Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 21 of 117
Found at i:6047313 original size:10 final size:10
Alignment explanation
Indices: 6047298--6047334 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
6047288 TGAAAGTCCT
6047298 AAAATTTTTA
1 AAAATTTTTA
6047308 AAAATTTTTA
1 AAAATTTTTA
6047318 AAAA-TTTTA
1 AAAATTTTTA
6047327 AAACATTT
1 AAA-ATTT
6047335 ATTTTCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.32
10 15 0.60
11 2 0.08
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:6047339 original size:34 final size:34
Alignment explanation
Indices: 6047301--6047385 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
6047291 AAGTCCTAAA
* *
6047301 ATTTTTAAAAATTTTTAA-AAATTTTAAAACATTT
1 ATTTTTGAAAATTTTTAAGAAATTTTAAAA-ATTC
* * **
6047335 ATTTTCGAAAACTTTTAAGAGTTTTTAAAAATTC
1 ATTTTTGAAAATTTTTAAGAAATTTTAAAAATTC
*
6047369 ATTTTTGAAAATATTTA
1 ATTTTTGAAAATTTTTA
6047386 TTTTTAAAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
34 32 0.78
35 9 0.22
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (34 bp):
ATTTTTGAAAATTTTTAAGAAATTTTAAAAATTC
Found at i:6047379 original size:15 final size:15
Alignment explanation
Indices: 6047356--6047394 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
6047346 CTTTTAAGAG
6047356 TTTTTAAAA-ATTCA
1 TTTTTAAAATATTCA
*
6047370 TTTTTGAAAATATTTA
1 TTTTT-AAAATATTCA
6047386 TTTTTAAAA
1 TTTTTAAAA
6047395 GCTCTTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 9 0.41
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (15 bp):
TTTTTAAAATATTCA
Found at i:6047403 original size:84 final size:84
Alignment explanation
Indices: 6047301--6047464 Score: 190
Period size: 84 Copynumber: 2.0 Consensus size: 84
6047291 AAGTCCTAAA
* *
6047301 ATTTTTAAAAATTTTTAAAAAT-TTTAAAACATTTATTTTCGAAAA-CTTTTAA-GAGTTTTTAA
1 ATTTTTAAAAACTCTTAAAAATGTTT-AAACATTTATTTTC-AAAATCTTTTAAGGA-TTTTTAA
6047363 AAATTCATTTTTGAAAATATTT
63 AAATTCATTTTTGAAAATATTT
* ** * * * *
6047385 ATTTTTAAAAGCTCTTAAAGGTGTTTGAACATTTATTTTCAAAATTTTTTTAGGATTTTTACAAA
1 ATTTTTAAAAACTCTTAAAAATGTTTAAACATTTATTTTCAAAATCTTTTAAGGATTTTTAAAAA
*
6047450 TTTATTTTTGAAAAT
66 TTCATTTTTGAAAAT
6047465 TTTGAATTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
83 4 0.06
84 58 0.87
85 5 0.07
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (84 bp):
ATTTTTAAAAACTCTTAAAAATGTTTAAACATTTATTTTCAAAATCTTTTAAGGATTTTTAAAAA
TTCATTTTTGAAAATATTT
Found at i:6049852 original size:32 final size:32
Alignment explanation
Indices: 6049808--6049873 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
6049798 TATTAATTTG
6049808 AAAATTATAAAAA-A-AAAAAAGAAAAGAAAGGC
1 AAAATTATAAAAACACAAAAAA-AAAA-AAAGGC
*
6049840 AAAA-TATCAAAAACACAAAAAAAAAAAAATGC
1 AAAATTAT-AAAAACACAAAAAAAAAAAAAGGC
6049872 AA
1 AA
6049874 GGTGAGAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
31 3 0.10
32 16 0.53
33 5 0.17
34 6 0.20
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.09
Consensus pattern (32 bp):
AAAATTATAAAAACACAAAAAAAAAAAAAGGC
Found at i:6052153 original size:15 final size:16
Alignment explanation
Indices: 6052135--6052164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6052125 AAAAAAAAAA
6052135 TTGAAA-TCCAAAACT
1 TTGAAACTCCAAAACT
6052150 TTGAAACTCCAAAAC
1 TTGAAACTCCAAAAC
6052165 CAAAACTCTA
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:0.23, G:0.07, T:0.23
Consensus pattern (16 bp):
TTGAAACTCCAAAACT
Found at i:6052589 original size:13 final size:13
Alignment explanation
Indices: 6052573--6052604 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
6052563 TAGGAACCAA
6052573 ATTTCAAAATGAC
1 ATTTCAAAATGAC
6052586 ATTTCAAAATGAC
1 ATTTCAAAATGAC
6052599 ATTTCA
1 ATTTCA
6052605 TCATCATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (13 bp):
ATTTCAAAATGAC
Found at i:6055945 original size:72 final size:72
Alignment explanation
Indices: 6055828--6056045 Score: 418
Period size: 72 Copynumber: 3.0 Consensus size: 72
6055818 AACAGTAGGT
6055828 TGCTAAGGACATGAAACATTTTGCAAAAAGATAGTCTTTAATTTTTTTTATTTTATGGATGTTTA
1 TGCTAAGGACATGAAACATTTTGCAAAAAGATAGTCTTTAATTTTTTTTATTTTATGGATGTTTA
*
6055893 TAAAGAA
66 CAAAGAA
*
6055900 TGCTAAGGACATGAAACATTTTGTAAAAAGATAGTCTTTAATTTTTTTTATTTTATGGATGTTTA
1 TGCTAAGGACATGAAACATTTTGCAAAAAGATAGTCTTTAATTTTTTTTATTTTATGGATGTTTA
6055965 CAAAGAA
66 CAAAGAA
6055972 TGCTAAGGACATGAAACATTTTGCAAAAAGATAGTCTTTAATTTTTTTTATTTTATGGATGTTTA
1 TGCTAAGGACATGAAACATTTTGCAAAAAGATAGTCTTTAATTTTTTTTATTTTATGGATGTTTA
6056037 CAAAGAA
66 CAAAGAA
6056044 TG
1 TG
6056046 ATATTTTGTT
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 143 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (72 bp):
TGCTAAGGACATGAAACATTTTGCAAAAAGATAGTCTTTAATTTTTTTTATTTTATGGATGTTTA
CAAAGAA
Found at i:6061432 original size:16 final size:15
Alignment explanation
Indices: 6061407--6061440 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
6061397 ATTTTTTATA
6061407 TTTTTGAAAATGAGAT
1 TTTTTGAAAATGA-AT
*
6061423 TTTTTTAAAATGAAT
1 TTTTTGAAAATGAAT
6061438 TTT
1 TTT
6061441 CAAGAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTTTGAAAATGAAT
Found at i:6072862 original size:15 final size:15
Alignment explanation
Indices: 6072844--6072875 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6072834 AAATACAAAA
6072844 TAATATAATATTATT
1 TAATATAATATTATT
*
6072859 TAATATAATCTTATT
1 TAATATAATATTATT
6072874 TA
1 TA
6072876 TAATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATATAATATTATT
Found at i:6084508 original size:2 final size:2
Alignment explanation
Indices: 6084501--6084552 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
6084491 TATTTATCTT
* * * * *
6084501 TA TA TA TA TA CA TA TA TA TA CA TA TA TA TA CA TG TG 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
6084543 TA TA TA TA TA
1 TA TA TA TA TA
6084553 AGTGTTAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6084552 original size:10 final size:10
Alignment explanation
Indices: 6084502--6084550 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
6084492 ATTTATCTTT
6084502 ATATATATAC
1 ATATATATAC
6084512 ATATATATAC
1 ATATATATAC
6084522 ATATATATAC
1 ATATATATAC
* * *
6084532 ATGTGTATAT
1 ATATATATAC
6084542 ATATATATA
1 ATATATATA
6084551 TAAGTGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (10 bp):
ATATATATAC
Found at i:6084557 original size:20 final size:21
Alignment explanation
Indices: 6084501--6084557 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
6084491 TATTTATCTT
*
6084501 TATATATATACA-TATATATA
1 TATATATATACAGTGTATATA
*
6084521 CATATATATACATGTGTATATA
1 TATATATATACA-GTGTATATA
6084543 TATATATATA-AGTGT
1 TATATATATACAGTGT
6084558 TAATAGCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.47
21 1 0.03
22 16 0.50
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (21 bp):
TATATATATACAGTGTATATA
Found at i:6091349 original size:2 final size:2
Alignment explanation
Indices: 6091338--6091367 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6091328 AAGAAATCAA
6091338 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6091368 AGGGAGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6097535 original size:3 final size:3
Alignment explanation
Indices: 6097527--6097551 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6097517 CACTACTTCT
6097527 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
6097552 CCAATAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6102369 original size:19 final size:20
Alignment explanation
Indices: 6102330--6102377 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
6102320 ATACCTGAAA
*
6102330 TAAATAAAAAAAATTATTTT
1 TAAATATAAAAAATTATTTT
*
6102350 TAAATATAAAATATTATTTT
1 TAAATATAAAAAATTATTTT
6102370 T-AATATAA
1 TAAATATAA
6102378 TTATAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATATAAAAAATTATTTT
Found at i:6102434 original size:36 final size:35
Alignment explanation
Indices: 6102369--6102437 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
6102359 AATATTATTT
6102369 TTAATATAATTATAAAAATAATTAAATATATATGA
1 TTAATATAATTATAAAAATAATTAAATATATATGA
**
6102404 TTAA-ATAATTAATTAAAAATAATTTTATATATAT
1 TTAATATAATT-A-TAAAAATAATTAAATATATAT
6102438 TAAATCGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 6 0.20
35 5 0.17
36 19 0.63
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAATATAATTATAAAAATAATTAAATATATATGA
Found at i:6102482 original size:3 final size:3
Alignment explanation
Indices: 6102474--6102507 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6102464 CTAATTCAAT
6102474 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6102508 GACTGGACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6102538 original size:17 final size:18
Alignment explanation
Indices: 6102516--6102550 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6102506 ATGACTGGAC
*
6102516 TTAAAACTCAA-TTTAAA
1 TTAAAAATCAACTTTAAA
6102533 TTAAAAATCAACTTTAAA
1 TTAAAAATCAACTTTAAA
6102551 ATATGGAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAATCAACTTTAAA
Found at i:6103535 original size:15 final size:15
Alignment explanation
Indices: 6103515--6103553 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6103505 ACGGAATGAG
*
6103515 TTGGAGCATGGGATA
1 TTGGAGCATGGGACA
* *
6103530 TTGGAGGATGGGCCA
1 TTGGAGCATGGGACA
6103545 TTGGAGCAT
1 TTGGAGCAT
6103554 TGGCTGGAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.41, T:0.26
Consensus pattern (15 bp):
TTGGAGCATGGGACA
Found at i:6103978 original size:24 final size:24
Alignment explanation
Indices: 6103902--6103979 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
6103892 ATCTATATAA
*
6103902 AAATTTTTAAA-AAAATTATTTTATT
1 AAATTTTTAAATATAATTA--TTATT
6103927 AAA--TTTAAATATAATTATTATT
1 AAATTTTTAAATATAATTATTATT
*
6103949 AAATTTTTAAAT-TATATTATTTTT
1 AAATTTTTAAATATA-ATTATTATT
*
6103973 ATATTTT
1 AAATTTT
6103980 ATATTTATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 8 0.17
23 8 0.17
24 27 0.59
25 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATTTTTAAATATAATTATTATT
Found at i:6103981 original size:13 final size:13
Alignment explanation
Indices: 6103965--6104010 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6103955 TTAAATTATA
6103965 TTATTTTTATATT
1 TTATTTTTATATT
*
6103978 TTATATTTATATT
1 TTATTTTTATATT
* *
6103991 GTATTATTATATT
1 TTATTTTTATATT
*
6104004 ATATTTT
1 TTATTTT
6104011 AAATTGTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TTATTTTTATATT
Found at i:6104602 original size:29 final size:29
Alignment explanation
Indices: 6104560--6104617 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6104550 CTAATAGTTA
6104560 GAATTCAGTCTGAACCAGTTCATATTTAT
1 GAATTCAGTCTGAACCAGTTCATATTTAT
6104589 GAATTCAGTCTGAACCAGTTCATATTTAT
1 GAATTCAGTCTGAACCAGTTCATATTTAT
6104618 TGAAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (29 bp):
GAATTCAGTCTGAACCAGTTCATATTTAT
Found at i:6112220 original size:3 final size:3
Alignment explanation
Indices: 6112214--6112261 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
6112204 TTTTTTTAAA
6112214 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6112262 TACATAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6118479 original size:9 final size:9
Alignment explanation
Indices: 6118467--6118519 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
6118457 TTCAAAAATC
6118467 TAAAAATTT
1 TAAAAATTT
6118476 TAAAAAATTCT
1 T-AAAAATT-T
* *
6118487 TTAAAATTC
1 TAAAAATTT
*
6118496 TAAAATTTT
1 TAAAAATTT
*
6118505 TGAAAATTT
1 TAAAAATTT
6118514 TAAAAA
1 TAAAAA
6118520 ATTCAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
9 19 0.56
10 13 0.38
11 2 0.06
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (9 bp):
TAAAAATTT
Found at i:6118481 original size:18 final size:19
Alignment explanation
Indices: 6118455--6118552 Score: 74
Period size: 22 Copynumber: 5.0 Consensus size: 19
6118445 TGTCAGTTGT
*
6118455 TTTTCAAAAA-TCTAAAAA
1 TTTTAAAAAATTCTAAAAA
*
6118473 TTTTAAAAAATTCTTTAAAA
1 TTTTAAAAAATTC-TAAAAA
* * * *
6118493 TTCT-AAAATTTTTGAAAA
1 TTTTAAAAAATTCTAAAAA
*
6118511 TTTTAAAAAATTCAAAAAATTA
1 TTTTAAAAAATTC-TAAAA--A
6118533 TTTTAAAAAATTCTCAAAAA
1 TTTTAAAAAATTCT-AAAAA
6118553 ATAAAAATAA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
18 17 0.28
19 14 0.23
20 12 0.20
22 18 0.30
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (19 bp):
TTTTAAAAAATTCTAAAAA
Found at i:6118483 original size:10 final size:10
Alignment explanation
Indices: 6118468--6118554 Score: 54
Period size: 10 Copynumber: 8.6 Consensus size: 10
6118458 TCAAAAATCT
6118468 AAAAATTTTA
1 AAAAATTTTA
6118478 AAAAATTCTT-
1 AAAAATT-TTA
* *
6118488 TAAAATTCT-
1 AAAAATTTTA
*
6118497 -AAAATTTTT
1 AAAAATTTTA
*
6118506 GAAAATTTTA
1 AAAAATTTTA
**
6118516 AAAAATTCAA
1 AAAAATTTTA
6118526 AAAATTATTTTA
1 AAAA--ATTTTA
*
6118538 AAAAATTCTCA
1 AAAAATT-TTA
6118549 AAAAAT
1 AAAAAT
6118555 AAAAATAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
8 7 0.11
9 1 0.02
10 35 0.57
11 10 0.16
12 8 0.13
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:6118538 original size:22 final size:24
Alignment explanation
Indices: 6118510--6118554 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
6118500 ATTTTTGAAA
6118510 ATTTTAAAAAA-T-TCAAAAAATT
1 ATTTTAAAAAATTCTCAAAAAATT
6118532 ATTTTAAAAAATTCTCAAAAAAT
1 ATTTTAAAAAATTCTCAAAAAAT
6118555 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 9 0.43
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (24 bp):
ATTTTAAAAAATTCTCAAAAAATT
Found at i:6118721 original size:20 final size:19
Alignment explanation
Indices: 6118697--6118751 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
6118687 TATTCAAAAT
* *
6118697 TTTTATAAATTTCTCAAACA
1 TTTTAAAAATTT-TAAAACA
6118717 TTTTAAAAATTTTAAAACA
1 TTTTAAAAATTTTAAAACA
* *
6118736 ATTTAAAAATTCTAAA
1 TTTTAAAAATTTTAAA
6118752 CTTTTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTAAAAATTTTAAAACA
Found at i:6118859 original size:17 final size:18
Alignment explanation
Indices: 6118815--6118851 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6118805 AAATTATCAT
* *
6118815 AATTCGAAAGTTTTTTAA
1 AATTCTAAAATTTTTTAA
6118833 AATTCTAAAATTTTTTAA
1 AATTCTAAAATTTTTTAA
6118851 A
1 A
6118852 TCTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTCTAAAATTTTTTAA
Found at i:6119022 original size:15 final size:17
Alignment explanation
Indices: 6118988--6119028 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
6118978 AACACTCCTT
6118988 AAAATTAAAAATATCTA
1 AAAATTAAAAATATCTA
*
6119005 AAAAATAAAAA-A-CTA
1 AAAATTAAAAATATCTA
6119020 AAAATTAAA
1 AAAATTAAA
6119029 TAAAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATTAAAAATATCTA
Found at i:6119042 original size:20 final size:18
Alignment explanation
Indices: 6119007--6119054 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
6118997 AATATCTAAA
*
6119007 AAATAAAAAACTAAAAATT
1 AAATAAAAAAC-AAAAAAT
6119026 AAATAAAAATACAAAAAAT
1 AAATAAAAA-ACAAAAAAT
*
6119045 ATATAAAAAA
1 AAATAAAAAA
6119055 TTGAAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.88
20 2 0.08
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATAAAAAACAAAAAAT
Found at i:6119324 original size:9 final size:9
Alignment explanation
Indices: 6119312--6119459 Score: 102
Period size: 9 Copynumber: 15.7 Consensus size: 9
6119302 TTTTTTAATT
6119312 TTTTTAAAA
1 TTTTTAAAA
*
6119321 TTTTCTAGAA
1 TTTT-TAAAA
** *
6119331 TTTGCACAA
1 TTTTTAAAA
6119340 TTTTTAAAA
1 TTTTTAAAA
*
6119349 TTTTATAAAT
1 TTTT-TAAAA
6119359 TTTTTAAAA
1 TTTTTAAAA
6119368 TTTTTAAAAA
1 TTTTT-AAAA
6119378 TTTTTAAAA
1 TTTTTAAAA
*
6119387 TATTTTAAATG
1 T-TTTTAAA-A
*
6119398 TTTTTAGAA
1 TTTTTAAAA
* *
6119407 TTTTTTAAT
1 TTTTTAAAA
6119416 TTTTTCAGAAA
1 TTTTT-A-AAA
*
6119427 -TTTTAAATT
1 TTTTTAAA-A
6119436 TTTTTGAAAA
1 TTTTT-AAAA
*
6119446 -TTTTAAAT
1 TTTTTAAAA
6119454 TTTTTA
1 TTTTTA
6119460 TATTTATTTG
Statistics
Matches: 108, Mismatches: 20, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
8 5 0.05
9 52 0.48
10 45 0.42
11 6 0.06
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:6119362 original size:19 final size:18
Alignment explanation
Indices: 6119340--6119503 Score: 131
Period size: 19 Copynumber: 8.8 Consensus size: 18
6119330 ATTTGCACAA
6119340 TTTTTAAAATTTTATAAAT
1 TTTTTAAAATTTT-TAAAT
*
6119359 TTTTTAAAATTTTTAAAAA
1 TTTTTAAAATTTTT-AAAT
6119378 TTTTTAAAATATTTTAAAT
1 TTTTTAAAAT-TTTTAAAT
* *
6119397 GTTTTTAGAATTTTTTAAT
1 -TTTTTAAAATTTTTAAAT
6119416 TTTTTCAGAAA-TTTTAAATT
1 TTTTT-A-AAATTTTTAAA-T
6119436 TTTTTGAAAA-TTTTAAAT
1 TTTTT-AAAATTTTTAAAT
* **
6119454 TTTTT-ATATTTATT-TGT
1 TTTTTAAAATTT-TTAAAT
*
6119471 TTTTT-AAATTTTAAAAT
1 TTTTTAAAATTTTTAAAT
*
6119488 TATTTTAGAATTTTTA
1 T-TTTTAAAATTTTTA
6119504 GTATTTTTGG
Statistics
Matches: 118, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
16 3 0.03
17 15 0.13
18 18 0.15
19 60 0.51
20 22 0.19
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTTAAAATTTTTAAAT
Found at i:6119464 original size:9 final size:9
Alignment explanation
Indices: 6119302--6119502 Score: 101
Period size: 10 Copynumber: 21.6 Consensus size: 9
6119292 TCCTTAATTC
*
6119302 TTTTTTAAT
1 TTTTTTAAA
6119311 TTTTTTAAAA
1 TTTTTT-AAA
*
6119321 TTTTCTAGAA
1 TTTTTTA-AA
**
6119331 -TTTGCACAA
1 TTTTTTA-AA
*
6119340 TTTTTAAAA
1 TTTTTTAAA
*
6119349 TTTTATAAA
1 TTTTTTAAA
6119358 TTTTTTAAAA
1 TTTTTT-AAA
*
6119368 TTTTTAAAAA
1 TTTTT-TAAA
*
6119378 TTTTTAAAA
1 TTTTTTAAA
*
6119387 TATTTTAAA
1 TTTTTTAAA
6119396 TGTTTTTAGAA
1 T-TTTTTA-AA
6119407 TTTTTT-AA
1 TTTTTTAAA
6119415 TTTTTTCAGAA
1 TTTTTT-A-AA
*
6119426 -ATTTTAAA
1 TTTTTTAAA
6119434 TTTTTTTGAAA
1 -TTTTTT-AAA
*
6119445 -ATTTTAAA
1 TTTTTTAAA
*
6119453 TTTTTTATA
1 TTTTTTAAA
*
6119462 TTTATTT--G
1 TTT-TTTAAA
6119470 TTTTTTAAA
1 TTTTTTAAA
*
6119479 -TTTTAAAA
1 TTTTTTAAA
6119487 TTATTTTAGAA
1 TT-TTTTA-AA
6119498 TTTTT
1 TTTTT
6119503 AGTATTTTTG
Statistics
Matches: 149, Mismatches: 23, Indels: 39
0.71 0.11 0.18
Matches are distributed among these distances:
7 3 0.02
8 23 0.15
9 54 0.36
10 57 0.38
11 12 0.08
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:6119716 original size:20 final size:20
Alignment explanation
Indices: 6119693--6119738 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
6119683 AGTTTTTATC
**
6119693 ATTTTTAAAAAAATTTTAGA
1 ATTTTTAAAAAAAAATTAGA
**
6119713 ATTTCAAAAAAAAAATTAGA
1 ATTTTTAAAAAAAAATTAGA
6119733 ATTTTT
1 ATTTTT
6119739 TTAGTTTTTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (20 bp):
ATTTTTAAAAAAAAATTAGA
Found at i:6119778 original size:13 final size:14
Alignment explanation
Indices: 6119755--6119785 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6119745 TTTTTAACCT
6119755 TTTACTTTTTTGAA
1 TTTACTTTTTTGAA
*
6119769 TTTATTTTTTTGAA
1 TTTACTTTTTTGAA
6119783 TTT
1 TTT
6119786 TTTTGAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTACTTTTTTGAA
Found at i:6121338 original size:21 final size:20
Alignment explanation
Indices: 6121296--6121339 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6121286 GTTGACTTAT
*
6121296 AGTAAAAAAAATTATAATAA
1 AGTAAAAAAAATTATAACAA
* *
6121316 AGTAAAAAATTATTGTAACAA
1 AGTAAAAAA-AATTATAACAA
6121337 AGT
1 AGT
6121340 GCGGCCAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.27
Consensus pattern (20 bp):
AGTAAAAAAAATTATAACAA
Found at i:6122419 original size:63 final size:66
Alignment explanation
Indices: 6122259--6122426 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 66
6122249 ACTGTTAGCC
* * *
6122259 AAAAACAACCAAAATATCAACATTTATCCAAAAAATAA-CCAAGACAAATGAGGGACGATGGAGA
1 AAAAAAAACCAAAATTTCAACATTTATTCAAAAAATAACCCAAGACAAATGAGGGACGATGGAG-
6122323 AA
65 AA
* *
6122325 AAAAAAAACCTAAATTTCAACATTTATTCAAAAAATAACCCAA-ACAAATGA-GGATGATGGAG-
1 AAAAAAAACCAAAATTTCAACATTTATTCAAAAAATAACCCAAGACAAATGAGGGACGATGGAGA
*
6122387 G
66 A
* * *
6122388 GAAAAAAACCCAAATTTCAACATTTGTTCAAAAAATAAC
1 AAAAAAAACCAAAATTTCAACATTTATTCAAAAAATAAC
6122427 TAAGAAAAAT
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
63 36 0.39
65 10 0.11
66 42 0.46
67 4 0.04
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.18
Consensus pattern (66 bp):
AAAAAAAACCAAAATTTCAACATTTATTCAAAAAATAACCCAAGACAAATGAGGGACGATGGAGA
A
Found at i:6122437 original size:63 final size:65
Alignment explanation
Indices: 6122259--6122438 Score: 222
Period size: 63 Copynumber: 2.8 Consensus size: 65
6122249 ACTGTTAGCC
* * *
6122259 AAAAACAACCAAAATATCAACATTTATCCAAAAAATAACCAAGACAAATGAGGGACGATGGAGAA
1 AAAAAAAACCAAAATTTCAACATTTATTCAAAAAATAACCAAGACAAATGAGGGACGATGGAG-A
6122324 A
65 A
* *
6122325 AAAAAAAACCTAAATTTCAACATTTATTCAAAAAATAACCCAA-ACAAATGA-GGATGATGGAG-
1 AAAAAAAACCAAAATTTCAACATTTATTCAAAAAATAA-CCAAGACAAATGAGGGACGATGGAGA
*
6122387 G
65 A
* * * * *
6122388 GAAAAAAACCCAAATTTCAACATTTGTTCAAAAAATAACTAAGAAAAATGA
1 AAAAAAAACCAAAATTTCAACATTTATTCAAAAAATAACCAAGACAAATGA
6122439 AAGCGTTGGA
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
62 3 0.03
63 42 0.42
65 10 0.10
66 42 0.42
67 4 0.04
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.18
Consensus pattern (65 bp):
AAAAAAAACCAAAATTTCAACATTTATTCAAAAAATAACCAAGACAAATGAGGGACGATGGAGAA
Found at i:6123148 original size:21 final size:20
Alignment explanation
Indices: 6123124--6123170 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
6123114 TTTATTTGAA
*
6123124 ATTATTAAAGAATAATTTTTT
1 ATTATTAAA-AATAAATTTTT
*
6123145 ATTATTAAAATTAAATTTTT
1 ATTATTAAAAATAAATTTTT
*
6123165 AATATT
1 ATTATT
6123171 TTATCAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTATTAAAAATAAATTTTT
Found at i:6127779 original size:40 final size:41
Alignment explanation
Indices: 6127718--6127796 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
6127708 GACTTTGATG
6127718 AGATGGGAAAACAAGAGAATAGGTTTGGATATACAGTAGGC
1 AGATGGGAAAACAAGAGAATAGGTTTGGATATACAGTAGGC
*
6127759 AGAT-GGAAAACAATG-TAATAGGTTTGGATATACAGTAG
1 AGATGGGAAAACAA-GAGAATAGGTTTGGATATACAGTAG
6127797 CGCATTTGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (41 bp):
AGATGGGAAAACAAGAGAATAGGTTTGGATATACAGTAGGC
Found at i:6132285 original size:52 final size:52
Alignment explanation
Indices: 6132219--6132375 Score: 219
Period size: 52 Copynumber: 3.0 Consensus size: 52
6132209 TGGACAAAAA
* *
6132219 GACTTGCAAAAGAAGAATTCTAAGAGAAAGATGATTCTTAATAGATAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAAGATGATTCTTAATAGACAAGTTT
*
6132271 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGA-GATTCTTAATAGACAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGA-GAAAGATGATTCTTAATAGACAAGTTT
* * * *
6132323 GACTTACAGGAGAAGAATTCTAAGAG-GAGAATGATTCTTAATGGACAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGAAAG-ATGATTCTTAATAGACAAGTTT
6132375 G
1 G
6132376 TATGGTTATA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
50 2 0.02
51 2 0.02
52 84 0.89
53 6 0.06
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGAAAGATGATTCTTAATAGACAAGTTT
Found at i:6133548 original size:11 final size:12
Alignment explanation
Indices: 6133526--6133554 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
6133516 TATAAAGAGA
6133526 ATTATATTTTTT
1 ATTATATTTTTT
6133538 ATTAT-TTTTTT
1 ATTATATTTTTT
6133549 ATTATA
1 ATTATA
6133555 ATTAATACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTATATTTTTT
Found at i:6137994 original size:71 final size:70
Alignment explanation
Indices: 6137858--6137995 Score: 231
Period size: 71 Copynumber: 2.0 Consensus size: 70
6137848 CATCCTAAAT
* * * *
6137858 GGATGAACACCAATAATAGTTAATAAGAAAAATTCACTATAAAAAGATGATACACAGATGGCAGA
1 GGATGAAAACCAATAATAGTTAATAAAAAAAATTCACCATAAAAAAATGATACACAGATGGCAGA
6137923 ATTTG
66 ATTTG
6137928 GGATGAAAACCAATAATAGTTAATAAAAAAAATTTCACCATAAAAAAATGATACACAGATGGCAG
1 GGATGAAAACCAATAATAGTTAATAAAAAAAA-TTCACCATAAAAAAATGATACACAGATGGCAG
6137993 AAT
65 AAT
6137996 ATTGAAGTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 30 0.48
71 33 0.52
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (70 bp):
GGATGAAAACCAATAATAGTTAATAAAAAAAATTCACCATAAAAAAATGATACACAGATGGCAGA
ATTTG
Found at i:6140246 original size:50 final size:50
Alignment explanation
Indices: 6140171--6140270 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
6140161 AGTTTATGTA
*
6140171 TACGTTTAACATTTTTGAGGTTTTAAAATTCACAAAACGATTAAAACATT
1 TACGTTTAACATTTTTGAGGTTTTAAAAGTCACAAAACGATTAAAACATT
6140221 TACGTTTAACATTTTTGAGGTTTTAAAAGTCACAAAACGATTAAAACATT
1 TACGTTTAACATTTTTGAGGTTTTAAAAGTCACAAAACGATTAAAACATT
6140271 ATCATGTACC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (50 bp):
TACGTTTAACATTTTTGAGGTTTTAAAAGTCACAAAACGATTAAAACATT
Found at i:6140284 original size:50 final size:50
Alignment explanation
Indices: 6140177--6140285 Score: 166
Period size: 50 Copynumber: 2.2 Consensus size: 50
6140167 TGTATACGTT
* * *
6140177 TAACATTTTTGAGGTTTTAAAATTCACAAAACGATTAAAACATTTACGTT
1 TAACATTTTTGAGGTTTTAAAAGTCACAAAACGATTAAAACATTTACATG
6140227 TAACATTTTTGAGGTTTTAAAAGTCACAAAACGATTAAAACA-TTATCATG
1 TAACATTTTTGAGGTTTTAAAAGTCACAAAACGATTAAAACATTTA-CATG
*
6140277 TACCATTTT
1 TAACATTTT
6140286 ATTTATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 3 0.06
50 51 0.94
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (50 bp):
TAACATTTTTGAGGTTTTAAAAGTCACAAAACGATTAAAACATTTACATG
Found at i:6140490 original size:3 final size:3
Alignment explanation
Indices: 6140475--6140522 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
6140465 ATTTTGAAAA
* *
6140475 ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6140523 CAATACATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:6148492 original size:21 final size:21
Alignment explanation
Indices: 6148450--6148508 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
6148440 TAATTGATTC
* * *
6148450 TATAAATTTGAATTACGTTAT
1 TATAAATTTTATTTACGATAT
*
6148471 TATAAATTTTATTTATGATAT
1 TATAAATTTTATTTACGATAT
*
6148492 TAAAAAGTTATTATTTA
1 TATAAA-TT-TTATTTA
6148509 ATTTTTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 22 0.71
22 2 0.06
23 7 0.23
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TATAAATTTTATTTACGATAT
Found at i:6149157 original size:18 final size:16
Alignment explanation
Indices: 6149126--6149176 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
6149116 TTTATTAAAA
6149126 TTTTA-ATTCATATTAT
1 TTTTATATT-ATATTAT
*
6149142 TTTCATATATTTTATTAT
1 TTT--TATATTATATTAT
6149160 TTTTATATTATATTAT
1 TTTTATATTATATTAT
6149176 T
1 T
6149177 ATATCATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 16 0.53
18 11 0.37
19 3 0.10
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATATTATATTAT
Found at i:6149168 original size:16 final size:17
Alignment explanation
Indices: 6149135--6149186 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 17
6149125 ATTTTAATTC
6149135 ATATTATTTTCATATATT
1 ATATTATTTT-ATATATT
*
6149153 TTATTATTTT-TATATT
1 ATATTATTTTATATATT
*
6149169 ATATTATTATATCATATT
1 ATATTATTTTAT-ATATT
6149187 TAAAATAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 14 0.48
17 1 0.03
18 14 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTATTTTATATATT
Found at i:6149175 original size:19 final size:18
Alignment explanation
Indices: 6149136--6149178 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
6149126 TTTTAATTCA
*
6149136 TATTATTTTCATATATTT
1 TATTATTTTCATATATAT
*
6149154 TATTATTTTTATATTATAT
1 TATTATTTTCATA-TATAT
6149173 TATTAT
1 TATTAT
6149179 ATCATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTATTTTCATATATAT
Found at i:6149434 original size:12 final size:12
Alignment explanation
Indices: 6149417--6149458 Score: 66
Period size: 12 Copynumber: 3.3 Consensus size: 12
6149407 TCGTAAAATG
6149417 TATGTTATTAAA
1 TATGTTATTAAA
6149429 TATGTTATTAAA
1 TATGTTATTAAA
6149441 TGTATGTTATTAAA
1 --TATGTTATTAAA
6149455 TATG
1 TATG
6149459 AATGTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 16 0.57
14 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (12 bp):
TATGTTATTAAA
Found at i:6149465 original size:16 final size:15
Alignment explanation
Indices: 6149410--6149469 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 15
6149400 AATTCACTCG
*
6149410 TAAAATGTATGTTAT
1 TAAAATGAATGTTAT
6149425 T-AAAT--ATGTTAT
1 TAAAATGAATGTTAT
*
6149437 T-AAATGTATGTTAT
1 TAAAATGAATGTTAT
6149451 TAAATATGAATGTTAT
1 TAAA-ATGAATGTTAT
6149467 TAA
1 TAA
6149470 TTCACTCGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
12 12 0.30
14 12 0.30
15 3 0.08
16 13 0.32
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (15 bp):
TAAAATGAATGTTAT
Found at i:6155093 original size:23 final size:25
Alignment explanation
Indices: 6155048--6155093 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
6155038 TGTTTTTTAT
*
6155048 TATTGATTGTTATCTATTACTTCTG
1 TATTGATTGTGATCTATTACTTCTG
*
6155073 TATTG-TTGTGAT-TATTGCTTC
1 TATTGATTGTGATCTATTACTTC
6155094 AGGCGCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 6 0.32
25 5 0.26
ACGTcount: A:0.17, C:0.11, G:0.15, T:0.57
Consensus pattern (25 bp):
TATTGATTGTGATCTATTACTTCTG
Found at i:6155718 original size:19 final size:19
Alignment explanation
Indices: 6155696--6155732 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6155686 TTTTAATATA
*
6155696 AAATAATAAATTACAAAAT
1 AAATAAAAAATTACAAAAT
*
6155715 AAATAAAAAATTATAAAA
1 AAATAAAAAATTACAAAA
6155733 ATACTAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAAAATTACAAAAT
Found at i:6156026 original size:16 final size:17
Alignment explanation
Indices: 6155986--6156029 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
6155976 ATTATAGTAA
*
6155986 TTAATATGTAGTTAAGT
1 TTAATATGTAATTAAGT
6156003 TT--TATGTAATTAA-T
1 TTAATATGTAATTAAGT
6156017 TTAATATGTAATT
1 TTAATATGTAATT
6156030 TAATAAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
16 9 0.38
17 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (17 bp):
TTAATATGTAATTAAGT
Found at i:6156928 original size:30 final size:29
Alignment explanation
Indices: 6156890--6156977 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 29
6156880 TTTTTATTAA
6156890 ATCTAAATAAATCTTTGAATTTTAATTTGCT
1 ATCTAAATAAATCTTT-AATTTTAATTTG-T
* * *
6156921 TTC-AAATAAATCCTTAAACTTTAATTTGT
1 ATCTAAATAAAT-CTTTAATTTTAATTTGT
6156950 ATCTAAATAAA-CTTTAATTCTTTAATTT
1 ATCTAAATAAATCTTTAA-T-TTTAATTT
6156978 ATACTAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
28 5 0.11
29 3 0.06
30 34 0.72
31 5 0.11
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (29 bp):
ATCTAAATAAATCTTTAATTTTAATTTGT
Found at i:6157101 original size:21 final size:18
Alignment explanation
Indices: 6157078--6157115 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6157068 ATAATAAAAA
*
6157078 AAAT-AAATAAT-TATTT
1 AAATAAAATAATAAATTT
6157094 AAATAAAATAATAAATTT
1 AAATAAAATAATAAATTT
6157112 AAAT
1 AAAT
6157116 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 7 0.37
18 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATAAAATAATAAATTT
Found at i:6157104 original size:30 final size:30
Alignment explanation
Indices: 6157030--6157104 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
6157020 GATAAAAGCA
* *
6157030 TATTTAAATACAAAT--TAAAAATAAAGATT
1 TATTTAAATA-AAATAAAAAAAATAAAGAAT
** * *
6157059 TATTTGGATATAATAAAAAAAATAAATAAT
1 TATTTAAATAAAATAAAAAAAATAAAGAAT
6157089 TATTTAAATAAAATAA
1 TATTTAAATAAAATAA
6157105 TAAATTTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
28 3 0.09
29 8 0.23
30 24 0.69
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (30 bp):
TATTTAAATAAAATAAAAAAAATAAAGAAT
Found at i:6157157 original size:56 final size:56
Alignment explanation
Indices: 6157086--6157205 Score: 188
Period size: 56 Copynumber: 2.1 Consensus size: 56
6157076 AAAAATAAAT
* * * *
6157086 AATTATTTAAATAAAATAAT-AAATTTAAATTTTTTTAAAAATATTTTAACCTTTTA
1 AATTACTTAAATAAAATAATAAAAATTAAAATTTTTAAAAAATATTTTAACC-TTTA
6157142 AATTACTTAAATAAAATAATAAAAATTAAAATTTTTAAAAAATATTTTAACCTTTA
1 AATTACTTAAATAAAATAATAAAAATTAAAATTTTTAAAAAATATTTTAACCTTTA
6157198 AATTACTT
1 AATTACTT
6157206 CTAATCCATT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 31 0.53
57 28 0.47
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (56 bp):
AATTACTTAAATAAAATAATAAAAATTAAAATTTTTAAAAAATATTTTAACCTTTA
Found at i:6160052 original size:20 final size:20
Alignment explanation
Indices: 6160027--6160065 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6160017 AAAATTTTAA
*
6160027 TTTGTATTATTTTTATATTT
1 TTTGTATAATTTTTATATTT
6160047 TTTGTATAATTTTTATATT
1 TTTGTATAATTTTTATATT
6160066 GTGTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTGTATAATTTTTATATTT
Found at i:6160077 original size:20 final size:20
Alignment explanation
Indices: 6160035--6160078 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6160025 AATTTGTATT
* *
6160035 ATTTTTATATTTTTTGTATA
1 ATTTTTATATTTGTTGTAAA
6160055 ATTTTTATATTGTGTT-TAAA
1 ATTTTTATATT-TGTTGTAAA
6160075 ATTT
1 ATTT
6160079 ATAGATCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (20 bp):
ATTTTTATATTTGTTGTAAA
Found at i:6160750 original size:27 final size:25
Alignment explanation
Indices: 6160697--6160759 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
6160687 TTATATATTT
* **
6160697 TGTTATATTTTATATAAAAATTATA
1 TGTTATAATTTATATAAAAAAAATA
6160722 TGTTATAATTTATATTCAAAAAAAATA
1 TGTTATAATTTATA-T-AAAAAAAATA
**
6160749 TGAAATAATTT
1 TGTTATAATTT
6160760 TTTTTACTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 13 0.42
26 1 0.03
27 17 0.55
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (25 bp):
TGTTATAATTTATATAAAAAAAATA
Found at i:6161486 original size:18 final size:18
Alignment explanation
Indices: 6161459--6161494 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6161449 AACTTAATTT
*
6161459 TATAATATATATTTAAAA
1 TATAAAATATATTTAAAA
*
6161477 TATAAAATATTTTTAAAA
1 TATAAAATATATTTAAAA
6161495 ACGACTTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAATATATTTAAAA
Found at i:6172831 original size:29 final size:32
Alignment explanation
Indices: 6172792--6172864 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
6172782 AAAATATTTC
* *
6172792 ATATGATATTTAAATTTA-AAA-TATT-TTTA
1 ATATAATATTTAAATTTATAAATTATTAATTA
6172821 ATATAATATTT-AATTTATAAATTTATTAATTA
1 ATATAATATTTAAATTTATAAA-TTATTAATTA
6172853 ATATAATATTTA
1 ATATAATATTTA
6172865 TTTTTAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 6 0.16
29 13 0.35
31 4 0.11
32 14 0.38
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (32 bp):
ATATAATATTTAAATTTATAAATTATTAATTA
Found at i:6172937 original size:31 final size:30
Alignment explanation
Indices: 6172868--6172939 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
6172858 ATATTTATTT
*
6172868 TTAATGAAATTAATTTTAAATGATAAAATAA
1 TTAAT-AAATAAATTTTAAATGATAAAATAA
*
6172899 TTAAATAAATAAATTTATAAAT-ATCATAATAA
1 TT-AATAAATAAATTT-TAAATGAT-AAAATAA
6172931 TTAATAAAT
1 TTAATAAAT
6172940 TTATAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (30 bp):
TTAATAAATAAATTTTAAATGATAAAATAA
Found at i:6172976 original size:29 final size:28
Alignment explanation
Indices: 6172939--6173000 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
6172929 AATTAATAAA
*
6172939 TTTATAATTTAAATATTATATTAAAAATAT
1 TTTATAATTTAAATATCATATT--AAATAT
6172969 TTTA-AATTTAAATATCATATTAAATAT
1 TTTATAATTTAAATATCATATTAAATAT
6172996 TTTAT
1 TTTAT
6173001 TATAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 10 0.33
29 16 0.53
30 4 0.13
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTATAATTTAAATATCATATTAAATAT
Found at i:6185412 original size:15 final size:16
Alignment explanation
Indices: 6185392--6185421 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6185382 ATTTATTTAT
6185392 TTAAATAT-AATAAAA
1 TTAAATATGAATAAAA
6185407 TTAAATATGAATAAA
1 TTAAATATGAATAAA
6185422 TGGATAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TTAAATATGAATAAAA
Found at i:6185942 original size:9 final size:9
Alignment explanation
Indices: 6185930--6185959 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6185920 ATAAATATAA
6185930 AAATATGTT
1 AAATATGTT
*
6185939 AAATGTGTT
1 AAATATGTT
6185948 AAATATGTT
1 AAATATGTT
6185957 AAA
1 AAA
6185960 CGTATATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (9 bp):
AAATATGTT
Found at i:6186295 original size:21 final size:22
Alignment explanation
Indices: 6186240--6186301 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
6186230 TTTTAATATT
* *
6186240 TAAAATTTATTTATTAAAAATTA
1 TAAAATTTA-ATATTAAAAATAA
*
6186263 TGAAACTTTAATATTAAAAA-AA
1 T-AAAATTTAATATTAAAAATAA
6186285 TAAAATTTAATATTAAA
1 TAAAATTTAATATTAAA
6186302 TACATTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 15 0.44
22 2 0.06
23 10 0.29
24 7 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAAATTTAATATTAAAAATAA
Found at i:6187632 original size:5 final size:6
Alignment explanation
Indices: 6187600--6187669 Score: 59
Period size: 6 Copynumber: 10.7 Consensus size: 6
6187590 AAAAATCTCG
* * *
6187600 TTTTGT TTTTAT TTTTGT ATTTAT TTTTAT TTTTAAT TATTTAT TATTTACTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT T-TTTAT T-TTTA--T
6187653 TTTTAT TTTTAT ATTTT
1 TTTTAT TTTTAT -TTTT
6187670 CGGTTTTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
6 30 0.56
7 15 0.28
8 7 0.13
9 2 0.04
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:6187632 original size:17 final size:16
Alignment explanation
Indices: 6187605--6187648 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
6187595 TCTCGTTTTG
*
6187605 TTTTTATTTTTGTATTTA
1 TTTTTA-TTTT-TAATTA
6187623 TTTTTATTTTTAATTA
1 TTTTTATTTTTAATTA
6187639 TTTATTATTT
1 TTT-TTATTT
6187649 ACTTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 10 0.42
18 6 0.25
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTTAATTA
Found at i:6187657 original size:8 final size:7
Alignment explanation
Indices: 6187619--6187669 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
6187609 TATTTTTGTA
6187619 TTTA-TT
1 TTTATTT
6187625 TTTATTT
1 TTTATTT
* *
6187632 TTAATTA
1 TTTATTT
*
6187639 TTTATTA
1 TTTATTT
6187646 TTTACTTT
1 TTTA-TTT
6187654 TTTATTT
1 TTTATTT
6187661 TTATATTT
1 TT-TATTT
6187669 T
1 T
6187670 CGGTTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 4 0.11
7 22 0.58
8 12 0.32
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTATTT
Found at i:6187657 original size:15 final size:14
Alignment explanation
Indices: 6187623--6187669 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
6187613 TTTGTATTTA
6187623 TTTTTATTTTTAAT
1 TTTTTATTTTTAAT
* *
6187637 TATTTATTATTTACT
1 TTTTTATT-TTTAAT
6187652 TTTTTATTTTTATAT
1 TTTTTATTTTTA-AT
6187667 TTT
1 TTT
6187670 CGGTTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTATTTTTAAT
Found at i:6188722 original size:13 final size:13
Alignment explanation
Indices: 6188683--6188725 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
6188673 CAGATTTATG
*
6188683 ATTTAAATATTAT
1 ATTTAAATATTAA
* *
6188696 ATTAAAAATTTTAA
1 ATT-TAAATATTAA
6188710 ATTTAAATATTAA
1 ATTTAAATATTAA
6188723 ATT
1 ATT
6188726 ACATATTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTAAATATTAA
Found at i:6188733 original size:27 final size:27
Alignment explanation
Indices: 6188683--6188735 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
6188673 CAGATTTATG
*
6188683 ATTTAAATATTATATTAAAAATTTTAA
1 ATTTAAATATTAAATTAAAAATTTTAA
* *
6188710 ATTTAAATATTAAATTACATATTTTA
1 ATTTAAATATTAAATTAAAAATTTTA
6188736 TCTTAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTAAATATTAAATTAAAAATTTTAA
Found at i:6189243 original size:17 final size:17
Alignment explanation
Indices: 6189221--6189265 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
6189211 TATTATAATA
6189221 ATTAAAATAAAATTTAT
1 ATTAAAATAAAATTTAT
*
6189238 ATTAAAA-AATAATTTTT
1 ATTAAAATAA-AATTTAT
*
6189255 ATTAAATTAAA
1 ATTAAAATAAA
6189266 TAAACTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAAAATAAAATTTAT
Found at i:6190323 original size:20 final size:20
Alignment explanation
Indices: 6190300--6190341 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6190290 CCATAAATAG
6190300 ATTTATTAATCTATTCA-AAA
1 ATTTATT-ATCTATTCATAAA
*
6190320 ATTTATTTTCTATTCATAAA
1 ATTTATTATCTATTCATAAA
6190340 AT
1 AT
6190342 CTAGGTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTATTATCTATTCATAAA
Found at i:6194399 original size:20 final size:19
Alignment explanation
Indices: 6194374--6194411 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6194364 TAACAAAATC
*
6194374 TTTTAATTTATTAATTTTAA
1 TTTTAATTT-TAAATTTTAA
6194394 TTTTAATTTTAAATTTTA
1 TTTTAATTTTAAATTTTA
6194412 TTTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAATTTTAAATTTTAA
Found at i:6202556 original size:2 final size:2
Alignment explanation
Indices: 6202549--6202580 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6202539 ATTAGCATAA
*
6202549 AT AT AT AT AT AT AT AC 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
6202581 CCGAGTTAAA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6202849 original size:11 final size:11
Alignment explanation
Indices: 6202833--6202873 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
6202823 ATATTATAAT
6202833 ATAATATAAAA
1 ATAATATAAAA
6202844 ATAATATAAATAA
1 ATAATAT-AA-AA
*
6202857 AAAATATAAAA
1 ATAATATAAAA
6202868 ATAATA
1 ATAATA
6202874 AAATTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 14 0.54
12 4 0.15
13 8 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:6202860 original size:16 final size:16
Alignment explanation
Indices: 6202828--6202877 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
6202818 ATATGATATT
6202828 ATAATAT-AATATAAAA
1 ATAATATAAATA-AAAA
6202844 ATAATATAAATAAAAA
1 ATAATATAAATAAAAA
*
6202860 AT-ATAAAAATAATAAA
1 ATAATATAAATAA-AAA
6202876 AT
1 AT
6202878 TTAAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 9 0.29
16 18 0.58
17 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAATATAAATAAAAA
Found at i:6202862 original size:24 final size:24
Alignment explanation
Indices: 6202835--6202903 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
6202825 ATTATAATAT
6202835 AATATAAAAATAATATAAATAAAA
1 AATATAAAAATAATATAAATAAAA
*
6202859 AATATAAAAATAATA-AAATTTAAA
1 AATATAAAAATAATATAAA-TAAAA
* *
6202883 ATTTTAAAAAT--TATAAATAAA
1 AATATAAAAATAATATAAATAAA
6202904 TTTATAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 5 0.13
23 6 0.15
24 28 0.72
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AATATAAAAATAATATAAATAAAA
Found at i:6202884 original size:15 final size:15
Alignment explanation
Indices: 6202835--6202883 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
6202825 ATTATAATAT
*
6202835 AATATAAAAATAATATA
1 AATA-AAAAAT-ATAAA
6202852 AATAAAAAATATAAA
1 AATAAAAAATATAAA
*
6202867 AATAATAAAATTTAAA
1 AATAA-AAAATATAAA
6202883 A
1 A
6202884 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 9 0.31
16 16 0.55
17 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAAAAATATAAA
Found at i:6205563 original size:19 final size:20
Alignment explanation
Indices: 6205515--6205563 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
6205505 GAAATTTTAT
6205515 AATAATT-TTTTAACTAAAA
1 AATAATTATTTTAACTAAAA
*
6205534 AATAATATATTTTTA-TAAAA
1 AATAAT-TATTTTAACTAAAA
6205554 AATAATTATT
1 AATAATTATT
6205564 AAAAATCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 10 0.37
20 12 0.44
21 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATTATTTTAACTAAAA
Found at i:6207275 original size:24 final size:27
Alignment explanation
Indices: 6207234--6207290 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 27
6207224 CCCTTCATTT
*
6207234 TTTTTTTTAGATATCTTAAAATTA-TA
1 TTTTTTTTAGACATCTTAAAATTATTA
6207260 TTTTTTTTA-ACA-CTTAAAATTATTA
1 TTTTTTTTAGACATCTTAAAATTATTA
6207285 TTTTTT
1 TTTTTT
6207291 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 10 0.34
25 10 0.34
26 9 0.31
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTTTTTAGACATCTTAAAATTATTA
Found at i:6207299 original size:23 final size:21
Alignment explanation
Indices: 6207235--6207317 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 21
6207225 CCTTCATTTT
6207235 TTTTTTTAGATATCTTAAAATTATA
1 TTTTTTTA-AT-T-TTAAAATTA-A
** *
6207260 TTTTTTTTAACACTTAAAATTAT
1 -TTTTTTTAA-TTTTAAAATTAA
6207283 TATTTTTTATATTTTAAAATTAA
1 T-TTTTTTA-ATTTTAAAATTAA
6207306 TTTTTTTAATTT
1 TTTTTTTAATTT
6207318 CCGTAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.08
22 8 0.17
23 17 0.35
24 10 0.21
25 1 0.02
26 8 0.17
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (21 bp):
TTTTTTTAATTTTAAAATTAA
Found at i:6207312 original size:24 final size:24
Alignment explanation
Indices: 6207233--6207312 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
6207223 TCCCTTCATT
6207233 TTTTTTTTTAGATATCTTAAAATTATA
1 TTTTTTTTT--ATATCTTAAAATTA-A
* *
6207260 TTTTTTTTAACA-CTTAAAATT-A
1 TTTTTTTTTATATCTTAAAATTAA
* *
6207282 TTATTTTTTATATTTTAAAATTAA
1 TTTTTTTTTATATCTTAAAATTAA
6207306 TTTTTTT
1 TTTTTTT
6207313 AATTTCCGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
22 10 0.23
23 8 0.18
24 16 0.36
25 2 0.05
27 8 0.18
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (24 bp):
TTTTTTTTTATATCTTAAAATTAA
Found at i:6215264 original size:21 final size:21
Alignment explanation
Indices: 6215240--6215281 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6215230 TTATTATTGC
* *
6215240 AATACTTAATTTTACTATTAT
1 AATAATTAATTTCACTATTAT
*
6215261 AATAATTAATTTCATTATTAT
1 AATAATTAATTTCACTATTAT
6215282 CACTATTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
AATAATTAATTTCACTATTAT
Found at i:6217949 original size:52 final size:52
Alignment explanation
Indices: 6217840--6217995 Score: 163
Period size: 52 Copynumber: 3.0 Consensus size: 52
6217830 TATAACCAAA
* * * ** **
6217840 CAAACTTGCCCATTAAGAATCCCTCTCTTTTTAGAATTCTTCTCCTATAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTATTGCAAGT
* *
6217892 TAAACTTGCCTATTACGAATCCCTTTCCTTTTAGAATTCTTCTATTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTATTGCAAGT
* * * *
6217944 CAAACTTACCTATTAAGAATCTTCTTT-CTCTT-GAAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-CCTTTCCTTTTAG-AATTCTTCTATTGCAAGT
6217996 ATTCTTGTCC
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
51 1 0.01
52 82 0.94
53 4 0.05
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTATTGCAAGT
Found at i:6218039 original size:11 final size:11
Alignment explanation
Indices: 6218021--6218059 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6218011 GCAATATCTG
6218021 ACAAATCTCAA
1 ACAAATCTCAA
* *
6218032 ATAAATCTCTA
1 ACAAATCTCAA
*
6218043 ACAAATCCCAA
1 ACAAATCTCAA
6218054 ACAAAT
1 ACAAAT
6218060 ATCTTAAGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:6218333 original size:25 final size:24
Alignment explanation
Indices: 6218302--6218400 Score: 81
Period size: 25 Copynumber: 4.0 Consensus size: 24
6218292 TTAAACCAAG
6218302 CTCTTCCCATATCTCGAACTGTCAA
1 CTCTTCCCATATCTCGAACT-TCAA
* * **
6218327 CTCTTCCCATGTCTCGAACCATCGG
1 CTCTTCCCATATCTCGAA-CTTCAA
* *
6218352 CTCTTCCCACATCTTGAATCTTCAA
1 CTCTTCCCATATCTCGAA-CTTCAA
* * *
6218377 CTCTTCTCATGTTTCGAACCTTCA
1 CTCTTCCCATATCTCGAA-CTTCA
6218401 GCTTTGATAC
Statistics
Matches: 56, Mismatches: 17, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
25 55 0.98
26 1 0.02
ACGTcount: A:0.20, C:0.36, G:0.09, T:0.34
Consensus pattern (24 bp):
CTCTTCCCATATCTCGAACTTCAA
Found at i:6218360 original size:50 final size:50
Alignment explanation
Indices: 6218301--6218396 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
6218291 CTTAAACCAA
*
6218301 GCTCTTCCCATATCTCGAA-CTGTCAACTCTTCCCATGTCTCGAACCATCG
1 GCTCTTCCCACATCTCGAATCT-TCAACTCTTCCCATGTCTCGAACCATCG
* * *
6218351 GCTCTTCCCACATCTTGAATCTTCAACTCTTCTCATGTTTCGAACC
1 GCTCTTCCCACATCTCGAATCTTCAACTCTTCCCATGTCTCGAACC
6218397 TTCAGCTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 39 0.95
51 2 0.05
ACGTcount: A:0.20, C:0.36, G:0.10, T:0.33
Consensus pattern (50 bp):
GCTCTTCCCACATCTCGAATCTTCAACTCTTCCCATGTCTCGAACCATCG
Found at i:6219824 original size:35 final size:37
Alignment explanation
Indices: 6219740--6219834 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 37
6219730 ATCAAAACAT
6219740 AATTATATAAATTTAAA-ATAAAATTTACATATAATAA
1 AATTATATAAATTTAAATATAAAATTTA-ATATAATAA
*
6219777 AA-T-T-TAAATTTAAATA-AAAATCTT-TTA-AATAA
1 AATTATATAAATTTAAATATAAAAT-TTAATATAATAA
6219809 AATTATATAAATTTAAATATAAAATT
1 AATTATATAAATTTAAATATAAAATT
6219835 AAATCTCACA
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
32 7 0.14
33 3 0.06
34 16 0.31
35 17 0.33
36 6 0.12
37 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (37 bp):
AATTATATAAATTTAAATATAAAATTTAATATAATAA
Found at i:6233002 original size:6 final size:6
Alignment explanation
Indices: 6232991--6233022 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6232981 CTTCAAAAGT
6232991 TTTTTG TTTTTG TTTTTG -TTTTG -TTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
6233023 ATTATTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:6234731 original size:17 final size:17
Alignment explanation
Indices: 6234709--6234744 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6234699 GGTAAATGTA
*
6234709 ATTATCAAAGTAATTTT
1 ATTATCAAAATAATTTT
*
6234726 ATTATCAAAATGATTTT
1 ATTATCAAAATAATTTT
6234743 AT
1 AT
6234745 CAATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTATCAAAATAATTTT
Found at i:6235143 original size:15 final size:16
Alignment explanation
Indices: 6235123--6235156 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
6235113 TTAGTTTAAA
6235123 AATATAAAA-AATTAT
1 AATATAAAATAATTAT
6235138 AATATAAAATAATTAT
1 AATATAAAATAATTAT
6235154 AAT
1 AAT
6235157 TTTATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:6235177 original size:18 final size:19
Alignment explanation
Indices: 6235140--6235177 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6235130 AAAATTATAA
* *
6235140 TATAAAATAATTATAATTT
1 TATAAAATAAATAAAATTT
6235159 TATAAAA-AAATAAAATTT
1 TATAAAATAAATAAAATTT
6235177 T
1 T
6235178 CATTCACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATAAAATAAATAAAATTT
Found at i:6235426 original size:21 final size:19
Alignment explanation
Indices: 6235394--6235432 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
6235384 TATAAAAATA
*
6235394 TACAAAATTAAATTAATTT
1 TACAAAATTAAATAAATTT
6235413 TACACAAATATAAATAAATT
1 TACA-AAAT-TAAATAAATT
6235433 ACTTCTCGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
TACAAAATTAAATAAATTT
Found at i:6235450 original size:2 final size:2
Alignment explanation
Indices: 6235443--6235480 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6235433 ACTTCTCGTG
*
6235443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6235481 ATTTTTCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6240206 original size:12 final size:13
Alignment explanation
Indices: 6240189--6240217 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6240179 AATTCAGTTT
6240189 TTTTTCTTTTT-C
1 TTTTTCTTTTTAC
6240201 TTTTTCTTTTTAC
1 TTTTTCTTTTTAC
6240214 TTTT
1 TTTT
6240218 GGATAACGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTTAC
Found at i:6247500 original size:18 final size:18
Alignment explanation
Indices: 6247479--6247523 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
6247469 TGTTATTCAT
6247479 AAAGGTCATGATTATATA
1 AAAGGTCATGATTATATA
6247497 AAAGGTCATGATTATATA
1 AAAGGTCATGATTATATA
6247515 AAAGGTCAT
1 AAAGGTCAT
6247524 AACCATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (18 bp):
AAAGGTCATGATTATATA
Found at i:6250543 original size:20 final size:20
Alignment explanation
Indices: 6250518--6250555 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6250508 TCAATTGGGG
6250518 AAAA-TTTGAGAGAAATCTGA
1 AAAATTTTGA-AGAAATCTGA
6250538 AAAATTTTGAAGAAATCT
1 AAAATTTTGAAGAAATCT
6250556 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (20 bp):
AAAATTTTGAAGAAATCTGA
Found at i:6251135 original size:18 final size:18
Alignment explanation
Indices: 6251112--6251153 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6251102 AAATGATTCT
6251112 ATAAAAAAATCTTTTCAA
1 ATAAAAAAATCTTTTCAA
* * *
6251130 ATAAAAAATTTTTTTCAT
1 ATAAAAAAATCTTTTCAA
6251148 ATAAAA
1 ATAAAA
6251154 TTTTCAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAAAATCTTTTCAA
Found at i:6252321 original size:3 final size:3
Alignment explanation
Indices: 6252313--6252351 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
6252303 TGAAATCAAT
6252313 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6252352 GAGATATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6252548 original size:3 final size:3
Alignment explanation
Indices: 6252540--6252568 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6252530 TGATTCCTTC
6252540 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6252569 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6252573 original size:3 final size:3
Alignment explanation
Indices: 6252567--6252606 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6252557 ATAATAATAA
6252567 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6252607 TTAACATTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6254450 original size:32 final size:31
Alignment explanation
Indices: 6254388--6254451 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
6254378 TAATTTCAAA
* *
6254388 TTTAAAAAAAAAAAAGTTAAAGAATCAATTT
1 TTTAAAAAAAAAAAAATTAAAGAATAAATTT
*
6254419 TTTAAAAAATAAAAAAATTCAAATAA-AAATTT
1 TTTAAAAAA-AAAAAAATT-AAAGAATAAATTT
6254451 T
1 T
6254452 GAAGAAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 9 0.32
32 14 0.50
33 5 0.18
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (31 bp):
TTTAAAAAAAAAAAAATTAAAGAATAAATTT
Found at i:6254576 original size:17 final size:17
Alignment explanation
Indices: 6254534--6254565 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6254524 TCAAAGTATC
6254534 AATTTTTTTTAGAAAAT
1 AATTTTTTTTAGAAAAT
6254551 AATTTTTTTTA-AAAA
1 AATTTTTTTTAGAAAA
6254566 AATGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTTTTTTAGAAAAT
Found at i:6254656 original size:59 final size:58
Alignment explanation
Indices: 6254585--6254707 Score: 176
Period size: 59 Copynumber: 2.1 Consensus size: 58
6254575 TTCAAGAAAC
* * * *
6254585 TTTTTTAAGAAAAGTTGAA-AGTATCAATTTTTCTTGAAGATAAAATTTTCAAAAGATA
1 TTTTTTAAGAAAAGTT-AAGAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAATA
*
6254643 TTTTTTGAGGAAAAGTTAAGAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAATA
1 TTTTTT-AAGAAAAGTTAAGAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAATA
6254702 TTTTTT
1 TTTTTT
6254708 TTTGGAGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
58 8 0.14
59 50 0.86
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (58 bp):
TTTTTTAAGAAAAGTTAAGAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAATA
Found at i:6262072 original size:2 final size:2
Alignment explanation
Indices: 6262065--6262116 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
6262055 CCCCTCTATT
* * * *
6262065 TA TA TA TA TA TA TA TA TG TA TA TA TG TG TG 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
*
6262107 TG TA TA TA TA
1 TA TA TA TA TA
6262117 ATGGTATACT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6262123 original size:12 final size:13
Alignment explanation
Indices: 6262071--6262124 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
6262061 TATTTATATA
6262071 TATATATATAT-G
1 TATATATATATGG
* *
6262083 TATATATGTGT-G
1 TATATATATATGG
*
6262095 TATATATATATATG
1 TATATATATAT-GG
6262109 TATATATA-ATGG
1 TATATATATATGG
6262121 TATA
1 TATA
6262125 CTTACGAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 24 0.69
13 2 0.06
14 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (13 bp):
TATATATATATGG
Found at i:6262123 original size:26 final size:26
Alignment explanation
Indices: 6262069--6262124 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
6262059 TCTATTTATA
*
6262069 TATATATATATATGTATATATGTGTG
1 TATATATATATATGTATATATATGTG
6262095 TATATATATATATGTATATATAATG-G
1 TATATATATATATGTATATAT-ATGTG
6262121 TATA
1 TATA
6262125 CTTACGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (26 bp):
TATATATATATATGTATATATATGTG
Found at i:6269674 original size:13 final size:14
Alignment explanation
Indices: 6269646--6269680 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
6269636 TTAAAAAAAT
6269646 ATTTTTCCATTTAAA
1 ATTTTT-CATTTAAA
6269661 ATTTTTCA-TTAAA
1 ATTTTTCATTTAAA
6269674 ATTTTTC
1 ATTTTTC
6269681 TTCATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
14 2 0.10
15 6 0.30
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTTCATTTAAA
Found at i:6271996 original size:21 final size:21
Alignment explanation
Indices: 6271955--6271996 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6271945 GAGGGGAGTA
*
6271955 TATAATCTAAAATAATTTAAT
1 TATAATCTAAAATAATGTAAT
* *
6271976 TATAATTTAAAATTATGTAAT
1 TATAATCTAAAATAATGTAAT
6271997 GTCTATCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAATCTAAAATAATGTAAT
Found at i:6272965 original size:2 final size:2
Alignment explanation
Indices: 6272958--6272996 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
6272948 AAATAAATAA
* *
6272958 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6272997 AAACACTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6276648 original size:19 final size:21
Alignment explanation
Indices: 6276610--6276648 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6276600 ATGGAAAAAA
*
6276610 GCAATTGATGAGGAAATGAAG
1 GCAATTGATGAAGAAATGAAG
6276631 GCAATTGA-GAAG-AATGAA
1 GCAATTGATGAAGAAATGAA
6276649 ACTTGGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (21 bp):
GCAATTGATGAAGAAATGAAG
Found at i:6283367 original size:2 final size:2
Alignment explanation
Indices: 6283360--6283385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6283350 CAAGATCAAA
6283360 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
6283386 TTGAGTAAAT
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:6284214 original size:17 final size:16
Alignment explanation
Indices: 6284194--6284232 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
6284184 TATAGTTTAT
*
6284194 AAAAAAATAAATAAAGA
1 AAAAAAAAAAAT-AAGA
6284211 AAAAGAAAAAAATAAGA
1 AAAA-AAAAAAATAAGA
6284228 AAAAA
1 AAAAA
6284233 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 12 0.60
18 7 0.35
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (16 bp):
AAAAAAAAAAATAAGA
Done.