Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 24 of 163
Found at i:7489751 original size:7 final size:7
Alignment explanation
Indices: 7489709--7489758 Score: 56
Period size: 6 Copynumber: 7.9 Consensus size: 7
7489699 GGGTTTCTCA
7489709 AAATG-G
1 AAATGAG
7489715 AAATG-G
1 AAATGAG
7489721 AAAT-AG
1 AAATGAG
*
7489727 CAATGA-
1 AAATGAG
7489733 AAATGA-
1 AAATGAG
7489739 AAATGAG
1 AAATGAG
7489746 AAATGAG
1 AAATGAG
7489753 AAATGA
1 AAATGA
7489759 TTCATTTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 25 0.64
7 14 0.36
ACGTcount: A:0.58, C:0.02, G:0.24, T:0.16
Consensus pattern (7 bp):
AAATGAG
Found at i:7491244 original size:24 final size:24
Alignment explanation
Indices: 7491217--7491262 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
7491207 ATAGACGAAA
* *
7491217 AAATTTTTGGTTTACCATGATAAG
1 AAATTTTCGATTTACCATGATAAG
7491241 AAATTTTCGATTTACCATGATA
1 AAATTTTCGATTTACCATGATA
7491263 CAACATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (24 bp):
AAATTTTCGATTTACCATGATAAG
Found at i:7496949 original size:3 final size:3
Alignment explanation
Indices: 7496941--7496968 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7496931 CTTTCTTTCG
7496941 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
7496969 TTTGAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:7510872 original size:22 final size:21
Alignment explanation
Indices: 7510832--7510901 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 21
7510822 GAGCAAAAAA
*
7510832 AATTGAGTGAATTTAAGAG-G
1 AATTGAGAGAATTTAAGAGAG
*
7510852 ATATTGAGAGCAATTTGAGAGAG
1 A-ATTGAGAG-AATTTAAGAGAG
* *
7510875 AATT--GAGAATGTGAGAGAG
1 AATTGAGAGAATTTAAGAGAG
7510894 AATTGAGA
1 AATTGAGA
7510902 TTGAATTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
19 15 0.36
20 4 0.10
21 9 0.21
22 12 0.29
23 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.31, T:0.26
Consensus pattern (21 bp):
AATTGAGAGAATTTAAGAGAG
Found at i:7525416 original size:15 final size:15
Alignment explanation
Indices: 7525396--7525443 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
7525386 TTAAGTATAA
*
7525396 ATATTAGATTAGATT
1 ATATTAGATTATATT
*
7525411 ATATTAGATTATAAT
1 ATATTAGATTATATT
*
7525426 ATATTATATTATATT
1 ATATTAGATTATATT
7525441 ATA
1 ATA
7525444 AAAGAAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
ATATTAGATTATATT
Found at i:7525428 original size:5 final size:5
Alignment explanation
Indices: 7525396--7525443 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
7525386 TTAAGTATAA
* * * *
7525396 ATATT AGATT AGATT ATATT AGATT ATAAT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA
7525444 AAAGAAACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (5 bp):
ATATT
Found at i:7526432 original size:22 final size:22
Alignment explanation
Indices: 7526407--7526483 Score: 84
Period size: 22 Copynumber: 3.4 Consensus size: 22
7526397 CTCTCTGATA
7526407 TTTAGCACGTCAGTGCTATCTG
1 TTTAGCACGTCAGTGCTATCTG
* *
7526429 TTTAGCACATCTA-TGCTCTCTG
1 TTTAGCACGTC-AGTGCTATCTG
*
7526451 ATATTTAGCACGTCAGTGCTTTCTG
1 ---TTTAGCACGTCAGTGCTATCTG
7526476 TTTAGCAC
1 TTTAGCAC
7526484 ATTTGTGCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
22 26 0.57
23 1 0.02
24 1 0.02
25 18 0.39
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (22 bp):
TTTAGCACGTCAGTGCTATCTG
Found at i:7526461 original size:25 final size:25
Alignment explanation
Indices: 7526396--7526475 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
7526386 ACTCTAGTGC
*
7526396 GCTCTCTGATATTTAGCACGTCAGT
1 GCTCTCTGATATTTAGCACATCAGT
*
7526421 GCTATCTG---TTTAGCACATCTA-T
1 GCTCTCTGATATTTAGCACATC-AGT
*
7526443 GCTCTCTGATATTTAGCACGTCAGT
1 GCTCTCTGATATTTAGCACATCAGT
*
7526468 GCTTTCTG
1 GCTCTCTG
7526476 TTTAGCACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 18 0.40
23 1 0.02
24 1 0.02
25 25 0.56
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATATTTAGCACATCAGT
Found at i:7526465 original size:47 final size:47
Alignment explanation
Indices: 7526396--7526485 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
7526386 ACTCTAGTGC
7526396 GCTCTCTGATATTTAGCACGTCAGTGCTATCTGTTTAGCACATCTAT
1 GCTCTCTGATATTTAGCACGTCAGTGCTATCTGTTTAGCACATCTAT
*
7526443 GCTCTCTGATATTTAGCACGTCAGTGCTTTCTGTTTAGCACAT
1 GCTCTCTGATATTTAGCACGTCAGTGCTATCTGTTTAGCACAT
7526486 TTGTGCTAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (47 bp):
GCTCTCTGATATTTAGCACGTCAGTGCTATCTGTTTAGCACATCTAT
Found at i:7526491 original size:22 final size:22
Alignment explanation
Indices: 7526407--7526493 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 22
7526397 CTCTCTGATA
* *
7526407 TTTAGCACGTCAGTGCTATCTG
1 TTTAGCACATCTGTGCTATCTG
* *
7526429 TTTAGCACATCTATGCTCTCTG
1 TTTAGCACATCTGTGCTATCTG
* * *
7526451 ATATTTAGCACGTCAGTGCTTTCTG
1 ---TTTAGCACATCTGTGCTATCTG
*
7526476 TTTAGCACATTTGTGCTA
1 TTTAGCACATCTGTGCTA
7526494 GAGGTGCTCA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
22 32 0.64
25 18 0.36
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (22 bp):
TTTAGCACATCTGTGCTATCTG
Found at i:7526684 original size:38 final size:39
Alignment explanation
Indices: 7526612--7526732 Score: 176
Period size: 39 Copynumber: 3.1 Consensus size: 39
7526602 TTTAAATTTA
* *
7526612 AAAAAATATTTTAAAATTATTTTAAAATTAAAAAAACTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAACTT
7526651 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAGTAA---
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAA--AACTT
*
7526689 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAACTT
7526728 AAAAA
1 AAAAA
7526733 ATAAATATAT
Statistics
Matches: 75, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
36 2 0.03
38 34 0.45
39 37 0.49
41 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (39 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAACTT
Found at i:7526745 original size:17 final size:17
Alignment explanation
Indices: 7526700--7526745 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
7526690 AAAAGTATTT
* *
7526700 TAAAAATATTTTAAAAT
1 TAAAAATATTTAAAAAA
*
7526717 TAAAAAAATTTAAAAAA
1 TAAAAATATTTAAAAAA
*
7526734 TAAATATATTTA
1 TAAAAATATTTA
7526746 TTATATCGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAAATATTTAAAAAA
Found at i:7530410 original size:13 final size:13
Alignment explanation
Indices: 7530392--7530457 Score: 96
Period size: 13 Copynumber: 5.1 Consensus size: 13
7530382 AGTTTGGCAA
7530392 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
7530405 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
7530418 TGATGTGGAAAAG
1 TGCTTTTGAAAAG
*
7530431 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
7530444 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
7530457 T
1 T
7530458 TCAGTTTCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:7533069 original size:23 final size:22
Alignment explanation
Indices: 7533043--7533091 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
7533033 TTTCTTTGCT
* * *
7533043 TTTTTTTATTGTTTTTATTACTA
1 TTTTCTTATTATTTTT-TCACTA
*
7533066 TTTTCTTGTTATTTTTTCACTA
1 TTTTCTTATTATTTTTTCACTA
7533088 TTTT
1 TTTT
7533092 ACTACCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTCTTATTATTTTTTCACTA
Found at i:7533074 original size:20 final size:22
Alignment explanation
Indices: 7533046--7533092 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
7533036 CTTTGCTTTT
7533046 TTTTATTGTT-TTTATT-ACTA
1 TTTTATTGTTATTTATTCACTA
* *
7533066 TTTTCTTGTTATTTTTTCACTA
1 TTTTATTGTTATTTATTCACTA
7533088 TTTTA
1 TTTTA
7533093 CTACCATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTATTGTTATTTATTCACTA
Found at i:7535476 original size:21 final size:21
Alignment explanation
Indices: 7535431--7535477 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
7535421 AAATAATAAA
*
7535431 ATAG-ATTATACATTATCTTT
1 ATAGTATTATACATTATATTT
*
7535451 ATAGTATTATATATTATGATTT
1 ATAGTATTATACATTAT-ATTT
7535473 -TAGTA
1 ATAGTA
7535478 AATTCACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 16 0.70
22 3 0.13
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (21 bp):
ATAGTATTATACATTATATTT
Found at i:7538240 original size:2 final size:2
Alignment explanation
Indices: 7538235--7538265 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7538225 TCTCTCTCTA
7538235 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
7538266 TTCTTCTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:7548633 original size:3 final size:3
Alignment explanation
Indices: 7548625--7548671 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
7548615 TGTTGAACAA
7548625 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7548672 AACACATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7560956 original size:20 final size:20
Alignment explanation
Indices: 7560931--7560978 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
7560921 CTCCAAATTT
**
7560931 TTATAAAATTACTGAATCTC
1 TTATAAAATTACCAAATCTC
*
7560951 TTATAAACTTACCAAATCTC
1 TTATAAAATTACCAAATCTC
*
7560971 TTACAAAA
1 TTATAAAA
7560979 CATTGTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (20 bp):
TTATAAAATTACCAAATCTC
Found at i:7563323 original size:81 final size:81
Alignment explanation
Indices: 7563188--7563348 Score: 261
Period size: 81 Copynumber: 2.0 Consensus size: 81
7563178 GAAGCTACGG
* * *
7563188 AGATCATTTTCGCCTTCCCGATTGGCTAATAGATTGGTTTCACCATTGAAGAGCAGAAAAAGTTT
1 AGATCATTTTCACCTTCCCGATTGGCTAACAGATTGGTGTCACCATTGAAGAGCAGAAAAAGTTT
*
7563253 GCAAAGAAGTGATGGC
66 GCAAAAAAGTGATGGC
*
7563269 AGATCATTTTCACCTTCCC-ATTTGGCTAACAGATTGGTGTCACCATTGAAGAGCAGAAAAGGTT
1 AGATCATTTTCACCTTCCCGA-TTGGCTAACAGATTGGTGTCACCATTGAAGAGCAGAAAAAGTT
7563333 TGCAAAAAAGTGATGG
65 TGCAAAAAAGTGATGG
7563349 ACCAATGAGT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
80 1 0.01
81 73 0.99
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (81 bp):
AGATCATTTTCACCTTCCCGATTGGCTAACAGATTGGTGTCACCATTGAAGAGCAGAAAAAGTTT
GCAAAAAAGTGATGGC
Found at i:7572004 original size:31 final size:31
Alignment explanation
Indices: 7571963--7572022 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
7571953 AATTTAGTTT
* *
7571963 CTTAATTAAAAA-CTTTAGAATAGTTCAATGA
1 CTTAAATAAAAATCTTTA-AATAATTCAATGA
*
7571994 CTTAAATAAAAATTTTTAAATAATTCAAT
1 CTTAAATAAAAATCTTTAAATAATTCAAT
7572023 AACTATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (31 bp):
CTTAAATAAAAATCTTTAAATAATTCAATGA
Found at i:7582290 original size:10 final size:9
Alignment explanation
Indices: 7582245--7582315 Score: 58
Period size: 9 Copynumber: 8.0 Consensus size: 9
7582235 TTTTAGTACG
7582245 ATAATTTTT
1 ATAATTTTT
*
7582254 ATATTTTTT
1 ATAATTTTT
*
7582263 ACAATTTTT
1 ATAATTTTT
* *
7582272 TTCTATTTTT
1 AT-AATTTTT
*
7582282 ATAACTTTT
1 ATAATTTTT
7582291 ATTAA-TTTT
1 A-TAATTTTT
7582300 -T-ATTTTT
1 ATAATTTTT
7582307 ATAATTTTT
1 ATAATTTTT
7582316 TTGTGACATG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
6 1 0.02
7 5 0.10
8 1 0.02
9 31 0.65
10 10 0.21
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (9 bp):
ATAATTTTT
Found at i:7585061 original size:33 final size:33
Alignment explanation
Indices: 7585024--7585088 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
7585014 TATGTTGGTC
*
7585024 GAAAAATGATGTCATTTTGTTGAGGCAGATTCT
1 GAAAAATGAGGTCATTTTGTTGAGGCAGATTCT
7585057 GAAAAATGAGGTCATTTTGTTGAGGCAGATTC
1 GAAAAATGAGGTCATTTTGTTGAGGCAGATTC
7585089 ATTTTCAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (33 bp):
GAAAAATGAGGTCATTTTGTTGAGGCAGATTCT
Found at i:7595318 original size:3 final size:3
Alignment explanation
Indices: 7595310--7595341 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
7595300 AATTCCCATC
7595310 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
7595342 ACACTAGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:7597623 original size:27 final size:27
Alignment explanation
Indices: 7597585--7597655 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
7597575 GGTGGAGGGC
* *
7597585 CTGCCATAGGCGGCACCAGTGATGCCA
1 CTGCCACAGGCGGCACCAATGATGCCA
* * * *
7597612 GTGGCAGAGGCGGCACCAATGGTGCCA
1 CTGCCACAGGCGGCACCAATGATGCCA
7597639 CTGCCACAGGCGGCACC
1 CTGCCACAGGCGGCACC
7597656 GGCCCTTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.21, C:0.34, G:0.34, T:0.11
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAATGATGCCA
Found at i:7597710 original size:15 final size:15
Alignment explanation
Indices: 7597692--7597749 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
7597682 TTGGCTGGGG
7597692 AAGAAAGGAAAGAAA
1 AAGAAAGGAAAGAAA
*
7597707 AAGAAAGGAAAGGAA
1 AAGAAAGGAAAGAAA
*
7597722 AGGAAAGGAGAAGAAA
1 AAGAAAGGA-AAGAAA
7597738 GAA-AAAGGAAAG
1 -AAGAAAGGAAAG
7597750 GAGAAGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 25 0.68
16 11 0.30
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAGAAAGGAAAGAAA
Found at i:7597717 original size:5 final size:5
Alignment explanation
Indices: 7597694--7597751 Score: 64
Period size: 5 Copynumber: 11.4 Consensus size: 5
7597684 GGCTGGGGAA
* * *
7597694 GAAAG GAAAG AAAAA GAAAG GAAAG GAAAG GAAAG GAGAA- GAAAG AAAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GA-AAG GAAAG -GAAAG
7597745 GAAAG GA
1 GAAAG GA
7597752 GAAGAAGAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 2 0.05
5 36 0.82
6 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:7598549 original size:156 final size:156
Alignment explanation
Indices: 7598069--7598624 Score: 848
Period size: 155 Copynumber: 3.6 Consensus size: 156
7598059 ATAAAATATG
* * * *
7598069 AAAAGAATGTAAAATAAT-AAAATACGAAAATAAAATA-TTTT-TTGAAAGTAAAAAAATC-CAG
1 AAAATAATGTAAAATAATAAAAATA-GAAAATAATATATTTTTATTGAAAGTAATAAAATCTGAG
*
7598130 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTT--TTTTACTAAATTTATTTTAAAAACACACT
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTT-TTAAATTTA-TTTAAAAACACACT
7598193 AAATTAATACATTTCAAACATAATGTACT
128 AAATTAATACATTTCAAACATAATGTACT
* * *
7598222 -AAA-AATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGG
1 AAAATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTATTGAAAGTAATAAAA-TCTGAG
* * * *
7598285 AAAAGAATACGAACAAAGGGCCAAAATAATGGTTAATTTTTGAAATTTATTT-AAAA-ACACTAA
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTTAAATTTATTTAAAAACACACTAA
7598348 ATTAATACATTTCAAACATAATGTACT
130 ATTAATACATTTCAAACATAATGTACT
*
7598375 AAAATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTATTGAAAGTAATAAAATCTGGGA
1 AAAATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTATTGAAAGTAATAAAATCTGAGA
*
7598440 AAAAAATACGAACAAAGGACCGAAATAAGGGTTAATTTTTTAAATTTATTTAAAAACACACTAAA
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTTAAATTTATTTAAAAACACACTAAA
7598505 TTAATACATTTCAAACATAATGTACT
131 TTAATACATTTCAAACATAATGTACT
7598531 AAAATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTATTGAAAGTAATAAAAT-T-AGA
1 AAAATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTATTGAAAGTAATAAAATCTGAGA
*
7598594 GAAAAAATACGAACAAAAGGCCGAAATAAGG
66 -AAAAAATACGAACAAAGGGCCGAAATAAGG
7598625 TTTTTTTACT
Statistics
Matches: 371, Mismatches: 20, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
151 24 0.06
152 12 0.03
153 48 0.13
154 63 0.17
155 120 0.32
156 100 0.27
157 4 0.01
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (156 bp):
AAAATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTATTGAAAGTAATAAAATCTGAGA
AAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTTAAATTTATTTAAAAACACACTAAA
TTAATACATTTCAAACATAATGTACT
Found at i:7603984 original size:39 final size:41
Alignment explanation
Indices: 7603941--7604019 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
7603931 ACTACCACAA
** *
7603941 TAACAATAATAA-TAGTTTTTTACTCAAAATAAT-ACTAAT
1 TAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAAT
7603980 TAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAA
1 TAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAA
7604020 AAATAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 12 0.34
40 18 0.51
41 5 0.14
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (41 bp):
TAACAATAATAATTAGGGTTTTACTAAAAATAATAACTAAT
Found at i:7604020 original size:13 final size:13
Alignment explanation
Indices: 7604002--7604027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7603992 TTAGGGTTTT
7604002 ACTAAAAATAATA
1 ACTAAAAATAATA
7604015 ACTAAAAATAATA
1 ACTAAAAATAATA
7604028 TAATGTAAAA
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
ACTAAAAATAATA
Found at i:7604630 original size:13 final size:13
Alignment explanation
Indices: 7604612--7604637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7604602 TTAGGGTTTT
7604612 ACTAAAAATAATA
1 ACTAAAAATAATA
7604625 ACTAAAAATAATA
1 ACTAAAAATAATA
7604638 TAATGTAAAA
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
ACTAAAAATAATA
Found at i:7605025 original size:25 final size:25
Alignment explanation
Indices: 7604987--7605034 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
7604977 CCTCCTCCTC
7604987 CTTCTTCTTCTTCTCCTTCAGCTCT
1 CTTCTTCTTCTTCTCCTTCAGCTCT
* *
7605012 CTTCTTCTTTTTCTCTTTCAGCT
1 CTTCTTCTTCTTCTCCTTCAGCT
7605035 GGGCTGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.04, C:0.35, G:0.04, T:0.56
Consensus pattern (25 bp):
CTTCTTCTTCTTCTCCTTCAGCTCT
Found at i:7605106 original size:27 final size:27
Alignment explanation
Indices: 7605062--7605126 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
7605052 ATAATTGAAG
* *
7605062 TGGTGCCGCCTTTGCCACAGGCACCAT
1 TGGTGCCGCCTCTACCACAGGCACCAT
7605089 TGGTGCCGCCTCTACCACAGGCACCAT
1 TGGTGCCGCCTCTACCACAGGCACCAT
7605116 TGGTGCCGCCT
1 TGGTGCCGCCT
7605127 GTGGCAGGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.14, C:0.38, G:0.26, T:0.22
Consensus pattern (27 bp):
TGGTGCCGCCTCTACCACAGGCACCAT
Found at i:7605528 original size:14 final size:15
Alignment explanation
Indices: 7605509--7605545 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
7605499 ATAAGCAAAC
7605509 AAATAAAT-AATTTT
1 AAATAAATGAATTTT
7605523 AAATAAATGAATTTT
1 AAATAAATGAATTTT
7605538 AATATAAA
1 AA-ATAAA
7605546 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 8 0.38
16 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATAAATGAATTTT
Found at i:7616707 original size:18 final size:18
Alignment explanation
Indices: 7616684--7616719 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7616674 GTAACTCTCA
7616684 GCAAAGCCTCCCATTGGT
1 GCAAAGCCTCCCATTGGT
7616702 GCAAAGCCTCCCATTGGT
1 GCAAAGCCTCCCATTGGT
7616720 TAGAGGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (18 bp):
GCAAAGCCTCCCATTGGT
Found at i:7618062 original size:49 final size:49
Alignment explanation
Indices: 7617990--7618094 Score: 203
Period size: 49 Copynumber: 2.2 Consensus size: 49
7617980 GCAAGATGAA
7617990 GGAACCAAAGAGCTTGGGAACTCTTCGTTTGGCCTATAACCATCTATCT
1 GGAACCAAAGAGCTTGGGAACTCTTCGTTTGGCCTATAACCATCTATCT
7618039 GGAACCAAAGAGCTTGGGAACTCTTCGTTTGGCCTATAACCATCTATCT
1 GGAACCAAAGAGCTTGGGAACTCTTCGTTTGGCCTATAACCATCTATCT
7618088 GG-ACCAA
1 GGAACCAA
7618095 TTCCTGACTG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 5 0.09
49 51 0.91
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (49 bp):
GGAACCAAAGAGCTTGGGAACTCTTCGTTTGGCCTATAACCATCTATCT
Found at i:7624003 original size:16 final size:16
Alignment explanation
Indices: 7623982--7624015 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
7623972 AACTGATTGA
7623982 TTTATACTCAGTTTCT
1 TTTATACTCAGTTTCT
7623998 TTTATACTCAGTTTCT
1 TTTATACTCAGTTTCT
7624014 TT
1 TT
7624016 CTTTGCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTATACTCAGTTTCT
Found at i:7629078 original size:20 final size:20
Alignment explanation
Indices: 7629055--7629094 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7629045 AATTTTTTAA
7629055 TTATAATTATAAT-TATATTT
1 TTATAATT-TAATATATATTT
*
7629075 TTATTATTTAATATATATTT
1 TTATAATTTAATATATATTT
7629095 ATTAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATAATTTAATATATATTT
Found at i:7633298 original size:17 final size:17
Alignment explanation
Indices: 7633276--7633308 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
7633266 TAAATTTTAA
7633276 AAATTAAAAATAAAAAT
1 AAATTAAAAATAAAAAT
7633293 AAATTAAAAATAAAAA
1 AAATTAAAAATAAAAA
7633309 AAAGAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATTAAAAATAAAAAT
Found at i:7636860 original size:30 final size:30
Alignment explanation
Indices: 7636784--7636869 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
7636774 CGGATGGTTT
*
7636784 CCCATTTGGCCCATGTTATAACCCATCTGACCA
1 CCCATTTGGCCCATG---TGACCCATCTGACCA
*
7636817 CCCA-TTGAACCCATGTGACCCATCTGACCA
1 CCCATTTG-GCCCATGTGACCCATCTGACCA
* *
7636847 CCCATTTGGCCCATCTGCCCCAT
1 CCCATTTGGCCCATGTGACCCAT
7636870 ATTCTTACCG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 30 0.65
31 3 0.07
32 3 0.07
33 10 0.22
ACGTcount: A:0.22, C:0.41, G:0.13, T:0.24
Consensus pattern (30 bp):
CCCATTTGGCCCATGTGACCCATCTGACCA
Found at i:7637506 original size:12 final size:12
Alignment explanation
Indices: 7637488--7637569 Score: 119
Period size: 12 Copynumber: 6.8 Consensus size: 12
7637478 GACCAAATTC
7637488 CTCATCATCAAA
1 CTCATCATCAAA
*
7637500 ATCATCATCAAA
1 CTCATCATCAAA
*
7637512 CTCATCATCGAA
1 CTCATCATCAAA
7637524 CTCATCATCAAA
1 CTCATCATCAAA
* *
7637536 TTCATCATCGAA
1 CTCATCATCAAA
7637548 CTCATCATCAAA
1 CTCATCATCAAA
*
7637560 ATCATCATCA
1 CTCATCATCA
7637570 CTTCCATCTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.40, C:0.30, G:0.02, T:0.27
Consensus pattern (12 bp):
CTCATCATCAAA
Found at i:7637710 original size:3 final size:3
Alignment explanation
Indices: 7637702--7637736 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
7637692 CTGGTTATTC
*
7637702 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCC CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
7637737 CTTTTGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.71, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:7644947 original size:18 final size:17
Alignment explanation
Indices: 7644924--7645099 Score: 78
Period size: 18 Copynumber: 10.0 Consensus size: 17
7644914 GAAGGAGAGG
7644924 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
7644942 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
7644959 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
7644975 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
7644993 GGAAAGAAAAGGAAAGGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
7645013 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
7645031 GGAAAGAAAAGGAAAGGAGAA
1 GG-AAG-AAA-GAAA-AAGAA
*
7645052 -G-AGAAAAAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* **
7645067 AGAAG-AAGAAGAGGGAA
1 GGAAGAAAGAA-AAAGAA
*
7645084 GGAAGGAA-AAAAAGAA
1 GGAAGAAAGAAAAAGAA
7645100 AATAAGGTAA
Statistics
Matches: 123, Mismatches: 21, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
15 13 0.11
16 16 0.13
17 19 0.15
18 32 0.26
19 23 0.19
20 17 0.14
21 3 0.02
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:7644957 original size:22 final size:23
Alignment explanation
Indices: 7644926--7645027 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
7644916 AGGAGAGGGG
*
7644926 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
7644948 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
7644970 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
7644996 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
7645020 AAGAAAAA
1 AAGAAAAA
7645028 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 10 0.17
24 32 0.53
25 5 0.08
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:7644984 original size:28 final size:28
Alignment explanation
Indices: 7644929--7645008 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
7644919 AGAGGGGAAG
7644929 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
7644954 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
7644988 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
7645009 GGGAGGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 8 0.17
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 6 0.13
34 17 0.37
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:7645002 original size:38 final size:36
Alignment explanation
Indices: 7644944--7645101 Score: 171
Period size: 38 Copynumber: 4.3 Consensus size: 36
7644934 GAAAGAAAGG
7644944 AAGAAAGAAAAAGAAG--GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
*
7644978 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAGAGGA
*
7645016 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAAGAGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAG-AG-GA
* * *
7645056 AA-AAAAAAGAAAGAAGAAGAAGAGGGAAGGA-AGGA
1 AAGAAAGAA-AAAGAAGAAGAAAAGGAAAGGAGAGGA
*
7645091 AAAAAAGAAAA
1 AAGAAAGAAAA
7645102 TAAGGTAATT
Statistics
Matches: 108, Mismatches: 8, Indels: 15
0.82 0.06 0.11
Matches are distributed among these distances:
34 15 0.14
35 7 0.06
36 7 0.06
38 62 0.57
39 8 0.07
40 9 0.08
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (36 bp):
AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
Found at i:7645004 original size:10 final size:10
Alignment explanation
Indices: 7644946--7645070 Score: 82
Period size: 10 Copynumber: 12.7 Consensus size: 10
7644936 AAGAAAGGAA
*
7644946 GAAAGAAAAA
1 GAAAGAAAAG
*
7644956 GAAGGAAAAG
1 GAAAGAAAAG
* *
7644966 GAAAGGAGAG
1 GAAAGAAAAG
7644976 GAAAG-AAA-
1 GAAAGAAAAG
7644984 GAAA-AAGAAG
1 GAAAGAA-AAG
7644994 GAAAGAAAAG
1 GAAAGAAAAG
***
7645004 GAAAGGGGAG
1 GAAAGAAAAG
7645014 GAAAG-AAA-
1 GAAAGAAAAG
7645022 GAAA-AATAAG
1 GAAAGAA-AAG
7645032 GAAAGAAAAG
1 GAAAGAAAAG
*
7645042 GAAAGGAGAAG
1 GAAA-GAAAAG
* *
7645053 AGAAAAAAAAA
1 -GAAAGAAAAG
7645064 GAAAGAA
1 GAAAGAA
7645071 GAAGAAGAGG
Statistics
Matches: 89, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
8 10 0.11
9 7 0.08
10 56 0.63
11 12 0.13
12 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:7645068 original size:32 final size:33
Alignment explanation
Indices: 7645017--7645100 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 33
7645007 AGGGGAGGAA
* *
7645017 AGAA-AGAAAAATAAGGAAAGAA-AAGGAA-AGG
1 AGAAGAGAAAAAAAAAGAAAGAAGAA-GAAGAGG
7645048 AGAAGAGAAAAAAAAAGAAAGAAGAAGAAGAGG
1 AGAAGAGAAAAAAAAAGAAAGAAGAAGAAGAGG
7645081 -GAAG-GAAGGAAAAAAAGAAA
1 AGAAGAGAA--AAAAAAAGAAA
7645101 ATAAGGTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
31 7 0.15
32 23 0.50
33 16 0.35
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (33 bp):
AGAAGAGAAAAAAAAAGAAAGAAGAAGAAGAGG
Found at i:7645075 original size:10 final size:10
Alignment explanation
Indices: 7644926--7645076 Score: 59
Period size: 10 Copynumber: 15.1 Consensus size: 10
7644916 AGGAGAGGGG
7644926 AAGAAGAAGA
1 AAGAAGAAGA
7644936 AAGAAAGGAAGA
1 AAG-AA-GAAGA
*
7644948 AAGAAAAAGA
1 AAGAAGAAGA
*
7644958 AGGAA-AAGGA
1 AAGAAGAA-GA
* *
7644968 AAGGAGAGGA
1 AAGAAGAAGA
7644978 AAG-A-AAGA
1 AAGAAGAAGA
7644986 AA-AAGAAGGA
1 AAGAAGAA-GA
7644996 AAGAA-AAGGA
1 AAGAAGAA-GA
** *
7645006 AAGGGGAGGA
1 AAGAAGAAGA
7645016 AAG-A-AAGA
1 AAGAAGAAGA
*
7645024 AA-AATAAGGA
1 AAGAAGAA-GA
7645034 AAGAA-AAGGA
1 AAGAAGAA-GA
*
7645044 AAGGAGAAGAGA
1 AAGAAG-A-AGA
* *
7645056 AAAAAAAAGA
1 AAGAAGAAGA
7645066 AAGAAGAAGA
1 AAGAAGAAGA
7645076 A
1 A
7645077 GAGGGAAGGA
Statistics
Matches: 108, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
8 12 0.11
9 7 0.06
10 63 0.58
11 11 0.10
12 14 0.13
13 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.01
Consensus pattern (10 bp):
AAGAAGAAGA
Found at i:7645699 original size:19 final size:18
Alignment explanation
Indices: 7645671--7645709 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
7645661 ATTGAAAGTA
7645671 ATTTTTTAATATTTTATT
1 ATTTTTTAATATTTTATT
*
7645689 ATTTTTGTAATGTTTTATT
1 ATTTTT-TAATATTTTATT
7645708 AT
1 AT
7645710 GGGTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
ATTTTTTAATATTTTATT
Found at i:7645734 original size:13 final size:13
Alignment explanation
Indices: 7645716--7645741 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7645706 TTATGGGTTT
7645716 TATAAAAAAATAA
1 TATAAAAAAATAA
7645729 TATAAAAAAATAA
1 TATAAAAAAATAA
7645742 AAAATTATCA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAAAAAAATAA
Found at i:7645795 original size:27 final size:28
Alignment explanation
Indices: 7645750--7645814 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 28
7645740 AAAAAATTAT
7645750 CAAAATAT-TATAACTTTTTTTTATTTAC
1 CAAAATATATATAAC-TTTTTTTATTTAC
7645778 CAAAATATATATAA-TTTTTTTATTTAC
1 CAAAATATATATAACTTTTTTTATTTAC
7645805 CAAAATATAT
1 CAAAATATAT
7645815 CAAAAAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 23 0.64
28 8 0.22
29 5 0.14
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (28 bp):
CAAAATATATATAACTTTTTTTATTTAC
Found at i:7649071 original size:61 final size:62
Alignment explanation
Indices: 7648960--7649077 Score: 161
Period size: 61 Copynumber: 1.9 Consensus size: 62
7648950 CCACTAATCC
* *
7648960 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
1 TAATAACTAACACAAAAATAATACTAAT-ATTTTATATACAAAATAATACTAACTAAAATTAT
*
7649023 TAATAACTAACTACAAAAATAATACTAAT-TTTT-TACTA-ACAATAATACTAACTAA
1 TAATAACTAAC-ACAAAAATAATACTAATATTTTATA-TACAAAATAATACTAACTAA
7649078 CATCTTAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 18 0.36
62 6 0.12
63 11 0.22
64 15 0.30
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (62 bp):
TAATAACTAACACAAAAATAATACTAATATTTTATATACAAAATAATACTAACTAAAATTAT
Found at i:7649091 original size:3 final size:3
Alignment explanation
Indices: 7649083--7649108 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7649073 ACTAACATCT
7649083 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
7649109 CTATAAAATT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:7649293 original size:11 final size:10
Alignment explanation
Indices: 7649275--7649310 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
7649265 AAATACCTTA
7649275 TTTTTCTCTT
1 TTTTTCTCTT
*
7649285 TTCTTTCTCTC
1 TT-TTTCTCTT
7649296 TTTTTCTCTT
1 TTTTTCTCTT
7649306 TTTTT
1 TTTTT
7649311 TCGCAGCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:7649446 original size:27 final size:27
Alignment explanation
Indices: 7649416--7649525 Score: 175
Period size: 27 Copynumber: 4.1 Consensus size: 27
7649406 GATTGGCAGG
*
7649416 ACTGGTGCCGCCAACCTGGTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
7649443 ACTGGTGCCGCCAACCTGCTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
**
7649470 ACTGGTGCCGCCAACCTGCTTCCCTTG
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
**
7649497 TTTGGTGCCGCCAACCTGCTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
7649524 AC
1 AC
7649526 CCAGGGAGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.11, C:0.45, G:0.20, T:0.25
Consensus pattern (27 bp):
ACTGGTGCCGCCAACCTGCTTCCCTCC
Found at i:7649574 original size:8 final size:8
Alignment explanation
Indices: 7649553--7649592 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
7649543 CAGTTCAGGT
*
7649553 TTTTTTTC
1 TTTTTTTA
7649561 TGTTTTTTA
1 T-TTTTTTA
*
7649570 TTTTTTTG
1 TTTTTTTA
7649578 TTTTTTTA
1 TTTTTTTA
7649586 TTTTTTT
1 TTTTTTT
7649593 GATATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.05, C:0.03, G:0.05, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:7649575 original size:16 final size:16
Alignment explanation
Indices: 7649553--7649593 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
7649543 CAGTTCAGGT
*
7649553 TTTTTTTCTGTTTTTTA
1 TTTTTTTGT-TTTTTTA
7649570 TTTTTTTGTTTTTTTA
1 TTTTTTTGTTTTTTTA
7649586 TTTTTTTG
1 TTTTTTTG
7649594 ATATATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.05, C:0.02, G:0.07, T:0.85
Consensus pattern (16 bp):
TTTTTTTGTTTTTTTA
Found at i:7649622 original size:22 final size:22
Alignment explanation
Indices: 7649594--7649636 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
7649584 TATTTTTTTG
7649594 ATATATTTTGATAAATAAAAAT
1 ATATATTTTGATAAATAAAAAT
*
7649616 ATATATTTTGGTAAATAAAAA
1 ATATATTTTGATAAATAAAAA
7649637 AAGTTATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (22 bp):
ATATATTTTGATAAATAAAAAT
Found at i:7650456 original size:75 final size:75
Alignment explanation
Indices: 7650362--7650700 Score: 455
Period size: 75 Copynumber: 4.4 Consensus size: 75
7650352 TTCCAGAAAC
* *
7650362 TTTATTATGTATTAATTTATAATTTCATTATTTCTGAAGGGTTTAAACATAATTTTTTAGGGGCT
1 TTTACTATATATTAATTTATAATTTCATTATTTCTGAAGGGTTTAAACATAATTTTTTAGGGGCT
7650427 AAAGTGTAAT
66 AAAGTGTAAT
7650437 TTTACTATATATTAATTTATAATTTCATTATTTCTGAAGGGTTTAAACATAATTTTTTAGGGGCT
1 TTTACTATATATTAATTTATAATTTCATTATTTCTGAAGGGTTTAAACATAATTTTTTAGGGGCT
7650502 AAAGTGTAAT
66 AAAGTGTAAT
* * * * * * **
7650512 TTTACTATATATTAATTTACAACTTCCTTATTTATAAGAAGATTGAATTGAAA-ATTTTTCATTT
1 TTTACTATATATTAATTTATAATTTCATTATTTCT--GAAG---G-GTTTAAACATAATT--TTT
*** *
7650576 TAAAAGTTAAAGTGTAAT
58 TAGGGGCTAAAGTGTAAT
7650594 TTTACTATATATTAATTTATAATTTCATTATTTCTGAAGGGTTTAAACATAATTTTTTAGGGGCT
1 TTTACTATATATTAATTTATAATTTCATTATTTCTGAAGGGTTTAAACATAATTTTTTAGGGGCT
7650659 AAAGTGTAAT
66 AAAGTGTAAT
* *
7650669 TTTACTATATATTAATTTAAAATTCCATTATT
1 TTTACTATATATTAATTTATAATTTCATTATT
7650701 CAAGAAACGG
Statistics
Matches: 227, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
75 151 0.67
76 5 0.02
77 9 0.04
80 9 0.04
81 5 0.02
82 48 0.21
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (75 bp):
TTTACTATATATTAATTTATAATTTCATTATTTCTGAAGGGTTTAAACATAATTTTTTAGGGGCT
AAAGTGTAAT
Found at i:7654516 original size:18 final size:18
Alignment explanation
Indices: 7654490--7654544 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
7654480 CCTAATTGCT
*
7654490 ACCCTAGCCCAAACAACA
1 ACCCAAGCCCAAACAACA
** *
7654508 ACCCAAGCCCAATTAATA
1 ACCCAAGCCCAAACAACA
*
7654526 ACCCCAGCCCAAACCAACA
1 ACCCAAGCCCAAA-CAACA
7654545 GCAGAGAAGC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
18 25 0.89
19 3 0.11
ACGTcount: A:0.44, C:0.44, G:0.05, T:0.07
Consensus pattern (18 bp):
ACCCAAGCCCAAACAACA
Found at i:7655899 original size:84 final size:85
Alignment explanation
Indices: 7655774--7655952 Score: 342
Period size: 84 Copynumber: 2.1 Consensus size: 85
7655764 TTTATTTTGG
*
7655774 TTTATTTATTCATTATTATTTTTTTAGAATTTGGTTTGTTTATTCTATTTTTGCCATTATCATTG
1 TTTATTTGTTCATTATTATTTTTTTAGAATTTGGTTTGTTTATTCTATTTTTGCCATTATCATTG
7655839 CAATTTTATCCTATCATTTA
66 CAATTTTATCCTATCATTTA
7655859 TTTATTTGTTCATTATTA-TTTTTTAGAATTTGGTTTGTTTATTCTATTTTTGCCATTATCATTG
1 TTTATTTGTTCATTATTATTTTTTTAGAATTTGGTTTGTTTATTCTATTTTTGCCATTATCATTG
7655923 CAATTTTATCCTATCATTTA
66 CAATTTTATCCTATCATTTA
7655943 TTTATTTGTT
1 TTTATTTGTT
7655953 ATTTTCAAAT
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 76 0.82
85 17 0.18
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.61
Consensus pattern (85 bp):
TTTATTTGTTCATTATTATTTTTTTAGAATTTGGTTTGTTTATTCTATTTTTGCCATTATCATTG
CAATTTTATCCTATCATTTA
Found at i:7660497 original size:22 final size:24
Alignment explanation
Indices: 7660471--7660514 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
7660461 GAAAAATATT
7660471 AAATAT-AT-ATTTTTTATTTTTA
1 AAATATAATGATTTTTTATTTTTA
*
7660493 AAATATAATGGTTTTTTATTTT
1 AAATATAATGATTTTTTATTTT
7660515 AAGTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 2 0.11
24 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (24 bp):
AAATATAATGATTTTTTATTTTTA
Found at i:7660656 original size:22 final size:22
Alignment explanation
Indices: 7660628--7660687 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
7660618 ATACAATTAA
* * *
7660628 TAATTTTAATAACAATTAGTTT
1 TAATTTTAATAAAAAATAATTT
*
7660650 TAATTTTATTAAAAAATAATTT
1 TAATTTTAATAAAAAATAATTT
*
7660672 TAATTTTAATTAAAAA
1 TAATTTTAATAAAAAA
7660688 CGGGCCGGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATTTTAATAAAAAATAATTT
Found at i:7664364 original size:44 final size:44
Alignment explanation
Indices: 7664293--7664411 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 44
7664283 CATGGCAAAT
* * ** *
7664293 CTTATCTCCCTGAAATTGCAGTA-GAGCATATTGAAGCCACTAGC
1 CTTATCTCCCTGAAGTTGCAG-AGGAGCAGATTGAAAACACAAGC
* * * *
7664337 CTTATCTCCTTGAAGTTGCAGAGGAGCAGGTTGAAAATACAAGT
1 CTTATCTCCCTGAAGTTGCAGAGGAGCAGATTGAAAACACAAGC
*
7664381 CTTATCTCCCTAAAGTTGCAGAGGAGCAGAT
1 CTTATCTCCCTGAAGTTGCAGAGGAGCAGAT
7664412 CATATTGAAC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
43 1 0.02
44 61 0.98
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGAGGAGCAGATTGAAAACACAAGC
Found at i:7664866 original size:18 final size:18
Alignment explanation
Indices: 7664840--7664889 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
7664830 CCTAATTGTT
*
7664840 ACCCTAGCCCAAACAACA
1 ACCCAAGCCCAAACAACA
** *
7664858 ACCCAAGCCCAATTAATA
1 ACCCAAGCCCAAACAACA
*
7664876 ACCCCAGCCCAAAC
1 ACCCAAGCCCAAAC
7664890 CAATAGCAGC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.44, G:0.06, T:0.08
Consensus pattern (18 bp):
ACCCAAGCCCAAACAACA
Found at i:7666318 original size:27 final size:28
Alignment explanation
Indices: 7666286--7666339 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
7666276 TTAGACCCAT
7666286 TTGTATTACATTTATAATT-TATTATTA
1 TTGTATTACATTTATAATTATATTATTA
** *
7666313 TTGTATTATTTTTATTATTATATTATT
1 TTGTATTACATTTATAATTATATTATT
7666340 GCTTGCATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (28 bp):
TTGTATTACATTTATAATTATATTATTA
Found at i:7666329 original size:17 final size:18
Alignment explanation
Indices: 7666302--7666339 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
7666292 TACATTTATA
*
7666302 ATTTATTATTATTGTATT
1 ATTTATTATTATTATATT
7666320 ATTT-TTATTATTATATT
1 ATTTATTATTATTATATT
7666337 ATT
1 ATT
7666340 GCTTGCATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTATTATTATTATATT
Found at i:7666371 original size:99 final size:100
Alignment explanation
Indices: 7666247--7666447 Score: 395
Period size: 99 Copynumber: 2.0 Consensus size: 100
7666237 ATCATTTATT
7666247 TAGTTGTTATTTTCAAATAGTTTCAAAATTTAGACCCATTTGTATTACATTTATAATTTATTATT
1 TAGTTGTTATTTTCAAATAGTTTCAAAATTTAGACCCATTTGTATTACATTTATAATTTATTATT
7666312 ATTGTATTATTTTTATTATTATATTATTGCTTGCA
66 ATTGTATTATTTTTATTATTATATTATTGCTTGCA
7666347 TAGTTGTTA-TTTCAAATAGTTTCAAAATTTAGACCCATTTGTATTACATTTATAATTTATTATT
1 TAGTTGTTATTTTCAAATAGTTTCAAAATTTAGACCCATTTGTATTACATTTATAATTTATTATT
7666411 ATTGTATTATTTTTATTATTATATTATTGCTTGCA
66 ATTGTATTATTTTTATTATTATATTATTGCTTGCA
7666446 TA
1 TA
7666448 ACTATTATTC
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 92 0.91
100 9 0.09
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (100 bp):
TAGTTGTTATTTTCAAATAGTTTCAAAATTTAGACCCATTTGTATTACATTTATAATTTATTATT
ATTGTATTATTTTTATTATTATATTATTGCTTGCA
Found at i:7666417 original size:27 final size:28
Alignment explanation
Indices: 7666385--7666438 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
7666375 TTAGACCCAT
7666385 TTGTATTACATTTATAATT-TATTATTA
1 TTGTATTACATTTATAATTATATTATTA
** *
7666412 TTGTATTATTTTTATTATTATATTATT
1 TTGTATTACATTTATAATTATATTATT
7666439 GCTTGCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (28 bp):
TTGTATTACATTTATAATTATATTATTA
Found at i:7666428 original size:17 final size:18
Alignment explanation
Indices: 7666401--7666438 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
7666391 TACATTTATA
*
7666401 ATTTATTATTATTGTATT
1 ATTTATTATTATTATATT
7666419 ATTT-TTATTATTATATT
1 ATTTATTATTATTATATT
7666436 ATT
1 ATT
7666439 GCTTGCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTATTATTATTATATT
Found at i:7668550 original size:11 final size:11
Alignment explanation
Indices: 7668534--7668560 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
7668524 GACATAAAAA
7668534 AATTATTAAAT
1 AATTATTAAAT
7668545 AATTATTAAAT
1 AATTATTAAAT
7668556 AATTA
1 AATTA
7668561 AAAAAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTATTAAAT
Found at i:7668737 original size:16 final size:16
Alignment explanation
Indices: 7668716--7668763 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
7668706 TATTTGAATT
*
7668716 TTTTAATGTAAACTA-A
1 TTTTAATATAAA-TATA
7668732 TTTTAATATAAATATA
1 TTTTAATATAAATATA
*
7668748 TTTTAAAATAAATATA
1 TTTTAATATAAATATA
7668764 ATCAAAGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 2 0.07
16 27 0.93
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTTAATATAAATATA
Found at i:7673324 original size:3 final size:3
Alignment explanation
Indices: 7673316--7673341 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7673306 CCCAAGCATA
7673316 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
7673342 TTAAATTTTT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:7674096 original size:17 final size:18
Alignment explanation
Indices: 7674076--7674113 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7674066 CAAATAATTC
*
7674076 AAAAAATA-AAATTTGAA
1 AAAAAATATAAAGTTGAA
*
7674093 AAAATATATAAAGTTGAA
1 AAAAAATATAAAGTTGAA
7674111 AAA
1 AAA
7674114 TAATTTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AAAAAATATAAAGTTGAA
Found at i:7679345 original size:20 final size:19
Alignment explanation
Indices: 7679288--7679347 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
7679278 AAAACCATGA
*
7679288 AATATAAAAATAT-AGAAT
1 AATATAAAAATATAATAAT
* *
7679306 ATTATAAAAAAATAATTAAT
1 AATATAAAAATATAA-TAAT
7679326 AATATAAAAATATTAATAAT
1 AATATAAAAATA-TAATAAT
7679346 AA
1 AA
7679348 AAATGATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 11 0.32
19 1 0.03
20 19 0.56
21 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AATATAAAAATATAATAAT
Found at i:7682767 original size:103 final size:103
Alignment explanation
Indices: 7682639--7683060 Score: 844
Period size: 103 Copynumber: 4.1 Consensus size: 103
7682629 GAAATTACTA
7682639 TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
1 TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
7682704 TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
66 TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
7682742 TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
1 TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
7682807 TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
66 TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
7682845 TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
1 TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
7682910 TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
66 TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
7682948 TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
1 TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
7683013 TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
66 TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
7683051 TAACCGAATT
1 TAACCGAATT
7683061 TTTTCGGTTT
Statistics
Matches: 319, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 319 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (103 bp):
TAACCGAATTAACCGACCTTCCAAAAATTTTAACCGTTAATCGAACCGAATTTTTTAAAAAAAAA
TTACCCGAACCGAAATTTTTTCGGTTAATAAGGTCGGT
Found at i:7684404 original size:8 final size:8
Alignment explanation
Indices: 7684391--7684421 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
7684381 TTATAAGCTT
7684391 TTATTATG
1 TTATTATG
7684399 TTATTATG
1 TTATTATG
*
7684407 TTATTATT
1 TTATTATG
7684415 TTATTAT
1 TTATTAT
7684422 TCCTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (8 bp):
TTATTATG
Found at i:7689557 original size:19 final size:19
Alignment explanation
Indices: 7689533--7689569 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
7689523 TATTTTTTTC
7689533 TTTTTTTAT-CCAATAACAT
1 TTTTTTTATACC-ATAACAT
7689552 TTTTTTTATACCATAACA
1 TTTTTTTATACCATAACA
7689570 AATATTCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTTTATACCATAACAT
Found at i:7692679 original size:94 final size:95
Alignment explanation
Indices: 7692542--7692731 Score: 364
Period size: 94 Copynumber: 2.0 Consensus size: 95
7692532 GAAAGAAGAG
*
7692542 AAAGAATACGGTAAAAAAGAGAAGAAAGTAATAACAACTTAGGGAGAGAAGAGAGAAGAGAAAGA
1 AAAGAATACGGTAAAAAAGAGAAAAAAGTAATAACAACTTAGGGAGAGAAGAGAGAAGAGAAAGA
7692607 AGACGGT-AAAAAAAAGATATCAACAGTTT
66 AGACGGTAAAAAAAAAGATATCAACAGTTT
7692636 AAAGAATACGGTAAAAAAGAGAAAAAAGTAATAACAACTTAGGGAGAGAAGAGAGAAGAGAAAGA
1 AAAGAATACGGTAAAAAAGAGAAAAAAGTAATAACAACTTAGGGAGAGAAGAGAGAAGAGAAAGA
7692701 AGACGGTAAAAAAAAAGATATCAACAGTTT
66 AGACGGTAAAAAAAAAGATATCAACAGTTT
7692731 A
1 A
7692732 GGGAGAGAAA
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 71 0.76
95 23 0.24
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.13
Consensus pattern (95 bp):
AAAGAATACGGTAAAAAAGAGAAAAAAGTAATAACAACTTAGGGAGAGAAGAGAGAAGAGAAAGA
AGACGGTAAAAAAAAAGATATCAACAGTTT
Found at i:7693019 original size:16 final size:15
Alignment explanation
Indices: 7693000--7693038 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
7692990 TTGTTATTTA
*
7693000 TTAAGTATTTTTGTAC
1 TTAA-TATTTTAGTAC
7693016 TTAAT-TTTTAGTAC
1 TTAATATTTTAGTAC
7693030 TTAATATTT
1 TTAATATTT
7693039 GTTTGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.62
15 4 0.19
16 4 0.19
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (15 bp):
TTAATATTTTAGTAC
Found at i:7706497 original size:37 final size:37
Alignment explanation
Indices: 7706425--7706497 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
7706415 CAAAAACCAA
** *
7706425 AAACCAAAAACAAAATTCCTATTTGAAAAATGTAGAG
1 AAACCAAAAACAAAATTCCTAGATGAAAAACGTAGAG
* *
7706462 AAACCAAAAACAAAATTGCTAGATGAAATACGTAGA
1 AAACCAAAAACAAAATTCCTAGATGAAAAACGTAGA
7706498 ACTTACTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (37 bp):
AAACCAAAAACAAAATTCCTAGATGAAAAACGTAGAG
Found at i:7714589 original size:29 final size:29
Alignment explanation
Indices: 7714556--7714619 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
7714546 GGGTAGATTG
* * *
7714556 AAAGATTGAAGATTTGAAGTTGGGTGGAT
1 AAAGATTGAAGATTTGAAATTGGCTGAAT
7714585 AAAGATTGAAGATTTGAAATTGGCTGAAT
1 AAAGATTGAAGATTTGAAATTGGCTGAAT
7714614 AAAGAT
1 AAAGAT
7714620 CAAATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.02, G:0.28, T:0.30
Consensus pattern (29 bp):
AAAGATTGAAGATTTGAAATTGGCTGAAT
Found at i:7714678 original size:18 final size:18
Alignment explanation
Indices: 7714657--7714691 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7714647 CTGTAATTAA
7714657 TTTAAATTTGATCTTTAG
1 TTTAAATTTGATCTTTAG
*
7714675 TTTAAATTTGATTTTTA
1 TTTAAATTTGATCTTTA
7714692 AAATTTTGAT
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:0.03, G:0.09, T:0.60
Consensus pattern (18 bp):
TTTAAATTTGATCTTTAG
Found at i:7718811 original size:3 final size:3
Alignment explanation
Indices: 7718803--7718828 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7718793 TTTTACAAAT
7718803 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
7718829 TTTACGTTAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:7725750 original size:457 final size:456
Alignment explanation
Indices: 7724896--7725801 Score: 1447
Period size: 457 Copynumber: 2.0 Consensus size: 456
7724886 ATTCCAATCA
* * *
7724896 ATGATATGACTAGTCTTGGCTATCGGAGCAGTTGAATCCACGAGTAGAGACATAGATGTATTCAT
1 ATGATATGAATAGTCTTGGCTATCAGAGCAGTTGAATCCACGAATAGAGACATAGATGTATTCAT
*
7724961 TGACAAAAGGATACATTGGACTGGACCCAAGATGAATTAATTATGAATCCATTTGTGAATTAATT
66 TGACAAAAGGATACATTGGACTGGACCCAAGATAAATTAATTATGAATCCATTTGTGAATTAATT
* *
7725026 CACTTGTGACATTCATGGTGTGATTTACCTAAATCCTAAATTAGTCACTGATCATGCATATGTAA
131 CACTTGTGACATTCATGGTGTGATTTACCTAAATCCTAAATTAGTCACTGACCACGCATATGTAA
* ** * * * * *
7725091 CTCATGTGCTTTGATATAAGTGGGGGTTTATGCTCTAAAGATGATCGAGTAGGATCATCCGTATG
196 CTCATGTGCTTTGATATAAATGAAGGCTTACGCTCTAAAAATGATCGAGCAGGATCAGCCGTATG
* *
7725156 TTGGTTACATGACTTGTGTATGGCATGGCTTTACTAGCAACAGTGGAATTCATAACTCAATTAAA
261 TTGGGTACATGACTTGTGTATGGCATGACTTTACTAGCAACAGTGGAATTCATAACTCAATTAAA
* *
7725221 GAGTTAACAATATCCTCTTATTGGCATTGTGTGGATTGATAAATATGGAATATGGCCACAGGTGT
326 GAGTTAACAATATCCTCTCATTGGCATTGTGTGGATTGATAAATATAGAATATGGCCACAGGTGT
* * *
7725286 CTTGTTCTCGAACGAGCAATTTAATCACAGTCATTTGTTGATAGTGATCATATTTAATCACAGTC
391 CTTGTTCTCAAACGAGCAATTTAATCACAGTCATTTGTTGACAATGATCATA-TTAATCACAGTC
7725351 AC
455 AC
*
7725353 ATGATATGAATAGTCTTGGCTATCAGAGCAGTTGACTCCACGAATAGAGACATAGATGTATTCAT
1 ATGATATGAATAGTCTTGGCTATCAGAGCAGTTGAATCCACGAATAGAGACATAGATGTATTCAT
** * * * * *
7725418 TGGTAGAATGATACATTGGACTGGATCCAAGATAAATTAATTCTGAATCCGTTTGTGAATTAATT
66 TGACAAAAGGATACATTGGACTGGACCCAAGATAAATTAATTATGAATCCATTTGTGAATTAATT
* *
7725483 CACTTGTGACATTCATGGTGTGATTTACCTAAATTCTGAATTAGTCACTGACCACGCATATGTAA
131 CACTTGTGACATTCATGGTGTGATTTACCTAAATCCTAAATTAGTCACTGACCACGCATATGTAA
7725548 CTCATGTGCTTTGATATAAATGAAGGCTTACGCTCTAAAAATGATCGAGCAGGAT-AGCCGGTAT
196 CTCATGTGCTTTGATATAAATGAAGGCTTACGCTCTAAAAATGATCGAGCAGGATCAGCC-GTAT
* *
7725612 GTTGGGTACATGACTTGTGTATGGCATGACTTTACTAGCAATAGTGGAATTCATAGCTCAATTAA
260 GTTGGGTACATGACTTGTGTATGGCATGACTTTACTAGCAACAGTGGAATTCATAACTCAATTAA
*
7725677 AGAGTTAACAATATCCTCTCATTGGCATTGTGTGGATTGATAAATATAGAATGTGGCCACAGGT-
325 AGAGTTAACAATATCCTCTCATTGGCATTGTGTGGATTGATAAATATAGAATATGGCCACAGGTG
* *
7725741 TGCTTGTTCTCAAATGAGCAATTTAATCACGGTCATTTGTTGACAATGATCATATTAATCA
390 T-CTTGTTCTCAAACGAGCAATTTAATCACAGTCATTTGTTGACAATGATCATATTAATCA
7725802 TTAAGAAGAC
Statistics
Matches: 411, Mismatches: 36, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
456 11 0.03
457 400 0.97
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (456 bp):
ATGATATGAATAGTCTTGGCTATCAGAGCAGTTGAATCCACGAATAGAGACATAGATGTATTCAT
TGACAAAAGGATACATTGGACTGGACCCAAGATAAATTAATTATGAATCCATTTGTGAATTAATT
CACTTGTGACATTCATGGTGTGATTTACCTAAATCCTAAATTAGTCACTGACCACGCATATGTAA
CTCATGTGCTTTGATATAAATGAAGGCTTACGCTCTAAAAATGATCGAGCAGGATCAGCCGTATG
TTGGGTACATGACTTGTGTATGGCATGACTTTACTAGCAACAGTGGAATTCATAACTCAATTAAA
GAGTTAACAATATCCTCTCATTGGCATTGTGTGGATTGATAAATATAGAATATGGCCACAGGTGT
CTTGTTCTCAAACGAGCAATTTAATCACAGTCATTTGTTGACAATGATCATATTAATCACAGTCA
C
Found at i:7726706 original size:11 final size:11
Alignment explanation
Indices: 7726690--7726737 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
7726680 ATTCCAAAAA
7726690 TAATATTATTT
1 TAATATTATTT
*
7726701 TAATATTAAATT
1 TAATATT-ATTT
*
7726713 TAATACTTATCT
1 TAATA-TTATTT
*
7726725 TAATAGTATTT
1 TAATATTATTT
7726736 TA
1 TA
7726738 TTAATTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 13 0.43
12 15 0.50
13 2 0.07
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (11 bp):
TAATATTATTT
Found at i:7729691 original size:44 final size:44
Alignment explanation
Indices: 7729643--7729738 Score: 156
Period size: 44 Copynumber: 2.2 Consensus size: 44
7729633 TTTATAAATA
*
7729643 TATATATACACATACTTTTATACATCTTCTATGCTTCATGATTT
1 TATATACACACATACTTTTATACATCTTCTATGCTTCATGATTT
* * *
7729687 TATATACATATATACTTTTATACATCTTCTATGCTTTATGATTT
1 TATATACACACATACTTTTATACATCTTCTATGCTTCATGATTT
7729731 TATATACA
1 TATATACA
7729739 TACTTATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (44 bp):
TATATACACACATACTTTTATACATCTTCTATGCTTCATGATTT
Found at i:7729739 original size:44 final size:44
Alignment explanation
Indices: 7729654--7729740 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
7729644 ATATATACAC
7729654 ATACTTTTATACATCTTCTATGCTTCATGATTTTATATACATAT
1 ATACTTTTATACATCTTCTATGCTTCATGATTTTATATACATAT
*
7729698 ATACTTTTATACATCTTCTATGCTTTATGATTTTATATACATA
1 ATACTTTTATACATCTTCTATGCTTCATGATTTTATATACATA
7729741 CTTATATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.51
Consensus pattern (44 bp):
ATACTTTTATACATCTTCTATGCTTCATGATTTTATATACATAT
Found at i:7732578 original size:20 final size:21
Alignment explanation
Indices: 7732553--7732598 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
7732543 CTAAATGTGC
7732553 ATATTTACATTTT-ATTCTTT
1 ATATTTACATTTTCATTCTTT
*
7732573 ATATTT-CGTTTTCATTCTTT
1 ATATTTACATTTTCATTCTTT
7732593 AT-TTTA
1 ATATTTA
7732599 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (21 bp):
ATATTTACATTTTCATTCTTT
Found at i:7736721 original size:77 final size:78
Alignment explanation
Indices: 7736623--7736777 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
7736613 TTTTAGGGAC
7736623 CTGAATTAAATTATATATTTTTATGATAGTAAAAATATAATTTCACCATTTTAATAGTATATATA
1 CTGAATTAAATTATATATTTTTATGATAGTAAAAATATAATTTCACCATTTTAATAGTATATATA
7736688 TTTATAATTTTTA
66 TTTATAATTTTTA
7736701 CTGAATTAAA-TATATATTTTTATGATAGTAAAAATATAATTTCACCATTTTAATAGTATATATA
1 CTGAATTAAATTATATATTTTTATGATAGTAAAAATATAATTTCACCATTTTAATAGTATATATA
7736765 TTTATAATTTTTA
66 TTTATAATTTTTA
7736778 AATGGTTAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 67 0.87
78 10 0.13
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (78 bp):
CTGAATTAAATTATATATTTTTATGATAGTAAAAATATAATTTCACCATTTTAATAGTATATATA
TTTATAATTTTTA
Found at i:7736742 original size:23 final size:23
Alignment explanation
Indices: 7736690--7736742 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
7736680 TATATATATT
* *
7736690 TATAATTTTTACTGAATTAAATA
1 TATAATTTTTACTGAAGTAAAAA
7736713 TAT-ATTTTTA-TGATAGTAAAAA
1 TATAATTTTTACTGA-AGTAAAAA
7736735 TATAATTT
1 TATAATTT
7736743 CACCATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (23 bp):
TATAATTTTTACTGAAGTAAAAA
Found at i:7746037 original size:1 final size:1
Alignment explanation
Indices: 7746033--7746063 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
7746023 AAAACACCTA
7746033 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7746064 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:7747535 original size:18 final size:18
Alignment explanation
Indices: 7747503--7747541 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
7747493 ATTAAAGTAC
7747503 TTTTATATCATTTAATAAT
1 TTTTATATCATTTAAT-AT
*
7747522 TTTTATATTA-TTAATAT
1 TTTTATATCATTTAATAT
7747539 TTT
1 TTT
7747542 AACAATCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATATCATTTAATAT
Found at i:7748382 original size:16 final size:15
Alignment explanation
Indices: 7748352--7748380 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7748342 ATATCTCTTT
7748352 TTTTTTAAATATTTA
1 TTTTTTAAATATTTA
7748367 TTTTTTAAATATTT
1 TTTTTTAAATATTT
7748381 TACTATATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTAAATATTTA
Found at i:7748630 original size:18 final size:18
Alignment explanation
Indices: 7748589--7748635 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
7748579 TTACAAGAGT
*
7748589 ATATACTTAATT-TTTAA
1 ATATATTTAATTATTTAA
7748606 A-AT-TTTAATTATTTAA
1 ATATATTTAATTATTTAA
7748622 ATATATTTAATTAT
1 ATATATTTAATTAT
7748636 AAAAGTAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 6 0.23
16 8 0.31
17 3 0.12
18 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTTAATTATTTAA
Found at i:7755319 original size:1 final size:1
Alignment explanation
Indices: 7755243--7755299 Score: 114
Period size: 1 Copynumber: 57.0 Consensus size: 1
7755233 ATCCAATCCT
7755243 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7755300 CCATTTTCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7756141 original size:22 final size:23
Alignment explanation
Indices: 7756104--7756146 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
7756094 TAAAAATGTT
*
7756104 AATAATTTGAAGTTGA-ATAAGA
1 AATAATTTAAAGTTGATATAAGA
*
7756126 AATAATTTAAATTTGATATAA
1 AATAATTTAAAGTTGATATAA
7756147 TCTAAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (23 bp):
AATAATTTAAAGTTGATATAAGA
Found at i:7760441 original size:12 final size:12
Alignment explanation
Indices: 7760424--7760450 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7760414 AGATTCAAAA
7760424 TGCTAGCAACTT
1 TGCTAGCAACTT
7760436 TGCTAGCAACTT
1 TGCTAGCAACTT
7760448 TGC
1 TGC
7760451 CACAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (12 bp):
TGCTAGCAACTT
Found at i:7761765 original size:78 final size:79
Alignment explanation
Indices: 7761659--7761818 Score: 313
Period size: 78 Copynumber: 2.0 Consensus size: 79
7761649 TAAAAATAAA
7761659 GAACACACAGATTTTACTTGAAAACCCTTTCGGGAAAAAACCACGGCCAGAGGAGAAGAAAATTC
1 GAACACACAGATTTTACTTGAAAACCCTTTCGGGAAAAAACCACGGCCAGAGGAGAAGAAAATTC
7761724 ACTATGTCGAATTT
66 ACTATGTCGAATTT
7761738 GAACAC-CAGATTTTACTTGAAAACCCTTTCGGGAAAAAACCACGGCCAGAGGAGAAGAAAATTC
1 GAACACACAGATTTTACTTGAAAACCCTTTCGGGAAAAAACCACGGCCAGAGGAGAAGAAAATTC
7761802 ACTATGTCGAATTT
66 ACTATGTCGAATTT
7761816 GAA
1 GAA
7761819 TTAATTACAA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 75 0.93
79 6 0.07
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (79 bp):
GAACACACAGATTTTACTTGAAAACCCTTTCGGGAAAAAACCACGGCCAGAGGAGAAGAAAATTC
ACTATGTCGAATTT
Found at i:7762089 original size:29 final size:29
Alignment explanation
Indices: 7762047--7762112 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
7762037 ACTTAATTCT
*
7762047 AACAAGTTCTTCATCGCGAACCCTCAATG
1 AACAAGTTCTTCATCGCGAACCCTCAACG
*
7762076 AACAAGTTCTTCATCGCGAACTCTCAACG
1 AACAAGTTCTTCATCGCGAACCCTCAACG
7762105 AACAAGTT
1 AACAAGTT
7762113 TTCCACCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (29 bp):
AACAAGTTCTTCATCGCGAACCCTCAACG
Found at i:7765076 original size:3 final size:3
Alignment explanation
Indices: 7765063--7765101 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
7765053 CATTAACCAA
7765063 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
7765102 ATGCTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:7779515 original size:42 final size:42
Alignment explanation
Indices: 7779373--7779502 Score: 197
Period size: 42 Copynumber: 3.1 Consensus size: 42
7779363 ATGGGTAGAG
* *
7779373 ACACGGACTGGGACATGACCGTGTGTCTCAAGTCAGTGAGTT
1 ACACGGGCTGGGACACGACCGTGTGTCTCAAGTCAGTGAGTT
*
7779415 ACACGGGCTGGGACACGACCGTGTGTCTCAAGTCAGGGAGTT
1 ACACGGGCTGGGACACGACCGTGTGTCTCAAGTCAGTGAGTT
* * * *
7779457 ACATGGGCTGGGACACGGCCGTATGTCTCAAATCAGTGAGTT
1 ACACGGGCTGGGACACGACCGTGTGTCTCAAGTCAGTGAGTT
7779499 ACAC
1 ACAC
7779503 AGGCGAAGAC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.22
Consensus pattern (42 bp):
ACACGGGCTGGGACACGACCGTGTGTCTCAAGTCAGTGAGTT
Found at i:7783906 original size:42 final size:42
Alignment explanation
Indices: 7783839--7783937 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
7783829 GCTATCTGGA
* *
7783839 CACACACTCATGTCCTTGCTTGTGTGGCTCACACAGACTGGG
1 CACACACCCATGTCCTTGCTTGTGTGGCTCACACAGACTAGG
** *
7783881 CACATGCCCATGTCCTTG-TTCGTGTGGCTCACACAGCCTAGG
1 CACACACCCATGTCCTTGCTT-GTGTGGCTCACACAGACTAGG
7783923 CACACACCCATGTCC
1 CACACACCCATGTCC
7783938 CTGACCCTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 2 0.04
42 47 0.96
ACGTcount: A:0.19, C:0.35, G:0.21, T:0.24
Consensus pattern (42 bp):
CACACACCCATGTCCTTGCTTGTGTGGCTCACACAGACTAGG
Found at i:7783949 original size:42 final size:42
Alignment explanation
Indices: 7783861--7783949 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
7783851 TCCTTGCTTG
* ** * ** *
7783861 TGTGGCTCACACAGACTGGGCACATGCCCATGTCCTTGTTCG
1 TGTGGCTCACACAGACTAGGCACACACCCATGTCCCTGACCC
*
7783903 TGTGGCTCACACAGCCTAGGCACACACCCATGTCCCTGACCC
1 TGTGGCTCACACAGACTAGGCACACACCCATGTCCCTGACCC
7783945 TGTGG
1 TGTGG
7783950 TTCTAAAGCG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.18, C:0.35, G:0.25, T:0.22
Consensus pattern (42 bp):
TGTGGCTCACACAGACTAGGCACACACCCATGTCCCTGACCC
Found at i:7786215 original size:20 final size:20
Alignment explanation
Indices: 7786190--7786229 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7786180 CTAGAGCAGG
*
7786190 ACAAAATAGAGCAGAACAGA
1 ACAAAACAGAGCAGAACAGA
* *
7786210 ACAAAACAGGGTAGAACAGA
1 ACAAAACAGAGCAGAACAGA
7786230 GTATGTATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.15, G:0.23, T:0.05
Consensus pattern (20 bp):
ACAAAACAGAGCAGAACAGA
Found at i:7792955 original size:21 final size:21
Alignment explanation
Indices: 7792916--7792955 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
7792906 TTTTTTCGAA
* *
7792916 TCGAGTCGAGTGAAATGAAAT
1 TCGAGTCGAATCAAATGAAAT
*
7792937 TCGAGTCGAATCAAGTGAA
1 TCGAGTCGAATCAAATGAA
7792956 TTTGTTAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (21 bp):
TCGAGTCGAATCAAATGAAAT
Found at i:7793270 original size:9 final size:9
Alignment explanation
Indices: 7793256--7793286 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
7793246 GTTAAACGAA
7793256 TCGAGTTAT
1 TCGAGTTAT
*
7793265 TCGAGTTAA
1 TCGAGTTAT
7793274 TCGAGTTAT
1 TCGAGTTAT
7793283 TCGA
1 TCGA
7793287 ATCAACTCNN
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:7805773 original size:21 final size:20
Alignment explanation
Indices: 7805749--7805787 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
7805739 CTCGTAAAAA
7805749 TGGTTATTTTAATAAACAATT
1 TGGTTATTTTAA-AAACAATT
* *
7805770 TGGTTTTTTTCAAAACAA
1 TGGTTATTTTAAAAACAA
7805788 CGATTTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (20 bp):
TGGTTATTTTAAAAACAATT
Found at i:7807123 original size:34 final size:35
Alignment explanation
Indices: 7807079--7807145 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
7807069 CAGTAAAATA
* *
7807079 TTTTCCGTAAAATAATTT-TTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
7807113 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
7807146 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:7811152 original size:95 final size:91
Alignment explanation
Indices: 7811028--7811249 Score: 286
Period size: 92 Copynumber: 2.4 Consensus size: 91
7811018 TTCAGGGTGC
**
7811028 AAAAAG-CCCTCAAACTTTTTTTAAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTTTTACACTC
1 AAAAAGACCCTCAAACTTTTTTT-AAAAAAAGCAATTAAG-CCC--CTAATTTTTTTTTACACTC
*
7811092 ATTTGGGTACTTGAACTTTCAAAATGCATA
62 AATTGGGTACTTGAACTTTCAAAATGCATA
* * * * *
7811122 AAAAATATCCTCAAACCTTTTTTTAAAAAAACCAATTAAGCCCCTAATTTTTTTTTGCATTCAAT
1 AAAAAGACCCTCAAA-CTTTTTTTAAAAAAAGCAATTAAGCCCCTAATTTTTTTTTACACTCAAT
*
7811187 TGGGTACTTGAACTTTCAAAATGCATC
65 TGGGTACTTGAACTTTCAAAATGCATA
* *
7811214 AAAAAGACCCTTAAAC-TTTTTCAAAAAAAGCAATTA
1 AAAAAGACCCTCAAACTTTTTTTAAAAAAAGCAATTA
7811250 GGACTCCGCT
Statistics
Matches: 112, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
90 18 0.16
91 1 0.01
92 55 0.49
94 8 0.07
95 22 0.20
96 8 0.07
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (91 bp):
AAAAAGACCCTCAAACTTTTTTTAAAAAAAGCAATTAAGCCCCTAATTTTTTTTTACACTCAATT
GGGTACTTGAACTTTCAAAATGCATA
Found at i:7811579 original size:18 final size:17
Alignment explanation
Indices: 7811530--7811588 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
7811520 AATAAAAATT
7811530 TTTATATATTTTATTAAAA
1 TTTAT-TATTTT-TTAAAA
*
7811549 TTTAATAATTTTTGTAAAA
1 TTT-ATTATTTTT-TAAAA
7811568 TTTATTATTTTTTATAAA
1 TTTATTATTTTTTA-AAA
7811586 TTT
1 TTT
7811589 TTTTCTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 2 0.06
18 15 0.43
19 16 0.46
20 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTATTATTTTTTAAAA
Found at i:7812260 original size:62 final size:62
Alignment explanation
Indices: 7812131--7812268 Score: 143
Period size: 62 Copynumber: 2.2 Consensus size: 62
7812121 AAACTTTCCA
* * * * *
7812131 AAAATTTTAAAATAATTTAATTTACATCTTTAAATTTTTTTTTCAATTATCATTCAACTTTT
1 AAAATTTTAAAATAATTTAATTTACATCTCTAAATTTTTTTTTAAAATATCATTAAACTCTT
* * * * *
7812193 AAAATTTTCAAATATTTTAATTT-GATCTACTAATTTTTTTTTTAAAATCTCATTAAATCTCTT
1 AAAATTTTAAAATAATTTAATTTACATCT-CTAAATTTTTTTTTAAAATATCATTAAA-CTCTT
*
7812256 AAATTCTTTAAAA
1 AAAAT-TTTAAAA
7812269 GTTCTAATTA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
61 4 0.07
62 43 0.70
63 8 0.13
64 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (62 bp):
AAAATTTTAAAATAATTTAATTTACATCTCTAAATTTTTTTTTAAAATATCATTAAACTCTT
Found at i:7817801 original size:17 final size:18
Alignment explanation
Indices: 7817769--7817802 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7817759 AAAGATTCTC
*
7817769 AAAATTAAACTCTTTTAA
1 AAAATTAAAATCTTTTAA
7817787 AAAATTAAAAT-TTTTA
1 AAAATTAAAATCTTTTA
7817803 TTTAAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTAAAATCTTTTAA
Found at i:7818692 original size:6 final size:6
Alignment explanation
Indices: 7818681--7818705 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7818671 GCTTCTCTAA
7818681 TTTAAT TTTAAT TTTAAT TTTAAT T
1 TTTAAT TTTAAT TTTAAT TTTAAT T
7818706 AAATTACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:7818971 original size:24 final size:23
Alignment explanation
Indices: 7818931--7818975 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
7818921 TCTCCTTCTC
7818931 TTTTACAATTCGATTTTGTTTTTT
1 TTTTACAATTCGATTTT-TTTTTT
* *
7818955 TTTTACAGTTC-AGTTTTTTTT
1 TTTTACAATTCGATTTTTTTTT
7818976 CATGAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 4 0.21
24 10 0.53
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTTACAATTCGATTTTTTTTTT
Found at i:7819218 original size:31 final size:31
Alignment explanation
Indices: 7819183--7819266 Score: 150
Period size: 31 Copynumber: 2.7 Consensus size: 31
7819173 CTTAACAACC
7819183 CAGTGACTTAAATAAAAACTTTCGAAAAGTT
1 CAGTGACTTAAATAAAAACTTTCGAAAAGTT
*
7819214 CAGTGACTTAAATAAAAACTTTCGAAGAGTT
1 CAGTGACTTAAATAAAAACTTTCGAAAAGTT
*
7819245 CAGCGACTTAAATAAAAACTTT
1 CAGTGACTTAAATAAAAACTTT
7819267 TGAATAATTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACTTTCGAAAAGTT
Found at i:7819278 original size:31 final size:30
Alignment explanation
Indices: 7819187--7819278 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 30
7819177 ACAACCCAGT
*
7819187 GACTTAAATAAAAACTTTCGAAAAGTTCAGT
1 GACTTAAATAAAAACTTTCGAAAA-TTCAGC
*
7819218 GACTTAAATAAAAACTTTCGAAGAGTTCAGC
1 GACTTAAATAAAAACTTTCGAA-AATTCAGC
*
7819249 GACTTAAATAAAAACTTTTGAATAATTCAG
1 GACTTAAATAAAAACTTTCGAA-AATTCAG
7819279 AGATCATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (30 bp):
GACTTAAATAAAAACTTTCGAAAATTCAGC
Found at i:7820224 original size:20 final size:20
Alignment explanation
Indices: 7820182--7820227 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
7820172 TCAAAGAAAC
* *
7820182 TAAAAAAAATAAAAATCTTA
1 TAAAATAAATAAAAATCTAA
7820202 TAAAATAAATAAAAGA-CTAA
1 TAAAATAAATAAAA-ATCTAA
7820222 TAAAAT
1 TAAAAT
7820228 TTGAAAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAAATAAATAAAAATCTAA
Found at i:7824578 original size:9 final size:9
Alignment explanation
Indices: 7824564--7824593 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
7824554 ATATTGGATC
7824564 TTTATTATA
1 TTTATTATA
7824573 TTTATTATA
1 TTTATTATA
7824582 TTTATTATA
1 TTTATTATA
7824591 TTT
1 TTT
7824594 GGGTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTATTATA
Done.