Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 8 of 214
Found at i:2481352 original size:18 final size:18
Alignment explanation
Indices: 2481331--2481762 Score: 227
Period size: 17 Copynumber: 25.0 Consensus size: 18
2481321 AAATTTAGTG
2481331 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
2481349 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
2481367 TCTTT-GTGTTTTCAAAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
2481385 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
2481402 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT--TCAAAAA
* *
2481422 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
2481440 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
2481457 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
2481475 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
2481491 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
2481509 TTCTCGCG-TTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
**
2481526 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
2481544 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
2481558 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
2481573 ---TCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
2481587 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
2481604 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
2481621 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
2481638 TTCCCGTG-TTTCAAAAAAAA
1 TTTTCGTGTTTTC---AAAAA
* *
2481658 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
2481676 ATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
2481695 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
2481712 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
2481728 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
2481746 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
2481763 AAACTTTCGT
Statistics
Matches: 319, Mismatches: 60, Indels: 71
0.71 0.13 0.16
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 9 0.03
15 3 0.01
16 21 0.07
17 124 0.39
18 113 0.35
19 12 0.04
20 27 0.08
21 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:2481451 original size:55 final size:53
Alignment explanation
Indices: 2481331--2481467 Score: 157
Period size: 55 Copynumber: 2.5 Consensus size: 53
2481321 AAATTTAGTG
** **
2481331 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTTTCAAAAA
* * * *
2481385 TTCTGGCGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTT--GTGTTTTCAAAAA
* *
2481440 TTTTCGTGTTTCACAAATTCTCGTGTTT
1 TTTTCGTGTTTCAAAAATTTTCGTGTTT
2481468 TCAAAAACTC
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
53 28 0.41
54 5 0.07
55 35 0.51
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (53 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTTTCAAAAA
Found at i:2481484 original size:73 final size:73
Alignment explanation
Indices: 2481344--2481485 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 73
2481334 TCGTGTTTTC
* * * *
2481344 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATTTTCGT
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
2481409 GTTTAAAA
66 GTTTAAAA
* * *
2481417 AAAAATTTACGTGTTTTCACAAAT-TTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAA-CTCC
1 AAAAATTTACGTGTTTTCAAAAATCTTT-GTGTTTTCAAAAATTCTCGCG-TTTCAAAAATCTCC
2481479 AGTGTTT
64 -GTGTTT
2481486 CAAAGTTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
72 19 0.32
73 40 0.68
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (73 bp):
AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
GTTTAAAA
Found at i:2481763 original size:18 final size:18
Alignment explanation
Indices: 2481334--2481762 Score: 207
Period size: 18 Copynumber: 24.8 Consensus size: 18
2481324 TTTAGTGTTT
*
2481334 TCGTGTTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
2481352 TCGTGTTTTCAAAAA-TC
1 TCGTGTTTTCAAAAATTC
*
2481369 TTTGTGTTTTCAAAAATTC
1 -TCGTGTTTTCAAAAATTC
* * *
2481388 TGGCG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
**
2481405 TCGTGTTTAAAAAAAAATT-
1 TCGTGTTT--TCAAAAATTC
* *
2481424 TACGTGTTTTCACAAATTT
1 T-CGTGTTTTCAAAAATTC
*
2481443 TCGTG-TTTCACAAATTC
1 TCGTGTTTTCAAAAATTC
*
2481460 TCGTGTTTTCAAAAACTC
1 TCGTGTTTTCAAAAATTC
**
2481478 -CAGTG-TTTCAAAGTTTC
1 TC-GTGTTTTCAAAAATTC
*
2481495 -CATGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* ** *
2481512 TCGCGTTTAAAAAAAAT-
1 TCGTGTTTTCAAAAATTC
2481529 TCGTG-TTTCAAAATATTC
1 TCGTGTTTTCAAAA-ATTC
**
2481547 TCG-CATTTC---AATT-
1 TCGTGTTTTCAAAAATTC
* **
2481560 T-TTGTTTT-TTAAA---
1 TCGTGTTTTCAAAAATTC
* *
2481573 TCGTG-TTTCAAAAAATG
1 TCGTGTTTTCAAAAATTC
*
2481590 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTC
*
2481607 TCGTG-TTTCTAAAATT-
1 TCGTGTTTTCAAAAATTC
*
2481623 TCCCTGTTTT-AAAAATTC
1 T-CGTGTTTTCAAAAATTC
* * *
2481641 CCGTG-TTTCAAAAAAAAATG
1 TCGTGTTTTC---AAAAATTC
*
2481661 TCGTGTTTTAAGAAAATT-
1 TCGTGTTTTCA-AAAATTC
* *
2481679 TCGTTTTTTCTAAAAATTT
1 TCGTGTTTTC-AAAAATTC
* *
2481698 TCGTG-TTTCTAAAATTT
1 TCGTGTTTTCAAAAATTC
*
2481715 TCGTG-TTT-ACAAATTC
1 TCGTGTTTTCAAAAATTC
2481731 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
2481749 TCGTGTTTT-AAAAA
1 TCGTGTTTTCAAAAA
2481763 AAACTTTCGT
Statistics
Matches: 316, Mismatches: 57, Indels: 77
0.70 0.13 0.17
Matches are distributed among these distances:
13 8 0.03
14 8 0.03
15 3 0.01
16 25 0.08
17 115 0.36
18 116 0.37
19 14 0.04
20 24 0.08
21 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:2493886 original size:252 final size:252
Alignment explanation
Indices: 2493441--2494231 Score: 1467
Period size: 252 Copynumber: 3.1 Consensus size: 252
2493431 CTTTCCAAGG
** *
2493441 AAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTC
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTC
*
2493506 ATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 ATATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
2493571 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCT
131 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCT
2493636 AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTATTTTTCA
196 AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTATTTTTCA
2493693 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTC
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTC
2493758 ATATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 ATATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
2493823 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCT
131 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCT
2493888 AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTATTTTTCA
196 AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTATTTTTCA
*
2493945 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTC
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTC
2494010 ATATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 ATATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
*
2494075 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAATCAACTCATATTGCT
131 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCT
* * ***
2494140 AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAATTTCTGTT-GTTAAAA
196 AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTATTTTTCA
*
2494196 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCT
2494232 CAGGACACGC
Statistics
Matches: 526, Mismatches: 13, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
251 37 0.07
252 489 0.93
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (252 bp):
AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTC
ATATTGCGAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCT
AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTATTTTTCA
Found at i:2494178 original size:123 final size:123
Alignment explanation
Indices: 2493448--2494194 Score: 950
Period size: 123 Copynumber: 6.0 Consensus size: 123
2493438 AGGAAAATCA
** *
2493448 ACTCATATCACGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
* *
2493513 GAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
*
2493571 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-AAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
* * ** ** *
2493635 TAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTAT-TTTTCAAAAATC
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGT-ATTT---TTAGT-TTATGTTTT---AAATT
*
2493699 A
123 G
* *
2493700 ACTCATATTGCGAGAGATGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
*
2493765 GAGAAGTGAGTTGAGCCT-AGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTCA-GGACACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
*
2493823 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-AAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
* * ** ** *
2493887 TAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTAT-TTTTCAAAAATC
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGT-ATTT---TTAGT-TTATGTTTT---AAATT
*
2493951 A
123 G
*
2493952 ACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
*
2494017 GAGAAGTGAGTTGAGCCT-AGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTCA-GGACACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
*
2494075 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTC-AAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
* * ** * * *
2494139 TAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAATTTCTGTTGTTAAA
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGTATTTTTAGTTTATGTT-TTAAA
2494195 AAAAATCAAC
Statistics
Matches: 540, Mismatches: 59, Indels: 50
0.83 0.09 0.08
Matches are distributed among these distances:
122 149 0.28
123 152 0.28
125 8 0.01
126 28 0.05
127 8 0.01
129 105 0.19
130 90 0.17
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (123 bp):
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
Found at i:2494384 original size:73 final size:72
Alignment explanation
Indices: 2494103--2494631 Score: 704
Period size: 72 Copynumber: 7.2 Consensus size: 72
2494093 GAGTTAAGCC
* * **
2494103 TTTT-AATTTATGTTTTTCAAAA-TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACG
2494166 CTGAGGTAA
65 CTGAGGT-A
* *
2494175 TTTT-AATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTT-TT--CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACA
2494239 CGCTGAGGTA
63 CGCTGAGGTA
* *
2494249 ATTTCAATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACGC
1 TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGC
2494314 TGAGGTA
66 TGAGGTA
*
2494321 TTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACG
*
2494386 TTGAGGTA
65 CTGAGGTA
* * * *
2494394 ATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAAGT
1 TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGC
2494459 TGAGGTA
66 TGAGGTA
* **
2494466 TTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATA
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACG
*
2494531 CTTAGGTA
65 CTGAGGTA
* * * * **
2494539 TTGTCAATTTTTTGTATGTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 TTTTCAA-TTTCTG--T-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGAC
*
2494604 ATGCTGAGGTA
62 ACGCTGAGGTA
*
2494615 TTTTCCATTTCTGTTTT
1 TTTTCAATTTCTGTTTT
2494632 TCAATTTATG
Statistics
Matches: 414, Mismatches: 33, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
71 2 0.00
72 150 0.36
73 130 0.31
74 15 0.04
75 61 0.15
76 56 0.14
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (72 bp):
TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGC
TGAGGTA
Found at i:2494405 original size:145 final size:146
Alignment explanation
Indices: 2494107--2494635 Score: 732
Period size: 145 Copynumber: 3.6 Consensus size: 146
2494097 TAAGCCTTTT
* * **
2494107 AATTTATGTTTTTCAAAA-TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
* *
2494171 GTAATTTT-AATTTCTG-TTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
66 GT-ATTTTCAATTTCTGCTT-TT--CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
* *
2494234 GGACACGCTGAGGTAATTTC
127 AGACACGTTGAGGTAATTTC
*
2494254 AATTTCTG-TTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
2494318 GTATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
66 GTATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
2494383 ACGTTGAGGTAATTTC
131 ACGTTGAGGTAATTTC
* * *
2494399 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAAGTTGAG
1 AATTTCTGTTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
2494463 GTATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
66 GTATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
2494528 ATAC-TT-AGGT-ATTGTC
131 --ACGTTGAGGTAATT-TC
* * * ** *
2494544 AATTTTTTGTATGTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCT
1 AA-TTTCTGT-T-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCT
* *
2494609 GAGGTATTTTCCATTTCTGTTTTTCAA
63 GAGGTATTTTCAATTTCTGCTTTTCAA
2494636 TTTATGTTTT
Statistics
Matches: 349, Mismatches: 23, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
144 3 0.01
145 189 0.54
146 21 0.06
147 63 0.18
148 3 0.01
149 70 0.20
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (146 bp):
AATTTCTGTTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
GTATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
ACGTTGAGGTAATTTC
Found at i:2494702 original size:86 final size:86
Alignment explanation
Indices: 2494553--2494770 Score: 330
Period size: 86 Copynumber: 2.5 Consensus size: 86
2494543 CAATTTTTTG
* *
2494553 TATG-TTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATT
1 TATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT
* **
2494617 TTCCATTTCTGTTTTTCAATT
66 TTCAATTTCTACTTTTCAATT
* * *
2494638 TATGTTTTCAAAAATCAATTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
1 TATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT
2494703 TTCAATTTCTACTTTTCAATT
66 TTCAATTTCTACTTTTCAATT
* *
2494724 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCT
1 TATG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
2494771 TTTAATTTTT
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 4 0.03
86 76 0.64
87 39 0.33
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (86 bp):
TATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT
TTCAATTTCTACTTTTCAATT
Found at i:2494806 original size:56 final size:56
Alignment explanation
Indices: 2494714--2494937 Score: 268
Period size: 55 Copynumber: 4.1 Consensus size: 56
2494704 TCAATTTCTA
* *
2494714 CTTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGC
1 CTTTT-AATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
2494769 CTTTTAATTTTTATTTTTCAAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
2494825 C--TT--TTTCTATTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTAATTTCTATTTTTC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
2494880 CTTTTGCAAATTCT-GTTTTC--AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT--AATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
2494935 CTT
1 CTT
2494938 GGCTCACACG
Statistics
Matches: 149, Mismatches: 9, Indels: 22
0.83 0.05 0.12
Matches are distributed among these distances:
52 11 0.07
54 14 0.09
55 79 0.53
56 34 0.23
57 2 0.01
60 5 0.03
61 4 0.03
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (56 bp):
CTTTTAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:2494974 original size:13 final size:14
Alignment explanation
Indices: 2494956--2494989 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2494946 CGCTGAGGTA
2494956 TTTTCAATTT-TGG
1 TTTTCAATTTCTGG
*
2494969 TTTTCAATTTCTGT
1 TTTTCAATTTCTGG
2494983 TTTTCAA
1 TTTTCAA
2494990 AAATCGACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.62
Consensus pattern (14 bp):
TTTTCAATTTCTGG
Found at i:2495091 original size:73 final size:73
Alignment explanation
Indices: 2494970--2495126 Score: 244
Period size: 73 Copynumber: 2.2 Consensus size: 73
2494960 CAATTTTGGT
* *
2494970 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTC-GGGACACG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGG-CACG
2495034 CTGAGGTAA
65 CTGAGGTAA
* * *
2495043 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCGCGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGGCACGC
*
2495108 TGAGGTAT
66 TGAGGTAA
2495116 TTTCAATTTCT
1 TTTCAATTTCT
2495127 ACTTTTCAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
73 74 0.96
74 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (73 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGGCACGC
TGAGGTAA
Found at i:2495162 original size:160 final size:158
Alignment explanation
Indices: 2494890--2495184 Score: 448
Period size: 160 Copynumber: 1.8 Consensus size: 158
2494880 CTTTTGCAAA
*
2494890 TTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACACGCTGAGGT
1 TTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTAGG--CACACGCTGAGGT
** * *
2494955 ATTTTCAATTTTGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTG
64 ATTTTCAATTTTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATGGCGAGAGGAGAGTTG
2495020 AGCCTCGGGACACGCTGAGGTAATTTCAAT
129 AGCCTCGGGACACGCTGAGGTAATTTCAAT
* * * *
2495050 TTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCGCGCTGAGGT
1 TTCTGTTT-TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-AGGCACACGCTGAGGT
*
2495114 ATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATGGCGAGAGGTGAGTT
64 ATTTTCAATTT-TACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATGGCGAGAGGAGAGTT
2495179 GAGCCT
128 GAGCCT
2495185 TTTTCTATTT
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
159 21 0.17
160 62 0.51
161 37 0.30
162 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (158 bp):
TTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTAGGCACACGCTGAGGTAT
TTTCAATTTTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATGGCGAGAGGAGAGTTGAG
CCTCGGGACACGCTGAGGTAATTTCAAT
Found at i:2495287 original size:55 final size:54
Alignment explanation
Indices: 2495128--2495296 Score: 203
Period size: 56 Copynumber: 3.1 Consensus size: 54
2495118 TCAATTTCTA
*
2495128 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATGGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * ******
2495183 CTTTTTCTATTTTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 C-TTTTCAATTTCT-GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
2495239 CTTTTGCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
2495294 CTT
1 CTT
2495297 GGCTCACGTG
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
55 42 0.46
56 50 0.54
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:2495612 original size:30 final size:30
Alignment explanation
Indices: 2495572--2495673 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
2495562 TTAAAAATAA
* *
2495572 AAATTACATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
2495602 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* * *
2495632 AAATTTCACTTAGACCCCTAAACCTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
2495662 AAATTTCATTTT
1 AAATTTCATTTT
2495674 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 4 0.07
30 57 0.93
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:2496915 original size:17 final size:17
Alignment explanation
Indices: 2496895--2496934 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2496885 TTTTTAAAAA
2496895 AAAAATT-TCATGTCTTC
1 AAAAATTCTCATGT-TTC
*
2496912 AAAATTTCTCATGTTTC
1 AAAAATTCTCATGTTTC
2496929 AAAAAT
1 AAAAAT
2496935 AATAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (17 bp):
AAAAATTCTCATGTTTC
Found at i:2497037 original size:16 final size:16
Alignment explanation
Indices: 2496989--2497037 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
2496979 TTTCTTTCTA
*
2496989 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
2497005 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
2497022 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
2497038 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:2497074 original size:20 final size:20
Alignment explanation
Indices: 2497036--2497072 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
2497026 ATTCGTGTTT
2497036 TCGTGTTTTCAAAAAAAATC
1 TCGTGTTTTCAAAAAAAATC
2497056 TCGTG-TTTCAAAAAAAA
1 TCGTGTTTTCAAAAAAAA
2497073 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (20 bp):
TCGTGTTTTCAAAAAAAATC
Found at i:2497080 original size:6 final size:6
Alignment explanation
Indices: 2497065--2497135 Score: 58
Period size: 6 Copynumber: 11.7 Consensus size: 6
2497055 CTCGTGTTTC
* * *
2497065 AAAA-A AAAATA AAAATA ATAATA ATAATA ATAAA-A ATAATA AATAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA A-AAATA AAAATA AA-AATA
2497113 AAAATA ATAAA-A AAAATTA AAAA
1 AAAATA A-AAATA AAAA-TA AAAA
2497136 AATTCTCGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 9 0.16
6 30 0.55
7 16 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:2497084 original size:3 final size:3
Alignment explanation
Indices: 2497072--2497122 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
2497062 TTCAAAAAAA
* * *
2497072 AAT AAA AAT AAT AAT AAT AAT AAT AAA AAT AAT AAAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
2497118 AAT AA
1 AAT AA
2497123 AAAAAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:2497084 original size:9 final size:9
Alignment explanation
Indices: 2497066--2497135 Score: 79
Period size: 9 Copynumber: 7.6 Consensus size: 9
2497056 TCGTGTTTCA
*
2497066 AAAAAAAAT
1 AAAAATAAT
2497075 AAAAATAAT
1 AAAAATAAT
*
2497084 AATAATAAT
1 AAAAATAAT
2497093 AATAAA-AAT
1 AA-AAATAAT
2497102 AATAAATAAT
1 AA-AAATAAT
2497112 AAAAATAAT
1 AAAAATAAT
*
2497121 AAAAAAAATT
1 AAAAATAA-T
2497131 AAAAA
1 AAAAA
2497136 AATTCTCGTG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
9 41 0.76
10 13 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:2497127 original size:12 final size:12
Alignment explanation
Indices: 2497075--2497137 Score: 67
Period size: 12 Copynumber: 5.3 Consensus size: 12
2497065 AAAAAAAAAT
*
2497075 AAAAATAATAAT
1 AAAAATAATAAA
*
2497087 AATAATAATAAA
1 AAAAATAATAAA
* *
2497099 AATAATAAATAAT
1 AAAAAT-AATAAA
2497112 AAAAATAATAAA
1 AAAAATAATAAA
2497124 AAAAAT--TAAA
1 AAAAATAATAAA
2497134 AAAA
1 AAAA
2497138 TTCTCGTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
10 8 0.18
12 27 0.60
13 10 0.22
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAATAATAAA
Found at i:2497223 original size:18 final size:18
Alignment explanation
Indices: 2497202--2497633 Score: 243
Period size: 18 Copynumber: 25.0 Consensus size: 18
2497192 AAATTTAGTG
2497202 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
2497220 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
2497238 TCTTT-GTGTTTTCAAAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
2497256 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
2497273 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT--TCAAAAA
* *
2497293 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
2497311 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
2497328 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
2497346 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
2497362 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * **
2497380 TTCTCGCGTTTAAAAAAA
1 TTTTCGTGTTTTCAAAAA
**
2497398 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
2497416 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
2497430 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
2497445 ---TCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
2497459 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
2497476 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
2497493 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
2497510 TTTCCGTG-TTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
2497529 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
2497547 ATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
2497566 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
2497583 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
2497599 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
2497617 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
2497634 AAAACTTTCG
Statistics
Matches: 319, Mismatches: 61, Indels: 69
0.71 0.14 0.15
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 9 0.03
15 3 0.01
16 21 0.07
17 112 0.35
18 125 0.39
19 22 0.07
20 20 0.06
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:2497283 original size:17 final size:17
Alignment explanation
Indices: 2497202--2497633 Score: 231
Period size: 17 Copynumber: 25.0 Consensus size: 17
2497192 AAATTTAGTG
2497202 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
2497220 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
2497238 TCTTT-GTGTTTTCAAAAA
1 T-TTTCGTG-TTTCAAAAA
* * *
2497256 TTCTGGCGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
*
2497273 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT---CAAAAA
* *
2497293 TTTACGTGTTTTCACAAA
1 TTTTCGTG-TTTCAAAAA
*
2497311 TTTTCGTGTTTCACAAA
1 TTTTCGTGTTTCAAAAA
*
2497328 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
2497346 -CTCCAGTGTTTC-AAAG
1 TTTTC-GTGTTTCAAAAA
* *
2497362 TTTCCATGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
2497380 TTCTCGCGTTTAAAAAAA
1 TTTTCGTGTTT-CAAAAA
**
2497398 AATTCGTGTTTCAAAATA
1 TTTTCGTGTTTCAAAA-A
* **
2497416 TTCTCGCATTTC---AA
1 TTTTCGTGTTTCAAAAA
***
2497430 TTTT--TGTTTTTTAAA
1 TTTTCGTGTTTCAAAAA
2497445 ---TCGTGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
* * *
2497459 ATGTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
*
2497476 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
* * *
2497493 TTTCCCTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
*
2497510 TTTCCGTGTTTCAAAAAAA
1 TTTTCGTGTTTC--AAAAA
* * *
2497529 ATGTCGTGTTTTAAGAAA
1 TTTTCGTGTTTCAA-AAA
* *
2497547 ATTTCGTTTTTTCTAAAAA
1 TTTTCG-TGTTTC-AAAAA
*
2497566 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
*
2497583 TTTTCGTGTTT-ACAAA
1 TTTTCGTGTTTCAAAAA
*
2497599 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* *
2497617 TTCTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
2497634 AAAACTTTCG
Statistics
Matches: 319, Mismatches: 67, Indels: 57
0.72 0.15 0.13
Matches are distributed among these distances:
12 4 0.01
14 12 0.04
15 3 0.01
16 15 0.05
17 131 0.41
18 109 0.34
19 28 0.09
20 14 0.04
21 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTTCGTGTTTCAAAAA
Found at i:2497322 original size:55 final size:53
Alignment explanation
Indices: 2497202--2497633 Score: 181
Period size: 53 Copynumber: 8.3 Consensus size: 53
2497192 AAATTTAGTG
** **
2497202 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTTTCAAAAA
* * * *
2497256 TTCTGGCGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTT--GTGTTTTCAAAAA
* * ** * ** *
2497311 TTTTCGTGTTTCACAAATTCTCGTGTTT-TCAAAAACTCCAGTG-TTTC-AAAG
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAAT-TTGTGTTTTCAAAAA
* * * * *
2497362 TTTCCATGTTTTCAAAAATTCTCGCGTTTAAAAAAAAATTCGTG-TTTCAAAATA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTTTCAAAA-A
* ** *** *
2497416 TTCTCGCATTTC---AATTTT--TGTTT---TTTAAA-TCGTG-TTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTTTCAAAAA
* * * ** *
2497459 ATGTCGTGTTTTAAAAATTTTCGTGTTT---CTAAAATTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTT--GTGTTTTCAAAAA
* * * * * *
2497510 TTTCCGTGTTTCAAAAAAAATGTCGTGTTT-TAAGAAAATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTC--AAAAATTTTCGTGTTTAAAAAAAAATTT-GTGTTTTC-AAAAA
* *
2497566 TTTTCGTGTTTCTAAAATTTTCGTGTTT----ACAAATTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATT-T-GTGTTTTCAAAAA
* *
2497617 TTCTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
2497634 AAAACTTTCG
Statistics
Matches: 286, Mismatches: 69, Indels: 49
0.71 0.17 0.12
Matches are distributed among these distances:
43 8 0.03
44 13 0.05
45 3 0.01
46 6 0.02
48 13 0.05
49 1 0.00
50 5 0.02
51 47 0.16
52 41 0.14
53 58 0.20
54 33 0.12
55 42 0.15
56 16 0.06
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (53 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTGTGTTTTCAAAAA
Found at i:2497355 original size:73 final size:73
Alignment explanation
Indices: 2497215--2497356 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 73
2497205 TCGTGTTTTC
* * * *
2497215 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATTTTCGT
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
2497280 GTTTAAAA
66 GTTTAAAA
* * *
2497288 AAAAATTTACGTGTTTTCACAAAT-TTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAA-CTCC
1 AAAAATTTACGTGTTTTCAAAAATCTTT-GTGTTTTCAAAAATTCTCGCG-TTTCAAAAATCTCC
2497350 AGTGTTT
64 -GTGTTT
2497357 CAAAGTTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
72 19 0.32
73 40 0.68
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (73 bp):
AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTCGCGTTTCAAAAATCTCCGT
GTTTAAAA
Found at i:2498666 original size:133 final size:133
Alignment explanation
Indices: 2498428--2498678 Score: 448
Period size: 133 Copynumber: 1.9 Consensus size: 133
2498418 AGTAGGTACA
2498428 TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTATTATCTGTTTTGATAA
1 TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTATTATCTGTTTTGATAA
*
2498493 GCTAATTGATTCAATTGTGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTACATTG
66 GCTAATTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTACATTG
2498558 GGG
131 GGG
*
2498561 TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTGTTATCTGTTTTGATAA
1 TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTATTATCTGTTTTGATAA
* * * *
2498626 GCTATTTGGTTCAATTATGTAATATGAATATATGATATTATGATTTTGCATGT
66 GCTAATTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGT
2498679 GCATTGGGCT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 112 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (133 bp):
TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTATTATCTGTTTTGATAA
GCTAATTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTACATTG
GGG
Found at i:2498854 original size:6 final size:6
Alignment explanation
Indices: 2498840--2498884 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
2498830 TAGACTAAGT
* **
2498840 TTTTTG TTTTGG TTTT-G TTTTGG GCTTGG TTTTGG TTTTGG TTTT
1 TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTT
2498885 TGCTTTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.00, C:0.02, G:0.29, T:0.69
Consensus pattern (6 bp):
TTTTGG
Found at i:2499140 original size:14 final size:14
Alignment explanation
Indices: 2499121--2499169 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2499111 CGACTTTGAA
2499121 TTTGAATTTTGGGT
1 TTTGAATTTTGGGT
** *
2499135 TTTGAATAAAT-GTT
1 TTTGAAT-TTTGGGT
2499149 TTTGAATTTTGGGT
1 TTTGAATTTTGGGT
2499163 TTTGAAT
1 TTTGAAT
2499170 AAATGTTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.55
Consensus pattern (14 bp):
TTTGAATTTTGGGT
Found at i:2499161 original size:28 final size:28
Alignment explanation
Indices: 2499121--2499193 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
2499111 CGACTTTGAA
2499121 TTTGAATTTTGGGTTTTGAATAAATGTT
1 TTTGAATTTTGGGTTTTGAATAAATGTT
2499149 TTTGAATTTTGGGTTTTGAATAAATGTT
1 TTTGAATTTTGGGTTTTGAATAAATGTT
* *
2499177 TTCGAACTTTGGGTTTT
1 TTTGAATTTTGGGTTTT
2499194 CAAATCATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.53
Consensus pattern (28 bp):
TTTGAATTTTGGGTTTTGAATAAATGTT
Found at i:2505733 original size:13 final size:13
Alignment explanation
Indices: 2505717--2505742 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2505707 CTGTGGAAAT
2505717 GTGCTTTTGAGAA
1 GTGCTTTTGAGAA
2505730 GTGCTTTTGAGAA
1 GTGCTTTTGAGAA
2505743 ATTTGAGTGT
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:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
GTGCTTTTGAGAA
Found at i:2509080 original size:21 final size:21
Alignment explanation
Indices: 2509038--2509080 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2509028 ATTTTCCACT
* *
2509038 TCTATTTTCTTTTCATTTTTC
1 TCTATTTCCTTTTCATTCTTC
2509059 TCTATTTCCTTTTTC-TTCTTC
1 TCTATTTCC-TTTTCATTCTTC
2509080 T
1 T
2509081 TCTAACCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
TCTATTTCCTTTTCATTCTTC
Found at i:2516392 original size:20 final size:20
Alignment explanation
Indices: 2516367--2516410 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2516357 TTGCATAGAT
2516367 TAAAAACTAAATTCAAAATA
1 TAAAAACTAAATTCAAAATA
* * *
2516387 TAAAAAGTTAATTTAAAATA
1 TAAAAACTAAATTCAAAATA
2516407 -AAAA
1 TAAAA
2516411 TATGTTACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAACTAAATTCAAAATA
Found at i:2516915 original size:13 final size:13
Alignment explanation
Indices: 2516897--2516950 Score: 65
Period size: 13 Copynumber: 3.9 Consensus size: 13
2516887 ATATTATCCA
2516897 ACCCAACCCAATT
1 ACCCAACCCAATT
2516910 ACCCAACCCAATT
1 ACCCAACCCAATT
2516923 ATCAACCTAACCCAATT
1 A-C--CC-AACCCAATT
2516940 A-CCAACCCAAT
1 ACCCAACCCAAT
2516951 AAAAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.22
13 16 0.43
14 1 0.03
16 2 0.05
17 10 0.27
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:2516935 original size:30 final size:30
Alignment explanation
Indices: 2516889--2516950 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2516879 AATAAATAAT
2516889 ATTATCCAACCCAACCCAATTACCCAACCCA
1 ATTATCCAACCCAACCCAATTA-CCAACCCA
*
2516920 ATTAT-CAACCTAACCCAATTACCAACCCA
1 ATTATCCAACCCAACCCAATTACCAACCCA
2516949 AT
1 AT
2516951 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 10 0.33
30 15 0.50
31 5 0.17
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.19
Consensus pattern (30 bp):
ATTATCCAACCCAACCCAATTACCAACCCA
Found at i:2516936 original size:17 final size:16
Alignment explanation
Indices: 2516889--2516946 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
2516879 AATAAATAAT
2516889 ATTATCCAACCCAACCCA
1 ATTAT-CAA-CCAACCCA
2516907 ATTA-C--CCAACCCA
1 ATTATCAACCAACCCA
2516920 ATTATCAACCTAACCCA
1 ATTATCAACC-AACCCA
*
2516937 ATTACCAACC
1 ATTATCAACC
2516947 CAATAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 12 0.34
14 1 0.03
16 3 0.09
17 15 0.43
18 4 0.11
ACGTcount: A:0.40, C:0.41, G:0.00, T:0.19
Consensus pattern (16 bp):
ATTATCAACCAACCCA
Found at i:2517125 original size:17 final size:17
Alignment explanation
Indices: 2517105--2517167 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
2517095 TAATTTCAAG
2517105 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
***
2517122 AATTATGTAATGATTCAA
1 AATTATGTAATG-TTTTT
*
2517140 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
2517159 AATTATGTA
1 AATTATGTA
2517168 GTGATTCAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 19 0.53
18 4 0.11
19 4 0.11
20 9 0.25
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:2517148 original size:37 final size:37
Alignment explanation
Indices: 2517102--2517176 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
2517092 TGTTAATTTC
*
2517102 AAGAATTATGTAATGTTTTTAATTATGTAATGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAATGATTCA
* *
2517139 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAATGATTCA
2517176 A
1 A
2517177 TTCGGGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAATGATTCA
Found at i:2517192 original size:9 final size:9
Alignment explanation
Indices: 2517175--2517205 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2517165 GTAGTGATTC
*
2517175 AATTCGGGT
1 AATTTGGGT
2517184 AATTTGGGT
1 AATTTGGGT
2517193 AATTTGGGT
1 AATTTGGGT
2517202 AATT
1 AATT
2517206 CGGTTAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (9 bp):
AATTTGGGT
Found at i:2517213 original size:9 final size:9
Alignment explanation
Indices: 2517175--2517213 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2517165 GTAGTGATTC
2517175 AATTCGGGT
1 AATTCGGGT
*
2517184 AATTTGGGT
1 AATTCGGGT
*
2517193 AATTTGGGT
1 AATTCGGGT
*
2517202 AATTCGGTT
1 AATTCGGGT
2517211 AAT
1 AAT
2517214 CAATTAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:2518486 original size:11 final size:11
Alignment explanation
Indices: 2518472--2518527 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
2518462 AAATTAAAAA
2518472 AAAAGTATTTT
1 AAAAGTATTTT
*
2518483 AAAATTATTTT
1 AAAAGTATTTT
2518494 -AAA--A-TTT
1 AAAAGTATTTT
2518501 AAATAGTATTTT
1 AAA-AGTATTTT
*
2518513 AAAAATATTTT
1 AAAAGTATTTT
2518524 AAAA
1 AAAA
2518528 TTAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 1 0.03
10 3 0.08
11 22 0.58
12 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:2523447 original size:18 final size:18
Alignment explanation
Indices: 2523407--2523450 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2523397 AATTTTTATG
**
2523407 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
2523425 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
2523443 CTTGGGTT
1 ATTGGGTT
2523451 TGGATTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:2532459 original size:19 final size:19
Alignment explanation
Indices: 2532435--2532474 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2532425 ACCATAGTTG
*
2532435 TAGTTTAGTTATATTTTTT
1 TAGTTTAGTTAGATTTTTT
* *
2532454 TAGTTTTGTTAGGTTTTTT
1 TAGTTTAGTTAGATTTTTT
2532473 TA
1 TA
2532475 CCAAAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (19 bp):
TAGTTTAGTTAGATTTTTT
Found at i:2533523 original size:17 final size:16
Alignment explanation
Indices: 2533501--2533556 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 16
2533491 TAAAATTTTA
2533501 ATAAATGATAAAAATAT
1 ATAAAT-ATAAAAATAT
*
2533518 ATAAAT-TATTAAATAT
1 ATAAATATA-AAAATAT
2533534 -TAAAT-TAAAAATAAT
1 ATAAATATAAAAAT-AT
2533549 ATAAATAT
1 ATAAATAT
2533557 TGTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 4 0.12
15 11 0.33
16 11 0.33
17 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
ATAAATATAAAAATAT
Found at i:2538713 original size:18 final size:19
Alignment explanation
Indices: 2538686--2538726 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
2538676 TTAAACCCTT
2538686 AAAAATCCCT-AACCTTAAC
1 AAAAATCCCTAAACC-TAAC
2538705 AAAAA-CCCTAAACCTAAC
1 AAAAATCCCTAAACCTAAC
2538723 AAAA
1 AAAA
2538727 TTAAAAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAATCCCTAAACCTAAC
Found at i:2540064 original size:23 final size:22
Alignment explanation
Indices: 2539999--2540065 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
2539989 TGATATTTTA
*
2539999 ATTATTTTTATATGTGAAATAT
1 ATTATATTTATATGTGAAATAT
* * *
2540021 TTTA-ATTAATTATTTGAAATAT
1 ATTATATTTA-TATGTGAAATAT
*
2540043 CATTATGTTTATATGTGAAATAT
1 -ATTATATTTATATGTGAAATAT
2540066 TTTAAATACA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 3 0.09
22 14 0.41
23 14 0.41
24 3 0.09
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.52
Consensus pattern (22 bp):
ATTATATTTATATGTGAAATAT
Found at i:2552574 original size:150 final size:148
Alignment explanation
Indices: 2552321--2552788 Score: 640
Period size: 151 Copynumber: 3.1 Consensus size: 148
2552311 TTTATTTATT
* * * *
2552321 AAAAAACACTA-TTTTCTTAAAAATTAAAGCTTTTTATTTTGAAGTAGTT---AAAAAAATTAAA
1 AAAAAACACTATTTTTCTTAAAGATTAAAGC-TTTTACTTTGAAATAGTTGAAAAAAAAATCAAA
* * *
2552382 ATTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAATTAAAAAAACAAATTTTTATTTTTCAAA
65 ACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAACAAATTTTTATTTTTCAAA
2552447 ATCTAAACTTTCTCCTTTTAA
130 ATCTAAACTTTCT--TTTTAA
* *
2552468 AAAAAATACTATTTTTCTTAAGGATTAAAGCTTTTACTTTGAAATAGTTGAAAAAAAAATCAAAA
1 AAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATAGTTGAAAAAAAAATCAAAA
*
2552533 CTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAAACAGATTTTTATTTTTCAAA
66 CTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACT-AAAAAAACAAATTTTTATTTTTCAAA
2552598 ATCTAAACTTTCTTTTTAAAA
130 ATCTAAACTTTCTTTTT--AA
* * * *
2552619 AAAAAAGATTATTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTGAAAAGAAAATCAAAA
1 AAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATAGTTGAAAAAAAAATCAAAA
* *
2552684 CTTTATTTTAAAAAATTAAAC-TTCTCTTTAAAATAACTAAAAAAACCATATTATTATTATTATT
66 CTTTATTTTAAAAATTTAAACTTTC-CTTTAAAATAACTAAAAAAA-CA-A--ATTTTTATT-TT
*
2552748 TCAAAATCTAAACTTTCTTCTTAA
125 TCAAAATCTAAACTTTCTTTTTAA
2552772 AAAAAACACTATTTTTC
1 AAAAAACACTATTTTTC
2552789 CCAAAATCAA
Statistics
Matches: 287, Mismatches: 21, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
147 26 0.09
148 17 0.06
149 4 0.01
150 57 0.20
151 135 0.47
153 17 0.06
154 8 0.03
155 23 0.08
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (148 bp):
AAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATAGTTGAAAAAAAAATCAAAA
CTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAACAAATTTTTATTTTTCAAAA
TCTAAACTTTCTTTTTAA
Found at i:2554902 original size:12 final size:12
Alignment explanation
Indices: 2554885--2554920 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2554875 TTAATTATAA
2554885 TACTATTATTAT
1 TACTATTATTAT
*
2554897 TACTATTATTAC
1 TACTATTATTAT
2554909 TACTATTATTAT
1 TACTATTATTAT
2554921 AGATGTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (12 bp):
TACTATTATTAT
Found at i:2555436 original size:18 final size:18
Alignment explanation
Indices: 2555404--2555809 Score: 80
Period size: 17 Copynumber: 22.6 Consensus size: 18
2555394 ATATTTTGAG
*
2555404 AACACGAAAATTTTTTTAA
1 AACACGAGAA-TTTTTTAA
2555423 AACACGAGAA--TTTTAGA
1 AACACGAGAATTTTTTA-A
* * *
2555440 AACACGAAAATTCTTAAA
1 AACACGAGAATTTTTTAA
* *
2555458 AACACGAAAATTTTTGAA
1 AACACGAGAATTTTTTAA
* **
2555476 AACACGA-AAATTTTTGG
1 AACACGAGAATTTTTTAA
* * *
2555493 ATCGCCGA-AATTTTTGAA
1 AAC-ACGAGAATTTTTTAA
*
2555511 AGCACGA-AATTTTTTGAA
1 AACACGAGAATTTTTT-AA
* *
2555529 AA-A-TATGAATTTTTTGA
1 AACACGA-GAATTTTTTAA
* * *
2555546 GACACGA-AAATTTTGAA
1 AACACGAGAATTTTTTAA
* *
2555563 AAC-CTGA-AAATTTTTAC
1 AACAC-GAGAATTTTTTAA
**
2555580 AACACG-GTAA-TTTGCAA
1 AACACGAG-AATTTTTTAA
* *
2555597 AACATGGGAATTTTTTTGAAA
1 AACACGAGAA-TTTTTT--AA
* * *
2555618 AACATGA-AAATTTTTGA
1 AACACGAGAATTTTTTAA
* * *
2555635 AATACGAAAATTTTTAGAA
1 AACACGAGAATTTTT-TAA
*
2555654 AACACGA-ATTTTTTTTGAA
1 AACACGAGA-ATTTTTT-AA
*
2555673 AACACGAAGATTTTTTTTGAA
1 AACACG-AGA-ATTTTTT-AA
**
2555694 AACACG-GAAACTTTTAA
1 AACACGAGAATTTTTTAA
*
2555711 AACAC-AGGAA-TTTTTGA
1 AACACGA-GAATTTTTTAA
* *
2555728 AACACGA-ATTTTTTTTTTCA
1 AACACGAGA---ATTTTTTAA
* * *
2555748 AACATGA-AAATTTTTGA
1 AACACGAGAATTTTTTAA
* *
2555765 AATACGAGAATTTTTT-T
1 AACACGAGAATTTTTTAA
* *
2555782 AATACG-GAATTTTTTGA
1 AACACGAGAATTTTTTAA
*
2555799 AATACGAGAAT
1 AACACGAGAAT
2555810 ATTAGAAACA
Statistics
Matches: 290, Mismatches: 63, Indels: 69
0.69 0.15 0.16
Matches are distributed among these distances:
16 17 0.06
17 111 0.38
18 77 0.27
19 43 0.15
20 16 0.06
21 26 0.09
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (18 bp):
AACACGAGAATTTTTTAA
Found at i:2555436 original size:36 final size:36
Alignment explanation
Indices: 2555396--2555559 Score: 124
Period size: 36 Copynumber: 4.6 Consensus size: 36
2555386 AAATAATTAT
* *
2555396 ATTTTGAGAACACGAAAATTTTTTTAAAACACGAGA
1 ATTTTGAGAACACGAAAATTTTTTAAAAACACGAAA
*
2555432 ATTTT-AGAAACACGAAAA-TTCTTAAAAACACGAAA
1 ATTTTGAG-AACACGAAAATTTTTTAAAAACACGAAA
* ** ***
2555467 ATTTTTGAAAACACGAAAATTTTTGGATCGC-CGAAA
1 A-TTTTGAGAACACGAAAATTTTTTAAAAACACGAAA
* * * *
2555503 TTTTTGA-AAGCACG-AAATTTTTTGAAAAATATGAAT
1 ATTTTGAGAA-CACGAAAATTTTTT-AAAAACACGAAA
*
2555539 TTTTTGAG-ACACGAAAATTTT
1 ATTTTGAGAACACGAAAATTTT
2555560 GAAAACCTGA
Statistics
Matches: 100, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
34 10 0.10
35 32 0.32
36 52 0.52
37 6 0.06
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (36 bp):
ATTTTGAGAACACGAAAATTTTTTAAAAACACGAAA
Found at i:2555504 original size:53 final size:53
Alignment explanation
Indices: 2555404--2555715 Score: 145
Period size: 53 Copynumber: 5.8 Consensus size: 53
2555394 ATATTTTGAG
* *
2555404 AACACGAAAATTTTTTTAAAACACGAGAATTTTAGAAACACGAAAATTCTTAAA
1 AACACGAAAA-TTTTTGAAAACACGAAAATTTTAGAAACACGAAAATTCTTAAA
* * * * * *
2555458 AACACGAAAATTTTTGAAAACACGAAAATTTTTGGATCGCCG-AAATTTTTGAA
1 AACACGAAAATTTTTGAAAACACGAAAATTTTAGAAAC-ACGAAAATTCTTAAA
* * * * * * * *
2555511 AGCACGAAATTTTTTGAAAAATATG-AATTTTTTGAGACACGAAAATT-TTGAA
1 AACACGAAAATTTTTG-AAAACACGAAAATTTTAGAAACACGAAAATTCTTAAA
* ** * * ** *
2555563 AAC-CTGAAAATTTTT-ACAACACGGTAATTTGCA-AAACATGGGAATTTTTTTGAAA
1 AACAC-GAAAATTTTTGAAAACACGAAAATTT-TAGAAACA--CGAAAATTCTT-AAA
* * ** * *
2555618 AACATGAAAATTTTTG-AAATACGAAAATTTTTAGAAAACACGAATTTTTTTTGAA
1 AACACGAAAATTTTTGAAAACACGAAAA-TTTTAG-AAACACGAA-AATTCTTAAA
* *
2555673 AACACGAAGATTTTTTTTGAAAACACGGAAACTTTTA-AAACAC
1 AACACGAA-A--ATTTTTGAAAACAC-GAAAATTTTAGAAACAC
2555716 AGGAATTTTT
Statistics
Matches: 194, Mismatches: 43, Indels: 39
0.70 0.16 0.14
Matches are distributed among these distances:
50 5 0.03
51 9 0.05
52 18 0.09
53 65 0.34
54 20 0.10
55 35 0.18
56 11 0.06
57 11 0.06
58 6 0.03
59 10 0.05
60 4 0.02
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.32
Consensus pattern (53 bp):
AACACGAAAATTTTTGAAAACACGAAAATTTTAGAAACACGAAAATTCTTAAA
Found at i:2555619 original size:21 final size:21
Alignment explanation
Indices: 2555590--2555695 Score: 66
Period size: 19 Copynumber: 5.4 Consensus size: 21
2555580 AACACGGTAA
* **
2555590 TTTGCAAAACATGGGAATTTT
1 TTTGAAAAACATGAAAATTTT
2555611 TTTGAAAAACATGAAAA--TT
1 TTTGAAAAACATGAAAATTTT
*
2555630 TTTGAAATAC--GAAAA-TTT
1 TTTGAAAAACATGAAAATTTT
* * *
2555648 TTAG-AAAACACG-AATTTTT
1 TTTGAAAAACATGAAAATTTT
* *
2555667 TTTG-AAAACACGAAGATTTTT
1 TTTGAAAAACATGAA-AATTTT
2555688 TTTGAAAA
1 TTTGAAAA
2555696 CACGGAAACT
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
17 9 0.13
18 7 0.10
19 26 0.37
20 1 0.01
21 24 0.34
22 3 0.04
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (21 bp):
TTTGAAAAACATGAAAATTTT
Found at i:2555667 original size:19 final size:21
Alignment explanation
Indices: 2555645--2555699 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
2555635 AATACGAAAA
*
2555645 TTTTTAGAAAACACG-A-ATT
1 TTTTTTGAAAACACGAAGATT
2555664 TTTTTTGAAAACACGAAGATT
1 TTTTTTGAAAACACGAAGATT
2555685 TTTTTTGAAAACACG
1 TTTTTTGAAAACACG
2555700 GAAACTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 1 0.03
21 18 0.55
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (21 bp):
TTTTTTGAAAACACGAAGATT
Found at i:2555708 original size:21 final size:20
Alignment explanation
Indices: 2555607--2555699 Score: 88
Period size: 19 Copynumber: 4.8 Consensus size: 20
2555597 AACATGGGAA
*
2555607 TTTTTTTGAAAAACATGAAA-
1 TTTTTTTG-AAAACACGAAAT
* *
2555627 -ATTTTTG-AAATACGAAA-
1 TTTTTTTGAAAACACGAAAT
* *
2555644 ATTTTTAGAAAACACG-AAT
1 TTTTTTTGAAAACACGAAAT
2555663 TTTTTTTGAAAACACGAAGAT
1 TTTTTTTGAAAACACGAA-AT
2555684 TTTTTTTGAAAACACG
1 TTTTTTTGAAAACACG
2555700 GAAACTTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
17 8 0.13
18 7 0.12
19 26 0.43
20 1 0.02
21 18 0.30
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (20 bp):
TTTTTTTGAAAACACGAAAT
Found at i:2555741 original size:17 final size:18
Alignment explanation
Indices: 2555604--2555742 Score: 83
Period size: 19 Copynumber: 7.6 Consensus size: 18
2555594 CAAAACATGG
*
2555604 GAATTTTTTTGAAAAACAT
1 GAATTTTTTTG-AAAACAC
** *
2555623 GAAAATTTTTG-AAATAC
1 GAATTTTTTTGAAAACAC
* *
2555640 GAAAATTTTTAGAAAACAC
1 G-AATTTTTTTGAAAACAC
2555659 GAATTTTTTTTGAAAACAC
1 GAA-TTTTTTTGAAAACAC
2555678 GAAGATTTTTTTTGAAAACAC
1 G-A-A-TTTTTTTGAAAACAC
**
2555699 GGAA-ACTTTT-AAAACAC
1 -GAATTTTTTTGAAAACAC
2555716 AGGAA--TTTTTG-AAACAC
1 --GAATTTTTTTGAAAACAC
2555733 GAATTTTTTT
1 GAATTTTTTT
2555743 TTTCAAACAT
Statistics
Matches: 98, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.03
17 27 0.28
18 18 0.18
19 29 0.30
20 2 0.02
21 18 0.18
22 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (18 bp):
GAATTTTTTTGAAAACAC
Found at i:2556543 original size:20 final size:20
Alignment explanation
Indices: 2556490--2556553 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
2556480 GACGTTGGGC
* *
2556490 CTGG-GCGCTGGGCCGAATG
1 CTGGTGCGCTGGGCCGGACG
*
2556509 CTGGTGCACTGGGCCGGACG
1 CTGGTGCGCTGGGCCGGACG
* *
2556529 CTGGTGCGCTTGGCCTGGGCG
1 CTGGTGCGCTGGGCC-GGACG
2556550 CTGG
1 CTGG
2556554 GCCTGCTGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
19 4 0.11
20 25 0.68
21 8 0.22
ACGTcount: A:0.06, C:0.28, G:0.47, T:0.19
Consensus pattern (20 bp):
CTGGTGCGCTGGGCCGGACG
Found at i:2556834 original size:5 final size:6
Alignment explanation
Indices: 2556788--2556838 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
2556778 TTTAAAATTT
** * *
2556788 TTTTTC TGTTTTC TTCCTC TTTTTC TTTCTA TTTTTC TTTTTC TTTTTC
1 TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
2556837 TT
1 TT
2556839 CTTCGGGCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:2557454 original size:30 final size:30
Alignment explanation
Indices: 2557379--2557545 Score: 110
Period size: 30 Copynumber: 5.6 Consensus size: 30
2557369 CAAAATATTT
* *
2557379 GGGGTAAAAATGTAATTTT-AGGAAAA-TAT-
1 GGGGTTAAAATGTAATTTTCA--AAAAGTTTA
*
2557408 GGGGCTAAAATGTAATTTTCAAAAAGTTTA
1 GGGGTTAAAATGTAATTTTCAAAAAGTTTA
* * ** *
2557438 GGGGTTAAAGTGTAATTTTGAGGAAGATTA
1 GGGGTTAAAATGTAATTTTCAAAAAGTTTA
* *
2557468 GGTGTTGAAATGTAATTTT-AGAAAAGTTT-
1 GGGGTTAAAATGTAATTTTCA-AAAAGTTTA
* * * * **
2557497 GAGGTCAAAATGTAAATTTCAAAAAATACA
1 GGGGTTAAAATGTAATTTTCAAAAAGTTTA
* *
2557527 AGGGTTAAAATTTAATTTT
1 GGGGTTAAAATGTAATTTT
2557546 TATTTTTTTG
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
28 4 0.04
29 39 0.38
30 61 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTCAAAAAGTTTA
Found at i:2557462 original size:60 final size:59
Alignment explanation
Indices: 2557379--2557511 Score: 146
Period size: 59 Copynumber: 2.3 Consensus size: 59
2557369 CAAAATATTT
2557379 GGGGTAAAAATGTAATTTTAGGAAAA-TATGGGGCTAAAATGTAATTTTCA-AAAAGTTTA
1 GGGGTAAAAATGTAATTTTAGGAAAATTA-GGGGCTAAAATGTAATTTT-AGAAAAGTTTA
* * * * * *
2557438 GGGGTTAAAGTGTAATTTTGAGGAAGATTAGGTGTTGAAATGTAATTTTAGAAAAGTTT-
1 GGGGTAAAAATGTAATTTT-AGGAAAATTAGGGGCTAAAATGTAATTTTAGAAAAGTTTA
* *
2557497 GAGGTCAAAATGTAA
1 GGGGTAAAAATGTAA
2557512 ATTTCAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
59 30 0.48
60 30 0.48
61 2 0.03
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (59 bp):
GGGGTAAAAATGTAATTTTAGGAAAATTAGGGGCTAAAATGTAATTTTAGAAAAGTTTA
Found at i:2560419 original size:51 final size:51
Alignment explanation
Indices: 2560361--2560468 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 51
2560351 TTTCATTCCA
* *
2560361 AATTTCCTTCCAAAATTCTGTCAAACCCATATTTAATTTCAATTTCCTCTC
1 AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCCCTC
*
2560412 AATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCCCTC
1 AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCCCTC
2560463 AATTTC
1 AATTTC
2560469 ATTTTTTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.28, G:0.01, T:0.42
Consensus pattern (51 bp):
AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCCCTC
Found at i:2560502 original size:29 final size:30
Alignment explanation
Indices: 2560469--2560531 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
2560459 CCTCAATTTC
*
2560469 ATTTTTTAAAATAA-TTTAAA-TTTTTTAT
1 ATTTTTAAAAATAATTTTAAATTTTTTTAT
2560497 ATTTTTAAAAATAATTTTAAATTTTTTTAT
1 ATTTTTAAAAATAATTTTAAATTTTTTTAT
2560527 ATTTT
1 ATTTT
2560532 CATCAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 13 0.41
29 6 0.19
30 13 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTTTAAAAATAATTTTAAATTTTTTTAT
Found at i:2562312 original size:18 final size:18
Alignment explanation
Indices: 2562289--2562323 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2562279 AGGTGTGTTT
*
2562289 CCTAACCCTTATATGTAC
1 CCTAACCCTTACATGTAC
2562307 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
2562324 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.06, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:2562886 original size:29 final size:29
Alignment explanation
Indices: 2562844--2563049 Score: 327
Period size: 29 Copynumber: 7.3 Consensus size: 29
2562834 TAATAAAAAC
2562844 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
2562873 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
2562902 CCTAATTTAATTAAAAACCCTAAACTCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
2562932 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
2562961 CCTGATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
2562990 CCTAATTTAATT--AAA----AACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
2563013 CCTAATTTAATTAAAAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
2563042 -CTAATTTA
1 CCTAATTTA
2563050 CATAATTTGA
Statistics
Matches: 165, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
23 20 0.12
25 3 0.02
27 3 0.02
28 8 0.05
29 103 0.62
30 28 0.17
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:2562895 original size:23 final size:23
Alignment explanation
Indices: 2562865--2563041 Score: 120
Period size: 23 Copynumber: 6.6 Consensus size: 23
2562855 TAAAAACCCT
2562865 AACCCTAACCTAATTTAATTAAAAA
1 AACCCTAACCTAATTTAATT--AAA
2562890 CCCTAACCCTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
2562917 AACCCTAAACTCTAACCTAATTTAATTAAA
1 AA--C----C-CTAACCTAATTTAATTAAA
2562947 AACCCTAACCCTAACCTGATTTAATTAAAAA
1 AACCCTAA-CCT-A----ATTTAATT--AAA
2562978 CCCTAACCCTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
2563005 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
2563028 AACCCTAACTCTAA
1 AACCCTAAC-CTAA
2563042 CTAATTTACA
Statistics
Matches: 128, Mismatches: 0, Indels: 45
0.74 0.00 0.26
Matches are distributed among these distances:
23 38 0.30
24 8 0.06
25 2 0.02
27 6 0.05
28 1 0.01
29 37 0.29
30 21 0.16
31 3 0.02
33 1 0.01
34 3 0.02
35 8 0.06
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:2562993 original size:88 final size:81
Alignment explanation
Indices: 2562844--2563049 Score: 324
Period size: 88 Copynumber: 2.5 Consensus size: 81
2562834 TAATAAAAAC
2562844 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
2562909 TAATTAAAAACCCTAAACTCTAA
66 TAATTAAAAA--C----C-CTAA
*
2562932 CCTAATTTAATTAAAAACCCTAACCCTAACCTGATTTAATTAAAAACCCTAACCCTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
2562997 TAATTAAAAACCCTAA
66 TAATTAAAAACCCTAA
*
2563013 CCTAATTTAATTAAAAACCCTAACTCTAA-CTAATTTA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTA
2563050 CATAATTTGA
Statistics
Matches: 115, Mismatches: 3, Indels: 8
0.91 0.02 0.06
Matches are distributed among these distances:
80 7 0.06
81 32 0.28
82 1 0.01
86 1 0.01
88 74 0.64
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (81 bp):
CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
TAATTAAAAACCCTAA
Found at i:2563111 original size:10 final size:10
Alignment explanation
Indices: 2563096--2563120 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2563086 TTTGGACTTA
2563096 ATAATTTTAC
1 ATAATTTTAC
2563106 ATAATTTTAC
1 ATAATTTTAC
2563116 ATAAT
1 ATAAT
2563121 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:2563207 original size:9 final size:9
Alignment explanation
Indices: 2563193--2563225 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2563183 TTTTACTAAA
2563193 AATTAATAC
1 AATTAATAC
2563202 AATTAATAC
1 AATTAATAC
2563211 AATT-AT-C
1 AATTAATAC
2563218 AATTAATA
1 AATTAATA
2563226 ATTGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.23
8 4 0.18
9 13 0.59
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (9 bp):
AATTAATAC
Found at i:2566458 original size:125 final size:125
Alignment explanation
Indices: 2566236--2566583 Score: 592
Period size: 123 Copynumber: 2.8 Consensus size: 125
2566226 CAAACTTGCT
*
2566236 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGTATCTTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGTATCCTGGTA
2566301 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGACCA
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGACCA
* *
2566361 ACTGTAGCAAAATCGCGTCCACGAGGGCCCGATTTCACAATTTCTTCTCAAATAGTATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGTATCCTGGTA
*
2566426 GAAGCGATTTTATACTATTTGCTCAGAAACGTC--AAAAAAATTATTTCTTACATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGACCA
* * * * *
2566484 ACTGTAGAAAAATCACGTCCACGAGGGTGTGATTTCATAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGTATCCTGGTA
*
2566549 GAAGCGATTTTATACTATTTACTCAGAAACGTCAA
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
2566584 CTCGAAATAA
Statistics
Matches: 209, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
123 114 0.55
125 95 0.45
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (125 bp):
ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGTATCCTGGTA
GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGACCA
Found at i:2573712 original size:2 final size:2
Alignment explanation
Indices: 2573705--2573733 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2573695 TATCTCTTAA
2573705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2573734 AAGAATCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2575475 original size:3 final size:3
Alignment explanation
Indices: 2575467--2575491 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2575457 GAACCGAAAG
2575467 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
2575492 ACAAGAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2577934 original size:20 final size:20
Alignment explanation
Indices: 2577909--2577946 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2577899 TAATTTTTTG
*
2577909 AATTTTATATATTTTTATCA
1 AATTTTAGATATTTTTATCA
*
2577929 AATTTTAGATTTTTTTAT
1 AATTTTAGATATTTTTAT
2577947 AATAACTTTT
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:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
AATTTTAGATATTTTTATCA
Found at i:2581823 original size:3 final size:3
Alignment explanation
Indices: 2581815--2581840 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2581805 ACCATATGAT
2581815 TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TA
2581841 ATCATTGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:2584047 original size:138 final size:138
Alignment explanation
Indices: 2583794--2584069 Score: 516
Period size: 138 Copynumber: 2.0 Consensus size: 138
2583784 TGTGAGGGAC
2583794 AACTTAGCCCTCACATACTTCTACACAATCGGCAACCTTAGGGCAATTGAAGACCTTAGAACAAA
1 AACTTAGCCCTCACATACTTCTACACAATCGGCAACCTTAGGGCAATTGAAGACCTTAGAACAAA
*
2583859 TACTAAAGTATGTTTATCTTTAGAGGGATCCTCTTTTTAACCTTACCAATACTTTGCAAAAGTCC
66 TACTAAAGTATGTTTATCTTTAGAGGGATCCTCTTTTTAACCTTACCAATACTTTGCAAAAATCC
2583924 CCCCTTAG
131 CCCCTTAG
*
2583932 AACTTAGCCCTCACATACTTCTACACAATCGGCAACCTTAGGGCAATTGAAGGCCTTAGAACAAA
1 AACTTAGCCCTCACATACTTCTACACAATCGGCAACCTTAGGGCAATTGAAGACCTTAGAACAAA
* *
2583997 TACTAAAGTATGTTTATCTTTAGAGGGATCCTCTTTTTAACCTTATCAATACTTTGCAAAAATCT
66 TACTAAAGTATGTTTATCTTTAGAGGGATCCTCTTTTTAACCTTACCAATACTTTGCAAAAATCC
2584062 CCCCTTAG
131 CCCCTTAG
2584070 CTTTCATTAT
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 134 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (138 bp):
AACTTAGCCCTCACATACTTCTACACAATCGGCAACCTTAGGGCAATTGAAGACCTTAGAACAAA
TACTAAAGTATGTTTATCTTTAGAGGGATCCTCTTTTTAACCTTACCAATACTTTGCAAAAATCC
CCCCTTAG
Found at i:2592919 original size:18 final size:18
Alignment explanation
Indices: 2592898--2592936 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2592888 TTTCTTCAAC
*
2592898 TTCTATTTCAAATTTCTT
1 TTCTATTTCAAATTCCTT
* *
2592916 TTCTGTTTCACATTCCTT
1 TTCTATTTCAAATTCCTT
2592934 TTC
1 TTC
2592937 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.59
Consensus pattern (18 bp):
TTCTATTTCAAATTCCTT
Found at i:2600277 original size:55 final size:58
Alignment explanation
Indices: 2600211--2600337 Score: 170
Period size: 55 Copynumber: 2.2 Consensus size: 58
2600201 TTCAAAAATA
* *
2600211 ATATTATTTTAATAGTTTTAATATTAAATTAAAT-TAA-ATTTA-ATAGATAACTATT
1 ATATTAATTTAATAGATTTAATATTAAATTAAATCTAATATTTATATAGATAACTATT
* * * * *
2600266 CTATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATT
1 ATATTAATTTAATAGATTTAATATTAAATTAAATCTAATATTTATATAGATAACTATT
2600324 ATATTAATTTAATA
1 ATATTAATTTAATA
2600338 TTAAAGTGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
55 30 0.49
56 3 0.05
57 5 0.08
58 23 0.38
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (58 bp):
ATATTAATTTAATAGATTTAATATTAAATTAAATCTAATATTTATATAGATAACTATT
Found at i:2602474 original size:17 final size:16
Alignment explanation
Indices: 2602448--2602480 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2602438 TAAATCCCAG
2602448 ATTTTGATACCCATAT
1 ATTTTGATACCCATAT
2602464 ATTTCTGATACCCATAT
1 ATTT-TGATACCCATAT
2602481 CTTTGACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTTGATACCCATAT
Found at i:2605561 original size:36 final size:36
Alignment explanation
Indices: 2605514--2605588 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
2605504 CTCATTCTAC
*
2605514 TAATATAAACATACCAAGCTAAATAAGTTCATGTTT
1 TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
*
2605550 TAATATAAACATACCAAGTTAAAGAAGTTCATGTTT
1 TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
2605586 TAA
1 TAA
2605589 CTTCCCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (36 bp):
TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
Found at i:2606339 original size:16 final size:16
Alignment explanation
Indices: 2606318--2606350 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2606308 GAATTTTTAA
2606318 TAATTA-TTAAGTAGTT
1 TAATTATTTAA-TAGTT
2606334 TAATTATTTAATAGTT
1 TAATTATTTAATAGTT
2606350 T
1 T
2606351 TATGTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
TAATTATTTAATAGTT
Found at i:2606572 original size:26 final size:27
Alignment explanation
Indices: 2606519--2606572 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
2606509 TTGAGTTAAT
*
2606519 AAATTCTCTTTGAGTTTTTCTTTAAAA
1 AAATTCTCTTTGAGTTTCTCTTTAAAA
*
2606546 AAATTCTC-TTGAGTTTCT-TTTAGAA
1 AAATTCTCTTTGAGTTTCTCTTTAAAA
2606571 AA
1 AA
2606573 GTTTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.32
26 9 0.36
27 8 0.32
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (27 bp):
AAATTCTCTTTGAGTTTCTCTTTAAAA
Found at i:2606800 original size:13 final size:13
Alignment explanation
Indices: 2606784--2606820 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2606774 TTATTCTATT
2606784 TTATTTATCTTAG
1 TTATTTATCTTAG
*
2606797 TTATTTATTTTAG
1 TTATTTATCTTAG
2606810 TTATTTTATCT
1 TTA-TTTATCT
2606821 GACTATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (13 bp):
TTATTTATCTTAG
Found at i:2616116 original size:14 final size:14
Alignment explanation
Indices: 2616099--2616132 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2616089 ATTAATAAAA
2616099 ATTCAATGAAAATG
1 ATTCAATGAAAATG
* *
2616113 ATTCAATGGAAATT
1 ATTCAATGAAAATG
2616127 ATTCAA
1 ATTCAA
2616133 ACTAATAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (14 bp):
ATTCAATGAAAATG
Found at i:2626629 original size:21 final size:21
Alignment explanation
Indices: 2626603--2626642 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2626593 TTGTACAAAC
2626603 TAAGCCTTTAAGCAAAGAAAT
1 TAAGCCTTTAAGCAAAGAAAT
2626624 TAAGCCTTTAAGCAAAGAA
1 TAAGCCTTTAAGCAAAGAA
2626643 GTTGATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (21 bp):
TAAGCCTTTAAGCAAAGAAAT
Found at i:2645515 original size:18 final size:18
Alignment explanation
Indices: 2645492--2645584 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
2645482 TACGACCGTT
2645492 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
2645510 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2645528 TACAGTACTATTTACGTA
1 TACGGTACTATTCACGTA
**
2645546 TACGACACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2645564 TACGATACTGTTCACGTA
1 TACGGTACTATTCACGTA
2645582 TAC
1 TAC
2645585 AGTAGTTGGG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2652196 original size:19 final size:18
Alignment explanation
Indices: 2652174--2652213 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2652164 AGTTTTGTTG
*
2652174 TTATATTACTAATTTTTAA
1 TTATATTACTAA-ATTTAA
*
2652193 TTATATTATTAAATTTAA
1 TTATATTACTAAATTTAA
2652211 TTA
1 TTA
2652214 ATCATGCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATATTACTAAATTTAA
Found at i:2654632 original size:309 final size:307
Alignment explanation
Indices: 2653774--2654972 Score: 1584
Period size: 309 Copynumber: 3.9 Consensus size: 307
2653764 CTGAACCCAT
* * * * * *
2653774 ATGATGAAATCACTTTCATGGCAAGACCTTAATAGGAATGCGACAATGGAAAAG-CTCAGAATGA
1 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGG-AAGGCCTCAGAATGA
* *
2653838 ATTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTCGGAC-AGAACATTTGGGGAGAGGTCATG
65 ATTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAG-ACATTTGGGGAGAGGTCATG
* ** * * * ** **
2653902 ATGTAAATTGTCAAAAGGTTTTTATGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAGTAGGTA
129 GTGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAATA
** *
2653967 CTAAAGCTATGTCTTTCATGTACTGAATA-TTTCTTCATATTGAATAAAACCCGTGGTTCCAAAT
194 CTAAAGCTATGTCTTTCATGTACCAAATATTTTC-TCATATTGAATAAAACTCGTGGTTCCAAAT
2654031 ATATATTAATTATCTTCTCCCTTTTATTCATTACAAATA-----T-----
258 ATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
* *
2654071 A--ATGAAATCACTCTCATGGCAAGACCTCAACACGAAGGCGACAATGGAGGGCCTCAGAATGAA
1 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGGCCTCAGAATGAA
* * * *
2654134 TTCAAGATTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTGTGGGGAGAGGTCATGG
66 TTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATT-TGGGGAGAGGTCATGG
* **
2654199 TGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAACAGGTAC
130 TGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAATAC
* * *
2654264 TAAAGTTATGTCTTTCATATACCAAATGTTTTCTCATATTGAATAAAACTCGTGGTTCCAAATAT
195 TAAAGCTATGTCTTTCATGTACCAAATATTTTCTCATATTGAATAAAACTCGTGGTTCCAAATAT
2654329 ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
260 ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
* *
2654377 ATGACGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAAGGCCTCAGAATGAT
1 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGGCCTCAGAATGA-
* * * * *
2654442 TTTTAAGGTTTTGATTAAAAGGAAAATAAGATTATTTAGGCAAGACATTTGGGGAGAGGTCATCG
65 ATTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGG
* * ** *
2654507 TGTAAATTATCAAAAAGCTTTTTATGCCATTGTTGGTAGGAGCCGCTAGAAAATAAGAACAAATA
130 TGTAAATTA-CCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAATA
* * * * *
2654572 CTAAAGTTATGTCTTTTATGTACCAAATATTTCCTTATATTGAATAAAATTCGTGGTTCCAAATA
194 CTAAAGCTATGTCTTTCATGTACCAAATATTTTCTCATATTGAATAAAACTCGTGGTTCCAAATA
* *
2654637 TATATTAATTATCTTATCCCTTTTATTCATTACAAATATTGGCTACCAT
259 TATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
* ** * *
2654686 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGTGACCTTGGAGGGCCTTAGAATGAA
1 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGGCCTCAGAATGAA
* * * *
2654751 TCCAAGGTTCTGATTAAAAGGAAAATAAGATTGTTTGGGCAAAAAATTTGGGGAGAGGTCATGGT
66 TTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGGT
* * * **
2654816 ATAAATTACCAAAAGCTTTTTACGCCGTTGTTGGTGGGAGCTGCTAGAAAATAAGAACAAATACT
131 GTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAATACT
* * * * *
2654881 AAAGCTATGTCTTTCATGTACCAAATGTTTTCTCGTATTGAACAAAACT-TTGGTTCCAAATAGA
196 AAAGCTATGTCTTTCATGTACCAAATATTTTCTCATATTGAATAAAACTCGTGGTTCCAAATATA
*
2654945 TATTAATTATCTTCTCCCTTTTAATCAT
261 TATTAATTATCTTCTCCCTTTTATTCAT
2654973 CGAGTGAATT
Statistics
Matches: 797, Mismatches: 87, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
294 2 0.00
295 91 0.11
296 167 0.21
297 5 0.01
301 1 0.00
306 40 0.05
307 93 0.12
308 145 0.18
309 253 0.32
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (307 bp):
ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGGCCTCAGAATGAA
TTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGGT
GTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAATACT
AAAGCTATGTCTTTCATGTACCAAATATTTTCTCATATTGAATAAAACTCGTGGTTCCAAATATA
TATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
Found at i:2655693 original size:78 final size:78
Alignment explanation
Indices: 2655501--2655733 Score: 240
Period size: 78 Copynumber: 3.0 Consensus size: 78
2655491 TTTCACAGTA
* * * * *
2655501 TTTT-CATGTTGTTGACCATTCTGGA-CCTCCTCTCTTGTTTCAGACAACATAAAGCATAAGCAT
1 TTTTCCATGTTGTTGACCATCCTAGACCCTCCTC-CCTGTCTCAGACTACATAAAGCATAAGCAT
2655564 ACTACTTAAA-ATG
65 ACTACTTAAATATG
* * * *
2655577 TTTTCTATGTTGTTGACCATCCTGGACCCTCCTTCCCTGTCTCAGACTACATTAAGCATAAACAT
1 TTTTCCATGTTGTTGACCATCCTAGACCCTCC-TCCCTGTCTCAGACTACATAAAGCATAAGCAT
2655642 ACTACTTAAAATATG
65 ACTACTT-AAATATG
*** * * * * **
2655657 TTTTCCATGTTGTTGATTTTCCTAGATCTTCC-CCCTGTTTCAAACTACATAAAGTGTAAGCATA
1 TTTTCCATGTTGTTGACCATCCTAGACCCTCCTCCCTGTCTCAGACTACATAAAGCATAAGCATA
2655721 CTACTTTAAATAT
66 CTAC-TTAAATAT
2655734 ATTAATGATA
Statistics
Matches: 131, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
76 4 0.03
77 19 0.15
78 73 0.56
79 7 0.05
80 28 0.21
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (78 bp):
TTTTCCATGTTGTTGACCATCCTAGACCCTCCTCCCTGTCTCAGACTACATAAAGCATAAGCATA
CTACTTAAATATG
Found at i:2658066 original size:37 final size:37
Alignment explanation
Indices: 2658005--2658083 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
2657995 TTATTACGAA
* * * *
2658005 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
*
2658042 GTCTTACCCGAACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
2658079 GTCTT
1 GTCTT
2658084 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
Found at i:2658280 original size:47 final size:47
Alignment explanation
Indices: 2658202--2658522 Score: 498
Period size: 47 Copynumber: 6.8 Consensus size: 47
2658192 CCCTTCGGGA
* * * * * * *
2658202 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2658249 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2658296 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2658343 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2658390 CTTATCACATATGTACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2658437 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2658484 CTTATCACATATATATACGCTTTCACATTCATCACATCG
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCG
2658523 AATCCTAAAT
Statistics
Matches: 253, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
47 225 0.89
49 28 0.11
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:2660444 original size:56 final size:56
Alignment explanation
Indices: 2660377--2660496 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
2660367 TATTAGTTTA
2660377 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
2660433 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
2660489 TTGCCCAT
1 TTGCCCAT
2660497 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:2661231 original size:9 final size:9
Alignment explanation
Indices: 2661217--2661281 Score: 62
Period size: 9 Copynumber: 7.2 Consensus size: 9
2661207 TTTACATTTA
2661217 TATATTAAT
1 TATATTAAT
2661226 TATATTAAT
1 TATATTAAT
2661235 TATATT-AT
1 TATATTAAT
*
2661243 TATATTACT
1 TATATTAAT
* *
2661252 AATTTTTAAT
1 TA-TATTAAT
2661262 TATATT-AT
1 TATATTAAT
*
2661270 TAATTTTAAT
1 T-ATATTAAT
2661280 TA
1 TA
2661282 ATCATGCTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
8 11 0.24
9 25 0.56
10 9 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATTAAT
Found at i:2661265 original size:19 final size:18
Alignment explanation
Indices: 2661221--2661281 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
2661211 CATTTATATA
* * *
2661221 TTAATTATATTAATTATA
1 TTAATTATATTACTAATT
2661239 TT-ATTATATTACTAATTT
1 TTAATTATATTACTAA-TT
*
2661257 TTAATTATATTATTAATT
1 TTAATTATATTACTAATT
2661275 TTAATTA
1 TTAATTA
2661282 ATCATGCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 11 0.30
18 14 0.38
19 12 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATTATATTACTAATT
Found at i:2661282 original size:22 final size:21
Alignment explanation
Indices: 2661228--2661283 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
2661218 ATATTAATTA
*
2661228 TATTAATTATATT-ATTATAT
1 TATTAATTTTATTAATTATAT
*
2661248 TACTAA-TTT-TTAATTATAT
1 TATTAATTTTATTAATTATAT
2661267 TATTAATTTTAATTAAT
1 TATTAATTTT-ATTAAT
2661284 CATGCTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.07
19 14 0.48
20 8 0.28
22 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTAATTTTATTAATTATAT
Found at i:2661458 original size:12 final size:12
Alignment explanation
Indices: 2661441--2661465 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2661431 AAACTTTTTT
2661441 CCCAATTAAAAA
1 CCCAATTAAAAA
2661453 CCCAATTAAAAA
1 CCCAATTAAAAA
2661465 C
1 C
2661466 AAATATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (12 bp):
CCCAATTAAAAA
Found at i:2661747 original size:84 final size:84
Alignment explanation
Indices: 2661606--2661775 Score: 250
Period size: 84 Copynumber: 2.0 Consensus size: 84
2661596 ATCAATAACA
*
2661606 TCCATAAAAAACAAACGCCATTCTTGAAACTCAAAAAATGAAGCAACAGACATGAAAGGAAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAACTCAAAAAATGAAGCAACAGACATGAAAGGAAAAAA
*
2661671 TAGTATGCATCATTCTACT
66 CAGTATGCATCATTCTACT
* * * * *
2661690 TCCATGAAAAACAAACACTATTCTTGAAACTCGAAAAATGCAGCAACAGACATGAAAGGGAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAACTCAAAAAATGAAGCAACAGACATGAAAGGAAAAAA
* * *
2661755 CGGTATGCATCGTTTTACT
66 CAGTATGCATCATTCTACT
2661774 TC
1 TC
2661776 GCTTTGAATC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.21
Consensus pattern (84 bp):
TCCATAAAAAACAAACACCATTCTTGAAACTCAAAAAATGAAGCAACAGACATGAAAGGAAAAAA
CAGTATGCATCATTCTACT
Found at i:2669170 original size:6 final size:6
Alignment explanation
Indices: 2669161--2669191 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2669151 ATATTATAGA
2669161 ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG A
1 ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG A
2669192 AAGGTGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.48, T:0.16
Consensus pattern (6 bp):
ATGGAG
Found at i:2671052 original size:308 final size:306
Alignment explanation
Indices: 2670488--2671324 Score: 1124
Period size: 308 Copynumber: 2.7 Consensus size: 306
2670478 GACTAAAATC
* * * * * *
2670488 ATATGATGAAATCACTTTCATGGCAAGATCTTAACAAGAATGCGACAATAGAGAGG-CTCAGAAT
1 ATATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAG-GGCCTCAGAAT
* * ** *
2670552 GAATTCAAAATTCTAATTAAAAGGAAAATAAGATTGTTCGTAC-AGA-ATATTTGGGAAGAGTTC
65 GAATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACAT-TTTGGG-AGAGATC
** * * ** *
2670615 ATGGTGTAAATTGTCAAAAGTTTTTTATGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAGTAG
128 ATGGTGTAAATTACCAAAAGCTTTTTATGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAA
*
2670680 GTACTAAAGCTATGTCTTTCATGTACCGAATATTTCTTCATATTGAATAAAACCCGTTGTTCCAA
193 GTACTAAAGCTATGTCTTTCATGTACC-AATATTTCTTCATATTGAATAAAACCCGTGGTTCCAA
*
2670745 ATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTGCA
257 ATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACA
* * * *
2670795 ATATGATGAAATCACTCCCATGGTAAGACCTCAACACGAAGGCGGCAATGGAGGGCCCCAGAATG
1 ATATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAGGGCCTCAGAATG
* * * * * *
2670860 AACTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTATGAGGAGAGGTCAT
66 AATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTG-GGAGAGATCAT
* * *
2670925 GGTGTAAATTACCAAAAGCTTTTTATGTCATTGTTGGGGGGAGCCACTAGAAAGTAAGAACATGT
130 GGTGTAAATTACCAAAAGCTTTTTATGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAGT
* * **
2670990 ACTAAAGCTATGTCTTTCATATACCAACTGTTT-TATCATATTGAATAAAACTTGTGGTTCCAAA
195 ACTAAAGCTATGTCTTTCATGTACCAA-TATTTCT-TCATATTGAATAAAACCCGTGGTTCCAAA
*
2671054 TATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACC
258 TATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACA
* * * *
2671103 ATATGATGAAATCACTCTCATGACAAGACCTCAACAAGAAGGTGGCAATGGAGGGCCTTAGAAAG
1 ATATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAGGGCCTCAGAATG
*
2671168 AATTCAATGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGAGAGATCATG
66 AATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGAGAGATCATG
* * * * * * *
2671233 GTGTAAAATACCAAAAAGCTTTTTAAGCCATTGTTGGTGGTAGGCGCTAGAAAATAAGAACAAAT
131 GTGTAAATTACC-AAAAGCTTTTTATGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAGT
2671298 ACTAAAGCTATGTCTTTCATGTACCAA
195 ACTAAAGCTATGTCTTTCATGTACCAA
2671325 ATGTGAAATA
Statistics
Matches: 462, Mismatches: 61, Indels: 13
0.86 0.11 0.02
Matches are distributed among these distances:
306 2 0.00
307 111 0.24
308 345 0.75
309 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (306 bp):
ATATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAGGGCCTCAGAATG
AATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGAGAGATCATG
GTGTAAATTACCAAAAGCTTTTTATGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAGTA
CTAAAGCTATGTCTTTCATGTACCAATATTTCTTCATATTGAATAAAACCCGTGGTTCCAAATAT
ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACA
Found at i:2673402 original size:11 final size:11
Alignment explanation
Indices: 2673386--2673411 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2673376 GTCCCTAAGA
2673386 TTTTTTATTTT
1 TTTTTTATTTT
2673397 TTTTTTATTTT
1 TTTTTTATTTT
2673408 TTTT
1 TTTT
2673412 GGAATTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:2689793 original size:56 final size:56
Alignment explanation
Indices: 2689717--2689826 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
2689707 ATGTTATAAT
* *
2689717 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTATAAAATGA
1 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTACAATTTAGTACAAAATGA
2689773 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTACAATTTAGTACAAAAT
1 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTACAATTTAGTACAAAAT
2689827 AAGTGTGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (56 bp):
GTAACTACCTATAATTTTAAATAACTTTGATTTAATTACAATTTAGTACAAAATGA
Found at i:2690571 original size:23 final size:24
Alignment explanation
Indices: 2690540--2690594 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
2690530 TAGGTTAGAT
2690540 AATT-AAATAATTAGGAATAATTA-
1 AATTAAAATAATTA-GAATAATTAG
2690563 AA-TAAAATAATTAGAATAATTAG
1 AATTAAAATAATTAGAATAATTAG
2690586 AATTAAAAT
1 AATTAAAAT
2690595 TTTGGGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.34
23 13 0.45
24 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
AATTAAAATAATTAGAATAATTAG
Found at i:2691974 original size:15 final size:14
Alignment explanation
Indices: 2691945--2691992 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
2691935 TGTTGTTTTC
*
2691945 TTAAAGCTTTTGATG
1 TTAAAGC-TTAGATG
*
2691960 TTAAATGGTTAGATG
1 TTAAA-GCTTAGATG
2691975 TT-AAGCTTAGATG
1 TTAAAGCTTAGATG
2691988 TTAAA
1 TTAAA
2691993 AATGACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 4 0.14
15 13 0.46
16 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (14 bp):
TTAAAGCTTAGATG
Found at i:2692058 original size:9 final size:9
Alignment explanation
Indices: 2692041--2692073 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2692031 AAAGAGGACT
*
2692041 ACAGCGTAA
1 ACAGTGTAA
2692050 ACAGTGTAA
1 ACAGTGTAA
2692059 ACAGTGTAA
1 ACAGTGTAA
2692068 ACAGTG
1 ACAGTG
2692074 GCATGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.18
Consensus pattern (9 bp):
ACAGTGTAA
Found at i:2694753 original size:82 final size:82
Alignment explanation
Indices: 2694612--2694769 Score: 262
Period size: 82 Copynumber: 1.9 Consensus size: 82
2694602 GAATGTAAGG
* *
2694612 GGTTGCTAAGTGTAGATTCTCCGAATCATTGATCAAAAAAGAGTTGCTAAGTGCCGATTCCCCAA
1 GGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAAAAAGAGTTGCTAAGTGCAGATTCCCCAA
2694677 ATCATAGATCAAAAAAT
66 ATCATAGATCAAAAAAT
* *
2694694 GGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCCCAA
1 GGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAAAAAGAGTTGCTAAGTGCAGATTCCCCAA
* *
2694759 ATTATTGATCA
66 ATCATAGATCA
2694770 GAAAGGGGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (82 bp):
GGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAAAAAGAGTTGCTAAGTGCAGATTCCCCAA
ATCATAGATCAAAAAAT
Found at i:2694775 original size:41 final size:41
Alignment explanation
Indices: 2694608--2694779 Score: 227
Period size: 41 Copynumber: 4.2 Consensus size: 41
2694598 CTTTGAATGT
* * *
2694608 AAGGGGTTGCTAAGTGTAGATTCTCCGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAA
* * * *
2694649 AAAGAGTTGCTAAGTGCCGATTCCCCAAATCATAGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAA
** * *
2694690 AAATGGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAA
* *
2694731 AAGGGGTTGCTAAGTGCAGATTCCCCAAATTATTGATCAGA
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAA
2694772 AAGGGGTT
1 AAGGGGTT
2694780 ACTATGTGTT
Statistics
Matches: 112, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAA
Found at i:2694865 original size:43 final size:41
Alignment explanation
Indices: 2694817--2695009 Score: 207
Period size: 43 Copynumber: 4.6 Consensus size: 41
2694807 ACTACAGGGT
2694817 GGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATGGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCAC-TGAT-GT-AAAGG
* * * *
2694860 GGTTGCTATGTGTTGATTCC-CCGTATCACTGAATATAAAGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCACTG-ATGTAAAGG
*
2694901 GGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCACTGAT-GT-AAAGG
*
2694944 GGTTGCTATA-TGTTGATTCC-CCGTATCACTGAT-TATAAGG
1 GGTTGCTA-AGTGCTGATTCCACCGTATCACTGATGTA-AAGG
*
2694984 TGGTTGCTAAGTACTGATTCCACCGT
1 -GGTTGCTAAGTGCTGATTCCACCGT
2695010 GTAATGGTTA
Statistics
Matches: 127, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
39 1 0.01
40 6 0.05
41 40 0.31
42 37 0.29
43 42 0.33
44 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCACTGATGTAAAGG
Found at i:2694874 original size:84 final size:83
Alignment explanation
Indices: 2694731--2695009 Score: 357
Period size: 84 Copynumber: 3.4 Consensus size: 83
2694721 ATTGATCAAA
* ** * ** *
2694731 AAGG-GGTTGCTAAGTGCAGATTCC-CCAAATTATTGAT-CAGAAAGGGGTTACTATGTGTTGAT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGAAAGGGGTTGCTATGTGTTGAT
* * * *
2694793 TTCCCATATCGCTAACTAC
66 TCCCCGTATCACTAA-TAT
* *
2694812 AGGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATGGTGAAAGGGGTTGCTATGTGTTGAT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGAAAGGGGTTGCTATGTGTTGAT
2694877 TCCCCGTATCACTGAATAT
66 TCCCCGTATCACT-AATAT
* *
2694896 AAAGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGAAAGGGGTTGCTATATGTTGAT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGAAAGGGGTTGCTATGTGTTGAT
*
2694961 TCCCCGTATCACTGATTAT
66 TCCCCGTATCACT-AATAT
*
2694980 AAGGTGGTTGCTAAGTACTGATTCCACCGT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGT
2695010 GTAATGGTTA
Statistics
Matches: 174, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
81 3 0.02
82 19 0.11
83 9 0.05
84 141 0.81
85 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (83 bp):
AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGAAAGGGGTTGCTATGTGTTGAT
TCCCCGTATCACTAATAT
Found at i:2694918 original size:41 final size:43
Alignment explanation
Indices: 2694815--2695009 Score: 215
Period size: 41 Copynumber: 4.6 Consensus size: 43
2694805 TAACTACAGG
*
2694815 GTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATGGTGAAA
1 GTGGTTGCTAAGTGCTGATTCCACCGTATCAC-TGATGATGAAA
* * *
2694858 GGGGTTGCTATGTGTTGATTCC-CCGTATCACTGAAT-AT-AAA
1 GTGGTTGCTAAGTGCTGATTCCACCGTATCACTG-ATGATGAAA
* *
2694899 GTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGAAA
1 GTGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGATGAAA
* * * *
2694942 GGGGTTGCTATA-TGTTGATTCC-CCGTATCACTGATTAT-AAG
1 GTGGTTGCTA-AGTGCTGATTCCACCGTATCACTGATGATGAAA
*
2694983 GTGGTTGCTAAGTACTGATTCCACCGT
1 GTGGTTGCTAAGTGCTGATTCCACCGT
2695010 GTAATGGTTA
Statistics
Matches: 126, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
40 1 0.01
41 43 0.34
42 38 0.30
43 43 0.34
44 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (43 bp):
GTGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGATGAAA
Found at i:2695162 original size:38 final size:37
Alignment explanation
Indices: 2695119--2695191 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
2695109 TGTGGAATTG
*
2695119 AATTGAATATTCACTAGAAAATGAAAAAGTGAAATTTA
1 AATTGAATAGTCACTA-AAAATGAAAAAGTGAAATTTA
* * * *
2695157 AATTGAATAGTGATTACAAGTGAAAAAGTGAAATT
1 AATTGAATAGTCACTAAAAATGAAAAAGTGAAATT
2695192 ATGAAAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 17 0.57
38 13 0.43
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (37 bp):
AATTGAATAGTCACTAAAAATGAAAAAGTGAAATTTA
Found at i:2700242 original size:29 final size:29
Alignment explanation
Indices: 2700193--2700249 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2700183 CAACGGTGCC
* *
2700193 TTCGAACCAATAACTCAGATATCACTTGG
1 TTCGAACCAACAACTCAGATACCACTTGG
* *
2700222 TTCGAACCAACAGCTCGGATACCACTTG
1 TTCGAACCAACAACTCAGATACCACTTG
2700250 TCACGGGGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (29 bp):
TTCGAACCAACAACTCAGATACCACTTGG
Found at i:2703149 original size:101 final size:101
Alignment explanation
Indices: 2702967--2703169 Score: 334
Period size: 101 Copynumber: 2.0 Consensus size: 101
2702957 ATTTTCCATA
* * *
2702967 ATAAATTGAATGGCTAAACAAGATTCGAAAGCAGAAGCAACTCAGCTTCTAGCACCTATTAAAAC
1 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
* * *
2703032 AGTATAGATTAGGATGGAACTATAACTAAAGATGAC
66 AGGATAGACTAAGATGGAACTATAACTAAAGATGAC
*
2703068 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAAC
1 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
*
2703133 AGGATAGACTAAGATGGAATTATAACTAAAGATGAC
66 AGGATAGACTAAGATGGAACTATAACTAAAGATGAC
2703169 A
1 A
2703170 AACTAAAAAG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.22
Consensus pattern (101 bp):
ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
AGGATAGACTAAGATGGAACTATAACTAAAGATGAC
Found at i:2709106 original size:23 final size:24
Alignment explanation
Indices: 2709075--2709129 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
2709065 TAGGTTAGAT
2709075 AATT-AAATAATTAGGAATAATTA-
1 AATTAAAATAATTA-GAATAATTAG
2709098 AA-TAAAATAATTAGAATAATTAG
1 AATTAAAATAATTAGAATAATTAG
2709121 AATTAAAAT
1 AATTAAAAT
2709130 TTTGGGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.34
23 13 0.45
24 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
AATTAAAATAATTAGAATAATTAG
Found at i:2709168 original size:15 final size:15
Alignment explanation
Indices: 2709148--2709191 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
2709138 AAGAAATTAA
2709148 AATTAAGTTTTTGGG
1 AATTAAGTTTTTGGG
2709163 AATTAA---TTTGGG
1 AATTAAGTTTTTGGG
2709175 AATTAAGTTTTTGGG
1 AATTAAGTTTTTGGG
2709190 AA
1 AA
2709192 ATAATTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.46
15 14 0.54
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (15 bp):
AATTAAGTTTTTGGG
Found at i:2709211 original size:27 final size:27
Alignment explanation
Indices: 2709146--2709212 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
2709136 TTAAGAAATT
* *
2709146 AAAATTAAGTTTTTGGGAATTAATTTGG
1 AAAA-TAAGTTTTTGGGAAATAATTTAG
* *
2709174 GAATTAAGTTTTTGGGAAATAATTTAG
1 AAAATAAGTTTTTGGGAAATAATTTAG
*
2709201 AAAATATGTTTT
1 AAAATAAGTTTT
2709213 ACTTGAACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.43
Consensus pattern (27 bp):
AAAATAAGTTTTTGGGAAATAATTTAG
Found at i:2715956 original size:46 final size:44
Alignment explanation
Indices: 2715852--2715959 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2715842 TGTCTTTAAC
** * * *
2715852 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
2715896 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
2715942 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2715960 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:2716850 original size:9 final size:9
Alignment explanation
Indices: 2716836--2716870 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2716826 TTCTATTCTG
2716836 TTTCTTTTC
1 TTTCTTTTC
*
2716845 TTTCTTTTT
1 TTTCTTTTC
*
2716854 TTTCTATTC
1 TTTCTTTTC
2716863 TTTCTTTT
1 TTTCTTTT
2716871 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:2716863 original size:18 final size:19
Alignment explanation
Indices: 2716836--2716875 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
2716826 TTCTATTCTG
*
2716836 TTTCTTTTCTTTCTTTT-T
1 TTTCTATTCTTTCTTTTGT
2716854 TTTCTATTCTTTCTTTTGT
1 TTTCTATTCTTTCTTTTGT
2716873 TTT
1 TTT
2716876 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTCTATTCTTTCTTTTGT
Found at i:2716892 original size:5 final size:5
Alignment explanation
Indices: 2716879--2716951 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
2716869 TTGTTTTATG
2716879 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
2716927 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
2716952 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:2716904 original size:19 final size:19
Alignment explanation
Indices: 2716880--2716922 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2716870 TGTTTTATGT
2716880 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
2716899 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
2716918 ATATA
1 ATATA
2716923 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:2716932 original size:24 final size:25
Alignment explanation
Indices: 2716886--2716950 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
2716876 ATGTATATAT
* *
2716886 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
2716910 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
2716935 TTACTATAATATAATA
1 ATAATATAATATAATA
2716951 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:2722101 original size:46 final size:44
Alignment explanation
Indices: 2721997--2722104 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2721987 TGTCTTTAAC
** * * *
2721997 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
2722041 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
2722087 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2722105 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:2723003 original size:19 final size:20
Alignment explanation
Indices: 2722981--2723021 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
2722971 TTCTATTCTG
*
2722981 TTTCTTTTCTTTCTTTT-TT
1 TTTCTATTCTTTCTTTTGTT
2723000 TTTCTATTCTTTCTTTTGTT
1 TTTCTATTCTTTCTTTTGTT
2723020 TT
1 TT
2723022 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTCTATTCTTTCTTTTGTT
Done.