Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_038053
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: 566589
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Found at i:128347 original size:24 final size:24
Alignment explanation
Indices: 128315--128363 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
128305 GGAATAATTC
* *
128315 CTCACCCTCAGGAGCCCGAAGTAA
1 CTCACCCTCAGCAGCCCCAAGTAA
* *
128339 CTCATCCTCATCAGCCCCAAGTAA
1 CTCACCCTCAGCAGCCCCAAGTAA
128363 C
1 C
128364 GAATCCGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.41, G:0.14, T:0.16
Consensus pattern (24 bp):
CTCACCCTCAGCAGCCCCAAGTAA
Left flanking sequence: Indices 127815 -- 128314
GAAGTCTTCATAGGGACTGTCAACGAAAGCCCCAAACCATTCATTAAGCAGGTTGACACAGTAAA
AGAACTCTCTTGTAGCCGCGCGAATGTATTTGCATGTCTTTCCGGGAGTCTCGCAATCCCAGCAG
TTGTATCCTTGGAAGTGACTTCTTGCAGTTCTACATTCTTCCTTTCGTATGTCTTCCTATACTTT
TGAGATGAGCTCGTCAAGGAAAAGCTATATTATCAGGCCAAATTCCGATCCGCTCCTCTTTCAGG
CGGTCTTTAGCTAGGAGCTTGAGTTCGATTCGGTAGAGAATCTCTGCACGATTCCGTTGCCTAAA
GTAGAAGTCCAGATTGGATATGAACTCTTGAGTGGCCCGTGTATGATAGTTTGTAGCATCTTGTG
CCCATTGGGGAAGAGGCAGGTCAAGGTCAAAATAACGGATTTGGACTTCTGGGGTCATCATCTGA
TGGTGGTAATTCTCTTTCTGGATCAACGGCTTCAGGGAATAATTC
Right flanking sequence: Indices 128364 -- 128863
GAATCCGAATGCCTATCTCCCGTTTCATAAGACTTTTCGGAAGAAACAATTGGATAAGAATCATA
GGCTGAATGAGCAGACGAATCGACCGAGGAAAGAGATGCTTACACACTAGAACACAACCTAACTC
TACTTCTTTTCTTTTTCCTGCAGCTATCTTCTCAACAGGTCAGTCAATATCAGTAGTGGAAAAAG
CAGACAGAGTAGTCCCCTGGTCATCAGTTAGTAGTTAAATAATCCCAGTAGTGGTCCTCTTGCCT
AGCGGAGTCAGCCCTTAATGGACAATGATAGGCAGACCAAAGATTGCACATCGCAGTCTAAGCGT
GCTTGCTTTGCGCACCGGCACAGCAGAATTGGAATCCGCTGGCAAAGCAAAGACAGCTTGATACT
TTACTTTGGTAAGGTAAGGTTAAAAAAGTGCGATGTCTTCCTGACTTGTTCAAGTCAGTTCTAAA
GCCCTTGCCCTATTCGCTTCACTCCTCTCAAAATATCGTAAGAGA
Found at i:131202 original size:18 final size:18
Alignment explanation
Indices: 131162--131204 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
131152 AAAGCCCTGC
131162 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
131181 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
131198 CATAGTC
1 CATAGTC
131205 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 130662 -- 131161
AAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACCATGCCTG
TCTGTTGGAGTGAATTGGATGATCGGGCCGAGGGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCC
TAATATGAACCTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTG
GCGCTTCAAAAGGCGAAACTCTCGTCGTAGTTTGGCGACCGGGCGGACACTTTTTGTTATCTAAA
GGCGAAGACTCTGAAGTGGGCGAACACTCGGCCCAGCAGGCGAACATGCCGGGCTCCGGCTCCGC
GCACCTGCTGACACCTTTCGAAGCACTTTCTAGTGTGCGCTTTAGTTTTCGAATGTGTCGTTCAG
CGTCACGAATGAAATTTCTCATTTCAGTGCTCGCCTTTTAAATCTTCAGTAGGGGCCTTTAGTCT
TTTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCTAAAGCCCTGC
Right flanking sequence: Indices 131205 -- 131704
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:246498 original size:21 final size:22
Alignment explanation
Indices: 246465--246507 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
246455 TACCGGAAGC
* *
246465 GAAGCTTCTGGCTCCC-CCTTT
1 GAAGCCTCCGGCTCCCTCCTTT
246486 GAAGCCTCCGGCTCCCTCCTTT
1 GAAGCCTCCGGCTCCCTCCTTT
246508 TCGTTCTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.09, C:0.42, G:0.19, T:0.30
Consensus pattern (22 bp):
GAAGCCTCCGGCTCCCTCCTTT
Left flanking sequence: Indices 245965 -- 246464
CTGCAGCTAATGTGACTGCAGATAAGTCTAAGACTTCTGAAGGGTTACGAAGGTAGAAGAACTTC
TTAGATATCATGGACATAGGGTGGCCCTAACAGCCTATTGATCGGGAAAAAGGGAAGGGACAATT
ATACCTTAGAAAAAGGTAGTAAATGGACTAACCTCATCGGTGAAGTGGCCTTCTTTCACGATGAT
CTGACCCTGACAGTTAGCGGACGTTGGCGATTTCGCTTCCGCGAGTGATGCCTGGCTAAAGCACT
CGAGCCTTGAAAAGGCGATCCCCATACCGCTTTCAGGATGACAACAGGAGAGACTATTACCTTAA
GTAGTAAGGAGTATAACGGCAGCTAGCGCTTTACTAATAGAATATCAAGTAAAGGGGACTTTATC
ATGATCTTACGAATCTACAACTCTCTTTACTGAGCGAGACTCTACCCAGATTTAAAGAATTCGCC
AAAGAGCCTTCTTCTAACTAGGAGAGTAAGCAAGCTACCGGAAGC
Right flanking sequence: Indices 246508 -- 247007
TCGTTCTACTTAGGTGGAGCAATCCGAACTCTCGACAGAATATAAAAGAGGTTTGTTTTTATTCC
TGTGTAGACACCTCAACGAACTCATGTGGACACTCCTCCGCCCGAGGACAATCTCTCAAAAATAC
ACATTAAGATGTTGACCCGTTTTTCTTTTCTTTGCTGATTCCTCTCAATGAAATTTGCCATGTTG
CACTAAGTTACTTACGGATGTATGCATGCGGTCCGGGAACACTTTGGGGTGAACACCCATCCGAA
CAAGTAGGGTCAATAGTTCAGCATTTAGGCCGTAACATTTAGCAACAAAAAAACCTTTAACCCAA
CAAGTGCTCTCCGAACCAAGCTAGATAGTCTCCTATCACTAGGCTCACCAACCAACCTGGACTTT
GATTCTTATTATTCCTACCGGATATCAAAACCATAAGGATTGTTTCCACCAGCCATGAGTTCCCA
TATGACATAAGCGCTCTTGGGTGGGCTGGGCCATTCCATCAAATC
Found at i:260154 original size:17 final size:17
Alignment explanation
Indices: 260111--260156 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
260101 GCAGTAAATG
*
260111 GAATAAACTAAGCAAGA
1 GAATAAACTAACCAAGA
*
260128 G-ATCAACTAACCAAGA
1 GAATAAACTAACCAAGA
*
260144 GAATGAACTAACC
1 GAATAAACTAACC
260157 CCAAGGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (17 bp):
GAATAAACTAACCAAGA
Left flanking sequence: Indices 259611 -- 260110
GAGCAAGCAGGAGTAGTCATATCTGCCTAGAAGGATTCGATAAAGAGAATGTGAGTGGGCAGGAG
ATCAATAGACACAGAAAGAGAAGACCAAAAGGAGCAGAAGGCACTCAGTTGTTTATGTGAAATCA
AGGAGCAGCAGGTTACACTTTTACACTTTTCCGAAGAGAGCTCAAAGCAATAAGATGAAAGATGA
GAAATGCTAGTAGATGAAAGATGGGATGAGATGCTAGCCTTAGCGCAGAAGATCAATCATTGAGC
CTTAGGCCACTACCGAGCAGCAATGGAGGATCATAACACTTGAGAGATGATCCCTACTTGAAAAG
GCGGAGACAATACCTCTTGTTTTGTTGCGACAAATCGAGTTTCAAAAGCCCATTTATCCATCACA
TTTTCAGGCACACCAGTCAAAGAGCCATCGGACCCATGAAAGTCCCCTTTTTTAATATACACAGC
CTTTGCCAGGATGTCTTTCATCAAGCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 260157 -- 260656
CCAAGGGATGATCTCGGATTGAAATCCAAGGCATGGTCCGCCCCAGGAAAAAAAAGAATTCCGAA
AACCCCACTAAAAAGAGCGATTGAGAGTGGATTTCAGGTTCGATAGTGTCGAGAAGGTATTAGCC
ACCGGTGACCGTACTTTCGTAAAAGCACCATTGGGCGGTGCTTCCTCTCTTTTTTCTGGAACCTC
GAACAAAAAATCGATCCCGCCATCAGCTCGACTAAGAGTTCCGAATCGAAAAAGTAAACTGAACT
TGACGGCCGAAAAAAACCGGTTTCTTAAGGGGGCGTAGCGCTTGCTTACTTTTTAGAGTAAGGAA
GAAAAGACAAGCAAAGTAAAGACCAGCGACACTTCCTCTTCCGGTCCGGAGGCTTAATCTTATAG
TTCTCCCTCTTATCTTCTGCTTACTATTGAAGTGGTTTTTCAACCGTTGCCTCGACTTGGTTAAA
TTGCATTTGTATTCGCTCAAATTCCGGCTGAATCCTCTGCCGGTA
Found at i:290044 original size:21 final size:21
Alignment explanation
Indices: 290005--290044 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
289995 CTTTTCGTTG
*
290005 GTCAACAACCAACTCTCTATA
1 GTCAAAAACCAACTCTCTATA
290026 GTCAAAAACACAACT-TCTA
1 GTCAAAAAC-CAACTCTCTA
290045 CAGGCCGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.42, C:0.30, G:0.05, T:0.23
Consensus pattern (21 bp):
GTCAAAAACCAACTCTCTATA
Left flanking sequence: Indices 289505 -- 290004
TCGAGGAACGTGTCTTGTTGGAACCGATGCCATCTTCGGGTGAATCCAGCGAAGCTAGCGTGAAT
CAGCAGCCTGTGATTCCCGAGCTGGAGCCTCCACTTATGGAGGAGAACGCCCGAAGAGCGGAGCT
ATATGGTCGATTGCGGACCAATTTGTGGGGGAGGCCTTATACCGAAGGGGCCCTAGAGTCTGTCG
TTGGCAGACAAGTGCCCATCGAAAAACACATTTTTGCCGCACTTGTGGAAGATGGGTACGATCCT
CAAGTTGTCTTTGAAAAAAGACATCTTATTCGGGGCTTTATTTTCTACCCGAATGGGGAGGCGCT
TAGTGAAAACACTTATGCCAATCATCTAACCGAAATTCTCAATTCGGGTACACGGCAAAGCCTTC
CATACCACCGGGTTATAAAAGCGATTCGAAACTCGGATCTCTTTTTATAACTGGGATCATCCCTC
TTTCACTTCTTTGGTGCATCTTTCTTTTTCCCATGCTTTTCGTTG
Right flanking sequence: Indices 290045 -- 290544
CAGGCCGTCTGTCTGGAGGGAAGAATTTTTTCTCAATCAATCATGCCTCAACTGGATAAATTCAC
TTATTTCACACAATTCTTCTGGTCATGCCTTTTCCTCTTTACTTTCTATATTCCCATATGCAATG
ATGGAGATGGAGTACTTGGGATCAGCAGAATTCTAAAACTACGGAACCAACTGGTTTCAAACCGG
GGGAACAACATCCGGAGCAACGACCCCAACAGTTTGGAGGATATCTTGAGAAAAGGTTTTAGCAC
CGGTGTATCCTATATGTACTCTAGTTTATTCGAAGTATCCCAATGGTGTAATGCCGTCGACTTAT
TGGGAAAAAGGAGGAAAATCACTTTGATCTCTTGTTTCGGAGAAATAAGTGGCTCACGAGGAATG
GAAAGAAACATATTATATTTGATCTCGAAGTCCTCATATAGCAGCGCTTCAAAAAATCCTGGATG
GGCGATCACTTGTAGGAATGACATAATGCTAATCCATGTTCCACA
Found at i:386646 original size:7 final size:7
Alignment explanation
Indices: 386634--386661 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
386624 GAGGGGAACC
386634 CTTACTA
1 CTTACTA
386641 CTTACTA
1 CTTACTA
386648 CTTACTA
1 CTTACTA
386655 CTTACTA
1 CTTACTA
386662 TATATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (7 bp):
CTTACTA
Left flanking sequence: Indices 386134 -- 386633
CAGACAGGTGTAGTCTAATGACTTGGTTTCCAAGAAGAATTCAATCATAAGCATGGAATCGGACA
AGCATTGGATTCTCGACCAGCCTTTTCTTGCTAACAAGCCATTCTAAAGTTCGATAGCAGCTTTT
GGACGAATTCCTATTCCGGAAAGTCACAAGTCAAGTGTAAGTACTATTCGATTTCGTTCAAAGCC
CTCCTACAGCTCCTGCTATTGCTAGAGGGATCTTCCGAGAAAGCGAAAGGCAACTCCCACTAGAG
GAGTAATGCTATTCTTAGGTACACCTACTATTGTGTATCATAATCAGTGAACTTCTTGCTGAGAT
AGTATATGGCTCTTTCCTTCCTACCTGTTTCATCGTGCTGACCAAGGACACAACTCATGGATGCT
ACCATTACTGACAGATACATCAGGAAAGGTCGACCAGGCGTTGGCGGGGAGCAAGGAAAAGCTAC
TCTGTCTGGCGATTGACATATTCTTTTGATTGAGAGAGGGGAACC
Right flanking sequence: Indices 386662 -- 387161
TATATAATATATAGAGTAGCGGGCACCATCTGGGGTCTCATTCCCCAGTACATAGGAGGGATATT
CCTTCTTATGTAAAGAAGTTTTACTGAGCACACAACGTGTTTAGTGAGATGGATTATGCTGTCTA
GCCATGTAGGACTAGTCTAGGCATAAAACACCGATGACGAAATTCTCTTGGCGAACGGAGCACTC
CCATAGGTATGGGTTGCCCTTTGGGTAACCGTACATTATTGGACTTTCTCCACTGCTTTTCAATG
GATTACTTTCATCTGAGATTTCTCAGGTGAGAGTAGTCTTTTGAAGACAGACCTGGTCGATACCA
GGCACCAGCCCCTGGGCTACCAAGGTAGTCCATTAAGGCAAGGGATTTAAGCTTGGCAGAGAAAT
CTACCATTCTTATCTCCTGGTGTTAGTATTCCCTTGTCTATCTTCCATTGATTGGCATTGGAGTA
CTCAGGATCTGTCTCTGGAGTATTATATAATAGGAAACCCATCAT
Found at i:443618 original size:20 final size:19
Alignment explanation
Indices: 443582--443628 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
443572 GACGATCTGG
*
443582 CTAATTATATATACTTCTAT
1 CTAATTAGATATACTTCT-T
443602 CTAATTAGATACT-CTTCTT
1 CTAATTAGATA-TACTTCTT
443621 CT-ATTAGA
1 CTAATTAGA
443629 AAGGCGAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
20 15 0.60
21 1 0.04
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.47
Consensus pattern (19 bp):
CTAATTAGATATACTTCTT
Left flanking sequence: Indices 443082 -- 443581
AATTCCGTTTCAAATGGTTTGAGCTTGGAAGCAACCTACTATCTATCGATAGGCGAGAACAGACT
GCTATTGGCTGCTTTGCCTATCTATTCTATTATGGCCGGCTTGGAGACATCAGAGGAAGACCATC
ATTTCTATCCGGGTACGATCATAGCTTCATTCATTCGTTGAACCTTGGGGATAACCATTAGCATT
GAGGTCAATCACCACACCACCTCTATCATACATACGACATTACATGACGCGAGAGTGCATGGTCA
ACACACACCTAAAGCGCCTACGTTCCGCTTGCAGCCAATACAACCACAACCTAACTTGCACGAGA
TTCAACAACCGAAACTACTGGTAGTCCCGAGGGGACGGCATCCTCCTATAATAGTTAGCAGTACT
GAACAAGCGAGTCATCGGTCGGGGGAAAGAAAAGGACCGCCTTTAAAAAGAAAAAAAAGGAAACG
CCCTTCGGAACAAAGGTGATTCTGTTCATGCTTCAGACGATCTGG
Right flanking sequence: Indices 443629 -- 444128
AAGGCGAACCTATAGGCCTGTTTTAGCGCGTTTCCAAAGCGGTTAGGTTGACTTTGGAAACGCTA
CTAAGGACCGGGTGAAGAATGAAAAACGTCCGCTAACGCCCACGGGATAAGATCTTTTTTAGATC
AGCAACGAATTCTTGTATCTACGAAGAAAGATTTCTCCCCGGGTTCAGACCCTAAATGCCATACC
TTGCTGAAGGCGATTCACGATAGAATCGCGCATAGTTCCGTTTGACCGAGATGTGAATGCCCGTG
ATCTGTTCGGTATAGTGATGGATTTCATGGCCGACGTCTAACCGGCACGAATACGCCGACATGAA
ACGAGTTCCCCGCGGAGCATTTTTTTTTTCTTTCGTTCTCGGACGTTTTGTTCGATTCCGGCACT
TGCGTTCTCATGCCCGGAACCCTCGCGATTGATTGGGAGAAAGAGCGAAAGCGAGAAAGATGGAT
TGTTATCCATCGGAAATCGATAGGAATTCCCCGGGGATTGCCTTA
Found at i:450668 original size:25 final size:24
Alignment explanation
Indices: 450630--450676 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
450620 CCGCTAGCTG
450630 TCACTCCTTGCCCTATTCGGTCGCT
1 TCACTCCTTGCCCT-TTCGGTCGCT
450655 TCACTCCTCT-CCCTTTCGGTCG
1 TCACTCCT-TGCCCTTTCGGTCG
450677 AGTTCTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 12 0.57
26 1 0.05
ACGTcount: A:0.06, C:0.43, G:0.15, T:0.36
Consensus pattern (24 bp):
TCACTCCTTGCCCTTTCGGTCGCT
Left flanking sequence: Indices 450130 -- 450629
TGTTCAATATCTCGGCTGCTCAAGAAGTTGGACTAGCTGCTCCTCCGACCCGGAGTGGATTCTAG
GGGAAGGGCAGAGCCTCACCTTGCAGTAGGAAGGTGTTCGTTGCTGGGACGGGTTCAAACTGGAC
TGAAGGGAGGAGGAATTAAATAGTCCTCTCTTCCTGGGGATTCATCACTGGCTAGGGCTTTCGAA
TCAAAGCATGGGCATCTGCAACTAAGAGGGAGCAGTAGATCGTCGATTGAAGAGCCAGGTCAGTA
AACTTCTATTGGGACTTCTATTGATTATAGATTCGACTATAGGGACTCCTAGCAACAAACTTGTA
TGACGGGGCCCCCATGGAGACGCCAGCCGGATCGACCAATAAATGATAGGCCAGAGGGATGGGCT
CATTCGACTAATTAGTGATCCCTGGCCCTACCTAACAAAGAGATGTCCCTAAACTAAAATAGGGG
ATTGGTTGGGAGTATTCCATAAAAATCTTTCTGATCCGCTAGCTG
Right flanking sequence: Indices 450677 -- 451176
AGTTCTTACAAACCTCTCCTTTCAGTCGAGCACTTCATACACTAGCCTGGAGAGATAGGAAAGAC
GCTCTGCTCTAAAGGGATCCTTCAAGACAAGCTGGCCGAACTGATGCTTAATGAGCATCACATTG
ATCGTATTAGGGAGATGTCCCCCTATTCAGATTTAAGGAAGGAGGCCTATCACTTCATTCAGGAT
AGGTTTCCTCCCCTGCATTATTATATATATAATTATAAACAAAGAAGAAAATCATTTTTTTATCC
AATTGTTCATTCCTGGGAAGAGGAAGAAGCAGATAGAGCAAGGGCCTCCTCTTCTTCCCGAAGTG
AGCGAATTGCATGTAGAGATCCTTAGGGGCTTATAGTTTAATTGGTTGAAACGTACCGCTCATAA
CGGTAATATTGTAGGTTCGAGCCCTACTAAGCCTACCACCCCCTTCTCTTCACCCGATACAAGAA
GGCAGTCGAAGTCCCCTCCACTCTTCATCAGTGCTTCAAATAGCA
Found at i:455467 original size:28 final size:29
Alignment explanation
Indices: 455435--455510 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
455425 CAATCGCTCA
*
455435 AGGTTTGAAGA-ACTCGACCATTAGGGAG
1 AGGTTCGAAGACACTCGACCATTAGGGAG
* *
455463 AGGTTCGTAGACGCTCGACCATTAGGGAG
1 AGGTTCGAAGACACTCGACCATTAGGGAG
* *
455492 AGGTTCGTAGACGCTCGAC
1 AGGTTCGAAGACACTCGAC
455511 TGGTAAGGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 9 0.20
29 35 0.80
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (29 bp):
AGGTTCGAAGACACTCGACCATTAGGGAG
Left flanking sequence: Indices 454935 -- 455434
GTAGTGGAGAGACAGAGATCACATTAGATTTCTACGGGAAAGCAAGAGTTTGAGCTATCAGCCAG
AAAGATCAAATTAGCATCGGATTCGGGTCGGACTTCACCGACGAGATTTGCAATAGTCATAGCGG
TGAATCAGAGCTTTGACTAGCCGGAATAGTAGTCAAGGTCTTCAAGCCTCATGTCGGCCAAGGCA
AGACAGCAAGCTACGAATAATCATCTAAGTGACTCTCCAGGCCGGGTTTAGGCCAAGAACCAGAA
GAAAGGGAACCCTTACCCGATACGGGAATGGGGATAGACTGATTAACCTACCTTTGGAGAGCAGC
GAATCCTTAGATTGCTACCAACTAGACTAACAGATAGAATGAAGAGAGTGCTGGACTTACATACG
TTATTTCCTACAAGACGGACTAGAGGATAGTACCTTGGACTGAGAGAGACTTTTTAGGCCATAAG
CGAGAGGGCCATGGTGCTAGAACTCAAAGAAGATTCAATCGCTCA
Right flanking sequence: Indices 455511 -- 456010
TGGTAAGGAGAGGAATGAAGTGAAGAATTGCCATTTTATGAGCTTGTAAGGCTCGTCGTTGAAGT
CCCCGAATAAAGGGGAAAGGGCTAAAAGTAGGCCGTTTGCTATTGCTATAAGGGCTGCTCGCCTT
TATAGCTTCGCTTTATTCAAGCGTTTTCGCACAATGAAGTGCATCCGGTGTCCGCGAGGCGAATG
ACCGGTTGTGAGATGGCGGACTCAGTCCGGGTCTTACCCATCTCTATATTTGGTTATTTAACCTC
ACTCTGATGACACTCAGAGTCCTTTTCTTGGTTAGAAGAGGTGCCTCCCCTCGGCTGTTTCTACA
GCCGTTTAGGCGAGTCTTGGTCCTTTTCAAGGTAGAAGTTTATTATAGATATCCACCTCACGGTG
GGATCGGACGGTGACGCGGAAGCCAGTCCAGCGGTAAGCTAATACCACTGGTTTGGAATTGGCTG
TCGCGCCAGGGCGTACCGGCTAGGAAGCACATTAGGAAACTAATA
Found at i:455480 original size:29 final size:29
Alignment explanation
Indices: 455447--455510 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
455437 GTTTGAAGAA
455447 CTCGACCATTAGGGAGAGGTTCGTAGACG
1 CTCGACCATTAGGGAGAGGTTCGTAGACG
455476 CTCGACCATTAGGGAGAGGTTCGTAGACG
1 CTCGACCATTAGGGAGAGGTTCGTAGACG
455505 CTCGAC
1 CTCGAC
455511 TGGTAAGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.20
Consensus pattern (29 bp):
CTCGACCATTAGGGAGAGGTTCGTAGACG
Left flanking sequence: Indices 454947 -- 455446
CAGAGATCACATTAGATTTCTACGGGAAAGCAAGAGTTTGAGCTATCAGCCAGAAAGATCAAATT
AGCATCGGATTCGGGTCGGACTTCACCGACGAGATTTGCAATAGTCATAGCGGTGAATCAGAGCT
TTGACTAGCCGGAATAGTAGTCAAGGTCTTCAAGCCTCATGTCGGCCAAGGCAAGACAGCAAGCT
ACGAATAATCATCTAAGTGACTCTCCAGGCCGGGTTTAGGCCAAGAACCAGAAGAAAGGGAACCC
TTACCCGATACGGGAATGGGGATAGACTGATTAACCTACCTTTGGAGAGCAGCGAATCCTTAGAT
TGCTACCAACTAGACTAACAGATAGAATGAAGAGAGTGCTGGACTTACATACGTTATTTCCTACA
AGACGGACTAGAGGATAGTACCTTGGACTGAGAGAGACTTTTTAGGCCATAAGCGAGAGGGCCAT
GGTGCTAGAACTCAAAGAAGATTCAATCGCTCAAGGTTTGAAGAA
Right flanking sequence: Indices 455511 -- 456010
TGGTAAGGAGAGGAATGAAGTGAAGAATTGCCATTTTATGAGCTTGTAAGGCTCGTCGTTGAAGT
CCCCGAATAAAGGGGAAAGGGCTAAAAGTAGGCCGTTTGCTATTGCTATAAGGGCTGCTCGCCTT
TATAGCTTCGCTTTATTCAAGCGTTTTCGCACAATGAAGTGCATCCGGTGTCCGCGAGGCGAATG
ACCGGTTGTGAGATGGCGGACTCAGTCCGGGTCTTACCCATCTCTATATTTGGTTATTTAACCTC
ACTCTGATGACACTCAGAGTCCTTTTCTTGGTTAGAAGAGGTGCCTCCCCTCGGCTGTTTCTACA
GCCGTTTAGGCGAGTCTTGGTCCTTTTCAAGGTAGAAGTTTATTATAGATATCCACCTCACGGTG
GGATCGGACGGTGACGCGGAAGCCAGTCCAGCGGTAAGCTAATACCACTGGTTTGGAATTGGCTG
TCGCGCCAGGGCGTACCGGCTAGGAAGCACATTAGGAAACTAATA
Found at i:455520 original size:29 final size:29
Alignment explanation
Indices: 455447--455523 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
455437 GTTTGAAGAA
* *
455447 CTCGACCATTAGGGAGAGGTTCGTAGACG
1 CTCGACCAGTAAGGAGAGGTTCGTAGACG
* *
455476 CTCGACCATTAGGGAGAGGTTCGTAGACG
1 CTCGACCAGTAAGGAGAGGTTCGTAGACG
**
455505 CTCGACTGGTAAGGAGAGG
1 CTCGACCAGTAAGGAGAGG
455524 AATGAAGTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.19
Consensus pattern (29 bp):
CTCGACCAGTAAGGAGAGGTTCGTAGACG
Left flanking sequence: Indices 454947 -- 455446
CAGAGATCACATTAGATTTCTACGGGAAAGCAAGAGTTTGAGCTATCAGCCAGAAAGATCAAATT
AGCATCGGATTCGGGTCGGACTTCACCGACGAGATTTGCAATAGTCATAGCGGTGAATCAGAGCT
TTGACTAGCCGGAATAGTAGTCAAGGTCTTCAAGCCTCATGTCGGCCAAGGCAAGACAGCAAGCT
ACGAATAATCATCTAAGTGACTCTCCAGGCCGGGTTTAGGCCAAGAACCAGAAGAAAGGGAACCC
TTACCCGATACGGGAATGGGGATAGACTGATTAACCTACCTTTGGAGAGCAGCGAATCCTTAGAT
TGCTACCAACTAGACTAACAGATAGAATGAAGAGAGTGCTGGACTTACATACGTTATTTCCTACA
AGACGGACTAGAGGATAGTACCTTGGACTGAGAGAGACTTTTTAGGCCATAAGCGAGAGGGCCAT
GGTGCTAGAACTCAAAGAAGATTCAATCGCTCAAGGTTTGAAGAA
Right flanking sequence: Indices 455524 -- 456023
AATGAAGTGAAGAATTGCCATTTTATGAGCTTGTAAGGCTCGTCGTTGAAGTCCCCGAATAAAGG
GGAAAGGGCTAAAAGTAGGCCGTTTGCTATTGCTATAAGGGCTGCTCGCCTTTATAGCTTCGCTT
TATTCAAGCGTTTTCGCACAATGAAGTGCATCCGGTGTCCGCGAGGCGAATGACCGGTTGTGAGA
TGGCGGACTCAGTCCGGGTCTTACCCATCTCTATATTTGGTTATTTAACCTCACTCTGATGACAC
TCAGAGTCCTTTTCTTGGTTAGAAGAGGTGCCTCCCCTCGGCTGTTTCTACAGCCGTTTAGGCGA
GTCTTGGTCCTTTTCAAGGTAGAAGTTTATTATAGATATCCACCTCACGGTGGGATCGGACGGTG
ACGCGGAAGCCAGTCCAGCGGTAAGCTAATACCACTGGTTTGGAATTGGCTGTCGCGCCAGGGCG
TACCGGCTAGGAAGCACATTAGGAAACTAATATGAATCCTACCCG
Found at i:463170 original size:23 final size:22
Alignment explanation
Indices: 463128--463171 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
463118 TAAGGCCCAA
463128 TATGCTAGTGCTAGTCTAGCTCC
1 TATGCTAGTGCTAG-CTAGCTCC
463151 TATGCTAGCTTGCTAG-TAGCT
1 TATGCTAG--TGCTAGCTAGCT
463172 TATATAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 13 0.68
25 6 0.32
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (22 bp):
TATGCTAGTGCTAGCTAGCTCC
Left flanking sequence: Indices 462628 -- 463127
GGGGGATTCTCTATTTCTTATCCTGCCCCTGACTTCATTTTAGAAAAGCAATCTCGAGAGGAAAA
AGTACTCGAATAGCCCCTCATTTCCCATAATCTTGTCTTGGAAGAGGCTCGACTGGACCCAGAAC
TTGACTCCACTTGCTGAGAATCTCATCTTGTGTGTTTTTTTCTTATTTTCGTAAGTAAGAATCTT
TCCTTTGTTTGGCTTGAGTTCCTTCTCATTTGTCAGGAGATGGAGTCATATGAGGTGAAACTCAT
TTGAAACGAAATGAGTTGATAAACGAAGACTCAGATTCCTCATATTGGTGGTTTCACAACTTGAT
CAGGGGCTGATAAGTGAGAAGGTCTTTCTATCCAGACACTAATCAGGCAGGTGAATGCGATAGCA
GTGTGTGCTGAGTCATGTATTCTGTTTTCGGAGAGCTAGAGAGACTAGGCCGCGGACATTGTGTA
GGCAGCGCAATAGTGCTTCTTACTCTACGGAGCGTTAAGGCCCAA
Right flanking sequence: Indices 463172 -- 463671
TATATAACTATACTGTACTAGCTTACGGATTGCTTTCCTTTCCTCTCACTGACTAGCTATACTAC
AGAAGGAATTGCTTCCCTGGCTTACGACTGGCATTACTACTTTCTAAGAACCGTGCTTTCAACCC
TTGGCTCGATTGCTTGACTGGAATCAGAGGAATTCATGGACAGCTACTGTTAAGAAGCATGAACT
CTTCATTCGCCTAGGTGTTTTCATATAAGTAAGATGCCTCCCGCTCGCACTCCCACTGATTGGAT
TGAACTGAGACTGGTACTAGTTGACTAAAAGGAGTACCTCTTAACTGAACAATCGTCGGAATGTG
TATAATAGTGCACTAAGAGACTTTCTTATAGTTATGATATCAAGTATTCTCAAATCCGCTAGTTG
AACCTTCTTCGGTCTCTTTCAGCGGGGAGGAAAACTCTTTCCGAGTTTTGGATGCTTGCTAAACA
ATTGAGAAGGATCTTAGCTCCCGGTGACCGGCTTTGCGGGACCGC
Found at i:504481 original size:7 final size:7
Alignment explanation
Indices: 504469--504496 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
504459 GAGGGGAACC
504469 CTTACTA
1 CTTACTA
504476 CTTACTA
1 CTTACTA
504483 CTTACTA
1 CTTACTA
504490 CTTACTA
1 CTTACTA
504497 TATATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (7 bp):
CTTACTA
Left flanking sequence: Indices 503969 -- 504468
CAGACAGGTGTAGTCTAATGACTTGGTTTCCAAGAAGAATTCAATCATAAGCATGGAATCGGACA
AGCATTGGATTCTCGACCAGCCTTTTCTTGCTAACAAGCCATTCTAAAGTTCGATAGCAGCTTTT
GGACGAATTCCTATTCCGGAAAGTCACAAGTCAAGTGTAAGTACTATTCGATTTCGTTCAAAGCC
CTCCTACAGCTCCTGCTATTGCTAGAGGGATCTTCCGAGAAAGCGAAAGGCAACTCCCACTAGAG
GAGTAATGCTATTCTTAGGTACACCTACTATTGTGTATCATAATCAGTGAACTTCTTGCTGAGAT
AGTATATGGCTCTTTCCTTCCTACCTGTTTCATCGTGCTGACCAAGGACACAACTCATGGATGCT
ACCATTACTGACAGATACATCAGGAAAGGTCGACCAGGCGTTGGCGGGGAGCAAGGAAAAGCTAC
TCTGTCTGGCGATTGACATATTCTTTTGATTGAGAGAGGGGAACC
Right flanking sequence: Indices 504497 -- 504996
TATATAATATATAGAGTAGCGGGCACCATCTGGGGTCTCATTCCCCAGTACATAGGAGGGATATT
CCTTCTTATGTAAAGAAGTTTTACTGAGCACACAACGTGTTTAGTGAGATGGATTATGCTGTCTA
GCCATGTAGGACTAGTCTAGGCATAAAACACCGATGACGAAATTCTCTTGGCGAACGGAGCACTC
CCATAGGTATGGGTTGCCCTTTGGGTAACCGTACATTATTGGACTTTCTCCACTGCTTTTCAATG
GATTACTTTCATCTGAGATTTCTCAGGTGAGAGTAGTCTTTTGAAGACAGACCTGGTCGATACCA
GGCACCAGCCCCTGGGCTACCAAGGTAGTCCATTAAGGCAAGGGATTTAAGCTTGGCAGAGAAAT
CTACCATTCTTATCTCCTGGTGTTAGTATTCCCTTGTCTATCTTCCATTGATTGGCATTGGAGTA
CTCAGGATCTGTCTCTGGAGTATTATATAATAGGAAACCCATCAT
Found at i:565867 original size:18 final size:18
Alignment explanation
Indices: 565846--565888 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
565836 CAACCTTGTT
565846 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
565864 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
565882 GACTATG
1 GACTATG
565889 GCAGGGCTTT
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:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 565346 -- 565845
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 565889 -- 566388
GCAGGGCTTTAGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTGA
AGATTTAAAAGGCGAGCACTGAAATGAGAAATTTCATTCGTGACGCTGAACGACACATTCGAAAA
CTAAAGCGCACACTAGAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCGGAGCCGGAGCCCGGCAT
GTTCGCCTGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTTTAGATAACAAAAAGTGTC
CGCCCGGTCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTAGGGCGACCGG
GCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGA
AGAGGGGGCAGAGATTCTTTCTCGAATTTTATTATATACAATCATTCTTCGTCTGCCCGGTTAAG
GATCGAGTATGAATATTCATTATAGATAGATACCCTGGTAACTGG
Done.