Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006936.1 Hibiscus syriacus cultivar Beakdansim tig00017808_pilon, whole genome shotgun sequence
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: 2176229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1194340 original size:9 final size:10
Alignment explanation
Indices: 1194323--1194355 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1194313 GCAAATTTTA
1194323 TTATAATTAT
1 TTATAATTAT
1194333 TTAT-ATTA-
1 TTATAATTAT
1194341 TTATAATTAT
1 TTATAATTAT
1194351 TTATA
1 TTATA
1194356 GTATTATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.19
9 8 0.38
10 9 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTATAATTAT
Found at i:1194343 original size:18 final size:18
Alignment explanation
Indices: 1194320--1194362 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1194310 TATGCAAATT
1194320 TTATTATAATTATTTATA
1 TTATTATAATTATTTATA
1194338 TTATTATAATTATTTATA
1 TTATTATAATTATTTATA
*
1194356 GTATTAT
1 TTATTAT
1194363 GACAAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATTATAATTATTTATA
Found at i:1199336 original size:6 final size:6
Alignment explanation
Indices: 1199321--1199350 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1199311 TAGAAAATAT
*
1199321 TTTTTG TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1199351 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:1203503 original size:27 final size:27
Alignment explanation
Indices: 1203471--1203526 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1203461 GTAATTTTAT
* *
1203471 CATTATATCTAATATTTAATATATACA
1 CATTATATCCAATATGTAATATATACA
* *
1203498 CATTATATCCCATATGTAATATCTACA
1 CATTATATCCAATATGTAATATATACA
1203525 CA
1 CA
1203527 AATTTGGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (27 bp):
CATTATATCCAATATGTAATATATACA
Found at i:1204224 original size:22 final size:22
Alignment explanation
Indices: 1204119--1204280 Score: 125
Period size: 22 Copynumber: 7.1 Consensus size: 22
1204109 TAATATATAA
*
1204119 TATATAGTTTTGTCAAAAA-ATAA
1 TATATAGTTTT-T-AAAAACATAT
* * * *
1204142 TATATGGGTTTTGAAAATATA-
1 TATATAGTTTTTAAAAACATAT
* *
1204163 TAGTATGGTTTCTAAAAACATA-
1 TA-TATAGTTTTTAAAAACATAT
*
1204185 TATTATAGTTTTTGAAAACATAT
1 TA-TATAGTTTTTAAAAACATAT
*
1204208 TATATAGTTTTAAAAAAACATAT
1 TATATAGTTTT-TAAAAACATAT
*
1204231 AATATATATATTTTTAAAAACATA-
1 --TATATA-GTTTTTAAAAACATAT
1204255 TAGTATAGTTTTTAAAAACATAT
1 TA-TATAGTTTTTAAAAACATAT
1204278 TAT
1 TAT
1204281 TATATAATTA
Statistics
Matches: 114, Mismatches: 16, Indels: 19
0.77 0.11 0.13
Matches are distributed among these distances:
21 6 0.05
22 63 0.55
23 26 0.23
25 15 0.13
26 4 0.04
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (22 bp):
TATATAGTTTTTAAAAACATAT
Found at i:1204252 original size:48 final size:45
Alignment explanation
Indices: 1204150--1204307 Score: 153
Period size: 46 Copynumber: 3.4 Consensus size: 45
1204140 AATATATGGG
* * *
1204150 TTTTGAAAATATA-TAGTATGGTTTCT-AAAAACATATATTATA-GT
1 TTTTGAAAACATATTA-TATAGTTT-TAAAAAACATATATTATATAT
1204194 TTTTGAAAACATATTATATAGTTTTAAAAAAACATATAATATATATAT
1 TTTTGAAAACATATTATATAGTTTT-AAAAAACATAT-AT-TATATAT
* * *
1204242 TTTTAAAAACATA-TAGTATAGTTTTTAAAAACATATTATTATATAA
1 TTTTGAAAACATATTA-TATAGTTTTAAAAAACATA-TATTATATAT
* *
1204288 TTATGAAAACATATAATATA
1 TTTTGAAAACATATTATATA
1204308 TATAGTTTTT
Statistics
Matches: 96, Mismatches: 9, Indels: 16
0.79 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 19 0.20
45 12 0.12
46 23 0.24
47 18 0.19
48 23 0.24
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.42
Consensus pattern (45 bp):
TTTTGAAAACATATTATATAGTTTTAAAAAACATATATTATATAT
Found at i:1204284 original size:23 final size:23
Alignment explanation
Indices: 1204170--1204284 Score: 130
Period size: 22 Copynumber: 5.0 Consensus size: 23
1204160 ATATAGTATG
*
1204170 GTTTCTAAAAACATA-TATTATA
1 GTTTTTAAAAACATATTATTATA
*
1204192 GTTTTTGAAAACATATTA-TATA
1 GTTTTTAAAAACATATTATTATA
*
1204214 GTTTTAAAAAAACATATAATATATATA
1 GTTTT-TAAAAACATAT--TAT-TATA
*
1204241 -TTTTTAAAAACATA-TAGTATA
1 GTTTTTAAAAACATATTATTATA
1204262 GTTTTTAAAAACATATTATTATA
1 GTTTTTAAAAACATATTATTATA
1204285 TAATTATGAA
Statistics
Matches: 78, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
21 4 0.05
22 38 0.49
23 17 0.22
25 11 0.14
26 4 0.05
27 4 0.05
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (23 bp):
GTTTTTAAAAACATATTATTATA
Found at i:1204310 original size:25 final size:23
Alignment explanation
Indices: 1204175--1204311 Score: 92
Period size: 22 Copynumber: 5.9 Consensus size: 23
1204165 GTATGGTTTC
*
1204175 TAAAAACATAT-AT-TATAGTTTT
1 TAAAAACATATAATATATA-TATT
*
1204197 TGAAAACATAT--TATATAGT-TT
1 TAAAAACATATAATATATA-TATT
1204218 TAAAAAAACATATAATATATATATTTT
1 T--AAAAACATATAATATATATA--TT
*
1204245 TAAAAACATATAGTATAGT-T-TT
1 TAAAAACATATAATATA-TATATT
*
1204267 TAAAAACATATTAT-TATATAATT
1 TAAAAACATATAATATATAT-ATT
*
1204290 ATGAAAACATATAATATATATA
1 -TAAAAACATATAATATATATA
1204312 GTTTTTGAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
20 1 0.01
21 7 0.07
22 30 0.32
23 11 0.12
24 14 0.15
25 27 0.29
26 1 0.01
27 3 0.03
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (23 bp):
TAAAAACATATAATATATATATT
Found at i:1204326 original size:25 final size:24
Alignment explanation
Indices: 1204110--1204330 Score: 87
Period size: 22 Copynumber: 9.5 Consensus size: 24
1204100 AATATATGAT
*
1204110 AATAT-ATAATATATAGTTTTGTCAA
1 AATATAAT-ATATATAGTTTT-TGAA
* * *
1204135 AAAAT-A-ATATATGGGTTTTGAA
1 AATATAATATATATAGTTTTTGAA
* * * *
1204157 AATAT-ATA-GTATGGTTTCTAAA
1 AATATAATATATATAGTTTTTGAA
*
1204179 AACAT-ATAT-TATAGTTTTTGAA
1 AATATAATATATATAGTTTTTGAA
* **
1204201 AACAT-AT-TATATAGTTTTAAAAAA
1 AATATAATATATATAGTTTT--TGAA
1204225 ACATATAATATATATA-TTTTT-AA
1 A-ATATAATATATATAGTTTTTGAA
* *
1204248 AA-A-CATATAGTATAGTTTTTAAA
1 AATATAATATA-TATAGTTTTTGAA
* * * *
1204271 AACATATTATTATATA-ATTATGAAA
1 AATATAATA-TATATAGTTTTTG-AA
1204296 ACATATAATATATATAGTTTTTG-A
1 A-ATATAATATATATAGTTTTTGAA
1204320 AATAT-ATATAT
1 AATATAATATAT
1204331 TTGAAAACAT
Statistics
Matches: 152, Mismatches: 27, Indels: 37
0.70 0.12 0.17
Matches are distributed among these distances:
20 5 0.03
21 6 0.04
22 63 0.41
23 22 0.14
24 9 0.06
25 23 0.15
26 18 0.12
27 6 0.04
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (24 bp):
AATATAATATATATAGTTTTTGAA
Found at i:1204354 original size:21 final size:21
Alignment explanation
Indices: 1204320--1204368 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1204310 TAGTTTTTGA
1204320 AATATATATATTTGAAAACAT
1 AATATATATATTTGAAAACAT
* *
1204341 ATTATATGAT-TTTGAAAATAT
1 AATATAT-ATATTTGAAAACAT
1204362 AATATAT
1 AATATAT
1204369 TGTATAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
AATATATATATTTGAAAACAT
Found at i:1204368 original size:26 final size:28
Alignment explanation
Indices: 1204339--1204403 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
1204329 ATTTGAAAAC
1204339 ATATTATAT-GATTTTGAAAATATA-AT
1 ATATTATATAGATTTTGAAAATATATAT
* * * *
1204365 ATATTGTATAGTTTTTTAATATATATAT
1 ATATTATATAGATTTTGAAAATATATAT
1204393 ATATATATATA
1 ATAT-TATATA
1204404 TATATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 8 0.26
27 12 0.39
28 6 0.19
29 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (28 bp):
ATATTATATAGATTTTGAAAATATATAT
Found at i:1204388 original size:2 final size:2
Alignment explanation
Indices: 1204383--1204420 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1204373 TAGTTTTTTA
1204383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1204421 TAAGCTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1205699 original size:13 final size:13
Alignment explanation
Indices: 1205651--1205701 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1205641 CTTGTAAATA
1205651 TTTATTTTTTTA-T
1 TTTA-TTTTTTACT
*
1205664 TTAATGTTTTTACT
1 TTTAT-TTTTTACT
*
1205678 TTTATTTTTTATT
1 TTTATTTTTTACT
1205691 TTGTATTTTTT
1 TT-TATTTTTT
1205702 TTATTTAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 1 0.03
13 18 0.56
14 13 0.41
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTATTTTTTACT
Found at i:1209087 original size:21 final size:21
Alignment explanation
Indices: 1209061--1209120 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
1209051 AAGGAACAAA
*
1209061 CACTGGACATACCTCATCAAG
1 CACTGGACACACCTCATCAAG
*
1209082 CACTGGACACATCTCATCAAG
1 CACTGGACACACCTCATCAAG
*
1209103 CACTAGACACACCTCATC
1 CACTGGACACACCTCATC
1209121 CTCACAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.37, G:0.12, T:0.18
Consensus pattern (21 bp):
CACTGGACACACCTCATCAAG
Found at i:1215534 original size:21 final size:20
Alignment explanation
Indices: 1215506--1215545 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1215496 CATTGCGGGA
*
1215506 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
1215526 ATTTCATGGCTTCAACAAAA
1 ATTT-ATGGCCTCAACAAAA
1215546 ACCTTGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:1229441 original size:72 final size:72
Alignment explanation
Indices: 1229319--1229474 Score: 190
Period size: 72 Copynumber: 2.2 Consensus size: 72
1229309 ATTCAATCTA
* * * * ** *
1229319 GACTCAACTTTACGATGAATGAGTCACCAACGATTTCAACTTCACGATGAATTATATCATGCCCA
1 GACTAAACTTCACGACGAATGAGTCACCAACGAATTCAACTTCACGATGAAGGATATCATGCACA
1229384 ATAGATT
66 ATAGATT
* *
1229391 GACTAAACTTCACGACGAATGAGTCACCTAA-GAATTCAACTTCATGATGAAGGATATCTTGCAC
1 GACTAAACTTCACGACGAATGAGTCACC-AACGAATTCAACTTCACGATGAAGGATATCATGCAC
*
1229455 AATATATT
65 AATAGATT
1229463 GACTCAAA-TTCA
1 GACT-AAACTTCA
1229475 TGGCAAAGGA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
72 67 0.93
73 5 0.07
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (72 bp):
GACTAAACTTCACGACGAATGAGTCACCAACGAATTCAACTTCACGATGAAGGATATCATGCACA
ATAGATT
Found at i:1230084 original size:20 final size:21
Alignment explanation
Indices: 1230012--1230085 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
1230002 AATATATGGT
* *
1230012 TTTTGAAAATATATAGTATAA
1 TTTTAAAAACATATAGTATAA
*
1230033 TTTCTAAAAACATATAGTATAGT
1 TTT-TAAAAACATATAGTATA-A
*
1230056 TTTTGAAAACATATTA-TATAA
1 TTTTAAAAACATA-TAGTATAA
1230077 TTTTAAAAA
1 TTTTAAAAA
1230086 AAACATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 11 0.25
22 28 0.64
23 5 0.11
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (21 bp):
TTTTAAAAACATATAGTATAA
Found at i:1230113 original size:26 final size:25
Alignment explanation
Indices: 1230038--1230141 Score: 65
Period size: 26 Copynumber: 4.2 Consensus size: 25
1230028 TATAATTTCT
* *
1230038 AAAAACATATA-GTATA-GTTTTTG
1 AAAAACATATATATATATTTTTTTG
* ***
1230061 -AAAACATAT-TATATAATTTTAAA
1 AAAAACATATATATATATTTTTTTG
1230084 AAAAACATATAATATATATTTTTTTG
1 AAAAACATAT-ATATATATTTTTTTG
*
1230110 AAAATATAATATATTATATAGTTTTTTT-
1 AAAA-A-CATATA-TATATA-TTTTTTTG
1230138 AAAA
1 AAAA
1230142 TAAAAAGTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
22 13 0.21
23 3 0.05
24 9 0.15
26 14 0.23
27 2 0.03
28 14 0.23
29 7 0.11
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (25 bp):
AAAAACATATATATATATTTTTTTG
Found at i:1230113 original size:28 final size:28
Alignment explanation
Indices: 1230077--1230146 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
1230067 TATTATATAA
*
1230077 TTTTAAAAAAAACATATAATATATA-TTT
1 TTTTAAAATAAA-ATATAATATATAGTTT
* *
1230105 TTTTGAAAATATAATATATTATATAGTTT
1 TTTT-AAAATAAAATATAATATATAGTTT
1230134 TTTTAAAATAAAA
1 TTTTAAAATAAAA
1230147 AGTAAAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 23 0.64
29 13 0.36
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTTAAAATAAAATATAATATATAGTTT
Found at i:1230197 original size:21 final size:20
Alignment explanation
Indices: 1230160--1230215 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
1230150 AAAATGTAAT
1230160 ATATATATATATATTGAAAAC
1 ATAT-TATATATATTGAAAAC
* *
1230181 ATATTATATGATTTTGAAAAT
1 ATATTATAT-ATATTGAAAAC
*
1230202 ATAATATATTATAT
1 ATATTATA-TATAT
1230216 AGTTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.17
21 23 0.79
22 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
ATATTATATATATTGAAAAC
Found at i:1230221 original size:26 final size:28
Alignment explanation
Indices: 1230181--1230245 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
1230171 TATTGAAAAC
1230181 ATATTATAT-GATTTTGAAAATATA-AT
1 ATATTATATAGATTTTGAAAATATATAT
* * *
1230207 ATATTATATAGTTTTTTTAATATATATAT
1 ATATTATATAG-ATTTTGAAAATATATAT
1230236 ATATATATAT
1 ATAT-TATAT
1230246 TAAGCTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 9 0.28
27 1 0.03
28 11 0.34
29 6 0.19
30 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (28 bp):
ATATTATATAGATTTTGAAAATATATAT
Found at i:1231547 original size:26 final size:26
Alignment explanation
Indices: 1231504--1231554 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1231494 ATTTTATGTT
*
1231504 CTTTTATTTTAGGTTTTTTACTTTTA
1 CTTTTATTTTAGGTTTTTTAATTTTA
*
1231530 CTTTTATTTTA-TTATTTTTAATTTT
1 CTTTTATTTTAGGT-TTTTTAATTTT
1231555 TATTTTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (26 bp):
CTTTTATTTTAGGTTTTTTAATTTTA
Found at i:1232772 original size:22 final size:22
Alignment explanation
Indices: 1232747--1232791 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1232737 TCAAAATGTG
1232747 CAAACAAGAGTAATGAATTGCT
1 CAAACAAGAGTAATGAATTGCT
* *
1232769 CAAATAAGGGTAATGAATTGCT
1 CAAACAAGAGTAATGAATTGCT
1232791 C
1 C
1232792 TACATTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.24
Consensus pattern (22 bp):
CAAACAAGAGTAATGAATTGCT
Found at i:1233282 original size:3 final size:3
Alignment explanation
Indices: 1233274--1233370 Score: 194
Period size: 3 Copynumber: 32.3 Consensus size: 3
1233264 GGTTAAAATA
1233274 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1233322 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1233370 A
1 A
1233371 GGAGGAGGAG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1233375 original size:3 final size:3
Alignment explanation
Indices: 1233369--1233413 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1233359 TGATGATGAT
1233369 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1233414 AAGTTAACGG
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:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:1235782 original size:169 final size:169
Alignment explanation
Indices: 1235504--1235952 Score: 467
Period size: 169 Copynumber: 2.7 Consensus size: 169
1235494 CACTATTTAT
* * * * *
1235504 GTCAATCATGCATTATGTTTGATGGGATAAGACACTATGATAT-GACAGAGATTCTCT-GAAAAA
1 GTCAATCATGCCTTATGTTTGATGGGATAAAACAC-ATGACATGGA-AGAAATTCTCTAGAAAAG
* * * * ** * * * *
1235567 GAAAAAACGCTTATTGTGGAAGGAGCCTTTCCTTTTAGCCAGATTTATTTGCATATTTCAGTCAA
64 GAAAAAACGCTTCTTGTGGAACGAGCCTTTCTTTTTTGTTAGATTTATCTACATACTTCAATCAA
* * *
1235632 TTATATGTAGATATAATGTTCCCATTTGAGGCACTACTCAC
129 TTATATGAAAATATAATGTTCCCAGTTGAGGCACTACTCAC
* * * * * *
1235673 GTTAATC-T-CATTTATGTTTGGTGGGATAAAACATTATGACATGGAAGAGATTTTCTA-AAAAT
1 GTCAATCATGC-CTTATGTTTGATGGGATAAAACA-CATGACATGGAAGAAATTCTCTAGAAAA-
* **** *
1235735 GGCAAAAGTTTTTCTTGTGCAACGAGCCTTTCTTTTTTGTTAGATTTATCTACATACTTCAATCA
63 GGAAAAAACGCTTCTTGTGGAACGAGCCTTTCTTTTTTGTTAGATTTATCTACATACTTCAATCA
* ** * * *
1235800 ATTATATGAAAATATGATGTTCTTAGTTGGGGCACTATTCAT
128 ATTATATGAAAATATAATGTTCCCAGTTGAGGCACTACTCAC
* * *
1235842 GTCAATCATGCCTTATGTTTGATGGGATAAGACACATGACATGGTAGAAATTCTCTAGAAAAGTA
1 GTCAATCATGCCTTATGTTTGATGGGATAAAACACATGACATGGAAGAAATTCTCTAGAAAAGGA
1235907 AAAAACGCTTCTTGTGGAACGAGCCTTTCTTTTTTGTTAGATTTAT
66 AAAAACGCTTCTTGTGGAACGAGCCTTTCTTTTTTGTTAGATTTAT
1235953 ATGGTAGATA
Statistics
Matches: 224, Mismatches: 48, Indels: 16
0.78 0.17 0.06
Matches are distributed among these distances:
167 1 0.00
168 41 0.18
169 156 0.70
170 25 0.11
171 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (169 bp):
GTCAATCATGCCTTATGTTTGATGGGATAAAACACATGACATGGAAGAAATTCTCTAGAAAAGGA
AAAAACGCTTCTTGTGGAACGAGCCTTTCTTTTTTGTTAGATTTATCTACATACTTCAATCAATT
ATATGAAAATATAATGTTCCCAGTTGAGGCACTACTCAC
Found at i:1236822 original size:36 final size:36
Alignment explanation
Indices: 1236782--1236876 Score: 138
Period size: 36 Copynumber: 2.6 Consensus size: 36
1236772 AAATTTAACC
*
1236782 ATAAACATTACATTTAGGACATAAAAACAACAAACT
1 ATAAACATTACATTAAGGACATAAAAACAACAAACT
* * *
1236818 ATAAATATTATATTAAGTACATAAAAACAACAAACT
1 ATAAACATTACATTAAGGACATAAAAACAACAAACT
1236854 -TAACACATTACATTAAGGACATA
1 ATAA-ACATTACATTAAGGACATA
1236877 CACATACCAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 3 0.06
36 48 0.94
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (36 bp):
ATAAACATTACATTAAGGACATAAAAACAACAAACT
Found at i:1238920 original size:16 final size:16
Alignment explanation
Indices: 1238899--1238932 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1238889 GTACATTTAA
1238899 ATATAAAAATACTTTT
1 ATATAAAAATACTTTT
*
1238915 ATATAAATATACTTTT
1 ATATAAAAATACTTTT
1238931 AT
1 AT
1238933 TCATACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATAAAAATACTTTT
Found at i:1239020 original size:17 final size:18
Alignment explanation
Indices: 1238985--1239019 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1238975 AATACTAATT
1238985 TATACAAGAAAAATAAAA
1 TATACAAGAAAAATAAAA
1239003 TATAC-AGAAAATATAAA
1 TATACAAGAAAA-ATAAA
1239020 TTCAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (18 bp):
TATACAAGAAAAATAAAA
Found at i:1241038 original size:26 final size:26
Alignment explanation
Indices: 1241009--1241064 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1240999 ATCGAGGTTG
* *
1241009 ATTTATTCATTTCAGAGCTTG-AGTGT
1 ATTTAGTCATTCCAGAGCTTGAAG-GT
*
1241035 ATTTAGTCATTCCAGGGCTTGAAGGT
1 ATTTAGTCATTCCAGAGCTTGAAGGT
1241061 ATTT
1 ATTT
1241065 TAGGTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.43
Consensus pattern (26 bp):
ATTTAGTCATTCCAGAGCTTGAAGGT
Found at i:1241101 original size:27 final size:28
Alignment explanation
Indices: 1241058--1241119 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
1241048 AGGGCTTGAA
*
1241058 GGTATTTTAGGTTATTTTACACTTCAGG
1 GGTATTTTAGGTTATTTTACACTTCAAG
**
1241086 GGTATTTT-GGTTATTTTACGGTTCAAG
1 GGTATTTTAGGTTATTTTACACTTCAAG
1241113 GGTATTT
1 GGTATTT
1241120 ATGTCATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.19, C:0.08, G:0.24, T:0.48
Consensus pattern (28 bp):
GGTATTTTAGGTTATTTTACACTTCAAG
Found at i:1241128 original size:27 final size:27
Alignment explanation
Indices: 1241058--1241128 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
1241048 AGGGCTTGAA
* *
1241058 GGTATTTTAGGTTATTTTACACTTCAGG
1 GGTATTTT-GGTCATTTTACACTTCAAG
* **
1241086 GGTATTTTGGTTATTTTACGGTTCAAG
1 GGTATTTTGGTCATTTTACACTTCAAG
1241113 GGTATTTAT-GTCATTT
1 GGTATTT-TGGTCATTT
1241129 CCTTCAGTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 29 0.76
28 9 0.24
ACGTcount: A:0.20, C:0.08, G:0.23, T:0.49
Consensus pattern (27 bp):
GGTATTTTGGTCATTTTACACTTCAAG
Found at i:1242842 original size:18 final size:18
Alignment explanation
Indices: 1242821--1242855 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1242811 ATTTGGTCCC
*
1242821 TTAATTAAATTAAATATT
1 TTAAATAAATTAAATATT
1242839 TTAAATAAATTAAATAT
1 TTAAATAAATTAAATAT
1242856 ATTTTACCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAATAAATTAAATATT
Found at i:1242943 original size:2 final size:2
Alignment explanation
Indices: 1242936--1242972 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1242926 TAAAAGTTAA
1242936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1242973 TAAATTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1243041 original size:2 final size:2
Alignment explanation
Indices: 1243030--1243068 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1243020 TGGCATTAAG
1243030 TA TA -A 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 TA TA TA
1243069 AATTATTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1243519 original size:88 final size:88
Alignment explanation
Indices: 1243370--1243550 Score: 328
Period size: 88 Copynumber: 2.1 Consensus size: 88
1243360 TCCGTCAACA
1243370 ATTAACAATTAATGACTTGATTGAGAACAATTAAATAGTTTAATAATCTGATTAACAAAATTGAA
1 ATTAACAATTAATGACTTGATTGAGAACAATTAAATAGTTTAATAATCTGATTAACAAAATTGAA
1243435 AGATTGATGATTAAAGTAAAATG
66 AGATTGATGATTAAAGTAAAATG
* *
1243458 ATTAACGATTAATGACTTGATTGAGAACAATTAAATAG-TTAGATAATTTGATTAACAAAATTGA
1 ATTAACAATTAATGACTTGATTGAGAACAATTAAATAGTTTA-ATAATCTGATTAACAAAATTGA
1243522 AAGATTGATGATTAAAGTAAAATG
65 AAGATTGATGATTAAAGTAAAATG
1243546 ATTAA
1 ATTAA
1243551 ATAATTAAAT
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
87 3 0.03
88 87 0.97
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (88 bp):
ATTAACAATTAATGACTTGATTGAGAACAATTAAATAGTTTAATAATCTGATTAACAAAATTGAA
AGATTGATGATTAAAGTAAAATG
Found at i:1244554 original size:2 final size:2
Alignment explanation
Indices: 1244547--1244639 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
1244537 GAAAGTAGAC
1244547 TA TA TA TA 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 TA TA TA TA
1244589 TA TA TA TA 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 TA TA TA TA
1244631 TA TA TA TA T
1 TA TA TA TA T
1244640 TAGTTTAAAC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1245373 original size:21 final size:20
Alignment explanation
Indices: 1245321--1245374 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1245311 TTTTGTTAAT
*
1245321 TTAAGATTATAT-ATATTTA
1 TTAAGATTATTTAATATTTA
* *
1245340 TTAATTATAATTTAATATTTA
1 TTAA-GATTATTTAATATTTA
1245361 TTAAGAATTATTTA
1 TTAAG-ATTATTTA
1245375 TTCTATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
21 18 0.67
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
TTAAGATTATTTAATATTTA
Found at i:1245493 original size:71 final size:71
Alignment explanation
Indices: 1245342--1245529 Score: 167
Period size: 71 Copynumber: 2.7 Consensus size: 71
1245332 TATATTTATT
* *
1245342 AATTATAATT-TA-ATATTTATTAAGAATTATTTATTCTATTAAATTATATTATTCCATTCCATT
1 AATTAAAATTATATATATTTATTAAGAATTATTTATTCTATTAAATTATATGATTCCATTCCATT
*
1245405 ATTATA
66 ATTAAA
* * * * * *
1245411 ATTTAATATTATATATATTTATTAAGAATTATTTTTTCTATTAGATTATACTGA-T-GATT-TAT
1 AATTAAAATTATATATATTTATTAAGAATTATTTATTCTATTAAATTATA-TGATTCCATTCCAT
1245473 ATATTAAA
65 -TATTAAA
* * * *
1245481 AATTAAGAATTATTTCT-TTTATT-A-AATTATATTATTTTAGTAAATTATA
1 AATTAA-AATTATATATATTTATTAAGAATTAT-TTATTCTATTAAATTATA
1245530 ATTTATTATA
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
68 6 0.06
69 24 0.25
70 22 0.23
71 42 0.44
72 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (71 bp):
AATTAAAATTATATATATTTATTAAGAATTATTTATTCTATTAAATTATATGATTCCATTCCATT
ATTAAA
Found at i:1245524 original size:18 final size:18
Alignment explanation
Indices: 1245488--1245529 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1245478 AAAAATTAAG
* *
1245488 AATTAT-TTCTTTTATTA
1 AATTATATTATTTTAGTA
1245505 AATTATATTATTTTAGTA
1 AATTATATTATTTTAGTA
1245523 AATTATA
1 AATTATA
1245530 ATTTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTATATTATTTTAGTA
Found at i:1245595 original size:13 final size:14
Alignment explanation
Indices: 1245571--1245619 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1245561 TTCTAATTAA
1245571 TAAATATATAATAT
1 TAAATATATAATAT
1245585 TAAAT-TATAATTAAT
1 TAAATATATAA-T-AT
*
1245600 AAATATATATAATAT
1 TAA-ATATATAATAT
1245615 TAAAT
1 TAAAT
1245620 TAAAAAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.17
14 8 0.28
15 8 0.28
16 3 0.10
17 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATATATAATAT
Found at i:1245610 original size:30 final size:28
Alignment explanation
Indices: 1245550--1245621 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
1245540 TATATATGAA
* * *
1245550 ATAATATTTATTTCTAATTAATAAATAT
1 ATAATATTAAATTATAATTAATAAATAT
1245578 ATAATATTAAATTATAATTAATAAATATAT
1 ATAATATTAAATTATAATTAAT-AA-ATAT
1245608 ATAATATTAAATTA
1 ATAATATTAAATTA
1245622 AAAAAGTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 19 0.49
29 2 0.05
30 18 0.46
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAATATTAAATTATAATTAATAAATAT
Found at i:1245612 original size:17 final size:15
Alignment explanation
Indices: 1245564--1245608 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
1245554 TATTTATTTC
1245564 TAATTAATAAATATA
1 TAATTAATAAATATA
*
1245579 TAA-TATTAAAT-TA
1 TAATTAATAAATATA
1245592 TAATTAATAAATATA
1 TAATTAATAAATATA
1245607 TA
1 TA
1245609 TAATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 5 0.19
14 14 0.54
15 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTAATAAATATA
Found at i:1249839 original size:15 final size:16
Alignment explanation
Indices: 1249821--1249853 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1249811 TTTTAAATTA
*
1249821 AAAATTTT-GTTTTTC
1 AAAATTTTCATTTTTC
1249836 AAAATTTTCATTTTTC
1 AAAATTTTCATTTTTC
1249852 AA
1 AA
1249854 TTTTGAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (16 bp):
AAAATTTTCATTTTTC
Found at i:1251616 original size:30 final size:30
Alignment explanation
Indices: 1251571--1251639 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
1251561 TTCTTTTGTA
*
1251571 CAAATGATCGATCCAAAAGTTTCTAGAATC
1 CAAAGGATCGATCCAAAAGTTTCTAGAATC
* * * *
1251601 CAAGGGATCGGTCCAAAAGTTTTTGGAATC
1 CAAAGGATCGATCCAAAAGTTTCTAGAATC
1251631 CAAAGGATC
1 CAAAGGATC
1251640 AATCTTTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (30 bp):
CAAAGGATCGATCCAAAAGTTTCTAGAATC
Found at i:1252933 original size:30 final size:30
Alignment explanation
Indices: 1252890--1253137 Score: 125
Period size: 30 Copynumber: 8.3 Consensus size: 30
1252880 TAGTTTACGC
*
1252890 ATTTTAATT-TTATCTTAAATTATTAAATAT
1 ATTTT-ATTCTTATCTTAACTTATTAAATAT
*
1252920 ATTTTATTCTTATCTTAACTTA--AAATTTT
1 ATTTTATTCTTATCTTAACTTATTAAA-TAT
* * *
1252949 ATTTTATTTTTATTTTAACTTA-AAAATAT
1 ATTTTATTCTTATCTTAACTTATTAAATAT
* * **
1252978 AGTTTATTCTTATCTTAATTTAAAAAAATAT
1 ATTTTATTCTTATCTTAACTT-ATTAAATAT
* *
1253009 AATTTATT-TCTAACTTAACTT-TTAAAAATAT
1 ATTTTATTCT-TATCTTAACTTATT--AAATAT
* * * *
1253040 ATCTTATTTTTATTTTAACTT-TGTACATAT
1 ATTTTATTCTTATCTTAACTTAT-TAAATAT
* * * * * ***
1253070 GTTATATTCTTAACTAAAATTATTAAACGC
1 ATTTTATTCTTATCTTAACTTATTAAATAT
* * *
1253100 ATTATT-TTCTCACCTTAAATTATTAAATAT
1 ATT-TTATTCTTATCTTAACTTATTAAATAT
*
1253130 AATTTATT
1 ATTTTATT
1253138 TTTCATATTT
Statistics
Matches: 165, Mismatches: 40, Indels: 26
0.71 0.17 0.11
Matches are distributed among these distances:
28 3 0.02
29 46 0.28
30 67 0.41
31 47 0.28
32 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTTTATTCTTATCTTAACTTATTAAATAT
Found at i:1252956 original size:29 final size:29
Alignment explanation
Indices: 1252890--1253060 Score: 148
Period size: 29 Copynumber: 5.7 Consensus size: 29
1252880 TAGTTTACGC
* *
1252890 ATTTTAATT-TTATCTTAAATTATTAAATAT
1 ATTTT-ATTCTTATCTTAACTTA-AAAATAT
* *
1252920 ATTTTATTCTTATCTTAACTTAAAATTTT
1 ATTTTATTCTTATCTTAACTTAAAAATAT
* *
1252949 ATTTTATTTTTATTTTAACTTAAAAATAT
1 ATTTTATTCTTATCTTAACTTAAAAATAT
* *
1252978 AGTTTATTCTTATCTTAATTTAAAAAAATAT
1 ATTTTATTCTTATCTTAACTT--AAAAATAT
* *
1253009 AATTTATT-TCTAACTTAACTTTTAAAAATAT
1 ATTTTATTCT-TATCTTAAC--TTAAAAATAT
* * *
1253040 ATCTTATTTTTATTTTAACTT
1 ATTTTATTCTTATCTTAACTT
1253061 TGTACATATG
Statistics
Matches: 115, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
29 51 0.44
30 18 0.16
31 43 0.37
32 1 0.01
33 2 0.02
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.56
Consensus pattern (29 bp):
ATTTTATTCTTATCTTAACTTAAAAATAT
Found at i:1252978 original size:58 final size:59
Alignment explanation
Indices: 1252890--1253002 Score: 165
Period size: 58 Copynumber: 1.9 Consensus size: 59
1252880 TAGTTTACGC
* *
1252890 ATTTTAATTTTATCTTAAATTATTAAATATATTTTATTCTTATCTTAACTTAAAATTTT
1 ATTTTAATTTTATCTTAAATTATAAAATATAGTTTATTCTTATCTTAACTTAAAATTTT
* * * *
1252949 ATTTTATTTTTATTTTAACTTA-AAAATATAGTTTATTCTTATCTTAATTTAAAA
1 ATTTTAATTTTATCTTAAATTATAAAATATAGTTTATTCTTATCTTAACTTAAAA
1253003 AAATATAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 29 0.60
59 19 0.40
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (59 bp):
ATTTTAATTTTATCTTAAATTATAAAATATAGTTTATTCTTATCTTAACTTAAAATTTT
Found at i:1253026 original size:31 final size:32
Alignment explanation
Indices: 1252914--1253061 Score: 93
Period size: 31 Copynumber: 4.9 Consensus size: 32
1252904 TTAAATTATT
* *
1252914 AAATATATTTTA-TTCTTATCTTAAC-TT-AA
1 AAATATAATTTATTTCTTAACTTAACTTTAAA
* * * **
1252943 AATTTTATTTTATTT-TTATTTTAAC-TT-AA
1 AAATATAATTTATTTCTTAACTTAACTTTAAA
* *
1252972 AAATATAGTTTA-TTCTTATCTTAA-TTTAAAA
1 AAATATAATTTATTTCTTAACTTAACTTT-AAA
*
1253003 AAATATAATTTATTTC-TAACTTAACTTTTAA
1 AAATATAATTTATTTCTTAACTTAACTTTAAA
**
1253034 AAATAT-ATCTTATTT-TTATTTTAACTTT
1 AAATATAAT-TTATTTCTTAACTTAACTTT
1253062 GTACATATGT
Statistics
Matches: 98, Mismatches: 12, Indels: 16
0.78 0.10 0.13
Matches are distributed among these distances:
28 2 0.02
29 42 0.43
30 4 0.04
31 44 0.45
32 6 0.06
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (32 bp):
AAATATAATTTATTTCTTAACTTAACTTTAAA
Found at i:1253236 original size:59 final size:63
Alignment explanation
Indices: 1253142--1253261 Score: 167
Period size: 59 Copynumber: 2.0 Consensus size: 63
1253132 TTTATTTTTC
* * *
1253142 ATATTTTATTATTCTCTTAACTTAAAAATTGATATTTTATTTTTATTTTAA-TTTAAAAATGT
1 ATATTTTATTATTATCTTAACTTAAAAATTGATATTTTACTTTTATCTTAATTTTAAAAATGT
* *
1253204 ATATTTTATTTTTATTTTAA-TTAAAAA-T-ATATTTTACTTTTATCTTAATTTTAAAAAT
1 ATATTTTATTATTATCTTAACTTAAAAATTGATATTTTACTTTTATCTTAATTTTAAAAAT
1253262 AAGATGATTG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 18 0.35
60 10 0.19
61 7 0.13
62 17 0.33
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (63 bp):
ATATTTTATTATTATCTTAACTTAAAAATTGATATTTTACTTTTATCTTAATTTTAAAAATGT
Found at i:1253262 original size:30 final size:30
Alignment explanation
Indices: 1253142--1253261 Score: 145
Period size: 31 Copynumber: 4.0 Consensus size: 30
1253132 TTTATTTTTC
* * *
1253142 ATATTTTATTATTCTCTTAACTTAAAAATT
1 ATATTTTATTTTTATCTTAATTTAAAAATT
*
1253172 GATATTTTATTTTTATTTTAATTTAAAAATGT
1 -ATATTTTATTTTTATCTTAATTTAAAAAT-T
*
1253204 ATATTTTATTTTTATTTTAA-TTAAAAA-T
1 ATATTTTATTTTTATCTTAATTTAAAAATT
*
1253232 ATATTTTACTTTTATCTTAATTTTAAAAAT
1 ATATTTTATTTTTATCTTAA-TTTAAAAAT
1253262 AAGATGATTG
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
28 19 0.24
30 14 0.18
31 45 0.57
32 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (30 bp):
ATATTTTATTTTTATCTTAATTTAAAAATT
Found at i:1255732 original size:120 final size:120
Alignment explanation
Indices: 1255519--1255761 Score: 486
Period size: 120 Copynumber: 2.0 Consensus size: 120
1255509 AGGGAGGATC
1255519 AGTGTGCTCCTCATATTCGTCCGTTTTGCTTTATTGAGGATTGGAATACCCACCCACAATTTCAA
1 AGTGTGCTCCTCATATTCGTCCGTTTTGCTTTATTGAGGATTGGAATACCCACCCACAATTTCAA
1255584 TCGTTTCTAGAATCAGTGTGGCAAGCTCATCACTCTTGGGAGGACAACATTGGAA
66 TCGTTTCTAGAATCAGTGTGGCAAGCTCATCACTCTTGGGAGGACAACATTGGAA
1255639 AGTGTGCTCCTCATATTCGTCCGTTTTGCTTTATTGAGGATTGGAATACCCACCCACAATTTCAA
1 AGTGTGCTCCTCATATTCGTCCGTTTTGCTTTATTGAGGATTGGAATACCCACCCACAATTTCAA
1255704 TCGTTTCTAGAATCAGTGTGGCAAGCTCATCACTCTTGGGAGGACAACATTGGAA
66 TCGTTTCTAGAATCAGTGTGGCAAGCTCATCACTCTTGGGAGGACAACATTGGAA
1255759 AGT
1 AGT
1255762 TTTGGGATTC
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (120 bp):
AGTGTGCTCCTCATATTCGTCCGTTTTGCTTTATTGAGGATTGGAATACCCACCCACAATTTCAA
TCGTTTCTAGAATCAGTGTGGCAAGCTCATCACTCTTGGGAGGACAACATTGGAA
Found at i:1262377 original size:25 final size:25
Alignment explanation
Indices: 1262349--1262397 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1262339 TTTTTTGAAA
*
1262349 TTTTGGCTTTTATTTTGTTTTTTTGT
1 TTTTGGCCTTT-TTTTGTTTTTTTGT
*
1262375 TTTTTGCCTTTTTTTGTTTTTTT
1 TTTTGGCCTTTTTTTGTTTTTTT
1262398 TTAAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.02, C:0.06, G:0.12, T:0.80
Consensus pattern (25 bp):
TTTTGGCCTTTTTTTGTTTTTTTGT
Found at i:1268946 original size:2 final size:2
Alignment explanation
Indices: 1268934--1268968 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1268924 TAAGTAATTA
1268934 AT AT A- 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
1268969 TCATTCACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1269019 original size:34 final size:35
Alignment explanation
Indices: 1268988--1269052 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 35
1268978 CGTAAATTGG
* *
1268988 TATTAAAT-TTATATG-TATTAAATG-TACAAA-T
1 TATTAAATGTTACATGTTACTAAATGTTACAAATT
1269019 TATTAAATGTTACATGTTACTAAATGTTACAAAT
1 TATTAAATGTTACATGTTACTAAATGTTACAAAT
1269053 GCTTATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 8 0.29
32 6 0.21
33 8 0.29
34 6 0.21
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (35 bp):
TATTAAATGTTACATGTTACTAAATGTTACAAATT
Found at i:1269203 original size:27 final size:27
Alignment explanation
Indices: 1269128--1269395 Score: 125
Period size: 27 Copynumber: 10.0 Consensus size: 27
1269118 TCACAATTGT
* *
1269128 ATAA-ATTTCATGCTTCGAGATGATGC
1 ATAATATTTCATCCTTTGAGATGATGC
* ** ** *
1269154 ACAATAGTTT-ATCAATCAAGATGATAC
1 ATAATA-TTTCATCCTTTGAGATGATGC
* *
1269181 ATAGTATTTCATCCTTTGGGATGATGC
1 ATAATATTTCATCCTTTGAGATGATGC
* * *
1269208 ACAATAGTTT-ATCATTCGAGATGAT-C
1 ATAATA-TTTCATCCTTTGAGATGATGC
* * * *
1269234 -TGCAGTATTCCATCATTTGTGATGATGC
1 AT--AATATTTCATCCTTTGAGATGATGC
* * * * * *
1269262 ATATTGTTCCACCCTTCGAGATGATGT
1 ATAATATTTCATCCTTTGAGATGATGC
* * *
1269289 ACAATGTTTCATCCTTTGTGATGATGC
1 ATAATATTTCATCCTTTGAGATGATGC
* * * * * **
1269316 ATAGTATTCCATTCTTCGAAATGATAT
1 ATAATATTTCATCCTTTGAGATGATGC
*
1269343 ATAATATTTCATCCTTTGTGATGATGC
1 ATAATATTTCATCCTTTGAGATGATGC
* *
1269370 ATAATATTACATTCC-TCGAGATGATG
1 ATAATATTTCA-TCCTTTGAGATGATG
1269396 TACTGTATTC
Statistics
Matches: 173, Mismatches: 59, Indels: 19
0.69 0.24 0.08
Matches are distributed among these distances:
26 9 0.05
27 153 0.88
28 10 0.06
29 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (27 bp):
ATAATATTTCATCCTTTGAGATGATGC
Found at i:1269204 original size:54 final size:53
Alignment explanation
Indices: 1269132--1269262 Score: 156
Period size: 54 Copynumber: 2.4 Consensus size: 53
1269122 AATTGTATAA
* *
1269132 ATTTCATGCTTCGAGATGATGCACAATAGTTTATCAATCAAGATGATACAT-AGT
1 ATTTCATCCTTTGAGATGATGCACAATAGTTTATCAATCAAGATGAT-C-TCAGT
* * *
1269186 ATTTCATCCTTTGGGATGATGCACAATAGTTTATCATTCGAGATGATCTGCAGT
1 ATTTCATCCTTTGAGATGATGCACAATAGTTTATCAATCAAGATGATCT-CAGT
* * *
1269240 ATTCCATCATTTGTGATGATGCA
1 ATTTCATCCTTTGAGATGATGCA
1269263 TATTGTTCCA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
52 1 0.01
53 1 0.01
54 65 0.97
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (53 bp):
ATTTCATCCTTTGAGATGATGCACAATAGTTTATCAATCAAGATGATCTCAGT
Found at i:1269280 original size:54 final size:54
Alignment explanation
Indices: 1269185--1269394 Score: 190
Period size: 54 Copynumber: 3.9 Consensus size: 54
1269175 TGATACATAG
* * * * * * * * *
1269185 TATTTCATCCTTTGGGATGATGCACAATAGTT-TATCATTCGAGATGATCTGCAG
1 TATTTCATCCTTTGTGATGATGCATAGTA-TTCCACCCTTCGAGATGATATACAA
* * * * *
1269239 TATTCCATCATTTGTGATGATGCATATTGTTCCACCCTTCGAGATGATGTACAA
1 TATTTCATCCTTTGTGATGATGCATAGTATTCCACCCTTCGAGATGATATACAA
* ** * *
1269293 TGTTTCATCCTTTGTGATGATGCATAGTATTCCATTCTTCGAAATGATATATAA
1 TATTTCATCCTTTGTGATGATGCATAGTATTCCACCCTTCGAGATGATATACAA
* * *
1269347 TATTTCATCCTTTGTGATGATGCATAATATTACATTCC-TCGAGATGAT
1 TATTTCATCCTTTGTGATGATGCATAGTATTCCA-CCCTTCGAGATGAT
1269395 GTACTGTATT
Statistics
Matches: 127, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
53 2 0.02
54 123 0.97
55 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (54 bp):
TATTTCATCCTTTGTGATGATGCATAGTATTCCACCCTTCGAGATGATATACAA
Found at i:1269334 original size:108 final size:108
Alignment explanation
Indices: 1269187--1269398 Score: 241
Period size: 108 Copynumber: 2.0 Consensus size: 108
1269177 ATACATAGTA
* * * * *
1269187 TTTCATCCTTTGGGATGATGCACAATAGTTTATCATTCGAGATGATCTGCAGTATTCCATCATTT
1 TTTCATCCTTTGGGATGATGCACAATAGTTCATCATTCGAAATGATATACAATATTCCATCATTT
* * *
1269252 GTGATGATGCATATTGTTCCA-CCCTTCGAGATGATGTACAATG
66 GTGATGATGCATAATATTACATCCC-TCGAGATGATGTACAATG
* * * * * *
1269295 TTTCATCCTTTGTGATGATGCATAGTA-TTCCATTC-TTCGAAATGATATATAATATTTCATCCT
1 TTTCATCCTTTGGGATGATGCACAATAGTT-CA-TCATTCGAAATGATATACAATATTCCATCAT
*
1269358 TTGTGATGATGCATAATATTACATTCCTCGAGATGATGTAC
64 TTGTGATGATGCATAATATTACATCCCTCGAGATGATGTAC
1269399 TGTATTCCAT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
107 2 0.02
108 80 0.93
109 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (108 bp):
TTTCATCCTTTGGGATGATGCACAATAGTTCATCATTCGAAATGATATACAATATTCCATCATTT
GTGATGATGCATAATATTACATCCCTCGAGATGATGTACAATG
Found at i:1274784 original size:259 final size:258
Alignment explanation
Indices: 1274129--1275015 Score: 1342
Period size: 257 Copynumber: 3.4 Consensus size: 258
1274119 CATCTTGCCC
* * * * * *
1274129 GAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGCCTGACAGATGATCC-GAA
1 GAAGGTCTTATAGATGGCCCGAAGGACTTATCATATTGTTCGAAAGACTTACAGATGA-CCTAAA
* * * * *
1274193 GGATTTAATCATCATGATCAAAAGACTTATTGATGTTCCGAAGGACTTACCGATTTTGGAAATAG
65 TGATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCGAAGGACTTACCGATTTTGGAAATAG
*
1274258 TTTACT-GGTAAGAATCTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA
130 TTTATTGGGTAAGAATCTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA
1274322 CAAAATGAGAAACTTTGGAAATTGTTTTCTCAATTTTTTTAAAATAATGTGGAAACATTCTGTCT
195 CAAAATGAGAAACTTT-GAAATTGTTTTCTCAATTTTTTTAAAATAATGTGGAAACATTCTGTCT
*
1274387 GAAGGTCTT-TGGATGGCCCGAAGGACTTATCATATTGTTCGAAAGACTTACAGATGACCTAAAT
1 GAAGGTCTTATAGATGGCCCGAAGGACTTATCATATTGTTCGAAAGACTTACAGATGACCTAAAT
*
1274451 GATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCGAATGACTTACCGATTTTGGAAATAGT
66 GATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCGAAGGACTTACCGATTTTGGAAATAGT
*
1274516 TTATTGGGTAAGAATCTTTGGAAATCGCCTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACAC
131 TTATTGGGTAAGAATCTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACAC
1274581 AAAATGAGAAACTTTAGAAATTGTTTTCTCAATTTTTTTAAAATAATGTGGAAACATTCTGTCT
196 AAAATGAGAAACTTT-GAAATTGTTTTCTCAATTTTTTTAAAATAATGTGGAAACATTCTGTCT
*
1274645 GAAGGTCTTATGGATGGCCCGAAGGACTTATCATATTGTTCGAAAGACTTACAGATGACCTAAAT
1 GAAGGTCTTATAGATGGCCCGAAGGACTTATCATATTGTTCGAAAGACTTACAGATGACCTAAAT
*
1274710 GATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCGAATGACTTACCGATTTTGGAAATAGT
66 GATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCGAAGGACTTACCGATTTTGGAAATAGT
* * *
1274775 TTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACA-
131 TTATTGGGTAAGAATCTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACAC
* * * * * * *
1274839 ATAAATGAGAAACTTTGAAAATTGCTTTCTC--GTTTTTCAAATTCATGTGAAAACA-TCATGGC
196 A-AAATGAGAAACTTTG-AAATTGTTTTCTCAATTTTTTTAAAATAATGTGGAAACATTC-TGTC
*
1274901 C
258 T
* * *
1274902 GAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTGCTT-GAAAGATTTACAGATGACCTGAA
1 GAAGGTCTTATAGATGGCCCGAAGGACTTATCATATTG-TTCGAAAGACTTACAGATGACCT-AA
* *
1274966 A-GATTTAATCATCATGCTCGAAAGAATTACTGATGGCCCGAAGGACTTAC
64 ATGATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCGAAGGACTTAC
1275016 TAAGTGAGAA
Statistics
Matches: 586, Mismatches: 35, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
256 4 0.01
257 230 0.39
258 146 0.25
259 206 0.35
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (258 bp):
GAAGGTCTTATAGATGGCCCGAAGGACTTATCATATTGTTCGAAAGACTTACAGATGACCTAAAT
GATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCGAAGGACTTACCGATTTTGGAAATAGT
TTATTGGGTAAGAATCTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACAC
AAAATGAGAAACTTTGAAATTGTTTTCTCAATTTTTTTAAAATAATGTGGAAACATTCTGTCT
Found at i:1276694 original size:2 final size:2
Alignment explanation
Indices: 1276687--1276714 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1276677 TATTGTTTAT
1276687 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
1276715 CACACACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1283377 original size:134 final size:134
Alignment explanation
Indices: 1283133--1283451 Score: 363
Period size: 134 Copynumber: 2.4 Consensus size: 134
1283123 ATGATTGTTT
* * ** ** *
1283133 TTCAGGGAAGATTGAATTAAACGTGATTTGCTTCGTTGCACTTCAAGAAAACCAAATATGAAAGA
1 TTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGTTCTTCAAGAAGACCAAATATGAAAGA
* * * * * * *
1283198 ACAAGAATCTGTTCCACTACTCTTTAGGGGATATCAGACTCGAGAAAATTTTTATCCACTTCAC-
66 ACAAGAATATGCTCAACTACTCTTTAGGAGAGATCAGACTCGAGAAAACTTTGATCCACTTCACT
1283262 CACTC
131 CA-TC
* * * * *
1283267 TTCAGGGAAGGTTGAATCGAATGTGATTTGCTTCACTGTTCTTCAGGAAGACTAAATCTGAAAGA
1 TTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGTTCTTCAAGAAGACCAAATATGAAAGA
* * *
1283332 AGAAGAATATGCTCAACTACTCTTTAGGAGAGATCAGACTTGAGAAGACTTTGATCCACTTCACT
66 ACAAGAATATGCTCAACTACTCTTTAGGAGAGATCAGACTCGAGAAAACTTTGATCCACTTCACT
*
1283397 GATC
131 CATC
* * * *
1283401 TTCAAGGAAGATTCAATCTAATGTGATTTGCTTCACT-TATCTTCATGAAGA
1 TTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGT-TCTTCAAGAAGA
1283452 TCGATCTTGA
Statistics
Matches: 155, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
133 1 0.01
134 153 0.99
135 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (134 bp):
TTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGTTCTTCAAGAAGACCAAATATGAAAGA
ACAAGAATATGCTCAACTACTCTTTAGGAGAGATCAGACTCGAGAAAACTTTGATCCACTTCACT
CATC
Found at i:1285514 original size:29 final size:27
Alignment explanation
Indices: 1285435--1285528 Score: 107
Period size: 28 Copynumber: 3.3 Consensus size: 27
1285425 AATGTAGTGA
1285435 TTGTAAAAATATAGGTTGTTATTGTAAT
1 TTGTAAAAATATA-GTTGTTATTGTAAT
*
1285463 ATGTAAAAATATGAGTTGTTATTGTAAT
1 TTGTAAAAATAT-AGTTGTTATTGTAAT
** *
1285491 TTGTAAAAAGTATATGTCATTATTTTAAT
1 TTGTAAAAA-TATA-GTTGTTATTGTAAT
*
1285520 TTATAAAAA
1 TTGTAAAAA
1285529 GATTTGTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 34 0.60
29 23 0.40
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (27 bp):
TTGTAAAAATATAGTTGTTATTGTAAT
Found at i:1285529 original size:29 final size:29
Alignment explanation
Indices: 1285481--1285644 Score: 147
Period size: 29 Copynumber: 5.7 Consensus size: 29
1285471 ATATGAGTTG
* * * *
1285481 TTATTGTAATTTGTAAAAAGTATATGTCA
1 TTATTGTAATTTATAAAAAGTATTTATCT
* * *
1285510 TTATTTTAATTTATAAAAAG-ATTTGTTT
1 TTATTGTAATTTATAAAAAGTATTTATCT
* *
1285538 TCTATTTTAAATTATAAAAA-TATTTATCCT
1 T-TATTGTAATTTATAAAAAGTATTTAT-CT
**
1285568 TTATTGTAATTTATAAGGAG-ATTTATCT
1 TTATTGTAATTTATAAAAAGTATTTATCT
* *
1285596 TCTATTATAATTTATAAAAAG-ATTTATCCA
1 T-TATTGTAATTTATAAAAAGTATTTAT-CT
1285626 TTATTGTAATTTATAAAAA
1 TTATTGTAATTTATAAAAA
1285645 AACTTTTGTC
Statistics
Matches: 112, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
28 9 0.08
29 99 0.88
30 4 0.04
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (29 bp):
TTATTGTAATTTATAAAAAGTATTTATCT
Found at i:1285572 original size:58 final size:58
Alignment explanation
Indices: 1285508--1285644 Score: 193
Period size: 58 Copynumber: 2.4 Consensus size: 58
1285498 AAGTATATGT
* * * * *
1285508 CATTATTTTAATTTATAAAAAGATTTGTTTTCTATTTTAAATTATAAAAATATTTATC
1 CATTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTATC
* ** *
1285566 CTTTATTGTAATTTATAAGGAGATTTATCTTCTATTATAATTTATAAAAAGATTTATC
1 CATTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTATC
1285624 CATTATTGTAATTTATAAAAA
1 CATTATTGTAATTTATAAAAA
1285645 AACTTTTGTC
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 67 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (58 bp):
CATTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTATC
Found at i:1285640 original size:87 final size:88
Alignment explanation
Indices: 1285511--1285672 Score: 202
Period size: 87 Copynumber: 1.8 Consensus size: 88
1285501 TATATGTCAT
* * ** * * * *
1285511 TATTTTAATTTATAAAAAGATTTGTTTTCTATTTTAAATTATAAAAATA-TTTATCCTTTATTGT
1 TATTATAATTTATAAAAAGATTTATCATCTATTGTAAATTATAAAAAAACTTTATCCTTAAATGT
1285575 AATTTATAAGGAGATTTATCTTC
66 AATTTATAAGGAGATTTATCTTC
* *
1285598 TATTATAATTTATAAAAAGATTTATCCAT-TATTGTAATTTATAAAAAAACTTTTGTCCTTAAAT
1 TATTATAATTTATAAAAAGATTTAT-CATCTATTGTAAATTATAAAAAAAC-TTTATCCTTAAAT
1285662 GTAATTTATAA
64 GTAATTTATAA
1285673 AAAATATTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
87 40 0.65
88 1 0.02
89 21 0.34
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (88 bp):
TATTATAATTTATAAAAAGATTTATCATCTATTGTAAATTATAAAAAAACTTTATCCTTAAATGT
AATTTATAAGGAGATTTATCTTC
Found at i:1286406 original size:30 final size:30
Alignment explanation
Indices: 1286372--1286433 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1286362 TAGGGAAATG
1286372 ATCTCAAGAAACACTAAAGTGAGGTTTCTA
1 ATCTCAAGAAACACTAAAGTGAGGTTTCTA
*
1286402 ATCTCAATAAACACTAAAGTGAGGTTTCTA
1 ATCTCAAGAAACACTAAAGTGAGGTTTCTA
1286432 AT
1 AT
1286434 GAAACGAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (30 bp):
ATCTCAAGAAACACTAAAGTGAGGTTTCTA
Found at i:1286673 original size:45 final size:45
Alignment explanation
Indices: 1286604--1286844 Score: 276
Period size: 45 Copynumber: 5.4 Consensus size: 45
1286594 GATACTACTG
* * *
1286604 AAAAG-TTGACTCCTCTCCGCGAGAAAGTCAAGAATCACAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * *** * *
1286648 GAAAGATTGACTTCTCTTTTTGAGAAAGTCAAGAGTAACAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * *
1286693 AAAAGATTAACTCCTCTTCATC-AGAGAGTCAAGAATGAGAACACT
1 AAAAGATTGACTCCTCTTCA-CGAGAAAGTCAAGAATGACAACACT
*
1286738 AAAAGATTG-CATTCTCTTCACGAGAAAGTCAAGGAA-GACAACACT
1 AAAAGATTGAC-TCCTCTTCACGAGAAAGTCAA-GAATGACAACACT
*
1286783 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGGAA-GATAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAATGACAACACT
1286828 AAAAGATTGACTCCTCT
1 AAAAGATTGACTCCTCT
1286845 ATCAATTTGT
Statistics
Matches: 167, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
44 6 0.04
45 157 0.94
46 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (45 bp):
AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
Found at i:1287233 original size:41 final size:41
Alignment explanation
Indices: 1287188--1287292 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 41
1287178 AAGGTCTTAT
*
1287188 AGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAAA
1 AGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTAAA
* * * * * *
1287229 AGATGACCCAAAGGATTTAATCATCATGTTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTAAA
*
1287271 TGATGGCCTCG-AGGACTTATCA
1 AGATGGCC-CGAAGGACTTATCA
1287293 ATTTTGGAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 19 0.37
42 31 0.61
43 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTAAA
Found at i:1287741 original size:20 final size:20
Alignment explanation
Indices: 1287687--1287733 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1287677 AAAACACCTT
1287687 GCCCGAAGGTCTTATAAATG
1 GCCCGAAGGTCTTATAAATG
*
1287707 GCCCGAAGGTCTTATAGATG
1 GCCCGAAGGTCTTATAAATG
1287727 GCCCGAA
1 GCCCGAA
1287734 TGACTTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (20 bp):
GCCCGAAGGTCTTATAAATG
Found at i:1288025 original size:41 final size:41
Alignment explanation
Indices: 1287980--1288083 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 41
1287970 AAGGTCTTAT
* **
1287980 AGATGGCCCGAAGGACTTATCATCTTACTCGAAATCCTGAC
1 AGATGGCCCGAAGGACTTATCATCATACTCGAAAGACTGAC
* * * * * *
1288021 AGATGACTCGGAGGATTTAATCATCATACTCGAAAGATTTAC
1 AGATGGCCCGAAGGACTT-ATCATCATACTCGAAAGACTGAC
*
1288063 TGATGGCCCGAAGGACTTATC
1 AGATGGCCCGAAGGACTTATC
1288084 GATTTTGGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
41 17 0.35
42 31 0.65
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTATCATCATACTCGAAAGACTGAC
Found at i:1288172 original size:258 final size:257
Alignment explanation
Indices: 1287110--1288205 Score: 1290
Period size: 258 Copynumber: 4.2 Consensus size: 257
1287100 ATTTAATATT
* * * * *
1287110 TTAAATGAGAAACTTTAAAAATCACTTTCTCATTTTCTTACAAATACCATATGAAAGCATCTTAC
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTT-TTA-AAAT--CATTTGAAAACATCATAC
* * *
1287175 CCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAAAAGATGACCCAA
62 CCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGA
*
1287240 AGGATTTAATCATCATGTTCGAAAGACTTACTGATGGCCTCG-AGGACTTATCAATTTTGGAAAT
127 AGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCC-CGAAGGACTTATCAATTTTGGAAAT
* * * *
1287304 AGTCTATTGGGTAAGAAACTTTGGAAATCGCTTTCTTACGTTTCAAAAAAATT-ATTTTCTGAAA
191 AGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTC-AAAAATTTCATTTTCTGAAA
1287368 ACA
255 ACA
* * * * *
1287371 CTGAATGAGAAACTTTGAAAATCGTTTTCTCATTTTTTTCAAATTCATTTGAAAACATCCTACCC
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCA-TTTTTT-AAAATCATTTGAAAACATCATACCC
* ** * * *
1287436 AAAGGTCTTACGGATGGCCCGAATGAC-TATCATCTTGCTCGAAAGACTTACAGATGACTCGAAG
64 GAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAG
* * ** * *
1287500 GATTTAATCATCATGCTCGAAAGACTTACTAATGACCTTAATGACTT-GCTAATTTTGGAAATAG
129 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATC-AATTTTGGAAATAG
* * * *
1287564 TTTACT-AGTAAGAAAATTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTGAAAATA
193 TTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA
*
1287628 TTAAATGAGAAACTTTGAAAATCGCTTTCTCA-TTTTTAAAATTCATGTGAAAACACCTTGCCCG
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTAAAA-TCATTTG-AAA-A-------C-
*
1287692 AAGGTCTTATAAATGGCCCGAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTGCTC-AAAG
55 -A--TC--AT--A---CCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAG
* * *
1287756 CCTGACAAATGATCCCGAAGGTTTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
110 ACTGACAGATGA-CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
* * * *
1287821 TTATTAATTTTGGAAATAGTTTACTCGATAAGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAA
174 TTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAA
*
1287886 ATTTCATTTTCTGAAAATA
239 ATTTCATTTTCTGAAAACA
* * * * * *
1287905 CTGAATGAGAAACTTTGGAAACCGCTTTCTCATTTTTTGAAAATCATTTTAAAACATCATGCCCG
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTT-AAAATCATTTGAAAACATCATACCCG
* ** * *
1287970 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTACTCGAAATCCTGACAGATGACTCGGAGG
65 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGG
* * *
1288035 ATTTAATCATCATACTCGAAAGATTTACTGATGGCCCGAAGGACTTATCGATTTTGGAAATAGTT
130 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTT
*
1288100 TATTGGGTAAGAAACTTTGGAAA-CTGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA
195 TACTGGGTAAGAAACTTTGGAAATC-GCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA
* *
1288163 TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAAT
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTAAAAT
1288206 AACTTAATTG
Statistics
Matches: 716, Mismatches: 85, Indels: 72
0.82 0.10 0.08
Matches are distributed among these distances:
254 3 0.00
255 11 0.02
256 10 0.01
257 80 0.11
258 290 0.41
259 54 0.08
261 32 0.04
262 5 0.01
263 2 0.00
264 1 0.00
265 2 0.00
266 1 0.00
267 1 0.00
268 2 0.00
269 1 0.00
270 1 0.00
272 1 0.00
275 40 0.06
276 81 0.11
277 84 0.12
278 10 0.01
279 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (257 bp):
TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTAAAATCATTTGAAAACATCATACCCGA
AGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGA
TTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTTT
ACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA
Found at i:1292774 original size:25 final size:25
Alignment explanation
Indices: 1292740--1292827 Score: 167
Period size: 25 Copynumber: 3.5 Consensus size: 25
1292730 CACATGTTGA
1292740 CTACCCATACATGGTATGATAAGTC
1 CTACCCATACATGGTATGATAAGTC
1292765 CTACCCATACATGGTATGATAAGTC
1 CTACCCATACATGGTATGATAAGTC
1292790 CTACCCATACATGGTATGATAAGTC
1 CTACCCATACATGGTATGATAAGTC
*
1292815 CTACCCAAACATG
1 CTACCCATACATG
1292828 CTTTCTACCC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (25 bp):
CTACCCATACATGGTATGATAAGTC
Found at i:1292891 original size:16 final size:16
Alignment explanation
Indices: 1292870--1292907 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1292860 AAATCCTAAC
1292870 CGCATGATATCTAATT
1 CGCATGATATCTAATT
1292886 CGCATGATATCTAATT
1 CGCATGATATCTAATT
*
1292902 TGCATG
1 CGCATG
1292908 CTTGTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (16 bp):
CGCATGATATCTAATT
Found at i:1294883 original size:39 final size:39
Alignment explanation
Indices: 1294829--1294904 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
1294819 AAACCTACTT
1294829 GGTTAAATAAACTTCAAAACAACTCAAAAATTATTCATA
1 GGTTAAATAAACTTCAAAACAACTCAAAAATTATTCATA
1294868 GGTTAAATAAACTTCAAAACAACTCAAAAATTATTCA
1 GGTTAAATAAACTTCAAAACAACTCAAAAATTATTCA
1294905 AAAAGTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.28
Consensus pattern (39 bp):
GGTTAAATAAACTTCAAAACAACTCAAAAATTATTCATA
Found at i:1295557 original size:14 final size:14
Alignment explanation
Indices: 1295535--1295573 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1295525 ATACACAAAT
*
1295535 GCATGGTGATTAGT
1 GCATGGTGATTAGC
* *
1295549 GCGTGGTGACTAGC
1 GCATGGTGATTAGC
1295563 GCATGGTGATT
1 GCATGGTGATT
1295574 TGTCTTTTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.13, G:0.38, T:0.31
Consensus pattern (14 bp):
GCATGGTGATTAGC
Found at i:1296037 original size:45 final size:44
Alignment explanation
Indices: 1295923--1296097 Score: 179
Period size: 45 Copynumber: 3.9 Consensus size: 44
1295913 TTGTGTTGCT
* * * **
1295923 AAAAATAAAATCAAATGATTAGTTCCTTTTGATTATTGAGTCGCC
1 AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTG-GTTGAG
* *
1295968 AAAATTTAAAATCAAAGGACTAGTTCCTTTTGATTACTTGGTTGTG
1 AAAA-TTAAAATCAAAGGATTAGTTCCTTTTGATTA-TTGGTTGAG
* * * * *
1296014 TAAATTAAAATCAAAGAATTAGTTCCTATCGAATATTGGTTTGAG
1 AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGG-TTGAG
* * *
1296059 AAAATTAAAATAAAAGGATTAGTTCATTTTTATTATTGG
1 AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGG
1296098 ATTACTAAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
44 4 0.04
45 65 0.61
46 34 0.32
47 3 0.03
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (44 bp):
AAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGGTTGAG
Found at i:1296287 original size:61 final size:58
Alignment explanation
Indices: 1296216--1296404 Score: 199
Period size: 58 Copynumber: 3.3 Consensus size: 58
1296206 AAAGAATATA
* * ***
1296216 AAGG-AAATAAATAACTGAATTTATTTCATTGTTAAAATCTTGCGTTGATTCTAACTTTGT
1 AAGGAAAATAAATAACTAAATTTATTTC-TT-TGAAAATCTT-AAATGATTCTAACTTTGT
* *
1296276 AAGGAAAATAAATAATTAAATTTATTTCTTTGAGAATCTTAAATGATTCTAACTTTGT
1 AAGGAAAATAAATAACTAAATTTATTTCTTTGAAAATCTTAAATGATTCTAACTTTGT
* ** *
1296334 AAGGAAAATGAATAGTTAAATTTATTT-TCTT-AAGAGTCTTAAATGATTCTAACTTTGT
1 AAGGAAAATAAATAACTAAATTTATTTCT-TTGAA-AATCTTAAATGATTCTAACTTTGT
1296392 AA-GAAAA-AAATAA
1 AAGGAAAATAAATAA
1296405 ATTGTCGAAT
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
56 4 0.04
57 7 0.06
58 67 0.59
59 8 0.07
60 6 0.05
61 21 0.19
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (58 bp):
AAGGAAAATAAATAACTAAATTTATTTCTTTGAAAATCTTAAATGATTCTAACTTTGT
Found at i:1296403 original size:118 final size:118
Alignment explanation
Indices: 1296261--1296541 Score: 324
Period size: 118 Copynumber: 2.4 Consensus size: 118
1296251 AATCTTGCGT
* ** *
1296261 TGATTCTAACTTTGTAAG--GAAAATAAATAATTAAATTTA-TTTCTTTGAGAATCTTAAATGAT
1 TGATTCTAACTTTGTAAGAAAAAAATAAATTGTTAAATTTATTTTC-TTGAGAATCGTAAATGAT
* * *
1296323 TCTA-ACTTTGTAAGGA-AAATGAATAGTTAAATTTATTTTCTTAAGAGTCTTAAA
65 TCTATA-TTT-TAAGAAGAAATAAATAGTTAAATTTATTTTCTTAAGAATCTTAAA
** ***
1296377 TGATTCTAACTTTGTAAGAAAAAAATAAATTGTCGAATTTATTTTCTTGAGAATCGTGGGTGATT
1 TGATTCTAACTTTGTAAGAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCGTAAATGATT
* *
1296442 CTATATTTTAAGAAGAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAA
66 CTATATTTTAAGAAGAAATAAATAGTTAAATTTATTTTCTTAAGAATCTTAAA
* * * *
1296495 AGATT-TTATTTTGTAA-AAATAAATAAATTGTTAAATTTATTTTCTTG
1 TGATTCTAACTTTGTAAGAAAAAAATAAATTGTTAAATTTATTTTCTTG
1296542 GAAATCTAGA
Statistics
Matches: 140, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
116 46 0.33
117 14 0.10
118 75 0.54
119 5 0.04
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.43
Consensus pattern (118 bp):
TGATTCTAACTTTGTAAGAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCGTAAATGATT
CTATATTTTAAGAAGAAATAAATAGTTAAATTTATTTTCTTAAGAATCTTAAA
Found at i:1296548 original size:58 final size:58
Alignment explanation
Indices: 1296261--1296541 Score: 300
Period size: 58 Copynumber: 4.8 Consensus size: 58
1296251 AATCTTGCGT
** **
1296261 TGATTCTAACTTTGTAAGGAAAATAAATAATTAAATTTA-TTTCTTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAAAAAAATAAATTGTTAAATTTATTTTC-TTGAGAATCTTAAA
** * * * *
1296319 TGATTCTAACTTTGTAAGGAAAATGAATAGTTAAATTTATTTTCTTAAGAGTCTTAAA
1 TGATTCTAACTTTGTAAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAA
** * ***
1296377 TGATTCTAACTTTGTAAGAAAAAAATAAATTGTCGAATTTATTTTCTTGAGAATCGTGGG
1 TGATTCTAACTTTGT-A-AAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAA
*
1296437 TGATTCTATA-TTT-TAAGAAGAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAA
1 TGATTCTA-ACTTTGTAA-AAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAA
* * *
1296495 AGATT-TTATTTTGTAAAAATAAATAAATTGTTAAATTTATTTTCTTG
1 TGATTCTAACTTTGTAAAAA-AAATAAATTGTTAAATTTATTTTCTTG
1296542 GAAATCTAGA
Statistics
Matches: 189, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
56 1 0.01
57 7 0.04
58 133 0.70
59 6 0.03
60 41 0.22
61 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.43
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAA
Found at i:1296771 original size:39 final size:39
Alignment explanation
Indices: 1296707--1296878 Score: 190
Period size: 39 Copynumber: 4.4 Consensus size: 39
1296697 TTCTAGTTTA
*
1296707 TAAAAGGAAATAAATTGTATA-ATTTATTTTTC-TGTTTTG
1 TAAAAGGAAATAAATCGT-TAGATTTA-TTTTCATGTTTTG
* * *
1296746 TAAAAGGAAATATATCGTTAGATTTATTTTCTTATTTTG
1 TAAAAGGAAATAAATCGTTAGATTTATTTTCATGTTTTG
* *
1296785 TAAAAGGAAATAAGTTGTT-GATTTATTTTCATGTTTTG
1 TAAAAGGAAATAAATCGTTAGATTTATTTTCATGTTTTG
* * *
1296823 TAGAAA-GAAATAAATCGTAAAATTTTATTTTAATGTTTTG
1 TA-AAAGGAAATAAATCGTTAGA-TTTATTTTCATGTTTTG
*
1296863 TAAAATGAAATAAATC
1 TAAAAGGAAATAAATC
1296879 CAATTCATAT
Statistics
Matches: 114, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
38 36 0.32
39 50 0.44
40 28 0.25
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.45
Consensus pattern (39 bp):
TAAAAGGAAATAAATCGTTAGATTTATTTTCATGTTTTG
Found at i:1296840 original size:77 final size:79
Alignment explanation
Indices: 1296707--1296877 Score: 215
Period size: 78 Copynumber: 2.2 Consensus size: 79
1296697 TTCTAGTTTA
* * *
1296707 TAAAAGGAAATAAATTGTATAATTTATTTTTCTGTTTTGTAAAAGGAAATATATCGTTAGA-TTT
1 TAAAAGGAAATAAATTGTATAATTTATTTTTCTGTTTTGTAAAAGGAAATAAATCGTAAAATTTT
**
1296771 ATTTTCTTATTTTG
66 ATTTTAATATTTTG
* *
1296785 TAAAAGGAAATAAGTTGT-TGATTTA-TTTTCATGTTTTGTAGAAA-GAAATAAATCGTAAAATT
1 TAAAAGGAAATAAATTGTATAATTTATTTTTC-TGTTTTGTA-AAAGGAAATAAATCGTAAAATT
*
1296847 TTATTTTAATGTTTTG
64 TTATTTTAATATTTTG
*
1296863 TAAAATGAAATAAAT
1 TAAAAGGAAATAAAT
1296878 CCAATTCATA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
76 5 0.06
77 28 0.35
78 47 0.59
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (79 bp):
TAAAAGGAAATAAATTGTATAATTTATTTTTCTGTTTTGTAAAAGGAAATAAATCGTAAAATTTT
ATTTTAATATTTTG
Found at i:1300170 original size:64 final size:65
Alignment explanation
Indices: 1300094--1300230 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 65
1300084 TACACTAGGG
* * * * * *
1300094 GTGCATCAGTACACTAATTACATTCGATGTTTC-AAAGAGCCAGGAGTGCATTAATGCATGGTTT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCAATGCATGGCTT
* * * ** *
1300158 GTGCATCGGTACACAAAATGCATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCAATGCATGGCTT
1300223 GTGCATCG
1 GTGCATCG
1300231 ATGCATGGCT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
64 28 0.47
65 32 0.53
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCAATGCATGGCTT
Found at i:1300228 original size:19 final size:19
Alignment explanation
Indices: 1300204--1300247 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1300194 ATATTCAAGA
1300204 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
1300223 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
1300242 GTGCAT
1 GTGCAT
1300248 TAGTACACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTT
Found at i:1300634 original size:18 final size:18
Alignment explanation
Indices: 1300611--1300648 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1300601 ATTTTCTTTC
*
1300611 AAAAAATCAATTTTTAAA
1 AAAAAATCAATTTTGAAA
1300629 AAAAAATCAATTTTGAAA
1 AAAAAATCAATTTTGAAA
1300647 AA
1 AA
1300649 TTACTCCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAAATCAATTTTGAAA
Found at i:1302951 original size:23 final size:23
Alignment explanation
Indices: 1302917--1302990 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
1302907 AACAGCAGAG
1302917 TGCATCGATGCATATTCAAGGAA
1 TGCATCGATGCATATTCAAGGAA
* * *
1302940 TGCATCGGTGCATCTTCATGG--
1 TGCATCGATGCATATTCAAGGAA
* *
1302961 TGTATCGATGCACATTCAA-GAGA
1 TGCATCGATGCATATTCAAGGA-A
1302984 TGCATCG
1 TGCATCG
1302991 GTACACTATC
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.03
21 14 0.36
23 24 0.62
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (23 bp):
TGCATCGATGCATATTCAAGGAA
Found at i:1302987 original size:44 final size:43
Alignment explanation
Indices: 1302915--1303015 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 43
1302905 TGAACAGCAG
* * *
1302915 AGTGCATCGATGCATATTCAAGGAATGCATCGGTGCATCT-TCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACA-CTATC-T
*
1302959 GGTGTATCGATGCACATTCAA-GAGATGCATCGGTACACTATCT
1 AGTGTATCGATGCACATTCAAGGA-ATGCATCGGTACACTATCT
1303002 AGTGTATCGATGCA
1 AGTGTATCGATGCA
1303016 TTATGCACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 18 0.36
44 32 0.64
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTATCT
Found at i:1307605 original size:20 final size:21
Alignment explanation
Indices: 1307566--1307605 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1307556 GAAGTTTTAA
* *
1307566 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
1307587 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
1307606 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:1309760 original size:64 final size:65
Alignment explanation
Indices: 1309674--1309829 Score: 226
Period size: 65 Copynumber: 2.4 Consensus size: 65
1309664 ATAAGACTTA
* * * * * *
1309674 GTGCATCGGTACACTAATTGCATTCGATGTTTCAAAGA-GCT-AGGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAA-ATACTCAAGAGTGCAACGATGCATGGCT
1309737 T
65 T
*
1309738 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCAACGATGCATGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATACTCAAGAGTGCAACGATGCATGGCTT
1309803 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
1309830 AATGGGTATG
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
63 1 0.01
64 35 0.42
65 47 0.57
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATACTCAAGAGTGCAACGATGCATGGCTT
Found at i:1310608 original size:19 final size:20
Alignment explanation
Indices: 1310562--1310605 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1310552 CTCTAAATCA
*
1310562 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATTCCATTTTG
1310582 TTTTTCAAAA-TCCAATTTTG
1 TTTTTCAAAATTCC-ATTTTG
1310602 TTTT
1 TTTT
1310606 CAACTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTCAAAATTCCATTTTG
Found at i:1311790 original size:19 final size:19
Alignment explanation
Indices: 1311734--1311804 Score: 106
Period size: 20 Copynumber: 3.6 Consensus size: 19
1311724 CTGCACATGC
*
1311734 AGTTTCAAAACTTTGAAGAA
1 AGTTTCAAAACTTTG-TGAA
1311754 AGTTTCAAAACTTTTGTGAA
1 AGTTTCAAAAC-TTTGTGAA
1311774 AGTTTCAAAACTTTGTGAA
1 AGTTTCAAAACTTTGTGAA
*
1311793 AGTATCAAAACT
1 AGTTTCAAAACT
1311805 CTTACTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 19 0.40
20 25 0.52
21 4 0.08
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (19 bp):
AGTTTCAAAACTTTGTGAA
Found at i:1311927 original size:19 final size:19
Alignment explanation
Indices: 1311903--1311954 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1311893 AATCTTAAAA
*
1311903 AAAGTTTCAAAACTCTTAC
1 AAAGTTTCAAAACTCGTAC
1311922 AAAGTTTCAAAACTCGTAC
1 AAAGTTTCAAAACTCGTAC
*
1311941 AAAGTTTCCAAACT
1 AAAGTTTCAAAACT
1311955 GTTAACAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (19 bp):
AAAGTTTCAAAACTCGTAC
Found at i:1314288 original size:604 final size:601
Alignment explanation
Indices: 1313370--1314518 Score: 1669
Period size: 604 Copynumber: 1.9 Consensus size: 601
1313360 AACGGTAGAA
* *
1313370 TAGTTCAAGGACATCACACTACTGGTCAGCCAGTAAGTAAATATGTTTTCACAATGGATAGATCA
1 TAGTTCAAGGACATCAAACTACTGGTCAGCCAGTAAGTAAATATGTTTTCACAAGGGATAGATCA
* *
1313435 AAGGAGGACAACTACCTATCCTAAGCAACTATCAATTGTAGATTCTATCACCACATAGGGTCAAA
66 AAGGAGAACAACTACATATCCTAAGCAACTATCAATTGTAGATTCTATCACCACATAGGGTCAAA
* *
1313500 ATGTTTTTAATAAATTGATAATTTCCTTCACGCGGAGAATGTTAGAAAAATTCGATAATTTTATA
131 ATGTTTTTAATAAATTGATAATTTCATTCACGCGGAGAATGTTAGAAAAATTCGATAATTTTAGA
* ** * *
1313565 GCTTTGAATGAGAAATCGATCCAAATATTGTTGAGGAAAATGTGGAACCAATTGTTGGTTCGTAC
196 GCTTTGAATAAGAAATCGATCCAAATATTGTTGAAAAAAATGTGGAACAAATTGTTGATTCGTAC
* * * * *
1313630 ATGTGTAGACGTGCATGATGTAGGTAACATGAATGTCTGAACCGATAAGGCTCTTTTGTGGGCTT
261 ATGTGTAGACATGCACGATGTAGGTAACATAAATGTCTGAACAGATAAGGCTCTTTTGTGCGCTT
*
1313695 ACGGATATTTTAATCCAAATGTGAAATATTT-TCATCAAATAAAGCATATCTTTTA-AAAAAATT
326 ACGGATATTTTAACCCAAATGTGAAATATTTGTCATCAAATAAAGCATATCTTTTACAAAAAATT
* *
1313758 GAAATTAAAAGGATAAATATTAAAATGTTTCTTTAATCAAAAACAATAATTTTGAAAATTGTTTG
391 GAAATTAAAAGGATAAATATTAAAATGTTCCTTTAAGC-AAAACAATAATTTTGAAAATTGTTTG
* * * * * *
1313823 ATTTCTTGATTCTCATTATTGCTTCATTAGGTCAAAACTTTCTAATGGTTCATAATGTGAAATCT
455 ATTGCTTGATTCTCATTAATGCTTCATTAGGTCAAAAATTTCCAATGGTTCACAATGTGAAATCC
* * **
1313888 TTATAAATACTGTGTAAACCTACTAGCTAGGATAAAACACACTTTAAAACAACTCAAAACTATTA
520 CTATAAACACCCTGTAAACCTACTAGCTAGGATAAAACACACTTTAAAACAACTCAAAACTATTA
1313953 AAAAAATTTCTCTCATC
585 AAAAAATTTCTCTCATC
*
1313970 TAGTTCAAGGACATCAAATCTACTGGTCAGCCAGTAAAGTAAATATGTTTTCACAAGGGA-AGGT
1 TAGTTCAAGGACATCAAA-CTACTGGTCAGCCAGT-AAGTAAATATGTTTTCACAAGGGATA-GA
* * * * *
1314034 TCAAAGGAGAACATCTACATATCCTATGTAATTATCGATTGTAGAGTT-TATCACCACATCA-GG
63 TCAAAGGAGAACAACTACATATCCTAAGCAACTATCAATTGTAGA-TTCTATCACCACAT-AGGG
* * * *
1314097 TCAAAATGTTTTTAATAAATTGATCAATTTCATTCATGCGGAGGATTGTTGGAAAATTTCGATAA
126 TCAAAATGTTTTTAATAAATTGAT-AATTTCATTCACGCGGA-GAATGTTAGAAAAATTCGATAA
* *
1314162 TTTTGGAGCTTTGAATAAGAAATTGATCCAAATATTGTTGAAAAAAATGTGGAACAAATTGTTGA
189 TTTTAGAGCTTTGAATAAGAAATCGATCCAAATATTGTTGAAAAAAATGTGGAACAAATTGTTGA
* * * * ** *
1314227 TTTGTACTTGTGTAGACATGCACGATGTAGGTAACATAAATGTTTGAACATATTTGGCTCTTTTT
254 TTCGTACATGTGTAGACATGCACGATGTAGGTAACATAAATGTCTGAACAGATAAGGCTCTTTTG
* * * *
1314292 TGCGCTTGCGGATATTTTAACCCAAATGTGAAATATTTGTCCTCAAATAGAGCATATCTTTTACG
319 TGCGCTTACGGATATTTTAACCCAAATGTGAAATATTTGTCATCAAATAAAGCATATCTTTTACA
* *
1314357 AAAAATTGAAATTAAAAGGATAAATATTAAAATGTTCCTTTAAGCAGAACAATAATTTTGGAAAT
384 AAAAATTGAAATTAAAAGGATAAATATTAAAATGTTCCTTTAAGCAAAACAATAATTTTGAAAAT
* * * *
1314422 TGTTTGATTGCTTTATTCTCCTTAATGTTTCATTAGGTCAAAAATTTCCAATTGTTCACAATGTG
449 TGTTTGATTGCTTGATTCTCATTAATGCTTCATTAGGTCAAAAATTTCCAATGGTTCACAATGTG
1314487 AAATCCCTATAAACACCCTGTAAACCTACTAG
514 AAATCCCTATAAACACCCTGTAAACCTACTAG
1314519 GTTAAATACA
Statistics
Matches: 482, Mismatches: 58, Indels: 13
0.87 0.10 0.02
Matches are distributed among these distances:
600 17 0.04
601 17 0.04
602 99 0.21
603 18 0.04
604 165 0.34
605 123 0.26
606 43 0.09
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (601 bp):
TAGTTCAAGGACATCAAACTACTGGTCAGCCAGTAAGTAAATATGTTTTCACAAGGGATAGATCA
AAGGAGAACAACTACATATCCTAAGCAACTATCAATTGTAGATTCTATCACCACATAGGGTCAAA
ATGTTTTTAATAAATTGATAATTTCATTCACGCGGAGAATGTTAGAAAAATTCGATAATTTTAGA
GCTTTGAATAAGAAATCGATCCAAATATTGTTGAAAAAAATGTGGAACAAATTGTTGATTCGTAC
ATGTGTAGACATGCACGATGTAGGTAACATAAATGTCTGAACAGATAAGGCTCTTTTGTGCGCTT
ACGGATATTTTAACCCAAATGTGAAATATTTGTCATCAAATAAAGCATATCTTTTACAAAAAATT
GAAATTAAAAGGATAAATATTAAAATGTTCCTTTAAGCAAAACAATAATTTTGAAAATTGTTTGA
TTGCTTGATTCTCATTAATGCTTCATTAGGTCAAAAATTTCCAATGGTTCACAATGTGAAATCCC
TATAAACACCCTGTAAACCTACTAGCTAGGATAAAACACACTTTAAAACAACTCAAAACTATTAA
AAAAATTTCTCTCATC
Found at i:1316463 original size:54 final size:54
Alignment explanation
Indices: 1316359--1316620 Score: 168
Period size: 54 Copynumber: 4.9 Consensus size: 54
1316349 ACAATATTCC
* * * *
1316359 ATCATTCGAGATGATGCATAATATTCTATCCTTCGAGATTATGTATATTATTTT
1 ATCATTCAAGATGATGCATAATATTCTATCCTTCGAGATGATGCACATTATTTT
* ** * *
1316413 ATCATTCAAGATGATGCATAGTATT-TCATTGTTCTAGATGATGCACATTATTTC
1 ATCATTCAAGATGATGCATAATATTCT-ATCCTTCGAGATGATGCACATTATTTT
* ** * * * * ** * **
1316467 ATCCTTTGAGATAATACACAATATTCCATTATTCGATATGATGCACATTATTCC
1 ATCATTCAAGATGATGCATAATATTCTATCCTTCGAGATGATGCACATTATTTT
* * * * * * * * *
1316521 ACCCTTCGAGATGATGCACAATATT-TCATCCTTTGTGATGATGCATAGTATTTC
1 ATCATTCAAGATGATGCATAATATTCT-ATCCTTCGAGATGATGCACATTATTTT
* * * * * *
1316575 ATCCTTCGAGATGATGCATTACATTCTATCATTCGAGGTGATGCAC
1 ATCATTCAAGATGATGCATAATATTCTATCCTTCGAGATGATGCAC
1316621 CGTATACTCA
Statistics
Matches: 161, Mismatches: 43, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
53 1 0.01
54 159 0.99
55 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (54 bp):
ATCATTCAAGATGATGCATAATATTCTATCCTTCGAGATGATGCACATTATTTT
Found at i:1316583 original size:81 final size:81
Alignment explanation
Indices: 1316325--1316620 Score: 254
Period size: 81 Copynumber: 3.7 Consensus size: 81
1316315 ACAGTTGTAT
* ** *
1316325 ATATTTCATCCTTC-AGGATGATATACAATATTCCATCATTCGAGATGATGCATAATA-TTCTAT
1 ATATTTCATCATTCGA-GATGATGCACAATATTCCATCATTCGAGATGATGCACAATATTTC-AT
* * *
1316388 CCTTCGAGATTATGTATA
64 CCTTTGAGATAATGCATA
* * * * * * ** * *
1316406 TTATTTTATCATTCAAGATGATGCATAGTATTTCATTGTTCTAGATGATGCACATTATTTCATCC
1 ATATTTCATCATTCGAGATGATGCACAATATTCCATCATTCGAGATGATGCACAATATTTCATCC
* *
1316471 TTTGAGATAATACACA
66 TTTGAGATAATGCATA
* * * * * *
1316487 ATATTCCATTATTCGATATGATGCACATTATTCCACCCTTCGAGATGATGCACAATATTTCATCC
1 ATATTTCATCATTCGAGATGATGCACAATATTCCATCATTCGAGATGATGCACAATATTTCATCC
* *
1316552 TTTGTGATGATGCATA
66 TTTGAGATAATGCATA
* * ** * * *
1316568 GTATTTCATCCTTCGAGATGATGCATTACATTCTATCATTCGAGGTGATGCAC
1 ATATTTCATCATTCGAGATGATGCACAATATTCCATCATTCGAGATGATGCAC
1316621 CGTATACTCA
Statistics
Matches: 164, Mismatches: 49, Indels: 4
0.76 0.23 0.02
Matches are distributed among these distances:
81 160 0.98
82 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (81 bp):
ATATTTCATCATTCGAGATGATGCACAATATTCCATCATTCGAGATGATGCACAATATTTCATCC
TTTGAGATAATGCATA
Found at i:1316593 original size:27 final size:27
Alignment explanation
Indices: 1316325--1316592 Score: 216
Period size: 27 Copynumber: 9.9 Consensus size: 27
1316315 ACAGTTGTAT
**
1316325 ATATTTCATCCTTC-AGGATGATATACA
1 ATATTTCATCCTTCGA-GATGATGCACA
* * *
1316352 ATATTCCATCATTCGAGATGATGCATA
1 ATATTTCATCCTTCGAGATGATGCACA
* * *
1316379 ATA-TTCTATCCTTCGAGATTATGTATA
1 ATATTTC-ATCCTTCGAGATGATGCACA
* * * * *
1316406 TTATTTTATCATTCAAGATGATGCATA
1 ATATTTCATCCTTCGAGATGATGCACA
* ** *
1316433 GTATTTCATTGTTCTAGATGATGCACA
1 ATATTTCATCCTTCGAGATGATGCACA
* * * *
1316460 TTATTTCATCCTTTGAGATAATACACA
1 ATATTTCATCCTTCGAGATGATGCACA
* ** *
1316487 ATATTCCATTATTCGATATGATGCACA
1 ATATTTCATCCTTCGAGATGATGCACA
* * *
1316514 TTATTCCACCCTTCGAGATGATGCACA
1 ATATTTCATCCTTCGAGATGATGCACA
* * *
1316541 ATATTTCATCCTTTGTGATGATGCATA
1 ATATTTCATCCTTCGAGATGATGCACA
*
1316568 GTATTTCATCCTTCGAGATGATGCA
1 ATATTTCATCCTTCGAGATGATGCA
1316593 TTACATTCTA
Statistics
Matches: 188, Mismatches: 50, Indels: 6
0.77 0.20 0.02
Matches are distributed among these distances:
26 2 0.01
27 183 0.97
28 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (27 bp):
ATATTTCATCCTTCGAGATGATGCACA
Found at i:1317932 original size:9 final size:9
Alignment explanation
Indices: 1317918--1317942 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1317908 ATGACCGGAG
1317918 TCGCCGCAC
1 TCGCCGCAC
1317927 TCGCCGCAC
1 TCGCCGCAC
1317936 TCGCCGC
1 TCGCCGC
1317943 CCCTTGAGAG
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:0.08, C:0.56, G:0.24, T:0.12
Consensus pattern (9 bp):
TCGCCGCAC
Found at i:1318037 original size:19 final size:20
Alignment explanation
Indices: 1317991--1318037 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
1317981 GGTTGACCGG
*
1317991 TTGGACCGGTCTGAATCGGT
1 TTGGACCGGTCTGAATCGAT
* * *
1318011 CTGAACCGG-CTGGATCGAT
1 TTGGACCGGTCTGAATCGAT
1318030 TTGGACCG
1 TTGGACCG
1318038 AGCCGAGCCG
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (20 bp):
TTGGACCGGTCTGAATCGAT
Found at i:1321133 original size:23 final size:23
Alignment explanation
Indices: 1321103--1321152 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1321093 ACATTGTTGG
1321103 ATGAATGAGGTTAGTCGTGTGTC
1 ATGAATGAGGTTAGTCGTGTGTC
1321126 ATGAATGAGGTTAGTCGTGTGTC
1 ATGAATGAGGTTAGTCGTGTGTC
1321149 ATGA
1 ATGA
1321153 GTTCATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.08, G:0.34, T:0.34
Consensus pattern (23 bp):
ATGAATGAGGTTAGTCGTGTGTC
Found at i:1323799 original size:995 final size:996
Alignment explanation
Indices: 1321126--1323866 Score: 5324
Period size: 996 Copynumber: 2.8 Consensus size: 996
1321116 GTCGTGTGTC
1321126 ATGAATGAGGTTAGTCGTGTGTCATGAGTTCATCATTATCTTAACAAGTTCAAGACTTGGTCACT
1 ATGAATGAGGTTAGTCGTGTGTCATGAGTTCATCATTATCTTAACAAGTTCAAGACTTGGTCACT
1321191 TAGTTAAGAGAAGAATTACTCATTGTCATTATGCACTAGTTTGAGGTACGTCCATTAGTGCTTAG
66 TAGTTAAGAGAAGAATTACTCATTGTCATTATGCACTAGTTTGAGGTACGTCCATTAGTGCTTAG
1321256 GTGATTAGTCTCACTATTACTTTTCCCATGTTTTTAAATTATTTTTCAAAAAGATGTTTCTATTA
131 GTGATTAGTCTCACTATTACTTTTCCCATGTTTTTAAATTATTTTTCAAAAAGATGTTTCTATTA
*
1321321 GAGTATGCCAAAGACTAATCATGAGATGATTGTAATGATATAATTTATTTATCGTGTTTATTGAA
196 GAGTATGCCAAAGACTAATCATGAGATGATTGTAATGATATACTTTATTTATCGTGTTTATTGAA
*
1321386 TAAAACATTGTCGTTATCTTTTTTTTTTTCAGTTATACTTTTGTGTCTTAAATAAACTAAAAGAT
261 TAAAGCATTGTCGTTATC--TTTTTTTTTCAGTTATACTTTTGTGTCTTAAATAAACTAAAAGAT
1321451 AATGAAGTCCATATAATAATATGATTATTCTTAAAAGGTCCTTGGTCGGGTATTATTGTGGGCAT
324 AATGAAGTCCATATAATAATATGATTATTCTTAAAAGGTCCTTGGTCGGGTATTATTGTGGGCAT
1321516 GAAAAATAATAATATGTTCAAGGCTAACATGTAGTTGATTCATGACAACGAGTTTTTATTGACAT
389 GAAAAATAATAATATGTTCAAGGCTAACATGTAGTTGATTCATGACAACGAGTTTTTATTGACAT
1321581 AAAGATGTCAAAATCGATACATGAGTATGTTGTTAGAGAACAACTTATTGGAATGACCCTCTAAA
454 AAAGATGTCAAAATCGATACATGAGTATGTTGTTAGAGAACAACTTATTGGAATGACCCTCTAAA
*
1321646 GGCATATGTCTTGGATTATTATGTGACAATCTCAACATTGCTCATGGTGATGACTACATCTATGA
519 GGCATATGTCTTGGATTATTATGTGACAATCTCAACATTGCTCATGGTGATGACTACATGTATGA
1321711 TCCTCAGACTTGAGATCATTATTATCTCAACATATATAGTCGTATGTTTTGATATAATTAAATGT
584 TCCTCAGACTTGAGATCATTATTATCTCAACATATATAGTCGTATGTTTTGATATAATTAAATGT
*
1321776 GTTTCGTAACCAGTTACATTATAAAGACTAATATTGGACATATCACGATATATGTAGTGGAGTGT
649 GTTTCGTAACCAGTTACATTATAAAGACTAATGTTGGACATATCACGATATATGTAGTGGAGTGT
1321841 TTGTGATCAAGATAGGATTTATCCTTCCTACATAAAAAGACAATTCACCTTATTTACTTTAAGGT
714 TTGTGATCAAGATAGGATTTATCCTTCCTACATAAAAAGACAATTCACCTTATTTACTTTAAGGT
1321906 TGAACTGTTATAAAAAGACAATTATTTCATAGCCTGGATTCGGGTGATTTATGTTGAGATAAACC
779 TGAACTGTTATAAAAAGACAATTATTTCATAGCCTGGATTCGGGTGATTTATGTTGAGATAAACC
1321971 TGATGAAATAACCTACGTACGTGAGAATGACTAGCCATTTTTTATGAAAAAATGTTGGATTGTTT
844 TGATGAAATAACCTACGTACGTGAGAATGACTAGCCATTTTTTATGAAAAAATGTTGGATTGTTT
1322036 TTCTAGTATACTTACTAGAATCATGAGGATATGTGGGCTACAGATATATATATATATATATATTT
909 TTCTAGTATACTTACTAGAATCATGAGGATATGTGGGCTACAGA-ATATATATATATATATATTT
1322101 TTGTTTTATTGCAAACATTGTTGG
973 TTGTTTTATTGCAAACATTGTTGG
*
1322125 ATGAATGAGGTTAGTCGTGTGTCATGAGTTCAACATTATCTTAACAAGTTCAAGACTTGGTCACT
1 ATGAATGAGGTTAGTCGTGTGTCATGAGTTCATCATTATCTTAACAAGTTCAAGACTTGGTCACT
1322190 TAGTTAAGAGAAGAATTACTCATTGTCATTATGCACTAGTTTGAGGTACGTCCATTAGTGCTTAG
66 TAGTTAAGAGAAGAATTACTCATTGTCATTATGCACTAGTTTGAGGTACGTCCATTAGTGCTTAG
1322255 GTGATTAGTCTCACTATTACTTTTCCCATGTTTTTAAATTATTTTTCAAAAAGATGTTTCTATTA
131 GTGATTAGTCTCACTATTACTTTTCCCATGTTTTTAAATTATTTTTCAAAAAGATGTTTCTATTA
1322320 GAGTATGCCAAAGACTAATCATGAGATGATTGTAATGATATACTTTATTTATCGTGTTTATTGAA
196 GAGTATGCCAAAGACTAATCATGAGATGATTGTAATGATATACTTTATTTATCGTGTTTATTGAA
1322385 TAAAGCATTGTCGTTATC-TTTTTTTTCAGTTATACTTTTGTGTCTTAAATAAACTAAAAGATAA
261 TAAAGCATTGTCGTTATCTTTTTTTTTCAGTTATACTTTTGTGTCTTAAATAAACTAAAAGATAA
1322449 TGAAGTCCATATAATAATATGATTATTCTTAAAAGGTCCTTGGTCGGGTATTATTGTGGGCATGA
326 TGAAGTCCATATAATAATATGATTATTCTTAAAAGGTCCTTGGTCGGGTATTATTGTGGGCATGA
1322514 AAAATAATAATATGTTCAAGGCTAACATGTAGTTGATTCATGACAACGAGTTTTTATTGACATAA
391 AAAATAATAATATGTTCAAGGCTAACATGTAGTTGATTCATGACAACGAGTTTTTATTGACATAA
1322579 AGATGTCAAAATCGATACATGAGTATGTTGTTAGAGAACAACTTATTGGAATGACCCTCTAAAGG
456 AGATGTCAAAATCGATACATGAGTATGTTGTTAGAGAACAACTTATTGGAATGACCCTCTAAAGG
1322644 CATATGTCTTGGATTATTATGTGACAATCTCAACATTGCTCATGGTGATGACTACATGTATGATC
521 CATATGTCTTGGATTATTATGTGACAATCTCAACATTGCTCATGGTGATGACTACATGTATGATC
1322709 CTCAGACTTGAGATCATTATTATCTCAACATATATAGTCGTATGTTTTGATATAATTAAATGTGT
586 CTCAGACTTGAGATCATTATTATCTCAACATATATAGTCGTATGTTTTGATATAATTAAATGTGT
1322774 TTCGTAACCAGTTACATTATAAAGACTAATGTTGGACATATCACGATATATGTAGTGGAGTGTTT
651 TTCGTAACCAGTTACATTATAAAGACTAATGTTGGACATATCACGATATATGTAGTGGAGTGTTT
1322839 GTGATCAAGATAGGATTTATCCTTCCTACATAAAAAGACAATTCACCTTATTTACTTTAAGGTTG
716 GTGATCAAGATAGGATTTATCCTTCCTACATAAAAAGACAATTCACCTTATTTACTTTAAGGTTG
1322904 AACTGTTATAAAAAGACAATTATTTCATAGCCTGGATTCGGGTGATTTATGTTGAGATAAACCTG
781 AACTGTTATAAAAAGACAATTATTTCATAGCCTGGATTCGGGTGATTTATGTTGAGATAAACCTG
1322969 ATGAAATAACCTACGTACGTGAGAATGACTAGCCATTTTTTATGAAAAAATGTTGGATTGTTTTT
846 ATGAAATAACCTACGTACGTGAGAATGACTAGCCATTTTTTATGAAAAAATGTTGGATTGTTTTT
1323034 CTAGTATACTTACTAGAATCATGAGGATATGTGGGCTACAG-ATATATATATATATATATTTTTG
911 CTAGTATACTTACTAGAATCATGAGGATATGTGGGCTACAGAATATATATATATATATATTTTTG
1323098 TTTTATTGCAAACATTGTTGG
976 TTTTATTGCAAACATTGTTGG
1323119 ATGAATGAGGTTAGTCGTGTGTCATGAGTTCATCATTATCTTAACAAGTTCAAGACTTGGTCACT
1 ATGAATGAGGTTAGTCGTGTGTCATGAGTTCATCATTATCTTAACAAGTTCAAGACTTGGTCACT
1323184 TAGTTAAGAGAAGAATTACTCATTGTCATTATGCACTAGTTTGAGGTACGTCCATTAGTGCTTAG
66 TAGTTAAGAGAAGAATTACTCATTGTCATTATGCACTAGTTTGAGGTACGTCCATTAGTGCTTAG
1323249 GTGATTAGTCTCACTATTACTTTTCCCATGTTTTTAAATTATTTTTCAAAAAGATGTTTCTATTA
131 GTGATTAGTCTCACTATTACTTTTCCCATGTTTTTAAATTATTTTTCAAAAAGATGTTTCTATTA
1323314 GAGTATGCCAAAGACTAATCATGAGATGATTGTAATGATATACTTTATTTATCGTGTTTATTGAA
196 GAGTATGCCAAAGACTAATCATGAGATGATTGTAATGATATACTTTATTTATCGTGTTTATTGAA
1323379 TAAAGCATTGTCGTTATCTTTTTTTTTCAGTTATACTTTTGTGTCTTAAATAAACTAAAAGATAA
261 TAAAGCATTGTCGTTATCTTTTTTTTTCAGTTATACTTTTGTGTCTTAAATAAACTAAAAGATAA
1323444 TGAAGTCCATATAATAATATGATTATTCTTAAAAGGTCCTTGGTCGGGTATTATTGTGGGCATGA
326 TGAAGTCCATATAATAATATGATTATTCTTAAAAGGTCCTTGGTCGGGTATTATTGTGGGCATGA
1323509 AAAATAATAATATGTTCAAGGCTAACATGTAGTTGATTCATGACAACGAGTTTTTATTGACATAA
391 AAAATAATAATATGTTCAAGGCTAACATGTAGTTGATTCATGACAACGAGTTTTTATTGACATAA
*
1323574 AGATGTCAAAATCGATACATGAGTATGTTGTTAGAGAACAACTTATTGGAATGAGCCTCTAAAGG
456 AGATGTCAAAATCGATACATGAGTATGTTGTTAGAGAACAACTTATTGGAATGACCCTCTAAAGG
*
1323639 CATATGTCTTGGATTATTATGTGACAATCTCAATATTGCTCATGGTGATGACTACATGTATGATC
521 CATATGTCTTGGATTATTATGTGACAATCTCAACATTGCTCATGGTGATGACTACATGTATGATC
* **
1323704 CTCATACTTGAGATCATTATTATCTCAACATATATAGTATTATGTTTTGATATAATTAAATGTGT
586 CTCAGACTTGAGATCATTATTATCTCAACATATATAGTCGTATGTTTTGATATAATTAAATGTGT
* *
1323769 TTCGTAGCCGGTTACATTATAAAGACTAATGTTGGACATATCACGATATATGTAGTGGAGTGTTT
651 TTCGTAACCAGTTACATTATAAAGACTAATGTTGGACATATCACGATATATGTAGTGGAGTGTTT
*
1323834 GTGATCAAGATAGGAATTATCCTTCCTACATAA
716 GTGATCAAGATAGGATTTATCCTTCCTACATAA
1323867 TAGGAGCTAT
Statistics
Matches: 1727, Mismatches: 14, Indels: 6
0.99 0.01 0.00
Matches are distributed among these distances:
994 321 0.19
995 461 0.27
996 670 0.39
999 275 0.16
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (996 bp):
ATGAATGAGGTTAGTCGTGTGTCATGAGTTCATCATTATCTTAACAAGTTCAAGACTTGGTCACT
TAGTTAAGAGAAGAATTACTCATTGTCATTATGCACTAGTTTGAGGTACGTCCATTAGTGCTTAG
GTGATTAGTCTCACTATTACTTTTCCCATGTTTTTAAATTATTTTTCAAAAAGATGTTTCTATTA
GAGTATGCCAAAGACTAATCATGAGATGATTGTAATGATATACTTTATTTATCGTGTTTATTGAA
TAAAGCATTGTCGTTATCTTTTTTTTTCAGTTATACTTTTGTGTCTTAAATAAACTAAAAGATAA
TGAAGTCCATATAATAATATGATTATTCTTAAAAGGTCCTTGGTCGGGTATTATTGTGGGCATGA
AAAATAATAATATGTTCAAGGCTAACATGTAGTTGATTCATGACAACGAGTTTTTATTGACATAA
AGATGTCAAAATCGATACATGAGTATGTTGTTAGAGAACAACTTATTGGAATGACCCTCTAAAGG
CATATGTCTTGGATTATTATGTGACAATCTCAACATTGCTCATGGTGATGACTACATGTATGATC
CTCAGACTTGAGATCATTATTATCTCAACATATATAGTCGTATGTTTTGATATAATTAAATGTGT
TTCGTAACCAGTTACATTATAAAGACTAATGTTGGACATATCACGATATATGTAGTGGAGTGTTT
GTGATCAAGATAGGATTTATCCTTCCTACATAAAAAGACAATTCACCTTATTTACTTTAAGGTTG
AACTGTTATAAAAAGACAATTATTTCATAGCCTGGATTCGGGTGATTTATGTTGAGATAAACCTG
ATGAAATAACCTACGTACGTGAGAATGACTAGCCATTTTTTATGAAAAAATGTTGGATTGTTTTT
CTAGTATACTTACTAGAATCATGAGGATATGTGGGCTACAGAATATATATATATATATATTTTTG
TTTTATTGCAAACATTGTTGG
Found at i:1325516 original size:43 final size:43
Alignment explanation
Indices: 1325468--1325710 Score: 159
Period size: 43 Copynumber: 5.4 Consensus size: 43
1325458 TTTCAAGAAA
1325468 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGACAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGACAGAC
* * * *
1325511 AAACGCCACAATAGATGTTGATATTTAGCGGCGTTTGGCGCGTTTGGAAGCC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-G-AC-------AGAC
* * *
1325563 AAACGCCACAATAGATGTTGATATTTAGCGGCATTTGGA-AGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-GACAGAC
* * * * ** ** *
1325606 AAACGCCGCAGTAGGTGTCGCTTTTTAGCGGCGTTTTTCCCAG
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGACAGAC
* * * * *
1325649 AAACGCCGCAGTAGGTGTTGATGTTTAGTGGCATTTTTATC--AC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGC-GTTTGA-CAGAC
*
1325692 AAACGCCGCAATAAGTGTT
1 AAACGCCGCAATAGGTGTT
1325711 AAGGTTTCGC
Statistics
Matches: 160, Mismatches: 28, Indels: 24
0.75 0.13 0.11
Matches are distributed among these distances:
43 113 0.71
44 5 0.03
45 2 0.01
52 40 0.25
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGACAGAC
Found at i:1325575 original size:95 final size:95
Alignment explanation
Indices: 1325468--1325641 Score: 251
Period size: 95 Copynumber: 1.8 Consensus size: 95
1325458 TTTCAAGAAA
* * * *
1325468 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-GACAGACAAACGCCACAATAGATGTTGA
1 AAACGCCACAATAGATGTTGATATTTAGCGGCATTTGGA-AGACAAACGCCACAATAGATGTCGA
1325532 TATTTAGCGGCGTTTGGCGCGTTTGGAAGCC
65 TATTTAGCGGCGTTTGGCGCGTTTGGAAGCC
* * * *
1325563 AAACGCCACAATAGATGTTGATATTTAGCGGCATTTGGAAGACAAACGCCGCAGTAGGTGTCGCT
1 AAACGCCACAATAGATGTTGATATTTAGCGGCATTTGGAAGACAAACGCCACAATAGATGTCGAT
*
1325628 TTTTAGCGGCGTTT
66 ATTTAGCGGCGTTT
1325642 TTCCCAGAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
95 67 0.97
96 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (95 bp):
AAACGCCACAATAGATGTTGATATTTAGCGGCATTTGGAAGACAAACGCCACAATAGATGTCGAT
ATTTAGCGGCGTTTGGCGCGTTTGGAAGCC
Found at i:1325739 original size:43 final size:42
Alignment explanation
Indices: 1325692--1325772 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 42
1325682 TTTTTATCAC
*
1325692 AAACGCCGCAATAAGTGTTAAGGTTTCGCGGCGTCTTTAGCTT
1 AAACGCCGCAATAAGTGTT-AGATTTCGCGGCGTCTTTAGCTT
* * *
1325735 AAACGCCGCAATATGTGTTTGATTTGGCGGCGTCTTTA
1 AAACGCCGCAATAAGTGTTAGATTTCGCGGCGTCTTTA
1325773 ATACAAATGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 16 0.47
43 18 0.53
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (42 bp):
AAACGCCGCAATAAGTGTTAGATTTCGCGGCGTCTTTAGCTT
Found at i:1326219 original size:21 final size:21
Alignment explanation
Indices: 1326152--1326208 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1326142 ATATGTTGCT
*
1326152 TCTCTTTGTGCTGCCGCTCCC
1 TCTCTTTGTGCTGCCGCTGCC
1326173 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
1326194 TCTCTTTGTGCTGCC
1 TCTCTTTGTGCTGCC
1326209 ACTGTTTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.00, C:0.39, G:0.21, T:0.40
Consensus pattern (21 bp):
TCTCTTTGTGCTGCCGCTGCC
Found at i:1326219 original size:42 final size:42
Alignment explanation
Indices: 1326152--1326234 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1326142 ATATGTTGCT
* * *
1326152 TCTCTTTGTGCTGCCGCTCCCTCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCACTCCCTCTCTCTCTGCTGCCGCTGCC
*** *
1326194 TCTCTTTGTGCTGCCACTGTTTCTCTCTCTGCTTCCGCTGC
1 TCTCTTTGTGCTGCCACTCCCTCTCTCTCTGCTGCCGCTGC
1326235 TGCTCTGGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.01, C:0.39, G:0.19, T:0.41
Consensus pattern (42 bp):
TCTCTTTGTGCTGCCACTCCCTCTCTCTCTGCTGCCGCTGCC
Found at i:1326226 original size:21 final size:21
Alignment explanation
Indices: 1326210--1326267 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
1326200 TGTGCTGCCA
*
1326210 CTGTTTCTCTCTCTGCTTCCG
1 CTGTTGCTCTCTCTGCTTCCG
* **
1326231 CTGCTGCTCTGGCTGCTTCCG
1 CTGTTGCTCTCTCTGCTTCCG
1326252 CTGTTGCTCTCTCTGC
1 CTGTTGCTCTCTCTGC
1326268 ATCCCTTGCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.00, C:0.38, G:0.21, T:0.41
Consensus pattern (21 bp):
CTGTTGCTCTCTCTGCTTCCG
Found at i:1333565 original size:46 final size:46
Alignment explanation
Indices: 1333498--1333588 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
1333488 TAGCGATTCT
*
1333498 GAAATAACTACATGGTCAAACAAGACAGAGGAACGAAGGCAAGTAC
1 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTAC
1333544 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTA
1 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTA
1333589 AGTACCTTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.49, C:0.15, G:0.24, T:0.11
Consensus pattern (46 bp):
GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTAC
Found at i:1334456 original size:42 final size:40
Alignment explanation
Indices: 1334410--1334632 Score: 130
Period size: 41 Copynumber: 5.4 Consensus size: 40
1334400 ATGTTAAAAA
*
1334410 ATTTGCGGCGTTTTTTGTCAAAACGCCACTAAAGTACGCAT
1 ATTTGCGGCGTTTTTTG-CAAAACGCCACTAAAGTACGAAT
* ** * *
1334451 CATTTGCGGCGTTTGTTAGCAAAACGCTGCTAAATTACTAAT
1 -ATTTGCGGCGTTT-TTTGCAAAACGCCACTAAAGTACGAAT
* * *
1334493 ACTTTGCGGCG-TTTCTACGAAAACGCCACTAAAGTACGAGT
1 A-TTTGCGGCGTTTTTTGC-AAAACGCCACTAAAGTACGAAT
* * * * * *
1334534 CTATAGTGGCGTTTTCATAC-GAACGCCACTAAAGTA-GAAGT
1 AT-TTGCGGCGTTTT-TTGCAAAACGCCACTAAAGTACGAA-T
* * * * * *
1334575 CTATAGCGGCGTTTTCATAC-AAACGCCACTAAAATACAAAT
1 AT-TTGCGGCGTTTT-TTGCAAAACGCCACTAAAGTACGAAT
1334616 ATTTTGCGGCGTTTTTT
1 A-TTTGCGGCGTTTTTT
1334633 ATAAAAACAC
Statistics
Matches: 145, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
40 6 0.04
41 87 0.60
42 46 0.32
43 6 0.04
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (40 bp):
ATTTGCGGCGTTTTTTGCAAAACGCCACTAAAGTACGAAT
Found at i:1334545 original size:41 final size:42
Alignment explanation
Indices: 1334498--1334607 Score: 158
Period size: 41 Copynumber: 2.7 Consensus size: 42
1334488 CTAATACTTT
1334498 GCGGCG-TTTC-TACGAAAACGCCACTAAAGTACG-AGTCTATA
1 GCGGCGTTTTCATACG-AAACGCCACTAAAGTA-GAAGTCTATA
*
1334539 GTGGCGTTTTCATACG-AACGCCACTAAAGTAGAAGTCTATA
1 GCGGCGTTTTCATACGAAACGCCACTAAAGTAGAAGTCTATA
1334580 GCGGCGTTTTCATAC-AAACGCCACTAAA
1 GCGGCGTTTTCATACGAAACGCCACTAAA
1334608 ATACAAATAT
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
40 1 0.02
41 54 0.86
42 4 0.06
43 4 0.06
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (42 bp):
GCGGCGTTTTCATACGAAACGCCACTAAAGTAGAAGTCTATA
Found at i:1334625 original size:41 final size:41
Alignment explanation
Indices: 1334513--1334630 Score: 137
Period size: 41 Copynumber: 2.9 Consensus size: 41
1334503 GTTTCTACGA
* * * *
1334513 AAACGCCACTAAAGTACGAGTCTATAGTGGCGTTTTCATAC
1 AAACGCCACTAAAGTACAAATATATAGCGGCGTTTTCATAC
* * * *
1334554 GAACGCCACTAAAGTAGAAGTCTATAGCGGCGTTTTCATAC
1 AAACGCCACTAAAGTACAAATATATAGCGGCGTTTTCATAC
* * *
1334595 AAACGCCACTAAAATACAAATATTTTGCGGCGTTTT
1 AAACGCCACTAAAGTACAAATATATAGCGGCGTTTT
1334631 TTATAAAAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTACAAATATATAGCGGCGTTTTCATAC
Found at i:1335088 original size:57 final size:57
Alignment explanation
Indices: 1334869--1335056 Score: 367
Period size: 57 Copynumber: 3.3 Consensus size: 57
1334859 ATTAAAACAG
1334869 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1334926 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
*
1334983 AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1335040 AAGTACTTATGCATAAA
1 AAGTACTTATGCATAAA
1335057 CAGTCTTCAC
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 130 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (57 bp):
AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
Found at i:1346271 original size:99 final size:99
Alignment explanation
Indices: 1346133--1346322 Score: 308
Period size: 99 Copynumber: 1.9 Consensus size: 99
1346123 ATATAATATT
* * * * *
1346133 ATATGTATACAATAAAGCTTGAGTTGTCCGTCTAGAGCAATTGGTTAATTGCCCCGTCTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTATAGAGCAATTGGTTAATCGCCCCGGCTTTATGG
*
1346198 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAACTAGCCTGATAAAGGTGATTATA
* *
1346232 ATATATATACAATAAAGCTTGGGTTGTCCCTATAGAGCAATTGGTTAATCGCTCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTATAGAGCAATTGGTTAATCGCCCCGGCTTTATGG
1346297 ATAAGATTCAACTAGCCTGATAAAGG
66 ATAAGATTCAACTAGCCTGATAAAGG
1346323 CAAATTAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 83 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGTTGTCCCTATAGAGCAATTGGTTAATCGCCCCGGCTTTATGG
ATAAGATTCAACTAGCCTGATAAAGGTGATTATA
Found at i:1348735 original size:19 final size:20
Alignment explanation
Indices: 1348695--1348738 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1348685 AAGAATTTTC
*
1348695 TTTTTTTTTGAAACATATAG
1 TTTTTTTTTGAAACAAATAG
1348715 TTTTTTTTT-AAA-AAATCAG
1 TTTTTTTTTGAAACAAAT-AG
1348734 TTTTT
1 TTTTT
1348739 GAAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.45
20 9 0.41
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTTTTTTTGAAACAAATAG
Found at i:1348777 original size:37 final size:36
Alignment explanation
Indices: 1348735--1348925 Score: 228
Period size: 37 Copynumber: 5.2 Consensus size: 36
1348725 AAAAATCAGT
1348735 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
1348771 TTTTTGAAAACATATAT-ATA-GT--TTTTGAAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
1348804 TTTTAAAAACATATATATAATATATAATCTTTGAAAACA
1 TTTT-GAAA-ATATATATAATATATAGT-TTTGAAAACA
* * **
1348843 CTTTGAGAATATATATAATATATTTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
1348879 TTTTGAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAA-ATATATATAATATATAG-TTTTGAAAACA
1348917 TTTTGAAAA
1 TTTTGAAAA
1348926 CATTTTGAAA
Statistics
Matches: 131, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
32 4 0.03
33 14 0.11
34 7 0.05
35 4 0.03
36 20 0.15
37 47 0.36
38 22 0.17
39 13 0.10
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:1348791 original size:32 final size:32
Alignment explanation
Indices: 1348752--1348822 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
1348742 AATATATATA
*
1348752 ATATATAG-TTTTGAAAACATTTTTGAAAACAT
1 ATATATAGTTTTTGAAAACA-TTTTAAAAACAT
1348784 ATATATAGTTTTTGAAAACATTTTAAAAACAT
1 ATATATAGTTTTTGAAAACATTTTAAAAACAT
1348816 ATATATA
1 ATATATA
1348823 ATATATAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
32 26 0.70
33 11 0.30
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (32 bp):
ATATATAGTTTTTGAAAACATTTTAAAAACAT
Found at i:1348900 original size:74 final size:69
Alignment explanation
Indices: 1348735--1348928 Score: 264
Period size: 74 Copynumber: 2.7 Consensus size: 69
1348725 AAAAATCAGT
1348735 TTTTGAAA-ATATATATAATATATAGTTTTGAAAACATTTTTGAAAACATATATATAGTTTTTGA
1 TTTTGAAACATATATATAATATATAGTTTTGAAAACA-TTTTGAAAACATATATATAGTTTTTGA
1348799 AAACA
65 AAACA
* * * * *
1348804 TTTTAAAAACATATATATAATATATAATCTTTGAAAACACTTTGAGAATATATATAATATATTTT
1 TTTT-GAAACATATATATAATATATAGT-TTTGAAAACATTTTGA-AA-ACATAT-ATATA-GTT
1348869 TTTGAAAACA
60 TTTGAAAACA
1348879 TTTTGAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAACAT
1 TTTTGAAACATATATATAATATATAG-TTTTGAAAACATTTTGAAAACAT
1348929 TTTGAAAACA
Statistics
Matches: 108, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
69 4 0.04
70 3 0.03
71 22 0.20
72 15 0.14
73 7 0.06
74 40 0.37
75 17 0.16
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (69 bp):
TTTTGAAACATATATATAATATATAGTTTTGAAAACATTTTGAAAACATATATATAGTTTTTGAA
AACA
Found at i:1348920 original size:11 final size:11
Alignment explanation
Indices: 1348906--1348939 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
1348896 AATATATAGT
1348906 TTTTGAAAACA
1 TTTTGAAAACA
1348917 TTTTGAAAACA
1 TTTTGAAAACA
1348928 TTTTGAAAACA
1 TTTTGAAAACA
1348939 T
1 T
1348940 ATATATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:1348972 original size:50 final size:48
Alignment explanation
Indices: 1348869--1348978 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 48
1348859 AATATATTTT
* *
1348869 TTTGAAAACATTTTGAAACATATATATAATATATAGTTTTTGAAAACAT
1 TTTGAAAACATTTTGAAACATATATAT-ATATATAGTTTTTGAAAAAAA
1348918 TTTGAAAACATTTTGAAAACATATATAT-TATATAG-TTTTGAAAAAAAAAA
1 TTTGAAAACATTTTG-AAACATATATATATATATAGTTTTTG---AAAAAAA
1348968 TTTGAAAACAT
1 TTTGAAAACAT
1348979 ATATATTATA
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
47 5 0.09
48 7 0.13
49 15 0.27
50 28 0.51
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.38
Consensus pattern (48 bp):
TTTGAAAACATTTTGAAACATATATATATATATAGTTTTTGAAAAAAA
Found at i:1348972 original size:124 final size:124
Alignment explanation
Indices: 1348793--1349033 Score: 285
Period size: 124 Copynumber: 1.9 Consensus size: 124
1348783 TATATATAGT
* * * *
1348793 TTTTGAAAACATTTTAAAAACATATATATAATATATAATCTTTGAAAACACTTTGAGAATATATA
1 TTTTGAAAACATTTTAAAAACATATATAT-ATATATAATCTTTGAAAAAAATTTGAAAACATATA
** * *
1348858 TAATATATTTTTTTGAAAA-CA-TTTTGAAA-CATATATATAATATATAGTTTTTGAAAACA
65 TAATATATAGTTTCGAAAATAATTTTTGAAAGC--ATATATAATATATAGTTTTTGAAAACA
* *
1348917 TTTTGAAAACATTTTGAAAACATATATAT-TATATAGT-TTTGAAAAAAAAAATTTGAAAACATA
1 TTTTGAAAACATTTTAAAAACATATATATATATATAATCTTTG---AAAAAAATTTGAAAACATA
* *
1348980 TATATTATATAGTTTCGAAAATAATTTTTGAAAGCATATATCATATATAGTTTT
63 TATAATATATAGTTTCGAAAATAATTTTTGAAAGCATATATAATATATAGTTTT
1349034 AAAATGATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
121 4 0.04
122 7 0.07
124 60 0.61
125 19 0.19
126 8 0.08
127 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (124 bp):
TTTTGAAAACATTTTAAAAACATATATATATATATAATCTTTGAAAAAAATTTGAAAACATATAT
AATATATAGTTTCGAAAATAATTTTTGAAAGCATATATAATATATAGTTTTTGAAAACA
Found at i:1349019 original size:38 final size:37
Alignment explanation
Indices: 1348928--1349060 Score: 144
Period size: 38 Copynumber: 3.5 Consensus size: 37
1348918 TTTGAAAACA
* *
1348928 TTTTGAAAACATATATATTATATAGTTTTGAAAAAAAAA
1 TTTTGAAAACATATATATTATATAG-TTTG-AAAATAAT
*
1348967 ATTTGAAAACATATATATTATATAGTTTCGAAAATAAT
1 TTTTGAAAACATATATATTATATAGTTT-GAAAATAAT
* * *
1349005 TTTTGAAAGCATATATCA-TATATAGTTTTAAAATGATT
1 TTTTGAAAACATATAT-ATTATATAGTTTGAAAAT-AAT
*
1349043 TTTTTAAAACATAT-TATT
1 TTTTGAAAACATATATATT
1349061 TTTAGTGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
36 1 0.01
37 7 0.09
38 47 0.58
39 26 0.32
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (37 bp):
TTTTGAAAACATATATATTATATAGTTTGAAAATAAT
Done.