Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001689.1 Kokia drynarioides strain JFW-HI SEQ_113365, 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: 86512
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 206 characters in sequence are not A, C, G, or T
Found at i:1131 original size:3 final size:3
Alignment explanation
Indices: 1125--1151 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1115 ACCCTCCTCC
1125 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1152 ATATGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1870 original size:27 final size:27
Alignment explanation
Indices: 1822--1873 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1812 GTTTAACTTT
* *
1822 TTTTTTAATTAATTACATAAATAATCA
1 TTTTTTAATTAAATACACAAATAATCA
*
1849 TTTTTTAATTAAATACGCAAATAAT
1 TTTTTTAATTAAATACACAAATAAT
1874 TTAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (27 bp):
TTTTTTAATTAAATACACAAATAATCA
Found at i:2142 original size:11 final size:11
Alignment explanation
Indices: 2109--2186 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 11
2099 TTTGGTTATT
2109 ATTTATTTTTA
1 ATTTATTTTTA
* *
2120 A--AATTTTAA
1 ATTTATTTTTA
2129 ATTTATTTTTA
1 ATTTATTTTTA
**
2140 ATTTA---AAA
1 ATTTATTTTTA
*
2148 ATATTATTTTAA
1 AT-TTATTTTTA
*
2160 ATTTATTTCTA
1 ATTTATTTTTA
2171 ATTTATTTTTA
1 ATTTATTTTTA
2182 ATTTA
1 ATTTA
2187 AAAATATTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
8 3 0.06
9 10 0.20
11 34 0.67
12 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTATTTTTA
Found at i:3733 original size:8 final size:8
Alignment explanation
Indices: 3720--3746 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3710 ATCTGCCCCA
3720 TCTCCACT
1 TCTCCACT
3728 TCTCCACT
1 TCTCCACT
3736 TCTCCACT
1 TCTCCACT
3744 TCT
1 TCT
3747 TCACCTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.48, G:0.00, T:0.41
Consensus pattern (8 bp):
TCTCCACT
Found at i:8763 original size:27 final size:29
Alignment explanation
Indices: 8731--8785 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
8721 TCTTTAAATA
* *
8731 AAATAAAATA-AAT-TTTAAAATATATAG
1 AAATAAAAAATAATATTAAAAATATATAG
8758 AAATAAAAAATAATATTAAAAATATATA
1 AAATAAAAAATAATATTAAAAATATATA
8786 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 3 0.12
29 12 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (29 bp):
AAATAAAAAATAATATTAAAAATATATAG
Found at i:27064 original size:29 final size:30
Alignment explanation
Indices: 27031--27093 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
27021 AAAAAGAGTG
* *
27031 ATTTTTGGATACCCAG-GGGCAAAATGGTA
1 ATTTTTGGACACCCAGAGGGAAAAATGGTA
* *
27060 A-TTTTGGACACTCTGAGGGAAAAATGGTA
1 ATTTTTGGACACCCAGAGGGAAAAATGGTA
27089 ATTTT
1 ATTTT
27094 GGGAAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 11 0.39
29 14 0.50
30 3 0.11
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (30 bp):
ATTTTTGGACACCCAGAGGGAAAAATGGTA
Found at i:27201 original size:59 final size:59
Alignment explanation
Indices: 27112--27271 Score: 159
Period size: 59 Copynumber: 2.7 Consensus size: 59
27102 TCGGGGTTAA
* *
27112 AAAAATTGAATTTTA-AACA-TTCGGGGGTAAAATGGTAATTTT-GGAAAATATCGA-GATC
1 AAAAATGGAATTTTAGAA-AGTTTGGGGGTAAAATGGTAATTTTAGGAAAA-AT-GAGGATC
* * * * * * *
27170 AAAAATGGAGTTTTTGGAATTTTGGGGGTAAAATGGAAATTTTAGGAAAAATTAGGGTC
1 AAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTAGGAAAAATGAGGATC
*
27229 AAAAATGGAATTTTAGAAAGTTTGGGGGTCAAAAT-ATAATTTT
1 AAAAATGGAATTTTAGAAAGTTTGGGGGT-AAAATGGTAATTTT
27272 TGGATAGTTT
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
58 14 0.17
59 58 0.70
60 11 0.13
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.33
Consensus pattern (59 bp):
AAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTAGGAAAAATGAGGATC
Found at i:27258 original size:30 final size:30
Alignment explanation
Indices: 27112--27262 Score: 98
Period size: 30 Copynumber: 5.1 Consensus size: 30
27102 TCGGGGTTAA
* * *
27112 AAAAATTGAATTTTA-AACATTCGGGGGT-
1 AAAAATGGAATTTTAGAAAATTTGGGGGTC
* * * * *
27140 -AAAATGGTAATTTTGGAAAATATCGAGATC
1 AAAAATGG-AATTTTAGAAAATTTGGGGGTC
* * * *
27170 AAAAATGGAGTTTTTGGAATTTTGGGGGT-
1 AAAAATGGAATTTTAGAAAATTTGGGGGTC
* *
27199 -AAAATGGAAATTTTAGGAAAAATT-AGGGTC
1 AAAAATGG-AATTTTA-GAAAATTTGGGGGTC
*
27229 AAAAATGGAATTTTAGAAAGTTTGGGGGTC
1 AAAAATGGAATTTTAGAAAATTTGGGGGTC
27259 AAAA
1 AAAA
27263 TATAATTTTT
Statistics
Matches: 89, Mismatches: 25, Indels: 16
0.68 0.19 0.12
Matches are distributed among these distances:
27 6 0.07
28 13 0.15
29 22 0.25
30 34 0.38
31 14 0.16
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.30
Consensus pattern (30 bp):
AAAAATGGAATTTTAGAAAATTTGGGGGTC
Found at i:28384 original size:3 final size:3
Alignment explanation
Indices: 28364--28455 Score: 51
Period size: 3 Copynumber: 29.7 Consensus size: 3
28354 TTTTATTAAA
* * * * * *
28364 ATT AAT ATT ATT AAT ATT ATT ATT AAT ATT CATT AATG CTA ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT
* * * *
28411 ATT CA-T ATTT ATT ATT AGT GTT ATT AGT AAT ATT ATT ATT ATT AT
1 ATT -ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28456 CAGTGACGAT
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
2 1 0.02
3 57 0.86
4 8 0.12
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:28436 original size:12 final size:12
Alignment explanation
Indices: 28369--28451 Score: 76
Period size: 12 Copynumber: 6.7 Consensus size: 12
28359 TTAAAATTAA
28369 TATTATTAATAT
1 TATTATTAATAT
28381 TATTATTAATAT
1 TATTATTAATAT
* **
28393 TCATTAATGCTAAT
1 T-ATTATTAAT-AT
*
28407 TATTATTCATATT
1 TATTATTAATA-T
* *
28420 TATTATTAGTGT
1 TATTATTAATAT
*
28432 TATTAGTAATAT
1 TATTATTAATAT
28444 TATTATTA
1 TATTATTA
28452 TTATCAGTGA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
12 31 0.56
13 21 0.38
14 3 0.05
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:29123 original size:6 final size:6
Alignment explanation
Indices: 29112--29187 Score: 77
Period size: 6 Copynumber: 13.0 Consensus size: 6
29102 TTACAATAAT
* * *
29112 TTTAAA TTTAAA TATAAA TTTAAA CTTAAA -TTAAA TTTAAAA TTTAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* *
29160 -CTAAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29188 ATGAGTTGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
5 12 0.21
6 39 0.68
7 6 0.11
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:29131 original size:12 final size:12
Alignment explanation
Indices: 29112--29187 Score: 77
Period size: 11 Copynumber: 6.5 Consensus size: 12
29102 TTACAATAAT
29112 TTTAAATTTAAA
1 TTTAAATTTAAA
*
29124 TATAAATTTAAA
1 TTTAAATTTAAA
*
29136 CTTAAA-TTAAA
1 TTTAAATTTAAA
*
29147 TTTAAAATTTAGA
1 TTT-AAATTTAAA
*
29160 -CTAAATTTAAA
1 TTTAAATTTAAA
*
29171 TTTAAA-ATAAA
1 TTTAAATTTAAA
29182 TTTAAA
1 TTTAAA
29188 ATGAGTTGAG
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
11 25 0.48
12 23 0.44
13 4 0.08
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:29177 original size:24 final size:25
Alignment explanation
Indices: 29113--29178 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 25
29103 TACAATAATT
*
29113 TTAAATTTAAATAT-AAATTTAAAC
1 TTAAATTTAAATTTAAAATTTAAAC
*
29137 TTAAA-TTAAATTTAAAATTTAGAC
1 TTAAATTTAAATTTAAAATTTAAAC
29161 -TAAATTTAAATTTAAAAT
1 TTAAATTTAAATTTAAAAT
29179 AAATTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.29
24 27 0.71
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (25 bp):
TTAAATTTAAATTTAAAATTTAAAC
Found at i:29189 original size:18 final size:17
Alignment explanation
Indices: 29100--29187 Score: 104
Period size: 17 Copynumber: 5.1 Consensus size: 17
29090 ACATTTTATT
* *
29100 ATTTACAATAATTTTAA
1 ATTTAAAATAAATTTAA
29117 ATTTAAATATAAATTTAA
1 ATTTAAA-ATAAATTTAA
* *
29135 ACTTAAATTAAATTTAAA
1 ATTTAAAATAAATTT-AA
* *
29153 ATTTAGACTAAATTTAA
1 ATTTAAAATAAATTTAA
29170 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
29187 A
1 A
29188 ATGAGTTGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
17 31 0.52
18 29 0.48
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:29780 original size:98 final size:98
Alignment explanation
Indices: 29607--30197 Score: 620
Period size: 98 Copynumber: 6.0 Consensus size: 98
29597 TCCTTTTCTG
* * * *
29607 CTTCTGAGGTA-TAAGGTTCGCCAATGCGACTTAAACCTTT-CCTTTTCGTCTTCGTGGTATTGG
1 CTTCTGAGGTACT-GGGTTCGCCATTGCGACTTAAACCTTTCCCTTGT-GTCTTCGTGGTACTGG
* * *
29670 ATCCGTCGTTGCGGCTTAGATCTTTCCTTTCATGT
64 ATCCGCCATTGCGGCTTAGATCTTTCCCTTCATGT
* * * *
29705 CTTTTGAGGTACTGGGTTCGCCATTGTGACTTAAACCTTTCCCTTGTGTCTTTGTGGTACTAGAT
1 CTTCTGAGGTACTGGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGAT
*
29770 CCACCATTGCGGCTTAGATCTTTCCCTTCATGT
66 CCGCCATTGCGGCTTAGATCTTTCCCTTCATGT
* *
29803 CTTCTGAGGTACTGGGTTCGCCATTGCGACTTAAACTTTTCCCTTGTGTCTTCGTGGTGCTGGAT
1 CTTCTGAGGTACTGGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGAT
* *
29868 CCGCCATTGCGGCTTAGATATTTCCCTTAATGT
66 CCGCCATTGCGGCTTAGATCTTTCCCTTCATGT
* ** *
29901 CTTCAGAGGTACTGGGTTTACCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTATTGGAT
1 CTTCTGAGGTACTGGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGAT
* * *
29966 CTGCCGTTGTGGCTTAGATCTTTCCCTTCATGT
66 CCGCCATTGCGGCTTAGATCTTTCCCTTCATGT
* * * * * * * *
29999 C-TCTAAGGTATTGGGTTCGTCATTGCGACTTAAATCTTTCCTTTTATTTCGTT-GTGGTACTAG
1 CTTCTGAGGTACTGGGTTCGCCATTGCGACTTAAACCTTTCC-CTTGTGTC-TTCGTGGTACTGG
* * * *
30062 ATTCGCCATTGCAGCTTAAATCTTTCCC-TCTTGTAT
64 ATCCGCCATTGCGGCTTAGATCTTTCCCTTCATG--T
* * * * * * * * * * *
30098 CTT-TGCGGTACT-AGATCTGCCGTTGCGGCTTAGATCTTTCCCTTTTATATCTTTGCGGTACTG
1 CTTCTGAGGTACTGGGTTC-GCCATTGCGACTTAAACCTTTCCC--TTGTGTCTTCGTGGTACTG
*
30161 GATCCGCCATTGCGGTCTTAGATCTTTCCCGTCATGT
63 GATCCGCCATTGCGG-CTTAGATCTTTCCCTTCATGT
30198 TCCATGGTGT
Statistics
Matches: 412, Mismatches: 68, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
97 37 0.09
98 293 0.71
99 37 0.09
100 28 0.07
101 13 0.03
102 4 0.01
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (98 bp):
CTTCTGAGGTACTGGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGAT
CCGCCATTGCGGCTTAGATCTTTCCCTTCATGT
Found at i:29827 original size:50 final size:50
Alignment explanation
Indices: 29678--30197 Score: 357
Period size: 50 Copynumber: 10.5 Consensus size: 50
29668 GGATCCGTCG
* *
29678 TTGCGGCTTAGATCTTTCCTTTCATGTCTTTTGAGGTACTGGGTTCGCCA
1 TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
* * * * * * * * * *
29728 TTGTGACTTAAACCTTTCCCTT-GTGTCTT-TGTGGTACTAGATCCACCA
1 TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
29776 TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
1 TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
* * * * * * *
29826 TTGCGACTTA-AACTTTTCCCTT-GTGTCTTC-GTGGTGCTGGATCCGCCA
1 TTGCGGCTTAGATC-TTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
* * * **
29874 TTGCGGCTTAGATATTTCCCTTAATGTCTTCAGAGGTACTGGGTTTACCA
1 TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
* * * * * * * *
29924 TTGCGACTTAAACCTTTCCCTT-GTGTCTTC-GTGGTA-TTGGATCTGCCG
1 TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTC-GCCA
* * * *
29972 TTGTGGCTTAGATCTTTCCCTTCATGTC-TCTAAGGTATTGGGTTCGTCA
1 TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
* * * * * * * * *
30021 TTGCGACTTAAATCTTTCCTTTTATTTCGT-TGTGGTACTAGATTCGCCA
1 TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
* * * * * * *
30070 TTGCAGCTTAAATCTTTCCC-TCTTGTATCTT-TGCGGTACT-AGATCTGCCG
1 TTGCGGCTTAGATCTTTCCCTTCATG--TCTTCTGAGGTACTGGGTTC-GCCA
* * * * *
30120 TTGCGGCTTAGATCTTTCCCTTTTATATCTT-TGCGGTACTGGATCCGCCA
1 TTGCGGCTTAGATCTTTCCC-TTCATGTCTTCTGAGGTACTGGGTTCGCCA
*
30170 TTGCGGTCTTAGATCTTTCCCGTCATGT
1 TTGCGG-CTTAGATCTTTCCCTTCATGT
30198 TCCATGGTGT
Statistics
Matches: 355, Mismatches: 97, Indels: 36
0.73 0.20 0.07
Matches are distributed among these distances:
47 4 0.01
48 92 0.26
49 100 0.28
50 142 0.40
51 15 0.04
52 2 0.01
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (50 bp):
TTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGAGGTACTGGGTTCGCCA
Found at i:37196 original size:6 final size:6
Alignment explanation
Indices: 37185--37271 Score: 67
Period size: 6 Copynumber: 15.0 Consensus size: 6
37175 TTACAATAAT
* * *
37185 TTTAAA TTTAAA TATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTTAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
* * *
37233 -CTAAA TTTAAA -ATAAA TTT-AA TCTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
37272 ATGAGTTGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
5 19 0.30
6 37 0.59
7 7 0.11
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:37201 original size:18 final size:18
Alignment explanation
Indices: 37180--37228 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
37170 ATTATTTACA
*
37180 ATAATTTTAAATTTAAAT
1 ATAAATTTAAATTTAAAT
*
37198 ATAAATTTAAACTTAAAT
1 ATAAATTTAAATTTAAAT
37216 -TAAATTTAAATTT
1 ATAAATTTAAATTT
37229 TAGACTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAAATTTAAATTTAAAT
Found at i:37225 original size:23 final size:24
Alignment explanation
Indices: 37186--37260 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 24
37176 TACAATAATT
37186 TTAAATTTAAATATAAATTTAAAC
1 TTAAATTTAAATATAAATTTAAAC
* *
37210 TTAAA-TTAAATTTAAATTTTAGAC
1 TTAAATTTAAATATAAA-TTTAAAC
*
37234 -TAAATTTAAA-ATAAATTTAATC
1 TTAAATTTAAATATAAATTTAAAC
37256 TTAAA
1 TTAAA
37261 ATAAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 5 0.12
23 22 0.51
24 16 0.37
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (24 bp):
TTAAATTTAAATATAAATTTAAAC
Found at i:37271 original size:23 final size:22
Alignment explanation
Indices: 37186--37271 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 22
37176 TACAATAATT
37186 TTAAATTTAAATATAAATTTAAAC
1 TTAAA-TTAAATATAAATTT-AAC
*
37210 TTAAATTAAATTTAAATTTTAGAC
1 TTAAATTAAATATAAA-TTTA-AC
37234 -TAAATTTAAA-ATAAATTTAATC
1 TTAAA-TTAAATATAAATTTAA-C
* *
37256 TTAAAATAAATTTAAA
1 TTAAATTAAATATAAA
37272 ATGAGTTGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.02
22 9 0.17
23 27 0.52
24 15 0.29
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (22 bp):
TTAAATTAAATATAAATTTAAC
Found at i:38894 original size:13 final size:13
Alignment explanation
Indices: 38876--38902 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38866 CGAGTCACTG
38876 ATCAAATTATATA
1 ATCAAATTATATA
38889 ATCAAATTATATA
1 ATCAAATTATATA
38902 A
1 A
38903 CTTTTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATCAAATTATATA
Found at i:42110 original size:18 final size:17
Alignment explanation
Indices: 42089--42133 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
42079 AATTTTGGAT
42089 TTTAAATTTATTCATAAA
1 TTTAAATTTATT-ATAAA
* *
42107 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTATAAA
42124 TTTAAATTTA
1 TTTAAATTTA
42134 AATTTGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTATAAA
Found at i:42112 original size:6 final size:6
Alignment explanation
Indices: 42103--42198 Score: 63
Period size: 6 Copynumber: 15.5 Consensus size: 6
42093 AATTTATTCA
** **
42103 TAAATT TAAATT T-GTTT TAAATT TAAATT TAAATT T-GTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
42149 TAAATT T-AGTT TAAATT CGGAATGATTT TAAATT TAAATCT TAAATT
1 TAAATT TAAATT TAAATT --TAA--A-TT TAAATT TAAAT-T TAAATT
42196 TAA
1 TAA
42199 GAATTCAGAA
Statistics
Matches: 69, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
5 10 0.14
6 45 0.65
7 7 0.10
8 2 0.03
9 2 0.03
10 1 0.01
11 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:42123 original size:11 final size:11
Alignment explanation
Indices: 42107--42149 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
42097 TATTCATAAA
42107 TTTAAATTTGT
1 TTTAAATTTGT
**
42118 TTTAAATTTAAA
1 TTTAAATTT-GT
42130 TTTAAATTTGT
1 TTTAAATTTGT
42141 TTTAAATTT
1 TTTAAATTT
42150 AAATTTAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTAAATTTGT
Found at i:42125 original size:17 final size:17
Alignment explanation
Indices: 42124--42165 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
42114 TTGTTTTAAA
42124 TTTAAATTTAAATTT-G
1 TTTAAATTTAAATTTAG
42140 TTTTAAATTTAAATTTAG
1 -TTTAAATTTAAATTTAG
42158 TTTAAATT
1 TTTAAATT
42166 CGGAATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTAAATTTAAATTTAG
Found at i:42129 original size:23 final size:23
Alignment explanation
Indices: 42103--42156 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
42093 AATTTATTCA
42103 TAAATTTAAATTTGTTTTAAATT
1 TAAATTTAAATTTGTTTTAAATT
42126 TAAATTTAAATTTGTTTTAAATT
1 TAAATTTAAATTTGTTTTAAATT
42149 TAAATTTA
1 TAAATTTA
42157 GTTTAAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TAAATTTAAATTTGTTTTAAATT
Found at i:43662 original size:30 final size:29
Alignment explanation
Indices: 43571--43817 Score: 143
Period size: 30 Copynumber: 8.4 Consensus size: 29
43561 TTTTTACCCG
*
43571 AACTTCC-AAAAATCTAGACTTTAACCCCAA
1 AACTTCCAAAAAAT-TA-ACTTTGACCCCAA
* * *
43601 AACTT-C-AAAAATTACCATTTTACCCCCA
1 AACTTCCAAAAAATTAAC-TTTGACCCCAA
43629 AACTTCCAAAAATATTAACTTTGACCCCAA
1 AACTTCCAAAAA-ATTAACTTTGACCCCAA
* * **
43659 AACTTCC-AAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAAATTAAC-TTTGACCCCAA
* *
43688 AACTTCCAAAAAATCTCAATTTTGACCTCAA
1 AACTTCCAAAAAAT-T-AACTTTGACCCCAA
* * * *
43719 AACTT-CTAAAAATTACCATTTTACCCTC-G
1 AACTTCCAAAAAATTAAC-TTTGACCC-CAA
* *
43748 AACCTCC-AAAAATTACATTTTTGACCCCAA
1 AACTTCCAAAAAATTA-A-CTTTGACCCCAA
* * *
43778 AAC-TCTAAAAAATT-ACTATTTTACCCCCA
1 AACTTCCAAAAAATTAAC--TTTGACCCCAA
43807 AACTTCCAAAA
1 AACTTCCAAAA
43818 TTCCATTTTT
Statistics
Matches: 167, Mismatches: 32, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
27 1 0.01
28 23 0.14
29 61 0.37
30 63 0.38
31 18 0.11
32 1 0.01
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.28
Consensus pattern (29 bp):
AACTTCCAAAAAATTAACTTTGACCCCAA
Found at i:43696 original size:59 final size:59
Alignment explanation
Indices: 43541--43860 Score: 309
Period size: 59 Copynumber: 5.4 Consensus size: 59
43531 GGAGGTCCCT
* *** * *
43541 AAACTGTCAAAAAATTA-CATTTTTTACCCGAACTTCCAAAAAT-CTAGACTTTAACCCCA
1 AAACT-TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATATTA-ACTTTGACCCCA
*
43600 AAACTT-CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATATTAACTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATATTAACTTTGACCCCA
* *
43658 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAA-ATCTCAATTTTGACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATAT-T-AACTTTGACCCCA
* * * *
43718 AAACTTCTAAAAATTACCATTTTACCCTCGAACCTCC-AAAA-ATTACATTTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATATTA-A-CTTTGACCCCA
* * * * *
43777 AAAC-TCTAAAAAATTACTATTTTACCCCCAAACTTCCAAAATTCCATT---TTTGACCCAA
1 AAACTTC-CAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT--ATTAACTTTGACCCCA
* *
43835 AAACTTTCAAAAATTACCCTTTTACC
1 AAACTTCCAAAAATTACCATTTTACC
43861 TCAGATGTCC
Statistics
Matches: 223, Mismatches: 25, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
57 9 0.04
58 75 0.34
59 88 0.39
60 48 0.22
63 3 0.01
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.30
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATATTAACTTTGACCCCA
Found at i:43832 original size:29 final size:28
Alignment explanation
Indices: 43594--43846 Score: 138
Period size: 29 Copynumber: 8.6 Consensus size: 28
43584 CTAGACTTTA
*
43594 ACCCCAAAACTTCAAAAATTACCA-TTTT
1 ACCCCAAAACTTCCAAAATT-CCATTTTT
* ** * *
43622 ACCCCCAAACTTCCAAAAATATTAACTTTG
1 ACCCCAAAACTTCC-AAAAT-TCCATTTTT
43652 ACCCCAAAACTTCCAAAAATTACCA-TTTT
1 ACCCCAAAACTTCC-AAAATT-CCATTTTT
** * *
43681 ACCCCCGAACTTCCAAAAAATCTCAATTTTG
1 ACCCCAAAACTTCC--AAAAT-TCCATTTTT
* *
43712 ACCTCAAAACTTCTAAAAATTACCA-TTTT
1 ACCCCAAAACTTC-CAAAATT-CCATTTTT
* * *
43741 ACCCTC-GAACCTCCAAAAATTACATTTTT
1 ACCC-CAAAACTTCC-AAAATTCCATTTTT
** *
43770 GACCCCAAAACTCTAAAAAATTAC-TATTTT
1 -ACCCCAAAACT-TCCAAAATTCCAT-TTTT
*
43800 ACCCCCAAACTTCCAAAATTCCATTTTT
1 ACCCCAAAACTTCCAAAATTCCATTTTT
* *
43828 GACCCAAAAACTTTCAAAA
1 -ACCCCAAAACTTCCAAAA
43847 ATTACCCTTT
Statistics
Matches: 172, Mismatches: 35, Indels: 35
0.71 0.14 0.14
Matches are distributed among these distances:
28 26 0.15
29 72 0.42
30 59 0.34
31 15 0.09
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.28
Consensus pattern (28 bp):
ACCCCAAAACTTCCAAAATTCCATTTTT
Found at i:43876 original size:58 final size:60
Alignment explanation
Indices: 43594--43885 Score: 318
Period size: 59 Copynumber: 5.0 Consensus size: 60
43584 CTAGACTTTA
* **
43594 ACCCCAAAAC-TTCAAAAATTACCATTTTACCCCCA-AACTTCCAAAAATAT-TAACTTTG
1 ACCCCAAAACTTTCAAAAATTACCATTTTACCCCCAGAACTTCCAAAAAT-TCCATTTTTG
* * *
43652 ACCCCAAAACTTCCAAAAATTACCATTTTACCCCC-GAACTTCCAAAAAATCTCAATTTTG
1 ACCCCAAAACTTTCAAAAATTACCATTTTACCCCCAGAACTTCCAAAAATTC-CATTTTTG
* * * *
43712 ACCTCAAAAC-TTCTAAAAATTACCATTTTACCCTC-GAACCTCCAAAAATTACATTTTTG
1 ACCCCAAAACTTTC-AAAAATTACCATTTTACCCCCAGAACTTCCAAAAATTCCATTTTTG
* * *
43771 ACCCCAAAACTCTAAAAAATTACTATTTTACCCCCA-AACTTCC-AAAATTCCATTTTTG
1 ACCCCAAAACTTTCAAAAATTACCATTTTACCCCCAGAACTTCCAAAAATTCCATTTTTG
* * * *
43829 ACCCAAAAACTTTCAAAAATTACCCTTTTA-CCTCAG-A-TGTCCAAAAATTCCGTTTTT
1 ACCCCAAAACTTTCAAAAATTACCATTTTACCCCCAGAACT-TCCAAAAATTCCATTTTT
43886 TATCCCGATT
Statistics
Matches: 199, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
56 1 0.01
57 8 0.04
58 63 0.32
59 78 0.39
60 49 0.25
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.30
Consensus pattern (60 bp):
ACCCCAAAACTTTCAAAAATTACCATTTTACCCCCAGAACTTCCAAAAATTCCATTTTTG
Found at i:46189 original size:2 final size:2
Alignment explanation
Indices: 46182--46206 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46172 AAATAATAAT
46182 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 T
46207 TTTATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48830 original size:59 final size:59
Alignment explanation
Indices: 48749--48860 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
48739 TTTTATATAT
48749 AAAAAAAACACTCTCATATTAATATTTGTTATTTTACAAGAAATTTTTAATTATTTAAA
1 AAAAAAAACACTCTCATATTAATATTTGTTATTTTACAAGAAATTTTTAATTATTTAAA
* * * *
48808 AAAAAAAACATTCTCATGTTAATATTTGTTATTTTATAAGAATTTTTTAATTA
1 AAAAAAAACACTCTCATATTAATATTTGTTATTTTACAAGAAATTTTTAATTA
48861 ATTTCTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (59 bp):
AAAAAAAACACTCTCATATTAATATTTGTTATTTTACAAGAAATTTTTAATTATTTAAA
Found at i:54625 original size:30 final size:31
Alignment explanation
Indices: 54589--54659 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
54579 GTTTACATTT
54589 CAGTCACTCAAC-TT-T-GAAAATGTGACAAAA
1 CAGTCACT-AACGTTATCGAAAA-GTGACAAAA
54619 CAGTCACTAACGTTATCGAAAAGTGACAAAA
1 CAGTCACTAACGTTATCGAAAAGTGACAAAA
*
54650 TAGTCACTAA
1 CAGTCACTAA
54660 TTAGCAGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.08
30 10 0.27
31 19 0.51
32 5 0.14
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.23
Consensus pattern (31 bp):
CAGTCACTAACGTTATCGAAAAGTGACAAAA
Found at i:54912 original size:52 final size:52
Alignment explanation
Indices: 54849--54950 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
54839 CCCCCCCCTG
54849 AAGAGCTGCTACAAACAGCAAGCTCACAACCAAAACCACAAAAACAGAACAA
1 AAGAGCTGCTACAAACAGCAAGCTCACAACCAAAACCACAAAAACAGAACAA
* * * * *
54901 AAGAGTTGCTACAGACAGCAAGCTCACAGCCAAAACCACGAATACAGAAC
1 AAGAGCTGCTACAAACAGCAAGCTCACAACCAAAACCACAAAAACAGAAC
54951 CACCGATCTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.49, C:0.28, G:0.15, T:0.08
Consensus pattern (52 bp):
AAGAGCTGCTACAAACAGCAAGCTCACAACCAAAACCACAAAAACAGAACAA
Found at i:61985 original size:17 final size:16
Alignment explanation
Indices: 61963--62012 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 16
61953 GGGAAAATAT
61963 TCGAATCTATACCGTTA
1 TCGAATC-ATACCGTTA
*
61980 TCGAATC-TACC-TTT
1 TCGAATCATACCGTTA
61994 TCG-ATCATACCGTTA
1 TCGAATCATACCGTTA
62009 TCGA
1 TCGA
62013 CACGTGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 3 0.11
14 9 0.32
15 9 0.32
17 7 0.25
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (16 bp):
TCGAATCATACCGTTA
Found at i:62710 original size:2 final size:2
Alignment explanation
Indices: 62703--62733 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62693 TCAAATGTTA
62703 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
62734 AGGTTTTAAT
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:63350 original size:22 final size:23
Alignment explanation
Indices: 63323--63364 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
63313 TAATTCATAA
63323 AAAAAAATGAAA-ATT-TTAAGG
1 AAAAAAATGAAATATTGTTAAGG
63344 AAAAAAATGAAATATTGTTAA
1 AAAAAAATGAAATATTGTTAA
63365 AATAGTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (23 bp):
AAAAAAATGAAATATTGTTAAGG
Found at i:74425 original size:4 final size:4
Alignment explanation
Indices: 74416--74440 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
74406 TGTTAAACTA
74416 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
74441 ATTTACCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:75745 original size:36 final size:36
Alignment explanation
Indices: 75693--75773 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
75683 TATTGTCATT
* *
75693 AGATCGATAGCGCGTCACTTCCAAACACAAAATAAG
1 AGATTGATAGCGCGTCAATTCCAAACACAAAATAAG
*
75729 AGATTGATAGCGCGTCAATTCCAAACATAAAATAAG
1 AGATTGATAGCGCGTCAATTCCAAACACAAAATAAG
75765 AGATTGATA
1 AGATTGATA
75774 ACACAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (36 bp):
AGATTGATAGCGCGTCAATTCCAAACACAAAATAAG
Found at i:75794 original size:21 final size:21
Alignment explanation
Indices: 75752--75794 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
75742 GTCAATTCCA
* * *
75752 AACATAAAATAAGAGATTGAT
1 AACACAAAATAAGAAATCGAT
75773 AACACAAAATAAGAAATCGAT
1 AACACAAAATAAGAAATCGAT
75794 A
1 A
75795 GCGCGTCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (21 bp):
AACACAAAATAAGAAATCGAT
Found at i:75812 original size:57 final size:57
Alignment explanation
Indices: 75716--75825 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
75706 GTCACTTCCA
* * *
75716 AACACAAAATAAGAGATTGATAGCGCGTCAATTCCAAACATAAAATAAGAGATTGAT
1 AACACAAAATAAGAAATCGATAGCGCGTCAATTCCAAACACAAAATAAGAGATTGAT
* * *
75773 AACACAAAATAAGAAATCGATAGCGCGTCCATTCTAAACACAAAATAATAGAT
1 AACACAAAATAAGAAATCGATAGCGCGTCAATTCCAAACACAAAATAAGAGAT
75826 CCATAGGGCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (57 bp):
AACACAAAATAAGAAATCGATAGCGCGTCAATTCCAAACACAAAATAAGAGATTGAT
Found at i:75820 original size:36 final size:36
Alignment explanation
Indices: 75773--75849 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
75763 AGAGATTGAT
* * *
75773 AACACAAAATAAGAAATCGATAGCGCGTCCATTCTA
1 AACACAAAATAAGAAATCCATAGCGCGTCAATTCCA
* * *
75809 AACACAAAATAATAGATCCATAGGGCGTCAATTCCA
1 AACACAAAATAAGAAATCCATAGCGCGTCAATTCCA
75845 AACAC
1 AACAC
75850 TTCTATAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.18
Consensus pattern (36 bp):
AACACAAAATAAGAAATCCATAGCGCGTCAATTCCA
Found at i:77091 original size:23 final size:24
Alignment explanation
Indices: 77045--77092 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
77035 TGCATATTAA
*
77045 AATTTTAATATTTATTAAAAATAG
1 AATTTTAATATCTATTAAAAATAG
* *
77069 AATTTTTATATCTA-TAAATATAG
1 AATTTTAATATCTATTAAAAATAG
77092 A
1 A
77093 TTTCAGACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AATTTTAATATCTATTAAAAATAG
Found at i:85742 original size:29 final size:30
Alignment explanation
Indices: 85707--86111 Score: 278
Period size: 29 Copynumber: 13.7 Consensus size: 30
85697 GTAAAACGGT
* *
85707 AATTTTTGGATGTTTTGGGGTCAAAAATAG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATAG
* *
85737 AATTTTTAGAAG-TTCGGGG-CTAAAAATGG
1 AATTTTTAGAAGTTTTGGGGTC-AAAAATAG
* * *
85766 AATTTTTGGAAATTTTAGGGGTTAAAAAT-G
1 AATTTTTAGAAGTTTT-GGGGTCAAAAATAG
*
85796 AGATTTTTAGAAGTTTGGGGGT-AAAAATAG
1 A-ATTTTTAGAAGTTTTGGGGTCAAAAATAG
* *
85826 AATTTTTAGAAGTTTTAGGGTC-AAAATGG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATAG
* * * * *
85855 GATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATAG
* * * **
85885 GATTTTTTGAAG-TCTGAGGG-CAAAAACGG
1 AATTTTTAGAAGTTTTG-GGGTCAAAAATAG
** * *
85914 AATTTTTAGAAGTTCAGAGGT-AAAAATAA
1 AATTTTTAGAAGTTTTGGGGTCAAAAATAG
* * **
85943 AATTTTTGGAAGTTTCGAGGGT-AAAAACGG
1 AATTTTTAGAAGTTTTG-GGGTCAAAAATAG
* * * *
85973 AATTTTTAAAAG-TTCGAAGGT-AAAAATGG
1 AATTTTTAGAAGTTTTG-GGGTCAAAAATAG
* *
86002 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATAG
* * *
86032 GATTTTTGGAAGTTTTGAGGGT-AAAAACAG
1 AATTTTTAGAAGTTTTG-GGGTCAAAAATAG
*** *
86062 AATTTTTAGAAGTTTCAAAGGT-AAAAATGG
1 AATTTTTAGAAGTTT-TGGGGTCAAAAATAG
86092 AATTTTTAGAAGTTTTGGGG
1 AATTTTTAGAAGTTTTGGGG
86112 GCTTCGAGGG
Statistics
Matches: 300, Mismatches: 59, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.00
29 142 0.47
30 131 0.44
31 26 0.09
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
AATTTTTAGAAGTTTTGGGGTCAAAAATAG
Found at i:85743 original size:30 final size:30
Alignment explanation
Indices: 85707--86111 Score: 325
Period size: 30 Copynumber: 13.7 Consensus size: 30
85697 GTAAAACGGT
* * * *
85707 AATTTTTGGATGTTTTGGGGTCAAAAATAG
1 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
85737 AATTTTTAGAAG-TTCGGGG-CTAAAAATGG
1 AATTTTTAGAAGTTTCGGGGTC-AAAAATGG
* * * *
85766 AATTTTTGGAAATTTTAGGGGTTAAAAAT-G
1 AATTTTTAG-AAGTTTCGGGGTCAAAAATGG
* *
85796 AGATTTTTAGAAGTTTGGGGGT-AAAAATAG
1 A-ATTTTTAGAAGTTTCGGGGTCAAAAATGG
**
85826 AATTTTTAGAAGTTTTAGGGTC-AAAATGG
1 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
* * *
85855 GATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
* * * *
85885 GATTTTTTGAAGTCT-GAGGG-CAAAAACGG
1 AATTTTTAGAAGTTTCG-GGGTCAAAAATGG
* **
85914 AATTTTTAGAAG-TTCAGAGGT-AAAAATAA
1 AATTTTTAGAAGTTTC-GGGGTCAAAAATGG
* *
85943 AATTTTTGGAAGTTTCGAGGGT-AAAAACGG
1 AATTTTTAGAAGTTTCG-GGGTCAAAAATGG
* *
85973 AATTTTTAAAAG-TTCGAAGGT-AAAAATGG
1 AATTTTTAGAAGTTTCG-GGGTCAAAAATGG
86002 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
1 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
* * * **
86032 GATTTTTGGAAGTTTTGAGGGT-AAAAACAG
1 AATTTTTAGAAGTTTCG-GGGTCAAAAATGG
**
86062 AATTTTTAGAAGTTTCAAAGGT-AAAAATGG
1 AATTTTTAGAAGTTTC-GGGGTCAAAAATGG
*
86092 AATTTTTAGAAGTTTTGGGG
1 AATTTTTAGAAGTTTCGGGG
86112 GCTTCGAGGG
Statistics
Matches: 301, Mismatches: 56, Indels: 37
0.76 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 137 0.46
30 139 0.46
31 23 0.08
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
AATTTTTAGAAGTTTCGGGGTCAAAAATGG
Found at i:85770 original size:59 final size:58
Alignment explanation
Indices: 85707--86105 Score: 351
Period size: 59 Copynumber: 6.8 Consensus size: 58
85697 GTAAAACGGT
* * *
85707 AATTTTTGGATGTTTTGGGGTCAAAAATAGAATTTTTAGAAGTTCGGGGCTAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAAGTTCGAGG-TAAAAATGG
* * * * *
85766 AATTTTTGGAAATTTTAGGGGTTAAAAAT-GAGATTTTTAGAAGTTTGGGGGTAAAAATAG
1 AATTTTTGGAAGTTTT-GGGGTCAAAAATGGA-ATTTTTAGAAG-TTCGAGGTAAAAATGG
* * * *
85826 AATTTTTAGAAGTTTTAGGGTC-AAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAAG-TTCGAGGT-AAAAATGG
* * * * **
85885 GATTTTTTGAAG-TCTGAGGG-CAAAAACGGAATTTTTAGAAGTTCAGAGGTAAAAATAA
1 AATTTTTGGAAGTTTTG-GGGTCAAAAATGGAATTTTTAGAAGTTC-GAGGTAAAAATGG
* * *
85943 AATTTTTGGAAGTTTCGAGGGT-AAAAACGGAATTTTTAAAAGTTCGAAGGTAAAAATGG
1 AATTTTTGGAAGTTTTG-GGGTCAAAAATGGAATTTTTAGAAGTTCG-AGGTAAAAATGG
* * * * * **
86002 AATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTTGAGGGTAAAAACAG
1 AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAAG-TTCGA-GGTAAAAATGG
* ***
86062 AATTTTTAGAAGTTTCAAAGGT-AAAAATGGAATTTTTAGAAGTT
1 AATTTTTGGAAGTTT-TGGGGTCAAAAATGGAATTTTTAGAAGTT
86106 TTGGGGGCTT
Statistics
Matches: 282, Mismatches: 43, Indels: 30
0.79 0.12 0.08
Matches are distributed among these distances:
58 49 0.17
59 135 0.48
60 89 0.32
61 9 0.03
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAAGTTCGAGGTAAAAATGG
Done.