Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008386.1 Corchorus capsularis cultivar CVL-1 contig08407, 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: 79787
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:174 original size:15 final size:15
Alignment explanation
Indices: 151--180 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
141 ATCGGTTGAA
*
151 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
166 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
181 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:2517 original size:25 final size:27
Alignment explanation
Indices: 2465--2517 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2455 TTACTCAACT
**
2465 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
2492 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
2517 A
1 A
2518 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:2619 original size:27 final size:25
Alignment explanation
Indices: 2589--2640 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2579 CATATTAGAA
*
2589 TTTTTAAAAATATATTCTTTTACAATT
1 TTTTTAAAAATA-A-ACTTTTACAATT
*
2616 TTTTTAGAAATAAACTTTTACAATT
1 TTTTTAAAAATAAACTTTTACAATT
2641 ATTCTACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 11 0.48
26 1 0.04
27 11 0.48
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTTAAAAATAAACTTTTACAATT
Found at i:6959 original size:22 final size:22
Alignment explanation
Indices: 6933--7030 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
6923 ATTACTGAAA
* *
6933 TTCATAGTGTGGTTATCAAAAT
1 TTCATATTGAGGTTATCAAAAT
* *
6955 TTCATAATGTGGTTA-CAAAAAT
1 TTCATATTGAGGTTATC-AAAAT
*
6977 TT--TATTGAAGGTAATCAAAAT
1 TTCATATTG-AGGTTATCAAAAT
*
6998 TTCATATTGAGTTTATCAAAAT
1 TTCATATTGAGGTTATCAAAAT
*
7020 TTCATAATGAG
1 TTCATATTGAG
7031 ATTAAGACGA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.06
21 12 0.19
22 43 0.67
23 5 0.08
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCATATTGAGGTTATCAAAAT
Found at i:7242 original size:22 final size:21
Alignment explanation
Indices: 7173--7307 Score: 92
Period size: 22 Copynumber: 6.1 Consensus size: 21
7163 TCATCAAATT
*
7173 AATTTCATATAGAGGTTA-CAA
1 AATTTCATA-GGAGGTTATCAA
* * * *
7194 AAGTTTCATAGTGTGGTGACCGA
1 AA-TTTCATAG-GAGGTTATCAA
*
7217 AATTTCATAGGATGGTTATCAG
1 AATTTCATAGGA-GGTTATCAA
* * *
7239 AATTTTATAGTGTGGTTATTAA
1 AATTTCATAG-GAGGTTATCAA
* *
7261 AATTTCACAGGGAGGTTATCAC
1 AATTTCATA-GGAGGTTATCAA
*
7283 AATTTCTTAAGGAGGTTATCAA
1 AATTTCAT-AGGAGGTTATCAA
7305 AAT
1 AAT
7308 AATATAGCAA
Statistics
Matches: 86, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
21 3 0.03
22 76 0.88
23 7 0.08
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (21 bp):
AATTTCATAGGAGGTTATCAA
Found at i:10742 original size:22 final size:22
Alignment explanation
Indices: 10712--10918 Score: 102
Period size: 22 Copynumber: 9.4 Consensus size: 22
10702 TCTAGCGTAG
*
10712 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* *
10735 AAATTTGATAACCTCATTATG-
1 AAATTTGATAACCACACTATGA
*
10756 AAATTTCGATAACCTTC-CTATG-
1 AAATTT-GATAACC-ACACTATGA
** *
10778 AAATTTGATAATAACCACAATGTA
1 AAATTTGATAACCA-CACTATG-A
*
10802 AAATTTTGATAACCACATTATGA
1 AAA-TTTGATAACCACACTATGA
* ** * *
10825 AATTTTGATAACCTTAGTGTGA
1 AAATTTGATAACCACACTATGA
* **
10847 AATTTTGATAATCTTC-CTATGA
1 AAATTTGATAA-CCACACTATGA
* * *
10869 AATTTTGTTAATCACACTAT-A
1 AAATTTGATAACCACACTATGA
* **
10890 AAA-TTGGTAACCGTACTATGA
1 AAATTTGATAACCACACTATGA
*
10911 AAAATTGA
1 AAATTTGA
10919 AAATTTTGAT
Statistics
Matches: 142, Mismatches: 31, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
20 12 0.08
21 20 0.14
22 82 0.58
23 11 0.08
24 8 0.06
25 9 0.06
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:10794 original size:68 final size:69
Alignment explanation
Indices: 10720--10858 Score: 201
Period size: 68 Copynumber: 2.0 Consensus size: 69
10710 AGAAATATTG
* * *
10720 ATAACCACACTGTGAAAA-TTTGATAACCTCATTATGAAATTTCGATAACCTTCCTATGAAA-TT
1 ATAACCACAATGT-AAAATTTTGATAACCACATTATGAAATTTCGATAACCTTACTATGAAATTT
10783 TGATA
65 TGATA
* * *
10788 ATAACCACAATGTAAAATTTTGATAACCACATTATGAAATTTTGATAACCTTAGTGTGAAATTTT
1 ATAACCACAATGTAAAATTTTGATAACCACATTATGAAATTTCGATAACCTTACTATGAAATTTT
10853 GATA
66 GATA
10857 AT
1 AT
10859 CTTCCTATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
67 4 0.06
68 50 0.79
69 9 0.14
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (69 bp):
ATAACCACAATGTAAAATTTTGATAACCACATTATGAAATTTCGATAACCTTACTATGAAATTTT
GATA
Found at i:11039 original size:22 final size:22
Alignment explanation
Indices: 11014--11097 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
11004 ATCTCTATGT
*
11014 AATTTTGATAACCTCCCCATAA
1 AATTTTGATAACCTCCCTATAA
* *
11036 AATTTTCATTACCTCCCTATAA
1 AATTTTGATAACCTCCCTATAA
* * * **
11058 AATCTTGTTAACTTCCCTAGGA
1 AATTTTGATAACCTCCCTATAA
11080 AATTTTGATAACCTCCCT
1 AATTTTGATAACCTCCCT
11098 CCCTATGAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (22 bp):
AATTTTGATAACCTCCCTATAA
Found at i:11192 original size:22 final size:21
Alignment explanation
Indices: 11164--11239 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 21
11154 CCTCTCTAAA
11164 AAATTTTGATAACTACACTAT
1 AAATTTTGATAACTACACTAT
11185 AAAGTTTTGATAACCT-CGA-TAT
1 AAA-TTTTGATAA-CTAC-ACTAT
* *
11207 GAAATTTTGGTAACCACACTATT
1 -AAATTTTGATAACTACACTA-T
11230 AAATTTTGAT
1 AAATTTTGAT
11240 GACCTTCATG
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
21 5 0.11
22 33 0.73
23 7 0.16
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAACTACACTAT
Found at i:11257 original size:44 final size:44
Alignment explanation
Indices: 11164--11261 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
11154 CCTCTCTAAA
* *
11164 AAATTTTGATAACTACACTATAAAGTTTTGATAACCTCGATATG
1 AAATTTTGGTAACCACACTATAAAGTTTTGATAACCTCGATATG
* *
11208 AAATTTTGGTAACCACACTATTAAA-TTTTGATGACCTTC-ATGTG
1 AAATTTTGGTAACCACACTA-TAAAGTTTTGATAACC-TCGATATG
*
11252 TAATTTTGGT
1 AAATTTTGGT
11262 TTGATTGTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 41 0.87
45 6 0.13
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (44 bp):
AAATTTTGGTAACCACACTATAAAGTTTTGATAACCTCGATATG
Found at i:12697 original size:16 final size:16
Alignment explanation
Indices: 12675--12720 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
12665 AATAAGTACT
*
12675 ATAACCCGAAACCGAT
1 ATAACCCGAAACCGAG
* *
12691 TTAACCC-AAATCGAG
1 ATAACCCGAAACCGAG
12706 ATAACCCGAAACCGA
1 ATAACCCGAAACCGA
12721 CAAAATCCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.13
Consensus pattern (16 bp):
ATAACCCGAAACCGAG
Found at i:16488 original size:51 final size:52
Alignment explanation
Indices: 16411--16516 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 52
16401 AAGACATGTG
*
16411 AAATTGTGCTAGACTTTATTTATGC-TGCTTTGGGAACTTAAAGTCATTGAA
1 AAATTGTGCTAGACTTTATTTATGCTTGCTTAGGGAACTTAAAGTCATTGAA
* *
16462 AAATTGTGCTAGACTTTTTTTCTGCTGTTGCTTAGGGAACTTAAAGTCATTGAA
1 AAATTGTGCTAGACTTTATTTATGC--TTGCTTAGGGAACTTAAAGTCATTGAA
16516 A
1 A
16517 GCAAAATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 23 0.47
54 26 0.53
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (52 bp):
AAATTGTGCTAGACTTTATTTATGCTTGCTTAGGGAACTTAAAGTCATTGAA
Found at i:21452 original size:14 final size:14
Alignment explanation
Indices: 21417--21452 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
21407 GCTGCTCATC
21417 TTTCGGTGTCGGTTT
1 TTTCGGT-TCGGTTT
21432 TTT-GGTTCGGTTT
1 TTTCGGTTCGGTTT
21445 TTTCGGTT
1 TTTCGGTT
21453 TTTATTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.50
14 7 0.35
15 3 0.15
ACGTcount: A:0.00, C:0.11, G:0.31, T:0.58
Consensus pattern (14 bp):
TTTCGGTTCGGTTT
Found at i:24582 original size:16 final size:16
Alignment explanation
Indices: 24561--24594 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
24551 TCCTAAATTA
24561 TTGCGCCAATGACATT
1 TTGCGCCAATGACATT
24577 TTGCGCCAATGACATT
1 TTGCGCCAATGACATT
24593 TT
1 TT
24595 TCCCCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (16 bp):
TTGCGCCAATGACATT
Found at i:28399 original size:52 final size:52
Alignment explanation
Indices: 28337--28444 Score: 207
Period size: 52 Copynumber: 2.1 Consensus size: 52
28327 GAAAATATTT
*
28337 AAAATAGATATAAACTTAAAATTAAAAAACTGTCATTAGGAATTCAACAAAA
1 AAAATAGATATAAACTTAAAATTAAAAAACTGTCATTAAGAATTCAACAAAA
28389 AAAATAGATATAAACTTAAAATTAAAAAACTGTCATTAAGAATTCAACAAAA
1 AAAATAGATATAAACTTAAAATTAAAAAACTGTCATTAAGAATTCAACAAAA
28441 AAAA
1 AAAA
28445 AACTGTCATT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.24
Consensus pattern (52 bp):
AAAATAGATATAAACTTAAAATTAAAAAACTGTCATTAAGAATTCAACAAAA
Found at i:28441 original size:26 final size:26
Alignment explanation
Indices: 28360--28443 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
28350 ACTTAAAATT
*
28360 AAAAAACTGTCATTAGGAATTCAACA
1 AAAAAACTGTCATTAAGAATTCAACA
* * *
28386 AAAAAAATAG--ATATAA-ACTT-AAAA
1 AAAAAACT-GTCAT-TAAGAATTCAACA
28410 TTAAAAAACTGTCATTAAGAATTCAACA
1 --AAAAAACTGTCATTAAGAATTCAACA
28438 AAAAAA
1 AAAAAA
28444 AAACTGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
24 3 0.07
25 6 0.14
26 25 0.58
27 6 0.14
28 3 0.07
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.23
Consensus pattern (26 bp):
AAAAAACTGTCATTAAGAATTCAACA
Found at i:28600 original size:29 final size:29
Alignment explanation
Indices: 28564--28621 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28554 TCTAATCGAG
28564 ACTTCTTCTTCTTCTTCTCCTCCTCTATT
1 ACTTCTTCTTCTTCTTCTCCTCCTCTATT
28593 ACTTCTTCTTCTTCTTCTCCTCCTCTATT
1 ACTTCTTCTTCTTCTTCTCCTCCTCTATT
28622 CTGCCAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.07, C:0.38, G:0.00, T:0.55
Consensus pattern (29 bp):
ACTTCTTCTTCTTCTTCTCCTCCTCTATT
Found at i:32218 original size:17 final size:17
Alignment explanation
Indices: 32196--32228 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32186 CTTTTTAAAA
32196 ATATATAGGCTACCTTG
1 ATATATAGGCTACCTTG
*
32213 ATATATAGGTTACCTT
1 ATATATAGGCTACCTT
32229 AAACAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (17 bp):
ATATATAGGCTACCTTG
Found at i:35091 original size:16 final size:16
Alignment explanation
Indices: 35070--35117 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
35060 ATGATGTCTA
35070 AGAATGAAAATCATAT
1 AGAATGAAAATCATAT
*
35086 AGAATGAAACATCATGT
1 AGAATGAAA-ATCATAT
*
35103 -GAGTGAAAAT-ATAT
1 AGAATGAAAATCATAT
35117 A
1 A
35118 ATGATAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 16 0.59
17 6 0.22
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (16 bp):
AGAATGAAAATCATAT
Found at i:35896 original size:13 final size:12
Alignment explanation
Indices: 35878--35911 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
35868 ACCAAGAACC
35878 TGAAAAAAAAAA
1 TGAAAAAAAAAA
35890 TTGAAAAAAAAAA
1 -TGAAAAAAAAAA
35903 -GAAAAAAAA
1 TGAAAAAAAA
35912 TTAAAAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (12 bp):
TGAAAAAAAAAA
Found at i:40942 original size:24 final size:24
Alignment explanation
Indices: 40911--40957 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40901 AAGTAGATTA
40911 TAATTAGATATT-ATTT-GATTTTG
1 TAATTAGAT-TTGATTTAGATTTTG
40934 TAATCTAGATTTGATTTAGATTTT
1 TAAT-TAGATTTGATTTAGATTTT
40958 ATCTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 9 0.43
25 6 0.29
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (24 bp):
TAATTAGATTTGATTTAGATTTTG
Found at i:41816 original size:41 final size:41
Alignment explanation
Indices: 41680--41824 Score: 204
Period size: 41 Copynumber: 3.5 Consensus size: 41
41670 AATAATATTG
*
41680 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAGAAATTGTCACTTTGGTAAATT
* * *
41721 AAAGTTA-CTGCTGACACTA-AAAGTTGTCACTTTGGTAAATT
1 AAAATTACCT-TTGACACCAGAAA-TTGTCACTTTGGTAAATT
* *
41762 GAAATTACTTTTGACACCAGAAATTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAGAAATTGTCACTTTGGTAAATT
41803 AAAATTACCTTTGACACCAGAA
1 AAAATTACCTTTGACACCAGAA
41825 GTGTTACTCC
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
40 4 0.04
41 81 0.91
42 4 0.04
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (41 bp):
AAAATTACCTTTGACACCAGAAATTGTCACTTTGGTAAATT
Found at i:41818 original size:82 final size:83
Alignment explanation
Indices: 41674--41879 Score: 233
Period size: 82 Copynumber: 2.5 Consensus size: 83
41664 AAAGTAAATA
* * * *
41674 ATATTGAAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAGTTACTGCTGACACT
1 ATATTG-AAATTACTTTTGACACCAGAAATTGTCACTTTGGTAAATTAAAATTACTGCTGACACC
***
41739 AAAAGTTGTCACTTTGGTA-
65 AAAAG-TGTCACTCCAGTAT
*
41758 A-ATTGAAATTACTTTTGACACCAGAAATTGTCACTTTGGTAAATTAAAATTACCT-TTGACACC
1 ATATTGAAATTACTTTTGACACCAGAAATTGTCACTTTGGTAAATTAAAATTA-CTGCTGACACC
* *
41821 AGAAGTGTTACTCCAGTAT
65 AAAAGTGTCACTCCAGTAT
41840 ATATT-ATAATTA-TTGTTGACACCAGAAATTGTCACCTTTG
1 ATATTGA-AATTACTT-TTGACACCAGAAATTGTCA-CTTTG
41880 AATTACCCCC
Statistics
Matches: 106, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
81 9 0.08
82 58 0.55
83 33 0.31
84 6 0.06
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (83 bp):
ATATTGAAATTACTTTTGACACCAGAAATTGTCACTTTGGTAAATTAAAATTACTGCTGACACCA
AAAGTGTCACTCCAGTAT
Found at i:42880 original size:25 final size:25
Alignment explanation
Indices: 42823--42873 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
42813 ACTCTTTAAC
42823 TAATTACTTCTCTTACTTTTACTCT
1 TAATTACTTCTCTTACTTTTACTCT
* *
42848 TAATTACTTCTTTTACTTTTGCTCT
1 TAATTACTTCTCTTACTTTTACTCT
42873 T
1 T
42874 TTCTACTGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.59
Consensus pattern (25 bp):
TAATTACTTCTCTTACTTTTACTCT
Found at i:42888 original size:32 final size:32
Alignment explanation
Indices: 42850--42943 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 32
42840 TTTACTCTTA
*
42850 ATTACTTCTTTTACTTTTGCTCTTTTCTACTG
1 ATTACTTCTTTTACTTTTACTCTTTTCTACTG
*
42882 CTTACTTCTTCTT-CTTTTACTCTTTCACTTCTACTG
1 ATTACTTCTT-TTACTTTTACTC-TT---TTCTACTG
*
42918 ATTACTTGTTTTACTTTTACTCTTTT
1 ATTACTTCTTTTACTTTTACTCTTTT
42944 ACTTTTACTG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
32 19 0.37
33 4 0.08
35 4 0.08
36 25 0.48
ACGTcount: A:0.13, C:0.23, G:0.04, T:0.60
Consensus pattern (32 bp):
ATTACTTCTTTTACTTTTACTCTTTTCTACTG
Found at i:42923 original size:36 final size:36
Alignment explanation
Indices: 42874--42969 Score: 122
Period size: 36 Copynumber: 2.7 Consensus size: 36
42864 TTTTGCTCTT
*
42874 TTCTACTGCTTACTTCTTCTTCTTTTACTCTTTCAC
1 TTCTACTGATTACTTCTTCTTCTTTTACTCTTTCAC
* *
42910 TTCTACTGATTACTTGTT-TTACTTTTACTCTTTTAC
1 TTCTACTGATTACTTCTTCTT-CTTTTACTCTTTCAC
* * *
42946 TTTTACTGATAACTTCTTCCTCTT
1 TTCTACTGATTACTTCTTCTTCTT
42970 ACTGATTGTC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
35 2 0.04
36 48 0.94
37 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.04, T:0.56
Consensus pattern (36 bp):
TTCTACTGATTACTTCTTCTTCTTTTACTCTTTCAC
Found at i:42945 original size:14 final size:14
Alignment explanation
Indices: 42926--42952 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42916 TGATTACTTG
42926 TTTTACTTTTACTC
1 TTTTACTTTTACTC
42940 TTTTACTTTTACT
1 TTTTACTTTTACT
42953 GATAACTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTACTTTTACTC
Found at i:42951 original size:20 final size:21
Alignment explanation
Indices: 42926--43012 Score: 60
Period size: 20 Copynumber: 4.3 Consensus size: 21
42916 TGATTACTTG
42926 TTTTACT-TTTACTCTTTTAC
1 TTTTACTGTTTACTCTTTTAC
* * * *
42946 TTTTACTGATAACT-TCTTCC
1 TTTTACTGTTTACTCTTTTAC
*
42966 TCTTACTGATTGT-CTCTTTTAC
1 TTTTACTG-TT-TACTCTTTTAC
42988 TTTTA-T-TTTACTC-TTTAC
1 TTTTACTGTTTACTCTTTTAC
43006 TCTTTAC
1 T-TTTAC
43013 CATTTTTTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
18 7 0.14
19 9 0.18
20 18 0.36
21 8 0.16
22 8 0.16
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (21 bp):
TTTTACTGTTTACTCTTTTAC
Found at i:43394 original size:38 final size:39
Alignment explanation
Indices: 43303--43508 Score: 278
Period size: 38 Copynumber: 5.3 Consensus size: 39
43293 GATTAATCCC
* *
43303 TTGACTCTTAATTACT-GA-TTTACTGATTACTATTTTTACC
1 TTGACTCTTAATTACTCAATTTTACTGATTACTA---TTACT
43343 TTGACTCTTAATTA-TCAATTTTACTGATTACTATTACT
1 TTGACTCTTAATTACTCAATTTTACTGATTACTATTACT
*
43381 TTGACTCATAATTA-TCAATTTTACTGATTACTATTACT
1 TTGACTCTTAATTACTCAATTTTACTGATTACTATTACT
* *
43419 TTGAGTCTTAATTACTTAATTTTACTGATTACTATTACT
1 TTGACTCTTAATTACTCAATTTTACTGATTACTATTACT
* * *
43458 TTGACTCTTAATTACTTAA-TTCACTGATTACTATTAGT
1 TTGACTCTTAATTACTCAATTTTACTGATTACTATTACT
43496 TTGACTCTTAATT
1 TTGACTCTTAATT
43509 TATTGGGGTA
Statistics
Matches: 154, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
38 83 0.54
39 42 0.27
40 15 0.10
41 14 0.09
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.50
Consensus pattern (39 bp):
TTGACTCTTAATTACTCAATTTTACTGATTACTATTACT
Found at i:43451 original size:77 final size:76
Alignment explanation
Indices: 43275--43508 Score: 273
Period size: 77 Copynumber: 3.1 Consensus size: 76
43265 TACTTTCTCC
* * * * *
43275 CTTAAGTATCAA-TTTACTGATTA--A-TCCCTTGACTCTTAATTACT-GATTTACTGATTACTA
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACTCATAATTACTCAATTTACTGATTACTA
*
43335 TTTTTACCTTGACT
66 ---TTACTTTGACT
43349 CTTAATTATCAATTTTACTGATTACTATTACTTTGACTCATAATTA-TCAATTTTACTGATTACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACTCATAATTACTCAA-TTTACTGATTACT
*
43413 ATTACTTTGAGT
65 ATTACTTTGACT
* * * *
43425 CTTAATTACTTAATTTTACTGATTACTATTACTTTGACTCTTAATTACTTAATTCACTGATTACT
1 CTTAATTA-TCAATTTTACTGATTACTATTACTTTGACTCATAATTACTCAATTTACTGATTACT
*
43490 ATTAGTTTGACT
65 ATTACTTTGACT
43502 CTTAATT
1 CTTAATT
43509 TATTGGGGTA
Statistics
Matches: 139, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
74 11 0.08
75 11 0.08
76 17 0.12
77 67 0.48
78 19 0.14
79 14 0.10
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (76 bp):
CTTAATTATCAATTTTACTGATTACTATTACTTTGACTCATAATTACTCAATTTACTGATTACTA
TTACTTTGACT
Found at i:44734 original size:15 final size:15
Alignment explanation
Indices: 44714--44745 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44704 TAACCGCCCA
*
44714 CTCTTTTCCTTCTTC
1 CTCTTTTCCTTCCTC
44729 CTCTTTTCCTTCCTC
1 CTCTTTTCCTTCCTC
44744 CT
1 CT
44746 TCCTCGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (15 bp):
CTCTTTTCCTTCCTC
Found at i:47218 original size:26 final size:26
Alignment explanation
Indices: 47166--47220 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
47156 TAAGCTAGCA
* * * *
47166 CTGAATTAAAAATAACTAAAGTGCCC
1 CTGAAGTAAAAATAACCAAAATACCC
*
47192 CTGAAGTAAAAATGACCAAAATACCC
1 CTGAAGTAAAAATAACCAAAATACCC
47218 CTG
1 CTG
47221 GGTGACTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.22, G:0.13, T:0.20
Consensus pattern (26 bp):
CTGAAGTAAAAATAACCAAAATACCC
Found at i:54882 original size:25 final size:25
Alignment explanation
Indices: 54831--54882 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
54821 AAATTGAAAT
*
54831 TTATAATTATTTTTAAATAATATAA
1 TTATAATTATTTTTAAATAATACAA
54856 TTAT-ATTAATTTTT-AATAATAACAA
1 TTATAATT-ATTTTTAAATAAT-ACAA
54881 TT
1 TT
54883 TAGAAATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATAATTATTTTTAAATAATACAA
Found at i:56212 original size:11 final size:11
Alignment explanation
Indices: 56169--56206 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
56159 TTCCTATATA
*
56169 AAATAAATTAT
1 AAATTAATTAT
56180 CAAA-TAATTAT
1 -AAATTAATTAT
56191 AAATTAATTAT
1 AAATTAATTAT
56202 AAATT
1 AAATT
56207 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:66828 original size:1 final size:1
Alignment explanation
Indices: 66822--66857 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
66812 AAGGGAAAAG
*
66822 TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
66858 CTTCTCTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:68804 original size:18 final size:19
Alignment explanation
Indices: 68781--68818 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
68771 GAAATAGTAT
68781 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
68799 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
68818 T
1 T
68819 ATGATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:72113 original size:31 final size:32
Alignment explanation
Indices: 72042--72120 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
72032 TAAGGCGTTT
* * * *
72042 CTTCTTCAAACGCCACCAGTTTGGGTCGCTTG
1 CTTCATCAAACGCCACCAGTTTGGGGCGATAG
* *
72074 CTTCATCAAACGCCTCCATTTTGGGGCGATAG
1 CTTCATCAAACGCCACCAGTTTGGGGCGATAG
72106 -TTCATCAAACGCCAC
1 CTTCATCAAACGCCAC
72121 TATTGTTCGG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 14 0.35
32 26 0.65
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.28
Consensus pattern (32 bp):
CTTCATCAAACGCCACCAGTTTGGGGCGATAG
Found at i:72415 original size:9 final size:9
Alignment explanation
Indices: 72401--72427 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
72391 TGCATTAAAG
72401 GAATCAAAA
1 GAATCAAAA
72410 GAATCAAAA
1 GAATCAAAA
72419 GAATCAAAA
1 GAATCAAAA
72428 TGTGTCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (9 bp):
GAATCAAAA
Found at i:72812 original size:15 final size:15
Alignment explanation
Indices: 72794--72826 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
72784 TCAAGGCGAG
72794 CTTGCTCTTCTTT-TT
1 CTTG-TCTTCTTTCTT
72809 CTTGTCTTCTTTCTT
1 CTTGTCTTCTTTCTT
72824 CTT
1 CTT
72827 CAATTCTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.00, C:0.27, G:0.06, T:0.67
Consensus pattern (15 bp):
CTTGTCTTCTTTCTT
Found at i:74937 original size:38 final size:38
Alignment explanation
Indices: 74890--74990 Score: 114
Period size: 28 Copynumber: 2.9 Consensus size: 38
74880 AATTACCACT
74890 AATTACTTAGGACTATATATTCTGTACAAAGTAATGCA
1 AATTACTTAGGACTATATATTCTGTACAAAGTAATGCA
*
74928 AATTACTTAGGA--AGATATT-T-T-----GT-ATGCA
1 AATTACTTAGGACTATATATTCTGTACAAAGTAATGCA
*
74956 AATTAATTAGGACTATATATTCTGTACAAAGTAAT
1 AATTACTTAGGACTATATATTCTGTACAAAGTAAT
74991 ACCAACTCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 20
0.68 0.04 0.27
Matches are distributed among these distances:
28 16 0.32
29 2 0.04
30 6 0.12
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 6 0.12
37 2 0.04
38 14 0.28
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (38 bp):
AATTACTTAGGACTATATATTCTGTACAAAGTAATGCA
Found at i:77212 original size:33 final size:32
Alignment explanation
Indices: 77171--77250 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 32
77161 TAAATTCTAT
77171 TATTTAGGGGCGTTTACTT-CTTAAATCGCCAC
1 TATTTAGGGGCGTTTACTTCCTTAAAT-GCCAC
* * **
77203 TATGTTAGGGGCATTTGCTTCCTTAGGTGCCAC
1 TAT-TTAGGGGCGTTTACTTCCTTAAATGCCAC
77236 TATTTAGGGGCGTTT
1 TATTTAGGGGCGTTT
77251 GTTTCATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 14 0.34
33 22 0.54
34 5 0.12
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (32 bp):
TATTTAGGGGCGTTTACTTCCTTAAATGCCAC
Found at i:77272 original size:32 final size:32
Alignment explanation
Indices: 77171--77265 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 32
77161 TAAATTCTAT
* *
77171 TATTTAGGGGCGTTTACTTCTTAAA-TCGCCAC
1 TATTTAGGGGCGTTTGCTTCATAAAGT-GCCAC
* * * *
77203 TATGTTAGGGGCATTTGCTTCCTTAGGTGCCAC
1 TAT-TTAGGGGCGTTTGCTTCATAAAGTGCCAC
*
77236 TATTTAGGGGCGTTTGTTTCATAAAGTGCC
1 TATTTAGGGGCGTTTGCTTCATAAAGTGCC
77266 CTTATTTTGC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
32 25 0.49
33 25 0.49
34 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (32 bp):
TATTTAGGGGCGTTTGCTTCATAAAGTGCCAC
Done.