Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 11 of 21
Found at i:1144502 original size:21 final size:20
Alignment explanation
Indices: 1144473--1144532 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
1144463 ATAAATAAAA
1144473 TATAAAATATAATGATTATAT
1 TATAAAATATAA-GATTATAT
* *
1144494 TATATAATATAAGTTTATA-
1 TATAAAATATAAGATTATAT
*
1144513 TA-AAAATTATAAAATTATAT
1 TATAAAA-TATAAGATTATAT
1144533 AAAAACTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.09
19 12 0.38
20 6 0.19
21 11 0.34
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
TATAAAATATAAGATTATAT
Found at i:1145598 original size:20 final size:20
Alignment explanation
Indices: 1145561--1145597 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
1145551 ATATTAATAT
1145561 ATTTTTATCTTTTATTTTAA
1 ATTTTTATCTTTTATTTTAA
1145581 ATTTTTAT-TTTTATTTT
1 ATTTTTATCTTTTATTTT
1145598 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTTATCTTTTATTTTAA
Found at i:1145599 original size:7 final size:6
Alignment explanation
Indices: 1145560--1145598 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
1145550 AATATTAATA
*
1145560 TATTTT TATCTTT TATTTT AAATTTT TATTTT TATTTT T
1 TATTTT TAT-TTT TATTTT -TATTTT TATTTT TATTTT T
1145599 TTAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:1145599 original size:13 final size:13
Alignment explanation
Indices: 1145560--1145599 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1145550 AATATTAATA
*
1145560 TATTTTTATCTTT
1 TATTTTTATTTTT
* *
1145573 TATTTTAAATTTT
1 TATTTTTATTTTT
1145586 TATTTTTATTTTT
1 TATTTTTATTTTT
1145599 T
1 T
1145600 TAAATATATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:1146037 original size:29 final size:28
Alignment explanation
Indices: 1145969--1146069 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 28
1145959 AAAATAAATA
*
1145969 TTATTTTTAAAATTTTAAAAA-TATAATT
1 TTATTTTTAAAATTTTAAAAATTAT-TTT
* **
1145997 TTA-ATAAAAAATTATTAAAAATTATTTT
1 TTATTTTTAAAATT-TTAAAAATTATTTT
* *
1146025 TTATTTTTAAAATTTATAAATATAATTTT
1 TTATTTTTAAAATTT-TAAAAATTATTTT
* *
1146054 ATATTTTTTAAATTTT
1 TTATTTTTAAAATTTT
1146070 GTAAGGGGTA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
27 7 0.12
28 17 0.29
29 34 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTATTTTTAAAATTTTAAAAATTATTTT
Found at i:1146128 original size:2 final size:2
Alignment explanation
Indices: 1146118--1146148 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1146108 AAAAGGTCAC
1146118 AT AT A- 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
1146149 GTATGTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1147255 original size:11 final size:12
Alignment explanation
Indices: 1147236--1147277 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1147226 ATAAAATGTT
1147236 ATATAAAAAATA
1 ATATAAAAAATA
*
1147248 AT-TAAAAAATT
1 ATATAAAAAATA
*
1147259 ATATAAAATATAA
1 ATATAAAAAAT-A
1147272 ATATAA
1 ATATAA
1147278 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 10 0.40
12 9 0.36
13 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATATAAAAAATA
Found at i:1147272 original size:30 final size:31
Alignment explanation
Indices: 1147235--1147300 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
1147225 AATAAAATGT
* *
1147235 TATATAAAAAATAATTAAAAAATTATATAAA
1 TATATAAAAAATAATTAAAAAATAATAGAAA
* *
1147266 -ATAT-AAATATAATTTAAAAATAATAGAAA
1 TATATAAAAAATAATTAAAAAATAATAGAAA
1147295 TATATA
1 TATATA
1147301 TATATCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (31 bp):
TATATAAAAAATAATTAAAAAATAATAGAAA
Found at i:1149077 original size:29 final size:27
Alignment explanation
Indices: 1149016--1149078 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 27
1149006 ATTTTGTCTA
*
1149016 ATAATATATTATTATTTTACTTATTTAT
1 ATAA-ATATTATTATTTTAATTATTTAT
1149044 -TAAATATTATT-TTTTAATTATAAATTAT
1 ATAAATATTATTATTTTAATTAT---TTAT
1149072 ATAAATA
1 ATAAATA
1149079 AGTTGAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 9 0.30
26 8 0.27
27 3 0.10
28 4 0.13
29 6 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
ATAAATATTATTATTTTAATTATTTAT
Found at i:1149906 original size:23 final size:23
Alignment explanation
Indices: 1149865--1149918 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1149855 TTTCTTACAC
* *
1149865 TAATAATATTTATTTATA-TATTAT
1 TAATAA-ATTTAATAATATTATT-T
1149889 TAATAAATTTAATAATATTATTT
1 TAATAAATTTAATAATATTATTT
1149912 TAATAAA
1 TAATAAA
1149919 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATAAATTTAATAATATTATTT
Found at i:1150833 original size:15 final size:15
Alignment explanation
Indices: 1150810--1150839 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1150800 CCATTATTAT
1150810 TATTATTAAAAAATA
1 TATTATTAAAAAATA
*
1150825 TATTTTTAAAAAATA
1 TATTATTAAAAAATA
1150840 AATAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTATTAAAAAATA
Found at i:1151050 original size:15 final size:14
Alignment explanation
Indices: 1151012--1151050 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1151002 ATTAATTATT
*
1151012 ATATTTAATATAAA
1 ATATTTTATATAAA
1151026 ATATTATTATATAAA
1 ATATT-TTATATAAA
1151041 ATAATTTTAT
1 AT-ATTTTAT
1151051 TAATTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 14 0.64
16 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATTTTATATAAA
Found at i:1152214 original size:11 final size:11
Alignment explanation
Indices: 1152198--1152229 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1152188 TCGTACAATT
1152198 ATATAATATAA
1 ATATAATATAA
1152209 ATATAATATAA
1 ATATAATATAA
1152220 A-ATAAT-TAA
1 ATATAATATAA
1152229 A
1 A
1152230 AAAACATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 4 0.19
10 5 0.24
11 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1152927 original size:21 final size:21
Alignment explanation
Indices: 1152902--1152941 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1152892 TATAATTTAT
1152902 TATAATAGTATCTATTATATC
1 TATAATAGTATCTATTATATC
* *
1152923 TATAATATTATTTATTATA
1 TATAATAGTATCTATTATA
1152942 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TATAATAGTATCTATTATATC
Found at i:1153254 original size:18 final size:18
Alignment explanation
Indices: 1153227--1153261 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1153217 AATTTAAAAA
*
1153227 ATTTACAAATTTTTTTAT
1 ATTTACAAATATTTTTAT
*
1153245 ATTTATAAATATTTTTA
1 ATTTACAAATATTTTTA
1153262 ATATAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTACAAATATTTTTAT
Found at i:1153265 original size:19 final size:18
Alignment explanation
Indices: 1153227--1153265 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1153217 AATTTAAAAA
*
1153227 ATTTACAAATTTTTTTAT
1 ATTTACAAATTTTTTAAT
*
1153245 ATTTATAAATATTTTTAAT
1 ATTTACAAAT-TTTTTAAT
1153264 AT
1 AT
1153266 AATAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTACAAATTTTTTAAT
Found at i:1154582 original size:18 final size:19
Alignment explanation
Indices: 1154559--1154602 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1154549 TTTTTTATAA
*
1154559 TAATATTTTAATAAT-ATT
1 TAATATTTTAAAAATAATT
1154577 TAATATTTTAAAAATAATT
1 TAATATTTTAAAAATAATT
*
1154596 AAATATT
1 TAATATT
1154603 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATATTTTAAAAATAATT
Found at i:1155052 original size:14 final size:15
Alignment explanation
Indices: 1155040--1155099 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
1155030 ATTAAAATTC
1155040 AAAAATAAAAATTTA
1 AAAAATAAAAATTTA
*
1155055 AAAAATAAATAA-ATA
1 AAAAATAAA-AATTTA
* * *
1155070 AAAGATAAACATTAGA
1 AAAAATAAAAATT-TA
1155086 AAAAGATAAAAATT
1 AAAA-ATAAAAATT
1155100 GCACAGTGTC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
14 1 0.03
15 19 0.56
16 6 0.18
17 8 0.24
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (15 bp):
AAAAATAAAAATTTA
Found at i:1160161 original size:17 final size:16
Alignment explanation
Indices: 1160117--1160163 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
1160107 TACGGCAAGA
*
1160117 AAAAAAATTAACATAAT
1 AAAAAAA-TAATATAAT
1160134 AAAAAATATAATATAAT
1 AAAAAA-ATAATATAAT
1160151 ATAAAAAATAATA
1 A-AAAAAATAATA
1160164 CAATTTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAAATAATATAAT
Found at i:1160172 original size:17 final size:18
Alignment explanation
Indices: 1160131--1160172 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1160121 AAATTAACAT
*
1160131 AATA-AAAAATATAATAT
1 AATATAAAAATATAATAC
1160148 AATATAAAAA-ATAATAC
1 AATATAAAAATATAATAC
*
1160165 AATTTAAA
1 AATATAAA
1160173 CACATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATAAAAATATAATAC
Found at i:1161701 original size:6 final size:6
Alignment explanation
Indices: 1161692--1161746 Score: 60
Period size: 6 Copynumber: 9.0 Consensus size: 6
1161682 AAGTGATAAA
*
1161692 AAATTT AAATTT AAA-TT AAATTT AAAAGTT AAGATTT AAATATT -AATTT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AA-ATTT AAAT-TT AAATTT
1161741 AAATTT
1 AAATTT
1161747 GAACAACTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 7 0.17
6 23 0.55
7 12 0.29
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:1161821 original size:6 final size:6
Alignment explanation
Indices: 1161812--1161861 Score: 82
Period size: 6 Copynumber: 8.0 Consensus size: 6
1161802 CATGCTCAAT
1161812 TTTAAA TTTAATTA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1161862 ATTTTTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 36 0.86
8 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:1162984 original size:2 final size:2
Alignment explanation
Indices: 1162977--1163012 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1162967 TAAGTAATGA
1162977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1163013 TGCATGCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1180741 original size:24 final size:22
Alignment explanation
Indices: 1180714--1180766 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
1180704 TCACGAAATA
1180714 TAAAAAATATAAATATT-TTAATTT
1 TAAAAAA-ATAAATATTATT--TTT
*
1180738 TAAATTAAATAAATATTATTTTT
1 TAAA-AAAATAAATATTATTTTT
1180761 TAAAAA
1 TAAAAA
1180767 TAATTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.04
23 7 0.28
24 13 0.52
25 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAAAAATAAATATTATTTTT
Found at i:1181001 original size:29 final size:30
Alignment explanation
Indices: 1180954--1181023 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
1180944 TGATATTATT
* *
1180954 ATTT-TATTTAAATAAATTTTTAAATTTTA
1 ATTTATATTTAAATAAATTTTTAAATATAA
*
1180983 ATTTATATTTAAAT-AATTTTTTAATATAA
1 ATTTATATTTAAATAAATTTTTAAATATAA
*
1181012 ATTAATATTTAA
1 ATTTATATTTAA
1181024 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTATATTTAAATAAATTTTTAAATATAA
Found at i:1181107 original size:27 final size:25
Alignment explanation
Indices: 1181046--1181107 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
1181036 AATTAATTAA
*
1181046 TTAAAAATAAAAAATAAAGATTTAT
1 TTAAAAATAAAAAACAAAGATTTAT
* *
1181071 TTATATAATAAAAATACAAAGATTATTT
1 TTA-AAAATAAAAA-ACAAAGATT-TAT
1181099 TTAAAAATA
1 TTAAAAATA
1181108 TAATATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 3 0.10
26 9 0.30
27 13 0.43
28 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (25 bp):
TTAAAAATAAAAAACAAAGATTTAT
Found at i:1181194 original size:23 final size:23
Alignment explanation
Indices: 1181168--1181251 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 23
1181158 ATATATAATT
1181168 ATATTATATAAAAATTAATTAAA
1 ATATTATATAAAAATTAATTAAA
* * *
1181191 ATATAAAATAAAATATT-ATAAAA
1 ATATTATATAAAA-ATTAATTAAA
* *
1181214 ATATAAATATAAAAAAAATTAAGTAAA
1 ATAT---TAT-ATAAAAATTAATTAAA
1181241 AT-TTATATAAA
1 ATATTATATAAA
1181252 TATATTATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
22 4 0.09
23 23 0.50
24 3 0.07
26 5 0.11
27 11 0.24
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (23 bp):
ATATTATATAAAAATTAATTAAA
Found at i:1181216 original size:11 final size:12
Alignment explanation
Indices: 1181168--1181259 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 12
1181158 ATATATAATT
1181168 ATATTATATAAA
1 ATATTATATAAA
1181180 A-ATTA-ATTAAA
1 ATATTATA-TAAA
* *
1181191 ATATAAAATAAA
1 ATATTATATAAA
1181203 ATATTATA-AAA
1 ATATTATATAAA
*
1181214 ATATAAATATAAAAA
1 ATAT---TATATAAA
*
1181229 AAATTA-AGTAAA
1 ATATTATA-TAAA
1181241 AT-TTATATAAA
1 ATATTATATAAA
1181252 TATATTAT
1 -ATATTAT
1181260 TTTAAAAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
10 1 0.02
11 24 0.38
12 23 0.37
13 5 0.08
14 4 0.06
15 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (12 bp):
ATATTATATAAA
Found at i:1181247 original size:29 final size:29
Alignment explanation
Indices: 1181189--1181255 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 29
1181179 AAATTAATTA
*
1181189 AAATATAAAATAAAATATTATAAAAATAT
1 AAATATAAAATAAAATATAATAAAAATAT
1181218 AAATATAAAA-AAAAT-TAAGTAAAATTTATAT
1 AAATATAAAATAAAATATAA-TAAAA---ATAT
1181249 AAATATA
1 AAATATA
1181256 TTATTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.06
28 10 0.30
29 10 0.30
31 11 0.33
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (29 bp):
AAATATAAAATAAAATATAATAAAAATAT
Found at i:1181642 original size:17 final size:17
Alignment explanation
Indices: 1181592--1181643 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1181582 AATTTGATTT
*
1181592 TTATATTTTTTAATTTAA
1 TTATA-TTTTTAATATAA
* * * *
1181610 GTAAATATTAAATATAA
1 TTATATTTTTAATATAA
1181627 TTATATTTTTAATATAA
1 TTATATTTTTAATATAA
1181644 AAATTATATT
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TTATATTTTTAATATAA
Found at i:1182522 original size:40 final size:38
Alignment explanation
Indices: 1182478--1182592 Score: 99
Period size: 40 Copynumber: 2.9 Consensus size: 38
1182468 ATTAATAATA
1182478 ATTTTTTTAATTTTATAAATAATTTAAAATTTTATTATGT
1 ATTTTTTTAATTTTATAAATAATTTAAAATTTTA-TAT-T
* * *
1182518 ATTTTATATT-ATTTTATAATTATATTTAAAAATATATATT
1 ATTTT-T-TTAATTTTATAAATA-ATTTAAAATTTTATATT
* *
1182558 ATTTTATTAATATTATTTATAA-AATTTAAAATTTT
1 ATTTTTTTAAT-TT-TATA-AATAATTTAAAATTTT
1182593 CGTATATGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 23 0.38
41 19 0.32
42 14 0.23
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (38 bp):
ATTTTTTTAATTTTATAAATAATTTAAAATTTTATATT
Found at i:1182558 original size:30 final size:32
Alignment explanation
Indices: 1182522--1182582 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
1182512 TTATGTATTT
1182522 TATATTATTTTA-TAAT-TATATTTA-AAAATA
1 TATATTATTTTATTAATAT-TATTTATAAAATA
1182552 TATATTATTTTATTAATATTATTTATAAAAT
1 TATATTATTTTATTAATATTATTTATAAAAT
1182583 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 12 0.43
31 10 0.36
32 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATATTATTTTATTAATATTATTTATAAAATA
Found at i:1188837 original size:22 final size:21
Alignment explanation
Indices: 1188798--1188850 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
1188788 AATAATATGT
* *
1188798 TAATATTTTATTAATATTTAAA
1 TAATTTTTTAATAATA-TTAAA
* *
1188820 TAATTTTTTAATATTATTAAT
1 TAATTTTTTAATAATATTAAA
*
1188841 TATTTTTTTA
1 TAATTTTTTA
1188851 TTATCATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTTTTTAATAATATTAAA
Found at i:1188839 original size:21 final size:19
Alignment explanation
Indices: 1188790--1188848 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1188780 TAATATCAAA
1188790 TAATATGTT-AAT-ATTTTAT
1 TAATAT-TTAAATAATTTT-T
1188809 TAATATTTAAATAATTTTT
1 TAATATTTAAATAATTTTT
* *
1188828 TAATATTATTAATTATTTTT
1 TAATATT-TAAATAATTTTT
1188848 T
1 T
1188849 TATTATCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 2 0.06
19 17 0.49
20 16 0.46
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TAATATTTAAATAATTTTT
Found at i:1190802 original size:14 final size:14
Alignment explanation
Indices: 1190783--1190809 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1190773 ATTCAATAAT
1190783 ATATTTATATATTA
1 ATATTTATATATTA
1190797 ATATTTATATATT
1 ATATTTATATATT
1190810 TTTATAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTATATATTA
Found at i:1190809 original size:22 final size:22
Alignment explanation
Indices: 1190781--1190825 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1190771 TTATTCAATA
1190781 ATATATTTATAT-ATTAATATTT
1 ATATATTTATATAATTAA-ATTT
*
1190803 ATATATTTTTATAATTAAATTT
1 ATATATTTATATAATTAAATTT
1190825 A
1 A
1190826 ATTAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATATTTATATAATTAAATTT
Found at i:1191126 original size:16 final size:15
Alignment explanation
Indices: 1191090--1191118 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1191080 TAAAAATAAA
1191090 AATATTTTTTATATT
1 AATATTTTTTATATT
1191105 AATA-TTTTTATATT
1 AATATTTTTTATATT
1191119 TTATTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATATTTTTTATATT
Found at i:1191137 original size:50 final size:51
Alignment explanation
Indices: 1191051--1191146 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 51
1191041 TTAGTTAAAT
1191051 TTAATTTATTTATATTTATTATTTATAATTAAAAATAAAAATATTTTTTATA
1 TTAATTTATTTATATTTATTATTTATAATTAAAAATAAAAA-ATTTTTTATA
*
1191103 TTAATATT-TTTATATTTTATTA-TTA-AATT-TAAATAAAAAATTTT
1 TTAAT-TTATTTATA-TTTATTATTTATAATTAAAAATAAAAAATTTT
1191147 AATTATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
49 5 0.12
50 9 0.22
51 4 0.10
52 14 0.34
53 9 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (51 bp):
TTAATTTATTTATATTTATTATTTATAATTAAAAATAAAAAATTTTTTATA
Found at i:1191159 original size:50 final size:52
Alignment explanation
Indices: 1191059--1191160 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 52
1191049 ATTTAATTTA
*
1191059 TTTATATTTATTATTTATAATTAAAAATAAAAATATTTTTTATATTAATATT
1 TTTATATTTATTATTTATAATTAAAAATAAAAATATTTTTTATATAAATATT
*
1191111 TTTATATTTTATTA-TTA-AATT-TAAATAAAAA-ATTTTAATTAT-TAAATATT
1 TTTATA-TTTATTATTTATAATTAAAAATAAAAATATTTT--TTATATAAATATT
1191161 AATTTAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
49 5 0.11
50 16 0.36
51 8 0.18
52 9 0.20
53 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (52 bp):
TTTATATTTATTATTTATAATTAAAAATAAAAATATTTTTTATATAAATATT
Found at i:1191447 original size:2 final size:2
Alignment explanation
Indices: 1191440--1191479 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1191430 AGATTGCAAA
* *
1191440 AT AT AT AT AT AT AT AT AT AT -T AT TT AT AT AT AT TT 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
1191480 GTATTAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:1191469 original size:21 final size:21
Alignment explanation
Indices: 1191443--1191484 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1191433 TTGCAAAATA
*
1191443 TATATATATATATATATTATT
1 TATATATATATATATAGTATT
*
1191464 TATATATATTTATATAGTATT
1 TATATATATATATATAGTATT
1191485 AAGATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATATATATATATAGTATT
Found at i:1192570 original size:22 final size:21
Alignment explanation
Indices: 1192545--1192586 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1192535 ATTTTAAAAA
1192545 ATAT-TTTTATAA-TAATATTT
1 ATATATTTTATAATTAA-ATTT
1192565 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1192586 A
1 A
1192587 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 13 0.65
22 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1192667 original size:13 final size:13
Alignment explanation
Indices: 1192649--1192673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192639 TAATTTTTAA
1192649 AAAAATAAAAATT
1 AAAAATAAAAATT
1192662 AAAAATAAAAAT
1 AAAAATAAAAAT
1192674 CCCTACCTAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATAAAAATT
Found at i:1198922 original size:27 final size:26
Alignment explanation
Indices: 1198852--1198929 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
1198842 GATATTTATT
* *
1198852 TATTTA-ATTATTAATATTTATAATTAA
1 TATTTATA-TATTTATAATTATAA-TAA
*
1198879 TATTTATATA-ATA-AATTATAATAA
1 TATTTATATATTTATAATTATAATAA
1198903 TATTTATTATATTTATAATTATAATAA
1 TATTTA-TATATTTATAATTATAATAA
1198930 ATATGATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 9 0.21
25 11 0.26
26 3 0.07
27 19 0.44
28 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TATTTATATATTTATAATTATAATAA
Found at i:1198942 original size:46 final size:46
Alignment explanation
Indices: 1198859--1198955 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 46
1198849 ATTTATTTAA
** *
1198859 TTATTAATATTTATAATTAATATTTATATAATAAATTATAATAATAT
1 TTATTAATATTTATAATTAATATAAATATAATAAATTA-AAAAATAT
* *
1198906 TTATT-ATATTTATAATT-ATAATAAATATGATTAATTAAAAAATAT
1 TTATTAATATTTATAATTAAT-ATAAATATAATAAATTAAAAAATAT
1198951 TTATT
1 TTATT
1198956 GTAATAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
45 14 0.32
46 25 0.57
47 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (46 bp):
TTATTAATATTTATAATTAATATAAATATAATAAATTAAAAAATAT
Found at i:1199085 original size:28 final size:30
Alignment explanation
Indices: 1199052--1199110 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1199042 TATTTAATAT
* *
1199052 AAATTTAT-TTATTTTTTA-ATATATAAAA
1 AAATTTATATTAATATTTAGATATATAAAA
1199080 AAATTTATATTAATATTTAGATATATAAAA
1 AAATTTATATTAATATTTAGATATATAAAA
1199110 A
1 A
1199111 TATAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 8 0.30
29 8 0.30
30 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
AAATTTATATTAATATTTAGATATATAAAA
Found at i:1199131 original size:24 final size:24
Alignment explanation
Indices: 1199086--1199134 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1199076 AAAAAAATTT
* * *
1199086 ATATTAATATTTAGATATATAAAA
1 ATATAAATATTTAGAAAAATAAAA
*
1199110 ATATAAATATTTATAAAAATAAAA
1 ATATAAATATTTAGAAAAATAAAA
1199134 A
1 A
1199135 ATTAAAGGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATATAAATATTTAGAAAAATAAAA
Found at i:1201264 original size:32 final size:31
Alignment explanation
Indices: 1201211--1201284 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
1201201 TATTTCTATT
* *
1201211 TTAAAACTTAATATTTATAAATTTAAATTAAA
1 TTAAAAATTAATAATTATAAA-TTAAATTAAA
* *
1201243 TTAAAAATTACATAATT-TAAATTGAATTATA
1 TTAAAAATTA-ATAATTATAAATTAAATTAAA
1201274 TTAAATAATTA
1 TTAAA-AATTA
1201285 TTATTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 13 0.36
32 18 0.50
33 5 0.14
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAAATTAATAATTATAAATTAAATTAAA
Found at i:1201824 original size:8 final size:8
Alignment explanation
Indices: 1201811--1201835 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1201801 TATTTTAAAC
1201811 ATAAAAAT
1 ATAAAAAT
1201819 ATAAAAAT
1 ATAAAAAT
1201827 ATAAAAAT
1 ATAAAAAT
1201835 A
1 A
1201836 AAATTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:1201950 original size:216 final size:208
Alignment explanation
Indices: 1201573--1202197 Score: 966
Period size: 216 Copynumber: 3.0 Consensus size: 208
1201563 TAAAGTGTAA
1201573 AAATTTATATAAATTTATAATATTTTAAACATAAAAATATAAAAATAAATTTTTCTCTAAATTAA
1 AAATTTATATAAATTTATAATATTTTAAACATAAAAATATAAAAATAAATTTTTCTCTAAATTAA
1201638 ATCACTATTACATATGTCATGAATTTAAACATGACATGAACACTTAAATTTTTCTTTAAGATGTG
66 ATCACTATTACATATGTCATGAATTTAAACATGACATGAACACTTAAATTTTTCTTTAAGATGTG
* * *
1201703 ATGTATTGAAACTCTACTTGAATACAATATAAAAAAAATAATTAAAACACAATATAAAAAATAAC
131 ATGTATTGAAACTCGACTTAAATACAATATAAAAAAAATAATTAAAACACAACATAAAAAATAAC
1201768 ATAATAAGAATAT
196 ATAATAAGAATAT
1201781 AAATTTATATAAATTTATAATATTTTAAACATAAAAATATAAAAATATAAAAATAAAATTTTCTC
1 AAATTTATATAAATTTATAATATTTTAAACATAAAAATAT-AAAA-AT--AAAT----TTTTCTC
*
1201846 TAAATTAAATCACTATTACATATGTCATGAATTTAAACATGACATGAATACTTAAATTTTTCTTT
58 TAAATTAAATCACTATTACATATGTCATGAATTTAAACATGACATGAACACTTAAATTTTTCTTT
* * *
1201911 AAGATGTGATGTATTGAAACTCGACTTAAATATAATATAAGAAAAATAATTAAAACACAACACAA
123 AAGATGTGATGTATTGAAACTCGACTTAAATACAATATAAAAAAAATAATTAAAACACAACA-TA
1201976 AAAAATAACATAATAAG-----
187 AAAAATAACATAATAAGAATAT
*
1201993 --A---ATATAAATTTATAATATTTTAAACATAAAAATATAAAAATAAATTTTTCTTTAAATTAA
1 AAATTTATATAAATTTATAATATTTTAAACATAAAAATATAAAAATAAATTTTTCTCTAAATTAA
*
1202053 ATCACTATTACATATGTCATGAATTTAAACATGACATGAACACTTAAATTTTTTTTTAAGATGTG
66 ATCACTATTACATATGTCATGAATTTAAACATGACATGAACACTTAAATTTTTCTTTAAGATGTG
* *
1202118 ATGTATTAAAACTCGACTTAAATACAATAT-AAAAAAATAATTAAAACATAACATAAAAAAATAA
131 ATGTATTGAAACTCGACTTAAATACAATATAAAAAAAATAATTAAAACACAACAT-AAAAAAT-A
*
1202182 ACATAATAATAATAT
194 ACATAATAAGAATAT
1202197 A
1 A
1202198 CAAATATATT
Statistics
Matches: 384, Mismatches: 16, Indels: 37
0.88 0.04 0.08
Matches are distributed among these distances:
198 28 0.07
199 115 0.30
203 4 0.01
205 2 0.01
206 4 0.01
207 34 0.09
208 40 0.10
209 4 0.01
210 3 0.01
212 4 0.01
216 128 0.33
217 18 0.05
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.35
Consensus pattern (208 bp):
AAATTTATATAAATTTATAATATTTTAAACATAAAAATATAAAAATAAATTTTTCTCTAAATTAA
ATCACTATTACATATGTCATGAATTTAAACATGACATGAACACTTAAATTTTTCTTTAAGATGTG
ATGTATTGAAACTCGACTTAAATACAATATAAAAAAAATAATTAAAACACAACATAAAAAATAAC
ATAATAAGAATAT
Found at i:1202740 original size:15 final size:16
Alignment explanation
Indices: 1202720--1202749 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1202710 TTAACTTATG
1202720 TTTGAATT-TTTTAAA
1 TTTGAATTATTTTAAA
1202735 TTTGAATTATTTTAA
1 TTTGAATTATTTTAA
1202750 TTTTATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (16 bp):
TTTGAATTATTTTAAA
Found at i:1202809 original size:16 final size:15
Alignment explanation
Indices: 1202790--1202864 Score: 64
Period size: 16 Copynumber: 4.9 Consensus size: 15
1202780 GATTTATACC
1202790 ATTTTAAGTTTGAATT
1 ATTTTAAGTTT-AATT
*
1202806 ATTTTCAA-TTTAAAT
1 ATTTT-AAGTTTAATT
1202821 -TTTTAAGTTTAAGTT
1 ATTTTAAGTTTAA-TT
* *
1202836 AATTTAAATTTAAATT
1 ATTTTAAGTTT-AATT
*
1202852 ATTTTAAATTTAA
1 ATTTTAAGTTTAA
1202865 GTAAATTTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.04
14 9 0.18
15 6 0.12
16 28 0.57
17 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (15 bp):
ATTTTAAGTTTAATT
Found at i:1202827 original size:30 final size:30
Alignment explanation
Indices: 1202791--1202873 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
1202781 ATTTATACCA
* *
1202791 TTTTAAGTTTGAA-TTATTTTCAATTTAAAT
1 TTTTAAGTTT-AAGTTAATTTAAATTTAAAT
1202821 TTTTAAGTTTAAGTTAATTTAAATTTAAATT
1 TTTTAAGTTTAAGTTAATTTAAATTTAAA-T
* *
1202852 ATTTTAAATTTAAGTAAATTTA
1 -TTTTAAGTTTAAGTTAATTTA
1202874 CGCTATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 2 0.04
30 24 0.52
31 1 0.02
32 19 0.41
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTTAAGTTTAAGTTAATTTAAATTTAAAT
Found at i:1202873 original size:16 final size:16
Alignment explanation
Indices: 1202822--1202873 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1202812 AATTTAAATT
*
1202822 TTTAAGTTTAAGTTAA
1 TTTAAATTTAAGTTAA
* *
1202838 TTTAAATTTAAATTAT
1 TTTAAATTTAAGTTAA
*
1202854 TTTAAATTTAAGTAAA
1 TTTAAATTTAAGTTAA
1202870 TTTA
1 TTTA
1202874 CGCTATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTAAATTTAAGTTAA
Found at i:1203871 original size:16 final size:16
Alignment explanation
Indices: 1203850--1203881 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1203840 ATATTATGAT
1203850 TTTTTTTAAAATTTAA
1 TTTTTTTAAAATTTAA
1203866 TTTTTTTAAAATTTAA
1 TTTTTTTAAAATTTAA
1203882 ATATGTTTGG
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTTAAAATTTAA
Found at i:1204101 original size:20 final size:20
Alignment explanation
Indices: 1204078--1204116 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1204068 TTTTAAATTC
1204078 AAAT-TATTATTTAGATAATA
1 AAATATATT-TTTAGATAATA
*
1204098 AAATATATTTTTATATAAT
1 AAATATATTTTTAGATAAT
1204117 TTTAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AAATATATTTTTAGATAATA
Found at i:1204137 original size:24 final size:25
Alignment explanation
Indices: 1204110--1204159 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1204100 ATATATTTTT
1204110 ATATAATTTT-AA-TTATAAAAATTA
1 ATATAATTTTAAATTTA-AAAAATTA
1204134 ATATAATTTTAAATTTAAAAAATTA
1 ATATAATTTTAAATTTAAAAAATTA
1204159 A
1 A
1204160 AAAAAACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 10 0.42
25 11 0.46
26 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATAATTTTAAATTTAAAAAATTA
Found at i:1204430 original size:2 final size:2
Alignment explanation
Indices: 1204423--1204449 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1204413 TTTCAAAGAA
1204423 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1204450 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1204454 original size:2 final size:2
Alignment explanation
Indices: 1204449--1204477 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1204439 TCTCTCTCTC
1204449 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
1204478 TAAAATGATA
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:1205955 original size:22 final size:22
Alignment explanation
Indices: 1205927--1205968 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1205917 AGTATTGGTC
1205927 ATTGGTTATTTGTTATCGACAT
1 ATTGGTTATTTGTTATCGACAT
1205949 ATTGGTTATTTGTTATCGAC
1 ATTGGTTATTTGTTATCGAC
1205969 GTGTCACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.50
Consensus pattern (22 bp):
ATTGGTTATTTGTTATCGACAT
Found at i:1206506 original size:19 final size:22
Alignment explanation
Indices: 1206484--1206535 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 22
1206474 TTAAATTTTT
1206484 TTTAAATATATAAA-A-AA-AA
1 TTTAAATATATAAATATAATAA
1206503 TTTAAA-A-ATAAATATAATAA
1 TTTAAATATATAAATATAATAA
1206523 TATTAAATATATA
1 T-TTAAATATATA
1206536 CTTATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 5 0.19
18 2 0.07
19 8 0.30
20 3 0.11
21 5 0.19
22 1 0.04
23 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAATATATAAATATAATAA
Found at i:1208645 original size:30 final size:31
Alignment explanation
Indices: 1208611--1208690 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
1208601 CATAATTATA
1208611 TTTAAGATATTATATAATTTATA-CATA-AAT
1 TTTAA-ATATTATATAATTTATATCATATAAT
*
1208641 TTTAAAATATTA-ATAATTTATATTATATAAT
1 TTT-AAATATTATATAATTTATATCATATAAT
1208672 TTTAAATATT-T-TAATTTAT
1 TTTAAATATTATATAATTTAT
1208691 CTTTATTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
29 18 0.40
30 19 0.42
31 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
TTTAAATATTATATAATTTATATCATATAAT
Found at i:1210920 original size:16 final size:16
Alignment explanation
Indices: 1210899--1210932 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1210889 TTTAAATAAT
*
1210899 TATTTAAAAATATTTA
1 TATTTAAAAATAATTA
*
1210915 TATTTAAATATAATTA
1 TATTTAAAAATAATTA
1210931 TA
1 TA
1210933 AAAATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTAAAAATAATTA
Found at i:1210944 original size:22 final size:22
Alignment explanation
Indices: 1210914--1210961 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1210904 AAAAATATTT
*
1210914 ATATTTAAATA-TAATTATAAAA
1 ATATATAAATATTAA-TATAAAA
1210936 ATATATAAATATTAATATAAAA
1 ATATATAAATATTAATATAAAA
1210958 ATAT
1 ATAT
1210962 TATGTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATATAAATATTAATATAAAA
Found at i:1210952 original size:28 final size:28
Alignment explanation
Indices: 1210889--1210955 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1210879 TTAATTTGGT
* *
1210889 TTTAA-ATAATTATTTAAAAATATTTATA
1 TTTAATATAATTA-TTAAAAATATATAAA
1210917 TTTAAATATAATTA-TAAAAATATATAAA
1 TTT-AATATAATTATTAAAAATATATAAA
1210945 TATTAATATAA
1 T-TTAATATAA
1210956 AAATATTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 23 0.68
29 4 0.12
30 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TTTAATATAATTATTAAAAATATATAAA
Found at i:1211990 original size:11 final size:11
Alignment explanation
Indices: 1211965--1211997 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1211955 TTTAATTTAT
*
1211965 TAAAATAA-AA
1 TAAAATAATTA
1211975 TAAAATAATTA
1 TAAAATAATTA
1211986 TAAAATAATTA
1 TAAAATAATTA
1211997 T
1 T
1211998 TTTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAATAATTA
Found at i:1212164 original size:8 final size:8
Alignment explanation
Indices: 1212153--1212210 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
1212143 AAAGCACTAA
1212153 ATAATTAT
1 ATAATTAT
*
1212161 ATAATTAA
1 ATAATTAT
1212169 ATAATTAT
1 ATAATTAT
*
1212177 AATATATTAAA
1 -ATA-ATT-AT
1212188 ATAATT-T
1 ATAATTAT
*
1212195 ATAATTAA
1 ATAATTAT
1212203 ATAATTAT
1 ATAATTAT
1212211 TACAATAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 6 0.15
8 21 0.52
9 6 0.15
10 6 0.15
11 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
ATAATTAT
Found at i:1212171 original size:16 final size:16
Alignment explanation
Indices: 1212150--1212210 Score: 88
Period size: 16 Copynumber: 3.7 Consensus size: 16
1212140 TATAAAGCAC
1212150 TAAATAATTATATAAT
1 TAAATAATTATATAAT
1212166 TAAATAATTATAATATAT
1 TAAATAATTAT-ATA-AT
1212184 TAAAATAATT-TATAAT
1 T-AAATAATTATATAAT
1212200 TAAATAATTAT
1 TAAATAATTAT
1212211 TACAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.20
16 15 0.37
17 6 0.15
18 4 0.10
19 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATAATTATATAAT
Found at i:1212191 original size:27 final size:28
Alignment explanation
Indices: 1212161--1212225 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
1212151 AAATAATTAT
1212161 ATAATTAAATAATT--ATAATATATTAAA
1 ATAATTAAATAATTAAATAAT-TATTAAA
* *
1212188 ATAATT-TATAATTAAATAATTATTACA
1 ATAATTAAATAATTAAATAATTATTAAA
1212215 ATAAATTAAAT
1 AT-AATTAAAT
1212226 GTTAGACTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.19
27 14 0.45
28 9 0.29
29 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAATTAAATAATTAAATAATTATTAAA
Found at i:1212687 original size:16 final size:16
Alignment explanation
Indices: 1212663--1212701 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1212653 AACGTGAGTA
1212663 TAAAAATATAATTTTT
1 TAAAAATATAATTTTT
*
1212679 TAAATATATAATTTTTT
1 TAAAAATATAA-TTTTT
1212696 TAAAAA
1 TAAAAA
1212702 AATTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAAAATATAATTTTT
Found at i:1212884 original size:22 final size:23
Alignment explanation
Indices: 1212859--1212925 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 23
1212849 TATCAAGATT
1212859 AATATAAATATAAAATATTT-TA
1 AATATAAATATAAAATATTTATA
1212881 AATATAAATATAACATATTAATTTATA
1 AATATAAATATAA-A-A-T-ATTTATA
*
1212908 AATAT-AATATAAACTATT
1 AATATAAATATAAAATATT
1212926 AAATTATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 16 0.41
23 2 0.05
24 1 0.03
25 2 0.05
26 11 0.28
27 7 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATAAATATAAAATATTTATA
Found at i:1212912 original size:27 final size:26
Alignment explanation
Indices: 1212859--1212937 Score: 87
Period size: 26 Copynumber: 3.1 Consensus size: 26
1212849 TATCAAGATT
1212859 AATATAAATATAAA-A-T-ATTT-TA
1 AATATAAATATAAATATTAATTTATA
1212881 AATATAAATATAACATATTAATTTATA
1 AATATAAATATAA-ATATTAATTTATA
*
1212908 AATAT-AATATAAACTATTAAATTATTA
1 AATATAAATATAAA-TATTAATTTA-TA
1212935 AAT
1 AAT
1212938 TTAATTATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
22 13 0.27
23 1 0.02
24 1 0.02
25 2 0.04
26 20 0.41
27 12 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (26 bp):
AATATAAATATAAATATTAATTTATA
Found at i:1212942 original size:27 final size:27
Alignment explanation
Indices: 1212858--1212942 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
1212848 GTATCAAGAT
* *
1212858 TAATATAAA-TATAAAATATTTTAAATA
1 TAATATAAACTATTAAAT-TATTAAATA
*
1212885 TAA-ATATAACATATTAATTTA-TAAATA
1 TAATATA-AAC-TATTAAATTATTAAATA
*
1212912 TAATATAAACTATTAAATTATTAAATT
1 TAATATAAACTATTAAATTATTAAATA
1212939 TAAT
1 TAAT
1212943 TATTTAATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 12 0.25
27 26 0.54
28 4 0.08
29 6 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATATAAACTATTAAATTATTAAATA
Found at i:1213803 original size:21 final size:21
Alignment explanation
Indices: 1213763--1213804 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1213753 AAATATTAAA
*
1213763 CTTAAATAATAATAATATTTT
1 CTTAAATAATAATAACATTTT
**
1213784 CTTAAATAATTTTAACATTTT
1 CTTAAATAATAATAACATTTT
1213805 AATATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
CTTAAATAATAATAACATTTT
Found at i:1220261 original size:19 final size:20
Alignment explanation
Indices: 1220199--1220262 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 20
1220189 AAATTAAAAT
*
1220199 TTATATAAATATAA-A-ATA
1 TTATATAAATATAATATAAA
* *
1220217 TT-T-TAAATATAATTTTAA
1 TTATATAAATATAATATAAA
1220235 -TATATAAATATAATATAAA
1 TTATATAAATATAATATAAA
1220254 TTAT-TAAAT
1 TTATATAAAT
1220263 TATTAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
16 9 0.25
17 2 0.06
18 4 0.11
19 18 0.50
20 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATATAAATATAATATAAA
Found at i:1220728 original size:12 final size:12
Alignment explanation
Indices: 1220711--1220745 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1220701 TAAGATTATT
1220711 ATTTATTTTAAA
1 ATTTATTTTAAA
1220723 ATTTA--TTAAA
1 ATTTATTTTAAA
1220733 ATTTATTTTAAA
1 ATTTATTTTAAA
1220745 A
1 A
1220746 ATATTTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.48
12 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTATTTTAAA
Found at i:1221296 original size:26 final size:26
Alignment explanation
Indices: 1221256--1221311 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
1221246 AATATAAACA
* *
1221256 TAAATATTAATATAAATA-AAATTTT
1 TAAATATTAAAATAAAAATAAATTTT
1221281 TAAATATTTAAAATAAAAATAAATTTT
1 TAAATA-TTAAAATAAAAATAAATTTT
1221308 TAAA
1 TAAA
1221312 CTTAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 6 0.22
26 10 0.37
27 11 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAATATTAAAATAAAAATAAATTTT
Found at i:1221522 original size:21 final size:21
Alignment explanation
Indices: 1221497--1221557 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 21
1221487 TTATATATTA
1221497 ATATAAAATTAAATTAATTTT
1 ATATAAAATTAAATTAATTTT
* * *
1221518 ATAT--ATTTATATAAATTTT
1 ATATAAAATTAAATTAATTTT
* *
1221537 TTATAAAATTAATATTTATTT
1 ATATAAAATTAA-ATTAATTT
1221558 AATTTAATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
19 15 0.52
21 8 0.28
22 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATAAAATTAAATTAATTTT
Found at i:1222683 original size:19 final size:19
Alignment explanation
Indices: 1222618--1222684 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 19
1222608 TTTACAAATA
1222618 ATTATAA-ATATAAT-TAAT
1 ATTATAATA-ATAATATAAT
*
1222636 ATTA-ATATAATTAATTATTAAA
1 ATTATA-ATAA-TAA-TA-TAAT
*
1222658 ATAATAATAATAATATAAT
1 ATTATAATAATAATATAAT
1222677 ATTATAAT
1 ATTATAAT
1222685 CCTTATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
17 1 0.03
18 6 0.16
19 14 0.37
20 3 0.08
21 3 0.08
22 10 0.26
23 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTATAATAATAATATAAT
Found at i:1223238 original size:15 final size:16
Alignment explanation
Indices: 1223198--1223239 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1223188 ATTTGGATCA
*
1223198 ATTTTATGATATTTAT
1 ATTTTATTATATTTAT
*
1223214 ATTTGGATTATATTTAT
1 ATTT-TATTATATTTAT
1223231 -TTTTATTAT
1 ATTTTATTAT
1223240 TATATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.23
16 7 0.32
17 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (16 bp):
ATTTTATTATATTTAT
Found at i:1223275 original size:24 final size:24
Alignment explanation
Indices: 1223248--1223310 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
1223238 ATTATATTTA
1223248 AAATATTAATTATTTATATAAATT
1 AAATATTAATTATTTATATAAATT
* *
1223272 AAATATTTA-TGTTT-TATAAATT
1 AAATATTAATTATTTATATAAATT
*
1223294 ATAATA-TATTTATTTAT
1 A-AATATTAATTATTTAT
1223311 GAATTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 10 0.32
23 12 0.39
24 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
AAATATTAATTATTTATATAAATT
Found at i:1225337 original size:17 final size:17
Alignment explanation
Indices: 1225287--1225343 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 17
1225277 AAAAAATGTT
1225287 AAAAATTAT-AATATATA
1 AAAAATTATAAATA-ATA
*
1225304 AAAATATATTTAGAATAATA
1 AAAA-AT-TATA-AATAATA
1225324 AAAAATTATAAAT-ATA
1 AAAAATTATAAATAATA
1225340 AAAA
1 AAAA
1225344 TAGTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 7 0.21
17 7 0.21
18 5 0.15
19 4 0.12
20 7 0.21
21 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAAATTATAAATAATA
Found at i:1225388 original size:21 final size:21
Alignment explanation
Indices: 1225357--1225428 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
1225347 TAAAATTATT
1225357 TTATCAAAAATTAATTTTTAAA
1 TTAT-AAAAATTAATTTTTAAA
* *
1225379 TCATAAAAATTTTATTTTTATAA
1 TTATAAAAA-TTAATTTTTA-AA
* * *
1225402 TTTTAAAATTTAATTATTAAA
1 TTATAAAAATTAATTTTTAAA
1225423 TTATAA
1 TTATAA
1225429 TTTTAATAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
21 12 0.30
22 20 0.50
23 8 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATAAAAATTAATTTTTAAA
Found at i:1225423 original size:13 final size:13
Alignment explanation
Indices: 1225396--1225448 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
1225386 AATTTTATTT
1225396 TTATAATTTTAAAA
1 TTATAATTTT-AAA
1225410 TT-TAATTATTAAA
1 TTATAATT-TTAAA
1225423 TTATAATTTT-AA
1 TTATAATTTTAAA
*
1225435 TAATAAATTTTAAA
1 TTAT-AATTTTAAA
1225449 ATTTTTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 5 0.15
13 18 0.53
14 11 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATAATTTTAAA
Found at i:1225451 original size:27 final size:27
Alignment explanation
Indices: 1225396--1225448 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1225386 AATTTTATTT
*
1225396 TTATAATTTTAAAATTTAATTATTAAA
1 TTATAATTTTAAAATTAAATTATTAAA
1225423 TTATAATTTTAATAA-TAAATT-TTAAA
1 TTATAATTTTAA-AATTAAATTATTAAA
1225449 ATTTTTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 17 0.71
28 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTATAATTTTAAAATTAAATTATTAAA
Found at i:1225873 original size:16 final size:16
Alignment explanation
Indices: 1225854--1225887 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1225844 ATTAATGTAT
1225854 TAAAAT-TTTATAAATA
1 TAAAATATTT-TAAATA
1225870 TAAAATATTTTAAATA
1 TAAAATATTTTAAATA
1225886 TA
1 TA
1225888 TTATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATATTTTAAATA
Found at i:1226257 original size:2 final size:2
Alignment explanation
Indices: 1226250--1226282 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1226240 ATCTCTTCCT
1226250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1226283 TAGAATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1226972 original size:31 final size:32
Alignment explanation
Indices: 1226931--1226997 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
1226921 AGTTTATATA
1226931 TATATATATATTAAAATATAAATTTAATC-TT
1 TATATATATATTAAAATATAAATTTAATCATT
* * * *
1226962 TATATTTATATTAAAATGTGAATTTAGTCATT
1 TATATATATATTAAAATATAAATTTAATCATT
1226994 TATA
1 TATA
1226998 ATGATTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (32 bp):
TATATATATATTAAAATATAAATTTAATCATT
Found at i:1227008 original size:32 final size:31
Alignment explanation
Indices: 1226938--1227009 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1226928 ATATATATAT
* *
1226938 ATATTAAAATATAAATTTAATCTTTATATTT
1 ATATTAAAATATAAATTTAATCTTTATAATG
* * *
1226969 ATATTAAAATGTGAATTTAGTCATTTATAATG
1 ATATTAAAATATAAATTTAATC-TTTATAATG
*
1227001 ATTTTAAAA
1 ATATTAAAA
1227010 ATTTATTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 19 0.56
32 15 0.44
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (31 bp):
ATATTAAAATATAAATTTAATCTTTATAATG
Found at i:1227937 original size:28 final size:26
Alignment explanation
Indices: 1227897--1227949 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
1227887 AATATTATTA
1227897 TTTTATTAATTTTTAATAATATAAATAT
1 TTTTATTAATTTTTAAT-AT-TAAATAT
1227925 TTTTAATT-ATTTTTAATATTAAATA
1 TTTT-ATTAATTTTTAATATTAAATA
1227950 AAAATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.25
27 2 0.08
28 13 0.54
29 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTATTAATTTTTAATATTAAATAT
Found at i:1227988 original size:24 final size:24
Alignment explanation
Indices: 1227947--1227996 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
1227937 TTAATATTAA
1227947 ATAAAAATTTAAAATTTTTAAAAAT
1 ATAAAAA-TTAAAATTTTTAAAAAT
1227972 ATAAAAA-TAAAATTTTTTAAAAAT
1 ATAAAAATTAAAA-TTTTTAAAAAT
1227996 A
1 A
1227997 ATTGTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.21
24 12 0.50
25 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAAAATTAAAATTTTTAAAAAT
Found at i:1228487 original size:14 final size:14
Alignment explanation
Indices: 1228458--1228635 Score: 61
Period size: 14 Copynumber: 12.4 Consensus size: 14
1228448 AACATTAATA
*
1228458 ATAACAATATTAAAT
1 ATAATAATA-TAAAT
1228473 ATAATAATATAAAT
1 ATAATAATATAAAT
1228487 ATAATACA-ATAAA-
1 ATAATA-ATATAAAT
*
1228500 ATAATTAAAATATAAT
1 ATAA-TAATATA-AAT
1228516 ATAAT-ATGATTCAAAT
1 ATAATAAT-A-T-AAAT
* *
1228532 ATAA-ATTTTAAAAT
1 ATAATAATAT-AAAT
*
1228546 TTAAATAATATAAA-
1 AT-AATAATATAAAT
* * *
1228560 ATATTAATGT-ATT
1 ATAATAATATAAAT
*
1228573 AAAATTAATATAAAT
1 ATAA-TAATATAAAT
*
1228588 A-AAAAATATTTTAAAT
1 ATAATAATA---TAAAT
1228604 ATAAT--TATAAA-
1 ATAATAATATAAAT
*
1228615 AAAATATATATAAAT
1 ATAATA-ATATAAAT
1228630 ATAATA
1 ATAATA
1228636 TGAATTTAAG
Statistics
Matches: 121, Mismatches: 20, Indels: 44
0.65 0.11 0.24
Matches are distributed among these distances:
11 4 0.03
12 5 0.04
13 17 0.14
14 42 0.35
15 28 0.23
16 22 0.18
17 3 0.02
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (14 bp):
ATAATAATATAAAT
Found at i:1228497 original size:24 final size:24
Alignment explanation
Indices: 1228470--1228522 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1228460 AACAATATTA
1228470 AATATAATAA-TATAAATATAATAC
1 AATATAATAATTA-AAATATAATAC
* *
1228494 AATAAAATAATTAAAATATAATAT
1 AATATAATAATTAAAATATAATAC
1228518 AATAT
1 AATAT
1228523 GATTCAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
AATATAATAATTAAAATATAATAC
Found at i:1228511 original size:19 final size:19
Alignment explanation
Indices: 1228455--1228535 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 19
1228445 GTTAACATTA
1228455 ATAATAACAAT-ATT-AAAT
1 ATAATAA-AATAATTAAAAT
* * *
1228473 ATAATAATATAAATATAAT
1 ATAATAAAATAATTAAAAT
*
1228492 ACAATAAAATAATTAAAAT
1 ATAATAAAATAATTAAAAT
* *
1228511 ATAATATAATATGATTCAAAT
1 ATAATA-AA-ATAATTAAAAT
1228532 ATAA
1 ATAA
1228536 ATTTTAAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
17 2 0.04
18 9 0.18
19 23 0.47
20 2 0.04
21 13 0.27
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (19 bp):
ATAATAAAATAATTAAAAT
Found at i:1228519 original size:21 final size:21
Alignment explanation
Indices: 1228495--1228535 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1228485 ATATAATACA
1228495 ATAAAATAATTAAAATATAAT
1 ATAAAATAATTAAAATATAAT
* * *
1228516 ATAATATGATTCAAATATAA
1 ATAAAATAATTAAAATATAA
1228536 ATTTTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
ATAAAATAATTAAAATATAAT
Found at i:1228601 original size:27 final size:27
Alignment explanation
Indices: 1228536--1228623 Score: 65
Period size: 27 Copynumber: 3.1 Consensus size: 27
1228526 TCAAATATAA
*
1228536 ATTTTAAAATTTAA-ATAATATAAAATATT
1 ATTTTAAAA-TTAATATAA-ATAAAA-AAT
1228565 AATGTATTAAAATTAATATAAATAAAAAAT
1 -AT-T-TTAAAATTAATATAAATAAAAAAT
*
1228595 ATTTT-AAATATAATTATAAA-AAAATAT
1 ATTTTAAAAT-TAA-TATAAATAAAAAAT
1228622 AT
1 AT
1228624 ATAAATATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
26 4 0.08
27 13 0.25
28 7 0.14
29 2 0.04
30 4 0.08
31 11 0.22
32 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
ATTTTAAAATTAATATAAATAAAAAAT
Found at i:1228603 original size:26 final size:27
Alignment explanation
Indices: 1228574--1228636 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
1228564 TAATGTATTA
*
1228574 AAAT-TAATATAAATAAAAAATAT-TTT
1 AAATATAATATAAA-AAAAAATATATAT
*
1228600 AAATATAAT-TATAAAAAAATATATAT
1 AAATATAATATAAAAAAAAATATATAT
1228626 AAATATAATAT
1 AAATATAATAT
1228637 GAATTTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 9 0.28
26 18 0.56
27 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AAATATAATATAAAAAAAAATATATAT
Found at i:1228948 original size:21 final size:21
Alignment explanation
Indices: 1228923--1228975 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1228913 ATACACATAC
1228923 ATATAAAA-ATTATTAAAAAAT
1 ATATAAAATATT-TTAAAAAAT
*
1228944 ATATAAAATATTTTATAAAAT
1 ATATAAAATATTTTAAAAAAT
*
1228965 AAAATAAAATA
1 -ATATAAAATA
1228976 AAAATTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATAAAATATTTTAAAAAAT
Found at i:1229400 original size:21 final size:20
Alignment explanation
Indices: 1229371--1229409 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1229361 TTGATAAAAT
*
1229371 AAAATTTAAAATTAATTATA
1 AAAATTTAAAATAAATTATA
*
1229391 AAAATATTAATATAAATTA
1 AAAAT-TTAAAATAAATTA
1229410 ATTTTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTTAAAATAAATTATA
Found at i:1230515 original size:19 final size:19
Alignment explanation
Indices: 1230488--1230524 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1230478 TTTGATTTTT
*
1230488 TATTGATTTATATTAATTA
1 TATTAATTTATATTAATTA
*
1230507 TATTAATTTGTATTAATT
1 TATTAATTTATATTAATT
1230525 TATAGTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATTTATATTAATTA
Found at i:1230520 original size:10 final size:10
Alignment explanation
Indices: 1230488--1230528 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
1230478 TTTGATTTTT
*
1230488 TATTGATTTA
1 TATTAATTTA
1230498 TATTAA-TTA
1 TATTAATTTA
*
1230507 TATTAATTTG
1 TATTAATTTA
1230517 TATTAATTTA
1 TATTAATTTA
1230527 TA
1 TA
1230529 GTCAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (10 bp):
TATTAATTTA
Found at i:1230775 original size:16 final size:16
Alignment explanation
Indices: 1230750--1230787 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1230740 TAATTTATAT
*
1230750 TTAAAAATTTTAAATA
1 TTAAATATTTTAAATA
*
1230766 TTAAATATTTTAAATT
1 TTAAATATTTTAAATA
1230782 TTAAAT
1 TTAAAT
1230788 TTTATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATATTTTAAATA
Found at i:1230782 original size:7 final size:7
Alignment explanation
Indices: 1230754--1230796 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1230744 TTATATTTAA
1230754 AAATTTT
1 AAATTTT
*
1230761 AAATATTA
1 AAAT-TTT
1230769 AATATTTT
1 AA-ATTTT
1230777 AAATTTT
1 AAATTTT
1230784 AAATTTT
1 AAATTTT
*
1230791 ATATTT
1 AAATTT
1230797 ACATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 21 0.68
8 8 0.26
9 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AAATTTT
Found at i:1231682 original size:24 final size:22
Alignment explanation
Indices: 1231642--1231691 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1231632 TACATAAAAT
1231642 TTAAAATTTAATAATATCATACA
1 TTAAAATTTAATAATAT-ATACA
* * *
1231665 TTAACAATTTATTTATATTTACA
1 TTAA-AATTTAATAATATATACA
1231688 TTAA
1 TTAA
1231692 TTTTAACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATTTAATAATATATACA
Found at i:1235775 original size:13 final size:13
Alignment explanation
Indices: 1235757--1235783 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1235747 TTACTTGGAC
1235757 TTGGGGGTAAGTA
1 TTGGGGGTAAGTA
1235770 TTGGGGGTAAGTA
1 TTGGGGGTAAGTA
1235783 T
1 T
1235784 CGGACACGGG
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:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (13 bp):
TTGGGGGTAAGTA
Found at i:1238848 original size:10 final size:9
Alignment explanation
Indices: 1238826--1238896 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 9
1238816 ACAATTGTAC
1238826 TTATA-ATT
1 TTATATATT
1238834 TTATATATT
1 TTATATATT
*
1238843 TATATAAATT
1 T-TATATATT
1238853 TTAATATATT
1 TT-ATATATT
1238863 TT-TAT-TT
1 TTATATATT
*
1238870 TTTTAT-TT
1 TTATATATT
* *
1238878 TTAAATTTT
1 TTATATATT
1238887 TTAT-TATT
1 TTATATATT
1238895 TT
1 TT
1238897 TCGTTATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 4 0.08
8 22 0.42
9 10 0.19
10 16 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATATATT
Found at i:1238874 original size:8 final size:8
Alignment explanation
Indices: 1238861--1238921 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
1238851 TTTTAATATA
1238861 TTTTTATT
1 TTTTTATT
1238869 TTTTTATT
1 TTTTTATT
**
1238877 TTTAAATTT
1 TTTTTA-TT
1238886 TTTATTATT
1 TTT-TTATT
1238895 TTTCGTTATT
1 TTT--TTATT
*
1238905 TTTTTAAT
1 TTTTTATT
*
1238913 ATTTTATT
1 TTTTTATT
1238921 T
1 T
1238922 GCTGTAATTG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
8 22 0.54
9 10 0.24
10 9 0.22
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTATT
Found at i:1238876 original size:14 final size:15
Alignment explanation
Indices: 1238859--1238891 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1238849 AATTTTAATA
*
1238859 TATTTTT-ATTTTTT
1 TATTTTTAAATTTTT
1238873 TATTTTTAAATTTTT
1 TATTTTTAAATTTTT
1238888 TATT
1 TATT
1238892 ATTTTTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TATTTTTAAATTTTT
Found at i:1239602 original size:16 final size:18
Alignment explanation
Indices: 1239569--1239604 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
1239559 GACCAATAAT
1239569 TTATATTTATATATTTTA
1 TTATATTTATATATTTTA
1239587 TTATA-TTATA-ATTTTA
1 TTATATTTATATATTTTA
1239603 TT
1 TT
1239605 TAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTTATATATTTTA
Found at i:1239639 original size:15 final size:14
Alignment explanation
Indices: 1239564--1239650 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 14
1239554 TTATAGACCA
1239564 ATAATTTATATTTAT
1 ATAATTTATA-TTAT
*
1239579 ATATTTTAT-TATATT
1 ATAATTTATAT-TA-T
1239594 ATAATTT-TATT-T
1 ATAATTTATATTAT
*
1239606 A-AA-ATATATTA-
1 ATAATTTATATTAT
1239617 ATAATTTATATTAT
1 ATAATTTATATTAT
**
1239631 ATAATTT-TAAAAT
1 ATAATTTATATTAT
1239644 ATAATTT
1 ATAATTT
1239651 CATCGTGTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
10 1 0.02
11 7 0.12
12 4 0.07
13 19 0.33
14 11 0.19
15 16 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATAATTTATATTAT
Found at i:1240719 original size:20 final size:19
Alignment explanation
Indices: 1240677--1240720 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1240667 AGTTTTATTT
** *
1240677 TTTTAATTAAATTTATTAC
1 TTTTAATTAAATTTAAAAA
1240696 TTTTAACTTAAATTTAAAAA
1 TTTTAA-TTAAATTTAAAAA
1240716 TTTTA
1 TTTTA
1240721 TCAATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAATTAAATTTAAAAA
Found at i:1240743 original size:17 final size:18
Alignment explanation
Indices: 1240713--1240750 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1240703 TTAAATTTAA
*
1240713 AAATTTTATCAATTTATTT
1 AAATTTTA-CAATTAATTT
1240732 AAATTTTA-AATTAATTT
1 AAATTTTACAATTAATTT
1240749 AA
1 AA
1240751 TTCAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTTTACAATTAATTT
Found at i:1241507 original size:19 final size:18
Alignment explanation
Indices: 1241466--1241509 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1241456 AAACATAAAT
* *
1241466 ATAATTTTTAATTATTTA
1 ATAATTTTTAAATATTAA
*
1241484 TTAATTTTATAAATATTAA
1 ATAATTTT-TAAATATTAA
1241503 ATAATTT
1 ATAATTT
1241510 AAAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAATTTTTAAATATTAA
Found at i:1241924 original size:91 final size:91
Alignment explanation
Indices: 1241820--1242042 Score: 250
Period size: 91 Copynumber: 2.5 Consensus size: 91
1241810 TTTAAAAATA
* * * *
1241820 ACTTAAACTTAAAATGATTTGAACAATTAAA-TATAAATAATTTGAACTTAAAATGATAAAATTT
1 ACTTAAATTTAAAATGATTTGAACAATTAAATTA-AAATAATATGAACATAAAATAATAAAATTT
* *
1241884 GATAAATTCAAATGTTAAATTTAATTG
65 AATAAATTCAAATATTAAATTTAATTG
* * * * *
1241911 ACTTAAATTTAAAATGATTTGAATACTTAACTTAAAATGATATGAACATAAAATAATCAAATTTA
1 ACTTAAATTTAAAATGATTTGAACAATTAAATTAAAATAATATGAACATAAAATAATAAAATTTA
* *
1241976 ATAATTTTAAATATTAAATTTAATTG
66 ATAAATTCAAATATTAAATTTAATTG
* * * ** * *
1242002 ACCTGAATTTAAAATAATTCAAATAATTAATTTAAAATAAT
1 ACTTAAATTTAAAATGATTTGAACAATTAAATTAAAATAAT
1242043 TAAATTTAAT
Statistics
Matches: 110, Mismatches: 21, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
91 108 0.98
92 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (91 bp):
ACTTAAATTTAAAATGATTTGAACAATTAAATTAAAATAATATGAACATAAAATAATAAAATTTA
ATAAATTCAAATATTAAATTTAATTG
Found at i:1242034 original size:23 final size:24
Alignment explanation
Indices: 1242007--1242133 Score: 104
Period size: 23 Copynumber: 5.3 Consensus size: 24
1241997 AATTGACCTG
1242007 AATTTAAAATAATTCAAATAATT-
1 AATTTAAAATAATTCAAATAATTA
1242030 AATTTAAAATAATT-AAATTTAA-TA
1 AATTTAAAATAATTCAAA--TAATTA
* * *
1242054 AATTTAAATATTAAATTCGATTGATTTA
1 AATTTAAA-A-T-AATTCAAAT-AATTA
* *
1242082 AATTT-AATTAATTTAAAT-ATTA
1 AATTTAAAATAATTCAAATAATTA
*
1242104 AATTTAAAATAATTTAAAT-ATTA
1 AATTTAAAATAATTCAAATAATTA
1242127 AATTTAA
1 AATTTAA
1242134 TTAATTTTAA
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
22 11 0.13
23 38 0.45
24 17 0.20
25 2 0.02
26 2 0.02
27 7 0.08
28 8 0.09
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
AATTTAAAATAATTCAAATAATTA
Found at i:1242066 original size:22 final size:22
Alignment explanation
Indices: 1242025--1242150 Score: 97
Period size: 23 Copynumber: 5.9 Consensus size: 22
1242015 ATAATTCAAA
*
1242025 TAATTAATTTAAAATAATTAAATT
1 TAATAAATTT-AAAT-ATTAAATT
1242049 TAATAAATTTAAATATTAAA--
1 TAATAAATTTAAATATTAAATT
** *
1242069 T--TCGA-TT-GAT-TTAAATT
1 TAATAAATTTAAATATTAAATT
*
1242086 TAATTAATTTAAATATTAAATT
1 TAATAAATTTAAATATTAAATT
*
1242108 TAAAATAATTTAAATATTAAATT
1 TAATA-AATTTAAATATTAAATT
*
1242131 TAATTAATTTTAAAT-TTAAA
1 TAA-TAAATTTAAATATTAAA
1242151 ATAATTTATA
Statistics
Matches: 82, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
15 5 0.06
16 2 0.02
17 3 0.04
18 2 0.02
19 2 0.02
20 3 0.04
21 2 0.02
22 21 0.26
23 32 0.39
24 10 0.12
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATAAATTTAAATATTAAATT
Found at i:1242077 original size:75 final size:74
Alignment explanation
Indices: 1241959--1242127 Score: 214
Period size: 75 Copynumber: 2.2 Consensus size: 74
1241949 GATATGAACA
* * * *
1241959 TAAAATAATCAAATTTAATAATTTTAAATATTAAATTTAATTGACCTGAATTTAAAATAATTCAA
1 TAAAATAATTAAATTTAATAAATTTAAATATTAAATTCAATTGACCTAAATTT-AAATAATTCAA
1242024 ATAATT-AATT
65 AT-ATTAAATT
* ** * *
1242034 TAAAATAATTAAATTTAATAAATTTAAATATTAAATTCGATTGATTTAAATTTAATTAATTTAAA
1 TAAAATAATTAAATTTAATAAATTTAAATATTAAATTCAATTGACCTAAATTTAAATAATTCAAA
1242099 TATTAAATT
66 TATTAAATT
1242108 TAAAATAATTTAAATATTAA
1 TAAAATAA-TTAAAT-TTAA
1242128 ATTTAATTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
73 3 0.04
74 23 0.28
75 52 0.63
76 4 0.05
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (74 bp):
TAAAATAATTAAATTTAATAAATTTAAATATTAAATTCAATTGACCTAAATTTAAATAATTCAAA
TATTAAATT
Found at i:1242142 original size:23 final size:22
Alignment explanation
Indices: 1242079--1242150 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 22
1242069 TTCGATTGAT
1242079 TTAAATTTAATTAATTTAAATA
1 TTAAATTTAATTAATTTAAATA
*
1242101 TTAAATTTAAAATAATTTAAATA
1 TTAAATTT-AATTAATTTAAATA
1242124 TTAAATTTAATTAATTTTAAAT-
1 TTAAATTTAATTAA-TTTAAATA
1242146 TTAAA
1 TTAAA
1242151 ATAATTTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.39
23 28 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAATTTAATTAATTTAAATA
Found at i:1242156 original size:39 final size:38
Alignment explanation
Indices: 1241959--1242158 Score: 164
Period size: 37 Copynumber: 5.3 Consensus size: 38
1241949 GATATGAACA
*
1241959 TAAAATAA-TCAAATTTAA-TAATTTTAAATATTAAATT
1 TAAAATAATTTAAATTTAATTAA-TTTAAATATTAAATT
* * ** * * *
1241996 T-AATTGACCTGAATTTAAAATAATTCAAATAATT-AATT
1 TAAAATAATTTAAATTT-AATTAATTTAAAT-ATTAAATT
*
1242034 TAAAATAA-TTAAATTTAATAAATTTAAATATTAAA-T
1 TAAAATAATTTAAATTTAATTAATTTAAATATTAAATT
** * *
1242070 TCGATTGATTTAAATTTAATTAATTTAAATATTAAATT
1 TAAAATAATTTAAATTTAATTAATTTAAATATTAAATT
*
1242108 TAAAATAATTTAAATATTAAATTTAA-TT-AATTTTAAATT
1 TAAAATAATTTAAAT-TT-AA-TTAATTTAAATATTAAATT
1242147 TAAAATAATTTA
1 TAAAATAATTTA
1242159 TAACTAAAAA
Statistics
Matches: 129, Mismatches: 23, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
36 12 0.09
37 44 0.34
38 31 0.24
39 34 0.26
40 4 0.03
41 4 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (38 bp):
TAAAATAATTTAAATTTAATTAATTTAAATATTAAATT
Found at i:1242183 original size:39 final size:36
Alignment explanation
Indices: 1242011--1242183 Score: 100
Period size: 37 Copynumber: 4.6 Consensus size: 36
1242001 GACCTGAATT
*
1242011 TAAAATAATTCAAATAATT-AATTTAAAATAA-TTAAA
1 TAAAA-AATTTAAA-AATTAAATTTAAAATAATTTAAA
* * ** * *
1242047 TTTAATAAATTTAAATATTAAA-TTCGATTGATTTAAA
1 --TAAAAAATTTAAAAATTAAATTTAAAATAATTTAAA
** *
1242084 TTTAATTAATTTAAATATTAAATTTAAAATAATTTAAA
1 --TAAAAAATTTAAAAATTAAATTTAAAATAATTTAAA
** *
1242122 TATTAAATTTAATTAATTTTAAATTTAAAATAATTTATAA
1 TAAAAAATTTAA--AA-ATTAAATTTAAAATAATTTA-AA
1242162 CTAAAAAATTTAAAAACTTAAA
1 -TAAAAAATTTAAAAA-TTAAA
1242184 AATATAAATT
Statistics
Matches: 107, Mismatches: 19, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
36 18 0.17
37 35 0.33
38 16 0.15
39 26 0.24
40 2 0.02
41 10 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (36 bp):
TAAAAAATTTAAAAATTAAATTTAAAATAATTTAAA
Done.