Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 18 of 45
Found at i:3323032 original size:2 final size:2
Alignment explanation
Indices: 3323025--3323062 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3323015 TTGTAGTTTC
3323025 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
3323063 GGCTTCAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3323948 original size:2 final size:2
Alignment explanation
Indices: 3323941--3323968 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3323931 GAAAATAAGA
3323941 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
3323969 GTTTATGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3324736 original size:27 final size:28
Alignment explanation
Indices: 3324697--3324749 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
3324687 TTTTTCACTT
*
3324697 AAATTACTATTTTTTACTT-GAAAAAGA
1 AAATTACTATTTTATACTTAGAAAAAGA
3324724 AAATTAC-ATTTTTATACTTAGAAAAA
1 AAATTACTA-TTTTATACTTAGAAAAA
3324750 AATATTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 16 0.70
28 6 0.26
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (28 bp):
AAATTACTATTTTATACTTAGAAAAAGA
Found at i:3325012 original size:14 final size:14
Alignment explanation
Indices: 3324953--3325012 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
3324943 TTAAAATATT
*
3324953 AAAAAATTAATTTA
1 AAAAAAATAATTTA
* *
3324967 AAATAAATTATTAATA
1 AAAAAAATAATT--TA
3324983 AATAAAAAT-ATATTA
1 AA-AAAAATAAT-TTA
3324998 AAAAAAATAATTTA
1 AAAAAAATAATTTA
3325012 A
1 A
3325013 TGACTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 19 0.51
15 6 0.16
16 6 0.16
17 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAAAATAATTTA
Found at i:3325829 original size:48 final size:48
Alignment explanation
Indices: 3325777--3325872 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
3325767 ACCTCCTATG
*
3325777 AAAATGG-TAAAAAAACAAAAACAG-TAAGAAATCAGTTTGAAACTGTTA
1 AAAATGGTTAAAAAAA-AAAAACAGAAAAGAAATCAG-TTGAAACTGTTA
* * *
3325825 AAAATGGTTAAAGAAAAGAAACAGAAAAGACATCAGTTGAAACTGTTA
1 AAAATGGTTAAAAAAAAAAAACAGAAAAGAAATCAGTTGAAACTGTTA
3325873 TTCTTACCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 26 0.62
49 16 0.38
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.20
Consensus pattern (48 bp):
AAAATGGTTAAAAAAAAAAAACAGAAAAGAAATCAGTTGAAACTGTTA
Found at i:3330969 original size:11 final size:11
Alignment explanation
Indices: 3330953--3331028 Score: 64
Period size: 11 Copynumber: 6.7 Consensus size: 11
3330943 TAAAAAAATT
3330953 TAAATATAATA
1 TAAATATAATA
*
3330964 TAAATATAAAA
1 TAAATATAATA
** *
3330975 TATTTTAAAATA
1 TA-AATATAATA
*
3330987 TAATTATAATA
1 TAAATATAATA
*
3330998 T-AATAAAATA
1 TAAATATAATA
3331008 TATTAATATAATA
1 TA--AATATAATA
3331021 TAAATATA
1 TAAATATA
3331029 TAAATTATTA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 8 0.16
11 26 0.51
12 7 0.14
13 10 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATATAATA
Found at i:3331004 original size:21 final size:19
Alignment explanation
Indices: 3330955--3331028 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 19
3330945 AAAAAATTTA
3330955 AATATAATATAAATATAA--
1 AATATAATA-AAATATAATT
**
3330973 AATATTTTAAAATATAATTAT
1 AATATAATAAAATATAA-T-T
3330994 AATATAATAAAATAT-ATT
1 AATATAATAAAATATAATT
3331012 AATATAATATAAATATA
1 AATATAATA-AAATATA
3331029 TAAATTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 8 0.17
18 17 0.37
19 7 0.15
20 1 0.02
21 13 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATAATAAAATATAATT
Found at i:3331015 original size:8 final size:9
Alignment explanation
Indices: 3330952--3331045 Score: 63
Period size: 11 Copynumber: 10.1 Consensus size: 9
3330942 TTAAAAAAAT
3330952 TTAAATATAA
1 TTAAATAT-A
3330962 TATAAATATA
1 T-TAAATATA
*
3330972 --AAATATT
1 TTAAATATA
3330979 TTAAAATATAA
1 TT-AAATAT-A
3330990 TTATAATATAA
1 TTA-AATAT-A
*
3331001 TAAAATATA
1 TTAAATATA
3331010 TT-AATATAA
1 TTAAATAT-A
3331019 TATAAATATA
1 T-TAAATATA
3331029 -TAAAT-TA
1 TTAAATATA
3331036 TTAAATATA
1 TTAAATATA
3331045 T
1 T
3331046 GTTTATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
7 8 0.12
8 15 0.22
9 7 0.10
10 16 0.23
11 23 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TTAAATATA
Found at i:3331020 original size:13 final size:14
Alignment explanation
Indices: 3330955--3331031 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 14
3330945 AAAAAATTTA
*
3330955 AATATAATATAAAT
1 AATATAATATATAT
* * *
3330969 -ATAAAATATTTTAA
1 AATATAATA-TATAT
3330983 AATATAATTATAATAT
1 AATATAA-TAT-ATAT
*
3330999 AATAAAATATAT-T
1 AATATAATATATAT
*
3331012 AATATAATATAAAT
1 AATATAATATATAT
3331026 -ATATAA
1 AATATAA
3331032 ATTATTAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
13 24 0.50
14 5 0.10
15 9 0.19
16 10 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATAATATATAT
Found at i:3331345 original size:23 final size:24
Alignment explanation
Indices: 3331301--3331346 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
3331291 AATTCTAATA
*
3331301 ATTACTTTTTTTAAAAATAAATTT
1 ATTACTTTTTATAAAAATAAATTT
3331325 ATTA-TTTTTATAATAAA-AAATT
1 ATTACTTTTTATAA-AAATAAATT
3331347 AAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTACTTTTTATAAAAATAAATTT
Found at i:3331431 original size:17 final size:17
Alignment explanation
Indices: 3331393--3331434 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3331383 CTTTGAATGA
3331393 TTTTAAAATTTTGATAT
1 TTTTAAAATTTTGATAT
* *
3331410 ATTTAAAATTATTTA-AT
1 TTTTAAAATT-TTGATAT
3331427 TTTTAAAA
1 TTTTAAAA
3331435 ATTAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAAAATTTTGATAT
Found at i:3339230 original size:34 final size:34
Alignment explanation
Indices: 3339187--3339253 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
3339177 CTACTAATAG
*
3339187 ACAATAATAGAGTGGAGAAATTAAAGGAATCAAC
1 ACAATAATAGAGTGAAGAAATTAAAGGAATCAAC
3339221 ACAATAATAGAGTGAAGAAATTAAAGGAATCAA
1 ACAATAATAGAGTGAAGAAATTAAAGGAATCAA
3339254 TGTTTTCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.18
Consensus pattern (34 bp):
ACAATAATAGAGTGAAGAAATTAAAGGAATCAAC
Found at i:3345234 original size:13 final size:13
Alignment explanation
Indices: 3345208--3345287 Score: 61
Period size: 15 Copynumber: 5.7 Consensus size: 13
3345198 TATAATATTT
3345208 TAAATATAATTATAA
1 TAAATA-AA-TATAA
3345223 TAAATAAATATAA
1 TAAATAAATATAA
**
3345236 TATAGATGCATATAA
1 TA-A-ATAAATATAA
*
3345251 TAAGTAAATATAA
1 TAAATAAATATAA
*
3345264 TATAGATACATATAA
1 TA-A-ATAAATATAA
*
3345279 TAATTAAAT
1 TAAATAAAT
3345288 CTAAAACCCA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
13 20 0.38
14 6 0.12
15 26 0.50
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:3345249 original size:28 final size:28
Alignment explanation
Indices: 3345218--3345287 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
3345208 TAAATATAAT
*
3345218 TATAATAAATAAATATAATATAGATGCA
1 TATAATAAATAAATATAATATAGATACA
*
3345246 TATAATAAGTAAATATAATATAGATACA
1 TATAATAAATAAATATAATATAGATACA
*
3345274 TATAATAATTAAAT
1 TATAATAAATAAAT
3345288 CTAAAACCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (28 bp):
TATAATAAATAAATATAATATAGATACA
Found at i:3345250 original size:15 final size:15
Alignment explanation
Indices: 3345218--3345280 Score: 71
Period size: 15 Copynumber: 4.5 Consensus size: 15
3345208 TAAATATAAT
*
3345218 TATAATA-A-ATAAA
1 TATAATATAGATACA
*
3345231 TATAATATAGATGCA
1 TATAATATAGATACA
*
3345246 TATAATA-AG-TAAA
1 TATAATATAGATACA
3345259 TATAATATAGATACA
1 TATAATATAGATACA
3345274 TATAATA
1 TATAATA
3345281 ATTAAATCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
13 16 0.39
14 5 0.12
15 20 0.49
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (15 bp):
TATAATATAGATACA
Found at i:3347219 original size:2 final size:2
Alignment explanation
Indices: 3347212--3347237 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3347202 AGTGTGGGGT
3347212 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3347238 AAGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3349478 original size:2 final size:2
Alignment explanation
Indices: 3349471--3349499 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3349461 ATCTCATTTC
3349471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3349500 GGTTACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3352237 original size:19 final size:20
Alignment explanation
Indices: 3352209--3352246 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3352199 AAATTTTTAA
3352209 TAAAAAAATTTTA-ATTTTT
1 TAAAAAAATTTTATATTTTT
*
3352228 TAAAATAATTTTATATTTT
1 TAAAAAAATTTTATATTTT
3352247 ATTTAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAAAAATTTTATATTTTT
Found at i:3354979 original size:24 final size:28
Alignment explanation
Indices: 3354921--3354981 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 28
3354911 AAATAGATGA
3354921 AATTTAATTAAATAAAATAAATTTATTT
1 AATTTAATTAAATAAAATAAATTTATTT
3354949 AATTTAATT-AA-AAAAT-AATTTATTT
1 AATTTAATTAAATAAAATAAATTTATTT
*
3354974 GA-TTAATT
1 AATTTAATT
3354982 TTATTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 6 0.19
25 10 0.31
26 5 0.16
27 2 0.06
28 9 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
AATTTAATTAAATAAAATAAATTTATTT
Found at i:3355139 original size:29 final size:29
Alignment explanation
Indices: 3355102--3355167 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 29
3355092 TTAAATATGG
*
3355102 TATAATATAAT-ATACATTTTTATGTAAT-A
1 TATAATATAATAATAC--TTTTATATAATAA
3355131 TATAATAT-ATAATACTTTTATATAATAA
1 TATAATATAATAATACTTTTATATAATAA
3355159 TATAA-ATAA
1 TATAATATAA
3355168 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 12 0.36
28 9 0.27
29 12 0.36
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (29 bp):
TATAATATAATAATACTTTTATATAATAA
Found at i:3355176 original size:27 final size:26
Alignment explanation
Indices: 3355103--3355195 Score: 75
Period size: 27 Copynumber: 3.5 Consensus size: 26
3355093 TAAATATGGT
* * *
3355103 ATAATAT-AATATACATTTTTATGTA
1 ATAATATAAATAAATATTTTTATATA
*
3355128 AT-ATATAATATATAATACTTTTATATA
1 ATAATATAA-ATA-AATATTTTTATATA
*
3355155 ATAATATAAATAAATTATTTTT-TAAA
1 ATAATATAAATAAA-TATTTTTATATA
*
3355181 ATAGATATAATTAAA
1 ATA-ATATAAATAAA
3355196 ATGGGTTGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
24 4 0.07
25 3 0.05
26 11 0.20
27 31 0.56
28 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
ATAATATAAATAAATATTTTTATATA
Found at i:3358837 original size:18 final size:20
Alignment explanation
Indices: 3358810--3358848 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3358800 GAAATAAGTA
3358810 TTTTATATATTTTTT-TAAT
1 TTTTATATATTTTTTCTAAT
3358829 TTTTA-ATATTTTTTCTAAT
1 TTTTATATATTTTTTCTAAT
3358848 T
1 T
3358849 AATTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATATATTTTTTCTAAT
Found at i:3359433 original size:25 final size:23
Alignment explanation
Indices: 3359405--3359450 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
3359395 TTTATTTACT
*
3359405 GTTAAAATTTGAAAATAAAAAACGG
1 GTTAAAAATT-AAAA-AAAAAACGG
3359430 GTTAAAAATTAAAAAAAAAAC
1 GTTAAAAATTAAAAAAAAAAC
3359451 TTCAAGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 4 0.20
25 9 0.45
ACGTcount: A:0.63, C:0.04, G:0.11, T:0.22
Consensus pattern (23 bp):
GTTAAAAATTAAAAAAAAAACGG
Found at i:3360074 original size:43 final size:44
Alignment explanation
Indices: 3359993--3360076 Score: 102
Period size: 43 Copynumber: 1.9 Consensus size: 44
3359983 TTGAGTTATT
* *
3359993 AAATTTTTAACTTTAAAGCTTTTAAATTATTTATTTCATTTTTC
1 AAATTTTTAACTTTAAAGATTTTAAATTATGTATTTCATTTTTC
*
3360037 AAATTTTTTA-TTTAAAGATTTTCACAATT-TGTA-TTCATTT
1 AAATTTTTAACTTTAAAGATTTT-A-AATTATGTATTTCATTT
3360077 AATATAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
43 18 0.51
44 13 0.37
45 4 0.11
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (44 bp):
AAATTTTTAACTTTAAAGATTTTAAATTATGTATTTCATTTTTC
Found at i:3360108 original size:23 final size:23
Alignment explanation
Indices: 3360068--3360113 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3360058 TCACAATTTG
*
3360068 TATTCATTTAATATAATAAATAA
1 TATTCATTTAATAAAATAAATAA
* *
3360091 TATTCATTTATTAAAATATATAA
1 TATTCATTTAATAAAATAAATAA
3360114 AATAATATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTCATTTAATAAAATAAATAA
Found at i:3360319 original size:21 final size:21
Alignment explanation
Indices: 3360289--3360341 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3360279 ATTTTAGTCG
*
3360289 CACCATTATAAT-ACTTAATCT
1 CACCACTATAATGAC-TAATCT
* *
3360310 TACTACTATAATGACTAATCT
1 CACCACTATAATGACTAATCT
3360331 CACCACTATAA
1 CACCACTATAA
3360342 CTATTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.34
Consensus pattern (21 bp):
CACCACTATAATGACTAATCT
Found at i:3363891 original size:28 final size:27
Alignment explanation
Indices: 3363856--3363921 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
3363846 AGCTTTCATA
*
3363856 TTTGACAAATACAAAGAAAATTATTATT
1 TTTGACAAATACAAA-AAAATCATTATT
* *
3363884 TTTGACAAACACAAAATAATCATTATT
1 TTTGACAAATACAAAAAAATCATTATT
3363911 TTTGACAAATA
1 TTTGACAAATA
3363922 AAATGACTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.59
28 14 0.41
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (27 bp):
TTTGACAAATACAAAAAAATCATTATT
Found at i:3364754 original size:5 final size:6
Alignment explanation
Indices: 3364732--3364783 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
3364722 ATACATCATT
* * *
3364732 TAAATA TAAAAA TAAAAA TAAAAA CTTAAAT TAAAAA -AAAAA CTAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA -TAAAAA TAAAAA TAAAAA -TAAAAA
3364781 TAA
1 TAA
3364784 TACTAAAGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 5 0.13
6 24 0.63
7 9 0.24
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (6 bp):
TAAAAA
Found at i:3364768 original size:26 final size:25
Alignment explanation
Indices: 3364731--3364780 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3364721 AATACATCAT
3364731 TTAAATATAAAAATAAAAATAAAAAC
1 TTAAATATAAAAA-AAAAATAAAAAC
3364757 TTAAAT-TAAAAAAAAAACTAAAAA
1 TTAAATATAAAAAAAAAA-TAAAAA
3364781 TAATACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 12 0.52
26 6 0.26
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (25 bp):
TTAAATATAAAAAAAAAATAAAAAC
Found at i:3366625 original size:12 final size:12
Alignment explanation
Indices: 3366586--3366638 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
3366576 TTATTTCATG
3366586 ATTTAAAATAAT
1 ATTTAAAATAAT
*
3366598 ATTAAAAATAAT
1 ATTTAAAATAAT
*
3366610 -TTTAAATTAAT
1 ATTTAAAATAAT
* *
3366621 ATTTATAATTA-
1 ATTTAAAATAAT
3366632 ATTTAAA
1 ATTTAAA
3366639 TAAAATAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 15 0.45
12 18 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTAAAATAAT
Found at i:3366636 original size:23 final size:22
Alignment explanation
Indices: 3366586--3366639 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
3366576 TTATTTCATG
*
3366586 ATTTAAAATAATATTAAAAATA
1 ATTTAAATTAATATTAAAAATA
* *
3366608 ATTTTAAATTAATATTTATAATTA
1 A-TTTAAATTAATA-TTAAAAATA
3366632 ATTTAAAT
1 ATTTAAAT
3366640 AAAATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 18 0.67
24 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTAAATTAATATTAAAAATA
Found at i:3374233 original size:50 final size:50
Alignment explanation
Indices: 3374172--3374272 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
3374162 GATCCTAAAA
* * *
3374172 AATAACATTTTAGAATCCA-TTTATAGATTCCTAAAAATTTATTAAAAATT
1 AATAACATTTTAGAAT-CATTTTATAGATGCCTAAAAAATTAATAAAAATT
3374222 AATAACATTTTAGAATCATTTTATAGATGCCTAAAAAATTAATAAAAATT
1 AATAACATTTTAGAATCATTTTATAGATGCCTAAAAAATTAATAAAAATT
3374272 A
1 A
3374273 TAGAGCAGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 2 0.04
50 45 0.96
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.38
Consensus pattern (50 bp):
AATAACATTTTAGAATCATTTTATAGATGCCTAAAAAATTAATAAAAATT
Found at i:3374447 original size:15 final size:15
Alignment explanation
Indices: 3374406--3374444 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3374396 TTTTTCTTTT
*
3374406 TTATATATTATTATA
1 TTATATATTATTAGA
3374421 TTATATCATTATT-GA
1 TTATAT-ATTATTAGA
3374436 TTATATATT
1 TTATATATT
3374445 TATAGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 13 0.59
16 6 0.27
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
TTATATATTATTAGA
Found at i:3374811 original size:18 final size:18
Alignment explanation
Indices: 3374773--3374811 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3374763 GATATTTAAA
*
3374773 AAAACTTTAAAAACATTT
1 AAAACTTTAAAAACATAT
* *
3374791 AAAATTTTAAAAATATAT
1 AAAACTTTAAAAACATAT
3374809 AAA
1 AAA
3374812 TATAAAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAACTTTAAAAACATAT
Found at i:3377224 original size:15 final size:14
Alignment explanation
Indices: 3377195--3377245 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
3377185 CATGTAATTA
3377195 ATATAATTA-ATTTT
1 ATATAATTATA-TTT
3377209 ATTATAATTATATTT
1 A-TATAATTATATTT
*
3377224 AATATATTTTATATTT
1 -ATATA-ATTATATTT
3377240 ATATAA
1 ATATAA
3377246 ATTTTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 1 0.03
15 20 0.65
16 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATAATTATATTT
Found at i:3377235 original size:16 final size:17
Alignment explanation
Indices: 3377216--3377280 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
3377206 TTTATTATAA
*
3377216 TTATATTTA-ATATATT
1 TTATATTTATATAAATT
3377232 TTATATTTATATAAATT
1 TTATATTTATATAAATT
*
3377249 TTA-ATATA-ATAATAATT
1 TTATATTTATAT-A-AATT
3377266 TT-TA-TTATATAAATT
1 TTATATTTATATAAATT
3377281 ATAAAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
15 6 0.15
16 17 0.41
17 18 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:3377251 original size:17 final size:16
Alignment explanation
Indices: 3377216--3377260 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3377206 TTTATTATAA
*
3377216 TTATATTTAATATATT
1 TTATATTTAATAAATT
3377232 TTATATTTATATAAATT
1 TTATATTTA-ATAAATT
*
3377249 TTA-ATATAATAA
1 TTATATTTAATAA
3377261 TAATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 13 0.50
17 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTAATAAATT
Found at i:3377260 original size:15 final size:16
Alignment explanation
Indices: 3377216--3377280 Score: 53
Period size: 18 Copynumber: 4.0 Consensus size: 16
3377206 TTTATTATAA
* *
3377216 TTATATTTAATATATT
1 TTATATATAATAAATT
*
3377232 TTATATTTATATAAATT
1 TTATATATA-ATAAATT
*
3377249 TTAATATAATAATAATTT
1 TT-ATAT-ATAATAAATT
3377267 TTAT-TAT-ATAAATT
1 TTATATATAATAAATT
3377281 ATAAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 6 0.14
15 2 0.05
16 10 0.24
17 10 0.24
18 12 0.29
19 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATATAATAAATT
Found at i:3377844 original size:30 final size:29
Alignment explanation
Indices: 3377798--3377868 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
3377788 TGTGTCAGAT
*
3377798 ATTAAATTTT-TAATTTTAATGATTAAAA
1 ATTAAATTTTATAATTTTAATGATAAAAA
*
3377826 ATTAAATTTTAATAATTTTAATTATAAAAA
1 ATTAAATTTT-ATAATTTTAATGATAAAAA
*
3377856 ATATATATTTTAT
1 AT-TAAATTTTAT
3377869 TATATATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 10 0.27
30 20 0.54
31 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
ATTAAATTTTATAATTTTAATGATAAAAA
Found at i:3380431 original size:19 final size:19
Alignment explanation
Indices: 3380391--3380428 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3380381 ATTAATTTAT
3380391 TAAAATTTATATAAATATA
1 TAAAATTTATATAAATATA
3380410 TAAAATTT-TA-AAATA-A
1 TAAAATTTATATAAATATA
3380426 TAA
1 TAA
3380429 TAAGATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 5 0.26
18 2 0.11
19 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTTATATAAATATA
Found at i:3380431 original size:27 final size:26
Alignment explanation
Indices: 3380346--3380427 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
3380336 TTATGATGAT
*
3380346 ATAATATAATTAT-TAAAA-TTT-AA
1 ATAATATAAATATATAAAATTTTAAA
* *
3380369 ATAATATAAAT-TATTAATTTATTAAA
1 ATAATATAAATATATAAAATT-TTAAA
*
3380395 ATTTATATAAATATATAAAATTTTAAA
1 A-TAATATAAATATATAAAATTTTAAA
3380422 ATAATA
1 ATAATA
3380428 ATAAGATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 1 0.02
23 13 0.28
24 1 0.02
25 2 0.04
26 7 0.15
27 15 0.33
28 7 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATAAAATTTTAAA
Found at i:3381402 original size:19 final size:17
Alignment explanation
Indices: 3381368--3381425 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 17
3381358 AAAATATATT
3381368 TTATAAAAATAATAATA
1 TTATAAAAATAATAATA
3381385 TTATAAAAATAATTTAATA
1 TTATAAAAATAA--TAATA
*
3381404 TTAAATTAAAATAAATAATA
1 TT--ATAAAAAT-AATAATA
3381424 TT
1 TT
3381426 TTATAACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 12 0.34
19 7 0.20
20 7 0.20
21 7 0.20
22 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTATAAAAATAATAATA
Found at i:3382618 original size:14 final size:13
Alignment explanation
Indices: 3382590--3382632 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
3382580 AAAGTAAATT
*
3382590 AATTATTTGATAA
1 AATTATTTTATAA
3382603 AATTATTTTTATAA
1 AATTA-TTTTATAA
*
3382617 AATTAAATTTATAA
1 AATT-ATTTTATAA
3382631 AA
1 AA
3382633 ATTTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 5 0.19
14 20 0.77
15 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
AATTATTTTATAA
Found at i:3382685 original size:17 final size:17
Alignment explanation
Indices: 3382664--3382712 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3382654 AAAAGCATTG
*
3382664 AATTTTAAATTTTAAAT
1 AATTTTAAATTTTAAAA
*
3382681 TATTTTATTAATTTTAAAA
1 AATTTTA--AATTTTAAAA
3382700 AATTATTAAATTT
1 AATT-TTAAATTT
3382713 ATTTTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 12 0.46
20 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTTAAATTTTAAAA
Found at i:3410257 original size:50 final size:51
Alignment explanation
Indices: 3410161--3410258 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 51
3410151 GATCCTAAAA
* *
3410161 AATAACATTTTAGAATCCATTTATAGATTCCTAAAAATTTATTAAAAACTT
1 AATAACATTTTAGAATCCATTTATAGATGCCTAAAAATTTAATAAAAACTT
3410212 AATAACATTTTAGAAT-CATTTATAGATCGCCTAAAAA-TTAATAAAAA
1 AATAACATTTTAGAATCCATTTATAGAT-GCCTAAAAATTTAATAAAAA
3410259 TTTATAGAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 20 0.45
51 24 0.55
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (51 bp):
AATAACATTTTAGAATCCATTTATAGATGCCTAAAAATTTAATAAAAACTT
Found at i:3410437 original size:15 final size:15
Alignment explanation
Indices: 3410396--3410434 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3410386 TTTTTCTTTT
*
3410396 TTATATATTATTATA
1 TTATATATTATTAGA
3410411 TTATATCATTATT-GA
1 TTATAT-ATTATTAGA
3410426 TTATATATT
1 TTATATATT
3410435 TATAGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 13 0.59
16 6 0.27
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
TTATATATTATTAGA
Found at i:3412284 original size:2 final size:2
Alignment explanation
Indices: 3412277--3412302 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3412267 GCTTTTGCGC
3412277 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
3412303 GTTGGTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3417168 original size:20 final size:21
Alignment explanation
Indices: 3417134--3417172 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3417124 GAGTAAATAT
*
3417134 TTTTTAATATTTATTTAATTA
1 TTTTTAATATCTATTTAATTA
3417155 TTTTTAA-ATCTATTTAAT
1 TTTTTAATATCTATTTAAT
3417173 ATTACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTAATATCTATTTAATTA
Found at i:3417668 original size:2 final size:2
Alignment explanation
Indices: 3417661--3417690 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3417651 CACCTGACCT
3417661 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3417691 TTAAGGCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3418510 original size:23 final size:22
Alignment explanation
Indices: 3418465--3418517 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
3418455 TTAGTTTTTT
*
3418465 TTTAAATTGATAAAAATATATA
1 TTTAAATTAATAAAAATATATA
3418487 TTTAATATTAATAATAAATA-ATA
1 TTTAA-ATTAATAA-AAATATATA
3418510 TTATAAAT
1 TT-TAAAT
3418518 AGTGAATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.19
23 14 0.52
24 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTTAAATTAATAAAAATATATA
Found at i:3420304 original size:22 final size:21
Alignment explanation
Indices: 3420272--3420314 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3420262 GTGCGGGCTT
3420272 ATTATATATAAATAAAAAAAA
1 ATTATATATAAATAAAAAAAA
* *
3420293 ATTATTATATAATTAATAAAAA
1 ATTA-TATATAAATAAAAAAAA
3420315 GGAGGACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTATATATAAATAAAAAAAA
Found at i:3420532 original size:19 final size:19
Alignment explanation
Indices: 3420492--3420546 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
3420482 ATAATATGAG
*
3420492 TTTAT-TAATATATAAAAAA
1 TTTATATAA-ATATATAAAA
*
3420511 TTTATATAAATATATAATA
1 TTTATATAAATATATAAAA
*
3420530 TTT-TA-AAATTTATAAAA
1 TTTATATAAATATATAAAA
3420547 GTAAATGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 10 0.32
18 2 0.06
19 16 0.52
20 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTATATAAATATATAAAA
Found at i:3423698 original size:48 final size:49
Alignment explanation
Indices: 3423641--3423739 Score: 146
Period size: 48 Copynumber: 2.0 Consensus size: 49
3423631 CAGCTGCCTC
* * **
3423641 TTAAATTTTATTAATTTTTTAGGCGTCTATAAAT-GATTCTAAATGTTA
1 TTAAATTTTAATAAATTTTTAGGAATCTATAAATGGATTCTAAATGTTA
*
3423689 TTAAGTTTTAATAAATTTTTAGGAATCTATAAATGGATTCTAAATGTTA
1 TTAAATTTTAATAAATTTTTAGGAATCTATAAATGGATTCTAAATGTTA
3423738 TT
1 TT
3423740 TTTTTAGGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 29 0.64
49 16 0.36
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.48
Consensus pattern (49 bp):
TTAAATTTTAATAAATTTTTAGGAATCTATAAATGGATTCTAAATGTTA
Found at i:3426300 original size:50 final size:50
Alignment explanation
Indices: 3426239--3426335 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 50
3426229 GATCCTAAAA
** * *
3426239 AATAACATTTTAGAATCCA-TTTATAGATTCCTAAAAATTTATTAAAACTT
1 AATAACATTTTAGAAT-CATTTTATAGACGCCTAAAAAATTAATAAAACTT
3426289 AATAACATTTTAGAATCATTTTATAGACGCCTAAAAAATTAATAAAA
1 AATAACATTTTAGAATCATTTTATAGACGCCTAAAAAATTAATAAAA
3426336 TTATAGAGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 2 0.05
50 40 0.95
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.36
Consensus pattern (50 bp):
AATAACATTTTAGAATCATTTTATAGACGCCTAAAAAATTAATAAAACTT
Found at i:3426512 original size:15 final size:15
Alignment explanation
Indices: 3426471--3426509 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3426461 TTTTTCTTTT
*
3426471 TTATATATTATTATA
1 TTATATATTATTAGA
3426486 TTATATCATTATT-GA
1 TTATAT-ATTATTAGA
3426501 TTATATATT
1 TTATATATT
3426510 TATAGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 13 0.59
16 6 0.27
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
TTATATATTATTAGA
Found at i:3428359 original size:2 final size:2
Alignment explanation
Indices: 3428352--3428377 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3428342 GCTTTTGCGC
3428352 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
3428378 GTTGGTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3432447 original size:2 final size:2
Alignment explanation
Indices: 3432440--3432475 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3432430 TGTGCCTTAA
3432440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3432476 AGGTCAGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3433024 original size:11 final size:11
Alignment explanation
Indices: 3432970--3433050 Score: 67
Period size: 11 Copynumber: 7.3 Consensus size: 11
3432960 TAAAATTTTG
3432970 ATAATATTAAAT
1 ATAATA-TAAAT
* * *
3432982 ATGATTTAAAA
1 ATAATATAAAT
3432993 ATAAT-TAAA-
1 ATAATATAAAT
3433002 ATAAATATTAAAT
1 AT-AATA-TAAAT
* *
3433015 ATTATATAAAA
1 ATAATATAAAT
*
3433026 ATAATATTAAT
1 ATAATATAAAT
3433037 ATAATATAAAT
1 ATAATATAAAT
3433048 ATA
1 ATA
3433051 TAAATATTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
9 2 0.04
10 7 0.13
11 33 0.60
12 11 0.20
13 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:3433043 original size:22 final size:24
Alignment explanation
Indices: 3432987--3433058 Score: 80
Period size: 22 Copynumber: 3.1 Consensus size: 24
3432977 TAAATATGAT
*
3432987 TTAAAAATAAT-T-AAAATAAATA
1 TTAAATATAATATAAAAATAAATA
*
3433009 TTAAATATTATATAAAAAT-AATA
1 TTAAATATAATATAAAAATAAATA
3433032 TT-AATATAATATAAATATATAAATA
1 TTAAATATAATATAAA-A-ATAAATA
3433057 TT
1 TT
3433059 TTTAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 21 0.50
23 8 0.19
24 7 0.17
25 6 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAAATATAATATAAAAATAAATA
Found at i:3433047 original size:33 final size:32
Alignment explanation
Indices: 3432970--3433049 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 32
3432960 TAAAATTTTG
*
3432970 ATAATATTAAATATGATTTAAAAATAATTAAA
1 ATAATATTAAATATGATATAAAAATAATTAAA
* *
3433002 ATAAATATTAAATATTATATAAAAATAATATTAAT
1 AT-AATATTAAATATGATATAAAAAT-A-ATTAAA
3433037 ATAATA-TAAATAT
1 ATAATATTAAATAT
3433050 ATAAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 2 0.05
33 28 0.67
34 5 0.12
35 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (32 bp):
ATAATATTAAATATGATATAAAAATAATTAAA
Found at i:3433108 original size:33 final size:33
Alignment explanation
Indices: 3433039--3433118 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
3433029 ATATTAATAT
* *
3433039 AATATAAATATATAAATATTTTTAAAATTTATAA
1 AATATAAAT-TATTAATATTATTAAAATTTATAA
3433073 AATATAAATTATTAATA-TATTAAAATTTATAAA
1 AATATAAATTATTAATATTATTAAAATTTAT-AA
*
3433106 AATATAAAATATT
1 AATATAAATTATT
3433119 TTAAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.29
33 21 0.50
34 9 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATAAATTATTAATATTATTAAAATTTATAA
Found at i:3433552 original size:15 final size:15
Alignment explanation
Indices: 3433483--3433552 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
3433473 ACTTAAATCA
*
3433483 AAAATAATTATAACTT
1 AAAATAATTA-AATTT
3433499 AAAATAATTTAAATTT
1 AAAATAA-TTAAATTT
* **
3433515 AAAAAAATTAAATAC
1 AAAATAATTAAATTT
*
3433530 ATAATAATTAAATTT
1 AAAATAATTAAATTT
*
3433545 AAACTAAT
1 AAAATAAT
3433553 CTAATTACTA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
15 23 0.53
16 17 0.40
17 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATAATTAAATTT
Found at i:3436749 original size:1 final size:1
Alignment explanation
Indices: 3436743--3436773 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
3436733 GTGAGTGGAC
*
3436743 GGGGGGGGGGGGGGGGGGGTGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3436774 TACGGGAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:3440922 original size:19 final size:17
Alignment explanation
Indices: 3440888--3440945 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 17
3440878 AAAATATATT
3440888 TTATAAAAATAATAATA
1 TTATAAAAATAATAATA
3440905 TTATAAAAATAATTTAATA
1 TTATAAAAATAA--TAATA
*
3440924 TTAAATTAAAATAAATAATA
1 TT--ATAAAAAT-AATAATA
3440944 TT
1 TT
3440946 TTATAACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 12 0.34
19 7 0.20
20 7 0.20
21 7 0.20
22 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTATAAAAATAATAATA
Found at i:3442141 original size:14 final size:13
Alignment explanation
Indices: 3442113--3442155 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
3442103 AAAGTAAATT
*
3442113 AATTATTTGATAA
1 AATTATTTTATAA
3442126 AATTATTTTTATAA
1 AATTA-TTTTATAA
*
3442140 AATTAAATTTATAA
1 AATT-ATTTTATAA
3442154 AA
1 AA
3442156 ATTTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 5 0.19
14 20 0.77
15 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
AATTATTTTATAA
Found at i:3443894 original size:19 final size:18
Alignment explanation
Indices: 3443860--3443928 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 18
3443850 AATCATTTTG
*
3443860 TTTTATATTAAAAATTATA
1 TTTTAAATT-AAAATTATA
3443879 TTATTAAATTAAAATTATA
1 TT-TTAAATTAAAATTATA
*
3443898 TTTTTATTAATTATTAATTATA
1 -TTTTA--AATTA-AAATTATA
3443920 TTTTAAATT
1 TTTTAAATT
3443929 TTTAAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
19 18 0.42
20 8 0.19
21 10 0.23
22 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAATTAAAATTATA
Found at i:3443907 original size:22 final size:22
Alignment explanation
Indices: 3443866--3443923 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 22
3443856 TTTGTTTTAT
* *
3443866 ATTAAAAATTATATTATTA--A
1 ATTATAAATTATATTTTTATTA
3443886 ATTA-AAATTATATTTTTATTA
1 ATTATAAATTATATTTTTATTA
*
3443907 ATTATTAATTATATTTT
1 ATTATAAATTATATTTT
3443924 AAATTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
20 4 0.12
21 5 0.15
22 11 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATAAATTATATTTTTATTA
Found at i:3443933 original size:19 final size:19
Alignment explanation
Indices: 3443872--3443938 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
3443862 TTATATTAAA
**
3443872 AATTATATTATTAAA-TTAA
1 AATTATATT-TTAAATTTTT
*
3443891 AATTATATTTTTATTAATTATT
1 AATTATA-TTTTA--AATTTTT
3443913 AATTATATTTTAAATTTTT
1 AATTATATTTTAAATTTTT
*
3443932 AAATATA
1 AATTATA
3443939 AAAAAATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 22 0.56
20 2 0.05
21 7 0.18
22 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTATATTTTAAATTTTT
Found at i:3445648 original size:21 final size:19
Alignment explanation
Indices: 3445606--3445645 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3445596 TTATACATAA
*
3445606 TAATATATTTATAAAGTTT
1 TAATATATTAATAAAGTTT
*
3445625 TAATATATTAAATAAAATTT
1 TAATATATT-AATAAAGTTT
3445645 T
1 T
3445646 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TAATATATTAATAAAGTTT
Found at i:3446451 original size:2 final size:2
Alignment explanation
Indices: 3446393--3446438 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3446383 ATTTTTCAGA
3446393 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3446435 TC TC
1 TC TC
3446439 CCCAAATCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3460906 original size:168 final size:168
Alignment explanation
Indices: 3460616--3460953 Score: 577
Period size: 168 Copynumber: 2.0 Consensus size: 168
3460606 TCTTATTTAT
* * *
3460616 TTGACCTCTTCTCCATTAGAGCACCTTCATTTTATTAATCGACCTAAGAAGTTGCAATATCAGTA
1 TTGACCTCTCCTCCATTAGAGCACCTTCATTTCATTAATCGACATAAGAAGTTGCAATATCAGTA
* *
3460681 GTAAACGAAATAAAACATCCTTGTTCATCCAAAAACATGTAATACTGTATAATTTCAATATCTAA
66 GTAAACGAAATAAAACATCCTTATTCATCCAAAAACATGTAATACGGTATAATTTCAATATCTAA
3460746 CTGATACATCAGGAAAGTTTTAATACTATCAAAGTAGG
131 CTGATACATCAGGAAAGTTTTAATACTATCAAAGTAGG
*
3460784 TTGACCTCTCCTCCATTAGAGCACCTTCGTTTCATTAATCGACATAAGAAGTTGCAATATCAGTA
1 TTGACCTCTCCTCCATTAGAGCACCTTCATTTCATTAATCGACATAAGAAGTTGCAATATCAGTA
* *
3460849 GTAAACGAAATAAAACATCCTTATTTATCCAAAAACATGTAATACGGTATGATTTCAATATCTAA
66 GTAAACGAAATAAAACATCCTTATTCATCCAAAAACATGTAATACGGTATAATTTCAATATCTAA
* **
3460914 CTGATACGTCAGGAAAGTTTTAATACTATTTAAGTAGG
131 CTGATACATCAGGAAAGTTTTAATACTATCAAAGTAGG
3460952 TT
1 TT
3460954 ATACAATGAA
Statistics
Matches: 159, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
168 159 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (168 bp):
TTGACCTCTCCTCCATTAGAGCACCTTCATTTCATTAATCGACATAAGAAGTTGCAATATCAGTA
GTAAACGAAATAAAACATCCTTATTCATCCAAAAACATGTAATACGGTATAATTTCAATATCTAA
CTGATACATCAGGAAAGTTTTAATACTATCAAAGTAGG
Found at i:3462360 original size:5 final size:5
Alignment explanation
Indices: 3462342--3462419 Score: 63
Period size: 5 Copynumber: 15.2 Consensus size: 5
3462332 TTTTTTTAAT
* *
3462342 ATATA AT-T- ATATA ATATAA ATATA ATATTAA AAATA ATTAAA ATATA
1 ATATA ATATA ATATA ATAT-A ATATA ATA-T-A ATATA A-TATA ATATA
*
3462389 ATATA AAATTA ATATA ATATA A-ATA ATATA A
1 ATATA ATA-TA ATATA ATATA ATATA ATATA A
3462420 ATTATCATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
3 2 0.03
4 6 0.10
5 34 0.58
6 14 0.24
7 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:3462366 original size:11 final size:11
Alignment explanation
Indices: 3462350--3462419 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
3462340 ATATATAATT
3462350 ATATAATATAA
1 ATATAATATAA
3462361 ATATAATATTAA
1 ATATAATA-TAA
*
3462373 AAATAAT-TAAA
1 ATATAATAT-AA
3462384 ATATAATATAA
1 ATATAATATAA
3462395 A-ATTAATAT-A
1 ATA-TAATATAA
3462405 ATATAA-AT-A
1 ATATAATATAA
3462414 ATATAA
1 ATATAA
3462420 ATTATCATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
9 9 0.17
10 7 0.13
11 26 0.50
12 10 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAATATAA
Found at i:3462385 original size:23 final size:21
Alignment explanation
Indices: 3462352--3462414 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 21
3462342 ATATAATTAT
3462352 ATAATATAAATATAATATTAAAA
1 ATAATA-AAATATAATA-TAAAA
3462375 ATAATTAAAATATAATATAAAA
1 ATAA-TAAAATATAATATAAAA
* *
3462397 TTAATATAATATAA-ATAA
1 ATAATAAAATATAATATAA
3462415 TATAAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 4 0.11
21 9 0.24
22 8 0.22
23 14 0.38
24 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATAAAATATAATATAAAA
Found at i:3462441 original size:24 final size:25
Alignment explanation
Indices: 3462389--3462470 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
3462379 TTAAAATATA
* *
3462389 ATATAAA--ATTAATATAATATAAATA
1 ATATAAATTATTAATAT-AT-TAATTT
* *
3462414 ATATAAATTA-TCATA-ATTTATTT
1 ATATAAATTATTAATATATTAATTT
3462437 CATATAAATTATTAATATATTAATTT
1 -ATATAAATTATTAATATATTAATTT
3462463 ATATAAAT
1 ATATAAAT
3462471 ATAATACAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
23 3 0.07
24 12 0.26
25 19 0.41
26 11 0.24
27 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATAAATTATTAATATATTAATTT
Found at i:3462457 original size:22 final size:23
Alignment explanation
Indices: 3462389--3462457 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
3462379 TTAAAATATA
** *
3462389 ATATAAAATTAATATAATATAAATA
1 ATAT-AAATT-ATATAATATATTTC
*
3462414 ATATAAATTATCATAATTTATTTC
1 ATATAAATTAT-ATAATATATTTC
3462438 ATATAAATTAT-TAATATATT
1 ATATAAATTATATAATATATT
3462458 AATTTATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.21
23 2 0.05
24 24 0.63
25 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATAAATTATATAATATATTTC
Found at i:3464334 original size:20 final size:19
Alignment explanation
Indices: 3464279--3464334 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 19
3464269 AATTTGAATT
*
3464279 TTATTAAAAATTTTAAATA
1 TTATTAAAAATTTTAAAAA
3464298 TTAATTAAAAA---TAAAAA
1 TT-ATTAAAAATTTTAAAAA
3464315 TATATTAAAAATTTTAAAAA
1 T-TATTAAAAATTTTAAAAA
3464335 AATTTCAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
17 14 0.45
18 1 0.03
19 2 0.06
20 14 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTATTAAAAATTTTAAAAA
Found at i:3465493 original size:20 final size:19
Alignment explanation
Indices: 3465470--3465507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3465460 TAAATAATTT
3465470 ATTT-AGTTTGATATGTTTAA
1 ATTTAAGTTT-ATAT-TTTAA
3465490 ATTTAAGTTTATATTTTA
1 ATTTAAGTTTATATTTTA
3465508 TTACGTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
ATTTAAGTTTATATTTTAA
Found at i:3468908 original size:2 final size:2
Alignment explanation
Indices: 3468901--3468937 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3468891 AGGAACCTTA
*
3468901 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3468938 GCAATTGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3469863 original size:2 final size:2
Alignment explanation
Indices: 3469858--3469891 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3469848 CTTAAGTGTG
3469858 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
3469892 CTTGTGCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3474380 original size:3 final size:3
Alignment explanation
Indices: 3474372--3474398 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3474362 TGATTAGTTG
3474372 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3474399 ACAAACATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3475357 original size:28 final size:28
Alignment explanation
Indices: 3475321--3475394 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 28
3475311 TTTAATTTTT
* * *
3475321 TTTATATATTTAAAAAATTATATTTATA
1 TTTAAATATATAAAAAATTATAATTATA
* ** *
3475349 TTTAAATATGTATTAAA-TATAATTATT
1 TTTAAATATATAAAAAATTATAATTATA
3475376 TTTAAA-ATATAAAAAATTA
1 TTTAAATATATAAAAAATTA
3475395 AAATAACATA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
26 7 0.19
27 16 0.44
28 13 0.36
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TTTAAATATATAAAAAATTATAATTATA
Found at i:3477179 original size:35 final size:38
Alignment explanation
Indices: 3477109--3477188 Score: 105
Period size: 35 Copynumber: 2.2 Consensus size: 38
3477099 ATGTGTAAGT
*
3477109 AATTTTTTATGAATAAAAAATTTACAAAAATATTA-TA
1 AATTTTTTATGAAAAAAAAATTTACAAAAATATTATTA
3477146 AATTTTTT-T-AAAAAAAAATTTA-AAAAATAATTATTA
1 AATTTTTTATGAAAAAAAAATTTACAAAAAT-ATTATTA
*
3477182 TATTTTT
1 AATTTTT
3477189 ATAATAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 6 0.15
35 16 0.41
36 9 0.23
37 8 0.21
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (38 bp):
AATTTTTTATGAAAAAAAAATTTACAAAAATATTATTA
Found at i:3479401 original size:2 final size:2
Alignment explanation
Indices: 3479394--3479426 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3479384 TTTGTATAAA
3479394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3479427 CACATTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3480616 original size:7 final size:7
Alignment explanation
Indices: 3480606--3480639 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
3480596 AACATTTAAT
3480606 AATTTTA
1 AATTTTA
3480613 AATTTTA
1 AATTTTA
3480620 AATTTT-
1 AATTTTA
3480626 AATATTTA
1 AAT-TTTA
3480634 AATTTT
1 AATTTT
3480640 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 19 0.76
8 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:3480620 original size:23 final size:22
Alignment explanation
Indices: 3480574--3480639 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
3480564 ATCGATTCCT
* **
3480574 AATTATAATTATTTTAAAAGTTA
1 AATT-TAATAATTTTAAATTTTA
3480597 ACATTTAATAATTTTAAATTTTA
1 A-ATTTAATAATTTTAAATTTTA
3480620 AATTT--TAATATTTAAATTTT
1 AATTTAATAAT-TTTAAATTTT
3480640 TTTATTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.11
21 10 0.26
22 4 0.11
23 17 0.45
24 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTAATAATTTTAAATTTTA
Found at i:3480669 original size:2 final size:2
Alignment explanation
Indices: 3480662--3480702 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3480652 TTATAATCTC
3480662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3480703 AAAAGGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3481216 original size:21 final size:21
Alignment explanation
Indices: 3481192--3481235 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
3481182 TTATTTTTAT
3481192 ATTAATATTT-TAAAAAATATA
1 ATTAA-ATTTATAAAAAATATA
3481213 ATTAAATTTAAATAAAAAATATA
1 ATTAAATTT--ATAAAAAATATA
3481236 TTTTATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
23 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAATTTATAAAAAATATA
Found at i:3481857 original size:16 final size:16
Alignment explanation
Indices: 3481836--3481869 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3481826 ATGAACTTAA
3481836 ATAGCTATTTATAGCC
1 ATAGCTATTTATAGCC
3481852 ATAGCTATTTATAGCC
1 ATAGCTATTTATAGCC
3481868 AT
1 AT
3481870 GCTTAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (16 bp):
ATAGCTATTTATAGCC
Found at i:3486366 original size:50 final size:51
Alignment explanation
Indices: 3486307--3486418 Score: 138
Period size: 50 Copynumber: 2.2 Consensus size: 51
3486297 GCTTAGAGTC
* *
3486307 AATAATTATAATC-ACCGCTTTTTATTATCAAAAATTAATAAAAAATAATT
1 AATAATTATAATCTACCGCTCTCTATTATCAAAAATTAATAAAAAATAATT
** * * * *
3486357 AATAATTATAA-CTACTTCTCTCTATTATTAAAAGTTAGTAAAAAATTATT
1 AATAATTATAATCTACCGCTCTCTATTATCAAAAATTAATAAAAAATAATT
3486407 AATAATTATAAT
1 AATAATTATAAT
3486419 TATTTCCTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 51 0.98
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (51 bp):
AATAATTATAATCTACCGCTCTCTATTATCAAAAATTAATAAAAAATAATT
Found at i:3486794 original size:129 final size:129
Alignment explanation
Indices: 3486564--3486824 Score: 495
Period size: 129 Copynumber: 2.0 Consensus size: 129
3486554 ATATATATAT
3486564 ATCTGTCAATCAACGTTTGGTACAGATTATGAACGAGACAAAGATAAGACAAAGACCAGACTAGA
1 ATCTGTCAATCAACGTTTGGTACAGATTATGAACGAGACAAAGATAAGACAAAGACCAGACTAGA
*
3486629 CAAGACAAGTACCCCACAGCTTAAATCTTTGTCTGATAACCAGACAGTGATCGGAGATTGTGAG
66 CAAGACAAGTACCCCACAGCTTAAATCTTTGTCTGATAACCAGACAGTGATCAGAGATTGTGAG
3486693 ATCTGTCAATCAACGTTTGGTACAGATTATGAACGAGACAAAGATAAGACAAAGACCAGACTAGA
1 ATCTGTCAATCAACGTTTGGTACAGATTATGAACGAGACAAAGATAAGACAAAGACCAGACTAGA
* *
3486758 CAAGACAAGTACCGCATAGCTTAAATCTTTGTCTGATAACCAGACAGTGATCAGAGATTGTGAG
66 CAAGACAAGTACCCCACAGCTTAAATCTTTGTCTGATAACCAGACAGTGATCAGAGATTGTGAG
3486822 ATC
1 ATC
3486825 AGAGATGAAT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (129 bp):
ATCTGTCAATCAACGTTTGGTACAGATTATGAACGAGACAAAGATAAGACAAAGACCAGACTAGA
CAAGACAAGTACCCCACAGCTTAAATCTTTGTCTGATAACCAGACAGTGATCAGAGATTGTGAG
Found at i:3489440 original size:6 final size:6
Alignment explanation
Indices: 3489429--3489455 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3489419 TACTGGTTGG
3489429 TGGCGA TGGCGA TGGCGA TGGCGA TGG
1 TGGCGA TGGCGA TGGCGA TGGCGA TGG
3489456 TGGTTCTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.19
Consensus pattern (6 bp):
TGGCGA
Found at i:3491807 original size:13 final size:13
Alignment explanation
Indices: 3491789--3491814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3491779 TATCATAGTT
3491789 TTTGTATTACGCC
1 TTTGTATTACGCC
3491802 TTTGTATTACGCC
1 TTTGTATTACGCC
3491815 CATTCTCTAC
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:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTGTATTACGCC
Found at i:3491904 original size:33 final size:32
Alignment explanation
Indices: 3491867--3491929 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 32
3491857 TGATATAATT
3491867 ATATAAATTTTAATA-AATTAATAATATTTATTA
1 ATATAAATTTTAATATAATT-AT-ATATTTATTA
3491900 ATATAAATTTTAATATAATTATATATTTAT
1 ATATAAATTTTAATATAATTATATATTTAT
3491930 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 8 0.28
33 17 0.59
34 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATAAATTTTAATATAATTATATATTTATTA
Found at i:3491927 original size:18 final size:19
Alignment explanation
Indices: 3491859--3491924 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 19
3491849 ATTTAAAATG
3491859 ATATAATTATATAAATTTTA
1 ATATAATTATAT-AATTTTA
3491879 ATA-AATTA-ATAATATTT-
1 ATATAATTATATAAT-TTTA
3491896 AT-TAA-TATA-AATTTTA
1 ATATAATTATATAATTTTA
3491912 ATATAATTATATA
1 ATATAATTATATA
3491925 TTTATATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
15 3 0.08
16 7 0.18
17 11 0.28
18 9 0.23
19 6 0.15
20 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATAATTATATAATTTTA
Found at i:3500271 original size:19 final size:21
Alignment explanation
Indices: 3500229--3500270 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3500219 TATGAATATA
3500229 TTAATAGTATTATATAATTTT
1 TTAATAGTATTATATAATTTT
*
3500250 TTAATA-TATATATATTATTTT
1 TTAATAGTAT-TATATAATTTT
3500271 ATTTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTAATAGTATTATATAATTTT
Found at i:3501855 original size:13 final size:13
Alignment explanation
Indices: 3501839--3501881 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
3501829 TAATTTTATA
3501839 ATATAATATAATT
1 ATATAATATAATT
* *
3501852 ATATTATATATTT
1 ATATAATATAATT
*
3501865 ATATCATATAATT
1 ATATAATATAATT
3501878 ATAT
1 ATAT
3501882 GACCTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:3502618 original size:71 final size:72
Alignment explanation
Indices: 3502492--3502666 Score: 181
Period size: 71 Copynumber: 2.4 Consensus size: 72
3502482 TAACTGACTT
* *** * *
3502492 ATAATTTATTATTTATATTTAATTAAATTAAAATAATTTTATCTACGATGTTAAATATAAGCTTC
1 ATAATTTATT-TTT-TATTTAATTAAATTAAAATAATTATATCTACGACACTAAATACAAACTTC
3502557 ACTTA-TGA
64 ACTTATTGA
* * * * * *
3502565 ATAATTTACTTTTTATTTAATTAAATTAATATTATTATATTTATGACACTAAATACAAACTTTAC
1 ATAATTTATTTTTTATTTAATTAAATTAAAATAATTATATCTACGACACTAAATACAAACTTCAC
**
3502630 TTATTTT
66 TTATTGA
3502637 ATAATTTATTTTTTAAATTTAATTAAATTA
1 ATAATTTATTTTTT--ATTTAATTAAATTA
3502667 GTATAATTTA
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
71 44 0.52
72 17 0.20
73 9 0.11
74 14 0.17
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (72 bp):
ATAATTTATTTTTTATTTAATTAAATTAAAATAATTATATCTACGACACTAAATACAAACTTCAC
TTATTGA
Found at i:3503513 original size:2 final size:2
Alignment explanation
Indices: 3503506--3503556 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
3503496 CTTTCTTTCT
*
3503506 AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3503548 AG AG AG AG A
1 AG AG AG AG A
3503557 ACACTCCGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3508080 original size:2 final size:2
Alignment explanation
Indices: 3508073--3508102 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3508063 GGATATCTAG
3508073 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
3508103 GTTTTTAACA
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:3509886 original size:6 final size:6
Alignment explanation
Indices: 3509875--3509913 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
3509865 TCCCAATTTG
*
3509875 TTTTTA TTTTTA TTTTTA TTTTTA --TTTA TTTCTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
3509914 TTTGAGGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.14
6 25 0.86
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:3516209 original size:23 final size:22
Alignment explanation
Indices: 3516166--3516209 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
3516156 TATAGTTATG
3516166 AAAATAATTAAAATACGATATAA
1 AAAATAATTAAAATAC-ATATAA
3516189 AAAATAATATAAACATA-ATAT
1 AAAATAAT-TAAA-ATACATAT
3516210 GAATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 12 0.63
24 4 0.21
25 3 0.16
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAATAATTAAAATACATATAA
Found at i:3518494 original size:2 final size:2
Alignment explanation
Indices: 3518487--3518522 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3518477 TCCCCTTAAT
3518487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3518523 AAGAGTAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3518749 original size:22 final size:22
Alignment explanation
Indices: 3518705--3518750 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3518695 TTTTTAGGCG
*
3518705 AAGAAAGAAATAAAAGAAGAGA
1 AAGAAAGAAATAAAAGAAAAGA
*
3518727 AAGAAAG-AGTAAAAGGAAAAGA
1 AAGAAAGAAATAAAA-GAAAAGA
3518749 AA
1 AA
3518751 ACTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (22 bp):
AAGAAAGAAATAAAAGAAAAGA
Found at i:3518843 original size:32 final size:33
Alignment explanation
Indices: 3518792--3518870 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
3518782 TTATATTTAA
* *
3518792 AATAATATATATTCATATAAATTTTGATATATT
1 AATAATTTATATTCATATAAATTTTAATATATT
* *
3518825 AATAATTTAT-TTTATATAAATTTTAATTTATT
1 AATAATTTATATTCATATAAATTTTAATATATT
*
3518857 TATATATTTATATT
1 AATA-ATTTATATT
3518871 TTATTATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 22 0.56
33 15 0.38
34 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (33 bp):
AATAATTTATATTCATATAAATTTTAATATATT
Found at i:3518878 original size:14 final size:15
Alignment explanation
Indices: 3518855--3518904 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
3518845 TTTTAATTTA
3518855 TTTATATATTTATAT
1 TTTATATATTTATAT
*
3518870 TTTAT-TATTAATAT
1 TTTATATATTTATAT
*
3518884 TTTATGTCATATTATAT
1 TTTATAT-AT-TTATAT
3518901 TTTA
1 TTTA
3518905 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 13 0.43
15 6 0.20
16 2 0.07
17 9 0.30
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTATATATTTATAT
Found at i:3519071 original size:12 final size:13
Alignment explanation
Indices: 3519039--3519072 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3519029 TTAAATTTAA
3519039 TAATTTTAAATAT
1 TAATTTTAAATAT
*
3519052 TTATTTTAAA-AT
1 TAATTTTAAATAT
3519064 TAATTTTAA
1 TAATTTTAA
3519073 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTTTAAATAT
Found at i:3526379 original size:59 final size:59
Alignment explanation
Indices: 3526287--3526466 Score: 238
Period size: 59 Copynumber: 3.1 Consensus size: 59
3526277 ATTTTTATCA
*
3526287 CACCCAAACTTTAGATCGCCACCAAGGCT-ACCAGATTCGCACACTAGGTGAGGCCAAGT
1 CACCCAAACTTTAGATCGCCACCAAGG-TGACCAGATTCGCACACTAGGTGACGCCAAGT
* * *
3526346 CACCCAAACTTTAGATCACCACCAAGGTGACCAGATTCGCGCACTAGGTGATGCCAAGT
1 CACCCAAACTTTAGATCGCCACCAAGGTGACCAGATTCGCACACTAGGTGACGCCAAGT
* * ** * *
3526405 CACCCGAACTTT-GACCGCCACCAAGGTGACCCAGATTAACACACTATGTGACACCAAGT
1 CACCCAAACTTTAGATCGCCACCAAGGTGA-CCAGATTCGCACACTAGGTGACGCCAAGT
3526464 CAC
1 CAC
3526467 TTAGACTCAG
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
58 16 0.15
59 91 0.85
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (59 bp):
CACCCAAACTTTAGATCGCCACCAAGGTGACCAGATTCGCACACTAGGTGACGCCAAGT
Found at i:3530867 original size:21 final size:22
Alignment explanation
Indices: 3530843--3530884 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3530833 TAAAAGCTGT
* *
3530843 AATTTTAATTATAAA-AATTAA
1 AATTCTAATAATAAAGAATTAA
3530864 AATTCTAATAATAAAGAATTA
1 AATTCTAATAATAAAGAATTA
3530885 CCTTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AATTCTAATAATAAAGAATTAA
Found at i:3531604 original size:32 final size:28
Alignment explanation
Indices: 3531555--3531622 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 28
3531545 ATTTATTTAT
3531555 TTATATAATTAATTAAAATATTTATATAAA
1 TTATATAATTAATTAAAATA-TTAT-TAAA
3531585 TATAATATAA-TATATTAAAATATTATTAAA
1 T-T-ATATAATTA-ATTAAAATATTATTAAA
3531615 TTATATAA
1 TTATATAA
3531623 ATTATTTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 6 0.17
29 1 0.03
30 6 0.17
31 7 0.20
32 15 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TTATATAATTAATTAAAATATTATTAAA
Found at i:3531680 original size:20 final size:20
Alignment explanation
Indices: 3531653--3531698 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
3531643 TATCTTAATA
3531653 TTTTTAATAATTATT-TTAT
1 TTTTTAATAATTATTATTAT
*
3531672 TTATTTAATTATTATTATTAT
1 TT-TTTAATAATTATTATTAT
3531693 TTTTTA
1 TTTTTA
3531699 TTTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 16 0.67
21 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTAATAATTATTATTAT
Found at i:3542985 original size:17 final size:16
Alignment explanation
Indices: 3542963--3543006 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
3542953 TTTATATAAT
*
3542963 AAATAAGAAAATTAAA
1 AAATAAGAAAATGAAA
*
3542979 GAAATAAGAAAATGGAA
1 -AAATAAGAAAATGAAA
3542996 AAATAAGAAAA
1 AAATAAGAAAA
3543007 AAAATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
AAATAAGAAAATGAAA
Found at i:3543532 original size:27 final size:29
Alignment explanation
Indices: 3543464--3543543 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 29
3543454 GATAGTAAAT
3543464 TATATTATATTACTTATTAAAAAATATATGTA
1 TATATT-TATTA--TATTAAAAAATATATGTA
*
3543496 TAGA--TA-TATATTAAAAAAT-TAT-TA
1 TATATTTATTATATTAAAAAATATATGTA
3543520 TATATTTATTATATTAAAAAATAT
1 TATATTTATTATATTAAAAAATAT
3543544 TTTATTGTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
24 5 0.12
25 3 0.07
26 13 0.31
27 13 0.31
28 3 0.07
29 2 0.05
32 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (29 bp):
TATATTTATTATATTAAAAAATATATGTA
Found at i:3543557 original size:26 final size:26
Alignment explanation
Indices: 3543478--3543557 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 26
3543468 TTATATTACT
* * *
3543478 TATTAAAAAATATATGTATAG-ATATA
1 TATTAAAAAATAT-TTTATTGTATTTA
3543504 TATTAAAAAATTATTATATATT-TA-TTA
1 TATTAAAAAA-TATT-T-TATTGTATTTA
3543531 TATTAAAAAATATTTTATTGTATTTA
1 TATTAAAAAATATTTTATTGTATTTA
3543557 T
1 T
3543558 TTTTAAAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
24 4 0.09
25 3 0.07
26 19 0.42
27 15 0.33
28 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
TATTAAAAAATATTTTATTGTATTTA
Found at i:3543885 original size:19 final size:20
Alignment explanation
Indices: 3543840--3543887 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
3543830 ATATTTAATT
**
3543840 ATTATTTAATATTAAATTTA
1 ATTATTTAATATTAAATAAA
3543860 ATT-TTTAATATTAAA-AAA
1 ATTATTTAATATTAAATAAA
3543878 ATTATTTAAT
1 ATTATTTAAT
3543888 TAATTAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTATTTAATATTAAATAAA
Found at i:3544019 original size:2 final size:2
Alignment explanation
Indices: 3544012--3544057 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3544002 CTAAACATAC
3544012 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
3544054 AT AT
1 AT AT
3544058 CAACTATCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3544340 original size:23 final size:23
Alignment explanation
Indices: 3544314--3544365 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3544304 TACTATATGG
3544314 TAAAAAATAAT-TAAAATATAAAA
1 TAAAAAATAATAT-AAATATAAAA
* * *
3544337 TAAAAAGTAATATAAATTTAATA
1 TAAAAAATAATATAAATATAAAA
3544360 TAAAAA
1 TAAAAA
3544366 TTTAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAAAAATAATATAAATATAAAA
Found at i:3544375 original size:14 final size:14
Alignment explanation
Indices: 3544350--3544420 Score: 63
Period size: 16 Copynumber: 4.7 Consensus size: 14
3544340 AAAGTAATAT
3544350 AAATTT-AATATAA
1 AAATTTAAATATAA
3544363 AAATTTAAATATATTA
1 AAATTTAAATATA--A
*
3544379 AAATTTATATAATAA
1 AAATTTAAAT-ATAA
*
3544394 AAATTATTAATATATTA
1 AAA-T-TTAA-ATATAA
3544411 AAATTTAAAT
1 AAATTTAAAT
3544421 TAATATACTG
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
13 6 0.12
14 8 0.17
15 8 0.17
16 12 0.25
17 12 0.25
18 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTTAAATATAA
Found at i:3544410 original size:32 final size:29
Alignment explanation
Indices: 3544350--3544418 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 29
3544340 AAAGTAATAT
3544350 AAATTTAATATAAAAATTTAAATATATTA
1 AAATTTAATATAAAAATTTAAATATATTA
*
3544379 AAATTTATATAATAAAAATTATTAATATATTA
1 AAATTTA-AT-ATAAAAATT-TAAATATATTA
3544411 AAATTTAA
1 AAATTTAA
3544419 ATTAATATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 7 0.19
30 2 0.06
31 10 0.28
32 17 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATTTAATATAAAAATTTAAATATATTA
Found at i:3544412 original size:18 final size:17
Alignment explanation
Indices: 3544360--3544413 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 17
3544350 AAATTTAATA
*
3544360 TAAAAATTTAAATATAT
1 TAAAAATTTTAATATAT
*
3544377 T-AAAA-TTT-ATATAA
1 TAAAAATTTTAATATAT
3544391 TAAAAATTATTAATATAT
1 TAAAAATT-TTAATATAT
3544409 TAAAA
1 TAAAA
3544414 TTTAAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.20
15 6 0.20
16 5 0.17
17 3 0.10
18 10 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAAATTTTAATATAT
Done.