Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 139 of 325
Found at i:42371586 original size:78 final size:79
Alignment explanation
Indices: 42371470--42371617 Score: 212
Period size: 78 Copynumber: 1.9 Consensus size: 79
42371460 TACTCGTTCA
**
42371470 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGA
42371534 TTTAGTAACTCGCAC
65 TTTAGTAACTCGCAC
* **
42371549 AATGCCTTCGGG-CTTAGCCCAGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
42371612 TTTAGT
65 TTTAGT
42371618 GTGACAGCCT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
77 3 0.05
78 45 0.73
79 14 0.23
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (79 bp):
AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
TTAGTAACTCGCAC
Found at i:42371617 original size:40 final size:40
Alignment explanation
Indices: 42371468--42371617 Score: 209
Period size: 40 Copynumber: 3.8 Consensus size: 40
42371458 GCTACTCGTT
*
42371468 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
42371508 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
42371548 C-AATGCCTTCGGG-CTTAGCCCAGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
42371586 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGT
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT
42371618 GTGACAGCCT
Statistics
Matches: 98, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
38 25 0.26
39 21 0.21
40 50 0.51
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42373422 original size:40 final size:40
Alignment explanation
Indices: 42373363--42373530 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
42373353 TGAATGATAC
* * *
42373363 CCGGGCTAAGTCCTGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
42373403 CCGGGCTAAGACCCAAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
42373443 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * * *
42373483 CCGGGTTAAGTCCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
42373523 CC-GGCTAA
1 CCGGGCTAA
42373531 ATTCCGAAGA
Statistics
Matches: 102, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
39 6 0.06
40 94 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:42373502 original size:80 final size:80
Alignment explanation
Indices: 42373363--42373530 Score: 187
Period size: 80 Copynumber: 2.1 Consensus size: 80
42373353 TGAATGATAC
* * * ** *
42373363 CCGGGCTAAGTCCTGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCAAAGGC-ATTC
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCAAAGGCAATT-
*
42373427 GTGCGAGTTGTTATAT
65 GTGCGAGTGGTTATAT
* * * * *
42373443 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGTCCCGAAGGCAATTG
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCAAAGGCAATTG
**
42373508 TGCTTGTGGTTATAT
66 TGCGAGTGGTTATAT
42373523 CC-GGCTAA
1 CCGGGCTAA
42373531 ATTCCGAAGA
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
79 6 0.08
80 64 0.88
81 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCAAAGGCAATTG
TGCGAGTGGTTATAT
Found at i:42377864 original size:19 final size:19
Alignment explanation
Indices: 42377840--42377880 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42377830 GAATCTTAAA
*
42377840 ATTC-AAATTTTTAATTTTG
1 ATTCAAAATTTTGAA-TTTG
42377859 ATTCAAAATTTTGAATTTG
1 ATTCAAAATTTTGAATTTG
42377878 ATT
1 ATT
42377881 AAGGCATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (19 bp):
ATTCAAAATTTTGAATTTG
Found at i:42377873 original size:55 final size:53
Alignment explanation
Indices: 42377807--42377916 Score: 159
Period size: 54 Copynumber: 2.0 Consensus size: 53
42377797 TGTTTTTTTC
* *
42377807 TTCAAAATTGAAATTTGGTTGAGGAATCTTAAAATTCAAA-TTTTTAATTTTGA
1 TTCAAAATTG-AATTTGATTAAGGAATCTTAAAATTCAAATTTTTTAATTTTGA
*
42377860 TTCAAAATTTTGAATTTGATTAAGGCATCTTAAAATTCAAATTTTTTAATTTTGA
1 TTCAAAA--TTGAATTTGATTAAGGAATCTTAAAATTCAAATTTTTTAATTTTGA
42377915 TT
1 TT
42377917 TATATTTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
53 7 0.14
54 26 0.51
55 18 0.35
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.46
Consensus pattern (53 bp):
TTCAAAATTGAATTTGATTAAGGAATCTTAAAATTCAAATTTTTTAATTTTGA
Found at i:42384410 original size:40 final size:40
Alignment explanation
Indices: 42384355--42384601 Score: 374
Period size: 40 Copynumber: 6.2 Consensus size: 40
42384345 TGAATGATAC
* * *
42384355 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
42384395 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
42384435 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
42384475 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
42384515 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATA-
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
42384554 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
42384594 CC-GGCTAA
1 CCGGGCTAA
42384602 ATTCCGAAGA
Statistics
Matches: 192, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
39 38 0.20
40 152 0.79
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:42392656 original size:40 final size:40
Alignment explanation
Indices: 42392601--42392847 Score: 374
Period size: 40 Copynumber: 6.2 Consensus size: 40
42392591 TGAATGATAC
* * *
42392601 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
42392641 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
42392681 CCGGGCTAAGACCCGAAGGCA-TTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
42392720 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
42392760 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
42392800 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
42392840 CC-GGCTAA
1 CCGGGCTAA
42392848 ATTCCGAAGA
Statistics
Matches: 192, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
39 44 0.23
40 146 0.76
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:42392812 original size:119 final size:120
Alignment explanation
Indices: 42392601--42392847 Score: 383
Period size: 119 Copynumber: 2.1 Consensus size: 120
42392591 TGAATGATAC
* *
42392601 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTG
* * *
42392666 TGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTTGTTATAT
66 TGCGAGTTGCTATACCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
*
42392720 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATATCCGGGCTAAGACCCGAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGCATTT
* **
42392784 GTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
65 GTGCGAGTTGCTATACCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
42392840 CC-GGCTAA
1 CCGGGCTAA
42392848 ATTCCGAAGA
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
119 97 0.83
120 20 0.17
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTTGCTATACCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
Found at i:42392856 original size:79 final size:80
Alignment explanation
Indices: 42392601--42392847 Score: 374
Period size: 79 Copynumber: 3.1 Consensus size: 80
42392591 TGAATGATAC
* * *
42392601 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGACCCGAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATATCCGGGCTAAGACCCGAAGGCATTT
42392665 GTGCGAGTTGTTATAT
65 GTGCGAGTTGTTATAT
42392681 CCGGGCTAAGACCCGAAGGCA-TTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
42392745 TGCGAGTTGTTATAT
66 TGCGAGTTGTTATAT
* * * *
42392760 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
** *
42392825 TGCTTGTGGTTATAT
66 TGCGAGTTGTTATAT
42392840 CC-GGCTAA
1 CCGGGCTAA
42392848 ATTCCGAAGA
Statistics
Matches: 155, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
79 80 0.52
80 75 0.48
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTTGTTATAT
Found at i:42398378 original size:5 final size:5
Alignment explanation
Indices: 42398368--42398428 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
42398358 AAAACTACTA
* * * *
42398368 AAAAT AAAAT AAAAG AAAGAC AAAAT AAAAT -AAAT CAGAAT AGAAGT
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT -AAAAT A-AAAT
42398415 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
42398429 AATAAATAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
4 4 0.09
5 31 0.69
6 10 0.22
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:42398392 original size:21 final size:24
Alignment explanation
Indices: 42398368--42398432 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 24
42398358 AAAACTACTA
42398368 AAAATAAAATAAAAGAA-AG-A-C
1 AAAATAAAATAAAAGAATAGAAGC
*
42398389 AAAATAAAATAAATCAGAATAGAAGT
1 AAAATAAAATAAA--AGAATAGAAGC
42398415 AAAATAAAATAAAA-AATA
1 AAAATAAAATAAAAGAATA
42398433 AATAGATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
21 13 0.34
23 8 0.21
24 3 0.08
25 1 0.03
26 13 0.34
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (24 bp):
AAAATAAAATAAAAGAATAGAAGC
Found at i:42400846 original size:40 final size:40
Alignment explanation
Indices: 42400719--42400848 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
42400709 ATGCTGGAAA
* * *
42400719 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
42400759 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
42400799 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
42400839 TTATATCCGG
1 TTATATCCGG
42400849 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:42408136 original size:124 final size:124
Alignment explanation
Indices: 42407914--42408138 Score: 326
Period size: 124 Copynumber: 1.8 Consensus size: 124
42407904 GAATTATGTG
* * * * * *
42407914 AAATGAAATATGGATGTGTAATGATTATCGATTTATGTGTGTATGAGTATTTGAATGATACCCGG
1 AAATGAAATATGAATGTCTAATGATTATCGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
* **
42407979 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
* *
42408038 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTCTAATGATTATCGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
*
42408103 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT
42408139 CCGGGTTAAG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 3 0.03
124 85 0.97
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (124 bp):
AAATGAAATATGAATGTCTAATGATTATCGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
Found at i:42408260 original size:40 final size:40
Alignment explanation
Indices: 42408133--42408262 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
42408123 TTGCTGGAAA
* * *
42408133 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
42408173 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
42408213 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
42408253 TTATATCCGG
1 TTATATCCGG
42408263 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:42411164 original size:20 final size:19
Alignment explanation
Indices: 42411139--42411204 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
42411129 TACTTCAGTA
42411139 CCCCTGATTGCACATACGTG
1 CCCCTGATTGCAC-TACGTG
* * * *
42411159 CCCCTGTTTGTACTTCGGTA
1 CCCCTGATTGCACTAC-GTG
*
42411179 CCCCTGATTGCACTTATGTG
1 CCCCTGATTGCAC-TACGTG
42411199 CCCCTG
1 CCCCTG
42411205 TTTACATTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.91
21 1 0.03
ACGTcount: A:0.14, C:0.35, G:0.20, T:0.32
Consensus pattern (19 bp):
CCCCTGATTGCACTACGTG
Found at i:42411201 original size:40 final size:40
Alignment explanation
Indices: 42411103--42411207 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 40
42411093 AACTATACCT
* *
42411103 TGATTGCACATATGTGCCACTATTTGTACTTCAGTACCCC
1 TGATTGCACATATGTGCCCCTGTTTGTACTTCAGTACCCC
* *
42411143 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGATTGCACATATGTGCCCCTGTTTGTACTTCAGTACCCC
*
42411183 TGATTGCACTTATGTGCCCCTGTTT
1 TGATTGCACATATGTGCCCCTGTTT
42411208 ACATTATGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.36
Consensus pattern (40 bp):
TGATTGCACATATGTGCCCCTGTTTGTACTTCAGTACCCC
Found at i:42415632 original size:7 final size:7
Alignment explanation
Indices: 42415578--42415632 Score: 62
Period size: 7 Copynumber: 8.3 Consensus size: 7
42415568 AAATAAGAAA
42415578 TAGGGTT
1 TAGGGTT
*
42415585 TAGTGTT
1 TAGGGTT
*
42415592 TAAGGTT
1 TAGGGTT
42415599 T-GGGTT
1 TAGGGTT
42415605 T-GGGTT
1 TAGGGTT
42415611 T-GGGTT
1 TAGGGTT
*
42415617 TGGGGTT
1 TAGGGTT
42415624 TAGGGTT
1 TAGGGTT
42415631 TA
1 TA
42415633 TAGTTTGTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
6 17 0.40
7 25 0.60
ACGTcount: A:0.11, C:0.00, G:0.42, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:42415647 original size:7 final size:6
Alignment explanation
Indices: 42415595--42415631 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
42415585 TAGTGTTTAA
42415595 GGTTTG GGTTTG GGTTTG GGTTTGG GGTTTAG GGTTT
1 GGTTTG GGTTTG GGTTTG GGTTT-G GGTTT-G GGTTT
42415632 ATAGTTTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.03, C:0.00, G:0.49, T:0.49
Consensus pattern (6 bp):
GGTTTG
Found at i:42418043 original size:142 final size:143
Alignment explanation
Indices: 42417764--42418045 Score: 458
Period size: 142 Copynumber: 2.0 Consensus size: 143
42417754 ATCTCACGTC
** *
42417764 GACTAGAATGAGTGACAATAGAATGTTTTAGAAAGCTTGAAATTTAGTTACCCAAATCTGTTGAA
1 GACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAATTTAGTTACCCAAATCTATTGAA
* * * *
42417829 AGCTTCAATTTGGGATTTTGACTTTGGTTTAAACTTAGTGTCTAGTTTGGGGTTCTAGATTTGTC
66 AGCTTCAATTTGGGATTTTGACTTAGGTCTAAACTTAGGGTCTAGTTTGGGGTTCTAGATTCGTC
*
42417894 TACGATTTGGGTT
131 TAAGATTTGGGTT
42417907 GACTAGAATGAGCAACAAT-GAATGTTTTAGAAAGCTTGAAATTTAGTTACCCAAATCTATTGAA
1 GACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAATTTAGTTACCCAAATCTATTGAA
* * *
42417971 AGTTTCAATTTGGGATTTTGACTTAGGTCTAAATTTAGGGTCTAGTTTGGGGTTTTAGATTCGTC
66 AGCTTCAATTTGGGATTTTGACTTAGGTCTAAACTTAGGGTCTAGTTTGGGGTTCTAGATTCGTC
42418036 TAAGATTTGG
131 TAAGATTTGG
42418046 TGATTTGATT
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
142 111 0.87
143 17 0.13
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (143 bp):
GACTAGAATGAGCAACAATAGAATGTTTTAGAAAGCTTGAAATTTAGTTACCCAAATCTATTGAA
AGCTTCAATTTGGGATTTTGACTTAGGTCTAAACTTAGGGTCTAGTTTGGGGTTCTAGATTCGTC
TAAGATTTGGGTT
Found at i:42425515 original size:47 final size:46
Alignment explanation
Indices: 42425446--42425665 Score: 209
Period size: 46 Copynumber: 4.8 Consensus size: 46
42425436 TATAATATCA
**
42425446 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAA-GTTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-C-TCAAGGCCG
* * * *
42425493 ATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTA-GCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTC-AAGGCCG
*
42425539 ATG-CATGTCCCAGACAT-GTCTTACAGTGGCTTACATCTCAAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCTCAAGGCCG
* * * *
42425585 ATG-CATGTCCCAAACAT-GTCTTACACTAGCACTCGTCTCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-G-GCTCATCTCAAGGCCG
* * *
42425631 ATGCCATGTCTCAGCCATGGTCTTACACTAGCTCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCA
42425666 CAATAACCCA
Statistics
Matches: 145, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
44 11 0.08
45 17 0.12
46 59 0.41
47 47 0.32
48 11 0.08
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTCAAGGCCG
Found at i:42428011 original size:11 final size:11
Alignment explanation
Indices: 42427995--42428022 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
42427985 GCCAGTGTAA
42427995 GACATGTCTAG
1 GACATGTCTAG
42428006 GACATGTCTAG
1 GACATGTCTAG
42428017 GACATG
1 GACATG
42428023 CATCGGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (11 bp):
GACATGTCTAG
Found at i:42428161 original size:50 final size:49
Alignment explanation
Indices: 42428008--42428221 Score: 233
Period size: 48 Copynumber: 4.4 Consensus size: 49
42427998 ATGTCTAGGA
* * * *
42428008 CATGTCTAGGACAT-GCATCGGC-CACGTTA-TCAGAGCCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCAC-CGATATTGAGAGCTAGTGTAAGAC
** * * *
42428055 CATGTCTGGGACATGGCATCGGCATTGAGA-CGAGAGCTAGTATAAGAC
1 CATGTCTGGGACATGGCATCGGCACCGATATTGAGAGCTAGTGTAAGAC
*
42428103 CATGTCTGGGACATGGCATCGGCACGGATATGTGAGAGCTAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCACCGATAT-TGAGAGCTAGTGTAAGAC
* * *
42428153 CATGTCTGGGACATGGCGTCGGC-CTCGATTTTGATAG-TCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCAC-CGATATTGAGAGCT-AGTGTAAGAC
42428202 CATGTCTGGGACATGGCATC
1 CATGTCTGGGACATGGCATC
42428222 AGCATTATAC
Statistics
Matches: 142, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
47 13 0.09
48 52 0.37
49 35 0.25
50 42 0.30
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (49 bp):
CATGTCTGGGACATGGCATCGGCACCGATATTGAGAGCTAGTGTAAGAC
Found at i:42428175 original size:98 final size:99
Alignment explanation
Indices: 42428039--42428221 Score: 262
Period size: 98 Copynumber: 1.9 Consensus size: 99
42428029 CCACGTTATC
*
42428039 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GACGAGAG-CTAGTATAAGA
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATGACGAGAGTC-AGTATAAGA
42428102 CCATGTCTGGGACATGGCATCGGCACGGATATGTG
65 CCATGTCTGGGACATGGCATCGGCACGGATATGTG
* * * *** * *
42428137 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTTGATAGTCAGTGTAAGAC
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATGACGAGAGTCAGTATAAGAC
42428202 CATGTCTGGGACATGGCATC
66 CATGTCTGGGACATGGCATC
42428222 AGCATTATAC
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
98 40 0.54
99 33 0.45
100 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (99 bp):
AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATGACGAGAGTCAGTATAAGAC
CATGTCTGGGACATGGCATCGGCACGGATATGTG
Found at i:42431439 original size:40 final size:40
Alignment explanation
Indices: 42431394--42431561 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
42431384 CGGAATACAA
*
42431394 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
42431434 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* **
42431474 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
42431514 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTATTAGC
42431554 CCGGATAT
1 CCGGATAT
42431562 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
Found at i:42431534 original size:80 final size:80
Alignment explanation
Indices: 42431394--42431561 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
42431384 CGGAATACAA
* * *
42431394 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
*
42431459 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
42431474 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACG--ACTAGCACAAA
*
42431537 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
42431554 CCGGATAT
1 CCGGATAT
42431562 CATTCAATTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 75 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:42438864 original size:17 final size:17
Alignment explanation
Indices: 42438842--42438891 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
42438832 TTGGGGTTTC
*
42438842 AAAAAAATAAAAAAAAG
1 AAAAAAAGAAAAAAAAG
42438859 AAAAAAAGAAAAAAAAG
1 AAAAAAAGAAAAAAAAG
42438876 AGGAAAAAGAGAAAAA
1 A--AAAAA-AGAAAAA
42438892 TGGAGAGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 17 0.59
19 5 0.17
20 7 0.24
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:42438875 original size:9 final size:9
Alignment explanation
Indices: 42438842--42438891 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
42438832 TTGGGGTTTC
*
42438842 AAAAAAATA
1 AAAAAAAGA
42438851 AAAAAAAG-
1 AAAAAAAGA
42438859 AAAAAAAGA
1 AAAAAAAGA
42438868 AAAAAAAGA
1 AAAAAAAGA
*
42438877 GGAAAAAGAGA
1 --AAAAAAAGA
42438888 AAAA
1 AAAA
42438892 TGGAGAGGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 8 0.22
9 20 0.56
11 8 0.22
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:42440133 original size:206 final size:206
Alignment explanation
Indices: 42439771--42440919 Score: 1638
Period size: 206 Copynumber: 5.6 Consensus size: 206
42439761 GTAGATCTAG
* *
42439771 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAA-CAAATCGAAGACATGGC
1 CTGAAGC-AGATCCAAGATGGTTTGGTATCCTTGTGCTTACAA-GAAGCAAATCGAAGACATAGC
* * * *
42439835 TAATTTGGCTTTCACGTGCTTGCGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
64 TGATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
* * **
42439900 GAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGAAGAGCAGACACATAGCAGATCTGGCCT
129 GAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCT
* * *
42439965 TCATATGTTTATA
194 TCAGATGATTAGA
42439978 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGAAGCAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGAAGCAAATCGAAGACATAGCTG
* * * *
42440043 ATTTGGTTTTCGCGTACTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTCTGCATTGTCAGA
66 ATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* ** * **
42440108 GAACAAATCAAAGTTTGGCGTCTCCAAATTCGATAGAGAGCAGACACATAGCAGATCTGGCCTTC
131 GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
42440173 -----A-T--A
196 AGATGATTAGA
* *
42440176 -TGAAGCAGATCCAAGATGATTTGGTATCCTTGTGTTTACAAGGAA-CAAATCGAAGACATAGCT
1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAA-GAAGCAAATCGAAGACATAGCT
* * * * * * *
42440239 AATTTGGCTTTCACGTGCTTACGATGAAACAAATTTAAGATGATTTGGCATCTCGGTATTTTCAG
65 GATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * *
42440304 AAAACAAATCGAAGTTTTGCATCTCCATATTCGACGGAGGGCAGACACATAACAGATCTAACCTT
130 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTT
42440369 CAGATGATTAGA
195 CAGATGATTAGA
* * *
42440381 CTGAAGCAGATCCAAGATAGTTTGGTATCCGTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGAAGCAAATCGAAGACATAGCTG
* * * *
42440446 ATTTCGTTTTCGCGTGCTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCATA
66 ATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * *
42440511 GAACAAATCAAAGTTTGCCGTCTCCATATTCGACGGAGGGTAGACACATAGCAAATCTAACCTTC
131 GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
42440576 AGATGATTAGA
196 AGATGATTAGA
* *
42440587 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGATATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGAAGCAAATCGAAGACATAGCTG
* * * * * *
42440652 ATTTGGTTTTCGCGTGCTTATGTTGAAGCAAGTCTAAGATGATTTGGAATCTCTGTGTTGTCAGA
66 ATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
42440717 GAACAAATCAAA-TATTGGCGTCTCCATATTCGATGGAGGGCAGACACATAGCAGATCTAACCTT
131 GAACAAATCAAAGT-TTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTT
42440781 CAGATGATTAGA
195 CAGATGATTAGA
* * * *
42440793 GTGAAGCAGATCCAAGATGGTTTGGTATCCTTATGCTTACAAGGAGCAAATTGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGAAGCAAATCGAAGACATAGCTG
42440858 ATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTC
66 ATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTC
42440920 CGGAAATAAA
Statistics
Matches: 843, Mismatches: 86, Indels: 27
0.88 0.09 0.03
Matches are distributed among these distances:
197 166 0.20
198 4 0.00
200 1 0.00
202 1 0.00
203 1 0.00
205 7 0.01
206 656 0.78
207 7 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (206 bp):
CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGAAGCAAATCGAAGACATAGCTG
ATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
AGATGATTAGA
Found at i:42440526 original size:403 final size:406
Alignment explanation
Indices: 42439771--42440919 Score: 1712
Period size: 403 Copynumber: 2.8 Consensus size: 406
42439761 GTAGATCTAG
* *
42439771 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATGGCT
1 CTGAAGC-AGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
42439836 AATTTGGCTTTCACGTGCTTGCGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 AATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * **
42439901 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGAAGAGCAGACACATAGCAGATCTGGCCTT
130 AGAACAAATC-AAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTT
* * * *
42439966 CATATGTTTATACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGAAGCAAATCG
194 CAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCG
*
42440031 AAGACATAGCTGATTTGGTTTTCGCGTACTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTC
259 AAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTC
* * *
42440096 TGCATTGTCAGAGAACAAATCAAAGTTTGGCGTCTCCAAATTCGATAGAGAGCAGACACATAGCA
324 TGTATTGTCAGAGAACAAATCAAAGTTTGCCGTCTCCAAATTCGACAGAGAGCAGACACATAGCA
* **
42440161 GATCTGGCCTTC-A-T-A
389 AATCTAACCTTCAATTAA
* *
42440176 -TGAAGCAGATCCAAGATGATTTGGTATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTA
1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTA
* * * *
42440240 ATTTGGCTTTCACGTGCTTACGATGAAACAAATTTAAGATGATTTGGCATCTCGGTATTTTCAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * * *
42440305 AAACAAATCGAAGTTTTGCATCTCCATATTCGACGGAGGGCAGACACATAACAGATCTAACCTTC
131 GAACAAATC-AAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
* *
42440370 AGATGATTAGACTGAAGCAGATCCAAGATAGTTTGGTATCCGTGTGCTTACAAGGAGCAAATCGA
195 AGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGA
*
42440435 AGACATAGCTGATTTCGTTTTCGCGTGCTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTCT
260 AGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTCT
* * * * *
42440500 GTATTGTCATAGAACAAATCAAAGTTTGCCGTCTCCATATTCGACGGAGGGTAGACACATAGCAA
325 GTATTGTCAGAGAACAAATCAAAGTTTGCCGTCTCCAAATTCGACAGAGAGCAGACACATAGCAA
42440565 ATCTAACCTTCAGATGATTAGA
390 ATCTAACCTTC--A--ATTA-A
* * *
42440587 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGATATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTA
* * * * * * *
42440652 ATTTGGTTTTCGCGTGCTTATGTTGAAGCAAGTCTAAGATGATTTGGAATCTCTGTGTTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* *
42440717 GAACAAATCAAATATTGGCGTCTCCATATTCGATGGAGGGCAGACACATAGCAGATCTAACCTTC
131 GAACAAATCAAGT-TTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
* * *
42440782 AGATGATTAGAGTGAAGCAGATCCAAGATGGTTTGGTATCCTTATGCTTACAAGGAGCAAATTGA
195 AGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGA
* *
42440847 AGACATAGCTGATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCT
260 AGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTCT
42440912 GTATTGTC
325 GTATTGTC
42440920 CGGAAATAAA
Statistics
Matches: 667, Mismatches: 67, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
403 357 0.54
404 6 0.01
408 1 0.00
409 1 0.00
411 4 0.01
412 298 0.45
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (406 bp):
CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTA
ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTCA
GATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAA
GACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAGTCTAAGATGATTTGGCATCTCTG
TATTGTCAGAGAACAAATCAAAGTTTGCCGTCTCCAAATTCGACAGAGAGCAGACACATAGCAAA
TCTAACCTTCAATTAA
Found at i:42442755 original size:16 final size:17
Alignment explanation
Indices: 42442734--42442768 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42442724 AAAAATTGTT
*
42442734 TTACTTTT-CTATATTA
1 TTACTTTTAATATATTA
42442750 TTACTTTTAATATATTA
1 TTACTTTTAATATATTA
42442767 TT
1 TT
42442769 TCATGTATTA
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:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (17 bp):
TTACTTTTAATATATTA
Found at i:42442954 original size:21 final size:23
Alignment explanation
Indices: 42442901--42442955 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
42442891 TATACTTTTA
42442901 TATTATATATTATATAATTATCT
1 TATTATATATTATATAATTATCT
* *
42442924 TATTAAATATGTATATTATT-T-T
1 TATTATATAT-TATATAATTATCT
42442946 T-TTATATATT
1 TATTATATATT
42442956 TTTAAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.04
21 7 0.25
22 2 0.07
23 10 0.36
24 8 0.29
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTATATATTATATAATTATCT
Found at i:42448592 original size:20 final size:20
Alignment explanation
Indices: 42448564--42448631 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
42448554 GTGGAAAATT
*
42448564 GATGTACTTCGGTACCCCTG
1 GATGCACTTCGGTACCCCTG
*
42448584 GATGCACTTAC-GTGCCCCT-
1 GATGCACTT-CGGTACCCCTG
* *
42448603 GTTGTACTGT-GGTACCCCTG
1 GATGCACT-TCGGTACCCCTG
*
42448623 AATGCACTT
1 GATGCACTT
42448632 ACGTGTCGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
19 14 0.39
20 21 0.58
21 1 0.03
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (20 bp):
GATGCACTTCGGTACCCCTG
Found at i:42448620 original size:39 final size:38
Alignment explanation
Indices: 42448566--42448766 Score: 222
Period size: 39 Copynumber: 5.2 Consensus size: 38
42448556 GGAAAATTGA
*
42448566 TGTACTTCGGTACCCCTGGATGCACTTACGTGCCCCTGT
1 TGTACTT-GGTACCCCTGAATGCACTTACGTGCCCCTGT
* ** *
42448605 TGTACTGTGGTACCCCTGAATGCACTTACGTGTCGTTAT
1 TGTACT-TGGTACCCCTGAATGCACTTACGTGCCCCTGT
* *
42448644 TGTACTTTGGGACCCCTGAATGCACTTACATGCCCCTGT
1 TGTAC-TTGGTACCCCTGAATGCACTTACGTGCCCCTGT
* *
42448683 TGTACTTCGGTATCCCTGGATGCACTTACGTGCCCCTGT
1 TGTACTT-GGTACCCCTGAATGCACTTACGTGCCCCTGT
* * * * * *
42448722 TGTACTTTGGCACCCCTGAACGCAATTACATTCCCTTGT
1 TGTAC-TTGGTACCCCTGAATGCACTTACGTGCCCCTGT
42448761 TGTACT
1 TGTACT
42448767 CCGATACTCC
Statistics
Matches: 135, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
38 3 0.02
39 128 0.95
40 4 0.03
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.33
Consensus pattern (38 bp):
TGTACTTGGTACCCCTGAATGCACTTACGTGCCCCTGT
Found at i:42448700 original size:78 final size:78
Alignment explanation
Indices: 42448566--42448766 Score: 251
Period size: 78 Copynumber: 2.6 Consensus size: 78
42448556 GGAAAATTGA
* * * *
42448566 TGTACTTCGGTACCCCTGGATGCACTTACGTGCCCCTGTTGTACTGTGGTACCCCTGAATGCACT
1 TGTACTTTGGCACCCCTGAATGCACTTACATGCCCCTGTTGTACTGTGGTACCCCTGAATGCACT
* **
42448631 TACGTGTCGTTAT
66 TACGTGCCCCTAT
* * *
42448644 TGTACTTTGGGACCCCTGAATGCACTTACATGCCCCTGTTGTACT-TCGGTATCCCTGGATGCAC
1 TGTACTTTGGCACCCCTGAATGCACTTACATGCCCCTGTTGTACTGT-GGTACCCCTGAATGCAC
*
42448708 TTACGTGCCCCTGT
65 TTACGTGCCCCTAT
* * * *
42448722 TGTACTTTGGCACCCCTGAACGCAATTACATTCCCTTGTTGTACT
1 TGTACTTTGGCACCCCTGAATGCACTTACATGCCCCTGTTGTACT
42448767 CCGATACTCC
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 1 0.01
78 106 0.99
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.33
Consensus pattern (78 bp):
TGTACTTTGGCACCCCTGAATGCACTTACATGCCCCTGTTGTACTGTGGTACCCCTGAATGCACT
TACGTGCCCCTAT
Found at i:42448719 original size:20 final size:20
Alignment explanation
Indices: 42448656--42448720 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
42448646 TACTTTGGGA
* *
42448656 CCCCTGAATGCACTTACATG
1 CCCCTGGATGCACTTACGTG
* * *
42448676 CCCCT-GTTGTACTT-CGGTA
1 CCCCTGGATGCACTTAC-GTG
*
42448695 TCCCTGGATGCACTTACGTG
1 CCCCTGGATGCACTTACGTG
42448715 CCCCTG
1 CCCCTG
42448721 TTGTACTTTG
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 1 0.03
19 11 0.34
20 19 0.59
21 1 0.03
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.29
Consensus pattern (20 bp):
CCCCTGGATGCACTTACGTG
Found at i:42453479 original size:23 final size:23
Alignment explanation
Indices: 42453453--42453497 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
42453443 GCAAATTCGA
*
42453453 AAAGAAATAAAAAGAAAAGAAAG
1 AAAGAAAGAAAAAGAAAAGAAAG
**
42453476 AAAGAAAGAAAGGGAAAAGAAA
1 AAAGAAAGAAAAAGAAAAGAAA
42453498 CTCATGACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (23 bp):
AAAGAAAGAAAAAGAAAAGAAAG
Found at i:42454658 original size:43 final size:43
Alignment explanation
Indices: 42454611--42454696 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
42454601 TATGTGATTG
42454611 ATATTAAAATGACAAAGATGAGAAATAAATATGAGATGAGAAA
1 ATATTAAAATGACAAAGATGAGAAATAAATATGAGATGAGAAA
* * * *
42454654 ATATTGAAATGACAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTAAAATGACAAAGATGAGAAATAAATATGAGATGAGAAA
42454697 TGAAATATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.23
Consensus pattern (43 bp):
ATATTAAAATGACAAAGATGAGAAATAAATATGAGATGAGAAA
Found at i:42454678 original size:16 final size:16
Alignment explanation
Indices: 42454617--42454681 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
42454607 ATTGATATTA
*
42454617 AAATGACAAAGATGAG
1 AAATGACAAATATGAG
42454633 AAAT---AAATATGAG
1 AAATGACAAATATGAG
* *
42454646 --ATGAGAAAATAT-TG
1 AAATGA-CAAATATGAG
42454660 AAATGACAAATATGAG
1 AAATGACAAATATGAG
42454676 AAATGA
1 AAATGA
42454682 TTATGAGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
11 2 0.05
13 8 0.21
14 1 0.03
15 12 0.32
16 15 0.39
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (16 bp):
AAATGACAAATATGAG
Found at i:42454706 original size:32 final size:32
Alignment explanation
Indices: 42454667--42454728 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
42454657 TTGAAATGAC
* *
42454667 AAATATGAGA-AATGATTATGAGATGAGAAATG
1 AAATATGAAATAATGAAT-TGAGATGAGAAATG
*
42454699 AAATATGAAATAATGAATTGAGATGTGAAA
1 AAATATGAAATAATGAATTGAGATGAGAAA
42454729 CTTGAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (32 bp):
AAATATGAAATAATGAATTGAGATGAGAAATG
Found at i:42462389 original size:29 final size:29
Alignment explanation
Indices: 42462346--42462465 Score: 163
Period size: 29 Copynumber: 4.2 Consensus size: 29
42462336 GAAAGCTTGT
*
42462346 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATATGATTTGGGCCTAATGGGCC
*
42462375 GTATGAATATGATTTGGGCCTAATGGGCC
1 ATATGAATATGATTTGGGCCTAATGGGCC
* * *
42462404 ATACGAATGTGATTTAGGCCTAATGGGCC
1 ATATGAATATGATTTGGGCCTAATGGGCC
*
42462433 ATATGAATGA-GA-TTGGGCCTAGTGGGCC
1 ATATGAAT-ATGATTTGGGCCTAATGGGCC
42462461 ATATG
1 ATATG
42462466 CATGTATGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 19 0.24
29 61 0.76
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (29 bp):
ATATGAATATGATTTGGGCCTAATGGGCC
Found at i:42463960 original size:43 final size:41
Alignment explanation
Indices: 42463868--42463980 Score: 127
Period size: 43 Copynumber: 2.7 Consensus size: 41
42463858 ATGTTTGGTG
* * *
42463868 TATAAGACCACGTCTGGGACATTGGCATCGTATTTGATTTCT
1 TATAAGACC-CGTCTAGGACATTGGCATCGTATTTGATTACA
* *
42463910 TACAAGACCCTGTCTAGGACAATGGCATCGATATTTGATTACA
1 TATAAGACCC-GTCTAGGACATTGGCATCG-TATTTGATTACA
* *
42463953 TGTAAGACTGCGTCTAGGACATTGGCAT
1 TATAAGAC-CCGTCTAGGACATTGGCAT
42463981 TTTACGAGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 25 0.42
43 32 0.54
44 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (41 bp):
TATAAGACCCGTCTAGGACATTGGCATCGTATTTGATTACA
Found at i:42467370 original size:27 final size:24
Alignment explanation
Indices: 42467316--42467374 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
42467306 TTCATGGTAT
*
42467316 TTTAGTAAATCCAAAATAAAAAAT
1 TTTAGTAAATCCAAAATAAAAAAA
42467340 TTTAGTAAATCCAAGAATTTAAAAAAA
1 TTTAGTAAATCCAA-AA--TAAAAAAA
42467367 TTTA-TAAA
1 TTTAGTAAA
42467375 GGCCTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 14 0.45
25 2 0.06
26 4 0.13
27 11 0.35
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (24 bp):
TTTAGTAAATCCAAAATAAAAAAA
Found at i:42475778 original size:71 final size:71
Alignment explanation
Indices: 42475694--42475857 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42475684 CGATTTGTCT
42475694 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42475759 CTTTCA
66 CTTTCA
42475765 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42475830 CTTTCA
66 CTTTCA
42475836 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42475858 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42475895 original size:71 final size:70
Alignment explanation
Indices: 42475694--42475891 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
42475684 CGATTTGTCT
* * * *
42475694 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
42475759 CTTTCA
65 CTTTCA
* * * *
42475765 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
42475830 CTTTCA
65 CTTTCA
* *
42475836 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
42475892 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42482887 original size:71 final size:71
Alignment explanation
Indices: 42482803--42482966 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42482793 CGATTTGTCT
42482803 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42482868 CTTTCA
66 CTTTCA
42482874 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42482939 CTTTCA
66 CTTTCA
42482945 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42482967 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42483004 original size:71 final size:70
Alignment explanation
Indices: 42482803--42483000 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
42482793 CGATTTGTCT
* * * *
42482803 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
42482868 CTTTCA
65 CTTTCA
* * * *
42482874 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
42482939 CTTTCA
65 CTTTCA
* *
42482945 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
42483001 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42486350 original size:15 final size:15
Alignment explanation
Indices: 42486330--42486361 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
42486320 TATTCGCATG
42486330 TCAAATCATAAACAA
1 TCAAATCATAAACAA
42486345 TCAAATCATAAACAA
1 TCAAATCATAAACAA
42486360 TC
1 TC
42486362 CATATTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (15 bp):
TCAAATCATAAACAA
Found at i:42488127 original size:71 final size:72
Alignment explanation
Indices: 42488045--42488206 Score: 229
Period size: 71 Copynumber: 2.3 Consensus size: 72
42488035 CATCATGTGT
* * * ** *
42488045 ACAAGAAAGCTACGAGACACCCTGTA-GTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACAC
1 ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGAGTGATTCCAAGTGAAGGACAC
42488109 CATGTAG
66 CATGTAG
* * *
42488116 ACAAGAGAGCTACGTGA-AAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGAAGGACAC
1 ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGAGTGATTCCAAGTGAAGGACAC
42488180 CATGTAG
66 CATGTAG
42488187 ACAAGAGAGCTACGAGACAA
1 ACAAGAGAGCTACGAGACAA
42488207 ATCGGTTAGG
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
70 3 0.04
71 74 0.94
72 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (72 bp):
ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGAGTGATTCCAAGTGAAGGACAC
CATGTAG
Found at i:42493116 original size:40 final size:39
Alignment explanation
Indices: 42493071--42493278 Score: 193
Period size: 40 Copynumber: 5.2 Consensus size: 39
42493061 CGGAATACAA
*
42493071 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42493111 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42493151 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
42493191 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
* ** * * *
42493231 CCGGGTATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
42493271 CCGGATAT
1 CCGGATAT
42493279 CATTCAATTG
Statistics
Matches: 139, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 4 0.03
40 132 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42493211 original size:80 final size:80
Alignment explanation
Indices: 42493071--42493277 Score: 229
Period size: 80 Copynumber: 2.6 Consensus size: 80
42493061 CGGAATACAA
* * *
42493071 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
42493135 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
42493151 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
42493215 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
* ** * ** * *
42493231 CCGGGTATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
42493278 TCATTCAATT
Statistics
Matches: 106, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
79 3 0.03
80 101 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:42501155 original size:40 final size:39
Alignment explanation
Indices: 42501110--42501317 Score: 193
Period size: 40 Copynumber: 5.2 Consensus size: 39
42501100 CGGAATACAA
*
42501110 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42501150 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42501190 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
42501230 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
* ** * * *
42501270 CCGGGTATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
42501310 CCGGATAT
1 CCGGATAT
42501318 CATTCAATTG
Statistics
Matches: 139, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 4 0.03
40 132 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42501250 original size:80 final size:80
Alignment explanation
Indices: 42501110--42501316 Score: 229
Period size: 80 Copynumber: 2.6 Consensus size: 80
42501100 CGGAATACAA
* * *
42501110 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
42501174 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
42501190 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
42501254 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
* ** * ** * *
42501270 CCGGGTATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
42501317 TCATTCAATT
Statistics
Matches: 106, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
79 3 0.03
80 101 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:42506452 original size:71 final size:72
Alignment explanation
Indices: 42506370--42506531 Score: 220
Period size: 71 Copynumber: 2.3 Consensus size: 72
42506360 CATCATGTGT
* * * ** *
42506370 ACAAGAAAGCTACGAGACACCCTGTA-GTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACAC
1 ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGAGTGATTCCAAGTGAAGGACAC
*
42506434 CATGTAG
66 CATATAG
* * *
42506441 ACAAGAGAGCTACGTGA-AAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGAAGGACAC
1 ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGAGTGATTCCAAGTGAAGGACAC
42506505 CATATAG
66 CATATAG
42506512 ACAAGAGAGCTACGAGACAA
1 ACAAGAGAGCTACGAGACAA
42506532 ATCGGTTAGG
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
70 3 0.04
71 73 0.94
72 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (72 bp):
ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGAGTGATTCCAAGTGAAGGACAC
CATATAG
Found at i:42508471 original size:41 final size:41
Alignment explanation
Indices: 42508403--42508522 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
42508393 CACATATATC
* *
42508403 ATACAATGACAATGTCCTAGACGTGGTCTTACACGAATCAA
1 ATACGATGACAATGTCCTAAACGTGGTCTTACACGAATCAA
* * * *
42508444 ATACGATGTCAATGTCCTAAACATGGTCTTACACATAATCAC
1 ATACGATGACAATGTCCTAAACGTGGTCTTACAC-GAATCAA
* * * *
42508486 ATATCGATGCCAACGTCCCAAACGTAGTCTTACACGA
1 ATA-CGATGACAATGTCCTAAACGTGGTCTTACACGA
42508523 GAACACATAT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 30 0.46
42 9 0.14
43 26 0.40
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (41 bp):
ATACGATGACAATGTCCTAAACGTGGTCTTACACGAATCAA
Found at i:42508517 original size:43 final size:43
Alignment explanation
Indices: 42508423--42508533 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
42508413 AATGTCCTAG
* * * *
42508423 ACGTGGTCTTACAC-GAATCAAATA-CGATGTCAATGTCCTAA
1 ACGTGGTCTTACACAGAATCACATATCGATGCCAACGTCCCAA
* *
42508464 ACATGGTCTTACACATAATCACATATCGATGCCAACGTCCCAA
1 ACGTGGTCTTACACAGAATCACATATCGATGCCAACGTCCCAA
*
42508507 ACGTAGTCTTACACGAGAA-CACATATC
1 ACGTGGTCTTACAC-AGAATCACATATC
42508534 AGAAACCCTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
41 13 0.22
42 8 0.14
43 34 0.59
44 3 0.05
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.24
Consensus pattern (43 bp):
ACGTGGTCTTACACAGAATCACATATCGATGCCAACGTCCCAA
Found at i:42513016 original size:42 final size:44
Alignment explanation
Indices: 42512915--42513032 Score: 143
Period size: 42 Copynumber: 2.7 Consensus size: 44
42512905 TGATATCATG
* * * * *
42512915 TAAGACTATGTCTGGAACATCGGCATCGATTTGAGATTTACGTG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGAGATTTACGTA
42512959 TAAGACCATGTCTGGGACATTGGCATCGTATAT-A-ATTT-CGTA
1 TAAGACCATGTCTGGGACATTGGCATCG-ATATGAGATTTACGTA
* *
42513001 TAAGACCCTGTCTGGGACAGTGGCATCGATAT
1 TAAGACCATGTCTGGGACATTGGCATCGATAT
42513033 TTGATAACAT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.06
42 29 0.44
43 4 0.06
44 26 0.39
45 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
TAAGACCATGTCTGGGACATTGGCATCGATATGAGATTTACGTA
Found at i:42522651 original size:46 final size:47
Alignment explanation
Indices: 42522495--42522753 Score: 189
Period size: 46 Copynumber: 5.5 Consensus size: 47
42522485 TTTGTGCGCT
* *
42522495 AGTGTAAG-ACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGAACATGTCTGGGACATGCATCGGCCTCGA-GATGAGAGCC
* * * * * * *
42522541 AGTGTAAGAACATGTCTAGGACATGGCAACGACATTGAGACGAGAGCT
1 AGTGTAAGAACATGTCTGGGACAT-GCATCGGCCTCGAGATGAGAGCC
42522589 AGTGTAAGAA-ATGTCTGGGACATGCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGAACATGTCTGGGACATGCATCGGCCTCGAGATG-AGAGCC
* * * * *
42522635 AGCGTAA-AACATGTCTGGGACATGCACCGG-CTATGAGAT--GCGTC
1 AGTGTAAGAACATGTCTGGGACATGCATCGGCCT-CGAGATGAGAGCC
* * * *
42522679 AGTGTATG-ACTCTGTCTAGGACATGGCATCGGCAC-AGAGATGTGAGAGCC
1 AGTGTAAGAAC-ATGTCTGGGACAT-GCATCGGC-CTCGAGA--TGAGAGCC
42522729 AGTGTAAG-ACGATGTCTGGGACATG
1 AGTGTAAGAAC-ATGTCTGGGACATG
42522754 GCGTCGGACA
Statistics
Matches: 164, Mismatches: 33, Indels: 29
0.73 0.15 0.13
Matches are distributed among these distances:
44 9 0.05
45 15 0.09
46 63 0.38
47 27 0.16
48 25 0.15
49 2 0.01
50 23 0.14
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (47 bp):
AGTGTAAGAACATGTCTGGGACATGCATCGGCCTCGAGATGAGAGCC
Found at i:42526297 original size:53 final size:53
Alignment explanation
Indices: 42526228--42526542 Score: 234
Period size: 53 Copynumber: 5.8 Consensus size: 53
42526218 TTCCTTTTTA
* * * * **
42526228 AACTTACCATTTCCATGTCTTGACATAGTCTTTTGTGGTATCCTTGCCTTATG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
* * * * *
42526281 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATA
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
* * * * * *
42526334 ATAGTTTATCAATGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTACG
1 A-A-CTCACCATTGCCATGCCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
* * * *
42526389 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
** * ** * * * * * * *
42526443 TAGTTTATTAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTCACCATTGCCATGCCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
* ** * **
42526498 AACTTACCAAAGCCATGCCTTGGCATGGTCTTATTTGGTATCCTT
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACGTGGTATCCTT
42526543 AAACCCTAAT
Statistics
Matches: 201, Mismatches: 57, Indels: 7
0.76 0.22 0.03
Matches are distributed among these distances:
53 83 0.41
54 37 0.18
55 81 0.40
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (53 bp):
AACTCACCATTGCCATGCCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
Found at i:42526365 original size:55 final size:55
Alignment explanation
Indices: 42526291--42526530 Score: 234
Period size: 55 Copynumber: 4.4 Consensus size: 55
42526281 AACTCACCAT
*
42526291 TGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAA
* * * * ** * * * *
42526346 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTACGA-A-CTCACCAT
1 TGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAA
* * *
42526399 TGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTATTAA
1 TGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAA
* *** * * ** *
42526454 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA-AACTTACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAA
* *
42526508 AGCCATGCCTTGGCATGGTCTTA
1 TGCCATGCCTTGACATGGTCTTA
42526531 TTTGGTATCC
Statistics
Matches: 144, Mismatches: 39, Indels: 5
0.77 0.21 0.03
Matches are distributed among these distances:
53 40 0.28
54 28 0.19
55 76 0.53
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (55 bp):
TGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAA
Found at i:42526429 original size:108 final size:107
Alignment explanation
Indices: 42526240--42526530 Score: 438
Period size: 108 Copynumber: 2.7 Consensus size: 107
42526230 CTTACCATTT
* **
42526240 CCATGTCTTGACATAGTCTTTTGTGGTATCCTTGCCTTATGAACTCACCATTGCCATGCCTTGGC
1 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTA-GAACTCACCATTGCCATGCCTTGGC
42526305 ATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAATG
65 ATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAATG
42526348 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTACGAACTCACCATTGCCATGCCTTGGC
1 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTA-GAACTCACCATTGCCATGCCTTGGC
* *
42526413 ATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTATTAATG
65 ATGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAATG
* * * * * **
42526456 CCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAAAGCCATGCCTTGG
1 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCC-T-TAGAACTCACCATTGCCATGCCTTGG
42526521 CATGGTCTTA
64 CATGGTCTTA
42526531 TTTGGTATCC
Statistics
Matches: 168, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
108 135 0.80
109 31 0.18
110 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (107 bp):
CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAGAACTCACCATTGCCATGCCTTGGCA
TGGTCTTACATGGGATCTTTGCCTTATAATAGTTTATCAATG
Found at i:42535760 original size:46 final size:46
Alignment explanation
Indices: 42535664--42535785 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 46
42535654 TGTTACACAA
*
42535664 TGTAAGACCATGTCTAGGACATGGCAAT-GACATCGAGACGAGAGCTAG
1 TGTAAGA-CATGTCTAGGACAT-GC-ATCGGCATCGAGACGAGAGCTAG
* *
42535712 TGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATGTA-AGCTAG
1 TGTAAGACATGTCTAGGACATGCATCGGCATCGAGACG-AGAGCTAG
* *
42535758 TGTAAGAAATGTCTGGGACATGCATCGG
1 TGTAAGACATGTCTAGGACATGCATCGG
42535786 GTATGAGATG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
45 2 0.03
46 43 0.64
47 15 0.22
48 7 0.10
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (46 bp):
TGTAAGACATGTCTAGGACATGCATCGGCATCGAGACGAGAGCTAG
Found at i:42536986 original size:30 final size:27
Alignment explanation
Indices: 42536942--42536997 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
42536932 ACACAAGCTA
*
42536942 GGACACGGGTGTGTCATGGCCGTGTGAG
1 GGACACGGGTGTGTCA-GGCAGTGTGAG
42536970 GGACACGGGCGTGTGTCAGGCAGTGTGA
1 GGACAC-GG-GTGTGTCAGGCAGTGTGA
42536998 AAGGCCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 11 0.44
30 8 0.32
ACGTcount: A:0.16, C:0.18, G:0.46, T:0.20
Consensus pattern (27 bp):
GGACACGGGTGTGTCAGGCAGTGTGAG
Found at i:42544774 original size:29 final size:29
Alignment explanation
Indices: 42544735--42544809 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
42544725 GGTTGAGAGA
* *
42544735 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
42544764 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
42544793 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
42544810 TGGTTGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:42544850 original size:2 final size:2
Alignment explanation
Indices: 42544845--42544869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42544835 GCGAACCCAC
42544845 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
42544870 TTTCTATCAA
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:42552682 original size:29 final size:29
Alignment explanation
Indices: 42552643--42552717 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
42552633 GGTTGAGAGA
* *
42552643 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
42552672 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
42552701 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
42552718 TGGTTGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:42557314 original size:44 final size:44
Alignment explanation
Indices: 42557156--42557330 Score: 217
Period size: 44 Copynumber: 3.9 Consensus size: 44
42557146 ATGGTTGAGC
42557156 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
*** * *
42557200 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGA
*
42557249 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* *
42557293 ACCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42557331 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 40 0.36
45 1 0.01
46 33 0.29
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Found at i:42560271 original size:15 final size:15
Alignment explanation
Indices: 42560251--42560314 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
42560241 GTATCTTGGG
42560251 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
42560266 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
42560281 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
42560296 TTTCTTTATTC-GG-
1 TTTCTTTATTCTGGA
42560309 TTTCTT
1 TTTCTT
42560315 GTTATCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.13
14 4 0.09
15 33 0.73
16 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:42562741 original size:46 final size:45
Alignment explanation
Indices: 42562691--42562866 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
42562681 TGGTTGAGCA
42562691 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
42562737 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
42562784 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
42562830 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42562867 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:42562847 original size:93 final size:93
Alignment explanation
Indices: 42562688--42562858 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
42562678 GGATGGTTGA
* *
42562688 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42562753 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
42562781 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42562846 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
42562859 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:42565286 original size:43 final size:43
Alignment explanation
Indices: 42565238--42565324 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
42565228 GAGAAAAGAA
*
42565238 TGAATATATTAAATGTGTATTCAAATCAGGTACGTTTGAAATG
1 TGAATATATGAAATGTGTATTCAAATCAGGTACGTTTGAAATG
* *
42565281 TGAATATATGAAATGTGTATTCGAATCAGGTATGTTTGAAATG
1 TGAATATATGAAATGTGTATTCAAATCAGGTACGTTTGAAATG
42565324 T
1 T
42565325 ATACTATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.38
Consensus pattern (43 bp):
TGAATATATGAAATGTGTATTCAAATCAGGTACGTTTGAAATG
Found at i:42572700 original size:49 final size:49
Alignment explanation
Indices: 42572628--42572721 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
42572618 TCAAGAAGGG
* *
42572628 ATAAATAGTAATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTAATAAGAGTGTAGACAATGGAAGACCAAGTTTAGCAATGT
* * *
42572677 ATAAATATTGATAAGAGTGTAGACAATGGAAGACCAATTTTAGCA
1 ATAAATAGTAATAAGAGTGTAGACAATGGAAGACCAAGTTTAGCA
42572722 TTACATGGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (49 bp):
ATAAATAGTAATAAGAGTGTAGACAATGGAAGACCAAGTTTAGCAATGT
Found at i:42576555 original size:46 final size:43
Alignment explanation
Indices: 42576334--42576556 Score: 157
Period size: 46 Copynumber: 4.8 Consensus size: 43
42576324 GGGTTAATTG
* * *
42576334 TGTGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCACATTACGA
1 TGTGC-AGTGTAAGACATGTCTAGGACATGCATCGGCTACA--A-GA
* *
42576381 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-AACGA
1 TGTG-CAGTGTAAGA-CATGTCTAGGACAT-GCATCGGC--T-ACAA-GA
* *
42576429 -GAGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCT-CAAGA
1 TGTGC-AGTGTAAGACATGTCTAGGACATGCATC-GGCTACAAGA
* * *
42576472 TGTAAACCAGTGTAAGACATGTATGGGACATGCATCGGCTACAAGA
1 TGT---GCAGTGTAAGACATGTCTAGGACATGCATCGGCTACAAGA
42576518 TGTGTCAGTGTAAGACGATGTCTAGGACATGGCATCGGC
1 TGTG-CAGTGTAAGAC-ATGTCTAGGACAT-GCATCGGC
42576557 ATTATACCCT
Statistics
Matches: 146, Mismatches: 13, Indels: 35
0.75 0.07 0.18
Matches are distributed among these distances:
43 2 0.01
44 14 0.10
45 15 0.10
46 58 0.40
47 31 0.21
48 24 0.16
50 1 0.01
51 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (43 bp):
TGTGCAGTGTAAGACATGTCTAGGACATGCATCGGCTACAAGA
Found at i:42581543 original size:25 final size:25
Alignment explanation
Indices: 42581495--42581543 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
42581485 CATAATTGAA
* * *
42581495 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
42581520 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
42581544 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:42584883 original size:29 final size:29
Alignment explanation
Indices: 42584824--42584927 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
42584814 GTGACGAGAT
* **
42584824 TGGCACTAAGTGTGC-ATGCTGGAAATATA
1 TGGCACTAAGTGTGCGA-GCTCGAAACGTA
**
42584853 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGAGCTCGAAACGTA
** * * *
42584882 TGGCACTGTGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGAGCTCGAAA-CGTA
42584911 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
42584928 AATCGAGTAT
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
28 2 0.03
29 56 0.95
30 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTCGAAACGTA
Found at i:42584965 original size:2 final size:2
Alignment explanation
Indices: 42584960--42584992 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42584950 GTGCGTACTC
42584960 TA TA 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 TA TA T
42584993 CTCCGATCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42592798 original size:29 final size:29
Alignment explanation
Indices: 42592765--42592837 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
42592755 GTGACGAGAT
42592765 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42592794 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42592823 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
42592838 GAGCTCGAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:42592865 original size:58 final size:59
Alignment explanation
Indices: 42592765--42592897 Score: 137
Period size: 58 Copynumber: 2.3 Consensus size: 59
42592755 GTGACGAGAT
* * * *
42592765 TGGCACTAAGTGTGC-ATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAAT-ATA
1 TGGCACTAAGTGTGCGATGCTCGAAAGATATGGCACTAAGTGTGCAGGCT-GAAATCACA
* * ** * * *
42592823 TGGCACTAAGTGTGCGA-GCTCGAAGGGTATGGCACTGTGTGTGCGGGCTTAAATCGCA
1 TGGCACTAAGTGTGCGATGCTCGAAAGATATGGCACTAAGTGTGCAGGCTGAAATCACA
42592881 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
42592898 AATCGAGTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 4 0.06
58 57 0.92
59 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (59 bp):
TGGCACTAAGTGTGCGATGCTCGAAAGATATGGCACTAAGTGTGCAGGCTGAAATCACA
Found at i:42597499 original size:15 final size:16
Alignment explanation
Indices: 42597473--42597505 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42597463 CATTTCACTA
*
42597473 TTATGTCTTTTTGTAT
1 TTATGTCTTTTTATAT
42597489 TTATGTC-TTTTATAT
1 TTATGTCTTTTTATAT
42597504 TT
1 TT
42597506 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.70
Consensus pattern (16 bp):
TTATGTCTTTTTATAT
Found at i:42612257 original size:37 final size:39
Alignment explanation
Indices: 42612198--42612300 Score: 94
Period size: 37 Copynumber: 2.8 Consensus size: 39
42612188 CAAAAATAGT
* *
42612198 ATTATTTTAATAGTTTAATATTAAATTAA-ATTTAA-T-
1 ATTATCTTAATAGTTTAATATTAAATTAATATTAAAGTG
* *
42612234 ACTTATCTTAATAGTATT-TTATTAATTTAATATTAAAGTG
1 A-TTATCTTAATAGT-TTAATATTAAATTAATATTAAAGTG
*
42612274 ATTATCTTAATA--TTAA-ATTTAATTAAT
1 ATTATCTTAATAGTTTAATATTAAATTAAT
42612301 GTTTATCTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
36 12 0.22
37 22 0.41
38 7 0.13
39 12 0.22
40 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (39 bp):
ATTATCTTAATAGTTTAATATTAAATTAATATTAAAGTG
Found at i:42612960 original size:31 final size:32
Alignment explanation
Indices: 42612885--42612960 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 32
42612875 TAACGTTTCT
* * *
42612885 TAATTA-GATGACCAAAAAATAAATTTACTAA
1 TAATTAGGATGACTAAAAAAGAAATTGACTAA
*
42612916 TAGTT-GGATGACTAAAAAAGAAATTGACTAA
1 TAATTAGGATGACTAAAAAAGAAATTGACTAA
42612947 TAATTAGGA-GACTA
1 TAATTAGGATGACTA
42612961 CTAGTGTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
31 35 0.92
32 3 0.08
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (32 bp):
TAATTAGGATGACTAAAAAAGAAATTGACTAA
Found at i:42612996 original size:13 final size:14
Alignment explanation
Indices: 42612978--42613009 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
42612968 GATGTACCCT
42612978 ATATTTTAT-ATTA
1 ATATTTTATAATTA
42612991 ATATTTTATAATTA
1 ATATTTTATAATTA
42613005 A-ATTT
1 ATATTT
42613010 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTTATAATTA
Found at i:42613252 original size:28 final size:28
Alignment explanation
Indices: 42613211--42613267 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
42613201 CGAGTATGGC
*
42613211 TTGCCCGTGTTTTGTATCGGGTTACTTA
1 TTGCCCGTGCTTTGTATCGGGTTACTTA
*
42613239 TTGCCCGTGCTTTGTATTGGGTTACTTA
1 TTGCCCGTGCTTTGTATCGGGTTACTTA
42613267 T
1 T
42613268 CATTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (28 bp):
TTGCCCGTGCTTTGTATCGGGTTACTTA
Found at i:42615458 original size:52 final size:52
Alignment explanation
Indices: 42615400--42615574 Score: 120
Period size: 53 Copynumber: 3.1 Consensus size: 52
42615390 TAATAATAAT
*
42615400 AAAATTACACTTTAATTTTCTCAAAATTGATAAAAATTAATTCAATTCTTTA
1 AAAATTACACTTTAATTTTATCAAAATTGATAAAAATTAATTCAATTCTTTA
* * * * * ** *
42615452 AAAATTATAAATATATAAACTATTAAAATAGCAAAATTTATAAAATTTTAAATT-AA-TAATAA
1 AAAATTA-CACT-T-T-AA-T-TT----TATCAAAATTGATAAAA-ATT-AATTCAATTCTTTA
*
42615514 TAAAATTACACTTTAATTTTTTCAAAATTGATAAAAAATTAATTCAATTCTTTA
1 -AAAATTACACTTTAATTTTATCAAAATTGAT-AAAAATTAATTCAATTCTTTA
42615568 AAAATTA
1 AAAATTA
42615575 TAAATATATA
Statistics
Matches: 89, Mismatches: 18, Indels: 31
0.64 0.13 0.22
Matches are distributed among these distances:
52 11 0.12
53 23 0.26
54 8 0.09
55 1 0.01
56 2 0.02
57 3 0.03
58 3 0.03
59 2 0.02
60 1 0.01
61 1 0.01
62 19 0.21
63 11 0.12
64 4 0.04
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (52 bp):
AAAATTACACTTTAATTTTATCAAAATTGATAAAAATTAATTCAATTCTTTA
Found at i:42615506 original size:115 final size:116
Alignment explanation
Indices: 42615371--42615605 Score: 427
Period size: 115 Copynumber: 2.0 Consensus size: 116
42615361 ATTCCTTTAT
*
42615371 AATTTATAAAATTTTGAATTAATAATAATAAAATTACACTTTAATTTTCTCAAAATTGAT-AAAA
1 AATTTATAAAATTTTAAATTAATAATAATAAAATTACACTTTAATTTTCTCAAAATTGATAAAAA
*
42615435 ATTAATTCAATTCTTTAAAAATTATAAATATATAAACTATTAAAATAGCAA
66 ATTAATTCAATTCTTTAAAAATTATAAATATATAAACTATTAAAATAGAAA
*
42615486 AATTTATAAAATTTTAAATTAATAATAATAAAATTACACTTTAATTTTTTCAAAATTGATAAAAA
1 AATTTATAAAATTTTAAATTAATAATAATAAAATTACACTTTAATTTTCTCAAAATTGATAAAAA
*
42615551 ATTAATTCAATTCTTTAAAAATTATAAATATATAGACTATTAAAATAGAAA
66 ATTAATTCAATTCTTTAAAAATTATAAATATATAAACTATTAAAATAGAAA
42615602 AATT
1 AATT
42615606 ATATTTTTAT
Statistics
Matches: 115, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
115 58 0.50
116 57 0.50
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.40
Consensus pattern (116 bp):
AATTTATAAAATTTTAAATTAATAATAATAAAATTACACTTTAATTTTCTCAAAATTGATAAAAA
ATTAATTCAATTCTTTAAAAATTATAAATATATAAACTATTAAAATAGAAA
Found at i:42615572 original size:31 final size:32
Alignment explanation
Indices: 42615510--42615578 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
42615500 TAAATTAATA
* * *
42615510 ATAATAAAATTACACTTTAATTTTTTCAAAATT
1 ATAA-AAAATTACACTTCAATTCTTTAAAAATT
42615543 GATAAAAAATTA-A-TTCAATTCTTTAAAAATT
1 -ATAAAAAATTACACTTCAATTCTTTAAAAATT
42615574 ATAAA
1 ATAAA
42615579 TATATAGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 5 0.16
31 15 0.47
32 1 0.03
33 7 0.22
34 4 0.12
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (32 bp):
ATAAAAAATTACACTTCAATTCTTTAAAAATT
Found at i:42621106 original size:22 final size:22
Alignment explanation
Indices: 42621040--42621106 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 22
42621030 AGGAAAATAG
* **
42621040 ACTTTTAGCGGCGCTTTTTTTA
1 ACTTTTAGCGGCGCTTTCTAAA
* * **
42621062 GCCTTTAGCGGCGC-CACTAAA
1 ACTTTTAGCGGCGCTTTCTAAA
42621083 ACTTTTAGCGGCGCTTTCTAAA
1 ACTTTTAGCGGCGCTTTCTAAA
42621105 AC
1 AC
42621107 GTCGCAAAAA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (22 bp):
ACTTTTAGCGGCGCTTTCTAAA
Found at i:42621177 original size:43 final size:43
Alignment explanation
Indices: 42621121--42621269 Score: 201
Period size: 43 Copynumber: 3.4 Consensus size: 43
42621111 CAAAAAACGT
* *
42621121 AAGGTTTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTC
1 AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
* *
42621164 AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGGCGCTAAAGGTT
1 AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
* *
42621207 AAGGCTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTATAAAGGCC
1 AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGC--TAAAGGTC
* *
42621252 ATGAC-TTTAGCGGCGTTT
1 AAGGCTTTTAGCGGCGTTT
42621270 TTTTAAATAA
Statistics
Matches: 95, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
43 73 0.77
44 13 0.14
45 9 0.09
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.28
Consensus pattern (43 bp):
AAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
Found at i:42622720 original size:9 final size:9
Alignment explanation
Indices: 42622706--42622827 Score: 109
Period size: 9 Copynumber: 12.9 Consensus size: 9
42622696 ATGTATTAGT
42622706 TAAGTTATG
1 TAAGTTATG
42622715 TAAGTTGTTATG
1 TAA---GTTATG
*
42622727 TACGTTATG
1 TAAGTTATG
*
42622736 TGAGTTATG
1 TAAGTTATG
*
42622745 TAAATTATG
1 TAAGTTATG
42622754 TAAGTTATG
1 TAAGTTATG
*
42622763 TAAATTATG
1 TAAGTTATG
42622772 TAAGTTGTTATG
1 TAA---GTTATG
* *
42622784 TAAATTACG
1 TAAGTTATG
*
42622793 TAAGTTATA
1 TAAGTTATG
*
42622802 TGAGTTATG
1 TAAGTTATG
42622811 TAAGTTATG
1 TAAGTTATG
*
42622820 TAATTTAT
1 TAAGTTAT
42622828 TGAAGTAATG
Statistics
Matches: 90, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
9 74 0.82
12 16 0.18
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:42622782 original size:48 final size:48
Alignment explanation
Indices: 42622730--42622822 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
42622720 TGTTATGTAC
* * * *
42622730 GTTATGTGAGTTATGTAAATTATGTAAGTTATGTAAATTATGTAAGTT
1 GTTATGTAAATTACGTAAATTATATAAGTTATGTAAATTATGTAAGTT
* * *
42622778 GTTATGTAAATTACGTAAGTTATATGAGTTATGTAAGTTATGTAA
1 GTTATGTAAATTACGTAAATTATATAAGTTATGTAAATTATGTAA
42622823 TTTATTGAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.44
Consensus pattern (48 bp):
GTTATGTAAATTACGTAAATTATATAAGTTATGTAAATTATGTAAGTT
Found at i:42622782 original size:57 final size:57
Alignment explanation
Indices: 42622710--42622827 Score: 164
Period size: 57 Copynumber: 2.1 Consensus size: 57
42622700 ATTAGTTAAG
** * * *
42622710 TTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATGTAAA
1 TTATGTAAGTTGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATGTAAA
* * *
42622767 TTATGTAAGTTGTTATGTAAATTACGTAAGTTATATGAGTTATGTAAGTTATGTAAT
1 TTATGTAAGTTGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATGTAAA
42622824 TTAT
1 TTAT
42622828 TGAAGTAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (57 bp):
TTATGTAAGTTGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATGTAAA
Found at i:42624371 original size:2 final size:2
Alignment explanation
Indices: 42624364--42624391 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42624354 TTTATATTTT
42624364 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
42624392 ATAAGTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42626752 original size:24 final size:25
Alignment explanation
Indices: 42626704--42626767 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
42626694 TGCGGAAGCG
*
42626704 GAGAGCGATGGCGAAGGGACGCAGAA
1 GAGA-CGACGGCGAAGGGACGCAGAA
*
42626730 GAGATGACGGCGAAGGGAC-CAGAA
1 GAGACGACGGCGAAGGGACGCAGAA
*
42626754 GAGACGATGGCGAA
1 GAGACGACGGCGAA
42626768 CAACGATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 17 0.50
25 13 0.38
26 4 0.12
ACGTcount: A:0.36, C:0.16, G:0.44, T:0.05
Consensus pattern (25 bp):
GAGACGACGGCGAAGGGACGCAGAA
Found at i:42627387 original size:158 final size:156
Alignment explanation
Indices: 42627017--42627387 Score: 357
Period size: 158 Copynumber: 2.4 Consensus size: 156
42627007 ATCTTTGAAG
* *
42627017 AAAACGACGCCG-TTCCTGTTAAGCACTAA--TGTTTTTTGCGGCGTTTATTT-AAAAAACGCCG
1 AAAACGACGCCGTTTTC-GTTAA--ACTAATCTGTTTTTTGC-GCGTTTTTTTAAAAAAACGCCG
* * *
42627078 CTAATCCCTATATACTCAACTAAAACGACGACGTGTACTATAAACTTGAATTATTTTGCGGCGTT
62 CAAATCCCTATATACTCAACTAAAACGACGAC-TGTACCATAAACTTGAATTATGTTGCGGCGTT
* *
42627143 TTTGAAAGCGCCACTAATACCCGTATATACT
126 TTTAAAAACGCCACTAATACCCGTATATACT
** * *
42627174 AAAACGGTGCCGTTTTCGTTAAACTAATCTGTATTTTGTG-GCG-TTTTCTATAAAAACGCCGCA
1 AAAACGACGCCGTTTTCGTTAAACTAATCTGT-TTTT-TGCGCGTTTTTTTAAAAAAACGCCGCA
* * * * * * *
42627237 AATCCCCTATATATTGAACTAAAACGACGA-TGCTTCCAGTACACTTTACTTCTGTTGCGGCGTT
64 AAT-CCCTATATACTCAACTAAAACGACGACTG-TACCA-TAAACTTGAATTATGTTGCGGCGTT
* *
42627301 TTTAAAAACGCCACTAGTACTC-TATCA-ATCT
126 TTTAAAAACGCCACTAATACCCGTAT-ATA-CT
* *
42627332 AAAACGACGCCGTTTTCTTTCAACT-ATACTGTTTTTTGCGCGTTTTTTTAAAAAAA
1 AAAACGACGCCGTTTTCGTTAAACTAAT-CTGTTTTTTGCGCGTTTTTTTAAAAAAA
42627388 GCCACTAATC
Statistics
Matches: 174, Mismatches: 26, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
155 5 0.03
156 8 0.05
157 51 0.29
158 108 0.62
159 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (156 bp):
AAAACGACGCCGTTTTCGTTAAACTAATCTGTTTTTTGCGCGTTTTTTTAAAAAAACGCCGCAAA
TCCCTATATACTCAACTAAAACGACGACTGTACCATAAACTTGAATTATGTTGCGGCGTTTTTAA
AAACGCCACTAATACCCGTATATACT
Found at i:42627983 original size:2 final size:2
Alignment explanation
Indices: 42627976--42628006 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42627966 AAACCTTTTA
42627976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42628007 AAGTTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42628400 original size:14 final size:14
Alignment explanation
Indices: 42628380--42628424 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
42628370 TCCTACACCT
42628380 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
42628394 TATACCCTAAA-TCA
1 TAAACCCTAAACT-A
42628408 TAAACCCTAAACTA
1 TAAACCCTAAACTA
42628422 TAA
1 TAA
42628425 TGATAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:42628708 original size:7 final size:7
Alignment explanation
Indices: 42628696--42628815 Score: 109
Period size: 7 Copynumber: 17.1 Consensus size: 7
42628686 AAAAATGCCA
42628696 CTAAACC
1 CTAAACC
42628703 CTAAACC
1 CTAAACC
42628710 CTAAACC
1 CTAAACC
*
42628717 CTAAACA
1 CTAAACC
*
42628724 CTAAACT
1 CTAAACC
42628731 CTAAACC
1 CTAAACC
*
42628738 CTTAACC
1 CTAAACC
*
42628745 CTTAACC
1 CTAAACC
*
42628752 CCAAACC
1 CTAAACC
*
42628759 CTTACACC
1 C-TAAACC
*
42628767 TTAAACTC
1 CTAAAC-C
42628775 C--AACC
1 CTAAACC
*
42628780 CTAACCC
1 CTAAACC
42628787 CTAAACC
1 CTAAACC
*
42628794 CTAAATC
1 CTAAACC
* *
42628801 ATAATCC
1 CTAAACC
42628808 CTAAACC
1 CTAAACC
42628815 C
1 C
42628816 ATAATTCATC
Statistics
Matches: 90, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 80 0.89
8 5 0.06
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:42629112 original size:41 final size:41
Alignment explanation
Indices: 42629055--42629274 Score: 327
Period size: 41 Copynumber: 5.4 Consensus size: 41
42629045 GTTATATGAC
42629055 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
42629096 TTTTAGCGGCGTTTTTCCAAAAGAGCCGCTAATGCTCTGG-
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* *
42629136 TTTTAGCGGCGTTTTTCCAAAAGCGCAGCTGATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * *
42629177 TTTTAGCGGCGTATTTCCAAAAGCACCACTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * * *
42629218 TTTTAGCGACGTTTTGCCAGAAGCGCCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
42629258 TTTTTGCGGCGTTTTTC
1 TTTTAGCGGCGTTTTTC
42629275 GCTATTGCTC
Statistics
Matches: 159, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 52 0.33
41 107 0.67
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:42629194 original size:81 final size:82
Alignment explanation
Indices: 42629055--42629274 Score: 329
Period size: 81 Copynumber: 2.7 Consensus size: 82
42629045 GTTATATGAC
42629055 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAG-
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGC
*
42629119 AGCCGCTAATGCTCTGG-
66 A-CCACTAATGCTCTGGT
* * *
42629136 TTTTAGCGGCGTTTTTCCAAAAGCGCAGCTGATGCTCTGGTTTTTAGCGGCGTATTTCCAAAAGC
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGC
42629201 ACCACTAATGCTCTGGT
66 ACCACTAATGCTCTGGT
* * * * *
42629218 TTTTAGCGACGTTTTGCCAGAAGCGCCGCTAATGCTCT-ATTTTTTGCGGCGTTTTTC
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTC
42629275 GCTATTGCTC
Statistics
Matches: 125, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
81 91 0.73
82 34 0.27
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGC
ACCACTAATGCTCTGGT
Found at i:42629272 original size:122 final size:122
Alignment explanation
Indices: 42629055--42629274 Score: 350
Period size: 122 Copynumber: 1.8 Consensus size: 122
42629045 GTTATATGAC
* * * * *
42629055 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTTCCAAAAGA
1 TTTTAGCGGCGTATTTCCAAAAGCACCACTAATGCTCTGGTTTTTAGCGACGTTTTGCCAAAAGA
*
42629120 GCCGCTAATGCTCTGGTTTTAGCGGCGTTTTTCCAAAAGCGCAGCTGATGCTCTGGT
66 GCCGCTAATGCTCTAGTTTTAGCGGCGTTTTTCCAAAAGCGCAGCTGATGCTCTGGT
* *
42629177 TTTTAGCGGCGTATTTCCAAAAGCACCACTAATGCTCTGGTTTTTAGCGACGTTTTGCCAGAAGC
1 TTTTAGCGGCGTATTTCCAAAAGCACCACTAATGCTCTGGTTTTTAGCGACGTTTTGCCAAAAGA
* *
42629242 GCCGCTAATGCTCTATTTTTTGCGGCGTTTTTC
66 GCCGCTAATGCTCTAGTTTTAGCGGCGTTTTTC
42629275 GCTATTGCTC
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
122 88 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (122 bp):
TTTTAGCGGCGTATTTCCAAAAGCACCACTAATGCTCTGGTTTTTAGCGACGTTTTGCCAAAAGA
GCCGCTAATGCTCTAGTTTTAGCGGCGTTTTTCCAAAAGCGCAGCTGATGCTCTGGT
Found at i:42629278 original size:30 final size:30
Alignment explanation
Indices: 42629244--42629303 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
42629234 CCAGAAGCGC
*
42629244 CGCTAATGCTCTATTTTTTGCGGCGTTTTT
1 CGCTAATGCTCTATTTTTAGCGGCGTTTTT
* * *
42629274 CGCTATTGCTCTGTTTTTAGTGGCGTTTTT
1 CGCTAATGCTCTATTTTTAGCGGCGTTTTT
42629304 GGTAAAACGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.08, C:0.18, G:0.22, T:0.52
Consensus pattern (30 bp):
CGCTAATGCTCTATTTTTAGCGGCGTTTTT
Found at i:42629372 original size:12 final size:12
Alignment explanation
Indices: 42629357--42629382 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42629347 GTTTTTTTAT
42629357 AAAACGCCGCTA
1 AAAACGCCGCTA
42629369 AAAACGCCGCTA
1 AAAACGCCGCTA
42629381 AA
1 AA
42629383 GCCCTATATT
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:42629871 original size:30 final size:30
Alignment explanation
Indices: 42629835--42629897 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
42629825 CGAGATGGCC
42629835 TAAAAGCCCTTTTAGTATTTTTATTGACTA
1 TAAAAGCCCTTTTAGTATTTTTATTGACTA
42629865 TAAAAGCCCTTTTAGTATTTTTATTGACTA
1 TAAAAGCCCTTTTAGTATTTTTATTGACTA
42629895 TAA
1 TAA
42629898 CAGAATACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (30 bp):
TAAAAGCCCTTTTAGTATTTTTATTGACTA
Found at i:42631665 original size:46 final size:46
Alignment explanation
Indices: 42631612--42631704 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
42631602 GCATAACTTA
*
42631612 GTCTCTATAAAGAAGACCACCCAAGGATTATACATCTTCAGCGCAT
1 GTCTCTATAAAGAAGACCACCCAAGGATTATACATCTTCAGCACAT
* **
42631658 GTCTCTATAAAGAAGATCACCTGAGGATTATACATCTTCAGCACAT
1 GTCTCTATAAAGAAGACCACCCAAGGATTATACATCTTCAGCACAT
42631704 G
1 G
42631705 CCGAAGTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (46 bp):
GTCTCTATAAAGAAGACCACCCAAGGATTATACATCTTCAGCACAT
Found at i:42633572 original size:29 final size:29
Alignment explanation
Indices: 42633530--42633597 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
42633520 AATTAGCTAC
* *
42633530 TTGATTCACCTTCTGCGTGTAAGGTAAGG
1 TTGAATCACCTTCTGCGTGTAAGATAAGG
*
42633559 TTGAATCACCTTCTGCGTGTAAGATAATG
1 TTGAATCACCTTCTGCGTGTAAGATAAGG
*
42633588 TTGAACCACC
1 TTGAATCACC
42633598 CTTCCCAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (29 bp):
TTGAATCACCTTCTGCGTGTAAGATAAGG
Found at i:42634209 original size:20 final size:20
Alignment explanation
Indices: 42634186--42634226 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42634176 CTTTAAATTG
42634186 ATTTGAATAAAAGCAAATCA
1 ATTTGAATAAAAGCAAATCA
* *
42634206 ATTTGATTAAAATCAAATCA
1 ATTTGAATAAAAGCAAATCA
42634226 A
1 A
42634227 AACGAGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (20 bp):
ATTTGAATAAAAGCAAATCA
Found at i:42640205 original size:15 final size:16
Alignment explanation
Indices: 42640175--42640212 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42640165 TTAAAAACTA
42640175 ATTTAAAAAAATATTT
1 ATTTAAAAAAATATTT
42640191 ATTTAAAAATAAT-TTT
1 ATTTAAAAA-AATATTT
*
42640207 TTTTAA
1 ATTTAA
42640213 CTTTTTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAAAAAATATTT
Found at i:42644822 original size:47 final size:46
Alignment explanation
Indices: 42644683--42644839 Score: 149
Period size: 47 Copynumber: 3.4 Consensus size: 46
42644673 AATAGCACAA
* * *
42644683 CCCAGATACGTCTTACACTAGCTATCTGTGTTGAGGCCGATGTATGT
1 CCCAGACACGTCTTACACTAG-TATCTCTGTTGAGGCCGATGCATGT
* * * * * * *
42644730 CCTAGACATGTCTTACATTAGCA-CAACTCTT-A-GCCGATGCGTGT
1 CCCAGACACGTCTTACACTAGTATC-TCTGTTGAGGCCGATGCATGT
* *
42644774 CCCAGACACATCTTACACTAGTTATCTTTGTTGAGGCCGATGCATGT
1 CCCAGACACGTCTTACACTAG-TATCTCTGTTGAGGCCGATGCATGT
*
42644821 CCCAGACATGTCTTACACT
1 CCCAGACACGTCTTACACT
42644840 GGCTCTCAAA
Statistics
Matches: 84, Mismatches: 21, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
44 27 0.32
45 6 0.07
46 6 0.07
47 45 0.54
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (46 bp):
CCCAGACACGTCTTACACTAGTATCTCTGTTGAGGCCGATGCATGT
Found at i:42646513 original size:52 final size:52
Alignment explanation
Indices: 42646446--42646549 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
42646436 TGAGGACTTT
42646446 CCTCCACGGAGAAACTTTCACAAATACCTTATCCCTGACTTCAAATTTAATC
1 CCTCCACGGAGAAACTTTCACAAATACCTTATCCCTGACTTCAAATTTAATC
42646498 CCTCCACGGAGAAACTTTCACAAATACCTTATCCCTGACTTCAAATTTAATC
1 CCTCCACGGAGAAACTTTCACAAATACCTTATCCCTGACTTCAAATTTAATC
42646550 TCTTTTCGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.29
Consensus pattern (52 bp):
CCTCCACGGAGAAACTTTCACAAATACCTTATCCCTGACTTCAAATTTAATC
Found at i:42652372 original size:47 final size:45
Alignment explanation
Indices: 42652254--42652377 Score: 151
Period size: 44 Copynumber: 2.7 Consensus size: 45
42652244 ATCTCCATTA
*
42652254 AGGCCGATGCATATCCCAGACATGTCTTACACTAGCACAACTCTT
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTT
* **** *
42652299 A-GCCGATGCGTGTCCCAGACATGTCTTACACTAGCTATTTTTGTT
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGC-ACAACTCTT
*
42652344 GAGGCTGATGCATGTCCCAGACATGTCTTACACT
1 -AGGCCGATGCATGTCCCAGACATGTCTTACACT
42652378 GGCTCTCAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 32 0.48
45 5 0.07
46 1 0.01
47 29 0.43
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (45 bp):
AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTT
Found at i:42656675 original size:24 final size:24
Alignment explanation
Indices: 42656614--42656676 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
42656604 GTGTTACAAT
*
42656614 CCCTATCACCAGACACCTGCAAAC
1 CCCTATCACTAGACACCTGCAAAC
* **
42656638 CCCTAT-ACTAGACACTTGCGGAC
1 CCCTATCACTAGACACCTGCAAAC
*
42656661 CTCTATCACTAGACAC
1 CCCTATCACTAGACAC
42656677 ATATGAACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.30, C:0.40, G:0.11, T:0.19
Consensus pattern (24 bp):
CCCTATCACTAGACACCTGCAAAC
Found at i:42656690 original size:24 final size:24
Alignment explanation
Indices: 42656614--42656710 Score: 79
Period size: 24 Copynumber: 4.1 Consensus size: 24
42656604 GTGTTACAAT
* * * *
42656614 CCCTATCACCAGACACCTGCAAAC
1 CCCTATCACTAGACACATACGAAC
* * *
42656638 CCCTAT-ACTAGACACTTGCGGAC
1 CCCTATCACTAGACACATACGAAC
* *
42656661 CTCTATCACTAGACACATATGAAC
1 CCCTATCACTAGACACATACGAAC
* * *
42656685 CCCTATCACCAGATACATGCGAAC
1 CCCTATCACTAGACACATACGAAC
42656709 CC
1 CC
42656711 TTATAGTGAA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 18 0.31
24 40 0.69
ACGTcount: A:0.32, C:0.38, G:0.11, T:0.19
Consensus pattern (24 bp):
CCCTATCACTAGACACATACGAAC
Found at i:42662206 original size:50 final size:51
Alignment explanation
Indices: 42662127--42662255 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
42662117 GACCATGGCA
* * *
42662127 ACAAGTGATAAGTGATAGCTTCGGATACACTTATCTGATCAAAGACAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAGCAAAGACAAATG
*
42662178 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAGCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAGCAAAGACAAATG
* *
42662228 ACAAGTGAAAAGTGGTAGCTTCGGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
42662256 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
50 46 0.65
51 25 0.35
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAGCAAAGACAAATG
Found at i:42662269 original size:31 final size:31
Alignment explanation
Indices: 42662231--42662378 Score: 224
Period size: 31 Copynumber: 4.8 Consensus size: 31
42662221 ACAAATGACA
42662231 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
42662262 AGTGAAAAGTGGTAGCTTCTGCTACCTGACC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
42662293 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * * *
42662324 AGTGAAAAATGGTAGCTCCAGCTACCTGTTC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
42662355 AGTGAATAGTGGTAGCTTCGGCTA
1 AGTGAAAAGTGGTAGCTTCGGCTA
42662379 TAAGTGACAA
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:42662467 original size:47 final size:47
Alignment explanation
Indices: 42662398--42662610 Score: 197
Period size: 47 Copynumber: 4.6 Consensus size: 47
42662388 AGTGATCCCC
* * *
42662398 GTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACT
1 GTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACT
* * * * *
42662445 GTATAAGACCATATCTGGGATATGGCATCAGTGAGACATGTGAT-TT
1 GTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACT
* * *
42662491 GTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTAC-
1 GTATAAGACCATAGCTGGGATATGGCATCG--GTGTGATATGTGA-TACT
* * * *
42662540 GTGTAAGACCATAGCTGGGCTATGGCATC-G-AT-ATATG-AATA-T
1 GTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACT
* *
42662582 GTGTAAGACCATAGCTGGGCTATGGCATC
1 GTATAAGACCATAGCTGGGATATGGCATC
42662611 ATTATGTGAA
Statistics
Matches: 144, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
42 31 0.22
43 1 0.01
44 5 0.03
45 1 0.01
46 27 0.19
47 39 0.27
48 10 0.07
49 30 0.21
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (47 bp):
GTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATACT
Found at i:42662553 original size:49 final size:48
Alignment explanation
Indices: 42662401--42662654 Score: 209
Period size: 42 Copynumber: 5.6 Consensus size: 48
42662391 GATCCCCGTA
* * * * * * *
42662401 TAAGACCATATCTGGGATATGGCATCG--GTGTGATATATGCTACTGTA
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTC-GTG
* * * * * *
42662448 TAAGACCATATCTGGGATATGGCATC-A-GTGAGACATGTGATTTGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCGTG
42662494 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATT-CGTG
*
42662543 TAAGACCATAGCTGGGCTATGGCATCGATATATGA-A--T-A-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCGTG
42662585 TAAGACCATAGCTGGGCTATGGCATC-ATTATGTGA-A---GA-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATCGA-TATGTGATATGTGATTCGTG
* **
42662627 TAAGACCATAGTTGAACTATGGCATCGA
1 TAAGACCATAGCTGGGCTATGGCATCGA
42662655 GAAAACGAAG
Statistics
Matches: 182, Mismatches: 18, Indels: 18
0.83 0.08 0.08
Matches are distributed among these distances:
41 1 0.01
42 64 0.35
43 1 0.01
44 1 0.01
45 1 0.01
46 27 0.15
47 37 0.20
48 13 0.07
49 37 0.20
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (48 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCGTG
Found at i:42665409 original size:25 final size:24
Alignment explanation
Indices: 42665376--42665423 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
42665366 GAGATGCGTT
*
42665376 TTTATTATAAAATATCACATTTTAG
1 TTTATTATAAAATAT-AAATTTTAG
42665401 TTTATTATAAAATATAAATTTTA
1 TTTATTATAAAATATAAATTTTA
42665424 AAAATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTATTATAAAATATAAATTTTAG
Found at i:42667086 original size:37 final size:37
Alignment explanation
Indices: 42667045--42667164 Score: 186
Period size: 37 Copynumber: 3.2 Consensus size: 37
42667035 AACCTTTAGT
*
42667045 TCGGGGCTTACCCGGACAAAATCTCCACCCGTGGTCA
1 TCGGGTCTTACCCGGACAAAATCTCCACCCGTGGTCA
*
42667082 TCGGGTCTTACCCGGACAAAATCGCCACCCGTGGTCA
1 TCGGGTCTTACCCGGACAAAATCTCCACCCGTGGTCA
* ** *
42667119 TCGGGTCTTACCCGGACATAATCTCCACATGTAGTCA
1 TCGGGTCTTACCCGGACAAAATCTCCACCCGTGGTCA
42667156 TCGGGTCTT
1 TCGGGTCTT
42667165 TAGAGCTCGG
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (37 bp):
TCGGGTCTTACCCGGACAAAATCTCCACCCGTGGTCA
Found at i:42667351 original size:47 final size:47
Alignment explanation
Indices: 42667282--42667719 Score: 705
Period size: 47 Copynumber: 9.3 Consensus size: 47
42667272 CCCTTCGGGA
* * * * *
42667282 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
42667329 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42667376 CTTATCACATATATGCACTTTCACATTCATCACATAGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42667423 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
42667470 CTTATCTCATATATGCACTTTCACATTCATCACATCGGTCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42667517 CTTATCACATATATACACTTTCACATTTATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42667564 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42667611 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42667658 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42667705 CTTATCACATATATA
1 CTTATCACATATATA
42667720 TATCTCATAC
Statistics
Matches: 367, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 367 1.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42667360 original size:25 final size:25
Alignment explanation
Indices: 42667332--42667411 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
42667322 ACTCGGCCTT
*
42667332 ATCACATATATACACTTTCACATTC
1 ATCACATATATGCACTTTCACATTC
* * *
42667357 ATCACAT-T-GGC-CATTCGACCTT-
1 ATCACATATATGCACTTTC-ACATTC
42667379 ATCACATATATGCACTTTCACATTC
1 ATCACATATATGCACTTTCACATTC
42667404 ATCACATA
1 ATCACATA
42667412 GGCCATTAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
22 11 0.26
23 6 0.14
24 7 0.16
25 19 0.44
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATGCACTTTCACATTC
Done.