Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 111 of 198
Found at i:35623550 original size:11 final size:11
Alignment explanation
Indices: 35623513--35623550 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
35623503 TCCTTCGTTG
35623513 ATCATCCCTCA
1 ATCATCCCTCA
*
35623524 AGCATCCCTCA
1 ATCATCCCTCA
35623535 ATCATCCCTCA
1 ATCATCCCTCA
*
35623546 TTCAT
1 ATCAT
35623551 TCTCATCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.26, C:0.42, G:0.03, T:0.29
Consensus pattern (11 bp):
ATCATCCCTCA
Found at i:35625762 original size:29 final size:30
Alignment explanation
Indices: 35625711--35625772 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
35625701 AATTATTTTA
35625711 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
35625741 TTGTTAATTTT-TTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
35625770 TTG
1 TTG
35625773 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:35625929 original size:13 final size:11
Alignment explanation
Indices: 35625894--35625923 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
35625884 TATATATATT
35625894 TAAAAATTATA
1 TAAAAATTATA
*
35625905 TAAAAATCATA
1 TAAAAATTATA
35625916 TAAAAATT
1 TAAAAATT
35625924 TAATATGGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:35629426 original size:58 final size:60
Alignment explanation
Indices: 35629362--35629477 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 60
35629352 ATCACTTTAA
*
35629362 TATTAAATTAATATAATACTTA-T-CAAGATAA-ATATTAGATTAAA-TATAATATTAAATC
1 TATTAAATTAATATAATACTTACTACAAGATAATA-ATTAAATTAAATTA-AATATTAAATC
*
35629420 TATTAAATTAATATAATATTTATCTACAAGATAATAATTAAATTAAATTAAATATTAA
1 TATTAAATTAATATAATACTTA-CTACAAGATAATAATTAAATTAAATTAAATATTAA
35629478 GATAATTGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
58 21 0.41
60 1 0.02
61 26 0.51
62 3 0.06
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (60 bp):
TATTAAATTAATATAATACTTACTACAAGATAATAATTAAATTAAATTAAATATTAAATC
Found at i:35629477 original size:61 final size:58
Alignment explanation
Indices: 35629362--35629562 Score: 158
Period size: 61 Copynumber: 3.2 Consensus size: 58
35629352 ATCACTTTAA
*
35629362 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATATAATATTAAATC
1 TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATATAATATTAAATC
*
35629420 TATTAAATTAATATAATATTTATCTACAAGAT-AATAATTAAATTAAAT-TAAATATTAAGATAA
1 TATTAAATTAATATAATACTTA--T-CAAGATAAAT-ATTAAATTAAATAT-AATATT---A-AA
35629483 TTGC
57 -T-C
* * * *
35629487 TTTAATATTAAATTAATAAAATAC-TATTAAGATAATTATTAAA-TCAATAGTAATATTAAATC
1 -----TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATA-TAATATTAAATC
*
35629549 TATTAAAATAATAT
1 TATTAAATTAATAT
35629563 CATTTTTGGA
Statistics
Matches: 115, Mismatches: 9, Indels: 39
0.71 0.06 0.24
Matches are distributed among these distances:
57 12 0.10
58 21 0.18
60 5 0.04
61 23 0.20
62 1 0.01
63 1 0.01
64 3 0.03
65 3 0.03
66 1 0.01
67 5 0.04
68 17 0.15
69 4 0.03
71 2 0.02
72 17 0.15
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (58 bp):
TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATATAATATTAAATC
Found at i:35630773 original size:51 final size:51
Alignment explanation
Indices: 35630709--35630896 Score: 224
Period size: 51 Copynumber: 3.7 Consensus size: 51
35630699 TATCGATGAA
* *
35630709 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* * * *
35630760 CCCATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT
* * *
35630811 CACGTGTGTGGGACTATGTGAAGGCTACTACGTAG-ACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGT-GTACCGATAAATA-TTGGT
35630861 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
35630897 TCGAATGATA
Statistics
Matches: 115, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
49 1 0.01
50 39 0.34
51 73 0.63
52 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:35630793 original size:26 final size:26
Alignment explanation
Indices: 35630713--35630795 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
35630703 GATGAACACG
*
35630713 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * * *
35630739 CGTGTA-T-CGATAAAT-AATGG-TCCCA
1 TGTGTAGTAC--TAAGTGAA-GGCTACTA
35630764 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
35630790 TGTGTA
1 TGTGTA
35630796 CCGAAAAGCT
Statistics
Matches: 41, Mismatches: 9, Indels: 14
0.64 0.14 0.22
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:35630896 original size:101 final size:102
Alignment explanation
Indices: 35630709--35630901 Score: 257
Period size: 101 Copynumber: 1.9 Consensus size: 102
35630699 TATCGATGAA
* * * *
35630709 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCCCATGTGTAGTAC
1 CACGTGTGTAGGACTATGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTAC
*
35630774 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTACGTGTACCGAAAAGCTTTGGT
* * *
35630811 CACGTGTGTGGGACTATGTGAAGGCTACTACGTAG-ACCG-TAAA-ACTTGATCACGTGTGTAGT
1 CACGTGTGTAGGACTATGTGAAGGCTACTACGT-GTACCGATAAATA-ATGATCACATGTGTAGT
* *
35630873 ACTATGTGAAGGCTACTACGTGTATCGAA
64 ACTAAGTGAAGGCTACTACGTGTACCGAA
35630902 TGATAATAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
100 1 0.01
101 43 0.54
102 34 0.43
103 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGGACTATGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTAC
TAAGTGAAGGCTACTACGTGTACCGAAAAGCTTTGGT
Found at i:35630928 original size:101 final size:102
Alignment explanation
Indices: 35630719--35630933 Score: 231
Period size: 101 Copynumber: 2.1 Consensus size: 102
35630709 CACGTGTGTA
* * *
35630719 GTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCCCATGTGTAGTACTAAGTGAAGG
1 GTACTATGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTACTAAGTGAAGG
* * * * * * *
35630784 CTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTG
66 CTACTACGTGTACCGAAAAGATATAGTAACATGGGTG
* * * *
35630821 GGACTATGTGAAGGCTACTACGTAG-ACCG-TAAA-ACTTGATCACGTGTGTAGTACTATGTGAA
1 GTACTATGTGAAGGCTACTACGT-GTACCGATAAATA-ATGATCACATGTGTAGTACTAAGTGAA
* *
35630883 GGCTACTACGTGTATCG-AATGATAATAGTAACATGGGTG
64 GGCTACTACGTGTACCGAAAAGAT-ATAGTAACATGGGTG
35630922 GTACTATGTGAA
1 GTACTATGTGAA
35630934 AACCCCCAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
100 5 0.05
101 62 0.67
102 25 0.27
103 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (102 bp):
GTACTATGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTACTAAGTGAAGG
CTACTACGTGTACCGAAAAGATATAGTAACATGGGTG
Found at i:35632365 original size:54 final size:54
Alignment explanation
Indices: 35632284--35632405 Score: 154
Period size: 54 Copynumber: 2.3 Consensus size: 54
35632274 TCCACCTGTA
* * * * *
35632284 TAACTCACTGAGTAGGGTCACATGGCCATGTCACAGGCCGTGTGCTAGACAAAG
1 TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCTAGACAAAG
* * * * *
35632338 TAACTCTCTGACTTGCGACACACGGCCATGTCGCAGGCCGTGTGCTAGGCCATG
1 TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCTAGACAAAG
35632392 TAACTCACTGACTT
1 TAACTCACTGACTT
35632406 AAAACATTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (54 bp):
TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCTAGACAAAG
Found at i:35634452 original size:23 final size:23
Alignment explanation
Indices: 35634407--35634452 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35634397 TGACATATTC
* **
35634407 TTTTATCTTTTATTTACTTAACT
1 TTTTATCTTTTAATTACCAAACT
*
35634430 TTTTTTCTTTTAATTACCAAACT
1 TTTTATCTTTTAATTACCAAACT
35634453 ACTACTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATCTTTTAATTACCAAACT
Found at i:35639106 original size:18 final size:20
Alignment explanation
Indices: 35639075--35639113 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
35639065 TTAAAAATAA
35639075 ATTTTCTAAAAATATT-TTT
1 ATTTTCTAAAAATATTATTT
35639094 ATTTTCT-AAAATATTATTT
1 ATTTTCTAAAAATATTATTT
35639113 A
1 A
35639114 CCAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTCTAAAAATATTATTT
Found at i:35642424 original size:26 final size:26
Alignment explanation
Indices: 35642388--35642444 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
35642378 ATAAACAAGT
35642388 AAAATAAAATTTAAAA-AAAAT-TAAA
1 AAAATAAAA-TTAAAATAAAATATAAA
*
35642413 AAAACTAAAATTAAAATAAAATATAAG
1 AAAA-TAAAATTAAAATAAAATATAAA
35642440 AAAAT
1 AAAAT
35642445 CAATATGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 10 0.36
26 11 0.39
27 7 0.25
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (26 bp):
AAAATAAAATTAAAATAAAATATAAA
Found at i:35643617 original size:11 final size:11
Alignment explanation
Indices: 35643593--35643625 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
35643583 TTCGGGTCTC
35643593 TAAACTAATA-A
1 TAAA-TAATATA
35643604 TAAATAATATA
1 TAAATAATATA
35643615 TAAATAATATA
1 TAAATAATATA
35643626 ATTAGTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATAATATA
Found at i:35644390 original size:3 final size:3
Alignment explanation
Indices: 35644382--35644422 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
35644372 CCGCTGCCCT
35644382 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
35644423 TTCAAGTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:35650946 original size:15 final size:17
Alignment explanation
Indices: 35650908--35650946 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
35650898 AAAAAATATC
35650908 AATTAAATTTCTACAAA
1 AATTAAATTTCTACAAA
35650925 AA-T-AATTT-TA-AAA
1 AATTAAATTTCTACAAA
35650938 AATTAAATT
1 AATTAAATT
35650947 CTAAGAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.25
14 3 0.15
15 9 0.45
16 1 0.05
17 2 0.10
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATTTCTACAAA
Found at i:35655075 original size:23 final size:23
Alignment explanation
Indices: 35655049--35655094 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35655039 TTTTAAACTC
35655049 AATCATTATGTTAGCCAAAGTTA
1 AATCATTATGTTAGCCAAAGTTA
35655072 AATCATTATGTTAGCCAAAGTTA
1 AATCATTATGTTAGCCAAAGTTA
35655095 TTTAAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
AATCATTATGTTAGCCAAAGTTA
Found at i:35656507 original size:14 final size:14
Alignment explanation
Indices: 35656488--35656527 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
35656478 TTGATTGGCA
35656488 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
35656502 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
35656516 GGAAAATGTTTT
1 GTAAAATGTTTT
35656528 ACATTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:35656549 original size:20 final size:20
Alignment explanation
Indices: 35656510--35656549 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35656500 CCGTAAAATG
**
35656510 ATTTCTGGAAAATGTTTTAC
1 ATTTCTGGAAAATGACTTAC
*
35656530 ATTTCTGTAAAATGACTTAC
1 ATTTCTGGAAAATGACTTAC
35656550 TGGAAAATAT
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:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
ATTTCTGGAAAATGACTTAC
Found at i:35656557 original size:35 final size:34
Alignment explanation
Indices: 35656497--35656562 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
35656487 AGTAAAATGT
* *
35656497 TTTCCGTAAAATGATTTCTGGAAAATGTTTTACA
1 TTTCCGTAAAATGATTACTGGAAAATATTTTACA
*
35656531 TTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTCCGTAAAATGA-TTACTGGAAAATATTTT
35656563 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (34 bp):
TTTCCGTAAAATGATTACTGGAAAATATTTTACA
Found at i:35658955 original size:15 final size:15
Alignment explanation
Indices: 35658935--35658966 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
35658925 GGACGGATAT
35658935 GGAGAAGAGGGAACC
1 GGAGAAGAGGGAACC
35658950 GGAGAAGAGGGAACC
1 GGAGAAGAGGGAACC
35658965 GG
1 GG
35658967 GGAAATGAAA
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:0.38, C:0.12, G:0.50, T:0.00
Consensus pattern (15 bp):
GGAGAAGAGGGAACC
Found at i:35660548 original size:29 final size:30
Alignment explanation
Indices: 35660515--35660571 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
35660505 GGGGTGGGAT
35660515 GGGAGCAAAAGTTATGGG-GGAAAGTGAGA
1 GGGAGCAAAAGTTATGGGAGGAAAGTGAGA
* *
35660544 GGGAGTAAAAGTTTTGGGAGGAAAGTGA
1 GGGAGCAAAAGTTATGGGAGGAAAGTGA
35660572 AGAAGTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.44, T:0.18
Consensus pattern (30 bp):
GGGAGCAAAAGTTATGGGAGGAAAGTGAGA
Found at i:35662509 original size:21 final size:21
Alignment explanation
Indices: 35662483--35662522 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35662473 TTACCATTAT
*
35662483 TGTTG-TAGTTGTTATTATTCA
1 TGTTGTTAGTTATT-TTATTCA
35662504 TGTTGTTAGTTATTTTATT
1 TGTTGTTAGTTATTTTATT
35662523 TATTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.62
Consensus pattern (21 bp):
TGTTGTTAGTTATTTTATTCA
Found at i:35666547 original size:10 final size:10
Alignment explanation
Indices: 35666503--35666566 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
35666493 AAAATTATTA
35666503 TTTTAGAAAAT
1 TTTTAG-AAAT
*
35666514 TTTTA-AATT
1 TTTTAGAAAT
* *
35666523 TTTTAATGTATT
1 TTTT-A-GAAAT
35666535 TTTTAGAAAT
1 TTTTAGAAAT
35666545 TTTTAGAAA-
1 TTTTAGAAAT
*
35666554 TTTTATAAAT
1 TTTTAGAAAT
35666564 TTT
1 TTT
35666567 ATAATTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.34
10 16 0.36
11 6 0.14
12 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (10 bp):
TTTTAGAAAT
Found at i:35667919 original size:25 final size:25
Alignment explanation
Indices: 35667884--35667950 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
35667874 CTCACCACAA
* *
35667884 CTCGTATGAGCTTATCGAT-TTGCAC
1 CTCGTAGGAGCTTACCGATATT-CAC
*
35667909 CTCGTAGGAGCTTACCGATATTCAG
1 CTCGTAGGAGCTTACCGATATTCAC
*
35667934 CTCGGAGGAGCTTACCG
1 CTCGTAGGAGCTTACCG
35667951 TTTATCGTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 35 0.95
26 2 0.05
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.28
Consensus pattern (25 bp):
CTCGTAGGAGCTTACCGATATTCAC
Found at i:35670562 original size:2 final size:2
Alignment explanation
Indices: 35670555--35670587 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35670545 TTTGTAAGTG
35670555 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35670588 TTAAAAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35676988 original size:23 final size:23
Alignment explanation
Indices: 35676939--35676993 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
35676929 TTTTTAGAAA
* * *
35676939 ATTCTGCAAAGCCTTTGTGGCGC
1 ATTCTGTAAAGCCTTTGTAGCAC
* *
35676962 ATTCTGTAAAGTCTTTGTAGCAT
1 ATTCTGTAAAGCCTTTGTAGCAC
35676985 ATTCTGTAA
1 ATTCTGTAA
35676994 CACCCTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (23 bp):
ATTCTGTAAAGCCTTTGTAGCAC
Found at i:35681347 original size:18 final size:19
Alignment explanation
Indices: 35681308--35681403 Score: 106
Period size: 19 Copynumber: 5.2 Consensus size: 19
35681298 ATTTTATATT
*
35681308 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGATTTA
*
35681327 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGATTTA
* *
35681345 TTAAATTAAAATAGAATTA
1 TTAAATGAAAATAGATTTA
*
35681364 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGATTTA
* * *
35681382 TTCAATTAAAATAGAGTTA
1 TTAAATGAAAATAGATTTA
35681401 TTA
1 TTA
35681404 CTTAATTAGA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
18 29 0.47
19 33 0.53
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGATTTA
Found at i:35681349 original size:37 final size:37
Alignment explanation
Indices: 35681308--35681403 Score: 165
Period size: 37 Copynumber: 2.6 Consensus size: 37
35681298 ATTTTATATT
*
35681308 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
*
35681345 TTAAATTAAAATAGAATTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
*
35681382 TTCAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
35681404 CTTAATTAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:35682092 original size:26 final size:28
Alignment explanation
Indices: 35682063--35682127 Score: 107
Period size: 29 Copynumber: 2.4 Consensus size: 28
35682053 ATTTTTTGGC
35682063 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
35682089 ATATTTTGGTAAATAAAAAAAAAGTTATA
1 ATATTTTGGTAAAT-AAAAAAAAGTTATA
35682118 ATATTTTGGT
1 ATATTTTGGT
35682128 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 14 0.39
28 7 0.19
29 15 0.42
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:35690647 original size:27 final size:27
Alignment explanation
Indices: 35690611--35690732 Score: 118
Period size: 27 Copynumber: 4.5 Consensus size: 27
35690601 ATTTGCCAAT
* * *
35690611 AAGGTCATTCTCTCAGAGTTCACCATA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* **
35690638 AAGTTTATTCTTTCAGAGTTCGTCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* **
35690665 AAGGTTATTCTTTCAAAGTTCGTCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* * *
35690692 AAGGTTATTCTTTTAGAGCTCGCCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* *
35690719 AAGGCTATTATTTC
1 AAGGTTATTCTTTC
35690733 CTAATGTGTT
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (27 bp):
AAGGTTATTCTTTCAGAGTTCACCACA
Found at i:35690675 original size:54 final size:54
Alignment explanation
Indices: 35690611--35690727 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 54
35690601 ATTTGCCAAT
* * * * * *
35690611 AAGGTCATTCTCTCAGAGTTCACCATAAAGTTTATTCTTTCAGAGTTCGTCACA
1 AAGGTTATTCTCTCAAAGTTCACCACAAAGGTTATTCTTTCAGAGCTCGCCACA
* ** *
35690665 AAGGTTATTCTTTCAAAGTTCGTCACAAAGGTTATTCTTTTAGAGCTCGCCACA
1 AAGGTTATTCTCTCAAAGTTCACCACAAAGGTTATTCTTTCAGAGCTCGCCACA
*
35690719 AAGGCTATT
1 AAGGTTATT
35690728 ATTTCCTAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (54 bp):
AAGGTTATTCTCTCAAAGTTCACCACAAAGGTTATTCTTTCAGAGCTCGCCACA
Found at i:35702843 original size:26 final size:26
Alignment explanation
Indices: 35702814--35702882 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
35702804 ATCCTCTCTC
35702814 AAGCCATATAACAGGAAGCTCACAAA
1 AAGCCATATAACAGGAAGCTCACAAA
*
35702840 AAGCTAT-TAATC-GGAAAGCTCACAAA
1 AAGCCATATAA-CAGG-AAGCTCACAAA
*
35702866 GAGCC-TAT--CAGGAAGCT
1 AAGCCATATAACAGGAAGCT
35702883 TATCCGGGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
23 6 0.17
24 2 0.06
25 6 0.17
26 22 0.61
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (26 bp):
AAGCCATATAACAGGAAGCTCACAAA
Found at i:35702965 original size:26 final size:26
Alignment explanation
Indices: 35702919--35702996 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
35702909 ATAAGAGTCA
* * * *
35702919 TAATCATGAAGTTCAAAAAGAACTTT
1 TAATCAGGAAGCTCAAGAAGAACCTT
* *
35702945 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCAAGAAGAACCTT
* *
35702971 TAATCGGGAAGCTCAAGAAGAGCCTT
1 TAATCAGGAAGCTCAAGAAGAACCTT
35702997 ATAACGGGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (26 bp):
TAATCAGGAAGCTCAAGAAGAACCTT
Found at i:35703004 original size:26 final size:26
Alignment explanation
Indices: 35702943--35703005 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
35702933 AAAAAGAACT
* *
35702943 TTTAATCAGGAAGCTCACGAAGAGCC
1 TTTAATCGGGAAGCTCAAGAAGAGCC
35702969 TTTAATCGGGAAGCTCAAGAAGAGCC
1 TTTAATCGGGAAGCTCAAGAAGAGCC
35702995 TTATAA-CGGGA
1 TT-TAATCGGGA
35703006 GCTTCGGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 31 0.91
27 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (26 bp):
TTTAATCGGGAAGCTCAAGAAGAGCC
Found at i:35705926 original size:50 final size:50
Alignment explanation
Indices: 35705815--35706063 Score: 264
Period size: 50 Copynumber: 4.8 Consensus size: 50
35705805 ATTTGGGCAA
*
35705815 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* * * *
35705871 AGAGGTCCCATGTAAGGCCATGTCTGGGATATGGCGTTGACACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * ***
35705921 AGAGGTCCCATGTAAGACTAAGTCTGGGACATGATGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
35705971 AGAGGTCCCCCGTAAGACCCTGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
35706021 AGAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35706064 TCTTATGATC
Statistics
Matches: 162, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
50 88 0.54
51 32 0.20
53 3 0.02
55 2 0.01
56 37 0.23
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:35707648 original size:42 final size:42
Alignment explanation
Indices: 35707591--35707703 Score: 181
Period size: 42 Copynumber: 2.7 Consensus size: 42
35707581 GTTTACAAAC
* *
35707591 AAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAA
*
35707633 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAA
* *
35707675 AAAAACGCCGCTAAAGATCATGTTATTTA
1 AAAAACGCCGCTAAAGACCATGTTCTTTA
35707704 ACAGCGTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAA
Found at i:35708363 original size:21 final size:21
Alignment explanation
Indices: 35708339--35708409 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
35708329 TTTTGCTCTG
* *
35708339 CTCTGCTTCTCTCGTTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
35708360 CTCTGCTTCCCTTACTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
35708381 CGCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
35708402 CTCTGCTT
1 CTCTGCTT
35708410 TAAGTTGTAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.04, C:0.44, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:35711081 original size:23 final size:24
Alignment explanation
Indices: 35711047--35711101 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
35711037 CTCCATATAA
*
35711047 ATAT-TAA-TAAGTTATGTAAGTT
1 ATATATAAGTAAGTTATGAAAGTT
35711069 AT-TATAAGTAAGTTATGAAAGTT
1 ATATATAAGTAAGTTATGAAAGTT
35711092 ATATATAAGT
1 ATATATAAGT
35711102 CATGTATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 1 0.03
22 5 0.17
23 16 0.55
24 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (24 bp):
ATATATAAGTAAGTTATGAAAGTT
Found at i:35711114 original size:31 final size:32
Alignment explanation
Indices: 35711077--35711138 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
35711067 TTATTATAAG
35711077 TAAGTTATGAAAGTTA-TATATAAGTCATGTA
1 TAAGTTATGAAAGTTATTATATAAGTCATGTA
* * *
35711108 TAAGTTATGTAAGTTATTATGTAAGTTATGT
1 TAAGTTATGAAAGTTATTATATAAGTCATGT
35711139 GTTGTGTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.44
Consensus pattern (32 bp):
TAAGTTATGAAAGTTATTATATAAGTCATGTA
Found at i:35711129 original size:12 final size:12
Alignment explanation
Indices: 35711112--35711232 Score: 67
Period size: 12 Copynumber: 10.1 Consensus size: 12
35711102 CATGTATAAG
35711112 TTATGTAAGTTA
1 TTATGTAAGTTA
35711124 TTATGTAAGTTA
1 TTATGTAAGTTA
*
35711136 TGTGTTGTGTAAGTT-
1 ----TTATGTAAGTTA
* *
35711151 TATATATAAATT-
1 T-TATGTAAGTTA
* *
35711163 TTATTTAAATTA
1 TTATGTAAGTTA
35711175 TGTATGTAAGTTA
1 T-TATGTAAGTTA
*
35711188 -TATATAAGTT-
1 TTATGTAAGTTA
*
35711198 TATATATAAG---
1 T-TATGTAAGTTA
35711208 TTATGTAAGTTA
1 TTATGTAAGTTA
35711220 TTATGTAAGTTA
1 TTATGTAAGTTA
35711232 T
1 T
35711233 GTGTTGTGTA
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
9 7 0.08
10 1 0.01
11 19 0.22
12 42 0.48
13 9 0.10
16 10 0.11
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:35711184 original size:36 final size:36
Alignment explanation
Indices: 35711143--35711214 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
35711133 TTATGTGTTG
*
35711143 TGTAAGTTTATATATAAATTT-TATTTAAATTATGTA
1 TGTAAG-TTATATATAAATTTATATATAAATTATGTA
* *
35711179 TGTAAGTTATATATAAGTTTATATATAAGTTATGTA
1 TGTAAGTTATATATAAATTTATATATAAATTATGTA
35711215 AGTTATTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (36 bp):
TGTAAGTTATATATAAATTTATATATAAATTATGTA
Found at i:35711211 original size:96 final size:95
Alignment explanation
Indices: 35711082--35711265 Score: 332
Period size: 96 Copynumber: 1.9 Consensus size: 95
35711072 ATAAGTAAGT
*
35711082 TATGAAAGTTATATATAAGTCATGTATAAGTTATGTAAGTTATTATGTAAGTTATGTGTTGTGTA
1 TATGAAAGTTATATATAAGTCATATATAAGTTATGTAAGTTATTATGTAAGTTATGTGTTGTGTA
35711147 AGTTTATATATAAATTTTATTTAAATTATG
66 AGTTTATATATAAATTTTATTTAAATTATG
* *
35711177 TATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTATGTAAGTTATGTGTTGTGT
1 TATGAAAGTTATATATAAG-TCATATATAAGTTATGTAAGTTATTATGTAAGTTATGTGTTGTGT
35711242 AAGTTTATATATAAATTTTATTTA
65 AAGTTTATATATAAATTTTATTTA
35711266 CGTATGTAAA
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
95 18 0.21
96 67 0.79
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.49
Consensus pattern (95 bp):
TATGAAAGTTATATATAAGTCATATATAAGTTATGTAAGTTATTATGTAAGTTATGTGTTGTGTA
AGTTTATATATAAATTTTATTTAAATTATG
Found at i:35711218 original size:21 final size:21
Alignment explanation
Indices: 35711192--35711234 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
35711182 AAGTTATATA
35711192 TAAGTT-TATATATAAGTTATG
1 TAAGTTAT-TATATAAGTTATG
*
35711213 TAAGTTATTATGTAAGTTATG
1 TAAGTTATTATATAAGTTATG
35711234 T
1 T
35711235 GTTGTGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (21 bp):
TAAGTTATTATATAAGTTATG
Found at i:35711274 original size:47 final size:46
Alignment explanation
Indices: 35711121--35711280 Score: 171
Period size: 47 Copynumber: 3.4 Consensus size: 46
35711111 GTTATGTAAG
35711121 TTATTATGTAAGTTATGTGTTGTGTAAGTTTATATATAAATTTTAT
1 TTATTATGTAAGTTATGTGTTGTGTAAGTTTATATATAAATTTTAT
* * * * * *
35711167 TTAAATTATGTATG-TAAGT-TATATATAAGTTTATATATAAGTTATGTAAG
1 TT--ATTATGTAAGTTATGTGT-TGTGTAAGTTTATATATAAATT-T-T-AT
35711217 TTATTATGTAAGTTATGTGTTGTGTAAGTTTATATATAAATTTTAT
1 TTATTATGTAAGTTATGTGTTGTGTAAGTTTATATATAAATTTTAT
* *
35711263 TTACGTATGTAAATTATG
1 TTA-TTATGTAAGTTATG
35711281 ATATGACTGA
Statistics
Matches: 91, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
46 7 0.08
47 36 0.40
48 20 0.22
49 24 0.26
50 4 0.04
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.51
Consensus pattern (46 bp):
TTATTATGTAAGTTATGTGTTGTGTAAGTTTATATATAAATTTTAT
Found at i:35711329 original size:19 final size:19
Alignment explanation
Indices: 35711290--35711334 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
35711280 GATATGACTG
*
35711290 ATAAATTTTTCAAATATAT
1 ATAAAATTTTCAAATATAT
35711309 ATAAAATTTT-AATATATAT
1 ATAAAATTTTCAA-ATATAT
35711328 ATTAAAA
1 A-TAAAA
35711335 ATGTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 16 0.70
20 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATTTTCAAATATAT
Found at i:35711329 original size:21 final size:22
Alignment explanation
Indices: 35711301--35711353 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
35711291 TAAATTTTTC
* *
35711301 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAAATGTATAT
*
35711322 ATATATAT-TAAAAATGTATAT
1 AAATATATATAAAAATGTATAT
35711343 AAATATATATA
1 AAATATATATA
35711354 TCAAAGATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATATATAAAAATGTATAT
Found at i:35712850 original size:16 final size:16
Alignment explanation
Indices: 35712829--35712905 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
35712819 GATTTTAGTA
35712829 AAGTATATATTCCAGC
1 AAGTATATATTCCAGC
**
35712845 AAGTATATATT-TGGC
1 AAGTATATATTCCAGC
*
35712860 ---CATATATTCCAGC
1 AAGTATATATTCCAGC
*
35712873 AACTGGAATATATTCCAGC
1 AA---GTATATATTCCAGC
35712892 AAGTATATATTCCA
1 AAGTATATATTCCA
35712906 AAGTTATAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.15
13 2 0.04
15 2 0.04
16 22 0.47
19 14 0.30
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.32
Consensus pattern (16 bp):
AAGTATATATTCCAGC
Found at i:35713554 original size:148 final size:148
Alignment explanation
Indices: 35713369--35713672 Score: 380
Period size: 148 Copynumber: 2.1 Consensus size: 148
35713359 AAGCTAAAAC
* * *
35713369 TTGTGGCGCTTAGAGCAAAAATGCCACAAATACCATGGACAAAACGACA-CTGTTATTGGATAAC
1 TTGTGGCGCTTAGAGCAAAAACGCCACAAATAACATGGACAAAACGACATC-GTTATTAGATAAC
* * * *
35713433 CATAAACATTTTTACGGCGTTTTATCAAAAGCGCCACTAATAAAAATAGGAAACGGCGTCGTTAC
65 CATAAACATTTTTACGGCGCTTTAGCAAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTAC
35713498 CTCAAC-CACTAATAAATAT
130 CTCAACTC-CTAATAAATAT
* * * *
35713517 TTGTGGCGCTT-GCAGTAAAAACGCCACTAATAACATGGACAAAATGGCATCGTTATTAGATAAC
1 TTGTGGCGCTTAG-AGCAAAAACGCCACAAATAACATGGACAAAACGACATCGTTATTAGATAAC
* * ** * * *
35713581 CTTAAACATTTTTGCGGCGCTTTAGCTGAAGCGCCACTAATAAAAGTAGGAAATGACGCCGTTTC
65 CATAAACATTTTTACGGCGCTTTAGCAAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTAC
* *
35713646 CTCAACTCGTAGTAAATAT
130 CTCAACTCCTAATAAATAT
35713665 TTGTGGCG
1 TTGTGGCG
35713673 TTTTTAAAAT
Statistics
Matches: 133, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
147 1 0.01
148 130 0.98
149 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (148 bp):
TTGTGGCGCTTAGAGCAAAAACGCCACAAATAACATGGACAAAACGACATCGTTATTAGATAACC
ATAAACATTTTTACGGCGCTTTAGCAAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTACC
TCAACTCCTAATAAATAT
Found at i:35714128 original size:7 final size:7
Alignment explanation
Indices: 35714116--35714191 Score: 64
Period size: 7 Copynumber: 10.3 Consensus size: 7
35714106 TTTGGGATTT
35714116 AACCTTA
1 AACCTTA
35714123 AACCTTA
1 AACCTTA
*
35714130 AACCCCTA
1 AA-CCTTA
35714138 AACCTTAA
1 AACCTT-A
35714146 AATCC-TA
1 AA-CCTTA
*
35714153 AGCCATTA
1 AACC-TTA
35714161 AACCCTTA
1 AA-CCTTA
*
35714169 AACCCTA
1 AACCTTA
35714176 AACCTTA
1 AACCTTA
*
35714183 AATCTTA
1 AACCTTA
35714190 AA
1 AA
35714192 ACCAACAACC
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
6 2 0.04
7 32 0.57
8 18 0.32
9 4 0.07
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.25
Consensus pattern (7 bp):
AACCTTA
Found at i:35714171 original size:8 final size:8
Alignment explanation
Indices: 35714118--35714184 Score: 54
Period size: 8 Copynumber: 8.9 Consensus size: 8
35714108 TGGGATTTAA
35714118 CCTTAAA-
1 CCTTAAAC
35714125 CCTTAAAC
1 CCTTAAAC
*
35714133 CCCTAAA-
1 CCTTAAAC
*
35714140 CCTTAAAAT
1 CCTT-AAAC
*
35714149 CC-TAAGC
1 CCTTAAAC
*
35714156 CATTAAAC
1 CCTTAAAC
35714164 CCTTAAAC
1 CCTTAAAC
35714172 CC-TAAA-
1 CCTTAAAC
35714178 CCTTAAA
1 CCTTAAA
35714185 TCTTAAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
6 2 0.04
7 21 0.44
8 23 0.48
9 2 0.04
ACGTcount: A:0.42, C:0.33, G:0.01, T:0.24
Consensus pattern (8 bp):
CCTTAAAC
Found at i:35714193 original size:15 final size:15
Alignment explanation
Indices: 35714116--35714194 Score: 72
Period size: 15 Copynumber: 5.3 Consensus size: 15
35714106 TTTGGGATTT
35714116 AACCTTAAACCTTAA
1 AACCTTAAACCTTAA
* *
35714131 ACCCCTAAACCTTAA
1 AACCTTAAACCTTAA
*
35714146 AATCC-TAAGCCATTAA
1 AA-CCTTAAACC-TTAA
* *
35714162 ACCCTTAAACCCT-A
1 AACCTTAAACCTTAA
*
35714176 AACCTTAAATCTTAA
1 AACCTTAAACCTTAA
35714191 AACC
1 AACC
35714195 AACAACCAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
14 11 0.22
15 27 0.54
16 12 0.24
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (15 bp):
AACCTTAAACCTTAA
Found at i:35714658 original size:21 final size:20
Alignment explanation
Indices: 35714591--35714658 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
35714581 GACTAAATGG
35714591 CCTAAACCCCAAACCTC-AAA
1 CCTAAACCCCAAACC-CAAAA
**
35714611 CCTTAAACCCCAAACTCCTAACC
1 CC-TAAACCCCAAAC-CC-AAAA
*
35714634 CCTAAACCCAAAACACCAAAA
1 CCTAAACCCCAAAC-CCAAAA
35714655 CCTA
1 CCTA
35714659 CATCATAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 14 0.37
23 3 0.08
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (20 bp):
CCTAAACCCCAAACCCAAAA
Found at i:35715367 original size:115 final size:113
Alignment explanation
Indices: 35715016--35715656 Score: 569
Period size: 115 Copynumber: 5.6 Consensus size: 113
35715006 TGGTTTCCCG
* * ** * * * *
35715016 TAAGCGCCACAAATTTTAGTATACATCAAGACCAAAACGCTGCGTTTTGGTTAAGGTATTCTACG
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
** * * * * **
35715081 GCGCTAGCCACAAATCTCCGCTACTACTATGCTTTAGCGGCG-TTTCACCG
66 GCGCT-TTCAAAAAGCGCCGCTAATACTAT-CTTTAGCGGCGTTTTC-CTA
* * * * * * *
35715131 TAAGCGGCAATAATTC-AAGTATACATCCAGACCAAAACGCTGCGTTTTGGTTCAGATATTTTGT
1 TAAGCGCCACTAATTCTAA-CATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGC
* * * *
35715195 GGCTCATCCAAAAAGCGCCGCTAATACTATCCTTTAGCGGCGTTTTCCAA
65 GGCGCTTTCAAAAAGCGCCGCTAATACTAT-CTTTAGCGGCGTTTTCCTA
** * *
35715245 TAAGCGCCACTAACGCTAACATACCTTAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
* * * * * *
35715310 GCGCTTTTACTAAAGCGCCGCTAATACTATCCTTTAACGGCATTTTACTG
66 GCGCTTTCA-AAAAGCGCCGCTAATACTAT-CTTTAGCGGCGTTTTCCTA
** * * *
35715360 TAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGCTGTGTTTTGGTTAAGATATTTTGCA
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
** ** ** * * *
35715425 GCGCTAGCCACGACTCACCGCTAATACTATGTTATAGCGGCGTTTTCGGTA
66 GCGCT-TTCAAAAAGCGCCGCTAATACTATCTT-TAGCGGCGTTTTC-CTA
* ** * * * **
35715476 -AA-CGCCGCTAATTCTAGTATA-AGCAAGACCAAAA-TGATGCGTTTTGGTTCAGATATTTCAC
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACT-CTGCGTTTTGGTTAAGATATTTTGC
* *
35715537 GGCGCTTTCAAAAAGCGCCGTTAATACTATCTGTTTGCGGCGTTTTCCTA
65 GGCGCTTTCAAAAAGCGCCGCTAATACTATCT-TTAGCGGCGTTTTCCTA
35715587 TAAGCGCCACTAATTCTAACATACATCAAGACC-AAACTCTGCG-TTTGGTTAAGATATTTTGCG
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
35715650 GCGCTTT
66 GCGCTTT
35715657 GCCATGCCTT
Statistics
Matches: 420, Mismatches: 93, Indels: 29
0.77 0.17 0.05
Matches are distributed among these distances:
111 2 0.00
112 55 0.13
113 61 0.15
114 117 0.28
115 183 0.44
116 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (113 bp):
TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
GCGCTTTCAAAAAGCGCCGCTAATACTATCTTTAGCGGCGTTTTCCTA
Found at i:35715419 original size:229 final size:226
Alignment explanation
Indices: 35715042--35715654 Score: 637
Period size: 229 Copynumber: 2.7 Consensus size: 226
35715032 TAGTATACAT
* * * ** * * *
35715042 CAAGACCAAAACGCTGCGTTTTGGTTAAGGTATTCTACGGCGCTAGCCACAAATCTCCGCTACTA
1 CAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTACGGCGCT-TTCACAAAGCGCCGCTAATA
* * * * * *
35715107 CTATGCTTTAGCGGCGTTTCACCGTAAGCGGCAATAATTCAAGTATACATCCAGACCAAAACGCT
65 CTAT-CTTTAGCGGCGTTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGCT
* * * *
35715172 GCGTTTTGGTTCAGATATTTTG-TG-GCTCATCCAAAAAGCGCCGCTAATACTATCCTT-TAGCG
129 GCGTTTTGGTTAAGATATTTTGCAGCGCT-AGCCAAAAAGCACCGCTAATACTAT-CTTATAGCG
*
35715234 GCGTTTTCCAATAAGCGCCACTAACGCTAACAT-AC
192 GCGTTTT-CAATAAACGCCACTAACGCTAACATAAC
* *
35715269 CTTAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTACTAAAGCGCCGCTAA
1 C--AAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTACGGCGCTTTCAC-AAAGCGCCGCTAA
* *
35715334 TACTATCCTTTAACGGCATTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACG
63 TACTAT-CTTTAGCGGCGTTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACG
* ** ** *
35715399 CTGTGTTTTGGTTAAGATATTTTGCAGCGCTAGCCACGACTCACCGCTAATACTATGTTATAGCG
127 CTGCGTTTTGGTTAAGATATTTTGCAGCGCTAGCCAAAAAGCACCGCTAATACTATCTTATAGCG
** * ** ** *
35715464 GCGTTTTCGGTAAACGCCGCTAATTCTAGTATAAG
192 GCGTTTTCAATAAACGCCACTAACGCTAACATAAC
* * * * *
35715499 CAAGACCAAAA-TGATGCGTTTTGGTTCAGATATTTCACGGCGCTTTCAAAAAGCGCCGTTAATA
1 CAAGACCAAAACT-CTGCGTTTTGGTTAAGATATTTTACGGCGCTTTCACAAAGCGCCGCTAATA
* * * ** *
35715563 CTATCTGTTTGCGGCGTTTTCCTATAAGCGCCACTAATTCTAACATACATCAAGACC-AAACTCT
65 CTATCT-TTAGCGGCGTTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGCT
*
35715627 GCG-TTTGGTTAAGATATTTTGCGGCGCT
129 GCGTTTTGGTTAAGATATTTTGCAGCGCT
35715655 TTGCCATGCC
Statistics
Matches: 322, Mismatches: 55, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
225 24 0.07
226 10 0.03
227 63 0.20
228 42 0.13
229 146 0.45
230 34 0.11
231 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (226 bp):
CAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTACGGCGCTTTCACAAAGCGCCGCTAATAC
TATCTTTAGCGGCGTTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGCTGC
GTTTTGGTTAAGATATTTTGCAGCGCTAGCCAAAAAGCACCGCTAATACTATCTTATAGCGGCGT
TTTCAATAAACGCCACTAACGCTAACATAAC
Found at i:35717604 original size:50 final size:50
Alignment explanation
Indices: 35717491--35717683 Score: 305
Period size: 50 Copynumber: 3.8 Consensus size: 50
35717481 GATAATAACA
* * **
35717491 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
35717542 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
35717592 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
35717642 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35717684 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 98 0.75
51 32 0.25
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:35719731 original size:21 final size:21
Alignment explanation
Indices: 35719701--35719768 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
35719691 ATGCTAAACT
35719701 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGGGTTGAACG
* * * *
35719722 GAAGCTCAT-AGGAGCTGAACA
1 GAAACCCATAAGG-GTTGAACG
*
35719743 GAAACCCATAAGGGTTAAACG
1 GAAACCCATAAGGGTTGAACG
*
35719764 AAAAC
1 GAAAC
35719769 TCTTATGAGT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.83
22 3 0.09
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (21 bp):
GAAACCCATAAGGGTTGAACG
Found at i:35719893 original size:24 final size:24
Alignment explanation
Indices: 35719866--35719977 Score: 188
Period size: 24 Copynumber: 4.7 Consensus size: 24
35719856 TAATTTTTCA
*
35719866 TCAATTCATCCTTTGTATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
*
35719890 TCAATTCATCATTTGCATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
*
35719914 TCAATTCATCCTTTACATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
35719938 TCAATTCATCCTTTGCATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
*
35719962 TCAATTCATCATTTGC
1 TCAATTCATCCTTTGC
35719978 CATAGAACTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (24 bp):
TCAATTCATCCTTTGCATTTACCG
Found at i:35724394 original size:26 final size:26
Alignment explanation
Indices: 35724359--35724419 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
35724349 CAATCAACTC
*
35724359 AAACTTAAGGGTCATCCAACCCATTT
1 AAACTCAAGGGTCATCCAACCCATTT
* * * *
35724385 AAGCTCAAGGGTCTTTCGACCCATTT
1 AAACTCAAGGGTCATCCAACCCATTT
35724411 AAACTCAAG
1 AAACTCAAG
35724420 CTCGCTAGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (26 bp):
AAACTCAAGGGTCATCCAACCCATTT
Found at i:35727590 original size:28 final size:26
Alignment explanation
Indices: 35727559--35727617 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 26
35727549 GAAATTAAAC
35727559 AAAATT-AAAAAGTATTTTAAAATATTTT
1 AAAATTAAAAAAGTA-TTT-AAA-ATTTT
35727587 AAAATTAAAAAAGTATTTAAAATTTT
1 AAAATTAAAAAAGTATTTAAAATTTT
35727613 AAAAT
1 AAAAT
35727618 ATTTTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.33
27 3 0.10
28 9 0.30
29 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (26 bp):
AAAATTAAAAAAGTATTTAAAATTTT
Found at i:35727598 original size:18 final size:18
Alignment explanation
Indices: 35727577--35727632 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
35727567 AAAGTATTTT
35727577 AAAATATTTTAAAATTAA
1 AAAATATTTTAAAATTAA
**
35727595 AAAAGTA-TTTAAAATTTT
1 AAAA-TATTTTAAAATTAA
*
35727613 AAAATATTTTAAATTTAA
1 AAAATATTTTAAAATTAA
35727631 AA
1 AA
35727633 TTAAAAAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 2 0.06
18 27 0.87
19 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AAAATATTTTAAAATTAA
Found at i:35727633 original size:24 final size:24
Alignment explanation
Indices: 35727601--35727649 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
35727591 TTAAAAAAGT
*
35727601 ATTTAAAATTTTAAAA-TATTTTAA
1 ATTTAAAA-TTAAAAAGTATTTTAA
35727625 ATTTAAAATTAAAAAGTATTTTAA
1 ATTTAAAATTAAAAAGTATTTTAA
35727649 A
1 A
35727650 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTTAAAATTAAAAAGTATTTTAA
Found at i:35731482 original size:4 final size:4
Alignment explanation
Indices: 35731467--35731495 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
35731457 TTGGTAAGGG
35731467 AATA AA-A AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
35731496 AGGTTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:35731977 original size:17 final size:18
Alignment explanation
Indices: 35731944--35731979 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35731934 TAATGAATAC
*
35731944 ATAAAATAATATTATATA
1 ATAAAAGAATATTATATA
35731962 ATAAAAGAAT-TTATATA
1 ATAAAAGAATATTATATA
35731979 A
1 A
35731980 AAATTAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAGAATATTATATA
Found at i:35734277 original size:21 final size:21
Alignment explanation
Indices: 35734253--35734307 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
35734243 TAGATAAAAA
* *
35734253 ATAAATATATATAAAATTATC
1 ATAAATATAAATAAAACTATC
* *
35734274 ATAAAGATAAATAATACTATC
1 ATAAATATAAATAAAACTATC
35734295 ATAAATATAAATA
1 ATAAATATAAATA
35734308 TTAATTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAATATAAATAAAACTATC
Found at i:35738530 original size:17 final size:16
Alignment explanation
Indices: 35738510--35738546 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
35738500 TTGTTTTACA
35738510 TTTTTTCCTTGTTCTGT
1 TTTTTTCCTTGTTCT-T
*
35738527 TTTTTTCCTTTTTCTT
1 TTTTTTCCTTGTTCTT
35738543 TTTT
1 TTTT
35738547 ATTTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTTTCCTTGTTCTT
Found at i:35738585 original size:33 final size:33
Alignment explanation
Indices: 35738534--35738633 Score: 116
Period size: 33 Copynumber: 3.0 Consensus size: 33
35738524 TGTTTTTTTC
35738534 CTTTTTC-TTTTTTATTTGTTTTTCTTTATTTA
1 CTTTTTCATTTTTTATTTGTTTTTCTTTATTTA
*
35738566 CTTTTTCAGTTTTTT-TTTGTTTTTCTTTATTTT
1 CTTTTTCA-TTTTTTATTTGTTTTTCTTTATTTA
*
35738599 CTTTATT-ATTTTCTTTATTTGTTTATCATTTATTT
1 CTTT-TTCA-TTT-TTTATTTGTTTTTC-TTTATTT
35738634 TATAATATTT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
32 7 0.12
33 25 0.42
34 11 0.19
35 9 0.15
36 7 0.12
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (33 bp):
CTTTTTCATTTTTTATTTGTTTTTCTTTATTTA
Found at i:35738609 original size:12 final size:12
Alignment explanation
Indices: 35738592--35738617 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35738582 TTGTTTTTCT
35738592 TTATTTTCTTTA
1 TTATTTTCTTTA
35738604 TTATTTTCTTTA
1 TTATTTTCTTTA
35738616 TT
1 TT
35738618 TGTTTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTCTTTA
Found at i:35738658 original size:23 final size:22
Alignment explanation
Indices: 35738628--35738695 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
35738618 TGTTTATCAT
*
35738628 TTATTTTATAATATTTTAAATG
1 TTATTTTATAATATTTTAAATA
35738650 TATATTTTA-AATATTTTATAATA
1 T-TATTTTATAATATTTTA-AATA
35738673 TTATTTT-TAA-ATTTT-AATA
1 TTATTTTATAATATTTTAAATA
35738692 TTAT
1 TTAT
35738696 AAAATATTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 8 0.19
21 5 0.12
22 18 0.43
23 11 0.26
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (22 bp):
TTATTTTATAATATTTTAAATA
Found at i:35738662 original size:22 final size:21
Alignment explanation
Indices: 35738628--35738711 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 21
35738618 TGTTTATCAT
*
35738628 TTATTTTATAATATTTTAAATG
1 TTATTTTA-AATATTTTAAATA
35738650 TATATTTTAAATATTTTATAATA
1 T-TATTTTAAATATTTTA-AATA
*
35738673 TTATTTTTAA-ATTTT-AATA
1 TTATTTTAAATATTTTAAATA
* *
35738692 TTA--TAAAATATTTAAAATA
1 TTATTTTAAATATTTTAAATA
35738711 T
1 T
35738712 ATTATTTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.06
18 4 0.08
19 12 0.23
21 5 0.09
22 18 0.34
23 11 0.21
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (21 bp):
TTATTTTAAATATTTTAAATA
Found at i:35738688 original size:21 final size:22
Alignment explanation
Indices: 35738620--35738695 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
35738610 TCTTTATTTG
*
35738620 TTTATCAT-TTATTTTATAATAT
1 TTTATAATATTATTTT-TAATAT
* *
35738642 TTTA-AATGTATATTTTAAATAT
1 TTTATAATAT-TATTTTTAATAT
35738664 TTTATAATATTATTTTTAA-A-
1 TTTATAATATTATTTTTAATAT
35738684 TTT-TAATATTAT
1 TTTATAATATTAT
35738696 AAAATATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
19 9 0.19
20 3 0.06
21 3 0.06
22 22 0.47
23 10 0.21
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (22 bp):
TTTATAATATTATTTTTAATAT
Found at i:35738841 original size:33 final size:32
Alignment explanation
Indices: 35738796--35738859 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
35738786 TAAAAATTAT
* *
35738796 TTTTTAAAATAATACTT-TATTTGAATATAATAA
1 TTTTAAAAATAATA-TTGTATTT-AATAAAATAA
35738829 TTTTAAAAATAATATTGTATTTAATAAAATA
1 TTTTAAAAATAATATTGTATTTAATAAAATA
35738860 CTATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTTAAAAATAATATTGTATTTAATAAAATAA
Found at i:35738878 original size:45 final size:43
Alignment explanation
Indices: 35738772--35738886 Score: 112
Period size: 45 Copynumber: 2.6 Consensus size: 43
35738762 TTTAAATGTA
35738772 TATTTTAAAAATTTTAAAAAT--TATTTTTTAAAATAATACTT
1 TATTTTAAAAATTTTAAAAATAATATTTTTTAAAATAATACTT
35738813 TATTTGAATATAATAATTTTAAAAATAATATTGTATTTAATAA-AATACTAT
1 TATTT---TA-AA-AATTTTAAAAATAATATT-T-TTTAA-AATAATACT-T
*
35738864 T-TTTTAAAAATTTTAAATATAAT
1 TATTTTAAAAATTTTAAAAATAAT
35738887 TGAAGAAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
41 5 0.08
44 2 0.03
45 16 0.26
46 14 0.23
47 2 0.03
48 4 0.06
49 1 0.02
50 14 0.23
51 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (43 bp):
TATTTTAAAAATTTTAAAAATAATATTTTTTAAAATAATACTT
Found at i:35738993 original size:20 final size:20
Alignment explanation
Indices: 35738947--35738995 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35738937 TAAGAATGTT
*
35738947 TTATAATATTAAAAAATTATA
1 TTATAAAATTAAAAAA-TATA
35738968 TT-TAAAATTCAAAAAA-ATA
1 TTATAAAATT-AAAAAATATA
35738987 TTATAAAAT
1 TTATAAAAT
35738996 ATTTAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 8 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TTATAAAATTAAAAAATATA
Found at i:35739002 original size:9 final size:10
Alignment explanation
Indices: 35738981--35739028 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
35738971 AAAATTCAAA
35738981 AAAATATTAT
1 AAAATATTAT
35738991 AAAATATT-T
1 AAAATATTAT
*
35739000 AAAATATACATTT
1 AAAATAT---TAT
35739013 AAAATATTAT
1 AAAATATTAT
35739023 AAAATA
1 AAAATA
35739029 AATAATAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 8 0.24
10 16 0.48
12 1 0.03
13 8 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATATTAT
Found at i:35739003 original size:22 final size:23
Alignment explanation
Indices: 35738946--35739032 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 23
35738936 TTAAGAATGT
* * *
35738946 TTTATAATATTAAAAAAT-TATA
1 TTTAAAATATTATAAAATAAATA
*
35738968 TTT-AAA-ATT-CAAAA-AAATA
1 TTTAAAATATTATAAAATAAATA
* *
35738987 TTATAAAATATT-TAAAATATACA
1 TT-TAAAATATTATAAAATAAATA
35739010 TTTAAAATATTATAAAATAAATA
1 TTTAAAATATTATAAAATAAATA
35739033 ATAAACAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
19 9 0.18
20 4 0.08
21 5 0.10
22 19 0.37
23 14 0.27
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTAAAATATTATAAAATAAATA
Found at i:35739076 original size:20 final size:20
Alignment explanation
Indices: 35739051--35739127 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 20
35739041 ATAAAGAAAA
35739051 ACAAAAAAATCAGAAAAAGG
1 ACAAAAAAATCAGAAAAAGG
* *
35739071 ACAAAAAAAACAG-AAAATG
1 ACAAAAAAATCAGAAAAAGG
*
35739090 --AAAAAAATGAGAAACAA--
1 ACAAAAAAATCAGAAA-AAGG
*
35739107 ATAAAAAAATCAGAAAAAGG
1 ACAAAAAAATCAGAAAAAGG
35739127 A
1 A
35739128 TAGCAGCAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 9 0.20
18 4 0.09
19 20 0.43
20 13 0.28
ACGTcount: A:0.73, C:0.08, G:0.13, T:0.06
Consensus pattern (20 bp):
ACAAAAAAATCAGAAAAAGG
Found at i:35739079 original size:28 final size:27
Alignment explanation
Indices: 35739047--35739127 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
35739037 ACAAATAAAG
*
35739047 AAAAACAAAAAAATCAGAAAAAGGACA
1 AAAAAAAAAAAAATCAGAAAAAGGACA
* * * * *
35739074 AAAAAAACAGAAAATGAAAAAAATGAGA
1 AAAAAAA-AAAAAATCAGAAAAAGGACA
*
35739102 AACAAATAAAAAAATCAGAAAAAGGA
1 AA-AAAAAAAAAAATCAGAAAAAGGA
35739128 TAGCAGCAGA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
27 6 0.15
28 31 0.76
29 4 0.10
ACGTcount: A:0.74, C:0.07, G:0.12, T:0.06
Consensus pattern (27 bp):
AAAAAAAAAAAAATCAGAAAAAGGACA
Found at i:35739086 original size:37 final size:36
Alignment explanation
Indices: 35739045--35739124 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 36
35739035 AAACAAATAA
35739045 AGAAAAACAAAAAAATCAGAAA-AAGGACAAAAAAAAC
1 AGAAAAACAAAAAAATCAGAAACAA--ACAAAAAAAAC
** * * *
35739082 AGAAAATGAAAAAAATGAGAAACAAATAAAAAAATC
1 AGAAAAACAAAAAAATCAGAAACAAACAAAAAAAAC
35739118 AGAAAAA
1 AGAAAAA
35739125 GGATAGCAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
36 15 0.42
37 19 0.53
38 2 0.06
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.06
Consensus pattern (36 bp):
AGAAAAACAAAAAAATCAGAAACAAACAAAAAAAAC
Found at i:35746722 original size:10 final size:10
Alignment explanation
Indices: 35746692--35746738 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
35746682 ATTTTTAGAG
35746692 ATTATATAAAA
1 ATTATA-AAAA
* *
35746703 ATTCTCAAAA
1 ATTATAAAAA
35746713 ATTAT-AAAA
1 ATTATAAAAA
*
35746722 ATAATAAAAA
1 ATTATAAAAA
35746732 ATTATAA
1 ATTATAA
35746739 TAGGGGTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 8 0.27
10 18 0.60
11 4 0.13
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:35746777 original size:10 final size:10
Alignment explanation
Indices: 35746762--35746786 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35746752 TTAAATTTTT
35746762 ATAACATTTA
1 ATAACATTTA
35746772 ATAACATTTA
1 ATAACATTTA
35746782 ATAAC
1 ATAAC
35746787 TTATATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAACATTTA
Found at i:35747133 original size:20 final size:19
Alignment explanation
Indices: 35747099--35747154 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
35747089 AATTTTTACA
*
35747099 AATTTTTATACTTTTAATT
1 AATTTTTATATTTTTAATT
* *
35747118 AGTTTTTTATATTTTTTTATT
1 A-ATTTTTATA-TTTTTAATT
35747139 AATTTTTATATTTTTA
1 AATTTTTATATTTTTA
35747155 TCATTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.20
20 16 0.53
21 8 0.27
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
AATTTTTATATTTTTAATT
Found at i:35747154 original size:18 final size:18
Alignment explanation
Indices: 35747083--35747173 Score: 67
Period size: 18 Copynumber: 4.8 Consensus size: 18
35747073 TTTCTTATAT
* **
35747083 TTTTTAAATTTTTACAAA
1 TTTTTATATTTTTATTAA
* *
35747101 TTTTTATACTTTTAATTAGT
1 TTTTTATA-TTTTTATTA-A
35747121 TTTTTATATTTTTTTATTAA
1 TTTTTATA--TTTTTATTAA
*
35747141 TTTTTATATTTTTA-TCA
1 TTTTTATATTTTTATTAA
*
35747158 TTTTAATTATTTTTAT
1 TTTTTA-TATTTTTAT
35747174 ATAAGTTTCT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
17 7 0.12
18 21 0.36
19 6 0.10
20 16 0.28
21 8 0.14
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTTATATTTTTATTAA
Found at i:35747257 original size:10 final size:10
Alignment explanation
Indices: 35747242--35747309 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
35747232 GAACATATTA
35747242 ATAATATTTT
1 ATAATATTTT
35747252 ATAATA--TT
1 ATAATATTTT
35747260 -TAATAGTTTT
1 ATAATA-TTTT
35747270 ATAAT-TTATT
1 ATAATATT-TT
35747280 A-AA-ATTTT
1 ATAATATTTT
* *
35747288 ATGATATTTG
1 ATAATATTTT
35747298 ATAAT-TTTT
1 ATAATATTTT
35747307 ATA
1 ATA
35747310 GATTTTCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
7 5 0.11
8 5 0.11
9 13 0.28
10 19 0.41
11 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (10 bp):
ATAATATTTT
Found at i:35747271 original size:18 final size:17
Alignment explanation
Indices: 35747243--35747296 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
35747233 AACATATTAA
35747243 TAATATTTTATAATATT
1 TAATATTTTATAATATT
*
35747260 TAATAGTTTTATAATTTAT
1 TAATA-TTTTATAATAT-T
* *
35747279 TAAAATTTTATGATATT
1 TAATATTTTATAATATT
35747296 T
1 T
35747297 GATAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.23
18 19 0.61
19 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TAATATTTTATAATATT
Found at i:35749273 original size:5 final size:5
Alignment explanation
Indices: 35749245--35749325 Score: 65
Period size: 5 Copynumber: 15.8 Consensus size: 5
35749235 TATAGTGAAA
* * * * * *
35749245 CATAT CTTAT CATAC CAGAG CATAT CATAAAT TATAC CATAT CA-ATT
1 CATAT CATAT CATAT CATAT CATAT CAT--AT CATAT CATAT CATA-T
*
35749292 CATAT CATAT CATAT CAGAT CATAT CATAT CATA
1 CATAT CATAT CATAT CATAT CATAT CATAT CATA
35749326 CAAAATCATA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
4 1 0.02
5 53 0.90
6 1 0.02
7 4 0.07
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.35
Consensus pattern (5 bp):
CATAT
Found at i:35750039 original size:48 final size:48
Alignment explanation
Indices: 35749954--35750045 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
35749944 AGCCCGTGTC
* * *
35749954 TGCACGATTTCACACGGCTGTGTGCCCCACATAGCCTACCCACAGGCT
1 TGCACGATTTCACACGACCGTGTGCCCCACACAGCCTACCCACAGGCT
* * * *
35750002 TGCATGATTTCACATGACCGTGTGCCCCGCACGGCCTACCCACA
1 TGCACGATTTCACACGACCGTGTGCCCCACACAGCCTACCCACA
35750046 CTACCGTGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (48 bp):
TGCACGATTTCACACGACCGTGTGCCCCACACAGCCTACCCACAGGCT
Found at i:35750205 original size:5 final size:5
Alignment explanation
Indices: 35750195--35750221 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
35750185 TGAGCATTCG
35750195 ATCGA ATCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA ATCGA AT
35750222 AAAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
ATCGA
Found at i:35751007 original size:30 final size:31
Alignment explanation
Indices: 35750968--35751027 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
35750958 TTGGGGTAGA
*
35750968 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
35750999 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
35751028 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:35751251 original size:18 final size:18
Alignment explanation
Indices: 35751228--35751264 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
35751218 TATAGTTTGA
*
35751228 TATTCGAGTTATTTGAAT
1 TATTCGAGTTATTCGAAT
35751246 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
35751264 T
1 T
35751265 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:35755611 original size:51 final size:51
Alignment explanation
Indices: 35755525--35755895 Score: 566
Period size: 51 Copynumber: 7.3 Consensus size: 51
35755515 GCTTCTAATC
* *
35755525 AGTGACAAGTGACAAGTAGTAGCTTCAGCTGCGCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
*
35755576 AGTGGCAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
* *
35755627 AGTGACAAGTGATAAGTAGTAGCTTCAACTACGCTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
35755678 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
* * *
35755729 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
* * *
35755780 AGTGACAAGTGATAAGTGGTAGCTT-AACTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
* * * * * *
35755830 AGTAAGAAGTGATAAGT-GATAGCTTTAGCTACACTTATTTGATCAGGGACA
1 AGTGACAAGTGATAAGTAG-TAGCTTCAGCTACGCTTATCTGATCAGTGACA
35755881 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
35755896 ATGTGATCCG
Statistics
Matches: 299, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
49 1 0.00
50 45 0.15
51 253 0.85
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
Found at i:35759666 original size:31 final size:29
Alignment explanation
Indices: 35759607--35759668 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
35759597 GTTTCACGTG
*
35759607 TATAATTGCACCAAATTAAAATTCATGTA
1 TATAATTGCACCAAAGTAAAATTCATGTA
* *
35759636 TATAATTGCACATTAAAGTAAAGTTCATGTA
1 TATAATTGCAC--CAAAGTAAAATTCATGTA
35759667 TA
1 TA
35759669 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
31 17 0.61
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (29 bp):
TATAATTGCACCAAAGTAAAATTCATGTA
Found at i:35759668 original size:29 final size:27
Alignment explanation
Indices: 35759605--35759671 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
35759595 AAGTTTCACG
*
35759605 TGTATAATTGCACCAAATTAAAATTCA
1 TGTATAATTGCACCAAAGTAAAATTCA
* *
35759632 TGTATATAATTGCACATTAAAGTAAAGTTCA
1 TG--TATAATTGCAC--CAAAGTAAAATTCA
35759663 TGTATAATT
1 TGTATAATT
35759672 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
29 18 0.55
31 13 0.39
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCACCAAAGTAAAATTCA
Found at i:35762646 original size:25 final size:25
Alignment explanation
Indices: 35762616--35762706 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
35762606 CCCGATTTTT
* *
35762616 AATAAACACAAAAAAATATTTTAAA
1 AATAAAAATAAAAAAATATTTTAAA
***
35762641 AATAAAAATAAATAAAA-AAAATAAA
1 AATAAAAATAAA-AAAATATTTTAAA
35762666 AATAAAAATAAAAAAATATTTTTAAA
1 AATAAAAATAAAAAAATA-TTTTAAA
*
35762692 ATTAAAAAATAAAAA
1 AAT-AAAAATAAAAA
35762707 TAAAAAAATA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
24 4 0.08
25 28 0.53
26 10 0.19
27 11 0.21
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
AATAAAAATAAAAAAATATTTTAAA
Found at i:35762647 original size:19 final size:16
Alignment explanation
Indices: 35762637--35762718 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 16
35762627 AAAAATATTT
35762637 TAAAAATAAAAATAA-A
1 TAAAAATAAAAA-AATA
35762653 TAAAAA-AAATAAAA-A
1 TAAAAATAAA-AAAATA
35762668 TAAAAATAAAAAAATA
1 TAAAAATAAAAAAATA
* *
35762684 TTTTTAAAAT-TAAAAA-A
1 ---TAAAAATAAAAAAATA
35762701 TAAAAATAAAAAAATA
1 TAAAAATAAAAAAATA
35762717 TA
1 TA
35762719 TTTATTATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
14 6 0.11
15 21 0.39
16 15 0.28
17 1 0.02
18 5 0.09
19 6 0.11
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAATAAAAAAATA
Found at i:35762653 original size:10 final size:10
Alignment explanation
Indices: 35762640--35762671 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
35762630 AATATTTTAA
35762640 AAATAAAAAT
1 AAATAAAAAT
35762650 AAATAAAAA-
1 AAATAAAAAT
35762659 AAATAAAAAT
1 AAATAAAAAT
35762669 AAA
1 AAA
35762672 AATAAAAAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:35762679 original size:50 final size:53
Alignment explanation
Indices: 35762616--35762716 Score: 145
Period size: 50 Copynumber: 2.0 Consensus size: 53
35762606 CCCGATTTTT
* *
35762616 AATAAACACAAAAAAATA-TTTTAAAAAT-AAAAATAAATA-AAAAAAATAAA
1 AATAAAAACAAAAAAATATTTTTAAAAATAAAAAATAAAAATAAAAAAATAAA
* *
35762666 AATAAAAATAAAAAAATATTTTTAAAATTAAAAAATAAAAATAAAAAAATA
1 AATAAAAACAAAAAAATATTTTTAAAAATAAAAAATAAAAATAAAAAAATA
35762717 TATTTATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
50 16 0.36
51 9 0.20
52 10 0.23
53 9 0.20
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (53 bp):
AATAAAAACAAAAAAATATTTTTAAAAATAAAAAATAAAAATAAAAAAATAAA
Found at i:35762711 original size:5 final size:6
Alignment explanation
Indices: 35762637--35762679 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
35762627 AAAAATATTT
*
35762637 TAAAAA TAAAAA TAAATAA AAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAA-AA TAAAAA TAAAAA TAAAAA TAAAAA
35762680 AATATTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:35763858 original size:28 final size:27
Alignment explanation
Indices: 35763819--35763875 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
35763809 AGAAACTAAA
* *
35763819 AACAAACATTCAACTAAAAAGAATGAT
1 AACAAACATTCAACTAAAAAAAATCAT
35763846 AACAAATCATTCAACTAAAAAAAATCAT
1 AACAAA-CATTCAACTAAAAAAAATCAT
35763874 AA
1 AA
35763876 AACGACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.61, C:0.16, G:0.04, T:0.19
Consensus pattern (27 bp):
AACAAACATTCAACTAAAAAAAATCAT
Found at i:35768616 original size:17 final size:15
Alignment explanation
Indices: 35768580--35768636 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 15
35768570 TATAAACAAT
35768580 ACAAAAATATTAAAA
1 ACAAAAATATTAAAA
*
35768595 ACAAAACTATTAAAATA
1 ACAAAAATATT-AAA-A
*
35768612 ACAAAAAAATATAAAA
1 ACAAAAATAT-TAAAA
*
35768628 ATAAAAATA
1 ACAAAAATA
35768637 AATTACAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 10 0.29
16 11 0.32
17 12 0.35
18 1 0.03
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (15 bp):
ACAAAAATATTAAAA
Found at i:35768710 original size:20 final size:18
Alignment explanation
Indices: 35768687--35768760 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
35768677 ATTTAAAAGC
35768687 TATAGAAAATTATTAAAATT
1 TATA-AAAA-TATTAAAATT
*
35768707 TATATAAAATATAAAAATAT
1 TATA-AAAATATTAAAAT-T
35768727 TATAAAAAGTA-TAAAA-T
1 TATAAAAA-TATTAAAATT
*
35768744 TATAAAACAAATTAAAA
1 TATAAAA-ATATTAAAA
35768761 ATATAAGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 9 0.20
18 6 0.13
19 16 0.35
20 15 0.33
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
TATAAAAATATTAAAATT
Found at i:35768730 original size:18 final size:19
Alignment explanation
Indices: 35768710--35768779 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 19
35768700 TAAAATTTAT
*
35768710 ATAAAA-TATAAAAATATT
1 ATAAAAGTATAAAAATATA
*
35768728 ATAAAAAGTATAAAATTATA
1 AT-AAAAGTATAAAAATATA
*
35768748 A-AACAAAT-TAAAAATATA
1 ATAA-AAGTATAAAAATATA
* *
35768766 AGAAAATTATAAAA
1 ATAAAAGTATAAAA
35768780 CTAATATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 17 0.40
19 14 0.33
20 11 0.26
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (19 bp):
ATAAAAGTATAAAAATATA
Found at i:35768757 original size:29 final size:28
Alignment explanation
Indices: 35768698--35768780 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
35768688 ATAGAAAATT
* *
35768698 ATTAAAATTTATATAAAA-TATAAAA-AT
1 ATTAAAA-ATATATAAAATTATAAAACAA
35768725 ATTATAAAA-AGTATAAAATTATAAAACAA
1 ATTA-AAAATA-TATAAAATTATAAAACAA
*
35768754 ATTAAAAATATAAGAAAATTATAAAAC
1 ATTAAAAATAT-ATAAAATTATAAAAC
35768781 TAATATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 1 0.02
27 11 0.23
28 15 0.32
29 20 0.43
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
ATTAAAAATATATAAAATTATAAAACAA
Found at i:35774128 original size:35 final size:35
Alignment explanation
Indices: 35774089--35774170 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 35
35774079 TATGTATTTT
**
35774089 TACTTTTTTTTTCTTTCTATTTTTTAAAATTTGAA
1 TACTTTTTTAATCTTTCTATTTTTTAAAATTTGAA
*
35774124 TACTTTTTTAATGTTTCTATTTTTTAAAATTTGAA
1 TACTTTTTTAATCTTTCTATTTTTTAAAATTTGAA
35774159 TACTTTTTTAAT
1 TACTTTTTTAAT
35774171 GTTCTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (35 bp):
TACTTTTTTAATCTTTCTATTTTTTAAAATTTGAA
Found at i:35774130 original size:18 final size:18
Alignment explanation
Indices: 35774109--35774166 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
35774099 TTCTTTCTAT
35774109 TTTTTAAAATTTGAATAC
1 TTTTTAAAATTTGAATAC
* ** *
35774127 TTTTT-TAATGTT-TCTAT
1 TTTTTAAAAT-TTGAATAC
35774144 TTTTTAAAATTTGAATAC
1 TTTTTAAAATTTGAATAC
35774162 TTTTT
1 TTTTT
35774167 TAATGTTCTC
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTTAAAATTTGAATAC
Found at i:35774132 original size:19 final size:19
Alignment explanation
Indices: 35774108--35774169 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
35774098 TTTCTTTCTA
35774108 TTTTTTAAAATTTGAATAC
1 TTTTTTAAAATTTGAATAC
** *
35774127 TTTTTTAATGTTT--CTA-
1 TTTTTTAAAATTTGAATAC
35774143 TTTTTTAAAATTTGAATAC
1 TTTTTTAAAATTTGAATAC
35774162 TTTTTTAA
1 TTTTTTAA
35774170 TGTTCTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 11 0.32
17 2 0.06
18 2 0.06
19 19 0.56
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTTTAAAATTTGAATAC
Found at i:35774171 original size:35 final size:35
Alignment explanation
Indices: 35774102--35774173 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
35774092 TTTTTTTTTC
35774102 TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
1 TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
35774137 TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
1 TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
35774172 TT
1 TT
35774174 CTCATAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (35 bp):
TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
Found at i:35775691 original size:23 final size:24
Alignment explanation
Indices: 35775639--35775699 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
35775629 TAGCTCGTAC
*
35775639 GAGCTTACCGATATATCAGCTCTTAT
1 GAGCTTACCG-T-TATCAGCTCTGAT
35775665 GAGCTTACCGTT-TCAGCT-TGAT
1 GAGCTTACCGTTATCAGCTCTGAT
*
35775687 AGAGCTAACCGTT
1 -GAGCTTACCGTT
35775700 CTTCAGTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 3 0.09
23 17 0.53
24 1 0.03
25 1 0.03
26 10 0.31
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (24 bp):
GAGCTTACCGTTATCAGCTCTGAT
Found at i:35781516 original size:9 final size:9
Alignment explanation
Indices: 35781502--35781530 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
35781492 CGTTAACGTG
35781502 TTGTAACAT
1 TTGTAACAT
35781511 TTGTAACAT
1 TTGTAACAT
35781520 TTGTAACAT
1 TTGTAACAT
35781529 TT
1 TT
35781531 TAGTCATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTGTAACAT
Found at i:35785125 original size:13 final size:13
Alignment explanation
Indices: 35785109--35785153 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
35785099 TCGAACCCCA
35785109 AACCTTAACCATG
1 AACCTTAACCATG
35785122 AACCTTAAACC-TG
1 AACCTT-AACCATG
*
35785135 AACCTCAAACCATG
1 AACCT-TAACCATG
35785149 AACCT
1 AACCT
35785154 CAAACCCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (13 bp):
AACCTTAACCATG
Found at i:35785765 original size:59 final size:60
Alignment explanation
Indices: 35785694--35785810 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 60
35785684 ATCAGTTTAA
* * * *
35785694 TATTAAATTAATATAATATTTATC-AATATAAATATTAAATTAAATTTAATATTAAATCT
1 TATTAAAATAATATAATACTTATCTAAGATAAATATTAAAGTAAATTTAATATTAAATCT
*
35785753 TATTAAAATAATATAATGCTTATCTATAAGATAAATATTAAAGTAAATTTAATATTAA
1 TATTAAAATAATATAATACTTATC--TAAGATAAATATTAAAGTAAATTTAATATTAA
35785811 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.42
62 29 0.58
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (60 bp):
TATTAAAATAATATAATACTTATCTAAGATAAATATTAAAGTAAATTTAATATTAAATCT
Found at i:35789425 original size:47 final size:47
Alignment explanation
Indices: 35789342--35789458 Score: 128
Period size: 47 Copynumber: 2.5 Consensus size: 47
35789332 TCTGTTCGAT
* * * * *
35789342 CAGTGGTTTATGCACAACGTATTTTATTCAGTAGTCATCTGCTCGAC
1 CAGTGGTTTATCCACAACATATTTTATTCAGCAGTCATCTACTCAAC
* *
35789389 TAGTGGTTTATCCACAACATATTTTAGTT-GGCAGTCATCTACTCAAC
1 CAGTGGTTTATCCACAACATATTTTA-TTCAGCAGTCATCTACTCAAC
* **
35789436 CAGTGGTTCATCCGTAACATATT
1 CAGTGGTTTATCCACAACATATT
35789459 AGCAGCTTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 56 0.97
48 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (47 bp):
CAGTGGTTTATCCACAACATATTTTATTCAGCAGTCATCTACTCAAC
Found at i:35790375 original size:21 final size:23
Alignment explanation
Indices: 35790331--35790375 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
35790321 TCGTCAGCTT
*
35790331 TTCTAAAAATAGACTAAATATTA
1 TTCTAAAAATAGAATAAATATTA
*
35790354 TTCT-AAAATA-AATAAATGTTA
1 TTCTAAAAATAGAATAAATATTA
35790375 T
1 T
35790376 AAATTGATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 6 0.30
23 4 0.20
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (23 bp):
TTCTAAAAATAGAATAAATATTA
Found at i:35795174 original size:47 final size:47
Alignment explanation
Indices: 35795120--35795236 Score: 126
Period size: 47 Copynumber: 2.5 Consensus size: 47
35795110 TTTGCTTGAT
*
35795120 CAGTGGTTTATCCACAATGTATTTTAGTCAACAATCATCTGCTCGAC
1 CAGTGGTTTATCCACAATGTATTTTAGTCAACAATCATCTACTCGAC
* * * ** * *
35795167 CAGTGGTTTATCCACGATATTTTTTAGTTGACAATCATTTACTTGAC
1 CAGTGGTTTATCCACAATGTATTTTAGTCAACAATCATCTACTCGAC
* * * *
35795214 CAATGGTTCATCCATAACGTATT
1 CAGTGGTTTATCCACAATGTATT
35795237 AGCAACTTTT
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (47 bp):
CAGTGGTTTATCCACAATGTATTTTAGTCAACAATCATCTACTCGAC
Found at i:35797871 original size:5 final size:5
Alignment explanation
Indices: 35797861--35797891 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
35797851 CTCGAAAATT
35797861 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
35797892 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:35799451 original size:16 final size:16
Alignment explanation
Indices: 35799430--35799468 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
35799420 TCATTTATTA
35799430 AATAAAA-ATTATCTT
1 AATAAAACATTATCTT
*
35799445 AATTAAAACATTATTTT
1 AA-TAAAACATTATCTT
35799462 AATAAAA
1 AATAAAA
35799469 TGATTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 10 0.48
17 9 0.43
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAAACATTATCTT
Found at i:35802675 original size:231 final size:229
Alignment explanation
Indices: 35802181--35802697 Score: 721
Period size: 230 Copynumber: 2.2 Consensus size: 229
35802171 AAGTTGTGAA
*
35802181 GAAAACGGCGTCGTTTTCTTATTACATTTAGTGGCGTTTTCTACAAAACGCCGCAACTATGTTTT
1 GAAAACGGCGTCGTTTTCTTATTACATTTAGTGGCG-TTT-TATAAAACGCCGCAACTATGTTTT
*** * ** * *
35802246 CTTTGTTACGGGAACGGCGTCGTTTTCCATTGTTATTAGTGGCGTTACACCCAAAACGCCGTAAA
64 CTTTGTTACAAAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAA
* *
35802311 TATATTTTAAAGATTACATGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACT
129 TATATTTTAAAGATTACAGGAGTTTACGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACT
* *
35802376 TATATATAAACGTCGCAAACTCGAAATGGTGTTACG
194 TATATATAAACGCCGCAAAATCGAAATGGTGTTACG
* * *
35802412 AAAAACGACGTCGTTTTCTTATTACATTTAGTGGCGTTTTAGATAAAACGCCGCAAGTATGTTTT
1 GAAAACGGCGTCGTTTTCTTATTACATTTAGTGGCGTTTT--ATAAAACGCCGCAACTATGTTTT
* * *
35802477 CTTTGTTACAAAAACGGCATCGTTTT-CAAGGATATTTGTGGCGTTACACCCAAAATGTCGCAAA
64 CTTTGTTACAAAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAA
* *
35802541 TATATTTTAAAGATTACAGGAGTTTACTTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCT
129 TATATTTTAAAGATTACAGGAGTTTACGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACT
*
35802606 TATATATAAACGCCGCAAAATTGAAATGGTGTTACG
194 TATATATAAACGCCGCAAAATCGAAATGGTGTTACG
* * *** *
35802642 GAAAACGGCGCCGTTTACTTAGTTGGTTTTAGTGGCGCTTTTATTAAACGCCGCAA
1 GAAAACGGCGTCGTTTTCTTA-TTACATTTAGTGGCG-TTTTATAAAACGCCGCAA
35802698 ATTTGCATTA
Statistics
Matches: 252, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
229 1 0.00
230 158 0.63
231 89 0.35
232 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (229 bp):
GAAAACGGCGTCGTTTTCTTATTACATTTAGTGGCGTTTTATAAAACGCCGCAACTATGTTTTCT
TTGTTACAAAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAATA
TATTTTAAAGATTACAGGAGTTTACGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACTTA
TATATAAACGCCGCAAAATCGAAATGGTGTTACG
Found at i:35803050 original size:19 final size:19
Alignment explanation
Indices: 35803028--35803071 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
35803018 CAGACATCTC
*
35803028 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
35803047 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
35803066 CCCCAA
1 CCCCAA
35803072 CGTAGTCCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:35805111 original size:20 final size:20
Alignment explanation
Indices: 35805086--35805150 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
35805076 TACAATTTCT
35805086 TAACTTATATAATATTAAGA
1 TAACTTATATAATATTAAGA
* *
35805106 TAACTTATTGTGGAATATT-ACA
1 TAACTTA-TAT--AATATTAAGA
*
35805128 TAACTTATATAATGTTAAGA
1 TAACTTATATAATATTAAGA
35805148 TAA
1 TAA
35805151 AAAATCGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 5 0.14
20 12 0.33
21 4 0.11
22 9 0.25
23 6 0.17
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (20 bp):
TAACTTATATAATATTAAGA
Found at i:35805183 original size:37 final size:37
Alignment explanation
Indices: 35805086--35805256 Score: 189
Period size: 37 Copynumber: 4.5 Consensus size: 37
35805076 TACAATTTCT
* * *
35805086 TAACTTATATAATATTAAGATAACTTATTGTGGAATATTACA
1 TAACTTATACAATATTAAGATAA--AATT-TCG-A-ATTACA
* * **
35805128 TAACTTATATAATGTTAAGATAAAAAATCGAATTACA
1 TAACTTATACAATATTAAGATAAAATTTCGAATTACA
* * *
35805165 TAACTTACACAATATTAAGGTAAAATTTCTAATTACA
1 TAACTTATACAATATTAAGATAAAATTTCGAATTACA
*
35805202 TAACTTATACAATATTAAGATAAAATTTTGAATTACA
1 TAACTTATACAATATTAAGATAAAATTTCGAATTACA
*
35805239 TAACTTATATAATATTAA
1 TAACTTATACAATATTAA
35805257 TATTACTTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
37 86 0.77
38 1 0.01
39 2 0.02
40 1 0.01
42 22 0.20
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.37
Consensus pattern (37 bp):
TAACTTATACAATATTAAGATAAAATTTCGAATTACA
Done.