Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: KP984758
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: 106343
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1048 original size:36 final size:36
Alignment explanation
Indices: 925--1032 Score: 216
Period size: 36 Copynumber: 3.0 Consensus size: 36
915 CAGCATAGAT
925 ATAGATATTTTCATAAAATAAATAGCTTATTTATGA
1 ATAGATATTTTCATAAAATAAATAGCTTATTTATGA
961 ATAGATATTTTCATAAAATAAATAGCTTATTTATGA
1 ATAGATATTTTCATAAAATAAATAGCTTATTTATGA
997 ATAGATATTTTCATAAAATAAATAGCTTATTTATGA
1 ATAGATATTTTCATAAAATAAATAGCTTATTTATGA
1033 TTGGCCAAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (36 bp):
ATAGATATTTTCATAAAATAAATAGCTTATTTATGA
Left flanking sequence: Indices 425 -- 924
CATTGGTGTTTTTTATTAATTTATTATCATTAAATTACATAATGATAAAAAAAAATATATATATA
TATTTTTTTGGGTGTATAGCTTAATTGGTAGAGCATTAGGCTTTTAACTTAATGGTCGCAGGTTC
AAGTCCTGCTATACCCAAATGTTCTTATAGAAGTTCCCCTGCCAGTTCATATGCGCATCAAAATA
TACATTGTACGTTGGCTCGTCTAGTCCGAGTAATTACGTTAAACTAAAATATATATATATATATT
TTTCTGTCTTTATGGCAGCTCACGCCCTTTTTTTCTTTGCGAAAAAAGGTCGCGGGCCTCTAATC
TAAGCTTAGATTGAGCGAAGAGAACGCTGCAGCCTTTGATGCGGCTCTGAAAAGAGAGAAGTTAA
TTAGGTGTTACCAATTACTTAACTATTTAACTTCTCTATATTATACAATCTGCAGCAATCCTGCA
TCCTGCAATTAAGGTTTGATAGCAACTGTAAACAACAGCATAGAT
Right flanking sequence: Indices 1033 -- 1532
TTGGCCAAATACATAATATTTTAGTATAGGCTATATATTATATATTGGCTAATGCTGTATTGATT
GTTGTTTCATTACAGCTAATTGCTGTTGGAATAAGGGCTCTAGTAAACTATAAGTTTCGATTATA
TGTGCCACGTTTGCGCTTTTCGGACAGTATTGGTGAAGCTGCCACCATGAAAAGTGGATTCCCGT
TATTTTCAAACTCCTAAGTAATCTACGTCACCGTCGACTTTAATTCATGAGATATGCGTCTCTTT
CATTAATTCTCTAAATTCTGCCAACCTATCTTATAAAATCCAGCCCGGCAGTATAATCAATACTA
GCTCGCTCGCATATATCCCCACATTCATTCGTCAAATCAGGTAATCTCTATTGAATAAGAGAGAA
GATATTGGTCTGAACTAAATAAATTGAATAAAAAGCTTCCGAGTACGCAAATAGTGGGAATACGT
CAGCAGCATTGGCAATCTAAAGTTAGGCTGGCAAAAGGTACAAGA
Found at i:30103 original size:12 final size:12
Alignment explanation
Indices: 30088--30112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30078 TATATATATA
30088 TATATATTTCAT
1 TATATATTTCAT
30100 TATATATTTCAT
1 TATATATTTCAT
30112 T
1 T
30113 TAGCAAGCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATTTCAT
Left flanking sequence: Indices 29588 -- 30087
CATCTGGATGTTAATAGGGCGCAACAAAAAATATATATATTTGCCGTTTTCTTTTTTGAGTTTTG
GAGAGTAAAATCTGCCAGACTAGGCAGGTGCATAGACCCCTTCGCCTTTTACTTAATCCGCAAGT
TTGGCGTTTACACGGTTCTTTTAGGATTAGGCAGGTACTATAGGTCCTCTGACTTCCAACTCGGA
CCATAGTGTACGGTTGAATCTCGCCGATATCACCTGTGAGCTATAGCGCTTGAGATGTCGTTTAG
TTCTCTGTCCCCATTATTTTGGGTAATCTGCTTCCATGCGTAAAAATATATCTATTTTTTTTCGT
CATTACCGTTCTTAGCCACCAGCAGGCTGAAAGCATAACAGTGTTCGTTCGTGTGATTCCCCGCG
TGCATTTTTTCCGCACTGGTTCGCTGTAGGGCAGGCTGACCCGAAAAGAACTGCGATTCTGCTTT
ATCATCTCATGCTAAATGAAATATATAATGAAATGTATATATATA
Right flanking sequence: Indices 30113 -- 30612
TAGCAAGCGCCAGCGGACTCGCGAAGGATTATTGAGCAGGCCGATAAACTAGCCGACAGCCGACG
AATATCTCCATTGCTGCTTCTGTGGCATGCTTTCTTTGCTATCGGGTAAGCCCTGAGCCTCTTGA
GCAGTAGTGCCTTTGTTGTAATCACAAGTGATCTAACGGCCGCCCCTAAGAAAGCCCCAGAAATT
CTATGGAAAATAGAAAAAGTAGAAGTAAGCTGTGGCTTATAAATGGTAAGATGAGGTGATAACGG
TCGATTAATTTTCATGTTTTTAGTTGACTTTGATTTTGACTCAAGGTGACAGGATTTGAACCTAT
GACCCTCTGTACCCAAAACAGATGCGCTACCAGACTGCGCTACACCTTGTCTGATGTTCCTTAAT
GAATATTTGATAAATGCTTAGACTGTTTGTTATTAAGCACCATACAAAAAAAACTAAGACTAATA
AAAACACTATATTTTTAACGCCACTGAAAAAAGCACTACCATCTC
Found at i:33729 original size:14 final size:14
Alignment explanation
Indices: 33710--33737 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33700 GCGGAGCAAA
33710 TGAGAGCGCGCGCG
1 TGAGAGCGCGCGCG
33724 TGAGAGCGCGCGCG
1 TGAGAGCGCGCGCG
33738 AATGTACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.50, T:0.07
Consensus pattern (14 bp):
TGAGAGCGCGCGCG
Left flanking sequence: Indices 33210 -- 33709
ACTTTCTACATAAACAGTGACTTCTATGGTTAAGCCCTATCGGGCCAGGTTAAAGGGCGCATGGA
GCGAATTATCATCCAACAGCCAGGAAGCGGCAGATTAGTATAACAGCGGATTAAGAATTCGCATG
TCGGAATAGTTTAGTCGGTTAGAACAGCGGGATCATAATTCGCACACGGGGGTTCAAATCCCTCT
TCCGATAGGAACTTTCGGATAGGAATTGAACCTACGTAGGCAAAAAAAAGATATATATATCTTTT
TTGCGCTGGTCACCAACCTTATCCTAAATTTTTTTTTCTATGATAGGCCACGGTAAAAAAAGATT
TACCATGTTTCTTAGGGTAACTAGAAATGCAACATAATAAATGTTGTTTTGACAAATAGATATTG
TTCACGAACTAAGTGGCTATACTGTTATGTTATATCAACAAAGTAGAACTAGCCGTGATGCTAGT
AGCTTCTGAATCATCATAGATAATTCATTGTTGTAGCGGAGCAAA
Right flanking sequence: Indices 33738 -- 34237
AATGTACGTTGCTCTGGCTTGTTGCAACATCAATTTAAGTAGGTCTACATGGCTTGCTTTCGAGC
GCCCTATTCATACGTAAGGTATAAAAAAATCAGGATAGAGGTGGTGGGAACGGGGCATTAAACGA
CATTATAACATAGGTCAGGGCCCTGTTATTGGACAAGCCATGTAGAAAACAAAAACGGTTAAAAG
CATCTCGAGAAGCGGTTGTATTTTATGTAGGTTATAATTAATAATTAGATTTATTTATAAATCTG
AAGTAAATCTGCATGTTATATATATGCCGTGACTTGAAAATACGTAAAGACTAAAATTACATATA
ACGGCGGCATCACCAGCGGCAATTCGATGTAGCCGACGCGTGGCCTGCGGCCCCGCAAGGCCGCG
GCGCTTTTCAGCGGCCGAAGGTTTTTTTCTGTTGGGTTTTACAAGATATCAAAATAAAATAAAGT
TAGAGAGCCCTGTGATTGGCGATTCTCGCCGGAGAGCACTTGTCT
Found at i:38679 original size:16 final size:16
Alignment explanation
Indices: 38658--38688 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
38648 GTAAAAAAAA
38658 TGACAAAGTAAAGATT
1 TGACAAAGTAAAGATT
38674 TGACAAAGTAAAGAT
1 TGACAAAGTAAAGAT
38689 AGAAGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (16 bp):
TGACAAAGTAAAGATT
Left flanking sequence: Indices 38158 -- 38657
TCTTATCGACGGAGTCGTTTGGCACCTCGATGTCGACTCATCACATCCTGGGGTTGAAGAAGGTC
CCAAGGGTTCGGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGAACGTCGTGAGACAG
TTCGGTTCCTATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACCCTAGTACGAGAGG
ACTGGGTTGGGTCAACCTATGGTGTACCGGTTGTTATGCCAATAGCAGCGCCGGGTAGCTAAGTT
GGTATAGAAGAACTGCTGAAAGCATCTAAGCGGGAAATCTTTCTCTATACAAGTTCTCATAAAAG
GTGAAAGACCATCACTTTGATAGGCGAGAGGTATAAACACCGTGAGGTGTGAAACAAGGCTTACG
ACTTGAGCTTACTCGTACTAATTATCTACTTTTCGGGAGCCCAGGGCTCTCCGGAGAGAACCTCT
TAATTGAGCAGAGATTGTTGCGATCTGTACGCAAAGTAAAAAAAA
Right flanking sequence: Indices 38689 -- 39188
AGAAGATTGACAAAGTAAAGATAGAAAGTTGTTCACATTTATGTTCTTCACATTTCTTCACATTT
ATGTTCTTCACATTTCTGTTGTTTACAGGACAAAGTAAAGAATGATTTATTATTCTGACAGCGCC
AGTCTATAAGTCTATAATTTCGCCTATAAATACAGCATTTTCGATATACAAGAAAAGGTACTATC
GGGTTGTTATGAGGTGAACCGATAAGCAAGTCTAGGTAGCCAAGTTTGATTTGTTCGGTAGCACT
TCGTTCTGTATACTTAGGTAGTGTTCTCTATACTGTAGCGGTGCTTGCACCGTCCTTATGGCAGT
ACTCGTGCAGCATGACGGGACATTAAACTTCAGCTAACCAAGCAAAACTTAGCCGAGTAATAAGC
CGAAGGCCTTATAGAGTCGGTCTTGTTTTTCAGACTTAGCTGAACTATAATTAGTTCTGTAGAAC
CCGGGTGCTAAGCGCAAGATTTGTACGTGGTTTTTCTCGTTACGG
Found at i:38700 original size:22 final size:23
Alignment explanation
Indices: 38668--38714 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
38658 TGACAAAGTA
38668 AAGATTTGACAAAGTAAAGATAG
1 AAGATTTGACAAAGTAAAGATAG
38691 AAGA-TTGACAAAGTAAAGATAG
1 AAGATTTGACAAAGTAAAGATAG
38713 AA
1 AA
38715 AGTTGTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.19
Consensus pattern (23 bp):
AAGATTTGACAAAGTAAAGATAG
Left flanking sequence: Indices 38168 -- 38667
GGAGTCGTTTGGCACCTCGATGTCGACTCATCACATCCTGGGGTTGAAGAAGGTCCCAAGGGTTC
GGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGAACGTCGTGAGACAGTTCGGTTCCT
ATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACCCTAGTACGAGAGGACTGGGTTGG
GTCAACCTATGGTGTACCGGTTGTTATGCCAATAGCAGCGCCGGGTAGCTAAGTTGGTATAGAAG
AACTGCTGAAAGCATCTAAGCGGGAAATCTTTCTCTATACAAGTTCTCATAAAAGGTGAAAGACC
ATCACTTTGATAGGCGAGAGGTATAAACACCGTGAGGTGTGAAACAAGGCTTACGACTTGAGCTT
ACTCGTACTAATTATCTACTTTTCGGGAGCCCAGGGCTCTCCGGAGAGAACCTCTTAATTGAGCA
GAGATTGTTGCGATCTGTACGCAAAGTAAAAAAAATGACAAAGTA
Right flanking sequence: Indices 38715 -- 39214
AGTTGTTCACATTTATGTTCTTCACATTTCTTCACATTTATGTTCTTCACATTTCTGTTGTTTAC
AGGACAAAGTAAAGAATGATTTATTATTCTGACAGCGCCAGTCTATAAGTCTATAATTTCGCCTA
TAAATACAGCATTTTCGATATACAAGAAAAGGTACTATCGGGTTGTTATGAGGTGAACCGATAAG
CAAGTCTAGGTAGCCAAGTTTGATTTGTTCGGTAGCACTTCGTTCTGTATACTTAGGTAGTGTTC
TCTATACTGTAGCGGTGCTTGCACCGTCCTTATGGCAGTACTCGTGCAGCATGACGGGACATTAA
ACTTCAGCTAACCAAGCAAAACTTAGCCGAGTAATAAGCCGAAGGCCTTATAGAGTCGGTCTTGT
TTTTCAGACTTAGCTGAACTATAATTAGTTCTGTAGAACCCGGGTGCTAAGCGCAAGATTTGTAC
GTGGTTTTTCTCGTTACGGAGCCTATAAGCATTTTTTAGCGTATG
Found at i:38740 original size:15 final size:15
Alignment explanation
Indices: 38720--38773 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
38710 TAGAAAGTTG
38720 TTCACATTTATGTTC
1 TTCACATTTATGTTC
38735 TTCAC----AT-TTC
1 TTCACATTTATGTTC
38745 TTCACATTTATGTTC
1 TTCACATTTATGTTC
*
38760 TTCACATTTCTGTT
1 TTCACATTTATGTT
38774 GTTTACAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
10 8 0.24
11 2 0.06
14 2 0.06
15 21 0.64
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.54
Consensus pattern (15 bp):
TTCACATTTATGTTC
Left flanking sequence: Indices 38220 -- 38719
GTCCCAAGGGTTCGGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGAACGTCGTGAGA
CAGTTCGGTTCCTATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACCCTAGTACGAG
AGGACTGGGTTGGGTCAACCTATGGTGTACCGGTTGTTATGCCAATAGCAGCGCCGGGTAGCTAA
GTTGGTATAGAAGAACTGCTGAAAGCATCTAAGCGGGAAATCTTTCTCTATACAAGTTCTCATAA
AAGGTGAAAGACCATCACTTTGATAGGCGAGAGGTATAAACACCGTGAGGTGTGAAACAAGGCTT
ACGACTTGAGCTTACTCGTACTAATTATCTACTTTTCGGGAGCCCAGGGCTCTCCGGAGAGAACC
TCTTAATTGAGCAGAGATTGTTGCGATCTGTACGCAAAGTAAAAAAAATGACAAAGTAAAGATTT
GACAAAGTAAAGATAGAAGATTGACAAAGTAAAGATAGAAAGTTG
Right flanking sequence: Indices 38774 -- 39273
GTTTACAGGACAAAGTAAAGAATGATTTATTATTCTGACAGCGCCAGTCTATAAGTCTATAATTT
CGCCTATAAATACAGCATTTTCGATATACAAGAAAAGGTACTATCGGGTTGTTATGAGGTGAACC
GATAAGCAAGTCTAGGTAGCCAAGTTTGATTTGTTCGGTAGCACTTCGTTCTGTATACTTAGGTA
GTGTTCTCTATACTGTAGCGGTGCTTGCACCGTCCTTATGGCAGTACTCGTGCAGCATGACGGGA
CATTAAACTTCAGCTAACCAAGCAAAACTTAGCCGAGTAATAAGCCGAAGGCCTTATAGAGTCGG
TCTTGTTTTTCAGACTTAGCTGAACTATAATTAGTTCTGTAGAACCCGGGTGCTAAGCGCAAGAT
TTGTACGTGGTTTTTCTCGTTACGGAGCCTATAAGCATTTTTTAGCGTATGACTATAGCAATGTT
ACAGTAGAAGCTTATATGGCTTCTGTTATCGCCCTAGAGAGTGAG
Found at i:38754 original size:25 final size:25
Alignment explanation
Indices: 38720--38770 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
38710 TAGAAAGTTG
38720 TTCACATTTATGTTCTTCACATTTC
1 TTCACATTTATGTTCTTCACATTTC
38745 TTCACATTTATGTTCTTCACATTTC
1 TTCACATTTATGTTCTTCACATTTC
38770 T
1 T
38771 GTTGTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCACATTTATGTTCTTCACATTTC
Left flanking sequence: Indices 38220 -- 38719
GTCCCAAGGGTTCGGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGAACGTCGTGAGA
CAGTTCGGTTCCTATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACCCTAGTACGAG
AGGACTGGGTTGGGTCAACCTATGGTGTACCGGTTGTTATGCCAATAGCAGCGCCGGGTAGCTAA
GTTGGTATAGAAGAACTGCTGAAAGCATCTAAGCGGGAAATCTTTCTCTATACAAGTTCTCATAA
AAGGTGAAAGACCATCACTTTGATAGGCGAGAGGTATAAACACCGTGAGGTGTGAAACAAGGCTT
ACGACTTGAGCTTACTCGTACTAATTATCTACTTTTCGGGAGCCCAGGGCTCTCCGGAGAGAACC
TCTTAATTGAGCAGAGATTGTTGCGATCTGTACGCAAAGTAAAAAAAATGACAAAGTAAAGATTT
GACAAAGTAAAGATAGAAGATTGACAAAGTAAAGATAGAAAGTTG
Right flanking sequence: Indices 38771 -- 39270
GTTGTTTACAGGACAAAGTAAAGAATGATTTATTATTCTGACAGCGCCAGTCTATAAGTCTATAA
TTTCGCCTATAAATACAGCATTTTCGATATACAAGAAAAGGTACTATCGGGTTGTTATGAGGTGA
ACCGATAAGCAAGTCTAGGTAGCCAAGTTTGATTTGTTCGGTAGCACTTCGTTCTGTATACTTAG
GTAGTGTTCTCTATACTGTAGCGGTGCTTGCACCGTCCTTATGGCAGTACTCGTGCAGCATGACG
GGACATTAAACTTCAGCTAACCAAGCAAAACTTAGCCGAGTAATAAGCCGAAGGCCTTATAGAGT
CGGTCTTGTTTTTCAGACTTAGCTGAACTATAATTAGTTCTGTAGAACCCGGGTGCTAAGCGCAA
GATTTGTACGTGGTTTTTCTCGTTACGGAGCCTATAAGCATTTTTTAGCGTATGACTATAGCAAT
GTTACAGTAGAAGCTTATATGGCTTCTGTTATCGCCCTAGAGAGT
Found at i:39941 original size:18 final size:18
Alignment explanation
Indices: 39918--39954 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39908 TTACAATCTG
39918 TACCTACCTTGTTATTAC
1 TACCTACCTTGTTATTAC
39936 TACCTACCTTGTTATTAC
1 TACCTACCTTGTTATTAC
39954 T
1 T
39955 TTGAATACCA
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:0.22, C:0.27, G:0.05, T:0.46
Consensus pattern (18 bp):
TACCTACCTTGTTATTAC
Left flanking sequence: Indices 39418 -- 39917
TGTTGTAATAACAAAAGAGATTAGTAAACAAAGAAAGAAAGAAAGGGTGATTTGCAGGCTCGCAT
TAACTCATGAAAATCAGTTAGGTTATTATGGATGCTTTTTCTTGCAATTAAACTTAAAGAAATAG
GGTGGTCGACAGACCACCTTTGTTTAAAGATAAATAGATTTTGCCTTTATTCAGTAAATCCTGGA
TATTACTTACAAGTAAATTTAACAAATTGGAAACCCTTAAACCAGTATAATAAAGTAAAAGAAAG
GCGGCTCTTTTTCTAGCTGGTACAAGTCCTTGGCATTTTACGGAAGCTAATATGAAGTGAAATTC
ATCTGGTGTTATACTGTCGCGTAATTCTTGCTTTTTGGCATTTTGTCTTTTTTGTCAATGAAAAA
CTGTTGCCAATTACCTGCATAATGCTGACTAACCTGCAGCTTATATTCGCTTATCTTACAAGTTT
CTTCTCTATCAATATCTACACCATTCAATCTTATCTTACAATCTG
Right flanking sequence: Indices 39955 -- 40454
TTGAATACCATGACTAGGAGGAAATAATAATTGTCTCATTTGATTAGGCGTCATGCCGTGTAAGG
CCTTATGTGGCCTATTATTATAGATTTTAATAGCTTCATGTAAAGCAGGATTATCCTGGTTTTTG
ATAATATTTGTTAGTGTTCGGAAAGTCCTTTGAACTATTTGATTTAAGGTTCCTGTGGCGGACTT
CACATTAAGTTTATCAAAATATTGGTTGAGCGATAAATATTCTGGGTTTGAATTTATGAACTTAA
CATTAGGTAAAAAACTGCTTACCGAGGATAGGCAATCTATCATATCCGCTAGATTGGGCGGGGTA
GCCTTGTAAAAGTGACTTACGATATGACGTGCTTTTACATCAATGATTGCAAAACAATATCCATA
ATCTCTCAATTGCTTACTGGCTATATAGAGTACATAATCCGAGTTTAAATATAGTTGCTTGTTAA
TATTTTGATGTTGCTTGTTAATATTTTGCTCGTGAGTTTTATGCA
Found at i:40424 original size:21 final size:21
Alignment explanation
Indices: 40398--40437 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
40388 TTTAAATATA
40398 GTTGCTTGTTAATATTTTGAT
1 GTTGCTTGTTAATATTTTGAT
40419 GTTGCTTGTTAATATTTTG
1 GTTGCTTGTTAATATTTTG
40438 CTCGTGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.57
Consensus pattern (21 bp):
GTTGCTTGTTAATATTTTGAT
Left flanking sequence: Indices 39898 -- 40397
CAATCTTATCTTACAATCTGTACCTACCTTGTTATTACTACCTACCTTGTTATTACTTTGAATAC
CATGACTAGGAGGAAATAATAATTGTCTCATTTGATTAGGCGTCATGCCGTGTAAGGCCTTATGT
GGCCTATTATTATAGATTTTAATAGCTTCATGTAAAGCAGGATTATCCTGGTTTTTGATAATATT
TGTTAGTGTTCGGAAAGTCCTTTGAACTATTTGATTTAAGGTTCCTGTGGCGGACTTCACATTAA
GTTTATCAAAATATTGGTTGAGCGATAAATATTCTGGGTTTGAATTTATGAACTTAACATTAGGT
AAAAAACTGCTTACCGAGGATAGGCAATCTATCATATCCGCTAGATTGGGCGGGGTAGCCTTGTA
AAAGTGACTTACGATATGACGTGCTTTTACATCAATGATTGCAAAACAATATCCATAATCTCTCA
ATTGCTTACTGGCTATATAGAGTACATAATCCGAGTTTAAATATA
Right flanking sequence: Indices 40438 -- 40937
CTCGTGAGTTTTATGCATTTCTGCTATGAATCATCATATATAGCAATATAGTAAGCGATAAATTG
CCCAATTATTGGTAATTATTGGTAAATTAGAAGAATATAGAGTAATTTCGAGAAGACGAAGAGCG
TAGCAGGTCGAAGCATCTGGAATAAATATGGAGCATCACCTTCTAACCTGTTCATCACAATACTC
TGTGATCACCTTCTAACCTGATAACCTGTTCGTTCTAACCTGATCTTCATCGCTTCGCGCCTTCT
AACCTTCTAACCTGATCACCTGTTCGTTCATCACAATACTCTGAACCTGATCACCTTCTAACCTG
ATCTTCATCACAATTTCTACGCATCATACTAAGCCTTTTTAGTAATAAATTTGTCTGTCGCCTTC
GGCTCAGTTTCTAACCTGATCACCTACGCATCACATTCATCACCTTCTAACCGGATAACCTTCCA
ATACGATCACCTGTTCCTTCTATTCTAATCTAATCTAATAGGTAA
Found at i:40940 original size:7 final size:7
Alignment explanation
Indices: 40928--40956 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
40918 TAATCTAATC
40928 TAATAGG
1 TAATAGG
40935 TAATAGG
1 TAATAGG
40942 TAATAGG
1 TAATAGG
40949 TAATAGG
1 TAATAGG
40956 T
1 T
40957 TAGGTCTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (7 bp):
TAATAGG
Left flanking sequence: Indices 40428 -- 40927
TAATATTTTGCTCGTGAGTTTTATGCATTTCTGCTATGAATCATCATATATAGCAATATAGTAAG
CGATAAATTGCCCAATTATTGGTAATTATTGGTAAATTAGAAGAATATAGAGTAATTTCGAGAAG
ACGAAGAGCGTAGCAGGTCGAAGCATCTGGAATAAATATGGAGCATCACCTTCTAACCTGTTCAT
CACAATACTCTGTGATCACCTTCTAACCTGATAACCTGTTCGTTCTAACCTGATCTTCATCGCTT
CGCGCCTTCTAACCTTCTAACCTGATCACCTGTTCGTTCATCACAATACTCTGAACCTGATCACC
TTCTAACCTGATCTTCATCACAATTTCTACGCATCATACTAAGCCTTTTTAGTAATAAATTTGTC
TGTCGCCTTCGGCTCAGTTTCTAACCTGATCACCTACGCATCACATTCATCACCTTCTAACCGGA
TAACCTTCCAATACGATCACCTGTTCCTTCTATTCTAATCTAATC
Right flanking sequence: Indices 40957 -- 41456
TAGGTCTAGAGATTCAATTCAATTCACTGAGCTTTCAAATTGCTGGTCGAATCCATGTCTTGTCA
TACCATTTTTCAAACCCCCATTCAAACCGAATATATTCCCGAAGTGACCCTTTTGTCAAAGCTGC
CAGTACAGAAGGCAGCTGCTTATAGTCCTAACAAAATTATTGTATAGTACGACACAAGGTTGACC
TCACCTCCACTATTTGTGCTATGCGGTTTATCATTCAGAAAATATAAACCATGTTGACAAACATA
GCATTTGTTTTATATAAAAAAAAAAAAACCGGCATCACTTACTCAAATTCAAGGTATGTCGAAAA
ATAAAAAGAGAATAAACTAGAAAAAAAAGAATAATAATGATCCTATGCTAATAAAACAAATTGTT
ATACGGAAAAAAGCCCAAGAGATTGAAAAAAAATCTCCATATATTCTTTTATTTCATTGTAGTGG
CTTGACAAGTCGACAATGGCGACAACTCAAAAATCTATTGTGTGC
Found at i:42285 original size:81 final size:81
Alignment explanation
Indices: 42150--42299 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
42140 AAAATACTCG
*
42150 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
42215 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
42231 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
42295 CCAAG
65 CCAAG
42300 TGAGCTCAGG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 41650 -- 42149
TTATACGGACAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGGTAATTTAGA
AATAACATCGGTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATCTTCTT
GTTTGAACAAGCCAATTTATGCTTCACCCGCTATACAAGAAAAGACGCAAGGAGGATTACTTAAT
AACCAGAGGATAACCACTTAGTAATTTGGACCCCCACTTTGCCAATTAAGGCCGTAGGCTTTATT
GACAGAACTGGGGCGCGTAGTTTGTAGCGAAGGTTTTTTTTTTCAATATTTTGAGAAACCCCCCA
AAAATATTTTTTGCTGCGAAAAGCAGCGCTTTCAAAGATTGTAACGATTTAAACTACTGGATGAT
TTGTTTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCAC
CTATTAAGTTATACTCGCCTTTCAATTTAGACATTAAAATACTCG
Right flanking sequence: Indices 42300 -- 42799
TGAGCTCAGGGAAGCAAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCAT
TTTATTTTATAGACATCCCCAGCTTATTCCGGCTCAGCTGGACCTGCGGCATTTTTTCAAATATT
TGAAAAAGATATAGTCCTTTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACTAGT
CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTGAATTGAATCTAACCACGGTTGCCTTGGC
AATAGCAATTACTCTTATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGAACT
AAAAGAAGATAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGGTTAAAATTTGGGGCTTTGT
TTTACGTAGTTTTGCCATCTATATAATATAATATAGTAAGAAATAATAAGTTGGCGAGGAAGTAA
AAAAAATATATATATATATATTTTTTTTTTAATTCGGTGGTCCTG
Found at i:45446 original size:21 final size:21
Alignment explanation
Indices: 45422--45463 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
45412 AAGCTGGAAA
45422 CGTAAAAAAATATATATATTG
1 CGTAAAAAAATATATATATTG
45443 CGTAAAAAAATATATATATTG
1 CGTAAAAAAATATATATATTG
45464 TTTTTTTTCA
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:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
CGTAAAAAAATATATATATTG
Left flanking sequence: Indices 44922 -- 45421
TTTCATTGGCGCTGTTGGAAAATCTGCACAAATAGGATTGCATACTCGGTTACCCGATGCAATGG
AGGGTTTTCGAATATTTGAGGGCTCTCATGTGCCAGTAGGTACATTATAACAATCTCACTGTATG
CTGGGATCGTCGAGCAAATGAGAGTCCCGATCGGAAAAATATCTCATTTTGACCAATCAGCAGGA
AACCTATAAGGGAAGGCCAAGCCCACCCAACAAAGTAAAGGCTGAAGGAGCTCTATAGGATCCTC
AGAGACTGTACGTGAGACCTCTTGTTAGAAATGGAATTTATCCTTGAAAAGAAAAGCCGGCCAGA
TTTAACTAAGATACGAAGCATTCTTTTGTCGTGAAGATTGAATCAGCTTTTTTTTAGATTATATA
GTCTAGATACGCAGGTCTTCTGGAATAGAAGGACCCGTCTAGGGTTTGGGCATGTAGAAAACCTT
GTATTGAATCAAATACGCCTCGTTATTTTGTTTATAAGCTGGAAA
Right flanking sequence: Indices 45464 -- 45963
TTTTTTTTCAGCGCGGCCTAATGTTACATTCCAACTTTCGGCTTGAGCCCAGCCTTATTGTCATC
CTTACCAAAGCGCCGCGCGCTGGATTTACCAGGACGCAGTTCAAAAAAGCTCAAATCTTTTCTGT
TGCTTCGCAAAATATATATATATTTGCAAGAAGCGTTGGGATGGGGCTAAGACGGTGTTTCATAT
ATAAAAGAAAAAAAACATCTTAGTTGTTAAGGACGCAGCATCCGTAAGATTCTTTTCTGGGAGAG
TCTTTATTTCATAAGTGGAAGATACAGTCCTTACTCTGGCTAGGCTTATCAGCTTATTACCTGAT
GCTCTCAAATATTATTTATTTGCCTTCTGGAAGCGTAAGAGGTTTTTAAAGAGTAGCCCACTCCA
GTATCTGCTTTGATTCATGCAGCTACTATGGTAACAGCAGGCGTTTTTATGATAGCAAGGTGCTC
CCCTTTATTCGAATATTCACCCACGGCTTTGATTGTGATTACTTT
Found at i:75927 original size:2 final size:2
Alignment explanation
Indices: 75920--75950 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
75910 AACGAATAAA
75920 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75951 TTTTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 75420 -- 75919
TGTGAATATCTATTATTCTCGGGCCCCAAGCAAGGGGCCACAAAACAGCACCCTTACTCTCCTAG
TCTATGTACATTGCTCTTTCTAGGAGGTTGGCTGCCCATCCTAGATATTCCTATTTTTCATGTGA
TTCCGGGTTCTATTTGGTTTAGTATAAAGATTCTTTTCTTTCTGTTTGTATATATATGGGTCCGT
GCAGCATTTCCACGATATCGTTATGACCAATTAATGAGACTTGGTTGGAAAGTATTCTTACCTTT
ATCATTAGCTTGGGTAGTTTTTGTATCTGGTGTTTTAGTAGCCTTTGACTGGCTCCCTTAATTCA
TTGAACAATTTCACTGCAGTACAATTAAAAAATATATATTTTTAATAAAAAAAAAACTCCGTTGA
ATAGCAGCTCGAAAACCAAATGAATTGATTAGAAGAAATATAAAATAATATATTTTATTCGTTCT
ATTAACTCCGTAAATGCAGGCTTTGAGCGTTCTAAAACGAATAAA
Right flanking sequence: Indices 75951 -- 76450
TTTTTTTTTATCTAAGGCCTTGTAATGATGGGTAAATCCTGCCCATGATGGATTGCGTTAATCAT
GAAGAACACCAAGTTTCCATGATCCGCGAAAACGAGAAAGCACGAAACATTAATATGTCAAGACG
ACTATCGATTCTTAAACAACCTATATTTTCTACATTTAACAATCATTTGATAGATTATCCAACCC
CGAGCAATATAAGTTATTGGTGGAGTTTTGGTTCGTTGGCTGGTCTTGGCTTGTTCATTCAGATA
ATTACAGGCGTTTTTTTAGCTATGCATTATACGCCTCATGTGGATTTAGCTTTCTTAAGCGTAGA
ACACATCATGAGGGATGTGAAAGGCGGCTGGTTGCTTCGTTATATGCATGCTAATGGGGCAAGTA
TGTTTTTTATTGTGGTTTATCTTCATATTTTTCGTGGTCTATATTATGGAAGTTATTCGAGTCCT
AGGGAATTAGTTTGGTGTCTTGGAGTTGTCATTTTACTTTTAATG
Found at i:75941 original size:13 final size:13
Alignment explanation
Indices: 75923--75948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
75913 GAATAAAATA
75923 TATATATATATAT
1 TATATATATATAT
75936 TATATATATATAT
1 TATATATATATAT
75949 ATTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Left flanking sequence: Indices 75423 -- 75922
GAATATCTATTATTCTCGGGCCCCAAGCAAGGGGCCACAAAACAGCACCCTTACTCTCCTAGTCT
ATGTACATTGCTCTTTCTAGGAGGTTGGCTGCCCATCCTAGATATTCCTATTTTTCATGTGATTC
CGGGTTCTATTTGGTTTAGTATAAAGATTCTTTTCTTTCTGTTTGTATATATATGGGTCCGTGCA
GCATTTCCACGATATCGTTATGACCAATTAATGAGACTTGGTTGGAAAGTATTCTTACCTTTATC
ATTAGCTTGGGTAGTTTTTGTATCTGGTGTTTTAGTAGCCTTTGACTGGCTCCCTTAATTCATTG
AACAATTTCACTGCAGTACAATTAAAAAATATATATTTTTAATAAAAAAAAAACTCCGTTGAATA
GCAGCTCGAAAACCAAATGAATTGATTAGAAGAAATATAAAATAATATATTTTATTCGTTCTATT
AACTCCGTAAATGCAGGCTTTGAGCGTTCTAAAACGAATAAAATA
Right flanking sequence: Indices 75949 -- 76448
ATTTTTTTTTTATCTAAGGCCTTGTAATGATGGGTAAATCCTGCCCATGATGGATTGCGTTAATC
ATGAAGAACACCAAGTTTCCATGATCCGCGAAAACGAGAAAGCACGAAACATTAATATGTCAAGA
CGACTATCGATTCTTAAACAACCTATATTTTCTACATTTAACAATCATTTGATAGATTATCCAAC
CCCGAGCAATATAAGTTATTGGTGGAGTTTTGGTTCGTTGGCTGGTCTTGGCTTGTTCATTCAGA
TAATTACAGGCGTTTTTTTAGCTATGCATTATACGCCTCATGTGGATTTAGCTTTCTTAAGCGTA
GAACACATCATGAGGGATGTGAAAGGCGGCTGGTTGCTTCGTTATATGCATGCTAATGGGGCAAG
TATGTTTTTTATTGTGGTTTATCTTCATATTTTTCGTGGTCTATATTATGGAAGTTATTCGAGTC
CTAGGGAATTAGTTTGGTGTCTTGGAGTTGTCATTTTACTTTTAA
Found at i:75941 original size:15 final size:15
Alignment explanation
Indices: 75921--75951 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
75911 ACGAATAAAA
75921 TATATATATATATAT
1 TATATATATATATAT
75936 TATATATATATATAT
1 TATATATATATATAT
75951 T
1 T
75952 TTTTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATATATATATAT
Left flanking sequence: Indices 75421 -- 75920
GTGAATATCTATTATTCTCGGGCCCCAAGCAAGGGGCCACAAAACAGCACCCTTACTCTCCTAGT
CTATGTACATTGCTCTTTCTAGGAGGTTGGCTGCCCATCCTAGATATTCCTATTTTTCATGTGAT
TCCGGGTTCTATTTGGTTTAGTATAAAGATTCTTTTCTTTCTGTTTGTATATATATGGGTCCGTG
CAGCATTTCCACGATATCGTTATGACCAATTAATGAGACTTGGTTGGAAAGTATTCTTACCTTTA
TCATTAGCTTGGGTAGTTTTTGTATCTGGTGTTTTAGTAGCCTTTGACTGGCTCCCTTAATTCAT
TGAACAATTTCACTGCAGTACAATTAAAAAATATATATTTTTAATAAAAAAAAAACTCCGTTGAA
TAGCAGCTCGAAAACCAAATGAATTGATTAGAAGAAATATAAAATAATATATTTTATTCGTTCTA
TTAACTCCGTAAATGCAGGCTTTGAGCGTTCTAAAACGAATAAAA
Right flanking sequence: Indices 75952 -- 76451
TTTTTTTTATCTAAGGCCTTGTAATGATGGGTAAATCCTGCCCATGATGGATTGCGTTAATCATG
AAGAACACCAAGTTTCCATGATCCGCGAAAACGAGAAAGCACGAAACATTAATATGTCAAGACGA
CTATCGATTCTTAAACAACCTATATTTTCTACATTTAACAATCATTTGATAGATTATCCAACCCC
GAGCAATATAAGTTATTGGTGGAGTTTTGGTTCGTTGGCTGGTCTTGGCTTGTTCATTCAGATAA
TTACAGGCGTTTTTTTAGCTATGCATTATACGCCTCATGTGGATTTAGCTTTCTTAAGCGTAGAA
CACATCATGAGGGATGTGAAAGGCGGCTGGTTGCTTCGTTATATGCATGCTAATGGGGCAAGTAT
GTTTTTTATTGTGGTTTATCTTCATATTTTTCGTGGTCTATATTATGGAAGTTATTCGAGTCCTA
GGGAATTAGTTTGGTGTCTTGGAGTTGTCATTTTACTTTTAATGA
Done.