Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022528.1 Corchorus olitorius cultivar O-4 contig22561, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 175698
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10779 original size:76 final size:76
Alignment explanation
Indices: 10628--10779 Score: 171
Period size: 76 Copynumber: 2.0 Consensus size: 76
10618 GACAAGGGCG
* * * * *
10628 CCGACTCCTCCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGACTTAAGACCTAGC
1 CCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGACTGAACACCCAGC
*
10693 TGGGCAGTGTC
66 TAGGCAGTGTC
* * * * *
10704 CCGACTCCACCTGGGTGCCCACATGGTTTGTC-TGAGGACCCATGTGATTTGCCTGATCACCCAG
1 CCGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAGCACCCATGTGATTTGACTGAACACCCAG
* *
10768 GTAGGCTGTGTC
65 CTAGGCAGTGTC
10780 ATAGCTCATC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
76 58 0.94
77 4 0.06
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.26
Consensus pattern (76 bp):
CCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGACTGAACACCCAGC
TAGGCAGTGTC
Found at i:11740 original size:27 final size:27
Alignment explanation
Indices: 11697--11748 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
11687 ATGATTTAGG
*
11697 GGTTACTAACTCCCTTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTTTCTTTTGA
* *
11724 GGTTACTAACACTCTTTTTTTTTTT
1 GGTTACTAACACCCTTTTTTCTTTT
11749 CAGTAGGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.56
Consensus pattern (27 bp):
GGTTACTAACACCCTTTTTTCTTTTGA
Found at i:17653 original size:76 final size:76
Alignment explanation
Indices: 17501--17653 Score: 173
Period size: 76 Copynumber: 2.0 Consensus size: 76
17491 GGACAAGGGC
* * * * *
17501 CCCGACTCCTCCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTTAAGACCTAG
1 CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
*
17566 CTGGGCAGTGT
66 CTAGGCAGTGT
* * * * *
17577 CCCGACTCCACTTGGGTGCCCACATGGTTTG-TTTGAGGACCCATGTGATTTGCCTGATCACCCA
1 CCCGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCA
* *
17641 GGTAGGCTGTGT
65 GCTAGGCAGTGT
17653 C
1 C
17654 ATAGCTCATC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
76 60 0.95
77 3 0.05
ACGTcount: A:0.15, C:0.31, G:0.27, T:0.27
Consensus pattern (76 bp):
CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
CTAGGCAGTGT
Found at i:20906 original size:4 final size:4
Alignment explanation
Indices: 20897--20923 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20887 TCCAAACATA
20897 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
20924 ACATAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:21832 original size:34 final size:34
Alignment explanation
Indices: 21789--21856 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
21779 AGGTGAAGGT
21789 CAGGGGAAAGAAGGGAACCCGAAAGACTACTCTA
1 CAGGGGAAAGAAGGGAACCCGAAAGACTACTCTA
*
21823 CAGGGGAAAGAAGGGAACCCGAAAGATTACTCTA
1 CAGGGGAAAGAAGGGAACCCGAAAGACTACTCTA
21857 AAAGGGAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.29, T:0.10
Consensus pattern (34 bp):
CAGGGGAAAGAAGGGAACCCGAAAGACTACTCTA
Found at i:21913 original size:21 final size:21
Alignment explanation
Indices: 21883--21931 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
21873 CTTTGAACTT
* *
21883 TCTGTTTTTTTTTGTGTTTTC
1 TCTGTATTTTTTGGTGTTTTC
*
21904 TCTGTATTTTTTGGTTTTTTC
1 TCTGTATTTTTTGGTGTTTTC
21925 TCT-TATT
1 TCTGTATT
21932 ATAATCCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.04, C:0.10, G:0.12, T:0.73
Consensus pattern (21 bp):
TCTGTATTTTTTGGTGTTTTC
Found at i:22699 original size:13 final size:13
Alignment explanation
Indices: 22681--22709 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22671 TGGCCTGCAG
22681 GGACTGCTGAGGT
1 GGACTGCTGAGGT
22694 GGACTGCTGAGGT
1 GGACTGCTGAGGT
22707 GGA
1 GGA
22710 GTGGGGCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.14, G:0.48, T:0.21
Consensus pattern (13 bp):
GGACTGCTGAGGT
Found at i:23795 original size:64 final size:64
Alignment explanation
Indices: 23724--23851 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
23714 TTTATTAGGA
* *
23724 AATGTAATTTCAAGGCAAAACAACCTCTTTTTGGTATTTTGTAATTTGGCCAAAGTAATAATTT
1 AATGTAATTTCAAGGAAAAACAACCTCTTTTTGGTATTTTGTAATTGGGCCAAAGTAATAATTT
23788 AATGTAATTTCAAGGAAAAACAACCTCTTTTTGGTATTTTGTAATTGGGCCAAAGTAATAATTT
1 AATGTAATTTCAAGGAAAAACAACCTCTTTTTGGTATTTTGTAATTGGGCCAAAGTAATAATTT
23852 TTTCTAAATG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (64 bp):
AATGTAATTTCAAGGAAAAACAACCTCTTTTTGGTATTTTGTAATTGGGCCAAAGTAATAATTT
Found at i:23934 original size:5 final size:5
Alignment explanation
Indices: 23919--23974 Score: 55
Period size: 5 Copynumber: 11.2 Consensus size: 5
23909 CGCTTTTAGT
*
23919 TAAAA -AAAA TAAAA TAAGA T-AAA TAAAA TAATAAA TAAAA TAATAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-A-AAA TAAAA TAA-AA
23965 T-AAA TAAAA T
1 TAAAA TAAAA T
23975 CTTTGCAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 10 0.23
5 24 0.56
6 5 0.12
7 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:23954 original size:12 final size:12
Alignment explanation
Indices: 23925--23968 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
23915 TAGTTAAAAA
23925 AAATAAAATAAGAT
1 AAATAAAAT-A-AT
23939 AAATAAAATAAT
1 AAATAAAATAAT
23951 AAATAAAATAAT
1 AAATAAAATAAT
23963 -AATAAA
1 AAATAAA
23969 TAAAATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.20
12 14 0.47
13 1 0.03
14 9 0.30
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:27192 original size:2 final size:2
Alignment explanation
Indices: 27185--27216 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27175 TGAACAAGAC
27185 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27217 CTAGTTAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27537 original size:13 final size:13
Alignment explanation
Indices: 27519--27543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27509 CTGATGCAAA
27519 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
27532 AAAAAAGAAAAA
1 AAAAAAGAAAAA
27544 AAGAATAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:28066 original size:97 final size:97
Alignment explanation
Indices: 27900--28096 Score: 394
Period size: 97 Copynumber: 2.0 Consensus size: 97
27890 ATTATGAATG
27900 TTATTAATCTTGTAATCTAAAATTACTAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGCT
1 TTATTAATCTTGTAATCTAAAATTACTAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGCT
27965 CTCTACAAACCTAATTGCCCTCTTGGATGATT
66 CTCTACAAACCTAATTGCCCTCTTGGATGATT
27997 TTATTAATCTTGTAATCTAAAATTACTAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGCT
1 TTATTAATCTTGTAATCTAAAATTACTAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGCT
28062 CTCTACAAACCTAATTGCCCTCTTGGATGATT
66 CTCTACAAACCTAATTGCCCTCTTGGATGATT
28094 TTA
1 TTA
28097 GTAACTTTTT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (97 bp):
TTATTAATCTTGTAATCTAAAATTACTAAAAAAATTATAAAAGGTATTAAAATAGCTATAATGCT
CTCTACAAACCTAATTGCCCTCTTGGATGATT
Found at i:30955 original size:692 final size:694
Alignment explanation
Indices: 29625--31014 Score: 2545
Period size: 692 Copynumber: 2.0 Consensus size: 694
29615 TAATCTACTA
*
29625 AAAAAGCTATAAAAGTTTTTAAAATTGTATTTATCAATCCTTACATTCTTAATAACATTAGTAAA
1 AAAAAGCTATAAAAGTTTTTAAAATTGTATTTACCAATCCTTACATTCTTAATAACATTAGTAAA
* *
29690 CTTTCATCAATGGTAAAGATTTACCATTTTTTTCCTCAAAAGTTACCGAAAAGGCTATAATAATT
66 CTTTCATCAATGGTAAAGATTTACCATTTTTTTCCTCAAAAGTTACCGAAAAAGCTATAATAATC
*
29755 ATAAAAAATGTATTATACTATCAACTAATTTAATGACCTTACACTATAAAGATACGTGCAATACT
131 ATAAAAAATGTATTATACTATCAACTAATTTAATGACCTTACACTATAAAGATACGTACAATACT
*
29820 GATTTTCTTATCTAAGATTAATTACTTAAAAGGTTATGGAAAACATTATAGTACTATCTAGATTG
196 GATTTTCTTATCTAAGATCAATTACTTAAAAGGTTATGGAAAACATTATAGTACTATCTAGATTG
29885 AAAGAACCTTACATCCTTATTAATTTTAGTAACCTTTTATCATCAATAAAGTGTTACAAATTTTA
261 AAAGAACCTTACATCCTTATTAATTTTAGTAACCTTTTATCATCAATAAAGTGTTACAAATTTTA
*
29950 TTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAATTGCATTTACCAATCCTTATTTTTT
326 TTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAATTGCAATTACCAATCCTTATTTTTT
* *
30015 AATAACATTAGTAAACTTTCATCAACGGTGAATATTTGTCATTTTTTTCTTAAAAGTTACTAAAA
391 AATAACATTAGTAAACTTTCATCAACGGTGAATATTTGCCATTTTTTTCTCAAAAGTTACTAAAA
**
30080 AACCTATAATGATCACAAAAGAGATATAGTACTATCCACTAATTCAATAACCTTACATCTTTTGT
456 AACCTATAATGATCACAAAAGAGATATAACACTATCCACTAATTCAATAACCTTACATCTTTTGT
30145 GATTTTGGTTATCATATTTCTTATTACTATTTTTTTGTAATTTTGATTATCATATTTCTCCAAAA
521 GATTTTGGTTATCATATTTCTTATTACTATTTTTTTGTAATTTTGATTATCATATTTCTCCAAAA
*
30210 TCTCACAATTCAACAAAACATACCCGGACCTATAAGTCAAATTTCCATATAAGGTTATAACTTAT
586 TCTCACAATTCAACAAAACATACCCGGACCTATAAGTCAAATTTCCATATAAGGTTACAACTTAT
*
30275 AACTAAACTTAATGCAACATAAGGAAGTATAAAATTAGGTGTAC
651 AACTAAACTTAATGCAACATAAGGAAGTAAAAAATTAGGTGTAC
* *
30319 AAAAA-CTATAAAAGTTTTTGAAATTGTATTTACCAATCCTTACATTCTTAATAACATTGGTAAA
1 AAAAAGCTATAAAAGTTTTTAAAATTGTATTTACCAATCCTTACATTCTTAATAACATTAGTAAA
*
30383 CTTTCATCAAT-GTGAAGATTTACCATTTTTTTCCCTCAAAAGTTACCGAAAAAGCTATAATAAT
66 CTTTCATCAATGGTAAAGATTTACCATTTTTTT-CCTCAAAAGTTACCGAAAAAGCTATAATAAT
* *
30447 CAT-AAAAATGTTTTGTACTATCAACTAATTTAATGACCTTACACTATAAAGATACGTACAATAC
130 CATAAAAAATGTATTATACTATCAACTAATTTAATGACCTTACACTATAAAGATACGTACAATAC
30511 TGATTTTCTTATCTAAGATCAATTACTTAAAAGGTTATGGAAAACATTATAGTACTATCTAGATT
195 TGATTTTCTTATCTAAGATCAATTACTTAAAAGGTTATGGAAAACATTATAGTACTATCTAGATT
*
30576 GAAAGAACCTTACATCCTTATTAATTTTAGTAACCTTTTATCATCAATAAAGTGTTACAATTTTT
260 GAAAGAACCTTACATCCTTATTAATTTTAGTAACCTTTTATCATCAATAAAGTGTTACAAATTTT
*
30641 ATTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAATTGTAATTACCAATCCTTATTTTT
325 ATTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAATTGCAATTACCAATCCTTA-TTTT
*
30706 TTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGCCATTTTTTTCTCAAAAGTTACTGA
389 TTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGCCATTTTTTTCTCAAAAGTTACTAA
*
30771 AAAACCTATAATGATCACAAAAGAGGTATAACACTATCCACTAATTCAATAACCTTACATCTTTT
454 AAAACCTATAATGATCACAAAAGAGATATAACACTATCCACTAATTCAATAACCTTACATCTTTT
30836 GTGATTTTGGTTATCATATTTCTTATTAC-ATTTTTTTGTAATTTTGATTATCATATTTCTCCAA
519 GTGATTTTGGTTATCATATTTCTTATTACTATTTTTTTGTAATTTTGATTATCATATTTCTCCAA
30900 AATCTCACAATTCAACAAAACATACCCGGACCTATAAGTCAAATTTCCATATAAGGTTACAACTT
584 AATCTCACAATTCAACAAAACATACCCGGACCTATAAGTCAAATTTCCATATAAGGTTACAACTT
30965 ATAACTAAACTTAATGCAACATAAGGAAGTAAAAAATTAGGTGTAC
649 ATAACTAAACTTAATGCAACATAAGGAAGTAAAAAATTAGGTGTAC
31011 AAAA
1 AAAA
31015 TTGGTTCCTA
Statistics
Matches: 673, Mismatches: 21, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
692 412 0.61
693 256 0.38
694 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (694 bp):
AAAAAGCTATAAAAGTTTTTAAAATTGTATTTACCAATCCTTACATTCTTAATAACATTAGTAAA
CTTTCATCAATGGTAAAGATTTACCATTTTTTTCCTCAAAAGTTACCGAAAAAGCTATAATAATC
ATAAAAAATGTATTATACTATCAACTAATTTAATGACCTTACACTATAAAGATACGTACAATACT
GATTTTCTTATCTAAGATCAATTACTTAAAAGGTTATGGAAAACATTATAGTACTATCTAGATTG
AAAGAACCTTACATCCTTATTAATTTTAGTAACCTTTTATCATCAATAAAGTGTTACAAATTTTA
TTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAATTGCAATTACCAATCCTTATTTTTT
AATAACATTAGTAAACTTTCATCAACGGTGAATATTTGCCATTTTTTTCTCAAAAGTTACTAAAA
AACCTATAATGATCACAAAAGAGATATAACACTATCCACTAATTCAATAACCTTACATCTTTTGT
GATTTTGGTTATCATATTTCTTATTACTATTTTTTTGTAATTTTGATTATCATATTTCTCCAAAA
TCTCACAATTCAACAAAACATACCCGGACCTATAAGTCAAATTTCCATATAAGGTTACAACTTAT
AACTAAACTTAATGCAACATAAGGAAGTAAAAAATTAGGTGTAC
Found at i:31757 original size:203 final size:202
Alignment explanation
Indices: 31405--31814 Score: 759
Period size: 203 Copynumber: 2.0 Consensus size: 202
31395 GCTTAATAAC
*
31405 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAATCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
31470 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
*
31535 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAATC
31600 CGATTTA
196 CGATTTA
31607 TTTATCAATGGTGAATGTTATT-ATTTTTTAAATCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAATCTAAGATTACTAACAAAGTTGTAGTGAATAA
31671 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
*
31736 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCCAAATTATAAAAGATATTAAAAA
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAA
31801 TCCGATTTA
194 TCCGATTTA
31810 TTTAT
1 TTTAT
31815 TATTAAGGAA
Statistics
Matches: 202, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
201 66 0.33
202 23 0.11
203 113 0.56
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAATCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAATC
CGATTTA
Found at i:37770 original size:2 final size:2
Alignment explanation
Indices: 37763--37796 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
37753 CTTTTAATCT
37763 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37797 GTAACAAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39855 original size:259 final size:259
Alignment explanation
Indices: 39396--39915 Score: 1040
Period size: 259 Copynumber: 2.0 Consensus size: 259
39386 CCTCTCCAAA
39396 AATTGTTAAGTTTTTAAATTATATCAATATTGGTTTTTTCAATCATCACATTCCGTCCCTTTCAC
1 AATTGTTAAGTTTTTAAATTATATCAATATTGGTTTTTTCAATCATCACATTCCGTCCCTTTCAC
39461 TCCAATTGCTTCCGTCAGCAATGAAGATGTGATTGATTCGAAAACCTCCTCGACAAGTCCATAAT
66 TCCAATTGCTTCCGTCAGCAATGAAGATGTGATTGATTCGAAAACCTCCTCGACAAGTCCATAAT
39526 TCATACAACAGACCTATCTCTTGACTCTGAGAAAAAAGTAAAAACAAAATTCTGCTCTTCATCCC
131 TCATACAACAGACCTATCTCTTGACTCTGAGAAAAAAGTAAAAACAAAATTCTGCTCTTCATCCC
39591 AATTTATGTACAAGTAACAATTCTCAGGCCGTTGTAAGACCAAACTATACAAAAACCGACTAAG
196 AATTTATGTACAAGTAACAATTCTCAGGCCGTTGTAAGACCAAACTATACAAAAACCGACTAAG
39655 AATTGTTAAGTTTTTAAATTATATCAATATTGGTTTTTTCAATCATCACATTCCGTCCCTTTCAC
1 AATTGTTAAGTTTTTAAATTATATCAATATTGGTTTTTTCAATCATCACATTCCGTCCCTTTCAC
39720 TCCAATTGCTTCCGTCAGCAATGAAGATGTGATTGATTCGAAAACCTCCTCGACAAGTCCATAAT
66 TCCAATTGCTTCCGTCAGCAATGAAGATGTGATTGATTCGAAAACCTCCTCGACAAGTCCATAAT
39785 TCATACAACAGACCTATCTCTTGACTCTGAGAAAAAAGTAAAAACAAAATTCTGCTCTTCATCCC
131 TCATACAACAGACCTATCTCTTGACTCTGAGAAAAAAGTAAAAACAAAATTCTGCTCTTCATCCC
39850 AATTTATGTACAAGTAACAATTCTCAGGCCGTTGTAAGACCAAACTATACAAAAACCGACTAAG
196 AATTTATGTACAAGTAACAATTCTCAGGCCGTTGTAAGACCAAACTATACAAAAACCGACTAAG
39914 AA
1 AA
39916 AACAAATTGA
Statistics
Matches: 261, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
259 261 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (259 bp):
AATTGTTAAGTTTTTAAATTATATCAATATTGGTTTTTTCAATCATCACATTCCGTCCCTTTCAC
TCCAATTGCTTCCGTCAGCAATGAAGATGTGATTGATTCGAAAACCTCCTCGACAAGTCCATAAT
TCATACAACAGACCTATCTCTTGACTCTGAGAAAAAAGTAAAAACAAAATTCTGCTCTTCATCCC
AATTTATGTACAAGTAACAATTCTCAGGCCGTTGTAAGACCAAACTATACAAAAACCGACTAAG
Found at i:39939 original size:17 final size:19
Alignment explanation
Indices: 39908--39942 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
39898 ACAAAAACCG
39908 ACTAAGAAAACAAATTGAA
1 ACTAAGAAAACAAATTGAA
39927 ACTAA-AAAA-AAATTGA
1 ACTAAGAAAACAAATTGA
39943 CTCAAACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (19 bp):
ACTAAGAAAACAAATTGAA
Found at i:43173 original size:17 final size:17
Alignment explanation
Indices: 43151--43192 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
43141 CAGGATATCA
43151 CAAACTCCGTTTGTTCC
1 CAAACTCCGTTTGTTCC
43168 CAAACTCCGTTTGTTCC
1 CAAACTCCGTTTGTTCC
43185 CAAACTCC
1 CAAACTCC
43193 ATCACTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31
Consensus pattern (17 bp):
CAAACTCCGTTTGTTCC
Found at i:61787 original size:33 final size:33
Alignment explanation
Indices: 61745--61827 Score: 166
Period size: 33 Copynumber: 2.5 Consensus size: 33
61735 ACCAGAAGAA
61745 AAAAAAAATTATGGCTTGCAATGTGCGACCAAC
1 AAAAAAAATTATGGCTTGCAATGTGCGACCAAC
61778 AAAAAAAATTATGGCTTGCAATGTGCGACCAAC
1 AAAAAAAATTATGGCTTGCAATGTGCGACCAAC
61811 AAAAAAAATTATGGCTT
1 AAAAAAAATTATGGCTT
61828 CCAAGAATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.23
Consensus pattern (33 bp):
AAAAAAAATTATGGCTTGCAATGTGCGACCAAC
Found at i:65589 original size:2 final size:2
Alignment explanation
Indices: 65582--65619 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
65572 CAAACTAATC
65582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65620 TCTATAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70140 original size:10 final size:10
Alignment explanation
Indices: 70120--70162 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
70110 GCAAAATGAA
70120 CCCGAAACCCG
1 CCCG-AACCCG
70131 CCCGAACCCG
1 CCCGAACCCG
*
70141 CCCGAGCCCG
1 CCCGAACCCG
70151 AACCCGAACCCG
1 --CCCGAACCCG
70163 AAATTACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 15 0.54
11 4 0.14
12 9 0.32
ACGTcount: A:0.23, C:0.56, G:0.21, T:0.00
Consensus pattern (10 bp):
CCCGAACCCG
Found at i:70149 original size:6 final size:6
Alignment explanation
Indices: 70117--70164 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
70107 CTGGCAAAAT
*
70117 GAACCC GAAACCC G--CCC GAACCC G--CCC GAGCCC GAACCC GAACCC
1 GAACCC G-AACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
70162 GAA
1 GAA
70165 ATTACCCGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
4 8 0.22
6 22 0.61
7 6 0.17
ACGTcount: A:0.29, C:0.50, G:0.21, T:0.00
Consensus pattern (6 bp):
GAACCC
Found at i:70450 original size:5 final size:5
Alignment explanation
Indices: 70439--70473 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
70429 TTAAATAATT
* *
70439 AAAGG GAAGG GAAGG AAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
70474 GGAGGGAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:70727 original size:20 final size:21
Alignment explanation
Indices: 70694--70740 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
70684 AAAAAAAAAG
* *
70694 AAAAAATTAGAAATTTTCAAC
1 AAAAAAATAGAAATCTTCAAC
70715 AAAAAAATA-AAATCTTC-AC
1 AAAAAAATAGAAATCTTCAAC
*
70734 AAGAAAA
1 AAAAAAA
70741 GAGATGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCAAC
Found at i:71899 original size:17 final size:17
Alignment explanation
Indices: 71879--71911 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
71869 TCCGATCCGA
71879 ACCCGA-ACGCGAACCCT
1 ACCCGAGAC-CGAACCCT
71896 ACCCGAGACCGAACCC
1 ACCCGAGACCGAACCC
71912 GAAAATACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.30, C:0.48, G:0.18, T:0.03
Consensus pattern (17 bp):
ACCCGAGACCGAACCCT
Found at i:71945 original size:32 final size:32
Alignment explanation
Indices: 71904--72010 Score: 135
Period size: 32 Copynumber: 3.3 Consensus size: 32
71894 CTACCCGAGA
* ** *
71904 CCGAACCCGAAAATACCTGAATCCGACATAAC
1 CCGAGCCCGAAAATACCCAAACCCGACATAAC
*
71936 CCGAGCCCGAAAATACCCAAACCCGACTTAAC
1 CCGAGCCCGAAAATACCCAAACCCGACATAAC
*
71968 CCGAGCCCGAAAATACCCAAACCCGA-AAATAC
1 CCGAGCCCGAAAATACCCAAACCCGACATA-AC
*
72000 CCGAACCCGAA
1 CCGAGCCCGAA
72011 GTACCTGAGC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
31 1 0.02
32 65 0.98
ACGTcount: A:0.40, C:0.38, G:0.13, T:0.08
Consensus pattern (32 bp):
CCGAGCCCGAAAATACCCAAACCCGACATAAC
Found at i:71985 original size:16 final size:16
Alignment explanation
Indices: 71904--72010 Score: 101
Period size: 16 Copynumber: 6.7 Consensus size: 16
71894 CTACCCGAGA
71904 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
* * *
71920 CTGAATCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
*
71936 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
* **
71952 CCAAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
*
71968 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
*
71984 CCAAACCCGAAAATAC
1 CCGAACCCGAAAATAC
72000 CCGAACCCGAA
1 CCGAACCCGAA
72011 GTACCTGAGC
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
15 5 0.07
16 59 0.86
17 5 0.07
ACGTcount: A:0.40, C:0.38, G:0.13, T:0.08
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:76561 original size:19 final size:18
Alignment explanation
Indices: 76528--76563 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
76518 TGGAAATAAT
76528 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
76546 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
76564 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:83908 original size:17 final size:17
Alignment explanation
Indices: 83885--83922 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
83875 AAAAAGACAT
* *
83885 TAAAAAAAA-GTTTGTA
1 TAAAAAAAACATTGGTA
83901 TAAAAAAAACATTGGTA
1 TAAAAAAAACATTGGTA
83918 TAAAA
1 TAAAA
83923 TTATTGTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (17 bp):
TAAAAAAAACATTGGTA
Found at i:95971 original size:15 final size:15
Alignment explanation
Indices: 95934--95973 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
95924 TTTTAGCGCG
*
95934 AAATTTCAAAATTCA
1 AAATTTGAAAATTCA
95949 AAATTTTGAAAATTCA
1 AAA-TTTGAAAATTCA
95965 AAATTTGAA
1 AAATTTGAA
95974 TTTCGGAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (15 bp):
AAATTTGAAAATTCA
Found at i:99890 original size:76 final size:76
Alignment explanation
Indices: 99715--100102 Score: 499
Period size: 76 Copynumber: 5.1 Consensus size: 76
99705 GTGGCATTCG
* * * * * * * * * *
99715 GCCGTTGATTGAGCAACGTCTGTGTGGACGCTTTGTCCCACTGACGTACGAACGAAGGGTGCCTG
1 GCCGTTGAGTGAGCAGCGTCTGCGTGGACGCTTTGTCTCACTAATGGACGAACG-GGGGCGCCAG
** *
99780 TCCAGGCACTCG
65 TTTAGGCACTCA
* * * *
99792 GCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTGTCTCACTAGTAGACGAACGGGGGCGCCAGT
1 GCCGTTGAGTGAGCAGCGTCTGCGTGGACGCTTTGTCTCACTAATGGACGAACGGGGGCGCCAGT
* * *
99857 TTAGACGCTTA
66 TTAGGCACTCA
* *
99868 GCCGTTGAGTGAGCAGCGTCTGCGTGGACGCTTTGTCTCACTAATGGACGAACGAGGGCATCC-G
1 GCCGTTGAGTGAGCAGCGTCTGCGTGGACGCTTTGTCTCACTAATGGACGAACGGGGGC-GCCAG
99932 TTTAGGCACTCA
65 TTTAGGCACTCA
* *
99944 GCCGTTGAGTGAGCAGCGTCTACGTGGACGCTTTGTCTCACAAATGGACGAACGGGGGCGCCAGT
1 GCCGTTGAGTGAGCAGCGTCTGCGTGGACGCTTTGTCTCACTAATGGACGAACGGGGGCGCCAGT
100009 TTAGGCACTCA
66 TTAGGCACTCA
*
100020 GCCGTTGAGTGAGCAGCGTCTGCGTTGACGCTTTGTCTCACTAATGGACGAACGGGGGCGCCAGT
1 GCCGTTGAGTGAGCAGCGTCTGCGTGGACGCTTTGTCTCACTAATGGACGAACGGGGGCGCCAGT
* *
100085 TCAGGCGCTCA
66 TTAGGCACTCA
*
100096 ACCGTTG
1 GCCGTTG
100103 TTTGAGACAT
Statistics
Matches: 270, Mismatches: 39, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
75 2 0.01
76 223 0.83
77 45 0.17
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.23
Consensus pattern (76 bp):
GCCGTTGAGTGAGCAGCGTCTGCGTGGACGCTTTGTCTCACTAATGGACGAACGGGGGCGCCAGT
TTAGGCACTCA
Found at i:109346 original size:27 final size:27
Alignment explanation
Indices: 109308--109365 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
109298 CCAAATATAT
*
109308 TTTTAAATTGCCATTATTAAAAAAT-A
1 TTTTAAATTGCCACTATTAAAAAATAA
* *
109334 TTTTAATTATGCCACTATTAAAATATAA
1 TTTTAAAT-TGCCACTATTAAAAAATAA
109362 TTTT
1 TTTT
109366 GTGTACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 7 0.26
27 15 0.56
28 5 0.19
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (27 bp):
TTTTAAATTGCCACTATTAAAAAATAA
Found at i:109518 original size:26 final size:26
Alignment explanation
Indices: 109487--109537 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
109477 ATTATTAAAA
* *
109487 TATTTTATTTTGAAATATTCAATTTT
1 TATTTTATTTAGAAAAATTCAATTTT
109513 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAATTCAATTT
109538 GTACAGTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTCAATTTT
Found at i:111051 original size:28 final size:31
Alignment explanation
Indices: 111020--111079 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 31
111010 CAATTCAATA
*
111020 TAATAATTT-AATTCTTT-AAT-TTTTTTAT
1 TAATAATTTCAATTATTTAAATATTTTTTAT
111048 TAATAATTTCAATTATTTAAATATTTTTTAT
1 TAATAATTTCAATTATTTAAATATTTTTTAT
111079 T
1 T
111080 TAAACGCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.32
29 7 0.25
30 3 0.11
31 9 0.32
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (31 bp):
TAATAATTTCAATTATTTAAATATTTTTTAT
Found at i:119954 original size:23 final size:24
Alignment explanation
Indices: 119916--119963 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
119906 ATAAAACAAC
*
119916 ACTAGCTCTTCCGGAGCCTT-AAT
1 ACTAGCTATTCCGGAGCCTTCAAT
*
119939 ACTAGCTATTCTGGAGCCTTCAAT
1 ACTAGCTATTCCGGAGCCTTCAAT
119963 A
1 A
119964 AATTTGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (24 bp):
ACTAGCTATTCCGGAGCCTTCAAT
Found at i:120171 original size:2 final size:2
Alignment explanation
Indices: 120164--120193 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
120154 CATAGAACGA
120164 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120194 CCAATATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120651 original size:21 final size:24
Alignment explanation
Indices: 120607--120686 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 24
120597 TATCTTAGAT
*
120607 ATAATATATATTATTAAATAAATA
1 ATAATATATATTACTAAATAAATA
120631 ATAA-ATATATT-CTAAAT-AAT-
1 ATAATATATATTACTAAATAAATA
*
120651 A-AATA-ATGAGTT-CAAAATAAATAA
1 ATAATATAT-A-TTACTAAATAAAT-A
120675 ATAATATATATT
1 ATAATATATATT
120687 TAATTACTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 10 0.22
22 8 0.17
23 7 0.15
24 7 0.15
25 5 0.11
26 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAATATATATTACTAAATAAATA
Found at i:135229 original size:44 final size:44
Alignment explanation
Indices: 135136--135229 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
135126 GACTCGAATT
* * *
135136 CTAAAATCCATACCTTACAAGTAGAACGACTCAAACCTCCAATC
1 CTAAAATCCAAACCTTACAAGCAGAACGACTCAAACCTCCAAAC
* *
135180 CTAAAATCCAAACCTTCCAAGCAGAGCGACTCAAACCT-CAAAC
1 CTAAAATCCAAACCTTACAAGCAGAACGACTCAAACCTCCAAAC
135223 CTTAAAA
1 C-TAAAA
135230 GTAGAAATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 5 0.11
44 39 0.89
ACGTcount: A:0.43, C:0.32, G:0.07, T:0.18
Consensus pattern (44 bp):
CTAAAATCCAAACCTTACAAGCAGAACGACTCAAACCTCCAAAC
Found at i:144367 original size:6 final size:6
Alignment explanation
Indices: 144356--144382 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
144346 TAGGGTTTAC
144356 TTTGAT TTTGAT TTTGAT TTTGAT TTT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTT
144383 TTATTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTGAT
Found at i:150908 original size:21 final size:21
Alignment explanation
Indices: 150879--150922 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
150869 ATATTTATAA
150879 CTTTATCAACTAACCTAGAGT
1 CTTTATCAACTAACCTAGAGT
*
150900 CTTTTTCAACTAACCTAGAGT
1 CTTTATCAACTAACCTAGAGT
150921 CT
1 CT
150923 AAACCTAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (21 bp):
CTTTATCAACTAACCTAGAGT
Found at i:150929 original size:13 final size:13
Alignment explanation
Indices: 150911--150936 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150901 TTTTTCAACT
150911 AACCTAGAGTCTA
1 AACCTAGAGTCTA
150924 AACCTAGAGTCTA
1 AACCTAGAGTCTA
150937 GAGGCTATTA
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:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
AACCTAGAGTCTA
Found at i:154643 original size:5 final size:5
Alignment explanation
Indices: 154633--154658 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
154623 GGGGATATGC
154633 AAACA AAACA AAACA AAACA AAACA A
1 AAACA AAACA AAACA AAACA AAACA A
154659 GCAACTTGGG
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:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:166721 original size:28 final size:29
Alignment explanation
Indices: 166669--166724 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
166659 TGCGAGCGCC
166669 GTATAACTATATATATTGTTATAAGAAAAA
1 GTATAACTATATATATTG-TATAAGAAAAA
*
166699 GTATAACTATATATATTG-GTAAGAAA
1 GTATAACTATATATATTGTATAAGAAA
166725 TAAAAAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 7 0.28
30 18 0.72
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (29 bp):
GTATAACTATATATATTGTATAAGAAAAA
Found at i:166730 original size:32 final size:30
Alignment explanation
Indices: 166669--166732 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
166659 TGCGAGCGCC
* *
166669 GTATAACTATATATATTGTTATAAGAAAAA
1 GTATAACTATATATATTGTAAAAAGAAAAA
*
166699 GTATAACTATATATATTGGTAAGAAATAAAAA
1 GTATAACTATATATATT-GTAA-AAAGAAAAA
166731 GT
1 GT
166733 GTTTAACGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 17 0.59
31 3 0.10
32 9 0.31
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.34
Consensus pattern (30 bp):
GTATAACTATATATATTGTAAAAAGAAAAA
Found at i:174095 original size:31 final size:30
Alignment explanation
Indices: 173998--174080 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
173988 GGGTTTAAGT
* *
173998 AAAATCTCGAATTTGAGTCTTTTGAATGAAT
1 AAAATCTTGAATTTGAGTC-TTTGAATGAAA
* * * *
174029 AAAATTTTGAGTTTGTGTTTTGTGAATGAAA
1 AAAATCTTGAATTTGAGTCTT-TGAATGAAA
174060 AAAATCTTGAATTTGAGTCTT
1 AAAATCTTGAATTTGAGTCTT
174081 ATAGATGAAG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 2 0.05
31 39 0.95
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (30 bp):
AAAATCTTGAATTTGAGTCTTTGAATGAAA
Done.