Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_062589
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: 315211
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Found at i:70460 original size:17 final size:17
Alignment explanation
Indices: 70433--70465 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
70423 ACTTGTGTCA
70433 GGGTAAAGCCCCCTTTAT
1 GGGTAAAG-CCCCTTTAT
70451 GGGT-AAGCCCCTTTA
1 GGGTAAAGCCCCTTTA
70466 GAGATAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 3 0.20
18 4 0.27
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (17 bp):
GGGTAAAGCCCCTTTAT
Left flanking sequence: Indices 69933 -- 70432
ATCGATCCTTAGTAATCGCGGGCCCCTAGTTGTTCACATAGATTTTTGCAGGCTCGAATAGGTGG
TTGGCTGCTGCGTCGTCGGAAGGGTCTTTTCCTTTGCTTGCGTAAGTTACCCTGCTTGCTATTCT
ATCACCCCTCGCCCGGCCTTTACTTGATTGATAGGGCTCCTTCACCAGGATCAATAGCCCAGCTA
CACTACCACTACCCGTAAGATAGAAGTAGGGCACTTCACTCACCTCAGAGAATGCACTACCTATC
TGTAATCAGTTCAGCTTAGAGTTGTTTGCTGACACACGCTACTATCACGCTGGTTGCTGCTTTCA
CTCGGATTCTCCTCGGGCGGATCAAGGGATATTGGCTTGGCTTGCGAAAGAACTTATAGTTGCAG
GATGGTTGGTTGACAGGTGTCTGGCTAGCAAAGAACCAGACAAAAAAAAACAAGTACAGTAGCGC
TATAGGCTATTTGATATAGTATAGCCGCGGAGACTACTTGTGTCA
Right flanking sequence: Indices 70466 -- 70965
GAGATAGGAAAACGGCCTAGCTGCTTTATTGAGGCAACATTGAGAATTTAAAAAAGAATTTGCTG
CTATTTCAGTGGTTGAAGTGCCGGTCGGCATTGCCTAAGTAACGTCCGACACTGTTTGCGCGCTT
CTCTCCTCTTCATTCAATGCAAAGACAACCGCCTGAGCGTCGCGTCTGACTCCAGCATCAGAGAA
GAAAGGCCCATATCTAATGCTTGCTTCAACCCGCACGAGATTGCCAAAATCTCAACGAGAGGAAA
CTCCGGCGCCCATACCTTTTGGTCTACACACCAAATCCTAATTAGCAAGATGGATCTTCCTCTTA
TATTTTTACCAAAAAAAGTTTTTCTGTTTAGCTTGTCAAGCCTAGAGCACACAGAAATAAGCAAC
TTGCCTATCGATATTAGGAGAACATAAGATATTCGATTTCTCAAAGCGCCCTGAAACCATGCAAA
AATCATCCAAACACTTTCTCTCAGCTTGAGAGCCTCAGAGAAACT
Found at i:91385 original size:21 final size:21
Alignment explanation
Indices: 91360--91401 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
91350 GAGGAACTAA
91360 AAAGAAGAGCTTTCGGTTTTT
1 AAAGAAGAGCTTTCGGTTTTT
91381 AAAGAAGAGCTTTCGGTTTTT
1 AAAGAAGAGCTTTCGGTTTTT
91402 GCACCGTCTT
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:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (21 bp):
AAAGAAGAGCTTTCGGTTTTT
Left flanking sequence: Indices 90860 -- 91359
CGAAATGAGAAAGAAGATGGTACACTCGAATTGTATTATTTAAGTGCTTATTGCTTGCCAAAGAT
CCTACTTCTACAATTGGTAGGTCACCGGGTTATTCAAATAAGTTGTGTTTTCTGTGGTTTTCCCA
TGTTACAACTTCTGTACCAATTCAGTCGATCCGGAATGGATCGGTTAAACATTCTATTAGGGAGC
CCGGTCTTGACTCTTCTGTGTGGTATTCATTCTTGTTCGGCTCTTGGAATCACATCCAGCAGTGG
TTGGAACAGCTCGCAAAATCCAACCACTTTACCTACTTCATTGCCCCCAACCGTTTCTCGTACCT
CTATTGAAACAGAATGGTTTCATGTTCCTTCATCGATTGGTTATTCCTCTCCGTTCGTATCTCTT
TTTCCAATTTCGGTCTCGATTAGTTTACAAGATTGAATGGCCTCCGGACTCTCGATTCGATTGTT
TTCCAAGAATGCTGCTGAGCCGGGTATGTAAGCGGGAGGAACTAA
Right flanking sequence: Indices 91402 -- 91901
GCACCGTCTTGCAGCTATTTAAATAATAATTATTTTAAATTATATATAATTATATAGATTTTTAT
TATTATAAAAACAAAACTTTTATTTTATAAGAAAGATTCTATATATGTCCAATCTCGAGTGGTTG
GTTCCACAGCATGCTCCTCGCTGCCCTATGGGGGGCAATACTCTCTTTCTCAAAGGCTCTGTTCA
TGCGAACCCCAAAGAGTCACTTGTTTTCCACTATCTCTCATCTGGCATCTCGGTTTAGGCGGAAG
GTTTCGTTTTCGCGCCGTCCAAAAAAGACGGATTCTAAGGGGTTAGAGAACTTTCCCCGCTGTCC
TTCTTTCAGCCGGTCCTAACTCCCTTCTCTTCTGGTTAATCCTATGAATCGGTAATCGGATCGGC
AACAGGTAAGAGGCTTTATCCGGGTTCAATTCCTTAATTCCGGATTAATTCCTTCGATGCGAGCG
GAGTATATCGAGAGACTCACCCACCGAGGACCGCCGTTGGCGCCT
Found at i:142333 original size:42 final size:42
Alignment explanation
Indices: 142269--142363 Score: 181
Period size: 42 Copynumber: 2.3 Consensus size: 42
142259 GCTCCTCAAC
*
142269 GGGCGGTTCCACCGGTGGAATGTTTGGGGCGGGCTCTCTACT
1 GGGCTGTTCCACCGGTGGAATGTTTGGGGCGGGCTCTCTACT
142311 GGGCTGTTCCACCGGTGGAATGTTTGGGGCGGGCTCTCTACT
1 GGGCTGTTCCACCGGTGGAATGTTTGGGGCGGGCTCTCTACT
142353 GGGCTGTTCCA
1 GGGCTGTTCCA
142364 AGTCCCTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.09, C:0.24, G:0.39, T:0.27
Consensus pattern (42 bp):
GGGCTGTTCCACCGGTGGAATGTTTGGGGCGGGCTCTCTACT
Left flanking sequence: Indices 141769 -- 142268
TAATAGGAATATTTCGTCTATTAAGGAGGATTCCCCGAATACCTAAAATAGAGATGATCATAGAA
AATGTGAAATATTTGATAAGATCCGTTTCGGAAACGTAGAATGTCAGAGAAATTCAAATGTTATA
ATAGCTCCTATATGAACTACTGGGAAGATCATAACGAAAAAGTAAAAGTGACCGAGATGCGAGGG
AAAAACTTTTGTTTAACATTTCCGGAAAGCCTCACGGCCTAGCGGACAGCGTCCCATCCACGCAT
GATTTTGATAAGCTCATCTCCTGCCTTAGCAGGAGTCTTCAAACTCCGGCGAATTTGCGGTTGGT
TCAGGTTTTCTATCACCTGGCCAATTTTAAGCCGCTTTTCCGCGTCAGCGGCGTCTATGTCCAAT
GCATCAATTACTTTTTGCATTACGTCCGTTCGTGGGGACCTCTCGGAAAAAGTGGATAGAAAGAG
CTGCACCCTCAGTTTGAGGTCTGACACCTCCACCTGCTCCTCAAC
Right flanking sequence: Indices 142364 -- 142863
AGTCCCTAAAGAGAGACTCCCCGCTTATGCCCGGGGCAGACGAACCAGGAAGCCGCTGCCCGACT
CCCTGGGAAGGCTGCGAATTGATTTCTTCCCCCGGTTCGGCAGGATTTTGAACCCAGTCAGAAAG
ACCCTCGAAAAAGGAAGAGGAAGGGTGGTCATCCCCCCCGGCCCCAGAAGGATTCATCATGAAAG
CGGTTGTTATTGTTTCTGCGTAAATGAAGTGAAACCAGAGCAAATTAGCGTAAATGAAGTGAAAC
CAGAGCAAATTAGAGAGTAGACTGACCACGAAAGTAGTTAAAACGTAAAAAAAAAAATTAAATAG
TAGTATGAGTGGAAAAGGCATCTTTATCTTTCTCCAAGAAAGCCATCGATAGATAAAGATCAAAG
AGAACATCAAAATGCTAAGAAGCACCCAATCAAAGGTAGTGAAAACAAGATTCTTTAAATTTCTC
CGTAGAAATATGGATAAGCATGTACTCATCAAACCTAAAAAAAAT
Found at i:142610 original size:30 final size:30
Alignment explanation
Indices: 142576--142636 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
142566 TATTGTTTCT
142576 GCGTAAATGAAGTGAAACCAGAGCAAATTA
1 GCGTAAATGAAGTGAAACCAGAGCAAATTA
142606 GCGTAAATGAAGTGAAACCAGAGCAAATTA
1 GCGTAAATGAAGTGAAACCAGAGCAAATTA
142636 G
1 G
142637 AGAGTAGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.13, G:0.25, T:0.16
Consensus pattern (30 bp):
GCGTAAATGAAGTGAAACCAGAGCAAATTA
Left flanking sequence: Indices 142076 -- 142575
GGCGAATTTGCGGTTGGTTCAGGTTTTCTATCACCTGGCCAATTTTAAGCCGCTTTTCCGCGTCA
GCGGCGTCTATGTCCAATGCATCAATTACTTTTTGCATTACGTCCGTTCGTGGGGACCTCTCGGA
AAAAGTGGATAGAAAGAGCTGCACCCTCAGTTTGAGGTCTGACACCTCCACCTGCTCCTCAACGG
GCGGTTCCACCGGTGGAATGTTTGGGGCGGGCTCTCTACTGGGCTGTTCCACCGGTGGAATGTTT
GGGGCGGGCTCTCTACTGGGCTGTTCCAAGTCCCTAAAGAGAGACTCCCCGCTTATGCCCGGGGC
AGACGAACCAGGAAGCCGCTGCCCGACTCCCTGGGAAGGCTGCGAATTGATTTCTTCCCCCGGTT
CGGCAGGATTTTGAACCCAGTCAGAAAGACCCTCGAAAAAGGAAGAGGAAGGGTGGTCATCCCCC
CCGGCCCCAGAAGGATTCATCATGAAAGCGGTTGTTATTGTTTCT
Right flanking sequence: Indices 142637 -- 143136
AGAGTAGACTGACCACGAAAGTAGTTAAAACGTAAAAAAAAAAATTAAATAGTAGTATGAGTGGA
AAAGGCATCTTTATCTTTCTCCAAGAAAGCCATCGATAGATAAAGATCAAAGAGAACATCAAAAT
GCTAAGAAGCACCCAATCAAAGGTAGTGAAAACAAGATTCTTTAAATTTCTCCGTAGAAATATGG
ATAAGCATGTACTCATCAAACCTAAAAAAAATAGAAAAAGGTTTTTTTTCATCTGGAACTTTTCA
AAATACTAAAATTCATTCGCTACACCAAGGCGAAAGGATTCGAACCTAAACAGATGCGCTGACCA
GACTGCGCTACACCTTGTCTTACCCACTCACTAGCTCTTCGTCGTTCGCCTCACCTCACTGCCGA
TCGCCGCGCTCCTTATCTACGCTAAATGTCCGTACCGTACGTTCTTTTTCGCGAAGAGCGACCTC
GACCGACCGAACCAACGCCTTATCAAACATACTTTGATTTTGTCA
Found at i:145963 original size:24 final size:24
Alignment explanation
Indices: 145931--145978 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
145921 AATCAGTCTT
145931 CTTGTATGGTTCCTGCTTGTTGGA
1 CTTGTATGGTTCCTGCTTGTTGGA
145955 CTTGTATGGTTCCTGCTTGTTGGA
1 CTTGTATGGTTCCTGCTTGTTGGA
145979 TAAGGAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.17, G:0.29, T:0.46
Consensus pattern (24 bp):
CTTGTATGGTTCCTGCTTGTTGGA
Left flanking sequence: Indices 145431 -- 145930
AGATGCATCTCAATGACAAAAACATAATGGATGGTGGTCTTTCAATCATTTTAAGTGTAAGTGTA
TATAGGAAACTAGCATATCGCTATACCTAGCTATAGGGAGACTCACTTGTTATGAGATTTCCATA
ATCCATGTTAAGGTGCGGGGACAAAATACTGCAAGAGATGTACCTATAGGTACTCAGAATAGCTG
CAGGTATCTTTAGTTTCCGGGTGAGAGGCCTCCATGGTTTGTTCATCAGCTCAGTTGGTTCAACG
ACATCGTAGTCTTTTCCATTTCCTAAACCGAAACCTTGGACCATATAGCATTCCCATAGCCATAA
GTTCCCTTGGTTTCAAAGAGCCGTGATCCAAATCGCCAGTTTGACTCCTCATCAGGACCTACTTT
GTTGACTTCATGAGTGACAACCTCCTCTCCATTTTAGACATCCCATTAGGCAGAGGCAGGGGAAG
CGGAGGCAATGCACTCTCCATAGCCATTTCATCCAAATCAGTCTT
Right flanking sequence: Indices 145979 -- 146478
TAAGGAAGGTGGCTAGCGTTGCTAAAGGACATGCTACCACCCCCTGTTTTGACAGCATCAGTATA
ACAATCTCGACAAAGATTGAATCGAAATCGCTCAGGTCAGTGAGTCCTCACCTACTCCTTATCAC
ACCCACAAGGTAGAATGTCCTCCCCGCGTTGATCGCTCATCACCTTTGCATCACACCCAGGAATG
GCACATGATGACCCTTTGACGCCATCTGAGGATGGTTGGCTTCGGATTCAATCACCTTGTCCATA
AGATGAGCTCGGGTAAGACTGTTGAATCCCCCAGTGAAGAGCGAATTGGACACATACTGTTCTTC
AACCTTCTGCGAAATGGATGGATCCATTGGCTGGTGTCGGAGGCCGTGTAGTTCATAAAGTCACC
ACTCCCAATTTCGCTATCGAGATCATCTCTGGAGTAGCTCATGTAGCGACCGGAGGAGGCGGCCG
AATGTGACTGTGGGAATTGGAGGCTTGCCGAGTGCATCGGGAATG
Found at i:242856 original size:31 final size:29
Alignment explanation
Indices: 242803--242878 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 29
242793 GTTGGAAAAA
* *
242803 AAGTAAAACTCCCTCTCCCTAAC-AGTCGAGT
1 AAGT-AAACTCCCT-TCCCTAACAAGT-AAGC
*
242834 AAGTGAAACTCCCTTACTCTAACAAGTAAGC
1 AAGT-AAACTCCCTT-CCCTAACAAGTAAGC
242865 AAGTAAACTCCCTT
1 AAGTAAACTCCCTT
242879 TGAATCTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 11 0.28
31 25 0.64
32 3 0.08
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.24
Consensus pattern (29 bp):
AAGTAAACTCCCTTCCCTAACAAGTAAGC
Left flanking sequence: Indices 242303 -- 242802
ACTTTAGGAGAGTCATATTTTCTGGTACGTCCATCTACTTATAAGCGGCCGGCTATGTTCTCTAA
ACTCATCTATTTCCTCTCGGCTCTCAGCGCAACGAGAAAGGATTCCCCAATAGCTGAGATTGGTA
CTAGAATTCGCGAATCTAGAGAGCACCAACGATGTTGACCGGGAGGGAAAGGAGCAATTAAAGCC
TTTCATCTCAATCAAATGACCGAAATGGAGACTCTATTCTTGTTGGCAAATGCAAATACGAATCC
ACTGATTTCCATCCCCATGTTCTCTGAGCAATGACCTTTGTTTCCAACAGTAATGGAGATTTGTT
GCAAACTGTCTCCGAATCCCGTGCTTTTCAAGTAAGCACCAACTCCTGTGATGTGTATTCCCCTC
CAGAGTCTGTCCTCAAACATGGCTTTCTTTGCCTTGACTTTATAAGTTTCATTCTCCACTAAGCT
TCTGAACTCTATGAATTTTTGAAAGATTTCGGACCGTTGGAAAAA
Right flanking sequence: Indices 242879 -- 243378
TGAATCTTATCCATTGAAGAAGACAGACTTCAAGACTGAAACCCGCCCTTTATTATTATATTATT
AGTAAGATAGGTTTGGAACTCGGGCTATAGTTATACTATATGCCCGGGCTTTTCTCGCTTGTTGC
TTTCTTTCTTCGCATGCTTTCGCGCATTTTTTAAAAATTTTTATTCTGGGGCGAACTCCCTATCT
TGATCGAAGTCCTGAAAGGCTTGGTTATGGTAGTCCCTCGGTCTATAAGATGTAGGCTTATCAAG
CTGAGGGAATTGCATAGTCAAGAGGAACTAAGTGCTGGTGATCGGAGCGTGGGGAACTCAGGCCG
CTGGTAGTAGAGGCAATGCAATTGAACCAATTTCCTTACACTCTAGCTGAGGGAGAGACTTTACC
TTTACTTAGAGAGGGGCAGCAATACTACTATGCTCTTCGGTGCTCGTAGGTTGACTTCCCTTATG
CACCCAGCCGCTTCACTAATGTGAATAGGTTATACAGAAGGGTGA
Found at i:245439 original size:39 final size:39
Alignment explanation
Indices: 245396--245474 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
245386 CGATTTTCTA
* *
245396 TTCACTCATGATCTGGCCTGGTCGACTCGATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
245435 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
245474 T
1 T
245475 GAAGGATGGG
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:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
Left flanking sequence: Indices 244896 -- 245395
GCCCACACCTGTGTAGAGTAGATCGTTCAACACCTGCGGCACAAACCTATTTTTGACCTATTGGT
CCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCAACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGAATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCGAGCAACCAGACTTAACATAAATGTAGTCACTGGAGCC
ATTCTAAAAAGGGAGAAATTAGCACTACTTGGTGAAATAGGTTCTTTTAGAATCAATTTCAAACC
ATCCGCTAGAGGTTGTAACAATCCGAACGCTCCCACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCGGCTGGAACAGCTATGTACGTTTTCGATTTTCTA
Right flanking sequence: Indices 245475 -- 245974
GAAGGATGGGACCTTTTCTCGAAAAACTCCGGATCGAGTTGAAGGTGGTGCAACATCGAATCTTG
TTACCTTACTTCGAATGGAATCTTAGCCCGCCTCACTTGCTTTCTGTACTGCATAAGGTTCTGAA
AGAAAGTAAAGGGATTTCCTTCTAACTAGTGGCTGAGAGTAAGCAAGCTACCTTCATTCAACAGA
TTTGTGGTTGAGTCAATAAGGGTCGGGAATCTTTGCTCTTCTCTTTTGCATTTCCGCTGCCTGCG
TTCTTCTTCGTGTCCGTACGTATCGCAAAGCTGGTCGACGCCAGCTGTAATGGTTCATTTCGGGA
GTTTGAACACCATCCCAAAAATACAACCCTGTCAAAGGTATTTAACCTTCCTTCCTTCTGAGTGG
AAATCCAATCCCGTTTTGTCTTTTTTGCATAAAAACCAAACTAATATAATATATATATATTTCTT
TTAAACCCGTTCTTCCGACCCCTCCAAAAATGACCTTCTCCAGTG
Found at i:270776 original size:27 final size:27
Alignment explanation
Indices: 270738--270800 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
270728 TAACAACAGA
270738 GCATCCCTCTCAAATATTAGAGCTCTT
1 GCATCCCTCTCAAATATTAGAGCTCTT
270765 GCATCCCTCTCAAATATTAGAGCTCTT
1 GCATCCCTCTCAAATATTAGAGCTCTT
270792 GCATCCCTC
1 GCATCCCTC
270801 GATTTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.32
Consensus pattern (27 bp):
GCATCCCTCTCAAATATTAGAGCTCTT
Left flanking sequence: Indices 270238 -- 270737
GGAGTTAGCTCAGTAGTACCGTGGGTAAGCAGTATGATTTTTATGAACCGCCCGAAAGAAAGATT
TATCTATGCCGGTATTTCACAATAGTCGCCGGGATCAGAGAATTAGACAAACCCCCCTCCGGTTA
GTAAGAATATTAAAGCTAAACAACTGCGACTGGTTGTAGGGCGTATAGCAACATAACAAGAATTG
ACACGATGAAAATCAGTGCATTTAAACGCACTGAAAGTGTAATATCCGCATCCTAAGGTTTTATG
CATCTGAATTGATCAATACCGTTCATGTGATCGTAAGCTCAATAACGTAGTGAAAGGCGCTGACG
AAGTGAAGTAATACCGGGCTTTTTATGCCACTTTTTAGTACTCGATAGCGAAAGATACACAAGGC
TGGGAAAGATTGACTTTAAAGGGCCTACATTCGTCTCTGTAAGCATTATAATCAACAACGCTTGA
CATAGTTTAATAAGATTCTTTAACAGCTTTCCGCTTAACAACAGA
Right flanking sequence: Indices 270801 -- 271300
GATTTATTATCAATTGGCACAGCGGATTCGAGAGCGGCATTTTAAGCATCTCCTTCAGCGCACAT
TGCCACCAATCTCCGTGGTTTTTCAATGGATTTCCTCGTAAACGAGTTTATCTTTTGACCAAAAG
CGTACTTTACCGTGGGTTTTCTCTCATAAAGAGATTGATTCGTCAGAACAGATTCTCTTCCGCAT
ACGGGCGGGATGCGAGGCTCGACGAGCGGGGGCAGTTGTTTGAGCAGCAGATGAAACTGGAATGA
AATAAAGTAATAAGCTGTTTTAACCGGGGGTAGTTGGTTATGGAGAGGATGCAAGGCACCTTAAT
ATGACATTATTTAAGAGATATATTCATTCTCTTTCTGCCCCCAGAACAACAAGCACTTATTGCAA
CCAATGCCACCCAATCCACGGCCAATCAATGCTTCAATGGACTCAGCTGCTTCATCCTCCCTTTC
AGGCTTTTGACTCGTAAACTCCGCATCGTAAATGGGCATCTTGAT
Found at i:272230 original size:5 final size:5
Alignment explanation
Indices: 272169--272216 Score: 73
Period size: 5 Copynumber: 9.8 Consensus size: 5
272159 CACCCCGGGG
272169 TATAC TATA- TCATAC TATAC TATAC TATAC TATAC TATA- TATAC TATA
1 TATAC TATAC T-ATAC TATAC TATAC TATAC TATAC TATAC TATAC TATA
272217 TTTATTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 5 0.12
5 34 0.85
6 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAC
Left flanking sequence: Indices 271669 -- 272168
ATTACTAAGCGATGGCAATTCTTGTTGCTAAGCGCTCCTGAATATTTGACTCTTGTACAATTTCT
CCTCTACTATAGTCTCATTCTGAAAGTCTTTTCTTCATGCTGCAAGTTGACTTCACCCCCTGCCG
TCGTAACAGCACTTTGGGCGGAAACGACTCTGTTATCTTGCATTAGAGATGAAAAAGAGCTCTCG
CTTTTGACCATGGAGATATATACCTACGACATTAGATCATCGAATTTCTCACTAGATGGAAGAAG
CTGAAAGATGTTGAATGCTTTCTATCACTAATATGTCAATCCGTTATTGAATCATCGAAGTCAAG
AAGAAGTGATGGGCTCGATATCGATATCAGATCCATAAGCGTTAAGAAAATCCCGAATATGCTGA
CCCGGGTGCAGTAAACGAACTTATATTCTCTTTGCTTTCTTTCAGAAGCTAAGCGCTACAACCTA
TAGCTTTAAATGAACCTTTCTCACATCCTTTATTTCACCCCGGGG
Right flanking sequence: Indices 272217 -- 272716
TTTATTATATTATAAGATATATATAATACAAACGGGTCACCCTACGGGTACCCCGCGGAAGCGGG
CACTGGACCGAGCTGAGGCGAGAGGAAAAACCCTACCAACCCCTATCCAATGGAAGAAGATACTT
ACAGAGAGTGAATGGATCACGGGTGTGGGACATGAACGTAGTCTTCATTCATTACATTGATTGTA
AGACTAATTCTTATGCTAACAACCTAAGTAACAAGCCTTTTCGCGGATAGACTTATGGAGTACAA
CTCGTGCTTTAAGCTTAAGACTCGTCTTATGAATGCCAAAAGGAACTATAAAGGAGCGCTTAGCG
ACAAAAACAACTAATTCGCTGTAGGTTGAAGCGGCAACAACAAGATTAAATGCCACAGGGCATAG
CCACAAGAATTGACTACGGGATGCGAGGAAAAGTCATGATAATATGACTTGGTAGCACGAGAAGA
AAGATACGATGGAATTGAACGGGAATCCCCCTGTTCTTCAACAAC
Found at i:296254 original size:18 final size:18
Alignment explanation
Indices: 296233--296269 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
296223 GTCACGGCCG
296233 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
296251 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
296269 A
1 A
296270 CAAGAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATCGTCACTATCATCA
Left flanking sequence: Indices 295733 -- 296232
TACTAATCGATAGGGCCTCATCGGTAAGTGCTACAAGATCTCGTACATTGGAACCCATGGTTATG
GACCCGAATCCATTAGTATAGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATATGAAAGAGT
GAAAAAGTGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCATGTATTTAATTTAT
TCGGAGCTATTAGAGCGGGATCCACTTTTTGGGGAATATGAGTCGAAGCAATAACAAGAATATTT
CTAGTGGAACATCTTTCACAATCCCTGGAGAGATAGTTCACTAATAAACCGAGGGATAAGTAATT
CGACTCATTCACATCCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATAGGTCTATTTCCGGCATCATATCCATAGTTAGCGCA
TTCATCATAGTTAGAAGCTCCAGCTCCGTATCAAGGTCACGGCCG
Right flanking sequence: Indices 296270 -- 296769
CAAGAAAACCCTTGGGCTTGTTATCCAGGAACTTGTTCAGAAATACTGTAATGAAAGGAACATAG
GAGTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTATCACTAAAAT
ACCCCTAGAGAGGGATAGGGCTAAACGGAGCGAAAAGGGTTTTCCATGAGATGGGAAATGAAAAC
TATTAGCCCCACAGGAGGTTTGTGAATAAGTAATTGTCTGATAATGAGCAAGGAATATCCGCCTT
TCTGCTAAACAGGATGTATTGAACTCATAATTCATTAGATACTTTTTATGAATGTCAACTAAGTA
TCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTCTTTGATAAATGAT
CACTATGAGTCAGACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGGTGGAGAACTGA
ACCAAGAATTCTCTTTCTTTATCACCAATCGAATCACTGTTCGAG
Found at i:308156 original size:18 final size:18
Alignment explanation
Indices: 308116--308158 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
308106 ACCGCCCTGC
308116 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
308135 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
308152 CATAGTC
1 CATAGTC
308159 AACAAGGTTT
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 307616 -- 308115
GAAAGCTTTTTTTTCAAGTGTCAGTAGCGGAACGTTCTGTCAATCGGGGAAGGTTTTTGGTGACA
ACACCTGGAGATATCAGAAGTGAGAATGCTGACATGAGTAACGAAAAATCCTGTGAAAAACACGA
TCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCAATCTACGCAGAGTGAATCGGTCCCTAAGGA
ACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACC
ATGCCTGTCTGTTGGAGCGAATTGAATGATCGGGCCGAGGGCAGCCCCCTCTTCCCCTCACTCTC
CTTTCCCTAATATGAACCTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTAC
GCGACTGGCGCTTCAAAAGACGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCCTTTACTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 308159 -- 308658
AACAAGGTTTAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:314906 original size:26 final size:23
Alignment explanation
Indices: 314858--314910 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
314848 AGGAATGGGT
314858 GAACGGGAAACCTGTTGTTAGGA
1 GAACGGGAAACCTGTTGTTAGGA
314881 GAACGGGAAACCTGTTGTTAGGA
1 GAACGGGAAACCTGTTGTTAGGA
*
314904 GGACGGG
1 GAACGGG
314911 GCCTGTTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.40, T:0.19
Consensus pattern (23 bp):
GAACGGGAAACCTGTTGTTAGGA
Left flanking sequence: Indices 314358 -- 314857
GTTATTTAAAACCAATAACAACGTAAAAAACACGTGGTTTTGCATGTAGGTGAAGGGTCAAATTG
ATCAAAAAAGGAACGCTCTCACTAAGTAAAACGGCTTTTCTAGGTTTTGTAGCTAGGGCTAGATG
GATTTCGTGTCAAAAGAAAAACGAGTGAAAAGACCATTTCAAGCAAAAAAGACGGGGTTTTAGAC
TTTTTTCCAAAAAGCATGCCACTTCACTTCTTATTCACTTCCTCACTTTGTTTACTTCGTAACCT
TTGGTATTGCGTCTCATCCAGGTGATTAATATCACGTCATAGCATTTCTTCCCCTGCTTCTGAAA
GAAAAGAATCATATGACTTACCTAGGCGGTTGTACCACTTGAAAGGTGACATTGAAGAAGCTGAA
TCGAAACTTATACGATATTGTAGAGAACCACTCTGAGTCTTTATTCCCCTAGTCTTCTTCGCATC
CTTACTTACCTCCTTATACTACTGTAAGCATATGAAGGAATGGGT
Right flanking sequence: Indices 314911 -- 315211
GCCTGTTGCCAAGGAGAACGGATAACATGGAAAGACAAGGAATACAAGGAAAGACAAGGAAAGCG
TGGGAGTTGCCGGGGTAACCTCCCTCTCCGGTCGAGTAACCTTCTACCTCTCCTTGTTGCCGAGG
AATGGAATTCCTATTCAAATTCCCGGGAAAGTCGACTTTGTTCGATAGTTCCCATCTCTCGATCA
CCCCACAAGAGAAGCCACTCGAACGAATAGCTCCTTTCTTGCCGTGGAATTCCTCAAAGCTATAA
TATAAATGGAATTCTCCCTTGACTCGATCTTTAAAAAAATT
Found at i:314967 original size:10 final size:10
Alignment explanation
Indices: 314939--314973 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
314929 CGGATAACAT
314939 GGAAAGACAA
1 GGAAAGACAA
*
314949 GG-AATACAA
1 GGAAAGACAA
314958 GGAAAGACAA
1 GGAAAGACAA
314968 GGAAAG
1 GGAAAG
314974 CGTGGGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.57, C:0.09, G:0.31, T:0.03
Consensus pattern (10 bp):
GGAAAGACAA
Left flanking sequence: Indices 314439 -- 314938
TCTCACTAAGTAAAACGGCTTTTCTAGGTTTTGTAGCTAGGGCTAGATGGATTTCGTGTCAAAAG
AAAAACGAGTGAAAAGACCATTTCAAGCAAAAAAGACGGGGTTTTAGACTTTTTTCCAAAAAGCA
TGCCACTTCACTTCTTATTCACTTCCTCACTTTGTTTACTTCGTAACCTTTGGTATTGCGTCTCA
TCCAGGTGATTAATATCACGTCATAGCATTTCTTCCCCTGCTTCTGAAAGAAAAGAATCATATGA
CTTACCTAGGCGGTTGTACCACTTGAAAGGTGACATTGAAGAAGCTGAATCGAAACTTATACGAT
ATTGTAGAGAACCACTCTGAGTCTTTATTCCCCTAGTCTTCTTCGCATCCTTACTTACCTCCTTA
TACTACTGTAAGCATATGAAGGAATGGGTGAACGGGAAACCTGTTGTTAGGAGAACGGGAAACCT
GTTGTTAGGAGGACGGGGCCTGTTGCCAAGGAGAACGGATAACAT
Right flanking sequence: Indices 314974 -- 315211
CGTGGGAGTTGCCGGGGTAACCTCCCTCTCCGGTCGAGTAACCTTCTACCTCTCCTTGTTGCCGA
GGAATGGAATTCCTATTCAAATTCCCGGGAAAGTCGACTTTGTTCGATAGTTCCCATCTCTCGAT
CACCCCACAAGAGAAGCCACTCGAACGAATAGCTCCTTTCTTGCCGTGGAATTCCTCAAAGCTAT
AATATAAATGGAATTCTCCCTTGACTCGATCTTTAAAAAAATT
Done.