Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 204 of 207
Found at i:61471880 original size:21 final size:21
Alignment explanation
Indices: 61471853--61471921 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
61471843 GCTTCTTTCA
*
61471853 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
61471874 TTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
61471895 CTGCTTCCCTCGTTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
61471916 CTGCTT
1 CTGCTT
61471922 TAAGTTGTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.01, C:0.41, G:0.20, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:61477442 original size:9 final size:9
Alignment explanation
Indices: 61477425--61477649 Score: 134
Period size: 9 Copynumber: 25.8 Consensus size: 9
61477415 TATGTATTAA
*
61477425 GTAAATTAT
1 GTAAGTTAT
61477434 GTAAGTTAT
1 GTAAGTTAT
*
61477443 GT-A-TTAA
1 GTAAGTTAT
*
61477450 GTAAGCTAT
1 GTAAGTTAT
* *
61477459 TTAAGTTGT
1 GTAAGTTAT
61477468 GT-A-TTAT
1 GTAAGTTAT
61477475 GTAAGTTAT
1 GTAAGTTAT
** *
61477484 CAAAGTAAT
1 GTAAGTTAT
*
61477493 GTATGTTAT
1 GTAAGTTAT
61477502 GTAAG-T-T
1 GTAAGTTAT
61477509 GTAAGTTAT
1 GTAAGTTAT
*
61477518 -TATGTATTAT
1 GTAAG--TTAT
*
61477528 GTAGGTTAT
1 GTAAGTTAT
61477537 GTAAGTTAT
1 GTAAGTTAT
*
61477546 GTAAGTTTT
1 GTAAGTTAT
61477555 GT-A-TTAT
1 GTAAGTTAT
**
61477562 GTAAGTCGT
1 GTAAGTTAT
61477571 GTAAGTTAT
1 GTAAGTTAT
* *
61477580 GTATGCTAT
1 GTAAGTTAT
*
61477589 GTAAGTAAT
1 GTAAGTTAT
61477598 GT-A-TTAT
1 GTAAGTTAT
61477605 GTAAGTTTAT
1 GTAAG-TTAT
*
61477615 ATAAGTTAATAT
1 GTAAG-T--TAT
*
61477627 GTAAGTAAT
1 GTAAGTTAT
61477636 GT-A-TTAT
1 GTAAGTTAT
61477643 GTAAGTT
1 GTAAGTT
61477650 TATATAAAAA
Statistics
Matches: 162, Mismatches: 36, Indels: 36
0.69 0.15 0.15
Matches are distributed among these distances:
7 31 0.19
8 15 0.09
9 91 0.56
10 14 0.09
11 4 0.02
12 7 0.04
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:61477445 original size:25 final size:25
Alignment explanation
Indices: 61477414--61477716 Score: 127
Period size: 25 Copynumber: 11.7 Consensus size: 25
61477404 TGATATATAT
*
61477414 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
61477439 TTATGTATTAAGTAAGCTATTTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* * **
61477464 TTGTGTATTATGTAAGTTATCAAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
61477489 TAATGTATGTTATGTAAG-T-TGTAAG
1 TTATGTA--TTAAGTAAGTTATGTAAG
* *
61477514 TTATTATGTATTATGTAGGTTATGTAAG
1 ---TTATGTATTAAGTAAGTTATGTAAG
**
61477542 TTATGTAAGTTTTGT-A-TTATGTAAG
1 TTATGT-A-TTAAGTAAGTTATGTAAG
** * * *
61477567 TCGTGTAAGTTATGTATGCTATGTAAG
1 TTATGT-A-TTAAGTAAGTTATGTAAG
* * *
61477594 TAATGTATTATGTAAGTTTATATAAG
1 TTATGTATTAAGTAAG-TTATGTAAG
*
61477620 TTA-ATATGTAAGTAATGTATTATGTAAG
1 TTATGTAT-TAAGTAA-G--TTATGTAAG
* * * *
61477648 TT-TATA-TAA-AAATTTTATATAAG
1 TTATGTATTAAGTAA-GTTATGTAAG
* *
61477671 TCATGTATTATGTAAGTTAACATGTAAG
1 TTATGTATTAAGTAAGTT---ATGTAAG
*
61477699 TTATGTATTATGTAAGTT
1 TTATGTATTAAGTAAGTT
61477717 TAATAACTGT
Statistics
Matches: 215, Mismatches: 41, Indels: 41
0.72 0.14 0.14
Matches are distributed among these distances:
23 9 0.04
24 3 0.01
25 96 0.45
26 31 0.14
27 28 0.13
28 48 0.22
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:61477448 original size:16 final size:16
Alignment explanation
Indices: 61477429--61477716 Score: 74
Period size: 16 Copynumber: 16.8 Consensus size: 16
61477419 TATTAAGTAA
61477429 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
* * *
61477445 ATTAAGTAAGCTATTT
1 ATTATGTAAGTTATGT
*
61477461 AAGTTGTGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
** *
61477477 AAGTTATCAAAGTAATGT
1 -A-TTATGTAAGTTATGT
*
61477495 ATGTTATGTAAGTTGTAAGTT
1 A--TTATGTAAG-T-TATG-T
61477516 ATTATGT-A-TTATGT
1 ATTATGTAAGTTATGT
61477530 AGGTTATGTAAGTTATGT
1 A--TTATGTAAGTTATGT
*
61477548 AAGTTTTGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
**
61477564 AAGTCGTGTAAGTTATGT
1 -A-TTATGTAAGTTATGT
*
61477582 ATGCTATGTAAGTAATGT
1 AT--TATGTAAGTTATGT
61477600 ATTATGTAAGTTTATATAAGTT
1 ATTATGTAAG--T-TAT--G-T
* *
61477622 AATATGTAAGTAATGT
1 ATTATGTAAGTTATGT
*
61477638 ATTATGTAAGTTTATAT
1 ATTATGTAAG-TTATGT
* *
61477655 AAAAATTTTATATAAGTCATGT
1 ----A--TTATGTAAGTTATGT
61477677 ATTATGTAAGTTA---
1 ATTATGTAAGTTATGT
*
61477690 A-CATGTAAGTTATGT
1 ATTATGTAAGTTATGT
61477705 ATTATGTAAGTT
1 ATTATGTAAGTT
61477717 TAATAACTGT
Statistics
Matches: 203, Mismatches: 35, Indels: 68
0.66 0.11 0.22
Matches are distributed among these distances:
12 10 0.05
13 1 0.00
14 2 0.01
15 4 0.02
16 81 0.40
17 13 0.06
18 51 0.25
19 12 0.06
20 3 0.01
21 4 0.02
22 14 0.07
23 8 0.04
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.45
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:61477551 original size:87 final size:87
Alignment explanation
Indices: 61477429--61477648 Score: 217
Period size: 87 Copynumber: 2.6 Consensus size: 87
61477419 TATTAAGTAA
* *
61477429 ATTATGTAAGTTATGTATTAAGTAAGCTATTTAAGTTGTGTATTATGTAAGTTATCAAAGTAATG
1 ATTATGTAAGTTATGTATTAAGTAAGCTATGTAAGTTGTGTATTATGTAAGTCATCAAAGTAATG
*
61477494 TATGTTATGTAAGTTGTAAGTT
66 TATGCTATGTAAGTTGTAAGTT
* * * * ** *
61477516 ATTATGT-A-TTATGTAGGTTATGTAAGTTATGTAAGTTTTGTATTATGTAAGTCGTGTAAGTTA
1 ATTATGTAAGTTATGTA--TTAAGTAAGCTATGTAAGTTGTGTATTATGTAAGTCATCAAAGTAA
61477579 TGTATGCTATGTAA---GTAA-TGT
64 TGTATGCTATGTAAGTTGTAAGT-T
* **
61477600 ATTATGTAAGTT-TATA-TAAGTTAA--TATGTAAGTAATGTATTATGTAAGT
1 ATTATGTAAGTTATGTATTAAG-TAAGCTATGTAAGTTGTGTATTATGTAAGT
61477649 TTATATAAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
81 23 0.20
82 3 0.03
83 4 0.04
84 12 0.11
85 11 0.10
86 3 0.03
87 57 0.50
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (87 bp):
ATTATGTAAGTTATGTATTAAGTAAGCTATGTAAGTTGTGTATTATGTAAGTCATCAAAGTAATG
TATGCTATGTAAGTTGTAAGTT
Found at i:61477563 original size:34 final size:37
Alignment explanation
Indices: 61477518--61477629 Score: 85
Period size: 34 Copynumber: 3.2 Consensus size: 37
61477508 TGTAAGTTAT
*
61477518 TATGTATTATGTAGGTTATGTAAGTTATGTAAG-T-T
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAT
** * *
61477553 T-TGTATTATGTAAGTCGTGTAAGTTATGTATGCTAT
1 TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAT
* * *
61477589 GTAAGTA--ATGT-A-TTATGTAAGTTTATATAAGTTAA
1 -TATGTATTATGTAAGTTATGTAAG-TTATGTAAGTTAT
61477624 TATGTA
1 TATGTA
61477630 AGTAATGTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
34 39 0.65
35 12 0.20
36 5 0.08
37 1 0.02
38 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (37 bp):
TATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAT
Found at i:61477631 original size:38 final size:38
Alignment explanation
Indices: 61477586--61477688 Score: 145
Period size: 38 Copynumber: 2.7 Consensus size: 38
61477576 TTATGTATGC
*
61477586 TATGTAAGTAATGTATTATGTAAGTTTATAT-AAGTTAA
1 TATGTAAGTAATGTATTATGTAAGTTTATATAAAATT-A
*
61477624 TATGTAAGTAATGTATTATGTAAGTTTATATAAAAATTT
1 TATGTAAGTAATGTATTATGTAAGTTTATAT-AAAATTA
* *
61477663 TATATAAGTCATGTATTATGTAAGTT
1 TATGTAAGTAATGTATTATGTAAGTT
61477689 AACATGTAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
38 31 0.53
39 24 0.41
40 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.46
Consensus pattern (38 bp):
TATGTAAGTAATGTATTATGTAAGTTTATATAAAATTA
Found at i:61477935 original size:13 final size:13
Alignment explanation
Indices: 61477917--61478002 Score: 81
Period size: 13 Copynumber: 6.8 Consensus size: 13
61477907 AAGTAATATA
61477917 TATTTAAGTAATG
1 TATTTAAGTAATG
*
61477930 TATTTAA--AATT
1 TATTTAAGTAATG
*
61477941 TATATAAGTTAAT-
1 TATTTAAG-TAATG
*
61477954 T-TGTAAGTAATG
1 TATTTAAGTAATG
*
61477966 TATTTAAGTAATT
1 TATTTAAGTAATG
*
61477979 TATTTAAGTAATA
1 TATTTAAGTAATG
*
61477992 TATTCAAGTAA
1 TATTTAAGTAA
61478003 ATTTTAGTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
11 13 0.21
12 6 0.10
13 39 0.64
14 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (13 bp):
TATTTAAGTAATG
Found at i:61478159 original size:12 final size:13
Alignment explanation
Indices: 61478133--61478163 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
61478123 TTAATAAGTT
61478133 AAAATAAATTGTA
1 AAAATAAATTGTA
61478146 AAAATAAATT-TA
1 AAAATAAATTGTA
61478158 AAAATA
1 AAAATA
61478164 TAATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAATAAATTGTA
Found at i:61478185 original size:18 final size:17
Alignment explanation
Indices: 61478148--61478191 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
61478138 AAATTGTAAA
61478148 AATAAATTTAAAAATAT
1 AATAAATTTAAAAATAT
* *
61478165 AATAAATATTGAAATTAT
1 AATAAAT-TTAAAAATAT
*
61478183 AATATATTT
1 AATAAATTT
61478192 TAACAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AATAAATTTAAAAATAT
Found at i:61478881 original size:14 final size:14
Alignment explanation
Indices: 61478862--61478888 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61478852 GAACAGCAAC
61478862 ATGATTAACTAAAG
1 ATGATTAACTAAAG
61478876 ATGATTAACTAAA
1 ATGATTAACTAAA
61478889 AAACCTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (14 bp):
ATGATTAACTAAAG
Found at i:61479595 original size:30 final size:30
Alignment explanation
Indices: 61479560--61479685 Score: 125
Period size: 30 Copynumber: 4.2 Consensus size: 30
61479550 AAAAAAATTG
* *
61479560 CATTTTGACCCCTATACTATTCAAAATTTA
1 CATTTTGACCCCTAAACTTTTCAAAATTTA
61479590 CATTTTGACCCC-AAACTTTTCTAAAA-TTA
1 CATTTTGACCCCTAAACTTTTC-AAAATTTA
** * *
61479619 CATTTCAACCCTTAAAATTTCTCAAAATTT-
1 CATTTTGACCCCTAAACTTT-TCAAAATTTA
* *
61479649 CATTTTAACCCCTAAAC-TTTCAAGAAATTA
1 CATTTTGACCCCTAAACTTTTCAA-AATTTA
61479679 CATTTTG
1 CATTTTG
61479686 GCCCATATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
28 4 0.05
29 25 0.32
30 46 0.58
31 4 0.05
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCAAAATTTA
Found at i:61480153 original size:14 final size:15
Alignment explanation
Indices: 61480125--61480153 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61480115 CAATCAAATA
61480125 AAGAAAAGAGAAGAG
1 AAGAAAAGAGAAGAG
61480140 AAGAAAAG-GAAGAG
1 AAGAAAAGAGAAGAG
61480154 GGGAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAGAAGAG
Found at i:61480282 original size:13 final size:12
Alignment explanation
Indices: 61480254--61480311 Score: 61
Period size: 12 Copynumber: 4.9 Consensus size: 12
61480244 AGAGGAAAAG
61480254 AAAGA-AAAGAAA
1 AAAGAGAAAG-AA
61480266 AAAGAGAGAAGAA
1 AAAGAGA-AAGAA
61480279 AAAGAGAAAGAA
1 AAAGAGAAAGAA
61480291 AAAGA-AAA-AA
1 AAAGAGAAAGAA
61480301 AATA-AGAAAGA
1 AA-AGAGAAAGA
61480312 CAGCAGGCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 5 0.12
11 7 0.17
12 16 0.39
13 10 0.24
14 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
AAAGAGAAAGAA
Found at i:61480866 original size:20 final size:20
Alignment explanation
Indices: 61480841--61480878 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61480831 AAAAATATTC
61480841 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
61480861 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
61480879 TTAGAATCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:61481125 original size:17 final size:16
Alignment explanation
Indices: 61481098--61481179 Score: 56
Period size: 17 Copynumber: 4.8 Consensus size: 16
61481088 TTTTTTTTTT
*
61481098 AAATTTCCGTGTTTCAA
1 AAATTT-CGTGTTTAAA
* *
61481115 AAATTCTCGTGAATAAAA
1 AAATT-TCGTG-TTTAAA
* **
61481133 AAAATTCGTGTTTTCA
1 AAATTTCGTGTTTAAA
*
61481149 AAATTCCCGTGTTTGAAA
1 AAATT-TCGTGTTT-AAA
61481167 AAATTTCGTGTTT
1 AAATTTCGTGTTT
61481180 TCGTGTTTTC
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
16 6 0.12
17 28 0.58
18 14 0.29
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
AAATTTCGTGTTTAAA
Found at i:61481180 original size:34 final size:35
Alignment explanation
Indices: 61481098--61481181 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
61481088 TTTTTTTTTT
*
61481098 AAATTTCCGTG-TTTCAAAAATTCTCGTGAATAAAA
1 AAATTT-CGTGTTTTCAAAAATTCCCGTGAATAAAA
* ** *
61481133 AAAATTCGTGTTTTC-AAAATTCCCGTGTTTGAAA
1 AAATTTCGTGTTTTCAAAAATTCCCGTGAATAAAA
61481167 AAATTTCGTGTTTTC
1 AAATTTCGTGTTTTC
61481182 GTGTTTTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 33 0.79
35 9 0.21
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (35 bp):
AAATTTCGTGTTTTCAAAAATTCCCGTGAATAAAA
Found at i:61481249 original size:19 final size:19
Alignment explanation
Indices: 61481226--61481409 Score: 123
Period size: 17 Copynumber: 9.7 Consensus size: 19
61481216 TTGGATGTTA
61481226 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
* * * *
61481245 CCGTG-TTT-GACAAATTT
1 TCGTGTTTTCAAAAAATTC
61481262 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
*
61481281 TCGTG-TTTC-AAAAATTT
1 TCGTGTTTTCAAAAAATTC
* *
61481298 TCGTGTTTTCAAAATTTTCATGTTT
1 TCGTGTTTTCAAAA-----A-ATTC
61481323 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
* *
61481342 TCGTGTTTTTTAAAAAAAT-
1 TCGTG-TTTTCAAAAAATTC
**
61481361 TCGTGTTTAAAAAAAATT-
1 TCGTGTTTTCAAAAAATTC
* *
61481379 TCATGTTTTC--AAAATTT
1 TCGTGTTTTCAAAAAATTC
*
61481396 TCATGTTTTCAAAA
1 TCGTGTTTTCAAAA
61481410 TTTTTCGTGT
Statistics
Matches: 131, Mismatches: 20, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
16 6 0.05
17 32 0.24
18 31 0.24
19 32 0.24
20 12 0.09
24 1 0.01
25 17 0.13
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (19 bp):
TCGTGTTTTCAAAAAATTC
Found at i:61481273 original size:36 final size:36
Alignment explanation
Indices: 61481226--61481311 Score: 145
Period size: 36 Copynumber: 2.4 Consensus size: 36
61481216 TTGGATGTTA
* *
61481226 TCGTGTTTTCAAAAAATTCCCGTGTTTGACAAATTT
1 TCGTGTTTTCAAAAAATTCCCGTGTTTCAAAAATTT
*
61481262 TCGTGTTTTCAAAAAATTCTCGTGTTTCAAAAATTT
1 TCGTGTTTTCAAAAAATTCCCGTGTTTCAAAAATTT
61481298 TCGTGTTTTCAAAA
1 TCGTGTTTTCAAAA
61481312 TTTTCATGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (36 bp):
TCGTGTTTTCAAAAAATTCCCGTGTTTCAAAAATTT
Found at i:61482561 original size:14 final size:14
Alignment explanation
Indices: 61482513--61482568 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
61482503 TATTATGCCT
*
61482513 AAAAAA-AACAAAA
1 AAAAAAGAAAAAAA
* *
61482526 ACAAAACAAAACAAA
1 AAAAAAGAAAA-AAA
61482541 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
*
61482555 GAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
61482569 TCAAGATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 5 0.14
14 19 0.53
15 12 0.33
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:61483781 original size:161 final size:161
Alignment explanation
Indices: 61483429--61484697 Score: 1783
Period size: 161 Copynumber: 7.9 Consensus size: 161
61483419 TATTTTTCAC
* * * * * *
61483429 TTTCTGTTTTTTTCAAATATCAACTCATAATACCAGAGGTGAGTTGAGCCTCGGGT--CATGCTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
*
61483492 AGGTA-TTTTTT-AATTTCGGTCTTTTTTTT---AAATCAACTCATATTGCGAGAAGTGAGTTGA
66 AGGTATTTTTTTAAATTTC--TTTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
61483552 GCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
129 GCCTCGGGTCGCACGCTGAGGTA-TTTTTTTAAA
61483586 TTTCTGTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
1 TTTCTG-TTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
*
61483651 GAGGTA-TTTTTTAAATTTCTATTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
65 GAGGTATTTTTTTAAATTTCT-TTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
** * *
61483715 GCCTCGGGTCGCATACCGAGGTATTTTTTAAAA
129 GCCTCGGGTCGCACGCTGAGGTATTTTTTTAAA
* * *
61483748 TTTCTGTTTTTTTCAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CATGCTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
*
61483811 AGGTATTTTTTTAAAATTTCTGTTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
66 AGGTATTTTTTT-AAATTTCT-TTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
* *
61483876 GCCTCGGATCGCACGCTGAGGTATTTTTTTTTAA
129 GCCTCGGGTCGCACGCTGAGGTA-TTTTTTTAAA
* *
61483910 TTTCTATTTTTTTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
1 TTTCT-GTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
61483975 GAGGTATTTTTTTTAAATTTCTGTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTT
65 GAGGTA-TTTTTTTAAATTTC--TTTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTT
61484040 GAGCCTCGGGTCGCACGCTGAGGTATTTTTTTAAA
127 GAGCCTCGGGTCGCACGCTGAGGTATTTTTTTAAA
* * *
61484075 TTTCTATTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT--CACGCTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
* * *
61484138 AGGTATTTTTTTTAAATTTCTGTTTTTCTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
66 AGGTA-TTTTTTTAAATTTCTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAG
61484203 CCTCGGGTCGCACGCTGAGGTATTTTTTTAAA
130 CCTCGGGTCGCACGCTGAGGTATTTTTTTAAA
* * *
61484235 TTTCTTTTTTTTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTTGGGTCGCACGCTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
*
61484300 AGGTATTTTTTTAAATTTCTGTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
66 AGGTATTTTTTTAAATTTCTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
* *
61484365 CTCGGGTCGCAAGCTGAGGTATTTTTTAAAAA
131 CTCGGGTCGCACGCTGAGGTATTTTTT-TAAA
*
61484397 TTTCTGTTTTTTT---AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGTTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
*
61484459 AGGTATTTTTTTAAATTTCTGTTTTTTTTTTCAAAAATCAACTCATATTGCGATAAGTGAGTTGA
66 AGGTATTTTTTTAAATTTC--TTTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
61484524 GCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
129 GCCTCGGGTCGCACGCTGAGGTA-TTTTTTTAAA
* * * *
61484558 TTTCTGTTTTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATG-
1 TTTCTG-TTT-TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGC
* * * * * *
61484622 TCGAGGTA-TTTTTT--A--T-TTTTGTTTTTCGAAGATCAACTCATAAT-CCAAAAGGTGAGTT
64 T-GAGGTATTTTTTTAAATTTCTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAA-GTGAGTT
*
61484680 GAGTCTCGGGTCGCACGC
127 GAGCCTCGGGTCGCACGC
61484698 CGAGCTGTTC
Statistics
Matches: 1017, Mismatches: 65, Indels: 59
0.89 0.06 0.05
Matches are distributed among these distances:
157 10 0.01
158 93 0.09
159 77 0.08
160 156 0.15
161 282 0.28
162 91 0.09
163 102 0.10
164 47 0.05
165 39 0.04
166 119 0.12
167 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (161 bp):
TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
AGGTATTTTTTTAAATTTCTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
CTCGGGTCGCACGCTGAGGTATTTTTTTAAA
Found at i:61483791 original size:80 final size:80
Alignment explanation
Indices: 61483429--61484697 Score: 1759
Period size: 80 Copynumber: 15.8 Consensus size: 80
61483419 TATTTTTCAC
* * * * * *
61483429 TTTCTGTTTTTTTCAAATATCAACTCATAATACCAGAGGTGAGTTGAGCCTCGGGT--CATGCTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
61483492 AGGTA-TTTTTT-AA
66 AGGTATTTTTTTAAA
* **
61483505 TTTCGGTCTTTTTT-TTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
1 TTTCTGT-TTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
61483569 GAGGTATTTTTTTTAAA
65 GAGGTA-TTTTTTTAAA
61483586 TTTCTGTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
1 TTTCTG-TTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
61483651 GAGGTA-TTTTTTAAA
65 GAGGTATTTTTTTAAA
* * **
61483666 TTTCTATTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCATAC
1 TTTC--TGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGC
* *
61483731 CGAGGTATTTTTTAAAA
64 TGAGGTATTTTTTTAAA
* * *
61483748 TTTCTGTTTTTTTCAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CATGCTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
61483811 AGGTATTTTTTTAAAA
66 AGGTATTTTTTT-AAA
* *
61483827 TTTCTGTTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCGCACGC
1 TTTCTG--TTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGC
*
61483892 TGAGGTATTTTTTTTTAA
64 TGAGGTA-TTTTTTTAAA
* *
61483910 TTTCTATTTTTTTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
1 TTTCT-GTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
61483975 GAGGTATTTTTTTTAAA
65 GAGGTA-TTTTTTTAAA
61483992 TTTCTGTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACG
1 TTTCTG---TTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACG
61484057 CTGAGGTATTTTTTTAAA
63 CTGAGGTATTTTTTTAAA
* * *
61484075 TTTCTATTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT--CACGCTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
61484138 AGGTATTTTTTTTAAA
66 AGGTA-TTTTTTTAAA
*
61484154 TTTCTGTTTTTCTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCT
1 TTTCTGTTTTT-TTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
61484219 GAGGTATTTTTTTAAA
65 GAGGTATTTTTTTAAA
* * *
61484235 TTTCTTTTTTTTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTTGGGTCGCACGCTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
61484300 AGGTATTTTTTTAAA
66 AGGTATTTTTTTAAA
*
61484315 TTTCTGTTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCAAGCT
1 TTTCTG-TTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
*
61484380 GAGGTATTTTTTAAAAA
65 GAGGTATTTTTT-TAAA
*
61484397 TTTCTGTTTTTTT---AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGTTG
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
61484459 AGGTATTTTTTTAAA
66 AGGTATTTTTTTAAA
*
61484474 TTTCTGTTTTTTTTTTCAAAAATCAACTCATATTGCGATAAGTGAGTTGAGCCTCGGGTCGCACG
1 TTTCTG---TTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACG
61484539 CTGAGGTATTTTTTTTAAA
63 CTGAGGTA-TTTTTTTAAA
* * * *
61484558 TTTCTGTTTTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATG-
1 TTTCTG-TTT-TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGC
61484622 TCGAGGTA-TTTTTT--A
64 T-GAGGTATTTTTTTAAA
* * * * * * *
61484637 TTT-T-TGTTTTTCGAAGATCAACTCATAAT-CCAAAAGGTGAGTTGAGTCTCGGGTCGCACGC
1 TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAA-GTGAGTTGAGCCTCGGGTCGCACGC
61484698 CGAGCTGTTC
Statistics
Matches: 1086, Mismatches: 69, Indels: 76
0.88 0.06 0.06
Matches are distributed among these distances:
74 3 0.00
75 39 0.04
76 43 0.04
77 15 0.01
78 98 0.09
79 33 0.03
80 239 0.22
81 221 0.20
82 170 0.16
83 139 0.13
84 86 0.08
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (80 bp):
TTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
AGGTATTTTTTTAAA
Found at i:61484999 original size:30 final size:29
Alignment explanation
Indices: 61484906--61484999 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
61484896 CGGAATTTAT
* *
61484906 ATTTTGACCCC-AAACTTTTCTAAAATTAC
1 ATTTTAACCCCTAAAC-TTTCAAAAATTAC
* * * *
61484935 ATTTGAACCCTTAAAATTTCTCAAAAGTT-C
1 ATTTTAACCCCT-AAACTT-TCAAAAATTAC
61484965 ATTTTAACCCCTAAACTTTCAAGAAATTAC
1 ATTTTAACCCCTAAACTTTCAA-AAATTAC
61484995 ATTTT
1 ATTTT
61485000 GGCCCATATT
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
28 4 0.08
29 17 0.34
30 19 0.38
31 10 0.20
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTTTAACCCCTAAACTTTCAAAAATTAC
Found at i:61485569 original size:12 final size:12
Alignment explanation
Indices: 61485554--61485595 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
61485544 AGAGGAAGAG
61485554 AAAGAAAAGAAA
1 AAAGAAAAGAAA
*
61485566 AAAGAGAAG-AA
1 AAAGAAAAGAAA
61485577 AAAGAAAA-AAA
1 AAAGAAAAGAAA
61485588 ATAAGAAA
1 A-AAGAAA
61485596 GACAGCAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:61485572 original size:18 final size:18
Alignment explanation
Indices: 61485549--61485586 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
61485539 GAAGAAGAGG
61485549 AAGAGAA-AGAAAAGAAAA
1 AAGAGAAGA-AAAAGAAAA
61485567 AAGAGAAGAAAAAGAAAA
1 AAGAGAAGAAAAAGAAAA
61485585 AA
1 AA
61485587 AATAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAGAGAAGAAAAAGAAAA
Found at i:61485575 original size:23 final size:23
Alignment explanation
Indices: 61485543--61485597 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
61485533 CGGCCCGAAG
*
61485543 AAGAGGAAGAGAAAGAAAAGAAAA-
1 AAGA-GAAGAAAAAGAAAA-AAAAT
61485567 AAGAGAAGAAAAAGAAAAAAAAT
1 AAGAGAAGAAAAAGAAAAAAAAT
61485590 AAGA-AAGA
1 AAGAGAAGA
61485598 CAGCAGGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 8 0.28
23 17 0.59
24 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (23 bp):
AAGAGAAGAAAAAGAAAAAAAAT
Found at i:61485593 original size:18 final size:18
Alignment explanation
Indices: 61485558--61485595 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
61485548 GAAGAGAAAG
*
61485558 AAAAGAAAAAAGAGAAGA
1 AAAAGAAAAAAAAGAAGA
*
61485576 AAAAGAAAAAAAATAAGA
1 AAAAGAAAAAAAAGAAGA
61485594 AA
1 AA
61485596 GACAGCAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAAAAGAAGA
Found at i:61486147 original size:20 final size:20
Alignment explanation
Indices: 61486122--61486159 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61486112 AAAAATATTC
61486122 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
61486142 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
61486160 TTAGAATCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:61486309 original size:17 final size:17
Alignment explanation
Indices: 61486282--61486327 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
61486272 AAAAAAATCG
61486282 TGTTTCAAAAATTT-TCA
1 TGTTTC-AAAATTTCTCA
*
61486299 TGTCTTCAAAATTTCTCG
1 TGT-TTCAAAATTTCTCA
61486317 TGTTTCAAAAT
1 TGTTTCAAAAT
61486328 AATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (17 bp):
TGTTTCAAAATTTCTCA
Found at i:61486338 original size:28 final size:28
Alignment explanation
Indices: 61486306--61486359 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
61486296 TCATGTCTTC
* * *
61486306 AAAATTTCTCGTGTTTCAAAATAATAAT
1 AAAATTTCCCGTGTTTAAAAAAAATAAT
61486334 AAAATTTCCCGTGTTTAAAAAAAATA
1 AAAATTTCCCGTGTTTAAAAAAAATA
61486360 TATTCCTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAATTTCCCGTGTTTAAAAAAAATAAT
Found at i:61486537 original size:19 final size:19
Alignment explanation
Indices: 61486514--61486691 Score: 119
Period size: 17 Copynumber: 9.8 Consensus size: 19
61486504 TTGGATGTTA
61486514 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
* * * *
61486533 CCGTG-TTT-GACAAATTT
1 TCGTGTTTTCAAAAAATTC
61486550 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
* *
61486569 TCGTGTTTTTAAAAAAAAT-
1 TCGTG-TTTTCAAAAAATTC
*
61486588 TCGTG-TTTAAAAAAATT-
1 TCGTGTTTTCAAAAAATTC
* * *
61486605 TCATGTTTTC-AAAATTTT
1 TCGTGTTTTCAAAAAATTC
61486623 TCGTG---TCAAAAAAATTC
1 TCGTGTTTTC-AAAAAATTC
* * * *
61486640 TCATGTATT-GAAAATTTC
1 TCGTGTTTTCAAAAAATTC
61486658 -CGTGTTTTCAAAAAAATTC
1 TCGTGTTTTC-AAAAAATTC
61486677 T-GTGTTTTCAAAAAA
1 TCGTGTTTTCAAAAAA
61486692 AATTTTTGTG
Statistics
Matches: 122, Mismatches: 24, Indels: 27
0.71 0.14 0.16
Matches are distributed among these distances:
15 2 0.02
17 47 0.39
18 26 0.21
19 35 0.29
20 12 0.10
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (19 bp):
TCGTGTTTTCAAAAAATTC
Found at i:61486626 original size:35 final size:34
Alignment explanation
Indices: 61486544--61486689 Score: 107
Period size: 35 Copynumber: 4.1 Consensus size: 34
61486534 CGTGTTTGAC
* * *
61486544 AAATTTTCGTGTTTTCAAAAAATTCTCGTGTTTTTAAA
1 AAATTTTCGTG-TTTAAAAAAATT-TCATG-TTTT-CA
**
61486582 AAAAATTCGTGTTTAAAAAAATTTCATGTTTTCA
1 AAATTTTCGTGTTTAAAAAAATTTCATGTTTTCA
* * *
61486616 AAATTTTTCGTG-TCAAAAAAATTCTCATGTATTGA
1 AAA-TTTTCGTGTTTAAAAAAATT-TCATGTTTTCA
* *
61486651 AAATTTCCGTGTTTTCAAAAAAA-TTCTGTGTTTTCA
1 AAATTTTCGTG-TTT-AAAAAAATTTC-ATGTTTTCA
61486687 AAA
1 AAA
61486690 AAAATTTTTG
Statistics
Matches: 87, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
34 21 0.24
35 24 0.28
36 15 0.17
37 18 0.21
38 9 0.10
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (34 bp):
AAATTTTCGTGTTTAAAAAAATTTCATGTTTTCA
Found at i:61486671 original size:36 final size:36
Alignment explanation
Indices: 61486514--61486677 Score: 142
Period size: 36 Copynumber: 4.6 Consensus size: 36
61486504 TTGGATGTTA
* *
61486514 TCGTGTTTTCAAAAAATTCCCGTG-TTTGACAAATTT
1 TCGTGTTTTCAAAAAATTCTCATGTTTTGA-AAATTT
* * **
61486550 TCGTGTTTTCAAAAAATTCTCGTGTTTTTAAAAAAAAT
1 TCGTGTTTTCAAAAAATTCTCATG-TTTT-GAAAATTT
* *
61486588 TCGTG-TTTAAAAAAATT-TCATGTTTTCAAAATTTT
1 TCGTGTTTTCAAAAAATTCTCATGTTTTGAAAA-TTT
*
61486623 TCGTG---TCAAAAAAATTCTCATGTATTGAAAATTT
1 TCGTGTTTTC-AAAAAATTCTCATGTTTTGAAAATTT
*
61486657 CCGTGTTTTCAAAAAAATTCT
1 TCGTGTTTTC-AAAAAATTCT
61486678 GTGTTTTCAA
Statistics
Matches: 106, Mismatches: 13, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
33 1 0.01
34 19 0.18
35 22 0.21
36 27 0.25
37 24 0.23
38 12 0.11
39 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (36 bp):
TCGTGTTTTCAAAAAATTCTCATGTTTTGAAAATTT
Found at i:61486692 original size:19 final size:19
Alignment explanation
Indices: 61486552--61486692 Score: 79
Period size: 19 Copynumber: 7.8 Consensus size: 19
61486542 ACAAATTTTC
61486552 GTGTTTTC-AAAAAATTCT
1 GTGTTTTCAAAAAAATTCT
*
61486570 CGTGTTTTTAAAAAAAATTC-
1 -GTG-TTTTCAAAAAAATTCT
61486590 GTG-TTT-AAAAAAATT-T
1 GTGTTTTCAAAAAAATTCT
* ***
61486606 CATGTTTTCAAAATTTTTC-
1 -GTGTTTTCAAAAAAATTCT
61486625 GTG---TCAAAAAAATTCT
1 GTGTTTTCAAAAAAATTCT
* * * * *
61486641 CATGTATT--GAAAATTTCC
1 -GTGTTTTCAAAAAAATTCT
61486659 GTGTTTTCAAAAAAATTCT
1 GTGTTTTCAAAAAAATTCT
61486678 GTGTTTTCAAAAAAA
1 GTGTTTTCAAAAAAA
61486693 ATTTTTGTGT
Statistics
Matches: 90, Mismatches: 18, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
15 9 0.10
16 9 0.10
17 12 0.13
18 12 0.13
19 34 0.38
20 5 0.06
21 9 0.10
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (19 bp):
GTGTTTTCAAAAAAATTCT
Found at i:61486693 original size:20 final size:19
Alignment explanation
Indices: 61486659--61486708 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
61486649 GAAAATTTCC
61486659 GTGTTTTC-AAAAAAATTCT
1 GTGTTTTCAAAAAAAATT-T
61486678 GTGTTTTCAAAAAAAATTT
1 GTGTTTTCAAAAAAAATTT
*
61486697 TTGTGTTTCAAA
1 GTGT-TTTCAAA
61486709 GATTTTCGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (19 bp):
GTGTTTTCAAAAAAAATTT
Found at i:61486739 original size:38 final size:37
Alignment explanation
Indices: 61486670--61486758 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 37
61486660 TGTTTTCAAA
*
61486670 AAAATTCT-GTGTTTTCAAAAAAAATTTTTGTGTTTC
1 AAAATTCTCGTGTTTTCAAAAAAAATTATTGTGTTTC
* * **
61486706 AAAGATTTTCGTGTTTTCTAAAATTATTATTGTGTTTC
1 AAA-ATTCTCGTGTTTTCAAAAAAAATTATTGTGTTTC
61486744 AAAATTCTCGTGTTT
1 AAAATTCTCGTGTTT
61486759 AAAAACAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.07
37 15 0.33
38 27 0.60
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (37 bp):
AAAATTCTCGTGTTTTCAAAAAAAATTATTGTGTTTC
Found at i:61486749 original size:19 final size:18
Alignment explanation
Indices: 61486697--61486749 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
61486687 AAAAAAATTT
*
61486697 TTGTGTTTCAAAGATTTTC
1 TTGTGTTTCAAA-ATTTTA
*
61486716 GTGT-TTTCTAAAATTATTA
1 TTGTGTTTC-AAAATT-TTA
61486735 TTGTGTTTCAAAATT
1 TTGTGTTTCAAAATT
61486750 CTCGTGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 7 0.25
19 17 0.61
20 4 0.14
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (18 bp):
TTGTGTTTCAAAATTTTA
Found at i:61488970 original size:16 final size:17
Alignment explanation
Indices: 61488951--61488984 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61488941 TATTTTTAAT
61488951 TGACA-CATTAAAATTA
1 TGACATCATTAAAATTA
*
61488967 TGACATTATTAAAATTA
1 TGACATCATTAAAATTA
61488984 T
1 T
61488985 TAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (17 bp):
TGACATCATTAAAATTA
Found at i:61489193 original size:14 final size:14
Alignment explanation
Indices: 61489174--61489228 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
61489164 TAAAGTAGCC
*
61489174 TAAACCCCAAACCT
1 TAAACCCTAAACCT
* *
61489188 TAAACCTTAAACCC
1 TAAACCCTAAACCT
*
61489202 CAAACTCCTAAACCT
1 TAAAC-CCTAAACCT
*
61489217 TAAACCCAAAAC
1 TAAACCCTAAAC
61489229 ACCAAAACCT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.16
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:61489216 original size:22 final size:21
Alignment explanation
Indices: 61489174--61489238 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
61489164 TAAAGTAGCC
*
61489174 TAAACCCCAAACCTTAAACCT
1 TAAACCCCAAACCCTAAACCT
61489195 TAAACCCCAAACTCCTAAACCT
1 TAAACCCCAAAC-CCTAAACCT
* *
61489217 TAAACCCAAAACACCAAAACCT
1 TAAACCCCAAAC-CCTAAACCT
61489239 ACATCATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 12 0.31
22 27 0.69
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (21 bp):
TAAACCCCAAACCCTAAACCT
Found at i:61489865 original size:114 final size:115
Alignment explanation
Indices: 61489580--61489872 Score: 306
Period size: 115 Copynumber: 2.6 Consensus size: 115
61489570 GTTTTTAACA
* * * *
61489580 AAGCGCCACTAATT-TTAGTATAAATCAAGACCAAAATGTTGCGTTTTGGTTATGGTATTTTGCG
1 AAGCGCCACTAATTCTTAGTATACATCAAGACCAAACT-TTGCGTTTTGGTTAAGATATTTTGCG
* * * * * *
61489644 GCGCTAGACACAAATCGCCGCTAATACTATGCTTTAGCGGCGTTTCACCGT
65 GCGCTAGACAAAAAGCGACGCAAATACTATCCGTTAGCGGCGTTTCACCGT
* * * * * *
61489695 AATCGCCACTAAATC-AAGTATACATCAAGAACAAAACGTTGCGTTTTGGTTTAGATATTTTGCG
1 AAGCGCCACTAATTCTTAGTATACATCAAG-ACCAAACTTTGCGTTTTGGTTAAGATATTTTGCG
** * ****
61489759 GCGCT-TCCAAAAAGCGACGCAAATACTATCCGTTAGTGGCGTTTTTGTGAT
65 GCGCTAGACAAAAAGCGACGCAAATACTATCCGTTAGCGGCGTTTCACCG-T
* *
61489810 AAGCGCCACTAATTCTTA-CATACCTCAAGACCAAACTTTGCGTTTTGGTTAAGATATTTTGCG
1 AAGCGCCACTAATTCTTAGTATACATCAAGACCAAACTTTGCGTTTTGGTTAAGATATTTTGCG
61489873 TGCTTTAACG
Statistics
Matches: 143, Mismatches: 31, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
114 62 0.43
115 75 0.52
116 6 0.04
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (115 bp):
AAGCGCCACTAATTCTTAGTATACATCAAGACCAAACTTTGCGTTTTGGTTAAGATATTTTGCGG
CGCTAGACAAAAAGCGACGCAAATACTATCCGTTAGCGGCGTTTCACCGT
Found at i:61489943 original size:198 final size:201
Alignment explanation
Indices: 61489673--61490075 Score: 514
Period size: 198 Copynumber: 2.0 Consensus size: 201
61489663 GCTAATACTA
* *
61489673 TGCTTTAGCGGCGTTTCACCGTAATCGCCACTAAATCAAGTATACATCAAGAACAAAACGTTGCG
1 TGCTTTAACGGCGTTTCACCGTAAGCGCCACTAAATCAAGTATACATCAAGAACAAAACGTTGCG
* * * * *
61489738 TTTTGGTTTAGATATTTTGCGGCGCTTC-CAAAAAGCGACGCAAATACTATCCGTTAGTGGCGTT
66 TTTTGGTTAAGATATTTTGCAGCGCTTCTCAAAAAGCGACGCAAATAATATCCGTTAGCGGCGGT
** * *
61489802 TTTGTGATAAGCGCCACTAATTCTTACATACCTCAAGACC-AAACTTTGCGTTTTGGTTAAGATA
131 TTACTG-TAAGCGCCACTAATT-TTACATACATCAAGACCAAAACGTTGCGTTTTGGTTAAGATA
61489866 TTTTGC-G
194 TTTTGCGG
* * *
61489873 TGCTTTAACGGCGTTTC-CC-TAAGCGCCATTAATTCTAGTATACATCAAG-ACAAAAAC-TATG
1 TGCTTTAACGGCGTTTCACCGTAAGCGCCACTAAATCAAGTATACATCAAGAAC-AAAACGT-TG
* * ** * * * *
61489934 CGTTTTGGTTAAGATATTTTGCAGCGCTTCTCACAAAGCGCCGTTATTAATATTCTTTCGCGGCG
64 CGTTTTGGTTAAGATATTTTGCAGCGCTTCTCAAAAAGCGACGCAAATAATATCCGTTAGCGGCG
*
61489999 GTTTACTGTAAGCGCCACTAATTTTATATACATCAAGACCAAAACGTTGCGTTTTGGTTAAGATA
129 GTTTACTGTAAGCGCCACTAATTTTACATACATCAAGACCAAAACGTTGCGTTTTGGTTAAGATA
61490064 TTTTGCGG
194 TTTTGCGG
61490072 TGCT
1 TGCT
61490076 AGCCACGAAT
Statistics
Matches: 175, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
197 18 0.10
198 105 0.60
199 36 0.21
200 16 0.09
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (201 bp):
TGCTTTAACGGCGTTTCACCGTAAGCGCCACTAAATCAAGTATACATCAAGAACAAAACGTTGCG
TTTTGGTTAAGATATTTTGCAGCGCTTCTCAAAAAGCGACGCAAATAATATCCGTTAGCGGCGGT
TTACTGTAAGCGCCACTAATTTTACATACATCAAGACCAAAACGTTGCGTTTTGGTTAAGATATT
TTGCGG
Found at i:61490170 original size:313 final size:313
Alignment explanation
Indices: 61489580--61490184 Score: 716
Period size: 313 Copynumber: 1.9 Consensus size: 313
61489570 GTTTTTAACA
* * * * * *
61489580 AAGCGCCACTAATTTTAGTATAAATCAAGACCAAAATGTTGCGTTTTGGTTATGGTATTTTGCGG
1 AAGCGCCACTAATTCTAGTATAAATCAAGACAAAAATGATGCGTTTTGGTTAAGATATTTTGCAG
* * * *
61489645 CGCTAGACACAAATCGCCGCTAATACTATGCTTTAGCGGCGTTTCACCGTAATCGCCACTAAATC
66 CGCTACACACAAAGCGCCGCTAATAATATGCTTTAGCGGCGTTTCACCGTAAGCGCCACTAAATC
* *
61489710 AAGTATACATCAAGAACAAAACGTTGCGTTTTGGTTTAGATATTTTGCGGCGCTTCCAAAAAGCG
131 AAGTATACATCAAGAACAAAACGTTGCGTTTTGGTTAAGATATTTTGCGGCGCTGCCAAAAAGCG
** * *** *
61489775 ACGCAAATACTATCCGTTAGTGGCGTTTTTGTGATAAGCGCCACTAATTCTTACATACCTCAAGA
196 ACGCAAATACTATAAGTTAGCGGCGTTTCACTGATAAGCGCCACTAATTCTTACATACATCAAGA
**
61489840 CCAAACTTTGCGTTTTGGTTAAGATATTTTGCGTGCTTTAACGGCGTTTCCCT
261 CCAAACGATGCGTTTTGGTTAAGATATTTTGCGTGCTTTAACGGCGTTTCCCT
* *
61489893 AAGCGCCATTAATTCTAGTATACATCAAGACAAAAACT-ATGCGTTTTGGTTAAGATATTTTGCA
1 AAGCGCCACTAATTCTAGTATAAATCAAGACAAAAA-TGATGCGTTTTGGTTAAGATATTTTGCA
* * * * * * * *
61489957 GCGCTTCTCACAAAGCGCCGTTATTAATATTCTTTCGCGGCGGTTT-ACTGTAAGCGCCACTAAT
65 GCGCTACACACAAAGCGCCGCTAATAATATGCTTTAGCGGC-GTTTCACCGTAAGCGCCACTAAA
** * * **
61490021 TTTA-TATACATCAAGACCAAAACGTTGCGTTTTGGTTAAGATATTTTGCGGTGCTAGCCACGAA
129 TCAAGTATACATCAAGAACAAAACGTTGCGTTTTGGTTAAGATATTTTGCGGCGCT-GCCAAAAA
* * * * * * *
61490085 TCGCCGCTAATACTATAATTTAGCGGCGTTTCACTG-TAGGTGCCACTAATTC-TAGTATACATC
193 GCGACGCAAATACTATAAGTTAGCGGCGTTTCACTGATAAGCGCCACTAATTCTTA-CATACATC
* *
61490148 AAGACCAAAACGATGTGTTTTGGTTCAGATATTTTGC
257 AAGACC-AAACGATGCGTTTTGGTTAAGATATTTTGC
61490185 AGCGCTTCCA
Statistics
Matches: 241, Mismatches: 46, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
311 2 0.01
312 74 0.31
313 160 0.66
314 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (313 bp):
AAGCGCCACTAATTCTAGTATAAATCAAGACAAAAATGATGCGTTTTGGTTAAGATATTTTGCAG
CGCTACACACAAAGCGCCGCTAATAATATGCTTTAGCGGCGTTTCACCGTAAGCGCCACTAAATC
AAGTATACATCAAGAACAAAACGTTGCGTTTTGGTTAAGATATTTTGCGGCGCTGCCAAAAAGCG
ACGCAAATACTATAAGTTAGCGGCGTTTCACTGATAAGCGCCACTAATTCTTACATACATCAAGA
CCAAACGATGCGTTTTGGTTAAGATATTTTGCGTGCTTTAACGGCGTTTCCCT
Found at i:61490321 original size:113 final size:114
Alignment explanation
Indices: 61489875--61490528 Score: 653
Period size: 114 Copynumber: 5.8 Consensus size: 114
61489865 ATTTTGCGTG
* * *
61489875 CTTTAACGGCG-TTTCCC-TAAGCGCCATTAATTCTAGTATACATCAAGACAAAAACTATGCGTT
1 CTTTAGCGGCGTTTTCCCGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTATGCGTT
* * * * *
61489938 TTGGTTAAGATATTTTGCAGCGCTTCTCACAAAGCGCCGTTATTAATATT
66 TTGGTTAAGATATTTTGCGGCGCTTC-CACAAAGCGCCGCTATTACTGTC
* * * * *
61489988 CTTTCGCGGCGGTTTACTGTAAGCGCCACTAATTTTA-TATACATCAAGACCAAAACGT-TGCGT
1 CTTTAGCGGCGTTTTCCCGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAAC-TATGCGT
* * * * * * *
61490051 TTTGGTTAAGATATTTTGCGGTGCTAGCCACGAATCGCCGCTAATACTATA
65 TTTGGTTAAGATATTTTGCGGCGCT-TCCACAAAGCGCCGCTATTACTGTC
* * * * * *
61490102 ATTTAGCGGCG-TTTCACTGTAGGTGCCACTAATTCTAGTATACATCAAGACCAAAACGATGTGT
1 CTTTAGCGGCGTTTTC-CCGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTATGCGT
* * *
61490166 TTTGGTTCAGATATTTTGCAGCGCTTCCATAAAGCGCCGCTATTACTGTC
65 TTTGGTTAAGATATTTTGCGGCGCTTCCACAAAGCGCCGCTATTACTGTC
* * * * * *
61490216 CTTTTGCGGCGTTTTCCCATAAACGCCACTAATTCTAGGATACCTCAAGACC-AAACTCTGCGTT
1 CTTTAGCGGCGTTTTCCCGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTATGCGTT
*
61490280 TTGGTTAAGATATTTTGCGGCGCTTCCAAAAAGCGCCGCTATTACTGTC
66 TTGGTTAAGATATTTTGCGGCGCTTCCACAAAGCGCCGCTATTACTGTC
* * * * * ** * *
61490329 CTTTAACGGCATTTTCCCGTAAACGCCACTACTTTTAGGGTACATCAAGACCGAAACGATGCGTT
1 CTTTAGCGGCGTTTTCCCGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTATGCGTT
***** * *
61490394 TTGGTTAAGATATTTTGCGGCGCTTTTTGGAAGCCGCCGGTAATAC-G--
66 TTGGTTAAGATATTTTGCGGCGCTTCCACAAAG-CGCCGCTATTACTGTC
* * * * *
61490441 CTGTAGTGGCGTTTTCCCATAATCGCCACTAATTCTAGTATACATCAAGACGAAAAC-ACTGCGT
1 CTTTAGCGGCGTTTTCCCGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTA-TGCGT
* *
61490505 TTTGGTTAAGAGATTTCGCGGCGC
65 TTTGGTTAAGATATTTTGCGGCGC
61490529 ATTGTGGTAA
Statistics
Matches: 450, Mismatches: 80, Indels: 23
0.81 0.14 0.04
Matches are distributed among these distances:
111 1 0.00
112 72 0.16
113 111 0.25
114 189 0.42
115 77 0.17
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (114 bp):
CTTTAGCGGCGTTTTCCCGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTATGCGTT
TTGGTTAAGATATTTTGCGGCGCTTCCACAAAGCGCCGCTATTACTGTC
Found at i:61492173 original size:285 final size:282
Alignment explanation
Indices: 61491592--61492540 Score: 1519
Period size: 285 Copynumber: 3.3 Consensus size: 282
61491582 TGCATGTTGA
* * * *
61491592 AAAAAAGTTAGTAAAACACTCTTACTTCAGCCATTTCTTCGTATTTTTTTTCTTCACATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTA-TTTTTTCCTCCGCATTTTATT
61491657 ACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAA
65 ACTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAA
* *
61491722 TTTAGTGTAAAAAAAGCTTATTCTTGCCCTTTGCTCGTATTATTTTCTCGAATTTTATTACTTTC
130 TTTAGTGTAAAAAAACCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAATTTTATTACTTTC
61491787 AA-AAAAAATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTT
195 AATAAAAAATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTT
61491851 GTATTAATTATTTCTGAATTTTT
260 GTATTAATTATTTCTGAATTTTT
61491874 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTT-CTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTCCTCCGCATTTTATTA
61491938 CTTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGT-TTTTTTAAAATTA
66 C-TTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTT-AAATTA
* ** *
61492002 ATTTAGTGTAAAAAAATTCTTATTCCTGCCCTTTGCTCGTATTATTTTCTTTAATTTTATTAATT
129 ATTTAGTGTAAAAAAA-CCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAATTTTATTACTT
*
61492067 TCAATAAAAAATTTTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTTTGTTTGAAAT
193 TCAATAAAAAA--TTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAAT
* *
61492132 ATCTATATTAATTATTTCTGAATTTTT
256 ATTTGTATTAATTATTTCTGAATTTTT
* * *
61492159 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTATTCGTATTTTTTCCTCCGTATTTTATTA
1 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTCCTCCGCATTTTATTA
*
61492224 CTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTTAAATTAAT
66 CTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAAT
* * * * * *
61492289 TTAGTGTAAAAAACCCCTTATTCCTGTCATTTGCTCATATTATTTTCCCGAATTTTATTACTTTA
131 TTAGTGTAAAAAA-ACCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAATTTTATTACTTTC
61492354 AATAAAAAAAAATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATA
195 AAT---AAAAAATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATA
61492419 TTTGTATTAATTATTTCTGAATTTTT
257 TTTGTATTAATTATTTCTGAATTTTT
* * * * *
61492445 TAAAAATTTTGTAAAACACTCTTCCCTCGGCCATTT-TTCGTATTTTTTCCTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTCCTCCGCATTTTATTA
*
61492509 CTTTAAAAAATTTCATAATTTCTAATTTTATA
66 CTTTAAAAAATATCATAATTTCTAATTTTATA
61492541 TTTTTACTTT
Statistics
Matches: 622, Mismatches: 33, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
280 20 0.03
281 77 0.12
282 89 0.14
283 6 0.01
285 295 0.47
286 129 0.21
288 6 0.01
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (282 bp):
AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTCCTCCGCATTTTATTA
CTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTATTTTTTAAATTAAT
TTAGTGTAAAAAAACCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAATTTTATTACTTTCA
ATAAAAAATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTG
TATTAATTATTTCTGAATTTTT
Found at i:61492976 original size:43 final size:42
Alignment explanation
Indices: 61492911--61493020 Score: 100
Period size: 43 Copynumber: 2.6 Consensus size: 42
61492901 AAAATTACAT
*
61492911 TTTTTTCTTTCT-TTTTCC-TTCCTCCCCTCTT-CTTCTTCTTC
1 TTTTTT-TTTCTCTTCTCCTTTCCTCCCCT-TTCCTTCTTCTTC
*** *
61492952 TTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TT-TTTTTTTCTCTTCTCCTTTCCTCCCCTTTCCTTCTTCTTC
*
61492995 TTTCTTTTTTCTTCCTCTCCTTTCCT
1 TTT-TTTTTTC-TCTTCTCCTTTCCT
61493021 TTTCTTTCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
41 7 0.12
42 12 0.21
43 25 0.44
44 13 0.23
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (42 bp):
TTTTTTTTTCTCTTCTCCTTTCCTCCCCTTTCCTTCTTCTTC
Found at i:61492998 original size:4 final size:4
Alignment explanation
Indices: 61492977--61493050 Score: 59
Period size: 4 Copynumber: 19.0 Consensus size: 4
61492967 CTCCTTTCCT
* * *
61492977 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCC TCTCC TTTCC TTTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTT-C -TTTC
61493025 TTTC TTTC TTTC TTTC -TTC -TTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
61493051 CCTCTCATTC
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
3 13 0.22
4 38 0.63
5 6 0.10
6 3 0.05
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:61493001 original size:44 final size:44
Alignment explanation
Indices: 61492940--61493042 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 44
61492930 TCCTCCCCTC
* *
61492940 TTCTTCTTCTTC-TTCTTTTTTTC-TCTTCTCCTTTCCTTTTCT
1 TTCTTCTTTTTCTTTCTTTTTTTCTTCCTCTCCTTTCCTTTTCT
61492982 TTCCTTCTTTTTCTTTC-TTTTTTCTTCCTCTCCTTTCCTTTTCT
1 TT-CTTCTTTTTCTTTCTTTTTTTCTTCCTCTCCTTTCCTTTTCT
*
61493026 TTCTT-TCTTTCTTTCTT
1 TTCTTCTTTTTCTTTCTT
61493043 CTTCTTTCCC
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
42 11 0.20
43 20 0.37
44 23 0.43
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (44 bp):
TTCTTCTTTTTCTTTCTTTTTTTCTTCCTCTCCTTTCCTTTTCT
Found at i:61493045 original size:38 final size:37
Alignment explanation
Indices: 61492914--61493046 Score: 112
Period size: 38 Copynumber: 3.5 Consensus size: 37
61492904 ATTACATTTT
*
61492914 TTTCTTTCTTT-TTCCTTCCTCCCCTCTTCTTCTTC-TTC
1 TTTCTTTCTTTCTT-CTTCCTCTCCT-TTCTT-TTCTTTC
* * * *
61492952 -TTCTTTTTTTC-TCTTCTCCTTTCCTTTTCTTTCCTTCTT
1 TTTCTTTCTTTCTTC-T-TCCTCTCC-TTTCTTTTCTT-TC
*
61492991 TTTCTTTCTTTTTTCTTCCTCTCCTTTCCTTTTCTTTC
1 TTTCTTTCTTTCTTCTTCCTCTCCTTT-CTTTTCTTTC
61493029 TTTCTTTCTTTCTTCTTC
1 TTTCTTTCTTTCTTCTTC
61493047 TTTCCCTCTC
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
36 1 0.01
37 13 0.17
38 33 0.44
39 16 0.21
40 10 0.13
41 2 0.03
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (37 bp):
TTTCTTTCTTTCTTCTTCCTCTCCTTTCTTTTCTTTC
Found at i:61500479 original size:51 final size:51
Alignment explanation
Indices: 61500403--61500620 Score: 303
Period size: 51 Copynumber: 4.3 Consensus size: 51
61500393 ACTTCTGATC
*
61500403 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAACTACACTTATCTGATCAGTGACA
* * * *
61500454 AGTGACAAATAATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTAGTAGCTTCAACTACACTTATCTGATCAGTGACA
* **
61500505 AGTGACAAGTGATAAATAGTAGCTTCAACTTTACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAACTACACTTATCTGATCAGTGACA
** * * *
61500556 AGTGACAAGTGATAAGCGGTGGCTT-AACTACACTTATTTGATCAGGGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAACTACACTTATCTGATCAGTGACA
*
61500606 AGTGAAAAGTGATAA
1 AGTGACAAGTGATAA
61500621 ATGTGATCCG
Statistics
Matches: 148, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 35 0.24
51 113 0.76
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAACTACACTTATCTGATCAGTGACA
Found at i:61512904 original size:22 final size:22
Alignment explanation
Indices: 61512869--61512911 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
61512859 ATTATAAAGC
*
61512869 ATAAAAATAAGTATTTATATAA
1 ATAAAAATAAGTATGTATATAA
**
61512891 ATAAAAATTCGTATGTATATA
1 ATAAAAATAAGTATGTATATA
61512912 CATATATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (22 bp):
ATAAAAATAAGTATGTATATAA
Found at i:61512929 original size:62 final size:62
Alignment explanation
Indices: 61512816--61512935 Score: 147
Period size: 62 Copynumber: 1.9 Consensus size: 62
61512806 AAATATGTAC
*
61512816 ATTTATATAAATGGAAAAAGTAGATATGTATATGTATATATATATTATAAAGCATAAAAATAAGT
1 ATTTATATAAAT-GAAAAAGTAGATATGTATA-GTACATATATATTATAAAG-ATAAAAATAAGT
* *
61512881 ATTTATATAAAT-AAAAATTCG-TATGTATA-TACATATATATTACATAAAGATAAAA
1 ATTTATATAAATGAAAAAGTAGATATGTATAGTACATATATATT--ATAAAGATAAAA
61512936 GGTATAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
60 11 0.22
61 6 0.12
62 14 0.28
63 7 0.14
65 12 0.24
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (62 bp):
ATTTATATAAATGAAAAAGTAGATATGTATAGTACATATATATTATAAAGATAAAAATAAGT
Found at i:61514375 original size:22 final size:24
Alignment explanation
Indices: 61514350--61514402 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 24
61514340 TTAAAATACG
61514350 TTAAAAATATTTTTTTT-TATTT-
1 TTAAAAATATTTTTTTTGTATTTA
*
61514372 TT-AAAATATTTTTTTTGTGTTTA
1 TTAAAAATATTTTTTTTGTATTTA
61514395 TTAAAAAT
1 TTAAAAAT
61514403 CGGGCTGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 6 0.22
23 2 0.07
24 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
TTAAAAATATTTTTTTTGTATTTA
Found at i:61519371 original size:14 final size:14
Alignment explanation
Indices: 61519350--61519383 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
61519340 TGATATGGGT
61519350 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
61519363 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
61519377 TTATAGG
1 TTATAGG
61519384 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:61523137 original size:23 final size:24
Alignment explanation
Indices: 61523103--61523147 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
61523093 GCCCGGCCCG
61523103 TTTTTAATTAAAATTAAAATTATT
1 TTTTTAATTAAAATTAAAATTATT
61523127 TTTTTAA-TAAAATTAAAATTA
1 TTTTTAATTAAAATTAAAATTA
61523148 ATTGCTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTTAATTAAAATTAAAATTATT
Found at i:61523159 original size:16 final size:16
Alignment explanation
Indices: 61523138--61523179 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
61523128 TTTTAATAAA
61523138 ATTAAAATTAATTGCT
1 ATTAAAATTAATTGCT
*
61523154 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGCT
*
61523170 AGTAAAATTA
1 ATTAAAATTA
61523180 TCAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTAAAATTAATTGCT
Found at i:61523249 original size:66 final size:59
Alignment explanation
Indices: 61523182--61523301 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
61523172 TAAAATTATC
* * *
61523182 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
61523240 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
61523299 AAA
1 AAA
61523302 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:61527384 original size:21 final size:20
Alignment explanation
Indices: 61527358--61527396 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
61527348 AATAATAGAT
*
61527358 TAATAACATATATAATAATGG
1 TAATAACAT-TAAAATAATGG
61527379 TAATAACATTAAAATAAT
1 TAATAACATTAAAATAAT
61527397 CAATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
TAATAACATTAAAATAATGG
Found at i:61527867 original size:9 final size:9
Alignment explanation
Indices: 61527850--61527886 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
61527840 TGAGTTTTCG
61527850 AATTCGAAT
1 AATTCGAAT
*
61527859 AACTCGAAT
1 AATTCGAAT
61527868 AATTCGAAT
1 AATTCGAAT
61527877 AATTCGAAT
1 AATTCGAAT
61527886 A
1 A
61527887 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:61527963 original size:21 final size:21
Alignment explanation
Indices: 61527922--61527964 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
61527912 ACCCCAAACT
* *
61527922 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
61527943 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
61527964 C
1 C
61527965 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:61528133 original size:30 final size:31
Alignment explanation
Indices: 61528099--61528158 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
61528089 AAACCTTTTA
*
61528099 TTTTCCCCCAAAATTTTTATTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
**
61528129 TTTTCCCTTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCA
61528159 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
Found at i:61530009 original size:22 final size:22
Alignment explanation
Indices: 61529984--61530066 Score: 63
Period size: 22 Copynumber: 3.9 Consensus size: 22
61529974 ATATTTCAAC
61529984 TATATTGATCTAAAATATTGTA
1 TATATTGATCTAAAATATTGTA
61530006 TATATTGGA-CTATTAAA-AGTT-T-
1 TATATT-GATCTA--AAATA-TTGTA
*
61530028 T-T-TT-ATATAAAATATTGTA
1 TATATTGATCTAAAATATTGTA
*
61530047 TATGTTGATCTAAAATATTG
1 TATATTGATCTAAAATATTG
61530067 CATAATCTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 22
0.67 0.03 0.31
Matches are distributed among these distances:
17 5 0.10
18 3 0.06
19 3 0.06
20 3 0.06
21 3 0.06
22 22 0.46
23 4 0.08
24 5 0.10
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (22 bp):
TATATTGATCTAAAATATTGTA
Found at i:61531483 original size:8 final size:8
Alignment explanation
Indices: 61531470--61531498 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
61531460 CACTAGAGAT
61531470 CAGTGTTA
1 CAGTGTTA
61531478 CAGTGTTA
1 CAGTGTTA
61531486 CAGTGTTA
1 CAGTGTTA
61531494 CAGTG
1 CAGTG
61531499 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:61531637 original size:23 final size:23
Alignment explanation
Indices: 61531585--61531637 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
61531575 AGTGTTATTG
61531585 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
61531608 TTTAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
61531631 ATCAGTG
1 ATCAGTG
61531638 TGGCACTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:61541557 original size:94 final size:93
Alignment explanation
Indices: 61541439--61541614 Score: 252
Period size: 94 Copynumber: 1.9 Consensus size: 93
61541429 TTAAGCAAGT
*
61541439 TAAATTTGTACTGGAGGTCTTGCTGTTAGCTAAAGTTGGCTAA-T-TTGATGATTGCCT-ATGTT
1 TAAATTTGTACTGGAGATCTTGCTGTTAGCTAAAGTTGG--AATTATTGATGATTG-CTGATGTT
61541501 TCTTTTAATTCCAAAAGATTACCGTTACCTAG
63 TCTTTTAA-TCCAAAAGATTACCGTTACCTAG
*
61541533 TAAACTTT-TACTGGAGATCTTGCTGTTAGCTAAAGTTGGAATTATTGATGATTGCTGATGTTTT
1 TAAA-TTTGTACTGGAGATCTTGCTGTTAGCTAAAGTTGGAATTATTGATGATTGCTGATGTTTC
*
61541597 TTTTTATCCAAAAGATTA
65 TTTTAATCCAAAAGATTA
61541615 AACGTTACGT
Statistics
Matches: 75, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
92 2 0.03
93 15 0.20
94 55 0.73
95 3 0.04
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (93 bp):
TAAATTTGTACTGGAGATCTTGCTGTTAGCTAAAGTTGGAATTATTGATGATTGCTGATGTTTCT
TTTAATCCAAAAGATTACCGTTACCTAG
Found at i:61546177 original size:67 final size:67
Alignment explanation
Indices: 61546100--61546234 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
61546090 TTCACTTTTG
61546100 TGTCTCTCTTTCATTTATCACCATGCAGTTTATTACTATGTACTTGGACTTAGGTGTGAGGGTAG
1 TGTCTCTCTTTCATTTATCACCATGCAGTTTATTACTATGTACTTGGACTTAGGTGTGAGGGTAG
61546165 GA
66 GA
61546167 TGTCTCTCTTTCATTTATCACCATGCAGTTTATTACTATGTACTTGGACTTAGGTGTGAGGGTAG
1 TGTCTCTCTTTCATTTATCACCATGCAGTTTATTACTATGTACTTGGACTTAGGTGTGAGGGTAG
61546232 GA
66 GA
61546234 T
1 T
61546235 ACAGTCATGC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (67 bp):
TGTCTCTCTTTCATTTATCACCATGCAGTTTATTACTATGTACTTGGACTTAGGTGTGAGGGTAG
GA
Found at i:61546718 original size:52 final size:52
Alignment explanation
Indices: 61546640--61546745 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
61546630 TAAGTTGTAT
61546640 TTGATACCCAAACATTCTTTCCTTAAATCTCATTGGCACATTCTTCCACTCA
1 TTGATACCCAAACATTCTTTCCTTAAATCTCATTGGCACATTCTTCCACTCA
*
61546692 TTGATACCCAAACATTCTTTCCTTAAATCTCATTGGTACATTCTTCCACTCA
1 TTGATACCCAAACATTCTTTCCTTAAATCTCATTGGCACATTCTTCCACTCA
61546744 TT
1 TT
61546746 TTTCCCAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (52 bp):
TTGATACCCAAACATTCTTTCCTTAAATCTCATTGGCACATTCTTCCACTCA
Found at i:61549004 original size:23 final size:23
Alignment explanation
Indices: 61548959--61549008 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
61548949 GGGTGTCAAT
*
61548959 GTTTAAATTAGTATTTATTTTTG
1 GTTTAAATTAGTATTTATATTTG
*
61548982 GTTTAAATTTGTATTTGA-ATTTG
1 GTTTAAATTAGTATTT-ATATTTG
61549005 GTTT
1 GTTT
61549009 TCATCACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (23 bp):
GTTTAAATTAGTATTTATATTTG
Found at i:61562188 original size:21 final size:22
Alignment explanation
Indices: 61562159--61562205 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
61562149 CAGAAAGAGT
*
61562159 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
*
61562181 GAGT-GTACTCCGCAGTAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
61562202 GAGT
1 GAGT
61562206 TTGAGCAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:61564293 original size:15 final size:15
Alignment explanation
Indices: 61564273--61564303 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
61564263 GTAGTGTGAC
61564273 TACCAAATTAATATT
1 TACCAAATTAATATT
61564288 TACCAAATTAATATT
1 TACCAAATTAATATT
61564303 T
1 T
61564304 CCGCTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (15 bp):
TACCAAATTAATATT
Found at i:61572384 original size:20 final size:20
Alignment explanation
Indices: 61572361--61572407 Score: 80
Period size: 18 Copynumber: 2.5 Consensus size: 20
61572351 TTTGGCGAAA
61572361 TCGTGTTTTGATCTTCGAGC
1 TCGTGTTTTGATCTTCGAGC
61572381 TCGTG--TTGATCTTCGAGC
1 TCGTGTTTTGATCTTCGAGC
61572399 TCGTGTTTT
1 TCGTGTTTT
61572408 TTTTTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 18 0.72
20 7 0.28
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.47
Consensus pattern (20 bp):
TCGTGTTTTGATCTTCGAGC
Found at i:61574843 original size:16 final size:16
Alignment explanation
Indices: 61574822--61574857 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
61574812 TGTTTCTCAG
61574822 TCTTCCTTGATAATGT
1 TCTTCCTTGATAATGT
61574838 TCTTCCTTGATAATGT
1 TCTTCCTTGATAATGT
61574854 TCTT
1 TCTT
61574858 TCATCTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (16 bp):
TCTTCCTTGATAATGT
Found at i:61578344 original size:26 final size:26
Alignment explanation
Indices: 61578309--61578380 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
61578299 ATATATTTTA
*
61578309 TTTTATTTTTTAATTTTAAAATACTTT
1 TTTTATTTTTTAATTTTAAAATA-ATT
*
61578336 TTTTATTTTTTATTTTTAAAATAA-T
1 TTTTATTTTTTAATTTTAAAATAATT
* *
61578361 TTTTAATGTTT-ATTTTAAAA
1 TTTTATTTTTTAATTTTAAAA
61578381 ATGGGTCGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 8 0.20
25 10 0.25
27 22 0.55
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTATTTTTTAATTTTAAAATAATT
Found at i:61578344 original size:27 final size:27
Alignment explanation
Indices: 61578309--61578364 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
61578299 ATATATTTTA
*
61578309 TTTTATTTTTTAATTTTAAAATACTTT
1 TTTTATTTTTTAATTTTAAAATAATTT
*
61578336 TTTTATTTTTTATTTTTAAAATAATTT
1 TTTTATTTTTTAATTTTAAAATAATTT
61578363 TT
1 TT
61578365 AATGTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTATTTTTTAATTTTAAAATAATTT
Found at i:61578381 original size:25 final size:25
Alignment explanation
Indices: 61578335--61578382 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
61578325 TAAAATACTT
* * *
61578335 TTTTTATTTTTTATTTTTAAAATAA
1 TTTTTAATGTTTATTTTAAAAATAA
61578360 TTTTTAATGTTTATTTTAAAAAT
1 TTTTTAATGTTTATTTTAAAAAT
61578383 GGGTCGGGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTTAATGTTTATTTTAAAAATAA
Found at i:61578887 original size:12 final size:12
Alignment explanation
Indices: 61578870--61578900 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
61578860 ACTTATTCGT
61578870 ATCAATTCTCAA
1 ATCAATTCTCAA
*
61578882 ATCAATTCTTAA
1 ATCAATTCTCAA
61578894 ATCAATT
1 ATCAATT
61578901 GGAACTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (12 bp):
ATCAATTCTCAA
Found at i:61581146 original size:11 final size:11
Alignment explanation
Indices: 61581132--61581158 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
61581122 AATATTAAAA
61581132 ATATATAGAAC
1 ATATATAGAAC
61581143 ATATATAGAAC
1 ATATATAGAAC
61581154 ATATA
1 ATATA
61581159 CAATACGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
ATATATAGAAC
Found at i:61581590 original size:14 final size:14
Alignment explanation
Indices: 61581540--61581592 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
61581530 GATAATAATA
*
61581540 AAAATAATAATATT
1 AAAATAAAAATATT
*
61581554 GAAATACAAAAGCTATT
1 AAAATA-AAAA--TATT
*
61581571 ATAATAAAAATATT
1 AAAATAAAAATATT
61581585 AAAATAAA
1 AAAATAAA
61581593 GTAATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 16 0.52
15 3 0.10
16 4 0.13
17 8 0.26
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (14 bp):
AAAATAAAAATATT
Found at i:61581658 original size:3 final size:3
Alignment explanation
Indices: 61581650--61581680 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
61581640 ACTAATGTAC
61581650 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
61581681 TTGAAATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:61581658 original size:123 final size:124
Alignment explanation
Indices: 61581444--61581674 Score: 299
Period size: 123 Copynumber: 1.9 Consensus size: 124
61581434 AAAAAGTAAA
* * *
61581444 TATAATAAAATGATATTAAAATAAAGTCATTAAAAACAGTAATATATGTATATATACATCTAATA
1 TATAATAAAA-GATATTAAAATAAAGTCAATAAAAACAGTAATACATATATATATACATC-AATA
* * * *
61581509 AGAATATATAGTAATGTTAATGATAATAATAAAAATAATAATATTGAAATACAAAAGCTAT
64 AGAATATACACTAATGTCAATAATAATAATAAAAATAATAATATTGAAATACAAAAGCTAT
* *
61581570 TATAATAAAA-ATATTAAAATAAAGT-AATAAAAACATTACTACATATATATATACAT-ACATGA
1 TATAATAAAAGATATTAAAATAAAGTCAATAAAAACAGTAATACATATATATATACATCA-AT-A
*
61581632 AG-ATATACACTAATGTACAATAATAATAATAATAATAATAATA
64 AGAATATACACTAATGT-CAATAATAATAATAAAAATAATAATA
61581675 ATAATATTGA
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
121 1 0.01
122 14 0.15
123 52 0.57
124 15 0.16
126 10 0.11
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (124 bp):
TATAATAAAAGATATTAAAATAAAGTCAATAAAAACAGTAATACATATATATATACATCAATAAG
AATATACACTAATGTCAATAATAATAATAAAAATAATAATATTGAAATACAAAAGCTAT
Found at i:61582961 original size:13 final size:13
Alignment explanation
Indices: 61582945--61582970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61582935 TTTATTTGGT
61582945 TTATTGGGTTTTG
1 TTATTGGGTTTTG
61582958 TTATTGGGTTTTG
1 TTATTGGGTTTTG
61582971 GGGTGGCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TTATTGGGTTTTG
Found at i:61584062 original size:31 final size:31
Alignment explanation
Indices: 61584027--61584097 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
61584017 TAAAGTTTTT
* **
61584027 ATTCAATGGCTTAAATGAAAACTTTTGAATA
1 ATTCAATGACTTAAATGAAAACTTTCAAATA
* * *
61584058 ATTCAGTAATTTAAATGAAAACTTTCAAATA
1 ATTCAATGACTTAAATGAAAACTTTCAAATA
61584089 ATTCAATGA
1 ATTCAATGA
61584098 TTATTTTATA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (31 bp):
ATTCAATGACTTAAATGAAAACTTTCAAATA
Found at i:61585542 original size:110 final size:114
Alignment explanation
Indices: 61585330--61585542 Score: 294
Period size: 110 Copynumber: 1.9 Consensus size: 114
61585320 TCAAAACCTT
*
61585330 AAATTTATTTCCAATTTTGCATAAAAAAATCATATTTTTTTCAAGGACAAAACACATGAAACACG
1 AAATTTATTCCCAATTTTGCATAAAAAAATCATATTTTTTTCAAGGACAAAACACATGAAACACG
*
61585395 AAATATAGCTGAATAAAACGACCCCAGAAGCTTACATTTCAATGCCTCC
66 AAATATAGCTAAATAAAACGACCCCAGAAGCTTACATTTCAATGCCTCC
* * * * *
61585444 AAATTTA-TCCCAATTTTGCATCAAAAATTCA-ATTTTTTT-AAGGATAAAACA-ATGAAATATG
1 AAATTTATTCCCAATTTTGCATAAAAAAATCATATTTTTTTCAAGGACAAAACACATGAAACACG
*
61585505 AAATATAGCTAAATTAAAA-GAACCCCA-AAGTTTACATT
66 AAATATAGCTAAA-TAAAACG-ACCCCAGAAGCTTACATT
61585543 ACAGCAAAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
110 31 0.35
111 22 0.25
112 8 0.09
113 21 0.24
114 7 0.08
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (114 bp):
AAATTTATTCCCAATTTTGCATAAAAAAATCATATTTTTTTCAAGGACAAAACACATGAAACACG
AAATATAGCTAAATAAAACGACCCCAGAAGCTTACATTTCAATGCCTCC
Found at i:61586203 original size:44 final size:42
Alignment explanation
Indices: 61586155--61586246 Score: 96
Period size: 44 Copynumber: 2.1 Consensus size: 42
61586145 GATACATGTC
61586155 TATTTAAATTTTGTTG-GAAAACATATGTTTCAATATTTTTAATG
1 TATTTAAA-TTTGTTGAG-AAACATATGTTTCAAT-TTTTTAATG
* * * **
61586199 TATTTTCAATTTGTTGAGAAACATTTGTTTTAATTTTTTTGTG
1 TA-TTTAAATTTGTTGAGAAACATATGTTTCAATTTTTTAATG
61586242 TATTT
1 TATTT
61586247 GATATATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
42 3 0.07
43 9 0.22
44 23 0.56
45 6 0.15
ACGTcount: A:0.28, C:0.04, G:0.12, T:0.55
Consensus pattern (42 bp):
TATTTAAATTTGTTGAGAAACATATGTTTCAATTTTTTAATG
Found at i:61587047 original size:20 final size:20
Alignment explanation
Indices: 61587024--61587067 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
61587014 AAACACCAAT
61587024 TTTTAAAAATATAAAAAATA
1 TTTTAAAAATATAAAAAATA
61587044 TTTTAAAAATATAAAAAATA
1 TTTTAAAAATATAAAAAATA
61587064 TTTT
1 TTTT
61587068 TTATTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTAAAAATATAAAAAATA
Found at i:61592570 original size:15 final size:15
Alignment explanation
Indices: 61592550--61592579 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
61592540 CTTTAATACA
61592550 ACCATTCTTGGTTGC
1 ACCATTCTTGGTTGC
61592565 ACCATTCTTGGTTGC
1 ACCATTCTTGGTTGC
61592580 TTTTCTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (15 bp):
ACCATTCTTGGTTGC
Found at i:61593940 original size:18 final size:16
Alignment explanation
Indices: 61593917--61593959 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 16
61593907 CACAAGTAAT
61593917 TTAAAAATTATAAACATA
1 TTAAAAATTA-AAA-ATA
61593935 TTAAAAAATTAAAAATA
1 TT-AAAAATTAAAAATA
61593952 TATAAAAA
1 T-TAAAAA
61593960 GTTCGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
19 8 0.35
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAAAAATA
Found at i:61593943 original size:19 final size:18
Alignment explanation
Indices: 61593919--61593959 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
61593909 CAAGTAATTT
61593919 AAAAATTATAAACATAT-TA
1 AAAAATTA-AAA-ATATATA
61593938 AAAAATTAAAAATATATA
1 AAAAATTAAAAATATATA
61593956 AAAA
1 AAAA
61593960 GTTCGTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATTAAAAATATATA
Found at i:61595539 original size:40 final size:40
Alignment explanation
Indices: 61595495--61595573 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
61595485 TACGTGGCAA
* * *
61595495 CAAAGCGCTCTTACGCGGACGCGCTTTGTTGCCACATAGG
1 CAAAGCGCGCTGACGCGGACGCGCTTTGCTGCCACATAGG
* *
61595535 CAAAGCGCGCTGACGTGGACGCGTTTTGCTGCCACATAG
1 CAAAGCGCGCTGACGCGGACGCGCTTTGCTGCCACATAG
61595574 CTCGCCCTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (40 bp):
CAAAGCGCGCTGACGCGGACGCGCTTTGCTGCCACATAGG
Found at i:61595743 original size:22 final size:22
Alignment explanation
Indices: 61595712--61595765 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
61595702 TCTCTCAATT
*
61595712 ATTT-TCTCAATTTCCTTTC-A
1 ATTTCTCTCAATTTCCTTCCAA
61595732 ATTTGCTCTCAATTTCCTTCCAA
1 ATTT-CTCTCAATTTCCTTCCAA
61595755 ATTTCTCTCAA
1 ATTTCTCTCAA
61595766 ATCCATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.13
22 21 0.70
23 5 0.17
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTCTCTCAATTTCCTTCCAA
Found at i:61595791 original size:51 final size:51
Alignment explanation
Indices: 61595727--61595826 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
61595717 CTCAATTTCC
*
61595727 TTTCAATTTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TTTCAATTTGCTCTCAATTTCCTCT-CAAATTTATCTCAAATCCATATTTAA
* * *
61595778 TTTCAATTTGCTCTCAATTTCCTCTTAAATTTATCTTAAATCCCTATTT
1 TTTCAATTTGCTCTCAATTTCCTCTCAAATTTATCTCAAATCCATATTT
61595827 TTAATTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.02, T:0.48
Consensus pattern (51 bp):
TTTCAATTTGCTCTCAATTTCCTCTCAAATTTATCTCAAATCCATATTTAA
Found at i:61596974 original size:7 final size:7
Alignment explanation
Indices: 61596962--61596987 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
61596952 TAGTCGATTG
61596962 GTATTTA
1 GTATTTA
61596969 GTATTTA
1 GTATTTA
61596976 GTATTTA
1 GTATTTA
61596983 GTATT
1 GTATT
61596988 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:61601057 original size:21 final size:21
Alignment explanation
Indices: 61601032--61601071 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61601022 ATGTAAGTTC
*
61601032 AAATATGT-TATAAATAATTCT
1 AAATAT-TATATAAAAAATTCT
61601053 AAATATTATATAAAAAATT
1 AAATATTATATAAAAAATT
61601072 AATAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATATTATATAAAAAATTCT
Found at i:61611548 original size:21 final size:20
Alignment explanation
Indices: 61611524--61611566 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
61611514 TAAAAAGTAA
*
61611524 AATTTAATTGATTGCAACATT
1 AATTAAATTGATTG-AACATT
* *
61611545 AATTAAATTTATTGACCATT
1 AATTAAATTGATTGAACATT
61611565 AA
1 AA
61611567 ATCATATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (20 bp):
AATTAAATTGATTGAACATT
Found at i:61614964 original size:21 final size:22
Alignment explanation
Indices: 61614921--61614966 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
61614911 TTATAGAGAT
* *
61614921 AAACTTGAATTTTTATGAGGAA
1 AAACATGAATTTTTATCAGGAA
*
61614943 AAACATGAATTTTTA-CATGAA
1 AAACATGAATTTTTATCAGGAA
61614964 AAA
1 AAA
61614967 AGCATTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (22 bp):
AAACATGAATTTTTATCAGGAA
Found at i:61616147 original size:30 final size:30
Alignment explanation
Indices: 61616080--61616154 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
61616070 GGTCATTTTT
* **
61616080 AATTATTAAATATAAACTTTTTTTTCTCAA
1 AATTATTAAATATAAAATTTTTTTAATCAA
61616110 AATTATTAAATATAAAATTGTTATTTAATC-A
1 AATTATTAAATATAAAATT-TT-TTTAATCAA
61616141 AA-TATTAACATATA
1 AATTATTAA-ATATA
61616155 TAAACATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 24 0.62
31 10 0.26
32 5 0.13
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (30 bp):
AATTATTAAATATAAAATTTTTTTAATCAA
Found at i:61616172 original size:18 final size:18
Alignment explanation
Indices: 61616142--61616179 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
61616132 ATTTAATCAA
*
61616142 ATATTAACATATATAAAC
1 ATATTAACATATAAAAAC
61616160 ATATTGAAC-TATAAAAAC
1 ATATT-AACATATAAAAAC
61616178 AT
1 AT
61616180 TTACATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATTAACATATAAAAAC
Found at i:61617518 original size:156 final size:156
Alignment explanation
Indices: 61617232--61617700 Score: 848
Period size: 156 Copynumber: 3.0 Consensus size: 156
61617222 GGAAAACCCT
* *
61617232 ACTGCTCCTGTATCTTATAATTCTGAGGAGGGAGTTGAATTGCTACCAAAGGTTTTAGATGATTG
1 ACTGCTCCTGTATCTTATAATTCTGAGGTGGGAGTTGAATTGCTACCAAAGGTTTTAGATGATTC
*
61617297 GACCATTGCCAACAGGATGGGTATGAATATGGAGCTGAACACTGAATTCCTACCATATCCTACAG
66 GACTATTGCCAACAGGATGGGTATGAATATGGAGCTGAACACTGAATTCCTACCATATCCTACAG
*
61617362 AAGATTCTACAAGTGCTAAAGAAATG
131 AAGATTCTACAAGTGCTAAAGAGATG
*
61617388 AGTGCTCCTGTATCTTATAATTCTGAGGTGGGAGTTGAATTGCTACCAAAGGTTTTAGATGATTC
1 ACTGCTCCTGTATCTTATAATTCTGAGGTGGGAGTTGAATTGCTACCAAAGGTTTTAGATGATTC
** *
61617453 GACTATTGCCAACAGGATCCGTATGAATATGGAGCTGAACACTGAATTGCTACCATATCCTACAG
66 GACTATTGCCAACAGGATGGGTATGAATATGGAGCTGAACACTGAATTCCTACCATATCCTACAG
61617518 AAGATTCTACAAGTGCTAAAGAGATG
131 AAGATTCTACAAGTGCTAAAGAGATG
*
61617544 ACTGCTCCTGTATTTTATAATTCTGAGGTGGGAGTTGAATTGCTACCAAAGGTTTTAGATGATTC
1 ACTGCTCCTGTATCTTATAATTCTGAGGTGGGAGTTGAATTGCTACCAAAGGTTTTAGATGATTC
*
61617609 GACTATTGCCAACAGGATGGGAATGAATATGGAGCTGAACACTGAATTCCTACCATATCCTACAG
66 GACTATTGCCAACAGGATGGGTATGAATATGGAGCTGAACACTGAATTCCTACCATATCCTACAG
61617674 AAGATTCTACAAGTGCTAAAGAGATG
131 AAGATTCTACAAGTGCTAAAGAGATG
61617700 A
1 A
61617701 ACATTGAATT
Statistics
Matches: 299, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
156 299 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (156 bp):
ACTGCTCCTGTATCTTATAATTCTGAGGTGGGAGTTGAATTGCTACCAAAGGTTTTAGATGATTC
GACTATTGCCAACAGGATGGGTATGAATATGGAGCTGAACACTGAATTCCTACCATATCCTACAG
AAGATTCTACAAGTGCTAAAGAGATG
Found at i:61620061 original size:54 final size:54
Alignment explanation
Indices: 61619960--61620069 Score: 130
Period size: 54 Copynumber: 2.0 Consensus size: 54
61619950 TCCACTCCTC
* * *
61619960 CATCTCTTTAGGACCTGTAGAATCTTCACTAGGCTTTGGTAACAATTCAATGTT
1 CATCTCTTTAGCACCTGTAGAATCTTCACTAGGATATGGTAACAATTCAATGTT
* ** * ** *
61620014 CATCTCTTTAGCACTTGTAGAATCTTCTGTAGGATATGTTAGGAATTCAGTGTT
1 CATCTCTTTAGCACCTGTAGAATCTTCACTAGGATATGGTAACAATTCAATGTT
61620068 CA
1 CA
61620070 GCTCCATATT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (54 bp):
CATCTCTTTAGCACCTGTAGAATCTTCACTAGGATATGGTAACAATTCAATGTT
Found at i:61620297 original size:156 final size:156
Alignment explanation
Indices: 61620013--61620481 Score: 848
Period size: 156 Copynumber: 3.0 Consensus size: 156
61620003 AATTCAATGT
*
61620013 TCATCTCTTTAGCACTTGTAGAATCTTCTGTAGGATATGTTAGGAATTCAGTGTTCAGCTCCATA
1 TCATCTCTTTAGCACTTGTAGAATCTTCTGTAGGATATGGTAGGAATTCAGTGTTCAGCTCCATA
*
61620078 TTCATTCCCATCCTGTTGGCAATAGTCGAATCATCTAAAACCTTTGGTAGCAATTCAACTCCCAC
66 TTCATACCCATCCTGTTGGCAATAGTCGAATCATCTAAAACCTTTGGTAGCAATTCAACTCCCAC
61620143 CTCAGAATTATAAGATACAGGAGCAG
131 CTCAGAATTATAAGATACAGGAGCAG
*
61620169 TCATCTCTTTAGCACTTGTAGAATCTTCTGTAGGATATGGTAGCAATTCAGTGTTCAGCTCCATA
1 TCATCTCTTTAGCACTTGTAGAATCTTCTGTAGGATATGGTAGGAATTCAGTGTTCAGCTCCATA
** *
61620234 TTCATACGGATCCTGTTGGCAATAGTCGAATCATCTAAAACCTTAGGTAGCAATTCAACTCCCAC
66 TTCATACCCATCCTGTTGGCAATAGTCGAATCATCTAAAACCTTTGGTAGCAATTCAACTCCCAC
*
61620299 CTCAGAATTATAAGATACAGGAGCAC
131 CTCAGAATTATAAGATACAGGAGCAG
*
61620325 TCATTTCTTTAGCACTTGTAGAATCTTCTGTAGGATATGGTAGGAATTCAGTGTTCAGCTCCATA
1 TCATCTCTTTAGCACTTGTAGAATCTTCTGTAGGATATGGTAGGAATTCAGTGTTCAGCTCCATA
* *
61620390 TTCATACCCATCCTGTTGGCAATGGTCCAATCATCTAAAACCTTTGGTAGCAATTCAACTCCCAC
66 TTCATACCCATCCTGTTGGCAATAGTCGAATCATCTAAAACCTTTGGTAGCAATTCAACTCCCAC
61620455 CTCAGAATTATAAGATACAGGAGCAG
131 CTCAGAATTATAAGATACAGGAGCAG
61620481 T
1 T
61620482 AGGATTTTCC
Statistics
Matches: 298, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 298 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (156 bp):
TCATCTCTTTAGCACTTGTAGAATCTTCTGTAGGATATGGTAGGAATTCAGTGTTCAGCTCCATA
TTCATACCCATCCTGTTGGCAATAGTCGAATCATCTAAAACCTTTGGTAGCAATTCAACTCCCAC
CTCAGAATTATAAGATACAGGAGCAG
Found at i:61625249 original size:24 final size:25
Alignment explanation
Indices: 61625216--61625271 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
61625206 GCATTGATGC
*
61625216 ACCTAAAAAT-GATCATGA-GTGCTT
1 ACCTATAAATAGATCAT-ATGTGCTT
61625240 ACCTATAAATCAGATCATATGTGCTT
1 ACCTATAAAT-AGATCATATGTGCTT
*
61625266 AACTAT
1 ACCTAT
61625272 GTTACACGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.33
25 1 0.04
26 17 0.63
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (25 bp):
ACCTATAAATAGATCATATGTGCTT
Found at i:61633084 original size:19 final size:19
Alignment explanation
Indices: 61633060--61633107 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
61633050 ATATATTAAA
*
61633060 AATTTTAAAAATAAATAAT
1 AATTTTAAAAATAAAGAAT
* *
61633079 AATTTTAAATATTAAGAAT
1 AATTTTAAAAATAAAGAAT
61633098 AA-TTTAAAAA
1 AATTTTAAAAA
61633108 ACTATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTTTAAAAATAAAGAAT
Found at i:61634333 original size:27 final size:26
Alignment explanation
Indices: 61634295--61634347 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
61634285 TAAATATGGA
61634295 TAAACTATAAAAATAGTCACTTTTGT
1 TAAACTATAAAAATAGTCACTTTTGT
*
61634321 TAAACTATAAAAATAGTTACTTTTGT
1 TAAACTATAAAAATAGTCACTTTTGT
61634347 T
1 T
61634348 TGTCTCAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (26 bp):
TAAACTATAAAAATAGTCACTTTTGT
Found at i:61644443 original size:26 final size:26
Alignment explanation
Indices: 61644414--61644467 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
61644404 AATTTCTACG
61644414 CTTTGATTTTTACATAATTTAGACTC
1 CTTTGATTTTTACATAATTTAGACTC
61644440 CTTTGATTTTTACATAATTTAGACTC
1 CTTTGATTTTTACATAATTTAGACTC
61644466 CT
1 CT
61644468 GTCCGTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (26 bp):
CTTTGATTTTTACATAATTTAGACTC
Found at i:61644601 original size:31 final size:30
Alignment explanation
Indices: 61644560--61644622 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
61644550 TATATAAGAA
*
61644560 TTGTTAAATTTCAGTTTTAATCCTTATATT
1 TTGTTAAATTTCAGATTTAATCCTTATATT
* *
61644590 TTGTTCAAATTTGAGATTTAATCTTTATATT
1 TTGTT-AAATTTCAGATTTAATCCTTATATT
61644621 TT
1 TT
61644623 AATATTGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (30 bp):
TTGTTAAATTTCAGATTTAATCCTTATATT
Found at i:61644756 original size:149 final size:150
Alignment explanation
Indices: 61644483--61644785 Score: 371
Period size: 149 Copynumber: 2.0 Consensus size: 150
61644473 TTCTTTTTCT
* *
61644483 TAATTTTCTTTTGACATGAGAAAACAATGGCTAAATTTCAGTATTAATCCCTCTACCTTTTTGAG
1 TAATTTTCTTTTGACATGAGAAAACAATGGCTAAATTTCAGTATTAATCCATCTACCTTTTTAAG
* ** * * * * * *
61644548 ATTATATAAGAATTGTTAAATTTCAGTTTTAATCCTTATATTTTGTTCAAATTTGAGATTTAATC
66 ATTATATAAGAATGGTTAAATTTCAAATTTAACCCCTATAATGTGCTCAAATTTAAGATTTAATC
* *
61644613 TTTATA-TTTTAATATTGACA
131 TCTATACTTTGAAT-TTGACA
* *
61644633 TAATTTTCTTTTGACATGAG-AAATAATGGCTAAATTTCAGT-TATAATTCATCTA-CTTTTTAA
1 TAATTTTCTTTTGACATGAGAAAACAATGGCTAAATTTCAGTAT-TAATCCATCTACCTTTTT-A
* ** *
61644695 AGATTATATAAGAATGGTTAAATTTTAAATTTGGCCCCTATAATGTGCTCAATTTTAAGATTTAA
64 AGATTATATAAGAATGGTTAAATTTCAAATTTAACCCCTATAATGTGCTCAAATTTAAGATTTAA
*
61644760 TCTCTATACTTTGAGTTTGACA
129 TCTCTATACTTTGAATTTGACA
61644782 TAAT
1 TAAT
61644786 CCAAATTAAA
Statistics
Matches: 130, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
148 7 0.05
149 98 0.75
150 25 0.19
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (150 bp):
TAATTTTCTTTTGACATGAGAAAACAATGGCTAAATTTCAGTATTAATCCATCTACCTTTTTAAG
ATTATATAAGAATGGTTAAATTTCAAATTTAACCCCTATAATGTGCTCAAATTTAAGATTTAATC
TCTATACTTTGAATTTGACA
Found at i:61648920 original size:149 final size:146
Alignment explanation
Indices: 61648649--61649080 Score: 519
Period size: 149 Copynumber: 2.9 Consensus size: 146
61648639 ATCAATCAAC
* *
61648649 CAACCAACAACTACAACAAATAAAAGAATCCCTTTATCTAAACATCAAATAAATCATTAAATTCC
1 CAACCAACAACTACAACAAAAAAAAGAAT-CCTTTATCTAAACATTAAATAAATCATTAAATTCC
** * * * *
61648714 ATAAAAAAAAAACACTGATTGTTGAAGATTCAAACGGGAAAACCCTCAAAGTTGTTTCCAAACTA
65 A-AGGAAAAAAACCCTAATTGTTGAAGATTCAAACGGGAAAACCCTCAAAATCGTTTCCAAACTA
*
61648779 TAAATAAATTTAAAAAAT
129 TAAATAAATTTAAAAAAG
* *
61648797 CAACCAACAACTACAACAAAAAAAAAGAATACCTTTATCTCAACATTAAATAAATCATTAATTTC
1 CAACCAACAACTACAAC-AAAAAAAAGAAT-CCTTTATCTAAACATTAAATAAATCATTAAATTC
* *
61648862 CAACGGAAAAAAACCCTAATTGTGGAAGATTCAAACGGGAAAACCCTCAAAATCGTTTCCAAACA
64 CAA-GGAAAAAAACCCTAATTGTTGAAGATTCAAACGGGAAAACCCTCAAAATCGTTTCCAAACT
*
61648927 ATAATTAAA-TTAAAAAAG
128 ATAAATAAATTTAAAAAAG
* * ** * * * ** * * * *
61648945 CCA-CATCCTCTTCAACTACAACGACAAT-CTTTATCTGAACAATAAATAAATTATTAAATTCCA
1 CAACCAACAACTACAACAAAAAAAAGAATCCTTTATCTAAACATTAAATAAATCATTAAATTCCA
* * * *
61649008 AGGAAAAAACCCCTAATTGTTGAAGATTCAAACGAGAAAACCCTCAAAATCGTTTTCAAACTACA
66 AGGAAAAAAACCCTAATTGTTGAAGATTCAAACGGGAAAACCCTCAAAATCGTTTCCAAACTATA
61649073 AATAAATT
131 AATAAATT
61649081 CAAAGCAGCC
Statistics
Matches: 245, Mismatches: 36, Indels: 10
0.84 0.12 0.03
Matches are distributed among these distances:
143 63 0.26
144 33 0.13
146 7 0.03
147 9 0.04
148 28 0.11
149 105 0.43
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (146 bp):
CAACCAACAACTACAACAAAAAAAAGAATCCTTTATCTAAACATTAAATAAATCATTAAATTCCA
AGGAAAAAAACCCTAATTGTTGAAGATTCAAACGGGAAAACCCTCAAAATCGTTTCCAAACTATA
AATAAATTTAAAAAAG
Found at i:61649893 original size:21 final size:21
Alignment explanation
Indices: 61649869--61649908 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
61649859 TTTTCGGATC
* *
61649869 GAGTTGAGTAAAATGAAGTTT
1 GAGTCGAGTAAAATCAAGTTT
*
61649890 GAGTCGAGTCAAATCAAGT
1 GAGTCGAGTAAAATCAAGT
61649909 GTAATTGTTT
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:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (21 bp):
GAGTCGAGTAAAATCAAGTTT
Found at i:61677316 original size:181 final size:181
Alignment explanation
Indices: 61677012--61677374 Score: 726
Period size: 181 Copynumber: 2.0 Consensus size: 181
61677002 GATGTTTTTT
61677012 AAGCAAAGTTTCGATTTTAATTATTGTAAATAAAAATAAATTTAGAGAGCTTTCTTCTCGTTTGA
1 AAGCAAAGTTTCGATTTTAATTATTGTAAATAAAAATAAATTTAGAGAGCTTTCTTCTCGTTTGA
61677077 GGTTTGAAATGGCTCGACTGTTAAAAAAAGTCTTACTTTTCGATTTAGAGTACCAAGTTAAGAAA
66 GGTTTGAAATGGCTCGACTGTTAAAAAAAGTCTTACTTTTCGATTTAGAGTACCAAGTTAAGAAA
61677142 AGATGTCAAATTCAAATAAAAAATGAATATTTAAGCTTTTTTATGTTAGGC
131 AGATGTCAAATTCAAATAAAAAATGAATATTTAAGCTTTTTTATGTTAGGC
61677193 AAGCAAAGTTTCGATTTTAATTATTGTAAATAAAAATAAATTTAGAGAGCTTTCTTCTCGTTTGA
1 AAGCAAAGTTTCGATTTTAATTATTGTAAATAAAAATAAATTTAGAGAGCTTTCTTCTCGTTTGA
61677258 GGTTTGAAATGGCTCGACTGTTAAAAAAAGTCTTACTTTTCGATTTAGAGTACCAAGTTAAGAAA
66 GGTTTGAAATGGCTCGACTGTTAAAAAAAGTCTTACTTTTCGATTTAGAGTACCAAGTTAAGAAA
61677323 AGATGTCAAATTCAAATAAAAAATGAATATTTAAGCTTTTTTATGTTAGGC
131 AGATGTCAAATTCAAATAAAAAATGAATATTTAAGCTTTTTTATGTTAGGC
61677374 A
1 A
61677375 TGATACTAAT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
181 182 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (181 bp):
AAGCAAAGTTTCGATTTTAATTATTGTAAATAAAAATAAATTTAGAGAGCTTTCTTCTCGTTTGA
GGTTTGAAATGGCTCGACTGTTAAAAAAAGTCTTACTTTTCGATTTAGAGTACCAAGTTAAGAAA
AGATGTCAAATTCAAATAAAAAATGAATATTTAAGCTTTTTTATGTTAGGC
Found at i:61679677 original size:232 final size:224
Alignment explanation
Indices: 61679324--61679775 Score: 518
Period size: 232 Copynumber: 2.0 Consensus size: 224
61679314 TTGCTTTTCT
* *
61679324 TTGTGGCTATTTCACCTAAAAAGCTAAAAAATAAATTTATCAGTTAAATTTGATTGAAATGCATA
1 TTGTGACTATTTCACCTAAAAAGCTAAAAAATAAATTTATCAGCTAAATTTGATTGAAAT-CATA
* * * * * *
61679389 TAAAAAATGGAAACAGCAAAATTCCAAGATGTTCATTTTCATATGTTCTTATTCTTTTAAAATTA
65 CAAAAAATAGAAACACCAAAATTCCAAGATATTCATTTCCATATGTTCTCATTCTTTTAAAATTA
* * * * * *
61679454 ACCCT-CAATGTCACAAAGAATAGCAAAACTACAAAAAAGAAGATCAAATTACACAATGTGTAAA
130 A-CATACAATGTCACAAAGAAAAACAAAACT---AAAAA-AAGACCAAATTAAAAAATGTGTAAA
*
61679518 TGTTGAGGGTTAATTTTTTTTAGAATCAAGACTAAA
190 TGTTGAGGATT-ATTTTTTTTAGAATCAAGACTAAA
* * * *
61679554 TTGTGACTCTTTCGCCTAGAAAAGCTAACAAAGA-AAATTTATTAGCTAATTTTGATTGAAAAT-
1 TTGTGACTATTTCACCTA-AAAAGCTAA-AAA-ATAAATTTATCAGCTAAATTTGATTG-AAATC
* *
61679617 ATACAAAAAATAGAAACACCAAAAAATT-CAAGATATT-AGTTTCCATCTTTTCTCATTCTTTTA
62 ATACAAAAAATAGAAACACC--AAAATTCCAAGATATTCA-TTTCCATATGTTCTCATTCTTTTA
* * *
61679680 AAATTAACATACAGTGTCACAAAGAAAAATAAAACTAAAAAAATACCAAATTAAAAAATGTGTAA
124 AAATTAACATACAATGTCACAAAGAAAAACAAAACTAAAAAAAGACCAAATTAAAAAATGTGTAA
*
61679745 ATGTTGAGGATTATTTTTTTTAGAATTAAGA
189 ATGTTGAGGATTATTTTTTTTAGAATCAAGA
61679776 TTGAATTAAC
Statistics
Matches: 189, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
227 18 0.10
228 31 0.16
229 5 0.03
230 15 0.08
231 29 0.15
232 80 0.42
233 11 0.06
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.32
Consensus pattern (224 bp):
TTGTGACTATTTCACCTAAAAAGCTAAAAAATAAATTTATCAGCTAAATTTGATTGAAATCATAC
AAAAAATAGAAACACCAAAATTCCAAGATATTCATTTCCATATGTTCTCATTCTTTTAAAATTAA
CATACAATGTCACAAAGAAAAACAAAACTAAAAAAAGACCAAATTAAAAAATGTGTAAATGTTGA
GGATTATTTTTTTTAGAATCAAGACTAAA
Found at i:61683702 original size:20 final size:20
Alignment explanation
Indices: 61683677--61683719 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
61683667 TTAGTCTCTA
61683677 AACCCAAAAATCAACTAACT
1 AACCCAAAAATCAACTAACT
61683697 AACCCAAAAATCAACTAACT
1 AACCCAAAAATCAACTAACT
61683717 AAC
1 AAC
61683720 ATTTCCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.56, C:0.30, G:0.00, T:0.14
Consensus pattern (20 bp):
AACCCAAAAATCAACTAACT
Found at i:61685022 original size:14 final size:14
Alignment explanation
Indices: 61684996--61685046 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
61684986 GAAAACAAAA
61684996 GAAATAAAATAAAG
1 GAAATAAAATAAAG
*
61685010 GAAATAAAGTAAAG
1 GAAATAAAATAAAG
* * *
61685024 TAAGTTAAAATAAAA
1 GAA-ATAAAATAAAG
61685039 G-AATAAAA
1 GAAATAAAA
61685047 GAAACAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.18
Consensus pattern (14 bp):
GAAATAAAATAAAG
Found at i:61685057 original size:17 final size:16
Alignment explanation
Indices: 61685035--61685068 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61685025 AAGTTAAAAT
61685035 AAAAGAATAAAAGAAAC
1 AAAAGAA-AAAAGAAAC
*
61685052 AAAAGAAGAAAGAAAC
1 AAAAGAAAAAAGAAAC
61685068 A
1 A
61685069 GAATAGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAC
Found at i:61685999 original size:24 final size:24
Alignment explanation
Indices: 61685945--61686016 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
61685935 TGTGTGAAGT
*
61685945 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
61685968 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
61685993 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
61686017 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:61686219 original size:37 final size:39
Alignment explanation
Indices: 61686160--61686255 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
61686150 CGGATAGATT
* * * *
61686160 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
61686197 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
61686236 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
61686256 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:61687858 original size:21 final size:21
Alignment explanation
Indices: 61687832--61687885 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
61687822 AAGGAGGTAA
*
61687832 TTTTACATTGACTGGAAAACC
1 TTTTACATTGACGGGAAAACC
*
61687853 TTTTACATTGACGGGAAAGCC
1 TTTTACATTGACGGGAAAACC
61687874 TTTTACATTGAC
1 TTTTACATTGAC
61687886 CATCCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (21 bp):
TTTTACATTGACGGGAAAACC
Found at i:61694694 original size:51 final size:52
Alignment explanation
Indices: 61694634--61694749 Score: 189
Period size: 51 Copynumber: 2.2 Consensus size: 52
61694624 AATGAGTACT
*
61694634 AAATTATAATTATGTTGGAACTTGGCTTTTAATTATAATAAGAAT-GGGACG
1 AAATTATAATTATGTTGGAACTTGGCTTTTAATAATAATAAGAATGGGGACG
* **
61694685 AAATTATAATTATGTTGGAACTTGTCTTTTAATAATAATACTAATGGGGACG
1 AAATTATAATTATGTTGGAACTTGGCTTTTAATAATAATAAGAATGGGGACG
61694737 AAATTATAATTAT
1 AAATTATAATTAT
61694750 ATTTGAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 41 0.68
52 19 0.32
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (52 bp):
AAATTATAATTATGTTGGAACTTGGCTTTTAATAATAATAAGAATGGGGACG
Found at i:61702255 original size:185 final size:182
Alignment explanation
Indices: 61701945--61702285 Score: 472
Period size: 185 Copynumber: 1.9 Consensus size: 182
61701935 TCTTGATCAG
* * * *
61701945 GCAAAAGTTAGTGAGGGTTTGTAAAGAAAAACCCTCACCGGCTTTTACTTGATAGATCAAAATGT
1 GCAAAAGTTAATGAGGGGTTGCAAAGAAAAACCCTCACCGGCTTTTACTTGATAGATCAAAATAT
* ***
61702010 TTACTTGGTTTACTTACTTAACTCTTAAAAAGCCATAGCTAGATTCTTAGAAATAGATCTAGAAG
66 TTACTCGGTTTACTTAAGAAACTCTTAAAAAGCCATAGCTAGATTCTTAGAAATAGATCTAGAAG
61702075 TTTACTCGACTCAATCACCTAGAAGGGGAAAAATTCTCTTCAACCAGGTGAA
131 TTTACTCGACTCAATCACCTAGAAGGGGAAAAATTCTCTTCAACCAGGTGAA
* * *
61702127 GCAAAAGTTAATGAGGGGTTGCAAAGGAAAGCCCTCA-CGGACTTTTGCTTGATAGAT-AAAGAT
1 GCAAAAGTTAATGAGGGGTTGCAAAGAAAAACCCTCACCGG-CTTTTACTTGATAGATCAAA-AT
* *
61702190 ATTTACTCGGTTTAATCATTAAGAAACTCTTAAAAAAG-CATAGTTAGATTGTTAGAAATAGATC
64 ATTTACTCGGTTT-A-C-TTAAGAAACTCTT-AAAAAGCCATAGCTAGATTCTTAGAAATAGATC
* *
61702254 TAGAAGTTTACTTGACTTAATCACCTAGAAGG
125 TAGAAGTTTACTCGACTCAATCACCTAGAAGG
61702286 AGAACCCCCC
Statistics
Matches: 138, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
181 6 0.04
182 60 0.43
183 1 0.01
184 1 0.01
185 64 0.46
186 6 0.04
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (182 bp):
GCAAAAGTTAATGAGGGGTTGCAAAGAAAAACCCTCACCGGCTTTTACTTGATAGATCAAAATAT
TTACTCGGTTTACTTAAGAAACTCTTAAAAAGCCATAGCTAGATTCTTAGAAATAGATCTAGAAG
TTTACTCGACTCAATCACCTAGAAGGGGAAAAATTCTCTTCAACCAGGTGAA
Found at i:61708367 original size:6 final size:6
Alignment explanation
Indices: 61708356--61708381 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
61708346 CGTTGAATCT
61708356 TGAGAA TGAGAA TGAGAA TGAGAA TG
1 TGAGAA TGAGAA TGAGAA TGAGAA TG
61708382 TAGGGAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (6 bp):
TGAGAA
Found at i:61715861 original size:179 final size:178
Alignment explanation
Indices: 61715562--61715920 Score: 682
Period size: 179 Copynumber: 2.0 Consensus size: 178
61715552 CTTGTCATCA
61715562 ATGAGTTAAATGTTGGGGGTTCAATATGGTTATTTTCTAGGGATAAAGTAACATTTAGTCTCTGA
1 ATGAGTTAAATGTTGGGGGTTCAATATGGTTATTTTCTAGGGATAAAGTAACATTTAGTCTCTGA
61715627 ATTTGACAATTTTTCGCAATTTGATCCATTAATTTTCTTTTGTCTATATTAGTCTCGGAACCAAA
66 ATTTGACAATTTTTCGCAATTTGATCCATTAATTTTCTTTTGTCTATATTAGTCTCGGAACCAAA
61715692 CAATCATTTCCGATCTTATCCCTGAATTTGGATTCAGTTAAGGTATTG
131 CAATCATTTCCGATCTTATCCCTGAATTTGGATTCAGTTAAGGTATTG
*
61715740 ATGAGTTAAATGTTGGGGGGTTCAATATGGTTATTTTCTAGGGATAAAGTAATATTTAGTCTCTG
1 ATGAGTTAAATGTT-GGGGGTTCAATATGGTTATTTTCTAGGGATAAAGTAACATTTAGTCTCTG
*
61715805 AATTTGACAATTTTTCGCAATTTGATCCCTTAATTTTCTTTTGTCTATATTAGTCTCGGAACCAA
65 AATTTGACAATTTTTCGCAATTTGATCCATTAATTTTCTTTTGTCTATATTAGTCTCGGAACCAA
*
61715870 GCAATCATTTCCGATCTTATCCCTGAATTTGGATTCAGTTAAGGTATTG
130 ACAATCATTTCCGATCTTATCCCTGAATTTGGATTCAGTTAAGGTATTG
61715919 AT
1 AT
61715921 AATGTGACAC
Statistics
Matches: 177, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
178 14 0.08
179 163 0.92
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (178 bp):
ATGAGTTAAATGTTGGGGGTTCAATATGGTTATTTTCTAGGGATAAAGTAACATTTAGTCTCTGA
ATTTGACAATTTTTCGCAATTTGATCCATTAATTTTCTTTTGTCTATATTAGTCTCGGAACCAAA
CAATCATTTCCGATCTTATCCCTGAATTTGGATTCAGTTAAGGTATTG
Done.