Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 13 of 255
Found at i:3744374 original size:20 final size:20
Alignment explanation
Indices: 3744303--3744434 Score: 69
Period size: 20 Copynumber: 6.3 Consensus size: 20
3744293 ATATATATAT
*
3744303 AAATAATATATAATAAATAATA
1 AAATAATA-ATAAT-GATAATA
*
3744325 AACAT-ATAAT-ATAATAATA
1 AA-ATAATAATAATGATAATA
* *
3744344 ATAT-ATAAATAATGATGATA
1 AAATAAT-AATAATGATAATA
*
3744364 AAATAATAATAACTTG-TGA-A
1 AAATAATAATAA--TGATAATA
*
3744384 AAATAATATATAATAAATAATA
1 AAATAATA-ATAAT-GATAATA
3744406 ATAAT-ATAAATAATGTATAATA
1 A-AATAAT-AATAATG-ATAATA
3744428 AAATAAT
1 AAATAAT
3744435 TTTATGATAT
Statistics
Matches: 89, Mismatches: 7, Indels: 28
0.72 0.06 0.23
Matches are distributed among these distances:
18 4 0.04
19 12 0.13
20 26 0.29
21 16 0.18
22 25 0.28
23 6 0.07
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATAATAATAATGATAATA
Found at i:3752470 original size:6 final size:6
Alignment explanation
Indices: 3752459--3752491 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3752449 AAAGGGGAGA
3752459 TCAAAG TCAAAG TCAAAG TCAAAG TCAAAG TCA
1 TCAAAG TCAAAG TCAAAG TCAAAG TCAAAG TCA
3752492 TGAGAAAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (6 bp):
TCAAAG
Found at i:3753947 original size:21 final size:21
Alignment explanation
Indices: 3753921--3753961 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3753911 AGACGAGCAA
* *
3753921 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3753942 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3753962 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3764373 original size:131 final size:131
Alignment explanation
Indices: 3764139--3764396 Score: 401
Period size: 131 Copynumber: 2.0 Consensus size: 131
3764129 CTATTCATTC
* * ** *
3764139 AAAAATTCTTTAAAACGAAGGCAATGTTCATTGTTTGGCAATTCGGGGAATCGTGCCCTATTGTG
1 AAAAATTCTTCAAAACAAAGGCAATGTTCATTGTTTGAAAATTCGGGGAATCGTGCCCTATCGTG
* * *
3764204 CCGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAATATTCCTTTGGAATTTCACTCATGTCTT
66 CCGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTCTT
3764269 T
131 T
* *
3764270 AAAAATTCTTCAAAACAAAGGTAATGTTCGA-TGTTTGAAAATTCGGGGAGTCGTGCCCTATCGT
1 AAAAATTCTTCAAAACAAAGGCAATGTTC-ATTGTTTGAAAATTCGGGGAATCGTGCCCTATCGT
*
3764334 GCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGT
65 GCCGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGT
3764397 TCTCCAAATC
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
131 114 0.99
132 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (131 bp):
AAAAATTCTTCAAAACAAAGGCAATGTTCATTGTTTGAAAATTCGGGGAATCGTGCCCTATCGTG
CCGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTCTT
T
Found at i:3765516 original size:13 final size:13
Alignment explanation
Indices: 3765498--3765522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3765488 ATTGGGCTAT
3765498 GTATATTATTGTG
1 GTATATTATTGTG
3765511 GTATATTATTGT
1 GTATATTATTGT
3765523 CTGTATTGTT
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:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
GTATATTATTGTG
Found at i:3766089 original size:130 final size:129
Alignment explanation
Indices: 3765850--3766181 Score: 451
Period size: 130 Copynumber: 2.6 Consensus size: 129
3765840 ATAATTATTC
*
3765850 GTTTAAAAAA-TCTTTAAAACGAAGGCAATATTCGATGTTTGGAAATTCGG-GCAATCGTGCCCT
1 GTTTAAAAAATTCTTTAAAA-GAAGGCAATGTTCGATGTTTGGAAATTCGGAG-AATCGTGCCCT
* *
3765913 ATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTCACTCA
64 ATCGTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCA
3765978 T
129 T
* *
3765979 GTTTAAAAAATTCTTTAAAATGAAGGCAACGTTCGATGTTTGGGAATTCGGAGAATCGTGCCCTA
1 GTTTAAAAAATTCTTTAAAA-GAAGGCAATGTTCGATGTTTGGAAATTCGGAGAATCGTGCCCTA
* *
3766044 TCGTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGGATATTCCTTTAGAATTTCACTCTT
65 TCGTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCAT
*** * * * * *
3766109 GTTTTCTAAATTC--TAAAACAAGGCAATGTTCAATGTCTAGAAATTC-GAGGATCGTGCCCTA-
1 GTTTAAAAAATTCTTTAAAAGAAGGCAATGTTCGATGTTTGGAAATTCGGAGAATCGTGCCCTAT
3766170 CTGTGCTGGGTT
66 C-GTGCTGGGTT
3766182 TCGGTTTTTT
Statistics
Matches: 182, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
125 1 0.01
126 24 0.13
127 22 0.12
128 5 0.03
129 10 0.05
130 119 0.65
131 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (129 bp):
GTTTAAAAAATTCTTTAAAAGAAGGCAATGTTCGATGTTTGGAAATTCGGAGAATCGTGCCCTAT
CGTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCAT
Found at i:3767787 original size:21 final size:21
Alignment explanation
Indices: 3767761--3767805 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3767751 TTTATGAGAA
*
3767761 TTAAAATATAAAAATAAAATT
1 TTAAAAGATAAAAATAAAATT
* * *
3767782 TTAAAAGATTAAATTATAATT
1 TTAAAAGATAAAAATAAAATT
3767803 TTA
1 TTA
3767806 TTAATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAAGATAAAAATAAAATT
Found at i:3768215 original size:14 final size:15
Alignment explanation
Indices: 3768196--3768286 Score: 76
Period size: 18 Copynumber: 5.5 Consensus size: 15
3768186 TCTTAGATGT
3768196 GATATG-CAATCTTA
1 GATATGACAATCTTA
3768210 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
*
3768227 GATATGATTGAAATCTTA
1 GATATGA---CAATCTTA
3768245 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
3768262 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
3768280 GATATGA
1 GATATGA
3768287 TATACAATCT
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
17 27 0.42
18 28 0.44
20 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:3768224 original size:17 final size:17
Alignment explanation
Indices: 3768184--3768300 Score: 146
Period size: 17 Copynumber: 6.5 Consensus size: 17
3768174 AATGATATGT
*
3768184 AATCTTAGATGTGATATGC
1 AATCTTAGATATGATA--C
3768203 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
3768220 AATCTTAGATATGATTGA-
1 AATCTTAGATATGA-T-AC
3768238 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
*
3768255 AATCTTAGATATGATTGC
1 AATCTTAGATATGA-TAC
3768273 AATCTTAGATATGATATAC
1 AATCTTAGATATG--ATAC
3768292 AATCTTAGA
1 AATCTTAGA
3768301 AGATATGATT
Statistics
Matches: 89, Mismatches: 3, Indels: 12
0.86 0.03 0.12
Matches are distributed among these distances:
16 1 0.01
17 30 0.34
18 30 0.34
19 27 0.30
20 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (17 bp):
AATCTTAGATATGATAC
Found at i:3768247 original size:35 final size:35
Alignment explanation
Indices: 3768184--3768300 Score: 189
Period size: 35 Copynumber: 3.3 Consensus size: 35
3768174 AATGATATGT
*
3768184 AATCTTAGATGTGATATGCAATCTTAGATATGATAC
1 AATCTTAGATATGAT-TGCAATCTTAGATATGATAC
*
3768220 AATCTTAGATATGATTGAAATCTTAGATATGATAC
1 AATCTTAGATATGATTGCAATCTTAGATATGATAC
3768255 AATCTTAGATATGATTGCAATCTTAGATATGATATAC
1 AATCTTAGATATGATTGCAATCTTAGATATG--ATAC
3768292 AATCTTAGA
1 AATCTTAGA
3768301 AGATATGATT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
35 49 0.64
36 14 0.18
37 13 0.17
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (35 bp):
AATCTTAGATATGATTGCAATCTTAGATATGATAC
Found at i:3774039 original size:15 final size:15
Alignment explanation
Indices: 3774019--3774074 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
3774009 CTTCTATTTC
3774019 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
*
3774034 AAAAAAAGAAAAG-A
1 AAAAAAAAAAAAGAA
* *
3774048 AAAAGAGAAAAAGAA
1 AAAAAAAAAAAAGAA
3774063 AAAAAAGAAAAA
1 AAAAAA-AAAAA
3774075 TGGAGAGGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.33
15 18 0.55
16 4 0.12
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:3774045 original size:23 final size:22
Alignment explanation
Indices: 3774019--3774074 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
3774009 CTTCTATTTC
3774019 AAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAGAAAAAAAAA
* * *
3774041 GAAAAGAAAAAGAGAAAAAGAAA
1 -AAAAAAAAAAAAGAAAAAAAAA
*
3774064 AAAAAGAAAAA
1 AAAAAAAAAAA
3774075 TGGAGAGGCC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAAGAAAAAAAAA
Found at i:3774423 original size:13 final size:14
Alignment explanation
Indices: 3774399--3774431 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3774389 TTTAATTTTC
3774399 AAAATTTCAAAAAA
1 AAAATTTCAAAAAA
*
3774413 AAAATTT-AAAATA
1 AAAATTTCAAAAAA
3774426 AAAATT
1 AAAATT
3774432 GCATTTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTTCAAAAAA
Found at i:3774467 original size:30 final size:30
Alignment explanation
Indices: 3774427--3774528 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
3774417 TTTAAAATAA
* *
3774427 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
3774457 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* **
3774487 AAATTTCACTTAAACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
3774517 AAATTTCATTTT
1 AAATTTCATTTT
3774529 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 4 0.07
30 57 0.93
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:3775428 original size:17 final size:17
Alignment explanation
Indices: 3775385--3775456 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 17
3775375 CCAGCCCAAC
3775385 AGAGAGAAAAAAAGAAAGAA
1 AGAGA-AAAAAAAG-AA-AA
3775405 AGAAGAAAAAAAAGAAAA
1 AG-AGAAAAAAAAGAAAA
3775423 AGAG-AAAAAAAGAAAA
1 AGAGAAAAAAAAGAAAA
3775439 A-AGAAAAAACAAGAAAA
1 AGAGAAAAAA-AAGAAAA
3775456 A
1 A
3775457 AGGGGTTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.04
16 18 0.37
17 10 0.20
18 4 0.08
19 2 0.04
20 10 0.20
21 3 0.06
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (17 bp):
AGAGAAAAAAAAGAAAA
Found at i:3775429 original size:28 final size:29
Alignment explanation
Indices: 3775389--3775446 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
3775379 CCCAACAGAG
* *
3775389 AGAAAAAAAGAAAGAAAGAAGAAA-AAAA
1 AGAAAAAAAGAAAAAAAGAAAAAAGAAAA
*
3775417 AGAAAAAGAGAAAAAAAGAAAAAAGAAAA
1 AGAAAAAAAGAAAAAAAGAAAAAAGAAAA
3775446 A
1 A
3775447 ACAAGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (29 bp):
AGAAAAAAAGAAAAAAAGAAAAAAGAAAA
Found at i:3775446 original size:8 final size:8
Alignment explanation
Indices: 3775389--3775457 Score: 68
Period size: 8 Copynumber: 8.0 Consensus size: 8
3775379 CCCAACAGAG
3775389 AGAAAAAA
1 AGAAAAAA
3775397 AGAAAGAAAGA
1 AG-AA-AAA-A
3775408 AGAAAAAAA
1 AG-AAAAAA
*
3775417 AGAAAAAG
1 AGAAAAAA
3775425 AGAAAAAA
1 AGAAAAAA
3775433 AG-AAAAA
1 AGAAAAAA
3775440 AGAAAAAACA
1 AG-AAAAA-A
3775450 AGAAAAAA
1 AGAAAAAA
3775458 GGGGTTCAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
7 7 0.13
8 17 0.32
9 14 0.26
10 9 0.17
11 6 0.11
ACGTcount: A:0.83, C:0.01, G:0.16, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:3775457 original size:17 final size:16
Alignment explanation
Indices: 3775393--3775458 Score: 89
Period size: 17 Copynumber: 4.0 Consensus size: 16
3775383 ACAGAGAGAA
*
3775393 AAAAAGAAAGAAAGAAG
1 AAAAA-AAAGAAAAAAG
3775410 AAAAAAAAG-AAAAAG
1 AAAAAAAAGAAAAAAG
3775425 AGAAAAAAAGAAAAAAG
1 A-AAAAAAAGAAAAAAG
3775442 AAAAAACAAGAAAAAAG
1 AAAAAA-AAGAAAAAAG
3775459 GGGTTCAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
15 6 0.13
16 17 0.38
17 22 0.49
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:3775619 original size:5 final size:5
Alignment explanation
Indices: 3775609--3775646 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
3775599 CATTTATATT
*
3775609 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTCAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
3775647 TTATTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:3775653 original size:5 final size:5
Alignment explanation
Indices: 3775645--3775674 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3775635 TTAATTCAAT
3775645 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3775675 AATACTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:3776022 original size:18 final size:18
Alignment explanation
Indices: 3776001--3776482 Score: 198
Period size: 17 Copynumber: 26.7 Consensus size: 18
3775991 AAATTTTTCA
3776001 TGTTTTCAAAAATTCTCG
1 TGTTTTCAAAAATTCTCG
**
3776019 TGTTTTCAAAAAAATT-TTA
1 TGTTTTC--AAAAATTCTCG
* *
3776038 T-TTTTCAAAATTTTTCG
1 TGTTTTCAAAAATTCTCG
*
3776055 TGTTTTCTAAAAATT-TCCA
1 TGTTTTC-AAAAATTCT-CG
* * *
3776074 T-ATTTCTAAAATTTTCG
1 TGTTTTCAAAAATTCTCG
**
3776091 TGTTTAAAAAAATT-TCG
1 TGTTTTCAAAAATTCTCG
* * * **
3776108 TATTTTCAAAATTTTTTTATTT
1 TGTTTTCAAAA----ATTCTCG
* *
3776130 TTTTTTCAACAATTCTCG
1 TGTTTTCAAAAATTCTCG
* *
3776148 AG-TTTCACAAATTCTCG
1 TGTTTTCAAAAATTCTCG
* * **
3776165 TGTTTT-AAAATTTTTTA
1 TGTTTTCAAAAATTCTCG
*
3776182 TGTTTTAAAAAATAAATTTCTCG
1 TGTTTT---CAA-AAA-TTCTCG
* *
3776205 TG-TTTCAAAAAAATTGTCA
1 TGTTTTC--AAAAATTCTCG
* *
3776224 TGTTTT-AAAAATTTTCA
1 TGTTTTCAAAAATTCTCG
*
3776241 TG-TTTCTAAAATGT-T--
1 TGTTTTCAAAAAT-TCTCG
*
3776256 TGTATTTCAAAAATCCTCG
1 TGT-TTTCAAAAATTCTCG
*
3776275 TGTTTTCAAAAATTCTCA
1 TGTTTTCAAAAATTCTCG
*
3776293 TG-TTT-AAAAAATCTTCG
1 TGTTTTCAAAAATTC-TCG
*
3776310 TGTTTTC-AAAATTCTAG
1 TGTTTTCAAAAATTCTCG
* *
3776327 TG-TTTCAAAAATTTTCA
1 TGTTTTCAAAAATTCTCG
* *
3776344 TGTTTTCAAAAATTTCCCC
1 TGTTTTCAAAAA-TTCTCG
3776363 TGTTTTCAAAAATTCTCG
1 TGTTTTCAAAAATTCTCG
* * * *
3776381 TATTTT-GAAAATTTTCT
1 TGTTTTCAAAAATTCTCG
3776398 TGTTTTCAAAAAAAACTT-TCG
1 TGTTTTC---AAAAA-TTCTCG
*
3776419 TGTTTT-ATAAA-TCTCCG
1 TGTTTTCAAAAATTCT-CG
3776436 TGTTTTCAAAAATTCTCG
1 TGTTTTCAAAAATTCTCG
* *
3776454 T-CTTTCAAAAATTTTCG
1 TGTTTTCAAAAATTCTCG
3776471 TGTTTTCAAAAA
1 TGTTTTCAAAAA
3776483 ATTGACCTTG
Statistics
Matches: 345, Mismatches: 73, Indels: 92
0.68 0.14 0.18
Matches are distributed among these distances:
15 3 0.01
16 21 0.06
17 135 0.39
18 96 0.28
19 37 0.11
20 13 0.04
21 18 0.05
22 17 0.05
23 5 0.01
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (18 bp):
TGTTTTCAAAAATTCTCG
Found at i:3776046 original size:36 final size:37
Alignment explanation
Indices: 3776003--3776123 Score: 135
Period size: 36 Copynumber: 3.4 Consensus size: 37
3775993 ATTTTTCATG
*
3776003 TTTTCAAAAATTCTCGTGTTTTCAAAAAAATTT-TAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTCTAT
* * *
3776039 TTTTCAAAATTTTTCGTGTTTTC-TAAAAATTTCCAT
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTCTAT
* *
3776075 ATTTCTAAAATTTTCGTG-TTT-AAAAAAATTTCGTA-
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTC-TAT
*
3776110 TTTTCAAAATTTTT
1 TTTTCAAAAATTTT
3776124 TTATTTTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
35 31 0.44
36 39 0.56
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (37 bp):
TTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTCTAT
Found at i:3776288 original size:52 final size:51
Alignment explanation
Indices: 3776224--3776481 Score: 152
Period size: 52 Copynumber: 4.9 Consensus size: 51
3776214 AAAATTGTCA
** * *
3776224 TGTTTT-AAAAATTTTCATGTTTCTAAAATGTT-TGTATTTCAAAAATCCTCG
1 TGTTTTCAAAAATTTTCATGTTTAAAAAATCTTCTGT-TTTC-AAAATCCTAG
* *
3776275 TGTTTTCAAAAATTCTCATGTTTAAAAAATCTTCGTGTTTTCAAAATTCTAG
1 TGTTTTCAAAAATTTTCATGTTTAAAAAATCTTC-TGTTTTCAAAATCCTAG
* * *
3776327 TG-TTTCAAAAATTTTCATGTTTTCAAAAAT-TTCCCCTGTTTTCAAAAATTCTCG
1 TGTTTTCAAAAATTTTCATG-TTTAAAAAATCTT---CTGTTTTC-AAAATCCTAG
* * * * *
3776381 TATTTT-GAAAATTTTCTTGTTTTCAAAAAAAACTTTCGTGTTTT-ATAAAT-CTCCG
1 TGTTTTCAAAAATTTTCATG-TTT--AAAAAATC-TTC-TGTTTTCA-AAATCCT-AG
* * * * *
3776436 TGTTTTCAAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTCAAAA
1 TGTTTTCAAAAATTTTCATGTTTAAAAAATCTTC-TGTTTTCAAAA
3776482 AATTGACCTT
Statistics
Matches: 167, Mismatches: 22, Indels: 35
0.75 0.10 0.16
Matches are distributed among these distances:
51 24 0.14
52 54 0.32
53 17 0.10
54 32 0.19
55 18 0.11
56 20 0.12
58 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (51 bp):
TGTTTTCAAAAATTTTCATGTTTAAAAAATCTTCTGTTTTCAAAATCCTAG
Found at i:3776303 original size:69 final size:69
Alignment explanation
Indices: 3776213--3776357 Score: 177
Period size: 69 Copynumber: 2.1 Consensus size: 69
3776203 CGTGTTTCAA
* * * * *
3776213 AAAAATTGTCATGTTTTAAAAATTTTCATG-TTTCTAAAATGT-TTGTATTTCAAAAATCCTCGT
1 AAAAATTCTCATGTTTAAAAAATCTTCATGTTTTC-AAAAT-TCTAGTATTTCAAAAATCCTCAT
3776276 GTTTTC
64 GTTTTC
* * **
3776282 AAAAATTCTCATGTTTAAAAAATCTTCGTGTTTTCAAAATTCTAGTGTTTCAAAAATTTTCATGT
1 AAAAATTCTCATGTTTAAAAAATCTTCATGTTTTCAAAATTCTAGTATTTCAAAAATCCTCATGT
3776347 TTTC
66 TTTC
3776351 AAAAATT
1 AAAAATT
3776358 TCCCCTGTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
68 1 0.02
69 60 0.92
70 4 0.06
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (69 bp):
AAAAATTCTCATGTTTAAAAAATCTTCATGTTTTCAAAATTCTAGTATTTCAAAAATCCTCATGT
TTTC
Found at i:3776408 original size:35 final size:34
Alignment explanation
Indices: 3776260--3776482 Score: 121
Period size: 35 Copynumber: 6.3 Consensus size: 34
3776250 AATGTTTGTA
* * * *
3776260 TTTCAAAAATCCTCGTGTTTTCAAAAATTCTCATG-
1 TTTCAAAAATTCTCGTATTTT--AAAATTTTCGTGT
* * * *
3776295 TTT-AAAAAATCTTCGTGTTTTCAAAATTCTAGTG-
1 TTTCAAAAATTC-TCGTATTTT-AAAATTTTCGTGT
* * * * *
3776329 TTTCAAAAATTTTCATGTTTTCAAAAATTTCCCCTGT
1 TTTCAAAAATTCTCGTATTTT--AAAATTT-TCGTGT
*
3776366 TTTCAAAAATTCTCGTATTTTGAAAATTTTCTTGT
1 TTTCAAAAATTCTCGTATTTT-AAAATTTTCGTGT
* * *
3776401 TTTCAAAAAAAACTT-TCGTGTTTTATAAATCTCCGTGT
1 TTTC---AAAAA-TTCTCGTATTTTA-AAATTTTCGTGT
* *
3776439 TTTCAAAAATTCTCGTCTTTCAAAAATTTTCGTGT
1 TTTCAAAAATTCTCGTATTT-TAAAATTTTCGTGT
3776474 TTTCAAAAA
1 TTTCAAAAA
3776483 ATTGACCTTG
Statistics
Matches: 149, Mismatches: 27, Indels: 24
0.75 0.14 0.12
Matches are distributed among these distances:
34 29 0.19
35 63 0.42
36 10 0.07
37 19 0.13
38 26 0.17
39 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (34 bp):
TTTCAAAAATTCTCGTATTTTAAAATTTTCGTGT
Found at i:3776520 original size:73 final size:73
Alignment explanation
Indices: 3776364--3776519 Score: 169
Period size: 73 Copynumber: 2.2 Consensus size: 73
3776354 AATTTCCCCT
** * * *
3776364 GTTTTC-AAAAATTCTCGTATTTTGAAAATTTTCTTGTTTTCAAAAAAAACTTTCGTGTTTTATA
1 GTTTTCAAAAAATTCTCGTATTTCAAAAATTTTCGTGTTTTC-AAAAAAACTTCCGTGTTTCATA
*
3776428 AATCTCCGT
65 AATCTCCGC
* *
3776437 GTTTTC-AAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTC-AAAAAA-TTGACCTTGTTTCAT
1 GTTTTCAAAAAATTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAACTT--CCGTGTTTCAT
*
3776499 AAATTTCCGC
64 AAATCTCCGC
3776509 G-TTTCAAAAAA
1 GTTTTCAAAAAA
3776520 AATCCTCGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
70 2 0.03
71 10 0.14
72 22 0.31
73 37 0.52
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (73 bp):
GTTTTCAAAAAATTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAACTTCCGTGTTTCATAA
ATCTCCGC
Found at i:3776587 original size:22 final size:22
Alignment explanation
Indices: 3776544--3776585 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3776534 ATAATTTATC
*
3776544 AAAATTTTTGTGTTTTCAAAAT
1 AAAATTTTTGTGTTTTAAAAAT
3776566 AAAA-TTTTGTGTTTTAAAAA
1 AAAATTTTTGTGTTTTAAAAA
3776586 ATTCTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
AAAATTTTTGTGTTTTAAAAAT
Found at i:3776675 original size:17 final size:18
Alignment explanation
Indices: 3776644--3776698 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
3776634 AAATTTTGTG
3776644 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
3776662 TTTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
3776679 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
3776697 TT
1 TT
3776699 ATTATTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 16 0.47
18 18 0.53
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:3777237 original size:45 final size:45
Alignment explanation
Indices: 3777183--3777275 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
3777173 ATTTTCAAAA
*
3777183 TTTCTTGTTCAAATTAACATTTAGTCGTGATCCTTAAATTTTTTG
1 TTTCTTGTTCAAATTAACATTTAGTCGCGATCCTTAAATTTTTTG
3777228 TTTCTTGTTCAAATTAACATTTAGTCGCGATCCTTAAATTTTTTG
1 TTTCTTGTTCAAATTAACATTTAGTCGCGATCCTTAAATTTTTTG
3777273 TTT
1 TTT
3777276 TCAAAAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.52
Consensus pattern (45 bp):
TTTCTTGTTCAAATTAACATTTAGTCGCGATCCTTAAATTTTTTG
Found at i:3781194 original size:43 final size:41
Alignment explanation
Indices: 3781140--3781259 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 41
3781130 AATTTAACGC
*
3781140 CTTAATCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCGAA
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCG-A
* * * * *
3781182 TCTTATCTCCCTAAGCAGTAGTGG-AGCAGATCCAAGA-TGCGA
1 -CTTAACCCCCTAAGCAGTAG-GGTAACAGGT-CAAAATTGCGA
*
3781224 CTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGTCAAAAT
3781260 ATAGCAGATC
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
40 5 0.08
41 23 0.38
42 1 0.02
43 26 0.43
44 6 0.10
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (41 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCGA
Found at i:3781734 original size:207 final size:207
Alignment explanation
Indices: 3781379--3782094 Score: 1193
Period size: 207 Copynumber: 3.5 Consensus size: 207
3781369 CGACGGAGAG
* *
3781379 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTG
3781444 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
* *
3781509 CATAGCAGATTTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTAGCATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
3781574 GCTTACAAGGAA
196 GCTTACAAGGAA
* * *
3781586 CAAATCGAAGGCATAGTTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTG
3781651 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
3781716 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
3781781 GCTTACAAGGAA
196 GCTTACAAGGAA
* * * *
3781793 CAAATCAAAGACATGGCTGATTTGGCTTTCCCGTGTTTACGTTGAAGCAAGTCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTG
* * *
3781858 GCATCTTTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCAACGGAGGACAGACA
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
* ** * * *
3781923 TATAGCAGATCTAACCTTCAGATGATTAGACTGAAGC-AGATCCAAGATGGTTTGGTATCCTTGT
131 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
*
3781987 GCTTACAA-GAG
196 GCTTACAAGGAA
* *
3781998 CAAATCGAAGACATAGCTGATTTGGCTTTCGCGTGTTTACGCTGAAGCAAATCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTG
* *
3782063 GCATCTCTGTATTGTCAGGGAACAAATTGAAG
66 GCATCTCTGTATTGTCAGAGAACAAATCGAAG
3782095 AAGCAGATTT
Statistics
Matches: 479, Mismatches: 30, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
205 91 0.19
206 34 0.07
207 354 0.74
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (207 bp):
CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTG
GCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACA
CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
GCTTACAAGGAA
Found at i:3782502 original size:17 final size:18
Alignment explanation
Indices: 3782489--3782613 Score: 100
Period size: 19 Copynumber: 6.9 Consensus size: 18
3782479 TAATCTTCAA
3782489 TGATATGCAATCTTAGATG
1 TGATATGCAATCTTAGA-G
3782508 TGATATGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
3782525 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
3782544 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
3782560 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
*
3782579 TGAT-TGCAATCTTAGATA
1 TGATATGCAATCTTAGA-G
*
3782597 TGATATACAATCTTAGA
1 TGATATGCAATCTTAGA
3782614 AGATATGATT
Statistics
Matches: 91, Mismatches: 5, Indels: 20
0.78 0.04 0.17
Matches are distributed among these distances:
15 2 0.02
16 3 0.03
17 24 0.26
18 28 0.31
19 30 0.33
20 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
TGATATGCAATCTTAGAG
Found at i:3782558 original size:35 final size:35
Alignment explanation
Indices: 3782496--3782613 Score: 200
Period size: 35 Copynumber: 3.3 Consensus size: 35
3782486 CAATGATATG
*
3782496 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
3782532 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
3782567 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
3782604 CAATCTTAGA
1 CAATCTTAGA
3782614 AGATATGATT
Statistics
Matches: 79, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
35 51 0.65
36 15 0.19
37 13 0.16
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:3788855 original size:20 final size:20
Alignment explanation
Indices: 3788830--3788872 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3788820 ATCAATATTC
3788830 TTATCCTGAATTTCAGGATT
1 TTATCCTGAATTTCAGGATT
* *
3788850 TTATCCTGAATTTTAGTATT
1 TTATCCTGAATTTCAGGATT
3788870 TTA
1 TTA
3788873 ATTTGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (20 bp):
TTATCCTGAATTTCAGGATT
Found at i:3790119 original size:85 final size:85
Alignment explanation
Indices: 3789976--3790145 Score: 286
Period size: 85 Copynumber: 2.0 Consensus size: 85
3789966 TAGCAAGTTT
*
3789976 CATTGGAATCAGAGTTGTGCAGCGATAGCGTGGTAATCAGTGCGAATGAGAAAATTTTAAATTTG
1 CATTGGAATCAGAGTTGTGCAGCGATAGCGTGGTAATCAGTGCGAATGAGAAAATTTTAAATTAG
3790041 GTGTTTAAGTATATGGTGTG
66 GTGTTTAAGTATATGGTGTG
* * * * *
3790061 CATTGTAATTAGAGTTGTGCAGCGATAGCGTGGTGATCAGTGTGAATGAGGAAATTTTAAATTAG
1 CATTGGAATCAGAGTTGTGCAGCGATAGCGTGGTAATCAGTGCGAATGAGAAAATTTTAAATTAG
3790126 GTGTTTAAGTATATGGTGTG
66 GTGTTTAAGTATATGGTGTG
3790146 ACAACGTGAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.34
Consensus pattern (85 bp):
CATTGGAATCAGAGTTGTGCAGCGATAGCGTGGTAATCAGTGCGAATGAGAAAATTTTAAATTAG
GTGTTTAAGTATATGGTGTG
Found at i:3791401 original size:20 final size:20
Alignment explanation
Indices: 3791368--3791417 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3791358 TAAAATAATT
* *
3791368 AATATATAAAGTAAT-TTAA
1 AATAAATAATGTAATCTTAA
3791387 AATAAAATAATGTAATCTTAA
1 AAT-AAATAATGTAATCTTAA
3791408 AATAAATAAT
1 AATAAATAAT
3791418 ATATGTAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 17 0.63
21 7 0.26
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (20 bp):
AATAAATAATGTAATCTTAA
Found at i:3791706 original size:27 final size:26
Alignment explanation
Indices: 3791659--3791747 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 26
3791649 ATATATGATA
*
3791659 ATTTAAAATAAAT-ATCGTGTAAAAAT
1 ATTTAAAATAAATAAT-ATGTAAAAAT
* *
3791685 ATTTCAAAATAAATAATATGT-ATAGT
1 ATTT-AAAATAAATAATATGTAAAAAT
* *
3791711 AGTTAAAATAAATAATATATATAAAAT
1 ATTTAAAATAAATAATATGTA-AAAAT
*
3791738 ATTTCAAATA
1 ATTTAAAATA
3791748 GATAGTAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
25 15 0.30
26 10 0.20
27 23 0.46
28 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (26 bp):
ATTTAAAATAAATAATATGTAAAAAT
Found at i:3793291 original size:16 final size:16
Alignment explanation
Indices: 3793270--3793331 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
3793260 TTTGGTTCAG
*
3793270 TGTAATGGAATAGGGT
1 TGTAATGGAATAGAGT
**
3793286 TGTAATGGAATAGAAC
1 TGTAATGGAATAGAGT
3793302 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
*
3793318 TGTAATAGAATAGA
1 TGTAATGGAATAGA
3793332 ACTGTAATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.40, C:0.02, G:0.29, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:3793306 original size:32 final size:32
Alignment explanation
Indices: 3793270--3793339 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
3793260 TTTGGTTCAG
* *
3793270 TGTAATGGAATAGGGTTGTAATGGAATAGAAC
1 TGTAATGGAATAGAGTTGTAATAGAATAGAAC
3793302 TGTAATGGAATAGAGTTGTAATAGAATAGAAC
1 TGTAATGGAATAGAGTTGTAATAGAATAGAAC
3793334 TGTAAT
1 TGTAAT
3793340 AGCAATTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.30
Consensus pattern (32 bp):
TGTAATGGAATAGAGTTGTAATAGAATAGAAC
Found at i:3793337 original size:16 final size:16
Alignment explanation
Indices: 3793286--3793341 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
3793276 GGAATAGGGT
*
3793286 TGTAATGGAATAGAAC
1 TGTAATAGAATAGAAC
* **
3793302 TGTAATGGAATAGAGT
1 TGTAATAGAATAGAAC
3793318 TGTAATAGAATAGAAC
1 TGTAATAGAATAGAAC
3793334 TGTAATAG
1 TGTAATAG
3793342 CAATTCAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.43, C:0.04, G:0.25, T:0.29
Consensus pattern (16 bp):
TGTAATAGAATAGAAC
Found at i:3793606 original size:21 final size:20
Alignment explanation
Indices: 3793578--3793617 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3793568 AATTTATTAT
3793578 TAATTATAATTTAACAATAA
1 TAATTATAATTTAACAATAA
*
3793598 TAATATATAATTTAATAATA
1 TAAT-TATAATTTAACAATA
3793618 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTATAATTTAACAATAA
Found at i:3793819 original size:12 final size:12
Alignment explanation
Indices: 3793789--3793823 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
3793779 TCTATGTTAC
3793789 TTAAAGAATAAT
1 TTAAAGAATAAT
3793801 TTAAAAGAATAAT
1 TT-AAAGAATAAT
3793814 TTAAAGAATA
1 TTAAAGAATA
3793824 TATTGTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
TTAAAGAATAAT
Found at i:3796440 original size:38 final size:38
Alignment explanation
Indices: 3796396--3796473 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
3796386 AAAAACGAAT
3796396 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
3796434 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
3796472 AA
1 AA
3796474 TAAATAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (38 bp):
AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
Found at i:3798646 original size:43 final size:43
Alignment explanation
Indices: 3798599--3798730 Score: 119
Period size: 44 Copynumber: 3.0 Consensus size: 43
3798589 TAACCAGCTC
3798599 CACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
1 CACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
* * * * *
3798642 CACTATCAA-TGCAG-GAAGGCAAGATCTTTTGTCTTCAACCAGC-T
1 CACTA-CAACCG-AGAG-AGGCAAGGT-TTGTGTCTTCGACCTGCTT
* *
3798686 CTA-TCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTT
1 C-ACT-ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
3798730 C
1 C
3798731 GCTGTCAATG
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
43 20 0.29
44 30 0.44
45 18 0.26
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (43 bp):
CACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
Found at i:3798664 original size:44 final size:43
Alignment explanation
Indices: 3798614--3798748 Score: 105
Period size: 44 Copynumber: 3.1 Consensus size: 43
3798604 CAACCGAGAG
3798614 AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTATCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTC-CTATCAATGCAGGA
* * * * * * *
3798658 AGGCAAGATCTTTTGTCTTCAACCAGC-T-CTATCACA-ACCGAAA
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCCTATCA-ATGCAG-GA
* * *
3798701 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGCTTC-CTATCAATGCAGGA
3798746 AGG
1 AGG
3798749 TAAGATCTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 8 0.12
43 15 0.23
44 21 0.32
45 16 0.24
46 6 0.09
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (43 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCCTATCAATGCAGGA
Found at i:3798677 original size:45 final size:44
Alignment explanation
Indices: 3798626--3798764 Score: 106
Period size: 45 Copynumber: 3.1 Consensus size: 44
3798616 GCAAGGTTTG
3798626 TGTCTTCGACCTGCTTCACTATCAATGCAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTC-CTATCAATGCAGGAAGGCAAGATCTTT
* * * * * * *
3798671 TGTCTTCAACCAGC-T-CTATCACA-ACCGAAAGAGGCAAGGT-TTG
1 TGTCTTCGACCTGCTTCCTATCA-ATGCAG-GA-AGGCAAGATCTTT
* * * *
3798714 TGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGTAAGATCTTT
1 TGTCTTCGACCTGCTTC-CTATCAATGCAGGAAGGCAAGATCTTT
3798759 TGTCTT
1 TGTCTT
3798765 TAACCAGCTC
Statistics
Matches: 68, Mismatches: 18, Indels: 16
0.67 0.18 0.16
Matches are distributed among these distances:
42 8 0.12
43 15 0.22
44 17 0.25
45 22 0.32
46 6 0.09
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (44 bp):
TGTCTTCGACCTGCTTCCTATCAATGCAGGAAGGCAAGATCTTT
Found at i:3798835 original size:42 final size:42
Alignment explanation
Indices: 3798788--3798922 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 42
3798778 TGTAACCAAT
3798788 GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
* ** ** * * * * *
3798830 GAAGGCAAGATCTACTTCTTTAACCAGCTCCACTG-TAAC-CAAT
1 GAAGGCAA-AGCTTGTT-TTCGATCTGCTTCGCTGTTAACGC-AG
3798873 GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
3798915 GAAGGCAA
1 GAAGGCAA
3798923 GATCTGCTGT
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
41 11 0.16
42 27 0.40
43 19 0.28
44 11 0.16
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (42 bp):
GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
Found at i:3798861 original size:85 final size:86
Alignment explanation
Indices: 3798538--3798935 Score: 455
Period size: 88 Copynumber: 4.6 Consensus size: 86
3798528 ATGCAAGGCT
* *
3798538 TTGTTTTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCAC
1 TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTGTCTTTAACCAGCTCCAC
* * *
3798602 TACAACCGA-GAGAGGCAAGGT
66 TACAACCAATGA-AGGCAAAGC
* * * * * * *
3798623 TTGTGTCTTCGACCTGCTTCACTATCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCT
1 TTGT-T-TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTGTCTTTAACCAGCTCC
* * *
3798688 A-TCACAACCGAAAG-AGGCAAGGT
64 ACT-ACAACC-AATGAAGGCAAAGC
* * * *
3798711 TTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGTAAGATCTTTTGTCTTTAACCAGCTCC
1 TTGT-T-TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTGTCTTTAACCAGCTCC
**
3798776 ACTGTAACCAATGAAGGCAAAGC
64 ACTACAACCAATGAAGGCAAAGC
* *
3798799 TTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTACT-TCTTTAACCAGCTCCAC
1 TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTGTCTTTAACCAGCTCCAC
**
3798863 TGTAACCAATGAAGGCAAAGC
66 TACAACCAATGAAGGCAAAGC
* *
3798884 TTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTGTCTT
1 TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTGTCTT
3798936 CACTGATCTG
Statistics
Matches: 275, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
85 88 0.32
86 41 0.15
87 40 0.15
88 103 0.37
89 2 0.01
90 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (86 bp):
TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTGTCTTTAACCAGCTCCAC
TACAACCAATGAAGGCAAAGC
Found at i:3800666 original size:26 final size:26
Alignment explanation
Indices: 3800617--3800666 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3800607 CTCTTTTTCT
*
3800617 TTTTATTTTTTTTATTTTGATTTTGA
1 TTTTATTTTTTTTATTTTCATTTTGA
* * *
3800643 TTTTGTTTTTTTTCTTTTCCTTTT
1 TTTTATTTTTTTTATTTTCATTTT
3800667 CCCTTGTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.08, C:0.06, G:0.06, T:0.80
Consensus pattern (26 bp):
TTTTATTTTTTTTATTTTCATTTTGA
Found at i:3803276 original size:19 final size:20
Alignment explanation
Indices: 3803247--3803295 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3803237 CACTTCGTGA
* *
3803247 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
3803266 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
3803286 AAATG-AATGC
1 AAATGTAATGC
3803296 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:3805187 original size:38 final size:38
Alignment explanation
Indices: 3805143--3805220 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
3805133 AAAAACGAAT
3805143 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
3805181 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
3805219 AA
1 AA
3805221 TAAATAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (38 bp):
AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
Found at i:3810449 original size:36 final size:34
Alignment explanation
Indices: 3810395--3810468 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
3810385 CTGGTCTAAT
*
3810395 ATGACATTCTTATATGATATATATGTTTCTGAAAAC
1 ATGACATTCTTATATG--ATATATGTTTATGAAAAC
* *
3810431 ATGACATTC-TAGTTTGATATATGTTTATGAAAAT
1 ATGACATTCTTA-TATGATATATGTTTATGAAAAC
3810465 ATGA
1 ATGA
3810469 TCTCTGATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 20 0.59
35 2 0.06
36 12 0.35
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (34 bp):
ATGACATTCTTATATGATATATGTTTATGAAAAC
Found at i:3810518 original size:32 final size:33
Alignment explanation
Indices: 3810445--3810521 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
3810435 CATTCTAGTT
*
3810445 TGATATATGTTTATGAAAATATGATCTCTGATC
1 TGATATATGTTTATGAAAATATGATCTATGATC
** * *
3810478 CAAAATATGTTTA-G-AAATATGACTTTATGATC
1 TGATATATGTTTATGAAAATATGA-TCTATGATC
3810510 TGATATATGTTT
1 TGATATATGTTT
3810522 CTGGTAATAC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
31 8 0.23
32 17 0.49
33 10 0.29
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (33 bp):
TGATATATGTTTATGAAAATATGATCTATGATC
Found at i:3812813 original size:13 final size:13
Alignment explanation
Indices: 3812795--3812837 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3812785 AATAAAAAAT
3812795 ATAAAGCAAATAC
1 ATAAAGCAAATAC
* *
3812808 ATAAAGAAAATGAA
1 ATAAAGCAAAT-AC
3812822 AT-AAGCAAATAC
1 ATAAAGCAAATAC
3812834 ATAA
1 ATAA
3812838 GTATACATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 18 0.75
14 3 0.12
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.16
Consensus pattern (13 bp):
ATAAAGCAAATAC
Found at i:3812914 original size:3 final size:3
Alignment explanation
Indices: 3812906--3813136 Score: 52
Period size: 3 Copynumber: 75.7 Consensus size: 3
3812896 AAAACGATAG
* * * *
3812906 TAA TAA TAA TAA AAA GGT-A TAA TAA T-A TAT TAGA TAG TAA -AA AAA
1 TAA TAA TAA TAA TAA --TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
3812951 TAA TAAA TAAA TAA -AA TAA TAA TAA TAG TAA TAA -AA -AA TGA TAA
1 TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
3812995 TAG TGA TAT TAG TAG TAA TAA TAA TAA T-A TGGAA TAA TAA TATA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T--AA TAA TAA TA-A TAA
* * * * * *
3813042 CAA TAA CAA CAA TAA T-A TGAA AAA TAA GAAA TAA CAA TACA GTAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA TAA TA-A -TAA TAA
* * * *
3813090 GT-T TAG TAA TAGA TCAC TAA TAA TAA TAG TAA -AA -AA TAA TAA TAA
1 -TAA TAA TAA TA-A T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3813135 TA
1 TA
3813137 TATTAGTAAG
Statistics
Matches: 168, Mismatches: 37, Indels: 46
0.67 0.15 0.18
Matches are distributed among these distances:
2 20 0.12
3 121 0.72
4 22 0.13
5 5 0.03
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:3812945 original size:37 final size:36
Alignment explanation
Indices: 3812901--3813039 Score: 105
Period size: 37 Copynumber: 3.9 Consensus size: 36
3812891 TAACGAAAAC
3812901 GATAGTAATAATAATAAAAAGGTATAATAATATATTA
1 GATAGTAATAATAATAAAAA-GTATAATAATATATTA
*
3812938 GATAGTAA-AAAAATAATAAA-TA-AATAA-A-A-TA
1 GATAGTAATAATAATAA-AAAGTATAATAATATATTA
* * * *
3812969 -ATAATAATAGTAATAAAAAATGATAATAGTGATATTA
1 GATAGTAATAATAATAAAAAGT-ATAATAAT-ATATTA
** *
3813006 G-TAGTAATAATAATAATATGGAATAATAATATAT
1 GATAGTAATAATAATAA-AAAGTATAATAATATAT
3813040 ACCAATAACA
Statistics
Matches: 79, Mismatches: 12, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
30 9 0.11
31 9 0.11
32 2 0.03
33 5 0.06
34 5 0.06
35 3 0.04
36 12 0.15
37 33 0.42
38 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (36 bp):
GATAGTAATAATAATAAAAAGTATAATAATATATTA
Found at i:3812968 original size:16 final size:15
Alignment explanation
Indices: 3812943--3812972 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3812933 TATTAGATAG
3812943 TAAAAAAATAATAAA
1 TAAAAAAATAATAAA
3812958 TAAATAAAATAATAA
1 TAAA-AAAATAATAA
3812973 TAATAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAAAATAATAAA
Found at i:3812988 original size:22 final size:19
Alignment explanation
Indices: 3812944--3812996 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 19
3812934 ATTAGATAGT
3812944 AAAAA-AATAATAAATAAA
1 AAAAATAATAATAAATAAA
*
3812962 TAAAATAATAATAATAGTAATA
1 AAAAATAATAATAA-A-TAA-A
*
3812984 AAAAATGATAATA
1 AAAAATAATAATA
3812997 GTGATATTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.14
19 8 0.29
20 1 0.04
21 3 0.11
22 12 0.43
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAAATAATAATAAATAAA
Found at i:3812994 original size:19 final size:20
Alignment explanation
Indices: 3812939--3812998 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
3812929 AATATATTAG
*
3812939 ATAGTAAAAAAATAAT-A-A
1 ATAGTAATAAAATAATAATA
3812957 ATA--AATAAAATAATAATA
1 ATAGTAATAAAATAATAATA
*
3812975 ATAGTAATAAAA-AATGATA
1 ATAGTAATAAAATAATAATA
3812994 ATAGT
1 ATAGT
3812999 GATATTAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 10 0.28
17 1 0.03
18 7 0.19
19 11 0.31
20 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (20 bp):
ATAGTAATAAAATAATAATA
Found at i:3813159 original size:3 final size:3
Alignment explanation
Indices: 3813151--3813206 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
3813141 AGTAAGGGTA
*
3813151 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
3813199 ATG ATG AT
1 ATG ATG AT
3813207 AATAATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3813211 original size:3 final size:3
Alignment explanation
Indices: 3813205--3813241 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3813195 GGTGATGATG
* *
3813205 ATA ATA ATA ATA ATA ATA ATA AGA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3813242 CTTATATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3814766 original size:11 final size:10
Alignment explanation
Indices: 3814740--3814778 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
3814730 TTATGTCTAA
3814740 AAAAGAATGGT
1 AAAA-AATGGT
3814751 AAAAAATTGGCT
1 AAAAAA-TGG-T
3814763 AAAAAATGGT
1 AAAAAATGGT
3814773 AAAAAA
1 AAAAAA
3814779 AAAGGCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.35
11 10 0.38
12 7 0.27
ACGTcount: A:0.62, C:0.03, G:0.18, T:0.18
Consensus pattern (10 bp):
AAAAAATGGT
Found at i:3814789 original size:22 final size:22
Alignment explanation
Indices: 3814740--3814789 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
3814730 TTATGTCTAA
**
3814740 AAAAGAATGGTAAAAAATTGGCT
1 AAAA-AATGGTAAAAAAAAGGCT
3814763 AAAAAATGGTAAAAAAAAAGGCT
1 AAAAAATGGT-AAAAAAAAGGCT
3814786 AAAA
1 AAAA
3814790 TAACCATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.62, C:0.04, G:0.18, T:0.16
Consensus pattern (22 bp):
AAAAAATGGTAAAAAAAAGGCT
Found at i:3817290 original size:18 final size:17
Alignment explanation
Indices: 3817260--3817302 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
3817250 AATCTGGGCG
3817260 TGTGGGCCACACGAGAA
1 TGTGGGCCACACGAGAA
* *
3817277 TGTGGGCTCACACGGGCA
1 TGTGGGC-CACACGAGAA
3817295 TGTGGGCC
1 TGTGGGCC
3817303 CATATTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.16
Consensus pattern (17 bp):
TGTGGGCCACACGAGAA
Found at i:3817643 original size:30 final size:30
Alignment explanation
Indices: 3817612--3817711 Score: 130
Period size: 30 Copynumber: 3.3 Consensus size: 30
3817602 CTTAGCTTTT
*
3817612 TCCACCACCAACTCCACTAGCCACACCTT-T
1 TCCACCACCAACTCCACTAGCCACA-CTTGC
*
3817642 TCCACCACCAAATCCACTAGCCACACTTGC
1 TCCACCACCAACTCCACTAGCCACACTTGC
** * *
3817672 TCCATTACCTACTCCACTAACCACACTTGC
1 TCCACCACCAACTCCACTAGCCACACTTGC
3817702 TCCACCACCA
1 TCCACCACCA
3817712 CTTGTACCTA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 3 0.05
30 56 0.95
ACGTcount: A:0.28, C:0.48, G:0.04, T:0.20
Consensus pattern (30 bp):
TCCACCACCAACTCCACTAGCCACACTTGC
Found at i:3818246 original size:24 final size:23
Alignment explanation
Indices: 3818198--3818258 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
3818188 CCTTTTTTGT
*
3818198 TATTATTATATTTCTTAATATTA
1 TATTATTATATTTCTTAATAATA
*
3818221 TATTATATATATATTCTT-TTAATA
1 TATTAT-TATAT-TTCTTAATAATA
*
3818245 TATTAGGTATATTT
1 TATTA-TTATATTT
3818259 TAAATTCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 8 0.25
24 19 0.59
25 5 0.16
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (23 bp):
TATTATTATATTTCTTAATAATA
Found at i:3818282 original size:2 final size:2
Alignment explanation
Indices: 3818275--3818339 Score: 50
Period size: 2 Copynumber: 34.5 Consensus size: 2
3818265 CTATATTACG
* * *
3818275 TA TA TA TA TA T- TA TA CTA T- TT TA TG TA TA TA TA TT TA -A TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3818315 T- TA TA T- TA TT TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3818340 TTTTTTTACA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
1 5 0.10
2 43 0.86
3 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (2 bp):
TA
Found at i:3818293 original size:25 final size:26
Alignment explanation
Indices: 3818265--3818335 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
3818255 ATTTTAAATT
*
3818265 CTATATTACGTATATATATATT-ATA
1 CTATATTATGTATATATATATTAATA
*
3818290 CTATTTTATGTATATATAT-TTAATA
1 CTATATTATGTATATATATATTAATA
* *
3818315 TTATATTATTTATATATATAT
1 CTATATTATGTATATATATAT
3818336 ATATTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.05
25 36 0.92
26 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (26 bp):
CTATATTATGTATATATATATTAATA
Found at i:3818305 original size:27 final size:26
Alignment explanation
Indices: 3818275--3818339 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 26
3818265 CTATATTACG
3818275 TATATATATATTATACTATTTTATGTATA
1 TATATATATATTATACTA-TTTA--TATA
* *
3818304 TATATTTAATATTATATTATTTATATA
1 TATATAT-ATATTATACTATTTATATA
3818331 TATATATAT
1 TATATATAT
3818340 TTTTTTTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 2 0.06
27 10 0.31
29 10 0.31
30 10 0.31
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TATATATATATTATACTATTTATATA
Found at i:3818385 original size:22 final size:24
Alignment explanation
Indices: 3818357--3818415 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
3818347 ACATGTTATC
3818357 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
3818379 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
3818404 TTATGTACATAT
1 TTATGTATATAT
3818416 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:3818405 original size:25 final size:25
Alignment explanation
Indices: 3818373--3818421 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3818363 ATATATCTTA
**
3818373 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
3818398 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
3818422 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:3818602 original size:16 final size:15
Alignment explanation
Indices: 3818578--3818625 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3818568 TAATTATTAT
*
3818578 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
3818594 TATTTTAATATTTTA
1 TATTTTAATATTTTA
3818609 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
3818625 T
1 T
3818626 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:3818613 original size:7 final size:8
Alignment explanation
Indices: 3818578--3818629 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3818568 TAATTATTAT
*
3818578 TATTCTAA
1 TATTTTAA
*
3818586 TATTTTGA
1 TATTTTAA
3818594 TATTTTAA
1 TATTTTAA
3818602 TATTTT-A
1 TATTTTAA
3818609 TATTTTATA
1 TATTTTA-A
*
3818618 TATTTTAT
1 TATTTTAA
3818626 TATT
1 TATT
3818630 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:3829599 original size:74 final size:73
Alignment explanation
Indices: 3829477--3830078 Score: 525
Period size: 74 Copynumber: 8.0 Consensus size: 73
3829467 CTTTTCAAGG
* * * *
3829477 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAAGCTGAGGTA-TTTTCAATTTC
3829542 TGTTTTTCA
65 TGTTTTTCA
* * *
3829551 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACAAGCTGAGGTATTTTTAAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAAGCTGAGGTA-TTTTCAATTTC
3829616 TGTTTTTCA
65 TGTTTTTCA
** * * *
3829625 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAAGCTGAGGTATTTTCAA--TTT
*
3829690 GTGTTTTAATTTATTTTTCA
64 CTG----------TTTTTCA
* * * *
3829710 AAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACA-TTGAGGTATTTTCAATTTA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA-AGCTGAGGTATTTTCAATTTC
** ***
3829774 T-CATCAAA
65 TGTTTTTCA
*** * * *
3829782 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGTTTCACACGTTGAGGTGTTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC--AAGACAAGCTGAGGTATTTTCAATTT
*
3829847 CTGTCTTTTAAAA
64 CTGT-TTTT--CA
* * * * *
3829860 AAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAGAC--GCTGAGGTAATTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAAGCTGAGGTATTTTCAATTTCT
* *
3829923 ATTTGTCA
66 GTTTTTCA
* * *
3829931 AAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCAAGACACA-TTGAGGTATTTTCAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA-AGCTGAGGTATTTTCAATTTC
*
3829995 TGTCTTTCAAAA
65 TGTTTTTC---A
* * * * *
3830007 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC--GCTGAGGTGTTTTCCATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAAGCTGAGGTATTTTCAATTTCT
*
3830070 GTTCTTCA
66 GTTTTTCA
3830078 A
1 A
3830079 TTTCTGTTTT
Statistics
Matches: 432, Mismatches: 69, Indels: 57
0.77 0.12 0.10
Matches are distributed among these distances:
71 40 0.09
72 38 0.09
73 29 0.07
74 179 0.41
75 5 0.01
76 42 0.10
78 36 0.08
83 4 0.01
85 59 0.14
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAAGCTGAGGTATTTTCAATTTCT
GTTTTTCA
Found at i:3829906 original size:233 final size:219
Alignment explanation
Indices: 3829699--3830444 Score: 524
Period size: 221 Copynumber: 3.2 Consensus size: 219
3829689 TGTGTTTTAA
* * *
3829699 TTTATTTTTCAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACATTGAGGTAT
1 TTTATTTGTCAAAA-TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACATTGAGGTAT
* ** *
3829764 TTTCAATTTATCATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGTTTCACACG
65 TTTCAATTTATCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-TAGCACAAG
* * *
3829829 TTGAGGT-GTTTTCAATTTCTGTCTTTTAAAAAAAATCAGCTCATATTGCAAGAGGTGAGTTGAA
129 CTGAGGTAGTTTTAAATTTCTGT-TTTT--AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAA
3829893 CCTC-AAG-ACGCTGAGGTAATTTCAATT
191 CCTCGAAGCACGCTGAGGTAATTTCAATT
*
3829920 TTTATTTGTCAAAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCAAGACACATTGAGGTAT
1 TTTATTTGTC-AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACATTGAGGTAT
* * * *
3829985 TTTCAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG-AC
65 TTTCAA-TT-TATC-TTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTAGCAC
*
3830049 --GCTGAGGTGTTTTCCATTTTTGTTCTTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGC
126 AAGCTGA-G-G---T--A-----GTT-TTAAATTTCTGTTTTT-AAAAA-ATCAACTCATATTGC
* * * *
3830112 GAGAGGTGAGTTGAGCCTCG-GGACACGCTGAGGTATTTTCAAATT
176 AAGAGGTGAGTTGAACCTCGAAG-CACGCTGAGGTAATTTC-AATT
* * * ** *
3830157 CTATT-TTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAG
1 -T-TTATTTGTC---AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACATTGAG
*
3830221 GTATTTTCAATTTCTGCTTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTG
61 GTATTTTCAA--------TTT--A----T-C--TTCAAAAAAATCAACTCATATTGCGAGAGGTG
** * * * *
3830286 AGTTGAGCCTCGGGTCACACGCTGAGG-CGTTTTCAATTTCTGCTTTTCAAAAGAATCAACTCAT
109 AGTTGAGCCTCTAG-CACAAGCTGAGGTAGTTTTAAATTTCTG-TTTTTAAAA-AATCAACTCAT
* * * * *
3830350 ATTGCAAGATGTGAGTTGAGCCTCG-GGTCACACGCTGAGGCATTTTCAATT
171 ATTGCAAGAGGTGAGTTGAACCTCGAAG---CACGCTGAGGTAATTTCAATT
** * *
3830401 TCTGCTTT-TCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAG
1 T-TTATTTGTC-AAAATCAACTCATATTGCGAGAGATGAGTTGAG
3830445 TCTCGGGCCA
Statistics
Matches: 433, Mismatches: 40, Indels: 84
0.78 0.07 0.15
Matches are distributed among these distances:
221 66 0.15
222 7 0.02
223 6 0.01
224 2 0.00
225 38 0.09
226 1 0.00
233 5 0.01
234 39 0.09
235 12 0.03
236 15 0.03
237 4 0.01
238 6 0.01
239 2 0.00
240 55 0.13
241 32 0.07
243 54 0.12
244 15 0.03
245 17 0.04
246 1 0.00
247 3 0.01
252 1 0.00
253 39 0.09
254 4 0.01
255 3 0.01
256 1 0.00
257 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (219 bp):
TTTATTTGTCAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACATTGAGGTATT
TTCAATTTATCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTAGCACAAGCT
GAGGTAGTTTTAAATTTCTGTTTTTAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCG
AAGCACGCTGAGGTAATTTCAATT
Found at i:3830068 original size:147 final size:148
Alignment explanation
Indices: 3829709--3830069 Score: 469
Period size: 147 Copynumber: 2.4 Consensus size: 148
3829699 TTTATTTTTC
* * * ** *
3829709 AAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACATTGAGGTATTTT-CA-ATT
1 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTATTTTCCATTTT
* * ** * *
3829772 TATCATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGTTTCACACGTTGAGGTG
64 TATCATC-AAAAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCG-AACACACATTGAGGTA
*
3829837 TTTTCAATTTCTGTCTTTTAAA
127 TTTTCAATTTCTGTCTTTCAAA
* * *
3829859 AAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAATTTCAATTTTTA
1 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTTCCATTTTTA
** *
3829924 TTTGTC-AAAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTC-AAGACACATTGAGGTATTT
66 -TCATCAAAAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCGAACACACATTGAGGTATTT
3829987 TCAATTTCTGTCTTTCAAA
130 TCAATTTCTGTCTTTCAAA
*
3830006 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTTTCCATTTTT
1 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTTCCATTTTT
3830070 GTTCTTCAAT
Statistics
Matches: 185, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
147 92 0.50
148 12 0.06
149 37 0.20
150 41 0.22
151 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (148 bp):
AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTTCCATTTTTA
TCATCAAAAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCGAACACACATTGAGGTATTTT
CAATTTCTGTCTTTCAAA
Found at i:3830199 original size:77 final size:76
Alignment explanation
Indices: 3830074--3830484 Score: 434
Period size: 77 Copynumber: 5.2 Consensus size: 76
3830064 ATTTTTGTTC
* *
3830074 TTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-ACAC
1 TTCAATTTCTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACAC
3830138 GCTGAGGTATT
66 GCTGAGGTATT
* *
3830149 TTCAAATTCTATTTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGG-AC
1 TTCAATTTCT-TTTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC
*
3830213 ACACTGAGGTATT
64 ACGCTGAGGTATT
3830226 TTCAATTTCTGCTTTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTG
1 TTCAA-TT-T-CTTTT---TTTC-A------AAAA-AATCAACTCATATTGCGAGAGGTGAGTTG
**
3830291 AGCCTCGGGTCACACGCTGAGGCGTT
52 AGCCTCGGG-CACACGCTGAGGTATT
** * * *
3830317 TTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCAAGATGTGAGTTGAGCCTCGGGTCACA
1 TTCAATTTCTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACA
*
3830382 CGCTGAGGCATT
65 CGCTGAGGTATT
** * *
3830394 TTCAATTTCTGCTTTTC--AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACA
1 TTCAATTTCTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACA
* *
3830457 CACTGAGGTCTT
65 CGCTGAGGTATT
* *
3830469 TTCAAATTCTGTTTTT
1 TTCAATTTCTTTTTTT
3830485 AATTTCTGCT
Statistics
Matches: 291, Mismatches: 27, Indels: 36
0.82 0.08 0.10
Matches are distributed among these distances:
75 72 0.25
76 4 0.01
77 131 0.45
78 4 0.01
79 4 0.01
80 2 0.01
81 2 0.01
82 3 0.01
84 1 0.00
85 4 0.01
88 7 0.02
89 38 0.13
90 2 0.01
91 17 0.06
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (76 bp):
TTCAATTTCTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACAC
GCTGAGGTATT
Found at i:3830243 original size:14 final size:14
Alignment explanation
Indices: 3830224--3830258 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3830214 CACTGAGGTA
*
3830224 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
3830238 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
3830252 TTTTCAA
1 TTTTCAA
3830259 AAGAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:3830279 original size:166 final size:162
Alignment explanation
Indices: 3829912--3830412 Score: 614
Period size: 166 Copynumber: 3.0 Consensus size: 162
3829902 GCTGAGGTAA
* * * ** *
3829912 TTTCAATTTTTATTTGTC-AAAAATCAACTCATATTGCGAGAGATAAGTTGAGCCTCAAGACACA
1 TTTCAATTTCTATTT-TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
* * * *
3829976 TTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAAC
65 CTGAGGTATTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * * * *
3830041 CTC--AAGACGCTGAGGTGTTTTCCATTTTTG-T
129 CTCGGGACACGCTGAGGTATTTTCAATTTCTGCT
*
3830072 TCTTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
1 T-TTCAATTTCT-ATTTTCAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
* * *
3830137 CGCTGAGGTATTTTCAAATTCTATTTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTG
63 CGCTGAGGTATTTTCAATTTCT-GTTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
*
3830202 AGCCTCGGGACACACTGAGGTATTTTCAATTTCTGCT
126 AGCCTCGGGACACGCTGAGGTATTTTCAATTTCTGCT
3830239 TTTCAATTTCTACTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTCAATTTCTA-TTTTCAAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--AC
** * * * *
3830304 ACGCTGAGGCGTTTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCAAGATGTGAGTTGA
62 ACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
*
3830369 GCCTCGGGTCACACGCTGAGGCATTTTCAATTTCTGCT
127 GCCTCGGG--ACACGCTGAGGTATTTTCAATTTCTGCT
3830407 TTTCAA
1 TTTCAA
3830413 AAATCAACTT
Statistics
Matches: 294, Mismatches: 32, Indels: 22
0.84 0.09 0.06
Matches are distributed among these distances:
160 1 0.00
161 11 0.04
162 7 0.02
163 55 0.19
164 40 0.14
165 2 0.01
166 118 0.40
167 6 0.02
168 54 0.18
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (162 bp):
TTTCAATTTCTATTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
TGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
CGGGACACGCTGAGGTATTTTCAATTTCTGCT
Found at i:3830305 original size:89 final size:92
Alignment explanation
Indices: 3830147--3830336 Score: 287
Period size: 89 Copynumber: 2.1 Consensus size: 92
3830137 CGCTGAGGTA
*
3830147 TTTTCAAATTCTATTTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGA
1 TTTTCAAATTCTATCTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGA
*
3830212 CACA-CTGAGGTATTTTCAATTTCTGC
66 CACACCTGAGGCATTTTCAATTTCTGC
* * * *
3830238 TTTTCAATTTCTA-CTTT-TCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 TTTTCAAATTCTATCTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGA
*
3830301 CACACGCTGAGGCGTTTTCAATTTCTGC
66 CACAC-CTGAGGCATTTTCAATTTCTGC
3830329 TTTTCAAA
1 TTTTCAAA
3830337 AGAATCAACT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
89 47 0.53
90 3 0.03
91 39 0.44
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (92 bp):
TTTTCAAATTCTATCTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGA
CACACCTGAGGCATTTTCAATTTCTGC
Found at i:3830497 original size:14 final size:13
Alignment explanation
Indices: 3830467--3830510 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3830457 CACTGAGGTC
*
3830467 TTTTCAAATTCTG
1 TTTTCAATTTCTG
*
3830480 TTTTTAATTTCTG
1 TTTTCAATTTCTG
*
3830493 CTTTTCAATTTCTA
1 -TTTTCAATTTCTG
3830507 TTTT
1 TTTT
3830511 TTCAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.64
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:3830511 original size:14 final size:14
Alignment explanation
Indices: 3830467--3830529 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
3830457 CACTGAGGTC
* *
3830467 TTTTCAAATTCTGT
1 TTTTCAATTTCTAT
**
3830481 TTTT-AATTTCTGC
1 TTTTCAATTTCTAT
3830494 TTTTCAATTTCTATT
1 TTTTCAATTTCTA-T
*
3830509 TTTTCAATTTATAT
1 TTTTCAATTTCTAT
3830523 TTTTCAA
1 TTTTCAA
3830530 AAATCAACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.22, C:0.13, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTTCAATTTCTAT
Found at i:3830514 original size:15 final size:15
Alignment explanation
Indices: 3830494--3830526 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3830484 TAATTTCTGC
*
3830494 TTTTCAATTTCTATT
1 TTTTCAATTTATATT
3830509 TTTTCAATTTATATT
1 TTTTCAATTTATATT
3830524 TTT
1 TTT
3830527 CAAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCAATTTATATT
Found at i:3830713 original size:14 final size:14
Alignment explanation
Indices: 3830690--3830724 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3830680 CGCTGTGGTG
* *
3830690 TTTTCCATTTCTGT
1 TTTTCAATTTCTGC
3830704 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
3830718 TTTTCAA
1 TTTTCAA
3830725 AAATCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:3830824 original size:14 final size:14
Alignment explanation
Indices: 3830779--3830841 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
3830769 CGCTGAGGTC
*
3830779 TTTTCAAATTCTGT
1 TTTTCAATTTCTGT
*
3830793 TTTT-AATTTCTGC
1 TTTTCAATTTCTGT
3830806 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
* *
3830820 TTTTCCAATTTATAT
1 TTTT-CAATTTCTGT
3830835 TTTTCAA
1 TTTTCAA
3830842 AAATCAACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:3830928 original size:117 final size:115
Alignment explanation
Indices: 3830691--3830929 Score: 284
Period size: 117 Copynumber: 2.1 Consensus size: 115
3830681 GCTGTGGTGT
* * * *
3830691 TTTCCATTTCTGTTTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 TTTCAATTTCTGTTTTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGA
* * * * **
3830756 GTCTCGGGCCACACGCTGAGGTCTTTTCAAATTCTGTTTTTAATTTCTGC
66 GCCTCGGGCCACACGCTGAGGTATTTTCAAAATCTGTTTTTAAATTAAGC
* *
3830806 TTTTCAATTTCTGTTTTTCCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGATATGAGTT
1 -TTTCAATTTCTGTTTTT-CAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTT
* * *
3830871 GAGCCTTGGGTTCACATG-TCGAGGTATTTTCAAAATCTGTTTTTCAAATTAAG-
64 GAGCCTCGGG-CCACACGCT-GAGGTATTTTCAAAATCTGTTTTT-AAATTAAGC
3830924 TTTCAA
1 TTTCAA
3830930 AAAAACCAAC
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
116 16 0.15
117 56 0.54
118 27 0.26
119 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (115 bp):
TTTCAATTTCTGTTTTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGA
GCCTCGGGCCACACGCTGAGGTATTTTCAAAATCTGTTTTTAAATTAAGC
Found at i:3831736 original size:30 final size:30
Alignment explanation
Indices: 3831702--3831864 Score: 222
Period size: 30 Copynumber: 5.4 Consensus size: 30
3831692 AATCTTAGCT
3831702 TTTTCCACCACCAACTCCACTAGCCACACC
1 TTTTCCACCACCAACTCCACTAGCCACACC
*
3831732 TTTTCCACCACCAACTCCACTAGCCACTCC
1 TTTTCCACCACCAACTCCACTAGCCACACC
3831762 TTTTCCACCACCAACTCCACTAGCCACACC
1 TTTTCCACCACCAACTCCACTAGCCACACC
*
3831792 TTTTCCACCACCAAATCCACTAGCCACA-C
1 TTTTCCACCACCAACTCCACTAGCCACACC
* ** * *
3831821 TTGCTCCATTACCTACTCCACTAACCACA-C
1 TT-TTCCACCACCAACTCCACTAGCCACACC
*
3831851 TTGCTCCACCACCA
1 TT-TTCCACCACCA
3831865 CTTGTACCTA
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
29 3 0.03
30 117 0.98
ACGTcount: A:0.26, C:0.48, G:0.04, T:0.22
Consensus pattern (30 bp):
TTTTCCACCACCAACTCCACTAGCCACACC
Found at i:3831738 original size:18 final size:18
Alignment explanation
Indices: 3831717--3831799 Score: 55
Period size: 18 Copynumber: 5.3 Consensus size: 18
3831707 CACCACCAAC
3831717 TCCACTAGCCACACCTTT
1 TCCACTAGCCACACCTTT
*
3831735 TCCACCA-CCA-A-C---
1 TCCACTAGCCACACCTTT
*
3831747 TCCACTAGCCACTCCTTT
1 TCCACTAGCCACACCTTT
*
3831765 TCCACCA-CCA-A-C---
1 TCCACTAGCCACACCTTT
3831777 TCCACTAGCCACACCTTT
1 TCCACTAGCCACACCTTT
3831795 TCCAC
1 TCCAC
3831800 CACCAAATCC
Statistics
Matches: 47, Mismatches: 6, Indels: 24
0.61 0.08 0.31
Matches are distributed among these distances:
12 12 0.26
13 6 0.13
14 1 0.02
15 4 0.09
16 1 0.02
17 6 0.13
18 17 0.36
ACGTcount: A:0.24, C:0.49, G:0.04, T:0.23
Consensus pattern (18 bp):
TCCACTAGCCACACCTTT
Found at i:3832389 original size:23 final size:22
Alignment explanation
Indices: 3832352--3832481 Score: 70
Period size: 22 Copynumber: 5.5 Consensus size: 22
3832342 CCTTTTTTGT
3832352 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TT-TTAATATTA
* *
3832375 TATTATATATATTCTT-TTAATA
1 TATTATATATATT-TTAATATTA
**
3832397 TATTAGGTATATTTTAA-ATTCTA
1 TATTATATATATTTTAATA-T-TA
*
3832420 TATTACGTATATATATATTATACTATTT
1 TATTA--TATATAT-T-TTA-A-TATTA
3832448 TATGTATATATA-TTTAATATTA
1 TAT-TATATATATTTTAATATTA
*
3832470 TATTATTTATAT
1 TATTATATATAT
3832482 ATATATATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
21 10 0.12
22 22 0.27
23 19 0.23
24 7 0.08
25 6 0.07
26 1 0.01
27 9 0.11
28 5 0.06
29 3 0.04
30 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (22 bp):
TATTATATATATTTTAATATTA
Found at i:3832445 original size:25 final size:26
Alignment explanation
Indices: 3832417--3832487 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
3832407 ATTTTAAATT
*
3832417 CTATATTACGTATATATATATT-ATA
1 CTATATTATGTATATATATATTAATA
*
3832442 CTATTTTATGTATATATAT-TTAATA
1 CTATATTATGTATATATATATTAATA
* *
3832467 TTATATTATTTATATATATAT
1 CTATATTATGTATATATATAT
3832488 ATTTTTTACA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.05
25 36 0.92
26 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (26 bp):
CTATATTATGTATATATATATTAATA
Found at i:3832482 original size:23 final size:23
Alignment explanation
Indices: 3832352--3832483 Score: 60
Period size: 25 Copynumber: 5.6 Consensus size: 23
3832342 CCTTTTTTGT
*
3832352 TATTA-TTATATTTCTTAATATTA
1 TATTATTTATATAT-TTAATATTA
** *
3832375 TATTA--TATATATTCTTTTAATA
1 TATTATTTATATATT-TAATATTA
**
3832397 TATTAGGTATAT-TTTAA-ATTCTA
1 TATTATTTATATATTTAATA-T-TA
* *
3832420 TATTACGTATATATATATT-ATACTA
1 TATTA--TTTATATAT-TTAATATTA
*
3832445 TTTTATGTATATATATTTAATATTA
1 TATTAT-T-TATATATTTAATATTA
3832470 TATTATTTATATAT
1 TATTATTTATATAT
3832484 ATATATTTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
21 2 0.02
22 17 0.21
23 22 0.27
24 8 0.10
25 28 0.34
26 2 0.02
27 3 0.04
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (23 bp):
TATTATTTATATATTTAATATTA
Found at i:3832552 original size:25 final size:25
Alignment explanation
Indices: 3832521--3832569 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3832511 ATATATCTTA
**
3832521 ACTATATTATATATGTATTTTTAAC
1 ACTATATTATATACATATTTTTAAC
*
3832546 ACTATATTATGTACATATTTTTAA
1 ACTATATTATATACATATTTTTAA
3832570 TATTATCACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (25 bp):
ACTATATTATATACATATTTTTAAC
Found at i:3832751 original size:16 final size:15
Alignment explanation
Indices: 3832727--3832774 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3832717 TAATTATTAT
*
3832727 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
3832743 TATTTTAATATTTTA
1 TATTTTAATATTTTA
3832758 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
3832774 T
1 T
3832775 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:3832762 original size:7 final size:8
Alignment explanation
Indices: 3832727--3832778 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3832717 TAATTATTAT
*
3832727 TATTCTAA
1 TATTTTAA
*
3832735 TATTTTGA
1 TATTTTAA
3832743 TATTTTAA
1 TATTTTAA
3832751 TATTTT-A
1 TATTTTAA
3832758 TATTTTATA
1 TATTTTA-A
*
3832767 TATTTTAT
1 TATTTTAA
3832775 TATT
1 TATT
3832779 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:3835088 original size:21 final size:22
Alignment explanation
Indices: 3835050--3835090 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3835040 TAAAATTTTA
3835050 AAATATTTAAAAATTAATTAAT
1 AAATATTTAAAAATTAATTAAT
*
3835072 AAATTTTTAAAAA-TAATTA
1 AAATATTTAAAAATTAATTA
3835091 TTATTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATATTTAAAAATTAATTAAT
Found at i:3844378 original size:18 final size:19
Alignment explanation
Indices: 3844355--3844392 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3844345 TAATAGTAGT
3844355 AATAATAATA-AAGTAATA
1 AATAATAATATAAGTAATA
* *
3844373 AATAATGATATTAGTAATA
1 AATAATAATATAAGTAATA
3844392 A
1 A
3844393 GTTAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
AATAATAATATAAGTAATA
Found at i:3844487 original size:24 final size:24
Alignment explanation
Indices: 3844422--3844487 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3844412 AAGTAATAGA
*
3844422 TAAATAA-ATATAAAAAGGAAGGTG
1 TAAATAATA-ATAAAAATGAAGGTG
* * *
3844446 TATAAT-ATAACAATAATGATGGTG
1 TA-AATAATAATAAAAATGAAGGTG
3844470 TAAATAATAATAAAAATG
1 TAAATAATAATAAAAATG
3844488 GCATTAGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
23 3 0.09
24 26 0.79
25 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.27
Consensus pattern (24 bp):
TAAATAATAATAAAAATGAAGGTG
Found at i:3844512 original size:6 final size:6
Alignment explanation
Indices: 3844497--3844528 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3844487 GGCATTAGGG
3844497 TAAA-A TAAATA TAAATA TAAATA TAAATA TAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAA
3844529 TGATAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAATA
Found at i:3844761 original size:3 final size:3
Alignment explanation
Indices: 3844755--3844788 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3844745 ATACCAAGGG
* *
3844755 TAA TAA TAA TAA TAA TAA TAA TAG TAC TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3844789 GATGATAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3844796 original size:18 final size:18
Alignment explanation
Indices: 3844764--3844798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3844754 GTAATAATAA
3844764 TAATAATAATAATAGTAC
1 TAATAATAATAATAGTAC
* *
3844782 TAATAATGATGATAGTA
1 TAATAATAATAATAGTA
3844799 AATATAATGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.34
Consensus pattern (18 bp):
TAATAATAATAATAGTAC
Found at i:3844970 original size:3 final size:3
Alignment explanation
Indices: 3844962--3845077 Score: 71
Period size: 3 Copynumber: 38.7 Consensus size: 3
3844952 AGAAAGAGAG
* *
3844962 ATA ATA ATA ATA ATA ATA ATA ATA ACA TATA TATA A-A ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA
* * * *
3845008 GTTA GA-A ATA A-A A-A ATA ATA GA-A GTA ATA ATA ATA ATG GTA ATA
1 -ATA -ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * *
3845052 AAA ATA AAA ATA ATA GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
3845078 GAGTTAAGTT
Statistics
Matches: 88, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
2 7 0.08
3 72 0.82
4 9 0.10
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:3847284 original size:21 final size:21
Alignment explanation
Indices: 3847258--3847302 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3847248 TTTATGAGAA
*
3847258 TTAAAATA-TAAATTTAAAATT
1 TTAAAAGATTAAA-TTAAAATT
*
3847279 TTAAAAGATTAAATTATAATT
1 TTAAAAGATTAAATTAAAATT
3847300 TTA
1 TTA
3847303 TTATTTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAAAAGATTAAATTAAAATT
Found at i:3848222 original size:25 final size:25
Alignment explanation
Indices: 3848188--3848237 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3848178 AAAGAAAGAA
3848188 AATTTGACTCGCCTTATTTCATTGC
1 AATTTGACTCGCCTTATTTCATTGC
3848213 AATTTGACTCGCCTTATTTCATTGC
1 AATTTGACTCGCCTTATTTCATTGC
3848238 CATTGATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (25 bp):
AATTTGACTCGCCTTATTTCATTGC
Found at i:3848293 original size:21 final size:19
Alignment explanation
Indices: 3848263--3848305 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
3848253 TGAAGATAAA
*
3848263 ATTTTAAAAATTAATTAATAT
1 ATTTTAAAAAATAA-TAAT-T
*
3848284 ATTTTTAAAAATAATAATT
1 ATTTTAAAAAATAATAATT
3848303 ATT
1 ATT
3848306 GATAAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTAAAAAATAATAATT
Found at i:3848414 original size:25 final size:25
Alignment explanation
Indices: 3848386--3848441 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
3848376 TATTATTTAA
3848386 AAAAATAAGTTCCTAAAAAGATACC
1 AAAAATAAGTTCCTAAAAAGATACC
3848411 AAAAATAAGTTCCTAAAAAGATACC
1 AAAAATAAGTTCCTAAAAAGATACC
3848436 AAAAAT
1 AAAAAT
3848442 CCAGTCATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.20
Consensus pattern (25 bp):
AAAAATAAGTTCCTAAAAAGATACC
Found at i:3848482 original size:8 final size:8
Alignment explanation
Indices: 3848469--3848495 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3848459 AGCAATATAA
3848469 TAAAGAAG
1 TAAAGAAG
3848477 TAAAGAAG
1 TAAAGAAG
3848485 TAAAGAAG
1 TAAAGAAG
3848493 TAA
1 TAA
3848496 TGGCAAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (8 bp):
TAAAGAAG
Found at i:3851599 original size:43 final size:43
Alignment explanation
Indices: 3851552--3851639 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
3851542 TAAAACCATT
* ** *
3851552 ATAATTTGTAAAAATATTTT-TTTTAAATTCCATTTGGTTTTTA
1 ATAATTCGTAAAAATATTTTAAATAAAATT-CATTTGGTTTTTA
*
3851595 ATAATTCGTAAAATTATTTTAAATAAAATTCATTTGGTTTTTA
1 ATAATTCGTAAAAATATTTTAAATAAAATTCATTTGGTTTTTA
3851638 AT
1 AT
3851640 TTTATAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 33 0.85
44 6 0.15
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (43 bp):
ATAATTCGTAAAAATATTTTAAATAAAATTCATTTGGTTTTTA
Found at i:3853369 original size:13 final size:14
Alignment explanation
Indices: 3853353--3853393 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
3853343 TTTACAGATA
3853353 CAGATA-ACAGAAT
1 CAGATATACAGAAT
3853366 CAGATATACAGAA-
1 CAGATATACAGAAT
* *
3853379 CAGGTATATAGAAT
1 CAGATATACAGAAT
3853393 C
1 C
3853394 CTACCCCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (14 bp):
CAGATATACAGAAT
Found at i:3863025 original size:18 final size:18
Alignment explanation
Indices: 3863002--3863047 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
3862992 TAAATTCACA
3863002 CTTTTTGCCTGCAAATTT
1 CTTTTTGCCTGCAAATTT
3863020 CTTTTTGCCTGCAAATTT
1 CTTTTTGCCTGCAAATTT
*
3863038 CCTTTTGCCT
1 CTTTTTGCCT
3863048 TTAATTCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.26, G:0.11, T:0.50
Consensus pattern (18 bp):
CTTTTTGCCTGCAAATTT
Found at i:3865660 original size:62 final size:62
Alignment explanation
Indices: 3865563--3865686 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
3865553 TTGAAAAATC
*
3865563 AAATGTTAGTGTATACAGTTTTGGCATTTTTTATGACACATGGCATAGAAGACTTGGCTATT
1 AAATGTTAGTGTATACAGTGTTGGCATTTTTTATGACACATGGCATAGAAGACTTGGCTATT
* *
3865625 AAATGTTAGTGTATACAGTGTTGGCGTTTTTTATGACACATGGCATAGAAGACTTGGTTATT
1 AAATGTTAGTGTATACAGTGTTGGCATTTTTTATGACACATGGCATAGAAGACTTGGCTATT
3865687 CTCTTCAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (62 bp):
AAATGTTAGTGTATACAGTGTTGGCATTTTTTATGACACATGGCATAGAAGACTTGGCTATT
Found at i:3867704 original size:25 final size:21
Alignment explanation
Indices: 3867657--3867700 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3867647 TGTGTAGGAG
3867657 TTATTTAGTTTGTTTTTATGA
1 TTATTTAGTTTGTTTTTATGA
*
3867678 TTATTTAGTTTGTTGTTATGA
1 TTATTTAGTTTGTTTTTATGA
3867699 TT
1 TT
3867701 GATTGTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (21 bp):
TTATTTAGTTTGTTTTTATGA
Found at i:3881677 original size:36 final size:36
Alignment explanation
Indices: 3881648--3881717 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
3881638 TTACTAAACC
*
3881648 CAAGATATCATAATATATTTATATAGTTACAAGACA
1 CAAGATATAATAATATATTTATATAGTTACAAGACA
* * *
3881684 CAAGGTATAATAATATATTTATATAATCACAAGA
1 CAAGATATAATAATATATTTATATAGTTACAAGA
3881718 AACCAAACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.33
Consensus pattern (36 bp):
CAAGATATAATAATATATTTATATAGTTACAAGACA
Found at i:3887018 original size:20 final size:20
Alignment explanation
Indices: 3886993--3887031 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3886983 TTTCCTCCCC
3886993 ATGTTGCTTTCCGACCAAAT
1 ATGTTGCTTTCCGACCAAAT
*
3887013 ATGTTGCTTTCTGACCAAA
1 ATGTTGCTTTCCGACCAAA
3887032 CAATGAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGTTGCTTTCCGACCAAAT
Found at i:3887430 original size:21 final size:21
Alignment explanation
Indices: 3887405--3887446 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3887395 ACCTGTTTAG
3887405 TGCCTTCAATCTCTAATCTAA
1 TGCCTTCAATCTCTAATCTAA
*
3887426 TGCCTTTAATCTCTAATCTAA
1 TGCCTTCAATCTCTAATCTAA
3887447 CACTTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.40
Consensus pattern (21 bp):
TGCCTTCAATCTCTAATCTAA
Found at i:3898688 original size:15 final size:16
Alignment explanation
Indices: 3898659--3898695 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3898649 CGAACGATGC
3898659 GATG-AAATGCAATGA
1 GATGCAAATGCAATGA
3898674 GATGCAAATGC-ATGA
1 GATGCAAATGCAATGA
3898689 -ATGCAAA
1 GATGCAAA
3898696 AAGGACATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (16 bp):
GATGCAAATGCAATGA
Found at i:3902865 original size:26 final size:28
Alignment explanation
Indices: 3902815--3902869 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
3902805 ATAGAAGATG
*
3902815 AAATATATACACAATATAATAATATAAT
1 AAATATATACACAATATAAAAATATAAT
*
3902843 AAATA-ATACA-AATTTAAAAATATAAT
1 AAATATATACACAATATAAAAATATAAT
3902869 A
1 A
3902870 CTTAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.60
27 5 0.20
28 5 0.20
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATATATACACAATATAAAAATATAAT
Found at i:3905115 original size:22 final size:22
Alignment explanation
Indices: 3905085--3905131 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3905075 TTCCAAGGTA
3905085 TATCCAATTAATGTCGCCAATG
1 TATCCAATTAATGTCGCCAATG
*
3905107 TATCTAATTAATGTCGCCAATG
1 TATCCAATTAATGTCGCCAATG
3905129 TAT
1 TAT
3905132 ATCTCAAGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (22 bp):
TATCCAATTAATGTCGCCAATG
Found at i:3906046 original size:24 final size:24
Alignment explanation
Indices: 3906019--3906066 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3906009 GACTATGAAG
*
3906019 ATAAAGTATTTAAAAA-ATTAATTA
1 ATAAA-TATTTAAAAATAATAATTA
*
3906043 ATAAATTTTTAAAAATAATAATTA
1 ATAAATATTTAAAAATAATAATTA
3906067 TTGATAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATAAATATTTAAAAATAATAATTA
Found at i:3909333 original size:160 final size:151
Alignment explanation
Indices: 3909063--3909403 Score: 472
Period size: 160 Copynumber: 2.2 Consensus size: 151
3909053 TATATTTTCT
* * *
3909063 AACATTACATTGATATTTTCTAACATTTGAGCAAGGGCAGTTTGACACTCAATCCAAATTTAACG
1 AACATTACATTGATATTTTTTAACATTTAAGCAAGGGCAGTTTGACAATCAATCCAAATTTAACG
3909128 AAACTAAAAATCAAATACAAAAATAATGCTTTTGTTTTTTGAAATGACTGAATATTTGACTTTTC
66 AAACTAAAAATCAAATACAAAAATAATGCTTTTGTTTTTTGAAATGACTGAATATTTGAC--TTC
* *
3909193 TCTTTCTTTTGATGTAATTTTG-
129 TCTTTCCTTTCATGTAATTTTGA
*
3909215 AACAATTACATTGATATTTTTTAACATTTAAGCAAGGG-GGTTTGACAATCAATCCAAATTTAAT
1 AAC-ATTACATTGATATTTTTTAACATTTAAGCAAGGGCAGTTTGACAATCAATCCAAATTT-A-
* *
3909279 GACTAAAAGAAACTAAAAATCAAATACTAAAGTAATGCTTTTGTTTTTTGAAATGACTGAATATT
63 -AC-----GAAACTAAAAATCAAATACAAAAATAATGCTTTTGTTTTTTGAAATGACTGAATATT
*
3909344 TGACTTCTCTTTCCTTTCATGTCATTTTGA
122 TGACTTCTCTTTCCTTTCATGTAATTTTGA
3909374 AACATTACATTGATATTTTCTT-ACATTTAA
1 AACATTACATTGATATTTT-TTAACATTTAA
3909404 TATATATATT
Statistics
Matches: 169, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
152 24 0.14
153 33 0.20
155 2 0.01
158 46 0.27
159 5 0.03
160 59 0.35
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (151 bp):
AACATTACATTGATATTTTTTAACATTTAAGCAAGGGCAGTTTGACAATCAATCCAAATTTAACG
AAACTAAAAATCAAATACAAAAATAATGCTTTTGTTTTTTGAAATGACTGAATATTTGACTTCTC
TTTCCTTTCATGTAATTTTGA
Found at i:3911431 original size:24 final size:24
Alignment explanation
Indices: 3911386--3911432 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3911376 ATTTAGTAGT
*
3911386 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTAATTAGC
3911410 ATAATATATTTTA-CATTAATTAG
1 ATAATATA-TTTAGCATTAATTAG
3911433 AATTAGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (24 bp):
ATAATATATTTAGCATTAATTAGC
Done.