Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010432.1 Corchorus capsularis cultivar CVL-1 contig10453, 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: 51301
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:1215 original size:82 final size:85
Alignment explanation
Indices: 1086--1246 Score: 238
Period size: 82 Copynumber: 1.9 Consensus size: 85
1076 GGATTTCTTA
* * *
1086 CTTAGAAGTTGATCTATTTATACTTGGATGTTCAACCATGGGGTTAGGATGGATCCCCATTT-CT
1 CTTAGAAGTTGATCTATTTATACTTGGATGTGCAACCACGGGATTAGGATGGATCCCCATTTACT
1150 TGGAATAGTCACTTGTTTTT
66 TGGAATAGTCACTTGTTTTT
* * * *
1170 CTTAGGAGTTGATCTCTTT-T-CTTGGATGTGCTACTACGGGATTAGGATGGATCCCCATTTACT
1 CTTAGAAGTTGATCTATTTATACTTGGATGTGCAACCACGGGATTAGGATGGATCCCCATTTACT
1233 TGGAATAGTCACTT
66 TGGAATAGTCACTT
1247 CTTAGCTCCT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
82 35 0.51
83 17 0.25
84 17 0.25
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (85 bp):
CTTAGAAGTTGATCTATTTATACTTGGATGTGCAACCACGGGATTAGGATGGATCCCCATTTACT
TGGAATAGTCACTTGTTTTT
Found at i:12395 original size:2 final size:2
Alignment explanation
Indices: 12388--12442 Score: 67
Period size: 2 Copynumber: 26.5 Consensus size: 2
12378 GACATGGGAG
*
12388 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA AA GTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
12432 GTA -A TA TA TA T
1 -TA TA TA TA TA T
12443 CAGTCAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 1 0.02
2 41 0.87
3 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:12669 original size:12 final size:12
Alignment explanation
Indices: 12652--12694 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
12642 TTAATACAGG
*
12652 TATCGATGGATA
1 TATCGACGGATA
12664 TATCGAACGGATA
1 TATCG-ACGGATA
12677 TATCGACGGATA
1 TATCGACGGATA
12689 TATCGA
1 TATCGA
12695 GGTATCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:14417 original size:20 final size:20
Alignment explanation
Indices: 14380--14438 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
14370 TATGGATATT
14380 TACGGATATATCGA--GATA
1 TACGGATATATCGACGGATA
14398 T-C-GATAAATATCGACGGATA
1 TACGGAT--ATATCGACGGATA
14418 TACGGATATATCGACGGATA
1 TACGGATATATCGACGGATA
14438 T
1 T
14439 TCCGTGACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 8 0.23
20 19 0.54
21 1 0.03
22 3 0.09
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (20 bp):
TACGGATATATCGACGGATA
Found at i:17628 original size:6 final size:6
Alignment explanation
Indices: 17617--17661 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
17607 CTGCTCATCA
* * *
17617 TCCTCT TCCTCT TCCTCT TCCTCC TCCTCC TCCTTT CTCCTCT TC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT -TCCTCT TC
17662 TTTCATCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
TCCTCT
Found at i:18845 original size:3 final size:3
Alignment explanation
Indices: 18837--18861 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18827 CCATGAGAAT
18837 AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC A
18862 TCCATGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:21499 original size:13 final size:14
Alignment explanation
Indices: 21475--21503 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21465 CCATTTTTCT
21475 ATTTCAAATATATA
1 ATTTCAAATATATA
21489 ATTTC-AATATATA
1 ATTTCAAATATATA
21502 AT
1 AT
21504 ACTCCCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTCAAATATATA
Found at i:21874 original size:45 final size:47
Alignment explanation
Indices: 21790--21881 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 47
21780 AAATTATAGT
* * * *
21790 AATTTAGCATGTTGACATATAGTAAATAGGAATAGTTAAATGTGTTTC
1 AATTAAGCATGTTGACA-ATAGCAAATAGGAATAATTAAACGTGTTTC
21838 AATTAAGCATGTTGAC-ATA-CAAATAGGAATAATTAAACGTGTTT
1 AATTAAGCATGTTGACAATAGCAAATAGGAATAATTAAACGTGTTT
21882 TAATCGTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 22 0.55
46 3 0.08
48 15 0.38
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (47 bp):
AATTAAGCATGTTGACAATAGCAAATAGGAATAATTAAACGTGTTTC
Found at i:22574 original size:33 final size:33
Alignment explanation
Indices: 22537--22633 Score: 101
Period size: 33 Copynumber: 2.9 Consensus size: 33
22527 GGCAGCTGAG
*
22537 CCATGGCCAAGCTGCCCTCCTGGGGCGGCACTA
1 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
* * *
22570 CCATGGCCAGGCCG-TCTCCCTGGGGCGGCCCTA
1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTA
*
22603 CCATGG--ATAGACCGCCCCCCTGGGGCGGCAC
1 CCATGGCCA-AG-CCGCCCTCCTGGGGCGGCAC
22634 CGGTACTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
31 1 0.02
32 3 0.06
33 47 0.90
34 1 0.02
ACGTcount: A:0.13, C:0.41, G:0.32, T:0.13
Consensus pattern (33 bp):
CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
Found at i:22795 original size:33 final size:32
Alignment explanation
Indices: 22705--22816 Score: 147
Period size: 32 Copynumber: 3.5 Consensus size: 32
22695 GCCTTGTCGC
*
22705 CCTAGT-GGGACGGCTAGCCGTGGCAGGGCCGT
1 CCTAGTGGGGA-GGCTAGCCGTGGCAGAGCCGT
*
22737 CCTAGTGGGGCGGCTAGCCGTGGCAGAGCCGT
1 CCTAGTGGGGAGGCTAGCCGTGGCAGAGCCGT
*
22769 CCTATTGGGGAGGTTCT-GCCGTGGCAGAGCCGT
1 CCTAGTGGGGAGG--CTAGCCGTGGCAGAGCCGT
*
22802 TCTAGTGGGGAGGCT
1 CCTAGTGGGGAGGCT
22817 CCGCGTGGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
31 2 0.03
32 37 0.52
33 30 0.42
34 2 0.03
ACGTcount: A:0.12, C:0.25, G:0.43, T:0.20
Consensus pattern (32 bp):
CCTAGTGGGGAGGCTAGCCGTGGCAGAGCCGT
Found at i:22899 original size:21 final size:19
Alignment explanation
Indices: 22873--22914 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
22863 CAAAAGTGTA
22873 AAAAAT-GGGACGGTGAATAGC
1 AAAAATAGGG-CGGT-AA-AGC
22894 AAAAATAGGGCGGTAAAGC
1 AAAAATAGGGCGGTAAAGC
22913 AA
1 AA
22915 CCCCCTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 10 0.50
22 3 0.15
ACGTcount: A:0.48, C:0.10, G:0.31, T:0.12
Consensus pattern (19 bp):
AAAAATAGGGCGGTAAAGC
Found at i:32235 original size:30 final size:30
Alignment explanation
Indices: 32200--32277 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
32190 GTAGAACAAA
* *
32200 ATCAGATTGTTCTCCTTCACAAACAAAGAG
1 ATCAGAATCTTCTCCTTCACAAACAAAGAG
*
32230 ATCAGAATCTTCTCCTTCAGAAACAAAGAG
1 ATCAGAATCTTCTCCTTCACAAACAAAGAG
32260 ATCAGAATCTTCCTCCTT
1 ATCAGAATCTT-CTCCTT
32278 GTCATACTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 38 0.86
31 6 0.14
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.28
Consensus pattern (30 bp):
ATCAGAATCTTCTCCTTCACAAACAAAGAG
Found at i:34073 original size:30 final size:31
Alignment explanation
Indices: 34010--34073 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
34000 ATGGTACTGG
* *
34010 TTGAGTTTTATAGCTGTAAAATTCATTTTTTA
1 TTGAGTTTTATAGCTGT-AAATCCATTTCTTA
34042 TTGA-TTTTATAGCTTGT-AATCCATTTCTTA
1 TTGAGTTTTATAGC-TGTAAATCCATTTCTTA
34072 TT
1 TT
34074 ATCGGACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 13 0.45
31 9 0.31
32 7 0.24
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (31 bp):
TTGAGTTTTATAGCTGTAAATCCATTTCTTA
Found at i:40670 original size:31 final size:31
Alignment explanation
Indices: 40635--40700 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
40625 AACTTTATGT
* *
40635 TTTCCGATTGTACCCTTGTT-TTTAAAACATA
1 TTTCCAATTGCACCCTT-TTATTTAAAACATA
40666 TTTCCAATTGCACCCTTTTATTTAAAACATA
1 TTTCCAATTGCACCCTTTTATTTAAAACATA
40697 TTTC
1 TTTC
40701 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGCACCCTTTTATTTAAAACATA
Found at i:41595 original size:19 final size:20
Alignment explanation
Indices: 41559--41596 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41549 TTACTATTAT
41559 TTTTCAATTTAATATTTTAC
1 TTTTCAATTTAATATTTTAC
41579 TTTT-AATTTCAAT-TTTTA
1 TTTTCAATTT-AATATTTTA
41597 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTCAATTTAATATTTTAC
Found at i:41817 original size:22 final size:21
Alignment explanation
Indices: 41763--42298 Score: 100
Period size: 22 Copynumber: 23.8 Consensus size: 21
41753 GTCTCTGTGA
*
41763 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAGGA-GG
* * *
41785 TTCTTATAATTTCATGAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
41807 TTATCAAAATTTCATAGTGTA-G
1 TTATCAAAATTTCATAG-G-AGG
* * *
41829 TTACCAAAATTTCAGATGGAAG
1 TTATCAAAATTTCATA-GGAGG
* ***
41851 TTATTAAAATTTCATAGTGTTA
1 TTATCAAAATTTCATAG-GAGG
*
41873 TTACCAAAATTTCATAGGATCAGG
1 TTATCAAAATTTCATAGG---AGG
* * *
41897 TTATTAAAATTTCTTAGGATGA
1 TTATCAAAATTTCATAGGA-GG
** *
41919 TTATTGAAATTTCATAGGGTAGTTAA
1 TTATCAAAATTTCATA-GG-AG---G
* * *
41945 TTATCACAATTTTATAGAAAGG
1 TTATCAAAATTTCATAG-GAGG
* * *
41967 GTATCAAAGAGATTATCA-A-AATG
1 TTATC-AA-A-ATT-TCATAGGAGG
* * *
41990 TCATAGAAGAATTTCATAGTGTGG
1 TTAT-CAA-AATTTCATAG-GAGG
* *
42014 TTAACAAAATTTCATTAGAAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
42036 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* * *
42058 TTATCAAAATTTTATACTGTGG
1 TTATCAAAATTTCATA-GGAGG
* *
42080 TTATCAAAATTCCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
42102 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * **
42127 AGTACCAAAATTTGATAAAAGG
1 -TTATCAAAATTTCATAGGAGG
*
42149 TTATC-AAATTTTATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
42169 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-G---AGG
* *
42195 TTATCAAAATTT-ATTGGAAGA
1 TTATCAAAATTTCATAGG-AGG
**
42216 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* *
42238 TTATCAAAATTTCAAAACGAGG
1 TTATCAAAATTTC-ATAGGAGG
* * * *
42260 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
*
42282 TTATCAGAATTTCATAG
1 TTATCAAAATTTCATAG
42299 ATGGGTCAAC
Statistics
Matches: 372, Mismatches: 92, Indels: 101
0.66 0.16 0.18
Matches are distributed among these distances:
19 2 0.01
20 18 0.05
21 36 0.10
22 212 0.57
23 30 0.08
24 24 0.06
25 23 0.06
26 17 0.05
27 2 0.01
28 8 0.02
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:41840 original size:44 final size:44
Alignment explanation
Indices: 41792--41909 Score: 152
Period size: 44 Copynumber: 2.6 Consensus size: 44
41782 TGGTTCTTAT
*
41792 AATTTCATGAGGAGGTTATCAAAATTTCATAGTG-TAGTTACCAA
1 AATTTCATGAGGAGGTTATTAAAATTTCATAGTGTTA-TTACCAA
*
41836 AATTTCA-GATGGAAGTTATTAAAATTTCATAGTGTTATTACCAA
1 AATTTCATGA-GGAGGTTATTAAAATTTCATAGTGTTATTACCAA
41880 AATTTCAT-AGGATCAGGTTATTAAAATTTC
1 AATTTCATGAGG---AGGTTATTAAAATTTC
41910 TTAGGATGAT
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
43 4 0.06
44 44 0.68
45 2 0.03
46 15 0.23
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (44 bp):
AATTTCATGAGGAGGTTATTAAAATTTCATAGTGTTATTACCAA
Found at i:42354 original size:22 final size:22
Alignment explanation
Indices: 42310--42361 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
42300 TGGGTCAACA
** *
42310 AAATTTT-ATAAAGAGTTTTTC
1 AAATTTTCATAAAGAGGCTATC
42331 AAATTTTCATAAAGAGGCTATC
1 AAATTTTCATAAAGAGGCTATC
42353 AAATTTTCA
1 AAATTTTCA
42362 AAATGTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATTTTCATAAAGAGGCTATC
Found at i:42495 original size:20 final size:20
Alignment explanation
Indices: 42467--42541 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
42457 TTATGGAGTA
42467 ATCAAAATTTCATGGAGGAT
1 ATCAAAATTTCATGGAGGAT
* **
42487 ATTAAAATTTCCGGGAGGAT
1 ATCAAAATTTCATGGAGGAT
* *
42507 ATCAAAATTTCATATGAAGATT
1 ATCAAAATTTCAT-GGAGGA-T
42529 ATCAAAATTTCAT
1 ATCAAAATTTCAT
42542 AGTTTAGTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 27 0.60
21 4 0.09
22 14 0.31
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (20 bp):
ATCAAAATTTCATGGAGGAT
Found at i:42704 original size:23 final size:23
Alignment explanation
Indices: 42652--42753 Score: 102
Period size: 23 Copynumber: 4.5 Consensus size: 23
42642 AAATTTTTAG
* * *
42652 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTATAAGGAAGT
*
42674 TTATCAAAATTTTATAAGGATGT
1 TTATCAAAATTTTATAAGGAAGT
42697 TTATCAAAATTTTAT-AGGAAGAT
1 TTATCAAAATTTTATAAGGAAG-T
* * *
42720 TTATCAAAATTTCAT-AGTAAGA
1 TTATCAAAATTTTATAAGGAAGT
*
42742 TTATCACAATTT
1 TTATCAAAATTT
42754 CATAGTGTGA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
22 34 0.49
23 35 0.51
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAAGGAAGT
Found at i:42758 original size:22 final size:22
Alignment explanation
Indices: 42506--42777 Score: 161
Period size: 22 Copynumber: 12.6 Consensus size: 22
42496 TCCGGGAGGA
42506 TATCAAAATTTCATA-TGAAGAT
1 TATCAAAATTTCATAGT-AAGAT
*
42528 TATCAAAATTTCATAGTTTAG-T
1 TATCAAAATTTCATAG-TAAGAT
* * * *
42550 TTTCAAAACTTCATAAG-AGGGT
1 TATCAAAATTTCAT-AGTAAGAT
**
42572 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATAGTAAGAT
* * * *
42594 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTAAGAT
** * ** *
42616 TATCAAAAAAT-ATTGGGAGGT
1 TATCAAAATTTCATAGTAAGAT
42637 TATCAAAATTT--T--T-AG-T
1 TATCAAAATTTCATAGTAAGAT
* *
42653 TATCAAGATTTCATAAGAAAG-T
1 TATCAAAATTTCAT-AGTAAGAT
* * * *
42675 TATCAAAATTTTATAAGGATGTT
1 TATCAAAATTTCAT-AGTAAGAT
* *
42698 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGTAAGA-T
42721 TATCAAAATTTCATAGTAAGAT
1 TATCAAAATTTCATAGTAAGAT
* **
42743 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTAAGAT
42765 TATCAAAATTTCA
1 TATCAAAATTTCA
42778 GAGTGTGATT
Statistics
Matches: 200, Mismatches: 37, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
20 1 0.00
21 19 0.09
22 126 0.63
23 39 0.19
24 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTAAGAT
Found at i:42782 original size:22 final size:22
Alignment explanation
Indices: 42506--42890 Score: 133
Period size: 22 Copynumber: 17.7 Consensus size: 22
42496 TCCGGGAGGA
*
42506 TATCAAAATTTCATA-TGAAGAT
1 TATCAAAATTTCATAGTG-TGAT
*
42528 TATCAAAATTTCATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
42550 TTTCAAAACTTCATAAGAG-GGT
1 TATCAAAATTTCAT-AGTGTGAT
* *
42572 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATAGTGTGAT
* * * *
42594 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTGTGAT
** * * * *
42616 TATCAAAAAAT-ATTGGGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
42637 TATCAAAATTT--T--T-AG-T
1 TATCAAAATTTCATAGTGTGAT
* * **
42653 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGTGTGA-T
* *
42675 TATCAAAATTTTATAAG-GATGTT
1 TATCAAAATTTCAT-AGTG-TGAT
* *
42698 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
**
42721 TATCAAAATTTCATAGTAAGAT
1 TATCAAAATTTCATAGTGTGAT
*
42743 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
42765 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
42787 TA-CTAACAA-TTCATA-TG-GAGGT
1 TATC-AA-AATTTCATAGTGTGA--T
* * * * *
42809 TTTTAAATTTTCATAATGTGGT
1 TATCAAAATTTCATAGTGTGAT
* *
42831 TATCAATATATCATA-TG-GAGGT
1 TATCAAAATTTCATAGTGTGA--T
* * *
42853 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-TGAT
42876 TATCAAAATTTCATA
1 TATCAAAATTTCATA
42891 TTCAGGTTTT
Statistics
Matches: 277, Mismatches: 57, Indels: 57
0.71 0.15 0.15
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 5 0.02
21 26 0.09
22 171 0.62
23 59 0.21
24 1 0.00
25 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:42898 original size:45 final size:44
Alignment explanation
Indices: 42819--42903 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 44
42809 TTTTAAATTT
* *
42819 TCATAATGTGGTTATCAATATATCATATGGAGGTTATCAACATC
1 TCATAATGTGGTTATCAAAATATCATATGCAGGTTATCAACATC
* * * *
42863 TCATAGTGTTGGTTATCAAAATTTCATATTCAGGTTTTCAA
1 TCATAATG-TGGTTATCAAAATATCATATGCAGGTTATCAA
42904 AATTCCTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 7 0.21
45 27 0.79
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (44 bp):
TCATAATGTGGTTATCAAAATATCATATGCAGGTTATCAACATC
Found at i:45425 original size:13 final size:13
Alignment explanation
Indices: 45407--45437 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
45397 CATATTCTAT
45407 TCTTTAACATTAA
1 TCTTTAACATTAA
45420 TCTTTAACATTAA
1 TCTTTAACATTAA
45433 TCTTT
1 TCTTT
45438 CTTCTTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (13 bp):
TCTTTAACATTAA
Found at i:48726 original size:21 final size:21
Alignment explanation
Indices: 48640--48716 Score: 91
Period size: 21 Copynumber: 3.3 Consensus size: 21
48630 ATGATGATGG
48640 ATTCAATATGATACCAATTAC
1 ATTCAATATGATACCAATTAC
48661 ATTCAATTTCAAGTTTGATACCAATTAC
1 ATTCAA--T--A---TGATACCAATTAC
48689 ATTCAATATGATACCAATTAC
1 ATTCAATATGATACCAATTAC
48710 ATTCAAT
1 ATTCAAT
48717 TATTAACCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
21 26 0.53
23 1 0.02
24 1 0.02
25 1 0.02
26 1 0.02
28 19 0.39
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36
Consensus pattern (21 bp):
ATTCAATATGATACCAATTAC
Found at i:50961 original size:2 final size:2
Alignment explanation
Indices: 50940--50988 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
50930 GAATTACCTG
* * * *
50940 AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50982 AT AT AT A
1 AT AT AT A
50989 GCTAGTGATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Done.