Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 24 of 27
Found at i:3364900 original size:21 final size:21
Alignment explanation
Indices: 3364876--3364931 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 21
3364866 ATTTTTTATT
3364876 TAATTTAATTAATTTAAATAA
1 TAATTTAATTAATTTAAATAA
*
3364897 TAATTT-TTTAA---AAATAA
1 TAATTTAATTAATTTAAATAA
*
3364914 T-ATTTAATAAATTTAAAT
1 TAATTTAATTAATTTAAAT
3364932 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
20 8 0.29
21 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTTAATTAATTTAAATAA
Found at i:3364970 original size:16 final size:18
Alignment explanation
Indices: 3364934--3364968 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3364924 ATTTAAATTT
3364934 ATTTTTTATATGTTTAAA
1 ATTTTTTATATGTTTAAA
3364952 ATTTTTTATAT-TTTAAA
1 ATTTTTTATATGTTTAAA
3364969 TTATGGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTTTTTATATGTTTAAA
Found at i:3365691 original size:120 final size:122
Alignment explanation
Indices: 3365486--3365725 Score: 448
Period size: 120 Copynumber: 2.0 Consensus size: 122
3365476 CAATTTATCC
* *
3365486 ACCGACACAATCGAGTGTTAGCAAATAAATTAAAATTTTACACTATAACTAACAAAGTGGATATC
1 ACCGACACAATCGAGTGTTAGCAAAGAAATTAAAATTTTACACTATAACTAACAAAGTGAATATC
3365551 AAATTTTAATTTAATTAATTTATGTAAAA-TTTAATTTTAA-TTTTTTTATTTATAT
66 AAATTTTAATTTAATTAATTTATGTAAAATTTTAATTTTAATTTTTTTTATTTATAT
3365606 ACCGACACAATCGAGTGTTAGCAAAGAAATTAAAATTTTACACTATAACTAACAAAGTGAATATC
1 ACCGACACAATCGAGTGTTAGCAAAGAAATTAAAATTTTACACTATAACTAACAAAGTGAATATC
3365671 AAATTTTAATTTAATTAATTTATGTAAAATTTTAATTTTAATTTTTTTTATTTAT
66 AAATTTTAATTTAATTAATTTATGTAAAATTTTAATTTTAATTTTTTTTATTTAT
3365726 GTGATCTTTA
Statistics
Matches: 116, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
120 92 0.79
121 11 0.09
122 13 0.11
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (122 bp):
ACCGACACAATCGAGTGTTAGCAAAGAAATTAAAATTTTACACTATAACTAACAAAGTGAATATC
AAATTTTAATTTAATTAATTTATGTAAAATTTTAATTTTAATTTTTTTTATTTATAT
Found at i:3367311 original size:17 final size:16
Alignment explanation
Indices: 3367289--3367343 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
3367279 TTTTTAAATT
3367289 ATTTTATATTTATATAA
1 ATTTTATA-TTATATAA
3367306 ATTTTAATAAATTA-AT-A
1 ATTTT-AT--ATTATATAA
3367323 A-TTTATATTATATAA
1 ATTTTATATTATATAA
3367338 ATTTTA
1 ATTTTA
3367344 AAATATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 4 0.12
16 7 0.22
17 7 0.22
18 4 0.12
19 3 0.09
20 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:3367337 original size:32 final size:34
Alignment explanation
Indices: 3367291--3367361 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 34
3367281 TTTAAATTAT
3367291 TTTATATTTATATAAATTTTAATAA-ATTAATA-A
1 TTTATATTTATATAAATTTTAA-AATATTAATATA
*
3367324 TTTATA-TTATATAAATTTTAAAATATTTATATA
1 TTTATATTTATATAAATTTTAAAATATTAATATA
3367357 TTTAT
1 TTTAT
3367362 TTAATTGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
31 2 0.06
32 21 0.60
33 12 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TTTATATTTATATAAATTTTAAAATATTAATATA
Found at i:3367773 original size:19 final size:19
Alignment explanation
Indices: 3367749--3367789 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3367739 ATTTTGATAA
3367749 ATATTATATATA-AATATAC
1 ATATTATATATATAAT-TAC
3367768 ATATTATATATATAATTAC
1 ATATTATATATATAATTAC
3367787 ATA
1 ATA
3367790 CTCATTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTATATATATAATTAC
Found at i:3368225 original size:21 final size:22
Alignment explanation
Indices: 3368184--3368226 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3368174 AATATGGATT
* *
3368184 TATTTTTTATTATTGTTAATAA
1 TATTTTTTATTATTATAAATAA
3368206 TATTTTTTATT-TTATAAATAA
1 TATTTTTTATTATTATAAATAA
3368227 AATTAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTTTTTATTATTATAAATAA
Found at i:3368617 original size:35 final size:35
Alignment explanation
Indices: 3368578--3368658 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 35
3368568 ATTGATATAT
3368578 TTTTATTATATTAAAATAATAAAATAAATTTTTAA
1 TTTTATTATATTAAAATAATAAAATAAATTTTTAA
* * * *
3368613 TTTTA-TA-ATT---TTATTTAAATAAATTTTTAT
1 TTTTATTATATTAAAATAATAAAATAAATTTTTAA
3368643 TTTTATTATAATTAAA
1 TTTTATTAT-ATTAAA
3368659 TAAAATTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
30 21 0.58
31 2 0.06
33 6 0.17
34 2 0.06
35 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTTATTATATTAAAATAATAAAATAAATTTTTAA
Found at i:3368648 original size:22 final size:24
Alignment explanation
Indices: 3368611--3368659 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3368601 ATAAATTTTT
3368611 AATTTTATAATTTTATT-TAAATA
1 AATTTTATAATTTTATTATAAATA
* *
3368634 AATTTT-TATTTTTATTATAATTA
1 AATTTTATAATTTTATTATAAATA
3368657 AAT
1 AAT
3368660 AAAATTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATTTTATAATTTTATTATAAATA
Found at i:3368849 original size:20 final size:21
Alignment explanation
Indices: 3368824--3368881 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
3368814 TAATTTGATT
3368824 TTAAAATAATTTTTTATA-AA
1 TTAAAATAATTTTTTATATAA
* *
3368844 TTAAAATTATTATTTA-ATAA
1 TTAAAATAATTTTTTATATAA
*
3368864 TAAAAATAATATTTTTAT
1 TTAAAATAAT-TTTTTAT
3368882 TTAAATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.03
20 24 0.80
21 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAATAATTTTTTATATAA
Found at i:3368931 original size:18 final size:19
Alignment explanation
Indices: 3368885--3368946 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
3368875 TTTTTATTTA
* *
3368885 AATTTTATTATGAAATATAT
1 AATTTTAATATAAAATA-AT
3368905 AATTATTAATATAAAATAAT
1 AATT-TTAATATAAAATAAT
*
3368925 -ATTTTAATATATAATAAAT
1 AATTTTAATATAAAAT-AAT
3368944 AAT
1 AAT
3368947 AAAATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.31
19 6 0.17
20 8 0.22
21 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTTAATATAAAATAAT
Found at i:3369226 original size:30 final size:29
Alignment explanation
Indices: 3369160--3369242 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
3369150 ATGTCATTAG
* *
3369160 TTAAATAAATTTTAAAATTTTAATTTATA
1 TTAAATAAATTTTTAATTTTTAATTTATA
* * *
3369189 TTAAATAAATTTTTCATTTTTCATTTTTA
1 TTAAATAAATTTTTAATTTTTAATTTATA
*
3369218 TATAAATAAATTTTTTATTTTTAAT
1 T-TAAATAAATTTTTAATTTTTAAT
3369243 AAAAGTTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 25 0.54
30 21 0.46
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TTAAATAAATTTTTAATTTTTAATTTATA
Found at i:3369320 original size:19 final size:19
Alignment explanation
Indices: 3369292--3369329 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3369282 ATATAAAAAA
*
3369292 TTTAAATATTTTTTAATAT
1 TTTAAATATTTTTAAATAT
*
3369311 TTTAATTATTTTTAAATAT
1 TTTAAATATTTTTAAATAT
3369330 AAGACACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTAAATATTTTTAAATAT
Found at i:3376469 original size:2 final size:2
Alignment explanation
Indices: 3376456--3376490 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3376446 GGAAACAAAC
* *
3376456 AT AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3376491 CTGTTCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3376557 original size:28 final size:28
Alignment explanation
Indices: 3376504--3376559 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3376494 TTCTCACAAC
* * **
3376504 AAATTTTTTTCTATATTTAATTATTTTT
1 AAATATTTTTATATATTTAAAAATTTTT
3376532 AAATATTTTTATATATTTAAAAATTTTT
1 AAATATTTTTATATATTTAAAAATTTTT
3376560 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
AAATATTTTTATATATTTAAAAATTTTT
Found at i:3378375 original size:21 final size:22
Alignment explanation
Indices: 3378342--3378383 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3378332 ATAAATTTAT
*
3378342 ATAATATTAATTA-TTAATATA
1 ATAAAATTAATTATTTAATATA
*
3378363 ATAAAATTTATTATTTAATAT
1 ATAAAATTAATTATTTAATAT
3378384 TTTAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATTAATTATTTAATATA
Found at i:3378419 original size:14 final size:16
Alignment explanation
Indices: 3378386--3378423 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
3378376 TTTAATATTT
3378386 TAAATATAATTATAATA
1 TAAAT-TAATTATAATA
3378403 TAAATTAATT-T-ATA
1 TAAATTAATTATAATA
3378417 TAAATTA
1 TAAATTA
3378424 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 5 0.24
17 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTAATTATAATA
Found at i:3378718 original size:20 final size:21
Alignment explanation
Indices: 3378695--3378733 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3378685 AAATAAATAT
3378695 TAAATATAATTA-ATAATTAA
1 TAAATATAATTATATAATTAA
*
3378715 TAAATATATTTATATAATT
1 TAAATATAATTATATAATT
3378734 TTAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAATATAATTATATAATTAA
Found at i:3378753 original size:14 final size:14
Alignment explanation
Indices: 3378698--3378753 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
3378688 TAAATATTAA
3378698 ATATAATTAATAATT
1 ATATAATTAA-AATT
* * *
3378713 A-ATAAATATATTT
1 ATATAATTAAAATT
**
3378726 ATATAATTTTAATT
1 ATATAATTAAAATT
3378740 ATATAATTAAAATT
1 ATATAATTAAAATT
3378754 TTAAATTTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
13 4 0.12
14 27 0.84
15 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATAATTAAAATT
Found at i:3378818 original size:20 final size:21
Alignment explanation
Indices: 3378795--3378839 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3378785 AAAAATATAT
*
3378795 ATTTAA-TTTTTATCTATTTA
1 ATTTAATTTTTTATCGATTTA
3378815 ATTTAATTTTTTATCGATTTA
1 ATTTAATTTTTTATCGATTTA
3378836 ATTT
1 ATTT
3378840 TTATTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTAATTTTTTATCGATTTA
Found at i:3378850 original size:16 final size:16
Alignment explanation
Indices: 3378809--3378850 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3378799 AATTTTTATC
*
3378809 TATTTAATTTAATTTT
1 TATTCAATTTAATTTT
*
3378825 T-TATCGATTTAATTTT
1 TAT-TCAATTTAATTTT
3378841 TATTCAATTT
1 TATTCAATTT
3378851 TTATATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTCAATTTAATTTT
Found at i:3379341 original size:3 final size:3
Alignment explanation
Indices: 3379333--3379364 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3379323 TATAAGTCTC
3379333 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3379365 AAATTCTTTA
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:3379605 original size:18 final size:18
Alignment explanation
Indices: 3379567--3379607 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3379557 TCGTATTTTA
* *
3379567 ATTAT-TATTTTTTTTAT
1 ATTATATATATTTTTCAT
3379584 -TTATATATATTTTTCAT
1 ATTATATATATTTTTCAT
3379601 ATTATAT
1 ATTATAT
3379608 CTTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.20
17 10 0.50
18 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTATATATATTTTTCAT
Found at i:3379746 original size:19 final size:19
Alignment explanation
Indices: 3379677--3379744 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
3379667 TAATTGATTG
*
3379677 GATTGATTTAAGTTCAATA
1 GATTGATTTAAGTTAAATA
* *
3379696 GAAAATT-AGTTAAGTTAGATA
1 G---ATTGATTTAAGTTAAATA
*
3379717 GATTGATTTAAGTTAAATT
1 GATTGATTTAAGTTAAATA
3379736 GAATTGATT
1 G-ATTGATT
3379745 AAAAGTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 13 0.34
20 7 0.18
21 12 0.32
22 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.18, T:0.41
Consensus pattern (19 bp):
GATTGATTTAAGTTAAATA
Found at i:3382422 original size:17 final size:17
Alignment explanation
Indices: 3382363--3382427 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 17
3382353 AATTTTTTTA
*
3382363 TTTAAA-AATTA-AAAT
1 TTTAAATAATTATATAT
*
3382378 TTTAAAT-ATTTTATA-
1 TTTAAATAATTATATAT
*
3382393 TTTAAAAACATTATATAT
1 TTTAAATA-ATTATATAT
*
3382411 TTTAAATAATTAAATAT
1 TTTAAATAATTATATAT
3382428 GGATATCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 15 0.38
16 2 0.05
17 15 0.38
18 7 0.18
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAATAATTATATAT
Found at i:3382865 original size:3 final size:3
Alignment explanation
Indices: 3382859--3382902 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3382849 AAACTCCTCC
3382859 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3382903 TTTATTGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3385805 original size:2 final size:2
Alignment explanation
Indices: 3385798--3385840 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3385788 TAGATTTGTG
3385798 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
3385840 T
1 T
3385841 GTCATGATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3386432 original size:27 final size:26
Alignment explanation
Indices: 3386400--3386452 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
3386390 AAAAATATAT
3386400 ATATATTTTATTATTTAATATATTAAAAA
1 ATAT-TTTTA-TATTTAATA-ATTAAAAA
*
3386429 ATATTTTTATATTTTATAATTAAA
1 ATATTTTTATATTTAATAATTAAA
3386453 TATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 8 0.35
28 5 0.22
29 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATATTTTTATATTTAATAATTAAAAA
Found at i:3386440 original size:35 final size:34
Alignment explanation
Indices: 3386386--3386470 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 34
3386376 CTCATGAATC
* * * *
3386386 TAAAAAAAATATATATATATTTTATTATTTAATA
1 TAAAAAAAATATTTTTATATTTTATAATTAAATA
*
3386420 TATTAAAAAATATTTTTATATTTTATAATTAAATA
1 TA-AAAAAAATATTTTTATATTTTATAATTAAATA
3386455 TAAATAAAAATATTTT
1 TAAA-AAAAATATTTT
3386471 ATTTATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
34 3 0.07
35 40 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
TAAAAAAAATATTTTTATATTTTATAATTAAATA
Found at i:3386833 original size:2 final size:2
Alignment explanation
Indices: 3386826--3386864 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3386816 TAGGCATTAT
3386826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3386865 GGGGTTTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3387430 original size:36 final size:37
Alignment explanation
Indices: 3387359--3387430 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
3387349 GTTATTCAAA
* * * * *
3387359 TTTAAATATTAAATATATATATATATATTTTAAATAT
1 TTTAAATATTAAAAATAAATAAAAATATTTAAAATAT
3387396 TTTAAATA-TAAAAATAAATAAAAATATTTAAAATA
1 TTTAAATATTAAAAATAAATAAAAATATTTAAAATA
3387431 AATGAGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 22 0.73
37 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (37 bp):
TTTAAATATTAAAAATAAATAAAAATATTTAAAATAT
Found at i:3387952 original size:42 final size:42
Alignment explanation
Indices: 3387903--3387983 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 42
3387893 ATTAAATATA
3387903 ATTAATATAATTAAAAATAAATAAATTTAAT-ATTTATATGTT
1 ATTAATAT-ATTAAAAATAAATAAATTTAATAATTTATATGTT
* ** * *
3387945 ATTAATATTTTAAATTTTAATATATTTAATAATTTATAT
1 ATTAATATATTAAAAATAAATAAATTTAATAATTTATAT
3387984 AATATTTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 17 0.52
42 16 0.48
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (42 bp):
ATTAATATATTAAAAATAAATAAATTTAATAATTTATATGTT
Found at i:3387999 original size:17 final size:17
Alignment explanation
Indices: 3387930--3388001 Score: 69
Period size: 17 Copynumber: 4.1 Consensus size: 17
3387920 TAAATAAATT
3387930 TAATATTTATATGTTAT-
1 TAATATTTATAT-TTATA
*
3387947 TAATATTTTAAATTT-TA
1 TAATA-TTTATATTTATA
3387964 -ATATATTTAATAATTTATA
1 TA-ATATTT-AT-ATTTATA
3387983 TAATATTTATATTTATA
1 TAATATTTATATTTATA
3388000 TA
1 TA
3388002 TTCGATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
16 5 0.11
17 20 0.43
18 12 0.26
19 8 0.17
20 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TAATATTTATATTTATA
Found at i:3389014 original size:15 final size:16
Alignment explanation
Indices: 3388994--3389023 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3388984 ATATATTTTA
3388994 TTTTTT-AAAAATAAC
1 TTTTTTCAAAAATAAC
3389009 TTTTTTCAAAAATAA
1 TTTTTTCAAAAATAA
3389024 TTTAAGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTTTCAAAAATAAC
Found at i:3390646 original size:35 final size:33
Alignment explanation
Indices: 3390595--3390660 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
3390585 AATCTTATAA
3390595 TTTATAAATAAATAATTAAAAATAAAAAATATT
1 TTTATAAATAAATAATTAAAAATAAAAAATATT
* **
3390628 TTTATTAATTAAATTAATTTTAAATAAAAAATA
1 TTTA-TAAATAAA-TAATTAAAAATAAAAAATA
3390661 CTTAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 4 0.14
34 7 0.25
35 17 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TTTATAAATAAATAATTAAAAATAAAAAATATT
Found at i:3396400 original size:155 final size:155
Alignment explanation
Indices: 3396207--3396513 Score: 614
Period size: 155 Copynumber: 2.0 Consensus size: 155
3396197 GATATTCTGT
3396207 AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
1 AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
3396272 AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
66 AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
3396337 CCGAGAATTTTCAGGGAAACCCTGA
131 CCGAGAATTTTCAGGGAAACCCTGA
3396362 AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
1 AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
3396427 AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
66 AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
3396492 CCGAGAATTTTCAGGGAAACCC
131 CCGAGAATTTTCAGGGAAACCC
3396514 CACCTGAACA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 152 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (155 bp):
AACAACAAAATTCAGGAGTAGATGTGACCTGGATGAGGGAAAAGTCTCTGCATGACCCCAAAGTC
AAAATTCTGTTACATGATATGATATACTGGTGTCTTTGGGTCCATTTTCTCGAGAAAACAATTTT
CCGAGAATTTTCAGGGAAACCCTGA
Found at i:3402981 original size:2 final size:2
Alignment explanation
Indices: 3402974--3402999 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3402964 AACGCAAAAC
3402974 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
3403000 GTGTGTGTGT
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:3403538 original size:36 final size:35
Alignment explanation
Indices: 3403495--3403565 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
3403485 CAGAAATTAC
3403495 CCCAAAAAAAAAAAAAGAAATCCCAGCAAATTTTA
1 CCCAAAAAAAAAAAAAGAAATCCCAGCAAATTTTA
*
3403530 CCCAAAAAAAAAAAAAGATATCCCAGCAAATTTTA
1 CCCAAAAAAAAAAAAAGAAATCCCAGCAAATTTTA
3403565 C
1 C
3403566 ATAAGACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.58, C:0.21, G:0.06, T:0.15
Consensus pattern (35 bp):
CCCAAAAAAAAAAAAAGAAATCCCAGCAAATTTTA
Found at i:3404256 original size:8 final size:7
Alignment explanation
Indices: 3404243--3404368 Score: 50
Period size: 6 Copynumber: 17.9 Consensus size: 7
3404233 AAAATTTTAA
3404243 ATATAATT
1 ATATAA-T
3404251 ATATAA-
1 ATATAAT
3404257 ATATAAT
1 ATATAAT
3404264 ATATAAAT
1 ATAT-AAT
*
3404272 AATATGAT
1 -ATATAAT
3404280 ATA-AAT
1 ATATAAT
*
3404286 ATAT-TT
1 ATATAAT
*
3404292 ATAAAAT
1 ATATAAT
* *
3404299 TTATAAA
1 ATATAAT
3404306 ATA-AAT
1 ATATAAT
3404312 -TATTAAT
1 ATA-TAAT
* *
3404319 TTATTAAA
1 ATA-TAAT
3404327 AT-TAAT
1 ATATAAT
3404333 ATA-AAT
1 ATATAAT
*
3404339 ATAAAAT
1 ATATAAT
*
3404346 ATTTAAAAT
1 A--TATAAT
3404355 ATATTAAT
1 ATA-TAAT
3404363 ATATAA
1 ATATAA
3404369 ATACATAAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
5 2 0.02
6 28 0.31
7 26 0.29
8 24 0.26
9 11 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:3404259 original size:14 final size:14
Alignment explanation
Indices: 3404240--3404298 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
3404230 TTAAAAATTT
3404240 TAAATATAATTATA
1 TAAATATAATTATA
3404254 TAAATATAA-TATA
1 TAAATATAATTATA
*
3404267 TAAATA-ATATGATA
1 TAAATATA-ATTATA
*
3404281 TAAATATATTTATA
1 TAAATATAATTATA
3404295 -AAAT
1 TAAAT
3404299 TTATAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 1 0.03
13 15 0.38
14 22 0.56
15 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:3404322 original size:29 final size:32
Alignment explanation
Indices: 3404288--3404348 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
3404278 ATATAAATAT
*
3404288 ATTTA-TAAAATT-TATAAA-ATAAATTATTA
1 ATTTATTAAAATTATATAAATATAAAATATTA
3404317 ATTTATTAAAATTAATATAAATATAAAATATT
1 ATTTATTAAAATT-ATATAAATATAAAATATT
3404349 TAAAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 5 0.19
30 7 0.26
32 6 0.22
33 9 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATTTATTAAAATTATATAAATATAAAATATTA
Found at i:3404371 original size:8 final size:8
Alignment explanation
Indices: 3404243--3404378 Score: 54
Period size: 8 Copynumber: 17.0 Consensus size: 8
3404233 AAAATTTTAA
*
3404243 ATATAATT
1 ATATAAAT
3404251 ATATAAAT
1 ATATAAAT
*
3404259 ATAATATAT
1 AT-ATAAAT
*
3404268 AAATAATAT
1 ATATAA-AT
3404277 GATATAAAT
1 -ATATAAAT
*
3404286 ATAT--TT
1 ATATAAAT
3404292 ATA-AAAT
1 ATATAAAT
*
3404299 TTAT-AA-
1 ATATAAAT
3404305 A-ATAAAT
1 ATATAAAT
*
3404312 -TATTAAT
1 ATATAAAT
*
3404319 TTATTAAAATT
1 ATA-T-AAA-T
3404330 AATATAAAT
1 -ATATAAAT
3404339 ATA-AAAT
1 ATATAAAT
*
3404346 ATTTAAAAT
1 ATAT-AAAT
*
3404355 ATATTAAT
1 ATATAAAT
3404363 ATATAAAT
1 ATATAAAT
*
3404371 ACATAAAT
1 ATATAAAT
3404379 TATTTAATTT
Statistics
Matches: 95, Mismatches: 17, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
5 2 0.02
6 6 0.06
7 16 0.17
8 38 0.40
9 19 0.20
10 10 0.11
11 2 0.02
12 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:3405339 original size:20 final size:20
Alignment explanation
Indices: 3405311--3405348 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3405301 GATGAAAATG
* *
3405311 TCTTTTATTTTTTTTATTTA
1 TCTTGTATTTTTTATATTTA
3405331 TCTTGTATTTTTTATATT
1 TCTTGTATTTTTTATATT
3405349 AAAAACTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (20 bp):
TCTTGTATTTTTTATATTTA
Found at i:3407833 original size:30 final size:31
Alignment explanation
Indices: 3407785--3407842 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
3407775 TGGTTAAGAG
** *
3407785 TTTATAGTTTATTTTATTATATA-AAATAAT
1 TTTATAGTTTATAATATTAAATATAAATAAT
*
3407815 TTTATATTTTATAATATTAAATATAAAT
1 TTTATAGTTTATAATATTAAATATAAAT
3407843 TTAATAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
TTTATAGTTTATAATATTAAATATAAATAAT
Found at i:3407853 original size:28 final size:28
Alignment explanation
Indices: 3407797--3407870 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
3407787 TATAGTTTAT
* *
3407797 TTTATTATA-TAAA-AT-AATTTTATAT
1 TTTATTATATTAAATATAAATTTAATAA
*
3407822 TTTATAATATTAAATATAAATTTAATAA
1 TTTATTATATTAAATATAAATTTAATAA
3407850 TTTATTAT-TTAAATAATAAAT
1 TTTATTATATTAAAT-ATAAAT
3407871 AAATTTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 8 0.20
26 4 0.10
27 8 0.20
28 21 0.51
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTATTATATTAAATATAAATTTAATAA
Found at i:3417817 original size:16 final size:18
Alignment explanation
Indices: 3417796--3417828 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3417786 TAATTTAAAT
3417796 ATTTT-AATT-TATTTTA
1 ATTTTAAATTATATTTTA
3417812 ATTTTAAATTATATTTT
1 ATTTTAAATTATATTTT
3417829 TTATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTAAATTATATTTTA
Found at i:3417831 original size:25 final size:23
Alignment explanation
Indices: 3417782--3417833 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 23
3417772 AATACATATA
3417782 ATTTTAATTTAAATATTTTAATTT
1 ATTTTAATTTAAATATTTT-ATTT
3417806 ATTTTAATTTTAAATTATATTT-TTT
1 ATTTTAA-TTTAAA-TAT-TTTATTT
3417831 ATT
1 ATT
3417834 AAAAAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 7 0.28
25 12 0.48
26 3 0.12
27 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTAATTTAAATATTTTATTT
Found at i:3418268 original size:16 final size:16
Alignment explanation
Indices: 3418249--3418294 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
3418239 AAATATAAAT
3418249 TTTAAATTCAAAATAA
1 TTTAAATTCAAAATAA
*
3418265 TTTATA-TCTAAAATAA
1 TTTAAATTC-AAAATAA
*
3418281 TTTAAATTTAAAAT
1 TTTAAATTCAAAAT
3418295 CAAACCTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 2 0.08
16 22 0.88
17 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAATTCAAAATAA
Found at i:3425129 original size:22 final size:22
Alignment explanation
Indices: 3425091--3425237 Score: 57
Period size: 22 Copynumber: 6.8 Consensus size: 22
3425081 AATACAATAC
* *
3425091 ATAATT-ATATATTATATAAAA
1 ATAATTAAAATATAATATAAAA
**
3425112 ATAATTAAAATATAATAT-ATT
1 ATAATTAAAATATAATATAAAA
3425133 ATAATTTAAAATATTAA-ATTAAATA
1 ATAA-TTAAAATA-TAATA-TAAA-A
*
3425158 ATAA-T-AAATAT-ATATAATTAT
1 ATAATTAAAATATAATATAA--AA
* *
3425179 ATGATATAAAATA-AATAATTAAA
1 ATAAT-TAAAATATAAT-ATAAAA
3425202 AT-A-T--AATATAATATAAAA
1 ATAATTAAAATATAATATAAAA
*
3425220 ATAA-TATGAATATAATAT
1 ATAATTA-AAATATAATAT
3425238 TATTATATAA
Statistics
Matches: 96, Mismatches: 11, Indels: 37
0.67 0.08 0.26
Matches are distributed among these distances:
18 11 0.11
19 5 0.05
20 5 0.05
21 16 0.17
22 35 0.36
23 9 0.09
24 8 0.08
25 7 0.07
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (22 bp):
ATAATTAAAATATAATATAAAA
Found at i:3425130 original size:5 final size:5
Alignment explanation
Indices: 3425120--3425271 Score: 74
Period size: 5 Copynumber: 31.4 Consensus size: 5
3425110 AAATAATTAA
* * * *
3425120 AATAT AATAT ATTAT AATTT AAAAT ATTA- AAT-T AA-AT AATAAT AA-AT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT-AT AATAT
* * *
3425167 ATATAT AAT-T -ATAT GATAT AAAAT AA-AT AATTAA AATAT AATAT AATAT
1 A-ATAT AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT
* * *
3425216 AAAAAT AATAT GAATAT AATAT --TAT TATAT AAATAT ATTA- AAT-T
1 -AATAT AATAT -AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
*
3425260 TATAT AATAT AA
1 AATAT AATAT AA
3425272 ATTATTAAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 34
0.68 0.12 0.21
Matches are distributed among these distances:
3 5 0.05
4 20 0.18
5 63 0.57
6 23 0.21
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:3425189 original size:46 final size:46
Alignment explanation
Indices: 3425110--3425360 Score: 130
Period size: 46 Copynumber: 5.5 Consensus size: 46
3425100 TATTATATAA
* *
3425110 AAATAATTA-AAATATAATATATTATA--ATTTAAAATATTA-AATT
1 AAATAATAATAAATATAATA-ATTATATGATATAAAATATTATAATT
*
3425153 AAATAATAATAAATATATATAATTATATGATATAAAATA-AATAATT
1 AAATAATAATAAATATA-ATAATTATATGATATAAAATATTATAATT
* * * *
3425199 AAA-ATATAATATAATATAAAAATAATATGA-ATATAATATTATTATAT
1 AAATA-ATAATA-AATATAATAATTATATGATATAAAATATTATAAT-T
* * * * *
3425246 AAAT-ATATTAAATTTATATAATATAAATTAT-TAAAATATTAATATTT
1 AAATAATAATAAATATA-ATAAT-TATATGATATAAAATATT-ATAATT
** * * * * *
3425293 ATAAT-ATTTTAAATATAATTATTTTAAT-ATATAAATTTTTATATTT
1 A-AATAATAATAAATATAATAATTAT-ATGATATAAAATATTATAATT
* * *
3425339 AAAAAATAA-ATATATAAAAATT
1 AAATAATAATAAATATAATAATT
3425361 TTTAAAATTT
Statistics
Matches: 160, Mismatches: 30, Indels: 34
0.71 0.13 0.15
Matches are distributed among these distances:
43 8 0.05
44 13 0.08
45 29 0.18
46 57 0.36
47 37 0.23
48 16 0.10
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.43
Consensus pattern (46 bp):
AAATAATAATAAATATAATAATTATATGATATAAAATATTATAATT
Found at i:3425250 original size:19 final size:19
Alignment explanation
Indices: 3425223--3425278 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
3425213 TATAAAAATA
*
3425223 ATATGAATATAATATTATT
1 ATATAAATATAATATTATT
* *
3425242 ATATAAATATATTA-AATT
1 ATATAAATATAATATTATT
3425260 -TATATAATATAA-ATTATT
1 ATATA-AATATAATATTATT
3425278 A
1 A
3425279 AAATATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 5 0.17
18 12 0.41
19 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATAAATATAATATTATT
Found at i:3425265 original size:32 final size:32
Alignment explanation
Indices: 3425202--3425295 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 32
3425192 AATAATTAAA
**
3425202 ATATAATAT-AA-TA-TAAAA-A-TAATATGA
1 ATATAATATAAATTATTAAAATATTAATATTT
*
3425229 ATATAATAT-TATTATATAAATATATTAA-ATTT
1 ATATAATATAAATTAT-TAAA-ATATTAATATTT
3425261 ATATAATATAAATTATTAAAATATTAATATTT
1 ATATAATATAAATTATTAAAATATTAATATTT
3425293 ATA
1 ATA
3425296 ATATTTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
27 10 0.18
28 2 0.04
30 4 0.07
31 8 0.15
32 23 0.42
33 8 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATTATTAAAATATTAATATTT
Found at i:3425300 original size:23 final size:22
Alignment explanation
Indices: 3425274--3425327 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 22
3425264 TAATATAAAT
3425274 TATTAAAATATTAA-TATTTATAA
1 TATTAAAATA-TAATTATTT-TAA
*
3425297 TATTTTAAATATAATTATTTTAA
1 TA-TTAAAATATAATTATTTTAA
3425320 TATATAAA
1 TAT-TAAA
3425328 TTTTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.04
23 13 0.50
24 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTAAAATATAATTATTTTAA
Found at i:3425309 original size:14 final size:15
Alignment explanation
Indices: 3425292--3425336 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
3425282 TATTAATATT
3425292 TATAATATTTTAA-A
1 TATAATATTTTAATA
3425306 TATAATTATTTTAATA
1 TATAA-TATTTTAATA
*
3425322 TATAA-ATTTTTATA
1 TATAATATTTTAATA
3425336 T
1 T
3425337 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 14 0.50
15 8 0.29
16 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATATTTTAATA
Found at i:3425710 original size:9 final size:8
Alignment explanation
Indices: 3425684--3425713 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3425674 GTCAGTTGAA
3425684 TAAATTAT
1 TAAATTAT
3425692 TAAATTAT
1 TAAATTAT
3425700 TAAATTTAT
1 TAAA-TTAT
3425709 TAAAT
1 TAAAT
3425714 AAATTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TAAATTAT
Found at i:3425722 original size:17 final size:17
Alignment explanation
Indices: 3425684--3425725 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3425674 GTCAGTTGAA
*
3425684 TAAA-TTATTAAATTAT
1 TAAATTTATTAAATAAT
3425700 TAAATTTATTAAATAAAT
1 TAAATTTATTAAAT-AAT
3425718 T-AATTTAT
1 TAAATTTAT
3425726 ATTAGTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 16 0.70
18 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTTATTAAATAAT
Found at i:3425922 original size:17 final size:17
Alignment explanation
Indices: 3425900--3425938 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3425890 TTCAAACTAA
3425900 TTAAATTCATTAAAATT
1 TTAAATTCATTAAAATT
* * *
3425917 TTAAATTTATTTAATTT
1 TTAAATTCATTAAAATT
3425934 TTAAA
1 TTAAA
3425939 AATTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAATTCATTAAAATT
Found at i:3427900 original size:24 final size:24
Alignment explanation
Indices: 3427851--3427901 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
3427841 ACACTGGTGA
*
3427851 TTTTACAATGAGAGTTTTCTCATT
1 TTTTACAATGAGAGTTCTCTCATT
3427875 TTTTAACAATGAGAGGTTCT-TC-TT
1 TTTT-ACAATGAGA-GTTCTCTCATT
3427899 TTT
1 TTT
3427902 CTTTGCTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.38
25 11 0.46
26 4 0.17
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (24 bp):
TTTTACAATGAGAGTTCTCTCATT
Found at i:3428519 original size:27 final size:28
Alignment explanation
Indices: 3428449--3428519 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 28
3428439 ATTCATAATT
*
3428449 AATTTAATTAATTTATGTAATAATTTTTA
1 AATTTAATT-ATTTATATAATAATTTTTA
* * *
3428478 AATTAAAATA-ATATATAATAA-TTTTA
1 AATTTAATTATTTATATAATAATTTTTA
*
3428504 AATTTTATTATTTATA
1 AATTTAATTATTTATA
3428520 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
26 12 0.36
27 13 0.39
28 1 0.03
29 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
AATTTAATTATTTATATAATAATTTTTA
Found at i:3429083 original size:21 final size:21
Alignment explanation
Indices: 3429057--3429096 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3429047 AAAATTTTTA
* *
3429057 TATAAATTTTATTATAAAATT
1 TATAAATATTAATATAAAATT
3429078 TATAAATATTAATATAAAA
1 TATAAATATTAATATAAAA
3429097 AATATTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAAATATTAATATAAAATT
Found at i:3430498 original size:2 final size:2
Alignment explanation
Indices: 3430491--3430533 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3430481 TTTCCTTCAA
3430491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3430533 A
1 A
3430534 GTTTTGCAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3431486 original size:5 final size:5
Alignment explanation
Indices: 3431476--3431598 Score: 90
Period size: 5 Copynumber: 23.8 Consensus size: 5
3431466 TTTATATTTG
* * * * *
3431476 TATAT TTTAT TATAT TATAAT ATATTT TATAT TATA- TAAAT TTTAA TATAT
1 TATAT TATAT TATAT TAT-AT -TATAT TATAT TATAT TATAT TATAT TATAT
*
3431527 TAATAAT TAATAT TATAT ATAAAT TAT-T TATAT TATAT TATAT TAT-T
1 T-AT-AT T-ATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT
* *
3431574 TATAT TATTTT TAAAT TATAT TATA
1 TATAT TA-TAT TATAT TATAT TATA
3431599 ATAATTTTTT
Statistics
Matches: 93, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
4 11 0.12
5 57 0.61
6 16 0.17
7 9 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:3431501 original size:20 final size:20
Alignment explanation
Indices: 3431476--3431617 Score: 84
Period size: 17 Copynumber: 7.0 Consensus size: 20
3431466 TTTATATTTG
3431476 TATATTTTATTATATTATAA
1 TATATTTTATTATATTATAA
3431496 TATA--TT-TTATATTAT-A
1 TATATTTTATTATATTATAA
* *
3431512 TAAATTTTAATATATTAATAA
1 TATATTTTATTATATT-ATAA
* * *
3431533 TTAATATTATATATAAATTAT-T
1 -T-ATATTTTAT-TATATTATAA
* *
3431555 TATATTATATTATATTATTTA
1 TATATTTTATTATATTA-TAA
3431576 TATTATTTTTAAATTATATTATAA
1 TA-TA-TTTT--ATTATATTATAA
3431600 TA-ATTTT-TTAT-TTATAA
1 TATATTTTATTATATTATAA
3431617 T
1 T
3431618 TAATATTGTG
Statistics
Matches: 97, Mismatches: 11, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
16 4 0.04
17 16 0.16
18 8 0.08
19 12 0.12
20 16 0.16
21 8 0.08
22 4 0.04
23 11 0.11
24 9 0.09
25 9 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATTTTATTATATTATAA
Found at i:3431522 original size:26 final size:28
Alignment explanation
Indices: 3431451--3431596 Score: 83
Period size: 26 Copynumber: 5.3 Consensus size: 28
3431441 AATCATTAAT
*
3431451 TTATAATAAATTA-AATTTATATTTGTATA
1 TTATATTAAATTATAA--TATATTTGTATA
* *
3431480 TTTTATTATATTATAATATATTT-TATA
1 TTATATTAAATTATAATATATTTGTATA
* **
3431507 TTATA-TAAATTTTAATATATTAATA-A
1 TTATATTAAATTATAATATATTTGTATA
*
3431533 TTAATATTATA-TATAA-AT-TATT-TATA
1 TT-ATATTAAATTATAATATAT-TTGTATA
* * * *
3431559 TTATATTATATTATTTATATTATTTTTAAA
1 TTATATTAAATTA-TAATA-TATTTGTATA
3431589 TTATATTA
1 TTATATTA
3431597 TAATAATTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
25 11 0.12
26 25 0.27
27 19 0.20
28 11 0.12
29 13 0.14
30 14 0.15
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TTATATTAAATTATAATATATTTGTATA
Found at i:3431536 original size:87 final size:82
Alignment explanation
Indices: 3431438--3431594 Score: 201
Period size: 87 Copynumber: 1.9 Consensus size: 82
3431428 AAGAAAAAAA
* *
3431438 ATTAATCATTAAT-TTATA-ATAAATTAAATTTATATTTGTATATTTTATTATATTATAATATAT
1 ATTAATAATTAATATTATATATAAATT--ATTTATA--T-TATATTATATTAT-TTATAATAT-T
*
3431501 TTTATATTATATAAATTTTAATAT
59 TTTAAATTATATAAATTTTAATAT
*
3431525 ATTAATAATTAATATTATATATAAATTATTTATATTATATTATATTATTTATATTATTTTTAAAT
1 ATTAATAATTAATATTATATATAAATTATTTATATTATATTATATTATTTATAATATTTTTAAAT
3431590 TATAT
66 TATAT
3431595 TATAATAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
82 12 0.19
83 8 0.12
84 12 0.19
85 1 0.02
87 19 0.30
88 5 0.08
89 7 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (82 bp):
ATTAATAATTAATATTATATATAAATTATTTATATTATATTATATTATTTATAATATTTTTAAAT
TATATAAATTTTAATAT
Found at i:3431595 original size:87 final size:84
Alignment explanation
Indices: 3431438--3431624 Score: 195
Period size: 87 Copynumber: 2.2 Consensus size: 84
3431428 AAGAAAAAAA
* * **
3431438 ATTAATCATTAAT-TTATAATAAATTAAATTTATATTTGTATATTTTATTATATTATAATATATT
1 ATTAATAATTAATATTATAATAAATT-AATTTATATTTGTATATTATATTATATTATAATATAAA
3431502 TTATATTAT-ATAAATTTTAATAT
65 TTATATTATAAT-AATTTT--T-T
* * *
3431525 ATTAATAATTAATATTATATATAAATT-ATTTATATTATATTATATTAT-TTATATTAT-TTTTA
1 ATTAATAATTAATATTATA-ATAAATTAATTTATATT-T-GTATATTATATTATATTATAATATA
3431587 AATTATATTATAATAATTTTTT
63 AATTATATTATAATAATTTTTT
*
3431609 ATTTATAATTAATATT
1 ATTAATAATTAATATT
3431625 GTGTATCATG
Statistics
Matches: 87, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
84 16 0.18
85 1 0.01
87 39 0.45
88 17 0.20
89 14 0.16
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (84 bp):
ATTAATAATTAATATTATAATAAATTAATTTATATTTGTATATTATATTATATTATAATATAAAT
TATATTATAATAATTTTTT
Found at i:3431605 original size:22 final size:20
Alignment explanation
Indices: 3431546--3431607 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
3431536 ATATTATATA
* *
3431546 TAAATTATTTATATTA-TAT
1 TAAATTATTTATATAATTTT
* *
3431565 TATATTATTTATATTATTTT
1 TAAATTATTTATATAATTTT
3431585 TAAATTATATTATAATAATTTT
1 TAAATTAT-TTAT-ATAATTTT
3431607 T
1 T
3431608 TATTTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 15 0.42
20 9 0.25
21 4 0.11
22 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TAAATTATTTATATAATTTT
Found at i:3431614 original size:22 final size:21
Alignment explanation
Indices: 3431564--3431615 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
3431554 TTATATTATA
*
3431564 TTATATTAT-TTATATTATTTT
1 TTAT-TTATATTATATAATTTT
* *
3431585 TAAATTATATTATAATAATTTT
1 TTATTTATATTAT-ATAATTTT
3431607 TTATTTATA
1 TTATTTATA
3431616 ATTAATATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.17
21 6 0.25
22 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTTATATTATATAATTTT
Found at i:3440359 original size:22 final size:23
Alignment explanation
Indices: 3440306--3440361 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
3440296 AAGACATAAA
3440306 TATTTTT-ATTATATTAAAATTT
1 TATTTTTAATTATATTAAAATTT
* *
3440328 TATTTATAATT-TATTAATA-TT
1 TATTTTTAATTATATTAAAATTT
3440349 TATTTTTTAATTA
1 TA-TTTTTAATTA
3440362 AATTGATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 21 0.75
23 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTTTAATTATATTAAAATTT
Found at i:3440623 original size:29 final size:30
Alignment explanation
Indices: 3440587--3440663 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
3440577 TTATTAAAAT
3440587 TATTATTTAAATAATAAAAAAT-TATTTTA
1 TATTATTTAAATAATAAAAAATATATTTTA
* * *
3440616 T-TTAATTTTAATTATAAAATATATATTTTA
1 TATT-ATTTAAATAATAAAAAATATATTTTA
3440646 TATT-TTTAAAATAATAAA
1 TATTATTT-AAATAATAAA
3440664 TTAAATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.05
29 19 0.49
30 16 0.41
31 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTATTTAAATAATAAAAAATATATTTTA
Found at i:3443513 original size:2 final size:2
Alignment explanation
Indices: 3443506--3443534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3443496 AAGAAGTTCA
3443506 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3443535 AGCTATCAAC
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3443895 original size:22 final size:22
Alignment explanation
Indices: 3443830--3443900 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
3443820 TAGATATAGA
* * *
3443830 ATTTTTATATAATTAATATATTT
1 ATTTTTATA-ATTTATTATAATT
* * *
3443853 GTTATTAT-ATTATATTTTAATT
1 ATTTTTATAATT-TATTATAATT
*
3443875 ATTTTTATAATTTATTATAATA
1 ATTTTTATAATTTATTATAATT
3443897 ATTT
1 ATTT
3443901 AATTTTAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
21 2 0.06
22 25 0.69
23 9 0.25
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (22 bp):
ATTTTTATAATTTATTATAATT
Found at i:3444505 original size:13 final size:14
Alignment explanation
Indices: 3444488--3444526 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
3444478 ATAAATTTTA
3444488 ATTTAAAATTAATT
1 ATTTAAAATTAATT
*
3444502 -TTTACAATTAATT
1 ATTTAAAATTAATT
*
3444515 AATTAAAATTAA
1 ATTTAAAATTAA
3444527 AAAAAAAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTAAAATTAATT
Found at i:3444758 original size:25 final size:25
Alignment explanation
Indices: 3444730--3444817 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 25
3444720 CTGAATATGG
*
3444730 TATAATATTAAAAATATAAATATGA
1 TATAATATTAAAAATATAAATATAA
*
3444755 TATAATATTAAAATATTTAAA-A-AA
1 TATAATATTAAAA-ATATAAATATAA
* * *
3444779 T-TAA-AATATAAATAT-GATATAA
1 TATAATATTAAAAATATAAATATAA
3444801 TATAATATTAAAAATAT
1 TATAATATTAAAAATAT
3444818 TTTATATAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.02
21 4 0.08
22 8 0.16
23 6 0.12
24 11 0.22
25 14 0.28
26 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
TATAATATTAAAAATATAAATATAA
Found at i:3444812 original size:29 final size:31
Alignment explanation
Indices: 3444778--3444847 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 31
3444768 TATTTAAAAA
3444778 ATTAAAATATAAATATGATATAAT-ATA-AT
1 ATTAAAATATAAATATGATATAATAATATAT
* *
3444807 ATTAAAA-AT--ATTTTATATAATAATATAT
1 ATTAAAATATAAATATGATATAATAATATAT
*
3444835 AATAAAATATAAA
1 ATTAAAATATAAA
3444848 ATTATATTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
26 10 0.30
27 3 0.09
28 10 0.30
29 9 0.27
31 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (31 bp):
ATTAAAATATAAATATGATATAATAATATAT
Found at i:3444823 original size:24 final size:24
Alignment explanation
Indices: 3444730--3444832 Score: 79
Period size: 24 Copynumber: 4.3 Consensus size: 24
3444720 CTGAATATGG
* *
3444730 TATAATATTAAAAATATAAATATGA
1 TATAATATTAAAAATAT-TATATAA
*
3444755 TATAATATT-AAAATATT-TAAAA
1 TATAATATTAAAAATATTATATAA
* * * *
3444777 AATTAA-AATATAAATATGATATAA
1 TA-TAATATTAAAAATATTATATAA
*
3444801 TATAATATTAAAAATATTTTAT-A
1 TATAATATTAAAAATATTATATAA
3444824 TAATAATAT
1 T-ATAATAT
3444833 ATAATAAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
22 6 0.10
23 14 0.23
24 31 0.52
25 9 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TATAATATTAAAAATATTATATAA
Found at i:3444845 original size:46 final size:46
Alignment explanation
Indices: 3444741--3444855 Score: 117
Period size: 46 Copynumber: 2.5 Consensus size: 46
3444731 ATAATATTAA
*
3444741 AAATATAAATATGATATAATATTAAAATATTTAAAAAATTAAAATAT
1 AAATA-AAATATAATATAATATTAAAATATTTAAAAAATTAAAATAT
** * * *
3444788 AAATATGATATAATATAATATTAAAAATATTTTATATAA-TAATATAT
1 AAATAAAATATAATATAATATT-AAAATA-TTTAAAAAATTAAAATAT
* *
3444835 -AATAAAATATAAAATTATATT
1 AAATAAAATATAATATAATATT
3444856 TGAGCATATT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
46 31 0.55
47 18 0.32
48 7 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (46 bp):
AAATAAAATATAATATAATATTAAAATATTTAAAAAATTAAAATAT
Found at i:3448843 original size:11 final size:12
Alignment explanation
Indices: 3448819--3448883 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 12
3448809 AATTAAAAAA
* *
3448819 TTATTACATATT
1 TTATTATATTTT
3448831 TTATT-TATTTT
1 TTATTATATTTT
3448842 TTATTATATTTT
1 TTATTATATTTT
*
3448854 ATAAATTATATATTT
1 -T-TATTATAT-TTT
*
3448869 TTATTTTTATTTT
1 TTA-TTATATTTT
3448882 TT
1 TT
3448884 TCTCAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 9 0.21
12 11 0.26
13 7 0.16
14 13 0.30
15 3 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTATATTTT
Found at i:3449235 original size:2 final size:2
Alignment explanation
Indices: 3449230--3449254 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3449220 TATATATATA
3449230 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 T
3449255 AACAAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3457907 original size:17 final size:17
Alignment explanation
Indices: 3457885--3457923 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3457875 ATGTAAATGT
*
3457885 AATATA-AAAAATTATTA
1 AATATATAAAAA-TAATA
3457902 AATATATAAAAATAATA
1 AATATATAAAAATAATA
3457919 AATAT
1 AATAT
3457924 GAATATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATATAAAAATAATA
Found at i:3458283 original size:2 final size:2
Alignment explanation
Indices: 3458276--3458301 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3458266 CAATTAGCGG
3458276 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
3458302 TATTTTGTTC
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:3462373 original size:14 final size:14
Alignment explanation
Indices: 3462354--3462380 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3462344 TTCATTTGAG
3462354 AATAAATAAAATAA
1 AATAAATAAAATAA
3462368 AATAAATAAAATA
1 AATAAATAAAATA
3462381 TATTTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAATAAAATAA
Found at i:3464852 original size:2 final size:2
Alignment explanation
Indices: 3464845--3464869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3464835 TCTTTCTGAT
3464845 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3464870 TATCCATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3466238 original size:6 final size:6
Alignment explanation
Indices: 3466221--3466250 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3466211 AACATATATG
*
3466221 TGTATA TTTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA
3466251 AATGTACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (6 bp):
TGTATA
Found at i:3466404 original size:2 final size:2
Alignment explanation
Indices: 3466397--3466438 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3466387 GCATGTGAGG
3466397 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
3466439 AAGAGAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3468024 original size:19 final size:19
Alignment explanation
Indices: 3467981--3468025 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3467971 TATATTCATT
**
3467981 AAACAAATAAATAAACCAA
1 AAACAAATAAATAAAAAAA
* *
3468000 ACACAAATAATTAAAAAAA
1 AAACAAATAAATAAAAAAA
3468019 AAACAAA
1 AAACAAA
3468026 GAAACTATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.76, C:0.13, G:0.00, T:0.11
Consensus pattern (19 bp):
AAACAAATAAATAAAAAAA
Found at i:3473038 original size:19 final size:20
Alignment explanation
Indices: 3472988--3473038 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
3472978 TTATTTTAAT
3472988 ATAATTTATAT-AAAATATA
1 ATAATTTATATAAAAATATA
* * *
3473007 ATAATATAAATAAAAATTTA
1 ATAATTTATATAAAAATATA
3473027 A-AATTTATATAA
1 ATAATTTATATAA
3473039 TAAAAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATTTATATAAAAATATA
Found at i:3474030 original size:20 final size:20
Alignment explanation
Indices: 3474002--3474055 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
3473992 AGCATACGTC
* *
3474002 ATAATTTTAATTAAAATTTA
1 ATAAATTTAATTAAAAATTA
*
3474022 ATAAATTTATTTAAAAATTA
1 ATAAATTTAATTAAAAATTA
3474042 A-ATAATTT-ATTAAA
1 ATA-AATTTAATTAAA
3474056 TCTGATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAATTTAATTAAAAATTA
Found at i:3474041 original size:27 final size:27
Alignment explanation
Indices: 3474010--3474097 Score: 77
Period size: 31 Copynumber: 3.0 Consensus size: 27
3474000 TCATAATTTT
*
3474010 AATTAAAATTTAATAAATTTATTTAAA
1 AATTAAAATTTATTAAATTTATTTAAA
*
3474037 AATTAAATAATTTATTAAATCTGATTTAATTA
1 AATT-AA-AATTTATTAAAT-TTATTTAA--A
* *
3474069 AATTTAAATTTTATTATTATTTATTTAAA
1 AA-TTAAAATTTATTA-AATTTATTTAAA
3474098 TATAATTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
27 4 0.08
28 2 0.04
29 12 0.24
30 7 0.14
31 15 0.31
32 7 0.14
33 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
AATTAAAATTTATTAAATTTATTTAAA
Found at i:3474133 original size:18 final size:17
Alignment explanation
Indices: 3474088--3474139 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 17
3474078 TTTATTATTA
3474088 TTTATTTAAATATAATT
1 TTTATTTAAATATAATT
* *
3474105 TTAATTAAAATAATAATT
1 TTTATTTAAAT-ATAATT
*
3474123 TTTATTTAAATTTAATT
1 TTTATTTAAATATAATT
3474140 ATAAAATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATTTAAATATAATT
Found at i:3474177 original size:18 final size:20
Alignment explanation
Indices: 3474133--3474178 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
3474123 TTTATTTAAA
3474133 TTTAATTATAAAATATATAATT
1 TTTAA-TATAAAATATAT-ATT
*
3474155 ATTAATAT-AAATATAT-TT
1 TTTAATATAAAATATATATT
3474173 TTTAAT
1 TTTAAT
3474179 TTTTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.32
20 8 0.36
21 3 0.14
22 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAATATAAAATATATATT
Found at i:3474245 original size:12 final size:11
Alignment explanation
Indices: 3474182--3474251 Score: 72
Period size: 12 Copynumber: 6.2 Consensus size: 11
3474172 TTTTAATTTT
3474182 TTAAATATAAA
1 TTAAATATAAA
*
3474193 -TAAATAATAAT
1 TTAAAT-ATAAA
3474204 TTAAATTTATAAA
1 TTAAA--TATAAA
*
3474217 TTAAAT-CAAA
1 TTAAATATAAA
3474227 TTAAATATAAA
1 TTAAATATAAA
3474238 TATAAATATAAA
1 T-TAAATATAAA
3474250 TT
1 TT
3474252 TAATTTTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
10 14 0.29
11 10 0.20
12 15 0.31
13 9 0.18
14 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAATATAAA
Found at i:3474266 original size:29 final size:28
Alignment explanation
Indices: 3474183--3474267 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
3474173 TTTAATTTTT
**
3474183 TAAATATAAATAAATAATAATTTAAATTTA
1 TAAATATAAATAAATTTTAATTTAAA--TA
* *
3474213 TAAAT-TAAATCAAA-TTAAATATAAATA
1 TAAATATAAAT-AAATTTTAATTTAAATA
*
3474240 TAAATATAAATTTAATTTTAATTTAAAT
1 TAAATATAAA-TAAATTTTAATTTAAAT
3474268 TTAATTTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
27 7 0.16
28 6 0.14
29 23 0.52
30 8 0.18
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAATATAAATAAATTTTAATTTAAATA
Found at i:3484299 original size:16 final size:15
Alignment explanation
Indices: 3484274--3484321 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
3484264 TAGCATTTTT
*
3484274 AAATTGATAAATTAAA
1 AAATTAATAAA-TAAA
3484290 AAATTAAT-AATAAA
1 AAATTAATAAATAAA
*
3484304 ATAATTAAAAAATAAA
1 A-AATTAATAAATAAA
3484320 AA
1 AA
3484322 GTCATTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 5 0.18
15 9 0.32
16 14 0.50
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAATTAATAAATAAA
Found at i:3484534 original size:16 final size:15
Alignment explanation
Indices: 3484515--3484563 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
3484505 AAAATAAAAA
3484515 AATAATAGAAATATAT
1 AATAATA-AAATATAT
*
3484531 AAT-ATAAAATTTA-
1 AATAATAAAATATAT
3484544 AATAATAAAA-ATAT
1 AATAATAAAATATAT
*
3484558 ATTAAT
1 AATAAT
3484564 TATTCCACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 5 0.18
14 17 0.61
15 3 0.11
16 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AATAATAAAATATAT
Found at i:3485086 original size:13 final size:11
Alignment explanation
Indices: 3485061--3485113 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
3485051 GATTCTTCCA
3485061 TTTTTTATAAT
1 TTTTTTATAAT
3485072 TTTTTTATAAT
1 TTTTTTATAAT
*
3485083 ATTTTGTTCAGACAT
1 -TTTT-TT-ATA-AT
3485098 TTTTTT-TAAT
1 TTTTTTATAAT
3485108 TTTTTT
1 TTTTTT
3485114 TCCTTTATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 8 0.22
11 12 0.33
12 4 0.11
13 4 0.11
14 6 0.17
15 2 0.06
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:3487065 original size:24 final size:24
Alignment explanation
Indices: 3487038--3487088 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
3487028 ATGATATAAA
3487038 TAAAAAATAAAT-ATATAAATATAT
1 TAAAAAATAAATAATATAAAT-TAT
** *
3487062 TAAAATTTATATAATATAAATTAT
1 TAAAAAATAAATAATATAAATTAT
3487086 TAA
1 TAA
3487089 TGAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAAAATAAATAATATAAATTAT
Found at i:3493026 original size:2 final size:2
Alignment explanation
Indices: 3493019--3493047 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3493009 CTGAATTTTC
3493019 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
3493048 GCTTTTTATC
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:3493218 original size:19 final size:18
Alignment explanation
Indices: 3493179--3493223 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
3493169 ATATTAAATA
3493179 ATTTTTAATATTTATATT
1 ATTTTTAATATTTATATT
3493197 ATTTTTAATATTT-TATT
1 ATTTTTAATATTTATATT
3493214 ATATTTTAAT
1 AT-TTTTAAT
3493224 TTATAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTAATATTTATATT
Found at i:3493233 original size:17 final size:17
Alignment explanation
Indices: 3493188--3493234 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
3493178 AATTTTTAAT
3493188 ATTTATATTAT-TTTTA
1 ATTTATATTATATTTTA
*
3493204 ATATTTTATTATATTTTA
1 AT-TTATATTATATTTTA
*
3493222 ATTTATAATATAT
1 ATTTATATTATAT
3493235 AAATATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 2 0.08
17 17 0.65
18 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATATTATATTTTA
Found at i:3495718 original size:14 final size:14
Alignment explanation
Indices: 3495699--3495727 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3495689 GAATAACTTA
3495699 TAATTATTACAGCC
1 TAATTATTACAGCC
3495713 TAATTATTACAGCC
1 TAATTATTACAGCC
3495727 T
1 T
3495728 TCCTATTCCT
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:0.21, G:0.07, T:0.38
Consensus pattern (14 bp):
TAATTATTACAGCC
Found at i:3496710 original size:20 final size:19
Alignment explanation
Indices: 3496685--3496733 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
3496675 TAATTATATT
3496685 TAAATTATTA-TATATTTATA
1 TAAATT-TTATTATATTT-TA
3496705 TAAATTTTATTTATATTTTA
1 TAAATTTTA-TTATATTTTA
3496725 TAAATTTTA
1 TAAATTTTA
3496734 ATAAAATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.11
20 17 0.63
21 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAAATTTTATTATATTTTA
Found at i:3496772 original size:27 final size:25
Alignment explanation
Indices: 3496712--3496772 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 25
3496702 ATATAAATTT
3496712 TATTTATATTTTATAAATTTTAATA
1 TATTTATATTTTATAAATTTTAATA
* * * * *
3496737 AAATCATATATTTATATTATTTTATTA
1 TATTTATAT-TTTATA-AATTTTAATA
3496764 TATTTATAT
1 TATTTATAT
3496773 CATATTTAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
25 6 0.23
26 6 0.23
27 14 0.54
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTTATATTTTATAAATTTTAATA
Found at i:3497083 original size:15 final size:15
Alignment explanation
Indices: 3497055--3497095 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3497045 TAAATAAAAT
3497055 TTAATAATCATTATC
1 TTAATAATCATTATC
*
3497070 TTAA-AATCATT-TA
1 TTAATAATCATTATC
*
3497083 TTAATAATAATTA
1 TTAATAATCATTA
3497096 ATAGCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAATAATCATTATC
Found at i:3497265 original size:2 final size:2
Alignment explanation
Indices: 3497258--3497286 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3497248 TGCTTCACAT
3497258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3497287 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3500148 original size:16 final size:16
Alignment explanation
Indices: 3500127--3500164 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3500117 TTGGGGCGAG
3500127 AACTTTGGTATTAGAA
1 AACTTTGGTATTAGAA
3500143 AACTTTGGTATTAGAA
1 AACTTTGGTATTAGAA
3500159 AACTTT
1 AACTTT
3500165 CGTCTCCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (16 bp):
AACTTTGGTATTAGAA
Found at i:3504524 original size:2 final size:2
Alignment explanation
Indices: 3504517--3504551 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3504507 CATTATGAGT
3504517 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3504552 GTGTGTCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3510423 original size:19 final size:19
Alignment explanation
Indices: 3510399--3510438 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
3510389 ATTTTAGATA
3510399 TAATTT-TTTTAATTTAAAT
1 TAATTTATTTT-ATTTAAAT
3510418 TAATTTATTTTATTTAAAT
1 TAATTTATTTTATTTAAAT
3510437 TA
1 TA
3510439 TTATTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATTTATTTTATTTAAAT
Found at i:3511779 original size:3 final size:3
Alignment explanation
Indices: 3511773--3511803 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3511763 TGATCTGTTG
3511773 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3511804 ACCCTCGTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3512947 original size:16 final size:18
Alignment explanation
Indices: 3512926--3512962 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
3512916 TGTAAATCGA
*
3512926 TTTTTAA-ATTTTAA-AT
1 TTTTTAATAATTTAATAT
3512942 TTTTTAATAATTTAATAT
1 TTTTTAATAATTTAATAT
3512960 TTT
1 TTT
3512963 AAAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAATAATTTAATAT
Found at i:3512974 original size:25 final size:24
Alignment explanation
Indices: 3512928--3512974 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
3512918 TAAATCGATT
** *
3512928 TTTAAATTTTAAATTTTTTAATAA
1 TTTAAATTTTAAAAATTATAATAA
3512952 TTTAATATTTTAAAAATTATAAT
1 TTTAA-ATTTTAAAAATTATAAT
3512975 TGAATATCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAAATTTTAAAAATTATAATAA
Found at i:3517613 original size:2 final size:2
Alignment explanation
Indices: 3517606--3517635 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3517596 TGACTTCTTA
3517606 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
3517636 TCAGGGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3519255 original size:26 final size:26
Alignment explanation
Indices: 3519219--3519270 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3519209 TTTATATTAA
*
3519219 ATTTTTAAATATAAATAATTTAATAT
1 ATTTTTAAATATAAATAATATAATAT
* **
3519245 ATTTTTTAATATTTATAATATAATAT
1 ATTTTTAAATATAAATAATATAATAT
3519271 TATATATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTTTAAATATAAATAATATAATAT
Found at i:3519268 original size:31 final size:31
Alignment explanation
Indices: 3519228--3519298 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
3519218 AATTTTTAAA
*
3519228 TATAA-ATAAT-TTAATATATTTTTTAA-TATT
1 TATAATATAATATT-ATATA-TATTTAATTATT
*
3519258 TATAATATAATATTATATATATTTAATTTTT
1 TATAATATAATATTATATATATTTAATTATT
3519289 TATAATATAA
1 TATAATATAA
3519299 ATCACAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 11 0.31
31 23 0.64
32 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TATAATATAATATTATATATATTTAATTATT
Found at i:3519270 original size:14 final size:14
Alignment explanation
Indices: 3519251--3519298 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
3519241 ATATATTTTT
3519251 TAATATTTATAATA
1 TAATATTTATAATA
*
3519265 TAATATTATATATATT
1 TAATATT-TATA-ATA
*
3519281 TAATTTTTTATAATA
1 TAA-TATTTATAATA
3519296 TAA
1 TAA
3519299 ATCACAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 9 0.32
17 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAATATTTATAATA
Found at i:3522029 original size:14 final size:12
Alignment explanation
Indices: 3522001--3522041 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
3521991 TAGATATACT
3522001 AATTT-AAAT-A
1 AATTTAAAATAA
3522011 AATTTAAATAATAA
1 AATTT-AA-AATAA
3522025 AATTTAAAATAA
1 AATTTAAAATAA
3522037 AATTT
1 AATTT
3522042 TAATGAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.19
12 11 0.41
13 5 0.19
14 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTTAAAATAA
Found at i:3522291 original size:9 final size:9
Alignment explanation
Indices: 3522274--3522361 Score: 55
Period size: 9 Copynumber: 10.6 Consensus size: 9
3522264 TAATATTAAA
*
3522274 TATAAATAT
1 TATATATAT
3522283 TATATATAT
1 TATATATAT
*
3522292 TAAATATAT
1 TATATATAT
3522301 TA-A-ATAT
1 TATATATAT
* *
3522308 T-T-TAAAA
1 TATATATAT
*
3522315 TATATTTAT
1 TATATATAT
*
3522324 TATATTTAT
1 TATATATAT
*
3522333 TACAT-TAT
1 TATATATAT
3522341 TAT-T-TAT
1 TATATATAT
*
3522348 TAAATATAT
1 TATATATAT
3522357 TATAT
1 TATAT
3522362 TTATATCATA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
7 14 0.23
8 8 0.13
9 40 0.65
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (9 bp):
TATATATAT
Found at i:3522346 original size:15 final size:15
Alignment explanation
Indices: 3522322--3522359 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3522312 AAATATATTT
*
3522322 ATTA-TATTTATTAC
1 ATTATTATTTATTAA
3522336 ATTATTATTTATTAA
1 ATTATTATTTATTAA
3522351 ATATATTAT
1 AT-TATTAT
3522360 ATTTATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 11 0.52
16 6 0.29
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTTATTAA
Found at i:3522890 original size:15 final size:14
Alignment explanation
Indices: 3522863--3522906 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
3522853 CTATTTATAA
*
3522863 TTTATTTATTAATT
1 TTTATTTAATAATT
3522877 TTTATTATAATAATTT
1 TTTATT-TAATAA-TT
*
3522893 TTTATTTAAAAATT
1 TTTATTTAATAATT
3522907 AATAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTATTTAATAATT
Done.