Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold303
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: 874694
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:601916 original size:11 final size:10
Alignment explanation
Indices: 601873--601914 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
601863 ATAAAAATAT
601873 AATTTTTT-A
1 AATTTTTTAA
601882 AATTTTTTAAA
1 AATTTTTT-AA
*
601893 AATATTTTAA
1 AATTTTTTAA
601903 AATTTTTTAA
1 AATTTTTTAA
601913 AA
1 AA
601915 ATAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.28
10 13 0.45
11 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:605152 original size:63 final size:63
Alignment explanation
Indices: 605053--605175 Score: 228
Period size: 63 Copynumber: 2.0 Consensus size: 63
605043 TTGTTGGCAT
*
605053 GTAAACTCGTTTAATCCCAAGTATCCCCTTCTCGGTCACCAATTTATCAAAAACAAAAAAGAC
1 GTAAACTCGTTTAATCCCAAGTATCCCCTTCTCGGTCACCAATTTATCAAAAAAAAAAAAGAC
*
605116 GTAAACTTGTTTAATCCCAAGTATCCCCTTCTCGGTCACCAATTTATCAAAAAAAAAAAA
1 GTAAACTCGTTTAATCCCAAGTATCCCCTTCTCGGTCACCAATTTATCAAAAAAAAAAAA
605176 AAAAAAGACC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (63 bp):
GTAAACTCGTTTAATCCCAAGTATCCCCTTCTCGGTCACCAATTTATCAAAAAAAAAAAAGAC
Found at i:615170 original size:2 final size:2
Alignment explanation
Indices: 615163--615214 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
615153 TGAAAGACAA
615163 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
615205 AG AG AG AG AG
1 AG AG AG AG AG
615215 GGTTCTCTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:617105 original size:153 final size:155
Alignment explanation
Indices: 616797--617106 Score: 606
Period size: 155 Copynumber: 2.0 Consensus size: 155
616787 TGTGGGTTCA
616797 ATTAAAAAAAAGAACAGAGAAAGAGCAAGGCTATATGTTTTGGATGTTTGTAGACTTTGTTGTAG
1 ATTAAAAAAAAGAACAGAGAAAGAGCAAGGCTATATGTTTTGGATGTTTGTAGACTTTGTTGTAG
616862 GCTATAGCTTCTAAGGCTTCGGGGTTTTTTATTTTTTTTTGAATCTCTAAATTCTGGAATACTTT
66 GCTATAGCTTCTAAGGCTTCGGGGTTTTTTATTTTTTTTTGAATCTCTAAATTCTGGAATACTTT
616927 TTGCTCTTCTTTTAACTGTCCTTTT
131 TTGCTCTTCTTTTAACTGTCCTTTT
616952 ATTAAAAAAAAGAACAGAGAAAGAGCAAGGCTATATGTTTTGGATGTTTGTAGACTTTGTTGTAG
1 ATTAAAAAAAAGAACAGAGAAAGAGCAAGGCTATATGTTTTGGATGTTTGTAGACTTTGTTGTAG
617017 GCTATAGCTTCTAAGGCTTCGGGG-TTTTT-TTTTTTTTTGAATCTCTAAATTCTGGAATACTTT
66 GCTATAGCTTCTAAGGCTTCGGGGTTTTTTATTTTTTTTTGAATCTCTAAATTCTGGAATACTTT
617080 TTGCTCTTCTTTTAACTGTCCTTTT
131 TTGCTCTTCTTTTAACTGTCCTTTT
617105 AT
1 AT
617107 CATGAACAGT
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
153 61 0.39
154 5 0.03
155 89 0.57
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (155 bp):
ATTAAAAAAAAGAACAGAGAAAGAGCAAGGCTATATGTTTTGGATGTTTGTAGACTTTGTTGTAG
GCTATAGCTTCTAAGGCTTCGGGGTTTTTTATTTTTTTTTGAATCTCTAAATTCTGGAATACTTT
TTGCTCTTCTTTTAACTGTCCTTTT
Found at i:619272 original size:2 final size:2
Alignment explanation
Indices: 619265--619306 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
619255 TGATTGTACG
619265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
619307 TGTTATGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:622110 original size:2 final size:2
Alignment explanation
Indices: 622103--622131 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
622093 ATGAATTTTG
622103 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
622132 TTAAAAAACA
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:622546 original size:17 final size:17
Alignment explanation
Indices: 622499--622547 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
622489 ATTTTTTTAA
622499 TAAAT-TAATTTTAAAGT
1 TAAATATAA-TTTAAAGT
622516 TAATATATAA-TTAAA-T
1 TAA-ATATAATTTAAAGT
622532 TAAATATAAGTTTAAA
1 TAAATATAA-TTTAAA
622548 ATATTTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.21
16 4 0.14
17 13 0.46
18 2 0.07
19 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
TAAATATAATTTAAAGT
Found at i:625335 original size:135 final size:136
Alignment explanation
Indices: 625092--625339 Score: 381
Period size: 136 Copynumber: 1.8 Consensus size: 136
625082 TATCTTTGTG
* * * *
625092 TTGTGGTCGTGGTCGGCTATTCTTGTCTTCTCAACACGCTCCCGAGTCCAACCCGTGAATCACTG
1 TTGTGGTCGTGGTCGGCAATTCTTATCTTCTCAACACGATCCCGAGTCCAAACCGTGAATCACTG
*
625157 GAAATTTATGTTCAAAAGATCCGCGAGATCCTGGAAATTACATTTTACACGCCACGCGTCGTTTT
66 GAAATTTATGTTCAAAAGATCCGCGAGATCCTAGAAATTACATTTTACACGCCACGCGTCGTTTT
625222 TTTATT
131 TTTATT
* * * * *
625228 TTGTGGTTGTGGTCGGCAATTCTTATCTTCTCAACAGGATCCCGAGTTCAAACCTTGAA-CTCTG
1 TTGTGGTCGTGGTCGGCAATTCTTATCTTCTCAACACGATCCCGAGTCCAAACCGTGAATCACTG
* *
625292 GAAATTTATGTTTAAAAGATCTGCGAGATCCTAGAAATTACATTTTAC
66 GAAATTTATGTTCAAAAGATCCGCGAGATCCTAGAAATTACATTTTAC
625340 GGATAAAAGG
Statistics
Matches: 100, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
135 49 0.49
136 51 0.51
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (136 bp):
TTGTGGTCGTGGTCGGCAATTCTTATCTTCTCAACACGATCCCGAGTCCAAACCGTGAATCACTG
GAAATTTATGTTCAAAAGATCCGCGAGATCCTAGAAATTACATTTTACACGCCACGCGTCGTTTT
TTTATT
Found at i:627222 original size:2 final size:2
Alignment explanation
Indices: 627215--627248 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
627205 AGAAGCTATG
627215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
627249 TCCCTCATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:627536 original size:3 final size:3
Alignment explanation
Indices: 627530--627563 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
627520 CCACTACTAT
*
627530 TTA TTA TTA TTA TTA TTA -TA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
627564 CATAATAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:627553 original size:17 final size:16
Alignment explanation
Indices: 627527--627563 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
627517 ATACCACTAC
*
627527 TATTTATTATTATTAT
1 TATTTATTATTATCAT
627543 TATTATATTATTATCAT
1 TATT-TATTATTATCAT
627560 TATT
1 TATT
627564 CATAATAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATTATTATCAT
Found at i:628196 original size:29 final size:31
Alignment explanation
Indices: 628164--628224 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
628154 TTTAGTTTAA
628164 AATTAAAATTA-TTAAAATTT-TTATTATTT
1 AATTAAAATTATTTAAAATTTATTATTATTT
* *
628193 AATTTAAATTATTTTAAATTTAATTATTATTT
1 AATTAAAATTATTTAAAATTT-ATTATTATTT
628225 CTTAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 10 0.37
30 8 0.30
32 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
AATTAAAATTATTTAAAATTTATTATTATTT
Found at i:628199 original size:21 final size:21
Alignment explanation
Indices: 628175--628217 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
628165 ATTAAAATTA
*
628175 TTAAAAT-TTTTATTATTTAAT
1 TTAAAATATTTTA-AATTTAAT
*
628196 TTAAATTATTTTAAATTTAAT
1 TTAAAATATTTTAAATTTAAT
628217 T
1 T
628218 ATTATTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAAATATTTTAAATTTAAT
Found at i:641252 original size:2 final size:2
Alignment explanation
Indices: 641245--641269 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
641235 ATTCGATGTT
641245 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
641270 CAATTAAACT
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:641565 original size:2 final size:2
Alignment explanation
Indices: 641552--641585 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
641542 AATATTTTAA
* *
641552 AT AT AG AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
641586 GTAAAAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:644924 original size:30 final size:28
Alignment explanation
Indices: 644869--644923 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
644859 ATGTAATAAA
644869 GATAATTTTTTTAAGGCTATTATATATT
1 GATAATTTTTTTAAGGCTATTATATATT
644897 GATAATTTTTTTAAGGCTATTATATAT
1 GATAATTTTTTTAAGGCTATTATATAT
644924 AGACTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.53
Consensus pattern (28 bp):
GATAATTTTTTTAAGGCTATTATATATT
Found at i:647144 original size:27 final size:27
Alignment explanation
Indices: 647093--647145 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
647083 TAAAAAAATG
* *
647093 ATACTTTAATTACATATATTTTTATAT
1 ATACTTTAATTACATATAATATTATAT
647120 ATACTTTAATTA-ATATAAATATTATA
1 ATACTTTAATTACATAT-AATATTATA
647146 ATATTCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
ATACTTTAATTACATATAATATTATAT
Found at i:647318 original size:14 final size:15
Alignment explanation
Indices: 647299--647328 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
647289 TTACAAACCA
647299 ATCAA-CAACGTCCC
1 ATCAACCAACGTCCC
647313 ATCAACCAACGTCCC
1 ATCAACCAACGTCCC
647328 A
1 A
647329 GGAAGGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.37, C:0.43, G:0.07, T:0.13
Consensus pattern (15 bp):
ATCAACCAACGTCCC
Found at i:647384 original size:2 final size:2
Alignment explanation
Indices: 647377--647401 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
647367 TTCTTTCCCC
647377 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
647402 TAGAAAGGAT
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:647573 original size:21 final size:22
Alignment explanation
Indices: 647547--647591 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
647537 TAATAATTAA
*
647547 ATTTTAATATTTAT-ATTTT-TT
1 ATTTTAA-AATTATGATTTTGTT
647568 ATTTTAAAATTATGATTTTGTT
1 ATTTTAAAATTATGATTTTGTT
647590 AT
1 AT
647592 AAAAATACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 12 0.57
22 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
ATTTTAAAATTATGATTTTGTT
Found at i:647875 original size:22 final size:21
Alignment explanation
Indices: 647834--647878 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
647824 TCAATGTAAA
*
647834 AAATATTTTTAAATGATAATT
1 AAATATTTTTAAATCATAATT
647855 AAATAATTTTT-AATCACTAATT
1 AAAT-ATTTTTAAATCA-TAATT
647877 AA
1 AA
647879 GTTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATATTTTTAAATCATAATT
Found at i:647884 original size:23 final size:23
Alignment explanation
Indices: 647849--647902 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
647839 TTTTTAAATG
*
647849 ATAATTAA-ATAATT-TTTAATC
1 ATAATTAAGTTAATTATTTAATC
*
647870 ACTAATTAAGTTAATTATTTTATC
1 A-TAATTAAGTTAATTATTTAATC
647894 ATAA-TAAGT
1 ATAATTAAGT
647903 GTCATTACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 1 0.04
22 12 0.43
23 8 0.29
24 7 0.25
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (23 bp):
ATAATTAAGTTAATTATTTAATC
Found at i:648451 original size:3 final size:3
Alignment explanation
Indices: 648443--648492 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
648433 GAAAAAACCG
* *
648443 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAAGT AAT AAT GAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AA-T AAT AAT AAT AAT AAT
648490 AAT
1 AAT
648493 GAAAATGGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 36 0.88
4 4 0.10
5 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:648624 original size:2 final size:2
Alignment explanation
Indices: 648619--648649 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
648609 TCTCTTCATT
648619 TC 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 TC T
648650 AGCTCGCTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:649933 original size:2 final size:2
Alignment explanation
Indices: 649928--649953 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
649918 AGATTGGATA
649928 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
649954 TTTGTCCCTT
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:652603 original size:2 final size:2
Alignment explanation
Indices: 652596--652633 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
652586 TAGCTTTCGA
*
652596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
652634 TCAAGATGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:656505 original size:29 final size:29
Alignment explanation
Indices: 656443--656505 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 29
656433 CTTAATTTAT
*
656443 TTAAAATAAAAATTTAATAATATAATTTA
1 TTAAAATAAAAATTTAATAATATAATATA
* *
656472 ATAAAATTAAAAATTTATGTAA-ATAA-ATA
1 TTAAAA-TAAAAATTTA-ATAATATAATATA
656501 TTAAA
1 TTAAA
656506 TTTATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 11 0.39
30 14 0.50
31 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
TTAAAATAAAAATTTAATAATATAATATA
Found at i:657007 original size:2 final size:2
Alignment explanation
Indices: 657000--657027 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
656990 GAAAATTCAC
657000 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
657028 CACACACACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:659045 original size:6 final size:6
Alignment explanation
Indices: 659034--659071 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
659024 CTGCCATCTC
*
659034 TTTTCT TTTTCT TTTTCT TTTT-T TTTT-T TTTTGT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
659072 TGTGTTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (6 bp):
TTTTCT
Found at i:659051 original size:12 final size:11
Alignment explanation
Indices: 659034--659071 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
659024 CTGCCATCTC
659034 TTTTCTTTTTCT
1 TTTTCTTTTT-T
659046 TTTTCTTTTTT
1 TTTTCTTTTTT
659057 TTTT-TTTTTGT
1 TTTTCTTTTT-T
659068 TTTT
1 TTTT
659072 TGTGTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.20
11 10 0.40
12 10 0.40
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:659740 original size:16 final size:18
Alignment explanation
Indices: 659705--659741 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
659695 AAAAAATTTA
*
659705 TTAATTTTTAACTTTTTT
1 TTAATTTTTAACTTTGTT
659723 TTAA-TTTT-ACTTTGTT
1 TTAATTTTTAACTTTGTT
659739 TTA
1 TTA
659742 TACTGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (18 bp):
TTAATTTTTAACTTTGTT
Found at i:666737 original size:16 final size:15
Alignment explanation
Indices: 666718--666765 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
666708 ATAAAAAATT
666718 ATTTAATAAAATTTAA
1 ATTTAA-AAAATTTAA
*
666734 ATTTAAAATAATTTTA
1 ATTTAAAA-AATTTAA
*
666750 ATTAAAAAAATTTAA
1 ATTTAAAAAATTTAA
666765 A
1 A
666766 CGTAAAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTAAAAAATTTAA
Found at i:666741 original size:26 final size:28
Alignment explanation
Indices: 666701--666756 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
666691 CGGTTAAATG
*
666701 AATTTAAATAAAAAATTA-TTTAA-TAA
1 AATTTAAATAAAAAATAATTTTAATTAA
**
666727 AATTTAAATTTAAAATAATTTTAATTAA
1 AATTTAAATAAAAAATAATTTTAATTAA
666755 AA
1 AA
666757 AAATTTAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.60
27 5 0.20
28 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AATTTAAATAAAAAATAATTTTAATTAA
Found at i:666772 original size:16 final size:15
Alignment explanation
Indices: 666701--666765 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
666691 CGGTTAAATG
666701 AATTTAAA-T-AAAA
1 AATTTAAATTAAAAA
* *
666714 AA-TT-ATTTAATAA
1 AATTTAAATTAAAAA
*
666727 AATTTAAATTTAAAAT
1 AATTTAAA-TTAAAAA
*
666743 AATTTTAATTAAAAA
1 AATTTAAATTAAAAA
666758 AATTTAAA
1 AATTTAAA
666766 CGTAAAATAC
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
11 1 0.03
12 3 0.08
13 7 0.18
14 2 0.05
15 14 0.36
16 12 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTTAAATTAAAAA
Found at i:666952 original size:60 final size:60
Alignment explanation
Indices: 666875--666993 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 60
666865 ACGGATTTAT
* *
666875 ATAATTTTATGTATTATAATTATATTTAAAAT-ATTATAT-TTATA-TAAATTTTAATATATTA
1 ATAATTTTATGTATTAT-A-TAT-TTTAAAATAATTATATATGATATTAAATTTAAAT-TATTA
* *
666936 ATAA-TTTATGTTTTATATATTTTAATATAATTATATATGATATTAAATTTAAATTATT
1 ATAATTTTATGTATTATATATTTTAAAATAATTATATATGATATTAAATTTAAATTATT
666994 TTTATATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
57 7 0.14
58 10 0.20
59 9 0.18
60 21 0.41
61 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (60 bp):
ATAATTTTATGTATTATATATTTTAAAATAATTATATATGATATTAAATTTAAATTATTA
Found at i:666963 original size:32 final size:33
Alignment explanation
Indices: 666878--666964 Score: 97
Period size: 32 Copynumber: 2.6 Consensus size: 33
666868 GATTTATATA
* *
666878 ATTTTATGTATTATAATTATATTTAAAATATTAT
1 ATTTTATATATTTTAA-TATATTTAAAATATTAT
*
666912 ATTTATATAAATTTTAATATA-TTAATAAT-TTAT
1 ATTT-TATATATTTTAATATATTTAA-AATATTAT
*
666945 GTTTTATATATTTTAATATA
1 ATTTTATATATTTTAATATA
666965 ATTATATATG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
32 15 0.33
33 11 0.24
34 11 0.24
35 9 0.20
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (33 bp):
ATTTTATATATTTTAATATATTTAAAATATTAT
Found at i:666999 original size:27 final size:27
Alignment explanation
Indices: 666965--667025 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
666955 TTTTAATATA
666965 ATTATATATGATATTAAATTTAAATTATT
1 ATTATATAT-A-ATTAAATTTAAATTATT
* * *
666994 TTTATATATAATTATATTTTAATTATT
1 ATTATATATAATTAAATTTAAATTATT
667021 ATTAT
1 ATTAT
667026 TTTTGTGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 19 0.68
28 1 0.04
29 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTATATATAATTAAATTTAAATTATT
Found at i:667024 original size:17 final size:18
Alignment explanation
Indices: 666951--667029 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 18
666941 TTATGTTTTA
*
666951 TATATTTTAATATAATTAT
1 TATATTTTAATAT-ATAAT
* *
666970 ATATGATATTAA-ATTTAAAT
1 -TAT-ATTTTAATATAT-AAT
666990 TAT-TTTT-ATATATAAT
1 TATATTTTAATATATAAT
*
667006 TATATTTTAAT-TATTAT
1 TATATTTTAATATATAAT
667023 TAT-TTTT
1 TATATTTT
667030 GTGATATCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
16 11 0.23
17 18 0.38
18 2 0.04
19 4 0.08
20 7 0.15
21 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (18 bp):
TATATTTTAATATATAAT
Found at i:675966 original size:25 final size:24
Alignment explanation
Indices: 675911--675966 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
675901 TAAAATTTAA
*
675911 ATAA-ATTAAAATTTATTTTTATT
1 ATAATATTAAAATTTAATTTTATT
*
675934 ATATTATTAAAATATTAATTTTA-T
1 ATAATATTAAAAT-TTAATTTTATT
675958 ATAAATATT
1 AT-AATATT
675967 TATATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.11
24 11 0.41
25 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATAATATTAAAATTTAATTTTATT
Found at i:676038 original size:20 final size:20
Alignment explanation
Indices: 675937--676038 Score: 61
Period size: 20 Copynumber: 5.0 Consensus size: 20
675927 TTTTATTATA
675937 TTATTAAA-ATAT-T-AATT
1 TTATTAAATATATATAAATT
**
675954 TTATATAAATATTTATATATTTT
1 TTAT-TAAATA--TATATAAATT
* *
675977 TATAATTAAATTTA-AAAAATT
1 T-T-ATTAAATATATATAAATT
*
675998 ATTATTAAATA-ATAATTAATT
1 -TTATTAAATATAT-ATAAATT
676019 TTATTAAATATATATAAATT
1 TTATTAAATATATATAAATT
676039 ATAAAAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
17 4 0.06
18 4 0.06
19 2 0.03
20 23 0.37
21 15 0.24
22 4 0.06
23 3 0.05
24 6 0.10
25 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTAAATATATATAAATT
Found at i:677342 original size:42 final size:42
Alignment explanation
Indices: 677295--677379 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
677285 TGTTTAATTG
677295 ATTTAATATGCCATTTTGTCAATGATTTGAACAGCCTTCAGC
1 ATTTAATATGCCATTTTGTCAATGATTTGAACAGCCTTCAGC
* * *
677337 ATTTAATATGCCATTTTTTCAATGTTTTGAACAGTCTTCAGC
1 ATTTAATATGCCATTTTGTCAATGATTTGAACAGCCTTCAGC
677379 A
1 A
677380 GGAATCAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (42 bp):
ATTTAATATGCCATTTTGTCAATGATTTGAACAGCCTTCAGC
Found at i:682195 original size:4 final size:4
Alignment explanation
Indices: 682186--682223 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
682176 TGAGGTATGT
682186 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
682224 GACGGGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:683496 original size:6 final size:6
Alignment explanation
Indices: 683484--683527 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
683474 TCAACTCCAG
* *
683484 CCCCAA TCCCAA TCCCAA CCCCAA CCCCAA CCCCAA CCCCAA CC
1 CCCCAA CCCCAA CCCCAA CCCCAA CCCCAA CCCCAA CCCCAA CC
683528 ACAGGGCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.32, C:0.64, G:0.00, T:0.05
Consensus pattern (6 bp):
CCCCAA
Found at i:685615 original size:15 final size:15
Alignment explanation
Indices: 685597--685651 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
685587 CAGTGGAGAT
*
685597 GAGGATGATGAGGAC
1 GAGGATGATGACGAC
* *
685612 GAGGATGACGATGAC
1 GAGGATGATGACGAC
*
685627 GACGATGATGACGAC
1 GAGGATGATGACGAC
*
685642 GATGATGATG
1 GAGGATGATG
685652 GTGGAGAGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.40, T:0.16
Consensus pattern (15 bp):
GAGGATGATGACGAC
Found at i:685621 original size:9 final size:9
Alignment explanation
Indices: 685603--685651 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
685593 AGATGAGGAT
*
685603 GATGAGGAC
1 GATGATGAC
*
685612 GAGGATGAC
1 GATGATGAC
*
685621 GATGACGAC
1 GATGATGAC
685630 GATGATGAC
1 GATGATGAC
* *
685639 GACGATGAT
1 GATGATGAC
685648 GATG
1 GATG
685652 GTGGAGAGGG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.39, T:0.16
Consensus pattern (9 bp):
GATGATGAC
Found at i:685636 original size:12 final size:12
Alignment explanation
Indices: 685621--685649 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
685611 CGAGGATGAC
685621 GATGACGACGAT
1 GATGACGACGAT
685633 GATGACGACGAT
1 GATGACGACGAT
685645 GATGA
1 GATGA
685650 TGGTGGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.17
Consensus pattern (12 bp):
GATGACGACGAT
Found at i:685683 original size:18 final size:18
Alignment explanation
Indices: 685656--685695 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
685646 ATGATGGTGG
*
685656 AGAGGGAGAGGAGGAAGA
1 AGAGGAAGAGGAGGAAGA
*
685674 AGAGGAAGAGGAGGAGGA
1 AGAGGAAGAGGAGGAAGA
685692 AGAG
1 AGAG
685696 CTTCAGCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (18 bp):
AGAGGAAGAGGAGGAAGA
Found at i:703507 original size:18 final size:19
Alignment explanation
Indices: 703467--703508 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
703457 TGAAGTTATT
*
703467 ATATT-ATACATTAACATA
1 ATATTAATAAATTAACATA
*
703485 TTATTAATAAATTAA-ATA
1 ATATTAATAAATTAACATA
703503 ATATTA
1 ATATTA
703509 TTTTATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATTAATAAATTAACATA
Found at i:704169 original size:2 final size:2
Alignment explanation
Indices: 704162--704195 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
704152 TACAGTAAAA
704162 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
704196 ACAACAGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:715462 original size:3 final size:3
Alignment explanation
Indices: 715450--715479 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
715440 AAAAAAAAAA
*
715450 ATT ATG ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
715480 TTTTGGGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:716521 original size:2 final size:2
Alignment explanation
Indices: 716516--716554 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
716506 TTTAGGTGTG
716516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
716555 GATGTTAAAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:719516 original size:25 final size:29
Alignment explanation
Indices: 719482--719542 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
719472 ATTAATATAT
* *
719482 TTTATTTTTAAAAT-TA-TAATTT-TTTAA
1 TTTATTTATAATATGTATTAATTTATTT-A
719509 TTTATTTATAATATGTATTAATTTATTTA
1 TTTATTTATAATATGTATTAATTTATTTA
719538 TTTAT
1 TTTAT
719543 AAATTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 12 0.41
28 2 0.07
29 12 0.41
30 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTATTTATAATATGTATTAATTTATTTA
Found at i:720439 original size:2 final size:2
Alignment explanation
Indices: 720432--720461 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
720422 ACCTTATCTG
720432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
720462 CAAATACAAA
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):
AT
Found at i:726806 original size:16 final size:16
Alignment explanation
Indices: 726785--726815 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
726775 TATACATCAA
*
726785 TTATATGTATATATAT
1 TTATATGTAAATATAT
726801 TTATATGTAAATATA
1 TTATATGTAAATATA
726816 AATTTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TTATATGTAAATATAT
Found at i:727125 original size:30 final size:27
Alignment explanation
Indices: 727089--727143 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 27
727079 AAAATTATGA
*
727089 TATTTTATTATATTATAATAATTTTTAACG
1 TATTTTA-TAT-TTAT-ATAAATTTTAACG
727119 TATTTTATATTTATATAAATTTTAA
1 TATTTTATATTTATATAAATTTTAA
727144 TATATTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 4 0.17
29 3 0.12
30 7 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TATTTTATATTTATATAAATTTTAACG
Found at i:727142 original size:17 final size:17
Alignment explanation
Indices: 727120--727218 Score: 71
Period size: 19 Copynumber: 5.6 Consensus size: 17
727110 TTTTTAACGT
727120 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
727137 ATTTTA-ATATAT-TAA
1 ATTTTATATTTATATAA
* *
727152 GAATTTAT-GTTATATAAA
1 -ATTTTATATTTATAT-AA
727170 ATTTTAATATTTATAT-A
1 ATTTT-ATATTTATATAA
727187 ATTATATCATATTTATAATAA
1 ATT-T-T-ATATTTAT-ATAA
*
727208 TTTTTATATTT
1 ATTTTATATTT
727219 TAATCATATT
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
15 3 0.05
16 13 0.20
17 15 0.23
18 11 0.17
19 16 0.25
20 3 0.05
21 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:727149 original size:27 final size:28
Alignment explanation
Indices: 727088--727218 Score: 65
Period size: 27 Copynumber: 4.5 Consensus size: 28
727078 AAAAATTATG
* *
727088 ATATTTTATTATATTATA-ATAATTTTTAAC
1 ATATTTTA-TAT-TTATATA-AAATTTTAAT
*
727118 GTATTTTATATTTATAT-AAATTTTAAT
1 ATATTTTATATTTATATAAAATTTTAAT
727145 ATATTAAGAATT-TATGTTATATAAAATTTTAAT
1 ATATT-----TTATAT-TTATATAAAATTTTAAT
* * * *
727178 AT-TTATATAATTATATCATATTTATAAT
1 ATATTTTATATTTATATAAAATTT-TAAT
727206 A-ATTTTTATATTT
1 ATA-TTTTATATTT
727219 TAATCATATT
Statistics
Matches: 79, Mismatches: 10, Indels: 25
0.69 0.09 0.22
Matches are distributed among these distances:
27 24 0.30
28 12 0.15
29 11 0.14
30 7 0.09
31 3 0.04
32 10 0.13
33 12 0.15
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTTTATATTTATATAAAATTTTAAT
Found at i:727220 original size:19 final size:19
Alignment explanation
Indices: 727164--727238 Score: 52
Period size: 19 Copynumber: 4.0 Consensus size: 19
727154 ATTTATGTTA
*
727164 TATAA-AATTTTAATA-TT
1 TATAATAATTTTTATATTT
*
727181 TAT-ATAA-TTATATCATATT
1 TATAATAATTTTTAT-AT-TT
727200 TATAATAATTTTTATATTT
1 TATAATAATTTTTATATTT
*
727219 TAATCAT-ATTTTTATTATTT
1 T-ATAATAATTTTTA-TATTT
727239 ATTTATATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.11
17 6 0.13
19 15 0.33
20 15 0.33
21 5 0.11
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TATAATAATTTTTATATTT
Found at i:727438 original size:25 final size:25
Alignment explanation
Indices: 727410--727461 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
727400 TAAAATCCAC
*
727410 TAATTATTAATAATTTATTTAATAT
1 TAATTATTAATAATTCATTTAATAT
727435 TAATTATTAATAATTCATTTAATAT
1 TAATTATTAATAATTCATTTAATAT
727460 TA
1 TA
727462 TACTTAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATTATTAATAATTCATTTAATAT
Found at i:729974 original size:13 final size:13
Alignment explanation
Indices: 729958--730000 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
729948 TTTTAAAAAA
729958 AAATTAAATATAT
1 AAATTAAATATAT
729971 AAA-TAAATATAT
1 AAATTAAATATAT
* *
729983 AACTTAAATATTT
1 AAATTAAATATAT
729996 AAATT
1 AAATT
730001 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAAATATAT
Found at i:731655 original size:22 final size:21
Alignment explanation
Indices: 731623--731663 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
731613 TTTAATTAAT
*
731623 TATTTTTATAAAATATAAAAAA
1 TATTTTAAT-AAATATAAAAAA
*
731645 TATTTTAATAATTATAAAA
1 TATTTTAATAAATATAAAA
731664 TCTTTTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTTTAATAAATATAAAAAA
Found at i:745608 original size:2 final size:2
Alignment explanation
Indices: 745601--745634 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
745591 GAGTGCTTTC
*
745601 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
745635 TGGATTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:746931 original size:14 final size:13
Alignment explanation
Indices: 746881--746924 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
746871 TATTTTGTAT
746881 TTAAATAT--ATA
1 TTAAATATAAATA
*
746892 TTATATATAAATA
1 TTAAATATAAATA
746905 TTAAATATAAATA
1 TTAAATATAAATA
746918 TTTAAAT
1 -TTAAAT
746925 GAAAATAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 7 0.25
13 15 0.54
14 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:748186 original size:27 final size:26
Alignment explanation
Indices: 748156--748241 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 26
748146 AATGTTAATT
748156 ATAATAATATTTTAAAAAGTATAATAA
1 ATAATAATATTTTAAAAA-TATAATAA
* * *
748183 ATAA-ATTATTTTTAAAATTTAATAA
1 ATAATAATATTTTAAAAATATAATAA
* *
748208 A-AATAATATATTAAATAA-AAAATAA
1 ATAATAATATTTTAAA-AATATAATAA
748233 AGTAATAAT
1 A-TAATAAT
748242 CAAAATTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
24 2 0.04
25 22 0.47
26 13 0.28
27 10 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAATAATATTTTAAAAATATAATAA
Found at i:752837 original size:27 final size:27
Alignment explanation
Indices: 752783--752892 Score: 91
Period size: 30 Copynumber: 3.8 Consensus size: 27
752773 TCTTCTTTAT
752783 ATATTTTAT-TTTATTATAATTATATTTAAA
1 ATATTTTATATTTA-TATAA--AT-TTTAAA
752813 ATATTTTATATTTATATAAATTTTAATA
1 ATATTTTATATTTATATAAATTTTAA-A
*
752841 TATTAATAATTTATA-TTATATAAATTTTATA
1 -A-T-AT--TTTATATTTATATAAATTTTAAA
752872 ATATTTTTATATTTATA-AAAT
1 ATA-TTTTATATTTATATAAAT
752893 ATTCATATTA
Statistics
Matches: 70, Mismatches: 1, Indels: 21
0.76 0.01 0.23
Matches are distributed among these distances:
27 15 0.21
28 9 0.13
29 3 0.04
30 16 0.23
31 7 0.10
32 14 0.20
33 6 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATTTTATATTTATATAAATTTTAAA
Found at i:752845 original size:47 final size:49
Alignment explanation
Indices: 752780--752871 Score: 118
Period size: 47 Copynumber: 1.9 Consensus size: 49
752770 GGATCTTCTT
* * *
752780 TATATATTTTATTTTATT-ATAA-TTATATT-TAAAATATTTTATATTTA
1 TATAAATTTTAATATATTAATAATTTATATTATAAAA-ATTTTATATTTA
*
752827 TATAAATTTTAATATATTAATAATTTATATTATATAAATTTTATA
1 TATAAATTTTAATATATTAATAATTTATATTATAAAAATTTTATA
752872 ATATTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 15 0.39
48 4 0.11
49 15 0.39
50 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (49 bp):
TATAAATTTTAATATATTAATAATTTATATTATAAAAATTTTATATTTA
Found at i:752849 original size:18 final size:17
Alignment explanation
Indices: 752802--752871 Score: 71
Period size: 16 Copynumber: 4.3 Consensus size: 17
752792 TTTATTATAA
752802 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
752818 TTATATTTATATAAATT
1 TTATATTTATATAAATT
752835 TTAATATATTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
752851 TTATA-TTATATAAATT
1 TTATATTTATATAAATT
752867 TTATA
1 TTATA
752872 ATATTTTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.06
14 2 0.04
15 5 0.11
16 18 0.38
17 8 0.17
18 8 0.17
19 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:752906 original size:27 final size:27
Alignment explanation
Indices: 752778--752906 Score: 86
Period size: 30 Copynumber: 4.5 Consensus size: 27
752768 CTGGATCTTC
752778 TTTATA-TATTTTAT-TTTATTATAATTAT
1 TTTATATTATTTTATATTTA-TATAA--AT
* *
752806 ATTTAAAATATTTTATATTTATATAAATT
1 -TTTATATTATTTTATATTTATATAAA-T
752835 TTAATATATTAATAATTTATA-TTATATAAAT
1 TT--TATATT-AT--TTTATATTTATATAAAT
*
752866 TTTATAATATTTTTATATTTATA-AAAT
1 TTTATATTA-TTTTATATTTATATAAAT
*
752893 ATTCATATTATTTT
1 -TTTATATTATTTT
752907 TTTATGTTAT
Statistics
Matches: 83, Mismatches: 6, Indels: 24
0.73 0.05 0.21
Matches are distributed among these distances:
27 14 0.17
28 16 0.19
29 12 0.14
30 17 0.20
31 9 0.11
32 9 0.11
33 6 0.07
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATATTATTTTATATTTATATAAAT
Found at i:758324 original size:31 final size:32
Alignment explanation
Indices: 758265--758328 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
758255 AGTCTGCGTT
*
758265 TGGGAGCCTCAGGCATCTTTTTTGAAGGTTGA
1 TGGGAGCCTCAGGCATCTTTTTTCAAGGTTGA
758297 TGGGAGCCTCAGGCATC-TTTTTCAAGGTTGA
1 TGGGAGCCTCAGGCATCTTTTTTCAAGGTTGA
758328 T
1 T
758329 AAAAGGAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (32 bp):
TGGGAGCCTCAGGCATCTTTTTTCAAGGTTGA
Found at i:761649 original size:22 final size:23
Alignment explanation
Indices: 761606--761649 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
761596 ATCATATCAC
*
761606 ATAAATATAATTTTTATAATTTA
1 ATAAATATAATTTTTACAATTTA
761629 ATAAATA-AA-TTTTACACATTT
1 ATAAATATAATTTTTACA-ATTT
761650 GAGTGACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAATATAATTTTTACAATTTA
Found at i:763049 original size:2 final size:2
Alignment explanation
Indices: 763042--763073 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
763032 TGGGCTTGTG
763042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
763074 GTATGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:763078 original size:4 final size:4
Alignment explanation
Indices: 763071--763097 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
763061 TATATATATA
763071 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
763098 ATACATGTAA
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:763438 original size:46 final size:44
Alignment explanation
Indices: 763388--763488 Score: 109
Period size: 46 Copynumber: 2.3 Consensus size: 44
763378 TAAAAAATAA
* * *
763388 TAAATTAAAATAAAAAATAAATA-TTTAATTGAGTAGTTTTTTTTTT
1 TAAATTAAAAGAAAAAA-AAATAGTTT--TTAAGTAGTTATTTTTTT
*
763434 TAAATTAAAAGATAAAAAAATAGTTTTTAAGTAGTTA--TTTTT
1 TAAATTAAAAGAAAAAAAAATAGTTTTTAAGTAGTTATTTTTTT
763476 TAAGATTAAAAGA
1 TAA-ATTAAAAGA
763489 TATAATTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
42 8 0.16
43 9 0.18
44 9 0.18
45 5 0.10
46 18 0.37
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (44 bp):
TAAATTAAAAGAAAAAAAAATAGTTTTTAAGTAGTTATTTTTTT
Found at i:769813 original size:4 final size:4
Alignment explanation
Indices: 769804--769837 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
769794 AATGCTGCGC
769804 CAGG CAGG CAGG CAGG CAGG CAGG CAGG CAGG CA
1 CAGG CAGG CAGG CAGG CAGG CAGG CAGG CAGG CA
769838 ATCAATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.47, T:0.00
Consensus pattern (4 bp):
CAGG
Found at i:770452 original size:42 final size:41
Alignment explanation
Indices: 770405--770483 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
770395 ATTAATTATA
770405 TTTAATAAATACAATTAA-TAATATAATATTTATATTTAAAAC
1 TTTAATAAATACAA-TAATTAATATAATA-TTATATTTAAAAC
* ** *
770447 TTTAATATATTTAATAATTTATATAATATTATATTTA
1 TTTAATAAATACAATAATTAATATAATATTATATTTA
770484 TAAATTAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 12 0.38
42 20 0.62
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (41 bp):
TTTAATAAATACAATAATTAATATAATATTATATTTAAAAC
Found at i:771097 original size:33 final size:32
Alignment explanation
Indices: 771060--771122 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
771050 AATTTAATTG
771060 AATATTTAAAA-ATTTTTAAAAAAATTATATTAA
1 AATA-TTAAAATATTTTTAAAAAAATT-TATTAA
*
771093 AATATTAAAATATTTTTAATAAAATTTATT
1 AATATTAAAATATTTTTAAAAAAATTTATT
771123 TATTATGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
AATATTAAAATATTTTTAAAAAAATTTATTAA
Found at i:775932 original size:2 final size:2
Alignment explanation
Indices: 775925--775950 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
775915 GCCACCAGCA
775925 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
775951 TTGTTAAGCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:776728 original size:15 final size:15
Alignment explanation
Indices: 776704--776747 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
776694 CAACCTTCGG
* *
776704 ATTATTAATATATTT
1 ATTATAAATATATAT
776719 ATTATAAATATATAT
1 ATTATAAATATATAT
* *
776734 ATTTTATATATATA
1 ATTATAAATATATA
776748 GTTTAGAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATAAATATATAT
Found at i:782711 original size:2 final size:2
Alignment explanation
Indices: 782704--782747 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
782694 CTTCATTTGC
782704 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
782745 AT A
1 AT A
782748 AACAAATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:783211 original size:16 final size:17
Alignment explanation
Indices: 783175--783212 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
783165 AATGATTCGC
*
783175 AAAAGCTTAATTTAATA
1 AAAAGATTAATTTAATA
783192 AAAAGATTAATTTAATA
1 AAAAGATTAATTTAATA
783209 AAAA
1 AAAA
783213 AATCATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAAGATTAATTTAATA
Found at i:784541 original size:17 final size:16
Alignment explanation
Indices: 784497--784556 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 16
784487 ATTTAAATAT
*
784497 ATATTAAAAAAATAAAA
1 ATATT-AAATAATAAAA
*
784514 ATTTTAAATAATATAAA
1 ATATTAAATAATA-AAA
* *
784531 ATATTATATAA-AAAT
1 ATATTAAATAATAAAA
*
784546 ATATGAAATAA
1 ATATTAAATAA
784557 AGTAATTATA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 11 0.31
16 8 0.23
17 16 0.46
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
ATATTAAATAATAAAA
Found at i:786910 original size:2 final size:2
Alignment explanation
Indices: 786903--786927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
786893 TCAAAAATAA
786903 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
786928 CACACAGGGG
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:788882 original size:15 final size:15
Alignment explanation
Indices: 788862--788891 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
788852 AAAAGGTTGG
788862 TTTCGAACTCCTTCA
1 TTTCGAACTCCTTCA
788877 TTTCGAACTCCTTCA
1 TTTCGAACTCCTTCA
788892 GCGCTCGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (15 bp):
TTTCGAACTCCTTCA
Found at i:789118 original size:13 final size:14
Alignment explanation
Indices: 789100--789131 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
789090 GTTGTAATTA
789100 AATATATTAAA-AT
1 AATATATTAAATAT
789113 AATATATTAAATAT
1 AATATATTAAATAT
789127 AATAT
1 AATAT
789132 TTTTTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATATTAAATAT
Found at i:801465 original size:28 final size:31
Alignment explanation
Indices: 801422--801487 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 31
801412 TTTAAATATT
*
801422 TAAATTT-ATATTG-TT-TTTAT-AAATA-A
1 TAAATTTAATATCGTTTATTTATAAAATACA
801448 TAAATTTAGATATCGTTTATTTATAAAATACA
1 TAAATTTA-ATATCGTTTATTTATAAAATACA
801480 TAAATTTA
1 TAAATTTA
801488 TGTTTATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.21
28 5 0.15
29 2 0.06
30 5 0.15
31 5 0.15
32 9 0.27
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (31 bp):
TAAATTTAATATCGTTTATTTATAAAATACA
Found at i:805540 original size:10 final size:11
Alignment explanation
Indices: 805515--805540 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
805505 ATCGAAGGCT
805515 TTTTTATCATG
1 TTTTTATCATG
805526 TTTTTATCATG
1 TTTTTATCATG
805537 TTTT
1 TTTT
805541 CTTAATGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTTATCATG
Found at i:807350 original size:23 final size:23
Alignment explanation
Indices: 807317--807400 Score: 93
Period size: 23 Copynumber: 3.6 Consensus size: 23
807307 ACTGGATGTC
807317 GATATGAATAAAATAATAAAATAA
1 GATAT-AATAAAATAATAAAATAA
*
807341 GATATAATAAAAT-ATATAAATAT
1 GATATAATAAAATAATA-AAATAA
*
807364 TATATAA-AAAATAATTAAAATGAA
1 GATATAATAAAATAA-TAAAAT-AA
807388 -ATATAATAAAATA
1 GATATAATAAAATA
807401 TGCTAATAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
22 8 0.15
23 30 0.58
24 14 0.27
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (23 bp):
GATATAATAAAATAATAAAATAA
Found at i:807397 original size:15 final size:14
Alignment explanation
Indices: 807323--807400 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 14
807313 TGTCGATATG
807323 AATAAA-ATAATAA
1 AATAAATATAATAA
807336 AATAAGATATAATAA
1 AATAA-ATATAATAA
*
807351 AATATATA-AATATTA
1 AATAAATATAATA--A
* *
807366 TATAAAAAATAATTAA
1 AAT-AAATATAA-TAA
807382 AATGAAATATAATAA
1 AAT-AAATATAATAA
807397 AATA
1 AATA
807401 TGCTAATAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
13 9 0.18
14 5 0.10
15 20 0.39
16 13 0.25
17 2 0.04
18 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AATAAATATAATAA
Found at i:811255 original size:16 final size:16
Alignment explanation
Indices: 811234--811266 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
811224 ACTGTCACAA
811234 TATATATATATAATAT
1 TATATATATATAATAT
*
811250 TATATATATATTATAT
1 TATATATATATAATAT
811266 T
1 T
811267 GGTACCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATATATATAATAT
Found at i:812019 original size:3 final size:3
Alignment explanation
Indices: 812011--812054 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
812001 TAAAACATAT
812011 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
812055 CAAGCTTGCA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:814460 original size:5 final size:5
Alignment explanation
Indices: 814441--814536 Score: 53
Period size: 5 Copynumber: 19.6 Consensus size: 5
814431 GATTTTAAAA
* * *
814441 ATAAT ATAAT -T-AT ATAAT ATAAAT AAAAT ATAA- A-AAA ATAAT -TAAA
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
814487 ATATT ACGTAAAT ATAAT ATAAT TTAA- ATAA- ATAAT ATAAT ATAAAT
1 ATAAT A--T-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT
814534 ATA
1 ATA
814537 TATCAAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 22
0.70 0.09 0.22
Matches are distributed among these distances:
3 4 0.06
4 14 0.20
5 39 0.55
6 10 0.14
7 1 0.01
8 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:815550 original size:8 final size:8
Alignment explanation
Indices: 815537--815578 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
815527 ATAAATTTTG
815537 ATATATTT
1 ATATATTT
815545 ATATATTT
1 ATATATTT
*
815553 ATAT-TAT
1 ATATATTT
*
815560 ATATATTA
1 ATATATTT
815568 ATAT-TTT
1 ATATATTT
815575 ATAT
1 ATAT
815579 CATATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATATTT
Found at i:815564 original size:15 final size:14
Alignment explanation
Indices: 815538--815578 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
815528 TAAATTTTGA
815538 TATATTTATATATT
1 TATATTTATATATT
815552 TATATTATATATATT
1 TATATT-TATATATT
*
815567 AATATTT-TATAT
1 TATATTTATATAT
815579 CATATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTTATATATT
Found at i:815596 original size:22 final size:20
Alignment explanation
Indices: 815545--815606 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 20
815535 TGATATATTT
*
815545 ATATATTTATATTATATATATTA
1 ATAT-TTTATA-TA-ATATTTTA
*
815568 ATATTTTATATCATATTTTA
1 ATATTTTATATAATATTTTA
815588 ATTATTTT-TAATAATATTT
1 A-TATTTTAT-ATAATATTT
815607 GTATTGAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.26
21 15 0.44
22 6 0.18
23 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTATATAATATTTTA
Found at i:818717 original size:17 final size:19
Alignment explanation
Indices: 818695--818747 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 19
818685 AATATATTAA
818695 AAAATTTATATAATAT-T-
1 AAAATTTATATAATATATC
818712 AAAA-TTAT-TAATATATC
1 AAAATTTATATAATATATC
818729 AAAATTTATATTAATATAT
1 AAAATTTATA-TAATATAT
818748 TTTGTATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.19
16 5 0.16
17 8 0.26
18 4 0.13
20 8 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATTTATATAATATATC
Found at i:818740 original size:20 final size:19
Alignment explanation
Indices: 818695--818747 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
818685 AATATATTAA
818695 AAAATTTATA-TAATAT-T
1 AAAATTTATATTAATATAT
818712 AAAA--T-TATTAATATAT
1 AAAATTTATATTAATATAT
818728 CAAAATTTATATTAATATAT
1 -AAAATTTATATTAATATAT
818748 TTTGTATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.07
15 7 0.23
16 1 0.03
17 8 0.27
19 1 0.03
20 11 0.37
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATTTATATTAATATAT
Found at i:820145 original size:4 final size:4
Alignment explanation
Indices: 820138--820163 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
820128 TTATACACAC
820138 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
820164 ATACATGCCC
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:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:824217 original size:2 final size:2
Alignment explanation
Indices: 824210--824246 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
824200 AATGAAACAT
824210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
824247 TCAGCTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:825987 original size:2 final size:2
Alignment explanation
Indices: 825980--826018 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
825970 TGCCCAAGGC
*
825980 AT AT AT AT GT 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 AT AT AT AT A
826019 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:826023 original size:2 final size:2
Alignment explanation
Indices: 826018--826043 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
826008 ATATATATAT
826018 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
826044 TCATATCAGC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:836865 original size:2 final size:2
Alignment explanation
Indices: 836858--836896 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
836848 GACCAACTTG
836858 AT AT AT AT 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 AT AT AT AT A
836897 ACATGAATTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:837547 original size:13 final size:14
Alignment explanation
Indices: 837524--837552 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
837514 TAATATTAAA
837524 AATATTTTTATATT
1 AATATTTTTATATT
837538 AATA-TTTTATATT
1 AATATTTTTATATT
837551 AA
1 AA
837553 AATAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:838192 original size:19 final size:20
Alignment explanation
Indices: 838155--838208 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
838145 ATATATTTTT
838155 ATAA-TTAAATTTAAATAAA-A
1 ATAATTTAAA-TT-AATAAATA
* *
838175 ATATTTTTAATTAATAAATA
1 ATAATTTAAATTAATAAATA
838195 ATAATTTAAATTAA
1 ATAATTTAAATTAA
838209 ATTATTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.21
20 18 0.64
21 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATTTAAATTAATAAATA
Found at i:838986 original size:23 final size:25
Alignment explanation
Indices: 838947--839013 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
838937 TTATTTTTAA
*
838947 ATTAATAAAAAATATTTTTAAAATT
1 ATTAATTAAAAATATTTTTAAAATT
* *
838972 -TTAATTAAAAA-ATTTATATAATT
1 ATTAATTAAAAATATTTTTAAAATT
838995 ATT-ATTATAAAATATTTTT
1 ATTAATTA-AAAATATTTTT
839014 TTAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 14 0.40
24 16 0.46
25 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTAATTAAAAATATTTTTAAAATT
Found at i:843836 original size:2 final size:2
Alignment explanation
Indices: 843823--843858 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
843813 AAAGGGAAGA
*
843823 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
843859 CACACACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:852386 original size:3 final size:3
Alignment explanation
Indices: 852378--852403 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
852368 TGCGACTGAC
852378 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
852404 TGATGATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:852424 original size:2 final size:2
Alignment explanation
Indices: 852419--852443 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
852409 ATGAGAGAAA
852419 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
852444 AGGACAATGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:853063 original size:3 final size:3
Alignment explanation
Indices: 853055--853098 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
853045 GTATTTATCT
*
853055 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
853099 GTTTTATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:861530 original size:19 final size:18
Alignment explanation
Indices: 861504--861543 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
861494 TAAATGAAAG
*
861504 TTAAAATTTTTAATATAT
1 TTAAAATTTATAATATAT
*
861522 TTAATAATTTATATTATAT
1 TTAA-AATTTATAATATAT
861541 TTA
1 TTA
861544 TATGTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAAATTTATAATATAT
Found at i:874313 original size:2 final size:2
Alignment explanation
Indices: 874306--874337 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
874296 GACATAAATA
874306 AT AT AT AT AT AT AT A- 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 AT A
874338 GAAGAGCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:874323 original size:15 final size:15
Alignment explanation
Indices: 874303--874335 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
874293 GTAGACATAA
874303 ATAATATATATATAT
1 ATAATATATATATAT
874318 ATAATATATATATAT
1 ATAATATATATATAT
874333 ATA
1 ATA
874336 TAGAAGAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATATATATATAT
Done.