Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_071229
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: 404807
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:36533 original size:29 final size:29
Alignment explanation
Indices: 36479--36534 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
36469 ACTGATGCCG
* *
36479 TGGGTCAAGCCCTTGTTTAGGCAACTACA
1 TGGGTCAAGCCCTTGTTTACGAAACTACA
36508 TGGGTCAA-CTCCTTGTTTACGAAACTA
1 TGGGTCAAGC-CCTTGTTTACGAAACTA
36535 ATTCGACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (29 bp):
TGGGTCAAGCCCTTGTTTACGAAACTACA
Left flanking sequence: Indices 35979 -- 36478
ACTAAGGTAAAGTGGTTCGACAGACGGTAGGGTACGACTGAAGCAATCCGATGGCTATTGTACAT
GTACGTGGGGTTGCAAGAGAGCATAGGAGCAAAGTCAGATTAGAACACTCTCCAAAGAAGTCCGA
AACGGATATTTTTGTATACGGAGACCGAGCTTCTATTCTAGAGGTTCCAGAGGGGCTGGCTTTGA
ATAGCCCAGAGGAAGAGGTCTATGAATATCCCAGTTTAAGTAGAGAGGGCCTTAGAGAGGAAGGT
GCATATCCTGTGAAAGCCTACAAAGCAGATAGAATAGACGAATTGCCCTATCAGCTATCAGAAAG
AGGCCAACAAGGCTTAGAAGTAGCTGTTAGCTTCGGTATTGAATTAGCTTCCTTAGCTTAGCAAC
TATAGATAGAGATAGGAAGGACTATCGGTTACGTCGATACAGGTTTCCGCGAGAGAACTCAAACT
ATAGGTTCGTCCAGGAACTATTCGCTTTTAAGTCAACTGATGCCG
Right flanking sequence: Indices 36535 -- 37034
ATTCGACTAAAAGGCGAGGAGAGCAGGGTTTCGCAGATAAACCGGGACTGCTGTGGTCCTTACCC
CCTAAGAGACTTCTTTGTGTTATCGTTCAACTGCTGCTACTCCCCGAGCATCAGCAGTATCACTT
GCTTTGCTTTATCGCTTCTCTCTTTAGTGCAATCAATCACTAACCGACCGATCAAAACGGGTGTT
CTAAAGCTCCTACGGTCCCATAGAACAAGGATTTTCGTGTTCTCCCCTACAACCCCCTGAGGAGA
ATCAGAGCGAGAGGAAGCCTTCGTTCAGCTATCAGTGCAGCGATCAAGAAATAACGACGAGCGGA
GGAAGCAGATTGGGAGGGTGGCCATATGTATATACCAAGAGCTAGTCTAGCTCTAGCATCAAGAA
CTACCCTTGAAGTAGCATCTTAGAACTCCTTAGTGGAGTCTAAAGGCACAATTAAGGCCAATAAA
GAAGCTCCTCCAACTTGTTCCGGAAAAGGCTAGTCACTGCTAGTA
Found at i:69892 original size:13 final size:13
Alignment explanation
Indices: 69874--69899 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69864 TGACAGTATT
69874 GCCTATAGTATAG
1 GCCTATAGTATAG
69887 GCCTATAGTATAG
1 GCCTATAGTATAG
69900 TAAGTAGATT
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GCCTATAGTATAG
Left flanking sequence: Indices 69374 -- 69873
GAGAGTTGCTCTTCCTTTGTTCAATCAGTTGACTTTGCTGCTATCATATATAAATAGTTGTATCA
GATCGCTACGCCCCTTAGGCGAGTTCCGTCACCGAGGGGAGAGAGCAAGTAGTATGCCATCGATC
AACTCTTACTTTGATCCTGGCAAGGGCAATGAAGAAAAAGTCCCTTCCTGTAGCTTGGCAGTAGG
ATTAGCTTGGTTAGCAGCAGTGGACGAGTCAGTGGAAGAGCCGGTAGCTTCGATTATCAAATTGC
TAAGTTTATTCTTAGCTCTCGAGGTAGTTAGTTCAGTGGTGAGGCAACTCAATACTCAATTAAGT
AAGTCACATATTTCCTTAGTCATAAGGTCTTCCTGGTCCTATCGAACCAGTCACTTCATACCTGG
ATCTTGTCCTTGCCTTAGCGCCTTAGCTTTCTTGGGCTAGGAACGAACCAGATAAAAGTAGTAGC
CTAGCAGTGATAGTATGCTTGAAAGCTTTCCTAGCTGACAGTATT
Right flanking sequence: Indices 69900 -- 70399
TAAGTAGATTGATTCGGCATAACCATAAGCGGTCTTGTAGGCCGGGCTAGTAGTTGTGGTGAGGT
ACTTGGGAATAAGAACTCCTCTTTTCAACCTTTTTCCCGTTTCCGAAAAAAGGAAATTGAGAAAG
TTTCACGATTGAACTCTCTTTCTATTAATGGAAATCCCATCGAAAGAGATGGGGGGAATCGAGAA
ATGGATCTTGTCACCTCTGCTCTGCCTCTACCAATTGGAGTAGAGCAAAGAAAACTCTGTCTGCT
GGTCAACATTTAATAAGTCCTGCCCAGAGGTAGGCATCGATTGAAGAAGAAAAGTCTCTATATAG
AATAAAAAAAGGAGCGAAGCAGCTCGACTGGTTGGAGAGGAGATCGAACAGCATAGGCTGGTAGT
CTTTCCGTCCTTCTCAGCGAGATTGGATAGGATTCCCTTTCTTTCAGGAATTCTTTGTTGTATAG
AAATAGGAAGAAAAGGCGTAGCTCTCTTTCTGCTGTTAGCAGGAT
Found at i:136827 original size:14 final size:14
Alignment explanation
Indices: 136808--136840 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
136798 CAAAGAGCCT
*
136808 TCTTATTCTATTAA
1 TCTTATTCCATTAA
136822 TCTTATTCCATTAA
1 TCTTATTCCATTAA
136836 T-TTAT
1 TCTTAT
136841 AGAAGGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (14 bp):
TCTTATTCCATTAA
Left flanking sequence: Indices 136308 -- 136807
CTAATAATTAATCATTCCTTCTTCTAGCTCCTATTGAATCCGCTTTTTCGTAAGAGAAGAGGAGT
AGAAATAGAAGGAAAAATCACCCAAGAAAGCAGTGAGCCAAGGAAGCAAGGGGACAAAGGGTTGG
TAGCCCGCTTACGGTCTCATTCGAGTCATTCTGGGCAAGACAGTCGGAAGCGAGCCAAAGCAGTA
GGACGTTCTCGGTTCAGTGTGCCAAGCCGCTTTCAAGCATTCCAGCGAGCCTCTTTTTTTTTTCT
TTTAGCTATCTCAACTCTTCGACTTCGAAAAACGAGGATTCTTTCTTCAGTGGAAGAGAAAGAAA
ACCCTCTATTACATCGACCCTTGCGTAGGAAAGATGGGGACCGGTGCGCGGACGACCCGGAGATA
GAGCTCGGAATCAGTAGAGCAGCAGAAGACCAACCCGCCCGGGTCTGTCGTCCTCTTCATTATAA
TCAAAAAAAAAAGTTTAAGTTTCAAAAAATTAGAGCAAAGAGCCT
Right flanking sequence: Indices 136841 -- 137340
AGAAGGTGGGATTCAATCCAGTCCCAAGCGTACCTGGAACTATCCTCTTTCCCGTCCTATTTTTG
ACTCTTCAACTAGAGGATTGGTTAGACCGATTGGACAGCTTTCCTTGGCCTTAATCATATAGTTA
CCTTATCTAAGTAAAGGAGTGAAGTTTGAAGTAGAGAGACAGTTCTTTTATCAATCAAATAGGCT
AGCTTCCTTGCTTGCATCCTTTCCTCTCTTTCAACATGAAATAAATATATCTGTCTCGACTGCCG
AATCCTGGACCGGAGAAGCTGCTAGCCTTCTTGGAAGCTAGAAAGAAAGCTAGCCTTCCTTCCCC
CCTGTAGCTATCTAAGGTTTGCCTGTAACCTTGCTCTCTATCGGCTAAAGCATGAAAGAGCTGTT
ACATAATAAGGTCTTATAGAATCATCTGTTCAAACCTATTCTCCGCATGCCATGTCTGTGCTTTA
CTGCCTTACTTGACTCTAGCATTTTCATGATTCTAGCGAAAGTTC
Found at i:165950 original size:15 final size:15
Alignment explanation
Indices: 165910--165950 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
165900 TGTTAGTAGT
165910 AGTAGTTCCAAAGCC
1 AGTAGTTCCAAAGCC
* *
165925 AGTCGTCCCAAAGCC
1 AGTAGTTCCAAAGCC
165940 AGTAGTTCCAA
1 AGTAGTTCCAA
165951 CCAAGTCAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (15 bp):
AGTAGTTCCAAAGCC
Left flanking sequence: Indices 165410 -- 165909
ACCTATTTTGGTTATAGCCTGGTCATTGTGTGCGATCGTTTAGTCCGGGAGGAGTGAACTACCAG
ATAGTCCAAGGCGACCTCGTCTTCGCACTTGACCCTCTCATTTGAACTGAACTCTTGTGCTTGAA
CAACGAACCCCGGGTGGGGAATTGGGGGAAGAAAGCTCAACAAAGGAAGAAAGCAGATAGCAGGT
ACTTTGCTTTGCTCAAGCACTTTGCTTTAGGTCGCAATCCTAGCACTGGCGAATTTTTCAACTCA
GCTGCCTAGGATTCTAAGTCCAATAAAAGAGGACCAAAAGTACCTCCTGCTTGACTCGCATCTCG
ACTTCTATCTCGACTTTCAATAACATGTGTTAAGCATGTAGCTAAATGGCATGTTGAAAGCCGAA
CTAAACCTAGTTCTCCTAGGAAAGATTGAGGAAAGAGATTGGTTTCGAGTTCTAGTAGGTAGCCA
GCATTTGTTATTTTTTATAGTACATATTATATTATTGTTAGTAGT
Right flanking sequence: Indices 165951 -- 166450
CCAAGTCAGCGACGCGAAGCGAAGGATAAATATCTTTTTTATTAGAAAGCAAGTCCGCCCCACGA
TTATAGTTATCTTATCTGTTAGTGAGAGCAAGCGAGGGAAGCTAGCGGTGGGAAGCCAACCAACG
ATTCTAGTTCTGCTCTTTCTGTTGAAAGCAAGCCGCCGGCGGGCGGTATTTATTCAAAAGTTGTC
GCTGAACCCTTCGATTCTTCCTCCGATGAAGCAGTCGAGAAGTCAATTGAAAAGGTACCATACCA
GCGGGGGATATCTCCATCGAAGTCTCCAAATCGAGAAAGGTTCTAATTGCCCTTAAATCATCGTT
TTAAGCCGCGTTCCGCTGATTAGATAGTTAAAATTCTCCATTAGACGCTTCAAATGACGATGACG
CCCATTTAATAAATGGATGAATTCTTCTAATTGTTCTGATTCTGAGAAAGCGGATTTGTCTGCTT
ATTCAAGGGATGAACCAGATTCTTCAACTGCAATTGAGGAAGCTG
Found at i:233722 original size:18 final size:18
Alignment explanation
Indices: 233699--233736 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
233689 ATACAAATCT
233699 AATACTAATAGAATAGAA
1 AATACTAATAGAATAGAA
* *
233717 AATACTAATATAATTGAA
1 AATACTAATAGAATAGAA
233735 AA
1 AA
233737 GAACTGTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (18 bp):
AATACTAATAGAATAGAA
Left flanking sequence: Indices 233199 -- 233698
TTCCGAAGGAACTGGAGTTACATTTCTTTTCCATTTCCATTCAAGAGTTCTTATGTGTTTCCGCG
CGCCTTTGAGACCCCGAAAAATGGACAAATTCCTTTTCTTAGGAACACATACAATATTCGTCACT
ACAAAAAGGATAATGGTAACCCCACCGTTAACTACTTCATTTATGAATTTCATAGTAATAGAAAT
ACATGTCCTACCGAAACAGAATTTGTAACTTGCTATCCTCTTGCCTAGCAGGCAAAGATTTACCT
CCGCGGAAAGGATGATTCATTCGTATCAAAACGAGAGTCCAACTACATTGCATTGCCAGAATCCA
TGTTGTATATTTGAAAGAGGTTGATCTCCTTGCTTCTCTCATGATACAACCCTCTTTCCGCTGAG
CCCCCTTTCTCCTCGGTCCACAGCACAGAGACAAAATGTAGGACTGGTGCCAAAAGTGAATCACG
GAAGAAAGGACTCACTGAGTCGGGATCACTAACTAATACAAATCT
Right flanking sequence: Indices 233737 -- 234236
GAACTGTCTTTTCTGTATACTTTCCCCGGTTCCGTTGCTACCGCGGGCTTTACGCAATCGATCGG
ATCATATAGATATCCCTTCAACACAACATAGGTCATCGAAAGGATCTCGGAGACCCACCAAAGCA
CGAAAGCCAGGATCTTTCAGAAAATGGATTCCTATTCGAAGAGTGCATAACCGCATGGATAAGCT
CACACTAACCCGTCAATTTTGAATCCAATTCGGGATTTTCCTATTGTTAGTTGGTATTTAGTTGT
CGGAAGGCAAATACTTCCTGTCCATTTTGATTTTAGAACTAGTGGAAAGAATTTGGAACAAAATA
AGGCAGCATTGATAGACCGTTGAATGAGAATGGGAATCGTCTTAGCAACTGGCTATAGCCATGAG
TAAAAGCCGCCGGGAGAGGAGAGACAATCTTTCATGAGAGAGGGACGAGCAAGTGACGGATTGGG
AAAAAAAATAGAAATAGAGGGCCAACTCTTCTAGTTGCGCCTCTA
Found at i:233730 original size:23 final size:23
Alignment explanation
Indices: 233693--233739 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
233683 TAACTAATAC
*
233693 AAATCTAATACTAATAGAATAGA
1 AAATCTAATACTAATAGAAAAGA
*
233716 AAATACTAATA-TAATTGAAAAGA
1 AAAT-CTAATACTAATAGAAAAGA
233739 A
1 A
233740 CTGTCTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.26
Consensus pattern (23 bp):
AAATCTAATACTAATAGAAAAGA
Left flanking sequence: Indices 233193 -- 233692
TACCATTTCCGAAGGAACTGGAGTTACATTTCTTTTCCATTTCCATTCAAGAGTTCTTATGTGTT
TCCGCGCGCCTTTGAGACCCCGAAAAATGGACAAATTCCTTTTCTTAGGAACACATACAATATTC
GTCACTACAAAAAGGATAATGGTAACCCCACCGTTAACTACTTCATTTATGAATTTCATAGTAAT
AGAAATACATGTCCTACCGAAACAGAATTTGTAACTTGCTATCCTCTTGCCTAGCAGGCAAAGAT
TTACCTCCGCGGAAAGGATGATTCATTCGTATCAAAACGAGAGTCCAACTACATTGCATTGCCAG
AATCCATGTTGTATATTTGAAAGAGGTTGATCTCCTTGCTTCTCTCATGATACAACCCTCTTTCC
GCTGAGCCCCCTTTCTCCTCGGTCCACAGCACAGAGACAAAATGTAGGACTGGTGCCAAAAGTGA
ATCACGGAAGAAAGGACTCACTGAGTCGGGATCACTAACTAATAC
Right flanking sequence: Indices 233740 -- 234239
CTGTCTTTTCTGTATACTTTCCCCGGTTCCGTTGCTACCGCGGGCTTTACGCAATCGATCGGATC
ATATAGATATCCCTTCAACACAACATAGGTCATCGAAAGGATCTCGGAGACCCACCAAAGCACGA
AAGCCAGGATCTTTCAGAAAATGGATTCCTATTCGAAGAGTGCATAACCGCATGGATAAGCTCAC
ACTAACCCGTCAATTTTGAATCCAATTCGGGATTTTCCTATTGTTAGTTGGTATTTAGTTGTCGG
AAGGCAAATACTTCCTGTCCATTTTGATTTTAGAACTAGTGGAAAGAATTTGGAACAAAATAAGG
CAGCATTGATAGACCGTTGAATGAGAATGGGAATCGTCTTAGCAACTGGCTATAGCCATGAGTAA
AAGCCGCCGGGAGAGGAGAGACAATCTTTCATGAGAGAGGGACGAGCAAGTGACGGATTGGGAAA
AAAAATAGAAATAGAGGGCCAACTCTTCTAGTTGCGCCTCTAACC
Found at i:304860 original size:21 final size:22
Alignment explanation
Indices: 304836--304877 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
304826 GCTCTGGAAG
304836 CTCCTCTGCTG-CACCCAAGTT
1 CTCCTCTGCTGCCACCCAAGTT
*
304857 CTCCTCTGCTGCCCCCCAAGT
1 CTCCTCTGCTGCCACCCAAGT
304878 GACAGAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.12, C:0.48, G:0.14, T:0.26
Consensus pattern (22 bp):
CTCCTCTGCTGCCACCCAAGTT
Left flanking sequence: Indices 304336 -- 304835
AAGTACCTATTCTTTTATATAAAAGATCAGGAAATCTCCACCGGAGAAGATCCGGATCCGGTACT
GCAAGAGGAAGATTCGCATCTGAGTAAGGGACATCCTCTGGGGTCAAGTATAAAAATAACTAATC
TGAAACCTCGGCTGATGAGGTTTCTTCTTTCTCCAACCTCTTGTGATCACCTTTCCCAGCTTTAT
TTTCTGCTGTGTACTTCACTGCCAAACCTACGTTTGCCTTCCTTTCTGCTTCAGCTTGCAACTTT
TTCTTTGCGGAAGCCCTTTTCCTTAGCATCTTCCTCCTCTGAGTTCTGGTCAGTTTGGGTGACTG
TGCCCCTACGGGTGTCCCTTCTGCAGCCTTCTTTTCAGACTTGGATTTCTGGACAGCAGACACCC
ATTGATCAGCAGGTGGAATGGGGACCTTAACCATCCTAGATTTCTCTGGAAAGTTAGGCATCTTC
CCAAACATTGCCAGCTGATTTGGTCTAGGTCTTCTGCTCTGGAAG
Right flanking sequence: Indices 304878 -- 305377
GACAGAACTGGCTGCTTGGGGACCAACTTCTGAGCAGCATCCTGTCTGGCAGAACCTAACTTGAT
GGCTCCAGAATCCACTAATTCTGCATGGAGGAGATTCGAACAGCTCTCACACATCCTATGCCTCA
AAACCTTCAGGTTTTCAACCAGTCTAGTCATTCCAGGAGGACTCTGCAATACCTGCTTGTATGTC
ATCCCAGTCTCACTTGCCCTCGAGGACTCAGAACCACTTTTCATCATCCCTTCAGTAGCATTCCA
TTGGTCAACTGACATGGCCTGCTTCCCTTTTCTTTCAGGAATGAGAAAATCCTCAAGTCCCATGG
CACACCTTGTGCCTGCACAGAGACTGAAGTATTCAGATTAATGCTAATCACATTCAAGTCAACTA
AAGAAGGAAAAGGAAACCTATCCACCCCCATCATCAAGAGGACATCGATTCATCTTGGCAGCTAC
CGATTACTTTTCTAGATGGGCAGAAGTGGTTTCGCTTAAAGAGGT
Found at i:310682 original size:18 final size:18
Alignment explanation
Indices: 310642--310684 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
310632 ACCGCCCTGC
310642 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
310661 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
310678 CATAGTC
1 CATAGTC
310685 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 310142 -- 310641
CGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTTGGAG
CGAATTGGATGATCGGGCCGAGGGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAATATGAAC
CTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAA
AGGCGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCGGACACTGATTGTTATCTAAAGGCGAA
GACTCTGAAGTGGGCGAACACTCGGCCCAGCGGGCGAACATGCCGGGCTCCGGCTCCGCGCACCT
GCTGACACCTTTCGAAGCACTTTCTAGTGTGCGCTAACGTTTTAGAATGTGTCGTTCAGCCTCAC
GAGTCTACAAGCCTTTATCATTTCAGTGCTCGCCTTTTGAATCTTCAGTAGGGGCCTTTAGTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 310685 -- 311184
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTAGTTGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:331514 original size:13 final size:13
Alignment explanation
Indices: 331496--331521 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
331486 TGACAGTATT
331496 GCCTATAGTATAG
1 GCCTATAGTATAG
331509 GCCTATAGTATAG
1 GCCTATAGTATAG
331522 TAAGTAGATT
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GCCTATAGTATAG
Left flanking sequence: Indices 330996 -- 331495
GAGAGTTGCTCTTCCTTTGTTCAATCAGTTGACTTTGCTGCTATCATATATAAATAGTTGTATCA
GATCGCTACGCCCCTTAGGCGAGTTCCGTCACCGAGGGGAGAGAGCAAGTAGTATGCCATCGATC
AACTCTTACTTTGATCCTGGCAAGGGCAATGAAGAAAAAGTCCCTTCCTGTAGCTTGGCAGTAGG
ATTAGCTTGGTTAGCAGCAGTGGACGAGTCAGTGGAAGAGCCGGTAGCTTCGATTATCAAATTGC
TAAGTTTATTCTTAGCTCTCGAGGTAGTTAGTTCAGTGGTGAGGCAACTCAATACTCAATTAAGT
AAGTCACATATTTCCTTAGTCATAAGGTCTTCCTGGTCCTATCGAACCAGTCACTTCATACCTGG
ATCTTGTCCTTGCCTTAGCGCCTTAGCTTTCTTGGGCTAGGAACGAACCAGATAAAAGTAGTAGC
CTAGCAGTGATAGTATGCTTGAAAGCTTTCCTAGCTGACAGTATT
Right flanking sequence: Indices 331522 -- 332021
TAAGTAGATTGATTCGGCATAACCATAAGCGGTCTTGTAGGCCGGGCTAGTAGTTGTGGTGAGGT
ACTTGGGAATAAGAACTCCTCTTTTCAACCTTTTTCCCGTTTCCGAAAAAAGGAAATTGAGAAAG
TTTCACGATTGAACTCTCTTTCTATTAATGGAAATCCCATCGAAAGAGATGGGGGGAATCGAGAA
ATGGATCTTGTCACCTCTGCTCTGCCTCTACCAATTGGAGTAGAGCAAAGAAAACTCTGTCTGCT
GGTCAACATTTAATAAGTCCTGCCCAGAGGTAGGCATCGATTGAAGAAGAAAAGTCTCTATATAG
AATAAAAAAAGGAGCGAAGCAGCTCGACTGGTTGGAGAGGAGATCGAACAGCATAGGCTGGTAGT
CTTTCCGTCCTTCTCAGCGAGATTGGATAGGATTCCCTTTCTTTCAGGAATTCTTTGTTGTATAG
AAATAGGAAGAAAAGGCGTAGCTCTCTTTCTGCTGTTAGCAGGAT
Found at i:372635 original size:12 final size:12
Alignment explanation
Indices: 372618--372642 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
372608 GATATTTTTT
372618 TTTTTTTACTTC
1 TTTTTTTACTTC
372630 TTTTTTTACTTC
1 TTTTTTTACTTC
372642 T
1 T
372643 GTGAGGGCGG
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTACTTC
Left flanking sequence: Indices 372118 -- 372617
ATTAGTTCAAGCAACCTATCAACCTAAGTTGTTGAAAGGGGCTGCTAGTTGTAGCGCGCTAGCGC
CCCTATAGAGTAAGACTCTTCTTCTGCGAGACTCCATCCAAATCCGCAACTCGTTGGTTGGTGTT
CAATTCTTTTTATTAAGACTATGCCTTCAATTCCATTCTTCGTCTTCCTAGTAGCAGTATTCTTG
CTCCACCCAACATGCATTTTAGAGTGCCGTGCCGGGGCGATAGGCGCGCCGCAGTCACGCATTCG
AGCAAGAGCCTTATTTTCCTTTGCAAGGTAATCAAAAACTAAAGAATGGATTAAAGTGATAGAGT
GTTATCAGGAGACGCTAGGCGTCGGAATTGAAAAGAAAATAAATAAGGGCTTTTTTTTTCGTCAG
CAGATTTCGCTCCTCAAGTTCTTGTTTGATCTGCCGCTGTTAGAACACCACAATATTCGTCCTTT
TGGGGTTAATGCTCTCAATGGTGAATCGATCATTCGATATTTTTT
Right flanking sequence: Indices 372643 -- 373142
GTGAGGGCGGAATGGAAGAAAAGTAATGAAACCTGCGATGGCTACTGAATAACCTCCTTTTACTT
TCTTAATAATAAAGCCTTTGACCTTTGTATTTGTTCGCCAAATCTTGTTCAGTTCCATCCAAGCT
CGGTTTTGTCTGAATCTTCGTGGAAGAAGAAGAAGCGGTTCACCAGCCACTACATCCAGGGATCT
CACCTTATCATTAAACCTGGCGGCTGCTCGCTTTTTGATCAGTGATTCACCGGCCACTAGATCGA
TGAAGAATCTCTCCAAAATCCGCTTTTTGATCAGTGATTCACCAGCCACTACATCCAGGGATCCC
ACCTTATTCTCAAACCTGGTAGCTCGGTTGATTGGCACTCCTGTGAGCTCATCTTGCATACAAAT
TCTGGGGGTCCCAGGTCCTGCATCCACCAAGAACATTTCTTCCCTTAAGCGTAAAACTTCAGATT
GTAAGGCGTTTCCACTACATAAAAAAAAACTTGAATTTGATCTTG
Found at i:377810 original size:5 final size:5
Alignment explanation
Indices: 377800--377825 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
377790 AGGAGCCCTA
377800 TCAAG TCAAG TCAAG TCAAG TCAAG T
1 TCAAG TCAAG TCAAG TCAAG TCAAG T
377826 AAAGGCCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCAAG
Left flanking sequence: Indices 377300 -- 377799
ATGAGACGCCCGCGCAAGGACCTCAATTCTCATTAGGAGGTCGAACCAAGGACCTATGGAAGTCG
GGGCTACCCCGTCCCCATGGGCAACGCAACAGTGTCCTGAGGGAGGAGTTTAGAGGCCTTATAGT
AGCACGGACTTCTTTTTCTTTCTAGGTCATGCGAAGGGGGCCAGTCCAAGATCGTACTGTTCCTC
TACAAAAACAACAGACGCTCTCAACGGCTAGGCGCCACTCTCTTTCTGAGTTATTCCAGCTTCTT
CATGATTTCGTGCCGCGGTGAACAAACAAAACCAAAAAAAAGAGGGCCGTCTCAGCGGAAGGAGA
AGGACCTGCTACGGCAGAGACTACTGACCCTCTTCTTGTTCCTAGCCGTCTGTTACGAGTCTGGG
AAGCCTGGAATCCTCAATATGAGGGATCCCTCAAAATAGAGAAGGGCGGGCAGGGCTTCCGCAAG
AGCCTCCCCCCTCTTCCCGGTCAAGATAGATGGGAAGGAGCCCTA
Right flanking sequence: Indices 377826 -- 378325
AAAGGCCAACACCAGTCTCTATATTGTTGTACGTAGACCTTTGTTTCAGGTCTTGTCAGAGCCTT
CCTCCTGCTAATCCGGCCATTTCCAAACCTTAGCTCGGCTAAATAGGCTCAATGATCTCTTTCTT
CGATAGGCCGGTCCGGCGCTCCGCGTAGAACTATTCGTACATGTTCCGACTCGCCGGTCATTATG
GATCTAGTGGCATGGCGAGGCAAGGGGGCATTGGAAAGACTAGACCATACTAAAGTAAAGAGGCA
TTCTGGAAGCGACTAGTCGCTTCTGGCGAAGCTTCTAGAAGGCCGACCACTACATAGAGAGATCC
ATATACCAGTCATGAGCGATAGCGAAGCCTAGAGAGGCGCAGGGCAGGATCGAAGAGCTTAGTGT
GAAAGGCTCCGAAAAGGAGCAGAGAAGGGGTTGTGCGCCCTCCGCCCCATCAACCTAATAATAAT
GAAGGGCTTTGATGCCAGCAAGCATCCTTGTAGTTGTTGGGGAGT
Found at i:395348 original size:20 final size:19
Alignment explanation
Indices: 395312--395353 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
395302 GACGATCTGG
*
395312 CTAATTATATATACTTCTAT
1 CTAATTATAGATACTTCT-T
395332 CTAATTATAGACT-CTTCTT
1 CTAATTATAGA-TACTTCTT
395351 CTA
1 CTA
395354 TTAGAAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 15 0.75
21 1 0.05
ACGTcount: A:0.31, C:0.19, G:0.02, T:0.48
Consensus pattern (19 bp):
CTAATTATAGATACTTCTT
Left flanking sequence: Indices 394812 -- 395311
AATGGTTTGAGCTTGGAAGCAACCTGCTATCTATCGATAGGCGAGAACAGACAGCTATTGGCTGC
TTCGCCTATCTATTCTATTATGGCCGGCTTGGAGACATCAGAGGAAGACCATCATCTCTATCCGG
GTACGATCATAGCTTCATTCATTCGTTGAACCTTGGGGATAACCAAACGCATTGAGGTCAATGAC
CACACCACCTCTATCATACATACGACATTACATGACGCGAGAGTGCATGGTCAACACACACCTAA
AGCGCCTACGTTCCGCTTGCAGCCAATACAACCACAACCTAACTTGCACGAGATTCAACAACCGA
AGCTACTAGTAGTCCCGAGGGGACGGCATCCTCCTATACTATAATAGTTAGCAGTACTGAACAAG
CGAGTCATCGGTCCGGGGAAAGAAAAGGACCGCCTTTGAAAAATAGAAAGGAATTATTTGACTTG
GCCTTCGGAACAAAGGTGATTCTGTTCATGCTTCAGACGATCTGG
Right flanking sequence: Indices 395354 -- 395853
TTAGAAGAACCTATAGGCCTGTTTTAGCGCGTTTCCAAAGGGTTAGGTTGACTTTGGAAACACTA
CTAAAGACCGGGTGAAGAATGAAAAACGTCCGCTAACGCCCACGGGATAAGATCTTTTTTAGATC
AGCAACGAATGTCTTGTATCTATGAAGAAAGATTTCTCCCCGGGTTCAGACCCTGAATGCCATAC
CTTGCTGAAGGCGATTCACGAGAGAATTGCGCATAGTTCCGTTTGACCGAGATGTGAATGCCCGT
GATCTGCTCGGTATAGTGATGGATTTCATGGCCGACGTCTAAGCGGCACGAATACGCCGACATGA
AAGGAGTTCCCCGCGGAGCATTTTTTCTTTCGTCCTCGGACGTTTTTTTTGTTCGATTCCGGCAC
TTGCGTTCTGATGCCCGGAACCCTCGCGATTGATTGGGAGAAAGAGCGAAAGCGAGAAAGATGGA
TTGTTATCCATCGGAAATCGATAGGAATTCCCCGGGGATGGATTG
Done.