Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 6 of 13
Found at i:1172325 original size:34 final size:34
Alignment explanation
Indices: 1172280--1172346 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1172270 AATAGGAATT
*
1172280 ACAATTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAATTTCTCTCTGA--TAAAAAGGAGAAAACAATA
1172315 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAATTTCTCTC-TGATAAAAAGGAGAAAACAA
1172347 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (34 bp):
ACAATTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:1172575 original size:36 final size:36
Alignment explanation
Indices: 1172524--1172598 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
1172514 CAACAAAATC
* *
1172524 ATGCTGCCAAGTTGGAGCAAATCAGCCGCCCCATTA
1 ATGCTGCCAACTTGGAGAAAATCAGCCGCCCCATTA
*
1172560 ATGCTGCCATCTTGGAGAAAATCAGCCGCCCCATTA
1 ATGCTGCCAACTTGGAGAAAATCAGCCGCCCCATTA
1172596 ATG
1 ATG
1172599 TTGTCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (36 bp):
ATGCTGCCAACTTGGAGAAAATCAGCCGCCCCATTA
Found at i:1172665 original size:20 final size:21
Alignment explanation
Indices: 1172642--1172682 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1172632 AACATTATGG
1172642 ATTATCA-ATCAACGTCGTAT
1 ATTATCACATCAACGTCGTAT
*
1172662 ATTATCACATCAACGTTGTAT
1 ATTATCACATCAACGTCGTAT
1172683 CAATAAACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (21 bp):
ATTATCACATCAACGTCGTAT
Found at i:1175119 original size:18 final size:18
Alignment explanation
Indices: 1175073--1175134 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
1175063 GGCTTGGGGA
1175073 TTTAAAT-TTTTTT--AT
1 TTTAAATATTTTTTAGAT
** *
1175088 TTTATTTATGTTTTAGAT
1 TTTAAATATTTTTTAGAT
1175106 TTTAAATATTTTTTTAG-T
1 TTTAAATA-TTTTTTAGAT
1175124 TTT-AATATTTT
1 TTTAAATATTTT
1175135 GGGTTTGGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.14
16 9 0.24
17 4 0.11
18 12 0.32
19 7 0.19
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTAAATATTTTTTAGAT
Found at i:1178736 original size:31 final size:31
Alignment explanation
Indices: 1178658--1178736 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
1178648 TAAAAAAACA
* * *
1178658 TAAATTTTAGTTACTTACGTTATCGTTTTAT
1 TAAATTTTGGTTACTTAAGATATCGTTTTAT
* * *
1178689 TAAGTTTTGATTACTTAAGATATTGTTTTAT
1 TAAATTTTGGTTACTTAAGATATCGTTTTAT
*
1178720 TAAATTTTGGTCACTTA
1 TAAATTTTGGTTACTTA
1178737 GACGTTGAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (31 bp):
TAAATTTTGGTTACTTAAGATATCGTTTTAT
Found at i:1196266 original size:23 final size:23
Alignment explanation
Indices: 1196240--1196284 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1196230 AAAAATATTT
*
1196240 TAATTATATATTTAATTATAATA
1 TAATTATAAATTTAATTATAATA
*
1196263 TAATTATAAATTTCATTATAAT
1 TAATTATAAATTTAATTATAAT
1196285 CCAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATTATAAATTTAATTATAATA
Found at i:1196283 original size:12 final size:12
Alignment explanation
Indices: 1196238--1196283 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1196228 ACAAAAATAT
*
1196238 TTTAATTATATA
1 TTTAATTATAAA
1196250 TTTAATTAT-AA
1 TTTAATTATAAA
*
1196261 TATAATTATAAA
1 TTTAATTATAAA
*
1196273 TTTCATTATAA
1 TTTAATTATAA
1196284 TCCAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATTATAAA
Found at i:1200290 original size:20 final size:20
Alignment explanation
Indices: 1200265--1200358 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
1200255 AATTGGGAAA
1200265 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1200285 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1200305 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1200326 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1200346 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1200359 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1200950 original size:20 final size:19
Alignment explanation
Indices: 1200904--1201069 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
1200894 ATAACCAAAA
*
1200904 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1200923 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1200942 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1200962 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1200978 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1200995 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1201009 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1201028 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1201048 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1201068 TC
1 TC
1201070 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1200985 original size:39 final size:39
Alignment explanation
Indices: 1200909--1200985 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
1200899 CAAAATCGCA
* **
1200909 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
1200948 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
1200986 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:1200994 original size:33 final size:33
Alignment explanation
Indices: 1200957--1201044 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1200947 GTTGCGATTT
* *
1200957 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1200990 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1201023 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1201045 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1203018 original size:42 final size:42
Alignment explanation
Indices: 1202958--1203041 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1202948 GTCTGACTCG
* * *
1202958 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1203000 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
1203042 ATTGTCATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1204458 original size:14 final size:14
Alignment explanation
Indices: 1204439--1204474 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1204429 ATTGTTTAAT
1204439 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1204453 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1204467 TGATTTGT
1 TGATTTGT
1204475 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1204625 original size:19 final size:19
Alignment explanation
Indices: 1204601--1204659 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1204591 GAAATTAGCG
1204601 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1204620 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1204634 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1204653 TTGCGAT
1 TTGCGAT
1204660 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1204625 original size:33 final size:34
Alignment explanation
Indices: 1204582--1204658 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
1204572 AAAAGTACTA
*
1204582 TCGCAATGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
* **
1204615 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
1204648 TCGCATTGCGA
1 TCGCATTGCGA
1204659 TAGTAATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (34 bp):
TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
Found at i:1206969 original size:12 final size:12
Alignment explanation
Indices: 1206952--1206976 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1206942 TCTTCGGGGA
1206952 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1206964 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1206976 C
1 C
1206977 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1207185 original size:24 final size:24
Alignment explanation
Indices: 1207151--1207204 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1207141 CTGAAACATC
* *
1207151 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1207175 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1207199 ATCAAA
1 ATCAAA
1207205 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1208291 original size:20 final size:20
Alignment explanation
Indices: 1208266--1208363 Score: 169
Period size: 20 Copynumber: 4.9 Consensus size: 20
1208256 ATTCATTTGA
1208266 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1208286 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1208306 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1208326 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1208346 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1208364 CGCAATGCGA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1208374 original size:34 final size:35
Alignment explanation
Indices: 1208288--1208375 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 35
1208278 GAAAATGGCT
1208288 ATCGCAATGCGAAAATGGCTATCGCAATGCGAAAATGG
1 ATCGCAATGCGAAAATGGCTATCGCAA-GCGAAAA--G
*
1208326 CTATCGCAACGCGAAAATGGCTATCGCAA-CGAGAAA-
1 --ATCGCAATGCGAAAATGGCTATCGCAAGCGA-AAAG
1208362 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1208376 TGAAAATAGC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
34 13 0.29
38 3 0.07
39 3 0.07
40 26 0.58
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.16
Consensus pattern (35 bp):
ATCGCAATGCGAAAATGGCTATCGCAAGCGAAAAG
Found at i:1208406 original size:14 final size:14
Alignment explanation
Indices: 1208387--1208440 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1208377 GAAAATAGCA
1208387 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1208401 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1208418 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1208434 TTGCGAT
1 TTGCGAT
1208441 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1208406 original size:33 final size:33
Alignment explanation
Indices: 1208369--1208439 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1208359 AAAATCGCAA
1208369 TGCGAAATGAAAATAGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATAGCATTGCGATTTTCTCGT
** ** ** *
1208402 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATAGCATTGCGATTTTCTCGT
1208435 TGCGA
1 TGCGA
1208440 TAGCCATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATAGCATTGCGATTTTCTCGT
Found at i:1208440 original size:33 final size:33
Alignment explanation
Indices: 1208384--1208459 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
1208374 AATGAAAATA
***
1208384 GCATTGCGATTTTCTCGTTGCGATTTTCATTTC
1 GCATTGCGATTTTCTCGTTGCGATAGCCATTTC
1208417 GCATTGCGATTTTCTCGTTGCGATAGCCATTTC
1 GCATTGCGATTTTCTCGTTGCGATAGCCATTTC
*
1208450 GCGTTGCGAT
1 GCATTGCGAT
1208460 AGTCTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (33 bp):
GCATTGCGATTTTCTCGTTGCGATAGCCATTTC
Found at i:1208566 original size:14 final size:14
Alignment explanation
Indices: 1208547--1208583 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1208537 CATCAATTAA
1208547 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1208561 ACAAATCATCTTTT
1 ACAAATCAACATTT
1208575 ACAAATCAA
1 ACAAATCAA
1208584 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1210474 original size:19 final size:19
Alignment explanation
Indices: 1210450--1210516 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1210440 GAAACTTAAA
1210450 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
1210469 ATCGCAACACGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1210489 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1210508 ATCGCAACG
1 ATCGCAACG
1210517 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1210485 original size:20 final size:19
Alignment explanation
Indices: 1210431--1210515 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 19
1210421 TAGTTTACTT
* **
1210431 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAA-TGACTA
*
1210451 TCGCAACGCGAAATGACTA
1 TCGCAACACGAAATGACTA
*
1210470 TCGCAACACGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
** **
1210490 TCGCAATGCGAAATGAAAA
1 TCGCAACACGAAATGACTA
1210509 TCGCAAC
1 TCGCAAC
1210516 GACAAAATCG
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 24 0.46
20 28 0.54
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:1210524 original size:14 final size:14
Alignment explanation
Indices: 1210505--1210562 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1210495 ATGCGAAATG
1210505 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1210519 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1210535 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1210551 AAAATCGCAACG
1 AAAATCGCAACG
1210563 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1210547 original size:32 final size:33
Alignment explanation
Indices: 1210489--1210567 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1210479 GGAAATGGCT
*
1210489 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1210522 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1210554 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1210568 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1210615 original size:14 final size:14
Alignment explanation
Indices: 1210596--1210653 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1210586 TTTCATTTCG
1210596 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1210610 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1210626 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1210642 CGTTGCGATTTT
1 CGTTGCGATTTT
1210654 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1210660 original size:33 final size:33
Alignment explanation
Indices: 1210579--1210669 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1210569 ACAAATCGCA
* *
1210579 TTGCAATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1210612 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1210644 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1210670 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1210688 original size:20 final size:19
Alignment explanation
Indices: 1210654--1210708 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1210644 TTGCGATTTT
*
1210654 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1210673 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1210693 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1210709 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1211921 original size:19 final size:20
Alignment explanation
Indices: 1211866--1211912 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1211856 GAAACTTAAA
1211866 ATCGCAACACGGAAATGGCT
1 ATCGCAACACGGAAATGGCT
1211886 ATCGCAACACGGAAATGGCT
1 ATCGCAACACGGAAATGGCT
1211906 ATCGCAA
1 ATCGCAA
1211913 TGCGAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACACGGAAATGGCT
Found at i:1211928 original size:19 final size:18
Alignment explanation
Indices: 1211906--1211963 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 18
1211896 GGAAATGGCT
1211906 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
1211925 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
1211939 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
1211957 ATCGCAA
1 ATCGCAA
1211964 CGACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 10 0.31
19 7 0.22
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:1211941 original size:14 final size:14
Alignment explanation
Indices: 1211922--1211979 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1211912 ATGCGAAATG
1211922 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1211936 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1211952 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1211968 AAAATCGCAACG
1 AAAATCGCAACG
1211980 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1211964 original size:32 final size:33
Alignment explanation
Indices: 1211906--1211984 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1211896 GGAAATGGCT
*
1211906 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1211939 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1211971 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1211985 CACAAATCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1212032 original size:14 final size:14
Alignment explanation
Indices: 1212013--1212070 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1212003 TTTCATTTCG
1212013 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1212027 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1212043 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1212059 CGTTGCGATTTT
1 CGTTGCGATTTT
1212071 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1212077 original size:33 final size:33
Alignment explanation
Indices: 1211996--1212086 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1211986 ACAAATCATA
* *
1211996 TTGCAATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1212029 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1212061 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1212087 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1212105 original size:20 final size:19
Alignment explanation
Indices: 1212071--1212125 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1212061 TTGCGATTTT
*
1212071 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1212090 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1212110 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1212126 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1212321 original size:24 final size:25
Alignment explanation
Indices: 1212290--1212337 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1212280 TACCTCGATG
*
1212290 TGTA-TTTTTGTAAAACATCATATA
1 TGTATTTTTTGTAAAACAGCATATA
1212314 TGTATTTTTTGTAAAACAGCATAT
1 TGTATTTTTTGTAAAACAGCATAT
1212338 CGATGTGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (25 bp):
TGTATTTTTTGTAAAACAGCATATA
Found at i:1212650 original size:19 final size:20
Alignment explanation
Indices: 1212596--1212662 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1212586 TAGTTTACTT
* *
1212596 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1212616 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1212636 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1212655 TCGCAACG
1 TCGCAACG
1212663 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1212670 original size:14 final size:14
Alignment explanation
Indices: 1212651--1212708 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1212641 ATGCGAAATG
1212651 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1212665 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1212681 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1212697 AAAATCGCAACG
1 AAAATCGCAACG
1212709 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1212677 original size:33 final size:33
Alignment explanation
Indices: 1212635--1212725 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1212625 GGAAATGGCT
1212635 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1212668 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1212700 ATCGCAACGCGAAATGAAAATTGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1212726 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1212761 original size:14 final size:14
Alignment explanation
Indices: 1212742--1212799 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1212732 TTGTGTTTCG
1212742 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1212756 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1212772 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1212788 CGTTGCGATTTT
1 CGTTGCGATTTT
1212800 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1212776 original size:32 final size:33
Alignment explanation
Indices: 1212737--1212815 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1212727 GCGATTTGTG
1212737 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1212769 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1212802 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1212816 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1212814 original size:19 final size:19
Alignment explanation
Indices: 1212756--1212873 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
1212746 GCGATTTTGT
1212756 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1212774 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1212788 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1212807 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
* **
1212827 TGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1212846 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1212866 TGTTGCGA
1 CGTTGCGA
1212874 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 11 0.14
19 25 0.32
20 28 0.35
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1214743 original size:14 final size:14
Alignment explanation
Indices: 1214724--1214759 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1214714 ATTGTTTAAT
1214724 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1214738 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1214752 TGATTTGT
1 TGATTTGT
1214760 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1214898 original size:19 final size:19
Alignment explanation
Indices: 1214876--1214943 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1214866 ATCGCAACGA
1214876 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
1214895 GAAAATCGCAATTCGAAAT
1 GAAAATCGCAATGCGAAAT
1214914 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1214928 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1214944 TTTTCATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 29 0.64
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1214987 original size:20 final size:20
Alignment explanation
Indices: 1214962--1215019 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1214952 TCGCATTGCG
*
1214962 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1214982 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1215002 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1215020 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1216108 original size:24 final size:24
Alignment explanation
Indices: 1216081--1216134 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1216071 GTATTCGAAA
* *
1216081 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1216105 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1216129 TTTGAT
1 TTTGAT
1216135 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1216326 original size:12 final size:12
Alignment explanation
Indices: 1216309--1216333 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1216299 ATATAATCCT
1216309 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1216321 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1216333 G
1 G
1216334 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1218648 original size:19 final size:19
Alignment explanation
Indices: 1218626--1218680 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
1218616 GGAAATTACT
1218626 ATCGCAATGAGAAATGAAA
1 ATCGCAATGAGAAATGAAA
*
1218645 ATCGCAACGAG--A-G--A
1 ATCGCAATGAGAAATGAAA
*
1218659 ATCGCAATGCGAAATGAAA
1 ATCGCAATGAGAAATGAAA
1218678 ATC
1 ATC
1218681 ACAACGCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
14 10 0.36
16 2 0.07
17 2 0.07
19 14 0.50
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGAGAAATGAAA
Found at i:1218673 original size:33 final size:33
Alignment explanation
Indices: 1218625--1218785 Score: 209
Period size: 33 Copynumber: 4.9 Consensus size: 33
1218615 CGGAAATTAC
*
1218625 TATCGCAATGAGAAATGAAAATCGCAACGAGAGA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGA-A
* **
1218659 -ATCGCAATGCGAAATGAAAATCACAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
* **
1218691 TTTCGCAATGCGAAATGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
* *
1218724 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 TATCGCAATGCGAAATGAAAATCGCAACGA-GAA
1218758 -ATCGCAATGCGAAATGAAAATCGCAACG
1 TATCGCAATGCGAAATGAAAATCGCAACG
1218786 CAAATTTAAT
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 113 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (33 bp):
TATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:1218967 original size:14 final size:14
Alignment explanation
Indices: 1218948--1218984 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1218938 CATCAATTAA
1218948 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1218962 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1218976 ACAAATCAA
1 ACAAATCAA
1218985 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1220410 original size:21 final size:21
Alignment explanation
Indices: 1220344--1220410 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1220334 GTGAATCGGG
*
1220344 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1220364 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1220386 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1220407 CTCT
1 CTCT
1220411 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1220429 original size:42 final size:41
Alignment explanation
Indices: 1220344--1220465 Score: 102
Period size: 42 Copynumber: 2.9 Consensus size: 41
1220334 GTGAATCGGG
* * * * *
1220344 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1220386 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * * *
1220428 CTCTTCAACGATAGAAGTGGACTCTTGAGGGATGATAG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAG
1220466 ACGAGTCGGG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1222496 original size:20 final size:19
Alignment explanation
Indices: 1222465--1222611 Score: 117
Period size: 20 Copynumber: 7.8 Consensus size: 19
1222455 TCTTTTGGTT
1222465 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1222484 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1222505 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1222524 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
* * *
1222538 GACCA-GACAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
*
1222557 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
1222577 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1222596 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1222612 TGCGATTTTG
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.09
16 1 0.01
17 3 0.03
18 1 0.01
19 44 0.41
20 47 0.44
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1222568 original size:19 final size:19
Alignment explanation
Indices: 1222465--1222616 Score: 145
Period size: 19 Copynumber: 8.1 Consensus size: 19
1222455 TCTTTTGGTT
*
1222465 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1222484 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1222504 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1222522 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
1222538 GACCA-GACAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
1222557 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1222577 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1222596 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1222615 GA
1 GA
1222617 TTTTGGTTTC
Statistics
Matches: 112, Mismatches: 12, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 50 0.45
20 45 0.40
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1223215 original size:20 final size:20
Alignment explanation
Indices: 1223190--1223242 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1223180 GCGCTATGTA
1223190 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1223210 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1223230 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1223243 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1223276 original size:20 final size:20
Alignment explanation
Indices: 1223251--1223304 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1223241 GATTTTGTAT
1223251 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1223271 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1223291 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1223305 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1223289 original size:61 final size:61
Alignment explanation
Indices: 1223191--1223307 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1223181 CGCTATGTAA
* * * * *
1223191 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1223252 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1223308 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1223323 original size:61 final size:61
Alignment explanation
Indices: 1223191--1223325 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1223181 CGCTATGTAA
* * * * * ** *
1223191 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1223252 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1223314 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1223326 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1223415 original size:21 final size:21
Alignment explanation
Indices: 1223375--1223415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1223365 ATTGTATACC
**
1223375 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1223396 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1223416 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1227327 original size:12 final size:11
Alignment explanation
Indices: 1227310--1227346 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1227300 CAAACTATAC
1227310 AAATATAGAAAA
1 AAATATA-AAAA
1227322 AAATAT-AAAA
1 AAATATAAAAA
1227332 AAAT-TAAAAA
1 AAATATAAAAA
1227342 AAATA
1 AAATA
1227347 AATTACTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.04
10 16 0.70
12 6 0.26
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (11 bp):
AAATATAAAAA
Found at i:1230270 original size:31 final size:31
Alignment explanation
Indices: 1230234--1230292 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1230224 AACTTAAAAG
*
1230234 AGTTTTGCAATACTGAGA-TTTAAATAATTTT
1 AGTTTTACAATACTGA-ATTTTAAATAATTTT
*
1230265 AGTTTTATAATACTGAATTTTAAATAAT
1 AGTTTTACAATACTGAATTTTAAATAAT
1230293 CCATACAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (31 bp):
AGTTTTACAATACTGAATTTTAAATAATTTT
Found at i:1230333 original size:22 final size:22
Alignment explanation
Indices: 1230308--1230385 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
1230298 CAACTACAAT
1230308 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
1230330 AATAAATCAATCCATA----CA
1 AATAAATCAATCCATATTTTAA
* *
1230348 AATAAATTAATCTATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
1230370 AATAAATCAATTCATA
1 AATAAATCAATCCATA
1230386 CTAATATATT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 15 0.33
22 30 0.67
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:1230365 original size:40 final size:40
Alignment explanation
Indices: 1230308--1230396 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
1230298 CAACTACAAT
*
1230308 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
1 AATAAATTAATCCATATTTTAAAATAAATCAATCCATACA
* * *
1230348 AATAAATTAATCTATATTTTAAAATAAATCAATTCATACT
1 AATAAATTAATCCATATTTTAAAATAAATCAATCCATACA
*
1230388 AATATATTA
1 AATAAATTA
1230397 TTTAAAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (40 bp):
AATAAATTAATCCATATTTTAAAATAAATCAATCCATACA
Found at i:1230402 original size:32 final size:31
Alignment explanation
Indices: 1230365--1230462 Score: 106
Period size: 32 Copynumber: 3.4 Consensus size: 31
1230355 TAATCTATAT
1230365 TTTAAAATAAATCAATTCATACTAATATATTA
1 TTTAAAATAAATCAATT-ATACTAATATATTA
1230397 TTTAAAATAAATC-A--AT--T--TATA-T-
1 TTTAAAATAAATCAATTATACTAATATATTA
*
1230419 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAAT-TATACTAATATATTA
1230451 TTTAAAATAAAT
1 TTTAAAATAAAT
1230463 TATTTTAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 20
0.72 0.01 0.26
Matches are distributed among these distances:
22 13 0.24
23 2 0.04
24 4 0.07
26 3 0.05
28 3 0.05
30 3 0.05
31 2 0.04
32 25 0.45
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTAAAATAAATCAATTATACTAATATATTA
Found at i:1230424 original size:22 final size:22
Alignment explanation
Indices: 1230397--1230439 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1230387 TAATATATTA
*
1230397 TTTAAAATAAATCAATTTATAT
1 TTTAAAATAAATCAATCTATAT
1230419 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
1230440 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:1230429 original size:54 final size:54
Alignment explanation
Indices: 1230347--1230462 Score: 189
Period size: 54 Copynumber: 2.1 Consensus size: 54
1230337 CAATCCATAC
* *
1230347 AAATAAATTAATCTATATTTTAAAATAAATCAAT-TCATACTAATATATTATTTA
1 AAATAAATCAATCTATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTA
*
1230401 AAATAAATCAATTTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTA
1 AAATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTA
1230455 AAATAAAT
1 AAATAAAT
1230463 TATTTTAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 57 0.98
55 1 0.02
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (54 bp):
AAATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTA
Found at i:1230448 original size:22 final size:22
Alignment explanation
Indices: 1230399--1230447 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1230389 ATATATTATT
* **
1230399 TAAAATAAATCAATTTATATTT
1 TAAAATAAATCAATCTATATAA
1230421 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
1230444 TAAA
1 TAAA
1230448 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:1230471 original size:15 final size:15
Alignment explanation
Indices: 1230442--1230572 Score: 124
Period size: 15 Copynumber: 8.5 Consensus size: 15
1230432 AATCTATACT
1230442 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1230456 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1230471 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1230493 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1230508 AATAAATTA-TTTAT
1 AATAAATTATTTTAA
*
1230522 AATAAATTA-TTTAT
1 AATAAATTATTTTAA
*
1230536 AATATATTATTTTAA
1 AATAAATTATTTTAA
*
1230551 AATATATTATTTTAA
1 AATAAATTATTTTAA
1230566 AATAAAT
1 AATAAAT
1230573 AACCTTATTA
Statistics
Matches: 100, Mismatches: 8, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
14 35 0.35
15 48 0.48
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1230488 original size:69 final size:66
Alignment explanation
Indices: 1230322--1230533 Score: 183
Period size: 72 Copynumber: 3.1 Consensus size: 66
1230312 AATCAATCCA
*** * * *
1230322 TATTTTAAAATAAATCAATCCATACAAATAAATTAATCTATATTTTAAAATAAATCAATTCATAC
1 TATTTTAAAATAAATCAATCCATA-TTTTAAAATAATC-A-ATTATAAAATAAAT-TATT--TA-
* *
1230387 TAATATAT
59 AAATAAAT
** *
1230395 TA-TTTAAAATAAATCAATTTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAAT
1 TATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAAT-TATA-AAATAAATTATTTAAAAT
1230459 AAAT
63 AAAT
* ** * *
1230463 TATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTATAATAAA
1 TATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATTATAAAATAAATTATTTAAAATAAA
1230528 T
66 T
1230529 TATTT
1 TATTT
1230534 ATAATATATT
Statistics
Matches: 116, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
66 25 0.22
67 3 0.03
68 13 0.11
69 29 0.25
70 2 0.02
71 12 0.10
72 30 0.26
73 2 0.02
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (66 bp):
TATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATTATAAAATAAATTATTTAAAATAAA
T
Found at i:1230588 original size:43 final size:42
Alignment explanation
Indices: 1230489--1230599 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 42
1230479 AATCCATATT
* * * * *
1230489 TTATAATAATTTATTTTAAAATAAATTATTTATAATAAATTAT
1 TTAT-ATAAATTATTTTAAAATATATTATTTAAAATAAATAAC
*
1230532 TTATAATATATTATTTTAAAATATATTATTTTAAAATAAATAACC
1 TTAT-ATAAATTATTTTAAAATATATTA-TTTAAAATAAATAA-C
1230577 TTAT-TAAATTA-TTTAAAAT-TATT
1 TTATATAAATTATTTTAAAATATATT
1230600 TTAATAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.07
42 8 0.14
43 31 0.53
44 12 0.20
45 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (42 bp):
TTATATAAATTATTTTAAAATATATTATTTAAAATAAATAAC
Found at i:1234072 original size:22 final size:21
Alignment explanation
Indices: 1234043--1234092 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
1234033 TTGCCACTGG
* *
1234043 AAAAAAACCCCTTTTTTAAAT
1 AAAAAAACACATTTTTTAAAT
1234064 ACAAAAAACACATTTTTTAAAT
1 A-AAAAAACACATTTTTTAAAT
1234086 AAAAAAA
1 AAAAAAA
1234093 TTGTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAAACACATTTTTTAAAT
Found at i:1239402 original size:69 final size:69
Alignment explanation
Indices: 1239313--1239485 Score: 256
Period size: 69 Copynumber: 2.5 Consensus size: 69
1239303 AGAAAGGCAG
* * * *
1239313 TCCACAAGATTCTTTCAGTTTTCGCTTTAATACGTTGGCAACTTCAGATGCTTGTTTAGATTTTT
1 TCCACAAGCTTCTTTAAGTTTTCGGTTTAATACGTTGGCAACTTCAGATGCTTGTTTAGATTTCT
1239378 ATGA
66 ATGA
* * * * *
1239382 TCTACAAGCTTCTTTAAGTTTTTGGTTTAATAAGTTGGTAACTTCAGGTGCTTGTTTAGATTTCT
1 TCCACAAGCTTCTTTAAGTTTTCGGTTTAATACGTTGGCAACTTCAGATGCTTGTTTAGATTTCT
1239447 ATGA
66 ATGA
*
1239451 TCCACAAGCATCTTTAAGTTTTCGGTTTAATACGT
1 TCCACAAGCTTCTTTAAGTTTTCGGTTTAATACGT
1239486 AGGTAATTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 91 1.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.44
Consensus pattern (69 bp):
TCCACAAGCTTCTTTAAGTTTTCGGTTTAATACGTTGGCAACTTCAGATGCTTGTTTAGATTTCT
ATGA
Found at i:1241718 original size:21 final size:19
Alignment explanation
Indices: 1241694--1241746 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1241684 AATTTGATTT
1241694 TTATTAATTCCAATTCTTATA
1 TTATTAATT--AATTCTTATA
*
1241715 TTATTTA-TAATTCTTATA
1 TTATTAATTAATTCTTATA
*
1241733 TTATAAATTTAATT
1 TTATTAA-TTAATT
1241747 TATAATCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 15 0.56
20 6 0.22
21 6 0.22
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTAATTAATTCTTATA
Found at i:1244183 original size:37 final size:38
Alignment explanation
Indices: 1244104--1244211 Score: 120
Period size: 37 Copynumber: 3.0 Consensus size: 38
1244094 AAGTATTAAA
** *
1244104 ATGGTTTTC-AAGTTTGGTAACCA--ACTTTGAAAAA-
1 ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
1244138 ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
1 ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
* * *
1244176 A-GTTTTTCAAAGTTTGGTAGATATTT-GTTGAAAAAT
1 ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
1244212 GATAATGGGA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
34 9 0.14
35 12 0.19
36 9 0.14
37 33 0.52
38 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (38 bp):
ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
Found at i:1244684 original size:37 final size:37
Alignment explanation
Indices: 1244602--1244710 Score: 120
Period size: 37 Copynumber: 3.1 Consensus size: 37
1244592 TGAAAGTATT
** *
1244602 AAAATGGTTTTC-AAGTTTGGTAACCA--ACTTTGAA
1 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAA
1244636 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTG-A
1 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAA
* * *
1244672 AAAATAGTTTTTCAAAGTTTGGTAGATATTT-GTTGAA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATATTTCTTTGAA
1244709 AA
1 AA
1244711 TGATAATGGG
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
34 12 0.19
35 12 0.19
36 9 0.14
37 31 0.48
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (37 bp):
AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAA
Found at i:1245095 original size:500 final size:503
Alignment explanation
Indices: 1243845--1245332 Score: 2770
Period size: 500 Copynumber: 3.0 Consensus size: 503
1243835 CAAAACTGCT
1243845 AAAACTAAAAGTAAACAATTAAAAACTATAATTATTTCACC-AAAATGTGTAG---ATTAAAGTT
1 AAAACTAAAAGTAAACAATTAAAAACTATAATTATTTCACCAAAAATGTGTAGATTATTAAAGTT
1243906 TGATATCAATTCACATACAACTATTTCATATACAAG-AAAATAATACAGTATTCCATTATACATG
66 TGATATCAATTCACATACAACTATTTCATATACAAGAAAAATAATACAGTATTCCATTATACATG
1243970 -AAACTATG--TCTG-TTGATAATCGGTTTTTGCTCATTACAAAGTTACTAAGAAAAAGGATTAA
131 AAAACTATGTCTCTGTTTGATAATCGGTTTTTGCTCATTACAAAGTTACTAAGAAAAAGGATTAA
1244031 AAATGGATAAATGACT-AAATGAAACATTAATTCTAATATAGACTACTACTTTCTAATTGTTGAA
196 AAATGGATAAATGACTAAAATGAAACATTAATTCTAATATAGACTACTACTTTCTAATTGTTGAA
1244095 AGTATTAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
261 AGTATTAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
1244160 TATTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTTGTTGAAAAATGATAATGGGATAA
326 TATTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTTGTTG-AAAATGATAATGGGATAA
1244225 TCACAATTAATCCCTAGGCTTTAGTGTATTTACAAGATTAAGTCCTTAAGTTTCAACTATAAATA
390 TCACAATTAATCCCTAGGCTTTAGTGTATTTACAAGATTAAGTCCTTAAGTTTCAAC-ATAAATA
1244290 CCCTAGCTCATTTAGCTTCAAAACTATCCCAAAAATCATTTCTTTCTCCA
454 CCCTAGCTCATTTAGCTTCAAAACTATCCCAAAAATCATTTCTTTCTCCA
1244340 AAAACTAAAAGTAAACAATTAAAAACTATAATTATTTCACCAAAAATGTGTAGATTATTAAAGTT
1 AAAACTAAAAGTAAACAATTAAAAACTATAATTATTTCACCAAAAATGTGTAGATTATTAAAGTT
*
1244405 TGATATCAATTCACATACAACTATTTCATATACAAGAAAAATTATACAGTATTCCA-T-TACATG
66 TGATATCAATTCACATACAACTATTTCATATACAAGAAAAATAATACAGTATTCCATTATACATG
1244468 AAAACTATGTCTCTGTTTGATAATCGG-TTTTGCTCATTAC-AAGTTACTAAGAAAAAGGATTAA
131 AAAACTATGTCTCTGTTTGATAATCGGTTTTTGCTCATTACAAAGTTACTAAGAAAAAGGATTAA
1244531 AAATGGATAAATGACTAAAATGAAACATTAATTCTAATATAGACTACTACTTTCTAATTGTTGAA
196 AAATGGATAAATGACTAAAATGAAACATTAATTCTAATATAGACTACTACTTTCTAATTGTTGAA
1244596 AGTATTAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
261 AGTATTAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
1244661 TATTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTTGTTGAAAATGATAATGGGATAAT
326 TATTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTTGTTGAAAATGATAATGGGATAAT
1244726 CACAATTAATCCCTAGGCTTTAGTGTATTTACAAGATTAAGTCCTTAAGTTTCAACATAAATACC
391 CACAATTAATCCCTAGGCTTTAGTGTATTTACAAGATTAAGTCCTTAAGTTTCAACATAAATACC
1244791 CTAGCTCA-TTAGCTTCAAAACTATCCCAAAAATCA-TTCTTTCTCCA
456 CTAGCTCATTTAGCTTCAAAACTATCCCAAAAATCATTTCTTTCTCCA
1244837 AAAACT-AAAGTAAACAATTAAAAACTATAATTATTTCACCAAAAATGTGTAGATTATTAAAGTT
1 AAAACTAAAAGTAAACAATTAAAAACTATAATTATTTCACCAAAAATGTGTAGATTATTAAAGTT
1244901 TGATATCAATTCACATACAACTATTTCATATACAAGAAAAATAATACAGTATTCCATTATACATG
66 TGATATCAATTCACATACAACTATTTCATATACAAGAAAAATAATACAGTATTCCATTATACATG
1244966 AAAACTATGTCTCTGTTTGATAATCGGTTTTTGCTCATTACAAAGTTACTAAGAAAAAGGATTAA
131 AAAACTATGTCTCTGTTTGATAATCGGTTTTTGCTCATTACAAAGTTACTAAGAAAAAGGATTAA
1245031 AAATGGATAAATGACTAAAATGAAACATTAATTCTAATATAGACTACTACTTTCTAATTGTTGAA
196 AAATGGATAAATGACTAAAATGAAACATTAATTCTAATATAGACTACTACTTTCTAATTGTTGAA
1245096 AGTATTAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
261 AGTATTAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
*
1245161 TATTTCTTTGGAAAATAGTTTTTCAAAGTTTGGTAG--ATTTGTTGAAAATGATAATGGGATAAT
326 TATTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTTGTTGAAAATGATAATGGGATAAT
1245224 CACAATTAAT-CCTAGGCTTTAGTGTATTTACAAGATT-AGTCCTTAAGTTTCAAC-TATAATAC
391 CACAATTAATCCCTAGGCTTTAGTGTATTTACAAGATTAAGTCCTTAAGTTTCAACATA-AATAC
1245286 CCTAGCTCATTTAGCTTCAAAACTATCCC-AAAATCATTTCTTTCTCC
455 CCTAGCTCATTTAGCTTCAAAACTATCCCAAAAATCATTTCTTTCTCC
1245333 CAATACTAGA
Statistics
Matches: 973, Mismatches: 3, Indels: 32
0.97 0.00 0.03
Matches are distributed among these distances:
495 43 0.04
496 162 0.17
497 74 0.08
498 103 0.11
499 84 0.09
500 320 0.33
501 176 0.18
502 11 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (503 bp):
AAAACTAAAAGTAAACAATTAAAAACTATAATTATTTCACCAAAAATGTGTAGATTATTAAAGTT
TGATATCAATTCACATACAACTATTTCATATACAAGAAAAATAATACAGTATTCCATTATACATG
AAAACTATGTCTCTGTTTGATAATCGGTTTTTGCTCATTACAAAGTTACTAAGAAAAAGGATTAA
AAATGGATAAATGACTAAAATGAAACATTAATTCTAATATAGACTACTACTTTCTAATTGTTGAA
AGTATTAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
TATTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTTGTTGAAAATGATAATGGGATAAT
CACAATTAATCCCTAGGCTTTAGTGTATTTACAAGATTAAGTCCTTAAGTTTCAACATAAATACC
CTAGCTCATTTAGCTTCAAAACTATCCCAAAAATCATTTCTTTCTCCA
Found at i:1249632 original size:21 final size:21
Alignment explanation
Indices: 1249608--1249668 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1249598 AACTTTGAAA
1249608 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1249629 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1249643 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1249664 AAATG
1 AAATG
1249669 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1249692 original size:72 final size:72
Alignment explanation
Indices: 1249570--1249753 Score: 234
Period size: 72 Copynumber: 2.6 Consensus size: 72
1249560 TGGGAGATTG
****
1249570 TTGAAAATGGTTTTC-AAGTTTGGT-AA-CCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
1 TTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
1249632 TGTTTCT
66 TGTTTCT
*
1249639 TTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-AAAAATAGTTTTTCAAAGTTTGGTAA
1 TTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAAT-GGTTTTCAAAGTTTGGTAA
1249703 ATGTTTCT
65 ATGTTTCT
* * *
1249711 TTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGAAAA
1 TTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAA
1249754 TGATAATGGG
Statistics
Matches: 100, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
69 15 0.15
70 9 0.09
71 8 0.08
72 34 0.34
73 8 0.08
74 26 0.26
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (72 bp):
TTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
TGTTTCT
Found at i:1249699 original size:37 final size:37
Alignment explanation
Indices: 1249600--1249753 Score: 235
Period size: 37 Copynumber: 4.2 Consensus size: 37
1249590 TGGTAACCAA
1249600 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
1249637 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1249672 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
1249709 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1249746 -GTTGAAAA
1 CTTTGAAAA
1249754 TGATAATGGG
Statistics
Matches: 111, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
35 30 0.27
36 16 0.14
37 65 0.59
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1250554 original size:12 final size:12
Alignment explanation
Indices: 1250525--1250568 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1250515 ATAAACTATT
1250525 TATAAT-TAATA
1 TATAATATAATA
1250536 T-TAATATAATA
1 TATAATATAATA
1250547 TATAATATAACT-
1 TATAATATAA-TA
1250559 TATAA-ATAAT
1 TATAATATAAT
1250569 CTAGTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.17
11 11 0.37
12 13 0.43
13 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAATATAATA
Found at i:1250723 original size:18 final size:18
Alignment explanation
Indices: 1250702--1250745 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1250692 TTTTATATGA
*
1250702 ATATAATATATAGTTTAT
1 ATATAATATATAGTATAT
*
1250720 ATATACTATATAGTATAT
1 ATATAATATATAGTATAT
1250738 ATACTAAT
1 ATA-TAAT
1250746 GAACTAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATAATATATAGTATAT
Found at i:1250741 original size:16 final size:17
Alignment explanation
Indices: 1250702--1250884 Score: 76
Period size: 16 Copynumber: 11.5 Consensus size: 17
1250692 TTTTATATGA
*
1250702 ATATAATATATAGTTTAT
1 ATATACTATATAG-TTAT
1250720 ATATACTATATAG-TAT
1 ATATACTATATAGTTAT
*
1250736 ATATACTA-AT-G-AACT
1 ATATACTATATAGTTA-T
1250751 A-ATA--ATATAGTT-T
1 ATATACTATATAGTTAT
* *
1250764 ATATAC-AAATATTTAT
1 ATATACTATATAGTTAT
*
1250780 ATATACTA-AT-G-AACT
1 ATATACTATATAGTTA-T
* *
1250795 ATATAATATATATTTAT
1 ATATACTATATAGTTAT
**
1250812 ATATA-TA-ATGAACTAT
1 ATATACTATAT-AGTTAT
* *
1250828 ATATA--ATGTA-TAAT
1 ATATACTATATAGTTAT
*
1250842 ATATACGATATAGTCTAT
1 ATATACTATATAGT-TAT
**
1250860 ATATGTTATATAGTTAT
1 ATATACTATATAGTTAT
1250877 ATATACTA
1 ATATACTA
1250885 ATAAGATAAT
Statistics
Matches: 125, Mismatches: 22, Indels: 37
0.68 0.12 0.20
Matches are distributed among these distances:
12 1 0.01
13 4 0.03
14 17 0.14
15 22 0.18
16 38 0.30
17 17 0.14
18 26 0.21
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.43
Consensus pattern (17 bp):
ATATACTATATAGTTAT
Found at i:1250782 original size:44 final size:46
Alignment explanation
Indices: 1250705--1250814 Score: 145
Period size: 46 Copynumber: 2.4 Consensus size: 46
1250695 TATATGAATA
* *
1250705 TAAT-ATATAGTTTATATATACTATATAGTATATATACTAATGAAC
1 TAATAATATAGTTTATATACACAATATAGTATATATACTAATGAAC
*
1250750 TAATAATATAGTTTATATACA-AATAT-TTATATATACTAATGAAC
1 TAATAATATAGTTTATATACACAATATAGTATATATACTAATGAAC
*
1250794 TATATAATATATATTTATATA
1 TA-ATAATATA-GTTTATATA
1250815 TATAATGAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
44 19 0.33
45 16 0.28
46 23 0.40
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (46 bp):
TAATAATATAGTTTATATACACAATATAGTATATATACTAATGAAC
Found at i:1250832 original size:28 final size:30
Alignment explanation
Indices: 1250772--1250846 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 30
1250762 TTATATACAA
1250772 ATATTTATATATACTAATGAACTATATAATAT
1 ATATTTATATATA-TAATGAAC-ATATAATAT
1250804 ATATTTATATATATAATGAAC-TAT-ATAT
1 ATATTTATATATATAATGAACATATAATAT
*
1250832 A-ATGTATAATATATA
1 ATATTTAT-ATATATA
1250847 CGATATAGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
27 5 0.12
28 12 0.29
29 3 0.07
31 8 0.20
32 13 0.32
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (30 bp):
ATATTTATATATATAATGAACATATAATAT
Found at i:1250843 original size:14 final size:13
Alignment explanation
Indices: 1250794--1250846 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
1250784 ACTAATGAAC
*
1250794 TATATAATATATATT
1 TATAT-ATATA-ATG
1250809 TATATATATAATG
1 TATATATATAATG
*
1250822 AACTATATATAATG
1 TA-TATATATAATG
1250836 TATAATATATA
1 TAT-ATATATA
1250847 CGATATAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 4 0.12
14 24 0.73
15 5 0.15
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (13 bp):
TATATATATAATG
Found at i:1250861 original size:18 final size:17
Alignment explanation
Indices: 1250840--1250882 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1250830 ATAATGTATA
1250840 ATATATACGATATAGTCT
1 ATATATACGATATAGT-T
***
1250858 ATATATGTTATATAGTT
1 ATATATACGATATAGTT
1250875 ATATATAC
1 ATATATAC
1250883 TAATAAGATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (17 bp):
ATATATACGATATAGTT
Found at i:1250919 original size:2 final size:2
Alignment explanation
Indices: 1250912--1251011 Score: 59
Period size: 2 Copynumber: 51.0 Consensus size: 2
1250902 TTAGGGTTTT
* * * *
1250912 TA TA TA TA TC TA TG TA AA T- TA TA T- TA TA GTA TA T- TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
1250952 TA TA -A TA TA TA GTT TA TA TA TA TA -A TA TA TA TA TGA -A TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* *
1250993 AA CTA TA GA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA
1251012 GGTCATATGC
Statistics
Matches: 74, Mismatches: 14, Indels: 20
0.69 0.13 0.19
Matches are distributed among these distances:
1 6 0.08
2 63 0.85
3 5 0.07
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1250971 original size:18 final size:18
Alignment explanation
Indices: 1250950--1251286 Score: 84
Period size: 18 Copynumber: 19.6 Consensus size: 18
1250940 GTATATTATT
1250950 TATATAATATATAGTTTA
1 TATATAATATATAGTTTA
1250968 TATAT-ATA-ATA---TA
1 TATATAATATATAGTTTA
* * *
1250981 TATATGAATATAAACTATA
1 TATAT-AATATATAGTTTA
* * *
1251000 GATAT-ATATATAGGTCA
1 TATATAATATATAGTTTA
** * *
1251017 TATGCAAAATATAGTATA
1 TATATAATATATAGTTTA
*
1251035 AATATAA-ACTATAG--TA
1 TATATAATA-TATAGTTTA
* * *
1251051 TATATTATATATAGGTCA
1 TATATAATATATAGTTTA
*
1251069 TATGTAAACTATATAG--T-
1 TATAT-AA-TATATAGTTTA
*
1251086 T-TAT-ATATATAGTTCA
1 TATATAATATATAGTTTA
*
1251102 TATGTAA-ACTATAGTTTA
1 TATATAATA-TATAGTTTA
* *
1251120 TATATAGT-TCATA-TGTA
1 TATATAATAT-ATAGTTTA
* *
1251137 AATATTAA-CTATAGTTTA
1 TATA-TAATATATAGTTTA
* *
1251155 TATGTAA-ACTATAGTTTG
1 TATATAATA-TATAGTTTA
1251173 TATA-AACTATATA-TTTA
1 TATATAA-TATATAGTTTA
* * *
1251190 TGTA-AA-CTATAGTTTG
1 TATATAATATATAGTTTA
1251206 TATA-AACTATATAGTTTA
1 TATATAA-TATATAGTTTA
*
1251224 TATGTAA-ACTATAG-TTA
1 TATATAATA-TATAGTTTA
1251241 GTATATAA-ACTATAGTTTA
1 -TATATAATA-TATAGTTTA
* *
1251260 TATGTAA-ACTATAGTTCA
1 TATATAATA-TATAGTTTA
1251278 TATA-AATAT
1 TATATAATAT
1251287 CAACCTTAGT
Statistics
Matches: 234, Mismatches: 50, Indels: 71
0.66 0.14 0.20
Matches are distributed among these distances:
13 14 0.06
14 1 0.00
15 7 0.03
16 28 0.12
17 48 0.21
18 116 0.50
19 13 0.06
20 7 0.03
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (18 bp):
TATATAATATATAGTTTA
Found at i:1250973 original size:20 final size:20
Alignment explanation
Indices: 1250945--1250982 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1250935 TTATAGTATA
*
1250945 TTATTTATATAATATATAGT
1 TTATATATATAATATATAGT
1250965 TTATATATATAATATATA
1 TTATATATATAATATATA
1250983 TATGAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTATATATATAATATATAGT
Found at i:1250984 original size:15 final size:15
Alignment explanation
Indices: 1250913--1251011 Score: 55
Period size: 15 Copynumber: 6.6 Consensus size: 15
1250903 TAGGGTTTTT
* *
1250913 ATATATATCTATGTA
1 ATATATATATATATA
1250928 A-AT-TATAT-TATA
1 ATATATATATATATA
* *
1250940 GTATATTATTTATATA
1 ATATA-TATATATATA
*
1250956 ATATATAGTTTATAT-
1 ATATATA-TATATATA
1250971 ATATAATATATATATGA
1 ATAT-ATATATATAT-A
* *
1250988 ATATAAACTATAGAT-
1 ATATATA-TATATATA
1251003 ATATATATA
1 ATATATATA
1251012 GGTCATATGC
Statistics
Matches: 66, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
12 3 0.05
13 6 0.09
14 4 0.06
15 23 0.35
16 20 0.30
17 10 0.15
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:1251034 original size:29 final size:29
Alignment explanation
Indices: 1250991--1251138 Score: 112
Period size: 29 Copynumber: 5.1 Consensus size: 29
1250981 TATATGAATA
*
1250991 TAAACTATAGATATATATATAGGTCATATG
1 TAAAATATAG-TATATATATAGGTCATATG
* * **
1251021 CAAAATATAGTATAAATATA-AAC-TATAG
1 TAAAATATAGTATATATATAGGTCATAT-G
1251049 T---ATATA-T-TATATATAGGTCATATG
1 TAAAATATAGTATATATATAGGTCATATG
*
1251073 TAAACTATATAGTTTATATATATAGTTCATATG
1 TAAA--ATATAG--TATATATATAGGTCATATG
* * *
1251106 TAAACTATAGTTTATATATAGTTCATATG
1 TAAAATATAGTATATATATAGGTCATATG
1251135 TAAA
1 TAAA
1251139 TATTAACTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
23 7 0.07
24 4 0.04
25 8 0.09
27 3 0.03
28 2 0.02
29 36 0.38
30 8 0.09
31 5 0.05
32 1 0.01
33 20 0.21
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (29 bp):
TAAAATATAGTATATATATAGGTCATATG
Found at i:1251072 original size:52 final size:47
Alignment explanation
Indices: 1250978--1251083 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 47
1250968 TATATATAAT
*
1250978 ATATATATGAATATAAACTATAGATATATATATAGGTCATATGCAAA
1 ATATATATAAATATAAACTATAGATATATATATAGGTCATATGCAAA
*
1251025 ATATAGTATAAATATAAACTATAGTATATATTATATATAGGTCATATGTAAA
1 ATATA-TATAAATATAAACTATAG---ATA-TATATATAGGTCATATGCAAA
*
1251077 CTATATA
1 ATATATA
1251084 GTTTATATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
47 5 0.10
48 17 0.33
51 5 0.10
52 24 0.47
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (47 bp):
ATATATATAAATATAAACTATAGATATATATATAGGTCATATGCAAA
Found at i:1251103 original size:33 final size:33
Alignment explanation
Indices: 1251039--1251138 Score: 129
Period size: 33 Copynumber: 3.1 Consensus size: 33
1251029 AGTATAAATA
* *
1251039 TAAACTATAGTA-TATATTATATATAGGTCATATG
1 TAAACTATA-TAGTTTA-TATATATAGTTCATATG
1251073 TAAACTATATAGTTTATATATATAGTTCATATG
1 TAAACTATATAGTTTATATATATAGTTCATATG
1251106 TAAAC--TATAG-TT-TATATATAGTTCATATG
1 TAAACTATATAGTTTATATATATAGTTCATATG
1251135 TAAA
1 TAAA
1251139 TATTAACTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
29 21 0.33
30 2 0.03
31 5 0.08
33 23 0.37
34 12 0.19
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (33 bp):
TAAACTATATAGTTTATATATATAGTTCATATG
Found at i:1251183 original size:69 final size:69
Alignment explanation
Indices: 1251006--1251274 Score: 198
Period size: 69 Copynumber: 3.9 Consensus size: 69
1250996 TATAGATATA
* * * * * * *
1251006 TATATAGGTCATATGCAAAATATAGTATAAATATAAACTATAGTATATATTATA-TATAGGTCAT
1 TATATAGTTTATATGTAAACTATAGT-TATATATAAACTATAGTTTATA-TAAACTATA-GT-AT
* *
1251070 ATGTAAAC
62 GTATAAAC
* * *
1251078 TATATAGTTTATA--T--A-TATAGTTCATATGTAAACTATAGTTTATATATAGT-TCA-TATGT
1 TATATAGTTTATATGTAAACTATAGTT-ATATATAAACTATAGTTTATATAAACTAT-AGTATGT
*
1251136 A-AATAT
64 ATAA-AC
* * * *
1251142 TAACTATAGTTTATATGTAAACTATAGTT-TGTATAAACTATATATTTATGTAAACTATAGTTTG
1 T-A-TATAGTTTATATGTAAACTATAGTTATATATAAACTATA-GTTTATATAAACTATAGTATG
1251206 TATAAAC
63 TATAAAC
1251213 TATATAGTTTATATGTAAACTATAGTTAGTATATAAACTATAGTTTATATGTAAACTATAGT
1 TATATAGTTTATATGTAAACTATAGTTA-TATATAAACTATAGTTTATA--TAAACTATAGT
1251275 TCATATAAAT
Statistics
Matches: 158, Mismatches: 20, Indels: 38
0.73 0.09 0.18
Matches are distributed among these distances:
63 2 0.01
64 5 0.03
65 2 0.01
66 17 0.11
67 26 0.16
68 2 0.01
69 36 0.23
70 17 0.11
71 27 0.17
72 24 0.15
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.42
Consensus pattern (69 bp):
TATATAGTTTATATGTAAACTATAGTTATATATAAACTATAGTTTATATAAACTATAGTATGTAT
AAAC
Found at i:1251235 original size:36 final size:36
Alignment explanation
Indices: 1251146--1251275 Score: 198
Period size: 36 Copynumber: 3.7 Consensus size: 36
1251136 AAATATTAAC
1251146 TATAGTTTATATGTAAACTATAGTTTGTATAAACTA
1 TATAGTTTATATGTAAACTATAGTTTGTATAAACTA
1251182 TATA--TT-TATGTAAACTATAGTTTGTATAAACTA
1 TATAGTTTATATGTAAACTATAGTTTGTATAAACTA
*
1251215 TATAGTTTATATGTAAACTATAGTTAGTATATAA--A
1 TATAGTTTATATGTAAACTATAGTTTGTATA-AACTA
1251250 CTATAGTTTATATGTAAACTATAGTT
1 -TATAGTTTATATGTAAACTATAGTT
1251276 CATATAAATA
Statistics
Matches: 88, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
33 31 0.35
34 2 0.02
35 3 0.03
36 50 0.57
37 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (36 bp):
TATAGTTTATATGTAAACTATAGTTTGTATAAACTA
Found at i:1251333 original size:18 final size:18
Alignment explanation
Indices: 1251036--1251336 Score: 129
Period size: 18 Copynumber: 16.9 Consensus size: 18
1251026 TATAGTATAA
1251036 ATATAAACTATAG-T-AT
1 ATATAAACTATAGTTCAT
* *
1251052 ATATTATA-TATAGGTCAT
1 ATA-TAAACTATAGTTCAT
*
1251070 ATGTAAACTATATAGTT--T
1 ATATAAAC--TATAGTTCAT
1251088 ATAT--A-TATAGTTCAT
1 ATATAAACTATAGTTCAT
* *
1251103 ATGTAAACTATAGTTTAT
1 ATATAAACTATAGTTCAT
** *
1251121 ATAT-AGTTCATA-TGT-AA
1 ATATAAACT-ATAGT-TCAT
* *
1251138 ATATTAACTATAGTTTAT
1 ATATAAACTATAGTTCAT
*
1251156 ATGTAAACTATAGTT--T
1 ATATAAACTATAGTTCAT
* *
1251172 GTATAAACTATA-TAT-TT
1 ATATAAACTATAGT-TCAT
*
1251189 ATGTAAACTATAGTT--T
1 ATATAAACTATAGTTCAT
* *
1251205 GTATAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTCAT
*
1251225 ATGTAAACTATAGTT-AGT
1 ATATAAACTATAGTTCA-T
*
1251243 ATATAAACTATAGTTTAT
1 ATATAAACTATAGTTCAT
*
1251261 ATGTAAACTATAGTTCAT
1 ATATAAACTATAGTTCAT
1251279 ATAAATATCAACCT-TAGTATACAT
1 AT--ATA--AA-CTATAGT-T-CAT
*
1251303 ATATATA-TATAGTTCAT
1 ATATAAACTATAGTTCAT
*
1251320 ATGTAAACTATAGTTCA
1 ATATAAACTATAGTTCA
1251337 CATAGTATAT
Statistics
Matches: 220, Mismatches: 31, Indels: 66
0.69 0.10 0.21
Matches are distributed among these distances:
13 7 0.03
15 5 0.02
16 28 0.13
17 41 0.19
18 101 0.46
19 5 0.02
20 16 0.07
22 9 0.04
23 3 0.01
24 5 0.02
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (18 bp):
ATATAAACTATAGTTCAT
Found at i:1251417 original size:6 final size:6
Alignment explanation
Indices: 1251408--1251454 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
1251398 AGTAGTAGTT
1251408 ATATAA ATATAA ATATAA ATAT-A A-ATAA ATATAA ATA-AA A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1251452 ATA
1 ATA
1251455 AACCTAAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.08
5 10 0.27
6 24 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
ATATAA
Found at i:1251437 original size:10 final size:10
Alignment explanation
Indices: 1251410--1251456 Score: 67
Period size: 10 Copynumber: 4.5 Consensus size: 10
1251400 TAGTAGTTAT
1251410 ATAAATATAAA
1 ATAAATAT-AA
1251421 TATAAATATAA
1 -ATAAATATAA
1251432 ATAAATATAA
1 ATAAATATAA
*
1251442 ATAAAAATAA
1 ATAAATATAA
1251452 ATAAA
1 ATAAA
1251457 CCTAAACCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
10 24 0.71
11 2 0.06
12 8 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAATATAA
Found at i:1251462 original size:16 final size:16
Alignment explanation
Indices: 1251410--1251454 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1251400 TAGTAGTTAT
*
1251410 ATAAATATAAATATAA
1 ATAAAAATAAATATAA
*
1251426 ATATAAATAAATATAA
1 ATAAAAATAAATATAA
1251442 ATAAAAATAAATA
1 ATAAAAATAAATA
1251455 AACCTAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAAATATAA
Found at i:1251560 original size:23 final size:21
Alignment explanation
Indices: 1251492--1251600 Score: 64
Period size: 21 Copynumber: 5.0 Consensus size: 21
1251482 AAATAAACCA
*
1251492 TAATATA-TATA-AACTATATAG
1 TAATATATTATATAA-T-TATAC
* *
1251513 TAATAAATTATATATTTATAC
1 TAATATATTATATAATTATAC
1251534 -AATATATTATTATAATTATAC
1 TAATATATTA-TATAATTATAC
*
1251555 ATAATATA-TAAATAAATTGTATAGC
1 -TAATATATTATAT-AA-T-TATA-C
*
1251580 TTATATAATTATATAATTATA
1 TAATAT-ATTATATAATTATA
1251601 AATAAACTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
20 8 0.12
21 22 0.32
22 9 0.13
23 12 0.17
24 10 0.14
25 4 0.06
26 4 0.06
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (21 bp):
TAATATATTATATAATTATAC
Found at i:1251700 original size:2 final size:2
Alignment explanation
Indices: 1251693--1251780 Score: 67
Period size: 2 Copynumber: 44.0 Consensus size: 2
1251683 CTTTATGCTA
* * *
1251693 AT AT AT AT AA ACT AT AT AGT TT AT AT AT A- AT AC AT AT AT -T AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* *
1251735 AT AT AA ACT AT AT AGT TT AT AT AT -T AT -T AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1251777 AT AT
1 AT AT
1251781 TAGTTGTTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
1 4 0.06
2 60 0.88
3 4 0.06
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1251719 original size:18 final size:18
Alignment explanation
Indices: 1251696--1251757 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 18
1251686 TATGCTAATA
1251696 TATATAAACTATATAGTT
1 TATATAAACTATATAGTT
1251714 TATATATAA-TACATATA-TT
1 TATATA-AACT--ATATAGTT
1251733 ATATATAAACTATATAGTT
1 -TATATAAACTATATAGTT
1251752 TATATA
1 TATATA
1251758 TTATTATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 18 0.47
19 8 0.21
20 12 0.32
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (18 bp):
TATATAAACTATATAGTT
Found at i:1251719 original size:20 final size:20
Alignment explanation
Indices: 1251694--1251758 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
1251684 TTTATGCTAA
1251694 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
1251714 TATATATAATAC-ATATA--T
1 TATATATAA-ACTATATAGTT
1251732 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
1251752 TATATAT
1 TATATAT
1251759 TATTATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
17 2 0.05
18 15 0.37
20 22 0.54
21 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATAAACTATATAGTT
Found at i:1251744 original size:38 final size:40
Alignment explanation
Indices: 1251693--1251779 Score: 142
Period size: 38 Copynumber: 2.2 Consensus size: 40
1251683 CTTTATGCTA
1251693 ATATATATAAACTATATAGTTTATATA-TAATACATATAT
1 ATATATATAAACTATATAGTTTATATATTAATACATATAT
* *
1251732 -TATATATAAACTATATAGTTTATATATTATTATATATAT
1 ATATATATAAACTATATAGTTTATATATTAATACATATAT
1251771 ATATATATA
1 ATATATATA
1251780 TTAGTTGTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 26 0.59
39 10 0.23
40 8 0.18
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (40 bp):
ATATATATAAACTATATAGTTTATATATTAATACATATAT
Found at i:1251746 original size:27 final size:27
Alignment explanation
Indices: 1251715--1251775 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
1251705 TATATAGTTT
1251715 ATATATAATACATATATTA-TATATAA
1 ATATATAATACATATATTATTATATAA
* ** *
1251741 ACTATATAGTTTATATATTATTATATAT
1 A-TATATAATACATATATTATTATATAA
1251769 ATATATA
1 ATATATA
1251776 TATATTAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.72
28 7 0.24
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATATAATACATATATTATTATATAA
Found at i:1252256 original size:202 final size:205
Alignment explanation
Indices: 1251813--1252585 Score: 922
Period size: 202 Copynumber: 3.8 Consensus size: 205
1251803 TTATTACTTA
* * *
1251813 TTTCTATTTATT-AATTGGTCCATAACTTTTTAAATGAGTATAATTTAGTACATTTTTGTATTAA
1 TTTCTATTT-TTAAATTGG-CC-CAAC-TTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAA
1251877 -TTCAACCT--CAATTTAAAATTATTTCGA-TTGAT-CC-C-TTTTGTGTTGTTTAATATATTTA
62 TTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATTTTGTGTTGTTTAATATATTTA
* * *
1251935 AATTTTATTTATAATTACATATTTGTTCAATTTAGTCCTCC-AGTTTTA-TTGCA-CTGAAATTG
127 AATTTTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTA
1251997 ACCATACTTATTAC
192 ACCATACTTATTAC
* ** *
1252011 TTATTTATTTTTAAATTGGCATAACTTTTAAATGGGTATAATTTAGTA-TTTTTTTTATTAATTT
1 TT-TCTATTTTTAAATTGGCCCAACTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTT
* *
1252075 CAACCTCAAAATTTAAAATTATTTTGATTTGA-CCC-C-TTTTGTGTTGTTTAATATATTTAAAT
65 CAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATTTTGTGTTGTTTAATATATTTAAA-
* *
1252137 TTTTATTTGTAATTTCATATTTGTTTAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTAAC
129 TTTTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTAAC
1252202 ACATACTTATTAC
194 -CATACTTATTAC
*
1252215 TTTCTA-TTTTAAATTGACCCAACTTTTAAATGGGTATAATTTAGTA---TTTTGTATTAATTTC
1 TTTCTATTTTTAAATTGGCCCAACTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTC
* * **
1252276 AACATCACAATTTAAAATTATTTCGATTGGATCCCTCATCAATGTGTTGTTTAAT-TATTTAAAT
66 AACCTCACAATTTAAAATTATTTCGATTTGATCCCTCAT-TTTGTGTTGTTTAATATATTTAAAT
* * * *
1252340 TTTATTTGTAATTTAATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGATC
130 TTTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATT-AAC
* *
1252405 CTTACTTATTTC
194 CATACTTATTAC
*
1252417 TTAATTCTATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTAT
1 -T--TTCTA-TTTTTAAATTGGCCC--AAC-TTTTAAATGGGTATAATTTAGTACTTTTTTGTAT
* * * * * *
1252482 TGATTTCAACCTCACAATTTAAAATTTTTTCAATTTGATCTCTCATCAATGTGTGTTGTTTAATT
59 TAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATC-C-C-TCATTTTGTGTTGTTTAATA
* *
1252547 TATTT-AATTTTTTTTATAATTTTATATTTGTTCAATTTA
121 TATTTAAATTTTATTTATAATTTCATATTTGTTCAATTTA
1252586 ATTCTTAAAT
Statistics
Matches: 501, Mismatches: 42, Indels: 47
0.85 0.07 0.08
Matches are distributed among these distances:
195 11 0.02
196 30 0.06
197 4 0.01
198 22 0.04
199 44 0.09
200 77 0.15
201 9 0.02
202 112 0.22
203 25 0.05
204 27 0.05
205 5 0.01
207 12 0.02
209 3 0.01
210 23 0.05
213 43 0.09
214 1 0.00
215 45 0.09
216 8 0.02
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.51
Consensus pattern (205 bp):
TTTCTATTTTTAAATTGGCCCAACTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTC
AACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATTTTGTGTTGTTTAATATATTTAAATT
TTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTAACCA
TACTTATTAC
Found at i:1257789 original size:2 final size:2
Alignment explanation
Indices: 1257782--1257813 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1257772 TATCTACACT
*
1257782 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1257814 AAAAGTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1259572 original size:7 final size:7
Alignment explanation
Indices: 1259560--1259590 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1259550 AAATGTTGAA
1259560 ATATTTT
1 ATATTTT
1259567 ATATTTT
1 ATATTTT
1259574 ATATTTT
1 ATATTTT
1259581 ATATTTT
1 ATATTTT
1259588 ATA
1 ATA
1259591 GTGAAATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
ATATTTT
Found at i:1261443 original size:21 final size:21
Alignment explanation
Indices: 1261418--1261554 Score: 138
Period size: 21 Copynumber: 6.6 Consensus size: 21
1261408 GTTTCCAGAT
* *
1261418 TCGCAACGCGAACTTCGATTA
1 TCGCAATGCGAACTTCGACTA
*
1261439 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1261460 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
1261480 TCGCAATGCGGTA-GTCGACTA
1 TCGCAATGC-GAACTTCGACTA
* *
1261501 TCGCAAAGCGAACTTAGACTA
1 TCGCAATGCGAACTTCGACTA
*
1261522 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
1261543 TCGCAATGCGAA
1 TCGCAATGCGAA
1261555 TATGTAAATC
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
20 16 0.16
21 81 0.84
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1261514 original size:83 final size:83
Alignment explanation
Indices: 1261418--1261580 Score: 290
Period size: 83 Copynumber: 2.0 Consensus size: 83
1261408 GTTTCCAGAT
* * *
1261418 TCGCAACGCGAACTTCGATTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAAAGCGAACTTAGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
*
1261483 CAATGCGGTAGTCGACTA
66 CAATGCGATAGTCGACTA
1261501 TCGCAAAGCGAACTTAGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAAAGCGAACTTAGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1261566 CAATGCGATAGTCGA
66 CAATGCGATAGTCGA
1261581 AGTTCACATT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (83 bp):
TCGCAAAGCGAACTTAGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
CAATGCGATAGTCGACTA
Found at i:1261566 original size:62 final size:61
Alignment explanation
Indices: 1261438--1261573 Score: 152
Period size: 62 Copynumber: 2.2 Consensus size: 61
1261428 AACTTCGATT
* * * *
1261438 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGGTAGTCGACT
1 ATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGGAAATCGCAATGCGATAGTC-ACA
* *
1261500 ATCGCAAAGCGAACTTAGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT-A-A
1 ATCGCAATGCGAACTTAGACTATCGCAATGCGAA-TATGGA-AATCGCAATGCG-ATA-GTCACA
1261562 ATCGCAATGCGA
1 ATCGCAATGCGA
1261574 TAGTCGAAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
62 46 0.73
63 13 0.21
64 2 0.03
65 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (61 bp):
ATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGGAAATCGCAATGCGATAGTCACA
Found at i:1261595 original size:21 final size:21
Alignment explanation
Indices: 1261569--1261620 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1261559 TAAATCGCAA
1261569 TGCGATAGTCGAAGTTCACAT
1 TGCGATAGTCGAAGTTCACAT
* * * *
1261590 TGCGATAATCTAAGTTCGCGT
1 TGCGATAGTCGAAGTTCACAT
1261611 TGCGATAGTC
1 TGCGATAGTC
1261621 CAAAATCGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCACAT
Found at i:1261724 original size:6 final size:6
Alignment explanation
Indices: 1261713--1261749 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1261703 GACACGTATT
*
1261713 ACCACG ACCACG TCCACG ACCACG A-CACG A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1261750 CGAGATGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:1261759 original size:5 final size:5
Alignment explanation
Indices: 1261750--1261800 Score: 77
Period size: 5 Copynumber: 10.4 Consensus size: 5
1261740 CGACACGACC
* *
1261750 CGAGA TGAGA TGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA
1261799 CG
1 CG
1261801 GCGACGGCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
4 4 0.09
5 40 0.91
ACGTcount: A:0.37, C:0.18, G:0.41, T:0.04
Consensus pattern (5 bp):
CGAGA
Found at i:1262455 original size:42 final size:42
Alignment explanation
Indices: 1262396--1263414 Score: 1057
Period size: 42 Copynumber: 24.5 Consensus size: 42
1262386 TGCGATTTTG
*
1262396 GACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1262438 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1262480 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1262522 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1262564 GACTATCGCAACGAATTTGGGATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1262606 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
1262648 GACTATCGCAACGAACTTGGACT--ATCGCAATGCGAA-TAT-
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACT-TC
* * **
1262687 GTA-AATCGCAATGCG-A--T--AGTCAAA--G-TTCGCG---TTGC
1 G-ACTATCGCAA--CGAATTTGGAAT-AAATCGCAACGCGAACTT-C
* * * * *** ** *
1262722 GAATCTGGAAACTG-ATTTGCG-ATACCGGAGATCGCGTTGCGATTTTG
1 GACTATCGCAAC-GAATTTG-GAATA----A-ATCGCAACGCGAACTTC
* * *
1262769 GACTATCGCAACGAATTTGGAATAAATCGTAACGCTAACTTT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1262811 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1262853 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1262895 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1262937 GACTATCGCAACGAATTTGGGATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1262979 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
1263021 GACTATCGCAACGAACTTGGACT--ATCGCAATGCGAA-TAT-
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACT-TC
* * **
1263060 GTA-AATCGCAATGCG-A--T--AGTCAAA--G-TTCGCG---TTGC
1 G-ACTATCGCAA--CGAATTTGGAAT-AAATCGCAACGCGAACTT-C
* * * * *** ** *
1263095 GAATCTGGAAACTG-ATTTGCG-ATACCGGAGATCGCGTTGCGATTTTG
1 GACTATCGCAAC-GAATTTG-GAATA----A-ATCGCAACGCGAACTTC
* * *
1263142 GACTATCGCAACGAATTTGGAATAAATCGTAACGCTAACTTT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1263184 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1263226 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1263268 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1263310 GACTATCGCAACGAATTTGGGATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1263352 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1263394 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
1263415 CTATCGCAAT
Statistics
Matches: 829, Mismatches: 90, Indels: 116
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.00
34 8 0.01
35 10 0.01
36 12 0.01
37 4 0.00
38 4 0.00
39 20 0.02
40 30 0.04
41 6 0.01
42 679 0.82
43 2 0.00
44 2 0.00
45 8 0.01
46 4 0.00
47 32 0.04
48 4 0.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1263068 original size:373 final size:373
Alignment explanation
Indices: 1262383--1263507 Score: 2178
Period size: 373 Copynumber: 3.0 Consensus size: 373
1262373 GAAATACCGT
* *
1262383 CGTTGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTCGACTATCGCA
1 CGTTGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCTAACTTTGACTATCGCA
* *
1262448 ACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAAT
66 ACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAATCGCAAC
* *
1262513 GCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGA
131 GCGAACTTCGACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGA
1262578 ATTTGGGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGA
196 ATTTGGGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGA
1262643 ACTTCGACTATCGCAACGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
261 ACTTCGACTATCGCAACGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1262708 AAAGTTCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCG
326 AAAGTTCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCG
1262756 CGTTGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCTAACTTTGACTATCGCA
1 CGTTGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCTAACTTTGACTATCGCA
*
1262821 ACGAATTTGGAATAAATCACAACGCGAACTTCGACTATCACAACGAACTTGGAATAAATCGCAAC
66 ACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAATCGCAAC
1262886 GCGAACTTCGACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGA
131 GCGAACTTCGACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGA
1262951 ATTTGGGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGA
196 ATTTGGGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGA
1263016 ACTTCGACTATCGCAACGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
261 ACTTCGACTATCGCAACGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1263081 AAAGTTCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCG
326 AAAGTTCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCG
1263129 CGTTGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCTAACTTTGACTATCGCA
1 CGTTGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCTAACTTTGACTATCGCA
1263194 ACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAATCGCAAC
66 ACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAATCGCAAC
1263259 GCGAACTTCGACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGA
131 GCGAACTTCGACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGA
1263324 ATTTGGGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGA
196 ATTTGGGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGA
1263389 ACTTCGACTATCGCAACGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
261 ACTTCGACTATCGCAACGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
*
1263454 GAAGTTCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCG
326 AAAGTTCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCG
1263502 CGTTGC
1 CGTTGC
1263508 AAATTATCGA
Statistics
Matches: 743, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
373 743 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (373 bp):
CGTTGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCTAACTTTGACTATCGCA
ACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAATCGCAAC
GCGAACTTCGACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGA
ATTTGGGATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGA
ACTTCGACTATCGCAACGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
AAAGTTCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCG
Found at i:1263847 original size:7 final size:7
Alignment explanation
Indices: 1263837--1263863 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1263827 TATATATTAT
1263837 ATATTTA
1 ATATTTA
1263844 ATATTTA
1 ATATTTA
1263851 ATATTTA
1 ATATTTA
1263858 ATATTT
1 ATATTT
1263864 TTTACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:1268575 original size:6 final size:7
Alignment explanation
Indices: 1268554--1268578 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1268544 AATTTCCATC
1268554 AAATAAA
1 AAATAAA
1268561 AAATAAA
1 AAATAAA
1268568 AAATAAA
1 AAATAAA
1268575 AAAT
1 AAAT
1268579 GACAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Done.