Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold341
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: 1349338
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:605431 original size:24 final size:24
Alignment explanation
Indices: 605362--605505 Score: 94
Period size: 24 Copynumber: 5.8 Consensus size: 24
605352 AAGTATATTT
605362 AAATAAA-AATTGTTATAAAATATA
1 AAATAAACAATTGTTATAAAATA-A
* * * *
605386 TGAAGAAATAATAATTGATATAAACTAA
1 --AA-ATA-AACAATTGTTATAAAATAA
* **
605414 AAATAAACAATTGTTATAAAGTGG
1 AAATAAACAATTGTTATAAAATAA
** * *
605438 CCATAAATAAATGTTATAAAATATA
1 AAATAAACAATTGTTATAAAATA-A
* *
605463 AAA-AAACAAGTGTTATAAAATAT
1 AAATAAACAATTGTTATAAAATAA
*
605486 AAACAAACAATTGTTATAAA
1 AAATAAACAATTGTTATAAA
605506 TAGATCAATC
Statistics
Matches: 91, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
23 3 0.03
24 63 0.69
25 3 0.03
26 4 0.04
27 2 0.02
28 3 0.03
29 13 0.14
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (24 bp):
AAATAAACAATTGTTATAAAATAA
Found at i:611372 original size:2 final size:2
Alignment explanation
Indices: 611365--611419 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
611355 AAACATTATT
* * * *
611365 TA TA TA TA TA TA TA -A T- TCA TA AA CA TT TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
611406 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
611420 AGTTTTTACT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.93
3 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:611392 original size:27 final size:28
Alignment explanation
Indices: 611348--611405 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 28
611338 GTTATAAGTA
611348 AATTCATAAACATTATTTATATATATATAT
1 AATTCATAAAC--TATTTATATATATATAT
*
611378 AATTCATAAAC-ATTTATTTATATATAT
1 AATTCATAAACTATTTATATATATATAT
611405 A
1 A
611406 TATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 16 0.59
30 11 0.41
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTCATAAACTATTTATATATATATAT
Found at i:611398 original size:31 final size:30
Alignment explanation
Indices: 611348--611409 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 30
611338 GTTATAAGTA
611348 AATTCATAAACATTATTTATATATATATAT
1 AATTCATAAACATTATTTATATATATATAT
611378 AATTCATAAACATTTATTTATATATATATAT
1 AATTCATAAACA-TTATTTATATATATATAT
611409 A
1 A
611410 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTCATAAACATTATTTATATATATATAT
Found at i:611849 original size:16 final size:16
Alignment explanation
Indices: 611828--611860 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
611818 TAAAATTGAA
611828 TAATA-TTGATATATTT
1 TAATATTTGAT-TATTT
611844 TAATATTTGATTATTT
1 TAATATTTGATTATTT
611860 T
1 T
611861 GACTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TAATATTTGATTATTT
Found at i:615971 original size:30 final size:30
Alignment explanation
Indices: 615936--616003 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
615926 CATTGTCTAT
615936 GGTGGCTGGCAGAGCTTAGGAAAAAGGTAA
1 GGTGGCTGGCAGAGCTTAGGAAAAAGGTAA
615966 GGTGGCTGGCAGAGCTTAGGAAAAAGGTAA
1 GGTGGCTGGCAGAGCTTAGGAAAAAGGTAA
615996 GGTGGCTG
1 GGTGGCTG
616004 AAGTTAATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.43, T:0.18
Consensus pattern (30 bp):
GGTGGCTGGCAGAGCTTAGGAAAAAGGTAA
Found at i:616368 original size:13 final size:13
Alignment explanation
Indices: 616350--616375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
616340 CACGATGATT
616350 TTGTATCGATACA
1 TTGTATCGATACA
616363 TTGTATCGATACA
1 TTGTATCGATACA
616376 AAACTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:618695 original size:16 final size:16
Alignment explanation
Indices: 618676--618712 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
618666 GTTTTAGGTC
618676 ATTTTAAGTTTAAATT
1 ATTTTAAGTTTAAATT
618692 ATTTTAAGTTTAAATT
1 ATTTTAAGTTTAAATT
618708 ATTTT
1 ATTTT
618713 GGATTCTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTTTAAGTTTAAATT
Found at i:619653 original size:20 final size:20
Alignment explanation
Indices: 619630--619682 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
619620 CAAAGCATAA
* *
619630 TGTATCGATACATCTGGATG
1 TGTATTGATACATCTAGATG
619650 TGTATTGATACATCTAGATG
1 TGTATTGATACATCTAGATG
619670 TGTATTGATACAT
1 TGTATTGATACAT
619683 ACAAGAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (20 bp):
TGTATTGATACATCTAGATG
Found at i:627731 original size:20 final size:19
Alignment explanation
Indices: 627693--627761 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
627683 ATTGTGCATT
*
627693 TATCGATACAATGATAATG
1 TATCGATACAAAGATAATG
*
627712 TATCGATATAAAGCATAATG
1 TATCGATACAAAG-ATAATG
*
627732 TATCGATACATCTAGAT-ATG
1 TATCGATACA--AAGATAATG
627752 TATCGATACA
1 TATCGATACA
627762 TACAAGGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
19 11 0.26
20 28 0.65
21 2 0.05
22 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (19 bp):
TATCGATACAAAGATAATG
Found at i:628722 original size:14 final size:15
Alignment explanation
Indices: 628703--628732 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
628693 TTCATTAACG
628703 AAAAGGAAAAA-AAA
1 AAAAGGAAAAAGAAA
628717 AAAAGGAAAAAGAAA
1 AAAAGGAAAAAGAAA
628732 A
1 A
628733 TTTTGACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGGAAAAAGAAA
Found at i:629984 original size:15 final size:15
Alignment explanation
Indices: 629966--629994 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
629956 TAAAGTTTAA
629966 ATTTTTAAAAAATAT
1 ATTTTTAAAAAATAT
629981 ATTTTTAAAAAATA
1 ATTTTTAAAAAATA
629995 AATTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTTAAAAAATAT
Found at i:630638 original size:30 final size:30
Alignment explanation
Indices: 630602--630686 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 30
630592 TTTTTTCTTG
*
630602 TATTTTATTTTTAATATAAATATTAATTAT
1 TATTTTATTTTTAATATAAATATTAATTAC
** * * *
630632 TATTTTA--CATAAAAT-AATTTTAATAAC
1 TATTTTATTTTTAATATAAATATTAATTAC
630659 TATTTTATTATTTAATATAAATA-TAATT
1 TATTTTATT-TTTAATATAAATATTAATT
630687 TTTAATTATT
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
27 16 0.40
28 5 0.12
30 16 0.40
31 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
TATTTTATTTTTAATATAAATATTAATTAC
Found at i:630653 original size:39 final size:36
Alignment explanation
Indices: 630617--630688 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
630607 TATTTTTAAT
*
630617 ATAAATATTAATTATTATTTTACATAAA-ATAATTTTA
1 ATAAATATT--TTATTATTTAACATAAATATAATTTTA
* *
630654 ATAACTATTTTATTATTTAATATAAATATAATTTT
1 ATAAATATTTTATTATTTAACATAAATATAATTTT
630689 TAATTATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 15 0.48
36 8 0.26
37 8 0.26
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (36 bp):
ATAAATATTTTATTATTTAACATAAATATAATTTTA
Found at i:630697 original size:34 final size:34
Alignment explanation
Indices: 630628--630697 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 34
630618 TAAATATTAA
*
630628 TTATTATTTTACATAAAATAATTTTAATAACTATT
1 TTATTATTTAACATAAAATAATTTT-ATAACTATT
* *
630663 TTATTATTTAATATAAATATAATTTT-TAATTATT
1 TTATTATTTAACATAAA-ATAATTTTATAACTATT
630697 T
1 T
630698 ATTGTATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 8 0.26
35 15 0.48
36 8 0.26
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (34 bp):
TTATTATTTAACATAAAATAATTTTATAACTATT
Found at i:634372 original size:68 final size:68
Alignment explanation
Indices: 634263--634445 Score: 246
Period size: 66 Copynumber: 2.7 Consensus size: 68
634253 TACTGCATTA
* * *
634263 ATTTGAATGAATAAGAACAAGAATCAGAAATTGGAAAATGAACAGAAAAAAACCATCATGCAGCA
1 ATTTGAATCAATAAGAACATGAATCAAAAATTGGAAAATGAACAGAAAAAAACCATCATGCAGCA
*
634328 TCC
66 ACC
* *
634331 ATTTGAAGT-AATAAGAACATGAATCAAAAACTGGAAAATGAAC--AAAAAACCCATCATGCAGC
1 ATTTGAA-TCAATAAGAACATGAATCAAAAATTGGAAAATGAACAGAAAAAAACCATCATGCAGC
634393 AACC
65 AACC
* ** *
634397 ATTTGAATCAAAAAGCGCATGAATAAAAAATTGGAAAATGAACAGAAAA
1 ATTTGAATCAATAAGAACATGAATCAAAAATTGGAAAATGAACAGAAAA
634446 CCATTATGCA
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
65 1 0.01
66 57 0.56
68 42 0.42
69 1 0.01
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.17
Consensus pattern (68 bp):
ATTTGAATCAATAAGAACATGAATCAAAAATTGGAAAATGAACAGAAAAAAACCATCATGCAGCA
ACC
Found at i:637883 original size:3 final size:3
Alignment explanation
Indices: 637875--637923 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
637865 ATTCATACAC
637875 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
637923 T
1 T
637924 GTTTTTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:638890 original size:21 final size:20
Alignment explanation
Indices: 638866--638926 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
638856 AATATTTTAT
638866 AATTTAAATTTATTTAAGTTA
1 AATTTAAATTTATTTAA-TTA
*
638887 AA-TTATTATTTATTTAATTA
1 AATTTA-AATTTATTTAATTA
* *
638907 AATAATAATTTTATTTAATT
1 AAT-TTAAATTTATTTAATT
638927 TTAATTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 8 0.24
21 23 0.70
22 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AATTTAAATTTATTTAATTA
Found at i:639136 original size:13 final size:12
Alignment explanation
Indices: 639118--639151 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
639108 ATCATTTTAG
639118 ATATAATATAAAA
1 ATATAATAT-AAA
639131 ATATAATAT-AA
1 ATATAATATAAA
639142 ATATAATATA
1 ATATAATATA
639152 TTTAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:640240 original size:22 final size:21
Alignment explanation
Indices: 640218--640265 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
640208 ATCATATTTA
640218 TATATTTAAAATATTATAA-T
1 TATATTTAAAATATTATAATT
*
640238 TATATTTAAAATATTTTATATT
1 TATATTTAAAATATTATA-ATT
640260 TATATT
1 TATATT
640266 ATTAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 17 0.68
21 1 0.04
22 7 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTTAAAATATTATAATT
Found at i:640258 original size:16 final size:16
Alignment explanation
Indices: 640211--640261 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 16
640201 TATTTATATC
640211 ATATTTATATATTTAAA
1 ATATTT-TATATTTAAA
640228 ATATTATAATTATATTTAAA
1 ATA-T-T--TTATATTTAAA
640248 ATATTTTATATTTA
1 ATATTTTATATTTA
640262 TATTATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 9 0.30
17 3 0.10
18 2 0.07
19 2 0.07
20 13 0.43
21 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTTTATATTTAAA
Found at i:640268 original size:16 final size:16
Alignment explanation
Indices: 640237--640283 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
640227 AATATTATAA
* *
640237 TTATATTTAAAATATT
1 TTATATTTATATTATT
640253 TTATATTTATATTA-T
1 TTATATTTATATTATT
*
640268 TAATAATTTATATTAT
1 TTAT-ATTTATATTAT
640284 ATAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTTATATTATT
Found at i:640272 original size:22 final size:22
Alignment explanation
Indices: 640211--640286 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
640201 TATTTATATC
* *
640211 ATATTTATA-TATTTAAAATATT
1 ATATTTATATTA-TTAATATTTT
* *
640233 ATAATTATATT-TAAAATATTTT
1 ATATTTATATTAT-TAATATTTT
*
640255 ATATTTATATTATTAATAATTT
1 ATATTTATATTATTAATATTTT
640277 ATATTATATA
1 ATATT-TATA
640287 AATTTTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.02
22 36 0.84
23 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTTATATTATTAATATTTT
Found at i:640283 original size:27 final size:26
Alignment explanation
Indices: 640229--640316 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 26
640219 ATATTTAAAA
* *
640229 TATTATAATTATA-T-TTAAAATA-T
1 TATTATATTTATATTATTAAAAAATT
*
640252 T-TTATATTTATATTATT-AATAATT
1 TATTATATTTATATTATTAAAAAATT
* *
640276 TA-TATTATATAAATT-TTAAAAAATT
1 TATTA-TATTTATATTATTAAAAAATT
640301 TA-TATATTTATATTAT
1 TATTATATTTATATTAT
640317 GTTCATATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
22 10 0.20
23 5 0.10
24 16 0.32
25 19 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTATATTTATATTATTAAAAAATT
Found at i:640727 original size:6 final size:6
Alignment explanation
Indices: 640707--640762 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
640697 GCCTAGTTGC
* * * *
640707 ATATAT A-ACTAT ATATCT ATATAT CTATAT ATCTAT ATATCT ATATAT
1 ATATAT ATA-TAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
640755 ATTTAT AT
1 ATATAT AT
640763 GATAATAAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
5 1 0.03
6 37 0.95
7 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:640761 original size:24 final size:24
Alignment explanation
Indices: 640707--640762 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
640697 GCCTAGTTGC
*
640707 ATATATAACTATATATCTATATAT
1 ATATATATCTATATATCTATATAT
*
640731 CTATATATCTATATATCTATATAT
1 ATATATATCTATATATCTATATAT
*
640755 ATTTATAT
1 ATATATAT
640763 GATAATAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATATATCTATATATCTATATAT
Found at i:640762 original size:8 final size:8
Alignment explanation
Indices: 640708--640754 Score: 85
Period size: 8 Copynumber: 5.9 Consensus size: 8
640698 CCTAGTTGCA
*
640708 TATATAAC
1 TATATATC
640716 TATATATC
1 TATATATC
640724 TATATATC
1 TATATATC
640732 TATATATC
1 TATATATC
640740 TATATATC
1 TATATATC
640748 TATATAT
1 TATATAT
640755 ATTTATATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (8 bp):
TATATATC
Found at i:641405 original size:2 final size:2
Alignment explanation
Indices: 641398--641426 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
641388 TCTATACCTC
641398 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 A
641427 ATTATTTTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:644361 original size:16 final size:17
Alignment explanation
Indices: 644340--644430 Score: 91
Period size: 16 Copynumber: 5.4 Consensus size: 17
644330 TCATTTCTCT
644340 CTTTCTTTTTTT-TTTC
1 CTTTCTTTTTTTCTTTC
644356 CTTTCTTTTTTTTCTTTC
1 CTTTC-TTTTTTTCTTTC
*
644374 C-TTCTTTTTTTCCTTC
1 CTTTCTTTTTTTCTTTC
644390 CTTTCTTCTTCCTTTC-TTC
1 CTTTCTT-TT--TTTCTTTC
*
644409 C-TTCTTCTTTTCTTTC
1 CTTTCTTTTTTTCTTTC
*
644425 TTTTCT
1 CTTTCT
644431 AGTTCAAAGT
Statistics
Matches: 64, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
15 4 0.06
16 20 0.31
17 20 0.31
18 12 0.19
19 4 0.06
20 4 0.06
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
CTTTCTTTTTTTCTTTC
Found at i:644367 original size:17 final size:17
Alignment explanation
Indices: 644340--644396 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
644330 TCATTTCTCT
644340 CTTTC-TTTTTTTTTTC
1 CTTTCTTTTTTTTTTTC
644356 CTTTCTTTTTTTTCTTTC
1 CTTTCTTTTTTTT-TTTC
**
644374 C-TTCTTTTTTTCCTTC
1 CTTTCTTTTTTTTTTTC
644390 CTTTCTT
1 CTTTCTT
644397 CTTCCTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 9 0.25
17 22 0.61
18 5 0.14
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
CTTTCTTTTTTTTTTTC
Found at i:644373 original size:4 final size:4
Alignment explanation
Indices: 644333--644427 Score: 54
Period size: 4 Copynumber: 23.8 Consensus size: 4
644323 ATTTTTCTCA
* * * * *
644333 TTTC TCTC TTTC TTT- TTTT TTTCC TTTC TTTTT TTTC TTTC CTTC TTTT
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC -TTTC TTTC TTTC TTTC TTTC
* * *
644382 TTTCC TTCC TTTC -TTC TTCC TTTC -TTC CTTC -TTC TTTTC TTTC TTT
1 TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTT
644428 TCTAGTTCAA
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
3 12 0.17
4 47 0.67
5 11 0.16
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:644409 original size:23 final size:21
Alignment explanation
Indices: 644374--644426 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
644364 TTTTTCTTTC
* *
644374 CTTCTTTTTTTCCTTCCTTTCTT
1 CTTCCTTTCTTCCTT-C-TTCTT
644397 CTTCCTTTCTTCCTTCTTCTT
1 CTTCCTTTCTTCCTTCTTCTT
644418 -TT-CTTTCTT
1 CTTCCTTTCTT
644427 TTCTAGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.25
20 2 0.07
21 5 0.18
22 1 0.04
23 13 0.46
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (21 bp):
CTTCCTTTCTTCCTTCTTCTT
Found at i:644412 original size:15 final size:15
Alignment explanation
Indices: 644383--644422 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
644373 CCTTCTTTTT
* *
644383 TTCCTTCCTTTCTTC
1 TTCCTTTCTTCCTTC
644398 TTCCTTTCTTCCTTC
1 TTCCTTTCTTCCTTC
*
644413 TTCTTTTCTT
1 TTCCTTTCTT
644423 TCTTTTCTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTCCTTTCTTCCTTC
Found at i:644497 original size:23 final size:23
Alignment explanation
Indices: 644471--644521 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
644461 CCACCATGCC
644471 TAAAAAT-TTAAACTTATAAAAAA
1 TAAAAATCTTAAACTT-TAAAAAA
* *
644494 T--AAATCTTAAACTTTTACAAA
1 TAAAAATCTTAAACTTTAAAAAA
644515 TAAAAAT
1 TAAAAAT
644522 ACATTGCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
21 10 0.43
22 8 0.35
23 5 0.22
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAAATCTTAAACTTTAAAAAA
Found at i:644681 original size:33 final size:33
Alignment explanation
Indices: 644574--644681 Score: 81
Period size: 33 Copynumber: 3.2 Consensus size: 33
644564 AAAAAACATA
* * *
644574 TTTAAATTTTCACAAATCAAAATAAATTATACT
1 TTTAAATTTTAACAAATAAAAATAAATAATACT
* * ** * **
644607 TTAAAAATTTAACCCGTATAATGAAATAAAAAATAAA
1 TTTAAATTTTAA--CAAATAA--AAATAAATAATACT
*
644644 TTTAAATTTTTACAAATAAAAATAAATAATACT
1 TTTAAATTTTAACAAATAAAAATAAATAATACT
644677 TTTAA
1 TTTAA
644682 TCAAATTAAT
Statistics
Matches: 53, Mismatches: 18, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
33 25 0.47
35 9 0.17
37 19 0.36
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (33 bp):
TTTAAATTTTAACAAATAAAAATAAATAATACT
Found at i:644710 original size:23 final size:23
Alignment explanation
Indices: 644701--644763 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
644691 TTAATCTTAC
644701 AAATAAAAATAAATTATACATTA
1 AAATAAAAATAAATTATACATTA
* * *
644724 AAATAAAAA-AATTTAAACTTCTA
1 AAATAAAAATAAATTATACAT-TA
*
644747 CAAATAACAATAAATTA
1 -AAATAAAAATAAATTA
644764 AACTTGAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 8 0.25
23 11 0.34
24 8 0.25
25 5 0.16
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATAAAAATAAATTATACATTA
Found at i:644766 original size:25 final size:23
Alignment explanation
Indices: 644636--644768 Score: 89
Period size: 22 Copynumber: 5.7 Consensus size: 23
644626 AATGAAATAA
*
644636 AAAATAAATTTAAATTTTTACAAAT
1 AAAATAAA-TTAAA-CTTTACAAAT
*
644661 AAAAATAAA-TAATACTTT--TAAT
1 -AAAATAAATTAA-ACTTTACAAAT
* * *
644683 CAAATTAATTAATC-TTACAAAT
1 AAAATAAATTAAACTTTACAAAT
* *
644705 AAAAATAAATTATACATTA-AAAT
1 -AAAATAAATTAAACTTTACAAAT
644728 AAAA-AAATTTAAACTTCTACAAAT
1 AAAATAAA-TTAAACTT-TACAAAT
644752 AACAATAAATTAAACTT
1 AA-AATAAATTAAACTT
644769 GAATAATCAT
Statistics
Matches: 84, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
20 2 0.02
21 10 0.12
22 19 0.23
23 16 0.19
24 15 0.18
25 11 0.13
26 11 0.13
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATAAATTAAACTTTACAAAT
Found at i:645142 original size:62 final size:65
Alignment explanation
Indices: 644999--645147 Score: 160
Period size: 66 Copynumber: 2.3 Consensus size: 65
644989 CTTATTTTTT
* * * * *
644999 AATTTTTTAATTTAAAATTTTTTATTTTATTAAAAGATCAATAATTAATATTTTGATTTTTTAAT
1 AATTTTTTAATTT--AA-TTTTTATTTTATTAAAAGATCAATAACTAACATGTTGATATTTTAAC
645064 ACA
63 ACA
* * *
645067 AATTTTTTAAATTTTATTTTTATTTTATTAAAA-ATTAATAACTAACATGTT-A-ATTTTAACAT
1 AATTTTTT-AATTTAATTTTTATTTTATTAAAAGATCAATAACTAACATGTTGATATTTTAACAC
*
645129 G
65 A
645130 AATTTTTTAATTTAATTT
1 AATTTTTTAATTTAATTT
645148 AATTTTTTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
62 9 0.13
63 15 0.21
64 1 0.01
65 14 0.20
66 17 0.24
67 1 0.01
68 8 0.11
69 5 0.07
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (65 bp):
AATTTTTTAATTTAATTTTTATTTTATTAAAAGATCAATAACTAACATGTTGATATTTTAACACA
Found at i:645153 original size:18 final size:18
Alignment explanation
Indices: 645130--645165 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
645120 TTTTAACATG
645130 AATTTTTTAATTTAATTT
1 AATTTTTTAATTTAATTT
*
645148 AATTTTTTAATTTTATTT
1 AATTTTTTAATTTAATTT
645166 GTGACGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
AATTTTTTAATTTAATTT
Found at i:646357 original size:11 final size:11
Alignment explanation
Indices: 646341--646383 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
646331 ATTTATTTTA
646341 TATATTTATGT
1 TATATTTATGT
*
646352 TATATTTATAT
1 TATATTTATGT
*
646363 TATTTTTTATGT
1 TA-TATTTATGT
*
646375 TATAATTAT
1 TATATTTAT
646384 ATTTAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (11 bp):
TATATTTATGT
Found at i:646361 original size:17 final size:17
Alignment explanation
Indices: 646328--646407 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 17
646318 TTTTCTTTTG
*
646328 TTTATTTATTTTATATA
1 TTTATTTATATTATATA
646345 TTTATGTTATATTTATATTA
1 TTTAT-TTATA-TTATA-TA
*
646365 TTT-TTTATGTTATA-A
1 TTTATTTATATTATATA
*
646380 TTATATTTAAATTAT-TA
1 TT-TATTTATATTATATA
*
646397 TATATTTATAT
1 TTTATTTATAT
646408 AAATTTTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
15 3 0.06
16 9 0.18
17 20 0.39
18 8 0.16
19 6 0.12
20 5 0.10
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTATTTATATTATATA
Found at i:646362 original size:6 final size:6
Alignment explanation
Indices: 646330--646407 Score: 51
Period size: 6 Copynumber: 13.5 Consensus size: 6
646320 TTCTTTTGTT
*
646330 TATTTA T-TTTA TATATT- TATGTTA TATTTA TA-TTA T-TTTT TATGTTA
1 TATTTA TATTTA TAT-TTA TAT-TTA TATTTA TATTTA TATTTA TAT-TTA
* * *
646377 TAATTA TATTTA -AATTA T-TATA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TAT
646408 AAATTTTTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
5 19 0.35
6 27 0.49
7 9 0.16
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:646371 original size:23 final size:24
Alignment explanation
Indices: 646326--646407 Score: 84
Period size: 23 Copynumber: 3.6 Consensus size: 24
646316 TTTTTTCTTT
*
646326 TGTT-TATTTATTTTATATATTTA
1 TGTTATATTTATATTATATATTTA
*
646349 TGTTATATTTATATTAT-TTTTTA
1 TGTTATATTTATATTATATATTTA
* *
646372 TGTTATAATTATATT-TA-AATTA
1 TGTTATATTTATATTATATATTTA
646394 T-TATATATTTATAT
1 TGT-TATATTTATAT
646408 AAATTTTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 1 0.02
22 15 0.30
23 23 0.46
24 11 0.22
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TGTTATATTTATATTATATATTTA
Found at i:646397 original size:20 final size:20
Alignment explanation
Indices: 646374--646422 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
646364 ATTTTTTATG
*
646374 TTATA-ATTATATTTAAATTA
1 TTATATATT-TATATAAATTA
*
646394 TTATATATTTATATAAATTT
1 TTATATATTTATATAAATTA
*
646414 TTACATATT
1 TTATATATT
646423 AATAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATATTTATATAAATTA
Found at i:646950 original size:49 final size:51
Alignment explanation
Indices: 646873--646971 Score: 175
Period size: 49 Copynumber: 2.0 Consensus size: 51
646863 TTCTAGCTAC
646873 TAAGATAAGAGGTTGTTGGCTTATTATATAATTATGTAGTATTCAAAATCGA
1 TAAGATAAGAGG-TGTTGGCTTATTATATAATTATGTAGTATTCAAAATCGA
646925 TAAGATAAGA-G-GTTGGCTTATTATATAATTATGTAGTATTCAAAATC
1 TAAGATAAGAGGTGTTGGCTTATTATATAATTATGTAGTATTCAAAATC
646972 AATACATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
49 36 0.77
51 1 0.02
52 10 0.21
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.38
Consensus pattern (51 bp):
TAAGATAAGAGGTGTTGGCTTATTATATAATTATGTAGTATTCAAAATCGA
Found at i:648302 original size:2 final size:2
Alignment explanation
Indices: 648295--648320 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
648285 AAAATTATTT
648295 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
648321 GATACACACA
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:648599 original size:20 final size:20
Alignment explanation
Indices: 648565--648604 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
648555 ATAAACATAA
*
648565 TTTTTACTTTTAAAAATAAAT
1 TTTTTACTTTGAAAAA-AAAT
648586 TTTTTA-TTTGAAAAAAAAT
1 TTTTTACTTTGAAAAAAAAT
648605 AAAGTATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTACTTTGAAAAAAAAT
Found at i:648736 original size:19 final size:20
Alignment explanation
Indices: 648698--648737 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
648688 TTTAAAATTC
648698 TAAATAATATATTTTATTTT
1 TAAATAATATATTTTATTTT
648718 TAAA-AATA-ATTTTATTTT
1 TAAATAATATATTTTATTTT
648736 TA
1 TA
648738 TTTGTCTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.60
19 4 0.20
20 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAAATAATATATTTTATTTT
Found at i:650035 original size:18 final size:19
Alignment explanation
Indices: 649980--650039 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 19
649970 AATTATACAT
* *
649980 TATATAAAAAATAT-TAAA
1 TATATAAATATTATATAAA
649998 -ATA-AAATATTATATAAA
1 TATATAAATATTATATAAA
*
650015 TATATAAATATTTTA-AAA
1 TATATAAATATTATATAAA
650033 TATATAA
1 TATATAA
650040 TATAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 13 0.36
19 9 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATATAAATATTATATAAA
Found at i:650065 original size:22 final size:23
Alignment explanation
Indices: 649987--650112 Score: 74
Period size: 22 Copynumber: 5.7 Consensus size: 23
649977 CATTATATAA
*
649987 AAAATAT-TAAAATAAA-ATATT
1 AAAATATATAATATAAATATATT
* * *
650008 -ATATAAAT-ATATAAATATTTT
1 AAAATATATAATATAAATATATT
650029 AAAATATATAATATAAAT-TATT
1 AAAATATATAATATAAATATATT
*
650051 AAAATATTATTTATATAAA-AT-TT
1 AAAATA-TA-TAATATAAATATATT
* *
650074 AAAA-ATTTTAAATATAAATATAAT
1 AAAATA-TAT-AATATAAATATATT
*
650098 ATAAT-TA-AATATAAA
1 AAAATATATAATATAAA
650113 AATAATATCA
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 10 0.12
21 14 0.17
22 25 0.31
23 19 0.23
24 13 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATATATAATATAAATATATT
Found at i:650105 original size:21 final size:21
Alignment explanation
Indices: 650081--650120 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
650071 TTTAAAAATT
*
650081 TTAAATATAAATATAATATAA
1 TTAAATATAAAAATAATATAA
650102 TTAAATATAAAAATAATAT
1 TTAAATATAAAAATAATAT
650121 CACTAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAATATAAAAATAATATAA
Found at i:650127 original size:21 final size:21
Alignment explanation
Indices: 650082--650128 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
650072 TTAAAAATTT
* *
650082 TAAATATAAATATAATATAAT
1 TAAATATAAAAATAATATAAC
*
650103 TAAATATAAAAATAATATCAC
1 TAAATATAAAAATAATATAAC
650124 TAAAT
1 TAAAT
650129 GAATTGTCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAATATAAAAATAATATAAC
Found at i:651539 original size:4 final size:4
Alignment explanation
Indices: 651530--651556 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
651520 GCCTGAGAGG
651530 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
651557 TCCAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:652514 original size:24 final size:25
Alignment explanation
Indices: 652481--652533 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
652471 AAAAAAGTGT
* * *
652481 AAAAATTTTAGGAGGATG-AGAAAA
1 AAAAAATTTAGCAAGATGAAGAAAA
*
652505 AAAAAATTTAGCAAGATGAAGAAGA
1 AAAAAATTTAGCAAGATGAAGAAAA
652530 AAAA
1 AAAA
652534 GGAAAACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (25 bp):
AAAAAATTTAGCAAGATGAAGAAAA
Found at i:652802 original size:21 final size:21
Alignment explanation
Indices: 652778--652828 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
652768 TATTAAATGA
652778 TAAAATATAAAT-AAAATATAT
1 TAAAATATAAATAAAAAT-TAT
*
652799 T-AAATAATAATTAAAAATTAT
1 TAAAAT-ATAAATAAAAATTAT
*
652820 TAAATTATA
1 TAAAATATA
652829 TTTATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 8 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAATATAAATAAAAATTAT
Found at i:652858 original size:25 final size:24
Alignment explanation
Indices: 652830--652895 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 24
652820 TAAATTATAT
*
652830 TTATATTAAAAATAAATTATTAAAA
1 TTATATTAAAAATAAA-TAATAAAA
* * ***
652855 TTATGTTTATGTTAAATAATAAAA
1 TTATATTAAAAATAAATAATAAAA
652879 TATATATTAAAAATAAA
1 T-TATATTAAAAATAAA
652896 ATAGATTAGA
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
TTATATTAAAAATAAATAATAAAA
Found at i:652890 original size:36 final size:34
Alignment explanation
Indices: 652744--652890 Score: 139
Period size: 31 Copynumber: 4.4 Consensus size: 34
652734 GATAAATGAT
* *
652744 TAAAAATTATTAAAAATATATTTATATTAAATGA
1 TAAAAATTATTAAAATTATATTTATATTAAATAA
* * *
652778 TAAAATATAAATAAAA-TATA-TTA-AAT-AATAA
1 TAAAA-ATTATTAAAATTATATTTATATTAAATAA
652809 TTAAAAATTATT-AAATTATATTTATATTAAA-AA
1 -TAAAAATTATTAAAATTATATTTATATTAAATAA
* *
652842 T--AAATTATTAAAATTATGTTTATGTTAAATAA
1 TAAAAATTATTAAAATTATATTTATATTAAATAA
652874 TAAAATATATATTAAAA
1 TAAAA-AT-TATTAAAA
652891 ATAAAATAGA
Statistics
Matches: 92, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
30 11 0.12
31 29 0.32
32 14 0.15
33 7 0.08
34 13 0.14
35 10 0.11
36 8 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (34 bp):
TAAAAATTATTAAAATTATATTTATATTAAATAA
Found at i:652951 original size:21 final size:21
Alignment explanation
Indices: 652867--652952 Score: 52
Period size: 21 Copynumber: 4.0 Consensus size: 21
652857 ATGTTTATGT
* **
652867 TAAATAATAAAATATATATTAA
1 TAAATAAAAAAAT-TATAAAAA
* *
652889 -AAATAAAATAGATTAGAAAAA
1 TAAATAAAA-AAATTATAAAAA
* *
652910 T-ATTAAAATAATT-TCATAAAA
1 TAAATAAAAAAATTAT-A-AAAA
652931 TAAATAAAAAAATTATAAAAA
1 TAAATAAAAAAATTATAAAAA
652952 T
1 T
652953 TTACTCTGTA
Statistics
Matches: 47, Mismatches: 11, Indels: 13
0.66 0.15 0.18
Matches are distributed among these distances:
20 4 0.09
21 28 0.60
22 14 0.30
23 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAATAAAAAAATTATAAAAA
Found at i:653494 original size:17 final size:17
Alignment explanation
Indices: 653469--653530 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
653459 AAAAGTTTTA
*
653469 AATTATTTATTTTTGTT
1 AATTATTTAATTTTGTT
*
653486 AATTTTTTAATTTTGTTT
1 AATTATTTAATTTTG-TT
*
653504 TATTAATTT-ATTTT-TT
1 AATT-ATTTAATTTTGTT
653520 -ATT-TTTAATTT
1 AATTATTTAATTT
653531 AAAGATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 3 0.08
14 4 0.11
15 3 0.08
16 2 0.05
17 13 0.34
18 10 0.26
19 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
AATTATTTAATTTTGTT
Found at i:653648 original size:18 final size:20
Alignment explanation
Indices: 653625--653662 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
653615 GAAATATTAT
653625 TTATTAAA-ATTT-TAAATA
1 TTATTAAATATTTATAAATA
653643 TTATTAAATATTTATAAATA
1 TTATTAAATATTTATAAATA
653663 ATTTATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAAATATTTATAAATA
Found at i:653657 original size:11 final size:11
Alignment explanation
Indices: 653622--653668 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
653612 TATGAAATAT
653622 TATTTATTAAA
1 TATTTATTAAA
653633 -A-TT-TTAAA
1 TATTTATTAAA
653641 TA-TTATTAAA
1 TATTTATTAAA
653651 TATTTA-TAAA
1 TATTTATTAAA
653661 TAATTTAT
1 T-ATTTAT
653669 CATTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
8 5 0.16
9 5 0.16
10 13 0.42
11 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTTATTAAA
Found at i:654317 original size:15 final size:15
Alignment explanation
Indices: 654297--654334 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
654287 GACCTATATG
654297 TTATTTTATCTAAAT-
1 TTATTTT-TCTAAATA
*
654312 TTATTTTTTTAAATA
1 TTATTTTTCTAAATA
654327 TTATTTTT
1 TTATTTTT
654335 AAAATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTTTCTAAATA
Found at i:654423 original size:14 final size:15
Alignment explanation
Indices: 654404--654433 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
654394 ATTAAAAATT
654404 TTATAATATT-TATA
1 TTATAATATTATATA
654418 TTATAATATTATATA
1 TTATAATATTATATA
654433 T
1 T
654434 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATAATATTATATA
Found at i:657458 original size:29 final size:29
Alignment explanation
Indices: 657390--657476 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
657380 CAAAGTTCAC
* *
657390 AAAT-TTTTATCAAATTAATTTTTATTTTT
1 AAATATTTTATCAAAATAA-TTTTATTTTA
** *
657419 AAATAAATTATCAAAATAATATTATTTTA
1 AAATATTTTATCAAAATAATTTTATTTTA
* * *
657448 AAATATTTTATTATAATATTTTTATTTTA
1 AAATATTTTATCAAAATAATTTTATTTTA
657477 TCACGTGAGA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 35 0.76
30 11 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
AAATATTTTATCAAAATAATTTTATTTTA
Found at i:657720 original size:15 final size:16
Alignment explanation
Indices: 657702--657731 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
657692 TATGAATTTT
657702 TTAATTAT-ATATTAA
1 TTAATTATAATATTAA
657717 TTAATTATAATATTA
1 TTAATTATAATATTA
657732 GTTTAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTATAATATTAA
Found at i:657778 original size:17 final size:17
Alignment explanation
Indices: 657756--657819 Score: 69
Period size: 16 Copynumber: 3.8 Consensus size: 17
657746 TATGTGATAA
*
657756 TATTAAAGTTATATTCT
1 TATTAAATTTATATTCT
* *
657773 TATT-AATTTTTAATTTTT
1 TATTAAATTTAT-A-TTCT
657791 TATTAAATTTATATTCT
1 TATTAAATTTATATTCT
657808 TATT-AATTTATA
1 TATTAAATTTATA
657820 GTGCTATTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 13 0.33
17 12 0.31
18 8 0.21
19 6 0.15
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTAAATTTATATTCT
Found at i:657865 original size:17 final size:17
Alignment explanation
Indices: 657823--657861 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
657813 ATTTATAGTG
* *
657823 CTATTACAATTTTTTAA
1 CTATTATAATTTTTAAA
657840 CTATTATAATTTTTAAA
1 CTATTATAATTTTTAAA
657857 C-ATTA
1 CTATTA
657862 ATAAATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (17 bp):
CTATTATAATTTTTAAA
Found at i:662531 original size:30 final size:30
Alignment explanation
Indices: 662497--662571 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
662487 TATATTAAAT
* *
662497 AATGTATCGACACATCTGGAAAAAAAATAG
1 AATGTATCGATACATCTGGAAAAAAAACAG
**
662527 AATGTATCGATACATCTGGGTAAAAAACAG
1 AATGTATCGATACATCTGGAAAAAAAACAG
662557 AATGTATCGATACAT
1 AATGTATCGATACAT
662572 GTATTGTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.24
Consensus pattern (30 bp):
AATGTATCGATACATCTGGAAAAAAAACAG
Found at i:666960 original size:14 final size:14
Alignment explanation
Indices: 666936--666977 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
666926 TAATATTCAA
666936 TCAACACTTGAACAC
1 TCAA-ACTTGAACAC
*
666951 TCAAACTTGAAAAC
1 TCAAACTTGAACAC
*
666965 TTAAACTTGAACA
1 TCAAACTTGAACA
666978 TGCAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.45, C:0.24, G:0.07, T:0.24
Consensus pattern (14 bp):
TCAAACTTGAACAC
Found at i:667430 original size:19 final size:19
Alignment explanation
Indices: 667406--667443 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
667396 TAACACAATT
* *
667406 AAATGCTAAATCTTTAATA
1 AAATGCAAAATCATTAATA
667425 AAATGCAAAATCATTAATA
1 AAATGCAAAATCATTAATA
667444 TACAAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
AAATGCAAAATCATTAATA
Found at i:668840 original size:18 final size:18
Alignment explanation
Indices: 668817--668852 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
668807 GGTTTGGCCA
668817 AAATTAAGTATCTATACT
1 AAATTAAGTATCTATACT
668835 AAATTAAGTATCTATACT
1 AAATTAAGTATCTATACT
668853 TAAAGTTTGG
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:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
AAATTAAGTATCTATACT
Found at i:675115 original size:18 final size:19
Alignment explanation
Indices: 675086--675137 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 19
675076 TTATACTTTC
*
675086 AATATATATTTAATTATC-
1 AATAAATATTTAATTATCA
* *
675104 AA-AAATTTTTTA-TATCA
1 AATAAATATTTAATTATCA
675121 AATAAATATTTAATTAT
1 AATAAATATTTAATTAT
675138 TTTTTATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
16 4 0.15
17 9 0.35
18 10 0.38
19 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAAATATTTAATTATCA
Found at i:675426 original size:17 final size:17
Alignment explanation
Indices: 675393--675438 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
675383 AATAAATAAT
* *
675393 AAAAATAATTAAA-TTA
1 AAAAATTATAAAATTTA
675409 AATAAA-TATAAAATTTA
1 AA-AAATTATAAAATTTA
675426 AAAAATTATAAAA
1 AAAAATTATAAAA
675439 ATATATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATTATAAAATTTA
Found at i:676300 original size:4 final size:4
Alignment explanation
Indices: 676293--676318 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
676283 TCTCTCTCTC
676293 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
676319 AGTTTTTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:685558 original size:2 final size:2
Alignment explanation
Indices: 685551--685611 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
685541 TTATAAGAAC
* **
685551 AT AT AT AT -T AT GT -T AT AT AT GC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
685591 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
685612 GAAAGAAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:694176 original size:23 final size:23
Alignment explanation
Indices: 694150--694204 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
694140 TATATATATT
*
694150 TTAAAAATTTATTTAGACATAAA
1 TTAAAAATTTATTTAAACATAAA
** *
694173 TTAATGATTTATTTAAATATAAA
1 TTAAAAATTTATTTAAACATAAA
*
694196 TTTAAAATT
1 TTAAAAATT
694205 AAATATTTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAAAAATTTATTTAAACATAAA
Found at i:694204 original size:30 final size:30
Alignment explanation
Indices: 694170--694294 Score: 107
Period size: 30 Copynumber: 4.2 Consensus size: 30
694160 ATTTAGACAT
*
694170 AAATTAATGATTTATTTAAATATAAATTTA
1 AAATTAATAATTTATTTAAATATAAATTTA
694200 AAATTAA-ATATTTATTT-AATAGTAAA-TTA
1 AAATTAATA-ATTTATTTAAATA-TAAATTTA
* * *
694229 AATGTTAATAATATATTTAAATAT-AATTAA
1 AA-ATTAATAATTTATTTAAATATAAATTTA
* **
694259 AAATATAAAAATTTATCAAAATA-AAATGTTA
1 AAAT-TAATAATTTATTTAAATATAAAT-TTA
694290 AAATT
1 AAATT
694295 TTTAAAAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
29 12 0.16
30 53 0.70
31 11 0.14
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (30 bp):
AAATTAATAATTTATTTAAATATAAATTTA
Found at i:694675 original size:19 final size:17
Alignment explanation
Indices: 694645--694680 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
694635 TAAGTAAAAG
694645 TTTTTTTGTGTATTTAA
1 TTTTTTTGTGTATTTAA
694662 TTTTTTTGTATGTATTTAA
1 TTTTTTTG--TGTATTTAA
694681 AAAAATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.69
Consensus pattern (17 bp):
TTTTTTTGTGTATTTAA
Found at i:695350 original size:31 final size:30
Alignment explanation
Indices: 695315--695374 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
695305 TTAAAATAAT
695315 AATTAA-TTTATAA-ACATATAATATTTATTTA
1 AATTAATTTTATAATA-AT-TAAT-TTTATTTA
695346 AATTAATTTTATAATAATTAATTTTATTT
1 AATTAATTTTATAATAATTAATTTTATTT
695375 TTTGTTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 7 0.26
31 10 0.37
32 9 0.33
33 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
AATTAATTTTATAATAATTAATTTTATTTA
Found at i:695364 original size:15 final size:15
Alignment explanation
Indices: 695310--695372 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 15
695300 TTATTTTAAA
695310 ATAATAATTAA-TTT
1 ATAATAATTAATTTT
695324 ATAA-ACATATAATATTT
1 ATAATA-AT-TAAT-TTT
*
695341 AT-TTAAATTAATTTT
1 ATAAT-AATTAATTTT
695356 ATAATAATTAATTTT
1 ATAATAATTAATTTT
695371 AT
1 AT
695373 TTTTTGTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
13 1 0.03
14 6 0.15
15 20 0.50
16 5 0.12
17 7 0.17
18 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAATAATTAATTTT
Found at i:695615 original size:18 final size:18
Alignment explanation
Indices: 695587--695645 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 18
695577 AATGTAAATA
695587 AATATTTTATAAATTATTT
1 AATA-TTTATAAATTATTT
695606 AATATTTATAAAATTAATTT
1 AATATTTAT-AAATT-ATTT
*
695626 ACATTATAATATAAATTATT
1 A-A-TAT-TTATAAATTATT
695646 GTTTATGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 5 0.15
19 9 0.26
20 5 0.15
21 4 0.12
22 8 0.24
23 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATTTATAAATTATTT
Found at i:700163 original size:79 final size:79
Alignment explanation
Indices: 700056--700614 Score: 520
Period size: 79 Copynumber: 7.1 Consensus size: 79
700046 TCATTGATGT
* * * * * * *
700056 TTTTATTTCTAAAATACCGAATTTCCACCATC-AGGGATATTCTAACCCTGTTATTTTCGAAGAG
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGA-GGATACTCCAACCCCGTTATTTTCGAAGGG
*
700120 ATACTCCAACCCGGA
65 ATACTCCAACCCCGA
* * * * *
700135 TTTTATTTCTAAAACATTGGTTTTCCACCATCGAGGATACTCCAACCTCATTATTTAT-GAGGGG
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTT-TCGAAGGG
700199 ATACTCCAACCCCGA
65 ATACTCCAACCCCGA
* * * * * *
700214 TTTTATTTTTAAAATACCGATTTTTCACAATCGAGGATACTCTAACCCCGTTATTTTCGAAGGGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCGAAGGGA
*
700279 CACTCCAACCCCGA
66 TACTCCAACCCCGA
** * ** * * *
700293 TTTTATTTCTAAAACATTTATTTTTCATAATCGGGGATACTCCAACCCCGTGA-TCTCTGAAGGG
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTC-GAAGGG
* * *
700357 ATACTCTAACCCTGG
65 ATACTCCAACCCCGA
* ** *
700372 TTTTATTT-TCAAAACGTCGATTTTCCATAATCGAGGATACTCCAACCCCGTTATTTTCG-AGAA
1 TTTTATTTCT-AAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCGAAG-G
* *
700435 CATACTCCAACCCTTG-
64 GATACTCCAACCC-CGA
* * * *
700451 TTTTATTTCTAAAACA-CTGATTTTCTACCATCAAGGATATTCCAACCCCGTTATTTTTGAAGGG
1 TTTTATTTCTAAAACATC-GATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCGAAGGG
* ***
700515 ATACTCTAACTTTGA
65 ATACTCCAACCCCGA
* * * * * * *
700530 TTTTATTTCCAAAACAACGATTTTCTACCATCGCGGATACTCCAACTCCGTTATTTTTGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCGAAGGGA
* *
700595 TACTCCAACCTCGT
66 TACTCCAACCCCGA
700609 TTTTAT
1 TTTTAT
700615 CTCCAAAGTA
Statistics
Matches: 396, Mismatches: 71, Indels: 26
0.80 0.14 0.05
Matches are distributed among these distances:
78 10 0.03
79 375 0.95
80 11 0.03
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCGAAGGGA
TACTCCAACCCCGA
Found at i:703705 original size:97 final size:95
Alignment explanation
Indices: 703539--703781 Score: 287
Period size: 97 Copynumber: 2.5 Consensus size: 95
703529 TTTTGGTTAA
* * * * * *
703539 AAAACGAGGTTGGAGTATCTCTTCAGATGAAT-AGGGTTGGAGTATCCTCGATGATGATAATTTA
1 AAAACAAGGTTGGAGTATCTCCTCGGATGAATGA-GGTTGAAGTATCC-CTATGATGACAATTTA
*
703603 GGCAAAAATAAGATTCAAATCTTGACAAGTTT
64 GGCAAAAATAAGATTCAAATCTTCACAAGTTT
*
703635 GAAAACAAGGTTGGAGTATCTCCTCGGATGATTGAGGTTGAAGTATCCCTATTGATGACAATTTA
1 -AAAACAAGGTTGGAGTATCTCCTCGGATGAATGAGGTTGAAGTATCCCTA-TGATGACAATTTA
*
703700 GGCAAAAATAAGATTTAAATCTTCACAAGTTT
64 GGCAAAAATAAGATTCAAATCTTCACAAGTTT
* * *
703732 AAAA-ATGGGTTGGAGTAT-TCCTTCGGAAGAATGAGATT-AGAGTATCCCTA
1 AAAACA-AGGTTGGAGTATCTCC-TCGGATGAATGAGGTTGA-AGTATCCCTA
703782 ATAAAAAAAA
Statistics
Matches: 128, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
95 5 0.04
96 40 0.31
97 82 0.64
98 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (95 bp):
AAAACAAGGTTGGAGTATCTCCTCGGATGAATGAGGTTGAAGTATCCCTATGATGACAATTTAGG
CAAAAATAAGATTCAAATCTTCACAAGTTT
Found at i:706209 original size:52 final size:52
Alignment explanation
Indices: 706134--706273 Score: 172
Period size: 52 Copynumber: 2.7 Consensus size: 52
706124 AACTGCCTGC
* * * * *
706134 ATGTATCGATACATTGAAGAATGTATCAATACGTTTAGGTCAAAAACCCAGA
1 ATGTATCAATACAATGAAAAATGTATCAATACATTTAGGTCAAAAACCCAAA
* * *
706186 ATGTATCAATACAATGAAAAATGTATCAATACATTTAGGTTAAAAGCTCAAA
1 ATGTATCAATACAATGAAAAATGTATCAATACATTTAGGTCAAAAACCCAAA
* * * *
706238 ATGTATTAATAAAATGAAAAATATATCGATACATTT
1 ATGTATCAATACAATGAAAAATGTATCAATACATTT
706274 TTTTTTTCAG
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (52 bp):
ATGTATCAATACAATGAAAAATGTATCAATACATTTAGGTCAAAAACCCAAA
Found at i:716716 original size:20 final size:20
Alignment explanation
Indices: 716669--716743 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
716659 AAAAAGACAT
*
716669 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
716688 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
716709 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
716729 AATGTATCGATACAT
1 AATGTATCGATACAT
716744 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:716737 original size:40 final size:39
Alignment explanation
Indices: 716666--716743 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
716656 GGTAAAAAGA
* *
716666 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
716705 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
716744 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:720350 original size:40 final size:40
Alignment explanation
Indices: 720305--720384 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
720295 TGATTAAAGA
* * *
720305 AAATTATGCAATCCTTGACAATCAATTATAACAACCATAT
1 AAATTATGCAAACCCTGACAATCAATTATAACAAACATAT
*
720345 AAATTATGTAAACCCTGACAATCAATTATAACAAACATAT
1 AAATTATGCAAACCCTGACAATCAATTATAACAAACATAT
720385 CATATGTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.29
Consensus pattern (40 bp):
AAATTATGCAAACCCTGACAATCAATTATAACAAACATAT
Found at i:724370 original size:24 final size:23
Alignment explanation
Indices: 724326--724384 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
724316 TTAATTTTTT
724326 AAAATAAAATATAAAATTATATA
1 AAAATAAAATATAAAATTATATA
*
724349 AAAATAAATATATCAACA-TATATA
1 AAAATAAA-ATAT-AAAATTATATA
*
724373 AAATTAAAATAT
1 AAAATAAAATAT
724385 TTGAATATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 12 0.38
24 17 0.53
25 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAAAATATAAAATTATATA
Found at i:724774 original size:21 final size:21
Alignment explanation
Indices: 724750--724790 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
724740 ATAATTAAAA
*
724750 ATATTTT-TTATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
724771 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
724791 AATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:726693 original size:34 final size:34
Alignment explanation
Indices: 726653--726724 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
726643 GTACCAAACC
726653 TTTTATTTCTTTCTACATAAGAAATGCTATACCT
1 TTTTATTTCTTTCTACATAAGAAATGCTATACCT
** *
726687 TTTTATTTCTTTCTACATGTGAAATGTTATACCT
1 TTTTATTTCTTTCTACATAAGAAATGCTATACCT
726721 TTTT
1 TTTT
726725 TAGTAATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (34 bp):
TTTTATTTCTTTCTACATAAGAAATGCTATACCT
Found at i:727197 original size:15 final size:15
Alignment explanation
Indices: 727177--727208 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
727167 AAATTTTCAC
727177 TATAAATGCAATACT
1 TATAAATGCAATACT
*
727192 TATAAATTCAATACT
1 TATAAATGCAATACT
727207 TA
1 TA
727209 ATTTTTCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (15 bp):
TATAAATGCAATACT
Found at i:728034 original size:3 final size:3
Alignment explanation
Indices: 728026--728065 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
728016 ATATATACAT
728026 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
728066 AACTGTTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:729529 original size:17 final size:17
Alignment explanation
Indices: 729507--729539 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
729497 ATATTATAAA
729507 TTTATATAAAATTTTAT
1 TTTATATAAAATTTTAT
*
729524 TTTATATAAATTTTTA
1 TTTATATAAAATTTTA
729540 AGCGTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATATAAAATTTTAT
Found at i:731021 original size:23 final size:23
Alignment explanation
Indices: 730991--731037 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
730981 ATCTAATTAG
730991 CCCTTAATCATTCAATTTTATGT
1 CCCTTAATCATTCAATTTTATGT
731014 CCCTTAATCATTCAATTTTATGT
1 CCCTTAATCATTCAATTTTATGT
731037 C
1 C
731038 TTACATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.47
Consensus pattern (23 bp):
CCCTTAATCATTCAATTTTATGT
Found at i:731907 original size:3 final size:3
Alignment explanation
Indices: 731899--731933 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
731889 TTTTGGTTAA
731899 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
731934 AAACCTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:732133 original size:18 final size:18
Alignment explanation
Indices: 732110--732144 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
732100 ATAAATCAAA
*
732110 AAATAAAAATTTTATTTG
1 AAATAAAAAGTTTATTTG
732128 AAATAAAAAGTTTATTT
1 AAATAAAAAGTTTATTT
732145 TTCTTGAAAA
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:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AAATAAAAAGTTTATTTG
Found at i:734716 original size:2 final size:2
Alignment explanation
Indices: 734709--734737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
734699 TTTTTGCCCA
734709 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
734738 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:734742 original size:2 final size:2
Alignment explanation
Indices: 734737--734761 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
734727 TCTCTCTCTC
734737 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
734762 GAACAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:736163 original size:21 final size:22
Alignment explanation
Indices: 736139--736194 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
736129 TTGAGAAAAA
736139 AATAATTATTAAAAAT-ATTAG
1 AATAATTATTAAAAATAATTAG
* *
736160 AAT-ATGAATAATAAATAATTAG
1 AATAATTATTAA-AAATAATTAG
*
736182 AA-ATTTATTAAAA
1 AATAATTATTAAAA
736195 TTGTGTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 6 0.22
21 9 0.33
22 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
AATAATTATTAAAAATAATTAG
Found at i:738140 original size:19 final size:19
Alignment explanation
Indices: 738118--738173 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
738108 TTTATATTAT
738118 ATTTTAATAATTATATAAA
1 ATTTTAATAATTATATAAA
738137 ATTTATAAT-ATTAT-T-AA
1 ATTT-TAATAATTATATAAA
*
738154 ATTTTTATATATATATATAA
1 ATTTTAATA-AT-TATATAA
738174 TCACAACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
16 3 0.10
17 6 0.20
18 3 0.10
19 12 0.40
20 5 0.17
21 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTAATAATTATATAAA
Found at i:738155 original size:17 final size:17
Alignment explanation
Indices: 738112--738158 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
738102 TATAATTTTA
*
738112 TATTATATTTTAATAAT
1 TATTAAATTTTAATAAT
738129 TATATAAAATTTATAAT-AT
1 TAT-T-AAATTT-TAATAAT
738148 TATTAAATTTT
1 TATTAAATTTT
738159 TATATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 9 0.35
18 2 0.08
19 10 0.38
20 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTAAATTTTAATAAT
Found at i:739773 original size:18 final size:18
Alignment explanation
Indices: 739739--739793 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
739729 TAAATACTTT
**
739739 ATATATATTAAACATATC
1 ATATATATTAATTATATC
739757 ATATATATTAATTATAT-
1 ATATATATTAATTATATC
* *
739774 TTAAATA-T-ATTATATC
1 ATATATATTAATTATATC
739790 ATAT
1 ATAT
739794 TTATATCTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 5 0.17
18 15 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATATATTAATTATATC
Found at i:739813 original size:29 final size:29
Alignment explanation
Indices: 739736--739828 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
739726 ACATAAATAC
* *
739736 TTTATATATATTAAACATATCATAT-ATA
1 TTTATATATATTAAATATATTATATCATA
*
739764 TTAAT-TATATTTAAATATATTATATCATA
1 TTTATATATA-TTAAATATATTATATCATA
*
739793 TTTATATCTATTAAATATATTAATATTCAT-
1 TTTATATATATTAAATATATT-ATA-TCATA
739823 TTTATA
1 TTTATA
739829 ATTAAAATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.07
28 17 0.31
29 18 0.33
30 12 0.22
31 4 0.07
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTATATATATTAAATATATTATATCATA
Found at i:739818 original size:37 final size:37
Alignment explanation
Indices: 739736--739813 Score: 93
Period size: 39 Copynumber: 2.1 Consensus size: 37
739726 ACATAAATAC
* *
739736 TTTATATATATTAAACATATCATATATATTAATTATA
1 TTTAAATATATTAAACATATCATATATATTAAATATA
* * *
739773 TTTAAATATATTATATCATATTTATATCTATTAAATATA
1 TTTAAATATATTA-AACATA-TCATATATATTAAATATA
739812 TT
1 TT
739814 AATATTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 12 0.35
38 5 0.15
39 17 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (37 bp):
TTTAAATATATTAAACATATCATATATATTAAATATA
Found at i:744032 original size:25 final size:25
Alignment explanation
Indices: 744004--744053 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
743994 GAACACTTGG
744004 TTCAAAGAATGATGGATAAGGCTAA
1 TTCAAAGAATGATGGATAAGGCTAA
744029 TTCAAAGAATGATGGATAAGGCTAA
1 TTCAAAGAATGATGGATAAGGCTAA
744054 AATTGAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (25 bp):
TTCAAAGAATGATGGATAAGGCTAA
Found at i:750825 original size:28 final size:28
Alignment explanation
Indices: 750762--751090 Score: 170
Period size: 28 Copynumber: 12.3 Consensus size: 28
750752 CAAGTTAAAA
* * *
750762 CCCACATGCGTTGGCACACAA-TCTAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
* * *
750789 CCCATATTCGTTGGCACATAAGTTTAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
*
750817 CCTACATTCGCTGGCAC----G--TAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
* * *
750839 CCCATATTCGCTGGCACGTAAGTTTAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
*
750867 CCCACATTCGTTGGCACATAAGTCTAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
**
750895 CTTACATTCGCTGG--CAT--G--TAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
* * * * *
750917 CCCATATTCACCGGCACGTAAGTTTAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
* * * *
750945 CCCACTTTCGCTAGCACGTAAGTCAAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
* * *
750973 CCCACATTAGTTGGCACATGAA-CCTAAG
1 CCCACATTCGCTGGCACAT-AAGTCTAAG
* ** * *
751001 CCCATATTCATTGGCACACAAGTCAAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
* * * *
751029 CCCACACTAGCAGGCATATAAG--TAAG
1 CCCACATTCGCTGGCACATAAGTCTAAG
* * * * *
751055 CCAACACTAGTTGGCACATGAGT-TAAAG
1 CCCACATTCGCTGGCACATAAGTCT-AAG
751083 CCCACATT
1 CCCACATT
751091 AGTTGTCATC
Statistics
Matches: 227, Mismatches: 58, Indels: 33
0.71 0.18 0.10
Matches are distributed among these distances:
22 32 0.14
24 4 0.02
26 25 0.11
27 21 0.09
28 143 0.63
29 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (28 bp):
CCCACATTCGCTGGCACATAAGTCTAAG
Found at i:750845 original size:50 final size:50
Alignment explanation
Indices: 750785--750888 Score: 163
Period size: 50 Copynumber: 2.1 Consensus size: 50
750775 GCACACAATC
* * *
750785 TAAGCCCATATTCGTTGGCACATAAGTTTAAGCCTACATTCGCTGGCACG
1 TAAGCCCATATTCGCTGGCACATAAGTTTAAGCCCACATTCGCTGGCACA
* *
750835 TAAGCCCATATTCGCTGGCACGTAAGTTTAAGCCCACATTCGTTGGCACA
1 TAAGCCCATATTCGCTGGCACATAAGTTTAAGCCCACATTCGCTGGCACA
750885 TAAG
1 TAAG
750889 TCTAAGCTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (50 bp):
TAAGCCCATATTCGCTGGCACATAAGTTTAAGCCCACATTCGCTGGCACA
Found at i:750847 original size:22 final size:22
Alignment explanation
Indices: 750813--750860 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
750803 CACATAAGTT
*
750813 TAAGCCTACATTCGCTGGCACG
1 TAAGCCCACATTCGCTGGCACG
*
750835 TAAGCCCATATTCGCTGGCACG
1 TAAGCCCACATTCGCTGGCACG
750857 TAAG
1 TAAG
750861 TTTAAGCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (22 bp):
TAAGCCCACATTCGCTGGCACG
Found at i:750876 original size:78 final size:78
Alignment explanation
Indices: 750785--750989 Score: 284
Period size: 78 Copynumber: 2.6 Consensus size: 78
750775 GCACACAATC
* * *
750785 TAAGCCCATATTCGTTGGCACATAAGTTTAAGCCTACATTCGCTGGCACGTAAGCCCATATTCGC
1 TAAGCCCACATTCGTTGGCACATAAGTCTAAGCCTACATTCGCTGGCACGTAAGCCCATATTCAC
*
750850 TGGCACGTAAGTT
66 CGGCACGTAAGTT
* *
750863 TAAGCCCACATTCGTTGGCACATAAGTCTAAGCTTACATTCGCTGGCATGTAAGCCCATATTCAC
1 TAAGCCCACATTCGTTGGCACATAAGTCTAAGCCTACATTCGCTGGCACGTAAGCCCATATTCAC
750928 CGGCACGTAAGTT
66 CGGCACGTAAGTT
* * * * * * * *
750941 TAAGCCCACTTTCGCTAGCACGTAAGTCAAAGCCCACATTAGTTGGCAC
1 TAAGCCCACATTCGTTGGCACATAAGTCTAAGCCTACATTCGCTGGCAC
750990 ATGAACCTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 111 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (78 bp):
TAAGCCCACATTCGTTGGCACATAAGTCTAAGCCTACATTCGCTGGCACGTAAGCCCATATTCAC
CGGCACGTAAGTT
Found at i:751093 original size:28 final size:28
Alignment explanation
Indices: 750733--751114 Score: 128
Period size: 28 Copynumber: 14.2 Consensus size: 28
750723 TATCAAAAGG
750733 AAGCCCACACTT-GTTGGCAC--AAGTTA
1 AAGCCCACA-TTAGTTGGCACATAAGTTA
* ** *
750759 AAACCCACATGCGTTGGCACACAA-TCT-
1 AAGCCCACATTAGTTGGCACATAAGT-TA
* * *
750786 AAGCCCATATTCGTTGGCACATAAGTTT
1 AAGCCCACATTAGTTGGCACATAAGTTA
* * *
750814 AAGCCTACATTCGCTGGCAC----G-T-
1 AAGCCCACATTAGTTGGCACATAAGTTA
* * * * *
750836 AAGCCCATATTCGCTGGCACGTAAGTTT
1 AAGCCCACATTAGTTGGCACATAAGTTA
*
750864 AAGCCCACATTCGTTGGCACATAAGTCT-
1 AAGCCCACATTAGTTGGCACATAAGT-TA
** * *
750892 AAGCTTACATTCGCTGG--CAT--G-T-
1 AAGCCCACATTAGTTGGCACATAAGTTA
* ** * *
750914 AAGCCCATATTCA-CCGGCACGTAAGTTT
1 AAGCCCACATT-AGTTGGCACATAAGTTA
* * * * * *
750942 AAGCCCACTTTCGCTAGCACGTAAGTCA
1 AAGCCCACATTAGTTGGCACATAAGTTA
**
750970 AAGCCCACATTAGTTGGCACATGAACCT-
1 AAGCCCACATTAGTTGGCACAT-AAGTTA
* * *
750998 AAGCCCATATTCA-TTGGCACACAAGTCA
1 AAGCCCACATT-AGTTGGCACATAAGTTA
* ** *
751026 AAGCCCACACTAGCAGGCATATAAG-T-
1 AAGCCCACATTAGTTGGCACATAAGTTA
* * *
751052 AAGCCAACACTAGTTGGCACATGAGTTA
1 AAGCCCACATTAGTTGGCACATAAGTTA
* *
751080 AAGCCCACATTAGTTGTCATC-TAAGTCA
1 AAGCCCACATTAGTTGGCA-CATAAGTTA
751108 AAGCCCA
1 AAGCCCA
751115 TACTAGCTGG
Statistics
Matches: 268, Mismatches: 60, Indels: 54
0.70 0.16 0.14
Matches are distributed among these distances:
22 30 0.11
23 1 0.00
24 4 0.01
25 1 0.00
26 41 0.15
27 28 0.10
28 158 0.59
29 5 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (28 bp):
AAGCCCACATTAGTTGGCACATAAGTTA
Found at i:751128 original size:28 final size:28
Alignment explanation
Indices: 751020--751129 Score: 100
Period size: 28 Copynumber: 4.0 Consensus size: 28
751010 ATTGGCACAC
* *
751020 AAGTCAAAGCCCACACTAGCAGGCATAT
1 AAGTCAAAGCCCACACTAGCTGGCATCT
* *
751048 AAGT--AAGCCAACACTAGTTGGCA-CAT
1 AAGTCAAAGCCCACACTAGCTGGCATC-T
* * * * *
751074 GAGTTAAAGCCCACATTAGTTGTCATCT
1 AAGTCAAAGCCCACACTAGCTGGCATCT
*
751102 AAGTCAAAGCCCATACTAGCTGGCATCT
1 AAGTCAAAGCCCACACTAGCTGGCATCT
751130 CGTAGGGAAG
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
26 20 0.31
28 43 0.67
29 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (28 bp):
AAGTCAAAGCCCACACTAGCTGGCATCT
Found at i:751511 original size:43 final size:42
Alignment explanation
Indices: 751434--751534 Score: 112
Period size: 43 Copynumber: 2.4 Consensus size: 42
751424 AAGAAGTAGG
* * **
751434 TGGGAGCACGAGCAACTGGCAGTAGCAAGTGATGAAAAAAAA
1 TGGGAGCACAAGCAACTGGCAGCAGCAAACGATGAAAAAAAA
* * * *
751476 TAGGGAGCACAAGCAACTGGTAGCAGTAAACGATGAAGAATAA
1 T-GGGAGCACAAGCAACTGGCAGCAGCAAACGATGAAAAAAAA
751519 TGGGAAGCACAAGCAA
1 TGGG-AGCACAAGCAA
751535 AGTGAAAAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 4 0.08
43 45 0.92
ACGTcount: A:0.44, C:0.15, G:0.30, T:0.12
Consensus pattern (42 bp):
TGGGAGCACAAGCAACTGGCAGCAGCAAACGATGAAAAAAAA
Found at i:752148 original size:4 final size:4
Alignment explanation
Indices: 752139--752191 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
752129 TGGACTAGAG
*
752139 AAGA AAGA AAG- AAG- AAGG AAGA AAGA AA-A AA-A AAGA AAGA AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
752182 AAGA AAGA AA
1 AAGA AAGA AA
752192 AAAATTGGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
3 15 0.33
4 30 0.67
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:752153 original size:7 final size:7
Alignment explanation
Indices: 752143--752190 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
752133 CTAGAGAAGA
752143 AAGAAAG
1 AAGAAAG
*
752150 AAGAAGG
1 AAGAAAG
752157 AAGAAAG
1 AAGAAAG
752164 -A-AAA-
1 AAGAAAG
752168 AA-AAAG
1 AAGAAAG
752174 AAAGAAAG
1 -AAGAAAG
752182 AAGAAAG
1 AAGAAAG
752189 AA
1 AA
752191 AAAAATTGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 7 0.20
6 1 0.03
7 23 0.66
8 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:752161 original size:18 final size:17
Alignment explanation
Indices: 752137--752186 Score: 70
Period size: 18 Copynumber: 3.1 Consensus size: 17
752127 AGTGGACTAG
752137 AGAAGAAAGAAAGAAGA
1 AGAAGAAAGAAAGAAGA
752154 AGGAAGAAAGAAA-AA-A
1 A-GAAGAAAGAAAGAAGA
752170 A-AAGAAAGAAAGAAGA
1 AGAAGAAAGAAAGAAGA
752186 A
1 A
752187 AGAAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.33
15 2 0.07
16 4 0.13
17 3 0.10
18 11 0.37
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AGAAGAAAGAAAGAAGA
Found at i:752178 original size:25 final size:24
Alignment explanation
Indices: 752137--752195 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
752127 AGTGGACTAG
* *
752137 AGAAGAAAGAAAGAAGAAGGAAGAA
1 AGAA-AAAAAAAGAAGAAAGAAGAA
752162 AGAAAAAAAAAGAAAGAAAGAAGAA
1 AGAAAAAAAAAG-AAGAAAGAAGAA
752187 AGAAAAAAA
1 AGAAAAAAA
752196 TTGGGTAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (24 bp):
AGAAAAAAAAAGAAGAAAGAAGAA
Found at i:752613 original size:3 final size:3
Alignment explanation
Indices: 752605--752629 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
752595 GTTTTAGAGA
752605 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
752630 TTGCTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:753105 original size:109 final size:109
Alignment explanation
Indices: 752909--753425 Score: 484
Period size: 109 Copynumber: 4.7 Consensus size: 109
752899 TCCTATTTAG
* * ** * ** ** *
752909 AATTTATTTTTGCATTAATTACGT-AGATTCGGATACTAAGGGATTGATCCCGAAATAAATCATT
1 AATTCATTTTTGCATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCCCGAAATAAATCATC
* * * *
752973 GTCTAGAGTCTTAAAGCGGCGTACGAATGCCCTTTACATAGGAA
66 GTCTAGAGTCTTAAAGCGACGTACGAACGCCCTTTATATAGGAT
* * * ** *
753017 AATTTATTTTTACATTAATTACGTAATATTTGGGCACCAAAAGATTGGCCATGAAATAAATAATC
1 AATTCATTTTTGCATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCCCGAAATAAATCATC
* ** * *
753082 GTCTAGAGTCTTAAAGTGACGTACGAACATCTTTTATATAGGAC
66 GTCTAGAGTCTTAAAGCGACGTACGAACGCCCTTTATATAGGAT
* * * ** * *
753126 AATTCATTTTTGCATTAATTATGTAATATTCAGGCACTAAGCGATTGGCCTCGAAATAAATTATC
1 AATTCATTTTTGCATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCCCGAAATAAATCATC
* * * *
753191 GTCTAAAGT-TGTAAAACGGCATACGAACGCCCTTTATATAGGAT
66 GTCTAGAGTCT-TAAAGCGACGTACGAACGCCCTTTATATAGGAT
** *
753235 AATTCATTTTTTTGCATTAATTACGTAAT-TTCGGGCACCAAAAGATTGGCCCCGAAATAGGTTA
1 AATTCA--TTTTTGCATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCCCGAAATAAATCA
* * * * * * * *
753299 TCATCTAAAATCATAAAACGACGTACAAATGCCCTTTGTATAGGAT
64 TCGTCTAGAGTCTTAAAGCGACGTACGAACGCCCTTTATATAGGAT
* * * * **
753345 AATTCATTTTTTGCACTAATTACATAA-ATTCGAGCATCAAAAGATTGGCCCCGAAATAGGTCAT
1 AATTCA-TTTTTGCATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCCCGAAATAAATCAT
*
753409 CGTCTAGAGTCATAAAG
65 CGTCTAGAGTCTTAAAG
753426 TGGCATATTA
Statistics
Matches: 336, Mismatches: 67, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
108 24 0.07
109 221 0.66
110 71 0.21
111 20 0.06
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (109 bp):
AATTCATTTTTGCATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCCCGAAATAAATCATC
GTCTAGAGTCTTAAAGCGACGTACGAACGCCCTTTATATAGGAT
Found at i:753447 original size:219 final size:218
Alignment explanation
Indices: 752957--753447 Score: 517
Period size: 219 Copynumber: 2.2 Consensus size: 218
752947 AGGGATTGAT
* * * * *
752957 CCCGAAATAAATCATTGTCTAGAGTCTTAAAGCGGCGTACGAATGCCCTTTACATAGGAAAATTT
1 CCCGAAATAAATCATCGTCTAGAGTCATAAAGCGGCATACGAACGCCCTTTATATAGGAAAATTT
* * *
753022 ATTTTTACATTAATTACGTAATATTTGGGCACCAAAAGATTGGCCATGAAATAAATAATCGTCTA
66 ATTTTTACATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCACGAAATAAATAATCATCTA
* * * ** * * **
753087 GAGTCTTAAAGTGACGTACGAACATCTTTTATATAGGACAATTCATTTTTGCATTAATTATGTAA
131 AAATCATAAAACGACGTACGAACATCCTTTATATAGGACAATTCATTTTTGCACTAATTACATAA
**
753152 TATTCAGGCACTAAGCGATTGGC
196 TATTCAGGCACTAAAAGATTGGC
* * * ** * *
753175 CTCGAAATAAATTATCGTCTAAAGTTGTAAAACGGCATACGAACGCCCTTTATATAGGATAATTC
1 CCCGAAATAAATCATCGTCTAGAGTCATAAAGCGGCATACGAACGCCCTTTATATAGGAAAATT-
* * * ** *
753240 ATTTTTTTGCATTAATTACGTAAT-TTCGGGCACCAAAAGATTGGCCCCGAAATAGGTTATCATC
65 -TATTTTTACATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCACGAAATAAATAATCATC
* *
753304 TAAAATCATAAAACGACGTAC-AA-ATGCCCTTTGTATAGGATAATTCATTTTTTGCACTAATTA
129 TAAAATCATAAAACGACGTACGAACAT--CCTTTATATAGGACAATTCA-TTTTTGCACTAATTA
753367 CATAA-ATTC-GAGCA-TCAAAAGATTGGC
191 CATAATATTCAG-GCACT-AAAAGATTGGC
** * ** *
753394 CCCGAAATAGGTCATCGTCTAGAGTCATAAAGTGGCATATTAACGCTCTTTATA
1 CCCGAAATAAATCATCGTCTAGAGTCATAAAGCGGCATACGAACGCCCTTTATA
753448 GAATTTATTT
Statistics
Matches: 221, Mismatches: 45, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
217 2 0.01
218 57 0.26
219 124 0.56
220 38 0.17
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (218 bp):
CCCGAAATAAATCATCGTCTAGAGTCATAAAGCGGCATACGAACGCCCTTTATATAGGAAAATTT
ATTTTTACATTAATTACGTAATATTCGGGCACCAAAAGATTGGCCACGAAATAAATAATCATCTA
AAATCATAAAACGACGTACGAACATCCTTTATATAGGACAATTCATTTTTGCACTAATTACATAA
TATTCAGGCACTAAAAGATTGGC
Found at i:755559 original size:21 final size:21
Alignment explanation
Indices: 755503--755559 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
755493 GTTATTATCA
* *
755503 AAATATTAAAAATATTTTTATAT
1 AAATATT--AAATAATTTTAAAT
* **
755526 TAATATTTTATAATTTTAAAT
1 AAATATTAAATAATTTTAAAT
755547 AAATATTAAATAA
1 AAATATTAAATAA
755560 AAATATTTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 20 0.77
23 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATTAAATAATTTTAAAT
Done.