Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 136 of 250
Found at i:43868225 original size:54 final size:54
Alignment explanation
Indices: 43867907--43868231 Score: 248
Period size: 54 Copynumber: 6.0 Consensus size: 54
43867897 TAAAATGGTG
* * ** * *
43867907 TTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTA
1 TTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAATCAAGGGTA
* * ** *
43867961 TTTCT-ATAATTTCTAGAAAGTTAAGGGTATTTCT-GTAATTTTGTAAATTAAGGGTA
1 TTT-TGGTAATTT-TACAAA-CCAAGGGTATTT-TGGTAATTTTGTAAATCAAGGGTA
** *** *
43868017 TTTTGGTAATTTTACAAATTAAGGGTATTTTGGTAATTTCACAAA-CCAGTGGTA
1 TTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAATCAAG-GGTA
* * ** *
43868071 TTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAA-CCAGAGGTA
1 TTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAATCAAG-GGTA
* * * * * *
43868125 TTATAGCAATTTTACAGACC-AGGGTATTTTGGTAATTTTACT-AATCGAGGGTA
1 TTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTT-GTAAATCAAGGGTA
** * * *
43868178 TTTTGGTAATTTTGTAAACCAAGGGTACTTTAGTAATTTTGTAAATCGAGGGTA
1 TTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAATCAAGGGTA
43868232 AAACAGTAAT
Statistics
Matches: 221, Mismatches: 39, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
53 42 0.19
54 129 0.58
55 12 0.05
56 38 0.17
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (54 bp):
TTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTGTAAATCAAGGGTA
Found at i:43868239 original size:27 final size:27
Alignment explanation
Indices: 43868209--43868312 Score: 136
Period size: 27 Copynumber: 3.9 Consensus size: 27
43868199 AGGGTACTTT
* *
43868209 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
43868236 AGTAATTCTATAAATCAAGGGTAAAAT
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
43868263 GGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* * *
43868290 AGTAATTATGTAAATCGGGGGTA
1 AGTAATTCTATAAATCGAGGGTA
43868313 CTTTGGTAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (27 bp):
AGTAATTCTATAAATCGAGGGTAAAAC
Found at i:43868241 original size:54 final size:54
Alignment explanation
Indices: 43868145--43868339 Score: 194
Period size: 54 Copynumber: 3.6 Consensus size: 54
43868135 TTTACAGACC
* ***** * *
43868145 AGGGTATTTTGGTAATTTTACT-AATCGAGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTACTTTGGTAATTTTA-TAAATCGAGGGTAAAACAGTAATTATGTAAATCA
* * * *
43868199 AGGGTACTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCA
1 AGGGTACTTTGGTAATTTTATAAATCGAGGGTAAAACAGTAATTATGTAAATCA
*** * *
43868253 AGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTATGTAAATCG
1 AGGGTACTTTGGTAATTTTATAAATCGAGGGTAAAACAGTAATTATGTAAATCA
* * *
43868307 GGGGTACTTTGGTAATTTTACAAGTCGAGGGTA
1 AGGGTACTTTGGTAATTTTATAAATCGAGGGTA
43868340 TTTCAATAAT
Statistics
Matches: 113, Mismatches: 27, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
53 1 0.01
54 112 0.99
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.34
Consensus pattern (54 bp):
AGGGTACTTTGGTAATTTTATAAATCGAGGGTAAAACAGTAATTATGTAAATCA
Found at i:43875396 original size:18 final size:19
Alignment explanation
Indices: 43875365--43875406 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
43875355 TTTTTTTAAA
*
43875365 TTTTTATTGAATTTCGTCTT
1 TTTTTATT-AATTTCGACTT
*
43875385 TTTTTATT-ATTTTGACTT
1 TTTTTATTAATTTCGACTT
43875403 TTTT
1 TTTT
43875407 GACTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (19 bp):
TTTTTATTAATTTCGACTT
Found at i:43878129 original size:146 final size:146
Alignment explanation
Indices: 43877937--43878229 Score: 577
Period size: 146 Copynumber: 2.0 Consensus size: 146
43877927 ATGTTACACT
43877937 ATAAATAGGTATTAAGCAATCAATTGTACCAAATGATATAGAAAATACAAGAAAACGAGCATACT
1 ATAAATAGGTATTAAGCAATCAATTGTACCAAATGATATAGAAAATACAAGAAAACGAGCATACT
*
43878002 AATACGAATAATAAATAGTTGAACTTGTTTTTGTTTGGTTGATTAAATTTGTGCATGTTGAGATA
66 AATACGAATAATAAATAGTTGAACTTCTTTTTGTTTGGTTGATTAAATTTGTGCATGTTGAGATA
43878067 TTTAGGGATGACCTAA
131 TTTAGGGATGACCTAA
43878083 ATAAATAGGTATTAAGCAATCAATTGTACCAAATGATATAGAAAATACAAGAAAACGAGCATACT
1 ATAAATAGGTATTAAGCAATCAATTGTACCAAATGATATAGAAAATACAAGAAAACGAGCATACT
43878148 AATACGAATAATAAATAGTTGAACTTCTTTTTGTTTGGTTGATTAAATTTGTGCATGTTGAGATA
66 AATACGAATAATAAATAGTTGAACTTCTTTTTGTTTGGTTGATTAAATTTGTGCATGTTGAGATA
43878213 TTTAGGGATGACCTAA
131 TTTAGGGATGACCTAA
43878229 A
1 A
43878230 GCATTGTTTG
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 146 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (146 bp):
ATAAATAGGTATTAAGCAATCAATTGTACCAAATGATATAGAAAATACAAGAAAACGAGCATACT
AATACGAATAATAAATAGTTGAACTTCTTTTTGTTTGGTTGATTAAATTTGTGCATGTTGAGATA
TTTAGGGATGACCTAA
Found at i:43881701 original size:16 final size:16
Alignment explanation
Indices: 43881677--43881710 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
43881667 TAGGAACGTC
*
43881677 AGCTGACCTAGGCTTA
1 AGCTAACCTAGGCTTA
43881693 AGCTAACCTAGGCTTA
1 AGCTAACCTAGGCTTA
43881709 AG
1 AG
43881711 GACGACAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (16 bp):
AGCTAACCTAGGCTTA
Found at i:43884623 original size:20 final size:20
Alignment explanation
Indices: 43884600--43884640 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
43884590 CTGTAGCGCT
*
43884600 ATCAAGGGCACCGAAGTGCA
1 ATCAAAGGCACCGAAGTGCA
*
43884620 ATCAAAGGCGCCGAAGTGCA
1 ATCAAAGGCACCGAAGTGCA
43884640 A
1 A
43884641 ATAAGGCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.24, G:0.29, T:0.10
Consensus pattern (20 bp):
ATCAAAGGCACCGAAGTGCA
Found at i:43890517 original size:40 final size:40
Alignment explanation
Indices: 43890434--43890653 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
43890424 ACCCAAGTAT
* ** * *
43890434 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
43890472 CTTCGGGCCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
43890512 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
43890552 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
43890592 CTTC-AGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
43890632 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
43890654 CATTCGAATA
Statistics
Matches: 153, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
38 11 0.07
39 17 0.11
40 122 0.80
41 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:43893370 original size:25 final size:26
Alignment explanation
Indices: 43893331--43893394 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
43893321 TTAGCTCTTA
*
43893331 TGAGCATCCCGATTAAA-GGCTCTTCG
1 TGAGCTTCCC-ATTAAATGGCTCTTCG
*
43893357 TGAGCTTCCCATTAAATTGGCTCTTTG
1 TGAGCTTCCCATTAAA-TGGCTCTTCG
*
43893384 TGACCTTCCCA
1 TGAGCTTCCCA
43893395 ATAGTGCTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.18
26 9 0.27
27 18 0.55
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (26 bp):
TGAGCTTCCCATTAAATGGCTCTTCG
Found at i:43893579 original size:24 final size:23
Alignment explanation
Indices: 43893531--43893582 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
43893521 AGCCCGGATA
* *
43893531 AGCTTCCTAATAGGCTCTTATTG
1 AGCTTCCTAAAAGGCTCTTAGTG
43893554 AGCTTCCTAAAATGGCTCTGT-GTG
1 AGCTTCCTAAAA-GGCTCT-TAGTG
43893578 AGCTT
1 AGCTT
43893583 TCCATTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
24 13 0.52
25 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (23 bp):
AGCTTCCTAAAAGGCTCTTAGTG
Found at i:43902940 original size:48 final size:48
Alignment explanation
Indices: 43902869--43903043 Score: 183
Period size: 48 Copynumber: 3.6 Consensus size: 48
43902859 GGTGTGCTAC
* * * *
43902869 TGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATGAGAGCCAA
1 TGTAAGACCATGTCTGGAACATGGCATCAGCCATGACATGAGAGCCAG
* * * ** *
43902917 TGTAAGACCATGTTTGGAACATGGCATC-GTCATTGAGACAAGAGCTAG
1 TGTAAGACCATGTCTGGAACATGGCATCAGCCA-TGACATGAGAGCCAG
* * * *
43902965 TGTAAAACCATGTCT-GAGACATGGCATCGGCCTTGACATGTGAGCCAG
1 TGTAAGACCATGTCTGGA-ACATGGCATCAGCCATGACATGAGAGCCAG
*
43903013 TGTAAGACCATGTTTGGAACATGGCATCAGC
1 TGTAAGACCATGTCTGGAACATGGCATCAGC
43903044 AATTCACCCT
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
47 5 0.05
48 93 0.91
49 4 0.04
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGAACATGGCATCAGCCATGACATGAGAGCCAG
Found at i:43903033 original size:96 final size:96
Alignment explanation
Indices: 43902864--43903040 Score: 273
Period size: 96 Copynumber: 1.8 Consensus size: 96
43902854 TGATAGGTGT
* * *
43902864 GCTACTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATGAGAGCCAATGTAAGACCATG
1 GCTACTGTAAAACCATGTCTGAGACATGGCATCAGCCACGACATGAGAGCCAATGTAAGACCATG
43902929 TTTGGAACATGGCATCGTCATTGAGACAAGA
66 TTTGGAACATGGCATCGTCATTGAGACAAGA
* * ** * *
43902960 GCTAGTGTAAAACCATGTCTGAGACATGGCATCGGCCTTGACATGTGAGCCAGTGTAAGACCATG
1 GCTACTGTAAAACCATGTCTGAGACATGGCATCAGCCACGACATGAGAGCCAATGTAAGACCATG
43903025 TTTGGAACATGGCATC
66 TTTGGAACATGGCATC
43903041 AGCAATTCAC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 72 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (96 bp):
GCTACTGTAAAACCATGTCTGAGACATGGCATCAGCCACGACATGAGAGCCAATGTAAGACCATG
TTTGGAACATGGCATCGTCATTGAGACAAGA
Found at i:43903401 original size:21 final size:21
Alignment explanation
Indices: 43903376--43903436 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 21
43903366 TTGTTACTTT
43903376 TTTATATGCAACTTACTAAGC
1 TTTATATGCAACTTACTAAGC
* *
43903397 -TT-TATGC--TTTACT---T
1 TTTATATGCAACTTACTAAGC
43903411 TTTATATGCAACTTACTAAGC
1 TTTATATGCAACTTACTAAGC
43903432 TTTAT
1 TTTAT
43903437 GCTTACTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 5 0.17
18 5 0.17
19 5 0.17
20 2 0.07
21 5 0.17
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (21 bp):
TTTATATGCAACTTACTAAGC
Found at i:43903402 original size:19 final size:19
Alignment explanation
Indices: 43903380--43903438 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
43903370 TACTTTTTTA
43903380 TATGCAACTTACTAAGCTT
1 TATGCAACTTACTAAGCTT
* **
43903399 TATGC--TTTACT--TTTT
1 TATGCAACTTACTAAGCTT
43903414 ATATGCAACTTACTAAGCTT
1 -TATGCAACTTACTAAGCTT
43903434 TATGC
1 TATGC
43903439 TTACTCCTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 5 0.17
18 5 0.17
19 10 0.34
20 2 0.07
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (19 bp):
TATGCAACTTACTAAGCTT
Found at i:43903417 original size:35 final size:36
Alignment explanation
Indices: 43903369--43903440 Score: 137
Period size: 35 Copynumber: 2.0 Consensus size: 36
43903359 GTTGATGTTG
43903369 TTACTTTTTTATATGCAACTTACTAAGCTTTATGCT
1 TTACTTTTTTATATGCAACTTACTAAGCTTTATGCT
43903405 TTAC-TTTTTATATGCAACTTACTAAGCTTTATGCT
1 TTACTTTTTTATATGCAACTTACTAAGCTTTATGCT
43903440 T
1 T
43903441 ACTCCTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 32 0.89
36 4 0.11
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (36 bp):
TTACTTTTTTATATGCAACTTACTAAGCTTTATGCT
Found at i:43904160 original size:19 final size:19
Alignment explanation
Indices: 43904114--43904153 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43904104 CTGTGTGGGA
*
43904114 CACGGGTCATGGACACGGG
1 CACGGGTCATGGACACAGG
*
43904133 CACGGGTCATGGGCACAGG
1 CACGGGTCATGGACACAGG
43904152 CA
1 CA
43904154 TGTGTCAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.40, T:0.10
Consensus pattern (19 bp):
CACGGGTCATGGACACAGG
Found at i:43905492 original size:18 final size:18
Alignment explanation
Indices: 43905469--43905514 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
43905459 CAACTCCCTA
43905469 TTCCAGAAGAGGTAATTG
1 TTCCAGAAGAGGTAATTG
43905487 TTCCAGAAGAGGTAATTG
1 TTCCAGAAGAGGTAATTG
43905505 TTCCAGAAGA
1 TTCCAGAAGA
43905515 ACAAATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (18 bp):
TTCCAGAAGAGGTAATTG
Found at i:43905521 original size:18 final size:18
Alignment explanation
Indices: 43905482--43905521 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43905472 CAGAAGAGGT
***
43905482 AATTGTTCCAGAAGAGGT
1 AATTGTTCCAGAAGAACA
43905500 AATTGTTCCAGAAGAACA
1 AATTGTTCCAGAAGAACA
43905518 AATT
1 AATT
43905522 CAACAACCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (18 bp):
AATTGTTCCAGAAGAACA
Found at i:43906556 original size:22 final size:22
Alignment explanation
Indices: 43906529--43906570 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
43906519 TATTTCAGTT
*
43906529 TACAGATATTAAGTTTATTTTC
1 TACAGAAATTAAGTTTATTTTC
43906551 TACAGAAATTAAGTTTATTT
1 TACAGAAATTAAGTTTATTT
43906571 GGTTTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (22 bp):
TACAGAAATTAAGTTTATTTTC
Found at i:43908809 original size:13 final size:15
Alignment explanation
Indices: 43908780--43908812 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
43908770 GGTGGAGAAA
43908780 ATAAATATTTGACAT
1 ATAAATATTTGACAT
43908795 ATAAATA-TT-ACAT
1 ATAAATATTTGACAT
43908808 ATAAA
1 ATAAA
43908813 GGAAAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (15 bp):
ATAAATATTTGACAT
Found at i:43912445 original size:15 final size:15
Alignment explanation
Indices: 43912425--43912454 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43912415 CAATTAGAAG
*
43912425 TCCTTAATTTTAGTT
1 TCCTTAATTATAGTT
43912440 TCCTTAATTATAGTT
1 TCCTTAATTATAGTT
43912455 CTCATTCTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (15 bp):
TCCTTAATTATAGTT
Found at i:43913204 original size:29 final size:30
Alignment explanation
Indices: 43913167--43913230 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
43913157 GAATTCATGA
* * *
43913167 TTAGAAGCTCCCTTCAATGAGTTC-CAAGG
1 TTAGGAGCTCCCTTCAAAGAGTTCTAAAGG
*
43913196 TTAGGAGCTCTCTTCAAAGAGTTCTAAAGG
1 TTAGGAGCTCCCTTCAAAGAGTTCTAAAGG
43913226 TTAGG
1 TTAGG
43913231 TTCTTCACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (30 bp):
TTAGGAGCTCCCTTCAAAGAGTTCTAAAGG
Found at i:43920785 original size:58 final size:58
Alignment explanation
Indices: 43920679--43920797 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 58
43920669 TTTGTCATGA
* *
43920679 CTTCATTAATCATCATTACGCAATAACACTTTTAACAAGAAGAGTTCATGCCTTGGAC
1 CTTCATCAATCATCATTACGCAATAACACTTTTAACAAGAAGAGTTCATACCTTGGAC
* * **
43920737 CTTCATCAATCATTATTATGCAATAACACTTTTAGTAGTAGAA-A-TTCATACCTTGGAC
1 CTTCATCAATCATCATTACGCAATAACACTTTTA--ACAAGAAGAGTTCATACCTTGGAC
43920795 CTT
1 CTT
43920798 AATATTTATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 47 0.89
59 1 0.02
60 5 0.09
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (58 bp):
CTTCATCAATCATCATTACGCAATAACACTTTTAACAAGAAGAGTTCATACCTTGGAC
Found at i:43927607 original size:7 final size:6
Alignment explanation
Indices: 43927579--43927629 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
43927569 ACCCAATCCA
* *
43927579 AAAATT AAAATT AAAATCT ACAAATT ACAATT -AAATT AATATAT AAAATT
1 AAAATT AAAATT AAAAT-T A-AAATT AAAATT AAAATT AAAAT-T AAAATT
43927629 A
1 A
43927630 TTTAATAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 4 0.11
6 20 0.54
7 9 0.24
8 4 0.11
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:43927636 original size:17 final size:18
Alignment explanation
Indices: 43927614--43927648 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43927604 TACAATTAAA
*
43927614 TTAATATATAAAA-TTAT
1 TTAATAGATAAAAGTTAT
43927631 TTAATAGATAAAAGTTAT
1 TTAATAGATAAAAGTTAT
43927649 ATGGTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
TTAATAGATAAAAGTTAT
Found at i:43927874 original size:5 final size:5
Alignment explanation
Indices: 43927864--43927891 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43927854 ATTACCGTAC
43927864 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
43927892 AATTTTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:43928273 original size:21 final size:21
Alignment explanation
Indices: 43928249--43928289 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43928239 TTTTGTTTTA
* *
43928249 TAAATAATAAATCTTAAAAAG
1 TAAAAAATAAATATTAAAAAG
*
43928270 TAAAAAATATATATTAAAAA
1 TAAAAAATAAATATTAAAAA
43928290 TCAACTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAAAATAAATATTAAAAAG
Found at i:43932243 original size:28 final size:28
Alignment explanation
Indices: 43932212--43932266 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
43932202 GTTAGTTTTA
* *
43932212 ATATATAATCGACTTTGCCGCCTGAATG
1 ATATATAATCAACTCTGCCGCCTGAATG
**
43932240 ATATATGGTCAACTCTGCCGCCTGAAT
1 ATATATAATCAACTCTGCCGCCTGAAT
43932267 ATTATAGTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (28 bp):
ATATATAATCAACTCTGCCGCCTGAATG
Found at i:43951422 original size:11 final size:10
Alignment explanation
Indices: 43951392--43951425 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
43951382 GGAGAGTACT
43951392 AAGAGTCAAA
1 AAGAGTCAAA
*
43951402 AAGAGCCAAA
1 AAGAGTCAAA
43951412 AACGAGTCAAA
1 AA-GAGTCAAA
43951423 AAG
1 AAG
43951426 GGACAAAATA
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:0.59, C:0.15, G:0.21, T:0.06
Consensus pattern (10 bp):
AAGAGTCAAA
Found at i:43951432 original size:21 final size:21
Alignment explanation
Indices: 43951394--43951433 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43951384 AGAGTACTAA
*
43951394 GAGTCAAAAAGAGCCAAAAAC
1 GAGTCAAAAAGAGACAAAAAC
*
43951415 GAGTCAAAAAGGGACAAAA
1 GAGTCAAAAAGAGACAAAA
43951434 TAGACCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.15, G:0.23, T:0.05
Consensus pattern (21 bp):
GAGTCAAAAAGAGACAAAAAC
Found at i:43957253 original size:22 final size:23
Alignment explanation
Indices: 43957228--43957279 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
43957218 CAAAAATTAC
43957228 AAAAGAAATTC-AAAATA-ATTTT
1 AAAA-AAATTCAAAAATATATTTT
*
43957250 -AAAAAATTCAAAAATATCTTTT
1 AAAAAAATTCAAAAATATATTTT
43957272 AAAAAAAT
1 AAAAAAAT
43957280 ATCTTCAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 4 0.15
23 7 0.27
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAAAAATTCAAAAATATATTTT
Found at i:43957256 original size:20 final size:22
Alignment explanation
Indices: 43957233--43957277 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
43957223 ATTACAAAAG
43957233 AAATTC-AAAATA-ATTTTAAA
1 AAATTCAAAAATATATTTTAAA
*
43957253 AAATTCAAAAATATCTTTTAAA
1 AAATTCAAAAATATATTTTAAA
43957275 AAA
1 AAA
43957278 ATATCTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 6 0.27
22 10 0.45
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATTCAAAAATATATTTTAAA
Found at i:43967499 original size:73 final size:74
Alignment explanation
Indices: 43967412--43967557 Score: 249
Period size: 73 Copynumber: 2.0 Consensus size: 74
43967402 GGCAAACTTA
*
43967412 AAAATTATTACCATCACCATAATAGTGCTTAGAAGAAACCAAGAAATAGGC-AAAGAAATAAAAC
1 AAAATTATTACCATCACCATAATAGTGCTTAGAAGAAACCAAGAAATAGCCAAAAGAAATAAAAC
43967476 ATAACATTG
66 ATAACATTG
* **
43967485 AAAATTATTACCATCACCATGATAGTGCTTAGAAGAAACCAAGAAATAGCCAAAAGAAATAATGC
1 AAAATTATTACCATCACCATAATAGTGCTTAGAAGAAACCAAGAAATAGCCAAAAGAAATAAAAC
43967550 ATAACATT
66 ATAACATT
43967558 ACCACTGATG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 49 0.72
74 19 0.28
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (74 bp):
AAAATTATTACCATCACCATAATAGTGCTTAGAAGAAACCAAGAAATAGCCAAAAGAAATAAAAC
ATAACATTG
Found at i:43967890 original size:1 final size:1
Alignment explanation
Indices: 43967884--43967950 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
43967874 ATTTAAACAT
* * * * * * * *
43967884 AAAAAAAAAAAAAACAAAAACAAAAAACAAAAAAAAAAACAAAAAACAAAAAAGACAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43967949 AA
1 AA
43967951 GAGAGGCAAG
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.88, C:0.10, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:43967908 original size:16 final size:15
Alignment explanation
Indices: 43967884--43967950 Score: 82
Period size: 16 Copynumber: 4.3 Consensus size: 15
43967874 ATTTAAACAT
43967884 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
43967899 AAAAACAAAAAACAAA-
1 AAAAA-AAAAAA-AAAC
43967915 AAAAAAAACAAAAAAC
1 AAAAAAAA-AAAAAAC
*
43967931 AAAAAAGACAAAAAAC
1 AAAAAA-AAAAAAAAC
43967947 AAAA
1 AAAA
43967951 GAGAGGCAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
15 11 0.24
16 31 0.67
17 4 0.09
ACGTcount: A:0.88, C:0.10, G:0.01, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:43967910 original size:19 final size:19
Alignment explanation
Indices: 43967886--43967950 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 19
43967876 TTAAACATAA
43967886 AAAAAAAAAAAACAAAAAC
1 AAAAAAAAAAAACAAAAAC
43967905 AAAAAACAAAAAA-AAAAAC
1 AAAAAA-AAAAAACAAAAAC
43967924 AAAAAACAAAAAAGACAAAAAAC
1 -AAAAA-AAAAAA-AC-AAAAAC
43967947 AAAA
1 AAAA
43967951 GAGAGGCAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
19 12 0.30
20 16 0.40
21 2 0.05
22 4 0.10
23 6 0.15
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAACAAAAAC
Found at i:43967922 original size:26 final size:27
Alignment explanation
Indices: 43967886--43967950 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 27
43967876 TTAAACATAA
43967886 AAAAAAAAAAAAC-AAAAACAAAAAAC
1 AAAAAAAAAAAACAAAAAACAAAAAAC
*
43967912 -AAAAAAAAAAACAAAAAACAAAAAAG
1 AAAAAAAAAAAACAAAAAACAAAAAAC
*
43967938 ACAAAAAACAAAA
1 A-AAAAAAAAAAA
43967951 GAGAGGCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 12 0.35
26 12 0.35
28 10 0.29
ACGTcount: A:0.88, C:0.11, G:0.02, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAAACAAAAAACAAAAAAC
Found at i:43970388 original size:22 final size:24
Alignment explanation
Indices: 43970345--43970388 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
43970335 ATTATATTGT
*
43970345 TAAATTGATATTTATAAATATTTA
1 TAAATTGATATTTAGAAATATTTA
*
43970369 TAAATT-A-ATTTAGAATTATT
1 TAAATTGATATTTAGAAATATT
43970389 AATTATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 1 0.06
24 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (24 bp):
TAAATTGATATTTAGAAATATTTA
Found at i:43970544 original size:18 final size:19
Alignment explanation
Indices: 43970500--43970544 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
43970490 AAAAAATTCT
*
43970500 TAATTATTTTTATTTGTTA
1 TAATTATTTTTATTTGTCA
*
43970519 TAAGTATTTTTATTT-TCA
1 TAATTATTTTTATTTGTCA
*
43970537 TATTTATT
1 TAATTATT
43970545 AATCAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
TAATTATTTTTATTTGTCA
Found at i:43971283 original size:24 final size:24
Alignment explanation
Indices: 43971239--43971285 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43971229 TTTTAACTTC
*
43971239 TTTTATTTATAAAATATTATTTAT
1 TTTTATTTATAAAATAATATTTAT
43971263 TTTTAATTTATAAAA-AATATTTA
1 TTTT-ATTTATAAAATAATATTTA
43971286 CCTGCAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATTTATAAAATAATATTTAT
Found at i:43971345 original size:30 final size:30
Alignment explanation
Indices: 43971310--43971368 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
43971300 AGGTGAGAAA
43971310 GAAATATATGGAAACATTGACTTGTGAGAC
1 GAAATATATGGAAACATTGACTTGTGAGAC
*
43971340 GAAATATATGGAAACATTGAGTTGTGAGA
1 GAAATATATGGAAACATTGACTTGTGAGA
43971369 TAGTTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (30 bp):
GAAATATATGGAAACATTGACTTGTGAGAC
Found at i:43974035 original size:7 final size:7
Alignment explanation
Indices: 43974023--43974055 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
43974013 GAGTCGATTC
43974023 GTATTTA
1 GTATTTA
43974030 GTATTTA
1 GTATTTA
43974037 GTATTTA
1 GTATTTA
*
43974044 CTATTTA
1 GTATTTA
43974051 GTATT
1 GTATT
43974056 ATGTATATAA
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:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:43974580 original size:30 final size:30
Alignment explanation
Indices: 43974521--43974617 Score: 115
Period size: 30 Copynumber: 3.3 Consensus size: 30
43974511 GATGATGACG
* *
43974521 CGGGCTCATCAACAGCG-CCACAGAATCAC
1 CGGGCCCATCAACAGCGCCCACACAATCAC
* * *
43974550 CGGGCCCATCAATAGTGCCCATACAATCAC
1 CGGGCCCATCAACAGCGCCCACACAATCAC
* *
43974580 CAGGCCCATCAACAGCGCCCACACAGTCAC
1 CGGGCCCATCAACAGCGCCCACACAATCAC
*
43974610 TGGGCCCA
1 CGGGCCCA
43974618 ATACTTTAAC
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
29 14 0.25
30 41 0.75
ACGTcount: A:0.29, C:0.40, G:0.20, T:0.11
Consensus pattern (30 bp):
CGGGCCCATCAACAGCGCCCACACAATCAC
Found at i:43975014 original size:21 final size:21
Alignment explanation
Indices: 43974954--43975015 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
43974944 CCAACACCCA
* *
43974954 CAACCAGATCCCCTATCGGAG
1 CAACCAGAACCCCTACCGGAG
* *
43974975 GAACCAGAATCCCC-GCCGGAG
1 CAACCAGAA-CCCCTACCGGAG
*
43974996 CAACCACAACCCCTACCGGA
1 CAACCAGAACCCCTACCGGA
43975016 AGCTGGACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.31, C:0.42, G:0.19, T:0.08
Consensus pattern (21 bp):
CAACCAGAACCCCTACCGGAG
Found at i:43975216 original size:54 final size:55
Alignment explanation
Indices: 43975134--43975259 Score: 141
Period size: 54 Copynumber: 2.3 Consensus size: 55
43975124 TATTGTTTCA
* * * *
43975134 TTTAATAAAATAAAAGTTGTTTTGAATAAAG-TA-ATTGT-AATTTACTTTTATATT
1 TTTAATAAAATAAAATTTCTTTTAAATAAAGCAATATTGTGAA--TACTTTTATATT
* * *
43975188 TTTAATAAAATAAAATTTCTTTTAAATAAGGCAATATTTTGAATATTTTTATATT
1 TTTAATAAAATAAAATTTCTTTTAAATAAAGCAATATTGTGAATACTTTTATATT
43975243 TTTAATAAAATATAAAT
1 TTTAATAAAATA-AAAT
43975260 AATGCAACAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
54 27 0.44
55 24 0.39
56 8 0.13
57 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (55 bp):
TTTAATAAAATAAAATTTCTTTTAAATAAAGCAATATTGTGAATACTTTTATATT
Found at i:43978410 original size:124 final size:126
Alignment explanation
Indices: 43978102--43978471 Score: 602
Period size: 125 Copynumber: 3.0 Consensus size: 126
43978092 GCCAAATAGG
** * *
43978102 AACTACTGTAGAAAAAGAGCGTCTTCATGGGAGCTTTTTTCAGTACTTTTGTTGACA-TGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* *
43978166 TGCTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTTTCAAAATTATTTTTTCAAA
66 TGCTTGAAGCGTTTTTGACACTATTTATTCAGAAACATCTTTTCAAAATTATTTTTTCAAA
* *
43978227 AACTACTGTAGAAAAATAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGGATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* * *
43978292 TGCTTGAAGCGTTTTTGACACTATTT-TTCAGAAACATCTTCTCAAAATTATTTTTTTAGA
66 TGCTTGAAGCGTTTTTGACACTATTTATTCAGAAACATCTTTTCAAAATTATTTTTTCAAA
43978352 AACTACTGTAGAAAAA-AGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
* *
43978416 TGCTTGAAGCGTTTTTGACACTATTTATTCATAAACATCTTTTTAAAATTATTTTT
66 TGCTTGAAGCGTTTTTGACACTATTTATTCAGAAACATCTTTTCAAAATTATTTTT
43978472 CAGATACATC
Statistics
Matches: 229, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
124 73 0.32
125 124 0.54
126 32 0.14
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTATTCAGAAACATCTTTTCAAAATTATTTTTTCAAA
Found at i:43981422 original size:38 final size:38
Alignment explanation
Indices: 43981367--43981443 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
43981357 TAGATGTTAG
*
43981367 GGACATCTCACTCTTTCGGCTTAAATTCCCCACTTTTT
1 GGACATATCACTCTTTCGGCTTAAATTCCCCACTTTTT
*
43981405 GGACATATCACTTTTTCGGCTTAAATTCCCCACTTTTT
1 GGACATATCACTCTTTCGGCTTAAATTCCCCACTTTTT
43981443 G
1 G
43981444 ACAACTCTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (38 bp):
GGACATATCACTCTTTCGGCTTAAATTCCCCACTTTTT
Found at i:43981441 original size:22 final size:22
Alignment explanation
Indices: 43981375--43981442 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
43981365 AGGGACATCT
*
43981375 CACTCTTTCGGCTTAAATTCCC
1 CACTTTTTCGGCTTAAATTCCC
*
43981397 CACTTTTT-GG---ACATAT---
1 CACTTTTTCGGCTTAAAT-TCCC
43981413 CACTTTTTCGGCTTAAATTCCC
1 CACTTTTTCGGCTTAAATTCCC
43981435 CACTTTTT
1 CACTTTTT
43981443 GACAACTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 16
0.65 0.06 0.30
Matches are distributed among these distances:
16 8 0.23
17 2 0.06
18 3 0.09
19 2 0.06
20 3 0.09
21 2 0.06
22 15 0.43
ACGTcount: A:0.19, C:0.29, G:0.09, T:0.43
Consensus pattern (22 bp):
CACTTTTTCGGCTTAAATTCCC
Found at i:43989649 original size:20 final size:20
Alignment explanation
Indices: 43989624--43989665 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
43989614 TGGGTTAGGG
43989624 ACACGGGCGTGTCCCAAACC
1 ACACGGGCGTGTCCCAAACC
43989644 ACACGGGCGTGTCCCAAACC
1 ACACGGGCGTGTCCCAAACC
43989664 AC
1 AC
43989666 CATGCATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.40, G:0.24, T:0.10
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAACC
Found at i:43992898 original size:19 final size:19
Alignment explanation
Indices: 43992858--43992912 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
43992848 GTAACAAAAT
* *
43992858 AAAATAAAAATAGATTCAAA
1 AAAAT-AAAATAAATTTAAA
*
43992878 AATAAAAAAATAAATTTAAA
1 AA-AATAAAATAAATTTAAA
*
43992898 AAAATAAAATCAATT
1 AAAATAAAATAAATT
43992913 GGTAAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 11 0.38
20 16 0.55
21 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATAAAATAAATTTAAA
Found at i:43992906 original size:20 final size:20
Alignment explanation
Indices: 43992858--43992906 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
43992848 GTAACAAAAT
*
43992858 AAAATAAAAATAGATTCAAA
1 AAAATAAAAATAAATTCAAA
*
43992878 AATAA-AAAAATAAATTTAAA
1 AA-AATAAAAATAAATTCAAA
43992898 AAAATAAAA
1 AAAATAAAA
43992907 TCAATTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATAAAAATAAATTCAAA
Found at i:44000750 original size:37 final size:37
Alignment explanation
Indices: 44000687--44000795 Score: 155
Period size: 37 Copynumber: 2.9 Consensus size: 37
44000677 AGGTCAGATG
* * * *
44000687 AAATCTCCACAAGAAGTTATCTGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCAGGTCTTACCCGGACA
* *
44000724 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCAGGTCTTACCCGGACA
*
44000761 TAATCTCCACACGTAGTCATCAGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCAGGTCTTACCCGGA
44000796 ATATATTTCC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCAGGTCTTACCCGGACA
Found at i:44000996 original size:48 final size:48
Alignment explanation
Indices: 44000937--44001273 Score: 584
Period size: 48 Copynumber: 7.0 Consensus size: 48
44000927 TATACACACG
* * * *
44000937 TCTCCTACATATTTCACACTAGCCCTTCGGCTTTACCACATATACGTA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
*
44000985 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
* *
44001033 TCTCATATATATTTCACATTAGCCATTCGGCTTTATCACATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
44001081 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
* *
44001129 TCTCATACATATTTCACATTAGCCATTCGGCTTTGCCACATATACCTA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
*
44001177 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACCTA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
44001225 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
44001273 T
1 T
44001274 ATTTATCTTG
Statistics
Matches: 277, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 277 1.00
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (48 bp):
TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
Found at i:44006576 original size:13 final size:13
Alignment explanation
Indices: 44006558--44006600 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
44006548 AAGATTTTTC
44006558 CTAAATATTATTA
1 CTAAATATTATTA
44006571 CTAAATA--ATT-
1 CTAAATATTATTA
*
44006581 CTAAATATTATCA
1 CTAAATATTATTA
44006594 CTAAATA
1 CTAAATA
44006601 ATTCTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 2 0.08
13 14 0.54
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
CTAAATATTATTA
Found at i:44006588 original size:23 final size:23
Alignment explanation
Indices: 44006558--44006609 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
44006548 AAGATTTTTC
*
44006558 CTAAATATTATTACTAAATAATT
1 CTAAATATTATCACTAAATAATT
44006581 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
44006604 CTAAAT
1 CTAAAT
44006610 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:44006622 original size:23 final size:23
Alignment explanation
Indices: 44006558--44006622 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
44006548 AAGATTTTTC
** *
44006558 CTAAATATTATTACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
** *
44006581 CTAAATATTATCACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
44006604 CTAAAT-TTAAAAATCAAAT
1 CTAAATATTAAAAAT-AAAT
44006623 TTAAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.14
23 32 0.86
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTAAAAATAAATAATT
Found at i:44007341 original size:22 final size:22
Alignment explanation
Indices: 44007299--44007341 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
44007289 TTAATGAAAT
* *
44007299 ATTATAAAAATTAAATGGATTC
1 ATTAAAAAAATTAAATAGATTC
*
44007321 ATTAAAAAAATTAATTAGATT
1 ATTAAAAAAATTAAATAGATT
44007342 TTTTTTAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTAAAAAAATTAAATAGATTC
Found at i:44007387 original size:18 final size:18
Alignment explanation
Indices: 44007355--44007392 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
44007345 TTTAACAATC
*
44007355 TCATTTTTGATTATATCTG
1 TCATTTTTGAATATAT-TG
44007374 TCATTTTT-AATATATTG
1 TCATTTTTGAATATATTG
44007391 TC
1 TC
44007393 TAAAACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.58
Consensus pattern (18 bp):
TCATTTTTGAATATATTG
Found at i:44007650 original size:30 final size:30
Alignment explanation
Indices: 44007591--44007650 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
44007581 TATATATTAT
*
44007591 ATTAAAAGGTCTAAGATCTTAACTGATGTG
1 ATTAAAAGGTCTAAGATCTTAACTAATGTG
* *
44007621 ATTATAAGGTCTAAGATCTTAATTAATGTG
1 ATTAAAAGGTCTAAGATCTTAACTAATGTG
44007651 GACGCCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (30 bp):
ATTAAAAGGTCTAAGATCTTAACTAATGTG
Found at i:44013074 original size:56 final size:56
Alignment explanation
Indices: 44013014--44013161 Score: 253
Period size: 56 Copynumber: 2.6 Consensus size: 56
44013004 TCTCATATAG
* *
44013014 GGTCTTACTGATACACATATATCGAAATCACATATCGATGCCAGCGTATTAAACGT
1 GGTCTTACTGACACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
*
44013070 GGTCTTACTCACACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
1 GGTCTTACTGACACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
44013126 GGTCTTACTCG-CACACATATATCGAAATCACATATC
1 GGTCTTACT-GACACACATATATCGAAATCACATATC
44013162 ACAAGTCGAA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
56 87 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (56 bp):
GGTCTTACTGACACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGT
Found at i:44015542 original size:21 final size:21
Alignment explanation
Indices: 44015516--44015559 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
44015506 ATATCGGTAA
44015516 TAGAATATCAAAGAGAATTTG
1 TAGAATATCAAAGAGAATTTG
*
44015537 TAGAATATGAAAGAGAATTTG
1 TAGAATATCAAAGAGAATTTG
44015558 TA
1 TA
44015560 TGACTCAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (21 bp):
TAGAATATCAAAGAGAATTTG
Found at i:44018244 original size:241 final size:241
Alignment explanation
Indices: 44017821--44018305 Score: 925
Period size: 241 Copynumber: 2.0 Consensus size: 241
44017811 GCATGAAAAG
*
44017821 AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTCGCATTGAAAATTTGGCGACATTT
1 AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTCGCATTGAAAATTTGGCGACATTA
*
44017886 CTTATACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
66 CTTACACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
44017951 AAGATTTGAATCTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
131 AAGATTTGAATCTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
44018016 TATCACTCGGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
196 TATCACTCGGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
* *
44018062 AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTTGCATTGAAAATTTGGTGACATTA
1 AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTCGCATTGAAAATTTGGCGACATTA
44018127 CTTACACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
66 CTTACACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
*
44018192 AAGATTTGAATTTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
131 AAGATTTGAATCTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
44018257 TATCACTCGGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
196 TATCACTCGGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
44018303 AAT
1 AAT
44018306 CTTTGTTTGC
Statistics
Matches: 239, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
241 239 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (241 bp):
AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTCGCATTGAAAATTTGGCGACATTA
CTTACACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
AAGATTTGAATCTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
TATCACTCGGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
Found at i:44024407 original size:15 final size:15
Alignment explanation
Indices: 44024383--44024413 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44024373 TAATGTCTTG
44024383 CAACTAGGATAAAAA
1 CAACTAGGATAAAAA
*
44024398 CAACTGGGATAAAAA
1 CAACTAGGATAAAAA
44024413 C
1 C
44024414 TTCTGTGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (15 bp):
CAACTAGGATAAAAA
Found at i:44024659 original size:36 final size:36
Alignment explanation
Indices: 44024619--44024691 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
44024609 CACTTTCCAT
**
44024619 TTTGCCTCATTGGCAACACTTTCAAAACT-TGTTGGG
1 TTTGCCTCATTAACAACACTTTCAAAA-TATGTTGGG
44024655 TTTGCCTCATTAACAACACTTTCAAAATATGTTGGG
1 TTTGCCTCATTAACAACACTTTCAAAATATGTTGGG
44024691 T
1 T
44024692 CACAATATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (36 bp):
TTTGCCTCATTAACAACACTTTCAAAATATGTTGGG
Found at i:44025921 original size:74 final size:74
Alignment explanation
Indices: 44025800--44025947 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
44025790 TTATGAATCT
44025800 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
1 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
44025865 TGACTTGTA
66 TGACTTGTA
44025874 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
1 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
44025939 TGACTTGTA
66 TGACTTGTA
44025948 CACTTTAATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (74 bp):
ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
TGACTTGTA
Found at i:44028211 original size:28 final size:27
Alignment explanation
Indices: 44028177--44028240 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
44028167 GTATTGTGAT
* *
44028177 TGTACTGTTTTGGGCATAGGCCCATAC
1 TGTACTGTTTAGGGCATAGGCCCAGAC
** *
44028204 TGTTACTGCATAGGGCTTAGGCCCAGAC
1 TG-TACTGTTTAGGGCATAGGCCCAGAC
44028232 TGTACTGTT
1 TGTACTGTT
44028241 AATGAATAGG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.33
Consensus pattern (27 bp):
TGTACTGTTTAGGGCATAGGCCCAGAC
Found at i:44028250 original size:33 final size:33
Alignment explanation
Indices: 44028201--44028263 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
44028191 CATAGGCCCA
* * * *
44028201 TACTGTTACTGCATAGGGCTTAGGCCCAGACTG
1 TACTGTTAATGAATAGGGCTCAAGCCCAGACTG
44028234 TACTGTTAATGAATAGGGCTCAAGCCCAGA
1 TACTGTTAATGAATAGGGCTCAAGCCCAGA
44028264 ACGTTACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (33 bp):
TACTGTTAATGAATAGGGCTCAAGCCCAGACTG
Found at i:44029440 original size:12 final size:12
Alignment explanation
Indices: 44029423--44029448 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44029413 AGAGTTTAAC
44029423 TATGATTAAACT
1 TATGATTAAACT
44029435 TATGATTAAACT
1 TATGATTAAACT
44029447 TA
1 TA
44029449 ATCACTTTAA
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:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
TATGATTAAACT
Found at i:44029580 original size:68 final size:67
Alignment explanation
Indices: 44029503--44029629 Score: 177
Period size: 68 Copynumber: 1.9 Consensus size: 67
44029493 TTAGATTAAA
*
44029503 TTTAATATTAAATCTTATTAAAATA-ATGT-AGATAAACATTAAATTAAATTTAATATTAAGATA
1 TTTAATATT-AAT-TTAATAAAATACAT-TAAGATAAACATTAAATTAAATTTAATATTAAGATA
44029566 TTCAC
63 TTCAC
**
44029571 TTTAATATTAATTTAATAAAATACTATTAAGATAAGTATTAAATTAAATTTAATATTAA
1 TTTAATATTAATTTAATAAAATAC-ATTAAGATAAACATTAAATTAAATTTAATATTAA
44029630 ACTATTAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
66 10 0.19
67 4 0.08
68 39 0.74
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (67 bp):
TTTAATATTAATTTAATAAAATACATTAAGATAAACATTAAATTAAATTTAATATTAAGATATTC
AC
Found at i:44031861 original size:48 final size:48
Alignment explanation
Indices: 44031806--44031903 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
44031796 ATTTCTCCAT
44031806 TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
1 TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
44031854 TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
1 TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
44031902 TT
1 TT
44031904 TCATTCATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (48 bp):
TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
Found at i:44034498 original size:41 final size:41
Alignment explanation
Indices: 44034424--44034611 Score: 177
Period size: 40 Copynumber: 4.6 Consensus size: 41
44034414 ATACTGGAAT
* * * *
44034424 TCTCACACATTAAGTGCCAAAACATAGCTGAAGCTATTTTAA
1 TCTCGCACACTAAGTGCC-ATATATAGCTGAAGCTATTTTAA
* * * *
44034466 TCTCGCACACTAAGTGCC-TTTCATAGCCGAAGCTATCTTAG
1 TCTCGCACACTAAGTGCCATAT-ATAGCTGAAGCTATTTTAA
* * *
44034507 TCTCGCACACTAAGTTCCACATATAGCTGAAGCTATTTCGAA
1 TCTCGCACACTAAGTGCCATATATAGCTGAAGCTATTT-TAA
* *
44034549 --TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCAA
1 TCTCGCACACTAAGTGCCATATATAGCTGAAGCTATTTTAA
* * *
44034588 -ATCACACATTAAGTGCCATATATA
1 TCTCGCACACTAAGTGCCATATATA
44034612 TATCCAAATC
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
39 2 0.02
40 54 0.45
41 47 0.39
42 18 0.15
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (41 bp):
TCTCGCACACTAAGTGCCATATATAGCTGAAGCTATTTTAA
Found at i:44035838 original size:35 final size:35
Alignment explanation
Indices: 44035792--44035858 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
44035782 AAAATCTTAC
* *
44035792 TAGTGAATAGGTTAGGGTATTGTTTTCTCATACCT
1 TAGTGAATAGGTTAGGGTACTATTTTCTCATACCT
44035827 TAGTGAATAGGTTAGGGTACTATTTTCTCATA
1 TAGTGAATAGGTTAGGGTACTATTTTCTCATA
44035859 GCATTCTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.42
Consensus pattern (35 bp):
TAGTGAATAGGTTAGGGTACTATTTTCTCATACCT
Found at i:44041044 original size:12 final size:12
Alignment explanation
Indices: 44041027--44041052 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44041017 CACACGCCAA
44041027 TGTGCTAGGCCG
1 TGTGCTAGGCCG
44041039 TGTGCTAGGCCG
1 TGTGCTAGGCCG
44041051 TG
1 TG
44041053 CCAAACCTGT
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:0.08, C:0.23, G:0.42, T:0.27
Consensus pattern (12 bp):
TGTGCTAGGCCG
Found at i:44041203 original size:32 final size:32
Alignment explanation
Indices: 44041156--44041228 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
44041146 ACACCAGAGG
*
44041156 ACACACGGCCGTGCAACATGACCGTGTGTCAC
1 ACACACGGCCATGCAACATGACCGTGTGTCAC
* *
44041188 ACACATGGCCATGCAACATGACTGTGTGTCAC
1 ACACACGGCCATGCAACATGACCGTGTGTCAC
44041220 ACACACGGC
1 ACACACGGC
44041229 TGAGACACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.16
Consensus pattern (32 bp):
ACACACGGCCATGCAACATGACCGTGTGTCAC
Found at i:44042157 original size:41 final size:41
Alignment explanation
Indices: 44042100--44042245 Score: 174
Period size: 40 Copynumber: 3.6 Consensus size: 41
44042090 ATACTCGAAT
*
44042100 TCTCGCACACTAAGTGCC-TTTCATAGCCGAAGCTATCTCAG
1 TCTCGCACACTAAGTGCCATAT-ATAGCCGAAGCTATCTCAG
* * * * *
44042141 TCTCGTACACTAAGTGCCACATATAGCCGTAGCTATTTCAAA
1 TCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTC-AG
44042183 T-T-GCACACTAAGTGCCATATATAGCCGAAGCTATCTC-G
1 TCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAG
**
44042221 GATCGCACACTAAGTGCCATATATA
1 TCTCGCACACTAAGTGCCATATATA
44042246 TATCCAAATC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.01
40 52 0.58
41 33 0.37
42 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (41 bp):
TCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAG
Found at i:44043582 original size:90 final size:90
Alignment explanation
Indices: 44043438--44043664 Score: 303
Period size: 90 Copynumber: 2.5 Consensus size: 90
44043428 TTTATTTTTT
* * **
44043438 GTTTTGATTTTTATTTCTAGAAGCGAGTTTTTTAAATTAGAATAAAATCTGTTTC-GATATTTAT
1 GTTTTGATTTTTATTTCCAAAAATGAG-TTTTTAAATTAGAATAAAATCTGTTTCAGA-ATTTAT
* * * *
44043502 TCCCGCCGTTTAATGGATTTTATTCCG
64 TCCCACCGCTCAATGGATTTTATTCCA
44043529 GTTTTGATTTTTATTTCCAAAAATGAGTTTTTAAATTAGAATAAAATCTGTTTCAGAATTTATTC
1 GTTTTGATTTTTATTTCCAAAAATGAGTTTTTAAATTAGAATAAAATCTGTTTCAGAATTTATTC
* *
44043594 CCATCGCTCAATGGATTTTTTTCCA
66 CCACCGCTCAATGGATTTTATTCCA
* * * *
44043619 ATTTTTATTTTTATTTCCAAAAATAAGTTTTTAAATTTGAATAAAA
1 GTTTTGATTTTTATTTCCAAAAATGAGTTTTTAAATTAGAATAAAA
44043665 AATTTTTCGC
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
90 96 0.79
91 25 0.21
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (90 bp):
GTTTTGATTTTTATTTCCAAAAATGAGTTTTTAAATTAGAATAAAATCTGTTTCAGAATTTATTC
CCACCGCTCAATGGATTTTATTCCA
Found at i:44043836 original size:48 final size:48
Alignment explanation
Indices: 44043784--44043880 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 48
44043774 TTATTGTGAT
*
44043784 TTAATTACTTAATTTTGTTTCA-AAATTT-AGTCTTGCCGTTTAACAAAA
1 TTAATT-CTTAATTTTGTTTCAGAAATTTAATTC-TGCCGTTTAACAAAA
* * * *
44043832 TTAATTTTTGATTTTGTTTCAGAACTTTAATTCTGTCGTTTAACAAAA
1 TTAATTCTTAATTTTGTTTCAGAAATTTAATTCTGCCGTTTAACAAAA
44043880 T
1 T
44043881 CAAAGGGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 13 0.31
48 26 0.62
49 3 0.07
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (48 bp):
TTAATTCTTAATTTTGTTTCAGAAATTTAATTCTGCCGTTTAACAAAA
Found at i:44052415 original size:21 final size:21
Alignment explanation
Indices: 44052389--44052429 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
44052379 TGGTAAGGAT
44052389 AATGTAGTGGCTAACGCACTG
1 AATGTAGTGGCTAACGCACTG
44052410 AATGTAGTGGCTAACGCACT
1 AATGTAGTGGCTAACGCACT
44052430 TAGCCATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (21 bp):
AATGTAGTGGCTAACGCACTG
Found at i:44057611 original size:18 final size:18
Alignment explanation
Indices: 44057556--44057603 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
44057546 GTAATAAGTG
44057556 ACGTTTTGAAAGTAAATA
1 ACGTTTTGAAAGTAAATA
44057574 ACGTTTTGAAAGTAAATA
1 ACGTTTTGAAAGTAAATA
44057592 ACGTTTTGAAAG
1 ACGTTTTGAAAG
44057604 AGAATAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (18 bp):
ACGTTTTGAAAGTAAATA
Found at i:44060529 original size:20 final size:19
Alignment explanation
Indices: 44060501--44060570 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
44060491 AAAAGTTAAA
*
44060501 AAAAATCAAAATAATTTTC
1 AAAATTCAAAATAATTTTC
*
44060520 AAATATTCAAAATAATTTTT
1 AAA-ATTCAAAATAATTTTC
*
44060540 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TC
44060559 AAAATTCTAAAA
1 AAAATTC-AAAA
44060571 ATTATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.09
19 20 0.44
20 21 0.47
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:44060548 original size:19 final size:19
Alignment explanation
Indices: 44060501--44060585 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 19
44060491 AAAAGTTAAA
* *
44060501 AAAAATCAAAATAATTTTC
1 AAAATTCAAAATAATTTTT
44060520 AAATATTCAAAATAATTTTT
1 AAA-ATTCAAAATAATTTTT
*
44060540 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
44060559 AAAATTCTAAAAATTATATTTTT
1 AAAATTC--AAAA-TA-ATTTTT
44060582 AAAA
1 AAAA
44060586 AATTATAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.07
19 20 0.36
20 17 0.31
21 4 0.07
22 1 0.02
23 5 0.09
24 4 0.07
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:44060578 original size:24 final size:25
Alignment explanation
Indices: 44060550--44060598 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
44060540 AAAATTCAAA
*
44060550 ATATTTAT-AAAAATTCTAAAAATT
1 ATATTTATAAAAAATTATAAAAATT
*
44060574 ATATTTTTAAAAAATTATAAAAATT
1 ATATTTATAAAAAATTATAAAAATT
44060599 TTGAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATTTATAAAAAATTATAAAAATT
Found at i:44069107 original size:15 final size:16
Alignment explanation
Indices: 44069076--44069108 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44069066 TGGGAACAAA
44069076 TGACCAAAAAAGTTTT
1 TGACCAAAAAAGTTTT
44069092 TGACCAAAAAAGTTTT
1 TGACCAAAAAAGTTTT
44069108 T
1 T
44069109 ACTTAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (16 bp):
TGACCAAAAAAGTTTT
Found at i:44082392 original size:31 final size:31
Alignment explanation
Indices: 44082346--44082414 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
44082336 TACTAGGCTG
*
44082346 AAGCC-TTTCATAATTCATAACACTGGGCCA
1 AAGCCTTTTCAAAATTCATAACACTGGGCCA
** **
44082376 AAGCCTTTTCAAAATTCATATTACTGGGCTG
1 AAGCCTTTTCAAAATTCATAACACTGGGCCA
44082407 AAGCCTTT
1 AAGCCTTT
44082415 ACTGTAAGCG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (31 bp):
AAGCCTTTTCAAAATTCATAACACTGGGCCA
Found at i:44082653 original size:24 final size:25
Alignment explanation
Indices: 44082606--44082653 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
44082596 CTGCTTTATC
**
44082606 ATAACTGGAGGCCTAGCCTCTTTTA
1 ATAACTGGAGGCAAAGCCTCTTTTA
*
44082631 ATAACTGG-GGCAAAGCCTTTTTT
1 ATAACTGGAGGCAAAGCCTCTTTT
44082654 GCACTTCCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (25 bp):
ATAACTGGAGGCAAAGCCTCTTTTA
Found at i:44082815 original size:25 final size:25
Alignment explanation
Indices: 44082787--44082835 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
44082777 ATAATTAAAC
* * *
44082787 CCTAGGGGTACAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
44082812 CCTAGGGGCAAAATAGTCATTTTT
1 CCTAGGGGCAAAATAGTCATTTTT
44082836 CATATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:44090773 original size:27 final size:27
Alignment explanation
Indices: 44090743--44090947 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
44090733 ATATTAAGTC
* *
44090743 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
44090770 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
44090798 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
44090825 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
44090852 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
44090879 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
44090906 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
44090933 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44090948 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.83
28 26 0.17
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:44090882 original size:54 final size:54
Alignment explanation
Indices: 44090743--44090946 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
44090733 ATATTAAGTC
* * * **
44090743 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
44090798 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
44090852 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
44090906 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
44090947 TGTACAATTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:44090912 original size:81 final size:81
Alignment explanation
Indices: 44090797--44090946 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
44090787 ATAATCAAAC
* * * * * *
44090797 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
44090862 GTGCATCATTTTCATT
66 GTGCATCATTTTCATT
* *
44090878 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
44090943 GTGC
66 GTGC
44090947 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTTCATT
Found at i:44098929 original size:27 final size:27
Alignment explanation
Indices: 44098899--44099103 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
44098889 ATATTAAGTC
* *
44098899 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
44098926 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
44098954 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
44098981 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
44099008 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
44099035 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
44099062 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
44099089 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44099104 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.83
28 26 0.17
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:44099038 original size:54 final size:54
Alignment explanation
Indices: 44098899--44099102 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
44098889 ATATTAAGTC
* * * **
44098899 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
44098954 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
44099008 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
44099062 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
44099103 TGTACAATTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:44099068 original size:81 final size:81
Alignment explanation
Indices: 44098953--44099102 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
44098943 ATAATCAAAC
* * * * * *
44098953 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
44099018 GTGCATCATTTTCATT
66 GTGCATCATTTTCATT
* *
44099034 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
44099099 GTGC
66 GTGC
44099103 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTTCATT
Found at i:44109435 original size:47 final size:47
Alignment explanation
Indices: 44109381--44109763 Score: 532
Period size: 47 Copynumber: 8.1 Consensus size: 47
44109371 TTAGGATTTT
** * * *
44109381 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
44109428 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG--CATATAT--GTGATAAGGCCGAATGGCCA
* *
44109479 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*** *
44109526 ATGTGATGAATGTGAACATTTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
44109573 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
44109620 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
44109667 ATGTGATGAATGTTAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
44109714 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
44109761 ATG
1 ATG
44109764 CGAAATGTGT
Statistics
Matches: 311, Mismatches: 21, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
47 263 0.85
49 11 0.04
51 37 0.12
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:44109649 original size:141 final size:141
Alignment explanation
Indices: 44109381--44109763 Score: 586
Period size: 141 Copynumber: 2.7 Consensus size: 141
44109371 TTAGGATTTT
** *
44109381 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGTATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
* *
44109446 TGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
65 ---ATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
44109511 AAGGCCGAATGGCCA
127 AAGGCCGAATGGCCA
* * * *
44109526 ATGTGATGAATGTGAACATTTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGTATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
**
44109591 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
66 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
44109656 CCGAATGGCCA
131 CCGAATGGCCA
* *
44109667 ATGTGATGAATGTTAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGTATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * *
44109732 TGTATATATGTGGTAAGGCCGAATGGCTAATG
66 TGTATATGTGTGATAAGGCCGAATGGCCAATG
44109764 CGAAATGTGT
Statistics
Matches: 216, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
141 159 0.74
144 1 0.00
145 56 0.26
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (141 bp):
ATGTGATGAATGTGAACATGTATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
CCGAATGGCCA
Found at i:44109919 original size:46 final size:46
Alignment explanation
Indices: 44109737--44109901 Score: 267
Period size: 46 Copynumber: 3.6 Consensus size: 46
44109727 GAACATGTAT
* * * *
44109737 ATATGTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATAAGATAG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATAG
44109783 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATAG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATAG
*
44109829 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATAG
* *
44109875 ATATGTGGTAAAGCCAAATGGCTAATG
1 ATATGAGGTAAAGCCGAATGGCTAATG
44109902 TGAGATATGT
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 112 1.00
ACGTcount: A:0.36, C:0.10, G:0.30, T:0.24
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATAG
Found at i:44116180 original size:37 final size:37
Alignment explanation
Indices: 44116130--44116208 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
44116120 TTATTACGAA
* *
44116130 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
44116167 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
44116204 GTCTT
1 GTCTT
44116209 TAGAGCTCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:44116405 original size:47 final size:47
Alignment explanation
Indices: 44116327--44117096 Score: 1353
Period size: 47 Copynumber: 16.4 Consensus size: 47
44116317 CCCTTCGGGA
* * * * * * *
44116327 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
44116374 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
44116421 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
44116468 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
44116515 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
44116562 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
44116609 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
44116656 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
44116703 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
44116750 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
44116797 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
44116844 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
44116891 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
44116938 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
44116985 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
44117032 CTTATCACATATATACACTTT-ACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
44117078 CTTATCACATATATACACT
1 CTTATCACATATATACACT
44117097 GTCTTGGCTG
Statistics
Matches: 699, Mismatches: 24, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
46 43 0.06
47 656 0.94
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:44138002 original size:14 final size:17
Alignment explanation
Indices: 44137968--44138008 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
44137958 ACCACATTAC
44137968 TTAGATGCAAAAACTTA
1 TTAGATGCAAAAACTTA
44137985 TTAGATG-AAAAA-TT-
1 TTAGATGCAAAAACTTA
44137999 TTAGA-GCAAA
1 TTAGATGCAAA
44138009 CTACCCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 8 0.35
15 2 0.09
16 5 0.22
17 7 0.30
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (17 bp):
TTAGATGCAAAAACTTA
Found at i:44153120 original size:28 final size:28
Alignment explanation
Indices: 44153050--44153120 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
44153040 GCAATCAAAT
* * *
44153050 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
44153078 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
44153106 ATGTCACTTAGTGTG
1 ATGGCACTTAGTGTG
44153121 AAAAATATCG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:44153128 original size:28 final size:28
Alignment explanation
Indices: 44153067--44153128 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
44153057 TCAGTGTACG
**
44153067 AAATATTGAGAATGGCACTTAGTGTGCG
1 AAATATTGAGAATGGCACTTAGTGTGAA
* *
44153095 AGATATTGAGAATGTCACTTAGTGTGAA
1 AAATATTGAGAATGGCACTTAGTGTGAA
44153123 AAATAT
1 AAATAT
44153129 CGAATGATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (28 bp):
AAATATTGAGAATGGCACTTAGTGTGAA
Found at i:44161035 original size:23 final size:23
Alignment explanation
Indices: 44160966--44161036 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 23
44160956 AAATGTCCAA
*
44160966 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
44160989 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
44161017 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
44161037 ATAATCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 19 0.46
24 1 0.02
28 21 0.51
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:44161062 original size:29 final size:28
Alignment explanation
Indices: 44160980--44161063 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
44160970 AACACACCAG
* *
44160980 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
44161008 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
*
44161036 TATAATCCATCCAAAACACACTAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
44161064 GCACAAAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 33 0.66
29 17 0.34
ACGTcount: A:0.46, C:0.30, G:0.04, T:0.20
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:44163328 original size:35 final size:35
Alignment explanation
Indices: 44163289--44163360 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
44163279 AAAAGTCACA
44163289 AAAACACAAAAATTTCAAGAAATAATCAAGAATTG
1 AAAACACAAAAATTTCAAGAAATAATCAAGAATTG
44163324 AAAACACAAAAATTTCAAGAAATAATCAAGAATTG
1 AAAACACAAAAATTTCAAGAAATAATCAAGAATTG
44163359 AA
1 AA
44163361 CTTACTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.19
Consensus pattern (35 bp):
AAAACACAAAAATTTCAAGAAATAATCAAGAATTG
Found at i:44172413 original size:40 final size:40
Alignment explanation
Indices: 44172369--44172465 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
44172359 CAACTATTTG
* * *
44172369 TGGCACGTT-GTGTGTGATTCGACATAGCTTTGGCTATATA
1 TGGCAC-TTAGTGTGCGATTCGACATAGCTTCGACTATATA
* * *
44172409 TGGCACTTAGTGTGCGATTTGAGATAGCTTCGACTATGTA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCGACTATATA
44172449 TGGCACTTAGTGTGCGA
1 TGGCACTTAGTGTGCGA
44172466 GATATCGAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
39 2 0.04
40 48 0.96
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTCGACATAGCTTCGACTATATA
Found at i:44172512 original size:28 final size:28
Alignment explanation
Indices: 44172446--44172516 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
44172436 CTTCGACTAT
44172446 GTATGGCACTTAGTGTGCGAGATATCGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
* * *
44172474 GTGTGGTACTTAGTGTGCGTGATATCGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
*
44172502 GTATGACACTTAGTG
1 GTATGGCACTTAGTG
44172517 CGAGGCATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.32
Consensus pattern (28 bp):
GTATGGCACTTAGTGTGCGAGATATCGA
Found at i:44175240 original size:28 final size:27
Alignment explanation
Indices: 44175208--44175567 Score: 223
Period size: 27 Copynumber: 13.3 Consensus size: 27
44175198 TTTAGTTTAC
44175208 AAAATTACTAAAATACCCTCGATTTTGT
1 AAAATTACTAAAATACCCTCGA-TTTGT
*
44175236 AAAATTACTAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTC-GATTTGT
*
44175263 AAAATTACTAAAATACCCCCTGATTTGT
1 AAAATTACTAAAATACCCTC-GATTTGT
*
44175291 AAAATTACTAAAATACCCTCGACTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* * *
44175318 AAAATTACCAAAGTACCCTCGATTTAT
1 AAAATTACTAAAATACCCTCGATTTGT
* **** * * *
44175345 AGAATTACTGTTTTACTCTTGATTTAT
1 AAAATTACTAAAATACCCTCGATTTGT
* **** **
44175372 AGAATTACTGTTTTACCCTCGATTTAC
1 AAAATTACTAAAATACCCTCGATTTGT
**
44175399 AAAATTATCGT--TTTACCCTCGA-TTGT
1 AAAATTA-C-TAAAATACCCTCGATTTGT
* * * **
44175425 GAAATTACTGAAATACCC-CTATAGGGT
1 AAAATTACTAAAATACCCTCGAT-TTGT
* * *
44175452 AGAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACTAAAATACCCTCGA-TTTGT
* *
44175479 AAAATTACCAAAATACCACT-GGTTTGT
1 AAAATTACTAAAATACC-CTCGATTTGT
* ** *
44175506 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* **
44175533 AAAATTACCAAAATATCCCT-GATTTAC
1 AAAATTACTAAAATA-CCCTCGATTTGT
44175560 AAAATTAC
1 AAAATTAC
44175568 AGAAAAACCC
Statistics
Matches: 273, Mismatches: 46, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.00
25 3 0.01
26 15 0.05
27 200 0.73
28 53 0.19
29 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTCGATTTGT
Found at i:44175276 original size:55 final size:55
Alignment explanation
Indices: 44175208--44175342 Score: 193
Period size: 55 Copynumber: 2.5 Consensus size: 55
44175198 TTTAGTTTAC
**
44175208 AAAATTACTAAAATACCCTCGATTTTGTAAAATTACTAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTCGATTTTGTAAAATTACTAAAATACCCTC-GACTTGT
*
44175263 AAAATTACTAAAATACCCCCTGA-TTTGTAAAATTACTAAAATACCCTCGACTTGT
1 AAAATTACTAAAATACCCTC-GATTTTGTAAAATTACTAAAATACCCTCGACTTGT
* *
44175318 AAAATTACCAAAGTACCCTCGATTT
1 AAAATTACTAAAATACCCTCGATTT
44175343 ATAGAATTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
54 2 0.03
55 66 0.93
56 3 0.04
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (55 bp):
AAAATTACTAAAATACCCTCGATTTTGTAAAATTACTAAAATACCCTCGACTTGT
Found at i:44175686 original size:27 final size:27
Alignment explanation
Indices: 44175616--44175712 Score: 72
Period size: 27 Copynumber: 3.6 Consensus size: 27
44175606 AAAACACTCT
* * * *
44175616 TGTAGGATGAAATGACTACAATACCCC
1 TGTAGGGTAAAATGACCATAATACCCC
* * *
44175643 TAATA-GGTAAAAAGACCGTAA-AGCCCC
1 T-GTAGGGTAAAATGACCATAATA-CCCC
* *
44175670 TGTAGGGTAAAGTGACCATAATACCCT
1 TGTAGGGTAAAATGACCATAATACCCC
*
44175697 TGTATGGTAAAATGAC
1 TGTAGGGTAAAATGAC
44175713 GAATATGCCC
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
26 3 0.06
27 46 0.88
28 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
TGTAGGGTAAAATGACCATAATACCCC
Found at i:44176365 original size:25 final size:25
Alignment explanation
Indices: 44176336--44176383 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
44176326 TTATAATGTG
44176336 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACTGTTTTGCCCCTAGGTA
*
44176361 AAAATGACTGTTTTGCCCTTAGG
1 AAAATGACTGTTTTGCCCCTAGG
44176384 GTTTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (25 bp):
AAAATGACTGTTTTGCCCCTAGGTA
Found at i:44176444 original size:20 final size:20
Alignment explanation
Indices: 44176410--44176485 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
44176400 GATACGTGGG
44176410 GTATGATAT--ACATGAT-T
1 GTATGATATGCACATGATAT
44176427 GATATGATATGCACATGATAT
1 G-TATGATATGCACATGATAT
* *
44176448 GCATGATATGCGCATGATAT
1 GTATGATATGCACATGATAT
*
44176468 GTATGAAATGCACATGAT
1 GTATGATATGCACATGAT
44176486 GAATTCATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
17 1 0.02
18 8 0.16
20 39 0.78
21 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
GTATGATATGCACATGATAT
Found at i:44176446 original size:11 final size:10
Alignment explanation
Indices: 44176430--44176468 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
44176420 CATGATTGAT
44176430 ATGATATGCAC
1 ATGATATGC-C
44176441 ATGATATG-C
1 ATGATATGCC
44176450 ATGATATGCGC
1 ATGATATGC-C
44176461 ATGATATG
1 ATGATATG
44176469 TATGAAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.35
11 17 0.65
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (10 bp):
ATGATATGCC
Found at i:44176588 original size:26 final size:26
Alignment explanation
Indices: 44176535--44176656 Score: 160
Period size: 25 Copynumber: 4.8 Consensus size: 26
44176525 GAGGAAGTGC
**
44176535 AAAAGGGCTTATG-CCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
44176560 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
44176586 AAAAGGCCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
44176612 AAAAGGGCTT-TACCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
44176637 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
44176657 ATTAAAGAGG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 42 0.50
26 42 0.50
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:44176632 original size:51 final size:52
Alignment explanation
Indices: 44176535--44176656 Score: 196
Period size: 51 Copynumber: 2.4 Consensus size: 52
44176525 GAGGAAGTGC
*
44176535 AAAAGGGCTTATG-CCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATACCCCAGTTTACCG
* *
44176586 AAAAGGCCTTATGCCCCAGTTTATTGAAAAGGGCTT-TACCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATACCCCAGTTTACCG
44176637 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
44176657 ATTAAAGAGG
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
50 10 0.15
51 34 0.52
52 22 0.33
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATACCCCAGTTTACCG
Found at i:44176860 original size:42 final size:42
Alignment explanation
Indices: 44176801--44176892 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
44176791 TAGTCTCCCC
*
44176801 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
*
44176843 AAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
44176885 AAATGGGC
1 AAATGGGC
44176893 CTATGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
Found at i:44183420 original size:39 final size:40
Alignment explanation
Indices: 44183364--44183470 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
44183354 TGATGAAAAA
* * *
44183364 TCGGCTATTTGTGGCACTTAGTGTGTGA-TCGACATAGCT
1 TCGGCTATATATGGCACTTAGTGTGCGATTCGACATAGCT
* * *
44183403 TTGGCTATATATGGCACTTAGTGTGCGATTTGAGATAGCT
1 TCGGCTATATATGGCACTTAGTGTGCGATTCGACATAGCT
44183443 TCGGCTATGA-ATGGCACTTAGTGTGCGA
1 TCGGCTAT-ATATGGCACTTAGTGTGCGA
44183471 GGTATCGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 24 0.41
40 34 0.58
41 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.35
Consensus pattern (40 bp):
TCGGCTATATATGGCACTTAGTGTGCGATTCGACATAGCT
Found at i:44183536 original size:28 final size:28
Alignment explanation
Indices: 44183453--44183538 Score: 109
Period size: 28 Copynumber: 3.1 Consensus size: 28
44183443 TCGGCTATGA
*
44183453 ATGGCACTTAGTGTGCGAGGTATCGAAT
1 ATGGCACTTAGTGTGCGAGGTATCGAGT
* * *
44183481 GTGGCACTTAGTGTGTGAGATATCGAGT
1 ATGGCACTTAGTGTGCGAGGTATCGAGT
* * *
44183509 ATGGCACTTAGTTTGCGAGGCATTGAGT
1 ATGGCACTTAGTGTGCGAGGTATCGAGT
44183537 AT
1 AT
44183539 TCAATGACAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.23, C:0.13, G:0.33, T:0.31
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAGGTATCGAGT
Found at i:44188472 original size:24 final size:25
Alignment explanation
Indices: 44188440--44188496 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 25
44188430 CAAGCTTTCT
44188440 TGGTTCTTTGTGAGA-TTCCCAA-TA
1 TGGTTCTTTGTGA-ACTTCCCAATTA
44188464 TGGTTCTTTGTGAACTTCCCAATTA
1 TGGTTCTTTGTGAACTTCCCAATTA
*
44188489 TGGCTCTT
1 TGGTTCTT
44188497 ATGAGCTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 1 0.03
24 20 0.67
25 9 0.30
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (25 bp):
TGGTTCTTTGTGAACTTCCCAATTA
Found at i:44188505 original size:24 final size:24
Alignment explanation
Indices: 44188444--44188507 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
44188434 CTTTCTTGGT
* * *
44188444 TCTTTGTGAGATTCCCAATATGGT
1 TCTTTATGAGCTTCCCAATATGGC
* *
44188468 TCTTTGTGAACTTCCCAATTATGGC
1 TCTTTATGAGCTTCCCAA-TATGGC
44188493 TC-TTATGAGCTTCCC
1 TCTTTATGAGCTTCCC
44188508 GTTATATGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 27 0.79
25 7 0.21
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (24 bp):
TCTTTATGAGCTTCCCAATATGGC
Found at i:44196344 original size:18 final size:18
Alignment explanation
Indices: 44196321--44196379 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
44196311 TAGCCCATTT
*
44196321 CAGTAACAGTCATCAGTG
1 CAGTAACAGTAATCAGTG
* *
44196339 CAGTAACCA-TGATCAATG
1 CAGTAA-CAGTAATCAGTG
*
44196357 TAGTAACAGTAATCAGTG
1 CAGTAACAGTAATCAGTG
44196375 CAGTA
1 CAGTA
44196380 TGCAAGCAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 2 0.06
18 29 0.88
19 2 0.06
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (18 bp):
CAGTAACAGTAATCAGTG
Found at i:44196663 original size:23 final size:23
Alignment explanation
Indices: 44196637--44196686 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
44196627 ACCCCATGCA
44196637 ATGCAACATA-ATATCATACATGG-
1 ATGCAACATACATAT-A-ACATGGC
44196660 ATGCAACATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
44196683 ATGC
1 ATGC
44196687 TCAAATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Done.