Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 30 of 143
Found at i:8841614 original size:30 final size:29
Alignment explanation
Indices: 8841452--8841614 Score: 154
Period size: 29 Copynumber: 5.5 Consensus size: 29
8841442 TAAATTGTCA
*
8841452 AAAAATTACATTTTAACCCTC-AAACTTTT
1 AAAAATTACATTTTAACCC-CAAAACTTTC
**
8841481 AAAAATTACATTTTTGAA-CTTAAAA-TTTC
1 AAAAATTACA-TTTT-AACCCCAAAACTTTC
* *
8841510 TAAAAATTACATTTTTACCCCTAAA-TTTAC
1 -AAAAATTACATTTTAACCCCAAAACTTT-C
* *
8841540 AAAAATTACATTTTTAACCCAAAAACTTCC
1 AAAAATTACA-TTTTAACCCCAAAACTTTC
* *
8841570 AAAAATTCCATTTTAACCCCAAAACTTGC
1 AAAAATTACATTTTAACCCCAAAACTTTC
8841599 AAAAATTACCATTTTA
1 AAAAATTA-CATTTTA
8841615 CCCTCGAACG
Statistics
Matches: 110, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
28 1 0.01
29 58 0.53
30 47 0.43
31 4 0.04
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCCAAAACTTTC
Found at i:8848845 original size:23 final size:23
Alignment explanation
Indices: 8848801--8848845 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
8848791 AACATAAAAT
**
8848801 TTTCTTTTGTTTTAACTTAATTC
1 TTTCTTTTGTTTTAACAAAATTC
8848824 TTTCTTTT-TTTTAATCAAAATT
1 TTTCTTTTGTTTTAA-CAAAATT
8848846 TCAAACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTCTTTTGTTTTAACAAAATTC
Found at i:8849998 original size:23 final size:23
Alignment explanation
Indices: 8849954--8849998 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
8849944 AACATAAAAT
**
8849954 TTTCTTTTGTTTTAACTTAATTC
1 TTTCTTTTGTTTTAACAAAATTC
8849977 TTTCTTTT-TTTTAATCAAAATT
1 TTTCTTTTGTTTTAA-CAAAATT
8849999 TCAAACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTCTTTTGTTTTAACAAAATTC
Found at i:8850350 original size:19 final size:19
Alignment explanation
Indices: 8850320--8850366 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
8850310 TTACTATTTG
8850320 TGTATG-TATGTA-TAATTA
1 TGTATGTTATGTACT-ATTA
*
8850338 TGTATGTTATGTACTGTTA
1 TGTATGTTATGTACTATTA
8850357 TGTATGTTAT
1 TGTATGTTAT
8850367 AGTCCATACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.23
19 19 0.73
20 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (19 bp):
TGTATGTTATGTACTATTA
Found at i:8850437 original size:21 final size:20
Alignment explanation
Indices: 8850412--8850574 Score: 78
Period size: 21 Copynumber: 8.3 Consensus size: 20
8850402 GATATGTAAA
8850412 TTATGTATGTTATGTTTAGTG
1 TTATGTATGTTATGTTTA-TG
* *
8850433 TTATGTTTG-TAT-ATT-TG
1 TTATGTATGTTATGTTTATG
8850450 -TATGTATGTTATGTTTACTG
1 TTATGTATGTTATGTTTA-TG
* * *
8850470 TTATGTATATTATATATGTATAA
1 TTATGTATGTTATGT-T-TAT-G
8850493 TTATGTATGTCT-TGTTTACTG
1 TTATGTATGT-TATGTTTA-TG
* *
8850514 TTATGTTTG-TAT-ATT-TG
1 TTATGTATGTTATGTTTATG
* * *
8850531 -TATGTATATCATG--TATA
1 TTATGTATGTTATGTTTATG
*
8850548 CTATGTATGTTATGTTTACTG
1 TTATGTATGTTATGTTTA-TG
8850569 TTATGT
1 TTATGT
8850575 TTGTATGATT
Statistics
Matches: 104, Mismatches: 20, Indels: 36
0.65 0.12 0.22
Matches are distributed among these distances:
16 14 0.13
17 10 0.10
18 13 0.12
19 5 0.05
20 8 0.08
21 36 0.35
22 4 0.04
23 13 0.12
24 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.17, T:0.56
Consensus pattern (20 bp):
TTATGTATGTTATGTTTATG
Found at i:8850461 original size:37 final size:37
Alignment explanation
Indices: 8850413--8850537 Score: 144
Period size: 37 Copynumber: 3.2 Consensus size: 37
8850403 ATATGTAAAT
*
8850413 TATGTATGTTATGTTTAGTGTTATGTTTGTATATTTG
1 TATGTATGTTATGTTTACTGTTATGTTTGTATATTTG
* *
8850450 TATGTATGTTATGTTTACTGTTATGTATATTATATATGTATAAT
1 TATGTATGTTATGTTTACTGTTATG--T-TTGTATAT-T-T--G
8850494 TATGTATGTCT-TGTTTACTGTTATGTTTGTATATTTG
1 TATGTATGT-TATGTTTACTGTTATGTTTGTATATTTG
8850531 TATGTAT
1 TATGTAT
8850538 ATCATGTATA
Statistics
Matches: 75, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
37 31 0.41
39 2 0.03
40 8 0.11
41 8 0.11
42 2 0.03
44 23 0.31
45 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.18, T:0.58
Consensus pattern (37 bp):
TATGTATGTTATGTTTACTGTTATGTTTGTATATTTG
Found at i:8850463 original size:55 final size:58
Alignment explanation
Indices: 8850336--8850463 Score: 154
Period size: 55 Copynumber: 2.2 Consensus size: 58
8850326 TATGTATAAT
** *
8850336 TATGTATGTTATGTACTGTTATGTATGTTATAGTCCATACTGTTTTGTTTGTATATTTG
1 TATGTATGTTATGTACAATTATGTATGTTATAGT-CATACTGTTATGTTTGTATATTTG
* * * * *
8850395 TATCTGTGATATGTA-AATTATGTATGTTAT-GT-TTAGTGTTATGTTTGTATATTTG
1 TATGTATGTTATGTACAATTATGTATGTTATAGTCATACTGTTATGTTTGTATATTTG
8850450 TATGTATGTTATGT
1 TATGTATGTTATGT
8850464 TTACTGTTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
55 31 0.53
57 2 0.03
58 13 0.22
59 12 0.21
ACGTcount: A:0.22, C:0.04, G:0.20, T:0.55
Consensus pattern (58 bp):
TATGTATGTTATGTACAATTATGTATGTTATAGTCATACTGTTATGTTTGTATATTTG
Found at i:8850562 original size:18 final size:18
Alignment explanation
Indices: 8850531--8850580 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
8850521 TGTATATTTG
* *
8850531 TATGTATATCATGTATAC
1 TATGTATGTTATGTATAC
*
8850549 TATGTATGTTATGTTTAC
1 TATGTATGTTATGTATAC
*
8850567 TGT-TATGTT-TGTAT
1 TATGTATGTTATGTAT
8850581 GATTGTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 4 0.15
17 6 0.22
18 17 0.63
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.54
Consensus pattern (18 bp):
TATGTATGTTATGTATAC
Found at i:8853728 original size:23 final size:22
Alignment explanation
Indices: 8853698--8853750 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
8853688 AGATAGATGA
*
8853698 ATGGTTTTATATAAATATAATAG
1 ATGGTTTT-TATAAATACAATAG
* * *
8853721 ATGGTTTTTTTAGATACAATGG
1 ATGGTTTTTATAAATACAATAG
8853743 ATGGTTTT
1 ATGGTTTT
8853751 GTTTAGATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (22 bp):
ATGGTTTTTATAAATACAATAG
Found at i:8853748 original size:22 final size:23
Alignment explanation
Indices: 8853720--8853764 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
8853710 AAATATAATA
8853720 GATGGTTTT-TTTAGATACAATG
1 GATGGTTTTGTTTAGATACAATG
8853742 GATGGTTTTGTTTAGATACAATG
1 GATGGTTTTGTTTAGATACAATG
8853765 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.44
Consensus pattern (23 bp):
GATGGTTTTGTTTAGATACAATG
Found at i:8856486 original size:3 final size:3
Alignment explanation
Indices: 8856478--8856536 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
8856468 GTGTTCCATA
8856478 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
8856526 TTC TTC TTC TT
1 TTC TTC TTC TT
8856537 TCTCGAAGCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:8857476 original size:31 final size:29
Alignment explanation
Indices: 8857435--8857511 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
8857425 ATAACGGCAC
* *
8857435 AATGATCAAAATATTATAAATTGATAACA-TT
1 AATGACCAAAATATAATAAATT-A-AA-ATTT
8857466 AATGACCAAAATATAATAAATTAAAATTT
1 AATGACCAAAATATAATAAATTAAAATTT
*
8857495 AATGACCAAAACATAAT
1 AATGACCAAAATATAAT
8857512 TTAAATCATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.02
29 20 0.48
30 1 0.02
31 20 0.48
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (29 bp):
AATGACCAAAATATAATAAATTAAAATTT
Found at i:8858487 original size:18 final size:19
Alignment explanation
Indices: 8858461--8858499 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
8858451 CAAAGTAAAT
* *
8858461 AAAATATTAAT-TTTTTTA
1 AAAAAATTAATATTTTATA
8858479 AAAAAATTAATATTTTATA
1 AAAAAATTAATATTTTATA
8858498 AA
1 AA
8858500 TACCGACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAAAATTAATATTTTATA
Found at i:8861915 original size:49 final size:49
Alignment explanation
Indices: 8861862--8862236 Score: 254
Period size: 49 Copynumber: 7.7 Consensus size: 49
8861852 TCATCTTCAG
* * *
8861862 GGTATAAGGTTCGTCATTGCGGCTTCAATCTTTCCCATTATTTTTCTAA
1 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCATTATTTTTCTAA
* * * * * * * *
8861911 GGTATAAAGTTCGTCGTTGCTGCTTCAACCTTTCCC-TCCATATCTCCAT
1 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCAT-TATTTTTCTAA
* * * *
8861960 GGTA-ATAGATTCGCCGTTACGGCTTCAATCTTTGCCATTATTTTTCTAA
1 GGTATA-AGGTTCGCCGTTGCGGCTTCAACCTTTCCCATTATTTTTCTAA
* * * * * *
8862009 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCTC-TCCATATCTCCAT
1 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCAT-TATTTTTCTAA
* * * * * **
8862058 GGTACAAGATTCACCGTTGCGGGTTTAATTTTTCCCATTATTTTTCTAA
1 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCATTATTTTTCTAA
* * * * * *
8862107 GGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCC-TCCATATCTCCAT
1 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCAT-TATTTTTCTAA
* ** * * * * * ** *
8862156 GGTACAAGAATCACCGTTGCGGTTTCAATCTTTCCAATAACGTCTCTAA
1 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCATTATTTTTCTAA
* * *
8862205 GGTACAAGGTCCGCCGTTGTGGCTTCAACCTT
1 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTT
8862237 CCCCTTCAAA
Statistics
Matches: 245, Mismatches: 73, Indels: 16
0.73 0.22 0.05
Matches are distributed among these distances:
48 4 0.02
49 237 0.97
50 4 0.02
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.37
Consensus pattern (49 bp):
GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCATTATTTTTCTAA
Found at i:8862005 original size:98 final size:98
Alignment explanation
Indices: 8861878--8862241 Score: 514
Period size: 98 Copynumber: 3.7 Consensus size: 98
8861868 AGGTTCGTCA
* * *
8861878 TTGCGGCTTCAATCTTTCCCATTATTTTTCTAAGGTATAAAGTTCGTCGTTGCTGCTTCAACCTT
1 TTGCGGCTTCAATCTTTCCCATTATTTTTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAACCTT
*
8861943 TCCCTCCATATCTCCATGGTA-ATAGATTCGCCG
66 TCCCTCCATATCTCCATGGTACA-AGATTCACCG
* *
8861976 TTACGGCTTCAATCTTTGCCATTATTTTTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAACCTT
1 TTGCGGCTTCAATCTTTCCCATTATTTTTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAACCTT
*
8862041 TCTCTCCATATCTCCATGGTACAAGATTCACCG
66 TCCCTCCATATCTCCATGGTACAAGATTCACCG
* * * *
8862074 TTGCGGGTTTAATTTTTCCCATTATTTTTCTAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTT
1 TTGCGGCTTCAATCTTTCCCATTATTTTTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAACCTT
*
8862139 TCCCTCCATATCTCCATGGTACAAGAATCACCG
66 TCCCTCCATATCTCCATGGTACAAGATTCACCG
* * * ** * * * *
8862172 TTGCGGTTTCAATCTTTCCAATAACGTCTCTAAGGTACAAGGTCCGCCGTTGTGGCTTCAACCTT
1 TTGCGGCTTCAATCTTTCCCATTATTTTTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAACCTT
*
8862237 CCCCT
66 TCCCT
8862242 TCAAACCTGT
Statistics
Matches: 237, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
98 236 1.00
99 1 0.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (98 bp):
TTGCGGCTTCAATCTTTCCCATTATTTTTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAACCTT
TCCCTCCATATCTCCATGGTACAAGATTCACCG
Found at i:8863123 original size:8 final size:7
Alignment explanation
Indices: 8863107--8863177 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
8863097 TGACCTCTTC
8863107 TTTTTCT
1 TTTTTCT
8863114 TTTTTC-
1 TTTTTCT
*
8863120 CTTTTCT
1 TTTTTCT
8863127 TTTTTC-
1 TTTTTCT
*
8863133 -TTCTCT
1 TTTTTCT
8863139 ATTTTT-T
1 -TTTTTCT
*
8863146 TCTTTCT
1 TTTTTCT
8863153 TTTTTCTT
1 TTTTTC-T
8863161 TTTTTCT
1 TTTTTCT
8863168 TCTTTT-T
1 T-TTTTCT
8863175 TTT
1 TTT
8863178 GGGTGAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
5 4 0.08
6 11 0.22
7 22 0.43
8 14 0.27
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:8863133 original size:26 final size:25
Alignment explanation
Indices: 8863104--8863163 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
8863094 CCTTGACCTC
*
8863104 TTCTTTTTCTTTTTTCCTTTTCTTTT
1 TTCTTTTTATTTTTTCC-TTTCTTTT
* *
8863130 TTCTTCTCTATTTTTTTCTTTCTTTT
1 TTCTT-TTTATTTTTTCCTTTCTTTT
8863156 TTCTTTTT
1 TTCTTTTT
8863164 TTCTTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.07
26 18 0.62
27 9 0.31
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (25 bp):
TTCTTTTTATTTTTTCCTTTCTTTT
Found at i:8863174 original size:12 final size:12
Alignment explanation
Indices: 8863113--8863177 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
8863103 CTTCTTTTTC
*
8863113 TTTTTTCCTT-T
1 TTTTTTTCTTCT
8863124 TCTTTTTTCTTCT
1 T-TTTTTTCTTCT
*
8863137 CTATTTTT-TTCT
1 -TTTTTTTCTTCT
*
8863149 TTCTTTT-TTC-
1 TTTTTTTCTTCT
8863159 TTTTTTTCTTCT
1 TTTTTTTCTTCT
8863171 TTTTTTT
1 TTTTTTT
8863178 GGGTGAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
10 6 0.14
11 12 0.27
12 19 0.43
13 6 0.14
14 1 0.02
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTCTTCT
Found at i:8863176 original size:19 final size:19
Alignment explanation
Indices: 8863109--8863175 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
8863099 ACCTCTTCTT
8863109 TTTCTTTTTTCCTTTTCTTT-
1 TTTCTTTTTT-CTTTT-TTTC
* * *
8863129 TTTCTTCTCTATTTTTTTC
1 TTTCTTTTTTCTTTTTTTC
8863148 TTTCTTTTTTCTTTTTTTC
1 TTTCTTTTTTCTTTTTTTC
8863167 -TTCTTTTTT
1 TTTCTTTTTT
8863176 TTGGGTGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.30
19 20 0.50
20 8 0.20
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTCTTTTTTCTTTTTTTC
Found at i:8867100 original size:21 final size:21
Alignment explanation
Indices: 8867076--8867135 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
8867066 TATATGCATG
*
8867076 ACTTGTATCGGTAGAAATTGC
1 ACTTGTATCGGTAGAAATAGC
* *
8867097 ACTTGTATTGGTAGAACTAGC
1 ACTTGTATCGGTAGAAATAGC
** *
8867118 ACAAGTATCGATAGAAAT
1 ACTTGTATCGGTAGAAAT
8867136 CTGTACAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAATAGC
Found at i:8876227 original size:12 final size:14
Alignment explanation
Indices: 8876200--8876232 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
8876190 TTGAAATCTG
8876200 TTTTATATTCTATT
1 TTTTATATTCTATT
8876214 TTTTATA-TCT-TT
1 TTTTATATTCTATT
8876226 TTTTATA
1 TTTTATA
8876233 AATGCCTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 3 0.16
14 7 0.37
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATATTCTATT
Found at i:8880474 original size:6 final size:6
Alignment explanation
Indices: 8880463--8880524 Score: 63
Period size: 6 Copynumber: 9.7 Consensus size: 6
8880453 GGCAACCCAA
*
8880463 TTTTAT TTTTAT TTTTCT TTATT-T TCTTTAT TTTTAT TTTTATTT TTTTAT
1 TTTTAT TTTTAT TTTTAT TT-TTAT T-TTTAT TTTTAT TTTTA--T TTTTAT
8880514 TTTTAGT TTTT
1 TTTTA-T TTTT
8880525 CTCTTGCACT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
6 33 0.67
7 10 0.20
8 6 0.12
ACGTcount: A:0.13, C:0.03, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:8880498 original size:25 final size:24
Alignment explanation
Indices: 8880463--8880526 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
8880453 GGCAACCCAA
8880463 TTTTATTTTTATTTTTCTTTATTT
1 TTTTATTTTTATTTTTCTTTATTT
8880487 TCTTTATTTTTA---TT-TTTATTT
1 T-TTTATTTTTATTTTTCTTTATTT
8880508 TTTTATTTTTAGTTTTTCT
1 TTTTATTTTTA-TTTTTCT
8880527 CTTGCACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 2 0.06
24 3 0.09
25 11 0.32
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (24 bp):
TTTTATTTTTATTTTTCTTTATTT
Found at i:8880511 original size:9 final size:9
Alignment explanation
Indices: 8880468--8880517 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
8880458 CCCAATTTTA
8880468 TTTTTATTT
1 TTTTTATTT
8880477 TTCTTTATTT
1 TT-TTTATTT
*
8880487 TCTTTATTT
1 TTTTTATTT
*
8880496 TTATTTTTATT
1 TT-TTTAT-TT
8880507 TTTTTATTT
1 TTTTTATTT
8880516 TT
1 TT
8880518 AGTTTTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 14 0.41
10 16 0.47
11 4 0.12
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTATTT
Found at i:8880512 original size:20 final size:20
Alignment explanation
Indices: 8880468--8880524 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
8880458 CCCAATTTTA
*
8880468 TTTTTA-TTTT-TCTTTATT
1 TTTTTATTTTTATTTTTATT
8880486 TTCTTTATTTTTATTTTTATT
1 TT-TTTATTTTTATTTTTATT
8880507 TTTTTATTTTTAGTTTTT
1 TTTTTATTTTTA-TTTTT
8880525 CTCTTGCACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 14 0.41
21 14 0.41
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTATTTTTATTTTTATT
Found at i:8883705 original size:20 final size:21
Alignment explanation
Indices: 8883651--8883705 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 21
8883641 AATAAACGGG
*
8883651 AAAGAAAGAAAGA-A-AAAAA
1 AAAGAAAGAAAGAGAGGAAAA
*
8883670 AAAGAAAGAAATAGAGGAAAA
1 AAAGAAAGAAAGAGAGGAAAA
*
8883691 AAAG-AAGAAGGAGAG
1 AAAGAAAGAAAGAGAG
8883706 AAAGATAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 12 0.40
20 10 0.33
21 8 0.27
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAGAGAGGAAAA
Found at i:8886695 original size:7 final size:7
Alignment explanation
Indices: 8886674--8886764 Score: 51
Period size: 7 Copynumber: 13.0 Consensus size: 7
8886664 GTTTCATGTA
*
8886674 TAGGATT
1 TAGGGTT
*
8886681 TAGAGTT
1 TAGGGTT
8886688 TAGGGTT
1 TAGGGTT
*
8886695 TCA-AGTT
1 T-AGGGTT
8886702 TAGGGTT
1 TAGGGTT
*
8886709 TAAGGTT
1 TAGGGTT
**
8886716 TATGATTT
1 TA-GGGTT
*
8886724 TA-AGTT
1 TAGGGTT
8886730 TAGGGTT
1 TAGGGTT
*
8886737 TAAGGTT
1 TAGGGTT
* *
8886744 TAAGTTT
1 TAGGGTT
8886751 TAGGGTT
1 TAGGGTT
*
8886758 TAAGGTT
1 TAGGGTT
8886765 ATGAATTTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
6 6 0.09
7 53 0.83
8 5 0.08
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.46
Consensus pattern (7 bp):
TAGGGTT
Found at i:8886701 original size:14 final size:13
Alignment explanation
Indices: 8886674--8886745 Score: 72
Period size: 14 Copynumber: 5.2 Consensus size: 13
8886664 GTTTCATGTA
*
8886674 TAGGATTTAGAGTT
1 TAGGGTTTA-AGTT
8886688 TAGGGTTTCAAGTT
1 TAGGGTTT-AAGTT
8886702 TAGGGTTTAAGGTT
1 TAGGGTTTAA-GTT
**
8886716 TATGATTTTAAGTT
1 TA-GGGTTTAAGTT
8886730 TAGGGTTTAAGGTT
1 TAGGGTTTAA-GTT
8886744 TA
1 TA
8886746 AGTTTTAGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
13 8 0.16
14 34 0.69
15 7 0.14
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.46
Consensus pattern (13 bp):
TAGGGTTTAAGTT
Found at i:8886705 original size:28 final size:28
Alignment explanation
Indices: 8886685--8886745 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
8886675 AGGATTTAGA
8886685 GTTTAGGGTTTCAAGTTTAGGGTTTAAG
1 GTTTAGGGTTTCAAGTTTAGGGTTTAAG
* * *
8886713 GTTTATGATTTTAAGTTTAGGGTTTAAG
1 GTTTAGGGTTTCAAGTTTAGGGTTTAAG
8886741 GTTTA
1 GTTTA
8886746 AGTTTTAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.48
Consensus pattern (28 bp):
GTTTAGGGTTTCAAGTTTAGGGTTTAAG
Found at i:8886752 original size:14 final size:14
Alignment explanation
Indices: 8886707--8886761 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
8886697 AAGTTTAGGG
*
8886707 TTTAAGGTTTATGAT
1 TTTAAGGTTTAAG-T
* *
8886722 TTTAA-GTTTAGGG
1 TTTAAGGTTTAAGT
8886735 TTTAAGGTTTAAGT
1 TTTAAGGTTTAAGT
*
8886749 TTTAGGGTTTAAG
1 TTTAAGGTTTAAG
8886762 GTTATGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
13 5 0.15
14 24 0.71
15 5 0.15
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (14 bp):
TTTAAGGTTTAAGT
Found at i:8886759 original size:28 final size:28
Alignment explanation
Indices: 8886697--8886752 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
8886687 TTAGGGTTTC
*
8886697 AAGTTTAGGGTTTAAGGTTTATGATTTT
1 AAGTTTAGGGTTTAAGGTTTAAGATTTT
8886725 AAGTTTAGGGTTTAAGGTTTAAG-TTTT
1 AAGTTTAGGGTTTAAGGTTTAAGATTTT
8886752 A
1 A
8886753 GGGTTTAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (28 bp):
AAGTTTAGGGTTTAAGGTTTAAGATTTT
Found at i:8886773 original size:21 final size:20
Alignment explanation
Indices: 8886679--8886764 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 20
8886669 ATGTATAGGA
8886679 TTTAGAGTTTAGGGTTTCAA-G
1 TTTA-AGTTTAGGGTTT-AAGG
* * * *
8886700 TTTAGGGTTTAAGGTTTATGAT
1 TTTA-AGTTTAGGGTTTAAG-G
8886722 TTTAAGTTTAGGGTTTAAGG
1 TTTAAGTTTAGGGTTTAAGG
8886742 TTTAAGTTTTAGGGTTTAAGG
1 TTTAAG-TTTAGGGTTTAAGG
8886763 TT
1 TT
8886765 ATGAATTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.13
21 43 0.80
22 4 0.07
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (20 bp):
TTTAAGTTTAGGGTTTAAGG
Found at i:8887008 original size:20 final size:21
Alignment explanation
Indices: 8886983--8887023 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
8886973 GTCCATTTGC
8886983 CCCGG-AGGAGTAGAGTATTG
1 CCCGGAAGGAGTAGAGTATTG
8887003 CCCGGAAGGAGTAGAGTATTG
1 CCCGGAAGGAGTAGAGTATTG
8887024 TGGTGGCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.27, C:0.15, G:0.39, T:0.20
Consensus pattern (21 bp):
CCCGGAAGGAGTAGAGTATTG
Found at i:8891828 original size:16 final size:16
Alignment explanation
Indices: 8891807--8891856 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
8891797 TGATGGTGAT
8891807 ATTATTTTTGTAATTA
1 ATTATTTTTGTAATTA
8891823 ATTATTTTT-TATATT-
1 ATTATTTTTGTA-ATTA
*
8891838 A-TATTTTGGTAATTA
1 ATTATTTTTGTAATTA
8891853 ATTA
1 ATTA
8891857 GTTAGGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 14 0.48
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
ATTATTTTTGTAATTA
Found at i:8892595 original size:20 final size:21
Alignment explanation
Indices: 8892570--8892612 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
8892560 TATTTACTAC
8892570 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
8892590 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
8892611 TA
1 TA
8892613 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:8892713 original size:23 final size:22
Alignment explanation
Indices: 8892687--8892764 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
8892677 CTATAACAAC
8892687 ATTAAATAACAAATCAATTAAAA
1 ATTAAATAACAAATCAA-TAAAA
*
8892710 ATTAAATTAAACAAAACAA-AAAA
1 ATTAAA-T-AACAAATCAATAAAA
* *
8892733 CTTAAAATAATCAAATTAACTAACAA
1 ATT-AAATAA-CAAATCAA-TAA-AA
8892759 ATTAAA
1 ATTAAA
8892765 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.05
23 19 0.44
24 4 0.09
25 14 0.33
26 4 0.09
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (22 bp):
ATTAAATAACAAATCAATAAAA
Found at i:8892795 original size:18 final size:18
Alignment explanation
Indices: 8892772--8892806 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8892762 AAAATATTTT
8892772 AAAATTAACCAAACTTAA
1 AAAATTAACCAAACTTAA
*
8892790 AAAATTAATCAAACTTA
1 AAAATTAACCAAACTTA
8892807 CATTTTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTAACCAAACTTAA
Found at i:8892984 original size:4 final size:4
Alignment explanation
Indices: 8892977--8893026 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
8892967 TCCTTCTTCC
8892977 TTCT TTC- TTCT TTC- TTCT TTCT TTCT TTCT TT-T TT-T TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
8893021 TT-T TTC
1 TTCT TTC
8893027 CTTCAAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 15 0.36
4 27 0.64
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTCT
Found at i:8892996 original size:7 final size:7
Alignment explanation
Indices: 8892962--8893026 Score: 76
Period size: 7 Copynumber: 9.1 Consensus size: 7
8892952 TCTCTTTCTC
*
8892962 CTTCTTC
1 CTTCTTT
*
8892969 CTTCTTC
1 CTTCTTT
8892976 CTTCTTT
1 CTTCTTT
8892983 CTTCTTT
1 CTTCTTT
8892990 CTTCTTT
1 CTTCTTT
8892997 CTTTCTTT
1 C-TTCTTT
*
8893005 CTTTTTT
1 CTTCTTT
*
8893012 TTTCTTT
1 CTTCTTT
*
8893019 CTTTTTT
1 CTTCTTT
8893026 C
1 C
8893027 CTTCAAATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
7 44 0.86
8 7 0.14
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
CTTCTTT
Found at i:8893015 original size:18 final size:19
Alignment explanation
Indices: 8892970--8893026 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 19
8892960 TCCTTCTTCC
*
8892970 TTCTTCCTTCTTTC-TTCT
1 TTCTTCTTTCTTTCTTTCT
8892988 TTCTTCTTTCTTTCTTTCT
1 TTCTTCTTTCTTTCTTTCT
*
8893007 TT-TTTTTTCTTTCTTT-T
1 TTCTTCTTTCTTTCTTTCT
8893024 TTC
1 TTC
8893027 CTTCAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 3 0.09
18 26 0.74
19 6 0.17
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (19 bp):
TTCTTCTTTCTTTCTTTCT
Found at i:8899285 original size:26 final size:26
Alignment explanation
Indices: 8899256--8899459 Score: 188
Period size: 26 Copynumber: 8.1 Consensus size: 26
8899246 CAGTTACTAA
* *
8899256 ATCGCTCTTACGAGCTAGTACAATAT
1 ATCGCTCTTACGAGCCAGTACAGTAT
* *
8899282 ATCGCTCTTTCTAGCCAGTACAGTAT
1 ATCGCTCTTACGAGCCAGTACAGTAT
*
8899308 ATCGCTCTTTCGAGCCAGTACAGTAT
1 ATCGCTCTTACGAGCCAGTACAGTAT
* * * *
8899334 ATCGCTCATACGAGCCAGTTCCGCAT
1 ATCGCTCTTACGAGCCAGTACAGTAT
* * * *
8899360 ATCGCTCTTTCAAGCCAGTGCAATAT
1 ATCGCTCTTACGAGCCAGTACAGTAT
* * *
8899386 ATCGCTCTTACAAGCCAGTTCATTAT
1 ATCGCTCTTACGAGCCAGTACAGTAT
8899412 ATCG--C-T-C---CCAGTACAGTAT
1 ATCGCTCTTACGAGCCAGTACAGTAT
* **
8899431 ATCACTCTTACGAGCCAGTTTAGTAT
1 ATCGCTCTTACGAGCCAGTACAGTAT
8899457 ATC
1 ATC
8899460 ACTCCCAGTA
Statistics
Matches: 146, Mismatches: 25, Indels: 14
0.79 0.14 0.08
Matches are distributed among these distances:
19 13 0.09
21 1 0.01
22 2 0.01
23 2 0.01
24 1 0.01
26 127 0.87
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (26 bp):
ATCGCTCTTACGAGCCAGTACAGTAT
Found at i:8899335 original size:52 final size:52
Alignment explanation
Indices: 8899256--8899418 Score: 209
Period size: 52 Copynumber: 3.1 Consensus size: 52
8899246 CAGTTACTAA
* * * * *
8899256 ATCGCTCTTACGAGCTAGTACAATATATCGCTCTTTCTAGCCAGTACAGTAT
1 ATCGCTCTTTCGAGCCAGTACAATATATCGCTCTTACAAGCCAGTTCAGTAT
* * * * *
8899308 ATCGCTCTTTCGAGCCAGTACAGTATATCGCTCATACGAGCCAGTTCCGCAT
1 ATCGCTCTTTCGAGCCAGTACAATATATCGCTCTTACAAGCCAGTTCAGTAT
* * *
8899360 ATCGCTCTTTCAAGCCAGTGCAATATATCGCTCTTACAAGCCAGTTCATTAT
1 ATCGCTCTTTCGAGCCAGTACAATATATCGCTCTTACAAGCCAGTTCAGTAT
8899412 ATCGCTC
1 ATCGCTC
8899419 CCAGTACAGT
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 94 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (52 bp):
ATCGCTCTTTCGAGCCAGTACAATATATCGCTCTTACAAGCCAGTTCAGTAT
Found at i:8899340 original size:78 final size:78
Alignment explanation
Indices: 8899256--8899418 Score: 209
Period size: 78 Copynumber: 2.1 Consensus size: 78
8899246 CAGTTACTAA
* * * * * * *
8899256 ATCGCTCTTACGAGCTAGTACAATATATCGCTCTTTCTAGCCAGTACAGTATATCGCTCTTTCGA
1 ATCGCTCATACGAGCCAGTACAACATATCGCTCTTTCAAGCCAGTACAATATATCGCTCTTACAA
8899321 GCCAGTACAGTAT
66 GCCAGTACAGTAT
* ** *
8899334 ATCGCTCATACGAGCCAGTTCCGCATATCGCTCTTTCAAGCCAGTGCAATATATCGCTCTTACAA
1 ATCGCTCATACGAGCCAGTACAACATATCGCTCTTTCAAGCCAGTACAATATATCGCTCTTACAA
* *
8899399 GCCAGTTCATTAT
66 GCCAGTACAGTAT
8899412 ATCGCTC
1 ATCGCTC
8899419 CCAGTACAGT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (78 bp):
ATCGCTCATACGAGCCAGTACAACATATCGCTCTTTCAAGCCAGTACAATATATCGCTCTTACAA
GCCAGTACAGTAT
Found at i:8899487 original size:45 final size:45
Alignment explanation
Indices: 8899374--8899490 Score: 162
Period size: 45 Copynumber: 2.6 Consensus size: 45
8899364 CTCTTTCAAG
* * * * *
8899374 CCAGTGCAATATATCGCTCTTACAAGCCAGTTCATTATATCGCTC
1 CCAGTACAGTATATCGCTCTTACGAGCCAGTTCAGTATATCACTC
* *
8899419 CCAGTACAGTATATCACTCTTACGAGCCAGTTTAGTATATCACTC
1 CCAGTACAGTATATCGCTCTTACGAGCCAGTTCAGTATATCACTC
*
8899464 CCAGTACAGTATATTGCTCTTACGAGC
1 CCAGTACAGTATATCGCTCTTACGAGC
8899491 TAGATGACAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (45 bp):
CCAGTACAGTATATCGCTCTTACGAGCCAGTTCAGTATATCACTC
Found at i:8899680 original size:24 final size:24
Alignment explanation
Indices: 8899651--8899867 Score: 272
Period size: 24 Copynumber: 8.9 Consensus size: 24
8899641 CAGCTAATGC
8899651 ACGTTTATGCTCGTCAGCCACTAT
1 ACGTTTATGCTCGTCAGCCACTAT
* * *
8899675 ATGTTTATGCTCGTTAGCCATTAT
1 ACGTTTATGCTCGTCAGCCACTAT
*
8899699 ACGTTTATGCTCATCAGCCACTAT
1 ACGTTTATGCTCGTCAGCCACTAT
* * *
8899723 ACATTTATGCTCGTCAACCGCTAT
1 ACGTTTATGCTCGTCAGCCACTAT
* *
8899747 ACGTTTATGCTTGTCAGCCATTGTAAT
1 ACGTTTATGCTCGTCAGCCA--CT-AT
8899774 ACGTTTATGCTCGTCAGCCACTAT
1 ACGTTTATGCTCGTCAGCCACTAT
* *
8899798 ACGTTTATGCTCGTCAACCACTGT
1 ACGTTTATGCTCGTCAGCCACTAT
* * *
8899822 ATGTTTATGCTTGTCAGCCACTGT
1 ACGTTTATGCTCGTCAGCCACTAT
*
8899846 ACGTTTATGCTCATCAGCCACT
1 ACGTTTATGCTCGTCAGCCACT
8899868 TAGATAAAAA
Statistics
Matches: 164, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
24 141 0.86
25 1 0.01
26 1 0.01
27 21 0.13
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (24 bp):
ACGTTTATGCTCGTCAGCCACTAT
Found at i:8902202 original size:13 final size:11
Alignment explanation
Indices: 8902163--8902194 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
8902153 TTATGCAAGG
8902163 TAACAATCTCA
1 TAACAATCTCA
8902174 TAACAATCTCA
1 TAACAATCTCA
8902185 TAACAATCTC
1 TAACAATCTC
8902195 GAATAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (11 bp):
TAACAATCTCA
Found at i:8903461 original size:24 final size:24
Alignment explanation
Indices: 8903426--8903506 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
8903416 AAACGTATAT
*
8903426 GCATAAATGTACAGTGGCTGACGA
1 GCATAAACGTACAGTGGCTGACGA
8903450 GCATAAACGTACAGTGGCTGACGA
1 GCATAAACGTACAGTGGCTGACGA
* * *
8903474 GCATAAATGTATAGTGGCTGACAA
1 GCATAAACGTACAGTGGCTGACGA
8903498 GCATAAACG
1 GCATAAACG
8903507 CATAAAAACT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (24 bp):
GCATAAACGTACAGTGGCTGACGA
Found at i:8903705 original size:45 final size:45
Alignment explanation
Indices: 8903631--8903752 Score: 147
Period size: 45 Copynumber: 2.7 Consensus size: 45
8903621 GAAGGTAAAT
* * * * *
8903631 GATATGTT-ATCTAGCTCGTAAGAGTGATATGCTGTACCGGGAGC
1 GATATGTTGAACTGGCTCGTAAGAGCGATATACTGTACCAGGAGC
* * *
8903675 GATATGTTGAACTGGCTCATAAGAGCGATATATTGTACTAGGAGC
1 GATATGTTGAACTGGCTCGTAAGAGCGATATACTGTACCAGGAGC
**
8903720 GATATACTGAACTGGCTCGTAAGAGCGATATAC
1 GATATGTTGAACTGGCTCGTAAGAGCGATATAC
8903753 AGCACTAGCT
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
44 8 0.12
45 57 0.88
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (45 bp):
GATATGTTGAACTGGCTCGTAAGAGCGATATACTGTACCAGGAGC
Found at i:8903752 original size:26 final size:26
Alignment explanation
Indices: 8903716--8903859 Score: 155
Period size: 26 Copynumber: 5.5 Consensus size: 26
8903706 ATTGTACTAG
8903716 GAGCGATATACTGAACTGGCTCGTAA
1 GAGCGATATACTGAACTGGCTCGTAA
* * * *
8903742 GAGCGATATACAGCACTAGCTCGAAA
1 GAGCGATATACTGAACTGGCTCGTAA
* * * *
8903768 GAGTGATATGCTGAACTGGCTCATAT
1 GAGCGATATACTGAACTGGCTCGTAA
* * *
8903794 GAGCGATATA-TTATACTAGCTCGAAA
1 GAGCGATATACTGA-ACTGGCTCGTAA
*
8903820 GAGCGATATACTGAACTGACTCGTAA
1 GAGCGATATACTGAACTGGCTCGTAA
*
8903846 GAGCGATTTACTGA
1 GAGCGATATACTGA
8903860 CTAAGCTTGT
Statistics
Matches: 92, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
25 2 0.02
26 88 0.96
27 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (26 bp):
GAGCGATATACTGAACTGGCTCGTAA
Found at i:8903798 original size:52 final size:52
Alignment explanation
Indices: 8903716--8903852 Score: 195
Period size: 52 Copynumber: 2.6 Consensus size: 52
8903706 ATTGTACTAG
8903716 GAGCGATATACTGAACTGGCTCGTAAGAGCGATATA-CAGCACTAGCTCGAAA
1 GAGCGATATACTGAACTGGCTCGTAAGAGCGATATATCA-CACTAGCTCGAAA
* * * * * *
8903768 GAGTGATATGCTGAACTGGCTCATATGAGCGATATATTATACTAGCTCGAAA
1 GAGCGATATACTGAACTGGCTCGTAAGAGCGATATATCACACTAGCTCGAAA
*
8903820 GAGCGATATACTGAACTGACTCGTAAGAGCGAT
1 GAGCGATATACTGAACTGGCTCGTAAGAGCGAT
8903853 TTACTGACTA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 72 0.99
53 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (52 bp):
GAGCGATATACTGAACTGGCTCGTAAGAGCGATATATCACACTAGCTCGAAA
Found at i:8911908 original size:23 final size:24
Alignment explanation
Indices: 8911882--8911935 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
8911872 CGTTTGTTTA
* *
8911882 ATGTTCACGAGCAT-TAAATGAAC
1 ATGTTCACGAACATATAAATAAAC
* *
8911905 ATGTTCATGAACATATAATTAAAC
1 ATGTTCACGAACATATAAATAAAC
8911929 ATGTTCA
1 ATGTTCA
8911936 TGAAAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (24 bp):
ATGTTCACGAACATATAAATAAAC
Found at i:8912745 original size:21 final size:20
Alignment explanation
Indices: 8912700--8912751 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
8912690 TGTGCTAGTT
*
8912700 CTACCGATACAAGTATGATTT
1 CTACCGATACAAGTATGA-TA
8912721 CTACCGATACAAGTCATGCA-A
1 CTACCGATACAAGT-ATG-ATA
8912742 CTACCGATAC
1 CTACCGATAC
8912752 CAAAACCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (20 bp):
CTACCGATACAAGTATGATA
Found at i:8917250 original size:19 final size:15
Alignment explanation
Indices: 8917215--8917262 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
8917205 GGGGATAGGG
8917215 TTTTTTCTTTTATTGTT
1 TTTTTTC-TTTATTG-T
8917232 CTTTATTTCTTTATCTGT
1 -TTT-TTTCTTTAT-TGT
8917250 TTTTTTCTTTATT
1 TTTTTTCTTTATT
8917263 TTGAGAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 9 0.32
17 3 0.11
18 9 0.32
19 6 0.21
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.77
Consensus pattern (15 bp):
TTTTTTCTTTATTGT
Found at i:8917544 original size:22 final size:22
Alignment explanation
Indices: 8917527--8917569 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8917517 CGAACGTTAT
*
8917527 ACGAACGGTTCA-CAAACGATTC
1 ACGAACAGTTCATCAAACG-TTC
8917549 ACGAACAGTTCATCAAACGTT
1 ACGAACAGTTCATCAAACGTT
8917570 TTATTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (22 bp):
ACGAACAGTTCATCAAACGTTC
Found at i:8919038 original size:19 final size:19
Alignment explanation
Indices: 8919011--8919050 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
8919001 AATTAAGCTG
8919011 AAGGTCAATAATATATATTA
1 AAGGTCAATAATATA-ATTA
8919031 AAGG-CAATAATATAATTA
1 AAGGTCAATAATATAATTA
8919049 AA
1 AA
8919051 TAATATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 10 0.50
20 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (19 bp):
AAGGTCAATAATATAATTA
Found at i:8937453 original size:70 final size:67
Alignment explanation
Indices: 8937322--8937454 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
8937312 ATAAACAATA
* * * *
8937322 TAATGGTTTTGCCTTTTAACTTAATGGGTAAATATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
8937387 CT
66 CT
* * *
8937389 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACGACGTAGTTTTGCCTTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTT
8937454 T
63 T
8937455 CTTATTCGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 19 0.34
68 2 0.04
70 35 0.62
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:8940256 original size:37 final size:41
Alignment explanation
Indices: 8940206--8940288 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 41
8940196 ATTAAAATAA
8940206 TAAAATAACATATA-ATTA-TA-T-T-TAAAAATATATTTTC
1 TAAAATAACATATAGATTATTATTGTATAAAAATA-ATTTTC
8940243 TAAAATTAA-ATATAGTATTATTATTGTATAAAAATAATTTTC
1 TAAAA-TAACATATAG-ATTATTATTGTATAAAAATAATTTTC
8940285 TAAA
1 TAAA
8940289 CTAAAATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
37 10 0.26
38 3 0.08
39 4 0.10
40 2 0.05
41 1 0.03
42 11 0.28
43 8 0.21
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (41 bp):
TAAAATAACATATAGATTATTATTGTATAAAAATAATTTTC
Found at i:8940681 original size:29 final size:32
Alignment explanation
Indices: 8940619--8940681 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 32
8940609 ATTTTAAATT
8940619 AATAAAAATAAAATTATATTTCAATCTTCTAA
1 AATAAAAATAAAATTATATTTCAATCTTCTAA
* *
8940651 AATAAAAAT-AACTTA-ATTT-AATCTTTTAA
1 AATAAAAATAAAATTATATTTCAATCTTCTAA
8940680 AA
1 AA
8940682 CTTATAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.38
30 4 0.14
31 5 0.17
32 9 0.31
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (32 bp):
AATAAAAATAAAATTATATTTCAATCTTCTAA
Found at i:8944627 original size:22 final size:22
Alignment explanation
Indices: 8944602--8944651 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
8944592 TTTTGTTTTT
8944602 TGTTGGCTTTATGATGACTTTA
1 TGTTGGCTTTATGATGACTTTA
* * *
8944624 TGTTAGCTTTATGTTGGCTTTA
1 TGTTGGCTTTATGATGACTTTA
*
8944646 TATTGG
1 TGTTGG
8944652 ATGTTATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (22 bp):
TGTTGGCTTTATGATGACTTTA
Found at i:8948997 original size:40 final size:40
Alignment explanation
Indices: 8948883--8949026 Score: 148
Period size: 40 Copynumber: 3.6 Consensus size: 40
8948873 GTTTTGGATA
*** *
8948883 AGAACTCAAGCTTTAACTTAGC-AGACTATGAGCCAGTGAT
1 AGAACTCAAGCTTCGGCTTAGCAAG-CTATGAGCCGGTGAT
8948923 AGAACTCAAGCTTCGGCTTAGCAAGCTATGAGCCGGTGAT
1 AGAACTCAAGCTTCGGCTTAGCAAGCTATGAGCCGGTGAT
* * * *
8948963 AGAATTCAAGCTTCGGCTTAGTAAGGTATTAGCCGGTG-T
1 AGAACTCAAGCTTCGGCTTAGCAAGCTATGAGCCGGTGAT
* * *
8949002 TGAACATTCAAGCTACGACTTAGCA
1 AGAAC--TCAAGCTTCGGCTTAGCA
8949027 GGCCACGAGA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 4 0.05
40 67 0.76
41 17 0.19
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (40 bp):
AGAACTCAAGCTTCGGCTTAGCAAGCTATGAGCCGGTGAT
Found at i:8950027 original size:21 final size:22
Alignment explanation
Indices: 8949990--8950039 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
8949980 TTATATTGTT
*
8949990 TCGGTAGTATGGAATTT-GAGTA
1 TCGGTAGTATAGAATTTAG-GTA
8950012 TCGGTAGT-TAGAATTTAGGTA
1 TCGGTAGTATAGAATTTAGGTA
8950033 TCGGTAG
1 TCGGTAG
8950040 AACTCTTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.36
Consensus pattern (22 bp):
TCGGTAGTATAGAATTTAGGTA
Found at i:8951071 original size:3 final size:3
Alignment explanation
Indices: 8951063--8951090 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8951053 ATCCCCGACA
8951063 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
8951091 AAACCCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:8953428 original size:10 final size:10
Alignment explanation
Indices: 8953413--8953470 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
8953403 TCAACAAAAA
8953413 TTAAAATAAT
1 TTAAAATAAT
8953423 TTAAAATAATT
1 TTAAAATAA-T
*
8953434 TTCAAAT--T
1 TTAAAATAAT
8953442 TTCAAAAT-AT
1 TT-AAAATAAT
*
8953452 TTAAAAAAAT
1 TTAAAATAAT
8953462 TCTAAAATA
1 T-TAAAATA
8953471 TATATAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 3 0.08
9 8 0.21
10 15 0.38
11 13 0.33
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAAATAAT
Found at i:8957816 original size:43 final size:43
Alignment explanation
Indices: 8957755--8957885 Score: 244
Period size: 43 Copynumber: 3.0 Consensus size: 43
8957745 ACATATGTGG
* *
8957755 TACCCCAGCCATCAGTACGGTGTCTGTTTATATAATTGTCCCC
1 TACCCCAACCATCGGTACGGTGTCTGTTTATATAATTGTCCCC
8957798 TACCCCAACCATCGGTACGGTGTCTGTTTATATAATTGTCCCC
1 TACCCCAACCATCGGTACGGTGTCTGTTTATATAATTGTCCCC
8957841 TACCCCAACCATCGGTACGGTGTCTGTTTATATAATTGTCCCC
1 TACCCCAACCATCGGTACGGTGTCTGTTTATATAATTGTCCCC
8957884 TA
1 TA
8957886 ACGATGCTAC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (43 bp):
TACCCCAACCATCGGTACGGTGTCTGTTTATATAATTGTCCCC
Found at i:8981974 original size:21 final size:21
Alignment explanation
Indices: 8981948--8981998 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
8981938 TTTTTAGTGC
* * *
8981948 CGGTAGAAGCATGATTTGTTT
1 CGGTAGAAGCATCACTTGTAT
*
8981969 CGGTAGAAGCTTCACTTGTAT
1 CGGTAGAAGCATCACTTGTAT
8981990 CGGTAGAAG
1 CGGTAGAAG
8981999 TATGCACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31
Consensus pattern (21 bp):
CGGTAGAAGCATCACTTGTAT
Found at i:8982954 original size:22 final size:22
Alignment explanation
Indices: 8982926--8982980 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
8982916 CTAATGAACA
** * *
8982926 GAGAGCACTAAGGTGTTATACG
1 GAGAGCACTAACATGCTAAACG
*
8982948 GAGAGCACGAACATGCTAAACG
1 GAGAGCACTAACATGCTAAACG
8982970 GAGAGCACTAA
1 GAGAGCACTAA
8982981 TCGTACTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (22 bp):
GAGAGCACTAACATGCTAAACG
Found at i:8989347 original size:16 final size:16
Alignment explanation
Indices: 8989326--8989377 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
8989316 TGAATTTTTT
8989326 ATTACAGCTTTATTCC
1 ATTACAGCTTTATTCC
*
8989342 ATTACAGCTTTATTCT
1 ATTACAGCTTTATTCC
* **
8989358 ATTACAACCCTATTCC
1 ATTACAGCTTTATTCC
8989374 ATTA
1 ATTA
8989378 TAATTCTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTACAGCTTTATTCC
Found at i:8991476 original size:30 final size:31
Alignment explanation
Indices: 8991373--8991487 Score: 94
Period size: 31 Copynumber: 3.7 Consensus size: 31
8991363 CAAACCTCAT
* * *
8991373 AATTTTGAAAATTTATCATTAAACA-TTTTAAA
1 AATTTTAAAAATTTA--ATTAAAGACTTCTAAA
*
8991405 AATTTTAAAATTTTTAATT--AGACTTCTAAA
1 AATTTTAAAA-ATTTAATTAAAGACTTCTAAA
* *
8991435 ATTTTTAAAAAATTTAATTAAAGGC-TCTAAA
1 AATTTT-AAAAATTTAATTAAAGACTTCTAAA
*
8991466 AATTTTAAAAACTTTGATTAAA
1 AATTTTAAAAA-TTTAATTAAA
8991488 CCACAAAAGT
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.03
30 23 0.34
31 27 0.40
32 12 0.18
33 4 0.06
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (31 bp):
AATTTTAAAAATTTAATTAAAGACTTCTAAA
Found at i:8991476 original size:31 final size:32
Alignment explanation
Indices: 8991401--8991487 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 32
8991391 TTAAACATTT
**
8991401 TAAAAATTTTAAAATTTTTAATT--AGACTTC
1 TAAAAATTTTAAAAAATTTAATTAAAGACTTC
* *
8991431 TAAAATTTTTAAAAAATTTAATTAAAGGC-TC
1 TAAAAATTTTAAAAAATTTAATTAAAGACTTC
* *
8991462 TAAAAATTTTAAAAACTTTGATTAAA
1 TAAAAATTTTAAAAAATTTAATTAAA
8991488 CCACAAAAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 20 0.42
31 25 0.52
32 3 0.06
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (32 bp):
TAAAAATTTTAAAAAATTTAATTAAAGACTTC
Found at i:8993325 original size:22 final size:22
Alignment explanation
Indices: 8993283--8993325 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8993273 TTTATTAATT
* *
8993283 TTTAAAAGATTTAATATTTTTA
1 TTTAAAAGATTAAATAATTTTA
8993305 TTTAAAAGA-TAAATAAATTTT
1 TTTAAAAGATTAAAT-AATTTT
8993326 TATCGTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTAAAAGATTAAATAATTTTA
Found at i:9005075 original size:18 final size:18
Alignment explanation
Indices: 9005044--9005093 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
9005034 GTTAATTTTT
* * *
9005044 TAATTCAAGCAATTCAGT
1 TAATTCGAGTAATTCAGG
*
9005062 TAATTCGATTAATTCAGG
1 TAATTCGAGTAATTCAGG
9005080 TAATTCGAGTAATT
1 TAATTCGAGTAATT
9005094 TTTTATACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (18 bp):
TAATTCGAGTAATTCAGG
Found at i:9014686 original size:33 final size:33
Alignment explanation
Indices: 9014649--9014754 Score: 98
Period size: 33 Copynumber: 3.4 Consensus size: 33
9014639 TTATACTGGA
9014649 ATCATTATACTAACCATACATATGTATATAAGT
1 ATCATTATACTAACCATACATATGTATATAAGT
* ** * * *
9014682 ATCA-TA-A-T-ACTATTGATCT-TATACT-GGA
1 ATCATTATACTAACCATACATATGTATA-TAAGT
9014710 ATCATTATACTAACCATACATATGTATATAAGT
1 ATCATTATACTAACCATACATATGTATATAAGT
*
9014743 ATCATAATACTA
1 ATCATTATACTA
9014755 TTGATCATAT
Statistics
Matches: 53, Mismatches: 13, Indels: 14
0.66 0.16 0.17
Matches are distributed among these distances:
28 9 0.17
29 10 0.19
30 2 0.04
31 2 0.04
32 10 0.19
33 20 0.38
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (33 bp):
ATCATTATACTAACCATACATATGTATATAAGT
Found at i:9014706 original size:61 final size:61
Alignment explanation
Indices: 9014636--9014760 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
9014626 ATACTTTGTC
9014636 ATCTTATACTGGAATCATTATACTAACCATACATATGTATATAAGTATCATAATACTATTG
1 ATCTTATACTGGAATCATTATACTAACCATACATATGTATATAAGTATCATAATACTATTG
9014697 ATCTTATACTGGAATCATTATACTAACCATACATATGTATATAAGTATCATAATACTATTG
1 ATCTTATACTGGAATCATTATACTAACCATACATATGTATATAAGTATCATAATACTATTG
9014758 ATC
1 ATC
9014761 ATATTTAACT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (61 bp):
ATCTTATACTGGAATCATTATACTAACCATACATATGTATATAAGTATCATAATACTATTG
Found at i:9018461 original size:6 final size:6
Alignment explanation
Indices: 9018431--9018473 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
9018421 CAATATTTTA
*
9018431 AATTAAT AATTACA AATTA- AATTAT AATTAT AATTAT AATTAT
1 AATT-AT AATTA-T AATTAT AATTAT AATTAT AATTAT AATTAT
9018474 TTCTATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
5 5 0.15
6 19 0.58
7 9 0.27
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTAT
Found at i:9022139 original size:16 final size:17
Alignment explanation
Indices: 9022112--9022146 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
9022102 ATTTTCTTTG
9022112 AATCCTTAAAATATTGA
1 AATCCTTAAAATATTGA
9022129 AATCCTT-AAATATTGA
1 AATCCTTAAAATATTGA
9022145 AA
1 AA
9022147 ACCTCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (17 bp):
AATCCTTAAAATATTGA
Found at i:9022155 original size:16 final size:16
Alignment explanation
Indices: 9022120--9022155 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9022110 TGAATCCTTA
* *
9022120 AAATATTGAAATCCTT
1 AAATATTGAAAACCTC
9022136 AAATATTGAAAACCTC
1 AAATATTGAAAACCTC
9022152 AAAT
1 AAAT
9022156 CGTTGAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.31
Consensus pattern (16 bp):
AAATATTGAAAACCTC
Found at i:9024072 original size:48 final size:48
Alignment explanation
Indices: 9024020--9024148 Score: 213
Period size: 48 Copynumber: 2.7 Consensus size: 48
9024010 TCTACCAACA
9024020 ACATTTTGAGCCTACAACATTCTGGTTTTGGAACACAAGATGGTAGTC
1 ACATTTTGAGCCTACAACATTCTGGTTTTGGAACACAAGATGGTAGTC
* *
9024068 ACATTTTGAGCCTACAACATTCTAGTTTTGGAACATAAGATGGTAGTC
1 ACATTTTGAGCCTACAACATTCTGGTTTTGGAACACAAGATGGTAGTC
* * *
9024116 ACATTTTGAGCATGCAAGATTCTGGTTTTGGAA
1 ACATTTTGAGCCTACAACATTCTGGTTTTGGAA
9024149 TACACCAATG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (48 bp):
ACATTTTGAGCCTACAACATTCTGGTTTTGGAACACAAGATGGTAGTC
Found at i:9025252 original size:15 final size:15
Alignment explanation
Indices: 9025229--9025263 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9025219 TTTTTGGAAT
* *
9025229 GATTAGGGATTTCAC
1 GATTTGGGATTGCAC
9025244 GATTTGGGATTGCAC
1 GATTTGGGATTGCAC
9025259 GATTT
1 GATTT
9025264 CGTTCTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (15 bp):
GATTTGGGATTGCAC
Found at i:9036155 original size:37 final size:38
Alignment explanation
Indices: 9036096--9036174 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 38
9036086 TTCGAAGCAA
** **
9036096 TAAAGTGACACCCAGTGTCTCATC-GGTCTAGCCGAAG
1 TAAAGTGACACCCAGTACCTCATCAAATCTAGCCGAAG
** *
9036133 TAAAGTGGTACCCAGTACCTCATCAAATCTATCCGAAG
1 TAAAGTGACACCCAGTACCTCATCAAATCTAGCCGAAG
9036171 TAAA
1 TAAA
9036175 ATAATGACAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (38 bp):
TAAAGTGACACCCAGTACCTCATCAAATCTAGCCGAAG
Found at i:9041791 original size:37 final size:38
Alignment explanation
Indices: 9041741--9041819 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 38
9041731 TTCAAAGCAA
** *
9041741 TAAAGTGACACCCAGTGTCTCATCG-GTCTAGT-CGAAG
1 TAAAGTGACACCCAGTACCTCATCGAATCTA-TCCGAAG
**
9041778 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGACACCCAGTACCTCATCGAATCTATCCGAAG
9041816 TAAA
1 TAAA
9041820 ATAATGACAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 22 0.63
38 13 0.37
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (38 bp):
TAAAGTGACACCCAGTACCTCATCGAATCTATCCGAAG
Found at i:9041982 original size:6 final size:6
Alignment explanation
Indices: 9041973--9041997 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9041963 TTCCAATTTT
9041973 ACTTTC ACTTTC ACTTTC ACTTTC A
1 ACTTTC ACTTTC ACTTTC ACTTTC A
9041998 ATTTTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (6 bp):
ACTTTC
Found at i:9048120 original size:32 final size:31
Alignment explanation
Indices: 9048034--9048143 Score: 90
Period size: 30 Copynumber: 3.6 Consensus size: 31
9048024 TTTCCCCTTC
*
9048034 TAAAATTT-ACCCATTTATTATGTT-TTT-TTT
1 TAAAATTTAACCCTTTTATT-T-TTATTTCTTT
* *
9048064 T-AAGTTAAACCCTTTTATTTTTATTT-TTGT
1 TAAAATTTAACCCTTTTATTTTTATTTCTT-T
*
9048094 TAAAATTTAACCTTTTGTATTTTTATTTCTTT
1 TAAAATTTAACCCTTT-TATTTTTATTTCTTT
*
9048126 TAAAA-GT-ACCCTTTTATT
1 TAAAATTTAACCCTTTTATT
9048144 ATGTTTCTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.03
29 14 0.21
30 19 0.29
31 12 0.18
32 17 0.26
33 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (31 bp):
TAAAATTTAACCCTTTTATTTTTATTTCTTT
Found at i:9048602 original size:110 final size:110
Alignment explanation
Indices: 9048405--9048611 Score: 310
Period size: 110 Copynumber: 1.9 Consensus size: 110
9048395 GTAATATTTT
* * * *
9048405 TTTTATTTTAGGAAATTAGAGAAATTGTGCCCTAACGTGTTGGGTATGGTTTTTTTGTTGAACCT
1 TTTTATTTCAGGAAATTAGAGAAATTGTGCCCTAACGTATTGGGTATGGATTTTCTGTTGAACCT
*
9048470 AAATAATTGAGTATCCTATTTAAAATCGATAAATGCTCAATGTTC
66 AAATAATTGAGCATCCTATTTAAAATCGATAAATGCTCAATGTTC
* *
9048515 TTTTATTTCAGGGAAA-TCGAGATATTGTGCCCTAACGTATTGGGTATGGATTTTCT-TTGAACC
1 TTTTATTTCA-GGAAATTAGAGAAATTGTGCCCTAACGTATTGGGTATGGATTTTCTGTTGAACC
*
9048578 TAAGTAATTGAGCATCCTATTTTAAAATCGATAA
65 TAAATAATTGAGCATCCTA-TTTAAAATCGATAA
9048612 GTGTTCTTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
109 24 0.28
110 58 0.67
111 5 0.06
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (110 bp):
TTTTATTTCAGGAAATTAGAGAAATTGTGCCCTAACGTATTGGGTATGGATTTTCTGTTGAACCT
AAATAATTGAGCATCCTATTTAAAATCGATAAATGCTCAATGTTC
Found at i:9052623 original size:6 final size:6
Alignment explanation
Indices: 9052604--9052654 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
9052594 AATTTAGAGG
*
9052604 TTAAA- TTAATT TTAAAT TT--AT TTAAAT TTAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
9052649 TATAAA
1 T-TAAA
9052655 ACAAATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 28 0.70
7 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:9052639 original size:22 final size:21
Alignment explanation
Indices: 9052604--9052645 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
9052594 AATTTAGAGG
*
9052604 TTAAATTAATTTTAAATTTAT
1 TTAAATTAAATTTAAATTTAT
9052625 TTAAATTTAAATTTAAATTTA
1 TTAAA-TTAAATTTAAATTTA
9052646 AATTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAATTAAATTTAAATTTAT
Found at i:9054761 original size:59 final size:57
Alignment explanation
Indices: 9054690--9055183 Score: 512
Period size: 59 Copynumber: 8.5 Consensus size: 57
9054680 AAGATTTCAG
* *
9054690 AAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTAACCTCG--ATTTCCAAAAATTACCATTTTACCCCCAAACTTTCC
* *
9054749 AAAATTCTA-TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
1 AAAATTCCATTTTTAACCTCGATTT--CCAAAAATTACCATTTTACCCCCAAACTTTCC
* * * * * *
9054807 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCTCGAAACTTTCC
1 AAAATTCCATTTTTAACCTC--GATTTCCAAAAATTACCATTTTACCCCCAAACTTTCC
* * * *
9054866 AAAATTCTATTTTTAACGTCGATTTCATCAAAAATTACCATTTTACCCCCGAACTCTCC
1 AAAATTCCATTTTTAACCTCGATTTC--CAAAAATTACCATTTTACCCCCAAACTTTCC
* * * *
9054925 AAAATTCCATTTTTAATCTCGATTTCACCAAAATTACCATTTTACCCCCGATCTTTCC
1 AAAATTCCATTTTTAACCTCGATTTC-CAAAAATTACCATTTTACCCCCAAACTTTCC
* *
9054983 AAAATTTCATTTTTAACC-CTGATTTCACCAAAAATTACCATTTTA-CCCTAAACTTTCC
1 AAAATTCCATTTTTAACCTC-GATTT--CCAAAAATTACCATTTTACCCCCAAACTTTCC
* * *
9055041 AAAATTCCATTTTTAACCTCGACTTTACC-AAAATTACCATTTTACCCCTAAAATTTCT
1 AAAATTCCATTTTTAACCTCGA-TTT-CCAAAAATTACCATTTTACCCCCAAACTTTCC
* * * * ** *
9055099 AAAATCCCATTTTTGACCCCGATTTCACTAAAAATTACCATTTTGCCCCC-AGGTATCC
1 AAAATTCCATTTTTAACCTCGATTTC-C-AAAAATTACCATTTTACCCCCAAACTTTCC
* *
9055157 AAAAGTCCCATTTTTAACCCCGATTTC
1 AAAA-TTCCATTTTTAACCTCGATTTC
9055184 ATCGTTTCTT
Statistics
Matches: 371, Mismatches: 47, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
56 4 0.01
57 24 0.06
58 168 0.45
59 171 0.46
60 1 0.00
61 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (57 bp):
AAAATTCCATTTTTAACCTCGATTTCCAAAAATTACCATTTTACCCCCAAACTTTCC
Found at i:9054784 original size:58 final size:59
Alignment explanation
Indices: 9054690--9055184 Score: 553
Period size: 58 Copynumber: 8.5 Consensus size: 59
9054680 AAGATTTCAG
* *
9054690 AAAATTCCATTTTTGACCTCGAAACTT--CCAAAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTAACCTCG--ATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* *
9054749 AAAATTCTA-TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
1 AAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* * * * * *
9054807 AAAATTCCATTTTTGACCCCAAAACTT--CCAAAAATTACCATTTTACCTCGAAACTTTCC
1 AAAATTCCATTTTTAACCTC--GATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* * * * *
9054866 AAAATTCTATTTTTAACGTCGATTTCATCAAAAATTACCATTTTACCCCCGAACTCTCC
1 AAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* * *
9054925 AAAATTCCATTTTTAATCTCGATTTCACC-AAAATTACCATTTTACCCCCGATCTTTCC
1 AAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* *
9054983 AAAATTTCATTTTTAACC-CTGATTTCACCAAAAATTACCATTTTA-CCCTAAACTTTCC
1 AAAATTCCATTTTTAACCTC-GATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* * *
9055041 AAAATTCCATTTTTAACCTCGACTTT-ACC-AAAATTACCATTTTACCCCTAAAATTTCT
1 AAAATTCCATTTTTAACCTCGA-TTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* * * * * ** *
9055099 AAAATCCCATTTTTGACCCCGATTTCACTAAAAATTACCATTTTGCCCCC-AGGTATCC
1 AAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* *
9055157 AAAAGTCCCATTTTTAACCCCGATTTCA
1 AAAA-TTCCATTTTTAACCTCGATTTCA
9055185 TCGTTTCTTC
Statistics
Matches: 374, Mismatches: 47, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
56 3 0.01
57 22 0.06
58 173 0.46
59 173 0.46
61 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
Found at i:9054868 original size:117 final size:116
Alignment explanation
Indices: 9054690--9055147 Score: 559
Period size: 117 Copynumber: 3.9 Consensus size: 116
9054680 AAGATTTCAG
* *
9054690 AAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATT
1 AAAATTCCATTTTTAACCTC--AACTTCCAAAAATTACCATTTTACCCCGAAACTTTCCAAAATT
9054755 CTA-TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
64 CTATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
* * *
9054807 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCTCGAAACTTTCCAAAATT
1 AAAATTCCATTTTTAACCTC--AACTTCCAAAAATTACCATTTTACCCCGAAACTTTCCAAAATT
* * ** *
9054872 CTATTTTTAACGTCGATTTCATCAAAAATTACCATTTTACCCCCGAACTCTCC
64 CTATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
* * * * *
9054925 AAAATTCCATTTTTAATCTCGATTTCACCAAAATTACCATTTTACCCCCG-ATCTTTCCAAAATT
1 AAAATTCCATTTTTAACCTCAACTTC-CAAAAATTACCATTTTA-CCCCGAAACTTTCCAAAATT
9054989 -TCATTTTTAACC-CTGATTTCACCAAAAATTACCATTTTA-CCCTAAACTTTCC
64 CT-ATTTTTAACCTC-GATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
* * * * *
9055041 AAAATTCCATTTTTAACCTCGACTTTACC-AAAATTACCATTTTACCCCTAAAATTTCTAAAATC
1 AAAATTCCATTTTTAACCTCAAC-TT-CCAAAAATTACCATTTTACCCCGAAACTTTCCAAAATT
* * * * *
9055105 CCATTTTTGACCCCGATTTCACTAAAAATTACCATTTTGCCCC
64 CTATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCC
9055148 CAGGTATCCA
Statistics
Matches: 297, Mismatches: 33, Indels: 22
0.84 0.09 0.06
Matches are distributed among these distances:
115 4 0.01
116 94 0.32
117 133 0.45
118 66 0.22
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (116 bp):
AAAATTCCATTTTTAACCTCAACTTCCAAAAATTACCATTTTACCCCGAAACTTTCCAAAATTCT
ATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
Found at i:9055133 original size:30 final size:29
Alignment explanation
Indices: 9055099--9055184 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
9055089 TAAAATTTCT
9055099 AAAATCCCATTTTTGACCCCGATTTCACTA
1 AAAATCCCATTTTTGACCCCGATTTCAC-A
* * * *
9055129 AAAATTACCA-TTTTGCCCCCAGGTATC-CA
1 AAAA-TCCCATTTTTGACCCC-GATTTCACA
* *
9055158 AAAGTCCCATTTTTAACCCCGATTTCA
1 AAAATCCCATTTTTGACCCCGATTTCA
9055185 TCGTTTCTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
28 8 0.19
29 12 0.29
30 14 0.33
31 8 0.19
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAATCCCATTTTTGACCCCGATTTCACA
Found at i:9057654 original size:14 final size:14
Alignment explanation
Indices: 9057635--9057665 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9057625 TCCCCACTTC
9057635 CCTTTAGCCTTTAA
1 CCTTTAGCCTTTAA
*
9057649 CCTTTAGCCTTTTA
1 CCTTTAGCCTTTAA
9057663 CCT
1 CCT
9057666 ATGCATAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.32, G:0.06, T:0.45
Consensus pattern (14 bp):
CCTTTAGCCTTTAA
Found at i:9060728 original size:52 final size:52
Alignment explanation
Indices: 9060627--9060864 Score: 329
Period size: 52 Copynumber: 4.6 Consensus size: 52
9060617 TGTGTATTTG
* * * *
9060627 ATACTCACAATGACACAGAGTCATC-GAACCT-TTAATCCGTAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCAG-ACCTCATAATCCGTAAAGGATTCAT
* * *
9060678 ATACTCACGATGACGCATAGTGATCAGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* * *
9060730 ATA-TACACGATGACACATAGTCATCGGACCTCGTAATCCGTAAAGGATCCAT
1 ATACT-CACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
*
9060782 ATACTCACGATGACACATAGTCATCAGATCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
*
9060834 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
9060865 ATTTCATTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
51 26 0.16
52 137 0.84
53 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
Found at i:9066990 original size:29 final size:28
Alignment explanation
Indices: 9066953--9067037 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
9066943 TTAGTAACAG
* *
9066953 GCATGACCTTTTGAGTCAACAAGGAGTAA
1 GCATGACC-TTTGGGTCAACAGGGAGTAA
*
9066982 GCATGACCTTTGGGTCAACTGGGAGTAA
1 GCATGACCTTTGGGTCAACAGGGAGTAA
* *
9067010 GCATAACCTTTGGGTCAATAGGGAGTAA
1 GCATGACCTTTGGGTCAACAGGGAGTAA
9067038 ATCAGATATT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 42 0.84
29 8 0.16
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (28 bp):
GCATGACCTTTGGGTCAACAGGGAGTAA
Found at i:9069007 original size:7 final size:7
Alignment explanation
Indices: 9068995--9069027 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
9068985 TCCCTGCTTC
9068995 CCTTTAG
1 CCTTTAG
9069002 CCTTTAG
1 CCTTTAG
*
9069009 CCTTTAA
1 CCTTTAG
9069016 CCTTTAG
1 CCTTTAG
9069023 CCTTT
1 CCTTT
9069028 TACCTATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.15, C:0.30, G:0.09, T:0.45
Consensus pattern (7 bp):
CCTTTAG
Found at i:9069014 original size:14 final size:14
Alignment explanation
Indices: 9068995--9069032 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
9068985 TCCCTGCTTC
*
9068995 CCTTTAGCCTTTAG
1 CCTTTAACCTTTAG
9069009 CCTTTAACCTTTAG
1 CCTTTAACCTTTAG
*
9069023 CCTTTTACCT
1 CCTTTAACCT
9069033 ATGCATAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.16, C:0.32, G:0.08, T:0.45
Consensus pattern (14 bp):
CCTTTAACCTTTAG
Found at i:9070821 original size:16 final size:16
Alignment explanation
Indices: 9070800--9070830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9070790 TTATGGATCC
9070800 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
9070816 CATTTTATCTTTATT
1 CATTTTACCTTTATT
9070831 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:9084463 original size:3 final size:3
Alignment explanation
Indices: 9084402--9084449 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
9084392 CCTCAGTTGA
9084402 AAT AAT -AT AAT 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
9084449 A
1 A
9084450 TGTTTATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9086448 original size:43 final size:41
Alignment explanation
Indices: 9086394--9086611 Score: 258
Period size: 41 Copynumber: 5.2 Consensus size: 41
9086384 GGTGTATAAA
* * * *
9086394 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGA-AATTGTAT
1 AAGGAAGACTCATGTCTCGGGATGAGAATGAGATTA-TGAAT
*
9086435 AAATGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 -AA-GGAAGACTCATGTCTCGGGATGAGAATGAGATTATGAAT
*
9086478 AAGGAAGACTCATGTCTCGGAATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGAAT
* * *
9086519 AAGGAAGACTCATGTCTCGGAAGGAGAATGAGATTATGATT
1 AAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGAAT
** * * **
9086560 AAGGAAGACTCATGTCTCGAAATGAGAACGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGAAT
9086601 AAAGGAAGACT
1 -AAGGAAGACT
9086612 TATGGCTAGA
Statistics
Matches: 159, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 112 0.70
42 14 0.09
43 32 0.20
44 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.24
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGAAT
Found at i:9093425 original size:43 final size:44
Alignment explanation
Indices: 9093355--9093478 Score: 125
Period size: 43 Copynumber: 2.9 Consensus size: 44
9093345 GAATATTTGG
* *
9093355 TGTATAAAAAGGAAGACTCATGCCTCGAGTTGAGCATGAGAAAT
1 TGTATAAAAAGGAAGACTCATGCCTCGAGATGAGAATGAGAAAT
* * *
9093399 TGTAT-AAATGGAATACTCATGTCTCGAGATGAGAATGAG--A-
1 TGTATAAAAAGGAAGACTCATGCCTCGAGATGAGAATGAGAAAT
* * *
9093439 T-TATAAATAAGGAAGACTCATGTCT-TAAATGAGAATGAGA
1 TGTATAAA-AAGGAAGACTCATGCCTCGAGATGAGAATGAGA
9093479 TTATGAATAA
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
39 3 0.04
40 15 0.22
41 16 0.24
43 29 0.43
44 5 0.07
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.26
Consensus pattern (44 bp):
TGTATAAAAAGGAAGACTCATGCCTCGAGATGAGAATGAGAAAT
Found at i:9093476 original size:40 final size:41
Alignment explanation
Indices: 9093357--9093514 Score: 171
Period size: 40 Copynumber: 3.9 Consensus size: 41
9093347 ATATTTGGTG
* ** *
9093357 TATAAA-AAGGAAGACTCATGCCTCGAGTTGAGCATGAGAAATT
1 TATAAATAAGGAAGACTCATGTCTCGAAATGAGAATGAG--A-T
* *
9093400 GTATAAAT--GGAATACTCATGTCTCGAGATGAGAATGAGAT
1 -TATAAATAAGGAAGACTCATGTCTCGAAATGAGAATGAGAT
*
9093440 TATAAATAAGGAAGACTCATGTCT-TAAATGAGAATGAGAT
1 TATAAATAAGGAAGACTCATGTCTCGAAATGAGAATGAGAT
* *
9093480 TATGAATAAGGAAGACCCATGTCTCGAAATGAGAA
1 TATAAATAAGGAAGACTCATGTCTCGAAATGAGAA
9093515 CGAGTGTAAC
Statistics
Matches: 100, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
39 7 0.07
40 37 0.37
41 24 0.24
43 26 0.26
44 6 0.06
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (41 bp):
TATAAATAAGGAAGACTCATGTCTCGAAATGAGAATGAGAT
Found at i:9100159 original size:190 final size:194
Alignment explanation
Indices: 9099879--9100254 Score: 449
Period size: 190 Copynumber: 2.0 Consensus size: 194
9099869 GGAAATGAGA
* * *
9099879 AAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGGTTGATATTTATGCATAAGTGCAT
1 AAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGAGATCTATGCATAAGTGCAT
* * * * * * *
9099944 ATTCTCGACAGCTCGTGAACAGCATCATTAGGG-ACAA-TTATA-TGC-TCAGATACTATATCAA
66 ACTCTCAAAAGCTCGTGAACAGCATCATTAGGGAACAATTTATAGTACAACAGACACCATATCAA
* * ** *
9100005 TGGCTGAGGTACCGCATATGTTGCGAGTCCTCGAAAGCTTGTGTGAGCAGTATCGTGACTTGGG
131 TGGCTGAGGTACCGCATACGTTGCAAGTCCTCGAAAGCTCATCTGAGCAGTATCGTGACTTGGG
* * * *
9100069 AAAGAGATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGGGA-CTATGC-TTATTGCAT
1 AAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGAGATCTATGCATAAGTGCAT
* * * * *
9100132 ACTCTCAAAAGCTCGTGTGAGCAGCATCGTTAGGGAATAATTTATAGTACAGACAGGCACCGTAT
66 ACTCTCAAAAGCTC--GTGAACAGCATCATTAGGGAACAATTTATAGTACA-ACAGACACCATAT
* *
9100197 CGATGGCTGGGGTACCGCATACGTTGCAAGTCCTCGAAAGCTCATCTGAGCAGTATCG
128 CAATGGCTGAGGTACCGCATACGTTGCAAGTCCTCGAAAGCTCATCTGAGCAGTATCG
9100255 AGTACTGGTA
Statistics
Matches: 153, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
188 18 0.12
189 5 0.03
190 61 0.40
191 3 0.02
192 5 0.03
193 2 0.01
195 59 0.39
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (194 bp):
AAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGAGATCTATGCATAAGTGCAT
ACTCTCAAAAGCTCGTGAACAGCATCATTAGGGAACAATTTATAGTACAACAGACACCATATCAA
TGGCTGAGGTACCGCATACGTTGCAAGTCCTCGAAAGCTCATCTGAGCAGTATCGTGACTTGGG
Found at i:9101728 original size:41 final size:41
Alignment explanation
Indices: 9101669--9101776 Score: 137
Period size: 41 Copynumber: 2.6 Consensus size: 41
9101659 TGGGTGTAAC
* *
9101669 AATGAGATTATGAATAAGGAAGACTCATGTCACG-GAATGTG
1 AATGAGATTATGATTAAGGAAGACTCATGTCACGAG-ATGGG
*
9101710 AATGAGATTATGATTAAGGAAGACTCATGTCTCGAGATGGG
1 AATGAGATTATGATTAAGGAAGACTCATGTCACGAGATGGG
* * *
9101751 AATGAGAATATGGTTAAAGAAAGACT
1 AATGAGATTATGATT-AAGGAAGACT
9101777 TATGGCTAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 49 0.83
42 10 0.17
ACGTcount: A:0.40, C:0.08, G:0.27, T:0.25
Consensus pattern (41 bp):
AATGAGATTATGATTAAGGAAGACTCATGTCACGAGATGGG
Found at i:9110678 original size:21 final size:21
Alignment explanation
Indices: 9110646--9110705 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
9110636 CAAAGATGTG
9110646 GGTGCAA-TTGATGAAGAATT
1 GGTGCAACTTGATGAAGAATT
*
9110666 GGTGCAACATGATGAAGAATT
1 GGTGCAACTTGATGAAGAATT
*
9110687 GGCGCAACTTGAT-AAGAAT
1 GGTGCAACTTGATGAAGAAT
9110706 CAGGCCACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 13 0.36
21 23 0.64
ACGTcount: A:0.37, C:0.10, G:0.28, T:0.25
Consensus pattern (21 bp):
GGTGCAACTTGATGAAGAATT
Found at i:9116794 original size:18 final size:18
Alignment explanation
Indices: 9116767--9116802 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9116757 AGACACTTCT
9116767 AATAGCATTTTAATTTTA
1 AATAGCATTTTAATTTTA
* *
9116785 AATAGTATTTTATTTTTA
1 AATAGCATTTTAATTTTA
9116803 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
AATAGCATTTTAATTTTA
Found at i:9117429 original size:27 final size:29
Alignment explanation
Indices: 9117382--9117443 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 29
9117372 AATTTATATC
* *
9117382 TTTATAATTTTTAAAAGATTAAATTA-AAT
1 TTTATAA-TTTTAAAAAATTAAAATATAAT
9117411 TTTATAA-TTTAAAAAATTAAAATATAAT
1 TTTATAATTTTAAAAAATTAAAATATAAT
9117439 TTTAT
1 TTTAT
9117444 TACTATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 15 0.50
28 8 0.27
29 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TTTATAATTTTAAAAAATTAAAATATAAT
Found at i:9118351 original size:21 final size:21
Alignment explanation
Indices: 9118340--9118394 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
9118330 TTCTCTCACT
9118340 GCTACCTCCGCTTCCCTCGCA
1 GCTACCTCCGCTTCCCTCGCA
9118361 GCTACCTCCGCTTCCCTCGCA
1 GCTACCTCCGCTTCCCTCGCA
9118382 GCTACCTCCGCTT
1 GCTACCTCCGCTT
9118395 TAAGTTGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.09, C:0.51, G:0.15, T:0.25
Consensus pattern (21 bp):
GCTACCTCCGCTTCCCTCGCA
Found at i:9120537 original size:8 final size:8
Alignment explanation
Indices: 9120521--9120552 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
9120511 CTGTTTTTAT
9120521 TAATTAAA
1 TAATTAAA
*
9120529 TATTTAAA
1 TAATTAAA
9120537 TAATTAAA
1 TAATTAAA
9120545 TAATTAAA
1 TAATTAAA
9120553 CATTTGGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAATTAAA
Found at i:9122199 original size:24 final size:21
Alignment explanation
Indices: 9122148--9122197 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
9122138 AAGAAAAGAC
9122148 TGAAGAAGGGAAGGGCGTGCG
1 TGAAGAAGGGAAGGGCGTGCG
9122169 TGAAGAAGGGAAGGGCGTGCG
1 TGAAGAAGGGAAGGGCGTGCG
9122190 TGAAGAAG
1 TGAAGAAG
9122198 AAGGTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.50, T:0.10
Consensus pattern (21 bp):
TGAAGAAGGGAAGGGCGTGCG
Found at i:9122619 original size:23 final size:21
Alignment explanation
Indices: 9122591--9122696 Score: 105
Period size: 23 Copynumber: 5.0 Consensus size: 21
9122581 TTTGTTATTA
9122591 ATATTAAGTAATTAATAATCTTT
1 ATATTAA-TAATTAATAAT-TTT
9122614 ATATTAAGTAATTAATAATATTT
1 ATATTAA-TAATTAATAAT-TTT
9122637 ATATTAAT-ATT-AT-A-TTT
1 ATATTAATAATTAATAATTTT
9122654 ATATTAATAATTAATATATTTTT
1 ATATTAATAATTAATA-A-TTTT
*
9122677 ATATTTAT-ATTAATATATTT
1 ATATTAATAATTAATA-ATTT
9122697 CGATTTAGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 14
0.82 0.02 0.15
Matches are distributed among these distances:
17 11 0.15
18 3 0.04
19 3 0.04
20 2 0.03
21 7 0.09
22 10 0.13
23 39 0.52
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (21 bp):
ATATTAATAATTAATAATTTT
Found at i:9122651 original size:17 final size:17
Alignment explanation
Indices: 9122631--9122692 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
9122621 GTAATTAATA
9122631 ATATTTATATTAATATT
1 ATATTTATATTAATATT
9122648 ATATTTATATTAATAATT
1 ATATTTATATTAAT-ATT
9122666 A-A--TATATT--T-TT
1 ATATTTATATTAATATT
9122677 ATATTTATATTAATAT
1 ATATTTATATTAATAT
9122693 ATTTCGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
11 3 0.08
12 1 0.03
13 1 0.03
14 6 0.16
15 6 0.16
16 1 0.03
17 16 0.42
18 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTATATTAATATT
Found at i:9122661 original size:29 final size:29
Alignment explanation
Indices: 9122629--9122692 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
9122619 AAGTAATTAA
9122629 TAATATTT-ATATTAATATTATATTTATAT
1 TAATATTTAATA-TAATATTATATTTATAT
* * *
9122658 TAATAATTAATATATTTTTATATTTATAT
1 TAATATTTAATATAATATTATATTTATAT
9122687 TAATAT
1 TAATAT
9122693 ATTTCGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TAATATTTAATATAATATTATATTTATAT
Found at i:9122737 original size:12 final size:12
Alignment explanation
Indices: 9122720--9122807 Score: 51
Period size: 12 Copynumber: 7.2 Consensus size: 12
9122710 TATATTTCTA
9122720 TATTATTTATTT
1 TATTATTTATTT
*
9122732 TATTATTCTA-TC
1 TATTATT-TATTT
9122744 TATTATTATATGTAT
1 TATTATT-TAT-T-T
9122759 TATTATTTTATTT
1 TATTA-TTTATTT
*
9122772 AAATTA-TTA-TT
1 -TATTATTTATTT
*
9122783 T-TTATTTA-GT
1 TATTATTTATTT
9122793 TATTATTTATATT
1 TATTATTTAT-TT
9122806 TA
1 TA
9122808 GTCTATTTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
9 3 0.05
10 5 0.08
11 9 0.15
12 20 0.34
13 6 0.10
14 6 0.10
15 8 0.14
16 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (12 bp):
TATTATTTATTT
Found at i:9122779 original size:20 final size:18
Alignment explanation
Indices: 9122756--9122800 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
9122746 TTATTATATG
9122756 TATTATTATTTTATTTAAAT
1 TATTATT-TTTTATTT-AAT
*
9122776 TATTA-TTTTTATTTAGT
1 TATTATTTTTTATTTAAT
9122793 TATTATTT
1 TATTATTT
9122801 ATATTTAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 7 0.30
18 10 0.43
19 1 0.04
20 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TATTATTTTTTATTTAAT
Found at i:9122808 original size:17 final size:17
Alignment explanation
Indices: 9122744--9122814 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
9122734 TTATTCTATC
*
9122744 TATTA-TTATATGTA-T
1 TATTATTTATATTTAGT
*
9122759 TATTATTT-TATTTAAAT
1 TATTATTTATATTT-AGT
*
9122776 TATTATTTTTATTTAGT
1 TATTATTTATATTTAGT
9122793 TATTATTTATATTTAGT
1 TATTATTTATATTTAGT
9122810 CTATT
1 -TATT
9122815 TAGAATTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
15 9 0.19
16 3 0.06
17 27 0.56
18 9 0.19
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (17 bp):
TATTATTTATATTTAGT
Found at i:9123153 original size:170 final size:170
Alignment explanation
Indices: 9122866--9123539 Score: 1093
Period size: 170 Copynumber: 4.0 Consensus size: 170
9122856 CGACAAATAC
* * * *
9122866 ACATCCACGGGAATTAGCTTATCCACCCCCCGAACAATACTATAAGAATCAGTACTGAACATCCC
1 ACATCCACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
* * * *
9122931 TCCTGTAATTATACTCGCGTCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATATAA
66 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCAGGCATTTGTTCATATATAA
* * *
9122996 TCTCACTAAAGAGGGTGCCATTTTCTTTGTTACTGTATAG
131 TCTCACTAAAGAGGGCGCCATTTTCATTATTACTGTATAG
* *
9123036 ACATCCACGGGAATTAGCTTATCGACCCCCCGAATAGTACTATAAGAATCAGTATTGAACATCCC
1 ACATCCACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
*
9123101 TCCTGTAATTGTACACGCGCCCATAGTAATAACATATTTAGGTTCAGGCATTTGTTCATATATAA
66 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCAGGCATTTGTTCATATATAA
9123166 TCTCACTAAAGAGGGCGCCATTTTCATTATTACTGTATAG
131 TCTCACTAAAGAGGGCGCCATTTTCATTATTACTGTATAG
* * *
9123206 ACATCCACGAGAATTAGCTTATTGACCCCTCGAATAGTACTATAAGAATCAGTATTGAACATCCC
1 ACATCCACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
*
9123271 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATATAA
66 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCAGGCATTTGTTCATATATAA
9123336 TCTCACTAAAGAGGGCGCCATTTTCATTATTACTGTATAG
131 TCTCACTAAAGAGGGCGCCATTTTCATTATTACTGTATAG
*
9123376 ACATCCACGAGAATTAGCTTATCGACCCCCCGAACAGTTA-TATAAGAATCATTATTGAACATCC
1 ACATCCACGAGAATTAGCTTATCGACCCCCCGAACAG-TACTATAAGAATCAGTATTGAACATCC
** * *
9123440 CTCCTGTAATTGTACACATGCCCATAGAAATAACATATTTAGGTTCAAGCATTTGTTC--ATATA
65 CTCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCAGGCATTTGTTCATATATA
* *
9123503 ATCTCACTAAAGAGGGCGTCATTTTCATTGTTACTGT
130 ATCTCACTAAAGAGGGCGCCATTTTCATTATTACTGT
9123540 TCCAATTGTT
Statistics
Matches: 475, Mismatches: 28, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
168 40 0.08
170 433 0.91
171 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (170 bp):
ACATCCACGAGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCAGGCATTTGTTCATATATAA
TCTCACTAAAGAGGGCGCCATTTTCATTATTACTGTATAG
Found at i:9124120 original size:41 final size:41
Alignment explanation
Indices: 9124061--9124231 Score: 173
Period size: 41 Copynumber: 4.2 Consensus size: 41
9124051 AAAATTTAAA
* * *
9124061 TAGCGGCGCTTATGGGAAAGCGCCGCTAATGCTCTGACCTT
1 TAGCGGCGCTTATAGGAAAGCGCCGCGAATACTCTGACCTT
* * *
9124102 TAGCGGCGCTTATAGGAAAGTGCCGCTAAT-GTCCTGACCTT
1 TAGCGGCGCTTATAGGAAAGCGCCGCGAATACT-CTGACCTT
** ** * * *
9124143 TAATGATGCTTACAGGAAAGCGCCACGAATACTGTGACCTT
1 TAGCGGCGCTTATAGGAAAGCGCCGCGAATACTCTGACCTT
* * * *
9124184 TAACGGTGCTTATAGGAAAGCGCCGCGAATACTGTGACTTT
1 TAGCGGCGCTTATAGGAAAGCGCCGCGAATACTCTGACCTT
9124225 TAGCGGC
1 TAGCGGC
9124232 ACTTTGACAT
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
40 1 0.01
41 106 0.98
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (41 bp):
TAGCGGCGCTTATAGGAAAGCGCCGCGAATACTCTGACCTT
Found at i:9125863 original size:17 final size:18
Alignment explanation
Indices: 9125831--9125864 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9125821 TATAGTAATT
*
9125831 ATATTAAAGGTAATAAAG
1 ATATTAAAGCTAATAAAG
9125849 ATATTAAA-CTAATAAA
1 ATATTAAAGCTAATAAA
9125865 ATTAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (18 bp):
ATATTAAAGCTAATAAAG
Found at i:9129849 original size:66 final size:66
Alignment explanation
Indices: 9129743--9129899 Score: 235
Period size: 66 Copynumber: 2.4 Consensus size: 66
9129733 CAAATTGCTC
* * *
9129743 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATCTA
1 AACTTAAAGAGGAGGCTACAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACCTA
9129808 A
66 A
* *
9129809 AACTTAAAGAGGAGGCTACAGTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACCTA
1 AACTTAAAGAGGAGGCTACAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACCTA
*
9129874 C
66 A
*
9129875 AACTTAAAGTGGAGGC-AGCAGCGAG
1 AACTTAAAGAGGAGGCTA-CAGCGAG
9129900 GCAAGCGGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
65 1 0.01
66 81 0.99
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTACAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACCTA
A
Found at i:9129936 original size:21 final size:21
Alignment explanation
Indices: 9129891--9129937 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
9129881 AAGTGGAGGC
* * *
9129891 AGCAGCGAGGCAAGCGGATGC
1 AGCAGCGAGGCAAGCGAAGGA
9129912 AGCAGCGAGGCAAGCGAAGGA
1 AGCAGCGAGGCAAGCGAAGGA
9129933 AGCAG
1 AGCAG
9129938 AGGCTACAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.43, T:0.02
Consensus pattern (21 bp):
AGCAGCGAGGCAAGCGAAGGA
Found at i:9130158 original size:15 final size:15
Alignment explanation
Indices: 9130138--9130166 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9130128 ATTTGAAGTT
9130138 ATTGGTTGGATTTGC
1 ATTGGTTGGATTTGC
9130153 ATTGGTTGGATTTG
1 ATTGGTTGGATTTG
9130167 AATTTACAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.34, T:0.48
Consensus pattern (15 bp):
ATTGGTTGGATTTGC
Found at i:9130323 original size:42 final size:43
Alignment explanation
Indices: 9130235--9130315 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 43
9130225 ATCTGTTATA
9130235 TTAGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCT
1 TTAGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCT
* *
9130278 TTAGCGGCGTTTGTGG-GAAAGCGCCGCTAAAGACCATG
1 TTAGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATG
9130316 TTCTTTAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 21 0.58
43 15 0.42
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.20
Consensus pattern (43 bp):
TTAGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCT
Done.