Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold498
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: 1804022
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 7 of 17
Found at i:593843 original size:34 final size:34
Alignment explanation
Indices: 593803--593871 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
593793 CAGTAAACAG
593803 AAAACTTAATGAAACACATGCCATAATCAGTAAA
1 AAAACTTAATGAAACACATGCCATAATCAGTAAA
593837 AAAACTTAATGAAACACATGCCATAATCAGTAAA
1 AAAACTTAATGAAACACATGCCATAATCAGTAAA
593871 A
1 A
593872 CATTAAACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (34 bp):
AAAACTTAATGAAACACATGCCATAATCAGTAAA
Found at i:598081 original size:19 final size:19
Alignment explanation
Indices: 598054--598110 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
598044 TTATATATTT
598054 TATTATATAAATATT-AATA
1 TATTATAT-AATATTAAATA
* *
598073 TATTTTATATTATTAAATA
1 TATTATATAATATTAAATA
*
598092 TATTA-A-AATTTTAAATA
1 TATTATATAATATTAAATA
598109 TA
1 TA
598111 AATTATATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 11 0.34
18 6 0.19
19 15 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATATAATATTAAATA
Found at i:598124 original size:24 final size:23
Alignment explanation
Indices: 598086--598130 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
598076 TTTATATTAT
*
598086 TAAATATATTAAAATTTTAAATA
1 TAAATATATTAAAATATTAAATA
*
598109 TAAATTATATTTAAATATTAAA
1 TAAA-TATATTAAAATATTAAA
598131 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATATATTAAAATATTAAATA
Found at i:599051 original size:18 final size:20
Alignment explanation
Indices: 599028--599069 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
599018 TTTGTATTTG
599028 ATAAAATTT-TA-AATTAAA
1 ATAAAATTTATATAATTAAA
*
599046 ATAAAATTTATATAATTAAT
1 ATAAAATTTATATAATTAAA
599066 ATAA
1 ATAA
599070 TAAAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAATTTATATAATTAAA
Found at i:599252 original size:21 final size:23
Alignment explanation
Indices: 599226--599271 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
599216 TTAAATATAT
599226 TATAATAAAAAAT-AATT-TAAA
1 TATAATAAAAAATAAATTATAAA
* *
599247 TATAATATAACATAAATTATAAA
1 TATAATAAAAAATAAATTATAAA
599270 TA
1 TA
599272 AAAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 4 0.19
23 6 0.29
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TATAATAAAAAATAAATTATAAA
Found at i:600442 original size:31 final size:30
Alignment explanation
Indices: 600405--600476 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
600395 TTAAATTTAA
600405 AATTATTTTAAAAAATTTAAATT-TTATAAT
1 AATTATTTTAAAAAA-TTAAATTATTATAAT
* **
600435 ATTTTATTTATATTAAATTAAATTATTATAAT
1 A-ATTATTT-TAAAAAATTAAATTATTATAAT
600467 AATTATTTTA
1 AATTATTTTA
600477 TTTTATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 3 0.09
31 19 0.54
32 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
AATTATTTTAAAAAATTAAATTATTATAAT
Found at i:600477 original size:17 final size:17
Alignment explanation
Indices: 600430--600489 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
600420 TTTAAATTTT
600430 ATAA-TATTTTATTTATA
1 ATAATTATTTTA-TTATA
* **
600447 TTAAATTAAATTATTATA
1 AT-AATTATTTTATTATA
*
600465 ATAATTATTTTATTTTA
1 ATAATTATTTTATTATA
*
600482 TTAATTAT
1 ATAATTAT
600490 AATAAATAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 20 0.61
18 8 0.24
19 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATTATTTTATTATA
Found at i:600777 original size:22 final size:22
Alignment explanation
Indices: 600746--600788 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
600736 TCTTTTTAAT
* *
600746 TAAATTTAAAAGTTAATAATTA
1 TAAATATAAAAATTAATAATTA
*
600768 TAAATATAAAAATTTATAATT
1 TAAATATAAAAATTAATAATT
600789 TTATTTATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAATATAAAAATTAATAATTA
Found at i:609495 original size:19 final size:19
Alignment explanation
Indices: 609468--609505 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
609458 TAAGAATTCA
609468 TATTATTATATTAAAATTT
1 TATTATTATATTAAAATTT
* *
609487 TATTTTTATATTAATATTT
1 TATTATTATATTAAAATTT
609506 ATAATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATTATATTAAAATTT
Found at i:613457 original size:14 final size:15
Alignment explanation
Indices: 613438--613468 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
613428 ACTTTTTAAA
613438 TATGTTATA-AAATT
1 TATGTTATACAAATT
613452 TATGTTATACAAATT
1 TATGTTATACAAATT
613467 TA
1 TA
613469 ATTTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (15 bp):
TATGTTATACAAATT
Found at i:613835 original size:49 final size:50
Alignment explanation
Indices: 613780--613881 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
613770 GCGAAAGCCT
* *
613780 ATATTTAT-TATTTATAAATAATAAAATTT-TA-AAAATTA-TTTTTATATTA
1 ATATTTATATATTT-T--ATAATAAAATTTAAATAAAATTATTTTTTAAATTA
*
613829 ATATTTATATATTTTATAATTAAATTTAAATAAAATTATTTTTTAAATTA
1 ATATTTATATATTTTATAATAAAATTTAAATAAAATTATTTTTTAAATTA
613879 ATA
1 ATA
613882 AATAATAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
47 11 0.24
48 1 0.02
49 16 0.35
50 18 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (50 bp):
ATATTTATATATTTTATAATAAAATTTAAATAAAATTATTTTTTAAATTA
Found at i:616429 original size:2 final size:2
Alignment explanation
Indices: 616424--616454 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
616414 AATTCATTTC
616424 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
616455 ATTAATTGAT
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:617967 original size:25 final size:25
Alignment explanation
Indices: 617917--617964 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
617907 TTTTAACTTA
*
617917 TAATTTTTTTATAATAATATTAAAT
1 TAATTTTTATATAATAATATTAAAT
*
617942 TAATTTTTATATAAT-TTATTAAA
1 TAATTTTTATATAATAATATTAAA
617965 ATTTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAATTTTTATATAATAATATTAAAT
Found at i:618093 original size:10 final size:10
Alignment explanation
Indices: 618078--618102 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
618068 GATCACTTCC
618078 TTTTTTTCTT
1 TTTTTTTCTT
618088 TTTTTTTCTT
1 TTTTTTTCTT
618098 TTTTT
1 TTTTT
618103 CTTTCTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:618329 original size:16 final size:16
Alignment explanation
Indices: 618304--618338 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
618294 AAAATATGTA
618304 TTTCTTTTTTTTCT-T
1 TTTCTTTTTTTTCTGT
618319 TTTCTTTTTTTTTCTGT
1 TTTC-TTTTTTTTCTGT
618336 TTT
1 TTT
618339 GAAATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 10 0.56
17 4 0.22
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTCTTTTTTTTCTGT
Found at i:622769 original size:15 final size:15
Alignment explanation
Indices: 622749--622780 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
622739 GAACAGATAG
622749 TTGATGGAAACTAAA
1 TTGATGGAAACTAAA
622764 TTGATGGAAACTAAA
1 TTGATGGAAACTAAA
622779 TT
1 TT
622781 AAACTAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (15 bp):
TTGATGGAAACTAAA
Found at i:628840 original size:3 final size:3
Alignment explanation
Indices: 628832--628864 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
628822 CAAAATGGAA
628832 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
628865 GGAAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:629193 original size:11 final size:11
Alignment explanation
Indices: 629177--629237 Score: 54
Period size: 10 Copynumber: 5.5 Consensus size: 11
629167 TTATAGTTCA
629177 AAATAATATTT
1 AAATAATATTT
629188 AAATAATATTTT
1 AAATAATA-TTT
*
629200 ATATTAATATTT
1 A-AATAATATTT
* *
629212 ATAT-ATTTTT
1 AAATAATATTT
*
629222 AATTAATA-TT
1 AAATAATATTT
629232 AAATAA
1 AAATAA
629238 AATAATTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
10 14 0.36
11 11 0.28
12 8 0.21
13 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATAATATTT
Found at i:629207 original size:24 final size:22
Alignment explanation
Indices: 629180--629237 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
629170 TAGTTCAAAA
629180 TAATATTTAAATAATATTTTATAT
1 TAATATTTAAATAAT-TTTTA-AT
*
629204 TAATATTTATAT-ATTTTTAAT
1 TAATATTTAAATAATTTTTAAT
629225 TAATA-TTAAATAA
1 TAATATTTAAATAA
629238 AATAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 5 0.16
21 8 0.26
22 5 0.16
23 2 0.06
24 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATATTTAAATAATTTTTAAT
Found at i:629209 original size:13 final size:14
Alignment explanation
Indices: 629180--629218 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
629170 TAGTTCAAAA
629180 TAATATTTA-A-A-
1 TAATATTTATATAT
629191 TAATATTT-TATAT
1 TAATATTTATATAT
629204 TAATATTTATATAT
1 TAATATTTATATAT
629218 T
1 T
629219 TTTAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 8 0.33
14 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATATTTATATAT
Found at i:630174 original size:3 final size:3
Alignment explanation
Indices: 630166--630206 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
630156 ATCAACTTTA
630166 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
630207 AGTGATGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:631365 original size:30 final size:30
Alignment explanation
Indices: 631315--631423 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
631305 AATTATTATA
631315 TTTTAA-TTATA-CTAAAATAAACATTTAAC
1 TTTTAATTTATATCT-AAATAAACATTTAAC
* ** *
631344 TTTTAATTTGTATCTAAATAAATTTTTAAA
1 TTTTAATTTATATCTAAATAAACATTTAAC
* * * *
631374 TTTTAAATTATATCAAAATAAATCA-GTAGC
1 TTTTAATTTATATCTAAATAAA-CATTTAAC
631404 TTTTAATTTATATCTAAATA
1 TTTTAATTTATATCTAAATA
631424 CATTAGTTAA
Statistics
Matches: 63, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
29 6 0.10
30 55 0.87
31 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (30 bp):
TTTTAATTTATATCTAAATAAACATTTAAC
Found at i:631394 original size:60 final size:59
Alignment explanation
Indices: 631302--631433 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 59
631292 CTTTACTTAG
* * *
631302 ATAAATTATTATATTTTAATTATACTAAAATAAA-CATTTAACTTTTAATTTGTATCTAA
1 ATAAATTATTAAATTTTAATTATACTAAAATAAATCA-GTAACTTTTAATTTATATCTAA
* *
631361 ATAAATTTTTAAATTTTAAATTATA-TCAAAATAAATCAGTAGCTTTTAATTTATATCTAA
1 ATAAATTATTAAATTTT-AATTATACT-AAAATAAATCAGTAACTTTTAATTTATATCTAA
*
631421 ATACATTAGTTAA
1 ATAAATTA-TTAA
631434 TGTAAATTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 16 0.26
60 40 0.65
61 6 0.10
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (59 bp):
ATAAATTATTAAATTTTAATTATACTAAAATAAATCAGTAACTTTTAATTTATATCTAA
Found at i:632534 original size:23 final size:23
Alignment explanation
Indices: 632473--632534 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
632463 TTTTTTATAA
*
632473 ATTTAAA-TAATTTA-AATTATT
1 ATTTAAATTAAATTATAATTATT
* * *
632494 ATTT-AATAATAATAATAATTTTT
1 ATTTAAATTA-AATTATAATTATT
632517 ATTTAAATTAAATTATAA
1 ATTTAAATTAAATTATAA
632535 AATATATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.06
21 5 0.16
22 3 0.10
23 17 0.55
24 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTAAATTAAATTATAATTATT
Found at i:633552 original size:2 final size:2
Alignment explanation
Indices: 633545--633571 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
633535 GATTGAGATC
633545 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
633572 CTTTTTTTTT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:633898 original size:10 final size:10
Alignment explanation
Indices: 633879--633917 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
633869 TGGATATGTA
*
633879 TAAATAAATT
1 TAAATTAATT
633889 TAAATTAATT
1 TAAATTAATT
*
633899 TAATTTAATT
1 TAAATTAATT
633909 T-AATTAATT
1 TAAATTAATT
633918 ATTTAATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TAAATTAATT
Found at i:633901 original size:5 final size:5
Alignment explanation
Indices: 633885--633917 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
633875 TGTATAAATA
*
633885 AATTT AAATT AATTT AATTT AATTT AA-TT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATT
633918 ATTTAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:633985 original size:19 final size:21
Alignment explanation
Indices: 633963--634001 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
633953 ATAAAAATAT
633963 ATAAA-TATTAAAT-AATAAA
1 ATAAATTATTAAATCAATAAA
*
633982 ATAAATTTTTAAATCAATAA
1 ATAAATTATTAAATCAATAA
634002 CCTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAAATTATTAAATCAATAAA
Found at i:634504 original size:22 final size:22
Alignment explanation
Indices: 634473--634535 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
634463 CAATATGATT
634473 AATAAAATAAATAAAATATAAA
1 AATAAAATAAATAAAATATAAA
* * **
634495 AATAATATAAGTATGATATAAA
1 AATAAAATAAATAAAATATAAA
*
634517 AATATAAATATACTAAAAT
1 AATA-AAATA-AATAAAAT
634536 TTATATAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 22 0.71
23 4 0.13
24 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (22 bp):
AATAAAATAAATAAAATATAAA
Found at i:636072 original size:25 final size:24
Alignment explanation
Indices: 636044--636130 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 24
636034 TTCGATATAT
636044 ATTTAAATATAAATATAAAAATTTA
1 ATTTAAATAT-AATATAAAAATTTA
636069 ATTTTTAAATAT-ATA-AAAAATTTTA
1 A--TTTAAATATAATATAAAAA-TTTA
* * *
636094 ATATATATAT-ATATAAAAA-TAA
1 ATTTAAATATAATATAAAAATTTA
* *
636116 ATCTAAATCTAATAT
1 ATTTAAATATAATAT
636131 TTTCCTCCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 9 0.18
23 14 0.27
24 10 0.20
25 9 0.18
27 9 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTTAAATATAATATAAAAATTTA
Found at i:636086 original size:23 final size:23
Alignment explanation
Indices: 636044--636113 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 23
636034 TTCGATATAT
636044 ATTTAA-ATAT-AA-ATATAAAA
1 ATTTAATATATAAATATATAAAA
* *
636064 ATTTAATTTTTAAATATATAAAAA
1 ATTTAATATATAAATATAT-AAAA
*
636088 ATTTTAATATATATATATATAAAA
1 A-TTTAATATATAAATATATAAAA
636112 AT
1 AT
636114 AAATCTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 6 0.15
21 2 0.05
22 2 0.05
23 5 0.12
24 10 0.25
25 15 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAATATATAAATATATAAAA
Found at i:638577 original size:20 final size:20
Alignment explanation
Indices: 638538--638597 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
638528 TTTATATATT
638538 TAATAA-TTAAATTTAA-AAA
1 TAATAATTTAAA-TTAATAAA
* *
638557 TAATATTTTTAATTAATAAA
1 TAATAATTTAAATTAATAAA
*
638577 TAGTAATTTAAATTAAATAAA
1 TAATAATTTAAATT-AATAAA
638598 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 9 0.27
20 18 0.55
21 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TAATAATTTAAATTAATAAA
Found at i:638586 original size:47 final size:46
Alignment explanation
Indices: 638505--638594 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 46
638495 TAAAAAAGTT
* **
638505 AAAATATTATTTTTATATTAATATTTATATATTTAATAATTAAATTTA
1 AAAATAATATTTTTATATTAATAAATATATATTT-A-AATTAAATTTA
638553 AAAATAATATTTTTA-ATTAATAAATAGTA-ATTTAAATTAAAT
1 AAAATAATATTTTTATATTAATAAATA-TATATTTAAATTAAAT
638595 AAAATAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
45 8 0.21
46 1 0.03
47 13 0.34
48 16 0.42
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (46 bp):
AAAATAATATTTTTATATTAATAAATATATATTTAAATTAAATTTA
Found at i:638642 original size:23 final size:23
Alignment explanation
Indices: 638611--638654 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
638601 AAAAATATAA
*
638611 TATTTAATATTAAATTTTAAATT
1 TATTAAATATTAAATTTTAAATT
**
638634 TATTAAATATTATTTTTTAAA
1 TATTAAATATTAAATTTTAAA
638655 ATAATTATAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTAAATATTAAATTTTAAATT
Found at i:638661 original size:23 final size:23
Alignment explanation
Indices: 638616--638661 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
638606 TATAATATTT
* *
638616 AATATTAAATTTTAAATTTATTA
1 AATATTAAATTTTAAAATAATTA
**
638639 AATATTATTTTTTAAAATAATTA
1 AATATTAAATTTTAAAATAATTA
638662 TATAAATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTAAATTTTAAAATAATTA
Found at i:639378 original size:18 final size:17
Alignment explanation
Indices: 639344--639396 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
639334 TTTTTAAAAT
639344 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
639361 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
639378 A-TTTAT-TTTAGATAA
1 ATTTTATATTTATATAA
639393 ATTT
1 ATTT
639397 ATGTAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.10
14 3 0.10
15 4 0.13
16 5 0.16
17 7 0.23
18 6 0.19
19 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:639890 original size:44 final size:46
Alignment explanation
Indices: 639827--639925 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 46
639817 TTAAATAAAT
* *
639827 TTAATTTAATT-TTTATTTATAA-ATTAAAACATA-AT-TATTTGAA
1 TTAATTAAATTATTTATTTATAATA-TAAAAAATATATATATTTGAA
639870 TTAAATTAAATTATTT-TTTATAATATAAAAAATATATATATTTG-A
1 TT-AATTAAATTATTTATTTATAATATAAAAAATATATATATTTGAA
639915 TTAA-TAAATTA
1 TTAATTAAATTA
639926 GTGAAAACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
43 9 0.18
44 25 0.51
45 9 0.18
46 6 0.12
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (46 bp):
TTAATTAAATTATTTATTTATAATATAAAAAATATATATATTTGAA
Found at i:643459 original size:19 final size:19
Alignment explanation
Indices: 643403--643460 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
643393 ATAAATATCA
643403 TTTTA-CATCATA-TTATAT
1 TTTTATCAT-ATATTTATAT
*
643421 TTTATATTATAT-TTTAATAT
1 TTT-TATCATATATTT-ATAT
643441 TTTTATCATATATTTATAT
1 TTTTATCATATATTTATAT
643460 T
1 T
643461 GTATATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 3 0.09
19 18 0.55
20 12 0.36
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATCATATATTTATAT
Found at i:643465 original size:13 final size:13
Alignment explanation
Indices: 643415--643466 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
643405 TTACATCATA
643415 TTATATTTTATA-
1 TTATATTTTATAT
643427 TTATATTTTAATAT
1 TTATATTTT-ATAT
* **
643441 TTTTATCATATAT
1 TTATATTTTATAT
*
643454 TTATATTGTATAT
1 TTATATTTTATAT
643467 AAAATTACGA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 9 0.28
13 17 0.53
14 6 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (13 bp):
TTATATTTTATAT
Found at i:644186 original size:2 final size:2
Alignment explanation
Indices: 644179--644203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
644169 TGTCCTAATC
644179 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
644204 ACTATTTTAT
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:645653 original size:28 final size:28
Alignment explanation
Indices: 645612--645678 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
645602 AAATTATAAT
* **
645612 ATTTAATTAATAAAAATATATTTAT-TTAA
1 ATTTAATT-TTAAAAATATATAAATATT-A
*
645641 ATTTAATTTTAAAATTATATAAATATTA
1 ATTTAATTTTAAAAATATATAAATATTA
645669 ATTTAATTTT
1 ATTTAATTTT
645679 TTAATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 23 0.70
29 10 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTTAATTTTAAAAATATATAAATATTA
Found at i:650642 original size:83 final size:80
Alignment explanation
Indices: 650492--650649 Score: 217
Period size: 83 Copynumber: 1.9 Consensus size: 80
650482 ATTGGTTCAA
* * * * * *
650492 ATCAAAATCAAATGCTATGATTAGTGAAGCTAATGTTTAATTAACTTTGGGAAAAAAAACTCATG
1 ATCAAAATCAAATGCTATGATTAGAGAAGCTAACGTTCAATTAACTTGGGGAAAAAAAAATAATG
650557 ATCACTTTTAGTCTC
66 ATCACTTTTAGTCTC
* *
650572 ATCAAAATTAAATGCTATGTGATTAGAGAATCTAACGTTCAATCTAACTTGGGGAAAAAAAAATA
1 ATCAAAATCAAATGCTA--TGATTAGAGAAGCTAACGTTCAAT-TAACTTGGGGAAAAAAAAATA
650637 ATGATCACTTTTA
63 ATGATCACTTTTA
650650 ATCTGATTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
80 16 0.24
82 20 0.30
83 31 0.46
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (80 bp):
ATCAAAATCAAATGCTATGATTAGAGAAGCTAACGTTCAATTAACTTGGGGAAAAAAAAATAATG
ATCACTTTTAGTCTC
Found at i:650768 original size:123 final size:123
Alignment explanation
Indices: 650572--651202 Score: 739
Period size: 123 Copynumber: 5.0 Consensus size: 123
650562 TTTTAGTCTC
* * * *
650572 ATCAAAATTAAATGCTATGTGATTAGAGAATCTAACGTTCAATCTAACTTGGGGAAAAAAAAATA
1 ATCAAAATTAAATGCTA--TGATTAGAGAAGCTAATGTTCAATC-AACTTTGGGAAAAAAAAATC
** **
650637 ATGATCACTTTTAATCTGATTGTTCAATTATAGACACATAAAAG-TTCCAATCGTCCATAATA
63 ATGATCACTTTTAATCTGA-TGTTCAATTATAGACACATAGGAGCTT-CAATTTTCCATAATA
* * *
650699 ATCAAAATTAAATTC-ATGCTCAGAGAAGCTAATGTTCAATCAACTTTGGGAAAAAAAAATCATG
1 ATCAAAATTAAATGCTATGATTAGAGAAGCTAATGTTCAATCAACTTTGGGAAAAAAAAATCATG
* * * *
650763 ATCACTTTTAATATCATGTTCGATTATACACACATAGGAGCTTCAATTTTCCATAATA
66 ATCACTTTTAATCTGATGTTCAATTATAGACACATAGGAGCTTCAATTTTCCATAATA
* * *
650821 ATCAAAATTAAATGCTATGATTAGAGAAGCTAATGTTCAATCAACTTTGGG-GAAAGAAATCATA
1 ATCAAAATTAAATGCTATGATTAGAGAAGCTAATGTTCAATCAACTTTGGGAAAAAAAAATCATG
* *
650885 ATCACTTTTAATCTGATATTCAATTATAGACACATAGGAGCATT-AATTTTCCATCATA
66 ATCACTTTTAATCTGATGTTCAATTATAGACACATAGGAGC-TTCAATTTTCCATAATA
* *
650943 ATTCAAAATTAAAAGCTTTGATTAGAGAAGCTAATGTTCAATCAACTTTGAGGAAAAAAAATAAT
1 A-TCAAAATTAAATGCTATGATTAGAGAAGCTAATGTTCAATCAACTTTG-GG-AAAAAAA-AA-
* * * *
651008 TCATGATCACTTCTAATCTGATGTTCAATTATAGACAGACAATACGAGCTTCAGTTTTCCATCAT
61 TCATGATCACTTTTAATCTGATGTTCAATTATAGAC--AC-ATAGGAGCTTCAATTTTCCATAAT
651073 AA
123 -A
* **
651075 ATCAAAATTAAATGCTTTGATTAGAGAAGCTAATGTTCAATCAACTTTGCAAAAAAAAAAAAAAA
1 ATCAAAATTAAATGCTATGATTAGAGAAGCTAATGTTCAATCAACTTTG-----GGAAAAAAAAA
* *
651140 TCATTATCACTTTTAATCTGATGTTCAATTATAGACAGACACATAGTAGCTTCAATTTTCCAT
61 TCATGATCACTTTTAATCTGATGTTCAATTAT----AGACACATAGGAGCTTCAATTTTCCAT
651203 CTTTGATGAT
Statistics
Matches: 438, Mismatches: 44, Indels: 38
0.84 0.08 0.07
Matches are distributed among these distances:
122 107 0.24
123 118 0.27
124 23 0.05
126 5 0.01
127 16 0.04
128 33 0.08
130 4 0.01
131 66 0.15
132 32 0.07
133 20 0.05
134 9 0.02
135 1 0.00
136 4 0.01
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (123 bp):
ATCAAAATTAAATGCTATGATTAGAGAAGCTAATGTTCAATCAACTTTGGGAAAAAAAAATCATG
ATCACTTTTAATCTGATGTTCAATTATAGACACATAGGAGCTTCAATTTTCCATAATA
Found at i:651868 original size:19 final size:21
Alignment explanation
Indices: 651829--651870 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
651819 AAATATTTTA
*
651829 AAATTATTTATTGAAATTATT
1 AAATTATTTATTGAAAATATT
651850 AAATTA-TTA-TGAAAATATT
1 AAATTATTTATTGAAAATATT
651869 AA
1 AA
651871 CCGATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 3 0.15
21 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
AAATTATTTATTGAAAATATT
Found at i:653687 original size:25 final size:24
Alignment explanation
Indices: 653649--653696 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
653639 TGTACTAGTT
653649 AAAAATTATTTAAT-CAATTTTTA
1 AAAAATTATTTAATACAATTTTTA
*
653672 AAAAATTTAATTTAATACATTTTTT
1 AAAAA-TT-ATTTAATACAATTTTT
653697 TATTGAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 7 0.33
26 7 0.33
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAAATTATTTAATACAATTTTTA
Found at i:655499 original size:60 final size:60
Alignment explanation
Indices: 655431--655549 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
655421 AGTAAATAAA
* * * * *
655431 TATAATCTATATACTATATAAATTTATGTAGTTAAAATTGTGTTTAATTCATTGATTACT
1 TATAATCTATATAATATATAAATTTACGGAATTAAAATTATGTTTAATTCATTGATTACT
655491 TATAATCTATATAATATATAAATTTACGGAATTAAAATTATGTTTAATTCATTGATTAC
1 TATAATCTATATAATATATAAATTTACGGAATTAAAATTATGTTTAATTCATTGATTAC
655550 GTAACGAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (60 bp):
TATAATCTATATAATATATAAATTTACGGAATTAAAATTATGTTTAATTCATTGATTACT
Found at i:656143 original size:5 final size:5
Alignment explanation
Indices: 656116--656156 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
656106 AAAAATTTAA
* *
656116 TAATT TACTT AAATT TAAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT T-AATT TAATT TAATT TAATT TAATT
656157 AAAAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (5 bp):
TAATT
Found at i:656188 original size:16 final size:16
Alignment explanation
Indices: 656133--656321 Score: 82
Period size: 16 Copynumber: 11.6 Consensus size: 16
656123 CTTAAATTTA
**
656133 AATTT-AATTTAATTT
1 AATTTAAATTTAAAAT
*
656148 AATTT-AA-TTAAAAA
1 AATTTAAATTTAAAAT
*
656162 AATTAATAATTTAAAAT
1 AATTTA-AATTTAAAAT
**
656179 AATTTAAATTTATCAT
1 AATTTAAATTTAAAAT
*
656195 AATCTAAATTTAAAAT
1 AATTTAAATTTAAAAT
** *
656211 AATTCGAATTAAAAAT
1 AATTTAAATTTAAAAT
* **
656227 AACTTAAATAATTAATTT
1 AATTTAAAT--TTAAAAT
* * *
656245 CACTTGAATTTAAAAT
1 AATTTAAATTTAAAAT
* *
656261 AA-TTAAATTTTATA-
1 AATTTAAATTTAAAAT
656275 AATTTAAATATTAACCTAATT
1 AATTTAAAT-TTAA---AA-T
***
656296 AATTTAAAACAAAAAT
1 AATTTAAATTTAAAAT
656312 AATTTAAATT
1 AATTTAAATT
656322 AATGAAATTT
Statistics
Matches: 126, Mismatches: 36, Indels: 23
0.68 0.19 0.12
Matches are distributed among these distances:
14 10 0.08
15 22 0.17
16 59 0.47
17 13 0.10
18 11 0.09
19 1 0.01
20 2 0.02
21 8 0.06
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:656649 original size:2 final size:2
Alignment explanation
Indices: 656642--656685 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
656632 ATATTTTATG
656642 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
656684 TA
1 TA
656686 AACACAACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:657429 original size:25 final size:24
Alignment explanation
Indices: 657396--657448 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
657386 TTAATAGTAA
*
657396 TAAT-TATTTATTATATTTAAATTT
1 TAATATATTTATTATATGTAAA-TT
* *
657420 TAATATATTTTTTATGTGTAAATT
1 TAATATATTTATTATATGTAAATT
657444 TAATA
1 TAATA
657449 AATGATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (24 bp):
TAATATATTTATTATATGTAAATT
Found at i:657547 original size:28 final size:29
Alignment explanation
Indices: 657523--657579 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
657513 AAAAAATTGA
*
657523 AGTAACAACACATAACATGATAAA-TAAT
1 AGTAACAACACATAACATAATAAATTAAT
**
657551 AGTAACAATGCATAACATAATAAA-TAAT
1 AGTAACAACACATAACATAATAAATTAAT
657579 A
1 A
657580 AGATATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.58, C:0.12, G:0.07, T:0.23
Consensus pattern (29 bp):
AGTAACAACACATAACATAATAAATTAAT
Found at i:658145 original size:27 final size:26
Alignment explanation
Indices: 658103--658155 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
658093 TAAAAAAATA
658103 TAAAATAATATGAATATATAAATATTT
1 TAAAATAATATGAATATA-AAATATTT
*
658130 TAAAATAAATAT-AATATAAATTATTT
1 TAAAAT-AATATGAATATAAAATATTT
658156 AATGTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TAAAATAATATGAATATAAAATATTT
Found at i:658477 original size:14 final size:15
Alignment explanation
Indices: 658441--658508 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 15
658431 AAATTTTATT
658441 AAATTATATTATTAAA
1 AAATT-TATTATTAAA
658457 AAATTTATTATT-AA
1 AAATTTATTATTAAA
*
658471 TAATTTAAATTATTTAAA
1 AAATTT--ATTA-TTAAA
658489 ATAA-TT-TTATTAAA
1 A-AATTTATTATTAAA
*
658503 TAATTT
1 AAATTT
658509 TAATAAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
13 2 0.05
14 14 0.33
15 10 0.23
16 9 0.21
17 2 0.05
18 4 0.09
19 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATTTATTATTAAA
Found at i:658499 original size:31 final size:29
Alignment explanation
Indices: 658431--658508 Score: 81
Period size: 32 Copynumber: 2.6 Consensus size: 29
658421 CATAAAATTT
*
658431 AAATTTTATT-A-AA-TTATATTATTAAA
1 AAATTTTATTAATAATTTAAATTATTAAA
658457 AAATTTATTATTAATAATTTAAATTATTTAAA
1 AAA-TT-TTATTAATAATTTAAATTA-TTAAA
658489 ATAATTTTATTAAATAATTT
1 A-AATTTTATT-AATAATTT
658509 TAATAAAAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
26 3 0.07
27 2 0.05
28 5 0.12
29 1 0.02
30 2 0.05
31 12 0.28
32 16 0.37
33 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AAATTTTATTAATAATTTAAATTATTAAA
Found at i:660278 original size:25 final size:25
Alignment explanation
Indices: 660246--660295 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
660236 AACTCATCTA
660246 AATTTAAAAAACTTATATCCAAATT
1 AATTTAAAAAACTTATATCCAAATT
*
660271 AATTTAAAAAATTTATATCCAAATT
1 AATTTAAAAAACTTATATCCAAATT
660296 TGAATCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (25 bp):
AATTTAAAAAACTTATATCCAAATT
Found at i:660747 original size:6 final size:5
Alignment explanation
Indices: 660718--660772 Score: 58
Period size: 5 Copynumber: 10.4 Consensus size: 5
660708 ACTTTATATT
*
660718 TTAAA TTAAA TTAAA TTAAA ATAAA TATAAA -TAATA TTAAA TTTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA T-TAAA TTAA-A TTAAA -TTAAA
660765 TTTAAA TT
1 -TTAAA TT
660773 TAATACGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 3 0.07
5 23 0.52
6 18 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:661271 original size:19 final size:19
Alignment explanation
Indices: 661246--661288 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
661236 AATTTACATA
661246 ATTTATTTAAAAAAATATT
1 ATTTATTTAAAAAAATATT
* *
661265 TTTTATTTAAATAAATATT
1 ATTTATTTAAAAAAATATT
661284 ATTTA
1 ATTTA
661289 CGGTTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATTTAAAAAAATATT
Found at i:662187 original size:28 final size:27
Alignment explanation
Indices: 662140--662192 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
662130 AAATTTATAT
* * *
662140 AAATATAAAATATTTTAAACGTAATTA
1 AAATATAAAAAATTATAAACATAATTA
662167 AAATATAAAAAATATATAAACATAAT
1 AAATATAAAAAAT-TATAAACATAAT
662193 ACGAATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (27 bp):
AAATATAAAAAATTATAAACATAATTA
Found at i:662470 original size:2 final size:2
Alignment explanation
Indices: 662463--662495 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
662453 GAATATGAAT
662463 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 T
662496 GTGTATGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:665692 original size:30 final size:31
Alignment explanation
Indices: 665649--665712 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
665639 TCAAAATTAA
* *
665649 AAAAATAAAAATAAAATTATTTTTTAAAATT
1 AAAAATAAAAATAAAAATATTTTTTAAAACT
*
665680 AAAAAT-AAAATAAAAATATTTTTTCAAACT
1 AAAAATAAAAATAAAAATATTTTTTAAAACT
665710 AAA
1 AAA
665713 CGGAGTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAAATAAAAATAAAAATATTTTTTAAAACT
Found at i:666295 original size:2 final size:2
Alignment explanation
Indices: 666290--666322 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
666280 CTTTGGTGTG
666290 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 T
666323 TGGGTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:666770 original size:16 final size:16
Alignment explanation
Indices: 666750--666782 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
666740 CTTTAAAATT
666750 AATATA-ATTAA-TAA
1 AATATATATTAACTAA
666764 AATATATATTAACTAA
1 AATATATATTAACTAA
666780 AAT
1 AAT
666783 TCGCATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 5 0.29
16 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATATATTAACTAA
Found at i:667139 original size:2 final size:2
Alignment explanation
Indices: 667132--667158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
667122 TATTCATCTT
667132 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
667159 GCATATGGAT
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:668719 original size:8 final size:8
Alignment explanation
Indices: 668694--668750 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
668684 CATAAATATA
668694 AATAATTAT
1 AATAATT-T
*
668703 AAAAATTT
1 AATAATTT
668711 AATAATTT
1 AATAATTT
668719 AATAATTT
1 AATAATTT
*
668727 ATATTATTT
1 A-ATAATTT
*
668736 TATAATATT
1 AATAAT-TT
668745 -ATAATT
1 AATAATT
668751 ATTTTTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
7 1 0.02
8 26 0.63
9 14 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
AATAATTT
Found at i:668774 original size:11 final size:10
Alignment explanation
Indices: 668724--668771 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
668714 AATTTAATAA
668724 TTTATATTAT
1 TTTATATTAT
*
668734 TTTATAATAT
1 TTTATATTAT
*
668744 TATA-ATTATT
1 TTTATATTA-T
*
668754 TTTAAATTAT
1 TTTATATTAT
668764 TTTATATT
1 TTTATATT
668772 TATATTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 3 0.10
10 24 0.77
11 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTATATTAT
Found at i:668850 original size:8 final size:8
Alignment explanation
Indices: 668839--668865 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
668829 TATTGTATCC
668839 ATAATTTT
1 ATAATTTT
668847 ATAATTTT
1 ATAATTTT
668855 ATAATTTT
1 ATAATTTT
668863 ATA
1 ATA
668866 TTATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATAATTTT
Found at i:676587 original size:3 final size:3
Alignment explanation
Indices: 676579--676627 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
676569 TGCATGAACA
676579 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
676627 T
1 T
676628 ATTATTATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:679310 original size:19 final size:19
Alignment explanation
Indices: 679266--679315 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
679256 ATATAAATAT
* * *
679266 ATAAATATGTTAAAATTTAT
1 ATAAATAT-ATAAAATATAA
679286 AT-AATATATAAAATATAA
1 ATAAATATATAAAATATAA
679304 ATAAATATATAA
1 ATAAATATATAA
679316 CTAATTAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 10 0.38
19 14 0.54
20 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAATATATAAAATATAA
Found at i:681846 original size:25 final size:25
Alignment explanation
Indices: 681818--681865 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
681808 TAGTATTATT
681818 TATTATTTTTAAAAAATTTTAAAAC
1 TATTATTTTTAAAAAATTTTAAAAC
* *
681843 TATTATTTTTATAATATTTTAAA
1 TATTATTTTTAAAAAATTTTAAA
681866 GTTGTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTATTTTTAAAAAATTTTAAAAC
Found at i:684509 original size:27 final size:25
Alignment explanation
Indices: 684463--684516 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
684453 ATTTATTAAT
684463 AATATTTAATATAATAAATTATAAC
1 AATATTTAATATAATAAATTATAAC
* *
684488 AATATTTATTATATTTATAATTATAAC
1 AATATTTAATATA-ATA-AATTATAAC
684515 AA
1 AA
684517 AATAGATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.48
26 2 0.08
27 11 0.44
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
AATATTTAATATAATAAATTATAAC
Found at i:684941 original size:23 final size:23
Alignment explanation
Indices: 684915--684964 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
684905 TGATTAGTTA
684915 ATTTTGATCAAAATTAAAATAAT
1 ATTTTGATCAAAATTAAAATAAT
* ** *
684938 ATTTTTATTTAAATTTAAATAAT
1 ATTTTGATCAAAATTAAAATAAT
684961 -TTTT
1 ATTTT
684965 ATATTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTTGATCAAAATTAAAATAAT
Found at i:684969 original size:23 final size:24
Alignment explanation
Indices: 684925--684975 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
684915 ATTTTGATCA
684925 AAATTAAAATAATATTTTTA-TTT
1 AAATTAAAATAATATTTTTATTTT
*
684948 AAATTTAAATAAT-TTTTATATTTT
1 AAATTAAAATAATATTTT-TATTTT
684972 AAAT
1 AAAT
684976 AATATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 4 0.16
23 14 0.56
24 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATTAAAATAATATTTTTATTTT
Found at i:685299 original size:21 final size:22
Alignment explanation
Indices: 685274--685321 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
685264 AGTTCATTCA
*
685274 TTAATTTTTTT-AATGTATTTT
1 TTAATTTTTTTAAATGTAATTT
*
685295 TTAATTTTTTTAAATTTAATTT
1 TTAATTTTTTTAAATGTAATTT
685317 TTAAT
1 TTAAT
685322 AATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTAATTTTTTTAAATGTAATTT
Found at i:686057 original size:41 final size:40
Alignment explanation
Indices: 685998--686085 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 40
685988 GGGTTAAATT
*
685998 TTTTATTTAATTTAAATTACT-AT-TT-ATATAATAAAATAATA
1 TTTTATTTAAATTAAATTA-TAATATTAATAT-A-AAAATAA-A
686039 TTTTATTTAAAATT-AATTATAATATTAATATAAAAATAAA
1 TTTTATTT-AAATTAAATTATAATATTAATATAAAAATAAA
686079 TTTTATT
1 TTTTATT
686086 ATTATTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
40 9 0.21
41 22 0.52
42 7 0.17
43 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (40 bp):
TTTTATTTAAATTAAATTATAATATTAATATAAAAATAAA
Found at i:687312 original size:2 final size:2
Alignment explanation
Indices: 687305--687363 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
687295 ATGATCTAAT
* * * * * *
687305 TA TA TA TA TA TA TA CA TG TT TG TG TA TA TA -A GA 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
687346 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
687364 GCTCTCATCG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (2 bp):
TA
Found at i:687647 original size:20 final size:22
Alignment explanation
Indices: 687622--687662 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
687612 ATTTAAAAAA
687622 AAAATTACATA-A-TTATATTT
1 AAAATTACATATATTTATATTT
*
687642 AAAATTATATATATTTATATT
1 AAAATTACATATATTTATATT
687663 ATATTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATTACATATATTTATATTT
Found at i:687666 original size:5 final size:5
Alignment explanation
Indices: 687645--687692 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
687635 TATATTTAAA
687645 ATTAT A-TAT ATTTAT ATTAT ATTAT AATTAT -TTAT ATTAT ATTAT ATT
1 ATTAT ATTAT A-TTAT ATTAT ATTAT -ATTAT ATTAT ATTAT ATTAT ATT
687693 TAAAATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.21
5 22 0.56
6 9 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:687670 original size:20 final size:21
Alignment explanation
Indices: 687645--687691 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
687635 TATATTTAAA
687645 ATTATATA-TATTTATATTAT
1 ATTATATATTATTTATATTAT
687665 ATTATA-ATTATTTATATTAT
1 ATTATATATTATTTATATTAT
687685 ATTATAT
1 ATTATAT
687692 TTAAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTATATATTATTTATATTAT
Found at i:688409 original size:22 final size:20
Alignment explanation
Indices: 688380--688430 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
688370 ATGAGGGATA
688380 TTTAATAAATTTATAATTTAT
1 TTTAATAAA-TTATAATTTAT
*
688401 TATTAAT-AATTGTAATTTAT
1 T-TTAATAAATTATAATTTAT
688421 TTTATATAAA
1 TTTA-ATAAA
688431 AAATAGAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 5 0.19
22 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTAATAAATTATAATTTAT
Found at i:688944 original size:29 final size:29
Alignment explanation
Indices: 688883--688944 Score: 67
Period size: 29 Copynumber: 2.1 Consensus size: 29
688873 ATGATTTTTT
*
688883 ATATAGTTTTTATTTATTTAATTTGATCG
1 ATATAGTTTTTATTTATTTAATTAGATCG
688912 ATATA-TTTTATATTTTATTT-ATATAGATC-
1 ATATAGTTTT-TA-TTTATTTAAT-TAGATCG
688941 ATAT
1 ATAT
688945 TTATTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
28 4 0.14
29 13 0.45
30 12 0.41
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (29 bp):
ATATAGTTTTTATTTATTTAATTAGATCG
Found at i:689982 original size:2 final size:2
Alignment explanation
Indices: 689977--690010 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
689967 GTATACACAC
689977 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
690011 CATAATAATA
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:690510 original size:27 final size:26
Alignment explanation
Indices: 690479--690551 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
690469 AAAAGCCACC
*
690479 CTTTGTGTTTGTCAAAAATGGT-AGTT
1 CTTTGTGTTTGTCAAAAATAGTGA-TT
* *
690505 ACTTTGTATTTGTAAAAAATAGTGATT
1 -CTTTGTGTTTGTCAAAAATAGTGATT
*
690532 CTTTTTTGTTTGTCAAAAAT
1 C-TTTGTGTTTGTCAAAAAT
690552 TGTGGCTTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 36 0.95
28 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (26 bp):
CTTTGTGTTTGTCAAAAATAGTGATT
Found at i:690569 original size:24 final size:24
Alignment explanation
Indices: 690537--690582 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
690527 TGATTCTTTT
690537 TTGTTTGTCAAAAATT-GTGGCTTG
1 TTGTTTGTC-AAAATTGGTGGCTTG
690561 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTCAAAATTGGTGGCT
690583 AATATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.20, C:0.09, G:0.26, T:0.46
Consensus pattern (24 bp):
TTGTTTGTCAAAATTGGTGGCTTG
Found at i:694740 original size:27 final size:27
Alignment explanation
Indices: 694709--694781 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
694699 AAAAGCCACC
* *
694709 CTTTGTGTTTGTCAAAAATAGTGGTTA
1 CTTTGTGTTTGTAAAAAATAGTGATTA
* * *
694736 CTTTGTATTTGTTAAAAATAGTGATTC
1 CTTTGTGTTTGTAAAAAATAGTGATTA
* *
694763 CTTTTTGTTTATAAAAAAT
1 CTTTGTGTTTGTAAAAAAT
694782 TATGGCTTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (27 bp):
CTTTGTGTTTGTAAAAAATAGTGATTA
Found at i:695726 original size:22 final size:22
Alignment explanation
Indices: 695687--695733 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
695677 ATATATATAA
*
695687 ATAAAGATAAATAGATACACAT
1 ATAAAAATAAATAGATACACAT
* * *
695709 ATAAAAATACATATATACATAT
1 ATAAAAATAAATAGATACACAT
695731 ATA
1 ATA
695734 CATATTGAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.28
Consensus pattern (22 bp):
ATAAAAATAAATAGATACACAT
Found at i:697326 original size:2 final size:2
Alignment explanation
Indices: 697313--697348 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
697303 GAAGGAAAGC
*
697313 AT AT AT AC 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
697349 TGCAATATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:697404 original size:54 final size:54
Alignment explanation
Indices: 697323--697443 Score: 233
Period size: 54 Copynumber: 2.2 Consensus size: 54
697313 ATATATACAT
*
697323 ATATATATATATATATATATATATATTGCAATATCCACTAAAAATCTTTCTGCC
1 ATATATGTATATATATATATATATATTGCAATATCCACTAAAAATCTTTCTGCC
697377 ATATATGTATATATATATATATATATTGCAATATCCACTAAAAATCTTTCTGCC
1 ATATATGTATATATATATATATATATTGCAATATCCACTAAAAATCTTTCTGCC
697431 ATATATGTATATA
1 ATATATGTATATA
697444 AATGCGTCCT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.41
Consensus pattern (54 bp):
ATATATGTATATATATATATATATATTGCAATATCCACTAAAAATCTTTCTGCC
Found at i:699221 original size:19 final size:20
Alignment explanation
Indices: 699184--699235 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
699174 TTTTTGCTAG
* *
699184 ATAATTAAA-ATATTATTTT
1 ATAATTAAATTTAATATTTT
*
699203 AT-ATTAATTTTAATATTTT
1 ATAATTAAATTTAATATTTT
699222 ATAATTAAATTTAA
1 ATAATTAAATTTAA
699236 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAATTAAATTTAATATTTT
Found at i:699238 original size:21 final size:19
Alignment explanation
Indices: 699197--699243 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 19
699187 ATTAAAATAT
*
699197 TATTTTATATTAATTTTAA
1 TATTTTATATTAATTTAAA
699216 TATTTTATAATTAAATTTAAA
1 TATTTTAT-ATT-AATTTAAA
699237 TAATTTT
1 T-ATTTT
699244 TTTATTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 3 0.12
21 8 0.33
22 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTATATTAATTTAAA
Found at i:700042 original size:14 final size:14
Alignment explanation
Indices: 700023--700070 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
700013 CTATCATTAG
700023 TTTATTAATTTATA
1 TTTATTAATTTATA
*
700037 TTTATTAATTTTATT
1 TTTATTAA-TTTATA
*
700052 TTTATTAATATATA
1 TTTATTAATTTATA
700066 TTTAT
1 TTTAT
700071 CATTCATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTAATTTATA
Found at i:700892 original size:32 final size:33
Alignment explanation
Indices: 700834--700909 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
700824 TAATACGAAA
*
700834 ATAATATAAATATATAAATATTTTAAAA-TTTAT
1 ATAATATAAATATATAAATATATTAAAACTTT-T
*
700867 ATAATATAAAT-TATTAATATATTAAAACTTTT
1 ATAATATAAATATATAAATATATTAAAACTTTT
700899 ATAAATATAAA
1 AT-AATATAAA
700910 ATACTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 17 0.44
33 22 0.56
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
ATAATATAAATATATAAATATATTAAAACTTTT
Found at i:701150 original size:24 final size:22
Alignment explanation
Indices: 701118--701162 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
701108 AAAATAATAA
701118 TTTAAATATTAAAATTATAAAATT
1 TTTAAATATT-AAATTA-AAAATT
701142 TTTAAATATTAAATTAAAAAT
1 TTTAAATATTAAATTAAAAAT
701163 AATTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.24
23 6 0.29
24 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAAATATTAAATTAAAAATT
Found at i:701682 original size:28 final size:30
Alignment explanation
Indices: 701615--701685 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
701605 TTATATTTAT
701615 TATTT-ATAATTAAA--AAAATAAAAATAA
1 TATTTAATAATTAAATCAAAATAAAAATAA
*
701642 TATTTTATAATTAAATCAAAATAAAAAT-A
1 TATTTAATAATTAAATCAAAATAAAAATAA
*
701671 T-TTTAATTATTAAAT
1 TATTTAATAATTAAAT
701686 ATTAATTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.13
28 21 0.54
29 2 0.05
30 11 0.28
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
TATTTAATAATTAAATCAAAATAAAAATAA
Found at i:702245 original size:22 final size:22
Alignment explanation
Indices: 702206--702277 Score: 83
Period size: 22 Copynumber: 3.1 Consensus size: 22
702196 TAAAAAATAA
702206 AATATTTAAAAATATTTTTATATT
1 AATATTT--AAATATTTTTATATT
*
702230 AATATTTATATATTTTTATAATT
1 AATATTTAAATATTTTTAT-ATT
*
702253 AA-ATTTAAATAATTTTTTTATT
1 AATATTTAAAT-ATTTTTATATT
702275 AAT
1 AAT
702278 TAAATAATGA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 23 0.55
23 12 0.29
24 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATATTTAAATATTTTTATATT
Found at i:702864 original size:17 final size:16
Alignment explanation
Indices: 702804--702861 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
702794 AAAATTAAAT
*
702804 ATAAATTAAATAATTTTA
1 ATAAAATAAAT-A-TTTA
*
702822 ATATCAAATAAATATTAA
1 ATA--AAATAAATATTTA
*
702840 ATATAATAAATATTTA
1 ATAAAATAAATATTTA
702856 ATAAAA
1 ATAAAA
702862 ATATACATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 16 0.48
18 9 0.27
19 1 0.03
20 7 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAATAAATATTTA
Found at i:703999 original size:25 final size:26
Alignment explanation
Indices: 703949--704001 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
703939 AAATAATATT
*
703949 AATTCAATAAAATAATTTATAAAAAA
1 AATTCAATAAAATAATTTAGAAAAAA
* *
703975 AATT-AATAAAATTA-TTAGAATAAA
1 AATTCAATAAAATAATTTAGAAAAAA
703999 AAT
1 AAT
704002 AAAGTTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 9 0.38
26 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AATTCAATAAAATAATTTAGAAAAAA
Found at i:704129 original size:44 final size:44
Alignment explanation
Indices: 704074--704158 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
704064 AATTACTTAA
*
704074 TTTTTACTAAAAAAATT-ATCCGCCTTCTACATAAAAAAAATTAC
1 TTTTTACTAAAAAAATTGAT-CACCTTCTACATAAAAAAAATTAC
* *
704118 TTTTTACTAAAAAAATTGATCACCTTCTACTTGAAAAAAAT
1 TTTTTACTAAAAAAATTGATCACCTTCTACATAAAAAAAAT
704159 ATATTTCTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.95
45 2 0.05
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (44 bp):
TTTTTACTAAAAAAATTGATCACCTTCTACATAAAAAAAATTAC
Found at i:704148 original size:23 final size:23
Alignment explanation
Indices: 704081--704158 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 23
704071 TAATTTTTAC
*
704081 TAAAAAAATTATCCGCCTTCTACA
1 TAAAAAAATTAT-CACCTTCTACA
* * *
704105 TAAAAAAA--ATTACTTTTTAC-
1 TAAAAAAATTATCACCTTCTACA
*
704125 TAAAAAAATTGATCACCTTCTACT
1 TAAAAAAATT-ATCACCTTCTACA
704149 TGAAAAAAAT
1 T-AAAAAAAT
704159 ATATTTCTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 8 0.19
21 6 0.14
22 2 0.05
23 9 0.21
24 9 0.21
25 8 0.19
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAAAAAATTATCACCTTCTACA
Found at i:704327 original size:2 final size:2
Alignment explanation
Indices: 704322--704346 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
704312 TTTTTTAATC
704322 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
704347 GAAAAAATGA
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:704494 original size:2 final size:2
Alignment explanation
Indices: 704487--704514 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
704477 CTCCTATCAA
704487 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
704515 GTGTGTGAAA
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:704600 original size:15 final size:16
Alignment explanation
Indices: 704582--704619 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
704572 TAATTTATAT
*
704582 TATTTAAATTTAAA-A
1 TATTTAAATATAAATA
704597 TA-TTAAATATAAATA
1 TATTTAAATATAAATA
704612 TATTTAAA
1 TATTTAAA
704620 AAATTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 10 0.50
15 5 0.25
16 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTAAATATAAATA
Found at i:705542 original size:7 final size:7
Alignment explanation
Indices: 705513--705559 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
705503 TAATAACTTT
705513 TATTATA
1 TATTATA
705520 TATTA-A
1 TATTATA
* *
705526 TAATAAA
1 TATTATA
705533 TATTATA
1 TATTATA
705540 TATTATA
1 TATTATA
705547 TTATATATA
1 -TAT-TATA
705556 TATT
1 TATT
705560 TATTATAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
6 5 0.15
7 19 0.56
8 6 0.18
9 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TATTATA
Found at i:706133 original size:21 final size:21
Alignment explanation
Indices: 706108--706195 Score: 99
Period size: 21 Copynumber: 4.0 Consensus size: 21
706098 ATTTTAAAAA
706108 ATATTTT-TAATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
706129 ATATTTTATAATTAAATTTAAAT
1 ATATTTTATAATTAAATTT--AT
706152 AAAATATTTT-TAATTAATATTTAT
1 ---ATATTTTATAATTAA-ATTTAT
706176 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
706196 AATAAAAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
21 23 0.39
22 14 0.24
23 2 0.03
24 2 0.03
25 7 0.12
26 11 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:706143 original size:26 final size:26
Alignment explanation
Indices: 706114--706190 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 26
706104 AAAAATATTT
706114 TTAATTAATATTTATATATTTTATAA
1 TTAATTAATATTTATATATTTTATAA
* *
706140 TTAAATTTAA-A--TA-AAATATT-T--
1 TT-AA-TTAATATTTATATATTTTATAA
706161 TTAATTAATATTTATATATTTTATAA
1 TTAATTAATATTTATATATTTTATAA
706187 TTAA
1 TTAA
706191 ATTTAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 2 0.05
22 2 0.05
23 6 0.16
24 6 0.16
25 2 0.05
26 6 0.16
27 3 0.08
28 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTAATTAATATTTATATATTTTATAA
Found at i:706158 original size:28 final size:26
Alignment explanation
Indices: 706129--706218 Score: 102
Period size: 21 Copynumber: 3.6 Consensus size: 26
706119 TAATATTTAT
706129 ATATTTTATAATTAAATTTAAATAAA
1 ATATTTTATAATTAAATTTAAATAAA
706155 ATATTTT-TAATTAATATTT--AT---
1 ATATTTTATAATTAA-ATTTAAATAAA
706176 ATATTTTATAATTAAATTTAAATAAAA
1 ATATTTTATAATTAAATTTAAAT-AAA
*
706203 ATATTATTTTAATTAA
1 ATATT-TTATAATTAA
706219 TAAATAATAA
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
21 11 0.20
22 7 0.13
23 2 0.04
24 2 0.04
25 7 0.13
26 11 0.20
27 5 0.09
28 9 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATTTTATAATTAAATTTAAATAAA
Found at i:706162 original size:47 final size:48
Alignment explanation
Indices: 706104--706241 Score: 210
Period size: 47 Copynumber: 2.9 Consensus size: 48
706094 AAATATTTTA
706104 AAAAATATTTTTAATTAATATTTATATATTTTATAATTAAATTTAAAT
1 AAAAATATTTTTAATTAATATTTATATATTTTATAATTAAATTTAAAT
706152 -AAAATATTTTTAATTAATATTTATATATTTTATAATTAAATTTAAAT
1 AAAAATATTTTTAATTAATATTTATATATTTTATAATTAAATTTAAAT
** *
706199 AAAAATATTATTTTAATTAATAAATA-ATAATTTA-AATTAAATT
1 AAAAATA-T-TTTTAATTAATATTTATATATTTTATAATTAAATT
706242 AATCAACCAA
Statistics
Matches: 84, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
47 47 0.56
48 15 0.18
49 8 0.10
50 14 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (48 bp):
AAAAATATTTTTAATTAATATTTATATATTTTATAATTAAATTTAAAT
Found at i:706236 original size:20 final size:18
Alignment explanation
Indices: 706190--706239 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
706180 TTTATAATTA
706190 AATTTAAA-TAAAAATAT
1 AATTTAAATTAAAAATAT
* *
706207 TATTTTAATTAATAAATAAT
1 AATTTAAATTAA-AAAT-AT
706227 AATTTAAATTAAA
1 AATTTAAATTAAA
706240 TTAATCAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.23
18 3 0.12
19 5 0.19
20 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTAAATTAAAAATAT
Found at i:706241 original size:25 final size:25
Alignment explanation
Indices: 706180--706244 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
706170 ATTTATATAT
706180 TTTATAATTAAATT--TAAATAAAAA
1 TTTA-AATTAAATTAATAAATAAAAA
* * *
706204 TATT-ATTTTAATTAATAAATAATAA
1 T-TTAAATTAAATTAATAAATAAAAA
706229 TTTAAATTAAATTAAT
1 TTTAAATTAAATTAAT
706245 CAACCAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
23 7 0.22
24 3 0.09
25 22 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTAAATTAAATTAATAAATAAAAA
Found at i:706407 original size:3 final size:3
Alignment explanation
Indices: 706399--706433 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
706389 GAGGTAGATA
*
706399 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
706434 GTTCATTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:707254 original size:2 final size:2
Alignment explanation
Indices: 707249--707301 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
707239 GTGAAGAAGG
707249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
707291 AT AT AT AT AT A
1 AT AT AT AT AT A
707302 CTTCTTGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:708440 original size:2 final size:2
Alignment explanation
Indices: 708433--708467 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
708423 ACCAACTGCT
708433 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
708468 TTTGAATTTA
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:708732 original size:2 final size:2
Alignment explanation
Indices: 708725--708750 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
708715 GACATGTCTG
708725 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
708751 GCTTTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:708993 original size:2 final size:2
Alignment explanation
Indices: 708988--709017 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
708978 CCAAAAAAGG
708988 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
709018 GCACCTTGCT
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:711403 original size:26 final size:26
Alignment explanation
Indices: 711374--711452 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 26
711364 AATTTTTTTA
*
711374 TTTAAAAAATTATTAAAATATTAATT
1 TTTAAAAAATAATTAAAATATTAATT
** * *
711400 TTTATTAGATAATTAAAATATTCATT
1 TTTAAAAAATAATTAAAATATTAATT
*** *
711426 TTTTCTATATAATTAAAATATT-ATT
1 TTTAAAAAATAATTAAAATATTAATT
711451 TT
1 TT
711453 ATATTAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 5 0.11
26 40 0.89
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (26 bp):
TTTAAAAAATAATTAAAATATTAATT
Found at i:711461 original size:22 final size:24
Alignment explanation
Indices: 711385--711461 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 24
711375 TTAAAAAATT
*
711385 ATTAAAATATTAATTTTTATTAGATA
1 ATTAAAATATTAATTTTTA-TA-TTA
* *
711411 ATTAAAATATTCATTTTTTCTATATA
1 ATTAAAATATT-AATTTTTATAT-TA
711437 ATTAAAATATT-A-TTTTATATTA
1 ATTAAAATATTAATTTTTATATTA
711459 ATT
1 ATT
711462 TTAATATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 5 0.11
23 7 0.16
26 26 0.59
27 6 0.14
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (24 bp):
ATTAAAATATTAATTTTTATATTA
Found at i:711469 original size:19 final size:19
Alignment explanation
Indices: 711433--711484 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
711423 ATTTTTTCTA
711433 TATAATTAAAATATT-AT-TT
1 TATAATT-AAAT-TTAATATT
*
711452 TAT-ATTAATTTTAATATT
1 TATAATTAAATTTAATATT
711470 TATAATTAAATTTAA
1 TATAATTAAATTTAA
711485 ATAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 2 0.07
17 5 0.18
18 8 0.29
19 13 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAATTAAATTTAATATT
Found at i:712563 original size:30 final size:29
Alignment explanation
Indices: 712527--712599 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 29
712517 TTATTATTTT
*
712527 TTAAAAAATTATTTAAGTATAAATTAAAAA
1 TTAAAAATTTATTTAAG-ATAAATTAAAAA
* *
712557 TTAAAAATTTATTTTGAGGTAAATTAAAAA
1 TTAAAAATTTA-TTTAAGATAAATTAAAAA
712587 TTAAAAATTTATT
1 TTAAAAATTTATT
712600 CAAAATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.05
30 32 0.82
31 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (29 bp):
TTAAAAATTTATTTAAGATAAATTAAAAA
Found at i:712624 original size:27 final size:26
Alignment explanation
Indices: 712581--712633 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
712571 TGAGGTAAAT
712581 TAAAAATTAAAAATTTATTCAAAATAA
1 TAAAAATTAAAAATTTA-TCAAAATAA
* *
712608 TAAAATATT-AAAGTTTATCTAAATAA
1 TAAAA-ATTAAAAATTTATCAAAATAA
712634 AATAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 12 0.52
28 3 0.13
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAAAATTAAAAATTTATCAAAATAA
Found at i:713139 original size:24 final size:24
Alignment explanation
Indices: 713112--713162 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
713102 ATACTACACG
713112 AAAAAAATAAT-TAAAATATAAAAT
1 AAAAAAATAATATAAAA-ATAAAAT
* * *
713136 AAAAATATGATATAAAAATAATAT
1 AAAAAAATAATATAAAAATAAAAT
713160 AAA
1 AAA
713163 TATAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAAAAATAATATAAAAATAAAAT
Found at i:713142 original size:22 final size:22
Alignment explanation
Indices: 713114--713173 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
713104 ACTACACGAA
713114 AAAAATAAT-TAAAATATAAAAT
1 AAAAATAATATAAAA-ATAAAAT
*
713136 AAAAATATGATATAAAAATAATAT
1 AAAAATA--ATATAAAAATAAAAT
*
713160 AAATATAATATAAA
1 AAAAATAATATAAA
713174 TATCTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 14 0.42
24 14 0.42
25 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAATAATATAAAAATAAAAT
Done.