Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 20 of 26
Found at i:3389641 original size:79 final size:79
Alignment explanation
Indices: 3389483--3389658 Score: 212
Period size: 79 Copynumber: 2.2 Consensus size: 79
3389473 TGGAGATAAC
* * *
3389483 AACGAGGCTGGAGTA-CCCATGATTATGGAAAATCGATGTTCTGGAAATAAAATTGGGATTGGAG
1 AACG-GGCTGGAGTATCCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAG
***
3389547 TATCCCCTTGGAAAT
65 TATCCCCTCAAAAAT
* * * *
3389562 AACAGGGCTGGAGTATCCC-TAATTATAGAAAATTGGTGTTTTGAAAATAAAATTGGGGTTGGAG
1 AAC-GGGCTGGAGTATCCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAG
3389626 TATCCCCTCAAAAAT
65 TATCCCCTCAAAAAT
*
3389641 AACGGGATTGGAGTATCC
1 AACGGG-CTGGAGTATCC
3389659 TCGCGAAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
78 3 0.04
79 76 0.92
80 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (79 bp):
AACGGGCTGGAGTATCCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAGT
ATCCCCTCAAAAAT
Found at i:3389654 original size:28 final size:28
Alignment explanation
Indices: 3389620--3389689 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
3389610 AAAATTGGGG
*
3389620 TTGGAGTATCCCCTCAAAAATAACGGGA
1 TTGGAGTATCCCCGCAAAAATAACGGGA
* * *
3389648 TTGGAGTATCCTCGCGAAAATAACGGGG
1 TTGGAGTATCCCCGCAAAAATAACGGGA
3389676 TTGGAGTATCCCCG
1 TTGGAGTATCCCCG
3389690 ATTATGAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (28 bp):
TTGGAGTATCCCCGCAAAAATAACGGGA
Found at i:3389733 original size:79 final size:79
Alignment explanation
Indices: 3389643--3390086 Score: 692
Period size: 79 Copynumber: 5.6 Consensus size: 79
3389633 TCAAAAATAA
* * *
3389643 CGGGATTGGAGTATCCTCGCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
*
3389708 TTTAGGAATAAAAT
66 TTTAGGAATAAAGT
* * * *
3389722 CGGGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCTCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
*
3389787 TTTAGGAATAAAGC
66 TTTAGGAATAAAGT
* * * *
3389801 CGAGGTTGGAGTATCCCCTCGAAAATAATGGGGTTAGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* *
3389866 TTTAGAAATAAAAT
66 TTTAGGAATAAAGT
* *
3389880 CGCGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
3389945 TTTAGGAATAAAGT
66 TTTAGGAATAAAGT
*
3389959 CGGGTTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
*
3390024 TTTAGGAATAAAGC
66 TTTAGGAATAAAGT
*
3390038 CGGGGTTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGAT
3390087 GATTAACGGG
Statistics
Matches: 333, Mismatches: 31, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
78 1 0.00
79 332 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTTAGGAATAAAGT
Found at i:3390073 original size:28 final size:28
Alignment explanation
Indices: 3390038--3390110 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 28
3390028 GGAATAAAGC
3390038 CGGGGTTGGAGTATCCCCTC-AGAAATAA
1 CGGGGTTGGAGTATCCCCTCGAG-AATAA
*
3390066 CGGGGTTGGAGTAT--CCTCGATGATTAA
1 CGGGGTTGGAGTATCCCCTCGA-GAATAA
3390093 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
3390111 GATTGTGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 4 0.10
27 19 0.47
28 15 0.38
29 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAGAATAA
Found at i:3390206 original size:51 final size:51
Alignment explanation
Indices: 3390093--3390331 Score: 266
Period size: 51 Copynumber: 4.6 Consensus size: 51
3390083 CGATGATTAA
* * *
3390093 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGAAAATAAAAC
** * * *
3390145 TAGAGTTGGAGTATCCCCGATTAT-AGTAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGAAAATAAAAC
* *
3390196 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAC
* * * * *
3390247 CGGAGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTT-AGGAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGA-AAATAAAAC
* * *
3390298 CAGGGTTGGAGTACCCCCCGATTATGAAAAATTG
1 CGGGGTTGGAGTA-TCCCCGATTGTGAAAAATTG
3390332 AGAAACTTAA
Statistics
Matches: 154, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
50 1 0.01
51 109 0.71
52 44 0.29
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAC
Found at i:3390284 original size:102 final size:103
Alignment explanation
Indices: 3390093--3390331 Score: 320
Period size: 102 Copynumber: 2.3 Consensus size: 103
3390083 CGATGATTAA
* * * *
3390093 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATTAGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTCGAAAATAAAATCAGAGTTGGAGTA
* *
3390158 TCCCCGATTATAGTAAATTGGTGTTTT-GAAAATAAAAC
66 TCCCCGATTATAGAAAATTAGTGTTTTAG-AAATAAAAC
*
3390196 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTCGAAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTCGAAAATAAAATCAGAGTTGGAGTA
* * * *
3390260 TCCTCGATTGTGGAAAATTAGTGTTTTAGGAATAAAAC
66 TCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAAC
* * *
3390298 CAGGGTTGGAGTACCCCCCGATTATGAAAAATTG
1 CGGGGTTGGAGTA-TCCCCGATTGTGAAAAATTG
3390332 AGAAACTTAA
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
102 66 0.55
103 54 0.45
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (103 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTCGAAAATAAAATCAGAGTTGGAGTA
TCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:3392654 original size:13 final size:13
Alignment explanation
Indices: 3392636--3392660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3392626 ATTGTAAAAT
3392636 GTATCGATACAAC
1 GTATCGATACAAC
3392649 GTATCGATACAA
1 GTATCGATACAA
3392661 TGAGCAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAC
Found at i:3392674 original size:20 final size:20
Alignment explanation
Indices: 3392644--3392750 Score: 72
Period size: 20 Copynumber: 5.8 Consensus size: 20
3392634 ATGTATCGAT
*
3392644 ACAACGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
3392664 GCAATGTATCG--ACAATGCA
1 ACAATGTATCGATACAATG-A
*
3392683 A-AATATATCGATAC-----
1 ACAATGTATCGATACAATGA
*
3392697 A--ATGTATCGATACATTGA
1 ACAATGTATCGATACAATGA
* *
3392715 ATAATGTATCGATACATTGA
1 ACAATGTATCGATACAATGA
*
3392735 ATAATGTATCGATACA
1 ACAATGTATCGATACA
3392751 TTTCCTTGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
13 11 0.15
14 1 0.01
18 15 0.21
19 1 0.01
20 44 0.61
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:3392751 original size:20 final size:20
Alignment explanation
Indices: 3392697--3392752 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
3392687 ATATCGATAC
3392697 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
3392717 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
3392737 AATGTATCGATACATT
1 AATGTATCGATACATT
3392753 TCCTTGGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:3393529 original size:40 final size:40
Alignment explanation
Indices: 3393484--3393575 Score: 184
Period size: 40 Copynumber: 2.3 Consensus size: 40
3393474 ATCCCACTTT
3393484 TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
1 TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
3393524 TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
1 TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
3393564 TTGAGGACAAAG
1 TTGAGGACAAAG
3393576 GAAGAGAAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (40 bp):
TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
Found at i:3393767 original size:28 final size:29
Alignment explanation
Indices: 3393739--3393821 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 29
3393729 GGACTAAAAA
3393739 GTGTCACCAACTCGTGTGGGCTTTGAAAG
1 GTGTCACCAACTCGTGTGGGCTTTGAAAG
** * *
3393768 GTGT--CCTGCTC-TTTGAGG-ATTGAAAG
1 GTGTCACCAACTCGTGTG-GGCTTTGAAAG
*
3393794 GTGCCACCAACTCGTGTGGGCTTTGAAA
1 GTGTCACCAACTCGTGTGGGCTTTGAAA
3393822 AGAAAAGGCG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
26 13 0.32
27 7 0.17
28 7 0.17
29 13 0.32
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (29 bp):
GTGTCACCAACTCGTGTGGGCTTTGAAAG
Found at i:3393860 original size:61 final size:58
Alignment explanation
Indices: 3393716--3394202 Score: 511
Period size: 55 Copynumber: 8.4 Consensus size: 58
3393706 ATAAAGTGCA
* * * * *
3393716 TCCTACTCTTTGAGGACTAAAAAGTGTCACCAACTCGTGTGGGCTTT----GAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
* * *
3393771 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-AAAGGCG
* **
3393832 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGAA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-AAAGGCG
* *
3393893 TCCTGCTCTTTGAGGACTGGAAAATACCACCAACTTGTGTGGGCTTT----GAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
* * *
3393948 TCTTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-GAAAG-AAAGGCG
* *
3394009 TCTTGCTCTTTGAGGACCGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG--A--CG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
* *
3394064 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT----GAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
* * *
3394119 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAA-G-AAAGGCG
3394180 TCCTGCTCTTTGAGGACTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
3394203 GTGAAAGAAG
Statistics
Matches: 378, Mismatches: 28, Indels: 47
0.83 0.06 0.10
Matches are distributed among these distances:
51 1 0.00
53 1 0.00
54 3 0.01
55 180 0.48
56 1 0.00
57 1 0.00
60 8 0.02
61 179 0.47
62 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (58 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
Found at i:3394142 original size:26 final size:26
Alignment explanation
Indices: 3394055--3394142 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
3394045 GTGTGGGCTT
*
3394055 TGAAAGACGTCCTGCTCTTTGAGGAC
1 TGAAAGGCGTCCTGCTCTTTGAGGAC
* ** * * *
3394081 TGAAAGGTG-CCACCAACTTATGTGGGC
1 TGAAAGGCGTCCTGC-TCTT-TGAGGAC
3394108 TTTGAAAGGCGTCCTGCTCTTTGAGGAC
1 --TGAAAGGCGTCCTGCTCTTTGAGGAC
3394136 TGAAAGG
1 TGAAAGG
3394143 TGCCACCAAC
Statistics
Matches: 44, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
25 3 0.07
26 17 0.39
27 5 0.11
28 5 0.11
29 11 0.25
30 3 0.07
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (26 bp):
TGAAAGGCGTCCTGCTCTTTGAGGAC
Found at i:3394192 original size:116 final size:112
Alignment explanation
Indices: 3393716--3394202 Score: 511
Period size: 116 Copynumber: 4.2 Consensus size: 112
3393706 ATAAAGTGCA
* * * * *
3393716 TCCTACTCTTTGAGGACTAAAAAGTGTCACCAACTCGTGTGGGCTTTG-AAAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTGCTCT
* * * *
3393780 TTGAGGATTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCG
65 TTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTG-AAAG-GAA--CG
**
3393832 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGAATCCT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG-----GCGTCCT
* *
3393897 GCTCTTTGAGGACTGGAAA-ATACCACCAACTTGTGTGGGCTTTGAAAGG--CA
60 GCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGAACG
* * *
3393948 TCTTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCTT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-----GAAAAGGCGTCCT
* *
3394013 GCTCTTTGAGGACCGAAAAATGCCACCAACTTGTGTGGGCTTTGAAA-G-ACG
60 GCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGAACG
* *
3394064 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTG-AAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTGCTCT
* * *
3394128 TTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAAGGTG
65 TTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTGAAAGG--AA--CG
3394180 TCCTGCTCTTTGAGGACTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
3394203 GTGAAAGAAG
Statistics
Matches: 318, Mismatches: 31, Indels: 45
0.81 0.08 0.11
Matches are distributed among these distances:
110 53 0.17
111 2 0.01
114 1 0.00
115 9 0.03
116 191 0.60
117 8 0.03
121 10 0.03
122 40 0.13
123 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (112 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTGCTCTT
TGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGAACG
Found at i:3395176 original size:1 final size:1
Alignment explanation
Indices: 3395172--3395234 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
3395162 CTTTTCTCTC
* * * * * * *
3395172 TTTTTTCTTTGTTTTGTTTTTTTTATTTTTTTTATTTTTTTTGTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3395235 GAAAAGAATG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:3395202 original size:27 final size:26
Alignment explanation
Indices: 3395172--3395235 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
3395162 CTTTTCTCTC
*
3395172 TTTTTTCTTTGTTTTGTTTTTTTTAT-
1 TTTTTTTTTTGTTTTGTTTTTTTT-TG
*
3395198 TTTTTTTATTTTTTTTGTTTTTTTTTG
1 TTTTTTT-TTTGTTTTGTTTTTTTTTG
3395225 TTTTTTTTTTG
1 TTTTTTTTTTG
3395236 AAAAGAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.03, C:0.02, G:0.08, T:0.88
Consensus pattern (26 bp):
TTTTTTTTTTGTTTTGTTTTTTTTTG
Found at i:3395232 original size:9 final size:9
Alignment explanation
Indices: 3395172--3395232 Score: 77
Period size: 9 Copynumber: 6.7 Consensus size: 9
3395162 CTTTTCTCTC
*
3395172 TTTTTTCTT
1 TTTTTTGTT
*
3395181 TGTTTTGTT
1 TTTTTTGTT
*
3395190 TTTTTTATT
1 TTTTTTGTT
*
3395199 TTTTTTATT
1 TTTTTTGTT
3395208 TTTTTTGTTT
1 TTTTTTG-TT
3395218 TTTTTTGTT
1 TTTTTTGTT
3395227 TTTTTT
1 TTTTTT
3395233 TTGAAAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
9 37 0.80
10 9 0.20
ACGTcount: A:0.03, C:0.02, G:0.07, T:0.89
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:3395233 original size:10 final size:10
Alignment explanation
Indices: 3395172--3395233 Score: 72
Period size: 10 Copynumber: 5.9 Consensus size: 10
3395162 CTTTTCTCTC
3395172 TTTTTTCTTTG
1 TTTTTT-TTTG
3395183 TTTTGTTTTT-
1 TTTT-TTTTTG
*
3395193 TTTATTTTTTT
1 TTT-TTTTTTG
3395204 TATTTTTTTTG
1 T-TTTTTTTTG
3395215 TTTTTTTTTG
1 TTTTTTTTTG
3395225 TTTTTTTTT
1 TTTTTTTTT
3395234 TGAAAAGAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
10 26 0.57
11 16 0.35
12 4 0.09
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3402943 original size:52 final size:52
Alignment explanation
Indices: 3402848--3403101 Score: 234
Period size: 52 Copynumber: 5.0 Consensus size: 52
3402838 GTAGAAAAGG
* * * *
3402848 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGAT-ACAAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGA-AAAGAA
* * * *
3402900 TGTCAATGTGCTGATTCACGGCCAGTGACATTAGACTTGAAGATGAAAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAA
* * *
3402952 TGCCAATGTGCTGATTCAAGGCCAGCG-CATTTGGCTTAGAA-ATGTTAAAG-A
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTA-AAGATG-AAAAGAA
* * * ** * *
3403003 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATG--ATG-G
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAA
* * * *
3403052 TGGCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAGGATGAAAAG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAG
3403102 GATGATAAAG
Statistics
Matches: 164, Mismatches: 31, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
49 40 0.24
51 41 0.25
52 82 0.50
53 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (52 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAA
Found at i:3403040 original size:103 final size:101
Alignment explanation
Indices: 3402848--3403091 Score: 244
Period size: 103 Copynumber: 2.4 Consensus size: 101
3402838 GTAGAAAAGG
* * *
3402848 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATACAAAGAATGTCAATGTGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATACAAAGAATGCCAATATGCTG
* ** * *
3402913 ATTCACGGCCAGTGACATTAGACTTGAAGATGAAAAGAA
66 ATTCAAGGCCAACGACATCAGACTTAAAGATG--AAG-A
**
3402952 TGCCAATGTGCTGATTCAAGGCCAGCGCAT-TT-GGCTTAGAA-ATGTTAAAG-ATGCCAATATG
1 TGCCAATGTGCTGATTCAAGGCCAGCG-ATATTGGGCTTA-AAGAT-ACAAAGAATGCCAATATG
* * * *
3403013 CTGATTCAAGGCCAACGATATCGGACTTAAAGATGATGG
63 CTGATTCAAGGCCAACGACATCAGACTTAAAGATGAAGA
* * * *
3403052 TGGCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAA
3403092 GGATGAAAAG
Statistics
Matches: 117, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
99 1 0.01
100 28 0.24
101 7 0.06
103 45 0.38
104 34 0.29
105 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (101 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATACAAAGAATGCCAATATGCTG
ATTCAAGGCCAACGACATCAGACTTAAAGATGAAGA
Found at i:3403306 original size:60 final size:62
Alignment explanation
Indices: 3403211--3403348 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 62
3403201 TTAAAGATGA
* * * * * *
3403211 TAAAAGATGAGAAGAGTGATAAAGATGCCAATATGCTGATTTAAGGCCAGCGATGTTGGGCT
1 TAAAAGATGAGAAGAATAATAAAGATGCCAATATGCTGATTCAAGACCAGCGATATTAGGCT
* *
3403273 TAAAA-ATGAGAA-AATAATAAAGGTGCGAATATGCTGATTCAAGACCAGCGATATTAGGCT
1 TAAAAGATGAGAAGAATAATAAAGATGCCAATATGCTGATTCAAGACCAGCGATATTAGGCT
*
3403333 T-AAAGATGTGAAGAAT
1 TAAAAGATGAGAAGAAT
3403349 GTCAATGTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
59 3 0.05
60 47 0.72
61 10 0.15
62 5 0.08
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (62 bp):
TAAAAGATGAGAAGAATAATAAAGATGCCAATATGCTGATTCAAGACCAGCGATATTAGGCT
Found at i:3403387 original size:52 final size:52
Alignment explanation
Indices: 3403304--3403425 Score: 174
Period size: 52 Copynumber: 2.3 Consensus size: 52
3403294 GGTGCGAATA
* * *
3403304 TGCTGATTCAAGACCAGCGATATTAGGCTTAAAGATGTGAAGAATGTCAATG
1 TGCTGATTCAAGGCCAGCGATATTAGGCTTAAAGATGAGAAGAATGCCAATG
* *
3403356 TGCTGATTCAAGGCTAGCGATGTT-GGACTTAAAGATGAGAAGAATGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAGATGAGAAGAATGCCAATG
*
3403408 TGTTGATTCAAGGCCAGC
1 TGCTGATTCAAGGCCAGC
3403426 AACATTGGGC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 2 0.03
52 60 0.97
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (52 bp):
TGCTGATTCAAGGCCAGCGATATTAGGCTTAAAGATGAGAAGAATGCCAATG
Found at i:3403498 original size:32 final size:33
Alignment explanation
Indices: 3403462--3403575 Score: 103
Period size: 32 Copynumber: 3.6 Consensus size: 33
3403452 CCAATTTGTA
* *
3403462 TGGGCTTTTGAA-AGGGTTGCCACTGA-CTTATG
1 TGGGCTTTTGAAGAAGGTTGCCAC-CACCTTATG
*
3403494 TGGGC-TTTGAAGAAGGTTGCCACCACCTTGTG
1 TGGGCTTTTGAAGAAGGTTGCCACCACCTTATG
* * * **
3403526 TGGGC-TTTAAAGAAAGTTGCCACCAACTCGTG
1 TGGGCTTTTGAAGAAGGTTGCCACCACCTTATG
*
3403558 TGGGCTTTAG-AGAAGGTT
1 TGGGCTTTTGAAGAAGGTT
3403576 CCTCTACTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
31 7 0.10
32 60 0.87
33 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (33 bp):
TGGGCTTTTGAAGAAGGTTGCCACCACCTTATG
Found at i:3403807 original size:28 final size:29
Alignment explanation
Indices: 3403746--3403819 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
3403736 TACATACAGC
3403746 AAGTGCCACTGA-TTGTGGATTCTGAAAAG
1 AAGTGCCACTGACTTGTGGA-TCTGAAAAG
*
3403775 -A-TGCCACTGACTTGTGGA-CTTAAAAG
1 AAGTGCCACTGACTTGTGGATCTGAAAAG
*
3403801 AAGTGCCACTGACTAGTGG
1 AAGTGCCACTGACTTGTGG
3403820 GCTTTGAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 7 0.17
27 10 0.25
28 23 0.57
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (29 bp):
AAGTGCCACTGACTTGTGGATCTGAAAAG
Found at i:3403829 original size:28 final size:28
Alignment explanation
Indices: 3403746--3403829 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
3403736 TACATACAGC
*
3403746 AAGTGCCACTGA-TTGT-GGATTCTGAA-
1 AAGTGCCACTGACTTGTGGGCTT-TGAAG
* **
3403772 AAGATGCCACTGACTTGTGGACTTAAAAG
1 AAG-TGCCACTGACTTGTGGGCTTTGAAG
*
3403801 AAGTGCCACTGACTAGTGGGCTTTGAAG
1 AAGTGCCACTGACTTGTGGGCTTTGAAG
3403829 A
1 A
3403830 GGGATTTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
26 3 0.07
27 9 0.20
28 28 0.61
29 6 0.13
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (28 bp):
AAGTGCCACTGACTTGTGGGCTTTGAAG
Found at i:3412453 original size:17 final size:17
Alignment explanation
Indices: 3412427--3412466 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3412417 ATTAAGGATT
3412427 ATGATAATAATTATGAA
1 ATGATAATAATTATGAA
* *
3412444 ATGATTATAATTATGAT
1 ATGATAATAATTATGAA
3412461 ATGATA
1 ATGATA
3412467 GACACTCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (17 bp):
ATGATAATAATTATGAA
Found at i:3413736 original size:14 final size:14
Alignment explanation
Indices: 3413717--3413744 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3413707 TGTATTTTTT
3413717 AAAATATATATATA
1 AAAATATATATATA
3413731 AAAATATATATATA
1 AAAATATATATATA
3413745 TTTTTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATATATATATA
Found at i:3414624 original size:2 final size:2
Alignment explanation
Indices: 3414617--3414643 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3414607 ATACGTGTAC
3414617 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3414644 AGCATTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3414849 original size:2 final size:2
Alignment explanation
Indices: 3414842--3414869 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3414832 ATATTTGAAA
3414842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3414870 CTTCGGGTCA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3417624 original size:3 final size:3
Alignment explanation
Indices: 3417610--3417669 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
3417600 GAATTCTAAA
*
3417610 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3417658 TAT TAT TAT TAT
1 TAT TAT TAT TAT
3417670 GTGAAACAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3422711 original size:25 final size:26
Alignment explanation
Indices: 3422664--3422712 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3422654 TAACTCTTAA
* **
3422664 TTTATATTTAAATATTTTTTTAATCT
1 TTTATATTTAAATAATTCATTAATCT
3422690 TTTATATTT-AATAATTCATTAAT
1 TTTATATTTAAATAATTCATTAAT
3422713 ATAAACCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATATTTAAATAATTCATTAATCT
Found at i:3423842 original size:79 final size:79
Alignment explanation
Indices: 3423743--3423888 Score: 213
Period size: 79 Copynumber: 1.8 Consensus size: 79
3423733 ATAACAACGA
* * *
3423743 GGCTGGAGTACCCATGATTATGGAAAATCGATGTTCTGGAAATAAAATTGGGATTGGAGTATCCC
1 GGCTGGAGTACCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAGTATCCC
3423808 CTTGGAAATAACAG
66 CTTGGAAATAACAG
* * * *
3423822 GGCTGGAGTATCCC-TAATTATAGAAAATTGGTGTTTTGAAAATAAAATTGGGGTTGGAGTATCC
1 GGCTGGAGTA-CCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAGTATCC
3423886 CCT
65 CCT
3423889 CAAAAATAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 56 0.95
80 3 0.05
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (79 bp):
GGCTGGAGTACCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAGTATCCC
CTTGGAAATAACAG
Found at i:3423896 original size:79 final size:79
Alignment explanation
Indices: 3423738--3423913 Score: 212
Period size: 79 Copynumber: 2.2 Consensus size: 79
3423728 TGGAGATAAC
* * *
3423738 AACGAGGCTGGAGTA-CCCATGATTATGGAAAATCGATGTTCTGGAAATAAAATTGGGATTGGAG
1 AACG-GGCTGGAGTATCCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAG
***
3423802 TATCCCCTTGGAAAT
65 TATCCCCTCAAAAAT
* * * *
3423817 AACAGGGCTGGAGTATCCC-TAATTATAGAAAATTGGTGTTTTGAAAATAAAATTGGGGTTGGAG
1 AAC-GGGCTGGAGTATCCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAG
3423881 TATCCCCTCAAAAAT
65 TATCCCCTCAAAAAT
*
3423896 AACGGGATTGGAGTATCC
1 AACGGG-CTGGAGTATCC
3423914 TCGCGAAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
78 3 0.04
79 76 0.92
80 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (79 bp):
AACGGGCTGGAGTATCCCATAATTATAGAAAATCGATGTTCTGAAAATAAAATTGGGATTGGAGT
ATCCCCTCAAAAAT
Found at i:3423909 original size:28 final size:28
Alignment explanation
Indices: 3423875--3423944 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
3423865 AAAATTGGGG
*
3423875 TTGGAGTATCCCCTCAAAAATAACGGGA
1 TTGGAGTATCCCCGCAAAAATAACGGGA
* * *
3423903 TTGGAGTATCCTCGCGAAAATAACGGGG
1 TTGGAGTATCCCCGCAAAAATAACGGGA
3423931 TTGGAGTATCCCCG
1 TTGGAGTATCCCCG
3423945 ATTATGAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (28 bp):
TTGGAGTATCCCCGCAAAAATAACGGGA
Found at i:3423988 original size:79 final size:79
Alignment explanation
Indices: 3423898--3424341 Score: 692
Period size: 79 Copynumber: 5.6 Consensus size: 79
3423888 TCAAAAATAA
* * *
3423898 CGGGATTGGAGTATCCTCGCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
*
3423963 TTTAGGAATAAAAT
66 TTTAGGAATAAAGT
* * * *
3423977 CGGGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCTCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
*
3424042 TTTAGGAATAAAGC
66 TTTAGGAATAAAGT
* * * *
3424056 CGAGGTTGGAGTATCCCCTCGAAAATAATGGGGTTAGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* *
3424121 TTTAGAAATAAAAT
66 TTTAGGAATAAAGT
* *
3424135 CGCGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
3424200 TTTAGGAATAAAGT
66 TTTAGGAATAAAGT
*
3424214 CGGGTTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
*
3424279 TTTAGGAATAAAGC
66 TTTAGGAATAAAGT
*
3424293 CGGGGTTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGAT
3424342 GATTAACGGG
Statistics
Matches: 333, Mismatches: 31, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
78 1 0.00
79 332 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTTAGGAATAAAGT
Found at i:3424328 original size:28 final size:28
Alignment explanation
Indices: 3424293--3424365 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 28
3424283 GGAATAAAGC
3424293 CGGGGTTGGAGTATCCCCTC-AGAAATAA
1 CGGGGTTGGAGTATCCCCTCGAG-AATAA
*
3424321 CGGGGTTGGAGTAT--CCTCGATGATTAA
1 CGGGGTTGGAGTATCCCCTCGA-GAATAA
3424348 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
3424366 GATTGTGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 4 0.10
27 19 0.47
28 15 0.38
29 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAGAATAA
Found at i:3424461 original size:51 final size:51
Alignment explanation
Indices: 3424348--3424586 Score: 266
Period size: 51 Copynumber: 4.6 Consensus size: 51
3424338 CGATGATTAA
* * *
3424348 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGAAAATAAAAC
** * * *
3424400 TAGAGTTGGAGTATCCCCGATTAT-AGTAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGAAAATAAAAC
* *
3424451 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAC
* * * * *
3424502 CGGAGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTT-AGGAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGA-AAATAAAAC
* * *
3424553 CAGGGTTGGAGTACCCCCCGATTATGAAAAATTG
1 CGGGGTTGGAGTA-TCCCCGATTGTGAAAAATTG
3424587 AGAAACTTAA
Statistics
Matches: 154, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
50 1 0.01
51 109 0.71
52 44 0.29
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAC
Found at i:3424539 original size:102 final size:103
Alignment explanation
Indices: 3424348--3424586 Score: 320
Period size: 102 Copynumber: 2.3 Consensus size: 103
3424338 CGATGATTAA
* * * *
3424348 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATTAGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTCGAAAATAAAATCAGAGTTGGAGTA
* *
3424413 TCCCCGATTATAGTAAATTGGTGTTTT-GAAAATAAAAC
66 TCCCCGATTATAGAAAATTAGTGTTTTAG-AAATAAAAC
*
3424451 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTCGAAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTCGAAAATAAAATCAGAGTTGGAGTA
* * * *
3424515 TCCTCGATTGTGGAAAATTAGTGTTTTAGGAATAAAAC
66 TCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAAC
* * *
3424553 CAGGGTTGGAGTACCCCCCGATTATGAAAAATTG
1 CGGGGTTGGAGTA-TCCCCGATTGTGAAAAATTG
3424587 AGAAACTTAA
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
102 66 0.55
103 54 0.45
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (103 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTCGAAAATAAAATCAGAGTTGGAGTA
TCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:3426911 original size:13 final size:13
Alignment explanation
Indices: 3426893--3426917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3426883 ATTGTAAAAT
3426893 GTATCGATACAAC
1 GTATCGATACAAC
3426906 GTATCGATACAA
1 GTATCGATACAA
3426918 TGAGCAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAC
Found at i:3426931 original size:20 final size:20
Alignment explanation
Indices: 3426901--3427007 Score: 72
Period size: 20 Copynumber: 5.8 Consensus size: 20
3426891 ATGTATCGAT
*
3426901 ACAACGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
3426921 GCAATGTATCG--ACAATGCA
1 ACAATGTATCGATACAATG-A
*
3426940 A-AATATATCGATAC-----
1 ACAATGTATCGATACAATGA
*
3426954 A--ATGTATCGATACATTGA
1 ACAATGTATCGATACAATGA
* *
3426972 ATAATGTATCGATACATTGA
1 ACAATGTATCGATACAATGA
*
3426992 ATAATGTATCGATACA
1 ACAATGTATCGATACA
3427008 TTTCCTTGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
13 11 0.15
14 1 0.01
18 15 0.21
19 1 0.01
20 44 0.61
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:3427008 original size:20 final size:20
Alignment explanation
Indices: 3426954--3427009 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
3426944 ATATCGATAC
3426954 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
3426974 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
3426994 AATGTATCGATACATT
1 AATGTATCGATACATT
3427010 TCCTTGGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:3427786 original size:40 final size:40
Alignment explanation
Indices: 3427741--3427832 Score: 184
Period size: 40 Copynumber: 2.3 Consensus size: 40
3427731 ATCCCACTTT
3427741 TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
1 TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
3427781 TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
1 TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
3427821 TTGAGGACAAAG
1 TTGAGGACAAAG
3427833 GAAGAGAAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (40 bp):
TTGAGGACAAAGAAAAAAAGAATGAAATAGGTCTTGCTCC
Found at i:3428024 original size:28 final size:29
Alignment explanation
Indices: 3427996--3428078 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 29
3427986 GGACTAAAAA
3427996 GTGTCACCAACTCGTGTGGGCTTTGAAAG
1 GTGTCACCAACTCGTGTGGGCTTTGAAAG
** * *
3428025 GTGT--CCTGCTC-TTTGAGG-ATTGAAAG
1 GTGTCACCAACTCGTGTG-GGCTTTGAAAG
*
3428051 GTGCCACCAACTCGTGTGGGCTTTGAAA
1 GTGTCACCAACTCGTGTGGGCTTTGAAA
3428079 AGAAAAGGCG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
26 13 0.32
27 7 0.17
28 7 0.17
29 13 0.32
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (29 bp):
GTGTCACCAACTCGTGTGGGCTTTGAAAG
Found at i:3428117 original size:61 final size:58
Alignment explanation
Indices: 3427973--3428459 Score: 511
Period size: 55 Copynumber: 8.4 Consensus size: 58
3427963 ATAAAGTGCA
* * * * *
3427973 TCCTACTCTTTGAGGACTAAAAAGTGTCACCAACTCGTGTGGGCTTT----GAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
* * *
3428028 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-AAAGGCG
* **
3428089 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGAA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-AAAGGCG
* *
3428150 TCCTGCTCTTTGAGGACTGGAAAATACCACCAACTTGTGTGGGCTTT----GAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
* * *
3428205 TCTTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-GAAAG-AAAGGCG
* *
3428266 TCTTGCTCTTTGAGGACCGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG--A--CG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
* *
3428321 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT----GAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
* * *
3428376 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAA-G-AAAGGCG
3428437 TCCTGCTCTTTGAGGACTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
3428460 GTGAAAGAAG
Statistics
Matches: 378, Mismatches: 28, Indels: 47
0.83 0.06 0.10
Matches are distributed among these distances:
51 1 0.00
53 1 0.00
54 3 0.01
55 180 0.48
56 1 0.00
57 1 0.00
60 8 0.02
61 179 0.47
62 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (58 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAGGCG
Found at i:3428399 original size:26 final size:26
Alignment explanation
Indices: 3428312--3428399 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
3428302 GTGTGGGCTT
*
3428312 TGAAAGACGTCCTGCTCTTTGAGGAC
1 TGAAAGGCGTCCTGCTCTTTGAGGAC
* ** * * *
3428338 TGAAAGGTG-CCACCAACTTATGTGGGC
1 TGAAAGGCGTCCTGC-TCTT-TGAGGAC
3428365 TTTGAAAGGCGTCCTGCTCTTTGAGGAC
1 --TGAAAGGCGTCCTGCTCTTTGAGGAC
3428393 TGAAAGG
1 TGAAAGG
3428400 TGCCACCAAC
Statistics
Matches: 44, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
25 3 0.07
26 17 0.39
27 5 0.11
28 5 0.11
29 11 0.25
30 3 0.07
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (26 bp):
TGAAAGGCGTCCTGCTCTTTGAGGAC
Found at i:3428449 original size:116 final size:112
Alignment explanation
Indices: 3427973--3428459 Score: 511
Period size: 116 Copynumber: 4.2 Consensus size: 112
3427963 ATAAAGTGCA
* * * * *
3427973 TCCTACTCTTTGAGGACTAAAAAGTGTCACCAACTCGTGTGGGCTTTG-AAAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTGCTCT
* * * *
3428037 TTGAGGATTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCG
65 TTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTG-AAAG-GAA--CG
**
3428089 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGAATCCT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG-----GCGTCCT
* *
3428154 GCTCTTTGAGGACTGGAAA-ATACCACCAACTTGTGTGGGCTTTGAAAGG--CA
60 GCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGAACG
* * *
3428205 TCTTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCGTCTT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-----GAAAAGGCGTCCT
* *
3428270 GCTCTTTGAGGACCGAAAAATGCCACCAACTTGTGTGGGCTTTGAAA-G-ACG
60 GCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGAACG
* *
3428321 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTG-AAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTGCTCT
* * *
3428385 TTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAAGGTG
65 TTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTGAAAGG--AA--CG
3428437 TCCTGCTCTTTGAGGACTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
3428460 GTGAAAGAAG
Statistics
Matches: 318, Mismatches: 31, Indels: 45
0.81 0.08 0.11
Matches are distributed among these distances:
110 53 0.17
111 2 0.01
114 1 0.00
115 9 0.03
116 191 0.60
117 8 0.03
121 10 0.03
122 40 0.13
123 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (112 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTGCTCTT
TGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGAACG
Found at i:3429433 original size:1 final size:1
Alignment explanation
Indices: 3429429--3429492 Score: 65
Period size: 1 Copynumber: 64.0 Consensus size: 1
3429419 CTTTTCTCTC
* * * * * * *
3429429 TTTTTTCTTTGTTTTGTTTTTTTTTATTTTTTTTATTTTTTTTGTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3429493 GAAAAGAATG
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:3429461 original size:28 final size:28
Alignment explanation
Indices: 3429429--3429490 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
3429419 CTTTTCTCTC
*
3429429 TTTTTTCTTTGTTTTGTTTTTTTTTATT
1 TTTTTTATTTGTTTTGTTTTTTTTTATT
* *
3429457 TTTTTTATTTTTTTTGTTTTTTTTTGTT
1 TTTTTTATTTGTTTTGTTTTTTTTTATT
3429485 TTTTTT
1 TTTTTT
3429491 TTGAAAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (28 bp):
TTTTTTATTTGTTTTGTTTTTTTTTATT
Found at i:3429491 original size:10 final size:10
Alignment explanation
Indices: 3429440--3429491 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
3429430 TTTTTCTTTG
3429440 TTTTGTTTTT
1 TTTTGTTTTT
*
3429450 TTTT-ATTTT
1 TTTTGTTTTT
*
3429459 TTTT-ATTTT
1 TTTTGTTTTT
3429468 TTTTGTTTTT
1 TTTTGTTTTT
3429478 TTTTGTTTTT
1 TTTTGTTTTT
3429488 TTTT
1 TTTT
3429492 TGAAAAGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
9 17 0.44
10 22 0.56
ACGTcount: A:0.04, C:0.00, G:0.06, T:0.90
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:3437257 original size:20 final size:20
Alignment explanation
Indices: 3437203--3437258 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
3437193 AAAATGCCTG
* *
3437203 AATGTATCGATACAATGAGC
1 AATGTATCGATACATTGAAC
*
3437223 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAC
3437243 AATGTATCGATACATT
1 AATGTATCGATACATT
3437259 TCCTTGGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAAC
Found at i:3437395 original size:21 final size:20
Alignment explanation
Indices: 3437365--3437403 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3437355 GTTGGGACCT
3437365 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
*
3437386 TGTATTGATACATTTAGA
1 TGTATCGATACATTTAGA
3437404 CAAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:3438185 original size:25 final size:26
Alignment explanation
Indices: 3438153--3438223 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
3438143 GCTTTAAATA
*
3438153 TAAAAAAATAAAAATAAATTTTTATT
1 TAAAAAAATAAAAATCAATTTTTATT
**
3438179 TCCAAAAATAAAAATCAA-TTTTATT
1 TAAAAAAATAAAAATCAATTTTTATT
*
3438204 TAAAACAATAAAAATCAATT
1 TAAAAAAATAAAAATCAATT
3438224 AGGAGAGGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 22 0.58
26 16 0.42
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAAAAAATAAAAATCAATTTTTATT
Found at i:3439999 original size:42 final size:42
Alignment explanation
Indices: 3439893--3440001 Score: 155
Period size: 42 Copynumber: 2.6 Consensus size: 42
3439883 AAGAGAAAGA
* * * *
3439893 AGAGATAGGAGGGATGATAGAAAGAGAGATAGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGGAGGAAAGATAGGAGAGATAAT
*
3439935 AGAGATAGAAGGGATGATAGGAGGAAAGATAGGAGAGATAAT
1 AGAGATAGGAGGGATGATAGGAGGAAAGATAGGAGAGATAAT
* *
3439977 AGAGAGAGGAGGGATGACAGGAGGA
1 AGAGATAGGAGGGATGATAGGAGGA
3440002 GGAGAGAAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.45, C:0.01, G:0.42, T:0.12
Consensus pattern (42 bp):
AGAGATAGGAGGGATGATAGGAGGAAAGATAGGAGAGATAAT
Found at i:3450889 original size:46 final size:46
Alignment explanation
Indices: 3450822--3450914 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
3450812 TATTCAAGTG
*
3450822 AACAAGTCCATTCCATGCTAAAAGAGATAACTATAAAACAAAGTTC
1 AACAAGCCCATTCCATGCTAAAAGAGATAACTATAAAACAAAGTTC
3450868 AACAAGCCCATTCCATGCTAAAAGAGATAACTATAAAACAAAGTTC
1 AACAAGCCCATTCCATGCTAAAAGAGATAACTATAAAACAAAGTTC
3450914 A
1 A
3450915 GGTAAAGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.20
Consensus pattern (46 bp):
AACAAGCCCATTCCATGCTAAAAGAGATAACTATAAAACAAAGTTC
Found at i:3451632 original size:114 final size:114
Alignment explanation
Indices: 3451447--3451659 Score: 340
Period size: 114 Copynumber: 1.9 Consensus size: 114
3451437 ATAAATTTTT
** * *
3451447 TATTAGTGTTTAAATTATTTGATATTAATTTAATTAATAAAATTATTAAAATTTTTAAAAAATAA
1 TATTAGTAATTAAATTATATGATATTAATTTAATTAATAAAATTATTAAAATTTTAAAAAAATAA
*
3451512 AATTATGATGCTTTAATATTTTAATTTATTTATATATATATATATATGA
66 AATTATGATGCTTTAATATTTTAATTTATATATATATATATATATATGA
3451561 TATTAGTAATTAAA-TATATGATATTAATTTAATTAAT-AAATTATTAAAATTTTAAATAAAAGT
1 TATTAGTAATTAAATTATATGATATTAATTTAATTAATAAAATTATTAAAATTTTAAA-AAAA-T
*
3451624 AAAATTATGATGTTTTAATATTTTAATTTATATATA
64 AAAATTATGATGCTTTAATATTTTAATTTATATATA
3451660 CATGTTTAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
112 18 0.20
113 26 0.29
114 47 0.52
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (114 bp):
TATTAGTAATTAAATTATATGATATTAATTTAATTAATAAAATTATTAAAATTTTAAAAAAATAA
AATTATGATGCTTTAATATTTTAATTTATATATATATATATATATATGA
Found at i:3451646 original size:104 final size:104
Alignment explanation
Indices: 3451447--3451659 Score: 245
Period size: 113 Copynumber: 2.0 Consensus size: 104
3451437 ATAAATTTTT
** * *
3451447 TATTAGTGTTTAAATTATTTGATATTAATTTAATTAATAAAATTATTAAAATTTTTAAAAAATAA
1 TATTAGTAATTAAATTATATGATATTAATTTAATTAATAAAATTATTAAAATTTTAAAAAAATAA
3451512 AATTATGATGCTTTAATATTTTAATTTATTTATATATATATATATATGA
66 AATTATGATG------T-TTTTAA-TTATTT-TA-ATATATATATATGA
3451561 TATTAGTAATTAAA-TATATGATATTAATTTAATTAAT-AAATTATTAAAATTTTAAATAAAAGT
1 TATTAGTAATTAAATTATATGATATTAATTTAATTAATAAAATTATTAAAATTTTAAA-AAAA-T
*
3451624 AAAATTATGATG-TTTTAA-TATTTTAATTTATATATA
64 AAAATTATGATGTTTTTAATTATTTTAATATATATATA
3451660 CATGTTTAAA
Statistics
Matches: 92, Mismatches: 5, Indels: 16
0.81 0.04 0.14
Matches are distributed among these distances:
102 10 0.11
103 2 0.02
104 5 0.05
106 6 0.07
112 18 0.20
113 26 0.28
114 25 0.27
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (104 bp):
TATTAGTAATTAAATTATATGATATTAATTTAATTAATAAAATTATTAAAATTTTAAAAAAATAA
AATTATGATGTTTTTAATTATTTTAATATATATATATGA
Found at i:3456289 original size:21 final size:21
Alignment explanation
Indices: 3456271--3456314 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3456261 GGATGAAATG
3456271 ATGCATTGGTTGGAGGAAAAA
1 ATGCATTGGTTGGAGGAAAAA
** *
3456292 ATGCATTTTTTGGATGAAAAA
1 ATGCATTGGTTGGAGGAAAAA
3456313 AT
1 AT
3456315 ACAACTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (21 bp):
ATGCATTGGTTGGAGGAAAAA
Found at i:3456323 original size:21 final size:21
Alignment explanation
Indices: 3456280--3456323 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3456270 GATGCATTGG
* **
3456280 TTGGAGGAAAAAATGCATTTT
1 TTGGAGGAAAAAATACAACTT
*
3456301 TTGGATGAAAAAATACAACTT
1 TTGGAGGAAAAAATACAACTT
3456322 TT
1 TT
3456324 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (21 bp):
TTGGAGGAAAAAATACAACTT
Found at i:3459661 original size:21 final size:22
Alignment explanation
Indices: 3459607--3459667 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
3459597 CTTTTATGAA
3459607 AATGTA-TCTTTGGATGAAATG
1 AATGTATTCTTTGGATGAAATG
* **
3459628 -ATGCATTGGTTGGATGAAA-G
1 AATGTATTCTTTGGATGAAATG
*
3459648 AATGTATTTTTTGGATGAAA
1 AATGTATTCTTTGGATGAAA
3459668 AAATACAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (22 bp):
AATGTATTCTTTGGATGAAATG
Found at i:3468332 original size:20 final size:20
Alignment explanation
Indices: 3468307--3468345 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3468297 TTATGTGAGC
3468307 AAGTATCTTGCAACTTCTAT
1 AAGTATCTTGCAACTTCTAT
*
3468327 AAGTATGTTGCAACTTCTA
1 AAGTATCTTGCAACTTCTA
3468346 ATATATTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (20 bp):
AAGTATCTTGCAACTTCTAT
Found at i:3485350 original size:28 final size:28
Alignment explanation
Indices: 3485297--3485360 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
3485287 TCTAAACTTT
* * *
3485297 TTAAAATTACAAATTAATCTTTAAATA-A
1 TTAAAA-TACAAATTAAGCATCAAATATA
3485325 TTAAAATACAAAATTAAGCATCAAATATA
1 TTAAAATAC-AAATTAAGCATCAAATATA
*
3485354 TCAAAAT
1 TTAAAAT
3485361 CAACACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 20 0.67
29 7 0.23
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (28 bp):
TTAAAATACAAATTAAGCATCAAATATA
Found at i:3493592 original size:2 final size:2
Alignment explanation
Indices: 3493585--3493612 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3493575 AAAGAAATAC
3493585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3493613 TTGGCATTGG
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3494841 original size:13 final size:14
Alignment explanation
Indices: 3494823--3494852 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3494813 GGATTGACTG
3494823 AATTAAAAATT-AA
1 AATTAAAAATTGAA
3494836 AATTAAAAATTGAA
1 AATTAAAAATTGAA
3494850 AAT
1 AAT
3494853 AATTATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AATTAAAAATTGAA
Found at i:3500602 original size:50 final size:50
Alignment explanation
Indices: 3500542--3500800 Score: 439
Period size: 50 Copynumber: 5.2 Consensus size: 50
3500532 TATACTTAGA
3500542 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
3500592 GTCAATAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
3500642 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
3500692 GTCAACAATTATGGCCACCTC-CTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATC
* * * * *
3500742 GTTAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
3500792 GTCAACAAT
1 GTCAACAAT
3500801 GGTAACAACT
Statistics
Matches: 200, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
49 1 0.00
50 198 0.99
51 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (50 bp):
GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:3501259 original size:8 final size:8
Alignment explanation
Indices: 3501221--3501253 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
3501211 ACTTATTTTT
3501221 AATAAAAA
1 AATAAAAA
3501229 AATAAAAA
1 AATAAAAA
3501237 AATAAAAA
1 AATAAAAA
3501245 AATAAAAA
1 AATAAAAA
3501253 A
1 A
3501254 GAAAAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:3505650 original size:20 final size:22
Alignment explanation
Indices: 3505613--3505652 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3505603 TTCAACCCTT
3505613 ATATTGTTTCCAACATAAATCC
1 ATATTGTTTCCAACATAAATCC
3505635 ATATTG-TTCC-ACATAAAT
1 ATATTGTTTCCAACATAAAT
3505653 TTTGGTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (22 bp):
ATATTGTTTCCAACATAAATCC
Found at i:3505953 original size:22 final size:22
Alignment explanation
Indices: 3505903--3505954 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
3505893 AATAAGAGCA
3505903 TTTTTTTTCTTTCTTGAAAGCT
1 TTTTTTTTCTTTCTTGAAAGCT
* *
3505925 ATGTTTTTAC-TTCTT-AAATGCT
1 -TTTTTTTTCTTTCTTGAAA-GCT
3505947 TTTTTTTT
1 TTTTTTTT
3505955 TTGTATTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 9 0.38
22 8 0.33
23 7 0.29
ACGTcount: A:0.15, C:0.12, G:0.08, T:0.65
Consensus pattern (22 bp):
TTTTTTTTCTTTCTTGAAAGCT
Found at i:3511764 original size:3 final size:3
Alignment explanation
Indices: 3511756--3511782 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3511746 CCACTTCAAG
3511756 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
3511783 GTTTGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:3515993 original size:39 final size:39
Alignment explanation
Indices: 3515950--3516063 Score: 140
Period size: 38 Copynumber: 2.9 Consensus size: 39
3515940 CTTTTAATGC
*
3515950 ATATTTGGTTTCATATGAATTTGATTAATCTTTTGATAA
1 ATATTTGGTTTCATATGAATTTGATTGATCTTTTGATAA
* ** **
3515989 ATATTTGGTTTTATATGAATTTGATTGAT-TTTTTTTGT
1 ATATTTGGTTTCATATGAATTTGATTGATCTTTTGATAA
* * *
3516027 ACATTTGGTTTCATATAAATTTGATTGATCTTGTGAT
1 ATATTTGGTTTCATATGAATTTGATTGATCTTTTGAT
3516064 CTTTTGATAT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
38 31 0.50
39 31 0.50
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.54
Consensus pattern (39 bp):
ATATTTGGTTTCATATGAATTTGATTGATCTTTTGATAA
Found at i:3516268 original size:58 final size:58
Alignment explanation
Indices: 3516193--3516302 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
3516183 TACTTTGAAT
* ** * *
3516193 AATGTATCAATACAATGTATCAATGCTTTGAATAATTTA-CTGATACATTTTCTTTCAA
1 AATGTATCAATAAAATGTATCAATAATTTAAATAATGTATC-GATACATTTTCTTTCAA
*
3516251 AATGTATCAATAAAATGTATCTATAATTTAAATAATGTATCGATACATTTTC
1 AATGTATCAATAAAATGTATCAATAATTTAAATAATGTATCGATACATTTTC
3516303 AAAATATATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 44 0.98
59 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (58 bp):
AATGTATCAATAAAATGTATCAATAATTTAAATAATGTATCGATACATTTTCTTTCAA
Found at i:3517345 original size:148 final size:146
Alignment explanation
Indices: 3517061--3517354 Score: 437
Period size: 148 Copynumber: 2.0 Consensus size: 146
3517051 GCTTCAATAC
3517061 ATTTCTAACTTAGTTATTTTTCTTGAATCAAATTGAAAATATTTTAAAAAATATTAAATTAATTT
1 ATTTCTAACTTAGTTATTTTTCTTGAATCAAATTGAAAATATTTTAAAAAATATTAAATTAATTT
* * * * * *
3517126 TCTTACCTTTTATTTTCTCAAAAATAGCGACCCAAATGAATATTTATACTTAGAATGTTTTTAAG
66 TCTTACCTTATATTTTCTCAAAAATAACGACCCAAATAAATATTTATACTCAAAATATTTTTAAG
3517191 ACAAGTTTAAGTGATT
131 ACAAGTTTAAGTGATT
* *
3517207 ATTTCTAAACTTAGTATTTTTTTCTTGAATCAAATTGAAAATATTTTGAAAAATATTAAATTAAT
1 ATTTCT-AACTTAGT-TATTTTTCTTGAATCAAATTGAAAATATTTTAAAAAATATTAAATTAAT
* ***
3517272 TTTCTTACCTCTAT-TTTTCTCAAAAATAATGTTTCAAATAAATATTTATACTCAAAATATTTTT
64 TTTCTTACCT-TATATTTTCTCAAAAATAACGACCCAAATAAATATTTATACTCAAAATATTTTT
*
3517336 GAGACAAGTTTAAGTGATT
128 AAGACAAGTTTAAGTGATT
3517355 TCAAGCTAAG
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
146 6 0.05
147 8 0.06
148 116 0.88
149 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (146 bp):
ATTTCTAACTTAGTTATTTTTCTTGAATCAAATTGAAAATATTTTAAAAAATATTAAATTAATTT
TCTTACCTTATATTTTCTCAAAAATAACGACCCAAATAAATATTTATACTCAAAATATTTTTAAG
ACAAGTTTAAGTGATT
Found at i:3517538 original size:20 final size:21
Alignment explanation
Indices: 3517513--3517561 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
3517503 AAATCCTCAT
3517513 TTGTATCGATACATATC-AAA
1 TTGTATCGATACATATCTAAA
3517533 TTGTATCGATACATATCTAAA
1 TTGTATCGATACATATCTAAA
3517554 -TGTATCGA
1 TTGTATCGA
3517562 AACTTTGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
TTGTATCGATACATATCTAAA
Found at i:3518140 original size:18 final size:18
Alignment explanation
Indices: 3518117--3518153 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3518107 AGCTACCTAT
3518117 TACATTGGACTAACTTGG
1 TACATTGGACTAACTTGG
3518135 TACATTGGACTAACTTGG
1 TACATTGGACTAACTTGG
3518153 T
1 T
3518154 TGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (18 bp):
TACATTGGACTAACTTGG
Found at i:3520533 original size:20 final size:20
Alignment explanation
Indices: 3520508--3520561 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3520498 ATTTGAAGCA
* *
3520508 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATGTACC
*
3520528 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTACC
3520548 ATGTATCGATACAA
1 ATGTATCGATACAA
3520562 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:3520615 original size:20 final size:20
Alignment explanation
Indices: 3520590--3520644 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3520580 TTGCCAGTTT
***
3520590 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTAAA
*
3520610 CATGTATTGATACAA-TAAA
1 CATGTATCGATACAATTAAA
3520629 CATGTATCGATACAAT
1 CATGTATCGATACAAT
3520645 GTATCGATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:3523140 original size:13 final size:13
Alignment explanation
Indices: 3523122--3523148 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3523112 ATAGTAACCC
3523122 ATGTATCGATACA
1 ATGTATCGATACA
3523135 ATGTATCGATACA
1 ATGTATCGATACA
3523148 A
1 A
3523149 AGAACATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3529548 original size:33 final size:33
Alignment explanation
Indices: 3529511--3529575 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
3529501 TTTGAAGCAA
* **
3529511 TGTATCGATACAATTTATTATGTATCGATACAT
1 TGTATCGATACAATGTACCATGTATCGATACAT
*
3529544 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
3529576 AACAGTGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:3529549 original size:13 final size:13
Alignment explanation
Indices: 3529531--3529555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3529521 CAATTTATTA
3529531 TGTATCGATACAT
1 TGTATCGATACAT
3529544 TGTATCGATACA
1 TGTATCGATACA
3529556 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3529629 original size:20 final size:20
Alignment explanation
Indices: 3529604--3529658 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
3529594 ACTGCAGTTT
3529604 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGTG
*
3529624 CATGTATTGATACAATTGTG
1 CATGTATCGATACAATTGTG
3529644 CATGTATCGATACAA
1 CATGTATCGATACAA
3529659 AGCATAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACAATTGTG
Found at i:3532411 original size:30 final size:31
Alignment explanation
Indices: 3532372--3532448 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
3532362 TTAATTGAAC
3532372 TTATTTAATTAAGTCCTTCAAATTTAA-CTT
1 TTATTTAATTAAGTCCTTCAAATTTAATCTT
* * *
3532402 TTTTTTAATTAAGTCTTTTAAATTTAATCTT
1 TTATTTAATTAAGTCCTTCAAATTTAATCTT
*
3532433 TTATTCAATTAAGTCC
1 TTATTTAATTAAGTCC
3532449 AACTTTATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 24 0.60
31 16 0.40
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (31 bp):
TTATTTAATTAAGTCCTTCAAATTTAATCTT
Found at i:3537626 original size:2 final size:2
Alignment explanation
Indices: 3537619--3537661 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3537609 GCAACTTTGC
3537619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3537661 A
1 A
3537662 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3537666 original size:2 final size:2
Alignment explanation
Indices: 3537661--3537710 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3537651 ATATATATAT
3537661 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3537703 AG AG AG AG
1 AG AG AG AG
3537711 CTTATAATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3537849 original size:2 final size:2
Alignment explanation
Indices: 3537842--3537875 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3537832 TATGGAAAAC
3537842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3537876 GATTAATGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3538803 original size:21 final size:24
Alignment explanation
Indices: 3538777--3538821 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
3538767 TTTTCATGAT
3538777 TATTT-AAATAA-AATTT-TTTAA
1 TATTTAAAATAATAATTTATTTAA
3538798 TATTTAAAATAATAATTTATTTAA
1 TATTTAAAATAATAATTTATTTAA
3538822 ATCAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 6 0.29
23 5 0.24
24 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTTAAAATAATAATTTATTTAA
Found at i:3538834 original size:20 final size:22
Alignment explanation
Indices: 3538811--3538857 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
3538801 TTAAAATAAT
*
3538811 AATTTATT-TAAATCAATT-TA
1 AATTTATTAAAAATCAATTATA
*
3538831 AA-TTATTAAAAATCTATTATA
1 AATTTATTAAAAATCAATTATA
3538852 AATTTA
1 AATTTA
3538858 ATTCAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 4 0.18
22 3 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTATTAAAAATCAATTATA
Found at i:3538897 original size:21 final size:20
Alignment explanation
Indices: 3538873--3538913 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3538863 ATTTAGATCA
*
3538873 AATTTATTAAATAAAATAAAT
1 AATTTAATAAAT-AAATAAAT
*
3538894 AATTTAATATATAAATAAAT
1 AATTTAATAAATAAATAAAT
3538914 TTATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTAATAAATAAATAAAT
Found at i:3538919 original size:21 final size:19
Alignment explanation
Indices: 3538872--3538922 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
3538862 AATTTAGATC
3538872 AAATTTA-TTAAATAAAAT
1 AAATTTATTTAAATAAAAT
*
3538890 AAA-TAATTTAATATATAAAT
1 AAATTTATTTAA-ATA-AAAT
3538910 AAATTTATTTAAA
1 AAATTTATTTAAA
3538923 ATAGATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.07
18 7 0.26
19 3 0.11
20 8 0.30
21 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTTATTTAAATAAAAT
Found at i:3544504 original size:21 final size:21
Alignment explanation
Indices: 3544480--3544523 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3544470 TTAAATATAT
3544480 TATTTTAAAAATAAAATAAAA
1 TATTTTAAAAATAAAATAAAA
*
3544501 TATTTTTAAAATAAAATAAAA
1 TATTTTAAAAATAAAATAAAA
3544522 TA
1 TA
3544524 ATTACTAACA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TATTTTAAAAATAAAATAAAA
Found at i:3545735 original size:16 final size:16
Alignment explanation
Indices: 3545714--3545745 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3545704 AGTTTTACAA
3545714 AAAATTTTTCAATTAT
1 AAAATTTTTCAATTAT
*
3545730 AAAATTTTTTAATTAT
1 AAAATTTTTCAATTAT
3545746 TATCAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTTTTCAATTAT
Found at i:3546837 original size:26 final size:26
Alignment explanation
Indices: 3546780--3546837 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
3546770 AAAAACAGAT
* *
3546780 TAAAAATTATTTAATTATTATTTTTT
1 TAAAAATTATTTAATTATTATATTTA
3546806 TAAAAATCTATTTAATGTATTA-ATTTA
1 TAAAAAT-TATTTAAT-TATTATATTTA
3546833 TAAAA
1 TAAAA
3546838 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.25
27 16 0.57
28 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TAAAAATTATTTAATTATTATATTTA
Found at i:3547823 original size:20 final size:20
Alignment explanation
Indices: 3547784--3547830 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3547774 AGTCTCAATA
3547784 ATTTAAAAATTATCAATTAT
1 ATTTAAAAATTATCAATTAT
* *
3547804 TTTTAAAAATTTATC-TTTAT
1 ATTTAAAAA-TTATCAATTAT
3547824 ATTTAAA
1 ATTTAAA
3547831 TTTATAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAAAATTATCAATTAT
Found at i:3548002 original size:22 final size:21
Alignment explanation
Indices: 3547959--3548002 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
3547949 ATAATTTTTA
*
3547959 TTTTATTTTAATTTTTTATCT
1 TTTTATTTTAATTTTCTATCT
3547980 TTTTAATTTT-ATTTTCTAGTCT
1 TTTT-ATTTTAATTTTCTA-TCT
3548002 T
1 T
3548003 ATTTCTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTTTAATTTTCTATCT
Found at i:3548760 original size:30 final size:29
Alignment explanation
Indices: 3548694--3548781 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
3548684 TTTATTATTT
* *
3548694 AAATTTAAATTAAATAATATT-ATATATTAA
1 AAATTTAAATTTAATAA-ATTAAT-TTTTAA
*
3548724 ATATTTAAATTTAATAAATTAATTTTTAAA
1 AAATTTAAATTTAATAAATTAATTTTT-AA
*
3548754 AAATTTAAATCTAATAAAAATTAATTTT
1 AAATTTAAATTTAAT--AAATTAATTTT
3548782 AAATTCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.12
30 32 0.65
32 11 0.22
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
AAATTTAAATTTAATAAATTAATTTTTAA
Found at i:3555067 original size:7 final size:7
Alignment explanation
Indices: 3555057--3555099 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
3555047 AATATTTAAT
3555057 AATTTTA
1 AATTTTA
3555064 AATTTTA
1 AATTTTA
3555071 AATTTTA
1 AATTTTA
3555078 ATATTTATA
1 A-ATTT-TA
*
3555087 ATTTTTTA
1 A-ATTTTA
3555095 AATTT
1 AATTT
3555100 AAGCTTAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 18 0.56
8 7 0.22
9 7 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
AATTTTA
Found at i:3555077 original size:23 final size:24
Alignment explanation
Indices: 3555051--3555099 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3555041 AAAAATAATA
3555051 TTTAATAATTT-TAA-ATTTTAAAT
1 TTTAAT-ATTTATAATATTTTAAAT
*
3555074 TTTAATATTTATAATTTTTTAAAT
1 TTTAATATTTATAATATTTTAAAT
3555098 TT
1 TT
3555100 AAGCTTAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 9 0.39
24 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTAATATTTATAATATTTTAAAT
Found at i:3555632 original size:3 final size:3
Alignment explanation
Indices: 3555624--3555658 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3555614 AATAGATGAG
3555624 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3555659 CATCCTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3556776 original size:2 final size:2
Alignment explanation
Indices: 3556769--3556804 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3556759 GTTAGAAGTA
3556769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3556805 GGCATTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3559318 original size:20 final size:20
Alignment explanation
Indices: 3559280--3559318 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3559270 TATAATATTG
*
3559280 ATAATAAATAAGTATTAAAC
1 ATAATAAATAAGTAATAAAC
* *
3559300 ATAATAAATTATTAATAAA
1 ATAATAAATAAGTAATAAA
3559319 TATATGTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
ATAATAAATAAGTAATAAAC
Found at i:3560540 original size:16 final size:15
Alignment explanation
Indices: 3560515--3560544 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3560505 TTATTTTAAT
3560515 ATTAAATAAATATTA
1 ATTAAATAAATATTA
3560530 ATTATAATAAATATT
1 ATTA-AATAAATATT
3560545 TAGTATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTAAATAAATATTA
Found at i:3560551 original size:16 final size:16
Alignment explanation
Indices: 3560519--3560552 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3560509 TTTAATATTA
*
3560519 AATAAATATTAATTAT
1 AATAAATATTAAGTAT
*
3560535 AATAAATATTTAGTAT
1 AATAAATATTAAGTAT
3560551 AA
1 AA
3560553 ATATAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAAATATTAAGTAT
Found at i:3560596 original size:39 final size:39
Alignment explanation
Indices: 3560499--3560596 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 39
3560489 TTAAAATTTA
*
3560499 AATATATTATTTTAATAT-TAAATAAATATTAATTATAAT
1 AATATAAT-TTTTAATATATAAATAAATATTAATTATAAT
*
3560538 AA-AT-ATTTAGTATAA-ATATAAATATATATTTAATT-TAAT
1 AATATAATTT--T-TAATATATAAATAAATA-TTAATTATAAT
3560577 AATATAATTTTTAATATATA
1 AATATAATTTTTAATATATA
3560597 GTAAAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
36 2 0.04
37 1 0.02
38 8 0.16
39 26 0.53
40 8 0.16
41 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (39 bp):
AATATAATTTTTAATATATAAATAAATATTAATTATAAT
Found at i:3562877 original size:22 final size:22
Alignment explanation
Indices: 3562852--3562894 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3562842 TTATTTTTTT
3562852 AAAAAATTACAAAT-TAAAAATA
1 AAAAAATT-CAAATATAAAAATA
*
3562874 AAAAAATTTAAATATAAAAAT
1 AAAAAATTCAAATATAAAAAT
3562895 TTAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAATTCAAATATAAAAATA
Found at i:3562886 original size:14 final size:14
Alignment explanation
Indices: 3562869--3562900 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3562859 TACAAATTAA
3562869 AAATAAAAAAATTT
1 AAATAAAAAAATTT
*
3562883 AAATATAAAAATTT
1 AAATAAAAAAATTT
3562897 AAAT
1 AAAT
3562901 TTTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATAAAAAAATTT
Found at i:3562958 original size:22 final size:22
Alignment explanation
Indices: 3562933--3562976 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3562923 AAATATTTTA
3562933 TTAACTGT-ATTAAATTTTAAAT
1 TTAACTGTCA-TAAATTTTAAAT
* *
3562955 TTAATTTTCATAAATTTTAAAT
1 TTAACTGTCATAAATTTTAAAT
3562977 CACAATGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAACTGTCATAAATTTTAAAT
Found at i:3566575 original size:18 final size:18
Alignment explanation
Indices: 3566554--3566591 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3566544 TTCCTTTTAC
3566554 ATTAAACATATTTTTT-TT
1 ATTAAACAT-TTTTTTCTT
*
3566572 ATTAAAGATTTTTTTCTT
1 ATTAAACATTTTTTTCTT
3566590 AT
1 AT
3566592 GTTTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTAAACATTTTTTTCTT
Found at i:3566741 original size:24 final size:24
Alignment explanation
Indices: 3566693--3566746 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
3566683 TTATTAAACA
3566693 TATTTATTAATTATTTAAGTATTT
1 TATTTATTAATTATTTAAGTATTT
* *
3566717 T-TTTATTGAATTATTTAATTGTTT
1 TATTTATT-AATTATTTAAGTATTT
3566741 TATTTA
1 TATTTA
3566747 GTTTGCTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 6 0.23
24 16 0.62
25 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TATTTATTAATTATTTAAGTATTT
Found at i:3572787 original size:16 final size:16
Alignment explanation
Indices: 3572766--3572799 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3572756 ACACACAAGT
3572766 GAATTTGGATTTGAAA
1 GAATTTGGATTTGAAA
3572782 GAATTTGGATTTGAAA
1 GAATTTGGATTTGAAA
3572798 GA
1 GA
3572800 TTGCAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (16 bp):
GAATTTGGATTTGAAA
Found at i:3574517 original size:15 final size:15
Alignment explanation
Indices: 3574497--3574528 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3574487 TTTCACATAT
3574497 TTTTCATTTCATGCA
1 TTTTCATTTCATGCA
3574512 TTTTCATTTCATGCA
1 TTTTCATTTCATGCA
3574527 TT
1 TT
3574529 CACGTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTTCATTTCATGCA
Found at i:3574591 original size:5 final size:5
Alignment explanation
Indices: 3574578--3574655 Score: 102
Period size: 5 Copynumber: 15.6 Consensus size: 5
3574568 ATTTCAAAAA
* * ** *
3574578 CATTT CATTG CATTA CATTT CATTT CATTT CATTT CATGG CATTT CATTG
1 CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT
*
3574628 CATTT CATTT CATTT CATTT TATTT CAT
1 CATTT CATTT CATTT CATTT CATTT CAT
3574656 GCATGAAAGT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 62 1.00
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (5 bp):
CATTT
Found at i:3574875 original size:116 final size:116
Alignment explanation
Indices: 3574697--3575050 Score: 604
Period size: 116 Copynumber: 3.1 Consensus size: 116
3574687 AACCTTTCAT
* *
3574697 CAACGACAAAGTAAGAAAATGATAATAAAAAAAAAAATAAAAGAAGCATCATGAGGGACAAAGAC
1 CAACGGCAAAGTAAGAAAATGATAAT-AAAAAAAAAACAAAAGAAGCATCATGAGGGACAAAGAC
*
3574762 AAATGTTGCAACACATGGGTGATGGAAAAACAACAAAGCAACATGAAAAAAG
65 AAATGCTGCAACACATGGGTGATGGAAAAACAACAAAGCAACATGAAAAAAG
3574814 CAACGGCAAAGTAAGAAAATGATAATAAAAAAAAAACAAAAGAAGCATCATGAGGGACAAAGACA
1 CAACGGCAAAGTAAGAAAATGATAATAAAAAAAAAACAAAAGAAGCATCATGAGGGACAAAGACA
3574879 AATGCTGCAACACATGGGTGATGGAAAAACAACAAAGCAACATGAAAAAAG
66 AATGCTGCAACACATGGGTGATGGAAAAACAACAAAGCAACATGAAAAAAG
*
3574930 CAACGGCAAAGTAAGAAAATGATAAT--AAAAAAAACAAAAGAAGCATCATGAGGGACAAAGGCA
1 CAACGGCAAAGTAAGAAAATGATAATAAAAAAAAAACAAAAGAAGCATCATGAGGGACAAAGACA
* * * *
3574993 AATGCTACAACACATGGGTGATGGAAAAACAGCAAAGCAACAAGTAAAAAG
66 AATGCTGCAACACATGGGTGATGGAAAAACAACAAAGCAACATGAAAAAAG
*
3575044 AAACGGC
1 CAACGGC
3575051 TACAAAAGGA
Statistics
Matches: 228, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
114 89 0.39
116 114 0.50
117 25 0.11
ACGTcount: A:0.56, C:0.14, G:0.20, T:0.11
Consensus pattern (116 bp):
CAACGGCAAAGTAAGAAAATGATAATAAAAAAAAAACAAAAGAAGCATCATGAGGGACAAAGACA
AATGCTGCAACACATGGGTGATGGAAAAACAACAAAGCAACATGAAAAAAG
Found at i:3575031 original size:57 final size:57
Alignment explanation
Indices: 3574740--3575031 Score: 154
Period size: 57 Copynumber: 5.1 Consensus size: 57
3574730 AAAATAAAAG
* * *
3574740 AAGCATCATGAGGGACAAAGACAAATGTTGCAACACATGGGTGATGGAAAAACAACA
1 AAGCATCATGAGGGACAAAGGCAAATGCTACAACACATGGGTGATGGAAAAACAACA
* *** * * * * ** *
3574797 AAGCAACATGAAAAAAGCAACGGCAAA-G-TA-AGA-AAAT-GATAATAAAAAAAAAACAAAA
1 AAGCATCATG-AGGGA-CAAAGGCAAATGCTACA-ACACATGGGTGAT---GGAAAAACAACA
* *
3574855 GAAGCATCATGAGGGACAAAGACAAATGCTGCAACACATGGGTGATGGAAAAACAACA
1 -AAGCATCATGAGGGACAAAGGCAAATGCTACAACACATGGGTGATGGAAAAACAACA
* *** * * * * ** *
3574913 AAGCAACATGAAAAAAGCAACGGCAAA-G-TA-AGA-AAAT-GATAATAAAAAAAACAAAA
1 AAGCATCATG-AGGGA-CAAAGGCAAATGCTACA-ACACATGGGTGAT-GGAAAAACAACA
*
3574969 GAAGCATCATGAGGGACAAAGGCAAATGCTACAACACATGGGTGATGGAAAAACAGCA
1 -AAGCATCATGAGGGACAAAGGCAAATGCTACAACACATGGGTGATGGAAAAACAACA
3575027 AAGCA
1 AAGCA
3575032 ACAAGTAAAA
Statistics
Matches: 162, Mismatches: 51, Indels: 44
0.63 0.20 0.17
Matches are distributed among these distances:
55 17 0.10
56 20 0.12
57 47 0.29
58 39 0.24
59 31 0.19
60 4 0.02
61 4 0.02
ACGTcount: A:0.53, C:0.14, G:0.21, T:0.11
Consensus pattern (57 bp):
AAGCATCATGAGGGACAAAGGCAAATGCTACAACACATGGGTGATGGAAAAACAACA
Found at i:3576029 original size:16 final size:15
Alignment explanation
Indices: 3575998--3576038 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
3575988 AAATTAGAAT
3575998 TAAAAAATAAAAAATAA
1 TAAAAAAT--AAAATAA
3576015 TAACAAAATAAAATAA
1 TAA-AAAATAAAATAA
3576031 TAAAAAAT
1 TAAAAAAT
3576039 TCTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 3 0.13
18 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAAAAATAAAATAA
Found at i:3580323 original size:22 final size:19
Alignment explanation
Indices: 3580293--3580341 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
3580283 TTAATGGCAT
3580293 TCATATTCATGACATTCATTCA
1 TCATATTCAT-A-A-TCATTCA
*
3580315 TCATTTTCATAATCATTCA
1 TCATATTCATAATCATTCA
3580334 TCAGTATT
1 TCA-TATT
3580342 TGCTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 1 0.04
22 9 0.38
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (19 bp):
TCATATTCATAATCATTCA
Found at i:3588622 original size:42 final size:41
Alignment explanation
Indices: 3588563--3589217 Score: 504
Period size: 42 Copynumber: 15.6 Consensus size: 41
3588553 TTTTTCTCTC
* * *
3588563 CCTCAGTCTGCTTGTCGGCCTTGACCCTAGAGACTTTCCTAT
1 CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-CTAT
* * * *
3588605 CCTCACTCTGCCTGTCGGCTTCGTCCCTGGAGACTTTTCAAT
1 CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTAT
* *
3588647 CCTCAGTCTACCTGTCGACTTTGACCCTGGAGACTTTTCT-T
1 CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTAT
* * * * * *
3588688 CTTTCAGTCTGCCTGTCAGCTTCGTCCTTGGAGACTTTCTTT
1 C-CTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTAT
* * *
3588730 CCCGCAGTCTGCCTGTCGGC-TTCATCCCTGGAGACTTTCTTT
1 -CCTCAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTCTAT
* * *
3588772 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAAC
1 -CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTAT
*
3588815 CCTCAGTCTGCCTGTCGACTTTGA-CCTAGGAGACTTTTCTTAT
1 CCTCAGTCTGCCTGTCGGCTTTGACCCT-GGAGAC-TTTC-TAT
* * **
3588858 CCTTCAGTTTGCTTGTCGGCTTTGACCCTGGAGACTGCCTCAT
1 CC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCT-AT
* * *
3588901 -CTAAAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCT-T
1 CCT-CAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTAT
*
3588941 CC-CATAGTCTGTCTGTCGGCTTTGACCCTGGAGACTTTTCT-T
1 CCTC--AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTAT
* * * * * *
3588983 CATTCAGTCTGCCTGTCGACTTCGTCCCTAGAGACTTTCTTT
1 C-CTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTAT
* * * *
3589025 CCCGCAGTCTGCCTGTCGGC-TTCATCCCTGGAGACTTTTTTT
1 -CCTCAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTCTAT
* * * * *
3589067 CCCTTAGTCTTCCTGTCGGCTTTGACCTTGGAGACTTTTCAAC
1 -CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTAT
* * *
3589110 CCTCAGTCTGCCTTTCGGCTTTGACTCGGGAGACTTTTCTTAT
1 CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC-TAT
* * * * *
3589153 CCTTA--ATGCCTGTAGGCTTTGACCATGGA-ACTTTCTTT
1 CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTAT
* * *
3589191 CCCTAAGTCTGCCCGTTGGCTTTGACC
1 -CCTCAGTCTGCCTGTCGGCTTTGACC
3589218 AGGGAGAATA
Statistics
Matches: 489, Mismatches: 96, Indels: 57
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.00
39 8 0.02
40 3 0.01
41 80 0.16
42 337 0.69
43 30 0.06
44 26 0.05
45 3 0.01
ACGTcount: A:0.13, C:0.31, G:0.20, T:0.36
Consensus pattern (41 bp):
CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTAT
Found at i:3590629 original size:16 final size:15
Alignment explanation
Indices: 3590598--3590638 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
3590588 AAATTAGAAT
3590598 TAAAAAATAAAAAATAA
1 TAAAAAAT--AAAATAA
3590615 TAACAAAATAAAATAA
1 TAA-AAAATAAAATAA
3590631 TAAAAAAT
1 TAAAAAAT
3590639 TCTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 3 0.13
18 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAAAAATAAAATAA
Found at i:3598459 original size:11 final size:11
Alignment explanation
Indices: 3598443--3598472 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3598433 TTTAGTTAAT
*
3598443 AATAATTAAAA
1 AATAATAAAAA
3598454 AATAATAAAAA
1 AATAATAAAAA
3598465 AATAATAA
1 AATAATAA
3598473 TTCTTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AATAATAAAAA
Found at i:3598717 original size:17 final size:17
Alignment explanation
Indices: 3598692--3598726 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3598682 AATTATAATT
3598692 TAAAAAATTATTAAATA
1 TAAAAAATTATTAAATA
* *
3598709 TAAATAATTATTACATA
1 TAAAAAATTATTAAATA
3598726 T
1 T
3598727 TTAATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAAAATTATTAAATA
Found at i:3599292 original size:17 final size:18
Alignment explanation
Indices: 3599270--3599303 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3599260 TTATAGTAAT
3599270 TTAATTT-AAATTTTAAA
1 TTAATTTGAAATTTTAAA
3599287 TTAATTTGAAATTTTAA
1 TTAATTTGAAATTTTAA
3599304 TATATTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTAATTTGAAATTTTAAA
Found at i:3600198 original size:22 final size:21
Alignment explanation
Indices: 3600173--3600220 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
3600163 TATTAGTTAA
*
3600173 AAATAATAAAAATAAAATTATT
1 AAATAA-AAAAATAAAATAATT
* *
3600195 AAATTAAATAAATTAAATAATT
1 AAA-TAAAAAAATAAAATAATT
3600217 AAAT
1 AAAT
3600221 GATATTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 18 0.82
23 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAAAAAATAAAATAATT
Found at i:3602738 original size:21 final size:22
Alignment explanation
Indices: 3602688--3602743 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
3602678 AATTTTAAAT
* *
3602688 ATTTATATAAATTTTAATATAA
1 ATTTAAATATATTTTAATATAA
**
3602710 AAAT-AATATATTTT-ATATAA
1 ATTTAAATATATTTTAATATAA
3602730 ATTTAAATATATTT
1 ATTTAAATATATTT
3602744 ATTTATTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 8 0.30
21 17 0.63
22 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTAAATATATTTTAATATAA
Done.