Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 43 of 193
Found at i:13089686 original size:47 final size:47
Alignment explanation
Indices: 13089597--13089686 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
13089587 TGTGTGTATA
* *
13089597 CCATTTTGGTATATAAATATATATTTTGTACTATTTTAGTAAATAAC
1 CCATTTTGATATATAAATATATATTTTGTACTATATTAGTAAATAAC
* * * *
13089644 CCATTTTGATATTTAATTAT-TATTTTTGTATTATATTGGTAAA
1 CCATTTTGATATATAAATATATA-TTTTGTACTATATTAGTAAA
13089687 CTTATGTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 2 0.06
47 34 0.94
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (47 bp):
CCATTTTGATATATAAATATATATTTTGTACTATATTAGTAAATAAC
Found at i:13091532 original size:45 final size:45
Alignment explanation
Indices: 13091461--13091549 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
13091451 CCCTAGCTCA
* *
13091461 TCAAGCCAAAGATATCAGCCTTAGTTTGACGAGCGACCGCAATAG
1 TCAAGCCAAAGATATCAGCCTGAGTTTGACGAGCCACCGCAATAG
* *
13091506 TCAAGCCAAGGATATCAGGCTGAGTTTGACGAGCCACCGCAATA
1 TCAAGCCAAAGATATCAGCCTGAGTTTGACGAGCCACCGCAATA
13091550 CTCTACTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCCTGAGTTTGACGAGCCACCGCAATAG
Found at i:13091871 original size:28 final size:28
Alignment explanation
Indices: 13091846--13091904 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
13091836 CTTGACTTGG
*
13091846 AACCATAAATCTTAAACCTTAAACTTAA
1 AACCATAAACCTTAAACCTTAAACTTAA
* * * *
13091874 AACCCTAAACCTTAAATCTTATACATAA
1 AACCATAAACCTTAAACCTTAAACTTAA
13091902 AAC
1 AAC
13091905 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (28 bp):
AACCATAAACCTTAAACCTTAAACTTAA
Found at i:13093219 original size:14 final size:14
Alignment explanation
Indices: 13093200--13093228 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13093190 CTAATTGCCG
13093200 CAATAATACCCTTC
1 CAATAATACCCTTC
13093214 CAATAATACCCTTC
1 CAATAATACCCTTC
13093228 C
1 C
13093229 CTCTATCAGA
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:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (14 bp):
CAATAATACCCTTC
Found at i:13094937 original size:4 final size:4
Alignment explanation
Indices: 13094917--13094982 Score: 80
Period size: 4 Copynumber: 16.2 Consensus size: 4
13094907 AACACATTAC
* * *
13094917 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
13094965 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
13094983 CCATTTATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
3 3 0.06
4 44 0.81
5 7 0.13
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:13094956 original size:21 final size:21
Alignment explanation
Indices: 13094924--13094983 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
13094914 TACCTTTCTT
13094924 TCCTTC-TTCTTTCTTTCCTC
1 TCCTTCTTTCTTTCTTTCCTC
*
13094944 TCCTTCTTTCTTTCTTT-CTT
1 TCCTTCTTTCTTTCTTTCCTC
*
13094964 TCTTTTCTTTCTTTCTTTCC
1 TC-CTTCTTTCTTTCTTTCC
13094984 CATTTATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.29
21 24 0.69
22 1 0.03
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
TCCTTCTTTCTTTCTTTCCTC
Found at i:13094981 original size:17 final size:16
Alignment explanation
Indices: 13094917--13094982 Score: 80
Period size: 17 Copynumber: 4.1 Consensus size: 16
13094907 AACACATTAC
*
13094917 CTTTCTTTCCTTC-TT
1 CTTTCTTTCTTTCTTT
* *
13094932 CTTTCTTTCCTCTCCTT
1 CTTTCTTT-CTTTCTTT
13094949 CTTTCTTTCTTTCTTT
1 CTTTCTTTCTTTCTTT
13094965 CTTTTCTTTCTTTCTTT
1 C-TTTCTTTCTTTCTTT
13094982 C
1 C
13094983 CCATTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
15 8 0.18
16 10 0.23
17 26 0.59
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
CTTTCTTTCTTTCTTT
Found at i:13098372 original size:38 final size:40
Alignment explanation
Indices: 13098321--13098414 Score: 93
Period size: 40 Copynumber: 2.4 Consensus size: 40
13098311 CTTTTCTGCC
* * * * *
13098321 TTTTCGTTAGATATCCATTTT-GA-ATGTCTTTTTTAACT
1 TTTTCATTTGATATCCATTTTAGATATATCTTTTTCAACA
* *
13098359 TTTTCATTTGATATTCGTTTTAGATATATCTTTTTCAACA
1 TTTTCATTTGATATCCATTTTAGATATATCTTTTTCAACA
* *
13098399 TTTTCATGTGTTATCC
1 TTTTCATTTGATATCC
13098415 CTTTCGATCA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
38 17 0.39
39 2 0.05
40 25 0.57
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (40 bp):
TTTTCATTTGATATCCATTTTAGATATATCTTTTTCAACA
Found at i:13100980 original size:21 final size:21
Alignment explanation
Indices: 13100956--13101005 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
13100946 TGTTCATACA
*
13100956 TCTTTCTTTCTGTTTTTATTC
1 TCTTTCTTTCTATTTTTATTC
* *
13100977 TC-TTCTTTTTATTTTTTTTC
1 TCTTTCTTTCTATTTTTATTC
*
13100997 TTTTTCTTT
1 TCTTTCTTT
13101006 TTCCTTCCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (21 bp):
TCTTTCTTTCTATTTTTATTC
Found at i:13101465 original size:21 final size:21
Alignment explanation
Indices: 13101439--13101484 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
13101429 CCTACAAGGT
* *
13101439 CACACGGTCGTGTGGCTCTCC
1 CACACGCTCGTGTGGCCCTCC
*
13101460 CACACGCTCGTGTGGCCCTTC
1 CACACGCTCGTGTGGCCCTCC
13101481 CACA
1 CACA
13101485 GGCCCATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.41, G:0.24, T:0.22
Consensus pattern (21 bp):
CACACGCTCGTGTGGCCCTCC
Found at i:13102476 original size:32 final size:32
Alignment explanation
Indices: 13102405--13102584 Score: 175
Period size: 32 Copynumber: 5.6 Consensus size: 32
13102395 ATCATTATAC
* * * *
13102405 AGTAAGCTCGTATGACCTAATCAAT-TAGTAAAC
1 AGTATGCTCGTAAGAGCT-ATCAATCT-GTAAAT
* * *
13102438 AATATGCTCGTAAGAACTATCAATCTATAAAT
1 AGTATGCTCGTAAGAGCTATCAATCTGTAAAT
* *
13102470 AGTATGCTTGTAAGAGCTATCAATCTGT-GAT
1 AGTATGCTCGTAAGAGCTATCAATCTGTAAAT
* *
13102501 CAGTATGCTCGTAAGAGCTATCAATTTGTGAAT
1 -AGTATGCTCGTAAGAGCTATCAATCTGTAAAT
* * * * *
13102534 AGTATGCTTGTAAGAGCTGTCAATTTGTGAAC
1 AGTATGCTCGTAAGAGCTATCAATCTGTAAAT
13102566 AGTATGCTCGTAAGAGCTA
1 AGTATGCTCGTAAGAGCTA
13102585 GCCCATCCAA
Statistics
Matches: 125, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
31 2 0.02
32 106 0.85
33 17 0.14
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (32 bp):
AGTATGCTCGTAAGAGCTATCAATCTGTAAAT
Found at i:13102557 original size:96 final size:97
Alignment explanation
Indices: 13102404--13102584 Score: 220
Period size: 96 Copynumber: 1.9 Consensus size: 97
13102394 AATCATTATA
*
13102404 CAGTAAGCTCGTATGACCTAATCAATTAGTAAACAATATGCTCGTAAGAACTATCAATCTATAAA
1 CAGTAAGCTCGTAAGACCTAATCAATTAGTAAACAATATGCTCGTAAGAACTATCAATCTATAAA
* *
13102469 TAGTATGCTTGTAAGAGCTATCAATCTGTGAT
66 CAGTATGCTCGTAAGAGCTATCAATCTGTGAT
* * * * * * * * * * * *
13102501 CAGTATGCTCGTAAGAGCT-ATCAATTTGTGAATAGTATGCTTGTAAGAGCTGTCAATTTGTGAA
1 CAGTAAGCTCGTAAGACCTAATCAATTAGTAAACAATATGCTCGTAAGAACTATCAATCTATAAA
13102565 CAGTATGCTCGTAAGAGCTA
66 CAGTATGCTCGTAAGAGCTA
13102585 GCCCATCCAA
Statistics
Matches: 69, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
96 53 0.77
97 16 0.23
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (97 bp):
CAGTAAGCTCGTAAGACCTAATCAATTAGTAAACAATATGCTCGTAAGAACTATCAATCTATAAA
CAGTATGCTCGTAAGAGCTATCAATCTGTGAT
Found at i:13102581 original size:64 final size:64
Alignment explanation
Indices: 13102424--13102584 Score: 232
Period size: 64 Copynumber: 2.5 Consensus size: 64
13102414 GTATGACCTA
* * * *
13102424 ATCAATTAGTAAACAATATGCTCGTAAGAACTATCAATCTATAAATAGTATGCTTGTAAGAGCT
1 ATCAATTTGTGAACAGTATGCTCGTAAGAGCTATCAATCTATAAATAGTATGCTTGTAAGAGCT
* * * * *
13102488 ATCAATCTGTGATCAGTATGCTCGTAAGAGCTATCAATTTGTGAATAGTATGCTTGTAAGAGCT
1 ATCAATTTGTGAACAGTATGCTCGTAAGAGCTATCAATCTATAAATAGTATGCTTGTAAGAGCT
*
13102552 GTCAATTTGTGAACAGTATGCTCGTAAGAGCTA
1 ATCAATTTGTGAACAGTATGCTCGTAAGAGCTA
13102585 GCCCATCCAA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 85 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (64 bp):
ATCAATTTGTGAACAGTATGCTCGTAAGAGCTATCAATCTATAAATAGTATGCTTGTAAGAGCT
Found at i:13102625 original size:34 final size:34
Alignment explanation
Indices: 13102580--13102805 Score: 224
Period size: 34 Copynumber: 6.6 Consensus size: 34
13102570 TGCTCGTAAG
*
13102580 AGCTAGCCCATCCAACACACCATATACTCATGTA
1 AGCTAACCCATCCAACACACCATATACTCATGTA
* *
13102614 AGCTAATCCATCCAACACACCATATACTCATGTG
1 AGCTAACCCATCCAACACACCATATACTCATGTA
* * ** *
13102648 AGCTAACCCGTCCCACACACCATATGGTCAT-AA
1 AGCTAACCCATCCAACACACCATATACTCATGTA
* * * * * *
13102681 GAGTTAACCCGTCCAACACACCATATGCTCGTATG
1 -AGCTAACCCATCCAACACACCATATACTCATGTA
* *
13102716 AGTTAACCCATCCAACACACCATATGCTC--GTA
1 AGCTAACCCATCCAACACACCATATACTCATGTA
* *
13102748 AGAACTAACCCATCCAACACACCATATACTCATATG
1 AG--CTAACCCATCCAACACACCATATACTCATGTA
**
13102784 AGCTAGTCCATCCAACACACCA
1 AGCTAACCCATCCAACACACCA
13102806 AATATACAGC
Statistics
Matches: 161, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.02
34 155 0.96
36 3 0.02
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.20
Consensus pattern (34 bp):
AGCTAACCCATCCAACACACCATATACTCATGTA
Found at i:13102667 original size:68 final size:68
Alignment explanation
Indices: 13102579--13102805 Score: 271
Period size: 68 Copynumber: 3.3 Consensus size: 68
13102569 ATGCTCGTAA
* * *
13102579 GAGCTAGCCCATCCAACACACCATATACTCATGTAAGCTAATCCATCCAACACACCATATACTCA
1 GAGCTAACCCATCCAACACACCATATGCTCATGTAAGCTAACCCATCCAACACACCATATACTCA
*
13102644 TGT
66 TAT
* * * * * * *
13102647 GAGCTAACCCGTCCCACACACCATATGGTCAT-AAGAGTTAACCCGTCCAACACACCATATGCTC
1 GAGCTAACCCATCCAACACACCATATGCTCATGTA-AGCTAACCCATCCAACACACCATATACTC
*
13102711 GTAT
65 ATAT
*
13102715 GAGTTAACCCATCCAACACACCATATGCTC--GTAAGAACTAACCCATCCAACACACCATATACT
1 GAGCTAACCCATCCAACACACCATATGCTCATGTAAG--CTAACCCATCCAACACACCATATACT
13102778 CATAT
64 CATAT
**
13102783 GAGCTAGTCCATCCAACACACCA
1 GAGCTAACCCATCCAACACACCA
13102806 AATATACAGC
Statistics
Matches: 131, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
66 2 0.02
67 2 0.02
68 127 0.97
ACGTcount: A:0.35, C:0.34, G:0.11, T:0.20
Consensus pattern (68 bp):
GAGCTAACCCATCCAACACACCATATGCTCATGTAAGCTAACCCATCCAACACACCATATACTCA
TAT
Found at i:13102756 original size:102 final size:102
Alignment explanation
Indices: 13102576--13102805 Score: 271
Period size: 102 Copynumber: 2.3 Consensus size: 102
13102566 AGTATGCTCG
* * *
13102576 TAAGAGCTAGCCCATCCAACACACCATATACTCATGTAAGCTAATCCATCCAACACACCATATAC
1 TAAGAGCTAACCCATCCAACACACCATATACTCATATAAGCTAACCCATCCAACACACCATATAC
** * * *
13102641 TCATGTGAGCTAACCCGTCCCACACACCATATGGTCA
66 TCATAAGAACTAACCCATCCAACACACCATATGGTCA
* * * * * * *
13102678 TAAGAGTTAACCCGTCCAACACACCATATGCTCGTATGAGTTAACCCATCCAACACACCATATGC
1 TAAGAGCTAACCCATCCAACACACCATATACTCATATAAGCTAACCCATCCAACACACCATATAC
* **
13102743 TCGTAAGAACTAACCCATCCAACACACCATATACTCA
66 TCATAAGAACTAACCCATCCAACACACCATATGGTCA
* **
13102780 TATGAGCTAGTCCATCCAACACACCA
1 TAAGAGCTAACCCATCCAACACACCA
13102806 AATATACAGC
Statistics
Matches: 105, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
102 105 1.00
ACGTcount: A:0.35, C:0.34, G:0.10, T:0.20
Consensus pattern (102 bp):
TAAGAGCTAACCCATCCAACACACCATATACTCATATAAGCTAACCCATCCAACACACCATATAC
TCATAAGAACTAACCCATCCAACACACCATATGGTCA
Found at i:13106461 original size:30 final size:30
Alignment explanation
Indices: 13106426--13106487 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
13106416 ATAATATCTT
13106426 ACAACAAACATATAGCACAGACAGAAACAC
1 ACAACAAACATATAGCACAGACAGAAACAC
* * ** *
13106456 ACAACAAGCATGTAGCATGGACAGAGACAC
1 ACAACAAACATATAGCACAGACAGAAACAC
13106486 AC
1 AC
13106488 CTCAAGCAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.08
Consensus pattern (30 bp):
ACAACAAACATATAGCACAGACAGAAACAC
Found at i:13106921 original size:12 final size:12
Alignment explanation
Indices: 13106904--13106941 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
13106894 AAAAAATCAA
13106904 CAGTCAATGGGT
1 CAGTCAATGGGT
*
13106916 CAGTCAACGGGT
1 CAGTCAATGGGT
13106928 C-GATCAATGGGT
1 CAG-TCAATGGGT
13106940 CA
1 CA
13106942 ACAGTTCGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 1 0.05
12 21 0.95
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (12 bp):
CAGTCAATGGGT
Found at i:13109260 original size:14 final size:14
Alignment explanation
Indices: 13109241--13109282 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
13109231 ACTCAACCAA
13109241 GATCGTTGACCGTT
1 GATCGTTGACCGTT
**
13109255 GATCGTTGACTATT
1 GATCGTTGACCGTT
13109269 GA-CAGTTGACCGTT
1 GATC-GTTGACCGTT
13109283 TAACCGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (14 bp):
GATCGTTGACCGTT
Found at i:13110535 original size:4 final size:4
Alignment explanation
Indices: 13110528--13110555 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
13110518 TAAATATATA
13110528 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
13110556 GGAATGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:13116489 original size:24 final size:24
Alignment explanation
Indices: 13116438--13116489 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
13116428 AACTTGCTCG
**
13116438 TTGATCGAACCTAACCCAAATCTG
1 TTGATCGAACCTAACCCAAATCCA
*
13116462 TTGATCGAACCTGAACCCAGA-CCA
1 TTGATCGAACCT-AACCCAAATCCA
13116486 TTGA
1 TTGA
13116490 CCATTGACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (24 bp):
TTGATCGAACCTAACCCAAATCCA
Found at i:13116524 original size:20 final size:20
Alignment explanation
Indices: 13116499--13116536 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13116489 ACCATTGACC
13116499 GTTGACCGTTAACTTTTTGG
1 GTTGACCGTTAACTTTTTGG
* *
13116519 GTTGACTGTTCACTTTTT
1 GTTGACCGTTAACTTTTT
13116537 TTGAGAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGACCGTTAACTTTTTGG
Found at i:13117676 original size:19 final size:19
Alignment explanation
Indices: 13117654--13117690 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13117644 CCGATTGGCA
13117654 CGACCCGAACCCATTGACT
1 CGACCCGAACCCATTGACT
* *
13117673 CGACCCGGACCCGTTGAC
1 CGACCCGAACCCATTGAC
13117691 CATTGACCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.43, G:0.22, T:0.14
Consensus pattern (19 bp):
CGACCCGAACCCATTGACT
Found at i:13118276 original size:2 final size:2
Alignment explanation
Indices: 13118269--13118298 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13118259 AATGTCATGC
13118269 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
13118299 CAAGCATGTG
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:13124446 original size:20 final size:20
Alignment explanation
Indices: 13124421--13124458 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13124411 AACCCAGATC
13124421 GTTGACCATTAACTTTTTGG
1 GTTGACCATTAACTTTTTGG
* *
13124441 GTTGACCGTTAGCTTTTT
1 GTTGACCATTAACTTTTT
13124459 TTGAGAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGACCATTAACTTTTTGG
Found at i:13125656 original size:12 final size:13
Alignment explanation
Indices: 13125634--13125662 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
13125624 TTGATAGTTT
13125634 CTTTGACTGTTGA
1 CTTTGACTGTTGA
13125647 CTTTGA-TGTTGA
1 CTTTGACTGTTGA
13125659 CTTT
1 CTTT
13125663 TTCTGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.52
Consensus pattern (13 bp):
CTTTGACTGTTGA
Found at i:13128385 original size:10 final size:11
Alignment explanation
Indices: 13128369--13128413 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
13128359 TTAATATTTA
13128369 ATATTTATAAT
1 ATATTTATAAT
13128380 -TATTTA-AAT
1 ATATTTATAAT
*
13128389 ATATTTATATT
1 ATATTTATAAT
*
13128400 TTA-TTATAAT
1 ATATTTATAAT
13128410 ATAT
1 ATAT
13128414 AAATTGATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
9 3 0.11
10 20 0.74
11 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATATTTATAAT
Found at i:13129062 original size:14 final size:14
Alignment explanation
Indices: 13129043--13129078 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
13129033 ACAATATCCA
13129043 AAAATAATAATAAC
1 AAAATAATAATAAC
*
13129057 AAAATAGTAATAAC
1 AAAATAATAATAAC
*
13129071 ATAATAAT
1 AAAATAAT
13129079 GAAATAACAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.25
Consensus pattern (14 bp):
AAAATAATAATAAC
Found at i:13129727 original size:21 final size:21
Alignment explanation
Indices: 13129684--13129727 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
13129674 ATAATTTTTT
* * *
13129684 TAAATTATAAAATTGTATAAA
1 TAAAATATAAAAATATATAAA
*
13129705 TAAAATATAAAAATATATTAA
1 TAAAATATAAAAATATATAAA
13129726 TA
1 TA
13129728 GTTTTTAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAATATAAAAATATATAAA
Found at i:13129865 original size:15 final size:15
Alignment explanation
Indices: 13129828--13129866 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
13129818 TTATTAATAT
*
13129828 ATTCCATACGGTTAA
1 ATTCCATTCGGTTAA
13129843 ATTCCATTCGGTTAA
1 ATTCCATTCGGTTAA
13129858 ATTCCATTC
1 ATTCCATTC
13129867 AGGCAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (15 bp):
ATTCCATTCGGTTAA
Found at i:13141659 original size:25 final size:26
Alignment explanation
Indices: 13141613--13141661 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
13141603 TTTCTGTTTT
*
13141613 CTTTCCTTCTTCAAAAATTTTGCTTC
1 CTTTCCTTCTTCAAAAAATTTGCTTC
13141639 CTTTCCTTCTT-AAAAAATTTGCT
1 CTTTCCTTCTTCAAAAAATTTGCT
13141662 GTTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.22, C:0.24, G:0.04, T:0.49
Consensus pattern (26 bp):
CTTTCCTTCTTCAAAAAATTTGCTTC
Found at i:13142258 original size:27 final size:27
Alignment explanation
Indices: 13142218--13142314 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 27
13142208 AAATGTGAGG
*
13142218 TTGGTGCCGTCTGTCAGGTAGGCATCT
1 TTGGTGCCGCCTGTCAGGTAGGCATCT
* * *
13142245 TTGGTGCCACCTGTCAGATAGACATCT
1 TTGGTGCCGCCTGTCAGGTAGGCATCT
* * ** *
13142272 CTAGTATCGCATGTCAGGTAGGCA-CTT
1 TTGGTGCCGCCTGTCAGGTAGGCATC-T
*
13142299 TTGGTGCCTCCTGTCA
1 TTGGTGCCGCCTGTCA
13142315 AATAGGCACT
Statistics
Matches: 51, Mismatches: 18, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
26 1 0.02
27 50 0.98
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (27 bp):
TTGGTGCCGCCTGTCAGGTAGGCATCT
Found at i:13142412 original size:18 final size:18
Alignment explanation
Indices: 13142389--13142424 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
13142379 TTTTTTAAAA
13142389 TTTTATTA-TTTAAATATT
1 TTTTATTAGTTT-AATATT
13142407 TTTTATTAGTTTAATATT
1 TTTTATTAGTTTAATATT
13142425 AAACAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTATTAGTTTAATATT
Found at i:13142714 original size:5 final size:6
Alignment explanation
Indices: 13142683--13142715 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
13142673 TTATATTATC
13142683 ATTTAA ATTTAA ATTTAA ATCTTAA A-TTAA ATT
1 ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATT
13142716 GTTGTGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:13143044 original size:6 final size:6
Alignment explanation
Indices: 13143033--13143064 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13143023 AATTAAATTA
13143033 AAAAAG AAAAAG AAAAAG -AAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
13143065 GATAAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:13156699 original size:28 final size:28
Alignment explanation
Indices: 13156662--13156719 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
13156652 AATTGAAATA
*
13156662 TTTTGGTGGAAGATAATTATTAACAATT
1 TTTTGGTGGAAGATAATTAATAACAATT
13156690 TTTTGGTGGAAGATAATTAATAACAATT
1 TTTTGGTGGAAGATAATTAATAACAATT
13156718 TT
1 TT
13156720 GATAACAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.43
Consensus pattern (28 bp):
TTTTGGTGGAAGATAATTAATAACAATT
Found at i:13157259 original size:12 final size:12
Alignment explanation
Indices: 13157244--13157305 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 12
13157234 ACAATTTTCA
13157244 CTAAATTTCTCT
1 CTAAATTTCTCT
* *
13157256 CTAAATGTCACT
1 CTAAATTTCTCT
13157268 C--AATTTCTCT
1 CTAAATTTCTCT
* *
13157278 CTAAATTTCACA
1 CTAAATTTCTCT
13157290 C-AAATTTCTCT
1 CTAAATTTCTCT
13157301 CTAAA
1 CTAAA
13157306 GCTCTCAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 8 0.21
11 9 0.23
12 22 0.56
ACGTcount: A:0.32, C:0.26, G:0.02, T:0.40
Consensus pattern (12 bp):
CTAAATTTCTCT
Found at i:13157299 original size:23 final size:23
Alignment explanation
Indices: 13157246--13157305 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 23
13157236 AATTTTCACT
*
13157246 AAATTTCTCTCTAAATGTCACTC
1 AAATTTCTCTCTAAATGTCACAC
*
13157269 -AATTTCTCTCTAAATTTCACAC
1 AAATTTCTCTCTAAATGTCACAC
13157291 AAATTTCTCTCTAAA
1 AAATTTCTCTCTAAA
13157306 GCTCTCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATTTCTCTCTAAATGTCACAC
Found at i:13157468 original size:19 final size:19
Alignment explanation
Indices: 13157441--13157506 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
13157431 GTAACAGTTA
*
13157441 ATTTTATTTTTTTAATATT
1 ATTTAATTTTTTTAATATT
13157460 ATTTAATTTTTTATAAT-TT
1 ATTTAATTTTTT-TAATATT
** *
13157479 AAATAATTTTTTAAATATT
1 ATTTAATTTTTTTAATATT
13157498 -TTTAATTTT
1 ATTTAATTTT
13157507 AATTTTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 10 0.26
19 25 0.64
20 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTAATTTTTTTAATATT
Found at i:13157469 original size:18 final size:18
Alignment explanation
Indices: 13157443--13157506 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
13157433 AACAGTTAAT
*
13157443 TTTATTTTTTTAATATTA
1 TTTAATTTTTTAATATTA
13157461 TTTAATTTTTT-ATAATTTA
1 TTTAATTTTTTAAT-A-TTA
**
13157480 AATAATTTTTTAAATATT-
1 TTTAATTTTTT-AATATTA
13157498 TTTAATTTT
1 TTTAATTTT
13157507 AATTTTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
17 2 0.05
18 18 0.49
19 14 0.38
20 1 0.03
21 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAATTTTTTAATATTA
Found at i:13157519 original size:14 final size:13
Alignment explanation
Indices: 13157495--13157524 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
13157485 TTTTTTAAAT
13157495 ATTTTTAATTTTA
1 ATTTTTAATTTTA
13157508 ATTTTATAATTTTA
1 ATTTT-TAATTTTA
13157522 ATT
1 ATT
13157525 AATATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTAATTTTA
Found at i:13157531 original size:20 final size:20
Alignment explanation
Indices: 13157448--13157532 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
13157438 TTAATTTTAT
* * * *
13157448 TTTTTTAATATTATTTAATT
1 TTTTATAATTTTAATTAATA
* *
13157468 TTTTATAA-TTTAAATAATT
1 TTTTATAATTTTAATTAATA
* *
13157487 TTTTAAATATTTTTAATT-TTAA
1 TTTT--ATAATTTTAATTAAT-A
13157509 TTTTATAATTTTAATTAATA
1 TTTTATAATTTTAATTAATA
13157529 TTTT
1 TTTT
13157533 TTTATAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
19 12 0.24
20 23 0.46
21 5 0.10
22 10 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATAATTTTAATTAATA
Found at i:13159090 original size:22 final size:22
Alignment explanation
Indices: 13159039--13159117 Score: 122
Period size: 22 Copynumber: 3.5 Consensus size: 22
13159029 AAGTACTTAA
*
13159039 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
*
13159061 CCAGTAGGCATACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
*
13159084 CAGTAGGCACACACAGTACAAT
1 CAGTAGGCACACACAGTGCAAT
13159106 CAGTAGGCACAC
1 CAGTAGGCACAC
13159118 GAGGTGCGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 32 0.62
23 20 0.38
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:13159138 original size:23 final size:23
Alignment explanation
Indices: 13159106--13159182 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
13159096 ACAGTACAAT
* ** *
13159106 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAACTGCAAAA
* *
13159129 TAGTAAGCACACAAACTGCAAAA
1 CAGTAAGCACACGAACTGCAAAA
*
13159152 CAGTAAGCACACGAAATGCAAAA
1 CAGTAAGCACACGAACTGCAAAA
13159175 CAGTAAGC
1 CAGTAAGC
13159183 GCGCTAGCGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (23 bp):
CAGTAAGCACACGAACTGCAAAA
Found at i:13159139 original size:45 final size:44
Alignment explanation
Indices: 13159039--13159141 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 44
13159029 AAGTACTTAA
*
13159039 CAGTAAGCACACACAGTGCAATCCAGTAGGCATACACAGTGCAAT
1 CAGTAAGCACACACAGTACAATCCAGTAGGCA-ACACAGTGCAAT
*
13159084 CAGTAGGCACACACAGTACAAT-CAGTAGGC-ACACGAGGTGCGAAAT
1 CAGTAAGCACACACAGTACAATCCAGTAGGCAACAC-A-GTGC--AAT
13159130 -AGTAAGCACACA
1 CAGTAAGCACACA
13159142 AACTGCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
42 4 0.08
43 1 0.02
44 12 0.24
45 31 0.61
46 3 0.06
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (44 bp):
CAGTAAGCACACACAGTACAATCCAGTAGGCAACACAGTGCAAT
Found at i:13161915 original size:20 final size:22
Alignment explanation
Indices: 13161877--13161931 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
13161867 TCTAAACCCT
*
13161877 TAAACCCTAATAATTAAAAAC-C
1 TAAACCCTAAT-TTTAAAAACTC
13161899 TAAA-CCTAATTTTAAAAACTC
1 TAAACCCTAATTTTAAAAACTC
13161920 TAAACCCTAATT
1 TAAACCCTAATT
13161932 AAACTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 8 0.27
21 11 0.37
22 11 0.37
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAACCCTAATTTTAAAAACTC
Found at i:13161933 original size:20 final size:18
Alignment explanation
Indices: 13161887--13161934 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 18
13161877 TAAACCCTAA
13161887 TAATTAAAAACCTAAACC
1 TAATTAAAAACCTAAACC
13161905 TAATTTTAAAAACTCTAAACCC
1 TAA--TTAAAAAC-CTAAA-CC
13161927 TAATTAAA
1 TAATTAAA
13161935 CTAAAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
20 13 0.50
21 5 0.19
22 5 0.19
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (18 bp):
TAATTAAAAACCTAAACC
Found at i:13162366 original size:22 final size:22
Alignment explanation
Indices: 13162338--13162381 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13162328 AAGCATGTCC
13162338 AGTTGGACGTGCTTTCTACACA
1 AGTTGGACGTGCTTTCTACACA
13162360 AGTTGGACGTGCTTTCTACACA
1 AGTTGGACGTGCTTTCTACACA
13162382 GGTGCTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (22 bp):
AGTTGGACGTGCTTTCTACACA
Found at i:13167599 original size:18 final size:18
Alignment explanation
Indices: 13167576--13167626 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
13167566 ATTCAATACT
13167576 TTAATTTGGGTAATTCGA
1 TTAATTTGGGTAATTCGA
*** *
13167594 TTAA-TTCAATCAATTCGG
1 TTAATTTGGGT-AATTCGA
13167612 TTAATTTGGGTAATT
1 TTAATTTGGGTAATT
13167627 TTTATACCAA
Statistics
Matches: 24, Mismatches: 7, Indels: 4
0.69 0.20 0.11
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (18 bp):
TTAATTTGGGTAATTCGA
Found at i:13168071 original size:3 final size:3
Alignment explanation
Indices: 13168063--13168090 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13168053 AAGGGCCCAA
13168063 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
13168091 AGGTTTCATG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:13168694 original size:149 final size:147
Alignment explanation
Indices: 13168497--13169002 Score: 632
Period size: 148 Copynumber: 3.4 Consensus size: 147
13168487 GATTTTGGAA
* * * *
13168497 AAAGTTTTGTTTTTTTAAAATAATCTCGAAATAAAAATTTTGATTTTTAAGGAAAATAGTGATTT
1 AAAGTTTTATTTTTTT-AACT-ATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTT
*
13168562 TCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAAAATGTTTTTTAGTTATTTTAAAGA
64 TCTTT-AAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAAAATGTTTTTTAGTCATTTTAAAG-
13168627 AAAAAGTTTAAATTTTTAAAC
127 AAAAAGTTTAAATTTTTAAAC
* *
13168648 AAAGTTTTATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTC
1 AAAGTTTTATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTTC
* ***
13168713 TTCAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAGCCTGTTTTTTAGTCATTTTAAAGAAAA
66 TTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAAAATGTTTTTTAGTCATTTTAAAGAAAA
13168778 AGTTTAAATTTTTAAAC
131 AGTTTAAATTTTTAAAC
* * * * **
13168795 AAAAATGTGA-TTTTTTAACTATTTCAAAATAAAAATTTAAATTTTTAAGTAAAATAGTGATTTT
1 -AAAGTTTTATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTT
* * *
13168859 CATTTTAAAAA-A-TAAGTTTAGATTTTTAAAAAAATAAAAATATGTTTTTTTAGTCATTTTAAA
65 C-TTTAAAAAAGAGAAAGTTTAGATTTTT--AAAAATAAAAAAATG-TTTTTTAGTCATTTTAAA
* *
13168922 GAAAAA-TTTACATTTGTAAAC
126 GAAAAAGTTTAAATTTTTAAAC
* * * **
13168943 AAAG---T-TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTGATGTAGTGATTTT
1 AAAGTTTTATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTT
13169003 GTTTTAATCA
Statistics
Matches: 313, Mismatches: 36, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
144 46 0.15
146 14 0.04
147 76 0.24
148 92 0.29
149 67 0.21
150 3 0.01
151 15 0.05
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (147 bp):
AAAGTTTTATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTTC
TTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAAAATGTTTTTTAGTCATTTTAAAGAAAA
AGTTTAAATTTTTAAAC
Found at i:13168780 original size:51 final size:49
Alignment explanation
Indices: 13168571--13168941 Score: 146
Period size: 50 Copynumber: 7.5 Consensus size: 49
13168561 TTCTTTAAAA
* * * *
13168571 AAAGAGAAAGTTTAGATTTTTAAAAATAAAAAAATG-TTTTTTAGTTATTTT
1 AAAGAAAAAGTTTAAATTTTTAAAAAT--AAAAGTGATTTTTTA-TCATTTT
* *** * * *
13168622 AAAGAAAAAAGTTTAAATTTTTAAACA-AAGTTTTATTTTTTTAACTATTTCG
1 AAAG-AAAAAGTTTAAATTTTTAAAAATAAAAGTGA-TTTTTTATC-ATTT-T
* ** * * * **
13168674 AAA-TAAAAGTTTGGATTTTTAAGTAA-AATAGTGATTTTCT-TCA--AA
1 AAAGAAAAAGTTTAAATTTTTAA-AAATAAAAGTGATTTTTTATCATTTT
* *
13168719 AAAGAGAAAGTTTAGATTTTTAAAAATAAAAGCCTG-TTTTTTAGTCATTTT
1 AAAGAAAAAGTTTAAATTTTTAAAAATAAAAG--TGATTTTTTA-TCATTTT
* * *
13168770 AAAGAAAAAGTTTAAATTTTTAAACAA-AAATGTGATTTTTTAACTATTTC
1 AAAGAAAAAGTTTAAATTTTTAAA-AATAAAAGTGATTTTTTATC-ATTTT
* * *
13168820 AAA-ATAAAAATTTAAATTTTTAAGTAA-AATAGTGA---TTT-TCATTTT
1 AAAGA-AAAAGTTTAAATTTTTAA-AAATAAAAGTGATTTTTTATCATTTT
* * *
13168865 AAA-AAATAAGTTTAGATTTTTAAAAAAATAAAAATATGTTTTTTTAGTCATTTT
1 AAAGAAA-AAGTTTAAATTTTT--AAAAAT-AAAA-GTGATTTTTTA-TCATTTT
* *
13168919 AAAGAAAAA-TTTACATTTGTAAA
1 AAAGAAAAAGTTTAAATTTTTAAA
13168942 CAAAGTTTTT
Statistics
Matches: 239, Mismatches: 50, Indels: 62
0.68 0.14 0.18
Matches are distributed among these distances:
44 2 0.01
45 25 0.10
46 23 0.10
47 10 0.04
48 6 0.03
49 13 0.05
50 60 0.25
51 49 0.21
52 27 0.11
53 9 0.04
54 12 0.05
55 3 0.01
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (49 bp):
AAAGAAAAAGTTTAAATTTTTAAAAATAAAAGTGATTTTTTATCATTTT
Found at i:13169500 original size:5 final size:5
Alignment explanation
Indices: 13169490--13169518 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
13169480 TATATTTATA
13169490 CCTTC CCTTC CCTTC CCTTC CCTTC CCTT
1 CCTTC CCTTC CCTTC CCTTC CCTTC CCTT
13169519 TCATTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
CCTTC
Found at i:13169617 original size:10 final size:10
Alignment explanation
Indices: 13169602--13169635 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
13169592 TTGTATAATG
13169602 TTTTATTTAT
1 TTTTATTTAT
13169612 TTTTATTTCAT
1 TTTTATTT-AT
*
13169623 ATTTATTTAT
1 TTTTATTTAT
13169633 TTT
1 TTT
13169636 CATATCTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:13169629 original size:21 final size:20
Alignment explanation
Indices: 13169603--13169653 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
13169593 TGTATAATGT
* *
13169603 TTTATTTATTTTTATTTCATA
1 TTTATTTATTTTCATATC-TA
13169624 TTTATTTATTTTCATATCTA
1 TTTATTTATTTTCATATCTA
13169644 TTATATTTAT
1 TT-TATTTAT
13169654 GGTTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTATTTTCATATCTA
Found at i:13169633 original size:15 final size:15
Alignment explanation
Indices: 13169613--13169651 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13169603 TTTATTTATT
*
13169613 TTTATTTCATATTTA
1 TTTATTTCATATCTA
13169628 TTTATTTTCATATCTA
1 TTTA-TTTCATATCTA
13169644 TTATATTT
1 TT-TATTT
13169652 ATGGTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 15 0.71
17 2 0.10
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTTCATATCTA
Found at i:13169638 original size:16 final size:16
Alignment explanation
Indices: 13169605--13169651 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
13169595 TATAATGTTT
*
13169605 TATTTATTTTTATTTCA
1 TATTTATTTAT-TTTCA
13169622 TATTTATTTATTTTCA
1 TATTTATTTATTTTCA
*
13169638 TATCTATTATATTT
1 TATTTATT-TATTT
13169652 ATGGTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATTTATTTTCA
Found at i:13172535 original size:61 final size:59
Alignment explanation
Indices: 13172437--13172606 Score: 209
Period size: 61 Copynumber: 2.8 Consensus size: 59
13172427 AACCCTGAGT
* * *
13172437 TTTCTAAAAATTCATTTTTGACCCACGAATTTTCTAAAATTTCATTTTTGGCCATC-GAAC
1 TTTCTAAAATTTCATTTTTGACCC-CGAACTTTCTAAAATTTCATTTTTGACC-TCTGAAC
*
13172497 TTTCTAAAATTTCATTTTTTGACCCTCGAACTTTCTAAAATTTCTTTTTTGACCTCTGAAC
1 TTTCTAAAATTTCA-TTTTTGACCC-CGAACTTTCTAAAATTTCATTTTTGACCTCTGAAC
* *
13172558 TTTTTAGAAATTTCA-TTTTGACCCCTAAACTTTCTAAAAATTTCATTTT
1 TTTCTA-AAATTTCATTTTTGACCCC-GAACTTTCT-AAAATTTCATTTT
13172607 AACCCTCAAA
Statistics
Matches: 97, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
59 1 0.01
60 32 0.33
61 56 0.58
62 8 0.08
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.46
Consensus pattern (59 bp):
TTTCTAAAATTTCATTTTTGACCCCGAACTTTCTAAAATTTCATTTTTGACCTCTGAAC
Found at i:13172618 original size:30 final size:30
Alignment explanation
Indices: 13172437--13172656 Score: 202
Period size: 30 Copynumber: 7.3 Consensus size: 30
13172427 AACCCTGAGT
* *
13172437 TTTCTAAAAA-TTCATTTTTGACCCACGAAT
1 TTTCTAAAAATTTCA-TTTTGACCCTCGAAC
* *
13172467 TTTCT-AAAATTTCATTTTTGGCCATCGAAC
1 TTTCTAAAAATTTCA-TTTTGACCCTCGAAC
13172497 TTTCT-AAAATTTCATTTTTTGACCCTCGAAC
1 TTTCTAAAAATTTCA--TTTTGACCCTCGAAC
*
13172528 TTTCT-AAAATTTCTTTTTTGA-CCTCTGAAC
1 TTTCTAAAAATTTC-ATTTTGACCCTC-GAAC
* * *
13172558 TTTTTAGAAATTTCATTTTGACCC-CTAAAC
1 TTTCTAAAAATTTCATTTTGACCCTC-GAAC
* *
13172588 TTTCTAAAAATTTCATTTTAACCCTCAAAC
1 TTTCTAAAAATTTCATTTTGACCCTCGAAC
* * * *
13172618 TTTTTAAAAATATCATTTTGACCCCCAAAC
1 TTTCTAAAAATTTCATTTTGACCCTCGAAC
13172648 TTT-TAAAAA
1 TTTCTAAAAA
13172657 AAATTATATT
Statistics
Matches: 165, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
29 14 0.08
30 114 0.69
31 37 0.22
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.43
Consensus pattern (30 bp):
TTTCTAAAAATTTCATTTTGACCCTCGAAC
Found at i:13173812 original size:18 final size:18
Alignment explanation
Indices: 13173789--13173832 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
13173779 GGTGACTTCC
13173789 ATTTTCGATTTTAAAAAT
1 ATTTTCGATTTTAAAAAT
13173807 ATTTTCGATTTTAAAAAT
1 ATTTTCGATTTTAAAAAT
13173825 ATTTTCGA
1 ATTTTCGA
13173833 AACTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTTTCGATTTTAAAAAT
Found at i:13176235 original size:21 final size:21
Alignment explanation
Indices: 13176202--13176244 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
13176192 GTTGAGAAGA
13176202 TTGAATTGAAAGCTCA-AATAG
1 TTGAATTGAAAGCT-AGAATAG
13176223 TTGAATT-AGAAGCTAGAATAG
1 TTGAATTGA-AAGCTAGAATAG
13176244 T
1 T
13176245 GAAGCTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (21 bp):
TTGAATTGAAAGCTAGAATAG
Found at i:13184888 original size:78 final size:77
Alignment explanation
Indices: 13184784--13185287 Score: 358
Period size: 78 Copynumber: 6.4 Consensus size: 77
13184774 CATTTTACAG
** * *
13184784 ATCTCTTACCCCGATCATGGGGCAGATCAAAGCATCCAAATCTCTTACCCTAATCAGAGGACAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCC-AATCTTTTACCTTAATCAGAGG-CAGA
**
13184849 TCAAAGACCGT-CA
64 TCAAAGACAATCCA
* * *
13184862 ATCTCTTACCCCGATCATGGGACAGATTGAAGCATCTAATCTTTTACCTTAATCAAAAGGCAGAT
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATC-AGAGGCAGAT
**
13184927 TGAAGACAATCCA
65 CAAAGACAATCCA
*
13184940 ATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTTACCTTAATCAGAAGGCAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATC-TTTTACCTTAATCAG-AGGCAGA
**
13185005 TTGAAGACAATCCA
64 TCAAAGACAATCCA
* ** * * * *
13185019 ATCTTTTACCTTGATCA-GAAGGCAGATTGAAGCATCCAATCTTTTACGTTAATAAGAAGGAAGA
1 ATCTCTTACCCCGATCATG-GGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAG-AGGCAGA
**
13185083 TTGAAGACACA-CCA
64 TCAAAGACA-ATCCA
*** * * * * *
13185097 ATCTCTTACCTTAATCA-GAAGACAGATTGAAGACAAACCAATCTTTTATCC-CAATCATGGGGC
1 ATCTCTTACCCCGATCATG-GGGCAGATTGAAG-C-ATCCAATCTTTTA-CCTTAATCA-GAGGC
* *
13185160 AGATTAAAG-C-ATCAA
61 AGATCAAAGACAATCCA
* ** ** * * * * * *
13185175 ATCTTTTACCCTAATCAAAGGGCAGATTGAAGATAATCTAATCTTTTACCCTAATTAGAGGGTAT
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAG--CATCCAATCTTTTACCTTAATCAGA-GGCAG
*
13185240 ATTAAAGACACA-CCA
63 ATCAAAGACA-ATCCA
* * * *
13185255 TTCTCTTACCCCAATCATGAGGCAGATCGAAGC
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGC
13185288 TATCATCCTA
Statistics
Matches: 353, Mismatches: 55, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
77 30 0.08
78 193 0.55
79 74 0.21
80 53 0.15
81 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (77 bp):
ATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAGGCAGATC
AAAGACAATCCA
Found at i:13184949 original size:40 final size:40
Alignment explanation
Indices: 13184884--13185229 Score: 336
Period size: 40 Copynumber: 8.8 Consensus size: 40
13184874 GATCATGGGA
*
13184884 CAGATTGAAG-C-ATCTAATCTTTTACCTTAATCAAAAGG
1 CAGATTGAAGACAATCCAATCTTTTACCTTAATCAAAAGG
* ** ***
13184922 CAGATTGAAGACAATCCAATCTCTTACCTCGATCATGGGG
1 CAGATTGAAGACAATCCAATCTTTTACCTTAATCAAAAGG
*
13184962 CAGATTGAAG-C-ATCCAATCTTTTTACCTTAATCAGAAGG
1 CAGATTGAAGACAATCCAATC-TTTTACCTTAATCAAAAGG
* *
13185001 CAGATTGAAGACAATCCAATCTTTTACCTTGATCAGAAGG
1 CAGATTGAAGACAATCCAATCTTTTACCTTAATCAAAAGG
*
13185041 CAGATTGAAG-C-ATCCAATCTTTTACGTTAAT-AAGAAGG
1 CAGATTGAAGACAATCCAATCTTTTACCTTAATCAA-AAGG
* * * *
13185079 AAGATTGAAGACACA-CCAATCTCTTACCTTAATCAGAAGA
1 CAGATTGAAGACA-ATCCAATCTTTTACCTTAATCAAAAGG
* * ***
13185119 CAGATTGAAGACAAACCAATCTTTTATCC-CAATCATGGGG
1 CAGATTGAAGACAATCCAATCTTTTA-CCTTAATCAAAAGG
* * * *
13185159 CAGATTAAAG-C-ATCAAATCTTTTACCCTAATCAAAGGG
1 CAGATTGAAGACAATCCAATCTTTTACCTTAATCAAAAGG
* * *
13185197 CAGATTGAAGATAATCTAATCTTTTACCCTAAT
1 CAGATTGAAGACAATCCAATCTTTTACCTTAAT
13185230 TAGAGGGTAT
Statistics
Matches: 255, Mismatches: 38, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
37 3 0.01
38 77 0.30
39 29 0.11
40 134 0.53
41 12 0.05
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (40 bp):
CAGATTGAAGACAATCCAATCTTTTACCTTAATCAAAAGG
Found at i:13185028 original size:79 final size:78
Alignment explanation
Indices: 13184784--13185107 Score: 404
Period size: 78 Copynumber: 4.1 Consensus size: 78
13184774 CATTTTACAG
* ** * *
13184784 ATCTCTTACCCCGATCATGGGGCAGATCAAAGCATCCAAATCTCTTACCCTAATCAG-AGGACAG
1 ATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCC-AATCTTTTACCTTAATCAGAAGG-CAG
** **
13184848 ATCAAAGACCGT-CA
64 ATTGAAGACAATCCA
* * * *
13184862 ATCTCTTACCCCGATCATGGGACAGATTGAAGCATCTAATCTTTTACCTTAATCAAAAGGCAGAT
1 ATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCAGAT
13184927 TGAAGACAATCCA
66 TGAAGACAATCCA
13184940 ATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTTACCTTAATCAGAAGGCAGA
1 ATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATC-TTTTACCTTAATCAGAAGGCAGA
13185005 TTGAAGACAATCCA
65 TTGAAGACAATCCA
* * * * * *
13185019 ATCTTTTACCTTGATCA-GAAGGCAGATTGAAGCATCCAATCTTTTACGTTAATAAGAAGGAAGA
1 ATCTCTTACCTCGATCATG-GGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCAGA
13185083 TTGAAGACACA-CCA
65 TTGAAGACA-ATCCA
13185097 ATCTCTTACCT
1 ATCTCTTACCT
13185108 TAATCAGAAG
Statistics
Matches: 219, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
77 27 0.12
78 119 0.54
79 73 0.33
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCAGAT
TGAAGACAATCCA
Found at i:13185218 original size:118 final size:118
Alignment explanation
Indices: 13184797--13185281 Score: 353
Period size: 118 Copynumber: 4.1 Consensus size: 118
13184787 TCTTACCCCG
* * * * ** **
13184797 ATCATGGGGCAGATCAAAGCATCCAAATCTCTTACCCTAATCAGAGGACAGATCAAAGACCGT-C
1 ATCATGAGGCAGATTAAAGCAT-CAAATCTCTTACCCTAATCAAAGGGCAGATTGAAGACAATCC
** * * * *
13184861 AATCTCTTACCCCGATCATG-GGACAGATTGAAG-C-ATCTAATCTTTTACCTTA
65 AATCTCTTACCCTAATCA-GAAGACAGATTGAAGACAAACCAATCTTTTACCTCA
** * * * **
13184913 ATCAAAAGGCAGATTGAAGACAATCCAATCTCTTA-CCTCGATCATGGGGCAGATTGAAG-C-AT
1 ATCATGAGGCAGATTAAAG-C-ATCAAATCTCTTACCCT-AATCAAAGGGCAGATTGAAGACAAT
* * * * **
13184975 CCAATCTTTTTACCTTAATCAGAAGGCAGATTGAAGACAATCCAATCTTTTACCTTG
63 CCAATC-TCTTACCCTAATCAGAAGACAGATTGAAGACAAACCAATCTTTTACCTCA
* * * ** * *
13185032 ATCA-GAAGGCAGATTGAAGCATCCAATCTTTTACGTTAAT-AAGAAGGAAGATTGAAGACACA-
1 ATCATG-AGGCAGATTAAAGCATCAAATCTCTTACCCTAATCAA-AGGGCAGATTGAAGACA-AT
*
13185094 CCAATCTCTTACCTTAATCAGAAGACAGATTGAAGACAAACCAATCTTTTATCC-CA
63 CCAATCTCTTACCCTAATCAGAAGACAGATTGAAGACAAACCAATCTTTTA-CCTCA
* * * *
13185150 ATCATGGGGCAGATTAAAGCATCAAATCTTTTACCCTAATCAAAGGGCAGATTGAAGATAATCTA
1 ATCATGAGGCAGATTAAAGCATCAAATCTCTTACCCTAATCAAAGGGCAGATTGAAGACAATCCA
* * * ** * * * * * *
13185215 ATCTTTTACCCTAATTAGAGGGTATATTAAAGACACACCATTCTCTTACCCCA
66 ATCTCTTACCCTAATCAGAAGACAGATTGAAGACAAACCAATCTTTTACCTCA
13185268 ATCATGAGGCAGAT
1 ATCATGAGGCAGAT
13185282 CGAAGCTATC
Statistics
Matches: 294, Mismatches: 56, Indels: 36
0.76 0.15 0.09
Matches are distributed among these distances:
115 1 0.00
116 25 0.09
117 74 0.25
118 149 0.51
119 44 0.15
120 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (118 bp):
ATCATGAGGCAGATTAAAGCATCAAATCTCTTACCCTAATCAAAGGGCAGATTGAAGACAATCCA
ATCTCTTACCCTAATCAGAAGACAGATTGAAGACAAACCAATCTTTTACCTCA
Found at i:13185850 original size:15 final size:15
Alignment explanation
Indices: 13185830--13185862 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
13185820 CTCGATTACC
13185830 GACCCTTGGACTTTT
1 GACCCTTGGACTTTT
13185845 GACCCTTGGACTTTT
1 GACCCTTGGACTTTT
13185860 GAC
1 GAC
13185863 TTCTCAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.36
Consensus pattern (15 bp):
GACCCTTGGACTTTT
Found at i:13186984 original size:29 final size:30
Alignment explanation
Indices: 13186939--13187043 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 30
13186929 CTAAACTTTC
** * *
13186939 CTAAAAATTCAAATTTAGC-CCCGAGTTTT
1 CTAAAAATTCATTTTTAACTCCCGAATTTT
*
13186968 CTAAAAATTCATTTTTAACTCTCGAATTTT
1 CTAAAAATTCATTTTTAACTCCCGAATTTT
* ** * * *
13186998 CTAAAATTTCATTTTTGGCTTCCAAACTTT
1 CTAAAAATTCATTTTTAACTCCCGAATTTT
*
13187028 CTAAAATTTCATTTTT
1 CTAAAAATTCATTTTT
13187044 TAACCCTCGA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 16 0.25
30 47 0.75
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (30 bp):
CTAAAAATTCATTTTTAACTCCCGAATTTT
Found at i:13187000 original size:30 final size:30
Alignment explanation
Indices: 13186964--13187074 Score: 109
Period size: 30 Copynumber: 3.6 Consensus size: 30
13186954 TAGCCCCGAG
*
13186964 TTTTCTAAAAATTCATTTTTAACTCTCGAA
1 TTTTCTAAAATTTCATTTTTAACTCTCGAA
** *
13186994 TTTTCTAAAATTTCATTTTTGGCT-TCCAAA
1 TTTTCTAAAATTTCATTTTTAACTCT-CGAA
* *
13187024 CTTTCTAAAATTTCATTTTTTAACCCTCG-A
1 TTTTCTAAAATTTCA-TTTTTAACTCTCGAA
*
13187054 TCTTTCTGGAAATTTCATTTT
1 T-TTTCT-AAAATTTCATTTT
13187075 GACCCCTAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
29 1 0.02
30 39 0.60
31 16 0.25
32 9 0.14
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (30 bp):
TTTTCTAAAATTTCATTTTTAACTCTCGAA
Found at i:13187086 original size:61 final size:60
Alignment explanation
Indices: 13186965--13187110 Score: 156
Period size: 61 Copynumber: 2.4 Consensus size: 60
13186955 AGCCCCGAGT
* * *
13186965 TTTCTAAAAATTCATTTTTAACTCTCGAATTTTCTAAAATTTCATTTTTGGCTTCCAAAC
1 TTTCTAAAAATTCATTTTTAACCCTCGAATTTTCTAAAATTTCATTTTTGACTCCCAAAC
* *
13187025 TTTCTAAAATTTCATTTTTTAACCCTCG-ATCTTTCTGGAAATTTCA-TTTTGAC-CCCTAAAC
1 TTTCTAAAAATTCA-TTTTTAACCCTCGAAT-TTTCT-AAAATTTCATTTTTGACTCCC-AAAC
*
13187086 TTTTTAAAAAATT-ATATTTTAACCC
1 TTTCT-AAAAATTCAT-TTTTAACCC
13187111 CTAAAACTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
60 18 0.25
61 41 0.56
62 14 0.19
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (60 bp):
TTTCTAAAAATTCATTTTTAACCCTCGAATTTTCTAAAATTTCATTTTTGACTCCCAAAC
Found at i:13192375 original size:18 final size:18
Alignment explanation
Indices: 13192354--13192390 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13192344 CCGTCCCCGA
13192354 CCACCTCCACCTCCGCCT
1 CCACCTCCACCTCCGCCT
* *
13192372 CCACGTCCACCTCTGCCT
1 CCACCTCCACCTCCGCCT
13192390 C
1 C
13192391 TAGAATTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.62, G:0.08, T:0.19
Consensus pattern (18 bp):
CCACCTCCACCTCCGCCT
Found at i:13204459 original size:16 final size:15
Alignment explanation
Indices: 13204423--13204459 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
13204413 TGCTGTAGTG
13204423 GAATAGAGTTGTAAA
1 GAATAGAGTTGTAAA
13204438 GTAATAGAGTTGTAATA
1 G-AATAGAGTTGTAA-A
13204455 GAATA
1 GAATA
13204460 AGGATGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 17 0.85
17 2 0.10
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (15 bp):
GAATAGAGTTGTAAA
Found at i:13204695 original size:57 final size:56
Alignment explanation
Indices: 13204634--13204785 Score: 189
Period size: 57 Copynumber: 2.6 Consensus size: 56
13204624 ATTATTAAAA
* *
13204634 TTTAATAAGATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATTATAT
1 TTTAATAA-ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAACAT
* * * *
13204691 TTTAACAAAATTATTATTAAATAAAATTAAATAAAATAATATATAATTTAATAACAT
1 TTTAA-TAAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAACAT
13204748 TTTCAATATAATTATTATTAAAATATGAA-TTAATAAAA
1 TTT-AATA-AATTATTATT-AAATAT-AATTTAATAAAA
13204786 ATCATAACAT
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
57 52 0.64
58 14 0.17
59 13 0.16
60 2 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (56 bp):
TTTAATAAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAACAT
Found at i:13218539 original size:45 final size:42
Alignment explanation
Indices: 13218440--13218546 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 42
13218430 AGTTACATCA
* * * *
13218440 CCATTCAATCTTTTACCCCTTATCTAGAGGAGTATATTAAAG
1 CCATTCAGTCTTTTACCCCTAATCTAGAGGAGTAAATGAAAG
*
13218482 CCATCATCCAGTCTTTTACCCCTAATCTAGAGGGGTAGAATGAAGTAG
1 CCAT--T-CAGTCTTTTACCCCTAATCTAGAGGAGTA-AATGAA--AG
13218530 CCATTCAGTCTTTTACC
1 CCATTCAGTCTTTTACC
13218547 TTAATCCAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
42 4 0.07
44 1 0.02
45 38 0.70
46 5 0.09
48 6 0.11
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (42 bp):
CCATTCAGTCTTTTACCCCTAATCTAGAGGAGTAAATGAAAG
Found at i:13218627 original size:42 final size:43
Alignment explanation
Indices: 13218539--13218702 Score: 169
Period size: 45 Copynumber: 3.8 Consensus size: 43
13218529 GCCATTCAGT
* * *
13218539 CTTTTACCT-TAATCCAGAAG-GACAGATTGAAACAACCATCCAAC
1 CTTTTACCTCTAATCCA-AAGAGGCAGGTTGAAGC--CCATCCAAC
13218583 CTTTTACCTCTAATCCAAAG-GGTCAGGTTGAAG-CCATCCAAC
1 CTTTTACCTCTAATCCAAAGAGG-CAGGTTGAAGCCCATCCAAC
* *
13218625 CTTTTACACT-TAATCCAGAGCGGCAGGTTGAAGCCATCATCCAAC
1 CTTTTAC-CTCTAATCCAAAGAGGCAGGTTGAAGCC--CATCCAAC
13218670 CTTTTACC-CATAATCCAAAGAGGCAGGTTGAAG
1 CTTTTACCTC-TAATCCAAAGAGGCAGGTTGAAG
13218703 TTACCAAGCG
Statistics
Matches: 105, Mismatches: 6, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
42 35 0.33
43 5 0.05
44 14 0.13
45 51 0.49
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
CTTTTACCTCTAATCCAAAGAGGCAGGTTGAAGCCCATCCAAC
Found at i:13218669 original size:87 final size:86
Alignment explanation
Indices: 13218539--13218702 Score: 226
Period size: 87 Copynumber: 1.9 Consensus size: 86
13218529 GCCATTCAGT
13218539 CTTTTACCTTAATCCAGAAGGACAGATTGAAACAACCATCCAACCTTTTACCTC-TAATCCAAAG
1 CTTTTACCTTAATCCAGAAGGACAGATTGAAACAACCATCCAACCTTTTACC-CATAATCCAAAG
13218603 -GGTCAGGTTGAAGCCATCCAAC
65 AGG-CAGGTTGAAGCCATCCAAC
* * * * *
13218625 CTTTTACACTTAATCCAG-AGCGGCAGGTTGAAGCCATCATCCAACCTTTTACCCATAATCCAAA
1 CTTTTAC-CTTAATCCAGAAG-GACAGATTGAAACAACCATCCAACCTTTTACCCATAATCCAAA
13218689 GAGGCAGGTTGAAG
64 GAGGCAGGTTGAAG
13218703 TTACCAAGCG
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
86 10 0.14
87 57 0.83
88 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (86 bp):
CTTTTACCTTAATCCAGAAGGACAGATTGAAACAACCATCCAACCTTTTACCCATAATCCAAAGA
GGCAGGTTGAAGCCATCCAAC
Found at i:13218719 original size:66 final size:66
Alignment explanation
Indices: 13218643--13218774 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
13218633 CTTAATCCAG
*
13218643 AGCGGCAGGTTGAAGCCATCATCCAACCTTTTACCCATAATCCAAAGAGGCAGGTTGAAGTTACC
1 AGCGGCAGGTTGAAGCCATCATCCAACATTTTACCCATAATCCAAAGAGGCAGGTTGAAGTTACC
13218708 A
66 A
* *
13218709 AGCGGTAGGTTGAAGCCATCATCCAACATTTTACCCATAATCCAGAGAGGCAGGTTGAAGTTACC
1 AGCGGCAGGTTGAAGCCATCATCCAACATTTTACCCATAATCCAAAGAGGCAGGTTGAAGTTACC
13218774 A
66 A
13218775 TCCAACCTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (66 bp):
AGCGGCAGGTTGAAGCCATCATCCAACATTTTACCCATAATCCAAAGAGGCAGGTTGAAGTTACC
A
Found at i:13218765 original size:45 final size:43
Alignment explanation
Indices: 13218715--13219117 Score: 182
Period size: 45 Copynumber: 9.2 Consensus size: 43
13218705 ACCAAGCGGT
13218715 AGGTTGAAGCCATCATCCAACATTTTACCCATAATCCAGAGAGGC
1 AGGTTGAAGCCATCATCCAAC-TTTTACCC-TAATCCAGAGAGGC
** * *
13218760 AGGTTGAAGTTACCATCCAACCTTTTACCCCTAATCCAAAG-GGAC
1 AGGTTGAAGCCATCATCCAA-CTTTTA-CCCTAATCCAGAGAGG-C
* * ** * * *
13218805 AAGTTGAAGTCGCCATTCAATCTTTTATCTCTAATCCAGAGGGGC
1 AGGTTGAAGCCATCATCCAA-CTTTTA-CCCTAATCCAGAGAGGC
** * * *
13218850 ATATTGAAGCCATCATCCAGTCTTTTAACCCTAACCCAAAGAGGC
1 AGGTTGAAGCCATCATCCA-ACTTTT-ACCCTAATCCAGAGAGGC
* * * * *
13218895 AGATTGAAGCTATCATCCAACCTTTTACCCTTAATTCAGAGGGGT
1 AGGTTGAAGCCATCATCCAA-CTTTTACCC-TAATCCAGAGAGGC
** * * *
13218940 AAATTGAAACCATCAT----C-----CCCTAATCTAGAGGGGC
1 AGGTTGAAGCCATCATCCAACTTTTACCCTAATCCAGAGAGGC
* * * *
13218974 AGGTTAAAGCCA-CAATCCAACATTTTACACCTAATCTAGAGGGGT
1 AGGTTGAAGCCATC-ATCCAAC-TTTTAC-CCTAATCCAGAGAGGC
* * * *
13219019 AGGTTGAAGTCACCATCTAATCTTTTACCCCTAATCCAGAGAGAC
1 AGGTTGAAGCCATCATCCAA-CTTTTA-CCCTAATCCAGAGAGGC
** * * * *
13219064 AAATTAAAGCCATTATCTAGACTTTTACCCCTAATCTAGA-AGGGC
1 AGGTTGAAGCCATCATCCA-ACTTTTA-CCCTAATCCAGAGA-GGC
*
13219109 AGATTGAAG
1 AGGTTGAAG
13219118 TTACAACACT
Statistics
Matches: 274, Mismatches: 59, Indels: 50
0.72 0.15 0.13
Matches are distributed among these distances:
33 1 0.00
34 21 0.08
35 3 0.01
38 1 0.00
40 1 0.00
44 8 0.03
45 228 0.83
46 11 0.04
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
AGGTTGAAGCCATCATCCAACTTTTACCCTAATCCAGAGAGGC
Found at i:13219416 original size:16 final size:16
Alignment explanation
Indices: 13219395--13219435 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
13219385 CATTTTTTTT
13219395 AACCCAAATAAAAAAA
1 AACCCAAATAAAAAAA
* *
13219411 AACCCAATTAAAACAA
1 AACCCAAATAAAAAAA
*
13219427 AACTCAAAT
1 AACCCAAAT
13219436 TCTTTAATCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.66, C:0.22, G:0.00, T:0.12
Consensus pattern (16 bp):
AACCCAAATAAAAAAA
Found at i:13220829 original size:11 final size:12
Alignment explanation
Indices: 13220813--13220855 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
13220803 ATTTACTAAC
13220813 ATTTAATTT-TT
1 ATTTAATTTATT
13220824 ATTTAATTTATT
1 ATTTAATTTATT
13220836 A-TT-ATTTATT
1 ATTTAATTTATT
13220846 ATTT-ATTTAT
1 ATTTAATTTAT
13220856 GGGTTATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.27
11 19 0.63
12 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTAATTTATT
Found at i:13233012 original size:26 final size:26
Alignment explanation
Indices: 13232982--13233033 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
13232972 TGAGATTGGA
* *
13232982 ACGTGGTAAGAGTTCCAATGAGAGTT
1 ACGTGGCAAGAGTTCCAAGGAGAGTT
13233008 ACGTGGCAAGAGTTCCAAGGAGAGTT
1 ACGTGGCAAGAGTTCCAAGGAGAGTT
13233034 GAAGGGACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (26 bp):
ACGTGGCAAGAGTTCCAAGGAGAGTT
Found at i:13236369 original size:18 final size:18
Alignment explanation
Indices: 13236335--13236388 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
13236325 TGCAGCTTTT
13236335 TTTTCTTTTTCTT-TTCTTA
1 TTTTCTTTTTCTTCTTC--A
13236354 TTTCTCTTTTTCTTCTTCA
1 TTT-TCTTTTTCTTCTTCA
13236373 TTTT-TATTTTCTTCTT
1 TTTTCT-TTTTCTTCTT
13236389 TTTATAACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.03
18 11 0.34
19 7 0.22
20 10 0.31
21 3 0.09
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTTCTTCTTCA
Found at i:13236383 original size:26 final size:27
Alignment explanation
Indices: 13236334--13236391 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
13236324 TTGCAGCTTT
* *
13236334 TTTTTCTTTTTCTTTTCTTATTTC-TC
1 TTTTTCTTCTTCATTTCTTATTTCTTC
13236360 TTTTTCTTCTTCATTT-TTATTTTCTTC
1 TTTTTCTTCTTCATTTCTTA-TTTCTTC
13236387 TTTTT
1 TTTTT
13236392 ATAACCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 3 0.11
26 18 0.64
27 7 0.25
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTTCTTCTTCATTTCTTATTTCTTC
Found at i:13236517 original size:27 final size:27
Alignment explanation
Indices: 13236479--13236534 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
13236469 TTTTGACGCC
13236479 ACCACCGCCACTCCCCGTTAGATTCCG
1 ACCACCGCCACTCCCCGTTAGATTCCG
* *
13236506 ACCATCGCCACTCCCCGTTGGATTCCG
1 ACCACCGCCACTCCCCGTTAGATTCCG
13236533 AC
1 AC
13236535 GTTGTTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.46, G:0.16, T:0.20
Consensus pattern (27 bp):
ACCACCGCCACTCCCCGTTAGATTCCG
Found at i:13237811 original size:18 final size:15
Alignment explanation
Indices: 13237769--13237805 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
13237759 TTTCTACTAT
13237769 TGCCACCTCCGCTAC
1 TGCCACCTCCGCTAC
13237784 TGCCACCTCCGCTAC
1 TGCCACCTCCGCTAC
13237799 TGCCACC
1 TGCCACC
13237806 ACCTCCACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.14, C:0.54, G:0.14, T:0.19
Consensus pattern (15 bp):
TGCCACCTCCGCTAC
Found at i:13240722 original size:43 final size:43
Alignment explanation
Indices: 13240661--13240749 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
13240651 GATTCGATCG
*
13240661 AACGCTCACCCCTAGCCATGCCTCCTTGACCTTGTTCTTCATC
1 AACGCTCACCCCTAGCCATGCCTCCTCGACCTTGTTCTTCATC
13240704 AACGCTCACCCCTAGCCATGCCTCCTCGACCTTGTTCTTCATC
1 AACGCTCACCCCTAGCCATGCCTCCTCGACCTTGTTCTTCATC
13240747 AAC
1 AAC
13240750 ACATTTACGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.18, C:0.43, G:0.11, T:0.28
Consensus pattern (43 bp):
AACGCTCACCCCTAGCCATGCCTCCTCGACCTTGTTCTTCATC
Found at i:13241962 original size:29 final size:29
Alignment explanation
Indices: 13241920--13241986 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
13241910 GAATATCGAT
*
13241920 GCCACACGGTCGTGTGTCAGGCTTTGTGA
1 GCCACACGATCGTGTGTCAGGCTTTGTGA
13241949 GCCACACGATCGTGTGTCAGGCTTTGTGA
1 GCCACACGATCGTGTGTCAGGCTTTGTGA
13241978 GCCACACGA
1 GCCACACGA
13241987 CACCACACGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24
Consensus pattern (29 bp):
GCCACACGATCGTGTGTCAGGCTTTGTGA
Found at i:13244991 original size:13 final size:13
Alignment explanation
Indices: 13244973--13244999 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13244963 GTAATGTGAA
13244973 GCGAGAAGGATAT
1 GCGAGAAGGATAT
13244986 GCGAGAAGGATAT
1 GCGAGAAGGATAT
13244999 G
1 G
13245000 TCTTCAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (13 bp):
GCGAGAAGGATAT
Found at i:13247916 original size:14 final size:16
Alignment explanation
Indices: 13247899--13247935 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
13247889 ATTAAAATAT
13247899 AAATTT-TA-AATTAA
1 AAATTTATATAATTAA
13247913 AAATTTATATAATT-A
1 AAATTTATATAATTAA
13247928 AAATTTAT
1 AAATTTAT
13247936 TGTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 11 0.52
16 4 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTTATATAATTAA
Found at i:13248026 original size:10 final size:9
Alignment explanation
Indices: 13248005--13248036 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
13247995 AAGTTTTATT
13248005 TTTTAATAA
1 TTTTAATAA
13248014 TTTTAATATA
1 TTTTAATA-A
13248024 TTTTAATAA
1 TTTTAATAA
13248033 TTTT
1 TTTT
13248037 CCCCTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTAATAA
Found at i:13248115 original size:37 final size:36
Alignment explanation
Indices: 13248074--13248162 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 36
13248064 ATATATATTC
13248074 AAATTTATATATTTTTTAAAAATATATATTAAAAATT
1 AAATTTATAT-TTTTTTAAAAATATATATTAAAAATT
* * *
13248111 AAA-TTAAATTTTTATTTTAAATTATATATTAAAAATT
1 AAATTTATA-TTTT-TTTAAAAATATATATTAAAAATT
13248148 --ATTT-TATTTTTTTAA
1 AAATTTATATTTTTTTAA
13248163 TTTTTTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
33 4 0.09
34 4 0.09
35 2 0.05
36 9 0.20
37 25 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
AAATTTATATTTTTTTAAAAATATATATTAAAAATT
Found at i:13248406 original size:17 final size:17
Alignment explanation
Indices: 13248386--13248484 Score: 72
Period size: 17 Copynumber: 5.5 Consensus size: 17
13248376 CTATTTTAAC
*
13248386 TTAAATTTGATTTTATT
1 TTAAATTTAATTTTATT
* * *
13248403 TTAACTTCAATTTTGTT
1 TTAAATTTAATTTTATT
13248420 TTAAATTTTAAATTTTAAATT
1 TTAAA-TTT-AATTTT--ATT
**
13248441 TTAAATTTTAAATTTTAAC
1 TTAAA-TTT-AATTTTATT
* *
13248460 TTAACTTAAATTTTATT
1 TTAAATTTAATTTTATT
13248477 TTAAATTT
1 TTAAATTT
13248485 CAACTTAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
17 30 0.48
18 4 0.06
19 11 0.17
21 18 0.29
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
TTAAATTTAATTTTATT
Found at i:13248430 original size:7 final size:7
Alignment explanation
Indices: 13248418--13248484 Score: 84
Period size: 7 Copynumber: 9.4 Consensus size: 7
13248408 TTCAATTTTG
13248418 TTTTAAA
1 TTTTAAA
13248425 TTTTAAA
1 TTTTAAA
13248432 TTTTAAA
1 TTTTAAA
13248439 TTTTAAA
1 TTTTAAA
13248446 TTTTAAA
1 TTTTAAA
*
13248453 TTTTAAC
1 TTTTAAA
13248460 TTAACTTAAA
1 TT---TTAAA
13248470 TTTT--A
1 TTTTAAA
13248475 TTTTAAA
1 TTTTAAA
13248482 TTT
1 TTT
13248485 CAACTTAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
5 5 0.09
7 42 0.79
10 6 0.11
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTTAAA
Found at i:13248473 original size:24 final size:24
Alignment explanation
Indices: 13248441--13248527 Score: 88
Period size: 24 Copynumber: 3.5 Consensus size: 24
13248431 ATTTTAAATT
13248441 TTAAATTTTAAATTTT-AACTT-AAC
1 TTAAATTTT--ATTTTAAACTTCAAC
*
13248465 TTAAATTTTATTTTAAATTTCAAC
1 TTAAATTTTATTTTAAACTTCAAC
* *
13248489 TTAAATTTTATTTTAACTTCTTCAAT
1 TTAAATTTTATTTTAA--ACTTCAAC
*
13248515 TTCAATTTTATTT
1 TTAAATTTTATTT
13248528 AATAAATTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
22 5 0.09
23 4 0.07
24 28 0.52
26 17 0.31
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAATTTTATTTTAAACTTCAAC
Found at i:13248480 original size:12 final size:12
Alignment explanation
Indices: 13248411--13248527 Score: 72
Period size: 14 Copynumber: 8.8 Consensus size: 12
13248401 TTTTAACTTC
*
13248411 AATTTTGTTTTA
1 AATTTTATTTTA
13248423 AATTTTAAATTTTA
1 AATTTT--ATTTTA
13248437 AATTTTAAATTTTA
1 AATTTT--ATTTTA
13248451 AATTTTAACTTAACTTA
1 AATTTT-A-TT---TTA
13248468 AATTTTATTTTA
1 AATTTTATTTTA
* **
13248480 AATTTCAACTTA
1 AATTTTATTTTA
13248492 AATTTTATTTTA
1 AATTTTATTTTA
* * *
13248504 ACTTCTTCAATTTC
1 AATT-TT-ATTTTA
13248518 AATTTTATTT
1 AATTTTATTT
13248528 AATAAATTTA
Statistics
Matches: 85, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
12 33 0.39
13 6 0.07
14 34 0.40
15 2 0.02
16 1 0.01
17 9 0.11
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (12 bp):
AATTTTATTTTA
Found at i:13251041 original size:12 final size:12
Alignment explanation
Indices: 13251024--13251049 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13251014 CCTAAACAGC
13251024 CCGATTGATCTT
1 CCGATTGATCTT
13251036 CCGATTGATCTT
1 CCGATTGATCTT
13251048 CC
1 CC
13251050 CAGTAGATGT
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:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (12 bp):
CCGATTGATCTT
Found at i:13253796 original size:29 final size:28
Alignment explanation
Indices: 13253745--13253810 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
13253735 AACTGTTTTA
*
13253745 TTATTTTTACTATGTAATTAATAATTAG
1 TTATATTTACTATGTAATTAATAATTAG
* *
13253773 TTATATTTACATATTTAATTAATAATTAT
1 TTATATTTAC-TATGTAATTAATAATTAG
13253802 TTATATTTA
1 TTATATTTA
13253811 TATTAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 9 0.26
29 25 0.74
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (28 bp):
TTATATTTACTATGTAATTAATAATTAG
Found at i:13254057 original size:34 final size:34
Alignment explanation
Indices: 13253969--13254058 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 34
13253959 TGTTAGAATT
* **
13253969 TTATTATTTTTGTTTCATTTGGTAGTTTTAAGTG
1 TTATTATTTTTGTTTCATTTTGTAGTTTTAAGCC
*
13254003 TTATTATTTTTGTTTCATTTTTTAGTTTTAAGCC
1 TTATTATTTTTGTTTCATTTTGTAGTTTTAAGCC
*
13254037 TTATCATTTTTGTTTCATTTTG
1 TTATTATTTTTGTTTCATTTTG
13254059 GTGAATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.64
Consensus pattern (34 bp):
TTATTATTTTTGTTTCATTTTGTAGTTTTAAGCC
Found at i:13260756 original size:17 final size:17
Alignment explanation
Indices: 13260734--13260772 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
13260724 AGGTGGAGAA
* * *
13260734 CTTGTTCGTTGAGAGTT
1 CTTGTTAGTAGAGAATT
13260751 CTTGTTAGTAGAGAATT
1 CTTGTTAGTAGAGAATT
13260768 CTTGT
1 CTTGT
13260773 CAAGTTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTAGTAGAGAATT
Found at i:13268921 original size:25 final size:25
Alignment explanation
Indices: 13268885--13268958 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
13268875 AAAGAGGTAG
* *
13268885 CCACATAAGCTTTCTAGAGAAATTA
1 CCACAAAAGCTTTCTAGAGAAATCA
* * * *
13268910 CGACAAAGGCTTTCCAAAGAAATCA
1 CCACAAAAGCTTTCTAGAGAAATCA
13268935 CCACAAAAGCTTTCTAGAGAAATC
1 CCACAAAAGCTTTCTAGAGAAATC
13268959 CGTGTTTGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.22
Consensus pattern (25 bp):
CCACAAAAGCTTTCTAGAGAAATCA
Found at i:13271000 original size:101 final size:101
Alignment explanation
Indices: 13270825--13271010 Score: 363
Period size: 101 Copynumber: 1.8 Consensus size: 101
13270815 AAAATGTTTA
13270825 GAACCACCACTCGAGAAAGAGGTCGTCGCTAGAGTCAAAAAATAACAATTCTAGAGACCTAATCA
1 GAACCACCACTCGAGAAAGAGGTCGTCGCTAGAGTCAAAAAATAACAATTCTAGAGACCTAATCA
13270890 CATTCGAACCCAGAGGTCGCGATAACACTCCACAAC
66 CATTCGAACCCAGAGGTCGCGATAACACTCCACAAC
*
13270926 GAACCACCACTCGAGAAAGAGGTCGTCGCTAGAGTCAAAAAATAACAATTTTAGAGACCTAATCA
1 GAACCACCACTCGAGAAAGAGGTCGTCGCTAGAGTCAAAAAATAACAATTCTAGAGACCTAATCA
13270991 CATTCGAACCCAGAGGTCGC
66 CATTCGAACCCAGAGGTCGC
13271011 TAGAGTCAAA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (101 bp):
GAACCACCACTCGAGAAAGAGGTCGTCGCTAGAGTCAAAAAATAACAATTCTAGAGACCTAATCA
CATTCGAACCCAGAGGTCGCGATAACACTCCACAAC
Found at i:13279789 original size:25 final size:25
Alignment explanation
Indices: 13279752--13279814 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
13279742 GTCATATAAT
* *
13279752 CTTTCCAG-GAAATCACCACAAAGG
1 CTTTCTAGAGAAATCACCACAAAAG
*
13279776 CTTTCTAGAGAAATCGCCACAAAAG
1 CTTTCTAGAGAAATCACCACAAAAG
13279801 CTTTCTAGAGAAAT
1 CTTTCTAGAGAAAT
13279815 TCGTGTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 7 0.20
25 28 0.80
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (25 bp):
CTTTCTAGAGAAATCACCACAAAAG
Found at i:13283703 original size:19 final size:20
Alignment explanation
Indices: 13283681--13283726 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
13283671 GATAAAAAAC
*
13283681 TTAAATATCTAA-TTAAATA
1 TTAAATATCAAATTTAAATA
*
13283700 TTAAA-ACCAAATTTAAATA
1 TTAAATATCAAATTTAAATA
*
13283719 TCAAATAT
1 TTAAATAT
13283727 TACATTAGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 4 0.19
19 16 0.76
20 1 0.05
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAATATCAAATTTAAATA
Found at i:13290472 original size:10 final size:11
Alignment explanation
Indices: 13290454--13290479 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13290444 TAATAATTTT
13290454 CTAAAAAAATA
1 CTAAAAAAATA
13290465 CTAAAAAAATA
1 CTAAAAAAATA
13290476 CTAA
1 CTAA
13290480 TACAGGGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (11 bp):
CTAAAAAAATA
Found at i:13290525 original size:27 final size:27
Alignment explanation
Indices: 13290487--13290538 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
13290477 TAATACAGGG
13290487 GTGGTGCCTACCTGACAGGCGGCACTA
1 GTGGTGCCTACCTGACAGGCGGCACTA
*
13290514 GTGGTGCCTACCTGTCAGGCGGCAC
1 GTGGTGCCTACCTGACAGGCGGCAC
13290539 CAACCCGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACTA
Found at i:13291092 original size:27 final size:27
Alignment explanation
Indices: 13291050--13291101 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
13291040 ATTCGGGTTT
13291050 GTGCCGCCTGATAGGTAGGCACCACTA
1 GTGCCGCCTGATAGGTAGGCACCACTA
13291077 GTGCCGCCTG-TCAGGTAGGCACCAC
1 GTGCCGCCTGAT-AGGTAGGCACCAC
13291102 CCCCGTATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.19, C:0.33, G:0.31, T:0.17
Consensus pattern (27 bp):
GTGCCGCCTGATAGGTAGGCACCACTA
Found at i:13300417 original size:18 final size:18
Alignment explanation
Indices: 13300394--13300432 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
13300384 ACACGTTACA
13300394 GTTACAGCTCATATGAGT
1 GTTACAGCTCATATGAGT
* * *
13300412 GTTACAGGTTATATGGGT
1 GTTACAGCTCATATGAGT
13300430 GTT
1 GTT
13300433 GGTCTTGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.38
Consensus pattern (18 bp):
GTTACAGCTCATATGAGT
Found at i:13300596 original size:69 final size:69
Alignment explanation
Indices: 13300494--13300639 Score: 211
Period size: 69 Copynumber: 2.1 Consensus size: 69
13300484 CCACAGCCTG
* *
13300494 TGTGAGAAGCATCGTGTAACCTAACATCCCGACCCACACCTCGTGTGAGCAGACCCATTTCACAG
1 TGTGAGCAGCATCGCGTAACCTAACATCCCGACCCACACCTCGTGTGAGCAGACCCATTTCACAG
13300559 CTCA
66 CTCA
* * * * * *
13300563 TGTGAGCAGCGTCGCGTAGCCTAACATCTCGACCCAGAGCTCGTGTGAGCAGGCCCATTTCACAG
1 TGTGAGCAGCATCGCGTAACCTAACATCCCGACCCACACCTCGTGTGAGCAGACCCATTTCACAG
*
13300628 CTCG
66 CTCA
13300632 TGTGAGCA
1 TGTGAGCA
13300640 TATATGATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (69 bp):
TGTGAGCAGCATCGCGTAACCTAACATCCCGACCCACACCTCGTGTGAGCAGACCCATTTCACAG
CTCA
Found at i:13300808 original size:265 final size:265
Alignment explanation
Indices: 13300335--13300835 Score: 804
Period size: 265 Copynumber: 1.9 Consensus size: 265
13300325 GATTCTCCAC
13300335 AGCTCGTGTGAGCAGACCCATTTCACAGCTCGTGTGAGCATATATGATTACACGTTACAGTTACA
1 AGCTCGTGTGAGCAGACCCATTTCACAGCTCGTGTGAGCATATATGATTACACGTTACAGTTACA
** * * * *
13300400 GCTCATATGAGTGTTACAGGTTATATGGGTGTTGGTCTTGGATGTCCTACCGATGGTTGAGGACT
66 GCTCATATGAGCATTACAGGTTATATGGGTGCTGGTCTCGGATGTCCTACCGATGGCTGAGGACC
* * * *
13300465 TGCATTTGTTGTGGATTCTCCACAGCCTGTGTGAGAAGCATCGTGTAACCTAACATCCCGACCCA
131 TACATTGGTTGAGGATTCTCCACAGCCCGTGTGAGAAGCATCGTGTAACCTAACATCCCGACCCA
*
13300530 CACCTCGTGTGAGCAGACCCATTTCACAGCTCATGTGAGCAGCGTCGCGTAGCCTAACATCTCGA
196 CACCTCGTGTGAGCAGACCCACTTCACAGCTCATGTGAGCAGCGTCGCGTAGCCTAACATCTCGA
13300595 CCCAG
261 CCCAG
* *
13300600 AGCTCGTGTGAGCAGGCCCATTTCACAGCTCGTGTGAGCATATATGATTACATGTTACAGTTACA
1 AGCTCGTGTGAGCAGACCCATTTCACAGCTCGTGTGAGCATATATGATTACACGTTACAGTTACA
* * *
13300665 GCTCATGTGAGCATTACAGGTTATATGGGTGCTGGTCTCGGATGTCCTATCGATGGCTGAGGTCC
66 GCTCATATGAGCATTACAGGTTATATGGGTGCTGGTCTCGGATGTCCTACCGATGGCTGAGGACC
* * * * *
13300730 TACATTGGTTGAGGATTCTCTACAGCCCGTGTGGGTAGCATCGTGTAGCCTAACATCTCGACCCA
131 TACATTGGTTGAGGATTCTCCACAGCCCGTGTGAGAAGCATCGTGTAACCTAACATCCCGACCCA
*
13300795 CAGCTCGTGTGAGCAGACCCACTTCACAGCTCATGTGAGCA
196 CACCTCGTGTGAGCAGACCCACTTCACAGCTCATGTGAGCA
13300836 TTAGAAGTTA
Statistics
Matches: 214, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
265 214 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (265 bp):
AGCTCGTGTGAGCAGACCCATTTCACAGCTCGTGTGAGCATATATGATTACACGTTACAGTTACA
GCTCATATGAGCATTACAGGTTATATGGGTGCTGGTCTCGGATGTCCTACCGATGGCTGAGGACC
TACATTGGTTGAGGATTCTCCACAGCCCGTGTGAGAAGCATCGTGTAACCTAACATCCCGACCCA
CACCTCGTGTGAGCAGACCCACTTCACAGCTCATGTGAGCAGCGTCGCGTAGCCTAACATCTCGA
CCCAG
Found at i:13304958 original size:3 final size:3
Alignment explanation
Indices: 13304950--13304990 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
13304940 AAAGGAAAGA
13304950 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
13304991 TAAGCATGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:13305209 original size:20 final size:20
Alignment explanation
Indices: 13305186--13305232 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
13305176 TTGATCTTGG
*
13305186 AAAAAAATTT-TATCTTTTAA
1 AAAAAAATTTAGAT-TTTTAA
13305206 AAAAAAATTTAGATTTTTAA
1 AAAAAAATTTAGATTTTTAA
13305226 AAAAAAA
1 AAAAAAA
13305233 AATATGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAAAATTTAGATTTTTAA
Found at i:13305304 original size:51 final size:49
Alignment explanation
Indices: 13305249--13305444 Score: 115
Period size: 51 Copynumber: 4.0 Consensus size: 49
13305239 TTTTTTATTC
13305249 ATTTTAAAGAAAAAGTTTAAATTTTTAATCAAAATTTTGATTTTTT-TAA
1 ATTTTAAA-AAAAAGTTTAAATTTTTAATCAAAATTTTGATTTTTTGTAA
* ** * ** **
13305298 CTATTTTGAAATAAAAGTTTTCATATTTAAGAAAAATAGTGA---TTT-TAA
1 --ATTTT-AAAAAAAAGTTTAAATTTTTAATCAAAATTTTGATTTTTTGTAA
* * *
13305346 A----AAAAATGAAAGTTTAGATTTTTCAATATAAAAATTT-ATTTTTTAGTAA
1 ATTTTAAAAA--AAAGTTTAAATTTTT-AAT-CAAAATTTTGATTTTTT-GTAA
* *
13305395 ATTTAAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGATTTTTTGTAA
1 ATTTTAAA-AAAAAGTTTAAATTTTTAATCAAAATTTTGATTTTTTGTAA
13305445 CTATTTCGAA
Statistics
Matches: 108, Mismatches: 21, Indels: 33
0.67 0.13 0.20
Matches are distributed among these distances:
41 4 0.04
43 12 0.11
44 3 0.03
45 5 0.05
46 1 0.01
47 3 0.03
48 6 0.06
49 4 0.04
50 11 0.10
51 37 0.34
52 17 0.16
53 3 0.03
54 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (49 bp):
ATTTTAAAAAAAAGTTTAAATTTTTAATCAAAATTTTGATTTTTTGTAA
Found at i:13305485 original size:147 final size:147
Alignment explanation
Indices: 13305213--13305581 Score: 458
Period size: 149 Copynumber: 2.5 Consensus size: 147
13305203 TAAAAAAAAA
* * * ** *
13305213 TTTAGATTTTTAAAAAAAAAAATATGTTTTTTA-TTCATTTTAAAGAAAAAGTTTAAATTTTTAA
1 TTTAGATTTTT-AAAATAAAAATTTATTTTTTAGTAAATTTAAAAGAAAAAGTTTAAATTTTTAA
* *
13305277 TCAAAATTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTTCATATTTAAGAAAAATAGTGA-T
65 ACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTCATATTTAAGAAAAATAGTGATT
13305341 TT-TAAAAAAAATGAAAG
130 TTCTAAAAAAAATGAAAG
*
13305358 TTTAGATTTTTCAATATAAAAATTTATTTTTTAGTAAATTTAAAAGAAAAAGTTTAAATTTTTAA
1 TTTAGATTTTT-AAAATAAAAATTTATTTTTTAGTAAATTTAAAAGAAAAAGTTTAAATTTTTAA
* *
13305423 ACAAAATTTTGATTTTTTGTAACTATTTCGAAATAAAAGCTTTT-ATCTTTAAGAAAAGTAGTGA
65 ACAAAATTTTGATTTTTT-TAACTATTTCGAAATAAAAG-TTTTCATATTTAAGAAAAATAGTGA
** *
13305487 TTTTCTTTAACAAATGAAAG
128 TTTTCTAAAAAAAATGAAAG
* * ** * ***
13305507 TTTAGATTTTTTTAAATAAAAATTTTTTTTTTAGTAGTTTTAAAATAAATTTTTTAAATTTTTAA
1 TTTAGA-TTTTTAAAATAAAAATTTATTTTTTAGTAAATTTAAAAGAAAAAGTTTAAATTTTTAA
*
13305572 AGAAAATTTT
65 ACAAAATTTT
13305582 TAAATTTTTA
Statistics
Matches: 193, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
145 28 0.15
146 45 0.23
147 37 0.19
148 7 0.04
149 71 0.37
150 5 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (147 bp):
TTTAGATTTTTAAAATAAAAATTTATTTTTTAGTAAATTTAAAAGAAAAAGTTTAAATTTTTAAA
CAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTCATATTTAAGAAAAATAGTGATTT
TCTAAAAAAAATGAAAG
Found at i:13305569 original size:22 final size:22
Alignment explanation
Indices: 13305544--13305602 Score: 95
Period size: 21 Copynumber: 2.7 Consensus size: 22
13305534 TTTTTAGTAG
13305544 TTTTAAA-ATAAATTTTTTAAAT
1 TTTTAAAGA-AAATTTTTTAAAT
13305566 TTTTAAAGAAAA-TTTTTAAAT
1 TTTTAAAGAAAATTTTTTAAAT
13305587 TTTTAAAGAAAATTTT
1 TTTTAAAGAAAATTTT
13305603 GATTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 21 0.60
22 13 0.37
23 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTTAAAGAAAATTTTTTAAAT
Found at i:13307042 original size:6 final size:6
Alignment explanation
Indices: 13307031--13307061 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
13307021 GCTAAACGTT
13307031 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC C
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC C
13307062 ATTCATTGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTTCCC
Found at i:13308517 original size:18 final size:18
Alignment explanation
Indices: 13308494--13308542 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 18
13308484 CCTGTCTTAT
13308494 TTCTTTACTGCTTTTGGG
1 TTCTTTACTGCTTTTGGG
* *
13308512 TTCTTT-C-ACTTTT-GT
1 TTCTTTACTGCTTTTGGG
13308527 TTCTTTACTGCTTTTG
1 TTCTTTACTGCTTTTG
13308543 ATTTGTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
15 7 0.28
16 6 0.24
17 6 0.24
18 6 0.24
ACGTcount: A:0.06, C:0.18, G:0.14, T:0.61
Consensus pattern (18 bp):
TTCTTTACTGCTTTTGGG
Found at i:13315009 original size:41 final size:43
Alignment explanation
Indices: 13314941--13315046 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 43
13314931 CTTGATGTTT
* *
13314941 AAAAGGAAGACTCATGTCTCTGGATGAGAATGAG-A-AT-GTGA
1 AAAAGGAAGACTCATGACTC-GAATGAGAATGAGAATATCGTGA
* * *
13314982 TAAAGGAAGACTCATGACTCGAAATGAGAGTGAGAATATCGTTA
1 AAAAGGAAGACTCATGACTCG-AATGAGAATGAGAATATCGTGA
*
13315026 AAAAGGAAGACTTATGACTCG
1 AAAAGGAAGACTCATGACTCG
13315047 GTAGAGCATA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
40 1 0.02
41 28 0.52
42 1 0.02
43 2 0.04
44 22 0.41
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (43 bp):
AAAAGGAAGACTCATGACTCGAATGAGAATGAGAATATCGTGA
Found at i:13317132 original size:109 final size:108
Alignment explanation
Indices: 13316825--13317132 Score: 382
Period size: 109 Copynumber: 2.8 Consensus size: 108
13316815 TTAGGCCTTG
* * * *
13316825 GATCGATGATATAAACTGTCGCGATGGATGAGATCTTGCATTTGTTGGGGATTCTCGATAGCTTG
1 GATCGATGATACAAACTGTCGCGATGGATGAGATCCTGCATATGTTGCGGATTCTCGATAGCTTG
* * * *
13316890 TATAAGCAGCATCATGAGCTAGTGACTATTGAATGGATACTAT
66 TGTGAGCAGCATCGTGAGCTGGTGACTATTGAATGGATACTAT
* * ** * *
13316933 GTTAAGATGATACAAACTGTCATGATGGTTGAGATCCTACATATGTTGCGGATTCTCGATAGCTT
1 GAT-CGATGATACAAACTGTCGCGATGGATGAGATCCTGCATATGTTGCGGATTCTCGATAGCTT
* *
13316998 GTGTGAGCAGCAACGTGAGTTGGTGACTATTGAATGGATACTAT
65 GTGTGAGCAGCATCGTGAGCTGGTGACTATTGAATGGATACTAT
* * * * *
13317042 GATCTGATGATACAAACCGTCGCGATGGCTAAGATCCTGCATATGTTACGGATTCTCAATAGCTT
1 GATC-GATGATACAAACTGTCGCGATGGATGAGATCCTGCATATGTTGCGGATTCTCGATAGCTT
* * *
13317107 GTGTGAGCAGTATCGTAAGCGGGTGA
65 GTGTGAGCAGCATCGTGAGCTGGTGA
13317133 TATAGGTCGT
Statistics
Matches: 167, Mismatches: 31, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
108 2 0.01
109 165 0.99
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (108 bp):
GATCGATGATACAAACTGTCGCGATGGATGAGATCCTGCATATGTTGCGGATTCTCGATAGCTTG
TGTGAGCAGCATCGTGAGCTGGTGACTATTGAATGGATACTAT
Found at i:13319842 original size:52 final size:52
Alignment explanation
Indices: 13319760--13320055 Score: 351
Period size: 52 Copynumber: 5.7 Consensus size: 52
13319750 AAATGCAAAA
* *
13319760 AGGTTCGATAACTATGTGTCATCGTAAGTATATGAATCCTTTACGGAATATG
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGAATATG
* *
13319812 AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAAATATG
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGAATATG
* * * * * * * *
13319864 AAGTCCAATGACTAAGTGTAATCATGAGTTTATGAATCCTTTATGGAATATG
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGAATATG
* * * *
13319916 AGG-TCTGATGACTAAGTGTCATCGTGAGTATATGAATCTTTTTCGGATTATG
1 AGGTTC-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGAATATG
* ** * * * *
13319968 AGGTCCGATGACTACATGTCATTGTGAGTACATGAATCCTTTACGGATTAAG
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGAATATG
* *
13320020 AGGTTCGATGACTATGTGTTATCGTGAGTAAATGAA
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAA
13320056 ATGAATCCCA
Statistics
Matches: 206, Mismatches: 36, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
51 1 0.00
52 204 0.99
53 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (52 bp):
AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGAATATG
Found at i:13324942 original size:15 final size:14
Alignment explanation
Indices: 13324911--13324940 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13324901 CCTCATTTCC
*
13324911 TTCATTTTTTTCTT
1 TTCATATTTTTCTT
13324925 TTCATATTTTTCTT
1 TTCATATTTTTCTT
13324939 TT
1 TT
13324941 TCCTGCCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TTCATATTTTTCTT
Found at i:13332800 original size:25 final size:25
Alignment explanation
Indices: 13332770--13332826 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
13332760 AAAGGTTGGT
*
13332770 AAAAAATTTTGACCTTTAAAAAAAA
1 AAAAAATTTAGACCTTTAAAAAAAA
* * **
13332795 AAAAAAATTAGACCTTTTAAAAATT
1 AAAAAATTTAGACCTTTAAAAAAAA
13332820 AAAAAAT
1 AAAAAAT
13332827 AATATTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (25 bp):
AAAAAATTTAGACCTTTAAAAAAAA
Done.