Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 25 of 444
Found at i:6494795 original size:54 final size:54
Alignment explanation
Indices: 6494736--6494844 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
6494726 AAGGTCTGAA
* *
6494736 TTTGATAAAAAAGGCATCGAGAATTGACTGCTTGCTTGTTGGTGATGGGGCAAC
1 TTTGATAAAAAAGGCATCGAGAATTGACTGCTTGCTTGCTGATGATGGGGCAAC
** *
6494790 TTTGATAAACCAGGTATCGAGAATTGACTGCTTGCTTGCTGATGATGGGGCAAC
1 TTTGATAAAAAAGGCATCGAGAATTGACTGCTTGCTTGCTGATGATGGGGCAAC
6494844 T
1 T
6494845 GACAGGATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (54 bp):
TTTGATAAAAAAGGCATCGAGAATTGACTGCTTGCTTGCTGATGATGGGGCAAC
Found at i:6499464 original size:2 final size:2
Alignment explanation
Indices: 6499457--6499502 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
6499447 TCATTGTGAA
*
6499457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6499498 A- AT AT
1 AT AT AT
6499503 TGATGAGCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6501732 original size:21 final size:21
Alignment explanation
Indices: 6501684--6501733 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
6501674 AAAAGATAAC
*
6501684 TTAATGATTAATTTAATTTAT
1 TTAATTATTAATTTAATTTAT
*
6501705 TTAAATTATTAA-TTAGTTTAT
1 TT-AATTATTAATTTAATTTAT
6501726 TATAATTA
1 T-TAATTA
6501734 AATAATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TTAATTATTAATTTAATTTAT
Found at i:6503420 original size:22 final size:23
Alignment explanation
Indices: 6503373--6503420 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6503363 CACTTCCACC
**
6503373 ATTTTCTTATTTGATAAACATTG
1 ATTTTCTTATTTGATAAACACAG
*
6503396 ATTTTCTTATTTG-TAAAGACAG
1 ATTTTCTTATTTGATAAACACAG
6503418 ATT
1 ATT
6503421 GACCTGAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (23 bp):
ATTTTCTTATTTGATAAACACAG
Found at i:6506056 original size:20 final size:20
Alignment explanation
Indices: 6506031--6506076 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
6506021 TTGATTCTAA
*
6506031 AAAAATTCACAAAAATTAT-T
1 AAAAATTC-CAAAAAATATAT
6506051 AAAAA-TCCAAAAAATATAT
1 AAAAATTCCAAAAAATATAT
6506070 AAAAATT
1 AAAAATT
6506077 AAACAAACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATTCCAAAAAATATAT
Found at i:6506063 original size:19 final size:20
Alignment explanation
Indices: 6506031--6506075 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
6506021 TTGATTCTAA
*
6506031 AAAAATTCACAAAAAT-TATT
1 AAAAATCCACAAAAATATA-T
6506051 AAAAATCCA-AAAAATATAT
1 AAAAATCCACAAAAATATAT
6506070 AAAAAT
1 AAAAAT
6506076 TAAACAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATCCACAAAAATATAT
Found at i:6506563 original size:13 final size:13
Alignment explanation
Indices: 6506545--6506572 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6506535 TGTTAACATT
6506545 GTTAAATTTTTTG
1 GTTAAATTTTTTG
6506558 GTTAAATTTTTTG
1 GTTAAATTTTTTG
6506571 GT
1 GT
6506573 GTTACATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (13 bp):
GTTAAATTTTTTG
Found at i:6506576 original size:15 final size:14
Alignment explanation
Indices: 6506544--6506582 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
6506534 TTGTTAACAT
6506544 TGTTAAATTTTTTG
1 TGTTAAATTTTTTG
6506558 -GTTAAATTTTTTGG
1 TGTTAAATTTTTT-G
*
6506572 TGTTACATTTT
1 TGTTAAATTTT
6506583 GAAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 1 0.05
15 9 0.41
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.62
Consensus pattern (14 bp):
TGTTAAATTTTTTG
Found at i:6510263 original size:41 final size:41
Alignment explanation
Indices: 6510185--6510263 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
6510175 CGTCAAATTG
* *
6510185 AAAGACAAAAGAAAATAATTCAATTCCAAATTGAAATAAAA
1 AAAGACAAAAGAAAATAATTCAACTCCAAATTAAAATAAAA
* * * *
6510226 AAAGAGAAAATAAAATAATTCAACTCTAACTTAAAATA
1 AAAGACAAAAGAAAATAATTCAACTCCAAATTAAAATA
6510264 GGAATACAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.22
Consensus pattern (41 bp):
AAAGACAAAAGAAAATAATTCAACTCCAAATTAAAATAAAA
Found at i:6512182 original size:3 final size:3
Alignment explanation
Indices: 6512174--6512297 Score: 57
Period size: 3 Copynumber: 42.7 Consensus size: 3
6512164 AAGCAATAGG
* * *
6512174 TAA TAA TAA -ATA TAA TAA TAA AAA T-A TAA TAT TAA -AGA TAA TAC
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * * *
6512218 TAA GT-A TAA T-A TAA TAA TAA TAA T-G TAA TAA TGA TAG TAA TGA
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
6512261 TGA CAA TAA TAA T-A TAA AAA GAA TAGA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA
6512298 GAAAAAATAG
Statistics
Matches: 90, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
2 12 0.13
3 72 0.80
4 6 0.07
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6512198 original size:14 final size:14
Alignment explanation
Indices: 6512174--6512249 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 14
6512164 AAGCAATAGG
6512174 TAATAATAAATATAA
1 TAATAA-AAATATAA
6512189 TAATAAAAATATAA
1 TAATAAAAATATAA
* * *
6512203 TATTAAAGATAATAC
1 TAATAAAAAT-ATAA
*
6512218 TAAGT-ATAATATAA
1 TAA-TAAAAATATAA
* *
6512232 TAATAATAATGTAA
1 TAATAAAAATATAA
6512246 TAAT
1 TAAT
6512250 GATAGTAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
13 1 0.02
14 34 0.68
15 14 0.28
16 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (14 bp):
TAATAAAAATATAA
Found at i:6512203 original size:26 final size:28
Alignment explanation
Indices: 6512174--6512237 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 28
6512164 AAGCAATAGG
*
6512174 TAATAATAAATATAATAATAA-A-AATA
1 TAATAATAAAGATAATAATAAGATAATA
* *
6512200 TAATATTAAAGATAATACTAAGTATAATA
1 TAATAATAAAGATAATAATAAG-ATAATA
6512229 TAATAATAA
1 TAATAATAA
6512238 TAATGTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 18 0.58
28 1 0.03
29 12 0.39
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (28 bp):
TAATAATAAAGATAATAATAAGATAATA
Found at i:6512290 original size:21 final size:21
Alignment explanation
Indices: 6512268--6512309 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
6512258 TGATGACAAT
*
6512268 AATAATATAAAAAGAATAGATAA
1 AATAATA-GAAAA-AATAGATAA
6512291 AATAATAGAAAAAATAGAT
1 AATAATAGAAAAAATAGAT
6512310 TTAAAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (21 bp):
AATAATAGAAAAAATAGATAA
Found at i:6513592 original size:22 final size:22
Alignment explanation
Indices: 6513535--6513597 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
6513525 TACGAGGACT
* *
6513535 GTGGCGGTATGGGACTGTTGTA
1 GTGGGGGTATGGGGCTGTTGTA
*
6513557 GTGGGGGTATGGGGCTGTTGTG
1 GTGGGGGTATGGGGCTGTTGTA
*
6513579 GTGGGGGTATGGGGTTGTT
1 GTGGGGGTATGGGGCTGTT
6513598 AGGGTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.08, C:0.05, G:0.54, T:0.33
Consensus pattern (22 bp):
GTGGGGGTATGGGGCTGTTGTA
Found at i:6514496 original size:68 final size:69
Alignment explanation
Indices: 6514375--6514525 Score: 211
Period size: 68 Copynumber: 2.2 Consensus size: 69
6514365 TTTTTTTGAC
* * *
6514375 AACAGAAATTGAAATTACTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAA
1 AACA-AAATTGAAAATACTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATACGAGTTG-AA
6514440 TT-AAA
64 TTGAAA
*
6514445 ACACAAAATTGAAAATACTCAGCGTG-CC-GAGGCTCAACTCACCTCTAGCAATACGAGTTGATT
1 A-ACAAAATTGAAAATACTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATACGAGTTGAAT
6514508 TGAAA
65 TGAAA
6514513 AACAAAATT-AAAA
1 AACAAAATTGAAAA
6514526 GGCTTAACTC
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
66 4 0.05
67 11 0.15
68 34 0.45
69 2 0.03
70 21 0.28
71 3 0.04
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (69 bp):
AACAAAATTGAAAATACTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATACGAGTTGAATT
GAAA
Found at i:6514535 original size:51 final size:50
Alignment explanation
Indices: 6514474--6514575 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 50
6514464 CAGCGTGCCG
**
6514474 AGGCTCAACTCACCTCTAGCAATACGAGTTGATTTGAAAAACA-AAATTAAA
1 AGGCTCAACTCACCTCTAGCAATACGAGTCAATTT--AAAACATAAATTAAA
* * *
6514525 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAATTAAA
1 AGGCTCAACTCACCTCTAGCAATACGAGTCAATTTAAAACATAAATTAAA
6514575 A
1 A
6514576 TACCCGGCGT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 6 0.13
50 9 0.20
51 30 0.67
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (50 bp):
AGGCTCAACTCACCTCTAGCAATACGAGTCAATTTAAAACATAAATTAAA
Found at i:6514679 original size:120 final size:118
Alignment explanation
Indices: 6514406--6514751 Score: 511
Period size: 120 Copynumber: 2.9 Consensus size: 118
6514396 GCGTGTCCTG
* * * * *
6514406 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAATTGAAAATACTCAGCGTG
1 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACA-TAAATT-AAAATAC-CCGCGTG
* *
6514471 --CCGAGGCTCAACTCACCTCTAGCAATACGAGTTGA-TTTGAAAAACAAAATTAAA
62 CCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAA
6514525 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAATTAAAATACCCGGCGTGCCC
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAATTAAAATACCC-GCGTGCCC
6514590 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
65 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAC-AAAATTAAA
*
6514645 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAGAATACCCGCGTGCCC
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAATTAA-AATACCCGCGTGCCC
*
6514710 CGAGGCTCAACTCACC-CTCGCAATATGAGCTGATTTTTGAAA
65 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAA
6514752 CAAAAGGAAT
Statistics
Matches: 211, Mismatches: 9, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
115 1 0.00
116 12 0.06
117 5 0.02
118 44 0.21
119 53 0.25
120 89 0.42
121 7 0.03
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (118 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAATTAAAATACCCGCGTGCCCC
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAA
Found at i:6514811 original size:73 final size:71
Alignment explanation
Indices: 6514645--6514917 Score: 208
Period size: 72 Copynumber: 3.9 Consensus size: 71
6514635 AAAAATTAAA
* * * * * * *
6514645 AGGCTTAACTCACCTCTCGCAATATGAGTCA-ATTTAAAAC-ATA-AACTAAGAATACC-C-GCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTGATTTTTGAAACAAAAGAATTAA-AATACCTCAGTG
* *
6514705 TGCCCCG
65 TGACCTG
6514712 AGGCTCAACTCACC-CTCGCAATATGAGCTGATTTTTGAAACAAAAGGAATTAAAATACCTCAGT
1 AGGCTCAACTCACCTCTCGCAATATGAG-TGATTTTTGAAACAAAA-GAATTAAAATACCTCAGT
6514776 GTGACCTG
64 GTGACCTG
** * * * * *
6514784 AGGCTTGACTCACCTCTCGCAATATGAGTCAATTTTTAAAAC-ATA-AACTAAAAAACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGT-GATTTTTGAAACAAAAGAATTAAAATACCTCA--G
6514847 TGTGACCTG
63 TGTGACCTG
* * * *
6514856 AGGCTCAACTCA--TTTCTCATATATGAGTTGATTTTTGAAA-ACATGAATTAAAGATACCTCAG
1 AGGCTCAACTCACCTCTCGCA-ATATGAG-TGATTTTTGAAACAAAAGAATTAAA-ATACCTCAG
6514918 AGTACCCAAA
Statistics
Matches: 163, Mismatches: 27, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
66 13 0.08
67 15 0.09
68 7 0.04
69 2 0.01
70 24 0.15
71 23 0.14
72 49 0.30
73 30 0.18
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTGATTTTTGAAACAAAAGAATTAAAATACCTCAGTGT
GACCTG
Found at i:6527530 original size:3 final size:3
Alignment explanation
Indices: 6527522--6527645 Score: 57
Period size: 3 Copynumber: 42.7 Consensus size: 3
6527512 AAGCAATAGG
* * *
6527522 TAA TAA TAA -ATA TAA TAA TAA AAA T-A TAA TAT TAA -AGA TAA TAC
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * * *
6527566 TAA GT-A TAA T-A TAA TAA TAA TAA T-G TAA TAA TGA TAG TAA TGA
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
6527609 TGA CAA TAA TAA T-A TAA AAA GAA TAGA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA
6527646 GTAAAAATAG
Statistics
Matches: 90, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
2 12 0.13
3 72 0.80
4 6 0.07
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6527546 original size:14 final size:14
Alignment explanation
Indices: 6527522--6527597 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 14
6527512 AAGCAATAGG
6527522 TAATAATAAATATAA
1 TAATAA-AAATATAA
6527537 TAATAAAAATATAA
1 TAATAAAAATATAA
* * *
6527551 TATTAAAGATAATAC
1 TAATAAAAAT-ATAA
*
6527566 TAAGT-ATAATATAA
1 TAA-TAAAAATATAA
* *
6527580 TAATAATAATGTAA
1 TAATAAAAATATAA
6527594 TAAT
1 TAAT
6527598 GATAGTAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
13 1 0.02
14 34 0.68
15 14 0.28
16 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (14 bp):
TAATAAAAATATAA
Found at i:6527551 original size:26 final size:28
Alignment explanation
Indices: 6527522--6527585 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 28
6527512 AAGCAATAGG
*
6527522 TAATAATAAATATAATAATAA-A-AATA
1 TAATAATAAAGATAATAATAAGATAATA
* *
6527548 TAATATTAAAGATAATACTAAGTATAATA
1 TAATAATAAAGATAATAATAAG-ATAATA
6527577 TAATAATAA
1 TAATAATAA
6527586 TAATGTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 18 0.58
28 1 0.03
29 12 0.39
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (28 bp):
TAATAATAAAGATAATAATAAGATAATA
Found at i:6528933 original size:22 final size:22
Alignment explanation
Indices: 6528903--6528965 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
6528893 TACGAGGACT
* *
6528903 GTGGCGGTATGGGACTGTTGTA
1 GTGGGGGTATGGGGCTGTTGTA
*
6528925 GTGGGGGTATGGGGCTGTTGTG
1 GTGGGGGTATGGGGCTGTTGTA
6528947 GTGGGGGTATGGGGCTGTT
1 GTGGGGGTATGGGGCTGTT
6528966 AGGGTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.08, C:0.06, G:0.54, T:0.32
Consensus pattern (22 bp):
GTGGGGGTATGGGGCTGTTGTA
Found at i:6529354 original size:2 final size:2
Alignment explanation
Indices: 6529347--6529386 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
6529337 TCATTGTGAA
*
6529347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AG AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6529387 TGATGAGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6531654 original size:21 final size:21
Alignment explanation
Indices: 6531606--6531655 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
6531596 AAAAGATAAC
*
6531606 TTAATGATTAATTTAATTTAT
1 TTAATTATTAATTTAATTTAT
6531627 TTAAATTATTAA-TTAATTTAT
1 TT-AATTATTAATTTAATTTAT
6531648 TATAATTA
1 T-TAATTA
6531656 AATAGTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAATTATTAATTTAATTTAT
Found at i:6535960 original size:19 final size:20
Alignment explanation
Indices: 6535936--6535981 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
6535926 TTGATTCTAA
6535936 AAAAATTAC-AAAAATGAT-T
1 AAAAATTACAAAAAAT-ATAT
*
6535955 AAAAA-TCCAAAAAATATAT
1 AAAAATTACAAAAAATATAT
6535974 AAAAATTA
1 AAAAATTA
6535982 AACAAGCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.18
19 17 0.77
20 1 0.05
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAATTACAAAAAATATAT
Found at i:6536727 original size:11 final size:11
Alignment explanation
Indices: 6536699--6536733 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
6536689 TTGACCTTTC
6536699 CAAGGTATGGG
1 CAAGGTATGGG
*
6536710 -TAGGTATGGG
1 CAAGGTATGGG
6536720 CAAGGTATGGG
1 CAAGGTATGGG
6536731 CAA
1 CAA
6536734 AGAATGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.29, C:0.09, G:0.43, T:0.20
Consensus pattern (11 bp):
CAAGGTATGGG
Found at i:6542142 original size:1 final size:1
Alignment explanation
Indices: 6542136--6542170 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
6542126 TTAGTACTTA
* *
6542136 TTTTTTTCTTCTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6542171 AAATTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:6542450 original size:118 final size:118
Alignment explanation
Indices: 6542289--6542524 Score: 400
Period size: 118 Copynumber: 2.0 Consensus size: 118
6542279 ATTATTTATT
*
6542289 TCGGTTAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCA
1 TCGGCTAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCA
*
6542354 AGCACCCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACC
66 AGCACCCTACCCCGGTTACTCAGTCAGTCACGATTTAAGCCATACTCATAACC
****
6542407 TCGGCTAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCA
1 TCGGCTAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCA
**
6542472 AGCACCCTACCCCGGTTACTCAGTCAGTCACGATTTAAGCTGTACTCATAACC
66 AGCACCCTACCCCGGTTACTCAGTCAGTCACGATTTAAGCCATACTCATAACC
6542525 ATGGAAAACA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 110 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (118 bp):
TCGGCTAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCA
AGCACCCTACCCCGGTTACTCAGTCAGTCACGATTTAAGCCATACTCATAACC
Found at i:6543350 original size:43 final size:42
Alignment explanation
Indices: 6543281--6543371 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
6543271 TGAAAAGGGG
* * *
6543281 TGTTTGGCTGCAGGTTTTGGGGATTCTAAAGCTGGAATAGGAC
1 TGTTTGGCTGCAGGATATGGGGATTCT-AAGCTGGAATAGAAC
* **
6543324 TGTTTGGCTGCAGAGATAT-GGTATTCTGGGCTGGAATAGAAC
1 TGTTTGGCTGCAG-GATATGGGGATTCTAAGCTGGAATAGAAC
6543366 TGTTTG
1 TGTTTG
6543372 ACAGCATGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 18 0.44
43 20 0.49
44 3 0.07
ACGTcount: A:0.21, C:0.11, G:0.34, T:0.34
Consensus pattern (42 bp):
TGTTTGGCTGCAGGATATGGGGATTCTAAGCTGGAATAGAAC
Found at i:6543509 original size:26 final size:26
Alignment explanation
Indices: 6543479--6543537 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
6543469 AATATTTAAC
*
6543479 TAAAATAAAAAAA-AAATAATAAATAA
1 TAAAAGAAAAAAATAAATAA-AAATAA
6543505 TAAAAGAAAAAAATAAATAAAAAT-A
1 TAAAAGAAAAAAATAAATAAAAATAA
6543530 -AAAAGAAA
1 TAAAAGAAA
6543538 GATTGGGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 8 0.26
25 1 0.03
26 16 0.52
27 6 0.19
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.15
Consensus pattern (26 bp):
TAAAAGAAAAAAATAAATAAAAATAA
Found at i:6543514 original size:24 final size:25
Alignment explanation
Indices: 6543487--6543537 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 25
6543477 ACTAAAATAA
6543487 AAAAAAAAT-AATAAATAAT-AAAAG
1 AAAAAAAATAAATAAA-AATAAAAAG
6543511 -AAAAAAATAAATAAAAATAAAAAG
1 AAAAAAAATAAATAAAAATAAAAAG
6543535 AAA
1 AAA
6543538 GATTGGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.46
24 11 0.46
25 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.14
Consensus pattern (25 bp):
AAAAAAAATAAATAAAAATAAAAAG
Found at i:6543518 original size:23 final size:24
Alignment explanation
Indices: 6543488--6543537 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
6543478 CTAAAATAAA
6543488 AAAAAAAT-AATAAATAAT-AAAAG
1 AAAAAAATAAATAAA-AATAAAAAG
6543511 AAAAAAATAAATAAAAATAAAAAG
1 AAAAAAATAAATAAAAATAAAAAG
6543535 AAA
1 AAA
6543538 GATTGGGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.14
Consensus pattern (24 bp):
AAAAAAATAAATAAAAATAAAAAG
Found at i:6550571 original size:18 final size:18
Alignment explanation
Indices: 6550544--6550619 Score: 107
Period size: 18 Copynumber: 4.2 Consensus size: 18
6550534 CAATCCCAAT
6550544 TACCGTATACGTGAATAG
1 TACCGTATACGTGAATAG
*
6550562 TACTGTATACGTGAATAG
1 TACCGTATACGTGAATAG
6550580 TACCGTATACGTGAATAG
1 TACCGTATACGTGAATAG
* * **
6550598 TGCCATATATATGAATAG
1 TACCGTATACGTGAATAG
6550616 TACC
1 TACC
6550620 ATAAATGGTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (18 bp):
TACCGTATACGTGAATAG
Found at i:6551182 original size:11 final size:11
Alignment explanation
Indices: 6551155--6551201 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
6551145 TTACCTTTCC
6551155 AAGGTATGGG-
1 AAGGTATGGGA
*
6551165 TAGGTATGGGA
1 AAGGTATGGGA
* *
6551176 AAGGTATGAGC
1 AAGGTATGGGA
6551187 AAGGTATGGGCA
1 AAGGTATGGG-A
6551199 AAG
1 AAG
6551202 AATGGGTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 9 0.31
11 17 0.59
12 3 0.10
ACGTcount: A:0.34, C:0.04, G:0.43, T:0.19
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:6551621 original size:16 final size:16
Alignment explanation
Indices: 6551600--6551630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6551590 TTTAATTTTT
6551600 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
6551616 TTTCAAATTTATATG
1 TTTCAAATATATATG
6551631 TTTTAACGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:6551728 original size:24 final size:25
Alignment explanation
Indices: 6551692--6551738 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
6551682 AATTTTTTAA
*
6551692 ATTTAACTCGAA-TAATTTCACTTG
1 ATTTAAATCGAATTAATTTCACTTG
* *
6551716 ATTTAAATTGAATTCATTTCACT
1 ATTTAAATCGAATTAATTTCACT
6551739 CGGCTCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (25 bp):
ATTTAAATCGAATTAATTTCACTTG
Found at i:6555115 original size:136 final size:136
Alignment explanation
Indices: 6554871--6555155 Score: 543
Period size: 136 Copynumber: 2.1 Consensus size: 136
6554861 CATTGGGCCT
**
6554871 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
6554936 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
6555001 ATATGC
131 ATATGC
*
6555007 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGTCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
6555072 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
6555137 ATATGC
131 ATATGC
6555143 AAGCCCATTTGGG
1 AAGCCCATTTGGG
6555156 GAGACTACTC
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 146 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:6555191 original size:21 final size:21
Alignment explanation
Indices: 6555162--6555209 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6555152 TGGGGAGACT
*
6555162 ACTCAACCC-ACCAACCACTAC
1 ACTCCACCCTACCAACCA-TAC
*
6555183 ACTCCACCCTACCAGCCATAC
1 ACTCCACCCTACCAACCATAC
6555204 ACTCCA
1 ACTCCA
6555210 TGTGGGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.33, C:0.52, G:0.02, T:0.12
Consensus pattern (21 bp):
ACTCCACCCTACCAACCATAC
Found at i:6556978 original size:26 final size:26
Alignment explanation
Indices: 6556942--6557051 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
6556932 CATGAATTTC
*
6556942 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
6556968 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
6556994 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
6557020 TTATCAT-AGAACATTTACCTAACCCA
1 TTATCATGA-AACATTTACCTAACCCA
6557046 TTATCA
1 TTATCA
6557052 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6557764 original size:21 final size:22
Alignment explanation
Indices: 6557740--6557813 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 22
6557730 AGTAAAATAT
6557740 ATAATATAATAA-AATTTATAA
1 ATAATATAATAATAATTTATAA
* *
6557761 ATAAAATGTATAATAA--TATAA
1 ATAATAT-AATAATAATTTATAA
6557782 ATAATATAATGAATAATTATATAA
1 ATAATATAAT-AATAATT-TATAA
6557806 ATAA-ATAA
1 ATAATATAA
6557814 AAAATAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 2 0.05
21 22 0.51
22 4 0.09
23 6 0.14
24 9 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (22 bp):
ATAATATAATAATAATTTATAA
Found at i:6557792 original size:24 final size:24
Alignment explanation
Indices: 6557760--6557813 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
6557750 AAAATTTATA
* *
6557760 AATAAAATGTATAATAATATAAAT
1 AATATAATGAATAATAATATAAAT
*
6557784 AATATAATGAATAATTATATAAAT
1 AATATAATGAATAATAATATAAAT
6557808 AA-ATAA
1 AATATAA
6557814 AAAATAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AATATAATGAATAATAATATAAAT
Found at i:6557826 original size:24 final size:24
Alignment explanation
Indices: 6557776--6557828 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
6557766 ATGTATAATA
** *
6557776 ATATAAATAATATAATGAATAATT
1 ATATAAATAATATAAAAAATAAAT
6557800 ATATAAATAA-ATAAAAAATAAGAT
1 ATATAAATAATATAAAAAATAA-AT
6557824 ATATA
1 ATATA
6557829 CTATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (24 bp):
ATATAAATAATATAAAAAATAAAT
Found at i:6561458 original size:26 final size:26
Alignment explanation
Indices: 6561429--6561536 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
6561419 TGATACAAAT
*
6561429 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
6561455 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
6561481 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
6561507 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
6561533 TGAT
1 TGAT
6561537 GGGAATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:6563052 original size:26 final size:26
Alignment explanation
Indices: 6563023--6563075 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
6563013 TTTACAGTTT
*
6563023 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCATAGG-GATAAATTGACCGAAA
* *
6563049 TACCCATAGGGTTAAATTGACCTAAA
1 TACCCATAGGGATAAATTGACCGAAA
6563075 T
1 T
6563076 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCATAGGGATAAATTGACCGAAA
Found at i:6565426 original size:11 final size:11
Alignment explanation
Indices: 6565412--6565454 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
6565402 ATAATATATA
6565412 ATACATATTAC
1 ATACATATTAC
*
6565423 ATACATATAATAT
1 ATACATAT--TAC
6565436 ATACATATTAC
1 ATACATATTAC
*
6565447 GTACATAT
1 ATACATAT
6565455 AATATTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (11 bp):
ATACATATTAC
Found at i:6565444 original size:24 final size:25
Alignment explanation
Indices: 6565407--6565459 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
6565397 ATTGTATAAT
6565407 ATATAATACATATTACATACATATA
1 ATATAATACATATTACATACATATA
*
6565432 ATAT-ATACATATTACGTACATATA
1 ATATAATACATATTACATACATATA
6565456 ATAT
1 ATAT
6565460 TATATGCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (25 bp):
ATATAATACATATTACATACATATA
Found at i:6565741 original size:20 final size:19
Alignment explanation
Indices: 6565687--6565744 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
6565677 TTTTTAATTA
6565687 TATTTATATTTT-AATTTT
1 TATTTATATTTTCAATTTT
* **
6565705 AATTTTAATATAATCAATTTT
1 TA-TTT-ATATTTTCAATTTT
6565726 TATTATATATTTTCAATTT
1 TATT-TATATTTTCAATTT
6565745 GTGTATTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 18 0.60
21 8 0.27
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATATTTTCAATTTT
Found at i:6565774 original size:40 final size:40
Alignment explanation
Indices: 6565730--6565810 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
6565720 AATTTTTATT
6565730 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
1 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
** * * * *
6565770 ATATATTTTTTATTTGTTTCTTGTTTTAATATTTGTTTTA
1 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
6565810 A
1 A
6565811 ATGTATTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (40 bp):
ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
Found at i:6567659 original size:28 final size:28
Alignment explanation
Indices: 6567628--6567696 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
6567618 CCCTCTGCCA
*
6567628 CCACCTGCTCCACCGCCCTGCAGCACAT
1 CCACTTGCTCCACCGCCCTGCAGCACAT
*
6567656 CCACTTGCTCCACCGCCCTGCAGCACCT
1 CCACTTGCTCCACCGCCCTGCAGCACAT
6567684 CCACTTGCTCCAC
1 CCACTTGCTCCAC
6567697 TTGCACCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.16, C:0.54, G:0.13, T:0.17
Consensus pattern (28 bp):
CCACTTGCTCCACCGCCCTGCAGCACAT
Found at i:6568658 original size:25 final size:23
Alignment explanation
Indices: 6568628--6568690 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 23
6568618 TTCTATGTTA
6568628 ATTTTAATGTTATTCATACTATTAT
1 ATTTTAATGTTATTCAT--TATTAT
6568653 ATTTTATTACTGTTA-TCATTATTAT
1 ATTTTA--A-TGTTATTCATTATTAT
*
6568678 ATTTTTAT-TTATT
1 ATTTTAATGTTATT
6568691 AGCATCCCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
23 1 0.03
25 17 0.52
27 5 0.15
28 5 0.15
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (23 bp):
ATTTTAATGTTATTCATTATTAT
Found at i:6568816 original size:2 final size:2
Alignment explanation
Indices: 6568809--6568973 Score: 91
Period size: 2 Copynumber: 87.0 Consensus size: 2
6568799 TATTCTTTTA
**
6568809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT ACT CC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* ** * *
6568851 -T AC GC AA AT AT AT AT -T A- AT AT -T AT AT -T AT GT 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
* * * *
6568888 -T TT TT AA AG AT -T 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
* * * * *
6568928 AT TT CAT AT AT -T AT GT AT AT AT TT TT A- AT AT AT -T AT GT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6568968 AT AT AT
1 AT AT AT
6568974 TATGTACATA
Statistics
Matches: 127, Mismatches: 23, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
1 11 0.09
2 114 0.90
3 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6568959 original size:35 final size:35
Alignment explanation
Indices: 6568933--6569003 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
6568923 TATATATTTC
* *
6568933 ATATATTATGTATATATTTTTAATATATTATGTAT
1 ATATATTATGTACATACTTTTAATATATTATGTAT
*
6568968 ATATATTATGTACATACTTTTAATATTATCATGTAT
1 ATATATTATGTACATACTTTTAATA-TATTATGTAT
6569004 TCATTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 23 0.72
36 9 0.28
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (35 bp):
ATATATTATGTACATACTTTTAATATATTATGTAT
Found at i:6569532 original size:26 final size:25
Alignment explanation
Indices: 6569502--6569557 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
6569492 TTATTTCCCT
6569502 TATTTTATTACTATTGACATTAGTAC
1 TATTTTATTACTATT-ACATTAGTAC
* * *
6569528 TATTTTTATTAGTATTACTTTATTAC
1 TA-TTTTATTACTATTACATTAGTAC
6569554 TATT
1 TATT
6569558 ACTACTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 2 0.08
26 12 0.46
27 12 0.46
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.57
Consensus pattern (25 bp):
TATTTTATTACTATTACATTAGTAC
Found at i:6569551 original size:14 final size:14
Alignment explanation
Indices: 6569505--6569560 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
6569495 TTTCCCTTAT
6569505 TTTATTACTATTGAC
1 TTTATTACTATT-AC
* *
6569520 ATTAGTACTATT--
1 TTTATTACTATTAC
*
6569532 TTTATTAGTATTAC
1 TTTATTACTATTAC
6569546 TTTATTACTATTAC
1 TTTATTACTATTAC
6569560 T
1 T
6569561 ACTAATATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
12 9 0.27
14 14 0.42
15 10 0.30
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (14 bp):
TTTATTACTATTAC
Found at i:6569596 original size:20 final size:20
Alignment explanation
Indices: 6569571--6569609 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6569561 ACTAATATCA
*
6569571 CTATTATTATTTTTTTATTG
1 CTATTATTATTATTTTATTG
6569591 CTATTATTATTATTTTATT
1 CTATTATTATTATTTTATT
6569610 TTTTACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (20 bp):
CTATTATTATTATTTTATTG
Found at i:6569602 original size:23 final size:23
Alignment explanation
Indices: 6569572--6569649 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
6569562 CTAATATCAC
*
6569572 TATTATTATTTT-TTTATTGCTA
1 TATTATTATTTTATTTATTACTA
*
6569594 TTATTATTATTTTATTTTTTACTA
1 -TATTATTATTTTATTTATTACTA
6569618 TATTATT-TTTTATTT-TTACTA
1 TATTATTATTTTATTTATTACTA
*
6569639 CTATTACTATT
1 -TATTATTATT
6569650 ATCATTACTA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
21 6 0.12
22 14 0.29
23 21 0.43
24 8 0.16
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.68
Consensus pattern (23 bp):
TATTATTATTTTATTTATTACTA
Found at i:6569686 original size:3 final size:3
Alignment explanation
Indices: 6569572--6569670 Score: 52
Period size: 3 Copynumber: 35.7 Consensus size: 3
6569562 CTAATATCAC
* ** *
6569572 TAT TAT TAT T-T TTT TAT TGC TAT TAT TAT TAT T-T TAT T-T T-T TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
6569616 TA- TAT TAT T-T T-T TAT TTT TAC TAC TAT TAC TAT TAT CAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6569661 TA- TAT TAT TA
1 TAT TAT TAT TA
6569671 GCATTTTTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
2 16 0.22
3 58 0.78
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6573200 original size:19 final size:18
Alignment explanation
Indices: 6573163--6573206 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
6573153 ATTTTAAATT
6573163 TTATTA-TTTTATGTATA
1 TTATTATTTTTATGTATA
*
6573180 TTATTATTTTATATTTATA
1 TTATTATTTT-TATGTATA
6573199 TTATTATT
1 TTATTATT
6573207 AAATACTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 3 0.12
19 15 0.62
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATTATTTTTATGTATA
Found at i:6573250 original size:18 final size:18
Alignment explanation
Indices: 6573224--6573288 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
6573214 GGAAATCCAT
*
6573224 TTATTTTATTATATATTA
1 TTATATTATTATATATTA
*
6573242 TTATATTATTTTATATGGTA
1 TTATATTATTATATAT--TA
* *
6573262 TATGTATTATTTATATTTTA
1 T-TATATTA-TTATATATTA
6573282 TTA-ATTA
1 TTATATTA
6573289 AATATTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
18 18 0.49
19 1 0.03
20 6 0.16
21 6 0.16
22 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTATATTATTATATATTA
Found at i:6573255 original size:20 final size:19
Alignment explanation
Indices: 6573232--6573288 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
6573222 ATTTATTTTA
6573232 TTATATATTATTATATTAT
1 TTATATATTATTATATTAT
*
6573251 TT-TATATGGTATATGTATTAT
1 TTATATAT--TAT-TATATTAT
*
6573272 TTATATTTTATTA-ATTA
1 TTATATATTATTATATTA
6573289 AATATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
18 9 0.29
19 3 0.10
20 6 0.19
21 9 0.29
22 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTATATATTATTATATTAT
Found at i:6573411 original size:41 final size:39
Alignment explanation
Indices: 6573351--6573442 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
6573341 AAAAATAATA
* *
6573351 AAATTATTTTTATTTATGTATATTATAAATTTATTTATTTT
1 AAATTATTATTATTTATGTATATTAT-AATTT-TATATTTT
*
6573392 AAATT-TTATTATTTGATGTATATTATTATTTTATATTTT
1 AAATTATTATTATTT-ATGTATATTATAATTTTATATTTT
*
6573431 ATATTATTATTA
1 AAATTATTATTA
6573443 AATACTGGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 11 0.24
40 18 0.40
41 16 0.36
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (39 bp):
AAATTATTATTATTTATGTATATTATAATTTTATATTTT
Found at i:6573488 original size:235 final size:227
Alignment explanation
Indices: 6573134--6573604 Score: 800
Period size: 235 Copynumber: 2.0 Consensus size: 227
6573124 TTAGTCCTCT
*
6573134 TATACTTATAAATTTATTTATTTTAAATTTTATTATTTTATGTATATTATTATTTTATATTTATA
1 TATA-TTATAAATTTATTTATTTTAAATTTTATTATTTGATGTATATTATTATTTTATATTTATA
*
6573199 TTATTATTAAATACTGGAAATCCATTTATTTTATTATATATTATTATATTATTTTATATGGTATA
65 TTATTATTAAATACTGGAAATCCATTTATTTTAATATATATTATTATATTATTTTATATGGTATA
6573264 TGTATTATTTATATTTTATTAATTAAATATTTTTTAAATATATGTATTATATATATTTTAAAATG
130 TGTATTATTTATATTTTATTAATTAAATA-TTTTT-AATATATGTATTATAT-TATTTTAAAATG
* *
6573329 TTAATTATGTATAAAAATAATAAAATTATTTTTATTTATG
192 ATAATTA--TAT--AAATAACAAAATTATTTTTATTTATG
6573369 TATATTATAAATTTATTTATTTTAAATTTTATTATTTGATGTATATTATTATTTTATATTTTATA
1 TATATTATAAATTTATTTATTTTAAATTTTATTATTTGATGTATATTATTATTTTATA-TTTATA
6573434 TTATTATTAAATACTGGAAATCCATTTATTTTAATATATATTATTATATTATTTTATATGGTATA
65 TTATTATTAAATACTGGAAATCCATTTATTTTAATATATATTATTATATTATTTTATATGGTATA
* *
6573499 TGTATTATTTATATTTTATTAATTAAATATTTTTAATATATGTATTATATTTTTTTTAAATGATA
130 TGTATTATTTATATTTTATTAATTAAATATTTTTAATATATGTATTATATTATTTTAAAATGATA
6573564 ATTATATAAATAACAAAATTATTTTTATTTATG
195 ATTATATAAATAACAAAATTATTTTTATTTATG
6573597 T-TATTATA
1 TATATTATA
6573605 TTATATGTTT
Statistics
Matches: 229, Mismatches: 6, Indels: 10
0.93 0.02 0.04
Matches are distributed among these distances:
227 7 0.03
228 26 0.11
230 3 0.01
232 16 0.07
233 16 0.07
234 58 0.25
235 103 0.45
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (227 bp):
TATATTATAAATTTATTTATTTTAAATTTTATTATTTGATGTATATTATTATTTTATATTTATAT
TATTATTAAATACTGGAAATCCATTTATTTTAATATATATTATTATATTATTTTATATGGTATAT
GTATTATTTATATTTTATTAATTAAATATTTTTAATATATGTATTATATTATTTTAAAATGATAA
TTATATAAATAACAAAATTATTTTTATTTATG
Found at i:6573491 original size:20 final size:19
Alignment explanation
Indices: 6573468--6573523 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
6573458 TTTATTTTAA
6573468 TATATATTATTATATTATT
1 TATATATTATTATATTATT
*
6573487 T-TATATGGTATATGTATTATT
1 TATATAT--TAT-TATATTATT
*
6573508 TATATTTTATTA-ATTA
1 TATATATTATTATATTA
6573524 AATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
18 9 0.30
19 2 0.07
20 6 0.20
21 9 0.30
22 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TATATATTATTATATTATT
Found at i:6573756 original size:27 final size:27
Alignment explanation
Indices: 6573710--6573765 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
6573700 AGTTTTAAAA
*
6573710 TTTTATAAATTACTATTAAACA-TTAT
1 TTTTATAAATTACTATTAAAAATTTAT
* *
6573736 TTTTATATATATATTATTAAAAATTTAT
1 TTTTATAAAT-TACTATTAAAAATTTAT
6573764 TT
1 TT
6573766 ATCACTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 10 0.40
28 6 0.24
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTATAAATTACTATTAAAAATTTAT
Found at i:6581241 original size:20 final size:20
Alignment explanation
Indices: 6581197--6581250 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
6581187 ATTACAAAAC
** *
6581197 AATTCAAAATAAATTTCTAA
1 AATTCAAAATATTTTTCAAA
*
6581217 TATTCAAAATATTTTTCAAA
1 AATTCAAAATATTTTTCAAA
6581237 AATTCCAAAA-ATTT
1 AATT-CAAAATATTT
6581251 CATAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTCAAAATATTTTTCAAA
Found at i:6584903 original size:24 final size:23
Alignment explanation
Indices: 6584874--6584919 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
6584864 TATGAAAACA
6584874 GTTAAACAAAATACT-ATATAAAAT
1 GTTAAA-AAAATA-TGATATAAAAT
*
6584898 GTTAAAATAATATGATATAAAA
1 GTTAAAAAAATATGATATAAAA
6584920 AGAACTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 13 0.65
24 6 0.30
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (23 bp):
GTTAAAAAAATATGATATAAAAT
Found at i:6588126 original size:29 final size:29
Alignment explanation
Indices: 6588056--6588129 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
6588046 TATACGACCA
*
6588056 ACCACACAGCCGTGTGGCTCACACGGCCT
1 ACCACACAGCCGTGTGGCTCACACAGCCT
* *
6588085 ACCACACAACCGTGTGGCTTACACAGCCT
1 ACCACACAGCCGTGTGGCTCACACAGCCT
**
6588114 ACCACATGGCCGTGTG
1 ACCACACAGCCGTGTG
6588130 ATATCAACAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.16
Consensus pattern (29 bp):
ACCACACAGCCGTGTGGCTCACACAGCCT
Found at i:6592187 original size:20 final size:19
Alignment explanation
Indices: 6592162--6592202 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
6592152 CAAAAAAAAG
6592162 AAATTCAAAATAAATTTTAA
1 AAATTCAAAAT-AATTTTAA
* *
6592182 AAATTCATAATCATTTTAA
1 AAATTCAAAATAATTTTAA
6592201 AA
1 AA
6592203 TTTTAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTCAAAATAATTTTAA
Found at i:6592231 original size:28 final size:27
Alignment explanation
Indices: 6592199--6592295 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 27
6592189 TAATCATTTT
6592199 AAAATTTTAAAACATTTATAAAAAAATC
1 AAAATTTTAAAA-ATTTATAAAAAAATC
* * * * *
6592227 AAAA-TTTATATATTTTTAAAAACTTATA
1 AAAATTTTAAAAATTTATAAAAA--AATC
* * *
6592255 AAAATTATAAAGAATATATAAAAAGATC
1 AAAATTTTAAA-AATTTATAAAAAAATC
6592283 AAAATTTTAAAAA
1 AAAATTTTAAAAA
6592296 AGTTCTAAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
26 10 0.19
27 7 0.13
28 22 0.42
29 4 0.08
30 9 0.17
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (27 bp):
AAAATTTTAAAAATTTATAAAAAAATC
Found at i:6595359 original size:29 final size:30
Alignment explanation
Indices: 6595325--6595384 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
6595315 AAAAAGTAAA
6595325 TTTA-TTTTTTTTCATCACAATTTTGTTGT
1 TTTATTTTTTTTTCATCACAATTTTGTTGT
6595354 TTTATTTTTTTTTCATCACAATTTTGTTGT
1 TTTATTTTTTTTTCATCACAATTTTGTTGT
6595384 T
1 T
6595385 ACTTCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (30 bp):
TTTATTTTTTTTTCATCACAATTTTGTTGT
Found at i:6599219 original size:71 final size:71
Alignment explanation
Indices: 6599132--6599293 Score: 324
Period size: 71 Copynumber: 2.3 Consensus size: 71
6599122 GATGTATCCT
6599132 ATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAG
1 ATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAG
6599197 GACACC
66 GACACC
6599203 ATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAG
1 ATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAG
6599268 GACACC
66 GACACC
6599274 ATGTAGACAAGAGAGCTACG
1 ATGTAGACAAGAGAGCTACG
6599294 AGACAAATCG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.19
Consensus pattern (71 bp):
ATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAG
GACACC
Found at i:6603712 original size:16 final size:16
Alignment explanation
Indices: 6603687--6603717 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6603677 CACCACTTGG
*
6603687 ATTGTTTGCCATTAAA
1 ATTGTCTGCCATTAAA
6603703 ATTGTCTGCCATTAA
1 ATTGTCTGCCATTAA
6603718 TCATAATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTGTCTGCCATTAAA
Found at i:6607803 original size:23 final size:21
Alignment explanation
Indices: 6607777--6607819 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
6607767 GTGAATCTAT
6607777 TATTGGTATTATATCTTATCATG
1 TATTGGTATTAT-TCTT-TCATG
**
6607800 TATTTTTATTATTCTTTCAT
1 TATTGGTATTATTCTTTCAT
6607820 ATTTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (21 bp):
TATTGGTATTATTCTTTCATG
Found at i:6612883 original size:30 final size:30
Alignment explanation
Indices: 6612842--6612903 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
6612832 TAATAAAGAT
* *
6612842 AAAATTATATTTACTCTTTTAAAAATTATA
1 AAAATTATATTTAATATTTTAAAAATTATA
*
6612872 AAAATTTTATTTAATATTTTAAAAATTATA
1 AAAATTATATTTAATATTTTAAAAATTATA
6612902 AA
1 AA
6612904 GATATAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
AAAATTATATTTAATATTTTAAAAATTATA
Found at i:6613695 original size:20 final size:20
Alignment explanation
Indices: 6613670--6613720 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
6613660 TACAAAAAAG
6613670 AAATTCAAAATAAATTTTAA
1 AAATTCAAAATAAATTTTAA
* * *
6613690 AAATTCATAAT-CATTTTTA
1 AAATTCAAAATAAATTTTAA
*
6613709 AAATTTAAAATA
1 AAATTCAAAATA
6613721 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATTCAAAATAAATTTTAA
Found at i:6614031 original size:24 final size:25
Alignment explanation
Indices: 6614002--6614049 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6613992 AATTTTTTTA
*
6614002 ATTTAACTCGAA-TAATTTCACTCG
1 ATTTAAATCGAATTAATTTCACTCG
* *
6614026 ATTTAAATTGAATTTATTTCACTC
1 ATTTAAATCGAATTAATTTCACTC
6614050 AACTCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (25 bp):
ATTTAAATCGAATTAATTTCACTCG
Found at i:6622386 original size:28 final size:28
Alignment explanation
Indices: 6622346--6622401 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
6622336 AAAATTACAT
6622346 AGTTTACAACTAAAGAACCTTGACTAAA
1 AGTTTACAACTAAAGAACCTTGACTAAA
*
6622374 AGTTTACAACTAAAGAACCTTGATTAAA
1 AGTTTACAACTAAAGAACCTTGACTAAA
6622402 TGTACAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (28 bp):
AGTTTACAACTAAAGAACCTTGACTAAA
Found at i:6627353 original size:29 final size:29
Alignment explanation
Indices: 6627311--6627369 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6627301 CATTGGAAAG
6627311 GCTTGTGAGCATTATTTGGATACCATGGA
1 GCTTGTGAGCATTATTTGGATACCATGGA
6627340 GCTTGTGAGCATTATTTGGATACCATGGA
1 GCTTGTGAGCATTATTTGGATACCATGGA
6627369 G
1 G
6627370 ATGTTGTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.34
Consensus pattern (29 bp):
GCTTGTGAGCATTATTTGGATACCATGGA
Found at i:6632976 original size:58 final size:58
Alignment explanation
Indices: 6632907--6633022 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
6632897 CAACCTCTGA
6632907 TTGTAAAGATATAGACTGTGAGAGATCTTATTCTATTAAGGTCTCCAACAAAATTGAC
1 TTGTAAAGATATAGACTGTGAGAGATCTTATTCTATTAAGGTCTCCAACAAAATTGAC
*
6632965 TTGTAAAGATATAGACTGTGAGAGATCTTATTCTATTAAGGTCTCCAGCAAAATTGAC
1 TTGTAAAGATATAGACTGTGAGAGATCTTATTCTATTAAGGTCTCCAACAAAATTGAC
6633023 ATCAACATAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (58 bp):
TTGTAAAGATATAGACTGTGAGAGATCTTATTCTATTAAGGTCTCCAACAAAATTGAC
Found at i:6634786 original size:16 final size:17
Alignment explanation
Indices: 6634754--6634786 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6634744 TTTATAAGTA
*
6634754 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
6634771 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
6634787 GTTTCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:6635391 original size:46 final size:46
Alignment explanation
Indices: 6635067--6635390 Score: 434
Period size: 46 Copynumber: 7.0 Consensus size: 46
6635057 TTATCTTTGA
* * * * *
6635067 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATAT
* *
6635113 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* * * * *
6635159 CACGTTGCTACGGTATCTTTCAACCATGGTCTTATTCATTTCCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
***
6635205 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
*
6635251 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* **
6635297 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* **
6635343 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
6635389 CA
1 CA
6635391 GAGAGCACAC
Statistics
Matches: 252, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 248 0.98
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
Found at i:6637102 original size:13 final size:12
Alignment explanation
Indices: 6637084--6637127 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
6637074 CCTTATTTTC
6637084 TTTCTCTTCACT
1 TTTCTCTTCACT
6637096 ATTTCTCTTCAC-
1 -TTTCTCTTCACT
6637108 TTTCTCTT-A-T
1 TTTCTCTTCACT
6637118 TTTCTCTTCA
1 TTTCTCTTCA
6637128 TTAACATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.31
11 9 0.31
13 11 0.38
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTCTCTTCACT
Found at i:6637123 original size:21 final size:24
Alignment explanation
Indices: 6637083--6637127 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
6637073 CCCTTATTTT
6637083 CTTTCTCTTCACTATTTCTCTTCA
1 CTTTCTCTTCACTATTTCTCTTCA
6637107 CTTTCTCTT-A-T-TTTCTCTTCA
1 CTTTCTCTTCACTATTTCTCTTCA
6637128 TTAACATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 1 0.05
24 9 0.43
ACGTcount: A:0.11, C:0.31, G:0.00, T:0.58
Consensus pattern (24 bp):
CTTTCTCTTCACTATTTCTCTTCA
Found at i:6638759 original size:18 final size:18
Alignment explanation
Indices: 6638735--6638832 Score: 60
Period size: 19 Copynumber: 5.4 Consensus size: 18
6638725 GATTACAAAA
*
6638735 AAAAAATCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
*
6638754 AAAAATTCTAAAATTTAT
1 AAAAATTCAAAAATTTAT
** * *
6638772 --ATTTTTAAAAAATTAT
1 AAAAATTCAAAAATTTAT
*
6638788 AAAAATTCTAAAAGATATAT
1 AAAAATTC-AAAA-ATTTAT
6638808 AAAAAAGTT-AAAAATTT-T
1 -AAAAA-TTCAAAAATTTAT
6638826 AAAAATT
1 AAAAATT
6638833 TCTAAAATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 15
0.68 0.15 0.17
Matches are distributed among these distances:
16 13 0.22
17 5 0.08
18 10 0.17
19 17 0.28
20 8 0.13
21 5 0.08
22 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:6638840 original size:9 final size:9
Alignment explanation
Indices: 6638774--6638839 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
6638764 AAATTTATAT
6638774 TTTTAAAAAA
1 TTTT-AAAAA
*
6638784 TTATAAAAA
1 TTTTAAAAA
*
6638793 TTCTAAAAGA
1 TTTTAAAA-A
*
6638803 TATATAAAAA
1 T-TTTAAAAA
**
6638813 AGTTAAAAA
1 TTTTAAAAA
6638822 TTTTAAAAA
1 TTTTAAAAA
6638831 TTTCTAAAA
1 TTT-TAAAA
6638840 TAATAATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 28 0.62
10 11 0.24
11 6 0.13
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:6640222 original size:32 final size:32
Alignment explanation
Indices: 6640186--6640249 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
6640176 TATTAACCAC
* *
6640186 ATCTTTAAAATAAATATAATTATTTAACTAAT
1 ATCTTTAAAATAAACATAACTATTTAACTAAT
* *
6640218 ATCTTTTAAATAAACATAACTATTTAATTAAT
1 ATCTTTAAAATAAACATAACTATTTAACTAAT
6640250 GTTGCTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (32 bp):
ATCTTTAAAATAAACATAACTATTTAACTAAT
Found at i:6642777 original size:22 final size:24
Alignment explanation
Indices: 6642722--6642781 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
6642712 GACTATATAT
*
6642722 AAAATATTAATAAATATAAAATAT
1 AAAATATTAATAAATATAAAATAA
* *
6642746 AAAATCATTAA-ATAT-TAAATTAA
1 AAAAT-ATTAATAAATATAAAATAA
6642769 AAAATATT-ATAAA
1 AAAATATTAATAAA
6642782 CATACAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 1 0.03
22 5 0.17
23 11 0.37
24 8 0.27
25 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATATTAATAAATATAAAATAA
Found at i:6644311 original size:17 final size:16
Alignment explanation
Indices: 6644275--6644350 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 16
6644265 ACAAACTGCA
6644275 AGCTCACCAA-ATGTACG
1 AGCTCACCAAGATG-A-G
*
6644292 AGCTCACCAAAGATGTG
1 AGCTCACC-AAGATGAG
6644309 AGCTCACCAAGACTGCA-
1 AGCTCACCAAGA-TG-AG
6644326 AGCTCACCAAGCATGAG
1 AGCTCACCAAG-ATGAG
6644343 AGCTCACC
1 AGCTCACC
6644351 TGCGAGCTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
16 5 0.10
17 40 0.78
18 3 0.06
19 3 0.06
ACGTcount: A:0.34, C:0.32, G:0.20, T:0.14
Consensus pattern (16 bp):
AGCTCACCAAGATGAG
Found at i:6644386 original size:8 final size:8
Alignment explanation
Indices: 6644373--6644400 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
6644363 ATTTTGCAAG
6644373 TTGCCAAC
1 TTGCCAAC
6644381 TTGCCAAC
1 TTGCCAAC
6644389 TTGCCAAC
1 TTGCCAAC
6644397 TTGC
1 TTGC
6644401 ACTGAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (8 bp):
TTGCCAAC
Found at i:6650220 original size:25 final size:25
Alignment explanation
Indices: 6650189--6650239 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6650179 AAGATTGATA
6650189 TATTTGAGGTGTCAAATCAGTTTAT
1 TATTTGAGGTGTCAAATCAGTTTAT
6650214 TATTTGAGGTGTCAAATCAGTTTAT
1 TATTTGAGGTGTCAAATCAGTTTAT
6650239 T
1 T
6650240 CATTGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (25 bp):
TATTTGAGGTGTCAAATCAGTTTAT
Found at i:6652824 original size:43 final size:43
Alignment explanation
Indices: 6652755--6652884 Score: 140
Period size: 43 Copynumber: 3.0 Consensus size: 43
6652745 AGCTCGTACA
* * * * *
6652755 ATGCCA-TATCCCAGATATGGTTTTACATGTTATCACATATCG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* ** *
6652797 ATGCCACTGTCCCAGACAGGGTCTTACACAAAATCA-ATTTACG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATAT-CG
6652840 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAATCACATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
6652883 AT
1 AT
6652885 AACCTAATGT
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
42 9 0.13
43 57 0.80
44 5 0.07
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:6658126 original size:20 final size:19
Alignment explanation
Indices: 6658103--6658141 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6658093 ATTATATCAT
6658103 TATTAAAATTATTAACAAAA
1 TATTAAAA-TATTAACAAAA
**
6658123 TATTTTAATATTAACAAAA
1 TATTAAAATATTAACAAAA
6658142 CATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTAAAATATTAACAAAA
Found at i:6662217 original size:41 final size:43
Alignment explanation
Indices: 6662148--6662231 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 43
6662138 AATTTGTGTA
*
6662148 TTGTTTTAAGAATTGTTTTAGTATTATTT-TTTATT-TATTTC
1 TTGTTTTAAGAATTGTTTTAGAATTATTTATTTATTATATTTC
* *
6662189 TTGTTTTAATATTTGTTTTA-AATGTATTTGATTTATTATATTT
1 TTGTTTTAAGAATTGTTTTAGAAT-TATTT-ATTTATTATATTT
6662232 TAAATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 2 0.06
41 23 0.64
43 6 0.17
44 5 0.14
ACGTcount: A:0.24, C:0.01, G:0.10, T:0.65
Consensus pattern (43 bp):
TTGTTTTAAGAATTGTTTTAGAATTATTTATTTATTATATTTC
Found at i:6662496 original size:31 final size:30
Alignment explanation
Indices: 6662424--6662498 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
6662414 TTGTAATTGG
*
6662424 TGATTAATTTAATTCTTTTTGAAAGATTAA
1 TGATAAATTTAATTCTTTTTGAAAGATTAA
6662454 TGATAAATTTAATTCTTTTTGAAAGATTAA
1 TGATAAATTTAATTCTTTTTGAAAGATTAA
6662484 TGATAAAATTTAATT
1 TGAT-AAATTTAATT
6662499 TAAAAAAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 33 0.77
31 10 0.23
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (30 bp):
TGATAAATTTAATTCTTTTTGAAAGATTAA
Found at i:6666341 original size:26 final size:24
Alignment explanation
Indices: 6666307--6666355 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
6666297 TAAATAAAAA
*
6666307 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAATATAA-AAA-CAAATAC
6666333 ATTTAAAAATATAAAAACAAATA
1 ATTTAAAAATATAAAAACAAATA
6666356 TTAAAACAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 13 0.59
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
ATTTAAAAATATAAAAACAAATAC
Found at i:6666486 original size:20 final size:22
Alignment explanation
Indices: 6666446--6666487 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
6666436 TTATATTAAA
6666446 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAA-GTAAATATG
6666469 ATTAAAAAT-AAA-TAAATAT
1 ATTAAAAATAAAAGTAAATAT
6666488 ATATATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
ATTAAAAATAAAAGTAAATATG
Found at i:6667839 original size:41 final size:41
Alignment explanation
Indices: 6667780--6667861 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
6667770 AATGTATCAG
*
6667780 GTATGGGGTGTTACAGAATATGTTGCTTATGCCTGTGCCAA
1 GTATGGGATGTTACAGAATATGTTGCTTATGCCTGTGCCAA
*
6667821 GTATGGGATGTTATAGAATATGTTGCTTATGCCTGTGCCAA
1 GTATGGGATGTTACAGAATATGTTGCTTATGCCTGTGCCAA
6667862 AGTGTGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.35
Consensus pattern (41 bp):
GTATGGGATGTTACAGAATATGTTGCTTATGCCTGTGCCAA
Found at i:6668436 original size:16 final size:17
Alignment explanation
Indices: 6668415--6668448 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6668405 GACTATATAG
*
6668415 AAAATAT-TAATAAATA
1 AAAATATATAAAAAATA
6668431 AAAATATATAAAAAATA
1 AAAATATATAAAAAATA
6668448 A
1 A
6668449 TATAAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATATAAAAAATA
Found at i:6668960 original size:16 final size:18
Alignment explanation
Indices: 6668934--6668966 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6668924 TTCAAATAAC
6668934 TAAATATATTTT-AAAGT
1 TAAATATATTTTGAAAGT
6668951 TAAA-ATATTTTGAAAG
1 TAAATATATTTTGAAAG
6668967 AATAATTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TAAATATATTTTGAAAGT
Found at i:6671748 original size:20 final size:21
Alignment explanation
Indices: 6671718--6671758 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
6671708 AAATTACAAA
6671718 AAAATAAATTCGA-AATAATTT
1 AAAATAAATTC-ATAATAATTT
6671739 AAAA-AAATTCATAATAATTT
1 AAAATAAATTCATAATAATTT
6671759 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 14 0.74
21 4 0.21
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAATAAATTCATAATAATTT
Found at i:6672355 original size:13 final size:11
Alignment explanation
Indices: 6672319--6672349 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
6672309 CCACTCGTAT
6672319 TAATTTTTATA
1 TAATTTTTATA
*
6672330 TTATTTTTATA
1 TAATTTTTATA
6672341 TAATTTTTA
1 TAATTTTTA
6672350 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:6675399 original size:3 final size:3
Alignment explanation
Indices: 6675391--6675428 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
6675381 TGAAAGCAAG
*
6675391 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6675429 ACCAATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6675525 original size:18 final size:18
Alignment explanation
Indices: 6675492--6675526 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6675482 ATAAGAATAA
*
6675492 AAAATATATACCTATATT
1 AAAATATATACATATATT
*
6675510 AAAATATATATATATAT
1 AAAATATATACATATAT
6675527 ATATAGCGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATATACATATATT
Found at i:6675527 original size:20 final size:20
Alignment explanation
Indices: 6675489--6675528 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6675479 ATAATAAGAA
*
6675489 TAAAAAATATATACCTATAT
1 TAAAAAATATATACATATAT
* *
6675509 TAAAATATATATATATATAT
1 TAAAAAATATATACATATAT
6675529 ATAGCGTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAAATATATACATATAT
Found at i:6675684 original size:25 final size:26
Alignment explanation
Indices: 6675640--6675697 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
6675630 GTATAAAGAT
6675640 ATAATAT-TAAAAAGATACATATA-C
1 ATAATATATAAAAAGATACATATACC
6675664 ATAATATATAAAAATGA-ACATATACC
1 ATAATATATAAAAA-GATACATATACC
6675690 AT-ATATAT
1 ATAATATAT
6675698 TAGAAATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.23
25 19 0.61
26 5 0.16
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (26 bp):
ATAATATATAAAAAGATACATATACC
Found at i:6675704 original size:26 final size:25
Alignment explanation
Indices: 6675638--6675704 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
6675628 ATGTATAAAG
*
6675638 ATATAATATTAAAAAGATACATATAC
1 ATAT-ATATTAAAATGATACATATAC
*
6675664 ATAATATATAAAAATGA-ACATATACC
1 AT-ATATATTAAAATGATACATATA-C
6675690 ATATATATTAGAAAT
1 ATATATATTA-AAAT
6675705 ACTAATAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 14 0.40
26 19 0.54
27 2 0.06
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.31
Consensus pattern (25 bp):
ATATATATTAAAATGATACATATAC
Found at i:6675919 original size:15 final size:16
Alignment explanation
Indices: 6675891--6675929 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
6675881 AAATATGTAC
*
6675891 ATAATATATAAAAAAT
1 ATAATATATAAAAAAA
6675907 ATAATAT-TAAAAAAA
1 ATAATATATAAAAAAA
6675922 ATAATATA
1 ATAATATA
6675930 CATAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATATATAAAAAAA
Found at i:6675929 original size:29 final size:30
Alignment explanation
Indices: 6675896--6675966 Score: 74
Period size: 32 Copynumber: 2.4 Consensus size: 30
6675886 TGTACATAAT
*
6675896 ATATAAAAAATATAA-TATTAAAAAAAATA
1 ATATAAAAAATAAAAGTATTAAAAAAAATA
* * *
6675925 ATATACATAATATAAAAGTATTTAAAATAATA
1 ATATA-A-AAAATAAAAGTATTAAAAAAAATA
6675957 A-ATAAAAAAT
1 ATATAAAAAAT
6675967 TGAAGAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
29 9 0.26
30 2 0.06
31 10 0.29
32 13 0.38
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (30 bp):
ATATAAAAAATAAAAGTATTAAAAAAAATA
Found at i:6676702 original size:40 final size:43
Alignment explanation
Indices: 6676611--6676702 Score: 100
Period size: 43 Copynumber: 2.2 Consensus size: 43
6676601 ATATATATAC
* * *
6676611 ATAAAAATGTACACTATTATATAATAATAATAATAATATAGAA
1 ATAAAAATGTACAATATAATATAATAATAATAATAATAAAGAA
* *
6676654 ATTCAAAAA-GTA-AATATAATATAATAATATTAA-AATAAAGTA
1 A-T-AAAAATGTACAATATAATATAATAATAATAATAATAAAGAA
6676696 ATAAAAA
1 ATAAAAA
6676703 ATAATACTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
40 5 0.12
41 1 0.02
42 8 0.19
43 19 0.45
44 4 0.10
45 5 0.12
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (43 bp):
ATAAAAATGTACAATATAATATAATAATAATAATAATAAAGAA
Found at i:6677280 original size:18 final size:18
Alignment explanation
Indices: 6677257--6677294 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
6677247 TGAGGAAAGA
6677257 AAAAAAAAGGAGAGAAGG
1 AAAAAAAAGGAGAGAAGG
6677275 AAAAAAAAGGAGAGAAGG
1 AAAAAAAAGGAGAGAAGG
6677293 AA
1 AA
6677295 GAGAGAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGGAGAGAAGG
Found at i:6677461 original size:10 final size:9
Alignment explanation
Indices: 6677446--6677496 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
6677436 ATGTATGTAC
6677446 AAAAAAAGA
1 AAAAAAAGA
*
6677455 GAAAAAAATA
1 -AAAAAAAGA
*
6677465 AAAAAATGA
1 AAAAAAAGA
6677474 AAAAGAAAGTA
1 AAAA-AAAG-A
6677485 AAAAAAA-A
1 AAAAAAAGA
6677493 AAAA
1 AAAA
6677497 GAAATTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 5 0.14
9 11 0.31
10 14 0.40
11 5 0.14
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:6677492 original size:30 final size:27
Alignment explanation
Indices: 6677446--6677532 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 27
6677436 ATGTATGTAC
*
6677446 AAAAA-AAGAGAAAAAAATAAAAAAATG
1 AAAAAGAAGA-AAAAAAAAAAAAAAATG
*
6677473 AAAAAGAAAGTAAAAAAAAAAAAAGAAATTT
1 AAAAAG-AAG-AAAAAAAAAAAAA-AAA-TG
* *
6677504 CAAAAGAAGAAAAAAAAAGAAGAAAATG
1 AAAAAGAAGAAAAAAAAA-AAAAAAATG
6677532 A
1 A
6677533 TGCCAATCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
27 5 0.10
28 1 0.02
29 26 0.54
30 10 0.21
31 6 0.12
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.08
Consensus pattern (27 bp):
AAAAAGAAGAAAAAAAAAAAAAAAATG
Found at i:6677495 original size:19 final size:19
Alignment explanation
Indices: 6677446--6677501 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
6677436 ATGTATGTAC
*
6677446 AAAAAAAGAGAAAA-AAAT
1 AAAAAAAGAAAAAAGAAAT
6677464 AAAAAAATG-AAAAAGAAAGT
1 AAAAAAA-GAAAAAAGAAA-T
6677484 AAAAAAA-AAAAAAGAAAT
1 AAAAAAAGAAAAAAGAAAT
6677502 TTCAAAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 12 0.36
19 13 0.39
20 8 0.24
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (19 bp):
AAAAAAAGAAAAAAGAAAT
Found at i:6684324 original size:40 final size:39
Alignment explanation
Indices: 6684264--6684374 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
6684254 ATCACGATTT
*
6684264 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAA-GCACTA
*
6684304 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAAG-CACTA
*
6684344 GCACAATGGCCTTCGGGTCTTAACCCGGATA
1 GCACAAT-GCCTTCGGGTCTTAGCCCGGATA
6684375 TAATTTCCAG
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
38 1 0.02
39 5 0.08
40 57 0.90
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.23
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAAGCACTA
Found at i:6691827 original size:40 final size:41
Alignment explanation
Indices: 6691696--6691891 Score: 342
Period size: 40 Copynumber: 4.8 Consensus size: 41
6691686 CATAGAGCAA
6691696 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGGGCAT
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGGGCAT
6691737 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGGGCAT
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGGGCAT
* *
6691778 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT-AGGGCAA
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGGGCAT
*
6691818 TAGCGGCGCTTTTGGTAAAACGCCACTAAAAGTC-GGGCAT
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGGGCAT
*
6691858 TAGCGGCGCTTTTGATAAAACGCCGCTAAAAGTC
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
6691892 ATATAACCCC
Statistics
Matches: 148, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
40 74 0.50
41 74 0.50
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGGGCAT
Found at i:6691849 original size:81 final size:81
Alignment explanation
Indices: 6691696--6691892 Score: 342
Period size: 81 Copynumber: 2.4 Consensus size: 81
6691686 CATAGAGCAA
* *
6691696 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGGGCATTAGCGGCGCTTTTGGTAAAACGCC
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGGGCAATAGCGGCGCTTTTGGTAAAACGCC
*
6691761 GCTAAAAGTCGGGGCAT
66 ACTAAAAGTC-GGGCAT
6691778 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGT-AGGGCAATAGCGGCGCTTTTGGTAAAACGCC
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGGGCAATAGCGGCGCTTTTGGTAAAACGCC
6691842 ACTAAAAGTCGGGCAT
66 ACTAAAAGTCGGGCAT
*
6691858 TAGCGGCGCTTTTGATAAAACGCCGCTAAAAGTCA
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCA
6691893 TATAACCCCT
Statistics
Matches: 110, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
80 38 0.35
81 39 0.35
82 33 0.30
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (81 bp):
TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGGGCAATAGCGGCGCTTTTGGTAAAACGCC
ACTAAAAGTCGGGCAT
Found at i:6691972 original size:37 final size:37
Alignment explanation
Indices: 6691930--6692000 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
6691920 AAAAATCATG
* * *
6691930 AACACTAATCTATAACTCCTAAAATACTAAACCCTTA
1 AACACTAAACCATAACTCCTAAAACACTAAACCCTTA
* *
6691967 AACACTAAACCATAACTTCTAAAACCCTAAACCC
1 AACACTAAACCATAACTCCTAAAACACTAAACCC
6692001 CAAAAAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (37 bp):
AACACTAAACCATAACTCCTAAAACACTAAACCCTTA
Found at i:6692126 original size:7 final size:7
Alignment explanation
Indices: 6692114--6692177 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
6692104 TTTATTTTTT
*
6692114 GGTTTAC
1 GGTTTAA
6692121 GGTTTAA
1 GGTTTAA
**
6692128 TATTTAA
1 GGTTTAA
6692135 GGTTTAA
1 GGTTTAA
* *
6692142 GGTCTAT
1 GGTTTAA
*
6692149 GGTTTAG
1 GGTTTAA
*
6692156 GGTTTTAT
1 GG-TTTAA
6692164 GGTTTAA
1 GGTTTAA
6692171 GGTTTAA
1 GGTTTAA
6692178 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:6692166 original size:15 final size:15
Alignment explanation
Indices: 6692130--6692180 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
6692120 CGGTTTAATA
*
6692130 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
6692144 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
6692159 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
6692174 TTAATGG
1 TTTATGG
6692181 CCATGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:6692779 original size:7 final size:7
Alignment explanation
Indices: 6692769--6692793 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6692759 AAATAAACTC
6692769 AAAATTT
1 AAAATTT
6692776 AAAATTT
1 AAAATTT
6692783 AAAATTT
1 AAAATTT
6692790 AAAA
1 AAAA
6692794 ATAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Done.