Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000083.1 Hibiscus syriacus cultivar Beakdansim tig00000151_pilon, 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: 92575
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7582 original size:17 final size:17
Alignment explanation
Indices: 7561--7599 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
7551 AACTAACACA
*
7561 AAAATTAGGAAAACTAC
1 AAAATCAGGAAAACTAC
* *
7578 GAAATCAGGACAACTAC
1 AAAATCAGGAAAACTAC
7595 AAAAT
1 AAAAT
7600 GGCAGAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (17 bp):
AAAATCAGGAAAACTAC
Found at i:10580 original size:10 final size:10
Alignment explanation
Indices: 10523--10602 Score: 54
Period size: 10 Copynumber: 7.5 Consensus size: 10
10513 TAATATTTTC
*
10523 GTTGATATAT
1 GTTGAAATAT
*
10533 GCTGAAATAT
1 GTTGAAATAT
10543 GCTATGAAATAT
1 G-T-TGAAATAT
10555 GTT-AAGATATGTT
1 GTTGAA-ATA---T
10568 GTTGAAATAT
1 GTTGAAATAT
*
10578 GTTGAGATAT
1 GTTGAAATAT
* *
10588 GCTGTAATAT
1 GTTGAAATAT
10598 GTTGA
1 GTTGA
10603 GACTATTTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
9 2 0.04
10 33 0.61
11 1 0.02
12 9 0.17
13 7 0.13
14 2 0.04
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.40
Consensus pattern (10 bp):
GTTGAAATAT
Found at i:10598 original size:20 final size:22
Alignment explanation
Indices: 10529--10604 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
10519 TTTCGTTGAT
* * * *
10529 ATATGCTGAAATATGCTATGAA
1 ATATGTTGAGATATGCTGTTAA
* *
10551 ATATGTTAAGATATGTTGTTGAA
1 ATATGTTGAGATATGCTGTT-AA
10574 ATATGTTGAGATATGCTG-T-A
1 ATATGTTGAGATATGCTGTTAA
10594 ATATGTTGAGA
1 ATATGTTGAGA
10605 CTATTTGAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 12 0.27
22 15 0.33
23 18 0.40
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (22 bp):
ATATGTTGAGATATGCTGTTAA
Found at i:15013 original size:2 final size:2
Alignment explanation
Indices: 15000--15033 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
14990 TTTTAAGAAA
15000 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15034 TTTATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15497 original size:12 final size:12
Alignment explanation
Indices: 15470--15507 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
15460 TATGACTAAT
15470 ATAATAA-TAAA
1 ATAATAATTAAA
15481 ATAATAATTAAA
1 ATAATAATTAAA
* *
15493 GTAATAATTTAA
1 ATAATAATTAAA
15505 ATA
1 ATA
15508 TATTGGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
ATAATAATTAAA
Found at i:15600 original size:29 final size:30
Alignment explanation
Indices: 15546--15602 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
15536 ATTAAATTGC
15546 AATAGTGACTAAAACATATAAAATTAAAGT
1 AATAGTGACTAAAACATATAAAATTAAAGT
* *
15576 AATAGT-ATTAAAATATA-AAATATTAAA
1 AATAGTGACTAAAACATATAAA-ATTAAA
15603 ATTAACAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.62
30 6 0.25
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.30
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAGT
Found at i:16430 original size:25 final size:24
Alignment explanation
Indices: 16394--16452 Score: 86
Period size: 22 Copynumber: 2.5 Consensus size: 24
16384 CTTGGTTGTA
*
16394 TCTTGCTGTCGTGGTCTCCTCGGGT
1 TCTTGCTCTCGT-GTCTCCTCGGGT
16419 TCTTGCTCTC--GTCTCCTCGGGT
1 TCTTGCTCTCGTGTCTCCTCGGGT
16441 TCTTGCTCTCGT
1 TCTTGCTCTCGT
16453 CGTTCTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 22 0.71
25 9 0.29
ACGTcount: A:0.00, C:0.32, G:0.25, T:0.42
Consensus pattern (24 bp):
TCTTGCTCTCGTGTCTCCTCGGGT
Found at i:16435 original size:22 final size:22
Alignment explanation
Indices: 16407--16453 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
16397 TGCTGTCGTG
16407 GTCTCCTCGGGTTCTTGCTCTC
1 GTCTCCTCGGGTTCTTGCTCTC
16429 GTCTCCTCGGGTTCTTGCTCTC
1 GTCTCCTCGGGTTCTTGCTCTC
16451 GTC
1 GTC
16454 GTTCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.23, T:0.40
Consensus pattern (22 bp):
GTCTCCTCGGGTTCTTGCTCTC
Found at i:16946 original size:3 final size:3
Alignment explanation
Indices: 16938--17020 Score: 85
Period size: 3 Copynumber: 26.3 Consensus size: 3
16928 TTTATTTATT
* *
16938 TAA TAA TAA AAA TAA AAA TATA TAA TTAA TAA TAA TAA TATA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TAA TA-A TAA -TAA
* **
16987 TAT TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17021 GAAATGAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
3 54 0.82
4 12 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:16966 original size:26 final size:26
Alignment explanation
Indices: 16938--16998 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
16928 TTTATTTATT
16938 TAATAATAAAAATA-AAAA-TATATAAT
1 TAATAATAAAAATATAAAATTA-AT-AT
* *
16964 TAATAATAATAATATATAATTAATAT
1 TAATAATAAAAATATAAAATTAATAT
16990 TAATAATAA
1 TAATAATAA
16999 TAATTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 24 0.77
27 5 0.16
28 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TAATAATAAAAATATAAAATTAATAT
Found at i:16977 original size:20 final size:20
Alignment explanation
Indices: 16948--17018 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
16938 TAATAATAAA
*
16948 AATAAAAATATATAATTAAT
1 AATAATAATATATAATTAAT
16968 AATAATAATATATAATTAAT
1 AATAATAATATATAATTAAT
*
16988 ATTAATAATA-ATAATTTTAAT
1 AATAATAATATATAA--TTAAT
17009 AATAATAATA
1 AATAATAATA
17019 ATGAAATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.09
20 28 0.61
21 14 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAATAATATATAATTAAT
Found at i:17438 original size:74 final size:74
Alignment explanation
Indices: 17302--18138 Score: 1398
Period size: 74 Copynumber: 11.4 Consensus size: 74
17292 GAGGTCTTAT
* * * *
17302 CATCTTGCATTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAATCTCCTGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
17367 TTTTGAAAA
66 TTTTGAAAA
* *
17376 CATCATGCACTGTAGGTCTTACAGATGACCCTAAGGCTTTAAATATCAAAAAGCTCCCGAAGGTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
17441 TTTTGAAAA
66 TTTTGAAAA
*
17450 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAA-ATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
17514 TTTTGAAAA
66 TTTTGAAAA
*
17523 CATAATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGC-
17588 TTTTTGAAAA
65 TTTTTGAAAA
* *
17598 CATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAA-ATCAAAAAGCTCCCAAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
17662 TTTTGAAAA
66 TTTTGAAAA
* * *
17671 CATCATGCACTGCAGGTCTTACAGATGACCATGAGGCTTTAAATATCAAAAAGCTCCCGAAGGTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
*
17736 TTTCTGAAAG
66 TTT-TGAAAA
*
17746 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTT-AA-ATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
17809 TTTTGAAAA
66 TTTTGAAAA
* *
17818 CATCATGCACTGCAGGTCTTATAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
*
17883 TTTTAAAAA
66 TTTTGAAAA
17892 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
17956 TTTTGAAAA
66 TTTTGAAAA
** *
17965 CATCATGCACTACAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
18030 TTTTGAAAA
66 TTTTGAAAA
* *
18039 CATCATGCGCTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCGAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
18103 TTTTGAAAA
66 TTTTGAAAA
*
18112 CATCATGCACTTTAGGTCTTACAGATG
1 CATCATGCACTGTAGGTCTTACAGATG
18139 TGGGAAATAA
Statistics
Matches: 717, Mismatches: 39, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
72 42 0.06
73 270 0.38
74 311 0.43
75 94 0.13
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (74 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
TTTTGAAAA
Found at i:17580 original size:147 final size:147
Alignment explanation
Indices: 17302--18138 Score: 1424
Period size: 147 Copynumber: 5.7 Consensus size: 147
17292 GAGGTCTTAT
* * * *
17302 CATCTTGCATTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAATCTCCTGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCAAAAAGCTCCCGAAGGCT
* *
17367 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTAAGGCTTTAAATATCAAAAAGCTC
65 TTTTGAAAACATCATGCACTGCAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
17432 CCGAAGGTTTTTTGAAAA
130 CCGAAGGTTTTTTGAAAA
*
17450 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
* *
17515 TTTGAAAACATAATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
66 TTTGAAAACATCATGCACTGCAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
17580 CGAAGGCTTTTTTGAAAA
131 CGAAGG-TTTTTTGAAAA
* *
17598 CATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAAATCAAAAAGCTCCCAAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
*
17663 TTTGAAAACATCATGCACTGCAGGTCTTACAGATGACCATGAGGCTTTAAATATCAAAAAGCTCC
66 TTTGAAAACATCATGCACTGCAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
*
17728 CGAAGGTTTTTCTGAAAG
131 CGAAGGTTTTT-TGAAAA
*
17746 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTT-AAATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
*
17810 TTTGAAAACATCATGCACTGCAGGTCTTATAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
66 TTTGAAAACATCATGCACTGCAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
* *
17875 CGAAGGCTTTTTAAAAA
131 CGAAGGTTTTTTGAAAA
17892 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
* *
17957 TTTGAAAACATCATGCACTACAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTTC
66 TTTGAAAACATCATGCACTGCAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
*
18022 CGAAGGCTTTTTGAAAA
131 CGAAGGTTTTTTGAAAA
* *
18039 CATCATGCGCTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCGAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
**
18104 TTTGAAAACATCATGCACTTTAGGTCTTACAGATG
66 TTTGAAAACATCATGCACTGCAGGTCTTACAGATG
18139 TGGGAAATAA
Statistics
Matches: 657, Mismatches: 29, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
146 43 0.07
147 388 0.59
148 226 0.34
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (147 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
TTTGAAAACATCATGCACTGCAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
CGAAGGTTTTTTGAAAA
Found at i:17695 original size:221 final size:221
Alignment explanation
Indices: 17302--18138 Score: 1403
Period size: 221 Copynumber: 3.8 Consensus size: 221
17292 GAGGTCTTAT
* * * *
17302 CATCTTGCATTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAATCTCCTGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
*
17367 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTAAGGCTTTAAATATCAAAAAGCTC
66 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
* *
17432 CCGAAGGTTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAAATCA
131 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAAATCA
17497 AAAAGCTCCCGAAGGCTTTTTGAAAA
196 AAAAGCTCCCGAAGGCTTTTTGAAAA
*
17523 CATAATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGC-
*
17588 TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAA-ATCAAAAAGCT
65 TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCT
* *
17652 CCCAAAGGCTTTTTGAAAACATCATGCACTGCAGGTCTTACAGATGACCATGAGGCTTTAAATAT
130 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAA-AT
* *
17717 CAAAAAGCTCCCGAAGGTTTTTCTGAAAG
194 CAAAAAGCTCCCGAAGGCTTTT-TGAAAA
*
17746 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTT-AA-ATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
* *
17809 TTTTGAAAACATCATGCACTGCAGGTCTTATAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
66 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
* *
17874 CCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCA
131 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAAATCA
17939 AAAAGCTCCCGAAGGCTTTTTGAAAA
196 AAAAGCTCCCGAAGGCTTTTTGAAAA
** *
17965 CATCATGCACTACAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
* *
18030 TTTTGAAAACATCATGCGCTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCGAAAAGCTC
66 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
*
18094 CCGAAGGCTTTTTGAAAACATCATGCACTTTAGGTCTTACAGATG
131 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
18139 TGGGAAATAA
Statistics
Matches: 576, Mismatches: 34, Indels: 13
0.92 0.05 0.02
Matches are distributed among these distances:
219 42 0.07
220 129 0.22
221 286 0.50
222 76 0.13
223 43 0.07
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (221 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAAATCA
AAAAGCTCCCGAAGGCTTTTTGAAAA
Found at i:23146 original size:14 final size:13
Alignment explanation
Indices: 23122--23163 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
23112 TGATTCAATT
23122 TTTTC-TTTTTTC
1 TTTTCTTTTTTTC
23134 TTGTTCTTTTTTTC
1 TT-TTCTTTTTTTC
23148 -TTTCTTTTTTTC
1 TTTTCTTTTTTTC
23160 TTTT
1 TTTT
23164 TTCTCTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 13 0.48
13 7 0.26
14 7 0.26
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:23148 original size:8 final size:8
Alignment explanation
Indices: 23120--23165 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
23110 CTTGATTCAA
23120 TTTTTTC-
1 TTTTTTCT
23127 TTTTTTCT
1 TTTTTTCT
23135 TGTTCTTT-T
1 T-TT-TTTCT
23144 TTTCTTTCT
1 TTT-TTTCT
23153 TTTTTTCT
1 TTTTTTCT
23161 TTTTT
1 TTTTT
23166 CTCTGATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.20
8 17 0.49
9 8 0.23
10 3 0.09
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (8 bp):
TTTTTTCT
Found at i:25665 original size:15 final size:17
Alignment explanation
Indices: 25647--25679 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25637 AAAACAATGT
25647 AATGTA-AAC-GCAAAA
1 AATGTATAACTGCAAAA
25662 AATGTATAACTGCAAAA
1 AATGTATAACTGCAAAA
25679 A
1 A
25680 TAAGAATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (17 bp):
AATGTATAACTGCAAAA
Found at i:27669 original size:5 final size:5
Alignment explanation
Indices: 27659--27686 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27649 TTATTCAGGA
27659 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
27687 TTAAAAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:30820 original size:94 final size:95
Alignment explanation
Indices: 30652--30847 Score: 261
Period size: 94 Copynumber: 2.1 Consensus size: 95
30642 ACTTGAAGAG
* * * *
30652 GTAGTATCGATACCATGGTAAGGGTATTGATACCAGGAATCATCAAATCTAAAATTGGTATCGGT
1 GTAGTATCAATACCATGGTAAGGGTATCGATACCAGGAATCATCAAACCTAAAATTGGTATCGAT
** *
30717 ACCGGAA-GGGGTATCAGTACCATAACATA
66 ACCAAAAGGGGGTATCAGTAACATAACATA
* *
30746 GTAGTATCAATACCATGGTAAGGGTATCGATACTAGGCAA-CATCGAACCTAAAATTGGTATCGA
1 GTAGTATCAATACCATGGTAAGGGTATCGATACCAGG-AATCATCAAACCTAAAATTGGTATCGA
* *
30810 TACCAAAAGGGGGTATCGGTAACATAGCATA
65 TACCAAAAGGGGGTATCAGTAACATAACATA
*
30841 GAAGTAT
1 GTAGTAT
30848 TGGTACCAGG
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 61 0.69
95 27 0.31
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (95 bp):
GTAGTATCAATACCATGGTAAGGGTATCGATACCAGGAATCATCAAACCTAAAATTGGTATCGAT
ACCAAAAGGGGGTATCAGTAACATAACATA
Found at i:30868 original size:95 final size:94
Alignment explanation
Indices: 30654--30875 Score: 232
Period size: 94 Copynumber: 2.4 Consensus size: 94
30644 TTGAAGAGGT
* * * * * * * *
30654 AGTATCGATACCATGGTAAGGGTATTGATACCAGG-AATCATCAAATCTAAAATTGGTATCGGTA
1 AGTATCAATACCAGGGTAAGAGTATCGATACTAGGCAA-CATCGAACCTAAAATTGGTATCGATA
** * *
30718 CCGGAAGGGGTATCAGTACCATAACATAGT
65 CCAAAAGGGGTATCAGTAACATAACATAGA
* *
30748 AGTATCAATACCATGGTAAGGGTATCGATACTAGGCAACATCGAACCTAAAATTGGTATCGATAC
1 AGTATCAATACCAGGGTAAGAGTATCGATACTAGGCAACATCGAACCTAAAATTGGTATCGATAC
* *
30813 CAAAAGGGGGTATCGGTAACATAGCATAGA
66 CAAAA-GGGGTATCAGTAACATAACATAGA
***
30843 AGTATTGGTACCAGGGT-AGTAGTATCGATACTA
1 AGTATCAATACCAGGGTAAG-AGTATCGATACTA
30876 TGGAGCCTGA
Statistics
Matches: 108, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
94 61 0.56
95 47 0.44
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (94 bp):
AGTATCAATACCAGGGTAAGAGTATCGATACTAGGCAACATCGAACCTAAAATTGGTATCGATAC
CAAAAGGGGTATCAGTAACATAACATAGA
Found at i:31271 original size:59 final size:59
Alignment explanation
Indices: 31194--31550 Score: 504
Period size: 59 Copynumber: 6.1 Consensus size: 59
31184 GATTACAAAA
* * ** *
31194 AGGGCACTTCATGTGCTAAAATGTTAAGAAATTCATACTAAGTGCATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
* *
31253 AGGGCATTTTGTGTGCTAACATGAGAA-AGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGA-AATTCATACTAAGTGTATGAATTTCCATAT
*
31312 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
* *
31371 AGGGCACTACGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
* * * *
31430 AGGGCACTACGTGTGCTAACATGGGAAGGAATTCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
* * * *
31489 -GAGGCACCTT-GTGTGCTAAAATGATAACAAATTCATCCTAAGTGTATGAATTTCCATAT
1 AG-GGCA-CTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
31548 AGG
1 AGG
31551 AAATATATAT
Statistics
Matches: 272, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
58 2 0.01
59 267 0.98
60 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:31972 original size:68 final size:68
Alignment explanation
Indices: 31894--32503 Score: 1040
Period size: 68 Copynumber: 9.0 Consensus size: 68
31884 AAAAGATTTA
* * *
31894 AGGCCTAACTGTGCATTTGACAAAAAGGTGTTAATTATGCCAGTTAGATGAAAGGCTGAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
31959 TTG
66 TTG
*
31962 AGGCCTAACTGTGCATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
32027 TTG
66 TTG
* *
32030 AGGCCTAACTGTGCATTTGTCAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
32095 TTG
66 TTG
*
32098 AGGCCTAACTGTGCATTTGACAGAAAGGCGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
32163 TTG
66 TTG
* *
32166 AGGCCTAACTGTGCATTTGACAGCAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
32231 TTG
66 TTG
* * * *
32234 TGGCCTAACTTTGCATTTGACAGAAAGGTGTTAATTATGCTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
32299 TTG
66 TTG
* *
32302 AGGCCTAACTGTGCATTTGACATAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
32367 TTG
66 TTG
* * *
32370 AGGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATACCAGTTACATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
32435 TTG
66 TTG
**
32438 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
32503 T
66 T
32504 GAGTAAAAGA
Statistics
Matches: 509, Mismatches: 33, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 509 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:32690 original size:46 final size:46
Alignment explanation
Indices: 32527--32698 Score: 201
Period size: 45 Copynumber: 3.8 Consensus size: 46
32517 GATGTATAAC
*
32527 AATGTATAATGATGTATAAAAGGCATGAAAGGATGCCATAAATG-A
1 AATGTATAATGATGTATAAAAGGCATGAATGGATGCCATAAATGAA
* * *
32572 AATGTATAACGGTGTATAAAAGACATGAAAT-GATGCCATAAAT-AA
1 AATGTATAATGATGTATAAAAGGCATG-AATGGATGCCATAAATGAA
*
32617 AATGTATAAT-AGTGTATAAAAAGGCATGAATGGTTGCCATAAATGAA
1 AATGTATAATGA-TGTAT-AAAAGGCATGAATGGATGCCATAAATGAA
* * *
32664 AATGCATAATGATGCATTATAA-GCATGAATGGATG
1 AATGTATAATGATGTA-TAAAAGGCATGAATGGATG
32699 TTTTCAACGA
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
45 54 0.50
46 34 0.32
47 17 0.16
48 2 0.02
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (46 bp):
AATGTATAATGATGTATAAAAGGCATGAATGGATGCCATAAATGAA
Found at i:33723 original size:2 final size:2
Alignment explanation
Indices: 33718--33745 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33708 CATTTTTTTA
33718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33746 TTGTTAGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33793 original size:18 final size:19
Alignment explanation
Indices: 33769--33817 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
33759 TAGAAAAATA
33769 ATATATATATAAACACTA-TT
1 ATATATATAT-AACA-TACTT
33789 ATATATA-ATAACATACTT
1 ATATATATATAACATACTT
33807 GATATATATAT
1 -ATATATATAT
33818 TGAACCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 6 0.23
19 9 0.35
20 9 0.35
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATATATATAACATACTT
Found at i:34038 original size:27 final size:27
Alignment explanation
Indices: 34006--34061 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
33996 TAAGTTATGG
34006 AGCCAGAGAAGCAAGCAGCCGTGGAGA
1 AGCCAGAGAAGCAAGCAGCCGTGGAGA
* * *
34033 AGCCAGATAATCAGGCAGCCGTGGAGA
1 AGCCAGAGAAGCAAGCAGCCGTGGAGA
34060 AG
1 AG
34062 GGAAGTTGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.36, T:0.07
Consensus pattern (27 bp):
AGCCAGAGAAGCAAGCAGCCGTGGAGA
Found at i:37619 original size:18 final size:18
Alignment explanation
Indices: 37596--37630 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37586 GAGGTAGGGA
*
37596 CTCTCGGTTTTATGGGGG
1 CTCTCGATTTTATGGGGG
*
37614 CTCTCGATTTTGTGGGG
1 CTCTCGATTTTATGGGG
37631 TTCTCAGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.17, G:0.37, T:0.40
Consensus pattern (18 bp):
CTCTCGATTTTATGGGGG
Found at i:37771 original size:2 final size:2
Alignment explanation
Indices: 37766--37797 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
37756 TAACACCTAG
37766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37798 TCGAACGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42962 original size:14 final size:14
Alignment explanation
Indices: 42939--42976 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
42929 TCTGTCTATA
*
42939 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
42952 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
42967 TGCAGGGATT
1 TGCAGGGATT
42977 ACTTTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:45379 original size:36 final size:35
Alignment explanation
Indices: 45306--45416 Score: 120
Period size: 36 Copynumber: 3.1 Consensus size: 35
45296 TAGAGTCATT
*
45306 TTTTTCTTAAAAATAAATTTTGTCTCGCTTGAG--AA
1 TTTTT-TT-AAAACAAATTTTGTCTCGCTTGAGACAA
*
45341 TTTTTTTAAGAACAAATTTTGTCTCACTTGAGACAA
1 TTTTTTTAA-AACAAATTTTGTCTCGCTTGAGACAA
* * *
45377 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGAC-A
1 TTT-TTTTAAAACAAATTTTGTCTCGCTTGAGACAA
45412 TTTTT
1 TTTTT
45417 CCTTTGAGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
33 2 0.03
34 23 0.35
35 9 0.14
36 27 0.42
37 4 0.06
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (35 bp):
TTTTTTTAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:46395 original size:133 final size:133
Alignment explanation
Indices: 45908--46379 Score: 558
Period size: 133 Copynumber: 3.6 Consensus size: 133
45898 AAACATTATC
* *
45908 CCTAAAGAT-TCCTAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCA
1 CCTAAAGATGGCC-AGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCA
* * * ** * * *
45972 TCACATAGGAGCCGCATAACCCCAAGATAACAAGCCGTCCTCATCGCGTAGGAACCGT-ATATCA
65 TCACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCGTCCTCATCGCGTAAGAACCGTGTTATCA
46036 TCAT
130 TCAT
* * *
46040 CCCTAAAGATGGCCAACCATCCTCATCATGTAGGAACCGTGTCATCCACCGACCAAATCTCCTCA
1 -CCTAAAGATGGCCAGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCA
* * ** *
46105 TCACGTAGAAGCCACGTCACCCTTAGATAACCAGTTGTCCTCATCACGTAAGAACCGTGTTATCA
65 TCACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCGTCCTCATCGCGTAAGAACCGTGTTATCA
46170 TC--
130 TCAT
* * * ** * *
46172 CCTAAAGACGGCCAGTCATCCTCATCACATAGGAATTGTGTCATCCCCCAACCAGATCTCCTCAT
1 CCTAAAGATGGCCAGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCAT
* * * * * *
46237 CACGTAGGAGTCGCGCCAACCTTAGATAACCAGCCATCCTCATCGCATAAGAATCGTGTTATCAT
66 CACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCGTCCTCATCGCGTAAGAACCGTGTTATCAT
46302 CAAT
131 C-AT
* * * * *
46306 CCTAAAGATGGTCAGCC-TCCTCATCGCGTAGAAACCGTGTCATCTACCGACCATATCTCCTCAT
1 CCTAAAGATGGCCAGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCAT
46370 CACGTAGGAG
66 CACGTAGGAG
46380 TTGTGTCATC
Statistics
Matches: 283, Mismatches: 51, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
131 110 0.39
133 150 0.53
134 23 0.08
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.22
Consensus pattern (133 bp):
CCTAAAGATGGCCAGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCAT
CACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCGTCCTCATCGCGTAAGAACCGTGTTATCAT
CAT
Found at i:46415 original size:264 final size:264
Alignment explanation
Indices: 45926--46418 Score: 607
Period size: 264 Copynumber: 1.9 Consensus size: 264
45916 TTCCTAGCCG
* * *
45926 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACATAGGAGCCGCATAA
1 TCCTCATCACATAGGAACCGTGTCATCCACCAACCAGATCTCCTCATCACATAGGAGCCGCACAA
* * *
45991 CCCCAAGATAACAAGCCGTCCTCATCGCGTAGGAACCGTATATCATCATCCCTAAAGATGGCCAA
66 CCCCAAGATAACAAGCCATCCTCATCGCATAAGAACCGTATATCATCATCCCTAAAGATGGCCAA
* *
46056 CCATCCTCATCATGTAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACGTAGAAGCCACG
131 CCATCCTCATCACGTAGAAACCGTGTCATCCACCGACCAAATCTCCTCATCACGTAGAAGCCACG
* ****
46121 TCACCCTTAGATAACCAGTTGTCCTCATCACGTAAGAACCGTGTTATCATCCCTAAAGACGGCCA
196 TCACCCTTAGACAACCACAACTCCTCATCACGTAAGAACCGTGTTATCATCCCTAAAGACGGCCA
46186 GTCA
261 GTCA
** * *
46190 TCCTCATCACATAGGAATTGTGTCATCCCCCAACCAGATCTCCTCATCACGTAGGAGTCGCGC-C
1 TCCTCATCACATAGGAACCGTGTCATCCACCAACCAGATCTCCTCATCACATAGGAG-C-CGCAC
** * * *
46254 AA-CCTTAGATAACCAGCCATCCTCATCGCATAAGAATCGTGTTATCATCAAT-CCTAAAGATGG
64 AACCCCAAGATAACAAGCCATCCTCATCGCATAAGAACCGT-ATATCATC-ATCCCTAAAGATGG
* * * * * * *
46317 TCAGCC-TCCTCATCGCGTAGAAACCGTGTCATCTACCGACCATATCTCCTCATCACGTAGGAGT
127 CCAACCATCCTCATCACGTAGAAACCGTGTCATCCACCGACCAAATCTCCTCATCACGTAGAAGC
*** * * *
46381 TGTGTCATCCTTAGACGACCACAACTCTTCATCACGTA
192 CACGTCACCCTTAGACAACCACAACTCCTCATCACGTA
46419 TGACAGTGTG
Statistics
Matches: 190, Mismatches: 35, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
264 160 0.84
265 25 0.13
266 5 0.03
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (264 bp):
TCCTCATCACATAGGAACCGTGTCATCCACCAACCAGATCTCCTCATCACATAGGAGCCGCACAA
CCCCAAGATAACAAGCCATCCTCATCGCATAAGAACCGTATATCATCATCCCTAAAGATGGCCAA
CCATCCTCATCACGTAGAAACCGTGTCATCCACCGACCAAATCTCCTCATCACGTAGAAGCCACG
TCACCCTTAGACAACCACAACTCCTCATCACGTAAGAACCGTGTTATCATCCCTAAAGACGGCCA
GTCA
Found at i:51650 original size:17 final size:17
Alignment explanation
Indices: 51628--51661 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
51618 CCTTGCATCT
51628 TCAAATAAGC-CGATAGA
1 TCAAATAA-CTCGATAGA
51645 TCAAATAACTCGATAGA
1 TCAAATAACTCGATAGA
51662 ATAGATCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (17 bp):
TCAAATAACTCGATAGA
Found at i:51951 original size:19 final size:20
Alignment explanation
Indices: 51927--51972 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
51917 GTTTATGCCA
51927 ATATTAAT-ATTAGATTAT-T
1 ATATTAATGATT-GATTATAT
*
51946 ATATTAATGATTTATTATAT
1 ATATTAATGATTGATTATAT
51966 ATATTAA
1 ATATTAA
51973 AATAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
ATATTAATGATTGATTATAT
Found at i:52126 original size:19 final size:18
Alignment explanation
Indices: 52082--52130 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
52072 AATTTTTTAT
*
52082 TAAAATAATATT-GAGTA
1 TAAAATAATATTAAAGTA
* *
52099 TATATTAATATTAAATGTA
1 TAAAATAATATTAAA-GTA
52118 TAAAATAATATTA
1 TAAAATAATATTA
52131 TTCATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 10 0.40
18 1 0.04
19 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAAATAATATTAAAGTA
Found at i:52204 original size:16 final size:18
Alignment explanation
Indices: 52175--52207 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
52165 GAAAATTATA
52175 AACAATATTAATTATATT
1 AACAATATTAATTATATT
52193 AACAAT-TT-ATTATAT
1 AACAATATTAATTATAT
52208 ATTATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (18 bp):
AACAATATTAATTATATT
Found at i:57333 original size:60 final size:59
Alignment explanation
Indices: 57266--57403 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
57256 TAAAGTAAAA
* *
57266 AAAATGATCCCTCGATTATAGGATATTACTTTGTTGAGTC-CTTCGACTATTAAAAGTTAC
1 AAAATGATCCCTCGATTATAGAATATTACTTTGTTGAGTCAC-TCGACTA-CAAAAGTTAC
* * * * *
57326 AAAATGATCCCCCGAGTATAGAATGTTGCTTTGTTGAGTCACTCGACTACAAAAGTTAT
1 AAAATGATCCCTCGATTATAGAATATTACTTTGTTGAGTCACTCGACTACAAAAGTTAC
* *
57385 AAAATGGTCACTCGATTAT
1 AAAATGATCCCTCGATTAT
57404 TCATTTTGTT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 23 0.35
60 42 0.64
61 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (59 bp):
AAAATGATCCCTCGATTATAGAATATTACTTTGTTGAGTCACTCGACTACAAAAGTTAC
Found at i:57685 original size:60 final size:60
Alignment explanation
Indices: 57601--57713 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
57591 AACAAATGAA
* * *
57601 TAGTTGGGTGACCATTTTATAACTTTTAATAG-TCGATGGACTCAACAAAGCAAAGTCCTG
1 TAGTTGGGTGACCATTTTACAACTTTTAATAGTTAGA-AGACTCAACAAAGCAAAGTCCTG
*
57661 TAGTTAGGG-GACTATTTTACAACTTTTAATAGTTAGAAGACTCAACAAAGCAA
1 TAGTT-GGGTGACCATTTTACAACTTTTAATAGTTAGAAGACTCAACAAAGCAA
57714 TATCCTATGG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
60 41 0.87
61 6 0.13
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (60 bp):
TAGTTGGGTGACCATTTTACAACTTTTAATAGTTAGAAGACTCAACAAAGCAAAGTCCTG
Found at i:57734 original size:60 final size:60
Alignment explanation
Indices: 57614--57737 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
57604 TTGGGTGACC
* * * * * * *
57614 ATTTTATAACTTTTAATAGTCGATGGACTCAACAAAGCAAAGTCCTGTAGTTAGGGGACT
1 ATTTTACAACTTTTAATAGTAGATAGACTCAACAAAGCAAAGTCCTATAGTCAAGAGACT
*
57674 ATTTTACAACTTTTAATAGTTAGA-AGACTCAACAAAGCAATA-TCCTATGGTCAAGAGACT
1 ATTTTACAACTTTTAATAG-TAGATAGACTCAACAAAGCAA-AGTCCTATAGTCAAGAGACT
57734 ATTT
1 ATTT
57738 GTATACGTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 50 0.93
61 4 0.07
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (60 bp):
ATTTTACAACTTTTAATAGTAGATAGACTCAACAAAGCAAAGTCCTATAGTCAAGAGACT
Found at i:59322 original size:23 final size:22
Alignment explanation
Indices: 59279--59322 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
59269 TTTTTTATTA
* *
59279 TTTTTCTCATTTGTTTTTTTTC
1 TTTTTCTCATTTATTTATTTTC
*
59301 TTTTTCCTCTTTTATTTATTTT
1 TTTTT-CTCATTTATTTATTTT
59323 TCATCTAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTCTCATTTATTTATTTTC
Found at i:62029 original size:95 final size:96
Alignment explanation
Indices: 61862--62105 Score: 330
Period size: 95 Copynumber: 2.5 Consensus size: 96
61852 AGTTGAATCC
* * * *
61862 GCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACTCCCCGTCTATACGGATAAGATTCAGCTAGC
1 GCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCGACTTTATGGATAAGATTCAGCTAGC
*
61927 CTGATAAAGGCGATTATAATATATAATA-AA-
66 CTAATAAAGGCGATTATAATATAT-ATACAAT
* * *
61957 GCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAACTTTATGGATAATATTCAGCTAGC
1 GCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCGACTTTATGGATAAGATTCAGCTAGC
*
62022 CTAATAAAGGTGATTATAATATATATACAAT
66 CTAATAAAGGCGATTATAATATATATACAAT
* * * *
62053 GATATTGAGCTGTCCCTCTAGAGTAATTGGTTAAACGCCCCGGCTTTATGGAT
1 G--CTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCGACTTTATGGAT
62106 TCAGCTAGCC
Statistics
Matches: 131, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
94 3 0.02
95 82 0.63
96 1 0.01
98 45 0.34
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (96 bp):
GCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACGCCCCGACTTTATGGATAAGATTCAGCTAGC
CTAATAAAGGCGATTATAATATATATACAAT
Found at i:63537 original size:125 final size:124
Alignment explanation
Indices: 63363--63733 Score: 472
Period size: 116 Copynumber: 3.0 Consensus size: 124
63353 CAATACAGGC
* * **
63363 TTGGATTTCAACTTCACGATGAATGATATTCAAGCCAAGGCT-ACACTTCACAACGAATGGGCCA
1 TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCA-ACTTCACAACGAATGGGCCA
*
63427 TCCACGGCTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCAAAATAT
65 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATC-AAATAT
* * * * *
63488 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCTAGGATCAACTTCACAACGAACGGGCCAT
1 TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
* * *
63553 CAACGGTTTCAACTTCACGCCGAAGGGAATCGTGCTTACCAGCAACA-T--TC----A-
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCAAATAT
*
63604 TTGGATTTCAACTTCACGACGAATGACATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
* * * *
63669 CCATGGTTTCAACTTCACGACGAAGGGAATCGTGCCCACAAGCAACAATGCCATCCAAATAT
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAAC-AT-TCAT-CAAATAT
63731 TTG
1 TTG
63734 ACTTCCTTAA
Statistics
Matches: 208, Mismatches: 26, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
116 99 0.48
117 2 0.01
121 1 0.00
122 3 0.01
124 1 0.00
125 97 0.47
126 2 0.01
127 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCAAATAT
Found at i:63881 original size:37 final size:36
Alignment explanation
Indices: 63840--63932 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
63830 ACAAGGAGTC
*
63840 GTCTCGCTTGAGACTAATTT-ACTCAAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTTCACTCAAAACAAA-TTTT
* * **
63877 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCACTCAAAACAAATTTT
*
63913 GTCTCTCTTGAGACAGTTTC
1 GTCTCTCTTGAGACAATTTC
63933 CCTTGAAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 28 0.56
37 22 0.44
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (36 bp):
GTCTCTCTTGAGACAATTTCACTCAAAACAAATTTT
Found at i:63920 original size:36 final size:37
Alignment explanation
Indices: 63865--63944 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 37
63855 AATTTACTCA
63865 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
63902 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
63938 AAACAAA
1 AAACAAA
63945 ATCTTTGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 36 0.84
37 7 0.16
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (37 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:64028 original size:37 final size:37
Alignment explanation
Indices: 63978--64107 Score: 158
Period size: 37 Copynumber: 3.6 Consensus size: 37
63968 AACAAATTTC
*
63978 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTT
1 GTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTT
* * * *
64015 GTCTCTCTTGAGACAGTTTC-CTTGAAAC-AAATTTC
1 GTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTT
* *
64050 GTCT-TCCTTGAGATAGTTTCTTTCGGAACTAAGTTTT
1 GTCTCT-CTTGAGACAGTTTCTTTTGGAACTAAGTTTT
*
64087 GTCTCTCTTGAGACAATTTCT
1 GTCTCTCTTGAGACAGTTTCT
64108 CTTGAAAACA
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
34 1 0.01
35 22 0.29
36 11 0.14
37 41 0.54
38 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (37 bp):
GTCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTT
Found at i:64068 original size:35 final size:35
Alignment explanation
Indices: 63960--64114 Score: 134
Period size: 37 Copynumber: 4.3 Consensus size: 35
63950 TGAATATGTG
*
63960 TTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGT
1 TTCCTTGAAACAAATTTCGTCTTCCTTGAGACAGT
* * * *
63995 TTCTTTTGGAACTAAGTTTTGTC-TCTCTTGAGACAGT
1 TTC-CTTGAAAC-AAATTTCGTCTTC-CTTGAGACAGT
*
64032 TTCCTTGAAACAAATTTCGTCTTCCTTGAGATAGT
1 TTCCTTGAAACAAATTTCGTCTTCCTTGAGACAGT
* * * * *
64067 TTCTTTCGGAACTAAGTTTTGTC-TCTCTTGAGACAAT
1 TTCCTT-GAAAC-AAATTTCGTCTTC-CTTGAGACAGT
64104 TTCTCTTGAAA
1 TTC-CTTGAAA
64115 ACAATCTTTG
Statistics
Matches: 94, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
35 26 0.28
36 21 0.22
37 45 0.48
38 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.41
Consensus pattern (35 bp):
TTCCTTGAAACAAATTTCGTCTTCCTTGAGACAGT
Found at i:64078 original size:72 final size:72
Alignment explanation
Indices: 63960--64114 Score: 265
Period size: 72 Copynumber: 2.1 Consensus size: 72
63950 TGAATATGTG
*
63960 TTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTG
1 TTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTCGGAACTAAGTTTTGTCTCTCTTG
*
64025 AGACAGT
66 AGACAAT
* *
64032 TTCCTTGAAACAAATTTCGTCTTCCTTGAGATAGTTTCTTTCGGAACTAAGTTTTGTCTCTCTTG
1 TTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTCGGAACTAAGTTTTGTCTCTCTTG
64097 AGACAAT
66 AGACAAT
64104 TTCTCTTGAAA
1 TTC-CTTGAAA
64115 ACAATCTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
72 71 0.91
73 7 0.09
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.41
Consensus pattern (72 bp):
TTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTCGGAACTAAGTTTTGTCTCTCTTG
AGACAAT
Found at i:64332 original size:84 final size:84
Alignment explanation
Indices: 64220--64390 Score: 234
Period size: 84 Copynumber: 2.0 Consensus size: 84
64210 GAAATACCAA
*
64220 ACCTTCGAGTTCGATTACACTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCAAGAAA
1 ACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCAAGAAA
64285 GGCTATTTGCCAACCAAAG
66 GGCTATTTGCCAACCAAAG
* * * * * * * * * *
64304 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGCAGCATAGCTTAAGTCAATAAT
1 ACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCAAGAAA
*
64369 GGTTATTTGCCAACCAAAG
66 GGCTATTTGCCAACCAAAG
64388 ACC
1 ACC
64391 AAACGAGTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (84 bp):
ACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCAAGAAA
GGCTATTTGCCAACCAAAG
Found at i:64636 original size:3 final size:3
Alignment explanation
Indices: 64630--64662 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
64620 GGTTTAATAA
64630 TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
64663 ATATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:65830 original size:20 final size:16
Alignment explanation
Indices: 65813--65847 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
65803 TTTTGTTTTG
65813 TTTTATTATTTTTGGTT
1 TTTTATTATTTTT-GTT
*
65830 TTTTATTATTTTTATT
1 TTTTATTATTTTTGTT
65846 TT
1 TT
65848 ATTTCTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTTATTATTTTTGTT
Found at i:65835 original size:14 final size:14
Alignment explanation
Indices: 65793--65850 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
65783 TTTTTTAATC
* *
65793 TTTTGTTTTGTTTT
1 TTTTGTTTTATTAT
65807 GTTTTGTTTTATTAT
1 -TTTTGTTTTATTAT
65822 TTTTGGTTTTTTATTAT
1 TTTT-G--TTTTATTAT
*
65839 TTTTATTTTATT
1 TTTTGTTTTATT
65851 TCTCAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 11 0.30
15 13 0.35
17 13 0.35
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (14 bp):
TTTTGTTTTATTAT
Found at i:65922 original size:105 final size:106
Alignment explanation
Indices: 65715--65927 Score: 383
Period size: 106 Copynumber: 2.0 Consensus size: 106
65705 TTTATCTTTT
*
65715 TTTTTGGTTTTTTATTATTTTTATTTTATTTCTCAATATTTTACTATTTTTACATAATTTTTTTT
1 TTTTTGGTTTTTTATTATTTTTATTTTATTTCTCAATATTTTACTATTTTTACATAATATTTTTT
* * *
65780 TCTTTTTTTAATCTTTTGTTTTGTTTTGTTTTGTTTTATTA
66 TCTTTTTTTAATCTTTTCTTTTGTTTTCTTTTATTTTATTA
65821 TTTTTGGTTTTTTATTATTTTTATTTTATTTCTCAATATTTTACTATTTTTACATAA-ATTTTTT
1 TTTTTGGTTTTTTATTATTTTTATTTTATTTCTCAATATTTTACTATTTTTACATAATATTTTTT
65885 TCTTTTTTTAATCTTTTCTTTTGTTTTCTTTTATTTTATTA
66 TCTTTTTTTAATCTTTTCTTTTGTTTTCTTTTATTTTATTA
65926 TT
1 TT
65928 GCTATTATAT
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 46 0.45
106 57 0.55
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (106 bp):
TTTTTGGTTTTTTATTATTTTTATTTTATTTCTCAATATTTTACTATTTTTACATAATATTTTTT
TCTTTTTTTAATCTTTTCTTTTGTTTTCTTTTATTTTATTA
Found at i:65977 original size:105 final size:104
Alignment explanation
Indices: 65727--65956 Score: 297
Period size: 106 Copynumber: 2.2 Consensus size: 104
65717 TTTGGTTTTT
* * *
65727 TATTATTTTTATTTTATTTCTCAATATTTTACTATTTTTACATAATTTTTTTTTCTTTTTTTAAT
1 TATTATTTTTATTTTATTTATCAATATTTCACTATTTTTACATAATATTTTTTTCTTTTTTTAAT
* * * * * *
65792 CTTTTGTTTTGTTTTGTTTTGTTTTATTATTTTTGGTTTTT
66 CTTTTCTTTTGTTTTCTTTTATTTTATTA--TTTGCTATTA
* *
65833 TATTATTTTTATTTTATTTCTCAATATTTTACTATTTTTACATAA-ATTTTTTTCTTTTTTTAAT
1 TATTATTTTTATTTTATTTATCAATATTTCACTATTTTTACATAATATTTTTTTCTTTTTTTAAT
65897 CTTTTCTTTTGTTTTCTTTTATTTTATTA-TTGCTATTA
66 CTTTTCTTTTGTTTTCTTTTATTTTATTATTTGCTATTA
65935 TA-TATATTTTA-TTTATTCTATC
1 TATTAT-TTTTATTTTATT-TATC
65957 TTTCTTCTCA
Statistics
Matches: 114, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
101 9 0.08
102 16 0.14
105 44 0.39
106 45 0.39
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.70
Consensus pattern (104 bp):
TATTATTTTTATTTTATTTATCAATATTTCACTATTTTTACATAATATTTTTTTCTTTTTTTAAT
CTTTTCTTTTGTTTTCTTTTATTTTATTATTTGCTATTA
Found at i:65993 original size:9 final size:8
Alignment explanation
Indices: 65971--66097 Score: 53
Period size: 8 Copynumber: 15.5 Consensus size: 8
65961 TTCTCACTTA
65971 TTTTTTAT
1 TTTTTTAT
65979 TGTTTTTAGT
1 T-TTTTTA-T
65989 TTTTTCTAT
1 TTTTT-TAT
65998 TTTTTGT-T
1 TTTTT-TAT
* * *
66006 CTCTTTAA
1 TTTTTTAT
66014 TTTTTTAT
1 TTTTTTAT
*
66022 TATCTTT-T
1 T-TTTTTAT
* *
66030 TTTATCAT
1 TTTTTTAT
*
66038 TTTTTCAT
1 TTTTTTAT
66046 TTTTTT-T
1 TTTTTTAT
* **
66053 CCTTTTTCC
1 -TTTTTTAT
*
66062 TCTTTTAT
1 TTTTTTAT
*
66070 TTATTTAT
1 TTTTTTAT
*
66078 TTATTTAT
1 TTTTTTAT
*
66086 TTATTTAT
1 TTTTTTAT
66094 TTTT
1 TTTT
66098 CATCTAACAT
Statistics
Matches: 89, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
7 4 0.04
8 60 0.67
9 21 0.24
10 4 0.04
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTTTTAT
Found at i:66012 original size:26 final size:26
Alignment explanation
Indices: 65969--66019 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
65959 TCTTCTCACT
* * *
65969 TATTTTTTATTGTTTTTAGTTTTTTC
1 TATTTTTTATTCTCTTTAATTTTTTC
*
65995 TATTTTTTGTTCTCTTTAATTTTTT
1 TATTTTTTATTCTCTTTAATTTTTT
66020 ATTATCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (26 bp):
TATTTTTTATTCTCTTTAATTTTTTC
Found at i:66074 original size:4 final size:4
Alignment explanation
Indices: 66065--66095 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
66055 TTTTTCCTCT
66065 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
66096 TTCATCTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:67955 original size:14 final size:14
Alignment explanation
Indices: 67936--67984 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
67926 TTGATTTAAA
67936 TTTTAATATTAATT
1 TTTTAATATTAATT
67950 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
67960 ATTAAATATTAATT
1 TTTTAATATTAATT
67974 TTTTAATATTA
1 TTTTAATATTA
67985 TATTATAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 6 0.22
13 1 0.04
14 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:68028 original size:21 final size:20
Alignment explanation
Indices: 68000--68067 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 20
67990 TAGATATTTA
68000 ATTTTATATCA-TA-TAAATT
1 ATTTTATAT-ATTATTAAATT
68019 ATTTTATATATTATTAAA--
1 ATTTTATATATTATTAAATT
*
68037 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA-TTAAATT
68057 ATTTTGATATA
1 ATTTT-ATATA
68068 AGTTTAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 3 0.07
18 14 0.34
19 11 0.27
20 9 0.22
21 4 0.10
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (20 bp):
ATTTTATATATTATTAAATT
Found at i:68562 original size:31 final size:31
Alignment explanation
Indices: 68525--68584 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
68515 TAGTTGTATG
* *
68525 AATTATTTAAATTTCAATATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
*
68556 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
68585 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:69173 original size:14 final size:13
Alignment explanation
Indices: 69147--69197 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
69137 CCATAAAAAT
69147 TATAAAAAATAAA
1 TATAAAAAATAAA
*
69160 TATAAAATACTAAA
1 TATAAAA-AATAAA
* *
69174 AATAAAAATTAAA
1 TATAAAAAATAAA
69187 TTATAAAAAAT
1 -TATAAAAAAT
69198 TTAAAAATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
TATAAAAAATAAA
Found at i:69193 original size:20 final size:20
Alignment explanation
Indices: 69143--69196 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
69133 TAAACCATAA
*
69143 AAATTATAAAAAATAAATAT
1 AAATTATAAAAAAAAAATAT
*
69163 AAAATACTAAAAATAAAAAT-T
1 AAATTA-TAAAAA-AAAAATAT
69184 AAATTATAAAAAA
1 AAATTATAAAAAA
69197 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
21 12 0.41
22 5 0.17
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATTATAAAAAAAAAATAT
Found at i:75422 original size:15 final size:13
Alignment explanation
Indices: 75396--75436 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
75386 TTTATCTTTT
75396 AAATTT-TATAAA
1 AAATTTATATAAA
75408 AATATTATATATAAA
1 AA-ATT-TATATAAA
75423 AAATTTAT-TAAA
1 AAATTTATATAAA
75435 AA
1 AA
75437 GTATATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.31
13 6 0.23
14 4 0.15
15 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATTTATATAAA
Found at i:75499 original size:14 final size:14
Alignment explanation
Indices: 75480--75510 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
75470 TTCGATGATT
75480 TTTTTATATAAATA
1 TTTTTATATAAATA
*
75494 TTTTTATTTAAATA
1 TTTTTATATAAATA
75508 TTT
1 TTT
75511 AGAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTATATAAATA
Found at i:76859 original size:60 final size:60
Alignment explanation
Indices: 76747--76879 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
76737 TCATATGACA
* * * * * * *
76747 ATTTTGTAACTTTTAATAGTCGAGTGACTCAATAAAACAACACCCTATAGTTGGAGAACC
1 ATTTTGTAACTTTCAATAGTCAAGAGACTCAACAAAACAACACCCTACAGTTGAAAAACC
* *
76807 ATTTTGTAACTTTCAATAGTCAAGAGACTCAACAAAATAATATCCC-ACAGTTGAAAAACC
1 ATTTTGTAACTTTCAATAGTCAAGAGACTCAACAAAACAACA-CCCTACAGTTGAAAAACC
76867 ATTTATG-AACTTT
1 ATTT-TGTAACTTT
76880 ACCATATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 57 0.92
61 5 0.08
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (60 bp):
ATTTTGTAACTTTCAATAGTCAAGAGACTCAACAAAACAACACCCTACAGTTGAAAAACC
Found at i:78668 original size:7 final size:7
Alignment explanation
Indices: 78656--78683 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
78646 CTTTCCTTCT
78656 CTCATCA
1 CTCATCA
78663 CTCATCA
1 CTCATCA
78670 CTCATCA
1 CTCATCA
78677 CTCATCA
1 CTCATCA
78684 TCTTCTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (7 bp):
CTCATCA
Found at i:81738 original size:77 final size:77
Alignment explanation
Indices: 81644--81794 Score: 266
Period size: 77 Copynumber: 2.0 Consensus size: 77
81634 TATTTTCTCG
* *
81644 TACCTCTTCATGGAGTTTCTTCACAAATTTAGCCTTGTTCTTGTCATCCTTGCTGATCACATGTT
1 TACCTCTTCATGAAGTTTCTTCACAAATTTAGCCTTGTTCTTGTCATCCTTGCTGATAACATGTT
81709 CAAAAGGCATCT
66 CAAAAGGCATCT
* *
81721 TACCTCTTTATGAAGTTTCTTCACGAATTTAGCCTTGTTCTTGTCATCCTTGCTGATAACATGTT
1 TACCTCTTCATGAAGTTTCTTCACAAATTTAGCCTTGTTCTTGTCATCCTTGCTGATAACATGTT
81786 CAAAAGGCA
66 CAAAAGGCA
81795 AAGGTAGTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (77 bp):
TACCTCTTCATGAAGTTTCTTCACAAATTTAGCCTTGTTCTTGTCATCCTTGCTGATAACATGTT
CAAAAGGCATCT
Found at i:85343 original size:59 final size:59
Alignment explanation
Indices: 85159--85331 Score: 253
Period size: 56 Copynumber: 3.0 Consensus size: 59
85149 TACATATTTG
85159 GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCA
1 GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCA
* * * * *
85218 AGATTGCACTAAAGTAT---TAGTGCATATGGTGGGAACAACCTTATGTGTCATAATCT
1 GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCA
* * *
85274 GGACTGCACTAAAGTATAACTAGTACAGATGGTGGGCACGACCTTATGTGTCATACTC
1 GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACTC
85332 GGGTTAGCAC
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
56 50 0.51
59 49 0.49
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (59 bp):
GGATTGCACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGTCATACTCA
Found at i:91719 original size:57 final size:58
Alignment explanation
Indices: 91649--91816 Score: 197
Period size: 55 Copynumber: 3.0 Consensus size: 58
91639 TGTATATTCG
*
91649 GGATTGCACTAAAGTATAACTA-TGCATATGGTGGGCACGACCTTATGTGTCATACTC
1 GGATTGCACTAAAGTATAACTAGTGCATATAGTGGGCACGACCTTATGTGTCATACTC
* * * * *
91706 GGATTGTACTAAAGTAT---TAGTGCGTATTGTGGGCACGACCTTATGTGACATATTC
1 GGATTGCACTAAAGTATAACTAGTGCATATAGTGGGCACGACCTTATGTGTCATACTC
* * * *
91761 GGACTGCAGTAAAGTATAACTAGTGCAGATAGT-GGCACGA-CTT-TATGTCATACTC
1 GGATTGCACTAAAGTATAACTAGTGCATATAGTGGGCACGACCTTATGTGTCATACTC
91816 G
1 G
91817 AGTTAGCACT
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
54 2 0.02
55 55 0.59
56 3 0.03
57 23 0.25
58 10 0.11
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (58 bp):
GGATTGCACTAAAGTATAACTAGTGCATATAGTGGGCACGACCTTATGTGTCATACTC
Done.