Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012652.1 Corchorus capsularis cultivar CVL-1 contig12673, 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: 49642
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2052 original size:15 final size:16
Alignment explanation
Indices: 2025--2054 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2015 TGGTAAAGTG
2025 AACCCGATCCGAAAAA
1 AACCCGATCCGAAAAA
2041 AACCCG-TCCGAAAA
1 AACCCGATCCGAAAA
2055 TCCGATCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.33, G:0.13, T:0.07
Consensus pattern (16 bp):
AACCCGATCCGAAAAA
Found at i:2355 original size:32 final size:32
Alignment explanation
Indices: 2319--2437 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 32
2309 TCTGACCAAA
** *
2319 ACCCAAACAGAACCCGAACCCGAATTAATCTG
1 ACCCAAACTTAACCCGAACCCGAATTAACCTG
*
2351 ACCCAAA-TTCAACCCGAACCCGAATTAACCTA
1 ACCCAAACTT-AACCCGAACCCGAATTAACCTG
*
2383 ACCCAAA-TTAACCCGAACCCAAATTAACCTG
1 ACCCAAACTTAACCCGAACCCGAATTAACCTG
*
2414 ACCCAAA-TCTAACCCGAACTCGAA
1 ACCCAAACT-TAACCCGAACCCGAA
2438 AATGACCCGA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 28 0.36
32 49 0.64
ACGTcount: A:0.41, C:0.36, G:0.08, T:0.14
Consensus pattern (32 bp):
ACCCAAACTTAACCCGAACCCGAATTAACCTG
Found at i:2359 original size:15 final size:15
Alignment explanation
Indices: 2336--2427 Score: 94
Period size: 15 Copynumber: 5.9 Consensus size: 15
2326 CAGAACCCGA
* *
2336 ACCCGAATTAATCTG
1 ACCCAAATTAACCTG
*
2351 ACCCAAATTCAACCCG
1 ACCCAAATT-AACCTG
* *
2367 AACCCGAATTAACCTA
1 -ACCCAAATTAACCTG
*
2383 ACCCAAATTAACCCG
1 ACCCAAATTAACCTG
2398 AACCCAAATTAACCTG
1 -ACCCAAATTAACCTG
2414 ACCCAAATCTAACC
1 ACCCAAAT-TAACC
2428 CGAACTCGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
15 28 0.44
16 27 0.43
17 8 0.13
ACGTcount: A:0.40, C:0.36, G:0.07, T:0.17
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:2403 original size:16 final size:16
Alignment explanation
Indices: 2329--2453 Score: 121
Period size: 16 Copynumber: 7.8 Consensus size: 16
2319 ACCCAAACAG
*
2329 AACCCGAACCCGAATT
1 AACCCGAACCCAAATT
* *
2345 AATCTG-ACCCAAATT
1 AACCCGAACCCAAATT
*
2360 CAACCCGAACCCGAATT
1 -AACCCGAACCCAAATT
*
2377 AA-CCTAACCCAAATT
1 AACCCGAACCCAAATT
2392 AACCCGAACCCAAATT
1 AACCCGAACCCAAATT
*
2408 AACCTG-ACCCAAATCT
1 AACCCGAACCCAAAT-T
* *
2424 AACCCGAACTCGAAAAT
1 AACCCGAAC-CCAAATT
*
2441 GACCCGAACCCAA
1 AACCCGAACCCAA
2454 CCTGACCCGC
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
15 29 0.33
16 36 0.41
17 19 0.22
18 4 0.05
ACGTcount: A:0.41, C:0.36, G:0.09, T:0.14
Consensus pattern (16 bp):
AACCCGAACCCAAATT
Found at i:6354 original size:30 final size:31
Alignment explanation
Indices: 6290--6357 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
6280 AATTTTATAT
* * *
6290 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
6321 TTTCCAATTGTACCCTT-TTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
6351 TTTCCAA
1 TTTCCAA
6358 ATTACCATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAACATA
Found at i:6432 original size:26 final size:27
Alignment explanation
Indices: 6382--6441 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
6372 ATAATATTTT
*
6382 AATTATTCCATTATTTTTTTAATCATA
1 AATTATTCAATTATTTTTTTAATCATA
6409 AATTATTCAATTA-TTTTTTAATCATA
1 AATTATTCAATTATTTTTTTAATCATA
6435 AATTATT
1 AATTATT
6442 AGATTATAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 20 0.62
27 12 0.38
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTATTCAATTATTTTTTTAATCATA
Found at i:6447 original size:26 final size:25
Alignment explanation
Indices: 6382--6448 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 25
6372 ATAATATTTT
*
6382 AATTATTCCATTATTTTTTTAATCATA
1 AATTATT-AATTA-TTTTTTAATCATA
6409 AATTATTCAATTATTTTTTAATCATA
1 AATTATT-AATTATTTTTTAATCATA
6435 AATTATTAGATTAT
1 AATTATTA-ATTAT
6449 AGAATACGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
25 1 0.03
26 25 0.66
27 12 0.32
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (25 bp):
AATTATTAATTATTTTTTAATCATA
Found at i:7064 original size:19 final size:20
Alignment explanation
Indices: 7037--7074 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
7027 TACTATTATT
7037 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
7057 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
7075 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:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:8330 original size:22 final size:23
Alignment explanation
Indices: 8302--8359 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
8292 TGTCTCTATG
8302 TGGTTATCAAAATTTCA-CAAGA
1 TGGTTATCAAAATTTCATCAAGA
* * * *
8324 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCATCAAGA
8347 -GGTTATCAAAATT
1 TGGTTATCAAAATT
8360 CCATAGTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (23 bp):
TGGTTATCAAAATTTCATCAAGA
Found at i:8425 original size:22 final size:22
Alignment explanation
Indices: 8400--8464 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
8390 AAGTTATCAA
*
8400 GTGGTTACCAAAATTTCATAGT
1 GTGGTTACCAAAATTTCATAGC
8422 GTGGTTACCAAAATTTCATAGC
1 GTGGTTACCAAAATTTCATAGC
*
8444 ATGGTTACCAAAATTTCATAG
1 GTGGTTACCAAAATTTCATAG
8465 GATCAGGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (22 bp):
GTGGTTACCAAAATTTCATAGC
Found at i:8498 original size:22 final size:22
Alignment explanation
Indices: 8470--8518 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
8460 CATAGGATCA
*
8470 GGTTATT-AGAATTTCTTAGGTT
1 GGTTATTGA-AATTTCTTAGGGT
8492 GGTTATTGAAATTTCTTAGGGT
1 GGTTATTGAAATTTCTTAGGGT
8514 GGTTA
1 GGTTA
8519 ATTATCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.04, G:0.27, T:0.47
Consensus pattern (22 bp):
GGTTATTGAAATTTCTTAGGGT
Found at i:8687 original size:44 final size:43
Alignment explanation
Indices: 8639--8949 Score: 132
Period size: 44 Copynumber: 7.0 Consensus size: 43
8629 TTTTATGGGG
8639 AGGTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATA-GA
* * *
8683 AGGTTAT-AAAAGTCTCAATTTCATAAG-G-AG-TACCAAAATTTGATAGA
1 AGGTTATCAAAA---T---TTT-AT-AGTGTGGTTATCAAAATTTCATAGA
* * * * ** * * *
8730 AAGTTATC-AAATCTCATAGAGTTATAAACGAAATTTCATAGAGA
1 AGGTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCAT--AGA
* * * * *
8774 TTAGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCG
1 --AGGTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATAG-A
** * * *
8820 AGGTTATCAAAATTACATAATGTGATTATCAGAATTTCATAGA
1 AGGTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATAGA
* * ** * *
8863 AGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAA
1 A-GGTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATAGA
* * *
8907 GAGGTTATC-AAATTTTCAAAATGTGATTA-CAAAAATTTCATAG
1 -AGGTTATCAAAATTTT-ATAGTGTGGTTATC-AAAATTTCATAG
8950 TGGTATTTCT
Statistics
Matches: 199, Mismatches: 46, Indels: 44
0.69 0.16 0.15
Matches are distributed among these distances:
39 2 0.01
40 3 0.02
41 1 0.01
42 10 0.05
43 13 0.07
44 103 0.52
45 3 0.02
46 7 0.04
47 35 0.18
48 13 0.07
49 4 0.02
50 3 0.02
51 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (43 bp):
AGGTTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATAGA
Found at i:8689 original size:22 final size:22
Alignment explanation
Indices: 8596--8924 Score: 78
Period size: 22 Copynumber: 14.7 Consensus size: 22
8586 CTTATAGTGT
*
8596 GGTTAACAAAATTTCATTATG-A
1 GGTTATCAAAATTTCA-TATGAA
* * ** *
8618 GGTTA-CTAATATTTTATGGGGA
1 GGTTATC-AAAATTTCATATGAA
* *
8640 GGTTATCAAAATTTTATAGTG-T
1 GGTTATCAAAATTTCATA-TGAA
8662 GGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATATGAA
*
8684 GGTTAT-AAAAGTCTCAATTTCAT-AA
1 GGTTATCAAAA-TTTC-A--T-ATGAA
* * *
8709 GGAGTACCAAAATTTGATA-GAA
1 GG-TTATCAAAATTTCATATGAA
* *
8731 AGTTATC-AAATCTCATA-G-A
1 GGTTATCAAAATTTCATATGAA
* *
8750 -GTTATAAACGAAATTTCATAGAGATTA
1 GGTTAT---CAAAATTTCATA-TGA--A
* *
8777 GATTATCAAAATTTCATAGTG-T
1 GGTTATCAAAATTTCATA-TGAA
* * *
8799 TGTTATCAAAATTTCA-AAGCGA
1 GGTTATCAAAATTTCATATG-AA
* *
8821 GGTTATCAAAATTACATAATG-T
1 GGTTATCAAAATTTCAT-ATGAA
* *
8843 GATTATCAGAATTTCATA-GAA
1 GGTTATCAAAATTTCATATGAA
* * * *
8864 GGGTCAACAAAATTTTATA-AAGA
1 -GGTTATCAAAATTTCATATGA-A
*
8887 GGTTATCAAAATTTCATA-AAGA
1 GGTTATCAAAATTTCATATGA-A
*
8909 GGTTATCAAATTTTCA
1 GGTTATCAAAATTTCA
8925 AAATGTGATT
Statistics
Matches: 230, Mismatches: 47, Indels: 60
0.68 0.14 0.18
Matches are distributed among these distances:
18 5 0.02
19 1 0.00
20 11 0.05
21 15 0.07
22 156 0.68
23 5 0.02
24 3 0.01
25 19 0.08
26 6 0.03
27 5 0.02
28 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATGAA
Found at i:8792 original size:25 final size:22
Alignment explanation
Indices: 8732--8924 Score: 97
Period size: 22 Copynumber: 8.7 Consensus size: 22
8722 TTGATAGAAA
*
8732 GTTATC-AAATCTCATAGAGTT
1 GTTATCAAAATTTCATAGAGTT
* * * *
8753 ATAAACGAAATTTCATAGAGATT
1 GTTATCAAAATTTCATAGAG-TT
*
8776 AGATTATCAAAATTTCATAGTGTT
1 -G-TTATCAAAATTTCATAGAGTT
* * **
8800 GTTATCAAAATTTCAAAGCGAG
1 GTTATCAAAATTTCATAGAGTT
*
8822 GTTATCAAAATTACATA-A-TGT
1 GTTATCAAAATTTCATAGAGT-T
* *
8843 GATTATCAGAATTTCATAGAAG-G
1 G-TTATCAAAATTTCATAG-AGTT
* * * * **
8866 GTCAACAAAATTTTATAAAGAG
1 GTTATCAAAATTTCATAGAGTT
* **
8888 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAAATTTCATAGAGTT
*
8910 GTTATCAAATTTTCA
1 GTTATCAAAATTTCA
8925 AAATGTGATT
Statistics
Matches: 132, Mismatches: 30, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
21 6 0.05
22 104 0.79
23 4 0.03
24 3 0.02
25 15 0.11
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGAGTT
Found at i:9098 original size:22 final size:22
Alignment explanation
Indices: 9030--9303 Score: 191
Period size: 22 Copynumber: 12.5 Consensus size: 22
9020 TTATGGAGTA
* *
9030 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGAGAGGTT
**
9050 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-AGAGGTT
*
9072 TTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGAGA-GGTT
* * *
9094 ATCAAAATTTCATAG-TATGTAG
1 ATCAAAATTTCATAGAGAGGT-T
*
9116 ATCAAAATTTCATAGAGAGATT
1 ATCAAAATTTCATAGAGAGGTT
*
9138 AACAAAATTTCATA-ATGAGGTT
1 ATCAAAATTTCATAGA-GAGGTT
** *
9160 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGAGAGGTT
* * *
9182 ATCAAGATTTCATAAAAAGGTT
1 ATCAAAATTTCATAGAGAGGTT
* *
9204 ATCAAAATTTTATAGGGAGGTT
1 ATCAAAATTTCATAGAGAGGTT
* * **
9226 AATCAAAATTTTATAGGAAAATTT
1 -ATCAAAATTTCATA-GAGAGGTT
* *
9250 ATCAAAATTTCATAGCGTGGTT
1 ATCAAAATTTCATAGAGAGGTT
* * * * *
9272 ATCACAATTTTATAGTGTGATT
1 ATCAAAATTTCATAGAGAGGTT
9294 ATCAAAATTT
1 ATCAAAATTT
9304 TAGAGTGTAA
Statistics
Matches: 196, Mismatches: 46, Indels: 22
0.74 0.17 0.08
Matches are distributed among these distances:
20 12 0.06
21 3 0.02
22 147 0.75
23 30 0.15
24 4 0.02
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGAGAGGTT
Found at i:9263 original size:68 final size:67
Alignment explanation
Indices: 9180--9305 Score: 162
Period size: 68 Copynumber: 1.9 Consensus size: 67
9170 CATAGGGAGG
* *
9180 TTATCAAGATTTCATAAAAAGGTTATCAAAATTTTATAGGGAGGTTAATCAAAATTTTATAGGAA
1 TTATCAAAATTTCATAAAAAGGTTATCAAAATTTTATAGGGAGATT-ATCAAAATTTTATAGGAA
9245 AAT
65 AAT
**** * * *
9248 TTATCAAAATTTCATAGCGTGGTTATCACAATTTTATAGTGTGATTATCAAAATTTTA
1 TTATCAAAATTTCATAAAAAGGTTATCAAAATTTTATAGGGAGATTATCAAAATTTTA
9306 GAGTGTAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 12 0.24
68 37 0.76
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (67 bp):
TTATCAAAATTTCATAAAAAGGTTATCAAAATTTTATAGGGAGATTATCAAAATTTTATAGGAAA
AT
Found at i:9304 original size:22 final size:22
Alignment explanation
Indices: 9202--9316 Score: 97
Period size: 22 Copynumber: 5.1 Consensus size: 22
9192 CATAAAAAGG
* * *
9202 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGTGTGA
**
9224 TTAATCAAAATTTTATAG-GAAAA
1 TT-ATCAAAATTTTATAGTG-TGA
* * *
9247 TTTATCAAAATTTCATAGCGTGG
1 -TTATCAAAATTTTATAGTGTGA
*
9270 TTATCACAATTTTATAGTGTGA
1 TTATCAAAATTTTATAGTGTGA
* *
9292 TTATCAAAATTTTAGAGTGTAA
1 TTATCAAAATTTTATAGTGTGA
9314 TTA
1 TTA
9317 CTAACAATTC
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
22 43 0.57
23 30 0.39
24 3 0.04
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTGTGA
Found at i:9509 original size:22 final size:21
Alignment explanation
Indices: 9470--9513 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
9460 CCTTAGGGAG
* *
9470 GTTAACAAAACTTCATAAGAAA
1 GTTAAAAAAAATTCATAA-AAA
*
9492 GTTAAAAAAAATTTATAAAAA
1 GTTAAAAAAAATTCATAAAAA
9513 G
1 G
9514 ATTCTCGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (21 bp):
GTTAAAAAAAATTCATAAAAA
Found at i:18101 original size:11 final size:11
Alignment explanation
Indices: 18087--18118 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
18077 TTTTTTTTTA
18087 CTCTTTTCTTT
1 CTCTTTTCTTT
18098 CTCTTTTCTTT
1 CTCTTTTCTTT
18109 CTCTTTTCTT
1 CTCTTTTCTT
18119 CTTCGACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTCTTTTCTTT
Found at i:18179 original size:13 final size:13
Alignment explanation
Indices: 18161--18187 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18151 ACCCATATTA
18161 TCTTTTCTTCTTC
1 TCTTTTCTTCTTC
18174 TCTTTTCTTCTTC
1 TCTTTTCTTCTTC
18187 T
1 T
18188 TCTTCTTCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TCTTTTCTTCTTC
Found at i:20818 original size:18 final size:18
Alignment explanation
Indices: 20795--20831 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20785 AATTTTCACC
*
20795 AAAAAAATTGAACTAAAA
1 AAAAAAATTGAAATAAAA
*
20813 AAAAAACTTGAAATAAAA
1 AAAAAAATTGAAATAAAA
20831 A
1 A
20832 TGTAAACACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAAAATTGAAATAAAA
Found at i:33170 original size:107 final size:105
Alignment explanation
Indices: 33037--33298 Score: 404
Period size: 107 Copynumber: 2.5 Consensus size: 105
33027 AGTTTAGCCT
*
33037 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
33102 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
33144 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
33209 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAT
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* **
33249 TAA-TTCACTAAGTTTAG-CTCAAATTAAAATTAAAATTTTTATTTT-AGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATT-TTATTTTTATTTTAAGGGT
33299 TAGGAAAATT
Statistics
Matches: 146, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
103 18 0.12
104 25 0.17
105 35 0.24
107 68 0.47
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:34967 original size:32 final size:32
Alignment explanation
Indices: 34931--35026 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
34921 AGCAAATGGA
34931 GAAGCAAATGTAGTTGAAGAAAGACCCTTTGT
1 GAAGCAAATGTAGTTGAAGAAAGACCCTTTGT
** * * *
34963 GAAGC-AATCCAGTTTG--G--AGA---ATGGA
1 GAAGCAAATGTAG-TTGAAGAAAGACCCTTTGT
34988 GAAGCAAATGTAGTTGAAGAAAGACCCTTTGT
1 GAAGCAAATGTAGTTGAAGAAAGACCCTTTGT
35020 GAAGCAA
1 GAAGCAA
35027 TCAGCAAGCT
Statistics
Matches: 45, Mismatches: 10, Indels: 18
0.62 0.14 0.25
Matches are distributed among these distances:
25 10 0.22
26 5 0.11
27 1 0.02
28 3 0.07
29 3 0.07
30 1 0.02
31 5 0.11
32 17 0.38
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (32 bp):
GAAGCAAATGTAGTTGAAGAAAGACCCTTTGT
Found at i:35048 original size:57 final size:57
Alignment explanation
Indices: 34921--35035 Score: 180
Period size: 57 Copynumber: 2.1 Consensus size: 57
34911 AGAATGAAGT
**
34921 AGCA-AATGGAGAAGCAAATGTAGTTGAAGAAAGACCCTTTGTGAAGCAATCCAGTT
1 AGCAGAATGGAGAAGCAAATGTAGTTGAAGAAAGACCCTTTGTGAAGCAATCCAGCA
* *
34977 TGGAGAATGGAGAAGCAAATGTAGTTGAAGAAAGACCCTTTGTGAAGCAAT-CAGCA
1 AGCAGAATGGAGAAGCAAATGTAGTTGAAGAAAGACCCTTTGTGAAGCAATCCAGCA
35033 AGC
1 AGC
35036 TGATTTTTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 6 0.12
57 46 0.88
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (57 bp):
AGCAGAATGGAGAAGCAAATGTAGTTGAAGAAAGACCCTTTGTGAAGCAATCCAGCA
Found at i:38050 original size:3 final size:3
Alignment explanation
Indices: 38042--38070 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38032 GCTTTTACCC
38042 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
38071 AGTACTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39105 original size:21 final size:22
Alignment explanation
Indices: 39067--39110 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
39057 GGGAAATCTC
39067 AAATCTGGAATGAAAGAGAAAAA
1 AAATCTGGAA-GAAAGAGAAAAA
39090 AAATCTGGAA-AAAGAGAAAAA
1 AAATCTGGAAGAAAGAGAAAAA
39111 TGAAAAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
23 10 0.48
ACGTcount: A:0.64, C:0.05, G:0.20, T:0.11
Consensus pattern (22 bp):
AAATCTGGAAGAAAGAGAAAAA
Found at i:43190 original size:40 final size:40
Alignment explanation
Indices: 43146--43269 Score: 96
Period size: 40 Copynumber: 3.1 Consensus size: 40
43136 GTAAAATGGT
43146 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
1 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
* * ** * * * * * *
43186 AAAATAGAGTTTTTAGTTGAGTAAAATAG---TAA-AATGGT-
1 AAAATATAATAGTTA--TAAGGATATTAGATTTAATTAT-ATA
43224 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
1 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
43264 AAAATA
1 AAAATA
43270 GAGTTTTTAG
Statistics
Matches: 56, Mismatches: 20, Indels: 16
0.61 0.22 0.17
Matches are distributed among these distances:
36 8 0.14
38 13 0.23
39 8 0.14
40 19 0.34
42 8 0.14
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (40 bp):
AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
Found at i:43217 original size:78 final size:78
Alignment explanation
Indices: 43129--43375 Score: 433
Period size: 78 Copynumber: 3.2 Consensus size: 78
43119 AAGTTTTAAT
43129 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
43194 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
43207 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
43272 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * * * *
43285 TAAAATAGTAAAAAGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
43350 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
43363 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
43376 ACCTAAACAA
Statistics
Matches: 163, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
78 161 0.99
79 2 0.01
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:46001 original size:17 final size:17
Alignment explanation
Indices: 45979--46033 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
45969 GTGGCAAGCT
45979 AGTAGGAATCAAGATTG
1 AGTAGGAATCAAGATTG
** *
45996 AGTAGG-AT-GTGACT-
1 AGTAGGAATCAAGATTG
*
46010 AGTAGGAATCAAGCTTG
1 AGTAGGAATCAAGATTG
46027 AGTAGGA
1 AGTAGGA
46034 TGTGCTTTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 4 0.14
17 13 0.46
ACGTcount: A:0.36, C:0.07, G:0.33, T:0.24
Consensus pattern (17 bp):
AGTAGGAATCAAGATTG
Found at i:46012 original size:31 final size:31
Alignment explanation
Indices: 45977--46037 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
45967 GAGTGGCAAG
45977 CTAGTAGGAATCAAGATTGAGTAGGATGTGA
1 CTAGTAGGAATCAAGATTGAGTAGGATGTGA
*
46008 CTAGTAGGAATCAAGCTTGAGTAGGATGTG
1 CTAGTAGGAATCAAGATTGAGTAGGATGTG
46038 CTTTTAATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.26
Consensus pattern (31 bp):
CTAGTAGGAATCAAGATTGAGTAGGATGTGA
Found at i:48026 original size:11 final size:11
Alignment explanation
Indices: 48012--48049 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
48002 ATTCATAACA
48012 AATTTATAATT
1 AATTTATAATT
48023 AATTTATAATT
1 AATTTATAATT
48034 -ATTTGATAATT
1 AATTT-ATAATT
*
48045 TATTT
1 AATTT
48050 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.