Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 117 of 145
Found at i:39193367 original size:2 final size:2
Alignment explanation
Indices: 39193324--39193349 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39193314 AAATCTTGTA
39193324 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
39193350 GATTTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39197823 original size:22 final size:22
Alignment explanation
Indices: 39197797--39197853 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
39197787 AAAAAACTAT
* *
39197797 TGTTTTGCTGCTGTTTTTCCAC
1 TGTTTTGCTGCTATTTTCCCAC
*
39197819 TGTTTTACTGCTATTTTCCCAC
1 TGTTTTGCTGCTATTTTCCCAC
*
39197841 TGTTTTGTTGCTA
1 TGTTTTGCTGCTA
39197854 CTATTTTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.09, C:0.21, G:0.16, T:0.54
Consensus pattern (22 bp):
TGTTTTGCTGCTATTTTCCCAC
Found at i:39198024 original size:142 final size:143
Alignment explanation
Indices: 39197858--39198144 Score: 549
Period size: 142 Copynumber: 2.0 Consensus size: 143
39197848 TTGCTACTAT
39197858 TTTGTTGTTATTGTTTGGATATTGTATATAACTCTTGTTTTTATTGATACTTTTACTATTATTTT
1 TTTGTTGTTATTGTTTGGATATTGTATATAACTCTTGTTTTTATTGATACTTTTACTATTATTTT
*
39197923 AGAGACATTTGCTTGTTAAGTTACACCTATCTTAGTGCTATTTAAGTATAAATATTTTTTAAATT
66 AGAGACATTTGCTTGTTAAGTTACACCTATCCTAGTGCTATTTAAGTATAAATATTTTTTAAATT
39197988 TATTTTCAATTTG
131 TATTTTCAATTTG
39198001 TTTGTTGTTATT-TTTGGATATTGTATATAACTCTTGTTTTTATTGATACTTTTACTATTATTTT
1 TTTGTTGTTATTGTTTGGATATTGTATATAACTCTTGTTTTTATTGATACTTTTACTATTATTTT
*
39198065 AGAGACATTTGCTTGTTAAGTTACACCTTTCCTAGTGCTATTTAAGTATAAATATTTTTTAAATT
66 AGAGACATTTGCTTGTTAAGTTACACCTATCCTAGTGCTATTTAAGTATAAATATTTTTTAAATT
39198130 TATTTTCAATTTG
131 TATTTTCAATTTG
39198143 TT
1 TT
39198145 GGGAAATATT
Statistics
Matches: 142, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
142 130 0.92
143 12 0.08
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.54
Consensus pattern (143 bp):
TTTGTTGTTATTGTTTGGATATTGTATATAACTCTTGTTTTTATTGATACTTTTACTATTATTTT
AGAGACATTTGCTTGTTAAGTTACACCTATCCTAGTGCTATTTAAGTATAAATATTTTTTAAATT
TATTTTCAATTTG
Found at i:39202746 original size:22 final size:22
Alignment explanation
Indices: 39202720--39202776 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
39202710 AAAAAACTAT
* *
39202720 TGTTTTGCTGCTGTTTTTCCAC
1 TGTTTTGCTGCTATTTTCCCAC
*
39202742 TGTTTTACTGCTATTTTCCCAC
1 TGTTTTGCTGCTATTTTCCCAC
*
39202764 TGTTTTGTTGCTA
1 TGTTTTGCTGCTA
39202777 CTATTTTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.09, C:0.21, G:0.16, T:0.54
Consensus pattern (22 bp):
TGTTTTGCTGCTATTTTCCCAC
Found at i:39208249 original size:3 final size:3
Alignment explanation
Indices: 39208241--39208280 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
39208231 CTAGGCCTAG
39208241 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
39208281 TAGTCCCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:39208656 original size:11 final size:11
Alignment explanation
Indices: 39208611--39208659 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
39208601 TATTTTTAAA
*
39208611 TTTTAAAATAC
1 TTTTAAAATAT
39208622 TTTTAAAATAT
1 TTTTAAAATAT
***
39208633 TTTTATTTTTAT
1 TTTTA-AAATAT
39208645 TTTTAAAATAT
1 TTTTAAAATAT
39208656 TTTT
1 TTTT
39208660 TTTTGTATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39208674 original size:24 final size:23
Alignment explanation
Indices: 39208622--39208676 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 23
39208612 TTTAAAATAC
39208622 TTTTAAAATATTTTTATTTTTAT
1 TTTTAAAATATTTTTATTTTTAT
39208645 TTTTAAAATATTTTT-TTTTGTAT
1 TTTTAAAATATTTTTATTTT-TAT
39208668 TTATTAAAA
1 TT-TTAAAA
39208677 ATCGGGCCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.13
23 20 0.67
24 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTAAAATATTTTTATTTTTAT
Found at i:39211333 original size:26 final size:26
Alignment explanation
Indices: 39211286--39211351 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 26
39211276 TGATATATGA
* *
39211286 CTCTTCGTGAGCTTCCCGATTAAAGG
1 CTCTTTGTGAGCTTCCCAATTAAAGG
* **
39211312 CTCTTTGTGAGCTTCCTAATTAATTG
1 CTCTTTGTGAGCTTCCCAATTAAAGG
*
39211338 CTCTCTG-GAGCTTC
1 CTCTTTGTGAGCTTC
39211352 TTGATATGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 7 0.21
26 27 0.79
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.38
Consensus pattern (26 bp):
CTCTTTGTGAGCTTCCCAATTAAAGG
Found at i:39211420 original size:24 final size:24
Alignment explanation
Indices: 39211371--39211436 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
39211361 CTCCCCTGAA
* * *
39211371 CTTCCCGATATATGGCTATTCGGAG
1 CTTCCCGTTA-ATGGCTCTTCAGAG
39211396 CTTCCCGTTAATGGCTCTTCAGAG
1 CTTCCCGTTAATGGCTCTTCAGAG
* * *
39211420 CTACCCATTATTGGCTC
1 CTTCCCGTTAATGGCTC
39211437 GCGTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (24 bp):
CTTCCCGTTAATGGCTCTTCAGAG
Found at i:39211535 original size:25 final size:25
Alignment explanation
Indices: 39211393--39211536 Score: 80
Period size: 25 Copynumber: 5.9 Consensus size: 25
39211383 TGGCTATTCG
*
39211393 GAGCTTCCCGTTA-ATGGCTCTTCA-
1 GAGCTTCCCGTTATATGGCTC-GCAT
* * *
39211417 GAGCTACCCATTAT-TGGCTCGCGT
1 GAGCTTCCCGTTATATGGCTCGCAT
** * **
39211441 GAGCTTCTTG-AATATGGCTCTTAT
1 GAGCTTCCCGTTATATGGCTCGCAT
** * * *
39211465 GAGCTTCTTGTTATATAGCCCGGAT
1 GAGCTTCCCGTTATATGGCTCGCAT
* ** *
39211490 AAGCTTCCCGTTATACAGCTCACAT
1 GAGCTTCCCGTTATATGGCTCGCAT
*
39211515 GAGCTTCCTGTTATATGGCTCG
1 GAGCTTCCCGTTATATGGCTCG
39211537 AGAGAGCGCA
Statistics
Matches: 87, Mismatches: 29, Indels: 7
0.71 0.24 0.06
Matches are distributed among these distances:
23 3 0.03
24 40 0.46
25 44 0.51
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCGCAT
Found at i:39215117 original size:51 final size:50
Alignment explanation
Indices: 39214944--39215121 Score: 146
Period size: 51 Copynumber: 3.5 Consensus size: 50
39214934 GATGGCCATG
* * ** *
39214944 TGTGTAGTGCTATGTGCAGGCTACTACGTGTACCAAAAAGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACGAAAGTGATAGGTCACA
* * * * * * *
39214994 TGTGTAGTACTGTGTGCAGGCTACTATGCGTACCGGATAGCT--TCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTA-C-GAAAG-TGATAGGTCACA
* * *
39215045 TGTGTAGTACTATATACAGGCTACTACGTGTATTGAATAGTGAT-GGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGAA-AGTGATAGGTCACA
*
39215096 TGTGTAGTACTATGTGTAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
39215122 TGTGAACCCG
Statistics
Matches: 97, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
50 31 0.32
51 63 0.65
52 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACGAAAGTGATAGGTCACA
Found at i:39215217 original size:42 final size:43
Alignment explanation
Indices: 39215129--39215386 Score: 271
Period size: 42 Copynumber: 6.1 Consensus size: 43
39215119 CTATGTGAAC
* * * * *
39215129 CCGTATCATTGATTAT-AAGGTGGTTGCAAATTGCTGATTCCA
1 CCGTATCCTTGATTATGAAAGAGGTTGCTAAGTGCTGATTCCA
* *
39215171 CCGTATCCTTGATTGTGAAAGAGGTTGCTATGTGCTGATTCC-
1 CCGTATCCTTGATTATGAAAGAGGTTGCTAAGTGCTGATTCCA
39215213 CCGTATCCTTGATTAT--AAGATGGTTGCTAAGTGCTGATTCCA
1 CCGTATCCTTGATTATGAAAGA-GGTTGCTAAGTGCTGATTCCA
* *
39215255 CCGTATCCTTGATTATGAAAG-GGTTTGCTATGTGCTGATTTC-
1 CCGTATCCTTGATTATGAAAGAGG-TTGCTAAGTGCTGATTCCA
* * * *
39215297 CCGTATCATTGATTAT-AAGGTGGTTCCTAAGTGCTGATTCCA
1 CCGTATCCTTGATTATGAAAGAGGTTGCTAAGTGCTGATTCCA
* * * *
39215339 CCGGGATCCTTTGAATATG-AGGTGGTTGCTAAGTGCTGATTCCA
1 CC-GTATCC-TTGATTATGAAAGAGGTTGCTAAGTGCTGATTCCA
39215383 CCGT
1 CCGT
39215387 GTAACGGTTA
Statistics
Matches: 184, Mismatches: 21, Indels: 21
0.81 0.09 0.09
Matches are distributed among these distances:
40 4 0.02
41 37 0.20
42 66 0.36
43 41 0.22
44 36 0.20
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (43 bp):
CCGTATCCTTGATTATGAAAGAGGTTGCTAAGTGCTGATTCCA
Found at i:39215274 original size:84 final size:83
Alignment explanation
Indices: 39215128--39215386 Score: 358
Period size: 84 Copynumber: 3.1 Consensus size: 83
39215118 ACTATGTGAA
* * *
39215128 CCCGTATCATTGATTATAAGGTGGTTGCAAATTGCTGATTCCACCGTATCCTTGATTGTGAAAGA
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAAAG-
39215193 GGTTGCTATGTGCTGATTC
65 GGTTGCTATGTGCTGATTC
* *
39215212 CCCGTATCCTTGATTATAAGATGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAAAGG
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAAAGG
*
39215277 GTTTGCTATGTGCTGATTT
66 G-TTGCTATGTGCTGATTC
* * * *
39215296 CCCGTATCATTGATTATAAGGTGGTTCCTAAGTGCTGATTCCACCGGGATCCTTTGAATATG-AG
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACC-GTATCC-TTGATTATGAAA
*
39215360 GTGGTTGCTAAGTGCTGATTC
64 G-GGTTGCTATGTGCTGATTC
39215381 CACCGT
1 C-CCGT
39215387 GTAACGGTTA
Statistics
Matches: 156, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
83 2 0.01
84 117 0.75
85 23 0.15
86 14 0.09
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (83 bp):
CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAAAGG
GTTGCTATGTGCTGATTC
Found at i:39222577 original size:26 final size:26
Alignment explanation
Indices: 39222528--39222578 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
39222518 CCCAATATAT
*
39222528 GGCTCTTCGTGAGCTTCTCGATTAAA
1 GGCTCTTCGTGAGCTTCTCAATTAAA
*
39222554 GGCTCTTTGTGAGCTTC-CTAATTAA
1 GGCTCTTCGTGAGCTTCTC-AATTAA
39222579 TGTCTTTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCTCAATTAAA
Found at i:39225961 original size:20 final size:20
Alignment explanation
Indices: 39225936--39225979 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
39225926 TAATATGGTA
39225936 AGAAAAGTGGAGAATTCTCT
1 AGAAAAGTGGAGAATTCTCT
39225956 AGAAAAGTGGAGAATTCTCT
1 AGAAAAGTGGAGAATTCTCT
39225976 AGAA
1 AGAA
39225980 TGTGTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (20 bp):
AGAAAAGTGGAGAATTCTCT
Found at i:39228747 original size:30 final size:30
Alignment explanation
Indices: 39228704--39228829 Score: 155
Period size: 30 Copynumber: 4.2 Consensus size: 30
39228694 AACAGTGAGT
* *
39228704 TACACAGCCTGGCAACACGGCCGTGCAACC
1 TACACGGCCTGGCAACACGGCCGTGTAACC
* *
39228734 TACACGGCTTGGCAACATGGCCGTGTAACC
1 TACACGGCCTGGCAACACGGCCGTGTAACC
* * *
39228764 TACACGACCTGGCGACACGGTCGTGTAACC
1 TACACGGCCTGGCAACACGGCCGTGTAACC
* *
39228794 TACACGGCTTGG-AGACACGGTCGTGTAACC
1 TACACGGCCTGGCA-ACACGGCCGTGTAACC
39228824 TACACG
1 TACACG
39228830 AACTAGACAC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.17
Consensus pattern (30 bp):
TACACGGCCTGGCAACACGGCCGTGTAACC
Found at i:39228797 original size:60 final size:60
Alignment explanation
Indices: 39228711--39228830 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 60
39228701 AGTTACACAG
*
39228711 CCTGGCAACACGGCCGTGCAACCTACACGGCTTGGCA-ACATGGCCGTGTAACCTACACGA
1 CCTGGCAACACGGCCGTGCAACCTACACGGCTTGG-AGACACGGCCGTGTAACCTACACGA
* * * *
39228771 CCTGGCGACACGGTCGTGTAACCTACACGGCTTGGAGACACGGTCGTGTAACCTACACGA
1 CCTGGCAACACGGCCGTGCAACCTACACGGCTTGGAGACACGGCCGTGTAACCTACACGA
39228831 ACTAGACACA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.24, C:0.33, G:0.27, T:0.17
Consensus pattern (60 bp):
CCTGGCAACACGGCCGTGCAACCTACACGGCTTGGAGACACGGCCGTGTAACCTACACGA
Found at i:39229644 original size:40 final size:41
Alignment explanation
Indices: 39229588--39229684 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 41
39229578 TGCCCTTTTC
*
39229588 TTTTATT-TACTTATTATTATT-TATTTATTA-TCTGTTCA-T
1 TTTTATTATATTTATTATT-TTGT-TTTATTATTCTGTTCATT
* *
39229627 TTTTATTATATTTATTATTTTGTTTTCTTATTCTGTTTATTT
1 TTTTATTATATTTATTATTTTGTTTTATTATTCTGTTCA-TT
*
39229669 TTTTATTATGTTTATT
1 TTTTATTATATTTATT
39229685 CCTGGTTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
39 15 0.31
40 18 0.37
42 16 0.33
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (41 bp):
TTTTATTATATTTATTATTTTGTTTTATTATTCTGTTCATT
Found at i:39229674 original size:17 final size:17
Alignment explanation
Indices: 39229638--39229684 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
39229628 TTTATTATAT
*
39229638 TTATTAT-TTTGTTTTC
1 TTATTATGTTTATTTTC
* *
39229654 TTATTCTGTTTATTTTT
1 TTATTATGTTTATTTTC
39229671 TTATTATGTTTATT
1 TTATTATGTTTATT
39229685 CCTGGTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (17 bp):
TTATTATGTTTATTTTC
Found at i:39230427 original size:13 final size:13
Alignment explanation
Indices: 39230409--39230434 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39230399 ATCGAGCCCA
39230409 CATATATGGAGCT
1 CATATATGGAGCT
39230422 CATATATGGAGCT
1 CATATATGGAGCT
39230435 TACTTTGGAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
CATATATGGAGCT
Found at i:39231018 original size:15 final size:15
Alignment explanation
Indices: 39230994--39231027 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
39230984 TGATCGAGCG
39230994 TGAT-CATATGAGGA
1 TGATCCATATGAGGA
39231008 TGATCCATATGAGGA
1 TGATCCATATGAGGA
39231023 TGATC
1 TGATC
39231028 GAGCGACGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (15 bp):
TGATCCATATGAGGA
Found at i:39231376 original size:6 final size:6
Alignment explanation
Indices: 39231355--39231397 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
39231345 AGTCTATTTG
* *
39231355 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT GTTTAT TGTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
39231398 CTTAAACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:39231389 original size:18 final size:17
Alignment explanation
Indices: 39231355--39231397 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
39231345 AGTCTATTTG
39231355 TTTTA-TTTTATTTTAT
1 TTTTATTTTTATTTTAT
39231371 TTTTATTTTTATGTTTAT
1 TTTTATTTTTAT-TTTAT
*
39231389 TGTTATTTT
1 TTTTATTTT
39231398 CTTAAACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 6 0.25
18 13 0.54
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTATTTTAT
Found at i:39235914 original size:30 final size:30
Alignment explanation
Indices: 39235878--39235935 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39235868 GGGTGAATAA
* **
39235878 GTTGCTCACACAAGTTGGCATTTTATCAGG
1 GTTGCTCACACAAGCTAACATTTTATCAGG
39235908 GTTGCTCACACAAGCTAACATTTTATCA
1 GTTGCTCACACAAGCTAACATTTTATCA
39235936 AAGTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (30 bp):
GTTGCTCACACAAGCTAACATTTTATCAGG
Found at i:39236358 original size:24 final size:24
Alignment explanation
Indices: 39236326--39236374 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
39236316 GCATAATGTT
39236326 TATATTTATCATGTTTGGAGGTGG
1 TATATTTATCATGTTTGGAGGTGG
39236350 TATATTTATCATGTTTGGAGGTGG
1 TATATTTATCATGTTTGGAGGTGG
39236374 T
1 T
39236375 TTAGTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.29, T:0.47
Consensus pattern (24 bp):
TATATTTATCATGTTTGGAGGTGG
Found at i:39238691 original size:18 final size:18
Alignment explanation
Indices: 39238679--39238845 Score: 174
Period size: 18 Copynumber: 9.3 Consensus size: 18
39238669 AGGTTCCTTC
*
39238679 GGCTTTTCGGGTTGTTTA
1 GGCTTTTCGGGTTCTTTA
*
39238697 GG-TTTCTCGGGTTCTTTG
1 GGCTTT-TCGGGTTCTTTA
* *
39238715 GGTTTTTCGGGTTCTTTT
1 GGCTTTTCGGGTTCTTTA
* *
39238733 GGTTTTTCGGGTGCTTTA
1 GGCTTTTCGGGTTCTTTA
*
39238751 GGCTTTTCGGGTTCTTTT
1 GGCTTTTCGGGTTCTTTA
* * *
39238769 GGTTTTTCTGGTACTTTA
1 GGCTTTTCGGGTTCTTTA
* * *
39238787 GGCTTCTCTGGTTCTTTG
1 GGCTTTTCGGGTTCTTTA
* * *
39238805 GGTTTTTCAGGTTCTTTG
1 GGCTTTTCGGGTTCTTTA
39238823 GGCTTTTCGGGTTCTTTA
1 GGCTTTTCGGGTTCTTTA
39238841 GGCTT
1 GGCTT
39238846 CTCAGGCTCC
Statistics
Matches: 125, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
17 3 0.02
18 119 0.95
19 3 0.02
ACGTcount: A:0.04, C:0.14, G:0.29, T:0.53
Consensus pattern (18 bp):
GGCTTTTCGGGTTCTTTA
Found at i:39238728 original size:54 final size:53
Alignment explanation
Indices: 39238652--39238845 Score: 192
Period size: 54 Copynumber: 3.6 Consensus size: 53
39238642 TTTCGGTGGT
** * * * *
39238652 GGTTCTTTTCGTTTCTCAGGTTCCTTCGGCTTTTCGGGTTGTTTAGGTTTCTCG
1 GGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTTTTCGGGTTGTTTAGGTTT-TCG
* *
39238706 GGTTCTTTGGGTTTTTCGGGTTCTTTTGGTTTTTCGGG-TGCTTTAGGCTTTTCG
1 GGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTTTTCGGGTTG-TTTAGG-TTTTCG
* * * * * * * *
39238760 GGTTCTTTTGGTTTTTCTGGTACTTTAGGCTTCTCTGGTTCTTTGGGTTTTTCA
1 GGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTTTTCGGGTTGTTTAGG-TTTTCG
*
39238814 GGTTCTTTGGGCTTTTCGGGTTCTTTAGGCTT
1 GGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTT
39238846 CTCAGGCTCC
Statistics
Matches: 115, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
53 2 0.02
54 109 0.95
55 4 0.03
ACGTcount: A:0.04, C:0.16, G:0.28, T:0.53
Consensus pattern (53 bp):
GGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTTTTCGGGTTGTTTAGGTTTTCG
Found at i:39238860 original size:36 final size:36
Alignment explanation
Indices: 39238652--39238860 Score: 202
Period size: 36 Copynumber: 5.8 Consensus size: 36
39238642 TTTCGGTGGT
** * *
39238652 GGTTCTTTTCGTTTCTCAGGTTCCTTCGGCTTTTCG
1 GGTTCTTTAGGTTTCTCAGGTTCTTTGGGCTTTTCG
* * *
39238688 GGTTGTTTAGGTTTCTCGGGTTCTTTGGGTTTTTCG
1 GGTTCTTTAGGTTTCTCAGGTTCTTTGGGCTTTTCG
* * * * *
39238724 GGTTCTTTTGGTTTTTCGGGTGCTTTAGGCTTTTCG
1 GGTTCTTTAGGTTTCTCAGGTTCTTTGGGCTTTTCG
* * * * * * *
39238760 GGTTCTTTTGGTTTTTCTGGTACTTTAGGCTTCTCT
1 GGTTCTTTAGGTTTCTCAGGTTCTTTGGGCTTTTCG
* *
39238796 GGTTCTTTGGGTTTTTCAGGTTCTTTGGGCTTTTCG
1 GGTTCTTTAGGTTTCTCAGGTTCTTTGGGCTTTTCG
* * *
39238832 GGTTCTTTAGGCTTCTCAGGCTCCTTGGG
1 GGTTCTTTAGGTTTCTCAGGTTCTTTGGG
39238861 TTTGGGAGGA
Statistics
Matches: 145, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 145 1.00
ACGTcount: A:0.04, C:0.17, G:0.28, T:0.51
Consensus pattern (36 bp):
GGTTCTTTAGGTTTCTCAGGTTCTTTGGGCTTTTCG
Found at i:39238860 original size:54 final size:53
Alignment explanation
Indices: 39238697--39238863 Score: 181
Period size: 54 Copynumber: 3.1 Consensus size: 53
39238687 GGGTTGTTTA
* * * * * *
39238697 GGTTTCTCGGGTTCTTTGGGTTTTTCGGGTTCTTTTGGTTTTTCGGGTGCTTTA
1 GGTTTTTCGGGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTTCTCGGCT-CTTTG
* * * * *
39238751 GGCTTTTCGGGTTCTTTTGGTTTTTCTGGTACTTTAGGCTTCTCTGGTTCTTTG
1 GGTTTTTCGGGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTTCTC-GGCTCTTTG
* * *
39238805 GGTTTTTCAGGTTCTTTGGGCTTTTCGGGTTCTTTAGGCTTCTCAGGCTCCTTG
1 GGTTTTTCGGGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTTCTC-GGCTCTTTG
39238859 GGTTT
1 GGTTT
39238864 GGGAGGAGGA
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
54 90 0.97
55 3 0.03
ACGTcount: A:0.04, C:0.16, G:0.29, T:0.51
Consensus pattern (53 bp):
GGTTTTTCGGGTTCTTTGGGTTTTTCGGGTTCTTTAGGCTTCTCGGCTCTTTG
Found at i:39241915 original size:40 final size:40
Alignment explanation
Indices: 39241846--39241923 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
39241836 CAAATTTGGG
*
39241846 CTTGCCTAAATATAGTTTTACTCAATTAAACTA-TTTTTAT
1 CTTGCCTAAATATAGTGTTACTCAATTAAA-TAGTTTTTAT
* *
39241886 CTTGGCTAAATATATGTGTTACT-AGTTAAATAGTTTTT
1 CTTGCCTAAATATA-GTGTTACTCAATTAAATAGTTTTT
39241924 TTTTCTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.06
40 24 0.73
41 7 0.21
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (40 bp):
CTTGCCTAAATATAGTGTTACTCAATTAAATAGTTTTTAT
Found at i:39243316 original size:18 final size:19
Alignment explanation
Indices: 39243283--39243321 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39243273 NNNNTTTTAA
* *
39243283 AAAAAAT-AGAATTTTTTT
1 AAAAAATAAAAATTTTATT
39243301 AAAAAATAAAAATTTTATT
1 AAAAAATAAAAATTTTATT
39243320 AA
1 AA
39243322 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAAAATAAAAATTTTATT
Found at i:39243901 original size:43 final size:43
Alignment explanation
Indices: 39243857--39244115 Score: 260
Period size: 43 Copynumber: 6.1 Consensus size: 43
39243847 ATAAAAGCCG
* * *
39243857 CTAAAGAGCATGACCTTTAGCGGCGCTTTTATCTCAAACGCCG
1 CTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAAACGCCA
*
39243900 CTAAAGAAT-ATGACCTTTAGCGGCGCTTTTATCACAAACACCA
1 CTAAAG-ATCATGACCTTTAGCGGCGCTTTTATCACAAACGCCA
* *
39243943 CTAAAGATCATGACCTTTAGCGGCACTTTTATCACAAAAGCCA
1 CTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAAACGCCA
* * ** * *
39243986 CTAAAAATCACGACCTTTAGCGATGC-TTTACCCAGAAACGCCA
1 CTAAAGATCATGACCTTTAGCGGCGCTTTTA-TCACAAACGCCA
* * * *
39244029 CTAAA-A-AATGACCTTTAGCGACGCTTTTATCTCAAACGACA
1 CTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAAACGCCA
* * * * * *
39244070 ATAAA-A-AATTATCTTTAGCGACGCTTTTTTCACAAACGCCA
1 CTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAAACGCCA
39244111 CTAAA
1 CTAAA
39244116 AGTACCGTTT
Statistics
Matches: 183, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
41 62 0.34
42 11 0.06
43 109 0.60
44 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (43 bp):
CTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAAACGCCA
Found at i:39243955 original size:86 final size:84
Alignment explanation
Indices: 39243857--39244115 Score: 299
Period size: 86 Copynumber: 3.1 Consensus size: 84
39243847 ATAAAAGCCG
*
39243857 CTAAAGAGCATGACCTTTAGCGGCGCTTTTATCTCAAACGCCGCTAAAGAATATGACCTTTAGCG
1 CTAAAGA-CATGACCTTTAGCGGCGCTTTTATCTCAAACGCCACTAAA-AATATGACCTTTAGCG
* *
39243922 GCGCTTTTATCACAAACACCA
64 ACGCTTTTATCACAAACGCCA
* * * *
39243943 CTAAAGATCATGACCTTTAGCGGCACTTTTATCACAAAAGCCACTAAAAATCACGACCTTTAGCG
1 CTAAAGA-CATGACCTTTAGCGGCGCTTTTATCTCAAACGCCACTAAAAAT-ATGACCTTTAGCG
* * *
39244008 ATGC-TTTACCCAGAAACGCCA
64 ACGCTTTTA-TCACAAACGCCA
* * * * * *
39244029 CTAAA-AAATGACCTTTAGCGACGCTTTTATCTCAAACGACAATAAAAA-ATTATCTTTAGCGAC
1 CTAAAGACATGACCTTTAGCGGCGCTTTTATCTCAAACGCCACTAAAAATATGACCTTTAGCGAC
*
39244092 GCTTTTTTCACAAACGCCA
66 GCTTTTATCACAAACGCCA
39244111 CTAAA
1 CTAAA
39244116 AGTACCGTTT
Statistics
Matches: 145, Mismatches: 25, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
82 28 0.19
83 3 0.02
84 35 0.24
85 8 0.06
86 71 0.49
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (84 bp):
CTAAAGACATGACCTTTAGCGGCGCTTTTATCTCAAACGCCACTAAAAATATGACCTTTAGCGAC
GCTTTTATCACAAACGCCA
Found at i:39246174 original size:7 final size:7
Alignment explanation
Indices: 39246162--39246186 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39246152 AGTCGATTGA
39246162 TATTTAG
1 TATTTAG
39246169 TATTTAG
1 TATTTAG
39246176 TATTTAG
1 TATTTAG
39246183 TATT
1 TATT
39246187 ATAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:39248231 original size:19 final size:19
Alignment explanation
Indices: 39248207--39248251 Score: 81
Period size: 19 Copynumber: 2.3 Consensus size: 19
39248197 TAAAATTATA
39248207 ATTTTTAGTTTTTGTATTTC
1 ATTTTTA-TTTTTGTATTTC
39248227 ATTTTTATTTTTGTATTTC
1 ATTTTTATTTTTGTATTTC
39248246 ATTTTT
1 ATTTTT
39248252 TTACAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.16, C:0.04, G:0.07, T:0.73
Consensus pattern (19 bp):
ATTTTTATTTTTGTATTTC
Found at i:39248373 original size:7 final size:7
Alignment explanation
Indices: 39248367--39248451 Score: 59
Period size: 7 Copynumber: 11.9 Consensus size: 7
39248357 AAATCATAAA
39248367 CCTTAAAC
1 CCTT-AAC
*
39248375 CCCTAAC
1 CCTTAAC
39248382 CCTTAAC
1 CCTTAAC
39248389 CCTTAAC
1 CCTTAAC
39248396 CCTTAAC
1 CCTTAAC
39248403 CAC-TAAC
1 C-CTTAAC
39248410 CAC-TAAC
1 C-CTTAAC
39248417 ACC-TAATC
1 -CCTTAA-C
*
39248425 CCTAAAC
1 CCTTAAC
* *
39248432 CCATAAT
1 CCTTAAC
*
39248439 CCATAAC
1 CCTTAAC
39248446 CCTTAA
1 CCTTAA
39248452 AATAGTAACT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
7 57 0.88
8 8 0.12
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.22
Consensus pattern (7 bp):
CCTTAAC
Found at i:39248382 original size:14 final size:14
Alignment explanation
Indices: 39248367--39248447 Score: 65
Period size: 14 Copynumber: 5.6 Consensus size: 14
39248357 AAATCATAAA
39248367 CCTTAAACCCCTAAC
1 CCTT-AACCCCTAAC
*
39248382 CCTTAACCCTTAAC
1 CCTTAACCCCTAAC
*
39248396 CCTTAACCACTAAC
1 CCTTAACCCCTAAC
*
39248410 CAC-TAACACCTAATC
1 C-CTTAACCCCTAA-C
* * *
39248425 CCTAAACCCATAAT
1 CCTTAACCCCTAAC
*
39248439 CCATAACCC
1 CCTTAACCC
39248448 TTAAAATAGT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
14 38 0.73
15 14 0.27
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTTAACCCCTAAC
Found at i:39248984 original size:40 final size:40
Alignment explanation
Indices: 39248889--39248986 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 40
39248879 TAATTTTTTT
* *
39248889 GCGGCGTTTTTTAAAAAGCCCCGCTAATGCCCGATCTATA
1 GCGGCGTTTTTCAAGAAGCCCCGCTAATGCCCGATCTATA
* * * * *
39248929 GCGGCGTTTTACAAGAAGCGCTGCTAATGCTCTATCTATA
1 GCGGCGTTTTTCAAGAAGCCCCGCTAATGCCCGATCTATA
*
39248969 GGGGCGTTTTTCAAGAAG
1 GCGGCGTTTTTCAAGAAG
39248987 TGTCACTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (40 bp):
GCGGCGTTTTTCAAGAAGCCCCGCTAATGCCCGATCTATA
Found at i:39248996 original size:40 final size:40
Alignment explanation
Indices: 39248912--39248999 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
39248902 AAAAGCCCCG
*
39248912 CTAATGCCCGATCTATAGCGGCGTTTTACAAGAAGCGCTG
1 CTAATGCCCGATCTATAGCGGCGTTTTACAAGAAGCGCTA
* * * * *
39248952 CTAATGCTCTATCTATAGGGGCGTTTTTCAAGAAGTG-TCA
1 CTAATGCCCGATCTATAGCGGCGTTTTACAAGAAGCGCT-A
39248992 CTAATGCC
1 CTAATGCC
39249000 ACTAAAGCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (40 bp):
CTAATGCCCGATCTATAGCGGCGTTTTACAAGAAGCGCTA
Found at i:39249089 original size:40 final size:40
Alignment explanation
Indices: 39249056--39249133 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
39249046 GGCATTCTTT
39249056 AAAAAGCGCCGCTAATGCT-ATACCTATAGCGGCAGTTTTC
1 AAAAAGCGCCGCTAATGCTCA-ACCTATAGCGGCAGTTTTC
39249096 AAAAAGCGCCGCTAATGCTCAACCTATAGCGGC-GTTTT
1 AAAAAGCGCCGCTAATGCTCAACCTATAGCGGCAGTTTT
39249134 TTATCCAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
39 5 0.14
40 31 0.84
41 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (40 bp):
AAAAAGCGCCGCTAATGCTCAACCTATAGCGGCAGTTTTC
Found at i:39249103 original size:155 final size:155
Alignment explanation
Indices: 39248814--39249134 Score: 457
Period size: 155 Copynumber: 2.1 Consensus size: 155
39248804 TAATTTTTTT
* *
39248814 GCGGCATTTTTCAAAAAGCGTCGCTAATGCCACTAAAGCTCAACATAAAACGACGACGTTGTGCT
1 GCGGCGTTTTTCAAAAAGCGTCACTAATGCCACTAAAGCTCAACATAAAACGACGACGTTGTGCT
* * * * *
39248879 TAATTTTTTTGCGGCGTTTTTTAAAAAGCCCCGCTAATGCCCGATCTATAGCGGCGTTTTACAAG
66 TAATTTTTTTGCGGCATTCTTTAAAAAGCCCCGCTAATGCCAGACCTATAGCGGCGTTTTACAAA
* * *
39248944 AAGCGCTGCTAATGCTCTATCTATA
131 AAGCGCCGCTAATGCTCAACCTATA
* * * *
39248969 GGGGCGTTTTTCAAGAAGTGTCACTAATGCCACTAAAGCTCAACATAAAGCGACGACGTTGTGCT
1 GCGGCGTTTTTCAAAAAGCGTCACTAATGCCACTAAAGCTCAACATAAAACGACGACGTTGTGCT
* * *
39249034 T-ATTTTTTATGCGGCATTCTTTAAAAAGCGCCGCTAATGCTATACCTATAGCGGCAGTTTT-CA
66 TAATTTTTT-TGCGGCATTCTTTAAAAAGCCCCGCTAATGCCAGACCTATAGCGGC-GTTTTACA
39249097 AAAAGCGCCGCTAATGCTCAACCTATA
129 AAAAGCGCCGCTAATGCTCAACCTATA
39249124 GCGGCGTTTTT
1 GCGGCGTTTTT
39249135 TATCCAAACG
Statistics
Matches: 146, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
154 7 0.05
155 134 0.92
156 5 0.03
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (155 bp):
GCGGCGTTTTTCAAAAAGCGTCACTAATGCCACTAAAGCTCAACATAAAACGACGACGTTGTGCT
TAATTTTTTTGCGGCATTCTTTAAAAAGCCCCGCTAATGCCAGACCTATAGCGGCGTTTTACAAA
AAGCGCCGCTAATGCTCAACCTATA
Found at i:39249949 original size:3 final size:3
Alignment explanation
Indices: 39249941--39249965 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39249931 ACCACATGAT
39249941 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
39249966 AACCCTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:39250083 original size:6 final size:6
Alignment explanation
Indices: 39250072--39250101 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
39250062 AGTTATTGTA
39250072 GTATCC GTATCC GTATCC GTATCC GTATCC
1 GTATCC GTATCC GTATCC GTATCC GTATCC
39250102 ACCACTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (6 bp):
GTATCC
Found at i:39251774 original size:2 final size:2
Alignment explanation
Indices: 39251767--39251821 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
39251757 CTCATTTGTA
* * *
39251767 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT CT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
39251809 AT AT AG AT AT AT A
1 AT AT AT AT AT AT A
39251822 GAAAGAGAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:39252008 original size:19 final size:17
Alignment explanation
Indices: 39251978--39252022 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
39251968 CGTGCGTGGA
*
39251978 AATATCATATTTAAGATAT
1 AATAT-ATATTTAA-AAAT
39251997 ATATATATATTTAAAAAT
1 A-ATATATATTTAAAAAT
39252015 AATATATA
1 AATATATA
39252023 AGAAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 4 0.17
19 9 0.38
20 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATATATATTTAAAAAT
Found at i:39252062 original size:22 final size:23
Alignment explanation
Indices: 39252008--39252064 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
39251998 TATATATATT
39252008 TAAAAATAATATATAAGAAATAA
1 TAAAAATAATATATAAGAAATAA
* *
39252031 TAAAATATAATATTTAA-AATTAA
1 TAAAA-ATAATATATAAGAAATAA
*
39252054 TAATAATAATA
1 TAAAAATAATA
39252065 ACAATACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.20
23 14 0.47
24 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAAATAATATATAAGAAATAA
Found at i:39257717 original size:27 final size:27
Alignment explanation
Indices: 39257664--39257717 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
39257654 CCCACACTGG
** *
39257664 TTTAAAATATTTCAATTTATATTTGAT
1 TTTAAAATAAATCAATTTATATGTGAT
39257691 TTTAAAATAAATCAATTTACT-TGTGAT
1 TTTAAAATAAATCAATTTA-TATGTGAT
39257718 ATATTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (27 bp):
TTTAAAATAAATCAATTTATATGTGAT
Found at i:39260913 original size:149 final size:149
Alignment explanation
Indices: 39260642--39260955 Score: 427
Period size: 149 Copynumber: 2.1 Consensus size: 149
39260632 AAAGTTCTGA
** *
39260642 TTTTTTTAAAAAAAAGAGAAAATTTAGATTTTTAAAAATAAAATTTATTTTTTAGTCATTTTAAA
1 TTTTTTTAAAAAAAAGAGAAAATTTAGATTTTTAAAAATAAAAAATATTTTTTAGCCATTTTAAA
* * * * *
39260707 GGAAAGTTTAAATTTTTAAAATAAATTTTTGATTTTTTTCAACTATTTCGGAATAAAAGCTTTGA
66 GGAAAGTTTAAA-TTTTAAAATAAATTTTTAATTTTTTTCAACCATTTCGAAATAAAACCTTTCA
*
39260772 TCTTTAAGAAAAACGGTGAT
130 TCTTTAAGAAAAACAGTGAT
* * *
39260792 TTTTTTTAAAAAAAATAGAAAGTTTAGATTTTTAAAAATAAAAAAAATGTTTTTTAGCCATTTTA
1 TTTTTTTAAAAAAAAGAGAAAATTTAGATTTTTAAAAAT--AAAAAATATTTTTTAGCCATTTTA
*
39260857 AAGGAAATTTTAAA-TTTAAAA-AAA-TTTTAATTTTTTTTCAACCATTTCGAAATAAAACCTTT
64 AAGGAAAGTTTAAATTTTAAAATAAATTTTTAA-TTTTTTTCAACCATTTCGAAATAAAACCTTT
**
39260919 CATCTTTAAGAAAAGTAGTGAT
128 CATCTTTAAGAAAAACAGTGAT
*
39260941 TTTTTTAAAAAAAAA
1 TTTTTTTAAAAAAAA
39260956 ATCACATATC
Statistics
Matches: 145, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
148 5 0.03
149 63 0.43
150 44 0.30
152 33 0.23
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (149 bp):
TTTTTTTAAAAAAAAGAGAAAATTTAGATTTTTAAAAATAAAAAATATTTTTTAGCCATTTTAAA
GGAAAGTTTAAATTTTAAAATAAATTTTTAATTTTTTTCAACCATTTCGAAATAAAACCTTTCAT
CTTTAAGAAAAACAGTGAT
Found at i:39261229 original size:25 final size:25
Alignment explanation
Indices: 39261201--39261265 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
39261191 AGATATATGA
*
39261201 CTCTTCGGAGCTTCCCTATTAAAGG
1 CTCTTCGGAGCTTCCCGATTAAAGG
* * *
39261226 CTCTTTCATGAGCTTCTCGATTAATGG
1 CTC-TTC-GGAGCTTCCCGATTAAAGG
*
39261253 CTCTCCGGAGCTT
1 CTCTTCGGAGCTT
39261266 TTCGATATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 9 0.28
26 5 0.16
27 18 0.56
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (25 bp):
CTCTTCGGAGCTTCCCGATTAAAGG
Found at i:39261335 original size:24 final size:25
Alignment explanation
Indices: 39261308--39261365 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
39261298 TGGCTTGTAT
*
39261308 GAGCTTCCCATTA-ATGGCTCTTC-A
1 GAGCTTCCCATTACATGGCTC-ACAA
* *
39261332 GAGCTTCTCTTTACATGGCTCACAA
1 GAGCTTCCCATTACATGGCTCACAA
39261357 GAGCTTCCC
1 GAGCTTCCC
39261366 GTTTATATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCATTACATGGCTCACAA
Found at i:39271641 original size:27 final size:25
Alignment explanation
Indices: 39271602--39271674 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 25
39271592 CCAGATATAT
39271602 GGCTCTTCGGAGCTTCCCGATTAAA
1 GGCTCTTCGGAGCTTCCCGATTAAA
* * *
39271627 GGCTTTTTCATGAGCTTCCCGATTAAT
1 GGC-TCTTC-GGAGCTTCCCGATTAAA
39271654 GGCTCTTCGGAGCTTCCCGAT
1 GGCTCTTCGGAGCTTCCCGAT
39271675 ATCGGCTCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 15 0.37
26 8 0.20
27 18 0.44
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.33
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCCGATTAAA
Found at i:39271763 original size:25 final size:23
Alignment explanation
Indices: 39271711--39271769 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 23
39271701 TAGCTCGTAT
*
39271711 GAGCTTCCCGTTAATGGCTCTTCG
1 GAGCTTCCCGTTAATGGC-CTTAG
39271735 GAGCTTCCCGTTACATGG-CTTAG
1 GAGCTTCCCGTTA-ATGGCCTTAG
39271758 AAGAGCTTCCCG
1 --GAGCTTCCCG
39271770 ATTATATGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 4 0.13
24 13 0.42
25 14 0.45
ACGTcount: A:0.17, C:0.29, G:0.25, T:0.29
Consensus pattern (23 bp):
GAGCTTCCCGTTAATGGCCTTAG
Found at i:39271788 original size:25 final size:26
Alignment explanation
Indices: 39271583--39271796 Score: 96
Period size: 24 Copynumber: 8.5 Consensus size: 26
39271573 CCACAGCTGT
* * *
39271583 TATGAGCGTCCAGA-TATATGGCTCT
1 TATGAGCTTCCCGATTATATGGCTCG
** * **
39271608 TCGGAGCTTCCCGATTA-AAGGCTTTT
1 TATGAGCTTCCCGATTATATGGC-TCG
*
39271634 TCATGAGCTTCCCGATTA-ATGGCTCT
1 T-ATGAGCTTCCCGATTATATGGCTCG
** *
39271660 TCGGAGCTTCCCGA-TAT-CGGCTCG
1 TATGAGCTTCCCGATTATATGGCTCG
* *
39271684 CT-TGAAG-TTCTCGA-TAT-TAGCTCG
1 -TATG-AGCTTCCCGATTATATGGCTCG
*
39271708 TATGAGCTTCCCG-TTA-ATGGCTCT
1 TATGAGCTTCCCGATTATATGGCTCG
** * *
39271732 TCGGAGCTTCCCG-TTACATGGCTTAG
1 TATGAGCTTCCCGATTATATGGC-TCG
*
39271758 -AAGAGCTTCCCGATTATAT-GCTCG
1 TATGAGCTTCCCGATTATATGGCTCG
39271782 TATGAGCATTCCCGA
1 TATGAGC-TTCCCGA
39271797 ATATGAATTG
Statistics
Matches: 144, Mismatches: 30, Indels: 29
0.71 0.15 0.14
Matches are distributed among these distances:
23 3 0.02
24 52 0.36
25 50 0.35
26 21 0.15
27 18 0.12
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (26 bp):
TATGAGCTTCCCGATTATATGGCTCG
Found at i:39273546 original size:39 final size:40
Alignment explanation
Indices: 39273501--39273603 Score: 145
Period size: 39 Copynumber: 2.5 Consensus size: 40
39273491 AAATATATTT
* *
39273501 ATTTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
39273540 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
39273580 ATTTTTGTTTTAAATTTTAAAATA
1 A--TTT-TTTT-AATTTTAAAATA
39273604 AATTTTTGGT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
39 30 0.53
40 8 0.14
42 3 0.05
43 4 0.07
44 12 0.21
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:39276439 original size:21 final size:21
Alignment explanation
Indices: 39276407--39276544 Score: 114
Period size: 21 Copynumber: 6.6 Consensus size: 21
39276397 GAAGCCCGAA
* *
39276407 AGCTTAACAGAAGCTCATGAG
1 AGCTAAACAGAAGCTCATAAG
*
39276428 AGCTAAATAGAAGCTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* *
39276449 AGCTAAACAGAAACCCATAAG
1 AGCTAAACAGAAGCTCATAAG
* * * * * *
39276470 GGTTGATCAGAAGCTCGTAAA
1 AGCTAAACAGAAGCTCATAAG
* *
39276491 AGCTTAACAGAAACTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* * * *
39276512 AGTTTAACAAAAGCTCGTAAG
1 AGCTAAACAGAAGCTCATAAG
*
39276533 AGCTGAACAGAA
1 AGCTAAACAGAA
39276545 ACTTGTATGA
Statistics
Matches: 89, Mismatches: 28, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 89 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.18
Consensus pattern (21 bp):
AGCTAAACAGAAGCTCATAAG
Found at i:39276459 original size:42 final size:42
Alignment explanation
Indices: 39276407--39276583 Score: 176
Period size: 42 Copynumber: 4.2 Consensus size: 42
39276397 GAAGCCCGAA
* * * * * *
39276407 AGCTTAACAGAAGCTCATGAGAGCTAAATAGAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAGAGTTTAATAGAAGCTCGTAAG
* * * * *
39276449 AGCTAAACAGAAACCCATAAG-GGTTGATCAGAAGCTCGTAAA
1 AGCTGAACAGAAACTCATAAGAGTTTAAT-AGAAGCTCGTAAG
* * *
39276491 AGCTTAACAGAAACTCATAAGAGTTTAACAAAAGCTCGTAAG
1 AGCTGAACAGAAACTCATAAGAGTTTAATAGAAGCTCGTAAG
** * *
39276533 AGCTGAACAGAAACTTGTATGAGTTGAATAGAAGCTCGTAAG
1 AGCTGAACAGAAACTCATAAGAGTTTAATAGAAGCTCGTAAG
39276575 AGCTGAACA
1 AGCTGAACA
39276584 AAAAGTAAAA
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 4 0.04
42 102 0.93
43 4 0.04
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.20
Consensus pattern (42 bp):
AGCTGAACAGAAACTCATAAGAGTTTAATAGAAGCTCGTAAG
Found at i:39276559 original size:84 final size:84
Alignment explanation
Indices: 39276405--39276583 Score: 207
Period size: 84 Copynumber: 2.1 Consensus size: 84
39276395 CAGAAGCCCG
* * * *
39276405 AAAGCTTAACAGAAGCTCATGAGAGCTAAATAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
1 AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAG
*
39276470 GGTTG-ATCAGAAGCTCGTA
66 AGTTGAAT-AGAAGCTCGTA
* * * * *** *
39276489 AAAGCTTAACAGAAACTCATAAGAGTTTAACAAAAGCTCGTAAGAGCTGAACAGAAACTTGTATG
1 AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAG
39276554 AGTTGAATAGAAGCTCGTA
66 AGTTGAATAGAAGCTCGTA
* *
39276573 AGAGCTGAACA
1 AAAGCTTAACA
39276584 AAAAGTAAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
84 77 0.97
85 2 0.03
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (84 bp):
AAAGCTTAACAGAAACTCATAAGAGCTAAACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAG
AGTTGAATAGAAGCTCGTA
Found at i:39276560 original size:21 final size:21
Alignment explanation
Indices: 39276407--39276583 Score: 113
Period size: 21 Copynumber: 8.4 Consensus size: 21
39276397 GAAGCCCGAA
* * * *
39276407 AGCTTAACAGAAGCTCATGAG
1 AGCTGAACAGAAACTCGTAAG
* * * *
39276428 AGCTAAATAGAAGCTCATAAG
1 AGCTGAACAGAAACTCGTAAG
* * *
39276449 AGCTAAACAGAAACCCATAAG
1 AGCTGAACAGAAACTCGTAAG
* * * * *
39276470 GGTTGATCAGAAGCTCGTAAA
1 AGCTGAACAGAAACTCGTAAG
* *
39276491 AGCTTAACAGAAACTCATAAG
1 AGCTGAACAGAAACTCGTAAG
* *
39276512 AGTTTAACA-AAAGCTCGTAAG
1 AGCTGAACAGAAA-CTCGTAAG
* *
39276533 AGCTGAACAGAAACTTGTATG
1 AGCTGAACAGAAACTCGTAAG
* * *
39276554 AGTTGAATAGAAGCTCGTAAG
1 AGCTGAACAGAAACTCGTAAG
39276575 AGCTGAACA
1 AGCTGAACA
39276584 AAAAGTAAAA
Statistics
Matches: 120, Mismatches: 34, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
20 3 0.03
21 114 0.95
22 3 0.03
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
AGCTGAACAGAAACTCGTAAG
Found at i:39281489 original size:23 final size:23
Alignment explanation
Indices: 39281455--39281498 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
39281445 TAAATTATAA
39281455 AATATATAAAAA-TAACAAAATAT
1 AATATATAAAAATTAA-AAAATAT
39281478 AATAT-TAGAAAATTAAAAAAT
1 AATATATA-AAAATTAAAAAAT
39281499 TAAGCTGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.11
23 14 0.74
24 3 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AATATATAAAAATTAAAAAATAT
Found at i:39284078 original size:74 final size:74
Alignment explanation
Indices: 39283957--39284180 Score: 448
Period size: 74 Copynumber: 3.0 Consensus size: 74
39283947 CTAACTTGCT
39283957 CATTTTTTGCAGTGAAGATACTAAAATGTAATTCAAAATATAATACATGTGATTTTATGATCAAA
1 CATTTTTTGCAGTGAAGATACTAAAATGTAATTCAAAATATAATACATGTGATTTTATGATCAAA
39284022 TAAGTGGGG
66 TAAGTGGGG
39284031 CATTTTTTGCAGTGAAGATACTAAAATGTAATTCAAAATATAATACATGTGATTTTATGATCAAA
1 CATTTTTTGCAGTGAAGATACTAAAATGTAATTCAAAATATAATACATGTGATTTTATGATCAAA
39284096 TAAGTGGGG
66 TAAGTGGGG
39284105 CATTTTTTGCAGTGAAGATACTAAAATGTAATTCAAAATATAATACATGTGATTTTATGATCAAA
1 CATTTTTTGCAGTGAAGATACTAAAATGTAATTCAAAATATAATACATGTGATTTTATGATCAAA
39284170 TAAGTGGGG
66 TAAGTGGGG
39284179 CA
1 CA
39284181 GAGACTATTC
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 150 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (74 bp):
CATTTTTTGCAGTGAAGATACTAAAATGTAATTCAAAATATAATACATGTGATTTTATGATCAAA
TAAGTGGGG
Found at i:39288266 original size:58 final size:58
Alignment explanation
Indices: 39288187--39288296 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
39288177 TAGTAGTTAC
* * *
39288187 TCAACTATTAGTAAGTATTTTTTGATCACTCAACTATGAAAAATTATAAAATGACCAT
1 TCAACTATTAGTAAATATTTTTTGATCACCCAACTATGAAAAATTACAAAATGACCAT
* * * * *
39288245 TCAATTATTAGTAAATTTTTTTTGGTTACCCAACTATGAAAAGTTACAAAAT
1 TCAACTATTAGTAAATATTTTTTGATCACCCAACTATGAAAAATTACAAAAT
39288297 AGCCACCTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (58 bp):
TCAACTATTAGTAAATATTTTTTGATCACCCAACTATGAAAAATTACAAAATGACCAT
Found at i:39292903 original size:2 final size:2
Alignment explanation
Indices: 39292898--39292930 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39292888 NNNNNNTCAA
39292898 AT AT AT 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 AT AT AT A
39292931 ATTATGACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39306502 original size:23 final size:23
Alignment explanation
Indices: 39306476--39306537 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
39306466 TAATATCCCG
39306476 AAAATTACTACTATAATACCTCA
1 AAAATTACTACTATAATACCTCA
* *
39306499 AAAATTACTACTATAATACTTCG
1 AAAATTACTACTATAATACCTCA
*
39306522 AAAATTACTACAATAA
1 AAAATTACTACTATAA
39306538 GAAAGTAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATTACTACTATAATACCTCA
Found at i:39306536 original size:20 final size:21
Alignment explanation
Indices: 39306466--39306536 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 21
39306456 ACTGTAATTG
39306466 TAATATCC-CGAAAATTACTAC
1 TAATA-CCTCGAAAATTACTAC
*
39306487 TATAATACCTCAAAAATTACTAC
1 --TAATACCTCGAAAATTACTAC
*
39306510 TATAATACTTCGAAAATTACTAC
1 --TAATACCTCGAAAATTACTAC
39306533 -AATA
1 TAATA
39306537 AGAAAGTAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
20 4 0.09
22 2 0.05
23 38 0.86
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (21 bp):
TAATACCTCGAAAATTACTAC
Found at i:39319945 original size:20 final size:20
Alignment explanation
Indices: 39319922--39319961 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39319912 TATTCAAACT
* *
39319922 ATATTACTTGAATAGTTATA
1 ATATTACATGAATAATTATA
*
39319942 ATATTAGATGAATAATTATA
1 ATATTACATGAATAATTATA
39319962 TGTCTTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
ATATTACATGAATAATTATA
Found at i:39321487 original size:27 final size:27
Alignment explanation
Indices: 39321449--39321503 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
39321439 CTTCCGGAAA
*
39321449 AGGTTTTAACCTTGAATGACGTATATT
1 AGGTTTTAACCTTGAATGACGCATATT
*
39321476 AGGTTTTAACCTTGAATGATGCATATT
1 AGGTTTTAACCTTGAATGACGCATATT
39321503 A
1 A
39321504 TGTATCAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (27 bp):
AGGTTTTAACCTTGAATGACGCATATT
Found at i:39326111 original size:13 final size:13
Alignment explanation
Indices: 39326093--39326117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39326083 ACCAACGATA
39326093 AAATTTTCACACG
1 AAATTTTCACACG
39326106 AAATTTTCACAC
1 AAATTTTCACAC
39326118 ATATAAATTA
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:39328356 original size:52 final size:51
Alignment explanation
Indices: 39328279--39328377 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 51
39328269 AAAAGTTTTG
*
39328279 GGGGTTTGGAGGGAAGTAAAGTTTTGAGAGAAAGCAAAAGGAAAAAAAAAA
1 GGGGTTTAGAGGGAAGTAAAGTTTTGAGAGAAAGCAAAAGGAAAAAAAAAA
* * *
39328330 GGGGTTTAGA-GGAAGTAACATTTTTTGGGAGAAAGTAAAAGGAAAAAA
1 GGGGTTTAGAGGGAAGTAA-A-GTTTTGAGAGAAAGCAAAAGGAAAAAA
39328378 CTTTTGAGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
50 8 0.19
51 10 0.24
52 24 0.57
ACGTcount: A:0.46, C:0.02, G:0.32, T:0.19
Consensus pattern (51 bp):
GGGGTTTAGAGGGAAGTAAAGTTTTGAGAGAAAGCAAAAGGAAAAAAAAAA
Found at i:39331713 original size:21 final size:21
Alignment explanation
Indices: 39331689--39331732 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
39331679 TACAATAATT
* * *
39331689 ATTTATTAGATGTTTATTAAA
1 ATTTAATAGATATTTATCAAA
*
39331710 ATTTAATATATATTTATCAAA
1 ATTTAATAGATATTTATCAAA
39331731 AT
1 AT
39331733 AATACCTATA
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:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
ATTTAATAGATATTTATCAAA
Found at i:39331955 original size:15 final size:16
Alignment explanation
Indices: 39331935--39331964 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39331925 AATACCCAAC
39331935 TTTTTTTT-CTTTTCT
1 TTTTTTTTCCTTTTCT
39331950 TTTTTTTTCCTTTTC
1 TTTTTTTTCCTTTTC
39331965 CGTGTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTTCCTTTTCT
Found at i:39334791 original size:304 final size:304
Alignment explanation
Indices: 39334235--39334842 Score: 1207
Period size: 304 Copynumber: 2.0 Consensus size: 304
39334225 TTTACATTAC
39334235 AAGAAAGAAACTTACTTTAGTAGATAATCTAAATAAGTGTATAATCCCGTAAAAGAATCGAAGTG
1 AAGAAAGAAACTTACTTTAGTAGATAATCTAAATAAGTGTATAATCCCGTAAAAGAATCGAAGTG
39334300 AGCATTTGATTCAAATACTAAAAAGGATTATTATGTCGTTTACAATTCTAATTGGAGAGATGGCT
66 AGCATTTGATTCAAATACTAAAAAGGATTATTATGTCGTTTACAATTCTAATTGGAGAGATGGCT
39334365 AGTCTTGGCTATCAAAACAGTTGACTCCACGGGTAGAGACGTAGATTTATTCATTGGTAGAATGA
131 AGTCTTGGCTATCAAAACAGTTGACTCCACGGGTAGAGACGTAGATTTATTCATTGGTAGAATGA
39334430 TACATTAGACTGGACCTAAGATGAATTAATTTTGAATACATTTGTAAATTAATTCACTTGTGACG
196 TACATTAGACTGGACCTAAGATGAATTAATTTTGAATACATTTGTAAATTAATTCACTTGTGACG
39334495 TTCATGGTGTGATTTACCTAAATCCTGAGTTAGTTGCTGACCAT
261 TTCATGGTGTGATTTACCTAAATCCTGAGTTAGTTGCTGACCAT
39334539 AAGAAAGAAACTTACTTTAGTAGATAATCTAAATAAGTGTATAATCCCGTAAAAGAATCGAAGTG
1 AAGAAAGAAACTTACTTTAGTAGATAATCTAAATAAGTGTATAATCCCGTAAAAGAATCGAAGTG
39334604 AGCATTTGATTCAAATACTAAAAAGGATTATTATGTCGTTTACAATTCTAATTGGAGAGATGGCT
66 AGCATTTGATTCAAATACTAAAAAGGATTATTATGTCGTTTACAATTCTAATTGGAGAGATGGCT
39334669 AGTCTTGGCTATCAAAACAGTTGACTCCACGGGTAGAGACGTAGATTTATTCATTGGTAGAATGA
131 AGTCTTGGCTATCAAAACAGTTGACTCCACGGGTAGAGACGTAGATTTATTCATTGGTAGAATGA
*
39334734 TACATTAGACTGGACCTAAGATGAATTAATTTTGAATACATTTGTAAATTCATTCACTTGTGACG
196 TACATTAGACTGGACCTAAGATGAATTAATTTTGAATACATTTGTAAATTAATTCACTTGTGACG
39334799 TTCATGGTGTGATTTACCTAAATCCTGAGTTAGTTGCTGACCAT
261 TTCATGGTGTGATTTACCTAAATCCTGAGTTAGTTGCTGACCAT
39334843 GCGTATGCAA
Statistics
Matches: 303, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
304 303 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (304 bp):
AAGAAAGAAACTTACTTTAGTAGATAATCTAAATAAGTGTATAATCCCGTAAAAGAATCGAAGTG
AGCATTTGATTCAAATACTAAAAAGGATTATTATGTCGTTTACAATTCTAATTGGAGAGATGGCT
AGTCTTGGCTATCAAAACAGTTGACTCCACGGGTAGAGACGTAGATTTATTCATTGGTAGAATGA
TACATTAGACTGGACCTAAGATGAATTAATTTTGAATACATTTGTAAATTAATTCACTTGTGACG
TTCATGGTGTGATTTACCTAAATCCTGAGTTAGTTGCTGACCAT
Found at i:39338092 original size:39 final size:39
Alignment explanation
Indices: 39338052--39338187 Score: 236
Period size: 39 Copynumber: 3.5 Consensus size: 39
39338042 ATTCACTTTT
* * * *
39338052 AAGCATATATCACATTACACATATAAGCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
39338091 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
39338130 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
39338169 AAGCATATATCACAATACT
1 AAGCATATATCACAATACT
39338188 TAAAAACATG
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:39338121 original size:17 final size:17
Alignment explanation
Indices: 39338094--39338160 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
39338084 AACATTTAAG
39338094 CATAT-ATCACAATACT
1 CATATAATCACAATACT
39338110 CATATAATCAC-ATAACATT
1 CATATAATCACAAT-AC--T
*
39338129 CAAGCATATATCACAATACT
1 C-A-TATA-ATCACAATACT
39338149 CATATAATCACA
1 CATATAATCACA
39338161 TAACATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
16 7 0.17
17 13 0.32
18 3 0.07
19 3 0.07
20 3 0.07
21 3 0.07
22 7 0.17
23 2 0.05
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.28
Consensus pattern (17 bp):
CATATAATCACAATACT
Found at i:39338257 original size:16 final size:15
Alignment explanation
Indices: 39338222--39338260 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
39338212 ACATAATGGT
*
39338222 CACATATCATATAAA
1 CACATATCAAATAAA
*
39338237 CACATATCACAATACA
1 CACATATCA-AATAAA
39338253 CACATATC
1 CACATATC
39338261 CATAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (15 bp):
CACATATCAAATAAA
Found at i:39342864 original size:48 final size:48
Alignment explanation
Indices: 39342809--39342904 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
39342799 AGTCGAGAAA
39342809 CGATTTAGACCGCTTGCACAAAGCACAGATAATAATTCAATTTAAGAT
1 CGATTTAGACCGCTTGCACAAAGCACAGATAATAATTCAATTTAAGAT
39342857 CGATTTAGACCGCTTGCACAAAGCACAGATAATAATTCAATTTAAGAT
1 CGATTTAGACCGCTTGCACAAAGCACAGATAATAATTCAATTTAAGAT
39342905 TTATTACTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (48 bp):
CGATTTAGACCGCTTGCACAAAGCACAGATAATAATTCAATTTAAGAT
Found at i:39344738 original size:10 final size:10
Alignment explanation
Indices: 39344723--39344754 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
39344713 TTTAAAATAC
39344723 TTTTTTTAAA
1 TTTTTTTAAA
39344733 -TTTTTTAAA
1 TTTTTTTAAA
39344742 TTTTTTTAAA
1 TTTTTTTAAA
39344752 TTT
1 TTT
39344755 AAAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:39344745 original size:8 final size:9
Alignment explanation
Indices: 39344724--39344754 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
39344714 TTAAAATACT
39344724 TTTTTTAAA
1 TTTTTTAAA
39344733 TTTTTTAAA
1 TTTTTTAAA
39344742 TTTTTTTAAA
1 -TTTTTTAAA
39344752 TTT
1 TTT
39344755 AAAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:39344763 original size:19 final size:19
Alignment explanation
Indices: 39344702--39344765 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
39344692 TTTTATTTTT
*
39344702 TATTTTTTT-ATTTTAAAA
1 TATTTTTTTAAATTTAAAA
**
39344720 TACTTTTTTTAAATTTTTTAA
1 TA-TTTTTTTAAA-TTTAAAA
39344741 -ATTTTTTTAAATTTAAAA
1 TATTTTTTTAAATTTAAAA
39344759 TATTTTT
1 TATTTTT
39344766 AAAATACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 7 0.19
19 23 0.62
20 2 0.05
21 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TATTTTTTTAAATTTAAAA
Found at i:39344777 original size:39 final size:38
Alignment explanation
Indices: 39344703--39344777 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
39344693 TTTATTTTTT
* ** *
39344703 ATTTTTTTATTTTAAAATACTTTTTTTAAATTTTTTAA
1 ATTTTTTTAATTTAAAATACTTTTTAAAAACTTTTTAA
39344741 ATTTTTTTAAATTTAAAATA-TTTTTAAAATACTTTTT
1 ATTTTTTT-AATTTAAAATACTTTTTAAAA-ACTTTTT
39344778 TTATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
38 15 0.48
39 16 0.52
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (38 bp):
ATTTTTTTAATTTAAAATACTTTTTAAAAACTTTTTAA
Found at i:39344784 original size:20 final size:18
Alignment explanation
Indices: 39344702--39344765 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
39344692 TTTTATTTTT
39344702 TATTTTTTTATTTTAAAA
1 TATTTTTTTATTTTAAAA
*
39344720 TACTTTTTTTAAATTTTTTAAA
1 TA-TTTTTTT--A-TTTTAAAA
* *
39344742 T-TTTTTTAAATTTAAAA
1 TATTTTTTTATTTTAAAA
39344759 TATTTTT
1 TATTTTT
39344766 AAAATACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 7 0.19
18 8 0.22
19 7 0.19
20 6 0.16
21 1 0.03
22 8 0.22
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTTTTATTTTAAAA
Found at i:39344784 original size:39 final size:37
Alignment explanation
Indices: 39344697--39344822 Score: 105
Period size: 37 Copynumber: 3.3 Consensus size: 37
39344687 AATATTTTTA
* *
39344697 TTTTTTATTTTTTTATTTTAAAATACTTTTTTTAAATT
1 TTTTTTATTTTTTTAATTTAAAATAC-TTTTTAAAATT
**
39344735 TTTTAAATTTTTTTAAATTTAAAATA-TTTTTAAAATACT
1 TTTTTTATTTTTTT-AATTTAAAATACTTTTTAAAAT--T
** * *
39344774 TTTTTTATTTTAAAATATTTTAAAATACTTTTT-TAA-T
1 TTTTTTATTTT--TTTAATTTAAAATACTTTTTAAAATT
39344811 TTTTTTATTTTT
1 TTTTTTATTTTT
39344823 AAAATAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
37 21 0.30
38 12 0.17
39 20 0.28
40 12 0.17
41 6 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (37 bp):
TTTTTTATTTTTTTAATTTAAAATACTTTTTAAAATT
Found at i:39344795 original size:29 final size:30
Alignment explanation
Indices: 39344742--39344813 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
39344732 ATTTTTTAAA
*
39344742 TTTTTTTAAATTTAAAATATTTTTAAAATAC
1 TTTTTTT-ATTTTAAAATATTTTTAAAATAC
39344773 TTTTTTTATTTTAAAATA-TTTTAAAATAC
1 TTTTTTTATTTTAAAATATTTTTAAAATAC
*
39344802 TTTTTTAATTTT
1 TTTTTTTATTTT
39344814 TTTATTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 22 0.56
30 10 0.26
31 7 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTTTTATTTTAAAATATTTTTAAAATAC
Found at i:39344822 original size:28 final size:28
Alignment explanation
Indices: 39344726--39344828 Score: 104
Period size: 29 Copynumber: 3.7 Consensus size: 28
39344716 AAAATACTTT
*
39344726 TTTTAA-ATTTTTTAAAT--TTTTTTAAA
1 TTTTAATATTTTTAAAATACTTTTTT-AA
* *
39344752 TTTAAAATATTTTTAAAATACTTTTTTTA
1 TTT-TAATATTTTTAAAATACTTTTTTAA
*
39344781 TTTTAAAATATTTTAAAATACTTTTTTAA
1 TTTTAATAT-TTTTAAAATACTTTTTTAA
**
39344810 TTTTTTTATTTTTAAAATA
1 TTTTAATATTTTTAAAATA
39344829 AATTTTTGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
26 3 0.05
27 2 0.03
28 24 0.38
29 28 0.44
30 6 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAATATTTTTAAAATACTTTTTTAA
Found at i:39348336 original size:22 final size:23
Alignment explanation
Indices: 39348299--39348341 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
39348289 ATTTTATTTT
39348299 CAATAAAAATGAATAATAAAATC
1 CAATAAAAATGAATAATAAAATC
*
39348322 CAAT-AAATTGAATAATAAAA
1 CAATAAAAATGAATAATAAAA
39348342 GAGGGCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (23 bp):
CAATAAAAATGAATAATAAAATC
Found at i:39359274 original size:16 final size:15
Alignment explanation
Indices: 39359232--39359278 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
39359222 TCTATACGAG
*
39359232 TAAATTTAATTCAAT
1 TAAATTCAATTCAAT
* *
39359247 TTAATACAATTCATAT
1 TAAATTCAATTCA-AT
39359263 TAAATTCAATTCAAT
1 TAAATTCAATTCAAT
39359278 T
1 T
39359279 CACATCTTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTCAATTCAAT
Found at i:39364564 original size:17 final size:18
Alignment explanation
Indices: 39364532--39364565 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39364522 GTTAACGACG
*
39364532 AAGAAGAAAAATAAAAGA
1 AAGAAGAAAAAGAAAAGA
39364550 AAGAA-AAAAAGAAAAG
1 AAGAAGAAAAAGAAAAG
39364566 GAGAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (18 bp):
AAGAAGAAAAAGAAAAGA
Found at i:39368567 original size:41 final size:41
Alignment explanation
Indices: 39368500--39368650 Score: 135
Period size: 41 Copynumber: 3.7 Consensus size: 41
39368490 TTTCGGGGGC
* *
39368500 TTTAGTGGCGTTTTTAGA-ATAT-CGCCGCTAATGCTTGAGGT
1 TTTAGCGGCGTTTTTA-ATA-ATGCGCCGCTAATGCTCGAGGT
* * *
39368541 TTTAGCGGCGTTTATAATAATGCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTAATAATGCGCCGCTAATGCTCGAGGT
* ** ** **
39368582 TTTAGTGGCGTTTTTTGTGTTGCGCCGCTAATGCTCGCTGT
1 TTTAGCGGCGTTTTTAATAATGCGCCGCTAATGCTCGAGGT
* * *
39368623 ATTAGCGGCGTTTTTGATAAAGCGCCGC
1 TTTAGCGGCGTTTTTAATAATGCGCCGC
39368651 AAAAAAAATA
Statistics
Matches: 87, Mismatches: 21, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
40 3 0.03
41 84 0.97
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAATAATGCGCCGCTAATGCTCGAGGT
Found at i:39368630 original size:82 final size:82
Alignment explanation
Indices: 39368495--39368650 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 82
39368485 TGACCTTTCG
* *
39368495 GGGGCTTTAGTGGCGTTTTTAGAATATCGCCGCTAATGCTTGAGGTTTTAGCGGCGTTTATAATA
1 GGGGCTTTAGTGGCGTTTTTAGAATATCGCCGCTAATGCTCGAGGTATTAGCGGCGTTTATAATA
*
39368560 ATGCGCCGCTAATGCTC
66 AAGCGCCGCTAATGCTC
* ** ** * *
39368577 GGGGCTTTAGTGGCGTTTTTTGTGT-TGCGCCGCTAATGCTCGCTGTATTAGCGGCGTTTTTGAT
1 GGGGCTTTAGTGGCGTTTTTAGAATAT-CGCCGCTAATGCTCGAGGTATTAGCGGCGTTTATAAT
39368641 AAAGCGCCGC
65 AAAGCGCCGC
39368651 AAAAAAAATA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
81 1 0.02
82 62 0.98
ACGTcount: A:0.16, C:0.19, G:0.30, T:0.35
Consensus pattern (82 bp):
GGGGCTTTAGTGGCGTTTTTAGAATATCGCCGCTAATGCTCGAGGTATTAGCGGCGTTTATAATA
AAGCGCCGCTAATGCTC
Found at i:39369266 original size:7 final size:7
Alignment explanation
Indices: 39369256--39369316 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
39369246 GATTTAAGGT
*
39369256 TTAGAGG
1 TTAGGGG
39369263 TTAGGGG
1 TTAGGGG
39369270 TTAGGGG
1 TTAGGGG
39369277 TTAGGGG
1 TTAGGGG
**
39369284 TTAGAAG
1 TTAGGGG
* *
39369291 TTAAGAG
1 TTAGGGG
39369298 TTAGGGAG
1 TTAGGG-G
*
39369306 TTAGGGT
1 TTAGGGG
39369313 TTAG
1 TTAG
39369317 ATCTTAATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
7 38 0.84
8 7 0.16
ACGTcount: A:0.25, C:0.00, G:0.44, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:39369323 original size:29 final size:28
Alignment explanation
Indices: 39369269--39369323 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
39369259 GAGGTTAGGG
*
39369269 GTTAGGGGTTAGGGGTTAGAAGTTAAGA
1 GTTAGGGGTTAGGGGTTAGAACTTAAGA
* *
39369297 GTTAGGGAGTTAGGGTTTAGATCTTAA
1 GTTAGGG-GTTAGGGGTTAGAACTTAA
39369324 TTAGTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (28 bp):
GTTAGGGGTTAGGGGTTAGAACTTAAGA
Found at i:39369589 original size:7 final size:7
Alignment explanation
Indices: 39369579--39369610 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
39369569 GATTTAAGGT
39369579 TTAGGGG
1 TTAGGGG
39369586 TTAGGGG
1 TTAGGGG
39369593 TTAGGGG
1 TTAGGGG
39369600 TTAGGGG
1 TTAGGGG
39369607 TTAG
1 TTAG
39369611 AAGTTGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:39370877 original size:7 final size:7
Alignment explanation
Indices: 39370867--39370927 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
39370857 GATTTAAGGT
*
39370867 TTAGAGG
1 TTAGGGG
39370874 TTAGGGG
1 TTAGGGG
39370881 TTAGGGG
1 TTAGGGG
39370888 TTAGGGG
1 TTAGGGG
**
39370895 TTAGAAG
1 TTAGGGG
* *
39370902 TTAAGAG
1 TTAGGGG
39370909 TTAGGGAG
1 TTAGGG-G
*
39370917 TTAGGGT
1 TTAGGGG
39370924 TTAG
1 TTAG
39370928 ATCTTAATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
7 38 0.84
8 7 0.16
ACGTcount: A:0.25, C:0.00, G:0.44, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:39370934 original size:29 final size:28
Alignment explanation
Indices: 39370880--39370934 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
39370870 GAGGTTAGGG
*
39370880 GTTAGGGGTTAGGGGTTAGAAGTTAAGA
1 GTTAGGGGTTAGGGGTTAGAACTTAAGA
* *
39370908 GTTAGGGAGTTAGGGTTTAGATCTTAA
1 GTTAGGG-GTTAGGGGTTAGAACTTAA
39370935 TTAGTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (28 bp):
GTTAGGGGTTAGGGGTTAGAACTTAAGA
Found at i:39371743 original size:7 final size:7
Alignment explanation
Indices: 39371733--39371764 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
39371723 GATTTAAGGT
39371733 TTAGGGG
1 TTAGGGG
39371740 TTAGGGG
1 TTAGGGG
39371747 TTAGGGG
1 TTAGGGG
39371754 TTAGGGG
1 TTAGGGG
39371761 TTAG
1 TTAG
39371765 AAGTTGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:39372872 original size:337 final size:333
Alignment explanation
Indices: 39372194--39373501 Score: 1674
Period size: 337 Copynumber: 4.0 Consensus size: 333
39372184 AACGACGTTG
* * * *
39372194 TTTCTGTTAATTTTTAGTGGC-GTTTGTTCATGAAACGCCGCAACAGCGACTTAAAATATTGGCT
1 TTTCTGTTAATTTATAGTGGCATTTTGTTCAGGAAACGCCGCAAAAGCGACTTAAAATATTGGCT
* * *
39372258 AAACGACGCCGTTTAGCTTAAGCAAATT-AATTGTTAGTGGCGTTTTTAAAGAAAATGCCACAAA
66 AAACGACGCCGTTTAGCTTAAGCAAATTAAATT-TTAGTGGCGTTTTTACAGAAAACGCCAGAAA
* * ** *
39372322 TGTGCATTAAAGCTTTATTAAACGGTGCTGTTTCGGACAAGAACTTTAATTTTTAGTGGCGCTTC
130 TGTGCATTAAAGCTTTATTAAACGGCGCCGTTTCGGATTAGAACTTTAATTTTTAGTGGCGCTTT
* *
39372387 TTAGAAACGCCGCAAATGTACAAGCAATAGCAGCGTTTTTCTAGAAACGCCGCAAAAGTGTCATA
195 TTAGAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTTTCTAGAAACGCCGCAAAAGTGTCTTA
* * *
39372452 AAATTTTGGCTAAACAACACCGTTTCTGTACACGAAATTTAACTTAGTATTTTCTCTATATTAAT
260 AAATTTTGGCTAAACGACTCCGTTTCTGTACACGAATTTTAACTTAG-A-TTTCTCTATATTAAT
*
39372517 CCAACGGCGCC
323 CCAATGGCGCC
* *
39372528 GTTTCTGTTAATTTATAGTGGCATTTTGTTCAGGAAACGTCGCAAAAGCGACTTAAAATATCGGC
1 -TTTCTGTTAATTTATAGTGGCATTTTGTTCAGGAAACGCCGCAAAAGCGACTTAAAATATTGGC
* * *
39372593 TAAACGACACTGTTTAGCTTAAGCAAATTAAATTTTAGTGGCGTTTTTACAGAAAACACCAGAAA
65 TAAACGACGCCGTTTAGCTTAAGCAAATTAAATTTTAGTGGCGTTTTTACAGAAAACGCCAGAAA
* *
39372658 TGTGCATTAAAGCTTTATTAAACGGTGCCGTTTCGGATTAGAACTTTAATTTTTAGTGGCGATTT
130 TGTGCATTAAAGCTTTATTAAACGGCGCCGTTTCGGATTAGAACTTTAATTTTTAGTGGCGCTTT
*
39372723 TTAAGAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTTTCTAGAAATGCCGCAAAAGTGTCTT
195 TT-AGAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTTTCTAGAAACGCCGCAAAAGTGTCTT
39372788 AAAATTTTGGCTAAACGACTCCGTTTCTGTACACGAATTTTAACTTAGAATTTTCTCTATATTAA
259 AAAATTTTGGCTAAACGACTCCGTTTCTGTACACGAATTTTAACTTAG-A-TTTCTCTATATTAA
39372853 TCCAATGGCGCC
322 TCCAATGGCGCC
** * *
39372865 ATTTCTGTTAATTTATAGTGGCATTTCATTCAGGAAACTCCGCAAAAGCGACTTAAAATATTGGT
1 -TTTCTGTTAATTTATAGTGGCATTTTGTTCAGGAAACGCCGCAAAAGCGACTTAAAATATTGGC
*
39372930 TAAACGACGCCGTTTAGCTTAAGCAAATTAAATTTTAGTGGCGTTTTTACAGAAAATGCCAGAAA
65 TAAACGACGCCGTTTAGCTTAAGCAAATTAAATTTTAGTGGCGTTTTTACAGAAAACGCCAGAAA
* *
39372995 TGTGCATTAAAGCTTTATTAAACAGCGTCGTTTCGGATTAGAACTTTAATTTTTAGTGGCGCTTT
130 TGTGCATTAAAGCTTTATTAAACGGCGCCGTTTCGGATTAGAACTTTAATTTTTAGTGGCGCTTT
* * * * * *
39373060 TCTAGAAGCACCACAAATGTACAAGAAATAGCGGCGTTTTTTTAGAAATGCCGCAAAAGTGTCTT
195 T-TAGAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTTTCTAGAAACGCCGCAAAAGTGTCTT
39373125 AAAATTTTGGCTAAACGA-TGCCGTTTCTGTACACGAATTTTAACTTAG------C-AT-TT--T
259 AAAATTTTGGCTAAACGACT-CCGTTTCTGTACACGAATTTTAACTTAGATTTCTCTATATTAAT
39373179 -C--T---G--
323 CCAATGGCGCC
* * * ** *
39373182 TTTTTGTTAATTTCTAGTGGCA-TTTGTGCACAAAACGCCGCAAAAGTGACTTAAAATATTGGCT
1 TTTCTGTTAATTTATAGTGGCATTTTGTTCAGGAAACGCCGCAAAAGCGACTTAAAATATTGGCT
* * * *
39373246 AAACGACCCCGTTTAGCTTAAGCAAATTAAATTTTAGTGGC-ATTTTACGGAAAACGCTAGAAAC
66 AAACGACGCCGTTTAGCTTAAGCAAATTAAATTTTAGTGGCGTTTTTACAGAAAACGCCAGAAA-
* * * * * * * *
39373310 TGTGCATTACAGCTTAATTGAACGACGCCATTTGGGATTAGAACTTTAATTTTTGGTGGCGTTTT
130 TGTGCATTAAAGCTTTATTAAACGGCGCCGTTTCGGATTAGAACTTTAATTTTTAGTGGCG--CT
* * * * * * * *
39373375 TTTTA-AAATGCCTCAAATGTGCTAGCAATAGCGGCGTTTTGTCAAAAAACGCCGTAAAAGTTTC
193 TTTTAGAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTT-TCTAGAAACGCCGCAAAAGTGTC
* * ** *
39373439 TTACAATTTTGGCTAAACGACGCCGTTTCTGTACATCGTGTTTTAACTTATCATTTCTCTATA
257 TTAAAATTTTGGCTAAACGACTCCGTTTCTGTACA-CGAATTTTAACTTA-GATTTCTCTATA
39373502 AGGCAGAACA
Statistics
Matches: 865, Mismatches: 88, Indels: 49
0.86 0.09 0.05
Matches are distributed among these distances:
314 18 0.02
315 154 0.18
316 71 0.08
317 16 0.02
319 1 0.00
322 1 0.00
324 2 0.00
325 3 0.00
327 2 0.00
328 2 0.00
329 1 0.00
335 20 0.02
336 154 0.18
337 419 0.48
338 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (333 bp):
TTTCTGTTAATTTATAGTGGCATTTTGTTCAGGAAACGCCGCAAAAGCGACTTAAAATATTGGCT
AAACGACGCCGTTTAGCTTAAGCAAATTAAATTTTAGTGGCGTTTTTACAGAAAACGCCAGAAAT
GTGCATTAAAGCTTTATTAAACGGCGCCGTTTCGGATTAGAACTTTAATTTTTAGTGGCGCTTTT
TAGAAACGCCGCAAATGTACAAGCAATAGCGGCGTTTTTCTAGAAACGCCGCAAAAGTGTCTTAA
AATTTTGGCTAAACGACTCCGTTTCTGTACACGAATTTTAACTTAGATTTCTCTATATTAATCCA
ATGGCGCC
Found at i:39373869 original size:13 final size:14
Alignment explanation
Indices: 39373838--39373869 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39373828 AAAGTACCGA
39373838 TCTTCTGTGTTTGT
1 TCTTCTGTGTTTGT
39373852 T-TTCTG-GTTTGT
1 TCTTCTGTGTTTGT
39373864 TCTTCT
1 TCTTCT
39373870 AATTGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 9 0.53
14 1 0.06
ACGTcount: A:0.00, C:0.16, G:0.19, T:0.66
Consensus pattern (14 bp):
TCTTCTGTGTTTGT
Found at i:39374630 original size:18 final size:18
Alignment explanation
Indices: 39374609--39374694 Score: 84
Period size: 18 Copynumber: 4.6 Consensus size: 18
39374599 CTTACACTAC
*
39374609 TTACTAAAATATATTTCA
1 TTACTAAAATATATTACA
*
39374627 TTACTTAAATATATTAC-
1 TTACTAAAATATATTACA
39374644 TTACTAAAATTTATAACTTACA
1 TTACTAAAA--TAT-A-TTACA
* *
39374666 TTAATTAAATATATTACA
1 TTACTAAAATATATTACA
39374684 TTACTTAAAAT
1 TTAC-TAAAAT
39374695 TTATATATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
17 8 0.15
18 23 0.42
19 9 0.16
20 4 0.07
21 4 0.07
22 7 0.13
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.44
Consensus pattern (18 bp):
TTACTAAAATATATTACA
Found at i:39374644 original size:31 final size:31
Alignment explanation
Indices: 39374586--39374644 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
39374576 AAATTTAAGT
* *
39374586 ATATATTACATTACTTACACTACTTACTAAA
1 ATATATTACATTACTTACAATAATTACTAAA
*
39374617 ATATATTTCATTACTTA-AATATATTACT
1 ATATATTACATTACTTACAATA-ATTACT
39374645 TACTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATATTACATTACTTACAATAATTACTAAA
Found at i:39374653 original size:17 final size:17
Alignment explanation
Indices: 39374606--39374664 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
39374596 TTACTTACAC
39374606 TACTTACTAAAATATAT
1 TACTTACTAAAATATAT
* *
39374623 TTCATTACTTAAATATAT
1 TAC-TTACTAAAATATAT
*
39374641 TACTTACTAAAATTTAT
1 TACTTACTAAAATATAT
*
39374658 AACTTAC
1 TACTTAC
39374665 ATTAATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (17 bp):
TACTTACTAAAATATAT
Found at i:39374677 original size:39 final size:38
Alignment explanation
Indices: 39374557--39374699 Score: 123
Period size: 39 Copynumber: 3.7 Consensus size: 38
39374547 TAACAGAATG
* * * *
39374557 TTAAATACATGACTTACTAAAATTTA-AGTATATATTACA
1 TTAAATATATTACTTACTAAAATTTATAAT-TACATTA-A
** * * * *
39374596 TTACTTACACTACTTACTAAAA--TAT-ATTTCATTAC
1 TTAAATATATTACTTACTAAAATTTATAATTACATTAA
39374631 TTAAATATATTACTTACTAAAATTTATAACTTACATTAA
1 TTAAATATATTACTTACTAAAATTTATAA-TTACATTAA
39374670 TTAAATATATTACATTACTTAAAATTTATA
1 TTAAATATATTAC-TTAC-TAAAATTTATA
39374700 TATATTTAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
35 18 0.22
36 5 0.06
37 6 0.07
38 1 0.01
39 38 0.46
40 4 0.05
41 11 0.13
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.43
Consensus pattern (38 bp):
TTAAATATATTACTTACTAAAATTTATAATTACATTAA
Found at i:39374876 original size:44 final size:45
Alignment explanation
Indices: 39374804--39374913 Score: 154
Period size: 44 Copynumber: 2.5 Consensus size: 45
39374794 AACTTACATA
39374804 ATAACATA-ATAACTTACATAA-TACACAACTTAATTAATAATATAC
1 ATAACATACATAA--TACATAATTACACAACTTAATTAATAATATAC
*
39374849 ATAACATACATAATACATAATTA-ACAACTTAATTAATATTATAC
1 ATAACATACATAATACATAATTACACAACTTAATTAATAATATAC
* *
39374893 ATATCATACATAATGCATAAT
1 ATAACATACATAATACATAAT
39374914 ACATAATACA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
44 46 0.77
45 10 0.17
46 4 0.07
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.33
Consensus pattern (45 bp):
ATAACATACATAATACATAATTACACAACTTAATTAATAATATAC
Found at i:39374913 original size:7 final size:7
Alignment explanation
Indices: 39374898--39374939 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
39374888 TATACATATC
39374898 ATACATA
1 ATACATA
*
39374905 ATGCATA
1 ATACATA
39374912 ATACATA
1 ATACATA
39374919 ATACATA
1 ATACATA
39374926 ACTTACATA
1 A--TACATA
39374935 ATACA
1 ATACA
39374940 GAACTTACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 24 0.77
9 7 0.23
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (7 bp):
ATACATA
Found at i:39374934 original size:16 final size:16
Alignment explanation
Indices: 39374791--39375172 Score: 235
Period size: 16 Copynumber: 22.9 Consensus size: 16
39374781 TATAAACTTG
39374791 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
39374808 CATAATAACTTACATAATA
1 C---ATAACTTACATAATA
* *
39374827 CACAACTTAATTAATAATATA
1 CATAACTT-A--CAT-A-ATA
*
39374848 CATAACATACATAATA
1 CATAACTTACATAATA
*
39374864 CATAA-TTA-A-CA-A
1 CATAACTTACATAATA
*
39374876 CTTAA-TTA-ATATTATA
1 CATAACTTACATA--ATA
* * *
39374892 CATATCATACATAATG
1 CATAACTTACATAATA
39374908 CATAA--TACATAATA
1 CATAACTTACATAATA
39374922 CATAACTTACATAATA
1 CATAACTTACATAATA
* * *
39374938 CAGAACTTACATTATG
1 CATAACTTACATAATA
* *
39374954 CACAACTTAATTAATATTATA
1 CATAACTT-A--CATA--ATA
*
39374975 CATAACTTAATTAATATTATA
1 CATAACTT-A--CATA--ATA
*
39374996 CATAACATACATAATA
1 CATAACTTACATAATA
*
39375012 CATAACTTACATAGTA
1 CATAACTTACATAATA
*
39375028 CATAACTAACATAATA
1 CATAACTTACATAATA
39375044 CATAACTTACATAATA
1 CATAACTTACATAATA
*
39375060 CATAACTTACATAGTA
1 CATAACTTACATAATA
* *
39375076 CACAACTAACATAATA
1 CATAACTTACATAATA
*
39375092 CACAACTTACATAATA
1 CATAACTTACATAATA
* *
39375108 CACAACTTACATAGCTTA
1 CATAACTTACATA--ATA
*
39375126 CAGAA--TACATAACTTA
1 CATAACTTACATAA--TA
*
39375142 CATAACTTATATAATA
1 CATAACTTACATAATA
*
39375158 CATAACCTACATAAT
1 CATAACTTACATAAT
39375173 TTACCAAATA
Statistics
Matches: 296, Mismatches: 42, Indels: 55
0.75 0.11 0.14
Matches are distributed among these distances:
12 9 0.03
13 1 0.00
14 14 0.05
15 3 0.01
16 182 0.61
17 6 0.02
18 20 0.07
19 6 0.02
20 17 0.06
21 38 0.13
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:39374934 original size:83 final size:81
Alignment explanation
Indices: 39374845--39375038 Score: 200
Period size: 83 Copynumber: 2.4 Consensus size: 81
39374835 AATTAATAAT
*
39374845 ATACATAACATACATAATACATAATTAACAACTTAATTAATATTATACATATCATACA-TAATGC
1 ATACATAACATACATAATACATAATTAACAACTTAATTAATATTATACATAACATA-ATTAAT--
39374909 ATAATACAT-A-ATACATA
63 ATAATACATAACATACATA
* * ** *
39374926 ACTTACAT-A-ATACAGAACTTACATTATGCACAACTTAATTAATATTATACATAACTTAATTAA
1 A--TACATAACATACATAA--TACATAATTAACAACTTAATTAATATTATACATAACATAATTAA
*
39374989 TATTATACATAACATACATA
62 TATAATACATAACATACATA
* * *
39375009 ATACATAACTTACATAGTACATAACTAACA
1 ATACATAACATACATAATACATAATTAACA
39375039 TAATACATAA
Statistics
Matches: 90, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
81 30 0.33
82 4 0.04
83 56 0.62
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.32
Consensus pattern (81 bp):
ATACATAACATACATAATACATAATTAACAACTTAATTAATATTATACATAACATAATTAATATA
ATACATAACATACATA
Found at i:39374981 original size:21 final size:21
Alignment explanation
Indices: 39374948--39375001 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
39374938 CAGAACTTAC
* *
39374948 ATTATGCACAACTTAATTAAT
1 ATTATACATAACTTAATTAAT
39374969 ATTATACATAACTTAATTAAT
1 ATTATACATAACTTAATTAAT
39374990 ATTATACATAAC
1 ATTATACATAAC
39375002 ATACATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTATACATAACTTAATTAAT
Found at i:39375118 original size:9 final size:9
Alignment explanation
Indices: 39374994--39375176 Score: 123
Period size: 9 Copynumber: 22.3 Consensus size: 9
39374984 ATTAATATTA
*
39374994 TACATAACA
1 TACATAACT
39375003 TACATAA--
1 TACATAACT
39375010 TACATAACT
1 TACATAACT
*
39375019 TACAT-A-G
1 TACATAACT
39375026 TACATAACT
1 TACATAACT
*
39375035 AACATAA--
1 TACATAACT
39375042 TACATAACT
1 TACATAACT
39375051 TACATAA--
1 TACATAACT
39375058 TACATAACT
1 TACATAACT
*
39375067 TACAT-A-G
1 TACATAACT
*
39375074 TACACAACT
1 TACATAACT
*
39375083 AACATAA--
1 TACATAACT
*
39375090 TACACAACT
1 TACATAACT
39375099 TACATAA--
1 TACATAACT
*
39375106 TACACAACT
1 TACATAACT
*
39375115 TACATAGCT
1 TACATAACT
*
39375124 TACAGAA--
1 TACATAACT
39375131 TACATAACT
1 TACATAACT
39375140 TACATAACT
1 TACATAACT
*
39375149 TATATAA--
1 TACATAACT
*
39375156 TACATAACC
1 TACATAACT
*
39375165 TACATAATT
1 TACATAACT
39375174 TAC
1 TAC
39375177 CAAATACATA
Statistics
Matches: 134, Mismatches: 22, Indels: 36
0.70 0.11 0.19
Matches are distributed among these distances:
7 52 0.39
8 4 0.03
9 78 0.58
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (9 bp):
TACATAACT
Found at i:39375118 original size:25 final size:25
Alignment explanation
Indices: 39374994--39375187 Score: 181
Period size: 25 Copynumber: 7.9 Consensus size: 25
39374984 ATTAATATTA
*
39374994 TACATAACATACATAATACATAACT
1 TACATAACTTACATAATACATAACT
*
39375019 TACAT-A-GTACATAACTAACATAA--
1 TACATAACTTACATAA-T-ACATAACT
39375042 TACATAACTTACATAATACATAACT
1 TACATAACTTACATAATACATAACT
* *
39375067 TACAT-A-GTACACAACTAACATAA--
1 TACATAACTTACATAA-T-ACATAACT
* *
39375090 TACACAACTTACATAATACACAACT
1 TACATAACTTACATAATACATAACT
* *
39375115 TACATAGCTTACAGAATACATAACT
1 TACATAACTTACATAATACATAACT
* *
39375140 TACATAACTTATATAATACATAACC
1 TACATAACTTACATAATACATAACT
*
39375165 TACATAATTTACCA-AATACATAA
1 TACATAACTTA-CATAATACATAA
39375188 ATATATATCA
Statistics
Matches: 138, Mismatches: 18, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
23 33 0.24
24 8 0.06
25 96 0.70
26 1 0.01
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (25 bp):
TACATAACTTACATAATACATAACT
Found at i:39380644 original size:21 final size:21
Alignment explanation
Indices: 39380620--39380670 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
39380610 CTACAACTTA
*
39380620 AAGCAGAGGC-AGCAGCGAGGG
1 AAGCAGAGGCTA-CAGCGAGAG
39380641 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTACAGCGAGAG
39380662 AAGCAGAGG
1 AAGCAGAGG
39380671 TTCAAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.43, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCTACAGCGAGAG
Found at i:39380713 original size:87 final size:86
Alignment explanation
Indices: 39380580--39380755 Score: 253
Period size: 87 Copynumber: 2.0 Consensus size: 86
39380570 GACCACAGTT
*
39380580 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCAGCAGCGAGGGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCAGCAGCGA-AGAAGC
*
39380645 AGAGGCTACAGCGAGAGAAGCA
65 AGAGGATACAGCGAGAGAAGCA
* * * * *
39380667 GAGGTTCAAAAGAAATATGAAGAGCTCCAGCTACAACTTGAAGCAGATGCGGCATCGAAGAAGCA
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCAGCAGCGAAGAAGCA
* * *
39380732 GAGGATGCAGTGAGGGAAGCA
66 GAGGATACAGCGAGAGAAGCA
39380753 GAG
1 GAG
39380756 CAGAGCAGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 26 0.33
87 53 0.67
ACGTcount: A:0.40, C:0.17, G:0.31, T:0.12
Consensus pattern (86 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCAGCAGCGAAGAAGCA
GAGGATACAGCGAGAGAAGCA
Found at i:39381183 original size:42 final size:43
Alignment explanation
Indices: 39381114--39381215 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 43
39381104 GCATTTGATT
*
39381114 GAAAAAGCGCCGCTAAAAGTCCGGTTCTATAGTGACGTTTGT-
1 GAAAAAGCGCCGCTAAAAGTCCGGTTCTATAGCGACGTTTGTG
* * *
39381156 GAGAAAA-CGCCGCTAAAAG-CCATGTTCTTTAGCGGCGTTTGTG
1 GA-AAAAGCGCCGCTAAAAGTCC-GGTTCTATAGCGACGTTTGTG
39381199 GAAAAAGCGCCGCTAAA
1 GAAAAAGCGCCGCTAAA
39381216 GAACATGACC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
41 2 0.04
42 34 0.65
43 16 0.31
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (43 bp):
GAAAAAGCGCCGCTAAAAGTCCGGTTCTATAGCGACGTTTGTG
Found at i:39381349 original size:42 final size:43
Alignment explanation
Indices: 39381149--39381408 Score: 282
Period size: 43 Copynumber: 6.1 Consensus size: 43
39381139 TCTATAGTGA
* **
39381149 CGTTTGT-GAGAAAA-CGCCGCTAAA-AGCCATGTTCTTTAGCGG
1 CGTTTGTAG-GAAAAGCGCCGCTAAAGA-ACATGACCTTTAGCGG
*
39381191 CGTTTGT-GGAAAAAGCGCCGCTAAAGAACATGACCTTTAGCTG
1 CGTTTGTAGG-AAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
* *
39381234 CATTTGTAGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCTG
1 CGTTTGTAGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
*
39381277 CATTTGTAGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
1 CGTTTGTAGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
* ** * *
39381320 CGTTTCTA-CTATAGCGCCACTAAAGAACATGACCTTTAGCGG
1 CGTTTGTAGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
* * ** *
39381362 CGTTTTTATTG--TTGCGCCGCTAAAGAACATGACTTTTAGCGG
1 CGTTTGTA-GGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
39381404 CGTTT
1 CGTTT
39381409 TGTTTCTATA
Statistics
Matches: 195, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 82 0.42
43 109 0.56
44 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (43 bp):
CGTTTGTAGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
Found at i:39381545 original size:22 final size:22
Alignment explanation
Indices: 39381502--39381545 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39381492 TAGTGGCGCT
* **
39381502 AAAAAGCGCCGCTAAATGCCTA
1 AAAAAACGCCGCTAAAAACCTA
39381524 AAAAAACGCCGCTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
39381546 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.27, G:0.14, T:0.11
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:39381747 original size:42 final size:42
Alignment explanation
Indices: 39381686--39381766 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
39381676 AAAAGTGGGT
* * *
39381686 ATATCTTTTGATTCGAAGATTGAGGG-TTTATATCTTAGTCTA
1 ATATCTTCTGATTCCAAGATTG-GGGATTTATATCATAGTCTA
39381728 ATATCTTCTGATTCCAAGATTGGGGATTTATATCATAGT
1 ATATCTTCTGATTCCAAGATTGGGGATTTATATCATAGT
39381767 TTAAGGTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (42 bp):
ATATCTTCTGATTCCAAGATTGGGGATTTATATCATAGTCTA
Found at i:39381813 original size:14 final size:14
Alignment explanation
Indices: 39381789--39381828 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
39381779 TTGATAAACT
*
39381789 GAAAAATTAAGTGTC
1 GAAAAA-TAAGTGTA
39381804 GAAAAATAAGTGTA
1 GAAAAATAAGTGTA
*
39381818 AAAAAATAAGT
1 GAAAAATAAGT
39381829 ATTGAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.57, C:0.03, G:0.17, T:0.23
Consensus pattern (14 bp):
GAAAAATAAGTGTA
Found at i:39382785 original size:122 final size:123
Alignment explanation
Indices: 39382645--39382889 Score: 483
Period size: 122 Copynumber: 2.0 Consensus size: 123
39382635 TAGTATAAAT
39382645 TGTAATTATATAATTATATATTTTTAAATTTAAAAAAATATCAATTATTATAAAAGTTATCAATA
1 TGTAATTATATAATTATATATTTTTAAATTTAAAAAAATATCAATTATTATAAAAGTTATCAATA
39382710 ATACTTGAAAATAATATTTAAACAATTAACAAAACATAAAATCGAATCATTGTTTATA
66 ATACTTGAAAATAATATTTAAACAATTAACAAAACATAAAATCGAATCATTGTTTATA
39382768 TGTAATTATA-AATTATATATTTTTAAATTTAAAAAAATATCAATTATTATAAAAGTTATCAATA
1 TGTAATTATATAATTATATATTTTTAAATTTAAAAAAATATCAATTATTATAAAAGTTATCAATA
39382832 ATACTTGAAAATAATATTTAAACAATTAACAAAACATAAAATCGAATCATTGTTTATA
66 ATACTTGAAAATAATATTTAAACAATTAACAAAACATAAAATCGAATCATTGTTTATA
39382890 ATATATGTTA
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 112 0.92
123 10 0.08
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39
Consensus pattern (123 bp):
TGTAATTATATAATTATATATTTTTAAATTTAAAAAAATATCAATTATTATAAAAGTTATCAATA
ATACTTGAAAATAATATTTAAACAATTAACAAAACATAAAATCGAATCATTGTTTATA
Found at i:39385123 original size:13 final size:13
Alignment explanation
Indices: 39385105--39385131 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39385095 AATAATAGGC
39385105 TTAATTTATAAAT
1 TTAATTTATAAAT
39385118 TTAATTTATAAAT
1 TTAATTTATAAAT
39385131 T
1 T
39385132 GATATTAAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTATAAAT
Found at i:39393435 original size:18 final size:17
Alignment explanation
Indices: 39393407--39393441 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39393397 NNNNNTAAGA
*
39393407 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39393424 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39393442 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39393672 original size:44 final size:45
Alignment explanation
Indices: 39393607--39393697 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
39393597 ACCTCTATTC
* * *
39393607 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
39393651 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
39393696 CA
1 CA
39393698 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:39393699 original size:16 final size:16
Alignment explanation
Indices: 39393678--39393713 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
39393668 GATTAGCTAT
39393678 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39393694 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39393710 TACA
1 TACA
39393714 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:39394935 original size:9 final size:9
Alignment explanation
Indices: 39394921--39394946 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39394911 TGTTTGAATA
39394921 GAAATGAAC
1 GAAATGAAC
39394930 GAAATGAAC
1 GAAATGAAC
39394939 GAAATGAA
1 GAAATGAA
39394947 TAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.23, T:0.12
Consensus pattern (9 bp):
GAAATGAAC
Done.