Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024618.1 Corchorus olitorius cultivar O-4 contig24651, 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: 43422
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:134 original size:11 final size:11
Alignment explanation
Indices: 118--143 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
108 AGATAATTTC
118 TTTTCTTCTAG
1 TTTTCTTCTAG
129 TTTTCTTCTAG
1 TTTTCTTCTAG
140 TTTT
1 TTTT
144 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:932 original size:15 final size:15
Alignment explanation
Indices: 902--943 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
892 TTACTTTGCT
902 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
918 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
933 TTGCTTTCTGT
1 TTGTTTTCTGT
944 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:4525 original size:21 final size:21
Alignment explanation
Indices: 4496--4537 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4486 AAAATCAGAA
*
4496 CAACCCCTGCTCAGGACTTGG
1 CAACCCCTGCCCAGGACTTGG
*
4517 CAACTCCTGCCCAGGACTTGG
1 CAACCCCTGCCCAGGACTTGG
4538 TATGTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.24, T:0.19
Consensus pattern (21 bp):
CAACCCCTGCCCAGGACTTGG
Found at i:4546 original size:71 final size:71
Alignment explanation
Indices: 4437--4608 Score: 256
Period size: 71 Copynumber: 2.4 Consensus size: 71
4427 AGTCCTGCCA
* * * *
4437 AGGACTTGACAACTCCTGCCCGGGACCTGGTCTGTTGAAAGACGGAAGAAAAATCAGAACAACCC
1 AGGACTTGGCAACTCCTGCCCAGGACTTGGTATGTTGAAAGACGGAAGAAAAATCAGAACAACCC
4502 CTG-CTC
66 CTGTC-C
* **
4508 AGGACTTGGCAACTCCTGCCCAGGACTTGGTATGTTGAAAGACGGAAGAAAATTCAGAACAAGTC
1 AGGACTTGGCAACTCCTGCCCAGGACTTGGTATGTTGAAAGACGGAAGAAAAATCAGAACAACCC
4573 CTGTCC
66 CTGTCC
4579 AGGACTTGGACAACTCCTGCCCAGGACTTG
1 AGGACTTGG-CAACTCCTGCCCAGGACTTG
4609 TTGCGGGAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
71 71 0.77
72 21 0.23
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (71 bp):
AGGACTTGGCAACTCCTGCCCAGGACTTGGTATGTTGAAAGACGGAAGAAAAATCAGAACAACCC
CTGTCC
Found at i:4596 original size:22 final size:22
Alignment explanation
Indices: 4566--4608 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4556 AAAATTCAGA
* *
4566 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
4588 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
4609 TTGCGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:6821 original size:33 final size:33
Alignment explanation
Indices: 6720--6857 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
6710 TTGCAAAGAG
* * * *
6720 TGTTTTAGATGTTGTTAGTGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
** * *
6753 TAATTTAAGTGTTGTTTGTGATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
6786 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC
* **
6819 TGTTTT-GGATGCTAATTGTGATGAAAAC-AAATC
1 TGTTTTAGG-TGTTGTTTGTGATG-AAACTAAATC
6852 TGTTTT
1 TGTTTT
6858 GGTTGATCAT
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
32 5 0.06
33 76 0.86
34 7 0.08
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
Found at i:8990 original size:71 final size:71
Alignment explanation
Indices: 8894--9084 Score: 285
Period size: 71 Copynumber: 2.7 Consensus size: 71
8884 ATTGAAGCCT
*
8894 AAAAA-CAGGACAAGTCCTGCCCAGGATTTGACAACTCCTGCCCAGGACCTGGTCTGCTGAAAGA
1 AAAAATCAGAACAAGTCCTGCCCAGGATTTGACAACTCCTGCCCAGGACCTGGTCTGCTGAAAGA
8958 CGGAAG
66 CGGAAG
* * * * *
8964 AAAAATCAGAACAACTCCTGCCCAGGACTTGATAACTCCTGCCCAGGACTTGGTCTGTTGAAAGA
1 AAAAATCAGAACAAGTCCTGCCCAGGATTTGACAACTCCTGCCCAGGACCTGGTCTGCTGAAAGA
9029 CGGAAG
66 CGGAAG
* * *
9035 AAAATTCAGAACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCAGGAC
1 AAAAATCAGAACAAGTCCTGCCCAGGA-TTTGACAACTCCTGCCCAGGAC
9085 TTGTTGCGGG
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
70 5 0.05
71 83 0.78
72 19 0.18
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (71 bp):
AAAAATCAGAACAAGTCCTGCCCAGGATTTGACAACTCCTGCCCAGGACCTGGTCTGCTGAAAGA
CGGAAG
Found at i:9002 original size:21 final size:21
Alignment explanation
Indices: 8976--9015 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
8966 AAATCAGAAC
8976 AACTCCTGCCCAGGACTTGAT
1 AACTCCTGCCCAGGACTTGAT
8997 AACTCCTGCCCAGGACTTG
1 AACTCCTGCCCAGGACTTG
9016 GTCTGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (21 bp):
AACTCCTGCCCAGGACTTGAT
Found at i:9075 original size:22 final size:22
Alignment explanation
Indices: 9045--9087 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9035 AAAATTCAGA
* *
9045 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
9067 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
9088 TTGCGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:14512 original size:22 final size:21
Alignment explanation
Indices: 14469--14517 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
14459 CCAGGTTCCC
14469 TCTTT-TTTT-TTTTCTTTCT
1 TCTTTCTTTTGTTTTCTTTCT
14488 TCTTCTCTTTTGTTTTC-TTCAT
1 TCTT-TCTTTTGTTTTCTTTC-T
14510 TCTTTCTT
1 TCTTTCTT
14518 AGTCGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.15
20 1 0.04
21 11 0.42
22 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (21 bp):
TCTTTCTTTTGTTTTCTTTCT
Found at i:22030 original size:2 final size:2
Alignment explanation
Indices: 22023--22058 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22013 AATAATTGAA
22023 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
22059 GATATTAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22394 original size:27 final size:29
Alignment explanation
Indices: 22332--22398 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 29
22322 GATTGTATAT
22332 GTGGTGGTGGTGGAGGTGGCGAGTAGACGG
1 GTGGTGGTGGTGGAGGTGGCGAGTAGAC-G
22362 GTGGTGGTGGTGGAGGTGGCGAGTAGACGG
1 GTGGTGGTGGTGGAGGTGGCGAGTAGAC-G
22392 GTGGTGG
1 GTGGTGG
22399 AGGGGAGTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.12, C:0.06, G:0.61, T:0.21
Consensus pattern (29 bp):
GTGGTGGTGGTGGAGGTGGCGAGTAGACG
Found at i:22406 original size:21 final size:24
Alignment explanation
Indices: 22337--22425 Score: 85
Period size: 30 Copynumber: 3.6 Consensus size: 24
22327 TATATGTGGT
22337 GGTGGTGGAGGTGGCGAGTAGACGGGTGG
1 GGTGGTGGAGGTGGCGAGTAGAC-----G
22366 TGGTGGTGGAGGTGGCGAGTAGACG
1 -GGTGGTGGAGGTGGCGAGTAGACG
*
22391 GGTGGTGGA-G-GG-GAGTAGACT
1 GGTGGTGGAGGTGGCGAGTAGACG
*
22412 GGTGGTGGCGGTGG
1 GGTGGTGGAGGTGG
22426 TGGTGGTGAC
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
21 16 0.29
22 3 0.05
23 3 0.05
24 9 0.16
25 1 0.02
30 23 0.42
ACGTcount: A:0.13, C:0.07, G:0.61, T:0.19
Consensus pattern (24 bp):
GGTGGTGGAGGTGGCGAGTAGACG
Found at i:22446 original size:51 final size:51
Alignment explanation
Indices: 22337--22470 Score: 151
Period size: 51 Copynumber: 2.6 Consensus size: 51
22327 TATATGTGGT
* * *
22337 GGTGGTGGAGGTGGCGAGTAGACGGGTGGTGGTGGTGGAGGTGGCGAGTAGACG
1 GGTGGTGGA-G-GG-GAGTAGACGGGTGGTGGCGGTGGAGGTGGCGACTAGACA
* * * * *
22391 GGTGGTGGAGGGGAGTAGACTGGTGGTGGCGGTGGTGGTGGTGACTGGGCA
1 GGTGGTGGAGGGGAGTAGACGGGTGGTGGCGGTGGAGGTGGCGACTAGACA
* *
22442 GGTGGTGGAGGAGAGTATACGGGTGGTGG
1 GGTGGTGGAGGGGAGTAGACGGGTGGTGG
22471 AGGAGAGTAG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 57 0.83
52 2 0.03
53 1 0.01
54 9 0.13
ACGTcount: A:0.14, C:0.07, G:0.59, T:0.20
Consensus pattern (51 bp):
GGTGGTGGAGGGGAGTAGACGGGTGGTGGCGGTGGAGGTGGCGACTAGACA
Found at i:22466 original size:21 final size:21
Alignment explanation
Indices: 22442--22488 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
22432 TGACTGGGCA
*
22442 GGTGGTGGAGGAGAGTATACG
1 GGTGGTGGAGGAGAGTAGACG
*
22463 GGTGGTGGAGGAGAGTAGACT
1 GGTGGTGGAGGAGAGTAGACG
22484 GGTGG
1 GGTGG
22489 AGGGGGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.55, T:0.19
Consensus pattern (21 bp):
GGTGGTGGAGGAGAGTAGACG
Found at i:22508 original size:21 final size:21
Alignment explanation
Indices: 22484--22563 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
22474 AGAGTAGACT
22484 GGTGGAGGGGGTGAAGAAACA
1 GGTGGAGGGGGTGAAGAAACA
* * * ***
22505 GGTGGTGGTGGCGAACTGACA
1 GGTGGAGGGGGTGAAGAAACA
*
22526 GGTGGAGGGGGTGGAGAATGGACA
1 GGTGGAGGGGGTGAAGAA---ACA
22550 GGTGGACGGGGGTG
1 GGTGGA-GGGGGTG
22564 GTGAGTAGAC
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 26 0.62
24 9 0.21
25 7 0.17
ACGTcount: A:0.23, C:0.07, G:0.56, T:0.14
Consensus pattern (21 bp):
GGTGGAGGGGGTGAAGAAACA
Found at i:22509 original size:42 final size:42
Alignment explanation
Indices: 22463--22543 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
22453 AGAGTATACG
* *
22463 GGTGGTGGAGGAG-AGTAGACTGGTGGAGGGGGTGAAGAAACA
1 GGTGGTGGAGGAGAACT-GACAGGTGGAGGGGGTGAAGAAACA
* * *
22505 GGTGGTGGTGGCGAACTGACAGGTGGAGGGGGTGGAGAA
1 GGTGGTGGAGGAGAACTGACAGGTGGAGGGGGTGAAGAA
22544 TGGACAGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.25, C:0.06, G:0.54, T:0.15
Consensus pattern (42 bp):
GGTGGTGGAGGAGAACTGACAGGTGGAGGGGGTGAAGAAACA
Found at i:22578 original size:25 final size:24
Alignment explanation
Indices: 22522--22606 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
22512 GTGGCGAACT
*
22522 GACAGGTGGAGGGGGTGGAGAATG
1 GACAGGTGGAGGGGGTGGAGAATA
* *
22546 GACAGGTGGACGGGGGTGGTGAGTA
1 GACAGGTGGA-GGGGGTGGAGAATA
* * * *
22571 GACTGGTGGTGGCGGTGGGGAATA
1 GACAGGTGGAGGGGGTGGAGAATA
**
22595 GATTGGTGGAGG
1 GACAGGTGGAGG
22607 TGGAGACGAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
24 31 0.62
25 19 0.38
ACGTcount: A:0.20, C:0.06, G:0.56, T:0.18
Consensus pattern (24 bp):
GACAGGTGGAGGGGGTGGAGAATA
Found at i:22596 original size:24 final size:24
Alignment explanation
Indices: 22560--22654 Score: 64
Period size: 24 Copynumber: 3.8 Consensus size: 24
22550 GGTGGACGGG
* *
22560 GGTGGTGAGTAGACTGGTGGTGGC
1 GGTGGGGAATAGACTGGTGGTGGC
* * *
22584 GGTGGGGAATAGATTGGTGGAGGT
1 GGTGGGGAATAGACTGGTGGTGGC
* * * * *
22608 GGAGACGAAGATACAACTGGTTGTGGC
1 GGTG-GGGA-ATA-GACTGGTGGTGGC
*
22635 GGTGGGGAATAGATTGGTGG
1 GGTGGGGAATAGACTGGTGG
22655 AGGTGGAGAC
Statistics
Matches: 49, Mismatches: 19, Indels: 6
0.66 0.26 0.08
Matches are distributed among these distances:
24 28 0.57
25 5 0.10
26 5 0.10
27 11 0.22
ACGTcount: A:0.21, C:0.06, G:0.49, T:0.23
Consensus pattern (24 bp):
GGTGGGGAATAGACTGGTGGTGGC
Found at i:22634 original size:51 final size:51
Alignment explanation
Indices: 22572--22690 Score: 211
Period size: 51 Copynumber: 2.3 Consensus size: 51
22562 TGGTGAGTAG
22572 ACTGGTGGTGGCGGTGGGGAATAGATTGGTGGAGGTGGAGACGAAGATACA
1 ACTGGTGGTGGCGGTGGGGAATAGATTGGTGGAGGTGGAGACGAAGATACA
*
22623 ACTGGTTGTGGCGGTGGGGAATAGATTGGTGGAGGTGGAGACGAAGATACA
1 ACTGGTGGTGGCGGTGGGGAATAGATTGGTGGAGGTGGAGACGAAGATACA
* *
22674 ACTGCTGGTGGAGGTGG
1 ACTGGTGGTGGCGGTGG
22691 AGACGAAGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.24, C:0.08, G:0.47, T:0.21
Consensus pattern (51 bp):
ACTGGTGGTGGCGGTGGGGAATAGATTGGTGGAGGTGGAGACGAAGATACA
Found at i:22639 original size:30 final size:29
Alignment explanation
Indices: 22598--22719 Score: 134
Period size: 30 Copynumber: 4.4 Consensus size: 29
22588 GGGAATAGAT
22598 TGGTGGAGGTGGAGACGAAGATACAACTGG
1 TGGTGGAGGTGGAGACGAAGATACAACT-G
* * *
22628 TTGTGGCGGTGG-G--G-A-ATA-GA-T-
1 TGGTGGAGGTGGAGACGAAGATACAACTG
22649 TGGTGGAGGTGGAGACGAAGATACAACTG
1 TGGTGGAGGTGGAGACGAAGATACAACTG
22678 CTGGTGGAGGTGGAGACGAAGATACAACTG
1 -TGGTGGAGGTGGAGACGAAGATACAACTG
22708 CTGGTGGAGGTG
1 -TGGTGGAGGTG
22720 AACGATTCCG
Statistics
Matches: 77, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
21 10 0.13
22 1 0.01
23 1 0.01
24 2 0.03
25 4 0.05
26 4 0.05
27 2 0.03
28 1 0.01
29 1 0.01
30 51 0.66
ACGTcount: A:0.26, C:0.10, G:0.44, T:0.20
Consensus pattern (29 bp):
TGGTGGAGGTGGAGACGAAGATACAACTG
Found at i:22984 original size:20 final size:21
Alignment explanation
Indices: 22959--23006 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
22949 TGGTGGGGAG
22959 GAGTAGACCGGGGGAGG-GGT
1 GAGTAGACCGGGGGAGGTGGT
* *
22979 GAGTAGACTGGTGGAGGTGGT
1 GAGTAGACCGGGGGAGGTGGT
*
23000 GAATAGA
1 GAGTAGA
23007 TAGGTGGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.25, C:0.06, G:0.52, T:0.17
Consensus pattern (21 bp):
GAGTAGACCGGGGGAGGTGGT
Found at i:23122 original size:21 final size:21
Alignment explanation
Indices: 23096--23166 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
23086 TTCTTGGACA
23096 GGTGGTGGAGGAGAGTAGACG
1 GGTGGTGGAGGAGAGTAGACG
* *
23117 GGTGGTGGTGGGGAGTAGACAG
1 GGTGGTGGAGGAGAGTAGAC-G
* * *
23139 GG-GGAGGAGGTGAGTAGACT
1 GGTGGTGGAGGAGAGTAGACG
*
23159 AGTGGTGG
1 GGTGGTGG
23167 TGGTGGTGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.90
22 3 0.08
ACGTcount: A:0.21, C:0.04, G:0.58, T:0.17
Consensus pattern (21 bp):
GGTGGTGGAGGAGAGTAGACG
Found at i:23128 original size:173 final size:171
Alignment explanation
Indices: 22839--23171 Score: 569
Period size: 173 Copynumber: 1.9 Consensus size: 171
22829 TGCTGGTGGC
22839 GGTGGTGATTGCTTTGGTGGCCTAATAGGAGTCACCGGAGATTGATCATATCCATCAGGTGCAGG
1 GGTGGTGATTGCTTTGGTGGCCTAATAGGAGTCACCGGAGATTGATCATATCCATCAGGTGCAGG
*
22904 TGCCGGTGTTTCTTGGACAGGTGGTGGAAGAGAGTAGACGGGAGGTGGTGGGGAGGAGTAGACCG
66 TGCCGGTGTTTCTTGGACAGGTGGTGGAAGAGAGTAGACGGGAGGTGGT--GG-GGAGTAGACAG
*
22969 GGGGAGG-GGTGAGTAGACTGGTGGAGGTGGTGAATAGATAGGT
128 GGGGAGGAGGTGAGTAGACTAGTGGAGGTGGTGAATAGATAGGT
* *
23012 GGTGGTGATTGCTTTGGTGGCCTAATAGGAGTCACTGGAGATTGATCATATCCATCAGGTGTAGG
1 GGTGGTGATTGCTTTGGTGGCCTAATAGGAGTCACCGGAGATTGATCATATCCATCAGGTGCAGG
* *
23077 TGCCGGTGTTTCTTGGACAGGTGGTGGAGGAGAGTAGACGGGTGGTGGTGGGGAGTAGACAGGGG
66 TGCCGGTGTTTCTTGGACAGGTGGTGGAAGAGAGTAGACGGGAGGTGGTGGGGAGTAGACAGGGG
*
23142 GAGGAGGTGAGTAGACTAGTGGTGGTGGTG
131 GAGGAGGTGAGTAGACTAGTGGAGGTGGTG
23172 GTGGTGATTG
Statistics
Matches: 152, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
170 17 0.11
171 25 0.16
173 110 0.72
ACGTcount: A:0.20, C:0.11, G:0.45, T:0.24
Consensus pattern (171 bp):
GGTGGTGATTGCTTTGGTGGCCTAATAGGAGTCACCGGAGATTGATCATATCCATCAGGTGCAGG
TGCCGGTGTTTCTTGGACAGGTGGTGGAAGAGAGTAGACGGGAGGTGGTGGGGAGTAGACAGGGG
GAGGAGGTGAGTAGACTAGTGGAGGTGGTGAATAGATAGGT
Found at i:23171 original size:21 final size:20
Alignment explanation
Indices: 23092--23171 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 20
23082 GTGTTTCTTG
*
23092 GACAGGTGGTGGAGGAGAGTA
1 GACA-GTGGTGGAGGTGAGTA
* * *
23113 GACGGGTGGTGGTGGGGAGTA
1 GAC-AGTGGTGGAGGTGAGTA
* *
23134 GACAGGGGGAGGAGGTGAGTA
1 GACA-GTGGTGGAGGTGAGTA
*
23155 GACTAGTGGTGGTGGTG
1 GAC-AGTGGTGGAGGTG
23172 GTGGTGATTG
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
21 44 0.98
22 1 0.02
ACGTcount: A:0.21, C:0.05, G:0.56, T:0.17
Consensus pattern (20 bp):
GACAGTGGTGGAGGTGAGTA
Found at i:28580 original size:14 final size:14
Alignment explanation
Indices: 28561--28596 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28551 ACTCATGGCC
28561 ATAATATATAAT-AT
1 ATAATA-ATAATAAT
28575 ATAATAATAATAAT
1 ATAATAATAATAAT
28589 ATAATAAT
1 ATAATAAT
28597 TGAATGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:30725 original size:12 final size:12
Alignment explanation
Indices: 30708--30732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30698 AAAACATGTT
30708 AACAATAGTCAA
1 AACAATAGTCAA
30720 AACAATAGTCAA
1 AACAATAGTCAA
30732 A
1 A
30733 GTTCAAACCA
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:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AACAATAGTCAA
Found at i:37917 original size:14 final size:14
Alignment explanation
Indices: 37898--37940 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
37888 TTTAGATCCT
37898 TACAAATATTAGTA
1 TACAAATATTAGTA
37912 TACAAATATTAGTA
1 TACAAATATTAGTA
37926 TACAAATATTAGTA
1 TACAAATATTAGTA
37940 T
1 T
37941 TATGTTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
TACAAATATTAGTA
Found at i:41225 original size:32 final size:32
Alignment explanation
Indices: 41189--41258 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
41179 AAAACATAAT
*
41189 TACATAATTAATTATTCTAAATGAAATAAAAA
1 TACATAATTAATTAATCTAAATGAAATAAAAA
*
41221 TACATAATTAATTAATCTAAATTAAATAAAAA
1 TACATAATTAATTAATCTAAATGAAATAAAAA
41253 TACATA
1 TACATA
41259 TTTATCCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.34
Consensus pattern (32 bp):
TACATAATTAATTAATCTAAATGAAATAAAAA
Done.