Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012999.1 Corchorus capsularis cultivar CVL-1 contig13020, 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: 67930
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1905 original size:73 final size:73
Alignment explanation
Indices: 1786--1924 Score: 233
Period size: 73 Copynumber: 1.9 Consensus size: 73
1776 TCCACTTCGG
* * *
1786 TTCTTTATACGAACCTTTAGTTCAACCTTCATAGGGGTTGAATTTGGATGTGGGTTGTATGCCTT
1 TTCTTTATACGAACCTTTAGTTCAACCTTCATAGGGGTGGAATTTGGATGTAGGCTGTATGCCTT
1851 TAGGATGA
66 TAGGATGA
* *
1859 TTCTTTATATGAACCTTTAGTTCAACCTTCGTAGGGGTGGAATTTGGATGTAGGCTGTATGCCTT
1 TTCTTTATACGAACCTTTAGTTCAACCTTCATAGGGGTGGAATTTGGATGTAGGCTGTATGCCTT
1924 T
66 T
1925 GGGAGGGTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (73 bp):
TTCTTTATACGAACCTTTAGTTCAACCTTCATAGGGGTGGAATTTGGATGTAGGCTGTATGCCTT
TAGGATGA
Found at i:2365 original size:29 final size:29
Alignment explanation
Indices: 2323--2397 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
2313 CTAACCGGCA
* *
2323 CCCTCTCCCAAGATGGTGGTTGTACAGCG
1 CCCTCTCCTAAGATGGTGGCTGTACAGCG
*
2352 CCCTCTCCTAAGATGGTGGCTGTACGGCG
1 CCCTCTCCTAAGATGGTGGCTGTACAGCG
* * *
2381 CCTTCTTCTAGGATGGT
1 CCCTCTCCTAAGATGGT
2398 TGGCGCGCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.15, C:0.29, G:0.28, T:0.28
Consensus pattern (29 bp):
CCCTCTCCTAAGATGGTGGCTGTACAGCG
Found at i:2546 original size:27 final size:28
Alignment explanation
Indices: 2516--2581 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
2506 AGCGTTCTAT
* *
2516 GCTTTGTAATCTTTGGGGGCG-ACTACC
1 GCTTTGTAATCTTCGAGGGCGTACTACC
2543 GCTTTGTGAA-CTTCGAGGGCGTACTACC
1 GCTTTGT-AATCTTCGAGGGCGTACTACC
2571 GCTTTGTAATC
1 GCTTTGTAATC
2582 CTTTAGGGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (28 bp):
GCTTTGTAATCTTCGAGGGCGTACTACC
Found at i:2589 original size:28 final size:26
Alignment explanation
Indices: 2516--2590 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 26
2506 AGCGTTCTAT
*
2516 GCTTTGTAATCTTTGGGGGCGACTACC
1 GCTTTGTAATCTTT-AGGGCGACTACC
*
2543 GCTTTGTGAA-CTTCGAGGGCGTACTACC
1 GCTTTGT-AATCTT-TAGGGCG-ACTACC
2571 GCTTTGTAATCCTTTAGGGC
1 GCTTTGTAAT-CTTTAGGGC
2591 ATAATTAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 17 0.43
28 20 0.50
29 3 0.08
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (26 bp):
GCTTTGTAATCTTTAGGGCGACTACC
Found at i:3407 original size:14 final size:14
Alignment explanation
Indices: 3388--3427 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
3378 TCTATATATA
3388 ATCAACCCTTTATT
1 ATCAACCCTTTATT
3402 ATCAACCC--T-TT
1 ATCAACCCTTTATT
3413 ATCAACCCTTTATT
1 ATCAACCCTTTATT
3427 A
1 A
3428 ATGAGAGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (14 bp):
ATCAACCCTTTATT
Found at i:3416 original size:11 final size:11
Alignment explanation
Indices: 3400--3425 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3390 CAACCCTTTA
3400 TTATCAACCCT
1 TTATCAACCCT
3411 TTATCAACCCT
1 TTATCAACCCT
3422 TTAT
1 TTAT
3426 TAATGAGAGG
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:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (11 bp):
TTATCAACCCT
Found at i:3806 original size:31 final size:31
Alignment explanation
Indices: 3768--3830 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
3758 CCATTCTCGA
*
3768 CGGTTTTCAGGTGAGTTCAGAGGAGAGTTTT
1 CGGTTTTCAGGTGAGTTCAGAGGAGAGATTT
*
3799 CGGTTTTCAGGTGAGTTTAGAGGAGAGATTT
1 CGGTTTTCAGGTGAGTTCAGAGGAGAGATTT
3830 C
1 C
3831 AGATTTTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.10, G:0.35, T:0.35
Consensus pattern (31 bp):
CGGTTTTCAGGTGAGTTCAGAGGAGAGATTT
Found at i:4401 original size:71 final size:71
Alignment explanation
Indices: 4317--4458 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
4307 GACATTGGTA
*
4317 CAATTTGCATTAAGCAATTTGAGTCTTCTCTACATTTTAAACTTGATGTTTCAAATTGTTGTTGA
1 CAATTTGCATTAAGCAATTTGAGTCTTCTCTACATTTTAAACTTGATGTTTCAAATTGTTGCTGA
4382 TATGGC
66 TATGGC
*
4388 CAATTTGCATTAAGCAATTTGAGTCTTCTCTACATTTTAAACTTTATGTTTCAAATTGTTGCTGA
1 CAATTTGCATTAAGCAATTTGAGTCTTCTCTACATTTTAAACTTGATGTTTCAAATTGTTGCTGA
4453 TATGGC
66 TATGGC
4459 AGAAACGGCA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (71 bp):
CAATTTGCATTAAGCAATTTGAGTCTTCTCTACATTTTAAACTTGATGTTTCAAATTGTTGCTGA
TATGGC
Found at i:5949 original size:24 final size:24
Alignment explanation
Indices: 5922--5968 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5912 CTAAATTGGG
*
5922 AACAAAAAATTGAGGATTGAACAA
1 AACAAAAAATAGAGGATTGAACAA
* *
5946 AACACAGAATAGAGGATTGAACA
1 AACAAAAAATAGAGGATTGAACA
5969 GTTAACCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.19, T:0.15
Consensus pattern (24 bp):
AACAAAAAATAGAGGATTGAACAA
Found at i:11430 original size:13 final size:13
Alignment explanation
Indices: 11412--11436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11402 TTGCCATCTT
11412 CGCCTTTTTACTA
1 CGCCTTTTTACTA
11425 CGCCTTTTTACT
1 CGCCTTTTTACT
11437 GACTTTAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (13 bp):
CGCCTTTTTACTA
Found at i:11780 original size:2 final size:2
Alignment explanation
Indices: 11773--11802 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11763 AACATTGACA
11773 AT 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
11803 GTTGCATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15953 original size:45 final size:46
Alignment explanation
Indices: 15902--15993 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
15892 ATTATTAAAT
*
15902 CTGAAAT-AAACGTAAAGATTAGAGGAGACAAGTTCCTCAAAGTTG
1 CTGAAATAAAACATAAAGATTAGAGGAGACAAGTTCCTCAAAGTTG
* *
15947 CTGAAATAAAACATAAAGATTAGAGGAGACAAGTTTCTCAAGGTTG
1 CTGAAATAAAACATAAAGATTAGAGGAGACAAGTTCCTCAAAGTTG
15993 C
1 C
15994 CAAGTCTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 7 0.16
46 36 0.84
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (46 bp):
CTGAAATAAAACATAAAGATTAGAGGAGACAAGTTCCTCAAAGTTG
Found at i:20254 original size:16 final size:16
Alignment explanation
Indices: 20213--20317 Score: 58
Period size: 16 Copynumber: 6.6 Consensus size: 16
20203 TCAGGTCGTT
*
20213 TTCGGGTTCGGATTAAA
1 TTCGGGTTCGGGTT-AA
*
20230 TT-GGG-TCGGGTTGA
1 TTCGGGTTCGGGTTAA
20244 TTCGGGTTCGGGTTAAA
1 TTCGGGTTCGGGTT-AA
* * ** *
20261 TT-TGGATCATGTTGA
1 TTCGGGTTCGGGTTAA
20276 TTCGGGTTCGGG-TAGA
1 TTCGGGTTCGGGTTA-A
* *
20292 TTTTGGG-TCAGGTTAA
1 -TTCGGGTTCGGGTTAA
20308 TTCGGGTTCG
1 TTCGGGTTCG
20318 AGTTCGGGTT
Statistics
Matches: 63, Mismatches: 17, Indels: 17
0.65 0.18 0.18
Matches are distributed among these distances:
14 3 0.05
15 18 0.29
16 30 0.48
17 12 0.19
ACGTcount: A:0.15, C:0.10, G:0.36, T:0.38
Consensus pattern (16 bp):
TTCGGGTTCGGGTTAA
Found at i:20280 original size:32 final size:32
Alignment explanation
Indices: 20213--20317 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 32
20203 TCAGGTCGTT
* *
20213 TTCGGGTTCGGATTAAA-TTGGGTCGGGTTGA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
* *
20244 TTCGGGTTCGGGTTAAATTTGGATCATGTTGA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
* *
20276 TTCGGGTTCGGG-TAGATTTTGGGTCAGGTTAA
1 TTCGGGTTCGGGTTA-AATTTGGGTCAGGTTGA
20308 TTCGGGTTCG
1 TTCGGGTTCG
20318 AGTTCGGGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
31 18 0.28
32 46 0.72
ACGTcount: A:0.15, C:0.10, G:0.36, T:0.38
Consensus pattern (32 bp):
TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
Found at i:20489 original size:20 final size:20
Alignment explanation
Indices: 20456--20494 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20446 TACATATGAA
*
20456 ATTTTCATAAATTATTATTT
1 ATTTTCATAAATTAGTATTT
20476 ATTTTCA-AATATTAGTATT
1 ATTTTCATAA-ATTAGTATT
20495 GAATTCAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTCATAAATTAGTATTT
Found at i:20593 original size:32 final size:32
Alignment explanation
Indices: 20514--20601 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 32
20504 TTTTTTCAGG
*
20514 TTCGGGTTCGGG-TTTTATCGGGTTTCAGATTT
1 TTCGGGTTCGGGATTTT-TTGGGTTTCAGATTT
* ** *
20546 TTTGGGTTC-TAATTTTTTGGGTTTGAGCA-TT
1 TTCGGGTTCGGGATTTTTTGGGTTTCAG-ATTT
20577 TTCGGGTTCGGGATTTTTTTGGGTT
1 TTCGGGTTCGGGA-TTTTTTGGGTT
20602 CGGATTCGGA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
31 19 0.43
32 14 0.32
33 11 0.25
ACGTcount: A:0.09, C:0.09, G:0.31, T:0.51
Consensus pattern (32 bp):
TTCGGGTTCGGGATTTTTTGGGTTTCAGATTT
Found at i:20607 original size:16 final size:17
Alignment explanation
Indices: 20514--20604 Score: 52
Period size: 15 Copynumber: 5.6 Consensus size: 17
20504 TTTTTTCAGG
20514 TTCGGGTTCGGG-TTTT
1 TTCGGGTTCGGGATTTT
* *
20530 ATCGGGTTTC-AGATTTT
1 TTCGGG-TTCGGGATTTT
**
20547 TT-GGGTTC-TAATTTT
1 TTCGGGTTCGGGATTTT
* *
20562 TT-GGGTTTGAGCA--TT
1 TTCGGGTTCG-GGATTTT
20577 TTCGGGTTCGGGATTTT
1 TTCGGGTTCGGGATTTT
*
20594 TTTGGGTTCGG
1 TTCGGGTTCGG
20605 ATTCGGACGG
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
15 21 0.37
16 15 0.26
17 21 0.37
ACGTcount: A:0.09, C:0.10, G:0.32, T:0.49
Consensus pattern (17 bp):
TTCGGGTTCGGGATTTT
Found at i:21497 original size:13 final size:13
Alignment explanation
Indices: 21479--21503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21469 TGTTGCTATT
21479 TTGTAGATCTAAG
1 TTGTAGATCTAAG
21492 TTGTAGATCTAA
1 TTGTAGATCTAA
21504 ATTTATGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTAGATCTAAG
Found at i:21590 original size:33 final size:33
Alignment explanation
Indices: 21553--21644 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
21543 CGCCCCAGGA
*
21553 GGACAAAGCCGCCCTCTTGGGGCGGCATGCCGT
1 GGACAAAGCCGCCCTCTTGGGGCGGCATGCCAT
*
21586 GGACAAAGCCGCCCTCTTGGGGCGGCATGCTAT
1 GGACAAAGCCGCCCTCTTGGGGCGGCATGCCAT
**
21619 GGACATTGCCGCCCTCTTGGGGCGGC
1 GGACAAAGCCGCCCTCTTGGGGCGGC
21645 TGTGCCACGA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.14, C:0.33, G:0.36, T:0.17
Consensus pattern (33 bp):
GGACAAAGCCGCCCTCTTGGGGCGGCATGCCAT
Found at i:21657 original size:33 final size:31
Alignment explanation
Indices: 21560--21661 Score: 114
Period size: 33 Copynumber: 3.1 Consensus size: 31
21550 GGAGGACAAA
* *
21560 GCCGCCCTCTTGGGGCGGCATGCCGTGGACAAA
1 GCCGCCCTCTTGGGGCGGCATGCC-AGGAC-AT
*
21593 GCCGCCCTCTTGGGGCGGCATGCTATGGACATT
1 GCCGCCCTCTTGGGGCGGCATGCCA-GGACA-T
* *
21626 GCCGCCCTCTTGGGGCGGCTGTGCCACGACAT
1 GCCGCCCTCTTGGGGCGGC-ATGCCAGGACAT
21658 GCCG
1 GCCG
21662 TCCCAGGAGG
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
32 6 0.10
33 50 0.83
34 4 0.07
ACGTcount: A:0.12, C:0.34, G:0.35, T:0.19
Consensus pattern (31 bp):
GCCGCCCTCTTGGGGCGGCATGCCAGGACAT
Found at i:21745 original size:10 final size:10
Alignment explanation
Indices: 21732--21763 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
21722 AGATTTTATA
21732 ATTATTAATT
1 ATTATTAATT
21742 ATTATTAATT
1 ATTATTAATT
21752 ATTATTAATT
1 ATTATTAATT
21762 AT
1 AT
21764 AATTTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTATTAATT
Found at i:21992 original size:29 final size:32
Alignment explanation
Indices: 21960--22038 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 32
21950 TTATTGTATG
*
21960 TTATTTTTGTAAGTAATTTTT-TATGT-TA-A
1 TTATTTTTGTAAGTAATTTTTGTAAGTATATA
* *
21989 TTATTATTGTATGTAATTTTTGTAAGTAATATA
1 TTATTTTTGTAAGTAATTTTTGTAAGT-ATATA
*
22022 TTTTTTTTGTAAGTAAT
1 TTATTTTTGTAAGTAAT
22039 ATTACAACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 19 0.47
30 4 0.10
32 2 0.05
33 15 0.38
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.59
Consensus pattern (32 bp):
TTATTTTTGTAAGTAATTTTTGTAAGTATATA
Found at i:22017 original size:13 final size:13
Alignment explanation
Indices: 21940--22018 Score: 54
Period size: 13 Copynumber: 5.9 Consensus size: 13
21930 CAGAGACATG
*
21940 TTTGTAA-TTATT
1 TTTGTAAGTAATT
* * *
21952 ATTGTATGTTATT
1 TTTGTAAGTAATT
21965 TTTGTAAGTAATT
1 TTTGTAAGTAATT
*
21978 TTT-TATGTTAATTAT
1 TTTGTAAG-TAA-T-T
*
21993 TATTGTATGTAATT
1 T-TTGTAAGTAATT
22007 TTTGTAAGTAAT
1 TTTGTAAGTAAT
22019 ATATTTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
12 8 0.15
13 31 0.57
14 3 0.06
15 3 0.06
16 5 0.09
17 4 0.07
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (13 bp):
TTTGTAAGTAATT
Found at i:22444 original size:2 final size:2
Alignment explanation
Indices: 22439--22478 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
22429 TGTGTGTGTG
* * *
22439 TA TA TA TA TA TA TA TA TA TA TT TA TT TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22479 ATTAAGCTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:25523 original size:41 final size:41
Alignment explanation
Indices: 25466--25707 Score: 240
Period size: 41 Copynumber: 5.8 Consensus size: 41
25456 TCTCTCTCTC
* *
25466 CAAAGTCCTCGAACACATTTATAACACAGAGACATCTATAT
1 CAAAGTCCCCAAACACATTTATAACACAGAGACATCTATAT
* * * *
25507 CAAAGTCCCCAAACACAGTTATAACACAG-GGCAATTCTCTTT
1 CAAAGTCCCCAAACACATTTATAACACAGAGAC-A-TCTATAT
* *
25549 CTAAAGTCCTCAAGCACATTTATAACACAGATG-CATCTATAT
1 C-AAAGTCCCCAAACACATTTATAACACAGA-GACATCTATAT
* * * *
25591 CAAAGTCCCCAAACACAATTATAACACAGGGGCACCTCTATTT
1 CAAAGTCCCCAAACACATTTATAACACA-GAG-ACATCTATAT
* * * *
25634 CAAA-TCCTCAAGCACATTTATAACACAAAGGCATCTATA-
1 CAAAGTCCCCAAACACATTTATAACACAGAGACATCTATAT
*
25673 CTAAAGTCCCCAAACACATTTATAACACAGGGACA
1 C-AAAGTCCCCAAACACATTTATAACACAGAGACA
25708 ATTATCTATT
Statistics
Matches: 161, Mismatches: 30, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
39 1 0.01
40 11 0.07
41 77 0.48
42 33 0.20
43 37 0.23
44 1 0.01
45 1 0.01
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (41 bp):
CAAAGTCCCCAAACACATTTATAACACAGAGACATCTATAT
Found at i:25559 original size:84 final size:82
Alignment explanation
Indices: 25448--25710 Score: 343
Period size: 84 Copynumber: 3.1 Consensus size: 82
25438 TACATCCCTA
*
25448 AGGGCATTTCTCTCTCTCCAAAGTCCTCGAA-CACATTTATAACACAGAGACATCTATATCAAAG
1 AGGGCAATTCTCT-T-T-CAAAGTCCTC-AAGCACATTTATAACACAGAG-CATCTATATCAAAG
*
25512 TCCCCAAACACAGTTATAACAC
61 TCCCCAAACACAATTATAACAC
25534 AGGGCAATTCTCTTTCTAAAGTCCTCAAGCACATTTATAACACAGATGCATCTATATCAAAGTCC
1 AGGGCAATTCTCTTTC-AAAGTCCTCAAGCACATTTATAACACAGA-GCATCTATATCAAAGTCC
25599 CCAAACACAATTATAACAC
64 CCAAACACAATTATAACAC
** * *
25618 AGGGGCACCTCTATTTCAAA-TCCTCAAGCACATTTATAACACAAAGGCATCTATA-CTAAAGTC
1 A-GGGCAATTCTCTTTCAAAGTCCTCAAGCACATTTATAACACAGA-GCATCTATATC-AAAGTC
*
25681 CCCAAACACATTTATAACAC
63 CCCAAACACAATTATAACAC
25701 AGGGACAATT
1 AGGG-CAATT
25711 ATCTATTATT
Statistics
Matches: 161, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
82 4 0.02
83 65 0.40
84 66 0.41
85 14 0.09
86 12 0.07
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.25
Consensus pattern (82 bp):
AGGGCAATTCTCTTTCAAAGTCCTCAAGCACATTTATAACACAGAGCATCTATATCAAAGTCCCC
AAACACAATTATAACAC
Found at i:25681 original size:83 final size:84
Alignment explanation
Indices: 25466--25704 Score: 351
Period size: 83 Copynumber: 2.9 Consensus size: 84
25456 TCTCTCTCTC
* *
25466 CAAAGTCCTCGAA-CACATTTATAACACAGAGACATCTATATCAAAGTCCCCAAACACAGTTATA
1 CAAAGTCCTC-AAGCACATTTATAACACAGAGGCATCTATATCAAAGTCCCCAAACACAATTATA
* *
25530 ACACA-GGGCAATTCTCTTT
65 ACACAGGGGCAACTCTATTT
*
25549 CTAAAGTCCTCAAGCACATTTATAACACAGATGCATCTATATCAAAGTCCCCAAACACAATTATA
1 C-AAAGTCCTCAAGCACATTTATAACACAGAGGCATCTATATCAAAGTCCCCAAACACAATTATA
*
25614 ACACAGGGGCACCTCTATTT
65 ACACAGGGGCAACTCTATTT
* *
25634 CAAA-TCCTCAAGCACATTTATAACACAAAGGCATCTATA-CTAAAGTCCCCAAACACATTTATA
1 CAAAGTCCTCAAGCACATTTATAACACAGAGGCATCTATATC-AAAGTCCCCAAACACAATTATA
25697 ACACAGGG
65 ACACAGGG
25705 ACAATTATCT
Statistics
Matches: 143, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
82 1 0.01
83 65 0.45
84 65 0.45
85 12 0.08
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.23
Consensus pattern (84 bp):
CAAAGTCCTCAAGCACATTTATAACACAGAGGCATCTATATCAAAGTCCCCAAACACAATTATAA
CACAGGGGCAACTCTATTT
Found at i:28010 original size:17 final size:18
Alignment explanation
Indices: 27985--28022 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
27975 ATTGTGTTTA
27985 TTATCTTTTAC-TACTTT
1 TTATCTTTTACTTACTTT
*
28002 TTATTTTTTACTTACTTT
1 TTATCTTTTACTTACTTT
28020 TTA
1 TTA
28023 ATTATTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATCTTTTACTTACTTT
Found at i:41401 original size:2 final size:2
Alignment explanation
Indices: 41394--41431 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
41384 CTCGTATTTT
*
41394 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41432 TAGATTGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:44372 original size:16 final size:15
Alignment explanation
Indices: 44352--44397 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
44342 AACCCGCCCG
44352 AACCCGAACCCGAAA
1 AACCCGAACCCGAAA
*
44367 ATACCCGAACCCGAGAC
1 A-ACCCGAACCCGA-AA
44384 AACCCGAACCCGAA
1 AACCCGAACCCGAA
44398 CCCGACCCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.41, C:0.41, G:0.15, T:0.02
Consensus pattern (15 bp):
AACCCGAACCCGAAA
Found at i:44407 original size:5 final size:6
Alignment explanation
Indices: 44338--44407 Score: 53
Period size: 6 Copynumber: 11.8 Consensus size: 6
44328 AAGTCAACGT
44338 CCCGAA CCCG-- CCCGAA CCCGAA CCCGAAAATA CCCGAA CCCGAGA --C-AA
1 CCCGAA CCCGAA CCCGAA CCCGAA CCCG---A-A CCCGAA CCCGA-A CCCGAA
44386 CCCGAA CCCGAA CCCG-A CCCGA
1 CCCGAA CCCGAA CCCGAA CCCGA
44408 GCCCAAGATC
Statistics
Matches: 53, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
3 1 0.02
4 5 0.09
5 7 0.13
6 32 0.60
7 2 0.04
9 1 0.02
10 5 0.09
ACGTcount: A:0.33, C:0.49, G:0.17, T:0.01
Consensus pattern (6 bp):
CCCGAA
Found at i:45193 original size:23 final size:23
Alignment explanation
Indices: 45159--45213 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
45149 TATCGAAAGT
45159 GAACCCGAACCCGACCCG-GACCC
1 GAACCCGAACCCGACCCGAG-CCC
* *
45182 GAACCCGGACCCGATCCGAGCCC
1 GAACCCGAACCCGACCCGAGCCC
45205 GAACCCGAA
1 GAACCCGAA
45214 AATACCCGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.27, C:0.47, G:0.24, T:0.02
Consensus pattern (23 bp):
GAACCCGAACCCGACCCGAGCCC
Found at i:45200 original size:17 final size:17
Alignment explanation
Indices: 45161--45212 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
45151 TCGAAAGTGA
45161 ACCCGAACCC-GACCCGG
1 ACCCGAACCCGGACCC-G
45178 ACCCGAACCCGGACCCG
1 ACCCGAACCCGGACCCG
* * *
45195 ATCCGAGCCCGAACCCG
1 ACCCGAACCCGGACCCG
45212 A
1 A
45213 AAATACCCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 26 0.84
18 5 0.16
ACGTcount: A:0.25, C:0.50, G:0.23, T:0.02
Consensus pattern (17 bp):
ACCCGAACCCGGACCCG
Found at i:45223 original size:16 final size:16
Alignment explanation
Indices: 45202--45291 Score: 132
Period size: 16 Copynumber: 5.8 Consensus size: 16
45192 CCGATCCGAG
45202 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
45218 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
45233 CCCGAACCCGAAAA-A
1 CCCGAACCCGAAAATA
*
45248 TCTCGAACCCGAAAATA
1 -CCCGAACCCGAAAATA
*
45265 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
45280 CCCGAACCCGAA
1 CCCGAACCCGAA
45292 CCCGCCCGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
15 30 0.45
16 36 0.54
17 1 0.01
ACGTcount: A:0.40, C:0.39, G:0.14, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:45233 original size:15 final size:15
Alignment explanation
Indices: 45202--45291 Score: 126
Period size: 15 Copynumber: 5.8 Consensus size: 15
45192 CCGATCCGAG
45202 CCCGAACCCGAAAATA
1 CCCGAACCCG-AAATA
45218 CCCGAACCCGAAATA
1 CCCGAACCCGAAATA
*
45233 CCCGAACCCGAAAAA
1 CCCGAACCCGAAATA
*
45248 TCTCGAACCCGAAAATA
1 -CCCGAACCCG-AAATA
*
45265 CCCGAACCCGAAGTA
1 CCCGAACCCGAAATA
45280 CCCGAACCCGAA
1 CCCGAACCCGAA
45292 CCCGCCCGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
15 35 0.52
16 28 0.42
17 4 0.06
ACGTcount: A:0.40, C:0.39, G:0.14, T:0.07
Consensus pattern (15 bp):
CCCGAACCCGAAATA
Found at i:45260 original size:6 final size:6
Alignment explanation
Indices: 45159--45213 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
45149 TATCGAAAGT
* * * *
45159 GAACCC GAACCC G-ACCC GGACCC GAACCC GGACCC G-ATCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
45205 GAACCC GAA
1 GAACCC GAA
45214 AATACCCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 9 0.22
6 32 0.78
ACGTcount: A:0.27, C:0.47, G:0.24, T:0.02
Consensus pattern (6 bp):
GAACCC
Found at i:45302 original size:47 final size:47
Alignment explanation
Indices: 45200--45305 Score: 158
Period size: 47 Copynumber: 2.3 Consensus size: 47
45190 ACCCGATCCG
45200 AGCCCGAACCCGAAAATACCCGAACCCGAAATACCCGAACCCGAAAA
1 AGCCCGAACCCGAAAATACCCGAACCCGAAATACCCGAACCCGAAAA
* * * **
45247 ATCTCGAACCCGAAAATACCCGAACCCGAAGTACCCGAACCCGAACC
1 AGCCCGAACCCGAAAATACCCGAACCCGAAATACCCGAACCCGAAAA
*
45294 CGCCCGAACCCG
1 AGCCCGAACCCG
45306 CCCAATTGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.37, C:0.42, G:0.16, T:0.06
Consensus pattern (47 bp):
AGCCCGAACCCGAAAATACCCGAACCCGAAATACCCGAACCCGAAAA
Found at i:47609 original size:51 final size:51
Alignment explanation
Indices: 47533--47634 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
47523 TTTAAATTAC
*
47533 TTTCATGAGAAAAGTGACCTGGTGGTGTTAAAGCACTTTCTCACTTTGGAG
1 TTTCATGAGAAAAGTGACCCGGTGGTGTTAAAGCACTTTCTCACTTTGGAG
47584 TTTCATGAGAAAAGTGACCCGGTGGTGTTAAAGCACTTTCTCACTTTGGAG
1 TTTCATGAGAAAAGTGACCCGGTGGTGTTAAAGCACTTTCTCACTTTGGAG
47635 AGAAAGTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (51 bp):
TTTCATGAGAAAAGTGACCCGGTGGTGTTAAAGCACTTTCTCACTTTGGAG
Found at i:54679 original size:18 final size:19
Alignment explanation
Indices: 54637--54680 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
54627 AGTTTTTCAG
* *
54637 TCAGTTTTTTTGAGTTAGT
1 TCAGTTTTTTTGAGTCAAT
54656 TCAGTTTTTTTGAGTCAAT
1 TCAGTTTTTTTGAGTCAAT
54675 T-AGTTT
1 TCAGTTT
54681 GAGTCTGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.18, C:0.07, G:0.18, T:0.57
Consensus pattern (19 bp):
TCAGTTTTTTTGAGTCAAT
Found at i:55402 original size:18 final size:20
Alignment explanation
Indices: 55360--55404 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
55350 GGGTTTACAC
* *
55360 ATTAATTAAAAACATTTTTA
1 ATTAATTAAAAACATATTAA
55380 ATTAATT-AAAA-ATATTAA
1 ATTAATTAAAAACATATTAA
55398 ATTAATT
1 ATTAATT
55405 TAAGTAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 12 0.52
19 4 0.17
20 7 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTAATTAAAAACATATTAA
Found at i:55780 original size:2 final size:2
Alignment explanation
Indices: 55773--55806 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55763 CAAATACAAG
55773 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
55807 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:55992 original size:20 final size:20
Alignment explanation
Indices: 55967--56008 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
55957 ATAACTAAAT
55967 ACTACACTAAGCCAAAGCCA
1 ACTACACTAAGCCAAAGCCA
55987 ACTACACTAAGCCAAAGCCA
1 ACTACACTAAGCCAAAGCCA
56007 AC
1 AC
56009 CCCCAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.36, G:0.10, T:0.10
Consensus pattern (20 bp):
ACTACACTAAGCCAAAGCCA
Found at i:61490 original size:20 final size:20
Alignment explanation
Indices: 61427--61491 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
61417 AAAATAAAGG
61427 AAAAT-ATTTTTTATTTTAGA
1 AAAATAATTTTTT-TTTTAGA
** * *
61447 AAACGCAA-TTTTTTTATCGCA
1 AAA-ATAATTTTTTTTTTAG-A
61468 AAAATAATTTTTTTTTTAGA
1 AAAATAATTTTTTTTTTAGA
61488 AAAA
1 AAAA
61492 ACGCAAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
20 14 0.42
21 18 0.55
22 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (20 bp):
AAAATAATTTTTTTTTTAGA
Done.