Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 19 of 29
Found at i:2790175 original size:2 final size:2
Alignment explanation
Indices: 2790168--2790192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2790158 AGACCTCTTT
2790168 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2790193 TAGAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2791039 original size:11 final size:11
Alignment explanation
Indices: 2791020--2791050 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2791010 AAATCACATT
2791020 GGATAAATTTTG
1 GGAT-AATTTTG
2791032 GGATAATTTTG
1 GGATAATTTTG
2791043 GGATAATT
1 GGATAATT
2791051 GGGAAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (11 bp):
GGATAATTTTG
Found at i:2792452 original size:2 final size:2
Alignment explanation
Indices: 2792445--2792470 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2792435 TTTATGTTAC
2792445 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2792471 GGCAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2794092 original size:2 final size:2
Alignment explanation
Indices: 2794085--2794117 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2794075 GCTCTCAAGT
*
2794085 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2794118 GAAATTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2795451 original size:2 final size:2
Alignment explanation
Indices: 2795444--2795477 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2795434 TTGACCATAC
2795444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2795478 TGAGTGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2797461 original size:3 final size:3
Alignment explanation
Indices: 2797453--2797483 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2797443 TTTCATTTAG
2797453 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2797484 ATGCTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2802800 original size:2 final size:2
Alignment explanation
Indices: 2802793--2802826 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2802783 CATTTGGCCA
2802793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2802827 TTCAAATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2806226 original size:2 final size:2
Alignment explanation
Indices: 2806219--2806248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2806209 TAAAGCACAG
2806219 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2806249 CAACCACGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2815306 original size:52 final size:50
Alignment explanation
Indices: 2815176--2815317 Score: 126
Period size: 52 Copynumber: 2.7 Consensus size: 50
2815166 GGGTTATTAA
* * *
2815176 AATAAATAAATAAAATGTGATATAAATATATAAATATTTTAAATTTTATAT
1 AATAAATATAT-AAATATAATATAAATATATAAATATTTTAAATTTTATAT
* * * * * *
2815227 AATATAATTTATTAATTTTTATTTAAATGTAT-AATATTTTATAATTTTTAATAT
1 AATA-AATATA-TAAATATAATATAAATATATAAATATTTTA-AA-TTTT-ATAT
2815281 AATAAATATATAAATATAATATAAATAT-TAAAATATT
1 AATAAATATATAAATATAATATAAATATAT-AAATATT
2815318 AAAATCTAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
51 14 0.20
52 33 0.46
53 16 0.23
54 8 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (50 bp):
AATAAATATATAAATATAATATAAATATATAAATATTTTAAATTTTATAT
Found at i:2815528 original size:2 final size:2
Alignment explanation
Indices: 2815521--2815547 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2815511 AAGGAAGTAA
2815521 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2815548 ATGAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2817656 original size:59 final size:59
Alignment explanation
Indices: 2817592--2817714 Score: 246
Period size: 59 Copynumber: 2.1 Consensus size: 59
2817582 AATTTAAATA
2817592 GATTTTAATAATAACGTGGACTAACATGTTAATAAAATTAGGTAAATAAATGATAGATG
1 GATTTTAATAATAACGTGGACTAACATGTTAATAAAATTAGGTAAATAAATGATAGATG
2817651 GATTTTAATAATAACGTGGACTAACATGTTAATAAAATTAGGTAAATAAATGATAGATG
1 GATTTTAATAATAACGTGGACTAACATGTTAATAAAATTAGGTAAATAAATGATAGATG
2817710 GATTT
1 GATTT
2817715 GATAAGCGGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (59 bp):
GATTTTAATAATAACGTGGACTAACATGTTAATAAAATTAGGTAAATAAATGATAGATG
Found at i:2818145 original size:14 final size:14
Alignment explanation
Indices: 2818113--2818161 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2818103 TTTAAAAAAT
*
2818113 TTAAAATTAAT-AA
1 TTAAAATAAATAAA
*
2818126 TGTAAAATAATTAAA
1 T-TAAAATAAATAAA
*
2818141 TTAAATTAAATAAA
1 TTAAAATAAATAAA
2818155 TTAAAAT
1 TTAAAAT
2818162 TTTTTAATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 1 0.03
14 25 0.86
15 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
TTAAAATAAATAAA
Found at i:2818926 original size:10 final size:10
Alignment explanation
Indices: 2818913--2818942 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2818903 TGTATTTTTC
2818913 AAATATATAT
1 AAATATATAT
2818923 AAATATATAT
1 AAATATATAT
*
2818933 ATATATATAT
1 AAATATATAT
2818943 TTTGATTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATATATAT
Found at i:2822608 original size:10 final size:10
Alignment explanation
Indices: 2822577--2822608 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2822567 GTGTGTGTGT
2822577 GTGAGAGAGA
1 GTGAGAGAGA
*
2822587 GAGAGAGAGA
1 GTGAGAGAGA
2822597 GTGAGAGAGA
1 GTGAGAGAGA
2822607 GT
1 GT
2822609 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.50, T:0.09
Consensus pattern (10 bp):
GTGAGAGAGA
Found at i:2824103 original size:15 final size:14
Alignment explanation
Indices: 2824083--2824122 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
2824073 TATTTTTTAA
*
2824083 AAAAAATTATATTT
1 AAAAAATTATATAT
*
2824097 AAGAAAATTAAATAT
1 AA-AAAATTATATAT
2824112 AAAAAATTATA
1 AAAAAATTATA
2824123 ATTTTTCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AAAAAATTATATAT
Found at i:2824549 original size:24 final size:22
Alignment explanation
Indices: 2824510--2824553 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
2824500 TTATGAGTGA
2824510 TTTTAAAAAAATGATAATTTAT
1 TTTTAAAAAAATGATAATTTAT
2824532 TTTTATAAAAAATCGATAATTT
1 TTTTA-AAAAAAT-GATAATTT
2824554 TAGTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTTAAAAAAATGATAATTTAT
Found at i:2824555 original size:25 final size:22
Alignment explanation
Indices: 2824510--2824560 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 22
2824500 TTATGAGTGA
*
2824510 TTTTAAAAAAATGATAATTTAT
1 TTTTAAAAAAATGATAATTTAG
2824532 TTTTATAAAAAATCGATAATTTTAG
1 TTTTA-AAAAAAT-GATAA-TTTAG
2824557 TTTT
1 TTTT
2824561 CTTTCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 7 0.28
24 5 0.20
25 8 0.32
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (22 bp):
TTTTAAAAAAATGATAATTTAG
Found at i:2828220 original size:21 final size:21
Alignment explanation
Indices: 2828194--2828236 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2828184 GGGGCAAAGT
*
2828194 AAGGTCGTCCGGATGTTCAGA
1 AAGGTCGTCCGGATGCTCAGA
* *
2828215 AAGGTCGTTCTGATGCTCAGA
1 AAGGTCGTCCGGATGCTCAGA
2828236 A
1 A
2828237 TCTTGAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (21 bp):
AAGGTCGTCCGGATGCTCAGA
Found at i:2828253 original size:28 final size:28
Alignment explanation
Indices: 2828213--2828266 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
2828203 CGGATGTTCA
* *
2828213 GAAAGGTCGTTCTGATGCTCAGAATCTT
1 GAAAGGCCGTTCTGATGCTAAGAATCTT
*
2828241 GAAAGGCCGTTCTGATGTTAAGAATC
1 GAAAGGCCGTTCTGATGCTAAGAATC
2828267 CCGTGCTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (28 bp):
GAAAGGCCGTTCTGATGCTAAGAATCTT
Found at i:2828562 original size:2 final size:2
Alignment explanation
Indices: 2828539--2828577 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2828529 GGCGCCATGT
* * *
2828539 TA TA AA TA TA AA TA TC TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2828578 TAGATTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2829103 original size:32 final size:31
Alignment explanation
Indices: 2829051--2829154 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 31
2829041 TAATTTAAAC
2829051 ATAATATAAA-ATATA-A-TAAAATAAAATAA
1 ATAATATAAATATATATATTAAAAT-AAATAA
**
2829080 ATAATATAAATATATATATTAAAATTCAT--
1 ATAATATAAATATATATATTAAAATAAATAA
*
2829109 ATAATATAAATTATTAATATATTAAAATTTATATAA
1 ATAATATAAA-TA-T-ATATATTAAAA--TAAATAA
2829145 AT-ATATAAAT
1 ATAATATAAAT
2829155 TTTAAATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
29 20 0.33
30 7 0.11
31 4 0.07
32 17 0.28
34 4 0.07
35 7 0.11
36 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
ATAATATAAATATATATATTAAAATAAATAA
Found at i:2829104 original size:14 final size:15
Alignment explanation
Indices: 2829057--2829181 Score: 56
Period size: 14 Copynumber: 8.6 Consensus size: 15
2829047 AAACATAATA
* *
2829057 TAAAATATAATAAAA
1 TAAAATATAATATAT
2829072 TAAAATA-AATA-A-
1 TAAAATATAATATAT
2829084 TATAAATAT-ATATAT
1 TA-AAATATAATATAT
*
2829099 TAAAAT-TCATATAAT
1 TAAAATATAATAT-AT
*
2829114 ATAAATTATTAATATAT
1 -TAAAATA-TAATATAT
2829131 TAAAAT-T--TATA-
1 TAAAATATAATATAT
2829142 TAAATATATAA-AT-T
1 TAAA-ATATAATATAT
* *
2829156 TTAAATATAATTATAA
1 TAAAATATAA-TATAT
2829172 TACAAATATA
1 TA-AAATATA
2829182 TCATAAATAA
Statistics
Matches: 86, Mismatches: 6, Indels: 34
0.68 0.05 0.27
Matches are distributed among these distances:
11 4 0.05
12 8 0.09
13 17 0.20
14 19 0.22
15 13 0.15
16 11 0.13
17 9 0.10
18 5 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAATATAATATAT
Found at i:2829110 original size:18 final size:17
Alignment explanation
Indices: 2829089--2829143 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
2829079 AATAATATAA
2829089 ATATATATATTAAAATT
1 ATATATATATTAAAATT
2829106 CATATA-ATA-T-AAATT
1 -ATATATATATTAAAATT
2829121 AT-TAATATATTAAAATT
1 ATAT-ATATATTAAAATT
2829138 -TATATA
1 ATATATA
2829144 AATATATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 1 0.03
14 3 0.09
15 8 0.25
16 6 0.19
17 9 0.28
18 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATATTAAAATT
Found at i:2829148 original size:18 final size:18
Alignment explanation
Indices: 2829089--2829158 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
2829079 AATAATATAA
* *
2829089 ATATATATATTAAAATTC
1 ATATAAATATTAAAATTT
2829107 ATAT-AATA-T-AAA-TT
1 ATATAAATATTAAAATTT
2829121 AT-TAATATATTAAAATTT
1 ATATAA-ATATTAAAATTT
*
2829139 ATATAAATATATAAATTTT
1 ATATAAATAT-TAAAATTT
2829158 A
1 A
2829159 AATATAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
13 1 0.02
14 4 0.10
15 6 0.14
16 2 0.05
17 6 0.14
18 12 0.29
19 11 0.26
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAAATATTAAAATTT
Found at i:2829158 original size:19 final size:20
Alignment explanation
Indices: 2829123--2829171 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2829113 TATAAATTAT
*
2829123 TAATATATTAAAATTTATATA
1 TAATATA-TAAAATTTAAATA
*
2829144 -AATATATAAATTTTAAATA
1 TAATATATAAAATTTAAATA
2829163 TAAT-TATAA
1 TAATATATAA
2829172 TACAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATATAAAATTTAAATA
Found at i:2829507 original size:5 final size:5
Alignment explanation
Indices: 2829491--2829579 Score: 58
Period size: 5 Copynumber: 17.2 Consensus size: 5
2829481 TACATATTTA
* *
2829491 TATAT CTATAT TATAT TCATAT TAT-T TTTTT ATATAT TATATT TATAT
1 TATAT -TATAT TATAT T-ATAT TATAT TATAT -TATAT TATA-T TATAT
* * *
2829539 TATAT TTTAAT T-TTT TATAT TATAT TAGT-T TATAT AATAT T
1 TATAT TAT-AT TATAT TATAT TATAT TA-TAT TATAT TATAT T
2829580 TTCAATTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
4 6 0.09
5 39 0.58
6 22 0.33
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:2829531 original size:26 final size:25
Alignment explanation
Indices: 2829497--2829565 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
2829487 TTTATATATC
* *
2829497 TATATTATATTCATATTATTTTTTTA
1 TATATTATATT-ATATTATATTTTAA
2829523 TATATTATATTTATATTATATTTTAA
1 TATATTATA-TTATATTATATTTTAA
* *
2829549 TTTTTTATATTATATTA
1 TATATTATATTATATTA
2829566 GTTTATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 8 0.21
26 28 0.74
27 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (25 bp):
TATATTATATTATATTATATTTTAA
Found at i:2829544 original size:31 final size:32
Alignment explanation
Indices: 2829487--2829564 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
2829477 ATTTTACATA
2829487 TTTATATATCTATA-TTATATTCATATTATT-TT
1 TTTATATAT-TATATTTATATTCATATT-TTATT
2829519 TTTATATATTATATTTATATT-ATATTTTAATT
1 TTTATATATTATATTTATATTCATATTTT-ATT
2829551 TTT-TATATTATATT
1 TTTATATATTATATT
2829565 AGTTTATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
30 2 0.05
31 20 0.47
32 21 0.49
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (32 bp):
TTTATATATTATATTTATATTCATATTTTATT
Found at i:2829571 original size:35 final size:35
Alignment explanation
Indices: 2829514--2829586 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
2829504 TATTCATATT
*
2829514 ATTTTTTTATATATTATATTTATATTATATTTT-A
1 ATTTTTTTATATATTATATTTATATAATATTTTCA
*
2829548 ATTTTTTATATTATATTA-GTTTATATAATATTTTCA
1 ATTTTTT-TA-TATATTATATTTATATAATATTTTCA
2829584 ATT
1 ATT
2829587 AATACGAGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 7 0.21
35 16 0.47
36 11 0.32
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (35 bp):
ATTTTTTTATATATTATATTTATATAATATTTTCA
Found at i:2829725 original size:2 final size:2
Alignment explanation
Indices: 2829720--2829749 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2829710 ACACACGCAC
2829720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2829750 GCACCGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2830038 original size:2 final size:2
Alignment explanation
Indices: 2830026--2830063 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2830016 TTATTCTTAC
*
2830026 AT AT A- AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2830064 GTCATCAGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2840066 original size:2 final size:2
Alignment explanation
Indices: 2840059--2840088 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2840049 ACTTGAATGC
2840059 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2840089 ACATATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:2841977 original size:36 final size:36
Alignment explanation
Indices: 2841930--2842001 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2841920 GTTTTAATAC
*
2841930 TTTGAATTTAGAAACTTTATATTTCTTAGAACATGT
1 TTTGAATTTAGAAACTTTATATTCCTTAGAACATGT
*
2841966 TTTGAATTTAGAAACTTTATCTTCCTTAGAACATGT
1 TTTGAATTTAGAAACTTTATATTCCTTAGAACATGT
2842002 CAAAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (36 bp):
TTTGAATTTAGAAACTTTATATTCCTTAGAACATGT
Found at i:2847795 original size:16 final size:17
Alignment explanation
Indices: 2847766--2847797 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2847756 ATCTTCGTAA
2847766 AAATTGAGGGTGACGTG
1 AAATTGAGGGTGACGTG
2847783 AAATTGA-GGTGACGT
1 AAATTGAGGGTGACGT
2847798 AGTCTCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.31, C:0.06, G:0.38, T:0.25
Consensus pattern (17 bp):
AAATTGAGGGTGACGTG
Found at i:2848139 original size:21 final size:22
Alignment explanation
Indices: 2848115--2848164 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2848105 TTTTTTATAA
2848115 ATAAAATATCATAAAAA-TATT
1 ATAAAATATCATAAAAATTATT
* **
2848136 ATAAATTATTTTAAAAATTATT
1 ATAAAATATCATAAAAATTATT
2848158 A-AAAATA
1 ATAAAATA
2848165 AAATATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAATATCATAAAAATTATT
Found at i:2848172 original size:26 final size:25
Alignment explanation
Indices: 2848113--2848205 Score: 77
Period size: 26 Copynumber: 3.8 Consensus size: 25
2848103 ATTTTTTTAT
**
2848113 AAATAAAATATCATAAAAA-TATT-
1 AAATAAAATATTTTAAAAATTATTA
*
2848136 --ATAAATTATTTTAAAAATTATTAA
1 AAATAAAATATTTTAAAAATTATT-A
** *
2848160 AAATAAAATATTTTAATTATAATTA
1 AAATAAAATATTTTAAAAATTATTA
* *
2848185 AATTATAATATTTTAAAAATT
1 AAATAAAATATTTTAAAAATT
2848206 CATAATAACA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
21 14 0.26
22 4 0.08
25 17 0.32
26 18 0.34
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATAAAATATTTTAAAAATTATTA
Found at i:2849594 original size:6 final size:6
Alignment explanation
Indices: 2849583--2849613 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2849573 CATATTCACA
2849583 TCCACC TCCACC TCCACC TCCACC TCCACC T
1 TCCACC TCCACC TCCACC TCCACC TCCACC T
2849614 TCATCTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.65, G:0.00, T:0.19
Consensus pattern (6 bp):
TCCACC
Found at i:2849939 original size:24 final size:26
Alignment explanation
Indices: 2849906--2849962 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 26
2849896 TGTCAAAAAA
2849906 TTATATAATTAAGTA-AAATATATT-T
1 TTAT-TAATTAAGTATAAATATATTAT
*
2849931 TTATTAATTAATTATTAAATATATTAT
1 TTATTAATTAAGTA-TAAATATATTAT
2849958 TTATT
1 TTATT
2849963 TAATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 9 0.32
25 4 0.14
26 9 0.32
27 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TTATTAATTAAGTATAAATATATTAT
Found at i:2856554 original size:16 final size:16
Alignment explanation
Indices: 2856533--2856563 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2856523 GGATATTTAG
2856533 AAAATCAGGAAATTTC
1 AAAATCAGGAAATTTC
*
2856549 AAAATCAGTAAATTT
1 AAAATCAGGAAATTT
2856564 GTAGATCTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (16 bp):
AAAATCAGGAAATTTC
Found at i:2861018 original size:16 final size:16
Alignment explanation
Indices: 2860997--2861027 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2860987 GATATTCTAG
2860997 AAAATCAGTAAATTTC
1 AAAATCAGTAAATTTC
2861013 AAAATCAGTAAATTT
1 AAAATCAGTAAATTT
2861028 GCAGATCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (16 bp):
AAAATCAGTAAATTTC
Found at i:2861073 original size:19 final size:18
Alignment explanation
Indices: 2861014--2861081 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
2861004 GTAAATTTCA
* *
2861014 AAATCAGTAAATTTGCAG
1 AAATCAGGAAATCTGCAG
*
2861032 --ATCTGGAAATCTGCAG
1 AAATCAGGAAATCTGCAG
2861048 AAATCAGGAAATCTGCTAG
1 AAATCAGGAAATCTGC-AG
*
2861067 AATTCAGGAAATCTG
1 AAATCAGGAAATCTG
2861082 GAAATCTGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
16 13 0.31
18 13 0.31
19 16 0.38
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (18 bp):
AAATCAGGAAATCTGCAG
Found at i:2863298 original size:13 final size:13
Alignment explanation
Indices: 2863266--2863291 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2863256 AAATAAAATG
2863266 GCATAGTTTTAAT
1 GCATAGTTTTAAT
2863279 GCATAGTTTTAAT
1 GCATAGTTTTAAT
2863292 TTCTAGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GCATAGTTTTAAT
Found at i:2865625 original size:2 final size:2
Alignment explanation
Indices: 2865618--2865653 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2865608 AGCCAGCAAC
*
2865618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2865654 GAGTGCTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2865815 original size:25 final size:25
Alignment explanation
Indices: 2865779--2865830 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
2865769 ATTTTTTAAA
*
2865779 AATAATTATATAAATTAACTAGATT
1 AATAATTATATAAATTAACTAAATT
*
2865804 AATAATTGTATAAATTAACTAAATT
1 AATAATTATATAAATTAACTAAATT
2865829 AA
1 AA
2865831 GTTTGGTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
AATAATTATATAAATTAACTAAATT
Found at i:2869421 original size:21 final size:21
Alignment explanation
Indices: 2869395--2869445 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
2869385 AATTAGCTGG
2869395 ATTTTGGCCCTTTCAAGATCT
1 ATTTTGGCCCTTTCAAGATCT
*
2869416 ATTTTGG-CCTTTCAAGATTT
1 ATTTTGGCCCTTTCAAGATCT
2869436 ATTTTGGCCC
1 ATTTTGGCCC
2869446 CGAGTCCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.45
Consensus pattern (21 bp):
ATTTTGGCCCTTTCAAGATCT
Found at i:2871079 original size:15 final size:16
Alignment explanation
Indices: 2871061--2871098 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2871051 AGCATATTAT
* *
2871061 ATTTAAAATTAATA-A
1 ATTTAAAATAAACAGA
2871076 ATTTAAAATAAACAGA
1 ATTTAAAATAAACAGA
2871092 ATTTAAA
1 ATTTAAA
2871099 TCAAAAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTTAAAATAAACAGA
Found at i:2883450 original size:17 final size:17
Alignment explanation
Indices: 2883417--2883452 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2883407 ATTCAATAAA
* *
2883417 CATATTACTTTCGAAAT
1 CATATTACTTACAAAAT
2883434 CATATTACTTACAAAAT
1 CATATTACTTACAAAAT
2883451 CA
1 CA
2883453 GGTTTATCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (17 bp):
CATATTACTTACAAAAT
Found at i:2883600 original size:31 final size:31
Alignment explanation
Indices: 2883559--2883744 Score: 183
Period size: 31 Copynumber: 6.0 Consensus size: 31
2883549 AAATTAGAAC
* *
2883559 AAAAATCACTATTCTAATCCGGTGGCACGGT
1 AAAAACCACTATTCTTATCCGGTGGCACGGT
*
2883590 AAAAACCACTATTCTAATCCGGTGGCACGGT
1 AAAAACCACTATTCTTATCCGGTGGCACGGT
* * ***
2883621 AAAAACTACTATTCTTATCCGATGGCACAAC
1 AAAAACCACTATTCTTATCCGGTGGCACGGT
* * *
2883652 AAAACCCACTATTCTTATCCGGTAGCACGGC
1 AAAAACCACTATTCTTATCCGGTGGCACGGT
* * * * *
2883683 GAAAATCACTGTTCTTATCTGGTGACACGGT
1 AAAAACCACTATTCTTATCCGGTGGCACGGT
** * * *
2883714 AAAAGTCACTATTCTTAACAGGTGGTACGGT
1 AAAAACCACTATTCTTATCCGGTGGCACGGT
2883745 TTGAAATCGA
Statistics
Matches: 127, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 127 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (31 bp):
AAAAACCACTATTCTTATCCGGTGGCACGGT
Found at i:2883715 original size:93 final size:93
Alignment explanation
Indices: 2883556--2883730 Score: 226
Period size: 93 Copynumber: 1.9 Consensus size: 93
2883546 CATAAATTAG
* * * *
2883556 AACAAAAATCACTATTCTAATCCGGTGGCACGGTAAAAACCACTATTCTAATCCGGTGGCACGGT
1 AACAAAAACCACTATTCTAATCCGGTAGCACGGCAAAAACCACTATTCTAATCCGGTGACACGGT
2883621 AAAAACT-ACTATTCTTATCCGATGGCAC
66 -AAAACTCACTATTCTTATCCGATGGCAC
* * * * * * *
2883649 AACAAAACCCACTATTCTTATCCGGTAGCACGGCGAAAATCACTGTTCTTATCTGGTGACACGGT
1 AACAAAAACCACTATTCTAATCCGGTAGCACGGCAAAAACCACTATTCTAATCCGGTGACACGGT
*
2883714 AAAAGTCACTATTCTTA
66 AAAACTCACTATTCTTA
2883731 ACAGGTGGTA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
92 5 0.07
93 64 0.93
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (93 bp):
AACAAAAACCACTATTCTAATCCGGTAGCACGGCAAAAACCACTATTCTAATCCGGTGACACGGT
AAAACTCACTATTCTTATCCGATGGCAC
Found at i:2884077 original size:29 final size:29
Alignment explanation
Indices: 2884023--2884078 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2884013 AAACTTTAAC
* *
2884023 AAAATCATCTTTAAAATCATATCAAAACA
1 AAAATCATCTTTAAAATCAAAACAAAACA
*
2884052 AAAATCA-CTTTCCAAATCAAAACAAAA
1 AAAATCATCTTT-AAAATCAAAACAAAA
2884079 AAATTACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (29 bp):
AAAATCATCTTTAAAATCAAAACAAAACA
Found at i:2889307 original size:31 final size:31
Alignment explanation
Indices: 2889263--2889323 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2889253 ATAAGTTAGA
2889263 ATAAAAATAACTATTCTAATCCAGTGGCACG
1 ATAAAAATAACTATTCTAATCCAGTGGCACG
* *
2889294 ATAAAAACT-ACTATTCTTATCCGGTGGCAC
1 ATAAAAA-TAACTATTCTAATCCAGTGGCAC
2889324 AGCAAAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (31 bp):
ATAAAAATAACTATTCTAATCCAGTGGCACG
Found at i:2889331 original size:31 final size:31
Alignment explanation
Indices: 2889272--2889444 Score: 204
Period size: 31 Copynumber: 5.6 Consensus size: 31
2889262 AATAAAAATA
* * * *
2889272 ACTATTCTAATCCAGTGGCAC-GATAAAAACT
1 ACTATTCTTATCCGGTGGCACAG-CAAAAACC
2889303 ACTATTCTTATCCGGTGGCACAGCAAAAACC
1 ACTATTCTTATCCGGTGGCACAGCAAAAACC
* * *
2889334 ACTATTATTATCCGGTGGCATAGCGAAAACC
1 ACTATTCTTATCCGGTGGCACAGCAAAAACC
* *
2889365 ACTATTCTCATCCGGTGGCACAGCGAAAACC
1 ACTATTCTTATCCGGTGGCACAGCAAAAACC
* * * *
2889396 ATTATTCTTATCCAGTGGCACGGCAAAAATC
1 ACTATTCTTATCCGGTGGCACAGCAAAAACC
*
2889427 ACTATTCTTAACCGGTGG
1 ACTATTCTTATCCGGTGG
2889445 TACGATTTGA
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
31 121 0.99
32 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (31 bp):
ACTATTCTTATCCGGTGGCACAGCAAAAACC
Found at i:2892390 original size:16 final size:16
Alignment explanation
Indices: 2892359--2892427 Score: 77
Period size: 16 Copynumber: 4.2 Consensus size: 16
2892349 TTTTCGAATT
*
2892359 ATTTTCGAATTTGGGTC
1 ATTTT-GAATTCGGGTC
2892376 ATTTTGAATTCGGGTC
1 ATTTTGAATTCGGGTC
**
2892392 ATTTTGTGTTCGGGTC
1 ATTTTGAATTCGGGTC
*
2892408 ATTTT-AGAGTCGGGTC
1 ATTTTGA-ATTCGGGTC
2892424 ATTT
1 ATTT
2892428 CAAGTTTGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 40 0.89
17 5 0.11
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (16 bp):
ATTTTGAATTCGGGTC
Found at i:2893094 original size:17 final size:17
Alignment explanation
Indices: 2893072--2893109 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2893062 GATACGTATA
2893072 TAATT-ATTATATTATTT
1 TAATTAATTA-ATTATTT
*
2893089 TAATTAATTAATTTTTT
1 TAATTAATTAATTATTT
2893106 TAAT
1 TAAT
2893110 AAAAAGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TAATTAATTAATTATTT
Found at i:2893527 original size:16 final size:16
Alignment explanation
Indices: 2893508--2893578 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
2893498 ATTATTCAAA
2893508 TCATTTCGAATTCGAG
1 TCATTTCGAATTCGAG
* *
2893524 TCATTTCGAATTTGAA
1 TCATTTCGAATTCGAG
*
2893540 TCATTTCGAATTTGAG
1 TCATTTCGAATTCGAG
* *
2893556 TTATTATAG-ATTCGAG
1 TCATT-TCGAATTCGAG
2893572 TCATTTC
1 TCATTTC
2893579 AGGTTTAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
15 1 0.02
16 43 0.93
17 2 0.04
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (16 bp):
TCATTTCGAATTCGAG
Found at i:2896403 original size:14 final size:12
Alignment explanation
Indices: 2896384--2896486 Score: 68
Period size: 14 Copynumber: 8.2 Consensus size: 12
2896374 ATATTTTTAA
2896384 TATATTCATATATT
1 TATATT-AT-TATT
2896398 TATATT-TTATT
1 TATATTATTATT
*
2896409 TATATTATTTTT
1 TATATTATTATT
2896421 TATATCATATTATAT
1 TATAT--TATTAT-T
*
2896436 TATAATTATTTTAT
1 TAT-ATTATTAT-T
2896450 TATATT-TTATT
1 TATATTATTATT
** *
2896461 TACGTTATATAAT
1 TATATTAT-TATT
2896474 TATATTA-TATT
1 TATATTATTATT
2896485 TA
1 TA
2896487 AATTTAACGT
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
11 20 0.28
12 14 0.19
13 11 0.15
14 21 0.29
15 4 0.06
16 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (12 bp):
TATATTATTATT
Found at i:2896408 original size:19 final size:19
Alignment explanation
Indices: 2896372--2896430 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
2896362 TTTTAATTAT
* * *
2896372 ATATATTTTTAATATATTC
1 ATATATTTATATTTTATTC
2896391 ATATATTTATATTTTATT-
1 ATATATTTATATTTTATTC
*
2896409 -TATA-TTATTTTTTATATC
1 ATATATTTATATTTTAT-TC
2896427 ATAT
1 ATAT
2896431 TATATTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.30
17 5 0.15
19 18 0.55
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATATTTATATTTTATTC
Found at i:2896416 original size:5 final size:5
Alignment explanation
Indices: 2896384--2896484 Score: 60
Period size: 5 Copynumber: 21.2 Consensus size: 5
2896374 ATATTTTTAA
* *
2896384 TATAT TCATA- TAT-T TATAT TTTATT TATAT TAT-T T-T-T TATAT CATAT
1 TATAT T-ATAT TATAT TATAT TATA-T TATAT TATAT TATAT TATAT TATAT
*
2896431 TATAT TATAAT TAT-T T-TAT TATAT TTTAT T-TACGT TATA- TA-AT
1 TATAT TAT-AT TATAT TATAT TATAT TATAT TATA--T TATAT TATAT
2896474 TATAT TATAT T
1 TATAT TATAT T
2896485 TAAATTTAAC
Statistics
Matches: 77, Mismatches: 5, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
3 5 0.06
4 18 0.23
5 38 0.49
6 14 0.18
7 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:2896429 original size:36 final size:39
Alignment explanation
Indices: 2896361--2896459 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 39
2896351 TATTTTAATA
*
2896361 ATTTTAATTATATATATTTTTAATATATTCATA-TAT-TTAT
1 ATTTTATTTATAT-TATTTTT--TATATTCATATTATATTAT
2896401 ATTTTATTTATATTATTTTTTATA-TCATATTATATTAT
1 ATTTTATTTATATTATTTTTTATATTCATATTATATTAT
* *
2896439 A-ATTATTT-TATTATATTTTAT
1 ATTTTATTTATATTATTTTTTAT
2896460 TTACGTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
36 17 0.31
37 13 0.24
38 5 0.09
39 7 0.13
40 12 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (39 bp):
ATTTTATTTATATTATTTTTTATATTCATATTATATTAT
Found at i:2896468 original size:24 final size:24
Alignment explanation
Indices: 2896397--2896490 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
2896387 ATTCATATAT
*
2896397 TTATATTTTATTTATATTATTTT-
1 TTATATTTTATTTAAATTATTTTA
2896420 TTATATCATATTATATTATAATTATTTTA
1 TTATAT--T-TTAT-TTA-AATTATTTTA
** * *
2896449 TTATATTTTATTTACGTTATATAA
1 TTATATTTTATTTAAATTATTTTA
*
2896473 TTATATTATATTTAAATT
1 TTATATTTTATTTAAATT
2896491 TAACGTATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
23 6 0.11
24 21 0.37
25 4 0.07
26 8 0.14
27 4 0.07
28 8 0.14
29 6 0.11
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (24 bp):
TTATATTTTATTTAAATTATTTTA
Found at i:2896476 original size:43 final size:42
Alignment explanation
Indices: 2896350--2896482 Score: 109
Period size: 43 Copynumber: 3.2 Consensus size: 42
2896340 ACAAAATTTG
* * *
2896350 ATATTTTAATAATTTTAATTATATATATTT-TTA-AT-ATATT
1 ATATTATAATTATTTTATTTATAT-TATTTGTTATATCATATT
* *
2896390 CATA-TAT-TTATATTTTATTTATATTATTTTTTATATCATATT
1 -ATATTATAAT-TATTTTATTTATATTATTTGTTATATCATATT
*
2896432 ATATTATAATTATTTTATTATATTTTATTTACGTTATAT-A-ATT
1 ATATTATAATTATTTTATT-TATATTATTT--GTTATATCATATT
2896475 ATATTATA
1 ATATTATA
2896483 TTTAAATTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
39 6 0.08
40 17 0.22
41 8 0.11
42 17 0.22
43 21 0.28
44 1 0.01
45 6 0.08
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (42 bp):
ATATTATAATTATTTTATTTATATTATTTGTTATATCATATT
Found at i:2896715 original size:2 final size:2
Alignment explanation
Indices: 2896708--2896760 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2896698 GAAAGTATTT
*
2896708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2896750 TA TA TA TA TA T
1 TA TA TA TA TA T
2896761 GATTGGATGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2897442 original size:4 final size:4
Alignment explanation
Indices: 2897433--2897466 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2897423 TTTGAAAGTT
2897433 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
2897467 CAACTCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:2901810 original size:2 final size:2
Alignment explanation
Indices: 2901803--2901839 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2901793 TACTTAGTTA
2901803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2901840 AAAGCCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2906941 original size:26 final size:26
Alignment explanation
Indices: 2906912--2906962 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2906902 AAAAAACCCG
2906912 TTTTTTTTCTTTAATGTTCTTTTTCC
1 TTTTTTTTCTTTAATGTTCTTTTTCC
* * *
2906938 TTTTTTTTTTTTCATTTTCTTTTTC
1 TTTTTTTTCTTTAATGTTCTTTTTC
2906963 ATTCTTTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTTTTTCTTTAATGTTCTTTTTCC
Found at i:2909877 original size:2 final size:2
Alignment explanation
Indices: 2909872--2909901 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2909862 GTGTGTGTGT
2909872 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2909902 ACCTCAAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2920850 original size:22 final size:23
Alignment explanation
Indices: 2920811--2920853 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2920801 AGATTATGAA
*
2920811 TATTAAAATTTTAATTTTAAATT
1 TATTAAAATATTAATTTTAAATT
*
2920834 TATT-AAATATTATTTTTAAA
1 TATTAAAATATTAATTTTAAA
2920854 AATAATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTAAAATATTAATTTTAAATT
Found at i:2923653 original size:2 final size:2
Alignment explanation
Indices: 2923646--2923674 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2923636 AGGTATTTCT
2923646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2923675 GTATTATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2925941 original size:2 final size:2
Alignment explanation
Indices: 2925934--2925963 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2925924 TGTATGTTCC
2925934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2925964 GGCATAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2933370 original size:11 final size:11
Alignment explanation
Indices: 2933354--2933378 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2933344 ACAAACCATC
2933354 AAGAAAAAAAA
1 AAGAAAAAAAA
2933365 AAGAAAAAAAA
1 AAGAAAAAAAA
2933376 AAG
1 AAG
2933379 CTTTAAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:2935660 original size:2 final size:2
Alignment explanation
Indices: 2935653--2935702 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
2935643 TGGTCTCACT
* *
2935653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2935695 GA TA TA TA
1 TA TA TA TA
2935703 GAGAGAGAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2942575 original size:13 final size:13
Alignment explanation
Indices: 2942559--2942583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2942549 TTTTTTAAAA
2942559 TATATTAATATTT
1 TATATTAATATTT
2942572 TATATTAATATT
1 TATATTAATATT
2942584 ATTAAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTAATATTT
Found at i:2944439 original size:3 final size:3
Alignment explanation
Indices: 2944433--2944458 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2944423 TCATCAAGCT
2944433 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
2944459 TTACCTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2949418 original size:11 final size:12
Alignment explanation
Indices: 2949402--2949440 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
2949392 GAACTATCAA
2949402 AAAGAAAA-AGG
1 AAAGAAAAGAGG
2949413 AAAGAAAAGAGG
1 AAAGAAAAGAGG
*
2949425 AAACAGAAAGAGG
1 AAAGA-AAAGAGG
2949438 AAA
1 AAA
2949441 ATAGTTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.32
12 7 0.28
13 10 0.40
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAGG
Found at i:2950971 original size:36 final size:36
Alignment explanation
Indices: 2950931--2950999 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
2950921 AGCAGGACTT
2950931 AACCTAAAAGAATACTTATTTCTTGGAAAACTACTA
1 AACCTAAAAGAATACTTATTTCTTGGAAAACTACTA
2950967 AACCTAAAAGAATACTTATTTCTTGGAAAACTA
1 AACCTAAAAGAATACTTATTTCTTGGAAAACTA
2951000 AGTGATTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (36 bp):
AACCTAAAAGAATACTTATTTCTTGGAAAACTACTA
Found at i:2952743 original size:2 final size:2
Alignment explanation
Indices: 2952738--2952777 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2952728 CTGGTGTGTG
2952738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2952778 ACTAGCATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2956429 original size:24 final size:26
Alignment explanation
Indices: 2956397--2956450 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
2956387 ATTCAAATAA
2956397 AAATCTTTAATTTTT-ATTTA-AAAT
1 AAATCTTTAATTTTTAATTTATAAAT
* *
2956421 AAATTTTTAATTTTTAATTTATATAT
1 AAATCTTTAATTTTTAATTTATAAAT
2956447 AAAT
1 AAAT
2956451 AAATCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 14 0.54
25 5 0.19
26 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
AAATCTTTAATTTTTAATTTATAAAT
Found at i:2956453 original size:30 final size:31
Alignment explanation
Indices: 2956402--2956460 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
2956392 AATAAAAATC
* * *
2956402 TTTAATTTTTATTTAAAATAAATTTTTAATT
1 TTTAATTTATATATAAAATAAATCTTTAATT
2956433 TTTAATTTATATAT-AAATAAATCTTTAA
1 TTTAATTTATATATAAAATAAATCTTTAA
2956461 CTTAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
TTTAATTTATATATAAAATAAATCTTTAATT
Found at i:2956468 original size:29 final size:29
Alignment explanation
Indices: 2956409--2956468 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
2956399 ATCTTTAATT
* * * *
2956409 TTTATTTAAAATAAATTTTTAATTTTTAA
1 TTTATATAAAATAAATCTTTAATCTTAAA
2956438 TTTATATATAAATAAATCTTTAA-CTTAAA
1 TTTATATA-AAATAAATCTTTAATCTTAAA
2956467 TT
1 TT
2956469 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTATATAAAATAAATCTTTAATCTTAAA
Found at i:2956494 original size:17 final size:16
Alignment explanation
Indices: 2956474--2956527 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
2956464 AAATTAATTT
2956474 TTTATTTAATATAAAAA
1 TTTATTTAA-ATAAAAA
2956491 TTTATTTAAAT-AAAA
1 TTTATTTAAATAAAAA
***
2956506 -TTAAAAAAATAAAAA
1 TTTATTTAAATAAAAA
2956521 TTTATTT
1 TTTATTT
2956528 GATTATAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 7 0.24
15 8 0.28
16 5 0.17
17 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTATTTAAATAAAAA
Found at i:2956499 original size:39 final size:40
Alignment explanation
Indices: 2956427--2956509 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
2956417 AAATAAATTT
* * *
2956427 TTAATTTTTAATTTATATATAAATAAATCTTTAACTTAAA
1 TTAATTTTTAATTTATATATAAATAAATATTTAAATAAAA
* *
2956467 TTAATTTTTTATTTA-ATATAAA-AATTTATTTAAATAAAA
1 TTAATTTTTAATTTATATATAAATAA-ATATTTAAATAAAA
2956506 TTAA
1 TTAA
2956510 AAAAATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.05
39 21 0.57
40 14 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (40 bp):
TTAATTTTTAATTTATATATAAATAAATATTTAAATAAAA
Found at i:2956596 original size:23 final size:25
Alignment explanation
Indices: 2956549--2956601 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
2956539 GATAAAAAAT
2956549 ATTTAAATATAATAAAAATATTAAA
1 ATTTAAATATAATAAAAATATTAAA
* *
2956574 ATTTAAATA-AATAAGATTA-TAAA
1 ATTTAAATATAATAAAAATATTAAA
2956597 ATTTA
1 ATTTA
2956602 GAGGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 9 0.35
24 8 0.31
25 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTTAAATATAATAAAAATATTAAA
Found at i:2957302 original size:14 final size:13
Alignment explanation
Indices: 2957283--2957334 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
2957273 TATATTTATT
2957283 TAAAAATTATAATA
1 TAAAAATTA-AATA
2957297 TAAAAATTAAATTA
1 TAAAAATTAAA-TA
2957311 TAAATAA--AAATA
1 TAAA-AATTAAATA
2957323 -AAAAATTAAATA
1 TAAAAATTAAATA
2957335 AATATAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 7 0.21
13 5 0.15
14 15 0.44
15 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAATTAAATA
Found at i:2957310 original size:19 final size:18
Alignment explanation
Indices: 2957286--2957321 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
2957276 ATTTATTTAA
2957286 AAATTATAATATAAAAATT
1 AAATTATAA-ATAAAAATT
2957305 AAATTATAAATAAAAAT
1 AAATTATAAATAAAAAT
2957322 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTATAAATAAAAATT
Found at i:2957333 original size:12 final size:12
Alignment explanation
Indices: 2957284--2957336 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
2957274 ATATTTATTT
2957284 AAAAATTATAATA
1 AAAAATTA-AATA
*
2957297 TAAAAATTAAATT
1 -AAAAATTAAATA
* *
2957310 ATAAATAAAAATA
1 AAAAAT-TAAATA
2957323 AAAAATTAAATA
1 AAAAATTAAATA
2957335 AA
1 AA
2957337 TATAAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 12 0.38
13 12 0.38
14 8 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAAATTAAATA
Found at i:2960224 original size:2 final size:2
Alignment explanation
Indices: 2960217--2960258 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2960207 TTTAGATTAC
2960217 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2960258 T
1 T
2960259 TCTTGGTCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2964698 original size:42 final size:42
Alignment explanation
Indices: 2964632--2964714 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
2964622 GGTACACAAT
* *
2964632 TTCCAGACTTCTCATTTGGGAACTTGACTAAAGAATGGGCAC
1 TTCCAGACTTCTCACTTGGAAACTTGACTAAAGAATGGGCAC
**
2964674 TTCCAGACTTCTCACTTGGAAACTTGACTGCAGAATGGGCA
1 TTCCAGACTTCTCACTTGGAAACTTGACTAAAGAATGGGCA
2964715 GGACAAAGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
TTCCAGACTTCTCACTTGGAAACTTGACTAAAGAATGGGCAC
Found at i:2968009 original size:25 final size:27
Alignment explanation
Indices: 2967981--2968038 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
2967971 AAATTTTATT
*
2967981 AAAATATTATTT-TTATAT-ATAATTA
1 AAAATATTATTTATTAAATAATAATTA
* *
2968006 AAAATTTTTATTTATTAAATAATAATTT
1 AAAA-TATTATTTATTAAATAATAATTA
2968034 AAAAT
1 AAAAT
2968039 TAAATTGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 4 0.15
26 7 0.26
27 6 0.22
28 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AAAATATTATTTATTAAATAATAATTA
Found at i:2973600 original size:2 final size:2
Alignment explanation
Indices: 2973593--2973618 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2973583 CATAACTATA
2973593 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
2973619 CCAATATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:2976555 original size:22 final size:21
Alignment explanation
Indices: 2976504--2976555 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
2976494 ACGTCACTTC
2976504 ATTTAATTA-AATAAATAAAA
1 ATTTAATTATAATAAATAAAA
** * *
2976524 AAATATTTATAATTAAATTAAA
1 ATTTAATTATAA-TAAATAAAA
2976546 ATTTAATTAT
1 ATTTAATTAT
2976556 CGAAAGATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 6 0.26
21 2 0.09
22 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTAATTATAATAAATAAAA
Found at i:2977477 original size:17 final size:17
Alignment explanation
Indices: 2977457--2977519 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
2977447 ACATAAAAAT
2977457 AATATTAATATAATTTA
1 AATATTAATATAATTTA
2977474 AATATATAA-AT-ATTTA
1 AATAT-TAATATAATTTA
* *
2977490 AA-ATTTTATATAATATA
1 AATA-TTAATATAATTTA
*
2977507 AATTATTATTATA
1 AA-TATTAATATA
2977520 TTAAAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
15 3 0.08
16 10 0.28
17 13 0.36
18 9 0.25
19 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATTAATATAATTTA
Found at i:2977502 original size:33 final size:32
Alignment explanation
Indices: 2977464--2977541 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
2977454 AATAATATTA
*
2977464 ATATAATTTAAATATATAAATAT-TTAAAATTTT
1 ATATAATATAAAT-TATAAATATATTAAAA-TTT
* *
2977497 ATATAATATAAATTATTATTATATTAAAATTT
1 ATATAATATAAATTATAAATATATTAAAATTT
2977529 ATATAAATATAAA
1 ATAT-AATATAAA
2977542 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.35
33 26 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATAATATAAATTATAAATATATTAAAATTT
Found at i:2977526 original size:17 final size:15
Alignment explanation
Indices: 2977483--2977533 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
2977473 AAATATATAA
2977483 ATAT-TTAAAATTTT
1 ATATATTAAAATTTT
*
2977497 ATATAATATAAATTATT
1 ATATATTA-AAATT-TT
2977514 ATTATATTAAAA-TTT
1 A-TATATTAAAATTTT
2977529 ATATA
1 ATATA
2977534 AATATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 8 0.26
15 5 0.16
16 6 0.19
17 6 0.19
18 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATTAAAATTTT
Found at i:2977549 original size:20 final size:20
Alignment explanation
Indices: 2977476--2977563 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
2977466 ATAATTTAAA
*
2977476 TATATAAATATTTAAA-ATTT
1 TATATAAATA-TAAAATATTT
*
2977496 TATAT-AATAT-AAAT-TAT
1 TATATAAATATAAAATATTT
*
2977513 TAT-T--ATATTAAA-A-TT
1 TATATAAATATAAAATATTT
2977528 TATATAAATATAAAATATTT
1 TATATAAATATAAAATATTT
*
2977548 TAAATAAA-ATAAAATA
1 TATATAAATATAAAATA
2977564 AAAATAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
15 8 0.14
16 5 0.09
17 8 0.14
18 8 0.14
19 13 0.23
20 14 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATAAATATAAAATATTT
Found at i:2977575 original size:17 final size:17
Alignment explanation
Indices: 2977549--2977594 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2977539 AAAATATTTT
2977549 AAAT-AAAATAAAATAA
1 AAATAAAAATAAAATAA
* *
2977565 AAATAAAAATATAATAC
1 AAATAAAAATAAAATAA
*
2977582 AAATAAATATAAA
1 AAATAAAAATAAA
2977595 TTACCAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAAAAATAAAATAA
Found at i:2977753 original size:16 final size:16
Alignment explanation
Indices: 2977721--2977752 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2977711 CATTTAACAT
2977721 ATAAATATATATAAAA
1 ATAAATATATATAAAA
2977737 ATAAATATAT-TAAAA
1 ATAAATATATATAAAA
2977752 A
1 A
2977753 AATTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATATATATAAAA
Found at i:2978603 original size:21 final size:20
Alignment explanation
Indices: 2978579--2978637 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
2978569 TAGATTATAT
*
2978579 AAATATTATTAATATTTAAA
1 AAATATAATTAATATTTAAA
*
2978599 AAA-ATTACATCAATAATTT-AA
1 AAATA-TA-ATTAAT-ATTTAAA
2978620 AAATATAATTAATATTTA
1 AAATATAATTAATATTTA
2978638 CAACTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 12 0.39
22 5 0.16
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATATAATTAATATTTAAA
Found at i:2978636 original size:19 final size:19
Alignment explanation
Indices: 2978579--2978637 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 19
2978569 TAGATTATAT
*
2978579 AAATATTATTAATATTTAA
1 AAATATAATTAATATTTAA
* *
2978598 AAAAATTACATCAATAATTTAA
1 AAATA-TA-ATTAAT-ATTTAA
2978620 AAATATAATTAATATTTA
1 AAATATAATTAATATTTA
2978638 CAACTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 9 0.28
20 6 0.19
21 7 0.22
22 10 0.31
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATAATTAATATTTAA
Found at i:2978723 original size:22 final size:23
Alignment explanation
Indices: 2978683--2978734 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
2978673 CCATATTTAT
2978683 ATATATATATATTACAAATATAA
1 ATATATATATATTACAAATATAA
*
2978706 ATATACTATAT-TTA-AAATATAT
1 ATATA-TATATATTACAAATATAA
2978728 AT-TATAT
1 ATATATAT
2978735 TCAACAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 2 0.07
22 9 0.33
23 8 0.30
24 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATATATATATTACAAATATAA
Found at i:2980722 original size:18 final size:18
Alignment explanation
Indices: 2980699--2980752 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2980689 TGTCGTATTA
2980699 TATTTATTATTATATTTT
1 TATTTATTATTATATTTT
* *
2980717 TATTTATTAAATATATTAT
1 TATTTATT-ATTATATTTT
*
2980736 AATTT-TATATTATATTT
1 TATTTAT-TATTATATTT
2980753 AAAATTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTATTATTATATTTT
Found at i:2980724 original size:27 final size:24
Alignment explanation
Indices: 2980694--2980753 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2980684 AATGATGTCG
*
2980694 TATTATATTTATTATTATATTTTTA
1 TATTATATTTA-TATTATAATTTTA
**
2980719 T-TTATTAAATATATTATAATTTTA
1 TATTA-TATTTATATTATAATTTTA
2980743 TATTATATTTA
1 TATTATATTTA
2980754 AAATTATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTATATTTATATTATAATTTTA
Found at i:2980749 original size:37 final size:36
Alignment explanation
Indices: 2980694--2980770 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
2980684 AATGATGTCG
** *
2980694 TATTATATTTATTATTATATTTTTATTTATTAAATA
1 TATTATATTTATTATTATATTTAAAATTATTAAATA
*
2980730 TATTATAATTT-TATATTATATTTAAAATTATTAAATT
1 TATTAT-ATTTAT-TATTATATTTAAAATTATTAAATA
2980767 TATT
1 TATT
2980771 TACTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 7 0.20
37 28 0.80
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (36 bp):
TATTATATTTATTATTATATTTAAAATTATTAAATA
Found at i:2980758 original size:19 final size:19
Alignment explanation
Indices: 2980720--2980772 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
2980710 ATATTTTTAT
* *
2980720 TTATTAAATATA-TTATAA
1 TTATTAAATTTATTTAAAA
*
2980738 TT-TTATATTATATTTAAAA
1 TTATTAAATT-TATTTAAAA
2980757 TTATTAAATTTATTTA
1 TTATTAAATTTATTTA
2980773 CTTAATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 13 0.46
20 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTAAATTTATTTAAAA
Found at i:2986781 original size:3 final size:3
Alignment explanation
Indices: 2986775--2986820 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2986765 CAACAACAAC
2986775 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2986821 TTTCAAGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2987085 original size:24 final size:24
Alignment explanation
Indices: 2987047--2987111 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 24
2987037 TGAATTACTA
*
2987047 TTTAATAATA-AATATAATATATATT
1 TTTAATATTATAATATAATA-ATA-T
2987072 TTTAA-ATT-TAATATAA-AATAT
1 TTTAATATTATAATATAATAATAT
2987093 TTTAATATTATAAT-TAATA
1 TTTAATATTATAATATAATA
2987112 GCGAAACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
21 6 0.17
22 9 0.26
23 6 0.17
24 9 0.26
25 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAATATTATAATATAATAATAT
Found at i:2989776 original size:20 final size:20
Alignment explanation
Indices: 2989751--2989799 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
2989741 GGTTCACGAT
*
2989751 AAAATTACCAAAATCAATAC
1 AAAATTACCAAAATCAACAC
2989771 AAAATTATACCAAAATCAACAC
1 AAAA-T-TACCAAAATCAACAC
2989793 AAAATTA
1 AAAATTA
2989800 TACTTGAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 2 0.08
22 18 0.69
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAATTACCAAAATCAACAC
Found at i:2989784 original size:22 final size:22
Alignment explanation
Indices: 2989756--2989802 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2989746 ACGATAAAAT
*
2989756 TACCAAAATCAATACAAAATTA
1 TACCAAAATCAACACAAAATTA
2989778 TACCAAAATCAACACAAAATTA
1 TACCAAAATCAACACAAAATTA
2989800 TAC
1 TAC
2989803 TTGAACATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (22 bp):
TACCAAAATCAACACAAAATTA
Found at i:2991880 original size:2 final size:2
Alignment explanation
Indices: 2991875--2991902 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2991865 GAAAAAAAAA
2991875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2991903 CCATGGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2994755 original size:2 final size:2
Alignment explanation
Indices: 2994748--2994776 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2994738 AAAGCCATTG
2994748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2994777 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2994781 original size:2 final size:2
Alignment explanation
Indices: 2994776--2994813 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2994766 ATATATATAT
2994776 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2994814 TGCTAAGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3002903 original size:2 final size:2
Alignment explanation
Indices: 3002898--3002938 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3002888 TGTAATAACA
3002898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3002939 CCAGAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3003288 original size:2 final size:2
Alignment explanation
Indices: 3003281--3003312 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3003271 GATTCTTTAT
*
3003281 CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3003313 AAAAAAAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3006131 original size:26 final size:24
Alignment explanation
Indices: 3006068--3006122 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
3006058 TCAATAACAT
*
3006068 TAATAATAATAAAAATTAATTATTA
1 TAATAA-AATTAAAATTAATTATTA
3006093 TAATAAAATTAAAATTAATAATATTA
1 TAATAAAATTAAAATTAAT--TATTA
3006119 TAAT
1 TAAT
3006123 TTATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 12 0.44
25 6 0.22
26 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAATAAAATTAAAATTAATTATTA
Found at i:3006235 original size:17 final size:17
Alignment explanation
Indices: 3006213--3006272 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
3006203 TATAATAAAT
*
3006213 TATTAAAACTATAATTA
1 TATTAAAAATATAATTA
*
3006230 TATTAAATAATAAAATGTA
1 TATTAAA-AATATAAT-TA
* *
3006249 -ATTAAAATTATATTTA
1 TATTAAAAATATAATTA
3006265 TATTAAAA
1 TATTAAAA
3006273 GAATTATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 2 0.06
17 19 0.54
18 12 0.34
19 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TATTAAAAATATAATTA
Found at i:3006257 original size:29 final size:28
Alignment explanation
Indices: 3006225--3006311 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 28
3006215 TTAAAACTAT
3006225 AATTATATTAAATAATAAAATGTAATTAA
1 AATTATATTAAATAATAAAAT-TAATTAA
*
3006254 AATTATATTTATATTAA-AAGAATT-ATTAA
1 AATTATA-TTA-AATAATAA-AATTAATTAA
*
3006283 AATTATAGT-AATAATAAAATTATATTAA
1 AATTATATTAAATAATAAAATTA-ATTAA
3006311 A
1 A
3006312 TAATAAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
26 8 0.16
27 2 0.04
28 7 0.14
29 19 0.39
30 6 0.12
31 7 0.14
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
AATTATATTAAATAATAAAATTAATTAA
Found at i:3006266 original size:35 final size:32
Alignment explanation
Indices: 3006194--3006271 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 32
3006184 ATTAAAATAG
*
3006194 TTATATGTATATAATAAATTATTAAAACTATAA
1 TTATAT-TAAATAATAAATTATTAAAACTATAA
* *
3006227 TTATATTAAATAATAAAATGTAATTAAAATTATAT
1 TTATATTAAATAAT-AAAT-T-ATTAAAACTATAA
3006262 TTATATTAAA
1 TTATATTAAA
3006272 AGAATTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
32 7 0.18
33 10 0.26
34 1 0.03
35 21 0.54
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (32 bp):
TTATATTAAATAATAAATTATTAAAACTATAA
Found at i:3006302 original size:17 final size:18
Alignment explanation
Indices: 3006280--3006320 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
3006270 AAAGAATTAT
3006280 TAAAATTATAGT-AATAA
1 TAAAATTATAGTAAATAA
*
3006297 TAAAATTATATTAAATAA
1 TAAAATTATAGTAAATAA
3006315 TAAAAT
1 TAAAAT
3006321 AAATTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAAATTATAGTAAATAA
Found at i:3006315 original size:18 final size:18
Alignment explanation
Indices: 3006225--3006320 Score: 72
Period size: 18 Copynumber: 5.2 Consensus size: 18
3006215 TTAAAACTAT
3006225 AATTATATTAAATAATAA
1 AATTATATTAAATAATAA
* *
3006243 AATGTA-ATTAAA-ATTAT
1 AAT-TATATTAAATAATAA
* *
3006260 ATTTATATTAAAAGAATTATTAA
1 AATTATATT---A-AA-TAATAA
*
3006283 AATTATAGT-AATAATAA
1 AATTATATTAAATAATAA
3006300 AATTATATTAAATAATAA
1 AATTATATTAAATAATAA
3006318 AAT
1 AAT
3006321 AAATTTGAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
16 2 0.03
17 21 0.34
18 22 0.36
19 2 0.03
20 1 0.02
21 2 0.03
23 11 0.18
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AATTATATTAAATAATAA
Found at i:3006706 original size:15 final size:16
Alignment explanation
Indices: 3006673--3006769 Score: 124
Period size: 16 Copynumber: 6.1 Consensus size: 16
3006663 CTGAATCTGT
* *
3006673 ATAAATCTAAATTTGA
1 ATAAATTTAAATTTAA
*
3006689 ATAAATTT-GATTTAA
1 ATAAATTTAAATTTAA
3006704 ATAAATTTAAATTTAA
1 ATAAATTTAAATTTAA
*
3006720 ATAAATTTAAACTTAA
1 ATAAATTTAAATTTAA
* * *
3006736 ATAAAATCAAATATAA
1 ATAAATTTAAATTTAA
3006752 ATAAATTTAAATTTAA
1 ATAAATTTAAATTTAA
3006768 AT
1 AT
3006770 TTATGGTCAA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
15 13 0.19
16 55 0.81
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (16 bp):
ATAAATTTAAATTTAA
Found at i:3006711 original size:10 final size:10
Alignment explanation
Indices: 3006711--3006763 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
3006701 TAAATAAATT
3006711 TAAATTTAAA
1 TAAATTTAAA
3006721 TAAATTTAAA
1 TAAATTTAAA
*
3006731 CTTAAA-TAAAA
1 --TAAATTTAAA
*
3006742 TCAAATATAAA
1 T-AAATTTAAA
3006753 TAAATTTAAA
1 TAAATTTAAA
3006763 T
1 T
3006764 TTAAATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 1 0.03
10 22 0.63
11 8 0.23
12 4 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAATTTAAA
Done.