Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 20 of 26
Found at i:3225302 original size:56 final size:56
Alignment explanation
Indices: 3225216--3225327 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
3225206 CACATGGCAC
3225216 CCATTTGTATAATATTAGCTTTGAACCTTGTTTATAATGCCCAAGGATATACTAAA
1 CCATTTGTATAATATTAGCTTTGAACCTTGTTTATAATGCCCAAGGATATACTAAA
* *
3225272 CCATTTGTATACTATTAGCTTTGAACCTTGTTTATAATGCCCAAGTATATACTAAA
1 CCATTTGTATAATATTAGCTTTGAACCTTGTTTATAATGCCCAAGGATATACTAAA
3225328 ATGCTAAGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (56 bp):
CCATTTGTATAATATTAGCTTTGAACCTTGTTTATAATGCCCAAGGATATACTAAA
Found at i:3232953 original size:14 final size:13
Alignment explanation
Indices: 3232921--3232982 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
3232911 AATATTTTAT
3232921 ATTTATATTAAT-
1 ATTTATATTAATA
*
3232933 TTTTATAATTAATA
1 ATTTAT-ATTAATA
3232947 ATTTATATTATATA
1 ATTTATATTA-ATA
*
3232961 AATTATA-TATATA
1 ATTTATATTA-ATA
3232974 TATTTATAT
1 -ATTTATAT
3232983 CATATTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 5 0.12
13 16 0.39
14 20 0.49
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTATATTAATA
Found at i:3233313 original size:23 final size:20
Alignment explanation
Indices: 3233287--3233333 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
3233277 TTAAATAAAA
*
3233287 TATTATATTA-ATCAT-TTT
1 TATTATATTATATTATATTT
3233305 TATTATATTATATTATATTT
1 TATTATATTATATTATATTT
3233325 TATT-TATTA
1 TATTATATTA
3233334 AATATGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 10 0.38
19 9 0.35
20 7 0.27
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATATTATATTATATTT
Found at i:3234342 original size:2 final size:2
Alignment explanation
Indices: 3234335--3234378 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3234325 TAACAATGGG
3234335 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3234377 GA
1 GA
3234379 CCGTTCTCAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3236272 original size:39 final size:39
Alignment explanation
Indices: 3236158--3236485 Score: 193
Period size: 36 Copynumber: 8.7 Consensus size: 39
3236148 GATGAAACGA
* * *
3236158 TAATTCGAGATAATCTGCATGATAAATACAATCAATAAC
1 TAATTCGAGATAATCTGCACGATAACTACTATCAATAAC
* * * * *
3236197 TATTTTTG-CAT-AT-TTCAC-ATTACTACTATCAATAAC
1 TA-ATTCGAGATAATCTGCACGATAACTACTATCAATAAC
*
3236233 TAATTCGAGATAATCTGCACGATAACTA-TAATTAATAAC
1 TAATTCGAGATAATCTGCACGATAACTACT-ATCAATAAC
* * * * * *
3236272 TATTTCTACAT-AT-TTCA-TATTACTACTATCAATAAC
1 TAATTCGAGATAATCTGCACGATAACTACTATCAATAAC
* * * *
3236308 TAATCCGAGATAATCTGCATGATAACTACAATCAACAAC
1 TAATTCGAGATAATCTGCACGATAACTACTATCAATAAC
* * * * *
3236347 TATTTCTG-CAT-AT-TTCAC-ATTACTACTATCAACAAC
1 TAATTC-GAGATAATCTGCACGATAACTACTATCAATAAC
* * *
3236383 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAC
1 TAATTCGAGATAATCTGCACGATAACTACTATCAATAAC
* * * * *
3236422 TATTTCTG-CAT-AT-TTCAC-ATTACTACTATCAACAAC
1 TAATTC-GAGATAATCTGCACGATAACTACTATCAATAAC
* * *
3236458 TAATCCAAGATAATCTGTACGATAACTA
1 TAATTCGAGATAATCTGCACGATAACTA
3236486 TGGAGGTTGA
Statistics
Matches: 213, Mismatches: 56, Indels: 40
0.69 0.18 0.13
Matches are distributed among these distances:
35 4 0.02
36 84 0.39
37 22 0.10
38 23 0.11
39 75 0.35
40 5 0.02
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (39 bp):
TAATTCGAGATAATCTGCACGATAACTACTATCAATAAC
Found at i:3236284 original size:75 final size:75
Alignment explanation
Indices: 3236158--3236485 Score: 512
Period size: 75 Copynumber: 4.4 Consensus size: 75
3236148 GATGAAACGA
* * * * *
3236158 TAATTCGAGATAATCTGCATGATAAATACAATCAATAACTATTTTTGCATATTTCACATTACTAC
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTCACATTACTAC
*
3236223 TATCAATAAC
66 TATCAACAAC
* * * * * *
3236233 TAATTCGAGATAATCTGCACGATAACTATAATTAATAACTATTTCTACATATTTCATATTACTAC
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTCACATTACTAC
*
3236298 TATCAATAAC
66 TATCAACAAC
*
3236308 TAATCCGAGATAATCTGCATGATAACTACAATCAACAACTATTTCTGCATATTTCACATTACTAC
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTCACATTACTAC
3236373 TATCAACAAC
66 TATCAACAAC
3236383 TAATCCGAGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTCACATTACTAC
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTCACATTACTAC
3236448 TATCAACAAC
66 TATCAACAAC
* *
3236458 TAATCCAAGATAATCTGTACGATAACTA
1 TAATCCGAGATAATCTGCACGATAACTA
3236486 TGGAGGTTGA
Statistics
Matches: 235, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 235 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (75 bp):
TAATCCGAGATAATCTGCACGATAACTACAATCAACAACTATTTCTGCATATTTCACATTACTAC
TATCAACAAC
Found at i:3236623 original size:15 final size:15
Alignment explanation
Indices: 3236603--3236641 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3236593 GGTAAACAGG
3236603 TGGTGGATGCACGGA
1 TGGTGGATGCACGGA
* *
3236618 TTGTGGATGCACGGG
1 TGGTGGATGCACGGA
3236633 TGGTGGATG
1 TGGTGGATG
3236642 GACAGGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.49, T:0.26
Consensus pattern (15 bp):
TGGTGGATGCACGGA
Found at i:3237685 original size:17 final size:17
Alignment explanation
Indices: 3237641--3237691 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
3237631 GTCAAACACG
* *
3237641 TAAAATAATTAAAAAAA
1 TAAAATTATTAATAAAA
* *
3237658 TAACA-TATTAATAATA
1 TAAAATTATTAATAAAA
3237674 TAAAATTATTAATTAAAA
1 TAAAATTATTAA-TAAAA
3237692 AAAGTATTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
16 12 0.46
17 10 0.38
18 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATTATTAATAAAA
Found at i:3239586 original size:15 final size:14
Alignment explanation
Indices: 3239566--3239605 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
3239556 TTATAGGCTT
3239566 TAAACTAATTATCCC
1 TAAACTAATTA-CCC
*
3239581 TAAACTAATTACTC
1 TAAACTAATTACCC
3239595 TAAACCTAATT
1 TAAA-CTAATT
3239606 CCACATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAACTAATTACCC
Found at i:3243785 original size:17 final size:16
Alignment explanation
Indices: 3243765--3243810 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
3243755 TTTTATTTTG
3243765 ATTTAATTTAAATAATT
1 ATTTAATTTAAATAA-T
*
3243782 ATTTAATAATAAA-AAT
1 ATTTAAT-TTAAATAAT
3243798 ATTTAATTTAAAT
1 ATTTAATTTAAAT
3243811 TTAATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 9 0.36
18 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAATTTAAATAAT
Found at i:3244031 original size:15 final size:16
Alignment explanation
Indices: 3244013--3244053 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3244003 AATTTGAATA
3244013 AAATTTTATTTAT-TT
1 AAATTTTATTTATATT
*
3244028 AAATTTAATTTATATT
1 AAATTTTATTTATATT
3244044 AAATTATTAT
1 AAATT-TTAT
3244054 ATTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 12 0.55
16 7 0.32
17 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATTTTATTTATATT
Found at i:3244047 original size:16 final size:16
Alignment explanation
Indices: 3243995--3244048 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
3243985 TGCTCGTGAG
*
3243995 TTAAATTAAATTTGA-A
1 TTAAATTTAATTT-ATA
* *
3244011 TAAAATTTTATTTAT-
1 TTAAATTTAATTTATA
3244026 TTAAATTTAATTTATA
1 TTAAATTTAATTTATA
3244042 TTAAATT
1 TTAAATT
3244049 ATTATATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 14 0.45
16 17 0.55
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTTAATTTATA
Found at i:3244057 original size:19 final size:17
Alignment explanation
Indices: 3244013--3244063 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 17
3244003 AATTTGAATA
3244013 AAATTT-TATTTAT-TT
1 AAATTTATATTTATATT
3244028 AAATTTA-ATTTATATT
1 AAATTTATATTTATATT
*
3244044 AAATTATTATATTTTTATT
1 AAA-T-TTATATTTATATT
3244063 A
1 A
3244064 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.40
16 5 0.17
17 1 0.03
18 3 0.10
19 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATTTATATTTATATT
Found at i:3244368 original size:15 final size:15
Alignment explanation
Indices: 3244338--3244378 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3244328 TATCCGGTAA
*
3244338 TTTATA-TATTTA-T
1 TTTATATTATATATT
3244351 TTTATATTTATATATT
1 TTTATA-TTATATATT
3244367 TTTATATTATAT
1 TTTATATTATAT
3244379 TTATGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATATTATATATT
Found at i:3244370 original size:21 final size:21
Alignment explanation
Indices: 3244337--3244388 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
3244327 TTATCCGGTA
*
3244337 ATTTATATA--TTTATTTTAT
1 ATTTATATATTTTTATATTAT
3244356 ATTTATATATTTTTATATTAT
1 ATTTATATATTTTTATATTAT
*
3244377 ATTTATGTATTT
1 ATTTATATATTT
3244389 ACGTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 9 0.31
21 20 0.69
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTATATATTTTTATATTAT
Found at i:3246487 original size:2 final size:2
Alignment explanation
Indices: 3246480--3246511 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3246470 TTTTTCCACT
*
3246480 GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3246512 CCATTTTCAT
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3248544 original size:19 final size:19
Alignment explanation
Indices: 3248520--3248558 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3248510 GTGATACAAT
3248520 AGACTCATCTTCCTGCAAA
1 AGACTCATCTTCCTGCAAA
3248539 AGACTCATCTTCCTGCAAA
1 AGACTCATCTTCCTGCAAA
3248558 A
1 A
3248559 TATAATAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.26
Consensus pattern (19 bp):
AGACTCATCTTCCTGCAAA
Found at i:3254429 original size:3 final size:3
Alignment explanation
Indices: 3254423--3254454 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3254413 TTTTAAAAAA
3254423 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3254455 ATATATATAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3254829 original size:135 final size:138
Alignment explanation
Indices: 3254509--3254862 Score: 499
Period size: 135 Copynumber: 2.6 Consensus size: 138
3254499 ACTCTTGATG
** *
3254509 AGTTATTTTATTAAATTT-AAAAATATTAAAAATAATGAGTAGTTTTTAGATGA-TAATTATCTT
1 AGTTATTTTATTAAATTTAAAAAATATTAAAAATGGTGAGTAGTTTTTAGA-GAGTAATTATTTT
* * *
3254572 TT-CAAAAATAAAAAAACTTAATTATTCGTAATTTTATTTTTATTCTTATAGCACTAAGTGTGAG
65 TTAAAAAAATAAAAAAACTTAA-TA-T--TAATTTTATATTTATTCTTATAACACTAAGTGTGAG
3254636 ACATCTAGTGAGT
126 ACATCTAGTGAGT
* * *
3254649 AGTTATTTTATTAAAGTTAAAAAATATTAAAAATGGTTAATAGTTTTTAGAGAGTAATTATTTTT
1 AGTTATTTTATTAAATTTAAAAAATATTAAAAATGGTGAGTAGTTTTTAGAGAGTAATTATTTTT
3254714 TAAAAAGAATAAAAGAAACTT-A-A-TAATTTTATATTTATT-TTATAACACTAAGTGTGAGACA
66 TAAAAA-AATAAAA-AAACTTAATATTAATTTTATATTTATTCTTATAACACTAAGTGTGAGACA
3254775 TCTAGTGAGT
129 TCTAGTGAGT
*
3254785 AG-TATTTTATTAAATTTAAAAAATATTAAAAATGGTGAGTAGTTTTTAGAGGGTAATTATTTTT
1 AGTTATTTTATTAAATTTAAAAAATATTAAAAATGGTGAGTAGTTTTTAGAGAGTAATTATTTTT
3254849 TAAAAAAATAAAAA
66 TAAAAAAATAAAAA
3254863 GATTTAAATA
Statistics
Matches: 196, Mismatches: 13, Indels: 17
0.87 0.06 0.08
Matches are distributed among these distances:
133 1 0.01
134 7 0.04
135 64 0.33
136 33 0.17
137 15 0.08
140 19 0.10
141 40 0.20
142 3 0.02
143 8 0.04
144 6 0.03
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (138 bp):
AGTTATTTTATTAAATTTAAAAAATATTAAAAATGGTGAGTAGTTTTTAGAGAGTAATTATTTTT
TAAAAAAATAAAAAAACTTAATATTAATTTTATATTTATTCTTATAACACTAAGTGTGAGACATC
TAGTGAGT
Found at i:3255966 original size:20 final size:19
Alignment explanation
Indices: 3255943--3255998 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
3255933 TATATGTATT
3255943 ATTTATTTAATATTAAAATA
1 ATTTATTTAA-ATTAAAATA
*
3255963 ATTTATTTAAATTTAAAATT
1 ATTTATTTAAA-TTAAAATA
*
3255983 TTTTATTTAAATTAAA
1 ATTTATTTAAATTAAA
3255999 TTGAATTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 6 0.18
20 27 0.82
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTATTTAAATTAAAATA
Found at i:3255975 original size:55 final size:57
Alignment explanation
Indices: 3255882--3255988 Score: 130
Period size: 55 Copynumber: 1.9 Consensus size: 57
3255872 TTCGAAATTT
* * *
3255882 TATTTTTTAATTTTATATTAAAAATCATATAATTAAA-TTAAATATTTATTATATATG
1 TATTATTTAATTTAATATTAAAAATAATATAATTAAATTTAAA-ATTTATTATATATG
* * *
3255939 TATTATTT-ATTTAATATT-AAAATAATTTATTTAAATTTAAAATTTTTTAT
1 TATTATTTAATTTAATATTAAAAATAATATAATTAAATTTAAAATTTATTAT
3255989 TTAAATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
55 22 0.51
56 14 0.33
57 7 0.16
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (57 bp):
TATTATTTAATTTAATATTAAAAATAATATAATTAAATTTAAAATTTATTATATATG
Found at i:3256377 original size:12 final size:12
Alignment explanation
Indices: 3256360--3256401 Score: 56
Period size: 10 Copynumber: 3.8 Consensus size: 12
3256350 AATTATTATT
3256360 TTTATATTAATA
1 TTTATATTAATA
3256372 TTTATA-TAAT-
1 TTTATATTAATA
3256382 TTTATATTAA-A
1 TTTATATTAATA
3256393 TTTA-ATTAA
1 TTTATATTAA
3256402 AAATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 11 0.39
11 11 0.39
12 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTATATTAATA
Found at i:3256439 original size:17 final size:17
Alignment explanation
Indices: 3256391--3256439 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
3256381 TTTTATATTA
3256391 AATTTAATTAAAAATAAT
1 AATTTAATT-AAAATAAT
*
3256409 AATTATTATT-AAATAAT
1 AATT-TAATTAAAATAAT
3256426 AATTTAATTAAAAT
1 AATTTAATTAAAAT
3256440 TAAATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 15 0.56
18 4 0.15
19 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTAATTAAAATAAT
Found at i:3256441 original size:22 final size:20
Alignment explanation
Indices: 3256396--3256449 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
3256386 TATTAAATTT
*
3256396 AATTAAA-AATAATAATTAT
1 AATTAAATAATAATAATTAA
*
3256415 TATTAAATAATAATTTAATTAA
1 AATTAAATAATAA--TAATTAA
*
3256437 AATTAAATTATAA
1 AATTAAATAATAA
3256450 AAAATTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 5 0.18
22 17 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTAAATAATAATAATTAA
Found at i:3256715 original size:17 final size:17
Alignment explanation
Indices: 3256665--3256722 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
3256655 ATAAGATAAA
3256665 AATAATTTTATATATATTTT
1 AATAATTTTA-A-ATA-TTT
*
3256685 AATAGTATTT-AATATTT
1 AATAAT-TTTAAATATTT
3256702 AATAATTTTAAATATATT
1 AATAATTTTAAATAT-TT
3256720 AAT
1 AAT
3256723 TTATATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 3 0.09
17 13 0.39
18 8 0.24
19 1 0.03
20 5 0.15
21 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATAATTTTAAATATTT
Found at i:3257027 original size:31 final size:31
Alignment explanation
Indices: 3256931--3257013 Score: 130
Period size: 31 Copynumber: 2.6 Consensus size: 31
3256921 GGGAATTAGA
3256931 GATCGTTTGGTAAGGTGCATCCAAATGCACTCC
1 GATC-TTT-GTAAGGTGCATCCAAATGCACTCC
*
3256964 GGTCTTTGTAAGGTGCATCCAAATGCACTCC
1 GATCTTTGTAAGGTGCATCCAAATGCACTCC
*
3256995 GATCTTTGTGAGGTGCATC
1 GATCTTTGTAAGGTGCATC
3257014 TGTATGCATT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 41 0.87
32 3 0.06
33 3 0.06
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (31 bp):
GATCTTTGTAAGGTGCATCCAAATGCACTCC
Found at i:3263441 original size:26 final size:26
Alignment explanation
Indices: 3263411--3263481 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 26
3263401 ACATTAATCA
* *
3263411 TATTTAGATTATAATTTTTTTATCGT
1 TATTTAAATTATAATTTTTTTATAGT
3263437 TATTTAAATTATAATTCTTTTTTTATAGT
1 TATTTAAATTATAA---TTTTTTTATAGT
3263466 TATTTAAATTATAATT
1 TATTTAAATTATAATT
3263482 CTTATATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 15 0.38
29 25 0.62
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (26 bp):
TATTTAAATTATAATTTTTTTATAGT
Found at i:3263467 original size:29 final size:29
Alignment explanation
Indices: 3263425--3263484 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
3263415 TAGATTATAA
*
3263425 TTTTTTTATCGTTATTTAAATTATAATTC
1 TTTTTTTATAGTTATTTAAATTATAATTC
3263454 TTTTTTTATAGTTATTTAAATTATAATTC
1 TTTTTTTATAGTTATTTAAATTATAATTC
3263483 TT
1 TT
3263485 ATATATTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.63
Consensus pattern (29 bp):
TTTTTTTATAGTTATTTAAATTATAATTC
Found at i:3263734 original size:2 final size:2
Alignment explanation
Indices: 3263727--3263788 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
3263717 TCTTTCTCTT
3263727 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
*
3263769 TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3263789 CTCATTAGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3264420 original size:21 final size:22
Alignment explanation
Indices: 3264396--3264440 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3264386 ATAAAAAAAT
3264396 AATTT-GATCAATGAAAAATTA
1 AATTTGGATCAATGAAAAATTA
* *
3264417 AATTTGGGTCAATGAAAACTTA
1 AATTTGGATCAATGAAAAATTA
3264439 AA
1 AA
3264441 CTATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (22 bp):
AATTTGGATCAATGAAAAATTA
Found at i:3264486 original size:20 final size:19
Alignment explanation
Indices: 3264453--3264501 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
3264443 ATTTTTTTTT
* *
3264453 TTAAATTATCTTTTTAAAACA
1 TTAAAATAT-TTTTCAAAA-A
3264474 TGTAAAATATTTTTCAAAAA
1 T-TAAAATATTTTTCAAAAA
3264494 TTAAAATA
1 TTAAAATA
3264502 GAATAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.28
20 2 0.08
21 9 0.36
22 7 0.28
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAAAATATTTTTCAAAAA
Found at i:3266561 original size:2 final size:2
Alignment explanation
Indices: 3266548--3266590 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3266538 TTCTCTTTAC
*
3266548 AT AT AC 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
3266590 A
1 A
3266591 ACTCATTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3268025 original size:19 final size:19
Alignment explanation
Indices: 3267992--3268028 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3267982 TGTCTATATA
3267992 TTTTTAATTTAATTTAATT
1 TTTTTAATTTAATTTAATT
3268011 TTTTATAATTT-ATTTAAT
1 TTTT-TAATTTAATTTAAT
3268029 CGTGACATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTAATTTAATTTAATT
Found at i:3274182 original size:16 final size:15
Alignment explanation
Indices: 3274159--3274201 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3274149 TAATAATATT
*
3274159 AAATATAATTATATA
1 AAATATAATTAAATA
*
3274174 AATATATAA-AAAATA
1 AA-ATATAATTAAATA
3274189 AAATATAATTAAA
1 AAATATAATTAAA
3274202 ATATGATACG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.26
15 11 0.48
16 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATAATTAAATA
Found at i:3274189 original size:23 final size:25
Alignment explanation
Indices: 3274140--3274189 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 25
3274130 TATTATTAAA
* * *
3274140 AATTATATTTAATAATATTAAATAT
1 AATTATATTAAATAATATAAAAAAT
3274165 AATTATA-TAAAT-ATATAAAAAAT
1 AATTATATTAAATAATATAAAAAAT
3274188 AA
1 AA
3274190 AATATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 11 0.50
24 4 0.18
25 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AATTATATTAAATAATATAAAAAAT
Found at i:3274202 original size:16 final size:16
Alignment explanation
Indices: 3274159--3274204 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
3274149 TAATAATATT
*
3274159 AAATATAATT-ATATA
1 AAATATAATTAAAATA
3274174 AATATATAA--AAAATA
1 AA-ATATAATTAAAATA
3274189 AAATATAATTAAAATA
1 AAATATAATTAAAATA
3274205 TGATACGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
16 12 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATAATTAAAATA
Found at i:3274310 original size:14 final size:16
Alignment explanation
Indices: 3274291--3274322 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3274281 AAATATTTTA
3274291 ATCATAAT-TAT-AAT
1 ATCATAATATATGAAT
3274305 ATCATAATATATGAAT
1 ATCATAATATATGAAT
3274321 AT
1 AT
3274323 AACGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
ATCATAATATATGAAT
Found at i:3277471 original size:22 final size:22
Alignment explanation
Indices: 3277446--3277491 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3277436 ATTGCATGCA
3277446 TAATTCATTACTTTTCTGCCCT
1 TAATTCATTACTTTTCTGCCCT
*
3277468 TAATTCATTACTTTTCTGGCCT
1 TAATTCATTACTTTTCTGCCCT
3277490 TA
1 TA
3277492 GTAAATGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.50
Consensus pattern (22 bp):
TAATTCATTACTTTTCTGCCCT
Found at i:3279534 original size:11 final size:11
Alignment explanation
Indices: 3279518--3279543 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3279508 GCTTCAGATG
3279518 TTTCATTTTAT
1 TTTCATTTTAT
3279529 TTTCATTTTAT
1 TTTCATTTTAT
3279540 TTTC
1 TTTC
3279544 TCCTTCAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:3280465 original size:30 final size:30
Alignment explanation
Indices: 3280431--3280511 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
3280421 ATTATTAAAG
* * *
3280431 TGATTTTATCGCAATTTATTACTATTATGA
1 TGATTTAATCACAATTTATTACTATTACGA
* *
3280461 TGATTTGATCACAATTTATTTCTATTACGA
1 TGATTTAATCACAATTTATTACTATTACGA
*
3280491 TGATTTAATAACAATTTATTA
1 TGATTTAATCACAATTTATTA
3280512 TTATAGTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (30 bp):
TGATTTAATCACAATTTATTACTATTACGA
Found at i:3280991 original size:19 final size:19
Alignment explanation
Indices: 3280965--3281022 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 19
3280955 AATTGTTATT
3280965 ATAAATATTTTTATTAT-A
1 ATAAATATTTTTATTATAA
3280983 ATAAAATATTTATTTAATTTATAA
1 AT-AAATA-TT-TTT-A-TTATAA
3281007 ATAAATATTTTTATTA
1 ATAAATATTTTTATTA
3281023 ATGATAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.06
19 8 0.24
20 3 0.09
21 6 0.18
22 3 0.09
23 9 0.26
24 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAAATATTTTTATTATAA
Found at i:3281029 original size:23 final size:22
Alignment explanation
Indices: 3280965--3281029 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
3280955 AATTGTTATT
*
3280965 ATAAATATTTTTATT-ATA-AT
1 ATAAATATTTTTATTAATATAA
*
3280985 A-AAATATTTAT-TTAATTTATAA
1 ATAAATATTTTTATTAA--TATAA
3281007 ATAAATATTTTTATTAATGATAA
1 ATAAATATTTTTATTAAT-ATAA
3281030 TATCTGTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
18 2 0.06
19 10 0.29
20 1 0.03
21 2 0.06
22 3 0.09
23 13 0.37
24 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAAATATTTTTATTAATATAA
Found at i:3281853 original size:73 final size:73
Alignment explanation
Indices: 3281767--3281910 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
3281757 CACCAAACAT
* * * *
3281767 AATTATCTAATCATCATATCGAATGGCTATGA-TTTTTAATATCATCACCCCAATACCAAACACT
1 AATTATCTAATCATCATATCAAATCGCTATGATTTTTTAATATAACCA-CCCAATACCAAACACT
3281831 AGATTTATG
65 AGATTTATG
* * * *
3281840 AATTATCTAATCATCATATCAAATCGCTTTGATTTTTTAGTATAACCACCCAATGCCAGACACTA
1 AATTATCTAATCATCATATCAAATCGCTATGATTTTTTAATATAACCACCCAATACCAAACACTA
3281905 GATTTA
66 GATTTA
3281911 GGGTTACTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 50 0.81
74 12 0.19
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (73 bp):
AATTATCTAATCATCATATCAAATCGCTATGATTTTTTAATATAACCACCCAATACCAAACACTA
GATTTATG
Found at i:3282648 original size:23 final size:25
Alignment explanation
Indices: 3282600--3282670 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
3282590 TTAAAAATAT
*
3282600 ATATAAATT-TA-TATATTATTAATA
1 ATATAAATTATATTATTTTATTAA-A
3282624 A-ATTAAATTATATTATTTTATTAAA
1 ATA-TAAATTATATTATTTTATTAAA
*
3282649 ATAAAAATTAT-TTATATTTATT
1 ATATAAATTATATTAT-TTTATT
3282671 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 1 0.03
24 11 0.28
25 17 0.43
26 11 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATAAATTATATTATTTTATTAAA
Found at i:3282881 original size:23 final size:25
Alignment explanation
Indices: 3282855--3282915 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 25
3282845 CTGCTTTACT
3282855 ATTTAATTAATTTTAAT-TT-ATAA
1 ATTTAATTAATTTTAATATTAATAA
3282878 A-TT--TTAATTTTAATAATTAATAA
1 ATTTAATTAATTTTAAT-ATTAATAA
3282901 ATTTAATATAATTTT
1 ATTTAAT-TAATTTT
3282916 TATGAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
20 11 0.35
22 4 0.13
23 6 0.19
24 2 0.06
26 1 0.03
27 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTAATTAATTTTAATATTAATAA
Found at i:3284026 original size:16 final size:15
Alignment explanation
Indices: 3284005--3284047 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
3283995 TATGTTTATA
*
3284005 AATTAAATTTGAATT
1 AATTAAATTTAAATT
* *
3284020 ATTTTAATTTTAAATT
1 A-ATTAAATTTAAATT
3284036 AATTAAATTTAA
1 AATTAAATTTAA
3284048 TATTTATATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATTAAATTTAAATT
Found at i:3284045 original size:22 final size:23
Alignment explanation
Indices: 3284020--3284065 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3284010 AATTTGAATT
3284020 ATTTTAAT-TTTAAATTAATTAA
1 ATTTTAATATTTAAATTAATTAA
*
3284042 A-TTTAATATTTATATTAATTAA
1 ATTTTAATATTTAAATTAATTAA
3284064 AT
1 AT
3284066 ATAAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTTAATATTTAAATTAATTAA
Found at i:3284073 original size:53 final size:53
Alignment explanation
Indices: 3283969--3284073 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
3283959 GTTAGATGAA
* * *
3283969 TTTAATATTAGATTAATTAAATTTAATATGTTTATAAATTAAATTTGAATTAT
1 TTTAATATTAAATTAATTAAATTTAATATGTTTATAAATTAAATATAAATTAT
* *
3284022 TTTAATTTTAAATTAATTAAATTTAATAT-TTATATTAATTAAATATAAATTA
1 TTTAATATTAAATTAATTAAATTTAATATGTT-TATAAATTAAATATAAATTA
3284074 ATTATATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 2 0.04
53 44 0.96
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (53 bp):
TTTAATATTAAATTAATTAAATTTAATATGTTTATAAATTAAATATAAATTAT
Found at i:3284127 original size:24 final size:24
Alignment explanation
Indices: 3284038--3284129 Score: 75
Period size: 24 Copynumber: 3.8 Consensus size: 24
3284028 TTTAAATTAA
*
3284038 TTAAATTT-AAT-ATTTATATTA-A
1 TTAAATTTAAATAATTTAT-TTATT
*
3284060 TTAAATATAAATTAATTATATTTATTAT
1 TTAAATTTAAA-TAATT-TATTTA-T-T
*
3284088 TTAAATTTATCA-AATTTATTTATT
1 TTAAATTTA-AATAATTTATTTATT
3284112 TTAAATTTAAATAATTTA
1 TTAAATTTAAATAATTTA
3284130 ACTTAACTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
22 7 0.12
23 3 0.05
24 17 0.30
25 7 0.12
26 9 0.16
27 4 0.07
28 8 0.14
29 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAAATTTAAATAATTTATTTATT
Found at i:3284175 original size:25 final size:23
Alignment explanation
Indices: 3284137--3284182 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
3284127 TTAACTTAAC
3284137 TATTTAAATATTTTTGAATTAAAAT
1 TATTT-AATATTTTT-AATTAAAAT
*
3284162 TATTTAATTTTTTTAATTAAA
1 TATTTAATATTTTTAATTAAA
3284183 TTAAATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 8 0.40
25 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTTAATATTTTTAATTAAAAT
Found at i:3284185 original size:22 final size:25
Alignment explanation
Indices: 3284137--3284182 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
3284127 TTAACTTAAC
3284137 TATTTAAATATTTTTGAATTAAAAT
1 TATTTAAATATTTTTGAATTAAAAT
*
3284162 TATTT-AAT-TTTTTTAATTAAA
1 TATTTAAATATTTTTGAATTAAA
3284183 TTAAATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 3 0.15
25 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TATTTAAATATTTTTGAATTAAAAT
Found at i:3286121 original size:35 final size:32
Alignment explanation
Indices: 3286058--3286125 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 32
3286048 AATTGCTTTC
*
3286058 TTTTTTTTAAAAAAAAAATGAATGAATTTAAA
1 TTTTTTTTAAAAAAAAAATGAATAAATTTAAA
* *
3286090 TTTTTTATTAAAAAAATTAATTTAATAAATTTAAA
1 TTTTTT-TTAAAAAAA--AAATGAATAAATTTAAA
3286125 T
1 T
3286126 ACTTTACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 6 0.20
33 9 0.30
35 15 0.50
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
TTTTTTTTAAAAAAAAAATGAATAAATTTAAA
Found at i:3286203 original size:28 final size:30
Alignment explanation
Indices: 3286168--3286223 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
3286158 AAATCATAAC
3286168 ATTTAAAT-TTAATAAAAA-TAA-TAAATAT
1 ATTTAAATATT-ATAAAAATTAATTAAATAT
3286196 ATTTAAATATTATAAAAATTAATTAAAT
1 ATTTAAATATTATAAAAATTAATTAAAT
3286224 TAATATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 15 0.60
29 5 0.20
30 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATTTAAATATTATAAAAATTAATTAAATAT
Found at i:3286823 original size:3 final size:3
Alignment explanation
Indices: 3286815--3286866 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
3286805 AACAAATGAC
3286815 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3286863 TAA T
1 TAA T
3286867 TATTATTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3286871 original size:3 final size:3
Alignment explanation
Indices: 3286865--3286899 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3286855 AATAATAATA
3286865 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3286900 AATCACAAAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3287258 original size:17 final size:18
Alignment explanation
Indices: 3287236--3287270 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3287226 AGTGTTTGTA
3287236 TTTAAATTTA-TTTATTT
1 TTTAAATTTATTTTATTT
3287253 TTTAAATTTATTTTATTT
1 TTTAAATTTATTTTATTT
3287271 ATGTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTAAATTTATTTTATTT
Found at i:3287286 original size:22 final size:22
Alignment explanation
Indices: 3287242--3287287 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3287232 TGTATTTAAA
* *
3287242 TTTATTTATTTTTTAAATTTAT
1 TTTATTTATTTTATAAATATAT
3287264 TTTATTTATGTTTAT-AATATAT
1 TTTATTTAT-TTTATAAATATAT
3287286 TT
1 TT
3287288 GATATCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTATTTATTTTATAAATATAT
Found at i:3287473 original size:43 final size:43
Alignment explanation
Indices: 3287426--3287513 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
3287416 TAAATTCAAA
*
3287426 TTAAATATTGAA-AAAATTTGTAAGAATGCTATCTTCCCTTATG
1 TTAAATATTGAACAAAA-TTGTAAGAATGCTATCTTCACTTATG
* * *
3287469 TTAAATTTTGAACAAAATTGTAAGTATGCTATCTTCATTTATG
1 TTAAATATTGAACAAAATTGTAAGAATGCTATCTTCACTTATG
3287512 TT
1 TT
3287514 TTGCCACCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 36 0.90
44 4 0.10
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.43
Consensus pattern (43 bp):
TTAAATATTGAACAAAATTGTAAGAATGCTATCTTCACTTATG
Found at i:3296748 original size:102 final size:102
Alignment explanation
Indices: 3296627--3296824 Score: 308
Period size: 102 Copynumber: 1.9 Consensus size: 102
3296617 ATAAATTTGT
* * *
3296627 ATTTTAAAGCAGTTATGTGGGTTTGAAGAAAACAAAAAATGTAAAAATTTGATCCGTTACGGTTT
1 ATTTTAAAGCAGTTATGTGGGTTTGAAGAAAACAAAAAATATAAAAAATTGATCCGTTACGATTT
3296692 TTAATTTTTGTACATTAACAATGAATTTTTTCTTTTA
66 TTAATTTTTGTACATTAACAATGAATTTTTTCTTTTA
* *
3296729 ATTTTAAAGC-GATTATGTGGGTTTGGATAAAACAAAAAATATAAAAAATTGATCCGTTACGATT
1 ATTTTAAAGCAG-TTATGTGGGTTTGAAGAAAACAAAAAATATAAAAAATTGATCCGTTACGATT
* * *
3296793 TTTATTTTTTGTACATTAATAATGATTTTTTT
65 TTTAATTTTTGTACATTAACAATGAATTTTTT
3296825 TATTTCATTT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 1 0.01
102 86 0.99
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (102 bp):
ATTTTAAAGCAGTTATGTGGGTTTGAAGAAAACAAAAAATATAAAAAATTGATCCGTTACGATTT
TTAATTTTTGTACATTAACAATGAATTTTTTCTTTTA
Found at i:3297038 original size:20 final size:19
Alignment explanation
Indices: 3297000--3297040 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3296990 AATAAAAAAA
* *
3297000 TAATTTTAATTTTAATATT
1 TAATTTTAAATTCAATATT
3297019 TAATTTTAAATTCAATTATT
1 TAATTTTAAATTCAA-TATT
3297039 TA
1 TA
3297041 TATTGAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATTTTAAATTCAATATT
Found at i:3298269 original size:22 final size:22
Alignment explanation
Indices: 3298228--3298269 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3298218 GCGAAAGTAA
*
3298228 TTTTTTATTTTATAATTTTAAT
1 TTTTTTATTATATAATTTTAAT
3298250 TTTTTTATTAT-TAATATTTA
1 TTTTTTATTATATAAT-TTTA
3298270 CGATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTATTATATAATTTTAAT
Found at i:3298801 original size:5 final size:5
Alignment explanation
Indices: 3298786--3298844 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
3298776 TAAAAATACT
* *
3298786 ATATGA ATATA ATAT- ATTTA ATA-A ATATA ATATA ATATA ATAT- ATTTAA
1 ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A
3298835 ATATA ATATA
1 ATATA ATATA
3298845 TATTAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
4 10 0.22
5 28 0.62
6 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:3298823 original size:28 final size:31
Alignment explanation
Indices: 3298786--3298844 Score: 97
Period size: 28 Copynumber: 2.0 Consensus size: 31
3298776 TAAAAATACT
3298786 ATATGAATATAATATATTT-AATA-AATATA
1 ATATGAATATAATATATTTAAATATAATATA
3298815 ATAT-AATATAATATATTTAAATATAATATA
1 ATATGAATATAATATATTTAAATATAATATA
3298845 TATTAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 14 0.50
29 8 0.29
30 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (31 bp):
ATATGAATATAATATATTTAAATATAATATA
Found at i:3298841 original size:25 final size:27
Alignment explanation
Indices: 3298786--3298844 Score: 86
Period size: 25 Copynumber: 2.2 Consensus size: 27
3298776 TAAAAATACT
3298786 ATATGAATATAATATATTTAATAAATATA
1 ATAT-AATATAATATATTT-ATAAATATA
3298815 ATATAATATAATATA-TT-TAAATATA
1 ATATAATATAATATATTTATAAATATA
3298840 ATATA
1 ATATA
3298845 TATTAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 13 0.43
27 2 0.07
28 11 0.37
29 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATAATATAATATATTTATAAATATA
Found at i:3298921 original size:24 final size:24
Alignment explanation
Indices: 3298870--3298921 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3298860 TAAAATTTTT
* * *
3298870 ATATTTAAATAATTAATATTATAT
1 ATATTTAAATAATTAATATAAAAA
* *
3298894 ATATTTATATGATTAATATAAAAA
1 ATATTTAAATAATTAATATAAAAA
3298918 ATAT
1 ATAT
3298922 AAAATATGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATTTAAATAATTAATATAAAAA
Found at i:3299959 original size:15 final size:15
Alignment explanation
Indices: 3299939--3299967 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3299929 AAAAATTTTA
3299939 AAAAATAATTAAAAC
1 AAAAATAATTAAAAC
3299954 AAAAATAATTAAAA
1 AAAAATAATTAAAA
3299968 TAATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAATTAAAAC
Found at i:3299986 original size:21 final size:20
Alignment explanation
Indices: 3299960--3300003 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3299950 AAACAAAAAT
3299960 AATTAAAATAATAAAATATAA
1 AATTAAAATAATAAAA-ATAA
* *
3299981 AATTAACATAATATAAATAA
1 AATTAAAATAATAAAAATAA
3300001 AAT
1 AAT
3300004 CTGACCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AATTAAAATAATAAAAATAA
Found at i:3303094 original size:15 final size:15
Alignment explanation
Indices: 3303042--3303101 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
3303032 TTATATTTTA
*
3303042 TAAATAAATTTAAAT
1 TAAATTAATTTAAAT
*
3303057 TAAATTTA-TT-AA-
1 TAAATTAATTTAAAT
3303069 TAAATAATAATTTAAAT
1 TAAAT--TAATTTAAAT
3303086 TAAATTAATTTAAAT
1 TAAATTAATTTAAAT
3303101 T
1 T
3303102 TAAAACATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 5 0.14
13 2 0.05
14 4 0.11
15 19 0.51
16 2 0.05
17 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTAATTTAAAT
Found at i:3303552 original size:6 final size:7
Alignment explanation
Indices: 3303535--3303560 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3303525 TACAATGAAT
3303535 TTTTTAC
1 TTTTTAC
3303542 TTTTTAC
1 TTTTTAC
3303549 TTTTTAC
1 TTTTTAC
3303556 TTTTT
1 TTTTT
3303561 TGAGGTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAC
Found at i:3304748 original size:4 final size:4
Alignment explanation
Indices: 3304739--3304764 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3304729 TAATATGTAA
3304739 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
3304765 GGTGAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3305037 original size:16 final size:16
Alignment explanation
Indices: 3305011--3305088 Score: 86
Period size: 16 Copynumber: 4.8 Consensus size: 16
3305001 TGATTAACTC
*
3305011 AAATATAAAATAATTTT
1 AAAT-TAAAATAATTTA
*
3305028 AATTTAAAATAATTTA
1 AAATTAAAATAATTTA
* *
3305044 AAATTAAAATGATCTA
1 AAATTAAAATAATTTA
3305060 AAATTAAAATAATTT-
1 AAATTAAAATAATTTA
*
3305075 CAATCTAAAATAAT
1 AAAT-TAAAATAAT
3305089 ACTAAATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
15 3 0.06
16 46 0.88
17 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (16 bp):
AAATTAAAATAATTTA
Found at i:3305108 original size:48 final size:49
Alignment explanation
Indices: 3305011--3305108 Score: 112
Period size: 48 Copynumber: 2.0 Consensus size: 49
3305001 TGATTAACTC
* * * **
3305011 AAATATAAAATAATTTTAATTTAAAATAATTTAAAATTAAAATGATCTA
1 AAATATAAAATAATTTCAATCTAAAATAATCTAAAATTAAAAAAATCTA
3305060 AAAT-TAAAATAATTTCAATCTAAAATAATACT-AAA-TAAAAAAACTCTA
1 AAATATAAAATAATTTCAATCTAAAATAAT-CTAAAATTAAAAAAA-TCTA
3305108 A
1 A
3305109 CTTTAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
47 6 0.14
48 31 0.74
49 5 0.12
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (49 bp):
AAATATAAAATAATTTCAATCTAAAATAATCTAAAATTAAAAAAATCTA
Found at i:3305475 original size:15 final size:14
Alignment explanation
Indices: 3305447--3305539 Score: 77
Period size: 14 Copynumber: 6.6 Consensus size: 14
3305437 GCTCAAGTAT
3305447 AATTT-AATAAAAA
1 AATTTAAATAAAAA
*
3305460 ATTTTAAATAAAAA
1 AATTTAAATAAAAA
* *
3305474 AA-TTAAATTTAAAT
1 AATTTAAA-TAAAAA
*
3305488 AATTTAAATTTAAAAT
1 AATTTAAA--TAAAAA
3305504 AATTTAAAT--AAA
1 AATTTAAATAAAAA
*
3305516 ATTTTAAATAAAAAA
1 AATTTAAAT-AAAAA
3305531 AATTTAAAT
1 AATTTAAAT
3305540 TATTTAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
12 10 0.15
13 9 0.14
14 16 0.25
15 16 0.25
16 14 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTTAAATAAAAA
Found at i:3305538 original size:27 final size:26
Alignment explanation
Indices: 3305447--3305539 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 26
3305437 GCTCAAGTAT
*
3305447 AATTTAATAAAAAATTTTAAATAAAAA
1 AATTTAA-ATAAAATTTTAAATAAAAA
* *
3305474 AA-TTAAATTTAAATAATTTAAATTTAAAAT
1 AATTTAAA--TAAA-ATTTTAAA--TAAAAA
3305504 AATTTAAATAAAATTTTAAATAAAAAA
1 AATTTAAATAAAATTTTAAAT-AAAAA
3305531 AATTTAAAT
1 AATTTAAAT
3305540 TATTTAAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
25 1 0.02
26 5 0.09
27 18 0.33
28 14 0.26
29 4 0.07
30 7 0.13
31 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTTAAATAAAATTTTAAATAAAAA
Found at i:3305549 original size:52 final size:54
Alignment explanation
Indices: 3305445--3305564 Score: 181
Period size: 52 Copynumber: 2.2 Consensus size: 54
3305435 TCGCTCAAGT
*
3305445 ATAATTTAATAAAAAATTTTAAATAAAAAAATTAAATTTAAATAATTTAAATTTAAA
1 ATAATTTAA-ATAAAATTTTAAAT-AAAAAA-TAAATTTAAATAATTTAAATTTAAA
*
3305502 ATAATTTAAATAAAATTTTAAAT-AAAAA-AAATTTAAATTATTTAAATTTAAA
1 ATAATTTAAATAAAATTTTAAATAAAAAATAAATTTAAATAATTTAAATTTAAA
3305554 ATAATTTAAAT
1 ATAATTTAAAT
3305565 TCAAAATAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
52 34 0.56
54 5 0.08
56 13 0.21
57 9 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (54 bp):
ATAATTTAAATAAAATTTTAAATAAAAAATAAATTTAAATAATTTAAATTTAAA
Found at i:3305588 original size:17 final size:16
Alignment explanation
Indices: 3305476--3305579 Score: 90
Period size: 16 Copynumber: 7.2 Consensus size: 16
3305466 AATAAAAAAA
3305476 TTAAATTT-AAATAAT
1 TTAAATTTAAAATAAT
3305491 TTAAATTTAAAATAAT
1 TTAAATTTAAAATAAT
3305507 TTAAA--TAAAAT--T
1 TTAAATTTAAAATAAT
3305519 TTAAA--T-AAA-AA-
1 TTAAATTTAAAATAAT
*
3305530 --AAATTT-AAATTAT
1 TTAAATTTAAAATAAT
3305543 TTAAATTTAAAATAAT
1 TTAAATTTAAAATAAT
*
3305559 TTAAATTCAAAATAAAT
1 TTAAATTTAAAAT-AAT
3305576 TTAA
1 TTAA
3305580 CTTTGAAATT
Statistics
Matches: 75, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
9 3 0.04
11 7 0.09
12 8 0.11
14 6 0.08
15 14 0.19
16 30 0.40
17 7 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:3306498 original size:17 final size:16
Alignment explanation
Indices: 3306462--3306499 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3306452 TTGAAAAATT
*
3306462 TTATA-TTTATAATTA
1 TTATATTTTATAATAA
3306477 TTATATTTTATAATAAA
1 TTATATTTTATAAT-AA
3306494 TTATAT
1 TTATAT
3306500 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 8 0.40
17 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTTTATAATAA
Found at i:3312484 original size:2 final size:2
Alignment explanation
Indices: 3312477--3312511 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3312467 AACTACAAAC
*
3312477 AT AT AT AT AT AT AT AT AT AT AT AT AC AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3312512 CTTATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3312983 original size:19 final size:21
Alignment explanation
Indices: 3312959--3313021 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
3312949 ATTCATAATA
3312959 ATATTAA-AATAATA-TTTTT
1 ATATTAATAATAATATTTTTT
* *
3312978 ATATTAATATTTATATTTTTT
1 ATATTAATAATAATATTTTTT
* *
3312999 ATATTAAT-TTTATATTTTTT
1 ATATTAATAATAATATTTTTT
3313019 ATA
1 ATA
3313022 ATTATATTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.17
20 20 0.50
21 13 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTAATAATAATATTTTTT
Found at i:3313018 original size:20 final size:21
Alignment explanation
Indices: 3312973--3313029 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
3312963 TAAAATAATA
3312973 TTTTTATATTAATATTTATAT
1 TTTTTATATTAATATTTATAT
3312994 TTTTTATATTAAT-TTTATAT
1 TTTTTATATTAATATTTATAT
3313014 TTTTTATAATT-ATATT
1 TTTTTAT-ATTAATATT
3313030 AGCGTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTATATTAATATTTATAT
Found at i:3313491 original size:28 final size:31
Alignment explanation
Indices: 3313456--3313512 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
3313446 TATAATTAAG
3313456 AAGTATTT-AAACAAATT-TAAA-AAATTGA
1 AAGTATTTAAAACAAATTATAAATAAATTGA
3313484 AAGTATTTAAAACAAATTATAAATAAATT
1 AAGTATTTAAAACAAATTATAAATAAATT
3313513 ACTTAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 8 0.31
29 9 0.35
30 4 0.15
31 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (31 bp):
AAGTATTTAAAACAAATTATAAATAAATTGA
Found at i:3313615 original size:25 final size:21
Alignment explanation
Indices: 3313558--3313617 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 21
3313548 AAATTATAAA
3313558 TTATAAATAAATCAAAATTTTAT
1 TTAT-AATAAAT-AAAATTTTAT
3313581 TTATAA-AAATAAATATATTTAT
1 TTATAATAAATAAA-AT-TTTAT
3313603 TTAATAATTAAATAA
1 TT-ATAA-TAAATAA
3313618 TTAATTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.09
21 6 0.19
22 9 0.28
23 8 0.25
25 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATAATAAATAAAATTTTAT
Found at i:3313627 original size:26 final size:22
Alignment explanation
Indices: 3313575--3313630 Score: 58
Period size: 26 Copynumber: 2.4 Consensus size: 22
3313565 TAAATCAAAA
3313575 TTTTATTTATAAAAATAAATAT
1 TTTTATTTATAAAAATAAATAT
* *
3313597 ATTTATTTAATAATTAAATAATTAAT
1 TTTTATTT-ATAA--AAATAAAT-AT
3313623 TTTTATTT
1 TTTTATTT
3313631 TATTCTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.26
23 4 0.15
25 7 0.26
26 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATTTATAAAAATAAATAT
Found at i:3321945 original size:25 final size:25
Alignment explanation
Indices: 3321914--3321965 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
3321904 CCTATAAATT
3321914 ATTAAAATTATATTT-ATAAATAATA
1 ATTAAAATTATATTTAAT-AATAATA
3321939 ATTAAAATTATATTTAATAATAATA
1 ATTAAAATTATATTTAATAATAATA
3321964 AT
1 AT
3321966 AAATAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTAAAATTATATTTAATAATAATA
Found at i:3321955 original size:12 final size:12
Alignment explanation
Indices: 3321915--3321955 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
3321905 CTATAAATTA
3321915 TTAAAATTATAT
1 TTAAAATTATAT
* *
3321927 TTATAAATAATAA
1 TTA-AAATTATAT
3321940 TTAAAATTATAT
1 TTAAAATTATAT
3321952 TTAA
1 TTAA
3321956 TAATAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTAAAATTATAT
Found at i:3322252 original size:17 final size:18
Alignment explanation
Indices: 3322220--3322253 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3322210 TTCCTTGTAA
*
3322220 TTTTTGCTTTCATTTTAG
1 TTTTTGCTTACATTTTAG
3322238 TTTTTGCTTAC-TTTTA
1 TTTTTGCTTACATTTTA
3322254 AATATCAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.68
Consensus pattern (18 bp):
TTTTTGCTTACATTTTAG
Found at i:3330944 original size:16 final size:17
Alignment explanation
Indices: 3330920--3330958 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3330910 TCGTTAAATA
3330920 TTTAATA-TTTTATTTT
1 TTTAATATTTTTATTTT
*
3330936 TTTATTATTTTTA-TTT
1 TTTAATATTTTTATTTT
3330952 TTTAATA
1 TTTAATA
3330959 ACTTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTAATATTTTTATTTT
Found at i:3331609 original size:12 final size:13
Alignment explanation
Indices: 3331589--3331621 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3331579 TTAATTTATA
3331589 TTATTTAAAAATT
1 TTATTTAAAAATT
*
3331602 TT-TTTAAAATTT
1 TTATTTAAAAATT
3331614 TTATTTAA
1 TTATTTAA
3331622 TATATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTTAAAAATT
Found at i:3332747 original size:25 final size:27
Alignment explanation
Indices: 3332719--3332779 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
3332709 AAATAATTAA
3332719 TAATTTAATATA-TATAA-ATAAATTT
1 TAATTTAATATACTATAATATAAATTT
*
3332744 TAATTT-ATATACTTATAATATATATTT
1 TAATTTAATATAC-TATAATATAAATTT
3332771 T--TTTAATAT
1 TAATTTAATAT
3332780 TGAAATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.16
25 9 0.29
26 9 0.29
27 8 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TAATTTAATATACTATAATATAAATTT
Found at i:3333174 original size:20 final size:19
Alignment explanation
Indices: 3333130--3333184 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
3333120 GCCCAACCCC
*
3333130 TTTTTTAATTTTATTTTTA
1 TTTTTTAATATTATTTTTA
*
3333149 TCTTTTAA-ATTATTTTAATA
1 TTTTTTAATATTATTTT--TA
3333169 TTTTTTAATAATTATT
1 TTTTTTAAT-ATTATT
3333185 ATTAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 7 0.24
19 7 0.24
20 9 0.31
22 6 0.21
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTAATATTATTTTTA
Found at i:3333966 original size:6 final size:6
Alignment explanation
Indices: 3333955--3333995 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
3333945 AACAAAATTA
*
3333955 TATATT TATATT T-TATT TATA-T TATATT TGATATT TGTATT
1 TATATT TATATT TATATT TATATT TATATT T-ATATT TATATT
3333996 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
5 10 0.32
6 15 0.48
7 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:3333973 original size:11 final size:11
Alignment explanation
Indices: 3333957--3333995 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
3333947 CAAAATTATA
3333957 TATTTATATTT
1 TATTTATATTT
*
3333968 TATTTATATTA
1 TATTTATATTT
3333979 TATTTGATATTT
1 TATTT-ATATTT
3333991 GTATT
1 -TATT
3333996 ATTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.62
12 5 0.21
13 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (11 bp):
TATTTATATTT
Found at i:3333995 original size:18 final size:16
Alignment explanation
Indices: 3333955--3334001 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
3333945 AACAAAATTA
3333955 TATATTTATATTTTATT
1 TATA-TTATATTTTATT
3333972 TATATTATATTTGATATT
1 TATATTATATTT--TATT
*
3333990 TGTATTAT-TTTT
1 TATATTATATTTT
3334002 TTAACTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.04
16 8 0.30
17 7 0.26
18 11 0.41
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (16 bp):
TATATTATATTTTATT
Found at i:3334119 original size:28 final size:28
Alignment explanation
Indices: 3334100--3334156 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
3334090 TTTATGTTAG
3334100 TTTCATATTATTTTTATATTATATTATA
1 TTTCATATTATTTTTATATTATATTATA
* *
3334128 TTTTATATTATTTTTCATGTTAT-TTATA
1 TTTCATATTATTTTT-ATATTATATTATA
3334156 T
1 T
3334157 CATATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (28 bp):
TTTCATATTATTTTTATATTATATTATA
Found at i:3334133 original size:17 final size:16
Alignment explanation
Indices: 3334104--3334138 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
3334094 TGTTAGTTTC
3334104 ATATTATTTTTATATT
1 ATATTATTTTTATATT
3334120 ATATTATATTTTATATT
1 ATATTAT-TTTTATATT
3334137 AT
1 AT
3334139 TTTTCATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATATTATTTTTATATT
Found at i:3334729 original size:33 final size:30
Alignment explanation
Indices: 3334665--3334734 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
3334655 TATTTATTTT
*
3334665 ATTAAAA-ATATTTTTATAATTAAATTTAA
1 ATTAAAATATATTTTTATAATTAAATTAAA
3334694 ATTAAAATATATTATTT-TAATTAAAATATAAAA
1 ATTAAAATATATT-TTTATAATT-AAAT-T-AAA
3334727 ATTAAAAT
1 ATTAAAAT
3334735 TTTAAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 7 0.20
30 10 0.29
31 7 0.20
32 1 0.03
33 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATTAAAATATATTTTTATAATTAAATTAAA
Found at i:3346847 original size:24 final size:25
Alignment explanation
Indices: 3346820--3346884 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
3346810 TTATTGATTT
3346820 TATTATTTAAATAATA-TTAAAAAA
1 TATTATTTAAATAATATTTAAAAAA
* *
3346844 TATT-TTTATAATAA-ATTTAAATAT
1 TATTATTTA-AATAATATTTAAAAAA
*
3346868 TTTTATTTTAAATAATA
1 TATTA-TTTAAATAATA
3346885 ATAAGAGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
23 5 0.15
24 18 0.55
25 5 0.15
26 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TATTATTTAAATAATATTTAAAAAA
Found at i:3352064 original size:2 final size:2
Alignment explanation
Indices: 3352016--3352044 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3352006 TATATGTACA
3352016 TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3352045 CGCATGCGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
TG
Found at i:3356472 original size:71 final size:69
Alignment explanation
Indices: 3356345--3356476 Score: 174
Period size: 71 Copynumber: 1.9 Consensus size: 69
3356335 AAAATAACAA
* * ** *
3356345 AAATAGTTATAAAAGGTAACATTAATAATACAGGTTCTAATTTAATAACAAATAATAGTAAAAGA
1 AAATAATTATAAAAGGTAACATTAATAATAAAACTTATAATTTAATAACAAATAATAGTAAAAGA
3356410 TAAT
66 TAAT
* **
3356414 AAATAATTATAAAAGGTAAACATTGATAAATAAAACTTATAATTTTGTAACAAATAATAGTAA
1 AAATAATTATAAAAGGT-AACATTAAT-AATAAAACTTATAATTTAATAACAAATAATAGTAA
3356477 TTTTATTGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 16 0.30
70 8 0.15
71 29 0.55
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (69 bp):
AAATAATTATAAAAGGTAACATTAATAATAAAACTTATAATTTAATAACAAATAATAGTAAAAGA
TAAT
Found at i:3357421 original size:20 final size:21
Alignment explanation
Indices: 3357366--3357421 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
3357356 TAAATTTTTA
3357366 TTAAATATTATA-TTATTAAAT
1 TTAAA-ATTATATTTATTAAAT
* *
3357387 TTAAAAATATTTTTATT-AA-
1 TTAAAATTATATTTATTAAAT
3357406 TTATAAATTATATTTA
1 TTA-AAATTATATTTA
3357422 ATATTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 3 0.10
20 16 0.55
21 10 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAAAATTATATTTATTAAAT
Found at i:3357424 original size:29 final size:28
Alignment explanation
Indices: 3357392--3357450 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
3357382 TAAATTTAAA
3357392 AATA-TTTTTATTAATTATAAATTATATTT
1 AATATTTTTTATT-ATTA-AAATTATATTT
*
3357421 AATATTTTTTATTATTAAAATTATTTTT
1 AATATTTTTTATTATTAAAATTATATTT
3357449 AA
1 AA
3357451 AATATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 12 0.43
29 8 0.29
30 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
AATATTTTTTATTATTAAAATTATATTT
Found at i:3357809 original size:17 final size:17
Alignment explanation
Indices: 3357763--3357799 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3357753 GATTTACTAT
3357763 ATTA-ATTATTTTTTAA
1 ATTATATTATTTTTTAA
3357779 ATTATATTATTTTTTACA
1 ATTATATTATTTTTTA-A
3357797 ATT
1 ATT
3357800 TGATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 11 0.58
18 4 0.21
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATATTATTTTTTAA
Found at i:3359063 original size:26 final size:27
Alignment explanation
Indices: 3359034--3359087 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
3359024 TTTTTTTGTA
* *
3359034 TATTTATTTTTTATT-ACTCATATTAC
1 TATTTACTTTTAATTAACTCATATTAC
*
3359060 TATTTACTTTTAATTAATTCATATTAC
1 TATTTACTTTTAATTAACTCATATTAC
3359087 T
1 T
3359088 TTCATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTTACTTTTAATTAACTCATATTAC
Found at i:3359167 original size:22 final size:19
Alignment explanation
Indices: 3359119--3359168 Score: 50
Period size: 22 Copynumber: 2.6 Consensus size: 19
3359109 TATTTATTAT
3359119 ATTATTATA-TAAAATAAA
1 ATTATTATATTAAAATAAA
*
3359137 A-TATAATATTACATAATAAA
1 ATTATTATATTA-A-AATAAA
3359157 ATTTATTATATT
1 A-TTATTATATT
3359169 TATTTTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.24
18 3 0.12
19 1 0.04
20 7 0.28
22 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTATTATATTAAAATAAA
Found at i:3359627 original size:19 final size:19
Alignment explanation
Indices: 3359575--3359646 Score: 56
Period size: 21 Copynumber: 3.6 Consensus size: 19
3359565 AAATTTATCA
*
3359575 TTAAATTAAATAAAAATAATT
1 TTAAATTAAA-AATAATAA-T
**
3359596 TTTTATTATAAAATAATAAT
1 TTAAATTA-AAAATAATAAT
* *
3359616 TTAAATTAAAAAT-TTTAT
1 TTAAATTAAAAATAATAAT
3359634 TTAAATTTAAAAA
1 TTAAA-TTAAAAA
3359647 ATACAAGTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 8 0.19
19 12 0.29
20 7 0.17
21 13 0.31
22 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAATTAAAAATAATAAT
Found at i:3359714 original size:8 final size:8
Alignment explanation
Indices: 3359692--3359732 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
3359682 GAAGAACTTG
3359692 ATATACAT
1 ATATACAT
3359700 AT-T-CAT
1 ATATACAT
3359706 ATATACAT
1 ATATACAT
*
3359714 ATATATAT
1 ATATACAT
*
3359722 ATATATAT
1 ATATACAT
3359730 ATA
1 ATA
3359733 CAAATTAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 5 0.17
7 2 0.07
8 23 0.77
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (8 bp):
ATATACAT
Found at i:3359822 original size:24 final size:23
Alignment explanation
Indices: 3359782--3359831 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
3359772 TATATCCAAT
** *
3359782 AATATTTTTATTTTTTATTTTATA
1 AATATTTTTATAATTTAATTTA-A
3359806 AATATTTTTATAATTTAATTTAA
1 AATATTTTTATAATTTAATTTAA
3359829 AAT
1 AAT
3359832 TTTATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
AATATTTTTATAATTTAATTTAA
Found at i:3360444 original size:20 final size:19
Alignment explanation
Indices: 3360394--3360450 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
3360384 AAATATTATT
3360394 TTTAAAAATAAAAATATGAA
1 TTTAAAAAT-AAAATATGAA
* *
3360414 ATAATAAAATAAAATATGAA
1 TTTA-AAAATAAAATATGAA
*
3360434 TTTAAATAATAATATAT
1 TTTAAA-AATAAAATAT
3360451 TTTAATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.07
20 23 0.77
21 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
TTTAAAAATAAAATATGAA
Found at i:3360447 original size:18 final size:17
Alignment explanation
Indices: 3360420--3360462 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3360410 TGAAATAATA
3360420 AAATAA-AATATGAATTT
1 AAATAATAATAT-AATTT
*
3360437 AAATAATAATATATTTT
1 AAATAATAATATAATTT
3360454 AATATAATA
1 AA-ATAATA
3360463 CACTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATAATAATATAATTT
Found at i:3361016 original size:3 final size:3
Alignment explanation
Indices: 3361010--3361042 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3361000 TAGTAGTAGT
3361010 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3361043 GCAACCTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3361773 original size:3 final size:3
Alignment explanation
Indices: 3361765--3361795 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3361755 TTTTAAATCT
3361765 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3361796 GCAAGCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3362068 original size:2 final size:2
Alignment explanation
Indices: 3362061--3362098 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3362051 TTCTTGGTTG
3362061 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
3362099 GTTTCCATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3362701 original size:13 final size:13
Alignment explanation
Indices: 3362685--3362728 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
3362675 TAAAAATCAG
3362685 TTTAATAAATTTA
1 TTTAATAAATTTA
3362698 TTTAAATAAATTTA
1 TTT-AATAAATTTA
**
3362712 TTTAATTTATTTA
1 TTTAATAAATTTA
3362725 TTTA
1 TTTA
3362729 TTTTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 15 0.54
14 13 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAATAAATTTA
Found at i:3362707 original size:14 final size:14
Alignment explanation
Indices: 3362688--3362716 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3362678 AAATCAGTTT
3362688 AATAAATTTATTTA
1 AATAAATTTATTTA
3362702 AATAAATTTATTTA
1 AATAAATTTATTTA
3362716 A
1 A
3362717 TTTATTTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAAATTTATTTA
Found at i:3362768 original size:23 final size:22
Alignment explanation
Indices: 3362733--3362783 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
3362723 TATTTATTTT
*
3362733 TTAAAATTAAATTATTAAATAAA
1 TTAAAATTAAATTA-AAAATAAA
* *
3362756 TTAATATTTAATTAAAAATAAA
1 TTAAAATTAAATTAAAAATAAA
3362778 -TAAAAT
1 TTAAAAT
3362784 ATATATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 5 0.21
22 7 0.29
23 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAATTAAATTAAAAATAAA
Found at i:3362934 original size:18 final size:18
Alignment explanation
Indices: 3362910--3362950 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3362900 GTTAAAATAA
3362910 AATTTGATTAATTT-TTT
1 AATTTGATTAATTTATTT
*
3362927 ATATTTGATTGATTTATTT
1 A-ATTTGATTAATTTATTT
3362946 AATTT
1 AATTT
3362951 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 16 0.76
19 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (18 bp):
AATTTGATTAATTTATTT
Found at i:3363030 original size:21 final size:21
Alignment explanation
Indices: 3363004--3363044 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3362994 ATTTTATTCA
3363004 TAATTT-ATAAAAAATATAAAT
1 TAATTTAATAAAAAAT-TAAAT
*
3363025 TAATTTAATTAAAAATTAAA
1 TAATTTAATAAAAAATTAAA
3363045 AAATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTTAATAAAAAATTAAAT
Found at i:3363108 original size:20 final size:20
Alignment explanation
Indices: 3363067--3363121 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3363057 TGATATATTT
* *
3363067 TAAAAAATT-ATTAAATTGA
1 TAAAAAATTAATTTAATTAA
*
3363086 TAAAAAATTAATTTATTTAA
1 TAAAAAATTAATTTAATTAA
3363106 TAAAAAATTAATTTAA
1 TAAAAAATTAATTTAA
3363122 AATATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAAAATTAATTTAATTAA
Found at i:3363240 original size:18 final size:17
Alignment explanation
Indices: 3363208--3363250 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
3363198 ATATCTTTAA
3363208 ATAATATATTTATATTATT
1 ATAAT-TATTTATATT-TT
3363227 -TAATTATTTAATATTTT
1 ATAATTATTT-ATATTTT
3363244 ATAATTA
1 ATAATTA
3363251 AATATTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATTATTTATATTTT
Found at i:3363254 original size:15 final size:16
Alignment explanation
Indices: 3363223--3363269 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
3363213 ATATTTATAT
* *
3363223 TATTTAA-TTATTTAA
1 TATTTAACTAATTAAA
*
3363238 TATTTTA-TAATTAAA
1 TATTTAACTAATTAAA
3363253 TATTTAACTAATTAAA
1 TATTTAACTAATTAAA
3363269 T
1 T
3363270 GATAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTAACTAATTAAA
Done.