Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_069590
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 306009
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:18844 original size:20 final size:20
Alignment explanation
Indices: 18819--18858 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
18809 ATGGCATCCA
*
18819 TTCTAGATTGTTCCATACTT
1 TTCTAGATTGATCCATACTT
* *
18839 TTCTAGTTTGATCTATACTT
1 TTCTAGATTGATCCATACTT
18859 GTATATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (20 bp):
TTCTAGATTGATCCATACTT
Left flanking sequence: Indices 18319 -- 18818
TCCCCTAATTCCTTCTCTGATATGAGGCCTATTAGCTTGACTCCTTTTTCTTCAAAAATTCTTTC
CAAGATTCTTAATGACAGGCTCAGTGTGGTTCTTCCTTCTATTATATCTTTGGAGCAGGCAGGCT
TTGTGCAAGGCAGATCTATTCATGAGAGCATTTGCCCGGCTCATGAACTTCTTGCTGATATCAAA
AAAAAGACCTATGGGGGTTATGATGAAGATTGATATGCAGAAAGCCTATGACAGACTAGACTGGT
CTTTTCTCATGGCTGTTCTTAAGAAGTTTGGTTTCTCTGATTCCTGGTGTAAGATTCTTTTTTCT
TGCATCAGCAATTGTTGGTATTCTGTTAGTGTGCAAGGTGAGCTGAATGCTTTCTTTAAATCTCA
CAGAGGAGTGAGGCAAGTAGAGCAGAATGTCCCGGATTGCTAAAAGGAGGCTTTGCCACGCAGGC
GCTTACTGGACACCCAAGTTGGCGTGGACGTCTGCATGGCATCCA
Right flanking sequence: Indices 18859 -- 19358
GTATATAATTCTCTATAAGAGTTTGGAGCCTTGTAAATTTATAGATATTTGTATAGAACACTCTA
GATACACAATTGTAGCCGTTAGATCGAGATGATCCTAACCGTCCATTGAGGAGGTGGAGGTGTCT
AAATAGGTGAGGCCTTCATTTGGCCAAACCATCCAAGCATTTGTAAACTTCTCTCTAGTGCAATA
CAAGTTCTCTACATTCTCCCTAACTCTCTCTTGTGTGCTTTCGGTCTTCTTGCCTAGTTCCTTCT
AGCTCACCATTCGGGTTAGACTGACTTAGCAACCAACAAGGGGTGTTGAAGCGCTAAGTGCCGCA
CGGTTGGCTTAGAATTGTCTAAGGCCGTGACAGTTGGTATCAGAGCTAAGGTTACGAGCGGGTCG
TAATCAAGGAAGAGCTAGACACGATGTCGGGAGTCACTGACGATGTTGCTGCTTCTGAGGTGAAT
AGGGGACGAGAGGTCGTTGCCCAAGATCCTGCCAAGAGGCATAGG
Found at i:51917 original size:39 final size:39
Alignment explanation
Indices: 51862--51940 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
51852 CCCATCCTTC
*
51862 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
*
51901 AATATCATGATCGGGTCGACTAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
51940 A
1 A
51941 TAGAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.23
Consensus pattern (39 bp):
AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 51362 -- 51861
TCCTTGACCCTTTTCTTTGAACACTGTTGAATGAGACTCCTACTTCTTTCAGGCTGATCTGCACT
ACAATCCTCTGATTCAGAAAGGCTGTTTCTTGTGGATATAGTCAACCTACTTACCATATTCCATG
GGATTGCACACGACAACCTTACTCTCATTGTCCAAATAAACTATCTTTTTATAACAATCAAGAGG
CTCATCACCGGGTCCAATAGACTGGATATTTCCAGCCAGACCGAGTTCTTCCATTAGTGCATATC
CAGCTTTCTCGTCGAAGAGAACTGAATTTCCTCTATTTGAAAGAAAAACTAGACTGATGAATCTT
TCAAATGCTATACCAGGATACTTTCCGCGAGAAAAGAGAGGCTGACATCTTTTCTTATCTATCTA
TTTTCGTAAATGAAGAAGATAAGTGAGAGCTTACTGACTGCATCTTCTAAGAAGGGCTTGGAAGA
AGAAATAGAATCTCCTTTCTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 51941 -- 52440
TAGAAAATAGAAAATGTACATAGCAGTTCCAGCTGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGATCATTTGGATTGTTACAACCTCTAGCAGATGGTTTTAAATTGATTATAAA
AGAACCTATTTCACCAAGTAGTGCAAATTTCTCCCTTTTTAGAATGGCTCCAGTGGCTACATTTA
TGTTAAGTCTGGTCGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATCCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGGTCG
GTCTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGG
TTTGTGCCGCAGGTGTTGAACGATCCACTCTACACAGGTGTGGGC
Found at i:75141 original size:16 final size:16
Alignment explanation
Indices: 75116--75155 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
75106 AAAGTGGAAA
*
75116 CTTTCCGCGGGATCCT
1 CTTTCTGCGGGATCCT
*
75132 CTTTCTGCGGGATGCT
1 CTTTCTGCGGGATCCT
75148 CTTT-TGCG
1 CTTTCTGCG
75156 CTACGATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.05, C:0.30, G:0.28, T:0.38
Consensus pattern (16 bp):
CTTTCTGCGGGATCCT
Left flanking sequence: Indices 74616 -- 75115
GGGCACTACTAACCAAGCCAAGCCCAGTTCCCGCCGATAGGCGCAGGTAGCTTGCTTCCAAGCCT
TGCCTTATATGATAGTTGTGGCCATGGCCCGAAGGAGCCTTAAGCACTTGTACAATGCTTCAAGT
CAAGGCTCCCTCCCACTCGTTGCCCAGAGCCTTTACTTTCCATGTTTTTAGTCAAATGCGCGCTA
GCGCGCTACAACTAGCACTTTTTTCTCTGAGAGGCTCGCTTCTTCCCGCCCCTTATTGAAAAAAA
AAGCGCGTTAGCGCTTTTACTTTTATTTATTATATAATACCTTCTTTCTACTTCTTTCTCAAAGT
AAAGCAAGCAACCTTTCGCCTTTATTTTTTTGAGGAGATATAAAAAGAAGCAACCTTACTAAGCA
AACGTAGGCTTGGGCTCGAAAGCAAGAAGCAACGGCTTTCGCGCTTGTTGGAGCTATTAAGCATC
TTAGACTATTCCATTCCATTTTTCAGCTGGACAGAAAAGTGGAAA
Right flanking sequence: Indices 75156 -- 75655
CTACGATGGAGTTTTTTACTCTTTAAGTGCGCCACTCCTTCTTTTGTCCTGTATCTGTAGCTGCT
TTTCCCGCACTCTCTTTTATCCCGCCGAAGGTCCCCCTTACGTAATAGGGGTTAAGTTAAGGGGG
GTGCACACCGTGGTCAAATCTGCATGAAAAACCGCGGGGAATCCTTAGTATTAAGTATTCTGCTC
CCGCACCCCCTATCTCTTAAAGGCTCTGCGCTCCCGCATTCTGATTGATCCTGTGCAATGTTGTA
ATCCTGCTGTTCCTTTATCCCCCGCTCCGCAGTTGCTGGAGACTTAGTCAGATTTTGAGCCTTTT
GCGGTACTGATTGATGTTATGGGGGATTACTTGGGTTGGCCGGACTGTTTGTTTGCGAAGGCCGA
AGGACTAAAAAATGAGGTTTTTGGTGTTATTGGACAGAATTGGTGCCGTTTTCCCACGCCTCCTT
TTCCATAATATGATTATGAGCTGCAGAACGCTTGAAGCTGGAATT
Found at i:88034 original size:27 final size:27
Alignment explanation
Indices: 88004--88055 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
87994 TATGGGTAGG
*
88004 AGTCAAGTGGAACATAGAATTGTTTGT
1 AGTCAAATGGAACATAGAATTGTTTGT
*
88031 AGTCAAATTGAACATAGAATTGTTT
1 AGTCAAATGGAACATAGAATTGTTT
88056 ATTGACAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (27 bp):
AGTCAAATGGAACATAGAATTGTTTGT
Left flanking sequence: Indices 87504 -- 88003
TGTAGGCGCCAACTCCCAGTTCTTTCTCTTCTTTCTTTTTTATCATCAAAAGAAGATTGCTGGAA
GAATAGAGATCCGGTCTTTCGTTCGCAACAAGGTAGCCATAGGGTGTACGAATAGCACTGATCGT
AGACCATCCAGATGCTTATGGGGCAGAACAGACCGATTGATTAGTTCCCGTGATCGTAGATCCAC
TTTAGCTAATGCAACTCGGGAAGAAGCTGCTAAGATCCCGTCGCTTACAAATGCTCCAGCGTGAA
ATAAAGACTTTTTTAGGTACAGGGATAAATTCGTACAATAGTGCGAGGACGGAAAAGAAAACGAC
CTTCTTTGATTTGACGCATGTTCTCCCAATAGTGCGAGTACTGACTTGTTCGTAGAAAAGAAGAG
TCCTGACTAGTATACCGTCTGCTATTCTTACTAAATCTCAAGATTGAATTGGTAGTTGTACAATT
GAACACGGTATGGGAACTATACAAATTGAACACGGTATGGGTAGG
Right flanking sequence: Indices 88056 -- 88555
ATTGACAAGTTTGTGGGTATGTGGTTTTTGCATTTCGTTCAATAGGGGGAACACGAGACCTATAA
AGAAAGGGGAATACAGATAAATGTTTTTTAGATTTTGACGCATTAGTAGGATTCATTCTTTTCCT
CTCCACAGATACCGAGATCTATCCTTAGATAGACGCACTATAAAGTTGAACAGGAAAGTTGAGAC
TGGCTTGTTCATGAGGCTAGTTCAGGAATTAAGGTTTTCTAGTTTCAATCTATAAATACCGTTTA
GCCCTCACTCGCCGGTGGGCTCACAACACTTGCTTTGTTGATTGAATCGATCGGGATGCCCTCGG
GGGCATCCCTCCCTGTTGTTGTTGATTGAACAGTGGAGATTCTCATACTTTTTAGCTGACTTCTT
GCTTCCTTCGTACATTAGCTGCACTAGACTGTTGAGCTATAGAGTTTAGACTGACTGACTCCATG
GCACTAGTTAATAGCTATCATAGATCGTTCCGGCCAGTGATCATT
Found at i:101251 original size:18 final size:18
Alignment explanation
Indices: 101211--101253 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
101201 ACCGCCCTGC
101211 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
101230 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
101247 CATAGTC
1 CATAGTC
101254 AACAAGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 100711 -- 101210
CGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTTGGAG
CGAATTGGATGATCGGGCCGAGGGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAATATGAAC
CTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAA
AGGCGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCGGACACTTTTTGTTATCTAAAGGCGAA
GACTCTGAAGTGGGCGAACACTCGGCCCAGCGGGCGAACATGCCGGGCTCCGGCTCCGCGCACCT
GCTGACACCTTTCGAAGCACTTTCTAGTGTGCGCTTTAGTTTTCGAATGTCTCGTTCAGCGTCAC
GAGTCTACAAGCCTTTCTCATTTCAGTGCTCGCCCTTTGAATCTTCAGTAGGGGCCTTTAGTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 101254 -- 101753
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAAGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:104487 original size:25 final size:25
Alignment explanation
Indices: 104459--104508 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
104449 AAATTGGGGT
104459 AGCTCAGGAACTATAGAATCTCTCA
1 AGCTCAGGAACTATAGAATCTCTCA
*
104484 AGCTCAGGAACTCTAGAATCTCTCA
1 AGCTCAGGAACTATAGAATCTCTCA
104509 GGAGTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (25 bp):
AGCTCAGGAACTATAGAATCTCTCA
Left flanking sequence: Indices 103959 -- 104458
GTGCCATTTCTTCTCTTGGAGGCAGGGCAATAGATTCATCTTGTCCTTGGCTTGTGAAGGGAATG
AGGTAGGGTAGCCAAAGCCCCCAACAAAGGGAGAGGGCAATCCTTCCCAAGTAATGCATAAGCAA
GATCAGGACTAGAGGGGTGTGAAGAGTAGGGGGATCTCTTGTGCAAAGCAAAGACAGGTACGTGC
TAGCAAAGAAGGGAAGTGGCAAGGGATTTCAAAGAAGAAGAAAGAAGAGAAAGTTAGTACACAGA
GTCTTCCCCTGCCTAATTGATCTAATGAGAAAGAAGTAGGCTAAGTCAAATAGAAAGTGTGTGTA
AACAATAAGTAATGACTTGCTTTGTGAGAGCTCAGTTTCTAAGACGAAGGCTAAGAATTCTCTAC
TAGAGGGATTGAAAAGATCGAGGGTAATTTCTGAGTCTTGATGGACCTTTCTTATTATAGGCCAA
AGGAATAGCTAAGGACTTCTTCCCTCATTCTCATCAAATTGGGGT
Right flanking sequence: Indices 104509 -- 105008
GGAGTTGAATAAACTCTTTTATGCTAGTGGAATTGGGAAGCATGATAAGTCCGTACTCCACATTC
TAGCTTCATCCTTGGTTTTCAAAGAAAGGAAACTTCAAAGACTGACAGAAGAGAAAGGTAAGATA
ATTCTTTCTGGCCTTAACTGAAAGCGGGGGAGGCCCAGGTCTACATACAGGTCTTGGATCAATAG
AATCCTCCGGGAAAGAATATCGGGATTAGTCTCCTTGCCATTGCTACTGTCTTTGAAAGTCTAGC
TATCCTCTCCTTGTCATGCTTAGTTATTCTGCATTGCTCCTTCTTCTGATCTTGCTTTCTTGCCT
TATAGAACTGACCTTTGTCCCCTCCTTCCGGTTTTCACTCACTTAAAGTCCATTCCTTGCTCTTG
CCTAGTTCTAGGCTTAGACGAAAGAGCTCATTCATAGATTCCATCTTTCTAGCATTTCATGTCTT
TCTTCCTTCAACTCTAATTCATGCCATGAATTGTTAAGTCCTTCT
Found at i:154236 original size:21 final size:21
Alignment explanation
Indices: 154212--154253 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
154202 AAAATTCCAC
154212 CTTAAAGCAACTGAGATATAT
1 CTTAAAGCAACTGAGATATAT
154233 CTTAAAGCAACTGAGATATAT
1 CTTAAAGCAACTGAGATATAT
154254 ATAATACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
CTTAAAGCAACTGAGATATAT
Left flanking sequence: Indices 153712 -- 154211
CATATGGAATAGGTCTCTGGCTTGCTCCTGTCTGCTCTTTGGTTATCTATCGGAAAGAGTCGTAA
TCTTTCCTTTCTGTCTACTCTACTATTGATTCCCTTAGGCTCGCTCAGTGCTAGTAAGTAATCTC
CTACCTTTACTTTAAAGAAAGGACATATCCAACGCCTCCAGGGTATGATCCTTAATCGAAAGCTA
TCTCCTTTTGCTTTCAGCCTTTCGGGACTGAAAGGCATCGACTCCTATCATAGCTCTTTCTGCCC
GTTACTGCTCTGTGGGCAACGGGCCGAAATAAATTACTATCGACCTAAACTGAAATAAAGTGAAA
GGGACCCACTACCCACTTCCCTTTCCCCGCCTCTGAAAAACAAAGAGCGGGCCTCGTTTTTCTTG
ACGAACCCACCGCACAAAAAAACGACACCCCCGACCTTAATCAACCTGAGAAAATAGAGAATCAA
AACCGACAACCAACTTGATAAAAGAAAGATATAAAAAAATTCCAC
Right flanking sequence: Indices 154254 -- 154753
ATAATACAATTTCTAGGAATTCTCCTCTTTGGGGTCCTAATTCTGTTAGAATCTTAAGAATCGTG
AGCAGGGATTCGATGGATTCTGAATCCTGATGGAGTGATATGACCGCGTCTTGTATTTGTTGAGC
CGGCGGTAAGGGCAGATTTTGGTATGTTAATTGTATCAATTTTTCTACTTCTGTGTGTATTGATT
CCATAAAGGAATCAATACACAGGTCAAATAAGTGCTCGGGGGCACTTTGGGTATTCAAGCCTTCT
AGGCTTCCATCTCTTAAAATTATAGCTAGAATTAGCGGGACATGTGCAATCTCTGCAATCAGAAC
TATGGAAATTGCCACTGAAGTAAGAAATTGTACGACTTGCTCGTGATTCACTTTTTTTTTCTTTC
CTTTTTTGATCTGAACATATAGAAAGGGAGTTCTTTCTTATGTGTAATAAAGATAACCAAAGTGT
TGGCTTTCAACAAAATACCTGGGAGGATTGTGTCAACAGGCCTCT
Found at i:172427 original size:15 final size:15
Alignment explanation
Indices: 172387--172433 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
172377 AGAAAGGTGA
172387 AAGAGCTACAGAA-G
1 AAGAGCTACAGAAGG
* *
172401 CAG-GCAACAGAAGG
1 AAGAGCTACAGAAGG
*
172415 AAGAGCTACAGAAGC
1 AAGAGCTACAGAAGG
172430 AAGA
1 AAGA
172434 CTAAGAACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 13 0.50
ACGTcount: A:0.49, C:0.17, G:0.30, T:0.04
Consensus pattern (15 bp):
AAGAGCTACAGAAGG
Left flanking sequence: Indices 171887 -- 172386
CTATCCTTTATCTTTCTCCTATGATTCCCAATATCCGTGGGATTTCCTCTAAAGCCTTTCTCTTT
AGTGACTCAAACAAAGAACCTTAGCGGATGGATGAAAGAAGTAACTGAAAGCAAGGATAATATCT
TATTTATCCCATCTAGGTATAGGGATAGATTGAATATTCCAGCGGTTGGTTGAAAAGATATACAA
TAATAAGAAGAGACTGATTGATATAGCATCTCACTAACTTAATCTCATGACTTTATAATATCACT
TTGTGAAAGTGCTCTCGATATGCCACCAAGAAGCCATTAGTGCAAGCTGGTATTTAGCTCGCTCC
TTAGATAAGCTATAGCTCCCTCTTTCTCGGTCAACCAAAAACAATGTAAAATGTATTAAATACCT
ATTCTTTGTTCTAATCAGCAAGCGGTATACGACAGCTTCGATAGCATCCTCTCCTCTTTCTGCTC
CAAATCCCTAGTTTAGAATGCAACGAATGAAGCGAAGAAAGGTGA
Right flanking sequence: Indices 172434 -- 172933
CTAAGAACTAGCTCGGCTTAAGGATTAGCTAGCTAGGAGTCTTTCTGTATATTCGAGACTTTATC
CCTCGGTTCTAAGTGCAAGGCTTTCTTAGCTGCGGTAACCCTGCTATGCAGGAATTCTTACAGTT
ATCTCAAATCTAAGCTTGGAACGACGAACCGGGAACACCTTCGTTTTCGCTTACCTGCTTAACCG
TTAGTTGTTAAGGATTAGCAGCACCGTCTACTAGCTAGAGCTGTGAAACCTGAGAGAGCCGGGTG
GGAACTCAAGACTAAGGCAGTAAGAAAGAGCTAGGATTAGTAGTTTGAGTTGGTTAGGCGGAATG
GGATCGAAGAGACTGTACCGAGAACCGGCTAACTGCCATGAAAGCAGAGAGAGCTACTGAGCAAC
GGAGGACAGAGCGAGAAAGATCTTGAACTCTTAAGCTTCATCCCTGTATGCATATTCCTATACCA
AAAGCAAGATAAGGGCGCGATGAATATTTACTGGATATAAGATAA
Found at i:177012 original size:19 final size:20
Alignment explanation
Indices: 176988--177033 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
176978 CCTTTCTATT
176988 TATAATAG-A-AGAAGTCTAA
1 TATAATAGTATAGAAGTCT-A
177007 TATAATTAGTATAGAAGTCTA
1 TATAA-TAGTATAGAAGTCTA
177028 TATAAT
1 TATAAT
177034 TAGCCAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 7 0.29
22 8 0.33
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (20 bp):
TATAATAGTATAGAAGTCTA
Left flanking sequence: Indices 176488 -- 176987
TTCCTATCGATTTCCGATGGATAACAATCCATCTTTCTCGCTTTCGCTCTTTCTCCCAATCAGTC
GCGAGGGTTCCGGGCATGAGAACGCAAGTGCCGGAATCAAACAAAAGGTCCGAACGTCCGAGGAC
GAAAGATAAAATGCTCCGCGGGGAAGTCGTTTCCATCTAGGATAGCGTATTCGTGCCGGTTAGAC
GTCGGCCATGAAATCCATCACTATACCGAGCAAATCATGGGCATTCACATCTCGGTCAAAGGGAA
CTGTGCGCGATTCTCTCGTGAATCGCCTTCAGCAAGGTATGGCATTCAGGGTCTTAACCCAGGGA
TAAATCTTTCTTCATAGATACAAGACATTCGTTGCTGATCTAAAAAAGATCTTCTCCCGTGGGCG
TTAGCGGACGTTTTTCATTTTTCACTCGGTCCTTACTTCCCAAAGCAAAGGTTTTTTTTAGGTTT
ACTTTGGAAAGGCGCTAAACAGGCCTATAGGTTCGCCTTTCTATT
Right flanking sequence: Indices 177034 -- 177533
TAGCCAAATCGTCTGAAGCATGAACAGAATCGCCTTTGTTCCGAAGGCCTAGCGAGTTAAGCGAG
TTCCTTTTTTCTTTTTTCAAAGGCAGTCCTTTTCTTTCCCCGGACCGATGACTCGCTTGTTCAGT
ACTGCTAACTCTTATTGGAGGATTCCGTCCCCTCGGGACTACCAGTAGCTTCGGTTGTTGAATCT
CGTGCAAGTTAGGTTGTGGTTGTATTGGCTGCAAGCGGAACGTAGGCGCTTTAGGTGTGTGTTGG
CCATGCACTCTCGCGTCGTGTAATGTCGTATGTATGATAGAGGTGGTGTGGTGATTGACCTCAAT
GCTAATGGTTATCCCCAAGGTTCAACGAATGAATGAAGCTATGCTATGATCGTACCCGGATAGAG
ATGATAGTCTTCCTCTGATGTCTCCAAGCCGGCCATAATAGAATCGATAGGCGAAGCAGCCAATA
GCAGTCTGTTCTCGCCTATCGATAGATAGCAGGTTGCTTCCAAGC
Found at i:225672 original size:32 final size:32
Alignment explanation
Indices: 225631--225693 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
225621 CTCCCAGATT
225631 CTTTAAAGGGTAAGTTGATTCTAGATTCTTTA
1 CTTTAAAGGGTAAGTTGATTCTAGATTCTTTA
225663 CTTTAAAGGGTAAGTTGATTCTAGATTCTTT
1 CTTTAAAGGGTAAGTTGATTCTAGATTCTTT
225694 CGGCGGGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (32 bp):
CTTTAAAGGGTAAGTTGATTCTAGATTCTTTA
Left flanking sequence: Indices 225131 -- 225630
GAGGGGAAGAATCGACGAGGAATCTAGACTAGAGAGGAATCTAGAACAGAAGTGAATAAAAAAGA
AAAAGCGTGAGGAGAATTAGAAACTCGATATGTTGGAAGGTGCAAAACTAATAGGGGCCGGAGCT
GCTACAATTGCTTCAGCGGGAGCTGCTATCGGTATTGGAAACGTCCTTAGTTCCTCGATTCATTC
CGTGGCTCGGAATCCATCATTGGCTAAACAATCATTTGGTTATGCCATTTTGGGCTTTGCTCTCA
CCGAAGCTATTGCATCGTTTGCCCCAATGATGGCCTTTCTGATCTCATCCGTATTCCGATCAAAG
AAGAAAAGAAAGAACGTCCTTTTTCCCTCTCAGTTCGTCGGTCAAACCAACGCCCGCTTGTTACC
CTTAGACTTACTTTTATGTAAAAAAATGAAATAATATATATATTATTATATTTCTTATTTTATTC
TATTATTATCCCCCATGGATAAATTAAGAGACTCGCTCCCAGATT
Right flanking sequence: Indices 225694 -- 226193
CGGCGGGCTTCCTCGTCTATCTGATTATAGCCTTTTTTACACATATAAAAGATAGGCAGGCCCTG
GAGAGGCTAGCTATTCAACATAAAGTAAATATTAAATTTGAGTATTCGTGGAAAGGGGTTTTCTT
GGATATCAATCATCCGGCTGAGAATATACTGGGAAACCATCCGAAAGATCATATAAGTCCGAAAG
ATAGTGTCAGTCCGAATTCAAGAAAGAAAGAGTAGAATTGGAAGTCAAGTAAGAAGGAAGGAGGC
TAGTCCCCGAAAATGCTCCGCGCCTAGGTTCTTTTGTCGTTGGGGCTTACACCTTGTGACTCATT
GATTCGGTCGAGCGTTCCTCGGGCGTCGATCAATCCTCAATCACAGGCCGCTCTGTCATTGTCTG
ATTTTTGGTTGTCTGATCACACTCGAAATTATGTATCTACTTATCATCTTTTTGCCCCTGCTCGG
TAGTTCCGTAGCAGGTTTTTTCGGACGTTTTCTAGGATCAGAAGG
Found at i:254829 original size:18 final size:18
Alignment explanation
Indices: 254789--254831 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
254779 ACCGCCCTGC
254789 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
254808 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
254825 CATAGTC
1 CATAGTC
254832 AACAAGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 254289 -- 254788
CGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTTGGAG
CGAATTGGATGATCGGGCCGAGGGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAATATGAAC
CTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAA
AGGCGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCGGACACTTTTTGTTATCTAAAGGCGAA
GACTCTGAAGTGGGCGAACACTCGGCCCAGCGGGCGAACATGCCGGGCTCCGGCTCCGCGCACCT
GCTGACACCTTTCGAAGCACTTTCTAGTGTGCGCTTTAGTTTTCGAATGTCTCGTTCAGCGTCAC
GAGTCTACAAGCCTTTCTCATTTCAGTGCTCGCCCTTTGAATCTTCAGTAGGGGCCTTTAGTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 254832 -- 255331
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAAGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:258065 original size:25 final size:25
Alignment explanation
Indices: 258037--258086 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
258027 AAATTGGGGT
258037 AGCTCAGGAACTATAGAATCTCTCA
1 AGCTCAGGAACTATAGAATCTCTCA
*
258062 AGCTCAGGAACTCTAGAATCTCTCA
1 AGCTCAGGAACTATAGAATCTCTCA
258087 GGAGTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (25 bp):
AGCTCAGGAACTATAGAATCTCTCA
Left flanking sequence: Indices 257537 -- 258036
GTGCCATTTCTTCTCTTGGAGGCAGGGCAATAGATTCATCTTGTCCTTGGCTTGTGAAGGGAATG
AGGTAGGGTAGCCAAAGCCCCCAACAAAGGGAGAGGGCAATCCTTCCCAAGTAATGCATAAGCAA
GATCAGGACTAGAGGGGTGTGAAGAGTAGGGGGATCTCTTGTGCAAAGCAAAGACAGGTACGTGC
TAGCAAAGAAGGGAAGTGGCAAGGGATTTCAAAGAAGAAGAAAGAAGAGAAAGTTAGTACACAGA
GTCTTCCCCTGCCTAATTGATCTAATGAGAAAGAAGTAGGCTAAGTCAAATAGAAAGTGTGTGTA
AACAATAAGTAATGACTTGCTTTGTGAGAGCTCAGTTTCTAAGACGAAGGCTAAGAATTCTCTAC
TAGAGGGATTGAAAAGATCGAGGGTAATTTCTGAGTCTTGATGGACCTTTCTTATTATAGGCCAA
AGGAATAGCTAAGGACTTCTTCCCTCATTCTCATCAAATTGGGGT
Right flanking sequence: Indices 258087 -- 258586
GGAGTTGAATAAACTCTTTTATGCTAGTGGAATTGGGAAGCATGATAAGTCCGTACTCCACATTC
TAGCTTCATCCTTGGTTTTCAAAGAAAGGAAACTTCAAAGACTGACAGAAGAGAAAGGTAAGATA
ATTCTTTCTGGCCTTAACTGAAAGCGGGGGAGGCCCAGGTCTACATACAGGTCTTGGATCAATAG
AATCCTCCGGGAAAGAATATCGGGATTAGTCTCCTTGCCATTGCTACTGTCTTTGAAAGTCTAGC
TATCCTCTCCTTGTCATGCTTAGTTATTCTGCATTGCTCCTTCTTCTGATCTTGCTTTCTTGCCT
TATAGAACTGACCTTTGTCCCCTCCTTCCGGTTTTCACTCACTTAAAGTCCATTCCTTGCTCTTG
CCTAGTTCTAGGCTTAGACGAAAGAGCTCATTCATAGATTCCATCTTTCTAGCATTTCATGTCTT
TCTTCCTTCAACTCTAATTCATGCCATGAATTGTTAAGTCCTTCT
Found at i:266883 original size:21 final size:21
Alignment explanation
Indices: 266857--266897 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
266847 GGCTAAGCTG
*
266857 CTAGTTGCCTTCTTAGCCTTC
1 CTAGTTGACTTCTTAGCCTTC
266878 CTAGTTGACTTCTTAGCCTT
1 CTAGTTGACTTCTTAGCCTT
266898 AAGGGCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.29, G:0.15, T:0.44
Consensus pattern (21 bp):
CTAGTTGACTTCTTAGCCTTC
Left flanking sequence: Indices 266357 -- 266856
TCAACGCAATGGGCGAGAAGGCTGACATGAAGGCTTTCATCGAAGGCAAAGCGGTGGGAATTCTC
TTTCAAGGCGGCCCGCACGACTCATCCTAAGTGAGGGCTTAGCCAACGAGACGTGCCTTTGGTGG
CATGGCTAGAAAGTGAAAGTGAAAGTCTTCAGCCTGAGAGTAAGCACCTAAAATAATGCCTTTTA
ATCGATCTTTTTATAGTTTTTAAAACCCTTATAAGACAGCTTTCACAGGCATTAGAGTAAAGATA
AATGGCCTTAACGCACGTTTTCCCGTTGGTCTAGTGGCATCCTAGATAGGTAGTATAAGAATAAA
TCTGCTAAACCCTTTGTGTTGACCTGCCTGCAAGTGGCTTCAAACACTCGCCTATTGAATAGTGC
GAGCTTGTTAGTCTTCCTTCCTGGGTGCTTGCCCGGGGTTGGTGTGAAGTACGCTCTTTAGCATC
GACCTTAAGGAGAGTTACTAACCTTCATCGTCGTTGGCTAAGCTG
Right flanking sequence: Indices 266898 -- 267397
AAGGGCTTGAAGAAGATAAGGGCATGGAGATTGACCCAGCTCATCGACCTTCTAGTAAAGCTAAG
CTGCTTAAAGAAATTGATAGTTTTCCGCATTCAAAATGTATGAACTCGGTTGTATGACTTCCGTC
CTTACTACTAAGGCTAGCTAGTTGCCTTCTTTGCCTTCCTCTGCTGCCCCGTGAGAGTGAGTTTG
TATGCCTGTTGGGTCTTTTCCTCACTAGGCAAATTATCAAGTCGATGCTCATATAACTGCATTTT
GATACTCTCACTTTTCCCTTCGATGAGCTGATCTTGAATTGCAAAAGTGATAGCTTATATAACTG
CATTTTGATACTTTTTTGAAGACGAGAAAGAGTTAGCCTTAAATGTCCCTATTCAATAGGCTTTC
TTTCTCCCTGTAGTTGGTCAACAACCAAATCTAGCTAGCAAGCAAGGTCATTAATACGCTAAAAG
AAGGCAGGCCCAAGATTTCCCCCTGTTTTTCCTAAAGAGAAATAT
Found at i:269321 original size:20 final size:21
Alignment explanation
Indices: 269293--269336 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
269283 CAAAGTCATT
269293 CTTAACTGTTTTTCCCCTT-C
1 CTTAACTGTTTTTCCCCTTAC
*
269313 CTTATCTGTTTTTCCCCTTAC
1 CTTAACTGTTTTTCCCCTTAC
269334 CTT
1 CTT
269337 TGCCTGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.09, C:0.34, G:0.05, T:0.52
Consensus pattern (21 bp):
CTTAACTGTTTTTCCCCTTAC
Left flanking sequence: Indices 268793 -- 269292
TCTCTTTGCCAGCAGGCTCCCACTTGCTGGTTCCGGGCTTGCTGGCCTATAATCCAGATTGATCT
ATTCAGATTGAGGAAACACCGAGTTCAGGTCTTCTTTCTATGCCCCAACTGGAGAAACTCTGAGA
TTTCTCACTATTCGTATGAAAATGGGGAAACAGTCTTTCTCAGACTCAAATCCTTCTTTTTTTAT
GCCACGGACTCCCCGAACGGACTTATAGCAGCAATACCAGCCAGAACCTCTGATGAGACCTATCC
ATCGTACTATCACTCTCCGCTATTAGAGAGGCTTTTCACCCACATGCGGGTCATCCTTCTCTAAT
ACCTGCTATAGGCAAGCTAAAATAAGGGTCCACCCTCATGCTTTAAGCCTATAATAGAAAGGGTA
TAAAGAGGTATCCTTAACGTGGTTTTTACCTAGGTAAAATAGCATTCTATTGGGATAAAAATCCC
CTGACATGTATTGGATGAAAGGTCCTAACTCCTAGCAAAGTCATT
Right flanking sequence: Indices 269337 -- 269836
TGCCTGTCTTGAAAGCTTCTGGCCGGGGAGATGCGGAACATTCTTTGCCTCATCTTTCATGCCTA
CCTACCATGCTAATCAAGATGGAAGATCTCATTTCGAATTTTAGTTTGGAAACTTCCCTAGTTGA
AATGGGTAACGTGTTCCGCTGCTTGGACTGACTCTTGCTATTGGAAACATATGCTCCCTAACGGT
TTGGGCCCTTCCTTTCGTTTGATGGCATGCGCCTTCTTAGAATAAGGCTAGGAGCTATTCTCCAG
TGATGGCTGCCTTCACCCTATGAGTGGGGTCTTTGCCTGGAAAAAAGGCTTTCACTATAGAAAAT
TCTCAAGTAGATGTTCCCTGAAATGGTGGCTATTTCTAAAGCAATGATTGCTAGGAAAGGTTTTG
CTGTCTAGCTCTTGCAAGCAAGGCGTGAAGCGATTCTCTTGAGCTCTAACCGGCTAAACCCGCTT
TGGTGGCCCGCCCCAAGTCTTGCCCATAGCTGACTTCTTTGCTAG
Found at i:299321 original size:21 final size:21
Alignment explanation
Indices: 299295--299335 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
299285 GGCTAAGCTG
*
299295 CTAGTTGCCTTCTTAGCCTTC
1 CTAGTTGACTTCTTAGCCTTC
299316 CTAGTTGACTTCTTAGCCTT
1 CTAGTTGACTTCTTAGCCTT
299336 AAGGGCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.29, G:0.15, T:0.44
Consensus pattern (21 bp):
CTAGTTGACTTCTTAGCCTTC
Left flanking sequence: Indices 298795 -- 299294
TCAACGCAATGGGCGAGAAGGCTGACATGAAGGCTTTCATCGAAGGCAAAGCGGTGGGAATTCTC
TTTCAAGGCGGCCCGCACGACTCATCCTAAGTGAGGGCTTAGCCAACGAGACGTGCCTTTGGTGG
CATGGCTAGAAAGTGAAAGTGAAAGTCTTCAGCCTGAGAGTAAGCACCTAAAATAATGCCTTTTA
ATCGATCTTTTTATAGTTTTTAAAACCCTTATAAGACAGCTTTCACAGGCATTAGAGTAAAGATA
AATGGCCTTAACGCACGTTTTCCCGTTGGTCTAGTGGCATCCTAGATAGGTAGTATAAGAATAAA
TCTGCTAAACCCTTTGTGTTGACCTGCCTGCAAGTGGCTTCAAACACTCGCCTATTGAATAGTGC
GAGCTTGTTAGTCTTCCTTCCTGGGTGCTTGCCCGGGGTTGGTGTGAAGTACGCTCTTTAGCATC
GACCTTAAGGAGAGTTACTAACCTTCATCGTCGTTGGCTAAGCTG
Right flanking sequence: Indices 299336 -- 299835
AAGGGCTTGAAGAAGATAAGGGCATGGAGATTGACCCAGCTCATCGACCTTCTAGTAAAGCTAAG
CTGCTTAAAGAAATTGATAGTTTTCCGCATTCAAAATGTATGAACTCGGTTGTATGACTTCCGTC
CTTACTACTAAGGCTAGCTAGTTGCCTTCTTTGCCTTCCTCTGCTGCCCCGTGAGAGTGAGTTTG
TATGCCTGTTGGGTCTTTTCCTCACTAGGCAAATTATCAAGTCGATGCTCATATAACTGCATTTT
GATACTCTCACTTTTCCCTTCGATGAGCTGATCTTGAATTGCAAAAGTGATAGCTTATATAACTG
CATTTTGATACTTTTTTGAAGACGAGAAAGAGTTAGCCTTAAATGTCCCTATTCAATAGGCTTTC
TTTCTCCCTGTAGTTGGTCAACAACCAAATCTAGCTAGCAAGCAAGGTCATTAATACGCTAAAAG
AAGGCAGGCCCAAGATTTCCCCCTGTTTTTCCTAAAGAGAAATAT
Done.