Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015030.1 Corchorus capsularis cultivar CVL-1 contig15051, 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: 69157
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:270 original size:15 final size:15
Alignment explanation
Indices: 250--368 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 15
240 ATTTATATTT
250 ATTATAATATATATA
1 ATTATAATATATATA
265 ATTATAATTATAATTTATA
1 ATTATAA-TAT-A--TATA
*
284 A-AATAAATATATATA
1 ATTAT-AATATATATA
299 A--AGTAA-ATATATA
1 ATTA-TAATATATATA
*
312 ATTACT-TTATATAT-
1 ATTA-TAATATATATA
326 ATTAT-ATATATAATAA
1 ATTATAATATAT-AT-A
* *
342 AGTA-AATACATATA
1 ATTATAATATATATA
356 ATTATAATATATA
1 ATTATAATATATA
369 ATTTATATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
13 14 0.17
14 13 0.16
15 30 0.37
16 11 0.13
17 2 0.02
18 5 0.06
19 7 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTATAATATATATA
Found at i:376 original size:11 final size:13
Alignment explanation
Indices: 258--371 Score: 64
Period size: 13 Copynumber: 8.8 Consensus size: 13
248 TTATTATAAT
258 ATATATAATTATA
1 ATATATAATTATA
271 AT-TATAATTTATA
1 ATATATAA-TTATA
*
284 A-A-ATAAATAT-
1 ATATATAATTATA
*
294 ATATA-AAGTA-A
1 ATATATAATTATA
305 ATATATAATTACT-
1 ATATATAATTA-TA
*
318 TTATATATATTAT-
1 ATATATA-ATTATA
*
331 ATATATAATAAAGTAA
1 ATATATAAT-TA-T-A
347 ATACATATAATTATA
1 AT--ATATAATTATA
362 ATATATAATT
1 ATATATAATT
372 TATATTTATT
Statistics
Matches: 79, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
10 1 0.01
11 13 0.16
12 16 0.20
13 30 0.38
14 5 0.06
15 3 0.04
16 3 0.04
17 1 0.01
18 7 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:1547 original size:33 final size:33
Alignment explanation
Indices: 1495--1601 Score: 137
Period size: 33 Copynumber: 3.2 Consensus size: 33
1485 AATTGCTCAT
* *
1495 GCCGCCCTACCTGGTGCGGCATTACCATGGCCAG
1 GCCGCCCT-CCTGGGGCGGCACTACCATGGCCAG
*
1529 GCCGTCCC-CCTGGGGCGGCCCTACCATGGCTCA-
1 GCCG-CCCTCCTGGGGCGGCACTACCATGGC-CAG
*
1562 ACCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1 GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1595 GCCGCCC
1 GCCGCCC
1602 ATGGCCAGGC
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
32 5 0.08
33 49 0.78
34 6 0.10
35 3 0.05
ACGTcount: A:0.12, C:0.44, G:0.30, T:0.14
Consensus pattern (33 bp):
GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
Found at i:1605 original size:15 final size:15
Alignment explanation
Indices: 1585--1615 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1575 GGCGGCACTA
1585 CCATGGCCAGGCCGC
1 CCATGGCCAGGCCGC
1600 CCATGGCCAGGCCGC
1 CCATGGCCAGGCCGC
1615 C
1 C
1616 TCCTTGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.48, G:0.32, T:0.06
Consensus pattern (15 bp):
CCATGGCCAGGCCGC
Found at i:1785 original size:33 final size:33
Alignment explanation
Indices: 1721--1946 Score: 330
Period size: 33 Copynumber: 6.9 Consensus size: 33
1711 AAAAAAACTT
* *
1721 GCCGCCCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* * *
1753 GCCGTCCTAGTGGGGCGGCTCCACCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
1786 ACCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* *
1819 GCCGCCCTAGTGGGGAGGCTCCGTCGTGCCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1852 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* *
1885 GCCGCCCTAGTGGGGAGCCTCCGTCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* *
1918 GCCGTCTTAGTGGGGAGGCTCCG-CGTGGC
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGC
1947 TAAGGGCAAA
Statistics
Matches: 176, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
32 25 0.14
33 151 0.86
ACGTcount: A:0.12, C:0.32, G:0.41, T:0.15
Consensus pattern (33 bp):
GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:2096 original size:3 final size:3
Alignment explanation
Indices: 2088--2115 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2078 AGAATTTGCA
2088 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2116 TATTTAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2483 original size:54 final size:54
Alignment explanation
Indices: 2401--2508 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
2391 AAACTACACA
* *
2401 TGCGGGGTTTAGAGAATATTTTTGAATTTTAAAAATAAAATTACTTCAGAAAAT
1 TGCGGGGTTTAGAGAATATTTTTGAATTTTAAAAACAAAATTAATTCAGAAAAT
2455 TGCGGGGTTTAGAGAATATTTTTGAATTTTAAAAACAAAATTAATTCAGAAAAT
1 TGCGGGGTTTAGAGAATATTTTTGAATTTTAAAAACAAAATTAATTCAGAAAAT
2509 GAGTATATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (54 bp):
TGCGGGGTTTAGAGAATATTTTTGAATTTTAAAAACAAAATTAATTCAGAAAAT
Found at i:3013 original size:20 final size:20
Alignment explanation
Indices: 2988--3027 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2978 TATCAGCTGA
2988 ATTTTGTTTTGACGTACTTG
1 ATTTTGTTTTGACGTACTTG
3008 ATTTTGTTTTGACGTACTTG
1 ATTTTGTTTTGACGTACTTG
3028 TGCTTTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.20, T:0.55
Consensus pattern (20 bp):
ATTTTGTTTTGACGTACTTG
Found at i:4698 original size:41 final size:41
Alignment explanation
Indices: 4641--4721 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
4631 AGAAGAAAGT
4641 TGCCCTCCCATGCTCTTCATTTACAGTAATATACCCTGAAG
1 TGCCCTCCCATGCTCTTCATTTACAGTAATATACCCTGAAG
4682 TGCCCTCCCATGCTCTTCATTTACAGTAATATACCCTGAA
1 TGCCCTCCCATGCTCTTCATTTACAGTAATATACCCTGAA
4722 AACTGTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.32
Consensus pattern (41 bp):
TGCCCTCCCATGCTCTTCATTTACAGTAATATACCCTGAAG
Found at i:17955 original size:2 final size:2
Alignment explanation
Indices: 17948--17978 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17938 CAGATCACAA
17948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17979 GGTCTTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19609 original size:2 final size:2
Alignment explanation
Indices: 19602--19628 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19592 ACAATTAACT
19602 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19629 GTTTTCTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22610 original size:15 final size:14
Alignment explanation
Indices: 22560--22651 Score: 56
Period size: 11 Copynumber: 7.0 Consensus size: 14
22550 TATGATTAGC
*
22560 TTTAATTAGTTAAT
1 TTTAATTAGTTTAT
** * *
22574 TAAAATTA-CTTAG
1 TTTAATTAGTTTAT
22587 TTT-ATTAGTTTAT
1 TTTAATTAGTTTAT
22600 GTTTAATTAG--TA-
1 -TTTAATTAGTTTAT
*
22612 TCTAATTAGTTTAT
1 TTTAATTAGTTTAT
22626 TATTAATTAG--TA-
1 T-TTAATTAGTTTAT
22638 TTTAATTAGTTTAT
1 TTTAATTAGTTTAT
22652 GATTAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.25
14 10 0.18
15 12 0.21
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (14 bp):
TTTAATTAGTTTAT
Found at i:22619 original size:26 final size:26
Alignment explanation
Indices: 22590--22657 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
22580 TACTTAGTTT
22590 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
22616 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
22642 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
22658 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:22718 original size:25 final size:24
Alignment explanation
Indices: 22666--22725 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
22656 AAAATGAAGG
*
22666 AAAATGAA-TTCGAAGATTTGTTA
1 AAAATGAAGTTCGAAGAGTTGTTA
*
22689 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTCGAAG-AGTTGTTA
* *
22714 GAAATTAAGTTC
1 AAAATGAAGTTC
22726 AGGGTTTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 8 0.27
24 6 0.20
25 16 0.53
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.33
Consensus pattern (24 bp):
AAAATGAAGTTCGAAGAGTTGTTA
Found at i:22841 original size:21 final size:21
Alignment explanation
Indices: 22796--22842 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
22786 CAAAAATGTA
* **
22796 AAAAGGGGGGCGATATTTAGC
1 AAAAGGAGGGCGATAAATAGC
*
22817 AAAAGGAGGGCGATAAATAGT
1 AAAAGGAGGGCGATAAATAGC
22838 AAAAG
1 AAAAG
22843 AAAAGGACAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.34, T:0.15
Consensus pattern (21 bp):
AAAAGGAGGGCGATAAATAGC
Found at i:25208 original size:116 final size:113
Alignment explanation
Indices: 24958--25188 Score: 266
Period size: 116 Copynumber: 2.0 Consensus size: 113
24948 AAACTTTTTG
* *
24958 GGAAGATATCATCCA-TAAAAAAACTTCAAAGTCTCCCTTTTAATTTTATGCTCTGTTAATGCAG
1 GGAAGAAATCATCCAGAAAAAAAACTTCAAAGTCTCCCTTTTAATTTTATGCTCTGTTAATGCAG
* * ** *** ** *
25022 AAAGAGTAATTATAACCCTAAAATCACCGTATATGCCAAATTTTTTTG
66 AAAGAGTAATTATAACCCTAAAATCACAGTAAACCCCAAAAAGTACTA
* * *
25070 GGAAGATATCATCCATAAAAAAAGCTTCAAAGTCTCCCCGTTTTAATTTTATGCTCTGTTAAATG
1 GGAAGAAATCATCCAGAAAAAAAACTTCAAAGTCT-CCC-TTTTAATTTTATGCTCTGTT-AATG
*
25135 CAGAAAGAGTAATTATAACCCTAAAATCAATAGATAAACCCCAAAAAGTACTA
63 CAGAAAGAGTAATTATAACCCTAAAATC-ACAG-TAAACCCCAAAAAGTACTA
25188 G
1 G
25189 TAAAAATGAT
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
112 15 0.15
113 17 0.17
114 3 0.03
115 20 0.20
116 32 0.32
117 2 0.02
118 11 0.11
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (113 bp):
GGAAGAAATCATCCAGAAAAAAAACTTCAAAGTCTCCCTTTTAATTTTATGCTCTGTTAATGCAG
AAAGAGTAATTATAACCCTAAAATCACAGTAAACCCCAAAAAGTACTA
Found at i:30723 original size:81 final size:81
Alignment explanation
Indices: 30588--30746 Score: 291
Period size: 81 Copynumber: 2.0 Consensus size: 81
30578 TATCCCATGC
*
30588 CATCTAGTATCCAGGATTTGACCCTGACTAATCCGGATCTGACCCGCGTCGCGCACCTGGTTATA
1 CATCTAGTATCCAGGATTTGACCCTGACTAATCCGGATCCGACCCGCGTCGCGCACCTGGTTATA
30653 GTGGGTGAGTCTCGGG
66 GTGGGTGAGTCTCGGG
* *
30669 CATCTAGTATCCAGGGTTTGACCCTGACTAATCCGGATCCGACCCGCGTCGCGCACCTGGTTATG
1 CATCTAGTATCCAGGATTTGACCCTGACTAATCCGGATCCGACCCGCGTCGCGCACCTGGTTATA
30734 GTGGGTGAGTCTC
66 GTGGGTGAGTCTC
30747 TCCCAAGGGG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (81 bp):
CATCTAGTATCCAGGATTTGACCCTGACTAATCCGGATCCGACCCGCGTCGCGCACCTGGTTATA
GTGGGTGAGTCTCGGG
Found at i:34135 original size:10 final size:10
Alignment explanation
Indices: 34120--34153 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
34110 TATAAATAAA
34120 TTTTTTTCA-
1 TTTTTTTCAT
34129 TTTTTTTCAAT
1 TTTTTTTC-AT
34140 TTTTTTTCAT
1 TTTTTTTCAT
34150 TTTT
1 TTTT
34154 CTGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.35
10 7 0.30
11 8 0.35
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:34459 original size:16 final size:16
Alignment explanation
Indices: 34434--34468 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34424 TCCCTCACCC
34434 AAATTTTTTTTAA-AA
1 AAATTTTTTTTAATAA
34449 AAATATTTTTTTAATAA
1 AAAT-TTTTTTTAATAA
34466 AAA
1 AAA
34469 AAAATGACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 9 0.50
17 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATTTTTTTTAATAA
Found at i:34466 original size:19 final size:17
Alignment explanation
Indices: 34436--34470 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
34426 CCTCACCCAA
34436 ATTTTTTTTAAAAAAAT
1 ATTTTTTTTAAAAAAAT
34453 ATTTTTTTAATAAAAAAA
1 ATTTTTTT--TAAAAAAA
34471 AATGACGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTTTTTTAAAAAAAT
Found at i:38659 original size:31 final size:30
Alignment explanation
Indices: 38573--38670 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
38563 TAAGTTGGGA
38573 CTCTCCCTTGGTGCGCGGCACTGGGGGAGT
1 CTCTCCCTTGGTGCGCGGCACTGGGGGAGT
* *
38603 CTCTCCCTTGGCGCGCAGCACTGGGGGAGT
1 CTCTCCCTTGGTGCGCGGCACTGGGGGAGT
*
38633 CTCTCCCCTGGTGCGCGGACACTGGGGGAGT
1 CTCTCCCTTGGTGCGCGG-CACTGGGGGAGT
38664 CTC-CCCT
1 CTCTCCCT
38671 GATGCGTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 46 0.75
31 15 0.25
ACGTcount: A:0.08, C:0.35, G:0.36, T:0.21
Consensus pattern (30 bp):
CTCTCCCTTGGTGCGCGGCACTGGGGGAGT
Found at i:41298 original size:26 final size:25
Alignment explanation
Indices: 41269--41335 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
41259 TGCACATCAA
* * *
41269 GGGGAGTCTCCCCTGGTGCGCTGTT
1 GGGGAGCCTCCCCTGGTACGCTGCT
*
41294 GGGGGAGCCTCCCTTGGTACGCTGCT
1 -GGGGAGCCTCCCCTGGTACGCTGCT
*
41320 AGGGAGCCTCCCCTGG
1 GGGGAGCCTCCCCTGG
41336 CGCGTATCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
25 14 0.40
26 21 0.60
ACGTcount: A:0.07, C:0.31, G:0.39, T:0.22
Consensus pattern (25 bp):
GGGGAGCCTCCCCTGGTACGCTGCT
Found at i:44177 original size:16 final size:16
Alignment explanation
Indices: 44157--44244 Score: 74
Period size: 16 Copynumber: 5.6 Consensus size: 16
44147 GAAGAGTGTG
*
44157 GGTGAGTATCTCACCG
1 GGTGAGTATCTCACCA
44173 GGTGAGTAT-TGCACCA
1 GGTGAGTATCT-CACCA
*
44189 GGTGAGTA-CTTACCA
1 GGTGAGTATCTCACCA
*
44204 GGTGAGTATTTGCACCA
1 GGTGAGTATCT-CACCA
** * *
44221 AATGAGTAT-TTACTA
1 GGTGAGTATCTCACCA
44236 GGTGAGTAT
1 GGTGAGTAT
44245 TTGTATTGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
15 23 0.40
16 24 0.41
17 11 0.19
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (16 bp):
GGTGAGTATCTCACCA
Found at i:44217 original size:32 final size:32
Alignment explanation
Indices: 44157--44247 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
44147 GAAGAGTGTG
* *
44157 GGTGAGTATCTCACCGGGTGAGTA-TTGCACCA
1 GGTGAGTA-CTTACCAGGTGAGTATTTGCACCA
44189 GGTGAGTACTTACCAGGTGAGTATTTGCACCA
1 GGTGAGTACTTACCAGGTGAGTATTTGCACCA
** * *
44221 AATGAGTATTTACTAGGTGAGTATTTG
1 GGTGAGTACTTACCAGGTGAGTATTTG
44248 TATTGGGTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.25
32 39 0.75
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (32 bp):
GGTGAGTACTTACCAGGTGAGTATTTGCACCA
Found at i:44244 original size:15 final size:15
Alignment explanation
Indices: 44157--44246 Score: 81
Period size: 15 Copynumber: 5.7 Consensus size: 15
44147 GAAGAGTGTG
* *
44157 GGTGAGTATCTCACCG
1 GGTGAGTAT-TTACCA
*
44173 GGTGAGTATTGCACCA
1 GGTGAGTATT-TACCA
*
44189 GGTGAGTACTTACCA
1 GGTGAGTATTTACCA
44204 GGTGAGTATTTGCACCA
1 GGTGAGTATTT--ACCA
** *
44221 AATGAGTATTTACTA
1 GGTGAGTATTTACCA
44236 GGTGAGTATTT
1 GGTGAGTATTT
44247 GTATTGGGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
15 27 0.44
16 22 0.35
17 13 0.21
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (15 bp):
GGTGAGTATTTACCA
Found at i:44370 original size:2 final size:2
Alignment explanation
Indices: 44363--44393 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44353 CATACATTAT
44363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44394 GCGTTGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44896 original size:1 final size:1
Alignment explanation
Indices: 44890--44921 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
44880 TTCAAAATGG
44890 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44922 CTGGAAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:47344 original size:31 final size:30
Alignment explanation
Indices: 47306--47471 Score: 144
Period size: 31 Copynumber: 5.5 Consensus size: 30
47296 TTTGGCTAAT
47306 TGCTCAAATAAGGGCCTAACGTTTGTAAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGT-AAAA
* **
47337 TGCTCAAATAAGGGCCTGATC-TTT-TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGTAAAA
*
47366 TGGTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGT-AAAA
* * **
47397 TGCTCAAATAAGGGCCCCATC-TTTG-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGTAAAA
* *
47426 TGGC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTG-TAAAA
*
47457 TACTCAAATAAGGGC
1 TGCTCAAATAAGGGC
47472 ATGTCTCACG
Statistics
Matches: 106, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
28 5 0.05
29 38 0.36
30 5 0.05
31 52 0.49
32 6 0.06
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTGTAAAA
Found at i:47382 original size:29 final size:28
Alignment explanation
Indices: 47340--47439 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
47330 GTAAAAATGC
47340 TCAAATAAGGGCCTGATCTTTTAATTTGG
1 TCAAATAAGGGCCT-ATCTTTTAATTTGG
* ** *
47369 TCAAATAAGGGCCTAACGTTTGTCAAAATGC
1 TCAAATAAGGGCCTATC-TTT-T-AATTTGG
* *
47400 TCAAATAAGGGCCCCATCTTTGAATTTGG
1 TCAAATAAGGG-CCTATCTTTTAATTTGG
*
47429 CCAAATAAGGG
1 TCAAATAAGGG
47440 TCTAACGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
28 2 0.04
29 31 0.55
30 1 0.02
31 18 0.32
32 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (28 bp):
TCAAATAAGGGCCTATCTTTTAATTTGG
Found at i:47402 original size:60 final size:60
Alignment explanation
Indices: 47309--47471 Score: 254
Period size: 60 Copynumber: 2.7 Consensus size: 60
47299 GGCTAATTGC
* ** *
47309 TCAAATAAGGGCCTAACGTTTGTAAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGG
47369 TCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGG
1 TCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGG
* * * *
47429 CCAAATAAGGGTCTAACGTTTGCCAAAATACTCAAATAAGGGC
1 TCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGC
47472 ATGTCTCACG
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGG
Found at i:47539 original size:31 final size:30
Alignment explanation
Indices: 47501--47699 Score: 131
Period size: 31 Copynumber: 6.6 Consensus size: 30
47491 AACTAAAACC
47501 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
*
47532 AGGCCCTTATTTGAGCATTTTCGATAACATT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
* ** * *
47563 GGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGAAACG-TT
* * ** *
47592 GGGCTCTTATTTGAGCATTTTTTATAACATT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
** *
47623 AGGCCCTTATTT-AGCCAAATTC-AAA-GATG
1 AGGCCCTTATTTGAG-CATTTTCGAAACG-TT
* *
47652 AGGCCCTTATTTGAACATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTCG-AAACGTT
*
47683 AGACCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
47700 ATTAGCCGTA
Statistics
Matches: 129, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
28 2 0.02
29 37 0.29
30 6 0.05
31 81 0.63
32 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTCGAAACGTT
Found at i:47608 original size:60 final size:60
Alignment explanation
Indices: 47532--47694 Score: 204
Period size: 60 Copynumber: 2.7 Consensus size: 60
47522 CGATAACGTT
* *
47532 AGGCCCTTATTTGAGCATTTTCGATAACATTGGGCCCTTATTTGGCCAAATTAAAAGATCG
1 AGGCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTAGCCAAATTAAAAGAT-G
* ** *
47593 -GGCTCTTATTTGAGCATTTTTTATAACATTAGGCCCTTATTTAGCCAAATTCAAAGATG
1 AGGCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTAGCCAAATTAAAAGATG
* * * *
47652 AGGCCCTTATTTGAACATTTTGGCA-AACGTTAGACCCTTATTT
1 AGGCCCTTATTTGAGCATTTTCG-ATAACATTAGGCCCTTATTT
47695 GAGCAATTAG
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 1 0.01
60 86 0.98
61 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (60 bp):
AGGCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTAGCCAAATTAAAAGATG
Found at i:48551 original size:29 final size:30
Alignment explanation
Indices: 48518--48587 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
48508 CGTTTAGACG
48518 TTTTGTCCCCC-GAACTTT-AATCTT-GGACA
1 TTTTG-CCCCCTGAA-TTTCAATCTTGGGACA
* *
48547 TTTTGCCCCCTGAATTTCAATTTTGGGACG
1 TTTTGCCCCCTGAATTTCAATCTTGGGACA
48577 TTTTGCCCCCT
1 TTTTGCCCCCT
48588 CAACCTAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 8 0.22
29 13 0.36
30 15 0.42
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.40
Consensus pattern (30 bp):
TTTTGCCCCCTGAATTTCAATCTTGGGACA
Found at i:48583 original size:30 final size:29
Alignment explanation
Indices: 48514--48587 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
48504 GTAGCGTTTA
48514 GACGTTTTGTCCCCC-GAACTTTAATCTTG
1 GACGTTTTG-CCCCCTGAACTTTAATCTTG
* *
48543 GACATTTTGCCCCCTGAA-TTTCAATTTTGG
1 GACGTTTTGCCCCCTGAACTTT-AATCTT-G
48573 GACGTTTTGCCCCCT
1 GACGTTTTGCCCCCT
48588 CAACCTAACG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.21
29 16 0.41
30 15 0.38
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.38
Consensus pattern (29 bp):
GACGTTTTGCCCCCTGAACTTTAATCTTG
Found at i:48811 original size:29 final size:29
Alignment explanation
Indices: 48757--48828 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
48747 TTAGGTTGTG
*
48757 GGGGCAAAACGTCCCAAAATTGAAGTTCA
1 GGGGCAAAACGTCCCAAAATTAAAGTTCA
* *
48786 GTGGGCAAAATGT-CCAAGATTAAAGTTCA
1 G-GGGCAAAACGTCCCAAAATTAAAGTTCA
48815 GGGAGCAAAACGTC
1 GGG-GCAAAACGTC
48829 TAAACGCTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.06
29 24 0.67
30 10 0.28
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (29 bp):
GGGGCAAAACGTCCCAAAATTAAAGTTCA
Found at i:50785 original size:12 final size:12
Alignment explanation
Indices: 50768--50800 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
50758 TCATCATGGA
50768 TCAGAGTTACAT
1 TCAGAGTTACAT
50780 TCAGAGTTACAT
1 TCAGAGTTACAT
*
50792 ACAGAGTTA
1 TCAGAGTTA
50801 TATTAGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (12 bp):
TCAGAGTTACAT
Found at i:51351 original size:24 final size:24
Alignment explanation
Indices: 51318--51367 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
51308 TCGTAGCCTT
51318 CTTAAGCTTAGGAAGATTACGAAG
1 CTTAAGCTTAGGAAGATTACGAAG
*
51342 CTTAATCTTAGGAAGATTACGAAG
1 CTTAAGCTTAGGAAGATTACGAAG
51366 CT
1 CT
51368 CATTTTGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (24 bp):
CTTAAGCTTAGGAAGATTACGAAG
Found at i:52982 original size:29 final size:30
Alignment explanation
Indices: 52943--53023 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
52933 TCTCGTTTTC
52943 AAAAGTTAATGGGGCAATTTGTCCCAAAA-
1 AAAAGTTAATGGGGCAATTTGTCCCAAAAG
* *
52972 AAAAGTTAATGGGCCAATTTATCCCAAAATG
1 AAAAGTTAATGGGGCAATTTGTCCCAAAA-G
*
53003 AATAGTTAA-GGGGCTAATTTG
1 AAAAGTTAATGGGGC-AATTTG
53024 GGTATTAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 27 0.61
30 4 0.09
31 13 0.30
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (30 bp):
AAAAGTTAATGGGGCAATTTGTCCCAAAAG
Found at i:54555 original size:63 final size:63
Alignment explanation
Indices: 54456--54581 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
54446 TTTCCTTGCA
54456 CTGACAGTCACCTTTGCTTCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG
1 CTGACAGTCACCTTTGCTTCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG
* *
54519 CTGACATTCACTTTTGCTTCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG
1 CTGACAGTCACCTTTGCTTCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG
54582 GATGAATTTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.43
Consensus pattern (63 bp):
CTGACAGTCACCTTTGCTTCAGTTTCATCTTTCTGTTGAGGTTGATCATTTACCGGAACTTTG
Found at i:64074 original size:2 final size:2
Alignment explanation
Indices: 64067--64097 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
64057 ATACTCTTCA
*
64067 CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
64098 ATGATTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Done.