Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 76 of 97
Found at i:30270186 original size:60 final size:57
Alignment explanation
Indices: 30270092--30270210 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 57
30270082 GCTTTGAGGA
30270092 GTCTTTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAAGTTTCGTT
1 GTCTTTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT--AAAGTTTCGTT
30270151 GNTCTTTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTTTCGTT
1 G-TCTTTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTTTCGTT
30270209 GT
1 GT
30270211 ATGCCTTAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
57 1 0.02
58 12 0.20
59 1 0.02
60 45 0.76
ACGTcount: A:0.18, C:0.12, G:0.19, T:0.50
Consensus pattern (57 bp):
GTCTTTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTTTCGTT
Found at i:30270228 original size:41 final size:40
Alignment explanation
Indices: 30270156--30270251 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 40
30270146 TCGTTGNTCT
30270156 TTTTTAAAGTTTC---GTTGCCTCAGTTTTGAGGAGTTC-A
1 TTTTTAAAGTTTCGTTGTTGCCTCAGTTTTGAGGAG-TCAA
*
30270193 TTTTTAAAGTTTCGTTGTATGCCTTAGTTTTGAGGAGTCATA
1 TTTTTAAAGTTTCGTTGT-TGCCTCAGTTTTGAGGAGTCA-A
*
30270235 TTTTTAAAATTTCGTTG
1 TTTTTAAAGTTTCGTTG
30270252 CCTCAGCTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
37 13 0.25
40 4 0.08
41 17 0.33
42 17 0.33
ACGTcount: A:0.21, C:0.10, G:0.20, T:0.49
Consensus pattern (40 bp):
TTTTTAAAGTTTCGTTGTTGCCTCAGTTTTGAGGAGTCAA
Found at i:30270276 original size:38 final size:37
Alignment explanation
Indices: 30270156--30270277 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 37
30270146 TCGTTGNTCT
**
30270156 TTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCA
1 TTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGCACA
* *
30270193 TTTTTAAAGTTTCGTTGTATGCCTTAGTTTTGAGGAGTCATA
1 TTTTTAAAGTTTC---GT-TGCCTCAGTTTTGAGGAG-CACA
* * *
30270235 TTTTTAAAATTTCGTTGCCTCAGCTTTGAAGAGCCACA
1 TTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAG-CACA
30270273 TTTTT
1 TTTTT
30270278 CTCTCAAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
37 13 0.19
38 23 0.33
39 2 0.03
40 2 0.03
41 17 0.24
42 13 0.19
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (37 bp):
TTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGCACA
Found at i:30270308 original size:1 final size:1
Alignment explanation
Indices: 30270302--30270553 Score: 162
Period size: 1 Copynumber: 252.0 Consensus size: 1
30270292 GAGTACAATT
* * * * * * * ** *
30270302 AAAAAAAACAAACAAACAAACAAAACAAAAAAAACAAAAAAAAAAACAAAAAAAAAGGAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * *
30270367 AAAAGAAAAAAAAATAAAAACAAAAAAAAGAAGAAAAAAAAGAACAAAAACAAAAACAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * ** * * *
30270432 AAACAAAAAACAAAAAAACAAAAAAAAACAAAAAAACAAAAAAACTAAAACAAAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
30270497 AAAAACAAAAAAAAAAACAAAAACAAACAAAAACAAAACAAAACAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30270554 GCTTTGGTAA
Statistics
Matches: 178, Mismatches: 73, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 178 1.00
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:30270336 original size:18 final size:17
Alignment explanation
Indices: 30270302--30270551 Score: 204
Period size: 18 Copynumber: 13.9 Consensus size: 17
30270292 GAGTACAATT
30270302 AAAAAAAACAAAC-AAAC
1 AAAAAAAA-AAACAAAAC
30270319 AAACAAAACAAAA-AAAAC
1 AAA-AAAA-AAAACAAAAC
*
30270337 AAAAAAAAAAACAAAAA
1 AAAAAAAAAAACAAAAC
* *
30270354 AAAAGGAAAAAAGAAAAGAAA
1 AAAA--AAAAAA-ACAA-AAC
30270375 AAAAAATAAAAACAAAA-
1 AAAAAA-AAAAACAAAAC
*
30270392 AAAAGAAGAAAAAAAAGAAC
1 AAAA-AA-AAAAACAA-AAC
*
30270412 AAAAACAAAAACAAAAC
1 AAAAAAAAAAACAAAAC
*
30270429 AAAAAACAAAAAACAAAAA
1 -AAAAA-AAAAAACAAAAC
30270448 AACAAAAAAAAACAAAA-
1 AA-AAAAAAAAACAAAAC
*
30270465 AAACAAAAAAACTAAAAC
1 AAAAAAAAAAAC-AAAAC
30270483 AAAAAAACAAAAACAAAAAC
1 -AAAAAA-AAAAAC-AAAAC
30270503 AAAAAAAAAAACAAAA-
1 AAAAAAAAAAACAAAAC
* *
30270519 ACAAACAAAAACAAAAC
1 AAAAAAAAAAACAAAAC
* *
30270536 AAAACAAAAAAGAAAA
1 AAAAAAAAAAACAAAA
30270552 AAGCTTTGGT
Statistics
Matches: 195, Mismatches: 18, Indels: 40
0.77 0.07 0.16
Matches are distributed among these distances:
16 27 0.14
17 44 0.23
18 56 0.29
19 39 0.20
20 22 0.11
21 7 0.04
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (17 bp):
AAAAAAAAAAACAAAAC
Found at i:30270352 original size:12 final size:12
Alignment explanation
Indices: 30270302--30270552 Score: 229
Period size: 12 Copynumber: 19.7 Consensus size: 12
30270292 GAGTACAATT
30270302 AAAAAAAACAAA
1 AAAAAAAACAAA
* *
30270314 CAAACAAACAAAA
1 AAAAAAAAC-AAA
30270327 CAAAAAAAACAAA
1 -AAAAAAAACAAA
30270340 AAAAAAAACAAA
1 AAAAAAAACAAA
30270352 AAAAAAGGAA-AAA
1 AAAAAA--AACAAA
30270365 AGAAAAGAAA-AAA
1 A-AAAA-AAACAAA
30270378 AAATAAAAACAAA
1 AAA-AAAAACAAA
* *
30270391 AAAAAGAAGAAA
1 AAAAAAAACAAA
*
30270403 AAAAAGAACAAA
1 AAAAAAAACAAA
*
30270415 AACAAAAACAAA
1 AAAAAAAACAAA
*
30270427 ACAAAAAACAAAAA
1 A-AAAAAA-ACAAA
30270441 ACAAAAAAACAAA
1 A-AAAAAAACAAA
*
30270454 AAAAAACAAAAAA
1 AAAAAA-AACAAA
30270467 ACAAAAAAACTAAA
1 A-AAAAAAAC-AAA
30270481 ACAAAAAAACAAA
1 A-AAAAAAACAAA
*
30270494 AACAAAAACAAA
1 AAAAAAAACAAA
30270506 AAAAAAAACAAA
1 AAAAAAAACAAA
30270518 AACAAACAAA-AACA
1 AA-AAA-AAACAA-A
*
30270532 AAACAAAACAAA
1 AAAAAAAACAAA
30270544 AAAGAAAAA
1 AAA-AAAAA
30270553 AGCTTTGGTA
Statistics
Matches: 203, Mismatches: 18, Indels: 35
0.79 0.07 0.14
Matches are distributed among these distances:
12 94 0.46
13 59 0.29
14 49 0.24
15 1 0.00
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:30270552 original size:18 final size:18
Alignment explanation
Indices: 30270302--30270553 Score: 213
Period size: 19 Copynumber: 13.7 Consensus size: 18
30270292 GAGTACAATT
*
30270302 AAAAAAAACAAAC-AAAC
1 AAAAAAAAAAAACAAAAC
*
30270319 AAACAAAACAAAA-AAAAC
1 AAA-AAAAAAAAACAAAAC
30270337 -AAAAAAAAAAACAAAA-
1 AAAAAAAAAAAACAAAAC
*
30270353 AAAAAGGAAAAAAGA-AAAGAA
1 AAAAA--AAAAAA-ACAAA-AC
30270374 AAAAAAATAAAAACAAAA-
1 AAAAAAA-AAAAACAAAAC
30270392 AAAAGAAGAAAAAA-AAGAAC
1 AAAA-AA-AAAAAACAA-AAC
*
30270412 -AAAAACAAAAACAAAAC
1 AAAAAAAAAAAACAAAAC
30270429 AAAAAACAAAAAACAAAA-
1 AAAAAA-AAAAAACAAAAC
30270447 AAACAAAAAAAAAC-AAA-
1 AAA-AAAAAAAAACAAAAC
*
30270464 AAAACAAAAAAACTAAAAC
1 AAAAAAAAAAAAC-AAAAC
30270483 AAAAAAACAAAAACAAAA-
1 AAAAAAA-AAAAACAAAAC
30270501 ACAAAAAAAAAAACAAAAAC
1 A-AAAAAAAAAAAC-AAAAC
30270521 AAACAAAAACAAAACAAAAC
1 AAA-AAAAA-AAAACAAAAC
30270541 AAAAAAGAAAAAA
1 AAAAAA-AAAAAA
30270554 GCTTTGGTAA
Statistics
Matches: 199, Mismatches: 7, Indels: 56
0.76 0.03 0.21
Matches are distributed among these distances:
16 17 0.09
17 27 0.14
18 46 0.23
19 67 0.34
20 32 0.16
21 10 0.05
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (18 bp):
AAAAAAAAAAAACAAAAC
Found at i:30271615 original size:34 final size:34
Alignment explanation
Indices: 30271572--30271639 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
30271562 ACGTCGAGAA
30271572 GAAGAAAGATTTAGGGAGAGAAGGGAGAAACACC
1 GAAGAAAGATTTAGGGAGAGAAGGGAGAAACACC
30271606 GAAGAAAGATTTAGGGAGAGAAGGGAGAAACACC
1 GAAGAAAGATTTAGGGAGAGAAGGGAGAAACACC
30271640 AATCATCTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.09, G:0.35, T:0.09
Consensus pattern (34 bp):
GAAGAAAGATTTAGGGAGAGAAGGGAGAAACACC
Found at i:30272384 original size:16 final size:15
Alignment explanation
Indices: 30272365--30272440 Score: 53
Period size: 16 Copynumber: 4.8 Consensus size: 15
30272355 AAAATTAGTC
30272365 AAAAATAAAAAATAA
1 AAAAATAAAAAATAA
* * *
30272380 TAAAATAATAAAGAGA
1 AAAAATAAAAAATA-A
* *
30272396 TAAAATGGGAAAAATAA
1 AAAAAT--AAAAAATAA
* *
30272413 AAAAACATAATAATAA
1 AAAAATA-AAAAATAA
30272429 AAAAATAAAAAA
1 AAAAATAAAAAA
30272441 ATAAGCGTAA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
15 15 0.33
16 20 0.44
17 5 0.11
18 5 0.11
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (15 bp):
AAAAATAAAAAATAA
Found at i:30272416 original size:8 final size:8
Alignment explanation
Indices: 30272405--30272444 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
30272395 ATAAAATGGG
30272405 AAAAATAA
1 AAAAATAA
* *
30272413 AAAAACAT
1 AAAAATAA
*
30272421 AATAATAA
1 AAAAATAA
30272429 AAAAATAA
1 AAAAATAA
30272437 AAAAATAA
1 AAAAATAA
30272445 GCGTAAACTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAATAA
Found at i:30275306 original size:29 final size:30
Alignment explanation
Indices: 30275242--30275335 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 30
30275232 ATTAGGGGTT
* *
30275242 ATTTGACTCAAAATAAAAATATAAGAGTTT
1 ATTTGACTCAAAATAAAAATATAAGACTTG
*
30275272 ATTTGACTCAAAAT-ACAATATAAGGACTTG
1 ATTTGACTCAAAATAAAAATATAA-GACTTG
* **
30275302 A-TTGA-GCGTAATAAAAATATAATGACTT-
1 ATTTGACTCAAAATAAAAATATAA-GACTTG
30275330 ATTTGA
1 ATTTGA
30275336 ATTTTTTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.09
29 29 0.55
30 19 0.36
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (30 bp):
ATTTGACTCAAAATAAAAATATAAGACTTG
Found at i:30275440 original size:78 final size:77
Alignment explanation
Indices: 30275289--30275445 Score: 201
Period size: 78 Copynumber: 2.0 Consensus size: 77
30275279 TCAAAATACA
* *
30275289 ATATAAGGACTTGATTGAGCGTAATAAAAATATAATGACTTATTTGAATTTTTTTAAAAATAGTT
1 ATATAAAGACTTGATTGAACGTAATAAAAATATAATGACTTATTTGAATTTTTTT-AAAATAGTT
**
30275354 TGGAGGCTTTTTT
65 AAGAGGCTTTTTT
* * *
30275367 ATATAAAGACTTGATTGAATGTAATAAAAATATAATGATTTATTTGAAAATTTTTTT-GAATAGC
1 ATATAAAGACTTGATTGAACGTAATAAAAATATAATGACTTATTTG--AATTTTTTTAAAATAG-
30275431 TTAAG-GGCTTTTTT
63 TTAAGAGGCTTTTTT
30275445 A
1 A
30275446 GATGTTATGC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 57 0.83
79 3 0.04
80 9 0.13
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (77 bp):
ATATAAAGACTTGATTGAACGTAATAAAAATATAATGACTTATTTGAATTTTTTTAAAATAGTTA
AGAGGCTTTTTT
Found at i:30281139 original size:30 final size:29
Alignment explanation
Indices: 30281105--30281165 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
30281095 TTCCATATCC
*
30281105 ATCAAACTAGAGTAGAGAGAATTCTGTACT
1 ATCAAACTAGAGTAGAGA-AATTCTGCACT
* *
30281135 ATCAAACTAGTGTAGAGAAATTTTGCACT
1 ATCAAACTAGAGTAGAGAAATTCTGCACT
30281164 AT
1 AT
30281166 ACTCTGTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (29 bp):
ATCAAACTAGAGTAGAGAAATTCTGCACT
Found at i:30288231 original size:237 final size:237
Alignment explanation
Indices: 30287582--30288491 Score: 1696
Period size: 237 Copynumber: 3.8 Consensus size: 237
30287572 TTATGTTTCC
* *
30287582 TACATTTGTTTGCATAGAGAAAGCGTTAGACAATTGCATAAGAAAATCCATTTTAAGTGATTGTA
1 TACATTTGTTTGCATAGAGAAAGCGTTAGACAATTGCATATGAAAATCCATTGTAAGTGATTGTA
* ** *
30287647 AAACAAATTTTTTCAGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
66 AAAAAAAAATTTTCTGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
30287712 AATCATAAGCATAATTACCAAACTCTGGATCATTTGGACCTTTATTTGATGGAGCATTTTCACCT
131 AATCATAAGCATAATTACCAAACTCTGGATCATTTGGACCTTTATTTGATGGAGCATTTTCACCT
*
30287777 CTGGACTCTGGATCATTTACACCTTTGTTGGTTGGAGTATTT
196 CTGGACTCTGGATCATTTACGCCTTTGTTGGTTGGAGTATTT
*
30287819 TACATTTGTTTGCATAGAGAAAGCGTTAGATAATTGCATA-GAAAATCCATTGTAAGTGATTGTA
1 TACATTTGTTTGCATAGAGAAAGCGTTAGACAATTGCATATGAAAATCCATTGTAAGTGATTGTA
*
30287883 AAAAAAAAAATTTCTGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
66 AAAAAAAAATTTTCTGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
*
30287948 AATCATAAGCATAATTACCAAACTCTGGGTCATTTGGACCTTTATTTGATGGAGCATTTTCACCT
131 AATCATAAGCATAATTACCAAACTCTGGATCATTTGGACCTTTATTTGATGGAGCATTTTCACCT
30288013 CTGGACTCTGGATCATTTACGCCTTTGTTGGTTGGAGTATTT
196 CTGGACTCTGGATCATTTACGCCTTTGTTGGTTGGAGTATTT
30288055 TACATTTGTTTGCATAGAGAAAGCGTTAGACAATTGCATATGAAAATCCATTGTAAGTGATTGTA
1 TACATTTGTTTGCATAGAGAAAGCGTTAGACAATTGCATATGAAAATCCATTGTAAGTGATTGTA
30288120 AAAAAAAAATTTTCTGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
66 AAAAAAAAATTTTCTGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
**
30288185 AATCATAAGCATAATTACCAAACTCTGGATCATTTGGATTTTTATTTGATGGAGCATTTTCACCT
131 AATCATAAGCATAATTACCAAACTCTGGATCATTTGGACCTTTATTTGATGGAGCATTTTCACCT
30288250 CTGGACTCTGGATCATTTACGCCTTTGTTGGTTGGAGTATTT
196 CTGGACTCTGGATCATTTACGCCTTTGTTGGTTGGAGTATTT
30288292 TACATTTGTTTGCATAGAGAAAGCGTTAGACAATTGCATATGAAAATCCATTGTAAGTGATTGTA
1 TACATTTGTTTGCATAGAGAAAGCGTTAGACAATTGCATATGAAAATCCATTGTAAGTGATTGTA
30288357 AAAAAAAAATTTTCTGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
66 AAAAAAAAATTTTCTGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
*
30288422 AATCATAAGCATAATTACCAAACTCTGGGTCATTTGGACCTTTATTTGATGGAGCATTTTCACCT
131 AATCATAAGCATAATTACCAAACTCTGGATCATTTGGACCTTTATTTGATGGAGCATTTTCACCT
30288487 CTGGA
196 CTGGA
30288492 TTCTTTGCTT
Statistics
Matches: 655, Mismatches: 17, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
236 227 0.35
237 428 0.65
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (237 bp):
TACATTTGTTTGCATAGAGAAAGCGTTAGACAATTGCATATGAAAATCCATTGTAAGTGATTGTA
AAAAAAAAATTTTCTGTCGATTGGATCATTACCTTTGGATTCTTTCACTGAACCTTTATATTCAG
AATCATAAGCATAATTACCAAACTCTGGATCATTTGGACCTTTATTTGATGGAGCATTTTCACCT
CTGGACTCTGGATCATTTACGCCTTTGTTGGTTGGAGTATTT
Found at i:30288627 original size:87 final size:87
Alignment explanation
Indices: 30288438--30288802 Score: 486
Period size: 87 Copynumber: 4.2 Consensus size: 87
30288428 AAGCATAATT
* ** * * * * *
30288438 ACCAAACTCTGGGTCATTTGGACCTTTATTTGATGGAGCATTTTCACCTCTGGATTCTTTGCTTG
1 ACCAAACTCTGGATCATTTACACCTTTGTTTGAAGGAGCATCTTCACCTTTGGATTCTTTGCCTG
30288503 -A--ATCACCATACCAATAAGC
66 AATTATCACCATACCAATAAGC
* * ** * * **
30288522 ACCGAACTCTGGATCATTTACACCTTTGTTGGTTGGAGTATTTTCAATTTTGGATTCTTTGCCTG
1 ACCAAACTCTGGATCATTTACACCTTTGTTTGAAGGAGCATCTTCACCTTTGGATTCTTTGCCTG
*
30288587 AATTATCACCGTACCAATAAGC
66 AATTATCACCATACCAATAAGC
* **
30288609 ACCAAACTCTGGATCATTTACACCTTTGTTTGTAGGAGCATCTTCACCTTTGGATTCTTTGTTTG
1 ACCAAACTCTGGATCATTTACACCTTTGTTTGAAGGAGCATCTTCACCTTTGGATTCTTTGCCTG
30288674 AATTATCACCATACCAATAAGC
66 AATTATCACCATACCAATAAGC
* *
30288696 ACCAAACTCTGGATCATTTACACCTTTGTTCGAAGGAGCATCTTCACCTTTGAAATT-TTTGCCT
1 ACCAAACTCTGGATCATTTACACCTTTGTTTGAAGGAGCATCTTCACCTTTG-GATTCTTTGCCT
30288760 GAATTATCACCATACCAATAAGC
65 GAATTATCACCATACCAATAAGC
*
30288783 ACCAAACTCCGGATCATTTA
1 ACCAAACTCTGGATCATTTA
30288803 TACCCTTTTG
Statistics
Matches: 248, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
84 53 0.21
85 1 0.00
87 191 0.77
88 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (87 bp):
ACCAAACTCTGGATCATTTACACCTTTGTTTGAAGGAGCATCTTCACCTTTGGATTCTTTGCCTG
AATTATCACCATACCAATAAGC
Found at i:30291755 original size:22 final size:22
Alignment explanation
Indices: 30291707--30291755 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
30291697 GAAATTGATT
* *
30291707 AGACTGGTTTTTAAGTATTGCG
1 AGACTGGTTTTTAAGCATTACG
*
30291729 AGACTGGTTTTTATGCATTACG
1 AGACTGGTTTTTAAGCATTACG
*
30291751 TGACT
1 AGACT
30291756 TAATCACTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.41
Consensus pattern (22 bp):
AGACTGGTTTTTAAGCATTACG
Found at i:30291824 original size:22 final size:22
Alignment explanation
Indices: 30291796--30291844 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
30291786 ACGCTATTGG
*
30291796 TTTTAGGTATTGCGTGACTGAT
1 TTTTAGGCATTGCGTGACTGAT
30291818 TTTTAGGCATTGCGTGACTGAT
1 TTTTAGGCATTGCGTGACTGAT
30291840 TTTTA
1 TTTTA
30291845 AGTAATGCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.47
Consensus pattern (22 bp):
TTTTAGGCATTGCGTGACTGAT
Found at i:30291926 original size:26 final size:26
Alignment explanation
Indices: 30291897--30292154 Score: 140
Period size: 26 Copynumber: 10.6 Consensus size: 26
30291887 AATGCTTATC
* * *
30291897 AACTAGTCACACAATACTTTATCAGA
1 AACTAGTCACGCAATACCTTATCAAA
30291923 AACTAGTCACGCAATACCTTATCAAA
1 AACTAGTCACGCAATACCTTATCAAA
30291949 AACTAGTCACGCAATACC----CAAA
1 AACTAGTCACGCAATACCTTATCAAA
** * * *
30291971 GTC-AGTAACACAATGCC-TATC--A
1 AACTAGTCACGCAATACCTTATCAAA
* *
30291993 A-CTAGTTACGCAATATCTTAT-AAGA
1 AACTAGTCACGCAATACCTTATCAA-A
* *
30292018 AACTAGTCATGCAATACTTTATCAAA
1 AACTAGTCACGCAATACCTTATCAAA
* *
30292044 AACTAGTCACACAATGCC----CAAA
1 AACTAGTCACGCAATACCTTATCAAA
** * *
30292066 GTC-AATCACGCAATGCC-TATC---
1 AACTAGTCACGCAATACCTTATCAAA
* * * *
30292087 AACTAGTCACACTATACTTTATCAGA
1 AACTAGTCACGCAATACCTTATCAAA
* *
30292113 AACTAGTCACACAATACCTTATAAAAA
1 AACTAGTCACGCAATACCTTAT-CAAA
*
30292140 AATTAGTCACGCAAT
1 AACTAGTCACGCAAT
30292155 GCCTAAAAAC
Statistics
Matches: 175, Mismatches: 38, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
21 25 0.14
22 30 0.17
23 7 0.04
24 2 0.01
25 2 0.01
26 92 0.53
27 17 0.10
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.24
Consensus pattern (26 bp):
AACTAGTCACGCAATACCTTATCAAA
Found at i:30292021 original size:95 final size:95
Alignment explanation
Indices: 30291886--30292154 Score: 378
Period size: 95 Copynumber: 2.8 Consensus size: 95
30291876 ACAAGTCACG
*
30291886 CAATGCTTATCAACTAGTCACACAATACTTTATCAGAAACTAGTCACGCAATACCTTATCAAAAA
1 CAATGCCTATCAACTAGTCACACAATACTTTATCAGAAACTAGTCACGCAATACCTTATCAAAAA
*
30291951 CTAGTCACGCAATACCCAAAGTCAGTAACA
66 CTAGTCACGCAATACCCAAAGTCAATAACA
* * * * *
30291981 CAATGCCTATCAACTAGTTACGCAATA-TCTTATAAGAAACTAGTCATGCAATACTTTATCAAAA
1 CAATGCCTATCAACTAGTCACACAATACT-TTATCAGAAACTAGTCACGCAATACCTTATCAAAA
* * * *
30292045 ACTAGTCACACAATGCCCAAAGTCAATCACG
65 ACTAGTCACGCAATACCCAAAGTCAATAACA
* * *
30292076 CAATGCCTATCAACTAGTCACACTATACTTTATCAGAAACTAGTCACACAATACCTTATAAAAAA
1 CAATGCCTATCAACTAGTCACACAATACTTTATCAGAAACTAGTCACGCAATACCTTAT-CAAAA
*
30292141 ATTAGTCACGCAAT
65 ACTAGTCACGCAAT
30292155 GCCTAAAAAC
Statistics
Matches: 150, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
94 1 0.01
95 132 0.88
96 17 0.11
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (95 bp):
CAATGCCTATCAACTAGTCACACAATACTTTATCAGAAACTAGTCACGCAATACCTTATCAAAAA
CTAGTCACGCAATACCCAAAGTCAATAACA
Found at i:30292184 original size:22 final size:23
Alignment explanation
Indices: 30292136--30292185 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
30292126 ATACCTTATA
*
30292136 AAAAAATTAGTCACGCAATGCCT
1 AAAAAACTAGTCACGCAATGCCT
* *
30292159 -AAAAACTAGTCACGTAAT-TCT
1 AAAAAACTAGTCACGCAATGCCT
30292180 AAAAAA
1 AAAAAA
30292186 TCACAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.22
Consensus pattern (23 bp):
AAAAAACTAGTCACGCAATGCCT
Found at i:30292347 original size:19 final size:21
Alignment explanation
Indices: 30292311--30292349 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
30292301 TTTATATATC
30292311 AAAAATCACTCTAAAATGCTT
1 AAAAATCACTCTAAAATGCTT
30292332 AAAAAT-ACTC-AAAATGCT
1 AAAAATCACTCTAAAATGCT
30292350 CACAGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAATCACTCTAAAATGCTT
Found at i:30298194 original size:49 final size:49
Alignment explanation
Indices: 30298137--30298250 Score: 219
Period size: 49 Copynumber: 2.3 Consensus size: 49
30298127 ATGAACAATA
*
30298137 TTATCTCAACAACCATAATCAATAAATATTATTCCAATTTTTATCTAAT
1 TTATCTCAACAACCATAATCAATAAATATTATTCCAATTTTCATCTAAT
30298186 TTATCTCAACAACCATAATCAATAAATATTATTCCAATTTTCATCTAAT
1 TTATCTCAACAACCATAATCAATAAATATTATTCCAATTTTCATCTAAT
30298235 TTATCTCAACAACCAT
1 TTATCTCAACAACCAT
30298251 TGACCTATTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.39
Consensus pattern (49 bp):
TTATCTCAACAACCATAATCAATAAATATTATTCCAATTTTCATCTAAT
Found at i:30298434 original size:17 final size:17
Alignment explanation
Indices: 30298412--30298444 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30298402 GAAAAGATAG
30298412 AAAATA-AAATGAAAAAC
1 AAAATAGAAA-GAAAAAC
30298429 AAAATAGAAAGAAAAA
1 AAAATAGAAAGAAAAA
30298445 GAAGAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAGAAAAAC
Found at i:30313642 original size:21 final size:20
Alignment explanation
Indices: 30313614--30313652 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
30313604 CTAGAGCTTA
30313614 AAGAAGAAAAAGAAGAAAAC
1 AAGAAGAAAAAGAAGAAAAC
**
30313634 AAGAGAGAAGCAGAAGAAA
1 AAGA-AGAAAAAGAAGAAA
30313653 GGAAGAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.69, C:0.05, G:0.26, T:0.00
Consensus pattern (20 bp):
AAGAAGAAAAAGAAGAAAAC
Found at i:30337944 original size:13 final size:12
Alignment explanation
Indices: 30337904--30337952 Score: 64
Period size: 12 Copynumber: 4.0 Consensus size: 12
30337894 AATAGAATAG
*
30337904 AAATAAATAAAT
1 AAATAAAAAAAT
30337916 AAATAAAAAAAT
1 AAATAAAAAAAT
30337928 AAATTAAAAGAAA-
1 AAA-TAAAA-AAAT
30337941 AAATAAAAAAAT
1 AAATAAAAAAAT
30337953 TTTAAAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.09
12 19 0.58
13 8 0.24
14 3 0.09
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:30338655 original size:35 final size:33
Alignment explanation
Indices: 30338587--30338681 Score: 93
Period size: 35 Copynumber: 2.8 Consensus size: 33
30338577 AACATGCTGA
* * *
30338587 TGCTCTGCTTTACTTGTATCCTTTCCAGTCTGC
1 TGCTATGCATTACTTGTATCCTTTACAGTCTGC
* * *
30338620 TTCTGCGTGCATTGCTTGTATCCTTTACA-TGCTGC
1 TGCT--ATGCATTACTTGTATCCTTTACAGT-CTGC
*
30338655 TGCTATGCTTTACTTGTATCCTTTACA
1 TGCTATGCATTACTTGTATCCTTTACA
30338682 ACTTTTGCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
33 23 0.46
34 1 0.02
35 26 0.52
ACGTcount: A:0.13, C:0.26, G:0.16, T:0.45
Consensus pattern (33 bp):
TGCTATGCATTACTTGTATCCTTTACAGTCTGC
Found at i:30338676 original size:33 final size:33
Alignment explanation
Indices: 30338578--30338681 Score: 111
Period size: 33 Copynumber: 3.1 Consensus size: 33
30338568 TTTGCTTGTA
* *
30338578 ACATGCTGATGCTCTGCTTTACTTGTATCCTTT
1 ACATGCTGCTGCTATGCTTTACTTGTATCCTTT
* * * * *
30338611 CCA-GTCTGCTTCTGCGTGCATTGCTTGTATCCTTT
1 ACATG-CTGCTGCT--ATGCTTTACTTGTATCCTTT
30338646 ACATGCTGCTGCTATGCTTTACTTGTATCCTTT
1 ACATGCTGCTGCTATGCTTTACTTGTATCCTTT
30338679 ACA
1 ACA
30338682 ACTTTTGCCT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
32 1 0.02
33 28 0.50
35 26 0.46
36 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.16, T:0.43
Consensus pattern (33 bp):
ACATGCTGCTGCTATGCTTTACTTGTATCCTTT
Found at i:30339092 original size:23 final size:23
Alignment explanation
Indices: 30339046--30339106 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
30339036 TTAAATCTAG
* *
30339046 TTATATTAGAATAACAATTCCTAA
1 TTATATTAGGATAA-GATTCCTAA
*
30339070 TTCTATTAGGATAAGATTCCTAA
1 TTATATTAGGATAAGATTCCTAA
30339093 TTATATTAGGATAA
1 TTATATTAGGATAA
30339107 AGTTATTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 21 0.64
24 12 0.36
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (23 bp):
TTATATTAGGATAAGATTCCTAA
Found at i:30343016 original size:2 final size:2
Alignment explanation
Indices: 30343009--30343043 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30342999 GGAATATAAT
30343009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30343044 CCATGATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30346400 original size:2 final size:2
Alignment explanation
Indices: 30346393--30346439 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
30346383 TTATGCAACA
30346393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30346435 AT AT A
1 AT AT A
30346440 ATCTAACTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30346932 original size:15 final size:15
Alignment explanation
Indices: 30346909--30346938 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30346899 AACATATTTA
*
30346909 TATTTTTTTAATTAT
1 TATTATTTTAATTAT
30346924 TATTATTTTAATTAT
1 TATTATTTTAATTAT
30346939 GACACCATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTAATTAT
Found at i:30349301 original size:101 final size:101
Alignment explanation
Indices: 30349126--30349308 Score: 294
Period size: 101 Copynumber: 1.8 Consensus size: 101
30349116 GAGGTACGAA
* *
30349126 CTAAGGTCTATTATTAGACAAAAAATGACAACATACAATTTGCATTTCAGAGAGAATGACAGGTT
1 CTAAGGTCTATTATTAGACAAAAAATGACAACATACAATTCGCATTTCAGAGAAAATGACAGGTT
30349191 TGGCATCTAAAATTACTGTTATTAGTAGCGTCACAC
66 TGGCATCTAAAATTACTGTTATTAGTAGCGTCACAC
* * * * **
30349227 CTAAGGTTTTTTATTAGACATAAAATGACAACATACAGTTCGCATTTTGGAGAAAATGACAGGTT
1 CTAAGGTCTATTATTAGACAAAAAATGACAACATACAATTCGCATTTCAGAGAAAATGACAGGTT
30349292 TGGCATCTAAAATTACT
66 TGGCATCTAAAATTACT
30349309 CCTAATATTG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 74 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (101 bp):
CTAAGGTCTATTATTAGACAAAAAATGACAACATACAATTCGCATTTCAGAGAAAATGACAGGTT
TGGCATCTAAAATTACTGTTATTAGTAGCGTCACAC
Found at i:30349526 original size:23 final size:23
Alignment explanation
Indices: 30349499--30349545 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
30349489 TAGGTATTTT
*
30349499 ATTTAT-TTTATTAGTTTAGTTTA
1 ATTTATATTTAAT-GTTTAGTTTA
*
30349522 ATTTATATTTAATGTTTATTTTA
1 ATTTATATTTAATGTTTAGTTTA
30349545 A
1 A
30349546 GTTAATGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (23 bp):
ATTTATATTTAATGTTTAGTTTA
Found at i:30350121 original size:101 final size:100
Alignment explanation
Indices: 30349945--30350146 Score: 395
Period size: 101 Copynumber: 2.0 Consensus size: 100
30349935 ATAATTTGCT
30349945 CTTGTGAATGATCCTTAATGTACCTCCAGCTCTTGAAAGCTCATGATGTTGATTTTCAGTCATTT
1 CTTGTGAATGATCCTTAATGTACCTCCAGCTCTTGAAAGCTCATGATGTTGATTTTCAGTCATTT
30350010 GCTGTGTTTTTAAAGGCGAAGGTTCTGTTTCTCTC
66 GCTGTGTTTTTAAAGGCGAAGGTTCTGTTTCTCTC
30350045 CNTTGTGAATGATCCTTAATGTACCTCCAGCTCTTGAAAGCTCATGATGTTGATTTTCAGTCATT
1 C-TTGTGAATGATCCTTAATGTACCTCCAGCTCTTGAAAGCTCATGATGTTGATTTTCAGTCATT
30350110 TGCTGTGTTTTTAAAGGCGAAGGTTCTGTTTCTCTC
65 TGCTGTGTTTTTAAAGGCGAAGGTTCTGTTTCTCTC
30350146 C
1 C
30350147 CTAGGGTATT
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
100 1 0.01
101 100 0.99
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (100 bp):
CTTGTGAATGATCCTTAATGTACCTCCAGCTCTTGAAAGCTCATGATGTTGATTTTCAGTCATTT
GCTGTGTTTTTAAAGGCGAAGGTTCTGTTTCTCTC
Found at i:30354711 original size:38 final size:38
Alignment explanation
Indices: 30354647--30354726 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
30354637 GTTGGATGGC
* * * *
30354647 GATATAGACCTCAATGGCGTTGGAGAGCTAGACGGTGA
1 GATATAGACCTCAATAGCATTAGAGAGCTAGACGGAGA
* *
30354685 GATATAGACCTCGATAGCATTAGAGAGCTGGACGGAGA
1 GATATAGACCTCAATAGCATTAGAGAGCTAGACGGAGA
30354723 GATA
1 GATA
30354727 ACTAAATCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.20
Consensus pattern (38 bp):
GATATAGACCTCAATAGCATTAGAGAGCTAGACGGAGA
Found at i:30357724 original size:34 final size:34
Alignment explanation
Indices: 30357681--30357748 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
30357671 ATCTTGGTTC
* *
30357681 TTCAGATCTTATTCCTTGGACTTGTTTGTTGAAA
1 TTCAGATCTTACTCCTTGGACTTGTTCGTTGAAA
*
30357715 TTCAGATCTTCCTCCTTGGACTTGTTCGTTGAAA
1 TTCAGATCTTACTCCTTGGACTTGTTCGTTGAAA
30357749 CTTTAAAGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (34 bp):
TTCAGATCTTACTCCTTGGACTTGTTCGTTGAAA
Found at i:30360825 original size:12 final size:12
Alignment explanation
Indices: 30360805--30360833 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30360795 ATAATTATGC
30360805 TTAAA-ACTTAA
1 TTAAACACTTAA
30360816 TTAAACACTTAA
1 TTAAACACTTAA
30360828 TTAAAC
1 TTAAAC
30360834 TCTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAACACTTAA
Found at i:30371245 original size:14 final size:14
Alignment explanation
Indices: 30371228--30371269 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
30371218 TTTAGAATAA
*
30371228 AATAATATTTTATT
1 AATAATATTATATT
*
30371242 AATAAAATTATATT
1 AATAATATTATATT
30371256 AA-AATATTAATATT
1 AATAATATT-ATATT
30371270 TAGTCAGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAATATTATATT
Found at i:30371705 original size:20 final size:20
Alignment explanation
Indices: 30371660--30371697 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30371650 TTTTGGCCCC
*
30371660 ATTTGACTTATTGGAGTATA
1 ATTTGACTCATTGGAGTATA
30371680 ATTTGACTCATTGGAGTA
1 ATTTGACTCATTGGAGTA
30371698 AGATTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTGACTCATTGGAGTATA
Found at i:30379780 original size:36 final size:36
Alignment explanation
Indices: 30379732--30379869 Score: 161
Period size: 36 Copynumber: 3.8 Consensus size: 36
30379722 ACGATGATTG
*
30379732 AAGCCCTGATGTGAGGGAAAGAATACCACACGAATA
1 AAGCCCAGATGTGAGGGAAAGAATACCACACGAATA
* * * *
30379768 AAGCCCAAATGTGGGGGAAAGAATACCATACAAATA
1 AAGCCCAGATGTGAGGGAAAGAATACCACACGAATA
* * *
30379804 AAGCCCAGATGT-AGGGGAAAAAATACCACAAGGATA
1 AAGCCCAGATGTGA-GGGAAAGAATACCACACGAATA
* * *
30379840 AAGCCCAGATATGGGGGTAAGAATACCACA
1 AAGCCCAGATGTGAGGGAAAGAATACCACA
30379870 TGTGTTAAGT
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (36 bp):
AAGCCCAGATGTGAGGGAAAGAATACCACACGAATA
Found at i:30379855 original size:72 final size:72
Alignment explanation
Indices: 30379732--30379867 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
30379722 ACGATGATTG
* * * *
30379732 AAGCCCTGATGTGAGGGAAAGAATACCACACGAATAAAGCCCAAATGTGGGGGAAAGAATACCAT
1 AAGCCCAGATGTGAGGGAAAAAATACCACAAGAATAAAGCCCAAATATGGGGGAAAGAATACCAT
30379797 ACAAATA
66 ACAAATA
* * *
30379804 AAGCCCAGATGT-AGGGGAAAAAATACCACAAGGATAAAGCCCAGATATGGGGGTAAGAATACCA
1 AAGCCCAGATGTGA-GGGAAAAAATACCACAAGAATAAAGCCCAAATATGGGGGAAAGAATACCA
30379868 CATGTGTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 1 0.02
72 55 0.98
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (72 bp):
AAGCCCAGATGTGAGGGAAAAAATACCACAAGAATAAAGCCCAAATATGGGGGAAAGAATACCAT
ACAAATA
Found at i:30389956 original size:21 final size:21
Alignment explanation
Indices: 30389914--30389956 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
30389904 CTTGTACCGG
*
30389914 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
30389935 TGGTGGTACTAGAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
30389956 T
1 T
30389957 TGACCAGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.37, T:0.23
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:30390371 original size:22 final size:22
Alignment explanation
Indices: 30390346--30390389 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30390336 TTTAAAACCA
30390346 CTTTAAAACCAAAAACTCTTAT
1 CTTTAAAACCAAAAACTCTTAT
*
30390368 CTTTAAAACCAAAAGCTCTTAT
1 CTTTAAAACCAAAAACTCTTAT
30390390 ACCAATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTTAT
Found at i:30395795 original size:129 final size:129
Alignment explanation
Indices: 30395565--30395816 Score: 407
Period size: 129 Copynumber: 2.0 Consensus size: 129
30395555 AACACTTTAA
* *
30395565 GATGATCATATGAGGGTTTTTCTTTAAATAAAAACTCCTATAGGGATTTTTCATCAAGTATTGGT
1 GATGATCATATGAGGGTTTTTCTTTAAATAAAAACTCATATAGGGATTTTCCATCAAGTATTGGT
30395630 GTGGATAGGATATTTATCAAGTATACTACTATTATTACACATTTGCCCCAATATCTTACTCTAG
66 GTGGATAGGATATTTATCAAGTATACTACTATTATTACACATTTGCCCCAATATCTTACTCTAG
* *
30395694 GATGATCATATGAGGGTTTTTCTTTCAATAAAAACTCATATGGGGATTTTCCATCTAA-TATTGG
1 GATGATCATATGAGGGTTTTTCTTTAAATAAAAACTCATATAGGGATTTTCCATC-AAGTATTGG
* * * **
30395758 TGTGGGTAGGATATTTATCAAGTATGCTACTGTTATTACACATTTTTCCCAATATCTTA
65 TGTGGATAGGATATTTATCAAGTATACTACTATTATTACACATTTGCCCCAATATCTTA
30395817 AAGGTAGATT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
129 111 0.98
130 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (129 bp):
GATGATCATATGAGGGTTTTTCTTTAAATAAAAACTCATATAGGGATTTTCCATCAAGTATTGGT
GTGGATAGGATATTTATCAAGTATACTACTATTATTACACATTTGCCCCAATATCTTACTCTAG
Found at i:30404198 original size:17 final size:18
Alignment explanation
Indices: 30404165--30404198 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30404155 TTTTAATTGT
*
30404165 AATTAGTTAATATATATA
1 AATTAGTTAAGATATATA
30404183 AATTAG-TAAGATATAT
1 AATTAGTTAAGATATAT
30404199 TTATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
AATTAGTTAAGATATATA
Found at i:30404291 original size:2 final size:2
Alignment explanation
Indices: 30404284--30404332 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
30404274 TAGCTATAGA
*
30404284 AT AT AT AT AT ACT AT AT AT AT A- AT AT AT A- AT AT A- AA AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30404324 AT AT AT AT A
1 AT AT AT AT A
30404333 ATAAAAAAAN
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
1 3 0.07
2 37 0.88
3 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:30404299 original size:9 final size:8
Alignment explanation
Indices: 30404284--30404332 Score: 59
Period size: 7 Copynumber: 6.4 Consensus size: 8
30404274 TAGCTATAGA
30404284 ATATATAT
1 ATATATAT
30404292 ATACTATAT
1 ATA-TATAT
30404301 ATATA-AT
1 ATATATAT
30404308 ATATA-AT
1 ATATATAT
*
30404315 ATA-AAAT
1 ATATATAT
30404322 ATATATAT
1 ATATATAT
30404330 ATA
1 ATA
30404333 ATAAAAAAAN
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 1 0.03
7 17 0.46
8 11 0.30
9 8 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATATAT
Found at i:30404337 original size:18 final size:18
Alignment explanation
Indices: 30404284--30404338 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
30404274 TAGCTATAGA
* *
30404284 ATATATATATACT-ATAT
1 ATATATATATAATAAAAT
30404301 ATATAATATATAATATAAAAT
1 ATAT-ATATAT-A-ATAAAAT
30404322 ATATATATATAATAAAA
1 ATATATATATAATAAAA
30404339 AAANNNNNNN
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 4 0.12
18 12 0.38
19 2 0.06
20 7 0.22
21 7 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATATATAATAAAAT
Found at i:30407420 original size:16 final size:16
Alignment explanation
Indices: 30407401--30407432 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30407391 TATATGTATG
30407401 TATATGTATACATACA
1 TATATGTATACATACA
*
30407417 TATATGTATGCATACA
1 TATATGTATACATACA
30407433 ACTTTATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (16 bp):
TATATGTATACATACA
Found at i:30407475 original size:72 final size:70
Alignment explanation
Indices: 30407399--30407656 Score: 220
Period size: 72 Copynumber: 3.6 Consensus size: 70
30407389 TATATATGTA
*
30407399 TGTATATGTA-TACATACATATATGTATGCATACAACTTTATGTATATGAGTTAATATATATGTT
1 TGTATATG-AGTA-ATACATATATGTATACATACAACTTTATGTATATGAGTTAATATATATGTT
30407463 TACATACC
64 TACATA-C
* * **
30407471 TGTATATGAGTTAATACATATATGTTTACATACAACTTTATATAACTTTAT-AACTAAGT-TAAT
1 TGTATATGAG-TAATACATATATGTATACATACAACTTTATGT-A---TATGAGTTAA-TAT-AT
* * **
30407534 ATATATATGTA-
59 ATGTTTACATAC
* * * * *
30407545 TGTATATG-TTAAATTCATATATGTATGCATACCACTTTATGTATTTGAGTTAATATATATGTTT
1 TGTATATGAGT-AATACATATATGTATACATACAACTTTATGTATATGAGTTAATATATATGTTT
30407609 ACATAC
65 ACATAC
* *
30407615 ATGTATATGAGTTAATACATTTATGTTTACATACAACTTTAT
1 -TGTATATGAG-TAATACATATATGTATACATACAACTTTAT
30407657 ATGACTTTAT
Statistics
Matches: 143, Mismatches: 28, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
69 12 0.08
70 5 0.03
71 9 0.06
72 61 0.43
73 30 0.21
74 8 0.06
75 5 0.03
76 13 0.09
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (70 bp):
TGTATATGAGTAATACATATATGTATACATACAACTTTATGTATATGAGTTAATATATATGTTTA
CATAC
Found at i:30407478 original size:32 final size:33
Alignment explanation
Indices: 30407439--30407503 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
30407429 TACAACTTTA
30407439 TGTATATGAGTTAAT-ATATATGTTTACATACC
1 TGTATATGAGTTAATAATATATGTTTACATACC
30407471 TGTATATGAGTTAATACATATATGTTTACATAC
1 TGTATATGAGTTAATA-ATATATGTTTACATAC
30407504 AACTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 15 0.48
34 16 0.52
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (33 bp):
TGTATATGAGTTAATAATATATGTTTACATACC
Found at i:30407503 original size:16 final size:16
Alignment explanation
Indices: 30407454--30407504 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
30407444 ATGAGTTAAT
30407454 ATATATGTTTACATACC
1 ATATATGTTTACATA-C
* *
30407471 TGTATATGAGTTA-ATAC
1 -ATATATG-TTTACATAC
30407488 ATATATGTTTACATAC
1 ATATATGTTTACATAC
30407504 A
1 A
30407505 ACTTTATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 1 0.04
18 9 0.33
19 3 0.11
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (16 bp):
ATATATGTTTACATAC
Found at i:30407609 original size:145 final size:146
Alignment explanation
Indices: 30407384--30407686 Score: 527
Period size: 145 Copynumber: 2.1 Consensus size: 146
30407374 GGGTTTTACA
*
30407384 TAATATATATATGTATGTATATGTATACATACATATATGTATGCATACAACTTTATGTATATGAG
1 TAATATATATATGTATGTATATGTATAAATACATATATGTATGCATACAACTTTATGTATATGAG
*
30407449 TTAATATATATGTTTACATACCTGTATATGAGTTAATACATATATGTTTACATACAACTTTATAT
66 TTAATATATATGTTTACATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATAT
30407514 AACTTTATAACTAAGT
131 AACTTTATAACTAAGT
* * *
30407530 TAATATATATATGTATGTATATGT-TAAATTCATATATGTATGCATACCACTTTATGTATTTGAG
1 TAATATATATATGTATGTATATGTATAAATACATATATGTATGCATACAACTTTATGTATATGAG
*
30407594 TTAATATATATGTTTACATACATGTATATGAGTTAATACATTTATGTTTACATACAACTTTATAT
66 TTAATATATATGTTTACATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATAT
* *
30407659 GACTTTATAATTAAGT
131 AACTTTATAACTAAGT
30407675 TAATATATATAT
1 TAATATATATAT
30407687 ATGTATGCAT
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
145 125 0.84
146 24 0.16
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.44
Consensus pattern (146 bp):
TAATATATATATGTATGTATATGTATAAATACATATATGTATGCATACAACTTTATGTATATGAG
TTAATATATATGTTTACATACATGTATATGAGTTAATACATATATGTTTACATACAACTTTATAT
AACTTTATAACTAAGT
Found at i:30407623 original size:18 final size:17
Alignment explanation
Indices: 30407600--30407649 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
30407590 TGAGTTAATA
30407600 TATATGTTTACATACAT
1 TATATGTTTACATACAT
*
30407617 GTATATGAGTTA-ATACAT
1 -TATATG-TTTACATACAT
30407635 T-TATGTTTACATACA
1 TATATGTTTACATACA
30407650 ACTTTATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 3 0.11
16 9 0.32
17 1 0.04
18 12 0.43
19 3 0.11
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (17 bp):
TATATGTTTACATACAT
Found at i:30407626 original size:32 final size:33
Alignment explanation
Indices: 30407583--30407649 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
30407573 ATACCACTTT
*
30407583 ATGTATTTGAGTTAAT-ATATATGTTTACATAC
1 ATGTATATGAGTTAATAATATATGTTTACATAC
*
30407615 ATGTATATGAGTTAATACATTTATGTTTACATAC
1 ATGTATATGAGTTAATA-ATATATGTTTACATAC
30407649 A
1 A
30407650 ACTTTATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 15 0.48
34 16 0.52
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (33 bp):
ATGTATATGAGTTAATAATATATGTTTACATAC
Found at i:30414363 original size:30 final size:30
Alignment explanation
Indices: 30414327--30414395 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
30414317 TCTTGATTGC
30414327 AAATGAAGAAGATGACAT-GCAAAGAGATGA
1 AAATGAAGAAGATGACATAG-AAAGAGATGA
* *
30414357 AGATGAAGAAGATGACATAGAAGGAGATGA
1 AAATGAAGAAGATGACATAGAAAGAGATGA
30414387 AAATGAAGA
1 AAATGAAGA
30414396 TCAAGATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.29, T:0.13
Consensus pattern (30 bp):
AAATGAAGAAGATGACATAGAAAGAGATGA
Found at i:30414394 original size:15 final size:14
Alignment explanation
Indices: 30414327--30414395 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 14
30414317 TCTTGATTGC
30414327 AAATGAAGAAGATG
1 AAATGAAGAAGATG
*
30414341 ACATGCAA-AGAGATG
1 AAATG-AAGA-AGATG
30414356 AAGATGAAGAAGATG
1 AA-ATGAAGAAGATG
* *
30414371 ACATAGAAGGAGATG
1 AAAT-GAAGAAGATG
30414386 AAAATGAAGA
1 -AAATGAAGA
30414396 TCAAGATCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
14 7 0.16
15 29 0.67
16 7 0.16
ACGTcount: A:0.54, C:0.04, G:0.29, T:0.13
Consensus pattern (14 bp):
AAATGAAGAAGATG
Found at i:30415135 original size:9 final size:9
Alignment explanation
Indices: 30415121--30415146 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30415111 GTATGTTATC
30415121 TTGTTATAT
1 TTGTTATAT
30415130 TTGTTATAT
1 TTGTTATAT
30415139 TTGTTATA
1 TTGTTATA
30415147 AATTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (9 bp):
TTGTTATAT
Found at i:30416649 original size:14 final size:15
Alignment explanation
Indices: 30416617--30416648 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30416607 TGGAACACCG
30416617 TTTCCAACGAAATTT
1 TTTCCAACGAAATTT
30416632 TTTCCAACGAAATTT
1 TTTCCAACGAAATTT
30416647 TT
1 TT
30416649 CGTCTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (15 bp):
TTTCCAACGAAATTT
Found at i:30432788 original size:25 final size:24
Alignment explanation
Indices: 30432766--30432897 Score: 149
Period size: 25 Copynumber: 5.3 Consensus size: 24
30432756 TGTAATCTAG
*
30432766 TTATCTTTACATTTTAAATATCTC
1 TTATCTATACATTTTAAATATCTC
** *
30432790 TTTATCTATACATTTT-TGTAATCTAT
1 -TTATCTATACATTTTAAAT-ATCT-C
*
30432816 TTATCTGTACATTTTAAATATCTC
1 TTATCTATACATTTTAAATATCTC
30432840 TGTATCTATACATTTTAAATATCTC
1 T-TATCTATACATTTTAAATATCTC
*
30432865 TGCATCTATACATTTTAAATATCTC
1 T-TATCTATACATTTTAAATATCTC
30432890 TTTATCTA
1 -TTATCTA
30432898 GTAAATCTGA
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
24 2 0.02
25 87 0.96
26 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.52
Consensus pattern (24 bp):
TTATCTATACATTTTAAATATCTC
Found at i:30432829 original size:50 final size:49
Alignment explanation
Indices: 30432754--30432897 Score: 189
Period size: 50 Copynumber: 2.9 Consensus size: 49
30432744 TAAATCTTAC
* *
30432754 TTTGTAATCTAGTTATCTTTACATTTTAAATATCTCTTTATCTATACATT
1 TTTGTAATCTATTTATCTATACATTTTAAATATCTCTTTATCTATACA-T
* *
30432804 TTTGTAATCTATTTATCTGTACATTTTAAATATCTCTGTATCTATACAT
1 TTTGTAATCTATTTATCTATACATTTTAAATATCTCTTTATCTATACAT
** * **
30432853 TTTAAATATCTCTGCATCTATACATTTTAAATATCTCTTTATCTA
1 TTTGTA-ATCTATTTATCTATACATTTTAAATATCTCTTTATCTA
30432898 GTAAATCTGA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 5 0.06
50 78 0.94
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.51
Consensus pattern (49 bp):
TTTGTAATCTATTTATCTATACATTTTAAATATCTCTTTATCTATACAT
Found at i:30435485 original size:22 final size:22
Alignment explanation
Indices: 30435460--30435503 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
30435450 TCATCAAACA
30435460 CTTTATTCTT-TTTTAT-TTTCAT
1 CTTT-TTCTTCTTTT-TCTTTCAT
30435482 CTTTTTCTTCTTTTTCTTTCAT
1 CTTTTTCTTCTTTTTCTTTCAT
30435504 TCACAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (22 bp):
CTTTTTCTTCTTTTTCTTTCAT
Found at i:30449836 original size:7 final size:6
Alignment explanation
Indices: 30449809--30449834 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30449799 TTGGTTCTCA
30449809 TTCTTT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT
30449835 TCAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTCTTT
Found at i:30451060 original size:2 final size:2
Alignment explanation
Indices: 30451055--30451079 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30451045 TATCTGTGTT
30451055 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30451080 GTATGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30451401 original size:15 final size:15
Alignment explanation
Indices: 30451381--30451411 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30451371 TTTCAATGAG
30451381 TCTTTTATTTTTTTT
1 TCTTTTATTTTTTTT
*
30451396 TCTTTTGTTTTTTTT
1 TCTTTTATTTTTTTT
30451411 T
1 T
30451412 TTTGTTGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.87
Consensus pattern (15 bp):
TCTTTTATTTTTTTT
Found at i:30461147 original size:24 final size:23
Alignment explanation
Indices: 30461120--30461196 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 23
30461110 ATAGTTGTGG
30461120 CAAAATATATAATAGAATACA-TGA
1 CAAAATATATAATA-AA-ACAGTGA
*
30461144 CAAAATATGTAATAAAACATGTGA
1 CAAAATATATAATAAAACA-GTGA
* ** *
30461168 CAAAACATATAGCAAAATATGTGA
1 CAAAATATATAATAAAACA-GTGA
30461192 CAAAA
1 CAAAA
30461197 CACATGACCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.07
23 2 0.04
24 40 0.89
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.22
Consensus pattern (23 bp):
CAAAATATATAATAAAACAGTGA
Found at i:30461163 original size:22 final size:24
Alignment explanation
Indices: 30461120--30461178 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
30461110 ATAGTTGTGG
30461120 CAAAATATATAATAGAATACATGA
1 CAAAATATATAATAGAATACATGA
*
30461144 CAAAATATGTAATA-AA-ACATGTGA
1 CAAAATATATAATAGAATACA--TGA
*
30461168 CAAAACATATA
1 CAAAATATATA
30461179 GCAAAATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 3 0.10
23 2 0.07
24 25 0.83
ACGTcount: A:0.58, C:0.10, G:0.08, T:0.24
Consensus pattern (24 bp):
CAAAATATATAATAGAATACATGA
Found at i:30461172 original size:12 final size:12
Alignment explanation
Indices: 30461141--30461198 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
30461131 ATAGAATACA
*
30461141 TGACAAAATATG
1 TGACAAAACATG
* *
30461153 TAATAAAACATG
1 TGACAAAACATG
*
30461165 TGACAAAACATA
1 TGACAAAACATG
*
30461177 T-AGCAAAATATG
1 TGA-CAAAACATG
30461189 TGACAAAACA
1 TGACAAAACA
30461199 CATGACCAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
11 1 0.03
12 33 0.94
13 1 0.03
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (12 bp):
TGACAAAACATG
Found at i:30461580 original size:13 final size:13
Alignment explanation
Indices: 30461562--30461587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30461552 GTAATATTAT
30461562 AATTAAAATAAAA
1 AATTAAAATAAAA
30461575 AATTAAAATAAAA
1 AATTAAAATAAAA
30461588 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATTAAAATAAAA
Found at i:30461662 original size:46 final size:45
Alignment explanation
Indices: 30461574--30461667 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 45
30461564 TTAAAATAAA
* * * * *
30461574 AAATTAAAATAAAATATATAATATAAGAATCAGAAATTAAAATNAG
1 AAATGAAAATAAAATATATAAGATAAGAATAAAAAATAAAAAT-AG
* *
30461620 AAATGAAAATAAAATATATAAGATTATAATAAAAAATAAAAATA-
1 AAATGAAAATAAAATATATAAGATAAGAATAAAAAATAAAAATAG
30461664 AAAT
1 AAAT
30461668 ATATGACATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 4 0.10
45 1 0.02
46 36 0.88
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.26
Consensus pattern (45 bp):
AAATGAAAATAAAATATATAAGATAAGAATAAAAAATAAAAATAG
Found at i:30461922 original size:15 final size:15
Alignment explanation
Indices: 30461904--30461938 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30461894 CATTGCTTAC
**
30461904 AATCACATTATTTGT
1 AATCACATTACCTGT
30461919 AATCACATTACCTGT
1 AATCACATTACCTGT
30461934 AATCA
1 AATCA
30461939 TTTTGCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (15 bp):
AATCACATTACCTGT
Found at i:30493180 original size:15 final size:16
Alignment explanation
Indices: 30493160--30493194 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
30493150 TTAATCTTTA
30493160 AAATAAAGCAAAAAG-
1 AAATAAAGCAAAAAGT
*
30493175 AAATAAATCAAAAAGT
1 AAATAAAGCAAAAAGT
30493191 AAAT
1 AAAT
30493195 TAATCTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (16 bp):
AAATAAAGCAAAAAGT
Found at i:30493194 original size:16 final size:15
Alignment explanation
Indices: 30493160--30493199 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
30493150 TTAATCTTTA
*
30493160 AAATAAAGCAAAAAG
1 AAATAAATCAAAAAG
30493175 AAATAAATCAAAAAG
1 AAATAAATCAAAAAG
*
30493190 TAAATTAATC
1 -AAATAAATC
30493200 TCTACACGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATAAATCAAAAAG
Found at i:30498528 original size:67 final size:67
Alignment explanation
Indices: 30498448--30498623 Score: 248
Period size: 67 Copynumber: 2.6 Consensus size: 67
30498438 AAGTTAGTTG
*
30498448 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTG-TAGGTTGTGATTGAGCCTTTGAAAAACC
1 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTG-TGAAAGGTTGTGATTGAGCCTTTGAAAAACC
30498512 ACT
65 ACT
* * * *
30498515 TTGGGTTTTGGTTGAACTCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCA
1 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTGAAAGGTTGTGATTGAGCCTTTGAAAAACCA
30498580 CT
66 CT
* * *
30498582 TTGGATTTTGGTTGATCCTG-GTAAAAACTATTGTGAAAGGTT
1 TTGGGTTTTGGTTGATCCCGTG-AAAAACCATTGTGAAAGGTT
30498624 TTGGCTAAAC
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
66 3 0.03
67 94 0.97
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (67 bp):
TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTGAAAGGTTGTGATTGAGCCTTTGAAAAACCA
CT
Found at i:30498544 original size:32 final size:32
Alignment explanation
Indices: 30498448--30498609 Score: 114
Period size: 35 Copynumber: 4.9 Consensus size: 32
30498438 AAGTTAGTTG
* * *
30498448 TTGGGTTTTGGTTGATCCCGTGAAAAACCATT
1 TTGGGTTTTGGTTGAGCCTGTGAAAAACCACT
* * *
30498480 GTTGTAGGTTGTGATTGAGCCTTTGAAAAACCACT
1 -TTG--GGTTTTGGTTGAGCCTGTGAAAAACCACT
*
30498515 TTGGGTTTTGGTTGA-ACTCGTGAAAAACCA-T
1 TTGGGTTTTGGTTGAGCCT-GTGAAAAACCACT
* * *
30498546 TGTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCACT
1 T-TG---GGTTTTGGTTGAGCCTGTGAAAAACCACT
* *
30498582 TTGGATTTTGGTTGATCCTG-GTAAAAAC
1 TTGGGTTTTGGTTGAGCCTGTG-AAAAAC
30498610 TATTGTGAAA
Statistics
Matches: 100, Mismatches: 19, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
31 5 0.05
32 40 0.40
33 3 0.03
34 3 0.03
35 45 0.45
36 4 0.04
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (32 bp):
TTGGGTTTTGGTTGAGCCTGTGAAAAACCACT
Found at i:30500977 original size:39 final size:39
Alignment explanation
Indices: 30500924--30501138 Score: 210
Period size: 39 Copynumber: 5.6 Consensus size: 39
30500914 GTGCCGGTAG
*
30500924 TGTGTGGTGTGGGAGAGCACATG-TCGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGAT-GATGATATATGCCA
* *
30500963 TGTGCGGTATGGGAGAGCACATGATAATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* * *
30501002 TGTGTGGTGTGGGAGAGCACATGATGATGATATATGTCG
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* * *
30501041 TGTGCGGTGTGGGAGTGCACATGACGAT-A-ATGGTG--A
1 TGTGCGGTGTGGGAGAGCACATGATGATGATAT-ATGCCA
* * * **
30501077 GGTACGGTGTGGGAGTGCATC-TGATGATGATAT-TGTAA
1 TGTGCGGTGTGGGAGAGCA-CATGATGATGATATATGCCA
* *
30501115 TGTGAGGTGTGGGAGTGCACATGA
1 TGTGCGGTGTGGGAGAGCACATGA
30501139 GCCGGAGGAG
Statistics
Matches: 149, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
36 25 0.17
37 5 0.03
38 25 0.17
39 93 0.62
40 1 0.01
ACGTcount: A:0.24, C:0.10, G:0.38, T:0.28
Consensus pattern (39 bp):
TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
Found at i:30501092 original size:36 final size:39
Alignment explanation
Indices: 30501007--30501138 Score: 116
Period size: 36 Copynumber: 3.5 Consensus size: 39
30500997 TGCCATGTGT
* * * *
30501007 GGTGTGGGAGAGCACATGATGATGATATATGT-CGTGTG-C
1 GGTGTGGGAGTGCACATGACGATGATAT-GGTAAG-GTGAC
*
30501046 GGTGTGGGAGTGCACATGACGAT-A-ATGGTGAGGT-AC
1 GGTGTGGGAGTGCACATGACGATGATATGGTAAGGTGAC
* * *
30501082 GGTGTGGGAGTGCATC-TGATGATGATATTGTAATGTGA-
1 GGTGTGGGAGTGCA-CATGACGATGATATGGTAAGGTGAC
30501120 GGTGTGGGAGTGCACATGA
1 GGTGTGGGAGTGCACATGA
30501139 GCCGGAGGAG
Statistics
Matches: 78, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
36 25 0.32
37 6 0.08
38 25 0.32
39 22 0.28
ACGTcount: A:0.23, C:0.09, G:0.40, T:0.27
Consensus pattern (39 bp):
GGTGTGGGAGTGCACATGACGATGATATGGTAAGGTGAC
Found at i:30502961 original size:14 final size:14
Alignment explanation
Indices: 30502942--30502968 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30502932 CGAAATTAAT
30502942 TAATTAACTAAAAC
1 TAATTAACTAAAAC
30502956 TAATTAACTAAAA
1 TAATTAACTAAAA
30502969 TTTAGATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:30509887 original size:7 final size:7
Alignment explanation
Indices: 30509877--30509906 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
30509867 TCTTTTTTCA
30509877 TCATTTT
1 TCATTTT
30509884 TCATTTAT
1 TCATTT-T
30509892 TCATTTT
1 TCATTTT
30509899 TCATTTT
1 TCATTTT
30509906 T
1 T
30509907 TTTTGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (7 bp):
TCATTTT
Found at i:30509908 original size:25 final size:26
Alignment explanation
Indices: 30509870--30509932 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
30509860 TCTCCTTTCT
**
30509870 TTTTTCATCATTTTTCATTTATT-CA
1 TTTTTCATTTTTTTTCATTTATTACA
** *
30509895 TTTTTCATTTTTTTTTGTTTATTATA
1 TTTTTCATTTTTTTTCATTTATTACA
*
30509921 TTTTTAATTTTT
1 TTTTTCATTTTT
30509933 ACTTGTTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
25 19 0.61
26 12 0.39
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTTTCATTTTTTTTCATTTATTACA
Found at i:30509909 original size:26 final size:26
Alignment explanation
Indices: 30509880--30509932 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
30509870 TTTTTCATCA
* *
30509880 TTTTTCATTTATT-CATTTTTCATTT
1 TTTTTTATTTATTACATTTTTAATTT
* *
30509905 TTTTTTGTTTATTATATTTTTAATTT
1 TTTTTTATTTATTACATTTTTAATTT
30509931 TT
1 TT
30509933 ACTTGTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTTTATTTATTACATTTTTAATTT
Found at i:30515353 original size:17 final size:17
Alignment explanation
Indices: 30515307--30515355 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
30515297 TTTAAAAAAT
*
30515307 TAATAATTAAATTATAA
1 TAATATTTAAATTATAA
*
30515324 -AAT-TTTTAATTATAA
1 TAATATTTAAATTATAA
30515339 TAATATTTAAATTATAA
1 TAATATTTAAATTATAA
30515356 ATAAAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 10 0.37
16 6 0.22
17 11 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATTATAA
Found at i:30515440 original size:28 final size:26
Alignment explanation
Indices: 30515409--30515462 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
30515399 ATGTTTAAAG
30515409 TATAAATTAATAATATTTTTTAAAAAAT
1 TATAAATTAATAATA--TTTTAAAAAAT
* *
30515437 TATAAATTATTCATATTTTAAAAAAT
1 TATAAATTAATAATATTTTAAAAAAT
30515463 AGAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.46
28 13 0.54
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TATAAATTAATAATATTTTAAAAAAT
Found at i:30521457 original size:55 final size:55
Alignment explanation
Indices: 30521372--30521482 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
30521362 AAAAGAATTC
* * *
30521372 ATTTGCACCTTGGTTGGCTGTCACTATTGAAGTAGAAATTTTTTTACGTTTGGAA
1 ATTTGCACCTTGGTTCGCTGTCACTATTGAAGTAGAAATTTTTTTAAGTCTGGAA
* *
30521427 ATTTTCACCTTGGTTCGTTGTCACTATTGAAGTAGAAATTTTTTTAAGTCTGGAA
1 ATTTGCACCTTGGTTCGCTGTCACTATTGAAGTAGAAATTTTTTTAAGTCTGGAA
30521482 A
1 A
30521483 GGGTCAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (55 bp):
ATTTGCACCTTGGTTCGCTGTCACTATTGAAGTAGAAATTTTTTTAAGTCTGGAA
Found at i:30521703 original size:16 final size:16
Alignment explanation
Indices: 30521673--30521716 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
30521663 CCAAAATTTA
*
30521673 GATTTTGATTCTTTTG
1 GATTTTTATTCTTTTG
*
30521689 GATTTTTATTTTTTTTG
1 GATTTTTA-TTCTTTTG
30521706 GCATTTTTATT
1 G-ATTTTTATT
30521717 GAATCCAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.29
17 10 0.42
18 7 0.29
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.68
Consensus pattern (16 bp):
GATTTTTATTCTTTTG
Found at i:30526902 original size:63 final size:64
Alignment explanation
Indices: 30526817--30526936 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 64
30526807 AGACAATATT
* * *
30526817 CCACACGTGGTGAATACATCTAGTGTAATGGATGATGGCATT-CACACGGTATGAGGCAACATG
1 CCACACATGGTGAATACATCTAGTATAATGGATGATGGCATTCCACACGATATGAGGCAACATG
* *
30526880 CCACACATGGTGAATGA-GTCTAGTATAATGGATGATGGCGTTCCACACGATATGAGG
1 CCACACATGGTGAAT-ACATCTAGTATAATGGATGATGGCATTCCACACGATATGAGG
30526937 TAATATTCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
63 36 0.72
64 14 0.28
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (64 bp):
CCACACATGGTGAATACATCTAGTATAATGGATGATGGCATTCCACACGATATGAGGCAACATG
Found at i:30532459 original size:20 final size:20
Alignment explanation
Indices: 30532436--30532504 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
30532426 ATAGACAAAA
30532436 CCATCTATCAATAAAT-TGGG
1 CCATCTATCAATAAATCT-GG
* *
30532456 CCATCTATCGATAGATCTGG
1 CCATCTATCAATAAATCTGG
* * *
30532476 CTATCTATCAATAGATCTAG
1 CCATCTATCAATAAATCTGG
*
30532496 TCATCTATC
1 CCATCTATC
30532505 CATGGATGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 40 0.98
21 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (20 bp):
CCATCTATCAATAAATCTGG
Found at i:30535667 original size:18 final size:18
Alignment explanation
Indices: 30535628--30535670 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30535618 GTTTTTGGTT
*
30535628 TTGATGATTGATCTTAAT
1 TTGATGATTGATCTTAAC
*
30535646 TTGATGA-TGATGTGTAAC
1 TTGATGATTGATCT-TAAC
30535664 TTGATGA
1 TTGATGA
30535671 GGAACTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (18 bp):
TTGATGATTGATCTTAAC
Found at i:30541210 original size:20 final size:20
Alignment explanation
Indices: 30541185--30541225 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
30541175 TATAGTTGTG
*
30541185 TCCTCCATTATA-AACAAACT
1 TCCTCCATCATAGAA-AAACT
30541205 TCCTCCATCATAGAAAAACT
1 TCCTCCATCATAGAAAAACT
30541225 T
1 T
30541226 TAAAAGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.29
Consensus pattern (20 bp):
TCCTCCATCATAGAAAAACT
Found at i:30547052 original size:54 final size:54
Alignment explanation
Indices: 30546990--30547097 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
30546980 CCTTAGGCTT
*
30546990 GGGTCAATGTATGGGATGTCCTTTCTTATGCTATCTCTACTGCACTACTTCATC
1 GGGTCAATGTATGGGATGTCCTTTCTTATGCTATCTATACTGCACTACTTCATC
*
30547044 GGGTCAATGTATGGGATGTCCTTTCTTATGCTGTCTATACTGCACTACTTCATC
1 GGGTCAATGTATGGGATGTCCTTTCTTATGCTATCTATACTGCACTACTTCATC
30547098 TTGTGACGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (54 bp):
GGGTCAATGTATGGGATGTCCTTTCTTATGCTATCTATACTGCACTACTTCATC
Found at i:30558103 original size:12 final size:12
Alignment explanation
Indices: 30558088--30558112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30558078 TTCAAGGGTG
30558088 GGTTCAAATTTT
1 GGTTCAAATTTT
30558100 GGTTCAAATTTT
1 GGTTCAAATTTT
30558112 G
1 G
30558113 AGCATGAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (12 bp):
GGTTCAAATTTT
Found at i:30559171 original size:64 final size:63
Alignment explanation
Indices: 30559067--30559228 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 63
30559057 ATCTTTGAAG
30559067 ATTATTTGCATTCAAGACTATTTGTTG--TTTTTATCCATTGTTGAAGACTGTTAATGATTTGCT
1 ATTATTTGC--TCAAGACTATTTGTTGTTTTTTTATCCATTGTTGAAGACTGTTAATGATTTGCT
* * * * *
30559130 ATTATTTGTTGAAGACTATTTGTTGTTTTTTTTATCCATTGTTGAATATTGTTAATGATTTGTT
1 ATTATTTGCTCAAGACTATTTGTTG-TTTTTTTATCCATTGTTGAAGACTGTTAATGATTTGCT
* *
30559194 GTTATTTGCTCAAGACTATTTATTGTTGTTTTTAT
1 ATTATTTGCTCAAGACTATTTGTTGTT-TTTTTAT
30559229 TTATGTTTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
61 15 0.17
63 10 0.12
64 61 0.71
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.54
Consensus pattern (63 bp):
ATTATTTGCTCAAGACTATTTGTTGTTTTTTTATCCATTGTTGAAGACTGTTAATGATTTGCT
Found at i:30560002 original size:40 final size:40
Alignment explanation
Indices: 30559958--30560036 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
30559948 CTCAATGATT
* *
30559958 GAAATTTATATATTGTTTTTTATCTTTGCAATTATGAGTA
1 GAAATTTATATATTGTTATTTATCTATGCAATTATGAGTA
* *
30559998 GAAATTTATATATTGTTATTTCTCTATGCAATTCTGAGT
1 GAAATTTATATATTGTTATTTATCTATGCAATTATGAGT
30560037 CACTAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.51
Consensus pattern (40 bp):
GAAATTTATATATTGTTATTTATCTATGCAATTATGAGTA
Found at i:30562919 original size:76 final size:76
Alignment explanation
Indices: 30562793--30562945 Score: 245
Period size: 76 Copynumber: 2.0 Consensus size: 76
30562783 TTTATGGTTG
* *
30562793 TTCTTTGGGTTTTAGCCACGTGCACAGAAACCTGATAGAAAACCCATCTTCTCAGCCCACAATTA
1 TTCTTTGGGTTTGAGCCACGTGCACAGAAACCTGATAGAAAACCCATCTTCTCAGCCAACAATTA
*
30562858 TTCTAGAGCAA
66 TTATAGAGCAA
*
30562869 TTCTTTGGGTTTGAGCCACGTGGACAGAAACCTGATA-AAGAACCCATCTTCTCAGCCAACAATT
1 TTCTTTGGGTTTGAGCCACGTGCACAGAAACCTGATAGAA-AACCCATCTTCTCAGCCAACAATT
*
30562933 ATTATCGAGCAA
65 ATTATAGAGCAA
30562945 T
1 T
30562946 ATGCTATGCA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 2 0.03
76 69 0.97
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (76 bp):
TTCTTTGGGTTTGAGCCACGTGCACAGAAACCTGATAGAAAACCCATCTTCTCAGCCAACAATTA
TTATAGAGCAA
Found at i:30563422 original size:15 final size:15
Alignment explanation
Indices: 30563398--30563428 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30563388 GTTGGTTAGG
30563398 GGAAGAAAAGAAGAA
1 GGAAGAAAAGAAGAA
*
30563413 GGAAGGAAAGAAGAA
1 GGAAGAAAAGAAGAA
30563428 G
1 G
30563429 AACGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (15 bp):
GGAAGAAAAGAAGAA
Found at i:30563428 original size:18 final size:18
Alignment explanation
Indices: 30563405--30563445 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
30563395 AGGGGAAGAA
* *
30563405 AAGAAGAAGGAAGGAAAG
1 AAGAAGAACGAAGAAAAG
*
30563423 AAGAAGAACGAATAAAAG
1 AAGAAGAACGAAGAAAAG
30563441 AAGAA
1 AAGAA
30563446 CTACCACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.29, T:0.02
Consensus pattern (18 bp):
AAGAAGAACGAAGAAAAG
Found at i:30563583 original size:35 final size:30
Alignment explanation
Indices: 30563542--30563621 Score: 94
Period size: 28 Copynumber: 2.7 Consensus size: 30
30563532 TTTAATATAT
*
30563542 TATTATTATTATTATTAAATTACAAAAATCAA
1 TATTATTATTATTATTAAA--ATAAAAATCAA
*
30563574 TATTATTATT-TT-TTAGAATAAAAATCAA
1 TATTATTATTATTATTAAAATAAAAATCAA
30563602 TATTATT-TTATTATTTAAAA
1 TATTATTATTATTA-TTAAAA
30563622 ATTATTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 2 0.05
28 19 0.45
30 9 0.21
31 2 0.05
32 10 0.24
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (30 bp):
TATTATTATTATTATTAAAATAAAAATCAA
Found at i:30564226 original size:355 final size:349
Alignment explanation
Indices: 30563738--30564737 Score: 1138
Period size: 355 Copynumber: 2.9 Consensus size: 349
30563728 GTATATAATA
* * * *
30563738 TATACTTAAAAATTTTATAAGTTATAATTTTTATAATGTTAACACAAAATA-AAAAGTAAATATA
1 TATAATTAATAATTTTATAAGTTATAATTTTTATAATATTAACATAAAATAGAAAA-TAAATATA
* * * * *
30563802 TTTATATTTAAAGTATATATAT--TAAAAGCATTTA-GT-GTATATATATAATAATAATTATATT
65 TTTATATTAAAAGTATATATATACTAAAAGTAATAATTTAGTATATATATAATAATAA-TATATT
* *
30563863 CCTTATAAATGAACCTAATATATATAAAGTAAATATATTAAAAGACATTACAAGGTAATTAGTAA
129 -CTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAGGTAATTAATAA
* *
30563928 TCATAGTTTCATGAATTAATTTAATTAATTTTATGAGTTTGTCCTTAATTAAATGAAATTAAAAA
193 TCATAATTTCATGAATTAATTTAATTAATTATATGAGTTTGTCCTTAATTAAATGAAATTAAAAA
* *
30563993 AAATAGTTAAGTTTCAAAACTATTATAATCTCATAACTTCTTTTTAAATAATTAAGTTTGTTTAT
258 AAATA-TTAAGTTTCAAAACTATTATAATCTCATAACTTCTCTTTAAATAA--AAGTTTGTATAT
*
30564058 TATAAGTTTATATAAA-AAA-A-CATATA-
320 TATAAGTTTATAAAAACAAAGAGCATATAT
* * * *
30564084 TAT-ATT-ATAA-TTTATAAGTTATAATTTTTATAATGTTAACA-ACAATAGAAAGTAAATATGT
1 TATAATTAATAATTTTATAAGTTATAATTTTTATAATATTAACATAAAATAGAAAATAAATATAT
* * *
30564145 TTATATTTAAAGTGTGTATATATATA-TACACAAATTAAAAATATTTTAGTATATATATAATAAT
66 TTATA-TTAAA---AGTATATATATACT--A-AAAGT---AATAATTTAGTATATATATAATAAT
*
30564209 AAGTATATTCTTTATAAATGAACCCAATATATATACAGTAAATATATTAAAAGACATTACAAGGT
121 AA-TATATTC-TTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAGGT
* * * *
30564274 AATTAATAATCATAATTTTATGAATTAATTTAATTAATTATATGGGTTTGTCCTTAATTACATCA
184 AATTAATAATCATAATTTCATGAATTAATTTAATTAATTATATGAGTTTGTCCTTAATTAAATGA
* * * *
30564339 AATTAAAAAAAATAACT-AGATTTCAAAACTATTATAATTTCATAA-TT-TCTCT---T-AAGGT
249 AATTAAAAAAAAT-ATTAAG-TTTCAAAACTATTATAATCTCATAACTTCTCTTTAAATAAAAGT
*
30564397 TTGTATATTATAAGTTTATAAAAACAAAGGAGTATATAT
312 TTGTATATTATAAGTTTATAAAAACAAA-GAGCATATAT
30564436 TATAATTAATAATTTTATAAGTTATAATTTTTATAATATTAACATAAAATAGAAAATAAATATAT
1 TATAATTAATAATTTTATAAGTTATAATTTTTATAATATTAACATAAAATAGAAAATAAATATAT
* * * *
30564501 TTATATTAAAAGTATATATATGCTAAAAGTATTAATTTA-TATA-ATATAGTAATTATAT-TTCT
66 TTATATTAAAAGTATATATATACTAAAAGTAATAATTTAGTATATATATAATAATAATATATTCT
* * * *
30564563 TATAAATGAACCCAATATATATAATGTATATATATTAAAAAAACATTACAAGTTAATTAATAATC
131 TATAAATGAACCCAATATATATAAAGTAAATATATT-AAAAGACATTACAAGGTAATTAATAATC
* ** * *
30564628 ATAATTTCATGAATTAATTTTATTAACAATAT-AGGTTTGTCTTTAATTATATGAAATT-AAAAA
195 ATAATTTCATGAATTAATTTAATTAATTATATGA-GTTTGTCCTTAATTAAATGAAATTAAAAAA
* * * *
30564691 AA-ATTAAATTCCAAAACTATTCTAATCTCAAAGAC-TCTCTTTAAATA
259 AATATTAAGTTTCAAAACTATTATAATCTCATA-ACTTCTCTTTAAATA
30564738 TATATATTAT
Statistics
Matches: 555, Mismatches: 62, Indels: 74
0.80 0.09 0.11
Matches are distributed among these distances:
340 22 0.04
341 3 0.01
342 63 0.11
343 116 0.21
344 6 0.01
345 13 0.02
346 17 0.03
347 33 0.06
348 3 0.01
349 2 0.00
350 9 0.02
351 6 0.01
352 13 0.02
353 9 0.02
354 10 0.02
355 207 0.37
356 23 0.04
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (349 bp):
TATAATTAATAATTTTATAAGTTATAATTTTTATAATATTAACATAAAATAGAAAATAAATATAT
TTATATTAAAAGTATATATATACTAAAAGTAATAATTTAGTATATATATAATAATAATATATTCT
TATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAGGTAATTAATAATCA
TAATTTCATGAATTAATTTAATTAATTATATGAGTTTGTCCTTAATTAAATGAAATTAAAAAAAA
TATTAAGTTTCAAAACTATTATAATCTCATAACTTCTCTTTAAATAAAAGTTTGTATATTATAAG
TTTATAAAAACAAAGAGCATATAT
Found at i:30564469 original size:16 final size:15
Alignment explanation
Indices: 30564435--30564472 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
30564425 GGAGTATATA
30564435 TTATAATTAATAATT
1 TTATAATTAATAATT
30564450 TTATAAGTT-ATAATTT
1 TTATAA-TTAATAA-TT
30564466 TTATAAT
1 TTATAAT
30564473 ATTAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTAATAATT
Found at i:30568115 original size:14 final size:15
Alignment explanation
Indices: 30568081--30568118 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
30568071 TAGATAATTA
30568081 TATTTTAT-TTTAGT
1 TATTTTATATTTAGT
*
30568095 TAATTTATATTTA-T
1 TATTTTATATTTAGT
30568109 TATTTTATAT
1 TATTTTATAT
30568119 ATTTGTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTTTATATTTAGT
Found at i:30568231 original size:76 final size:75
Alignment explanation
Indices: 30568141--30568284 Score: 225
Period size: 76 Copynumber: 1.9 Consensus size: 75
30568131 TTTTATATTG
* * * *
30568141 TAATTTAATTATTATATGTTGATTTTGAAGTATTTAATTAAATATTTTTTAATTAATCATTATTA
1 TAATATAATTATTATATGTTGAGTTTGAAGTATTTAATTAAATATTTGTTAATTAATCAGTATTA
30568206 TATTATGTAA
66 TATTATGTAA
* *
30568216 TAATATAATATATTATATGTTGAGTTTGAAGTATTTAATTAAATATTTGTTAATTTATTAGTATT
1 TAATATAAT-TATTATATGTTGAGTTTGAAGTATTTAATTAAATATTTGTTAATTAATCAGTATT
30568281 ATAT
65 ATAT
30568285 AATAATAGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 8 0.13
76 54 0.87
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (75 bp):
TAATATAATTATTATATGTTGAGTTTGAAGTATTTAATTAAATATTTGTTAATTAATCAGTATTA
TATTATGTAA
Found at i:30575676 original size:27 final size:27
Alignment explanation
Indices: 30575638--30575693 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
30575628 TTTTACCAAG
30575638 ATGTTTTAAGCTAGTCCAGTATTTTAA
1 ATGTTTTAAGCTAGTCCAGTATTTTAA
*
30575665 ATGTTTTAAGCTAGTCCATTATTTTAA
1 ATGTTTTAAGCTAGTCCAGTATTTTAA
30575692 AT
1 AT
30575694 TTTGTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.46
Consensus pattern (27 bp):
ATGTTTTAAGCTAGTCCAGTATTTTAA
Found at i:30589659 original size:2 final size:2
Alignment explanation
Indices: 30589654--30589683 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30589644 ATATATATAA
30589654 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30589684 TAAATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30596108 original size:45 final size:45
Alignment explanation
Indices: 30596044--30596133 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
30596034 TACTAAGTCA
30596044 ATGCATATTAAAAGCATGTAGCCTACTGTTGTAATAAAAACTATC
1 ATGCATATTAAAAGCATGTAGCCTACTGTTGTAATAAAAACTATC
30596089 ATGCATATTAAAAGCATGTAGCCTACTGTTGTAATAAAAACTATC
1 ATGCATATTAAAAGCATGTAGCCTACTGTTGTAATAAAAACTATC
30596134 TTCACTTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (45 bp):
ATGCATATTAAAAGCATGTAGCCTACTGTTGTAATAAAAACTATC
Found at i:30606023 original size:39 final size:39
Alignment explanation
Indices: 30605980--30606061 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
30605970 GATTTTTTTT
*
30605980 TATAAAATTAAAGTACGTTCGTGCAACGCACTCATGTAA
1 TATAAAATTAAAGTACGTTCATGCAACGCACTCATGTAA
* * * * * *
30606019 TATAAAATTAGAGTATGTTCATGTAATGCATTCGTGTAA
1 TATAAAATTAAAGTACGTTCATGCAACGCACTCATGTAA
30606058 TATA
1 TATA
30606062 GGCAAAACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (39 bp):
TATAAAATTAAAGTACGTTCATGCAACGCACTCATGTAA
Found at i:30606981 original size:21 final size:21
Alignment explanation
Indices: 30606957--30606997 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
30606947 AAAAAATAGA
30606957 AAAATAGAAAAAAGAAAGAAT
1 AAAATAGAAAAAAGAAAGAAT
*
30606978 AAAATAGGAAAAAGAAAGAA
1 AAAATAGAAAAAAGAAAGAA
30606998 CAAGCAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (21 bp):
AAAATAGAAAAAAGAAAGAAT
Found at i:30608045 original size:27 final size:27
Alignment explanation
Indices: 30608000--30608143 Score: 119
Period size: 29 Copynumber: 5.1 Consensus size: 27
30607990 ATTAAAACAA
* *
30608000 AAATATTTTATCTTGTCTAAATTGAGAT
1 AAATATTTT-TCTTGTCTAAATTAAGAC
* * *
30608028 AAATATGTTTCTTATCTAGATTAAGAC
1 AAATATTTTTCTTGTCTAAATTAAGAC
*
30608055 AAATTATTTTTCTTGTCTTAAATTAAAAC
1 AAA-TATTTTTCTTGTC-TAAATTAAGAC
* * *
30608084 AAACATACTTTCTTGTTTAAATTAAGACC
1 AAATAT-TTTTCTTGTCTAAATTAAGA-C
* *
30608113 AAACATGTTTT-TTCATCTAAATTAAGAC
1 AAATAT-TTTTCTT-GTCTAAATTAAGAC
30608141 AAA
1 AAA
30608144 CATGTTAAAG
Statistics
Matches: 94, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
27 17 0.18
28 36 0.38
29 41 0.44
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (27 bp):
AAATATTTTTCTTGTCTAAATTAAGAC
Found at i:30608131 original size:86 final size:86
Alignment explanation
Indices: 30607981--30608143 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 86
30607971 ATGACAACTT
* * * * *
30607981 TTGTCTTTAATTAAAACAAAAATATTTTATCTTGTCTAAATTGAGATAAATATGTTTCTTATCTA
1 TTGTCTTAAATTAAAACAAAAATATCTTATCTTGTCTAAATTAAGACAAACATGTTTCTTATCTA
*
30608046 GATTAAGACAAATTATTTTTC
66 AATTAAGACAAATTATTTTTC
* * *
30608067 TTGTCTTAAATTAAAACAAACATA-CTT-TCTTGTTTAAATTAAGACCAAACATGTTTTTTCATC
1 TTGTCTTAAATTAAAACAAAAATATCTTATCTTGTCTAAATTAAGA-CAAACATGTTTCTT-ATC
30608130 TAAATTAAGACAAA
64 TAAATTAAGACAAA
30608144 CATGTTAAAG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 15 0.23
85 13 0.20
86 38 0.58
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (86 bp):
TTGTCTTAAATTAAAACAAAAATATCTTATCTTGTCTAAATTAAGACAAACATGTTTCTTATCTA
AATTAAGACAAATTATTTTTC
Found at i:30613648 original size:35 final size:35
Alignment explanation
Indices: 30613578--30613897 Score: 358
Period size: 35 Copynumber: 9.1 Consensus size: 35
30613568 CACTTGATTA
* *
30613578 AAATTGTTTAATTAAG---TTGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
30613610 AAATTATTTAATTAAATCATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
30613645 AAATCGTTTAATCAAGTCATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
**** * *
30613680 AAATTAAACAATTAAGTTATTGGGCCTACTTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
30613715 AAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATT
1 AAA-TTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
30613751 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* *
30613787 AAATTGTTTAATTAAGTTATTAGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
30613822 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
*
30613858 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
30613893 AAATT
1 AAATT
30613898 AAACTATTAA
Statistics
Matches: 239, Mismatches: 43, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
32 14 0.06
35 140 0.59
36 82 0.34
37 3 0.01
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:30613794 original size:71 final size:71
Alignment explanation
Indices: 30613578--30613895 Score: 385
Period size: 71 Copynumber: 4.5 Consensus size: 71
30613568 CACTTGATTA
* * * *
30613578 AAATTGTTTAATTAAG---TTGTGCCTAATTAACT-AAATTATTTAATTAAATCATTGGGCCTAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTATTGGGCCTAA
30613639 TTAATT
66 TTAATT
* * * *** * *
30613645 AAATCGTTTAATCAAGTCATTGGGCCTAATTAATT-AAATTAAACAATTAAGTTATTGGGCCTAC
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTATTGGGCCTAA
*
30613709 TTGATT
66 TTAATT
* * * *
30613715 AAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAATTGTTGGGCTTA
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTATTGGGCCTA
30613780 ATTAATT
65 ATTAATT
* * * * *
30613787 AAATTGTTTAATTAAGTTATTAGGCCTAATTGATTAAAATTGTTTAATTAAATTGTTGGGCTTAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTATTGGGCCTAA
30613852 TTAATT
66 TTAATT
*
30613858 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAA
30613896 TTAAACTATT
Statistics
Matches: 218, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
67 14 0.06
70 45 0.21
71 130 0.60
72 29 0.13
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (71 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTATTGGGCCTAA
TTAATT
Found at i:30616158 original size:3 final size:3
Alignment explanation
Indices: 30616150--30616174 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30616140 ATATAGATAT
30616150 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
30616175 GCCATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:30618147 original size:28 final size:28
Alignment explanation
Indices: 30618116--30618514 Score: 464
Period size: 28 Copynumber: 13.8 Consensus size: 28
30618106 TTTTATTTTA
30618116 TCTAAATTAAGACAAATATGTTTTCTTG
1 TCTAAATTAAGACAAATATGTTTTCTTG
*
30618144 TCTAGATTAAGACAAAAACTAT-TTTTCTTG
1 TCTAAATTAAGAC--AAA-TATGTTTTCTTG
* *
30618174 TCTTAAATTAAGACAAACATATTTTCTTG
1 TC-TAAATTAAGACAAATATGTTTTCTTG
*
30618203 TTTAAATTAAGACAAATATGTTTTCTTG
1 TCTAAATTAAGACAAATATGTTTTCTTG
*
30618231 TCTAGATTAAGACAAAAACTAT-TTTTCTTG
1 TCTAAATTAAGAC--AAA-TATGTTTTCTTG
* *
30618261 TCTTAAATTAAGACAAACATATTTTCTTG
1 TC-TAAATTAAGACAAATATGTTTTCTTG
*
30618290 TTTAAATTAAGACAAATATGTTTTCTTG
1 TCTAAATTAAGACAAATATGTTTTCTTG
*
30618318 TCTAGATTAAGACAAAAACTAT-TTTTCTTG
1 TCTAAATTAAGAC--AAA-TATGTTTTCTTG
* *
30618348 TCTTAAATTAAGACAAACATATTTTCTTG
1 TC-TAAATTAAGACAAATATGTTTTCTTG
*
30618377 TTTAAATTAAGACAAATATGTTTTCTTG
1 TCTAAATTAAGACAAATATGTTTTCTTG
*
30618405 TCTAGATTAAGACAAAAACTAT-TTTTCTTG
1 TCTAAATTAAGAC--AAA-TATGTTTTCTTG
* *
30618435 TCTTAAATTAAGACAAACATATTTTCTTG
1 TC-TAAATTAAGACAAATATGTTTTCTTG
*
30618464 TTTAAATTAAGACTAAATATGTTTTCTTG
1 TCTAAATTAAGAC-AAATATGTTTTCTTG
*
30618493 TCTAAATTAAAACAAATATGTT
1 TCTAAATTAAGACAAATATGTT
30618515 AAAGCTGTCA
Statistics
Matches: 321, Mismatches: 29, Indels: 42
0.82 0.07 0.11
Matches are distributed among these distances:
28 145 0.45
29 72 0.22
30 52 0.16
31 52 0.16
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.42
Consensus pattern (28 bp):
TCTAAATTAAGACAAATATGTTTTCTTG
Found at i:30618181 original size:59 final size:58
Alignment explanation
Indices: 30618097--30618508 Score: 472
Period size: 59 Copynumber: 7.1 Consensus size: 58
30618087 TTTAATTACA
* * *
30618097 ACAAAAATATTTTATTTTATC-TAAATTAAGACAAATATGTTTTCTTGTCTAGATTAAG
1 ACAAAAATATTTT-TCTTGTCTTAAATTAAGACAAATATGTTTTCTTGTCTAAATTAAG
* * *
30618155 ACAAAAACTATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAG
1 ACAAAAA-TATTTTTCTTGTCTTAAATTAAGACAAATATGTTTTCTTGTCTAAATTAAG
*
30618214 AC--AAATATGTTTTCTTGTC-TAGATTAAGACAAAAACTAT-TTTTCTTGTCTTAAATTAAG
1 ACAAAAATAT-TTTTCTTGTCTTAAATTAAGAC--AAA-TATGTTTTCTTGTC-TAAATTAAG
* *
30618273 ACAAACATA-TTTTCTTGT-TTAAATTAAGACAAATATGTTTTCTTGTCTAGATTAAG
1 ACAAAAATATTTTTCTTGTCTTAAATTAAGACAAATATGTTTTCTTGTCTAAATTAAG
* * *
30618329 ACAAAAACTATTTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAG
1 ACAAAAA-TATTTTTCTTGTCTTAAATTAAGACAAATATGTTTTCTTGTCTAAATTAAG
*
30618388 AC--AAATATGTTTTCTTGTC-TAGATTAAGACAAAAACTAT-TTTTCTTGTCTTAAATTAAG
1 ACAAAAATAT-TTTTCTTGTCTTAAATTAAGAC--AAA-TATGTTTTCTTGTC-TAAATTAAG
* *
30618447 ACAAACATA-TTTTCTTGT-TTAAATTAAGACTAAATATGTTTTCTTGTCTAAATTAAA
1 ACAAAAATATTTTTCTTGTCTTAAATTAAGAC-AAATATGTTTTCTTGTCTAAATTAAG
30618504 ACAAA
1 ACAAA
30618509 TATGTTAAAG
Statistics
Matches: 307, Mismatches: 24, Indels: 47
0.81 0.06 0.12
Matches are distributed among these distances:
56 43 0.14
57 57 0.19
58 58 0.19
59 141 0.46
61 8 0.03
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (58 bp):
ACAAAAATATTTTTCTTGTCTTAAATTAAGACAAATATGTTTTCTTGTCTAAATTAAG
Found at i:30618230 original size:87 final size:87
Alignment explanation
Indices: 30618082--30618508 Score: 757
Period size: 87 Copynumber: 4.9 Consensus size: 87
30618072 AGGGTAACTT
* * * *
30618082 TTGTCTTTAATTACA-ACAAAAATATTTTATTTTATCTAAATTAAGACAAATATGTTTTCTTGTC
1 TTGTCTTAAATTA-AGACAAACATATTTTCTTGT-T-TAAATTAAGACAAATATGTTTTCTTGTC
30618146 TAGATTAAGACAAAAACTATTTTTC
63 TAGATTAAGACAAAAACTATTTTTC
30618171 TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGACAAATATGTTTTCTTGTCTAG
1 TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGACAAATATGTTTTCTTGTCTAG
30618236 ATTAAGACAAAAACTATTTTTC
66 ATTAAGACAAAAACTATTTTTC
30618258 TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGACAAATATGTTTTCTTGTCTAG
1 TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGACAAATATGTTTTCTTGTCTAG
30618323 ATTAAGACAAAAACTATTTTTC
66 ATTAAGACAAAAACTATTTTTC
30618345 TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGACAAATATGTTTTCTTGTCTAG
1 TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGACAAATATGTTTTCTTGTCTAG
30618410 ATTAAGACAAAAACTATTTTTC
66 ATTAAGACAAAAACTATTTTTC
30618432 TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGACTAAATATGTTTTCTTGTCTA
1 TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGAC-AAATATGTTTTCTTGTCTA
* *
30618497 AATTAAAACAAA
65 GATTAAGACAAA
30618509 TATGTTAAAG
Statistics
Matches: 330, Mismatches: 6, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
87 272 0.82
88 31 0.09
89 27 0.08
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (87 bp):
TTGTCTTAAATTAAGACAAACATATTTTCTTGTTTAAATTAAGACAAATATGTTTTCTTGTCTAG
ATTAAGACAAAAACTATTTTTC
Found at i:30619897 original size:22 final size:22
Alignment explanation
Indices: 30619863--30619910 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
30619853 CAAGTAGAAG
*
30619863 AAAACAATGCAAAAAAAAAA-A
1 AAAACAATACAAAAAAAAAACA
30619884 AAAAGCAATACAAAAAAAAAACA
1 AAAA-CAATACAAAAAAAAAACA
30619907 AAAA
1 AAAA
30619911 AAAAAGAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 15 0.62
23 5 0.21
ACGTcount: A:0.81, C:0.10, G:0.04, T:0.04
Consensus pattern (22 bp):
AAAACAATACAAAAAAAAAACA
Found at i:30619898 original size:16 final size:14
Alignment explanation
Indices: 30619876--30619920 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
30619866 ACAATGCAAA
30619876 AAAAAAAAAAAAGC
1 AAAAAAAAAAAAGC
*
30619890 AATACAAAAAAAAAAC
1 AA-A-AAAAAAAAAGC
30619906 AAAAAAAAAAGAAGC
1 AAAAAAAAAA-AAGC
30619921 GTTCAAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.35
15 5 0.19
16 12 0.46
ACGTcount: A:0.82, C:0.09, G:0.07, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAAGC
Found at i:30623548 original size:26 final size:26
Alignment explanation
Indices: 30623493--30623550 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
30623483 TGCTTCCTTC
* * *
30623493 AAAATGACTTGGATGAATGACGGCTG
1 AAAATGACTTGGAAGAATGACAGCTA
*
30623519 AAAATGATTTGGAAGAAT-ACTAGCTA
1 AAAATGACTTGGAAGAATGAC-AGCTA
30623545 AAAATG
1 AAAATG
30623551 CTTAATGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (26 bp):
AAAATGACTTGGAAGAATGACAGCTA
Found at i:30634645 original size:23 final size:23
Alignment explanation
Indices: 30634619--30634674 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
30634609 ACTCAAGGTT
*
30634619 GCAGTGCTGAGGAAG-CCAAGGCC
1 GCAGTGCTG-GGAAGAACAAGGCC
* * *
30634642 GCAGTGTTGGGGAGAACAAGGCT
1 GCAGTGCTGGGAAGAACAAGGCC
30634665 GCAGTGCTGG
1 GCAGTGCTGG
30634675 TGAAAGGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.23, C:0.20, G:0.43, T:0.14
Consensus pattern (23 bp):
GCAGTGCTGGGAAGAACAAGGCC
Found at i:30660946 original size:42 final size:41
Alignment explanation
Indices: 30660873--30660951 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 41
30660863 AATGTTATAG
* * *
30660873 AGAAGAGTTATATGTGAAAAGCTATACAAAAACAAGTTAAA
1 AGAAGAGTTATACGTGAAAAGCTACAAAAAAACAAGTTAAA
* * *
30660914 AGAAGAAGTTGTACGTGAAAAGGTACAAAAAAAGAAGT
1 AGAAG-AGTTATACGTGAAAAGCTACAAAAAAACAAGT
30660952 CGTACGTGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 5 0.16
42 26 0.84
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.19
Consensus pattern (41 bp):
AGAAGAGTTATACGTGAAAAGCTACAAAAAAACAAGTTAAA
Found at i:30661165 original size:18 final size:18
Alignment explanation
Indices: 30661142--30661184 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
30661132 TTCACTGTTA
30661142 TTTGTGCGAAGTAATTAT
1 TTTGTGCGAAGTAATTAT
*
30661160 TTTGTGCGAGGTAATTAT
1 TTTGTGCGAAGTAATTAT
*
30661178 TCTGTGC
1 TTTGTGC
30661185 AAGATAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (18 bp):
TTTGTGCGAAGTAATTAT
Done.