Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 5 of 433
Found at i:1382690 original size:14 final size:14
Alignment explanation
Indices: 1382683--1382710 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1382673 TAAATAATAT
1382683 ACCCTAAACTATAA
1 ACCCTAAACTATAA
1382697 ACCCTAAACTATAA
1 ACCCTAAACTATAA
1382711 TGATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
ACCCTAAACTATAA
Found at i:1382924 original size:11 final size:11
Alignment explanation
Indices: 1382908--1382939 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1382898 TAAACTCCAA
*
1382908 CCTTAAACTAC
1 CCTTAAACCAC
1382919 CCTTAAACCAC
1 CCTTAAACCAC
1382930 CCTTAAACCA
1 CCTTAAACCA
1382940 TGATCCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (11 bp):
CCTTAAACCAC
Found at i:1383201 original size:30 final size:31
Alignment explanation
Indices: 1383144--1383201 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1383134 TTTAAAATTA
*
1383144 TTTTAAAAAATAGTATTTTCATTTTTTTCAT
1 TTTTAAAAAATAGTATTTTCATGTTTTTCAT
*
1383175 TTTTAACAAATA-T-TTTTCTATGTTTTT
1 TTTTAAAAAATAGTATTTTC-ATGTTTTT
1383202 ACTTTCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 8 0.33
31 11 0.46
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTTAAAAAATAGTATTTTCATGTTTTTCAT
Found at i:1383444 original size:40 final size:40
Alignment explanation
Indices: 1383399--1383523 Score: 164
Period size: 40 Copynumber: 3.1 Consensus size: 40
1383389 AAACTCTTTT
* *
1383399 GCGGCGCTTTTTGAAAAACGCAGCTATAGGTGTACCTATA
1 GCGGCGCTTCTTAAAAAACGCAGCTATAGGTGTACCTATA
* *
1383439 GCGGCGCTTCTAAAAAAACGCCA-CTATAGGTGTACTTATA
1 GCGGCGCTTCTTAAAAAACG-CAGCTATAGGTGTACCTATA
* * *
1383479 GCGGCGCTTCTTAAAAAACGCCGCTAAAGATGTACCTA-A
1 GCGGCGCTTCTTAAAAAACGCAGCTATAGGTGTACCTATA
1383518 GCGGCG
1 GCGGCG
1383524 TTTTTAAGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 8 0.11
40 64 0.86
41 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (40 bp):
GCGGCGCTTCTTAAAAAACGCAGCTATAGGTGTACCTATA
Found at i:1383648 original size:40 final size:40
Alignment explanation
Indices: 1383593--1383700 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
1383583 AAACTCTTTT
1383593 GCGGCGCTTTTTGAAAAACGCCGCTAAAGGTGTACCTATA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAAGGTGTACCTATA
* *
1383633 GCGGCGCGTGTTGAAAAACGCCGCTAAAGGTGTACCTATA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAAGGTGTACCTATA
*
1383673 GCGGCGCTTTTTAAAAAACGCCGCTAAA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAA
1383701 AACGCTGCTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (40 bp):
GCGGCGCTTTTTGAAAAACGCCGCTAAAGGTGTACCTATA
Found at i:1383713 original size:11 final size:12
Alignment explanation
Indices: 1383686--1383715 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1383676 GCGCTTTTTA
1383686 AAAAACGCCGCT
1 AAAAACGCCGCT
*
1383698 AAAAACGCTGCT
1 AAAAACGCCGCT
1383710 AAAAAC
1 AAAAAC
1383716 CTGTTTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.27, G:0.13, T:0.10
Consensus pattern (12 bp):
AAAAACGCCGCT
Found at i:1383811 original size:12 final size:12
Alignment explanation
Indices: 1383794--1383821 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1383784 TCTCCTCCAA
1383794 TAAATCATTCAT
1 TAAATCATTCAT
1383806 TAAATCATTCAT
1 TAAATCATTCAT
1383818 TAAA
1 TAAA
1383822 AATCTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAATCATTCAT
Found at i:1384669 original size:16 final size:16
Alignment explanation
Indices: 1384635--1384688 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1384625 ATTGAAGAGG
**
1384635 AAATTAGAAAGATGGA
1 AAATTAGAAAGATAAA
*
1384651 AAATTAAAAAGATAAAAA
1 AAATTAGAAAGAT--AAA
*
1384669 AAAATAGAAAGATAAA
1 AAATTAGAAAGATAAA
1384685 AAAT
1 AAAT
1384689 ACGTGCATCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
AAATTAGAAAGATAAA
Found at i:1389283 original size:21 final size:21
Alignment explanation
Indices: 1389259--1389299 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1389249 GCCGTTATAT
* *
1389259 ACTTATAACAGCATTTGAGAC
1 ACTTATAAAAACATTTGAGAC
1389280 ACTTATAAAAACATTTGAGA
1 ACTTATAAAAACATTTGAGA
1389300 TTCATATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (21 bp):
ACTTATAAAAACATTTGAGAC
Found at i:1389411 original size:18 final size:19
Alignment explanation
Indices: 1389390--1389440 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1389380 CTTTAATAAA
*
1389390 ATTTA-TAAATATAATTTC
1 ATTTAGTAAATATAATATC
* * *
1389408 ATTTATTAAAGATTATATC
1 ATTTAGTAAATATAATATC
1389427 ATTTAGTAAATATA
1 ATTTAGTAAATATA
1389441 TGATTAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (19 bp):
ATTTAGTAAATATAATATC
Found at i:1400117 original size:23 final size:25
Alignment explanation
Indices: 1400085--1400131 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
1400075 CTTTAATCTA
1400085 AACTCAAAATTAA-CTTAAATAAAT
1 AACTCAAAATTAACCTTAAATAAAT
1400109 AACTC-AAATTAACCTTAAATAAA
1 AACTCAAAATTAACCTTAAATAAA
1400132 CCAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (25 bp):
AACTCAAAATTAACCTTAAATAAAT
Found at i:1404722 original size:47 final size:47
Alignment explanation
Indices: 1404668--1404761 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
1404658 AATATGTATC
* *
1404668 GAATTTGATTTTCAGTATTCAAAATTCAAATCTGATCTGATTTGTGT
1 GAATTTGATTTTCAGTATTCAAAACTCAAATCTAATCTGATTTGTGT
*
1404715 GAATTTGATTTTCAGTATTCAAAACTCGAATCTAATCTGATTTGTGT
1 GAATTTGATTTTCAGTATTCAAAACTCAAATCTAATCTGATTTGTGT
1404762 TTCATGATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (47 bp):
GAATTTGATTTTCAGTATTCAAAACTCAAATCTAATCTGATTTGTGT
Found at i:1405831 original size:42 final size:38
Alignment explanation
Indices: 1405784--1405864 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 38
1405774 TAATATTAGA
*
1405784 TAGATTATATT-AATTTTTATGTTTGATTTTAGTATATAATTT
1 TAGATTATATTGAA--TTTAAGTTTGA-TTTA--ATATAATTT
1405826 TAGATTATATTGAATTTAAGTTTGATTTAATATAATTT
1 TAGATTATATTGAATTTAAGTTTGATTTAATATAATTT
1405864 T
1 T
1405865 GTGTTAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
38 10 0.27
40 4 0.11
41 10 0.27
42 11 0.30
43 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (38 bp):
TAGATTATATTGAATTTAAGTTTGATTTAATATAATTT
Found at i:1425275 original size:48 final size:48
Alignment explanation
Indices: 1425185--1425280 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
1425175 ATATTAACTT
** *
1425185 TATTACGATTTAGATTTATTTGATTCTTTTTAACTGTGTATGGATTAA
1 TATTACGATTTAGATTTATTTGATTCTTTTTAACAATATATGGATTAA
* *
1425233 TATTACGATTTGGATTTATTTGATTCTTTTTCACAATATATGGATTAA
1 TATTACGATTTAGATTTATTTGATTCTTTTTAACAATATATGGATTAA
1425281 ATCAATTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (48 bp):
TATTACGATTTAGATTTATTTGATTCTTTTTAACAATATATGGATTAA
Found at i:1437790 original size:3 final size:3
Alignment explanation
Indices: 1437782--1437813 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1437772 TAACAAGGAT
1437782 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1437814 CAATCACATA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1440049 original size:9 final size:9
Alignment explanation
Indices: 1440009--1440059 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
1439999 TTTTTTAAAG
1440009 TTTTAATTT
1 TTTTAATTT
1440018 TCTTTATATATT
1 T-TTTA-AT-TT
*
1440030 CTTTAGA-TT
1 TTTTA-ATTT
1440039 TTTTAATTT
1 TTTTAATTT
1440048 TTTTAATTT
1 TTTTAATTT
1440057 TTT
1 TTT
1440060 AAAAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.03
9 21 0.60
10 4 0.11
11 7 0.20
12 2 0.06
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTAATTT
Found at i:1441142 original size:3 final size:3
Alignment explanation
Indices: 1441134--1441167 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1441124 ATCAAAACCC
* *
1441134 ATA ATA ATA TTG ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1441168 CCCAATAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1451713 original size:16 final size:17
Alignment explanation
Indices: 1451694--1451731 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1451684 AAGCTAAATT
*
1451694 TAAATTTAAA-TAAAAA
1 TAAATTAAAATTAAAAA
1451710 TAAATTAAAATTAAAAA
1 TAAATTAAAATTAAAAA
1451727 -AAATT
1 TAAATT
1451732 GAATGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATTAAAATTAAAAA
Found at i:1451713 original size:22 final size:20
Alignment explanation
Indices: 1451688--1451730 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
1451678 CAAAGAAAGC
*
1451688 TAAATTTAAATTTAAATAAAAA
1 TAAA-TTAAAATTAAA-AAAAA
1451710 TAAATTAAAATTAAAAAAAA
1 TAAATTAAAATTAAAAAAAA
1451730 T
1 T
1451731 TGAATGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATTAAAATTAAAAAAAA
Found at i:1458611 original size:23 final size:22
Alignment explanation
Indices: 1458585--1458627 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1458575 TAATTTAGGT
*
1458585 ATATTTCATATTTTTTTAAAAAA
1 ATATTT-ATATTATTTTAAAAAA
*
1458608 ATATTTTTATTATTTTAAAA
1 ATATTTATATTATTTTAAAA
1458628 TTATTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTATATTATTTTAAAAAA
Found at i:1465490 original size:18 final size:18
Alignment explanation
Indices: 1465467--1465505 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1465457 ATACAATTTA
1465467 ATTAT-ATTTGAATAAAAT
1 ATTATAATTT-AATAAAAT
1465485 ATTATAATTTAATAAAAT
1 ATTATAATTTAATAAAAT
1465503 ATT
1 ATT
1465506 GTGCCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTATAATTTAATAAAAT
Found at i:1468700 original size:2 final size:2
Alignment explanation
Indices: 1468693--1468724 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1468683 TGAGAAAAGA
1468693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1468725 TTGATTCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1470359 original size:24 final size:21
Alignment explanation
Indices: 1470319--1470363 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
1470309 AAATATTAAA
1470319 TATATATTTTTAATTAACATTT
1 TATATATTTTTAATTAA-ATTT
1470341 TATATATTTTTATATTTAAATTT
1 TATATATTTTTA-A-TTAAATTT
1470364 AAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.57
23 5 0.24
24 4 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATATTTTTAATTAAATTT
Found at i:1473665 original size:28 final size:28
Alignment explanation
Indices: 1473597--1473675 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
1473587 GAATCATTCG
* *
1473597 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* *
1473625 ATATCTCACACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* * *
1473653 ATATTTCGTACACTGAGTACCAT
1 ATATTTCGCACACTAAGTGCCAT
1473676 ATTTGATTGC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:1477175 original size:31 final size:32
Alignment explanation
Indices: 1477137--1477198 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
1477127 TTGATCATTA
1477137 AATTATTC-GAAAG-TTTTTATTTAAGTCACCG
1 AATTATTCAG-AAGTTTTTTATTTAAGTCACCG
1477168 AATTATTCAGAAGTTCTTTTTATTTAAGTCA
1 AATTATTCAGAAG-T-TTTTTATTTAAGTCA
1477199 TTAGATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 11 0.41
32 1 0.04
34 15 0.56
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (32 bp):
AATTATTCAGAAGTTTTTTATTTAAGTCACCG
Found at i:1480305 original size:18 final size:18
Alignment explanation
Indices: 1480282--1480319 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1480272 AATATATATT
*
1480282 AACCCAAGTATCCAACCC
1 AACCCAAGTACCCAACCC
*
1480300 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
1480318 AA
1 AA
1480320 TCATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.45, G:0.03, T:0.11
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:1480312 original size:13 final size:13
Alignment explanation
Indices: 1480296--1480320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1480286 CAAGTATCCA
1480296 ACCCAACCCAATT
1 ACCCAACCCAATT
1480309 ACCCAACCCAAT
1 ACCCAACCCAAT
1480321 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:1480364 original size:5 final size:6
Alignment explanation
Indices: 1480345--1480386 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
1480335 ATAATTGAAT
1480345 AAATAA AAATAA AAATAAA AAACTAA AAATAA AAATGAA AAA
1 AAATAA AAATAA AAAT-AA AAA-TAA AAATAA AAAT-AA AAA
1480387 CATATAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 17 0.52
7 15 0.45
8 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:1480371 original size:14 final size:13
Alignment explanation
Indices: 1480345--1480379 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
1480335 ATAATTGAAT
1480345 AAAT-AAAAATAA
1 AAATAAAAAATAA
1480357 AAATAAAAAACTAA
1 AAATAAAAAA-TAA
1480371 AAATAAAAA
1 AAATAAAAA
1480380 TGAAAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 5 0.24
14 12 0.57
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:1480373 original size:20 final size:20
Alignment explanation
Indices: 1480348--1480387 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1480338 ATTGAATAAA
1480348 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
*
1480368 TAAAAATAAAAATGAAAAAC
1 TAAAAATAAAAATAAAAAAC
1480388 ATATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:1480419 original size:9 final size:9
Alignment explanation
Indices: 1480405--1480454 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
1480395 TTTATACAAA
*
1480405 TAATTCGGG
1 TAATTCGGT
*
1480414 TAATTCGGA
1 TAATTCGGT
*
1480423 TAATTCAGT
1 TAATTCGGT
*
1480432 TAATTCGTT
1 TAATTCGGT
1480441 TAATTCGGT
1 TAATTCGGT
1480450 TAATT
1 TAATT
1480455 TTATACTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:1482050 original size:25 final size:24
Alignment explanation
Indices: 1482022--1482087 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
1482012 ACTGAATAAT
1482022 TAATTAATT-CAATAACTGTAATGA-A
1 TAATT-ATTACAATAA-T-TAATGACA
*
1482047 TAATTCTTACAATAATTAATGACA
1 TAATTATTACAATAATTAATGACA
*
1482071 TAATT-TTACAAAAATTA
1 TAATTATTACAATAATTA
1482088 CAAAATGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 17 0.46
24 9 0.24
25 11 0.30
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (24 bp):
TAATTATTACAATAATTAATGACA
Found at i:1482079 original size:23 final size:23
Alignment explanation
Indices: 1482031--1482087 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
1482021 TTAATTAATT
1482031 CAATAACTGTAATGAATAATTCTTA
1 CAATAA-T-TAATGAATAATTCTTA
1482056 CAATAATTAATGACATAATT-TTA
1 CAATAATTAATGA-ATAATTCTTA
*
1482079 CAAAAATTA
1 CAATAATTA
1482088 CAAAATGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 17 0.57
24 7 0.23
25 6 0.20
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (23 bp):
CAATAATTAATGAATAATTCTTA
Found at i:1482406 original size:9 final size:9
Alignment explanation
Indices: 1482392--1482432 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
1482382 AAAAAAGACT
1482392 TTAAATCAA
1 TTAAATCAA
1482401 TTAAATCAA
1 TTAAATCAA
1482410 --AAATCAA
1 TTAAATCAA
1482417 TATAAATCAA
1 T-TAAATCAA
1482427 TTAAAT
1 TTAAAT
1482433 TAATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (9 bp):
TTAAATCAA
Found at i:1482415 original size:16 final size:17
Alignment explanation
Indices: 1482394--1482426 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1482384 AAAAGACTTT
1482394 AAATCAAT-TAAATCAA
1 AAATCAATATAAATCAA
1482410 AAATCAATATAAATCAA
1 AAATCAATATAAATCAA
1482427 TTAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATCAATATAAATCAA
Found at i:1486990 original size:31 final size:32
Alignment explanation
Indices: 1486923--1486990 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 32
1486913 TAAAAAAATC
* * *
1486923 AATTTGACTCTTTTTCAAAAGGTTGATGGTCA
1 AATTTGACTATTTTTCAAAAGGTTGAAGGCCA
* * *
1486955 AATTTTACTATTTTT-AAGAGGTTGAAGGCCT
1 AATTTGACTATTTTTCAAAAGGTTGAAGGCCA
1486986 AATTT
1 AATTT
1486991 AACATACACA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (32 bp):
AATTTGACTATTTTTCAAAAGGTTGAAGGCCA
Found at i:1491900 original size:2 final size:2
Alignment explanation
Indices: 1491893--1491926 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1491883 TACAACTTGA
1491893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1491927 GCGCGCACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1498668 original size:18 final size:18
Alignment explanation
Indices: 1498645--1498679 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1498635 AATTTAACAA
1498645 TAAAAAT-ATATATTTTTT
1 TAAAAATGAT-TATTTTTT
1498663 TAAAAATGATTATTTTT
1 TAAAAATGATTATTTTT
1498680 AAATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAAAAATGATTATTTTTT
Found at i:1501725 original size:2 final size:2
Alignment explanation
Indices: 1501718--1501750 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1501708 CCATCTTATG
1501718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1501751 TATCATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1508254 original size:105 final size:105
Alignment explanation
Indices: 1508136--1508350 Score: 421
Period size: 105 Copynumber: 2.0 Consensus size: 105
1508126 AAAATGCAAT
1508136 GAACTGGCTCGAACACGTGACTAAAACTAAAGAATGATAAAAAATCGTAATAAATTATAAAAAAA
1 GAACTGGCTCGAACACGTGACTAAAACTAAAGAATGATAAAAAATCGTAATAAATTATAAAAAAA
*
1508201 ATCCAAACCTTGAAACTAAATGATTTAACTCAAAATGTTA
66 ATCCAAACCCTGAAACTAAATGATTTAACTCAAAATGTTA
1508241 GAACTGGCTCGAACACGTGACTAAAACTAAAGAATGATAAAAAATCGTAATAAATTATAAAAAAA
1 GAACTGGCTCGAACACGTGACTAAAACTAAAGAATGATAAAAAATCGTAATAAATTATAAAAAAA
1508306 ATCCAAACCCTGAAACTAAATGATTTAACTCAAAATGTTA
66 ATCCAAACCCTGAAACTAAATGATTTAACTCAAAATGTTA
1508346 GAACT
1 GAACT
1508351 TAAAATTTTA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 109 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (105 bp):
GAACTGGCTCGAACACGTGACTAAAACTAAAGAATGATAAAAAATCGTAATAAATTATAAAAAAA
ATCCAAACCCTGAAACTAAATGATTTAACTCAAAATGTTA
Found at i:1518856 original size:45 final size:45
Alignment explanation
Indices: 1518805--1518894 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1518795 ATTATGTCTC
1518805 AAATTGATGAAAAGATTGTGAAACATTTTATGTAGTATAATTGTA
1 AAATTGATGAAAAGATTGTGAAACATTTTATGTAGTATAATTGTA
1518850 AAATTGATGAAAAGATTGTGAAACATTTTATGTAGTATAATTGTA
1 AAATTGATGAAAAGATTGTGAAACATTTTATGTAGTATAATTGTA
1518895 TACCTTATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (45 bp):
AAATTGATGAAAAGATTGTGAAACATTTTATGTAGTATAATTGTA
Found at i:1526730 original size:29 final size:30
Alignment explanation
Indices: 1526644--1526753 Score: 100
Period size: 31 Copynumber: 3.6 Consensus size: 30
1526634 ATCAAATCAA
* *
1526644 AATTAAAGCTTTATGTATA-CATTTCAACTAT
1 AATTAAAG-TTTATGTATATAATTAC-ACTAT
* * *
1526675 AATTAGAGTTTCACGTGTATAATTACACTA-
1 AATTAAAGTTT-ATGTATATAATTACACTAT
1526705 AATTAAAGTTTATGTATATAATTACA-TATT
1 AATTAAAGTTTATGTATATAATTACACTA-T
*
1526735 AATTTAAAATTTATGTATA
1 AA-TTAAAGTTTATGTATA
1526754 ATTTTGAGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.03
29 13 0.20
30 15 0.23
31 31 0.48
32 4 0.06
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (30 bp):
AATTAAAGTTTATGTATATAATTACACTAT
Found at i:1526754 original size:29 final size:27
Alignment explanation
Indices: 1526690--1526756 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 27
1526680 GAGTTTCACG
*
1526690 TGTATAATTACACTAAATTAAAGTTTA
1 TGTATAATTACACTAAATTAAAATTTA
1526717 TGTATATAATTACA-TATTAATTTAAAATTTA
1 TG--TATAATTACACTA--AA-TTAAAATTTA
1526748 TGTATAATT
1 TGTATAATT
1526757 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 2 0.06
28 2 0.06
29 17 0.50
30 2 0.06
31 11 0.32
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (27 bp):
TGTATAATTACACTAAATTAAAATTTA
Found at i:1527389 original size:14 final size:14
Alignment explanation
Indices: 1527358--1527388 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1527348 CCTTTGGTTG
1527358 TTTTCTGTTTCTTT
1 TTTTCTGTTTCTTT
1527372 TTTTCT-TTTCTTT
1 TTTTCTGTTTCTTT
1527385 TTTT
1 TTTT
1527389 TTTCTGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (14 bp):
TTTTCTGTTTCTTT
Found at i:1535320 original size:27 final size:25
Alignment explanation
Indices: 1535264--1535328 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 25
1535254 GGTTGAATCG
*
1535264 AATTTT-ATTATAATTATTTAATAA
1 AATTTTAATTTTAATTATTTAATAA
*
1535288 AATTTTACAATTTTAATTTTTTAATAA
1 AATTTT--AATTTTAATTATTTAATAA
**
1535315 TTTTTTAATTTTAA
1 AATTTTAATTTTAA
1535329 ATCAAACTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
24 6 0.18
25 8 0.24
27 20 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
AATTTTAATTTTAATTATTTAATAA
Found at i:1539878 original size:6 final size:6
Alignment explanation
Indices: 1539867--1539896 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1539857 TCAGGTTCCC
1539867 ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT
1539897 TTGTATGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:1540157 original size:66 final size:66
Alignment explanation
Indices: 1540051--1540435 Score: 617
Period size: 66 Copynumber: 5.8 Consensus size: 66
1540041 CAAAAGGAAA
* *
1540051 AAAGAGAAAATAACCTCATTGATGTTGGTGTGGCTGCAAATAACCCAGTCTGCATCGACAAAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
1540116 G
66 G
* * *
1540117 AAAGAGAAAATAACGTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTCTGCATCGACGAAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
1540182 G
66 G
* * *
1540183 AAAGAGAATATAACCTCATTGATGGTTGTGTGGCTGCAAATAACCCAGTATGCATGGACAAAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
1540248 G
66 G
* *
1540249 CAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATGGACAAAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
1540314 G
66 G
* * * *
1540315 CAAGAGAAAATAACCTAATTGATGGTGGTGTGGCTGCATATAACCCAGTATGCATCGAAAAAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
1540380 G
66 G
* * *
1540381 AAAGAGAATATAACCTAATTGACGGTGGTGTGGCTGCAAATAACCCAGTATGCAT
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCAT
1540436 TCTCAAAATG
Statistics
Matches: 299, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 299 1.00
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (66 bp):
AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
G
Found at i:1542977 original size:28 final size:31
Alignment explanation
Indices: 1542926--1542991 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
1542916 AAATGTTAAG
* *
1542926 AAAACTATATATAAAATTT---TAATAAATT
1 AAAAATATATATAAAATTTAAATATTAAATT
1542954 AAAAATATATA-AAAATATTAAATATTAAATT
1 AAAAATATATATAAAAT-TTAAATATTAAATT
1542985 AAAAATA
1 AAAAATA
1542992 ACATAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 5 0.16
28 12 0.38
31 15 0.47
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAAATATATATAAAATTTAAATATTAAATT
Found at i:1542980 original size:26 final size:28
Alignment explanation
Indices: 1542926--1542982 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1542916 AAATGTTAAG
* *
1542926 AAAACTATATATAAAATTTTAATAAATT
1 AAAAATATATATAAAATATTAATAAATT
*
1542954 AAAAATATATA-AAAATATTAA-ATATT
1 AAAAATATATATAAAATATTAATAAATT
1542980 AAA
1 AAA
1542983 TTAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 7 0.27
27 9 0.35
28 10 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAAATATATATAAAATATTAATAAATT
Found at i:1544797 original size:16 final size:16
Alignment explanation
Indices: 1544757--1544797 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1544747 CCTAGTTAGG
1544757 TTGGTTTTGAATTGTAT
1 TTGGTTTT-AATTGTAT
1544774 TTGG-TTTAAGTTGT-T
1 TTGGTTTTAA-TTGTAT
1544789 TTGGTTTTA
1 TTGGTTTTA
1544798 GGTGGATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.32
16 11 0.50
17 4 0.18
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (16 bp):
TTGGTTTTAATTGTAT
Found at i:1546539 original size:4 final size:4
Alignment explanation
Indices: 1546530--1546571 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
1546520 CTTCAACAAT
1546530 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1546572 GTTTGATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:1548433 original size:24 final size:24
Alignment explanation
Indices: 1548401--1548455 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
1548391 TTCTAAATTT
*
1548401 GTAAAATAATAAGTTAATATAATG
1 GTAAAATAATAAGTTAATATAATA
1548425 GTAAAATAATAAGTTAATATAATA
1 GTAAAATAATAAGTTAATATAATA
1548449 GTAAAAT
1 GTAAAAT
1548456 TGCATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (24 bp):
GTAAAATAATAAGTTAATATAATA
Found at i:1548446 original size:13 final size:13
Alignment explanation
Indices: 1548406--1548448 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1548396 AATTTGTAAA
1548406 ATAATAAGTTAAT
1 ATAATAAGTTAAT
* *
1548419 ATAAT--GGTAAA
1 ATAATAAGTTAAT
1548430 ATAATAAGTTAAT
1 ATAATAAGTTAAT
1548443 ATAATA
1 ATAATA
1548449 GTAAAATTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (13 bp):
ATAATAAGTTAAT
Found at i:1552777 original size:29 final size:30
Alignment explanation
Indices: 1552721--1552779 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1552711 GAATCTGATC
*
1552721 AAATCAAAATTTCATATATAAAACTGCACA
1 AAATCAAAATTTAATATATAAAACTGCACA
* * *
1552751 AAATCAAAA-TTAATGTATACAATTGCACA
1 AAATCAAAATTTAATATATAAAACTGCACA
1552780 TTAAACTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATCAAAATTTAATATATAAAACTGCACA
Found at i:1558404 original size:42 final size:42
Alignment explanation
Indices: 1558357--1558440 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1558347 TGATTACCCA
* * *
1558357 TTTCTCGTTTTTTTAATTATAATGGAAATCGCTGAGTTTATC
1 TTTCTCGCTTTTCTAATTATAATGGAAATCGCTGAGTCTATC
* * *
1558399 TTTCTCGCTTTTCTGATTATATTGGGAATCGCTGAGTCTATC
1 TTTCTCGCTTTTCTAATTATAATGGAAATCGCTGAGTCTATC
1558441 GACTTAGATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (42 bp):
TTTCTCGCTTTTCTAATTATAATGGAAATCGCTGAGTCTATC
Found at i:1560909 original size:14 final size:14
Alignment explanation
Indices: 1560870--1560915 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1560860 TTCTGAAATT
1560870 TTTTTCATGGGAAAA
1 TTTTT-ATGGGAAAA
**
1560885 TTTGCAT--GAAAA
1 TTTTTATGGGAAAA
1560897 TTTTTATGGGAAAA
1 TTTTTATGGGAAAA
1560911 TTTTT
1 TTTTT
1560916 CTCCAGCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 10 0.40
14 12 0.48
15 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (14 bp):
TTTTTATGGGAAAA
Found at i:1566751 original size:19 final size:19
Alignment explanation
Indices: 1566727--1566785 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
1566717 TTCGTTTGAA
1566727 GTATTTTCCGTCAAAATTC
1 GTATTTTCCGTCAAAATTC
*
1566746 GTATTTTCCATCAAAATTC
1 GTATTTTCCGTCAAAATTC
**
1566765 ACCATTTTCCGTCAAAATTC
1 -GTATTTTCCGTCAAAATTC
1566785 G
1 G
1566786 CCGTCAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (19 bp):
GTATTTTCCGTCAAAATTC
Found at i:1567520 original size:30 final size:31
Alignment explanation
Indices: 1567487--1567580 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
1567477 TTAGTATCTT
*
1567487 TATTTTACTCAACTTATAAATTTCGTCCCT-
1 TATTTTACTCAACTTATAAATTTAGTCCCTC
* *
1567517 TATTTTA---AA-TTTTATAA-TTAGTCCCTG
1 TATTTTACTCAACTTATA-AATTTAGTCCCTC
*
1567544 TATCTTACTCAACTTATAAATTTAGT-CCTC
1 TATTTTACTCAACTTATAAATTTAGTCCCTC
1567574 TATTTTA
1 TATTTTA
1567581 TTAGTTTACC
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
26 12 0.24
27 10 0.20
30 20 0.39
31 9 0.18
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (31 bp):
TATTTTACTCAACTTATAAATTTAGTCCCTC
Found at i:1567552 original size:57 final size:57
Alignment explanation
Indices: 1567470--1567580 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 57
1567460 CTGGTCAAAC
* * * *
1567470 TTTATAATTAGTATCTTTATTTTACTCAACTTATAAATTTCGTCC-CTTATTTTAAAT
1 TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCTC-TATTTTAAAT
*
1567527 TTTATAATTAGTCCCTGTATCTTACTCAACTTATAAATTTAGTCCTCTATTTTA
1 TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCTCTATTTTA
1567581 TTAGTTTACC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 47 0.98
58 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (57 bp):
TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCTCTATTTTAAAT
Found at i:1567570 original size:31 final size:29
Alignment explanation
Indices: 1567490--1567571 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 29
1567480 GTATCTTTAT
*
1567490 TTTACTCAACTTATAAATTTCGTCCCTTA
1 TTTACTCAACTTATAAATTTAGTCCCTTA
* *
1567519 TTT--T-AAATTTTATAA-TTAGTCCCTGTA
1 TTTACTCAACTTATA-AATTTAGTCCCT-TA
1567546 TCTTACTCAACTTATAAATTTAGTCC
1 T-TTACTCAACTTATAAATTTAGTCC
1567572 TCTATTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
26 14 0.34
27 6 0.15
28 2 0.05
29 3 0.07
30 3 0.07
31 13 0.32
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTACTCAACTTATAAATTTAGTCCCTTA
Found at i:1572896 original size:16 final size:16
Alignment explanation
Indices: 1572861--1572905 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1572851 ATCTTTATTT
*
1572861 GAATAAATGTAGAGCGAA
1 GAATAAA-G-AGAACGAA
1572879 GAATAAAGAGAACGAA
1 GAATAAAGAGAACGAA
*
1572895 GAACAAAGAGA
1 GAATAAAGAGA
1572906 GCAATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.68
17 1 0.04
18 7 0.28
ACGTcount: A:0.58, C:0.07, G:0.27, T:0.09
Consensus pattern (16 bp):
GAATAAAGAGAACGAA
Found at i:1576739 original size:22 final size:23
Alignment explanation
Indices: 1576709--1576754 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1576699 CAGTCCACGT
1576709 ATAAGTTATAAAAATTCAAAAAA
1 ATAAGTTATAAAAATTCAAAAAA
* *
1576732 ATAA-TTATAAATATTTAAAAAA
1 ATAAGTTATAAAAATTCAAAAAA
1576754 A
1 A
1576755 CGTCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAGTTATAAAAATTCAAAAAA
Found at i:1577832 original size:2 final size:2
Alignment explanation
Indices: 1577825--1577864 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1577815 AAAACATTAA
1577825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1577865 ACATCGGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1583753 original size:40 final size:40
Alignment explanation
Indices: 1583708--1583790 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
1583698 ACTGATAGTC
* *
1583708 TGGATACGTCAACATGACATTGGTCTACATATAGTTAAGT
1 TGGATACGTCAACATGAAATTGGTCTACATATAATTAAGT
*
1583748 TGGATATGTCAACATGAAATTGGTCTACATATAATTAAGT
1 TGGATACGTCAACATGAAATTGGTCTACATATAATTAAGT
1583788 TGG
1 TGG
1583791 CACCATCGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (40 bp):
TGGATACGTCAACATGAAATTGGTCTACATATAATTAAGT
Found at i:1598450 original size:2 final size:2
Alignment explanation
Indices: 1598443--1598475 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1598433 AAGCTGCATT
1598443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1598476 GAGAATTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1599143 original size:2 final size:2
Alignment explanation
Indices: 1599136--1599172 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1599126 TCTGTGCTTT
1599136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1599173 TAAATTATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1599414 original size:2 final size:2
Alignment explanation
Indices: 1599409--1599467 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1599399 TAAACATTAG
1599409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1599451 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1599468 GATAAAGATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1601430 original size:14 final size:14
Alignment explanation
Indices: 1601395--1601432 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1601385 ATCGAAATTT
*
1601395 TAAATTTTAAAAAA
1 TAAATATTAAAAAA
*
1601409 TACA-ATTAAAAAA
1 TAAATATTAAAAAA
1601422 TAAATATTAAA
1 TAAATATTAAA
1601433 TCCACAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATATTAAAAAA
Found at i:1603779 original size:31 final size:31
Alignment explanation
Indices: 1603725--1603785 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1603715 ACAATTTGGT
* *
1603725 CACTGAATTATTTAAAAAATTTTATTTAAGC
1 CACTGAACTATTTAAAAAATTTTAATTAAGC
**
1603756 CACTGAACTATTTAAAATTTTTTAATTAAG
1 CACTGAACTATTTAAAAAATTTTAATTAAG
1603786 TCATTGGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (31 bp):
CACTGAACTATTTAAAAAATTTTAATTAAGC
Found at i:1612826 original size:25 final size:25
Alignment explanation
Indices: 1612792--1612841 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1612782 AAAAGTACTA
1612792 AAAGTGTTTGATGCATGTTCTTTGG
1 AAAGTGTTTGATGCATGTTCTTTGG
1612817 AAAGTGTTTGATGCATGTTCTTTGG
1 AAAGTGTTTGATGCATGTTCTTTGG
1612842 CATTGGTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.44
Consensus pattern (25 bp):
AAAGTGTTTGATGCATGTTCTTTGG
Found at i:1618179 original size:2 final size:2
Alignment explanation
Indices: 1618172--1618201 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1618162 AATTATTTTA
1618172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1618202 TTGTACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1624282 original size:42 final size:42
Alignment explanation
Indices: 1624234--1624313 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
1624224 TTATTCATCT
1624234 TAAATTTGACTTCAAAAATTAAAGCTATATTCGATTTTATTC
1 TAAATTTGACTTCAAAAATTAAAGCTATATTCGATTTTATTC
* * * *
1624276 TAAATTTGACTTGAAAATTTAAAGTTATATTCTATTTT
1 TAAATTTGACTTCAAAAATTAAAGCTATATTCGATTTT
1624314 GACTTAATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (42 bp):
TAAATTTGACTTCAAAAATTAAAGCTATATTCGATTTTATTC
Found at i:1629419 original size:48 final size:48
Alignment explanation
Indices: 1629326--1629421 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1629316 ATGCTTAAAG
1629326 TAAGCCACTTGTGAATATTTGTTAAGGAAAGAAAAGAAAAGCTTAGAT
1 TAAGCCACTTGTGAATATTTGTTAAGGAAAGAAAAGAAAAGCTTAGAT
1629374 TAAGCCACTTGTGAATATTTGTTAAGGAAAGAAAAGAAAAGCTTAGAT
1 TAAGCCACTTGTGAATATTTGTTAAGGAAAGAAAAGAAAAGCTTAGAT
1629422 CCCACATTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (48 bp):
TAAGCCACTTGTGAATATTTGTTAAGGAAAGAAAAGAAAAGCTTAGAT
Found at i:1633095 original size:25 final size:25
Alignment explanation
Indices: 1633061--1633110 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1633051 GTCTCATCGA
1633061 GTAGAATATGAAACCATAATAATAT
1 GTAGAATATGAAACCATAATAATAT
1633086 GTAGAATATGAAACCATAATAATAT
1 GTAGAATATGAAACCATAATAATAT
1633111 TATTCAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (25 bp):
GTAGAATATGAAACCATAATAATAT
Found at i:1636699 original size:2 final size:2
Alignment explanation
Indices: 1636692--1636723 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1636682 ACTTTAAGAA
1636692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1636724 GTCTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1640699 original size:567 final size:567
Alignment explanation
Indices: 1639625--1640765 Score: 2255
Period size: 567 Copynumber: 2.0 Consensus size: 567
1639615 GATTGAATCG
1639625 AAAAAAAACTGTCTAAAACCAGGTTTTTTGATTCTTTGGGTTATAGTTTTAATTTGTGGCTAATA
1 AAAAAAAACTGTCTAAAACCAGGTTTTTTGATTCTTTGGGTTATAGTTTTAATTTGTGGCTAATA
1639690 TTATTAAATTTTAGCCCAATTTTATCCAATCCTACTAATAACCTGTTGACCCATCTAGCAGAAGG
66 TTATTAAATTTTAGCCCAATTTTATCCAATCCTACTAATAACCTGTTGACCCATCTAGCAGAAGG
1639755 GGCTGTGCTGATTCTTTTGATATTTTCATGGGTTGCTTACCTCTTTTGTGGAGAGTCGAAATCAT
131 GGCTGTGCTGATTCTTTTGATATTTTCATGGGTTGCTTACCTCTTTTGTGGAGAGTCGAAATCAT
1639820 GGGCTGCTTACCTATGTAGAGGAAATGTAATGGTTGTGGAATTATGAAGGAGACGTTGGAATATC
196 GGGCTGCTTACCTATGTAGAGGAAATGTAATGGTTGTGGAATTATGAAGGAGACGTTGGAATATC
1639885 AAAAGAAAGAAAAGGTAATAACATTTACGAAGAGTTGAATATATATGGTTTAATTGGTGATGAAT
261 AAAAGAAAGAAAAGGTAATAACATTTACGAAGAGTTGAATATATATGGTTTAATTGGTGATGAAT
1639950 TTGGTTTTTAAAATATTTGTTTATAATTTGAATTTTTTGAGTTTGATGCACGTTTTTAACAATAA
326 TTGGTTTTTAAAATATTTGTTTATAATTTGAATTTTTTGAGTTTGATGCACGTTTTTAACAATAA
1640015 TTTAACAAATATTCATTTTATAGGTGTAGCGACGTAAAAATTTTGGTTTGGGGTCGCTAATTGGG
391 TTTAACAAATATTCATTTTATAGGTGTAGCGACGTAAAAATTTTGGTTTGGGGTCGCTAATTGGG
1640080 GCGATCTAGTGAAAAAGTTTGAAAACTGAAGTTCAATTTTGAAATAAAAAGGAGTCGCCACCGAT
456 GCGATCTAGTGAAAAAGTTTGAAAACTGAAGTTCAATTTTGAAATAAAAAGGAGTCGCCACCGAT
1640145 CCTTTTTTATAGGTGTGATCGGACACCTATTAAATCTATTTTTTAAA
521 CCTTTTTTATAGGTGTGATCGGACACCTATTAAATCTATTTTTTAAA
1640192 AAAAAAAACTGTCTAAAACCAGGTTTTTTGATTCTTTGGGTTATAGTTTTAATTTGTGGCTAATA
1 AAAAAAAACTGTCTAAAACCAGGTTTTTTGATTCTTTGGGTTATAGTTTTAATTTGTGGCTAATA
1640257 TTATTAAATTTTAGCCCAATTTTATCCAATCCTACTAATAACCTGTTGACCCATCTAGCAGAAGG
66 TTATTAAATTTTAGCCCAATTTTATCCAATCCTACTAATAACCTGTTGACCCATCTAGCAGAAGG
1640322 GGCTGTGCTGATTCTTTTGATATTTTCATGGGTTGCTTACCTCTTTTGTGGAGAGTCGAAATCAT
131 GGCTGTGCTGATTCTTTTGATATTTTCATGGGTTGCTTACCTCTTTTGTGGAGAGTCGAAATCAT
1640387 GGGCTGCTTACCTATGTAGAGGAAATGTAATGGTTGTGGAATTATGAAGGAGACGTTGGAATATC
196 GGGCTGCTTACCTATGTAGAGGAAATGTAATGGTTGTGGAATTATGAAGGAGACGTTGGAATATC
1640452 AAAAGAAAGAAAAGGTAATAACATTTACGAAGAGTTGAATATATATGGTTTAATTGGTGATGAAT
261 AAAAGAAAGAAAAGGTAATAACATTTACGAAGAGTTGAATATATATGGTTTAATTGGTGATGAAT
1640517 TTGGTTTTTAAAATATTTGTTTATAATTTGAATTTTTTGAGTTTGATGCACGTTTTTAACAATAA
326 TTGGTTTTTAAAATATTTGTTTATAATTTGAATTTTTTGAGTTTGATGCACGTTTTTAACAATAA
*
1640582 TTTAACAAATATTCATTTTATAGGTGTAGCGACGTAAAAATTTTGGTTTGGGGTTGCTAATTGGG
391 TTTAACAAATATTCATTTTATAGGTGTAGCGACGTAAAAATTTTGGTTTGGGGTCGCTAATTGGG
1640647 GCGATCTAGTGAAAAAGTTTGAAAACTGAAGTTCAATTTTGAAATAAAAAGGAGTCGCCACCGAT
456 GCGATCTAGTGAAAAAGTTTGAAAACTGAAGTTCAATTTTGAAATAAAAAGGAGTCGCCACCGAT
*
1640712 CCTTTTTTATAGGTGTGATCGGACACCTATTAAATCTATTTTTTTAA
521 CCTTTTTTATAGGTGTGATCGGACACCTATTAAATCTATTTTTTAAA
*
1640759 AACAAAA
1 AAAAAAA
1640766 GAAGGCTAAG
Statistics
Matches: 571, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
567 571 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (567 bp):
AAAAAAAACTGTCTAAAACCAGGTTTTTTGATTCTTTGGGTTATAGTTTTAATTTGTGGCTAATA
TTATTAAATTTTAGCCCAATTTTATCCAATCCTACTAATAACCTGTTGACCCATCTAGCAGAAGG
GGCTGTGCTGATTCTTTTGATATTTTCATGGGTTGCTTACCTCTTTTGTGGAGAGTCGAAATCAT
GGGCTGCTTACCTATGTAGAGGAAATGTAATGGTTGTGGAATTATGAAGGAGACGTTGGAATATC
AAAAGAAAGAAAAGGTAATAACATTTACGAAGAGTTGAATATATATGGTTTAATTGGTGATGAAT
TTGGTTTTTAAAATATTTGTTTATAATTTGAATTTTTTGAGTTTGATGCACGTTTTTAACAATAA
TTTAACAAATATTCATTTTATAGGTGTAGCGACGTAAAAATTTTGGTTTGGGGTCGCTAATTGGG
GCGATCTAGTGAAAAAGTTTGAAAACTGAAGTTCAATTTTGAAATAAAAAGGAGTCGCCACCGAT
CCTTTTTTATAGGTGTGATCGGACACCTATTAAATCTATTTTTTAAA
Found at i:1642050 original size:3 final size:3
Alignment explanation
Indices: 1642042--1642119 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
1642032 GTATATGCAT
1642042 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1642090 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1642120 TGAAAATACA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1642598 original size:21 final size:22
Alignment explanation
Indices: 1642574--1642623 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
1642564 TTAGGGAAGG
1642574 GGAGAAAGA-AAAAAAAGGAGA
1 GGAGAAAGAGAAAAAAAGGAGA
* *
1642595 GGAG-AAGAGAGAAAAGGGAGA
1 GGAGAAAGAGAAAAAAAGGAGA
1642616 GGAGAAAG
1 GGAGAAAG
1642624 GAGAGAGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (22 bp):
GGAGAAAGAGAAAAAAAGGAGA
Found at i:1643651 original size:44 final size:44
Alignment explanation
Indices: 1643566--1643653 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
1643556 GATGTACGCC
* * *
1643566 TTGTAGCTTCAATTCGCTCCAATGTAACTTCACGGATATGAGAT
1 TTGTAGCTTCAATTCACTCCAATGTAACTTCACGAAGATGAGAT
*
1643610 TTGTAGCTTCAATTTACTTCC-ATGTAACTTCA-GAAAGATGAGAT
1 TTGTAGCTTCAATTCAC-TCCAATGTAACTTCACG-AAGATGAGAT
1643654 CTACATCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 34 0.89
45 3 0.08
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (44 bp):
TTGTAGCTTCAATTCACTCCAATGTAACTTCACGAAGATGAGAT
Found at i:1643992 original size:54 final size:54
Alignment explanation
Indices: 1643871--1644072 Score: 235
Period size: 54 Copynumber: 3.7 Consensus size: 54
1643861 ATTGACTCCT
* ** ** *
1643871 AAGGCTCAACTCACTTCTCGCAATATGGGTTGATTTTTTTGAAAAACAAAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAATTGA--TTTTAAAAAAACAGAAATTAA
* * * *
1643927 AAGG-TATAACTCACCTCTCGCAATATGAGTTGCTTTTAAAAAAACAGCAATTAA
1 AAGGCT-CAACTCACCTCTCGCAATATGAATTGATTTTAAAAAAACAGAAATTAA
* **
1643981 AAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTGAAAAAGTAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTAAAAAAACAGAAATTAA
* *
1644035 AAGGTTCAACCCACCTCTCGCAATATGAATTGATTTTA
1 AAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTA
1644073 GATTTAATAG
Statistics
Matches: 126, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
54 97 0.77
55 2 0.02
56 27 0.21
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTAAAAAAACAGAAATTAA
Found at i:1644072 original size:108 final size:108
Alignment explanation
Indices: 1643871--1644072 Score: 282
Period size: 108 Copynumber: 1.9 Consensus size: 108
1643861 ATTGACTCCT
* **
1643871 AAGGCTCAACTCACTTCTCGCAATATGGGTTGATTTTTTTGAAAAACAAAAATTAAAAGGTATAA
1 AAGGCTCAACTCACCTCTCGCAATATGAATTGA--TTTTTGAAAAACAAAAATTAAAAGGTATAA
* * *
1643936 CTCACCTCTCGCAATATGAGTTGCTTTTAAAAAAACAGCAATTAA
64 CCCACCTCTCGCAATATGAATTGATTTTAAAAAAACAGCAATTAA
* *
1643981 AAGGCTCAACTCACCTCTCGCAATATGAATTGA-TTTTGAAAAAGTAGAAATTAAAAGGT-TCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTGAAAAA-CAAAAATTAAAAGGTAT-AA
1644044 CCCACCTCTCGCAATATGAATTGATTTTA
64 CCCACCTCTCGCAATATGAATTGATTTTA
1644073 GATTTAATAG
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
107 11 0.13
108 41 0.50
110 30 0.37
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (108 bp):
AAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTGAAAAACAAAAATTAAAAGGTATAACC
CACCTCTCGCAATATGAATTGATTTTAAAAAAACAGCAATTAA
Found at i:1644193 original size:71 final size:71
Alignment explanation
Indices: 1644040--1644287 Score: 327
Period size: 71 Copynumber: 3.5 Consensus size: 71
1644030 ATTAAAAGGT
* * * * * *
1644040 TCAACCCACCTCTCGCAATATGAATTGATTTTAGATTTA-ATAGGAATTGAAATTACGTCAGCGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGA--AACATA--AATTGAAATTACCTCAACGT
* ** *
1644104 GCCCCGAGGT
62 GTCTTGAGGC
*
1644114 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1644179 TGAGGC
66 TGAGGC
*
1644185 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTCAAATTACCTCAACGTGTCT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
1644250 TGAGGC
66 TGAGGC
* *
1644256 TCAACTCACCTTTCGCAATATGAGCTGATTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTT
1644288 CTTGGAAAAC
Statistics
Matches: 158, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
71 123 0.78
72 1 0.01
73 3 0.02
74 31 0.20
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (71 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCT
TGAGGC
Found at i:1661736 original size:77 final size:76
Alignment explanation
Indices: 1661450--1662447 Score: 1054
Period size: 70 Copynumber: 13.5 Consensus size: 76
1661440 CAAGTGACAG
*
1661450 AAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AATTTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCA
1661509 ATTTATGTTTC
66 ATTTATGTTTC
1661520 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AATTTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCA
1661579 ATTTATGTTTC
66 ATTTATGTTTC
*
1661590 AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGG-----T-AATTTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCA
1661649 ATTTATGTTTC
66 ATTTATGTTTC
*
1661660 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA-TTTC
1661725 AATTTATGTTTC
65 AATTTATGTTTC
*
1661737 AAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AATTTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCA
1661796 ATTTATGTTTC
66 ATTTATGTTTC
* *
1661807 AAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGG-----T-AATTTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCA
1661866 ATTTATGTTTC
66 ATTTATGTTTC
*
1661877 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA-TTTC
1661942 AATTTATGTTTC
65 AATTTATGTTTC
*
1661954 AAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AATTTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCA
1662013 ATTTATGTTTC
66 ATTTATGTTTC
** * * *
1662024 AAAAATCAACTC--A-T-----AGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAGTCTC
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA-----
*
1662081 TACTTTCTAATTTCTGTTCATC
60 -A-TTTC-AATTTATGTT--TC
* * *
1662103 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTC-AGCTCACACGCTGAGGTATTTTCA
1 ---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACACGTTGAGGTAATTTCA
*
1662167 ATTTCTGTTTTTCAATTTCTGTTCGTC
60 A--------TTTCAATTTATGTT--TC
1662194 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC-
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCA
*
1662258 ---TGT-TTTC
66 ATTTATGTTTC
1662265 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
*
1662330 ----TGT-TTTC
65 AATTTATGTTTC
** *
1662337 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
*
1662402 ----TGT-TTTC
65 AATTTATGTTTC
*
1662409 AAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1662448 GGTTCACATG
Statistics
Matches: 837, Mismatches: 35, Indels: 109
0.85 0.04 0.11
Matches are distributed among these distances:
63 26 0.03
68 1 0.00
69 2 0.00
70 334 0.40
71 21 0.03
72 137 0.16
73 32 0.04
74 6 0.01
75 3 0.00
76 8 0.01
77 139 0.17
78 4 0.00
79 2 0.00
81 12 0.01
83 1 0.00
84 1 0.00
85 1 0.00
86 18 0.02
88 37 0.04
89 17 0.02
91 31 0.04
92 4 0.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (76 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCA
ATTTATGTTTC
Found at i:1661818 original size:217 final size:218
Alignment explanation
Indices: 1661450--1662447 Score: 1286
Period size: 217 Copynumber: 4.5 Consensus size: 218
1661440 CAAGTGACAG
* *
1661450 AAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA-TTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1661508 AATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
66 AATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
1661573 ATTTCAATTTATGTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTT
131 ATTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTT
1661637 GAGGTAATTTCAATTTATGTTTC
196 GAGGTAATTTCAATTTATGTTTC
1661660 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
*
1661725 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
66 AATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
*
1661790 ATTTCAATTTATGTTTC-AAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAAGACACGTT
131 ATTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTT
1661854 GAGGTAATTTCAATTTATGTTTC
196 GAGGTAATTTCAATTTATGTTTC
1661877 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
*
1661942 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
66 AATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
* ** * *
1662007 ATTTCAATTTATGTTTCAAAAATCAACTC--A-T-----AGGTGAGTTGAGCCTCGGGGCACGCT
131 ATTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTT
*
1662064 GAGGTATTTTCAGTCTCTACTTTCTAATTTCTGTTCATC
196 GAGG-----T-A------A-TTTC-AATTTATGTT--TC
* ** * *
1662103 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCAA
1 ---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA--AAACACGTTGAGGTAATTTCAA
*
1662168 TTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAA
61 -------TTTTCAATTTATGTT--TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAA
* *
1662233 GACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
117 GACACGTTGAGGTAATTTCAATTTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAA
*
1662298 GCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC
181 GCCTCAAGACACGTTGAGGTAATTTCAATTTATG-TTTC
** * *
1662337 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAA-TTT
1 AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTT
* *
1662401 C----TGT-TTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC
65 CAATTTATGTTTC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1662448 GGTTCACATG
Statistics
Matches: 707, Mismatches: 30, Indels: 95
0.85 0.04 0.11
Matches are distributed among these distances:
210 74 0.10
215 5 0.01
216 4 0.01
217 339 0.48
218 13 0.02
222 5 0.01
223 4 0.01
224 9 0.01
226 2 0.00
229 37 0.05
230 19 0.03
231 22 0.03
232 31 0.04
234 2 0.00
235 8 0.01
236 6 0.01
237 1 0.00
238 14 0.02
240 66 0.09
241 16 0.02
243 2 0.00
244 2 0.00
249 26 0.04
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (218 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
AATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
ATTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTT
GAGGTAATTTCAATTTATGTTTC
Found at i:1661823 original size:147 final size:140
Alignment explanation
Indices: 1661450--1662038 Score: 971
Period size: 147 Copynumber: 4.1 Consensus size: 140
1661440 CAAGTGACAG
*
1661450 AAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1661515 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
66 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
1661580 TTTATGTTTC
131 TTTATGTTTC
*
1661590 AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
*
1661655 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAA
66 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA
1661720 TTTTCAATTTATGTTTC
125 -TTTCAATTTATGTTTC
*
1661737 AAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
* *
1661802 GTTTCAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGTAATTTCAA
66 GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
1661867 TTTATGTTTC
131 TTTATGTTTC
*
1661877 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACACGTTGAGGTAATTTCAATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG-----T-AA-TTTC
*
1661942 AATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
59 AATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
1662007 ATTTCAATTTATGTTTC
124 ATTTCAATTTATGTTTC
1662024 AAAAATCAACTCATA
1 -AAAATCAACTCATA
1662039 GGTGAGTTGA
Statistics
Matches: 421, Mismatches: 13, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
140 183 0.43
141 2 0.00
142 1 0.00
145 2 0.00
146 4 0.01
147 215 0.51
148 14 0.03
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (140 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
GTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
TTTATGTTTC
Found at i:1662180 original size:14 final size:14
Alignment explanation
Indices: 1662161--1662189 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1662151 CGCTGAGGTA
1662161 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
1662175 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
1662189 T
1 T
1662190 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:1662196 original size:91 final size:87
Alignment explanation
Indices: 1662038--1662263 Score: 278
Period size: 88 Copynumber: 2.6 Consensus size: 87
1662028 ATCAACTCAT
** * * * **
1662038 AGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAGTCTCT-ACTTTCTAATTTCTGTTCAT
1 AGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCTAATTTCTGTTCAT
1662102 CAAAAAAATCAACTCATATTGCGAG
66 C---AAAATCAACTCATATTGCGAG
*
1662127 AGGTGAGTTGAGTCTC-AGCTCACACGCTGAGGTATTTTCAATTTCTGTTTTTC-AATTTCTGTT
1 AGGTGAGTTGAGCCTCAAG---ACACGCTGAGGTATTTTCAATTTCTGTTTTTCTAATTTCTGTT
*
1662190 CGTCAAAATCAACTCATATTGCGAG
63 CATCAAAATCAACTCATATTGCGAG
* *
1662215 AGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTT
1 AGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTT
1662264 CAAAAATCAA
Statistics
Matches: 121, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
86 28 0.23
88 37 0.31
89 17 0.14
91 35 0.29
92 4 0.03
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (87 bp):
AGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCTAATTTCTGTTCAT
CAAAATCAACTCATATTGCGAG
Found at i:1662293 original size:72 final size:72
Alignment explanation
Indices: 1662176--1662526 Score: 474
Period size: 72 Copynumber: 4.7 Consensus size: 72
1662166 AATTTCTGTT
*
1662176 TTTCAATTTCTGTTCGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTCTGTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGT
1662240 TGAGGTAA
65 TGAGGTAA
1662248 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
1662313 GAGGTAA
66 GAGGTAA
* **
1662320 TTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
*
1662385 GAGGTAT
66 GAGGTAA
* *
1662392 TTTCAATTTCTGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACA
1 TTTCAATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACA
* *
1662456 TGCTGAGGT-A
62 CGTTGAGGTAA
1662466 TTCTCAATTTCTGTCTTTCAAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TT-TCAATTTCTGT-TTTC-------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1662527 TTCAGATCAC
Statistics
Matches: 252, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
71 2 0.01
72 154 0.61
73 34 0.13
74 2 0.01
75 21 0.08
76 4 0.02
82 35 0.14
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (72 bp):
TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
GAGGTAA
Found at i:1662519 original size:387 final size:378
Alignment explanation
Indices: 1661791--1662551 Score: 1018
Period size: 387 Copynumber: 2.0 Consensus size: 378
1661781 GTTGAGGTAA
*
1661791 TTTCAATTTATGTTTCAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAAGACACGTTGA
1 TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGA
1661856 GGTAATTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACAC
66 GGTAATTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACAC
**
1661921 GTTGAGGTAATTTCAATTTTCAATTTATGTTTCAAAATCAACTCATATGGCGAGAGGTGAGTTGA
131 GTTGAGGTAATTTCAATTTTC-A--TATGTTTCAAAATCAACTCATATGGCGAGAAATGAGTTGA
*
1661986 GCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATCAACTCATAGGTGAGTTGAGC
193 GCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATCAACTCAGAGGTGAGTTGAGC
* * * ** **
1662051 CTCGGGGCACGCTGAGGTATTTTCAGTCTCTACTTTCTAATTTCTGTTCATCAAAAAAATCAACT
258 CTCGGGGCACGCTGAGGTATTCTCAATCTCTACTGTC--ATTTC--TAAAAAAAAAAAATCAACT
* *
1662116 CATATTGCGAGAGGTGAGTTGAG-TCTCAGCTCACACGCTGAGGTATTTTCAATTTCTGTT
319 CATATTGCGAGAGGTGAGTTGAGCT-TCAGATCACACACTGAGGTATTTTCAATTTCTGTT
* *
1662176 TTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
1 TTTCAATTTATGTT--TCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTT
* *
1662241 GAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
64 GAGGTAATTTCAATTTATG-TTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAA
* *
1662306 ACACGTTGAGGTAATTTCAA-TTTC-TGT-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTT
127 ACACGTTGAGGTAATTTCAATTTTCATATGTTTCAAAA-TCAACTCATATGGCGAGAAATGAGTT
* *
1662368 GAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAAAAAATCAACTTATATTGCGAGA
191 GAGCCTCAAGACACGTTGAGGTAATTTCAATTTATG-TTTC-AAAAATCAAC------T-C-AGA
**
1662433 GGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTCTCAAT-T-T-CTGTC-TTTC-AAAAAAAA
246 GGTGAGTTGAGCCTCGGGGCAC--GCTGAGGTATTCTCAATCTCTACTGTCATTTCTAAAAAAAA
*
1662493 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGTGGTATTTT
309 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTT
1662552 TTCAATTTAC
Statistics
Matches: 334, Mismatches: 24, Indels: 34
0.85 0.06 0.09
Matches are distributed among these distances:
383 8 0.02
384 59 0.18
385 17 0.05
386 10 0.03
387 123 0.37
388 9 0.03
389 59 0.18
390 4 0.01
392 1 0.00
393 5 0.01
394 23 0.07
395 1 0.00
396 15 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (378 bp):
TTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGA
GGTAATTTCAATTTATGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAACAC
GTTGAGGTAATTTCAATTTTCATATGTTTCAAAATCAACTCATATGGCGAGAAATGAGTTGAGCC
TCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAAATCAACTCAGAGGTGAGTTGAGCCTC
GGGGCACGCTGAGGTATTCTCAATCTCTACTGTCATTTCTAAAAAAAAAAAATCAACTCATATTG
CGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTCAATTTCTGTT
Found at i:1662924 original size:44 final size:45
Alignment explanation
Indices: 1662841--1662939 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 45
1662831 TGAAGTTGTT
* *
1662841 AATCTTATAT-TTCTGAAGTCACAGTAAAGCAGATCGAAGCTACA
1 AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
* * ** *
1662885 AATCTTATATCCT-TGAAGTTACATTAAAGTGGATTGAAGCCACA
1 AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
* *
1662929 AAGCATATATC
1 AATCTTATATC
1662940 AGAAGATGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (45 bp):
AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
Found at i:1663290 original size:35 final size:35
Alignment explanation
Indices: 1663251--1663321 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1663241 CACTTGCCTC
*
1663251 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
*
1663286 TTCCCATTCTCCCATGCTGTCTGCCACCAACACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
1663321 T
1 T
1663322 CACACACCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.18, C:0.46, G:0.10, T:0.25
Consensus pattern (35 bp):
TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
Found at i:1663795 original size:32 final size:29
Alignment explanation
Indices: 1663724--1663810 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 29
1663714 AAAGAGGGGA
*
1663724 AGCAAAAAAAAAATCCAGCAAAAAATTCC
1 AGCAAAAAAAAAATCCAGAAAAAAATTCC
* *
1663753 AGCACCAAAAAAAATTTCCAGAAAAAAATTTTC
1 AGCA--AAAAAAAA-ATCCAGAAAAAAA-TTCC
*
1663786 AGCAAAAAAAAAA-CCAAAAAAAAAT
1 AGCAAAAAAAAAATCCAGAAAAAAAT
1663811 AGAACGACCC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.02
29 14 0.29
31 16 0.33
32 11 0.22
33 7 0.14
ACGTcount: A:0.64, C:0.17, G:0.06, T:0.13
Consensus pattern (29 bp):
AGCAAAAAAAAAATCCAGAAAAAAATTCC
Found at i:1664080 original size:11 final size:11
Alignment explanation
Indices: 1664055--1664092 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1664045 CGACCGGATT
*
1664055 TCCCTTC-CCC
1 TCCCTTCTCTC
1664065 TCCCTTCTCTC
1 TCCCTTCTCTC
1664076 TCCCTTCTCTC
1 TCCCTTCTCTC
1664087 TTCCCT
1 -TCCCT
1664093 CTTTCTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 7 0.28
11 13 0.52
12 5 0.20
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (11 bp):
TCCCTTCTCTC
Found at i:1664638 original size:2 final size:2
Alignment explanation
Indices: 1664631--1664755 Score: 61
Period size: 2 Copynumber: 65.5 Consensus size: 2
1664621 CTAATATGTG
* *
1664631 TA TA TA TA TA TA TA TA TA T- TA TG TG TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1664671 T- TA TG TA TA TA TG TCA T- TA GT- TA TA TA TT TC T- TA TG TA TA
1 TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
1664711 TA T- TC T- TA AA TA CTA T- TA TA TA CA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1664751 TA TA T
1 TA TA T
1664756 TTTAAATTCC
Statistics
Matches: 95, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
1 9 0.09
2 82 0.86
3 4 0.04
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1664696 original size:31 final size:30
Alignment explanation
Indices: 1664631--1664713 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
1664621 CTAATATGTG
* *
1664631 TATATATATATA-TATATAT-TATGTGTAT
1 TATATATATATATTATGTATATATGTGCAT
1664659 TATATATATATATTATGTATATATGT-CAT
1 TATATATATATATTATGTATATATGTGCAT
* *
1664688 TAGTTATATATTTCTTATGTATATAT
1 TA--TATATATATATTATGTATATAT
1664714 TCTTAAATAC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.26
29 10 0.21
30 5 0.11
31 20 0.43
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.54
Consensus pattern (30 bp):
TATATATATATATTATGTATATATGTGCAT
Found at i:1665982 original size:15 final size:17
Alignment explanation
Indices: 1665964--1665995 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1665954 AATTTATGAA
1665964 ATATA-ATAAAA-TAAT
1 ATATATATAAAAGTAAT
1665979 ATATATATAAAAGTAAT
1 ATATATATAAAAGTAAT
1665996 GAAACAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 6 0.40
17 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
ATATATATAAAAGTAAT
Found at i:1666371 original size:38 final size:40
Alignment explanation
Indices: 1666304--1666383 Score: 110
Period size: 38 Copynumber: 2.0 Consensus size: 40
1666294 TGAAATAAAT
1666304 AATAATAATTTAAAAAGAAATAAAGTTAGAATAAAAATAA
1 AATAATAATTTAAAAAGAAATAAAGTTAGAATAAAAATAA
* * * *
1666344 AATAA-AATTTAGAAAGGATTAAA-TTAGAATAGAAATAA
1 AATAATAATTTAAAAAGAAATAAAGTTAGAATAAAAATAA
1666382 AA
1 AA
1666384 ATACAGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 16 0.44
39 15 0.42
40 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (40 bp):
AATAATAATTTAAAAAGAAATAAAGTTAGAATAAAAATAA
Found at i:1666385 original size:39 final size:41
Alignment explanation
Indices: 1666295--1666386 Score: 118
Period size: 39 Copynumber: 2.3 Consensus size: 41
1666285 ACAAAATATT
1666295 GAAATAAATAATAATAATTTAAAAAGAAATAAAGTTAGAATA
1 GAAATAAA-AATAATAATTTAAAAAGAAATAAAGTTAGAATA
* * * *
1666337 AAAAT-AAAATAA-AATTTAGAAAGGATTAAA-TTAGAATA
1 GAAATAAAAATAATAATTTAAAAAGAAATAAAGTTAGAATA
1666375 GAAATAAAAATA
1 GAAATAAAAATA
1666387 CAGATGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 12 0.27
39 21 0.48
40 5 0.11
41 2 0.05
42 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (41 bp):
GAAATAAAAATAATAATTTAAAAAGAAATAAAGTTAGAATA
Found at i:1667615 original size:13 final size:13
Alignment explanation
Indices: 1667599--1667631 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1667589 CTTTGTACAC
1667599 GGACTTTTTTAAT
1 GGACTTTTTTAAT
1667612 GGAC-TTTTTAAT
1 GGACTTTTTTAAT
1667624 GGACTTTT
1 GGACTTTT
1667632 AAAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (13 bp):
GGACTTTTTTAAT
Found at i:1670313 original size:30 final size:30
Alignment explanation
Indices: 1670256--1670313 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1670246 AATCCCGAGC
*
1670256 TTAGGGGCAAAAATGTAAATATGCAAAAGT
1 TTAGGGGCAAAAATGTAAATATCCAAAAGT
* * *
1670286 TTAGGGGCAAAATTGTAATTTTCCAAAA
1 TTAGGGGCAAAAATGTAAATATCCAAAA
1670314 TTTGAGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (30 bp):
TTAGGGGCAAAAATGTAAATATCCAAAAGT
Found at i:1670783 original size:46 final size:46
Alignment explanation
Indices: 1670733--1670907 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
1670723 TGGTTGAGCA
1670733 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
1670779 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
1670824 CATCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
1670871 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1670908 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 23 0.21
46 50 0.47
47 23 0.21
49 3 0.03
50 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1670888 original size:92 final size:93
Alignment explanation
Indices: 1670730--1670900 Score: 299
Period size: 92 Copynumber: 1.8 Consensus size: 93
1670720 GGATGGTTGA
* *
1670730 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1670795 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
1670823 GCATCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1670887 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
1670901 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 51 0.69
93 23 0.31
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:1677840 original size:30 final size:30
Alignment explanation
Indices: 1677784--1677840 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1677774 AATCCCGAGC
*
1677784 TAGGGGCAAAAATGTAAATATGCAAAAGTT
1 TAGGGGCAAAAATGTAAATATCCAAAAGTT
* * *
1677814 TAGGGGCAAAATTGTAATTTTCCAAAA
1 TAGGGGCAAAAATGTAAATATCCAAAA
1677841 TTTGAGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAAATATCCAAAAGTT
Found at i:1678312 original size:46 final size:46
Alignment explanation
Indices: 1678262--1678437 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
1678252 TGGTTGAGCA
1678262 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
1678308 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* **
1678353 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
1678401 CCCGAGCTCGTTGAGTTGAGTCCAAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1678438 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 63 0.59
47 28 0.26
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1678418 original size:93 final size:93
Alignment explanation
Indices: 1678259--1678430 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
1678249 GGATGGTTGA
***
1678259 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
*
1678324 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCAAGTTCGTGAAATGTAACTAG
* *
1678352 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
1678417 TGAGTCCAAGTTCG
66 TGAGTCCAAGTTCG
1678431 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAAATGTAACTAG
Found at i:1680288 original size:2 final size:2
Alignment explanation
Indices: 1680281--1680310 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1680271 CATATGCATG
1680281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1680311 GGCTTACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1682473 original size:31 final size:31
Alignment explanation
Indices: 1682411--1682476 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1682401 AATAGCTCAA
* *
1682411 TGACTTAAATAAAAACTTTTGAATAAGTTAG
1 TGACTTAAATAAAAACTTTTCAAAAAGTTAG
*
1682442 TGACTTAAATGAAAAC-TTTCAAAAAGTTTAG
1 TGACTTAAATAAAAACTTTTCAAAAAG-TTAG
1682473 TGAC
1 TGAC
1682477 CAAATTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTCAAAAAGTTAG
Found at i:1688818 original size:4 final size:4
Alignment explanation
Indices: 1688809--1688838 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1688799 TTTGGGAGGT
1688809 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1688839 GTATGTGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1688874 original size:23 final size:23
Alignment explanation
Indices: 1688844--1688890 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1688834 TTATTGTATG
1688844 TGTGAAGCATATTATGAGAGAAA
1 TGTGAAGCATATTATGAGAGAAA
1688867 TGTGAAGCATATTATGAGAGAAA
1 TGTGAAGCATATTATGAGAGAAA
1688890 T
1 T
1688891 CTTGTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (23 bp):
TGTGAAGCATATTATGAGAGAAA
Found at i:1692777 original size:19 final size:19
Alignment explanation
Indices: 1692753--1692792 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1692743 AGTTTACTCT
1692753 TTAATCTAATGTACAAGGA
1 TTAATCTAATGTACAAGGA
1692772 TTAATCTAATGTACAAGGA
1 TTAATCTAATGTACAAGGA
1692791 TT
1 TT
1692793 GACTTACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
TTAATCTAATGTACAAGGA
Found at i:1707718 original size:8 final size:8
Alignment explanation
Indices: 1707707--1707748 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
1707697 GATAATAAAA
1707707 TTATAATT
1 TTATAATT
*
1707715 TTATCATT
1 TTATAATT
1707723 TTA-ATATT
1 TTATA-ATT
1707731 TTATAATT
1 TTATAATT
1707739 TTATAATT
1 TTATAATT
1707747 TT
1 TT
1707749 TAAATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 29 0.97
9 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATAATT
Found at i:1708882 original size:18 final size:18
Alignment explanation
Indices: 1708859--1708933 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
1708849 ACCGTTTACG
1708859 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
1708877 GTACTATTCACGTATACG
1 GTACTATTCACGTATACA
* * * *
1708895 GCACTATTTACGAATACG
1 GTACTATTCACGTATACA
*
1708913 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
1708931 GTA
1 GTA
1708934 GTTGGGATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:1714891 original size:12 final size:12
Alignment explanation
Indices: 1714874--1714899 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1714864 TCACTCGTGG
1714874 CAATCTTTTCAT
1 CAATCTTTTCAT
1714886 CAATCTTTTCAT
1 CAATCTTTTCAT
1714898 CA
1 CA
1714900 TTAGGGTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (12 bp):
CAATCTTTTCAT
Found at i:1725468 original size:33 final size:30
Alignment explanation
Indices: 1725408--1725477 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
1725398 AAGAAAATAT
*
1725408 ATATATATATATATAAATAATAGTATTAGAA
1 ATATATATATATATAAATAATAATATTA-AA
* *
1725439 ATCATATAGTATATATAACTGATAATATTAAA
1 AT-ATATA-TATATATAAATAATAATATTAAA
1725471 ATATATA
1 ATATATA
1725478 CATAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 9 0.26
33 18 0.53
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
ATATATATATATATAAATAATAATATTAAA
Found at i:1725702 original size:3 final size:3
Alignment explanation
Indices: 1725694--1725741 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1725684 ACAAGGATAT
1725694 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1725742 TTGAAACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1725867 original size:3 final size:3
Alignment explanation
Indices: 1725847--1725922 Score: 134
Period size: 3 Copynumber: 25.3 Consensus size: 3
1725837 AATGTATTTC
* *
1725847 AAT AAC AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1725895 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1725923 TTGAAATGCA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1726426 original size:11 final size:12
Alignment explanation
Indices: 1726396--1726427 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1726386 AAAGAAAAAA
1726396 AAGAGAG-AGGG
1 AAGAGAGAAGGG
1726407 AAGAGAGAAGGG
1 AAGAGAGAAGGG
1726419 -AGAGAGAAG
1 AAGAGAGAAG
1726428 AGAGGGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (12 bp):
AAGAGAGAAGGG
Found at i:1726573 original size:11 final size:12
Alignment explanation
Indices: 1726539--1726565 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1726529 TATATATATA
1726539 TTTGTATATTTT
1 TTTGTATATTTT
1726551 TTTGTATATTTT
1 TTTGTATATTTT
1726563 TTT
1 TTT
1726566 TATGTTTTAA
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:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTGTATATTTT
Found at i:1726985 original size:35 final size:34
Alignment explanation
Indices: 1726932--1727013 Score: 128
Period size: 35 Copynumber: 2.4 Consensus size: 34
1726922 GCAGGTGCGG
* *
1726932 TGGGAGTGTGTGATGGTGCTGGTGGCAGACAGCA
1 TGGGAGAGTGGGATGGTGCTGGTGGCAGACAGCA
1726966 TGGGAGAGTGGGAGTGGTGCTGGTGGCAGACAGCA
1 TGGGAGAGTGGGA-TGGTGCTGGTGGCAGACAGCA
*
1727001 TAGGAGAGTGGGA
1 TGGGAGAGTGGGA
1727014 AGAGGCAAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 11 0.25
35 33 0.75
ACGTcount: A:0.21, C:0.10, G:0.50, T:0.20
Consensus pattern (34 bp):
TGGGAGAGTGGGATGGTGCTGGTGGCAGACAGCA
Found at i:1729944 original size:76 final size:75
Alignment explanation
Indices: 1729854--1730250 Score: 352
Period size: 76 Copynumber: 5.2 Consensus size: 75
1729844 TATCGTGACT
* * ** *
1729854 TTCGGTTTTTTAACAATTCGCTTGATTTAATCTCGTGA-TAGTCATTTTTATGGTCTGTTGATTT
1 TTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACT-GTCATTTTTACGGTCTGTT-ATTT
*
1729918 AAGATTG-AGACC
64 AAGATCGCA-ACC
* * * * * * * *
1729930 ATCGGTTTTCTAACAATTTG-TTGATTTAATATTGCAACTGTCATTTTTACGATCCGCTTATCTA
1 TTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCATTTTTACGGTCTG-TTATTTA
1729994 AGATCGCAACC
65 AGATCGCAACC
* * * **
1730005 TTTGATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTGTCATTTTTACGGTCTGCTTATTTA
1 TTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCATTTTTACGGTCTG-TTATTTA
* **
1730070 AGATTGTGACC
65 AGATCGCAACC
* * * ** * *
1730081 TTCGATTTTCTAACAGTTCACTTGCTTTAATCTCGCAACTACCATTTTTACGGTCCGCTAATTTA
1 TTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCATTTTTACGGTCTG-TTATTTA
*
1730146 ATATCGCAACC
65 AGATCGCAACC
* * * *
1730157 TTCAGTTTTCTAATAGTACGCTTGATTTAATCTCGCAACTGTCATTTTTATGG-CTCGTTGATTT
1 TTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCATTTTTACGGTCT-GTT-ATTT
* * * *
1730221 AATATCACGACT
64 AAGATCGCAACC
1730233 TTCGGTTTTCTAACAGTT
1 TTCGGTTTTCTAACAGTT
1730251 TGCTAATTCA
Statistics
Matches: 258, Mismatches: 57, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
75 57 0.22
76 201 0.78
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (75 bp):
TTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCATTTTTACGGTCTGTTATTTAA
GATCGCAACC
Done.