Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 5 of 167
Found at i:1362485 original size:42 final size:43
Alignment explanation
Indices: 1362430--1362512 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 43
1362420 TAGGTTTTGA
* *
1362430 GGTTAGAGGTTTTAGGGCTTGGGGCTTGGTGCTTGGGGTTTAG
1 GGTTAGAGGTTTTAGGGCTTGAGGCTTGGGGCTTGGGGTTTAG
* * *
1362473 GGTTAG-GGTTTTAGGGTTTGAGGTTTGGGGTTTGGGGTTT
1 GGTTAGAGGTTTTAGGGCTTGAGGCTTGGGGCTTGGGGTTT
1362513 GTGGCGTGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 29 0.83
43 6 0.17
ACGTcount: A:0.08, C:0.04, G:0.47, T:0.41
Consensus pattern (43 bp):
GGTTAGAGGTTTTAGGGCTTGAGGCTTGGGGCTTGGGGTTTAG
Found at i:1362513 original size:7 final size:7
Alignment explanation
Indices: 1362407--1362513 Score: 61
Period size: 7 Copynumber: 15.0 Consensus size: 7
1362397 TAAGGTATTA
1362407 GGGTTTG
1 GGGTTTG
*
1362414 GGGTTTTA
1 GGG-TTTG
*
1362422 GGTTTTG
1 GGGTTTG
* *
1362429 AGGTTAG
1 GGGTTTG
* *
1362436 AGGTTTTA
1 -GGGTTTG
*
1362444 GGGCTTG
1 GGGTTTG
*
1362451 GGGCTTG
1 GGGTTTG
* *
1362458 GTGCTTG
1 GGGTTTG
*
1362465 GGGTTTA
1 GGGTTTG
*
1362472 GGGTTAG
1 GGGTTTG
* *
1362479 GGTTTTA
1 GGGTTTG
1362486 GGGTTTG
1 GGGTTTG
*
1362493 AGGTTTG
1 GGGTTTG
1362500 GGGTTTG
1 GGGTTTG
1362507 GGGTTTG
1 GGGTTTG
1362514 TGGCGTGGGG
Statistics
Matches: 72, Mismatches: 26, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
7 64 0.89
8 8 0.11
ACGTcount: A:0.08, C:0.03, G:0.47, T:0.42
Consensus pattern (7 bp):
GGGTTTG
Found at i:1362551 original size:7 final size:7
Alignment explanation
Indices: 1362541--1363531 Score: 1093
Period size: 7 Copynumber: 135.9 Consensus size: 7
1362531 CTCGGCGCTC
1362541 GGGTTTA
1 GGGTTTA
1362548 GGGTTTA
1 GGGTTTA
*
1362555 GAGTTTA
1 GGGTTTA
*
1362562 GAGATTTA
1 G-GGTTTA
*
1362570 GGGCTTA
1 GGGTTTA
1362577 GGGTTTTTA
1 GGG--TTTA
1362586 GGGTTTA
1 GGGTTTA
1362593 GGGTTTA
1 GGGTTTA
1362600 GGGTTTA
1 GGGTTTA
*
1362607 GGGTTTG
1 GGGTTTA
*
1362614 GGGTTTG
1 GGGTTTA
*
1362621 GGGTTTG
1 GGGTTTA
1362628 GGGTTTA
1 GGGTTTA
*
1362635 GCGTTT-
1 GGGTTTA
*
1362641 GGCATTTA
1 GG-GTTTA
*
1362649 GGGTTTGG
1 GGGTTT-A
1362657 GGGTTTA
1 GGGTTTA
1362664 GGGTTTA
1 GGGTTTA
1362671 GGGTCTTA
1 GGGT-TTA
*
1362679 GTGTCTTA
1 GGGT-TTA
1362687 GGGTTTA
1 GGGTTTA
*
1362694 GGGTCTA
1 GGGTTTA
1362701 GGGTTTTA
1 GGG-TTTA
1362709 GGGTTTA
1 GGGTTTA
1362716 GGGTTTA
1 GGGTTTA
*
1362723 GGATTTA
1 GGGTTTA
*
1362730 GGGATTA
1 GGGTTTA
*
1362737 GGGTTTG
1 GGGTTTA
*
1362744 GGGTTTG
1 GGGTTTA
*
1362751 GGGTTTG
1 GGGTTTA
*
1362758 GGGTTTGG
1 GGGTTT-A
1362766 GGGTTTA
1 GGGTTTA
1362773 GGGTTTTA
1 GGG-TTTA
1362781 GGGTTTTA
1 GGG-TTTA
1362789 GGGTTTA
1 GGGTTTA
1362796 GGGTTTTA
1 GGG-TTTA
*
1362804 TCGGGGTTTG
1 ---GGGTTTA
*
1362814 GGGTTTG
1 GGGTTTA
1362821 GGGTTTTA
1 GGG-TTTA
*
1362829 GGGGTTTG
1 -GGGTTTA
1362837 GGGTTTTA
1 GGG-TTTA
*
1362845 GGGGTTCA
1 -GGGTTTA
1362853 GGGTTTTA
1 GGG-TTTA
1362861 GGGGTTTTA
1 -GGG-TTTA
*
1362870 GGGGTTA
1 GGGTTTA
1362877 GGGTTTA
1 GGGTTTA
*
1362884 GGGGTTA
1 GGGTTTA
*
1362891 GGGTTCA
1 GGGTTTA
*
1362898 GGGTTCA
1 GGGTTTA
*
1362905 GGGTTCA
1 GGGTTTA
*
1362912 GGGTTCA
1 GGGTTTA
*
1362919 GGGTTCA
1 GGGTTTA
1362926 GGGTTTTA
1 GGG-TTTA
1362934 GGGTTTA
1 GGGTTTA
*
1362941 GGGTTCA
1 GGGTTTA
1362948 GGGGTTTA
1 -GGGTTTA
*
1362956 GGGTTCA
1 GGGTTTA
1362963 GGGGTTTA
1 -GGGTTTA
*
1362971 GGGTTCA
1 GGGTTTA
1362978 GGGGTTTA
1 -GGGTTTA
*
1362986 GGGTTCA
1 GGGTTTA
*
1362993 GGGTTCA
1 GGGTTTA
*
1363000 GGGTTCA
1 GGGTTTA
*
1363007 GGGTTCA
1 GGGTTTA
*
1363014 GGGTTCA
1 GGGTTTA
*
1363021 GGGTTCA
1 GGGTTTA
*
1363028 GGGTTCA
1 GGGTTTA
*
1363035 GGGTTCA
1 GGGTTTA
*
1363042 GGGTTCA
1 GGGTTTA
*
1363049 GGGTTCA
1 GGGTTTA
*
1363056 GGGTTCA
1 GGGTTTA
*
1363063 GGGTTCA
1 GGGTTTA
1363070 GGGTTTTA
1 GGG-TTTA
*
1363078 GGGTTCA
1 GGGTTTA
*
1363085 GGGTTCA
1 GGGTTTA
1363092 GGGTTTTA
1 GGG-TTTA
*
1363100 GGGTTCA
1 GGGTTTA
1363107 GGGTTTA
1 GGGTTTA
1363114 TGGGTTTA
1 -GGGTTTA
1363122 GGGTTTA
1 GGGTTTA
*
1363129 GGGGTTCA
1 -GGGTTTA
1363137 GGGTTTA
1 GGGTTTA
*
1363144 GGGTTTTG
1 GGG-TTTA
1363152 GGGTTTA
1 GGGTTTA
*
1363159 GGGTTTT
1 GGGTTTA
*
1363166 GGGGTTA
1 GGGTTTA
1363173 GGGTTTA
1 GGGTTTA
*
1363180 GGGGTTA
1 GGGTTTA
*
1363187 GGGTTTTG
1 GGG-TTTA
1363195 GGGTTTA
1 GGGTTTA
*
1363202 GGGTTTTG
1 GGG-TTTA
1363210 GGGTTTA
1 GGGTTTA
*
1363217 GGGTTTTG
1 GGG-TTTA
*
1363225 GGGTTTT
1 GGGTTTA
*
1363232 GGGTTTTG
1 GGG-TTTA
*
1363240 GGGTTTT
1 GGGTTTA
1363247 GGGTTTTA
1 GGG-TTTA
1363255 GGGGTTTA
1 -GGGTTTA
1363263 GGGTTTTA
1 GGG-TTTA
1363271 GGGGTTTA
1 -GGGTTTA
1363279 GGGTTTA
1 GGGTTTA
1363286 GGGTTTA
1 GGGTTTA
1363293 GGGTTTA
1 GGGTTTA
1363300 GGGTTTTA
1 GGG-TTTA
1363308 GGGTTTA
1 GGGTTTA
1363315 GGGTTTA
1 GGGTTTA
1363322 GGGTTTA
1 GGGTTTA
1363329 GGGTTTA
1 GGGTTTA
1363336 GGGTTTA
1 GGGTTTA
1363343 GGGTTTA
1 GGGTTTA
1363350 GGGTTTA
1 GGGTTTA
1363357 GGGTTTA
1 GGGTTTA
1363364 GGGTTTA
1 GGGTTTA
1363371 GGGTTTA
1 GGGTTTA
1363378 GGGTTTA
1 GGGTTTA
1363385 GGGTTTA
1 GGGTTTA
1363392 GGGTTTA
1 GGGTTTA
1363399 GGGTTTA
1 GGGTTTA
1363406 GGGTTTA
1 GGGTTTA
1363413 GGGTTTA
1 GGGTTTA
1363420 GGGTTTA
1 GGGTTTA
1363427 GGGTTTA
1 GGGTTTA
1363434 GGGTTTA
1 GGGTTTA
1363441 GGGTTTA
1 GGGTTTA
1363448 GGGGTTTA
1 -GGGTTTA
1363456 GGGTTTA
1 GGGTTTA
1363463 GGGTTTA
1 GGGTTTA
1363470 GGGTTTA
1 GGGTTTA
1363477 GGGTTTA
1 GGGTTTA
1363484 GGGTTTA
1 GGGTTTA
1363491 GGGTTTA
1 GGGTTTA
1363498 GGGTTTA
1 GGGTTTA
1363505 GGGTTTA
1 GGGTTTA
1363512 GGGTTTA
1 GGGTTTA
1363519 GGGTTTA
1 GGGTTTA
1363526 GGGTTT
1 GGGTTT
1363532 NNNNNNNNNN
Statistics
Matches: 878, Mismatches: 67, Indels: 78
0.86 0.07 0.08
Matches are distributed among these distances:
6 1 0.00
7 662 0.75
8 183 0.21
9 26 0.03
10 3 0.00
11 3 0.00
ACGTcount: A:0.12, C:0.03, G:0.44, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:1368620 original size:21 final size:21
Alignment explanation
Indices: 1368596--1368638 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1368586 AAATTAATTT
* *
1368596 AAAATTAATATTTATTGTTTA
1 AAAAATAATATTTAATGTTTA
*
1368617 AAAAATATTATTTAATGTTTA
1 AAAAATAATATTTAATGTTTA
1368638 A
1 A
1368639 CAGAGTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AAAAATAATATTTAATGTTTA
Found at i:1369033 original size:10 final size:9
Alignment explanation
Indices: 1369007--1369032 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1368997 TTTAAAGAAT
1369007 AATTTTTTG
1 AATTTTTTG
1369016 AATTTTTTG
1 AATTTTTTG
1369025 AATTTTTT
1 AATTTTTT
1369033 TTAAAATTTA
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:0.08, T:0.69
Consensus pattern (9 bp):
AATTTTTTG
Found at i:1375251 original size:21 final size:20
Alignment explanation
Indices: 1375223--1375262 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1375213 ATTTACCTCC
*
1375223 AAGTTTGAGACTTAGCTTCT
1 AAGTTTGAAACTTAGCTTCT
1375243 AAGTCTTGAAACTTAGCTTC
1 AAGT-TTGAAACTTAGCTTC
1375263 CTAACAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
AAGTTTGAAACTTAGCTTCT
Found at i:1378293 original size:21 final size:23
Alignment explanation
Indices: 1378267--1378317 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
1378257 GTTTTAAAAA
1378267 TTGTTTTAGTA-TTATTTTTAT-
1 TTGTTTTAGTATTTATTTTTATG
*
1378288 TTGTTTTAGTATTTGTTTTTATG
1 TTGTTTTAGTATTTATTTTTATG
1378311 TT-TTTTA
1 TTGTTTTA
1378318 AATATATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.41
22 14 0.52
23 2 0.07
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.73
Consensus pattern (23 bp):
TTGTTTTAGTATTTATTTTTATG
Found at i:1378300 original size:12 final size:12
Alignment explanation
Indices: 1378267--1378306 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1378257 GTTTTAAAAA
1378267 TTGTTTTAGTA-
1 TTGTTTTAGTAT
*
1378278 TTATTTT--TAT
1 TTGTTTTAGTAT
1378288 TTGTTTTAGTAT
1 TTGTTTTAGTAT
1378300 TTGTTTT
1 TTGTTTT
1378307 TATGTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 2 0.08
10 6 0.25
11 6 0.25
12 10 0.42
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.72
Consensus pattern (12 bp):
TTGTTTTAGTAT
Found at i:1378347 original size:27 final size:25
Alignment explanation
Indices: 1378297--1378347 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
1378287 TTTGTTTTAG
* *
1378297 TATTTGTTTTTATGTTTTTTAAATA
1 TATTTGTTTTTATATTTTTAAAATA
1378322 TATTTGATTTATTATATTTTTAAAAT
1 TATTTG-TTT-TTATATTTTTAAAAT
1378348 TTTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (25 bp):
TATTTGTTTTTATATTTTTAAAATA
Found at i:1404385 original size:21 final size:21
Alignment explanation
Indices: 1404361--1404400 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1404351 AAAAATGAAA
1404361 TAAAAATAAAGAAAACAAAAT
1 TAAAAATAAAGAAAACAAAAT
** *
1404382 TAAATCTAAATAAAACAAA
1 TAAAAATAAAGAAAACAAA
1404401 TAAATGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (21 bp):
TAAAAATAAAGAAAACAAAAT
Found at i:1407244 original size:16 final size:16
Alignment explanation
Indices: 1407219--1407253 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1407209 TTTCTATTGA
*
1407219 TCTATTCTTCCAATTT
1 TCTATCCTTCCAATTT
*
1407235 TCTATCCTTCCTATTT
1 TCTATCCTTCCAATTT
1407251 TCT
1 TCT
1407254 TTTCACTTTA
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:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (16 bp):
TCTATCCTTCCAATTT
Found at i:1413050 original size:17 final size:17
Alignment explanation
Indices: 1413028--1413061 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1413018 GATCACAACT
1413028 TCGTTTATTAAAGAGTC
1 TCGTTTATTAAAGAGTC
1413045 TCGTTTATTAAAGAGTC
1 TCGTTTATTAAAGAGTC
1413062 AAAAAGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
TCGTTTATTAAAGAGTC
Found at i:1419318 original size:22 final size:22
Alignment explanation
Indices: 1419286--1419377 Score: 96
Period size: 22 Copynumber: 4.2 Consensus size: 22
1419276 TACGAGTTTT
* **
1419286 GCACTTTGGTGCTCTCTATTTA
1 GCACTTCGGTGCTCTCTGCTTA
* *
1419308 GCACTTCGGTGCTGTTTGCTTA
1 GCACTTCGGTGCTCTCTGCTTA
* *
1419330 GCA-TTTGGTGCTCTCTGCTTG
1 GCACTTCGGTGCTCTCTGCTTA
* *
1419351 GCACTTCGGTACTCTCTGTTTA
1 GCACTTCGGTGCTCTCTGCTTA
1419373 GCACT
1 GCACT
1419378 ATAATGCTCT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 17 0.30
22 39 0.70
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.41
Consensus pattern (22 bp):
GCACTTCGGTGCTCTCTGCTTA
Found at i:1419374 original size:43 final size:44
Alignment explanation
Indices: 1419281--1419377 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 44
1419271 GCTTGTACGA
* * * * *
1419281 GTTTTGCACTTTGGTGCTCTCTATTTAGCACTTCGGTGCTGTTT
1 GTTTAGCACTTTGGTGCTCTCTACTTAGCACTTCGGTACTCTCT
* * *
1419325 GCTTAGCA-TTTGGTGCTCTCTGCTTGGCACTTCGGTACTCTCT
1 GTTTAGCACTTTGGTGCTCTCTACTTAGCACTTCGGTACTCTCT
1419368 GTTTAGCACT
1 GTTTAGCACT
1419378 ATAATGCTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
43 36 0.84
44 7 0.16
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.43
Consensus pattern (44 bp):
GTTTAGCACTTTGGTGCTCTCTACTTAGCACTTCGGTACTCTCT
Found at i:1422475 original size:12 final size:12
Alignment explanation
Indices: 1422458--1422491 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1422448 CGGCCCGCCC
1422458 ATATTAATTTTT
1 ATATTAATTTTT
*
1422470 ATATTATTTTTT
1 ATATTAATTTTT
1422482 ATA-TAATTTT
1 ATATTAATTTT
1422492 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1422733 original size:22 final size:22
Alignment explanation
Indices: 1422707--1422755 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1422697 ATATCCAAAC
1422707 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * **
1422729 CATAATAGTAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
1422751 AATAA
1 AATAA
1422756 GGAGAAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:1422754 original size:11 final size:11
Alignment explanation
Indices: 1422715--1422754 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1422705 ACAATAACAA
1422715 CAAAATAGTAG
1 CAAAATAGTAG
* *
1422726 CAACATAATAG
1 CAAAATAGTAG
*
1422737 TAAAATAGTAG
1 CAAAATAGTAG
1422748 CAAAATA
1 CAAAATA
1422755 AGGAGAAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:1423119 original size:32 final size:32
Alignment explanation
Indices: 1423078--1423140 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1423068 AATTAATAAT
*
1423078 AAATATTATATAATTTAATTAAAATTGGTATG
1 AAATATTATATAATTTAATTAAAATTAGTATG
1423110 AAATATTATATAATTTAATTAAAATTAGTAT
1 AAATATTATATAATTTAATTAAAATTAGTAT
1423141 ACAAAGTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.44
Consensus pattern (32 bp):
AAATATTATATAATTTAATTAAAATTAGTATG
Found at i:1427725 original size:22 final size:22
Alignment explanation
Indices: 1427689--1427730 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1427679 ACAACCTACA
*
1427689 TAATAATAAAAATATTATTATT
1 TAATAATAAAAATATCATTATT
**
1427711 TAATAATAATTATATCATTA
1 TAATAATAAAAATATCATTA
1427731 ATAAAGTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATAATAAAAATATCATTATT
Found at i:1427985 original size:15 final size:15
Alignment explanation
Indices: 1427961--1427999 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1427951 GAATTGAAAA
*
1427961 ATAAATATTATATAT
1 ATAAAAATTATATAT
*
1427976 ATAAAAATTATATTT
1 ATAAAAATTATATAT
1427991 ACTAAAAAT
1 A-TAAAAAT
1428000 AATTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAAATTATATAT
Found at i:1428076 original size:41 final size:41
Alignment explanation
Indices: 1428031--1428109 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
1428021 TTGATTTTAT
* *
1428031 AAATAAAATAGTTATTAATTAAAAAGATGAATTAAAAATAA
1 AAATAAAAAAGTTATTAATTAAAAACATGAATTAAAAATAA
* * *
1428072 AAATAAAAAATTTATTAATTATAAACATTAATTAAAAA
1 AAATAAAAAAGTTATTAATTAAAAACATGAATTAAAAA
1428110 AAACTTGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (41 bp):
AAATAAAAAAGTTATTAATTAAAAACATGAATTAAAAATAA
Found at i:1437813 original size:14 final size:14
Alignment explanation
Indices: 1437788--1437821 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1437778 AAAGAATTAA
1437788 AGAAACAAAGAAAC
1 AGAAACAAAGAAAC
1437802 A-AAACAAAAGAAAC
1 AGAAAC-AAAGAAAC
1437816 AGAAAC
1 AGAAAC
1437822 GAAGTAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.74, C:0.15, G:0.12, T:0.00
Consensus pattern (14 bp):
AGAAACAAAGAAAC
Found at i:1443764 original size:14 final size:14
Alignment explanation
Indices: 1443739--1443772 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1443729 AAAGAATTAA
1443739 AGAAACAAAGAAAC
1 AGAAACAAAGAAAC
1443753 A-AAACAAAAGAAAC
1 AGAAAC-AAAGAAAC
1443767 AGAAAC
1 AGAAAC
1443773 GAAGTAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.74, C:0.15, G:0.12, T:0.00
Consensus pattern (14 bp):
AGAAACAAAGAAAC
Found at i:1446734 original size:18 final size:18
Alignment explanation
Indices: 1446711--1446751 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1446701 NAAAAAAAAA
1446711 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
1446729 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
1446747 AGAAA
1 AGAAA
1446752 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:1446867 original size:3 final size:3
Alignment explanation
Indices: 1446861--1446886 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1446851 GATGAAAGAA
1446861 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1446887 AGTATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1455047 original size:190 final size:189
Alignment explanation
Indices: 1454725--1455105 Score: 672
Period size: 190 Copynumber: 2.0 Consensus size: 189
1454715 GGTGAAAACA
1454725 AAAGGATAGATTCGACATCCGTTAAGCTGAATAATGAACGATGCACTTCTTTGCAAACAAGCCTG
1 AAAGGATAGATTCGACATCCGTTAAGCTGAATAATGAACGATGCACTTCTTTGCAAACAAGCCTG
* * *
1454790 ATGAATACTCACAAGGTTGCATGCTGTGGCTCATGCTACGTTCTTAACTAAATACTACTCTAATA
66 ATGAATACTCACAAGGCTACATGCTGTGGCCCATGCTACGTTCTTAACTAAATACTACTCTAATA
*
1454855 AAAAATTTCTAGATGTACAGAGATGATCACCCGACTCTTGGACGTGGAAAAGCATATTG
131 AAAAATTTCTAGACGTACAGAGATGATCACCCGACTCTTGGACGTGGAAAAGCATATTG
* * *
1454914 AAAGGATGGATTGGACATCCGTTAAGCTGAAGTAATGAACGATGCAGTTCTTTGCAAACAAGCCT
1 AAAGGATAGATTCGACATCCGTTAAGCTGAA-TAATGAACGATGCACTTCTTTGCAAACAAGCCT
*
1454979 GATGAATACTCACAAGGCTACATGCTGTGGCCCATGCTACGTTCTTAACTAAATACTGCTCTAAT
65 GATGAATACTCACAAGGCTACATGCTGTGGCCCATGCTACGTTCTTAACTAAATACTACTCTAAT
*
1455044 AAAAAATTTCTAGACGTGCAGAGATGATCACCCGACTCTTGGACGTGGAAAAGCATATTG
130 AAAAAATTTCTAGACGTACAGAGATGATCACCCGACTCTTGGACGTGGAAAAGCATATTG
1455104 AA
1 AA
1455106 GGGGTGAGAT
Statistics
Matches: 182, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
189 29 0.16
190 153 0.84
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (189 bp):
AAAGGATAGATTCGACATCCGTTAAGCTGAATAATGAACGATGCACTTCTTTGCAAACAAGCCTG
ATGAATACTCACAAGGCTACATGCTGTGGCCCATGCTACGTTCTTAACTAAATACTACTCTAATA
AAAAATTTCTAGACGTACAGAGATGATCACCCGACTCTTGGACGTGGAAAAGCATATTG
Found at i:1455351 original size:55 final size:53
Alignment explanation
Indices: 1455275--1455487 Score: 160
Period size: 55 Copynumber: 3.9 Consensus size: 53
1455265 ACTTGTTATG
* *
1455275 TAACAATCAATTTGAACATATAAACAATTTATTCAAAATAAGCAATATTTCAACA
1 TAACAATCAATTTAAACATATAAACAATCTATT-AAAA-AAGCAATATTTCAACA
* * * * *
1455330 TAACAATCCATTTAAATATATAAACAATCAATTAAAAAAGGAAGTAGTATTCCATCA
1 TAACAATCAATTTAAACATATAAACAATCTATTAAAAAAGCAA-TA-T-TT-CAACA
* * ** *
1455387 TAACAATCGATTTAAACATATAAATAATCTATTTAAAAGAAATAACATTTCAACA
1 TAACAATCAATTTAAACATATAAACAATCTA-TTAAAA-AAGCAATATTTCAACA
* * ** * * *
1455442 TGATAATTTATTTAAACATAAAAAACAATCGATT-GAAAAG-AATATT
1 TAACAATCAATTTAAACAT-ATAAACAATCTATTAAAAAAGCAATATT
1455488 CTAGCATAAC
Statistics
Matches: 126, Mismatches: 25, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
52 5 0.04
53 7 0.06
54 8 0.06
55 50 0.40
56 13 0.10
57 32 0.25
58 7 0.06
59 4 0.03
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.31
Consensus pattern (53 bp):
TAACAATCAATTTAAACATATAAACAATCTATTAAAAAAGCAATATTTCAACA
Found at i:1455481 original size:112 final size:112
Alignment explanation
Indices: 1455275--1455480 Score: 250
Period size: 112 Copynumber: 1.8 Consensus size: 112
1455265 ACTTGTTATG
* * * * *
1455275 TAACAATCAATTTGAACATATAAACAATTTATTCAAAATAAGCAATATTTCAACATAACAATCCA
1 TAACAATCAATTTAAACATATAAACAATCTATTCAAAAGAAACAACATTTCAACATAACAATCCA
* *
1455340 TTTAAATATATAAACAATCAATTAAAAAAGGAAGTAGTATTCCATCA
66 TTTAAACATAAAAACAATCAATTAAAAAAGGAAGTAGTATTCCATCA
* * * * * * **
1455387 TAACAATCGATTTAAACATATAAATAATCTATTTAAAAGAAATAACATTTCAACATGATAATTTA
1 TAACAATCAATTTAAACATATAAACAATCTATTCAAAAGAAACAACATTTCAACATAACAATCCA
* *
1455452 TTTAAACATAAAAAACAATCGATTGAAAA
66 TTTAAACAT-AAAAACAATCAATTAAAAA
1455481 GAATATTCTA
Statistics
Matches: 76, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
112 60 0.79
113 16 0.21
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (112 bp):
TAACAATCAATTTAAACATATAAACAATCTATTCAAAAGAAACAACATTTCAACATAACAATCCA
TTTAAACATAAAAACAATCAATTAAAAAAGGAAGTAGTATTCCATCA
Found at i:1459323 original size:30 final size:30
Alignment explanation
Indices: 1459287--1459343 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
1459277 CTCTCGTATG
1459287 CGTACTATCATATATGAATATCCTTTTCTA
1 CGTACTATCATATATGAATATCCTTTTCTA
1459317 CGTACTATCATATATGAATATCCTTTT
1 CGTACTATCATATATGAATATCCTTTT
1459344 TTTCATTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (30 bp):
CGTACTATCATATATGAATATCCTTTTCTA
Found at i:1464259 original size:29 final size:28
Alignment explanation
Indices: 1464226--1464288 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
1464216 GGAAATAGTT
* *
1464226 AATTT-ATATCTATTTTTTAATTCTTTTAA
1 AATTTAATATATATTTTTT-ATT-TATTAA
1464255 AATTTTAATATATATTTTTTATTTATTAA
1 AA-TTTAATATATATTTTTTATTTATTAA
1464284 AATTT
1 AATTT
1464289 TATACATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.10
29 9 0.30
30 6 0.20
31 12 0.40
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
AATTTAATATATATTTTTTATTTATTAA
Found at i:1464289 original size:29 final size:31
Alignment explanation
Indices: 1464231--1464290 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
1464221 TAGTTAATTT
* *
1464231 ATATCTATTTTTTAATTCTTTTAAAATTTTA
1 ATATATATTTTTTAATTCTATTAAAATTTTA
1464262 ATATATATTTTTT-ATT-TATTAAAATTTTA
1 ATATATATTTTTTAATTCTATTAAAATTTTA
1464291 TACATACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.44
30 3 0.11
31 12 0.44
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (31 bp):
ATATATATTTTTTAATTCTATTAAAATTTTA
Found at i:1468303 original size:33 final size:33
Alignment explanation
Indices: 1468261--1468327 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1468251 CATCTCCATA
* **
1468261 AAAAGTCATACAAAGTCATTTTGGTTACTTTAG
1 AAAAGTCATACAAAATCATTAGGGTTACTTTAG
1468294 AAAAGTCATACAAAATCATTAGGGTTACTTTAG
1 AAAAGTCATACAAAATCATTAGGGTTACTTTAG
1468327 A
1 A
1468328 TAAACATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (33 bp):
AAAAGTCATACAAAATCATTAGGGTTACTTTAG
Found at i:1470625 original size:31 final size:30
Alignment explanation
Indices: 1470557--1470625 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
1470547 CTTCATTGTC
1470557 TAGTGACTTAAACAAAAACTTTCGAATAGT
1 TAGTGACTTAAACAAAAACTTTCGAATAGT
* **
1470587 TATGTGACTTGAATGAAAACATTT-GAATAGTT
1 TA-GTGACTTAAACAAAAAC-TTTCGAATAG-T
1470619 TAGTGAC
1 TAGTGAC
1470626 CATTTTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 2 0.06
31 25 0.76
32 6 0.18
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.33
Consensus pattern (30 bp):
TAGTGACTTAAACAAAAACTTTCGAATAGT
Found at i:1473407 original size:35 final size:35
Alignment explanation
Indices: 1473368--1473440 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
1473358 ATTGAGTAAA
*
1473368 AAAGGACAAATAAAGTGATGCTATTTTTTATTAAT
1 AAAGGACAAATAAAGCGATGCTATTTTTTATTAAT
*
1473403 AAAGGACAAATAAAGCGATGCTGTTTTTTATTAAT
1 AAAGGACAAATAAAGCGATGCTATTTTTTATTAAT
1473438 AAA
1 AAA
1473441 ATACTGTAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (35 bp):
AAAGGACAAATAAAGCGATGCTATTTTTTATTAAT
Found at i:1476484 original size:25 final size:26
Alignment explanation
Indices: 1476446--1476515 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 26
1476436 TTTAAAATTT
*
1476446 TTAAAAAATGATTAATTTATTCATT-A
1 TTAAAAAA-AATTAATTTATTCATTAA
* **
1476472 TTAAAAAAAATT-ATTAATTTTTTAA
1 TTAAAAAAAATTAATTTATTCATTAA
*
1476497 CT-AAAAAAATTAATTTATT
1 TTAAAAAAAATTAATTTATT
1476516 TATTGATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
24 17 0.47
25 11 0.31
26 8 0.22
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (26 bp):
TTAAAAAAAATTAATTTATTCATTAA
Found at i:1493100 original size:29 final size:28
Alignment explanation
Indices: 1493064--1493120 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1493054 AAATTAATAG
1493064 TGATAAAA-TTACACTTTAACCC-TTAAAA
1 TGATAAAATTTA-A-TTTAACCCTTTAAAA
1493092 TGATAAAAATTTAATTTAACCCTTTAAAA
1 TGAT-AAAATTTAATTTAACCCTTTAAAA
1493121 ATTACAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 12 0.46
29 11 0.42
30 3 0.12
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (28 bp):
TGATAAAATTTAATTTAACCCTTTAAAA
Found at i:1496101 original size:26 final size:25
Alignment explanation
Indices: 1496065--1496130 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
1496055 CTTATATATA
1496065 TAATATTATTTATTTTAAATTTTTT
1 TAATATTATTTATTTTAAATTTTTT
*
1496090 TAATATTCATTTATTTTAAGTTTTCTT
1 TAATATT-ATTTATTTTAAATTTT-TT
*
1496117 GT-ATATTGTTTATT
1 -TAATATTATTTATT
1496131 CGAACCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 7 0.19
26 21 0.58
27 7 0.19
28 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (25 bp):
TAATATTATTTATTTTAAATTTTTT
Found at i:1496113 original size:25 final size:25
Alignment explanation
Indices: 1496065--1496113 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1496055 CTTATATATA
*
1496065 TAATATTATTTATTTTAAATTTTTT
1 TAATATTATTTATTTTAAAGTTTTT
1496090 TAATATTCATTTATTTT-AAGTTTT
1 TAATATT-ATTTATTTTAAAGTTTT
1496114 CTTGTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TAATATTATTTATTTTAAAGTTTTT
Found at i:1496206 original size:2 final size:2
Alignment explanation
Indices: 1496199--1496238 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1496189 TAGATTGTTG
* *
1496199 TA TA TA TA TT TA TA TT TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1496239 TTTGTTGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1502686 original size:32 final size:32
Alignment explanation
Indices: 1502650--1502728 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
1502640 TCATACCTTT
* * * *
1502650 TAAATAGATATAATTATTCAATTAATATATCC
1 TAAATAGATATAACTATTCAAATAACATATCA
*
1502682 TAAATAGATATAACTATTCAAATAACATTTCA
1 TAAATAGATATAACTATTCAAATAACATATCA
*
1502714 TAAATAAATATAACT
1 TAAATAGATATAACT
1502729 TCAAGTAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.37
Consensus pattern (32 bp):
TAAATAGATATAACTATTCAAATAACATATCA
Found at i:1505742 original size:21 final size:22
Alignment explanation
Indices: 1505716--1505760 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1505706 TGATATTACA
1505716 TTATTATTATTTT-CTTTCTAT
1 TTATTATTATTTTCCTTTCTAT
* *
1505737 TTATTATTTTTTTCCTTTTTAT
1 TTATTATTATTTTCCTTTCTAT
1505759 TT
1 TT
1505761 TATTTTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTATTATTTTCCTTTCTAT
Found at i:1506516 original size:36 final size:34
Alignment explanation
Indices: 1506451--1506517 Score: 80
Period size: 36 Copynumber: 1.9 Consensus size: 34
1506441 TTATATATCA
*** *
1506451 ATATTATATTATGTATATTTCTTTTTTAAATACT
1 ATATTATATTATGTATATTTAGATATTAAATACT
1506485 ATATATATATGTATGTATATTTAGATATTAAAT
1 ATAT-TATAT-TATGTATATTTAGATATTAAAT
1506518 GTATGATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 4 0.15
35 5 0.19
36 18 0.67
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (34 bp):
ATATTATATTATGTATATTTAGATATTAAATACT
Found at i:1506678 original size:17 final size:17
Alignment explanation
Indices: 1506656--1506718 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
1506646 TTAAATATTG
1506656 TATTTTTATTATGTATA
1 TATTTTTATTATGTATA
* * *
1506673 TATTTTTAATACGGATA
1 TATTTTTATTATGTATA
*
1506690 CATTTTTTATTACTCGTATA
1 TA-TTTTTATTA-T-GTATA
1506710 TATATTTTA
1 TAT-TTTTA
1506719 ATATTGTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 15 0.44
18 8 0.24
19 1 0.03
20 10 0.29
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (17 bp):
TATTTTTATTATGTATA
Found at i:1506730 original size:35 final size:33
Alignment explanation
Indices: 1506641--1506731 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 33
1506631 TACTGTGTAA
1506641 ATATTTTAAATATTGTA-TTTTTATTATGTATAT
1 ATATTTT-AATATTGTATTTTTTATTATGTATAT
**
1506674 AT-TTTTAATACGGATACATTTTTTATTACTCGTATAT
1 ATATTTTAATATTG-T--ATTTTTTATTA-T-GTATAT
1506711 ATATTTTAATATTGTATTTTT
1 ATATTTTAATATTGTATTTTT
1506732 ATTGTTATGC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
31 5 0.11
32 5 0.11
33 2 0.04
34 1 0.02
35 15 0.32
36 1 0.02
37 9 0.19
38 9 0.19
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (33 bp):
ATATTTTAATATTGTATTTTTTATTATGTATAT
Found at i:1506803 original size:24 final size:24
Alignment explanation
Indices: 1506757--1506803 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1506747 CTTTAATACT
* *
1506757 ATATCATTTTTATTTTTATTTTTC
1 ATATCATTCTTATGTTTATTTTTC
1506781 ATATCA-TCTTATGTTTATGTTTT
1 ATATCATTCTTATGTTTAT-TTTT
1506804 TCAAACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (24 bp):
ATATCATTCTTATGTTTATTTTTC
Found at i:1507072 original size:3 final size:3
Alignment explanation
Indices: 1507064--1507117 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
1507054 AATTTTACTT
* * * *
1507064 TTA TTA TTA CTA CTA -TA TTA TTA TTA TTA TTA TCA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1507111 TTA TTA T
1 TTA TTA T
1507118 CATATTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1507333 original size:3 final size:3
Alignment explanation
Indices: 1507325--1507375 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
1507315 TATCTCTAAC
* *
1507325 TAT TAT TAT TTT GTAT ATAT TAT TAT CTA- TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT -TAT -TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
1507372 TAT T
1 TAT T
1507376 CTTTATTGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.77
4 7 0.17
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1507347 original size:14 final size:15
Alignment explanation
Indices: 1507325--1507375 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1507315 TATCTCTAAC
* *
1507325 TATTATTATTTTGTA
1 TATTATTATTATCTA
1507340 TA-TATTATTATCTA
1 TATTATTATTATCTA
1507354 TATTATTATTAT-TA
1 TATTATTATTATCTA
1507368 CTATTATT
1 -TATTATT
1507376 CTTTATTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 14 0.44
15 18 0.56
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (15 bp):
TATTATTATTATCTA
Found at i:1511838 original size:11 final size:11
Alignment explanation
Indices: 1511822--1511850 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1511812 TCCCATTTGA
1511822 GAATTCTTAAG
1 GAATTCTTAAG
1511833 GAATTCTTAAG
1 GAATTCTTAAG
1511844 GAATTCT
1 GAATTCT
1511851 ATTTGTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (11 bp):
GAATTCTTAAG
Found at i:1514230 original size:30 final size:31
Alignment explanation
Indices: 1514186--1514244 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1514176 AATTAAATAA
1514186 AACAAATAAAAGAAA-CAAAAAGAAAAGAAG
1 AACAAATAAAAGAAATCAAAAAGAAAAGAAG
** * *
1514216 AACAAATAGTAGAAATGAAAGAGAAAAGA
1 AACAAATAAAAGAAATCAAAAAGAAAAGA
1514245 GGGAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (31 bp):
AACAAATAAAAGAAATCAAAAAGAAAAGAAG
Found at i:1514377 original size:18 final size:18
Alignment explanation
Indices: 1514354--1514390 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1514344 TTTTTTTAGA
1514354 ATCTTAGTATTAAATACT
1 ATCTTAGTATTAAATACT
1514372 ATCTTAGTATTAAATACT
1 ATCTTAGTATTAAATACT
1514390 A
1 A
1514391 CCTAGTCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (18 bp):
ATCTTAGTATTAAATACT
Found at i:1515552 original size:33 final size:32
Alignment explanation
Indices: 1515464--1515557 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 32
1515454 TAATATAATT
*
1515464 AATA-ATTTTAATAA-TAATAA-ACATCTAAT-A
1 AATATATTTTAATAATTAATAATA-A-ATAATAA
*
1515494 AATATATTTTACTAATTAATAATAAATAATAA
1 AATATATTTTAATAATTAATAATAAATAATAA
*
1515526 AATATCTTTTCAATAATT-ATACATAAATAATA
1 AATATATTTT-AATAATTAATA-ATAAATAATA
1515558 CAAGTGTACT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
30 4 0.07
31 13 0.24
32 20 0.37
33 17 0.31
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.39
Consensus pattern (32 bp):
AATATATTTTAATAATTAATAATAAATAATAA
Found at i:1520062 original size:12 final size:12
Alignment explanation
Indices: 1520045--1520080 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1520035 ATTCATTTGA
1520045 CATTCATGCATT
1 CATTCATGCATT
1520057 CATTCATGCATT
1 CATTCATGCATT
*
1520069 CATTCATACATT
1 CATTCATGCATT
1520081 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:1530077 original size:75 final size:76
Alignment explanation
Indices: 1529985--1530203 Score: 284
Period size: 75 Copynumber: 2.9 Consensus size: 76
1529975 TATATTTTTT
* *
1529985 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAAT
1530050 TTCTGT-TGTC
66 TTCTGTCTGTC
** * *
1530060 AAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAAT
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAAT
* * *
1530125 TTTTATCTTTC
66 TTCTGTCTGTC
* * * *
1530136 --AAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGG-CATGTTGAGTTAATTTCAA
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACATGCTGAGGTAATTTCAA
1530198 TTTCTG
65 TTTCTG
1530204 CTTTTAAATT
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
74 55 0.45
75 65 0.53
76 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (76 bp):
AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAAT
TTCTGTCTGTC
Found at i:1530176 original size:74 final size:73
Alignment explanation
Indices: 1529967--1530200 Score: 279
Period size: 74 Copynumber: 3.1 Consensus size: 73
1529957 AATTTCTGCT
* *
1529967 TTTCAATTTATATTTTTTAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTCAATTTATA--TTTTCAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
1530032 CGCTGAGGTAA
63 TGCTGAGGTAA
* * * **
1530043 TTTCAATTTCTGTTGTCAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAT
1 TTTCAATTTATATTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAT
*
1530108 GCTGAGGTAT
64 GCTGAGGTAA
* * * *
1530118 TTTCAATTTTTATCTTTCAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCATG
1 TTTCAATTTATAT-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATG
* *
1530183 TTGAGTTAA
65 CTGAGGTAA
1530192 TTTCAATTT
1 TTTCAATTT
1530201 CTGCTTTTAA
Statistics
Matches: 135, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
74 60 0.44
75 56 0.41
76 19 0.14
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (73 bp):
TTTCAATTTATATTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGC
TGAGGTAA
Found at i:1530273 original size:90 final size:88
Alignment explanation
Indices: 1530117--1530293 Score: 257
Period size: 90 Copynumber: 2.0 Consensus size: 88
1530107 TGCTGAGGTA
* *
1530117 TTTTCAATTTTTATCTTTCAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCAT
1 TTTTAAATTTATATCTTTCAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCAT
*
1530182 GTTGAGTTAATTTCAATTTCTGC
66 GTTGAGGTAATTTCAATTTCTGC
* * **
1530205 TTTTAAATTTATATTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGCGTTGAGCCTC-AGGA
1 TTTTAAATTTATATCTTTC-AAAAAA-TCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGG-
1530269 CATGTTGAGGTAATTTCAATTTCTG
63 CATGTTGAGGTAATTTCAATTTCTG
1530294 TTGTCAAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
88 16 0.20
89 9 0.11
90 54 0.68
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (88 bp):
TTTTAAATTTATATCTTTCAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCAT
GTTGAGGTAATTTCAATTTCTGC
Found at i:1530305 original size:239 final size:240
Alignment explanation
Indices: 1529880--1530381 Score: 756
Period size: 239 Copynumber: 2.1 Consensus size: 240
1529870 GAGTTGAGTC
* * * *
1529880 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGT
1 TTTCAATTTCTATCTTTCAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCACGT
* * *
1529945 TGAGGTAATTTTAATTTCTGCTTTTCAATTTATATTTTTTAAAAAAATTCAACTCATATTGCGAG
66 TGAGGTAATTTCAATTTCTGCTTTTAAATTTATATTTTTCAAAAAAATTCAACTCATATTGCGAG
1530010 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTC-AAAAAAAATCAACT
131 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAAAATCAACT
* * *
1530074 CATATTGCGAGAAATGAGTTGAGCCTCAAG-ACATGCTGAGGTAT
196 CATATTGCGAGAAACGAGTTGAGCCTCAAGCACACGCCGAGGTAT
* *
1530118 TTTCAATTTTTATCTTTCAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCATG
1 TTTCAATTTCTATCTTTC-AAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCACG
*
1530183 TTGAGTTAATTTCAATTTCTGCTTTTAAATTTATATTTTTCAAAAAAATTCAACTCATATTGCGA
65 TTGAGGTAATTTCAATTTCTGCTTTTAAATTTATATTTTTCAAAAAAATTCAACTCATATTGCGA
* * *
1530248 GAGGTGCGTTGAGCCTCAGGACATGTTGAGGTAATTTCAATTTCTGTTGTCAAAAAAAAAATCAA
130 GAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTC-AAAAAAAAATCAA
* * * * *
1530313 CTCGTATTGTGAGAGACGAGTTGAGCCTTAGGTCACACGCCGAGGTAT
194 CTCATATTGCGAGAAACGAGTTGAGCCTCAAG-CACACGCCGAGGTAT
* *
1530361 TTTCAATTTCTGTTTTTCAAA
1 TTTCAATTTCTATCTTTCAAA
1530382 TTTTGCCTTT
Statistics
Matches: 235, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
238 15 0.06
239 152 0.65
241 38 0.16
242 3 0.01
243 27 0.11
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (240 bp):
TTTCAATTTCTATCTTTCAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCAAGGCACGT
TGAGGTAATTTCAATTTCTGCTTTTAAATTTATATTTTTCAAAAAAATTCAACTCATATTGCGAG
AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAAAATCAACT
CATATTGCGAGAAACGAGTTGAGCCTCAAGCACACGCCGAGGTAT
Found at i:1530313 original size:77 final size:78
Alignment explanation
Indices: 1530224--1530374 Score: 187
Period size: 77 Copynumber: 1.9 Consensus size: 78
1530214 TATATTTTTC
* ** * * **
1530224 AAAAAAATTCAACTCATATTGCGAGAGGTGCGTTGAGCCTCAGG-ACATGTTGAGGTAATTTCAA
1 AAAAAAAATCAACTCATATTGCGAGAGACGAGTTGAGCCTCAGGCACACGCCGAGGTAATTTCAA
1530288 TTTCTGTTGTCAA
66 TTTCTGTTGTCAA
* * * *
1530301 AAAAAAAATCAACTCGTATTGTGAGAGACGAGTTGAGCCTTAGGTCACACGCCGAGGTATTTTCA
1 AAAAAAAATCAACTCATATTGCGAGAGACGAGTTGAGCCTCAGG-CACACGCCGAGGTAATTTCA
1530366 ATTTCTGTT
65 ATTTCTGTT
1530375 TTTCAAATTT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 37 0.61
79 24 0.39
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (78 bp):
AAAAAAAATCAACTCATATTGCGAGAGACGAGTTGAGCCTCAGGCACACGCCGAGGTAATTTCAA
TTTCTGTTGTCAA
Found at i:1530440 original size:91 final size:91
Alignment explanation
Indices: 1530302--1530468 Score: 228
Period size: 91 Copynumber: 1.8 Consensus size: 91
1530292 TGTTGTCAAA
* * * *
1530302 AAAAAAATCAACTCGTATTGTGAGAGACGAGTTGAGCCTTAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGACGAGTTGAGCCTTAGGTCACACGCCAAGCTATTTTCAA
*
1530367 TTTCTGTTTTTCAAATTTTGCCTTTC
66 TTTCTATTTTTCAAATTTTGCCTTTC
* * ** *
1530393 AAAAAGATCGACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGCTCACACGCTAAGCTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGACGAGTTGAGCCTTAGG-TCACACGCCAAGCTATTTTCA
1530457 ATTTCTATTTTT
65 ATTTCTATTTTT
1530469 ATTGTCTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
90 2 0.03
91 63 0.97
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (91 bp):
AAAAAAATCAACTCATATTGCGAGAGACGAGTTGAGCCTTAGGTCACACGCCAAGCTATTTTCAA
TTTCTATTTTTCAAATTTTGCCTTTC
Found at i:1532568 original size:12 final size:12
Alignment explanation
Indices: 1532551--1532578 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1532541 TACTTATGTT
1532551 TTATATATTATA
1 TTATATATTATA
1532563 TTATATATTATA
1 TTATATATTATA
1532575 TTAT
1 TTAT
1532579 TAAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATATTATA
Found at i:1534682 original size:21 final size:21
Alignment explanation
Indices: 1534657--1534710 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1534647 ACGGCCTGAG
*
1534657 ACACGGGTGTGTCCCATGACC
1 ACACGGGCGTGTCCCATGACC
* * *
1534678 TCACGGGCGTGTCCCTTGGCC
1 ACACGGGCGTGTCCCATGACC
1534699 ACACGGGCGTGT
1 ACACGGGCGTGT
1534711 ATGCCTTGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.13, C:0.33, G:0.33, T:0.20
Consensus pattern (21 bp):
ACACGGGCGTGTCCCATGACC
Found at i:1547986 original size:28 final size:28
Alignment explanation
Indices: 1547955--1548018 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1547945 TTTGACTCAG
* * *
1547955 CAAGCCTTCCGTTATGAATTG-GGTCACA
1 CAAGCCTTCCGTAATGAAATGACG-CACA
*
1547983 CAAGCCTTCTGTAATGAAATGACGCACA
1 CAAGCCTTCCGTAATGAAATGACGCACA
1548011 CAAGCCTT
1 CAAGCCTT
1548019 AGAGAATCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (28 bp):
CAAGCCTTCCGTAATGAAATGACGCACA
Found at i:1555308 original size:26 final size:26
Alignment explanation
Indices: 1555272--1555323 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1555262 GAGCAAAATG
1555272 TATGTCTATTTAAAACGAATCATGCT
1 TATGTCTATTTAAAACGAATCATGCT
1555298 TATGTCTATTTAAAACGAATCATGCT
1 TATGTCTATTTAAAACGAATCATGCT
1555324 CAAATTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (26 bp):
TATGTCTATTTAAAACGAATCATGCT
Found at i:1556283 original size:17 final size:17
Alignment explanation
Indices: 1556261--1556300 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
1556251 AATCAACCTT
1556261 CACCTCCGGCACCAATC
1 CACCTCCGGCACCAATC
*
1556278 CACCT-C--CACCGATC
1 CACCTCCGGCACCAATC
1556292 CACCTCCGG
1 CACCTCCGG
1556301 TCCTTCACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
14 12 0.63
15 1 0.05
16 1 0.05
17 5 0.26
ACGTcount: A:0.20, C:0.55, G:0.12, T:0.12
Consensus pattern (17 bp):
CACCTCCGGCACCAATC
Found at i:1558592 original size:25 final size:25
Alignment explanation
Indices: 1558563--1558641 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 25
1558553 GATCTTTGCT
1558563 TAATTTCATATGCTCTAACTTACAG
1 TAATTTCATATGCTCTAACTTACAG
*
1558588 TAATTTCATATGCT-TCAA---AAAG
1 TAATTTCATATGCTCT-AACTTACAG
1558610 TAATTTCATATGCTCTAACTTACAG
1 TAATTTCATATGCTCTAACTTACAG
1558635 TAATTTC
1 TAATTTC
1558642 TTTTTGCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
22 19 0.40
23 1 0.02
24 1 0.02
25 26 0.55
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.41
Consensus pattern (25 bp):
TAATTTCATATGCTCTAACTTACAG
Found at i:1559035 original size:18 final size:17
Alignment explanation
Indices: 1559008--1559162 Score: 74
Period size: 18 Copynumber: 9.0 Consensus size: 17
1558998 AATATTAAGA
1559008 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
1559025 ATTTCTATTAAA-T-TAT
1 ATTT-TATTAAATTATAT
* *
1559041 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
1559055 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* *
1559074 AGTATTA-TATATTATA-
1 A-TTTTATTAAATTATAT
1559090 ATTTTATTAAATTCATAT
1 ATTTTATTAAATT-ATAT
*** *
1559108 AAGAATATTTAATATTA-AGA
1 -ATTTTA-TTAA-ATTATA-T
1559128 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
1559145 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
1559163 TTAATAATAT
Statistics
Matches: 102, Mismatches: 18, Indels: 35
0.66 0.12 0.23
Matches are distributed among these distances:
13 2 0.02
14 5 0.05
15 10 0.10
16 10 0.10
17 23 0.23
18 32 0.31
19 9 0.09
20 8 0.08
21 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:1559078 original size:121 final size:120
Alignment explanation
Indices: 1558765--1559191 Score: 739
Period size: 120 Copynumber: 3.5 Consensus size: 120
1558755 GAATATAATG
* *
1558765 ATTTGATTAAATTATATATTTTTACTAAATTATATTTTTAATAATAATTATTTTAAATTATATTT
1 ATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTTTAAATTATATTT
1558830 TATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGA
64 TATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGA
*
1558887 ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1558952 TAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAAATATTAAGA
66 TAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTT-AATATTAAGA
*
1559008 ATTTTATTAAATTATATATTTCTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
* * *
1559073 TAGTATTATATATTATAATTTTATTAAATTCATATAAGAATATTTAATATTAAGA
66 TAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGA
* *
1559128 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAAT-ATTATGTTAAATTATCTTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1559192 AATTATTTAT
Statistics
Matches: 293, Mismatches: 11, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
119 19 0.06
120 128 0.44
121 115 0.39
122 31 0.11
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (120 bp):
ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
TAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGA
Found at i:1559079 original size:22 final size:23
Alignment explanation
Indices: 1559054--1559096 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1559044 TAATAATAAT
*
1559054 TATTTTAAATTAT-ATTTTATAG
1 TATTATAAATTATAATTTTATAG
*
1559076 TATTATATATTATAATTTTAT
1 TATTATAAATTATAATTTTAT
1559097 TAAATTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTATAAATTATAATTTTATAG
Found at i:1559198 original size:25 final size:27
Alignment explanation
Indices: 1559143--1559207 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 27
1559133 ATTAAATTAT
*
1559143 ATATTT-TTATTAAATTATATTTAATA
1 ATATTTATTGTTAAATTATATTTAATA
*
1559169 ATA-TTA-TGTTAAATTATCTTTTAA-A
1 ATATTTATTGTTAAATTAT-ATTTAATA
*
1559194 TTATTTATTGTTAA
1 ATATTTATTGTTAA
1559208 TAATAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 15 0.47
26 11 0.34
27 6 0.19
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (27 bp):
ATATTTATTGTTAAATTATATTTAATA
Found at i:1559211 original size:120 final size:120
Alignment explanation
Indices: 1558765--1559303 Score: 727
Period size: 120 Copynumber: 4.5 Consensus size: 120
1558755 GAATATAATG
* *
1558765 ATTTGATTAAATTATATATTTTTACTAAATTATATTTTTAATAATAATTATTTTAAATTATATTT
1 ATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTTTAAATTATATTT
* *
1558830 TATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGA
64 TATAGTATTATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
*
1558887 ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
* *
1558952 TAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAAATATTAAGA
66 TAGTATTATATATTATAATTTTAGTAAATTCATATAAGAATATTT-AATATTAAGA
*
1559008 ATTTTATTAAATTATATATTTCTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
*
1559073 TAGTATTATATATTATAATTTTATTAAATTCATATAAGAATATTTAATATTAAGA
66 TAGTATTATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
* *
1559128 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAAT-ATTATGTTAAATTATCTTTTA
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
* * * * * *
1559192 -A--ATTATTTATTGTTAA---TAATAATTTACCA-A-AACAAATTTCTGCTAATTATTAAGA
66 TAGTATTATATATT-ATAATTTTAGTAAATT--CATATAA-GAATAT-T--TAA-TATTAAGA
* * *
1559247 ATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAAT
1 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT-TTTAAAT
1559304 ATGATTAAAT
Statistics
Matches: 385, Mismatches: 21, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
114 9 0.02
115 5 0.01
116 12 0.03
117 3 0.01
118 4 0.01
119 67 0.17
120 133 0.35
121 121 0.31
122 31 0.08
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (120 bp):
ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
TAGTATTATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
Found at i:1559275 original size:18 final size:17
Alignment explanation
Indices: 1559247--1559281 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1559237 ATTATTAAGA
*
1559247 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1559264 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1559282 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1559281 original size:16 final size:16
Alignment explanation
Indices: 1559247--1559301 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
1559237 ATTATTAAGA
1559247 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
1559264 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
1559280 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
1559294 ATGTTTAA
1 AT-TTTAA
1559302 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:1559551 original size:17 final size:16
Alignment explanation
Indices: 1559517--1559573 Score: 105
Period size: 16 Copynumber: 3.5 Consensus size: 16
1559507 GATTTGCTAT
1559517 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1559533 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1559550 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1559566 TACACCTC
1 TACACCTC
1559574 GTATCTATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 24 0.60
17 16 0.40
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1569238 original size:18 final size:17
Alignment explanation
Indices: 1569211--1569249 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1569201 GGCAAGTATT
1569211 AATATTAAAATAAAAAA
1 AATATTAAAATAAAAAA
* *
1569228 AATACTTAAAATTAAATA
1 AATA-TTAAAATAAAAAA
1569246 AATA
1 AATA
1569250 AAGTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AATATTAAAATAAAAAA
Found at i:1574410 original size:13 final size:13
Alignment explanation
Indices: 1574392--1574416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1574382 CTAATGGACA
1574392 ATATGAAATAATT
1 ATATGAAATAATT
1574405 ATATGAAATAAT
1 ATATGAAATAAT
1574417 ATGAAAAAAA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
ATATGAAATAATT
Found at i:1574616 original size:23 final size:23
Alignment explanation
Indices: 1574544--1574616 Score: 58
Period size: 26 Copynumber: 3.0 Consensus size: 23
1574534 CTGAAACCAA
* *
1574544 TTAAAGTAAA-AAGATATGTAAAGT
1 TTAAAATAAATAATATATG-AAA-T
* *
1574568 TTAAAAAAAATAATATATAAAAAAAT
1 TTAAAATAAATAATATAT---GAAAT
1574594 TTAAAATAAATAATATATGAAAT
1 TTAAAATAAATAATATATGAAAT
1574617 GATTCAGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
23 4 0.10
24 8 0.21
25 6 0.15
26 18 0.46
27 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (23 bp):
TTAAAATAAATAATATATGAAAT
Found at i:1574627 original size:26 final size:26
Alignment explanation
Indices: 1574570--1574635 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1574560 TGTAAAGTTT
* *
1574570 AAAAAAAATAATATATAAAAAAATTT
1 AAAATAAATAATATATAAAAAAATTC
* **
1574596 AAAATAAATAATATATGAAATGATTC
1 AAAATAAATAATATATAAAAAAATTC
* *
1574622 AGAATAAACAATAT
1 AAAATAAATAATAT
1574636 GCAAAAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (26 bp):
AAAATAAATAATATATAAAAAAATTC
Found at i:1574930 original size:27 final size:26
Alignment explanation
Indices: 1574783--1575049 Score: 89
Period size: 26 Copynumber: 10.4 Consensus size: 26
1574773 ATAAAAGAGC
*
1574783 TTAAAATAAAT-A-ATATAAAAGT-T
1 TTAAAATAAATAATATATAAAAATAT
* ** *
1574806 TTAAAATGAGGAACATATAAAACA-AT
1 TTAAAATAAATAATATATAAAA-ATAT
* *
1574832 TTAAACTAAATACTATATATGAAAAT-T
1 TTAAAATAAATA--ATATATAAAAATAT
*
1574859 TT-AAATAGATAATA-ATACATAAAGTAGT
1 TTAAAATAAATAATATATA-A-AAA-TA-T
* *
1574887 TTAAAATAAAGAGTATATAAAAATAT
1 TTAAAATAAATAATATATAAAAATAT
** *
1574913 TTAAAAATAAATAATATATGGAAA-GT
1 TT-AAAATAAATAATATATAAAAATAT
* * *
1574939 TCAAAATAAA-AATA-ATAAAAAGGAAC
1 TTAAAATAAATAATATATAAAAA--TAT
*** * *
1574965 TTAAAGCGATTAACATATAGAATAATA-
1 TTAAAATAAATAATATATA-AA-AATAT
** *
1574992 -T-ATCTAAATAACATATAAAAAT-T
1 TTAAAATAAATAATATATAAAAATAT
1575015 TT-AAATAAATAATATAT-AAAATAGT
1 TTAAAATAAATAATATATAAAAATA-T
1575040 TTAAAATAAA
1 TTAAAATAAA
1575050 AGGTATCTAA
Statistics
Matches: 176, Mismatches: 41, Indels: 51
0.66 0.15 0.19
Matches are distributed among these distances:
23 23 0.13
24 24 0.14
25 33 0.19
26 35 0.20
27 26 0.15
28 18 0.10
29 12 0.07
30 5 0.03
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.30
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAAATAT
Found at i:1575031 original size:24 final size:26
Alignment explanation
Indices: 1574996--1575049 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
1574986 ATAATATATC
*
1574996 TAAATAACATATAAAA-A-TTTTAAA
1 TAAATAACATATAAAATAGTTTAAAA
*
1575020 TAAATAATATATAAAATAGTTTAAAA
1 TAAATAACATATAAAATAGTTTAAAA
1575046 TAAA
1 TAAA
1575050 AGGTATCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 15 0.58
25 1 0.04
26 10 0.38
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
TAAATAACATATAAAATAGTTTAAAA
Found at i:1575924 original size:16 final size:16
Alignment explanation
Indices: 1575905--1575951 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1575895 AAAAAAAATA
1575905 GAAATAAAAAGAAGA-T
1 GAAATAAAAAGAA-ACT
1575921 GAAATAAAACA-AAACT
1 GAAATAAAA-AGAAACT
1575937 GAAATAAACAAGAAA
1 GAAATAAA-AAGAAA
1575952 ACTTAGATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 21 0.78
17 5 0.19
ACGTcount: A:0.70, C:0.06, G:0.13, T:0.11
Consensus pattern (16 bp):
GAAATAAAAAGAAACT
Found at i:1578171 original size:17 final size:16
Alignment explanation
Indices: 1578141--1578184 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
1578131 AATTCATAAT
1578141 TCAATTTCCAATCAATA
1 TCAATTT-CAATCAATA
1578158 TACAATTTCAATCAATA
1 T-CAATTTCAATCAATA
1578175 TCAA-TTCAAT
1 TCAATTTCAAT
1578185 ACATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.23
16 3 0.12
17 11 0.42
18 6 0.23
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.36
Consensus pattern (16 bp):
TCAATTTCAATCAATA
Found at i:1578855 original size:11 final size:11
Alignment explanation
Indices: 1578835--1578870 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1578825 TAAAACCCTA
*
1578835 TTTTTCCTTTC
1 TTTTTTCTTTC
1578846 TTTTTTCTTTC
1 TTTTTTCTTTC
*
1578857 TCTTTTCTTTC
1 TTTTTTCTTTC
1578868 TTT
1 TTT
1578871 CCTTCCCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:1584242 original size:31 final size:27
Alignment explanation
Indices: 1584206--1584271 Score: 69
Period size: 31 Copynumber: 2.3 Consensus size: 27
1584196 TAATTCTAAA
1584206 AAAAATTAATAAACTTAGTCCTCAACATTT
1 AAAAATT-ATAAACTTAGTCCT-AAC-TTT
* *
1584236 ACAAAATCTATCAATTTAGTCCTAACTTT
1 A-AAAAT-TATAAACTTAGTCCTAACTTT
1584265 AAAAATT
1 AAAAATT
1584272 GAGAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 5 0.16
29 4 0.12
30 4 0.12
31 17 0.53
32 1 0.03
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAAATTATAAACTTAGTCCTAACTTT
Found at i:1584242 original size:62 final size:62
Alignment explanation
Indices: 1584149--1584269 Score: 138
Period size: 62 Copynumber: 2.0 Consensus size: 62
1584139 TATAAAATGT
* ** * * * * *
1584149 TTAATAAATTTAGCGCTCAATGTTTATAAAATTTATTATTTTAGTTCTAA-TTCTAAAAAAAA
1 TTAATAAACTTAGCGCTCAACATTTACAAAATCTATCAATTTAGTCCTAACTT-TAAAAAAAA
1584211 TTAATAAACTTAGTC-CTCAACATTTACAAAATCTATCAATTTAGTCCTAACTTTAAAAA
1 TTAATAAACTTAG-CGCTCAACATTTACAAAATCTATCAATTTAGTCCTAACTTTAAAAA
1584270 TTGAGAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
62 46 0.94
63 3 0.06
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (62 bp):
TTAATAAACTTAGCGCTCAACATTTACAAAATCTATCAATTTAGTCCTAACTTTAAAAAAAA
Found at i:1586269 original size:15 final size:15
Alignment explanation
Indices: 1586249--1586356 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
1586239 TTTATGGAAA
1586249 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
1586264 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
1586278 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* ***
1586294 ATCAAATAT-TGAAA
1 ATCAAAGATATGGGT
1586308 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
1586324 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
1586338 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
1586354 ATC
1 ATC
1586357 GAGATATTGG
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
14 11 0.17
15 43 0.66
16 11 0.17
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:1586286 original size:30 final size:30
Alignment explanation
Indices: 1586245--1586356 Score: 172
Period size: 30 Copynumber: 3.7 Consensus size: 30
1586235 CATATTTATG
*
1586245 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
*
1586275 GAAAGTCAAAGATATGGGTATCAAAT-ATT
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
1586304 GAAAAGTCAAAGATATGGGTATCAAATATTG
1 G-AAAGTCAAAGATATGGGTATCAAATAATA
1586335 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
1586357 GAGATATTGG
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
29 3 0.04
30 71 0.93
31 2 0.03
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.25
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:1586343 original size:60 final size:60
Alignment explanation
Indices: 1586245--1586365 Score: 199
Period size: 60 Copynumber: 2.0 Consensus size: 60
1586235 CATATTTATG
1586245 GAAAATCAAAGATATGGGTATCAAATAATAGAAAGTCAAAGATATGGGTATC-AAATATT
1 GAAAATCAAAGATATGGGTATCAAATAATAGAAAGTCAAAGATATGGGTATCGAAATATT
* * *
1586304 GAAAAGTCAAAGATATGGGTATCAAATATTGGAAAGTCAAAGATATGGGTATCGAGATATT
1 GAAAA-TCAAAGATATGGGTATCAAATAATAGAAAGTCAAAGATATGGGTATCGAAATATT
1586365 G
1 G
1586366 GCATAATAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 5 0.09
60 45 0.79
61 7 0.12
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.26
Consensus pattern (60 bp):
GAAAATCAAAGATATGGGTATCAAATAATAGAAAGTCAAAGATATGGGTATCGAAATATT
Found at i:1590962 original size:15 final size:15
Alignment explanation
Indices: 1590942--1591019 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
1590932 TTTATGGAAA
1590942 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
1590957 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
1590971 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
1590987 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
1591001 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
1591017 ATC
1 ATC
1591020 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:1590971 original size:30 final size:30
Alignment explanation
Indices: 1590935--1591019 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
1590925 ATCCATATTT
*
1590935 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
1590965 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
1590995 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
1591020 GAGATATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:1597275 original size:10 final size:10
Alignment explanation
Indices: 1597260--1597302 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
1597250 ATAATTAATT
1597260 AATTTTTAAA
1 AATTTTTAAA
1597270 AATTTTT-AA
1 AATTTTTAAA
*
1597279 AATTTATAAA
1 AATTTTTAAA
* *
1597289 AATATTAAAA
1 AATTTTTAAA
1597299 AATT
1 AATT
1597303 AATTAATTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:1597299 original size:19 final size:19
Alignment explanation
Indices: 1597260--1597299 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1597250 ATAATTAATT
* * *
1597260 AATTTTTAAAAATTTTTAA
1 AATTTATAAAAATATTAAA
1597279 AATTTATAAAAATATTAAA
1 AATTTATAAAAATATTAAA
1597298 AA
1 AA
1597300 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTATAAAAATATTAAA
Found at i:1599045 original size:21 final size:22
Alignment explanation
Indices: 1599005--1599055 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1598995 TGTATATACG
* *
1599005 TATATTTTATGTACATTATGTA
1 TATATTTTATATACATTATGCA
* *
1599027 TATATTTTA-ATATATTATGCG
1 TATATTTTATATACATTATGCA
1599048 TATATTTT
1 TATATTTT
1599056 GTTTTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (22 bp):
TATATTTTATATACATTATGCA
Found at i:1599665 original size:20 final size:23
Alignment explanation
Indices: 1599631--1599671 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1599621 TACTAACATA
1599631 TATATATACTATGTA-ATTTTAT
1 TATATATACTATGTACATTTTAT
1599653 TATAT-TACT-TGTACATTTT
1 TATATATACTATGTACATTTT
1599672 TATATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (23 bp):
TATATATACTATGTACATTTTAT
Found at i:1599677 original size:21 final size:21
Alignment explanation
Indices: 1599629--1599677 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1599619 ATTACTAACA
1599629 TATATATATACTATGTAATTT
1 TATATATATACTATGTAATTT
1599650 TAT-TATATTACT-TGTACATTT
1 TATATATA-TACTATGTA-ATTT
1599671 T-TATATA
1 TATATATA
1599678 CCATGCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATATACTATGTAATTT
Found at i:1601469 original size:18 final size:18
Alignment explanation
Indices: 1601437--1601477 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1601427 CTTAAAATCT
* *
1601437 TTAAAAATTACAAAATTA
1 TTAAAAACTAAAAAATTA
1601455 TTAAAAACTAAAAAATTA
1 TTAAAAACTAAAAAATTA
1601473 -TAAAA
1 TTAAAA
1601478 TTATCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAACTAAAAAATTA
Found at i:1601477 original size:26 final size:27
Alignment explanation
Indices: 1601439--1601503 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
1601429 TAAAATCTTT
* * *
1601439 AAAAATTACAAAATTATTAAAA-ACTA
1 AAAAATTATAAAATTATCAAAACAATA
1601465 AAAAATTATAAAATTATCAAAACAATA
1 AAAAATTATAAAATTATCAAAACAATA
*
1601492 TAAAA-TATAAAA
1 AAAAATTATAAAA
1601504 AAATACAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 27 0.79
27 7 0.21
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (27 bp):
AAAAATTATAAAATTATCAAAACAATA
Found at i:1601503 original size:17 final size:19
Alignment explanation
Indices: 1601464--1601513 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
1601454 ATTAAAAACT
*
1601464 AAAAAATTATAAAATTATC
1 AAAAAAATATAAAATTATC
*
1601483 AAAACAATATAAAA-TAT-
1 AAAAAAATATAAAATTATC
*
1601500 AAAAAAATACAAAA
1 AAAAAAATATAAAA
1601514 ATTTACTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 12 0.44
18 3 0.11
19 12 0.44
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAAAATATAAAATTATC
Found at i:1601686 original size:63 final size:63
Alignment explanation
Indices: 1601587--1601773 Score: 374
Period size: 63 Copynumber: 3.0 Consensus size: 63
1601577 CTAGAGTTTG
1601587 AACATTAATCATTGTCTCTTGGAAGGATACCATCGAATATGATAGTTTTATAATTCAATTTTA
1 AACATTAATCATTGTCTCTTGGAAGGATACCATCGAATATGATAGTTTTATAATTCAATTTTA
1601650 AACATTAATCATTGTCTCTTGGAAGGATACCATCGAATATGATAGTTTTATAATTCAATTTTA
1 AACATTAATCATTGTCTCTTGGAAGGATACCATCGAATATGATAGTTTTATAATTCAATTTTA
1601713 AACATTAATCATTGTCTCTTGGAAGGATACCATCGAATATGATAGTTTTATAATTCAATTT
1 AACATTAATCATTGTCTCTTGGAAGGATACCATCGAATATGATAGTTTTATAATTCAATTT
1601774 ATAGGAATTT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 124 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (63 bp):
AACATTAATCATTGTCTCTTGGAAGGATACCATCGAATATGATAGTTTTATAATTCAATTTTA
Found at i:1602301 original size:20 final size:19
Alignment explanation
Indices: 1602278--1602345 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
1602268 TTTTTTTACT
* *
1602278 ATTTTTTATAATCTTTTATG
1 ATTTTTTATAA-ATTTTATA
*
1602298 ATTTTTAATAAATTTTATA
1 ATTTTTTATAAATTTTATA
* *
1602317 ATTTTTTACAATATTGTA-A
1 ATTTTTTATAA-ATTTTATA
1602336 ATTTTTTATA
1 ATTTTTTATA
1602346 GTTTCTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 25 0.62
20 15 0.38
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTTTTATAAATTTTATA
Found at i:1602323 original size:10 final size:10
Alignment explanation
Indices: 1602269--1602345 Score: 61
Period size: 10 Copynumber: 7.9 Consensus size: 10
1602259 GATGCAATAT
1602269 TTTTTTACT-A
1 TTTTTTA-TAA
1602279 TTTTTTATAA
1 TTTTTTATAA
* *
1602289 TCTTTTATGA
1 TTTTTTATAA
*
1602299 TTTTTAATAA
1 TTTTTTATAA
*
1602309 -ATTTTATAA
1 TTTTTTATAA
*
1602318 TTTTTTACAA
1 TTTTTTATAA
* *
1602328 TATTGTA-AA
1 TTTTTTATAA
1602337 TTTTTTATA
1 TTTTTTATA
1602346 GTTTCTAAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
9 15 0.29
10 36 0.71
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:1612272 original size:22 final size:22
Alignment explanation
Indices: 1612231--1612272 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1612221 GAAAAGTATT
*
1612231 AAATTTATTTTAAAATATATAA
1 AAATTTATATTAAAATATATAA
1612253 AAATTATATATTAAAA-ATAT
1 AAATT-TATATTAAAATATAT
1612273 TTTTAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTTATATTAAAATATATAA
Found at i:1612317 original size:10 final size:10
Alignment explanation
Indices: 1612304--1612353 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
1612294 AAAAAATTCA
1612304 AAAAATTATT
1 AAAAATTATT
1612314 AAAAATTA-T
1 AAAAATTATT
*
1612323 AAAAA--AAT
1 AAAAATTATT
*
1612331 AAAAAGTATT
1 AAAAATTATT
1612341 AAAAATTAATT
1 AAAAATT-ATT
1612352 AA
1 AA
1612354 TTATTAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 1 0.03
8 6 0.18
9 6 0.18
10 16 0.47
11 5 0.15
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAATTATT
Found at i:1612326 original size:20 final size:20
Alignment explanation
Indices: 1612303--1612353 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 20
1612293 TAAAAAATTC
*
1612303 AAAAAATTATTAAAAATTAT
1 AAAAAATTATTAAAAAGTAT
1612323 AAAAAA--A-TAAAAAGTAT
1 AAAAAATTATTAAAAAGTAT
*
1612340 TAAAAATTAATTAA
1 AAAAAATT-ATTAA
1612354 TTATTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
17 14 0.56
18 1 0.04
20 7 0.28
21 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAAATTATTAAAAAGTAT
Found at i:1613608 original size:18 final size:17
Alignment explanation
Indices: 1613587--1613644 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
1613577 AAAATTATCA
1613587 AAAACTTAAAAAAGTTAT
1 AAAA-TTAAAAAAGTTAT
1613605 AAAATTATAAAAA-TATAT
1 AAAATTA-AAAAAGT-TAT
*
1613623 ATAAATATAAAAAAGTAAT
1 A-AAAT-TAAAAAAGTTAT
1613642 AAA
1 AAA
1613645 TTTTATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 4 0.12
18 15 0.44
19 12 0.35
20 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATTAAAAAAGTTAT
Found at i:1614585 original size:31 final size:31
Alignment explanation
Indices: 1614550--1614617 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1614540 CATCTAAAGG
1614550 ACTGAA-CTAGGAACGTTTGATAACATTAGGA
1 ACTGAATC-AGGAACGTTTGATAACATTAGGA
* ** *
1614581 ACTGAATCGGGTGCGTTTGATAACATTAGGG
1 ACTGAATCAGGAACGTTTGATAACATTAGGA
1614612 ACTGAA
1 ACTGAA
1614618 GTGGGCTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (31 bp):
ACTGAATCAGGAACGTTTGATAACATTAGGA
Found at i:1632317 original size:16 final size:16
Alignment explanation
Indices: 1632296--1632329 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1632286 CAAAGCCATA
1632296 CAAGAGTTACCTCCAC
1 CAAGAGTTACCTCCAC
1632312 CAAGAGTTACCTCCAC
1 CAAGAGTTACCTCCAC
1632328 CA
1 CA
1632330 CGTACTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.38, G:0.12, T:0.18
Consensus pattern (16 bp):
CAAGAGTTACCTCCAC
Found at i:1633246 original size:15 final size:15
Alignment explanation
Indices: 1633228--1633258 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1633218 CAAAATTTCA
1633228 AAAAAAAAAAAAATT
1 AAAAAAAAAAAAATT
*
1633243 AAAAAAATAAAAATT
1 AAAAAAAAAAAAATT
1633258 A
1 A
1633259 CATTTTGACA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAAAAAAAAATT
Found at i:1633293 original size:30 final size:29
Alignment explanation
Indices: 1633253--1633368 Score: 117
Period size: 30 Copynumber: 3.9 Consensus size: 29
1633243 AAAAAAATAA
* *
1633253 AAATTACATTTTGACACCTAAACTTTTC-CT
1 AAATTTCATTTTGAC-CCTAAAC-TTTCATT
*
1633283 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCATT
* *
1633313 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGA-CCCTAAACTTTCATT
* * *
1633343 AAATTTCATTTTAATCCTAAATTTTC
1 AAATTTCATTTTGACCCTAAACTTTC
1633369 TAAAAATTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 16 0.22
30 54 0.74
31 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCATT
Found at i:1637548 original size:67 final size:67
Alignment explanation
Indices: 1637440--1637569 Score: 251
Period size: 67 Copynumber: 1.9 Consensus size: 67
1637430 AGCAGTACGA
1637440 TAGGGACATTCACGCGTATGAAGGAACTCTCAAAGAAAAAGAAATGCAACTTAACTTCTTGATCA
1 TAGGGACATTCACGCGTATGAAGGAACTCTCAAAGAAAAAGAAATGCAACTTAACTTCTTGATCA
1637505 AT
66 AT
*
1637507 TAGGGACATTCACGCGTATGAAGGAACTCTCAAAGAAAAAGAAATGCAACTTGACTTCTTGAT
1 TAGGGACATTCACGCGTATGAAGGAACTCTCAAAGAAAAAGAAATGCAACTTAACTTCTTGAT
1637570 TAATGAAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (67 bp):
TAGGGACATTCACGCGTATGAAGGAACTCTCAAAGAAAAAGAAATGCAACTTAACTTCTTGATCA
AT
Found at i:1643353 original size:73 final size:73
Alignment explanation
Indices: 1643234--1643379 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
1643224 AATATTTGTC
1643234 CGTTGAGAAATATTGTTGCGCTCTGGTTTAGGTAGCTCGGAGACTCAGACAATATATGTTGTATC
1 CGTTGAGAAATATTGTTGCGCTCTGGTTTAGGTAGCTCGGAGACTCAGACAATATATGTTGTATC
1643299 ACACGACA
66 ACACGACA
*
1643307 CGTTGAGAAATATTGTTGCGCTCTGGTTTGGGTAGCTCGGAGACTCAGACAATATATGTTGTATC
1 CGTTGAGAAATATTGTTGCGCTCTGGTTTAGGTAGCTCGGAGACTCAGACAATATATGTTGTATC
*
1643372 ATACGACA
66 ACACGACA
1643380 TGGCTAATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (73 bp):
CGTTGAGAAATATTGTTGCGCTCTGGTTTAGGTAGCTCGGAGACTCAGACAATATATGTTGTATC
ACACGACA
Found at i:1646143 original size:187 final size:187
Alignment explanation
Indices: 1645823--1646198 Score: 544
Period size: 187 Copynumber: 2.0 Consensus size: 187
1645813 GACATGCTCT
**
1645823 AAACAAAAGAAATGTCAAGCATTACCCGGATAAGAATTTGATAAGTGCAAGATCTTCAAAGCAAG
1 AAACAAAAGAAATGTCAAGCATTACCCGGATAAGAATTTGATAAGCACAAGATCTTCAAAGCAAG
*
1645888 AACAAAGTTTAACCAAGGGCAAAAAGGTGATATCTGAGAAACGTCGATTACTCGTAAAGCTCGAA
66 AACAAAGTTCAACCAAGGGCAAAAAGGTGATATCTGAGAAACGTCGATTACTCGTAAAGCTCGAA
* * *
1645953 GACAGGTATGAGGCCTGAAGAGAAGGTCGAGAATCAAAGCAATGAACGCAGATCCTC
131 GACAGGTATAAGGCCTGAAGAGAAAGTCGAGAATCAAAGCAATGAACACAGATCCTC
* * *
1646010 AAACAAAAGAAATGTTAAGCATTACCTGGATGAA-AATTTGATAAGCACAAGAGTC-TCAAAGTA
1 AAACAAAAGAAATGTCAAGCATTACCCGGAT-AAGAATTTGATAAGCACAAGA-TCTTCAAAGCA
* * * * *
1646073 AGAACAAAGTTCAATC-GGTGGC-AGAAGAGTGATATCTGAGAAACGTCGATTGCTCGTGAAGCT
64 AGAACAAAGTTCAACCAAG-GGCAAAAAG-GTGATATCTGAGAAACGTCGATTACTCGTAAAGCT
* *
1646136 TGAAGACATGTATAAGGCCTGAAGAGAAAGTCGAGAATCAAAGCAATGAACACAGATCCTC
127 CGAAGACAGGTATAAGGCCTGAAGAGAAAGTCGAGAATCAAAGCAATGAACACAGATCCTC
1646197 AA
1 AA
1646199 CAATCGTGGC
Statistics
Matches: 169, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
186 5 0.03
187 160 0.95
188 4 0.02
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (187 bp):
AAACAAAAGAAATGTCAAGCATTACCCGGATAAGAATTTGATAAGCACAAGATCTTCAAAGCAAG
AACAAAGTTCAACCAAGGGCAAAAAGGTGATATCTGAGAAACGTCGATTACTCGTAAAGCTCGAA
GACAGGTATAAGGCCTGAAGAGAAAGTCGAGAATCAAAGCAATGAACACAGATCCTC
Found at i:1650552 original size:109 final size:109
Alignment explanation
Indices: 1650416--1650835 Score: 788
Period size: 109 Copynumber: 3.9 Consensus size: 109
1650406 TAAATTCAAT
* **
1650416 AGGATATTT-GACAATTTGGTTAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTTAG-CTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1650480 ATTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
65 ATTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
1650525 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1650590 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
1650634 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1650699 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
1650743 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
*
1650808 TTTCCAAACGCAAAATATTGCCTTATTT
66 TTTCCAAACGCAAAACATTGCCTTATTT
1650836 GGAAATATTT
Statistics
Matches: 306, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
109 305 1.00
110 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (109 bp):
AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
Found at i:1651449 original size:24 final size:22
Alignment explanation
Indices: 1651422--1651472 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1651412 ATATATGCAC
*
1651422 ATATATATATTAAGATATATGG
1 ATATATATAATAAGATATATGG
*
1651444 ATATATATAATAAGATATATAG
1 ATATATATAATAAGATATATGG
1651466 ATATATA
1 ATATATA
1651473 ACTAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
ATATATATAATAAGATATATGG
Found at i:1651473 original size:20 final size:21
Alignment explanation
Indices: 1651424--1651482 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
1651414 ATATGCACAT
* *
1651424 ATATATATTAAGATATATGGAT
1 ATATATAATAAGATATAT-GAG
1651446 ATATATAATAAGATATAT-AG
1 ATATATAATAAGATATATGAG
1651466 ATATATAACTAA-ATATA
1 ATATATAA-TAAGATATA
1651483 ATATTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 17 0.50
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATATAATAAGATATATGAG
Found at i:1653688 original size:44 final size:44
Alignment explanation
Indices: 1653640--1653866 Score: 187
Period size: 44 Copynumber: 5.2 Consensus size: 44
1653630 CAATGTAGGA
1653640 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
* * * * ** * * *
1653684 AGGCAAGGT-TTGTGTCTTCGACCTGCT-TCACTGTCAA-TGTAGG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCT-A-TCACAACCGAAAG
1653727 AAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
1 -AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
* * * * ** * * *
1653772 AGGCAAGGT-TTGTGTCTTCGACCTGCT-TCACTGTCAA-TGTAGG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCT-A-TCACAACCGAAAG
*
1653815 AAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAG
1 -AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
1653860 AGGCAAG
1 AGGCAAG
1653867 GTTTGTGTCT
Statistics
Matches: 134, Mismatches: 37, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
42 2 0.01
43 38 0.28
44 55 0.41
45 38 0.28
46 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (44 bp):
AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
Found at i:1653696 original size:88 final size:88
Alignment explanation
Indices: 1653414--1654000 Score: 773
Period size: 88 Copynumber: 6.7 Consensus size: 88
1653404 AGCTTCAATG
** * * ** * *
1653414 CAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATC
** * *
1653477 TGCT-TCTTTAACTAGCTCCA-CTA
65 TTTTGTCTTCAACCAGCTCCATC-A
* ** * * * *
1653500 CAATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATC
** *
1653563 TGCT-TCTTTAACCAGCTCCA-CTA
65 TTTTGTCTTCAACCAGCTCCATC-A
*
1653586 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
*
1653651 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCCATCA
1653674 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
*
1653739 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCCATCA
1653762 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
1653827 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCCATCA
* *
1653850 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATC-
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
*
1653914 TTT-TCTTTAACCAGCTCCA-CTA
66 TTTGTCTTCAACCAGCTCCATC-A
* * *
1653936 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTATCAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
1654001 GTAACTTCAT
Statistics
Matches: 468, Mismatches: 27, Indels: 11
0.92 0.05 0.02
Matches are distributed among these distances:
85 6 0.01
86 170 0.36
87 40 0.09
88 251 0.54
89 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (88 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGTAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCCATCA
Found at i:1656179 original size:7 final size:8
Alignment explanation
Indices: 1656154--1656183 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1656144 CTATTTTGAC
1656154 TTTGATTTT
1 TTTGA-TTT
1656163 TTTGATTT
1 TTTGATTT
1656171 TTTGATTT
1 TTTGATTT
1656179 TTTGA
1 TTTGA
1656184 ATTCATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (8 bp):
TTTGATTT
Found at i:1657504 original size:114 final size:114
Alignment explanation
Indices: 1657300--1657527 Score: 429
Period size: 114 Copynumber: 2.0 Consensus size: 114
1657290 CGACAATACG
*
1657300 TGCGTTGAATAAGCTTTGATACAACTCCTTATATGACATCGGAATTGGCGTGCATTGAAGGTTCT
1 TGCGTTGAATAAGCTTTGATACAACTCCTTATATGACATCGGAATTGGCGTGAATTGAAGGTTCT
* *
1657365 CAGTGCCTTGCTTCACATACGATTCTTGTCTAGATGAACCTTGCTGACT
66 CAGTGCCTTGCTTCACATACAATTCTTATCTAGATGAACCTTGCTGACT
1657414 TGCGTTGAATAAGCTTTGATACAACTCCTTATATGACATCGGAATTGGCGTGAATTGAAGGTTCT
1 TGCGTTGAATAAGCTTTGATACAACTCCTTATATGACATCGGAATTGGCGTGAATTGAAGGTTCT
1657479 CAGTGCCTTGCTTCACATACAATTCTTATCTAGATGAACCTTGCTGACT
66 CAGTGCCTTGCTTCACATACAATTCTTATCTAGATGAACCTTGCTGACT
1657528 AGTAATCACC
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (114 bp):
TGCGTTGAATAAGCTTTGATACAACTCCTTATATGACATCGGAATTGGCGTGAATTGAAGGTTCT
CAGTGCCTTGCTTCACATACAATTCTTATCTAGATGAACCTTGCTGACT
Found at i:1658819 original size:19 final size:20
Alignment explanation
Indices: 1658790--1658838 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1658780 CACTTCGTGA
* *
1658790 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
1658809 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
1658829 AAATG-AATGC
1 AAATGTAATGC
1658839 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:1660358 original size:109 final size:109
Alignment explanation
Indices: 1660222--1660423 Score: 352
Period size: 109 Copynumber: 1.9 Consensus size: 109
1660212 TAAATTCAAT
*
1660222 AGGATATTTGACAATTTGGTTAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1660287 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
* *
1660331 AGGATATTT-AGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTTGA-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
*
1660395 ATTTCCAAACGCAAAATATTGCCTTATTT
65 ATTTCCAAACGCAAAACATTGCCTTATTT
1660424 GGAAATATTT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
108 1 0.01
109 87 0.99
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (109 bp):
AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
Done.