Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008285.1 Hibiscus syriacus cultivar Beakdansim tig00110948_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: 146154
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1881 original size:20 final size:20
Alignment explanation
Indices: 1835--1881 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
1825 TCCCGTATCA
1835 TTTACCGGTTTTTATCATTT
1 TTTACCGGTTTTTATCATTT
*
1855 TGATACCGG-TTTTATCATATT
1 T-TTACCGGTTTTTATCAT-TT
1876 TTTACC
1 TTTACC
1882 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (20 bp):
TTTACCGGTTTTTATCATTT
Found at i:12100 original size:9 final size:9
Alignment explanation
Indices: 12082--12123 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
12072 CATTTTAACC
12082 TTTAAATAT
1 TTTAAATAT
*
12091 TTTAATTAT
1 TTTAAATAT
*
12100 TTAAAATA-
1 TTTAAATAT
12108 TTTAAATAT
1 TTTAAATAT
*
12117 TTAAAAT
1 TTTAAAT
12124 TGTTTGTACA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAATAT
Found at i:12104 original size:17 final size:17
Alignment explanation
Indices: 12085--12123 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
12075 TTTAACCTTT
*
12085 AAATATTTTAATTATTTA
1 AAATA-TTTAAATATTTA
12103 AAATATTTAAATATTTA
1 AAATATTTAAATATTTA
12120 AAAT
1 AAAT
12124 TGTTTGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATTTAAATATTTA
Found at i:12114 original size:8 final size:8
Alignment explanation
Indices: 12082--12121 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
12072 CATTTTAACC
12082 TTTAAATA
1 TTTAAATA
*
12090 TTTTAATTA
1 -TTTAAATA
12099 TTTAAAATA
1 TTT-AAATA
12108 TTTAAATA
1 TTTAAATA
12116 TTTAAA
1 TTTAAA
12122 ATTGTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAATA
Found at i:12793 original size:24 final size:20
Alignment explanation
Indices: 12740--12797 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
12730 TTTCCCTTGA
*
12740 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
12760 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
12783 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
12798 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:12908 original size:64 final size:63
Alignment explanation
Indices: 12785--12921 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
12775 TCTTTAACAT
* * *
12785 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAA-AGA
* * * ** *
12849 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACATTCGATGTTTTCAT-TTTAAAGA
12912 GTGCATCGAT
1 GTGCATCGAT
12922 ACACATTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
63 18 0.29
64 44 0.71
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:16448 original size:23 final size:24
Alignment explanation
Indices: 16399--16448 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
16389 CCACTAGGGG
*
16399 CTATGAAATTTATCCCGAATGACCA
1 CTATGAAA-TTATCCCGAAGGACCA
* *
16424 CTATGAAA-TATCCTGAAGGATCA
1 CTATGAAATTATCCCGAAGGACCA
16447 CT
1 CT
16449 GTATATCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (24 bp):
CTATGAAATTATCCCGAAGGACCA
Found at i:17225 original size:24 final size:20
Alignment explanation
Indices: 17172--17229 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
17162 TTCCCCTTGA
*
17172 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
17192 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
17215 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
17230 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:27875 original size:5 final size:5
Alignment explanation
Indices: 27856--27900 Score: 72
Period size: 5 Copynumber: 8.8 Consensus size: 5
27846 TAAAACCTGC
*
27856 AAAAT AAGAT AAAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
27901 ATAATTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:27915 original size:6 final size:6
Alignment explanation
Indices: 27864--27925 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 6
27854 GCAAAATAAG
* *
27864 ATAAAA ATAA-A ATAA-A ATAA-A ATAA-A ATAA-A ATAAAA ATAATTA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAA-TA
*
27908 ATGATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA
27926 GTTAAATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
5 25 0.49
6 22 0.43
7 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.26
Consensus pattern (6 bp):
ATAATA
Found at i:27925 original size:22 final size:21
Alignment explanation
Indices: 27890--27930 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
27880 ATAAAATAAA
27890 ATAAAATAAAAATAATTAATG
1 ATAAAATAAAAATAATTAATG
* *
27911 ATAATAATAATAATAGTTAA
1 ATAA-AATAAAAATAATTAA
27931 ATTAAAACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
ATAAAATAAAAATAATTAATG
Found at i:28607 original size:261 final size:259
Alignment explanation
Indices: 28069--28808 Score: 968
Period size: 261 Copynumber: 2.8 Consensus size: 259
28059 TGATACTACC
* * * ** *
28069 AGATGACCCGAATGATTT-ATTCATTATGCTTGAAAGACTTA-CATGGCCTTAATGACTTAATC-
1 AGATGACCCGAATGATTTAATT-ATCATGCTCGAAAGACTTATGATGGCCCAAATGACTT-ACCA
* * *
28131 ATCTTGGAAATAGTTTACTAGGTAATAAATTTTGGAAATCG-TTTCTTACTTTTTCAAAAAATTC
64 ATTTTGGAAATAGTTTACTAGGTAATAAACTTTGGAAATCGTTTTCTTAC-TTTTCAAAAATTTC
*
28195 AATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGTTTTCTCATCTTTTGAAAATCATGT
128 AATTTTCAAAAAAGATTTAAATGAGAAACTTTGGAAATCGTTTTCTCATCTTTTGAAAATCATGT
**
28260 GAAAACATCATGCCCGAAGGTCTTATGGATGACCCGAAAGACTTATCATCTTGCTCGAAAGGCTT
193 GAAAACATCCCGCCCGAAGGTCTTATGGATGACCCGAAAGACTTATCATCTTGCTCGAAAGGCTT
28325 AT
258 AT
* ** * *
28327 AGATTAAGCGAAAGATTTAATTATCATGCTCGAAAGACTTATTGATGGCCCGAATGACTTACCAA
1 AGATGACCCGAATGATTTAATTATCATGCTCGAAAGACTTA-TGATGGCCCAAATGACTTACCAA
* * *
28392 TTTTAGAAATAGTTTACTAGGTAATAAACTTTGGAAATCGTTTTCTTACTTTCCAAATATTTCAA
65 TTTTGGAAATAGTTTACTAGGTAATAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCAA
* * *
28457 TTTTCAAAAAATATTTAAATGAGAAAATTTGGTAATCGTTTTCTCATCATTTTGAAAATCATGTG
130 TTTTCAAAAAAGATTTAAATGAGAAACTTTGGAAATCGTTTTCTCATC-TTTTGAAAATCATGTG
* * * * *
28522 AAAACATCCCGCCCGAAGTTCTTATGGATGGCCCTAAGGGCTTATCATCTTGCTCGAAAGGCTTA
194 AAAACATCCCGCCCGAAGGTCTTATGGATGACCCGAAAGACTTATCATCTTGCTCGAAAGGCTTA
28587 T
259 T
** *
28588 AGATGACCCGAATGATTTAATCCTCATGCTCGAAAGACTTACTGATGGCTCAAATGACTTACCAA
1 AGATGACCCGAATGATTTAATTATCATGCTCGAAAGACTTA-TGATGGCCCAAATGACTTACCAA
* * * **
28653 TTTTGGAAATAGTTTACTAGATAAGAAACTTTGGAAATTGGTTTCTCTTTTTTTTCAAAAATTTC
65 TTTTGGAAATAGTTTACTAGGTAATAAACTTTGGAAA-TCGTTT-TCTTACTTTTCAAAAATTTC
* * * ** *
28718 AATTTTCACACAAGATTTAAATGAGAAACTTTAGAAATCACTTTCTTATCTTTTGAAAATCATGT
128 AATTTTCAAAAAAGATTTAAATGAGAAACTTTGGAAATCGTTTTCTCATCTTTTGAAAATCATGT
** *
28783 G-AAACATCCTACCCGTAGGTCTTATG
193 GAAAACATCCCGCCCGAAGGTCTTATG
28809 AATAGTGTTG
Statistics
Matches: 417, Mismatches: 57, Indels: 13
0.86 0.12 0.03
Matches are distributed among these distances:
258 31 0.07
259 5 0.01
260 109 0.26
261 194 0.47
262 21 0.05
263 57 0.14
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (259 bp):
AGATGACCCGAATGATTTAATTATCATGCTCGAAAGACTTATGATGGCCCAAATGACTTACCAAT
TTTGGAAATAGTTTACTAGGTAATAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCAAT
TTTCAAAAAAGATTTAAATGAGAAACTTTGGAAATCGTTTTCTCATCTTTTGAAAATCATGTGAA
AACATCCCGCCCGAAGGTCTTATGGATGACCCGAAAGACTTATCATCTTGCTCGAAAGGCTTAT
Found at i:31084 original size:20 final size:20
Alignment explanation
Indices: 31055--31104 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
31045 ATCTTTTCGA
31055 CTCGACTCGATTCGAAAAAG
1 CTCGACTCGATTCGAAAAAG
* *
31075 CTCGATTCGATTTGAAAAAG
1 CTCGACTCGATTCGAAAAAG
31095 CTCGACTCGA
1 CTCGACTCGA
31105 ATTAACTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
CTCGACTCGATTCGAAAAAG
Found at i:32700 original size:21 final size:19
Alignment explanation
Indices: 32668--32706 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
32658 TTTTAAGTAT
*
32668 TTTAATTAGAATTTTCTTC
1 TTTAATTAGAATTATCTTC
32687 TTTAATTTAGGAATTATCTT
1 TTTAA-TTA-GAATTATCTT
32707 TACTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (19 bp):
TTTAATTAGAATTATCTTC
Found at i:37424 original size:23 final size:21
Alignment explanation
Indices: 37398--37471 Score: 87
Period size: 23 Copynumber: 3.5 Consensus size: 21
37388 CCCGTGAGGG
37398 GTATCGATACATATTCAAGGAAT
1 GTATCGATACATATTCAAGG--T
* *
37421 GTATCGGTACACATTCAAGGT
1 GTATCGATACATATTCAAGGT
* *
37442 GTATCGATACATA-ACAAGGG
1 GTATCGATACATATTCAAGGT
37462 GTATCGATAC
1 GTATCGATAC
37472 CTAGGTATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.33
21 12 0.27
23 18 0.40
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (21 bp):
GTATCGATACATATTCAAGGT
Found at i:39840 original size:64 final size:63
Alignment explanation
Indices: 39717--39857 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
39707 TCTTTAACAT
* * * *
39717 GTGCATCGATGAACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGA
* * * * *
39780 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATG-TTTCTTCTTTAAAG
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTTCAT-TTTAAAG
39843 A
63 A
*
39844 GTACATCGATGCAC
1 GTGCATCGATGCAC
39858 ATTGAATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 20 0.31
64 45 0.69
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGA
Found at i:41842 original size:12 final size:12
Alignment explanation
Indices: 41825--41851 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41815 ATGATGATTC
41825 TCCAACGTCATG
1 TCCAACGTCATG
41837 TCCAACGTCATG
1 TCCAACGTCATG
41849 TCC
1 TCC
41852 GTTTACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:50240 original size:17 final size:17
Alignment explanation
Indices: 50218--50267 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
50208 TATTTTGTTT
50218 TGTGTTTGAGTTCTCAA
1 TGTGTTTGAGTTCTCAA
50235 TGTG-TT--GTT-T---
1 TGTGTTTGAGTTCTCAA
50245 TGTGTTTGAGTTCTCAA
1 TGTGTTTGAGTTCTCAA
50262 TGTGTT
1 TGTGTT
50268 GGTCTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 14
0.65 0.00 0.35
Matches are distributed among these distances:
10 4 0.15
11 2 0.08
13 4 0.15
14 4 0.15
16 2 0.08
17 10 0.38
ACGTcount: A:0.12, C:0.08, G:0.26, T:0.54
Consensus pattern (17 bp):
TGTGTTTGAGTTCTCAA
Found at i:50279 original size:27 final size:27
Alignment explanation
Indices: 50212--50279 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
50202 ATATTATATT
* *
50212 TTGTTTTGTGTTTGAGTTCTCAATGTG
1 TTGTCTTGTCTTTGAGTTCTCAATGTG
* *
50239 TTGTTTTGTGTTTGAGTTCTCAATGTG
1 TTGTCTTGTCTTTGAGTTCTCAATGTG
50266 TTGGTCTT-TCTTTG
1 TT-GTCTTGTCTTTG
50280 TTGCAGCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 34 0.89
28 4 0.11
ACGTcount: A:0.09, C:0.09, G:0.25, T:0.57
Consensus pattern (27 bp):
TTGTCTTGTCTTTGAGTTCTCAATGTG
Found at i:50280 original size:33 final size:27
Alignment explanation
Indices: 50212--50268 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
50202 ATATTATATT
50212 TTGTTTTGTGTTTGAGTTCTCAATGTG
1 TTGTTTTGTGTTTGAGTTCTCAATGTG
50239 TTGTTTTGTGTTTGAGTTCTCAATGTG
1 TTGTTTTGTGTTTGAGTTCTCAATGTG
50266 TTG
1 TTG
50269 GTCTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.11, C:0.07, G:0.26, T:0.56
Consensus pattern (27 bp):
TTGTTTTGTGTTTGAGTTCTCAATGTG
Found at i:53472 original size:7 final size:7
Alignment explanation
Indices: 53460--53490 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
53450 GTCAAAGAAA
53460 GTCAACG
1 GTCAACG
53467 GTCAACG
1 GTCAACG
*
53474 GTCAATG
1 GTCAACG
53481 GTCAACG
1 GTCAACG
53488 GTC
1 GTC
53491 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:53537 original size:19 final size:19
Alignment explanation
Indices: 53494--53538 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
53484 AACGGTCGGG
*
53494 TCGGGTCAGACCGGTCAAA
1 TCGGTTCAGACCGGTCAAA
53513 -CTGGTTCAGACCGGTCAAA
1 TC-GGTTCAGACCGGTCAAA
53532 TCGGTTC
1 TCGGTTC
53539 GAACCGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 21 0.91
20 1 0.04
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (19 bp):
TCGGTTCAGACCGGTCAAA
Found at i:53553 original size:10 final size:10
Alignment explanation
Indices: 53503--53596 Score: 72
Period size: 9 Copynumber: 9.7 Consensus size: 10
53493 GTCGGGTCAG
53503 ACCGG-TCAA
1 ACCGGTTCAA
* *
53512 ACTGGTTCAG
1 ACCGGTTCAA
53522 ACCGG-TCAA
1 ACCGGTTCAA
* *
53531 ATCGGTTCGA
1 ACCGGTTCAA
*
53541 ACCGGTTGAA
1 ACCGGTTCAA
53551 ACCGG-TCAA
1 ACCGGTTCAA
53560 ACCGG-TCAGA
1 ACCGGTTCA-A
* *
53570 ACCGATTGAAA
1 ACCGGTT-CAA
53581 ACCGGTT-AA
1 ACCGGTTCAA
53590 ACCGGTT
1 ACCGGTT
53597 TCCAGCAGCC
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
9 31 0.46
10 27 0.40
11 8 0.12
12 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:53555 original size:29 final size:31
Alignment explanation
Indices: 53522--53596 Score: 102
Period size: 29 Copynumber: 2.5 Consensus size: 31
53512 ACTGGTTCAG
* *
53522 ACCGGTCAAATCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGATTGAAA
53551 ACCGGTCAAACCGG-TCAGAACCGATTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGATTGAAA
*
53581 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
53597 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.05
29 22 0.55
30 15 0.38
31 1 0.03
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGATTGAAA
Found at i:60842 original size:7 final size:7
Alignment explanation
Indices: 60829--60866 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
60819 GTCAAAGAAA
60829 GTCAACG
1 GTCAACG
*
60836 ATCAACG
1 GTCAACG
60843 GTCAACG
1 GTCAACG
*
60850 GTCAATG
1 GTCAACG
60857 GTCAACG
1 GTCAACG
60864 GTC
1 GTC
60867 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:60878 original size:17 final size:17
Alignment explanation
Indices: 60856--60890 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
60846 AACGGTCAAT
*
60856 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
60873 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
60890 G
1 G
60891 TCGGGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:60940 original size:10 final size:9
Alignment explanation
Indices: 60894--60941 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
60884 GGGTCGGTCG
*
60894 GGTCATACC
1 GGTCAAACC
*
60903 GGTCAAATC
1 GGTCAAACC
*
60912 GGTTCGAACC
1 GG-TCAAACC
60922 GGTCAAACC
1 GGTCAAACC
60931 GGTCAGAACC
1 GGTCA-AACC
60941 G
1 G
60942 ATTGAAAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 20 0.62
10 12 0.38
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:67953 original size:2 final size:2
Alignment explanation
Indices: 67946--67974 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
67936 TAGAGTAATT
67946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67975 CACCAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:80367 original size:6 final size:6
Alignment explanation
Indices: 80356--80392 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
80346 AAGAAGAAAG
* *
80356 AAGACA AAGACA AAGACA AAGACA AAAACA AAAACA A
1 AAGACA AAGACA AAGACA AAGACA AAGACA AAGACA A
80393 GGAAGGCACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.73, C:0.16, G:0.11, T:0.00
Consensus pattern (6 bp):
AAGACA
Found at i:83076 original size:27 final size:27
Alignment explanation
Indices: 83046--83100 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
83036 AGTCCTAATG
83046 CAAATAATATTTCTTCACCGAATTTCA
1 CAAATAATATTTCTTCACCGAATTTCA
83073 CAAATAATATTTCTTCACCGAATTTCA
1 CAAATAATATTTCTTCACCGAATTTCA
83100 C
1 C
83101 TCCAAGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (27 bp):
CAAATAATATTTCTTCACCGAATTTCA
Found at i:89932 original size:19 final size:19
Alignment explanation
Indices: 89891--89932 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
89881 ATGACCAATA
* * *
89891 AATTCGCAACGTGATCTCG
1 AATTCGCAACGCGAACTCC
89910 AATTCGCAACGCGAACTCC
1 AATTCGCAACGCGAACTCC
89929 AATT
1 AATT
89933 TCCAAATTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:90016 original size:20 final size:19
Alignment explanation
Indices: 89991--90060 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
89981 CTGAATTTCA
89991 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTT-TG
*
90011 AATTCGCAACGCGAATTTTG
1 AATTCGCAACTCG-ATTTTG
**
90031 TTTTCGCAACTCGATTTTCG
1 AATTCGCAACTCGATTTT-G
90051 AATTCGCAAC
1 AATTCGCAAC
90061 ACAAATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.12
20 33 0.79
21 4 0.10
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (19 bp):
AATTCGCAACTCGATTTTG
Found at i:90038 original size:40 final size:40
Alignment explanation
Indices: 89993--90069 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
89983 GAATTTCAAA
* *
89993 TTCGCAACTCGA-TTTCTGAATTCGCAACGCGAATTTTGTT
1 TTCGCAACTCGATTTTC-GAATTCGCAACACAAATTTTGTT
90033 TTCGCAACTCGATTTTCGAATTCGCAACACAAATTTT
1 TTCGCAACTCGATTTTCGAATTCGCAACACAAATTTT
90070 AATTTTGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCGAATTCGCAACACAAATTTTGTT
Found at i:90080 original size:40 final size:40
Alignment explanation
Indices: 89993--90080 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
89983 GAATTTCAAA
* * *
89993 TTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTTGTT
1 TTCGCAACTCGATTTCTGAATTCGCAACACAAATTTTATT
90033 TTCGCAACTCGATTT-TCGAATTCGCAACACAAATTTTAATT
1 TTCGCAACTCGATTTCT-GAATTCGCAACACAAATTTT-ATT
90074 TT-GCAAC
1 TTCGCAAC
90081 AAGTTTTAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 1 0.02
40 38 0.88
41 4 0.09
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (40 bp):
TTCGCAACTCGATTTCTGAATTCGCAACACAAATTTTATT
Found at i:90087 original size:18 final size:18
Alignment explanation
Indices: 90061--90099 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
90051 AATTCGCAAC
*
90061 ACAAATTTTAATTTTGCA
1 ACAAATTTTAATTTCGCA
* *
90079 ACAAGTTTTAGTTTCGCA
1 ACAAATTTTAATTTCGCA
90097 ACA
1 ACA
90100 CAAATGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (18 bp):
ACAAATTTTAATTTCGCA
Found at i:92011 original size:76 final size:78
Alignment explanation
Indices: 91842--92009 Score: 245
Period size: 76 Copynumber: 2.2 Consensus size: 78
91832 TTGCTCAGAG
** *
91842 GGAACCGATTCCCCCCTAAATGGTTTTGGCCCCGAGATTTCCAGAATGCTCGGAGGGAACCGATT
1 GGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAGGGAACCGATT
91907 CCCCCCCATAGGA
66 CCCCCCCATAGGA
* *
91920 GGAACCGATT-CCCCCTAAACAGTTTT-GCTCCGAGAATTCCAGTATGCTCGGAGGGAACCGA-T
1 GGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAGGGAACCGATT
*
91982 CCCCCCCA-AGGG
66 CCCCCCCATAGGA
*
91994 GGTACCGATTCCCCCC
1 GGAACCGATTCCCCCC
92010 CTTGTACAAC
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
74 12 0.15
75 14 0.17
76 32 0.39
77 14 0.17
78 10 0.12
ACGTcount: A:0.23, C:0.34, G:0.24, T:0.20
Consensus pattern (78 bp):
GGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAGGGAACCGATT
CCCCCCCATAGGA
Found at i:92248 original size:18 final size:17
Alignment explanation
Indices: 92208--92249 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
92198 ATTGATCAAT
*
92208 AACAAGAAACATCAAGC
1 AACAAGAAACATCAAGA
92225 AACAAGAAATCAT-AGAGA
1 AACAAGAAA-CATCA-AGA
92243 AACAAGA
1 AACAAGA
92250 GAGAAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.62, C:0.17, G:0.14, T:0.07
Consensus pattern (17 bp):
AACAAGAAACATCAAGA
Found at i:97807 original size:21 final size:21
Alignment explanation
Indices: 97781--97864 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
97771 TTTTGGTGCA
* *
97781 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCACT
* **
97802 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCACT
*
97823 GAAGGGGAACCGATTCCCCCCACA
1 G-A-GGGAACCGA-TCCCCCCACT
* *
97847 G-GGGAATCGATACCCCCA
1 GAGGGAACCGATCCCCCCA
97865 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
20 7 0.14
21 26 0.52
22 1 0.02
23 9 0.18
24 7 0.14
ACGTcount: A:0.24, C:0.37, G:0.25, T:0.14
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCACT
Found at i:99801 original size:9 final size:8
Alignment explanation
Indices: 99779--99829 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
99769 TGTTTCAACA
99779 TTTTGGAT
1 TTTTGGAT
99787 ATTTTGGAT
1 -TTTTGGAT
99796 TGTTT-GAT
1 T-TTTGGAT
99804 TTTGTGGAT
1 TTT-TGGAT
*
99813 TGTTGGA-
1 TTTTGGAT
99820 TTTTGGAT
1 TTTTGGAT
99828 TT
1 TT
99830 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:99813 original size:17 final size:17
Alignment explanation
Indices: 99781--99824 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
99771 TTTCAACATT
99781 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
99798 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
99815 TTGGATTTTG
1 TTGGATTTTG
99825 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:100576 original size:76 final size:76
Alignment explanation
Indices: 100432--100598 Score: 221
Period size: 76 Copynumber: 2.2 Consensus size: 76
100422 TTGCTCAGAG
** * *
100432 GGAACCGATTCCCCCTAAATGGTTTTGGCCCCGAGATTTCCAGAATGCTCGGAGGAAACCGAT-T
1 GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAGGAAACCGATCC
100496 CCCCCCATAGGA
66 CCCCCCA-AGGA
* * *
100508 GGAACCGATTCCCCCTAAACAGTTTT-GCTCCGAGAATTCCAGTATGCTCGGAGGGAACCGATCC
1 GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAGGAAACCGAT-C
*
100572 CCCCCCCAAGGG
65 CCCCCCCAAGGA
*
100584 GGTACCGATTCCCCC
1 GGAACCGATTCCCCC
100599 CTTGTACAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
75 32 0.40
76 41 0.51
77 7 0.09
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (76 bp):
GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAGGAAACCGATCC
CCCCCCAAGGA
Found at i:100837 original size:18 final size:17
Alignment explanation
Indices: 100797--100838 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
100787 ATTGATCAAT
*
100797 AACAAGAAACATCAAGC
1 AACAAGAAACATCAAGA
100814 AACAAGAAATCAT-AGAGA
1 AACAAGAAA-CATCA-AGA
100832 AACAAGA
1 AACAAGA
100839 GAGAAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.62, C:0.17, G:0.14, T:0.07
Consensus pattern (17 bp):
AACAAGAAACATCAAGA
Found at i:103758 original size:450 final size:450
Alignment explanation
Indices: 102917--103763 Score: 1417
Period size: 450 Copynumber: 1.9 Consensus size: 450
102907 CATACAAGGT
* *
102917 TTGTTGGGTTATAGGGTCCATCGATCACCCTTAGGGATTCTATCATGTATGGGCGCGATATCGGT
1 TTGTTGGGTTATAGGGTCCAGCGATCACCCTTAGGGATTCTATCATGTATGGGCGCGATATCAGT
* * * * *
102982 GCATGACTGCCCAACCTGCCGAGGTCCACGTATTCCTTGCGAAGCCCCTAGGCCCGCCCGCAGTA
66 GCATGACTACCCAACCTGCCGAGGCCCACATATGCCTTGCGAAGCCCCTAGGCCCGCCCGCAGCA
* * **
103047 CGCTATATATGCGGGGCTCTGCAATGCCGTGGTGAACTGTAGGGGTGCCCCACAAGAATTTACCT
131 CGCTATAGATGCGGGGCTCTGCAATGCCGTGGTGAACTATAGGGGTGCCCCACAAGAATCCACCT
* *
103112 TGGCTTGGGGGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGACCCACTTACTTA
196 TGGCTTGGGGGAACCCAATGATCACCCACTACAAAGATATGAGGTTAAAATGACCCACCTACTTA
* * * *
103177 TCACCAATTGGTTTTAAGAAGGAATGGTGATCATTCGCTTCAGAAATCTGTGGTTAAGCGTGCTT
261 CCACCAATTGGTTTTAAGAAGGAAAGATGACCATTCGCTTCAGAAATCTGTGGTTAAGCGTGCTT
*
103242 GGACTAAAGGAAATCCAAGGATGGGTGACCCACTGGGAAGTTGTTCAGAAATGAATGACTCGATC
326 GGACTAAAGGAAATCCAAGGATGGGTGACCCACTAGGAAGTTGTTCAGAAATGAATGACTCGATC
103307 CTAACAACTGGTATCAGAGCAGGTTGCAGGTTCGAATCCCCCAGGTGTCGTTGGGGGTGA
391 CTAACAACTGGTATCAGAGCAGGTTGCAGGTTCGAATCCCCCAGGTGTCGTTGGGGGTGA
* * *
103367 TTGTTGGGTTATGGGGTCTAGCGATCACCCTTAGGGATTCTATCGTGTATGGGCGCGATATCAGT
1 TTGTTGGGTTATAGGGTCCAGCGATCACCCTTAGGGATTCTATCATGTATGGGCGCGATATCAGT
* *
103432 G-AGTGACTACCCAACCTGCCGAGGCCCACATGTGCCTTGCGAAGCCCCTAGGCCCGCCCGTAGC
66 GCA-TGACTACCCAACCTGCCGAGGCCCACATATGCCTTGCGAAGCCCCTAGGCCCGCCCGCAGC
*
103496 ACGCTATAGATGCGGGGCTCTGCAATGCCGTGGTGAACTATGGGGGTGCCCCACAAGAATCCACC
130 ACGCTATAGATGCGGGGCTCTGCAATGCCGTGGTGAACTATAGGGGTGCCCCACAAGAATCCACC
* * *
103561 TTGGCTTGGGGGAACCCAATGATCACCCACTATAAAGATATGATGTTAAAATGGCCCACCTACTT
195 TTGGCTTGGGGGAACCCAATGATCACCCACTACAAAGATATGAGGTTAAAATGACCCACCTACTT
*
103626 ACCACCAATTGGTTTTAAGAAGGAAAGATGACCATTCGCTTCAGAACTCTGTGGTTAAGCGTGCT
260 ACCACCAATTGGTTTTAAGAAGGAAAGATGACCATTCGCTTCAGAAATCTGTGGTTAAGCGTGCT
*
103691 TGGACTAAGGGAAATCCAAGGATGGGTGACCCACTAGGAAGTTGTTCAGAAATGAATGACTCGAT
325 TGGACTAAAGGAAATCCAAGGATGGGTGACCCACTAGGAAGTTGTTCAGAAATGAATGACTCGAT
103756 CCTAACAA
390 CCTAACAA
103764 GGTTGACCTG
Statistics
Matches: 367, Mismatches: 29, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
449 1 0.00
450 366 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (450 bp):
TTGTTGGGTTATAGGGTCCAGCGATCACCCTTAGGGATTCTATCATGTATGGGCGCGATATCAGT
GCATGACTACCCAACCTGCCGAGGCCCACATATGCCTTGCGAAGCCCCTAGGCCCGCCCGCAGCA
CGCTATAGATGCGGGGCTCTGCAATGCCGTGGTGAACTATAGGGGTGCCCCACAAGAATCCACCT
TGGCTTGGGGGAACCCAATGATCACCCACTACAAAGATATGAGGTTAAAATGACCCACCTACTTA
CCACCAATTGGTTTTAAGAAGGAAAGATGACCATTCGCTTCAGAAATCTGTGGTTAAGCGTGCTT
GGACTAAAGGAAATCCAAGGATGGGTGACCCACTAGGAAGTTGTTCAGAAATGAATGACTCGATC
CTAACAACTGGTATCAGAGCAGGTTGCAGGTTCGAATCCCCCAGGTGTCGTTGGGGGTGA
Found at i:103887 original size:18 final size:18
Alignment explanation
Indices: 103864--103900 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
103854 CAAGCAAAAG
*
103864 AAAATCAAAATCGCAATC
1 AAAATCAAAATCCCAATC
103882 AAAATCAAAATCCCAATC
1 AAAATCAAAATCCCAATC
103900 A
1 A
103901 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.57, C:0.24, G:0.03, T:0.16
Consensus pattern (18 bp):
AAAATCAAAATCCCAATC
Found at i:104193 original size:20 final size:20
Alignment explanation
Indices: 104168--104210 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
104158 ATCGCAACGT
* *
104168 GAATTTGACTTTTGTGTTGC
1 GAATTTGACTTTCGCGTTGC
104188 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGCGTTGC
104208 GAA
1 GAA
104211 AGTGTACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.42
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGC
Found at i:104371 original size:64 final size:64
Alignment explanation
Indices: 104269--104419 Score: 223
Period size: 64 Copynumber: 2.4 Consensus size: 64
104259 AATTTAAAAC
*
104269 AACAAATCAACTTTTAAAAATCAATTAAACAAGTAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTAAAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
* *** * *
104333 AACAAATCAACTTTTAGAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTAAAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*
104397 AACAAATCAAC-TTTACAAATCAA
1 AACAAATCAACTTTTAAAAATCAA
104420 CTTTTACAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
63 11 0.14
64 68 0.86
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTAAAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:104414 original size:13 final size:14
Alignment explanation
Indices: 104398--104430 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
104388 CATCAATTAA
104398 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
104411 ACAAATCAACTTTT
1 ACAAATCAACTTTT
104425 ACAAAT
1 ACAAAT
104431 ACATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:105784 original size:21 final size:20
Alignment explanation
Indices: 105760--105835 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 20
105750 GTGGGAGAGA
105760 CCTCTTGAACGATGACAGGTG
1 CCTCTTGAACGATGACAGG-G
* *
105781 CCTCTTGAACGGTAGGA-GGGG
1 CCTCTTGAAC-G-ATGACAGGG
* * *
105802 CTTCTTGAAAGATGATATGGG
1 CCTCTTGAACGATGACA-GGG
105823 CCTCTTGAACGAT
1 CCTCTTGAACGAT
105836 AGGAGAGGCC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 3 0.07
20 1 0.02
21 33 0.77
22 3 0.07
23 3 0.07
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (20 bp):
CCTCTTGAACGATGACAGGG
Found at i:105808 original size:42 final size:41
Alignment explanation
Indices: 105753--105861 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 41
105743 TCGAACGGTG
* *
105753 GGAGAGACCTCTTGAACGATGACAGGTGCCTCTTGAACGGTA
1 GGAGAGGCCTCTTGAACGATGACAGG-GCCTCTTGAACGATA
* * * *
105795 GGAGGGGCTTCTTGAAAGATGATATGGGCCTCTTGAACGATA
1 GGAGAGGCCTCTTGAACGATGACA-GGGCCTCTTGAACGATA
* *
105837 GGAGAGGCCTATTTAACGATGACAG
1 GGAGAGGCCTCTTGAACGATGACAG
105862 ATGAATCGGG
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
41 1 0.02
42 51 0.94
43 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (41 bp):
GGAGAGGCCTCTTGAACGATGACAGGGCCTCTTGAACGATA
Found at i:105845 original size:21 final size:20
Alignment explanation
Indices: 105753--105857 Score: 61
Period size: 21 Copynumber: 5.0 Consensus size: 20
105743 TCGAACGGTG
*
105753 GGAGAGACCTCTTGAACGAT
1 GGAGAGGCCTCTTGAACGAT
* *
105773 -GACAGGTGCCTCTTGAACGGT
1 GGAGA-G-GCCTCTTGAACGAT
* * *
105794 AGGAGGGGCTTCTTGAAAGAT
1 -GGAGAGGCCTCTTGAACGAT
*
105815 -GATATGGGCCTCTTGAACGAT
1 GGAGA--GGCCTCTTGAACGAT
* *
105836 AGGAGAGGCCTATTTAACGAT
1 -GGAGAGGCCTCTTGAACGAT
105857 G
1 G
105858 ACAGATGAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
19 5 0.08
20 2 0.03
21 49 0.79
22 1 0.02
23 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (20 bp):
GGAGAGGCCTCTTGAACGAT
Found at i:108375 original size:20 final size:21
Alignment explanation
Indices: 108350--108392 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
108340 TCTGAGAGAT
*
108350 GGAGAT-GGACGGATTTCGCC
1 GGAGATGGGACGGATGTCGCC
108370 GGAGATGGGGACGGATGTCGCC
1 GGAGAT-GGGACGGATGTCGCC
108392 G
1 G
108393 TAGAGAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.19, C:0.19, G:0.47, T:0.16
Consensus pattern (21 bp):
GGAGATGGGACGGATGTCGCC
Found at i:108518 original size:19 final size:20
Alignment explanation
Indices: 108496--108533 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
108486 AATATTGTGT
108496 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
108515 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
108534 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:108563 original size:18 final size:20
Alignment explanation
Indices: 108540--108586 Score: 80
Period size: 18 Copynumber: 2.5 Consensus size: 20
108530 TAAACGCGCT
108540 TTGCGAATTTGAC-T-TGTG
1 TTGCGAATTTGACTTCTGTG
108558 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
108578 TTGCGAATT
1 TTGCGAATT
108587 ACAAATTCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 13 0.48
19 1 0.04
20 13 0.48
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:108600 original size:20 final size:20
Alignment explanation
Indices: 108577--108626 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
108567 TGACTTCTGT
108577 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* *
108597 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
108617 GTTGCGAATT
1 GTTGCGAATT
108627 TGGAAACTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:123593 original size:12 final size:13
Alignment explanation
Indices: 123566--123606 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
123556 CTAAGTTTTT
123566 TAAATTTTAAATA
1 TAAATTTTAAATA
*
123579 TAAATTTT-TATA
1 TAAATTTTAAATA
123591 T-AATTTTAAAATA
1 TAAATTTT-AAATA
123604 TAA
1 TAA
123607 TATTATTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 6 0.26
12 4 0.17
13 12 0.52
14 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAATTTTAAATA
Found at i:123597 original size:24 final size:23
Alignment explanation
Indices: 123561--123606 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
123551 GTCTACTAAG
123561 TTTTTTAAATTTT-AAATATAAA
1 TTTTTTAAATTTTAAAATATAAA
123583 TTTTTATATAATTTTAAAATATAA
1 TTTTT-TA-AATTTTAAAATATAA
123607 TATTATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 2 0.10
24 6 0.29
25 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTTAAATTTTAAAATATAAA
Found at i:137039 original size:2 final size:2
Alignment explanation
Indices: 137032--137056 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
137022 AATAAGAAAA
137032 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 A
137057 AACTTCTTTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:141155 original size:59 final size:59
Alignment explanation
Indices: 141070--141208 Score: 167
Period size: 59 Copynumber: 2.4 Consensus size: 59
141060 AATTGATCTT
* * *
141070 TAAACTTTTGGATATTCTATTTTCATCCC-CAACTATGAT-TCTCATT-TAAATTAGTCCC
1 TAAACTTTTGAATATTCTAATTTCATCCCTAAACTATG-TCTCTCATTCTAAA-TAGTCCC
* * *
141128 TAAACTTTTTGAACATTCTAATTTCATCCCTAAACTATGTCTCTCTTTCTAAATGGTCCC
1 TAAAC-TTTTGAATATTCTAATTTCATCCCTAAACTATGTCTCTCATTCTAAATAGTCCC
*
141188 CAAACTTTTGAATATTCTAAT
1 TAAACTTTTGAATATTCTAAT
141209 GGTATCCCCA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
58 5 0.07
59 37 0.54
60 23 0.33
61 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.42
Consensus pattern (59 bp):
TAAACTTTTGAATATTCTAATTTCATCCCTAAACTATGTCTCTCATTCTAAATAGTCCC
Found at i:141462 original size:58 final size:58
Alignment explanation
Indices: 141341--141464 Score: 130
Period size: 58 Copynumber: 2.1 Consensus size: 58
141331 TAGTATACAT
* * * *
141341 ATAGTTTGGGATGAAATTGAATGTTCAAAAAGTTTATGGACTAATTTAGAATAAAGGTT
1 ATAGTTTGGGATGAAATTGAATGTTC-AAAAGTTGATGAACTAATTTAGAAGAAAGGTC
*
141400 ATAGTTTGGGGAT-AAAGTTGAAATGTTC-AAAGTTGA-GAACTAATTTAGAAGGATA-GTC
1 ATAGTTT-GGGATGAAA-TTG-AATGTTCAAAAGTTGATGAACTAATTTAGAA-GAAAGGTC
141458 ATAGTTT
1 ATAGTTT
141465 AAAAAATGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
58 22 0.39
59 19 0.34
60 8 0.14
61 7 0.12
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (58 bp):
ATAGTTTGGGATGAAATTGAATGTTCAAAAGTTGATGAACTAATTTAGAAGAAAGGTC
Done.