Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 12 of 26
Found at i:1633879 original size:18 final size:17
Alignment explanation
Indices: 1633822--1633879 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
1633812 ATAATATTTA
*
1633822 AAATAATTTAAATTTTT
1 AAATAATTTAAATTATT
* *
1633839 ATATAAATTTTAATATATT
1 AAAT-AATTTAAAT-TATT
1633858 -AATAATTTAAATTATGT
1 AAATAATTTAAATTAT-T
1633875 AAATA
1 AAATA
1633880 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 3 0.09
17 12 0.38
18 14 0.44
19 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATAATTTAAATTATT
Found at i:1634131 original size:11 final size:11
Alignment explanation
Indices: 1634115--1634160 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
1634105 CTTATCCTTG
1634115 AAATATAAATA
1 AAATATAAATA
*
1634126 AAATATAAAAAA
1 AAATAT-AAATA
1634138 AAATCATAAATA
1 AAAT-ATAAATA
*
1634150 TAATATAAATA
1 AAATATAAATA
1634161 TATAAATACG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 13 0.43
12 15 0.50
13 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATATAAATA
Found at i:1635469 original size:26 final size:29
Alignment explanation
Indices: 1635416--1635471 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
1635406 TAATTTAATT
*
1635416 TTATAACTTTAAATTATTTTTATTTATTA
1 TTATAACTTTAAATTATTTTTATATATTA
*
1635445 TTATAA-TTTATA-TATTTTTA-ATATTA
1 TTATAACTTTAAATTATTTTTATATATTA
1635471 T
1 T
1635472 CTTTCTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 8 0.32
28 5 0.20
29 6 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TTATAACTTTAAATTATTTTTATATATTA
Found at i:1635471 original size:29 final size:29
Alignment explanation
Indices: 1635393--1635471 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
1635383 AAATATAACA
1635393 TAAATTATTAATTTAATTTAATTTTATAACTT
1 TAAATTATT--TTTAATTT-ATTTTATAACTT
1635425 TAAATTATTTTT-ATTTATTATTATAA-TT
1 TAAATTATTTTTAATTTATT-TTATAACTT
*
1635453 TATA-TATTTTTAATATTAT
1 TAAATTATTTTTAAT-TTAT
1635472 CTTTCTTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
27 7 0.16
28 10 0.23
29 14 0.33
30 3 0.07
32 9 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
TAAATTATTTTTAATTTATTTTATAACTT
Found at i:1640433 original size:23 final size:21
Alignment explanation
Indices: 1640398--1640440 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1640388 TATGATCAAA
1640398 TTTTTTTAATATTTTAATATT
1 TTTTTTTAATATTTTAATATT
*
1640419 TTTTTTATAATTATTTTCATAT
1 TTTTTT-TAA-TATTTTAATAT
1640441 CTAAATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTTAATATTTTAATATT
Found at i:1645781 original size:24 final size:23
Alignment explanation
Indices: 1645740--1645784 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
1645730 ATTTAAAAAA
1645740 TTTTAAACTATATTTTTTTTATT
1 TTTTAAACTATATTTTTTTTATT
1645763 TTTTAAA-TATATATATTTTTTA
1 TTTTAAACTATAT-T-TTTTTTA
1645785 ATTAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 8 0.40
24 7 0.35
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTAAACTATATTTTTTTTATT
Found at i:1646970 original size:28 final size:28
Alignment explanation
Indices: 1646939--1647026 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
1646929 TCTCCATCTA
*
1646939 TTATATAAATATTTTATTTTTTTAATAT
1 TTATATAAATATTTTATTTTTTAAATAT
* *
1646967 TTATATATAGTA-TTTA-TATTTAAATAT
1 TTATATA-AATATTTTATTTTTTAAATAT
** *
1646994 ACATAATAAA-ATTTAATTTTTTAAATAT
1 TTAT-ATAAATATTTTATTTTTTAAATAT
1647022 TTATA
1 TTATA
1647027 AAAAATAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
26 1 0.02
27 16 0.35
28 26 0.57
29 3 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
TTATATAAATATTTTATTTTTTAAATAT
Found at i:1647027 original size:28 final size:27
Alignment explanation
Indices: 1646951--1647032 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
1646941 ATATAAATAT
* **
1646951 TTTATTTTTTTAATATTTATATATAGTA
1 TTTATTTTTTAAATATTTATA-ATAAAA
* **
1646979 TTTA-TATTTAAATATACATAATAAAA
1 TTTATTTTTTAAATATTTATAATAAAA
1647005 TTTAATTTTTTAAATATTTATAA-AAAA
1 TTT-ATTTTTTAAATATTTATAATAAAA
1647032 T
1 T
1647033 AAAATTATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
26 7 0.16
27 18 0.42
28 18 0.42
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (27 bp):
TTTATTTTTTAAATATTTATAATAAAA
Found at i:1647332 original size:2 final size:2
Alignment explanation
Indices: 1647325--1647356 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1647315 AACCCAGCCG
1647325 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
1647357 GACAATTAGG
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:1647394 original size:16 final size:16
Alignment explanation
Indices: 1647375--1647432 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
1647365 GGCAGGTTTA
*
1647375 AAATTATTTTATATTT
1 AAATTATTTTAAATTT
1647391 AAATTATTTTAAATTT
1 AAATTATTTTAAATTT
*
1647407 AAA-TATTTTTGAATTT
1 AAATTA-TTTTAAATTT
1647423 AAATTTATTT
1 AAA-TTATTT
1647433 AAGTTTGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.05
16 30 0.81
17 3 0.08
18 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:1647434 original size:32 final size:32
Alignment explanation
Indices: 1647371--1647456 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
1647361 ATTAGGCAGG
* *
1647371 TTTAAAATTATTTTATATTTAAATTATTTTAAA
1 TTTAAATTTATTTGA-ATTTAAATTATTTTAAA
*
1647404 TTTAAATATT-TTTGAATTTAAATT-TATTTAAG
1 TTTAAAT-TTATTTGAATTTAAATTAT-TTTAAA
**
1647436 TTTGGATTTATTTGAATTTAA
1 TTTAAATTTATTTGAATTTAA
1647457 TTTTTTTGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.07
32 30 0.67
33 10 0.22
34 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (32 bp):
TTTAAATTTATTTGAATTTAAATTATTTTAAA
Found at i:1647491 original size:14 final size:15
Alignment explanation
Indices: 1647459--1647507 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
1647449 GAATTTAATT
1647459 TTTTTGAGTTTGAAA
1 TTTTTGAGTTTGAAA
*
1647474 -TTTTGGGTTT-AAA
1 TTTTTGAGTTTGAAA
1647487 TTTTTTTGAGTTTG-AA
1 --TTTTTGAGTTTGAAA
1647503 TTTTT
1 TTTTT
1647508 TTTAGTTCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
16 11 0.39
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.61
Consensus pattern (15 bp):
TTTTTGAGTTTGAAA
Found at i:1647493 original size:16 final size:16
Alignment explanation
Indices: 1647388--1647514 Score: 91
Period size: 16 Copynumber: 8.1 Consensus size: 16
1647378 TTATTTTATA
* * *
1647388 TTTAAATTATTTTAAA
1 TTTAAATTTTTTTGAG
* *
1647404 TTTAAATATTTTTGAA
1 TTTAAATTTTTTTGAG
* *
1647420 TTTAAATTTATTTAAG
1 TTTAAATTTTTTTGAG
** * *
1647436 TTTGGATTTATTTGAA
1 TTTAAATTTTTTTGAG
1647452 TTT-AATTTTTTTGAG
1 TTTAAATTTTTTTGAG
*
1647467 TTTGAAA---TTTTGGG
1 TTT-AAATTTTTTTGAG
1647481 TTTAAATTTTTTTGAG
1 TTTAAATTTTTTTGAG
* *
1647497 TTTGAATTTTTTTTAG
1 TTTAAATTTTTTTGAG
1647513 TT
1 TT
1647515 CGGGTTTGAA
Statistics
Matches: 88, Mismatches: 18, Indels: 10
0.76 0.16 0.09
Matches are distributed among these distances:
13 3 0.03
14 9 0.10
15 12 0.14
16 62 0.70
17 2 0.02
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (16 bp):
TTTAAATTTTTTTGAG
Found at i:1647681 original size:18 final size:18
Alignment explanation
Indices: 1647658--1647692 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1647648 ACAAAAGATA
1647658 ATATATA-ATTAAA-CAT
1 ATATATATATTAAATCAT
1647674 ATATATATATTAAATCAT
1 ATATATATATTAAATCAT
1647692 A
1 A
1647693 AAAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATATATTAAATCAT
Found at i:1648114 original size:18 final size:18
Alignment explanation
Indices: 1648066--1648114 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
1648056 AATAAATATT
1648066 TAAAAATTA-ATTTTATA
1 TAAAAATTATATTTTATA
*
1648083 TACAAATATATATTTTA-A
1 TAAAAAT-TATATTTTATA
1648101 TAAATAATTATATT
1 TAAA-AATTATATT
1648115 AAAAATAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.22
18 12 0.44
19 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAAATTATATTTTATA
Found at i:1648128 original size:32 final size:30
Alignment explanation
Indices: 1648046--1648161 Score: 85
Period size: 32 Copynumber: 3.7 Consensus size: 30
1648036 GTAATATACA
1648046 ATATTATAATAATAAATA-TTTAAAAATTAATT
1 ATATTA-AA-AATAAATATTTTAAAAA-TAATT
* * *
1648078 TTATATACAAATATATATTTTAATAAATAATT
1 ATAT-TAAAAATAAATATTTTAA-AAATAATT
* *
1648110 ATATTAAAAATAACATATTATAACAA-AATT
1 ATATTAAAAATAA-ATATTTTAAAAATAATT
* *
1648140 TTACTTAAAAAT-AATAATTTAA
1 ATA-TTAAAAATAAATATTTTAA
1648162 TAATTTACTT
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
29 7 0.10
30 7 0.10
31 24 0.35
32 25 0.37
33 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
ATATTAAAAATAAATATTTTAAAAATAATT
Found at i:1648941 original size:23 final size:21
Alignment explanation
Indices: 1648910--1648952 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1648900 ATTTTTTTAA
1648910 TAAAATCAAATTTAATTTAAATT
1 TAAAATCAAATTT--TTTAAATT
*
1648933 TAAACTCAAATTTTTTAAAT
1 TAAAATCAAATTTTTTAAAT
1648953 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATCAAATTTTTTAAATT
Found at i:1655788 original size:2 final size:2
Alignment explanation
Indices: 1655781--1655834 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1655771 GTTTCTCTTT
1655781 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
1655823 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1655835 AATTCTTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1656095 original size:45 final size:45
Alignment explanation
Indices: 1656001--1656101 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
1655991 ATATAAAAAC
* *
1656001 TTATATTATTATTTAAAATAACATAAAAATTAAAATATTATATTT
1 TTATATTAATATTTAAAATAACATAAAAATTAAAATATTATATTA
* ** *
1656046 TTATATTAATATTTATAATTAA-ATTCAAATTAAAAATATTTTA-TA
1 TTATATTAATATTTA-AAATAACATAAAAATT-AAAATATTATATTA
*
1656091 TTATATAAATA
1 TTATATTAATA
1656102 GTAATTCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
45 32 0.68
46 15 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (45 bp):
TTATATTAATATTTAAAATAACATAAAAATTAAAATATTATATTA
Found at i:1656527 original size:2 final size:2
Alignment explanation
Indices: 1656522--1656550 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1656512 TTGGTTTTTT
1656522 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1656551 ATATATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1656563 original size:6 final size:6
Alignment explanation
Indices: 1656554--1656611 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
1656544 TGTGTGTATA
*
1656554 TATATT TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1656602 TATATG TATA
1 TATATG TATA
1656612 AAGGAAATTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:1661677 original size:21 final size:21
Alignment explanation
Indices: 1661653--1661698 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1661643 ATAAACCGAG
1661653 GGTTAGGAAACCGGAT-AGACC
1 GGTTAGGAAACCGGATAAG-CC
* *
1661674 GGTTAGGGAACGGGATAAGCC
1 GGTTAGGAAACCGGATAAGCC
1661695 GGTT
1 GGTT
1661699 GGTTCATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.28, C:0.15, G:0.39, T:0.17
Consensus pattern (21 bp):
GGTTAGGAAACCGGATAAGCC
Found at i:1662129 original size:21 final size:22
Alignment explanation
Indices: 1662097--1662145 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1662087 AAAGACAATT
*
1662097 AATATAAAAAT-ATTTTTAAAA
1 AATATAAAAATAATTATTAAAA
1662118 AATA-AAATAATAATTATTAAAA
1 AATATAAA-AATAATTATTAAAA
*
1662140 TATATA
1 AATATA
1662146 GAATGATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.13
21 7 0.30
22 12 0.52
23 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAAAAATAATTATTAAAA
Found at i:1662305 original size:22 final size:24
Alignment explanation
Indices: 1662271--1662319 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
1662261 TTATGTTTTG
*
1662271 TTTATTATATAATTTTATAAAATT
1 TTTATTATATAATATTATAAAATT
* *
1662295 TTTATT-T-TAATATTATCAATTT
1 TTTATTATATAATATTATAAAATT
1662317 TTT
1 TTT
1662320 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 15 0.68
23 1 0.05
24 6 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTATTATATAATATTATAAAATT
Found at i:1662708 original size:18 final size:18
Alignment explanation
Indices: 1662685--1662737 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
1662675 AAAAATAATC
1662685 ATTATTATTTATAAATAT
1 ATTATTATTTATAAATAT
*
1662703 ATTATTATTAAT-AATAT
1 ATTATTATTTATAAATAT
1662720 -TTATTTAATTTATAAATA
1 ATTA-TT-ATTTATAAATA
1662738 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.10
17 7 0.23
18 16 0.53
19 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATTATTTATAAATAT
Found at i:1663561 original size:38 final size:37
Alignment explanation
Indices: 1663454--1663561 Score: 91
Period size: 38 Copynumber: 2.8 Consensus size: 37
1663444 TCACATGCAA
*
1663454 CACATGTAACATTAAAAATTATTACTTTAAAAATTAAAT
1 CACAAGTAACATTAAAAATTATTACTTT--AAATTAAAT
*
1663493 CTA-AA-TCATCATTCAAATAA-TATT--TATTAAATCTAAAT
1 C-ACAAGT-AACATT-AAA-AATTATTACT-TTAAAT-TAAAT
1663531 CACAAGTAACATTAAAAATTATTACTTTAAA
1 CACAAGTAACATTAAAAATTATTACTTTAAA
1663562 AATTAAAAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 23
0.68 0.04 0.28
Matches are distributed among these distances:
36 2 0.04
37 12 0.22
38 20 0.36
39 11 0.20
40 8 0.15
41 2 0.04
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (37 bp):
CACAAGTAACATTAAAAATTATTACTTTAAATTAAAT
Found at i:1667178 original size:23 final size:23
Alignment explanation
Indices: 1667143--1667194 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1667133 TAACTGAAAG
1667143 ATTAAAAACTTATTTAGATACAA
1 ATTAAAAACTTATTTAGATACAA
* * * *
1667166 GTTAAAAATTTATTTGGATATAA
1 ATTAAAAACTTATTTAGATACAA
1667189 ATTAAA
1 ATTAAA
1667195 TGTTAAGTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (23 bp):
ATTAAAAACTTATTTAGATACAA
Found at i:1668393 original size:19 final size:19
Alignment explanation
Indices: 1668366--1668404 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1668356 TCAAAAAATA
*
1668366 ATTTATTAATTATAATTTT
1 ATTTATTAACTATAATTTT
* *
1668385 ATTTTTTAACTATCATTTT
1 ATTTATTAACTATAATTTT
1668404 A
1 A
1668405 ATTAATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTATTAACTATAATTTT
Found at i:1671459 original size:4 final size:4
Alignment explanation
Indices: 1671450--1671474 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1671440 GTAATATCTC
1671450 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
1671475 GTAGCAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:1671906 original size:21 final size:22
Alignment explanation
Indices: 1671881--1671930 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1671871 TTTATGAGAA
*
1671881 ATATTTTTAATTTATTTTA-AT
1 ATATTTTTAATTTATATTATAT
**
1671902 ATATTAATAATTTATATTATAT
1 ATATTTTTAATTTATATTATAT
*
1671924 AAATTTT
1 ATATTTT
1671931 AATATGTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTAATTTATATTATAT
Found at i:1671947 original size:32 final size:32
Alignment explanation
Indices: 1671894--1671955 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1671884 TTTTTAATTT
*
1671894 ATTTTAATATATTAATAATTTATATTATATAA
1 ATTTTAATATATTAATAATTTATATCATATAA
* *
1671926 ATTTTAATATGTT-TTATATTTATATCATAT
1 ATTTTAATATATTAATA-ATTTATATCATAT
1671956 TTTATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (32 bp):
ATTTTAATATATTAATAATTTATATCATATAA
Found at i:1671962 original size:27 final size:26
Alignment explanation
Indices: 1671912--1671976 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
1671902 ATATTAATAA
1671912 TTTATATTATATAAATTTTAATATGT
1 TTTATATTATATAAATTTTAATATGT
* *
1671938 TTTATATTTATATCATATTTTATATTATAT
1 TTTATA-TTATAT-AAATTTTA-A-TATGT
1671968 TTTA-ATTAT
1 TTTATATTAT
1671977 TTTTTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 6 0.18
27 6 0.18
28 11 0.33
29 2 0.06
30 8 0.24
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTATATTATATAAATTTTAATATGT
Found at i:1671975 original size:11 final size:12
Alignment explanation
Indices: 1671939--1671986 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
1671929 TTAATATGTT
1671939 TTATA-TTTATA
1 TTATATTTTATA
*
1671950 TCATATTTTATA
1 TTATATTTTATA
1671962 TTATATTTTA-A
1 TTATATTTTATA
1671973 TTAT-TTTT-TA
1 TTATATTTTATA
1671983 TTAT
1 TTAT
1671987 TTTCATCTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 9 0.27
11 9 0.27
12 15 0.45
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:1672854 original size:5 final size:5
Alignment explanation
Indices: 1672834--1672867 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
1672824 TCATCAACTA
1672834 TATAT GTATA- TATAT TATAT TATAT TATAT TATA
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATA
1672868 CAATTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:1678061 original size:17 final size:17
Alignment explanation
Indices: 1678006--1678074 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
1677996 CTTGAACTAA
1678006 AATTTATCATTATATAAAAT
1 AATTTAT-ATTA-A-AAAAT
*
1678026 AA-TTAT-TT-AAATAT
1 AATTTATATTAAAAAAT
*
1678040 TATTTATATTAAAAAAT
1 AATTTATATTAAAAAAT
*
1678057 AATTTA-ATAAAAAAAT
1 AATTTATATTAAAAAAT
1678073 AA
1 AA
1678075 AAGTTCTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 5 0.12
15 5 0.12
16 13 0.32
17 12 0.29
19 4 0.10
20 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTATATTAAAAAAT
Found at i:1678645 original size:21 final size:21
Alignment explanation
Indices: 1678621--1678686 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1678611 TAATATGATA
1678621 AATTTATATAATAATAAAAAT
1 AATTTATATAATAATAAAAAT
* *
1678642 AATTAAT-TAACTAATTAAAAT
1 AATTTATATAA-TAATAAAAAT
*
1678663 -ATTTAAATAA-ATATATAAAAT
1 AATTTATATAATA-ATA-AAAAT
1678684 AAT
1 AAT
1678687 AGATATTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
19 1 0.03
20 9 0.26
21 23 0.66
22 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTATATAATAATAAAAAT
Found at i:1678844 original size:16 final size:17
Alignment explanation
Indices: 1678825--1678862 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1678815 CTTAATATTT
1678825 ATAAAATATTAT-ATAA
1 ATAAAATATTATAATAA
*
1678841 AT-AAATATTTTAATAA
1 ATAAAATATTATAATAA
1678857 ATAAAA
1 ATAAAA
1678863 CATAAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 8 0.42
17 3 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAAATATTATAATAA
Found at i:1679454 original size:19 final size:20
Alignment explanation
Indices: 1679432--1679480 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
1679422 TTTTTTAAAT
1679432 AAATTTATTTTTTTAC-TTA
1 AAATTTATTTTTTTACATTA
* *
1679451 AAATGTA-TCTTTTACATTA
1 AAATTTATTTTTTTACATTA
1679470 AATATTT-TTTT
1 AA-ATTTATTTT
1679481 AAAATACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
18 7 0.30
19 11 0.48
20 5 0.22
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (20 bp):
AAATTTATTTTTTTACATTA
Found at i:1681452 original size:15 final size:16
Alignment explanation
Indices: 1681432--1681488 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1681422 TTTTATATAA
*
1681432 AAAAAATTTTAATT-T
1 AAAAAATTATAATTAT
1681447 AAAAAATTATAATTAT
1 AAAAAATTATAATTAT
* *
1681463 -AAATATTAAAATTTAT
1 AAAAAATTATAA-TTAT
*
1681479 TAAAAATTAT
1 AAAAAATTAT
1681489 TTTTTATAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 22 0.65
16 5 0.15
17 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAAATTATAATTAT
Found at i:1682195 original size:23 final size:23
Alignment explanation
Indices: 1682151--1682195 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1682141 TTTTAAAAAC
*
1682151 TTTAATTATAAAAATATATTAAT
1 TTTAATTATAAAAAAATATTAAT
*
1682174 TTTAATTA-AAAATAAATTTTAA
1 TTTAATTATAAAA-AAATATTAA
1682196 ATATTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAATTATAAAAAAATATTAAT
Found at i:1682735 original size:3 final size:3
Alignment explanation
Indices: 1682722--1682752 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1682712 CCAAAGCTAT
*
1682722 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1682753 ATTTACTGTA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1683205 original size:14 final size:14
Alignment explanation
Indices: 1683186--1683214 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1683176 GAAAATTGTG
1683186 CCAAAATACTTCTC
1 CCAAAATACTTCTC
1683200 CCAAAATACTTCTC
1 CCAAAATACTTCTC
1683214 C
1 C
1683215 TCATATTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (14 bp):
CCAAAATACTTCTC
Found at i:1683422 original size:17 final size:18
Alignment explanation
Indices: 1683388--1683422 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1683378 TGAATAACTT
*
1683388 AATTAAATATATTTATAA
1 AATTAAATATAATTATAA
1683406 AATTAAAT-TAATTATAA
1 AATTAAATATAATTATAA
1683423 TAAGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAAATATAATTATAA
Found at i:1684280 original size:3 final size:3
Alignment explanation
Indices: 1684265--1684295 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1684255 TTTTATTCGG
*
1684265 AGA AGA GGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1684296 TTCTTGATCA
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1688743 original size:22 final size:22
Alignment explanation
Indices: 1688676--1688743 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
1688666 AAATTATCAT
1688676 TATATAATAATTTAGATTTAAAAA
1 TATATAA-AATTTAGA-TTAAAAA
* **
1688700 -ATATCAAATTTATCTTAAAAA
1 TATATAAAATTTAGATTAAAAA
1688721 TATATTAAAATTTA-ATTAAAAA
1 TATA-TAAAATTTAGATTAAAAA
1688743 T
1 T
1688744 TTTAAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 7 0.19
22 17 0.46
23 13 0.35
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (22 bp):
TATATAAAATTTAGATTAAAAA
Found at i:1688803 original size:20 final size:20
Alignment explanation
Indices: 1688778--1688818 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1688768 TTTAATTATA
1688778 ATATTAATTAATTATTA-AAT
1 ATATTAATTAA-TATTATAAT
1688798 ATATTAATTAATATTATAAT
1 ATATTAATTAATATTATAAT
1688818 A
1 A
1688819 ATAAAGTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATTAATATTATAAT
Found at i:1689475 original size:26 final size:26
Alignment explanation
Indices: 1689446--1689528 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
1689436 ATTTTTTTTT
1689446 TTAATTTTAGATCATTAAATTTAATA
1 TTAATTTTAGATCATTAAATTTAATA
*
1689472 TTAATTTATAGATCA-TAAATTTTTAATT
1 TTAATTT-TAGATCATTAAA--TTTAATA
* * *
1689500 TTATTTATTAAATTATTAAATTT-ATA
1 TTAATT-TTAGATCATTAAATTTAATA
1689526 TTA
1 TTA
1689529 TTAAAAAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 16 0.34
27 10 0.21
28 16 0.34
29 5 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTAATTTTAGATCATTAAATTTAATA
Found at i:1689486 original size:27 final size:27
Alignment explanation
Indices: 1689446--1689528 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
1689436 ATTTTTTTTT
1689446 TTAATTT-TAGATCATTAAATTTAATA
1 TTAATTTATAGATCATTAAATTTAATA
1689472 TTAATTTATAGATCA-TAAATTTTTAAT-
1 TTAATTTATAGATCATTAAA--TTTAATA
* * *
1689499 TTTATTTATTAAATTATTAAATTT-ATA
1 TTAATTTA-TAGATCATTAAATTTAATA
1689526 TTA
1 TTA
1689529 TTAAAAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
26 13 0.28
27 19 0.40
28 11 0.23
29 4 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTAATTTATAGATCATTAAATTTAATA
Found at i:1689521 original size:22 final size:21
Alignment explanation
Indices: 1689487--1689533 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1689477 TTATAGATCA
*
1689487 TAAATTTTTAATTT-TATTTAT
1 TAAATTTTAAATTTATA-TTAT
1689508 TAAATTATTAAATTTATATTAT
1 TAAATT-TTAAATTTATATTAT
1689530 TAAA
1 TAAA
1689534 AAAAGTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 15 0.65
23 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAATTTTAAATTTATATTAT
Found at i:1689719 original size:22 final size:22
Alignment explanation
Indices: 1689693--1689734 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1689683 ACTTAATAAA
1689693 ATTAAT-ATAAATAATTTAATTT
1 ATTAATAATAAA-AATTTAATTT
*
1689715 ATTAATAATAAAATTTTAAT
1 ATTAATAATAAAAATTTAAT
1689735 ATGATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAATAATAAAAATTTAATTT
Found at i:1690186 original size:11 final size:11
Alignment explanation
Indices: 1690127--1690185 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
1690117 AATTAATAAA
1690127 AAATTAAAATT
1 AAATTAAAATT
1690138 AAATT-AAATT
1 AAATTAAAATT
* * *
1690148 TAA-TACAATC
1 AAATTAAAATT
1690158 AAATTAAATATT
1 AAATTAAA-ATT
* *
1690170 ATATTTAAATT
1 AAATTAAAATT
1690181 AAATT
1 AAATT
1690186 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
9 1 0.03
10 12 0.33
11 15 0.42
12 8 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:1690711 original size:24 final size:23
Alignment explanation
Indices: 1690671--1690774 Score: 70
Period size: 24 Copynumber: 4.4 Consensus size: 23
1690661 ATATTTATAT
1690671 AAATATAATAT-TAAAATATAATA
1 AAATATAATATAT-AAATATAATA
**
1690694 AAATATAAATATATAAATATTTTA
1 AAATAT-AATATATAAATATAATA
*
1690718 AAATAT-ATGATATAAAT-TATTA
1 AAATATAAT-ATATAAATATAATA
* * * * *
1690740 ATATATAAAATTTATATAAATATA
1 AAATATAATATATAAATATA-ATA
1690764 AAATATTAATA
1 AAATA-TAATA
1690775 ATTATTTTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
22 17 0.27
23 16 0.25
24 25 0.40
25 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (23 bp):
AAATATAATATATAAATATAATA
Found at i:1690769 original size:13 final size:13
Alignment explanation
Indices: 1690667--1690774 Score: 51
Period size: 13 Copynumber: 7.7 Consensus size: 13
1690657 AAACATATTT
*
1690667 ATATAAATATAAT
1 ATATAAATATAAA
*
1690680 AT-TAAA-ATATA
1 ATATAAATATAAA
1690691 ATA-AAATATAAA
1 ATATAAATATAAA
1690703 TATATAAATATTTTAAA
1 -ATATAAATA---TAAA
*
1690720 ATATATGATATAAA
1 ATATA-AATATAAA
*
1690734 TTATTAATATATAAAA
1 ATA-TAA-ATAT-AAA
1690750 TTTATATAAATATAAA
1 ---ATATAAATATAAA
*
1690766 ATATTAATA
1 ATATAAATA
1690775 ATTATTTTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 28
0.67 0.07 0.26
Matches are distributed among these distances:
11 8 0.11
12 8 0.11
13 13 0.18
14 11 0.15
15 6 0.08
16 11 0.15
17 11 0.15
18 3 0.04
19 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (13 bp):
ATATAAATATAAA
Found at i:1690820 original size:63 final size:62
Alignment explanation
Indices: 1690667--1690820 Score: 149
Period size: 63 Copynumber: 2.5 Consensus size: 62
1690657 AAACATATTT
*
1690667 ATATAAATATA-ATAT-TAAAATATAATA-AAATATAAATATATAAATATTTTAAAATATATG
1 ATATAAATATATAAATATAAAATA-AATATAAATATAAATATATAAATATTTTAAAATATATG
** * * *
1690727 ATATAAAT-TATTAATATATAAAATTTATATAAATATAAAATATTAATAATTATTTTTATAT-TA
1 ATATAAATATA-TAA-ATATAAAATAAATATAAATAT-AAATA-T-ATAAATATTTTAAAATATA
1690790 TG
61 TG
*
1690792 ATA-AGATATATAAATATAAAATAAATATA
1 ATATAAATATATAAATATAAAATAAATATA
1690821 TAATTATTAA
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
59 2 0.03
60 8 0.11
61 1 0.01
62 5 0.07
63 26 0.34
64 11 0.14
65 10 0.13
66 13 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (62 bp):
ATATAAATATATAAATATAAAATAAATATAAATATAAATATATAAATATTTTAAAATATATG
Found at i:1691146 original size:19 final size:19
Alignment explanation
Indices: 1691122--1691169 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1691112 TTTAATTTAT
* *
1691122 TAAAATAATTATTTTATTA
1 TAAAATAATTAATGTATTA
*
1691141 TAAAATTATTTAATGTATTA
1 TAAAA-TAATTAATGTATTA
1691161 TAAAA-AATT
1 TAAAATAATT
1691170 TATTATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 5 0.21
20 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAAAATAATTAATGTATTA
Found at i:1691147 original size:16 final size:17
Alignment explanation
Indices: 1691117--1691151 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1691107 CATTGTTTAA
1691117 TTTATTAAAATAATTAT
1 TTTATTAAAATAATTAT
*
1691134 TTTATTATAA-AATTAT
1 TTTATTAAAATAATTAT
1691150 TT
1 TT
1691152 AATGTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATTAAAATAATTAT
Found at i:1692262 original size:13 final size:14
Alignment explanation
Indices: 1692235--1692271 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1692225 TAAATAAATT
1692235 TATTTTATATTTAA
1 TATTTTATATTTAA
1692249 TATTTTAT-TTTAA
1 TATTTTATATTTAA
1692262 TACTTTTATA
1 TA-TTTTATA
1692272 CGCACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTATATTTAA
Found at i:1692833 original size:3 final size:3
Alignment explanation
Indices: 1692825--1692856 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1692815 TAAAAAATAT
1692825 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1692857 TTGTTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1695524 original size:16 final size:17
Alignment explanation
Indices: 1695500--1695536 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1695490 TTAATTTTAA
1695500 ATATGTTAAAAAT-ATT
1 ATATGTTAAAAATAATT
*
1695516 ATATTTTAAAAATAATT
1 ATATGTTAAAAATAATT
1695533 ATAT
1 ATAT
1695537 AAATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
ATATGTTAAAAATAATT
Found at i:1697296 original size:2 final size:2
Alignment explanation
Indices: 1697285--1697315 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1697275 GGATCCTTAA
1697285 AT AT -T 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
1697316 TGAAGAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1701504 original size:2 final size:2
Alignment explanation
Indices: 1701497--1701524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1701487 CACAGTGTGC
1701497 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
1701525 TTAAGCATAA
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:1702609 original size:24 final size:23
Alignment explanation
Indices: 1702572--1702634 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
1702562 TTAAGAGTTA
*
1702572 ATTTATAATTTATAATTTTTTATT
1 ATTTAT-ATATATAATTTTTTATT
*
1702596 TTTTAATATATATATATTTTTTATT
1 ATTT-ATATATATA-ATTTTTTATT
*
1702621 ATTTATATGTATAA
1 ATTTATATATATAA
1702635 GATTTATTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 17 0.52
25 15 0.45
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
ATTTATATATATAATTTTTTATT
Found at i:1702627 original size:16 final size:18
Alignment explanation
Indices: 1702592--1702628 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1702582 TATAATTTTT
1702592 TATTTTTTAATATATATA
1 TATTTTTTAATATATATA
* *
1702610 TATTTTTTATTATTTATA
1 TATTTTTTAATATATATA
1702628 T
1 T
1702629 GTATAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTTTAATATATATA
Found at i:1702639 original size:25 final size:25
Alignment explanation
Indices: 1702582--1702639 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
1702572 ATTTATAATT
*
1702582 TATA-ATTTTTTATTTTTTAATATA
1 TATAGATTTTTTATTATTTAATATA
* *
1702606 TATATATTTTTTATTATTT-ATATG
1 TATAGATTTTTTATTATTTAATATA
1702630 TATAAGATTT
1 TAT-AGATTT
1702640 ATTCGTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (25 bp):
TATAGATTTTTTATTATTTAATATA
Found at i:1708608 original size:76 final size:78
Alignment explanation
Indices: 1708507--1708710 Score: 218
Period size: 76 Copynumber: 2.6 Consensus size: 78
1708497 GAGATAATAA
* * * * *
1708507 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
1708571 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* * **
1708583 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* *
1708648 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * *
1708662 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1708711 GAAATAACGA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 7 0.07
76 47 0.45
77 2 0.02
78 3 0.03
79 45 0.43
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:1708702 original size:28 final size:28
Alignment explanation
Indices: 1708662--1708733 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1708652 GGAATAAAGC
** *
1708662 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1708690 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1708718 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1708734 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1708791 original size:52 final size:50
Alignment explanation
Indices: 1708722--1708891 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
1708712 AAATAACGAG
* * *
1708722 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
1708774 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
1708827 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
1708878 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1708892 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:1708910 original size:28 final size:28
Alignment explanation
Indices: 1708865--1708946 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
1708855 AGTGTTTTAA
* *
1708865 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1708892 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
1708919 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1708947 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:1711381 original size:13 final size:13
Alignment explanation
Indices: 1711363--1711388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1711353 ACAAAGATCC
1711363 ATGTATCGATACA
1 ATGTATCGATACA
1711376 ATGTATCGATACA
1 ATGTATCGATACA
1711389 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1711384 original size:33 final size:33
Alignment explanation
Indices: 1711342--1711408 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1711332 AAAATTTCCA
***
1711342 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1711375 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1711408 A
1 A
1711409 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1711452 original size:19 final size:18
Alignment explanation
Indices: 1711428--1711495 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1711418 CAGTAGCTAA
1711428 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1711447 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1711462 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1711479 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1711496 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1711468 original size:13 final size:13
Alignment explanation
Indices: 1711450--1711474 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1711440 ACAATACTTA
1711450 TGTATCGATACAT
1 TGTATCGATACAT
1711463 TGTATCGATACA
1 TGTATCGATACA
1711475 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1711472 original size:32 final size:32
Alignment explanation
Indices: 1711431--1711493 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1711421 TAGCTAATTA
*
1711431 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1711463 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1711494 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1711575 original size:21 final size:21
Alignment explanation
Indices: 1711551--1711607 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1711541 CATTTGTAGG
1711551 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1711572 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1711593 ATGTATCGATACATT
1 ATGTATCGATACATT
1711608 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1711638 original size:16 final size:16
Alignment explanation
Indices: 1711617--1711648 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1711607 TTAAATTTTT
1711617 TTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTCAA
1711633 TTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTCAA
1711649 ACACTTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTTTTTCAA
Found at i:1712325 original size:55 final size:55
Alignment explanation
Indices: 1712241--1713694 Score: 2210
Period size: 55 Copynumber: 26.4 Consensus size: 55
1712231 ATAAATTGTA
* * * *
1712241 TCCTGCTCATTGAGGAGT-AAAAGGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAA-GTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
1712296 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCCACTTGTATGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * * *
1712351 TCCTGCTTTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1712406 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
1712461 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGGGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1712516 TCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1712571 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1712626 TCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1712681 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1712736 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1712791 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1712846 TCCTGCTCGTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1712901 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1712956 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1713011 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1713066 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1713121 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1713176 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1713231 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1713286 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1713341 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1713396 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1713451 TCCTGCTCGTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1713506 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1713561 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1713616 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1713671 TCCTGCTCTTTGGGGACTAAAAAG
1 TCCTGCTCTTTGAGGACTGAAAAG
1713695 CGGAAGGAGA
Statistics
Matches: 1317, Mismatches: 56, Indels: 52
0.92 0.04 0.04
Matches are distributed among these distances:
54 35 0.03
55 1246 0.95
56 36 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:1712430 original size:26 final size:26
Alignment explanation
Indices: 1712401--1712486 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
1712391 GGGCTTTAAG
1712401 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
1712427 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
1712455 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
1712482 AGGTG
1 AGGTG
1712487 CCACCAACTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.29
27 9 0.20
28 9 0.20
29 8 0.18
30 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:1712701 original size:26 final size:26
Alignment explanation
Indices: 1712672--1712816 Score: 91
Period size: 26 Copynumber: 5.3 Consensus size: 26
1712662 GTGTGGGCTT
*
1712672 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
1712698 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
1712725 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
** *
1712753 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
1712780 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
1712808 TGAAAGGTG
1 TGAAAGGTG
1712817 CCACCAACTT
Statistics
Matches: 88, Mismatches: 17, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
25 6 0.07
26 25 0.28
27 18 0.20
28 17 0.19
29 16 0.18
30 6 0.07
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:1713090 original size:26 final size:26
Alignment explanation
Indices: 1713006--1713091 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
1712996 GGGCTTTGAG
*
1713006 AGGTGTCCTGCTCTTTGAGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
1713032 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
1713060 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
1713087 AGGTG
1 AGGTG
1713092 CCACCAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 9 0.20
28 8 0.18
29 8 0.18
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:1714710 original size:21 final size:21
Alignment explanation
Indices: 1714676--1714728 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1714666 CTCTCTTTTC
* *
1714676 CTTTGTTTTGTTTTTTGTT-CT
1 CTTT-TTTTTTTTTTTTTTGCT
*
1714697 TTTTTTTTTTTTTTTTTTGCT
1 CTTTTTTTTTTTTTTTTTGCT
1714718 CTTTTTTTTTT
1 CTTTTTTTTTT
1714729 GAAGAGAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (21 bp):
CTTTTTTTTTTTTTTTTTGCT
Found at i:1714712 original size:23 final size:23
Alignment explanation
Indices: 1714654--1714728 Score: 78
Period size: 23 Copynumber: 3.1 Consensus size: 23
1714644 CTTAAGTAGG
* *
1714654 TTTTTTTCTTTTCTCTCTTTTCCTTT
1 TTTTTTTTTTTTGT-TCTTTT--TTT
* *
1714680 GTTTTGTTTTTTGTTCTTTTTTT
1 TTTTTTTTTTTTGTTCTTTTTTT
*
1714703 TTTTTTTTTTTTGCTCTTTTTTT
1 TTTTTTTTTTTTGTTCTTTTTTT
1714726 TTT
1 TTT
1714729 GAAGAGAAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 26 0.62
25 6 0.14
26 10 0.24
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (23 bp):
TTTTTTTTTTTTGTTCTTTTTTT
Found at i:1723840 original size:23 final size:24
Alignment explanation
Indices: 1723795--1723843 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1723785 TTTTATATGG
*
1723795 TTGATATTTTAAAATATCGATAGT
1 TTGATATTTTAAAATATCAATAGT
1723819 TTGATA-TTTAAGAATAT-AATAGT
1 TTGATATTTTAA-AATATCAATAGT
1723842 TT
1 TT
1723844 TATTCATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (24 bp):
TTGATATTTTAAAATATCAATAGT
Found at i:1725214 original size:2 final size:2
Alignment explanation
Indices: 1725207--1725235 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1725197 ATTCTTCTAA
1725207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1725236 AATTAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1726657 original size:13 final size:14
Alignment explanation
Indices: 1726631--1726659 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1726621 ACTTAATGTC
1726631 ATTAAATAAAATAT
1 ATTAAATAAAATAT
1726645 ATTAAAT-AAATAT
1 ATTAAATAAAATAT
1726658 AT
1 AT
1726660 AATAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTAAATAAAATAT
Found at i:1728545 original size:14 final size:15
Alignment explanation
Indices: 1728513--1728548 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1728503 AAAGTCGAAA
1728513 AAAATTTTAAATATT
1 AAAATTTTAAATATT
*
1728528 AAAATTTT-AATTTT
1 AAAATTTTAAATATT
1728542 AAAATTT
1 AAAATTT
1728549 ACTAAATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATTTTAAATATT
Found at i:1729358 original size:24 final size:23
Alignment explanation
Indices: 1729304--1729358 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
1729294 AATATTGACA
*
1729304 TAAA-TATTAAAATATTAATTAT
1 TAAACTATTAAAATATTAATCAT
* *
1729326 TAAATTATTAAAACTATTTATCAT
1 TAAACTATTAAAA-TATTAATCAT
*
1729350 TTAACTATT
1 TAAACTATT
1729359 GATTTTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 8 0.30
24 15 0.56
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAACTATTAAAATATTAATCAT
Found at i:1729534 original size:12 final size:12
Alignment explanation
Indices: 1729517--1729548 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1729507 TTTACAATTA
1729517 TCAAATAAATAT
1 TCAAATAAATAT
1729529 TCAAATAAATAT
1 TCAAATAAATAT
*
1729541 TAAAATAA
1 TCAAATAA
1729549 TAATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (12 bp):
TCAAATAAATAT
Found at i:1729596 original size:230 final size:232
Alignment explanation
Indices: 1729057--1729717 Score: 916
Period size: 230 Copynumber: 2.8 Consensus size: 232
1729047 AATAGCAAAA
* * *
1729057 TCAACATAAATATTAAATTATTAATTATTAAAATATTAAAAACTATTTATTATTAAAATATTAAT
1 TCAA-ATAAATATTAAAATATTAATTATTAAATTATT-AAAACTATTTATTATTAAACTATT-A-
* * * * * * * * *
1729122 ATTTTAATATCAATATTCCAAATTGTAATGTTTTAATCATAA-GATTTAATACTAAAATATTATA
62 A--TT--T-TCAATATT-AAAATAGTAATATTTCAATAATAATG-GTTAAAAATAAAATAATATA
* * ** *
1729186 TTAATATTAAATACTTCAAATAGACTATTTATTATTAAAATTTTAATTATATTAATATTTAAAAT
120 TTAATATTAAATACTTAAAATATACTATTTATTATTAAAACATTAATTATATAAATATTTAAAAT
1729251 ATTATAACTATTATTAGAAATATTATTTTACAATTATCAAATAAATAT
185 ATTATAACTATTATTAGAAATATTATTTTACAATTATCAAATAAATAT
* * * * *
1729299 TGACATAAATATTAAAATATTAATTATTAAATTATTAAAACTATTTATCATTTAACTATTGATTT
1 TCAAATAAATATTAAAATATTAATTATTAAATTATTAAAACTATTTATTATTAAACTATTAATTT
1729364 TCAATATTAAAATAGTAATATTTCAATAATAATGGTTAAAAATAAAATAATATATTAATATTAAA
66 TCAATATTAAAATAGTAATATTTCAATAATAATGGTTAAAAATAAAATAATATATTAATATTAAA
*
1729429 TACTTAAAATATACCATTTATTATTAAAACATTAATTATATAAATATTTAAAATATTATAACTAT
131 TACTTAAAATATACTATTTATTATTAAAACATTAATTATATAAATATTTAAAATATTATAACTAT
1729494 TATTAG-AA-ATTATTTTACAATTATCAAATAAATAT
196 TATTAGAAATATTATTTTACAATTATCAAATAAATAT
* *
1729529 TCAAATAAATATTAAAATAATAATTATTAAATTATTAAAACTATTTATTGTTAAACTATTAATTT
1 TCAAATAAATATTAAAATATTAATTATTAAATTATTAAAACTATTTATTATTAAACTATTAATTT
* *
1729594 TCAATATGAAAATAGTAATATTTCAATAATAATGGTTAAAAATAAAATAATGTATTAATATTAAA
66 TCAATATTAAAATAGTAATATTTCAATAATAATGGTTAAAAATAAAATAATATATTAATATTAAA
*
1729659 TAATTAAAATAATACTATTTATTATTAAAACATTAATTATATAGAGAT-TTTAAAATATT
131 TACTTAAAAT-ATACTATTTATTATTAAAACATTAATTATATA-A-ATATTTAAAATATT
1729718 TAAAATATAA
Statistics
Matches: 381, Mismatches: 34, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
230 157 0.41
231 33 0.09
232 123 0.32
233 11 0.03
234 1 0.00
236 2 0.01
238 1 0.00
240 21 0.06
241 30 0.08
242 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (232 bp):
TCAAATAAATATTAAAATATTAATTATTAAATTATTAAAACTATTTATTATTAAACTATTAATTT
TCAATATTAAAATAGTAATATTTCAATAATAATGGTTAAAAATAAAATAATATATTAATATTAAA
TACTTAAAATATACTATTTATTATTAAAACATTAATTATATAAATATTTAAAATATTATAACTAT
TATTAGAAATATTATTTTACAATTATCAAATAAATAT
Found at i:1729694 original size:29 final size:26
Alignment explanation
Indices: 1729629--1729694 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 26
1729619 ATAATAATGG
*
1729629 TTAAAAA-TAAAATAATGTATTAATA
1 TTAAAAATTAAAATAATCTATTAATA
*
1729654 TTAAATAATTAAAATAATACTATTTATTA
1 TTAAA-AATTAAAATAAT-CTA-TTAATA
1729683 TTAAAACATTAA
1 TTAAAA-ATTAA
1729695 TTATATAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 5 0.15
26 2 0.06
27 9 0.26
28 3 0.09
29 15 0.44
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (26 bp):
TTAAAAATTAAAATAATCTATTAATA
Found at i:1729777 original size:23 final size:23
Alignment explanation
Indices: 1729751--1729795 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1729741 TTTATTTTTA
*
1729751 TTAATATTTTTAATATTA-AAATC
1 TTAATACTTTT-ATATTAGAAATC
1729774 TTAATACTTTTATATTAGAAAT
1 TTAATACTTTTATATTAGAAAT
1729796 ATTTATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAATACTTTTATATTAGAAATC
Found at i:1729990 original size:30 final size:28
Alignment explanation
Indices: 1729940--1730016 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 28
1729930 TCTTAAATAC
1729940 TATTTTATTAAAATATTAAATTAATATTAA
1 TATTTTATTAAAATATTAAA-TAATATT-A
1729970 TATTTTATTATTAAA-A-TAAATAATATTA
1 TATTTTATTA--AAATATTAAATAATATTA
*
1729998 TA--TTAATAAAATA-TAAATA
1 TATTTTATTAAAATATTAAATA
1730017 TTAAAAATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
24 3 0.07
25 7 0.16
26 5 0.12
28 3 0.07
29 7 0.16
30 14 0.33
31 1 0.02
32 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTTTATTAAAATATTAAATAATATTA
Found at i:1731467 original size:16 final size:17
Alignment explanation
Indices: 1731433--1731490 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
1731423 AAATTATGAA
1731433 TATATAAATATTTTAAATT
1 TATATAAATA--TTAAATT
1731452 TATATAAATA-TAAA-T
1 TATATAAATATTAAATT
1731467 TAT-TAATATATTAAATT
1 TATATAA-ATATTAAATT
1731484 T-TATAAA
1 TATATAAA
1731491 AAATATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.09
15 7 0.20
16 10 0.29
17 5 0.14
19 10 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATAAATATTAAATT
Found at i:1731495 original size:34 final size:33
Alignment explanation
Indices: 1731420--1731504 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
1731410 AGACACGAAA
* * *
1731420 AAAAAATTATGAATATATAAATATTTTAAATTTAT
1 AAAAAA-TATAAAT-TATTAATATATTAAATTTAT
*
1731455 -ATAAATATAAATTATTAATATATTAAATTTTAT
1 AAAAAATATAAATTATTAATATATTAAA-TTTAT
*
1731488 AAAAAATATAAAATATT
1 AAAAAATATAAATTATT
1731505 TTAAATATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
32 13 0.31
33 11 0.26
34 18 0.43
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (33 bp):
AAAAAATATAAATTATTAATATATTAAATTTAT
Found at i:1731497 original size:40 final size:40
Alignment explanation
Indices: 1731423--1731499 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
1731413 CACGAAAAAA
**
1731423 AAATTATGAATATATAAATATTTTAAATTTATATAAATAT
1 AAATTATGAATATATAAATATTTTAAATAAATATAAATAT
*
1731463 AAATTATTAATATATTAAAT-TTTATAAA-AAATATAAA
1 AAATTATGAATATA-TAAATATTT-TAAATAAATATAAA
1731500 ATATTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 23 0.72
41 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (40 bp):
AAATTATGAATATATAAATATTTTAAATAAATATAAATAT
Found at i:1732148 original size:20 final size:19
Alignment explanation
Indices: 1732096--1732150 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1732086 TAAATTAAAT
* *
1732096 TAATTTTATATAT-TTTTA
1 TAATTTTTTATATGATTTA
1732114 TAATTTTTTATATGATTTA
1 TAATTTTTTATATGATTTA
1732133 T-ATTTATTTAATATGATT
1 TAATTT-TTT-ATATGATT
1732151 GTTATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.50
19 8 0.25
20 8 0.25
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TAATTTTTTATATGATTTA
Found at i:1732718 original size:3 final size:3
Alignment explanation
Indices: 1732710--1732759 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
1732700 CCTCCAATCC
*
1732710 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
1732756 TAA T
1 TAA T
1732760 GTCTAACTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1738764 original size:3 final size:3
Alignment explanation
Indices: 1738756--1738784 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1738746 ACCATGAAAA
1738756 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1738785 ACCAGGAATT
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1740258 original size:28 final size:28
Alignment explanation
Indices: 1740176--1740250 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
1740166 TCTCGCTTTT
* *
1740176 TCTTTAATAATTAAAATTATTAAAATTTAA
1 TCTTTAATAACTAAAATTA--ATAATTTAA
1740206 TCTTTAATAACTAAAATTAATAATTTAA
1 TCTTTAATAACTAAAATTAATAATTTAA
*
1740234 TACTTT-ATCACTAAAAT
1 T-CTTTAATAACTAAAAT
1740251 ACGTAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 19 0.46
29 4 0.10
30 18 0.44
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (28 bp):
TCTTTAATAACTAAAATTAATAATTTAA
Found at i:1740979 original size:21 final size:23
Alignment explanation
Indices: 1740926--1740986 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
1740916 GCTTGTAGAT
1740926 TAATTTTATTATTTAAAAATATTA
1 TAATTTTA-TATTTAAAAATATTA
* * *
1740950 AAATATTAT-TTTAAATAT-TTA
1 TAATTTTATATTTAAAAATATTA
*
1740971 TAATTTTATAATTAAA
1 TAATTTTATATTTAAA
1740987 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 10 0.33
22 13 0.43
23 1 0.03
24 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTTTATATTTAAAAATATTA
Found at i:1741224 original size:21 final size:21
Alignment explanation
Indices: 1741187--1741226 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1741177 TGTGTGTTAA
1741187 TAAAAAATAATTATTTTAATT
1 TAAAAAATAATTATTTTAATT
*
1741208 TAAAATAAT-ATTTTTTTAA
1 TAAAA-AATAATTATTTTAA
1741227 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAAAATAATTATTTTAATT
Found at i:1741227 original size:16 final size:17
Alignment explanation
Indices: 1741190--1741233 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
1741180 GTGTTAATAA
1741190 AAAATAATTATTTTAATTT
1 AAAATAA-TATTTT-ATTT
1741209 AAAATAATATTTT-TTT
1 AAAATAATATTTTATTT
*
1741225 AAAAAAATA
1 AAAATAATA
1741234 AAAATAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 11 0.46
18 6 0.25
19 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATAATATTTTATTT
Found at i:1741610 original size:25 final size:24
Alignment explanation
Indices: 1741552--1741630 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 24
1741542 AATAGTTTTA
*
1741552 AAATTTTAAAAAATTATTTTTATATT
1 AAATTTTAAAAAATT-TTTATA-ATT
* *
1741578 -AATATTAATAAATTTTATATAATT
1 AAATTTTAAAAAATTTT-TATAATT
*
1741602 AAATTTTAAAAATATTTTTTATTATT
1 AAATTTTAAAAA-A-TTTTTATAATT
1741628 AAA
1 AAA
1741631 AATAAATCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 5 0.12
25 24 0.56
26 10 0.23
27 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AAATTTTAAAAAATTTTTATAATT
Found at i:1741649 original size:47 final size:50
Alignment explanation
Indices: 1741552--1741649 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 50
1741542 AATAGTTTTA
** *** *
1741552 AAATTTTAAAAAATTATTTTTATATTAATATTAATAAATTTTATATAATT
1 AAATTTTAAAAAATTATTTTTATATTAATAAAAATAAATCAAATAAAATT
*
1741602 AAATTTT-AAAAA-TATTTTT-TATTATTAAAAATAAATCAAATAAAATT
1 AAATTTTAAAAAATTATTTTTATATTAATAAAAATAAATCAAATAAAATT
1741649 A
1 A
1741650 TTTAAATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
47 22 0.54
48 7 0.17
49 5 0.12
50 7 0.17
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (50 bp):
AAATTTTAAAAAATTATTTTTATATTAATAAAAATAAATCAAATAAAATT
Found at i:1741899 original size:15 final size:16
Alignment explanation
Indices: 1741891--1741927 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1741881 AAAATTATTT
1741891 TTTTAAAAATAATTAA
1 TTTTAAAAATAATTAA
1741907 TTTTAAAAAATAA-TAA
1 TTTT-AAAAATAATTAA
1741923 TTTTA
1 TTTTA
1741928 TATTAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 11 0.55
17 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTTAAAAATAATTAA
Found at i:1741910 original size:17 final size:16
Alignment explanation
Indices: 1741890--1741927 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1741880 TAAAATTATT
*
1741890 TTTTTAAAAATAATTAA
1 TTTTAAAAAATAA-TAA
1741907 TTTTAAAAAATAATAA
1 TTTTAAAAAATAATAA
1741923 TTTTA
1 TTTTA
1741928 TATTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAAAAATAATAA
Found at i:1742156 original size:18 final size:17
Alignment explanation
Indices: 1742129--1742181 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
1742119 ATACATACCT
*
1742129 TTTAAATTATATTATTAA
1 TTTATATTATATT-TTAA
1742147 TTTAT-TT-TATTTTAA
1 TTTATATTATATTTTAA
*
1742162 TTTATTATTATCTTTTAA
1 TTTA-TATTATATTTTAA
1742180 TT
1 TT
1742182 GTTATCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 8 0.27
16 5 0.17
17 4 0.13
18 13 0.43
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATATTATATTTTAA
Found at i:1742529 original size:25 final size:25
Alignment explanation
Indices: 1742478--1742527 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
1742468 TTAAAAAATT
1742478 TATTAATTATAAATAATATAATAAA
1 TATTAATTATAAATAATATAATAAA
1742503 TATTAATT-TAAATAAAATATAATAA
1 TATTAATTATAAAT--AATATAATAA
1742528 TAAACTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 8 0.35
26 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TATTAATTATAAATAATATAATAAA
Found at i:1742724 original size:14 final size:14
Alignment explanation
Indices: 1742686--1742729 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1742676 ATAATGTTAT
*
1742686 TAATAGATTTTAAA
1 TAATATATTTTAAA
*
1742700 TTATATA-TTTAAA
1 TAATATATTTTAAA
1742713 TAATATATTTTAAA
1 TAATATATTTTAAA
1742727 TAA
1 TAA
1742730 ATTAGTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TAATATATTTTAAA
Found at i:1742738 original size:27 final size:26
Alignment explanation
Indices: 1742681--1742753 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 26
1742671 TTTACATAAT
* * *
1742681 GTTATTAATAGATTTTAAATTATATA
1 GTTAATAATATATTTTAAATAATATA
*
1742707 TTTAAATAATATATTTTAAATAA-ATTA
1 GTT-AATAATATATTTTAAATAATA-TA
* *
1742734 GTTAATAAAATATTTAAAAT
1 GTTAATAATATATTTTAAAT
1742754 TTTAAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 18 0.47
27 20 0.53
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
GTTAATAATATATTTTAAATAATATA
Found at i:1742775 original size:29 final size:30
Alignment explanation
Indices: 1742719--1742784 Score: 73
Period size: 33 Copynumber: 2.2 Consensus size: 30
1742709 TAAATAATAT
1742719 ATTTTAAATAAATTAGTTAATAAAATATTTAAA
1 ATTTTAAATAAATTA--TAATAAAATA-TTAAA
* *
1742752 ATTTTAAATAAATTA-AA-AATATATTAAT
1 ATTTTAAATAAATTATAATAAAATATTAAA
1742780 ATTTT
1 ATTTT
1742785 TTAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 9 0.29
29 5 0.16
30 2 0.06
33 15 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
ATTTTAAATAAATTATAATAAAATATTAAA
Found at i:1742986 original size:3 final size:3
Alignment explanation
Indices: 1742978--1743022 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1742968 CTCCATTTGC
1742978 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1743023 AGCTTTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1744811 original size:25 final size:25
Alignment explanation
Indices: 1744764--1744812 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1744754 ATTTTAATTT
* * *
1744764 TTTTAAAAATTAATTAAATATAATA
1 TTTTAAAAATAAAATAAACATAATA
*
1744789 TTTTAAAAATAAAATCAACATAAT
1 TTTTAAAAATAAAATAAACATAAT
1744813 TTAAGTCATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
TTTTAAAAATAAAATAAACATAATA
Found at i:1746352 original size:2 final size:2
Alignment explanation
Indices: 1746345--1746370 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1746335 ACATACATAC
1746345 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
1746371 TGTAAGCTGT
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):
AT
Found at i:1752583 original size:14 final size:14
Alignment explanation
Indices: 1752544--1752597 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
1752534 TTTTTGATTA
*
1752544 TATAATAATATATAT
1 TATATTAATATA-AT
*
1752559 TAT-TTTA-ATAAT
1 TATATTAATATAAT
1752571 TATATTAATATAAT
1 TATATTAATATAAT
1752585 T-TATATAATATAA
1 TATAT-TAATATAA
1752598 GAAATAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 5 0.15
13 9 0.27
14 16 0.48
15 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTAATATAAT
Found at i:1755894 original size:17 final size:17
Alignment explanation
Indices: 1755872--1755905 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1755862 GAGTTTATAC
1755872 TATAAAAATAAAAAAAT
1 TATAAAAATAAAAAAAT
*
1755889 TATAAAAATAATAAAAT
1 TATAAAAATAAAAAAAT
1755906 ATTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TATAAAAATAAAAAAAT
Found at i:1756627 original size:30 final size:29
Alignment explanation
Indices: 1756593--1756656 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
1756583 TCCTTTAATT
1756593 TTTTTTCTATTTTTCTATATTCATGTTACC
1 TTTTTTCTATTTTTCTATATTCATGTTA-C
*
1756623 TTTTTTTTATTTTTCTATATTCATGTTAC
1 TTTTTTCTATTTTTCTATATTCATGTTAC
1756652 TTTTT
1 TTTTT
1756657 ATTTTTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.16, C:0.12, G:0.03, T:0.69
Consensus pattern (29 bp):
TTTTTTCTATTTTTCTATATTCATGTTAC
Found at i:1756661 original size:26 final size:28
Alignment explanation
Indices: 1756594--1756664 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 28
1756584 CCTTTAATTT
1756594 TTTTTCTATTTTTCTATATTCATGTTACC
1 TTTTT-TATTTTTCTATATTCATGTTACC
1756623 TTTTTTTTATTTTTCTATATTCATGTTA-C
1 --TTTTTTATTTTTCTATATTCATGTTACC
1756652 -TTTTTATTTTTCT
1 TTTTTTATTTTTCT
1756665 TTCCATTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
26 13 0.32
29 1 0.03
30 21 0.52
31 5 0.12
ACGTcount: A:0.15, C:0.13, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTTATTTTTCTATATTCATGTTACC
Found at i:1757848 original size:3 final size:3
Alignment explanation
Indices: 1757840--1757874 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1757830 AATTATGTAC
1757840 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1757875 CGTCTTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1765093 original size:2 final size:2
Alignment explanation
Indices: 1765088--1765120 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1765078 TGTGTGTGTT
1765088 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 A
1765121 ACACCTTTGC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1765409 original size:34 final size:34
Alignment explanation
Indices: 1765371--1765440 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1765361 TCTTTGTTAA
1765371 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
1 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
1765405 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
1 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
1765439 GA
1 GA
1765441 GAATGTTAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.40
Consensus pattern (34 bp):
GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
Done.