Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 2 of 15
Found at i:316948 original size:22 final size:21
Alignment explanation
Indices: 316855--316949 Score: 54
Period size: 22 Copynumber: 4.4 Consensus size: 21
316845 TAGTAGAAGA
* *
316855 TTAATAACATAATAATAA-ATG
1 TTAATAATATAGTAATAATA-G
*
316876 ATTAATAATAT-GTAAAAAATAG
1 -TTAATAATATAGT-AATAATAG
* *
316898 TTGATAATATATTAATAA-A-
1 TTAATAATATAGTAATAATAG
316917 TTAATGATAATATAGTACATAATAG
1 TT-A--ATAATATAGTA-ATAATAG
316942 TTAATAAT
1 TTAATAAT
316950 GTATTAGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
19 2 0.04
20 1 0.02
21 14 0.25
22 30 0.54
23 5 0.09
24 2 0.04
25 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
TTAATAATATAGTAATAATAG
Found at i:317512 original size:14 final size:15
Alignment explanation
Indices: 317476--317512 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
317466 AACAAAGTCA
317476 ATAA-TTTAAAAACT
1 ATAATTTTAAAAACT
317490 ATAATTTTTAAAAA-T
1 ATAA-TTTTAAAAACT
317505 ATAATTTT
1 ATAATTTT
317513 TTTTTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.38
15 5 0.24
16 8 0.38
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATTTTAAAAACT
Found at i:317514 original size:16 final size:16
Alignment explanation
Indices: 317480--317513 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
317470 AAGTCAATAA
317480 TTTAAAAACTATAATT
1 TTTAAAAACTATAATT
317496 TTTAAAAA-TATAATT
1 TTTAAAAACTATAATT
317511 TTT
1 TTT
317514 TTTTTAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAAAAACTATAATT
Found at i:322476 original size:3 final size:3
Alignment explanation
Indices: 322468--322493 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
322458 CTAACAGGAA
322468 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
322494 TCTAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:330754 original size:16 final size:17
Alignment explanation
Indices: 330690--330755 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 17
330680 CTTTCTTTTT
* *
330690 TTTTAATTTTTA-AATA
1 TTTTAATTATTACTATA
*
330706 TATTAATATATTACTAT-
1 TTTTAAT-TATTACTATA
* *
330723 TTTTTATTA-TATTATA
1 TTTTAATTATTACTATA
330739 TTTTAATTATTA-TATA
1 TTTTAATTATTACTATA
330755 T
1 T
330756 AATATTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
15 5 0.13
16 21 0.54
17 11 0.28
18 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTATTACTATA
Found at i:330795 original size:21 final size:21
Alignment explanation
Indices: 330728--330795 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
330718 ACTATTTTTT
* *
330728 ATTATATTATATTTTAAT-TA
1 ATTATATAATATTTAAATATA
*
330748 TTATATATAATATTTAAATTTTATA
1 AT-TATATAATATTTAAA---TATA
*
330773 ATTATATCATATTTAAATATA
1 ATTATATAATATTTAAATATA
330794 AT
1 AT
330796 ATAACCCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.03
21 19 0.50
24 15 0.39
25 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATATAATATTTAAATATA
Found at i:330798 original size:42 final size:44
Alignment explanation
Indices: 330697--330799 Score: 108
Period size: 45 Copynumber: 2.4 Consensus size: 44
330687 TTTTTTTAAT
* * *
330697 TTTTAAATAT-AT-TAATATATTACTATTTTTTATTATATTATA
1 TTTTAAATATAATATAATATATTACAATTTTTAATTATATCATA
*
330739 TTTTAATTATTATATATAATAT-TTA-AATTTTATAATTATATCATA
1 TTTTAAATA-TA-ATATAATATATTACAATTTT-TAATTATATCATA
330784 -TTTAAATATAATATAA
1 TTTTAAATATAATATAA
330800 CCCAAATCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
42 14 0.27
43 3 0.06
44 12 0.24
45 16 0.31
46 6 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (44 bp):
TTTTAAATATAATATAATATATTACAATTTTTAATTATATCATA
Found at i:341457 original size:20 final size:20
Alignment explanation
Indices: 341434--341496 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
341424 TATGTAAACA
341434 TAAACATAAATAAAATTTAT
1 TAAACATAAATAAAATTTAT
341454 TAAACAT--ATCAAAA-TT-T
1 TAAACATAAAT-AAAATTTAT
*
341471 TAAATATAAATATAATATTTAT
1 TAAACATAAATA-AA-ATTTAT
341493 TAAA
1 TAAA
341497 TATATTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
17 7 0.20
18 5 0.14
19 8 0.23
20 8 0.23
21 2 0.06
22 5 0.14
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAACATAAATAAAATTTAT
Found at i:341498 original size:16 final size:16
Alignment explanation
Indices: 341477--341507 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
341467 ATTTTAAATA
341477 TAAATATAATATTTAT
1 TAAATATAATATTTAT
*
341493 TAAATATATTATTTA
1 TAAATATAATATTTA
341508 ATAATATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATATAATATTTAT
Found at i:342572 original size:39 final size:36
Alignment explanation
Indices: 342534--342610 Score: 86
Period size: 39 Copynumber: 2.1 Consensus size: 36
342524 GTGAGTTTAT
*
342534 ATTTAATATATTAATATATTAATAATATATATTATTTAT
1 ATTTAATATATTAATA-AATAA-AATA-ATATTATTTAT
*
342573 -TAATAATATATTAATAAATAAAATAATATTATTT-T
1 AT-TTAATATATTAATAAATAAAATAATATTATTTAT
342608 ATT
1 ATT
342611 AAAAAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
35 1 0.03
36 10 0.30
37 4 0.12
38 5 0.15
39 13 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
ATTTAATATATTAATAAATAAAATAATATTATTTAT
Found at i:342575 original size:20 final size:21
Alignment explanation
Indices: 342539--342583 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
342529 TTTATATTTA
342539 ATATATTAATATATTAATAAT
1 ATATATTAATATATTAATAAT
*
342560 ATATATT-ATTTATTAATAAT
1 ATATATTAATATATTAATAAT
342580 ATAT
1 ATAT
342584 TAATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATTAATATATTAATAAT
Found at i:342661 original size:17 final size:18
Alignment explanation
Indices: 342552--342670 Score: 57
Period size: 18 Copynumber: 6.4 Consensus size: 18
342542 TATTAATATA
*
342552 TTAATAATA-TATATTAT
1 TTAATAAAATTATATTAT
* *
342569 TTATTAATAA-TATATTAA
1 TTAATAA-AATTATATTAT
* *
342587 TAAATAAAATAATATTATT
1 TTAATAAAATTATATTA-T
* *
342606 TTATTAAAAAATTTAAATATAAT
1 TTA--ATAAAA-TT--ATATTAT
* *
342629 TATAA-ATAATTTTATT-T
1 T-TAATAAAATTATATTAT
342646 TTAATAAAATTATATTAT
1 TTAATAAAATTATATTAT
342664 TTAATAA
1 TTAATAA
342671 TTAATAATAT
Statistics
Matches: 75, Mismatches: 16, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
16 3 0.04
17 19 0.25
18 30 0.40
19 2 0.03
20 2 0.03
21 8 0.11
22 2 0.03
23 2 0.03
24 7 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATAAAATTATATTAT
Found at i:342677 original size:40 final size:40
Alignment explanation
Indices: 342544--342678 Score: 93
Period size: 40 Copynumber: 3.4 Consensus size: 40
342534 ATTTAATATA
* * *
342544 TTAATATATTAATAATATATATTATTTATTAATAA-TATATTAA
1 TTAATA-ATTAATAAT-TTTATT-TTTAATAA-AATTATATTAT
* * *
342587 TAAATAA--AATAATATTATTTTATTAA-AAAATT-TA-AAT
1 TTAATAATTAATAATTTTA-TTT-TTAATAAAATTATATTAT
* * *
342624 ATAATTATAAATAATTTTATTTTTAATAAAATTATATTAT
1 TTAATAATTAATAATTTTATTTTTAATAAAATTATATTAT
342664 TTAATAATTAATAAT
1 TTAATAATTAATAAT
342679 ATATAAATTT
Statistics
Matches: 70, Mismatches: 14, Indels: 19
0.68 0.14 0.18
Matches are distributed among these distances:
37 9 0.13
38 13 0.19
39 17 0.24
40 25 0.36
42 1 0.01
43 5 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (40 bp):
TTAATAATTAATAATTTTATTTTTAATAAAATTATATTAT
Found at i:342691 original size:59 final size:60
Alignment explanation
Indices: 342544--342691 Score: 135
Period size: 59 Copynumber: 2.5 Consensus size: 60
342534 ATTTAATATA
* *
342544 TTAATATATTAATAATATATATTATTTATTAATAATATATTAATAAATAAAATAATATTATT
1 TTAATA-ATTAATAATATATA-AATTTATAAATAATATATTAATAAATAAAATAATATTATT
* ** * * * *
342606 TTATTAAAAAATTTAA-ATAT-AA-TTATAAATAATTTTATT-TTTAATAAAATTATATTA-T
1 TTAATAATTAA--TAATATATAAATTTATAAATAA-TATATTAATAAATAAAATAATATTATT
342664 TTAATAATTAATAATATATAAATTTATA
1 TTAATAATTAATAATATATAAATTTATA
342692 TTTTATTAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
56 3 0.04
57 4 0.06
58 11 0.16
59 29 0.43
60 6 0.09
61 3 0.04
62 9 0.13
63 3 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (60 bp):
TTAATAATTAATAATATATAAATTTATAAATAATATATTAATAAATAAAATAATATTATT
Found at i:345344 original size:22 final size:22
Alignment explanation
Indices: 345296--345344 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
345286 TTCACGTTCC
*
345296 ATATTTACATTTTTATTATATT
1 ATATTTACATTTTTATTATACT
* *
345318 TTATTTTCATTATTT-TTATACT
1 ATATTTACATT-TTTATTATACT
345340 ATATT
1 ATATT
345345 CATATTATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (22 bp):
ATATTTACATTTTTATTATACT
Found at i:347241 original size:2 final size:2
Alignment explanation
Indices: 347234--347261 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
347224 GGCATTGTAA
347234 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
347262 TGCGCATGAT
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:348260 original size:14 final size:14
Alignment explanation
Indices: 348241--348271 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
348231 TGGAGATAGT
*
348241 AGAAAGCGCGAGAG
1 AGAAAGAGCGAGAG
348255 AGAAAGAGCGAGAG
1 AGAAAGAGCGAGAG
348269 AGA
1 AGA
348272 TGGGGAGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.42, T:0.00
Consensus pattern (14 bp):
AGAAAGAGCGAGAG
Found at i:354935 original size:22 final size:22
Alignment explanation
Indices: 354905--354956 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
354895 ATATCATTTA
*
354905 AATT-TAATT-TTTTATGATTAT
1 AATTATAATTATTATAT-ATTAT
*
354926 AATTATAATTATTATATTTTAT
1 AATTATAATTATTATATATTAT
354948 AATTA-AATT
1 AATTATAATT
354957 GTGTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.30
22 14 0.52
23 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTATAATTATTATATATTAT
Found at i:356152 original size:15 final size:14
Alignment explanation
Indices: 356132--356170 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
356122 TGATTCTGGG
356132 TTTTCCTTCTTCTTT
1 TTTTCCTTCTT-TTT
*
356147 TTTTCCTTCATTTT
1 TTTTCCTTCTTTTT
*
356161 TTTTCATTCT
1 TTTTCCTTCT
356171 GATTTTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCCTTCTTTTT
Found at i:356161 original size:14 final size:15
Alignment explanation
Indices: 356132--356165 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
356122 TGATTCTGGG
*
356132 TTTTCCTTCTTCTTT
1 TTTTCCTTCATCTTT
356147 TTTTCCTTCAT-TTT
1 TTTTCCTTCATCTTT
356161 TTTTC
1 TTTTC
356166 ATTCTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCCTTCATCTTT
Found at i:357863 original size:1 final size:1
Alignment explanation
Indices: 357857--357882 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
357847 GAACCCTTAA
357857 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
357883 AAAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:360046 original size:25 final size:25
Alignment explanation
Indices: 360012--360062 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
360002 AAGAAAAGAG
360012 TGATTTAATTTTATGGATGAATTGT
1 TGATTTAATTTTATGGATGAATTGT
360037 TGATTTAATTTTATGGATGAATTGT
1 TGATTTAATTTTATGGATGAATTGT
360062 T
1 T
360063 CTTAATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (25 bp):
TGATTTAATTTTATGGATGAATTGT
Found at i:360276 original size:2 final size:2
Alignment explanation
Indices: 360269--360300 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
360259 GTCATTTATG
360269 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
360301 GAAGGAGAGA
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:365078 original size:16 final size:16
Alignment explanation
Indices: 365047--365089 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
365037 TTTAATATTT
*
365047 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATT-A
365064 ATAAAA-TTATAATTA
1 ATAAAATTTATAATTA
*
365079 ATAAATTTTAT
1 ATAAAATTTAT
365090 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAAATTTATAATTA
Found at i:365443 original size:11 final size:12
Alignment explanation
Indices: 365410--365458 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
365400 TATATAAAAA
* *
365410 ATAAAATATGAT
1 ATAAAAAATAAT
365422 ATAAAAAATAAT
1 ATAAAAAATAAT
*
365434 -TAAAACATAAT
1 ATAAAAAATAAT
*
365445 ATAAAAATTAAT
1 ATAAAAAATAAT
365457 AT
1 AT
365459 GATATGAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:365446 original size:23 final size:23
Alignment explanation
Indices: 365398--365456 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
365388 TACTACTTTA
* *
365398 AATATATAAAA-AA-TAAAATAT
1 AATATAAAAAATAATTAAAACAT
*
365419 GATATAAAAAATAATTAAAACAT
1 AATATAAAAAATAATTAAAACAT
*
365442 AATATAAAAATTAAT
1 AATATAAAAAATAAT
365457 ATGATATGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 9 0.29
22 2 0.06
23 20 0.65
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AATATAAAAAATAATTAAAACAT
Found at i:365757 original size:20 final size:20
Alignment explanation
Indices: 365734--365778 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
365724 AATTATTAAT
*
365734 ATATAAAAATTTATATAAAA
1 ATATAAAAATTTAAATAAAA
* *
365754 ATATAATATTTTAAATAAAA
1 ATATAAAAATTTAAATAAAA
365774 A-ATAA
1 ATATAA
365779 TATAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAAAAATTTAAATAAAA
Found at i:365773 original size:19 final size:20
Alignment explanation
Indices: 365746--365803 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
365736 ATAAAAATTT
365746 ATATAAAAATATAATATTTTA
1 ATAT-AAAATATAATATTTTA
* *
365767 A-ATAAAAAATAATA--TAA
1 ATATAAAATATAATATTTTA
365784 ATATAAATATATAATATTTT
1 ATATAAA-ATATAATATTTT
365804 TTTTCTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 17 0.59
20 2 0.07
21 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAAATATAATATTTTA
Found at i:365799 original size:22 final size:24
Alignment explanation
Indices: 365745--365799 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 24
365735 TATAAAAATT
* *
365745 TATATAAAAATATAATATTTTAAA
1 TATATAATAATATAATATTATAAA
* *
365769 TAAAAAATAATATAA-A-TATAAA
1 TATATAATAATATAATATTATAAA
365791 TATATAATA
1 TATATAATA
365800 TTTTTTTTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 12 0.48
23 1 0.04
24 12 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TATATAATAATATAATATTATAAA
Found at i:365868 original size:14 final size:14
Alignment explanation
Indices: 365803--365861 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
365793 TATAATATTT
*
365803 TTTTTCTTTCTTCC
1 TTTTTCTTTCTTTC
*
365817 TTTTTCTTTTTTTC
1 TTTTTCTTTCTTTC
*
365831 TCTTTCATTT-TTTC
1 TTTTTC-TTTCTTTC
365845 ATTTTT-TTTCTTTC
1 -TTTTTCTTTCTTTC
365859 TTT
1 TTT
365862 CTTTTTCGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 6 0.16
14 25 0.66
15 7 0.18
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTCTTTC
Found at i:366045 original size:38 final size:35
Alignment explanation
Indices: 365969--366053 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 35
365959 TTAATATTTT
*
365969 AATTATTTATATTTTAAAATATTAATAAATAAAAA
1 AATTATTAATATTTTAAAATATTAATAAATAAAAA
* *
366004 AATTATTAATAATGTTTAAAA-ATTATTAAATATTAATA
1 AATTATTAAT-AT-TTTAAAATATTAATAAATA--AAAA
*
366042 AATTATTGATAT
1 AATTATTAATAT
366054 ATCTCTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
35 9 0.21
36 12 0.29
37 9 0.21
38 12 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (35 bp):
AATTATTAATATTTTAAAATATTAATAAATAAAAA
Found at i:369489 original size:10 final size:10
Alignment explanation
Indices: 369474--369504 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
369464 TATTATCATA
369474 TTTAATTTTT
1 TTTAATTTTT
369484 TTTAA-TTTT
1 TTTAATTTTT
369493 TTTAATTTTT
1 TTTAATTTTT
369503 TT
1 TT
369505 ATATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTAATTTTT
Found at i:369501 original size:18 final size:19
Alignment explanation
Indices: 369459--369534 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 19
369449 TGAGTTTATG
*
369459 TTTTTTATTATCATATTTAATT
1 TTTTTTAATAT-AT-TTTAA-T
*
369481 TTTTTTAAT-TTTTTTAAT
1 TTTTTTAATATATTTTAAT
*
369499 TTTTTT-ATATATTTAAAT
1 TTTTTTAATATATTTTAAT
369517 TTTTTTAAATTATATTTT
1 TTTTTT-AA-TATATTTT
369535 TATATTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
17 2 0.04
18 20 0.44
19 5 0.11
20 2 0.04
21 8 0.18
22 8 0.18
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTAATATATTTTAAT
Found at i:369520 original size:19 final size:18
Alignment explanation
Indices: 369459--369523 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
369449 TGAGTTTATG
369459 TTTTTTATTATCATATTTAA
1 TTTTTT-TTAT-ATATTTAA
* *
369479 TTTTTTTTAATTTTTTTAA
1 TTTTTTTT-ATATATTTAA
369498 -TTTTTTTATATATTTAA
1 TTTTTTTTATATATTTAA
*
369515 ATTTTTTTA
1 TTTTTTTTA
369524 AATTATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 8 0.21
18 15 0.38
19 8 0.21
20 8 0.21
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTTATATATTTAA
Found at i:369527 original size:10 final size:9
Alignment explanation
Indices: 369474--369524 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
369464 TATTATCATA
369474 TTTAATTTTT
1 TTTAA-TTTT
369484 TTTAATTTT
1 TTTAATTTT
369493 TTTAATTTT
1 TTTAATTTT
*
369502 TTT-ATATAT
1 TTTAAT-TTT
*
369511 TTAAATTTT
1 TTTAATTTT
369520 TTTAA
1 TTTAA
369525 ATTATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 2 0.06
9 26 0.74
10 7 0.20
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTAATTTT
Found at i:372423 original size:14 final size:13
Alignment explanation
Indices: 372404--372434 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
372394 TGCACCCATA
372404 CATCCATCATCATT
1 CATCCATCATCA-T
372418 CATCCATCATCAT
1 CATCCATCATCAT
372431 CATC
1 CATC
372435 GGCGTCAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (13 bp):
CATCCATCATCAT
Found at i:372651 original size:14 final size:14
Alignment explanation
Indices: 372632--372661 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
372622 TTTTTGATTG
*
372632 ATAATATATGTGTT
1 ATAATATATGAGTT
372646 ATAATATATGAGTT
1 ATAATATATGAGTT
372660 AT
1 AT
372662 TCTTTGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
ATAATATATGAGTT
Found at i:373171 original size:27 final size:27
Alignment explanation
Indices: 373124--373176 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
373114 AAAACCCGCT
*
373124 AAAGAGGAAAACCTTGACAAAGAGAAC
1 AAAGAGAAAAACCTTGACAAAGAGAAC
*
373151 AAAGAGAAAAATCC-TGGCAAAGAGAA
1 AAAGAGAAAAA-CCTTGACAAAGAGAA
373177 AAACCAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.57, C:0.13, G:0.23, T:0.08
Consensus pattern (27 bp):
AAAGAGAAAAACCTTGACAAAGAGAAC
Found at i:376072 original size:1 final size:1
Alignment explanation
Indices: 376066--376091 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
376056 AGACTACATT
376066 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
376092 GTAAGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:376995 original size:2 final size:2
Alignment explanation
Indices: 376988--377018 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
376978 GTCCTTTATG
376988 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 A
377019 AAAAGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:378168 original size:2 final size:2
Alignment explanation
Indices: 378161--378195 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
378151 AAGATCTTAG
378161 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 T
378196 GAAGAGTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:381519 original size:14 final size:14
Alignment explanation
Indices: 381502--381553 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
381492 AATGAAAGAA
*
381502 ATATATTAATTTTT
1 ATATTTTAATTTTT
* * *
381516 ATATGGTTAAATTTA
1 ATAT-TTTAATTTTT
381531 ATATTTTAATTTTT
1 ATATTTTAATTTTT
381545 ATATTTTAA
1 ATATTTTAA
381554 AATATTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (14 bp):
ATATTTTAATTTTT
Found at i:381556 original size:29 final size:30
Alignment explanation
Indices: 381501--381561 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
381491 TAATGAAAGA
381501 AATATATTAATTTTTATATGGTTAAAT-TT
1 AATATATTAATTTTTATATGGTTAAATATT
* *
381530 AATATTTTAATTTTTATAT-TTTAAAATATT
1 AATATATTAATTTTTATATGGTT-AAATATT
381560 AA
1 AA
381562 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 22 0.79
30 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
AATATATTAATTTTTATATGGTTAAATATT
Found at i:381798 original size:15 final size:15
Alignment explanation
Indices: 381780--381829 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
381770 TATTATAATT
381780 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
* *
381795 TT-AAAATATTAAAT
1 TTAAAAATATAAAAA
*
381809 TTAATAATATAAAAA
1 TTAAAAATATAAAAA
381824 TTAAAA
1 TTAAAA
381830 TATTTTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:381800 original size:14 final size:14
Alignment explanation
Indices: 381783--381832 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
381773 TATAATTTTA
381783 AAAATATAAAAATT
1 AAAATATAAAAATT
* *
381797 AAAATATTAAATTT
1 AAAATATAAAAATT
381811 AATAATATAAAAATT
1 AA-AATATAAAAATT
381826 AAAATAT
1 AAAATAT
381833 TTTTTTCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:381817 original size:29 final size:31
Alignment explanation
Indices: 381770--381833 Score: 105
Period size: 29 Copynumber: 2.1 Consensus size: 31
381760 TTTTTTTATT
381770 TATTATAATTTTAAAAATATAAAAATTAAAA
1 TATTATAATTTTAAAAATATAAAAATTAAAA
*
381801 TATTA-AA-TTTAATAATATAAAAATTAAAA
1 TATTATAATTTTAAAAATATAAAAATTAAAA
381830 TATT
1 TATT
381834 TTTTTCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 25 0.78
30 2 0.06
31 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TATTATAATTTTAAAAATATAAAAATTAAAA
Found at i:393866 original size:3 final size:3
Alignment explanation
Indices: 393860--393885 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
393850 AAGCTAAAAA
393860 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
393886 TCAAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:401927 original size:2 final size:2
Alignment explanation
Indices: 401898--401946 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
401888 TTAATTTATC
* * *
401898 TA TA TG TA TA TC TA TA TT TA TA -A 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
401939 TA TA TA TA
1 TA TA TA TA
401947 ATAAGAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:403543 original size:2 final size:2
Alignment explanation
Indices: 403536--403565 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
403526 GTAAAATCTG
403536 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
403566 ATTTAAATGA
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):
TA
Found at i:404787 original size:15 final size:14
Alignment explanation
Indices: 404741--404817 Score: 70
Period size: 14 Copynumber: 5.5 Consensus size: 14
404731 TTAAATTTAA
*
404741 AATAATTTTTAATT
1 AATATTTTTTAATT
404755 -ATATTTTTTATATT
1 AATATTTTTTA-ATT
404769 --TATTATTTTAATT
1 AATATT-TTTTAATT
**
404782 AATATTTAATAATT
1 AATATTTTTTAATT
*
404796 AAATAATTTTTAATT
1 -AATATTTTTTAATT
404811 AATATTT
1 AATATTT
404818 ATAAAAATCG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 16 0.31
14 20 0.39
15 15 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATATTTTTTAATT
Found at i:405458 original size:2 final size:2
Alignment explanation
Indices: 405451--405486 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
405441 AATAAATCCT
405451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
405487 GGGCATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:417767 original size:2 final size:2
Alignment explanation
Indices: 417760--417860 Score: 60
Period size: 2 Copynumber: 50.5 Consensus size: 2
417750 CTTTCTTTCC
* * * * * *
417760 TA TA TA TA TA TA TA TA TA TA TA TC TC TA TA CA CA CA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * ** * * *
417802 AA TA TA TA TA TA TA TA CA CG TA CTA -A AA GA AA 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
*
417844 TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA T
417861 TGGCCATAAC
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.01
2 78 0.96
3 2 0.02
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.40
Consensus pattern (2 bp):
TA
Found at i:419968 original size:10 final size:10
Alignment explanation
Indices: 419940--419976 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
419930 TTCTTCTTTA
419940 TTCTTTTCAT
1 TTCTTTTCAT
419950 TTCCTTTTCAT
1 TT-CTTTTCAT
*
419961 TTCTTTTCCT
1 TTCTTTTCAT
419971 TTCTTT
1 TTCTTT
419977 GCCTTTTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCTTTTCAT
Found at i:427708 original size:2 final size:2
Alignment explanation
Indices: 427703--427731 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
427693 TATGTTTTTC
427703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
427732 AATAAAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:433524 original size:3 final size:3
Alignment explanation
Indices: 433516--433543 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
433506 GTTCCCCCCA
433516 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
433544 TTGTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:437462 original size:20 final size:20
Alignment explanation
Indices: 437437--437475 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
437427 CTATGACTTC
437437 GGAAGCAGGGTATAAATGGG
1 GGAAGCAGGGTATAAATGGG
437457 GGAAGCAGGGTATAAATGG
1 GGAAGCAGGGTATAAATGG
437476 TAGTAACAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.44, T:0.15
Consensus pattern (20 bp):
GGAAGCAGGGTATAAATGGG
Found at i:440901 original size:2 final size:2
Alignment explanation
Indices: 440894--440938 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
440884 TAGAGATAAC
440894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
440936 TA T
1 TA T
440939 TTCTCCTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:449788 original size:2 final size:2
Alignment explanation
Indices: 449781--449814 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
449771 TAATAATTGG
449781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
449815 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:449819 original size:2 final size:2
Alignment explanation
Indices: 449814--449840 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
449804 TATATATATA
449814 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
449841 TTATATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:450062 original size:5 final size:5
Alignment explanation
Indices: 450052--450076 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
450042 ATTGGTATGT
450052 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
450077 AGGAAGTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:451297 original size:6 final size:6
Alignment explanation
Indices: 451286--451315 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
451276 ATCTTACAAA
451286 AAAAAT AAAAAT AAAAAT AAAAAT ATAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT A-AAAA
451316 ACAGAACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:461882 original size:14 final size:14
Alignment explanation
Indices: 461865--461891 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
461855 AAATTTTAAT
461865 TTTAATTTTTATAA
1 TTTAATTTTTATAA
461879 TTTAATTTTTATA
1 TTTAATTTTTATA
461892 TTTTCAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATAA
Found at i:462706 original size:2 final size:2
Alignment explanation
Indices: 462701--462734 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
462691 GTCAAATCTG
462701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
462735 TACTATAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:462908 original size:9 final size:8
Alignment explanation
Indices: 462883--462911 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
462873 TTATCATATA
462883 TTTT-ATT
1 TTTTAATT
462890 TTTTAATT
1 TTTTAATT
462898 TTTTAATT
1 TTTTAATT
462906 TTTTAA
1 TTTTAA
462912 AATATCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTAATT
Found at i:464625 original size:25 final size:25
Alignment explanation
Indices: 464597--464651 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
464587 TTTTTTATTT
464597 ATTTATAAATATTAATATAAA-AATA
1 ATTTATAAATATT-ATATAAATAATA
* * * *
464622 ATTTTTTATTATTTTATAAATAATA
1 ATTTATAAATATTATATAAATAATA
464647 ATTTA
1 ATTTA
464652 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTATAAATATTATATAAATAATA
Found at i:464631 original size:36 final size:36
Alignment explanation
Indices: 464584--464653 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
464574 AAAGATTTTT
*
464584 TAATTTTTTATT-TATTTATAAATATTAATATAAAAA
1 TAATTTTTTATTAT-TTTATAAATAATAATATAAAAA
*
464620 TAATTTTTTATTATTTTATAAATAATAATTTAAA
1 TAATTTTTTATTATTTTATAAATAATAATATAAA
464654 TTTTTAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
TAATTTTTTATTATTTTATAAATAATAATATAAAAA
Found at i:466719 original size:20 final size:19
Alignment explanation
Indices: 466694--466733 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
466684 CTTATTATTC
* *
466694 TATGATTTAGAATTACTTAA
1 TATGATTAAAAATTA-TTAA
466714 TATGATTAAAAATTATTAA
1 TATGATTAAAAATTATTAA
466733 T
1 T
466734 TCTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (19 bp):
TATGATTAAAAATTATTAA
Found at i:467665 original size:2 final size:2
Alignment explanation
Indices: 467658--467688 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
467648 TGATTTTCAA
467658 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 T
467689 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:467693 original size:2 final size:2
Alignment explanation
Indices: 467688--467712 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
467678 TCTCTCTCTC
467688 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
467713 GTATGTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:478631 original size:2 final size:2
Alignment explanation
Indices: 478624--478654 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
478614 CAAAATCAAT
478624 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 T
478655 TTTCTTCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:482315 original size:7 final size:7
Alignment explanation
Indices: 482277--482305 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
482267 TAATTTTTTC
482277 TTTAATA
1 TTTAATA
482284 TTTAATA
1 TTTAATA
482291 TTTAATA
1 TTTAATA
482298 TTTAATA
1 TTTAATA
482305 T
1 T
482306 AATAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAATA
Found at i:483313 original size:25 final size:22
Alignment explanation
Indices: 483257--483313 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
483247 AATAGTGATT
*
483257 AAATT-AA-TAAATTTATTTAA
1 AAATTAAATTAAATTTATATAA
483277 AAATTAAATTAAATTTATAATATA
1 AAATTAAATTAAATTTAT-ATA-A
*
483301 AAATATAATTTAA
1 AAAT-TAAATTAA
483314 CATGTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 5 0.17
21 2 0.07
22 9 0.30
23 2 0.07
24 5 0.17
25 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATTAAATTAAATTTATATAA
Found at i:483766 original size:18 final size:19
Alignment explanation
Indices: 483743--483782 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
483733 AAAAATCATT
*
483743 ATATAAA-ATTTTTTATAA
1 ATATAAATATTTTTGATAA
483761 ATATAAATATTTTTGATAA
1 ATATAAATATTTTTGATAA
483780 ATA
1 ATA
483783 CATTTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATATAAATATTTTTGATAA
Found at i:483976 original size:3 final size:3
Alignment explanation
Indices: 483968--483997 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
483958 CATTATTTAT
483968 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
483998 TATTCATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:484087 original size:23 final size:22
Alignment explanation
Indices: 484047--484102 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
484037 TTATTATATT
* *
484047 TAATATAAAATTATTTTTTAAA
1 TAATATAAAATTAATTTTAAAA
*
484069 TAATATATTAATTAATTTTAAAA
1 TAATATA-AAATTAATTTTAAAA
484092 TATATCATAAA
1 TA-AT-ATAAA
484103 GATATACAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 7 0.26
23 14 0.52
24 3 0.11
25 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATATAAAATTAATTTTAAAA
Found at i:484323 original size:12 final size:12
Alignment explanation
Indices: 484306--484331 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
484296 GGATTTCCAT
484306 AATTAATAAATA
1 AATTAATAAATA
484318 AATTAATAAATA
1 AATTAATAAATA
484330 AA
1 AA
484332 AACAAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTAATAAATA
Found at i:486036 original size:20 final size:20
Alignment explanation
Indices: 486011--486048 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
486001 TGTTTCATGC
*
486011 CATTGGACCCTTCGTAATAA
1 CATTGGACCCTTCATAATAA
486031 CATTGGACCCTTCATAAT
1 CATTGGACCCTTCATAAT
486049 GACAGTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (20 bp):
CATTGGACCCTTCATAATAA
Found at i:493632 original size:24 final size:24
Alignment explanation
Indices: 493562--493658 Score: 92
Period size: 24 Copynumber: 4.0 Consensus size: 24
493552 TAAATATATA
*
493562 TAATATATTTATATA--TAA-AAT
1 TAATATTTTTATATATTTAATAAT
*
493583 TAATATTATTTATATTATATTCATAAT
1 TAATATT-TTTATA-TAT-TTAATAAT
*
493610 TAATATTTTGATATATTTAATAAT
1 TAATATTTTTATATATTTAATAAT
* *
493634 TTATATTTTTTTATATTTATATAAT
1 TAATATTTTTATATATTTA-ATAAT
493659 CCATGCAACA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
21 6 0.10
22 6 0.10
23 2 0.03
24 23 0.37
25 8 0.13
26 7 0.11
27 10 0.16
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (24 bp):
TAATATTTTTATATATTTAATAAT
Found at i:493831 original size:3 final size:3
Alignment explanation
Indices: 493825--493854 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
493815 AGTTTACTAC
493825 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
493855 ATATTTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:493955 original size:2 final size:2
Alignment explanation
Indices: 493948--493996 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
493938 CGTGTGCCCA
493948 CT CT CT CT CT CT 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 CT CT CT CT CT CT
493990 CT CT CT C
1 CT CT CT C
493997 ACACGCGCGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:494100 original size:23 final size:23
Alignment explanation
Indices: 494071--494114 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
494061 AGCTCATCTC
*
494071 CTCTCGTCCTCTCTTATTTTCCT
1 CTCTCGTCCTCTCTCATTTTCCT
**
494094 CTCTCGTTTTCTCTCATTTTC
1 CTCTCGTCCTCTCTCATTTTC
494115 TTCTGAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.05, C:0.36, G:0.05, T:0.55
Consensus pattern (23 bp):
CTCTCGTCCTCTCTCATTTTCCT
Found at i:500438 original size:2 final size:2
Alignment explanation
Indices: 500431--500458 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
500421 TGTTCTCTAA
500431 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
500459 GGTTCCGTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:503070 original size:8 final size:8
Alignment explanation
Indices: 503055--503087 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
503045 GATTGTTAGA
503055 ATTT-TAT
1 ATTTATAT
503062 ATTTATAT
1 ATTTATAT
503070 ATTTATAT
1 ATTTATAT
*
503078 ATATATAT
1 ATTTATAT
503086 AT
1 AT
503088 GGGCTAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTATAT
Found at i:509691 original size:50 final size:50
Alignment explanation
Indices: 509611--509712 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
509601 TAAGGATGAA
*
509611 AGCATGGATTTTGTTCAAAACCTGAAGAAGTCTCAAATTTCTAAATTTAC
1 AGCAAGGATTTTGTTCAAAACCTGAAGAAGTCTCAAATTTCTAAATTTAC
509661 AGCAAGGATTTTGTTCAAAACCTGAAGAAGTCTCAAATTTCTAAATTTAC
1 AGCAAGGATTTTGTTCAAAACCTGAAGAAGTCTCAAATTTCTAAATTTAC
509711 AG
1 AG
509713 ATCCAATCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (50 bp):
AGCAAGGATTTTGTTCAAAACCTGAAGAAGTCTCAAATTTCTAAATTTAC
Found at i:516694 original size:7 final size:7
Alignment explanation
Indices: 516684--516743 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
516674 TTTTTTTTAT
516684 TTTAATA
1 TTTAATA
516691 TTTAATA
1 TTTAATA
516698 TTTAATA
1 TTTAATA
516705 -TTAATTTAA
1 TTTAA--T-A
*
516714 TCTAATA
1 TTTAATA
*
516721 TATAATA
1 TTTAATA
*
516728 TATTTATA
1 T-TTAATA
516736 TTTAATA
1 TTTAATA
516743 T
1 T
516744 ATTATATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
6 4 0.09
7 28 0.65
8 7 0.16
9 1 0.02
10 3 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (7 bp):
TTTAATA
Found at i:516775 original size:30 final size:30
Alignment explanation
Indices: 516739--516806 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
516729 ATTTATATTT
** *
516739 AATATATTATATAATTTTTATTATAAT-AAA
1 AATATATTATATAATAATTATAAT-ATGAAA
* *
516769 AATATATAATATTATAATTATAATATGAAA
1 AATATATTATATAATAATTATAATATGAAA
516799 AATATATT
1 AATATATT
516807 TTATTAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
AATATATTATATAATAATTATAATATGAAA
Found at i:516832 original size:22 final size:22
Alignment explanation
Indices: 516776--516836 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
516766 AAAAATATAT
*
516776 AATATTATAATTA-TAATATGAAA
1 AATATTA-AATTATTAA-ATAAAA
**
516799 AATA-TATTTTATTAAATAAAA
1 AATATTAAATTATTAAATAAAA
516820 AATATTAAATTATTAAA
1 AATATTAAATTATTAAA
516837 AATATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 12 0.39
22 15 0.48
23 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATTAAATTATTAAATAAAA
Found at i:518232 original size:2 final size:2
Alignment explanation
Indices: 518225--518264 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
518215 AATGTTAAGA
518225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
518265 CCCTTACAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:525713 original size:3 final size:3
Alignment explanation
Indices: 525707--525732 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
525697 TGAAAATCAA
525707 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
525733 ATGTACTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:533836 original size:17 final size:17
Alignment explanation
Indices: 533812--533857 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
533802 AATTAAAATA
*
533812 AAAT-AATTTTTATTTT
1 AAATAAATTTTAATTTT
533828 AAATAAATTTTAATTTT
1 AAATAAATTTTAATTTT
533845 -AATCAAATTTTAA
1 AAAT-AAATTTTAA
533858 ATAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATAAATTTTAATTTT
Found at i:533870 original size:16 final size:17
Alignment explanation
Indices: 533804--533871 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 17
533794 ATAAAATAAA
* * *
533804 TTAAAATAAAATAATTT
1 TTAATATAAATTAAATT
* *
533821 TTATTTTAAA-TAAATT
1 TTAATATAAATTAAATT
* * *
533837 TTAATTTTAATCAAATT
1 TTAATATAAATTAAATT
533854 TTAA-ATAAATTAAATT
1 TTAATATAAATTAAATT
533870 TT
1 TT
533872 TTTATGATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
16 24 0.60
17 16 0.40
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATATAAATTAAATT
Found at i:536691 original size:28 final size:30
Alignment explanation
Indices: 536617--536692 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 30
536607 TATTTTTGAA
*
536617 AATTTTTATTTAAATTTAATAAAAAGTTAT
1 AATTTTTATTAAAATTTAATAAAAAGTTAT
** *
536647 AATTTATT-TTATTATTTAA-AAATA-TTAT
1 AATTT-TTATTAAAATTTAATAAAAAGTTAT
536675 AATTTTTATTAAAATTTA
1 AATTTTTATTAAAATTTA
536693 TTATTTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.05
28 17 0.45
29 4 0.11
30 13 0.34
31 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
AATTTTTATTAAAATTTAATAAAAAGTTAT
Found at i:536698 original size:19 final size:21
Alignment explanation
Indices: 536647--536699 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
536637 AAAAAGTTAT
*
536647 AATTTATT-TTATTATTTAAA
1 AATTTATTATTTTTATTTAAA
*
536667 AATATTATAATTTTTA-TT-AA
1 AAT-TTATTATTTTTATTTAAA
536687 AATTTATTATTTT
1 AATTTATTATTTT
536700 ATAAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.32
20 8 0.29
21 6 0.21
22 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTATTATTTTTATTTAAA
Found at i:537495 original size:20 final size:20
Alignment explanation
Indices: 537470--537510 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
537460 AAATTTAAAT
537470 TTATATAAAATACTATATTA
1 TTATATAAAATACTATATTA
*
537490 TTATATAAAATATTATATTA
1 TTATATAAAATACTATATTA
537510 T
1 T
537511 ATTAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATAAAATACTATATTA
Found at i:537513 original size:22 final size:22
Alignment explanation
Indices: 537470--537531 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 22
537460 AAATTTAAAT
*
537470 TTATATAAAATACTATA-T-TA
1 TTATATAAAATATTATATTATA
537490 TTATATAAAATATTATATTATA
1 TTATATAAAATATTATATTATA
* *
537512 TTA-ATTAATTATTATTATTA
1 TTATATAAAATATTA-TATTA
537532 AATTTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 16 0.44
21 10 0.28
22 10 0.28
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATATAAAATATTATATTATA
Found at i:537720 original size:14 final size:14
Alignment explanation
Indices: 537701--537756 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
537691 TTTTATTTAT
537701 AAAATTTAAATTAA
1 AAAATTTAAATTAA
*
537715 AAAATTT-ATTTAA
1 AAAATTTAAATTAA
* *
537728 AAAAATAAATATTAA
1 AAAATTTAA-ATTAA
**
537743 ATCATTTAAATTAA
1 AAAATTTAAATTAA
537757 TTATAATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
13 10 0.31
14 13 0.41
15 9 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATTTAAATTAA
Found at i:537731 original size:13 final size:13
Alignment explanation
Indices: 537692--537731 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
537682 CGATAATTTT
*
537692 TTTATTTATAAAA
1 TTTATTTAAAAAA
*
537705 TTTAAATTAAAAAA
1 TTT-ATTTAAAAAA
537719 TTTATTTAAAAAA
1 TTTATTTAAAAAA
537732 ATAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTATTTAAAAAA
Found at i:538569 original size:3 final size:3
Alignment explanation
Indices: 538561--538597 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
538551 TACTTTTTAT
*
538561 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
538598 ATGACTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:538718 original size:22 final size:21
Alignment explanation
Indices: 538693--538733 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
538683 AAAAAATTAA
538693 ATATAATTATAAAAATAATATT
1 ATATAATT-TAAAAATAATATT
* *
538715 ATATTATTTTAAAATAATA
1 ATATAATTTAAAAATAATA
538734 AAATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATAATTTAAAAATAATATT
Found at i:544742 original size:16 final size:16
Alignment explanation
Indices: 544721--544751 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
544711 TCAAGTTAAG
*
544721 ATAAATTATTTTAAAT
1 ATAAATTATATTAAAT
544737 ATAAATTATATTAAA
1 ATAAATTATATTAAA
544752 ATTTTTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAATTATATTAAAT
Found at i:545522 original size:12 final size:12
Alignment explanation
Indices: 545463--545522 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
545453 ATTTAATTTT
*
545463 TAATTTTTTATA
1 TAATTTTTAATA
*
545475 T-ATTTTTATTA
1 TAATTTTTAATA
* *
545486 AAATTTTAAATA
1 TAATTTTTAATA
*
545498 TAAATAATTTAATA
1 T-AAT-TTTTAATA
545512 TAATTTTTAAT
1 TAATTTTTAAT
545523 TTTAAAAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
11 8 0.22
12 15 0.42
13 6 0.17
14 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAATTTTTAATA
Found at i:545546 original size:27 final size:27
Alignment explanation
Indices: 545481--545546 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
545471 TATATATTTT
* *
545481 TATTAAA-ATTTTAAATATAAATAATT
1 TATTAAATATTTTAAATATAAAAAATA
* * *
545507 TAATATAAT-TTTTAATTTTAAAAAATA
1 TATTA-AATATTTTAAATATAAAAAATA
545534 TATTAAATATTTT
1 TATTAAATATTTT
545547 GATTATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTAAATATTTTAAATATAAAAAATA
Found at i:545627 original size:32 final size:32
Alignment explanation
Indices: 545592--545653 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
545582 TTCAATCTCT
*
545592 TTTTTAAAATTAAAT-TTTTTATTTAAATTTA
1 TTTTTAAAATAAAATATTTTTATTTAAATTTA
545623 TTTTTAAAATAAAATATTTTTATTTAAATTT
1 TTTTTAAAATAAAATATTTTTATTTAAATTT
545654 TTAATTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTTAAAATAAAATATTTTTATTTAAATTTA
Found at i:545662 original size:32 final size:31
Alignment explanation
Indices: 545595--545662 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
545585 AATCTCTTTT
* *
545595 TTAAAATTAAATTTTTTATTTAAATTTATTT
1 TTAAAATAAAATTTTTTATTTAAATTTATTA
545626 TTAAAATAAAATATTTTTATTTAAATTT-TTAA
1 TTAAAATAAAAT-TTTTTATTTAAATTTATT-A
545658 TTAAA
1 TTAAA
545663 CAAATAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TTAAAATAAAATTTTTTATTTAAATTTATTA
Found at i:546393 original size:16 final size:17
Alignment explanation
Indices: 546324--546405 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 17
546314 AAAATATATA
546324 AATTAAATATATTATTTT
1 AATT-AATATATTATTTT
* * *
546342 TATTAAATTAACATAATTATT
1 AATT-AA-T-ATATTATT-TT
*
546363 AA-TAATATTTTATTTT
1 AATTAATATATTATTTT
*
546379 ATTTAA-ATATTATTTT
1 AATTAATATATTATTTT
546395 AATTAATATAT
1 AATTAATATAT
546406 ATAATAACAT
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
16 17 0.35
17 12 0.24
18 7 0.14
19 3 0.06
20 7 0.14
21 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTAATATATTATTTT
Found at i:546462 original size:23 final size:23
Alignment explanation
Indices: 546436--546489 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
546426 TTTACATAAT
*
546436 AATAATTTTTAACAAATATTTA-A
1 AATAATTTTCAACAAA-ATTTATA
*
546459 AATAATTTTCAATAAAATTTATA
1 AATAATTTTCAACAAAATTTATA
*
546482 AAAAATTT
1 AATAATTT
546490 ATTTAATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAATTTTCAACAAAATTTATA
Found at i:546541 original size:3 final size:3
Alignment explanation
Indices: 546533--546569 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
546523 TAAGGAAAAG
546533 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
546570 CAAAATTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:546981 original size:20 final size:21
Alignment explanation
Indices: 546940--546981 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
546930 TCTCATTCTC
*
546940 AAAATATTTTTATATTAATTA
1 AAAATATTTTTATAATAATTA
546961 AAAAT-TTTTTA-AATAAGTTA
1 AAAATATTTTTATAATAA-TTA
546981 A
1 A
546982 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATATTTTTATAATAATTA
Found at i:547012 original size:29 final size:27
Alignment explanation
Indices: 546954--547051 Score: 67
Period size: 29 Copynumber: 3.4 Consensus size: 27
546944 TATTTTTATA
* *
546954 TTAATTAAAAATTTTTTAAATAAGTT-AAT
1 TTAATTAAAAA--ATTTAAA-AATTTAAAT
546983 TTAATTAAAAAATATATAAAAATTTAAAT
1 TTAATTAAAAAAT-T-TAAAAATTTAAAT
*
547012 TAAAATT--AAAATTTAAAATATTTAATAT
1 T-TAATTAAAAAATTTAAAA-ATTTAA-AT
*
547040 TTATTTAAAAAA
1 TTAATTAAAAAA
547052 AATTATTCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
26 5 0.09
27 11 0.20
28 13 0.23
29 23 0.41
30 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
TTAATTAAAAAATTTAAAAATTTAAAT
Found at i:547118 original size:17 final size:16
Alignment explanation
Indices: 547096--547131 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
547086 ATATTTGTAC
*
547096 TTTTTAAAAAGTAATTA
1 TTTTTAAAAA-AAATTA
547113 TTTTTAAAAAAAATTA
1 TTTTTAAAAAAAATTA
547129 TTT
1 TTT
547132 ATATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTTTAAAAAAAATTA
Found at i:547181 original size:26 final size:26
Alignment explanation
Indices: 547155--547205 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
547145 TTTTAAAAAA
547155 TTTACTCATAAAATGAAT-ATAATAAAT
1 TTTACT-ATAAAAT-AATAATAATAAAT
*
547182 TTTAGTATAAAATAATAATAATAA
1 TTTACTATAAAATAATAATAATAA
547206 TAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 14 0.64
27 5 0.23
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
TTTACTATAAAATAATAATAATAAAT
Found at i:548301 original size:11 final size:10
Alignment explanation
Indices: 548285--548430 Score: 62
Period size: 10 Copynumber: 14.8 Consensus size: 10
548275 ATTTAGATAT
548285 TTATATTTTA
1 TTATATTTTA
548295 TTGATATATTT-
1 TT-ATAT-TTTA
*
548306 TTATATTATAA
1 TTATATT-TTA
548317 TTATATTTTA
1 TTATATTTTA
*
548327 --A-ATATTA
1 TTATATTTTA
548334 TT-TATTTCTA
1 TTATATTT-TA
548344 -T-TATTTTA
1 TTATATTTTA
* *
548352 ATATATTAATAA
1 TTATATT--TTA
*
548364 TT-TATATTA
1 TTATATTTTA
548373 -TATATTTTA
1 TTATATTTTA
*
548382 ATATA-TTTA
1 TTATATTTTA
*
548391 -TATATTAATA
1 TTATATT-TTA
548401 TTATATTTTA
1 TTATATTTTA
*
548411 TTATTTTTCATA
1 TTATATTT--TA
548423 TTATATTT
1 TTATATTT
548431 ATAATTATTC
Statistics
Matches: 104, Mismatches: 13, Indels: 36
0.68 0.08 0.24
Matches are distributed among these distances:
7 5 0.05
8 8 0.08
9 24 0.23
10 30 0.29
11 22 0.21
12 15 0.14
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (10 bp):
TTATATTTTA
Found at i:548338 original size:18 final size:18
Alignment explanation
Indices: 548299--548412 Score: 76
Period size: 19 Copynumber: 6.3 Consensus size: 18
548289 ATTTTATTGA
*
548299 TATATTTTTATATTATAAT
1 TATATTTTAATATTAT-AT
548318 TATATTTTAAATATTAT-T
1 TATATTTT-AATATTATAT
* * * *
548336 TAT-TTCTATTATTTTAA
1 TATATTTTAATATTATAT
*
548353 TATATTAATAAT-TTATATT
1 TATATT-TTAATATTATA-T
548372 ATATATTTTAATA-TAT-T
1 -TATATTTTAATATTATAT
*
548389 TATATATTAATATTATAT
1 TATATTTTAATATTATAT
*
548407 TTTATT
1 TATATT
548413 ATTTTTCATA
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
16 17 0.23
17 10 0.14
18 15 0.21
19 18 0.25
20 13 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTTAATATTATAT
Found at i:548366 original size:26 final size:25
Alignment explanation
Indices: 548320--548373 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
548310 ATTATAATTA
* * *
548320 TATTTTAAATATTATTTATTTCTAT
1 TATTTTAAATATTAATAATTTATAT
548345 TATTTTAATATATTAATAATTTATAT
1 TATTTTAA-ATATTAATAATTTATAT
548371 TAT
1 TAT
548374 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTTTAAATATTAATAATTTATAT
Found at i:548424 original size:36 final size:36
Alignment explanation
Indices: 548352--548436 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 36
548342 TATTATTTTA
548352 ATATATTAATAATTTATATTATATATTTTAATATATTT
1 ATATATTAATAATTTATATTATATATTTT-ATATA-TT
*
548390 ATATATTAAT-A-TTATATTTTATTATTTT-TCATATT
1 ATATATTAATAATTTATATTATA-TATTTTAT-ATATT
548425 ATAT-TT-ATAATT
1 ATATATTAATAATT
548437 ATTCTATCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
33 2 0.05
34 3 0.07
35 8 0.19
36 12 0.29
37 7 0.17
38 10 0.24
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (36 bp):
ATATATTAATAATTTATATTATATATTTTATATATT
Found at i:548428 original size:41 final size:41
Alignment explanation
Indices: 548328--548437 Score: 112
Period size: 38 Copynumber: 2.8 Consensus size: 41
548318 TATATTTTAA
*
548328 ATATTATT-TATTTC-TATTAT-TTTAATATATTAATAATTT
1 ATATTATTATTTTTCATATTATATTT-ATATATTAATAATTT
548367 ATATTA-TATATTTT-A-A-TATATTTATATATTAAT-ATTAT
1 ATATTATTAT-TTTTCATATTATATTTATATATTAATAATT-T
*
548405 ATTTTATTATTTTTCATATTATATTTATA-ATTA
1 ATATTATTATTTTTCATATTATATTTATATATTA
548438 TTCTATCTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
37 3 0.05
38 24 0.40
39 15 0.25
40 8 0.13
41 10 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (41 bp):
ATATTATTATTTTTCATATTATATTTATATATTAATAATTT
Found at i:548819 original size:34 final size:35
Alignment explanation
Indices: 548776--548841 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
548766 CGATAAACTT
548776 TTAATTATATCAAATTAAATTAT-TAAATTTTTTTA
1 TTAATTATATCAAATT-AATTATATAAATTTTTTTA
* *
548811 TTAA-TATATTAAATTAATTATATTAATTTTT
1 TTAATTATATCAAATTAATTATATAAATTTTT
548842 AAATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 18 0.64
35 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (35 bp):
TTAATTATATCAAATTAATTATATAAATTTTTTTA
Found at i:548848 original size:20 final size:22
Alignment explanation
Indices: 548796--548885 Score: 64
Period size: 21 Copynumber: 4.3 Consensus size: 22
548786 CAAATTAAAT
* *
548796 TATTAAATT-TTTTTATTAATA
1 TATTAAATTAATTATATTAATA
548817 TATTAAATTAATTATATTAAT-
1 TATTAAATTAATTATATTAATA
* * *
548838 TTTTAAA-TAATTTTAATAA-A
1 TATTAAATTAATTATATTAATA
* * *
548858 AATTAATTTAA-TATATATAATT
1 TATTAAATTAATTATAT-TAATA
548880 TATTAA
1 TATTAA
548886 TAAAAAATTA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
20 17 0.33
21 21 0.40
22 14 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTAAATTAATTATATTAATA
Found at i:548867 original size:15 final size:15
Alignment explanation
Indices: 548849--548899 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
548839 TTTAAATAAT
548849 TTTAATAAAAATTAA
1 TTTAATAAAAATTAA
*
548864 TTTAATATATATAATTTA
1 TTTAATA-A-A-AATTAA
548882 -TTAATAAAAAATTAA
1 TTTAAT-AAAAATTAA
548897 TTT
1 TTT
548900 TATATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 12 0.41
16 4 0.14
17 7 0.24
18 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAATAAAAATTAA
Found at i:548869 original size:32 final size:33
Alignment explanation
Indices: 548841--548905 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
548831 TATTAATTTT
548841 TAAATAA-TT-TTAAT-AAAAATTAATTTAATA
1 TAAATAATTTATTAATAAAAAATTAATTTAATA
* *
548871 TATATAATTTATTAATAAAAAATTAATTTTATA
1 TAAATAATTTATTAATAAAAAATTAATTTAATA
548904 TA
1 TA
548906 TTTATTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 6 0.20
31 2 0.07
32 5 0.17
33 17 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TAAATAATTTATTAATAAAAAATTAATTTAATA
Done.