Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011106.1 Corchorus capsularis cultivar CVL-1 contig11127, 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: 97080
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:14361 original size:45 final size:45
Alignment explanation
Indices: 14310--14402 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
14300 GGTGGAAATA
14310 CTTTGGAGGCAGAGGAGGAAGCTTAGGAAGAGGAGGGCATGGCGT
1 CTTTGGAGGCAGAGGAGGAAGCTTAGGAAGAGGAGGGCATGGCGT
* *
14355 CTTTGGAGGCAGAGGAGGAAGCTTGGGAAGAGGAGGGCATGGCTT
1 CTTTGGAGGCAGAGGAGGAAGCTTAGGAAGAGGAGGGCATGGCGT
14400 CTT
1 CTT
14403 GGGGAATGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.25, C:0.12, G:0.45, T:0.18
Consensus pattern (45 bp):
CTTTGGAGGCAGAGGAGGAAGCTTAGGAAGAGGAGGGCATGGCGT
Found at i:14425 original size:18 final size:18
Alignment explanation
Indices: 14399--14434 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
14389 GGGCATGGCT
*
14399 TCTTGGGGAATGGAGGAA
1 TCTTCGGGAATGGAGGAA
*
14417 TCTTCGGGAGTGGAGGAA
1 TCTTCGGGAATGGAGGAA
14435 GTGGCTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.08, G:0.44, T:0.22
Consensus pattern (18 bp):
TCTTCGGGAATGGAGGAA
Found at i:14617 original size:24 final size:21
Alignment explanation
Indices: 14539--14627 Score: 97
Period size: 21 Copynumber: 4.1 Consensus size: 21
14529 GTACACTGGT
* * *
14539 GGCTTGTAGACAGGAACTGGT
1 GGCTTGTAGACTGGAACAGGA
*
14560 GGCTTGTAGACAGGAACAGGA
1 GGCTTGTAGACTGGAACAGGA
*
14581 GGCTTGTACACTGGAACAGGA
1 GGCTTGTAGACTGGAACAGGA
*
14602 GGTTTCTTGTAGACTGGAACCGGA
1 GG---CTTGTAGACTGGAACAGGA
14626 GG
1 GG
14628 GGGCTTATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
21 40 0.68
24 19 0.32
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (21 bp):
GGCTTGTAGACTGGAACAGGA
Found at i:14680 original size:33 final size:33
Alignment explanation
Indices: 14643--14715 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
14633 TATATACCGG
* *
14643 TGGAGGAAG-TGGTGGTTTCTTGTATACTGGCAC
1 TGGAGGAAGAT-GTGGTTTCTTGTAAACTGGAAC
* *
14676 TGGAGGAGGATTTGGTTTCTTGTAAACTGGAAC
1 TGGAGGAAGATGTGGTTTCTTGTAAACTGGAAC
14709 TGGAGGA
1 TGGAGGA
14716 GGCTTGTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.22, C:0.10, G:0.37, T:0.32
Consensus pattern (33 bp):
TGGAGGAAGATGTGGTTTCTTGTAAACTGGAAC
Found at i:14716 original size:33 final size:33
Alignment explanation
Indices: 14655--14717 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
14645 GAGGAAGTGG
* *
14655 TGGTTTCTTGTATACTGGCACTGGAGGAGGATT
1 TGGTTTCTTGTAAACTGGAACTGGAGGAGGATT
14688 TGGTTTCTTGTAAACTGGAACTGGAGGAGG
1 TGGTTTCTTGTAAACTGGAACTGGAGGAGG
14718 CTTGTAGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.35, T:0.33
Consensus pattern (33 bp):
TGGTTTCTTGTAAACTGGAACTGGAGGAGGATT
Found at i:14745 original size:21 final size:21
Alignment explanation
Indices: 14695--14897 Score: 199
Period size: 21 Copynumber: 9.2 Consensus size: 21
14685 ATTTGGTTTC
* *
14695 TTGTAAACTGGAACTGGAGGAGGC
1 TTGTAGACTGGAACT---GGAGGT
* *
14719 TTGTAGACTGGAACAGGCGGT
1 TTGTAGACTGGAACTGGAGGT
*
14740 TTGTAGATTGGAACTGGAGGT
1 TTGTAGACTGGAACTGGAGGT
* * *
14761 TTGTAAACTGGAACCGGAGGAGGC
1 TTGTAGACTGGAA-C--TGGAGGT
* *
14785 TTGTAGACTGGAACCGGAGGC
1 TTGTAGACTGGAACTGGAGGT
14806 TTGTAGACTGGAACTGGAGGT
1 TTGTAGACTGGAACTGGAGGT
*
14827 TTGTACACTGGAACTGGAGGT
1 TTGTAGACTGGAACTGGAGGT
* * *
14848 TTGTACACTGGAACCGGAGGAGGC
1 TTGTAGACTGGAA-C--TGGAGGT
14872 TTGTAGACTGGAACTGGAGGT
1 TTGTAGACTGGAACTGGAGGT
14893 TTGTA
1 TTGTA
14898 AATTGGGACC
Statistics
Matches: 152, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
21 101 0.66
22 2 0.01
23 2 0.01
24 47 0.31
ACGTcount: A:0.25, C:0.13, G:0.37, T:0.25
Consensus pattern (21 bp):
TTGTAGACTGGAACTGGAGGT
Found at i:14756 original size:45 final size:43
Alignment explanation
Indices: 14695--14897 Score: 189
Period size: 45 Copynumber: 4.6 Consensus size: 43
14685 ATTTGGTTTC
* *
14695 TTGTAAACTGGAACTGGAGGAGGCTTGTAGACTGGAACAGGCGGT
1 TTGTAGACTGGAACT--AGGAGGCTTGTAGACTGGAACAGGAGGT
* * * *
14740 TTGTAGATTGGAACT-GGAGGTTTGTAAACTGGAACCGGAGGAGGC
1 TTGTAGACTGGAACTAGGAGGCTTGTAGACTGGAA-C--AGGAGGT
* *
14785 TTGTAGACTGGAAC-CGGAGGCTTGTAGACTGGAACTGGAGGT
1 TTGTAGACTGGAACTAGGAGGCTTGTAGACTGGAACAGGAGGT
* * * *
14827 TTGTACACTGGAACT-GGAGGTTTGTACACTGGAACCGGAGGAGGC
1 TTGTAGACTGGAACTAGGAGGCTTGTAGACTGGAA-C--AGGAGGT
*
14872 TTGTAGACTGGAACT-GGAGGTTTGTA
1 TTGTAGACTGGAACTAGGAGGCTTGTA
14898 AATTGGGACC
Statistics
Matches: 133, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
42 52 0.39
43 2 0.02
44 1 0.01
45 78 0.59
ACGTcount: A:0.25, C:0.13, G:0.37, T:0.25
Consensus pattern (43 bp):
TTGTAGACTGGAACTAGGAGGCTTGTAGACTGGAACAGGAGGT
Found at i:14765 original size:66 final size:66
Alignment explanation
Indices: 14695--14899 Score: 290
Period size: 66 Copynumber: 3.1 Consensus size: 66
14685 ATTTGGTTTC
* * *
14695 TTGTAAACTGGAACTGGAGGAGGCTTGTAGACTGGAACAGGCGGTTTGTAGATTGGAACTGGAGG
1 TTGTAAACTGGAACTGGAGGAGGCTTGTAGACTGGAACAGGAGGCTTGTAGACTGGAACTGGAGG
14760 T
66 T
* *
14761 TTGTAAACTGGAACCGGAGGAGGCTTGTAGACTGGAACCGGAGGCTTGTAGACTGGAACTGGAGG
1 TTGTAAACTGGAACTGGAGGAGGCTTGTAGACTGGAACAGGAGGCTTGTAGACTGGAACTGGAGG
14826 T
66 T
* * *
14827 TTGTACACTGGAACT---GGAGGTTTGTACACTGGAACCGGAGGAGGCTTGTAGACTGGAACTGG
1 TTGTAAACTGGAACTGGAGGAGGCTTGTAGACTGGAA-C--AGGAGGCTTGTAGACTGGAACTGG
14889 AGGT
63 AGGT
14893 TTGTAAA
1 TTGTAAA
14900 TTGGGACCGG
Statistics
Matches: 125, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
63 17 0.14
64 1 0.01
66 107 0.86
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.24
Consensus pattern (66 bp):
TTGTAAACTGGAACTGGAGGAGGCTTGTAGACTGGAACAGGAGGCTTGTAGACTGGAACTGGAGG
T
Found at i:14818 original size:87 final size:87
Alignment explanation
Indices: 14713--14897 Score: 307
Period size: 87 Copynumber: 2.1 Consensus size: 87
14703 TGGAACTGGA
* * *
14713 GGAGGCTTGTAGACTGGAACAGGCGGTTTGTAGATTGGAACTGGAGGTTTGTAAACTGGAACCGG
1 GGAGGCTTGTAGACTGGAACAGGAGGTTTGTACACTGGAACTGGAGGTTTGTAAACTGGAACCGG
14778 AGGAGGCTTGTAGACTGGAACC
66 AGGAGGCTTGTAGACTGGAACC
* *
14800 GGAGGCTTGTAGACTGGAACTGGAGGTTTGTACACTGGAACTGGAGGTTTGTACACTGGAACCGG
1 GGAGGCTTGTAGACTGGAACAGGAGGTTTGTACACTGGAACTGGAGGTTTGTAAACTGGAACCGG
*
14865 AGGAGGCTTGTAGACTGGAACT
66 AGGAGGCTTGTAGACTGGAACC
*
14887 GGAGGTTTGTA
1 GGAGGCTTGTA
14898 AATTGGGACC
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.24, C:0.14, G:0.38, T:0.24
Consensus pattern (87 bp):
GGAGGCTTGTAGACTGGAACAGGAGGTTTGTACACTGGAACTGGAGGTTTGTAAACTGGAACCGG
AGGAGGCTTGTAGACTGGAACC
Found at i:18206 original size:62 final size:62
Alignment explanation
Indices: 18108--18226 Score: 202
Period size: 62 Copynumber: 1.9 Consensus size: 62
18098 ATCCACCCCT
* * * *
18108 AGTCAAGATGGATGGAGGTTTAAATTCATCTTGAGAGAGATCTCGAGTTTGAGTTCAGTTCG
1 AGTCAAGATGGATGGAGGTTGAAATTCACCTCGAGAGAGATCTCGAGTTTAAGTTCAGTTCG
18170 AGTCAAGATGGATGGAGGTTGAAATTCACCTCGAGAGAGATCTCGAGTTTAAGTTCA
1 AGTCAAGATGGATGGAGGTTGAAATTCACCTCGAGAGAGATCTCGAGTTTAAGTTCA
18227 AGTCCGACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (62 bp):
AGTCAAGATGGATGGAGGTTGAAATTCACCTCGAGAGAGATCTCGAGTTTAAGTTCAGTTCG
Found at i:28023 original size:2 final size:2
Alignment explanation
Indices: 28016--28042 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28006 TCATCATGTG
28016 AT AT AT 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 A
28043 GTTGGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28406 original size:22 final size:22
Alignment explanation
Indices: 28381--28423 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
28371 AGAAGACTAC
28381 AAATTGATTCAACTACTAAAAT
1 AAATTGATTCAACTACTAAAAT
28403 AAATTGATTCAACTACTAAAA
1 AAATTGATTCAACTACTAAAA
28424 CAAAGATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (22 bp):
AAATTGATTCAACTACTAAAAT
Found at i:39184 original size:20 final size:20
Alignment explanation
Indices: 39159--39210 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
39149 GACGTGGTAT
39159 TGCCACATGGCACCAAAAAA
1 TGCCACATGGCACCAAAAAA
*
39179 TGCCACATGACACCAAAAAA
1 TGCCACATGGCACCAAAAAA
*
39199 TGCCACGTGGCA
1 TGCCACATGGCA
39211 ACGCCATGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.31, G:0.17, T:0.12
Consensus pattern (20 bp):
TGCCACATGGCACCAAAAAA
Found at i:56091 original size:14 final size:14
Alignment explanation
Indices: 56072--56099 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56062 TTGCAGACTT
56072 CTCAGATTTTCTCA
1 CTCAGATTTTCTCA
56086 CTCAGATTTTCTCA
1 CTCAGATTTTCTCA
56100 AATATATCTT
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:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
CTCAGATTTTCTCA
Found at i:56611 original size:14 final size:14
Alignment explanation
Indices: 56592--56619 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56582 TTGCAGACTT
56592 CTCAGATTTTCTCA
1 CTCAGATTTTCTCA
56606 CTCAGATTTTCTCA
1 CTCAGATTTTCTCA
56620 AATATATCTT
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:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
CTCAGATTTTCTCA
Found at i:57060 original size:523 final size:521
Alignment explanation
Indices: 55999--57228 Score: 2107
Period size: 523 Copynumber: 2.4 Consensus size: 521
55989 TGACCTTTTA
* *
55999 CTTTCCCGTCATTCACACGTTTCTGGCCTTTTCCACGATTCTTCCGTCCTTTTCCGTTCGTCATT
1 CTTTCCCGCCATTCACACGTTTCTGGCCTTTTCCACGATTCTTCCGTCCTTTTCCGTTCGCCATT
56064 GCAGACTTCTCAGATTTTCTCACTCAGATTTTCTCAAATATATCTTTTGAAGTTTTAGCGAAAAT
66 GCAGACTTCTCAGATTTTCTCACTCAGATTTTCTCAAATATATCTTTTGAAGTTTTAGCGAAAAT
56129 GAGAAAATGTGGTATCTTATTTTATTTTATAGTAGCTGGTTTGACTAC-GGCCCATTT-CTCAAT
131 GAGAAAATGTGGTATCTTATTTTATTTTATAGTAGCTGGTTTGACTACGGGCCCATTTAC-CAAT
**
56192 TGTAATAATTTTTTACTAGTAGACTAGTAGTAATAATCTTGAGCCAGAATGGCTCTTGGACTTCA
195 TGTAATAATTTTTTACTAGTAGACTAGTAGTAATAATCTTGAGCCAGAATGGCTCCCGGACTTCA
* *
56257 ACGAGAAATCATTGCTATAATATTACCTATATCATCATTTAGTGTAAACTTTGTGTCATTTTTAC
260 ACGAGAAATCATTGCTATAATATTACCTATATCACCATTTAGTGTAAACATTGTGTCATTTTTAC
* *
56322 GAGTGTTTTATACATAAAAATCCAAATAATGTAATAGGCTATGAATACATTGAATTCTGATAGTG
325 GAGTGTTTTATACATAAAAATCAAAATAATGTAATAAGCTATGAATACATTGAATTCTGATAGTG
* * *
56387 CGGATCTATCAAATCAATCAATTTCATTTGATTCTAGCGTTGATGGAAATTAATTAATTAATTAA
390 CGGATCTATCAAATCAATCAATTTCATTCGATTCTAGCGTTGATGGAAATAAATAAATTAATTAA
* *
56452 TTACCTCTCTTTTTGCGCTCAGGTCCCAATCCCGATCTCTTGCCATGACCTTTTCCTTTCCCGCC
455 TTACCTCTCTTTTTGCACTCAGGTCCCAATCCCGATCCCTTGCCATGACCTTTTCCTTTCCCGCC
56517 TC
520 TC
56519 CTTTCCCGCCATTCACACGTTTCTGGCCTTTTCCACGATTCTTCCGTCCTTTTCCGTTCGCCATT
1 CTTTCCCGCCATTCACACGTTTCTGGCCTTTTCCACGATTCTTCCGTCCTTTTCCGTTCGCCATT
56584 GCAGACTTCTCAGATTTTCTCACTCAGATTTTCTCAAATATATCTTTTGAAGTTTTAGCGAAAAT
66 GCAGACTTCTCAGATTTTCTCACTCAGATTTTCTCAAATATATCTTTTGAAGTTTTAGCGAAAAT
*
56649 GAGAAAATGTGGTATCTTATTTTATTTTATAGTAGCTGGTTTAACTACGGGCCCATTTACCAATT
131 GAGAAAATGTGGTATCTTATTTTATTTTATAGTAGCTGGTTTGACTACGGGCCCATTTACCAATT
56714 GTAATAATTTTTTACTAGTAGACTAGTAGTAATAATCTTGAGCCAGAATGAG-TCCCGGACTTCA
196 GTAATAATTTTTTACTAGTAGACTAGTAGTAATAATCTTGAGCCAGAATG-GCTCCCGGACTTCA
56778 ACGAGAAATCATTGCTATAATATTACCTATATCACCATTTAGTGTAAACATTGTGTCATTTTTAC
260 ACGAGAAATCATTGCTATAATATTACCTATATCACCATTTAGTGTAAACATTGTGTCATTTTTAC
*
56843 GAGTGTTTTATACATAAAAATCGAAATATAATGTAATAAGTTATGAATACATTGAATTCTGATAG
325 GAGTGTTTTATACATAAAAATC-AAA-ATAATGTAATAAGCTATGAATACATTGAATTCTGATAG
56908 TGCGGATCTATCAAATCAATCAATTTCATTCGATTCTAGCGTTGATGGAAATAAATAAATTAATT
388 TGCGGATCTATCAAATCAATCAATTTCATTCGATTCTAGCGTTGATGGAAATAAATAAATTAATT
* *
56973 AATTACCTCTCTTTTTGCACTCAGGTCCCGATCCCGGTCCCTTGCCATGACCTTTTCCTTTCCCG
453 AATTACCTCTCTTTTTGCACTCAGGTCCCAATCCCGATCCCTTGCCATGACCTTTTCCTTTCCCG
*
57038 CCTT
518 CCTC
*
57042 CTTTCCCGCCATTCACACGTTTCTGGCCTTTTCCACGATTCTTCCGTCCTTTTTCGTTCGCCATT
1 CTTTCCCGCCATTCACACGTTTCTGGCCTTTTCCACGATTCTTCCGTCCTTTTCCGTTCGCCATT
*
57107 GC--A------A-A----CT-TCTCAGATTTTCTCAAATATATCTTTTGAAGTTTTAGCGAAAAT
66 GCAGACTTCTCAGATTTTCTCACTCAGATTTTCTCAAATATATCTTTTGAAGTTTTAGCGAAAAT
* *
57158 GAGAAAATGTGGTATCTTATTTTATTTTATAGTAGCTGGTTTGACTATGGGTCCATTTACCAATT
131 GAGAAAATGTGGTATCTTATTTTATTTTATAGTAGCTGGTTTGACTACGGGCCCATTTACCAATT
57223 GTAATA
196 GTAATA
57229 CTCCCTTCGT
Statistics
Matches: 682, Mismatches: 23, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
509 111 0.16
510 2 0.00
514 1 0.00
515 1 0.00
520 175 0.26
521 160 0.23
522 4 0.01
523 228 0.33
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (521 bp):
CTTTCCCGCCATTCACACGTTTCTGGCCTTTTCCACGATTCTTCCGTCCTTTTCCGTTCGCCATT
GCAGACTTCTCAGATTTTCTCACTCAGATTTTCTCAAATATATCTTTTGAAGTTTTAGCGAAAAT
GAGAAAATGTGGTATCTTATTTTATTTTATAGTAGCTGGTTTGACTACGGGCCCATTTACCAATT
GTAATAATTTTTTACTAGTAGACTAGTAGTAATAATCTTGAGCCAGAATGGCTCCCGGACTTCAA
CGAGAAATCATTGCTATAATATTACCTATATCACCATTTAGTGTAAACATTGTGTCATTTTTACG
AGTGTTTTATACATAAAAATCAAAATAATGTAATAAGCTATGAATACATTGAATTCTGATAGTGC
GGATCTATCAAATCAATCAATTTCATTCGATTCTAGCGTTGATGGAAATAAATAAATTAATTAAT
TACCTCTCTTTTTGCACTCAGGTCCCAATCCCGATCCCTTGCCATGACCTTTTCCTTTCCCGCCT
C
Found at i:60632 original size:28 final size:27
Alignment explanation
Indices: 60568--60621 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
60558 TATTTCTGGA
*
60568 AAACAAGGGAAAGGGATAATTAAAAAG
1 AAACAAGGGAAAGGGACAATTAAAAAG
60595 AAACAAGGGAAAGGGACAATTAAAAAG
1 AAACAAGGGAAAGGGACAATTAAAAAG
60622 GAACCGAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.59, C:0.06, G:0.26, T:0.09
Consensus pattern (27 bp):
AAACAAGGGAAAGGGACAATTAAAAAG
Found at i:61925 original size:120 final size:121
Alignment explanation
Indices: 61706--61948 Score: 461
Period size: 120 Copynumber: 2.0 Consensus size: 121
61696 AGTTAGACTG
*
61706 AAACGCTAATCTATGAGCCAACAAATAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCT
1 AAACACTAATCTATGAGCCAACAAATAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCT
61771 ATACTCATAACTAAACTACCTATCTACCAAATACATAAATAAACAAATTACAAATA
66 ATACTCATAACTAAACTACCTATCTACCAAATACATAAATAAACAAATTACAAATA
61827 AAACACTAATCTATGAGCCAACAAATAAACCCAGTG-AATCTCATTACAATTCAAATAAATCTCT
1 AAACACTAATCTATGAGCCAACAAATAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCT
*
61891 ATGCTCATAACTAAACTACCTATCTACCAAATACATAAATAAACAAATTACAAATA
66 ATACTCATAACTAAACTACCTATCTACCAAATACATAAATAAACAAATTACAAATA
61947 AA
1 AA
61949 TTCACATCCC
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
120 85 0.71
121 35 0.29
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.25
Consensus pattern (121 bp):
AAACACTAATCTATGAGCCAACAAATAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCT
ATACTCATAACTAAACTACCTATCTACCAAATACATAAATAAACAAATTACAAATA
Found at i:78835 original size:31 final size:31
Alignment explanation
Indices: 78800--78941 Score: 149
Period size: 31 Copynumber: 4.9 Consensus size: 31
78790 GGCATGCCAC
78800 GTGTCACTTTTTGGTACACGTGGCGTGACAT
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
* *
78831 GTGTCACATTTTGGTACACATGGCGTGACAT
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
* *
78862 GTGTCACTTTTTGATACATGT-G-GT-AC--
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
* * *
78888 --G--ACTTTTTGGTACATGTGGCGTGCCAC
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
*
78915 ATGTCACTTTTTGGTACACGTGGCGTG
1 GTGTCACTTTTTGGTACACGTGGCGTG
78942 CCACGTCGGA
Statistics
Matches: 93, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
22 15 0.16
23 1 0.01
24 3 0.03
25 1 0.01
28 2 0.02
29 3 0.03
30 1 0.01
31 67 0.72
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (31 bp):
GTGTCACTTTTTGGTACACGTGGCGTGACAT
Found at i:78882 original size:19 final size:21
Alignment explanation
Indices: 78858--78905 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
78848 ACATGGCGTG
78858 ACATGTGT-C-ACTTTTTGAT
1 ACATGTGTACGACTTTTTGAT
*
78877 ACATGTGGTACGACTTTTTGGT
1 ACATGT-GTACGACTTTTTGAT
78899 ACATGTG
1 ACATGTG
78906 GCGTGCCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
21 2 0.08
22 15 0.60
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.42
Consensus pattern (21 bp):
ACATGTGTACGACTTTTTGAT
Found at i:78961 original size:84 final size:83
Alignment explanation
Indices: 78805--78961 Score: 181
Period size: 84 Copynumber: 1.9 Consensus size: 83
78795 GCCACGTGTC
** * *
78805 ACTTTTTGGTACACGTGGCGTGACATGTGTCACATTTTGGTACACATGGCGTGACATGTGTCACT
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACATTTTGGTACACATGGCGTGACACGTGACAC-
**
78870 TTTTGATACATGTGGTACG
65 TCGTGATACATGTGGTACG
* * * * *
78889 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCGTGCCACGTCGGACA
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACATTTTGGTACACATGGCGTGACACGT--GACA
78954 C-CGTGATA
64 CTCGTGATA
78962 GAATCGTTTG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
84 56 0.93
86 4 0.07
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (83 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACATTTTGGTACACATGGCGTGACACGTGACACT
CGTGATACATGTGGTACG
Found at i:86405 original size:16 final size:18
Alignment explanation
Indices: 86384--86416 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
86374 AAATATAGTA
86384 ATTTTTG-A-TATGTGAC
1 ATTTTTGCACTATGTGAC
86400 ATTTTTGCACTATGTGA
1 ATTTTTGCACTATGTGA
86417 TTGTTTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (18 bp):
ATTTTTGCACTATGTGAC
Found at i:96985 original size:21 final size:21
Alignment explanation
Indices: 96942--96985 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
96932 AAAAAAGGGG
* *
96942 TTGCTAAATACCGCCTTAGTT
1 TTGCTAAATACCGCCTCACTT
96963 TTGCTAAATACCGTCC-CACTT
1 TTGCTAAATACCG-CCTCACTT
96984 TT
1 TT
96986 TACACCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (21 bp):
TTGCTAAATACCGCCTCACTT
Done.