Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 22 of 27
Found at i:3321532 original size:15 final size:16
Alignment explanation
Indices: 3321502--3321534 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3321492 AAATATTAAA
3321502 TATAAATATTTATTTAT
1 TATAAATA-TTATTTAT
3321519 TATAAATA-TATTTAT
1 TATAAATATTATTTAT
3321534 T
1 T
3321535 TTTTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATAAATATTATTTAT
Found at i:3324491 original size:3 final size:3
Alignment explanation
Indices: 3324478--3324520 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
3324468 AATAAAAGTC
*
3324478 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3324521 CTTTAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3325151 original size:15 final size:15
Alignment explanation
Indices: 3325122--3325161 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3325112 AATTTTTTAT
3325122 TTTTTTAATTT--AA
1 TTTTTTAATTTAAAA
3325135 TTATTTT-ATTTAAAA
1 TT-TTTTAATTTAAAA
3325150 TTTTTTAATTTA
1 TTTTTTAATTTA
3325162 GGTAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 6 0.26
14 8 0.35
15 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTTAATTTAAAA
Found at i:3326756 original size:26 final size:26
Alignment explanation
Indices: 3326727--3326780 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
3326717 TATTTAATAA
**
3326727 ATTTAAATTTTTATAAAAAAATTAAT
1 ATTTAAATTTAAATAAAAAAATTAAT
*
3326753 ATTTAAATTTAAATAAAAAATTTAAT
1 ATTTAAATTTAAATAAAAAAATTAAT
3326779 AT
1 AT
3326781 ATTATTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAAATTTAAATAAAAAAATTAAT
Found at i:3326787 original size:25 final size:24
Alignment explanation
Indices: 3326739--3326793 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
3326729 TTAAATTTTT
3326739 ATAAAAAAATTAATATTTAAATTTAA
1 ATAAAAAAATTAATATTT-AATTT-A
*
3326765 ATAAAAAATTTAATATATT-ATTTA
1 ATAAAAAAATTAATAT-TTAATTTA
3326789 ATAAA
1 ATAAA
3326794 CTTTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 6 0.22
25 4 0.15
26 15 0.56
27 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAAAAAAATTAATATTTAATTTA
Found at i:3329241 original size:2 final size:2
Alignment explanation
Indices: 3329234--3329274 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3329224 TAGATTTGAT
3329234 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3329275 TCTTTTGAAC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3334231 original size:24 final size:24
Alignment explanation
Indices: 3334199--3334247 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3334189 CATACGTTTA
** *
3334199 ATTTTAATTTTTTTGGATTAAATG
1 ATTTTAATTTCGTTGGAATAAATG
3334223 ATTTTAATTTCGTTGGAATAAATG
1 ATTTTAATTTCGTTGGAATAAATG
3334247 A
1 A
3334248 GTGTTTGCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (24 bp):
ATTTTAATTTCGTTGGAATAAATG
Found at i:3334466 original size:2 final size:2
Alignment explanation
Indices: 3334461--3334502 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3334451 TATACATGTT
*
3334461 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3334503 AACTTGATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3334991 original size:18 final size:18
Alignment explanation
Indices: 3334967--3335009 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
3334957 CCATGTTTAT
3334967 AATATTTTATTATTAAAA
1 AATATTTTATTATTAAAA
* *
3334985 TATA-TTTATTTTTAAAA
1 AATATTTTATTATTAAAA
3335002 AATATTTT
1 AATATTTT
3335010 TTACGTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTTTATTATTAAAA
Found at i:3337979 original size:2 final size:2
Alignment explanation
Indices: 3337972--3338019 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3337962 TGATTGCATT
*
3337972 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3338014 TA TA TA
1 TA TA TA
3338020 AAACTAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3349322 original size:13 final size:13
Alignment explanation
Indices: 3349296--3349334 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3349286 ATATCTATAT
3349296 TTAAATAT--ATA
1 TTAAATATAAATA
3349307 TTAAATATAAATA
1 TTAAATATAAATA
*
3349320 TTAAATAAAAATA
1 TTAAATATAAATA
3349333 TT
1 TT
3349335 TTAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.32
13 17 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:3349881 original size:21 final size:18
Alignment explanation
Indices: 3349855--3349898 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
3349845 AATATTAAAT
*
3349855 TTTTTTATATAATTAATTATA
1 TTTTTTACATAA--AATT-TA
3349876 TTTTTTACATAAAATTTA
1 TTTTTTACATAAAATTTA
3349894 TTTTT
1 TTTTT
3349899 CTTTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 4 0.18
21 11 0.50
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTTACATAAAATTTA
Found at i:3349891 original size:23 final size:22
Alignment explanation
Indices: 3349848--3349891 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3349838 ATAATTTAAT
* *
3349848 ATTAAATTTTTTTATATAATTA
1 ATTAAATTTTTTCATAAAATTA
*
3349870 ATTATATTTTTTACATAAAATT
1 ATTAAATTTTTT-CATAAAATT
3349892 TATTTTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTAAATTTTTTCATAAAATTA
Found at i:3350373 original size:28 final size:27
Alignment explanation
Indices: 3350342--3350411 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 27
3350332 CATAAAATAT
3350342 TAAATTAAATTTATTTAC-AAGGCTT-CTA
1 TAAA-TAAATTTATTTACTAA-G-TTGCTA
3350370 TAAATAAATTATATTTACTAAGTTGCTA
1 TAAATAAATT-TATTTACTAAGTTGCTA
3350398 TAAATAAATTTATT
1 TAAATAAATTTATT
3350412 CTAGTAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 12 0.31
28 25 0.64
29 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (27 bp):
TAAATAAATTTATTTACTAAGTTGCTA
Found at i:3350698 original size:24 final size:24
Alignment explanation
Indices: 3350671--3350720 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3350661 AAAAGTTTTT
3350671 ATTTTTATATATT-T-ATTATATAAA
1 ATTTTTATAT-TTATAATTAT-TAAA
3350695 ATTTTTATATTTATAATTATTAAA
1 ATTTTTATATTTATAATTATTAAA
3350719 AT
1 AT
3350721 CATGATTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.08
24 17 0.71
25 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTTTATATTTATAATTATTAAA
Found at i:3364618 original size:23 final size:23
Alignment explanation
Indices: 3364566--3364632 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
3364556 AATATTTCTC
* * *
3364566 TTTATCTTTC-TGTCTCTTTGCC
1 TTTATCTTTCTTTTTTCTTTGCA
*
3364588 TTTCTCTTTCTTTTTTCTTTGCA
1 TTTATCTTTCTTTTTTCTTTGCA
3364611 TTTATCTTACTCTTCTTTTCTT
1 TTTATCTT--TCTT-TTTTCTT
3364633 ATACTTTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 9 0.25
23 16 0.44
25 4 0.11
26 7 0.19
ACGTcount: A:0.06, C:0.24, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTATCTTTCTTTTTTCTTTGCA
Found at i:3365433 original size:22 final size:20
Alignment explanation
Indices: 3365401--3365441 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
3365391 GAAAAAAAAA
3365401 TAATTAAAAAAATAATTTTAT
1 TAATT-AAAAAATAATTTTAT
*
3365422 TAATGTAAAAAATATTTTTA
1 TAAT-TAAAAAATAATTTTA
3365442 AAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATTAAAAAATAATTTTAT
Found at i:3365447 original size:14 final size:15
Alignment explanation
Indices: 3365428--3365457 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3365418 TTATTAATGT
3365428 AAAAAATATT-TTTA
1 AAAAAATATTATTTA
3365442 AAAAAATATTATTTA
1 AAAAAATATTATTTA
3365457 A
1 A
3365458 TAAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAAATATTATTTA
Found at i:3365575 original size:32 final size:31
Alignment explanation
Indices: 3365534--3365593 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3365524 TAACTTTAAA
3365534 CCTTTAAAATATAAAAAAATAAAATTTAAAAC
1 CCTTTAAAATAT-AAAAAATAAAATTTAAAAC
*
3365566 CCTTTAAAATATAAAATATAAAATTTAA
1 CCTTTAAAATATAAAAAATAAAATTTAA
3365594 TTTATTAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (31 bp):
CCTTTAAAATATAAAAAATAAAATTTAAAAC
Found at i:3366244 original size:28 final size:28
Alignment explanation
Indices: 3366204--3366263 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
3366194 CACCTTTACC
3366204 ATTACCCTATGTGGGAGGAGAGAAAGAA
1 ATTACCCTATGTGGGAGGAGAGAAAGAA
3366232 ATTACCCTATGTGGGAGGAGAGAAAGAA
1 ATTACCCTATGTGGGAGGAGAGAAAGAA
3366260 ATTA
1 ATTA
3366264 GTGTTTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (28 bp):
ATTACCCTATGTGGGAGGAGAGAAAGAA
Found at i:3366885 original size:14 final size:14
Alignment explanation
Indices: 3366861--3366893 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3366851 TAAGCTAATG
3366861 ATAAATTTAAATTT
1 ATAAATTTAAATTT
3366875 -TAAATTTTAAATTT
1 ATAAA-TTTAAATTT
3366889 ATAAA
1 ATAAA
3366894 ATATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 9 0.53
15 4 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAATTTAAATTT
Found at i:3367289 original size:20 final size:21
Alignment explanation
Indices: 3367261--3367299 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3367251 TCATTAAATT
3367261 TTTAATTTT-AATAATTAAAA
1 TTTAATTTTCAATAATTAAAA
* *
3367281 TTTATTTTTCGATAATTAA
1 TTTAATTTTCAATAATTAA
3367300 GTATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTAATTTTCAATAATTAAAA
Found at i:3367876 original size:6 final size:6
Alignment explanation
Indices: 3367859--3367931 Score: 62
Period size: 6 Copynumber: 11.8 Consensus size: 6
3367849 ATATGTTTAA
* *
3367859 TATATAT TATATT TATATT TAAAATT T-TA-A TATATT TAATTATT TATATT
1 TATAT-T TATATT TATATT T-ATATT TATATT TATATT T-A-TATT TATATT
3367909 TATA-T TATTATT TATATT TATAT
1 TATATT TA-TATT TATATT TATAT
3367932 AAATAATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
4 1 0.02
5 6 0.11
6 28 0.51
7 15 0.27
8 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:3367918 original size:18 final size:18
Alignment explanation
Indices: 3367897--3367931 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3367887 AATATATTTA
3367897 ATTATTTATATTTATATT
1 ATTATTTATATTTATATT
3367915 ATTATTTATATTTATAT
1 ATTATTTATATTTATAT
3367932 AAATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTATTTATATTTATATT
Found at i:3372623 original size:3 final size:3
Alignment explanation
Indices: 3372615--3372643 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3372605 AAATCGAGAC
3372615 GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3372644 AGGGTTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3375456 original size:3 final size:3
Alignment explanation
Indices: 3375448--3375483 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3375438 TAAATGCATC
3375448 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3375484 CTAGAACGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3376129 original size:183 final size:183
Alignment explanation
Indices: 3375821--3376185 Score: 694
Period size: 183 Copynumber: 2.0 Consensus size: 183
3375811 AGCTTCGCAG
* * *
3375821 TTACATGGTTACCTCACAATTATTGGTCTGAAAGCAAGCTAAGGCAGGAATTCCAAGCCCCATGA
1 TTACATGGTTACCTCACAATTATTGGCCTGAAAGCAAGCTAAGACACGAATTCCAAGCCCCATGA
*
3375886 AAATGTTATATCAGAATTATGGCTCAGCTGTTCATCCATATAAAACTTGACTTGATATATCTAAA
66 AAATGTTATATCAGAATTATGGCTCAGCTGTTCATCCATATAAAACTTGACTTCATATATCTAAA
3375951 AGTTTGCTTCAAAACTAGAAAGCACATTCCACGAGTTCAATTAGAGATCGCCA
131 AGTTTGCTTCAAAACTAGAAAGCACATTCCACGAGTTCAATTAGAGATCGCCA
3376004 TTACATGGTTACCTCACAATTATTGGCCTGAAAGCAAGCTAAGACACGAATTCCAAGCCCCATGA
1 TTACATGGTTACCTCACAATTATTGGCCTGAAAGCAAGCTAAGACACGAATTCCAAGCCCCATGA
3376069 AAATGTTATATCAGAATTATGGCTCAGCTGTTCATCCATATAAAACTTGACTTCATATATCTAAA
66 AAATGTTATATCAGAATTATGGCTCAGCTGTTCATCCATATAAAACTTGACTTCATATATCTAAA
3376134 AGTTTGCTTCAAAACTAGAAAGCACATTCCACGAGTTCAATTAGAGATCGCC
131 AGTTTGCTTCAAAACTAGAAAGCACATTCCACGAGTTCAATTAGAGATCGCC
3376186 CCAGCAAGCC
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 178 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (183 bp):
TTACATGGTTACCTCACAATTATTGGCCTGAAAGCAAGCTAAGACACGAATTCCAAGCCCCATGA
AAATGTTATATCAGAATTATGGCTCAGCTGTTCATCCATATAAAACTTGACTTCATATATCTAAA
AGTTTGCTTCAAAACTAGAAAGCACATTCCACGAGTTCAATTAGAGATCGCCA
Found at i:3384379 original size:29 final size:29
Alignment explanation
Indices: 3384320--3384379 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3384310 ATTAAATTTT
** **
3384320 TAATTTTAATAATTAAAATTTAATTTTAA
1 TAATTTTAATAATTAAAAAATAATTAAAA
3384349 TAATTTTAA-ATATTAAAAAATAATTAAAA
1 TAATTTTAATA-ATTAAAAAATAATTAAAA
3384378 TA
1 TA
3384380 TTTACTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATTTTAATAATTAAAAAATAATTAAAA
Found at i:3404024 original size:352 final size:344
Alignment explanation
Indices: 3403271--3404122 Score: 1104
Period size: 352 Copynumber: 2.5 Consensus size: 344
3403261 AAAATTAAAG
* *
3403271 CAATTTTTTCAAAGAGTTATGTTTTAAATACGACTATCACGGTATTTGCAGGAGCCAACAATGAT
1 CAATTTTTTC-AAGAGTTATGTTTTAAATACGACTACCATGGTATTTGCAGGAGCCAACAATGAT
* * * *
3403336 GGGAAACGAGGGGAGGGTGGTTACAGAGATGAAAATGGCTACCGAAATG--AG-TTCAGAGGCCG
65 GGGAAACCAGGGAAGGGTGGTTATAGAGATGAAAATGGCTACCGAAACGACAGCTTCAGAGGCCG
* * *
3403398 AGGGAACTTCAATGGTAACCAGAACTCTTATCATAAATATGTTTGTAACATTAATATAATGTGTA
130 AGGGAACTTCAATGGTAGCCATAACTCTTATCATAAATATGTTTATAACATTAATATAATGTGTA
**
3403463 TAAAAAGATTTTCTCTCTTATTTGAACTCTACAGCGCTGAATAAAATATCCCAACTAAACCCAAA
195 TAAAAAGATTTTCTCTCTTATGAGAACTCTACAGCGCTGAATAAAATATCCCAACTAAACCCAAA
* *
3403528 ACTATATTAACTAAAATTAAAGCCGATGATTAATTGTGTTAGTTAAAATAAATGAAGTAAGGAAC
260 ACTATATTAAATAAAATTAAAGCCGATGATTAATTGTGTTAGCTAAAATAAATGAAGTAAGGAAC
*
3403593 AAATATAGGTAAAGTAGTAT
325 AAATAGAGGTAAAGTAGTAT
**
3403613 CAATTTTTTTTCGAAGAGTTATGTTTTAAATACGACTAGAATGGTATTTGCAGGAGCCAACAATG
1 CAA--TTTTTTC-AAGAGTTATGTTTTAAATACGACTACCATGGTATTTGCAGGAGCCAACAATG
* * * * * *
3403678 AAGGGCAACCAGAGAAGGGTGGTTATAGAGATGGAAATGGCTACCAAAACGACAGCTTCGGAGGC
63 ATGGGAAACCAGGGAAGGGTGGTTATAGAGATGAAAATGGCTACCGAAACGACAGCTTCAGAGGC
* * * *
3403743 CGAGGGAACTTCAATGGTAGCCATAACTGTTGTCGTAAATATGTTTTATAACA-TAGTATGAATG
128 CGAGGGAACTTCAATGGTAGCCATAACTCTTATCATAAATATG-TTTATAACATTAATAT-AATG
* * *
3403807 TGTATAAAAGGATTTTCTCTCTTACTAGAGAACTTTACAGCGCTGAATAAAGTATCCCAACTAAA
191 TGTATAAAAAGATTTTCTCTCTTA-T-GAGAACTCTACAGCGCTGAATAAAATATCCCAACTAAA
*** * *
3403872 CTTGAAACTGTATTAAATAAAATTAAAGCC-AGTGATTATATTTTAGTGTTAGCTAAATTAAATG
254 CCCAAAACTATATTAAATAAAATTAAAGCCGA-TGATTA-A--TT-GTGTTAGCTAAAATAAATG
* * *
3403936 AAGTAATGAACAACTAGAGGTCAA-TAGTAT
314 AAGTAAGGAACAAATAGAGGTAAAGTAGTAT
* *
3403966 CAATTATTTTCAATGAGTTATGTTTTAAATACGACTACCATGGTATTTGCAGGAGCCAACCATGG
1 CAATT-TTTTCAA-GAGTTATGTTTTAAATACGACTACCATGGTATTTGCAGGAGCCAACAATGA
** * * *
3404031 TGGGAAACCAGGGTGGGGTGGTTATAGAGATGAAAATGGCTACCGAAACGACAACTTCAAAGTCC
64 TGGGAAACCAGGGAAGGGTGGTTATAGAGATGAAAATGGCTACCGAAACGACAGCTTCAGAGGCC
* * *
3404096 AAGGGAACGTCAATAGTAGCCATAACT
129 GAGGGAACTTCAATGGTAGCCATAACT
3404123 TTGGAAGAAA
Statistics
Matches: 439, Mismatches: 55, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
342 3 0.01
344 98 0.22
346 2 0.00
347 51 0.12
348 35 0.08
349 2 0.00
350 65 0.15
351 5 0.01
352 130 0.30
353 11 0.03
354 37 0.08
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (344 bp):
CAATTTTTTCAAGAGTTATGTTTTAAATACGACTACCATGGTATTTGCAGGAGCCAACAATGATG
GGAAACCAGGGAAGGGTGGTTATAGAGATGAAAATGGCTACCGAAACGACAGCTTCAGAGGCCGA
GGGAACTTCAATGGTAGCCATAACTCTTATCATAAATATGTTTATAACATTAATATAATGTGTAT
AAAAAGATTTTCTCTCTTATGAGAACTCTACAGCGCTGAATAAAATATCCCAACTAAACCCAAAA
CTATATTAAATAAAATTAAAGCCGATGATTAATTGTGTTAGCTAAAATAAATGAAGTAAGGAACA
AATAGAGGTAAAGTAGTAT
Found at i:3405286 original size:17 final size:17
Alignment explanation
Indices: 3405266--3405300 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3405256 ACCTTTTCTA
3405266 ATTTTT-TTATATTTTAT
1 ATTTTTATT-TATTTTAT
3405283 ATTTTTATTTATTTTAT
1 ATTTTTATTTATTTTAT
3405300 A
1 A
3405301 ATTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTTATTTATTTTAT
Found at i:3405454 original size:11 final size:11
Alignment explanation
Indices: 3405440--3405540 Score: 71
Period size: 11 Copynumber: 8.7 Consensus size: 11
3405430 AAAATGATTT
*
3405440 TAAATATTATA
1 TAAATATAATA
3405451 TAAATATAATA
1 TAAATATAATA
*
3405462 TAAAAATAAT-
1 TAAATATAATA
3405472 TAAAATATAATA
1 T-AAATATAATA
* *
3405484 TTATATATGATA
1 -TAAATATAATA
3405496 TATAA-ATAATA
1 TA-AATATAATA
*
3405507 TAATATAAAATA
1 TAA-ATATAATA
3405519 TTAATATATTAATA
1 -TAA-ATA-TAATA
*
3405533 TATATATA
1 TAAATATA
3405541 TATTTTAGAT
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
10 2 0.03
11 39 0.54
12 17 0.24
13 10 0.14
14 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
TAAATATAATA
Found at i:3405461 original size:5 final size:5
Alignment explanation
Indices: 3405442--3405540 Score: 59
Period size: 5 Copynumber: 20.2 Consensus size: 5
3405432 AATGATTTTA
* * * *
3405442 AATAT TATAT AAATAT AATAT AAAAAT AATTAA AATAT AATAT TATAT
1 AATAT AATAT -AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT
*
3405490 -ATGAT -ATAT AA-AT AATAT AATAT AAAAT -AT-T AATAT -AT-T AATAT
1 AAT-AT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
3405534 ATATAT A
1 A-ATAT A
3405541 TATTTTAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
3 2 0.03
4 15 0.20
5 41 0.55
6 16 0.22
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:3405512 original size:23 final size:22
Alignment explanation
Indices: 3405478--3405542 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
3405468 TAATTAAAAT
*
3405478 ATAATATTATATATGATATATAA
1 ATAATATAATATAT-ATATATAA
* *
3405501 ATAATATAATATA-AAATATTA
1 ATAATATAATATATATATATAA
3405522 AT-ATATTAATATATATATATA
1 ATAATA-TAATATATATATATA
3405543 TTTTAGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.09
21 15 0.43
22 5 0.14
23 12 0.34
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAATATAATATATATATATAA
Found at i:3405543 original size:16 final size:16
Alignment explanation
Indices: 3405442--3405544 Score: 59
Period size: 16 Copynumber: 7.0 Consensus size: 16
3405432 AATGATTTTA
*
3405442 AATAT-TATATAAATAT
1 AATATATATATATAT-T
* *
3405458 AATATAAAAATA-ATT
1 AATATATATATATATT
3405473 AA-A-ATATA-ATATT
1 AATATATATATATATT
3405486 -ATATATGATATATA--
1 AATATAT-ATATATATT
3405500 AATA-ATATA-ATA-T
1 AATATATATATATATT
*
3405513 AAAATAT-TAATATATT
1 AATATATAT-ATATATT
3405529 AATATATATATATATT
1 AATATATATATATATT
3405545 TTAGATATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
12 5 0.07
13 14 0.21
14 8 0.12
15 12 0.18
16 24 0.35
17 5 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
AATATATATATATATT
Found at i:3413733 original size:41 final size:41
Alignment explanation
Indices: 3413688--3413770 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
3413678 AAACCAGCCC
3413688 TTTTAACACCGAATCCATATAAGTGGCAAAAATTGAAGCAA
1 TTTTAACACCGAATCCATATAAGTGGCAAAAATTGAAGCAA
* * *
3413729 TTTTAGCACTGAATCCATATAAGTGGCAAAAATTGAGGCAA
1 TTTTAACACCGAATCCATATAAGTGGCAAAAATTGAAGCAA
3413770 T
1 T
3413771 CTAGAAGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.27
Consensus pattern (41 bp):
TTTTAACACCGAATCCATATAAGTGGCAAAAATTGAAGCAA
Found at i:3422115 original size:15 final size:15
Alignment explanation
Indices: 3422085--3422143 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
3422075 GATGCTATTT
3422085 ATAATAATTAATTATA
1 ATAAT-ATTAATTATA
*
3422101 ATAATATTTATTAT-
1 ATAATATTAATTATA
3422115 AT-ATA-TAATTATA
1 ATAATATTAATTATA
3422128 ATAA-ATATAA-TATA
1 ATAATAT-TAATTATA
3422142 AT
1 AT
3422144 GTAATTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 6 0.16
13 6 0.16
14 9 0.24
15 11 0.30
16 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATATTAATTATA
Found at i:3422126 original size:27 final size:25
Alignment explanation
Indices: 3422080--3422131 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
3422070 TTATTGATGC
3422080 TATTTATAATAATTAATTATAATAA
1 TATTTATAATAATTAATTATAATAA
*
3422105 TATTTATTATATATATAATTATAATAA
1 TATTTATAATA-AT-TAATTATAATAA
3422132 ATATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 10 0.42
26 2 0.08
27 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTTATAATAATTAATTATAATAA
Found at i:3429827 original size:2 final size:2
Alignment explanation
Indices: 3429820--3429849 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3429810 AATTTTTAAA
3429820 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
3429850 CAAAGTTCTT
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:3437766 original size:19 final size:19
Alignment explanation
Indices: 3437738--3437790 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
3437728 TAAACAATTA
* *
3437738 AAATTTTTAATATTATATAT
1 AAATTATTAA-ATTATAAAT
3437758 -AATTATTAAATTATAAAT
1 AAATTATTAAATTATAAAT
*
3437776 AAATTAATAAATTAT
1 AAATTATTAAATTAT
3437791 CATTACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.28
19 21 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTATTAAATTATAAAT
Found at i:3438254 original size:32 final size:33
Alignment explanation
Indices: 3438198--3438260 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
3438188 TTTTTTTGAA
*
3438198 TTTAATAAAAATTATATATTAAATAATATTTTT
1 TTTAATAAAAATTATATATAAAATAATATTTTT
3438231 TTTAA-AAAAATTA-ATAATAAAATAATATTT
1 TTTAATAAAAATTATAT-ATAAAATAATATTT
3438261 AATTAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 2 0.07
32 21 0.75
33 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TTTAATAAAAATTATATATAAAATAATATTTTT
Found at i:3438841 original size:15 final size:15
Alignment explanation
Indices: 3438823--3438864 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3438813 TTATTTATTT
3438823 ATTTTATATTTTTAA
1 ATTTTATATTTTTAA
* *
3438838 ATTTTATA-TATTAT
1 ATTTTATATTTTTAA
3438852 ATTTATATATTTT
1 ATTT-TATATTTT
3438865 ATATAACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.36
15 12 0.55
16 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTATATTTTTAA
Found at i:3438854 original size:22 final size:22
Alignment explanation
Indices: 3438826--3438936 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 22
3438816 TTTATTTATT
*
3438826 TTATATTTTTAAATTTTATATA
1 TTATATTTATAAATTTTATATA
*
3438848 TTATATTTATATATTTTATATAACATAA
1 TTATATTTATA-AATTT-TAT---AT-A
*
3438876 TTATATTTA-AAATATTATATA
1 TTATATTTATAAATTTTATATA
3438897 TT-TA--TATAAATTTTAATATA
1 TTATATTTATAAATTTT-ATATA
**
3438917 TTA-ATAAAT-AATTTTATATA
1 TTATATTTATAAATTTTATATA
3438937 AATTTTAATA
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 15 0.21
21 9 0.12
22 14 0.19
23 4 0.06
24 3 0.04
25 3 0.04
26 3 0.04
27 3 0.04
28 10 0.14
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATTTATAAATTTTATATA
Found at i:3438866 original size:15 final size:15
Alignment explanation
Indices: 3438806--3438904 Score: 75
Period size: 14 Copynumber: 6.9 Consensus size: 15
3438796 AGTGATTAGA
*
3438806 TTTATATTTATTTA-
1 TTTATATTTATATAT
3438820 TTTAT-TTTATAT-T
1 TTTATATTTATATAT
*
3438833 TTTAAATTT-TATAT
1 TTTATATTTATATAT
*
3438847 ATTATATTTATATAT
1 TTTATATTTATATAT
* *
3438862 TTTATA-TAACATA-
1 TTTATATTTATATAT
* *
3438875 ATTATATTTAAAATAT
1 TTTATATTT-ATATAT
*
3438891 TATATATTTATATA
1 TTTATATTTATATA
3438905 AATTTTAATA
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
13 18 0.28
14 22 0.34
15 18 0.28
16 7 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTATATTTATATAT
Found at i:3439072 original size:22 final size:21
Alignment explanation
Indices: 3439047--3439106 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
3439037 ATGAATTATG
*
3439047 ATTTTATATGTTATATTAATAT
1 ATTTTATAT-TTATATTAAGAT
3439069 ATTTTA-ATTATTATATTTAAGAT
1 ATTTTATA-T-TTATA-TTAAGAT
*
3439092 ATTATATATTTATAT
1 ATTTTATATTTATAT
3439107 AAATTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 2 0.06
22 17 0.53
23 12 0.38
24 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
ATTTTATATTTATATTAAGAT
Found at i:3439083 original size:14 final size:15
Alignment explanation
Indices: 3439050--3439106 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
3439040 AATTATGATT
*
3439050 TTATATGTTATATTA
1 TTATATTTTATATTA
*
3439065 ATATATTTTA-ATTA
1 TTATATTTTATATTA
* *
3439079 TTATATTTAAGA-TA
1 TTATATTTTATATTA
3439093 TTATATATTTATAT
1 TTATAT-TTTATAT
3439107 AAATTAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
14 20 0.61
15 13 0.39
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TTATATTTTATATTA
Found at i:3439119 original size:19 final size:17
Alignment explanation
Indices: 3439095--3439129 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
3439085 TTAAGATATT
3439095 ATATATTTATATAAATTAA
1 ATATA-TTA-ATAAATTAA
3439114 ATATATTAATAAATTA
1 ATATATTAATAAATTA
3439130 TGTAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATTAATAAATTAA
Found at i:3439197 original size:9 final size:11
Alignment explanation
Indices: 3439175--3439205 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
3439165 ATGTATAATA
3439175 TTTATATTATT
1 TTTATATTATT
3439186 TTTA-ATTATT
1 TTTATATTATT
3439196 TTTATATTAT
1 TTTATATTAT
3439206 ATTCGTGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATATTATT
Found at i:3444142 original size:2 final size:2
Alignment explanation
Indices: 3444137--3444164 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3444127 TTCTTTTTTG
3444137 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
3444165 CAAATATTTA
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:3444365 original size:20 final size:20
Alignment explanation
Indices: 3444318--3444372 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
3444308 TTAATTATGA
3444318 ATTTTAAATATTTTATAATG
1 ATTTTAAATATTTTATAATG
3444338 ATTATTAAA-ATTTTATATTAT-
1 ATT-TTAAATATTTTATA--ATG
*
3444359 ATTTTAATTATTTT
1 ATTTTAAATATTTT
3444373 TATATATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 15 0.50
21 13 0.43
22 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTAAATATTTTATAATG
Found at i:3444389 original size:22 final size:21
Alignment explanation
Indices: 3444345--3444406 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 21
3444335 ATGATTATTA
*
3444345 AAATTTTATATTATATTTTAAT
1 AAATTTT-TATTATATTTAAAT
*
3444367 -TATTTTTA-TATA-TTAAAT
1 AAATTTTTATTATATTTAAAT
3444385 AAATTTTTAATTATATTTAAAT
1 AAATTTTT-ATTATATTTAAAT
3444407 TTATCGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 5 0.15
19 10 0.30
20 3 0.09
21 9 0.27
22 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AAATTTTTATTATATTTAAAT
Found at i:3444400 original size:40 final size:40
Alignment explanation
Indices: 3444306--3444407 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 40
3444296 TCAAAATCGC
* *
3444306 TTTTAATTATGAATTTTAAATATTTTATAATGATTATTAAAA
1 TTTTAATTAT--ATTTTAATTATTTTATAATGATTAATAAAA
*
3444348 TTTTATATTATATTTTAATTATTTT-TATAT-ATTAAATAAAT
1 TTTTA-ATTATATTTTAATTATTTTATA-ATGATT-AATAAAA
*
3444389 TTTTAATTATATTTAAATT
1 TTTTAATTATATTTTAATT
3444408 TATCGTATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
40 18 0.34
41 25 0.47
42 5 0.09
43 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (40 bp):
TTTTAATTATATTTTAATTATTTTATAATGATTAATAAAA
Found at i:3444785 original size:13 final size:12
Alignment explanation
Indices: 3444757--3444786 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3444747 TCACTTGTAC
3444757 AAAAACTTGAAG
1 AAAAACTTGAAG
3444769 AAAAACTTGAAG
1 AAAAACTTGAAG
3444781 AAAAAC
1 AAAAAC
3444787 AAAATGAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.63, C:0.10, G:0.13, T:0.13
Consensus pattern (12 bp):
AAAAACTTGAAG
Found at i:3446882 original size:2 final size:2
Alignment explanation
Indices: 3446875--3446911 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3446865 GCTGTAGACA
3446875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3446912 AACAGGTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3447427 original size:2 final size:2
Alignment explanation
Indices: 3447422--3447451 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3447412 CATTTTTTTC
3447422 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3447452 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3448550 original size:16 final size:17
Alignment explanation
Indices: 3448529--3448561 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3448519 CTTTCCATTG
3448529 AAATAAA-AATTCTTAA
1 AAATAAATAATTCTTAA
*
3448545 AAATAAATAATTTTTAA
1 AAATAAATAATTCTTAA
3448562 CTTCTTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATAAATAATTCTTAA
Found at i:3449710 original size:23 final size:24
Alignment explanation
Indices: 3449678--3449732 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
3449668 AATAATTTCG
3449678 AATATGAATATAAAAAAAATTT-AA
1 AATAT-AATATAAAAAAAATTTAAA
*
3449702 AATATAATATATAAAAAATTTAAA
1 AATATAATATAAAAAAAATTTAAA
3449726 AATATAA
1 AATATAA
3449733 CATTAAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
AATATAATATAAAAAAAATTTAAA
Found at i:3451510 original size:20 final size:20
Alignment explanation
Indices: 3451473--3451510 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3451463 TTCGAATTTG
*
3451473 AATTAAAATTTTATAATACT
1 AATTAAAATATTATAATACT
3451493 AATTAAAAATATTA-AATA
1 AATT-AAAATATTATAATA
3451511 TATTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAAATATTATAATACT
Found at i:3452859 original size:2 final size:2
Alignment explanation
Indices: 3452854--3452890 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3452844 AATTTTACTC
3452854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3452891 TTGAAGGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3454634 original size:12 final size:12
Alignment explanation
Indices: 3454580--3454640 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
3454570 AACTGTCGGA
*
3454580 GTCCCAGTAGTT
1 GTCCCAGTGGTT
* *
3454592 GTGCCGGTGGTT
1 GTCCCAGTGGTT
*
3454604 GTCCCGGTGGTT
1 GTCCCAGTGGTT
3454616 GTCCCAGTGGTT
1 GTCCCAGTGGTT
* *
3454628 GTTCCAGTTGTT
1 GTCCCAGTGGTT
3454640 G
1 G
3454641 GGGTCGTGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.07, C:0.21, G:0.36, T:0.36
Consensus pattern (12 bp):
GTCCCAGTGGTT
Found at i:3458198 original size:15 final size:15
Alignment explanation
Indices: 3458183--3458225 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
3458173 AATTAAAAAA
3458183 TATATAATTATTAAAT
1 TATA-AATTATTAAAT
*
3458199 TTTAAATTATTAAAT
1 TATAAATTATTAAAT
3458214 TATTAAA-TATTA
1 TA-TAAATTATTA
3458226 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATAAATTATTAAAT
Found at i:3458199 original size:23 final size:23
Alignment explanation
Indices: 3458173--3458221 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3458163 TTAGCATAAG
3458173 AATTAAAAAATA-TATAATTATTA
1 AATTAAAAAATATTA-AATTATTA
** *
3458196 AATTTTAAATTATTAAATTATTA
1 AATTAAAAAATATTAAATTATTA
3458219 AAT
1 AAT
3458222 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTAAAAAATATTAAATTATTA
Found at i:3458211 original size:8 final size:8
Alignment explanation
Indices: 3458188--3458225 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
3458178 AAAAATATAT
3458188 AATTATTA
1 AATTATTA
3458196 AATT-TTA
1 AATTATTA
3458203 AATTATTA
1 AATTATTA
3458211 AATTATTA
1 AATTATTA
3458219 AA-TATTA
1 AATTATTA
3458226 TTTTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AATTATTA
Found at i:3458430 original size:2 final size:2
Alignment explanation
Indices: 3458423--3458452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3458413 ATAATAAAAC
3458423 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
3458453 GTAAAGCATT
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:3458994 original size:31 final size:31
Alignment explanation
Indices: 3458959--3459020 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3458949 TTACCCAGGT
*
3458959 AAATATTGATGTCAAA-TTTAATTTATTTTAA
1 AAATATTAAT-TCAAAGTTTAATTTATTTTAA
* *
3458990 AAATATTAATTTAAAGTTTAATTTTTTTTAA
1 AAATATTAATTCAAAGTTTAATTTATTTTAA
3459021 TAGGTTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (31 bp):
AAATATTAATTCAAAGTTTAATTTATTTTAA
Found at i:3459606 original size:20 final size:20
Alignment explanation
Indices: 3459590--3459626 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
3459580 TATATTTTTG
3459590 TTGATTTTGTTTAATTTATA
1 TTGATTTTGTTTAATTTATA
*
3459610 TTTATTTTG-TTAATTTA
1 TTGATTTTGTTTAATTTA
3459627 ATAGGAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (20 bp):
TTGATTTTGTTTAATTTATA
Found at i:3473588 original size:20 final size:22
Alignment explanation
Indices: 3473573--3473614 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3473563 AAAATATTTT
3473573 AAAAAT-AATTATAATATAATA
1 AAAAATAAATTATAATATAATA
3473594 AAAAATAAAATTATAATATAA
1 AAAAAT-AAATTATAATATAA
3473615 ACGTACGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAATAAATTATAATATAATA
Found at i:3473649 original size:19 final size:19
Alignment explanation
Indices: 3473622--3473661 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3473612 TAAACGTACG
*
3473622 AATTGTTAAATCTAACAAA
1 AATTATTAAATCTAACAAA
3473641 AATTATTAAATCTAACAAA
1 AATTATTAAATCTAACAAA
3473660 AA
1 AA
3473662 GAACCCGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (19 bp):
AATTATTAAATCTAACAAA
Found at i:3473848 original size:17 final size:17
Alignment explanation
Indices: 3473815--3473849 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3473805 TTAACATAAA
**
3473815 TATATTTAATATTTTTT
1 TATATTTAATAGATTTT
3473832 TATATTTAATAGATTTT
1 TATATTTAATAGATTTT
3473849 T
1 T
3473850 TTTTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TATATTTAATAGATTTT
Found at i:3484850 original size:41 final size:42
Alignment explanation
Indices: 3484787--3484867 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 42
3484777 TATAAATGAG
*
3484787 TAAATATTGTTTTAGAATTAAAAGAAATCATAAATATTGACA
1 TAAATATTGTTTTAGAAATAAAAGAAATCATAAATATTGACA
*
3484829 TAAATATTG-TTTAGAAATAAAAGAAGTCATAAATATTGA
1 TAAATATTGTTTTAGAAATAAAAGAAATCATAAATATTGA
3484868 TATTATTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 28 0.76
42 9 0.24
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (42 bp):
TAAATATTGTTTTAGAAATAAAAGAAATCATAAATATTGACA
Found at i:3485348 original size:18 final size:19
Alignment explanation
Indices: 3485311--3485349 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3485301 TATGAATATG
**
3485311 AATATATAATAATCTTTTA
1 AATATATAATAAAATTTTA
3485330 AATATATAA-AAAATTTTA
1 AATATATAATAAAATTTTA
3485348 AA
1 AA
3485350 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATATAATAAAATTTTA
Found at i:3486307 original size:2 final size:2
Alignment explanation
Indices: 3486302--3486326 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3486292 AAAAAAGGCA
3486302 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 A
3486327 CACACACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3487849 original size:15 final size:15
Alignment explanation
Indices: 3487829--3487869 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
3487819 CAAAGTAATA
3487829 TATTAAAATTTATAT
1 TATTAAAATTTATAT
*
3487844 TATTAAAATTTTTTAT
1 TATTAAAA-TTTATAT
3487860 TATTTAAAAT
1 TA-TTAAAAT
3487870 ATTTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 9 0.39
17 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAAAATTTATAT
Found at i:3487862 original size:16 final size:16
Alignment explanation
Indices: 3487829--3487878 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 16
3487819 CAAAGTAATA
3487829 TATTAAAA-TTTATAT
1 TATTAAAATTTTATAT
*
3487844 TATTAAAATTTTTTAT
1 TATTAAAATTTTATAT
3487860 TATTTAAAATATTTATAT
1 TA-TTAAAAT-TTTATAT
3487878 T
1 T
3487879 TAATACATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 8 0.27
16 8 0.27
17 7 0.23
18 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAAAATTTTATAT
Found at i:3487878 original size:18 final size:17
Alignment explanation
Indices: 3487836--3487878 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
3487826 ATATATTAAA
3487836 ATTTATATTATTAAAAT
1 ATTTATATTATTAAAAT
*
3487853 -TTTTTATTATTTAAAAT
1 ATTTATATTA-TTAAAAT
3487870 ATTTATATT
1 ATTTATATT
3487879 TAATACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTATATTATTAAAAT
Found at i:3487888 original size:17 final size:16
Alignment explanation
Indices: 3487831--3487891 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
3487821 AAGTAATATA
3487831 TTAAAAT-TTATATTA-
1 TTAAAATATT-TATTAT
*
3487846 TTAAAATTTTTTATTAT
1 TTAAAA-TATTTATTAT
3487863 TTAAAATATTTA-TAT
1 TTAAAATATTTATTAT
3487878 TTAATACATATTTA
1 TTAA-A-ATATTTA
3487892 AATATAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 13 0.32
16 12 0.30
17 15 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAAATATTTATTAT
Found at i:3488000 original size:30 final size:36
Alignment explanation
Indices: 3487924--3487995 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
3487914 TTTTTAAATG
*
3487924 TATTAAAATTTTTTTAAAATTAAATATATATATTAA
1 TATTAAAATTTATTTAAAATTAAATATATATATTAA
* *
3487960 TATTACAATTTATTT-AAATTAAACTATATAAATTAA
1 TATTAAAATTTATTTAAAATTAAA-TATATATATTAA
3487996 AATTTCACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 8 0.25
36 24 0.75
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (36 bp):
TATTAAAATTTATTTAAAATTAAATATATATATTAA
Found at i:3488354 original size:5 final size:5
Alignment explanation
Indices: 3488340--3488371 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3488330 AAAATATGAC
3488340 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3488372 TTCAGTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:3496916 original size:23 final size:23
Alignment explanation
Indices: 3496873--3496917 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3496863 AAAAATATCG
*
3496873 ATATTAAAATTTAAATTTTAAAT
1 ATATTAAAATTTAAATATTAAAT
*
3496896 ATATT-AAATATTATATATTAAA
1 ATATTAAAAT-TTAAATATTAAA
3496918 AATAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTAAAATTTAAATATTAAAT
Found at i:3504349 original size:17 final size:18
Alignment explanation
Indices: 3504327--3504360 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3504317 ATGATTGTTA
3504327 TTTTATAATT-ATATTTT
1 TTTTATAATTAATATTTT
*
3504344 TTTTATTATTAATATTT
1 TTTTATAATTAATATTT
3504361 ATAATTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATAATTAATATTTT
Found at i:3504997 original size:2 final size:2
Alignment explanation
Indices: 3504990--3505028 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3504980 AAAAGGCTAT
3504990 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3505029 ATTTATCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3511186 original size:2 final size:2
Alignment explanation
Indices: 3511179--3511214 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3511169 AATACTCCGC
3511179 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3511215 GTCCACCGCA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3512450 original size:16 final size:17
Alignment explanation
Indices: 3512429--3512465 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3512419 TATTTATATT
*
3512429 TAAATA-TTTATAAATA
1 TAAATATTTTATAAAAA
3512445 TAAATATTTTATAAAAA
1 TAAATATTTTATAAAAA
3512462 TAAA
1 TAAA
3512466 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATATTTTATAAAAA
Found at i:3512472 original size:17 final size:17
Alignment explanation
Indices: 3512434--3512472 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3512424 ATATTTAAAT
* *
3512434 ATTTATAAATATAAATA
1 ATTTATAAAAATAAAAA
*
3512451 TTTTATAAAAATAAAAA
1 ATTTATAAAAATAAAAA
3512468 ATTTA
1 ATTTA
3512473 AATAATATGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTATAAAAATAAAAA
Found at i:3513206 original size:6 final size:6
Alignment explanation
Indices: 3513189--3513218 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3513179 AAACTGGCTT
3513189 TTTTGTC TTTTGC TTTTGC TTTTGC TTTTG
1 TTTTG-C TTTTGC TTTTGC TTTTGC TTTTG
3513219 TAGATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.00, C:0.13, G:0.17, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:3518485 original size:9 final size:9
Alignment explanation
Indices: 3518471--3518498 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3518461 TGTTTTTCAC
3518471 TTTTATTTA
1 TTTTATTTA
3518480 TTTTATTTA
1 TTTTATTTA
3518489 TTTTATTTA
1 TTTTATTTA
3518498 T
1 T
3518499 GTCTAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTATTTA
Found at i:3518631 original size:25 final size:26
Alignment explanation
Indices: 3518589--3518649 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
3518579 ACATATTTAA
* **
3518589 AAAAT-TATATAAATATATTTTTATT
1 AAAATATAAATAAATATATAATTATT
3518614 AAAATATAAATAAA-ATATAATTATT
1 AAAATATAAATAAATATATAATTATT
*
3518639 -AAATATGAATA
1 AAAATATAAATA
3518650 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 10 0.32
25 14 0.45
26 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAATATAAATAAATATATAATTATT
Found at i:3523819 original size:3 final size:3
Alignment explanation
Indices: 3523811--3523848 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3523801 AGAATCTACT
3523811 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3523849 TTATTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3523853 original size:3 final size:3
Alignment explanation
Indices: 3523847--3523871 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3523837 ATAATAATAA
3523847 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3523872 GTATCCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3524065 original size:2 final size:2
Alignment explanation
Indices: 3524058--3524108 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
3524048 AGTAGGCATA
*
3524058 AT AT AT AT AT AT AT TT 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
3524100 AT AT AT AT A
1 AT AT AT AT A
3524109 ATAGACTTTT
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:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3525193 original size:2 final size:2
Alignment explanation
Indices: 3525186--3525222 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3525176 GGTTGTTTCG
3525186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3525223 ATCAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3526137 original size:2 final size:2
Alignment explanation
Indices: 3526130--3526156 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3526120 TCTATTAATC
3526130 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3526157 TCCTGGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3527688 original size:2 final size:2
Alignment explanation
Indices: 3527642--3527676 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3527632 CATAATATTC
*
3527642 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3527677 TCTCTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3529229 original size:37 final size:35
Alignment explanation
Indices: 3529188--3529262 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
3529178 AAATACTATA
* *
3529188 TATTATATATTATATGTCATTCAAATATTAAAAAAAT
1 TATTATAAAATATATGTCA-T-AAATATTAAAAAAAT
* * *
3529225 TATTATAAAATATTTTTTATAAATATTAAAAAAAT
1 TATTATAAAATATATGTCATAAATATTAAAAAAAT
3529260 TAT
1 TAT
3529263 AAAATTATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 18 0.55
36 1 0.03
37 14 0.42
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (35 bp):
TATTATAAAATATATGTCATAAATATTAAAAAAAT
Found at i:3531100 original size:2 final size:2
Alignment explanation
Indices: 3531093--3531124 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3531083 AATCAGACCA
3531093 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
3531125 CCCCAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3542052 original size:20 final size:22
Alignment explanation
Indices: 3542008--3542056 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3541998 TAATTTTATT
3542008 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
3542030 TAAATATTAA-TA-AAAAATA-A
1 TAAAT-TTAATTATAAAAATATA
3542050 T-AATTTA
1 TAAATTTA
3542057 TTAATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 2 0.08
21 7 0.27
22 7 0.27
23 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:3550165 original size:26 final size:27
Alignment explanation
Indices: 3550126--3550199 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
3550116 TATAAATTTA
*
3550126 TTTATATTTAATTTAAA-AATATATAT
1 TTTAAATTTAATTTAAATAATATATAT
* *
3550152 TTTAAATTTTATTTAAATTTATATATAT
1 TTTAAATTTAATTTAAA-TAATATATAT
*
3550180 TTATAAATGATAATTTAAAT
1 TT-TAAAT-TTAATTTAAAT
3550200 TTATTTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 15 0.38
28 10 0.26
29 6 0.15
30 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
TTTAAATTTAATTTAAATAATATATAT
Found at i:3550196 original size:30 final size:28
Alignment explanation
Indices: 3550144--3550210 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 28
3550134 TAATTTAAAA
* *
3550144 ATATATATTTTAAATTTTATTTAAATTT
1 ATATATATTTTAAATATAATTTAAATTT
3550172 ATATATATTTATAAATGATAATTTAAATTT
1 ATATATATTT-TAAAT-ATAATTTAAATTT
*
3550202 ATTTATATT
1 ATATATATT
3550211 ATATTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 10 0.29
29 5 0.15
30 19 0.56
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
ATATATATTTTAAATATAATTTAAATTT
Found at i:3550428 original size:18 final size:17
Alignment explanation
Indices: 3550406--3550450 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
3550396 AATTTGATTC
3550406 ATTTTTAAA-TATATTT
1 ATTTTTAAATTATATTT
3550422 AATTTTTAAATTATATTT
1 -ATTTTTAAATTATATTT
*
3550440 ATTTTAAAATT
1 ATTTTTAAATT
3550451 TAATATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTAAATTATATTT
Found at i:3550450 original size:17 final size:17
Alignment explanation
Indices: 3550393--3550450 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
3550383 ACTTTAGAGA
*
3550393 TAAAATT-TGATTCATTT
1 TAAAATTAT-ATTTATTT
*
3550410 TTAAA-TATATTTAATTT
1 TAAAATTATATTT-ATTT
*
3550427 TTAAATTATATTTATTT
1 TAAAATTATATTTATTT
3550444 TAAAATT
1 TAAAATT
3550451 TAATATGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 4 0.11
17 24 0.69
18 7 0.20
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TAAAATTATATTTATTT
Found at i:3550793 original size:3 final size:3
Alignment explanation
Indices: 3550785--3550837 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
3550775 GATGGGCTTG
3550785 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3550833 ATT AT
1 ATT AT
3550838 ATATGCTTGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3553546 original size:3 final size:3
Alignment explanation
Indices: 3553538--3553571 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3553528 TGATAGCAAG
3553538 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3553572 CAATTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3557669 original size:21 final size:21
Alignment explanation
Indices: 3557621--3557669 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3557611 ATTATAGTAT
*
3557621 AATAATGTATATAAATATAAA
1 AATAATTTATATAAATATAAA
*
3557642 AATAATTTATATAATTGA-AAA
1 AATAATTTATATAAAT-ATAAA
3557663 AATAATT
1 AATAATT
3557670 GAGTTAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AATAATTTATATAAATATAAA
Found at i:3563499 original size:37 final size:37
Alignment explanation
Indices: 3563457--3563537 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
3563447 TATTTTTCTA
* *
3563457 TGGATTGGCGCTGCCACCCAAATTCTAACAATCATAG
1 TGGATTGGCACTGCCACCCAAATACTAACAATCATAG
* *
3563494 TGGATTGGCATTGCCACCCAAATACTGACAATCATAG
1 TGGATTGGCACTGCCACCCAAATACTAACAATCATAG
3563531 TGGATTG
1 TGGATTG
3563538 ACCAAGCCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (37 bp):
TGGATTGGCACTGCCACCCAAATACTAACAATCATAG
Found at i:3563547 original size:37 final size:37
Alignment explanation
Indices: 3563469--3563554 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
3563459 GATTGGCGCT
* * *
3563469 GCCACCCAAATTCTAACAATCATAGTGGATTGGCATT
1 GCCACCCAAATACTAACAATCATAGTGGATTGCCATA
*
3563506 GCCACCCAAATACTGACAATCATAGTGGATTGACCA-A
1 GCCACCCAAATACTAACAATCATAGTGGATTG-CCATA
*
3563543 GCCACTCAAATA
1 GCCACCCAAATA
3563555 TTACTTGTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 41 0.95
38 2 0.05
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (37 bp):
GCCACCCAAATACTAACAATCATAGTGGATTGCCATA
Found at i:3569331 original size:21 final size:21
Alignment explanation
Indices: 3569283--3569331 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3569273 ATTATAGTAT
*
3569283 AATAATGTATATAAATATAAA
1 AATAATTTATATAAATATAAA
*
3569304 AATAATTTATATAATTGA-AAA
1 AATAATTTATATAAAT-ATAAA
3569325 AATAATT
1 AATAATT
3569332 GAGTTAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AATAATTTATATAAATATAAA
Found at i:3575161 original size:37 final size:37
Alignment explanation
Indices: 3575119--3575199 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
3575109 TATTTTTCTA
* *
3575119 TGGATTGGCGCTGCCACCCAAATTCTAACAATCATAG
1 TGGATTGGCACTGCCACCCAAATACTAACAATCATAG
* *
3575156 TGGATTGGCATTGCCACCCAAATACTGACAATCATAG
1 TGGATTGGCACTGCCACCCAAATACTAACAATCATAG
3575193 TGGATTG
1 TGGATTG
3575200 ACCAAGCCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (37 bp):
TGGATTGGCACTGCCACCCAAATACTAACAATCATAG
Found at i:3575209 original size:37 final size:37
Alignment explanation
Indices: 3575131--3575216 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
3575121 GATTGGCGCT
* * *
3575131 GCCACCCAAATTCTAACAATCATAGTGGATTGGCATT
1 GCCACCCAAATACTAACAATCATAGTGGATTGCCATA
*
3575168 GCCACCCAAATACTGACAATCATAGTGGATTGACCA-A
1 GCCACCCAAATACTAACAATCATAGTGGATTG-CCATA
*
3575205 GCCACTCAAATA
1 GCCACCCAAATA
3575217 TTACTTGTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 41 0.95
38 2 0.05
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (37 bp):
GCCACCCAAATACTAACAATCATAGTGGATTGCCATA
Found at i:3578740 original size:21 final size:22
Alignment explanation
Indices: 3578716--3578763 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3578706 GTTATAGTAT
3578716 AATAATG-TATATAAAT-ATAAA
1 AATAATGTTATATAAATGA-AAA
*
3578737 AAT-ATGTTATATAATTGAAAA
1 AATAATGTTATATAAATGAAAA
3578758 AATAAT
1 AATAAT
3578764 TGAGTTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 17 0.74
22 3 0.13
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (22 bp):
AATAATGTTATATAAATGAAAA
Found at i:3578921 original size:18 final size:18
Alignment explanation
Indices: 3578880--3578923 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3578870 TCAATATTTA
*
3578880 AAATATTAAATAAATTTTT
1 AAAT-TTAAATAAATTATT
3578899 AAATTTAAATAAATTAATT
1 AAATTTAAATAAATT-ATT
3578918 -AATTTA
1 AAATTTA
3578924 TAAATTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTTAAATAAATTATT
Found at i:3578921 original size:26 final size:26
Alignment explanation
Indices: 3578875--3578929 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3578865 TTTTCTCAAT
* *
3578875 ATTTAAAATATTAAATAAATTTTTAA
1 ATTTAAAAAATTAAATAAATTTATAA
*
3578901 ATTTAAATAAATT-AATTAATTTATAA
1 ATTTAAA-AAATTAAATAAATTTATAA
3578927 ATT
1 ATT
3578930 CTTTTAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTAAAAAATTAAATAAATTTATAA
Found at i:3581501 original size:3 final size:3
Alignment explanation
Indices: 3581493--3581535 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3581483 TGATAGCAAG
3581493 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3581536 CAATTCCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3582998 original size:21 final size:21
Alignment explanation
Indices: 3582952--3583014 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
3582942 TGTGGAGGAT
* *
3582952 CATAAAATTT-TTTTTGTTGGA
1 CATAAAATTTGATTTTGTT-TA
*
3582973 AATAAATATTTGATTTT-TTTA
1 CATAAA-ATTTGATTTTGTTTA
3582994 CATAAAATTTGATTTTGTTTA
1 CATAAAATTTGATTTTGTTTA
3583015 ACATTATGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 10 0.29
21 15 0.43
22 6 0.17
23 4 0.11
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (21 bp):
CATAAAATTTGATTTTGTTTA
Found at i:3583005 original size:20 final size:22
Alignment explanation
Indices: 3582974--3583014 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
3582964 TTTGTTGGAA
3582974 ATAAATATTTGATTTT-TTTAC
1 ATAAATATTTGATTTTGTTTAC
3582995 ATAAA-ATTTGATTTTGTTTA
1 ATAAATATTTGATTTTGTTTA
3583015 ACATTATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (22 bp):
ATAAATATTTGATTTTGTTTAC
Found at i:3585634 original size:21 final size:21
Alignment explanation
Indices: 3585586--3585634 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3585576 ATTATAGTAT
*
3585586 AATAATGTATATAAATATAAA
1 AATAATTTATATAAATATAAA
*
3585607 AATAATTTATATAATTGA-AAA
1 AATAATTTATATAAAT-ATAAA
3585628 AATAATT
1 AATAATT
3585635 GAGTTAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AATAATTTATATAAATATAAA
Found at i:3591317 original size:37 final size:37
Alignment explanation
Indices: 3591273--3591356 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 37
3591263 TTATTTTTCC
* *
3591273 GTGGATTGACGCTACCACCCAAATTCTAACAATCATA
1 GTGGATTGACACTACCACCCAAATACTAACAATCATA
* * * *
3591310 GTGGATTGGCACTGCCACTCAAATACTGACAATCATA
1 GTGGATTGACACTACCACCCAAATACTAACAATCATA
3591347 GTGGATTGAC
1 GTGGATTGAC
3591357 TAAGCCACTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (37 bp):
GTGGATTGACACTACCACCCAAATACTAACAATCATA
Found at i:3591364 original size:37 final size:37
Alignment explanation
Indices: 3591273--3591371 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 37
3591263 TTATTTTTCC
* * * * *
3591273 GTGGATTGACGCTACCACCCAAATTCTAACAATCATA
1 GTGGATTGGCACTGCCACTCAAATACTAACAATCATA
*
3591310 GTGGATTGGCACTGCCACTCAAATACTGACAATCATA
1 GTGGATTGGCACTGCCACTCAAATACTAACAATCATA
3591347 GTGGATT-G-ACTAAGCCACTCAAATA
1 GTGGATTGGCACT--GCCACTCAAATA
3591372 TTACTTGTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
35 3 0.06
36 1 0.02
37 50 0.93
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (37 bp):
GTGGATTGGCACTGCCACTCAAATACTAACAATCATA
Found at i:3592297 original size:21 final size:23
Alignment explanation
Indices: 3592264--3592309 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3592254 TTTGTTGAAA
*
3592264 ATAAAATTTTGATTTT-TTTTAC
1 ATAAAATTTTGATTTTGTTTGAC
3592286 ATAAAA-TTTGATTTTGTTTGAC
1 ATAAAATTTTGATTTTGTTTGAC
3592308 AT
1 AT
3592310 TATGTCGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (23 bp):
ATAAAATTTTGATTTTGTTTGAC
Found at i:3594925 original size:21 final size:21
Alignment explanation
Indices: 3594877--3594925 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3594867 ATTATAGTAT
*
3594877 AATAATGTATATAAATATAAA
1 AATAATTTATATAAATATAAA
*
3594898 AATAATTTATATAATTGA-AAA
1 AATAATTTATATAAAT-ATAAA
3594919 AATAATT
1 AATAATT
3594926 GAGTTAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AATAATTTATATAAATATAAA
Found at i:3595121 original size:25 final size:25
Alignment explanation
Indices: 3595085--3595135 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
3595075 TAATTAATCT
* * *
3595085 ATAAATTTTTCT-AATCTTAACAAA
1 ATAAATTCTTCTCAAACTTAAAAAA
3595109 ATAAGATTCTTCTCAAACTTAAAAAA
1 ATAA-ATTCTTCTCAAACTTAAAAAA
3595135 A
1 A
3595136 AAAAAGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 11 0.50
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAAATTCTTCTCAAACTTAAAAAA
Found at i:3600607 original size:37 final size:37
Alignment explanation
Indices: 3600563--3600646 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 37
3600553 TTATTTTTCC
* *
3600563 GTGGATTGACGCTACCACCCAAATTCTAACAATCATA
1 GTGGATTGACACTACCACCCAAATACTAACAATCATA
* * * *
3600600 GTGGATTGGCACTGCCACTCAAATACTGACAATCATA
1 GTGGATTGACACTACCACCCAAATACTAACAATCATA
3600637 GTGGATTGAC
1 GTGGATTGAC
3600647 TAAGCCACTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (37 bp):
GTGGATTGACACTACCACCCAAATACTAACAATCATA
Done.