Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold156
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: 2697547
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 6 of 14
Found at i:1138440 original size:2 final size:2
Alignment explanation
Indices: 1138433--1138461 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1138423 TAAAGGCAAC
1138433 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
1138462 AAATATAGTG
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:1138746 original size:16 final size:17
Alignment explanation
Indices: 1138727--1138771 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1138717 TTACGTTGCG
*
1138727 TATTAATTTTTAT-ATA
1 TATTAATTTATATCATA
1138743 TATTGAATTTATATCATA
1 TATT-AATTTATATCATA
*
1138761 TTTTAATTTAT
1 TATTAATTTAT
1138772 CGTATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.16
17 15 0.60
18 6 0.24
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTAATTTATATCATA
Found at i:1140073 original size:20 final size:20
Alignment explanation
Indices: 1140050--1140088 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1140040 TATTAATATA
* *
1140050 TAATTTTTTTTATAAAAATG
1 TAATATTTTATATAAAAATG
1140070 TAATATTTTATATAAAAAT
1 TAATATTTTATATAAAAAT
1140089 ACAAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TAATATTTTATATAAAAATG
Found at i:1140268 original size:17 final size:17
Alignment explanation
Indices: 1140244--1140298 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
1140234 ATGAATTGAG
1140244 ATAT-AATATGAATATA
1 ATATAAATATGAATATA
** *
1140260 ATATAAATAAAAAAATA
1 ATATAAATATGAATATA
1140277 ATATAAATATG-ATATTA
1 ATATAAATATGAATA-TA
1140294 ATATA
1 ATATA
1140299 CGAATATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 6 0.19
17 25 0.81
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (17 bp):
ATATAAATATGAATATA
Found at i:1140437 original size:14 final size:14
Alignment explanation
Indices: 1140385--1140443 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
1140375 AAAACAACAT
1140385 AAATAT-AATATTAA
1 AAATATAAATA-TAA
1140399 AAAT-T-AAT-T-A
1 AAATATAAATATAA
*
1140409 AAATA-AAATA-CA
1 AAATATAAATATAA
1140421 AAATATAAATATAA
1 AAATATAAATATAA
1140435 AAATATAAA
1 AAATATAAA
1140444 AAATATTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
10 5 0.13
11 4 0.11
12 6 0.16
13 9 0.24
14 14 0.37
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATATAAATATAA
Found at i:1150574 original size:27 final size:29
Alignment explanation
Indices: 1150540--1150593 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
1150530 AATCTTAAGT
1150540 ATTATTTAAT-TATTATTTTT-TTAAAAA
1 ATTATTTAATATATTATTTTTATTAAAAA
1150567 ATTATTTAATATATTATTTTTATTAAA
1 ATTATTTAATATATTATTTTTATTAAA
1150594 TTTATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 10 0.40
28 10 0.40
29 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
ATTATTTAATATATTATTTTTATTAAAAA
Found at i:1150598 original size:27 final size:26
Alignment explanation
Indices: 1150540--1150593 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
1150530 AATCTTAAGT
1150540 ATTATTTAATTATTATTTTTTTAAAAA
1 ATTATTTAATTATTATTTTTTT-AAAA
1150567 ATTATTTAATATATTATTTTTATTAAA
1 ATTATTTAAT-TATTATTTTT-TTAAA
1150594 TTTATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 10 0.40
28 13 0.52
29 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
ATTATTTAATTATTATTTTTTTAAAA
Found at i:1151701 original size:2 final size:2
Alignment explanation
Indices: 1151694--1151724 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1151684 ATTGATTATC
1151694 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 T
1151725 TAAAAATAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1152092 original size:21 final size:21
Alignment explanation
Indices: 1152015--1152099 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 21
1152005 TTAATATTTT
*
1152015 TATTAAGCGTGTTAGGTAAATA
1 TATTAAGTGTGTTAGGT-AATA
* * *
1152037 TATTATA-TGTATTATGTGATA
1 TATTA-AGTGTGTTAGGTAATA
*
1152058 TGTT-AG-GTG--A-GTAATA
1 TATTAAGTGTGTTAGGTAATA
*
1152074 TATTAAGTGTGTTAGGTAATG
1 TATTAAGTGTGTTAGGTAATA
1152095 TATTA
1 TATTA
1152100 GGTAAACATA
Statistics
Matches: 47, Mismatches: 9, Indels: 15
0.66 0.13 0.21
Matches are distributed among these distances:
16 8 0.17
17 3 0.06
18 3 0.06
19 3 0.06
20 1 0.02
21 16 0.34
22 12 0.26
23 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.44
Consensus pattern (21 bp):
TATTAAGTGTGTTAGGTAATA
Found at i:1156791 original size:34 final size:34
Alignment explanation
Indices: 1156701--1156801 Score: 112
Period size: 37 Copynumber: 2.9 Consensus size: 34
1156691 ATTAAGTGTA
* * *
1156701 TTAGGTAAACATATTAAGTGTGTTAAGTGGTATT
1 TTAGGGAAACATATTAAGTGTGTTAAGTGATATG
* * *
1156735 TTAAGTGACTAATATATTAAGTGTGTTAAGTGATGTG
1 TT-AGGGA--AACATATTAAGTGTGTTAAGTGATATG
*
1156772 TTAGGGAAACATATTAAGTGTGTTAGGTGA
1 TTAGGGAAACATATTAAGTGTGTTAAGTGA
1156802 ACTTATTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
34 23 0.42
35 3 0.05
36 4 0.07
37 25 0.45
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.39
Consensus pattern (34 bp):
TTAGGGAAACATATTAAGTGTGTTAAGTGATATG
Found at i:1156853 original size:20 final size:20
Alignment explanation
Indices: 1156815--1156853 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1156805 TATTTTGTAT
* * *
1156815 AAATAAATCTATTATAAAAA
1 AAATAAATATAATAAAAAAA
1156835 AAATAAATATAATAAAAAA
1 AAATAAATATAATAAAAAA
1156854 TACAATTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAATATAATAAAAAAA
Found at i:1160224 original size:3 final size:3
Alignment explanation
Indices: 1160216--1160247 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1160206 AGTGACGTCA
1160216 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
1160248 ATAGATTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1160570 original size:29 final size:29
Alignment explanation
Indices: 1160533--1160645 Score: 113
Period size: 32 Copynumber: 3.7 Consensus size: 29
1160523 AAATAATTTA
1160533 ATTTAATAAAAA-ATATTTATTTTTTAATT
1 ATTTAATAAAAATATATTTATTTTTTAA-T
*
1160562 TTTTAATAAAAATATTTATTTATTTTTTAAT
1 ATTTAATAAAAATA--TATTTATTTTTTAAT
* *
1160593 ATTTAA-AAAATATTTATTTATTTTTTTTAAA
1 ATTTAATAAAA-ATATATTTA--TTTTTTAAT
*
1160624 ATTTGATAAAAAATATATTTAT
1 ATTTAAT-AAAAATATATTTAT
1160646 ATCTTTAAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
29 17 0.24
30 6 0.09
31 21 0.30
32 22 0.31
33 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
ATTTAATAAAAATATATTTATTTTTTAAT
Found at i:1160816 original size:16 final size:16
Alignment explanation
Indices: 1160792--1160822 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1160782 GAAATTATCT
*
1160792 TTAATTTATTATTAAA
1 TTAAATTATTATTAAA
1160808 TTAAATTATTATTAA
1 TTAAATTATTATTAA
1160823 GTTATATTCT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATTATTATTAAA
Found at i:1160987 original size:14 final size:14
Alignment explanation
Indices: 1160970--1161010 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1160960 AAAATCAGTT
1160970 AAAGAAAAAATAAA
1 AAAGAAAAAATAAA
* *
1160984 AAAGAAAAGAGAAA
1 AAAGAAAAAATAAA
1160998 AAAGTAAAAAATA
1 AAAG-AAAAAATA
1161011 TATAAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (14 bp):
AAAGAAAAAATAAA
Found at i:1161231 original size:24 final size:25
Alignment explanation
Indices: 1161178--1161235 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
1161168 TCTTTTTTAA
1161178 TAAAAATAATATAATATATTAATAT
1 TAAAAATAATATAATATATTAATAT
* *
1161203 CAAAATTAATAT-ATATAATTAA-AT
1 TAAAAATAATATAATAT-ATTAATAT
1161227 TAAAAATAA
1 TAAAAATAA
1161236 GTTTAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAAATAATATAATATATTAATAT
Found at i:1161672 original size:2 final size:2
Alignment explanation
Indices: 1161667--1161694 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1161657 TAATCAAAAA
1161667 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
1161695 TGGGTCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1167530 original size:24 final size:24
Alignment explanation
Indices: 1167498--1167558 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
1167488 TTTATCAACG
* *
1167498 AATTTGTCTCTATGATACCAAACA
1 AATTTGTCTATACGATACCAAACA
* *
1167522 AATTTGTCTATACGATACTAAACG
1 AATTTGTCTATACGATACCAAACA
1167546 AATTTGTCTATAC
1 AATTTGTCTATAC
1167559 CATGAGAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (24 bp):
AATTTGTCTATACGATACCAAACA
Found at i:1172919 original size:16 final size:16
Alignment explanation
Indices: 1172898--1172928 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1172888 TTAAATAACA
*
1172898 TAAAATTATTTTTATT
1 TAAAATTAATTTTATT
1172914 TAAAATTAATTTTAT
1 TAAAATTAATTTTAT
1172929 ATATTAATAT
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:0.00, T:0.58
Consensus pattern (16 bp):
TAAAATTAATTTTATT
Found at i:1172954 original size:38 final size:33
Alignment explanation
Indices: 1172868--1172989 Score: 95
Period size: 38 Copynumber: 3.4 Consensus size: 33
1172858 AAGTTGATCT
*
1172868 AATACTTTTTAAATTATTA-TTTAAATAACATAAAA
1 AATATTTTTTAAA-TATTATTTTAAAT-A-ATAAAA
* *
1172903 TTATTTTTATTTAAA-ATTAATTTTATATATTAATATAAA
1 -AATATTT-TTTAAATATT-ATTTTA-A-A-TAATA-AAA
1172942 AATAATTTTTTAAATATTATTTTAAATAATAAAA
1 AAT-ATTTTTTAAATATTATTTTAAATAATAAAA
*
1172976 TATATTTTTTAAAT
1 AATATTTTTTAAAT
1172990 CTGTTGAGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
33 11 0.15
34 5 0.07
35 8 0.11
36 6 0.08
37 11 0.15
38 18 0.25
39 11 0.15
40 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (33 bp):
AATATTTTTTAAATATTATTTTAAATAATAAAA
Found at i:1172967 original size:26 final size:27
Alignment explanation
Indices: 1172923--1172973 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1172913 TTAAAATTAA
*
1172923 TTTTATATATTAATATAAA-AATAATT
1 TTTTAAATATTAATATAAATAATAATT
* *
1172949 TTTTAAATATTATTTTAAATAATAA
1 TTTTAAATATTAATATAAATAATAA
1172974 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTTAAATATTAATATAAATAATAATT
Found at i:1173211 original size:3 final size:3
Alignment explanation
Indices: 1173203--1173239 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1173193 CTAAAAATAA
1173203 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1173240 ATGCTCTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1175178 original size:7 final size:7
Alignment explanation
Indices: 1175127--1175179 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
1175117 TAAATATAAA
1175127 AAATATAT
1 AAATAT-T
1175135 AAATATT
1 AAATATT
*
1175142 AAAAATT
1 AAATATT
*
1175149 AAATTTT
1 AAATATT
*
1175156 AAATTTT
1 AAATATT
1175163 AAATTTATT
1 AAA--TATT
1175172 AAATATT
1 AAATATT
1175179 A
1 A
1175180 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
7 27 0.69
8 6 0.15
9 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AAATATT
Found at i:1177586 original size:6 final size:6
Alignment explanation
Indices: 1177572--1177601 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1177562 TAATTCATGC
*
1177572 CAATTT CAATAT CAATAT CAATAT CAATAT
1 CAATAT CAATAT CAATAT CAATAT CAATAT
1177602 GACAGTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (6 bp):
CAATAT
Found at i:1178031 original size:3 final size:3
Alignment explanation
Indices: 1178023--1178055 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1178013 GTGGGTACAT
1178023 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1178056 TCTCTTAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1178183 original size:24 final size:25
Alignment explanation
Indices: 1178143--1178191 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1178133 AAAGTTTTTT
1178143 TTTTCTTTTAAAGAATATTTTGTAAC
1 TTTTCTTTTAAAGAATATTTT-TAAC
1178169 TTTT-TTTTAAA-AATATTTTTAAC
1 TTTTCTTTTAAAGAATATTTTTAAC
1178192 ATATATAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 8 0.35
25 7 0.30
26 4 0.17
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTCTTTTAAAGAATATTTTTAAC
Found at i:1181523 original size:21 final size:22
Alignment explanation
Indices: 1181499--1181547 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1181489 AAAAATTAAA
1181499 TTAAATTT-TTTTTTATATTAT
1 TTAAATTTATTTTTTATATTAT
* *
1181520 TTAAATTTAATTTTTTATTTTTT
1 TTAAATTT-ATTTTTTATATTAT
1181543 TTAAA
1 TTAAA
1181548 ATATTCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
23 16 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTAAATTTATTTTTTATATTAT
Found at i:1184824 original size:15 final size:15
Alignment explanation
Indices: 1184804--1184834 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1184794 GTGGGCACTA
1184804 CTAAACCATGCCAAG
1 CTAAACCATGCCAAG
1184819 CTAAACCATGCCAAG
1 CTAAACCATGCCAAG
1184834 C
1 C
1184835 CTAGCTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.35, G:0.13, T:0.13
Consensus pattern (15 bp):
CTAAACCATGCCAAG
Found at i:1192900 original size:21 final size:19
Alignment explanation
Indices: 1192869--1192907 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1192859 AATCTGCCTT
*
1192869 TTTTTGTTTTAATTATTTA
1 TTTTTGTTTTAAATATTTA
1192888 TTTTTGATATTTAAATATTT
1 TTTTTG-T-TTTAAATATTT
1192908 TTAGATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTTGTTTTAAATATTTA
Found at i:1193635 original size:26 final size:26
Alignment explanation
Indices: 1193601--1193655 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1193591 CGGAGTTTGT
* * *
1193601 ATTTCATTGCAGTTAGGAGTTGTTAA
1 ATTTAATTGCAGTTAGGAATTCTTAA
* *
1193627 ATTTAATTGTAGTTTGGAATTCTTAA
1 ATTTAATTGCAGTTAGGAATTCTTAA
1193653 ATT
1 ATT
1193656 CATGCAACCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (26 bp):
ATTTAATTGCAGTTAGGAATTCTTAA
Found at i:1198260 original size:5 final size:5
Alignment explanation
Indices: 1198252--1198282 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1198242 AAGAACTGAC
1198252 AGGAA AGGAA AGGAA AGGAA AGGAA AGGAA A
1 AGGAA AGGAA AGGAA AGGAA AGGAA AGGAA A
1198283 ATGAGCGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
AGGAA
Found at i:1207648 original size:48 final size:48
Alignment explanation
Indices: 1207548--1207655 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 48
1207538 CTATTCTAGG
* * **
1207548 AATTGTTCTAAACAAAAATTGTTTTTTATAAAAGCTGTTATCTATAAA
1 AATTGTTCTAAACAAAAATTGTTCTTTATAAAAGCTATTATAAATAAA
** * * * *
1207596 AATTGTTCTAAGTAAAAGTTGTTCTTTATAAAAGTTATTCTAAATAAC
1 AATTGTTCTAAACAAAAATTGTTCTTTATAAAAGCTATTATAAATAAA
1207644 AATTGTTCTAAA
1 AATTGTTCTAAA
1207656 TAAGTGCTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (48 bp):
AATTGTTCTAAACAAAAATTGTTCTTTATAAAAGCTATTATAAATAAA
Found at i:1207650 original size:32 final size:32
Alignment explanation
Indices: 1207575--1207652 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
1207565 ATTGTTTTTT
* * * *
1207575 ATAAAAGCTGTTATCTATAAAAATTGTTCTAA
1 ATAAAAGTTGTTCTTTATAAAAATTATTCTAA
* *
1207607 GTAAAAGTTGTTCTTTATAAAAGTTATTCTAA
1 ATAAAAGTTGTTCTTTATAAAAATTATTCTAA
1207639 ATAACAA-TTGTTCT
1 ATAA-AAGTTGTTCT
1207653 AAATAAGTGC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (32 bp):
ATAAAAGTTGTTCTTTATAAAAATTATTCTAA
Found at i:1207655 original size:16 final size:16
Alignment explanation
Indices: 1207550--1207658 Score: 76
Period size: 16 Copynumber: 6.8 Consensus size: 16
1207540 ATTCTAGGAA
* *
1207550 TTGTTCTAAACAAAAA
1 TTGTTCTAAATAAAAG
* **
1207566 TTGTTTTTTATAAAAG
1 TTGTTCTAAATAAAAG
* * ** *
1207582 CTGTTATCTATAAAAA
1 TTGTTCTAAATAAAAG
*
1207598 TTGTTCTAAGTAAAAG
1 TTGTTCTAAATAAAAG
**
1207614 TTGTTCTTTATAAAAG
1 TTGTTCTAAATAAAAG
*
1207630 TTATTCTAAATAACAA-
1 TTGTTCTAAATAA-AAG
1207646 TTGTTCTAAATAA
1 TTGTTCTAAATAA
1207659 GTGCTATTTT
Statistics
Matches: 70, Mismatches: 22, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
16 68 0.97
17 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (16 bp):
TTGTTCTAAATAAAAG
Found at i:1207814 original size:16 final size:16
Alignment explanation
Indices: 1207700--1207825 Score: 108
Period size: 16 Copynumber: 7.8 Consensus size: 16
1207690 ATATTTCGGG
1207700 TAATAATTATTTTAAA
1 TAATAATTATTTTAAA
* *
1207716 CAAAAAATTATTTTAAA
1 -TAATAATTATTTTAAA
** * *
1207733 TAGGAGTTTTTTTAAA
1 TAATAATTATTTTAAA
* * *
1207749 TAGTAACTATTCTAAA
1 TAATAATTATTTTAAA
1207765 TAATAATTATTTTAAA
1 TAATAATTATTTTAAA
* * *
1207781 TAAAAATTGTTATAAA
1 TAATAATTATTTTAAA
*
1207797 TAATAATTATTTTGAA
1 TAATAATTATTTTAAA
* *
1207813 TATTAATTGTTTT
1 TAATAATTATTTT
1207826 TGAATAAAGT
Statistics
Matches: 85, Mismatches: 24, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
16 71 0.84
17 14 0.16
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATAATTATTTTAAA
Found at i:1208224 original size:2 final size:2
Alignment explanation
Indices: 1208217--1208253 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1208207 CCCCGGTCAT
* *
1208217 TA TA TA TA TA CA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1208254 GAAAACAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1212249 original size:13 final size:13
Alignment explanation
Indices: 1212220--1212261 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1212210 TAAAGACGAG
1212220 AAATTATC-TTTA
1 AAATTATCTTTTA
*
1212232 TAATTATCTTTTA
1 AAATTATCTTTTA
*
1212245 AAATTATGTTTTCA
1 AAATTATCTTTT-A
1212259 AAA
1 AAA
1212262 AACTTTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 7 0.28
13 14 0.56
14 4 0.16
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (13 bp):
AAATTATCTTTTA
Found at i:1216975 original size:5 final size:5
Alignment explanation
Indices: 1216955--1216994 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
1216945 TTACCAAAGC
1216955 AAAT- AAAT- AAAT- AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
1216995 GTAAGTTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.34
5 23 0.66
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:1217904 original size:2 final size:2
Alignment explanation
Indices: 1217897--1217927 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1217887 GGTGCGGATT
*
1217897 TA TA TA TA CA 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 T
1217928 TAAGTCGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1218176 original size:13 final size:14
Alignment explanation
Indices: 1218158--1218190 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1218148 ATTTAGAATT
1218158 ATTTATA-AATTAA
1 ATTTATACAATTAA
1218171 ATTTATACGAATTAA
1 ATTTATAC-AATTAA
1218186 ATTTA
1 ATTTA
1218191 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
15 11 0.61
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTTATACAATTAA
Found at i:1219261 original size:20 final size:21
Alignment explanation
Indices: 1219233--1219287 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
1219223 TATGATGTGA
*
1219233 TATAAAAATAATA-TAAATAT-
1 TATATAAATAATATTAAA-ATC
1219253 TATATAAAT-ATATTAAAATC
1 TATATAAATAATATTAAAATC
*
1219273 AATATAAATAA-ATTA
1 TATATAAATAATATTA
1219288 TTAATGTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 5 0.17
20 24 0.80
21 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TATATAAATAATATTAAAATC
Found at i:1223549 original size:15 final size:16
Alignment explanation
Indices: 1223516--1223550 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1223506 ATATATATAG
1223516 TTTTGCGAGAAGGGTT
1 TTTTGCGAGAAGGGTT
1223532 TTTTGCGAGAAGGGTT
1 TTTTGCGAGAAGGGTT
1223548 TTT
1 TTT
1223551 CTCAGGACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.34, T:0.43
Consensus pattern (16 bp):
TTTTGCGAGAAGGGTT
Found at i:1223597 original size:3 final size:3
Alignment explanation
Indices: 1223589--1223633 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1223579 ATCTCGCCTA
1223589 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
1223634 CCATGGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1226653 original size:2 final size:2
Alignment explanation
Indices: 1226646--1226672 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1226636 TTATTTCAAC
1226646 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 A
1226673 CATCAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1227097 original size:17 final size:18
Alignment explanation
Indices: 1227073--1227113 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1227063 CCATTATTTT
1227073 AAAAATTT-TAAAAATAA
1 AAAAATTTATAAAAATAA
* *
1227090 AGAAATTTATCAAAATAA
1 AAAAATTTATAAAAATAA
1227108 AAAAAT
1 AAAAAT
1227114 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATTTATAAAAATAA
Found at i:1227577 original size:31 final size:28
Alignment explanation
Indices: 1227542--1227625 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 28
1227532 AATAATAAGG
* *
1227542 TAAAGAGATAAGTATATTTTTAATCAAATCT
1 TAAAGAAATAAGTATATTTTT--T-AAATAT
1227573 TAAAGAAATAAGTGAGTATTTTTTAAATAT
1 TAAAGAAATAAGT-A-TATTTTTTAAATAT
1227603 T-AAGAAAGTAAGTATATTTTTTA
1 TAAAGAAA-TAAGTATATTTTTTA
1227626 TAAAACTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
28 9 0.19
29 7 0.15
30 11 0.23
31 13 0.27
32 1 0.02
33 7 0.15
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.40
Consensus pattern (28 bp):
TAAAGAAATAAGTATATTTTTTAAATAT
Found at i:1238170 original size:19 final size:19
Alignment explanation
Indices: 1238148--1238184 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1238138 AAAATATAAG
1238148 AAAAAAAT-A-GAAATTAA
1 AAAAAAATAATGAAATTAA
*
1238165 AAAAAAATCATGAAATTAA
1 AAAAAAATAATGAAATTAA
1238184 A
1 A
1238185 GAATTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 9 0.50
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAAAAATAATGAAATTAA
Found at i:1248006 original size:22 final size:23
Alignment explanation
Indices: 1247981--1248023 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1247971 TTGCAGTTCA
1247981 TGTTAAACC-CATTATTTTGCCT
1 TGTTAAACCTCATTATTTTGCCT
* *
1248003 TGTTCAACCTTATTATTTTGC
1 TGTTAAACCTCATTATTTTGC
1248024 AGTAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (23 bp):
TGTTAAACCTCATTATTTTGCCT
Found at i:1248274 original size:89 final size:89
Alignment explanation
Indices: 1248118--1248297 Score: 288
Period size: 89 Copynumber: 2.0 Consensus size: 89
1248108 GTGAGAGCAT
* * * *
1248118 TCCGGGAGTAGAGTCCTGATTGCAACGGGTCGATGTGTGAGATTAAGCCTCTCAGATCGTCTTCG
1 TCCGGGAGTAAAATCCTGATTGCAACGGGTCGATCTGTGAGATTAAGCCTCTCAGATCGTCTCCG
*
1248183 GAAGGAGACTATACCTCCAGCAAC
66 GAAGGAGAATATACCTCCAGCAAC
* *
1248207 TCCGGGAGTAAAATCCTGATTGCAATGGGTCGATCTGTGAGATTATGCCTCTCAGATCGTCTCCG
1 TCCGGGAGTAAAATCCTGATTGCAACGGGTCGATCTGTGAGATTAAGCCTCTCAGATCGTCTCCG
*
1248272 GAAGGAGAATATGCCTCCAGCAAC
66 GAAGGAGAATATACCTCCAGCAAC
1248296 TC
1 TC
1248298 TGAAAATACC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (89 bp):
TCCGGGAGTAAAATCCTGATTGCAACGGGTCGATCTGTGAGATTAAGCCTCTCAGATCGTCTCCG
GAAGGAGAATATACCTCCAGCAAC
Found at i:1255033 original size:20 final size:21
Alignment explanation
Indices: 1255010--1255060 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1255000 ATATTCAAAA
1255010 TTTATTTAATA-TTAAATTTT
1 TTTATTTAATATTTAAATTTT
***
1255030 TTTAAAAAATATTTAAATTTT
1 TTTATTTAATATTTAAATTTT
*
1255051 TAT-TTTAATA
1 TTTATTTAATA
1255061 AATTGACCAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATTTAATATTTAAATTTT
Found at i:1258670 original size:14 final size:14
Alignment explanation
Indices: 1258648--1258680 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1258638 CTTATTTTTA
1258648 TTAAATAAATAAAT
1 TTAAATAAATAAAT
*
1258662 TTAATTAAATAAAT
1 TTAAATAAATAAAT
1258676 TTAAA
1 TTAAA
1258681 CAATTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAATAAATAAAT
Found at i:1262163 original size:14 final size:14
Alignment explanation
Indices: 1262127--1262164 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
1262117 TATATATACA
1262127 TAAAT-TAAAATTT
1 TAAATATAAAATTT
1262140 TAATAATATAAAATTT
1 T-A-AATATAAAATTT
1262156 TAAATATAA
1 TAAATATAA
1262165 TTATAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 8 0.36
15 4 0.18
16 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATATAAAATTT
Found at i:1262309 original size:25 final size:24
Alignment explanation
Indices: 1262260--1262315 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 24
1262250 CAAATTAAAT
*
1262260 ATTTATAAATTTTAAAATATTTAA
1 ATTTATTAATTTTAAAATATTTAA
*
1262284 ATTTATTAATTTATATAATATTTAA
1 ATTTATTAATTT-TAAAATATTTAA
1262309 ATTTATT
1 ATTTATT
1262316 TATTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTATTAATTTTAAAATATTTAA
Found at i:1262313 original size:17 final size:17
Alignment explanation
Indices: 1262291--1262324 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1262281 TAAATTTATT
1262291 AATTTATATAATATTTA
1 AATTTATATAATATTTA
* *
1262308 AATTTATTTATTATTTA
1 AATTTATATAATATTTA
1262325 TTTACTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTATATAATATTTA
Found at i:1266422 original size:71 final size:71
Alignment explanation
Indices: 1266306--1266443 Score: 258
Period size: 71 Copynumber: 1.9 Consensus size: 71
1266296 AACTTCATAA
1266306 GATAGTAACAACAACCATGTGATAAAGAGAAATAACACGTAAAAGGGAAGATCCTGTGAAGTTGT
1 GATAGTAACAACAACCATGTGATAAAGAGAAATAACACGTAAAAGGGAAGATCCTGTGAAGTTGT
1266371 TTGTAT
66 TTGTAT
* *
1266377 GATAGTGACAACAACCATTTGATAAAGAGAAATAACACGTAAAAGGGAAGATCCTGTGAAGTTGT
1 GATAGTAACAACAACCATGTGATAAAGAGAAATAACACGTAAAAGGGAAGATCCTGTGAAGTTGT
1266442 TT
66 TT
1266444 TAACTTCAGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (71 bp):
GATAGTAACAACAACCATGTGATAAAGAGAAATAACACGTAAAAGGGAAGATCCTGTGAAGTTGT
TTGTAT
Found at i:1269062 original size:2 final size:2
Alignment explanation
Indices: 1269055--1269085 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1269045 AAACTAAAAC
1269055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1269086 AACCCTGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1272022 original size:228 final size:227
Alignment explanation
Indices: 1271637--1272936 Score: 1086
Period size: 228 Copynumber: 5.7 Consensus size: 227
1271627 CTAGAGTTCG
* * * * *
1271637 ACCATCCTCCAA-CTGCTTCCCAGCAAAGATCAACCTCTGCTGGTCTGGAGGAATCCCCTCCTTG
1 ACCATCCT-CAAGCTGTTTACCAGCAAAGATTAACCTCTGCTGGTCAGGAGGAATCCCTTCCTTG
* * * * * * **
1271701 TCCTGGATCTTTGCTTTCACATTGTCAATCGTGTCTGAGCTCTCAACCTCCAGGGTAATGGTTTT
65 TCCTGAATCTTGGCTTTGACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAAGTAATGGTTTT
* * * * * * * * * * *
1271766 ACCTGTCAAG-GTCTTGACAAATATCTGCATCCCTCCTCTAAGGCGCAAAACCAAATGCAAGGTT
130 ACCAGT-AAGAGTTTTCACAAAGATCTGCATCCCACCACTAAGACG-AAAACCAAGTGGAGGGTA
* *
1271830 GACTCCTTTTGGATGTTATAATCTGCAAGCGTCCT
193 GACTCCTTTTGGATGTTGTAATCTGCAAGGGTCCT
* * * * *
1271865 CCCATCCTCAAGCTGCTTT-CCGGCAAAGATTAACCTCTGTTGGTCAGGTGGGATACCC-TCCTT
1 ACCATCCTCAAGCTG-TTTACCAGCAAAGATTAACCTCTGCTGGTCAGGAGGAAT-CCCTTCCTT
* * * *
1271928 ATCTTGAATCTTGGCTTTAACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAAAGTAATGGTTT
64 GTCCTGAATCTTGGCTTTGACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAAGTAATGGTTT
* * ** *
1271993 TACCAGTCAA-AGTTTTCACAAAAATCTGCATTCCACCACGCAGACGAAGCACCAAGTGGAGGGT
129 TACCAGT-AAGAGTTTTCACAAAGATCTGCATCCCACCACTAAGACGAA-AACCAAGTGGAGGGT
* * * *
1272057 TGA-TTCTTTCTGGATATTGTAATCTGCAAGTGTCCT
192 AGACTCCTTT-TGGATGTTGTAATCTGCAAGGGTCCT
* * * * * * * * *
1272093 CCCATCCTCCAGCTGTTTGCCAGCGAAA-ATCAGCCTCTGTTGATCTGGTGGAATCCCTTCCTTG
1 ACCATCCTCAAGCTGTTTACCAGC-AAAGATTAACCTCTGCTGGTCAGGAGGAATCCCTTCCTTG
* * * * * *
1272157 TCCTGGATCTTAGCTTTGACATTGTCAATTGTGTCAGAACTCTCAACTTCCAAAGTAATAGTCTT
65 TCCTGAATCTTGGCTTTGACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAAGTAATGGT-TT
* * * * * * ** *
1272222 T-CCTGTGAGAGTCTTCACAAAAATTTGCATACCACCACGCAGACGTAACACC-AGATGGAGGGT
129 TACCAGTAAGAGTTTTCACAAAGATCTGCATCCCACCACTAAGACG-AAAACCAAG-TGGAGGGT
* * * * *
1272285 AGACTCCTTCTGAATGTTATAGTCTGCAAGGGTTCT
192 AGACTCCTTTTGGATGTTGTAATCTGCAAGGGTCCT
* * * * *
1272321 ACCATCTTCAAGCTGTTTCCCAGCAAAAATTAGCCTCTGCTGGTCAGGTGGAATACCC-TCCTTG
1 ACCATCCTCAAGCTGTTTACCAGCAAAGATTAACCTCTGCTGGTCAGGAGGAAT-CCCTTCCTTG
* * * * * * *
1272385 TCCTGAATCTTGGAC-TTAACGTTATCAATTGTATCAGAACTCTCCACCTCCAAAGTGATAGTTT
65 TCCTGAATCTTGG-CTTTGACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAAGTAATGGTTT
* * * * *
1272449 TTCCAGTAAGAGTTTTTACAAAGATCTGCATGCCACCCCTAAGACG-AAGCACAAGGTGGAGGGT
129 TACCAGTAAGAGTTTTCACAAAGATCTGCATCCCACCACTAAGACGAAAAC-CAA-GTGGAGGGT
* * *
1272513 AGACT-CTTTCTGGATGTTGTAATCAGCAAGGGTGCG
192 AGACTCCTTT-TGGATGTTGTAATCTGCAAGGGTCCT
* * * *
1272549 GCCATCCTCAAGTTGTTTACCAGCAAAGA-TAAGCCTCTGCTGGTCTGGAGGGATCCCTTCCTTG
1 ACCATCCTCAAGCTGTTTACCAGCAAAGATTAA-CCTCTGCTGGTCAGGAGGAATCCCTTCCTTG
* * * * * * * * * *
1272613 TCTTGGATCTTGGCCTTGACATTATCGATTGTGTCAGAGCTTTCCACCT-CAAGGGTGATTGTCT
65 TCCTGAATCTTGGCTTTGACATTATCAATTGTGTCAGAGCTCTCAACCTCCAA-AGTAATGGTTT
* * * * * * * *
1272677 TGCCGGTAAGAGTTTTCACAAAGATCTGCATGCCACCCCTGAGACGAAGGA-CAAGGTGAAGAGT
129 TACCAGTAAGAGTTTTCACAAAGATCTGCATCCCACCACTAAGACGAA-AACCAA-GTGGAGGGT
* * * * *
1272741 AGACTCCTTTTGGATGTTGTAGTCAGCAAGAGTGCG
192 AGACTCCTTTTGGATGTTGTAATCTGCAAGGGTCCT
* * * *
1272777 ACCATCCTCAAGCTGTTTTCCGGCAAAGA-TAAGCCTCTGTTGGTCAGGAGGGATCCCTTCCTTG
1 ACCATCCTCAAGCTGTTTACCAGCAAAGATTAA-CCTCTGCTGGTCAGGAGGAATCCCTTCCTTG
* * * * * * ** *
1272841 TCTTGAATCTTGGCCTTGACATTATCAATTGTGTCTGAGCTTTCCACCTCGAGGGTAATGGTCTT
65 TCCTGAATCTTGGCTTTGACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAAGTAATGGTTTT
1272906 ACCAGTAAGAGTTTTCACAAAGATCTGCATC
130 ACCAGTAAGAGTTTTCACAAAGATCTGCATC
1272937 TGTTGTCAAC
Statistics
Matches: 896, Mismatches: 146, Indels: 60
0.81 0.13 0.05
Matches are distributed among these distances:
226 2 0.00
227 38 0.04
228 828 0.92
229 28 0.03
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (227 bp):
ACCATCCTCAAGCTGTTTACCAGCAAAGATTAACCTCTGCTGGTCAGGAGGAATCCCTTCCTTGT
CCTGAATCTTGGCTTTGACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAAGTAATGGTTTTA
CCAGTAAGAGTTTTCACAAAGATCTGCATCCCACCACTAAGACGAAAACCAAGTGGAGGGTAGAC
TCCTTTTGGATGTTGTAATCTGCAAGGGTCCT
Found at i:1272440 original size:456 final size:452
Alignment explanation
Indices: 1271569--1272935 Score: 1445
Period size: 456 Copynumber: 3.0 Consensus size: 452
1271559 AAATCAGAAA
* * * * * * * * * * *
1271569 CCACCACGGAGGCGAAGGACAAGATGCAGAGTGGACTCCTTCTGGATATTGTAGTCAGCTAGAGT
1 CCACCACGAAGACGAAGCACAAGGTGGAGGGTAGACTCTTTCTGGATATTGTAATCAGCAAGGGT
* * * * * * *
1271634 TCGACCATCCTCCAACTGCTTCCCAGCAAAGATCAACCTCTGCTGGTCTGGAGGAATCCCCTCCT
66 CCGCCCATCCTCCAGCTGTTTACCAGCAAAGATCAGCCTCTGCTGGTCTGGAGGAATCCCTTCCT
* * * * * *
1271699 TGTCCTGGATCTTTGCTTTCACATTGTCAATCGTGTCTGAGCTCTCAACCTCCAGGGTAATGGT-
131 TGTCCTGGATCTTAGCTTTGACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAAGGTAATAGTC
* * * * * * * *
1271763 TTTACCTGTCAAG-GTCTTGACAAATATCTGCATCCCTCCTCTAAGGCGCAAAACCAAATGCAA-
196 TTT-CCTGT-AAGAGTCTTCACAAAAATCTGCATACCACCAC-GAGACG-AAAACCAGATG-AAG
* * * *
1271826 GGTTGACTCCTTTTGGATGTTATAATCTGCAAGCGTCCTCCCATCCTCAAGCTGCTTTCCGGCAA
256 GGTAGACTCCTTTTGGATGTTATAGTCTGCAAGAGTCCTACCATCCTCAAGCTG-TTTCCGGCAA
* * *
1271891 AGATTAACCTCTGTTGGTCAGGTGGGATACCCTCCTTATCTTGAATCTTGGCTTTAACATTGTCA
320 AGATTAGCCTCTGTTGGTCAGGTGGGATACCCTCCTTGTCTTGAATCTTGGC-TTAACATTATCA
* *
1271956 ATTGTGTCAGAGCTCTCAACCTCCAAAGTAATGGTTTTACCAGTCAA-AGTTTTCACAAAAATCT
384 ATTGTGTCAGAGCTCTCCACCTCCAAAGTAATGGTTTTACCAGT-AAGAGTTTTCACAAAGATCT
*
1272020 GCATT
448 GCATG
* * * * *
1272025 CCACCACGCAGACGAAGCACCAA-GTGGAGGGTTGATTCTTTCTGGATATTGTAATCTGCAAGTG
1 CCACCACGAAGACGAAGCA-CAAGGTGGAGGGTAGACTCTTTCTGGATATTGTAATCAGCAAGGG
* * * * *
1272089 TCCTCCCATCCTCCAGCTGTTTGCCAGCGAAA-ATCAGCCTCTGTTGATCTGGTGGAATCCCTTC
65 TCCGCCCATCCTCCAGCTGTTTACCAGC-AAAGATCAGCCTCTGCTGGTCTGGAGGAATCCCTTC
* * *
1272153 CTTGTCCTGGATCTTAGCTTTGACATTGTCAATTGTGTCAGAACTCTCAACTTCCAAAGTAATAG
129 CTTGTCCTGGATCTTAGCTTTGACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAAGGTAATAG
* * * *
1272218 TCTTTCCTGTGAGAGTCTTCACAAAAATTTGCATACCACCACGCAGACGTAACACCAGATGGAGG
194 TCTTTCCTGTAAGAGTCTTCACAAAAATCTGCATACCACCACG-AGACG-AAAACCAGATGAAGG
* * * * * *
1272283 GTAGACTCCTTCTGAATGTTATAGTCTGCAAGGGTTCTACCATCTTCAAGCTGTTTCCCAGCAAA
257 GTAGACTCCTTTTGGATGTTATAGTCTGCAAGAGTCCTACCATCCTCAAGCTGTTT-CCGGCAAA
* * * * *
1272348 AATTAGCCTCTGCTGGTCAGGTGGAATACCCTCCTTGTCCTGAATCTTGGACTTAACGTTATCAA
321 GATTAGCCTCTGTTGGTCAGGTGGGATACCCTCCTTGTCTTGAATCTTGG-CTTAACATTATCAA
* * * * * *
1272413 TTGTATCAGAACTCTCCACCTCCAAAGTGATAGTTTTTCCAGTAAGAGTTTTTACAAAGATCTGC
385 TTGTGTCAGAGCTCTCCACCTCCAAAGTAATGGTTTTACCAGTAAGAGTTTTCACAAAGATCTGC
1272478 ATG
450 ATG
* * *
1272481 CCACCCCTAAGACGAAGCACAAGGTGGAGGGTAGACTCTTTCTGGATGTTGTAATCAGCAAGGGT
1 CCACCACGAAGACGAAGCACAAGGTGGAGGGTAGACTCTTTCTGGATATTGTAATCAGCAAGGGT
* * * * * *
1272546 GCGGCCATCCTCAAGTTGTTTACCAGCAAAGATAAGCCTCTGCTGGTCTGGAGGGATCCCTTCCT
66 CCGCCCATCCTCCAGCTGTTTACCAGCAAAGATCAGCCTCTGCTGGTCTGGAGGAATCCCTTCCT
* * * * * * * * *
1272611 TGTCTTGGATCTTGGCCTTGACATTATCGATTGTGTCAGAGCTTTCCACCT-CAAGGGTGATTGT
131 TGTCCTGGATCTTAGCTTTGACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAA-GGTAATAGT
* * * * * * * * * *
1272675 CTTGCCGGTAAGAGTTTTCACAAAGATCTGCATGCCACCCCTGAGACGAAGGACAAGGTGAAGAG
195 CTTTCCTGTAAGAGTCTTCACAAAAATCTGCATACCACCAC-GAGACGAA-AACCAGATGAAGGG
* * * *
1272740 TAGACTCCTTTTGGATGTTGTAGTCAGCAAGAGTGCGACCATCCTCAAGCTGTTTTCCGGCAAAG
258 TAGACTCCTTTTGGATGTTATAGTCTGCAAGAGTCCTACCATCCTCAAGCTG-TTTCCGGCAAAG
* * *
1272805 ATAAGCCTCTGTTGGTCAGGAGGGAT-CCCTTCCTTGTCTTGAATCTTGGCCTTGACATTATCAA
322 ATTAGCCTCTGTTGGTCAGGTGGGATACCC-TCCTTGTCTTGAATCTTGG-CTTAACATTATCAA
* * * ** *
1272869 TTGTGTCTGAGCTTTCCACCTCGAGGGTAATGGTCTTACCAGTAAGAGTTTTCACAAAGATCTGC
385 TTGTGTCAGAGCTCTCCACCTCCAAAGTAATGGTTTTACCAGTAAGAGTTTTCACAAAGATCTGC
1272934 AT
450 AT
1272936 CTGTTGTCAA
Statistics
Matches: 749, Mismatches: 146, Indels: 32
0.81 0.16 0.03
Matches are distributed among these distances:
455 22 0.03
456 713 0.95
457 14 0.02
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.29
Consensus pattern (452 bp):
CCACCACGAAGACGAAGCACAAGGTGGAGGGTAGACTCTTTCTGGATATTGTAATCAGCAAGGGT
CCGCCCATCCTCCAGCTGTTTACCAGCAAAGATCAGCCTCTGCTGGTCTGGAGGAATCCCTTCCT
TGTCCTGGATCTTAGCTTTGACATTGTCAATTGTGTCAGAGCTCTCAACCTCCAAGGTAATAGTC
TTTCCTGTAAGAGTCTTCACAAAAATCTGCATACCACCACGAGACGAAAACCAGATGAAGGGTAG
ACTCCTTTTGGATGTTATAGTCTGCAAGAGTCCTACCATCCTCAAGCTGTTTCCGGCAAAGATTA
GCCTCTGTTGGTCAGGTGGGATACCCTCCTTGTCTTGAATCTTGGCTTAACATTATCAATTGTGT
CAGAGCTCTCCACCTCCAAAGTAATGGTTTTACCAGTAAGAGTTTTCACAAAGATCTGCATG
Found at i:1273224 original size:35 final size:35
Alignment explanation
Indices: 1273138--1273208 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
1273128 ACACAAAGCA
*
1273138 TAATATATCAAGCAATCAGAAGTCAAAATCAATAC
1 TAATATATCAAGCAATCAGAAATCAAAATCAATAC
1273173 TAATATATCAAGCAATCAGAAATCAAAATCAATAC
1 TAATATATCAAGCAATCAGAAATCAAAATCAATAC
1273208 T
1 T
1273209 TCTTGTCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (35 bp):
TAATATATCAAGCAATCAGAAATCAAAATCAATAC
Found at i:1275976 original size:228 final size:227
Alignment explanation
Indices: 1275184--1276004 Score: 962
Period size: 228 Copynumber: 3.6 Consensus size: 227
1275174 TTGCTTCCCT
* * * *
1275184 GCAAATATCAGCCTCTGCTGGTCTGGGGGGATCCCTTCCTTATCCTGGATCTTGGCCTTCACATT
1 GCAAAGATAAGCCTCTGCTGGTCTGGAGGGATCCCTTCCTTATCTTGGATCTTGGCCTTCACATT
* * * * * * * * * * * *
1275249 GTCAATGGTGTCTGAGCTTTCAACTTCCAGGGTAATGGTCTTTCCCGTCAAGGTCTTCACAAAAA
66 ATCAATGGTGTCAGAGCTTTCCACCTCAAGGGTGATAGTCTTGCCAGTGAGGGTCTTAACAAAAA
* * * * *
1275314 TTTGCATCCCACCACGAAGGCGAAGCACCAAGTGGAGGGTCGACTCCTTTTGAATATTGTAGTCT
131 TTTGCATACCACCACGAA-GCGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTGTAGTCA
* ** *
1275379 GCAAGGGTCCTCCCATCCTCAAGCTGCTTACCA
195 GCAAGGGTACGGCCATCCTCAAGCTGTTTACCA
* * * * * *
1275412 GCAAAAATCAA-CCTCTGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATTTTGGCCTTGACAT
1 GCAAAGAT-AAGCCTCTGCTGGTCTGGAGGGATCCCTTCCTTATCTTGGATCTTGGCCTTCACAT
* * * * * * * * * * *
1275476 TGTCAATTGTGTCAGAGCTCTCCACTTCCAGGGTGATAGTTTTCCCGGTAAGTGTCTTTACAAAA
65 TATCAATGGTGTCAGAGCTTTCCACCTCAAGGGTGATAGTCTTGCCAGTGAGGGTCTTAACAAAA
* * * *
1275541 ATCTGCATACCACCACGAAGACGGAGCACCAAGTGAAGGGTGGATTCCTTTTGGATGTTGTAGTC
130 ATTTGCATACCACCACGAAG-CGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTGTAGTC
* *
1275606 AGCCAA-GGTGCGGCCATCCTCAAGTTGTTTACCA
194 AG-CAAGGGTACGGCCATCCTCAAGCTGTTTACCA
* *
1275640 GCAAAGATAAGCCTCTGCTGGTCTGGAGGAATCCCTTCCTTGTCTTGGATCTTGGCCTTCACATT
1 GCAAAGATAAGCCTCTGCTGGTCTGGAGGGATCCCTTCCTTATCTTGGATCTTGGCCTTCACATT
* *
1275705 ATCAATGGTGTCAGAGCTTTCTACCTCAAGGGTGATAGTCTTGCCAGTGAGGGTCTTAACAAAGA
66 ATCAATGGTGTCAGAGCTTTCCACCTCAAGGGTGATAGTCTTGCCAGTGAGGGTCTTAACAAAAA
* * * * *
1275770 TTTGCATACCACCCCTCAAGCGAAGGACCAAGTGGAGCGTGGACTCCTTCTGGATGTTGTAGTCA
131 TTTGCATACCACCAC-GAAGCGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTGTAGTCA
* *
1275835 GCTAGGGTACGGCCATCCTCCAGCTGTTTACCA
195 GCAAGGGTACGGCCATCCTCAAGCTGTTTACCA
* * * * * *
1275868 GCAAAGATAAGTCTCTGTTGGTCCGGTGGGATTCCTTCCTTATCTTGGATCTTGGCCTTGACATT
1 GCAAAGATAAGCCTCTGCTGGTCTGGAGGGATCCCTTCCTTATCTTGGATCTTGGCCTTCACATT
* * * *
1275933 ATCAATGGTGTCAGAGCTTTCCACCTCAAGGGTGATGGTCTTGCCAGTGAGGGTCTTGACGAAGA
66 ATCAATGGTGTCAGAGCTTTCCACCTCAAGGGTGATAGTCTTGCCAGTGAGGGTCTTAACAAAAA
1275998 TTTGCAT
131 TTTGCAT
1276005 CTATTTTGAA
Statistics
Matches: 507, Mismatches: 80, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
227 5 0.01
228 495 0.98
229 7 0.01
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (227 bp):
GCAAAGATAAGCCTCTGCTGGTCTGGAGGGATCCCTTCCTTATCTTGGATCTTGGCCTTCACATT
ATCAATGGTGTCAGAGCTTTCCACCTCAAGGGTGATAGTCTTGCCAGTGAGGGTCTTAACAAAAA
TTTGCATACCACCACGAAGCGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTGTAGTCAG
CAAGGGTACGGCCATCCTCAAGCTGTTTACCA
Found at i:1280520 original size:59 final size:59
Alignment explanation
Indices: 1280473--1280620 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 59
1280463 GTGATGTGTA
*
1280473 AATCTAGGTCGCCTTGATGGCGGTCTAAGTTTAGGCGACTTGGTGTCACTTAGTGTGGT
1 AATCTAGGTCGCCTTGATGGCGATCTAAGTTTAGGCGACTTGGTGTCACTTAGTGTGGT
** * * * * *
1280532 AATCTAGGTTTCTTTGGTGGCGATCTAAGTTTAGGTGACTTGGCGTCACTTAATGT-GT
1 AATCTAGGTCGCCTTGATGGCGATCTAAGTTTAGGCGACTTGGTGTCACTTAGTGTGGT
* * * *
1280590 GAAT-TTGGTCTCCTTGGTGACGATCTAAGTT
1 -AATCTAGGTCGCCTTGATGGCGATCTAAGTT
1280621 CATAGTGTGA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
58 25 0.33
59 51 0.67
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (59 bp):
AATCTAGGTCGCCTTGATGGCGATCTAAGTTTAGGCGACTTGGTGTCACTTAGTGTGGT
Found at i:1287930 original size:18 final size:18
Alignment explanation
Indices: 1287907--1287945 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1287897 ACTTGATTCG
1287907 TTTTTAAAAAAATTTATT
1 TTTTTAAAAAAATTTATT
***
1287925 TTTTTATTTAAATTTATT
1 TTTTTAAAAAAATTTATT
1287943 TTT
1 TTT
1287946 AAATTTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTAAAAAAATTTATT
Found at i:1287951 original size:18 final size:18
Alignment explanation
Indices: 1287916--1287966 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
1287906 GTTTTTAAAA
**
1287916 AAATTTATTTTTTTATTT
1 AAATTTATTTTTAAATTT
1287934 AAATTTATTTTTAAATTT
1 AAATTTATTTTTAAATTT
*
1287952 AAATTT-TTTTAAAAT
1 AAATTTATTTTTAAAT
1287967 ATTTCAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AAATTTATTTTTAAATTT
Found at i:1288359 original size:2 final size:2
Alignment explanation
Indices: 1288354--1288382 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1288344 AAAAAAAGAT
1288354 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
1288383 CCATGGAGCT
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:1290424 original size:21 final size:22
Alignment explanation
Indices: 1290398--1290454 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
1290388 TTTATATATT
1290398 TTAAATATATTAAAAATTTT-A
1 TTAAATATATTAAAAATTTTAA
* *
1290419 TTAAATTTATTAAAATTTTTAAA
1 TTAAATATATTAAAAATTTT-AA
1290442 TTAAATAT-TTAAA
1 TTAAATATATTAAA
1290455 TACTCAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.58
22 5 0.16
23 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAATATATTAAAAATTTTAA
Found at i:1290582 original size:34 final size:33
Alignment explanation
Indices: 1290530--1290595 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
1290520 TTTTAAGTAA
*
1290530 CTCACAAATTACTTGAATCATTCTAAATCCTTAC
1 CTCACAAATTACTGGAATCATT-TAAATCCTTAC
* * * *
1290564 CTCACAAGTTGCTGGAATCGTTTACATCCTTA
1 CTCACAAATTACTGGAATCATTTAAATCCTTA
1290596 GGAATCGTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (33 bp):
CTCACAAATTACTGGAATCATTTAAATCCTTAC
Found at i:1294286 original size:23 final size:24
Alignment explanation
Indices: 1294232--1294292 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
1294222 AAAAATAAAA
1294232 AATT-AATTTTAT-ATTAAAATTT
1 AATTAAATTTTATAATTAAAATTT
*
1294254 -A-TATATTTTTATAATT-AAATTT
1 AATTA-AATTTTATAATTAAAATTT
*
1294276 AATTAAATTTTTTAATT
1 AATTAAATTTTATAATT
1294293 TTTATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 13 0.42
23 14 0.45
24 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTAAATTTTATAATTAAAATTT
Found at i:1298537 original size:22 final size:22
Alignment explanation
Indices: 1298509--1298574 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
1298499 TTCTGAGTAG
1298509 CATTCATAAATTTATATCAAGA
1 CATTCATAAATTTATATCAAGA
1298531 CATTCATAAATTTATATCAAGA
1 CATTCATAAATTTATATCAAGA
*
1298553 CATTCATAAACTTATATCAAGA
1 CATTCATAAATTTATATCAAGA
1298575 AATCAAGTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (22 bp):
CATTCATAAATTTATATCAAGA
Found at i:1300652 original size:2 final size:2
Alignment explanation
Indices: 1300639--1300670 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1300629 ATAAGTTGTA
*
1300639 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
1300671 TTGTTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1302368 original size:7 final size:7
Alignment explanation
Indices: 1302350--1302404 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
1302340 TATTTTTTAA
1302350 TTAAT-T
1 TTAATAT
1302356 TT-ATAT
1 TTAATAT
1302362 TTAATA-
1 TTAATAT
1302368 TT--TAT
1 TTAATAT
1302373 TTAATAT
1 TTAATAT
1302380 TTAA-A-
1 TTAATAT
1302385 TTATATAT
1 TTA-ATAT
1302393 TTAATAT
1 TTAATAT
1302400 TTAAT
1 TTAAT
1302405 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
4 2 0.05
5 7 0.17
6 9 0.22
7 20 0.49
8 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTAATAT
Found at i:1302373 original size:11 final size:11
Alignment explanation
Indices: 1302345--1302407 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
1302335 ATACATATTT
* *
1302345 TTTAATTAATT
1 TTTATTTAATA
1302356 TTATATTTAATA
1 TT-TATTTAATA
1302368 TTTATTTAATA
1 TTTATTTAATA
1302379 TTTA---AATTA
1 TTTATTTAA-TA
*
1302388 TATATTTAATA
1 TTTATTTAATA
1302399 TTTAATTTA
1 TTT-ATTTA
1302408 TTTAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
11 19 0.45
12 16 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTATTTAATA
Found at i:1302395 original size:20 final size:20
Alignment explanation
Indices: 1302353--1302408 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1302343 TTTTTAATTA
* *
1302353 ATTTTATATTT-AA-TATTT
1 ATTTAATATTTAAATTATAT
1302371 ATTTAATATTTAAATTATAT
1 ATTTAATATTTAAATTATAT
*
1302391 ATTTAATATTTAATTTAT
1 ATTTAATATTTAAATTAT
1302409 TTAAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 10 0.30
19 2 0.06
20 21 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAATATTTAAATTATAT
Found at i:1302676 original size:2 final size:2
Alignment explanation
Indices: 1302669--1302694 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1302659 AAATTTTCTA
1302669 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
1302695 TTCCTTATTG
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:1303297 original size:2 final size:2
Alignment explanation
Indices: 1303290--1303316 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1303280 TCTGATCATT
1303290 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1303317 TCTAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1303428 original size:16 final size:18
Alignment explanation
Indices: 1303396--1303428 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1303386 GTGCTCTTTT
1303396 ATTTTTGTTTCCTTCTTA
1 ATTTTTGTTTCCTTCTTA
1303414 ATTTTT-TTT-CTTCTT
1 ATTTTTGTTTCCTTCTT
1303429 TTCGTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.73
Consensus pattern (18 bp):
ATTTTTGTTTCCTTCTTA
Found at i:1303748 original size:3 final size:3
Alignment explanation
Indices: 1303740--1303776 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1303730 TAGCTCATTC
*
1303740 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1303777 TAATTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1316335 original size:12 final size:12
Alignment explanation
Indices: 1316296--1316336 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1316286 GCTTGACATC
1316296 TCATCATCACCA
1 TCATCATCACCA
*
1316308 TCAGCATCACCA
1 TCATCATCACCA
*
1316320 TCATCATCACAA
1 TCATCATCACCA
1316332 TCATC
1 TCATC
1316337 CACTTCCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.34, C:0.39, G:0.02, T:0.24
Consensus pattern (12 bp):
TCATCATCACCA
Found at i:1320589 original size:11 final size:11
Alignment explanation
Indices: 1320575--1320609 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1320565 TGCAATTCAG
1320575 TTACTCTCTCT
1 TTACTCTCTCT
*
1320586 TTACTCTTTCT
1 TTACTCTCTCT
*
1320597 TTAGTCTCTCT
1 TTACTCTCTCT
1320608 TT
1 TT
1320610 GTCTGCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.29, G:0.03, T:0.60
Consensus pattern (11 bp):
TTACTCTCTCT
Found at i:1338420 original size:19 final size:21
Alignment explanation
Indices: 1338396--1338443 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
1338386 ATCACTTAAG
1338396 ATAAATATAA-TATAA-AAAA
1 ATAAATATAATTATAATAAAA
*
1338415 ATAAATA-AATTATAATTAAA
1 ATAAATATAATTATAATAAAA
1338435 A-AAATATAA
1 ATAAATATAA
1338444 GTTACATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 17 0.68
20 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAATATAATTATAATAAAA
Found at i:1338434 original size:23 final size:23
Alignment explanation
Indices: 1338396--1338440 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1338386 ATCACTTAAG
1338396 ATAAATATAATATAAAAAAATAA
1 ATAAATATAATATAAAAAAATAA
1338419 ATAAATTATAAT-TAAAAAAATA
1 ATAAA-TATAATATAAAAAAATA
1338441 TAAGTTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAAATATAATATAAAAAAATAA
Found at i:1338551 original size:19 final size:19
Alignment explanation
Indices: 1338518--1338556 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1338508 TTATAACTTA
*
1338518 ATAAATTACATAAATATAAT
1 ATAAATTACACAAAT-TAAT
1338538 ATAAA-TACACAAATTAAT
1 ATAAATTACACAAATTAAT
1338556 A
1 A
1338557 CGACTACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAATTACACAAATTAAT
Found at i:1343890 original size:29 final size:29
Alignment explanation
Indices: 1343848--1343909 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
1343838 ACTGCTTGTT
1343848 AAAATAAGGCTGTGTCCATGAGTGTAAAG
1 AAAATAAGGCTGTGTCCATGAGTGTAAAG
* * *
1343877 AAAATGAGGCTGTGTCCGTGTGTGTAAAG
1 AAAATAAGGCTGTGTCCATGAGTGTAAAG
1343906 AAAA
1 AAAA
1343910 AACCAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.29, T:0.24
Consensus pattern (29 bp):
AAAATAAGGCTGTGTCCATGAGTGTAAAG
Found at i:1346077 original size:78 final size:78
Alignment explanation
Indices: 1345948--1346103 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 78
1345938 TATAAGCTCA
* **
1345948 AGATTTAATTGCAGTCCAAAATTATAATAGTGCAACAGTGACTTGGAGATGAAGTAGGCACTACA
1 AGATTTAATTGCAGTCCAAAATTATAATAGGGCAACAGCAACTTGGAGATGAAGTAGGCACTACA
*
1346013 TATGTGCTAACCT
66 AATGTGCTAACCT
1346026 AGATTTAATTGCAGTCCAAAATTATAATAGGGCAACAGCAACTTGGAGATGAAGTAGGCACTACA
1 AGATTTAATTGCAGTCCAAAATTATAATAGGGCAACAGCAACTTGGAGATGAAGTAGGCACTACA
1346091 AATGTGCTAACCT
66 AATGTGCTAACCT
1346104 TGTAGCATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (78 bp):
AGATTTAATTGCAGTCCAAAATTATAATAGGGCAACAGCAACTTGGAGATGAAGTAGGCACTACA
AATGTGCTAACCT
Found at i:1350998 original size:19 final size:20
Alignment explanation
Indices: 1350974--1351027 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
1350964 TTTTAAATAA
1350974 AAATATAT-TAATTATATTT
1 AAATATATGTAATTATATTT
*
1350993 AAATATATGTTATTATATTT
1 AAATATATGTAATTATATTT
1351013 ATTAA-ATATGTAATT
1 A--AATATATGTAATT
1351028 TTAATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 8 0.27
20 11 0.37
21 9 0.30
22 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
AAATATATGTAATTATATTT
Found at i:1351994 original size:10 final size:10
Alignment explanation
Indices: 1351981--1352013 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1351971 TTGATTAATT
1351981 AAAAAT-TTA
1 AAAAATATTA
1351990 AAAAATATTA
1 AAAAATATTA
*
1352000 AAAAATAATA
1 AAAAATATTA
1352010 AAAA
1 AAAA
1352014 TAAATATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATATTA
Found at i:1358758 original size:15 final size:15
Alignment explanation
Indices: 1358738--1358766 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1358728 GTTCTTTTCA
1358738 TATGTAAATAACAGG
1 TATGTAAATAACAGG
1358753 TATGTAAATAACAG
1 TATGTAAATAACAG
1358767 ACAAATGAAT
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:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (15 bp):
TATGTAAATAACAGG
Found at i:1360496 original size:19 final size:20
Alignment explanation
Indices: 1360455--1360500 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1360445 TTGAATTGGT
1360455 TTAAAATAATATATTTTTAA
1 TTAAAATAATATATTTTTAA
1360475 TTAAAATAATATATTTTT-A
1 TTAAAATAATATATTTTTAA
1360494 TTAAAAT
1 TTAAAAT
1360501 TTAATTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAATAATATATTTTTAA
Found at i:1368862 original size:2 final size:2
Alignment explanation
Indices: 1368857--1368888 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1368847 AAAAAAAAGG
1368857 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1368889 ATCTTGCTTG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1370759 original size:18 final size:19
Alignment explanation
Indices: 1370721--1370760 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1370711 TTTATTTTTT
*
1370721 TATGAAATTATATTATAAG
1 TATGAAATTATAATATAAG
*
1370740 TATGCAATTATAAT-TAAG
1 TATGAAATTATAATATAAG
1370758 TAT
1 TAT
1370761 TATGTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (19 bp):
TATGAAATTATAATATAAG
Found at i:1370976 original size:11 final size:11
Alignment explanation
Indices: 1370960--1370984 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1370950 ATTTTAAAAT
1370960 TAAAAAATATA
1 TAAAAAATATA
1370971 TAAAAAATATA
1 TAAAAAATATA
1370982 TAA
1 TAA
1370985 TTTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAAAATATA
Found at i:1371021 original size:24 final size:23
Alignment explanation
Indices: 1370977--1371023 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1370967 TATATAAAAA
* *
1370977 ATATATAATTTTATTTTTTAATT
1 ATATATAAATTTATTTATTAATT
1371000 ATATATAAATTTATTTAATTAATT
1 ATATATAAATTTATTT-ATTAATT
1371024 TAATTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATATAAATTTATTTATTAATT
Found at i:1371630 original size:19 final size:17
Alignment explanation
Indices: 1371603--1371645 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1371593 ATTTATATAA
*
1371603 AAATTAATTAATTTAAATC
1 AAATAAATTAA-TT-AATC
1371622 AAATAAATTAATTAATC
1 AAATAAATTAATTAATC
1371639 -AATAAAT
1 AAATAAAT
1371646 AAACATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 2 0.09
19 10 0.43
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATAAATTAATTAATC
Found at i:1371633 original size:23 final size:24
Alignment explanation
Indices: 1371603--1371675 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 24
1371593 ATTTATATAA
*
1371603 AAATTAATTAATTTAAATCAA-AT
1 AAATTAATTAATTTAAATAAACAT
*
1371626 AAATTAATTAATCAATAAATAAACAT
1 AAATTAATTAAT--TTAAATAAACAT
1371652 ATAATTAAATTAATTTAATATAAA
1 A-AATT-AATTAATTTAA-ATAAA
1371676 ATTAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 12 0.29
25 7 0.17
26 6 0.15
27 9 0.22
28 7 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATTAATTAATTTAAATAAACAT
Found at i:1371693 original size:21 final size:21
Alignment explanation
Indices: 1371639--1371694 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
1371629 TTAATTAATC
* * *
1371639 AATAAATAAACATATAATTAA
1 AATAAATTAATATAAAATTAA
* *
1371660 ATTAATTTAATATAAAATTAA
1 AATAAATTAATATAAAATTAA
*
1371681 AATAAATTCATATA
1 AATAAATTAATATA
1371695 TAATATTTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
AATAAATTAATATAAAATTAA
Found at i:1373027 original size:2 final size:2
Alignment explanation
Indices: 1373020--1373050 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1373010 GCTATGTTCA
1373020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1373051 CATCATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1373454 original size:2 final size:2
Alignment explanation
Indices: 1373447--1373488 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1373437 TCGTGTTAAT
1373447 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
1373489 GCTTACAGGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1373745 original size:24 final size:21
Alignment explanation
Indices: 1373707--1373751 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 21
1373697 GACCTGGTCA
1373707 TAAAAATAAATTAAATACAAT
1 TAAAAATAAATTAAATACAAT
1373728 TAAAAATAATAATATAAATACAAT
1 TAAAAAT-A-AAT-TAAATACAAT
1373752 ACATACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 3 0.14
24 10 0.48
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATAAATTAAATACAAT
Found at i:1374542 original size:12 final size:13
Alignment explanation
Indices: 1374527--1374556 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1374517 TTTAATTTTA
1374527 ATTTT-AAAAATT
1 ATTTTAAAAAATT
1374539 ATTTTAAAAAATT
1 ATTTTAAAAAATT
1374552 ATTTT
1 ATTTT
1374557 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTTAAAAAATT
Found at i:1374652 original size:20 final size:21
Alignment explanation
Indices: 1374627--1374678 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
1374617 TTCATATTTT
1374627 TTATTTTATTTCTAAT-ATTA
1 TTATTTTATTTCTAATAATTA
* *
1374647 TTA-TTTATTTATTATAATTA
1 TTATTTTATTTCTAATAATTA
*
1374667 TTTTTTTATTTC
1 TTATTTTATTTC
1374679 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 10 0.38
20 9 0.35
21 7 0.27
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTTTATTTCTAATAATTA
Found at i:1374925 original size:21 final size:19
Alignment explanation
Indices: 1374895--1374946 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1374885 ATATGAGTAT
*
1374895 AATAAAATAAATTAAT-TA
1 AATATAATAAATTAATATA
*
1374913 GAATATGAGATAAAATAATATA
1 -AATAT-A-ATAAATTAATATA
1374935 AATATAATAAAT
1 AATATAATAAAT
1374947 ATATATATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 14 0.52
22 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
AATATAATAAATTAATATA
Found at i:1374948 original size:30 final size:30
Alignment explanation
Indices: 1374884--1374942 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1374874 ATAATTATAT
*
1374884 AATATGAGTATAATAAAATAAATTAATTAG
1 AATATGAGTAAAATAAAATAAATTAATTAG
*
1374914 AATATGAGATAAAATAATATAAATATAAT
1 AATATGAG-TAAAATAAAATAAAT-TAAT
1374943 AAATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
31 13 0.52
32 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATGAGTAAAATAAAATAAATTAATTAG
Found at i:1375690 original size:2 final size:2
Alignment explanation
Indices: 1375678--1375724 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
1375668 TAAACTCTTC
* *
1375678 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1375720 A- AT AT
1 AT AT AT
1375725 TTCATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1384503 original size:144 final size:144
Alignment explanation
Indices: 1384328--1384610 Score: 455
Period size: 144 Copynumber: 2.0 Consensus size: 144
1384318 AAAATAAAAG
*
1384328 AAAACCAAACCTACATTATTCATTCTTTTATTTATACTATACATTATTAGGTATAAAATTCTAAA
1 AAAACCAAACCTACATTATTCATTCTTTTATTTATACTATACATTATTAGGAATAAAATTCTAAA
1384393 GAAATACACATATATATACATAT-GAT-TAAGATAATAATGATTAAATTGATG-GTAACATAATG
66 GAAATACACATATATATACATATAGATATAAGATAATAATGATTAAATTGATGAG-AACATAATG
1384455 AAAAACAATGGTCGGAT
130 --AAACAATGGTCGGAT
* *
1384472 AAAACCCAACCTACATTATTCATTCTTTTATTTATACTATACATTATTAGGAATAAATTTCTAAA
1 AAAACCAAACCTACATTATTCATTCTTTTATTTATACTATACATTATTAGGAATAAAATTCTAAA
* * * *
1384537 GAAATGCACATATATATATATATATATATAAGATAATAATGATTGAATTGATGAGAACATAATGA
66 GAAATACACATATATATACATATAGATATAAGATAATAATGATTAAATTGATGAGAACATAATGA
1384602 AACAATGGT
131 AACAATGGT
1384611 TAGATAGTCT
Statistics
Matches: 129, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
144 93 0.72
145 2 0.02
146 33 0.26
147 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.35
Consensus pattern (144 bp):
AAAACCAAACCTACATTATTCATTCTTTTATTTATACTATACATTATTAGGAATAAAATTCTAAA
GAAATACACATATATATACATATAGATATAAGATAATAATGATTAAATTGATGAGAACATAATGA
AACAATGGTCGGAT
Found at i:1384794 original size:3 final size:3
Alignment explanation
Indices: 1384786--1384814 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1384776 TGAGCATATA
1384786 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1384815 AAATTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1385072 original size:2 final size:2
Alignment explanation
Indices: 1385065--1385096 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1385055 CACCATAACA
1385065 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
1385097 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:1387650 original size:11 final size:11
Alignment explanation
Indices: 1387634--1387658 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1387624 TATATATATA
1387634 TATGTAAAGTT
1 TATGTAAAGTT
1387645 TATGTAAAGTT
1 TATGTAAAGTT
1387656 TAT
1 TAT
1387659 CCACAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (11 bp):
TATGTAAAGTT
Found at i:1392161 original size:26 final size:24
Alignment explanation
Indices: 1392131--1392181 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 24
1392121 CGTCTATTTG
1392131 TATTATATTTATATATATTAT-TAAAT
1 TATTATATTT-T-TA-ATTATATAAAT
1392157 TATTATATTTTTAATTATATAAAT
1 TATTATATTTTTAATTATATAAAT
1392181 T
1 T
1392182 TTAAGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.21
24 8 0.33
25 1 0.04
26 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTATATTTTTAATTATATAAAT
Found at i:1392165 original size:16 final size:16
Alignment explanation
Indices: 1392139--1392210 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
1392129 TGTATTATAT
1392139 TTATATATATTATTAAA
1 TTATATATATT-TTAAA
*
1392156 TTAT-TATATTTTTAA
1 TTATATATATTTTAAA
*
1392171 TTATATAAATTTTAAGA
1 TTATATATATTTTAA-A
* * *
1392188 TATATATTTATTTGATA
1 T-TATATATATTTTAAA
1392205 TTATAT
1 TTATAT
1392211 TTTAATTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 8 0.18
16 19 0.42
17 8 0.18
18 10 0.22
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTATATATATTTTAAA
Found at i:1392225 original size:16 final size:16
Alignment explanation
Indices: 1392141--1392225 Score: 63
Period size: 15 Copynumber: 5.4 Consensus size: 16
1392131 TATTATATTT
1392141 ATATATATTATTAAATTA
1 ATATATATT-TT-AATTA
*
1392159 TTATAT-TTTTAATT-
1 ATATATATTTTAATTA
* *
1392173 ATATAAATTTTAA--G
1 ATATATATTTTAATTA
* *
1392187 ATATATA-TTTATTTG
1 ATATATATTTTAATTA
1392202 ATATTATATTTTAATTA
1 ATA-TATATTTTAATTA
1392219 ATATATA
1 ATATATA
1392226 CATTTCATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
13 4 0.07
14 10 0.19
15 14 0.26
16 10 0.19
17 11 0.20
18 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATATATATTTTAATTA
Found at i:1399827 original size:20 final size:20
Alignment explanation
Indices: 1399785--1399823 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1399775 GTAATATTAA
*
1399785 AAATATTTAAACTCAAATAT
1 AAATAATTAAACTCAAATAT
1399805 AAATAATTAAACT-AAATAT
1 AAATAATTAAACTCAAATAT
1399824 TAAAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATTAAACTCAAATAT
Found at i:1401979 original size:33 final size:35
Alignment explanation
Indices: 1401885--1401997 Score: 88
Period size: 36 Copynumber: 3.1 Consensus size: 35
1401875 TTGAATTGGG
* * *
1401885 TTTATTATTAAATATTAATAAAATTTAAAATATTTA
1 TTTATTATTAAATAATAATTAAA-TAAAAATATTTA
* **
1401921 TTTAATATTTTATAATTAAATTTAAATAAAAATA-TT-
1 TTTATTATTAAATAA-T-AA-TTAAATAAAAATATTTA
1401957 TTTATTATTAAATAATAATTAAAATAAATTAAT-TTTA
1 TTTATTATTAAATAATAATT-AAATAAA--AATATTTA
1401994 TTTA
1 TTTA
1401998 AATTAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
33 2 0.03
34 9 0.15
35 1 0.02
36 28 0.47
37 7 0.12
38 9 0.15
39 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
TTTATTATTAAATAATAATTAAATAAAAATATTTA
Found at i:1401982 original size:28 final size:27
Alignment explanation
Indices: 1401924--1401980 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
1401914 ATATTTATTT
*
1401924 AATATTTTATAATTAAATTTAAATAAA
1 AATATTTTATAATTAAATATAAATAAA
* *
1401951 AATATTTTTATTATTAAATAATAATTAAA
1 AATA-TTTTATAATTAAAT-ATAAATAAA
1401980 A
1 A
1401981 TAAATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.16
28 13 0.52
29 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATATTTTATAATTAAATATAAATAAA
Found at i:1402318 original size:24 final size:26
Alignment explanation
Indices: 1402281--1402334 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
1402271 ATTTTGATGA
* *
1402281 TTTTAAAATTAAATTAA-ATTAATTT
1 TTTTAAAATAAAATCAACATTAATTT
1402306 TTTTAAAA-AAAATCAACATTAATTT
1 TTTTAAAATAAAATCAACATTAATTT
1402331 TTTT
1 TTTT
1402335 TATTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTAAAATAAAATCAACATTAATTT
Found at i:1404501 original size:31 final size:32
Alignment explanation
Indices: 1404463--1404523 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
1404453 CGTTAATATT
*
1404463 TATTTAATAACATT-T-ATATAAAATATTTACG
1 TATTTAATAAAATTATAATAT-AAATATTTACG
1404494 TATTTAATAAAATTATAATATAAATATTTA
1 TATTTAATAAAATTATAATATAAATATTTA
1404524 TTTAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 13 0.48
32 10 0.37
33 4 0.15
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (32 bp):
TATTTAATAAAATTATAATATAAATATTTACG
Found at i:1404525 original size:28 final size:27
Alignment explanation
Indices: 1404457--1404529 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 27
1404447 ATATCACGTT
*
1404457 AATATTTATTTAATAACATTTATATAA
1 AATATTTATTTAATAAAATTTATATAA
1404484 AATATTTACGTATTTAATAAAA-TTATAATATA
1 AATA-TT---TATTTAATAAAATTTAT-ATA-A
1404516 AATATTTATTTAAT
1 AATATTTATTTAAT
1404530 TTATATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
27 4 0.10
28 10 0.26
30 4 0.10
31 16 0.41
32 5 0.13
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (27 bp):
AATATTTATTTAATAAAATTTATATAA
Found at i:1404941 original size:21 final size:21
Alignment explanation
Indices: 1404925--1404982 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1404915 TTAAATTAGT
*
1404925 TATTATAATAATAAAATTAAA
1 TATTATAAAAATAAAATTAAA
*
1404946 TGTTATAAAAATAAAATTAAA
1 TATTATAAAAATAAAATTAAA
*
1404967 -A-T-TAATAATAAAATTA
1 TATTATAAAAATAAAATTA
1404983 TGTATTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 13 0.39
19 1 0.03
21 19 0.58
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TATTATAAAAATAAAATTAAA
Found at i:1404943 original size:26 final size:21
Alignment explanation
Indices: 1404927--1404966 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1404917 AAATTAGTTA
*
1404927 TTATAATAATAAAATTAAATG
1 TTATAAAAATAAAATTAAATG
1404948 TTATAAAAATAAAATTAAA
1 TTATAAAAATAAAATTAAA
1404967 ATTAATAATA
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:0.03, T:0.35
Consensus pattern (21 bp):
TTATAAAAATAAAATTAAATG
Found at i:1405385 original size:21 final size:20
Alignment explanation
Indices: 1405361--1405404 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1405351 TAAACTTTTT
1405361 AATTAAAAGATTAAT-AAAATA
1 AATT-AAAG-TTAATGAAAATA
*
1405382 AATTAAAGTTATTGAAAATA
1 AATTAAAGTTAATGAAAATA
1405402 AAT
1 AAT
1405405 ACTAGCAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (20 bp):
AATTAAAGTTAATGAAAATA
Found at i:1406762 original size:24 final size:24
Alignment explanation
Indices: 1406735--1406783 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1406725 TATTTATAAT
1406735 AATATTTTATTAAAAATTAATTTA
1 AATATTTTATTAAAAATTAATTTA
1406759 AATATTTTATTAAAAATTAATTTA
1 AATATTTTATTAAAAATTAATTTA
1406783 A
1 A
1406784 CATCATCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATTTTATTAAAAATTAATTTA
Found at i:1408016 original size:11 final size:12
Alignment explanation
Indices: 1407992--1408031 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 12
1407982 GTTAAAATTT
*
1407992 ATATTTTATTAA
1 ATATATTATTAA
1408004 ATATATT-TTAA
1 ATATATTATTAA
1408015 ATAT-TTATTAA
1 ATATATTATTAA
1408026 ATATAT
1 ATATAT
1408032 AGATAACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 2 0.08
11 16 0.64
12 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATATTATTAA
Done.