Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, 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: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 6 of 402
Found at i:750459 original size:19 final size:19
Alignment explanation
Indices: 750417--750459 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
750407 ATTTGAGGCT
**
750417 AAAAACTAGGAACCTCGTT
1 AAAAACTAGGAACCTCGCC
* *
750436 GAAAACTAGGAATCTCGCC
1 AAAAACTAGGAACCTCGCC
750455 AAAAA
1 AAAAA
750460 TTCGCCAGAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAAACTAGGAACCTCGCC
Found at i:751286 original size:21 final size:20
Alignment explanation
Indices: 751244--751283 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
751234 ATTAATAAAA
751244 AAGATATCTAAAAAAATTTT
1 AAGATATCTAAAAAAATTTT
* *
751264 AAGATTTCTAAGAAAATTTT
1 AAGATATCTAAAAAAATTTT
751284 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
AAGATATCTAAAAAAATTTT
Found at i:753526 original size:18 final size:18
Alignment explanation
Indices: 753503--753538 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
753493 CAGATCAGCA
753503 CTCTAATGAAGGTTCAAG
1 CTCTAATGAAGGTTCAAG
753521 CTCTAATGAAGGTTCAAG
1 CTCTAATGAAGGTTCAAG
753539 TACAGGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (18 bp):
CTCTAATGAAGGTTCAAG
Found at i:756242 original size:100 final size:100
Alignment explanation
Indices: 756082--756280 Score: 346
Period size: 100 Copynumber: 2.0 Consensus size: 100
756072 ATGCTTTTCA
*
756082 TTATGAAATGTTTTATGAAATTGATGTTTGGTTGATATGATATCTGGGATACTAGTTTCTATGTA
1 TTATGAAATGTTTTATGAAATTGATGTTTGGTTGATATGATATCTGGGATACTAGATTCTATGTA
* *
756147 TATTTTGTATCTGTATATTCAGTTTATGCTGAAAG
66 TATTTTGTATCCGTATATTCAATTTATGCTGAAAG
756182 TTATGAAATGTTTTATGAAATTGATGTTTGGGTTGATATGATATCTGGGATACTA-ATTCTATGT
1 TTATGAAATGTTTTATGAAATTGATGTTT-GGTTGATATGATATCTGGGATACTAGATTCTATGT
*
756246 ATATTTTGTATCCGTTTATTCAATTTATGCTGAAA
65 ATATTTTGTATCCGTATATTCAATTTATGCTGAAA
756281 TCCATGTGCA
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
100 69 0.73
101 25 0.27
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.47
Consensus pattern (100 bp):
TTATGAAATGTTTTATGAAATTGATGTTTGGTTGATATGATATCTGGGATACTAGATTCTATGTA
TATTTTGTATCCGTATATTCAATTTATGCTGAAAG
Found at i:761818 original size:55 final size:55
Alignment explanation
Indices: 761734--761840 Score: 187
Period size: 55 Copynumber: 1.9 Consensus size: 55
761724 TCCTGCACAG
* *
761734 CTAACGTTATCCTGTCTGTATGGTATGAACATAACACACCTACTAATTGCGGCAT
1 CTAACGTTATCCTGTCTGTATGGTATGAACATAAAACACCCACTAATTGCGGCAT
*
761789 CTAACGTTGTCCTGTCTGTATGGTATGAACATAAAACACCCACTAATTGCGG
1 CTAACGTTATCCTGTCTGTATGGTATGAACATAAAACACCCACTAATTGCGG
761841 GTCGATTGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (55 bp):
CTAACGTTATCCTGTCTGTATGGTATGAACATAAAACACCCACTAATTGCGGCAT
Found at i:765459 original size:2 final size:2
Alignment explanation
Indices: 765452--765496 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
765442 TTTATTATTT
765452 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
765494 TC T
1 TC T
765497 TTTTTCCCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:796990 original size:28 final size:27
Alignment explanation
Indices: 796949--797021 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
796939 TAAACAAAAG
796949 CCACTAACACACATCTAACTTCCATAAA
1 CCACTAACACACATCTAACTT-CATAAA
* *
796977 CCACTAATAAACATCTAACTTCATAAA
1 CCACTAACACACATCTAACTTCATAAA
*
797004 CTACTAACACACATCTAA
1 CCACTAACACACATCTAA
797022 TTGTTCATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (27 bp):
CCACTAACACACATCTAACTTCATAAA
Found at i:825339 original size:30 final size:30
Alignment explanation
Indices: 825304--825363 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
825294 ATGCATGAAT
825304 TTATATATTATAATATTATTAATAAGCTAC
1 TTATATATTATAATATTATTAATAAGCTAC
825334 TTATATATTATAATATTATTAATAAGCTAC
1 TTATATATTATAATATTATTAATAAGCTAC
825364 AAAATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (30 bp):
TTATATATTATAATATTATTAATAAGCTAC
Found at i:825846 original size:20 final size:20
Alignment explanation
Indices: 825809--825848 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
825799 ATACTATTTC
* **
825809 ATTAAAATTCACTGAAATAA
1 ATTAAAATTAACAAAAATAA
825829 ATTAAAATTAACAAAAATAA
1 ATTAAAATTAACAAAAATAA
825849 TTGATATTAT
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:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (20 bp):
ATTAAAATTAACAAAAATAA
Found at i:826486 original size:45 final size:45
Alignment explanation
Indices: 826417--826502 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
826407 CGTGACCCTT
* *
826417 ACCATTCTCGAATGGCCCGCACACACAAAAGTTATACCGGCCCCC
1 ACCACTCTCGAATGGCCCGCACACACAAAAGCTATACCGGCCCCC
*
826462 ACCACTCTCGAATGGTCCGCACACACAAAAGCTATACCGGC
1 ACCACTCTCGAATGGCCCGCACACACAAAAGCTATACCGGC
826503 TACCACTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.30, C:0.38, G:0.16, T:0.15
Consensus pattern (45 bp):
ACCACTCTCGAATGGCCCGCACACACAAAAGCTATACCGGCCCCC
Found at i:827057 original size:2 final size:2
Alignment explanation
Indices: 827050--827075 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
827040 TCCATTGCTT
827050 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
827076 GACATTACAT
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:827147 original size:2 final size:2
Alignment explanation
Indices: 827140--827168 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
827130 TCAATTCCTT
827140 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 T
827169 TGGCTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:830020 original size:3 final size:3
Alignment explanation
Indices: 830006--830054 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
829996 CGACGAGGAA
*
830006 GAT GAT GGT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
830054 G
1 G
830055 TGTTTCCTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:834696 original size:23 final size:24
Alignment explanation
Indices: 834668--834715 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
834658 ATTTAATTAC
*
834668 TTAATTA-ACATAAATAATTTTTT
1 TTAATTATACATAAATAATATTTT
* *
834691 TTAATTATATATAAATGATATTTT
1 TTAATTATACATAAATAATATTTT
834715 T
1 T
834716 ACTTTACATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTAATTATACATAAATAATATTTT
Found at i:843483 original size:2 final size:2
Alignment explanation
Indices: 843434--843471 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
843424 CTTCTCCATT
843434 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
843472 CACTTGTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:843802 original size:14 final size:14
Alignment explanation
Indices: 843782--843815 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
843772 TTAGCCACGC
843782 TTCTTTTTCCT-TT
1 TTCTTTTTCCTGTT
843795 TTCTTTTTCCTGTT
1 TTCTTTTTCCTGTT
843809 TTCTTTT
1 TTCTTTT
843816 AACAGCCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
TTCTTTTTCCTGTT
Found at i:892549 original size:23 final size:22
Alignment explanation
Indices: 892516--892566 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
892506 AAAAAAATAA
892516 TAAAAATTATTATAATTAT-ACT
1 TAAAAATTATTATAATTATGA-T
892538 TAAAAATATATTATAATTATGAT
1 TAAAAAT-TATTATAATTATGAT
892561 TAAAAA
1 TAAAAA
892567 ATACTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.26
23 19 0.70
24 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TAAAAATTATTATAATTATGAT
Found at i:892576 original size:23 final size:23
Alignment explanation
Indices: 892516--892577 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
892506 AAAAAAATAA
*
892516 TAAAAAT-TATTATAATTATACT
1 TAAAAATATATAATAATTATACT
*
892538 TAAAAATATATTATAATTATGA-T
1 TAAAAATATATAATAATTAT-ACT
892561 TAAAAA-ATACTAATAAT
1 TAAAAATATA-TAATAAT
892578 AATTTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 10 0.28
23 25 0.69
24 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAAATATATAATAATTATACT
Found at i:892619 original size:21 final size:20
Alignment explanation
Indices: 892594--892632 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
892584 ATATTAAATA
892594 AAATTTATTAAATTAATATTT
1 AAATTTATTAAA-TAATATTT
*
892615 AAATTTATTTAATAATAT
1 AAATTTATTAAATAATAT
892633 GATAAACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTTATTAAATAATATTT
Found at i:892638 original size:21 final size:21
Alignment explanation
Indices: 892586--892638 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
892576 ATAATTTTAT
892586 ATTAA-ATA-AAATTTATTAA
1 ATTAATATATAAATTTATTAA
* *
892605 ATTAATATTTAAATTTATTTA
1 ATTAATATATAAATTTATTAA
892626 A-TAATATGATAAA
1 ATTAATAT-ATAAA
892639 CTCAATCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.18
20 8 0.29
21 15 0.54
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTAATATATAAATTTATTAA
Found at i:901367 original size:2 final size:2
Alignment explanation
Indices: 901360--901408 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
901350 GTTTGTGGTC
*
901360 AT AT AT AT AT AT AC AT AT AT AT A- AT AT A- AT AT A- 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
*
901399 A- AA AT AT AT A
1 AT AT AT AT AT A
901409 ATTCTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:901378 original size:14 final size:13
Alignment explanation
Indices: 901360--901408 Score: 64
Period size: 14 Copynumber: 3.7 Consensus size: 13
901350 GTTTGTGGTC
901360 ATATATATATATA
1 ATATATATATATA
901373 CATATATATAATATA
1 -ATATATAT-ATATA
901388 ATATA-ATATATA
1 ATATATATATATA
*
901400 AAATATATA
1 ATATATATA
901409 ATTCTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 9 0.28
13 5 0.16
14 13 0.41
15 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATATATATA
Found at i:901379 original size:12 final size:11
Alignment explanation
Indices: 901360--901408 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 11
901350 GTTTGTGGTC
901360 ATATATATATA
1 ATATATATATA
*
901371 TACATATATATA
1 -ATATATATATA
901383 ATATA-ATATA
1 ATATATATATA
901393 ATATATA-A-A
1 ATATATATATA
901402 ATATATA
1 ATATATA
901409 ATTCTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.24
10 11 0.32
11 5 0.15
12 10 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATATATATA
Found at i:901795 original size:2 final size:2
Alignment explanation
Indices: 901788--901812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
901778 AGTTTAATAA
901788 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
901813 CACGTACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:901849 original size:49 final size:49
Alignment explanation
Indices: 901795--901895 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
901785 TAAATATATA
901795 TATATATATATATATATACACGTACATAAACAGTTTATGGTCTTCGATT
1 TATATATATATATATATACACGTACATAAACAGTTTATGGTCTTCGATT
901844 TATATATATATATATATACACGTACATAAACAGTTTATGGTCTTCGATT
1 TATATATATATATATATACACGTACATAAACAGTTTATGGTCTTCGATT
901893 TAT
1 TAT
901896 CAGGCTGACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (49 bp):
TATATATATATATATATACACGTACATAAACAGTTTATGGTCTTCGATT
Found at i:903284 original size:62 final size:62
Alignment explanation
Indices: 903183--903302 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 62
903173 AGAATGTAAA
*
903183 ACTCTAAATCATAAACCTCCTAACAAGGTTACAAATCAATCGGACCACGGATCGACTTTCGT
1 ACTCTAAATCATAAACCTCCTAACAAGGTTACAAATCAATCAGACCACGGATCGACTTTCGT
* * * * * *
903245 ACTCTGAATCATAAACCTCCTGACAAGGTTCCTATTCAATCAGACCACGGATTGACTT
1 ACTCTAAATCATAAACCTCCTAACAAGGTTACAAATCAATCAGACCACGGATCGACTT
903303 CCGTTCAACC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (62 bp):
ACTCTAAATCATAAACCTCCTAACAAGGTTACAAATCAATCAGACCACGGATCGACTTTCGT
Found at i:911518 original size:2 final size:2
Alignment explanation
Indices: 911511--911540 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
911501 TGTATGTATG
911511 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
911541 ATAGCTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:916023 original size:2 final size:2
Alignment explanation
Indices: 916016--916042 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
916006 ATTTAACTCG
916016 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 T
916043 GTATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:927040 original size:21 final size:23
Alignment explanation
Indices: 927010--927063 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
927000 TTTATTATTT
*
927010 TATATA-AAAATTT-ATT-TAAA
1 TATATATAAAATTTCATTAAAAA
*
927030 TATATTTAAAATTTCATTAAAAA
1 TATATATAAAATTTCATTAAAAA
927053 TATATATAAAA
1 TATATATAAAA
927064 CAAAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 3 0.11
23 13 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATATAAAATTTCATTAAAAA
Found at i:927710 original size:29 final size:29
Alignment explanation
Indices: 927678--927733 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
927668 CCCAAGGCGT
*
927678 TAGTCAACTTTCAAAAGCTAGTAGCATGG
1 TAGTCAACTTTCAAAAACTAGTAGCATGG
* *
927707 TAGTCAATTTTCAAAAACTGGTAGCAT
1 TAGTCAACTTTCAAAAACTAGTAGCAT
927734 AGAGGTACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (29 bp):
TAGTCAACTTTCAAAAACTAGTAGCATGG
Found at i:932148 original size:54 final size:54
Alignment explanation
Indices: 932060--932225 Score: 206
Period size: 54 Copynumber: 3.0 Consensus size: 54
932050 ATCAGAGTAC
* *
932060 CCAACAGTAAGGAAAGGATTTGGGTTTTTAAAATCAAACAAAAATTTCTTGGTT
1 CCAACAGTAAGGAAAGGATTTGGGTTTTTGAAATCAAACAAAAATTTATTGGTT
* * * * *
932114 CTAACGGTAAGGAAAGGATTTAGGTTTTCGAAATCAAACAAACAAAAATTTATTAGTT
1 CCAACAGTAAGGAAAGGATTTGGGTTTTTGAAAT----CAAACAAAAATTTATTGGTT
* * *
932172 CCAACAATAGGGAAAGGATTTGGGTTTTTGAAATCAAACAAAAATTTTTTGGTT
1 CCAACAGTAAGGAAAGGATTTGGGTTTTTGAAATCAAACAAAAATTTATTGGTT
932226 TAGTTGTGGA
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
54 47 0.51
58 46 0.49
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (54 bp):
CCAACAGTAAGGAAAGGATTTGGGTTTTTGAAATCAAACAAAAATTTATTGGTT
Found at i:932186 original size:58 final size:58
Alignment explanation
Indices: 932060--932213 Score: 172
Period size: 58 Copynumber: 2.7 Consensus size: 58
932050 ATCAGAGTAC
* * * * * *
932060 CCAACAGTAAGGAAAGGATTTGGGTTTT--TAA--AATCAAACAAAAATTTCTTGGTT
1 CCAACAATAAGGAAAGGATTTAGGTTTTCGAAATCAAACAAACAAAAATTTATTAGTT
* **
932114 CTAACGGTAAGGAAAGGATTTAGGTTTTCGAAATCAAACAAACAAAAATTTATTAGTT
1 CCAACAATAAGGAAAGGATTTAGGTTTTCGAAATCAAACAAACAAAAATTTATTAGTT
* * *
932172 CCAACAATAGGGAAAGGATTTGGGTTTTTGAAATCAAACAAA
1 CCAACAATAAGGAAAGGATTTAGGTTTTCGAAATCAAACAAA
932214 AATTTTTTGG
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 25 0.30
56 2 0.02
58 56 0.67
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.29
Consensus pattern (58 bp):
CCAACAATAAGGAAAGGATTTAGGTTTTCGAAATCAAACAAACAAAAATTTATTAGTT
Found at i:937461 original size:21 final size:22
Alignment explanation
Indices: 937436--937480 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
937426 CCATTCTCTC
*
937436 TTTTCTT-TTTATTTTTTTGGT
1 TTTTCTTCTTTATTTTCTTGGT
*
937457 TTTTCTTCTTTCTTTTCTTGGT
1 TTTTCTTCTTTATTTTCTTGGT
937479 TT
1 TT
937481 GCGACAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.78
Consensus pattern (22 bp):
TTTTCTTCTTTATTTTCTTGGT
Found at i:939759 original size:24 final size:25
Alignment explanation
Indices: 939728--939781 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
939718 AAAGTTAATC
* *
939728 TATT-TAATATTTGAATTTTAAAAT
1 TATTATAATATTTAAATTATAAAAT
939752 T-TTATAATATTTAAATTATAAAAT
1 TATTATAATATTTAAATTATAAAAT
939776 TATTAT
1 TATTAT
939782 TTAATATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 2 0.08
24 20 0.77
25 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATTATAATATTTAAATTATAAAAT
Found at i:939954 original size:17 final size:17
Alignment explanation
Indices: 939934--939967 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
939924 TATATAATTC
*
939934 ATTATAATATTTTTTTA
1 ATTATAACATTTTTTTA
939951 ATTATAACATTTTTTTA
1 ATTATAACATTTTTTTA
939968 TAAAATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATAACATTTTTTTA
Found at i:940191 original size:28 final size:27
Alignment explanation
Indices: 940156--940213 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
940146 TTTATTGTTA
*
940156 AAACTTAA-AAAATCATAAAATATTTAT
1 AAACTTAATAAAAT-ATAAAATACTTAT
**
940183 AAACTTTAATATTATATAAAATACTTAT
1 AAAC-TTAATAAAATATAAAATACTTAT
940211 AAA
1 AAA
940214 AAAGCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 19 0.73
29 3 0.12
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (27 bp):
AAACTTAATAAAATATAAAATACTTAT
Found at i:945716 original size:10 final size:10
Alignment explanation
Indices: 945697--945737 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
945687 AAATTATAAA
945697 TAAT-ATTTT
1 TAATAATTTT
945706 TAATAATTTT
1 TAATAATTTT
*
945716 TTATATATTTT
1 TAATA-ATTTT
945727 TAATAATTTT
1 TAATAATTTT
945737 T
1 T
945738 TATATTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 4 0.14
10 15 0.54
11 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TAATAATTTT
Found at i:945718 original size:11 final size:12
Alignment explanation
Indices: 945695--945739 Score: 62
Period size: 11 Copynumber: 4.1 Consensus size: 12
945685 TTAAATTATA
945695 AATAATATTTTT
1 AATAATATTTTT
945707 AATAAT-TTTTT
1 AATAATATTTTT
945718 -AT-ATATTTTT
1 AATAATATTTTT
945728 AATAAT-TTTTT
1 AATAATATTTTT
945739 A
1 A
945740 TATTTAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.07
10 7 0.23
11 13 0.43
12 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATAATATTTTT
Found at i:945724 original size:21 final size:21
Alignment explanation
Indices: 945699--945742 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
945689 ATTATAAATA
945699 ATATTTTTAATAATTTTTTAT
1 ATATTTTTAATAATTTTTTAT
945720 ATATTTTTAATAATTTTTTAT
1 ATATTTTTAATAATTTTTTAT
945741 AT
1 AT
945743 TTAACTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATATTTTTAATAATTTTTTAT
Found at i:947304 original size:29 final size:29
Alignment explanation
Indices: 947272--947336 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
947262 GATACAAATC
* ** *
947272 AAAAAATAAAAATTTATTTAAATATAATA
1 AAAAAATAAAAACTTAAATAAATAGAATA
* *
947301 AAAATATATAAACTTAAATAAATAGAATA
1 AAAAAATAAAAACTTAAATAAATAGAATA
*
947330 ATAAAAT
1 AAAAAAT
947337 TCGAATGCTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAAAATAAAAACTTAAATAAATAGAATA
Found at i:956135 original size:17 final size:17
Alignment explanation
Indices: 956113--956147 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
956103 AAAAACAAAG
956113 GTATGTGATAAATCTAT
1 GTATGTGATAAATCTAT
956130 GTATGTGATAAATCTAT
1 GTATGTGATAAATCTAT
956147 G
1 G
956148 CTGTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (17 bp):
GTATGTGATAAATCTAT
Found at i:956727 original size:6 final size:6
Alignment explanation
Indices: 956716--956743 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
956706 ATTCATTTTC
956716 CTCTGT CTCTGT CTCTGT CTCTGT CTCT
1 CTCTGT CTCTGT CTCTGT CTCTGT CTCT
956744 CTCTGAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.14, T:0.50
Consensus pattern (6 bp):
CTCTGT
Found at i:963086 original size:17 final size:17
Alignment explanation
Indices: 963060--963093 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
963050 AAGTTTCACA
*
963060 TTAAAAATTTTTTAAAT
1 TTAAAAATTTATTAAAT
*
963077 TTAAATATTTATTAAAT
1 TTAAAAATTTATTAAAT
963094 ATTTTACTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTATTAAAT
Found at i:974001 original size:8 final size:8
Alignment explanation
Indices: 973988--974016 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
973978 AAATAATTTT
973988 TTTTTTAA
1 TTTTTTAA
973996 TTTTTTAA
1 TTTTTTAA
974004 TTTTTTAA
1 TTTTTTAA
974012 TTTTT
1 TTTTT
974017 ATCTTGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAA
Found at i:981917 original size:25 final size:25
Alignment explanation
Indices: 981889--981950 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 25
981879 TTTTTATTAA
981889 AATTTTTTTTAATCATAATTATAAT
1 AATTTTTTTTAATCATAATTATAAT
* *
981914 AA--TTTTTTAATTATAATTGTAAT
1 AATTTTTTTTAATCATAATTATAAT
* *
981937 GATTATTTTTAATC
1 AATTTTTTTTAATC
981951 TCTCTATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 20 0.67
25 10 0.33
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (25 bp):
AATTTTTTTTAATCATAATTATAAT
Found at i:986817 original size:59 final size:58
Alignment explanation
Indices: 986704--986838 Score: 164
Period size: 59 Copynumber: 2.3 Consensus size: 58
986694 AAAATTTTTA
* * * * * *
986704 TTTTAAACATTTTATTTTTAAGAAAAATTGATACTTTCAATTTTTTCCTAAAAATATTAT
1 TTTTAAACTTTTTATTTTTAAGAAAAATTAATACTTTCAACTTTCTCCCAAAAAT-GT-T
*
986764 TTTTAAACTTTTTATTTTTAAG-AAAATTAATACTTTCAACTTTCTCCCCAAAATGTT
1 TTTTAAACTTTTTATTTTTAAGAAAAATTAATACTTTCAACTTTCTCCCAAAAATGTT
* *
986821 TTTGAAAATTTTTATTTT
1 TTTTAAACTTTTTATTTT
986839 AGAAACTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
57 17 0.26
58 1 0.02
59 27 0.41
60 21 0.32
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (58 bp):
TTTTAAACTTTTTATTTTTAAGAAAAATTAATACTTTCAACTTTCTCCCAAAAATGTT
Found at i:986869 original size:72 final size:73
Alignment explanation
Indices: 986774--986914 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 73
986764 TTTTAAACTT
**
986774 TTTATTTTTAAGAAAATTAATACTTTCAACTTTCTC-CCCAAA-A-TGTTTTTGAAAATTTTTAT
1 TTTATTTTTAAGAAAATTAATACTTTCAACTTTCTCTCAAAAATATTGTTTTTGAAAA-TTTTAT
986836 TTTAGAAAC
65 TTTAGAAAC
* * *
986845 TTTATTTTTAAAGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAATTTTAT
1 TTTATTTTT-AAGAAAATTAATACTTTCAACTTTCTCTCAAAAATATTGTTTTTGAAAATTTTAT
986910 TTTAG
65 TTTAG
986915 GAAAATCATT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
71 9 0.15
72 25 0.41
73 4 0.07
74 12 0.20
75 11 0.18
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.50
Consensus pattern (73 bp):
TTTATTTTTAAGAAAATTAATACTTTCAACTTTCTCTCAAAAATATTGTTTTTGAAAATTTTATT
TTAGAAAC
Found at i:987804 original size:19 final size:18
Alignment explanation
Indices: 987762--987827 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
987752 GATAAAAATC
*
987762 TAAAAAATAATAATAAACA
1 TAAAAAATAATACTAAA-A
*
987781 AAAAAAATAATACTAATAA
1 TAAAAAATAATACTAA-AA
987800 T-AAAAATAAATACATAAAA
1 TAAAAAAT-AATAC-TAAAA
987819 TAAATAAAT
1 TAAA-AAAT
987828 TAAAAAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 6 0.15
19 23 0.59
20 6 0.15
21 4 0.10
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAAAATAATACTAAAA
Found at i:987805 original size:22 final size:22
Alignment explanation
Indices: 987763--987822 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
987753 ATAAAAATCT
987763 AAAA-AATAATAATAAACAAAA
1 AAAATAATAATAATAAACAAAA
*
987784 AAAATAATACTAATAATA-AAAA
1 AAAATAATAATAATAA-ACAAAA
*
987806 TAAATACATAA-AATAAA
1 AAAATA-ATAATAATAAA
987823 TAAATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 5 0.15
22 24 0.73
23 4 0.12
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAATAATAATAATAAACAAAA
Found at i:988121 original size:44 final size:44
Alignment explanation
Indices: 988013--988258 Score: 251
Period size: 44 Copynumber: 5.5 Consensus size: 44
988003 TTTTCTTAAT
* * **
988013 CAAAGCTCCTCTAATCAGAGGCTCAATGACTTTAAAAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTT-GGAAAAATAAA
* * * *
988058 CAAGGCTCCTTTAAGCAGAGGCTCAATGACTTTGGAAAGATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAA
* * * *
988102 CAAAACTCATCTAACCAGAGGCTCAACGACTTTGGACAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAA
* * * *
988146 TAAGGCTCCTTTAAGCAGAGGTTCAACGACTTT-GAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAA
* * *
988189 CAAAGCTTCTCTAAACAGAGGCTCAACAACTTTGAGAAAAAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTG-G----AAAAATAAA
*
988238 CAAAGCTCCTCTAATCAGAGG
1 CAAAGCTCCTCTAAGCAGAGG
988259 TTTAACAACT
Statistics
Matches: 164, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
43 35 0.21
44 70 0.43
45 31 0.19
49 28 0.17
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (44 bp):
CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAA
Found at i:988177 original size:88 final size:86
Alignment explanation
Indices: 988013--988236 Score: 277
Period size: 88 Copynumber: 2.5 Consensus size: 86
988003 TTTTCTTAAT
* * ** *
988013 CAAAGCTCCTCTAATCAGAGGCTCAATGACTTTAAAAAAAATAAACAAGGCTCCTTTAAGCAGAG
1 CAAAGCT-CTCTAAACAGAGGCTCAACGACTTT-GGAAAAATAAATAAGGCTCCTTTAAGCAGAG
* *
988078 GCTCAATGACTTTGGAAAGATAAA
64 GCTCAACGACTTT-GAAAAATAAA
* * *
988102 CAAAACTCATCTAACCAGAGGCTCAACGACTTTGGACAAATAAATAAGGCTCCTTTAAGCAGAGG
1 CAAAGCTC-TCTAAACAGAGGCTCAACGACTTTGGAAAAATAAATAAGGCTCCTTTAAGCAGAGG
*
988167 TTCAACGACTTTGAAAAATAAA
65 CTCAACGACTTTGAAAAATAAA
* *
988189 CAAAGCTTCTCTAAACAGAGGCTCAACAACTTTGAGAAAAAAAAATAA
1 CAAAGC-TCTCTAAACAGAGGCTCAACGACTTTG-GAAAAATAAATAA
988237 ACAAAGCTCC
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
87 37 0.32
88 52 0.44
89 28 0.24
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (86 bp):
CAAAGCTCTCTAAACAGAGGCTCAACGACTTTGGAAAAATAAATAAGGCTCCTTTAAGCAGAGGC
TCAACGACTTTGAAAAATAAA
Found at i:988367 original size:87 final size:87
Alignment explanation
Indices: 988263--988463 Score: 230
Period size: 87 Copynumber: 2.3 Consensus size: 87
988253 CAGAGGTTTA
* * * *** *
988263 ACAACTTTT-AAAGAAATAAATTGCTCCTTTAAACA-ATGGCATTGCAATTTTGAAAAAAATAAA
1 ACAACTTTTGAAA-AAATAAATTGCTCATCTAAACAGA-AGCACCACAACTTTGAAAAAAATAAA
*
988326 TTG-TTCATCTAAACAGAGGCAACC
64 TTGTTTC-TCTAAACAGAGACAACC
* * *
988350 CCGACTTTTGAAAAAATAAATTGCTCATCTAAATAGAAGCACCACAACTTTGAAAAAAATAAATT
1 ACAACTTTTGAAAAAATAAATTGCTCATCTAAACAGAAGCACCACAACTTTGAAAAAAATAAATT
*
988415 GTTTCTCTAAATAGAGACAACC
66 GTTTCTCTAAACAGAGACAACC
*
988437 ATAACTTTTGAAAAAATAAA-TGCTCAT
1 ACAACTTTTGAAAAAATAAATTGCTCAT
988464 TGACAATCAT
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
86 7 0.07
87 82 0.85
88 7 0.07
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (87 bp):
ACAACTTTTGAAAAAATAAATTGCTCATCTAAACAGAAGCACCACAACTTTGAAAAAAATAAATT
GTTTCTCTAAACAGAGACAACC
Found at i:988371 original size:44 final size:45
Alignment explanation
Indices: 988310--988457 Score: 189
Period size: 44 Copynumber: 3.4 Consensus size: 45
988300 GGCATTGCAA
* * *
988310 TTTTGAAAAAAATAAATTGTTCATCTAAACAGAGGCAACCCCGAC
1 TTTTGAAAAAAATAAATTGTTCATCTAAATAGAGGCAACCACAAC
* *
988355 TTTTG-AAAAAATAAATTGCTCATCTAAATAGAAGC-ACCACAAC
1 TTTTGAAAAAAATAAATTGTTCATCTAAATAGAGGCAACCACAAC
* *
988398 -TTTGAAAAAAATAAATTGTTTC-TCTAAATAGAGACAACCATAAC
1 TTTTGAAAAAAATAAATTG-TTCATCTAAATAGAGGCAACCACAAC
988442 TTTTG-AAAAAATAAAT
1 TTTTGAAAAAAATAAAT
988458 GCTCATTGAC
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
42 4 0.04
43 30 0.33
44 47 0.52
45 9 0.10
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.28
Consensus pattern (45 bp):
TTTTGAAAAAAATAAATTGTTCATCTAAATAGAGGCAACCACAAC
Found at i:1001285 original size:15 final size:16
Alignment explanation
Indices: 1001260--1001299 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1001250 CTCATTGTAT
*
1001260 TAAATATTTATTTTA-A
1 TAAA-ATTTATTTAATA
1001276 TAAAATTTATTTAATA
1 TAAAATTTATTTAATA
1001292 TAAAATTT
1 TAAAATTT
1001300 TTATTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAATTTATTTAATA
Found at i:1001290 original size:14 final size:16
Alignment explanation
Indices: 1001260--1001291 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1001250 CTCATTGTAT
1001260 TAAATATTTATTTTAA
1 TAAATATTTATTTTAA
1001276 TAAA-ATTTA-TTTAA
1 TAAATATTTATTTTAA
1001290 TA
1 TA
1001292 TAAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATATTTATTTTAA
Found at i:1008565 original size:17 final size:16
Alignment explanation
Indices: 1008515--1008565 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
1008505 AATTAATTAA
*
1008515 AATTTTATTTATATATT
1 AATTTTATTTATA-AAT
1008532 AA-TTTATTATAATAAAT
1 AATTTTATT-T-ATAAAT
1008549 AAGTTTTATTTATAAAT
1 AA-TTTTATTTATAAAT
1008566 TAATAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 6 0.21
17 13 0.45
18 4 0.14
19 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
AATTTTATTTATAAAT
Found at i:1030453 original size:21 final size:23
Alignment explanation
Indices: 1030428--1030477 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1030418 AAATAAGATA
1030428 TAATAATATAATT-TA-A-AATTT
1 TAATAA-ATAATTATACATAATTT
1030449 TAATAAA-AATTATACATAATTT
1 TAATAAATAATTATACATAATTT
1030471 TAATAAA
1 TAATAAA
1030478 ATAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.15
20 3 0.12
21 7 0.27
22 12 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAATAATTATACATAATTT
Found at i:1030492 original size:22 final size:22
Alignment explanation
Indices: 1030444--1030494 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1030434 TATAATTTAA
* * *
1030444 AATTTTAATAAAAATTATACAT
1 AATTTTAATAAAAATAAAAAAT
1030466 AATTTTAAT-AAAATAAAAAAT
1 AATTTTAATAAAAATAAAAAAT
1030487 ATATTTTA
1 A-ATTTTA
1030495 TATTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTTTAATAAAAATAAAAAAT
Found at i:1032578 original size:30 final size:31
Alignment explanation
Indices: 1032527--1032592 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1032517 CATTAAATTA
*
1032527 AAAT-TTTAATTAGAGTGAAAAT-AGATATTT
1 AAATATTTAATTAGAGTGAAAATAAAAT-TTT
*
1032557 AAATATTTAATTTGA-TGAAAATAAAATTTT
1 AAATATTTAATTAGAGTGAAAATAAAATTTT
1032587 AAATAT
1 AAATAT
1032593 GAATTCTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (31 bp):
AAATATTTAATTAGAGTGAAAATAAAATTTT
Found at i:1032653 original size:29 final size:27
Alignment explanation
Indices: 1032601--1032656 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
1032591 ATGAATTCTC
*
1032601 AATAAAAATAAAAAATTAATTAATTAT
1 AATAAAAATAAAAAATTAACTAATTAT
*
1032628 AATAAAATATTAAAAATTTAACTAATTAT
1 AATAAAA-A-TAAAAAATTAACTAATTAT
1032657 TAAAATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.28
28 1 0.04
29 17 0.68
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AATAAAAATAAAAAATTAACTAATTAT
Found at i:1041503 original size:12 final size:12
Alignment explanation
Indices: 1041488--1041512 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1041478 TCATAAATTA
1041488 TAATATAATATT
1 TAATATAATATT
1041500 TAATATAATATT
1 TAATATAATATT
1041512 T
1 T
1041513 TAAATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATATAATATT
Found at i:1041535 original size:30 final size:29
Alignment explanation
Indices: 1041499--1041567 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 29
1041489 AATATAATAT
1041499 TTAATATAATATTTTAAATTTAAAAAATTTA
1 TTAATATAATATTTTAAA-TT-AAAAATTTA
*
1041530 -TAATATAATA-TTTAAATTATAAATTTA
1 TTAATATAATATTTTAAATTAAAAATTTA
1041557 TTAAT-TAATAT
1 TTAATATAATAT
1041568 ATCATTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
27 13 0.37
28 6 0.17
29 6 0.17
30 10 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAATATAATATTTTAAATTAAAAATTTA
Found at i:1041651 original size:31 final size:32
Alignment explanation
Indices: 1041616--1041680 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
1041606 CATTATTTAA
* *
1041616 AATTAATCATATTAA-AAGTAAAA-ACTACTTT
1 AATTAAT-AAATTAATAAGTAAAATACTACATT
*
1041647 AATTAATAAATTAATAATTAAAATACTACATT
1 AATTAATAAATTAATAAGTAAAATACTACATT
1041679 AA
1 AA
1041681 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 6 0.21
31 14 0.48
32 9 0.31
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (32 bp):
AATTAATAAATTAATAAGTAAAATACTACATT
Found at i:1051181 original size:3 final size:3
Alignment explanation
Indices: 1051173--1051216 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1051163 GAAAGATAGT
1051173 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1051217 TTTTCAGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1051480 original size:18 final size:18
Alignment explanation
Indices: 1051454--1051518 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
1051444 CAAAAGTTAG
*
1051454 TTTTTTTTATAAGTTGTA
1 TTTTATTTATAAGTTGTA
* * *
1051472 TTTTATTTATCCAGTTTTT
1 TTTTATTTAT-AAGTTGTA
*
1051491 TTTTTTTTATAAGTTGTA
1 TTTTATTTATAAGTTGTA
1051509 TTTTATTTAT
1 TTTTATTTAT
1051519 CCAAAAGAAG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
18 23 0.62
19 14 0.38
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTTATTTATAAGTTGTA
Found at i:1068335 original size:13 final size:13
Alignment explanation
Indices: 1068317--1068346 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1068307 AAATTTCAGT
*
1068317 TATTTTATTTTTA
1 TATTTTAATTTTA
1068330 TATTTTAATTTTA
1 TATTTTAATTTTA
1068343 TATT
1 TATT
1068347 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTTAATTTTA
Found at i:1077113 original size:11 final size:11
Alignment explanation
Indices: 1077097--1077148 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
1077087 ATCTCATAAA
*
1077097 AAATTTGTTTG
1 AAATTTGTTAG
1077108 AAATTTGTTAG
1 AAATTTGTTAG
* *
1077119 AGATTTATTAG
1 AAATTTGTTAG
* *
1077130 AGATTTGTTTG
1 AAATTTGTTAG
1077141 AAATTTGT
1 AAATTTGT
1077149 CAGATATTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (11 bp):
AAATTTGTTAG
Found at i:1077277 original size:52 final size:52
Alignment explanation
Indices: 1077221--1077328 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
1077211 AATATGTAAA
1077221 TTTGACTTACA-AGAGAAAAATTT-TAAAAGGAAAGAGATTCTTAATAGGCAAG
1 TTTGACTTACAGA-AG-AAAATTTCTAAAAGGAAAGAGATTCTTAATAGGCAAG
* * * * *
1077273 TTTGACTTACAGAAGAAAATTTCTAAGATGAGAGGGATTCTTAATGGGCAAG
1 TTTGACTTACAGAAGAAAATTTCTAAAAGGAAAGAGATTCTTAATAGGCAAG
1077325 TTTG
1 TTTG
1077329 TATAGTTATA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 7 0.14
52 41 0.84
53 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (52 bp):
TTTGACTTACAGAAGAAAATTTCTAAAAGGAAAGAGATTCTTAATAGGCAAG
Found at i:1077862 original size:31 final size:31
Alignment explanation
Indices: 1077824--1077908 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
1077814 AGGCTTTTAA
*
1077824 CCCAACAAGTGGTATCAAAGCTGTGGTGATC
1 CCCAACAAGTGGTATCAGAGCTGTGGTGATC
*
1077855 CCCAACAAGTGGTATCAGAGCTGTGGTGTTC
1 CCCAACAAGTGGTATCAGAGCTGTGGTGATC
1077886 CCCAACAAGTGGTATCAGAGCTG
1 CCCAACAAGTGGTATCAGAGCTG
1077909 AAGGTTTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (31 bp):
CCCAACAAGTGGTATCAGAGCTGTGGTGATC
Found at i:1077987 original size:24 final size:24
Alignment explanation
Indices: 1077960--1078008 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1077950 AGAGTCGAAG
1077960 GTTCGAGACGT-GAAAGAGCTGAAA
1 GTTCGAGACGTGGAAAGAGCT-AAA
* *
1077984 GTTCGAGATGTGGGAAGAGCTAAA
1 GTTCGAGACGTGGAAAGAGCTAAA
1078008 G
1 G
1078009 GTTTGGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.35, C:0.10, G:0.37, T:0.18
Consensus pattern (24 bp):
GTTCGAGACGTGGAAAGAGCTAAA
Found at i:1078122 original size:25 final size:24
Alignment explanation
Indices: 1078094--1078153 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
1078084 AAAATTTAAA
**
1078094 ATGTGATAAGAGTTGAAGATTCAAG
1 ATGTGA-AAGAGCCGAAGATTCAAG
*
1078119 ATGTGGAAAGAGCCGAAGGTTCAAG
1 ATGT-GAAAGAGCCGAAGATTCAAG
*
1078144 ACGTGAAAGA
1 ATGTGAAAGA
1078154 ACTGAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 6 0.20
25 22 0.73
26 2 0.07
ACGTcount: A:0.40, C:0.08, G:0.32, T:0.20
Consensus pattern (24 bp):
ATGTGAAAGAGCCGAAGATTCAAG
Found at i:1078187 original size:177 final size:175
Alignment explanation
Indices: 1077866--1078218 Score: 571
Period size: 177 Copynumber: 2.0 Consensus size: 175
1077856 CCAACAAGTG
**
1077866 GTATCAGAGCTGTGGTGTTCCCCAACAAGTGGTATCAGAGCTGAAGGTTTAAAATGTGAGAAGAG
1 GTATCAGAGCTGTGGTGTTCCCCAACAAGTGGTATCAGAGCTGAAAATTTAAAATGTGAGAAGAG
* * * *
1077931 TTAGATTCAAGATATGAAAAGAGTCGAAGGTTCGAGACGTGAAAGAGCTGAAAGTTCGAGATGTG
66 TTAGATTCAAGATATGAAAAGAGCCGAAGGTTCAAGACGTGAAAGAACTGAAAGTTAGAGATGTG
* *
1077996 GGAAGAGCTAAAGGTTTGGGAAGTGCATGGTTTGAGACATGAGAA
131 GGAAAAGCTAAAGGTTTGGGAAGTGCATGATTTGAGACATGAGAA
* *
1078041 GTATCAGAGCTGTGGTGTTCTCCAACAAGTGGTATCAGAGCTGAAAATTTAAAATGTGATAAGAG
1 GTATCAGAGCTGTGGTGTTCCCCAACAAGTGGTATCAGAGCTGAAAATTTAAAATGTGAGAAGAG
* *
1078106 TTGAAGATTCAAGATGTGGAAAGAGCCGAAGGTTCAAGACGTGAAAGAACTGAAAGTTAGAGATG
66 TT--AGATTCAAGATATGAAAAGAGCCGAAGGTTCAAGACGTGAAAGAACTGAAAGTTAGAGATG
*
1078171 TGGGAAAAGCTAAAGGTTTGGGAAGTGCATGATTTGAGACATGGGAA
129 TGGGAAAAGCTAAAGGTTTGGGAAGTGCATGATTTGAGACATGAGAA
1078218 G
1 G
1078219 AAGCAATTCT
Statistics
Matches: 163, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
175 63 0.39
177 100 0.61
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.24
Consensus pattern (175 bp):
GTATCAGAGCTGTGGTGTTCCCCAACAAGTGGTATCAGAGCTGAAAATTTAAAATGTGAGAAGAG
TTAGATTCAAGATATGAAAAGAGCCGAAGGTTCAAGACGTGAAAGAACTGAAAGTTAGAGATGTG
GGAAAAGCTAAAGGTTTGGGAAGTGCATGATTTGAGACATGAGAA
Found at i:1078580 original size:52 final size:52
Alignment explanation
Indices: 1078492--1078648 Score: 217
Period size: 52 Copynumber: 3.0 Consensus size: 52
1078482 TGGACAAGAA
* *
1078492 GACTTGCAAAAGAAGAATTCTAAGA-GAAAGGAGATTCTTAATAGGTAGGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGG-GATTCTTAATAGGTAAGTTT
* * *
1078544 GACTTGCAAGAGAAGAATTTTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
* * * *
1078596 GACTTACAGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
1078648 G
1 G
1078649 TATGGTTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 86 0.93
53 6 0.07
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
Found at i:1088083 original size:46 final size:46
Alignment explanation
Indices: 1088012--1088105 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
1088002 CACTTCTTTT
1088012 TCGATATCAAACAGCTCAAAAGTTGAAGCTCATACATTTTATAATG
1 TCGATATCAAACAGCTCAAAAGTTGAAGCTCATACATTTTATAATG
*
1088058 TCGATATCAAACAGCTCAAATGTTGAAGCTCATACATTTTATAATG
1 TCGATATCAAACAGCTCAAAAGTTGAAGCTCATACATTTTATAATG
1088104 TC
1 TC
1088106 AAAAATTGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (46 bp):
TCGATATCAAACAGCTCAAAAGTTGAAGCTCATACATTTTATAATG
Found at i:1105617 original size:2 final size:2
Alignment explanation
Indices: 1105610--1105648 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1105600 CCCAAATAAA
1105610 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1105649 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1106847 original size:17 final size:18
Alignment explanation
Indices: 1106825--1106859 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1106815 AATTATCTAA
1106825 GTTTTA-AAAATATTTAT
1 GTTTTACAAAATATTTAT
1106842 GTTTTATCAAAATATTTA
1 GTTTTA-CAAAATATTTA
1106860 ATATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (18 bp):
GTTTTACAAAATATTTAT
Found at i:1107930 original size:128 final size:129
Alignment explanation
Indices: 1107783--1108040 Score: 419
Period size: 129 Copynumber: 2.0 Consensus size: 129
1107773 TAAACTTTGT
* * *
1107783 CGAAAAATTTAATCGAAAAATTCAAATATTCATTCCAAAAACCCAGTTTTCCAAAAAAATTT-AA
1 CGAAAAATTTAATCAAAAAATTCAAATATTCACTCCAAAAACCCAATTTTCCAAAAAAATTTCAA
* *
1107847 AAATTCTCAAATTTCTCTAGATTACTTCAAAAACCCTCTAGAAATATAAACCTAATCCCAAAAA
66 AAATTCTCAAATTTCTCTAGATTACTTCAAAAACACTCTAGAAACATAAACCTAATCCCAAAAA
* * *
1107911 CGAAAAATTTAATCAAAAAATTCAAATATTCACTCTAAAAACCCAATTTTCTAAAAAAATTTCAG
1 CGAAAAATTTAATCAAAAAATTCAAATATTCACTCCAAAAACCCAATTTTCCAAAAAAATTTCAA
* *
1107976 AAATTCTTAGATTTCTCTAGATTACTTCAAAAACACTCTAGAAACATAAACCTAATCCCAAAAA
66 AAATTCTCAAATTTCTCTAGATTACTTCAAAAACACTCTAGAAACATAAACCTAATCCCAAAAA
1108040 C
1 C
1108041 CCAAATCTAA
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
128 57 0.48
129 62 0.52
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (129 bp):
CGAAAAATTTAATCAAAAAATTCAAATATTCACTCCAAAAACCCAATTTTCCAAAAAAATTTCAA
AAATTCTCAAATTTCTCTAGATTACTTCAAAAACACTCTAGAAACATAAACCTAATCCCAAAAA
Found at i:1108060 original size:20 final size:20
Alignment explanation
Indices: 1108032--1108078 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1108022 TAAACCTAAT
*
1108032 CCCAAAAAC-CCAAATCTAAA
1 CCCAGAAACTCCAAATC-AAA
* *
1108052 CCTAGAAACTTCAAATCAAA
1 CCCAGAAACTCCAAATCAAA
1108072 CCCAGAA
1 CCCAGAA
1108079 TTTCCAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.51, C:0.32, G:0.04, T:0.13
Consensus pattern (20 bp):
CCCAGAAACTCCAAATCAAA
Found at i:1108086 original size:20 final size:22
Alignment explanation
Indices: 1108041--1108086 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
1108031 TCCCAAAAAC
*
1108041 CCAAATCTAAACCTAGAAACTT
1 CCAAATCTAAACCCAGAAACTT
*
1108063 -CAAATC-AAACCCAG-AATTT
1 CCAAATCTAAACCCAGAAACTT
1108082 CCAAA
1 CCAAA
1108087 AATCAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.48, C:0.28, G:0.04, T:0.20
Consensus pattern (22 bp):
CCAAATCTAAACCCAGAAACTT
Found at i:1108451 original size:3 final size:3
Alignment explanation
Indices: 1108443--1108586 Score: 158
Period size: 3 Copynumber: 50.3 Consensus size: 3
1108433 AGAAAGAAAA
* * *
1108443 AAT AAT AAT AA- AAT AAT AAT AAT AGT AAT AAT AAT GAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * *
1108490 AAT AAT GGT AAT AAT -AT AAT -AT AAC AA- AAT AAT GAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1108533 AAT AGT AAT -GT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1108580 AAT AAT A
1 AAT AAT A
1108587 TAGTATAGTA
Statistics
Matches: 118, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
2 13 0.11
3 105 0.89
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1108548 original size:57 final size:56
Alignment explanation
Indices: 1108443--1108604 Score: 187
Period size: 57 Copynumber: 3.0 Consensus size: 56
1108433 AGAAAGAAAA
* *
1108443 AATAATAATAA-AATAATAATAATAGTAATAATAATGATA-ATAGTAA--TAATAAT
1 AATAATAATAATAATAATAACAATAATAATAATAAT-ATAGATAGTAATGTAATAAT
**
1108496 GGTAATAAT-ATAAT-ATAACAA-AATAATGATATAATATA-ATAGTAATGTAATAAT
1 AATAATAATAATAATAATAACAATAATAAT-A-ATAATATAGATAGTAATGTAATAAT
*
1108550 AATAATAATAATAATAATAATAATAATAATAATAATATAGTATAGTAATGTAATA
1 AATAATAATAATAATAATAACAATAATAATAATAATATAG-ATAGTAATGTAATA
1108605 CAAAAATAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
51 5 0.05
52 18 0.20
53 15 0.16
54 14 0.15
55 13 0.14
56 7 0.08
57 20 0.22
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (56 bp):
AATAATAATAATAATAATAACAATAATAATAATAATATAGATAGTAATGTAATAAT
Found at i:1108913 original size:65 final size:64
Alignment explanation
Indices: 1108841--1108986 Score: 181
Period size: 65 Copynumber: 2.3 Consensus size: 64
1108831 TCATGAATTG
* **
1108841 AAAAAATAAAATGATCTGGACTAAGCTAAGATC-AAATCAGATGACCGAGATTGAGCTGTCAA-T
1 AAAAAATAAAATGATCTGGACTAAGCTAAGATCAAAAT-AGATGACCGAAATTGAGCCAT-AAGT
1108904 CA
64 -A
* * * *
1108906 AAAAAATAAAATGATCTAGACTGAGCTGAGATCAAAATAGGTGACCGAAATTGAGCCATAAGTA
1 AAAAAATAAAATGATCTGGACTAAGCTAAGATCAAAATAGATGACCGAAATTGAGCCATAAGTA
1108970 AAAAAA-AAAATGATCTG
1 AAAAAATAAAATGATCTG
1108987 AACTGAGTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 10 0.14
64 9 0.13
65 48 0.68
66 4 0.06
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (64 bp):
AAAAAATAAAATGATCTGGACTAAGCTAAGATCAAAATAGATGACCGAAATTGAGCCATAAGTA
Found at i:1109059 original size:56 final size:56
Alignment explanation
Indices: 1108972--1109083 Score: 125
Period size: 56 Copynumber: 2.0 Consensus size: 56
1108962 CATAAGTAAA
* * * *
1108972 AAAAAAAATGATCTGAACTGAGTCAAAATCAAACGATTGGGACTGAGCTACAAGTC
1 AAAAAAAATGATCTGAACTGAGTCAAAATCAAACGATCGAGACTAAGCCACAAGTC
* * * * ** *
1109028 AAAAAAAATGATTTGGATTGAGTTATGATCAAATGATCGAGACTAAGCCACAAGTC
1 AAAAAAAATGATCTGAACTGAGTCAAAATCAAACGATCGAGACTAAGCCACAAGTC
1109084 TGAAAAATGG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (56 bp):
AAAAAAAATGATCTGAACTGAGTCAAAATCAAACGATCGAGACTAAGCCACAAGTC
Found at i:1110132 original size:19 final size:18
Alignment explanation
Indices: 1110110--1110151 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1110100 TTTTTTCTCA
*
1110110 TTTTTTCCT-CTTTTTTGT
1 TTTTTTTCTACTTTTTT-T
*
1110128 TTTTTTTTTACTTTTTTT
1 TTTTTTTCTACTTTTTTT
1110146 TTTTTT
1 TTTTTT
1110152 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (18 bp):
TTTTTTTCTACTTTTTTT
Found at i:1110146 original size:14 final size:15
Alignment explanation
Indices: 1110127--1110161 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1110117 CTCTTTTTTG
*
1110127 TTTTTTTTTTACTTT
1 TTTTTTTTTTAATTT
1110142 TTTTTTTTTTAATTT
1 TTTTTTTTTTAATTT
1110157 TTTTT
1 TTTTT
1110162 ACAGGCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTAATTT
Found at i:1112755 original size:15 final size:15
Alignment explanation
Indices: 1112732--1112761 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1112722 GAACCTTAAT
*
1112732 TTTATAATGTATAAA
1 TTTAAAATGTATAAA
1112747 TTTAAAATGTATAAA
1 TTTAAAATGTATAAA
1112762 ACCCTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TTTAAAATGTATAAA
Found at i:1114991 original size:13 final size:13
Alignment explanation
Indices: 1114970--1115048 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 13
1114960 AGATGATAAA
1114970 AAAAT-TAAATAT-
1 AAAATATAAA-ATC
1114982 AAAATATAAAATC
1 AAAATATAAAATC
1114995 AAAATATAAAAAATC
1 AAAATAT--AAAATC
* *
1115010 AAATAAAATTAAATC
1 -AA-AATATAAAATC
* *
1115025 AAAAAATAAAATT
1 AAAATATAAAATC
*
1115038 AAAATAGAAAA
1 AAAATATAAAA
1115049 AAAAACCTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
12 7 0.13
13 29 0.53
14 2 0.04
15 11 0.20
16 2 0.04
17 4 0.07
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (13 bp):
AAAATATAAAATC
Found at i:1115009 original size:15 final size:15
Alignment explanation
Indices: 1114989--1115035 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1114979 TATAAAATAT
1114989 AAAATCAAAATATAA
1 AAAATCAAAATATAA
1115004 AAAATC-AAATA-AA
1 AAAATCAAAATATAA
*
1115017 ATTAAATCAAAAAATAA
1 A--AAATCAAAATATAA
1115034 AA
1 AA
1115036 TTAAAATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
13 3 0.11
14 5 0.19
15 12 0.44
16 4 0.15
17 3 0.11
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATCAAAATATAA
Found at i:1115013 original size:20 final size:19
Alignment explanation
Indices: 1114970--1115050 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 19
1114960 AGATGATAAA
* *
1114970 AAAATTAAATATAAAATAT
1 AAAATAAAATATAAAAAAT
1114989 AAAATCAAAATATAAAAAAT
1 AAAAT-AAAATATAAAAAAT
*
1115009 CAAATAAAATTAAATCAAAAAAT
1 AAAATAAAA-T--AT-AAAAAAT
*
1115032 AAAATTAAAATAGAAAAAA
1 AAAA-TAAAATATAAAAAA
1115051 AAACCTGTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
19 9 0.18
20 23 0.45
21 1 0.02
22 2 0.04
23 11 0.22
24 5 0.10
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.22
Consensus pattern (19 bp):
AAAATAAAATATAAAAAAT
Found at i:1115894 original size:3 final size:3
Alignment explanation
Indices: 1115861--1115959 Score: 86
Period size: 3 Copynumber: 35.0 Consensus size: 3
1115851 AGAATAAAAA
* * * *
1115861 AAT AA- AAT AAA AAT AAT GAT AAT AGT AAT AAT AAT GAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1115907 AAT -AT ATAT AGT AAT -AT AAT AAT AAT AAT AAT AAT -AT AAT -AT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1115949 AGT -AT AAT AAT
1 AAT AAT AAT AAT
1115960 GTAATACAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
2 13 0.17
3 60 0.79
4 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1115927 original size:37 final size:38
Alignment explanation
Indices: 1115879--1115965 Score: 131
Period size: 37 Copynumber: 2.3 Consensus size: 38
1115869 AAAAATAATG
*
1115879 ATAATAGTAATAATAATGATAATAATATAATATA-TATA
1 ATAATA-TAATAATAATAATAATAATATAATATAGTATA
*
1115917 GTAATATAATAATAATAATAATAATATAATATAGTATA
1 ATAATATAATAATAATAATAATAATATAATATAGTATA
*
1115955 ATAATGTAATA
1 ATAATATAATA
1115966 CAAAAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 26 0.59
38 18 0.41
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (38 bp):
ATAATATAATAATAATAATAATAATATAATATAGTATA
Found at i:1115964 original size:43 final size:40
Alignment explanation
Indices: 1115872--1115975 Score: 115
Period size: 37 Copynumber: 2.5 Consensus size: 40
1115862 ATAAAATAAA
*
1115872 AATAATGATAATAGTAATAATAATGATAATAATATAATATAT
1 AATAATG-TAATA-TAATAATAATAATAATAATATAATATAT
1115914 -AT-A-GTAATATAATAATAATAATAATAATATAATATAGTAT
1 AATAATGTAATATAATAATAATAATAATAATAT-A-ATA-TAT
* *
1115954 AATAATGTAATACAAAAATAAT
1 AATAATGTAATATAATAATAAT
1115976 GACAATAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
37 20 0.38
38 6 0.11
39 4 0.08
40 4 0.08
41 4 0.08
42 1 0.02
43 14 0.26
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.35
Consensus pattern (40 bp):
AATAATGTAATATAATAATAATAATAATAATATAATATAT
Found at i:1115983 original size:43 final size:40
Alignment explanation
Indices: 1115872--1115983 Score: 113
Period size: 40 Copynumber: 2.7 Consensus size: 40
1115862 ATAAAATAAA
1115872 AATAATGATAATAGTAATAATAATGATAATAATATAATATATAT
1 AATAATG-TAATA--AATAATAATGA-AATAATATAATATATAT
* *
1115916 AGTAATATAAT-AATAATAAT--AATAATATAATATAGTAT
1 AATAATGTAATAAATAATAATGAAATAATATAATATA-TAT
*
1115954 AATAATGTAATACAAAAATAATGACAATAA
1 AATAATGTAATA-AATAATAATGA-AATAA
1115984 AAAAAATCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
37 14 0.25
38 12 0.21
40 17 0.30
43 9 0.16
44 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (40 bp):
AATAATGTAATAAATAATAATGAAATAATATAATATATAT
Found at i:1116856 original size:5 final size:5
Alignment explanation
Indices: 1116846--1116872 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1116836 TTGGATAAAT
1116846 TTGCA TTGCA TTGCA TTGCA TTGCA TT
1 TTGCA TTGCA TTGCA TTGCA TTGCA TT
1116873 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTGCA
Found at i:1127264 original size:40 final size:40
Alignment explanation
Indices: 1127220--1127304 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
1127210 TAATTTATTT
1127220 TACGATGTTCAATTATACTTTACAAAATTAAAATAATAAA
1 TACGATGTTCAATTATACTTTACAAAATTAAAATAATAAA
* *
1127260 TACGATGTTCAATTATATTTTATAAAATTAAAATAATAAA
1 TACGATGTTCAATTATACTTTACAAAATTAAAATAATAAA
1127300 TACGA
1 TACGA
1127305 ATAAAGGGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.36
Consensus pattern (40 bp):
TACGATGTTCAATTATACTTTACAAAATTAAAATAATAAA
Found at i:1133016 original size:2 final size:2
Alignment explanation
Indices: 1133009--1133039 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1132999 TTATGGATTT
*
1133009 TA TA TA TA TA AA 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 T
1133040 TTACACTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1137538 original size:2 final size:2
Alignment explanation
Indices: 1137531--1137561 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1137521 TGATTCCTTG
1137531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1137562 GCTTTTGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1147557 original size:33 final size:32
Alignment explanation
Indices: 1147513--1147589 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
1147503 AAAAATATAA
* * **
1147513 ATTAAATTAAATATATATTTTTTATATTTTTAT
1 ATTAAAATAAATATATAATACTTA-ATTTTTAT
1147546 ATTAAAATAAAT-TATAATACTTAATTTTTAT
1 ATTAAAATAAATATATAATACTTAATTTTTAT
1147577 A-TAAAATATAATA
1 ATTAAAATA-AATA
1147590 AAAATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 7 0.18
31 12 0.32
32 8 0.21
33 11 0.29
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTAAAATAAATATATAATACTTAATTTTTAT
Found at i:1148599 original size:13 final size:13
Alignment explanation
Indices: 1148581--1148605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1148571 ATTCCATCAC
1148581 TATCAAATGACAA
1 TATCAAATGACAA
1148594 TATCAAATGACA
1 TATCAAATGACA
1148606 CAGAAGATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (13 bp):
TATCAAATGACAA
Found at i:1148668 original size:69 final size:69
Alignment explanation
Indices: 1148590--1148728 Score: 235
Period size: 69 Copynumber: 2.0 Consensus size: 69
1148580 CTATCAAATG
*
1148590 ACAATATCAAATGACACAGAAGATAGGTTTTTAAAAAATAAGATAATTTTTTTAATTA-ACAATT
1 ACAATATCAAATGACACAGAAAATAGGTTTTTAAAAAATAAGATAATTTTTTTAATTATA-AATT
1148654 ATATA
65 ATATA
* *
1148659 ACAATATCAAATGATACAGAAAATAGTTTTTTAAAAAATAAGATAATTTTTTTAATTATAAATTA
1 ACAATATCAAATGACACAGAAAATAGGTTTTTAAAAAATAAGATAATTTTTTTAATTATAAATTA
1148724 TATA
66 TATA
1148728 A
1 A
1148729 TTTTAAATTT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 65 0.98
70 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (69 bp):
ACAATATCAAATGACACAGAAAATAGGTTTTTAAAAAATAAGATAATTTTTTTAATTATAAATTA
TATA
Found at i:1150782 original size:38 final size:38
Alignment explanation
Indices: 1150701--1150783 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
1150691 AAATATAGAA
* *
1150701 ATAAAAAATTAAATTAAATTATATATTTTTAATTTGTT
1 ATAAAAAATTAAATTAAATTATATATTTTTAATATATT
*
1150739 ATAAAAAATTAATATTATA-TATAT-TTATTTAAATATATT
1 ATAAAAAATTAA-ATTAAATTATATATT-TTT-AATATATT
1150778 -TAAAAA
1 ATAAAAA
1150784 TCTTATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
37 2 0.05
38 26 0.67
39 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (38 bp):
ATAAAAAATTAAATTAAATTATATATTTTTAATATATT
Found at i:1151083 original size:17 final size:18
Alignment explanation
Indices: 1151051--1151084 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1151041 ATAATAAATT
1151051 TTTAATATAATATTTAAA
1 TTTAATATAATATTTAAA
*
1151069 TTTAA-ATAATTTTTAA
1 TTTAATATAATATTTAA
1151085 TATGATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATATAATATTTAAA
Found at i:1151092 original size:29 final size:31
Alignment explanation
Indices: 1151033--1151101 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 31
1151023 ATGAATTACT
1151033 TTTAAA-TTATAATAAATTTTTAATATAATA
1 TTTAAATTTATAATAAATTTTTAATATAATA
*
1151063 TTTAAATTTA-AAT-AATTTTTAATATGATA
1 TTTAAATTTATAATAAATTTTTAATATAATA
1151092 TTT-AATTTAT
1 TTTAAATTTAT
1151102 CAATTTATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 6 0.17
29 18 0.50
30 9 0.25
31 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TTTAAATTTATAATAAATTTTTAATATAATA
Found at i:1151112 original size:28 final size:28
Alignment explanation
Indices: 1151033--1151119 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 28
1151023 ATGAATTACT
1151033 TTTAAATTATAATAAATTTTTAATATAATA
1 TTTAAATT-TAAT-AATTTTTAATATAATA
*
1151063 TTTAAATTTAAATAATTTTTAATATGATA
1 TTTAAATTT-AATAATTTTTAATATAATA
1151092 TTT-AATTT-ATCAATTTATTAAT-TAATA
1 TTTAAATTTAAT-AATTT-TTAATATAATA
1151119 T
1 T
1151120 ACATATTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.04
27 10 0.19
28 10 0.19
29 19 0.37
30 11 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (28 bp):
TTTAAATTTAATAATTTTTAATATAATA
Found at i:1152107 original size:18 final size:19
Alignment explanation
Indices: 1152081--1152116 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1152071 AAAGGTGATA
1152081 GAAAATAAAAA-AAAAATT
1 GAAAATAAAAATAAAAATT
*
1152099 GAAAGTAAAAATAAAAAT
1 GAAAATAAAAATAAAAAT
1152117 GTGATTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (19 bp):
GAAAATAAAAATAAAAATT
Found at i:1152835 original size:19 final size:19
Alignment explanation
Indices: 1152811--1152847 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1152801 CACTTATGAA
1152811 TTTAAACAAATTTAAATAT
1 TTTAAACAAATTTAAATAT
**
1152830 TTTAAATGAATTTAAATA
1 TTTAAACAAATTTAAATA
1152848 ATATTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTAAACAAATTTAAATAT
Found at i:1152843 original size:10 final size:9
Alignment explanation
Indices: 1152809--1152868 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
1152799 TACACTTATG
*
1152809 AATTTAAACA
1 AATTTAAA-T
1152819 AATTTAAAT
1 AATTTAAAT
*
1152828 ATTTTAAAT
1 AATTTAAAT
1152837 GAATTTAAAT
1 -AATTTAAAT
1152847 AATATTAAAT
1 AAT-TTAAAT
**
1152857 AAAGTAAAT
1 AATTTAAAT
1152866 AAT
1 AAT
1152869 CATATATCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
9 18 0.43
10 24 0.57
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (9 bp):
AATTTAAAT
Found at i:1152864 original size:29 final size:29
Alignment explanation
Indices: 1152806--1152865 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
1152796 GCATACACTT
***
1152806 ATGAATTTAAACAAATTTAAATATTTTAA
1 ATGAATTTAAACAAATTTAAATAAAGTAA
*
1152835 ATGAATTTAAA-TAATATTAAATAAAGTAA
1 ATGAATTTAAACAAAT-TTAAATAAAGTAA
1152864 AT
1 AT
1152866 AATCATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (29 bp):
ATGAATTTAAACAAATTTAAATAAAGTAA
Found at i:1162284 original size:14 final size:14
Alignment explanation
Indices: 1162265--1162294 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1162255 GTATTCCAAA
1162265 AAAAAAAAAAAAGT
1 AAAAAAAAAAAAGT
*
1162279 AAAAAAAAAAATGT
1 AAAAAAAAAAAAGT
1162293 AA
1 AA
1162295 GCTTAGCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAAAAGT
Found at i:1163568 original size:3 final size:3
Alignment explanation
Indices: 1163560--1163614 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1163550 ATTAAGAAAT
1163560 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1163608 TAA TAA T
1 TAA TAA T
1163615 GCAAACGTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1163950 original size:28 final size:24
Alignment explanation
Indices: 1163878--1163956 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 24
1163868 CAATTTGAAA
*
1163878 ATTAAAAA-ATATATAAATATAAAT
1 ATTAAAAATTTATATAAAT-TAAAT
* **
1163902 ATTTAAAATTTATATTTATTAAAT
1 ATTAAAAATTTATATAAATTAAAT
*
1163926 ATTAAGAGAATAATTATATAAATTAATT
1 ATTAA-A-AAT--TTATATAAATTAAAT
1163954 ATT
1 ATT
1163957 TTTTTTTGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 16 0.38
25 8 0.19
26 3 0.07
28 15 0.36
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (24 bp):
ATTAAAAATTTATATAAATTAAAT
Found at i:1173698 original size:34 final size:34
Alignment explanation
Indices: 1173655--1173723 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1173645 GCAAGTGATT
*
1173655 CAGTTCTCTTTATCAGGTATGCTATAGTCACATA
1 CAGTTCTCTTTATCAGGTATGCTATAATCACATA
1173689 CAGTTCTCTTTATCAGGTATGCTATAATCACATA
1 CAGTTCTCTTTATCAGGTATGCTATAATCACATA
1173723 C
1 C
1173724 TGCAATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (34 bp):
CAGTTCTCTTTATCAGGTATGCTATAATCACATA
Found at i:1176655 original size:2 final size:2
Alignment explanation
Indices: 1176643--1176762 Score: 70
Period size: 2 Copynumber: 61.5 Consensus size: 2
1176633 TAAGTACCTC
* * *
1176643 TA TA AA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * * *
1176685 TA TT TA CA CA -A TA TA -A AA T- TA -A AA AA AA TA TA TT TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1176723 -A TCA GTA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1176763 TTCATTTGTT
Statistics
Matches: 96, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
1 5 0.05
2 88 0.92
3 2 0.02
4 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1180348 original size:2 final size:2
Alignment explanation
Indices: 1180341--1180366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1180331 TAAACTGAGA
1180341 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
1180367 GCCCAAACGT
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):
AT
Found at i:1181045 original size:46 final size:46
Alignment explanation
Indices: 1180992--1181084 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1180982 TTCCAAGCAA
1180992 AATTCATGAAATTCAAGTACTCCACATTGTAGTTTTCAGCGTGGAC
1 AATTCATGAAATTCAAGTACTCCACATTGTAGTTTTCAGCGTGGAC
1181038 AATTCATGAAATTCAAGTACTCCACATTGTAGTTTTCAGCGTGGAC
1 AATTCATGAAATTCAAGTACTCCACATTGTAGTTTTCAGCGTGGAC
1181084 A
1 A
1181085 GCCGGCCAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (46 bp):
AATTCATGAAATTCAAGTACTCCACATTGTAGTTTTCAGCGTGGAC
Found at i:1185402 original size:20 final size:18
Alignment explanation
Indices: 1185379--1185428 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
1185369 CTGACCACAG
1185379 TTTTCTTTTTCTTTCTTT
1 TTTTCTTTTTCTTTCTTT
* *
1185397 CCTTTTCTTCTGCTTTCTTT
1 --TTTTCTTTTTCTTTCTTT
*
1185417 TTTTTTTTTTCT
1 TTTTCTTTTTCT
1185429 GATTATTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTCTTTCTTT
Found at i:1189860 original size:39 final size:38
Alignment explanation
Indices: 1189806--1189944 Score: 147
Period size: 39 Copynumber: 3.6 Consensus size: 38
1189796 CTGGGGCCAA
1189806 CAACTGAGATTTTTCTTCAGTGCATTCTATTGGTGTCAG
1 CAACTGAGATTTTTCTTCAGTGCATTCT-TTGGTGTCAG
*
1189845 CAACTGAGATTTTTCTTCA--GCATACTCTTTTGGTGCCAG
1 CAACTGAGATTTTTCTTCAGTGCAT--TC-TTTGGTGTCAG
* * ** *
1189884 CAACTGAGATTTTTCGTCAATATACTCTTTCGGTGTCAG
1 CAACTGAGATTTTTCTTCAGTGCATTCTTT-GGTGTCAG
* *
1189923 CAACTGAGGTTTCTCTTCAGTG
1 CAACTGAGATTTTTCTTCAGTG
1189945 TATTGAACAC
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
37 4 0.05
38 3 0.04
39 74 0.89
40 1 0.01
41 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (38 bp):
CAACTGAGATTTTTCTTCAGTGCATTCTTTGGTGTCAG
Found at i:1192318 original size:23 final size:23
Alignment explanation
Indices: 1192273--1192318 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1192263 AAGTTTGTGG
** *
1192273 AAATTTTTTATAAATGATTTAAT
1 AAATTTTTTATAAAAAATATAAT
*
1192296 AAATTTTTTTTAAAAAATATAAT
1 AAATTTTTTATAAAAAATATAAT
1192319 TAATAGATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATTTTTTATAAAAAATATAAT
Found at i:1192556 original size:13 final size:13
Alignment explanation
Indices: 1192538--1192562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192528 TCTCTCAATT
1192538 TTTTAATTTTTAA
1 TTTTAATTTTTAA
1192551 TTTTAATTTTTA
1 TTTTAATTTTTA
1192563 TTTAATCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:1195291 original size:52 final size:52
Alignment explanation
Indices: 1195137--1195292 Score: 174
Period size: 52 Copynumber: 3.0 Consensus size: 52
1195127 TATAACCATA
* * * *
1195137 CAAACTTGCCCATTAAGAATCC-CTCTC-CTCTAGAATTCTTCTTCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTTCTCT-TAAAATTCTTCTTTTGTAAGT
* * * *
1195188 TAAACTTGCCTATTAAAAAT-CTCTTTTCTTTTAAAATTCTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCCTC-TTTCTCTTAAAATTCTTCTTTTGTAAGT
* * *
1195240 CAAACTTGTCTATTAAGAATCCTCTTTCTCTTAAAATTTTTCTTTTATAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTTCTCTTAAAATTCTTCTTTTGTAAGT
1195292 C
1 C
1195293 TTCTTGTCCA
Statistics
Matches: 86, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
50 1 0.01
51 18 0.21
52 63 0.73
53 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.44
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCTCTTTCTCTTAAAATTCTTCTTTTGTAAGT
Done.