Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1723
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: 37269
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Found at i:4757 original size:2 final size:2
Alignment explanation
Indices: 4750--4784 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4740 AAACTCAATC
*
4750 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4785 ACTAAAACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4810 original size:28 final size:28
Alignment explanation
Indices: 4778--4853 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
4768 ATATATGTAT
* *
4778 ATATATAACTAAAACTGAACTT-AATACC
1 ATATATAACTAAAA-TCAAATTGAATACC
* *
4806 GTATATAACCAAAATCAAATTGAATACC
1 ATATATAACTAAAATCAAATTGAATACC
* *
4834 ATATATAACTGAAATAAAAT
1 ATATATAACTAAAATCAAAT
4854 CAAACTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 5 0.13
28 34 0.87
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (28 bp):
ATATATAACTAAAATCAAATTGAATACC
Found at i:7800 original size:118 final size:119
Alignment explanation
Indices: 7586--7820 Score: 347
Period size: 118 Copynumber: 2.0 Consensus size: 119
7576 TTTTAAATGG
*
7586 ACTTAACCTTTTTGTCTTAAACCCATTTTTTTAGTATAAATATTTTTTGTCTAAACTCTCATAAA
1 ACTTAACCTTTTTGTCTTAAACCCATTTTTTTAGTATAAACATTTTTTGTCTAAACTCTCATAAA
* * *
7651 TATCGATAGGCCTTCACGCTTGGACGCATCCAAAATAATTTTAAAAACAAAAGA
66 TATCGATAGGCCTTCAAGCTTGGACGAATCCAAAATAATATTAAAAACAAAAGA
7705 ACTTAACCTTTTTGTC-TACAA-CCATTTTTTTAGTAT-AACA-TTTTTGTCTAAAACT-T-ATT
1 ACTTAACCTTTTTGTCTTA-AACCCATTTTTTTAGTATAAACATTTTTTGTCT-AAACTCTCA-T
7764 ATAATATCGAATAGGCCTTCAAGCTTGGACGAATCCAAAATAATATTAAAAACAAAA
63 A-AATATCG-ATAGGCCTTCAAGCTTGGACGAATCCAAAATAATATTAAAAACAAAA
7821 AAGTCATCAC
Statistics
Matches: 107, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
115 1 0.01
116 12 0.11
117 15 0.14
118 61 0.57
119 18 0.17
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (119 bp):
ACTTAACCTTTTTGTCTTAAACCCATTTTTTTAGTATAAACATTTTTTGTCTAAACTCTCATAAA
TATCGATAGGCCTTCAAGCTTGGACGAATCCAAAATAATATTAAAAACAAAAGA
Found at i:8995 original size:20 final size:16
Alignment explanation
Indices: 8953--9071 Score: 78
Period size: 16 Copynumber: 7.0 Consensus size: 16
8943 TTTTTACCCA
8953 GATGTATCGATACATT
1 GATGTATCGATACATT
8969 GATGTATCGATACATGTAT
1 GATGTATCGATACA--T-T
*
8988 GAATGTATCGATATATT
1 G-ATGTATCGATACATT
* * *** * *
9005 -CTGTCTTTTTACCTA
1 GATGTATCGATACATT
*
9020 GATATATCGATACATT
1 GATGTATCGATACATT
9036 GATGTATCGATACATGTAT
1 GATGTATCGATACA--T-T
9055 GAATGTATCGATACATT
1 G-ATGTATCGATACATT
9072 CTTCAATGTA
Statistics
Matches: 76, Mismatches: 18, Indels: 17
0.68 0.16 0.15
Matches are distributed among these distances:
15 7 0.09
16 34 0.45
17 2 0.03
18 4 0.05
19 4 0.05
20 25 0.33
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (16 bp):
GATGTATCGATACATT
Found at i:9011 original size:67 final size:67
Alignment explanation
Indices: 8903--9073 Score: 315
Period size: 67 Copynumber: 2.6 Consensus size: 67
8893 TTTTAACTAA
*
8903 ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCCAGATGTATCGATACAT
1 ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCCAGATATATCGATACAT
8968 TG
66 TG
*
8970 ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCTAGATATATCGATACAT
1 ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCCAGATATATCGATACAT
9035 TG
66 TG
*
9037 ATGTATCGATACATGTATGAATGTATCGATACATTCT
1 ATGTATCGATACATGTATGAATGTATCGATATATTCT
9074 TCAATGTATT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 101 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (67 bp):
ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCCAGATATATCGATACAT
TG
Found at i:9061 original size:87 final size:83
Alignment explanation
Indices: 8953--9122 Score: 216
Period size: 87 Copynumber: 2.0 Consensus size: 83
8943 TTTTTACCCA
* * *
8953 GATGTATCGATACATTGATGTATCGATACATGT-ATGAATGTATCGATATATTCTGTCTTTTTAC
1 GATGTATCGATACATTGATGTATCGATACAT-TCATCAATGTATCGATACATTCTATCTTTTTAC
*
9017 CTAGATATATCGATACATT
65 CCAGATATATCGATACATT
* *
9036 GATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATTGATACATTCTATCTTTT
1 GATGTATCGATACA--T-TG-ATGTATCGATACATTCATCAATGTATCGATACATTCTATCTTTT
* *
9101 TTCCCAGATGTATCGATACATT
62 TACCCAGATATATCGATACATT
9123 TTTTTAGTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
83 14 0.19
85 1 0.01
86 3 0.04
87 56 0.76
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (83 bp):
GATGTATCGATACATTGATGTATCGATACATTCATCAATGTATCGATACATTCTATCTTTTTACC
CAGATATATCGATACATT
Found at i:9079 original size:20 final size:20
Alignment explanation
Indices: 9037--9093 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
9027 CGATACATTG
* *
9037 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
9057 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
9077 ATGTATTGATACATTCT
1 ATGTATCGATACATTCT
9094 ATCTTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:12636 original size:11 final size:11
Alignment explanation
Indices: 12608--12641 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12598 CAATTTGAAT
* *
12608 TTTATAATATT
1 TTTATATTATA
12619 TTTATATTATA
1 TTTATATTATA
12630 TTTATATTATA
1 TTTATATTATA
12641 T
1 T
12642 AAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTATATTATA
Found at i:15409 original size:28 final size:26
Alignment explanation
Indices: 15354--15406 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
15344 ATAAAATTAT
15354 TATTTTATTTAATATTAATTATAAAA
1 TATTTTATTTAATATTAATTATAAAA
15380 TATTTTAATATTAATATTAA-TATAAAA
1 TATTTT-AT-TTAATATTAATTATAAAA
15407 ATAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.24
27 9 0.36
28 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTTTATTTAATATTAATTATAAAA
Found at i:15416 original size:28 final size:28
Alignment explanation
Indices: 15362--15419 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
15352 ATTATTTTAT
***
15362 TTAATATTAATTATAAAATATTTTAATA
1 TTAATATTAATTATAAAATAAAATAATA
15390 TTAATATTAA-TATAAAAATAAAATAATA
1 TTAATATTAATTAT-AAAATAAAATAATA
15418 TT
1 TT
15420 TTAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TTAATATTAATTATAAAATAAAATAATA
Found at i:16107 original size:51 final size:52
Alignment explanation
Indices: 16031--16169 Score: 181
Period size: 51 Copynumber: 2.7 Consensus size: 52
16021 TTTGGAAAGA
* * *
16031 AAATGTATTGATAAATTTTTCATTGTATCGATACATTCTAG-GTTTTAACCT
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGAGTTTTAACCC
* * *
16082 AAATGTATCAATACATTTTTCATTGTATCGATACATTCTAGATTTTTGACCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGAGTTTTAACCC
* * * *
16134 AAATATATCGATACATTCTTCAATGTATCAATACAT
1 AAATGTATCGATACATTTTTCATTGTATCGATACAT
16170 GTAAGCTATT
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 38 0.50
52 38 0.50
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGAGTTTTAACCC
Found at i:18615 original size:80 final size:80
Alignment explanation
Indices: 18477--18787 Score: 365
Period size: 80 Copynumber: 3.9 Consensus size: 80
18467 TCACCATCGG
* * *
18477 GGATACTTCAACCCCGTCTTTACTTCTAAAA-ACCAAAATTTTCATCTTAGGAGATACTCCAACC
1 GGATACTCCAACCCCATCTTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAACC
* *
18541 CTATCAATTCTGAAG
66 CCATCAATTCTGAAA
*
18556 GGATACTCCAACCCCATCGTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAACC
1 GGATACTCCAACCCCATCTTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAACC
* *
18621 CTATCAATTCCGAAA
66 CCATCAATTCTGAAA
* * *** * * *
18636 GGATACTCCAACCCCGT-TCTTACTTTTAAAACATTGAATTTCTTCGTCTTTGGGGATACTCCAA
1 GGATACTCCAACCCCATCT-TTACTTCTAAAACACCAAAATT-TTCATCTTAGGGGATACTCCAA
**
18700 CCCCATCGTTTCTGAAA
64 CCCCATCAATTCTGAAA
* * * * * * *
18717 GGATACTCCAACTCCATTTTTATTTCCAAAACATCAAAATTTTTATCTCAGGGGATACTCCAACC
1 GGATACTCCAACCCCATCTTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAACC
18782 CCATCA
66 CCATCA
18788 TTTTCGAGTG
Statistics
Matches: 196, Mismatches: 32, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
79 28 0.14
80 103 0.53
81 64 0.33
82 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (80 bp):
GGATACTCCAACCCCATCTTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAACC
CCATCAATTCTGAAA
Found at i:18910 original size:109 final size:109
Alignment explanation
Indices: 18768--19026 Score: 337
Period size: 109 Copynumber: 2.4 Consensus size: 109
18758 TTTATCTCAG
* * * * *
18768 GGGATACTCCAACCCCATCATTTTCGAGTGGATACTCTAACCTCATCAATTCCAAAGA-GATACT
1 GGGATACTCCAACCCCATCATTTCCAAGTGGATACTCCAACCCCACCAATT-CAAAGAGGATACT
18832 TCAACACC-GTTTTTACTTCTAAAACATTGAATTTCTTCATCTCTA
65 TCAAC-CCTGTTTTTACTTCTAAAACATTGAATTTCTTCATCTCTA
* **
18877 GGGATACTCCAACCCCATCGTTTCCAAAG-GGATACTCCAACCCCACCAATTCTGAGAGGATACT
1 GGGATACTCCAACCCCATCATTTCC-AAGTGGATACTCCAACCCCACCAATTCAAAGAGGATACT
*
18941 TCAACCCTGTTTTTACTTTTAAAACATTGAATTTCTTCATCTCTA
65 TCAACCCTGTTTTTACTTCTAAAACATTGAATTTCTTCATCTCTA
* * * * *
18986 -GGATACTCCAACGCCACCATTTTCGAGGGGATACTCCAACC
1 GGGATACTCCAACCCCATCATTTCCAAGTGGATACTCCAACC
19027 TCGATTTTCA
Statistics
Matches: 132, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
107 2 0.02
108 39 0.30
109 89 0.67
110 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (109 bp):
GGGATACTCCAACCCCATCATTTCCAAGTGGATACTCCAACCCCACCAATTCAAAGAGGATACTT
CAACCCTGTTTTTACTTCTAAAACATTGAATTTCTTCATCTCTA
Found at i:25599 original size:2 final size:2
Alignment explanation
Indices: 25592--25618 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25582 ATTATCAATA
25592 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 A
25619 AACACCAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26371 original size:31 final size:31
Alignment explanation
Indices: 26313--26371 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
26303 ACGTTAGTAT
*
26313 TAATTTTTATTTTTAAAAGTTTTAAAATCAA
1 TAATTTTTATTTTTAAAAGTTTAAAAATCAA
26344 TAATATTTT-TTTTT-AAAGATTTAAAAAT
1 TAAT-TTTTATTTTTAAAAG-TTTAAAAAT
26372 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 17 0.68
32 4 0.16
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (31 bp):
TAATTTTTATTTTTAAAAGTTTAAAAATCAA
Found at i:26678 original size:11 final size:11
Alignment explanation
Indices: 26658--26688 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
26648 AGCTTTACCG
26658 TTTTTATTTCTC
1 TTTTT-TTTCTC
26670 TTTTTTTTCTC
1 TTTTTTTTCTC
26681 TTTTTTTT
1 TTTTTTTT
26689 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:27382 original size:20 final size:21
Alignment explanation
Indices: 27346--27386 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
27336 GTATTTAGAT
27346 AATTAAATTAAATTTATTTTAG
1 AATTAAATT-AATTTATTTTAG
27368 AATTAAATT-ATTTATTTTA
1 AATTAAATTAATTTATTTTA
27387 TTAGATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTAAATTAATTTATTTTAG
Found at i:28511 original size:23 final size:23
Alignment explanation
Indices: 28462--28512 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
28452 TGAATTTTTC
*
28462 AAAAATAAATTTAAAAAAATTTG
1 AAAAATAAATTTAAAAAAATATG
28485 AAAAATGAAATTTAAGAAAAA-AT-
1 AAAAAT-AAATTTAA-AAAAATATG
28508 AAAAA
1 AAAAA
28513 GAAGAGGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 11 0.44
24 9 0.36
25 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAAATAAATTTAAAAAAATATG
Found at i:28512 original size:24 final size:23
Alignment explanation
Indices: 28462--28512 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
28452 TGAATTTTTC
* *
28462 AAAAATAAATTTAAAAAAATTTG
1 AAAAATAAATTTAAAAAAATATA
28485 AAAAATGAAATTTAAGAAAAA-ATA
1 AAAAAT-AAATTTAA-AAAAATATA
28509 AAAA
1 AAAA
28513 GAAGAGGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 13 0.54
25 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAAATAAATTTAAAAAAATATA
Found at i:30858 original size:14 final size:14
Alignment explanation
Indices: 30839--30865 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30829 GTTAGCTTGC
30839 TTTTTTTCTCTCTT
1 TTTTTTTCTCTCTT
30853 TTTTTTTCTCTCT
1 TTTTTTTCTCTCT
30866 CTTATGGTTA
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:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTTCTCTCTT
Found at i:30864 original size:16 final size:15
Alignment explanation
Indices: 30839--30868 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30829 GTTAGCTTGC
30839 TTTTTTTCTCTCTTT
1 TTTTTTTCTCTCTTT
30854 TTTTTTCTCTCTCTT
1 TTTTTT-TCTCTCTT
30869 ATGGTTAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTCTCTCTTT
Found at i:30915 original size:19 final size:21
Alignment explanation
Indices: 30891--30935 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
30881 CTTTTTTCTC
30891 TTTTTTC-ATCTTC-TTTTT-A
1 TTTTTTCGAT-TTCATTTTTAA
30910 TTTTTTCGATTTCATTTTTAA
1 TTTTTTCGATTTCATTTTTAA
30931 TTTTT
1 TTTTT
30936 GTTTTTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
21 6 0.26
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTTCGATTTCATTTTTAA
Found at i:33128 original size:15 final size:15
Alignment explanation
Indices: 33110--33147 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
33100 GTTAGCTTGC
33110 TTTTTTTCTCTCTTT
1 TTTTTTTCTCTCTTT
*
33125 TTTTCTTCTCTCTTT
1 TTTTTTTCTCTCTTT
33140 TATTTTTT
1 T-TTTTTT
33148 GATTTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTCTCTTT
Found at i:33173 original size:20 final size:20
Alignment explanation
Indices: 33137--33187 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
33127 TTCTTCTCTC
*
33137 TTTTATTTTTTGATTTCA-T
1 TTTTAATTTTTGATTTCACT
*
33156 TTTTAATTTTTGTTTTTCACTT
1 TTTTAATTTTTG-ATTTCAC-T
33178 TTTTAATTTT
1 TTTTAATTTT
33188 AAAAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 5 0.19
22 11 0.41
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTAATTTTTGATTTCACT
Found at i:34437 original size:13 final size:13
Alignment explanation
Indices: 34419--34448 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34409 CTCGATTTTT
*
34419 TTTTTGATTATTG
1 TTTTTGATTATTA
34432 TTTTTGATTATTA
1 TTTTTGATTATTA
34445 TTTT
1 TTTT
34449 CAGTGCATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (13 bp):
TTTTTGATTATTA
Found at i:34703 original size:19 final size:19
Alignment explanation
Indices: 34679--34717 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
34669 GAGTACAATC
* *
34679 ATTTAAATATATTAAAAAT
1 ATTTAAAAAAATTAAAAAT
34698 ATTTAAAAAAATTAAAAAT
1 ATTTAAAAAAATTAAAAAT
34717 A
1 A
34718 CATATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTAAAAAAATTAAAAAT
Found at i:36473 original size:18 final size:18
Alignment explanation
Indices: 36446--36484 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36436 AAACTATAAG
*
36446 TTTTGTAAAAT-TAATTAT
1 TTTTGGAAAATGTAA-TAT
36464 TTTTGGAAAATGTAATAT
1 TTTTGGAAAATGTAATAT
36482 TTT
1 TTT
36485 CTGTTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (18 bp):
TTTTGGAAAATGTAATAT
Done.