Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 29
Found at i:5487127 original size:31 final size:31
Alignment explanation
Indices: 5487085--5487152 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
5487075 TTACTAAAAA
* *
5487085 TAGGTGTCTAACGTTTTCTCCGTTACCATTT
1 TAGGTGACTAACGTTTTCTCCATTACCATTT
*
5487116 TGGGTGACTAACGTTTTCTCCATTACCATTT
1 TAGGTGACTAACGTTTTCTCCATTACCATTT
5487147 TAGGTG
1 TAGGTG
5487153 CTCAGACGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.43
Consensus pattern (31 bp):
TAGGTGACTAACGTTTTCTCCATTACCATTT
Found at i:5488075 original size:2 final size:2
Alignment explanation
Indices: 5488068--5488092 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5488058 ACCGCCTGGG
5488068 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
5488093 GTTCTTCCCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5494144 original size:13 final size:15
Alignment explanation
Indices: 5494126--5494157 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
5494116 TTTGAATCAC
5494126 CCTTTTTT-TCC-TT
1 CCTTTTTTCTCCTTT
5494139 CCTTTTTTCTCCTTT
1 CCTTTTTTCTCCTTT
5494154 CCTT
1 CCTT
5494158 GTAGTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CCTTTTTTCTCCTTT
Found at i:5496756 original size:13 final size:12
Alignment explanation
Indices: 5496733--5496757 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5496723 AAAAAAAATC
5496733 ACTAATTTTTTT
1 ACTAATTTTTTT
5496745 ACTAATTTTTTT
1 ACTAATTTTTTT
5496757 A
1 A
5496758 AAATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
ACTAATTTTTTT
Found at i:5497120 original size:26 final size:25
Alignment explanation
Indices: 5497067--5497132 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
5497057 TAAAAAAATC
5497067 AAATTTTAGTAAAAAAAATATTTTA
1 AAATTTTAGTAAAAAAAATATTTTA
* * *
5497092 AAATTTTAGTGAAAAATATTTTTTA
1 AAATTTTAGTAAAAAAAATATTTTA
* *
5497117 AAA-ATTAGTTAAAAAA
1 AAATTTTAGTAAAAAAA
5497133 TCAAATTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 10 0.29
25 25 0.71
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
AAATTTTAGTAAAAAAAATATTTTA
Found at i:5500203 original size:27 final size:27
Alignment explanation
Indices: 5500173--5500247 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
5500163 GGATGGAAGG
** * *
5500173 AAATGAATGAAATACCCTTGAAGTGTA
1 AAATGAACAAAATACCCCTAAAGTGTA
*
5500200 AAATGACCAAAATACCCCTAAAGTGTA
1 AAATGAACAAAATACCCCTAAAGTGTA
*
5500227 AAATGACCAAAAATACCCCTA
1 AAATGAAC-AAAATACCCCTA
5500248 TAATGAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 30 0.71
28 12 0.29
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (27 bp):
AAATGAACAAAATACCCCTAAAGTGTA
Found at i:5500240 original size:28 final size:27
Alignment explanation
Indices: 5500182--5500247 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
5500172 GAAATGAATG
* *
5500182 AAATACCCTTGAAGTGTAAAATGACCA
1 AAATACCCCTAAAGTGTAAAATGACCA
5500209 AAATACCCCTAAAGTGTAAAATGACCAA
1 AAATACCCCTAAAGTGTAAAATGACC-A
5500237 AAATACCCCTA
1 AAATACCCCTA
5500248 TAATGAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 24 0.67
28 12 0.33
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.20
Consensus pattern (27 bp):
AAATACCCCTAAAGTGTAAAATGACCA
Found at i:5503547 original size:58 final size:60
Alignment explanation
Indices: 5503437--5503560 Score: 171
Period size: 58 Copynumber: 2.1 Consensus size: 60
5503427 TTTGTATGAG
* *
5503437 ACATCTCCAATAAATAACTTCCTCTTATACCATTTAAACATATTTATGAGTATTTCTAAA
1 ACATCTCCAATAAATAACTTCCTCTTATACCAGTTAAACATATTTATAAGTATTTCTAAA
* * * * *
5503497 ACATCTCCAATAAA-AA-TTCCTTTTATGCTAGTTAGACATATTTCTAAGTATTTCTAAA
1 ACATCTCCAATAAATAACTTCCTCTTATACCAGTTAAACATATTTATAAGTATTTCTAAA
5503555 ACATCT
1 ACATCT
5503561 ATAAAAACTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 41 0.72
59 2 0.04
60 14 0.25
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (60 bp):
ACATCTCCAATAAATAACTTCCTCTTATACCAGTTAAACATATTTATAAGTATTTCTAAA
Found at i:5504353 original size:22 final size:21
Alignment explanation
Indices: 5504321--5504364 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
5504311 GAAATTTTAA
5504321 ATTTTTTATATTAATTA-TTT
1 ATTTTTTATATTAATTAGTTT
*
5504341 ATTTTATTAATATTATTTAGTTT
1 ATTTT-TT-ATATTAATTAGTTT
5504364 A
1 A
5504365 AAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 9 0.45
23 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTTTTTATATTAATTAGTTT
Found at i:5505768 original size:2 final size:2
Alignment explanation
Indices: 5505761--5505795 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5505751 ATTTATATTC
5505761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5505796 CAATATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5511771 original size:64 final size:62
Alignment explanation
Indices: 5511700--5511820 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 62
5511690 TTGGACTCTC
*
5511700 AGTGCATCGGTGCAT-TAAGAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTG
1 AGTGCATCGATGCATGT-A-AGTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAAGCCTG
*
5511764 AGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAA
1 AGTGCATCGATGCAT-GTAAGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAA
5511821 CTTAATTGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
63 8 0.15
64 43 0.81
65 1 0.02
66 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATGTAAGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAAGCCTG
Found at i:5511833 original size:64 final size:65
Alignment explanation
Indices: 5511720--5511862 Score: 188
Period size: 64 Copynumber: 2.2 Consensus size: 65
5511710 TGCATTAAGA
*
5511720 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGG-TAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGACTGAGTGCATCGATGCATGGAT-T
5511784 -
65 G
*
5511784 GTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAACTTA-ATTG-GTGCATCGATGCATGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAA---AGACTGAGTGCATCGATGCATGGA
5511846 TTG
63 TTG
*
5511849 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
5511863 CACTTTGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
63 8 0.11
64 46 0.65
65 16 0.23
66 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGACTGAGTGCATCGATGCATGGATTG
Found at i:5511850 original size:20 final size:20
Alignment explanation
Indices: 5511825--5511862 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5511815 TGAAAACTTA
5511825 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
5511845 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
5511863 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:5517727 original size:22 final size:21
Alignment explanation
Indices: 5517685--5517724 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5517675 GAGTTTATTT
*
5517685 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5517706 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5517725 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5519505 original size:21 final size:21
Alignment explanation
Indices: 5519481--5519524 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5519471 CCAGAGGAGG
*
5519481 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
5519502 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
5519523 AG
1 AG
5519525 CTCCCGGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:5525596 original size:14 final size:14
Alignment explanation
Indices: 5525574--5525603 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5525564 TGGTCACCTC
5525574 TGTTGTTTTTTTTT
1 TGTTGTTTTTTTTT
*
5525588 TGTTTTTTTTTTTT
1 TGTTGTTTTTTTTT
5525602 TG
1 TG
5525604 AGAAAACTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
TGTTGTTTTTTTTT
Found at i:5529109 original size:31 final size:31
Alignment explanation
Indices: 5529071--5529226 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
5529061 AGGGTCGAGG
*
5529071 GTTTACCTATGTTCTTCGGGACATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
5529102 GTTTACCTATATTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5529133 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5529164 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
5529195 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
5529226 G
1 G
5529227 GTTCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5532907 original size:18 final size:17
Alignment explanation
Indices: 5532884--5532918 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5532874 TAATTATATG
*
5532884 TGATTATCTGTATTACAT
1 TGATTATATGTA-TACAT
5532902 TGATTATATGTATACAT
1 TGATTATATGTATACAT
5532919 GACTAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (17 bp):
TGATTATATGTATACAT
Found at i:5533525 original size:31 final size:31
Alignment explanation
Indices: 5533487--5533641 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
5533477 AGGGTCGAGG
*
5533487 GTTTACCTATGTTCTTTGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
5533518 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
5533549 GTTTACCTATGTTCTTCGGGACATATGG-TT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
* *
5533579 GTTTACTTATGTTCTTCGGGATATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
* * *
5533610 GATTACCTAGGTTCTTCGGAATC-TATGGATT
1 GTTTACCTATGTTCTTCGGGA-CATATGGATT
5533641 G
1 G
5533642 GTCCTTCGGG
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
30 28 0.25
31 86 0.75
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.43
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGATT
Found at i:5533605 original size:61 final size:62
Alignment explanation
Indices: 5533487--5533641 Score: 233
Period size: 61 Copynumber: 2.5 Consensus size: 62
5533477 AGGGTCGAGG
*
5533487 GTTTACCTATGTTCTTTGGGACATATGGATTGTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATTGTTTACCTATGTTCTTCGGGACATATGGATT
* *
5533549 GTTTACCTATGTTCTTCGGGACATATGG-TTGTTTACTTATGTTCTTCGGGATATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATTGTTTACCTATGTTCTTCGGGACATATGGATT
* * *
5533610 GATTACCTAGGTTCTTCGGAATC-TATGGATTG
1 GTTTACCTATGTTCTTCGGGA-CATATGGATTG
5533642 GTCCTTCGGG
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
61 54 0.64
62 31 0.36
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.43
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGATTGTTTACCTATGTTCTTCGGGACATATGGATT
Found at i:5534287 original size:29 final size:30
Alignment explanation
Indices: 5534245--5534310 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
5534235 GGGGTGTTAC
*
5534245 ACACAC-AGTGACCTCCATGGTTGCATGGA
1 ACACACGAGTGACCTCCATGGTCGCATGGA
*
5534274 ACACACGA-TGACCTCTATGGTCGCATGGA
1 ACACACGAGTGACCTCCATGGTCGCATGGA
*
5534303 GCACACGA
1 ACACACGA
5534311 CAACCTAGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (30 bp):
ACACACGAGTGACCTCCATGGTCGCATGGA
Found at i:5552145 original size:14 final size:15
Alignment explanation
Indices: 5552126--5552158 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5552116 ATATTATAAC
5552126 ATTTT-AGATTTAAT
1 ATTTTAAGATTTAAT
*
5552140 ATTTTAAGCTTTAAT
1 ATTTTAAGATTTAAT
5552155 ATTT
1 ATTT
5552159 AAAATTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTTTAAGATTTAAT
Found at i:5560580 original size:19 final size:17
Alignment explanation
Indices: 5560548--5560582 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
5560538 AGCGTTCCAA
5560548 ACTTATCCAAGTCATTC
1 ACTTATCCAAGTCATTC
5560565 ACTTAATCCTAAGTCATT
1 ACTT-ATCC-AAGTCATT
5560583 GAGGTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (17 bp):
ACTTATCCAAGTCATTC
Found at i:5564027 original size:2 final size:2
Alignment explanation
Indices: 5564020--5564084 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
5564010 TGTTAAAACA
5564020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5564062 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
5564085 GATGATATTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5564850 original size:30 final size:29
Alignment explanation
Indices: 5564799--5564857 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5564789 TTAAAATTTT
5564799 AAAATTATATTGAAACAAAAAAATATTCCC
1 AAAATTATATTGAAAC-AAAAAATATTCCC
**
5564829 AAAATTATAATT-AAATTAAAAATATTCCC
1 AAAATTAT-ATTGAAACAAAAAATATTCCC
5564858 TCTGATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 12 0.46
30 11 0.42
31 3 0.12
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATTATATTGAAACAAAAAATATTCCC
Found at i:5575882 original size:229 final size:227
Alignment explanation
Indices: 5575477--5575925 Score: 772
Period size: 229 Copynumber: 2.0 Consensus size: 227
5575467 GTAAATTATC
* * * *
5575477 TATCCTTTTTATAAAAGTGTTCATACTTATTTCACTATGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTATGAAAACATATTTATTATTATATTTAGT
**
5575542 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
5575607 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTG
5575672 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
5575705 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACT-ATGAAAACATATTTATTATTATATTTAG
*
5575770 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* * *
5575835 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATT
5575900 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
5575926 GCAGTTTTAA
Statistics
Matches: 208, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 38 0.18
229 170 0.82
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTATGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:5576014 original size:20 final size:19
Alignment explanation
Indices: 5575991--5576036 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
5575981 CGATATACCA
*
5575991 GGTAAAAATATGATAAAACC
1 GGTAAAAA-AAGATAAAACC
5576011 GGTAACAAAAAGATAAAACC
1 GGTAA-AAAAAGATAAAACC
5576031 GGTAAA
1 GGTAAA
5576037 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (19 bp):
GGTAAAAAAAGATAAAACC
Found at i:5576204 original size:17 final size:19
Alignment explanation
Indices: 5576165--5576207 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
5576155 ATGTAAAAAT
5576165 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
5576185 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
5576202 ATGATA
1 ATGATA
5576208 CCAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:5578481 original size:21 final size:21
Alignment explanation
Indices: 5578434--5578498 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
5578424 AAGACAATCA
* *
5578434 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
5578456 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
5578476 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
5578497 AG
1 AG
5578499 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:5578569 original size:33 final size:33
Alignment explanation
Indices: 5578532--5578597 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
5578522 AAATTGATGG
*
5578532 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
5578565 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
5578598 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:5580413 original size:19 final size:19
Alignment explanation
Indices: 5580389--5580437 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5580379 AATGTAGGGT
5580389 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
5580408 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
5580427 TATTTTTGTAT
1 TAATTTTGTAT
5580438 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5580901 original size:199 final size:199
Alignment explanation
Indices: 5580556--5581924 Score: 2627
Period size: 199 Copynumber: 6.9 Consensus size: 199
5580546 CAATATGGCC
* *
5580556 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
5580621 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
5580686 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
5580751 ATGGAA
194 ATGGAA
5580757 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5580822 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
* *
5580887 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTTGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
5580951 GGAA
196 GGAA
5580955 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5581020 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5581085 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
5581150 GGAA
196 GGAA
5581154 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5581219 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
5581284 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
5581349 GGAA
196 GGAA
*
5581353 AACAGGGTGCACCCATAAAGTGTCAATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5581418 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5581483 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
5581547 GGAA
196 GGAA
5581551 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5581615 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5581680 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
5581745 GGAA
196 GGAA
5581749 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5581814 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5581879 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
5581925 CTAATTTAAA
Statistics
Matches: 1154, Mismatches: 11, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
197 140 0.12
198 308 0.27
199 647 0.56
200 24 0.02
201 35 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:5581535 original size:397 final size:398
Alignment explanation
Indices: 5580556--5581926 Score: 2631
Period size: 397 Copynumber: 3.4 Consensus size: 398
5580546 CAATATGGCC
* *
5580556 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
5580621 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
5580686 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTTCCAGAATGA
5580751 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
194 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
5580816 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
259 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
* *
5580881 TGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTTGATA-TTTTTTTCCAGA
324 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
5580945 ATGAATGGAA
389 ATGAATGGAA
5580955 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5581020 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
5581085 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTTCCAGAATGAAT
5581150 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
5581215 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
5581280 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
*
5581345 GAAAGGAA
391 GAATGGAA
*
5581353 AACAGGGTGCACCCATAAAGTGTCAATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5581418 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5581483 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTTCCAGAATGAAT
5581547 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
5581611 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
5581676 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
5581741 GAATGGAA
391 GAATGGAA
5581749 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5581814 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5581879 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
5581927 AATTTAAATA
Statistics
Matches: 960, Mismatches: 10, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
396 337 0.35
397 368 0.38
398 220 0.23
399 35 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (398 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTTCCAGAATGAAT
GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
GAATGGAA
Found at i:5583406 original size:18 final size:18
Alignment explanation
Indices: 5583385--5583446 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
5583375 AGCGGTCGCA
5583385 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
5583403 GAAGATGATGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
5583421 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
5583439 GAAGATGA
1 GAAGATGA
5583447 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:5583409 original size:6 final size:6
Alignment explanation
Indices: 5583385--5583476 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
5583375 AGCGGTCGCA
* * * * * *
5583385 GAAGAT GAAGCT GACGAT GAAGAT GATGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
5583433 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
5583477 TGATCCAAAC
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.22
Consensus pattern (6 bp):
GAAGAT
Found at i:5583414 original size:3 final size:3
Alignment explanation
Indices: 5583400--5583480 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
5583390 TGAAGCTGAC
* * * * ** *
5583400 GAT GAA GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
5583448 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
5583481 CCAAACAAGT
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.36, C:0.05, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:5583439 original size:36 final size:36
Alignment explanation
Indices: 5583388--5583464 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
5583378 GGTCGCAGAA
*
5583388 GATGAAGCTGACGATGAAGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGACGATGATGAC
* *
5583424 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGATGACGATGATGAC
5583460 GATGA
1 GATGA
5583465 TGATGAAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGATGACGATGATGAC
Found at i:5583480 original size:12 final size:12
Alignment explanation
Indices: 5583388--5583476 Score: 79
Period size: 12 Copynumber: 7.4 Consensus size: 12
5583378 GGTCGCAGAA
*
5583388 GATGAAGCTGAC
1 GATGAAGATGAC
*
5583400 GATGAAGATGAT
1 GATGAAGATGAC
*
5583412 GATGATGATGAC
1 GATGAAGATGAC
* *
5583424 GATGAAGCTGGC
1 GATGAAGATGAC
*
5583436 GATGAAGATGAT
1 GATGAAGATGAC
* * *
5583448 GACGATGATGAT
1 GATGAAGATGAC
* *
5583460 GATGATGATGAA
1 GATGAAGATGAC
5583472 GATGA
1 GATGA
5583477 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:5585256 original size:183 final size:183
Alignment explanation
Indices: 5584948--5585656 Score: 1283
Period size: 183 Copynumber: 3.9 Consensus size: 183
5584938 CTTTCAACAT
** * * *
5584948 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
5585013 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5585078 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
5585131 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
5585196 GGTCTACAACCTATATCGATACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5585261 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
5585314 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
5585379 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
5585444 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
5585497 TTTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
5585562 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
5585627 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
5585657 GTAATTTTAA
Statistics
Matches: 509, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 509 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:5588158 original size:25 final size:25
Alignment explanation
Indices: 5588124--5588188 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
5588114 TTATCATTAA
5588124 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
5588149 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
* *
5588174 ATTTAAGTATATACA
1 ATTTAGGTATGTACA
5588189 TCTTTTGAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:5588517 original size:22 final size:22
Alignment explanation
Indices: 5588472--5588517 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
5588462 ATTACATAAC
**
5588472 TTTTAAAAAAAGTATCGATTCT
1 TTTTAAAAAAAGTATCGACACT
* *
5588494 TTTTATAAAAAGTATGGACACT
1 TTTTAAAAAAAGTATCGACACT
5588516 TT
1 TT
5588518 CAATATAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (22 bp):
TTTTAAAAAAAGTATCGACACT
Found at i:5588570 original size:23 final size:23
Alignment explanation
Indices: 5588540--5588598 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
5588530 TAAACATATG
5588540 ATGTAATAGGTAGCCCTTATACA
1 ATGTAATAGGTAGCCCTTATACA
* ** *
5588563 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCCCTTATACA
5588586 ATGTAATAGGTAG
1 ATGTAATAGGTAG
5588599 TGGTTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (23 bp):
ATGTAATAGGTAGCCCTTATACA
Found at i:5588605 original size:23 final size:23
Alignment explanation
Indices: 5588535--5588607 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
5588525 ATAGGTAAAC
* **
5588535 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
5588558 ATACAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
5588581 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
5588604 ATAT
1 ATAT
5588608 TATAAAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:5588648 original size:20 final size:20
Alignment explanation
Indices: 5588607--5588648 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
5588597 AGTGGTTATA
* *
5588607 TTATAAAGTGTCTATCATTT
1 TTATAAAGTGTCCATCACTT
5588627 TTATAAAAGTGTCCAT-ACTT
1 TTAT-AAAGTGTCCATCACTT
5588647 TT
1 TT
5588649 TTCACTGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (20 bp):
TTATAAAGTGTCCATCACTT
Found at i:5588910 original size:25 final size:25
Alignment explanation
Indices: 5588876--5588926 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5588866 ACAACAAATC
*
5588876 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
5588901 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
5588926 A
1 A
5588927 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:5589336 original size:18 final size:18
Alignment explanation
Indices: 5589315--5589351 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5589305 GTAATTGGAG
5589315 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5589333 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5589351 T
1 T
5589352 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5589359 original size:24 final size:24
Alignment explanation
Indices: 5589307--5589353 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5589297 TTTCATATGT
* *
5589307 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
5589331 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
5589354 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:5589653 original size:39 final size:39
Alignment explanation
Indices: 5589610--5589696 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
5589600 TCCGATGCTC
*
5589610 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
5589649 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
5589688 ATCAAAATC
1 ATCAAAATC
5589697 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:5590133 original size:23 final size:23
Alignment explanation
Indices: 5590102--5590174 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
5590092 ATAGGTAAAC
*
5590102 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
5590125 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
5590148 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
5590171 ATAT
1 ATAT
5590175 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5591016 original size:22 final size:23
Alignment explanation
Indices: 5590981--5591023 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5590971 TATTGTACTT
**
5590981 TATAATATTTCCGGT-TAAATAA
1 TATAATATAACCGGTCTAAATAA
5591003 TATAATATAACCGGTCTAAAT
1 TATAATATAACCGGTCTAAAT
5591024 TTTAACCGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (23 bp):
TATAATATAACCGGTCTAAATAA
Found at i:5592066 original size:75 final size:75
Alignment explanation
Indices: 5591926--5592078 Score: 200
Period size: 75 Copynumber: 2.0 Consensus size: 75
5591916 CCAGCAACAC
* ** * *
5591926 CTGTACCACCTTGTTGCACGTCTTCATGTACACTCTGATTGTTAGACCCCATGTGTTATCCACTA
1 CTGTAACACCTTGTTGCAAATCTTCATGTACACTCTGATTGCTAGACCCCACGTGTTATCCACTA
5591991 GGTAA-GAACT
66 GGTAATG-ACT
* * * * *
5592001 CTGTAACACCTTGTTGCAAATCTTCATGTACACTGTGATTGCTAGACTCCACGTTTTGTCTACTA
1 CTGTAACACCTTGTTGCAAATCTTCATGTACACTCTGATTGCTAGACCCCACGTGTTATCCACTA
5592066 GGTAATGACT
66 GGTAATGACT
5592076 CTG
1 CTG
5592079 CACGAGTAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
75 66 0.99
76 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (75 bp):
CTGTAACACCTTGTTGCAAATCTTCATGTACACTCTGATTGCTAGACCCCACGTGTTATCCACTA
GGTAATGACT
Found at i:5601781 original size:2 final size:2
Alignment explanation
Indices: 5601774--5601809 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5601764 TTTAAATACA
5601774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5601810 TACTTTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5602856 original size:27 final size:28
Alignment explanation
Indices: 5602821--5602877 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
5602811 AAAATATATT
*
5602821 TATTAATATTTCGAATAATATAATATAA
1 TATTAATATTTCGAATAATATAATAAAA
** *
5602849 TATT-ATATTTTTAATATTATAATAAAA
1 TATTAATATTTCGAATAATATAATAAAA
5602876 TA
1 TA
5602878 ATCAATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
TATTAATATTTCGAATAATATAATAAAA
Found at i:5602938 original size:53 final size:50
Alignment explanation
Indices: 5602840--5602942 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 50
5602830 TTCGAATAAT
*
5602840 ATAATATAATATTATATTTTTAATATTATAATAAAATAATCAATTATTATA
1 ATAATATAATATTATATTTTT-ATATTATAATAAAATAATAAATTATTATA
* *
5602891 ATAATATAAGATATTATATTTTT-TATTTTAATAATATATAGTAAATTATTAT
1 ATAATAT-A-ATATTATATTTTTATATTATAATAA-A-ATAATAAATTATTAT
5602943 TAAAATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
51 17 0.38
52 2 0.04
53 26 0.58
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (50 bp):
ATAATATAATATTATATTTTTATATTATAATAAAATAATAAATTATTATA
Found at i:5603060 original size:34 final size:34
Alignment explanation
Indices: 5603022--5603133 Score: 78
Period size: 34 Copynumber: 3.4 Consensus size: 34
5603012 TTATATATTT
5603022 AATATTAATATAATA-ATCTAATAATATTTTAATA
1 AATA-TAATATAATACATCTAATAATATTTTAATA
* * * *
5603056 AATAT-ATGTAAAATATACTAATTAATATTTTTA-A
1 AATATAATATAATACAT-CTAA-TAATATTTTAATA
*
5603090 AATATAATATAA-ACA-CT-AT--TACTTTAATA
1 AATATAATATAATACATCTAATAATATTTTAATA
5603119 AATAATTAATATAAT
1 AAT-A-TAATATAAT
5603134 TTATAATATT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
28 6 0.10
29 4 0.06
30 2 0.03
31 9 0.14
32 8 0.13
33 3 0.05
34 16 0.25
35 15 0.24
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (34 bp):
AATATAATATAATACATCTAATAATATTTTAATA
Found at i:5603070 original size:23 final size:23
Alignment explanation
Indices: 5603023--5603095 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
5603013 TATATATTTA
5603023 ATATTAATATAATA-ATCTAATAAT
1 ATATTAATA-AATATATCTAA-AAT
* *
5603047 ATTTTAATAAATATATGTAAAAT
1 ATATTAATAAATATATCTAAAAT
* * * *
5603070 ATACTAATTAATATTTTTAAAAT
1 ATATTAATAAATATATCTAAAAT
5603093 ATA
1 ATA
5603096 ATATAAACAC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 28 0.68
24 13 0.32
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (23 bp):
ATATTAATAAATATATCTAAAAT
Found at i:5603161 original size:31 final size:31
Alignment explanation
Indices: 5603137--5603216 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 31
5603127 ATATAATTTA
5603137 TAATATTTTTATTTCAATAAAATATAACAATAT
1 TAATATTTTTA-TT-AATAAAATATAACAATAT
5603170 TAATATTTTTATTAATAAAATTATAA-AA-A-
1 TAATATTTTTATTAATAAAA-TATAACAATAT
*
5603199 TAATA-TTTTAATAATAAA
1 TAATATTTTTATTAATAAA
5603217 TAAATTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
28 12 0.27
29 5 0.11
30 1 0.02
31 9 0.20
32 7 0.16
33 11 0.24
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
TAATATTTTTATTAATAAAATATAACAATAT
Found at i:5603699 original size:19 final size:20
Alignment explanation
Indices: 5603656--5603709 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
5603646 TATAATTATT
5603656 TTATTTATAAAAA-ATTAGAA
1 TTATTTATAAAAATATTA-AA
*
5603676 ATATTTATAAAAATATT-AA
1 TTATTTATAAAAATATTAAA
*
5603695 TTATTATTTAAAAAT
1 TTATT-TATAAAAAT
5603710 TATTTGGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.21
20 20 0.69
21 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTATTTATAAAAATATTAAA
Found at i:5610357 original size:14 final size:15
Alignment explanation
Indices: 5610338--5610367 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5610328 ATGATAAATG
5610338 ATTAT-AAATATATT
1 ATTATAAAATATATT
5610352 ATTATAAAATATATT
1 ATTATAAAATATATT
5610367 A
1 A
5610368 AATTCAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:5612469 original size:21 final size:21
Alignment explanation
Indices: 5612445--5612496 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
5612435 TTAACTCACT
5612445 AAAATTTAAAAATAAATTTTA
1 AAAATTTAAAAATAAATTTTA
5612466 AAAATTTAAAAATAAATTTTA
1 AAAATTTAAAAATAAATTTTA
*
5612487 AACATTTAAA
1 AAAATTTAAA
5612497 TTTATAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATTTAAAAATAAATTTTA
Found at i:5613428 original size:32 final size:32
Alignment explanation
Indices: 5613381--5613447 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
5613371 ATAATCGAAT
** * * * *
5613381 AATTTAAAATTTAACTTTCATCTTTTTTTATA
1 AATTTAAAAAATAACTCTCAACATTTTTCATA
5613413 AATTTAAAAAATAACTCTCAACATTTTTCATA
1 AATTTAAAAAATAACTCTCAACATTTTTCATA
5613445 AAT
1 AAT
5613448 AAATAATGTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (32 bp):
AATTTAAAAAATAACTCTCAACATTTTTCATA
Found at i:5613725 original size:32 final size:32
Alignment explanation
Indices: 5613689--5613817 Score: 93
Period size: 32 Copynumber: 4.0 Consensus size: 32
5613679 ACATGTAATA
* * * *
5613689 ATGTGGTATATGTCATGTCATCATGTTAAGTG
1 ATGTGATATATATCATATCATCATATTAAGTG
* *
5613721 ATGTGATATAAAT-ATTATCATCATTTTAAGTG
1 ATGTGATATATATCA-TATCATCATATTAAGTG
* * * *
5613753 ATGTGACACATGTCATATCATTATATT-AGATG
1 ATGTGATATATATCATATCATCATATTAAG-TG
* * *
5613785 ATGT-AGTATGTATCATGTCATCATCTTAAGTG
1 ATGTGA-TATATATCATATCATCATATTAAGTG
5613817 A
1 A
5613818 CAGATCAATA
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
31 4 0.05
32 67 0.91
33 3 0.04
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (32 bp):
ATGTGATATATATCATATCATCATATTAAGTG
Found at i:5614823 original size:2 final size:2
Alignment explanation
Indices: 5614816--5614857 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5614806 AGACCATTAA
5614816 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5614858 TTCAATTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5615673 original size:36 final size:35
Alignment explanation
Indices: 5615592--5615729 Score: 204
Period size: 35 Copynumber: 3.9 Consensus size: 35
5615582 AAATAAACAA
**
5615592 TTGAATCGAAAGTGCTTATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
* *
5615627 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-AC
5615663 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
* * *
5615698 TCGAATCGAAAGTGTCGATGCTTCCTTTCGTT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTT
5615730 ATTCTTCTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
35 60 0.65
36 33 0.35
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
Found at i:5615708 original size:71 final size:71
Alignment explanation
Indices: 5615592--5615735 Score: 243
Period size: 71 Copynumber: 2.0 Consensus size: 71
5615582 AAATAAACAA
** *
5615592 TTGAATCGAAAGTGCTTATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTCGAATCGAAAGTGCCGATGCTTCCTTTCG
*
5615657 TTCTTC
66 TTATTC
*
5615663 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTCGAATCGAAAGTGTCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTCGAATCGAAAGTGCCGATGCTTCCTTTCG
5615728 TTATTC
66 TTATTC
5615734 TT
1 TT
5615736 CTTATTCACC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (71 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTCGAATCGAAAGTGCCGATGCTTCCTTTCG
TTATTC
Found at i:5617540 original size:20 final size:20
Alignment explanation
Indices: 5617517--5617565 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5617507 TTGTGAAATG
5617517 TTTTGGAACATCAAAGAATA
1 TTTTGGAACATCAAAGAATA
** *
5617537 TTTTATAACATCATAGAATA
1 TTTTGGAACATCAAAGAATA
5617557 TTTTGGAAC
1 TTTTGGAAC
5617566 TATGAAGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (20 bp):
TTTTGGAACATCAAAGAATA
Found at i:5618152 original size:13 final size:13
Alignment explanation
Indices: 5618134--5618159 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5618124 CAAGTTTATT
5618134 GCCATGATAATGA
1 GCCATGATAATGA
5618147 GCCATGATAATGA
1 GCCATGATAATGA
5618160 TGTTTGTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GCCATGATAATGA
Found at i:5618311 original size:27 final size:27
Alignment explanation
Indices: 5618271--5618328 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
5618261 AAGAATCATC
*
5618271 GGTGGTGATGGGGTGGTTTACAGGTTT
1 GGTGGTGATAGGGTGGTTTACAGGTTT
**
5618298 GGTGGTGATAGGGTGGTTTATGGGTTT
1 GGTGGTGATAGGGTGGTTTACAGGTTT
5618325 GGTG
1 GGTG
5618329 ATGTGAACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.10, C:0.02, G:0.50, T:0.38
Consensus pattern (27 bp):
GGTGGTGATAGGGTGGTTTACAGGTTT
Found at i:5620993 original size:31 final size:32
Alignment explanation
Indices: 5620953--5621037 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 32
5620943 TATTTTGGTC
*
5620953 ACTTT-AATTT-TTTTTAAATTTAATTACT-TA
1 ACTTTCAATTTATTTTT-AATTTAATCACTCTA
**
5620983 ACTTTCAATTTATTCCTAATTTAATCACTCTA
1 ACTTTCAATTTATTTTTAATTTAATCACTCTA
*
5621015 ACTTTCAAATTTATTTTTTATTT
1 ACTTTC-AATTTATTTTTAATTT
5621038 TTACTTATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 5 0.11
31 16 0.36
32 11 0.24
33 13 0.29
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (32 bp):
ACTTTCAATTTATTTTTAATTTAATCACTCTA
Found at i:5621022 original size:32 final size:32
Alignment explanation
Indices: 5620969--5621029 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
5620959 ATTTTTTTTA
*
5620969 AATTTAATTACTTAACTTTC-AATTTATTCCT
1 AATTTAATCACTTAACTTTCAAATTTATTCCT
5621000 AATTTAATCACTCTAACTTTCAAATTTATT
1 AATTTAATCACT-TAACTTTCAAATTTATT
5621030 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 11 0.41
32 8 0.30
33 8 0.30
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.49
Consensus pattern (32 bp):
AATTTAATCACTTAACTTTCAAATTTATTCCT
Found at i:5627680 original size:24 final size:24
Alignment explanation
Indices: 5627648--5627704 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
5627638 AAGATGGCTG
5627648 ATGAGAATGTCACTATAGTTGCAA
1 ATGAGAATGTCACTATAGTTGCAA
5627672 ATGAGAATGTCACTATAGTTGCAA
1 ATGAGAATGTCACTATAGTTGCAA
5627696 ATGAGAATG
1 ATGAGAATG
5627705 ATGGTAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (24 bp):
ATGAGAATGTCACTATAGTTGCAA
Found at i:5630801 original size:3 final size:3
Alignment explanation
Indices: 5630793--5630889 Score: 106
Period size: 3 Copynumber: 31.7 Consensus size: 3
5630783 GGCCCGTTTG
* * *
5630793 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* * *
5630840 TTA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5630888 TA
1 TA
5630890 TTTAAATGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.03
3 70 0.89
4 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5633014 original size:27 final size:25
Alignment explanation
Indices: 5632981--5633056 Score: 95
Period size: 25 Copynumber: 3.0 Consensus size: 25
5632971 TTTAAATAAA
5632981 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTT-AA-TAAGTTAAT
*
5633008 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATATTTTTAATAAGTTAAT
5633033 -ATAAAAATATTTTT--TAAGTTAAT
1 AAT-AAAATATTTTTAATAAGTTAAT
5633056 A
1 A
5633057 TATATAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.20
24 2 0.04
25 19 0.42
26 2 0.04
27 13 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AATAAAATATTTTTAATAAGTTAAT
Found at i:5633033 original size:25 final size:24
Alignment explanation
Indices: 5632981--5633069 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 24
5632971 TTTAAATAAA
*
5632981 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAA-ATATTT-AA-TAAGTTAAT
5633008 AATAAAATATATTTAATAAGTTAAT
1 AATAAAA-ATATTTAATAAGTTAAT
**
5633033 -ATAAAAATATTTTTTAAGTTAAT
1 AATAAAAATATTTAATAAGTTAAT
5633056 ATATATAAAATATT
1 A-ATA-AAAATATT
5633070 ATGAATTTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
23 15 0.27
24 6 0.11
25 12 0.21
26 10 0.18
27 13 0.23
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (24 bp):
AATAAAAATATTTAATAAGTTAAT
Found at i:5633050 original size:23 final size:24
Alignment explanation
Indices: 5632982--5633058 Score: 93
Period size: 23 Copynumber: 3.1 Consensus size: 24
5632972 TTAAATAAAA
*
5632982 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATATATTT--ATTAAGTTAAT
*
5633008 AATAAAATATATTTAATAAGTTAAT
1 -ATAAAATATATTTATTAAGTTAAT
*
5633033 ATAAAA-ATATTTTTTAAGTTAAT
1 ATAAAATATATTTATTAAGTTAAT
5633056 ATA
1 ATA
5633059 TATAAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.39
24 6 0.13
25 10 0.22
27 12 0.26
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
ATAAAATATATTTATTAAGTTAAT
Found at i:5635713 original size:2 final size:2
Alignment explanation
Indices: 5635708--5635764 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
5635698 AAGAAAAATA
5635708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5635750 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
5635765 AATGTTAGGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5636326 original size:12 final size:12
Alignment explanation
Indices: 5636305--5636347 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
5636295 AGATAAAAAT
*
5636305 AATAAGAAATAA
1 AATAAAAAATAA
5636317 AATAAAAAATAA
1 AATAAAAAATAA
5636329 AATAAAATAATAA
1 AATAAAA-AATAA
5636342 AATAAA
1 AATAAA
5636348 TAAAAAGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:5636333 original size:17 final size:17
Alignment explanation
Indices: 5636311--5636352 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
5636301 AAATAATAAG
5636311 AAATAAAATAA-AAAAT
1 AAATAAAATAATAAAAT
5636327 AAAATAAAATAATAAAAT
1 -AAATAAAATAATAAAAT
5636345 AAATAAAA
1 AAATAAAA
5636353 AGGACTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATAAAATAATAAAAT
Found at i:5639384 original size:12 final size:12
Alignment explanation
Indices: 5639352--5639386 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5639342 ATTTTACATC
*
5639352 AAGTTTTTCATT
1 AAGTTTTTCTTT
5639364 AAG-TTTTCTTT
1 AAGTTTTTCTTT
5639375 AAGTTTTTCTTT
1 AAGTTTTTCTTT
5639387 TTGTGTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (12 bp):
AAGTTTTTCTTT
Found at i:5641911 original size:141 final size:141
Alignment explanation
Indices: 5641683--5641954 Score: 375
Period size: 141 Copynumber: 1.9 Consensus size: 141
5641673 GTTGCTCCCC
* * * *
5641683 AGACTCAGAAAAACCAACCCAAAGGACTCAAAAGTGAATAACCAAAGGAATTTATCATAAAACCT
1 AGACTCAGAAAAACCAACCCAAAGAACTCAAAAGCGAACAACCAAAGAAATTTATCATAAAACCT
* * * *
5641748 CTTTTTCCTACTAGATTTGCTAAGTCCAAGAAAGAAGCAGAAGAGAAAGAAATTCTTGAGACATT
66 CATTTTCCCACTAGATTCGCTAAGTCCAAGAAAGAAGCAGAAGAGAAACAAATTCTTGAGACATT
5641813 TTGCGAGATCA
131 TTGCGAGATCA
* * * *
5641824 AGACTCA-AAACAACCAACCCAAAGAACTTAAAAGCGAACGACCGAAGAAATTTGTCATAAAACC
1 AGACTCAGAAA-AACCAACCCAAAGAACTCAAAAGCGAACAACCAAAGAAATTTATCATAAAACC
** * * *
5641888 TCATTTTCCCGTTAGATTCGCTAAGTCCAAGAAAGAAGTAGAATAGAAACAAATTCTTGAGATAT
65 TCATTTTCCCACTAGATTCGCTAAGTCCAAGAAAGAAGCAGAAGAGAAACAAATTCTTGAGACAT
5641953 TT
130 TT
5641955 CGCAAGATTG
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
140 3 0.03
141 110 0.97
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.22
Consensus pattern (141 bp):
AGACTCAGAAAAACCAACCCAAAGAACTCAAAAGCGAACAACCAAAGAAATTTATCATAAAACCT
CATTTTCCCACTAGATTCGCTAAGTCCAAGAAAGAAGCAGAAGAGAAACAAATTCTTGAGACATT
TTGCGAGATCA
Found at i:5644464 original size:12 final size:12
Alignment explanation
Indices: 5644434--5644468 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5644424 GTTTTACATC
*
5644434 AAGTTTTTCATT
1 AAGTTTTTCTTT
5644446 AAG-TTTTCTTT
1 AAGTTTTTCTTT
5644457 AAGTTTTTCTTT
1 AAGTTTTTCTTT
5644469 TTTGTGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (12 bp):
AAGTTTTTCTTT
Found at i:5650219 original size:23 final size:22
Alignment explanation
Indices: 5650167--5650221 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
5650157 CCTTCATGCA
5650167 TGCT-TTGGTTTAAAGCTCGAG
1 TGCTGTTGGTTTAAAGCTCGAG
*
5650188 T--TGTTGGTTTAAAGCTTGAG
1 TGCTGTTGGTTTAAAGCTCGAG
5650208 TTGCTGTTGGTTTA
1 -TGCTGTTGGTTTA
5650222 TTAAATAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 16 0.55
21 2 0.07
23 10 0.34
ACGTcount: A:0.16, C:0.09, G:0.29, T:0.45
Consensus pattern (22 bp):
TGCTGTTGGTTTAAAGCTCGAG
Found at i:5650841 original size:40 final size:39
Alignment explanation
Indices: 5650797--5650885 Score: 108
Period size: 42 Copynumber: 2.2 Consensus size: 39
5650787 AATAAGGTAT
*
5650797 ATAATTAGCGGCGTTTATG-AGTAAAAACGACACTATAAAC
1 ATAATTAGCGGCATTTATGAAG--AAAACGACACTATAAAC
*
5650837 ATAATTATTAGCGGCATTTGTGAAGAAAACGACACTATAAAC
1 AT-A--ATTAGCGGCATTTATGAAGAAAACGACACTATAAAC
5650879 ATAATTA
1 ATAATTA
5650886 TTCACGATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
39 4 0.09
40 2 0.05
41 2 0.05
42 19 0.44
43 14 0.33
44 2 0.05
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (39 bp):
ATAATTAGCGGCATTTATGAAGAAAACGACACTATAAAC
Found at i:5651945 original size:31 final size:31
Alignment explanation
Indices: 5651910--5651978 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
5651900 AACATTTAGT
*
5651910 CCGTTTACAATATGGTCCCCGACGTAATCGA
1 CCGTTTACAATATGGTCCCCGACATAATCGA
* *
5651941 CCGTTTGCAATATGGTCCCCGACATAATCGG
1 CCGTTTACAATATGGTCCCCGACATAATCGA
5651972 CCGTTTA
1 CCGTTTA
5651979 ACATCGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (31 bp):
CCGTTTACAATATGGTCCCCGACATAATCGA
Found at i:5670281 original size:37 final size:37
Alignment explanation
Indices: 5670231--5670332 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
5670221 TTTCGTCCTA
* *
5670231 CTAGGATTCAAACTTCTAAAAATATGATAAAATTTTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTTG
* *
5670268 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTA
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTTG
** * *
5670305 CTATTATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
5670333 TTACAAGCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTTG
Found at i:5671038 original size:10 final size:10
Alignment explanation
Indices: 5671019--5671053 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
5671009 TATACATACA
5671019 TTTT-TATAT
1 TTTTATATAT
5671028 TTTTATATAT
1 TTTTATATAT
5671038 TTTTATATAT
1 TTTTATATAT
5671048 TTTTAT
1 TTTTAT
5671054 TTTATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.16
10 21 0.84
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATATAT
Found at i:5671041 original size:18 final size:18
Alignment explanation
Indices: 5671018--5671079 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
5671008 TTATACATAC
5671018 ATTTTTATAT-TTTTATAT
1 ATTTTTATATATTTT-TAT
5671036 ATTTTTATATATTTTTAT
1 ATTTTTATATATTTTTAT
*
5671054 TTTATTTATACTATTTATT-T
1 ATT-TTTATA-TATTT-TTAT
5671074 ATTTTT
1 ATTTTT
5671080 CATTATGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.39
19 13 0.34
20 8 0.21
21 2 0.05
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTATATATTTTTAT
Found at i:5672411 original size:19 final size:20
Alignment explanation
Indices: 5672375--5672412 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5672365 ACCTTACTAA
*
5672375 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
5672395 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
5672413 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:5675822 original size:16 final size:15
Alignment explanation
Indices: 5675803--5675852 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
5675793 GGCAAAAATA
5675803 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAAGAA-C
5675819 AAAAAAGAAGAA-AAC
1 AAAAAAGAA-AAGAAC
5675834 AAAAAAG-AAAGAAC
1 AAAAAAGAAAAGAAC
5675848 AAAAA
1 AAAAA
5675853 TCAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.06
14 9 0.28
15 8 0.25
16 11 0.34
17 2 0.06
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGAAC
Found at i:5676496 original size:22 final size:22
Alignment explanation
Indices: 5676471--5676526 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
5676461 AGCTACCCCA
* *
5676471 TCAAACCTTTGAGCATTAAATG
1 TCAAACCTTTGAACATCAAATG
* *
5676493 TCAAATCTTTTAACATCAAATG
1 TCAAACCTTTGAACATCAAATG
*
5676515 TCAAACATTTGA
1 TCAAACCTTTGA
5676527 CCAAACACAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
TCAAACCTTTGAACATCAAATG
Found at i:5678748 original size:106 final size:106
Alignment explanation
Indices: 5677472--5678747 Score: 2032
Period size: 106 Copynumber: 12.0 Consensus size: 106
5677462 ATATCGTGCC
* * * *
5677472 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5677537 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
5677578 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
5677643 AATTTTAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
5677684 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAACTTCCG
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5677749 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGTATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
5677790 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5677855 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
5677896 ACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGGATCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
5677961 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
5678002 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
5678067 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
5678108 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
5678173 AATTTTGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
5678214 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5678279 AATTTCGGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
5678320 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5678385 AATTTCAGAGCCAATTTCAACTTCATAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
5678426 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCTCTAGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
5678491 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
5678532 ACTCGAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
5678597 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
5678638 ACTCGAGATAACACAAGTTCAACTTCACAACGGAGGGACGGTTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
5678703 GATTCCAGAGCCAATTTCAACTTCAC-GACGGAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
5678744 ACTC
1 ACTC
5678748 GGAACAATGC
Statistics
Matches: 1094, Mismatches: 75, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
106 1094 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:5680050 original size:23 final size:23
Alignment explanation
Indices: 5680022--5680068 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
5680012 TATATATATA
5680022 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTT-TTTCATT
5680045 TATTTATTATAATTTTTTTCATT
1 TATTTATTATAATTTTTTTCATT
5680068 T
1 T
5680069 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATTATAATTTTTTTCATT
Found at i:5680093 original size:10 final size:10
Alignment explanation
Indices: 5680078--5680129 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
5680068 TTTCTTTGCG
5680078 TTATATTATA
1 TTATATTATA
*
5680088 TTATATTTCTA
1 TTATA-TTATA
5680099 TTATA-TATA
1 TTATATTATA
5680108 TATATATATATA
1 T-TATAT-TATA
5680120 TATATATTAT
1 T-TATATTAT
5680130 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.11
10 9 0.25
11 12 0.33
12 11 0.31
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATATTATA
Found at i:5680107 original size:2 final size:2
Alignment explanation
Indices: 5680079--5680126 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
5680069 TTCTTTGCGT
* *
5680079 TA TA T- TA TA T- TA TA TT TC TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5680118 TA TA TA TA T
1 TA TA TA TA T
5680127 TATTATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:5680358 original size:17 final size:18
Alignment explanation
Indices: 5680336--5680373 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5680326 ATTTTTATAT
*
5680336 TTTTATATATA-TTTTTA
1 TTTTATATATACTATTTA
*
5680353 TTTTATTTATACTATTTA
1 TTTTATATATACTATTTA
5680371 TTT
1 TTT
5680374 ATTTTCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATATATACTATTTA
Found at i:5680368 original size:20 final size:21
Alignment explanation
Indices: 5680322--5680378 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
5680312 TATATTATAC
5680322 ATAC-ATTTTTATATTTTTAT
1 ATACTATTTTTATATTTTTAT
5680342 ATA-TATTTTTAT-TTTATT-T
1 ATACTATTTTTATATTT-TTAT
5680361 ATACTATTTATT-TATTTT
1 ATACTATTT-TTATATTTT
5680379 CATTAGGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
19 7 0.22
20 20 0.62
21 5 0.16
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (21 bp):
ATACTATTTTTATATTTTTAT
Found at i:5680376 original size:22 final size:22
Alignment explanation
Indices: 5680275--5680378 Score: 67
Period size: 22 Copynumber: 4.6 Consensus size: 22
5680265 TTTCTTTTTC
5680275 ATTTATTTATTATTATTGT-TACT
1 ATTTATTTATT-TTATT-TATACT
5680298 ATTTAGTATT-TTATTATATTATACAT
1 ATTTA-T-TTATT-TTAT-TTATAC-T
* *
5680324 ACATT-TTTATATT-TTTATA-T
1 A-TTTATTTATTTTATTTATACT
5680344 ATATT-TTTATTTTATTTATACT
1 AT-TTATTTATTTTATTTATACT
5680366 ATTTATTTATTTT
1 ATTTATTTATTTT
5680379 CATTAGGTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 23
0.71 0.04 0.25
Matches are distributed among these distances:
20 11 0.17
21 8 0.12
22 16 0.24
23 6 0.09
24 13 0.20
25 8 0.12
26 2 0.03
27 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTATTTATTTTATTTATACT
Found at i:5683527 original size:25 final size:25
Alignment explanation
Indices: 5683498--5683547 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5683488 AATGTATAAT
5683498 TTAAAAGTTTTACATTAAACTACAA
1 TTAAAAGTTTTACATTAAACTACAA
*
5683523 TTAAAAGTTTTGCATTAAACTACAA
1 TTAAAAGTTTTACATTAAACTACAA
5683548 ATGAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (25 bp):
TTAAAAGTTTTACATTAAACTACAA
Found at i:5684891 original size:37 final size:36
Alignment explanation
Indices: 5684819--5684891 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
5684809 TTATATTTTA
*
5684819 AATTTTGTAAAAAAATTATATAAATATTATGAATTT
1 AATTTTGTAAAAAAATTATATAAATATTATCAATTT
* *
5684855 AATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 AATTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
5684892 GTAATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 23 0.72
37 9 0.28
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (36 bp):
AATTTTGTAAAAAAATTATATAAATATTATCAATTT
Found at i:5685073 original size:20 final size:20
Alignment explanation
Indices: 5685037--5685074 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5685027 ATCCTATTCC
**
5685037 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
5685057 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
5685075 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:5692364 original size:23 final size:23
Alignment explanation
Indices: 5692338--5692381 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
5692328 AATTCTTAAT
5692338 AGGGTTTCAAGGTTTTATACTTG
1 AGGGTTTCAAGGTTTTATACTTG
5692361 AGGGTTTCAAGGTTTTATACT
1 AGGGTTTCAAGGTTTTATACT
5692382 GATAAGAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (23 bp):
AGGGTTTCAAGGTTTTATACTTG
Found at i:5693296 original size:35 final size:35
Alignment explanation
Indices: 5693250--5693320 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
5693240 GTACTATGAA
5693250 ATTAATGAAATATGGATAAAGTCGTAACTCTAAGT
1 ATTAATGAAATATGGATAAAGTCGTAACTCTAAGT
5693285 ATTAATGAAATATGGATAAAGTCGTAACTCTAAGT
1 ATTAATGAAATATGGATAAAGTCGTAACTCTAAGT
5693320 A
1 A
5693321 CCGATTCTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (35 bp):
ATTAATGAAATATGGATAAAGTCGTAACTCTAAGT
Found at i:5694176 original size:3 final size:3
Alignment explanation
Indices: 5694168--5694199 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5694158 ATTTTTTGTT
5694168 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5694200 GAGTAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5703619 original size:21 final size:21
Alignment explanation
Indices: 5703587--5703657 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 21
5703577 GGCAAGCAAC
5703587 TTTGGAAAAATGATTTTCAAAG
1 TTTGG-AAAATGATTTTCAAAG
*
5703609 TTTGGCAAATG--TTTC----
1 TTTGGAAAATGATTTTCAAAG
*
5703624 TTT-GAAAATGGTTTTCAAAG
1 TTTGGAAAATGATTTTCAAAG
*
5703644 TTTGGTAAATGATT
1 TTTGGAAAATGATT
5703658 CTTTAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 15
0.67 0.07 0.26
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
19 4 0.11
20 3 0.08
21 13 0.34
22 5 0.13
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (21 bp):
TTTGGAAAATGATTTTCAAAG
Found at i:5703703 original size:37 final size:36
Alignment explanation
Indices: 5703592--5703703 Score: 138
Period size: 35 Copynumber: 3.1 Consensus size: 36
5703582 GCAACTTTGG
* *
5703592 AAAAATGATTTTCAAAGTTTGGCAAATGTTTCTTTG-
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTC-TTGA
* *
5703628 -AAAATGGTTTTCAAAGTTTGGTAAATGATTCTTTA
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTGA
* *
5703663 AAAAATGGTTTTTCAAAGTTTGGTAGATGTTTGTTGA
1 AAAAATGG-TTTTCAAAGTTTGGTAAATGTTTCTTGA
5703700 AAAA
1 AAAA
5703704 TTGTAATGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
34 2 0.03
35 28 0.43
36 7 0.11
37 28 0.43
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTGA
Found at i:5708282 original size:37 final size:36
Alignment explanation
Indices: 5708175--5708292 Score: 150
Period size: 35 Copynumber: 3.3 Consensus size: 36
5708165 TGGCAACCAA
* *
5708175 CTTTGAAAAAATGATTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAAA-GGTTTTCAAAGTTTGGTAAATGTTT
*
5708212 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAAGGTTTTCAAAGTTTGGTAAATGTTT
* *
5708247 CTTTGAAAAAAGGTTTTTTAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAAGG-TTTTCAAAGTTTGGTAAATGTTT
*
5708284 -GTTGAAAAA
1 CTTTGAAAAA
5708293 TTGTAATGGG
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 28 0.39
36 18 0.25
37 26 0.36
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAAAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:5711093 original size:25 final size:25
Alignment explanation
Indices: 5711036--5711093 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
5711026 ATGGTAATTT
* *
5711036 AAAAATATATATATATAATTTTAAAT
1 AAAAAAAT-TATATATAATTTTAAAA
*
5711062 ATAAAAATTATATAT-ATTTTAAAA
1 AAAAAAATTATATATAATTTTAAAA
5711086 AAAGAAAA
1 AAA-AAAA
5711094 CACATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.37
25 11 0.41
26 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAAAAATTATATATAATTTTAAAA
Found at i:5712921 original size:2 final size:2
Alignment explanation
Indices: 5712914--5712975 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
5712904 CAAGCCAGAC
5712914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5712956 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
5712976 GGGAAAACTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5719894 original size:34 final size:32
Alignment explanation
Indices: 5719841--5719910 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
5719831 ACCTTACAAC
* *
5719841 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
5719873 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
5719907 TCCC
1 TCCC
5719911 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:5720150 original size:20 final size:22
Alignment explanation
Indices: 5720125--5720164 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5720115 AGTCGTATAT
5720125 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
5720145 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
5720165 TATACTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:5720216 original size:21 final size:21
Alignment explanation
Indices: 5720192--5720234 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5720182 CCCATAATAG
*
5720192 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
5720213 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
5720234 A
1 A
5720235 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:5720310 original size:22 final size:21
Alignment explanation
Indices: 5720270--5720309 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5720260 CTGTTGAACA
5720270 GGGGGGGAATCGGTACCCCAT
1 GGGGGGGAATCGGTACCCCAT
5720291 GGGGGGGAATCGGTACCCC
1 GGGGGGGAATCGGTACCCC
5720310 CTGGACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.45, T:0.12
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCAT
Found at i:5720372 original size:21 final size:21
Alignment explanation
Indices: 5720347--5720423 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
5720337 AAAACCTGCA
5720347 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
5720368 GGGGGTATCTGTA---CCT--
1 GGGGGTATCTGTACCCCCTGG
5720384 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
5720404 GGGGGAAATCTATACCCCCT
1 GGGGG-TATCTGTACCCCCT
5720424 TGGCAATCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
15 12 0.26
18 6 0.13
21 17 0.36
22 12 0.26
ACGTcount: A:0.14, C:0.27, G:0.34, T:0.25
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:5720389 original size:15 final size:15
Alignment explanation
Indices: 5720369--5720397 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5720359 ACCCCCTGGG
5720369 GGGGTATCTGTACCT
1 GGGGTATCTGTACCT
5720384 GGGGTATCTGTACC
1 GGGGTATCTGTACC
5720398 CCCTGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.34, T:0.31
Consensus pattern (15 bp):
GGGGTATCTGTACCT
Found at i:5722442 original size:32 final size:33
Alignment explanation
Indices: 5722406--5722475 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
5722396 ACCTTACAAC
* * *
5722406 TCCCTAGTTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTACACGGGCTAAACTAGAACATT
*
5722438 TCCCTAGCTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAGCTTTACACGGGCTAAACTAGAACATT
5722471 TCCCT
1 TCCCT
5722476 TTACAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 11 0.33
33 22 0.67
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (33 bp):
TCCCTAGCTTTACACGGGCTAAACTAGAACATT
Found at i:5722712 original size:20 final size:22
Alignment explanation
Indices: 5722687--5722726 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5722677 AGTCGTATAT
5722687 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
5722707 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
5722727 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:5722793 original size:21 final size:22
Alignment explanation
Indices: 5722754--5722797 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5722744 CCCATAATAG
5722754 AGGGAATCGATACCCCCTTCAT
1 AGGGAATCGATACCCCCTTCAT
5722776 AGGGAATCGATA-CCCCTTCAT
1 AGGGAATCGATACCCCCTTCAT
5722797 A
1 A
5722798 ATATTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (22 bp):
AGGGAATCGATACCCCCTTCAT
Found at i:5722910 original size:15 final size:15
Alignment explanation
Indices: 5722890--5722919 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5722880 AAACCTACAG
5722890 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
5722905 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
5722920 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:5722930 original size:22 final size:22
Alignment explanation
Indices: 5722905--5722947 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5722895 ATCTGTACCC
* *
5722905 GGGGTATCTGTACCCCCTGGGG
1 GGGGAATCTATACCCCCTGGGG
5722927 GGGGAATCTATACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
5722948 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (22 bp):
GGGGAATCTATACCCCCTGGGG
Found at i:5723105 original size:34 final size:29
Alignment explanation
Indices: 5723037--5723096 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
5723027 AAACTTTGAA
* *
5723037 TAAATTCAATTACGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATCTTG
5723066 TAAATTCAATTCAAGTCCAAAAACCATCTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATCTTG
5723097 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATCTTG
Done.