Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 23
Found at i:2491106 original size:14 final size:13
Alignment explanation
Indices: 2491084--2491128 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
2491074 ACTTAACATT
2491084 AAAAAAATAAAAA
1 AAAAAAATAAAAA
2491097 AAAAACAATAATAAA
1 AAAAA-AATAA-AAA
*
2491112 AAAATAAGTAAAAA
1 AAAA-AAATAAAAA
2491126 AAA
1 AAA
2491129 GTAAAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.18
14 11 0.39
15 11 0.39
16 1 0.04
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (13 bp):
AAAAAAATAAAAA
Found at i:2491109 original size:40 final size:40
Alignment explanation
Indices: 2491057--2491162 Score: 112
Period size: 39 Copynumber: 2.7 Consensus size: 40
2491047 ACTATGAATC
** *
2491057 AAAACAAATAATAATAAACTTAACATTAAAAAAA-TAAAAAA
1 AAAAC-AATAATAATAAAAATAA-ATAAAAAAAAGTAAAAAA
*
2491098 AAAACAATAATAA-AAAAATAAGTAAAAAAAAGTAAAAAA
1 AAAACAATAATAATAAAAATAAATAAAAAAAAGTAAAAAA
*
2491137 ACAAC-ATAA-AATAAAAATAAAATAAA
1 AAAACAATAATAATAAAAAT-AAATAAA
2491163 CATGAATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
37 2 0.04
38 18 0.32
39 23 0.41
40 8 0.14
41 5 0.09
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (40 bp):
AAAACAATAATAATAAAAATAAATAAAAAAAAGTAAAAAA
Found at i:2491112 original size:13 final size:12
Alignment explanation
Indices: 2491084--2491156 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 12
2491074 ACTTAACATT
2491084 AAAAAAATAA-A
1 AAAAAAATAATA
*
2491095 AAAAAAACAATAA
1 AAAAAAATAAT-A
2491108 TAAAAAAATAAGTA
1 -AAAAAAATAA-TA
2491122 AAAAAAAGTAA-A
1 AAAAAAA-TAATA
2491134 AAAACAACATAA-A
1 AAAA-AA-ATAATA
*
2491147 ATAAAAATAA
1 AAAAAAATAA
2491157 AATAAACATG
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
11 13 0.25
12 7 0.13
13 17 0.33
14 14 0.27
15 1 0.02
ACGTcount: A:0.81, C:0.04, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:2491117 original size:25 final size:24
Alignment explanation
Indices: 2491083--2491162 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
2491073 AACTTAACAT
2491083 TAAAAAAATAAAAAAAAAACAATAA
1 TAAAAAAATAAAAAAAAAA-AATAA
* *
2491108 TAAAAAAATAAGTAAAAAAAAGTAA
1 TAAAAAAATAA-AAAAAAAAAATAA
* *
2491133 AAAAACAACATAAAATAAAAATAA-AA
1 TAAAA-AA-ATAAAA-AAAAAAAATAA
2491159 TAAA
1 TAAA
2491163 CATGAATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
25 19 0.43
26 15 0.34
27 10 0.23
ACGTcount: A:0.80, C:0.04, G:0.03, T:0.14
Consensus pattern (24 bp):
TAAAAAAATAAAAAAAAAAAATAA
Found at i:2491135 original size:38 final size:38
Alignment explanation
Indices: 2491084--2491156 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 38
2491074 ACTTAACATT
2491084 AAAAAAATAAAAAAAA-AACAATAATAA-AAAAATAAGTA
1 AAAAAAATAAAAAAAACAAC-ATAA-AATAAAAATAAGTA
2491122 AAAAAAAGT-AAAAAAACAACATAAAATAAAAATAA
1 AAAAAAA-TAAAAAAAACAACATAAAATAAAAATAA
2491157 AATAAACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
37 2 0.06
38 26 0.81
39 4 0.12
ACGTcount: A:0.81, C:0.04, G:0.03, T:0.12
Consensus pattern (38 bp):
AAAAAAATAAAAAAAACAACATAAAATAAAAATAAGTA
Found at i:2491735 original size:2 final size:2
Alignment explanation
Indices: 2491728--2491778 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2491718 TTATGTTTAC
2491728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2491770 TA TA TA TA T
1 TA TA TA TA T
2491779 CAACATTTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2493147 original size:42 final size:41
Alignment explanation
Indices: 2493034--2493147 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
2493024 GCCCGAAGGT
* * * * *
2493034 CTTATGGATGACCCGAAGGACTTATCATCTTTCTCGAAAGA
1 CTTATAGATAACCTGAAGGACTTATCATCATGCTCGAAAGA
* *
2493075 CTTATAGATAACCTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATAACCTGAAGGACTT-ATCATCATGCTCGAAAGA
***
2493117 CTTACT-GATGGTCTGAAGGACTTACTCATCA
1 CTTA-TAGATAACCTGAAGGACTTA-TCATCA
2493148 AGAAACCCTT
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
41 20 0.34
42 37 0.64
43 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (41 bp):
CTTATAGATAACCTGAAGGACTTATCATCATGCTCGAAAGA
Found at i:2493496 original size:255 final size:255
Alignment explanation
Indices: 2493135--2493652 Score: 835
Period size: 255 Copynumber: 2.0 Consensus size: 255
2493125 TGGTCTGAAG
*
2493135 GACTTACTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAA
1 GACTTACTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCGTAGTTATCAAGGAACCCCTAAA
* *
2493200 AATTAGGCTTCGCTTCCTTTTAAAAAACTTTTGGAGATAATCATCAAGAAACCCCTGAAAATCAA
66 AATTAGGCTTAGCTTCCTTATAAAAAACTTTTGGAGATAATCATCAAGAAACCCCTGAAAATCAA
*
2493265 GCTTAGTTTCTAAAAACTCATTTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCTCGAAGGAC
131 GCTTAGTTTCTAAAAACTCATTTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGAC
* *
2493330 TTATCATCT-TGCTCGAAAGACTTAAAGATGGCCCGAATAACTTACGTATCA-AGCTCGAAA
196 TTATCATCTGT-CTCAAAAGACTTAAAGATGGCCCGAATAACTTACGCATCATA-CTCGAAA
* * * *
2493390 GACTTAGTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCGTAGTTGTTAAGGAACCCTTAAA
1 GACTTACTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCGTAGTTATCAAGGAACCCCTAAA
2493455 AATTAGGCTTAGCTTCCTTAT-AAAAACTCTTTGGAGATAATCATCAAGAAACCCCTGAAAATCA
66 AATTAGGCTTAGCTTCCTTATAAAAAACT-TTTGGAGATAATCATCAAGAAACCCCTGAAAATCA
* * * *
2493519 GGCTTAGTTTCTAAAAACTCATTTGAAAACATCCTGCTCGAATGTTTTATGGATGGCCCGAAGGA
130 AGCTTAGTTTCTAAAAACTCATTTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGA
* * *
2493584 CTTATCATCTGTCTTAAAAGACTTACAGATGGCCCGAATGACTTACGCATCATACTCGAAA
195 CTTATCATCTGTCTCAAAAGACTTAAAGATGGCCCGAATAACTTACGCATCATACTCGAAA
2493645 GACTTACT
1 GACTTACT
2493653 GATGGCCCGA
Statistics
Matches: 242, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
254 7 0.03
255 233 0.96
256 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (255 bp):
GACTTACTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCGTAGTTATCAAGGAACCCCTAAA
AATTAGGCTTAGCTTCCTTATAAAAAACTTTTGGAGATAATCATCAAGAAACCCCTGAAAATCAA
GCTTAGTTTCTAAAAACTCATTTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGAC
TTATCATCTGTCTCAAAAGACTTAAAGATGGCCCGAATAACTTACGCATCATACTCGAAA
Found at i:2493672 original size:20 final size:20
Alignment explanation
Indices: 2493603--2493672 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
2493593 TGTCTTAAAA
*
2493603 GACTTACAGATGGCCCGAAT
1 GACTTACTGATGGCCCGAAT
** * *
2493623 GACTTAC-GCATCATACTCGAAA
1 GACTTACTG-AT--GGCCCGAAT
2493645 GACTTACTGATGGCCCGAAT
1 GACTTACTGATGGCCCGAAT
2493665 GACTTACT
1 GACTTACT
2493673 CATCAAGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 22 0.58
22 14 0.37
23 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
GACTTACTGATGGCCCGAAT
Found at i:2493823 original size:59 final size:58
Alignment explanation
Indices: 2493720--2493831 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 58
2493710 GTTGTCAAAG
2493720 AACCCCTAAAAATTAGGCTTAACTTCCTTTTAAAAACTCATTGAAAATAATCATCAAGA
1 AACCCCTAAAAATTAGGCTTAACTTCCTTTTAAAAACTCATTGAAAAT-ATCATCAAGA
* * *
2493779 AACCCCTAAAAATTAGGCTTAGA-TT-CTTTTGAAAATTGCTTTGAAAATATCAT
1 AACCCCTAAAAATTAGGCTTA-ACTTCCTTTTAAAAACT-CATTGAAAATATCAT
2493832 GTTGTTTGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 15 0.31
59 32 0.67
60 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (58 bp):
AACCCCTAAAAATTAGGCTTAACTTCCTTTTAAAAACTCATTGAAAATATCATCAAGA
Found at i:2494655 original size:41 final size:41
Alignment explanation
Indices: 2494528--2494655 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 41
2494518 TTTATAACTA
* *
2494528 AAACGTCGCAATAGA-GTTGTTTATAGTGACGTTTCTTCAAC
1 AAACGTCGCAATA-ATGTTGTTTATAGTGGCGTTTGTTCAAC
* * * * *
2494569 AAACGCCGCAATAGT-TTGTTAATTTTGTGGCATTTGTAT-AA-
1 AAACGTCGCAATAATGTTGTT--TATAGTGGCGTTTGT-TCAAC
* *
2494610 AAACGTCGCGATAATGTTGTTTATAGTGGTGTTTGTTCAAC
1 AAACGTCGCAATAATGTTGTTTATAGTGGCGTTTGTTCAAC
2494651 AAACG
1 AAACG
2494656 ATGCTATATA
Statistics
Matches: 66, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
39 1 0.02
40 18 0.27
41 29 0.44
42 17 0.26
43 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (41 bp):
AAACGTCGCAATAATGTTGTTTATAGTGGCGTTTGTTCAAC
Found at i:2494674 original size:82 final size:82
Alignment explanation
Indices: 2494527--2494681 Score: 181
Period size: 82 Copynumber: 1.9 Consensus size: 82
2494517 GTTTATAACT
* **
2494527 AAAACGTCGCAATAGAGTTGTTTATAGTGACGTTTCTTCAACAAACGCCGCAATAGTTTGTTAAT
1 AAAACGTCGCAATAGAGTTGTTTATAGTGACGTTTCTTCAACAAACGACGCAATAGTAAGTTAAT
*
2494592 TTTGTGGCATTTGTATA
66 TTAGTGGCATTTGTATA
* ** * *
2494609 AAAACGTCGCGATA-ATGTTGTTTATAGTGGTGTTTGTTCAACAAACGATGCTATATAG-AAG-T
1 AAAACGTCGCAATAGA-GTTGTTTATAGTGACGTTTCTTCAACAAACGACGC-A-ATAGTAAGTT
2494671 AATTTAGTGGC
63 AATTTAGTGGC
2494682 GTTTATCAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
81 1 0.02
82 54 0.89
83 2 0.03
84 4 0.07
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (82 bp):
AAAACGTCGCAATAGAGTTGTTTATAGTGACGTTTCTTCAACAAACGACGCAATAGTAAGTTAAT
TTAGTGGCATTTGTATA
Found at i:2495248 original size:22 final size:22
Alignment explanation
Indices: 2495223--2495267 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2495213 AAGTGTTTTT
2495223 TTGCTTTCGAATAGAAAAATAA
1 TTGCTTTCGAATAGAAAAATAA
* *
2495245 TTGCTTTCTAATAGGAAAATAA
1 TTGCTTTCGAATAGAAAAATAA
2495267 T
1 T
2495268 ACCTTCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
TTGCTTTCGAATAGAAAAATAA
Found at i:2496616 original size:41 final size:41
Alignment explanation
Indices: 2496565--2496673 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 41
2496555 ATATGATTAA
* *
2496565 TTTAGCGGCGTTTGTGAGAAAATGCCGAAATAGCAATAAAC
1 TTTAGTGGCGTTTGTGAGAAAACGCCGAAATAGCAATAAAC
* * * ** *
2496606 TTTAGTGGCGTTTTTGAGAAAACGCCGCAATATCCTTATAC
1 TTTAGTGGCGTTTGTGAGAAAACGCCGAAATAGCAATAAAC
**
2496647 TTTAGTGGCGTTTGTGACCAAACGCCG
1 TTTAGTGGCGTTTGTGAGAAAACGCCG
2496674 TTATATCCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (41 bp):
TTTAGTGGCGTTTGTGAGAAAACGCCGAAATAGCAATAAAC
Found at i:2496762 original size:41 final size:42
Alignment explanation
Indices: 2496717--2496795 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
2496707 AAAACGCCGT
*
2496717 AATAGTTTTGTCATTTAGTGGCGTTTTT-TAATAAATGCCTC
1 AATAGTTTTGTCATTTAGGGGCGTTTTTGTAATAAATGCCTC
**
2496758 AATAGTTTTGTGTTTTAGGGGCGTTTTTGTAATAAATG
1 AATAGTTTTGTCATTTAGGGGCGTTTTTGTAATAAATG
2496796 TTGTATAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 25 0.74
42 9 0.26
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.47
Consensus pattern (42 bp):
AATAGTTTTGTCATTTAGGGGCGTTTTTGTAATAAATGCCTC
Found at i:2496807 original size:42 final size:42
Alignment explanation
Indices: 2496717--2496835 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 42
2496707 AAAACGCCGT
** *
2496717 AATAGTTTTGTCATTTAGTGGCGTTTTT-TAATAAATGCCTC
1 AATAGTTTTGTGTTTTAGGGGCGTTTTTGTAATAAATGCCTC
* *
2496758 AATAGTTTTGTGTTTTAGGGGCGTTTTTGTAATAAATG-TTG
1 AATAGTTTTGTGTTTTAGGGGCGTTTTTGTAATAAATGCCTC
* * * *
2496799 TATAAGTTTGGCGTTTTAGGGGCATTTTTGTAATAAA
1 AAT-AGTTTTGTGTTTTAGGGGCGTTTTTGTAATAAA
2496836 CGTCGCCATT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 28 0.42
42 39 0.58
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (42 bp):
AATAGTTTTGTGTTTTAGGGGCGTTTTTGTAATAAATGCCTC
Found at i:2500541 original size:21 final size:21
Alignment explanation
Indices: 2500523--2500629 Score: 117
Period size: 21 Copynumber: 5.1 Consensus size: 21
2500513 ATGAAGCAAG
*
2500523 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGTAGCAGC
**
2500544 GGAAGCAGCTAGAGTAGCAGC
1 GGAAGCAGAGAGAGTAGCAGC
**
2500565 GGAAGCAGCTAGAGTAGCAGC
1 GGAAGCAGAGAGAGTAGCAGC
* *
2500586 GGAAGCAGAGAGAGAAGCAGT
1 GGAAGCAGAGAGAGTAGCAGC
* *
2500607 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGTA-GCAGC
2500628 GG
1 GG
2500630 CAGAACAGAG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
20 1 0.01
21 74 0.99
ACGTcount: A:0.36, C:0.18, G:0.42, T:0.05
Consensus pattern (21 bp):
GGAAGCAGAGAGAGTAGCAGC
Found at i:2500605 original size:42 final size:41
Alignment explanation
Indices: 2500515--2500644 Score: 118
Period size: 42 Copynumber: 3.1 Consensus size: 41
2500505 AGCGAAAAAT
**
2500515 GAAGCAAGGGAAGCAGAGAGAGCAGCAGCGGAAGCAGCTAGA
1 GAAGC-AGGGAAGCAGAGAGAGCAGCAGCGGAAGCAGAGAGA
* ** *
2500557 GTAGCAGCGGAAGCAGCTAGAGTAGCAGCGGAAGCAGAGAGA
1 GAAGCAG-GGAAGCAGAGAGAGCAGCAGCGGAAGCAGAGAGA
* * * * *
2500599 GAAGCAGTGGCAGCACAGAGAG-AGGCAGCGGCAGAACAGAGA
1 GAAGCAG-GGAAGCAGAGAGAGCA-GCAGCGGAAGCAGAGAGA
2500641 GAAG
1 GAAG
2500645 TAATATATCA
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
41 3 0.04
42 68 0.96
ACGTcount: A:0.38, C:0.17, G:0.41, T:0.04
Consensus pattern (41 bp):
GAAGCAGGGAAGCAGAGAGAGCAGCAGCGGAAGCAGAGAGA
Found at i:2500631 original size:21 final size:21
Alignment explanation
Indices: 2500526--2500644 Score: 89
Period size: 21 Copynumber: 5.7 Consensus size: 21
2500516 AAGCAAGGGA
* * *
2500526 AGCAGAGAGAGCAGCAGCGGA
1 AGCACAGAGAGAAGCAGCGGC
* * *
2500547 AGCAGC-TAGAGTAGCAGCGGA
1 AGCA-CAGAGAGAAGCAGCGGC
* * *
2500568 AGCAGC-TAGAGTAGCAGCGGA
1 AGCA-CAGAGAGAAGCAGCGGC
* *
2500589 AGCAGAGAGAGAAGCAGTGGC
1 AGCACAGAGAGAAGCAGCGGC
*
2500610 AGCACAGAGAGAGGCAGCGGC
1 AGCACAGAGAGAAGCAGCGGC
*
2500631 AGAACAGAGAGAAG
1 AGCACAGAGAGAAG
2500645 TAATATATCA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.38, C:0.18, G:0.40, T:0.04
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGCGGC
Found at i:2501025 original size:43 final size:46
Alignment explanation
Indices: 2500978--2501074 Score: 121
Period size: 43 Copynumber: 2.2 Consensus size: 46
2500968 TACATTTAGT
*
2500978 GGCGTTTGT-GATAAAAATGCCGCGAAATCGCAAGACATA-T-TGC
1 GGCGTTTGTCGACAAAAATGCCGCGAAATCGCAAGACATATTCTGC
* ** *
2501021 GGCGTTT-TCGACGAAAATGCCGTTAAATCTCAAGACATATTCTGC
1 GGCGTTTGTCGACAAAAATGCCGCGAAATCGCAAGACATATTCTGC
2501066 GGCGTTTGT
1 GGCGTTTGT
2501075 AGGAAAACGC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
43 32 0.71
44 1 0.02
45 10 0.22
46 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (46 bp):
GGCGTTTGTCGACAAAAATGCCGCGAAATCGCAAGACATATTCTGC
Found at i:2501134 original size:41 final size:39
Alignment explanation
Indices: 2501055--2501152 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 39
2501045 AAATCTCAAG
* * *
2501055 ACATATTCTGCGGCGTTTGTAGGAAAACGCCGCTAAATATCA
1 ACATCTTCTGCGGCG-TTGTAGGAAAACACCGC-AAA-ATAA
* * *
2501097 ACATCTTCTGCGACGTTGTAGGAAAACACGGGAAAATAA
1 ACATCTTCTGCGGCGTTGTAGGAAAACACCGCAAAATAA
*
2501136 ACATCTACTGCGGCGTT
1 ACATCTTCTGCGGCGTT
2501153 TGTGAAGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
39 18 0.38
40 3 0.06
41 14 0.29
42 13 0.27
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (39 bp):
ACATCTTCTGCGGCGTTGTAGGAAAACACCGCAAAATAA
Found at i:2505102 original size:10 final size:10
Alignment explanation
Indices: 2505076--2505142 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 10
2505066 TTTGAGAGGT
2505076 TTTCTTTCTTC
1 TTTCTTT-TTC
2505087 TTTCTTTCTT-
1 TTTCTTT-TTC
2505097 TTTCTTTTTC
1 TTTCTTTTTC
*
2505107 TTTTTTTTTC
1 TTTCTTTTTC
2505117 TCTT-TTTTT-
1 T-TTCTTTTTC
*
2505126 TTCTCTTTTTT
1 TT-TCTTTTTC
2505137 TTTCTT
1 TTTCTT
2505143 CTGTTTTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
8 1 0.02
9 4 0.08
10 31 0.62
11 14 0.28
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:2505108 original size:12 final size:11
Alignment explanation
Indices: 2505075--2505184 Score: 78
Period size: 12 Copynumber: 9.2 Consensus size: 11
2505065 ATTTGAGAGG
*
2505075 TTTTCTTTCTT
1 TTTTTTTTCTT
* *
2505086 CTTTCTTTCTT
1 TTTTTTTTCTT
2505097 TTTCTTTTTC-T
1 TTT-TTTTTCTT
2505108 TTTTTTTTCTCT
1 TTTTTTTTCT-T
2505120 TTTTTTTTCTCT
1 TTTTTTTTCT-T
2505132 TTTTTTTTCTT
1 TTTTTTTTCTT
*
2505143 CTGTTTTTTATGTT
1 -T-TTTTTT-TCTT
*
2505157 TTTCATTTTATATT
1 TTT--TTTT-TCTT
2505171 TTTTTCTTTCTT
1 TTTTT-TTTCTT
2505183 TT
1 TT
2505185 CTATCTTTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
10 6 0.07
11 17 0.20
12 38 0.45
13 9 0.11
14 14 0.17
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:2505126 original size:22 final size:21
Alignment explanation
Indices: 2505091--2505138 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 21
2505081 TTCTTCTTTC
2505091 TTTCTTTTTCTTTTTCTTTTTT
1 TTTCTTTTT-TTTTTCTTTTTT
2505113 TTTCTCTTTTTTTTTCTCTTTTT
1 TTTCT-TTTTTTTTTCT-TTTTT
2505136 TTT
1 TTT
2505139 TCTTCTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTCTTTTTTTTTTCTTTTTT
Found at i:2505132 original size:24 final size:24
Alignment explanation
Indices: 2505075--2505151 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 24
2505065 ATTTGAGAGG
*
2505075 TTTTCTTTCTTCTTTCTTTCTTTTTCT
1 TTTTCTTT-TTTTTTC-TTCTTTTT-T
2505102 TTTTCTTTTTTTTTC-TCTTTTTT
1 TTTTCTTTTTTTTTCTTCTTTTTT
*
2505125 TTTCTCTTTTTTTTTCTTCTGTTTT
1 TTT-TCTTTTTTTTTCTTCTTTTTT
2505150 TT
1 TT
2505152 ATGTTTTTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.09
24 19 0.41
25 9 0.20
26 6 0.13
27 8 0.17
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (24 bp):
TTTTCTTTTTTTTTCTTCTTTTTT
Found at i:2505220 original size:22 final size:22
Alignment explanation
Indices: 2505179--2505221 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2505169 TTTTTTTCTT
*
2505179 TCTTTTCTATCTTTTTTCTATA
1 TCTTTTCTATCTTTTCTCTATA
2505201 TCTTTTCT-TCTTTCTCTCTAT
1 TCTTTTCTATCTTT-TCTCTAT
2505222 GTTGTCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.67
Consensus pattern (22 bp):
TCTTTTCTATCTTTTCTCTATA
Found at i:2508601 original size:21 final size:20
Alignment explanation
Indices: 2508568--2508660 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
2508558 AACAAGTTGA
* *
2508568 AATTTAACAAATAT-GGTTTC
1 AATTTGACAAA-ATCGGTTAC
* * *
2508588 AATTTGACGAAATAGGTAAC
1 AATTTGACAAAATCGGTTAC
*
2508608 AAATTTGACAAAATCGGTTAA
1 -AATTTGACAAAATCGGTTAC
* *
2508629 AATTTGACAAAATCGATTTC
1 AATTTGACAAAATCGGTTAC
*
2508649 AATTTGAGAAAA
1 AATTTGACAAAA
2508661 CCGATATAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 41 0.69
21 16 0.27
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (20 bp):
AATTTGACAAAATCGGTTAC
Found at i:2511163 original size:22 final size:22
Alignment explanation
Indices: 2511137--2511181 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2511127 AATGTATTAA
2511137 TGTTGTAAGTTAATTTGGAATG
1 TGTTGTAAGTTAATTTGGAATG
2511159 TGTTGTAAGTTAATTTGGAATG
1 TGTTGTAAGTTAATTTGGAATG
2511181 T
1 T
2511182 TATTGGCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (22 bp):
TGTTGTAAGTTAATTTGGAATG
Found at i:2511224 original size:12 final size:12
Alignment explanation
Indices: 2511207--2511244 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2511197 AGCGGGGAGA
2511207 AGAAGAGAAGGT
1 AGAAGAGAAGGT
*
2511219 AGAAGAAAAGGT
1 AGAAGAGAAGGT
*
2511231 ACAAGAGAAGGT
1 AGAAGAGAAGGT
2511243 AG
1 AG
2511245 TAGGGGGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.37, T:0.08
Consensus pattern (12 bp):
AGAAGAGAAGGT
Found at i:2512229 original size:226 final size:225
Alignment explanation
Indices: 2511833--2512425 Score: 739
Period size: 226 Copynumber: 2.6 Consensus size: 225
2511823 AATGTACACG
* ** * * *
2511833 TAATATGTTGATAATACTGATAATAAATCAAGTAATTAATATATATATTTTTATCGTCGGATTTC
1 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACCTAT-T-TTGTTATAGTCGGATATC
* * * *
2511898 TAAGGCCCCATCAGCTTTAAACAGTCGCTACCTATTACATTAAATAAGCGCTATTTGTTATGTTA
64 TAAGGCCCCATCAGCTTTAAACAGACGCTACCTATTACATTAAATAAACACTACTTGTTATGTTA
* *
2511963 TTATGGTTGATAATGTGTCCAGTAATTAACCTATTTTGTTATCGTCATATTTTTAAGGCTCCATC
129 TTATGGTTGATAATGTGTCCAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATC
* *
2512028 AACTTAAACTTTTGTAAGATTTTAGGCGCTACA
194 AACTTAAACTTTGGTAACATTTTAGGCGCT-CA
* *
2512061 TAATATGTTAATAATACTGATAACAAATCAAGTAATTAACCTATTTTGTTATAGTTGGATATCTA
1 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACCTATTTTGTTATAGTCGGATATCTA
*
2512126 AGGCCTCATCAGAC-TTAAACAGACGCTACCTATTACATTAAATAAACACTACTTGTTATGTTAT
66 AGGCCCCATCAG-CTTTAAACAGACGCTACCTATTACATTAAATAAACACTACTTGTTATGTTAT
** *
2512190 TATGGTTGATAATGT-TCCAAGTAATTAATTTATTTTGTTATCGTCGGATTTCTAAGGCTCCATC
130 TATGGTTGATAATGTGTCC-AGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATC
* *
2512254 AGCTTAAACTTTGGTAACATTTTAGGCTCTCA
194 AACTTAAACTTTGGTAACATTTTAGGCGCTCA
* * * * *
2512286 TAATATGTTGATAATATTAATAAC-AATCAAGTAATTAACCTATTTTGTTATCGTCGAATTTCTA
1 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACCTATTTTGTTATAGTCGGATATCTA
* * * * * ** * * * *
2512350 AAGTCCCATCAGTTTTAAAAATG-CGCTACTTATTACGGTACATAAGA-GCTACCT-ATATGTTA
66 AGGCCCCATCAGCTTTAAACA-GACGCTACCTATTACATTAAATAA-ACACTACTTGTTATGTTA
2512412 TTATGGTTGATAAT
129 TTATGGTTGATAAT
2512426 ATTTTTAATA
Statistics
Matches: 319, Mismatches: 41, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
223 21 0.07
224 74 0.23
225 28 0.09
226 154 0.48
227 2 0.01
228 40 0.13
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (225 bp):
TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACCTATTTTGTTATAGTCGGATATCTA
AGGCCCCATCAGCTTTAAACAGACGCTACCTATTACATTAAATAAACACTACTTGTTATGTTATT
ATGGTTGATAATGTGTCCAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAA
CTTAAACTTTGGTAACATTTTAGGCGCTCA
Found at i:2517941 original size:29 final size:29
Alignment explanation
Indices: 2517907--2517994 Score: 167
Period size: 29 Copynumber: 3.0 Consensus size: 29
2517897 CCTAAATTAA
*
2517907 TTTGATGTCATTGCTTACATTAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2517936 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2517965 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2517994 T
1 T
2517995 AGGTGAAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2522654 original size:29 final size:29
Alignment explanation
Indices: 2522620--2522678 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2522610 CCTAAATTAA
2522620 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2522649 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2522678 T
1 T
2522679 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2530059 original size:18 final size:19
Alignment explanation
Indices: 2530032--2530080 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
2530022 GGATTATCAG
*
2530032 TGGTCCTTCGGGACT-TAA
1 TGGTCATTCGGGACTATAA
* *
2530050 TGGTCATTCGAGA-TATAG
1 TGGTCATTCGGGACTATAA
2530068 TGGT-ATTCGGGAC
1 TGGTCATTCGGGAC
2530081 AAATATTCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (19 bp):
TGGTCATTCGGGACTATAA
Found at i:2532513 original size:18 final size:19
Alignment explanation
Indices: 2532478--2532514 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2532468 CACGGAATGT
2532478 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2532498 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2532515 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2532736 original size:35 final size:37
Alignment explanation
Indices: 2532665--2532737 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
2532655 GTTGGAAAAT
* *
2532665 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
*
2532702 ATTTATATAATTT-TTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAAATT-AAAATCATAAA
2532737 A
1 A
2532738 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 13 0.41
36 7 0.22
37 12 0.38
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
Found at i:2552574 original size:20 final size:19
Alignment explanation
Indices: 2552549--2552591 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
2552539 ACGGTTTTTT
*
2552549 TATTTTCTTA-TAATATATAA
1 TATTTT-TTATTAAAATAT-A
2552569 TATTTTTTATTAAAATATA
1 TATTTTTTATTAAAATATA
2552588 TATT
1 TATT
2552592 AAGGTTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTTTATTAAAATATA
Found at i:2553672 original size:22 final size:23
Alignment explanation
Indices: 2553647--2553690 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2553637 AATTAAGTTT
2553647 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
2553669 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
2553691 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:2562571 original size:20 final size:20
Alignment explanation
Indices: 2562546--2562585 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2562536 TAACTCAACA
*
2562546 GGGTATATGTTCCCCCTGGG
1 GGGTATATGTACCCCCTGGG
* *
2562566 GGGTATCTGTACCCTCTGGG
1 GGGTATATGTACCCCCTGGG
2562586 CAATCTGGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.35, T:0.30
Consensus pattern (20 bp):
GGGTATATGTACCCCCTGGG
Found at i:2562948 original size:12 final size:12
Alignment explanation
Indices: 2562916--2562949 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2562906 AGAAAATCAT
*
2562916 TTTGAAATCAAA
1 TTTGAAATTAAA
2562928 TTTGAAATTAAA
1 TTTGAAATTAAA
*
2562940 TTTGGAATTA
1 TTTGAAATTA
2562950 CTCCCCCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (12 bp):
TTTGAAATTAAA
Found at i:2565143 original size:22 final size:23
Alignment explanation
Indices: 2565094--2565153 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2565084 TTGATTCCCT
*
2565094 AAAGGGGGAATCGATACCCATTC
1 AAAGGGGGAATCGATACCCATGC
*
2565117 AAAGGGGGAATCGGTACCCATGC
1 AAAGGGGGAATCGATACCCATGC
*
2565140 -AAGGGGGTATCGAT
1 AAAGGGGGAATCGAT
2565154 TCCTAGCTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 12 0.36
23 21 0.64
ACGTcount: A:0.32, C:0.18, G:0.33, T:0.17
Consensus pattern (23 bp):
AAAGGGGGAATCGATACCCATGC
Found at i:2566699 original size:23 final size:22
Alignment explanation
Indices: 2566654--2566718 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
2566644 TTTTTAATTA
*
2566654 TATTTTTTTATTTATTTACTATAT
1 TATTTTTTTATTTA--TATTATAT
*
2566678 TCCTTTTTTTATTTATATTATAT
1 T-ATTTTTTTATTTATATTATAT
*
2566701 TATTTTTATTATATATAT
1 TATTTTT-TTATTTATAT
2566719 CTTATATCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.14
23 17 0.49
24 1 0.03
25 12 0.34
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTTTTATTTATATTATAT
Found at i:2566705 original size:14 final size:14
Alignment explanation
Indices: 2566686--2566725 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2566676 ATTCCTTTTT
2566686 TTATTTATATTATA
1 TTATTTATATTATA
*
2566700 TTATTTTTATTATA
1 TTATTTATATTATA
2566714 TATATCTTATAT
1 T-TAT-TTATAT
2566726 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:2566890 original size:18 final size:18
Alignment explanation
Indices: 2566845--2566901 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2566835 CTATTTTTGT
* *
2566845 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
2566862 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
2566880 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
2566898 TTTT
1 TTTT
2566902 TTTCTTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:2566898 original size:13 final size:13
Alignment explanation
Indices: 2566882--2566906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2566872 TTACTTTATT
2566882 TTATTTTTTTCTA
1 TTATTTTTTTCTA
2566895 TTATTTTTTTCT
1 TTATTTTTTTCT
2566907 TAATATCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:2566957 original size:36 final size:37
Alignment explanation
Indices: 2566895--2566978 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 37
2566885 TTTTTTTCTA
*
2566895 TTATTT-TTTT-CTTAATATCATGTATATCT-TTATTTT
1 TTATTTGTTTTACTTAATAT-ATATATATCTATTA-TTT
*
2566931 TTATTTGTTTTACTTAATAT-TATATATTTATTATTT
1 TTATTTGTTTTACTTAATATATATATATCTATTATTT
*
2566967 TTACTTGTTTTA
1 TTATTTGTTTTA
2566979 GTAAATACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 27 0.64
37 7 0.17
38 8 0.19
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.67
Consensus pattern (37 bp):
TTATTTGTTTTACTTAATATATATATATCTATTATTT
Found at i:2567161 original size:25 final size:27
Alignment explanation
Indices: 2567108--2567166 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
2567098 TTTTGTTTAT
* *
2567108 TTTTATTTTTTTATTATTTTTTACGTG
1 TTTTATTATTTTATCATTTTTTACGTG
*
2567135 TTTTATTATTTT-TCATTTTTT-CTTG
1 TTTTATTATTTTATCATTTTTTACGTG
2567160 TTTTATT
1 TTTTATT
2567167 TATTATTCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 10 0.34
26 8 0.28
27 11 0.38
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (27 bp):
TTTTATTATTTTATCATTTTTTACGTG
Found at i:2567169 original size:26 final size:28
Alignment explanation
Indices: 2567108--2567170 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
2567098 TTTTGTTTAT
*
2567108 TTTTATTT-TTTTATTATTTTTTACGTG
1 TTTTATTTATTTTATCATTTTTTACGTG
*
2567135 TTTTA-TTATTTT-TCATTTTTT-CTTG
1 TTTTATTTATTTTATCATTTTTTACGTG
2567160 TTTTATTTATT
1 TTTTATTTATT
2567171 ATTCTCGCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 8 0.25
26 15 0.47
27 9 0.28
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (28 bp):
TTTTATTTATTTTATCATTTTTTACGTG
Found at i:2570279 original size:13 final size:12
Alignment explanation
Indices: 2570247--2570292 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 12
2570237 CAATCAGAAC
2570247 AAAAAGAGAAAA
1 AAAAAGAGAAAA
2570259 AAGCAAAGAGAAAA
1 AA--AAAGAGAAAA
2570273 TAAAAAGAGAAAA
1 -AAAAAGAGAAAA
2570286 AATAAAG
1 AA-AAAG
2570293 GAAGATTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.13
13 14 0.47
14 10 0.33
15 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:2570487 original size:69 final size:69
Alignment explanation
Indices: 2570369--2570506 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
2570359 GATTCAAACT
* * * *
2570369 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAACCATTTATGAATAACTGAACCACTCCACTCGAAGATCATAGAGCA
2570434 TCAA
66 TCAA
*
2570438 ATGAGATTGATCAAGCACAACCATTTATGAATAACTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAACCATTTATGAATAACTGAACCACTCCACTCGAAGATCATAGAGCA
2570503 TCAA
66 TCAA
2570507 GAGAGAGACA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.24
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAACCATTTATGAATAACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:2572001 original size:37 final size:38
Alignment explanation
Indices: 2571946--2572020 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
2571936 GAAGATTTTA
* * *
2571946 TCTCGCTTGAGATAGTTTCCCTTGAAACA-AAATATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
*
2571983 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
2572021 AAAACATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (38 bp):
TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
Found at i:2572084 original size:37 final size:39
Alignment explanation
Indices: 2572041--2572115 Score: 118
Period size: 37 Copynumber: 2.0 Consensus size: 39
2572031 TCTTGAAATG
* *
2572041 AATTTTGTCTCTCTTGAGATAGTTTC-C-CTTGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTCTTGAAACAA
2572078 AATTTTGTCTCCCTTGAGACAGTTTCTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTCTTGAAACA
2572116 TAAACATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 24 0.71
38 1 0.03
39 9 0.26
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (39 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTCTTGAAACAA
Found at i:2572169 original size:104 final size:102
Alignment explanation
Indices: 2571946--2572187 Score: 394
Period size: 104 Copynumber: 2.4 Consensus size: 102
2571936 GAAGATTTTA
*
2571946 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
* * *
2572011 ATAAACATTGAAAACATTTCTCTTGAAATGAATTTTG
66 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
*
2572048 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTCTTGAA
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAG-TT-TCTCTTGAA
2572113 ACATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
64 ACATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
* * *
2572152 TCTCTTTTGAGACAGTTTCCCTTGAAACAAATTATT
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATT
2572188 TGAATATGTT
Statistics
Matches: 129, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
102 50 0.39
103 2 0.02
104 77 0.60
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
Found at i:2572285 original size:25 final size:25
Alignment explanation
Indices: 2572250--2572315 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 25
2572240 GGAACTTAGT
2572250 TTTC-TCTCTCTTGAGACAGTCAAA
1 TTTCGTCTCTCTTGAGACAGTCAAA
2572274 TTTCGTCTCTCTTGA-A-A--CAAA
1 TTTCGTCTCTCTTGAGACAGTCAAA
2572295 TTTCGTCTCTCTTGAGACAGT
1 TTTCGTCTCTCTTGAGACAGT
2572316 TTCCCTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
21 19 0.51
22 1 0.03
23 2 0.05
24 5 0.14
25 10 0.27
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (25 bp):
TTTCGTCTCTCTTGAGACAGTCAAA
Found at i:2572394 original size:52 final size:50
Alignment explanation
Indices: 2572317--2572415 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 50
2572307 TGAGACAGTT
**
2572317 TCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAAAAAAAATTTATC
1 TCCCTTGAAACAAAATCTTCAAATTTATTTCCCCTAAAAAAAAATTTATC
* *
2572367 TCCCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACAAAATTT
1 TCCCTTG-AA-ACAAAATCTTCAAATTTATTTCCCCTAAAAAAAAATTT
2572416 TGTTTTCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 7 0.16
51 2 0.05
52 34 0.79
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.35
Consensus pattern (50 bp):
TCCCTTGAAACAAAATCTTCAAATTTATTTCCCCTAAAAAAAAATTTATC
Found at i:2573364 original size:110 final size:110
Alignment explanation
Indices: 2573166--2573401 Score: 293
Period size: 110 Copynumber: 2.2 Consensus size: 110
2573156 TCCCAGTTTC
* ** *
2573166 AGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAATACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTAAACTCAAGACAACACAAGCTCAACTTCACAA
* *
2573231 CGAAGGGGCGACTGATTGTCAACAAATAACTTTTCAGTTTCATTT
66 CGAAAGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTT
* * * * *
2573276 AGAGTCAATTTCAACTTCACAGTGAAGGATATTAAACTCGAGATAACACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTAAACTCAAGACAACACAAGCTCAACTTCACAA
* * * *
2573341 CGAAAGGGCGGCTGGCTGTCAACAAATAA-TTTCCCAG-TTC---C
66 CGAAAGGGCGACTGACTGTCAACAAATAACTTT-TCAGTTTCATTT
2573382 AGAGCCAATTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
2573402 GATGGAGGAT
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
106 19 0.17
109 6 0.06
110 84 0.77
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (110 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTAAACTCAAGACAACACAAGCTCAACTTCACAA
CGAAAGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTT
Found at i:2574806 original size:14 final size:14
Alignment explanation
Indices: 2574787--2574826 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2574777 ATTCCTTTTT
2574787 TTATTTATATTATA
1 TTATTTATATTATA
*
2574801 TTATTTTTATTATA
1 TTATTTATATTATA
2574815 TATATCTTATAT
1 T-TAT-TTATAT
2574827 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:2574896 original size:2 final size:2
Alignment explanation
Indices: 2574889--2574913 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2574879 ATTTACTATG
2574889 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2574914 TTTCTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2575020 original size:18 final size:18
Alignment explanation
Indices: 2574970--2575035 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
2574960 ATATTCTATT
*
2574970 TTTATTTTTATTTATTTA-
1 TTTA-TTTTATTTTTTTAC
* * *
2574988 TATATATTATATTTTTAC
1 TTTATTTTATTTTTTTAC
2575006 TTTATTTTATTTTTTT-C
1 TTTATTTTATTTTTTTAC
2575023 TATTATTTT-TTTT
1 T-TTATTTTATTTT
2575036 CTTAATATCA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 16 0.41
18 23 0.59
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTATTTTTTTAC
Found at i:2575028 original size:31 final size:31
Alignment explanation
Indices: 2574938--2575017 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
2574928 ATTTTATACG
* * *
2574938 TTTTTATATATATTT-TTTCT-TAATATTCTA
1 TTTTTATTTATATTTATTTATAT-ATATTATA
*
2574968 TTTTTATTTTTATTTATTTATATATATTATA
1 TTTTTATTTATATTTATTTATATATATTATA
2574999 TTTTTACTTTAT-TTTATTT
1 TTTTTA-TTTATATTTATTT
2575018 TTTTCTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 13 0.31
31 24 0.57
32 5 0.12
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (31 bp):
TTTTTATTTATATTTATTTATATATATTATA
Found at i:2589624 original size:30 final size:30
Alignment explanation
Indices: 2589590--2589693 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 30
2589580 TCCCGAATAT
2589590 TTAATTTCAATTAATTAAATATAGATTTAA
1 TTAATTTCAATTAATTAAATATAGATTTAA
* * * * *
2589620 TTAATTTGAAATAATAAAATCCCTAAAAAATGATT-A
1 TTAATTTCAATTAATTAAA----T-ATAGAT--TTAA
*
2589656 TTAAATTCCAATTAATTAAATATAGATTTAA
1 TT-AATTTCAATTAATTAAATATAGATTTAA
2589687 TTAATTT
1 TTAATTT
2589694 GAAATAATAA
Statistics
Matches: 53, Mismatches: 12, Indels: 18
0.64 0.14 0.22
Matches are distributed among these distances:
30 22 0.42
31 3 0.06
32 4 0.08
33 1 0.02
34 1 0.02
35 4 0.08
36 3 0.06
37 15 0.28
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (30 bp):
TTAATTTCAATTAATTAAATATAGATTTAA
Found at i:2602566 original size:330 final size:330
Alignment explanation
Indices: 2601965--2602627 Score: 1317
Period size: 330 Copynumber: 2.0 Consensus size: 330
2601955 CAACATGGTT
*
2601965 AGAATATGCAGGAATTCCTCATCTGAAATATGCAGGAAAATGATACAATCATCGACATTAAATAA
1 AGAATATGCAGGAACTCCTCATCTGAAATATGCAGGAAAATGATACAATCATCGACATTAAATAA
2602030 ATGTGCACGGCGAGGTCCACCACGACAAATGCGAAGGCCACAAATACTTCCTCGTTGTTGTTCAA
66 ATGTGCACGGCGAGGTCCACCACGACAAATGCGAAGGCCACAAATACTTCCTCGTTGTTGTTCAA
2602095 TATGGAGAAAGTATGATAGCCCCTGAGCGCATATAACAGACAAAAATGGCGATATGGAATCCCCT
131 TATGGAGAAAGTATGATAGCCCCTGAGCGCATATAACAGACAAAAATGGCGATATGGAATCCCCT
2602160 TAACGAAGGCCTTGTTGTAGAGCGAAAGCATTAGTAAGGCTACTATTGATCCGAACTCGGTATGT
196 TAACGAAGGCCTTGTTGTAGAGCGAAAGCATTAGTAAGGCTACTATTGATCCGAACTCGGTATGT
2602225 AATAGTGGAGACAGAAGATAAGATAAGCTCAACCCAAGTGTTGCAAACCCCAACCATAGCATCAT
261 AATAGTGGAGACAGAAGATAAGATAAGCTCAACCCAAGTGTTGCAAACCCCAACCATAGCATCAT
2602290 GCTAC
326 GCTAC
2602295 AGAATATGCAGGAACTCCTCATCTGAAATATGCAGGAAAATGATACAATCATCGACATTAAATAA
1 AGAATATGCAGGAACTCCTCATCTGAAATATGCAGGAAAATGATACAATCATCGACATTAAATAA
2602360 ATGTGCACGGCGAGGTCCACCACGACAAATGCGAAGGCCACAAATACTTCCTCGTTGTTGTTCAA
66 ATGTGCACGGCGAGGTCCACCACGACAAATGCGAAGGCCACAAATACTTCCTCGTTGTTGTTCAA
2602425 TATGGAGAAAGTATGATAGCCCCTGAGCGCATATAACAGACAAAAATGGCGATATGGAATCCCCT
131 TATGGAGAAAGTATGATAGCCCCTGAGCGCATATAACAGACAAAAATGGCGATATGGAATCCCCT
2602490 TAACGAAGGCCTTGTTGTAGAGCGAAAGCATTAGTAAGGCTACTATTGATCCGAACTCGGTATGT
196 TAACGAAGGCCTTGTTGTAGAGCGAAAGCATTAGTAAGGCTACTATTGATCCGAACTCGGTATGT
2602555 AATAGTGGAGACAGAAGATAAGATAAGCTCAACCCAAGTGTTGCAAACCCCAACCATAGCATCAT
261 AATAGTGGAGACAGAAGATAAGATAAGCTCAACCCAAGTGTTGCAAACCCCAACCATAGCATCAT
2602620 GCTAC
326 GCTAC
2602625 AGA
1 AGA
2602628 GAAATGGCCT
Statistics
Matches: 332, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
330 332 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (330 bp):
AGAATATGCAGGAACTCCTCATCTGAAATATGCAGGAAAATGATACAATCATCGACATTAAATAA
ATGTGCACGGCGAGGTCCACCACGACAAATGCGAAGGCCACAAATACTTCCTCGTTGTTGTTCAA
TATGGAGAAAGTATGATAGCCCCTGAGCGCATATAACAGACAAAAATGGCGATATGGAATCCCCT
TAACGAAGGCCTTGTTGTAGAGCGAAAGCATTAGTAAGGCTACTATTGATCCGAACTCGGTATGT
AATAGTGGAGACAGAAGATAAGATAAGCTCAACCCAAGTGTTGCAAACCCCAACCATAGCATCAT
GCTAC
Found at i:2605888 original size:36 final size:36
Alignment explanation
Indices: 2605846--2605921 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2605836 TTATAGCTAA
*
2605846 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2605882 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2605918 AAAA
1 AAAA
2605922 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2610415 original size:15 final size:15
Alignment explanation
Indices: 2610397--2610426 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2610387 CCACGGTGCT
2610397 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2610412 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
2610427 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:2610891 original size:36 final size:36
Alignment explanation
Indices: 2610849--2610924 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2610839 TTATAGCTAA
*
2610849 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2610885 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2610921 AAAA
1 AAAA
2610925 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2611993 original size:13 final size:14
Alignment explanation
Indices: 2611958--2612000 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
2611948 CAACCCACAC
*
2611958 TGAGTCAAATCAGT
1 TGAGTCAACTCAGT
2611972 TGAGTCAACTCA-T
1 TGAGTCAACTCAGT
*
2611985 TGGGTCAACTC-GT
1 TGAGTCAACTCAGT
2611998 TGA
1 TGA
2612001 CTTTGACCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (14 bp):
TGAGTCAACTCAGT
Found at i:2614461 original size:30 final size:30
Alignment explanation
Indices: 2614390--2614461 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
2614380 GGTCAACTCG
* *
2614390 TTGACTTTGACCGAGTCAACCTATTGACCA
1 TTGACTTTGACCGAATCAACCCATTGACCA
* * * * * *
2614420 ATCACTATGACCGAATCAACCCGTTTACCT
1 TTGACTTTGACCGAATCAACCCATTGACCA
2614450 TTGACTTTGACC
1 TTGACTTTGACC
2614462 AAAAAGTTAA
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (30 bp):
TTGACTTTGACCGAATCAACCCATTGACCA
Found at i:2619306 original size:416 final size:412
Alignment explanation
Indices: 2618498--2619337 Score: 1122
Period size: 416 Copynumber: 2.0 Consensus size: 412
2618488 TATGTTTAAT
* *
2618498 TATAGTGAAAAATATATTGTCACAAAGATTTCCATCCATATTTTTTTGCGCAAAAAAGTCATATA
1 TATAGTAAAAAATATATTGTCACAAAGATTTCCATCCATATTTTTTTGCACAAAAAAGTCATATA
* *
2618563 ATGACAAATTTTGTAACTATAAATGTTAATAATTATTACATAAAACATTGTCACAAAAAATAATG
66 ATAACAAATTTTGTAACTATAAATGTTAATAATTATTACAGAAAACATTGTCACAAAAAATAATG
* * *
2618628 ATATTCACGTTTTTTGTGACAAATTATATTTATAGTTATAAATTTTAACTATAGTGATAGCATAT
131 ATATTCACGATTTTTGTGACAAATTATACTTATAGTTATAAATTTTAACTATAGTGATAACATAT
* * * *
2618693 ATTAATCGTCATAATTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGACAATTTTTATAA
196 ATTAATCG-CATAAATATTTTTCTCAACTTTTTTGTTTCAAAAGCTATATTGACAAGTTTTATAA
* * *
2618758 TTATAATTTATAATTATTGTTATAGAAAAAATATCATATCAATAAAATTCAAGTTTTTTGTATTA
260 TTATAATTTATAATAATTGTTATAGAAAAAATATCACATCAATAAAATTCAAGTTTTTTGTAATA
* * *
2618823 AATTATTTTTTTACTTATATATTTTAATCATTATGAAAAATTATACTATCAAAATTATTTCTCCC
325 AATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAAAA-TAATTATCCC
*
2618888 TATTTTTTTAATGTCAAAAATGTTA
389 TA-TTTTTTAATGCCAAAAATGTTA
* * *
2618913 TATAGTAACAAAATATATTTTCATAAAGATTTTCC-TCTATATTTTTTTGCACTAGAAAAA-TCA
1 TATAGTAA-AAAATATATTGTCACAAAGA-TTTCCATCCATATTTTTTTGCAC-A-AAAAAGTCA
** * * * *
2618976 TATTGTAATAATTTTTGTAACTATAAGTGTTTATAATTATTACAGAAAACATTGTCACAAAAAAT
62 TATAATAACAAATTTTGTAACTATAAATGTTAATAATTATTACAGAAAACATTGTCACAAAAAAT
* * * * *
2619041 AATGGTATTCAC-ATTTTTGTGAGAAATTATACTTGTAGTTATAAATTTTAATTATAGTTATAAC
127 AATGATATTCACGATTTTTGTGACAAATTATACTTATAGTTATAAATTTTAACTATAGTGATAAC
* *
2619105 ATATATT-AT-G-ATAAATATTTTTTTCAACTTTTTTTTGTTTCAAAAAGCTATATTGATAAGTT
192 ATATATTAATCGCATAAATATTTTTCTCAAC--TTTTTTGTTTC-AAAAGCTATATTGACAAGTT
* *
2619167 TTGTAATTATAATTTATAGTAATTGTTATAGAAAAAATTATCACATCAGATAATAAAATTCAAGT
254 TTATAATTATAATTTATAATAATTGTTATAGAAAAAA-TATCACATC----AATAAAATTCAAGT
* *
2619232 TTTTTGTAATCAATTA-TTTTGTATTTATATATTTTAATCATTATGAAAAATTATACTAT-AAAA
314 TTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAAAA
**
2619295 -AATTATCCCTATTTTTTGGTGCCAAAAATGTTA
379 TAATTATCCCTATTTTTTAATGCCAAAAATGTTA
2619328 TATAGTAAAA
1 TATAGTAAAA
2619338 GTTTTATAGT
Statistics
Matches: 373, Mismatches: 40, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
412 15 0.04
414 14 0.04
415 87 0.23
416 102 0.27
417 77 0.21
418 9 0.02
419 41 0.11
420 28 0.08
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (412 bp):
TATAGTAAAAAATATATTGTCACAAAGATTTCCATCCATATTTTTTTGCACAAAAAAGTCATATA
ATAACAAATTTTGTAACTATAAATGTTAATAATTATTACAGAAAACATTGTCACAAAAAATAATG
ATATTCACGATTTTTGTGACAAATTATACTTATAGTTATAAATTTTAACTATAGTGATAACATAT
ATTAATCGCATAAATATTTTTCTCAACTTTTTTGTTTCAAAAGCTATATTGACAAGTTTTATAAT
TATAATTTATAATAATTGTTATAGAAAAAATATCACATCAATAAAATTCAAGTTTTTTGTAATAA
ATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAAAATAATTATCCCTA
TTTTTTAATGCCAAAAATGTTA
Found at i:2623275 original size:21 final size:19
Alignment explanation
Indices: 2623251--2623293 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2623241 TTGATTTTAT
*
2623251 AATTTAACTTAATTGTGATAA
1 AATTT-ACTT-ATTGTAATAA
*
2623272 AATTTACTTTTTGTAATAA
1 AATTTACTTATTGTAATAA
2623291 AAT
1 AAT
2623294 AATTGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (19 bp):
AATTTACTTATTGTAATAA
Found at i:2623964 original size:23 final size:23
Alignment explanation
Indices: 2623934--2623985 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
2623924 AGGGTAAACT
*
2623934 CGTTGACTTTGACCTAGTCAACC
1 CGTTGACTTTGACCGAGTCAACC
2623957 CGTTGACTTTGACCGAGTCAACC
1 CGTTGACTTTGACCGAGTCAACC
2623980 CGTTGA
1 CGTTGA
2623986 TCGTTCACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (23 bp):
CGTTGACTTTGACCGAGTCAACC
Found at i:2624015 original size:30 final size:30
Alignment explanation
Indices: 2623957--2624030 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 30
2623947 CTAGTCAACC
* * *
2623957 CGTTGACTTTGACCGAGTCAACCCGTTGAT
1 CGTTCACTTTGACCGAATCAACACGTTGAT
* * *
2623987 CGTTCACTTTGGCCGAATCAACATGTTGAC
1 CGTTCACTTTGACCGAATCAACACGTTGAT
* *
2624017 CTTTGACTTTGACC
1 CGTTCACTTTGACC
2624031 AAAAAGTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (30 bp):
CGTTCACTTTGACCGAATCAACACGTTGAT
Found at i:2625782 original size:31 final size:31
Alignment explanation
Indices: 2625744--2625820 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
2625734 TAAGGTGACC
* *
2625744 CTTGGGTAGTCTCTGTGGCACCGAGATA-TTT
1 CTTGGGTAGCCTCTGTGACACCGAGA-ACTTT
* *
2625775 CTTGGGTAGGCCTCCGTGACCCCGAGAACTTT
1 CTTGGGTA-GCCTCTGTGACACCGAGAACTTT
*
2625807 CTTGGGTAGGCTCT
1 CTTGGGTAGCCTCT
2625821 CAGGCCTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
31 13 0.34
32 25 0.66
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.31
Consensus pattern (31 bp):
CTTGGGTAGCCTCTGTGACACCGAGAACTTT
Found at i:2634956 original size:22 final size:22
Alignment explanation
Indices: 2634928--2634980 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
2634918 AAACATTTCT
2634928 ATGGCAGTTTACTCATCAGAAA
1 ATGGCAGTTTACTCATCAGAAA
2634950 ATGGCAGTTTACTCATCAGAAA
1 ATGGCAGTTTACTCATCAGAAA
*
2634972 TTGGCAGTT
1 ATGGCAGTT
2634981 AGAGTGGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (22 bp):
ATGGCAGTTTACTCATCAGAAA
Found at i:2642931 original size:3 final size:3
Alignment explanation
Indices: 2642923--2642998 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
2642913 ATCCTTATCT
2642923 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2642971 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2642999 AGAAATGCCC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2649379 original size:20 final size:20
Alignment explanation
Indices: 2649354--2649405 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2649344 GGAAGGGTAA
2649354 TATCGATACTCTTGACTGAG
1 TATCGATACTCTTGACTGAG
2649374 TATCGATACTCTTGACTGAG
1 TATCGATACTCTTGACTGAG
2649394 TATCGATACTCT
1 TATCGATACTCT
2649406 GAGGTGGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (20 bp):
TATCGATACTCTTGACTGAG
Found at i:2652040 original size:31 final size:31
Alignment explanation
Indices: 2651998--2652107 Score: 177
Period size: 31 Copynumber: 3.5 Consensus size: 31
2651988 AGGGTCAAGG
*
2651998 GTTTACCTATGTTATTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2652029 GTTTACTTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2652060 GTTTACCTATGTTCTTCGGGACATA-GAGACT
1 GTTTACCTATGTTCTTCGGGACATATG-GACT
*
2652091 GTTTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
2652108 AGGATCTATG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
30 1 0.01
31 73 0.99
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2656457 original size:31 final size:31
Alignment explanation
Indices: 2656419--2656543 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
2656409 AGGGTCGAGG
2656419 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2656450 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2656481 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2656512 GTTTACCTAGGTTCTTCAGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2656543 G
1 G
2656544 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2657778 original size:15 final size:15
Alignment explanation
Indices: 2657758--2657794 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2657748 TACCTTTTAT
2657758 TTTAAATAATTTACC
1 TTTAAATAATTTACC
*
2657773 TTTAAATAGTTTACC
1 TTTAAATAATTTACC
2657788 TTTAAAT
1 TTTAAAT
2657795 GGTAAATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (15 bp):
TTTAAATAATTTACC
Found at i:2657802 original size:7 final size:7
Alignment explanation
Indices: 2657790--2657818 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2657780 AGTTTACCTT
2657790 TAAATGG
1 TAAATGG
2657797 TAAATGG
1 TAAATGG
2657804 TAAATGG
1 TAAATGG
2657811 TAAATGG
1 TAAATGG
2657818 T
1 T
2657819 GTTTATCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (7 bp):
TAAATGG
Found at i:2658033 original size:16 final size:16
Alignment explanation
Indices: 2658012--2658044 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2658002 ACCTTTGTTT
2658012 CACTTGCGACTCGTCA
1 CACTTGCGACTCGTCA
2658028 CACTTGCGACTCGTCA
1 CACTTGCGACTCGTCA
2658044 C
1 C
2658045 CCAACGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.39, G:0.18, T:0.24
Consensus pattern (16 bp):
CACTTGCGACTCGTCA
Found at i:2665964 original size:16 final size:16
Alignment explanation
Indices: 2665945--2665978 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2665935 TCGTTAATTG
*
2665945 TTAAGCTCGTTGCTCA
1 TTAAGCTCGATGCTCA
2665961 TTAAGCTCGATGCTCA
1 TTAAGCTCGATGCTCA
2665977 TT
1 TT
2665979 GCTCGCCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (16 bp):
TTAAGCTCGATGCTCA
Found at i:2668503 original size:42 final size:41
Alignment explanation
Indices: 2668416--2668511 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
2668406 GATTGTGGCG
* * * * *
2668416 TTTTTAGACAAACGCCGCTACAGATAAGTATTTTAATGGCAT
1 TTTTTAG-CAAACGCCGCGAAAAATAAGTACTTTAACGGCAT
* *
2668458 TTTTTAGCAAACGCCGCGAAAAATATGTACTTTAGCGGCAT
1 TTTTTAGCAAACGCCGCGAAAAATAAGTACTTTAACGGCAT
*
2668499 TTTTTAGAAAACG
1 TTTTTAGCAAACG
2668512 GGTTAATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 39 0.85
42 7 0.15
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (41 bp):
TTTTTAGCAAACGCCGCGAAAAATAAGTACTTTAACGGCAT
Found at i:2671057 original size:43 final size:43
Alignment explanation
Indices: 2670930--2671207 Score: 249
Period size: 43 Copynumber: 6.5 Consensus size: 43
2670920 GGCCTTTGTA
* * * *
2670930 TCCAAAAACGCCGCTAAAGATCT-AACCTTTT-CCGTAGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCA-TTTAT
* * * * *
2670972 TCCAAAAATGCCGCTATAGCTCT-GACCTTTTGCGACGTTTAT
1 TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCATTTAT
* *
2671014 TCCAAAAATGCCGCTATAGATCTCAACCTTTTACGGCATTTAT
1 TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCATTTAT
* * * * * * *
2671057 TCGAAAAACGTCGCTATAGATCTCGACCTTTTACAGCGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCATTTAT
* * * *
2671100 TCTAAAAACGCCACTATAGATCTTAA-CTTTTGCGGCGTTTAT
1 TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCATTTAT
* * *** * *
2671142 TCCCAAAACACATATATAGATCTCGACCTTTTGCGGCATTTGT
1 TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCATTTAT
*
2671185 TCCAAAAATGCCGCTATAGATCT
1 TCCAAAAACGCCGCTATAGATCT
2671208 TGAACTTTTG
Statistics
Matches: 188, Mismatches: 45, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
42 84 0.45
43 104 0.55
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (43 bp):
TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCATTTAT
Found at i:2671075 original size:85 final size:84
Alignment explanation
Indices: 2670924--2671207 Score: 281
Period size: 85 Copynumber: 3.3 Consensus size: 84
2670914 ATTAGTGGCC
* * * * * *
2670924 TTTGTATCCAAAAACGCCGCTAAAGATCTAACCTTTTCCGTAGTTTGTTCCAAAAATGCCGCTAT
1 TTTGT-TCCAAAAACGCCGCTATAGATCTAACCTTTTCGGCA-TTTATTCCAAAAACGTCGCTAT
*
2670989 AGCTCT-GACCTTTTGCGACG
64 AGATCTCGACCTTTTGCGACG
* * *
2671009 TTTATTCCAAAAATGCCGCTATAGATCTCAACCTTTTACGGCATTTATTCGAAAAACGTCGCTAT
1 TTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTT-CGGCATTTATTCCAAAAACGTCGCTAT
*
2671074 AGATCTCGACCTTTTAC-AGCG
64 AGATCTCGACCTTTTGCGA-CG
* * * * *
2671095 TTTGTTCTAAAAACGCCACTATAGATCTTAA-CTTTTGCGGCGTTTATTCCCAAAACACAT--AT
1 TTTGTTCCAAAAACGCCGCTATAGATC-TAACCTTTT-CGGCATTTATT-CCAAAA-ACGTCGCT
* *
2671157 ATAGATCTCGACCTTTTGCGGCA
62 ATAGATCTCGACCTTTTGCGACG
*
2671180 TTTGTTCCAAAAATGCCGCTATAGATCT
1 TTTGTTCCAAAAACGCCGCTATAGATCT
2671208 TGAACTTTTG
Statistics
Matches: 165, Mismatches: 26, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
84 22 0.13
85 95 0.58
86 44 0.27
87 4 0.02
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (84 bp):
TTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTCGGCATTTATTCCAAAAACGTCGCTATAG
ATCTCGACCTTTTGCGACG
Found at i:2671160 original size:128 final size:128
Alignment explanation
Indices: 2670930--2671216 Score: 319
Period size: 128 Copynumber: 2.2 Consensus size: 128
2670920 GGCCTTTGTA
* * * * * *
2670930 TCCAAAAACGCCGCTAAAGATCT--AACCTTTT-CCGTAGTTTGTTCCAAAAATGCCGCTATAGC
1 TCCAAAAACGCCGCTATAGATCTCGAA-CTTTTACAG-CGTTTGTTCCAAAAACGCCACTATAGA
* ** * *
2670992 TCTGACCTTTTGCGACGTTTATTCCAAAAATGCCGCTATAGATCTCAACCTTTTACGGCATTTAT
64 TCTGAACTTTTGCGACGTTTATTCCAAAAACACAGATATAGATCTCAACCTTTTACGGCATTTAT
* * * *
2671057 TCGAAAAACGTCGCTATAGATCTCGACCTTTTACAGCGTTTGTTCTAAAAACGCCACTATAGATC
1 TCCAAAAACGCCGCTATAGATCTCGAACTTTTACAGCGTTTGTTCCAAAAACGCCACTATAGATC
* * * * * * *
2671122 TTAACTTTTGCGGCGTTTATTCCCAAAACACATATATAGATCTCGACCTTTTGCGGCATTTGT
66 TGAACTTTTGCGACGTTTATTCCAAAAACACAGATATAGATCTCAACCTTTTACGGCATTTAT
* *
2671185 TCCAAAAATGCCGCTATAGATCTTGAACTTTT
1 TCCAAAAACGCCGCTATAGATCTCGAACTTTT
2671217 GCGACGATTT
Statistics
Matches: 130, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
127 20 0.15
128 107 0.82
129 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (128 bp):
TCCAAAAACGCCGCTATAGATCTCGAACTTTTACAGCGTTTGTTCCAAAAACGCCACTATAGATC
TGAACTTTTGCGACGTTTATTCCAAAAACACAGATATAGATCTCAACCTTTTACGGCATTTAT
Found at i:2671761 original size:36 final size:36
Alignment explanation
Indices: 2671713--2671782 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2671703 AAATGCTAAA
* *
2671713 GTGTACCGATACACCCTTCAGTGTATCCATACACTG
1 GTGTACCAATACACCCTGCAGTGTATCCATACACTG
*
2671749 GTGTACCAATACACTCTGCAGTGTATCCATACAC
1 GTGTACCAATACACCCTGCAGTGTATCCATACAC
2671783 CCTGGCTGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (36 bp):
GTGTACCAATACACCCTGCAGTGTATCCATACACTG
Found at i:2671780 original size:20 final size:19
Alignment explanation
Indices: 2671712--2671783 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 19
2671702 AAAATGCTAA
* *
2671712 AGTGTACCGATACACCCTTC
1 AGTGTACCAATACA-CCTGC
2671732 AGTGTATCC-ATACA-CTG-
1 AGTGTA-CCAATACACCTGC
2671749 -GTGTACCAATACACTCTGC
1 AGTGTACCAATACAC-CTGC
2671768 AGTGTATCC-ATACACC
1 AGTGTA-CCAATACACC
2671784 CTGGCTGCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
15 2 0.05
16 10 0.23
18 5 0.11
19 1 0.02
20 22 0.50
21 4 0.09
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (19 bp):
AGTGTACCAATACACCTGC
Found at i:2671848 original size:21 final size:21
Alignment explanation
Indices: 2671816--2671856 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2671806 TTTGAATTTA
*
2671816 ATGAAGGTGTACCGATACCCT
1 ATGAAGGTGTACCAATACCCT
2671837 ATGAATGG-GTACCAATACCC
1 ATGAA-GGTGTACCAATACCC
2671857 CCTGTTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
ATGAAGGTGTACCAATACCCT
Found at i:2671928 original size:20 final size:20
Alignment explanation
Indices: 2671905--2671943 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2671895 TCAAACGACT
2671905 CAAAACATCCCCAACGGCTC
1 CAAAACATCCCCAACGGCTC
2671925 CAAAACATCCCCAACGGCT
1 CAAAACATCCCCAACGGCT
2671944 AGATATGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.44, G:0.10, T:0.10
Consensus pattern (20 bp):
CAAAACATCCCCAACGGCTC
Found at i:2674702 original size:12 final size:12
Alignment explanation
Indices: 2674685--2674710 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2674675 GGGGGAGCTT
2674685 TGATTTTTCAAA
1 TGATTTTTCAAA
2674697 TGATTTTTCAAA
1 TGATTTTTCAAA
2674709 TG
1 TG
2674711 TCAAATTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (12 bp):
TGATTTTTCAAA
Found at i:2674825 original size:18 final size:20
Alignment explanation
Indices: 2674784--2674831 Score: 82
Period size: 18 Copynumber: 2.5 Consensus size: 20
2674774 ATAACAAATT
2674784 TATAACAAAATGTTTTTCGA
1 TATAACAAAATGTTTTTCGA
2674804 TATAACAAAATG-TTTT-GA
1 TATAACAAAATGTTTTTCGA
2674822 TATAACAAAA
1 TATAACAAAA
2674832 AGTGGGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 12 0.43
19 4 0.14
20 12 0.43
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (20 bp):
TATAACAAAATGTTTTTCGA
Found at i:2674931 original size:18 final size:21
Alignment explanation
Indices: 2674908--2674956 Score: 77
Period size: 18 Copynumber: 2.5 Consensus size: 21
2674898 TATATTTTCC
2674908 AACAATTGGTAT-CTTTT-T-
1 AACAATTGGTATCCTTTTGTA
2674926 AACAATTGGTATCCTTTTGTA
1 AACAATTGGTATCCTTTTGTA
2674947 AACAATTGGT
1 AACAATTGGT
2674957 GCCTTTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.43
19 5 0.18
20 1 0.04
21 10 0.36
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (21 bp):
AACAATTGGTATCCTTTTGTA
Found at i:2675312 original size:36 final size:36
Alignment explanation
Indices: 2675265--2675334 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
2675255 AATGTAATTA
*
2675265 GTGTACAGATACACCCTGCAGTGTATGCATACACTG
1 GTGTACAGATACACCCTGCAGTGTATCCATACACTG
* * *
2675301 GTGTACCGATACACTCTGTAGTGTATCCATACAC
1 GTGTACAGATACACCCTGCAGTGTATCCATACAC
2675335 CCTGACTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (36 bp):
GTGTACAGATACACCCTGCAGTGTATCCATACACTG
Found at i:2675332 original size:20 final size:18
Alignment explanation
Indices: 2675273--2675335 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 18
2675263 TAGTGTACAG
*
2675273 ATACACCCTGCAGTGTATGC
1 ATACA-CCTG-AGTGTATCC
2675293 ATACA-CTG-GTGTA-CC
1 ATACACCTGAGTGTATCC
2675308 GATACACTCTGTAGTGTATCC
1 -ATACAC-CTG-AGTGTATCC
2675329 ATACACC
1 ATACACC
2675336 CTGACTACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
15 1 0.03
16 10 0.28
18 6 0.17
19 1 0.03
20 16 0.44
21 2 0.06
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (18 bp):
ATACACCTGAGTGTATCC
Found at i:2675404 original size:21 final size:21
Alignment explanation
Indices: 2675378--2675418 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2675368 TTTGAATTTA
*
2675378 ATGAAGGTGTACCGATACCCT
1 ATGAAGGGGTACCGATACCCT
2675399 ATGAAGGGGTACCGATACCC
1 ATGAAGGGGTACCGATACCC
2675419 CCTGTTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (21 bp):
ATGAAGGGGTACCGATACCCT
Found at i:2676203 original size:20 final size:20
Alignment explanation
Indices: 2676174--2676219 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2676164 CCTTGGATCG
*
2676174 TGCATAGCAGTACACGGGCA
1 TGCATGGCAGTACACGGGCA
2676194 TGCATGGCAGTACACGGGCA
1 TGCATGGCAGTACACGGGCA
2676214 TGCATG
1 TGCATG
2676220 TATCAGTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (20 bp):
TGCATGGCAGTACACGGGCA
Found at i:2682297 original size:19 final size:19
Alignment explanation
Indices: 2682255--2682297 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2682245 AAATGATATC
* *
2682255 TTTTTAAAAATTGATATCAA
1 TTTTTAAAAATTCATAAC-A
2682275 TTTTT-AAAATTCATAACA
1 TTTTTAAAAATTCATAACA
2682293 TTTTT
1 TTTTT
2682298 GGATACCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 10 0.48
20 5 0.24
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTTAAAAATTCATAACA
Found at i:2685018 original size:28 final size:28
Alignment explanation
Indices: 2684964--2685018 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2684954 TATGGTGCAA
2684964 TCACAGTTACAAGGCACTAAATGTGCCG
1 TCACAGTTACAAGGCACTAAATGTGCCG
*
2684992 TCACAGTTACAGGGCACTAAATGTGCC
1 TCACAGTTACAAGGCACTAAATGTGCC
2685019 ATACAATTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (28 bp):
TCACAGTTACAAGGCACTAAATGTGCCG
Found at i:2685161 original size:16 final size:17
Alignment explanation
Indices: 2685140--2685174 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2685130 TCGTACAGGA
*
2685140 AAAGAAAA-AGTACATG
1 AAAGAAAACAATACATG
2685156 AAAGAAAACAATACATG
1 AAAGAAAACAATACATG
2685173 AA
1 AA
2685175 TACATAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (17 bp):
AAAGAAAACAATACATG
Found at i:2687767 original size:29 final size:29
Alignment explanation
Indices: 2687735--2688003 Score: 180
Period size: 29 Copynumber: 9.1 Consensus size: 29
2687725 ATTTGAGATA
*
2687735 AAAATAAATTATATTTTTACAAGTTAA-AT
1 AAAATAAAATATATTTTTA-AAGTTAATAT
*
2687764 AAAAATAAAATATATTTTTTAAGTTAATAT
1 -AAAATAAAATATATTTTTAAAGTTAATAT
* *
2687794 AAGACT-AAA-ATATTTTTAAA-TTAAAAT
1 AA-AATAAAATATATTTTTAAAGTTAATAT
2687821 AAAAATAAAATATATTTTTTAAA-TTAATAT
1 -AAAATAAAATATA-TTTTTAAAGTTAATAT
2687851 AAAACTAAAATATATTTTT-AAGTTAATAT
1 AAAA-TAAAATATATTTTTAAAGTTAATAT
* * * *
2687880 AAAAGTAAAATATA-TCTGATAATTTAAGAT
1 AAAA-TAAAATATATTTTTA-AAGTTAATAT
****
2687910 AAAAATGAAATATATATTTTTTAAAACCCCAT-T
1 -AAAAT-AAA-ATATA-TTTTT-AAAGTTAATAT
* *
2687943 AAGATAAAA-ATTATTTTTAAAAGTTAAGAT
1 AAAATAAAATA-TATTTTT-AAAGTTAATAT
* *
2687973 AAGAATAAAATATATTATTAAA-TTAAGAT
1 AA-AATAAAATATATTTTTAAAGTTAATAT
2688002 AA
1 AA
2688004 GATTATAATA
Statistics
Matches: 192, Mismatches: 27, Indels: 41
0.74 0.10 0.16
Matches are distributed among these distances:
27 8 0.04
28 19 0.10
29 64 0.33
30 62 0.32
31 22 0.11
32 10 0.05
33 1 0.01
34 5 0.03
35 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATAAAATATATTTTTAAAGTTAATAT
Found at i:2687912 original size:59 final size:58
Alignment explanation
Indices: 2687720--2687930 Score: 228
Period size: 59 Copynumber: 3.6 Consensus size: 58
2687710 TTTTGAATAC
* *
2687720 TTTTAATTTGAGATAAAAATAAATTATATTTTTACAAGTTAAATAAAAATAAAATATATT
1 TTTTAATTTAAGATAAAAATAAAATATATTTTT--AAGTTAAATAAAAATAAAATATATT
* * * * *
2687780 TTTTAAGTTAATATAAGACT-AAA-ATATTTTTAAATTAAAATAAAAATAAAATATATT
1 TTTTAATTTAAGATAAAAATAAAATATATTTTTAAGTT-AAATAAAAATAAAATATATT
* * * * *
2687837 TTTTAAATTAATATAAAACTAAAATATATTTTTAAGTTAATATAAAAGTAAAATATATC
1 TTTTAATTTAAGATAAAAATAAAATATATTTTTAAGTTAA-ATAAAAATAAAATATATT
**
2687896 TGATAATTTAAGATAAAAATGAAATATATATTTTT
1 TTTTAATTTAAGATAAAAAT-AAA-ATATATTTTT
2687931 TAAAACCCCA
Statistics
Matches: 128, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
56 4 0.03
57 38 0.30
58 13 0.10
59 45 0.35
60 18 0.14
61 10 0.08
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (58 bp):
TTTTAATTTAAGATAAAAATAAAATATATTTTTAAGTTAAATAAAAATAAAATATATT
Found at i:2688005 original size:29 final size:29
Alignment explanation
Indices: 2687720--2688003 Score: 216
Period size: 30 Copynumber: 9.6 Consensus size: 29
2687710 TTTTGAATAC
* * *
2687720 TTTTAATTTGAGATAAAAATAAATTATAT
1 TTTTAAATTAAGATAAAAATAAAATATAT
2687749 TTTTACAAGTTAA-ATAAAAATAAAATATATT
1 TTTTA-AA-TTAAGATAAAAATAAAATATA-T
* * * *
2687780 TTTTAAGTTAATATAAGACT-AAA-ATAT
1 TTTTAAATTAAGATAAAAATAAAATATAT
*
2687807 TTTTAAATTAAAATAAAAATAAAATATATT
1 TTTTAAATTAAGATAAAAATAAAATATA-T
* *
2687837 TTTTAAATTAATATAAAACTAAAATATAT
1 TTTTAAATTAAGATAAAAATAAAATATAT
* * *
2687866 TTTTAAGTTAATATAAAAGTAAAATATAT
1 TTTTAAATTAAGATAAAAATAAAATATAT
** *
2687895 CTGATAATTTAAGATAAAAATGAAATATATATT
1 -TTTTAAATTAAGATAAAAAT-AAA-ATATA-T
***** * *
2687928 TTTTAAAACCCCATTAAGATAAAA-ATTAT
1 TTTTAAATTAAGATAAAAATAAAATA-TAT
*
2687957 TTTTAAAAGTTAAGATAAGAATAAAATATAT
1 TTTT-AAA-TTAAGATAAAAATAAAATATAT
*
2687988 TATTAAATTAAGATAA
1 TTTTAAATTAAGATAA
2688004 GATTATAATA
Statistics
Matches: 202, Mismatches: 38, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
27 17 0.08
28 6 0.03
29 58 0.29
30 74 0.37
31 30 0.15
32 16 0.08
33 1 0.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTTAAATTAAGATAAAAATAAAATATAT
Found at i:2688135 original size:37 final size:35
Alignment explanation
Indices: 2688077--2688301 Score: 145
Period size: 37 Copynumber: 6.1 Consensus size: 35
2688067 TATAGTATGC
**
2688077 AAAAGATTTTTGAAAACTTATATAATATATGTTTTTT
1 AAAA-ATTTTT-AAAAAATATATAATATATGTTTTTT
*
2688114 AAAAATGTTTTAAAAAATTATATAATATA-GTTTTTAA
1 AAAAAT-TTTTAAAAAA-TATATAATATATGTTTTT-T
* * * *
2688151 AAAAACATTTT-GAAAATATATAATATATGGTTTAT
1 AAAAA-TTTTTAAAAAATATATAATATATGTTTTTT
* * * *
2688186 -AACATTTTTGAAAACATATATATTATATAGTTTTTAA
1 AAAAATTTTT-AAAAAATATATAATATAT-GTTTTT-T
*
2688223 AAAAACATTTT-AAAAATATATAATATAT-TCTTTTT
1 AAAAA-TTTTTAAAAAATATATAATATATGT-TTTTT
* * *
2688258 AAAACATTTTGAAAACATATATATAATAAATATTTTTT
1 AAAA-ATTTTTAAAA-A-ATATATAATATATGTTTTTT
2688296 AGAAAA
1 A-AAAA
2688302 AACATTTTGA
Statistics
Matches: 146, Mismatches: 24, Indels: 35
0.71 0.12 0.17
Matches are distributed among these distances:
33 4 0.03
34 3 0.02
35 33 0.23
36 32 0.22
37 44 0.30
38 22 0.15
39 8 0.05
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (35 bp):
AAAAATTTTTAAAAAATATATAATATATGTTTTTT
Found at i:2688171 original size:72 final size:73
Alignment explanation
Indices: 2688084--2688387 Score: 336
Period size: 72 Copynumber: 4.1 Consensus size: 73
2688074 TGCAAAAGAT
*
2688084 TTTTGAAAACTTATATAATATATGTTTTTTAAAA-ATGTTTTAAAAAAT-TATATAATATAGTTT
1 TTTTGAAAA--TATATAATATATGTTTTTTAAAACAT-TTTGAAAAAATATATATAATATAGTTT
2688147 TTAAAAAAACA
63 TTAAAAAAACA
* * * *
2688158 TTTTGAAAATATATAATATATG--GTTTATAACATTTTTGAAAACATATATATTATATAGTTTTT
1 TTTTGAAAATATATAATATATGTTTTTTAAAACA-TTTTGAAAAAATATATATAATATAGTTTTT
2688221 AAAAAAACA
65 AAAAAAACA
* * *
2688230 TTTTAAAAATATATAATATAT-TCTTTTTAAAACATTTTGAAAACATATATATAATAAATATTTT
1 TTTTGAAAATATATAATATATGT-TTTTTAAAACATTTTGAAAAAATATATATAAT--ATAGTTT
2688294 TTAGAAAAAACA
63 TTA-AAAAAACA
* * * *
2688306 TTTTGAAAACATATATTATATAG--TTTTAAAACATTTTGAAAATATATACATATTATATAG-TT
1 TTTTGAAAATATATAATATAT-GTTTTTTAAAACATTTTGAAAA-A-ATATATATAATATAGTTT
2688368 TTAAAAAAACA
63 TTAAAAAAACA
*
2688379 TTTCGAAAA
1 TTTTGAAAA
2688388 CCTTTTTTTT
Statistics
Matches: 199, Mismatches: 18, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
70 6 0.03
71 10 0.05
72 59 0.30
73 36 0.18
74 22 0.11
75 31 0.16
76 26 0.13
77 9 0.05
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (73 bp):
TTTTGAAAATATATAATATATGTTTTTTAAAACATTTTGAAAAAATATATATAATATAGTTTTTA
AAAAAACA
Found at i:2688337 original size:33 final size:36
Alignment explanation
Indices: 2688300--2688373 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
2688290 TTTTTTAGAA
2688300 AAAACATTTTG-AAA-ACAT-ATATTATATAGTTTT
1 AAAACATTTTGAAAATACATAATATTATATAGTTTT
*
2688333 AAAACATTTTGAAAATATATACATATTATATAGTTTT
1 AAAACATTTTGAAAATACATA-ATATTATATAGTTTT
2688370 AAAA
1 AAAA
2688374 AAACATTTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 11 0.31
34 3 0.08
35 3 0.08
37 19 0.53
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (36 bp):
AAAACATTTTGAAAATACATAATATTATATAGTTTT
Found at i:2689539 original size:4 final size:4
Alignment explanation
Indices: 2689530--2689560 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2689520 TTTTGATCTT
2689530 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2689561 TTGCAACATT
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:2689678 original size:4 final size:4
Alignment explanation
Indices: 2689664--2689763 Score: 57
Period size: 4 Copynumber: 24.8 Consensus size: 4
2689654 ATTACCCTTT
* *
2689664 TTTA CTTA TTTA TTTAA TTTAA TTTA -TTA -TTA TATTA TTATA TATA
1 TTTA TTTA TTTA TTT-A TTT-A TTTA TTTA TTTA T-TTA TT-TA TTTA
* * * *
2689710 TATA TATTA -TT- TTTA TTTA TTT- TTTCT TTTA TTTT TTTA TTTA TTTT
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA
2689757 TTTA TTT
1 TTTA TTT
2689764 TTTTTCTCAT
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
3 13 0.17
4 44 0.56
5 21 0.27
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:2689691 original size:35 final size:32
Alignment explanation
Indices: 2689603--2689692 Score: 76
Period size: 35 Copynumber: 2.7 Consensus size: 32
2689593 AGTATTTAAC
*
2689603 ATTTTTTTAATTTAACTTTATT-CTTTTTTATT
1 ATTTATTTAATTTAA-TTTATTACTTTTTTATT
* * *
2689635 TTTTATTTTCA-TTATTATTATTACCCTTTTTTACTT
1 ATTTA-TTTAATTTAAT-TTATTA--CTTTTTTA-TT
2689671 ATTTATTTAATTTAATTTATTA
1 ATTTATTTAATTTAATTTATTA
2689693 TTATATTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
31 1 0.02
32 11 0.25
33 4 0.09
35 18 0.41
36 10 0.23
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (32 bp):
ATTTATTTAATTTAATTTATTACTTTTTTATT
Found at i:2689740 original size:12 final size:12
Alignment explanation
Indices: 2689725--2689846 Score: 67
Period size: 12 Copynumber: 9.8 Consensus size: 12
2689715 ATTATTTTTA
2689725 TTTATTTTTTCT
1 TTTATTTTTTCT
2689737 TTTATTTTTT-T
1 TTTATTTTTTCT
2689748 ATTTATTTTTT-T
1 -TTTATTTTTTCT
2689760 ATTT-TTTTTCTCATT
1 -TTTATTTTT-TC--T
*
2689775 TTTACTTTTTTTT
1 TTTA-TTTTTTCT
*
2689788 CTTTAATTTTTCT
1 -TTTATTTTTTCT
*
2689801 TTAATTTTATT-T
1 TTTATTTT-TTCT
*
2689813 TCTA--TTTTCT
1 TTTATTTTTTCT
*
2689823 TTTAACTTTTTCT
1 TTT-ATTTTTTCT
2689836 TTTATTCTTTT
1 TTTATT-TTTT
2689847 ATTCTTGCCT
Statistics
Matches: 87, Mismatches: 9, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
9 2 0.02
10 5 0.06
11 7 0.08
12 37 0.43
13 22 0.25
14 7 0.08
15 2 0.02
16 5 0.06
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTTTTCT
Found at i:2689744 original size:11 final size:11
Alignment explanation
Indices: 2689716--2689841 Score: 72
Period size: 11 Copynumber: 11.5 Consensus size: 11
2689706 TATATATATA
*
2689716 TTATTTTT-AT
1 TTATTTTTCTT
2689726 TTATTTTTTCTT
1 TTA-TTTTTCTT
2689738 TTA--TTT-TT
1 TTATTTTTCTT
*
2689746 TTATTTATTTTT
1 TTATTT-TTCTT
2689758 TTATTTTT-TT
1 TTATTTTTCTT
2689768 TCTCATTTTTAC-T
1 T-T-ATTTTT-CTT
2689781 TT-TTTTTCTT
1 TTATTTTTCTT
*
2689791 TAATTTTTCTT
1 TTATTTTTCTT
*
2689802 TAATTTTAT-TT
1 TTATTTT-TCTT
2689813 TCTA-TTTTCTT
1 T-TATTTTTCTT
2689824 TTAACTTTTTCTT
1 TT-A-TTTTTCTT
2689837 TTATT
1 TTATT
2689842 CTTTTATTCT
Statistics
Matches: 95, Mismatches: 3, Indels: 35
0.71 0.02 0.26
Matches are distributed among these distances:
8 5 0.05
9 4 0.04
10 16 0.17
11 37 0.39
12 22 0.23
13 11 0.12
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATTTTTCTT
Found at i:2689775 original size:24 final size:24
Alignment explanation
Indices: 2689719--2689775 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
2689709 ATATATATTA
2689719 TTTTT-ATTTATTTTTTCTTTTAT
1 TTTTTCATTTATTTTTTCTTTTAT
*
2689742 TTTTTTATTTATTTTTT-TATTT-T
1 TTTTTCATTTATTTTTTCT-TTTAT
2689765 TTTTCTCATTT
1 TTTT-TCATTT
2689776 TTACTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTCATTTATTTTTTCTTTTAT
Found at i:2689776 original size:19 final size:19
Alignment explanation
Indices: 2689736--2689789 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
2689726 TTATTTTTTC
*
2689736 TTTTATTTTTTTAT-TTATTT
1 TTTTATTTTTTT-TCTCA-TT
2689756 TTTTATTTTTTTTCTCA-T
1 TTTTATTTTTTTTCTCATT
2689774 TTTTACTTTTTTTTCT
1 TTTTA-TTTTTTTTCT
2689790 TTAATTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 6 0.19
19 11 0.35
20 14 0.45
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTTTTCTCATT
Found at i:2693185 original size:27 final size:26
Alignment explanation
Indices: 2693110--2693176 Score: 116
Period size: 26 Copynumber: 2.5 Consensus size: 26
2693100 CCCTCTGTCT
*
2693110 AATCACCAAGAGAACAAGGAAAATGC
1 AATCACCAAGAGAACGAGGAAAATGC
2693136 AATCACCAAGAGAACGAGGAAAATGC
1 AATCACCAAGAGAACGAGGAAAATGC
2693162 AATCACCAAGGAGAA
1 AATCACCAA-GAGAA
2693177 GGGTAAAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 34 0.87
27 5 0.13
ACGTcount: A:0.52, C:0.19, G:0.21, T:0.07
Consensus pattern (26 bp):
AATCACCAAGAGAACGAGGAAAATGC
Found at i:2694177 original size:95 final size:95
Alignment explanation
Indices: 2694053--2694312 Score: 373
Period size: 94 Copynumber: 2.7 Consensus size: 95
2694043 AGATTATAAT
* * *
2694053 ATTAT-ATATATAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAACTTTAT
1 ATTATAATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
2694117 GGATAAGATTCAGCTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
* * *
2694147 ATTATAATATACAATAAAGCTCGAGTTGTCCCTCTAGAGCAATTGGTTAAATG-CCCGACTTTAT
1 ATTATAATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
*
2694211 GGATAATATTCAGCTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
* * *
2694241 ATTATAATAT-CTATACAACGATATTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGACT
1 ATTATAATATACAATA-AA-G--CTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACT
2694305 TTATGGAT
62 TTATGGAT
2694313 CCAGCTAGAC
Statistics
Matches: 147, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
93 4 0.03
94 56 0.38
95 43 0.29
97 30 0.20
98 14 0.10
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
GGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:2695305 original size:84 final size:84
Alignment explanation
Indices: 2695064--2695959 Score: 1014
Period size: 84 Copynumber: 10.5 Consensus size: 84
2695054 AAAGCACCTT
* * * *
2695064 CAACAAAAGACCTTTGAGTTCAATTATACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
2695129 GGCGAGAAGGGTTATCTGC
66 GGCGAGAAGGGCTATCTGC
*
2695148 CAACAAAAGACCTTCGAGTT-TATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
2695212 GGCGAGAAGGGCTATCTGC
66 GGCGAGAAGGGCTATCTGC
** *
2695231 CAACAAAAGATATTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
2695296 GGCGAGAAGGGCTAT-TCGC
66 GGCGAGAAGGGCTATCT-GC
*
2695315 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
2695380 AGTGAGAAGGGCTATCTAC
66 GGCGAGAAGGGCTATCTGC
* *
2695399 CAACAAAAGACCTGAGAGACCTTCGAGTTCGATTACTCTCAGCTCAAAGGCACATCCAATTTACA
1 CAAC---A-A----A-AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCA
* * ** * *
2695464 GAATAACTCAAGGAAAAAAGGGTTATCTGTC
55 GCATAGCTCAAGGCGAGAAGGGCTATCTG-C
* * *
2695495 AAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGCACATCATTTGCAACATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
2695560 GGATG-GAAGGGCTATATGC
66 GG-CGAGAAGGGCTATCTGC
*
2695579 CAACAAAATACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
2695644 AGTGAGAAGGGCTATCTGC
66 GGCGAGAAGGGCTATCTGC
* * * * * *
2695663 CAACAAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGACATATCCAGTAT--AGCATAACTC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CA-TTTGCAGCATAGCTC
* * *
2695726 AAGGCAAGAAGGGTTATCTGT
64 AAGGCGAGAAGGGCTATCTGC
* * * * *
2695747 CAACAAAAGACCTTCGAGTTAGATTACATTCAGCTCAAAGGTATATCAAATTTACAGCATAGCTC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTC
* * * **
2695812 AAGGCGAGAATGACTATTTAT
64 AAGGCGAGAAGGGCTATCTGC
* * * * *
2695833 CAAC-CAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGACATATCAAATTTACAGCATAGCTC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTC
* * * *
2695897 AAGGTGAGAAGGGTTATTTGT
64 AAGGCGAGAAGGGCTATCTGC
* * * *
2695918 CAAC-AAATACCTTCGAGTTTGATTACATTCAGCTCAAGGGCA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
2695960 TGTCAGATTT
Statistics
Matches: 707, Mismatches: 82, Indels: 45
0.85 0.10 0.05
Matches are distributed among these distances:
83 81 0.11
84 343 0.49
85 138 0.20
86 31 0.04
87 38 0.05
88 2 0.00
92 2 0.00
93 39 0.06
94 1 0.00
95 28 0.04
96 4 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (84 bp):
CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
GGCGAGAAGGGCTATCTGC
Found at i:2696799 original size:40 final size:39
Alignment explanation
Indices: 2696753--2696921 Score: 142
Period size: 39 Copynumber: 4.5 Consensus size: 39
2696743 TTTGAAAACT
*
2696753 TATATAATATATGGTTTTTTTTAAAA-ATATTTTAAAAAA
1 TATATAATATATGGTTTTTTTTAAAACACATTTT-AAAAA
* * * *
2696792 TTATATAATATATAG-TTTTTTAAAAAAACATTTTGAAAA
1 -TATATAATATATGGTTTTTTTTAAAACACATTTTAAAAA
*
2696831 TATATAACATATGG----TTTT-AAA-ACATTTTGAAAACA
1 TATATAATATATGGTTTTTTTTAAAACACATTTT-AAAA-A
* * * *
2696866 TATATATTATATAG--TTTATTAAAAGACATTTTAAAAA
1 TATATAATATATGGTTTTTTTTAAAACACATTTTAAAAA
2696903 TATATAATATATGGTTTTT
1 TATATAATATATGGTTTTT
2696922 AAAACATTGT
Statistics
Matches: 106, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
33 7 0.07
34 6 0.06
35 15 0.14
37 16 0.15
38 19 0.18
39 24 0.23
40 19 0.18
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (39 bp):
TATATAATATATGGTTTTTTTTAAAACACATTTTAAAAA
Found at i:2696919 original size:72 final size:75
Alignment explanation
Indices: 2696753--2696929 Score: 227
Period size: 73 Copynumber: 2.4 Consensus size: 75
2696743 TTTGAAAACT
* *
2696753 TATATAATATATGGTTTTTTTTAAAA-ATATTTTAAAAAATTATATAATATATAGTTTTTTAAAA
1 TATATAATATATGG---TTTTTAAAACAT-TTTGAAAAAATTATATAATATATAGTTTATTAAAA
*
2696817 AAACATTTTGAAAA
62 AAACATTTTAAAAA
* * * *
2696831 TATATAACATATGG-TTTTAAAACATTTTGAAAACA-TATATATTATATAGTTTATT-AAAAGAC
1 TATATAATATATGGTTTTTAAAACATTTTGAAAAAATTATATAATATATAGTTTATTAAAAAAAC
2696893 ATTTTAAAAA
66 ATTTTAAAAA
2696903 TATATAATATATGGTTTTTAAAACATT
1 TATATAATATATGGTTTTTAAAACATT
2696930 GTTTTCAAAC
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
72 28 0.31
73 30 0.34
74 16 0.18
75 2 0.02
78 13 0.15
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (75 bp):
TATATAATATATGGTTTTTAAAACATTTTGAAAAAATTATATAATATATAGTTTATTAAAAAAAC
ATTTTAAAAA
Found at i:2697497 original size:18 final size:19
Alignment explanation
Indices: 2697463--2697498 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2697453 TATTTAACGT
*
2697463 TTTTTATTTTACTTTATTC
1 TTTTTATTTTACATTATTC
2697482 TTTTTATTTT-CATTATT
1 TTTTTATTTTACATTATT
2697499 ATTATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTATTTTACATTATTC
Found at i:2697561 original size:14 final size:14
Alignment explanation
Indices: 2697530--2697579 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
2697520 CTATTTAATT
*
2697530 TATTATATTATTATTA
1 TATTAT-TTTTTA-TA
2697546 TATTATTTTTTATA
1 TATTATTTTTTATA
2697560 TATT-TTTTTTA-A
1 TATTATTTTTTATA
*
2697572 TTTTATTT
1 TATTATTT
2697580 ATTTTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.13
13 10 0.32
14 6 0.19
15 5 0.16
16 6 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTATTTTTTATA
Found at i:2697580 original size:23 final size:24
Alignment explanation
Indices: 2697521--2697581 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
2697511 TTTACTTATC
*
2697521 TATTTAATTTATTATATTATTATTA
1 TATTTTATTTA-TATATTATTATTA
* * *
2697546 TATTATTTTTTATATATTTTTTTTA
1 TATT-TTATTTATATATTATTATTA
2697571 -ATTTTATTTAT
1 TATTTTATTTAT
2697582 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 7 0.23
24 3 0.10
25 15 0.50
26 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTTTATTTATATATTATTATTA
Found at i:2697589 original size:11 final size:11
Alignment explanation
Indices: 2697528--2697645 Score: 55
Period size: 12 Copynumber: 10.2 Consensus size: 11
2697518 ATCTATTTAA
2697528 TTTATTATATTAT
1 TTTATT-TATT-T
2697541 TATTATATTATTT
1 T-TTAT-TTATTT
*
2697554 TTTATATA-TT
1 TTTATTTATTT
*
2697564 TTT-TTTA-AT
1 TTTATTTATTT
2697573 TTTATTTATTT
1 TTTATTTATTT
*
2697584 TTTATTTTGACTT
1 TTTA-TTT-ATTT
*
2697597 TTT-TTTCTTCT
1 TTTATTTATT-T
**
2697608 TTCCTTTGATTT
1 TTTATTT-ATTT
*
2697620 ATTATTTTATTAT
1 TTTA-TTTATT-T
2697633 TTTATTTATTT
1 TTTATTTATTT
2697644 TT
1 TT
2697646 CCCCCTAATA
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
9 7 0.09
10 10 0.12
11 16 0.20
12 21 0.26
13 18 0.22
14 8 0.10
15 1 0.01
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTATTTATTT
Done.