Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 5 of 32
Found at i:510950 original size:102 final size:101
Alignment explanation
Indices: 510805--511022 Score: 328
Period size: 102 Copynumber: 2.1 Consensus size: 101
510795 AAGTGGGAGA
*** * * * * *
510805 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGAAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
510870 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
510906 ATTGTTGATTAAATGAAAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-AAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
510971 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
511008 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
511023 GTGGTTTTTA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGAAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:511518 original size:11 final size:11
Alignment explanation
Indices: 511502--511535 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
511492 TATTATTTTA
*
511502 AATATAATTAT
1 AATATAAATAT
511513 AATATAAATAT
1 AATATAAATAT
511524 AATATAAATAT
1 AATATAAATAT
511535 A
1 A
511536 TAAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATAAATAT
Found at i:511522 original size:17 final size:16
Alignment explanation
Indices: 511500--511548 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
511490 TATATTATTT
511500 TAAATATAATTATAATA
1 TAAATATAATTATAA-A
511517 TAAATATAA-TATAAA
1 TAAATATAATTATAAA
*
511532 TATATA-AATTATTAAA
1 TAAATATAATTA-TAAA
511548 T
1 T
511549 TTATGGTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.07
15 8 0.28
16 10 0.34
17 9 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATATAATTATAAA
Found at i:511815 original size:5 final size:5
Alignment explanation
Indices: 511805--511859 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
511795 AAAAAATTAA
*
511805 AATAT AATAT AATAT -ATAAT AATA- AAAAT AATAT AAATAT AATAT AA-AT
1 AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT -AATAT AATAT AATAT
511854 -ATAT AA
1 AATAT AA
511860 ATTTATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
3 1 0.02
4 9 0.21
5 25 0.60
6 7 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:511846 original size:11 final size:11
Alignment explanation
Indices: 511804--511856 Score: 79
Period size: 11 Copynumber: 4.6 Consensus size: 11
511794 TAAAAAATTA
511804 AAATATAATAT
1 AAATATAATAT
511815 AATATATAATAAT
1 AA-ATATAAT-AT
*
511828 AAAAATAATAT
1 AAATATAATAT
511839 AAATATAATAT
1 AAATATAATAT
511850 AAATATA
1 AAATATA
511857 TAAATTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 21 0.55
12 13 0.34
13 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATAATAT
Found at i:511854 original size:17 final size:17
Alignment explanation
Indices: 511804--511946 Score: 59
Period size: 19 Copynumber: 8.3 Consensus size: 17
511794 TAAAAAATTA
511804 AAATAT-AATATAATAT
1 AAATATAAATATAATAT
*
511820 ATAATAATAAAAATAATAT
1 A-AAT-ATAAATATAATAT
*
511839 AAATATAATATAAATATAT
1 AAATATAA-ATATA-ATAT
*
511858 AAATTTATTAAAT-TTATAT
1 AAA--TA-TAAATATAATAT
*
511877 AAA-ATAAAT-TATTAT
1 AAATATAAATATAATAT
* *
511892 -AATATTAAA-ATTTATTT
1 AAATA-TAAATA-TAATAT
*
511909 AAATAT-AATAT-TTAT
1 AAATATAAATATAATAT
* *
511924 AAATATAATTAAAATAT
1 AAATATAAATATAATAT
511941 ATAATA
1 A-AATA
511947 ATCTATAAAC
Statistics
Matches: 95, Mismatches: 15, Indels: 32
0.67 0.11 0.23
Matches are distributed among these distances:
14 2 0.02
15 18 0.19
16 12 0.13
17 16 0.17
18 16 0.17
19 24 0.25
21 4 0.04
22 3 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATAAATATAATAT
Found at i:511871 original size:9 final size:10
Alignment explanation
Indices: 511835--511879 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
511825 AATAAAAATA
*
511835 ATATAAATATA
1 ATATAAAT-TT
511846 ATATAAA--T
1 ATATAAATTT
511854 ATATAAATTT
1 ATATAAATTT
511864 AT-TAAATTT
1 ATATAAATTT
511873 ATATAAA
1 ATATAAA
511880 ATAAATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 7 0.23
9 9 0.30
10 7 0.23
11 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATAAATTT
Found at i:511884 original size:32 final size:31
Alignment explanation
Indices: 511841--511944 Score: 79
Period size: 32 Copynumber: 3.2 Consensus size: 31
511831 AATAATATAA
*
511841 ATATAATATAAATATATAAATTTATTAAATTT
1 ATATAAAATAAAT-TATAAATTTATTAAATTT
511873 ATATAAAATAAATTATTATAA--TATTAAAATTT
1 ATATAAAATAAATTA-TA-AATTTATT-AAATTT
* * *
511905 ATTTAAATATAATATTTATAAATATAATTAAA-AT
1 ATATAAA-ATAA-A-TTATAAAT-TTATTAAATTT
511939 ATATAA
1 ATATAA
511945 TAATCTATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
31 6 0.10
32 26 0.45
33 8 0.14
34 9 0.16
35 6 0.10
36 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATAAAATAAATTATAAATTTATTAAATTT
Found at i:511938 original size:26 final size:23
Alignment explanation
Indices: 511889--511941 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
511879 AATAAATTAT
* *
511889 TATAATATTAAAATTTATTTAAA
1 TATAATATTAAAATTAATTAAAA
511912 TATAATATTTATAAATATAATTAAAA
1 TATAATA-TTA-AAAT-TAATTAAAA
511938 TATA
1 TATA
511942 TAATAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 3 0.12
25 4 0.16
26 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAATTAATTAAAA
Found at i:512872 original size:3 final size:3
Alignment explanation
Indices: 512864--512892 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
512854 CTAGGAATGT
512864 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
512893 TTCTTGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:513255 original size:26 final size:26
Alignment explanation
Indices: 513226--513281 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
513216 AATAATTAAG
* *
513226 AAAAATTTAAGAAAATCATAAAAAGT
1 AAAAATATAAAAAAATCATAAAAAGT
** *
513252 AAAAATATAAAAAAATGTTAAAAATT
1 AAAAATATAAAAAAATCATAAAAAGT
513278 AAAA
1 AAAA
513282 TAATAATATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (26 bp):
AAAAATATAAAAAAATCATAAAAAGT
Found at i:513607 original size:28 final size:27
Alignment explanation
Indices: 513573--513637 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 27
513563 ATTATATATA
513573 TTATTAAATTATCAAATCTATTAACTTT
1 TTATTAAATTATCAAATCTATTAA-TTT
* *
513601 TTATTAAAATATTAAATCTATTAATTT
1 TTATTAAATTATCAAATCTATTAATTT
513628 TTAATTAAAT
1 TT-ATTAAAT
513638 CAATTGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
TTATTAAATTATCAAATCTATTAATTT
Found at i:513716 original size:8 final size:7
Alignment explanation
Indices: 513688--513712 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
513678 AATTTGAAGT
513688 AAATAAA
1 AAATAAA
513695 AAATAAA
1 AAATAAA
513702 AAATAAA
1 AAATAAA
513709 AAAT
1 AAAT
513713 TAAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:521703 original size:16 final size:18
Alignment explanation
Indices: 521671--521708 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
521661 AAGTTTTATC
521671 ATAATTAAATAATTAATT
1 ATAATTAAATAATTAATT
521689 ATAA-TAAAT-ATTAATT
1 ATAATTAAATAATTAATT
521705 ATAA
1 ATAA
521709 ATATAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 5 0.25
18 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTAAATAATTAATT
Found at i:525575 original size:18 final size:20
Alignment explanation
Indices: 525527--525576 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
525517 AGATATGAAC
* *
525527 ATATATAAAAAATAATTATA
1 ATATATATAAAATAATCATA
525547 ATATAATATAAAATAA-CATA
1 ATAT-ATATAAAATAATCATA
525567 A-ATATATAAA
1 ATATATATAAA
525577 CATATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.26
19 2 0.07
20 8 0.30
21 10 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATATATAAAATAATCATA
Found at i:525598 original size:17 final size:17
Alignment explanation
Indices: 525578--525627 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
525568 ATATATAAAC
525578 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
525595 ATA-T-AAA-TTAT-TA
1 ATATTAAAATTTATATA
525608 ATTTATTAAAATTTATATA
1 A--TATTAAAATTTATATA
525627 A
1 A
525628 CATATATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.11
14 4 0.15
15 5 0.19
16 2 0.07
17 6 0.22
18 4 0.15
19 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:525602 original size:33 final size:32
Alignment explanation
Indices: 525559--525631 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
525549 ATAATATAAA
525559 ATAACATAAATATATAAACATATTAAAATTTAT
1 ATAACATAAAT-TATAAACATATTAAAATTTAT
* * **
525592 ATAATATAAATTATTAATTTATTAAAATTTAT
1 ATAACATAAATTATAAACATATTAAAATTTAT
525624 ATAACATA
1 ATAACATA
525632 TATCATTTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (32 bp):
ATAACATAAATTATAAACATATTAAAATTTAT
Found at i:525656 original size:10 final size:10
Alignment explanation
Indices: 525641--525687 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
525631 ATATCATTTC
525641 AAATATAATT
1 AAATATAATT
525651 AAATAT-A-T
1 AAATATAATT
*
525659 AAAAATATATT
1 AAATATA-ATT
525670 AAATATAATAT
1 AAATATAAT-T
525681 AAATATA
1 AAATATA
525688 TAAAACTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
8 6 0.19
9 1 0.03
10 9 0.29
11 15 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATATAATT
Found at i:525666 original size:20 final size:21
Alignment explanation
Indices: 525641--525687 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
525631 ATATCATTTC
525641 AAATATAATTAAATAT-ATAA
1 AAATATAATTAAATATAATAA
*
525661 AAATAT-ATTAAATATAATAT
1 AAATATAATTAAATATAATAA
525681 AAATATA
1 AAATATA
525688 TAAAACTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATAATTAAATATAATAA
Found at i:525991 original size:2 final size:2
Alignment explanation
Indices: 525984--526016 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
525974 TCAAGAACCA
525984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
526017 ATTAAGGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:529507 original size:22 final size:20
Alignment explanation
Indices: 529481--529530 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
529471 TTTTAGTATA
*
529481 TTATTTTTAACATTATAAATTT
1 TTATTTTT-ACAAT-TAAATTT
* *
529503 TTATTTGTACAATTAGATTT
1 TTATTTTTACAATTAAATTT
529523 TTATTTTT
1 TTATTTTT
529531 TATCTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 13 0.54
21 4 0.17
22 7 0.29
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (20 bp):
TTATTTTTACAATTAAATTT
Found at i:540437 original size:23 final size:24
Alignment explanation
Indices: 540407--540452 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
540397 AAGTTTTTAA
* *
540407 TTTTTTAA-ATTAATATGTAAAAT
1 TTTTTTAATAATAAAATGTAAAAT
540430 TTTTTTAATAATAAAATGTAAAA
1 TTTTTTAATAATAAAATGTAAAA
540453 AAAGTAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTTTTAATAATAAAATGTAAAAT
Found at i:540527 original size:22 final size:23
Alignment explanation
Indices: 540493--540537 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
540483 ATATTTTTTT
*
540493 AAATTAATTTATTATAAA-ATTTA
1 AAATTAATATATTA-AAATATTTA
540516 AAATT-ATATATTAAAATATTTA
1 AAATTAATATATTAAAATATTTA
540538 TATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 12 0.60
23 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATTAATATATTAAAATATTTA
Found at i:543380 original size:16 final size:16
Alignment explanation
Indices: 543359--543390 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
543349 AAACATATTT
*
543359 TTTATTTTAAATTTAA
1 TTTATTATAAATTTAA
543375 TTTATTATAAATTTAA
1 TTTATTATAAATTTAA
543391 AAATTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATTATAAATTTAA
Found at i:543877 original size:34 final size:34
Alignment explanation
Indices: 543808--543888 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
543798 TTTTATCTTG
* * *
543808 TTTTAAAATAAATTATTATTTTAATTAGTGATTT
1 TTTTAAAATAAATTATCATTTTAATCAGTCATTT
543842 TTTTAAAA-AAATTATCATTTTAAATCA-TCATTT
1 TTTTAAAATAAATTATCATTTT-AATCAGTCATTT
543875 TTTTATTAAATAAA
1 TTTTA--AAATAAA
543889 ATGATGAGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 22 0.55
34 12 0.30
35 3 0.08
36 3 0.08
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (34 bp):
TTTTAAAATAAATTATCATTTTAATCAGTCATTT
Found at i:545821 original size:2 final size:2
Alignment explanation
Indices: 545814--545857 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
545804 ACTCCTGCAA
545814 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
545856 AT
1 AT
545858 GAGTATGTTA
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):
AT
Found at i:547231 original size:81 final size:81
Alignment explanation
Indices: 547096--547259 Score: 292
Period size: 81 Copynumber: 2.0 Consensus size: 81
547086 CTTTTAATTG
* * *
547096 AATTTAATATCGTTAATTAAATATCAATAAAAATATAAAAATAATTTATATTATTACAAATTTAT
1 AATTTAATATCGTGAATCAAATATCAATAAAAATATAAAAATAATTTATATTATTAAAAATTTAT
547161 TATTTGAAATATTATA
66 TATTTGAAATATTATA
*
547177 AATTTGATATCGTGAATCAAATATCAATAAAAATATAAAAATAATTTATATTATTAAAAATTTAT
1 AATTTAATATCGTGAATCAAATATCAATAAAAATATAAAAATAATTTATATTATTAAAAATTTAT
547242 TATTTGAAATATTATA
66 TATTTGAAATATTATA
547258 AA
1 AA
547260 AATTACCTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (81 bp):
AATTTAATATCGTGAATCAAATATCAATAAAAATATAAAAATAATTTATATTATTAAAAATTTAT
TATTTGAAATATTATA
Found at i:547440 original size:15 final size:17
Alignment explanation
Indices: 547420--547457 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
547410 ATCTACTGTT
547420 TTTAAAATA-TTTAA-A
1 TTTAAAATATTTTAATA
*
547435 TTTAAATTATTTTAATA
1 TTTAAAATATTTTAATA
547452 TTTAAA
1 TTTAAA
547458 TTTATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 5 0.25
17 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATATTTTAATA
Found at i:547456 original size:17 final size:17
Alignment explanation
Indices: 547420--547473 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
547410 ATCTACTGTT
*
547420 TTTAAAATA-TTTAA-A
1 TTTAAATTATTTTAATA
547435 TTTAAATTATTTTAATA
1 TTTAAATTATTTTAATA
*
547452 TTTAAATT-TATTTATTA
1 TTTAAATTAT-TTTAATA
547469 TTTAA
1 TTTAA
547474 TCTTGTACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 8 0.24
16 6 0.18
17 20 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTATTTTAATA
Found at i:547523 original size:18 final size:18
Alignment explanation
Indices: 547500--547554 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 18
547490 TAAATCGATT
547500 ATAAATTATTTATAAATA
1 ATAAATTATTTATAAATA
*
547518 ATAAATTAAATATTTTAAATA
1 ATAAATT--AT-TTATAAATA
*
547539 AAAAATTATTTA-AAAT
1 ATAAATTATTTATAAAT
547555 TAAAATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.13
18 9 0.29
19 2 0.06
20 2 0.06
21 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATTATTTATAAATA
Found at i:547538 original size:21 final size:23
Alignment explanation
Indices: 547501--547546 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
547491 AAATCGATTA
*
547501 TAAATTATTTATAAATAATAAAT
1 TAAATTATTTATAAATAAAAAAT
547524 TAAA-TATTT-TAAATAAAAAAT
1 TAAATTATTTATAAATAAAAAAT
547545 TA
1 TA
547547 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 5 0.23
23 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATTATTTATAAATAAAAAAT
Found at i:555040 original size:30 final size:28
Alignment explanation
Indices: 554970--555049 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 28
554960 GAAATTACTA
*
554970 TTTAAAT-AATA-AAAAATACTTTTAAT
1 TTTAAATAAATATAAAAATAATTTTAAT
*
554996 TATAAATATTAATATAAAAATAATTTATAAT
1 TTTAAATA--AATATAAAAATAATTT-TAAT
* *
555027 TTTATAATAAATATTAATATAAT
1 TTTA-AATAAATATAAAAATAAT
555050 CATATATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 6 0.14
29 4 0.09
30 22 0.51
31 7 0.16
32 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
TTTAAATAAATATAAAAATAATTTTAAT
Found at i:560049 original size:16 final size:17
Alignment explanation
Indices: 560019--560051 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
560009 AAATCAATTC
*
560019 AATTCATAATTTTTTAA
1 AATTCATAATATTTTAA
560036 AATT-ATAATATTTTAA
1 AATTCATAATATTTTAA
560052 TTTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTCATAATATTTTAA
Found at i:561261 original size:13 final size:15
Alignment explanation
Indices: 561226--561276 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 15
561216 GATAAATTAA
*
561226 TATTTAAATTTATAT
1 TATTTAAATATATAT
561241 TATTTAAATAT-TAT
1 TATTTAAATATATAT
561255 T-TTTAAATATA-AT
1 TATTTAAATATATAT
*
561268 TATATAAAT
1 TATTTAAAT
561277 TAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 12 0.38
14 10 0.31
15 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTAAATATATAT
Found at i:561280 original size:13 final size:13
Alignment explanation
Indices: 561218--561282 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
561208 ATAAAAAAGA
561218 TAAATTAA-TATT
1 TAAATTAATTATT
561230 TAAATTTATATTATT
1 TAAA-TTA-ATTATT
*
561245 TAAATATTATT-TT
1 TAAAT-TAATTATT
*
561258 TAAATATAATTATA
1 TAAAT-TAATTATT
561272 TAAATTAATTA
1 TAAATTAATTA
561283 AAATTATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
12 4 0.09
13 21 0.47
14 11 0.24
15 9 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATTAATTATT
Found at i:565945 original size:17 final size:17
Alignment explanation
Indices: 565909--565948 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
565899 GTATAATTAT
565909 TTAA-TTTAAAAAATAA
1 TTAATTTTAAAAAATAA
*
565925 -TAATTTTATAAAATAA
1 TTAATTTTAAAAAATAA
565941 TTAATTTT
1 TTAATTTT
565949 TATTATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTTTAAAAAATAA
Found at i:566064 original size:45 final size:45
Alignment explanation
Indices: 565989--566081 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 45
565979 TTTTTAAAAC
* *
565989 ATTTAGAATAATAATTTTATATTTTCTTATTGAATGT-TTATTTTA
1 ATTTAGAATAATAATTTTATATTTTCTTATTAAAT-TATTATTATA
* *
566034 ATTTAGATATAGT-ATTTTAT-TTTATTTTATTAAATTATTATTATA
1 ATTTAGA-ATAATAATTTTATATTT-TCTTATTAAATTATTATTATA
566079 ATT
1 ATT
566082 ATTTAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
44 4 0.10
45 33 0.80
46 4 0.10
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.59
Consensus pattern (45 bp):
ATTTAGAATAATAATTTTATATTTTCTTATTAAATTATTATTATA
Found at i:567886 original size:2 final size:2
Alignment explanation
Indices: 567879--567917 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
567869 ATGACAATAA
567879 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
567918 ATCACTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:575546 original size:2 final size:2
Alignment explanation
Indices: 575539--575585 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
575529 GAGCTCACAA
* *
575539 AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG AG AG AG AT AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
575581 AG AG A
1 AG AG A
575586 TGATAACCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:575914 original size:2 final size:2
Alignment explanation
Indices: 575907--575941 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
575897 TGTTACTAAA
575907 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
575942 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:575973 original size:24 final size:24
Alignment explanation
Indices: 575906--575995 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
575896 ATGTTACTAA
* *
575906 AATAT-ATATATATATAT-ATATAT
1 AATATAATATATATAAATAAAAT-T
575929 AATATAATATATA-AAATTAAAATT
1 AATATAATATATATAAA-TAAAATT
575953 AATATAATATATATAAATAAATATT
1 AATATAATATATATAAATAAA-ATT
*
575978 -TTATAAT-TATAATAAATA
1 AATATAATATAT-ATAAATA
575996 TAAAATATCT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
23 10 0.17
24 39 0.67
25 9 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AATATAATATATATAAATAAAATT
Found at i:576265 original size:13 final size:13
Alignment explanation
Indices: 576242--576272 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
576232 AATTTATCTA
*
576242 TATTATTTATATT
1 TATTATTTATAAT
576255 TATTATTTATAAT
1 TATTATTTATAAT
576268 TATTA
1 TATTA
576273 AAAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATTTATAAT
Found at i:580589 original size:33 final size:33
Alignment explanation
Indices: 580523--580598 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
580513 TTGAAAAACT
* * * **
580523 TTAAAAATGATATTTATTTCTTATACTGTTAAA
1 TTAAAAATAATATTTATCTCTAATACTACTAAA
*
580556 TTAAAAATAATATTTATCTCTAATATTACTAAA
1 TTAAAAATAATATTTATCTCTAATACTACTAAA
*
580589 TTCAAAATAA
1 TTAAAAATAA
580599 AAAAATATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (33 bp):
TTAAAAATAATATTTATCTCTAATACTACTAAA
Found at i:583898 original size:2 final size:2
Alignment explanation
Indices: 583891--583920 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
583881 AAAGTTTGAA
583891 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
583921 TTACCGTAGG
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:586777 original size:20 final size:21
Alignment explanation
Indices: 586752--586792 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
586742 AAATCTAGAG
586752 TTATATTAGG-TATTTTATAT
1 TTATATTAGGCTATTTTATAT
*
586772 TTATATTAGGCTTTTTTATAT
1 TTATATTAGGCTATTTTATAT
586793 CCCATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (21 bp):
TTATATTAGGCTATTTTATAT
Found at i:586933 original size:2 final size:2
Alignment explanation
Indices: 586926--586968 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
586916 TTAGTAGCCT
586926 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
586968 A
1 A
586969 TCAATGTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:592739 original size:8 final size:8
Alignment explanation
Indices: 592726--592755 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
592716 GACTGAAACT
592726 AAAAAAAG
1 AAAAAAAG
592734 AAAAAAAG
1 AAAAAAAG
*
592742 AAAACAAG
1 AAAAAAAG
592750 AAAAAA
1 AAAAAA
592756 GCTTGCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:594162 original size:11 final size:11
Alignment explanation
Indices: 594121--594183 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
594111 TATTATTAAG
594121 TAAA-TAAATT
1 TAAATTAAATT
594131 TAAA-T-AATT
1 TAAATTAAATT
* **
594140 TAATTTTTATT
1 TAAATTAAATT
*
594151 TTAATTAAATT
1 TAAATTAAATT
594162 TAAATT-AATT
1 TAAATTAAATT
594172 TAAATTTAAATT
1 TAAA-TTAAATT
594184 ATTTATAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
9 7 0.17
10 14 0.33
11 17 0.40
12 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:594174 original size:16 final size:16
Alignment explanation
Indices: 594125--594197 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 16
594115 ATTAAGTAAA
594125 TAAATTTAAA-TAATT
1 TAAATTTAAATTAATT
* **
594140 TAATTTTTATTTTAA-T
1 TAA-ATTTAAATTAATT
594156 TAAATTTAAATTAATT
1 TAAATTTAAATTAATT
594172 TAAATTTAAATT-ATT
1 TAAATTTAAATTAATT
594187 TATAATTTAAA
1 TA-AATTTAAA
594198 CTTGACTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
15 16 0.33
16 29 0.60
17 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTTAAATTAATT
Found at i:594177 original size:10 final size:10
Alignment explanation
Indices: 594121--594177 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
594111 TATTATTAAG
*
594121 TAAATAAATT
1 TAAATTAATT
594131 TAAA-TAATT
1 TAAATTAATT
* *
594140 TAATTTTTATT
1 TAA-ATTAATT
*
594151 TTAATTAAATT
1 TAAATT-AATT
594162 TAAATTAATT
1 TAAATTAATT
594172 TAAATT
1 TAAATT
594178 TAAATTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
9 7 0.19
10 16 0.43
11 14 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TAAATTAATT
Found at i:594196 original size:27 final size:28
Alignment explanation
Indices: 594134--594196 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
594124 ATAAATTTAA
** *
594134 ATAATTTAATTTTTATTTTAATTAAATTT
1 ATAATTTAATTTAAATTTAAATT-AATTT
594163 A-AA-TTAATTTAAATTTAAATT-ATTT
1 ATAATTTAATTTAAATTTAAATTAATTT
594188 ATAATTTAA
1 ATAATTTAA
594197 ACTTGACTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 5 0.17
26 2 0.07
27 19 0.66
28 2 0.07
29 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATAATTTAATTTAAATTTAAATTAATTT
Found at i:594394 original size:4 final size:4
Alignment explanation
Indices: 594385--594424 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
594375 TAATTTTAAA
*
594385 AATT AATT AATT AATT AA-T AATT AATT AAAT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT A
594425 TGATAATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:594407 original size:19 final size:19
Alignment explanation
Indices: 594380--594422 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
594370 TTACTTAATT
* *
594380 TTAAAAATTAATTAATTAA
1 TTAATAATTAATTAAATAA
594399 TTAATAATTAATTAAATAA
1 TTAATAATTAATTAAATAA
594418 TTAAT
1 TTAAT
594423 TATGATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAATAATTAATTAAATAA
Found at i:594969 original size:32 final size:31
Alignment explanation
Indices: 594878--594985 Score: 93
Period size: 32 Copynumber: 3.5 Consensus size: 31
594868 TTTATATATT
* *
594878 TATATCAATATATTTATATTAT-T-TTTTTAA
1 TATATTAATA-ATTTATATTATATAATTTTAA
594908 TTATATTTAA-AATTT-TA-TATA-AATTTTAA
1 -TATA-TTAATAATTTATATTATATAATTTTAA
594937 TATATTAATAATTTATATTATATAATTATTAA
1 TATATTAATAATTTATATTATATAATT-TTAA
* *
594969 TATTTTATATATTTTAT
1 TATATTA-ATAATTTAT
594986 TTTTATTACG
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
27 4 0.06
28 12 0.19
29 10 0.16
30 8 0.12
31 9 0.14
32 13 0.20
33 8 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (31 bp):
TATATTAATAATTTATATTATATAATTTTAA
Found at i:595662 original size:21 final size:21
Alignment explanation
Indices: 595620--595668 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
595610 CTCAATATTT
*
595620 ATAAT-ATTTTTTATTATTAA
1 ATAATAATTTTTTATTATAAA
*
595640 ATTATAATTTTTTA-TATAAAA
1 ATAATAATTTTTTATTAT-AAA
595661 ATAATAAT
1 ATAATAAT
595669 AATATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAATAATTTTTTATTATAAA
Found at i:597586 original size:33 final size:32
Alignment explanation
Indices: 597544--597661 Score: 100
Period size: 31 Copynumber: 3.6 Consensus size: 32
597534 AAAAGTTAAA
597544 ATATAATATAATATAAATAAATATTTTA-AATTT
1 ATATAATATAA-AT-AATAAATATTTTATAATTT
* *
597577 ATATAATATAAATTATTAATATTTTATAATTT
1 ATATAATATAAATAATAAATATTTTATAATTT
* * *
597609 TTATAATTATAAAATATTTTAAATATATTATAA--T
1 ATATAA-TAT-AAATA--ATAAATATTTTATAATTT
597643 ATATAATA-AAATATATAAA
1 ATATAATATAAATA-ATAAA
597662 AAATATGAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
30 5 0.07
31 16 0.23
32 12 0.17
33 16 0.23
34 10 0.14
36 12 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATATAATATAAATAATAAATATTTTATAATTT
Found at i:597590 original size:15 final size:14
Alignment explanation
Indices: 597549--597598 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
597539 TTAAAATATA
597549 ATATAATATAAA-T
1 ATATAATATAAATT
* * *
597562 AAATATTTTAAATTT
1 ATATAATATAAA-TT
597577 ATATAATATAAATT
1 ATATAATATAAATT
597591 AT-TAATAT
1 ATATAATAT
597599 TTTATAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 15 0.52
14 4 0.14
15 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:597595 original size:23 final size:25
Alignment explanation
Indices: 597554--597606 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
597544 ATATAATATA
*
597554 ATATAA-ATAAATATTTTAA-ATTT
1 ATATAATATAAATATATTAATATTT
597577 ATATAATATAAAT-TATTAATATTT
1 ATATAATATAAATATATTAATATTT
597601 -TATAAT
1 ATATAAT
597607 TTTTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATAATATAAATATATTAATATTT
Found at i:597624 original size:27 final size:28
Alignment explanation
Indices: 597529--597648 Score: 95
Period size: 27 Copynumber: 4.2 Consensus size: 28
597519 ATTACAAATA
* * *
597529 ATATAAAA-AGTTAAAATATAATATAAT
1 ATATAAAATATTTTAAATATATTATAAT
* *
597556 ATAAATAAATATTTTAAATTTA-TATAAT
1 ATATA-AAATATTTTAAATATATTATAAT
* *
597584 ATAAATTATTAATATTTTATAAT-TTTTATAAT
1 AT--A-TA-AAATATTTTA-AATATATTATAAT
597616 -TATAAAATATTTTAAATATATTATAAT
1 ATATAAAATATTTTAAATATATTATAAT
597643 ATATAA
1 ATATAA
597649 TAAAATATAT
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
26 3 0.04
27 21 0.28
28 18 0.24
29 10 0.13
30 1 0.01
31 13 0.17
32 9 0.12
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATAAAATATTTTAAATATATTATAAT
Found at i:597639 original size:21 final size:20
Alignment explanation
Indices: 597614--597662 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
597604 AATTTTTATA
**
597614 ATTATAAAATATTTTAAATAT
1 ATTATAAAATATAATAAA-AT
*
597635 ATTATAATATATAATAAAAT
1 ATTATAAAATATAATAAAAT
597655 A-TATAAAA
1 ATTATAAAA
597663 AATATGAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATAAAATATAATAAAAT
Found at i:597643 original size:10 final size:10
Alignment explanation
Indices: 597543--597660 Score: 54
Period size: 9 Copynumber: 12.2 Consensus size: 10
597533 AAAAAGTTAA
*
597543 AATATAATAT
1 AATATATTAT
*
597553 AATATA-AAT
1 AATATATTAT
*
597562 AA-ATATTTT
1 AATATATTAT
*
597571 AA-ATTTATAT
1 AATATAT-TAT
597581 AATATAAATTATT
1 AATAT--ATTA-T
*
597594 AATATTTTAT
1 AATATATTAT
*
597604 AAT-TTTTAT
1 AATATATTAT
*
597613 AAT-TA-TAA
1 AATATATTAT
*
597621 AATATTTTA-
1 AATATATTAT
597630 AATATATTAT
1 AATATATTAT
*
597640 AATATATAAT
1 AATATATTAT
*
597650 AAAATA-TAT
1 AATATATTAT
597659 AA
1 AA
597661 AAAATATGAA
Statistics
Matches: 85, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
8 8 0.09
9 33 0.39
10 30 0.35
11 5 0.06
12 2 0.02
13 7 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATATATTAT
Found at i:597833 original size:9 final size:9
Alignment explanation
Indices: 597802--597866 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
597792 AATAATTTTA
597802 ATATTAAA-
1 ATATTAAAT
597810 ATATT-AA-
1 ATATTAAAT
597817 A-ATTAAAT
1 ATATTAAAT
*
597825 ATTTTAAAT
1 ATATTAAAT
597834 ATATTAAATTT
1 ATATTAAA--T
*
597845 ATATTTAAT
1 ATATTAAAT
597854 ATA-TAAAT
1 ATATTAAAT
*
597862 TTATT
1 ATATT
597867 GCATATGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
6 3 0.07
7 5 0.11
8 12 0.26
9 18 0.39
11 8 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
ATATTAAAT
Found at i:598502 original size:3 final size:3
Alignment explanation
Indices: 598494--598532 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
598484 ATTTTTCTTA
598494 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
598533 GTGAAGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:599327 original size:28 final size:30
Alignment explanation
Indices: 599295--599355 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
599285 AACGATATAT
*
599295 ATATTTTAAA-AT-TTTAT-ATAAATATAAA
1 ATATTTTAAATATAATTATGATAAA-ATAAA
599323 ATATTTTAAATATAATTATGATAAAATAAA
1 ATATTTTAAATATAATTATGATAAAATAAA
599353 ATA
1 ATA
599356 CACAAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.34
29 2 0.07
30 12 0.41
31 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
ATATTTTAAATATAATTATGATAAAATAAA
Found at i:599733 original size:19 final size:19
Alignment explanation
Indices: 599709--599759 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
599699 TGATACTTAT
*
599709 AATTATAAAATATAATAAA
1 AATTATTAAATATAATAAA
*
599728 AATTATTAAATAT-ATTAA
1 AATTATTAAATATAATAAA
599746 AATT-TTAAATATAA
1 AATTATTAAATATAA
599760 ATGTAATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 9 0.31
19 12 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTATTAAATATAATAAA
Found at i:600202 original size:16 final size:17
Alignment explanation
Indices: 600173--600206 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
600163 TGTGTAAAAT
*
600173 TTTTTATTTTAAATTTA
1 TTTTTATTTAAAATTTA
600190 TTTTTA-TTAAAATTTA
1 TTTTTATTTAAAATTTA
600206 T
1 T
600207 ATATTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTATTTAAAATTTA
Found at i:601440 original size:24 final size:23
Alignment explanation
Indices: 601398--601442 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
601388 AAAATTTTGA
*
601398 TATATTTCATAATTTATATAATT
1 TATATTTCATAATTGATATAATT
601421 TATATTTACATAATTGATATAA
1 TATATTT-CATAATTGATATAA
601443 AAATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TATATTTCATAATTGATATAATT
Found at i:601691 original size:28 final size:28
Alignment explanation
Indices: 601660--601737 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 28
601650 ACCCTCAATT
601660 TTTTATTTTATTAAATAAAAATTT-ATA
1 TTTTATTTTATTAAATAAAAATTTAATA
** *
601687 CTTTTATTACATTAAA-ATAAACTTTAATA
1 -TTTTATTTTATTAAATA-AAAATTTAATA
601716 TTTTAATTTGTATTCAAATAAA
1 TTTT-ATTT-TATT-AAATAAA
601738 CCCTAAACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.03
28 23 0.59
29 6 0.15
30 3 0.08
31 5 0.13
32 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (28 bp):
TTTTATTTTATTAAATAAAAATTTAATA
Found at i:601737 original size:30 final size:30
Alignment explanation
Indices: 601701--601776 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
601691 TATTACATTA
*
601701 AAATAAACTTTAATATTTTAATTTGTAT-T
1 AAATAAACTTTAATATTTTAATTTATATCT
**
601730 CAAATAAACCCTAA-ACTTTTAATTTATATCT
1 -AAATAAACTTTAATA-TTTTAATTTATATCT
*
601761 AAATAACCTTTAATAT
1 AAATAAACTTTAATAT
601777 AATTAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 1 0.03
30 34 0.92
31 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.43
Consensus pattern (30 bp):
AAATAAACTTTAATATTTTAATTTATATCT
Found at i:605734 original size:18 final size:18
Alignment explanation
Indices: 605713--605752 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
605703 AATAATGATT
605713 AATTTAAAAAGTATTTAA
1 AATTTAAAAAGTATTTAA
** *
605731 AATTTTTAAATTATTTAA
1 AATTTAAAAAGTATTTAA
605749 AATT
1 AATT
605753 ATAATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTTAAAAAGTATTTAA
Found at i:605751 original size:10 final size:10
Alignment explanation
Indices: 605714--605754 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
605704 ATAATGATTA
*
605714 ATTTAAAAAGT
1 ATTT-AAAATT
605725 ATTTAAAATT
1 ATTTAAAATT
605735 -TTT-AAATT
1 ATTTAAAATT
605743 ATTTAAAATT
1 ATTTAAAATT
605753 AT
1 AT
605755 AATATTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
8 5 0.19
9 6 0.22
10 12 0.44
11 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
ATTTAAAATT
Found at i:605822 original size:20 final size:21
Alignment explanation
Indices: 605789--605829 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
605779 TATGAATTAA
605789 ATATTATTAATAAT-ATTTAT
1 ATATTATTAATAATCATTTAT
**
605809 ATATTATTTTTAATCATTTAT
1 ATATTATTAATAATCATTTAT
605830 TCTATATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTATTAATAATCATTTAT
Found at i:607223 original size:18 final size:19
Alignment explanation
Indices: 607184--607225 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
607174 GAATTCTCTA
607184 ATTTTTAATTTTATTAATTT
1 ATTTTTAATTTTA-TAATTT
607204 ATTTTTGAATTTTA-AA-TT
1 ATTTTT-AATTTTATAATTT
607222 ATTT
1 ATTT
607226 ATTCATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
19 2 0.10
20 6 0.29
21 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTAATTTTATAATTT
Found at i:608485 original size:3 final size:3
Alignment explanation
Indices: 608477--608520 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
608467 AAATTGATGC
608477 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
608521 ACATAAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:609836 original size:14 final size:15
Alignment explanation
Indices: 609819--609847 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
609809 TAATTATAAA
609819 AATATATAAA-AATT
1 AATATATAAATAATT
609833 AATATATAAATAATT
1 AATATATAAATAATT
609848 TTATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATATAAATAATT
Found at i:610471 original size:25 final size:24
Alignment explanation
Indices: 610423--610477 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
610413 TTTTTATTGA
*
610423 TAAA-ATTTTTAAAAAATATATTT
1 TAAATATTTTGAAAAAATATATTT
610446 TAAATATTTTGAATAAAATA-ATTTT
1 TAAATATTTTGAA-AAAATATA-TTT
610471 TAAATAT
1 TAAATAT
610478 ATGTTTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 8 0.29
25 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAAATATTTTGAAAAAATATATTT
Found at i:611115 original size:2 final size:2
Alignment explanation
Indices: 611110--611141 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
611100 ACAATTATTC
*
611110 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
611142 TACAACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:611586 original size:25 final size:27
Alignment explanation
Indices: 611540--611589 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
611530 AGTTAAAAAT
*
611540 TTTAAAATTTTATTCAAGTAAAATTTA
1 TTTAAAATTATATTCAAGTAAAATTTA
*
611567 TTTAAAATTATCTTC-A-TAAAATT
1 TTTAAAATTATATTCAAGTAAAATT
611590 CGTTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 1 0.05
27 13 0.62
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTAAAATTATATTCAAGTAAAATTTA
Found at i:611595 original size:25 final size:27
Alignment explanation
Indices: 611540--611595 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
611530 AGTTAAAAAT
* *
611540 TTTAAAATTTTATTCAAGTAAAATTTA
1 TTTAAAATTATATTCAAGTAAAATTCA
* *
611567 TTTAAAATTATCTTC-A-TAAAATTCG
1 TTTAAAATTATATTCAAGTAAAATTCA
611592 TTTA
1 TTTA
611596 TTTAAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 11 0.44
26 1 0.04
27 13 0.52
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTAAAATTATATTCAAGTAAAATTCA
Found at i:612347 original size:33 final size:32
Alignment explanation
Indices: 612271--612347 Score: 75
Period size: 33 Copynumber: 2.3 Consensus size: 32
612261 TAAAAATATT
* * *
612271 ATTATATTAATATTTATAATTAAATTTAAATA
1 ATTAAATTATTATTTATAATAAAATTTAAATA
**
612303 AAAAAATTTATTATTTA-AATAATAATTTAAATTA
1 ATTAAA-TTATTATTTATAATAA-AATTTAAA-TA
612337 ATTAAATTATT
1 ATTAAATTATT
612348 TCGAATTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
32 7 0.20
33 22 0.63
34 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATTAAATTATTATTTATAATAAAATTTAAATA
Found at i:612749 original size:2 final size:2
Alignment explanation
Indices: 612742--612773 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
612732 TCTCTTTCAC
612742 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
612774 GATCCAAAAA
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:613223 original size:16 final size:16
Alignment explanation
Indices: 613167--613230 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 16
613157 TTATAAATAA
613167 ATTTAAA-TAAAAATAAT
1 ATTTAAATTAAAAAT--T
* *
613184 TTTTAATATTAAATAATA
1 ATTTAA-ATTAAA-AATT
613202 ATTTAAATTAAAAATT
1 ATTTAAATTAAAAATT
*
613218 ATTTAATTTAAAA
1 ATTTAAATTAAAA
613231 CTTAACCCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 15 0.38
17 11 0.28
18 6 0.15
19 4 0.10
20 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAAATTAAAAATT
Found at i:613560 original size:2 final size:2
Alignment explanation
Indices: 613553--613584 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
613543 TTATTAAATA
613553 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
613585 TGGAGTTTCC
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:616635 original size:24 final size:21
Alignment explanation
Indices: 616608--616677 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 21
616598 TTTTACAAAA
616608 AATTAAAAGCATATATACATAGTT
1 AATTAAAAGCATATA-A-ATA-TT
616632 AATTAAAATGCATA-AAATATT
1 AATTAAAA-GCATATAAATATT
616653 AATTATAAAG-ATAT-AATATAT
1 AATTA-AAAGCATATAAATAT-T
616674 AATT
1 AATT
616678 TAAATCTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
20 8 0.19
21 13 0.31
22 6 0.14
23 1 0.02
24 9 0.21
25 5 0.12
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (21 bp):
AATTAAAAGCATATAAATATT
Found at i:620781 original size:2 final size:2
Alignment explanation
Indices: 620774--620807 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
620764 GTCCTCAGGT
620774 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
620808 GCATGTGCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:627136 original size:1 final size:1
Alignment explanation
Indices: 627130--627154 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
627120 TATGACTATT
627130 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
627155 AAACAACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:634373 original size:121 final size:121
Alignment explanation
Indices: 634159--634400 Score: 484
Period size: 121 Copynumber: 2.0 Consensus size: 121
634149 TTAACAAATA
634159 TACCAACATTTCTATTTACATCTCTCATGGTAAATGGTTATGGTTTTCTTATGAGCAGTTGATAG
1 TACCAACATTTCTATTTACATCTCTCATGGTAAATGGTTATGGTTTTCTTATGAGCAGTTGATAG
634224 TTAAAGTTTGTCTCAAAGCCCTAACCAAATTCCAAGATATTCCCAGGTACGAATTC
66 TTAAAGTTTGTCTCAAAGCCCTAACCAAATTCCAAGATATTCCCAGGTACGAATTC
634280 TACCAACATTTCTATTTACATCTCTCATGGTAAATGGTTATGGTTTTCTTATGAGCAGTTGATAG
1 TACCAACATTTCTATTTACATCTCTCATGGTAAATGGTTATGGTTTTCTTATGAGCAGTTGATAG
634345 TTAAAGTTTGTCTCAAAGCCCTAACCAAATTCCAAGATATTCCCAGGTACGAATTC
66 TTAAAGTTTGTCTCAAAGCCCTAACCAAATTCCAAGATATTCCCAGGTACGAATTC
634401 CCAACTTTCG
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (121 bp):
TACCAACATTTCTATTTACATCTCTCATGGTAAATGGTTATGGTTTTCTTATGAGCAGTTGATAG
TTAAAGTTTGTCTCAAAGCCCTAACCAAATTCCAAGATATTCCCAGGTACGAATTC
Found at i:634703 original size:2 final size:2
Alignment explanation
Indices: 634696--634738 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
634686 TCGTCCATAT
634696 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
634738 T
1 T
634739 TTTGGTTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:635223 original size:13 final size:14
Alignment explanation
Indices: 635205--635238 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
635195 ATTATTAATT
635205 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
635218 TTATTAAATTTTTA
1 TTATTAAATTTATA
635232 TTATTAA
1 TTATTAA
635239 TAAATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:635226 original size:30 final size:32
Alignment explanation
Indices: 635192--635259 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
635182 ATTTATGTCA
* *
635192 TAAATTATTAATT-TTATTAAATTATATTA-T
1 TAAATTATTAATTATTAATAAATTAAATTACT
*
635222 TAAATT-TTTATTATTAATAAATTAAATTACT
1 TAAATTATTAATTATTAATAAATTAAATTACT
*
635253 TACATTA
1 TAAATTA
635260 AATTCATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 5 0.16
30 20 0.65
31 6 0.19
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (32 bp):
TAAATTATTAATTATTAATAAATTAAATTACT
Found at i:635414 original size:22 final size:23
Alignment explanation
Indices: 635377--635423 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
635367 TAGTATAAAT
635377 AATTTAATTTATTAA-TAATAAA
1 AATTTAATTTATTAATTAATAAA
635399 AATTTAA-TTATATAATTTAATAAA
1 AATTTAATTTAT-TAA-TTAATAAA
635423 A
1 A
635424 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
24 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAATTTATTAATTAATAAA
Found at i:635450 original size:27 final size:26
Alignment explanation
Indices: 635404--635454 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
635394 ATAAAAATTT
*
635404 AATTATATAATTTAATAAAATTAAAA
1 AATTATATAATCTAATAAAATTAAAA
635430 AATT-TATAATCTATATAAAAATTAA
1 AATTATATAATCTA-AT-AAAATTAA
635455 TATTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 6 0.27
27 8 0.36
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AATTATATAATCTAATAAAATTAAAA
Found at i:636149 original size:17 final size:17
Alignment explanation
Indices: 636127--636159 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
636117 AATTTACACC
*
636127 TAAATAAATTTTTAATA
1 TAAATAAACTTTTAATA
636144 TAAATAAACTTTTAAT
1 TAAATAAACTTTTAAT
636160 TTATTTATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAAACTTTTAATA
Found at i:636217 original size:24 final size:23
Alignment explanation
Indices: 636176--636233 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
636166 ATGTACAAAT
636176 TAAAAAATAAAAAATTATTTAGA
1 TAAAAAATAAAAAATTATTTAGA
*
636199 TAAAATATAAAAAATTTATTTA-A
1 TAAAAAATAAAAAA-TTATTTAGA
636222 -AAAAAAGTAAAA
1 TAAAAAA-TAAAA
636234 TAGTTCAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 5 0.16
23 19 0.61
24 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (23 bp):
TAAAAAATAAAAAATTATTTAGA
Found at i:636909 original size:2 final size:2
Alignment explanation
Indices: 636904--636934 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
636894 ACACACACTG
636904 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
636935 ATACATATAT
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:637163 original size:24 final size:25
Alignment explanation
Indices: 637130--637192 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
637120 TCAATTGAAT
*
637130 ATATTGATTTTTTAAAA-ATATTAA
1 ATATTAATTTTTTAAAATATATTAA
*
637154 ATATTAATTTTTTAAAATATATTTA
1 ATATTAATTTTTTAAAATATATTAA
*
637179 ATGGTTAATTTTTT
1 AT-ATTAATTTTTT
637193 GTATTAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 16 0.47
25 8 0.24
26 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (25 bp):
ATATTAATTTTTTAAAATATATTAA
Found at i:637292 original size:30 final size:27
Alignment explanation
Indices: 637236--637294 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 27
637226 CTCAAATTTC
* *
637236 AATATACAATATATGTAAATAAAATAT
1 AATATACAATATAAGTAAAAAAAATAT
637263 AATATACAATGATCAAGTTAAAAAAAATAT
1 AATATACAAT-AT-AAG-TAAAAAAAATAT
637293 AA
1 AA
637295 AGCATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 2 0.07
29 2 0.07
30 13 0.48
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (27 bp):
AATATACAATATAAGTAAAAAAAATAT
Found at i:639990 original size:83 final size:83
Alignment explanation
Indices: 639903--640067 Score: 276
Period size: 83 Copynumber: 2.0 Consensus size: 83
639893 TTTATTTATA
*
639903 TATTTTAATCAATATAATATTTAATTTCATATGCTGGTAGATAACGTTAATATTTTTTTTAACTA
1 TATTTTAATCAATATAATATTTAATTTCATATGCTGGTAGATAACATTAATATTTTTTTTAACTA
639968 CAATCCCTCTTTTTAAAT
66 CAATCCCTCTTTTTAAAT
* *
639986 TATTTTAATCAGTATAATATTTAATTTCATATGCTGTTAGATAACATTAATATTTTTTTTAACTA
1 TATTTTAATCAATATAATATTTAATTTCATATGCTGGTAGATAACATTAATATTTTTTTTAACTA
* **
640051 CGATCTTTCTTTTTAAA
66 CAATCCCTCTTTTTAAA
640068 ATTAAAAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (83 bp):
TATTTTAATCAATATAATATTTAATTTCATATGCTGGTAGATAACATTAATATTTTTTTTAACTA
CAATCCCTCTTTTTAAAT
Found at i:640116 original size:25 final size:25
Alignment explanation
Indices: 640061--640116 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
640051 CGATCTTTCT
*
640061 TTTTAAAATTAAAAATTAAATCATTA
1 TTTT-AAATTAAAAATTAAATAATTA
*
640087 GTTTAAATTAAAAATT-AATAAATTA
1 TTTTAAATTAAAAATTAAAT-AATTA
640112 TTTTA
1 TTTTA
640117 TTTGATACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 3 0.12
25 20 0.77
26 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTTAAATTAAAAATTAAATAATTA
Found at i:640649 original size:18 final size:17
Alignment explanation
Indices: 640616--640650 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
640606 TTTAGTTAAA
*
640616 AAATTATATATTTATAT
1 AAATTATATATATATAT
640633 AAATTATGATATATATAT
1 AAATTAT-ATATATATAT
640651 TATTTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
AAATTATATATATATAT
Found at i:640869 original size:20 final size:19
Alignment explanation
Indices: 640846--640887 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
640836 TATATAAAAT
640846 AATAAAAAAATATAATTTTA
1 AATAAAAAAATAT-ATTTTA
* *
640866 AATATAAATATATATTTTA
1 AATAAAAAAATATATTTTA
640885 AAT
1 AAT
640888 TATATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAAAAAAATATATTTTA
Found at i:640874 original size:18 final size:20
Alignment explanation
Indices: 640853--640897 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
640843 AATAATAAAA
640853 AAATATA-ATTTTAAA-TAT
1 AAATATATATTTTAAATTAT
640871 AAATATATATTTTAAATTAT
1 AAATATATATTTTAAATTAT
640891 ATAATAT
1 A-AATAT
640898 GAATCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.29
19 8 0.33
20 4 0.17
21 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATATATTTTAAATTAT
Found at i:642881 original size:3 final size:3
Alignment explanation
Indices: 642873--642903 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
642863 CTCTTAGTTC
*
642873 ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
642904 CAAGTCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:644861 original size:2 final size:2
Alignment explanation
Indices: 644854--644886 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
644844 GTCTAGACGA
644854 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
644887 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:649515 original size:2 final size:2
Alignment explanation
Indices: 649510--649540 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
649500 CCTTTTTTCC
649510 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
649541 GGGATTTTAA
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:650184 original size:15 final size:15
Alignment explanation
Indices: 650164--650194 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
650154 TTTAAATCTT
650164 ATAATATATTATTTA
1 ATAATATATTATTTA
*
650179 ATAATATTTTATTTA
1 ATAATATATTATTTA
650194 A
1 A
650195 GACGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATATATTATTTA
Found at i:651081 original size:17 final size:17
Alignment explanation
Indices: 651046--651087 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
651036 TCTATAATAA
651046 AAATCATATCATTTAATT
1 AAAT-ATATCATTTAATT
651064 AAATATAT-ATTTATATT
1 AAATATATCATTTA-ATT
651081 AAATATA
1 AAATATA
651088 ATACTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 14 0.61
18 4 0.17
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATATCATTTAATT
Found at i:651099 original size:17 final size:17
Alignment explanation
Indices: 651061--651099 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
651051 ATATCATTTA
*
651061 ATTAAATATATATTTAT
1 ATTAAATATATACTTAT
651078 ATTAAATATAATACTTAT
1 ATTAAATAT-ATACTTAT
651096 -TTAA
1 ATTAA
651100 TATTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAAATATATACTTAT
Found at i:651124 original size:20 final size:20
Alignment explanation
Indices: 651056--651127 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
651046 AAATCATATC
651056 ATTTA-ATT-AAATATA--T
1 ATTTATATTAAAATATACTT
651072 ATTTATATTAAATATAATACTT
1 ATTTATATTAAA-AT-ATACTT
*
651094 ATTTAATATTAAAAT-TATTT
1 ATTT-ATATTAAAATATACTT
651114 AATTTATATTAAAA
1 -ATTTATATTAAAA
651128 AAATTTAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.11
17 3 0.06
18 2 0.04
19 2 0.04
20 16 0.34
21 4 0.09
22 7 0.15
23 8 0.17
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTATATTAAAATATACTT
Found at i:651133 original size:20 final size:20
Alignment explanation
Indices: 651072--651135 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
651062 TTAAATATAT
*
651072 ATTTATATTAAATATAATACTT-
1 ATTTATATTAAA-A-AA-ATTTA
**
651094 ATTTAATATTAAAATTATTTA
1 ATTT-ATATTAAAAAAATTTA
651115 ATTTATATTAAAAAAATTTA
1 ATTTATATTAAAAAAATTTA
651135 A
1 A
651136 ATTAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 18 0.51
21 4 0.11
22 5 0.14
23 8 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTATATTAAAAAAATTTA
Found at i:651138 original size:21 final size:21
Alignment explanation
Indices: 651094--651140 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
651084 TATAATACTT
**
651094 ATTTAATATTAAAATTATTTA
1 ATTTAATATTAAAAAAATTTA
651115 ATTT-ATATTAAAAAAATTTA
1 ATTTAATATTAAAAAAATTTA
*
651135 AATTAA
1 ATTTAA
651141 ATAATTCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTAATATTAAAAAAATTTA
Found at i:651453 original size:1 final size:1
Alignment explanation
Indices: 651447--651473 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
651437 CTTCGGCCAG
651447 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
651474 CAATCTTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:654481 original size:2 final size:2
Alignment explanation
Indices: 654474--654503 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
654464 TTTATAGCTA
654474 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
654504 AATGCCACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:658571 original size:15 final size:14
Alignment explanation
Indices: 658547--658598 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 14
658537 ATTTATGTTA
*
658547 AATTTGATTAACTTT
1 AATTTAATTAA-TTT
658562 AATTTAATTAATTT
1 AATTTAATTAATTT
658576 AATATTTAATTTAA-TT
1 -A-ATTTAA-TTAATTT
658592 AATTTAA
1 AATTTAA
658599 ATATAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 9 0.27
15 12 0.36
16 8 0.24
17 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
AATTTAATTAATTT
Found at i:658574 original size:9 final size:9
Alignment explanation
Indices: 658560--658598 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
658550 TTGATTAACT
658560 TTAATTTAA
1 TTAATTTAA
658569 TTAATTTAATA
1 TTAATTT-A-A
658580 TTTAATTTAA
1 -TTAATTTAA
658590 TTAATTTAA
1 TTAATTTAA
658599 ATATAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 16 0.59
10 2 0.07
11 2 0.07
12 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATTTAA
Found at i:658583 original size:21 final size:21
Alignment explanation
Indices: 658559--658598 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
658549 TTTGATTAAC
658559 TTTAATTTAATTAATTTAATA
1 TTTAATTTAATTAATTTAATA
658580 TTTAATTTAATTAATTTAA
1 TTTAATTTAATTAATTTAA
658599 ATATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATTTAATTAATTTAATA
Found at i:658620 original size:15 final size:15
Alignment explanation
Indices: 658591--658671 Score: 63
Period size: 16 Copynumber: 5.1 Consensus size: 15
658581 TTAATTTAAT
*
658591 TAATTTAAATATAAAA
1 TAATTAAAAT-TAAAA
658607 TAATTAAAATTAAATA
1 TAATTAAAATTAAA-A
* *
658623 TTAAATTTAAATTTAAA
1 -T-AATTAAAATTAAAA
*
658640 TAATTTAAATTTAAAA
1 TAA-TTAAAATTAAAA
* *
658656 TAATTCAAACTAAAA
1 TAATTAAAATTAAAA
658671 T
1 T
658672 TAATCTAATC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
15 16 0.31
16 23 0.44
17 2 0.04
18 11 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTAAAATTAAAA
Found at i:658637 original size:49 final size:49
Alignment explanation
Indices: 658567--658675 Score: 145
Period size: 49 Copynumber: 2.3 Consensus size: 49
658557 ACTTTAATTT
*
658567 AATT-AAT-TTAATATTTAATTTAATTAATTTAAATATAAAATAATTAA
1 AATTAAATATTAATATTTAATTTAAATAATTTAAATATAAAATAATTAA
* *
658614 AATTAAATATTAA-ATTTAAATTTAAATAATTTAAATTTAAAATAATTCA
1 AATTAAATATTAATATTT-AATTTAAATAATTTAAATATAAAATAATTAA
*
658663 AACTAAA-ATTAAT
1 AATTAAATATTAAT
658676 CTAATCCGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
47 4 0.07
48 12 0.22
49 38 0.70
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (49 bp):
AATTAAATATTAATATTTAATTTAAATAATTTAAATATAAAATAATTAA
Found at i:658640 original size:6 final size:6
Alignment explanation
Indices: 658571--658654 Score: 56
Period size: 6 Copynumber: 14.3 Consensus size: 6
658561 TAATTTAATT
* *
658571 AATTTA ATATTT- AATTT- AA-TT- AATTTA AATATAA AATAATTA AAATTA
1 AATTTA A-ATTTA AATTTA AATTTA AATTTA AAT-TTA AAT--TTA AATTTA
658619 AATATTA AATTTA AATTTA AA--T- AATTTA AATTTA AA
1 AAT-TTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
658655 ATAATTCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
3 2 0.03
4 5 0.08
5 9 0.14
6 29 0.45
7 15 0.23
8 5 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:661374 original size:21 final size:22
Alignment explanation
Indices: 661350--661407 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
661340 ATTCTAACAG
661350 TAAATTTAATTTATATT-AT-AT
1 TAAATTTAATTTA-ATTAATAAT
661371 TAAATTTAATTTAATTAATAAT
1 TAAATTTAATTTAATTAATAAT
*
661393 TAAATAT-ATTTAATT
1 TAAATTTAATTTAATT
661408 TGATTTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.09
21 23 0.68
22 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATTTAATTTAATTAATAAT
Done.