Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 10 of 356
Found at i:3426720 original size:13 final size:13
Alignment explanation
Indices: 3426699--3426728 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3426689 TTAAAAATTT
*
3426699 TAAATTTTAAAAA
1 TAAAATTTAAAAA
3426712 TAAAATTTAAAAA
1 TAAAATTTAAAAA
3426725 TAAA
1 TAAA
3426729 GAATATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAATTTAAAAA
Found at i:3430961 original size:11 final size:11
Alignment explanation
Indices: 3430942--3431002 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
3430932 GTAATTATTT
3430942 AATTAATATAA
1 AATTAATATAA
* *
3430953 AATTTATATTA
1 AATTAATATAA
3430964 AATTCAATTATAA
1 AATT-AA-TATAA
*
3430977 AATT-ATACAA
1 AATTAATATAA
*
3430987 ATATTAATAGAA
1 A-ATTAATATAA
3430999 AATT
1 AATT
3431003 GTTTTTTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 5 0.12
11 20 0.50
12 7 0.17
13 8 0.20
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (11 bp):
AATTAATATAA
Found at i:3433866 original size:18 final size:19
Alignment explanation
Indices: 3433843--3433885 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
3433833 TTCATATCCC
*
3433843 TTTTTTTTTTTC-TTCTAA
1 TTTTTTTTGTTCGTTCTAA
*
3433861 -TTTTTTTGTTCGTTGTAA
1 TTTTTTTTGTTCGTTCTAA
3433879 TTTTTTT
1 TTTTTTT
3433886 AAATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 5 0.24
19 6 0.29
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTTTTTGTTCGTTCTAA
Found at i:3449394 original size:19 final size:19
Alignment explanation
Indices: 3449354--3449400 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3449344 TAAAATGGTA
*
3449354 TAATATTAATATTATTTTT
1 TAATATTAATATTATTTGT
*
3449373 TAATATTTATA-TATTATGT
1 TAATATTAATATTATT-TGT
3449392 TAAT-TTAAT
1 TAATATTAAT
3449401 TTTGAGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TAATATTAATATTATTTGT
Found at i:3454968 original size:15 final size:14
Alignment explanation
Indices: 3454950--3454979 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3454940 AGTTTCTCTC
3454950 TTTCTTTTTTCTTTT
1 TTTCTTTTTT-TTTT
3454965 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
3454979 T
1 T
3454980 ATGGTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:3462445 original size:66 final size:66
Alignment explanation
Indices: 3462339--3462469 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
3462329 CATAACTTAT
* *
3462339 AAATTTTACCATTTAATTCGGTCTACATTCGTTATCCATTAATACATAACAGTCAACAGTCAATA
1 AAATTTTACCATTTAATCCGGTCTACATTCGTTATCCATTAATACATAACAATCAACAGTCAATA
3462404 A
66 A
3462405 AAATTTTACCATTTAATCCGGTCTACATTCGTTATCCATTAATACATAACAATCAACAGTCAATA
1 AAATTTTACCATTTAATCCGGTCTACATTCGTTATCCATTAATACATAACAATCAACAGTCAATA
3462470 TTTATCAACC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (66 bp):
AAATTTTACCATTTAATCCGGTCTACATTCGTTATCCATTAATACATAACAATCAACAGTCAATA
A
Found at i:3462582 original size:18 final size:16
Alignment explanation
Indices: 3462559--3462620 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 16
3462549 TCAGTAGCAT
3462559 TCAGTTACTCTATAACAG
1 TCAGTTA-TC-ATAACAG
3462577 TCAGTTATACAATAACAG
1 TCAGTTAT-C-ATAACAG
*
3462595 TCATTTATTCAGTAACAG
1 TCAGTTA-TCA-TAACAG
*
3462613 TCAATTAT
1 TCAGTTAT
3462621 TCCGTAGCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.08
18 34 0.89
19 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (16 bp):
TCAGTTATCATAACAG
Found at i:3462621 original size:18 final size:18
Alignment explanation
Indices: 3462570--3462622 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
3462560 CAGTTACTCT
* *
3462570 ATAACAGTCAGTTATACA
1 ATAACAGTCAATTATTCA
*
3462588 ATAACAGTCATTTATTCA
1 ATAACAGTCAATTATTCA
*
3462606 GTAACAGTCAATTATTC
1 ATAACAGTCAATTATTC
3462623 CGTAGCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (18 bp):
ATAACAGTCAATTATTCA
Found at i:3464856 original size:22 final size:22
Alignment explanation
Indices: 3464826--3464893 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
3464816 TGCACAAACG
3464826 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
** *
3464848 TGCAGAGAGCAC-AAATGTACTA
1 AACAGAGAGCACTAAA-GTGCTA
*
3464870 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
3464893 A
1 A
3464894 TAATAGAACA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
21 3 0.08
22 25 0.69
23 6 0.17
24 2 0.06
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:3464906 original size:30 final size:29
Alignment explanation
Indices: 3464870--3464926 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
3464860 AAATGTACTA
3464870 AACAGAGAGCACTTAACGTGCTAATAATAG
1 AACAGAGAGCAC-TAACGTGCTAATAATAG
*
3464900 AACAGAGAGCACTAATGTGCTAATAAT
1 AACAGAGAGCACTAACGTGCTAATAAT
3464927 CAGAGAGCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (29 bp):
AACAGAGAGCACTAACGTGCTAATAATAG
Found at i:3466039 original size:21 final size:21
Alignment explanation
Indices: 3465998--3466039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3465988 TTCGTCCCTG
* **
3465998 CTATTCTGTTTGTTTTTTTTT
1 CTATTCTGTTTCTTTACTTTT
3466019 CTATTCTGTTTCTTTACTTTT
1 CTATTCTGTTTCTTTACTTTT
3466040 TTTATGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.71
Consensus pattern (21 bp):
CTATTCTGTTTCTTTACTTTT
Found at i:3466058 original size:7 final size:7
Alignment explanation
Indices: 3466048--3466136 Score: 64
Period size: 7 Copynumber: 13.3 Consensus size: 7
3466038 TTTTTATGTT
3466048 TTATATA
1 TTATATA
3466055 -T-TATA
1 TTATATA
3466060 TTATATA
1 TTATATA
*
3466067 TAATATA
1 TTATATA
*
3466074 ATA-ATA
1 TTATATA
*
3466080 TAATATA
1 TTATATA
3466087 TTATATA
1 TTATATA
3466094 TTA-ATA
1 TTATATA
*
3466100 CTTAAATA
1 -TTATATA
3466108 TTA-A-A
1 TTATATA
3466113 TTAATATA
1 TT-ATATA
*
3466121 ATATATA
1 TTATATA
*
3466128 ATATATA
1 TTATATA
3466135 TT
1 TT
3466137 TTTATATAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
5 7 0.11
6 11 0.17
7 43 0.65
8 5 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (7 bp):
TTATATA
Found at i:3470253 original size:22 final size:23
Alignment explanation
Indices: 3470204--3470253 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3470194 TATAATTTCT
**
3470204 TTATAAAATTATATCAACATTGA
1 TTATAAAATTATATCAACAAGGA
* *
3470227 ATATAAATTTATAT-AACAAGGA
1 TTATAAAATTATATCAACAAGGA
3470249 TTATA
1 TTATA
3470254 TATATCAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (23 bp):
TTATAAAATTATATCAACAAGGA
Found at i:3479048 original size:19 final size:20
Alignment explanation
Indices: 3479024--3479073 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3479014 TTTTAAATTA
3479024 AAATTAAATTAT-AAGAATG
1 AAATTAAATTATAAAGAATG
*
3479043 AAATTAAATTATAAAGAATT
1 AAATTAAATTATAAAGAATG
*
3479063 AAATTTAATTA
1 AAATTAAATTA
3479074 AATAAAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (20 bp):
AAATTAAATTATAAAGAATG
Found at i:3487040 original size:16 final size:17
Alignment explanation
Indices: 3487009--3487041 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3486999 TTCATAAGTA
3487009 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
3487026 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
3487042 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:3487435 original size:45 final size:46
Alignment explanation
Indices: 3487337--3487453 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 46
3487327 TGACATAGTG
* * **
3487337 TCTTTCAACTATGGTCTTACTCATTTTCTTTCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCCCGTCAGGTTGCCATGGTA
* * *
3487383 TATTTCAACCATGGTCTTATTCA-TTCCCGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCCCGTCAGGTTGCCATGGTA
* *
3487428 TCTTTCAACCATGTTCTTACACATTT
1 TCTTTCAACCATGGTCTTACTCATTT
3487454 TATGTAACAC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 37 0.63
46 22 0.37
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACTCATTTCCCGTCAGGTTGCCATGGTA
Found at i:3488882 original size:50 final size:50
Alignment explanation
Indices: 3488767--3488909 Score: 205
Period size: 50 Copynumber: 2.8 Consensus size: 50
3488757 GATAATAACA
* ** * *
3488767 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
3488818 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
3488868 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
3488910 TTACCCAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 48 0.59
51 33 0.41
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:3489025 original size:13 final size:13
Alignment explanation
Indices: 3489004--3489034 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3488994 GCTTAGATCA
*
3489004 TCATCAAATAAAT
1 TCATAAAATAAAT
3489017 TCATAAAATAAAT
1 TCATAAAATAAAT
3489030 TCATA
1 TCATA
3489035 GTTTCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:3490179 original size:46 final size:46
Alignment explanation
Indices: 3490116--3490354 Score: 397
Period size: 46 Copynumber: 5.2 Consensus size: 46
3490106 TTGGGCCATT
* *
3490116 ACATTTTATATCCTGTTGCCATGGTGTCTTTCAACCATGGTCTTAC
1 ACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGGTCTTAC
* *
3490162 ATATTTCATATCATGTTGCAATGGTGTCTTTCAACCATGGTCTTAC
1 ACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGGTCTTAC
* *
3490208 ACATTTCATATCATGTTGCCATGGTATCTTTCAACCTTGGTCTTAC
1 ACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGGTCTTAC
* *
3490254 ACATTTCATATCCTGTTGTCATGGTGTCTTTCAACCATGGTCTTAC
1 ACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGGTCTTAC
*
3490300 ACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 ACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGGTCTTAC
3490346 ACATTTCAT
1 ACATTTCAT
3490355 TTCAGAAAGC
Statistics
Matches: 178, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 178 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
ACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGGTCTTAC
Found at i:3493223 original size:21 final size:21
Alignment explanation
Indices: 3493187--3493241 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
3493177 TTAGTTTTTC
3493187 TTATAAAATTAAATCAAATAAAT
1 TTATAAAA-TAAATC-AATAAAT
3493210 TTATAAAA-AAATCAATAAAT
1 TTATAAAATAAATCAATAAAT
3493230 TATGATAAAATA
1 T-T-ATAAAATA
3493242 TAATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.28
21 6 0.21
22 6 0.21
23 9 0.31
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
TTATAAAATAAATCAATAAAT
Found at i:3493240 original size:19 final size:21
Alignment explanation
Indices: 3493187--3493239 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 21
3493177 TTAGTTTTTC
3493187 TTATAAAATTAAATCAAATAAAT
1 TTATAAAA--AAATCAAATAAAT
3493210 TTATAAAAAAATC-AATAAAT
1 TTATAAAAAAATCAAATAAAT
3493230 TATGATAAAA
1 T-T-ATAAAA
3493240 TATAATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.29
21 6 0.21
22 6 0.21
23 8 0.29
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (21 bp):
TTATAAAAAAATCAAATAAAT
Found at i:3493260 original size:17 final size:17
Alignment explanation
Indices: 3493234--3493293 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
3493224 ATAAATTATG
3493234 ATAAAA-TATAATATTT
1 ATAAAATTATAATATTT
3493250 ATAAAATTATAATACATGTT
1 ATAAAATTATAAT--AT-TT
3493270 ATAAAATCTATACA-ATTT
1 ATAAAAT-TATA-ATATTT
3493288 A-AAAAT
1 ATAAAAT
3493294 ACAAAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.16
17 11 0.29
18 3 0.08
19 4 0.11
20 9 0.24
21 4 0.11
22 1 0.03
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
ATAAAATTATAATATTT
Found at i:3501596 original size:27 final size:27
Alignment explanation
Indices: 3501558--3501615 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
3501548 TTTCATGAAT
3501558 GAGATAGTTTTCATGTAGCCAGAAAAG
1 GAGATAGTTTTCATGTAGCCAGAAAAG
3501585 GAGATAGTTTTCATGTAGCCAGAAAAG
1 GAGATAGTTTTCATGTAGCCAGAAAAG
3501612 GAGA
1 GAGA
3501616 ACATGAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.24
Consensus pattern (27 bp):
GAGATAGTTTTCATGTAGCCAGAAAAG
Found at i:3513568 original size:23 final size:23
Alignment explanation
Indices: 3513525--3513570 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3513515 ATATACCAAT
**
3513525 ATTTTTTTTAATTAGCTAAATAG
1 ATTTTTTTTAATTAGAGAAATAG
3513548 ATTTTTTTTAATTAGAGAAATAG
1 ATTTTTTTTAATTAGAGAAATAG
3513571 GTGGATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (23 bp):
ATTTTTTTTAATTAGAGAAATAG
Found at i:3515589 original size:19 final size:20
Alignment explanation
Indices: 3515559--3515599 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
3515549 AAAATCAAAT
3515559 TAATTTTCAAAATTTTAAAA
1 TAATTTTCAAAATTTTAAAA
3515579 TAATTTT-AAAATTTTAAAA
1 TAATTTTCAAAATTTTAAAA
3515598 TA
1 TA
3515600 TTTATAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATTTTCAAAATTTTAAAA
Found at i:3515669 original size:21 final size:22
Alignment explanation
Indices: 3515643--3515683 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3515633 AGTTATAAAT
3515643 TTAAAAAAACTAA-AAAATATA
1 TTAAAAAAACTAATAAAATATA
*
3515664 TTAAAAAATCTAATAAAATA
1 TTAAAAAAACTAATAAAATA
3515684 ATAATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAAAAAAACTAATAAAATATA
Found at i:3519798 original size:18 final size:17
Alignment explanation
Indices: 3519759--3519810 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
3519749 TGATTGAATT
3519759 GTTGAATTGAAAGAGAA
1 GTTGAATTGAAAGAGAA
* * *
3519776 TTTGAGATTTAAAGTGAA
1 GTTGA-ATTGAAAGAGAA
*
3519794 GTTGAATTGAATGAGAA
1 GTTGAATTGAAAGAGAA
3519811 ATATATATGT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (17 bp):
GTTGAATTGAAAGAGAA
Found at i:3519879 original size:24 final size:25
Alignment explanation
Indices: 3519832--3519879 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
3519822 AGTATTGAAT
*
3519832 TGTATTTTGATTTGTGAATGGAAAG
1 TGTATTTTGATTTGTGAAAGGAAAG
3519857 TGTA-TTTGATTT-TGAAAGTGAAA
1 TGTATTTTGATTTGTGAAAG-GAAA
3519880 TCGTGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (25 bp):
TGTATTTTGATTTGTGAAAGGAAAG
Found at i:3521601 original size:15 final size:15
Alignment explanation
Indices: 3521578--3521625 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
3521568 TATCAAATTT
3521578 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
3521593 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
3521608 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
3521622 ATAT
1 ATAT
3521626 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:3522149 original size:23 final size:23
Alignment explanation
Indices: 3522121--3522178 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
3522111 TAATATTCCG
3522121 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
3522144 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
3522167 AGTGTGTTTGGG
1 GGTGTGTTTGGG
3522179 AGGAATCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.09, C:0.03, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:3522304 original size:18 final size:19
Alignment explanation
Indices: 3522283--3522323 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3522273 AATGAAATGA
3522283 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
3522301 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
3522320 GAAA
1 GAAA
3522324 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:3526606 original size:13 final size:13
Alignment explanation
Indices: 3526588--3526620 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3526578 TTAATTAATT
3526588 AAATAAAATAAAG
1 AAATAAAATAAAG
*
3526601 AAATAAAATAGAG
1 AAATAAAATAAAG
3526614 AAATAAA
1 AAATAAA
3526621 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (13 bp):
AAATAAAATAAAG
Found at i:3526693 original size:13 final size:13
Alignment explanation
Indices: 3526663--3526700 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3526653 AAAACGAAAC
3526663 AGAG-AAGAACAGG
1 AGAGAAAGAA-AGG
*
3526676 GGAGAAAGAAAGG
1 AGAGAAAGAAAGG
3526689 AGAGAAAGAAAG
1 AGAGAAAGAAAG
3526701 AAAGGGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.58, C:0.03, G:0.39, T:0.00
Consensus pattern (13 bp):
AGAGAAAGAAAGG
Found at i:3526713 original size:17 final size:17
Alignment explanation
Indices: 3526678--3526711 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3526668 AGAACAGGGG
3526678 AGAAAGAAAGGAGAGAA
1 AGAAAGAAAGGAGAGAA
3526695 AGAAAGAAAGG-GAGAA
1 AGAAAGAAAGGAGAGAA
3526711 A
1 A
3526712 AGGGAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGGAGAGAA
Found at i:3526979 original size:15 final size:15
Alignment explanation
Indices: 3526959--3527002 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
3526949 CAAATTTATG
*
3526959 TTGATTGAAATCATT
1 TTGATTGAAATCATA
*
3526974 TTGATTG-AATTATA
1 TTGATTGAAATCATA
3526988 TTGATTGAAAT-ATA
1 TTGATTGAAATCATA
3527002 T
1 T
3527003 ATTATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (15 bp):
TTGATTGAAATCATA
Found at i:3526993 original size:14 final size:14
Alignment explanation
Indices: 3526954--3527002 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3526944 TTTATCAAAT
*
3526954 TTATGTTGATTGAAA
1 TTATATTGATTG-AA
* *
3526969 TCATTTTGATTGAA
1 TTATATTGATTGAA
3526983 TTATATTGATTGAA
1 TTATATTGATTGAA
*
3526997 ATATAT
1 TTATAT
3527003 ATTATATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (14 bp):
TTATATTGATTGAA
Found at i:3527515 original size:23 final size:23
Alignment explanation
Indices: 3527487--3527544 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
3527477 TAATATTCCA
3527487 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
3527510 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
3527533 GGTGTGTTTGGG
1 GGTGTGTTTGGG
3527545 AGGAATCCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.07, C:0.03, G:0.43, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:3527670 original size:18 final size:19
Alignment explanation
Indices: 3527649--3527689 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3527639 AATGAAATGA
3527649 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
3527667 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
3527686 GAAA
1 GAAA
3527690 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:3528760 original size:42 final size:40
Alignment explanation
Indices: 3528711--3528824 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 40
3528701 TTCATTTTCT
* * *
3528711 TGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TGATGCCATAG-CCAGCTATGGTCTTACACATATTCACAT-A
*
3528753 TGATGCCATAGCCCAGCTATGGTCTTACAAATATTCACATA
1 TGATGCCATAG-CCAGCTATGGTCTTACACATATTCACATA
3528794 TCGATGCCATAGCCTAGCTATGGTCTTACAC
1 T-GATGCCATAGCC-AGCTATGGTCTTACAC
3528825 GGATCACATA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
41 4 0.06
42 60 0.94
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (40 bp):
TGATGCCATAGCCAGCTATGGTCTTACACATATTCACATA
Found at i:3528956 original size:48 final size:48
Alignment explanation
Indices: 3528745--3528983 Score: 253
Period size: 48 Copynumber: 5.0 Consensus size: 48
3528735 TTACACATCT
*
3528745 TCACATAAT-GATGCCATAGCCCAGCTATGGTCTTACA---A--ATAT-
1 TCACAT-ATCGATGCCATAGCCCAGCTATGGTCTTACACGGATCACATA
*
3528787 TCACATATCGATGCCATAGCCTAGCTATGGTCTTACACGGATCACATA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGGATCACATA
* * * * * * *
3528835 TCTC--ACCGATGCCATATCCTAGATATGGTCTTACACAGAAGCACATAA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACAC-GGATCACAT-A
* * *
3528883 TCACATCACACTGATGCCATAGCCCAACTATGGTCTTATACGGATCACATA
1 TCACAT-A-TC-GATGCCATAGCCCAGCTATGGTCTTACACGGATCACATA
3528934 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGGATCACATA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGGATCACATA
3528982 TC
1 TC
3528984 TCACTGATGC
Statistics
Matches: 163, Mismatches: 20, Indels: 22
0.80 0.10 0.11
Matches are distributed among these distances:
41 2 0.01
42 33 0.20
45 1 0.01
46 29 0.18
47 10 0.06
48 46 0.28
49 1 0.01
50 1 0.01
51 8 0.05
52 8 0.05
53 24 0.15
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (48 bp):
TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGGATCACATA
Found at i:3529886 original size:46 final size:46
Alignment explanation
Indices: 3529817--3530108 Score: 286
Period size: 46 Copynumber: 6.6 Consensus size: 46
3529807 TGATGTCATA
* * * * *
3529817 GTATCTTTCAACTATAGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATGTCACGTTGCCATG
*
3529863 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* *
3529909 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* * *
3529955 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCAT-
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* ** *
3530000 G----------CCATGGTCTTACACATTTCACATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* * * * *
3530036 GTATCTTT-AACCATGATCTTACACATTTCATATCAGGTTGCCACG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* *
3530081 GTATCTTTCAACCATGGTTTTACACATT
1 GTATCTTTCAACCATGGTCTTACTCATT
3530109 CCATATCAGA
Statistics
Matches: 217, Mismatches: 17, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
35 33 0.15
36 1 0.00
45 45 0.21
46 138 0.64
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
Found at i:3530012 original size:35 final size:35
Alignment explanation
Indices: 3529966--3530035 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
3529956 TATCTTTCAA
*
3529966 CCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 CCATGGTCTTACACATTTCACATCAGGTTGCCATG
3530001 CCATGGTCTTACACATTTCACATCAGGTTGCCATG
1 CCATGGTCTTACACATTTCACATCAGGTTGCCATG
3530036 GTATCTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (35 bp):
CCATGGTCTTACACATTTCACATCAGGTTGCCATG
Found at i:3530019 original size:81 final size:80
Alignment explanation
Indices: 3529920--3530078 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 80
3529910 TATCTTTCAA
** * *
3529920 CCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 CCATGGTCTTACACATTTCACATCACGTTGCCATGGTATCTTT-AACCATGATCTTACACATTTC
3529985 ATATCAGGTTGCCATG
65 ATATCAGGTTGCCATG
*
3530001 CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTAACCATGATCTTACACATTTCA
1 CCATGGTCTTACACATTTCACATCACGTTGCCATGGTATCTTTAACCATGATCTTACACATTTCA
3530066 TATCAGGTTGCCA
66 TATCAGGTTGCCA
3530079 CGGTATCTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
80 34 0.47
81 39 0.53
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.36
Consensus pattern (80 bp):
CCATGGTCTTACACATTTCACATCACGTTGCCATGGTATCTTTAACCATGATCTTACACATTTCA
TATCAGGTTGCCATG
Found at i:3530056 original size:45 final size:46
Alignment explanation
Indices: 3530001--3530117 Score: 182
Period size: 45 Copynumber: 2.6 Consensus size: 46
3529991 GGTTGCCATG
* *
3530001 CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTT-AA
1 CCATGGTCTTACACATTTCATATCAGGTTGCCACGGTATCTTTCAA
*
3530046 CCATGATCTTACACATTTCATATCAGGTTGCCACGGTATCTTTCAA
1 CCATGGTCTTACACATTTCATATCAGGTTGCCACGGTATCTTTCAA
* *
3530092 CCATGGTTTTACACATTCCATATCAG
1 CCATGGTCTTACACATTTCATATCAG
3530118 AGAGCACACT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
45 40 0.62
46 25 0.38
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (46 bp):
CCATGGTCTTACACATTTCATATCAGGTTGCCACGGTATCTTTCAA
Found at i:3530104 original size:126 final size:127
Alignment explanation
Indices: 3529874--3530117 Score: 391
Period size: 126 Copynumber: 1.9 Consensus size: 127
3529864 TATCTTTCAA
* ** * **
3529874 CCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTC
1 CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTC
* *
3529939 ATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
66 ATATCACGTTGCCACGGTATCTTTCAACCATGGTCTTACACATTCCATATCAGGTTGCCATG
3530001 CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTT-AACCATGATCTTACACATTTC
1 CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTC
* *
3530065 ATATCAGGTTGCCACGGTATCTTTCAACCATGGTTTTACACATTCCATATCAG
66 ATATCACGTTGCCACGGTATCTTTCAACCATGGTCTTACACATTCCATATCAG
3530118 AGAGCACACT
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
126 67 0.63
127 40 0.37
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (127 bp):
CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTC
ATATCACGTTGCCACGGTATCTTTCAACCATGGTCTTACACATTCCATATCAGGTTGCCATG
Found at i:3540383 original size:52 final size:51
Alignment explanation
Indices: 3540312--3540520 Score: 275
Period size: 52 Copynumber: 4.1 Consensus size: 51
3540302 ATCAAGTGAT
* * *
3540312 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGT-G
* *
3540364 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* *
3540415 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
*
3540462 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-AAGTG
3540514 ATAAGTG
1 A-AAGTG
3540521 GCTACACTTA
Statistics
Matches: 141, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
46 43 0.30
51 1 0.01
52 92 0.65
53 5 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:3540434 original size:98 final size:97
Alignment explanation
Indices: 3540298--3540520 Score: 231
Period size: 98 Copynumber: 2.3 Consensus size: 97
3540288 TTTGAGTACT
* * *
3540298 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTAC-ACT-TATCTGATCAAGTGA-CAA
1 TCTGATCAAGTGA-CAAGTGATAAGTGATAGCTATAGCTACGACTATA-CTGATC---TGATCAA
* * *
3540360 GTG-GAAAGTGATAAGTGATAGCTTCGGCTACACTTA
61 GAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
3540396 TCTGATCAAGTGACAAGTGAAAAGTGATAAG-TGATAGCTTCGGCTATACTTATCTGATCAAGAG
1 TCTGATCAAGTGACAAGTGATAAGTGAT-AGCT-ATAGCTACGACTATACTGATCTGATCAAGAG
*
3540460 ACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
64 ACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
3540494 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGAC-AAGTGATAAGTG
3540521 GCTACACTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
96 3 0.03
97 18 0.17
98 64 0.61
99 18 0.17
100 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAGTGATAAGTGATAGCTATAGCTACGACTATACTGATCTGATCAAGAGAC
AAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:3540493 original size:46 final size:44
Alignment explanation
Indices: 3540416--3540595 Score: 192
Period size: 37 Copynumber: 4.3 Consensus size: 44
3540406 TGACAAGTGA
*
3540416 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTT--GCTACACTTATCTGATCAAGAGAC
3540462 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TT-GCTACACTTATCTGATCAAGAGAC
*
3540508 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
3540545 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGGGAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
3540582 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
3540596 CATACGTAAG
Statistics
Matches: 125, Mismatches: 5, Indels: 15
0.86 0.03 0.10
Matches are distributed among these distances:
36 9 0.07
37 58 0.46
38 1 0.01
39 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 51 0.41
47 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (44 bp):
AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
Found at i:3540528 original size:37 final size:37
Alignment explanation
Indices: 3540484--3540593 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
3540474 GATAGCTTTA
3540484 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
3540521 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
3540558 GCTACACTTATCTGATCAAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
3540594 ATCATACGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 12 0.17
37 58 0.83
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:3564573 original size:12 final size:12
Alignment explanation
Indices: 3564556--3564588 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3564546 GATACTCCGT
3564556 AAATATTTATAA
1 AAATATTTATAA
3564568 AAATATTTATAA
1 AAATATTTATAA
3564580 AAATATTTA
1 AAATATTTA
3564589 CGGATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATATTTATAA
Found at i:3564852 original size:38 final size:38
Alignment explanation
Indices: 3564800--3564885 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
3564790 CAAATGAGGT
* *
3564800 ACTGGGTACC-ACTTTACTTCG-GCTAGGCCGATAAGAC
1 ACTGGGTGCCAACTTTACTTCGAACTA-GCCGATAAGAC
* * *
3564837 ACTGGGTGCCAACTTTACTTCGAACTATCCGATGAGTC
1 ACTGGGTGCCAACTTTACTTCGAACTAGCCGATAAGAC
3564875 ACTGGGTGCCA
1 ACTGGGTGCCA
3564886 TTCTAGTGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 9 0.21
38 30 0.71
39 3 0.07
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (38 bp):
ACTGGGTGCCAACTTTACTTCGAACTAGCCGATAAGAC
Found at i:3566648 original size:21 final size:21
Alignment explanation
Indices: 3566613--3566662 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3566603 TATATAACTT
* *
3566613 TATAATTAAT-ATTTTAATTAT
1 TATAATTATTGATTTT-ATTAA
3566634 TA-AATTATTGATTTTATTAA
1 TATAATTATTGATTTTATTAA
3566654 TATAATTAT
1 TATAATTAT
3566663 ACTTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TATAATTATTGATTTTATTAA
Found at i:3576547 original size:32 final size:32
Alignment explanation
Indices: 3576456--3576548 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 32
3576446 CAATCAAAAT
3576456 TGAACCCCACATATATGCGAACCATTATGTATG
1 TGAACCCCACATATATGCGAACCA-TATGTATG
* *
3576489 TGAATCCC-CATATATGCGAGCCATATGTATG
1 TGAACCCCACATATATGCGAACCATATGTATG
* * *
3576520 TGAACCCCACATATTTGCAAACTATATGT
1 TGAACCCCACATATATGCGAACCATATGT
3576549 GAACCCCCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 15 0.29
32 30 0.58
33 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (32 bp):
TGAACCCCACATATATGCGAACCATATGTATG
Found at i:3579332 original size:24 final size:22
Alignment explanation
Indices: 3579305--3579354 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
3579295 ATAAATTAAT
*
3579305 TAAATCTAAAATATGTAGAAAATA
1 TAAATATAAAATATG-A-AAAATA
* *
3579329 TAAATATATAATGTGAAAAATA
1 TAAATATAAAATATGAAAAATA
3579351 TAAA
1 TAAA
3579355 AAAATCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 1 0.04
24 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (22 bp):
TAAATATAAAATATGAAAAATA
Found at i:3581351 original size:16 final size:16
Alignment explanation
Indices: 3581322--3581392 Score: 52
Period size: 19 Copynumber: 4.1 Consensus size: 16
3581312 TAATATTAAA
* *
3581322 ATATATACATGATAAT
1 ATATATAAAAGATAAT
3581338 ATATATAAAAGATATATGT
1 ATATATAAAAGATA-A--T
*
3581357 ATATATAAATATATAAT
1 ATATATAAA-AGATAAT
*
3581374 ATAATATTAAAATATAAT
1 AT-ATA-TAAAAGATAAT
3581392 A
1 A
3581393 AGAGAACATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 12 0.26
17 4 0.09
18 11 0.24
19 15 0.33
20 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (16 bp):
ATATATAAAAGATAAT
Found at i:3581380 original size:18 final size:17
Alignment explanation
Indices: 3581333--3581392 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 17
3581323 TATATACATG
*
3581333 ATAATAT-ATATAAAAG
1 ATAATATAATATAAAAT
*
3581349 ATATATGTATATATAAATAT
1 ATA-ATATA-ATATAAA-AT
3581369 ATAATATAATATTAAAAT
1 ATAATATAATA-TAAAAT
3581387 ATAATA
1 ATAATA
3581393 AGAGAACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 3 0.08
17 3 0.08
18 11 0.31
19 15 0.42
20 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATATAATATAAAAT
Found at i:3581606 original size:3 final size:3
Alignment explanation
Indices: 3581598--3581633 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3581588 AAGCATAAAC
*
3581598 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3581634 CATTGGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3581755 original size:23 final size:25
Alignment explanation
Indices: 3581729--3581778 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
3581719 TGTATACACG
3581729 TACATAATAAAAATA-T-ATACTAA
1 TACATAATAAAAATAGTAATACTAA
*
3581752 TACATAATAATAATAGTAATACTAA
1 TACATAATAAAAATAGTAATACTAA
3581777 TA
1 TA
3581779 ATGCTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 14 0.58
24 1 0.04
25 9 0.38
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (25 bp):
TACATAATAAAAATAGTAATACTAA
Found at i:3583238 original size:4 final size:4
Alignment explanation
Indices: 3583231--3583255 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3583221 AACAAGTGAA
3583231 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
3583256 GAGGGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3587390 original size:16 final size:17
Alignment explanation
Indices: 3587364--3587402 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3587354 TTGTGTATAT
3587364 ATTTCAATAAAAATC-AA
1 ATTT-AATAAAAATCAAA
*
3587381 ATTTAATAAAGATCAAA
1 ATTTAATAAAAATCAAA
3587398 ATTTA
1 ATTTA
3587403 TGTATCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (17 bp):
ATTTAATAAAAATCAAA
Found at i:3589185 original size:16 final size:16
Alignment explanation
Indices: 3589166--3589208 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3589156 TATTGTTTTT
3589166 AAAAAATATTTTTGAG
1 AAAAAATATTTTTGAG
* * *
3589182 AAAAAACACTTTTGGG
1 AAAAAATATTTTTGAG
3589198 ATAAAAATATT
1 A-AAAAATATT
3589209 ACTAAACAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.33
Consensus pattern (16 bp):
AAAAAATATTTTTGAG
Found at i:3589923 original size:16 final size:15
Alignment explanation
Indices: 3589901--3589939 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
3589891 ATACTAAAAA
3589901 TATAATTTATGAT-TT
1 TATAATTTAT-ATATT
3589916 TAATAATTTATATATT
1 T-ATAATTTATATATT
3589932 TATAATTT
1 TATAATTT
3589940 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TATAATTTATATATT
Found at i:3591995 original size:16 final size:17
Alignment explanation
Indices: 3591970--3592011 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
3591960 ATGACTCCCT
*
3591970 TTTTAATTTTT-TAAAA
1 TTTTATTTTTTGTAAAA
*
3591986 TTTTATTTTTTGTATAA
1 TTTTATTTTTTGTAAAA
3592003 TTTT-TTTTT
1 TTTTATTTTT
3592012 AAAATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTATTTTTTGTAAAA
Found at i:3603530 original size:22 final size:23
Alignment explanation
Indices: 3603505--3603551 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3603495 AGGTGATGAT
*
3603505 TTAATTAACATACT-TT-TTTTTA
1 TTAACTAACAT-CTCTTATTTTTA
3603527 TTAACTAACATCTCTTATTTTTA
1 TTAACTAACATCTCTTATTTTTA
3603550 TT
1 TT
3603552 GACTCCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 12 0.55
23 8 0.36
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAACTAACATCTCTTATTTTTA
Found at i:3603895 original size:87 final size:85
Alignment explanation
Indices: 3603734--3603896 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 85
3603724 AATTAAACTA
3603734 ATATCACTTTCTTATCATAATAAATAAAATTGTAAAAAAAATCCTTTCATTTGTAACCCTAATAC
1 ATATCACTTTCTTATCATAATAAATAAAATTGTAAAAAAAATCCTTTCATTTGTAACCCTAATAC
3603799 ATCTTATATGATATATACTG
66 ATCTTATATGATATATACTG
*
3603819 ATATCACTTTCTTATCATAATAAATAAAATTGTAAAAAAAAAATCCTTTTATTTGTAACCCTAAT
1 ATATCACTTTCTTATCATAATAAATAAAATTGT--AAAAAAAATCCTTTCATTTGTAACCCTAAT
3603884 ACATCTTATATGA
64 ACATCTTATATGA
3603897 GAAAATGATA
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
85 33 0.44
87 42 0.56
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (85 bp):
ATATCACTTTCTTATCATAATAAATAAAATTGTAAAAAAAATCCTTTCATTTGTAACCCTAATAC
ATCTTATATGATATATACTG
Found at i:3610148 original size:36 final size:36
Alignment explanation
Indices: 3610101--3610175 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
3610091 AATGCTCTTG
3610101 CATGCTTACTTATTTTGGTGATTCACTCTTTTATAC
1 CATGCTTACTTATTTTGGTGATTCACTCTTTTATAC
3610137 CATGCTTACTTATTTTGGTGATTCACTCTTTTATAC
1 CATGCTTACTTATTTTGGTGATTCACTCTTTTATAC
3610173 CAT
1 CAT
3610176 ATAACTAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (36 bp):
CATGCTTACTTATTTTGGTGATTCACTCTTTTATAC
Found at i:3611821 original size:35 final size:33
Alignment explanation
Indices: 3611782--3611848 Score: 80
Period size: 35 Copynumber: 2.0 Consensus size: 33
3611772 TTTTTTAGAA
3611782 TAAACAAACTTTGTTAATAAAAATATTAAAAATTT
1 TAAACAAACTTTGTTAAT-AAAA-ATTAAAAATTT
*** *
3611817 TAAACTTGCTTTTTTAATAAAAATTAAAAATT
1 TAAACAAACTTTGTTAATAAAAATTAAAAATT
3611849 AACAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 10 0.36
34 4 0.14
35 14 0.50
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (33 bp):
TAAACAAACTTTGTTAATAAAAATTAAAAATTT
Found at i:3620449 original size:20 final size:20
Alignment explanation
Indices: 3620410--3620450 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3620400 AATTCGAAAT
* *
3620410 GTTTAGAGTTTAGTGTTCGA
1 GTTTAGAGTTTAGAGATCGA
*
3620430 GTTTAGAGTTTGGAGATCGA
1 GTTTAGAGTTTAGAGATCGA
3620450 G
1 G
3620451 ATTCAAGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.34, T:0.39
Consensus pattern (20 bp):
GTTTAGAGTTTAGAGATCGA
Found at i:3638880 original size:14 final size:14
Alignment explanation
Indices: 3638861--3638887 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3638851 GAGCTAGTAC
3638861 GGTTGAAATGGAAT
1 GGTTGAAATGGAAT
3638875 GGTTGAAATGGAA
1 GGTTGAAATGGAA
3638888 ATGAAATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (14 bp):
GGTTGAAATGGAAT
Found at i:3639331 original size:20 final size:21
Alignment explanation
Indices: 3639294--3639332 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3639284 TTTCTTTCTT
* *
3639294 TTATTTTTTAATATTATTAGA
1 TTATTTTATAATAGTATTAGA
3639315 TTATTTTATAA-AGTATTA
1 TTATTTTATAATAGTATTA
3639333 TTGTAGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TTATTTTATAATAGTATTAGA
Found at i:3641350 original size:14 final size:14
Alignment explanation
Indices: 3641326--3641363 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
3641316 ATAATAAAAC
3641326 AGAATGAAAATATACA
1 AGAA-GAAAATA-ACA
3641342 A-AAGAAAATAACA
1 AGAAGAAAATAACA
3641355 AGAAGAAAA
1 AGAAGAAAA
3641364 AATTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 14 0.67
15 2 0.10
16 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.13, T:0.11
Consensus pattern (14 bp):
AGAAGAAAATAACA
Found at i:3641858 original size:24 final size:24
Alignment explanation
Indices: 3641830--3641875 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3641820 AGGGTGGTTT
* *
3641830 AGTGGGGTGATGGGGTTAGTGGCA
1 AGTGGGATGATGGAGTTAGTGGCA
3641854 AGTGGGATGATGGAGTTAGTGG
1 AGTGGGATGATGGAGTTAGTGG
3641876 TTGGTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.02, G:0.52, T:0.26
Consensus pattern (24 bp):
AGTGGGATGATGGAGTTAGTGGCA
Found at i:3644530 original size:15 final size:15
Alignment explanation
Indices: 3644510--3644543 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3644500 AGAGTTTGAG
3644510 AAGTACTGTATTATA
1 AAGTACTGTATTATA
3644525 AAGTACTGTATTATA
1 AAGTACTGTATTATA
3644540 AAGT
1 AAGT
3644544 GTAGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (15 bp):
AAGTACTGTATTATA
Found at i:3649345 original size:31 final size:31
Alignment explanation
Indices: 3649272--3649347 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
3649262 GGACTGTTTA
*
3649272 AAATTTTTTT-AATAGTTTAGTGATTTAAAT
1 AAATTTTTTTAAATAGTTCAGTGATTTAAAT
**
3649302 AAAAATTTTTAAATAGTTCAGTGATTTAAAT
1 AAATTTTTTTAAATAGTTCAGTGATTTAAAT
3649333 AAATTTTTTTAAATA
1 AAATTTTTTTAAATA
3649348 ATTTAATGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 8 0.20
31 32 0.80
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (31 bp):
AAATTTTTTTAAATAGTTCAGTGATTTAAAT
Found at i:3650383 original size:41 final size:42
Alignment explanation
Indices: 3650338--3650419 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 42
3650328 CAACTGTATT
*
3650338 GAATTA-AAGTGCAGATATTTTATAATTTAACCAAAT-AAATC
1 GAATTAGAAG-GCAGATACTTTATAATTTAACCAAATGAAATC
* * * *
3650379 GAATTAGAAGGGATATACTTTATGATTTAATCAAATGAAAT
1 GAATTAGAAGGCAGATACTTTATAATTTAACCAAATGAAAT
3650420 TGAAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 27 0.79
42 7 0.21
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (42 bp):
GAATTAGAAGGCAGATACTTTATAATTTAACCAAATGAAATC
Found at i:3664286 original size:31 final size:30
Alignment explanation
Indices: 3664251--3664310 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
3664241 ATAAAATGAT
**
3664251 TATTGAACTATTCAAATTTTTTTATTTAAAC
1 TATTGAACTATTCAAA-AATTTTATTTAAAC
*
3664282 TATTGAACTATTTAAAAATTTTATTTAAA
1 TATTGAACTATTCAAAAATTTTATTTAAA
3664311 GTACTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (30 bp):
TATTGAACTATTCAAAAATTTTATTTAAAC
Found at i:3664773 original size:188 final size:188
Alignment explanation
Indices: 3664456--3664832 Score: 736
Period size: 188 Copynumber: 2.0 Consensus size: 188
3664446 TTCTAGTCTC
3664456 AAAGCAATGCCAGGATTTCCAAGGGAAGATCTATGACAATAAAGCTTGAATCATTCCAATGGAAG
1 AAAGCAATGCCAGGATTTCCAAGGGAAGATCTATGACAATAAAGCTTGAATCATTCCAATGGAAG
3664521 ACAAAACCACTTGACATGAATAATTCTAGGGGGTCCTTTGGCTTTAAGGTGCAAAGGAAAAGCCA
66 ACAAAACCACTTGACATGAATAATTCTAGGGGGTCCTTTGGCTTTAAGGTGCAAAGGAAAAGCCA
* *
3664586 AGAACTCGCCCGCAAGAGAGAGAACCTTAAGAATAACGGAGTTTTCATAATACGGCTT
131 AGAACTAGCCCGCAAGAGAGAGAACCTTAAGAATAACGGAGTTTTCATAATACAGCTT
3664644 AAAGCAATGCCAGGATTTCCAAGGGAAGATCTATGACAATAAAGCTTGAATCATTCCAATGGAAG
1 AAAGCAATGCCAGGATTTCCAAGGGAAGATCTATGACAATAAAGCTTGAATCATTCCAATGGAAG
3664709 ACAAAACCACTTGACATGAATAATTCTAGGGGGTCCTTTGGCTTTAAGGTGCAAAGGAAAAGCCA
66 ACAAAACCACTTGACATGAATAATTCTAGGGGGTCCTTTGGCTTTAAGGTGCAAAGGAAAAGCCA
3664774 AGAACTAGCCCGCAAGAGAGAGAACCTTAAGAATAACGGAGTTTTCATAATACAGCTT
131 AGAACTAGCCCGCAAGAGAGAGAACCTTAAGAATAACGGAGTTTTCATAATACAGCTT
3664832 A
1 A
3664833 TTAAAGACGA
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
188 187 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (188 bp):
AAAGCAATGCCAGGATTTCCAAGGGAAGATCTATGACAATAAAGCTTGAATCATTCCAATGGAAG
ACAAAACCACTTGACATGAATAATTCTAGGGGGTCCTTTGGCTTTAAGGTGCAAAGGAAAAGCCA
AGAACTAGCCCGCAAGAGAGAGAACCTTAAGAATAACGGAGTTTTCATAATACAGCTT
Found at i:3674117 original size:15 final size:15
Alignment explanation
Indices: 3674076--3674122 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3674066 CCTATTTCGT
3674076 AATATATCAAAAAGA
1 AATATATCAAAAAGA
* *
3674091 ATTATGACCAAAAAGA
1 AATAT-ATCAAAAAGA
*
3674107 AATCTATCAAAAAGA
1 AATATATCAAAAAGA
3674122 A
1 A
3674123 TTCAAATAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.19
Consensus pattern (15 bp):
AATATATCAAAAAGA
Found at i:3688237 original size:9 final size:9
Alignment explanation
Indices: 3688173--3688286 Score: 53
Period size: 9 Copynumber: 12.9 Consensus size: 9
3688163 TTTTAGAATT
*
3688173 ATTTTTAAA
1 ATTTTTATA
3688182 ATTTTTATA
1 ATTTTTATA
3688191 ATTTTTA-A
1 ATTTTTATA
**
3688199 A-TAATATAA
1 ATTTTTAT-A
* *
3688208 ATTGTGA-A
1 ATTTTTATA
3688216 ATTTTTATAA
1 ATTTTTAT-A
3688226 ATTTTTATA
1 ATTTTTATA
3688235 ATTATTT-TAA
1 ATT-TTTAT-A
* * *
3688245 AATTTAAAA
1 ATTTTTATA
3688254 ATTATTT-TA
1 ATT-TTTATA
3688263 ATTTTT-T-
1 ATTTTTATA
*
3688270 ATTTTTAGA
1 ATTTTTATA
3688279 ATTTTTAT
1 ATTTTTAT
3688287 TTTTGTAATT
Statistics
Matches: 78, Mismatches: 16, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
7 9 0.12
8 12 0.15
9 38 0.49
10 19 0.24
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (9 bp):
ATTTTTATA
Found at i:3688245 original size:19 final size:19
Alignment explanation
Indices: 3688223--3688271 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
3688213 GAAATTTTTA
3688223 TAAATTTTTATAATTATTT
1 TAAATTTTTATAATTATTT
* * *
3688242 TAAAATTTAAAAATTATTT
1 TAAATTTTTATAATTATTT
*
3688261 TAATTTTTTAT
1 TAAATTTTTAT
3688272 TTTTAGAATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAAATTTTTATAATTATTT
Found at i:3688283 original size:16 final size:16
Alignment explanation
Indices: 3688261--3688299 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3688251 AAAATTATTT
3688261 TAATTTTTTATTTTTAG
1 TAATTTTTTATTTTT-G
3688278 -AA-TTTTTATTTTTG
1 TAATTTTTTATTTTTG
3688292 TAATTTTT
1 TAATTTTT
3688300 GTTCAGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.05
15 13 0.65
16 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (16 bp):
TAATTTTTTATTTTTG
Found at i:3688448 original size:23 final size:23
Alignment explanation
Indices: 3688415--3688465 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3688405 AATTTGAAAA
* *
3688415 TTGAATTACTT-ATTCGAATTGAC
1 TTGAATAACTTGATTCG-ATTAAC
*
3688438 TTGAATAACTTGATTTGATTAAC
1 TTGAATAACTTGATTCGATTAAC
3688461 TTGAA
1 TTGAA
3688466 ATTCAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (23 bp):
TTGAATAACTTGATTCGATTAAC
Found at i:3689955 original size:25 final size:25
Alignment explanation
Indices: 3689921--3689969 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3689911 CGTTAACTCG
3689921 ACTCGATTTGACTC-AAAAACATTTT
1 ACTCGATTTGACTCGAAAAA-ATTTT
*
3689946 ACTCGATTTGATTCGAAAAAATTT
1 ACTCGATTTGACTCGAAAAAATTT
3689970 CAAGTTGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (25 bp):
ACTCGATTTGACTCGAAAAAATTTT
Found at i:3696102 original size:47 final size:47
Alignment explanation
Indices: 3696051--3696146 Score: 124
Period size: 47 Copynumber: 2.0 Consensus size: 47
3696041 AAAATATAAG
* * * *
3696051 ATAATTGAGTGATAAAAA-ATAATTTAAATGATTATT-TTGTTATTTTT
1 ATAATTAAGTGA-AAAAATATAA-TTAAATGAGTATTAATGTAATTTTT
3696098 ATAATTAAGTGAAAAAATATAATTAAATGAGTATTAATGTAATTTTT
1 ATAATTAAGTGAAAAAATATAATTAAATGAGTATTAATGTAATTTTT
3696145 AT
1 AT
3696147 TTTTTTATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 17 0.40
47 26 0.60
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (47 bp):
ATAATTAAGTGAAAAAATATAATTAAATGAGTATTAATGTAATTTTT
Found at i:3705314 original size:17 final size:19
Alignment explanation
Indices: 3705292--3705333 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
3705282 TCGAAAGAGA
*
3705292 AAAAAACT-CA-AAAAAAT
1 AAAAAACTCCACAAAAAAG
3705309 AAAAAA-TCCACAAAAAAG
1 AAAAAACTCCACAAAAAAG
3705327 AAAAAAC
1 AAAAAAC
3705334 ACAAGAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 8 0.38
18 12 0.57
ACGTcount: A:0.76, C:0.14, G:0.02, T:0.07
Consensus pattern (19 bp):
AAAAAACTCCACAAAAAAG
Found at i:3721658 original size:24 final size:20
Alignment explanation
Indices: 3721640--3721680 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3721630 TTTGAATAAG
3721640 AAATGGTGAAGGATTTTGAA
1 AAATGGTGAAGGATTTTGAA
3721660 AAATGGTGAAGGATTTT-AA
1 AAATGGTGAAGGATTTTGAA
3721679 AA
1 AA
3721681 GGAGAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (20 bp):
AAATGGTGAAGGATTTTGAA
Found at i:3731339 original size:51 final size:51
Alignment explanation
Indices: 3731284--3731383 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
3731274 CTACCACATA
* *
3731284 ACATGTAA-CACATCCATAATGAACTCGGACCTCTCAACGAGCTTGGATGTT
1 ACATG-AATCACATCCATAATGAACTCGAACCTCTCAACGAGCTCGGATGTT
* *
3731335 ACATGAATCGCATCCATTATGAACTCGAACCTCTCAACGAGCTCGGATG
1 ACATGAATCACATCCATAATGAACTCGAACCTCTCAACGAGCTCGGATG
3731384 CTCGCATCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 2 0.05
51 42 0.95
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (51 bp):
ACATGAATCACATCCATAATGAACTCGAACCTCTCAACGAGCTCGGATGTT
Found at i:3746386 original size:44 final size:45
Alignment explanation
Indices: 3746330--3746420 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 45
3746320 ACTAAATAAA
* * *
3746330 ATCTCTCTCTTAAAGTGTAACGTTGTACATAG-AAAAAAATATAC
1 ATCTCTCTCTTAAAATGTAACATTGTACAAAGAAAAAAAATATAC
*
3746374 ATCTCTCTCTTAAAATGTTACATTGTACAAAGAAAAAAAATATAC
1 ATCTCTCTCTTAAAATGTAACATTGTACAAAGAAAAAAAATATAC
3746419 AT
1 AT
3746421 ATAATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 28 0.67
45 14 0.33
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (45 bp):
ATCTCTCTCTTAAAATGTAACATTGTACAAAGAAAAAAAATATAC
Found at i:3749804 original size:2 final size:2
Alignment explanation
Indices: 3749797--3749824 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3749787 TCATGGGCTC
3749797 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3749825 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3753558 original size:22 final size:21
Alignment explanation
Indices: 3753532--3753573 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3753522 CTTTTATCAT
*
3753532 TTTAATCGTTAATTATTTTTAG
1 TTTAATCATTAATT-TTTTTAG
3753554 TTTAATCATTAATTTTTTTA
1 TTTAATCATTAATTTTTTTA
3753574 AAATAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTAATCATTAATTTTTTTAG
Found at i:3754087 original size:13 final size:13
Alignment explanation
Indices: 3754069--3754094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3754059 TTACAAGTAT
3754069 AATGAAAATTTTA
1 AATGAAAATTTTA
3754082 AATGAAAATTTTA
1 AATGAAAATTTTA
3754095 GGTTAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AATGAAAATTTTA
Found at i:3754184 original size:22 final size:22
Alignment explanation
Indices: 3754158--3754203 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3754148 TCTTTTATGT
3754158 TTTTTTAACTT-ACTTCTTCTTC
1 TTTTTTAA-TTCACTTCTTCTTC
* *
3754180 TTTTTTCATTCTCTTCTTCTTC
1 TTTTTTAATTCACTTCTTCTTC
3754202 TT
1 TT
3754204 CCTTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTTAATTCACTTCTTCTTC
Found at i:3755051 original size:14 final size:14
Alignment explanation
Indices: 3755032--3755070 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
3755022 TAAATTTGAT
3755032 TTTTAATTTATATA
1 TTTTAATTTATATA
*
3755046 TTTTAATATTATATT
1 TTTTAAT-TTATATA
3755061 TTTATAATTT
1 TTT-TAATTT
3755071 TATTAATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 11 0.50
16 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTAATTTATATA
Found at i:3755057 original size:15 final size:13
Alignment explanation
Indices: 3755030--3755064 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
3755020 TCTAAATTTG
3755030 ATTTTTAATTTAT
1 ATTTTTAATTTAT
3755043 ATATTTTAATATTAT
1 AT-TTTTAAT-TTAT
3755058 ATTTTTA
1 ATTTTTA
3755065 TAATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 12 0.60
15 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTTTAATTTAT
Found at i:3755741 original size:17 final size:17
Alignment explanation
Indices: 3755706--3755744 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3755696 CTTTAGAATT
*
3755706 TTTTTAAAAAGTTATAA
1 TTTTTAAAAAATTATAA
3755723 TTTTTAAAAAA-TATAA
1 TTTTTAAAAAATTATAA
*
3755739 ATTTTA
1 TTTTTA
3755745 GATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTTTAAAAAATTATAA
Found at i:3760203 original size:24 final size:24
Alignment explanation
Indices: 3760161--3760210 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
3760151 TCATCAACAG
* * *
3760161 ATTTTACTACCATCGAAACCATCC
1 ATTTTACTACCACCAAAACCAACC
*
3760185 ATTTTACTATCACCAAAACCAACC
1 ATTTTACTACCACCAAAACCAACC
3760209 AT
1 AT
3760211 CCTTCCCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.32, G:0.02, T:0.28
Consensus pattern (24 bp):
ATTTTACTACCACCAAAACCAACC
Found at i:3760208 original size:28 final size:28
Alignment explanation
Indices: 3760177--3760244 Score: 73
Period size: 32 Copynumber: 2.3 Consensus size: 28
3760167 CTACCATCGA
3760177 AACCATCCATTTTACTATCACCAAAACC
1 AACCATCCATTTTACTATCACCAAAACC
* **
3760205 AACCATCCTTCCCTTTTACTATCACTGAAACC
1 AACCA----TCCATTTTACTATCACCAAAACC
3760237 AACCATCC
1 AACCATCC
3760245 TTATCATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
28 8 0.24
32 25 0.76
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.26
Consensus pattern (28 bp):
AACCATCCATTTTACTATCACCAAAACC
Found at i:3760225 original size:32 final size:32
Alignment explanation
Indices: 3760186--3760246 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3760176 AAACCATCCA
3760186 TTTTACTATCACCAAAACCAACCATCCTTCCC
1 TTTTACTATCACCAAAACCAACCATCCTTCCC
**
3760218 TTTTACTATCACTGAAACCAACCATCCTT
1 TTTTACTATCACCAAAACCAACCATCCTT
3760247 ATCATTGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (32 bp):
TTTTACTATCACCAAAACCAACCATCCTTCCC
Found at i:3774310 original size:3 final size:3
Alignment explanation
Indices: 3774302--3774335 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3774292 CCCTTTCATC
3774302 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3774336 TTATATTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3778555 original size:30 final size:28
Alignment explanation
Indices: 3778494--3778561 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
3778484 AAAAACCTAC
* *
3778494 ATTAATTTTCTATAATGAAAGTTAAATA
1 ATTACTTTTCTATAATGAAAGATAAATA
* *
3778522 ATTACTTTTCATATAATTAAGAGATAATTA
1 ATTACTTTTC-TATAATGAA-AGATAAATA
3778552 ATTACCTTTT
1 ATTA-CTTTT
3778562 TCTGTACCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 9 0.27
29 8 0.24
30 11 0.33
31 5 0.15
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (28 bp):
ATTACTTTTCTATAATGAAAGATAAATA
Found at i:3779025 original size:14 final size:15
Alignment explanation
Indices: 3779006--3779041 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3778996 AGATAATAGA
3779006 AAATAAAG-AAAAAG
1 AAATAAAGTAAAAAG
*
3779020 AAATAAAGTTAAAAG
1 AAATAAAGTAAAAAG
3779035 AAATAAA
1 AAATAAA
3779042 AGAATTGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (15 bp):
AAATAAAGTAAAAAG
Found at i:3781929 original size:104 final size:109
Alignment explanation
Indices: 3781810--3782034 Score: 273
Period size: 110 Copynumber: 2.1 Consensus size: 109
3781800 GCTAGAGATA
* * * *
3781810 TAAAAAAAAATTGGTGCTGACCA-GTAGATGGCTGGCACCAGGT-ATTTTTTGTGTCCCAA-GCC
1 TAAAAAAAAATTGGTGCTGACCATGTA-ATAGCTGGCACCAGGTAATTTTTCGAGTCCCAAGGCA
* *
3781872 A-A-TTTTTTTACTTTGGAACACTGATGGCTGGCACCAGTGAATT
65 ATATTTTTTTTACTTTGGAACACTGATGGCCGGCACCAGGGAATT
* * *
3781915 TAAAAAAAAA-TGGTGCTGACCATGTAATAGCTGGCACTAGGTACATTTTTCGAGTCCTAAGGTA
1 TAAAAAAAAATTGGTGCTGACCATGTAATAGCTGGCACCAGGTA-ATTTTTCGAGTCCCAAGGCA
* * *
3781979 ATATTTTTTTTTACTTTGGGACACTGATTGCCGGCACCAGGGTATT
65 ATA-TTTTTTTTACTTTGGAACACTGATGGCCGGCACCAGGGAATT
3782025 TAAAAAAAAA
1 TAAAAAAAAA
3782035 AATTTGGGTG
Statistics
Matches: 101, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
104 26 0.26
105 13 0.13
106 13 0.13
107 2 0.02
108 1 0.01
110 46 0.46
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (109 bp):
TAAAAAAAAATTGGTGCTGACCATGTAATAGCTGGCACCAGGTAATTTTTCGAGTCCCAAGGCAA
TATTTTTTTTACTTTGGAACACTGATGGCCGGCACCAGGGAATT
Found at i:3782995 original size:21 final size:21
Alignment explanation
Indices: 3782971--3783020 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
3782961 ACCATAGAAG
3782971 ATGGTGATGAAGGGTCTGATA
1 ATGGTGATGAAGGGTCTGATA
3782992 ATGGTGATGAAGGGTCTGATA
1 ATGGTGATGAAGGGTCTGATA
3783013 ATGGTGAT
1 ATGGTGAT
3783021 CAGTCCCACT
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:0.28, C:0.04, G:0.38, T:0.30
Consensus pattern (21 bp):
ATGGTGATGAAGGGTCTGATA
Found at i:3783609 original size:91 final size:91
Alignment explanation
Indices: 3783486--3783705 Score: 309
Period size: 91 Copynumber: 2.4 Consensus size: 91
3783476 TTATATTTAC
* *
3783486 ATATACAAAAAAATACGAACATTCTAATAAATTAATACACGAAAATATAAAAACGAAACCTTAAA
1 ATATA-AAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAACGAAACCTTAAA
* *
3783551 TCATAAACAAGTACATTAAGTATACAA
65 TCATAAACAACTACATTAAATATACAA
* *
3783578 ATATAAAAAAAATACAAACATTCTAAGAAATTAATATACGAAAATATAAAAATGAAACCTTAAAT
1 ATATAAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAACGAAACCTTAAAT
* * * *
3783643 CCTAGACAACTACATTAAATTTACAG
66 CATAAACAACTACATTAAATATACAA
*
3783669 ATAT-AAAAAAATACAAAAATTCTAAAGAAA-TAATACA
1 ATATAAAAAAAATACAAACATTCT-AAGAAATTAATACA
3783706 ATTATTTTGA
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
90 24 0.21
91 86 0.75
92 5 0.04
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.24
Consensus pattern (91 bp):
ATATAAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAACGAAACCTTAAAT
CATAAACAACTACATTAAATATACAA
Found at i:3793058 original size:20 final size:21
Alignment explanation
Indices: 3793033--3793081 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3793023 GACAACCTCT
3793033 AAATATAAA-AAAATTTTAAA
1 AAATATAAATAAAATTTTAAA
* *
3793053 AAATATAAATTAATTTTTAAA
1 AAATATAAATAAAATTTTAAA
3793074 AAATATAA
1 AAATATAA
3793082 TTTTTTAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATAAATAAAATTTTAAA
Found at i:3804552 original size:24 final size:24
Alignment explanation
Indices: 3804520--3804567 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3804510 AGAAAGACAC
3804520 ATCATCTACTTAGATAGTCGATTA
1 ATCATCTACTTAGATAGTCGATTA
3804544 ATCATCTACTTAGATAGTCGATTA
1 ATCATCTACTTAGATAGTCGATTA
3804568 GTGACCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (24 bp):
ATCATCTACTTAGATAGTCGATTA
Found at i:3805226 original size:16 final size:16
Alignment explanation
Indices: 3805215--3805245 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3805205 GTTTTTTTAT
*
3805215 ATTTATTATTTTTAAA
1 ATTTAATATTTTTAAA
3805231 ATTTAATATTTTTAA
1 ATTTAATATTTTTAA
3805246 TAAATCACAC
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAATATTTTTAAA
Found at i:3809126 original size:16 final size:16
Alignment explanation
Indices: 3809105--3809139 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3809095 GCATATCACT
3809105 CACCTTTAATCAGTAC
1 CACCTTTAATCAGTAC
3809121 CACCTTTAATCAGTAC
1 CACCTTTAATCAGTAC
3809137 CAC
1 CAC
3809140 AGATGCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.29
Consensus pattern (16 bp):
CACCTTTAATCAGTAC
Found at i:3812855 original size:11 final size:11
Alignment explanation
Indices: 3812839--3812877 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3812829 AGATTGAATT
*
3812839 TTTTTTTACAA
1 TTTTTTTACTA
*
3812850 TTTTTTATATTA
1 TTTTTT-TACTA
3812862 TTTTTTTACTA
1 TTTTTTTACTA
3812873 TTTTT
1 TTTTT
3812878 AATAATGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTTACTA
Found at i:3815852 original size:23 final size:23
Alignment explanation
Indices: 3815825--3815869 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3815815 TACAAAGTAG
3815825 TTTTAATAATTTGTAATTTAGAT
1 TTTTAATAATTTGTAATTTAGAT
* *
3815848 TTTTAGTAATTTTTAATTTAGA
1 TTTTAATAATTTGTAATTTAGA
3815870 AAATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTTAATAATTTGTAATTTAGAT
Found at i:3821043 original size:14 final size:14
Alignment explanation
Indices: 3821026--3821056 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3821016 GTTATCATGA
3821026 TATTATTATATTGT
1 TATTATTATATTGT
*
3821040 TATTATTTTATTGT
1 TATTATTATATTGT
3821054 TAT
1 TAT
3821057 GGTTTGAATA
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:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
TATTATTATATTGT
Found at i:3830358 original size:30 final size:31
Alignment explanation
Indices: 3830307--3830365 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3830297 AAAAGTTAAA
*
3830307 CTTTTAAAAATTTTGAAAATTTTCATTAATT
1 CTTTTAAAAATTTTGAAAATTTTAATTAATT
3830338 CTTTTAAAAATTTT-AAAATTTTAATTAA
1 CTTTTAAAAATTTTGAAAATTTTAATTAA
3830366 GCCCTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (31 bp):
CTTTTAAAAATTTTGAAAATTTTAATTAATT
Found at i:3835209 original size:23 final size:25
Alignment explanation
Indices: 3835167--3835212 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
3835157 AAGAATTTTA
*
3835167 AAAAATAAAAAAAGTCTAAATATTC
1 AAAAATAAAAAAAGTATAAATATTC
3835192 AAAAAT-AAAAAA-TATAAATAT
1 AAAAATAAAAAAAGTATAAATAT
3835213 AAATATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAATAAAAAAAGTATAAATATTC
Found at i:3835600 original size:41 final size:41
Alignment explanation
Indices: 3835521--3835624 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 41
3835511 ACCCTAATAT
* *
3835521 AAACATTAAAATA-ATATTAAAATAATTGTATAAAAAATTTA
1 AAACAATAAAATATATATTAAAATAATTGAATAAAAAA-TTA
* **
3835562 AATA-AATAAAATATATA-TAAAATTATTGAATATTAAATTA
1 AA-ACAATAAAATATATATTAAAATAATTGAATAAAAAATTA
*
3835602 AAACAATACAAATAT-TTTTAAAA
1 AAACAATA-AAATATATATTAAAA
3835625 AAATAATATG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
39 1 0.02
40 10 0.19
41 37 0.71
42 4 0.08
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (41 bp):
AAACAATAAAATATATATTAAAATAATTGAATAAAAAATTA
Found at i:3837038 original size:4 final size:4
Alignment explanation
Indices: 3837031--3837057 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3837021 TCTTTCCATT
3837031 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3837058 CAGTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3837807 original size:39 final size:39
Alignment explanation
Indices: 3837753--3837831 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3837743 GCTTTCTAAT
3837753 TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
1 TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
3837792 TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
1 TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
3837831 T
1 T
3837832 TCAAATGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (39 bp):
TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
Found at i:3840454 original size:27 final size:27
Alignment explanation
Indices: 3840393--3840445 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3840383 AAAGTTCATT
*
3840393 AGCTAAATTTAAAAAAAAACACTTAAA
1 AGCTAAATTTAAAAAAAAAAACTTAAA
3840420 AGCTAAATTTAAAAAAAAAAACTTAA
1 AGCTAAATTTAAAAAAAAAAACTTAA
3840446 GACTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.23
Consensus pattern (27 bp):
AGCTAAATTTAAAAAAAAAAACTTAAA
Found at i:3842661 original size:29 final size:30
Alignment explanation
Indices: 3842608--3842687 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
3842598 ATCTTAAAAT
* *
3842608 TATATATGAATTATGATTTAATGTGCAATTA
1 TATATATAAATTTTGATTT-ATGTGCAATTA
* *
3842639 TATATATAAATTTTGATTT-TGTGTAATTT
1 TATATATAAATTTTGATTTATGTGCAATTA
*
3842668 TATATTTAAAATTTTGATTT
1 TATATAT-AAATTTTGATTT
3842688 GATTCCATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.33
30 12 0.28
31 17 0.40
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.54
Consensus pattern (30 bp):
TATATATAAATTTTGATTTATGTGCAATTA
Found at i:3854761 original size:43 final size:46
Alignment explanation
Indices: 3854711--3854796 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
3854701 AGATTAATTA
* *
3854711 AGTGATCAAATT-AA-AAAATTGATAATTGGGT-GAAAAAAAAAGT
1 AGTGATCAAATTGAAGAAAATTAATAATTGAGTAGAAAAAAAAAGT
*
3854754 AGTGATCAAATTGAAGCAAATTAATAATTGAGTAGAAAAAAAA
1 AGTGATCAAATTGAAGAAAATTAATAATTGAGTAGAAAAAAAA
3854797 GACAATATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 12 0.32
44 2 0.05
45 14 0.38
46 9 0.24
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.24
Consensus pattern (46 bp):
AGTGATCAAATTGAAGAAAATTAATAATTGAGTAGAAAAAAAAAGT
Found at i:3858694 original size:26 final size:25
Alignment explanation
Indices: 3858636--3858695 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
3858626 TTATTTATTT
3858636 AAATATATATAATTAAACCAAAATA
1 AAATATATATAATTAAACCAAAATA
* *
3858661 AAATTATATATATTTGAAA-CACAATCA
1 AAA-TATATATAATT-AAACCAAAAT-A
3858688 AAATATAT
1 AAATATAT
3858696 TTTATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 3 0.10
26 20 0.67
27 7 0.23
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (25 bp):
AAATATATATAATTAAACCAAAATA
Done.