Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006069.1 Corchorus capsularis cultivar CVL-1 contig06087, 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: 54794
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:521 original size:22 final size:21
Alignment explanation
Indices: 407--588 Score: 141
Period size: 22 Copynumber: 8.2 Consensus size: 21
397 ATCTCTATGA
*
407 GGTTATCAAAATTTCATAAGAT
1 GGTTATCAAAATTTCAT-AGGT
* * *
429 GGTTATTACAATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGGT
*
451 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GT
* * *
473 GGTTACCAAAATTTCAAATGGA
1 GGTTATCAAAATTTCATA-GGT
*
495 AGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GT
*
517 GGTTA-CCAAATTTCATAGGAT
1 GGTTATCAAAATTTCATAGG-T
* *
538 CAGGTTATTAAAATTTCTTAGGTT
1 --GGTTATCAAAATTTCATAGG-T
**
562 GGTTATTGAAATTTCATAGGGT
1 GGTTATCAAAATTTCATA-GGT
584 GGTTA
1 GGTTA
589 ATTATCACAA
Statistics
Matches: 127, Mismatches: 25, Indels: 16
0.76 0.15 0.10
Matches are distributed among these distances:
20 1 0.01
21 16 0.13
22 90 0.71
23 8 0.06
24 12 0.09
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGT
Found at i:649 original size:22 final size:21
Alignment explanation
Indices: 624--745 Score: 86
Period size: 22 Copynumber: 5.6 Consensus size: 21
614 ATCAAAGAGA
*
624 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
646 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
668 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* * * * *
690 TTA-CTAATTTTGATGGGGAGA
1 TTATCAAAATTTCAT-AGGAGG
* *
711 TTATCAAAATTTTATAGTGCGG
1 TTATCAAAATTTCATAG-GAGG
733 TTATCAAAATTTC
1 TTATCAAAATTTC
746 GTATGAAGCT
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 17 0.22
22 54 0.70
23 5 0.06
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:1015 original size:22 final size:22
Alignment explanation
Indices: 882--1029 Score: 95
Period size: 22 Copynumber: 6.7 Consensus size: 22
872 AAAATTCCAG
* *
882 TATCAAAATTTCAAAAACGAGGT
1 TATCAAAATTTCATAAA-GAGAT
* * * *
905 TATCAAAATTACAGAATGTGAT
1 TATCAAAATTTCATAAAGAGAT
* * * *
927 TATCACAATTTCATAGAGGGGT
1 TATCAAAATTTCATAAAGAGAT
* * * *
949 CAACAAAATTTTATAAA-AAAGT
1 TATCAAAATTTCATAAAGAGA-T
971 TATCAAAATTTCATAAAGAGAT
1 TATCAAAATTTCATAAAGAGAT
* *
993 TATCAAATTTTCA-AAATGTGAT
1 TATCAAAATTTCATAAA-GAGAT
1015 TA-CAAAAATTTCATA
1 TATC-AAAATTTCATA
1030 GTGGTATTTA
Statistics
Matches: 93, Mismatches: 27, Indels: 10
0.72 0.21 0.08
Matches are distributed among these distances:
21 4 0.04
22 72 0.77
23 17 0.18
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (22 bp):
TATCAAAATTTCATAAAGAGAT
Found at i:1158 original size:22 final size:22
Alignment explanation
Indices: 1130--1686 Score: 197
Period size: 22 Copynumber: 25.5 Consensus size: 22
1120 TCAGGGAGGA
1130 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
1152 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1174 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
1196 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * **
1217 AGATCAAAATTTCATAGGGACAT
1 -TATCAAAATTTCATATGAAGGT
*
1240 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
1262 TATCAAAAAATCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
1284 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
1300 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
1322 TATCAAAATTTTATAGGGAGGTTT
1 TATCAAAATTTCATATGAAGG--T
* * *
1346 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
* *
1369 TATCAAAATTTCATTACG-AGCT
1 TATCAAAATTTCA-TATGAAGGT
* * *
1391 TATCACAATTTCATA-GTATGAT
1 TATCAAAATTTCATATG-AAGGT
* * * *
1413 TATCAAAATTTTAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
1435 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
1457 TTTTAAATTTTCATAACG-GGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
1479 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * ***
1501 TATCAACATCTCATAGTGTTCGT
1 TATCAAAATTTCATA-TGAAGGT
1524 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
1546 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
1568 CT-TCAAAATTCCTTA-GAGAGGT
1 -TATCAAAATTTCATATGA-AGGT
* *
1590 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
1612 TA-AAAAAATT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
1632 TCTCGAAATTACATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
1654 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
1676 TATCAAAATTT
1 TATCAAAATTT
1687 AATAATGGAA
Statistics
Matches: 400, Mismatches: 93, Indels: 84
0.69 0.16 0.15
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
20 14 0.04
21 28 0.07
22 273 0.68
23 47 0.12
24 25 0.06
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:1187 original size:44 final size:43
Alignment explanation
Indices: 1130--1686 Score: 218
Period size: 44 Copynumber: 12.8 Consensus size: 43
1120 TCAGGGAGGA
*
1130 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAG-TTAGT
* *
1174 TTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAG-TATGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTA-GT
* * * ** * * *
1217 AGATCAAAATTTCATAGGGACATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTA-GT
** *
1262 TATCAAAAAATCATAAGGAGGTTATCAAAA-TT--T-G-TAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAGT
* * * **
1300 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTA-G--T
* * *
1346 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATTACG--AGCT
1 TATCAAAATTTCATAAGAAG-GTTATCAAAATTTCA-TA-GTTAG-T
* * * * *
1391 TATCACAATTTCAT-AGTATGATTATCAAAATTTTAGAGTGT-GAT
1 TATCAAAATTTCATAAG-AAGGTTATCAAAATTTCATAGT-TAG-T
* * * * * **
1435 TA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACG-GGGT
1 TATC-AA-AATTTCATAAGAAGGTTATCAAAATTTCAT-A-GTTAGT
* * * * * * *
1479 TATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTCGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATA--GTTAGT
**
1524 TATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATA-TTGAGGT
1 TATCAAAATTTCA-TAAGAAGGTTATCAAAATTTCATAGTT-A-GT
* * * *
1568 CT-TCAAAA-TTCCTTAGAGAGGTTAACAAAATTTCATAAG-AAGGT
1 -TATCAAAATTTCATAAGA-AGGTTATCAAAATTTCAT-AGTTA-GT
* * * * * * *
1612 TA-AAAAAATT-ATAAAAAGGTTCTCGAAATTACATAGTATCGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGT-TAGT
* *
1654 TATTAAAATTTCATAGGAAGGTTATCAAAATTT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTT
1687 AATAATGGAA
Statistics
Matches: 376, Mismatches: 95, Indels: 84
0.68 0.17 0.15
Matches are distributed among these distances:
38 27 0.07
39 3 0.01
41 4 0.01
42 27 0.07
43 27 0.07
44 195 0.52
45 54 0.14
46 22 0.06
47 14 0.04
48 2 0.01
49 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAGT
Found at i:1374 original size:23 final size:23
Alignment explanation
Indices: 1299--1379 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
1289 AAATTTGTAG
* * * *
1299 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
1321 TTATCAAAATTTTATAGGGAGGTT
1 TTATCAAAATTTTATA-GGAAGAT
1345 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
1368 TTATCAAAATTT
1 TTATCAAAATTT
1380 CATTACGAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 14 0.29
23 19 0.39
24 16 0.33
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:1625 original size:20 final size:22
Alignment explanation
Indices: 1586--1632 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
1576 TTCCTTAGAG
* *
1586 AGGTTAACAAAATTTCATAAGA
1 AGGTTAACAAAAATTCATAAAA
1608 AGGTTAA-AAAAATT-ATAAAA
1 AGGTTAACAAAAATTCATAAAA
1628 AGGTT
1 AGGTT
1633 CTCGAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 6 0.26
22 7 0.30
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (22 bp):
AGGTTAACAAAAATTCATAAAA
Found at i:2697 original size:39 final size:39
Alignment explanation
Indices: 2641--2717 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
2631 TCTTGCCACC
*
2641 TCTCAAACGTGACGATACGTTGTCAATGGCGGAATTGAT
1 TCTCAAACGTGACGATACATTGTCAATGGCGGAATTGAT
*
2680 TCTCAAACGTGATGATACATTGTCAATGGCGGAATTGA
1 TCTCAAACGTGACGATACATTGTCAATGGCGGAATTGA
2718 GTTGGCTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (39 bp):
TCTCAAACGTGACGATACATTGTCAATGGCGGAATTGAT
Found at i:5007 original size:2 final size:2
Alignment explanation
Indices: 4995--5027 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4985 AGTATTTTAA
4995 AT AT A- 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
5028 TTTACTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10233 original size:26 final size:26
Alignment explanation
Indices: 10183--10235 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
10173 AAATTAGTGC
10183 AAAAACTAATTTTATACTATTAATTA
1 AAAAACTAATTTTATACTATTAATTA
10209 AAAAACTAATTTTATACTATTAATTA
1 AAAAACTAATTTTATACTATTAATTA
10235 A
1 A
10236 TAATAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAAACTAATTTTATACTATTAATTA
Found at i:11604 original size:319 final size:319
Alignment explanation
Indices: 11025--11610 Score: 1064
Period size: 319 Copynumber: 1.8 Consensus size: 319
11015 TGTGCAACAT
*
11025 CTTGAATTAACACTGCTCGACCTGCAATAGATAACATTTTGCCCTTCCAGCTTTTAATTCTTTTC
1 CTTGAATTAACACTGCTCGACCTGCAATAGATAACATTTTGCCCTTCCAGCTTTTAATTCTCTTC
* *
11090 CATAATCTGTCTTTTATCGCTTCCAATTATGCTCTCTTTGACTTGCCAACCATTATTAGCATACC
66 CATAATCTGTCTTTTATCGCCTCCAATTATGCTCTCTTTAACTTGCCAACCATTATTAGCATACC
* *
11155 AAGATACTTGTCTTTCGCTAAAATCTTTTGTAACCCCAAACTCTGCATGATGCAATTGTGATACT
131 AAGATACTTGTCTTTCGCTAAAATCTTTTGTAACCCCAAACTATGCATGATGCAATTGCGATACT
*
11220 GCTCATGCACATTCTTACTAAACAACACAACAGATTTCTCTACATTAATCATCTGTCCCGAAGCC
196 GCTCAGGCACATTCTTACTAAACAACACAACAGATTTCTCTACATTAATCATCTGTCCCGAAGCC
11285 ACTTCAATAATGGTTGACCTGCAATAGCTTGAATTAATCATCTGTCCCGAAGCCAATAA
261 ACTTCAATAATGGTTGACCTGCAATAGCTTGAATTAATCATCTGTCCCGAAGCCAATAA
11344 CTTGAATTAACACTGCTCGACCTGCAATAGATAACATTTTGCCCTTCCAGCTTTTAATTCTCTTC
1 CTTGAATTAACACTGCTCGACCTGCAATAGATAACATTTTGCCCTTCCAGCTTTTAATTCTCTTC
* *
11409 CATAATCTGTCTTTTATCGCCTCCAATTATGGTCTCTTTAACTTGCCAACCATTATTGGCATACC
66 CATAATCTGTCTTTTATCGCCTCCAATTATGCTCTCTTTAACTTGCCAACCATTATTAGCATACC
*
11474 AAGATACTTGTCTTTCGCTAAAATCTTTTGTACCCCCAAACTATGCATGATGCAATTGCGATACT
131 AAGATACTTGTCTTTCGCTAAAATCTTTTGTAACCCCAAACTATGCATGATGCAATTGCGATACT
* * *
11539 GCTCAGGCACATTCTTACTAAACAACATAGCAGATTTGTCTACATTAATCATCTGTCCCGAAGCC
196 GCTCAGGCACATTCTTACTAAACAACACAACAGATTTCTCTACATTAATCATCTGTCCCGAAGCC
11604 ACTTCAA
261 ACTTCAA
11611 AAGCTTTCAA
Statistics
Matches: 255, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
319 255 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (319 bp):
CTTGAATTAACACTGCTCGACCTGCAATAGATAACATTTTGCCCTTCCAGCTTTTAATTCTCTTC
CATAATCTGTCTTTTATCGCCTCCAATTATGCTCTCTTTAACTTGCCAACCATTATTAGCATACC
AAGATACTTGTCTTTCGCTAAAATCTTTTGTAACCCCAAACTATGCATGATGCAATTGCGATACT
GCTCAGGCACATTCTTACTAAACAACACAACAGATTTCTCTACATTAATCATCTGTCCCGAAGCC
ACTTCAATAATGGTTGACCTGCAATAGCTTGAATTAATCATCTGTCCCGAAGCCAATAA
Found at i:27100 original size:6 final size:7
Alignment explanation
Indices: 27084--27108 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27074 TTTAGGGTGG
27084 TTTTAAT
1 TTTTAAT
27091 TTTTAAT
1 TTTTAAT
27098 TTTTAAT
1 TTTTAAT
27105 TTTT
1 TTTT
27109 TTTAAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:30409 original size:20 final size:20
Alignment explanation
Indices: 30384--30424 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
30374 CGATCAGACT
* *
30384 AAAATATTAAATTAAAAGAA
1 AAAATATGAAATGAAAAGAA
30404 AAAATATGAAATGAAAAGAA
1 AAAATATGAAATGAAAAGAA
30424 A
1 A
30425 TACTAATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (20 bp):
AAAATATGAAATGAAAAGAA
Found at i:39744 original size:75 final size:75
Alignment explanation
Indices: 39657--39806 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
39647 CCTCTTTTTA
39657 TTTTCTTTCCCTCCCATCCCCTCAAATCCAAACATAGCACAAGATCTACCCTTGTTTTCACTATA
1 TTTTCTTTCCCTCCCATCCCCTCAAATCCAAACATAGCACAAGATCTACCCTTGTTTTCACTATA
39722 ATAATTCTCT
66 ATAATTCTCT
39732 TTTTCTTTCCCTCCCATCCCCTCAAATCCAAACATAGCACAAGATCTACCCTTGTTTTCACTATA
1 TTTTCTTTCCCTCCCATCCCCTCAAATCCAAACATAGCACAAGATCTACCCTTGTTTTCACTATA
39797 ATAATTCTCT
66 ATAATTCTCT
39807 AACAGTCCCC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.27, C:0.33, G:0.04, T:0.36
Consensus pattern (75 bp):
TTTTCTTTCCCTCCCATCCCCTCAAATCCAAACATAGCACAAGATCTACCCTTGTTTTCACTATA
ATAATTCTCT
Found at i:43103 original size:22 final size:22
Alignment explanation
Indices: 43058--43119 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
43048 TTCTAGGGAG
* *
43058 ATTACTAAAATTTTATAAGAAA
1 ATTACTATAATTTCATAAGAAA
* *
43080 ATTACTATAATTTCATAGGTAA
1 ATTACTATAATTTCATAAGAAA
*
43102 ATTGGC-ATAATTTCATAA
1 ATT-ACTATAATTTCATAA
43120 TCAAGTTACC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (22 bp):
ATTACTATAATTTCATAAGAAA
Found at i:43294 original size:22 final size:22
Alignment explanation
Indices: 43264--43352 Score: 71
Period size: 22 Copynumber: 4.0 Consensus size: 22
43254 TTTAGTCACA
43264 AAAATTTCATAGAGAGATTACT
1 AAAATTTCATAGAGAGATTACT
*
43286 AGAATTTCATAGCTA-AG-TTA-T
1 AAAATTTCATAG--AGAGATTACT
43307 CAAAATTTCATAG-GA-ATGTTACT
1 -AAAATTTCATAGAGAGA--TTACT
* *
43330 AAAATTTCATAGGGAGGTTACT
1 AAAATTTCATAGAGAGATTACT
43352 A
1 A
43353 GAACTTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 46 0.85
23 5 0.09
24 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAGAGAGATTACT
Found at i:43329 original size:44 final size:47
Alignment explanation
Indices: 43212--43341 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 47
43202 ATAGTAAGGT
* * * *
43212 TACAAAAATTTCA-AAAGGAGAATACTAGAATTTCATAGGTAATTTAG
1 TACAAAAATTTCATAGA-GAGATTACTAGAATTTCATAGCTAAGTTAG
43259 TCACAAAAATTTCATAGAGAGATTACTAGAATTTCATAGCTAAGTTA-
1 T-ACAAAAATTTCATAGAGAGATTACTAGAATTTCATAGCTAAGTTAG
*
43306 T-C-AAAATTTCATAG-GA-ATGTTACTAAAATTTCATAG
1 TACAAAAATTTCATAGAGAGA--TTACTAGAATTTCATAG
43342 GGAGGTTACT
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
42 1 0.01
43 2 0.03
44 28 0.38
45 1 0.01
47 2 0.03
48 38 0.51
49 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (47 bp):
TACAAAAATTTCATAGAGAGATTACTAGAATTTCATAGCTAAGTTAG
Found at i:47670 original size:30 final size:29
Alignment explanation
Indices: 47603--47674 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
47593 ACACCGAACC
****
47603 GTCAAATAAGCCCCTGAACTATTATTTCG
1 GTCAAATAAGCCCCTGAACTATTAAAAAG
* *
47632 GCCAAATAAGCCCCTGAACTCTTAAAAAAG
1 GTCAAATAAGCCCCTGAACTATT-AAAAAG
47662 GTCAAATAAGCCC
1 GTCAAATAAGCCC
47675 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAG
Found at i:48473 original size:71 final size:71
Alignment explanation
Indices: 48329--48484 Score: 181
Period size: 74 Copynumber: 2.2 Consensus size: 71
48319 GTAGATATAT
* * *
48329 ATATATATTATAATAATGATAATACGTAGATATATTATATAATAATAACAACAATGGCAGGGAGG
1 ATATATATAATAATAATAATAATACGTAGATATATTATATAATAATAACAACAATGACA--GA-G
** *
48394 GGATAGTAG
63 AAAAAGTAG
* *
48403 ATATATATAATAATGATAATAATACGTAGATATATTATATAATAATAACAACATATATACA-A-A
1 ATATATATAATAATAATAATAATACGTAGATATATTATATAATAATAACAACA-AT-GACAGAGA
48466 AAAAGTAG
64 AAAAGTAG
48474 ATATATATAAT
1 ATATATATAAT
48485 CACTCAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
71 17 0.24
73 1 0.01
74 50 0.69
75 2 0.03
76 2 0.03
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.31
Consensus pattern (71 bp):
ATATATATAATAATAATAATAATACGTAGATATATTATATAATAATAACAACAATGACAGAGAAA
AAGTAG
Done.