Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chrUn_random
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: 10571689
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 1662808 characters in sequence are not A, C, G, or T
File 4 of 30
Found at i:1114777 original size:69 final size:69
Alignment explanation
Indices: 1114695--1114832 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
1114685 TCAGACAAGG
1114695 AGATAAGGCAAGCAGGACCAAAATGAAGGTTGTCATGGGAGTTATCTGCCATTTCATTGAAATCA
1 AGATAAGGCAAGCAGGACCAAAATGAAGGTTGTCATGGGAGTTATCTGCCATTTCATTGAAATCA
1114760 ATTA
66 ATTA
1114764 AGATAAGGCAAGCAGGACCAAAATGAAGGTTGTCATGGGAGTTATCTGCCATTTCATTGAAATCA
1 AGATAAGGCAAGCAGGACCAAAATGAAGGTTGTCATGGGAGTTATCTGCCATTTCATTGAAATCA
1114829 ATTA
66 ATTA
1114833 TAACACAAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (69 bp):
AGATAAGGCAAGCAGGACCAAAATGAAGGTTGTCATGGGAGTTATCTGCCATTTCATTGAAATCA
ATTA
Found at i:1115429 original size:59 final size:59
Alignment explanation
Indices: 1115354--1115472 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
1115344 CTGTATACTT
*
1115354 AATGCACTATGTAATAGGACAAGGTAATTAATGGCTTTACATATTTGTTGGAATGACTA
1 AATGCACTATGTAATAGGACAAGGTAATTAATGGCTTTACATATTCGTTGGAATGACTA
*
1115413 AATGCACTATGTAATAGGACAAGGTAATTAATGGCTTTACGTATTCGTTGGAATGACTA
1 AATGCACTATGTAATAGGACAAGGTAATTAATGGCTTTACATATTCGTTGGAATGACTA
1115472 A
1 A
1115473 GTGAAAATAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (59 bp):
AATGCACTATGTAATAGGACAAGGTAATTAATGGCTTTACATATTCGTTGGAATGACTA
Found at i:1117643 original size:19 final size:19
Alignment explanation
Indices: 1117619--1117656 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1117609 CCATTTGACT
1117619 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
1117638 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
1117657 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:1122360 original size:13 final size:13
Alignment explanation
Indices: 1122342--1122366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1122332 TTTCAGAAAA
1122342 TTTATAAAATCAT
1 TTTATAAAATCAT
1122355 TTTATAAAATCA
1 TTTATAAAATCA
1122367 CAATTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:1123762 original size:19 final size:19
Alignment explanation
Indices: 1123738--1123775 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1123728 CTACCAAACC
*
1123738 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
1123757 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
1123776 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:1167583 original size:11 final size:11
Alignment explanation
Indices: 1167549--1167611 Score: 74
Period size: 11 Copynumber: 5.8 Consensus size: 11
1167539 CTAAACCTAT
1167549 CAAAATTTGCA
1 CAAAATTTGCA
* *
1167560 CAAAAATGGCA
1 CAAAATTTGCA
*
1167571 CAAAATTTACA
1 CAAAATTTGCA
* *
1167582 CAAAAGTTGTA
1 CAAAATTTGCA
1167593 C-AAATTTGCA
1 CAAAATTTGCA
1167603 CAAAATTTG
1 CAAAATTTG
1167612 TACAGAATTC
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
10 8 0.20
11 33 0.80
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (11 bp):
CAAAATTTGCA
Found at i:1167597 original size:21 final size:21
Alignment explanation
Indices: 1167573--1167620 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1167563 AAATGGCACA
1167573 AAATTTACACAAAAGTTGTAC
1 AAATTTACACAAAAGTTGTAC
* *
1167594 AAATTTGCACAAAATTTGTAC
1 AAATTTACACAAAAGTTGTAC
1167615 AGAATT
1 A-AATT
1167621 CACTAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATTTACACAAAAGTTGTAC
Found at i:1172636 original size:25 final size:26
Alignment explanation
Indices: 1172578--1172637 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
1172568 GTGGTCGCAA
*
1172578 CCAC-GTATATCAACTTGTGGCCTAG
1 CCACAGTATATCAACCTGTGGCCTAG
* *
1172603 CCACA-TATATCATCCTGTGGCCTTG
1 CCACAGTATATCAACCTGTGGCCTAG
1172628 CCA-AGTATAT
1 CCACAGTATAT
1172638 ATATCACAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (26 bp):
CCACAGTATATCAACCTGTGGCCTAG
Found at i:1174572 original size:18 final size:19
Alignment explanation
Indices: 1174533--1174580 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1174523 TTAATATTTT
1174533 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
*
1174552 AATATTATTTTATT-TTAA
1 AATATTATTTTATTAATAA
*
1174570 AATATTCTTTT
1 AATATTATTTT
1174581 CACCCATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTATTTTATTAATAA
Found at i:1177401 original size:28 final size:28
Alignment explanation
Indices: 1177359--1177417 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1177349 GGACAAATGT
**
1177359 CCTGGTGGTGGAAAATTACTGTTTTGCC
1 CCTGGTGGTGGAAAATTACCATTTTGCC
1177387 CCTGG-GGTGGCAAAATTACCATTTTGCC
1 CCTGGTGGTGG-AAAATTACCATTTTGCC
1177415 CCT
1 CCT
1177418 AGATAGTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACCATTTTGCC
Found at i:1188430 original size:21 final size:21
Alignment explanation
Indices: 1188388--1188430 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1188378 CTTGTACCGG
*
1188388 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
1188409 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
1188430 T
1 T
1188431 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:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:1193394 original size:27 final size:27
Alignment explanation
Indices: 1193345--1193431 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
1193335 CTTACACACC
*
1193345 ATGTTCAAAAAAAATGTTATTACATGCA
1 ATGTTGAAAAAAAA-GTTATTACATGCA
*
1193373 ATGTTGAAAAAAAAGTTGTTACATG-A
1 ATGTTGAAAAAAAAGTTATTACATGCA
* * *
1193399 TATGTTGAAAAAAAATTTATTACACGCC
1 -ATGTTGAAAAAAAAGTTATTACATGCA
1193427 ATGTT
1 ATGTT
1193432 TAAGTTGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 37 0.73
28 13 0.25
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (27 bp):
ATGTTGAAAAAAAAGTTATTACATGCA
Found at i:1193554 original size:28 final size:28
Alignment explanation
Indices: 1193523--1193585 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1193513 TTGTTATATG
**
1193523 CCATGTTGAAAAAAAAATTTATTACACA
1 CCATGTTGAAAAAAAAAGGTATTACACA
*
1193551 CCATGTTGAAAAAAAAAGGTATTACACG
1 CCATGTTGAAAAAAAAAGGTATTACACA
1193579 CCATGTT
1 CCATGTT
1193586 TAAGGTGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (28 bp):
CCATGTTGAAAAAAAAAGGTATTACACA
Found at i:1193567 original size:182 final size:182
Alignment explanation
Indices: 1193221--1193566 Score: 432
Period size: 182 Copynumber: 1.9 Consensus size: 182
1193211 GCACACCATA
* * *
1193221 TTGAAAAAAAATTTATTATACACCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCCTAGTGA
1 TTGAAAAAAAATTTATTACACACCATGTTTAAGGTGTTTAACTCCAACAGTTTATATCCTAGTGA
* * * * *
1193286 AATACTAAGATAGAGACCAAGTTACACGCTATGTTTAAAAAATAATATACTTACACACCATGTTC
66 AATACAAAGAAAAAGACCAAGTTACACGCTATGATTAAAAAATAATATACTTACACACCATGTTA
**
1193351 AAAAAAAATGTTATTACATGCAATGTTGAAAAAAAAGTTGTTACATGATATG
131 AAAAAAAATGTTATTACACACAATGTTGAAAAAAAAGTTGTTACATGATATG
* * * *
1193403 TTGAAAAAAAATTTATTACACGCCATGTTTAAGTTGTTTAATTCTAACAGTTTATATCCTAGTGA
1 TTGAAAAAAAATTTATTACACACCATGTTTAAGGTGTTTAACTCCAACAGTTTATATCCTAGTGA
* ** * * **
1193468 AATACAAAGAAAAAGACCAAGTTACATGCCT-T-ATTGCAAAATAAGT-T-GTTATATGCCATGT
66 AATACAAAGAAAAAGACCAAGTTACACG-CTATGATTAAAAAATAA-TATACTTACACACCATGT
*
1193529 TGAAAAAAAAAT-TTATTACACACCATGTTGAAAAAAAA
129 T-AAAAAAAAATGTTATTACACACAATGTTGAAAAAAAA
1193567 AGGTATTACA
Statistics
Matches: 139, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
180 34 0.24
181 19 0.14
182 84 0.60
183 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (182 bp):
TTGAAAAAAAATTTATTACACACCATGTTTAAGGTGTTTAACTCCAACAGTTTATATCCTAGTGA
AATACAAAGAAAAAGACCAAGTTACACGCTATGATTAAAAAATAATATACTTACACACCATGTTA
AAAAAAAATGTTATTACACACAATGTTGAAAAAAAAGTTGTTACATGATATG
Found at i:1201382 original size:73 final size:73
Alignment explanation
Indices: 1201263--1201443 Score: 256
Period size: 73 Copynumber: 2.5 Consensus size: 73
1201253 AAAATGCTCG
* * *
1201263 TAGTCGACTAACTATGCTTCTTAGTTGATTAAGTCGTCTCTGTCTTTGAATCC-AGTTTTTGGCA
1 TAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCATCTCTGTCTTTGAA-CCTAGTTTCTGGCA
*
1201327 GTAAGCTTT
65 GGAAGCTTT
* * *
1201336 TAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCATCTTTGTCTTTGAACCTGGTTTCTGGTAG
1 TAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCATCTCTGTCTTTGAACCTAGTTTCTGGCAG
1201401 GAAGCTTT
66 GAAGCTTT
* * *
1201409 TAGTCGACTAACCATGCTTCTTGGTCGACTAAGTC
1 TAGTCGACTAACTATGCTTCTTAGTCGATTAAGTC
1201444 TTTTCTGTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 2 0.02
73 95 0.98
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (73 bp):
TAGTCGACTAACTATGCTTCTTAGTCGATTAAGTCATCTCTGTCTTTGAACCTAGTTTCTGGCAG
GAAGCTTT
Found at i:1204868 original size:2 final size:2
Alignment explanation
Indices: 1204861--1204894 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1204851 TAAACAAAAT
1204861 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1204895 AACATGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1205872 original size:12 final size:12
Alignment explanation
Indices: 1205855--1205879 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1205845 TTAGGCAACC
1205855 ATATATATACAT
1 ATATATATACAT
1205867 ATATATATACAT
1 ATATATATACAT
1205879 A
1 A
1205880 CACACATGTT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATACAT
Found at i:1206438 original size:15 final size:14
Alignment explanation
Indices: 1206409--1206440 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
1206399 AGTTTTCTAA
1206409 AGAAAGAGTGAGAG
1 AGAAAGAGTGAGAG
1206423 AGAAAGAGTCGAGAG
1 AGAAAGAGT-GAGAG
1206438 AGA
1 AGA
1206441 GATAGGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.41, T:0.06
Consensus pattern (14 bp):
AGAAAGAGTGAGAG
Found at i:1223766 original size:6 final size:6
Alignment explanation
Indices: 1223755--1223779 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1223745 GCTTATGATC
1223755 TATAAA TATAAA TATAAA TATAAA T
1 TATAAA TATAAA TATAAA TATAAA T
1223780 TCTTAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:1286213 original size:28 final size:29
Alignment explanation
Indices: 1286165--1286228 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1286155 ATAAATTTTT
* **
1286165 AAAAATTACACTTTTGCCCCCGTAAAGTG
1 AAAAATTACACTTTTGACCCCAAAAAGTG
* *
1286194 AAAAATTACA-TTTTTACCCCAAAAATTG
1 AAAAATTACACTTTTGACCCCAAAAAGTG
1286222 AAAAATT
1 AAAAATT
1286229 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.30
Consensus pattern (29 bp):
AAAAATTACACTTTTGACCCCAAAAAGTG
Found at i:1295428 original size:20 final size:20
Alignment explanation
Indices: 1295403--1295487 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 20
1295393 AGTGACAAAA
1295403 ATTTTATATTTTTTTATTTT
1 ATTTTATATTTTTTTATTTT
*
1295423 ATTTTATATTTTTATATTTT
1 ATTTTATATTTTTTTATTTT
* **
1295443 -TGTATATATATTTTTT-TCAT
1 AT-TTTATAT-TTTTTTATTTT
1295463 ATTTCTATATTTTTATTATTATT
1 ATTT-TATATTTTT-TTATT-TT
1295486 AT
1 AT
1295488 ATTTTTTCGT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 1 0.02
20 32 0.64
21 13 0.26
22 1 0.02
23 3 0.06
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (20 bp):
ATTTTATATTTTTTTATTTT
Found at i:1295472 original size:33 final size:36
Alignment explanation
Indices: 1295404--1295494 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 36
1295394 GTGACAAAAA
* * * *
1295404 TTTTA-TATTTTTTTATTTTATTTTATATTTTTATAT
1 TTTTAGTATTATTATATTTT-TTTCATATTTCTATAT
1295440 TTTT-GTA-TA-TATATTTTTTTCATATTTCTATAT
1 TTTTAGTATTATTATATTTTTTTCATATTTCTATAT
*
1295473 TTTTATTATTATTATATTTTTT
1 TTTTAGTATTATTATATTTTTT
1295495 CGTAAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
33 18 0.39
34 9 0.20
35 3 0.07
36 16 0.35
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (36 bp):
TTTTAGTATTATTATATTTTTTTCATATTTCTATAT
Found at i:1295475 original size:17 final size:15
Alignment explanation
Indices: 1295403--1295493 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 15
1295393 AGTGACAAAA
*
1295403 ATTTTATATTTTTTT
1 ATTTTATATTTTTAT
*
1295418 ATTTTAT-TTTATAT
1 ATTTTATATTTTTAT
*
1295432 -TTTTATATTTTTGT
1 ATTTTATATTTTTAT
* *
1295446 ATATATATTTTTTTCAT
1 AT-TTTATATTTTT-AT
1295463 ATTTCTATATTTTTATT
1 ATTT-TATATTTTTA-T
1295480 ATTATTATATTTTT
1 ATT-TTATATTTTT
1295494 TCGTAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
13 6 0.10
14 10 0.17
15 8 0.13
16 11 0.18
17 24 0.40
18 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (15 bp):
ATTTTATATTTTTAT
Found at i:1295744 original size:22 final size:21
Alignment explanation
Indices: 1295712--1295752 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1295702 TTATAAGTTT
1295712 ATTATTTTA-TTATATATTTGA
1 ATTATTTTATTTAT-TATTTGA
1295733 ATTATTTTTATTTATTATTT
1 ATTA-TTTTATTTATTATTT
1295753 TTATCNNNNN
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
ATTATTTTATTTATTATTTGA
Found at i:1297294 original size:37 final size:37
Alignment explanation
Indices: 1297240--1297692 Score: 514
Period size: 37 Copynumber: 12.0 Consensus size: 37
1297230 TAATGACATT
* * *
1297240 TTTAAGAATAAACTCCTCAAAATTGAGGCAACGAAA-
1 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* **
1297276 TTTAAAAAATGAATTCCTCAAAGTTGAGGCAACGAAAC
1 TTT-AAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* ** * *
1297314 TTTTTAAAATGAACTCCTCAAAGTTGAGGCGACAAAAC
1 -TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* * * *
1297352 TTTAAAAATGAACTCCTCGAAGCTAAGGCAATGAAAC
1 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
*
1297389 TTTAAAAATGAACTCCTCAAAACTGAGGCAATGAAAC
1 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* * *
1297426 TTTAAAAATGAACTCCTCAAAATTGAGGCCATGAAAC
1 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* *
1297463 TTTTAAAAAATGAACTCCTTAAAGCTGAGGCAACGAAAC
1 -TTT-AAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* *
1297502 TTCTAAAAATGAACTCTTTAAAACTGAGGCAAC-AAGAC
1 TT-TAAAAATGAACTCCTCAAAACTGAGGCAACGAA-AC
*
1297540 TTTAAAAATTGAACTCCTCAAAACTGAGGCAACGAGAC
1 TTTAAAAA-TGAACTCCTCAAAACTGAGGCAACGAAAC
* * *
1297578 TTTGAAGATGAACTCCTCAAAACTGAGGCAACCAAAGC
1 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAA-C
* * *
1297616 TTTTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGTATC
1 --TTT-AAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
*
1297656 TTTAAAAATGAATTCCTCAAAACTGAGGCAACGAAAC
1 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
1297693 CTTTTTTTCT
Statistics
Matches: 360, Mismatches: 44, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
36 3 0.01
37 192 0.53
38 100 0.28
39 34 0.09
40 4 0.01
41 27 0.08
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (37 bp):
TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
Found at i:1297341 original size:75 final size:75
Alignment explanation
Indices: 1297238--1297698 Score: 516
Period size: 75 Copynumber: 6.1 Consensus size: 75
1297228 GGTAATGACA
* * * **
1297238 TTTTTAAGAATAAACTCCTCAAAATTGAGGCAACGAAA-TTTAAAAAATGAATTCCTCAAAGTTG
1 TTTTTAA-AATGAACTCCTCAAAACTGAGGCAACGAAACTTT-AAAAATGAACTCCTCAAAACTG
1297302 AGGCAACGAAAC
64 AGGCAACGAAAC
** * * * * *
1297314 TTTTTAAAATGAACTCCTCAAAGTTGAGGCGACAAAACTTTAAAAATGAACTCCTCGAAGCTAAG
1 TTTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAG
*
1297379 GCAATGAAAC
66 GCAACGAAAC
* * *
1297389 -TTTAAAAATGAACTCCTCAAAACTGAGGCAATGAAACTTTAAAAATGAACTCCTCAAAATTGAG
1 TTTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAG
* *
1297453 GCCATGAAAC
66 GCAACGAAAC
* * * * *
1297463 TTTTAAAAAATGAACTCCTTAAAGCTGAGGCAACGAAACTTCTAAAAATGAACTCTTTAAAACTG
1 TTTT-TAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT-TAAAAATGAACTCCTCAAAACTG
1297528 AGGCAAC-AAGAC
64 AGGCAACGAA-AC
* * * *
1297540 -TTTAAAAATTGAACTCCTCAAAACTGAGGCAACGAGACTTTGAAGATGAACTCCTCAAAACTGA
1 TTTTTAAAA-TGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGA
*
1297604 GGCAACCAAAGC
65 GGCAACGAAA-C
* * * *
1297616 TTTTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGTATCTTTAAAAATGAATTCCTCAAAACTG
1 TTTTT--AAAATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTG
1297681 AGGCAACGAAACC
64 AGGCAACGAAA-C
1297694 TTTTT
1 TTTTT
1297699 TTCTTCTATG
Statistics
Matches: 329, Mismatches: 45, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
74 63 0.19
75 90 0.27
76 79 0.24
77 30 0.09
78 63 0.19
79 4 0.01
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (75 bp):
TTTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAG
GCAACGAAAC
Found at i:1309843 original size:20 final size:20
Alignment explanation
Indices: 1309818--1309857 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1309808 AGTGACAAAA
*
1309818 ATTTTATATTTTTTTATTTT
1 ATTTTATATTTTTATATTTT
1309838 ATTTTATATTTTTATATTTT
1 ATTTTATATTTTTATATTTT
1309858 GTATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (20 bp):
ATTTTATATTTTTATATTTT
Found at i:1309981 original size:16 final size:16
Alignment explanation
Indices: 1309958--1310003 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
1309948 NNNNNNNNNN
1309958 TTTATTTTTTATTTT-
1 TTTATTTTTTATTTTA
1309973 TTATATTTTTTATTTTA
1 TT-TATTTTTTATTTTA
1309990 TTTATTTATTTATT
1 TTTATTT-TTTATT
1310004 AATGTCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.07
16 18 0.64
17 8 0.29
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTTTTATTTTA
Found at i:1310003 original size:8 final size:7
Alignment explanation
Indices: 1309958--1310000 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1309948 NNNNNNNNNN
1309958 TTTATTT
1 TTTATTT
1309965 TTTATTT
1 TTTATTT
1309972 TTTATATT
1 TTTAT-TT
*
1309980 TTT-TAT
1 TTTATTT
1309986 TTTATTT
1 TTTATTT
1309993 ATTTATTT
1 -TTTATTT
1310001 ATTAATGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 4 0.13
7 15 0.48
8 12 0.39
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTATTT
Found at i:1310346 original size:20 final size:21
Alignment explanation
Indices: 1310301--1310352 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
1310291 CATGGTATTT
*
1310301 TTTTATTTATTATTTATTTTA
1 TTTTATTTATTATTTATGTTA
*
1310322 ATTTATTT-TTA-TTACTGTTA
1 TTTTATTTATTATTTA-TGTTA
1310342 TTTTATTTATT
1 TTTTATTTATT
1310353 TGTAGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 14 0.54
21 9 0.35
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTTATTATTTATGTTA
Found at i:1310365 original size:25 final size:25
Alignment explanation
Indices: 1310314--1310365 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1310304 TATTTATTAT
* * *
1310314 TTATTTTAATTTATTTTTATTACTG
1 TTATTTTAATTTATTTGTATAAATG
1310339 TTATTTT-ATTTATTTGTAGTAAATG
1 TTATTTTAATTTATTTGTA-TAAATG
1310364 TT
1 TT
1310366 TTTCTAAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (25 bp):
TTATTTTAATTTATTTGTATAAATG
Found at i:1311442 original size:17 final size:17
Alignment explanation
Indices: 1311420--1311457 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1311410 GTTGAAGGGA
*
1311420 TTTTTTT-TGTTGCTAG
1 TTTTTTTATTTTGCTAG
*
1311436 TTTTTTTATTTTGCTTG
1 TTTTTTTATTTTGCTAG
1311453 TTTTT
1 TTTTT
1311458 CTGGCTTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.05, C:0.05, G:0.13, T:0.76
Consensus pattern (17 bp):
TTTTTTTATTTTGCTAG
Found at i:1317428 original size:15 final size:16
Alignment explanation
Indices: 1317403--1317432 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1317393 TGGATTTTTT
1317403 AAAACAACTTTAAAAC
1 AAAACAACTTTAAAAC
1317419 AAAA-AACTTTAAAA
1 AAAACAACTTTAAAA
1317433 TCCAAAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAACAACTTTAAAAC
Found at i:1324438 original size:20 final size:20
Alignment explanation
Indices: 1324413--1324458 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1324403 TTTTGACCCC
*
1324413 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGAAGTATA
*
1324433 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
1324453 ATTTGA
1 ATTTGA
1324459 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:1324534 original size:28 final size:27
Alignment explanation
Indices: 1324503--1324555 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1324493 TTTGGAGTAT
*
1324503 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
1324531 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
1324556 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:1324561 original size:28 final size:28
Alignment explanation
Indices: 1324503--1324561 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1324493 TTTGGAGTAT
* *
1324503 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
1324531 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
1324559 AGG
1 AGG
1324562 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:1331829 original size:15 final size:17
Alignment explanation
Indices: 1331800--1331831 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1331790 AATTTAAACC
1331800 AAAAAATGATGAATTTT
1 AAAAAATGATGAATTTT
1331817 AAAAAAT-AT-AATTTT
1 AAAAAATGATGAATTTT
1331832 CTGAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAAAAATGATGAATTTT
Found at i:1354994 original size:2 final size:2
Alignment explanation
Indices: 1354987--1355073 Score: 131
Period size: 2 Copynumber: 42.0 Consensus size: 2
1354977 TGAATATTTA
1354987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT ACT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T A-T
1355032 ANT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1355074 TCCACCAATT
Statistics
Matches: 82, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
1 1 0.01
2 71 0.87
3 10 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1356486 original size:28 final size:27
Alignment explanation
Indices: 1356447--1356500 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
1356437 ATGTCCTGAT
*
1356447 GGTGGAAAATTATAATTTTACCCCTAG
1 GGTGGAAAATTACAATTTTACCCCTAG
*
1356474 GGTGGTAAAATTACCATTTTACCCCTA
1 GGTGG-AAAATTACAATTTTACCCCTA
1356501 TGCTCCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTAG
Found at i:1381565 original size:2 final size:2
Alignment explanation
Indices: 1381560--1381587 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1381550 GAAAAAAATA
1381560 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
1381588 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1382219 original size:5 final size:5
Alignment explanation
Indices: 1382191--1382265 Score: 93
Period size: 5 Copynumber: 15.4 Consensus size: 5
1382181 GGTGGGAGAG
*
1382191 AAAG- AAAG- AAAG- AAAGA AACGA AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
* *
1382238 AAAGA AAGGA AAAGA AAATA ATAAGA AA
1 AAAGA AAAGA AAAGA AAAGA A-AAGA AA
1382266 GGGAAATGGG
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
4 12 0.19
5 47 0.75
6 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:1382296 original size:25 final size:24
Alignment explanation
Indices: 1382268--1382352 Score: 91
Period size: 25 Copynumber: 3.3 Consensus size: 24
1382258 ATAAGAAAGG
*
1382268 GAAATGGGCATGGCCCAACAAAATA
1 GAAATGGGCATGGCCCAATAAAA-A
*
1382293 GAAAATTGGACATGGCCCAATAAAGGAA
1 G-AAA-TGGGCATGGCCCAATAAA--AA
1382321 G-AATGGGCATGGCCCAATTAAAAA
1 GAAATGGGCATGGCCCAA-TAAAAA
1382345 GAAATGGG
1 GAAATGGG
1382353 AGAAGTCCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
24 3 0.06
25 20 0.39
26 9 0.18
27 16 0.31
28 2 0.04
29 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.27, T:0.14
Consensus pattern (24 bp):
GAAATGGGCATGGCCCAATAAAAA
Found at i:1384445 original size:12 final size:11
Alignment explanation
Indices: 1384414--1384464 Score: 84
Period size: 11 Copynumber: 4.5 Consensus size: 11
1384404 AGCTTTTAGG
*
1384414 TTTAAAGTTGG
1 TTTAAAGTTGT
1384425 TTTAAAGTTGT
1 TTTAAAGTTGT
1384436 TTTAAAAGTTGT
1 TTT-AAAGTTGT
1384448 TTTAAAGTTGT
1 TTTAAAGTTGT
1384459 TTTAAA
1 TTTAAA
1384465 ATTTATAGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
11 27 0.71
12 11 0.29
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (11 bp):
TTTAAAGTTGT
Found at i:1384445 original size:23 final size:23
Alignment explanation
Indices: 1384417--1384465 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1384407 TTTTAGGTTT
1384417 AAAGTTGGTTTAAAGTTGTTTTA
1 AAAGTTGGTTTAAAGTTGTTTTA
*
1384440 AAAGTTGTTTTAAAGTTGTTTTA
1 AAAGTTGGTTTAAAGTTGTTTTA
1384463 AAA
1 AAA
1384466 TTTATAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (23 bp):
AAAGTTGGTTTAAAGTTGTTTTA
Found at i:1385247 original size:14 final size:14
Alignment explanation
Indices: 1385228--1385254 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1385218 CAAAATTAAT
1385228 TAATTAACTAAAAC
1 TAATTAACTAAAAC
1385242 TAATTAACTAAAA
1 TAATTAACTAAAA
1385255 TTAAAATCAA
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:1386365 original size:20 final size:19
Alignment explanation
Indices: 1386340--1386381 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1386330 AATAATAAAC
1386340 AAATTAAAAGAAATAACATA
1 AAATTAAAAGAAATAAC-TA
* *
1386360 AAATTAAAATAACTAACTA
1 AAATTAAAAGAAATAACTA
1386379 AAA
1 AAA
1386382 GTAACCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (19 bp):
AAATTAAAAGAAATAACTA
Found at i:1393477 original size:15 final size:15
Alignment explanation
Indices: 1393459--1393505 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1393449 TAAAGATCAG
1393459 AGGTTTTGATTTTAA
1 AGGTTTTGATTTTAA
*
1393474 AGGTTTGGATTTTAA
1 AGGTTTTGATTTTAA
* *
1393489 AGTTTTTGGTTTTAA
1 AGGTTTTGATTTTAA
1393504 AG
1 AG
1393506 TTGTTTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
AGGTTTTGATTTTAA
Found at i:1393567 original size:14 final size:15
Alignment explanation
Indices: 1393542--1393574 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1393532 TGCGTGGCCC
1393542 AAGTTAAGTTAAGTT
1 AAGTTAAGTTAAGTT
1393557 AAGTT-AGTTAAGTT
1 AAGTTAAGTTAAGTT
1393571 AAGT
1 AAGT
1393575 CAGGTTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (15 bp):
AAGTTAAGTTAAGTT
Found at i:1393581 original size:19 final size:19
Alignment explanation
Indices: 1393543--1393582 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1393533 GCGTGGCCCA
*
1393543 AGTTAAGTTAAGTTAAGTT
1 AGTTAAGTTAAGTCAAGTT
*
1393562 AGTTAAGTTAAGTCAGGTT
1 AGTTAAGTTAAGTCAAGTT
1393581 AG
1 AG
1393583 GTAGAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (19 bp):
AGTTAAGTTAAGTCAAGTT
Found at i:1393584 original size:5 final size:5
Alignment explanation
Indices: 1393542--1393574 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1393532 TGCGTGGCCC
1393542 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTT AAGT
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGT
1393575 CAGGTTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:1394816 original size:28 final size:27
Alignment explanation
Indices: 1394777--1394829 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1394767 TATCCTGGTA
*
1394777 GTGGAAAATTACAATTTTGCCCCTAAG
1 GTGGAAAATTACAATTTTACCCCTAAG
*
1394804 GTGGCAAAATTACCATTTTACCCCTA
1 GTGG-AAAATTACAATTTTACCCCTA
1394830 TACACCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (27 bp):
GTGGAAAATTACAATTTTACCCCTAAG
Found at i:1394896 original size:20 final size:20
Alignment explanation
Indices: 1394871--1394916 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1394861 CTTTTAAACC
1394871 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
1394891 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
1394911 TCAAAT
1 TCAAAT
1394917 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:1395937 original size:28 final size:29
Alignment explanation
Indices: 1395896--1395960 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1395886 GTCTATGGGC
* *
1395896 AATTTTTCAGTTTT-TTGGGCAAAAATGT
1 AATTTTTCACTTTTATGGGGCAAAAATGT
*
1395924 AATTTTTCACTTTTACTGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-TGGGGCAAAAATGT
*
1395954 AAATTTT
1 AATTTTT
1395961 AAAAATTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 13 0.42
30 18 0.58
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (29 bp):
AATTTTTCACTTTTATGGGGCAAAAATGT
Found at i:1399210 original size:12 final size:12
Alignment explanation
Indices: 1399193--1399222 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1399183 GCCACTTGTC
1399193 ATTGTAATTATT
1 ATTGTAATTATT
1399205 ATTGTAATTATT
1 ATTGTAATTATT
1399217 ATTGTA
1 ATTGTA
1399223 CCCTAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (12 bp):
ATTGTAATTATT
Found at i:1410950 original size:20 final size:20
Alignment explanation
Indices: 1410921--1410960 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1410911 CTTCAAGCAC
*
1410921 TATTAGCAATTATCATCAAG
1 TATTAGCAATCATCATCAAG
*
1410941 TATTATCAATCATCATCAAG
1 TATTAGCAATCATCATCAAG
1410961 CATTCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (20 bp):
TATTAGCAATCATCATCAAG
Found at i:1413827 original size:60 final size:60
Alignment explanation
Indices: 1413763--1413876 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
1413753 TTGTAACCCA
* *
1413763 GAAACAGA-AGGTTTCTTGCTGTAGCGAGATT-TTTTCTCACTGCAGCGAAATTCAACTAAT
1 GAAACAGACA-GTTTCTCGCTGCAGCGAGATTCTTTT-TCACTGCAGCGAAATTCAACTAAT
* * * *
1413823 GAAACAGACAGTTTCTCGTTGCAGCGAGATTCTTTTTCGCTGTAGGGAAATTCA
1 GAAACAGACAGTTTCTCGCTGCAGCGAGATTCTTTTTCACTGCAGCGAAATTCA
1413877 TTCTCACTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 41 0.89
61 5 0.11
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (60 bp):
GAAACAGACAGTTTCTCGCTGCAGCGAGATTCTTTTTCACTGCAGCGAAATTCAACTAAT
Found at i:1414211 original size:19 final size:19
Alignment explanation
Indices: 1414183--1414290 Score: 56
Period size: 19 Copynumber: 5.5 Consensus size: 19
1414173 CACACTCGGC
*
1414183 TCGTGTACATCCCCCCACA
1 TCGTGCACATCCCCCCACA
* **
1414202 TCGTGCACATAACCGGCACCA
1 TCGTGCACAT-CCCCCCA-CA
**
1414223 TCGTGTGCATTCCCCCTCACA
1 TCGTGCACA-TCCCCC-CACA
*****
1414244 TCGTGCACAATTAGTGC-CA
1 TCGTGCAC-ATCCCCCCACA
*
1414263 TCGTGTACATCCCCCCACA
1 TCGTGCACATCCCCCCACA
1414282 TCGTGCACA
1 TCGTGCACA
1414291 CGGGCACTAT
Statistics
Matches: 60, Mismatches: 23, Indels: 12
0.63 0.24 0.13
Matches are distributed among these distances:
18 3 0.05
19 28 0.47
20 5 0.08
21 20 0.33
22 4 0.07
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (19 bp):
TCGTGCACATCCCCCCACA
Found at i:1414227 original size:40 final size:37
Alignment explanation
Indices: 1414183--1414290 Score: 128
Period size: 40 Copynumber: 2.8 Consensus size: 37
1414173 CACACTCGGC
1414183 TCGTGTACATCCCCCCACATCGTGCACATAACCG-GCACCA
1 TCGTGTACATCCCCCCACATCGTGCACATAA--GTG--CCA
* *
1414223 TCGTGTGCATTCCCCCTCACATCGTGCACAATTAGTGCCA
1 TCGTGTACA-TCCCCC-CACATCGTGCAC-ATAAGTGCCA
1414263 TCGTGTACATCCCCCCACATCGTGCACA
1 TCGTGTACATCCCCCCACATCGTGCACA
1414291 CGGGCACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
37 1 0.02
38 12 0.20
39 6 0.10
40 19 0.31
41 7 0.11
42 13 0.21
43 3 0.05
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (37 bp):
TCGTGTACATCCCCCCACATCGTGCACATAAGTGCCA
Found at i:1415156 original size:7 final size:7
Alignment explanation
Indices: 1415148--1415180 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1415138 AACGTGAGAG
*
1415148 GGAAGAG
1 GGAAGAA
1415155 GGAAGAA
1 GGAAGAA
1415162 GGAAGAA
1 GGAAGAA
1415169 GGAAGAA
1 GGAAGAA
1415176 -GAAGA
1 GGAAGA
1415181 CAAGCTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (7 bp):
GGAAGAA
Found at i:1418500 original size:32 final size:33
Alignment explanation
Indices: 1418464--1418563 Score: 105
Period size: 32 Copynumber: 3.0 Consensus size: 33
1418454 CTTTAGCAAT
1418464 GGTTTTTCACGGGATCAACCAAAACCCAA-AAC
1 GGTTTTTCACGGGATCAACCAAAACCCAACAAC
** * * *
1418496 GGTTTTTCAAAGGCTCAACCACAACCTACAACAAT
1 GGTTTTTCACGGGATCAACCAAAACC--CAACAAC
*
1418531 GGTTTTT-ACCGAGATCAACCAAAACCCAACAAC
1 GGTTTTTCA-CGGGATCAACCAAAACCCAACAAC
1418564 TAACTTTTCT
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
32 22 0.42
33 6 0.11
34 4 0.08
35 21 0.40
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.20
Consensus pattern (33 bp):
GGTTTTTCACGGGATCAACCAAAACCCAACAAC
Found at i:1430122 original size:15 final size:15
Alignment explanation
Indices: 1430102--1430139 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1430092 CAGATATTTT
1430102 GATTTTAAAGCTTTA
1 GATTTTAAAGCTTTA
* *
1430117 GATTTTAAAGTTTTT
1 GATTTTAAAGCTTTA
1430132 GATTTTAA
1 GATTTTAA
1430140 GGTTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (15 bp):
GATTTTAAAGCTTTA
Found at i:1442801 original size:20 final size:19
Alignment explanation
Indices: 1442778--1442831 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1442768 TAAATATAAA
1442778 TAACATAAAACT-AACATTAT
1 TAACATAAAA-TAAACATT-T
*
1442798 TAACTTAAAATAAACATTT
1 TAACATAAAATAAACATTT
* *
1442817 AAACATAAATTAAAC
1 TAACATAAAATAAAC
1442832 TACACTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (19 bp):
TAACATAAAATAAACATTT
Found at i:1442933 original size:25 final size:25
Alignment explanation
Indices: 1442899--1442958 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
1442889 GCATAATTAG
1442899 GTATTTAATGTCCCATTAAATATGT
1 GTATTTAATGTCCCATTAAATATGT
1442924 GTATTTAATGTCCCATTAAATATGT
1 GTATTTAATGTCCCATTAAATATGT
1442949 GTATTTAATG
1 GTATTTAATG
1442959 CACACATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (25 bp):
GTATTTAATGTCCCATTAAATATGT
Found at i:1445675 original size:35 final size:34
Alignment explanation
Indices: 1445636--1445745 Score: 127
Period size: 35 Copynumber: 3.2 Consensus size: 34
1445626 TGATCCCAGT
1445636 AAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTG
1 AAAAACCATTGTTG-AGGTTGTGGTTGAGCCTTTG
* * * **
1445671 AAAAATCACT-TTG-GGTTTTGGTTGAGCCCGTG
1 AAAAACCATTGTTGAGGTTGTGGTTGAGCCTTTG
1445703 AAAAACCATTG-TGACAGGTTGTGGTTGAGCCTTTG
1 AAAAACCATTGTTG--AGGTTGTGGTTGAGCCTTTG
1445738 AAAAACCA
1 AAAAACCA
1445746 CTTTGGGTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
32 26 0.43
34 3 0.05
35 32 0.52
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (34 bp):
AAAAACCATTGTTGAGGTTGTGGTTGAGCCTTTG
Found at i:1445692 original size:67 final size:67
Alignment explanation
Indices: 1445614--1445775 Score: 238
Period size: 67 Copynumber: 2.4 Consensus size: 67
1445604 AAATTGGTTG
* * *
1445614 TTGGGTTTTGGTTGATCCCAGT-AAAAACCATTGTTG-TAGGTTGTGGTTGAGCCTTTGAAAAAT
1 TTGGGTTTTGGTTGAGCCC-GTGAAAAACCATTG-TGACAGGTTGTGGTTGAGCCTTTGAAAAAC
1445677 CACT
64 CACT
1445681 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGACAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGACAGGTTGTGGTTGAGCCTTTGAAAAACCA
1445746 CT
66 CT
* * *
1445748 TTGGGTTTTAGTTTAGCACGTGAAAAAC
1 TTGGGTTTTGGTTGAGCCCGTGAAAAAC
1445776 TAGTGTAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
66 4 0.05
67 83 0.95
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.35
Consensus pattern (67 bp):
TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGACAGGTTGTGGTTGAGCCTTTGAAAAACCA
CT
Found at i:1445698 original size:32 final size:32
Alignment explanation
Indices: 1445652--1445754 Score: 127
Period size: 32 Copynumber: 3.1 Consensus size: 32
1445642 CATTGTTGTA
*
1445652 GGTTGTGGTTGAGCCTTTGAAAAATCACTTTG
1 GGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
* **
1445684 GGTTTTGGTTGAGCCCGTGAAAAACCA-TTGTG
1 GGTTGTGGTTGAGCCTTTGAAAAACCACTT-TG
1445716 ACAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
1 ---GGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
1445751 GGTT
1 GGTT
1445755 TTAGTTTAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
31 2 0.03
32 29 0.49
35 26 0.44
36 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (32 bp):
GGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
Found at i:1450532 original size:20 final size:20
Alignment explanation
Indices: 1450499--1450538 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1450489 GAATTTGCGT
1450499 CAAATATATCGATACATTTG
1 CAAATATATCGATACATTTG
* *
1450519 CAAATCTATTGATACATTTG
1 CAAATATATCGATACATTTG
1450539 GTTCTAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (20 bp):
CAAATATATCGATACATTTG
Found at i:1452276 original size:31 final size:31
Alignment explanation
Indices: 1452236--1452307 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
1452226 GGTTGATTTC
* * *
1452236 TTTTGATTTCCTTTATTCCTCTTTTCTTGAT
1 TTTTCATTTCCTTTATTCCACTTTTCTTAAT
*
1452267 TTTTCATTTCCTTTATTTCACTTTTCTTAAT
1 TTTTCATTTCCTTTATTCCACTTTTCTTAAT
1452298 TTTTCATTTC
1 TTTTCATTTC
1452308 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.12, C:0.19, G:0.03, T:0.65
Consensus pattern (31 bp):
TTTTCATTTCCTTTATTCCACTTTTCTTAAT
Found at i:1452292 original size:16 final size:16
Alignment explanation
Indices: 1452242--1452292 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1452232 TTTCTTTTGA
*
1452242 TTTCCTTTATTCCTCT
1 TTTCCTTTATTTCTCT
* * *
1452258 TTT-CTTGATTTTTCA
1 TTTCCTTTATTTCTCT
*
1452273 TTTCCTTTATTTCACT
1 TTTCCTTTATTTCTCT
1452289 TTTC
1 TTTC
1452293 TTAATTTTTC
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTCCTTTATTTCTCT
Found at i:1452307 original size:15 final size:15
Alignment explanation
Indices: 1452258--1452309 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1452248 TTATTCCTCT
*
1452258 TTTCTTGATTTTTCA
1 TTTCTTAATTTTTCA
* ** *
1452273 TTTCCTTTATTTCACT
1 TTT-CTTAATTTTTCA
1452289 TTTCTTAATTTTTCA
1 TTTCTTAATTTTTCA
1452304 TTTCTT
1 TTTCTT
1452310 TTTTTAAATA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.13, C:0.17, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTCTTAATTTTTCA
Found at i:1454538 original size:33 final size:34
Alignment explanation
Indices: 1454501--1454591 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 34
1454491 GGTGGTCAAT
*
1454501 TTTTGAAAGAGGAAAGAGAGGTTGTGCTG-CTGG
1 TTTTGAAAGAGGAAAGAGAGGTTGTGCTGTATGG
* * * **
1454534 TTTTGAGAGAGGAAAAAAAGGTTGTGCTGTTATTT
1 TTTTGAAAGAGGAAAGAGAGGTTGTGCTG-TATGG
1454569 TTTTGAAAGAGGAAAGAGAGGTT
1 TTTTGAAAGAGGAAAGAGAGGTT
1454592 ATGCCACTGG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 26 0.55
35 21 0.45
ACGTcount: A:0.32, C:0.03, G:0.34, T:0.31
Consensus pattern (34 bp):
TTTTGAAAGAGGAAAGAGAGGTTGTGCTGTATGG
Found at i:1455942 original size:42 final size:43
Alignment explanation
Indices: 1455885--1455976 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 43
1455875 TTGGGTGATA
* *
1455885 ATGATGACCCAGCTATGTGCGTGT-GGGAGTGCACATAAGCTG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACAGAAGCTG
* *
1455927 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCATAGGAGCTG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACAGAAGCTG
1455970 ATGATGA
1 ATGATGA
1455977 TGGGATGGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 23 0.51
43 22 0.49
ACGTcount: A:0.26, C:0.16, G:0.35, T:0.23
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACAGAAGCTG
Found at i:1456007 original size:2 final size:2
Alignment explanation
Indices: 1456000--1456048 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1455990 ATGATGATGG
1456000 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
1456042 AT AT AT A
1 AT AT AT A
1456049 AATGTGTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1456270 original size:108 final size:107
Alignment explanation
Indices: 1456097--1456311 Score: 315
Period size: 108 Copynumber: 2.0 Consensus size: 107
1456087 GTAATACATA
* * *
1456097 TGAATCTTGTATGTTAAACCTTCATAATTTCTAAGCATGTTCAAGTTGATTTTGTCTTTACAGCT
1 TGAATCTTGCATGTTAAACCTTCATAATTTCTAAGCATGTTCAAGTTCATTTTGCCTTTACAGCT
*
1456162 AAATGGCCTTTCCTTGAGAGAATGAAAATTTGTTGTTGGTGT
66 AAATGGCCTTTCCTTGAGAGAATGAAAACTTGTTGTTGGTGT
* * **
1456204 NTGAATCTTGCATGTTGAACCTTGGA-AATTTCTAAGCATGTTCAAGTTCATTTTGCCTTTGTAG
1 -TGAATCTTGCATGTTAAACCTT-CATAATTTCTAAGCATGTTCAAGTTCATTTTGCCTTTACAG
* *
1456268 CTAAATGGCCTTTTCTTGGGAGAATGAAAACTTGTTGTTGGTGT
64 CTAAATGGCCTTTCCTTGAGAGAATGAAAACTTGTTGTTGGTGT
1456312 CCTGTTTCTT
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 95 0.99
109 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.41
Consensus pattern (107 bp):
TGAATCTTGCATGTTAAACCTTCATAATTTCTAAGCATGTTCAAGTTCATTTTGCCTTTACAGCT
AAATGGCCTTTCCTTGAGAGAATGAAAACTTGTTGTTGGTGT
Found at i:1457528 original size:22 final size:20
Alignment explanation
Indices: 1457500--1457552 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
1457490 GCGATTAGAG
1457500 AAAGAAAGAAAATAGAAGAA
1 AAAGAAAGAAAATAGAAGAA
* *
1457520 AGAGAGAAA-AATAGTGGAAGAA
1 A-A-AGAAAGAA-AATAGAAGAA
1457542 AAAGAAAGAAA
1 AAAGAAAGAAA
1457553 GGAAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 14 0.52
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.06
Consensus pattern (20 bp):
AAAGAAAGAAAATAGAAGAA
Found at i:1459019 original size:19 final size:19
Alignment explanation
Indices: 1458991--1459028 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1458981 CCATTTAACT
* *
1458991 TATTGGAGTATGATTTGAG
1 TATTGAAGTATAATTTGAG
1459010 TATTGAAGTATAATTTGAG
1 TATTGAAGTATAATTTGAG
1459029 GGTTTGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTGAAGTATAATTTGAG
Found at i:1463988 original size:28 final size:29
Alignment explanation
Indices: 1463947--1464006 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
1463937 GTCTATGGGC
*
1463947 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
1463975 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
1464005 AA
1 AA
1464007 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:1464293 original size:20 final size:20
Alignment explanation
Indices: 1464268--1464306 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1464258 GGAAGAAAAA
1464268 AAGAAAAACCAAAGAGAAAC
1 AAGAAAAACCAAAGAGAAAC
**
1464288 AAGAAAATTCAAAGAGAAA
1 AAGAAAAACCAAAGAGAAA
1464307 TTCGCGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.10, G:0.15, T:0.05
Consensus pattern (20 bp):
AAGAAAAACCAAAGAGAAAC
Found at i:1471959 original size:22 final size:23
Alignment explanation
Indices: 1471931--1471981 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1471921 AGAGCATGGC
1471931 TTAAAG-ATCAGAGCTTTTGGTT
1 TTAAAGAATCAGAGCTTTTGGTT
* *
1471953 TTAAAGATATTAGGGCTTTTGGTT
1 TTAAAGA-ATCAGAGCTTTTGGTT
1471977 TTAAA
1 TTAAA
1471982 ATTTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.24
24 19 0.76
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (23 bp):
TTAAAGAATCAGAGCTTTTGGTT
Found at i:1472815 original size:328 final size:327
Alignment explanation
Indices: 1472218--1472872 Score: 1265
Period size: 328 Copynumber: 2.0 Consensus size: 327
1472208 ACTGCACCTA
1472218 CTTTTCGAGCAGCACCTGCTGCTGAGCCTACTAACATTTCTCCACCTCTTCCACCACCTACTGTT
1 CTTTTCGAGCAGCACCTGCTGCTGAGCCTACTAACATTTCTCCACCTCTTCCACCACCTACTGTT
1472283 ACTCCTGTTGTTCCTGCCATGTCTCTTGAGGCAATCCAAGCATTAGTAGCTTTTCTTAATGTCAT
66 ACTCCTGTTGTTCCTGCCATGTCTCTTGAGGCAATCCAAGCATTAGTAGCTTTTCTTAATGTCAT
1472348 TATGGGCCAGGCTCAAGCTAGTCAAGTCCCTCCTGTTGTTCCCCCAGCAGTATCTCCAGTGCCAC
131 TATGGGCCAGGCTCAAGCTAGTCAAGTCCCTCCTGTTGTTCCCCCAGCAGTATCTCCAGTGCCAC
1472413 CACAACCACCTCCTGTTCCACCACCAATGCCAGATGTCTCCATTTCCAAAAAGCTTAAGGAAGCT
196 CACAACCACCTCCTGTTCCACCACCAATGCCAGATGTCTCCATTTCCAAAAAGCTTAAGGAAGCT
1472478 AGGCAGTTGGTTTGCACTTCTTTTGTTGGTGATTTGGATGCAACCGGAGCTAAAGATTGGATTAC
261 AGGCAGTTGGTTTGCACTTCTTTTGTTGGTGATTTGGATGCAACCGGAGCTAAAGATTGGATTAC
1472543 TC
326 TC
*
1472545 NCTTTTCGAGCAGCACTTGCTGCTGAGCCTACTAACATTTCTCCACCTCTTCCACCACCTACTGT
1 -CTTTTCGAGCAGCACCTGCTGCTGAGCCTACTAACATTTCTCCACCTCTTCCACCACCTACTGT
1472610 TACTCCTGTTGTTCCTGCCATGTCTCTTGAGGCAATCCAAGCATTAGTAGCTTTTCTTAATGTCA
65 TACTCCTGTTGTTCCTGCCATGTCTCTTGAGGCAATCCAAGCATTAGTAGCTTTTCTTAATGTCA
1472675 TTATGGGCCAGGCTCAAGCTAGTCAAGTCCCTCCTGTTGTTCCCCCAGCAGTATCTCCAGTGCCA
130 TTATGGGCCAGGCTCAAGCTAGTCAAGTCCCTCCTGTTGTTCCCCCAGCAGTATCTCCAGTGCCA
* * *
1472740 CCCCCACCACCTCTTGTTCCACCACCAATGCCAGATGTCTCCATTTCCAAAAAGCTTAAGGAAGC
195 CCACAACCACCTCCTGTTCCACCACCAATGCCAGATGTCTCCATTTCCAAAAAGCTTAAGGAAGC
1472805 TAGGCAGTTGGTTTGCACTTCTTTTGTTGGTGATTTGGATGCAACCGGAGCTAAAGATTGGATTA
260 TAGGCAGTTGGTTTGCACTTCTTTTGTTGGTGATTTGGATGCAACCGGAGCTAAAGATTGGATTA
1472870 CTC
325 CTC
1472873 AGGTAACAGA
Statistics
Matches: 323, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
328 323 1.00
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (327 bp):
CTTTTCGAGCAGCACCTGCTGCTGAGCCTACTAACATTTCTCCACCTCTTCCACCACCTACTGTT
ACTCCTGTTGTTCCTGCCATGTCTCTTGAGGCAATCCAAGCATTAGTAGCTTTTCTTAATGTCAT
TATGGGCCAGGCTCAAGCTAGTCAAGTCCCTCCTGTTGTTCCCCCAGCAGTATCTCCAGTGCCAC
CACAACCACCTCCTGTTCCACCACCAATGCCAGATGTCTCCATTTCCAAAAAGCTTAAGGAAGCT
AGGCAGTTGGTTTGCACTTCTTTTGTTGGTGATTTGGATGCAACCGGAGCTAAAGATTGGATTAC
TC
Found at i:1474989 original size:28 final size:27
Alignment explanation
Indices: 1474952--1475005 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
1474942 ATTTGGAGTA
*
1474952 TAGGGGTAAAATGGTAATTTTACCACCC
1 TAGGGATAAAATGGTAATTTT-CCACCC
*
1474980 TAGGGATAAAATTGTAATTTTCCACC
1 TAGGGATAAAATGGTAATTTTCCACC
1475006 ACCAGGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (27 bp):
TAGGGATAAAATGGTAATTTTCCACCC
Found at i:1476146 original size:15 final size:16
Alignment explanation
Indices: 1476116--1476150 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1476106 ATAAAATATT
1476116 ATGTTTTTCAATTAAA
1 ATGTTTTTCAATTAAA
* *
1476132 ATGTTTTTTAATAAAA
1 ATGTTTTTCAATTAAA
1476148 ATG
1 ATG
1476151 AGATTTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
ATGTTTTTCAATTAAA
Found at i:1489121 original size:13 final size:13
Alignment explanation
Indices: 1489103--1489127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1489093 AGAGAAATTG
1489103 TGATTTTATAAAA
1 TGATTTTATAAAA
1489116 TGATTTTATAAA
1 TGATTTTATAAA
1489128 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:1492094 original size:2 final size:2
Alignment explanation
Indices: 1492089--1492144 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
1492079 TATATATATA
*
1492089 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1492131 TG TG TG TG TA TG TG
1 TG TG TG TG TG TG TG
1492145 GAGTTGCGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.02, C:0.02, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:1494648 original size:28 final size:28
Alignment explanation
Indices: 1494606--1494659 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1494596 AATAAAATAG
* * * *
1494606 AAGAAAGAGAGAAAGAGAGAAAAAGGAA
1 AAGAAAGAAAAAAAGAAAAAAAAAGGAA
1494634 AAGAAAGAAAAAAAGAAAAAAAAAGG
1 AAGAAAGAAAAAAAGAAAAAAAAAGG
1494660 TAAACTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (28 bp):
AAGAAAGAAAAAAAGAAAAAAAAAGGAA
Found at i:1497032 original size:13 final size:14
Alignment explanation
Indices: 1497004--1497036 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1496994 ATTTATCTTT
1497004 TATTTTAAAACTTA
1 TATTTTAAAACTTA
*
1497018 TATTTT-AAGCTTA
1 TATTTTAAAACTTA
1497031 TATTTT
1 TATTTT
1497037 GGTTTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (14 bp):
TATTTTAAAACTTA
Found at i:1604650 original size:20 final size:20
Alignment explanation
Indices: 1604625--1604662 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1604615 CCACTTACTA
1604625 AATTTCCAAAACCA-TTATTC
1 AATTT-CAAAACCAGTTATTC
1604645 AATTTCAAAACCAGTTAT
1 AATTTCAAAACCAGTTAT
1604663 AAAACTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (20 bp):
AATTTCAAAACCAGTTATTC
Found at i:1610809 original size:19 final size:19
Alignment explanation
Indices: 1610785--1610822 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1610775 CCATTTAACT
*
1610785 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
1610804 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
1610823 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:1615566 original size:20 final size:20
Alignment explanation
Indices: 1615541--1615578 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1615531 TTTTGGCCCC
1615541 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
1615561 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
1615579 NNNNNNNNNN
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:1615701 original size:4 final size:4
Alignment explanation
Indices: 1615679--1615762 Score: 69
Period size: 4 Copynumber: 22.5 Consensus size: 4
1615669 NNNNNNNNNN
*
1615679 ATTT TTTT ATTT -TTT -TTT ATTT ATTT ATTT A-TT A-TT ATTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT
1615724 ATTT AATTT ATTT A-TT A-TT A-TT ATTT -TTT -TTT AATTT AT
1 ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT AT
1615763 GTGTCTACAG
Statistics
Matches: 71, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
3 27 0.38
4 34 0.48
5 10 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:1615717 original size:28 final size:28
Alignment explanation
Indices: 1615685--1615762 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
1615675 NNNNATTTTT
1615685 TTATTTTTTTTTATTTATTTATTTATTA
1 TTATTTTTTTTTATTTATTTATTTATTA
*
1615713 TTA-TTTTATTTATTTAATTTATTTATTA
1 TTATTTTTTTTTATTT-ATTTATTTATTA
*
1615741 TTATTATTTTTTT-TTAATTTAT
1 TTATT-TTTTTTTATTTATTTAT
1615763 GTGTCTACAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 11 0.25
28 24 0.55
29 3 0.07
30 6 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (28 bp):
TTATTTTTTTTTATTTATTTATTTATTA
Found at i:1615738 original size:32 final size:30
Alignment explanation
Indices: 1615690--1615762 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 30
1615680 TTTTTTTATT
*
1615690 TTTTTTTATTTATTTATTTATTATTATTTTA
1 TTTTTTAATTTATTTA-TTATTATTATTTTA
1615721 TTTATTTAATTTATTTATTATTATTA-TTT-
1 TTT-TTTAATTTATTTATTATTATTATTTTA
1615750 TTTTTTAATTTAT
1 TTTTTTAATTTAT
1615763 GTGTCTACAG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 10 0.25
29 3 0.08
30 3 0.08
31 12 0.30
32 12 0.30
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (30 bp):
TTTTTTAATTTATTTATTATTATTATTTTA
Found at i:1622248 original size:29 final size:29
Alignment explanation
Indices: 1622216--1622352 Score: 105
Period size: 26 Copynumber: 4.9 Consensus size: 29
1622206 ATATGTCGTA
1622216 TAACAACAATATTTTTTTAACATGACATG
1 TAACAACAATATTTTTTTAACATGACATG
* * *
1622245 TAACAATAATATTTTTTTTTCAACATGGCGTG
1 TAACAACAATA--TTTTTTT-AACATGACATG
*
1622277 TAACAAC----TTTTTTTAACCATGACGTG
1 TAACAACAATATTTTTTTAA-CATGACATG
1622303 T---AAC-ATATTTTTTT-ACAT-AGCATG
1 TAACAACAATATTTTTTTAACATGA-CATG
*
1622327 TAACAACAGTATTTTTTTCAACATGA
1 TAACAACAATATTTTTTT-AACATGA
1622353 TGTATAACAA
Statistics
Matches: 86, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
23 4 0.05
24 7 0.08
25 3 0.03
26 23 0.27
27 3 0.03
28 9 0.10
29 10 0.12
30 4 0.05
31 8 0.09
32 15 0.17
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (29 bp):
TAACAACAATATTTTTTTAACATGACATG
Found at i:1622481 original size:69 final size:69
Alignment explanation
Indices: 1622385--1622579 Score: 282
Period size: 69 Copynumber: 2.8 Consensus size: 69
1622375 TCGTCACAAG
* * * * * *
1622385 TTTTTGTACATAGTGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTACTTGACTTGTTA
1 TTTTTGTACATAGCGTGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
1622450 AATA
66 AATA
* * *
1622454 TTTTTGTACATAGCATGTGACATGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
1 TTTTTGTACATAGCGTGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
*
1622519 CATA
66 AATA
* *
1622523 TTTTTGTACATAGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATG
1 TTTTTGTACATAGCGTGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTACATG
1622580 GCATGTAACA
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 112 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (69 bp):
TTTTTGTACATAGCGTGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
AATA
Found at i:1622517 original size:24 final size:24
Alignment explanation
Indices: 1622483--1622533 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1622473 ACATGCTAAC
* *
1622483 CATGACTTGTCACAGGTTTTTGTA
1 CATGACCTGTCACAGATTTTTGTA
*
1622507 CATGACCTGTCACATATTTTTGTA
1 CATGACCTGTCACAGATTTTTGTA
1622531 CAT
1 CAT
1622534 AGCGTGTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (24 bp):
CATGACCTGTCACAGATTTTTGTA
Found at i:1622595 original size:114 final size:114
Alignment explanation
Indices: 1622454--1622817 Score: 469
Period size: 114 Copynumber: 3.2 Consensus size: 114
1622444 TTGTTAAATA
* *
1622454 TTTTTGTACATAGCATGTGACATGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
1 TTTTTGTACATAGCATGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
*
1622519 CATATTTTTGTACATAGCGTGTAACACGCTAACCATGGCTTGTCACAGG
66 CATATTTTTGTACATAGCGTGTAACACGCTAACCATGGCTTGTCACAAG
* * * ***
1622568 TTTTTGTACATGGCATGTAACAAGCTAACCATAACTTGTCACAGGTTTTTGCACATGGGTTGTCA
1 TTTTTGTACATAGCATGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
* * * * *
1622633 CATATTTTTGTACATGGCATGTAACAAGCTAACCATGACTTATCACATA-
66 CATATTTTTGTACATAGCGTGTAACACGCTAACCATGGCTTGTCACA-AG
* ** * * * *
1622682 TTTTTGTACATAGCGTGTAACACCCTAACCATGGCTTGTCACAAGTTTTTGTACATAACGTGTCA
1 TTTTTGTACATAGCATGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
* * *
1622747 CATATTTTTGTCCACAGCGTGTAACACGCTAACCATAGCTTGTCACAAG
66 CATATTTTTGTACATAGCGTGTAACACGCTAACCATGGCTTGTCACAAG
* * *
1622796 TTTTTGTATATGGCGTGTAACA
1 TTTTTGTACATAGCATGTAACA
1622818 TCATAGCGTG
Statistics
Matches: 212, Mismatches: 36, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
113 1 0.00
114 211 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (114 bp):
TTTTTGTACATAGCATGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTACATGACCTGTCA
CATATTTTTGTACATAGCGTGTAACACGCTAACCATGGCTTGTCACAAG
Found at i:1622624 original size:45 final size:45
Alignment explanation
Indices: 1622514--1622625 Score: 152
Period size: 45 Copynumber: 2.5 Consensus size: 45
1622504 GTACATGACC
** * * * **
1622514 TGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCATGGCT
1 TGTCACAGGTTTTTGTACATGGCATGTAACAAGCTAACCATAACT
1622559 TGTCACAGGTTTTTGTACATGGCATGTAACAAGCTAACCATAACT
1 TGTCACAGGTTTTTGTACATGGCATGTAACAAGCTAACCATAACT
*
1622604 TGTCACAGGTTTTTGCACATGG
1 TGTCACAGGTTTTTGTACATGG
1622626 GTTGTCACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (45 bp):
TGTCACAGGTTTTTGTACATGGCATGTAACAAGCTAACCATAACT
Found at i:1622640 original size:24 final size:24
Alignment explanation
Indices: 1622603--1622649 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1622593 TAACCATAAC
*
1622603 TTGTCACAGGTTTTTGCACATGGG
1 TTGTCACAGATTTTTGCACATGGG
* *
1622627 TTGTCACATATTTTTGTACATGG
1 TTGTCACAGATTTTTGCACATGG
1622650 CATGTAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (24 bp):
TTGTCACAGATTTTTGCACATGGG
Found at i:1622686 original size:69 final size:69
Alignment explanation
Indices: 1622552--1622692 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
1622542 ACACGCTAAC
* * *
1622552 CATGGCTTGTCACAGGTTTTTGTACATGGCATGTAACAAGCTAACCATAACTTGTCACAGGTTTT
1 CATGGCTTGTCACAGATTTTTGTACATGGCATGTAACAAGCTAACCATAACTTATCACAGATTTT
1622617 TGCA
66 TGCA
* * * *
1622621 CATGGGTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGACTTATCACATATTTT
1 CATGGCTTGTCACAGATTTTTGTACATGGCATGTAACAAGCTAACCATAACTTATCACAGATTTT
*
1622686 TGTA
66 TGCA
1622690 CAT
1 CAT
1622693 AGCGTGTAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (69 bp):
CATGGCTTGTCACAGATTTTTGTACATGGCATGTAACAAGCTAACCATAACTTATCACAGATTTT
TGCA
Found at i:1622701 original size:45 final size:45
Alignment explanation
Indices: 1622630--1622744 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
1622620 ACATGGGTTG
* * *
1622630 TCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGACTTA
1 TCACATATTTTTGTACATAGCGTGTAACAACCTAACCATGACTTA
* * *
1622675 TCACATATTTTTGTACATAGCGTGTAACACCCTAACCATGGCTTG
1 TCACATATTTTTGTACATAGCGTGTAACAACCTAACCATGACTTA
*
1622720 TCACA-AGTTTTTGTACATAACGTGT
1 TCACATA-TTTTTGTACATAGCGTGT
1622745 CACATATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 1 0.02
45 61 0.98
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (45 bp):
TCACATATTTTTGTACATAGCGTGTAACAACCTAACCATGACTTA
Found at i:1622767 original size:24 final size:24
Alignment explanation
Indices: 1622718--1622768 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1622708 AACCATGGCT
*
1622718 TGTCACAAGTTTTTGTACATAACG
1 TGTCACAAGTTTTTGTACACAACG
* *
1622742 TGTCACATA-TTTTTGTCCACAGCG
1 TGTCACA-AGTTTTTGTACACAACG
1622766 TGT
1 TGT
1622769 AACACGCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (24 bp):
TGTCACAAGTTTTTGTACACAACG
Found at i:1622813 original size:69 final size:69
Alignment explanation
Indices: 1622675--1622803 Score: 222
Period size: 69 Copynumber: 1.9 Consensus size: 69
1622665 CCATGACTTA
* *
1622675 TCACATATTTTTGTACATAGCGTGTAACACCCTAACCATGGCTTGTCACAAGTTTTTGTACATAA
1 TCACATATTTTTGTACACAGCGTGTAACACCCTAACCATAGCTTGTCACAAGTTTTTGTACATAA
1622740 CGTG
66 CGTG
* *
1622744 TCACATATTTTTGTCCACAGCGTGTAACACGCTAACCATAGCTTGTCACAAGTTTTTGTA
1 TCACATATTTTTGTACACAGCGTGTAACACCCTAACCATAGCTTGTCACAAGTTTTTGTA
1622804 TATGGCGTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 56 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (69 bp):
TCACATATTTTTGTACACAGCGTGTAACACCCTAACCATAGCTTGTCACAAGTTTTTGTACATAA
CGTG
Found at i:1624491 original size:19 final size:19
Alignment explanation
Indices: 1624447--1624484 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1624437 CCATTTAACT
* *
1624447 TATTCGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
1624466 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
1624485 GTTTGGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:1634221 original size:20 final size:19
Alignment explanation
Indices: 1634198--1634246 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1634188 ATAAAAAATA
*
1634198 AAAAGAGAAAAGATAGAAAC
1 AAAAGAGAAAA-AAAGAAAC
1634218 AAAAGA-AAACAAAAGAAAC
1 AAAAGAGAAA-AAAAGAAAC
1634237 AAAA-AGAAAA
1 AAAAGAGAAAA
1634247 TGTTGTACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.08
19 17 0.65
20 7 0.27
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAGAGAAAAAAAGAAAC
Found at i:1634229 original size:10 final size:10
Alignment explanation
Indices: 1634214--1634246 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1634204 GAAAAGATAG
1634214 AAACAAAAGA
1 AAACAAAAGA
1634224 AAACAAAAG-
1 AAACAAAAGA
1634233 AAACAAAAAGA
1 AAAC-AAAAGA
1634244 AAA
1 AAA
1634247 TGTTGTACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.19
10 14 0.67
11 3 0.14
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (10 bp):
AAACAAAAGA
Found at i:1634791 original size:111 final size:111
Alignment explanation
Indices: 1634583--1634806 Score: 272
Period size: 111 Copynumber: 2.0 Consensus size: 111
1634573 AACCGGTTGG
* * * *
1634583 GGAGGAAAGCCTTTGGGTAGCCAGTGAAAAGGGAGAGGCGAAAGATCCAAGCGATGATAGGATAG
1 GGAGGAAAACCTTTGGGTAGCCAGCGAAAAGGGAGAGGAGAAAGATCCAAGCGACGATAGGATAG
**
1634648 AAACGAGGAGAGCCAACTAACGATTTGGAGAGATCTAGAGGTTTTT
66 AAACGAGGAGAGCCAACTAACGATTTAAAGAGATCTAGAGGTTTTT
* * * * *
1634694 GGAGGAAAACTTTTGGGTAGTCAGCGAAAAGGGAGAGGAGAAAGATCCGAGCGGCGGTAGGATAG
1 GGAGGAAAACCTTTGGGTAGCCAGCGAAAAGGGAGAGGAGAAAGATCCAAGCGACGATAGGATAG
* * ** *
1634759 AAATG-GGAAGAGCCGA-TCGGCGGTTTAAAGAGATCTAGAGGTTTTT
66 AAACGAGG-AGAGCCAACT-AACGATTTAAAGAGATCTAGAGGTTTTT
1634805 GG
1 GG
1634807 GGGAGGCCAT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
110 3 0.03
111 92 0.97
ACGTcount: A:0.33, C:0.12, G:0.37, T:0.18
Consensus pattern (111 bp):
GGAGGAAAACCTTTGGGTAGCCAGCGAAAAGGGAGAGGAGAAAGATCCAAGCGACGATAGGATAG
AAACGAGGAGAGCCAACTAACGATTTAAAGAGATCTAGAGGTTTTT
Found at i:1638344 original size:14 final size:14
Alignment explanation
Indices: 1638304--1638371 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
1638294 CAAAGAAGAT
* **
1638304 AATACATATAAAGG
1 AATATATATAAATA
*
1638318 AATATAAATAAATA
1 AATATATATAAATA
1638332 AATATATATAAATA
1 AATATATATAAATA
* *
1638346 ATACAATATAAAAATA
1 A-A-TATATATAAATA
*
1638362 AAAATATATA
1 AATATATATA
1638372 TAGTTAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
14 31 0.70
15 2 0.05
16 11 0.25
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (14 bp):
AATATATATAAATA
Found at i:1640461 original size:19 final size:19
Alignment explanation
Indices: 1640439--1640476 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1640429 CCATTTGAAT
1640439 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
1640458 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
1640477 GTTGAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:1640540 original size:27 final size:28
Alignment explanation
Indices: 1640510--1640568 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1640500 TCTCGGTATT
1640510 TTTTG-AAGCATAGGGATAAAATGGTAA
1 TTTTGCAAGCATAGGGATAAAATGGTAA
* * * * *
1640537 TTTTGCCATCCTAGGGGTAAAATTGTAA
1 TTTTGCAAGCATAGGGATAAAATGGTAA
1640565 TTTT
1 TTTT
1640569 ACACACCCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.37
Consensus pattern (28 bp):
TTTTGCAAGCATAGGGATAAAATGGTAA
Found at i:1644953 original size:15 final size:16
Alignment explanation
Indices: 1644933--1644973 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1644923 CAGATATTTT
1644933 GATTTTAAAG-CATTG
1 GATTTTAAAGTCATTG
*
1644948 GATTTTAAAGTCTTTG
1 GATTTTAAAGTCATTG
1644964 G-TTTTAAAGT
1 GATTTTAAAGT
1644974 TGTTTTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (16 bp):
GATTTTAAAGTCATTG
Found at i:1645056 original size:5 final size:5
Alignment explanation
Indices: 1645016--1645055 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
1645006 CCCCAAGTCC
* *
1645016 AGTTA AGTTA AGATA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
1645056 GATTGAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (5 bp):
AGTTA
Found at i:1646466 original size:20 final size:20
Alignment explanation
Indices: 1646441--1646486 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1646431 TTTTGGCCCC
1646441 ATTTGACTTATTGGAGTAAG
1 ATTTGACTTATTGGAGTAAG
1646461 ATTTGACTTATTGGAGTAAG
1 ATTTGACTTATTGGAGTAAG
1646481 ATTTGA
1 ATTTGA
1646487 GGTTTAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTAAG
Found at i:1655893 original size:15 final size:15
Alignment explanation
Indices: 1655852--1655898 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1655842 AAAAATTATT
*
1655852 ATATAATAAATTAGTCA
1 ATATAATAAA-TA-TAA
1655869 ATAT-ATAAATATAA
1 ATATAATAAATATAA
1655883 ATATAATAAATATAA
1 ATATAATAAATATAA
1655898 A
1 A
1655899 AGAACAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 6 0.21
15 13 0.46
16 5 0.18
17 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
ATATAATAAATATAA
Found at i:1657498 original size:11 final size:12
Alignment explanation
Indices: 1657466--1657491 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1657456 TCTATTTCTA
1657466 TTTGACATTTTG
1 TTTGACATTTTG
1657478 TTTGACATTTTG
1 TTTGACATTTTG
1657490 TT
1 TT
1657492 GAAATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTGACATTTTG
Found at i:1657575 original size:12 final size:12
Alignment explanation
Indices: 1657541--1657588 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1657531 CATTATACAA
* *
1657541 ATAAATCAAATA
1 ATAAATAAAATC
1657553 ATAAACTTAAAATC
1 ATAAA--TAAAATC
1657567 ATAAATAAAATC
1 ATAAATAAAATC
*
1657579 AAAAATAAAA
1 ATAAATAAAA
1657589 ATCAAACAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 21 0.68
14 10 0.32
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
ATAAATAAAATC
Found at i:1657591 original size:13 final size:13
Alignment explanation
Indices: 1657561--1657601 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
1657551 TAATAAACTT
*
1657561 AAAATCATAAAT-
1 AAAATCAAAAATA
1657573 AAAATCAAAAATA
1 AAAATCAAAAATA
1657586 AAAATCAAACAATA
1 AAAATCAAA-AATA
1657600 AA
1 AA
1657602 TTATGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 11 0.42
13 9 0.35
14 6 0.23
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATCAAAAATA
Found at i:1664255 original size:16 final size:16
Alignment explanation
Indices: 1664234--1664264 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1664224 TCCAAGTTTA
1664234 ACAAAATAAGAAAAAC
1 ACAAAATAAGAAAAAC
*
1664250 ACAAAATTAGAAAAA
1 ACAAAATAAGAAAAA
1664265 AAAAACTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
ACAAAATAAGAAAAAC
Found at i:1664947 original size:20 final size:21
Alignment explanation
Indices: 1664911--1664952 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1664901 AATTTAAAGC
1664911 AAAATAACATGAAATTAAACT
1 AAAATAACATGAAATTAAACT
*
1664932 AAAATAAC-TTAAATTAAACT
1 AAAATAACATGAAATTAAACT
1664952 A
1 A
1664953 TTCATCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAATAACATGAAATTAAACT
Found at i:1671242 original size:37 final size:37
Alignment explanation
Indices: 1671192--1671267 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
1671182 CGAAACACAT
1671192 ATCCAAAAATCCAGCCATCATGCTTGTGACATTCGAC
1 ATCCAAAAATCCAGCCATCATGCTTGTGACATTCGAC
*
1671229 ATCCAAAAGTCCAGCCATCATGCTTGTGACATTCGAC
1 ATCCAAAAATCCAGCCATCATGCTTGTGACATTCGAC
1671266 AT
1 AT
1671268 GTCCATATCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (37 bp):
ATCCAAAAATCCAGCCATCATGCTTGTGACATTCGAC
Found at i:1673179 original size:19 final size:19
Alignment explanation
Indices: 1673151--1673189 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1673141 TATTTTAAGA
1673151 TATGTCTTGCATGTTTATT
1 TATGTCTTGCATGTTTATT
*
1673170 TATGTTTTGCATGTTTATT
1 TATGTCTTGCATGTTTATT
1673189 T
1 T
1673190 TTGAGATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (19 bp):
TATGTCTTGCATGTTTATT
Done.