Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 114 of 199
Found at i:34651848 original size:21 final size:22
Alignment explanation
Indices: 34651823--34651866 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
34651813 CACTCTTCCT
34651823 TTTCTTCATCGATTATTGCAGG
1 TTTCTTCATCGATTATTGCAGG
34651845 TTCTTCTTCATCGATTATTGCA
1 -T-TTCTTCATCGATTATTGCA
34651867 ATGTTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTCTTCATCGATTATTGCAGG
Found at i:34651881 original size:24 final size:24
Alignment explanation
Indices: 34651830--34651884 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
34651820 CCTTTTCTTC
* *
34651830 ATCGATTATTGCAGGTTCTTCTTC
1 ATCGATTATTGCAGGTTCTACTTA
*
34651854 ATCGATTATTGCAATGTTC-ACTTA
1 ATCGATTATTGC-AGGTTCTACTTA
34651878 ATCGATT
1 ATCGATT
34651885 TCCCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (24 bp):
ATCGATTATTGCAGGTTCTACTTA
Found at i:34653319 original size:22 final size:22
Alignment explanation
Indices: 34653304--34653366 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
34653294 TTGTTTTAAT
34653304 ATTGTTCTTGATTTGTTCTGAAA
1 ATTGTT-TTGATTTGTTCTGAAA
* *
34653327 ATTGTTTTGA-TAGTCTGCTGGAA
1 ATTGTTTTGATTTGT-T-CTGAAA
34653350 ATTGTTCTTGATTTGTT
1 ATTGTT-TTGATTTGTT
34653367 AGTGAGTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.09
22 5 0.15
23 17 0.52
24 5 0.15
25 3 0.09
ACGTcount: A:0.19, C:0.08, G:0.21, T:0.52
Consensus pattern (22 bp):
ATTGTTTTGATTTGTTCTGAAA
Found at i:34657372 original size:47 final size:47
Alignment explanation
Indices: 34657319--34657562 Score: 263
Period size: 47 Copynumber: 5.3 Consensus size: 47
34657309 ATGATTTTAG
* * * *
34657319 TAAATTCATATAAGAATATTTATTATTAAGAATT-TTATAAAATTATA
1 TAAATTCATATAAGAAAATTTATTAGTAATAATTATT-TTAAATTATA
* *
34657366 TAAATTCATATAAGAAAATTTATTA-TCAAAAATT-TTATGAAATTATA
1 TAAATTCATATAAGAAAATTTATTAGT-AATAATTATT-TTAAATTATA
** *
34657413 T--A-T--TATAATTAAATTATATTTAATAATAATTATTTTAAATTATA
1 TAAATTCATATAAGAAAATT-TA-TTAGTAATAATTATTTTAAATTATA
*
34657457 CAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
1 TAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
* *
34657504 CAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTTTA
1 TAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
34657551 TTAAA-TCATATA
1 -TAAATTCATATA
34657563 TTTTAATTAA
Statistics
Matches: 173, Mismatches: 13, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
42 10 0.06
43 2 0.01
44 19 0.11
45 4 0.02
46 2 0.01
47 121 0.70
48 5 0.03
49 10 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (47 bp):
TAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
Found at i:34657432 original size:16 final size:17
Alignment explanation
Indices: 34657411--34657456 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
34657401 TATGAAATTA
34657411 TATATTATAATTA-AAT
1 TATATTATAATTATAAT
*
34657427 TATATT-TAATAATAAT
1 TATATTATAATTATAAT
*
34657443 TATTTTA-AATTATA
1 TATATTATAATTATA
34657457 CAAATTCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATTATAATTATAAT
Found at i:34657438 original size:18 final size:17
Alignment explanation
Indices: 34657405--34657450 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
34657395 AAATTTTATG
34657405 AAATTATATATT-ATAATT
1 AAATTATAT-TTAATAA-T
34657423 AAATTATATTTAATAAT
1 AAATTATATTTAATAAT
34657440 -AATTAT-TTTAA
1 AAATTATATTTAA
34657451 ATTATACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.19
16 6 0.22
17 3 0.11
18 13 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATATTTAATAAT
Found at i:34657525 original size:91 final size:91
Alignment explanation
Indices: 34657319--34657547 Score: 238
Period size: 91 Copynumber: 2.5 Consensus size: 91
34657309 ATGATTTTAG
* * * *
34657319 TAAATTCATATAAGAATATTTATTATTAAGAATT-TTATAAAATTATATAAATTCATATAAGAAA
1 TAAATTCATATAAGAATATTTA-TAGTAATAATTATT-TTAAATTATACAAATTCATATAAGAAA
34657383 ATTTATTATCAAAAATTTTATGAAATTA
64 ATTTATTATCAAAAATTTTATGAAATTA
*
34657411 TATATT-ATAATTAA-ATTATATTTA-A-TAATAATTATTTTAAATTATACAAATTCATATAAGA
1 TAAATTCAT-A-TAAGA--ATATTTATAGTAATAATTATTTTAAATTATACAAATTCATATAAGA
* *
34657472 AAATTTATTAGT-AATAATTATT-TTAAATTA
62 AAATTTATTA-TCAAAAATT-TTATGAAATTA
*
34657502 TACAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATT
1 T--AAATTCATATAAGAATATTTA-TAGTAATAATTATTTTAAATT
34657548 TTATTAAATC
Statistics
Matches: 115, Mismatches: 8, Indels: 26
0.77 0.05 0.17
Matches are distributed among these distances:
91 62 0.54
92 16 0.14
93 10 0.09
94 27 0.23
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (91 bp):
TAAATTCATATAAGAATATTTATAGTAATAATTATTTTAAATTATACAAATTCATATAAGAAAAT
TTATTATCAAAAATTTTATGAAATTA
Found at i:34657610 original size:59 final size:61
Alignment explanation
Indices: 34657544--34657713 Score: 186
Period size: 59 Copynumber: 2.8 Consensus size: 61
34657534 AATTATTTTA
34657544 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCA-TATT-A-
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTT-ATTATTAAG
* ** * * ** * * * *
34657603 TATTTTATTGTATCATATATTATGATTTTAGTAAATTCATATAAGAA-TATTTATTATTAAG
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTA-ATAATAATTATTTATTATTAAG
*
34657664 AATTTTATTAAATCATATATTTGAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT
34657714 GTTAAAATAT
Statistics
Matches: 83, Mismatches: 23, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
58 1 0.01
59 38 0.46
60 13 0.16
61 31 0.37
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (61 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTATTATTAAG
Found at i:34657672 original size:15 final size:16
Alignment explanation
Indices: 34657644--34657673 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34657634 TAAATTCATA
34657644 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
34657660 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
34657674 AATCATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:34657953 original size:16 final size:16
Alignment explanation
Indices: 34657932--34657968 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
34657922 TTGATTTGCT
34657932 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
34657948 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
34657964 ATTAC
1 ATTAC
34657969 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:34658891 original size:37 final size:37
Alignment explanation
Indices: 34658844--34658924 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
34658834 GTCCAATTAA
* *
34658844 AAAATGTGTATCAATTATCTTATTATATGTGTAGACT
1 AAAAGGTGTATCAATTATCTTATTACATGTGTAGACT
* * *
34658881 AAAAGGTGTATCAATTATTTTCTTACATGTGTAGCCT
1 AAAAGGTGTATCAATTATCTTATTACATGTGTAGACT
34658918 AAAAGGT
1 AAAAGGT
34658925 TTAAATAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (37 bp):
AAAAGGTGTATCAATTATCTTATTACATGTGTAGACT
Found at i:34664734 original size:19 final size:18
Alignment explanation
Indices: 34664712--34664747 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34664702 ATTCTAGACT
34664712 TTAACTTTTAACTTTTTTA
1 TTAACTTTTAA-TTTTTTA
*
34664731 TTAATTTTTAATTTTTT
1 TTAACTTTTAATTTTTT
34664748 GAATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTAACTTTTAATTTTTTA
Found at i:34664776 original size:21 final size:21
Alignment explanation
Indices: 34664749--34664802 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
34664739 TAATTTTTTG
*
34664749 AATTTTTAAAAATATTTCTATA
1 AATTTTTAAAAATATTT-TACA
* *
34664771 AA-TTTTAATAATGTTTTACA
1 AATTTTTAAAAATATTTTACA
34664791 AATTTTTAAAAA
1 AATTTTTAAAAA
34664803 GCTAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 20 0.74
22 2 0.07
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (21 bp):
AATTTTTAAAAATATTTTACA
Found at i:34664809 original size:29 final size:29
Alignment explanation
Indices: 34664776--34664831 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
34664766 CTATAAATTT
34664776 TAATAATGTTTTACAAA-T-TTTTAAAAAGC
1 TAAT-ATGTTTTA-AAATTATTTTAAAAAGC
*
34664805 TAATATTTTTTAAAATTATTTTAAAAA
1 TAATATGTTTTAAAATTATTTTAAAAA
34664832 AATTAAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.12
28 8 0.33
29 13 0.54
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (29 bp):
TAATATGTTTTAAAATTATTTTAAAAAGC
Found at i:34670780 original size:30 final size:30
Alignment explanation
Indices: 34670733--34670810 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 30
34670723 CAACCCAATC
* * *
34670733 ATAAAAATTACAAATAATTTCATAAATAAAA
1 ATAAAAA-TAAAAATAATTTAAAAAATAAAA
34670764 ATAAAAATAAAAATAATTTAAAAAATAAAA
1 ATAAAAATAAAAATAATTTAAAAAATAAAA
34670794 ATAAAAATAAAATATAA
1 ATAAAAATAAAA-ATAA
34670811 ATAGGCACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 32 0.74
31 11 0.26
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (30 bp):
ATAAAAATAAAAATAATTTAAAAAATAAAA
Found at i:34670813 original size:6 final size:6
Alignment explanation
Indices: 34670756--34670811 Score: 69
Period size: 6 Copynumber: 9.2 Consensus size: 6
34670746 ATAATTTCAT
**
34670756 AAATAA AAATAA AAATAA AAAT-A ATTTAAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAAT-AA AAATAA AAATAA AAATAA
34670804 AATATAA A
1 AA-ATAA A
34670812 TAGGCACATG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
5 3 0.07
6 32 0.74
7 8 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:34675429 original size:105 final size:104
Alignment explanation
Indices: 34675222--34675434 Score: 381
Period size: 104 Copynumber: 2.0 Consensus size: 104
34675212 TTACTCTGGT
* *
34675222 AAGATAAAGTCAGGAGTGGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACCAAAA
1 AAGATAAAATCAGGAGTAGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACCAAAA
34675287 AAATGCTTACACATATATATACATTTACGTACATTTATA
66 AAATGCTTACACATATATATACATTTACGTACATTTATA
34675326 AAGATAAAATCAGGAGTAGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACCAAAA
1 AAGATAAAATCAGGAGTAGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACC-AAA
* *
34675391 AAAATGCTTACACGTTTATATACATTTACGTACATTTATA
65 AAAATGCTTACACATATATATACATTTACGTACATTTATA
34675431 AAGA
1 AAGA
34675435 ATTGTGTTAA
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 59 0.57
105 45 0.43
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (104 bp):
AAGATAAAATCAGGAGTAGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACCAAAA
AAATGCTTACACATATATATACATTTACGTACATTTATA
Found at i:34675691 original size:23 final size:23
Alignment explanation
Indices: 34675661--34675714 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
34675651 TTTAAAAGTT
* *
34675661 AAATATTATTTTATCCTAATATC
1 AAATATTATGTAATCCTAATATC
*
34675684 AAATATTATGTAATCCTAATATT
1 AAATATTATGTAATCCTAATATC
34675707 AAATATTA
1 AAATATTA
34675715 ATTACAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATATTATGTAATCCTAATATC
Found at i:34678727 original size:13 final size:14
Alignment explanation
Indices: 34678703--34678731 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34678693 CATGCTTTTG
34678703 AACACTTTGATCAT
1 AACACTTTGATCAT
34678717 AACAC-TTGATCAT
1 AACACTTTGATCAT
34678730 AA
1 AA
34678732 ATCAACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (14 bp):
AACACTTTGATCAT
Found at i:34693723 original size:25 final size:25
Alignment explanation
Indices: 34693695--34693749 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
34693685 CTGAATGTTT
** *
34693695 TCAGTACAGTCTATCTATAGTATTC
1 TCAGTACACACTATCTATAGCATTC
* *
34693720 TCAGTATACACTATCTATAGCATTT
1 TCAGTACACACTATCTATAGCATTC
34693745 TCAGT
1 TCAGT
34693750 TTTTAAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (25 bp):
TCAGTACACACTATCTATAGCATTC
Found at i:34698908 original size:22 final size:21
Alignment explanation
Indices: 34698869--34698913 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
34698859 ATTATGAATA
34698869 TTAATTTATAATATAATTAATT
1 TTAATTTATAATATAATT-ATT
*
34698891 TTAATTT-TAATCTAAATTATT
1 TTAATTTATAATAT-AATTATT
34698912 TT
1 TT
34698914 GTGTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATTTATAATATAATTATT
Found at i:34706130 original size:16 final size:16
Alignment explanation
Indices: 34706109--34706179 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
34706099 GTTTGATTCA
*
34706109 CTATAATGGAATAGGG
1 CTATAATGGAATAGAG
*
34706125 CTATAATTGAATAGAG
1 CTATAATGGAATAGAG
* *
34706141 CTGTAATGGAATAAAG
1 CTATAATGGAATAGAG
* * *
34706157 TTGTAATGGAATAAAG
1 CTATAATGGAATAGAG
*
34706173 CTGTAAT
1 CTATAAT
34706180 TAGTAATTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.30
Consensus pattern (16 bp):
CTATAATGGAATAGAG
Found at i:34706361 original size:25 final size:26
Alignment explanation
Indices: 34706333--34706383 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
34706323 GATGACCATT
*
34706333 GTTATTGTT-ATTAAATTTTAATAAA
1 GTTATTGTTAAATAAATTTTAATAAA
*
34706358 GTTATTGTTAAATATATTTTAATAAA
1 GTTATTGTTAAATAAATTTTAATAAA
34706384 TAAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (26 bp):
GTTATTGTTAAATAAATTTTAATAAA
Found at i:34706491 original size:57 final size:56
Alignment explanation
Indices: 34706385--34706513 Score: 125
Period size: 57 Copynumber: 2.2 Consensus size: 56
34706375 TTTAATAAAT
* * * * * *
34706385 AAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATAAAATTCAATA
1 AAATAATATATAATTTAATAACATTATAACATAATTATTATGAAATAAAAATC-ATA
* * *
34706442 AAATAATATATAATTTAATAACATTCATAATATTATTA-TATGAATTAAAAATCATA
1 AAATAATATATAATTTAATAACATT-ATAACATAATTATTATGAAATAAAAATCATA
34706498 ATATATAATATTATAA
1 A-A-ATAATA-TATAA
34706514 AAATAATATA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
56 4 0.07
57 35 0.59
58 15 0.25
59 5 0.08
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (56 bp):
AAATAATATATAATTTAATAACATTATAACATAATTATTATGAAATAAAAATCATA
Found at i:34710118 original size:33 final size:33
Alignment explanation
Indices: 34710081--34710268 Score: 116
Period size: 33 Copynumber: 5.7 Consensus size: 33
34710071 CTTTATTCTA
* *
34710081 TGTTTACTGTCCCAGCAGACTATTTCTATTTCG
1 TGTTTATTGTCCCAACAGACTATTTCTATTTCG
* ** *
34710114 TGTTTATTGTCCTAACAGACTAACTCTATTTTG
1 TGTTTATTGTCCCAACAGACTATTTCTATTTCG
* ** *
34710147 TGTTTATTGTCTCAATGGATTATTTCT-TTTCCG
1 TGTTTATTGTCCCAACAGACTATTTCTATTT-CG
* * * * *
34710180 TGTTTAATGT-CTAGACGGGCTATATT-TGTTTCG
1 TGTTTATTGTCCCA-ACAGACTAT-TTCTATTTCG
* * * * *
34710213 TGTTTACTGT-CCAGA-TGAACTATATATGTTTCG
1 TGTTTATTGTCCCA-ACAG-ACTATTTCTATTTCG
34710246 TGTTTATTGTCCCAACAGACTAT
1 TGTTTATTGTCCCAACAGACTAT
34710269 CTATGTAGAT
Statistics
Matches: 120, Mismatches: 27, Indels: 16
0.74 0.17 0.10
Matches are distributed among these distances:
32 6 0.05
33 105 0.88
34 9 0.08
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTTTATTGTCCCAACAGACTATTTCTATTTCG
Found at i:34719490 original size:138 final size:138
Alignment explanation
Indices: 34719227--34719490 Score: 424
Period size: 138 Copynumber: 1.9 Consensus size: 138
34719217 AGAGAACATA
* *
34719227 AATATAATTAATGTATGAATTTGATTCATACAAAATATTAATTGTATGTATTTTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
* * *
34719292 TAATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGGCGTGGAAATTAATATTCTT
66 TAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACGTGGAAATGAATATTCTT
34719357 TTGGAAAG
131 TTGGAAAG
34719365 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
* * *
34719430 TAATATTAACAATTATATTAATTAATTT-TGATCAAAATATAAAAGACATTGGAAA-GAATAT
66 TAATATAAACAATTATATTAATTAATTTCAG-TCAAAATATAAAAGAC-GTGGAAATGAATAT
34719491 AATTTTGTTT
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
137 1 0.01
138 109 0.94
139 6 0.05
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.40
Consensus pattern (138 bp):
AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
TAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACGTGGAAATGAATATTCTT
TTGGAAAG
Found at i:34719557 original size:75 final size:75
Alignment explanation
Indices: 34719478--34719616 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 75
34719468 ATAAAAGACA
* *
34719478 TTGGAAAGAATATAATT-TTGTTTTCTAACTTTCCATTTGCCTTCTTTATTAATAA-AGAAATAA
1 TTGGAAAGAATATAATTCAT-TTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGAG-AATAA
34719541 TGATATATTCTT
64 TGATATATTCTT
* *
34719553 TTGGAAATAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGAGAATAAT
1 TTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGAGAATAAT
34719617 CCTAGTTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
75 55 0.95
76 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.46
Consensus pattern (75 bp):
TTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGAGAATAATG
ATATATTCTT
Found at i:34719576 original size:22 final size:22
Alignment explanation
Indices: 34719534--34719575 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34719524 TATTAATAAA
34719534 GAAATAATGATATATTCTTTTG
1 GAAATAATGATATATTCTTTTG
34719556 GAAATAAT-ATA-ATTCATTTT
1 GAAATAATGATATATTC-TTTT
34719576 TCTAACTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (22 bp):
GAAATAATGATATATTCTTTTG
Found at i:34720203 original size:27 final size:27
Alignment explanation
Indices: 34720173--34720237 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
34720163 ATTACAAATT
34720173 GGGTTCGCCAGTTGATTTGGCGAGCTG
1 GGGTTCGCCAGTTGATTTGGCGAGCTG
* * *
34720200 GGGTTCTCCAATTGATTTGGCGAGTTG
1 GGGTTCGCCAGTTGATTTGGCGAGCTG
34720227 GGGTTCGCCAG
1 GGGTTCGCCAG
34720238 ATGGTTTAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.12, C:0.18, G:0.38, T:0.31
Consensus pattern (27 bp):
GGGTTCGCCAGTTGATTTGGCGAGCTG
Found at i:34720249 original size:27 final size:27
Alignment explanation
Indices: 34720173--34720264 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
34720163 ATTACAAATT
* *
34720173 GGGTTCGCCAGTTGATTTGGCGAGCTG
1 GGGTTCGCCAGATGATTTGGCGAGTTG
*
34720200 GGGTTCTCCA-ATTGATTTGGCGAGTTG
1 GGGTTCGCCAGA-TGATTTGGCGAGTTG
* * *
34720227 GGGTTCGCCAGATGGTTTAGCGAATTG
1 GGGTTCGCCAGATGATTTGGCGAGTTG
* *
34720254 GTGTTCACCAG
1 GGGTTCGCCAG
34720265 TCAAAGTCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 53 0.98
28 1 0.02
ACGTcount: A:0.15, C:0.17, G:0.36, T:0.32
Consensus pattern (27 bp):
GGGTTCGCCAGATGATTTGGCGAGTTG
Found at i:34723987 original size:17 final size:17
Alignment explanation
Indices: 34723965--34724001 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
34723955 AATTTTTGAA
34723965 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
34723982 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
34723999 TTA
1 TTA
34724002 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:34725282 original size:46 final size:46
Alignment explanation
Indices: 34725230--34725507 Score: 484
Period size: 46 Copynumber: 6.0 Consensus size: 46
34725220 CCATGGGAAA
* * *
34725230 TTGTGAAAAGTAGATATGGTGTTTCGGTGAAGAAAACCATACTAAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
34725276 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
34725322 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
34725368 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
34725414 TTGTGAAAAGTAGGCATGGTGTTTCAATGAAGAAAACCATACTGAT
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
34725460 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
34725506 TT
1 TT
34725508 ATAGCATTGT
Statistics
Matches: 221, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 221 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:34729568 original size:20 final size:20
Alignment explanation
Indices: 34729539--34729583 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
34729529 CTATTTATGC
* *
34729539 ACATATTC-AAGAGACTTAA
1 ACATATTCAAACACACTTAA
34729558 ACATCATTCAAACACACTTAA
1 ACAT-ATTCAAACACACTTAA
34729579 ACATA
1 ACATA
34729584 CCATTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 13 0.59
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.24
Consensus pattern (20 bp):
ACATATTCAAACACACTTAA
Found at i:34739356 original size:95 final size:95
Alignment explanation
Indices: 34739193--34739370 Score: 329
Period size: 95 Copynumber: 1.9 Consensus size: 95
34739183 TATTATTTAG
*
34739193 AATATACCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGGTACAATTATGATATTGCATGT
1 AATATACCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGATACAATTATGATATTGCATGT
34739258 TTGTTTATGTTTCATGCATTATACGAATGC
66 TTGTTTATGTTTCATGCATTATACGAATGC
* *
34739288 AATATGCCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGATGCAATTATGATATTGCATGT
1 AATATACCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGATACAATTATGATATTGCATGT
34739353 TTGTTTATGTTTCATGCA
66 TTGTTTATGTTTCATGCA
34739371 CGAATGCATC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (95 bp):
AATATACCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGATACAATTATGATATTGCATGT
TTGTTTATGTTTCATGCATTATACGAATGC
Found at i:34743949 original size:13 final size:14
Alignment explanation
Indices: 34743919--34743951 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34743909 TCAATAATCA
34743919 AAAAATAGAAAATG
1 AAAAATAGAAAATG
*
34743933 AAAATTAGAAAAT-
1 AAAAATAGAAAATG
34743946 AAAAAT
1 AAAAAT
34743952 GAATATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (14 bp):
AAAAATAGAAAATG
Found at i:34746518 original size:19 final size:19
Alignment explanation
Indices: 34746489--34746534 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
34746479 GTTAAAGATG
*
34746489 TTATT-AAAATAAT-TTTTC
1 TTATTCAAAAT-ATGTTTTA
34746507 TTATTCAAAATATGTTTTA
1 TTATTCAAAATATGTTTTA
34746526 TTATTCAAA
1 TTATTCAAA
34746535 GTTATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (19 bp):
TTATTCAAAATATGTTTTA
Found at i:34746838 original size:19 final size:20
Alignment explanation
Indices: 34746814--34746858 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
34746804 TCAAAATTTT
34746814 ATTTTAATATTT-TT-TATAC
1 ATTTTAAT-TTTATTATATAC
*
34746833 ATTTTAATTTTATTATGTAC
1 ATTTTAATTTTATTATATAC
34746853 ATTTTA
1 ATTTTA
34746859 TTACCTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 10 0.43
20 10 0.43
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTAATTTTATTATATAC
Found at i:34752120 original size:22 final size:21
Alignment explanation
Indices: 34752080--34752120 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
34752070 AGTTTTAAGT
**
34752080 TTAGTTTTCTCTAGGTTTTCC
1 TTAGTTTTCTCTACATTTTCC
34752101 TTAGTTTTTCTCTACATTTT
1 TTAG-TTTTCTCTACATTTT
34752121 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.61
Consensus pattern (21 bp):
TTAGTTTTCTCTACATTTTCC
Found at i:34758801 original size:28 final size:26
Alignment explanation
Indices: 34758730--34758803 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
34758720 CACGCTATAA
*
34758730 AAAGGAAGCATTTGTGGCAATCTATG
1 AAAGGAAGCCTTTGTGGCAATCTATG
* * *
34758756 AAATGAAAGTCTTTGTGGCGATCTATGG
1 AAA-GGAAGCCTTTGTGGCAATCTAT-G
*
34758784 AAAGGAATGCCTTCGTGGCA
1 AAAGGAA-GCCTTTGTGGCA
34758804 GATTCTAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.08
27 21 0.57
28 13 0.35
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (26 bp):
AAAGGAAGCCTTTGTGGCAATCTATG
Found at i:34759023 original size:27 final size:26
Alignment explanation
Indices: 34758967--34759084 Score: 94
Period size: 27 Copynumber: 4.4 Consensus size: 26
34758957 GCGTGTGGCT
* * * * *
34758967 AACTCTAAAGGACTGTAGATATGGTA
1 AACTCTGAAGGAATGAATATATGGTG
34758993 AACTCT-AAGAGAATGATATATATGGTG
1 AACTCTGAAG-GAATGA-ATATATGGTG
* *
34759020 AACTCTGAAGGAACAGAATATATGGCG
1 AACTCTGAAGGAA-TGAATATATGGTG
* ** *
34759047 AACTCTGAAGGAATAGCACGTATGGCG
1 AACTCTGAAGGAAT-GAATATATGGTG
34759074 AACTCTGAAGG
1 AACTCTGAAGG
34759085 GACGGTTCTA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
25 3 0.04
26 10 0.13
27 59 0.77
28 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (26 bp):
AACTCTGAAGGAATGAATATATGGTG
Found at i:34786283 original size:19 final size:19
Alignment explanation
Indices: 34786259--34786312 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
34786249 AATATGCAGG
*
34786259 TTTTTTTACTCTTTTTGTTT
1 TTTTTTTACT-ATTTTGTTT
*
34786279 TTTTTTTACTATTTTGTTG
1 TTTTTTTACTATTTTGTTT
*
34786298 TTTTTTCACTATTTT
1 TTTTTTTACTATTTT
34786313 ATTACCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (19 bp):
TTTTTTTACTATTTTGTTT
Found at i:34786339 original size:14 final size:14
Alignment explanation
Indices: 34786322--34786352 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34786312 TATTACCTTT
34786322 TTACTATTATGTTG
1 TTACTATTATGTTG
*
34786336 TTACTATTTTGTTG
1 TTACTATTATGTTG
34786350 TTA
1 TTA
34786353 TATATAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:34788140 original size:19 final size:19
Alignment explanation
Indices: 34788116--34788167 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 19
34788106 AAAAAGATTA
34788116 TTTTTAATTTAATTTAATT-T
1 TTTTTAATTTAA-TT-ATTGT
34788136 TTTTATAATTTAATTA-TGT
1 TTTT-TAATTTAATTATTGT
34788155 TCTTTTAATTTAA
1 T-TTTTAATTTAA
34788168 AATTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 9 0.31
21 8 0.28
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTTAATTTAATTATTGT
Found at i:34793136 original size:20 final size:20
Alignment explanation
Indices: 34793103--34793141 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34793093 TGAATTTTGT
*
34793103 AAAAATCAGAGTGAAATAGG
1 AAAAAACAGAGTGAAATAGG
* *
34793123 AAAAAACAGTGTGATATAG
1 AAAAAACAGAGTGAAATAG
34793142 TGAGCCAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAAAACAGAGTGAAATAGG
Found at i:34796830 original size:15 final size:15
Alignment explanation
Indices: 34796810--34796839 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34796800 CACTTTTCCA
34796810 TTTTATGCATAATAT
1 TTTTATGCATAATAT
34796825 TTTTATGCATAATAT
1 TTTTATGCATAATAT
34796840 CCCACTCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTTATGCATAATAT
Found at i:34798768 original size:3 final size:3
Alignment explanation
Indices: 34798760--34798823 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
34798750 CCACTTAAGA
*
34798760 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
34798808 AAG AAG AA- AAG AAG AA
1 AAG AAG AAG AAG AAG AA
34798824 CCTTCTTCAG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34798894 original size:3 final size:3
Alignment explanation
Indices: 34798886--34798974 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
34798876 CAATTTAACA
34798886 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
34798934 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
34798975 CCTGCTTCAG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34809162 original size:20 final size:20
Alignment explanation
Indices: 34809137--34809177 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
34809127 CACATGGTAG
*
34809137 TGTGTTTGAAAACCGTAACT
1 TGTGTTGGAAAACCGTAACT
*
34809157 TGTGTTGGGAAACCGTAACT
1 TGTGTTGGAAAACCGTAACT
34809177 T
1 T
34809178 TGCTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (20 bp):
TGTGTTGGAAAACCGTAACT
Found at i:34810599 original size:12 final size:11
Alignment explanation
Indices: 34810567--34810601 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
34810557 ACACTTCCCC
*
34810567 ACACCCCTCAA
1 ACACTCCTCAA
34810578 ACACTCCTCAA
1 ACACTCCTCAA
34810589 ACACTTCCTCAA
1 ACAC-TCCTCAA
34810601 A
1 A
34810602 TTTTACCTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.37, C:0.46, G:0.00, T:0.17
Consensus pattern (11 bp):
ACACTCCTCAA
Found at i:34817381 original size:20 final size:20
Alignment explanation
Indices: 34817356--34817396 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
34817346 CACATGGTAA
*
34817356 TGTGTTTGAAAACCATAACT
1 TGTGTTGGAAAACCATAACT
*
34817376 TGTGTTGGGAAACCATAACT
1 TGTGTTGGAAAACCATAACT
34817396 T
1 T
34817397 TACTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
TGTGTTGGAAAACCATAACT
Found at i:34862715 original size:29 final size:29
Alignment explanation
Indices: 34862683--34862757 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
34862673 TTTTTTTTAA
*
34862683 ATTTACCGAAATGGGCCAGGTATTTTATT
1 ATTTACCGAAATGGGCCAGGCATTTTATT
34862712 ATTTACCGAAATGGGCCAGGCATTTTATT
1 ATTTACCGAAATGGGCCAGGCATTTTATT
*
34862741 ATTTACCGGAATGGGCC
1 ATTTACCGAAATGGGCC
34862758 CTTTTCCCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (29 bp):
ATTTACCGAAATGGGCCAGGCATTTTATT
Found at i:34863041 original size:12 final size:12
Alignment explanation
Indices: 34863024--34863077 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
34863014 AACTAATCCT
34863024 CTCTCAAATTTC
1 CTCTCAAATTTC
*
34863036 CTCTC-AATTTG
1 CTCTCAAATTTC
*
34863047 CTTTCAAA-TTC
1 CTCTCAAATTTC
34863058 CT-TCAAAATTT-
1 CTCTC-AAATTTC
34863069 CTCTCAAAT
1 CTCTCAAAT
34863078 CCATATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
10 2 0.06
11 22 0.63
12 11 0.31
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:34863094 original size:51 final size:51
Alignment explanation
Indices: 34863039--34863136 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
34863029 AAATTTCCTC
*
34863039 TCAATTTGCTTTCAAATTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCTCAAATTCCTCT-AAAATTTCTCTCAAATCCATATTTATTT
* * * *
34863090 TCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTT
34863137 TTAAATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:34864291 original size:7 final size:7
Alignment explanation
Indices: 34864279--34864311 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
34864269 TAGTTGATTG
34864279 GTATTTA
1 GTATTTA
34864286 GTATTTA
1 GTATTTA
34864293 GTATTTA
1 GTATTTA
34864300 GTATTTA
1 GTATTTA
34864307 GTATT
1 GTATT
34864312 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:34864959 original size:18 final size:18
Alignment explanation
Indices: 34864932--34864971 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34864922 CAGGTGCGTT
* *
34864932 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
34864950 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
34864968 TCCT
1 TCCT
34864972 TTTTCTAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:34865269 original size:21 final size:21
Alignment explanation
Indices: 34865229--34865275 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
34865219 ATGCCCTATT
*
34865229 GGAAGAACCAGAATCCCCGCC
1 GGAAGAACCACAATCCCCGCC
34865250 GGAAGAACCACAA-CCGCCGCC
1 GGAAGAACCACAATCC-CCGCC
*
34865271 AGAAG
1 GGAAG
34865276 CTGGACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.36, C:0.36, G:0.26, T:0.02
Consensus pattern (21 bp):
GGAAGAACCACAATCCCCGCC
Found at i:34865544 original size:15 final size:15
Alignment explanation
Indices: 34865524--34865587 Score: 62
Period size: 15 Copynumber: 4.5 Consensus size: 15
34865514 GACAAACCTT
34865524 AAACCCTTAACTTAA
1 AAACCCTTAACTTAA
*
34865539 AAACCC-TAAC--CA
1 AAACCCTTAACTTAA
** *
34865551 TGACCCTTAAATTAA
1 AAACCCTTAACTTAA
*
34865566 AAACCCTTAACCTAA
1 AAACCCTTAACTTAA
34865581 AAACCCT
1 AAACCCT
34865588 AAACCCTTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
12 5 0.14
13 3 0.08
14 4 0.11
15 25 0.68
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.22
Consensus pattern (15 bp):
AAACCCTTAACTTAA
Found at i:34865591 original size:22 final size:22
Alignment explanation
Indices: 34865566--34866103 Score: 673
Period size: 22 Copynumber: 24.7 Consensus size: 22
34865556 CTTAAATTAA
*
34865566 AAACCCTTAACCTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
*
34865588 AAACCCTTAACTTAAAAATCCT
1 AAACCCTTAACTTAAAAACCCT
* *
34865610 AACCCCTTAACCTAAAAA-CCT
1 AAACCCTTAACTTAAAAACCCT
* * * *
34865631 TAACCATTAACTTTAAAACCGT
1 AAACCCTTAACTTAAAAACCCT
*
34865653 AAACCCTGAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
* *
34865675 -AGCCCTTAACTTTATAAACCCTT
1 AAACCCTTAAC-TTAAAAACCC-T
* * *
34865698 AAACCATTAAATTAAAACCCCT
1 AAACCCTTAACTTAAAAACCCT
*
34865720 AAACCCTTAACTT-AGAACCCAT
1 AAACCCTTAACTTAAAAACCC-T
*
34865742 AAACCCTTAACCTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
* *
34865764 -AACCCTTAACTTTAAAATCCT
1 AAACCCTTAACTTAAAAACCCT
*
34865785 AAACCCTTAACTTAAAACCCCT
1 AAACCCTTAACTTAAAAACCCT
34865807 AAACCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
* *
34865829 AACCCCTTAACTTAAAAACACT
1 AAACCCTTAACTTAAAAACCCT
*
34865851 AACCCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
34865873 -AACCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
*
34865894 AACCCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
*
34865916 AACCCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
*
34865938 AAACCCTTAACATAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
*
34865960 -AACCCTTAACTTTAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
* *
34865981 AAACCCTTAAATT-AAAACCCAC
1 AAACCCTTAACTTAAAAACCC-T
* *
34866003 AAACCCTTAACCTAAAAACTCT
1 AAACCCTTAACTTAAAAACCCT
34866025 -AACCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
* *
34866046 -AACCCTTAACTTTAAAATCCT
1 AAACCCTTAACTTAAAAACCCT
*
34866067 AAACCCTTAAATTAAAAACCCT
1 AAACCCTTAACTTAAAAACCCT
34866089 -AACCCTTAACTTAAA
1 AAACCCTTAACTTAAA
34866104 TATAATTTGA
Statistics
Matches: 445, Mismatches: 59, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
21 145 0.33
22 272 0.61
23 21 0.05
24 7 0.02
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (22 bp):
AAACCCTTAACTTAAAAACCCT
Found at i:34865592 original size:15 final size:15
Alignment explanation
Indices: 34865563--34865592 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34865553 ACCCTTAAAT
*
34865563 TAAAAACCCTTAACC
1 TAAAAACCCTAAACC
34865578 TAAAAACCCTAAACC
1 TAAAAACCCTAAACC
34865593 CTTAACTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAACCCTAAACC
Found at i:34865642 original size:43 final size:43
Alignment explanation
Indices: 34865566--34866103 Score: 608
Period size: 43 Copynumber: 12.4 Consensus size: 43
34865556 CTTAAATTAA
* *
34865566 AAACCCTTAACCTAAAAACCCTAAACCCTTAACTTAAAAATCCT
1 AAACCCTTAACTTAAAAA-CCTAAACCCTTAACTTAAAAACCCT
* * * * * *
34865610 AACCCCTTAACCTAAAAACCTTAACCATTAACTTTAAAACCGT
1 AAACCCTTAACTTAAAAACCTAAACCCTTAACTTAAAAACCCT
* * *
34865653 AAACCCTGAACTTAAAAACCCT-AGCCCTTAACTTTATAAACCCTT
1 AAACCCTTAACTTAAAAA-CCTAAACCCTTAAC-TTAAAAACCC-T
* * * *
34865698 AAACCATTAAATTAAAACCCCTAAACCCTTAACTT-AGAACCCAT
1 AAACCCTTAACTTAAAA-ACCTAAACCCTTAACTTAAAAACCC-T
* * *
34865742 AAACCCTTAACCTAAAAACCCT-AACCCTTAACTTTAAAATCCT
1 AAACCCTTAACTTAAAAA-CCTAAACCCTTAACTTAAAAACCCT
*
34865785 AAACCCTTAACTTAAAACCCCTAAACCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAA-ACCTAAACCCTTAACTTAAAAACCCT
* *
34865829 AACCCCTTAACTTAAAAACACTAACCCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAAC-CTAAACCCTTAACTTAAAAACCCT
*
34865873 -AACCCTTAACTTAAAAACCCTAACCCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAA-CCTAAACCCTTAACTTAAAAACCCT
* *
34865916 AACCCCTTAACTTAAAAACCCTAAACCCTTAACATAAAAACCCT
1 AAACCCTTAACTTAAAAA-CCTAAACCCTTAACTTAAAAACCCT
* * *
34865960 -AACCCTTAACTTTAAAACCCTAAACCCTTAAATT-AAAACCCAC
1 AAACCCTTAAC-TTAAAAACCTAAACCCTTAACTTAAAAACCC-T
*
34866003 AAACCCTTAACCTAAAAACTCT-AACCCTTAACTTAAAAACCCT
1 AAACCCTTAACTTAAAAAC-CTAAACCCTTAACTTAAAAACCCT
* *
34866046 -AACCCTTAACTTTAAAATCCTAAACCCTTAAATTAAAAACCCT
1 AAACCCTTAAC-TTAAAAACCTAAACCCTTAACTTAAAAACCCT
34866089 -AACCCTTAACTTAAA
1 AAACCCTTAACTTAAA
34866104 TATAATTTGA
Statistics
Matches: 424, Mismatches: 51, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
42 24 0.06
43 192 0.45
44 179 0.42
45 20 0.05
46 9 0.02
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (43 bp):
AAACCCTTAACTTAAAAACCTAAACCCTTAACTTAAAAACCCT
Found at i:34865667 original size:65 final size:65
Alignment explanation
Indices: 34865517--34866100 Score: 675
Period size: 65 Copynumber: 9.0 Consensus size: 65
34865507 TTTAATTGAC
* * * * * *
34865517 AAACCTTAAACCCTTAACTTAAAAACCCT-AACCATGACCCTTAAATTAA---AAACCCTTAACC
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTA-ACTTAAA--AACCCTAACCCTTAACT
*
34865578 TAA
63 TTA
* * * * *
34865581 AAACCCTAAACCCTTAACTTAAAAATCCTAACCCCTTAACCTAAAAACCTTAACCATTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
* * * * * *
34865646 AAACCGTAAACCCTGAACTTAAAAACCCT-AGCCCTTAACTTTATAAACCCTTAAACCATTAA-A
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAAC-TTAAAAACCC-T-AACCCTTAACT
34865709 TTA
63 TTA
* *
34865712 AAACCCCTAAACCCTTAACTT-AGAACCCATAAACCCTTAACCTAAAAACCCTAACCCTTAACTT
1 AAA-CCCTAAACCCTTAACTTAAAAACCC-TAAACCCTTAACTTAAAAACCCTAACCCTTAACTT
34865776 TA
64 TA
* * *
34865778 AAATCCTAAACCCTTAACTTAAAACCCCTAAACCCTTAACTTAAAAACCCTAACCCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAA-CCCTTAACTTT
34865843 A
65 A
* * *
34865844 AAACACTAACCCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACCCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAA-CCCTTAACTTT
34865908 A
65 A
* *
34865909 AAACCCTAACCCCTTAACTTAAAAACCCTAAACCCTTAACATAAAAACCCTAACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
* * * * *
34865974 AAACCCTAAACCCTTAAATT-AAAACCCACAAACCCTTAACCTAAAAACTCTAACCCTTAACTTA
1 AAACCCTAAACCCTTAACTTAAAAACCC-TAAACCCTTAACTTAAAAACCCTAACCCTTAACTTT
34866038 A
65 A
* * *
34866039 AAACCCT-AACCCTTAACTTTAAAATCCTAAACCCTTAAATTAAAAACCCTAACCCTTAACTT
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTT
34866101 AAATATAATT
Statistics
Matches: 453, Mismatches: 51, Indels: 32
0.85 0.10 0.06
Matches are distributed among these distances:
62 2 0.00
64 90 0.20
65 236 0.52
66 83 0.18
67 33 0.07
68 9 0.02
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (65 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
Found at i:34865715 original size:87 final size:87
Alignment explanation
Indices: 34865566--34866103 Score: 646
Period size: 87 Copynumber: 6.2 Consensus size: 87
34865556 CTTAAATTAA
* * *
34865566 AAACCCTTAACCTAAAAACCCTAAACCCTTAACTTAAAAATCCTAACCCCTTAACC-TAAAAACC
1 AAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAA-CCCTTAACCTTAAAACCC
* * * *
34865630 TTAACCATTAACTTTAAAACCGT
65 TAAACCCTTAACTTAAAAACCCT
* * * * *
34865653 AAACCCTGAACTTAAAAACCCT-AGCCCTTAACTTTATAAACCCTTAAACCATTAA-ATTAAAAC
1 AAACCCTTAACTTAAAAACCCTAAACCCTTAAC-TTAAAAACCC-T-AACCCTTAACCTTAAAA-
*
34865716 CCCTAAACCCTTAACTT-AGAACCCAT
62 CCCTAAACCCTTAACTTAAAAACCC-T
* * *
34865742 AAACCCTTAACCTAAAAACCCT-AACCCTTAACTTTAAAATCCTAAACCCTTAA-CTTAAAACCC
1 AAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACCTTAAAA-CC
34865805 CTAAACCCTTAACTTAAAAACCCT
64 CTAAACCCTTAACTTAAAAACCCT
* * *
34865829 AACCCCTTAACTTAAAAACACTAACCCCTTAACTTAAAAACCCTAACCCTTAA-CTTAAAAACCC
1 AAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTT-AAAACCC
*
34865893 TAACCCCTTAACTTAAAAACCCT
65 TAAACCCTTAACTTAAAAACCCT
* * *
34865916 AACCCCTTAACTTAAAAACCCTAAACCCTTAACATAAAAACCCTAACCCTTAACTTTAAAACCCT
1 AAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTTAAAACCCT
* *
34865981 AAACCCTTAAATT-AAAACCCAC
66 AAACCCTTAACTTAAAAACCC-T
* * * *
34866003 AAACCCTTAACCTAAAAACTCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTTAAAATCCT
1 AAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTTAAAACCCT
*
34866067 AAACCCTTAAATTAAAAACCCT
66 AAACCCTTAACTTAAAAACCCT
34866089 -AACCCTTAACTTAAA
1 AAACCCTTAACTTAAA
34866104 TATAATTTGA
Statistics
Matches: 397, Mismatches: 42, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
85 14 0.04
86 69 0.17
87 214 0.54
88 54 0.14
89 46 0.12
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (87 bp):
AAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTTAAAACCCT
AAACCCTTAACTTAAAAACCCT
Found at i:34869532 original size:125 final size:125
Alignment explanation
Indices: 34869250--34869817 Score: 730
Period size: 125 Copynumber: 4.5 Consensus size: 125
34869240 CCTAAACATG
* * *
34869250 CTACTGTAGAAAAAGCGCGTTCAAGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
34869315 TAGAAGCG-ATTTTATACTATTTGCTCAGAAACG-CTAAGTCGAAATTATTTTTCCAAGAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTC-AACTCGAAATTATTTTTCCAAGAC
* * *
34869374 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAACATGCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * * * * *
34869438 CTTGCAGCGTTGTTTTATACTATATGCTCAGAAATGTCAACTCAAAATTATTTTT-CAGGAC
65 CTTGAAGCGTT-TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
* ** * *
34869499 CTACTATAGCAAAAATGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTTATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
34869564 TTGAAGCGTTTTTTAAAACTATTTGCTCAAAAACGTTAACTCGAAATTATTTCTTCCAAGAC
66 TTGAAGCGTTTTTT-AAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAAGAC
* * * *
34869626 CAACTGTAGCAAAAGCGAGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
34869691 TTGAAGCATTTTTTAAACTATTTGCTCAGAAACGTAAAGTCGAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
* * * * * *
34869751 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
34869816 TT
66 TT
34869818 TGATTTTATC
Statistics
Matches: 382, Mismatches: 54, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
123 2 0.01
124 66 0.17
125 164 0.43
126 75 0.20
127 75 0.20
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
Found at i:34869751 original size:252 final size:249
Alignment explanation
Indices: 34869250--34869817 Score: 773
Period size: 252 Copynumber: 2.3 Consensus size: 249
34869240 CCTAAACATG
* * * *
34869250 CTACTGTAG-AAAAAGCGCGTTCAAGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
1 CTACTATAGCAAAAA-CGCGTACACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTG
* * * * *
34869314 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGCTAAGTCGAAATTATTTTTCCAAGACCTACT
65 CTTGAAGCGATTTTAAACTATTTGCTCAAAAACGCTAACTCGAAATTATTTTTCCAAGACCAACT
* * *
34869379 GTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATGCTGCTTGCA
130 GTAGCAAAAGCGAGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGCTTGAA
* * * *
34869444 GCGTTGTTTTATACTATATGCTCAGAAATGTCAACTCAAAATTATTTTTCAGGAC
195 GCATTGTTTTAAACTATATGCTCAGAAACGTAAACTCAAAATTATTTTTCAGGAC
* * *
34869499 CTACTATAGCAAAAATGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTTATAAAGCATCCTGC
1 CTACTATAGCAAAAACGCGTACACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
34869564 TTGAAGCGTTTTTTAAAACTATTTGCTCAAAAACGTTAACTCGAAATTATTTCTTCCAAGACCAA
66 TTGAAGCG-ATTTT-AAACTATTTGCTCAAAAACGCTAACTCGAAATTATTT-TTCCAAGACCAA
**
34869629 CTGTAGCAAAAGCGAGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGTATCCTGCTT
128 CTGTAGCAAAAGCGAGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAACATCCTGCTT
* * *
34869693 GAAGCATT-TTTTAAACTATTTGCTCAGAAACGTAAAGTCGAAATTATTTTTCCAGGAC
192 GAAGCATTGTTTTAAACTATATGCTCAGAAACGTAAACTCAAAATTATTTTT-CAGGAC
* * * * * *
34869751 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCTGC
1 CTACTATAGCAAAAACGCGTACACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTGC
34869816 TT
66 TT
34869818 TGATTTTATC
Statistics
Matches: 280, Mismatches: 33, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
249 60 0.21
250 9 0.03
251 70 0.25
252 139 0.50
253 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (249 bp):
CTACTATAGCAAAAACGCGTACACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGATTTTAAACTATTTGCTCAAAAACGCTAACTCGAAATTATTTTTCCAAGACCAACTG
TAGCAAAAGCGAGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGCTTGAAG
CATTGTTTTAAACTATATGCTCAGAAACGTAAACTCAAAATTATTTTTCAGGAC
Found at i:34882804 original size:10 final size:11
Alignment explanation
Indices: 34882789--34882817 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
34882779 AAATAATTCT
34882789 TTTAAAAAA-A
1 TTTAAAAAATA
34882799 TTTAAAAAATA
1 TTTAAAAAATA
34882810 TTTAAAAA
1 TTTAAAAA
34882818 TGCATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:34882976 original size:28 final size:28
Alignment explanation
Indices: 34882945--34882999 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
34882935 TTCTTTGAAA
*
34882945 TAAATATATATAAAATT-TAAAAATTCTT
1 TAAAAATATAT-AAATTATAAAAATTCTT
34882973 TAAAAATATATAAATTATAAAAATTCT
1 TAAAAATATATAAATTATAAAAATTCT
34883000 AAGGATTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAAAATATATAAATTATAAAAATTCTT
Found at i:34886871 original size:12 final size:12
Alignment explanation
Indices: 34886854--34886905 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
34886844 AAGCTTTTTC
34886854 TTTTAGAAGTTG
1 TTTTAGAAGTTG
*
34886866 TTTTAGAAGCTG
1 TTTTAGAAGTTG
* *
34886878 TTTTA-ACA-ATC
1 TTTTAGA-AGTTG
34886889 TTTTAGAAGTTG
1 TTTTAGAAGTTG
34886901 TTTTA
1 TTTTA
34886906 ACAATATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (12 bp):
TTTTAGAAGTTG
Found at i:34886893 original size:23 final size:23
Alignment explanation
Indices: 34886866--34886917 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
34886856 TTAGAAGTTG
*
34886866 TTTTAGAAGCTGTTTTAACAATC
1 TTTTAGAAGCTGTTTTAACAATA
*
34886889 TTTTAGAAGTTGTTTTAACAATA
1 TTTTAGAAGCTGTTTTAACAATA
34886912 TTTTAG
1 TTTTAG
34886918 GTTGTGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (23 bp):
TTTTAGAAGCTGTTTTAACAATA
Found at i:34890107 original size:19 final size:20
Alignment explanation
Indices: 34890070--34890108 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
34890060 GTGATTTTTG
* *
34890070 GAAAAATTAATTTCGATCAA
1 GAAAAATTAAGTTCAATCAA
34890090 GAAAAATTAAGTT-AATCAA
1 GAAAAATTAAGTTCAATCAA
34890109 ATTAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (20 bp):
GAAAAATTAAGTTCAATCAA
Found at i:34890504 original size:17 final size:17
Alignment explanation
Indices: 34890487--34890519 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34890477 ATAATATTAT
34890487 TTTAA-TAAATTTAATA
1 TTTAATTAAATTTAATA
*
34890503 TTTAATTTAATTTAATA
1 TTTAATTAAATTTAATA
34890520 CTTATCCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTAAATTTAATA
Found at i:34901453 original size:26 final size:26
Alignment explanation
Indices: 34901415--34901464 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
34901405 GGAATAAATT
**
34901415 GAAGAAATTGACGTGAAAAAAAGAGA
1 GAAGAAAAAGACGTGAAAAAAAGAGA
*
34901441 GAAGAAAAAGACGTGAAAAGAAGA
1 GAAGAAAAAGACGTGAAAAAAAGA
34901465 TGGGTATCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.60, C:0.04, G:0.28, T:0.08
Consensus pattern (26 bp):
GAAGAAAAAGACGTGAAAAAAAGAGA
Found at i:34901513 original size:6 final size:6
Alignment explanation
Indices: 34901502--34901528 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34901492 TTCCTATTTC
34901502 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
34901529 GAAGATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:34908073 original size:13 final size:13
Alignment explanation
Indices: 34908057--34908090 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
34908047 TGTGGTACAT
34908057 GACCGTGTGGGCA
1 GACCGTGTGGGCA
* *
34908070 GACCATGTGGGTA
1 GACCGTGTGGGCA
34908083 GACCGTGT
1 GACCGTGT
34908091 AACTCTCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.41, T:0.21
Consensus pattern (13 bp):
GACCGTGTGGGCA
Found at i:34919628 original size:16 final size:16
Alignment explanation
Indices: 34919607--34919638 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34919597 GTTTTGTTGC
*
34919607 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
34919623 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
34919639 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:34919836 original size:46 final size:43
Alignment explanation
Indices: 34919776--34919860 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
34919766 CATGGTGGAT
*
34919776 TCAGCACACAGCAACCACCCTCTGTAATCAATGATATCCGGTGGGA
1 TCAGCACACAGCAACCA-CCT-TATAATCAATGATA-CCGGTGGGA
* *
34919822 TCAGCACATAGCAACCACCTTATAATTAATGATACCGGT
1 TCAGCACACAGCAACCACCTTATAATCAATGATACCGGT
34919861 TCACATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 12 0.33
45 3 0.08
46 16 0.44
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (43 bp):
TCAGCACACAGCAACCACCTTATAATCAATGATACCGGTGGGA
Found at i:34919924 original size:51 final size:51
Alignment explanation
Indices: 34919866--34920056 Score: 210
Period size: 51 Copynumber: 3.8 Consensus size: 51
34919856 CCGGTTCACA
** * *
34919866 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACATGACCATCACTATCTGGTACACG
* * * ** *
34919917 TAGTAGCCTGCACATAGTACCACACACGTGATCGA--AGCTATCTGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACACATGA-CCATCA-CTATCTGGTACACG
* *
34919968 TAGTAGCCTGCACATAGTACTACACATACGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACATGACC-ATCACTATCTGGTACACG
*
34920018 TAGTAGCCTGCACATAGTACTATACACATGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACATGACCATCACT
34920057 TTCACTTTCA
Statistics
Matches: 115, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
49 4 0.03
50 41 0.36
51 67 0.58
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACATGACCATCACTATCTGGTACACG
Found at i:34920071 original size:101 final size:103
Alignment explanation
Indices: 34919860--34920082 Score: 242
Period size: 101 Copynumber: 2.2 Consensus size: 103
34919850 ATGATACCGG
**
34919860 TTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCC
1 TTCACATAGTAGCCTGCACATAGTACTACACATACGACCATCACTATCCGATACACGTAGTAGCC
* * **
34919925 TGCACATAGTACCACACACGTGATCGAAGCTATCTGGT
66 TGCACATAGTACCACACACATGATCCAAGCTATCTACT
* * * *
34919963 AT-GCATAGTAGCCTGCACATAGTACTACACATACGACCTATCA-T-TCTGGTACACGTAGTAGC
1 TTCACATAGTAGCCTGCACATAGTACTACACATACGACC-ATCACTATCCGATACACGTAGTAGC
* * *
34920025 CTGCACATAGTACTATACACATGA-CCATCA-CTTTC-ACT
65 CTGCACATAGTACCACACACATGATCCA--AGCTATCTACT
* *
34920063 TTCACATAGTGGCCTACACA
1 TTCACATAGTAGCCTGCACA
34920083 CAGTCCATGC
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
100 4 0.04
101 55 0.56
102 35 0.35
103 5 0.05
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (103 bp):
TTCACATAGTAGCCTGCACATAGTACTACACATACGACCATCACTATCCGATACACGTAGTAGCC
TGCACATAGTACCACACACATGATCCAAGCTATCTACT
Found at i:34922142 original size:16 final size:16
Alignment explanation
Indices: 34922121--34922154 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
34922111 TTGGGTTGAG
*
34922121 AAAATTATTTAATTAA
1 AAAATTAATTAATTAA
34922137 AAAATTAATTAATTAA
1 AAAATTAATTAATTAA
34922153 AA
1 AA
34922155 TTATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTAATTAATTAA
Found at i:34926760 original size:147 final size:147
Alignment explanation
Indices: 34926492--34926787 Score: 463
Period size: 147 Copynumber: 2.0 Consensus size: 147
34926482 GAGGGGATTT
34926492 TATAAAATGGCGCTATTTTTTTTAAAGTAAAATTAATTTTTGTGGCGTTTTTTATAAAACGCCGC
1 TATAAAATGGCGCTATTTTTTTTAAAGTAAAATTAATTTTTGTGGCGTTTTTTATAAAACGCCGC
* * * * *
34926557 TATTTCTTACATTTTGCGGTGTTTTTGTGAAAAAATGCTGCAACAAATTATTTCATTTGGAATAA
66 TATTGCTTACATTTTGCGGTGTTTTTAT-AAAAAACGCCGCAAAAAATTATTTCATTTGGAATAA
34926622 AACGACACTGTTTTGCTA
130 AACGACACTGTTTTGCTA
* *
34926640 TATAAAATGGCGCTA-TTTTTTTAAAGTAAAATTATTTTTTGTGTCG-TTTTTATAAAAACGCCG
1 TATAAAATGGCGCTATTTTTTTTAAAGTAAAATTAATTTTTGTGGCGTTTTTTAT-AAAACGCCG
*
34926703 CTATTGCTTACCTTTTGCGGTGTTTTTCAT-AAAAACGCCGCAAAAAAATTATTTCATTTGGAAT
65 CTATTGCTTACATTTTGCGGTGTTTTT-ATAAAAAACGCCGC-AAAAAATTATTTCATTTGGAAT
34926767 AAAACGACACTGTTTTGCTA
128 AAAACGACACTGTTTTGCTA
34926787 T
1 T
34926788 GCTAAAAATC
Statistics
Matches: 137, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
146 16 0.12
147 105 0.77
148 16 0.12
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (147 bp):
TATAAAATGGCGCTATTTTTTTTAAAGTAAAATTAATTTTTGTGGCGTTTTTTATAAAACGCCGC
TATTGCTTACATTTTGCGGTGTTTTTATAAAAAACGCCGCAAAAAATTATTTCATTTGGAATAAA
ACGACACTGTTTTGCTA
Found at i:34927620 original size:14 final size:14
Alignment explanation
Indices: 34927597--34927649 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
34927587 ACTAACTCTT
*
34927597 AACCCTAAACCACA
1 AACCCCAAACCACA
*
34927611 AACCCCAAACCCCA
1 AACCCCAAACCACA
* * *
34927625 AACTCCTAACCACT
1 AACCCCAAACCACA
*
34927639 AACCCTAAACC
1 AACCCCAAACC
34927650 TTATTTAATT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.43, C:0.47, G:0.00, T:0.09
Consensus pattern (14 bp):
AACCCCAAACCACA
Found at i:34927621 original size:21 final size:20
Alignment explanation
Indices: 34927597--34927649 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
34927587 ACTAACTCTT
*
34927597 AACCCTAAACCACAAACCCCA
1 AACCCTAAACC-CAAACCACA
* * *
34927618 AACCCCAAACTCCTAACCACT
1 AACCCTAAAC-CCAAACCACA
34927639 AACCCTAAACC
1 AACCCTAAACC
34927650 TTATTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.43, C:0.47, G:0.00, T:0.09
Consensus pattern (20 bp):
AACCCTAAACCCAAACCACA
Found at i:34927895 original size:14 final size:15
Alignment explanation
Indices: 34927878--34927910 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
34927868 CTTAAATCAG
*
34927878 AATCCCTGA-TCCAT
1 AATCCCTAATTCCAT
34927892 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
34927907 AATC
1 AATC
34927911 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:34928376 original size:41 final size:41
Alignment explanation
Indices: 34928317--34928516 Score: 247
Period size: 41 Copynumber: 4.9 Consensus size: 41
34928307 AAATGTTTTT
*
34928317 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * ** *
34928358 GCGGCGCATCTTGGAAAACGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
** * **
34928399 GCGATGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
** **
34928440 GCGGCGCTTTTTCAAAAACGATGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
34928481 GCGGCGCTTTTTTTAAAAACGCCGCTAAAGCCCTGA
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAGCCCTGA
34928517 AAGGTAGAAA
Statistics
Matches: 133, Mismatches: 25, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
41 110 0.83
42 23 0.17
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:34940951 original size:43 final size:43
Alignment explanation
Indices: 34940900--34940993 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
34940890 GAGTCCTCAG
* * * *
34940900 TGCATCATCAGATAAACCGAAGCAAATATATTGGCACACATAA
1 TGCATCATCAAACAAACCGAAGCAAATATACTGACACACATAA
* *
34940943 TGTATCATCAAACAAACCGAAGCAAATATACTGACACACATAG
1 TGCATCATCAAACAAACCGAAGCAAATATACTGACACACATAA
34940986 TGCATCAT
1 TGCATCAT
34940994 TGGAAAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.21
Consensus pattern (43 bp):
TGCATCATCAAACAAACCGAAGCAAATATACTGACACACATAA
Found at i:34941400 original size:14 final size:14
Alignment explanation
Indices: 34941381--34941414 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34941371 AATCACATGA
*
34941381 ATGTATATATGCAT
1 ATGTATATATACAT
*
34941395 ATGTATATATATAT
1 ATGTATATATACAT
34941409 ATGTAT
1 ATGTAT
34941415 TGAACTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (14 bp):
ATGTATATATACAT
Found at i:34941574 original size:9 final size:9
Alignment explanation
Indices: 34941560--34941586 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
34941550 TACATCCAAG
34941560 TTTAATTTA
1 TTTAATTTA
34941569 TTTAATTTA
1 TTTAATTTA
34941578 TTTAATTTA
1 TTTAATTTA
34941587 GTCCCTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTAATTTA
Found at i:34944766 original size:18 final size:19
Alignment explanation
Indices: 34944745--34944780 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
34944735 ATAGATTTCC
34944745 TTTTATTTTTTG-ATTTTA
1 TTTTATTTTTTGCATTTTA
*
34944763 TTTTCTTTTTTGCATTTT
1 TTTTATTTTTTGCATTTT
34944781 TCGGCTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTTATTTTTTGCATTTTA
Found at i:34945634 original size:25 final size:21
Alignment explanation
Indices: 34945582--34945626 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
34945572 AATAATAGCA
*
34945582 TAATTTATTATATATATTTTT
1 TAATTTATTATAAATATTTTT
34945603 TAATTTATTATAAATCATTATTT
1 TAATTTATTATAAAT-ATT-TTT
34945626 T
1 T
34945627 GAGATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 3 0.14
23 4 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTTATTATAAATATTTTT
Found at i:34950824 original size:6 final size:6
Alignment explanation
Indices: 34950815--34950873 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
34950805 AGGAGGAAGA
* ** *
34950815 AAAATC AAAATC AAAATC AAAAGC AAAAAGA AAAATC AAAATC AAAGTC
1 AAAATC AAAATC AAAATC AAAATC -AAAATC AAAATC AAAATC AAAATC
*
34950864 AAAGTC AAAA
1 AAAATC AAAA
34950874 AATGAAAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 41 0.89
7 5 0.11
ACGTcount: A:0.68, C:0.14, G:0.07, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:34950837 original size:31 final size:31
Alignment explanation
Indices: 34950811--34950874 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
34950801 AAAAAGGAGG
34950811 AAGAAAAATCAAAATCAAAATCAAAAGCAAA
1 AAGAAAAATCAAAATCAAAATCAAAAGCAAA
*
34950842 AAGAAAAATCAAAATCAAAGTC-AAAGTCAAA
1 AAGAAAAATCAAAATCAAAATCAAAAG-CAAA
34950873 AA
1 AA
34950875 ATGAAAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.69, C:0.12, G:0.08, T:0.11
Consensus pattern (31 bp):
AAGAAAAATCAAAATCAAAATCAAAAGCAAA
Found at i:34953140 original size:44 final size:43
Alignment explanation
Indices: 34953091--34953938 Score: 160
Period size: 44 Copynumber: 19.3 Consensus size: 43
34953081 GATAACAGAT
* *
34953091 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACAC-AGC
* * * * * * * * *
34953135 CTTGCCTCCCTGGATTG-CAGTGGAGCAGGTTGAAAATAACAGAT
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGA-CACAG-C
* * *
34953179 CTTGTCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAGC
*** * * * * * * *
34953223 CTTGCCTTCCTGGGTTG-CAGCGGAGCAGGTTGAAAATAGCAGAT
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAG-C
* * *
34953267 CTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCAGA
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAGC
* *** * * * * * * **
34953311 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTGAAAATAGCATAT
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CA-GC
* ** **
34953355 CTTGCCTTCCTGCACCGATGGCAAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAGC
* * * * * * *
34953399 CTTGCCTCCCTAG-ATTG-CAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTTCCT-GCACTGACAGTGAAGCAGATCGAAGACA-CAG-C
* * *
34953443 CTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCAGA
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAGC
* *** * * ** * * *
34953487 CTTGCCTCCCTGGGTTG-CAG-CAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGCACTGACAGTGA-AGCAGATCGAAGACA-CAG-C
** * *
34953531 CTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACAGCAGA
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAGC
* * * * * * ** * * **
34953575 CTTGCCTCCCT-AAGTTG-CAGCGGAGCAGGTTAAAAATAGCAAAT
1 CTTGCCTTCCTGCA-CTGACAGTGAAGCAGATCGAAGACA-C-AGC
* * * *
34953619 CTTGCCTTCCTGCACCGACAGCGAAGCTGATCGAAGACACCAGT
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAGC
*** * * * * * **
34953663 CTTGCC-TCCATGGGTTG-CAGCGGAA-CAGGTTGAAAATAGCAAAT
1 CTTGCCTTCC-TGCACTGACAG-TGAAGCAGATCGAAGACA-C-AGC
*
34953707 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCAAAGACACCAGC
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAGC
* ** * * * * * * *
34953751 CTTGCCTCCCTAG-GTTG-CAGCGGAGCAGGTTGAAAATAGCAGAT
1 CTTGCCTTCCT-GCACTGACAGTGAAGCAGATCGAAGACA-CAG-C
* * * * *
34953795 CTTGCCTTCCTTCACCGACAGCGAAACAAATCGAAGACACTAGC
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACAC-AGC
* * * * * * * * *
34953839 CTTACCTCCCTGGATTG-CAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACA-CAG-C
* * *
34953883 CTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACCCCAGC
1 CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGA-CACAGC
* *
34953927 CTTACCTCCCTG
1 CTTGCCTTCCTG
34953939 GGTTACAGCG
Statistics
Matches: 543, Mismatches: 226, Indels: 70
0.65 0.27 0.08
Matches are distributed among these distances:
42 1 0.00
43 148 0.27
44 241 0.44
45 152 0.28
46 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (43 bp):
CTTGCCTTCCTGCACTGACAGTGAAGCAGATCGAAGACACAGC
Found at i:34953974 original size:88 final size:88
Alignment explanation
Indices: 34953077--34953962 Score: 1205
Period size: 88 Copynumber: 10.1 Consensus size: 88
34953067 AACAGATCAG
* * *
34953077 TGAAGATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
34953142 CCCTGGATTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * * **
34953165 TGAAAATAACAGATCTTGTCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
34953230 TCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * ** *
34953253 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCAGACTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
34953318 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* ** *
34953341 TGAAAATAGCATATCTTGCCTTCCTGCACCGATGGCAAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
34953406 CCCTAGATTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * ** *
34953429 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACACCAGACTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
34953494 CCCTGGGTTGCAGCAGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
34953517 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACAGCAGACTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
**
34953582 CCCTAAGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
34953605 TAAAAATAGCAAATCTTGCCTTCCTGCACCGACAGCGAAGCTGATCGAAGACACCAGTCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
34953670 CCATGGGTTGCAGCGGAACAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
34953693 TGAAAATAGCAAATCTTGCCTTCCTGCACTGACAGTGAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
34953758 CCCTAGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * * *
34953781 TGAAAATAGCAGATCTTGCCTTCCTTCACCGACAGCGAAACAAATCGAAGACACTAGCCTTACCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
34953846 CCCTGGATTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * ** * *
34953869 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGCAGATCGAAGACCCCAGCCTTACCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
34953934 CCCTGGGTTACAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
34953957 TGAAAA
1 TGAAAA
34953963 ATATAGATCT
Statistics
Matches: 705, Mismatches: 93, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 705 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (88 bp):
TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGT
Found at i:34954099 original size:128 final size:127
Alignment explanation
Indices: 34953953--34954479 Score: 849
Period size: 128 Copynumber: 4.1 Consensus size: 127
34953943 ACAGCGGAGC
* * *
34953953 AGGTTGAAAAATATAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACGAATCTT
1 AGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGA-GAATCTT
34954018 ATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAAT
65 ATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAAT
34954081 AGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGAGAATCTT
1 AGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGAC-GAGAATCTT
* *
34954146 ATCTTCAAGAGTAAGGAAGCAAATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGCAAT
65 ATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAAT
*
34954209 AGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATCGAAGACG-GTAAATCT
1 AGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGAG--AATCT
* * * * *
34954273 TATCTTCAAGAGTAGGGAAGCAGATTTAAGCCATAAGTCCTATCTCCCTGGTCTGCAGTGTAGT
64 TATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAAT
* *
34954337 AGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGAGAAATCTT
1 AGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGAG-AATCTT
* * * *
34954402 ATCTTCAAGAGTAAGGAAGCAGATTTAAGCCGCTAGTCTTATCTCCCTGGTCAGCAGTTGAAT
65 ATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAAT
34954465 AGGTTGGAAATTACA
1 AGGTTGGAAATTACA
34954480 AATCCTATCT
Statistics
Matches: 370, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
126 1 0.00
127 1 0.00
128 365 0.99
129 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (127 bp):
AGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGAGAATCTTA
TCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAAT
Found at i:34955980 original size:25 final size:21
Alignment explanation
Indices: 34955928--34955972 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
34955918 AATAATAGCA
*
34955928 TAATTTATTATATATATTTTT
1 TAATTTATTATAAATATTTTT
34955949 TAATTTATTATAAATCATTATTT
1 TAATTTATTATAAAT-ATT-TTT
34955972 T
1 T
34955973 GAGATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 3 0.14
23 4 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTTATTATAAATATTTTT
Found at i:34957927 original size:24 final size:23
Alignment explanation
Indices: 34957896--34957941 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
34957886 ATATGCGATT
* * *
34957896 CAAAAATTTTATGTTCCTTTCAC
1 CAAAAAATTTACGTTCCATTCAC
34957919 CAAAAAATTTACGTTCCATTCAC
1 CAAAAAATTTACGTTCCATTCAC
34957942 ATTGAAATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (23 bp):
CAAAAAATTTACGTTCCATTCAC
Found at i:34958117 original size:24 final size:25
Alignment explanation
Indices: 34958064--34958123 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
34958054 TGGAATGATT
* *
34958064 TTTATATATTTTTTCTTTTACTAGCA
1 TTTATATA-TTTTTATTTTACTAGAA
*
34958090 -TTATATATTTTTATTTTATTA-AA
1 TTTATATATTTTTATTTTACTAGAA
*
34958113 TTTATAGATTT
1 TTTATATATTT
34958124 AAGTAACTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 21 0.72
25 7 0.24
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.63
Consensus pattern (25 bp):
TTTATATATTTTTATTTTACTAGAA
Found at i:34958209 original size:25 final size:26
Alignment explanation
Indices: 34958142--34958206 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 26
34958132 TGATTTTTTA
* *
34958142 ATAA-TTATAATATAATACAAAATAT
1 ATAATTTATAATATAATATAAAATAC
* * * *
34958167 TTAATTT-TCATATGATATAAATTAC
1 ATAATTTATAATATAATATAAAATAC
34958192 ATAATTTATAATATA
1 ATAATTTATAATATA
34958207 TATTAGGATA
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (26 bp):
ATAATTTATAATATAATATAAAATAC
Found at i:34967114 original size:37 final size:37
Alignment explanation
Indices: 34967064--34967137 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
34967054 GTGGAAAATA
34967064 GATGCTTCAGTTATAAGGTGGAAATATTATTTGCATC
1 GATGCTTCAGTTATAAGGTGGAAATATTATTTGCATC
34967101 GATGCTTCAGTTATAAGGTGGAAATATTATTTGCATC
1 GATGCTTCAGTTATAAGGTGGAAATATTATTTGCATC
34967138 TACTTTCTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (37 bp):
GATGCTTCAGTTATAAGGTGGAAATATTATTTGCATC
Found at i:34967926 original size:18 final size:18
Alignment explanation
Indices: 34967899--34967933 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34967889 TCCAACTCAT
*
34967899 CATCTTCATCTCCACCTC
1 CATCTCCATCTCCACCTC
*
34967917 CATCTCCATCTCTACCT
1 CATCTCCATCTCCACCT
34967934 TAATCTAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.49, G:0.00, T:0.34
Consensus pattern (18 bp):
CATCTCCATCTCCACCTC
Found at i:34968420 original size:5 final size:5
Alignment explanation
Indices: 34968410--34968440 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
34968400 GCATAGGCTC
34968410 AATCA AATCA AATCA AATCA AATCA AA-CA AA
1 AATCA AATCA AATCA AATCA AATCA AATCA AA
34968441 AAAACTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (5 bp):
AATCA
Found at i:34968762 original size:6 final size:6
Alignment explanation
Indices: 34968736--34968775 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
34968726 GTTAAATGAA
34968736 TTCATT TCTCATT TCTCATT TTCATT TTCATT TTCATT TT
1 TTCATT T-TCATT T-TCATT TTCATT TTCATT TTCATT TT
34968776 TGAGAAAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 20 0.61
7 13 0.39
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (6 bp):
TTCATT
Found at i:34970249 original size:97 final size:96
Alignment explanation
Indices: 34970107--34970300 Score: 361
Period size: 97 Copynumber: 2.0 Consensus size: 96
34970097 ATGTATGAAA
34970107 CAACACAAATCAACCCCAACAAATACCTTGATTGTCGTCCAACCCCTTGCATGATTCATGCATGA
1 CAACACAAATCAACCCCAACAAATACCTTGATTGTCGTCCAACCCCTTGCATGATTCATGCATGA
*
34970172 AATCAAGCATGAATCAAGTAACCACTTAATC
66 AATCAAGCATGAATCAAGCAACCACTTAATC
34970203 CAACACAAATCAACCCCCAACAAATACCTTGATTGTCGTCCAACCCCTTGCATGATTCATGCATG
1 CAACACAAATCAA-CCCCAACAAATACCTTGATTGTCGTCCAACCCCTTGCATGATTCATGCATG
*
34970268 AAATCAAGCATGAATCAAGCAACCGCTTAATC
65 AAATCAAGCATGAATCAAGCAACCACTTAATC
34970300 C
1 C
34970301 TCATCCCACA
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 13 0.14
97 82 0.86
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (96 bp):
CAACACAAATCAACCCCAACAAATACCTTGATTGTCGTCCAACCCCTTGCATGATTCATGCATGA
AATCAAGCATGAATCAAGCAACCACTTAATC
Found at i:34972436 original size:17 final size:17
Alignment explanation
Indices: 34972414--34972446 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
34972404 TCCCAGATTT
34972414 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
34972431 TGATACCCATATCTTT
1 TGATACCCATATCTTT
34972447 GACTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:34975703 original size:41 final size:40
Alignment explanation
Indices: 34975646--34975790 Score: 175
Period size: 41 Copynumber: 3.5 Consensus size: 40
34975636 TTTAACATAT
34975646 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCC-GATTCAGA
* *
34975687 TCACCGGCACTTAGCCTGCTAGGTTTATAACCAGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCC-GATTCAGA
* * * * **
34975728 TCACTGGCACTTAGCCTGCTAGACTTAAAGTCCGAATCATT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAG-CCGATTCAGA
34975769 TCACCGGC-CTTAAGCCTGCTAG
1 TCACCGGCACTT-AGCCTGCTAG
34975791 ACACAAAGTC
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 3 0.03
41 85 0.94
42 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCGATTCAGA
Found at i:34975799 original size:41 final size:41
Alignment explanation
Indices: 34975740--34975886 Score: 215
Period size: 41 Copynumber: 3.6 Consensus size: 41
34975730 ACTGGCACTT
* * * *
34975740 AGCCTGCTAGACTTAAAGTCCG-AATCATTTCACCGGCCTTA
1 AGCCTGCTAGACATAAAGTCTGAAAT-AATTCACCGGCATTA
*
34975781 AGCCTGCTAGACACAAAGTCTGAAATAATTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATTA
*
34975822 AGTCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATTA
*
34975863 AGCCTACTAGACATAAAGTCTGAA
1 AGCCTGCTAGACATAAAGTCTGAA
34975887 TACCACGGAT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 93 0.97
42 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATTA
Found at i:34976252 original size:61 final size:63
Alignment explanation
Indices: 34976149--34976615 Score: 254
Period size: 61 Copynumber: 7.3 Consensus size: 63
34976139 AACTCAAAGC
* * * * * *
34976149 ATACATT-GGCTAACATACATATAATTCA-TATGA-TTAATTTCAACCTATCAAATTCA-ATAT
1 ATACATTCGGCTAACATATATATAATTCATTA-AATTTCATTTCAACTTATAAAACTCACATAT
* *
34976209 ATACATTCGGCTAACATATATGTAATTCATTAAATTTCA-TTCAACTTACAAAACTCAGCATAT
1 ATACATTCGGCTAACATATATATAATTCATTAAATTTCATTTCAACTTATAAAACTCA-CATAT
* * ** * *
34976272 ATATATTCGGCTAA-ATATATATAGAATTTATGCAATTT-ATTTTATCTTATAAAACTCA-A-AT
1 ATACATTCGGCTAACATATATAT--AATTCATTAAATTTCATTTCAACTTATAAAACTCACATAT
* * * * *
34976333 ATACATT-GACTAACGCATATATATATACGATTCA-TACATTTTATTTTAACTTATAAAATTCAA
1 ATACATTCGGCTAA--C--ATATATATA--ATTCATTAAATTTCATTTCAACTTATAAAACTC--
34976396 AACATATAT
58 -AC--ATAT
* * *
34976405 ATACATTCGGCTAACATATATGTAATTCATTAAATTTCA-TTCAACTTACAAAACCCAGCATAT
1 ATACATTCGGCTAACATATATATAATTCATTAAATTTCATTTCAACTTATAAAACTCA-CATAT
** *
34976468 AT--ATTCGGCTAA-ATATATATAGAATTTC-TGCAATTT-ATTTTAACTTATAAAACTCA-A-A
1 ATACATTCGGCTAACATATATAT--AA-TTCATTAAATTTCATTTCAACTTATAAAACTCACATA
34976526 T
63 T
* * * * * *
34976527 ATACATT-GACTAACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAA
1 ATACATTCGGCTAACATATATATA-ATTC-ATT-A-A-ATTTCATTTCAACTTATAAAACTC---
34976591 ACATATAT
58 AC--ATAT
34976599 ATACATTCGGCTAACAT
1 ATACATTCGGCTAACAT
34976616 TTTTATACAA
Statistics
Matches: 313, Mismatches: 46, Indels: 83
0.71 0.10 0.19
Matches are distributed among these distances:
59 7 0.02
60 26 0.08
61 64 0.20
62 36 0.12
63 29 0.09
64 35 0.11
65 48 0.15
67 18 0.06
68 9 0.03
69 8 0.03
71 3 0.01
72 18 0.06
73 12 0.04
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (63 bp):
ATACATTCGGCTAACATATATATAATTCATTAAATTTCATTTCAACTTATAAAACTCACATAT
Found at i:34976376 original size:65 final size:65
Alignment explanation
Indices: 34976307--34976590 Score: 212
Period size: 65 Copynumber: 4.4 Consensus size: 65
34976297 ATTTATGCAA
*
34976307 TTTATTTTATCTTATAAAACTCAAATATACATTGACTAACGCATATATATATACGATTCATACAT
1 TTTATTTTAACTTATAAAACTCAAATATACATTGACTAACGCATATATATATACGATTCATACAT
* * * * * *
34976372 TTTATTTTAACTTATAAAATTCAAAACATATATAT-AC-ATTCGGC-TA-ACATATATGTAATTC
1 TTTATTTTAACTTATAAAACTC-AAATATACAT-TGACTA-AC-GCATATATATATACG--ATTC
*
34976433 ATTAAAT
60 A-TACAT
* * * * * * * * *
34976440 TTCA-TTCAACTTACAAAACCCAGCATATATATTCGGCTAA---ATATATATAGA--ATTTC-TG
1 TTTATTTTAACTTATAAAACTCA-AATATACATT-GACTAACGCATATATATATACGA-TTCATA
*
34976498 CAA
63 CAT
* *
34976501 TTTATTTTAACTTATAAAACTCAAATATACATTGACTAACACATATATATATACAATTCATACAT
1 TTTATTTTAACTTATAAAACTCAAATATACATTGACTAACGCATATATATATACGATTCATACAT
*
34976566 TTTATTTTAACTTATAAAATTCAAA
1 TTTATTTTAACTTATAAAACTCAAA
34976591 ACATATATAT
Statistics
Matches: 165, Mismatches: 33, Indels: 42
0.69 0.14 0.17
Matches are distributed among these distances:
60 5 0.03
61 13 0.08
62 16 0.10
63 13 0.08
64 3 0.02
65 58 0.35
66 20 0.12
67 28 0.17
68 8 0.05
69 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (65 bp):
TTTATTTTAACTTATAAAACTCAAATATACATTGACTAACGCATATATATATACGATTCATACAT
Found at i:34976630 original size:196 final size:195
Alignment explanation
Indices: 34976205--34976615 Score: 761
Period size: 194 Copynumber: 2.1 Consensus size: 195
34976195 ATCAAATTCA
*
34976205 ATATATACATTCGGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACTCAGCAT
1 ATATATACATTCGGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACCCAGCA-
*
34976270 ATATATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTATCTTATAAAACTCAAATAT
65 ATATATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAAACTCAAATAT
* *
34976335 ACATTGACTAACGCATATATATATACGATTCATACATTTTATTTTAACTTATAAAATTCAAAACA
130 ACATTGACTAACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACA
34976400 T
195 T
34976401 ATATATACATTCGGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACCCAGC-A
1 ATATATACATTCGGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACCCAGCAA
*
34976465 TATATATTCGGCTAAATATATATAGAATTTCTGCAATTTATTTTAACTTATAAAACTCAAATATA
66 TATATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAAACTCAAATATA
34976530 CATTGACTAACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACAT
131 CATTGACTAACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACAT
34976595 ATATATACATTCGGCTAACAT
1 ATATATACATTCGGCTAACAT
34976616 TTTTATACAA
Statistics
Matches: 210, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
194 148 0.70
196 62 0.30
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (195 bp):
ATATATACATTCGGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACCCAGCAA
TATATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAAACTCAAATATA
CATTGACTAACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACAT
Found at i:34978919 original size:17 final size:17
Alignment explanation
Indices: 34978897--34978946 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
34978887 TCCCAGATTT
34978897 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
34978914 TGATACCGATATCTTTC
1 TGATACCCATATCTTTC
34978931 TGATACCCATATCTTT
1 TGATACCCATATCTTT
34978947 GACTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:34985591 original size:6 final size:6
Alignment explanation
Indices: 34985582--34985636 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
34985572 GAATTTGAAC
34985582 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
34985630 TATTTT T
1 TATTTT T
34985637 TAGATTTGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:34993631 original size:18 final size:18
Alignment explanation
Indices: 34993608--34993643 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
34993598 TTCTTGTTGA
34993608 AAAATAATTAAATATTAT
1 AAAATAATTAAATATTAT
*
34993626 AAAATAATTAAATTTTAT
1 AAAATAATTAAATATTAT
34993644 TACAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATAATTAAATATTAT
Found at i:35010787 original size:6 final size:6
Alignment explanation
Indices: 35010769--35010813 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
35010759 TGCAAATGAA
* *
35010769 TCATTT CTCATTT TCATTT TCATTT TCAATTT CCATTT CCATTT T
1 TCATTT -TCATTT TCATTT TCATTT TC-ATTT TCATTT TCATTT T
35010814 GAGAAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 24 0.69
7 11 0.31
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (6 bp):
TCATTT
Found at i:35010793 original size:12 final size:12
Alignment explanation
Indices: 35010769--35010813 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
35010759 TGCAAATGAA
35010769 TCATTTCTCATTT
1 TCATTT-TCATTT
35010782 TCATTTTCATTT
1 TCATTTTCATTT
*
35010794 TCAATTTCCATTT
1 TC-ATTTTCATTT
*
35010807 CCATTTT
1 TCATTTT
35010814 GAGAAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 12 0.43
13 16 0.57
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTTCATTT
Found at i:35010793 original size:19 final size:19
Alignment explanation
Indices: 35010769--35010813 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
35010759 TGCAAATGAA
*
35010769 TCATTTCTC-ATTTTCATTT
1 TCATTT-TCAATTTCCATTT
35010788 TCATTTTCAATTTCCATTT
1 TCATTTTCAATTTCCATTT
*
35010807 CCATTTT
1 TCATTTT
35010814 GAGAAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (19 bp):
TCATTTTCAATTTCCATTT
Found at i:35010927 original size:21 final size:19
Alignment explanation
Indices: 35010884--35010931 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
35010874 CATTTCTGAA
35010884 TATTTTTCATTTCTCTCTT
1 TATTTTTCATTTCTCTCTT
*
35010903 TATTTTTCATTTCTCTATT
1 TATTTTTCATTTCTCTCTT
*
35010922 T-TTATTCATT
1 TATTTTTCATT
35010932 ATGTTCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTCATTTCTCTCTT
Found at i:35024147 original size:95 final size:92
Alignment explanation
Indices: 35024044--35024273 Score: 262
Period size: 93 Copynumber: 2.4 Consensus size: 92
35024034 GTTTGTCAAT
* * * ** *
35024044 TAAATTAATTATAATATTTTTTAAATTAGATTAGGTTTCGTGTTTATTGTTTTTTAAGAAAAAAT
1 TAAATTAATTATAA-ATTTTTAAAATTAGATTAGGTTTAGAG-TTAAAGGTTTTTAAG-AAAAAT
* * *
35024109 CAATTAAATTAGGATTTAGGGTTACTTGAG
63 CAAATAAATTAGGATTCAAGGTTACTTGAG
* * * * *
35024139 TAATTTAATTAAAAAATTTAAAAATTAGATTAGGGTTTAGAGTTAAAGGTTTTTAAGGAAAATCA
1 TAAATTAATTATAAATTTTTAAAATTAGATTA-GGTTTAGAGTTAAAGGTTTTTAAGAAAAATCA
*
35024204 AATAAATTAGGGTTCAAGGTTACTTGAG
65 AATAAATTAGGATTCAAGGTTACTTGAG
35024232 TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
1 TAAATTAATTATAAATTTTT--AAAATTAGATTA-GGTTTAG
35024274 GGTTTTTAAG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
93 47 0.42
94 27 0.24
95 39 0.35
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.41
Consensus pattern (92 bp):
TAAATTAATTATAAATTTTTAAAATTAGATTAGGTTTAGAGTTAAAGGTTTTTAAGAAAAATCAA
ATAAATTAGGATTCAAGGTTACTTGAG
Found at i:35024226 original size:93 final size:96
Alignment explanation
Indices: 35024094--35024273 Score: 267
Period size: 93 Copynumber: 1.9 Consensus size: 96
35024084 TGTTTATTGT
* * * *
35024094 TTTTTAAGAAAAAATCAATTAAATTAGGATTTAGGGTTACTTGAGTAATTTAATTA-AAAAATTT
1 TTTTTAAGAAAAAATCAAATAAATTAGGATTCAAGGTTACTTGAGTAAATTAATTATAAAAATTT
35024158 -AAAAATTAGATTAGGGTTTAGAGTTAAAGG
66 AAAAAATTAGATTAGGGTTTAGAGTTAAAGG
* * **
35024188 TTTTTAAG-GAAAATCAAATAAATTAGGGTTCAAGGTTACTTGAGTAAATTAATTATAAATTTTT
1 TTTTTAAGAAAAAATCAAATAAATTAGGATTCAAGGTTACTTGAGTAAATTAATTATAAAAATTT
35024252 AAAAAATTAGATTAGGGTTTAG
66 AAAAAATTAGATTAGGGTTTAG
35024274 GGTTTTTAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
93 41 0.54
94 14 0.18
95 21 0.28
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.38
Consensus pattern (96 bp):
TTTTTAAGAAAAAATCAAATAAATTAGGATTCAAGGTTACTTGAGTAAATTAATTATAAAAATTT
AAAAAATTAGATTAGGGTTTAGAGTTAAAGG
Found at i:35024885 original size:18 final size:18
Alignment explanation
Indices: 35024859--35024901 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35024849 GACTAGAAAA
* * *
35024859 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
35024877 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
35024895 AGGATAC
1 AGGATAC
35024902 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:35025566 original size:7 final size:7
Alignment explanation
Indices: 35025556--35025581 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35025546 CATAATACAT
35025556 AATACTA
1 AATACTA
35025563 AATACTA
1 AATACTA
35025570 AATACTA
1 AATACTA
35025577 AATAC
1 AATAC
35025582 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:35026768 original size:11 final size:11
Alignment explanation
Indices: 35026752--35026786 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
35026742 TTTTTTAAAT
35026752 AGGAATTTGAG
1 AGGAATTTGAG
*
35026763 AGGAATTTGAA
1 AGGAATTTGAG
35026774 AGGAATTTGAG
1 AGGAATTTGAG
35026785 AG
1 AG
35026787 AATAATAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (11 bp):
AGGAATTTGAG
Done.