Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 9 of 21
Found at i:1183949 original size:7 final size:7
Alignment explanation
Indices: 1183937--1183976 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
1183927 ATTTATGTAT
1183937 TTATATA
1 TTATATA
1183944 TTATATA
1 TTATATA
1183951 TTATAT-
1 TTATATA
1183957 TTA-ATA
1 TTATATA
1183963 -TAT-TA
1 TTATATA
1183968 TTATATA
1 TTATATA
1183975 TT
1 TT
1183977 TACATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 6 0.21
6 6 0.21
7 17 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:1183956 original size:14 final size:14
Alignment explanation
Indices: 1183937--1183976 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 14
1183927 ATTTATGTAT
1183937 TTATATATTATATA
1 TTATATATTATATA
1183951 TTATAT-TTA-ATA
1 TTATATATTATATA
1183963 -TAT-TATTATATA
1 TTATATATTATATA
1183975 TT
1 TT
1183977 TACATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
10 1 0.04
11 6 0.26
12 6 0.26
13 4 0.17
14 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATATTATATA
Found at i:1183992 original size:30 final size:29
Alignment explanation
Indices: 1183956--1184038 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 29
1183946 ATATATTATA
1183956 TTTAATATATTATTATATATTTACATAAAT
1 TTTAATATATTATTAT-TATTTACATAAAT
* * * *
1183986 TTTAATATATGAATAATTTATATAATATAAAT
1 TTTAATATAT-TATTA-TTAT-TTACATAAAT
*
1184018 CTTAATATATTATTATTATTT
1 TTTAATATATTATTATTATTT
1184039 TTATATATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
29 1 0.02
30 14 0.33
31 9 0.21
32 18 0.43
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (29 bp):
TTTAATATATTATTATTATTTACATAAAT
Found at i:1183995 original size:20 final size:19
Alignment explanation
Indices: 1183929--1183995 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
1183919 CTTTAATAAT
* *
1183929 TTATGTATTT-ATATATTA
1 TTATATATTTAATAAATTA
*
1183947 TATATTATATTTAATATATTA
1 T-TA-TATATTTAATAAATTA
1183968 TTATATATTTACATAAATT-
1 TTATATATTTA-ATAAATTA
1183987 TTAATATAT
1 TT-ATATAT
1183996 GAATAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.02
19 12 0.29
20 20 0.48
21 9 0.21
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
TTATATATTTAATAAATTA
Found at i:1184055 original size:23 final size:24
Alignment explanation
Indices: 1184025--1184085 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
1184015 AATCTTAATA
*
1184025 TATTATTATTAT-TTTT-ATATAT
1 TATTATAATTATATTTTCATATAT
*
1184047 T-TT-TAATTAATATTTTCATATTT
1 TATTATAATT-ATATTTTCATATAT
1184070 TATTATAATTATATTT
1 TATTATAATTATATTT
1184086 AAATTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 4 0.12
21 4 0.12
22 5 0.16
23 6 0.19
24 8 0.25
25 5 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTATAATTATATTTTCATATAT
Found at i:1184289 original size:15 final size:13
Alignment explanation
Indices: 1184269--1184323 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 13
1184259 AAATACGAAA
1184269 ATATAAAGTAATAAT
1 ATATAAA-T-ATAAT
1184284 ATATAAAATTATATAT
1 ATAT-AAA-TATA-AT
1184300 AATATAAATATAAT
1 -ATATAAATATAAT
1184314 ATATAAATAT
1 ATATAAATAT
1184324 GTACGAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 10 0.28
14 2 0.06
15 11 0.31
16 9 0.25
17 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
ATATAAATATAAT
Found at i:1185557 original size:18 final size:20
Alignment explanation
Indices: 1185532--1185633 Score: 72
Period size: 18 Copynumber: 5.2 Consensus size: 20
1185522 AATAAATTTA
1185532 ATAATTTATATATTTAT-TT
1 ATAATTTATATATTTATATT
*
1185551 A-AATTTATATTTTTATATT
1 ATAATTTATATATTTATATT
*
1185570 ATAA-TTATAT-TTACGATATT
1 ATAATTTATATATT--TATATT
**
1185590 ATATATTTATATAAATTT-TAAC
1 ATA-ATTTATAT--ATTTATATT
*
1185612 AT-ATTTATATATTTATTTT
1 ATAATTTATATATTTATATT
1185631 ATA
1 ATA
1185634 TTTGTATTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 21
0.69 0.09 0.23
Matches are distributed among these distances:
18 20 0.31
19 13 0.20
20 18 0.28
21 1 0.02
22 10 0.16
25 2 0.03
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (20 bp):
ATAATTTATATATTTATATT
Found at i:1185945 original size:23 final size:23
Alignment explanation
Indices: 1185911--1185961 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1185901 GTCAACCTAA
1185911 TTTT-TTTTTAAAATTT-TACATT
1 TTTTATTTTTAAAATTTATA-ATT
1185933 TTTTATTTTTAAAATTTATAATT
1 TTTTATTTTTAAAATTTATAATT
1185956 TTTTAT
1 TTTTAT
1185962 GATAATACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.15
23 21 0.78
24 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTATTTTTAAAATTTATAATT
Found at i:1186062 original size:13 final size:13
Alignment explanation
Indices: 1186044--1186068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1186034 TGATTAATGG
1186044 TACTTAAATTTTA
1 TACTTAAATTTTA
1186057 TACTTAAATTTT
1 TACTTAAATTTT
1186069 GAAAAATCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
TACTTAAATTTTA
Found at i:1187576 original size:20 final size:21
Alignment explanation
Indices: 1187551--1187598 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
1187541 TTTTTATTTG
1187551 ATATATTTATAATTTTTT-AA
1 ATATATTTATAATTTTTTAAA
*
1187571 ATATATATATAATTTTTTAAA
1 ATATATTTATAATTTTTTAAA
1187592 ATATATT
1 ATATATT
1187599 GATATCTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATATTTATAATTTTTTAAA
Found at i:1187576 original size:22 final size:22
Alignment explanation
Indices: 1187532--1187598 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 22
1187522 TTTTCTATGT
**
1187532 TATTTA-AATTTTTTATTTGATA
1 TATTTATAATTTTTTAAAT-ATA
1187554 TATTTATAATTTTTTAAATATA
1 TATTTATAATTTTTTAAATATA
1187576 TA--TATAATTTTTTAAA-ATA
1 TATTTATAATTTTTTAAATATA
1187595 TATT
1 TATT
1187599 GATATCTAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 5 0.12
20 14 0.35
22 11 0.28
23 10 0.25
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (22 bp):
TATTTATAATTTTTTAAATATA
Found at i:1188184 original size:21 final size:21
Alignment explanation
Indices: 1188160--1188199 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1188150 TATTTTTATT
1188160 TAAAT-TTAATTAAAAAATATA
1 TAAATATTAA-TAAAAAATATA
1188181 TAAATATTAATAAAAAATA
1 TAAATATTAATAAAAAATA
1188200 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:1189221 original size:20 final size:21
Alignment explanation
Indices: 1189191--1189230 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1189181 TTAATAATAA
*
1189191 TTTATTATATTTTATATTTAT
1 TTTATTATATTTAATATTTAT
1189212 TTTATT-TATTTAATATTTA
1 TTTATTATATTTAATATTTA
1189231 AAAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATTATATTTAATATTTAT
Found at i:1189237 original size:15 final size:14
Alignment explanation
Indices: 1189219--1189275 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 14
1189209 TATTTTATTT
1189219 ATTTAATATTTAAAA
1 ATTT-ATATTTAAAA
*
1189234 ATTTTATATATTAAAT
1 A-TTTATAT-TTAAAA
1189250 ATTTATAATTTAAAA
1 ATTTAT-ATTTAAAA
*
1189265 AATTATATTTA
1 ATTTATATTTA
1189276 TATATAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.14
15 20 0.56
16 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTATATTTAAAA
Found at i:1189519 original size:3 final size:3
Alignment explanation
Indices: 1189511--1189555 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1189501 CACAAAAGCA
*
1189511 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1189556 GCTAATTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1194164 original size:20 final size:20
Alignment explanation
Indices: 1194129--1194177 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1194119 AAATAATATT
* *
1194129 TTTATAAATTTTAATT-TAA
1 TTTATTAATTTAAATTATAA
*
1194148 TTTAATTAATTTAAATTATTA
1 TTT-ATTAATTTAAATTATAA
1194169 TTTATTAAT
1 TTTATTAAT
1194178 AAAACATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 17 0.68
21 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTAATTTAAATTATAA
Found at i:1194202 original size:23 final size:22
Alignment explanation
Indices: 1194143--1194211 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
1194133 TAAATTTTAA
**
1194143 TTTAATTTAATTAATTTAAAT-T
1 TTTAATTT-ATTAATAAAAATAT
*
1194165 ATT-ATTTATTAATAAAACATAT
1 TTTAATTTATTAATAAAA-ATAT
1194187 TTTAATTTAATT-ATAAAAATAT
1 TTTAATTT-ATTAATAAAAATAT
1194209 TTT
1 TTT
1194212 TTTAGATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 8 0.21
21 6 0.15
22 12 0.31
23 10 0.26
24 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAATTTATTAATAAAAATAT
Found at i:1194212 original size:23 final size:23
Alignment explanation
Indices: 1194168--1194211 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1194158 TTAAATTATT
1194168 ATTTATTAATAAAACATATTTTA
1 ATTTATTAATAAAACATATTTTA
1194191 ATTTAATT-ATAAAA-ATATTTT
1 ATTT-ATTAATAAAACATATTTT
1194212 TTTAGATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 10 0.50
24 3 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTATTAATAAAACATATTTTA
Found at i:1194404 original size:13 final size:13
Alignment explanation
Indices: 1194383--1194423 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1194373 ATTTTATATT
1194383 TTATTTAAATAAA
1 TTATTTAAATAAA
*
1194396 TTATGTAAATAAA
1 TTATTTAAATAAA
*
1194409 TT-TTTTAATAAA
1 TTATTTAAATAAA
1194421 TTA
1 TTA
1194424 AAAATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
TTATTTAAATAAA
Found at i:1194529 original size:14 final size:14
Alignment explanation
Indices: 1194510--1194549 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1194500 TAATTACATC
1194510 ATATTTTGGTAAAA
1 ATATTTTGGTAAAA
*
1194524 ATATTTTGATAAAA
1 ATATTTTGGTAAAA
*
1194538 ATACTTTGGTAA
1 ATATTTTGGTAA
1194550 CAATTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (14 bp):
ATATTTTGGTAAAA
Found at i:1194609 original size:9 final size:9
Alignment explanation
Indices: 1194595--1194619 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1194585 AAATTTTACT
1194595 TAATAAAGA
1 TAATAAAGA
1194604 TAATAAAGA
1 TAATAAAGA
1194613 TAATAAA
1 TAATAAA
1194620 CTTAACCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (9 bp):
TAATAAAGA
Found at i:1196908 original size:2 final size:2
Alignment explanation
Indices: 1196903--1196928 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1196893 TTTCTTTAGT
1196903 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
1196929 ACTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1197319 original size:12 final size:12
Alignment explanation
Indices: 1197296--1197336 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
1197286 ATTAAATAAT
1197296 ATTATA-TTTAA
1 ATTATATTTTAA
1197307 ATTATATTTTAA
1 ATTATATTTTAA
*
1197319 A-TATAATTTAA
1 ATTATATTTTAA
*
1197330 AATATAT
1 ATTATAT
1197337 ATCACTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTATATTTTAA
Found at i:1198351 original size:3 final size:3
Alignment explanation
Indices: 1198343--1198387 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1198333 CCACAGGATT
1198343 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1198388 TTCACTTAAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1199054 original size:15 final size:15
Alignment explanation
Indices: 1198941--1199047 Score: 64
Period size: 14 Copynumber: 7.3 Consensus size: 15
1198931 AGAAATTCAC
*
1198941 ATAATTATTATTTA-A
1 ATAA-TATTATATATA
1198956 ATAATATT-TATA-A
1 ATAATATTATATATA
*
1198969 TATAATATTATA-ATT
1 -ATAATATTATATATA
* *
1198984 ATAATTTTAT-TATT
1 ATAATATTATATATA
* *
1198998 TTAAT-TTTTATATTA
1 ATAATATTATATA-TA
* *
1199013 ATCATAATTAAATATA
1 ATAAT-ATTATATATA
1199029 ATAATATTATATATA
1 ATAATATTATATATA
1199044 ATAA
1 ATAA
1199048 CTATATAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
13 7 0.10
14 31 0.43
15 23 0.32
16 6 0.08
17 5 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAATATTATATATA
Found at i:1203156 original size:4 final size:4
Alignment explanation
Indices: 1203147--1203223 Score: 104
Period size: 4 Copynumber: 19.8 Consensus size: 4
1203137 TCTGTATAAT
* *
1203147 ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
1203195 ATAC ATAC AT-- ATAT ATAT ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1203224 TATATATATA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.03
4 64 0.97
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:1203176 original size:20 final size:20
Alignment explanation
Indices: 1203151--1203245 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
1203141 TATAATATAC
1203151 ATACATACATACATACATAT
1 ATACATACATACATACATAT
1203171 ATACATACATACATACATAT
1 ATACATACATACATACATAT
1203191 ATACATACATACAT--ATAT
1 ATACATACATACATACATAT
* *
1203209 ATATATACATACATATATAT
1 ATACATACATACATACATAT
* * *
1203229 ATATATATATATATACA
1 ATACATACATACATACA
1203246 CGAATGAAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
18 17 0.25
20 52 0.75
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.35
Consensus pattern (20 bp):
ATACATACATACATACATAT
Found at i:1203226 original size:12 final size:12
Alignment explanation
Indices: 1203145--1203245 Score: 107
Period size: 12 Copynumber: 8.6 Consensus size: 12
1203135 AGTCTGTATA
1203145 ATATACATACAT
1 ATATACATACAT
*
1203157 ACATACATACAT
1 ATATACATACAT
1203169 ATATACATACAT
1 ATATACATACAT
* *
1203181 ACATACATATAT
1 ATATACATACAT
*
1203193 ACATACATACAT
1 ATATACATACAT
*
1203205 ATAT--ATATAT
1 ATATACATACAT
* *
1203215 ACATACATATAT
1 ATATACATACAT
* *
1203227 ATATATATATAT
1 ATATACATACAT
1203239 ATATACA
1 ATATACA
1203246 CGAATGAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
10 8 0.11
12 68 0.89
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATACATACAT
Found at i:1203228 original size:4 final size:4
Alignment explanation
Indices: 1203167--1203243 Score: 73
Period size: 4 Copynumber: 19.2 Consensus size: 4
1203157 ACATACATAC
* * * * * * *
1203167 ATAT ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
1203215 ACAT ACAT ATAT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1203244 CACGAATGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:1204154 original size:2 final size:2
Alignment explanation
Indices: 1204147--1204173 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1204137 TCATAAATAA
1204147 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
1204174 AATGGCTAGC
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:1204544 original size:13 final size:13
Alignment explanation
Indices: 1204511--1204537 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1204501 TAATTTAAAT
1204511 TAAATTAATTTTA
1 TAAATTAATTTTA
1204524 TAAATTAATTTTA
1 TAAATTAATTTTA
1204537 T
1 T
1204538 TATTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATTAATTTTA
Found at i:1204545 original size:18 final size:18
Alignment explanation
Indices: 1204503--1204561 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
1204493 ATTTATTTTA
* *
1204503 ATTTAAATTAAATTAATT
1 ATTTAAATTAATTTTATT
1204521 -TTATAAATTAATTTTATT
1 ATT-TAAATTAATTTTATT
*
1204539 ATTTAAAATATATTTTA-T
1 ATTTAAATTA-ATTTTATT
1204557 ATTTA
1 ATTTA
1204562 TATTTTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 25 0.71
19 8 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTAAATTAATTTTATT
Found at i:1204577 original size:32 final size:30
Alignment explanation
Indices: 1204500--1204577 Score: 72
Period size: 32 Copynumber: 2.6 Consensus size: 30
1204490 ATTATTTATT
*
1204500 TTAA-TTTA-AATTAAATTAATTTTATAAA
1 TTAATTTTATAATTAAAATAATTTTATAAA
* *
1204528 TTAATTTTATTATTTAAAATATATTTTAT-AT
1 TTAATTTTA-TAATTAAAATA-ATTTTATAAA
1204559 TTATATTTTTATAATTAAA
1 TTA-A-TTTTATAATTAAA
1204578 TTTAAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 4 0.10
29 4 0.10
31 12 0.30
32 15 0.38
33 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTAATTTTATAATTAAAATAATTTTATAAA
Found at i:1204638 original size:60 final size:58
Alignment explanation
Indices: 1204499--1204638 Score: 133
Period size: 60 Copynumber: 2.4 Consensus size: 58
1204489 AATTATTTAT
* * * * * *
1204499 TTTAATTTAAATTAAATTAATTTTATAAATTAATTTTATTATTTAAAATATATTTTATA
1 TTTAATATAATTTAAATAAATTTAATAAATTAATTATATTA-TTAAAATATATTTTAAA
* *
1204558 TTT-ATAT-TTTTATAATTAAATTTAAATTAAATTAATTCATATTA-TAAAATTTATTTTAAA
1 TTTAATATAATTTA-AA-TAAATTT-AA-TAAATTAATT-ATATTATTAAAATATATTTTAAA
1204618 TTTAATATAATTTAAATAAAT
1 TTTAATATAATTTAAATAAAT
1204639 AAATAATTTG
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
57 3 0.05
58 5 0.08
59 9 0.14
60 23 0.35
61 16 0.25
62 9 0.14
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.54
Consensus pattern (58 bp):
TTTAATATAATTTAAATAAATTTAATAAATTAATTATATTATTAAAATATATTTTAAA
Found at i:1207987 original size:23 final size:23
Alignment explanation
Indices: 1207957--1208003 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1207947 GCGAGTAAAG
1207957 TAAGAGTGGAAAATGGAAATGAT
1 TAAGAGTGGAAAATGGAAATGAT
1207980 TAAGAGTGGAAAATGGAAATGAT
1 TAAGAGTGGAAAATGGAAATGAT
1208003 T
1 T
1208004 CCTGCAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (23 bp):
TAAGAGTGGAAAATGGAAATGAT
Found at i:1208990 original size:23 final size:23
Alignment explanation
Indices: 1208964--1209008 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1208954 TAATAATATT
*
1208964 ATTTA-ATATTTTTGAATTTTAAA
1 ATTTATATATTTAT-AATTTTAAA
*
1208987 ATTTATTTATTTATAATTTTAA
1 ATTTATATATTTATAATTTTAA
1209009 TCTTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTATATATTTATAATTTTAAA
Found at i:1209204 original size:2 final size:2
Alignment explanation
Indices: 1209197--1209228 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1209187 ATCTCATTCA
1209197 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
1209229 TTAAATTCTA
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:1215000 original size:2 final size:2
Alignment explanation
Indices: 1214987--1215027 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1214977 TCCTTTAGAA
*
1214987 AG AG AA AG AG AG AG AG 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 AG AG AG AG AG AG AG AG A
1215028 ATCGGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1215221 original size:15 final size:16
Alignment explanation
Indices: 1215201--1215230 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1215191 TACTTAACGT
1215201 AAAAGAAAA-AAAAAA
1 AAAAGAAAAGAAAAAA
1215216 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
1215231 CAATCTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAA
Found at i:1216140 original size:16 final size:16
Alignment explanation
Indices: 1216121--1216151 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1216111 TTAATATTTT
1216121 TTTAAATTAAATTAAA
1 TTTAAATTAAATTAAA
*
1216137 TTTAAATTAATTTAA
1 TTTAAATTAAATTAA
1216152 TTATTTATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAATTAAATTAAA
Found at i:1216170 original size:30 final size:29
Alignment explanation
Indices: 1216136--1216230 Score: 79
Period size: 33 Copynumber: 3.1 Consensus size: 29
1216126 ATTAAATTAA
* *
1216136 ATTTAAATTAATTTAATTATTTATTATATT
1 ATTTAAATTAATTTAATTA-ATATGATATT
1216166 ATTTAAATATTAATTTTATATTAATATGATATT
1 ATTT-AA-ATTAA-TTTA-ATTAATATGATATT
*
1216199 -TTTATAATTAAATTTAA-TAA-ATAATATT
1 ATTTA-AATT-AATTTAATTAATATGATATT
1216227 ATTT
1 ATTT
1216231 TTATTTTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
28 7 0.13
29 6 0.11
30 5 0.09
31 10 0.18
32 11 0.20
33 12 0.22
34 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
ATTTAAATTAATTTAATTAATATGATATT
Found at i:1216774 original size:25 final size:26
Alignment explanation
Indices: 1216715--1216768 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
1216705 TTAAATTATT
* *
1216715 ATTTAATAATAAATAATAATTTTTTA
1 ATTTAATTATAAATAATAATTTTTAA
1216741 ATTTAATTATAAA-AAT-ATTTTTAA
1 ATTTAATTATAAATAATAATTTTTAA
1216765 ATTT
1 ATTT
1216769 TTATTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 11 0.42
25 3 0.12
26 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTAATTATAAATAATAATTTTTAA
Found at i:1220897 original size:13 final size:13
Alignment explanation
Indices: 1220879--1220903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1220869 TATCTAATAG
1220879 TATTTTATTTATT
1 TATTTTATTTATT
1220892 TATTTTATTTAT
1 TATTTTATTTAT
1220904 ATTTTTAACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:1230914 original size:36 final size:36
Alignment explanation
Indices: 1230819--1230915 Score: 104
Period size: 36 Copynumber: 2.7 Consensus size: 36
1230809 AAAGCTGTTG
* * * * *
1230819 GGTGTTAGCAATGGTATTGGACCTAGCCGTCCTGTT
1 GGTGTTAGCAATGGTATCGGGCCTGGCCGGCCTATT
* * * *
1230855 AGTGTTAGCAGTGGGATCAGGCCTGGCCGGCCTATT
1 GGTGTTAGCAATGGTATCGGGCCTGGCCGGCCTATT
*
1230891 GGTGTTAGCAATGGTAACGGGCCTG
1 GGTGTTAGCAATGGTATCGGGCCTG
1230916 TTCAGCCTGT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.18, C:0.20, G:0.35, T:0.28
Consensus pattern (36 bp):
GGTGTTAGCAATGGTATCGGGCCTGGCCGGCCTATT
Found at i:1232093 original size:16 final size:16
Alignment explanation
Indices: 1232074--1232105 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1232064 AAGTGTTTCA
1232074 CTTTCAAAGTTTTAGC
1 CTTTCAAAGTTTTAGC
1232090 CTTTCAAAGTTTTAGC
1 CTTTCAAAGTTTTAGC
1232106 ATTAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (16 bp):
CTTTCAAAGTTTTAGC
Found at i:1240282 original size:2 final size:2
Alignment explanation
Indices: 1240275--1240310 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1240265 CATTGAATTT
* *
1240275 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1240311 ATCTTATCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1240489 original size:21 final size:21
Alignment explanation
Indices: 1240440--1240489 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 21
1240430 AGTAAATTTC
1240440 ATAATTCATATATTTGTTATAT
1 ATAATT-ATATATTTGTTATAT
*
1240462 AT-A-TATATA-TTGTTGTATT
1 ATAATTATATATTTGTTATA-T
1240481 ATAATTATA
1 ATAATTATA
1240490 ATTAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
18 7 0.29
19 8 0.33
20 2 0.08
21 5 0.21
22 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (21 bp):
ATAATTATATATTTGTTATAT
Found at i:1250564 original size:19 final size:20
Alignment explanation
Indices: 1250523--1250565 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1250513 ATCATTTATA
* *
1250523 TTTTTAAACTCTCTATTGTC
1 TTTTCAAACTCTCTATTGAC
*
1250543 TTTTCAAACTCTTTATT-AC
1 TTTTCAAACTCTCTATTGAC
1250562 TTTT
1 TTTT
1250566 TCAAGTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTCAAACTCTCTATTGAC
Found at i:1255250 original size:11 final size:11
Alignment explanation
Indices: 1255234--1255317 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
1255224 AAATTAAATG
1255234 ATATAAATAAA
1 ATATAAATAAA
1255245 ATAT-AATAATA
1 ATATAAATAA-A
1255256 ATATAAATTTATAA
1 ATATAAA--TA-AA
*
1255270 ATTTATAA-AAA
1 ATATA-AATAAA
1255281 ATATAAAT-AA
1 ATATAAATAAA
*
1255291 TTAATAAATAAA
1 AT-ATAAATAAA
* *
1255303 ATTTATAT-AA
1 ATATAAATAAA
1255313 ATATA
1 ATATA
1255318 TCACCCTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
10 16 0.28
11 25 0.44
12 6 0.11
14 7 0.12
15 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAATAAA
Found at i:1256258 original size:6 final size:6
Alignment explanation
Indices: 1256249--1256282 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1256239 TTTTAATCAT
* *
1256249 ATATAT ATATAT ATATAG ATATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
1256283 TGTAACTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (6 bp):
ATATAG
Found at i:1260955 original size:10 final size:11
Alignment explanation
Indices: 1260922--1261027 Score: 59
Period size: 10 Copynumber: 10.3 Consensus size: 11
1260912 CTTTAGTTAA
*
1260922 TTTTATACAA-
1 TTTTATATAAT
1260932 TTTTATATAA-
1 TTTTATATAAT
1260942 TTTTAT-TAATT
1 TTTTATATAA-T
1260953 TTTTATATAAT
1 TTTTATATAAT
*
1260964 TTTTA-A-AAG
1 TTTTATATAAT
* *
1260973 CTTTATA-ATT
1 TTTTATATAAT
*
1260983 TTTTGTATAA-
1 TTTTATATAAT
*
1260993 -TTTAGATAACT
1 TTTTATATAA-T
* *
1261004 TTTGATAT-AC
1 TTTTATATAAT
1261014 TTTTATATAAT
1 TTTTATATAAT
1261025 TTT
1 TTT
1261028 GATACTTCTT
Statistics
Matches: 72, Mismatches: 15, Indels: 17
0.69 0.14 0.16
Matches are distributed among these distances:
9 16 0.22
10 30 0.42
11 18 0.25
12 8 0.11
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (11 bp):
TTTTATATAAT
Found at i:1260958 original size:11 final size:12
Alignment explanation
Indices: 1260932--1260967 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1260922 TTTTATACAA
1260932 TTTTATATAA--
1 TTTTATATAATT
1260942 TTTTAT-TAATT
1 TTTTATATAATT
1260953 TTTTATATAATT
1 TTTTATATAATT
1260965 TTT
1 TTT
1260968 AAAAGCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 6 0.26
11 6 0.26
12 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATATAATT
Found at i:1260965 original size:31 final size:30
Alignment explanation
Indices: 1260922--1261114 Score: 99
Period size: 31 Copynumber: 6.2 Consensus size: 30
1260912 CTTTAGTTAA
*
1260922 TTTTATACAATTTTATATAATTTTATTAATT
1 TTTTATATAATTTTATATAATTTTA-TAATT
* *
1260953 TTTTATATAATTTT-TAAAAGCTTTATAATT
1 TTTTATATAATTTTATATAA-TTTTATAATT
* * *
1260983 TTTTGTATAA-TTTAGATAACTTTTGAT-ATAC
1 TTTTATATAATTTTATATAA-TTTT-ATAAT-T
** *
1261014 TTTTATATAATTTTGATACTTCTTAATATAATT
1 TTTTATATAATTTT-ATA-TAATT-TTATAATT
* * * *
1261047 TATTA-AT-ATTTGATATAATTTTAATCACT
1 TTTTATATAATTTTATATAATTTT-ATAATT
* ** *
1261076 TTTAATATAATTTTAATATTTTTTGTAAAATT
1 TTTTATATAATTTT-ATATAATTT-TATAATT
1261108 TTTTATA
1 TTTTATA
1261115 ACCTTTACAA
Statistics
Matches: 117, Mismatches: 31, Indels: 27
0.67 0.18 0.15
Matches are distributed among these distances:
28 1 0.01
29 13 0.11
30 31 0.26
31 36 0.31
32 21 0.18
33 11 0.09
34 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (30 bp):
TTTTATATAATTTTATATAATTTTATAATT
Found at i:1261012 original size:21 final size:21
Alignment explanation
Indices: 1260983--1261031 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1260973 CTTTATAATT
1260983 TTTTG-TATA-ATTTAGATAA
1 TTTTGATATACATTTAGATAA
* *
1261002 CTTTTGATATACTTTTATATAA
1 -TTTTGATATACATTTAGATAA
1261024 TTTTGATA
1 TTTTGATA
1261032 CTTCTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 12 0.48
22 8 0.32
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (21 bp):
TTTTGATATACATTTAGATAA
Found at i:1261063 original size:41 final size:39
Alignment explanation
Indices: 1261018--1261096 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 39
1261008 ATATACTTTT
*
1261018 ATATAATTTTGAT-ACTTCTTAATATAATTTATTAATATTTG
1 ATATAATTTTAATCACTT-TTAATATAA-TT-TTAATATTTG
1261059 ATATAATTTTAATCACTTTTAATATAATTTTAATATTT
1 ATATAATTTTAATCACTTTTAATATAATTTTAATATTT
1261097 TTTGTAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 9 0.25
40 2 0.06
41 21 0.58
42 4 0.11
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (39 bp):
ATATAATTTTAATCACTTTTAATATAATTTTAATATTTG
Found at i:1261091 original size:21 final size:20
Alignment explanation
Indices: 1261010--1261097 Score: 94
Period size: 21 Copynumber: 4.4 Consensus size: 20
1261000 AACTTTTGAT
*
1261010 ATACTTTT-ATATAATTTTG
1 ATACTTTTAATATAATTTTA
1261029 ATACTTCTTAATATAATTTATTA
1 ATACTT-TTAATATAA-TT-TTA
*
1261052 ATA--TTTGATATAATTTTA
1 ATACTTTTAATATAATTTTA
1261070 ATCACTTTTAATATAATTTTA
1 AT-ACTTTTAATATAATTTTA
1261091 ATA-TTTT
1 ATACTTTT
1261098 TTGTAAAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
18 5 0.08
19 13 0.22
20 11 0.19
21 23 0.39
22 2 0.03
23 5 0.08
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (20 bp):
ATACTTTTAATATAATTTTA
Found at i:1261108 original size:41 final size:41
Alignment explanation
Indices: 1261022--1261109 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 41
1261012 ACTTTTATAT
* * *
1261022 AATTTTGATACTTCTTAATATAATTTATTAATATTTGATAT
1 AATTTTAATACTTCTTAATATAATTTAATAATATTTGATAA
* *
1261063 AATTTTAATCACTT-TTAATATAATTTTAATATTTTTTG-TAA
1 AATTTTAAT-ACTTCTTAATATAA-TTTAATAATATTTGATAA
1261104 AATTTT
1 AATTTT
1261110 TTATAACCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 25 0.62
42 15 0.38
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (41 bp):
AATTTTAATACTTCTTAATATAATTTAATAATATTTGATAA
Found at i:1261196 original size:21 final size:20
Alignment explanation
Indices: 1261167--1261207 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1261157 ACATTTTGAG
*
1261167 ATAATTTTGATAATATTTATA
1 ATAACTTTGAT-ATATTTATA
*
1261188 ATAACTTTGATATTTTTATA
1 ATAACTTTGATATATTTATA
1261208 TTTTTTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
ATAACTTTGATATATTTATA
Found at i:1261331 original size:21 final size:21
Alignment explanation
Indices: 1261287--1261378 Score: 86
Period size: 21 Copynumber: 4.5 Consensus size: 21
1261277 GTAACATTTA
*
1261287 ATATGATTTTGATAA-T-TT-
1 ATATAATTTTGATAAGTATTG
*
1261305 ATATAATTTTGATAAGTAGTG
1 ATATAATTTTGATAAGTATTG
* *
1261326 ATATAATTTTAACAAGT-TTG
1 ATATAATTTTGATAAGTATTG
*
1261346 AATATAATTTTGGTAA-TATTTG
1 -ATATAATTTTGATAAGTA-TTG
1261368 ATATAATTTTG
1 ATATAATTTTG
1261379 TTAGATCTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
18 14 0.23
19 1 0.02
20 4 0.07
21 38 0.63
22 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (21 bp):
ATATAATTTTGATAAGTATTG
Found at i:1261400 original size:9 final size:10
Alignment explanation
Indices: 1261386--1261442 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
1261376 TTGTTAGATC
1261386 TTAATAA-TT
1 TTAATAATTT
1261395 TTAATAATTT
1 TTAATAATTT
*
1261405 TTAATATAATT
1 TTAATA-ATTT
* *
1261416 ATAATACTTTT
1 TTAATA-ATTT
*
1261427 TTGATAATTT
1 TTAATAATTT
1261437 TTAATA
1 TTAATA
1261443 TAATTTTGAT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
9 7 0.19
10 16 0.43
11 14 0.38
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (10 bp):
TTAATAATTT
Found at i:1261415 original size:21 final size:21
Alignment explanation
Indices: 1261283--1261415 Score: 80
Period size: 21 Copynumber: 6.6 Consensus size: 21
1261273 GTTAGTAACA
*
1261283 TTTAATATGATTTTGATAA--
1 TTTAATATAATTTTGATAATT
*
1261302 TTT-ATATAATTTTGATAAGT
1 TTTAATATAATTTTGATAATT
** * * * *
1261322 AGTGATATAATTTTAACAAGT
1 TTTAATATAATTTTGATAATT
* * *
1261343 TTGAATATAATTTTGGTAATA
1 TTTAATATAATTTTGATAATT
* *
1261364 TTTGATATAATTTTGTTAGA-T
1 TTTAATATAATTTTGATA-ATT
* *
1261385 CTT-A-ATAATTTTAATAATT
1 TTTAATATAATTTTGATAATT
1261404 TTTAATATAATT
1 TTTAATATAATT
1261416 ATAATACTTT
Statistics
Matches: 85, Mismatches: 22, Indels: 12
0.71 0.18 0.10
Matches are distributed among these distances:
18 15 0.18
19 16 0.19
20 3 0.04
21 50 0.59
22 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTAATATAATTTTGATAATT
Found at i:1261449 original size:21 final size:21
Alignment explanation
Indices: 1261425--1261499 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
1261415 TATAATACTT
1261425 TTTTGATAATTTTTAATATAA
1 TTTTGATAATTTTTAATATAA
* * *
1261446 TTTTGATAACTATTGATATAA
1 TTTTGATAATTTTTAATATAA
*
1261467 TTGTT-ATAATATTTAATATAA
1 TT-TTGATAATTTTTAATATAA
1261488 TTTTGATAATTT
1 TTTTGATAATTT
1261500 GAGGAAACTA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTGATAATTTTTAATATAA
Found at i:1261559 original size:21 final size:21
Alignment explanation
Indices: 1261535--1261596 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
1261525 ATAATGTTTT
**
1261535 TAACATTTATAATCGTTTTAA
1 TAACATTTATAATAATTTTAA
*
1261556 TAACTTTTGAT-ATAATTTTAA
1 TAACATTT-ATAATAATTTTAA
* *
1261577 TTACAGTTTATAATTATTTT
1 TAACA-TTTATAATAATTTT
1261597 GATATAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.53
Consensus pattern (21 bp):
TAACATTTATAATAATTTTAA
Found at i:1265162 original size:2 final size:2
Alignment explanation
Indices: 1265155--1265193 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1265145 TATCCAAATC
1265155 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
1265194 GAGAGAGAGA
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:1265198 original size:2 final size:2
Alignment explanation
Indices: 1265193--1265224 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1265183 ATATATATAT
1265193 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
1265225 CATATGATTA
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):
AG
Found at i:1265617 original size:2 final size:2
Alignment explanation
Indices: 1265610--1265643 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1265600 TGTTTGTTTT
1265610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1265644 AGGTTCTTAT
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):
TA
Found at i:1268380 original size:19 final size:19
Alignment explanation
Indices: 1268356--1268397 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1268346 TCAAACTCGG
*
1268356 TCTTAGGAAGTAGGAGCTA
1 TCTTAGGAAGGAGGAGCTA
1268375 TCTTAGGAAGGAGGAGCTA
1 TCTTAGGAAGGAGGAGCTA
1268394 TCTT
1 TCTT
1268398 TTTCCCATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.29
Consensus pattern (19 bp):
TCTTAGGAAGGAGGAGCTA
Found at i:1272565 original size:28 final size:29
Alignment explanation
Indices: 1272524--1272586 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
1272514 GAAATAAAAA
* *
1272524 ATAATTAATTATTAAAT-ATATTTTATTAT
1 ATAA-TAATTATTAAATAATATCTTATAAT
1272553 ATAATAATTATTAAATAATATCTTATAAT
1 ATAATAATTATTAAATAATATCTTATAAT
1272582 A-AATA
1 ATAATA
1272587 TAATCTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
ATAATAATTATTAAATAATATCTTATAAT
Found at i:1273816 original size:18 final size:19
Alignment explanation
Indices: 1273793--1273840 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1273783 TTAATTATTA
*
1273793 TAATTTATTT-GATTTAAT
1 TAATTTATTTAAATTTAAT
1273811 TAATTT-TTTAAATTTAAT
1 TAATTTATTTAAATTTAAT
*
1273829 CAATTTAATTTA
1 TAATTT-ATTTA
1273841 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
20 4 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TAATTTATTTAAATTTAAT
Found at i:1277468 original size:19 final size:18
Alignment explanation
Indices: 1277433--1277533 Score: 63
Period size: 19 Copynumber: 5.6 Consensus size: 18
1277423 TTGATTGAAT
*
1277433 TTAAATATAATAT-TTTAA
1 TTAAAT-TAATTTATTTAA
1277451 TTAAATTAATTTAATTTAA
1 TTAAATTAATTT-ATTTAA
1277470 -TATAATT-A-TTATTTAA
1 TTA-AATTAATTTATTTAA
*
1277486 TT-AA-TAATTTATATTTTAT
1 TTAAATTAA-TT-TA-TTTAA
1277505 TTAAATTTAA-TTATTTAA
1 TTAAA-TTAATTTATTTAA
1277523 TATAAATTAAT
1 T-TAAATTAAT
1277534 ATAAACTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 27
0.69 0.03 0.28
Matches are distributed among these distances:
14 1 0.02
15 3 0.05
16 6 0.09
17 9 0.14
18 20 0.30
19 21 0.32
20 3 0.05
22 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAATTAATTTATTTAA
Found at i:1277470 original size:5 final size:5
Alignment explanation
Indices: 1277446--1277533 Score: 56
Period size: 5 Copynumber: 17.2 Consensus size: 5
1277436 AATATAATAT
* * *
1277446 TTTAA -TTAA ATTAA TTTAA TTTAA TATAA TTATTA TTTAA TTAATAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA TT--TAA
* * *
1277493 TTTATA TTTTA TTTAAA TTTAA -TT-A TTTAA TATAA ATTAA T
1 TTTA-A TTTAA TTT-AA TTTAA TTTAA TTTAA TTTAA TTTAA T
1277534 ATAAACTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.12
5 38 0.59
6 12 0.19
7 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TTTAA
Found at i:1277494 original size:33 final size:33
Alignment explanation
Indices: 1277430--1277533 Score: 95
Period size: 37 Copynumber: 2.9 Consensus size: 33
1277420 AATTTGATTG
1277430 AATTTAAATATAATATTTTAATTAAATTAATTT
1 AATTTAAATATAATATTTTAATTAAATTAATTT
1277463 AATTT-AATATAATTATTATTTAATTAATAATTTATATTT
1 AATTTAAATATAA-TA-T-TTTAATT-A-AA-TTA-ATTT
* *
1277502 TATTTAAATTTAAT-TATTTAATATAAATTAAT
1 AATTTAAATATAATAT-TTTAAT-TAAATTAAT
1277534 ATAAACTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
32 7 0.12
33 7 0.12
34 3 0.05
35 10 0.17
36 3 0.05
37 11 0.18
38 4 0.07
39 9 0.15
40 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATTTAAATATAATATTTTAATTAAATTAATTT
Found at i:1277977 original size:149 final size:149
Alignment explanation
Indices: 1277809--1278103 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
1277799 CGAGAAATTG
1277809 GTCGATTCTCATTTATTTATTTATTTTTAAAAAATATTTTTTGACCTATAAACATTGAAAATATA
1 GTCGATTCTCATTTATTTATTTATTTTTAAAAAATATTTTTTGACCTATAAACATTGAAAATATA
*
1277874 AAACTACAGACTCTCAAAAACAAAGATTAACCAAACTGATGCTAAATTTGTAATGTTATTGTTGA
66 AAACTACAGACACTCAAAAACAAAGATTAACCAAACTGATGCTAAATTTGTAATGTTATTGTTGA
1277939 TTAAATGAGTGTAAAGATT
131 TTAAATGAGTGTAAAGATT
1277958 GTCGATTCTCATTTATTTATTTATTTTTAAAAAATATTTTTTGACCTATAAACATTGAAAATATA
1 GTCGATTCTCATTTATTTATTTATTTTTAAAAAATATTTTTTGACCTATAAACATTGAAAATATA
1278023 AAACTACAGACACTCAAAAACAAAGATTAACCAAACTGATGCTAAATTTGTAATGTTATTGTTGA
66 AAACTACAGACACTCAAAAACAAAGATTAACCAAACTGATGCTAAATTTGTAATGTTATTGTTGA
1278088 TTAAATGAGTGTAAAG
131 TTAAATGAGTGTAAAG
1278104 TGATTTAATT
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 145 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (149 bp):
GTCGATTCTCATTTATTTATTTATTTTTAAAAAATATTTTTTGACCTATAAACATTGAAAATATA
AAACTACAGACACTCAAAAACAAAGATTAACCAAACTGATGCTAAATTTGTAATGTTATTGTTGA
TTAAATGAGTGTAAAGATT
Found at i:1278175 original size:50 final size:49
Alignment explanation
Indices: 1278113--1278286 Score: 204
Period size: 50 Copynumber: 3.5 Consensus size: 49
1278103 GTGATTTAAT
* * **
1278113 TATTCTTTATCAATCTTTGATAATCGAGAGAGATGGTCGTAATTGTTGA
1 TATTCTTCATCAATCTTTGACAATCGAGAGAGATGACCGTAATTGTTGA
* * *
1278162 CTATTCTTCATCAACCTTTGACAATCGAGAGAGTTGACCGTAATTATTGA
1 -TATTCTTCATCAATCTTTGACAATCGAGAGAGATGACCGTAATTGTTGA
* * * *
1278212 TAATTCTTCATCAATTTTTGACAATCGAAAAAGATGACCGTAATTGTTCA
1 T-ATTCTTCATCAATCTTTGACAATCGAGAGAGATGACCGTAATTGTTGA
* *
1278262 TTATTCTTCACCAAGCTTTGACAAT
1 -TATTCTTCATCAATCTTTGACAAT
1278287 AGAAAAAGGT
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
49 1 0.01
50 103 0.98
51 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (49 bp):
TATTCTTCATCAATCTTTGACAATCGAGAGAGATGACCGTAATTGTTGA
Found at i:1278292 original size:50 final size:50
Alignment explanation
Indices: 1278111--1278309 Score: 200
Period size: 50 Copynumber: 4.0 Consensus size: 50
1278101 AAGTGATTTA
* * * * * **
1278111 ATTATTCTTTATCAATCTTTGATAATCGAGAGAGATGGTCGTAATTGTTG
1 ATTATTCTTCATCAACCTTTGACAATCGAAAAAGATGACCGTAATTGTTG
* * * * *
1278161 ACTATTCTTCATCAACCTTTGACAATCGAGAGAGTTGACCGTAATTATTG
1 ATTATTCTTCATCAACCTTTGACAATCGAAAAAGATGACCGTAATTGTTG
* ** *
1278211 ATAATTCTTCATCAATTTTTGACAATCGAAAAAGATGACCGTAATTGTTC
1 ATTATTCTTCATCAACCTTTGACAATCGAAAAAGATGACCGTAATTGTTG
* * * * * *
1278261 ATTATTCTTCACCAAGCTTTGACAATAGAAAAAGGTGATCGCAATTGTT
1 ATTATTCTTCATCAACCTTTGACAATCGAAAAAGATGACCGTAATTGTT
1278310 AACTCTAAGC
Statistics
Matches: 124, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 124 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (50 bp):
ATTATTCTTCATCAACCTTTGACAATCGAAAAAGATGACCGTAATTGTTG
Found at i:1282760 original size:50 final size:50
Alignment explanation
Indices: 1282680--1282935 Score: 305
Period size: 50 Copynumber: 5.1 Consensus size: 50
1282670 GCAAAGTGAT
* * * **
1282680 TTGAGTATTCTTCATCAACCTTTGATAATCGAGAGAGGTGGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * *
1282730 TTGACTATTCTTTACCAACTTTTGACAATCGAGAGAGGTGACCGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * * * *
1282780 TTGACTATTCTTCATCAACCTTTGACAATCAAGAGAAGTGACTGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * * * **
1282830 TTGACTATTCTTCACTAACTTTTAACAATCGAGAGAGATGATTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * * *
1282880 TTGACTATTCTTCACCAACCTTTGACAATAGAAAAAAGTGACCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
1282930 TTGACT
1 TTGACT
1282936 TTAAGCATCT
Statistics
Matches: 173, Mismatches: 33, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 173 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
Found at i:1283108 original size:14 final size:15
Alignment explanation
Indices: 1283083--1283111 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1283073 TATTATTGTG
1283083 TTTAATTTTTATTTT
1 TTTAATTTTTATTTT
1283098 TTTAA-TTTTATTTT
1 TTTAATTTTTATTTT
1283112 AATTATGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTAATTTTTATTTT
Found at i:1284486 original size:22 final size:22
Alignment explanation
Indices: 1284452--1284493 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1284442 TAGATTTAAT
* *
1284452 ATATTTTTTAAATATAAATTAG
1 ATATGTTTAAAATATAAATTAG
*
1284474 ATATGTTTAAAATTTAAATT
1 ATATGTTTAAAATATAAATT
1284494 TTAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
ATATGTTTAAAATATAAATTAG
Found at i:1285017 original size:7 final size:7
Alignment explanation
Indices: 1285005--1285085 Score: 58
Period size: 7 Copynumber: 10.7 Consensus size: 7
1284995 TACATTTAAA
1285005 TATTTAT
1 TATTTAT
1285012 TATTTAT
1 TATTTAT
1285019 ATATATTAT
1 -TAT-TTAT
1285028 TAATTTAT
1 T-ATTTAT
* *
1285036 AATTTTAAAA
1 TA-TTT--AT
1285046 TATTTAT
1 TATTTAT
1285053 ATATTTA-
1 -TATTTAT
1285060 TATTTTAT
1 TA-TTTAT
1285068 T-TTTAT
1 TATTTAT
1285074 TATTTAT
1 TATTTAT
1285081 TATTT
1 TATTT
1285086 TATATTTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
6 8 0.13
7 23 0.38
8 18 0.30
9 9 0.15
10 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TATTTAT
Found at i:1285052 original size:25 final size:25
Alignment explanation
Indices: 1285019--1285066 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
1285009 TATTATTTAT
1285019 ATATATTAT-TAATTTATAATTTTAAA
1 ATATATTATAT-ATTTAT-ATTTTAAA
1285045 ATAT-TTATATATTTATATTTTA
1 ATATATTATATATTTATATTTTA
1285067 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
25 10 0.48
26 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATATTATATATTTATATTTTAAA
Found at i:1285079 original size:13 final size:15
Alignment explanation
Indices: 1284998--1285085 Score: 76
Period size: 17 Copynumber: 5.8 Consensus size: 15
1284988 TTTTAATTAC
*
1284998 ATTTAAATATTTATT
1 ATTTATATATTTATT
1285013 ATTTATATATATTATT
1 ATTTATATAT-TTATT
*
1285029 AATTTATA-ATTTTAAAAT
1 -ATTTATATA-TTT--ATT
1285047 ATTTATATATTTA-T
1 ATTTATATATTTATT
*
1285061 ATTT-TATTTTTATT
1 ATTTATATATTTATT
1285075 ATTTAT-TATTT
1 ATTTATATATTT
1285086 TATATTTTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
13 7 0.11
14 14 0.23
15 11 0.18
16 8 0.13
17 18 0.30
18 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATATATTTATT
Found at i:1285091 original size:7 final size:7
Alignment explanation
Indices: 1285007--1285094 Score: 54
Period size: 8 Copynumber: 11.6 Consensus size: 7
1284997 CATTTAAATA
1285007 TTTATTAT
1 TTTA-TAT
1285015 TTATATAT
1 TT-TATAT
* *
1285023 ATTATTAA
1 TTTA-TAT
1285031 TTTATAAT
1 TTTAT-AT
*
1285039 TTTAAAAT
1 TTT-ATAT
1285047 ATTTATAT
1 -TTTATAT
1285055 ATTTATAT
1 -TTTATAT
1285063 TTTAT-T
1 TTTATAT
1285069 TTTAT-T
1 TTTATAT
1285075 ATTTATTAT
1 -TTTA-TAT
1285084 TTTATAT
1 TTTATAT
1285091 TTTA
1 TTTA
1285095 AAATAATTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
6 7 0.11
7 19 0.29
8 33 0.50
9 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTATAT
Found at i:1285104 original size:10 final size:10
Alignment explanation
Indices: 1285091--1285138 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
1285081 TATTTTATAT
1285091 TTTAAAATAA
1 TTTAAAATAA
*
1285101 TTTAATATAA
1 TTTAAAATAA
1285111 --T-AAA-AA
1 TTTAAAATAA
1285117 TTATAAAATAA
1 TT-TAAAATAA
1285128 TTTAAAATAA
1 TTTAAAATAA
1285138 T
1 T
1285139 AAATAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
6 2 0.06
7 2 0.06
8 1 0.03
9 1 0.03
10 21 0.68
11 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTTAAAATAA
Found at i:1285104 original size:53 final size:58
Alignment explanation
Indices: 1284989--1285109 Score: 155
Period size: 53 Copynumber: 2.2 Consensus size: 58
1284979 TTTATTTCAT
*
1284989 TTTAATTACATTTAAATATTTATTATTTATATATATTATTAATTTATAATTTTAAAATA
1 TTTAA-TATATTTAAATATTTATTATTTATATATATTATTAATTTATAATTTTAAAATA
* *
1285048 TTT-ATATATTTATAT-TTTATT-TTTAT-TAT-TTATTATTTTAT-ATTTTAAAATAA
1 TTTAATATATTTAAATATTTATTATTTATATATATTATTAATTTATAATTTTAAAAT-A
1285101 TTTAATATA
1 TTTAATATA
1285110 ATAAAAATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
52 10 0.18
53 15 0.26
54 8 0.14
55 5 0.09
56 6 0.11
57 9 0.16
58 1 0.02
59 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (58 bp):
TTTAATATATTTAAATATTTATTATTTATATATATTATTAATTTATAATTTTAAAATA
Found at i:1285153 original size:21 final size:21
Alignment explanation
Indices: 1285111--1285178 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1285101 TTTAATATAA
* *
1285111 TAAAAAT-TATAAAATAAT-T
1 TAAAAATATAAAAAATTATCT
1285130 T-AAAATAATAAATAAA-TATCT
1 TAAAAAT-ATAAA-AAATTATCT
*
1285151 TAAAAATATAAAAAATTATTT
1 TAAAAATATAAAAAATTATCT
1285172 TAAAAAT
1 TAAAAAT
1285179 TTTATAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 5 0.12
19 1 0.03
20 8 0.20
21 21 0.52
22 5 0.12
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAATATAAAAAATTATCT
Found at i:1285349 original size:2 final size:2
Alignment explanation
Indices: 1285342--1285367 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1285332 TTATTTGTCT
1285342 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1285368 ATTCTCGATT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1285871 original size:15 final size:15
Alignment explanation
Indices: 1285851--1285885 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1285841 GGAGATGAGA
1285851 TTATTTTATTTCTTT
1 TTATTTTATTTCTTT
*
1285866 TTATTTTATTTGTTT
1 TTATTTTATTTCTTT
1285881 TTATT
1 TTATT
1285886 GAAATAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (15 bp):
TTATTTTATTTCTTT
Found at i:1285967 original size:20 final size:20
Alignment explanation
Indices: 1285943--1286031 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 20
1285933 TTATTAATTA
1285943 ATATTAAAAAATATTATAAT
1 ATATTAAAAAATATTATAAT
* * *
1285963 TTATTTATAAATATAATTTTAAT
1 ATA-TTA-AAAAAT-ATTATAAT
*
1285986 ATA-T--ATAATATTAT-AT
1 ATATTAAAAAATATTATAAT
*
1286002 ATACT-AAAAATATTATATAT
1 ATATTAAAAAATATTATA-AT
1286022 ATATTAAAAA
1 ATATTAAAAA
1286032 TATAAAATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
16 5 0.10
17 5 0.10
18 12 0.23
20 8 0.15
21 8 0.15
22 5 0.10
23 9 0.17
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTAAAAAATATTATAAT
Found at i:1285993 original size:15 final size:14
Alignment explanation
Indices: 1285967--1286024 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 14
1285957 TATAATTTAT
* *
1285967 TTATAAATATAATT
1 TTATATATATAATA
1285981 TTAATATATATAATA
1 TT-ATATATATAATA
1285996 TTATATATACTAAAAATA
1 TTATATATA-T---AATA
1286014 TTATATATATA
1 TTATATATATA
1286025 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 10 0.27
15 13 0.35
17 1 0.03
18 13 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATATATATAATA
Found at i:1286032 original size:20 final size:20
Alignment explanation
Indices: 1285997--1286034 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1285987 TATATAATAT
1285997 TATATATACTAAAAATATTA
1 TATATATACTAAAAATATTA
*
1286017 TATATATATTAAAAATAT
1 TATATATACTAAAAATAT
1286035 AAAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATATACTAAAAATATTA
Found at i:1286041 original size:20 final size:20
Alignment explanation
Indices: 1285998--1286041 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1285988 ATATAATATT
* *
1285998 ATATATACTAAAAATATTAT
1 ATATATACTAAAAATATAAA
*
1286018 ATATATATTAAAAATATAAA
1 ATATATACTAAAAATATAAA
1286038 ATAT
1 ATAT
1286042 TTTTACGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATATACTAAAAATATAAA
Found at i:1287199 original size:2 final size:2
Alignment explanation
Indices: 1287192--1287230 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1287182 CCAAATCTTC
1287192 AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T 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 AT A
1287231 GTGTATCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1287926 original size:22 final size:21
Alignment explanation
Indices: 1287894--1287935 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1287884 ATTTTGTTTA
1287894 AAAATTATTTAATTATTATTTT
1 AAAATTATTTAATTA-TATTTT
* *
1287916 AAAATTTTTTATTTATATTT
1 AAAATTATTTAATTATATTT
1287936 AATATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AAAATTATTTAATTATATTTT
Found at i:1294651 original size:2 final size:2
Alignment explanation
Indices: 1294644--1294669 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1294634 TTTATTTTTA
1294644 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
1294670 TCTAACTTCA
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:1295790 original size:20 final size:21
Alignment explanation
Indices: 1295749--1295792 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1295739 TTTTTTAAAT
*
1295749 AAATTAATTAATAAAAATTAA
1 AAATAAATTAATAAAAATTAA
*
1295770 AAATAAATTAA-AAATATTAA
1 AAATAAATTAATAAAAATTAA
1295790 AAA
1 AAA
1295793 ATTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATAAATTAATAAAAATTAA
Found at i:1295793 original size:21 final size:22
Alignment explanation
Indices: 1295743--1295812 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 22
1295733 ATAATATTTT
*
1295743 TTAAATAAATTAATTAATAAAAA
1 TTAAA-AAATAAATTAATAAAAA
*
1295766 TT-AAAAATAAATTAA-AAATA
1 TTAAAAAATAAATTAATAAAAA
1295786 TTAAAAAATTAATATTTAATTAAAAA
1 TTAAAAAA-TAA-A-TTAA-TAAAAA
1295812 T
1 T
1295813 CGAGTGAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.16
21 15 0.39
22 5 0.13
23 3 0.08
24 4 0.11
26 5 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAAAAATAAATTAATAAAAA
Found at i:1297259 original size:3 final size:3
Alignment explanation
Indices: 1297251--1297278 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1297241 TGAAACTTTA
1297251 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1297279 CGTATGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1298262 original size:22 final size:21
Alignment explanation
Indices: 1298225--1298266 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1298215 AATATTAATA
**
1298225 TAAAATAATATTCTAATATTTT
1 TAAAATAATAAACTAA-ATTTT
1298247 TAAAATAATAAACTAAATTT
1 TAAAATAATAAACTAAATTT
1298267 ATTGATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAATAATAAACTAAATTTT
Found at i:1300377 original size:9 final size:9
Alignment explanation
Indices: 1300359--1300442 Score: 57
Period size: 9 Copynumber: 9.1 Consensus size: 9
1300349 TAGATCACGA
1300359 AAAT-TATT
1 AAATATATT
1300367 AAATATATT
1 AAATATATT
1300376 AAA-ATTATT
1 AAATA-TATT
*
1300385 AAATATTAAT
1 AAATA-TATT
1300395 ATAATATATT
1 A-AATATATT
* *
1300405 AATTA-AAT
1 AAATATATT
1300413 AAATCATATT
1 AAAT-ATATT
* *
1300423 AATTTTATTT
1 AAATATA-TT
1300433 AAATATATT
1 AAATATATT
1300442 A
1 A
1300443 TCTTATGTTA
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
8 10 0.17
9 23 0.39
10 22 0.37
11 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (9 bp):
AAATATATT
Found at i:1300581 original size:12 final size:12
Alignment explanation
Indices: 1300564--1300588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1300554 AGTTTCATAT
1300564 ATCTTACCAGAA
1 ATCTTACCAGAA
1300576 ATCTTACCAGAA
1 ATCTTACCAGAA
1300588 A
1 A
1300589 AACCGACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
ATCTTACCAGAA
Found at i:1303330 original size:17 final size:17
Alignment explanation
Indices: 1303305--1303343 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1303295 ACGCATGAAG
*
1303305 AATAAAAATATAAATTT
1 AATATAAATATAAATTT
*
1303322 AATATAAATATATATTT
1 AATATAAATATAAATTT
*
1303339 TATAT
1 AATAT
1303344 TTATATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATAAATATAAATTT
Found at i:1307700 original size:14 final size:14
Alignment explanation
Indices: 1307681--1307709 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1307671 CTATCTTAAA
1307681 TACTTATTTAATAT
1 TACTTATTTAATAT
1307695 TACTTATTTAATAT
1 TACTTATTTAATAT
1307709 T
1 T
1307710 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TACTTATTTAATAT
Found at i:1308135 original size:23 final size:22
Alignment explanation
Indices: 1308109--1308163 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
1308099 TTTAAATTAT
*
1308109 ATTTAATAATAAATATTATATAA
1 ATTTAATAATAAA-AATATATAA
*
1308132 ATTTAATTATAAAAATATATAA
1 ATTTAATAATAAAAATATATAA
1308154 ATTTATATAA
1 ATTTA-ATAA
1308164 AATTTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTAATAATAAAAATATATAA
Found at i:1308140 original size:33 final size:34
Alignment explanation
Indices: 1308103--1308177 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 34
1308093 AATCTGTTTA
1308103 AATTATATTTAATA-ATAAATATTATAT-AAATTT
1 AATTATATTTAATATATAAAT-TTATATAAAATTT
**
1308136 AATTATA-AAAATATATAAATTTATATAAAATTT
1 AATTATATTTAATATATAAATTTATATAAAATTT
*
1308169 -ATTTTATTT
1 AATTATATTT
1308178 TATTAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
32 15 0.44
33 19 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
AATTATATTTAATATATAAATTTATATAAAATTT
Found at i:1308153 original size:22 final size:22
Alignment explanation
Indices: 1308109--1308165 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1308099 TTTAAATTAT
* *
1308109 ATTTAATAATAAATATTATATAA
1 ATTTAATTATAAA-AATATATAA
1308132 ATTTAATTATAAAAATATATAA
1 ATTTAATTATAAAAATATATAA
1308154 ATTT-A-TATAAAA
1 ATTTAATTATAAAA
1308166 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 7 0.22
21 1 0.03
22 12 0.38
23 12 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTAATTATAAAAATATATAA
Found at i:1309389 original size:24 final size:22
Alignment explanation
Indices: 1309349--1309394 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
1309339 TTAAAATATA
1309349 TTATATTTATTTAATTTATTTT
1 TTATATTTATTTAATTTATTTT
*
1309371 TTATATTTATATTTTATTTATTTT
1 TTATA-TT-TATTTAATTTATTTT
1309395 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 2 0.10
24 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATATTTATTTAATTTATTTT
Found at i:1309389 original size:33 final size:31
Alignment explanation
Indices: 1309328--1309404 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 31
1309318 TAATATAAAA
1309328 TTAATTTATTTTTAAAATATATTATATTTAT
1 TTAATTTATTTTTAAAATATATTATATTTAT
*
1309359 TTAATTTATTTTT--TATAT-TTATATTTTAT
1 TTAATTTATTTTTAAAATATATTATA-TTTAT
* *
1309388 TTATTTTAAATTTTAAA
1 TTAATTT-ATTTTTAAA
1309405 TAAATTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 5 0.13
29 15 0.39
30 5 0.13
31 13 0.34
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TTAATTTATTTTTAAAATATATTATATTTAT
Found at i:1312307 original size:2 final size:2
Alignment explanation
Indices: 1312300--1312334 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1312290 ATTCAACTCA
1312300 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 A
1312335 AAAGGTGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1318321 original size:3 final size:3
Alignment explanation
Indices: 1318315--1318353 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
1318305 AAACAGAACA
1318315 AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA-T AAT A
1318354 TCATTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1318347 original size:7 final size:7
Alignment explanation
Indices: 1318317--1318470 Score: 129
Period size: 7 Copynumber: 23.9 Consensus size: 7
1318307 ACAGAACAAA
1318317 TAATAA-
1 TAATAAT
1318323 TAATAA-
1 TAATAAT
1318329 TAATAA-
1 TAATAAT
1318335 TAATAAT
1 TAATAAT
1318342 TAATAAT
1 TAATAAT
1318349 TAAT-AT
1 TAATAAT
* *
1318355 CATTAAT
1 TAATAAT
1318362 TAAT-AT
1 TAATAAT
1318368 TAATAAT
1 TAATAAT
*
1318375 TATTAAT
1 TAATAAT
*
1318382 TATTAAT
1 TAATAAT
1318389 TAATAA-
1 TAATAAT
1318395 -AA-AGA-
1 TAATA-AT
1318400 -AATAAT
1 TAATAAT
1318406 TAATAAT
1 TAATAAT
*
1318413 TAGT-AT
1 TAATAAT
* *
1318419 CATTAAT
1 TAATAAT
1318426 TAATAAT
1 TAATAAT
1318433 TAATAA-
1 TAATAAT
1318439 T-AT-AT
1 TAATAAT
1318444 TAATAAT
1 TAATAAT
1318451 TAATAAT
1 TAATAAT
*
1318458 TATTAAT
1 TAATAAT
1318465 TAATAA
1 TAATAA
1318471 AAAAAGAAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 21
0.78 0.08 0.13
Matches are distributed among these distances:
4 2 0.02
5 9 0.07
6 36 0.29
7 77 0.62
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (7 bp):
TAATAAT
Found at i:1318352 original size:4 final size:4
Alignment explanation
Indices: 1318338--1318468 Score: 72
Period size: 4 Copynumber: 35.0 Consensus size: 4
1318328 ATAATAATAA
*
1318338 TAAT TAA- TAAT TAAT ATCAT TAAT TAA- T-AT TAA- TAAT T-AT TAAT
1 TAAT TAAT TAAT TAAT -TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
* * * * * *
1318382 T-AT TAAT TAAT AAAAA GAAA TAAT TAA- TAAT TAGT ATCAT TAAT TAA-
1 TAAT TAAT TAAT -TAAT TAAT TAAT TAAT TAAT TAAT -TAAT TAAT TAAT
1318429 TAAT TAA- TAA- TATAT TAA- TAAT TAA- TAAT T-AT TAAT TAAT
1 TAAT TAAT TAAT TA-AT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1318469 AAAAAAAGAA
Statistics
Matches: 100, Mismatches: 11, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
2 1 0.01
3 34 0.34
4 56 0.56
5 9 0.09
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (4 bp):
TAAT
Found at i:1331406 original size:5 final size:5
Alignment explanation
Indices: 1331396--1331475 Score: 55
Period size: 5 Copynumber: 16.8 Consensus size: 5
1331386 ATTAAAAAAT
* * *
1331396 TATAA TATAA TATAA TATGA TA-AA TATAA -ATAT TTTAA -AT-A TAATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T-ATAA
* *
1331443 TATAA TAAAA TAT-T TA-AA TATAA TATGAA TATA
1 TATAA TATAA TATAA TATAA TATAA TAT-AA TATA
1331476 TTAATTAATA
Statistics
Matches: 57, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
3 1 0.02
4 11 0.19
5 38 0.67
6 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:1331453 original size:18 final size:18
Alignment explanation
Indices: 1331432--1331486 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1331422 TAAATATTTT
*
1331432 AAATATAATAATATAATA
1 AAATATATTAATATAATA
1331450 AAATAT-TTAAATATAATA
1 AAATATATT-AATATAATA
*
1331468 TGAATATATTAAT-TAATA
1 -AAATATATTAATATAATA
1331486 A
1 A
1331487 TTAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 1 0.03
18 20 0.65
19 8 0.26
20 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATATATTAATATAATA
Found at i:1331458 original size:26 final size:30
Alignment explanation
Indices: 1331404--1331467 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 30
1331394 ATTATAATAT
1331404 AATATAAT-ATGATAAATATAAATATTTTA
1 AATATAATAATGATAAATATAAATATTTTA
1331433 AATATAATAAT-AT-AATA-AAATA-TTTA
1 AATATAATAATGATAAATATAAATATTTTA
1331459 AATATAATA
1 AATATAATA
1331468 TGAATATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 13 0.38
27 5 0.15
28 4 0.12
29 10 0.29
30 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
AATATAATAATGATAAATATAAATATTTTA
Found at i:1331474 original size:29 final size:31
Alignment explanation
Indices: 1331404--1331475 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 31
1331394 ATTATAATAT
1331404 AATATAATATG-ATA-AATATAAATATTTTA
1 AATATAATATGAATATAATATAAATATTTTA
1331433 AATAT-A-AT-AATATAATA-AAATA-TTTA
1 AATATAATATGAATATAATATAAATATTTTA
1331459 AATATAATATGAATATA
1 AATATAATATGAATATA
1331476 TTAATTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
26 9 0.24
27 11 0.29
28 7 0.18
29 11 0.29
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (31 bp):
AATATAATATGAATATAATATAAATATTTTA
Found at i:1331883 original size:19 final size:19
Alignment explanation
Indices: 1331859--1331901 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
1331849 TAAATATAGA
1331859 AATATTTT-ATATAATATAT
1 AATATTTTAATATAAT-TAT
1331878 AATATTTTAAATATAATTAT
1 AATATTTT-AATATAATTAT
1331898 AATA
1 AATA
1331902 AATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
20 7 0.32
21 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATTTTAATATAATTAT
Found at i:1331927 original size:18 final size:17
Alignment explanation
Indices: 1331906--1331943 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1331896 ATAATAAATA
*
1331906 AAAATATATAAATATAAT
1 AAAATACATAAAT-TAAT
1331924 AAAATACATAAATTAAT
1 AAAATACATAAATTAAT
1331941 AAA
1 AAA
1331944 TTATTTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATACATAAATTAAT
Found at i:1334275 original size:23 final size:22
Alignment explanation
Indices: 1334247--1334302 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
1334237 TTAAGTACAA
1334247 ATAATTTATTT-TTATAAAATAAT
1 ATAATTTATTTATTA-AAAAT-AT
*
1334270 ATAATTTGATTTATTAATAATAT
1 ATAATTT-ATTTATTAAAAATAT
1334293 ATAAATTTAT
1 AT-AATTTAT
1334303 AATATCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 13 0.45
24 13 0.45
25 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATAATTTATTTATTAAAAATAT
Found at i:1334932 original size:2 final size:2
Alignment explanation
Indices: 1334918--1334965 Score: 64
Period size: 2 Copynumber: 24.0 Consensus size: 2
1334908 TAAATAAATT
1334918 TA TA TA TGA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA -A
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
1334960 TA TA TA
1 TA TA TA
1334966 CACATGCACA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1336686 original size:2 final size:2
Alignment explanation
Indices: 1336679--1336710 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1336669 TATAATTCCC
1336679 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
1336711 TCTTCTTATT
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
Done.