Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1298
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: 42122
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:1536 original size:20 final size:21
Alignment explanation
Indices: 1497--1536 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1487 CCCGTCTAGC
*
1497 TCAAGCTCAAATCCAGCTTAT
1 TCAAGCTCAAATCCAACTTAT
*
1518 TCAAGCTC-GATCCAACTTA
1 TCAAGCTCAAATCCAACTTA
1537 CCTGAGCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.28
Consensus pattern (21 bp):
TCAAGCTCAAATCCAACTTAT
Found at i:1595 original size:30 final size:30
Alignment explanation
Indices: 1561--1656 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
1551 AGCTCACTCC
1561 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
1591 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
1621 CAGCTCAACTTTAG-TCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
1650 TAGCTCA
1 TAGCTCA
1657 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:1798 original size:15 final size:14
Alignment explanation
Indices: 1777--1815 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 14
1767 TCGTAACGAA
1777 AAAAAAAAAGGAAATC
1 AAAAAAAAA--AAATC
1793 AAAAAAAAAAAATC
1 AAAAAAAAAAAATC
1807 AAAAAAAAA
1 AAAAAAAAA
1816 TTTTGAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.61
16 9 0.39
ACGTcount: A:0.85, C:0.05, G:0.05, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAAAATC
Found at i:2192 original size:11 final size:11
Alignment explanation
Indices: 2178--2211 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2168 AAAAAATTTG
2178 ATTGAAAAAAA
1 ATTGAAAAAAA
2189 ATTGAAAAAAA
1 ATTGAAAAAAA
*
2200 AGTGAAAAAAA
1 ATTGAAAAAAA
2211 A
1 A
2212 ATCGAGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:3137 original size:5 final size:5
Alignment explanation
Indices: 3127--3169 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
3117 AAGAGAAAAC
3127 AAAGA AAAGA AAAG- AAA-A AAAGA AAAGA AATA-A AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA-AGA AAAGA AAAGA
3170 GAGGCAAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 7 0.21
5 26 0.76
6 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:3150 original size:18 final size:19
Alignment explanation
Indices: 3120--3156 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
3110 TCTTGTAAAG
3120 AGAAAACAAAGAAAAGAAA
1 AGAAAACAAAGAAAAGAAA
3139 AGAAAA-AAAGAAAAGAAA
1 AGAAAACAAAGAAAAGAAA
3157 TAAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (19 bp):
AGAAAACAAAGAAAAGAAA
Found at i:3162 original size:18 final size:17
Alignment explanation
Indices: 3122--3162 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
3112 TTGTAAAGAG
*
3122 AAAACAAAGAAAAGAAA
1 AAAAAAAAGAAAAGAAA
3139 AGAAAAAAAGAAAAGAAA
1 A-AAAAAAAGAAAAGAAA
*
3157 TAAAAA
1 AAAAAA
3163 GAAAAGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGAAAAGAAA
Found at i:3247 original size:11 final size:12
Alignment explanation
Indices: 3215--3245 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3205 TTGAGAGAAC
3215 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3227 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3239 TTGAAAA
1 TTGAAAA
3246 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:5456 original size:30 final size:30
Alignment explanation
Indices: 5422--5518 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
5412 AGCTCACTCC
5422 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
5452 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
5482 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
5512 TAGCTCA
1 TAGCTCA
5519 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:13177 original size:29 final size:29
Alignment explanation
Indices: 13144--13212 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
13134 TAATAATTAG
*
13144 ATATGTCCTAA-TTAGTTTAAGTGTTTTAA
1 ATATGTCCTAATTTA-TTCAAGTGTTTTAA
13173 ATATGTCCTAATTTATTCAAGTGTTTTAA
1 ATATGTCCTAATTTATTCAAGTGTTTTAA
13202 ATATGTCCTAA
1 ATATGTCCTAA
13213 ACTAATACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 35 0.92
30 3 0.08
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (29 bp):
ATATGTCCTAATTTATTCAAGTGTTTTAA
Found at i:15536 original size:20 final size:20
Alignment explanation
Indices: 15513--15559 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
15503 GGGTTAAGAT
*
15513 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
15533 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
15553 TGAGCTG
1 TGAGCTG
15560 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:20852 original size:23 final size:22
Alignment explanation
Indices: 20800--20852 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
20790 TCCACGTCTT
*
20800 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
20822 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
20845 TTTCTTTT
1 TTTCTTTT
20853 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:21452 original size:18 final size:18
Alignment explanation
Indices: 21429--21466 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
21419 GCACCTAGGG
21429 CTGGTTATCCCTATCTTC
1 CTGGTTATCCCTATCTTC
21447 CTGGTTATCCCTATCTTC
1 CTGGTTATCCCTATCTTC
21465 CT
1 CT
21467 TAATTGGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.34, G:0.11, T:0.45
Consensus pattern (18 bp):
CTGGTTATCCCTATCTTC
Found at i:23804 original size:19 final size:18
Alignment explanation
Indices: 23768--23807 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23758 TTTCCACTCG
*
23768 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
23786 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
23805 TTT
1 TTT
23808 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:23939 original size:18 final size:17
Alignment explanation
Indices: 23880--23940 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
23870 GCACTCTTTC
*
23880 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
23899 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
*
23916 TGTTTCTTTTTCAGTTTCT
1 T-TTTCTTTTTCAATTT-T
23935 TTTTCT
1 TTTTCT
23941 CTCGTCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 23 0.64
19 9 0.25
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:24974 original size:24 final size:23
Alignment explanation
Indices: 24920--24997 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
24910 GGATAATTAA
**
24920 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
24943 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
24967 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
24988 GAAATAGTAT
1 GAAATGGTAT
24998 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:24982 original size:21 final size:21
Alignment explanation
Indices: 24956--25022 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
24946 TTGGTATTTG
24956 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
24977 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
24998 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
25021 GG
1 GG
25023 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:29286 original size:17 final size:17
Alignment explanation
Indices: 29261--29315 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
29251 TCTCTTTTCA
*
29261 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
29278 TTCTTTTTTTTTTCATTT
1 TTC-TTTTTTTTTGAATT
* *
29296 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
29313 TTC
1 TTC
29316 GTCTTTTCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:29289 original size:18 final size:18
Alignment explanation
Indices: 29266--29307 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29256 TTTCATTCTC
*
29266 TTTTTTTGAATTTTCTTT
1 TTTTTTTCAATTTTCTTT
*
29284 TTTTTTTCATTTTTCTTT
1 TTTTTTTCAATTTTCTTT
29302 TCTTTT
1 T-TTTT
29308 GTATTTTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTCAATTTTCTTT
Found at i:29313 original size:18 final size:19
Alignment explanation
Indices: 29276--29327 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
29266 TTTTTTTGAA
*
29276 TTTTCTTTT-TTTTTTCAT
1 TTTTCTTTTCTTTTGTCAT
29294 TTTTCTTTTCTTTTGT-AT
1 TTTTCTTTTCTTTTGTCAT
29312 TTTCGTCTTTTCTTTT
1 TTT--TCTTTTCTTTT
29328 TCTCTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 14 0.47
19 5 0.17
20 11 0.37
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTTCTTTTCTTTTGTCAT
Found at i:31537 original size:15 final size:16
Alignment explanation
Indices: 31517--31555 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
31507 CCGTATGCAA
31517 TTTTTTTTTTTCAA-T
1 TTTTTTTTTTTCAACT
*
31532 TTTTTTTTTTTGAACT
1 TTTTTTTTTTTCAACT
31548 TTTTTTTT
1 TTTTTTTT
31556 ACGCACCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTTCAACT
Found at i:31872 original size:24 final size:23
Alignment explanation
Indices: 31818--31895 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
31808 GGATAATTAA
**
31818 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
31841 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
31865 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
31886 GAAATAGTAT
1 GAAATGGTAT
31896 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:31880 original size:21 final size:21
Alignment explanation
Indices: 31854--31920 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
31844 TTGGTATTTG
31854 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
31875 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
31896 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
31919 GG
1 GG
31921 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:33533 original size:14 final size:13
Alignment explanation
Indices: 33514--33563 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
33504 ACTAGCTCTC
33514 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
33527 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAT
33541 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
33554 TTTTTTTTCA
1 TTTTTTTTCA
33564 CAACTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 23 0.64
14 13 0.36
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:33552 original size:27 final size:27
Alignment explanation
Indices: 33514--33566 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
33504 ACTAGCTCTC
33514 TTTTTTTTCAAATTTTTTTTTCACAAT
1 TTTTTTTTCAAATTTTTTTTTCACAAT
33541 TTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTCAAATTTTTTTTTCACAA
33567 CTTGATAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTTTTTCAAATTTTTTTTTCACAAT
Found at i:33622 original size:13 final size:12
Alignment explanation
Indices: 33604--33646 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
33594 TGGAAACTAG
*
33604 TTTTTTTTCGAA
1 TTTTTTTTTGAA
33616 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
33628 TTTTTTTTTGAG
1 TTTTTTTTTGAA
33640 TTTTTTT
1 TTTTTTT
33647 CAAGAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:38619 original size:19 final size:18
Alignment explanation
Indices: 38583--38622 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38573 TTTCCACTCG
*
38583 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
38601 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
38620 TTT
1 TTT
38623 TTTGTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:39687 original size:13 final size:13
Alignment explanation
Indices: 39669--39717 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
39659 AAACTAGCTC
39669 TTTTTTCACAATT
1 TTTTTTCACAATT
39682 TTTTTTCACAATT
1 TTTTTTCACAATT
39695 TTTTTTCA-AATT
1 TTTTTTCACAATT
39707 TTTTTTCACAA
1 TTTTTTCACAA
39718 CTTGATATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.34
13 23 0.66
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTTTCACAATT
Found at i:39706 original size:25 final size:26
Alignment explanation
Indices: 39669--39717 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
39659 AAACTAGCTC
39669 TTTTTTCACAATTTTTTTTCACAATT
1 TTTTTTCACAATTTTTTTTCACAATT
39695 TTTTTTCA-AATTTTTTTTCACAA
1 TTTTTTCACAATTTTTTTTCACAA
39718 CTTGATATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTTCACAATTTTTTTTCACAATT
Found at i:39770 original size:12 final size:12
Alignment explanation
Indices: 39753--39790 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
39743 ATGGAAACCA
39753 AATTTTTTTTTG
1 AATTTTTTTTTG
*
39765 AATTTTTTTTTC
1 AATTTTTTTTTG
39777 AAGTTTTTTTTTG
1 AA-TTTTTTTTTG
39790 A
1 A
39791 GAAACTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.71
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:41144 original size:22 final size:24
Alignment explanation
Indices: 41108--41151 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
41098 TAATGATGTG
*
41108 CAAACTATAACATAATTAAAAACA
1 CAAACTATAACATAACTAAAAACA
41132 CAAACTA-AA-ATAACTAAAAA
1 CAAACTATAACATAACTAAAAA
41152 TTAATGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 2 0.11
24 7 0.37
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (24 bp):
CAAACTATAACATAACTAAAAACA
Done.