Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007840.1 Hibiscus syriacus cultivar Beakdansim tig00110194_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: 1104544
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:518511 original size:37 final size:35
Alignment explanation
Indices: 518421--518523 Score: 118
Period size: 35 Copynumber: 2.8 Consensus size: 35
518411 CGGGTCGGAT
* * *
518421 ATATATATATATATATATATTTAAATTAAATATATAA
1 ATAT-TATATATTTTTA-ATTTAATTTAAATATATAA
518458 ATATTATATATTTTTAATTTAATTTAAATATATAA
1 ATATTATATATTTTTAATTTAATTTAAATATATAA
*
518493 TTA-TATATAATTAATTTAATTTAATTTAAAT
1 ATATTATAT-ATT--TTTAATTTAATTTAAAT
518524 TTAAATTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
34 5 0.08
35 23 0.39
36 10 0.17
37 21 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
ATATTATATATTTTTAATTTAATTTAAATATATAA
Found at i:518526 original size:6 final size:6
Alignment explanation
Indices: 518505--518538 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
518495 ATATATAATT
518505 AATTT- AATTT- AATTTA AATTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
518539 TTAATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:519000 original size:24 final size:25
Alignment explanation
Indices: 518956--519004 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
518946 CGCTTGTTGA
518956 AGGGATATATCGGGACCTTCTTATT
1 AGGGATATATCGGGACCTTCTTATT
*
518981 AGGGCTATATC-GGACCTTCTTATT
1 AGGGATATATCGGGACCTTCTTATT
519005 GTAGACTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (25 bp):
AGGGATATATCGGGACCTTCTTATT
Found at i:521546 original size:31 final size:31
Alignment explanation
Indices: 521508--521694 Score: 324
Period size: 31 Copynumber: 6.0 Consensus size: 31
521498 CCCGAATGAC
521508 CAGTCCATA-GATCCCGAAGAATC-TAGGTAAA
1 CAGTCCATATG-TCCCGAAGAA-CATAGGTAAA
521539 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
521570 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
521601 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
521632 CCGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
521663 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
521694 C
1 C
521695 CCTCGACCCT
Statistics
Matches: 150, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
30 1 0.01
31 148 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:522451 original size:64 final size:63
Alignment explanation
Indices: 522343--522566 Score: 222
Period size: 64 Copynumber: 3.5 Consensus size: 63
522333 TAATGAAGGT
* ** * * * **
522343 ATGCATCGATGCACTACTGATGCATCGATGCATAAAATGTATTCGATGTTGT-ATTATTGCTGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTT-TCACTATTAATGAG
* *
522407 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAATGAG
* * *
522471 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATTAATGAG
** *
522534 AGTGCATCGATGCA-TACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
522567 ATTCAAACAA
Statistics
Matches: 137, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
63 21 0.15
64 113 0.82
65 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAATGAG
Found at i:524760 original size:21 final size:21
Alignment explanation
Indices: 524736--524790 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
524726 AAGCCATGAA
524736 TGTATCGATGCACTATGAGTG
1 TGTATCGATGCACTATGAGTG
524757 TGTATCGATGCACTATGAGTG
1 TGTATCGATGCACTATGAGTG
* *
524778 TGCACCGATGCAC
1 TGTATCGATGCAC
524791 CAAGACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
TGTATCGATGCACTATGAGTG
Found at i:524831 original size:20 final size:20
Alignment explanation
Indices: 524806--524858 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
524796 CAAATTTGAA
524806 GGTGCATCGATGCAGTAAGG
1 GGTGCATCGATGCAGTAAGG
*
524826 GGTGCATCGATACAGTAAGG
1 GGTGCATCGATGCAGTAAGG
*
524846 GGTGCATTGATGC
1 GGTGCATCGATGC
524859 TCAATATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.23
Consensus pattern (20 bp):
GGTGCATCGATGCAGTAAGG
Found at i:525902 original size:2 final size:2
Alignment explanation
Indices: 525889--525934 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
525879 AATATGTATG
525889 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
525932 TA T
1 TA T
525935 TATGTTTGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:527669 original size:20 final size:20
Alignment explanation
Indices: 527619--527675 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
527609 TAAAAATCAT
*
527619 AAAATATTAT-AATTTCATTA
1 AAAATATTATAAATTT-ATAA
*
527639 AAAAT-TT-TAAAATTATAA
1 AAAATATTATAAATTTATAA
527657 AAAATATTATAAATTTATA
1 AAAATATTATAAATTTATA
527676 TAAATGTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 9 0.29
19 8 0.26
20 14 0.45
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATATTATAAATTTATAA
Found at i:527994 original size:16 final size:17
Alignment explanation
Indices: 527968--528024 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
527958 TTAAGAAAAT
*
527968 TTAAGAATTATTAGAA-A
1 TTAA-AATTATTAAAACA
527985 TTAAAATTATTAAAACA
1 TTAAAATTATTAAAACA
* * *
528002 TAAAAAATATTATAACA
1 TTAAAATTATTAAAACA
528019 TTAAAA
1 TTAAAA
528025 AATTACTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 10 0.29
17 24 0.71
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (17 bp):
TTAAAATTATTAAAACA
Found at i:528007 original size:17 final size:17
Alignment explanation
Indices: 527973--528035 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
527963 AAAATTTAAG
* *
527973 AATTATTAGAA-ATTAA
1 AATTATTAAAACATAAA
527989 AATTATTAAAACATAAA
1 AATTATTAAAACATAAA
* *
528006 AAATATTATAACATTAAAA
1 AATTATTAAAACA-T-AAA
*
528025 AATTACTAAAA
1 AATTATTAAAA
528036 AATATACATT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 10 0.27
17 15 0.41
18 1 0.03
19 11 0.30
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (17 bp):
AATTATTAAAACATAAA
Found at i:530153 original size:20 final size:20
Alignment explanation
Indices: 530128--530167 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
530118 ATAGTTTACC
530128 CTAAATTTTATATAATGCAA
1 CTAAATTTTATATAATGCAA
530148 CTAAATTTTATATAATGCAA
1 CTAAATTTTATATAATGCAA
530168 ATTATCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
CTAAATTTTATATAATGCAA
Found at i:536362 original size:23 final size:23
Alignment explanation
Indices: 536336--536380 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
536326 CACCACAGCT
*
536336 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
536359 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
536381 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:536618 original size:149 final size:149
Alignment explanation
Indices: 536359--536662 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
536349 CGAAGTGCCC
*
536359 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
536424 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
536489 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
536508 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
536573 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
536638 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
536657 CGTAGA
1 CGTAGA
536663 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:537491 original size:18 final size:18
Alignment explanation
Indices: 537470--537504 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
537460 TCTCATCTAG
537470 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
537488 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
537505 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:538112 original size:21 final size:21
Alignment explanation
Indices: 538088--538132 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
538078 TCTTGTTCGT
* *
538088 TTGAAAGGGTATCGGTTCCCC
1 TTGAAAGGGTACCGATTCCCC
*
538109 TTGAATGGGTACCGATTCCCC
1 TTGAAAGGGTACCGATTCCCC
538130 TTG
1 TTG
538133 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAAGGGTACCGATTCCCC
Found at i:541290 original size:23 final size:23
Alignment explanation
Indices: 541264--541308 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
541254 CACCACAGCT
*
541264 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
541287 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
541309 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:541546 original size:149 final size:149
Alignment explanation
Indices: 541287--541590 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
541277 CGAAGTGCCC
*
541287 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
541352 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
541417 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
541436 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
541501 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
541566 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
541585 CGTAGA
1 CGTAGA
541591 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:542418 original size:18 final size:18
Alignment explanation
Indices: 542397--542431 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
542387 TCCCATCTAG
542397 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
542415 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
542432 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:543039 original size:21 final size:21
Alignment explanation
Indices: 543015--543059 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
543005 TCTTGTTCGT
* *
543015 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
543036 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
543057 TTG
1 TTG
543060 TCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:550123 original size:14 final size:14
Alignment explanation
Indices: 550104--550138 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
550094 CGGTTCTGGC
550104 CGGTTCACTAATAG
1 CGGTTCACTAATAG
550118 CGGTTCACTAATAG
1 CGGTTCACTAATAG
550132 CGGTTCA
1 CGGTTCA
550139 ACCGGTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (14 bp):
CGGTTCACTAATAG
Found at i:551003 original size:2 final size:2
Alignment explanation
Indices: 550996--551021 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
550986 ATTTAAAGAT
550996 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
551022 GGGTAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:551291 original size:35 final size:35
Alignment explanation
Indices: 551245--551356 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
551235 AAAACAATCC
* * *
551245 TCAATTTCATTCTAACCCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
551280 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * *
551315 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
551350 TTAATTT
1 TCAATTT
551357 AAGGGTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:552730 original size:35 final size:35
Alignment explanation
Indices: 552690--552799 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 35
552680 TCTAAACCTT
* * *
552690 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
* *
552725 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATA
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
* * *
552760 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
552795 AAATT
1 AAATT
552800 TAGGAATGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
Found at i:553271 original size:31 final size:30
Alignment explanation
Indices: 553230--553310 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 30
553220 AATTTTAAAA
**
553230 TATTATATTTTAATCACTTATTTTATTGATT
1 TATTATATTTTAATCACTTACATTATTGA-T
* * *
553261 TATTAAATTTTAATTATTTACATTATTGAT
1 TATTATATTTTAATCACTTACATTATTGAT
553291 TATTATATTTTAATCACTTA
1 TATTATATTTTAATCACTTA
553311 ACTGTTAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 18 0.43
31 24 0.57
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (30 bp):
TATTATATTTTAATCACTTACATTATTGAT
Found at i:554798 original size:30 final size:30
Alignment explanation
Indices: 554748--554837 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
554738 TTTGATCGAA
* *
554748 TTTAGGGATTAAATTGATATTTTATATAAAG
1 TTTAGGG-TCAAAATGATATTTTATATAAAG
* *
554779 TTTAGGGTCAAAATGATATTTTATCTGAAG
1 TTTAGGGTCAAAATGATATTTTATATAAAG
* * * *
554809 TTCAAGGTC-AAATTAGTATTCTATATAAA
1 TTTAGGGTCAAAATGA-TATTTTATATAAA
554838 ATTCAGGGGT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 5 0.10
30 36 0.75
31 7 0.15
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (30 bp):
TTTAGGGTCAAAATGATATTTTATATAAAG
Found at i:555026 original size:30 final size:31
Alignment explanation
Indices: 554990--555066 Score: 129
Period size: 30 Copynumber: 2.5 Consensus size: 31
554980 TTTAAGTCCC
*
554990 TAACATGATTGAGGGTTTCATTC-AAAAAAA
1 TAACATGGTTGAGGGTTTCATTCAAAAAAAA
555020 TAACATGGTTGAGGGTTTCATTCAAAAAAAAA
1 TAACATGGTTGAGGGTTTCATTC-AAAAAAAA
555052 TAACATGGTTGAGGG
1 TAACATGGTTGAGGG
555067 ATTAGAATTG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 22 0.50
32 22 0.50
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (31 bp):
TAACATGGTTGAGGGTTTCATTCAAAAAAAA
Found at i:556241 original size:2 final size:2
Alignment explanation
Indices: 556234--556265 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
556224 CAAGCAACTC
556234 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
556266 CATTCACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:573576 original size:12 final size:12
Alignment explanation
Indices: 573559--573601 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
573549 GAAGGTTGGG
573559 AGAAAAGAAAGA
1 AGAAAAGAAAGA
573571 AGAAAAGATAAGA
1 AGAAAAGA-AAGA
573584 GAGAAAATAGAAAGA
1 -AG-AAA-AGAAAGA
573599 AGA
1 AGA
573602 GAAAAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.30
13 5 0.19
14 4 0.15
15 7 0.26
16 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (12 bp):
AGAAAAGAAAGA
Found at i:577814 original size:2 final size:2
Alignment explanation
Indices: 577807--577860 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
577797 TTCAATTGTT
577807 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
577849 TA TA TA TA TA TA
1 TA TA TA TA TA TA
577861 CCTTTGACAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:583687 original size:17 final size:18
Alignment explanation
Indices: 583650--583688 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
583640 ATATTGTGTA
*
583650 TTTAATTTATTTAAGTAT
1 TTTAAGTTATTTAAGTAT
583668 TTTAAGTTATTTAA-TAT
1 TTTAAGTTATTTAAGTAT
583685 TTTA
1 TTTA
583689 CTTATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTAAGTTATTTAAGTAT
Found at i:584019 original size:18 final size:18
Alignment explanation
Indices: 583981--584018 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
583971 ATATTGTGTA
*
583981 TTTAATTTATTTAAGTAT
1 TTTAAGTTATTTAAGTAT
583999 TTTAAGTTATTTAA-TAT
1 TTTAAGTTATTTAAGTAT
584016 TTT
1 TTT
584019 TCTTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTAAGTTATTTAAGTAT
Found at i:584142 original size:331 final size:330
Alignment explanation
Indices: 583541--584204 Score: 1283
Period size: 331 Copynumber: 2.0 Consensus size: 330
583531 CCTTTCTATA
583541 AATACCCTCATCCTCAATCACTTTCATCACACCAAATTCTCTCAATTTCTCTCAAATACTCTTAT
1 AATACCCTCATCCTCAATCACTTTCATCACACCAAATTCTCTCAATTTCTCTCAAATACTCTTAT
583606 ATTCTCCGTTTAAGGTATATTTTATTATATTTTAATATTGTGTATTTAATTTATTTAAGTATTTT
66 ATTCTCCGTTTAAGGTATATTTTATTATATTTTAATATTGTGTATTTAATTTATTTAAGTATTTT
*
583671 AAGTTATTTAATATTTTACTTATATAATTTTTTTTGCAGAAATGTAATGGAAGACGGTCTACTTC
131 AAGTTATTTAATATTTTACTTATATAATTTTTTTTGCAGAAATATAATGGAAGACGGTCTACTTC
*
583736 GCTTGGATAGAAATTATATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTA
196 GCTTGGATAGAAATCATATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTA
583801 ATTTAAATTATTAGTAATAATTTGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAATT
261 ATTTAAATTATTAGTAATAATTTGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAATT
583866 TTTGT
326 TTTGT
583871 AATACCCTCATCCTCAATCACTTTCATCACACCAAATTCTCTCAATTTCTCTCAAATACTCTTAT
1 AATACCCTCATCCTCAATCACTTTCATCACACCAAATTCTCTCAATTTCTCTCAAATACTCTTAT
*
583936 ATTCTCTGTTTAAGGTATATTTTATTATATTTTTAATATTGTGTATTTAATTTATTTAAGTATTT
66 ATTCTCCGTTTAAGGTATATTTTATTATA-TTTTAATATTGTGTATTTAATTTATTTAAGTATTT
*
584001 TAAGTTATTTAATATTTTTCTTATATAATTTTTTTTGCAGAAATATAATGGAAGACGGTCTACTT
130 TAAGTTATTTAATATTTTACTTATATAATTTTTTTTGCAGAAATATAATGGAAGACGGTCTACTT
584066 CGCTTGGATAGAAATCATATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTT
195 CGCTTGGATAGAAATCATATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTT
584131 AATTTAAATTATTAGTAATAATTTGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAT
260 AATTTAAATTATTAGTAATAATTTGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAT
584196 TTTTGT
325 TTTTGT
584202 AAT
1 AAT
584205 TATTTATTTT
Statistics
Matches: 329, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
330 93 0.28
331 236 0.72
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (330 bp):
AATACCCTCATCCTCAATCACTTTCATCACACCAAATTCTCTCAATTTCTCTCAAATACTCTTAT
ATTCTCCGTTTAAGGTATATTTTATTATATTTTAATATTGTGTATTTAATTTATTTAAGTATTTT
AAGTTATTTAATATTTTACTTATATAATTTTTTTTGCAGAAATATAATGGAAGACGGTCTACTTC
GCTTGGATAGAAATCATATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTA
ATTTAAATTATTAGTAATAATTTGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAATT
TTTGT
Found at i:586274 original size:35 final size:33
Alignment explanation
Indices: 586235--586319 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
586225 GTATTTCAGT
586235 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
586270 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
586305 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
586320 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:589979 original size:49 final size:51
Alignment explanation
Indices: 589918--590029 Score: 149
Period size: 53 Copynumber: 2.2 Consensus size: 51
589908 GGTAGTTGCA
* *
589918 CCGCGCCT-TATATAATTATATC-AG-TTAAAGGTATGGCGCGGCCCCTGCC
1 CCGCG-CTATATATAATTATATCAAGATTAAAGGTAAGGCGCGGCCCCTGAC
*
589967 CCGCGCTATATATAATTATGTCAGAGATTTAAAGGTAAGGCGCGGCCCCTGAC
1 CCGCGCTATATATAATTATATCA-AGA-TTAAAGGTAAGGCGCGGCCCCTGAC
590020 CCGCGCTATA
1 CCGCGCTATA
590030 CCCTACGTGG
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
48 2 0.04
49 18 0.33
51 2 0.04
53 33 0.60
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (51 bp):
CCGCGCTATATATAATTATATCAAGATTAAAGGTAAGGCGCGGCCCCTGAC
Found at i:591552 original size:35 final size:34
Alignment explanation
Indices: 591506--591617 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
591496 AAAACAATCC
*
591506 TCAATTTTATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTTATTCTAAACC-CAAATTCCAAAATAAT
*
591541 TCAATTTTATTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTTTATTCTAAACCC-AAATTCCAAAATAAT
** * *
591576 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTTATTCT-AAACCCAAATTCCAAAATAAT
*
591611 TTAATTT
1 TCAATTT
591618 CTGTCTTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 61 0.90
36 6 0.09
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (34 bp):
TCAATTTTATTCTAAACCCAAATTCCAAAATAAT
Found at i:592723 original size:35 final size:33
Alignment explanation
Indices: 592675--592786 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 33
592665 ATTCCTCCTT
*
592675 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTT-GAATTTGGG-TTTAGAATG
*
592710 TAATTGAATTATTTTGAAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTG-AATTT-GGGTTTAGAATG
* *
592745 AAATTGAATTACTTTGGAATTTGGGGTTTATAATG
1 AAATTGAATTA-TTTTGAATTT-GGGTTTAGAATG
592780 AAATTGA
1 AAATTGA
592787 GGAATGTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
34 1 0.01
35 60 0.88
36 7 0.10
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.43
Consensus pattern (33 bp):
AAATTGAATTATTTTGAATTTGGGTTTAGAATG
Found at i:596525 original size:2 final size:2
Alignment explanation
Indices: 596520--596553 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
596510 AAATTGTAAG
596520 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
596554 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:596577 original size:44 final size:45
Alignment explanation
Indices: 596525--596615 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 45
596515 GTAAGATATA
* *
596525 TATATATATATATATATATATATATATATTTAAATTTAAAT-TAAATAG
1 TATATA-ATAT-TATAAATA-AT-TAAATTTAAATTTAAATATAAATAG
596573 TATATAATATTATAAATAATTAAATTTAAATTTAAATATAAAT
1 TATATAATATTATAAATAATTAAATTTAAATTTAAATATAAAT
596616 TGAAATAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 16 0.40
45 7 0.17
46 7 0.17
47 4 0.10
48 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (45 bp):
TATATAATATTATAAATAATTAAATTTAAATTTAAATATAAATAG
Found at i:596596 original size:38 final size:41
Alignment explanation
Indices: 596533--596610 Score: 117
Period size: 38 Copynumber: 2.0 Consensus size: 41
596523 TATATATATA
* *
596533 TATATATATATATATATATATTTAAATTTAAA-TTAAATAG
1 TATATATATATATATAAATAATTAAATTTAAATTTAAATAG
596573 TATATA-ATAT-TATAAATAATTAAATTTAAATTTAAATA
1 TATATATATATATATAAATAATTAAATTTAAATTTAAATA
596611 TAAATTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 18 0.51
39 11 0.31
40 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (41 bp):
TATATATATATATATAAATAATTAAATTTAAATTTAAATAG
Found at i:596903 original size:21 final size:21
Alignment explanation
Indices: 596874--596926 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
596864 ATTCTGACTA
596874 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
596895 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
596916 TCGCAATGCGA
1 TCGCATTGCGA
596927 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:596996 original size:21 final size:20
Alignment explanation
Indices: 596916--597008 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
596906 TTTTCCTAAT
596916 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
596936 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
596957 TCGCATTGCGATTACGTAAAA
1 TCGCAATGCGAATACGT-AAA
*
596978 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
596998 TCACAATGCGA
1 TCGCAATGCGA
597009 TTTACATAGC
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:596999 original size:41 final size:41
Alignment explanation
Indices: 596916--597010 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
596906 TTTTCCTAAT
* *
596916 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATATGGAAAA
* * *
596957 TCGCATTGCGATTACGTAAAATCGCAATGCGAATAT-GTAAA
1 TCGCAATGCGATTACGT-AAATCGCAACGCGAATATGGAAAA
*
596998 TCACAATGCGATT
1 TCGCAATGCGATT
597011 TACATAGCGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 30 0.65
42 16 0.35
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (41 bp):
TCGCAATGCGATTACGTAAATCGCAACGCGAATATGGAAAA
Found at i:597605 original size:20 final size:20
Alignment explanation
Indices: 597580--597628 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
597570 CAACGAGTGA
597580 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
597600 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
597620 ATCGCAACG
1 ATCGCAACG
597629 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:597711 original size:20 final size:20
Alignment explanation
Indices: 597641--597727 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
597631 AGAATCGCAA
*
597641 TGCGATTTTTATTTT-GCGT
1 TGCGATTTTCATTTTCGCGT
** **
597660 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
597680 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
597700 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
597720 TGCGATTT
1 TGCGATTT
597728 AAAGTTTCAG
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 10 0.18
20 47 0.82
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:597735 original size:20 final size:20
Alignment explanation
Indices: 597692--597735 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
597682 CGATAGTCAT
** *
597692 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
597712 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
597732 TTTC
1 TTTC
597736 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:599606 original size:20 final size:20
Alignment explanation
Indices: 599581--599675 Score: 139
Period size: 20 Copynumber: 5.0 Consensus size: 20
599571 AGAATAGTTT
599581 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
599601 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
599621 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
599637 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
599655 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
599675 A
1 A
599676 TTGCGATTCT
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
14 7 0.10
16 4 0.06
17 4 0.06
18 4 0.06
20 48 0.72
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:599715 original size:20 final size:20
Alignment explanation
Indices: 599688--599837 Score: 170
Period size: 20 Copynumber: 7.8 Consensus size: 20
599678 GCGATTCTCT
**
599688 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
599708 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
**
599728 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
* *
599747 CATTGCGAT--TC----TCT
1 CGTTGCGATAGTCATTTTCG
599761 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
599781 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCG
599801 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
599821 CGTTGCTATAGTCATTT
1 CGTTGCGATAGTCATTT
599838 GCAGATTCTA
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
14 10 0.09
16 2 0.02
17 2 0.02
19 13 0.12
20 84 0.76
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:599816 original size:73 final size:74
Alignment explanation
Indices: 599675--599826 Score: 234
Period size: 73 Copynumber: 2.1 Consensus size: 74
599665 TGCGAAAATG
* **
599675 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGTTGCGATTTT
1 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCACGTTGCGATAGT
599740 CA-TTTCGC
66 CATTTTCGC
** *
599748 ATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCACGTTGCGATAGT
1 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCACGTTGCGATAGT
599813 CATTTTCGC
66 CATTTTCGC
*
599822 GTTGC
1 ATTGC
599827 TATAGTCATT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 61 0.86
74 10 0.14
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (74 bp):
ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCACGTTGCGATAGT
CATTTTCGC
Found at i:600404 original size:21 final size:20
Alignment explanation
Indices: 600313--600411 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
600303 GACTCACCTG
600313 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
600333 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGG-CCCTC
** *
600355 TCATCCCTCAAGAGTCTCCTC
1 TCATCGTTCAAGAGGC-CCTC
* * *
600376 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
600397 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
600412 TCTCTCCCAA
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
20 3 0.05
21 51 0.88
22 1 0.02
23 3 0.05
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:600410 original size:42 final size:43
Alignment explanation
Indices: 600310--600420 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 43
600300 CCCGACTCAC
* * * *
600310 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
* **
600352 CTATCATCCCTCAAGA-GTCTCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
*
600394 CTGTCATCGTTGAAGAGGTCT-CTCCCA
1 CTGTCATCGTTCAAGAGGTCTCCTCCCA
600421 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 5 0.09
42 47 0.84
43 4 0.07
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
Found at i:601795 original size:14 final size:14
Alignment explanation
Indices: 601776--601811 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
601766 ATTGTTTAAT
601776 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
601790 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
601804 TGATTTGT
1 TGATTTGT
601812 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:601963 original size:33 final size:33
Alignment explanation
Indices: 601913--602007 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
601903 AAAACAGACT
* ** *
601913 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
601947 ATCGCAATGCGAAATGAAAATCGCAACGGGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
601980 ATCGCAATGCGAAAATAAAAATCGCAAC
1 ATCGCAATGCG-AAATGAAAATCGCAAC
602008 ACGAAACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:602039 original size:19 final size:19
Alignment explanation
Indices: 602017--602104 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
602007 CACGAAACTA
* *
602017 ATTTCGCGTTGTGATTTTC
1 ATTTCGCATTGCGATTTTC
602036 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
* *
602054 A---CCCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
602070 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
602089 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
602105 CTCTCATTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.14
16 4 0.07
18 4 0.07
19 30 0.53
20 11 0.19
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:602115 original size:52 final size:50
Alignment explanation
Indices: 602017--602155 Score: 152
Period size: 52 Copynumber: 2.7 Consensus size: 50
602007 CACGAAACTA
* * *
602017 ATTTCGCGTTGTGATTTTCATTTTCGCATTGCGATTCACCCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTCA-TTTCGCATTGCGATTCACCCATTGCGA--GTC
* * *
602070 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGAGTC
1 ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCACCCATTGCGAGTC
** *
602120 ATTTCCGCGTTGCGATAGTCAATTCCGCATTGCGAT
1 ATTT-CGCGTTGCGATTTTC-ATTTCGCATTGCGAT
602156 AGTCATTTCC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 6 0.08
51 12 0.16
52 38 0.51
53 18 0.24
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (50 bp):
ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCACCCATTGCGAGTC
Found at i:602145 original size:20 final size:20
Alignment explanation
Indices: 602116--602195 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
602106 TCTCATTGCG
*
602116 AGTCATTTCCGCGTTGCGAT
1 AGTCAATTCCGCGTTGCGAT
*
602136 AGTCAATTCCGCATTGCGAT
1 AGTCAATTCCGCGTTGCGAT
* *
602156 AGTCATTTCCGTGTTGCGAT
1 AGTCAATTCCGCGTTGCGAT
602176 AGTCATATT-CGCGTTGCGAT
1 AGTCA-ATTCCGCGTTGCGAT
602196 TTCTGCGTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
20 50 0.96
21 2 0.04
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.35
Consensus pattern (20 bp):
AGTCAATTCCGCGTTGCGAT
Found at i:602163 original size:40 final size:40
Alignment explanation
Indices: 602109--602195 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
602099 GCGATTCTCT
602109 CATTGCG--AGTCATTTCCGCGTTGCGATAGTCA-ATTCCG
1 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATT-CG
*
602147 CATTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCG
1 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
*
602187 CGTTGCGAT
1 CATTGCGAT
602196 TTCTGCGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 7 0.16
40 34 0.77
41 3 0.07
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (40 bp):
CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
Found at i:605561 original size:20 final size:20
Alignment explanation
Indices: 605538--605624 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
605528 TAGAATCTCG
605538 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
605558 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
605578 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
*
605599 CTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
605619 TTGCGA
1 TTGCGA
605625 ATTAGGAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.02
20 39 0.71
21 15 0.27
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:605639 original size:21 final size:21
Alignment explanation
Indices: 605614--605666 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
605604 ATTTACGTAT
*
605614 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
605635 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
605656 TCGCAATGCGA
1 TCGCAATGCGA
605667 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:605882 original size:28 final size:29
Alignment explanation
Indices: 605836--605890 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
605826 TTTCTCTTTA
*
605836 AATAATTTAAATTTCTTTT-TATCAATTTG
1 AATAATTTAAAATTCTTTTAT-TCAATTTG
605865 AATAA-TTAAAATTCTTTTATTCAATT
1 AATAATTTAAAATTCTTTTATTCAATT
605891 AGATTCGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (29 bp):
AATAATTTAAAATTCTTTTATTCAATTTG
Found at i:605983 original size:29 final size:29
Alignment explanation
Indices: 605950--606007 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
605940 AATGGATTTG
605950 TAGCGCATTAAAAGAATGCTTAGATATCA
1 TAGCGCATTAAAAGAATGCTTAGATATCA
*
605979 TAGCGCATTAAATGAATGCTTAGATATCA
1 TAGCGCATTAAAAGAATGCTTAGATATCA
606008 CATTGATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (29 bp):
TAGCGCATTAAAAGAATGCTTAGATATCA
Found at i:608692 original size:16 final size:16
Alignment explanation
Indices: 608671--608713 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
608661 AAAAAAGACC
608671 CAAATCCCTAAAAACT
1 CAAATCCCTAAAAACT
608687 CAAATCCCTAAAAACT
1 CAAATCCCTAAAAACT
608703 CAAATCCCTAA
1 CAAATCCCTAA
608714 TCCTAACCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.19
Consensus pattern (16 bp):
CAAATCCCTAAAAACT
Found at i:608878 original size:12 final size:12
Alignment explanation
Indices: 608861--608886 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
608851 ATTTGGTTCA
608861 TCAATTTTATCG
1 TCAATTTTATCG
608873 TCAATTTTATCG
1 TCAATTTTATCG
608885 TC
1 TC
608887 GAGTAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (12 bp):
TCAATTTTATCG
Found at i:609065 original size:29 final size:28
Alignment explanation
Indices: 609009--609095 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 28
608999 ATAGTTGAAA
* * *
609009 TTAAGATTTTC-AATTTTTTGGGTTTTT
1 TTAAGATTTGCAAAGTTTTTAGGTTTTT
609036 TTAAAGATTTGCAAAGTTTTTAGGTTTTT
1 TT-AAGATTTGCAAAGTTTTTAGGTTTTT
* * *
609065 TTAAGATTTTCAAATTTTTTGAGATTTTT
1 TTAAGATTTGCAAAGTTTTT-AGGTTTTT
609094 TT
1 TT
609096 TAATAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.04
28 24 0.47
29 25 0.49
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (28 bp):
TTAAGATTTGCAAAGTTTTTAGGTTTTT
Found at i:609288 original size:2 final size:2
Alignment explanation
Indices: 609281--609317 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
609271 TTAAGCTCTT
609281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
609318 GACTTTAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:615740 original size:22 final size:20
Alignment explanation
Indices: 615692--615740 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
615682 GTTGGTCAAA
615692 TATATATAATTAAAAATATT
1 TATATATAATTAAAAATATT
* * *
615712 AAAATATAATTTAATAATTATT
1 TATATATAA-TTAA-AAATATT
615734 TATATAT
1 TATATAT
615741 TTTATTTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATATAATTAAAAATATT
Found at i:619567 original size:23 final size:23
Alignment explanation
Indices: 619524--619567 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
619514 CACATGATGA
*
619524 ATTTATAATTTTTAAAAAAATTT
1 ATTTATAAATTTTAAAAAAATTT
619547 ATTT-TAAATTTTATAAAAAAT
1 ATTTATAAATTTTA-AAAAAAT
619568 CTGTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTATAAATTTTAAAAAAATTT
Found at i:620680 original size:30 final size:30
Alignment explanation
Indices: 620646--620729 Score: 71
Period size: 36 Copynumber: 2.6 Consensus size: 30
620636 AACTTTTTTT
620646 ATATTTTTAATTTGTAAA-AAAATTATATAA
1 ATATTTTTAATTTGTAAAGAAAA-TATATAA
*
620676 ATATTATGAATTTAATTTTTTAAAGAAAATATATAA
1 ATA-T-T---TTTAA-TTTGTAAAGAAAATATATAA
*
620712 ATATTTTACAATTTGTAA
1 ATATTTT-TAATTTGTAA
620730 TATTATACAA
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
30 3 0.07
31 9 0.21
32 3 0.07
34 1 0.02
35 6 0.14
36 17 0.40
37 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (30 bp):
ATATTTTTAATTTGTAAAGAAAATATATAA
Found at i:620725 original size:37 final size:35
Alignment explanation
Indices: 620651--620725 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
620641 TTTTTATATT
*
620651 TTTAATTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTGTAAAAAAATTATATAAATATTATCAA
* *
620686 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTGTAAA-AAAATTATATAAATATTAT-CAA
620723 TTT
1 TTT
620726 GTAATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 20 0.59
37 9 0.26
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (35 bp):
TTTAATTTGTAAAAAAATTATATAAATATTATCAA
Found at i:636864 original size:26 final size:27
Alignment explanation
Indices: 636819--636870 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
636809 ATTATTTGAT
* *
636819 TAAATTGATATAATTTAATTAAATATC
1 TAAATCGATATAAATTAATTAAATATC
*
636846 TAAATCGA-ATAAATTAATTATATAT
1 TAAATCGATATAAATTAATTAAATAT
636871 AATTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
TAAATCGATATAAATTAATTAAATATC
Found at i:644462 original size:252 final size:254
Alignment explanation
Indices: 644012--644520 Score: 914
Period size: 252 Copynumber: 2.0 Consensus size: 254
644002 TTTAACAACT
644012 TATATTTTTAATATTAAAGTAAAATACATAAAAGTTTATTGAATATATATTTTTTATAAAAATTT
1 TATATTTTTAATATTAAAGTAAAATACATAAAAGTTTATTGAATATATATTTTTTATAAAAATTT
644077 TACACATAATATATATATATATATATATTATCTTTTCAAAAAAACATAAACATACGTACAATGAT
66 TACACATAATATATATATATATATATATTATCTTTTCAAAAAAACATAAACATACGTACAATGAT
* * *
644142 ATAAATACGTGTTTATTTTTAGGTATCAAGAAATTGAGAGATGTACATATCTACATTGGTATAAG
131 ATAAATACGTGTTTATTTCTAGGTATCAAGAAATTGAGAGATATACATATCTACATTGGTACAAG
*
644207 TATGCGCTTATTTCTTCA-TTTTTTCTTAGTTTTTTCATGCTATATATGAATTGTACAA
196 TATGCGCTTATTTCTTCATTTTTTTCCTAGTTTTTTCATGCTATATATGAATTGTACAA
*
644265 TATATTTTTAATATTAAAGTAAAATACATAAAAGTTTATTGAATATAT-TTTTTTATAAAATTTT
1 TATATTTTTAATATTAAAGTAAAATACATAAAAGTTTATTGAATATATATTTTTTATAAAAATTT
644329 TACACATAATATATATATATATATATATTATCTTTTCAAAAAAACATAAACATACGTACAATGAT
66 TACACATAATATATATATATATATATATTATCTTTTCAAAAAAACATAAACATACGTACAATGAT
* * * *
644394 ATAAATATGTGTTTATTTCTAGGTATCAGGATATTGAGAGATATTCATATCTACATTGGTACAAG
131 ATAAATACGTGTTTATTTCTAGGTATCAAGAAATTGAGAGATATACATATCTACATTGGTACAAG
644459 TATGCGCTTATTTCTTCATTTTTTTTCCTAGTTTTTTCATGCTATATATGAATTGTACAA
196 TATGCGCTTATTTCTTCA-TTTTTTTCCTAGTTTTTTCATGCTATATATGAATTGTACAA
644519 TA
1 TA
644521 AAATATCATA
Statistics
Matches: 245, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
252 156 0.64
253 48 0.20
254 41 0.17
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (254 bp):
TATATTTTTAATATTAAAGTAAAATACATAAAAGTTTATTGAATATATATTTTTTATAAAAATTT
TACACATAATATATATATATATATATATTATCTTTTCAAAAAAACATAAACATACGTACAATGAT
ATAAATACGTGTTTATTTCTAGGTATCAAGAAATTGAGAGATATACATATCTACATTGGTACAAG
TATGCGCTTATTTCTTCATTTTTTTCCTAGTTTTTTCATGCTATATATGAATTGTACAA
Found at i:645687 original size:88 final size:88
Alignment explanation
Indices: 645534--645700 Score: 289
Period size: 88 Copynumber: 1.9 Consensus size: 88
645524 AAAAATCATA
** *
645534 AGTACCTCCAATATCAGTGGATTTTGCATCACTGTACTAAGAACACGAGAGACCGACTTGTTGAT
1 AGTACCTCCAATATCACAGGATTTTGCATCACTGTACTAAGAACACGAGAGACCGACTTGCTGAT
645599 GGTCCCATCTGCATAGAAAGTCC
66 GGTCCCATCTGCATAGAAAGTCC
* *
645622 AGTACCTCCAATATCCCAGGATTTTGCATCACTGTACTAAGTACACGAGAGACCGACTTGCTGAT
1 AGTACCTCCAATATCACAGGATTTTGCATCACTGTACTAAGAACACGAGAGACCGACTTGCTGAT
645687 GGTCCCATCTGCAT
66 GGTCCCATCTGCAT
645701 TAACCCAAGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (88 bp):
AGTACCTCCAATATCACAGGATTTTGCATCACTGTACTAAGAACACGAGAGACCGACTTGCTGAT
GGTCCCATCTGCATAGAAAGTCC
Found at i:653098 original size:6 final size:6
Alignment explanation
Indices: 653087--653113 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
653077 TCCCGCCCCC
653087 CTCCCT CTCCCT CTCCCT CTCCCT CTC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTC
653114 ATTTTCACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:659283 original size:15 final size:15
Alignment explanation
Indices: 659247--659294 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
659237 TATAAAATTT
**
659247 TAAAAAATATAAATT
1 TAAAAAATATAAAAA
* *
659262 TATAAAATTTTAAAAA
1 TA-AAAAATATAAAAA
659278 TAAAAAATATAAAAA
1 TAAAAAATATAAAAA
659293 TA
1 TA
659295 TCTAAAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAAATATAAAAA
Found at i:659285 original size:25 final size:25
Alignment explanation
Indices: 659233--659291 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
659223 TAATGGTATC
*
659233 AATTTATAAAATTTTAAAAAATATA
1 AATTTATAAAATTTTAAAAAATAAA
659258 AATTTATAAAATTTT-AAAAATAAA
1 AATTTATAAAATTTTAAAAAATAAA
*
659282 AA-ATATAAAA
1 AATTTATAAAA
659292 ATATCTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 10 0.31
25 15 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATTTATAAAATTTTAAAAAATAAA
Found at i:659293 original size:8 final size:8
Alignment explanation
Indices: 659249--659295 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
659239 TAAAATTTTA
659249 AAAAATAT
1 AAAAATAT
**
659257 AAATTTAT
1 AAAAATAT
* *
659265 AAAATTTT
1 AAAAATAT
659273 AAAAATA-
1 AAAAATAT
659280 AAAAATAT
1 AAAAATAT
659288 AAAAATAT
1 AAAAATAT
659296 CTAAAAACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 7 0.22
8 25 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AAAAATAT
Found at i:661250 original size:18 final size:19
Alignment explanation
Indices: 661227--661269 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
661217 CAGCAGCACA
*
661227 TAACTGCTC-TTAACAAGC
1 TAACTGCTCGTTAACAAAC
661245 TAACTGCTCGTTTAACAAAC
1 TAACTGCTCG-TTAACAAAC
661265 TAACT
1 TAACT
661270 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (19 bp):
TAACTGCTCGTTAACAAAC
Found at i:663279 original size:63 final size:63
Alignment explanation
Indices: 663175--663295 Score: 174
Period size: 63 Copynumber: 1.9 Consensus size: 63
663165 TATTAACCAT
*
663175 CTCGTCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
1 CTCGGCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
* * *
663238 CTCGGCTTCATTATGTACTT-CTGCATTAC-CATCTTCTTCATGCACGGTGGTGGTATTT
1 CTCGGCTTCATTATG-AATTGCTGCATTACTCA-CTTCTTCATGCACGGTGATGATATTT
663296 AGTAACTGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
62 2 0.04
63 47 0.90
64 3 0.06
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.40
Consensus pattern (63 bp):
CTCGGCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
Found at i:665878 original size:18 final size:19
Alignment explanation
Indices: 665855--665897 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
665845 CAGCAGCACA
*
665855 TAACTGCT-TTTAACAAGC
1 TAACTGCTCTTTAACAAAC
665873 TAACTGCTCGTTTAACAAAC
1 TAACTGCTC-TTTAACAAAC
665893 TAACT
1 TAACT
665898 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (19 bp):
TAACTGCTCTTTAACAAAC
Found at i:669025 original size:2 final size:2
Alignment explanation
Indices: 669018--669057 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
669008 TACCATAATA
669018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
669058 ATTATAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:669411 original size:29 final size:29
Alignment explanation
Indices: 669369--669426 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
669359 CAAAGCATGC
669369 ATCCCACCCACCAGCTGTCCATCGCCACT
1 ATCCCACCCACCAGCTGTCCATCGCCACT
669398 ATCCCACCCACCAGCTGTCCATCGCCACT
1 ATCCCACCCACCAGCTGTCCATCGCCACT
669427 GTCGCCCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.52, G:0.10, T:0.17
Consensus pattern (29 bp):
ATCCCACCCACCAGCTGTCCATCGCCACT
Found at i:671353 original size:59 final size:60
Alignment explanation
Indices: 671242--671429 Score: 193
Period size: 59 Copynumber: 3.2 Consensus size: 60
671232 TATTTGGATG
* * * * * *
671242 AATTTGAGAATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTAAAATGAGAGTCAT
1 AATTTGAGGATGAAAATAGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
* * * * * *
671302 ATTTTGAGGAT-AAAATGGAATCTTCAAAAGTTTAAGGACTAGTATAGAATGA-AGTCAT
1 AATTTGAGGATGAAAATAGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
* * * * *
671360 AGTCTG-GGAATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAATCAG
1 AATTTGAGG-ATGAAAATAGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
671420 AATTTGAGGA
1 AATTTGAGGA
671430 CATATGACAC
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
57 2 0.02
58 12 0.12
59 68 0.67
60 18 0.18
61 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.29
Consensus pattern (60 bp):
AATTTGAGGATGAAAATAGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
Found at i:672631 original size:2 final size:2
Alignment explanation
Indices: 672594--672621 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
672584 TCCCTTTTTA
672594 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
672622 TAAGATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:679675 original size:38 final size:37
Alignment explanation
Indices: 679632--679707 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 37
679622 ATTTGGGGAC
679632 TTTGCAACTCACTTTTTCTGCCATCTATGTGGGGAGAT
1 TTTGCAACTCACTTTTTCTGCCATCTATGT-GGGAGAT
679670 TTTGCAACTCACTTTTTCTGCCATCTATGTGGGAGAT
1 TTTGCAACTCACTTTTTCTGCCATCTATGTGGGAGAT
679707 T
1 T
679708 CGAGAGGGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 8 0.21
38 30 0.79
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (37 bp):
TTTGCAACTCACTTTTTCTGCCATCTATGTGGGAGAT
Found at i:694027 original size:149 final size:151
Alignment explanation
Indices: 693745--694198 Score: 569
Period size: 149 Copynumber: 3.0 Consensus size: 151
693735 CTACATGACC
* * * * ***
693745 GGAATTGGCTCTCATTATTCTGGTAAACCAATGTTTGAAAAAGATGTCATAGCTGATGGAGAAGG
1 GGAATTGGTTCCCATTATCCTGGTAAAGCAATAAGTGAAAAAGATGTCATAGCTGATGGAGAAGG
* * * * ** *
693810 CTCTAGATA-CAAAACCAAAGTAGAGCATGGTAAGGTAGTTTCAGATTTCTTGATGCCACTGGAG
66 CTCTAGGTATCAGAACCAATGTAGAGCAGGGTGGGGTAGTTTCAGATTTGTTGATGCCACTGGAG
*
693874 ATGGGAACGCAATCCCCGAGT
131 ATGGGAATGCAATCCCCGAGT
* * *
693895 GGAATTGGTT-CCATTATCCTGGTAAAGTAATACGTGAAAAAGATGTCATAGCTGATAGAGAAGG
1 GGAATTGGTTCCCATTATCCTGGTAAAGCAATAAGTGAAAAAGATGTCATAGCTGATGGAGAAGG
* * * * * ** * *
693959 CTCTAGGTATC-GAAGCATTGTAGAGCAGGGTGGGGTAGTTTTAGGTTTGATGGCGCCAGTGAAG
66 CTCTAGGTATCAGAACCAATGTAGAGCAGGGTGGGGTAGTTTCAGATTTGTTGATGCCACTGGAG
*
694023 ATGGGAATGCAATCCTCGAGT
131 ATGGGAATGCAATCCCCGAGT
* *
694044 GGAATTGGTTCCCATTATCGTGGTAAAGCAATAAGTGAAAAAAATGTCATAGCTGATGGAGAAGG
1 GGAATTGGTTCCCATTATCCTGGTAAAGCAATAAGTGAAAAAGATGTCATAGCTGATGGAGAAGG
*
694109 CTCTA-G-ATGCAGAACCAATGTAGAGCAGGGTGGGGTAGTTTCAGATGTGTTGATGCCACTGGA
66 CTCTAGGTAT-CAGAACCAATGTAGAGCAGGGTGGGGTAGTTTCAGATTTGTTGATGCCACTGGA
*
694172 GATGGGAATGCAATCCCCTAGT
130 GATGGGAATGCAATCCCCGAGT
694194 -GAATT
1 GGAATT
694199 CTGTTTTCAG
Statistics
Matches: 256, Mismatches: 44, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
148 2 0.01
149 128 0.50
150 126 0.49
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.26
Consensus pattern (151 bp):
GGAATTGGTTCCCATTATCCTGGTAAAGCAATAAGTGAAAAAGATGTCATAGCTGATGGAGAAGG
CTCTAGGTATCAGAACCAATGTAGAGCAGGGTGGGGTAGTTTCAGATTTGTTGATGCCACTGGAG
ATGGGAATGCAATCCCCGAGT
Found at i:695138 original size:30 final size:30
Alignment explanation
Indices: 695102--695158 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
695092 CTCTAAAATT
695102 TAATCTAATGGCCTAGTTTAATAAAAAAAA
1 TAATCTAATGGCCTAGTTTAATAAAAAAAA
695132 TAATCTAATGGCCTAGTTTAATAAAAA
1 TAATCTAATGGCCTAGTTTAATAAAAA
695159 TATGGGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (30 bp):
TAATCTAATGGCCTAGTTTAATAAAAAAAA
Found at i:699936 original size:26 final size:26
Alignment explanation
Indices: 699903--699954 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
699893 GAGCGTACGA
699903 GGGAATGTCCTTAAAGCTACAGGGAG
1 GGGAATGTCCTTAAAGCTACAGGGAG
699929 GGGAATGTCCTTAAAGCTACAGGGAG
1 GGGAATGTCCTTAAAGCTACAGGGAG
699955 TCGCACTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (26 bp):
GGGAATGTCCTTAAAGCTACAGGGAG
Found at i:704637 original size:164 final size:162
Alignment explanation
Indices: 704347--704672 Score: 568
Period size: 165 Copynumber: 2.0 Consensus size: 162
704337 CTTGCACCCA
704347 ACTAGGAATGATTAGGGTAGTACCCATAGAATATACTGACCTTGATCTTCCCTGTCTAGAAAGGG
1 ACTAGGAATGATTAGGGTAGTACCCATAGAATATACTGACCTTGATCTTCCCTGTCTAGAAAGGG
704412 CACAGCAACCACATTGGATTACCCTTCCTATACTGAATAGAATAGTCCAGTCCCAATAATTTAGT
66 CACAGCAACCACATTGGATTACCCTTCC-ATACTGAATAGAATAGTCCAGTCCCAATAATTTAGT
704477 CAACCC-TTCTTCTGGATGGCAGTAGTTAATTC
130 CAACCCTTTCTTCTGGATGGCAGTAGTTAATTC
*
704509 ACTAGGAATGATTAGGGTAGTACCCATAGCCATATACTGACCTTGATCTTCCCACTGTCTAGAAA
1 ACTAGGAATGATTAGGGTAGTACCCATAG-AATATACTGACCTTGATCTT-CC-CTGTCTAGAAA
704574 GGGCATCAGCAACCACATTGGACTTACCCTTCC-TA-TGAATAGAATAGTCCAGTCCCAATAATT
63 GGGCA-CAGCAACCACATTGGA-TTACCCTTCCATACTGAATAGAATAGTCCAGTCCCAATAATT
704637 TAGTCAACCCTTTCTTCTGGATGGCAGTAGTTAATT
126 TAGTCAACCCTTTCTTCTGGATGGCAGTAGTTAATT
704673 TCTGCTCTAA
Statistics
Matches: 157, Mismatches: 1, Indels: 9
0.94 0.01 0.05
Matches are distributed among these distances:
162 29 0.18
163 19 0.12
164 40 0.25
165 43 0.27
166 16 0.10
167 10 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (162 bp):
ACTAGGAATGATTAGGGTAGTACCCATAGAATATACTGACCTTGATCTTCCCTGTCTAGAAAGGG
CACAGCAACCACATTGGATTACCCTTCCATACTGAATAGAATAGTCCAGTCCCAATAATTTAGTC
AACCCTTTCTTCTGGATGGCAGTAGTTAATTC
Found at i:708208 original size:12 final size:12
Alignment explanation
Indices: 708188--708217 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
708178 TCTTCTTCTC
*
708188 CTCCCCGTTCAT
1 CTCCTCGTTCAT
708200 CTCCTCGTTCAT
1 CTCCTCGTTCAT
708212 CTCCTC
1 CTCCTC
708218 CGACTGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.50, G:0.07, T:0.37
Consensus pattern (12 bp):
CTCCTCGTTCAT
Found at i:712379 original size:6 final size:6
Alignment explanation
Indices: 712370--712401 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
712360 ATTTTCTTCC
*
712370 GCCTCT GCCTCT GCCTCT GCCTCT GTCTCT GC
1 GCCTCT GCCTCT GCCTCT GCCTCT GCCTCT GC
712402 TAGGGTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.47, G:0.19, T:0.34
Consensus pattern (6 bp):
GCCTCT
Found at i:712644 original size:17 final size:17
Alignment explanation
Indices: 712617--712655 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
712607 AATTTACAAT
712617 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
712633 TAATTATAAATAATATC
1 TAATTATAAATAATATC
712650 TAATTA
1 TAATTA
712656 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:727655 original size:18 final size:17
Alignment explanation
Indices: 727634--727667 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
727624 ATTTTAATTT
727634 TTTTATATATTTTATATC
1 TTTTATATA-TTTATATC
*
727652 TTTTATGTATTTATAT
1 TTTTATATATTTATAT
727668 TAAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTATATATTTATATC
Found at i:727891 original size:18 final size:18
Alignment explanation
Indices: 727864--727898 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
727854 AGAAGACAAC
727864 ATACACAATCATAAAAAT
1 ATACACAATCATAAAAAT
*
727882 ATACATAATCATAAAAA
1 ATACACAATCATAAAAA
727899 GTGATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (18 bp):
ATACACAATCATAAAAAT
Found at i:728254 original size:11 final size:11
Alignment explanation
Indices: 728198--728254 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
728188 AACAATGAGT
*
728198 AATTAAAACAA
1 AATTAAAATAA
*
728209 AATTAAAATAT
1 AATTAAAATAA
* *
728220 AATCTTAAATAT
1 AAT-TAAAATAA
*
728232 AATTTAAA-AA
1 AATTAAAATAA
728242 AATTAAAATAA
1 AATTAAAATAA
728253 AA
1 AA
728255 ACTAAGTATC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 8 0.21
11 21 0.54
12 10 0.26
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (11 bp):
AATTAAAATAA
Found at i:750267 original size:31 final size:31
Alignment explanation
Indices: 750231--750290 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
750221 AACTTAAAAG
750231 AGTTTTACAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
750262 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
750291 CATACAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:750419 original size:16 final size:16
Alignment explanation
Indices: 750398--750429 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
750388 AGTTTTATAG
750398 AATAAAATTTATAAAT
1 AATAAAATTTATAAAT
750414 AATAAAATTTATAAAT
1 AATAAAATTTATAAAT
750430 GATCATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAAATTTATAAAT
Found at i:752667 original size:31 final size:32
Alignment explanation
Indices: 752621--752714 Score: 106
Period size: 31 Copynumber: 3.0 Consensus size: 32
752611 CTCTGATTGG
*
752621 ATTT-AGGAGTTAAATTGATATTTTATCTAAA
1 ATTTAAGGAGTCAAATTGATATTTTATCTAAA
*
752652 ATTTAAGGA-TCAAATTGATATATTATCT-AA
1 ATTTAAGGAGTCAAATTGATATTTTATCTAAA
* **
752682 ATTTTAGGAGTTTAATT-AGTATTTTATCTAAA
1 ATTTAAGGAGTCAAATTGA-TATTTTATCTAAA
752714 A
1 A
752715 ATTATACATA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
30 11 0.21
31 35 0.66
32 7 0.13
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (32 bp):
ATTTAAGGAGTCAAATTGATATTTTATCTAAA
Found at i:753455 original size:8 final size:8
Alignment explanation
Indices: 753444--753470 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
753434 TCTAGTTTTC
753444 CTCCCTCT
1 CTCCCTCT
753452 CTCCCTCT
1 CTCCCTCT
753460 CTCCCTCT
1 CTCCCTCT
753468 CTC
1 CTC
753471 TTTTGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (8 bp):
CTCCCTCT
Found at i:759485 original size:269 final size:258
Alignment explanation
Indices: 758949--759517 Score: 764
Period size: 260 Copynumber: 2.2 Consensus size: 258
758939 CTTATTTATA
* * *
758949 TATTTAATAAAAATATTTTTTTATTATTTCGGGTCGGATCGGTCGGTTTTCTAATTCATACATTC
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGTCGGATTTCTAATTCATACATTC
* *
759014 GGGTCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGGTCGGTTTTTTAAGTGTGATATTCAGGT
66 GGGTCGGGTTCGGTGAAACTTTATTTTGGTCGGCTCGGT--GTTTTTTAAGTGTGATATTCAGGT
* * *
759079 CAGGTCGAGTTCGGGTTTAGGGTGAAATATACTCGACCCGAAAATATATATAATTTTGCCTTATA
129 CAGGTCGAGTTCGGGTTTAGGGTGAAATAGACTCGACCCGAAAAAATATATAATTTTACCTTATA
* * * *
759144 TATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAATCACTGTTTT
194 TATTTAGGAATAATTACAATAATACCCATATATATATAATTATATTTCAATTAAATCACTGTTTT
* *
759209 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATCGGATTTCTAATTCATATATT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGG-TCGGATTTCTAATTCATACATT
**
759274 CGGGTCGGG-TCGGTGAAACTTTATTTTGGTCGGCTCGGT-TTTTTTAAAGTGTGATATTTGGGT
65 CGGGTCGGGTTCGGTGAAACTTTATTTTGGTCGGCTCGGTGTTTTTT-AAGTGTGATATTCAGGT
* * * * *
759337 CGGGTCGGGTTTGGGTTTAGGGTGAAAAATACCCGACTTGACCCGACCCAAAAAATATATATTTT
129 CAGGTCGAGTTCGGGTTTAGGGTG--AAATA---GACTCGACCCG----AAAAAATATATAATTT
* *
759402 TACCTTATATATTTAGGAATTATTACAATAATACCTATATATATATATATATATATTTCAATTAA
185 TACCTTATATATTTAGGAATAATTACAATAATACCCATATATATATA-AT-TATATTTCAATTAA
*
759467 GTCACTGTTTT
248 ATCACTGTTTT
759478 TATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGT
1 TATTGAATAAAAATA-TTTTTTTATTATTTCGGGTCGGGT
759518 TTCTAATTCA
Statistics
Matches: 270, Mismatches: 25, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
257 6 0.02
258 36 0.13
260 72 0.27
261 29 0.11
263 9 0.03
267 56 0.21
268 2 0.01
269 37 0.14
270 23 0.09
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.41
Consensus pattern (258 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGTCGGATTTCTAATTCATACATTC
GGGTCGGGTTCGGTGAAACTTTATTTTGGTCGGCTCGGTGTTTTTTAAGTGTGATATTCAGGTCA
GGTCGAGTTCGGGTTTAGGGTGAAATAGACTCGACCCGAAAAAATATATAATTTTACCTTATATA
TTTAGGAATAATTACAATAATACCCATATATATATAATTATATTTCAATTAAATCACTGTTTT
Found at i:765078 original size:32 final size:32
Alignment explanation
Indices: 765032--765103 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
765022 ATCACAAAAA
* * *
765032 GTCGAGTCGGGTGAAAGATATATATTTTTTGG
1 GTCGGGTCGGGTGAAAGATATAAAATTTTTGG
* *
765064 GTCGGGTCGGGTGAAGGATGTAAAATTTTTGG
1 GTCGGGTCGGGTGAAAGATATAAAATTTTTGG
*
765096 ATCGGGTC
1 GTCGGGTC
765104 AGGTTGGCCG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.22, C:0.08, G:0.36, T:0.33
Consensus pattern (32 bp):
GTCGGGTCGGGTGAAAGATATAAAATTTTTGG
Found at i:766525 original size:37 final size:38
Alignment explanation
Indices: 766474--766559 Score: 138
Period size: 38 Copynumber: 2.3 Consensus size: 38
766464 TTTTATCTAG
*
766474 GTCGGGTCGAGTTTTTT-AAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGA
* *
766511 GTCGGGTCGGGTTTTTTAAAGTGTGATATTCGGTTCGG
1 GTCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGA
766549 GTCGGGTCGGG
1 GTCGGGTCGGG
766560 ATTAGGGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 16 0.36
38 29 0.64
ACGTcount: A:0.13, C:0.12, G:0.40, T:0.36
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGA
Found at i:767114 original size:18 final size:17
Alignment explanation
Indices: 767077--767123 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
767067 TATGGAATTG
*
767077 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
767094 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
767112 GATTCTAATTCC
1 GATTCCAATTCC
767124 CTCATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:767818 original size:257 final size:249
Alignment explanation
Indices: 767441--767988 Score: 734
Period size: 257 Copynumber: 2.2 Consensus size: 249
767431 TCGGGTAAGG
* *
767441 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGATCGAGTCGGTTTTTTTAATTGTGATATTC
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGAGTCGGTTTTTTTAAGTGTGATATTC
* * * *
767506 GGGTCGGGTCGAGTTCGGGTTTATAGTGAAAAATACCCAACCCAAAAATATATATAATTTTATCT
66 -GAT--GATCGAGTTCGGGTTTAGAGTGAAAAATACCCAACCCAAAAATATATATAATTTTACCT
*
767571 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATA-AT-T-TTTTTCAATTAAGTCAC
128 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATATATATATTTTTCAATTAAGTAAC
* *
767633 TG-TTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTTGGGTCGGATTTCTAATTCATATA
193 TGTTTTTATTG------AAT-A-TTTTTT-TTATTTCGGGTCGGGTCGAATTTCTAATTCATATA
767697 T
249 T
* *
767698 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGT-GGGATCAGTTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGAG-TC-GGTTTTTTTAAGTGTGATAT
* *
767762 TC-AT-ATCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAA-ATATATAATTTT
64 TCGATGATCGAGTTCGGGTTTAGAGTGAAAAATACCC-A----ACCCAAAAATATATATAATTTT
767824 ACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATATATATTTTTCAATTAAG
124 ACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATATATATTTTTCAATTAAG
*
767889 TAATTGTTTTTATTGAATATTTTTTTTATTTCGGGTCGGGTCGAATTTCTAATTCATATAT
189 TAACTGTTTTTATTGAATATTTTTTTTATTTCGGGTCGGGTCGAATTTCTAATTCATATAT
*
767950 TCGAGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCG
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCG
767989 GGTCTCAGAT
Statistics
Matches: 264, Mismatches: 15, Indels: 28
0.86 0.05 0.09
Matches are distributed among these distances:
252 70 0.27
253 34 0.13
254 2 0.01
255 3 0.01
256 3 0.01
257 95 0.36
258 31 0.12
259 1 0.00
260 17 0.06
261 8 0.03
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.41
Consensus pattern (249 bp):
TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGAGTCGGTTTTTTTAAGTGTGATATTC
GATGATCGAGTTCGGGTTTAGAGTGAAAAATACCCAACCCAAAAATATATATAATTTTACCTTAT
ATATTTAGGAATAATTACAATAATACCCCTCTATATATATATATATTTTTCAATTAAGTAACTGT
TTTTATTGAATATTTTTTTTATTTCGGGTCGGGTCGAATTTCTAATTCATATAT
Found at i:771627 original size:32 final size:31
Alignment explanation
Indices: 771591--771667 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
771581 TGGGGCCACG
*
771591 GGGCCTACCTAAGAATACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAAT-CATCTCAGGGCCGCA
** *
771623 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAATCATCTCAGGGCCGCA
*
771654 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
771668 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAATCATCTCAGGGCCGCA
Found at i:778979 original size:297 final size:295
Alignment explanation
Indices: 778432--779026 Score: 1131
Period size: 297 Copynumber: 2.0 Consensus size: 295
778422 TATATAATTT
778432 TATTTTCTTTAAATTTTTTACTTGATATGACAAGTCGTTATACATTATAAATGTCATGTTTTCAC
1 TATTTTCTTTAAATTTTTTACTTGATATGACAAGTCGTTATACATTATAAATGTCATGTTTTCAC
778497 GACAAATTAATGAATAGAAATAAGACAAATCAGCCCACCAACTCTTCAAGTCTCGTTCCATTTTC
66 GACAAATTAATGAATAGAAATAAGACAAATCAGCCCACCAACTCTTCAAGTCTCGTTCCATTTTC
778562 AGGGTTGAGTCTCGGCTGTGTTTGTCTCTCCAGTTTCATGTGTTTCAAACTTTGGTGGTAGGGCA
131 AGGGTTGAGTCTCGGCTGTGTTTGTCTCTCCAGTTTCATGTGTTTCAAACTTTGGTGGTAGGGCA
778627 ATCAAAACTTATCCCATAATTTAGACCTGATATGAATATCATACGATGCCATATATATAATGTTA
196 ATCAAAACTTATCCCATAATTTAGACCTGATATGAATATCATACGATGCCATATATATAATGTTA
778692 T-ATATAATTAATTATTATAAAATTATTAAACCCTA
261 TAATATAATTAATTATTATAAAATTATTAAA-CCTA
778727 TATTTTCTTTAAATTTTTTACTTGATATGACAAGTCGTTATACATTATAAATGTCATGTTTTTCA
1 TATTTTCTTTAAATTTTTTACTTGATATGACAAGTCGTTATACATTATAAATGTCATG-TTTTCA
778792 CGACAAATTAATTGAATAGAAATAAGACAAATCAGCCCACCAACTCTTCAAGTCTCGTTCCATTT
65 CGACAAATTAA-TGAATAGAAATAAGACAAATCAGCCCACCAACTCTTCAAGTCTCGTTCCATTT
778857 TCAGGGTTGAGTCTCGGCTGTGTTTGTCTCTCCAGTTTCATGTGTTTCAAACTTTGGTGGTAGGG
129 TCAGGGTTGAGTCTCGGCTGTGTTTGTCTCTCCAGTTTCATGTGTTTCAAACTTTGGTGGTAGGG
778922 CAATCAATAACTTATCCCATAATTTAGACCTGATATGAATATCATACGATG-CATATATATAATG
194 CAATCAA-AACTTATCCCATAATTTAGACCTGATATGAATATCATACGATGCCATATATATAATG
778986 TTATACATATAATTAATTATTATAAAATTATTAAACCTA
258 TTATA-ATATAATTAATTATTATAAAATTATTAAACCTA
779025 TA
1 TA
779027 ATACTTTAAT
Statistics
Matches: 295, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
295 58 0.20
296 17 0.06
297 142 0.48
298 49 0.17
299 29 0.10
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (295 bp):
TATTTTCTTTAAATTTTTTACTTGATATGACAAGTCGTTATACATTATAAATGTCATGTTTTCAC
GACAAATTAATGAATAGAAATAAGACAAATCAGCCCACCAACTCTTCAAGTCTCGTTCCATTTTC
AGGGTTGAGTCTCGGCTGTGTTTGTCTCTCCAGTTTCATGTGTTTCAAACTTTGGTGGTAGGGCA
ATCAAAACTTATCCCATAATTTAGACCTGATATGAATATCATACGATGCCATATATATAATGTTA
TAATATAATTAATTATTATAAAATTATTAAACCTA
Found at i:785640 original size:15 final size:15
Alignment explanation
Indices: 785597--785640 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
785587 AGGATTTTTT
785597 ATTAAAATAATATATA
1 ATTAAAATAA-ATATA
*
785613 ATT-AGATATAATATA
1 ATTAAAATA-AATATA
785628 ATTAAAATAAATA
1 ATTAAAATAAATA
785641 ATGATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
ATTAAAATAAATATA
Found at i:786747 original size:51 final size:51
Alignment explanation
Indices: 786685--786824 Score: 226
Period size: 51 Copynumber: 2.7 Consensus size: 51
786675 GATTTGGCGT
* * *
786685 CACGTGTGGTATAGCGCGCACCCTGTACCGCGCTATACGGTGACATGATTTA
1 CACGTG-GGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATGACTTA
786737 CACGTGGGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATGACTTA
1 CACGTGGGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATGACTTA
* *
786788 CACGTGGGTATAGCGCACCCCCTGTTCCGCGCTATAC
1 CACGTGGGTATAGCGCGCCCCCTGTACCGCGCTATAC
786825 ATTTTATATG
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 77 0.93
52 6 0.07
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (51 bp):
CACGTGGGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATGACTTA
Found at i:787055 original size:15 final size:15
Alignment explanation
Indices: 787032--787079 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
787022 TCGTTATAAA
* *
787032 TTTTGTTATAATTGT
1 TTTTATTATAATTAT
*
787047 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
787062 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
787078 TT
1 TT
787080 AAAAAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.67
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:790420 original size:35 final size:34
Alignment explanation
Indices: 790335--790421 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
790325 ATTTGGTATT
*
790335 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
790369 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
790407 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
790422 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:791026 original size:18 final size:18
Alignment explanation
Indices: 791003--791041 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
790993 ATGGAAAGGC
*
791003 TGCGGCATCATATATGGT
1 TGCGGCATCATAAATGGT
791021 TGCGGCATCATAAATGGT
1 TGCGGCATCATAAATGGT
791039 TGC
1 TGC
791042 AGTGGCTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (18 bp):
TGCGGCATCATAAATGGT
Found at i:792810 original size:10 final size:10
Alignment explanation
Indices: 792791--792828 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
792781 CTTAAACAGA
*
792791 GAGAGTATTT
1 GAGAGAATTT
792801 GAGAGAATTT
1 GAGAGAATTT
*
792811 GAAAGAATTT
1 GAGAGAATTT
792821 GAGAGAAT
1 GAGAGAAT
792829 ATGGTATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:794855 original size:2 final size:2
Alignment explanation
Indices: 794848--794900 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
794838 AAAAGAGTGT
794848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
794890 TA TA TA TA TA T
1 TA TA TA TA TA T
794901 TAATATTGCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:805578 original size:23 final size:24
Alignment explanation
Indices: 805538--805598 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
805528 AAGGCAAATG
* *
805538 AAACGTGCCACAAGAGTAAAG-TA
1 AAACGTGCCAAAATAGTAAAGCTA
*
805561 AAACGTGTCAAAATAGTAAAGCTA
1 AAACGTGCCAAAATAGTAAAGCTA
805585 AAACGTGCCAAAAT
1 AAACGTGCCAAAAT
805599 GGCAAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.16
Consensus pattern (24 bp):
AAACGTGCCAAAATAGTAAAGCTA
Found at i:810762 original size:21 final size:22
Alignment explanation
Indices: 810738--810783 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
810728 TTCAAATCCG
* *
810738 AAAATAATAATAACAA-TAAAA
1 AAAAGAATAAAAACAACTAAAA
*
810759 AAAAGAATAAAAATAACTAAAA
1 AAAAGAATAAAAACAACTAAAA
810781 AAA
1 AAA
810784 GTTATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (22 bp):
AAAAGAATAAAAACAACTAAAA
Found at i:810773 original size:24 final size:22
Alignment explanation
Indices: 810740--810783 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
810730 CAAATCCGAA
*
810740 AATAATAATAACAATAAAAAAAAG
1 AATAAAAATAAC--TAAAAAAAAG
810764 AATAAAAATAACTAAAAAAA
1 AATAAAAATAACTAAAAAAA
810784 GTTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (22 bp):
AATAAAAATAACTAAAAAAAAG
Found at i:817882 original size:23 final size:23
Alignment explanation
Indices: 817842--817905 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
817832 CATTTTGATA
*
817842 AAAATATTAATTATTAATGTATTT
1 AAAATA-TAATTATTAATATATTT
* *
817866 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAATATATTT
817889 AACAATATAATATATTA
1 AA-AATATAAT-TATTA
817906 TAATAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.47
24 13 0.38
25 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAATATATTT
Found at i:818090 original size:30 final size:30
Alignment explanation
Indices: 818027--818099 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
818017 TTTTCTTAAA
818027 AATATTATTAAATTATTAATAATAAATAAT
1 AATATTATTAAATTATTAATAATAAATAAT
* *
818057 AATATGTATTTAA-TATTAATATAATAATCTAAT
1 AATAT-TATTAAATTATT-A-ATAATAA-ATAAT
818090 AATATT-TTAA
1 AATATTATTAA
818100 TAAAAATACT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
30 9 0.25
31 10 0.28
32 8 0.22
33 9 0.25
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
AATATTATTAAATTATTAATAATAAATAAT
Found at i:818122 original size:24 final size:24
Alignment explanation
Indices: 818072--818142 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
818062 GTATTTAATA
*
818072 TTAATATAATAAT-CTAATAATAT-T
1 TTAATA-AA-AATACTAAAAATATAT
*
818096 TTAATAAAAATACTTAAAATATAT
1 TTAATAAAAATACTAAAAATATAT
* * *
818120 TTATTAATAATTCTAAAAATATA
1 TTAATAAAAATACTAAAAATATA
818143 ATATGCTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 3 0.08
23 10 0.26
24 26 0.67
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAATAAAAATACTAAAAATATAT
Found at i:818286 original size:14 final size:14
Alignment explanation
Indices: 818242--818288 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
818232 AAAATTTTAG
*
818242 AAATAATATTTTAAT
1 AAATAATA-TTAAAT
*
818257 -AATAATATTAGCAT
1 AAATAATATTA-AAT
818271 AAATAATATTAAAT
1 AAATAATATTAAAT
818285 AAAT
1 AAAT
818289 TGTTATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 2 0.07
14 15 0.56
15 10 0.37
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:829768 original size:21 final size:21
Alignment explanation
Indices: 829742--829787 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
829732 GAGTTCTGGG
* *
829742 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
829763 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
829784 CAAG
1 CAAG
829788 CGACAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Done.