Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold90
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: 1653315
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.32
Warning! 63894 characters in sequence are not A, C, G, or T
File 7 of 10
Found at i:984777 original size:39 final size:39
Alignment explanation
Indices: 984711--984828 Score: 112
Period size: 39 Copynumber: 3.0 Consensus size: 39
984701 CAAATTCTAT
* ** * * * *
984711 TAAAAAATTTATGTATTAATCACATATTTCAGATTCTAA
1 TAAAAAATCTATACATTAATTATATATTTTAGATTTTAA
* *
984750 TAAATAATCTATACATT-ATTAATATATTTTAAATTTTAA
1 TAAAAAATCTATACATTAATT-ATATATTTTAGATTTTAA
* * *
984789 TAAAAAATTTATATATTAATTATATTTTTTAGATTTTAA
1 TAAAAAATCTATACATTAATTATATATTTTAGATTTTAA
984828 T
1 T
984829 TAATTATAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
38 2 0.03
39 58 0.92
40 3 0.05
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (39 bp):
TAAAAAATCTATACATTAATTATATATTTTAGATTTTAA
Found at i:988288 original size:2 final size:2
Alignment explanation
Indices: 988281--988305 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
988271 TTTCCAGGCA
988281 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
988306 TGTGCAACAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:992292 original size:17 final size:19
Alignment explanation
Indices: 992239--992308 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 19
992229 TAATGTAAAT
* *
992239 AAATACTTT-ATATTT-TT
1 AAATAATTTAATATTTATA
*
992256 AAATTATTTAATATTTATA
1 AAATAATTTAATATTTATA
992275 AAATAATTTAA-A-TTATA
1 AAATAATTTAATATTTATA
* *
992292 ATATAA-TTATTATTTAT
1 AAATAATTTAATATTTAT
992309 GTTTTAGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
16 3 0.07
17 18 0.42
18 11 0.26
19 11 0.26
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATAATTTAATATTTATA
Found at i:992368 original size:147 final size:149
Alignment explanation
Indices: 992108--992415 Score: 337
Period size: 150 Copynumber: 2.1 Consensus size: 149
992098 ATATTTCTAA
* * * *
992108 TAAATTATTATTTTTTATAAAAATAATTTAAATCATATTATAATTATTACATTTTTTATTAATTG
1 TAAATTATTAATATTTATAAAAATAATTTAAATCATAATATAATTATTACATGTTTTATTAATTG
*
992173 ATAAAGAGGATAGAAAGAAAAATATAATAAAGAAAAAAACAAAAAA-TTTAGAAAATTAA-TGTA
66 ATAAAGAGGATAGAAAGAAAAATATAATAAAGAAAAAAACAAAAAATTTTACAAAATTAATTGTA
* *
992236 AATAAATACTTTATATTTT
131 AATAAATAATTTATATGTT
* *
992255 TAAATTATTTAATATTTAT-AAAATAATTTAAATTATAATATAATTATTATTTATGTTTTAGTTA
1 TAAATTA-TTAATATTTATAAAAATAATTTAAATCATAATATAATTATTA--CATGTTTTA-TTA
* * * * * *
992319 ATTTATAAAGATGATA-AAATG-AAGA-A-AA-AAGGAAAAACATAAAACAATTTTTACAAAATT
62 ATTGATAAAGAGGATAGAAA-GAAAAATATAATAAAGAAAAAAACAAAA-AA-TTTTACAAAATT
*
992379 AATTTTAAATAAATAATTTATATGTT
124 AATTGTAAATAAATAATTTATATGTT
*
992405 TATA-TATTAAT
1 TAAATTATTAAT
992416 TATAATTCCA
Statistics
Matches: 135, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
146 13 0.10
147 39 0.29
148 15 0.11
149 27 0.20
150 41 0.30
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (149 bp):
TAAATTATTAATATTTATAAAAATAATTTAAATCATAATATAATTATTACATGTTTTATTAATTG
ATAAAGAGGATAGAAAGAAAAATATAATAAAGAAAAAAACAAAAAATTTTACAAAATTAATTGTA
AATAAATAATTTATATGTT
Found at i:996622 original size:76 final size:77
Alignment explanation
Indices: 996421--996653 Score: 249
Period size: 76 Copynumber: 3.0 Consensus size: 77
996411 ATCCCCGATT
* * * * * * *
996421 ATGAAAAATCGGTGTTCTAGAAATAAAAATTGGGGTTGGAGTATCCCCTCGAAAATAACAGGATT
1 ATGAAAAATTGATGTTTTAGAAAT-AAAACTGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTT
996486 GGAGTATCC-CTG
65 GGAGTATCCTCTG
* * * * *
996498 ATTATAGAAATTAATATTTTAGAAAT-AAAGTCGGGGTTGGGGTATCCCCTCAAAAATAACGGGG
1 ATGA-A-AAATTGATGTTTTAGAAATAAAACT-GGGGTTGGAGTATCCCCTCAAAAATAACGGGG
*
996562 CTGGAGTATCCTC-G
63 TTGGAGTATCCTCTG
* * *
996576 ATGAAAAATTGATGTTTTAGAAATAAAACTGGGGTTGAAGTGTCCCCTCAGAAATAACGGGGTTG
1 ATGAAAAATTGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTG
*
996641 AAGTATCCT-TG
66 GAGTATCCTCTG
996652 AT
1 AT
996654 TGTGGAAAGT
Statistics
Matches: 128, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
76 58 0.45
77 12 0.09
78 43 0.34
79 15 0.12
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (77 bp):
ATGAAAAATTGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTG
GAGTATCCTCTG
Found at i:996701 original size:79 final size:76
Alignment explanation
Indices: 996421--996701 Score: 181
Period size: 76 Copynumber: 3.6 Consensus size: 76
996411 ATCCCCGATT
* * * ** * * **
996421 ATGAAAAATCGGTGTTCTAGAAATAAAAATTGGGGTTGGAGTATCCCCTCGAAAATAACAGGATT
1 ATGAAAAATCGATGTTTTAGAAATAAAAA-TGGAGTTAAAGTATCCCCTCAAAAATAACGGGGCT
*
996486 GGAGTATCC-CTG
65 GAAGTATCCTC-G
* ** * * * ***
996498 ATTATAGAAATTAATATTTTAGAAAT-AAAGTCGGGGTTGGGGTATCCCCTCAAAAATAACGGGG
1 ATGA-A-AAATCGATGTTTTAGAAATAAAAAT-GGAGTTAAAGTATCCCCTCAAAAATAACGGGG
*
996562 CTGGAGTATCCTCG
63 CTGAAGTATCCTCG
* * * * * * *
996576 ATGAAAAATTGATGTTTTAGAAATAAAACTGGGGTTGAAGTGTCCCCTCAGAAATAACGGGGTTG
1 ATGAAAAATCGATGTTTTAGAAATAAAAATGGAGTTAAAGTATCCCCTCAAAAATAACGGGGCTG
*
996641 AAGTATCCTTG
66 AAGTATCCTCG
* * *
996652 ATTGTGGAAAGTCGGTGTTTT-GAAAATAAAAATGGAGTTAAAGTATCCCC
1 A---TGAAAAATCGATGTTTTAG-AAATAAAAATGGAGTTAAAGTATCCCC
996702 GATTATAGAA
Statistics
Matches: 164, Mismatches: 31, Indels: 16
0.78 0.15 0.08
Matches are distributed among these distances:
76 57 0.35
77 9 0.05
78 47 0.29
79 51 0.31
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (76 bp):
ATGAAAAATCGATGTTTTAGAAATAAAAATGGAGTTAAAGTATCCCCTCAAAAATAACGGGGCTG
AAGTATCCTCG
Found at i:996773 original size:51 final size:50
Alignment explanation
Indices: 996667--996802 Score: 143
Period size: 51 Copynumber: 2.7 Consensus size: 50
996657 GGAAAGTCGG
** * *
996667 TGTTTTGAAAATAAAAAT-GGAGTTAAAGTATCCCCGATTATAGAAAGTGGG
1 TGTTTTG-AAAT-AAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATGGA
*
996718 TGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTA-AGAAAAATTGA
1 TGTTTT-GAAATAAAATCGGAGTTGGAGTATCCCCGATTATAG-AAAATGGA
*
996769 TGTTTTGGAAATGAAATCGG-GATTGGAGTATCCC
1 TGTTTT-GAAATAAAATCGGAG-TTGGAGTATCCC
996803 TGAGATGAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
50 8 0.11
51 65 0.88
52 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (50 bp):
TGTTTTGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATGGA
Found at i:999173 original size:13 final size:13
Alignment explanation
Indices: 999155--999180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
999145 ACAAAGATCG
999155 ATGTATCGATACA
1 ATGTATCGATACA
999168 ATGTATCGATACA
1 ATGTATCGATACA
999181 TTGAATAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1001168 original size:12 final size:12
Alignment explanation
Indices: 1001153--1001221 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
1001143 ATTTATAAAA
1001153 ATAATTTAAATT
1 ATAATTTAAATT
* *
1001165 ATAATATAAATG
1 ATAATTTAAATT
**
1001177 A-ATATTTATAAAA
1 ATA-ATTTA-AATT
1001190 ATAATTTAAATT
1 ATAATTTAAATT
*
1001202 ATAATATAAATT
1 ATAATTTAAATT
*
1001214 ATTATTTA
1 ATAATTTA
1001222 TATAAATTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
11 1 0.02
12 34 0.77
13 8 0.18
14 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (12 bp):
ATAATTTAAATT
Found at i:1001187 original size:37 final size:37
Alignment explanation
Indices: 1001140--1001228 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
1001130 TAAATTCTTT
1001140 AATATTTATAAAAATAATTTAAATTATAATATAAATG
1 AATATTTATAAAAATAATTTAAATTATAATATAAATG
*
1001177 AATATTTATAAAAATAATTTAAATTATAATATAAATT
1 AATATTTATAAAAATAATTTAAATTATAATATAAATG
* *
1001214 ATTATTTATATAAAT
1 AATATTTATAAAAAT
1001229 TATTGTTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (37 bp):
AATATTTATAAAAATAATTTAAATTATAATATAAATG
Found at i:1009613 original size:22 final size:21
Alignment explanation
Indices: 1009570--1009610 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1009560 CAAATTTCTT
1009570 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
1009592 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
1009611 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:1011255 original size:35 final size:35
Alignment explanation
Indices: 1011209--1011275 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
1011199 AAGGGGGAGA
*
1011209 GAAAGGAGAAAATATGTGCAAATAATTTTTTTTTT
1 GAAAGGAGAAAATATGTGCAAATAAATTTTTTTTT
1011244 GAAAGGAGAAAATATGTGCAAATAAATTTTTT
1 GAAAGGAGAAAATATGTGCAAATAAATTTTTT
1011276 GATTAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.36
Consensus pattern (35 bp):
GAAAGGAGAAAATATGTGCAAATAAATTTTTTTTT
Found at i:1011284 original size:35 final size:35
Alignment explanation
Indices: 1011209--1011284 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
1011199 AAGGGGGAGA
**
1011209 GAAAGGAGAAAATATGTGCAAATAATTTTTTTTTT
1 GAAAGGAGAAAATATGTGCAAATAATTTTTTGATT
1011244 GAAAGGAGAAAATATGTGCAAATAAATTTTTTGATT
1 GAAAGGAGAAAATATGTGCAAAT-AATTTTTTGATT
1011280 -AAAGG
1 GAAAGG
1011285 GGGAGAATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 28 0.74
36 10 0.26
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (35 bp):
GAAAGGAGAAAATATGTGCAAATAATTTTTTGATT
Found at i:1011908 original size:20 final size:19
Alignment explanation
Indices: 1011884--1011947 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
1011874 CACATTTAAT
1011884 TGTATCGATACATGTTGCA
1 TGTATCGATACATGTTGCA
1011903 TAGTATCGATACA---T---
1 T-GTATCGATACATGTTGCA
1011917 TGTATCGATACATGTTGCA
1 TGTATCGATACATGTTGCA
1011936 TTGTATCGATAC
1 -TGTATCGATAC
1011948 TTGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 22 0.59
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTGCA
Found at i:1011923 original size:13 final size:13
Alignment explanation
Indices: 1011905--1011929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1011895 ATGTTGCATA
1011905 GTATCGATACATT
1 GTATCGATACATT
1011918 GTATCGATACAT
1 GTATCGATACAT
1011930 GTTGCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1011924 original size:33 final size:33
Alignment explanation
Indices: 1011882--1011947 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1011872 TACACATTTA
1011882 ATTGTATCGATACATGTTGCATAGTATCGATAC
1 ATTGTATCGATACATGTTGCATAGTATCGATAC
*
1011915 ATTGTATCGATACATGTTGCATTGTATCGATAC
1 ATTGTATCGATACATGTTGCATAGTATCGATAC
1011948 TTGAAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (33 bp):
ATTGTATCGATACATGTTGCATAGTATCGATAC
Found at i:1012038 original size:13 final size:13
Alignment explanation
Indices: 1012020--1012045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1012010 TACACAAAGT
1012020 ATGTATCGATACA
1 ATGTATCGATACA
1012033 ATGTATCGATACA
1 ATGTATCGATACA
1012046 CCATAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1012062 original size:33 final size:32
Alignment explanation
Indices: 1012002--1012065 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1011992 TAGCCAAACT
*
1012002 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGAATGTATCGATACAA
1012034 TGTATCGATACACCATAA-AATGTATCGATACA
1 TGTATCGATACA-CA-AAGAATGTATCGATACA
1012066 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 15 0.52
34 2 0.07
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAGAATGTATCGATACAA
Found at i:1013444 original size:19 final size:19
Alignment explanation
Indices: 1013397--1013451 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1013387 CTGCCAGTTT
***
1013397 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TAAA
*
1013417 CATGCATCGATACAATAAA
1 CATGTATCGATACAATAAA
1013436 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1013452 GTATCGATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:1014304 original size:22 final size:22
Alignment explanation
Indices: 1014279--1014320 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1014269 TTTTAGTTAT
*
1014279 AAAAATTACATTTTTTTCATCC
1 AAAAAATACATTTTTTTCATCC
**
1014301 AAAAAATGTATTTTTTTCAT
1 AAAAAATACATTTTTTTCAT
1014321 TTAATCAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAAAATACATTTTTTTCATCC
Found at i:1014886 original size:2 final size:2
Alignment explanation
Indices: 1014879--1014935 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
1014869 GAACAAAAAC
* *
1014879 TA TA TA TA TA TA TA TA TA TA AA TA AA TA -A 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
1014920 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1014936 ATGTAATGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1015460 original size:24 final size:23
Alignment explanation
Indices: 1015433--1015478 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1015423 AATGTATTAA
*
1015433 AAAAATTTAAAAATAATTATTTTT
1 AAAAA-TTAAAAATAATGATTTTT
*
1015457 AAAAATTAAAACTAATGATTTT
1 AAAAATTAAAAATAATGATTTT
1015479 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AAAAATTAAAAATAATGATTTTT
Found at i:1016043 original size:20 final size:21
Alignment explanation
Indices: 1016020--1016065 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1016010 ATAAGTTATT
1016020 ATTTTATTAACATT-TAAATA
1 ATTTTATTAACATTATAAATA
* * *
1016040 ATTTTTTTAATATTATTAATA
1 ATTTTATTAACATTATAAATA
1016061 ATTTT
1 ATTTT
1016066 TTATTATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTATTAACATTATAAATA
Found at i:1016103 original size:14 final size:14
Alignment explanation
Indices: 1016084--1016135 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
1016074 TGTTATTATT
1016084 TTAAAATATAAAAA
1 TTAAAATATAAAAA
1016098 TTAAAA-A-AATAAA
1 TTAAAATATAA-AAA
1016111 TTTAATAATATAAAAA
1 -TTAA-AATATAAAAA
1016127 TTAAAATAT
1 TTAAAATAT
1016136 TTTTTATCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.06
13 4 0.12
14 15 0.45
15 6 0.18
16 4 0.12
17 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:1017340 original size:3 final size:3
Alignment explanation
Indices: 1017332--1017368 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1017322 TCACTTTAAA
1017332 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1017369 TTGCATATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1017674 original size:20 final size:20
Alignment explanation
Indices: 1017649--1017725 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
1017639 TTTTCACAAT
*
1017649 TTGTATTGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1017669 TTGTATCGATACATT-TTGCA
1 TTGTATCGATACATTGTT-CA
*
1017689 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
*
1017709 TTGTATCGATATATTGT
1 TTGTATCGATACATTGT
1017726 ATCAATACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.04
20 48 0.94
21 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1017725 original size:33 final size:33
Alignment explanation
Indices: 1017688--1017772 Score: 161
Period size: 33 Copynumber: 2.6 Consensus size: 33
1017678 TACATTTTGC
1017688 ATTGTATCGATACATTGCTCATTGTATCGATAT
1 ATTGTATCGATACATTGCTCATTGTATCGATAT
*
1017721 ATTGTATCAATACATTGCTCATTGTATCGATAT
1 ATTGTATCGATACATTGCTCATTGTATCGATAT
1017754 ATTGTATCGATACATTGCT
1 ATTGTATCGATACATTGCT
1017773 TGAATGTATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.42
Consensus pattern (33 bp):
ATTGTATCGATACATTGCTCATTGTATCGATAT
Found at i:1020138 original size:51 final size:51
Alignment explanation
Indices: 1020076--1020292 Score: 229
Period size: 51 Copynumber: 4.3 Consensus size: 51
1020066 TTTCTTCTCA
* * *
1020076 GGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAATCG
1 GGGATACTCCAACT-CCGATTTTATTTCCAAAACATCAATTTTTCGTAATCG
* * * **
1020127 GGGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGTAATCG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCGTAATCG
* * * * **
1020178 AGGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGTAATCG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCGTAATCG
* * * * ** *
1020229 AGGATACTCCAACTCCGATTTTATTTTCAAAATACCAATTTTTCACAATTG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCGTAATCG
1020280 GGGATACTCCAAC
1 GGGATACTCCAAC
1020293 CCCGTTATTT
Statistics
Matches: 144, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
51 143 0.99
52 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCGTAATCG
Found at i:1020397 original size:28 final size:29
Alignment explanation
Indices: 1020358--1020431 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
1020348 TTCTTTCATA
* *
1020358 ATCGGGGGTACTCTAACCCCGTTATTT-C
1 ATCGGGGATACTCCAACCCCGTTATTTCC
*
1020386 ATCGGGGATACTCCAATCCCGTTATTTCC
1 ATCGGGGATACTCCAACCCCGTTATTTCC
*
1020415 A-AGGGGATACTCCAACC
1 ATCGGGGATACTCCAACC
1020432 TCGATTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTATTTCC
Found at i:1020527 original size:28 final size:27
Alignment explanation
Indices: 1020468--1020541 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
1020458 TTTCACAATT
*
1020468 GGGGATACTCCAACCCCGTTATTTCATC
1 GGGGATACTCTAACCCCGTTATTTCA-C
*
1020496 GGGGATACTCTAACCCTGTTATTTTCGA-
1 GGGGATACTCTAACCCCGTTA-TTTC-AC
*
1020524 GGGGATACTCTAATCCCG
1 GGGGATACTCTAACCCCG
1020542 GCTTTATATC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 35 0.88
29 4 0.10
30 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (27 bp):
GGGGATACTCTAACCCCGTTATTTCAC
Found at i:1020612 original size:110 final size:108
Alignment explanation
Indices: 1020279--1020666 Score: 458
Period size: 110 Copynumber: 3.6 Consensus size: 108
1020269 TTTCACAATT
* * *
1020279 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATATCTAAAACTAT
1 GGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCC-GACTTTATATCTAAAAAT-T
* *
1020344 TGATTTCTTTCATAATCGGGGGTACTCTAACCCCGTTATTTCATC
64 TGATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATC
* * * * *
1020389 GGGGATACTCCAATCCC-GTTATTTCCAAGGGGATACTCCAACCTCGATTTTAT-TTTTAAAATA
1 GGGGATACTCCAA-CCCTGTTATTTCCGAGGGGATACTCCAACC-CGACTTTATATCTAAAAATT
** * * * *
1020452 CCAATT-TTTCACAATTGGGGATACTCCAACCCCGTTATTTCATC
64 TGATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATC
* * * *
1020496 GGGGATACTCTAACCCTGTTATTTTCGAGGGGATACTCTAATCCCGGCTTTATATCTAAAAATGT
1 GGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAA-CCCGACTTTATATCTAAAAAT-T
1020561 TGATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATC
64 TGATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATC
* * * * * *
1020606 GGGGATACTCTAATCTTGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAA
1 GGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAA-CCCGACTTTATATCTAAAA
1020667 TACCAATTTT
Statistics
Matches: 233, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
106 3 0.01
107 74 0.32
108 12 0.05
109 9 0.04
110 131 0.56
111 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (108 bp):
GGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCGACTTTATATCTAAAAATTTG
ATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATC
Found at i:1020614 original size:28 final size:26
Alignment explanation
Indices: 1020578--1020651 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 26
1020568 TTTCATAATA
*
1020578 GGGGGTACTCCAACCCCGTTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTC--C
* * **
1020606 GGGGATACTCTAATCTTGTTATTTCC
1 GGGGATACTCCAACCCCGTTATTTCC
1020632 GAGGAGATACTCCAACCCCG
1 G-GG-GATACTCCAACCCCG
1020652 ATTTTATTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 31 0.89
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (26 bp):
GGGGATACTCCAACCCCGTTATTTCC
Found at i:1020656 original size:217 final size:217
Alignment explanation
Indices: 1020279--1020698 Score: 662
Period size: 217 Copynumber: 1.9 Consensus size: 217
1020269 TTTCACAATT
*
1020279 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATATCTAAAACTAT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATATCTAAAAATAT
* *
1020344 TGATTTCTTTCATAATCGGGGGTACTCTAACCCCGTTATTTCATCGGGGATACTCCAATCCCGTT
66 TGATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATCGGGGATACTCCAATCCCGTT
* * * * *
1020409 ATTTCCAAGGGGATACTCCAACCTCGATTTTATTTTTAAAATACCAATTTTTCACAATTGGGGAT
131 ATTTCCAAGGAGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCGGGGAT
1020474 ACTCCAACCCCGTTATTTCATC
196 ACTCCAACCCCGTTATTTCATC
* * * * *
1020496 GGGGATACTCTAACCCTGTTATTTTCGAGGGGATACTCTAATCCC-GGCTTTATATCTAAAAATG
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCTGGCTTTATATCTAAAAATA
* **
1020560 TTGATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATCGGGGATACTCTAATCTTGT
65 TTGATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATCGGGGATACTCCAATCCCGT
*
1020625 TATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCGGGGA
130 TATTTCCAAGGAGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCGGGGA
*
1020690 TACTTCAAC
195 TACTCCAAC
1020699 TCCAATTTTA
Statistics
Matches: 184, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
217 181 0.98
218 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (217 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATATCTAAAAATAT
TGATTTCTTTCATAATAGGGGGTACTCCAACCCCGTTATTTCATCGGGGATACTCCAATCCCGTT
ATTTCCAAGGAGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCGGGGAT
ACTCCAACCCCGTTATTTCATC
Found at i:1020707 original size:51 final size:51
Alignment explanation
Indices: 1020637--1020752 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
1020627 TTTCCGAGGA
* *
1020637 GATACTCCAACCCCGATTTTA-TTTCTAAAATACCAATTT-TCCACAATCGGG
1 GATACTCCAACCCCAATTTTATTTTC-AAAACACCAATTTCT-CACAATCGGG
* * *
1020688 GATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTCTCACAATTGGG
1 GATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTCTCACAATCGGG
1020739 GATACTCCAACCCC
1 GATACTCCAACCCC
1020753 GTTATTTCTG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 51 0.91
52 5 0.09
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (51 bp):
GATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTCTCACAATCGGG
Found at i:1020820 original size:79 final size:78
Alignment explanation
Indices: 1020686--1020949 Score: 300
Period size: 79 Copynumber: 3.3 Consensus size: 78
1020676 TCCACAATCG
* * * * * * **
1020686 GGGATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTCTCACAATTGGGGATACTCCAACC
1 GGGATACTCCAACCCCGACTTTATTTTCAAAATACCGATTTCTCACAATCAGGGATACTCCAACC
**
1020751 CCGTTA-TTTCTGA
66 CTATTATTTTC-GA
**
1020764 GAGGATACTCCAACCCCGACTTTA-TTTCTAAAATATTGATTTCTCACAATCAGGGATACTCCAA
1 G-GGATACTCCAACCCCGACTTTATTTTC-AAAATACCGATTTCTCACAATCAGGGATACTCCAA
1020828 CCCTATTATTTTCGTA
64 CCCTATTATTTTCG-A
* *
1020844 GGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTT-TCTATAATCAGGGATACTCCAAC
1 GGGATACTCCAACCCCGACTTTATTTTCAAAATACCGATTTCTC-ACAATCAGGGATACTCCAAC
1020908 CCTATTATTTTCGA
65 CCTATTATTTTCGA
* * *
1020922 GGAGTTACTCCAACCCCGATTTTTTTTT
1 GG-GATACTCCAACCCCGACTTTATTTT
1020950 GTTATTTCTA
Statistics
Matches: 161, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
78 10 0.06
79 141 0.88
80 10 0.06
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (78 bp):
GGGATACTCCAACCCCGACTTTATTTTCAAAATACCGATTTCTCACAATCAGGGATACTCCAACC
CTATTATTTTCGA
Found at i:1029669 original size:2 final size:2
Alignment explanation
Indices: 1029662--1029691 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1029652 CACCTTTAGA
1029662 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
1029692 TCATAACATT
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:1031294 original size:31 final size:31
Alignment explanation
Indices: 1031251--1031311 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1031241 TTCTTTTTTC
*
1031251 TTTTTTTGCTTTCATACTGTTAAATATGATT
1 TTTTTTTGCTTTCAAACTGTTAAATATGATT
*
1031282 TTTTTTTTCTTTCAAACTGTTAAATATGAT
1 TTTTTTTGCTTTCAAACTGTTAAATATGAT
1031312 GATCTGATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (31 bp):
TTTTTTTGCTTTCAAACTGTTAAATATGATT
Found at i:1032755 original size:2 final size:2
Alignment explanation
Indices: 1032748--1032802 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1032738 ACTTGCTTAC
1032748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1032790 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1032803 AATCTGGTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1034989 original size:6 final size:6
Alignment explanation
Indices: 1034980--1035009 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1034970 GTGAAAGTAG
*
1034980 GGGCAG GGGCAA GGGCAA GGGCAA GGGCAA
1 GGGCAA GGGCAA GGGCAA GGGCAA GGGCAA
1035010 CTTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.53, T:0.00
Consensus pattern (6 bp):
GGGCAA
Found at i:1035469 original size:25 final size:25
Alignment explanation
Indices: 1035435--1035487 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1035425 GGGTCTTGCA
1035435 CCAGACTCAAGTTCAATAATATGAT
1 CCAGACTCAAGTTCAATAATATGAT
1035460 CCAGACTCAAGTTCAATAATATGAT
1 CCAGACTCAAGTTCAATAATATGAT
1035485 CCA
1 CCA
1035488 CCTTTAGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (25 bp):
CCAGACTCAAGTTCAATAATATGAT
Found at i:1038036 original size:3 final size:3
Alignment explanation
Indices: 1038028--1038070 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1038018 GAAAGGTTTA
*
1038028 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1038071 GTATTAAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1044429 original size:3 final size:3
Alignment explanation
Indices: 1044421--1044468 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1044411 TCTTTCTCAA
1044421 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1044469 CTGTAGAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1050237 original size:1 final size:1
Alignment explanation
Indices: 1050231--1050256 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1050221 GGCACCGACC
1050231 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1050257 GAGAAAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1050380 original size:15 final size:15
Alignment explanation
Indices: 1050356--1050471 Score: 64
Period size: 15 Copynumber: 7.7 Consensus size: 15
1050346 TTTAAATATA
1050356 AATATAAAATATATTT
1 AATAT-AAATATATTT
1050372 AATATAAATATATTT
1 AATATAAATATATTT
* *
1050387 AATTTTAAA-ATTTTT
1 AA-TATAAATATATTT
*
1050402 AATAT--AT-T-TTA
1 AATATAAATATATTT
*
1050413 AAAATTAAATTATTATTT
1 AATA-TAAA-TA-TATTT
*
1050431 ATATTTAAATATATATT
1 A-ATATAAATATAT-TT
* *
1050448 AA-ATAAAAATATTA
1 AATATAAATATATTT
1050462 AATATAAATA
1 AATATAAATA
1050472 CTTAAAAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
11 5 0.07
12 3 0.04
14 6 0.08
15 34 0.45
16 14 0.18
17 6 0.08
18 7 0.09
19 1 0.01
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATAAATATATTT
Found at i:1050461 original size:13 final size:13
Alignment explanation
Indices: 1050443--1050481 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1050433 ATTTAAATAT
1050443 ATATTAAATAAAA
1 ATATTAAATAAAA
*
1050456 ATATTAAATATAA
1 ATATTAAATAAAA
1050469 ATACTTAAA-AAAA
1 ATA-TTAAATAAAA
1050482 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATTAAATAAAA
Found at i:1055438 original size:33 final size:33
Alignment explanation
Indices: 1055396--1055462 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1055386 GCGGCTGGGG
* *
1055396 CATAACATCGACCACTTTGGGTTAGGTGACTTA
1 CATAACATCGACCACTTTAGGTTAGATGACTTA
1055429 CATAACATCGACCACTTTAGGTTAGATGACTTA
1 CATAACATCGACCACTTTAGGTTAGATGACTTA
1055462 C
1 C
1055463 CCCAAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (33 bp):
CATAACATCGACCACTTTAGGTTAGATGACTTA
Found at i:1062820 original size:18 final size:18
Alignment explanation
Indices: 1062797--1062904 Score: 58
Period size: 21 Copynumber: 5.3 Consensus size: 18
1062787 ATCTTCTTCT
1062797 CTCCTCCTCCTATCATCC
1 CTCCTCCTCCTATCATCC
*
1062815 CTCCT-CTCTCTATTATCTTTC
1 CTCCTCCTC-CTATCATC---C
1062836 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
*
1062857 CTCCTATCTCTACTATC-TCTC
1 CTCC--TC-CTCCTATCATC-C
1062878 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
1062899 CTCCTC
1 CTCCTC
1062905 TCTCTTCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 32
0.66 0.04 0.30
Matches are distributed among these distances:
17 3 0.04
18 16 0.23
19 4 0.06
20 4 0.06
21 22 0.31
22 4 0.06
23 4 0.06
24 10 0.14
25 3 0.04
ACGTcount: A:0.10, C:0.47, G:0.02, T:0.41
Consensus pattern (18 bp):
CTCCTCCTCCTATCATCC
Found at i:1062846 original size:42 final size:42
Alignment explanation
Indices: 1062800--1062918 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1062790 TTCTTCTCTC
* *
1062800 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTTTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1062842 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1062884 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1062919 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1062859 original size:12 final size:11
Alignment explanation
Indices: 1062834--1062908 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 11
1062824 CTATTATCTT
*
1062834 TCCTGTCTCTCC
1 TCCTATCTC-CC
1062846 TCCTATCATCCC
1 TCCTATC-TCCC
1062858 TCCTATCT--C
1 TCCTATCTCCC
*
1062867 TACTATCT--C
1 TCCTATCTCCC
*
1062876 TCCTGTCTCTCC
1 TCCTATCTC-CC
1062888 TCCTATCATCCC
1 TCCTATC-TCCC
*
1062900 TCCTCTCTC
1 TCCTATCTC
1062909 TTCTTTCTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
9 15 0.29
11 3 0.06
12 30 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.48, G:0.03, T:0.40
Consensus pattern (11 bp):
TCCTATCTCCC
Found at i:1067343 original size:4 final size:4
Alignment explanation
Indices: 1067334--1067372 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
1067324 AAACAAATCA
*
1067334 AAAT AAAT AAAT AAAT AAAT GAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1067373 CACCTCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1068531 original size:50 final size:49
Alignment explanation
Indices: 1068456--1068590 Score: 198
Period size: 50 Copynumber: 2.7 Consensus size: 49
1068446 AAAAATGCCT
* *
1068456 GAATGTATCGATATATTGAGAAATGTATCGATACATCTAGGTAAAACCAA
1 GAATGTATCGATACAATGA-AAATGTATCGATACATCTAGGTAAAACCAA
* * *
1068506 GAATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAACACCCA
1 GAATGTATCGATACAATGAA-AATGTATCGATACATCTAGGTAAAACCAA
1068556 GAATGTATCGATACAATGAAGAATGTATCGATACA
1 GAATGTATCGATACAATGAA-AATGTATCGATACA
1068591 AATTGTGAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 1 0.01
50 77 0.99
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (49 bp):
GAATGTATCGATACAATGAAAATGTATCGATACATCTAGGTAAAACCAA
Found at i:1074380 original size:20 final size:22
Alignment explanation
Indices: 1074336--1074389 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 22
1074326 TTCAACAAAT
1074336 TGTATCGATACA-ATAGGGTAA
1 TGTATCGATACATATAGGGTAA
*
1074357 TGTATCGATACATA-AGTG-AA
1 TGTATCGATACATATAGGGTAA
1074377 TGTATCGATACAT
1 TGTATCGATACAT
1074390 GTCTTAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 15 0.48
21 15 0.48
22 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (22 bp):
TGTATCGATACATATAGGGTAA
Found at i:1074560 original size:52 final size:51
Alignment explanation
Indices: 1074446--1074562 Score: 146
Period size: 52 Copynumber: 2.3 Consensus size: 51
1074436 CTAGAATGAA
*
1074446 AATGTATCGATACATTCTGGGCTTTGACCCAAATGAATCGATACATTCTTC
1 AATGTATCGATACATTCTGGGCTTTGACCCAAATGAATCGATACATCCTTC
* ** * *
1074497 ATTGTATCGATACATTCTAGGTTTTTGACCTAAATGTATCGATACATCCATT-
1 AATGTATCGATACATTCT-GGGCTTTGACCCAAATGAATCGATACATCC-TTC
*
1074549 AATGTAACGATACA
1 AATGTATCGATACA
1074563 AGCAAGCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 17 0.30
52 37 0.66
53 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (51 bp):
AATGTATCGATACATTCTGGGCTTTGACCCAAATGAATCGATACATCCTTC
Found at i:1086011 original size:57 final size:57
Alignment explanation
Indices: 1085935--1086255 Score: 288
Period size: 57 Copynumber: 5.6 Consensus size: 57
1085925 TATGACTTAA
* * * * *
1085935 TGGCATCCCTTCTCAAAGTCTACAACTTCGTGGCACCCCTTTTAAAGTCCACAACTTTG
1 TGGCA-CCCTT-TTAAAGTCCATAACTCCGTGGCACCCCTTTTAAAGTCCACAACTTCG
** ** * * *
1085994 TGGTGCCCTTTTAAAGTCCATAACTTTGTGGCACCTCTTTTAAAGTCCATAACTCCG
1 TGGCACCCTTTTAAAGTCCATAACTCCGTGGCACCCCTTTTAAAGTCCACAACTTCG
* * ** * * *
1086051 TGGCACCCTTTTAAAGTCTAAAACTTTGCGGTA-CCC-TTTAAAGTCCACAACTTCA
1 TGGCACCCTTTTAAAGTCCATAACTCCGTGGCACCCCTTTTAAAGTCCACAACTTCG
* * * *
1086106 TGGCACCTACTTTTTAAGTCCATAACTCCATAGCA-CCCTTTTAAAGTCCACAACTCCG
1 TGGCACC--CTTTTAAAGTCCATAACTCCGTGGCACCCCTTTTAAAGTCCACAACTTCG
*** * * * *
1086164 TGGCATATTTTTAAAGTCCATAACTCCGTGACAGCCCTTTTAAAGTCCATAACTTCA
1 TGGCACCCTTTTAAAGTCCATAACTCCGTGGCACCCCTTTTAAAGTCCACAACTTCG
* * *
1086221 TGGCACCTTTTTAAAGTCCACAACTCCTTGGCACC
1 TGGCACCCTTTTAAAGTCCATAACTCCGTGGCACC
1086256 TGTCACAACG
Statistics
Matches: 211, Mismatches: 47, Indels: 10
0.79 0.18 0.04
Matches are distributed among these distances:
55 23 0.11
56 23 0.11
57 135 0.64
58 27 0.13
59 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.31
Consensus pattern (57 bp):
TGGCACCCTTTTAAAGTCCATAACTCCGTGGCACCCCTTTTAAAGTCCACAACTTCG
Found at i:1086076 original size:85 final size:85
Alignment explanation
Indices: 1085965--1086245 Score: 341
Period size: 85 Copynumber: 3.3 Consensus size: 85
1085955 TACAACTTCG
* *
1085965 TGGCACCCCTTTTAAAGTCCACAACTTTGTGGTGCCCTTTTAAAGTCCATAACTTTGTGGCACCT
1 TGGCA-CCCTTTTAAAGTCCACAACTTTGTGGTACCCTTTTAAAGTCCATAACTTCGTGGCACCT
*
1086030 CTTTTAAAGTCCATAACTCCG
65 CTTTTAAAGTCCATAACTCCA
* * * * *
1086051 TGGCACCCTTTTAAAGTCTAAAACTTTGCGGTACCC-TTTAAAGTCCACAACTTCATGGCACCTA
1 TGGCACCCTTTTAAAGTCCACAACTTTGTGGTACCCTTTTAAAGTCCATAACTTCGTGGCACCT-
*
1086115 CTTTTTAAGTCCATAACTCCA
65 CTTTTAAAGTCCATAACTCCA
* ** * *** * *
1086136 TAGCACCCTTTTAAAGTCCACAACTCCGTGGCATATTTTTAAAGTCCATAACTCCGTGACAGCC-
1 TGGCACCCTTTTAAAGTCCACAACTTTGTGGTACCCTTTTAAAGTCCATAACTTCGTGGCA-CCT
*
1086200 CTTTTAAAGTCCATAACTTCA
65 CTTTTAAAGTCCATAACTCCA
*
1086221 TGGCACCTTTTTAAAGTCCACAACT
1 TGGCACCCTTTTAAAGTCCACAACT
1086246 CCTTGGCACC
Statistics
Matches: 165, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
84 24 0.15
85 114 0.69
86 25 0.15
87 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (85 bp):
TGGCACCCTTTTAAAGTCCACAACTTTGTGGTACCCTTTTAAAGTCCATAACTTCGTGGCACCTC
TTTTAAAGTCCATAACTCCA
Found at i:1086256 original size:28 final size:28
Alignment explanation
Indices: 1085935--1086255 Score: 275
Period size: 28 Copynumber: 11.2 Consensus size: 28
1085925 TATGACTTAA
* * *
1085935 TGGCATCCCTTCTCAAAGTCTACAACTTCG
1 TGGCA-CCCTT-TTAAAGTCCACAACTCCG
**
1085965 TGGCACCCCTTTTAAAGTCCACAACTTTG
1 TGGCA-CCCTTTTAAAGTCCACAACTCCG
** * **
1085994 TGGTGCCCTTTTAAAGTCCATAACTTTG
1 TGGCACCCTTTTAAAGTCCACAACTCCG
*
1086022 TGGCACCTCTTTTAAAGTCCATAACTCCG
1 TGGCACC-CTTTTAAAGTCCACAACTCCG
* * **
1086051 TGGCACCCTTTTAAAGTCTAAAACTTTG
1 TGGCACCCTTTTAAAGTCCACAACTCCG
* * * *
1086079 CGGTACCC-TTTAAAGTCCACAACTTCA
1 TGGCACCCTTTTAAAGTCCACAACTCCG
* * *
1086106 TGGCACCTACTTTTTAAGTCCATAACTCCA
1 TGGCACC--CTTTTAAAGTCCACAACTCCG
*
1086136 TAGCACCCTTTTAAAGTCCACAACTCCG
1 TGGCACCCTTTTAAAGTCCACAACTCCG
*** *
1086164 TGGCATATTTTTAAAGTCCATAACTCCG
1 TGGCACCCTTTTAAAGTCCACAACTCCG
* * * *
1086192 TGACAGCCCTTTTAAAGTCCATAACTTCA
1 TGGCA-CCCTTTTAAAGTCCACAACTCCG
* *
1086221 TGGCACCTTTTTAAAGTCCACAACTCCT
1 TGGCACCCTTTTAAAGTCCACAACTCCG
1086249 TGGCACC
1 TGGCACC
1086256 TGTCACAACG
Statistics
Matches: 240, Mismatches: 46, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
27 20 0.08
28 121 0.50
29 67 0.28
30 32 0.13
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.31
Consensus pattern (28 bp):
TGGCACCCTTTTAAAGTCCACAACTCCG
Found at i:1087272 original size:79 final size:78
Alignment explanation
Indices: 1087143--1087318 Score: 187
Period size: 79 Copynumber: 2.2 Consensus size: 78
1087133 CCCTTGGAGT
* *
1087143 ACGGAGTTGGAGTGCATCCCTCGATGAAAAATTTAATACTTTGGAGATAAAAACGGGATAGGAGT
1 ACGGAGTTGGAGT--ATCCCTCGATGAAAAATTTAATACTTTGAAAATAAAAACGGGATAGGAGT
* * *
1087208 ATCCTCT-TGAAAATA
64 AGCCTATAAG-AAATA
* * * *
1087223 ATGGAGTTGGAGTATCCC-CGA-GACAAAAGTTTTAATATTTTGAAAATAAAAACGGGGTTGGAG
1 ACGGAGTTGGAGTATCCCTCGATGA-AAAA--TTTAATACTTTGAAAATAAAAACGGGATAGGAG
1087286 TAGCCTATAAGAAATA
63 TAGCCTATAAGAAATA
*
1087302 ACGGGGTTGGAGTATCC
1 ACGGAGTTGGAGTATCC
1087319 ATAAAACGAG
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
76 2 0.02
77 7 0.09
78 5 0.06
79 54 0.67
80 13 0.16
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (78 bp):
ACGGAGTTGGAGTATCCCTCGATGAAAAATTTAATACTTTGAAAATAAAAACGGGATAGGAGTAG
CCTATAAGAAATA
Found at i:1087378 original size:29 final size:28
Alignment explanation
Indices: 1087346--1087400 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1087336 TTGTTGTACA
* *
1087346 AAAAAAAACTAGGGTTGGAGTATCCCCTC
1 AAAAAAAACGA-GGTTGAAGTATCCCCTC
*
1087375 AAAAATAACGAGGTTGAAGTATCCCC
1 AAAAAAAACGAGGTTGAAGTATCCCC
1087401 GAAGGTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (28 bp):
AAAAAAAACGAGGTTGAAGTATCCCCTC
Found at i:1087501 original size:28 final size:28
Alignment explanation
Indices: 1087432--1087504 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
1087422 TGGAAATATA
*
1087432 AATGGGGTTAGAGTATCTCCTCGAAAAC
1 AATGGGGTTAGAGTATCTCCTCAAAAAC
** * * *
1087460 AACAGGGCTGGAGTATCTCCTTAAAAAC
1 AATGGGGTTAGAGTATCTCCTCAAAAAC
1087488 AATGGGGTTAGAGTATC
1 AATGGGGTTAGAGTATC
1087505 CCTGATGGTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (28 bp):
AATGGGGTTAGAGTATCTCCTCAAAAAC
Found at i:1090228 original size:21 final size:21
Alignment explanation
Indices: 1090183--1090235 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1090173 GCAGTATGCA
1090183 GTATCGATAC-ATTCACTTAT
1 GTATCGATACAATTCACTTAT
*
1090203 GTATCGATACAATT-ACTATTT
1 GTATCGATACAATTCACT-TAT
1090224 GTATCGATACAA
1 GTATCGATACAA
1090236 ATTATAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (21 bp):
GTATCGATACAATTCACTTAT
Found at i:1090391 original size:27 final size:27
Alignment explanation
Indices: 1090331--1090391 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
1090321 TCTATAGTAC
*
1090331 CCCTTTAAAGTCCACAACTTCATGGCA
1 CCCTTTTAAGTCCACAACTTCATGGCA
** *
1090358 CATTTTTAAGTCCATAACTTCATGGCA
1 CCCTTTTAAGTCCACAACTTCATGGCA
1090385 CCCTTTT
1 CCCTTTT
1090392 CAAAGCTCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTTCATGGCA
Found at i:1090391 original size:28 final size:28
Alignment explanation
Indices: 1090329--1090405 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 28
1090319 TGTCTATAGT
*
1090329 ACCCCTTTAAAGTCCACAACTTCATGGC
1 ACCCTTTTAAAGTCCACAACTTCATGGC
* * *
1090357 A-CATTTTTAAGTCCATAACTTCATGGC
1 ACCCTTTTAAAGTCCACAACTTCATGGC
1090384 ACCCTTTTCAAAGCTCACACAA
1 ACCCTTTT-AAAG-TC-CACAA
1090406 GTCGGTGGCA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 23 0.61
28 6 0.16
29 3 0.08
30 2 0.05
31 4 0.11
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.29
Consensus pattern (28 bp):
ACCCTTTTAAAGTCCACAACTTCATGGC
Found at i:1090474 original size:33 final size:31
Alignment explanation
Indices: 1090380--1090606 Score: 224
Period size: 31 Copynumber: 7.2 Consensus size: 31
1090370 CATAACTTCA
* *
1090380 TGGCACCCTTTTCAAAGCTCACACAAGTCGG
1 TGGCAACCTTTTCAAAGCCCACACAAGTCGG
* *
1090411 TGGCAACCTTCTCAAAGCCCACACAGGTCGG
1 TGGCAACCTTTTCAAAGCCCACACAAGTCGG
* * *
1090442 TGGTAACTCTTTTCAAAAGTCCACACATGTCGG
1 TGGCAAC-CTTTTC-AAAGCCCACACAAGTCGG
* *
1090475 TGGCAACCTTCTCAAAGCCCACACAAGTTGG
1 TGGCAACCTTTTCAAAGCCCACACAAGTCGG
*
1090506 TGGCAACCCTTTTCAAAAGCCCACACAAGTCGA
1 TGGCAA-CCTTTTC-AAAGCCCACACAAGTCGG
* * * **
1090539 TGGTAACCCTTTCCAAACCCCACACAAGTCCA
1 TGGCAA-CCTTTTCAAAGCCCACACAAGTCGG
* *
1090571 TGGCAATCC-TTTCAAAAACCCA-ACAAGTCAG
1 TGGCAA-CCTTTTC-AAAGCCCACACAAGTCGG
1090602 TGGCA
1 TGGCA
1090607 TCTTCTTCTA
Statistics
Matches: 165, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
31 69 0.42
32 46 0.28
33 50 0.30
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (31 bp):
TGGCAACCTTTTCAAAGCCCACACAAGTCGG
Found at i:1090487 original size:64 final size:63
Alignment explanation
Indices: 1090380--1090606 Score: 248
Period size: 64 Copynumber: 3.6 Consensus size: 63
1090370 CATAACTTCA
*
1090380 TGGC-ACCCTTTTC-AAAGCTCACACAAGTCGGTGGCAACCTTCTCAAAGCCCACACAGGTCGG
1 TGGCAACCCTTTTCAAAAGC-CACACAAGTCGGTGGCAACCTTCTCAAAGCCCACACAAGTCGG
* * * *
1090442 TGGTAACTCTTTTCAAAAGTCCACACATGTCGGTGGCAACCTTCTCAAAGCCCACACAAGTTGG
1 TGGCAACCCTTTTCAAAAG-CCACACAAGTCGGTGGCAACCTTCTCAAAGCCCACACAAGTCGG
* * * *
1090506 TGGCAACCCTTTTCAAAAGCCCACACAAGTCGATGGTAACCCTT-TCCAAACCCCACACAAGTCC
1 TGGCAACCCTTTTCAAAAG-CCACACAAGTCGGTGGCAA-CCTTCT-CAAAGCCCACACAAGTCG
*
1090570 A
63 G
* * *
1090571 TGGCAATCC-TTTCAAAAACC-CAACAAGTCAGTGGCA
1 TGGCAACCCTTTTCAAAAGCCAC-ACAAGTCGGTGGCA
1090607 TCTTCTTCTA
Statistics
Matches: 139, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
62 4 0.03
63 21 0.15
64 86 0.62
65 28 0.20
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (63 bp):
TGGCAACCCTTTTCAAAAGCCACACAAGTCGGTGGCAACCTTCTCAAAGCCCACACAAGTCGG
Found at i:1090757 original size:52 final size:52
Alignment explanation
Indices: 1090674--1090976 Score: 238
Period size: 52 Copynumber: 5.8 Consensus size: 52
1090664 CATCTCTTTC
* * * * *
1090674 TAAGTCCAATGTTGCTAGCCTCGAATCAGTACATTGGCACTCTTCTT-ATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTCTT-TTCATCTT
* * * *
1090726 TAAGTCCAATGTCGTTGGCCTTGAATTAGTACATAAGCAC-CTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTCTTT-TCATCTT
** * * * * * * *
1090778 TAAGTCTGATATCACTAGCCTTGAATCAGCATATTGGCAC-CTTTATAATTTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTCTTT-TCATCTT
* ** * * *
1090830 TAAGCCCAATGTCATTGGCCTTGAATCAACACATTAGCATTCTTCTCAT-TT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTCTTTTCATCTT
* * * * *
1090881 TAAGTCCAATGTTGCTGGCTTTGAATTAGCACATTAGCATTTTTTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTCTTTTCATCTT
* * **
1090933 TAAGTCCGATGTCGCTGG-CTGTGAATCAACGTATTAGCACTCTT
1 TAAGTCCAATGTCGCTGGCCT-TGAATCAGCACATTAGCACTCTT
1090977 CTCACCCTTA
Statistics
Matches: 195, Mismatches: 51, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
50 1 0.01
51 47 0.24
52 144 0.74
53 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (52 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTCTTTTCATCTT
Found at i:1090905 original size:51 final size:51
Alignment explanation
Indices: 1090827--1090980 Score: 173
Period size: 51 Copynumber: 3.0 Consensus size: 51
1090817 CCTTTATAAT
* ** *
1090827 TTTTAAGCCCAATGTCATTGGCCTTGAATCAACACATTAGCATTCTTCTCA
1 TTTTAAGTCCAATGTCGCTGGCTTTGAATCAACACATTAGCATTCTTCTCA
* * * * *
1090878 TTTTAAGTCCAATGTTGCTGGCTTTGAATTAGCACATTAGCATTTTTTTCA
1 TTTTAAGTCCAATGTCGCTGGCTTTGAATCAACACATTAGCATTCTTCTCA
* * ** *
1090929 TCTTTAAGTCCGATGTCGCTGGCTGTGAATCAACGTATTAGCACTCTTCTCA
1 T-TTTAAGTCCAATGTCGCTGGCTTTGAATCAACACATTAGCATTCTTCTCA
1090981 CCCTTATCAT
Statistics
Matches: 83, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 43 0.52
52 40 0.48
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (51 bp):
TTTTAAGTCCAATGTCGCTGGCTTTGAATCAACACATTAGCATTCTTCTCA
Found at i:1095874 original size:39 final size:40
Alignment explanation
Indices: 1095815--1095896 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 40
1095805 ATGCGCTTGA
*
1095815 CCCTGGCGATAGGGCGAATGAGGCGTGCCCCACTTAAT-T
1 CCCTAGCGATAGGGCGAATGAGGCGTGCCCCACTTAATAT
1095854 CCCTAGCGATAGGGCGAATGAGGCGTGCCCCACTTAATAT
1 CCCTAGCGATAGGGCGAATGAGGCGTGCCCCACTTAATAT
1095894 CCC
1 CCC
1095897 CACTTCAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 37 0.90
40 4 0.10
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (40 bp):
CCCTAGCGATAGGGCGAATGAGGCGTGCCCCACTTAATAT
Found at i:1102005 original size:2 final size:2
Alignment explanation
Indices: 1101998--1102024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1101988 ATTATATGTG
1101998 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 T
1102025 TCTAAAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1104231 original size:22 final size:20
Alignment explanation
Indices: 1104182--1104257 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
1104172 AAAAACCCAG
1104182 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATGAGA
1104202 AATGTATCGATACAATTGTA-A
1 AATGTATCGATACAA-TG-AGA
* * **
1104223 GCATGTATCGATACATTGACT
1 -AATGTATCGATACAATGAGA
*
1104244 AATGTATTGATACA
1 AATGTATCGATACA
1104258 TTTCCTTAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
20 28 0.60
21 5 0.11
22 14 0.30
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:1109399 original size:31 final size:31
Alignment explanation
Indices: 1109361--1109450 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
1109351 TTATGGGAAC
**
1109361 AATTTAAGCTCATGTTTAAGAGCAATATGAT
1 AATTTAAGCTCATACTTAAGAGCAATATGAT
* * * *
1109392 AGTTTAAGCTCTTACTTAGGAGCATTATGAT
1 AATTTAAGCTCATACTTAAGAGCAATATGAT
* *
1109423 AATTTAAGCTTATACCTAAGAGCAATAT
1 AATTTAAGCTCATACTTAAGAGCAATAT
1109451 TTTTTATTTA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (31 bp):
AATTTAAGCTCATACTTAAGAGCAATATGAT
Found at i:1110978 original size:22 final size:22
Alignment explanation
Indices: 1110952--1110995 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1110942 ATATTTGATA
*
1110952 ATTTTTACCTTAGTAAAAAAAT
1 ATTTTTACCATAGTAAAAAAAT
* *
1110974 ATTTTTAGCATAGTAAACAAAT
1 ATTTTTACCATAGTAAAAAAAT
1110996 GGTGGAGGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (22 bp):
ATTTTTACCATAGTAAAAAAAT
Found at i:1115953 original size:13 final size:13
Alignment explanation
Indices: 1115935--1115960 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1115925 ACATTAGTTT
1115935 TGTATCGATACAA
1 TGTATCGATACAA
1115948 TGTATCGATACAA
1 TGTATCGATACAA
1115961 AGCTACCTCA
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1124063 original size:30 final size:32
Alignment explanation
Indices: 1124006--1124176 Score: 165
Period size: 32 Copynumber: 5.5 Consensus size: 32
1123996 CCAAAAGCCT
* *
1124006 ACGACTCAGTGGCA-C-CCTT-CTCAAAGTCC
1 ACGACTCAGTGGCATCATCTTCCTCCAAGTCC
** *
1124035 ATAACTCAGTGGAATC-TCTT-CTCCAAGTCC
1 ACGACTCAGTGGCATCATCTTCCTCCAAGTCC
*
1124065 ACGACTCAGTGGCATCATTTTCCTCCAAGTCC
1 ACGACTCAGTGGCATCATCTTCCTCCAAGTCC
* * * *
1124097 ATGACTTAGTGGCATCATTTTCCTCTAAGTCC
1 ACGACTCAGTGGCATCATCTTCCTCCAAGTCC
* * *
1124129 ACGACTCAGTGGCATCCTTTTGCTTCCAAGT-C
1 ACGACTCAGTGGCATCATCTT-CCTCCAAGTCC
*
1124161 ACGACTTAGTGGCATC
1 ACGACTCAGTGGCATC
1124177 CTTTTTCTTC
Statistics
Matches: 120, Mismatches: 18, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.09
30 26 0.22
31 3 0.03
32 73 0.61
33 7 0.06
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (32 bp):
ACGACTCAGTGGCATCATCTTCCTCCAAGTCC
Found at i:1124095 original size:32 final size:32
Alignment explanation
Indices: 1124029--1124216 Score: 179
Period size: 32 Copynumber: 5.9 Consensus size: 32
1124019 ACCCTTCTCA
** * *
1124029 AAGTCCATAACTCAGTGGAATC-TCTT-CTCC
1 AAGTCCACGACTCAGTGGCATCATTTTCCTCC
1124059 AAGTCCACGACTCAGTGGCATCATTTTCCTCC
1 AAGTCCACGACTCAGTGGCATCATTTTCCTCC
* * *
1124091 AAGTCCATGACTTAGTGGCATCATTTTCCTCT
1 AAGTCCACGACTCAGTGGCATCATTTTCCTCC
* *
1124123 AAGTCCACGACTCAGTGGCATCCTTTTGCTTCC
1 AAGTCCACGACTCAGTGGCATCATTTT-CCTCC
* * * *
1124156 AAGT-CACGACTTAGTGGCATCCTTTTTCTTCT
1 AAGTCCACGACTCAGTGGCAT-CATTTTCCTCC
* *
1124188 AAGTCCACAACTCTA-TGGCA-CTTTTTCCT
1 AAGTCCACGACTC-AGTGGCATCATTTTCCT
1124217 TTTTAAAGCT
Statistics
Matches: 134, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.14
31 11 0.08
32 80 0.60
33 23 0.17
34 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.34
Consensus pattern (32 bp):
AAGTCCACGACTCAGTGGCATCATTTTCCTCC
Found at i:1124136 original size:64 final size:63
Alignment explanation
Indices: 1124029--1124216 Score: 204
Period size: 64 Copynumber: 3.0 Consensus size: 63
1124019 ACCCTTCTCA
* * * * *
1124029 AAGTCCATAACTCAGTGGAATCTCTT-CTCCAAGTCCACGACTCAGTGGCATCATTTTCCTCC
1 AAGTCCATGACTTAGTGGCATCTTTTCCTCTAAGTCCACGACTCAGTGGCATCATTTTCCTCC
* *
1124091 AAGTCCATGACTTAGTGGCATCATTTTCCTCTAAGTCCACGACTCAGTGGCATCCTTTTGCTTCC
1 AAGTCCATGACTTAGTGGCATC-TTTTCCTCTAAGTCCACGACTCAGTGGCATCATTTT-CCTCC
* * * *
1124156 AAGT-CACGACTTAGTGGCATCCTTTTTCTTCTAAGTCCACAACTCTA-TGGCA-CTTTTTCCT
1 AAGTCCATGACTTAGTGGCAT-C-TTTTCCTCTAAGTCCACGACTC-AGTGGCATCATTTTCCT
1124217 TTTTAAAGCT
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
62 19 0.18
63 5 0.05
64 49 0.45
65 34 0.31
66 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.34
Consensus pattern (63 bp):
AAGTCCATGACTTAGTGGCATCTTTTCCTCTAAGTCCACGACTCAGTGGCATCATTTTCCTCC
Found at i:1124193 original size:65 final size:64
Alignment explanation
Indices: 1124059--1124216 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 64
1124049 TCTCTTCTCC
*
1124059 AAGTCCACGACTCAGTGGCATCATTTTCCTCCAAGTCCATGACTTAGTGGCATCATTTTCCTCT
1 AAGTCCACGACTCAGTGGCATCATTTTCCTCCAAGTCCACGACTTAGTGGCATCATTTTCCTCT
* * * *
1124123 AAGTCCACGACTCAGTGGCATCCTTTTGCTTCCAAGT-CACGACTTAGTGGCATCCTTTTTCTTC
1 AAGTCCACGACTCAGTGGCATCATTTT-CCTCCAAGTCCACGACTTAGTGGCAT-CATTTTCCTC
1124187 T
64 T
* *
1124188 AAGTCCACAACTCTA-TGGCA-CTTTTTCCT
1 AAGTCCACGACTC-AGTGGCATCATTTTCCT
1124217 TTTTAAAGCT
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.02
64 46 0.55
65 34 0.41
66 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (64 bp):
AAGTCCACGACTCAGTGGCATCATTTTCCTCCAAGTCCACGACTTAGTGGCATCATTTTCCTCT
Found at i:1124257 original size:35 final size:34
Alignment explanation
Indices: 1124211--1124278 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1124201 TATGGCACTT
*
1124211 TTTCCTTTTTAAAG-CTCACAACTCCGTGGCACCCC
1 TTTCCCTTTT-AAGTCT-ACAACTCCGTGGCACCCC
*
1124246 TTTCCCTTTTAAGTCTACAACTCCGTGGGACCC
1 TTTCCCTTTTAAGTCTACAACTCCGTGGCACCC
1124279 TTCTCAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 19 0.63
35 11 0.37
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.32
Consensus pattern (34 bp):
TTTCCCTTTTAAGTCTACAACTCCGTGGCACCCC
Found at i:1124632 original size:27 final size:27
Alignment explanation
Indices: 1124465--1124630 Score: 215
Period size: 27 Copynumber: 6.1 Consensus size: 27
1124455 TGACACTTCT
* *
1124465 CACCCTTTTAAGCCCACGACTCCATGT
1 CACCCTTTTAAGCCCATGACTCCATGG
* * *
1124492 CACCCTTTTATGGCCATAACTCCATGG
1 CACCCTTTTAAGCCCATGACTCCATGG
* *
1124519 CGCCCTTTTAAGCCCATGACTCTATGG
1 CACCCTTTTAAGCCCATGACTCCATGG
*
1124546 CACCCTTTTAAGCCCACGACTCCATGG
1 CACCCTTTTAAGCCCATGACTCCATGG
**
1124573 CACCCTTTTAAGCCCATGACTCTGTGG
1 CACCCTTTTAAGCCCATGACTCCATGG
* * *
1124600 CACCTTTTTAAGTCCATAACTCCATGG
1 CACCCTTTTAAGCCCATGACTCCATGG
1124627 CACC
1 CACC
1124631 TTCTTCTTTT
Statistics
Matches: 118, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 118 1.00
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.28
Consensus pattern (27 bp):
CACCCTTTTAAGCCCATGACTCCATGG
Found at i:1124692 original size:32 final size:32
Alignment explanation
Indices: 1124605--1124702 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
1124595 TGTGGCACCT
* *
1124605 TTTTAAGTCCATAACTCCATGGCACCTTCTTC
1 TTTTAAGTCCATAACTCCGTGGCACCTTTTTC
* * *
1124637 TTTTCAAAGCCCACAACTCCGTGGAACCTTTTTC
1 TTTT--AAGTCCATAACTCCGTGGCACCTTTTTC
* *
1124671 TTTTAAGTCTATAACTCCGTGGCACCCTTTTC
1 TTTTAAGTCCATAACTCCGTGGCACCTTTTTC
1124703 AAAGCCCACA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 27 0.50
34 27 0.50
ACGTcount: A:0.21, C:0.31, G:0.11, T:0.37
Consensus pattern (32 bp):
TTTTAAGTCCATAACTCCGTGGCACCTTTTTC
Found at i:1124730 original size:32 final size:32
Alignment explanation
Indices: 1124689--1124757 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
1124679 CTATAACTCC
1124689 GTGGC-ACCCTTTTC-AAAGCCCACACAAGTCG
1 GTGGCAACCC-TTTCAAAAGCCCACACAAGTCG
* *
1124720 GTGGCAACCCTTTCAAAAGCCCACACGAGTTG
1 GTGGCAACCCTTTCAAAAGCCCACACAAGTCG
1124752 GTGGCA
1 GTGGCA
1124758 TCTATTTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 9 0.26
32 25 0.74
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (32 bp):
GTGGCAACCCTTTCAAAAGCCCACACAAGTCG
Found at i:1124889 original size:52 final size:52
Alignment explanation
Indices: 1124830--1125214 Score: 283
Period size: 52 Copynumber: 7.5 Consensus size: 52
1124820 CCAATGTCTC
* * *
1124830 TGGCCTTGAATCAGCTTATTAGCATCTTCAATATTCCTAAGTCC-AACATCGT
1 TGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAG-CCTAATATCGT
* * * * *
1124882 TGGCCTTGAATCAACACATTGGGACCCTT--ATCA-TCTTTAAGCCTAATATCGT
1 TGGCCTTGAATCAGCATATTGGCA-TCTTCAAT-ATTC-CTAAGCCTAATATCGT
* *
1124934 TGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAGCCTAATGTCGC
1 TGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAGCCTAATATCGT
* * * * * * *
1124986 TAGCCTTGAATCAGCACATTGGTACCTTC-AT-TT-TTAAGTCC-GATATCAT
1 TGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAG-CCTAATATCGT
* * *
1125035 TGGCCTTGAATCAGCATATTGGCATCTTTAATATTCCTAAGCCTAATGTTGT
1 TGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAGCCTAATATCGT
* * * * * *
1125087 TGGCCTTGAATCAGTACATTGGCATTCTTC--TCTTCTTCAAGACTAATTTCGT
1 TGGCCTTGAATCAGCATATTGGCA-TCTTCAATATTCCT-AAGCCTAATATCGT
* * * * * * *
1125139 T-GCCTGTAAATCAGCACATTGACATTCTTCGCATCTT--TAAGCCCAATATCGC
1 TGGCCT-TGAATCAGCATATTGGCA-TCTTC-AATATTCCTAAGCCTAATATCGT
*
1125191 TAGCCTTGAATCAGCATATTGGCA
1 TGGCCTTGAATCAGCATATTGGCA
1125215 CCCTTGTCAT
Statistics
Matches: 262, Mismatches: 52, Indels: 38
0.74 0.15 0.11
Matches are distributed among these distances:
49 32 0.12
50 6 0.02
51 24 0.09
52 180 0.69
53 16 0.06
55 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.35
Consensus pattern (52 bp):
TGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAGCCTAATATCGT
Found at i:1124947 original size:104 final size:100
Alignment explanation
Indices: 1124760--1125108 Score: 416
Period size: 101 Copynumber: 3.4 Consensus size: 100
1124750 TGGTGGCATC
* * * * * *
1124760 TATTTCTAAG-CTCAATGTCGCTGGCCTTGAATTAGCACTTTAGCACCTTCATCTTTAAGTCCAA
1 TATTCCTAAGCCT-AATGTCGTTGGCCTTGAATCAGCACATTGGGACCTTCATCTTTAAGTCCAA
* * *
1124824 TGTCTCTGGCCTTGAATCAGCTTATTAGCATCTTCAA
65 TATCT-TGGCCTTGAATCAGCATATTGGCATCTTCAA
** *
1124861 TATTCCTAAGTCC-AACATCGTTGGCCTTGAATCAACACATTGGGACCCTTATCATCTTTAAG-C
1 TATTCCTAAG-CCTAATGTCGTTGGCCTTGAATCAGCACATTGGGA-CC-T-TCATCTTTAAGTC
1124924 CTAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCAA
62 C-AATATC-TTGGCCTTGAATCAGCATATTGGCATCTTCAA
* * * * *
1124965 TATTCCTAAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGTACCTTCATTTTTAAGTCCGAT
1 TATTCCTAAGCCTAATGTCGTTGGCCTTGAATCAGCACATTGGGACCTTCATCTTTAAGTCCAAT
*
1125030 ATCATTGGCCTTGAATCAGCATATTGGCATCTTTAA
66 ATC-TTGGCCTTGAATCAGCATATTGGCATCTTCAA
* *
1125066 TATTCCTAAGCCTAATGTTGTTGGCCTTGAATCAGTACATTGG
1 TATTCCTAAGCCTAATGTCGTTGGCCTTGAATCAGCACATTGG
1125109 CATTCTTCTC
Statistics
Matches: 213, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
101 118 0.55
102 5 0.02
103 8 0.04
104 81 0.38
105 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (100 bp):
TATTCCTAAGCCTAATGTCGTTGGCCTTGAATCAGCACATTGGGACCTTCATCTTTAAGTCCAAT
ATCTTGGCCTTGAATCAGCATATTGGCATCTTCAA
Found at i:1125061 original size:101 final size:100
Alignment explanation
Indices: 1124760--1125267 Score: 427
Period size: 104 Copynumber: 4.9 Consensus size: 100
1124750 TGGTGGCATC
* * * *
1124760 TATTTCTAAG-CTCAATGTCGCTGGCCTTGAATTAGCACTTTAGCACCTTCATCTTTAAGTCCAA
1 TATTCCTAAGCCT-AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* * *
1124824 TGTCTCTGGCCTTGAATCAGCTTATTAGCATCTTCAA
65 TATCT-TGGCCTTGAATCAGCATATTGGCATCTTCAA
** * * *
1124861 TATTCCTAAGTCC-AACATCGTTGGCCTTGAATCAACACATTGGGACCCTTATCATCTTTAAG-C
1 TATTCCTAAG-CCTAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CC-T-TCATCTTTAAGTC
1124924 CTAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCAA
62 C-AATATC-TTGGCCTTGAATCAGCATATTGGCATCTTCAA
* * * *
1124965 TATTCCTAAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGTACCTTCATTTTTAAGTCCGAT
1 TATTCCTAAGCCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
*
1125030 ATCATTGGCCTTGAATCAGCATATTGGCATCTTTAA
66 ATC-TTGGCCTTGAATCAGCATATTGGCATCTTCAA
* * * * *
1125066 TATTCCTAAGCCTAATGTTGTTGGCCTTGAATCAGTACATTGGCATTCTTC-TCTTCTTCAAGAC
1 TATTCCTAAGCCTAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCATC-T-TT-AAGTC
* * * * * *
1125130 TAATTTCGTT-GCCTGTAAATCAGCACATTGACATTCTTCGCA
62 CAATATC-TTGGCCT-TGAATCAGCATATTGGCA-TCTTC-AA
* * * * * *
1125172 TCTT--TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCCTTGTCATCTTTTAAGGC
1 TATTCCTAAGCCTAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CC-T-TCATC-TTTAAGTC
* * * *
1125235 CAATGTCACTGGCCTTGAATTAGCATAATGGCA
62 CAATATC-TTGGCCTTGAATCAGCATATTGGCA
1125268 CAAGCCCAAT
Statistics
Matches: 328, Mismatches: 59, Indels: 36
0.78 0.14 0.09
Matches are distributed among these distances:
101 120 0.37
102 10 0.03
103 14 0.04
104 139 0.42
105 29 0.09
106 12 0.04
107 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (100 bp):
TATTCCTAAGCCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
ATCTTGGCCTTGAATCAGCATATTGGCATCTTCAA
Found at i:1125153 original size:205 final size:206
Alignment explanation
Indices: 1124763--1125267 Score: 556
Period size: 205 Copynumber: 2.4 Consensus size: 206
1124753 TGGCATCTAT
* * * * *
1124763 TTCTAAG-CTCAATGTCGCTGGCCTTGAATTAGCACTTTAGCACCTTCATCTTTAAGTCCAATGT
1 TTCTAAGCCT-AATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATGT
* *
1124827 C-TCTGGCCTTGAATCAGCTTATTAGCATCTTCAATATTCCTAAGTCCAACATCGTTGGCCTTGA
65 CAT-TGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAGTCCAACATCGTTGGCCTTGA
* * * * * *
1124891 ATCAACACATTGGGACCCTTATCATCTTTAAGCCTAATATCGTTGGCCTTGAATCAGCATATTGG
129 ATCAACACATTGGCACCCTTATCATCTTCAAGACTAATATCGTTGGCCTTAAATCAGCACATTGA
1124956 CA-TCTTC-AATA
194 CATTCTTCGAATA
* * *
1124967 TTCCTAAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGTACCTTCATTTTTAAGTCCGATAT
1 TT-CTAAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATGT
* ** *
1125032 CATTGGCCTTGAATCAGCATATTGGCATCTTTAATATTCCTAAG-CCTAATGTTGTTGGCCTTGA
65 CATTGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAGTCC-AACATCGTTGGCCTTGA
** ** * * *
1125096 ATCAGTACATTGGCATTCTTCTCTTCTTCAAGACTAATTTCGTT-GCCTGTAAATCAGCACATTG
129 ATCAACACATTGGCACCCTTATCATCTTCAAGACTAATATCGTTGGCCT-TAAATCAGCACATTG
* *
1125160 ACATTCTTCGCATC
193 ACATTCTTCGAATA
* * * *
1125174 TT-TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCCTTGTCATCTTTTAAGGCCAA
1 TTCTAAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCA-CC-T-TCAT-TTTTAAGTCCAA
* * *
1125238 TGTCACTGGCCTTGAATTAGCATAATGGCA
62 TGTCATTGGCCTTGAATCAGCATATTGGCA
1125268 CAAGCCCAAT
Statistics
Matches: 251, Mismatches: 39, Indels: 17
0.82 0.13 0.06
Matches are distributed among these distances:
204 8 0.03
205 188 0.75
206 10 0.04
207 5 0.02
208 4 0.02
209 36 0.14
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (206 bp):
TTCTAAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATGTC
ATTGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAGTCCAACATCGTTGGCCTTGAAT
CAACACATTGGCACCCTTATCATCTTCAAGACTAATATCGTTGGCCTTAAATCAGCACATTGACA
TTCTTCGAATA
Found at i:1125353 original size:49 final size:49
Alignment explanation
Indices: 1125275--1125854 Score: 356
Period size: 49 Copynumber: 11.7 Consensus size: 49
1125265 GCACAAGCCC
* *
1125275 AATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCT
1 AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCT
* *
1125324 ACTATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGTCT
1 AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCT
* * * * * *
1125373 AATGTCAGTTGGCCGTGAATCAGCACATTGACATTCTTCGCATCTTTAAGCCT
1 AATATC-GCTGGCCTTGAATCAGCACATTGGCA-CCTT--CATCTTTAAGTCT
* * * * * *
1125426 AATATCACTAGCCTTGAATCAACATATTGGCACCCTTGTCATCTTTTAAGACC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCA-CC-T-TCATC-TTTAAGTCT
* * * **
1125479 AATGTCACTGGCCTTGAATCAGCACGTTGG------CA----TAACCCT
1 AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCT
* * *
1125518 AATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCT
* * * * * *
1125567 ACTGTCGTTGGCCTTGAATCAGCACATTGACACC-TCAAACTTTAAGTCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTTTAAGTCT
* * * *
1125616 ACTATCACTGGCCTTGAATTAGCACATTGGCACTTTCATCTTTAAGTCT
1 AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCT
* * * * * * * * *
1125665 GATATCGCTGGCCTTAAATCAGCATATTGGCATCTTTAAT-TCCTATGCCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCATCT-TTAAGTCT
* * * * * *
1125715 AATGTCGCTGGCATTGAATCAACACATTGGCATTCTTCTCATCTTCAAGGCT
1 AATATCGCTGGCCTTGAATCAGCACATTGGCA--CCT-TCATCTTTAAGTCT
* * * * * * * * * *
1125767 AATGTCGTTGGTCGTGAATCAACACATTGACATTCTGTGCATATTTAAGCCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCA-CCT-T-CATCTTTAAGTCT
* * **
1125819 AATATCGTTGGCCTTGAATCCGCATGTTGGCACCTT
1 AATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1125855 AATCATTGTT
Statistics
Matches: 407, Mismatches: 99, Indels: 49
0.73 0.18 0.09
Matches are distributed among these distances:
39 29 0.07
44 2 0.00
45 2 0.00
48 2 0.00
49 157 0.39
50 61 0.15
51 12 0.03
52 90 0.22
53 51 0.13
54 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (49 bp):
AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCT
Found at i:1125468 original size:243 final size:243
Alignment explanation
Indices: 1124777--1125696 Score: 812
Period size: 243 Copynumber: 3.7 Consensus size: 243
1124767 AAGCTCAATG
* * * *
1124777 TCGCTGGCCTTGAATTAGCACT-TTAGCACCTTCATCTTTAAGTCCAATGTC-TCTGGCCTTGAA
1 TCGCTGGCCTTGAATCAGCA-TATTGGCACCTTCATCTTTAAGTCTACTGTCGT-TGGCCTTGAA
** * * * * * * * *
1124840 TCAGCTTATTAGCATCTTCAATATTCCTAAGTCCAACATC-GTTGGCCTTGAATCAACACATTGG
64 TCAGCACATTGGCACCTTC-ATCTT--TAAGTCTAATATCAGTTGGCCGTGAATCAGCACATTGA
* ** ** * * *
1124904 GACCCTTATCATCTTTAAGCCTAATATCGTTGGCCTTGAATCAGCATATTGGCA-TC-T-TCAAT
126 CATTCTTCGCATCTTTAAGCCTAATATCGCTAGCCTTGAATCAGCATATTGGCACCCTTGTC-AT
* * * * * * * *
1124966 ATTCCTAAG-CCTAATGTCGCTAGCCTTGAATCAGCACATTGGTACCTTCATTTTTAAGTCC-GA
190 CTT-TTAAGACC-AATGTCACTGGCCTTGAATCAGCACAATGG------CA----CAA-CCCTAA
1125029 TA
242 TA
** * * * * * *
1125031 TCATTGGCCTTGAATCAGCATATTGGCATCTTTAATATTCCTAAGCCTAATGTTGTTGGCCTTGA
1 TCGCTGGCCTTGAATCAGCATATTGGCA-CCTTCATCTT--TAAGTCTACTGTCGTTGGCCTTGA
* * * * *
1125096 ATCAGTACATTGGCATTCTTC-TCTTCTTCAAGACTAATTTC-GTT-GCCTGTAAATCAGCACAT
63 ATCAGCACATTGGCA-CCTTCATC-T-TT-AAGTCTAATATCAGTTGGCC-GTGAATCAGCACAT
*
1125158 TGACATTCTTCGCATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCCTTGTC
123 TGACATTCTTCGCATCTTTAAGCCTAATATCGCTAGCCTTGAATCAGCATATTGGCACCCTTGTC
* * *
1125223 ATCTTTTAAGGCCAATGTCACTGGCCTTGAATTAGCATAATGGCACAAGCCC-AATA
188 ATCTTTTAAGACCAATGTCACTGGCCTTGAATCAGCACAATGGCACAA-CCCTAATA
* * * *
1125279 TTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTACTATCGCTGGCCTTAAATC
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTACTGTCGTTGGCCTTGAATC
*
1125344 AGCACATTGGCACCTTCATCTTTAAGTCTAATGTCAGTTGGCCGTGAATCAGCACATTGACATTC
66 AGCACATTGGCACCTTCATCTTTAAGTCTAATATCAGTTGGCCGTGAATCAGCACATTGACATTC
* *
1125409 TTCGCATCTTTAAGCCTAATATCACTAGCCTTGAATCAACATATTGGCACCCTTGTCATCTTTTA
131 TTCGCATCTTTAAGCCTAATATCGCTAGCCTTGAATCAGCATATTGGCACCCTTGTCATCTTTTA
** *
1125474 AGACCAATGTCACTGGCCTTGAATCAGCACGTTGGCATAACCCTAATA
196 AGACCAATGTCACTGGCCTTGAATCAGCACAATGGCACAACCCTAATA
* *
1125522 TCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCACTGTCGTTGGCCTTGAATC
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTACTGTCGTTGGCCTTGAATC
* * * * * * * *
1125587 AGCACATTGACACC-TCAAACTTTAAGTCCACTATCA-CTGGCCTTGAATTAGCACATTGGCA--
66 AGCACATTGGCACCTTC-ATCTTTAAGTCTAATATCAGTTGGCCGTGAATCAGCACATTGACATT
* * * * *
1125648 CTT-TCATCTTTAAGTCTGATATCGCTGGCCTTAAATCAGCATATTGGCA
130 CTTCGCATCTTTAAGCCTAATATCGCTAGCCTTGAATCAGCATATTGGCA
1125697 TCTTTAATTC
Statistics
Matches: 557, Mismatches: 90, Indels: 53
0.80 0.13 0.08
Matches are distributed among these distances:
239 39 0.07
240 3 0.01
242 36 0.06
243 213 0.38
244 8 0.01
245 34 0.06
247 7 0.01
248 33 0.06
252 2 0.00
253 1 0.00
254 22 0.04
255 7 0.01
256 5 0.01
257 101 0.18
258 37 0.07
259 7 0.01
260 2 0.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (243 bp):
TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTACTGTCGTTGGCCTTGAATC
AGCACATTGGCACCTTCATCTTTAAGTCTAATATCAGTTGGCCGTGAATCAGCACATTGACATTC
TTCGCATCTTTAAGCCTAATATCGCTAGCCTTGAATCAGCATATTGGCACCCTTGTCATCTTTTA
AGACCAATGTCACTGGCCTTGAATCAGCACAATGGCACAACCCTAATA
Found at i:1125474 original size:53 final size:49
Alignment explanation
Indices: 1124780--1125268 Score: 216
Period size: 52 Copynumber: 9.5 Consensus size: 49
1124770 CTCAATGTCG
* * * * *
1124780 CTGGCCTTGAATTAGCACTTTAGCACCTTCATCTTTAAGTCC-AATGTCT
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAG-CCTAATATCA
** * * * * *
1124829 CTGGCCTTGAATCAGCTTATTAGCATCTTCAATATTCCTAAGTCC-AACATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTT--TAAG-CCTAATATCA
* * * *
1124881 TTGGCCTTGAATCAACACATTGGGACCCTTATCATCTTTAAGCCTAATATCG
1 CTGGCCTTGAATCAGCACATTGGCA-CC-T-TCATCTTTAAGCCTAATATCA
* * * * * *
1124933 TTGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAGCCTAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTT--TAAGCCTAATATCA
* * * *
1124985 CTAGCCTTGAATCAGCACATTGGTACCTTCATTTTTAAGTCC-GATATCA
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAG-CCTAATATCA
* * * * * * **
1125034 TTGGCCTTGAATCAGCATATTGGCATCTTTAATATTCCTAAGCCTAATGTTG
1 CTGGCCTTGAATCAGCACATTGGCA-CCTTCATCTT--TAAGCCTAATATCA
* * * * *
1125086 TTGGCCTTGAATCAGTACATTGGCATTCTTC-TCTTCTTCAAGACTAATTTC-
1 CTGGCCTTGAATCAGCACATTGGCA-CCTTCATC-T-TT-AAGCCTAATATCA
* * * * * * *
1125137 GTTGCCTGTAAATCAGCACATTGACATTCTTCGCATCTTTAAGCCCAATATCG
1 CTGGCCT-TGAATCAGCACATTGGCA-CCTT--CATCTTTAAGCCTAATATCA
* * *
1125190 CTAGCCTTGAATCAGCATATTGGCACCCTTGTCATCTTTTAAGGCC-AATGTCA
1 CTGGCCTTGAATCAGCACATTGGCA-CC-T-TCATC-TTTAA-GCCTAATATCA
* * *
1125243 CTGGCCTTGAATTAGCATAATGGCAC
1 CTGGCCTTGAATCAGCACATTGGCAC
1125269 AAGCCCAATA
Statistics
Matches: 340, Mismatches: 73, Indels: 51
0.73 0.16 0.11
Matches are distributed among these distances:
49 56 0.16
50 18 0.05
51 16 0.05
52 193 0.57
53 42 0.12
54 11 0.03
55 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (49 bp):
CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGCCTAATATCA
Found at i:1125493 original size:53 final size:49
Alignment explanation
Indices: 1124780--1125696 Score: 468
Period size: 49 Copynumber: 18.5 Consensus size: 49
1124770 CTCAATGTCG
* * * * *
1124780 CTGGCCTTGAATTAGCACTTTAGCACCTTCATCTTTAAGTCCAATGTCT
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
** * * * * *
1124829 CTGGCCTTGAATCAGCTTATTAGCATCTTCAATATTCCTAAGTCCAACATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTT--TAAGTCCAATATCA
* * * *
1124881 TTGGCCTTGAATCAACACATTGGGACCCTTATCATCTTTAAG-CCTAATATCG
1 CTGGCCTTGAATCAGCACATTGGCA-CC-T-TCATCTTTAAGTCC-AATATCA
* * * * * *
1124933 TTGGCCTTGAATCAGCATATTGGCATCTTCAATATTCCTAAG-CCTAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTT--TAAGTCC-AATATCA
* * * *
1124985 CTAGCCTTGAATCAGCACATTGGTACCTTCATTTTTAAGTCCGATATCA
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
* * * * * * **
1125034 TTGGCCTTGAATCAGCATATTGGCATCTTTAATATTCCTAAG-CCTAATGTTG
1 CTGGCCTTGAATCAGCACATTGGCA-CCTTCATCTT--TAAGTCC-AATATCA
* * * * * *
1125086 TTGGCCTTGAATCAGTACATTGGCATTCTTC-TCTTCTTCAAGACTAATTTC-
1 CTGGCCTTGAATCAGCACATTGGCA-CCTTCATC-T-TT-AAGTCCAATATCA
* * * * * * *
1125137 GTTGCCTGTAAATCAGCACATTGACATTCTTCGCATCTTTAAGCCCAATATCG
1 CTGGCCT-TGAATCAGCACATTGGCA-CCTT--CATCTTTAAGTCCAATATCA
* * * *
1125190 CTAGCCTTGAATCAGCATATTGGCACCCTTGTCATCTTTTAAGGCCAATGTCA
1 CTGGCCTTGAATCAGCACATTGGCA-CC-T-TCATC-TTTAAGTCCAATATCA
* * * * **
1125243 CTGGCCTTGAATTAGCATAATGG------CA-C---AAGCCCAATATTG
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
* * * *
1125282 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCTACTATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
* * *
1125331 CTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGTCTAATGTCA
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
* * * *
1125380 GTTGGCCGTGAATCAGCACATTGACATTCTTCGCATCTTTAAG-CCTAATATCA
1 -CTGGCCTTGAATCAGCACATTGGCA-CCTT--CATCTTTAAGTCC-AATATCA
* * * * *
1125433 CTAGCCTTGAATCAACATATTGGCACCCTTGTCATCTTTTAAGACCAATGTCA
1 CTGGCCTTGAATCAGCACATTGGCA-CC-T-TCATC-TTTAAGTCCAATATCA
* * *
1125486 CTGGCCTTGAATCAGCACGTTGG------CA----TAA-CCCTAATATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC-AATATCA
* * * * *
1125525 CTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCACTGTCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
* * * *
1125574 TTGGCCTTGAATCAGCACATTGACACC-TCAAACTTTAAGTCCACTATCA
1 CTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTTTAAGTCCAATATCA
* * ** *
1125623 CTGGCCTTGAATTAGCACATTGGCACTTTCATCTTTAAGTCTGATATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
* *
1125672 CTGGCCTTAAATCAGCATATTGGCA
1 CTGGCCTTGAATCAGCACATTGGCA
1125697 TCTTTAATTC
Statistics
Matches: 671, Mismatches: 137, Indels: 120
0.72 0.15 0.13
Matches are distributed among these distances:
38 2 0.00
39 58 0.09
43 1 0.00
44 4 0.01
45 4 0.01
46 1 0.00
48 2 0.00
49 215 0.32
50 43 0.06
51 19 0.03
52 215 0.32
53 92 0.14
54 11 0.02
55 4 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (49 bp):
CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
Found at i:1125827 original size:52 final size:52
Alignment explanation
Indices: 1125711--1125838 Score: 123
Period size: 52 Copynumber: 2.5 Consensus size: 52
1125701 TAATTCCTAT
* * ** * * *
1125711 GCCCAATGTCGCTGGCATTGAATCAACACATTGGCATTCTTCTCATCTTCAA
1 GCCCAATATCGTTGGCCGTGAATCAACACATTGACATTCTTCGCATATTCAA
* * * * *
1125763 GGCTAATGTCGTTGGTCGTGAATCAACACATTGACATTCTGT-GCATATTTAA
1 GCCCAATATCGTTGGCCGTGAATCAACACATTGACATTCT-TCGCATATTCAA
*
1125815 GCCCAATATCGTTGGCCTTGAATC
1 GCCCAATATCGTTGGCCGTGAATC
1125839 CGCATGTTGG
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
52 59 0.98
53 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (52 bp):
GCCCAATATCGTTGGCCGTGAATCAACACATTGACATTCTTCGCATATTCAA
Found at i:1128055 original size:31 final size:31
Alignment explanation
Indices: 1128017--1128078 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1128007 GGATTCTGTA
1128017 AATGAGTTCGTGACACTCATACCACTCTTTC
1 AATGAGTTCGTGACACTCATACCACTCTTTC
1128048 AATGAGTTCGTGACACTCATACCACTCTTTC
1 AATGAGTTCGTGACACTCATACCACTCTTTC
1128079 CCTTTTGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (31 bp):
AATGAGTTCGTGACACTCATACCACTCTTTC
Found at i:1133462 original size:21 final size:21
Alignment explanation
Indices: 1133436--1133477 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1133426 CTCCTTGCAC
*
1133436 TTCATTTATTTTC-TTTTTTAA
1 TTCA-TTATTTTCATTTGTTAA
1133457 TTCATTATTTTCATTTGTTAA
1 TTCATTATTTTCATTTGTTAA
1133478 AATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (21 bp):
TTCATTATTTTCATTTGTTAA
Found at i:1139664 original size:195 final size:193
Alignment explanation
Indices: 1139330--1139720 Score: 667
Period size: 195 Copynumber: 2.0 Consensus size: 193
1139320 CCAATAAACT
*
1139330 TTACAAACAAATCTCGCACAAATTGAAAAAAAAAACAATGAAAGTGAAAGAAAATAAGAATAATG
1 TTACAAACAAATCTCGCACAAATTG-AAAAAAAAACAATGAAAGTGAAAGAAAATAAAAATAATG
* *
1139395 AACTGAGGTATTTATAATAGAGCAAACTAATTTATGCATTAGTTTCACATTTTTTCGCACTTTGT
65 AACTGAGGTATTTATAATAGAGCAAAATAATTTATACATTAGTTTCACATTTTTTCGCACTTTGT
1139460 CGTGTCATTAATCAATTTTTTTCTATCATGCCAGAAAGAATTTGAGACCCCATGCAACTGTCATA
130 CGTGTCATTAATCAA-TTTTTT-TATCATGCCAGAAAGAATTTGAGA-CCCATGCAACTGTCATA
1139525 TC
192 TC
*
1139527 TTACAAACAAATCTCGCACAAATTG-AAAAAAAATAATGAAAGTGAAAGAAAATAAAAATAATGA
1 TTACAAACAAATCTCGCACAAATTGAAAAAAAAACAATGAAAGTGAAAGAAAATAAAAATAATGA
* *
1139591 ACTGAGGTATTTATAATAGAGTAAAATAATTTATACATTAGTTTCACATTTTTTCTCACTTTGTC
66 ACTGAGGTATTTATAATAGAGCAAAATAATTTATACATTAGTTTCACATTTTTTCGCACTTTGTC
* *
1139656 GTGTCATTAATCAATTTTTTTATCGTGTCAGAAAGAATTTGAGACCCATGCAACTGTCATATC
131 GTGTCATTAATCAATTTTTTTATCATGCCAGAAAGAATTTGAGACCCATGCAACTGTCATATC
1139719 TT
1 TT
1139721 TTGGGTTCTA
Statistics
Matches: 186, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
192 21 0.11
193 22 0.12
194 6 0.03
195 112 0.60
197 25 0.13
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (193 bp):
TTACAAACAAATCTCGCACAAATTGAAAAAAAAACAATGAAAGTGAAAGAAAATAAAAATAATGA
ACTGAGGTATTTATAATAGAGCAAAATAATTTATACATTAGTTTCACATTTTTTCGCACTTTGTC
GTGTCATTAATCAATTTTTTTATCATGCCAGAAAGAATTTGAGACCCATGCAACTGTCATATC
Found at i:1139824 original size:87 final size:87
Alignment explanation
Indices: 1139700--1139911 Score: 280
Period size: 87 Copynumber: 2.4 Consensus size: 87
1139690 GAATTTGAGA
* * * *
1139700 CCCATGCAACTGTCATATCTTTTGGGTTCTAAGAAATTTATAAGGCATTAGTCAAATATTTTTTG
1 CCCATGCATCTGTCATATC-TTCGGGTTCTAAGAAATTCATAAGGCATTAGTCAAATATTTTCTG
1139765 TAATGTCAAAAGGAATCTAATAC
65 TAATGTCAAAAGGAATCTAATAC
* * * * *
1139788 CCCATGCATTTGTTATATCTTCGGGTTCTAAAAAATTCATTAGGGATTAGTCAAATATTTTCTGT
1 CCCATGCATCTGTCATATCTTCGGGTTCTAAGAAATTCATAAGGCATTAGTCAAATATTTTCTGT
** * *
1139853 CGTGTTAAAAGGAATCTGATAC
66 AATGTCAAAAGGAATCTAATAC
*
1139875 CCCATGCATCTGTCACATCTTCCGGGTTCTAAGAAAT
1 CCCATGCATCTGTCATATCTT-CGGGTTCTAAGAAAT
1139912 ATATTATCAA
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
87 76 0.72
88 30 0.28
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (87 bp):
CCCATGCATCTGTCATATCTTCGGGTTCTAAGAAATTCATAAGGCATTAGTCAAATATTTTCTGT
AATGTCAAAAGGAATCTAATAC
Found at i:1145138 original size:20 final size:21
Alignment explanation
Indices: 1145113--1145152 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1145103 CTATTACGTT
*
1145113 TATAATCATAA-TATATTTAA
1 TATAATCAAAATTATATTTAA
*
1145133 TATAATTAAAATTATATTTA
1 TATAATCAAAATTATATTTA
1145153 TAATCATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAATCAAAATTATATTTAA
Found at i:1145548 original size:20 final size:20
Alignment explanation
Indices: 1145523--1145570 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
1145513 ATAATAGAAG
1145523 AAAAAAAAG-TAAAGGAAAGA
1 AAAAAAAAGTTAAA-GAAAGA
1145543 AAAAAAAAGTTAAAGAAAGA
1 AAAAAAAAGTTAAAGAAAGA
1145563 AAAAAAAA
1 AAAAAAAA
1145571 TATGTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (20 bp):
AAAAAAAAGTTAAAGAAAGA
Found at i:1145610 original size:16 final size:17
Alignment explanation
Indices: 1145591--1145625 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1145581 TTATTTAGAT
*
1145591 AAATTTTT-TAAAATTA
1 AAATTTTTAAAAAATTA
1145607 AAATTTTTAAAAAATTA
1 AAATTTTTAAAAAATTA
1145624 AA
1 AA
1145626 CGTATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTTTAAAAAATTA
Found at i:1146894 original size:21 final size:22
Alignment explanation
Indices: 1146845--1146927 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 22
1146835 TATGATTATT
*
1146845 TTTATTATTT-TTAAAAAATAA
1 TTTATTATTTAATAAAAAATAA
* *
1146866 TTGA-TATTTAATATAAAAT-A
1 TTTATTATTTAATAAAAAATAA
*
1146886 TTTATTATTGTATTTAAAAAATAA
1 TTTATTATT-TA-ATAAAAAATAA
**
1146910 TTTAAGATTTAATAAAAA
1 TTTATTATTTAATAAAAA
1146928 TATTTTGTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
20 9 0.19
21 14 0.29
22 8 0.17
23 9 0.19
24 8 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTATTATTTAATAAAAAATAA
Found at i:1146902 original size:44 final size:43
Alignment explanation
Indices: 1146841--1146933 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 43
1146831 AAAATATGAT
* * *
1146841 TATTTTTATTATTTTTAAAAAATAA-TTGATATTTAATATAAAA
1 TATTTTTATTATATTTAAAAAATAATTTAAGATTTAATA-AAAA
*
1146884 TATTTATTATTGTATTTAAAAAATAATTTAAGATTTAATAAAAA
1 TATTT-TTATTATATTTAAAAAATAATTTAAGATTTAATAAAAA
1146928 TATTTT
1 TATTTT
1146934 GTAATTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 6 0.14
44 27 0.61
45 11 0.25
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (43 bp):
TATTTTTATTATATTTAAAAAATAATTTAAGATTTAATAAAAA
Found at i:1146993 original size:54 final size:53
Alignment explanation
Indices: 1146898--1147601 Score: 685
Period size: 54 Copynumber: 13.8 Consensus size: 53
1146888 TATTATTGTA
* * * *
1146898 TTTAAAAAATAATTTAAGATTTAATA-AAAATAT-TTTGTAATTTTTATTATT
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAATTTTTATTATT
* * *
1146949 TTTAACTAGTAATTTGAAATTTAATATAAAATATATTCTTTAATTTTTATTATG
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATATT-TTTAATTTTTATTATT
* *
1147003 TTTAAATAATAATTTGAGATTTAATATAAAATATATTCTTTAATTTTTATTATG
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATATT-TTTAATTTTTATTATT
* * *
1147057 TTTAAATAATAATTTGAGATTTAATAT-AAA-ATATTTTTATTTTTTA-AATT
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAATTTTTATTATT
* * * * **
1147107 TTTAAAAATTATTTTGAGCTTTAATATAAAATAT-TTTGAAATTTCTTATTATT
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAATTT-TTATTATT
*
1147160 TTTAAATAGTAATTT-ATGATTTAATAT-AAA-AT-TTTTTAATTTTTATCATTT
1 TTTAAATAGTAATTTGA-GATTTAATATAAAATATATTTTTAATTTTTATTA-TT
*
1147211 TTTAAA-AATAATTT-AGAATTTAATATAAAAATATATTTTTAATTTTTA-T-TT
1 TTTAAATAGTAATTTGAG-ATTTAATAT-AAAATATATTTTTAATTTTTATTATT
* *
1147262 TTTAAATAGTAATTTGAGATTCAATATAAAATATATTTTTTTATTTTTATTATT
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATA-TTTTTAATTTTTATTATT
* ** *
1147316 TTTAAATAGTTATTCAAGATTTAATATAAAATAT-TTTTAAATTTTTATTATT
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAATTTTTATTATT
*
1147368 TTTAAAAAGTAATTTGAGATTTAATAT-AAA-ATATTTTT-A-TTTT-TTA--
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAATTTTTATTATT
* *
1147414 ---AAA-AGTAATTTGGGATGTAATATAAAATAT-TTTTTAA--TTT-TTA--
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAATTTTTATTATT
* * *
1147457 -TT--ATAGTAATTTTG-GATTTAAGATAAAATTTATTTTT--TTATTTTTTATTT
1 TTTAAATAGTAA-TTTGAGATTTAATATAAAATATATTTTTAATT-TTTATTA-TT
* *
1147507 TTTAAATAGTAATTTGGGATTTAATATAAAATATATTTTTTAATTTTTACTATTT
1 TTTAAATAGTAATTTGAGATTTAATATAAAATATA-TTTTTAATTTTTATTA-TT
* *
1147562 TTTAAATAATAATTT-ACAATTTAATATAAAATATATTTTT
1 TTTAAATAGTAATTTGA-GATTTAATATAAAATATATTTTT
1147602 TAAATAGTAA
Statistics
Matches: 554, Mismatches: 56, Indels: 83
0.80 0.08 0.12
Matches are distributed among these distances:
42 18 0.03
43 18 0.03
44 22 0.04
45 9 0.02
46 3 0.01
47 3 0.01
48 3 0.01
49 5 0.01
50 50 0.09
51 84 0.15
52 94 0.17
53 57 0.10
54 147 0.27
55 39 0.07
56 2 0.00
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (53 bp):
TTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTTAATTTTTATTATT
Found at i:1147403 original size:35 final size:38
Alignment explanation
Indices: 1147361--1147448 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 38
1147351 TTTAAATTTT
*
1147361 TATTATTTTTAAAAAGTAATTTGAGATTTAATATAAAA
1 TATTATTTTTAAAAAGTAATTTGAGATGTAATATAAAA
*
1147399 TATTTTTATTTTTTAAAAAGTAATTTGGGATGTAATATAAAA
1 TA---TTA-TTTTTAAAAAGTAATTTGAGATGTAATATAAAA
1147441 TATT-TTTT
1 TATTATTTT
1147449 AATTTTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
37 4 0.09
38 2 0.05
39 2 0.05
41 3 0.07
42 33 0.75
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (38 bp):
TATTATTTTTAAAAAGTAATTTGAGATGTAATATAAAA
Found at i:1147489 original size:313 final size:306
Alignment explanation
Indices: 1146842--1147604 Score: 772
Period size: 313 Copynumber: 2.5 Consensus size: 306
1146832 AAATATGATT
* * * * *
1146842 ATTT-TTATTATTTTTAAA-AAATAATTGAT-ATTTAATATAAAA-TATTT-ATTATTGT-A--T
1 ATTTATTATTATTTTTAAATAGA-AATTTATGATTTAATATAAAATTTTTTAATTTTTATCATTT
* *
1146899 TTAAAAAATAATTTAAGATTTAATAAAAATATTTTGTAATTTTTATTATTTTTAACTAGTAATTT
65 TTTAAAAATAATTTAAGATTTAATAAAAATATTTTGTAATTTTTATTATTTTTAAATAGTAATTT
* **
1146964 GAAATTTAATATAAAATATATTCTTTAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATA
130 GAAATTCAATATAAAATATATTCTTTAATTTTTATTATGTTTAAATAATAATTCAAGATTTAATA
*
1147029 TAAAATATATTCTTTAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATATAAAATATTTT
195 TAAAATATATTCTTAAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATATAAAATATTTT
* * * *
1147094 TATTTTTTAAATTTTTAAAAATTATTTTGAGCTTTAATATAAAATATTTTGAA
260 TA----TT--ATTTTTAAAAAGTAATTTGAGATGTAATATAAAATATTTTGAA
* *
1147147 ATTTCTTATTATTTTTAAATAGTAATTTATGATTTAATATAAAATTTTTTAATTTTTATCATTTT
1 ATTTATTATTATTTTTAAATAGAAATTTATGATTTAATATAAAATTTTTTAATTTTTATCATTTT
*
1147212 TTAAAAATAATTT-AGAATTTAATATAAAAATATATTTTTAATTTTTA-T-TTTTTAAATAGTAA
66 TTAAAAATAATTTAAG-ATTT-A-ATAAAAATAT-TTTGTAATTTTTATTATTTTTAAATAGTAA
* * * * * *
1147274 TTTGAGATTCAATATAAAATATATTTTTTTATTTTTATTATTTTTAAATAGTTATTCAAGATTTA
127 TTTGAAATTCAATATAAAATATATTCTTTAATTTTTATTATGTTTAAATAATAATTCAAGATTTA
*
1147339 ATATAAAATAT-TT-TTAAATTTTTATTATTTTTAAA-AAGTAATTTGAGATTTAATATAAAATA
192 ATATAAAATATATTCTTAAATTTTTATTATGTTTAAATAA-TAATTTGAGATTTAATATAAAATA
*
1147401 TTTTTA-T-TTTTTAAAAAGTAATTTGGGATGTAATATAAAATA-TTT---
256 TTTTTATTATTTTTAAAAAGTAATTTGAGATGTAATATAAAATATTTTGAA
* * ** * *
1147446 -TTTA--ATT-TTTATT--ATAGTAATTT-TGGATTTAAGATAAAATTTATTTTTTTATTTTTTA
1 ATTTATTATTATTT-TTAAATAGAAATTTAT-GATTTAATATAAAATTT-TTTAATT-TTTATCA
* ** * *
1147504 TTTTTTAAATAGTAATTTGGGATTTAATATAAAATATATTTTTTAATTTTTACTATTTTTTAAAT
62 TTTTTTAAA-AATAATTTAAGATTT-A-ATAAAA-ATATTTTGTAATTTTTATTA-TTTTTAAAT
* * *
1147569 AATAATTT-ACAATTTAATATAAAATATATTTTTTAA
122 AGTAATTTGA-AATTCAATATAAAATATATTCTTTAA
1147605 ATAGTAAATT
Statistics
Matches: 397, Mismatches: 37, Indels: 53
0.82 0.08 0.11
Matches are distributed among these distances:
293 1 0.00
294 26 0.07
295 8 0.02
296 19 0.05
297 33 0.08
298 9 0.02
299 1 0.00
300 39 0.10
302 3 0.01
303 30 0.08
305 4 0.01
306 21 0.05
307 14 0.04
308 4 0.01
309 6 0.02
310 3 0.01
311 52 0.13
312 20 0.05
313 81 0.20
314 11 0.03
315 12 0.03
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (306 bp):
ATTTATTATTATTTTTAAATAGAAATTTATGATTTAATATAAAATTTTTTAATTTTTATCATTTT
TTAAAAATAATTTAAGATTTAATAAAAATATTTTGTAATTTTTATTATTTTTAAATAGTAATTTG
AAATTCAATATAAAATATATTCTTTAATTTTTATTATGTTTAAATAATAATTCAAGATTTAATAT
AAAATATATTCTTAAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATATAAAATATTTTT
ATTATTTTTAAAAAGTAATTTGAGATGTAATATAAAATATTTTGAA
Found at i:1147507 original size:53 final size:53
Alignment explanation
Indices: 1147441--1147602 Score: 198
Period size: 55 Copynumber: 3.0 Consensus size: 53
1147431 TAATATAAAA
* * * *
1147441 TATTTTTTAATTTTTATTATAGTAATTTTGGATTTAAGATAAAATTTATTTTTT
1 TATTTTTTATTTTTTA-AATAGTAATTTGGGATTTAAGATAAAATATATTTTTT
*
1147495 TATTTTTTATTTTTTAAATAGTAATTTGGGATTTAATATAAAATATATTTTTT
1 TATTTTTTATTTTTTAAATAGTAATTTGGGATTTAAGATAAAATATATTTTTT
* * *** *
1147548 AATTTTTACTATTTTTTAAATAATAATTTACAATTTAATATAAAATATATTTTTT
1 TATTTTT--TATTTTTTAAATAGTAATTTGGGATTTAAGATAAAATATATTTTTT
1147603 AAATAGTAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
53 39 0.41
54 15 0.16
55 42 0.44
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (53 bp):
TATTTTTTATTTTTTAAATAGTAATTTGGGATTTAAGATAAAATATATTTTTT
Found at i:1147548 original size:19 final size:19
Alignment explanation
Indices: 1147526--1147604 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 19
1147516 TAATTTGGGA
1147526 TTTAATATAAAATATATTT
1 TTTAATATAAAATATATTT
**
1147545 TTTAAT-T--TTTACTATTT
1 TTTAATATAAAATA-TATTT
* ***
1147562 TTTAA-ATAATAATTTACAA
1 TTTAATATAA-AATATATTT
1147581 TTTAATATAAAATATATTT
1 TTTAATATAAAATATATTT
1147600 TTTAA
1 TTTAA
1147605 ATAGTAAATT
Statistics
Matches: 42, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
16 2 0.05
17 11 0.26
18 1 0.02
19 23 0.55
20 5 0.12
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAATATAAAATATATTT
Found at i:1147602 original size:38 final size:38
Alignment explanation
Indices: 1147557--1147637 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
1147547 TAATTTTTAC
*
1147557 TATTTTTTAAATAAT-AATTTACAATTTAATATAAAATA
1 TATTTTTTAAATAATAAATTGA-AATTTAATATAAAATA
* * *
1147595 TATTTTTTAAATAGTAAATTGAGATTTTATATAAAATA
1 TATTTTTTAAATAATAAATTGAAATTTAATATAAAATA
1147633 T-TTTT
1 TATTTT
1147638 AAATTTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 4 0.11
38 29 0.76
39 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (38 bp):
TATTTTTTAAATAATAAATTGAAATTTAATATAAAATA
Found at i:1147707 original size:104 final size:105
Alignment explanation
Indices: 1147595--1147877 Score: 373
Period size: 106 Copynumber: 2.7 Consensus size: 105
1147585 ATATAAAATA
* * *
1147595 TATTTTTTAAATAGTAAATTGAGATTTTATATAAAATATTTTTAAATTTTTCTATTTTTAAATAA
1 TATTTTTTAAATAGT-AATTAAGATTTAATATAAAATATTTTTAAATTTTTTTATTTTTAAATAA
* *
1147660 TAATTCAAGATTTAATAT-AAA-ATGTTTTTATTTTTTTAT
65 TAATTCAAGATTTAATATAAAATATATTTTTAATTTTTTAT
* *
1147699 TATTTTTTATGA-AGTAATTCAA-ATTTAATATAAAATAGTTTTT-TATTTTTTTATTTTTTAAA
1 TATTTTTTA-AATAGTAATT-AAGATTTAATATAAAATA-TTTTTAAATTTTTTTA-TTTTTAAA
1147761 TAATAACTT-AAGATTTAATATAAAATATATTTTTAATTTTTTAT
62 TAATAA-TTCAAGATTTAATATAAAATATATTTTTAATTTTTTAT
*
1147805 TA-TTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAAATTTTTATTATTTTTAAATA
1 TATTTTTTAAATAGTAATT-AAGATTTAATATAAAATATTTTTAAATTTTT-TTATTTTTAAATA
1147869 ATAATTCAA
64 ATAATTCAA
1147878 AATTAAAAAA
Statistics
Matches: 157, Mismatches: 10, Indels: 22
0.83 0.05 0.12
Matches are distributed among these distances:
103 26 0.17
104 45 0.29
105 28 0.18
106 55 0.35
107 3 0.02
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (105 bp):
TATTTTTTAAATAGTAATTAAGATTTAATATAAAATATTTTTAAATTTTTTTATTTTTAAATAAT
AATTCAAGATTTAATATAAAATATATTTTTAATTTTTTAT
Found at i:1147729 original size:52 final size:52
Alignment explanation
Indices: 1147598--1147877 Score: 349
Period size: 52 Copynumber: 5.4 Consensus size: 52
1147588 TAAAATATAT
* * * * *
1147598 TTTTTAAATAGTAAATT-GAGATTTTATATAAAATATTTTTAAATTTTT-CTA
1 TTTTTAAATAAT-AATTCAAGATTTAATATAAAATATTTTTAATTTTTTATTA
* *
1147649 TTTTTAAATAATAATTCAAGATTTAATATAAAATGTTTTTATTTTTTTATTA
1 TTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAATTTTTTATTA
* *
1147701 TTTTT-TATGAAGTAATTCAA-ATTTAATATAAAATAGTTTTTTA-TTTTT-TTA
1 TTTTTAAAT-AA-TAATTCAAGATTTAATATAAAATA-TTTTTAATTTTTTATTA
1147752 TTTTTTAAATAATAACTT-AAGATTTAATATAAAATATATTTTTAATTTTTTATTA
1 -TTTTTAAATAATAA-TTCAAGATTTAATAT-AAA-ATATTTTTAATTTTTTATTA
*
1147807 TTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAAATTTTTATTA
1 TTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAATTTTTTATTA
1147859 TTTTTAAATAATAATTCAA
1 TTTTTAAATAATAATTCAA
1147878 AATTAAAAAA
Statistics
Matches: 201, Mismatches: 14, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
50 4 0.02
51 47 0.23
52 84 0.42
53 29 0.14
54 34 0.17
55 3 0.01
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (52 bp):
TTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAATTTTTTATTA
Found at i:1147756 original size:493 final size:503
Alignment explanation
Indices: 1146842--1147874 Score: 1329
Period size: 493 Copynumber: 2.0 Consensus size: 503
1146832 AAATATGATT
*
1146842 ATTTTTATTATTTTTAAAAAATAA-TTGATATTTAATATAAAATATTTATTATTGTATTTAAAAA
1 ATTTTTATTATTTTT-AAAAATAATTTGAGATTTAATATAAAATATTTATTATTGTATTTAAAAA
*
1146906 ATAATTTAAGATTTAATAAAAATATTTTGTAATTTTTATTATTTTTAACTAGTAATTTGAAATTT
65 ATAATTTAAGATGTAATAAAAATATTTTGTAA-TTTTATTA--TTTAACTAGTAATTTGAAATTT
*
1146971 AATATAAAATATATTCTTTAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATATAAAATA
127 AAGATAAAATATATTCTTTAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATATAAAATA
* *
1147036 TATTCTTTAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATATAAAATATTTTTATTTTT
192 TATTCTTTAATTTTTACTATGTTTAAATAATAATTTGAAATTTAATATAAAATA---TTATTTTT
* *
1147101 TAAATTTTTAAAAATTATTTTGAGCTTTAATATAAAATATTTTGAAATTTCTTATTATTTTTAAA
254 TAAA---TTAAAAA-TA-TTTGAGATTTAATATAAAATATTTTGAAATTTCTTACTATTTTTAAA
* * * *
1147166 TAGTAATTTATGATTTAATATAAAATTTTTTAATTTTTATCATTTTTTAAAAATAATTTAGAATT
314 TAATAATTCAAGATTTAATATAAAATTTTTTAATTTTTATCATTTTTTAAAAATAATTCAGAATT
* * *
1147231 TAATATAAAAATATATTTTTAATTTTTATTTTTTAAATAGTAATTTGAGATTCAATATAAAATAT
379 TAATATAAAAATATATTTTTAATTTTTATTTTTTAAATAATAACTTAAGATTCAATATAAAATAT
* * *
1147296 ATTTTT-TTATTTTTATTATTTTTAAATAGTTATTCAAGATTTAATATAAAATATTTTTAA
444 ATTTTTAAT-TTTTTATTATTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAA
1147356 ATTTTTATTATTTTTAAAAAGTAATTTGAGATTTAATATAAAATATTT-TTATT-T-TTTAAAAA
1 ATTTTTATTATTTTTAAAAA-TAATTTGAGATTTAATATAAAATATTTATTATTGTATTTAAAAA
* ** * *
1147418 GTAATTTGGGATGTAATATAAAATATTTTTTAA-TTT-TTA-TT-A-TAGTAATTTTG-GATTTA
65 ATAATTTAAGATGTAATA-AAAATATTTTGTAATTTTATTATTTAACTAGTAA-TTTGAAATTTA
* * * * *
1147477 AGATAAAATTTATTTTTTTATTTTTTATT-T-TTTAAATAGTAATTTGGGATTTAATATAAAATA
128 AGATAAAATATA-TTCTTTAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATATAAAATA
* *
1147540 TATTTTTTAATTTTTACTATTTTTTAAATAATAATTT-ACAATTTAATATAAAATA-TATTTTTT
192 TATTCTTTAATTTTTACTA-TGTTTAAATAATAATTTGA-AATTTAATATAAAATATTATTTTTT
** * *
1147603 AAA-TAGTAA-A-TTGAGATTTTATATAAAATATTTTTAAATTT-TT-CTATTTTTAAATAATAA
255 AAATTAAAAATATTTGAGATTTAATATAAAATATTTTGAAATTTCTTACTATTTTTAAATAATAA
* * * *
1147663 TTCAAGATTTAATATAAAATGTTTTTATTTTTTTATTATTTTTTATGAAGTAATTCA-AATTTAA
320 TTCAAGATTTAATATAAAAT-TTTTTA-ATTTTTATCATTTTTTA-AAAATAATTCAGAATTTAA
* *
1147727 TAT-AAAATAGT-TTTTTATTTTTTTATTTTTTAAATAATAACTTAAGATTTAATATAAAATATA
382 TATAAAAATA-TATTTTTA-ATTTTTATTTTTTAAATAATAACTTAAGATTCAATATAAAATATA
1147790 TTTTTAATTTTTTATTATTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAA
445 TTTTTAATTTTTTATTATTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAA
1147849 ATTTTTATTATTTTTAAATAATAATT
1 ATTTTTATTATTTTTAAA-AATAATT
1147875 CAAAATTAAA
Statistics
Matches: 466, Mismatches: 39, Indels: 49
0.84 0.07 0.09
Matches are distributed among these distances:
491 33 0.07
492 20 0.04
493 171 0.37
494 11 0.02
495 1 0.00
497 4 0.01
501 11 0.02
504 49 0.11
505 53 0.11
506 19 0.04
507 2 0.00
510 3 0.01
511 3 0.01
512 22 0.05
513 19 0.04
514 23 0.05
515 22 0.05
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (503 bp):
ATTTTTATTATTTTTAAAAATAATTTGAGATTTAATATAAAATATTTATTATTGTATTTAAAAAA
TAATTTAAGATGTAATAAAAATATTTTGTAATTTTATTATTTAACTAGTAATTTGAAATTTAAGA
TAAAATATATTCTTTAATTTTTATTATGTTTAAATAATAATTTGAGATTTAATATAAAATATATT
CTTTAATTTTTACTATGTTTAAATAATAATTTGAAATTTAATATAAAATATTATTTTTTAAATTA
AAAATATTTGAGATTTAATATAAAATATTTTGAAATTTCTTACTATTTTTAAATAATAATTCAAG
ATTTAATATAAAATTTTTTAATTTTTATCATTTTTTAAAAATAATTCAGAATTTAATATAAAAAT
ATATTTTTAATTTTTATTTTTTAAATAATAACTTAAGATTCAATATAAAATATATTTTTAATTTT
TTATTATTTTTAAATAATAATTCAAGATTTAATATAAAATATTTTTAA
Found at i:1148429 original size:16 final size:17
Alignment explanation
Indices: 1148408--1148448 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1148398 TTTTAATTAT
1148408 TTTTAAGTTTGAA-TCA
1 TTTTAAGTTTGAAGTCA
*
1148424 TTTTAA-TTTTAAGTCA
1 TTTTAAGTTTGAAGTCA
1148440 TTTT-AGTTT
1 TTTTAAGTTT
1148449 CCGATCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.59
Consensus pattern (17 bp):
TTTTAAGTTTGAAGTCA
Found at i:1148650 original size:15 final size:14
Alignment explanation
Indices: 1148627--1148669 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1148617 ATCACATGTT
* *
1148627 TTTTTATTTTTTTC
1 TTTTAATTTTTTTA
*
1148641 TTTTAAATTTTATTA
1 TTTT-AATTTTTTTA
1148656 TTTTAATTTTTTTA
1 TTTTAATTTTTTTA
1148670 AGTTAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTAATTTTTTTA
Found at i:1149046 original size:23 final size:21
Alignment explanation
Indices: 1149003--1149046 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
1148993 ATAGTATTAT
* *
1149003 TAAAATAATATTAATACAATA
1 TAAAATAATATAAATAAAATA
1149024 TAAAATATATTATAAATAAAATA
1 TAAAATA-A-TATAAATAAAATA
1149047 ATTAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAATAATATAAATAAAATA
Found at i:1149563 original size:2 final size:2
Alignment explanation
Indices: 1149556--1149582 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1149546 GTCCAATGAT
1149556 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1149583 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1150883 original size:25 final size:23
Alignment explanation
Indices: 1150839--1150912 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
1150829 TAGGGTGAAT
*
1150839 AAATAAATTT-TTAATTTTTTTA
1 AAATAATTTTATTAATTTTTTTA
1150861 AAATAAAATTTTATTAATTTTTTTA
1 AAAT--AATTTTATTAATTTTTTTA
1150886 TAAATAATTTTATTAATTTTTTATA
1 -AAATAATTTTATTAATTTTTT-TA
1150911 AA
1 AA
1150913 TTATTTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
22 4 0.09
24 24 0.52
25 14 0.30
26 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATAATTTTATTAATTTTTTTA
Found at i:1150886 original size:12 final size:12
Alignment explanation
Indices: 1150869--1150920 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1150859 TAAAATAAAA
*
1150869 TTTTATTAATTT
1 TTTTATAAATTT
**
1150881 TTTTATAAATAA
1 TTTTATAAATTT
*
1150893 TTTTATTAA-TT
1 TTTTATAAATTT
1150904 TTTTATAAATTAT
1 TTTTATAAATT-T
1150917 TTTT
1 TTTT
1150921 TTATAAATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 8 0.26
12 18 0.58
13 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTATAAATTT
Found at i:1150920 original size:14 final size:15
Alignment explanation
Indices: 1150897--1150928 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1150887 AAATAATTTT
*
1150897 ATTAATTTTTTATAA
1 ATTATTTTTTTATAA
1150912 ATTATTTTTTTATAA
1 ATTATTTTTTTATAA
1150927 AT
1 AT
1150929 CATAGTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTTTTTTATAA
Found at i:1150920 original size:24 final size:24
Alignment explanation
Indices: 1150837--1150919 Score: 109
Period size: 23 Copynumber: 3.5 Consensus size: 24
1150827 TTTAGGGTGA
*
1150837 ATAAATAAATTT-TTAATTTTTTT
1 ATAAATAATTTTATTAATTTTTTT
1150860 A-AAATAAAATTTTATTAATTTTTTT
1 ATAAAT--AATTTTATTAATTTTTTT
1150885 ATAAATAATTTTATTAA-TTTTTT
1 ATAAATAATTTTATTAATTTTTTT
*
1150908 ATAAATTATTTT
1 ATAAATAATTTT
1150920 TTTATAAATC
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.07
23 18 0.33
24 16 0.30
25 12 0.22
26 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATAAATAATTTTATTAATTTTTTT
Found at i:1155300 original size:19 final size:19
Alignment explanation
Indices: 1155253--1155293 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1155243 CTCTCCACTC
*
1155253 CTTTAT-TTATCTTGTTCT
1 CTTTATGTTTTCTTGTTCT
*
1155271 CTTTATGTTTTCTTTTTCT
1 CTTTATGTTTTCTTGTTCT
1155290 CTTT
1 CTTT
1155294 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.71
Consensus pattern (19 bp):
CTTTATGTTTTCTTGTTCT
Found at i:1157927 original size:53 final size:53
Alignment explanation
Indices: 1157845--1157951 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
1157835 GAGTTACATA
1157845 TATGAATGAATGAATAAATGAATGGGGCAGCATTTACTGAAATGCATTAGGTG
1 TATGAATGAATGAATAAATGAATGGGGCAGCATTTACTGAAATGCATTAGGTG
*
1157898 TATGAATGAATGAATAAATGAATGTGGCAGCATTTACTGAAATGCATTAGGTG
1 TATGAATGAATGAATAAATGAATGGGGCAGCATTTACTGAAATGCATTAGGTG
1157951 T
1 T
1157952 TAAGCAATTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.30
Consensus pattern (53 bp):
TATGAATGAATGAATAAATGAATGGGGCAGCATTTACTGAAATGCATTAGGTG
Found at i:1159696 original size:22 final size:22
Alignment explanation
Indices: 1159662--1159709 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1159652 TTTTCTTTGA
* * *
1159662 TTTTTTGACTTTTCTTTGACTTT
1 TTTTTTCACTTTTATTTCA-TTT
1159685 TTTTTTCA-TTTTATTTCATTT
1 TTTTTTCACTTTTATTTCATTT
1159706 TTTT
1 TTTT
1159710 CAAAAAGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTTTCACTTTTATTTCATTT
Found at i:1162381 original size:19 final size:19
Alignment explanation
Indices: 1162347--1162393 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1162337 AGGAGTGGAC
*
1162347 AAAACAAACA-AAAGAAAA
1 AAAACAAAGAGAAAGAAAA
*
1162365 AAAAGAAAGAGAAAGAAAA
1 AAAACAAAGAGAAAGAAAA
1162384 AAAACAAAGA
1 AAAACAAAGA
1162394 AAAAACAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAACAAAGAGAAAGAAAA
Found at i:1162392 original size:13 final size:13
Alignment explanation
Indices: 1162376--1162422 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1162366 AAAGAAAGAG
1162376 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
* *
1162389 AAAGAAAAAACAG
1 AAAGAAAAAAAAC
*
1162402 AAAAAAAATAAAAC
1 AAAGAAAA-AAAAC
1162416 AAA-AAAA
1 AAAGAAAA
1162423 CAACAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Done.