Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_pilon, 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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 27
Found at i:3443759 original size:24 final size:25
Alignment explanation
Indices: 3443712--3443773 Score: 108
Period size: 24 Copynumber: 2.5 Consensus size: 25
3443702 ATCACTATAT
3443712 AATCAAATTGATGTTTTTTTTAAAGA
1 AATCAAATTGATG-TTTTTTTAAAGA
3443738 AATCAAATTGATG-TTTTTTAAAGA
1 AATCAAATTGATGTTTTTTTAAAGA
3443762 AATCAAATTGAT
1 AATCAAATTGAT
3443774 ATTAAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 23 0.64
26 13 0.36
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (25 bp):
AATCAAATTGATGTTTTTTTAAAGA
Found at i:3447249 original size:3 final size:3
Alignment explanation
Indices: 3447241--3447275 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3447231 CTTTCATAGC
3447241 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3447276 TCAATTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3447419 original size:96 final size:96
Alignment explanation
Indices: 3447255--3447447 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
3447245 TATTATTATT
3447255 ATTATTATTATTATTATTATTTCAATTTTATTTTTCAATCATAGCTTTCCAGAGAATTCAATCTA
1 ATTATTATTATTATTATTATTTCAATTTTATTTTTCAATCATAGCTTTCCAGAGAATTCAATCTA
3447320 AAGGAGTTTTCTCTGCATGAAAAAAGCTAAC
66 AAGGAGTTTTCTCTGCATGAAAAAAGCTAAC
*
3447351 ATTATTATTATTATTATTATTTCCATTTTATTTTTCAATCATAGCTTTCCAGAGAATTCAATCTA
1 ATTATTATTATTATTATTATTTCAATTTTATTTTTCAATCATAGCTTTCCAGAGAATTCAATCTA
3447416 AAGGAGTTTTCTCTGCATGAAAAAAGCTAAC
66 AAGGAGTTTTCTCTGCATGAAAAAAGCTAAC
3447447 A
1 A
3447448 ATTTAACATC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (96 bp):
ATTATTATTATTATTATTATTTCAATTTTATTTTTCAATCATAGCTTTCCAGAGAATTCAATCTA
AAGGAGTTTTCTCTGCATGAAAAAAGCTAAC
Found at i:3447625 original size:4 final size:4
Alignment explanation
Indices: 3447616--3449106 Score: 2697
Period size: 4 Copynumber: 373.8 Consensus size: 4
3447606 GGTTCTTATT
3447616 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3447664 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3447712 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3447760 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3447808 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
3447856 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
3447904 ATGC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3447952 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448000 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
3448048 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
3448096 ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
3448144 ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
3448192 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
3448240 ATAC ATGC ATGC ATAC ATTC ATGC ATGTAT GTAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC A--TAC ATAC ATAC ATAC ATAC ATAC
3448290 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448338 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448386 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
3448434 ATGC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC ATGC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448482 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448530 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
3448578 ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
3448626 ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
3448674 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448722 ATAC ATAC ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448768 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448816 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448864 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448912 ATAC ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3448958 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3449004 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
3449052 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATCC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3449100 ATAC ATA
1 ATAC ATA
3449107 TATGTATGGG
Statistics
Matches: 1446, Mismatches: 33, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
2 6 0.00
4 1439 1.00
6 1 0.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:3450860 original size:51 final size:50
Alignment explanation
Indices: 3450784--3450897 Score: 156
Period size: 51 Copynumber: 2.3 Consensus size: 50
3450774 TTAGCAGTAA
* * **
3450784 AGCGCGCCCACTGCACCGCGCTATACAATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCACTATACAATGAGCTGGCGCCACGT-GGGTAT
**
3450835 AGCGCGCCCCCTGCACCGCACTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCACTATACAATGAGCTGGCGCCACGTGGGTAT
*
3450885 AGCGCGGCCCCTG
1 AGCGCGCCCCCTG
3450898 TAGCGCGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
50 18 0.32
51 38 0.68
ACGTcount: A:0.17, C:0.35, G:0.32, T:0.17
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCACTATACAATGAGCTGGCGCCACGTGGGTAT
Found at i:3451036 original size:10 final size:10
Alignment explanation
Indices: 3451021--3451055 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3451011 TTTATCACAC
3451021 CAAATTCTCT
1 CAAATTCTCT
3451031 CAAATTCTCT
1 CAAATTCTCT
3451041 -AAATTTCTCT
1 CAAA-TTCTCT
3451051 CAAAT
1 CAAAT
3451056 ATTCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:3451060 original size:12 final size:12
Alignment explanation
Indices: 3451024--3451062 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 12
3451014 ATCACACCAA
3451024 ATTCTCTC-AA-
1 ATTCTCTCAAAT
3451034 ATTCTCT-AAAT
1 ATTCTCTCAAAT
3451045 -TTCTCTCAAAT
1 ATTCTCTCAAAT
3451056 ATTCTCT
1 ATTCTCT
3451063 TTTTAAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 15 0.60
11 4 0.16
12 6 0.24
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTCTCTCAAAT
Found at i:3451316 original size:110 final size:111
Alignment explanation
Indices: 3451185--3451405 Score: 354
Period size: 110 Copynumber: 2.0 Consensus size: 111
3451175 TGGAAATAAT
* *
3451185 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
* * * *
3451250 TATTTAGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
3451295 ATATCTCGACACTTTGTTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
3451360 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
3451406 TTTTTGTAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 68 0.67
111 33 0.33
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.47
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:3457208 original size:50 final size:51
Alignment explanation
Indices: 3457128--3457248 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 51
3457118 CCCTACGTGG
* * **
3457128 CGTATAGCGCGCTGCAGGGGCCGCGTTATA-CCCACGTGGCACCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGCCGCGCTATACCCCACGTGGCACCAAATCAC
** *
3457178 CGTATAGCGCGGTGCAGAGGG-CGCGCTATACCCCACGTGGTGCCAAATCAT
1 CGTATAGCGCGGTGCAG-GGGCCGCGCTATACCCCACGTGGCACCAAATCAC
*
3457229 CGTATTGCGCGGTGCAGGGG
1 CGTATAGCGCGGTGCAGGGG
3457249 GTGCGGTGCA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 27 0.44
51 34 0.56
ACGTcount: A:0.18, C:0.31, G:0.34, T:0.17
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGCCGCGCTATACCCCACGTGGCACCAAATCAC
Found at i:3457256 original size:14 final size:14
Alignment explanation
Indices: 3457237--3457263 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3457227 ATCGTATTGC
3457237 GCGGTGCAGGGGGT
1 GCGGTGCAGGGGGT
3457251 GCGGTGCAGGGGG
1 GCGGTGCAGGGGG
3457264 CGCGCTTTAC
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:0.07, C:0.15, G:0.67, T:0.11
Consensus pattern (14 bp):
GCGGTGCAGGGGGT
Found at i:3464425 original size:22 final size:22
Alignment explanation
Indices: 3464400--3464446 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3464390 AAGCGTGAAG
* * * *
3464400 AAGAAGAACAGAAGGAGAGGAA
1 AAGAAAAAAAGAACGAGAGAAA
3464422 AAGAAAAAAAGAACGAGAGAAA
1 AAGAAAAAAAGAACGAGAGAAA
3464444 AAG
1 AAG
3464447 CTCAGGAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.66, C:0.04, G:0.30, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAGAACGAGAGAAA
Found at i:3468159 original size:3 final size:3
Alignment explanation
Indices: 3468151--3468210 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
3468141 ACTTATTTAT
* *
3468151 TTA TTA TTA TTA TTA TAA TTA TTA TAA TTA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
3468196 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
3468211 AAAAATAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3469616 original size:17 final size:17
Alignment explanation
Indices: 3469591--3469625 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3469581 TAAATATATA
3469591 TATAATAAATATTAATT
1 TATAATAAATATTAATT
* *
3469608 TATATTAAATCTTAATT
1 TATAATAAATATTAATT
3469625 T
1 T
3469626 GATTTTACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATAAATATTAATT
Found at i:3469954 original size:19 final size:22
Alignment explanation
Indices: 3469930--3469977 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 22
3469920 TGAATTCTTA
*
3469930 AATTTTTAA-TAATATAG-A-C
1 AATTTTTAATTAATAAAGTACC
3469949 AATTTTTAATTAATAAAGTACC
1 AATTTTTAATTAATAAAGTACC
3469971 AATTTTT
1 AATTTTT
3469978 GGCGTTGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 7 0.28
21 1 0.04
22 8 0.32
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (22 bp):
AATTTTTAATTAATAAAGTACC
Found at i:3470388 original size:17 final size:17
Alignment explanation
Indices: 3470366--3470402 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3470356 CTTTTCAAAT
3470366 TTTTTATA-TACTTTATA
1 TTTTTATATTA-TTTATA
3470383 TTTTTATATTATTTATA
1 TTTTTATATTATTTATA
3470400 TTT
1 TTT
3470403 CATTTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTATATTATTTATA
Found at i:3481086 original size:21 final size:20
Alignment explanation
Indices: 3481060--3481137 Score: 97
Period size: 19 Copynumber: 3.9 Consensus size: 20
3481050 CTTGAAGAAA
3481060 AAAAAAAGAAGAACAAAAAAG
1 AAAAAAAGAAGAA-AAAAAAG
*
3481081 AAAAAAAATGAGGAAAAAAAAG
1 -AAAAAAA-GAAGAAAAAAAAG
3481103 AAAAAAA-AAGAAAAAAAA-
1 AAAAAAAGAAGAAAAAAAAG
*
3481121 AAGAAAAGAAGAAAAAA
1 AAAAAAAGAAGAAAAAA
3481138 GAGGGGGTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.12
19 19 0.37
21 7 0.14
22 14 0.27
23 5 0.10
ACGTcount: A:0.83, C:0.01, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAAAGAAGAAAAAAAAG
Found at i:3481087 original size:10 final size:10
Alignment explanation
Indices: 3481060--3481137 Score: 86
Period size: 10 Copynumber: 7.6 Consensus size: 10
3481050 CTTGAAGAAA
3481060 AAAAAAAGAAG
1 AAAAAAA-AAG
*
3481071 AACAAAAAAG
1 AAAAAAAAAG
3481081 AAAAAAAATGAG
1 AAAAAAAA--AG
*
3481093 GAAAAAAAAG
1 AAAAAAAAAG
3481103 AAAAAAAAAG
1 AAAAAAAAAG
3481113 AAAAAAAAA-
1 AAAAAAAAAG
* *
3481122 AGAAAAGAAG
1 AAAAAAAAAG
3481132 AAAAAA
1 AAAAAA
3481138 GAGGGGGTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
9 7 0.12
10 35 0.61
11 6 0.11
12 9 0.16
ACGTcount: A:0.83, C:0.01, G:0.14, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3481087 original size:22 final size:21
Alignment explanation
Indices: 3481059--3481127 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 21
3481049 GCTTGAAGAA
3481059 AAAAAAAAGAAGAACAAAAAAG
1 AAAAAAAAGAAGAA-AAAAAAG
*
3481081 AAAAAAAATGAGGAAAAAAAAG
1 AAAAAAAA-GAAGAAAAAAAAG
3481103 AAAAAAAAAGAA-AAAAAAAAG
1 -AAAAAAAAGAAGAAAAAAAAG
3481124 AAAA
1 AAAA
3481128 GAAGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.09
21 9 0.21
22 17 0.40
23 13 0.30
ACGTcount: A:0.84, C:0.01, G:0.13, T:0.01
Consensus pattern (21 bp):
AAAAAAAAGAAGAAAAAAAAG
Found at i:3481135 original size:16 final size:15
Alignment explanation
Indices: 3481054--3481139 Score: 66
Period size: 15 Copynumber: 5.3 Consensus size: 15
3481044 ATTATGCTTG
3481054 AAGAAAAAAAAAAGAA
1 AAGAAAAAAAAAA-AA
*
3481070 GAACAAAAAAGAAAAAA
1 -AAGAAAAAA-AAAAAA
3481087 AATGAGGAAAAAAAAGAAA
1 AA-GA--AAAAAAAA-AAA
3481106 AA-AAAAGAAAAAAAA
1 AAGAAAA-AAAAAAAA
* *
3481121 AAGAAAAGAAGAAAA
1 AAGAAAAAAAAAAAA
3481136 AAGA
1 AAGA
3481140 GGGGGTCAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
15 18 0.31
16 11 0.19
17 12 0.21
18 7 0.12
19 10 0.17
ACGTcount: A:0.83, C:0.01, G:0.15, T:0.01
Consensus pattern (15 bp):
AAGAAAAAAAAAAAA
Found at i:3482033 original size:114 final size:114
Alignment explanation
Indices: 3481833--3482172 Score: 509
Period size: 114 Copynumber: 3.0 Consensus size: 114
3481823 AAGTGCTACG
*
3481833 TTCTCATAGTAGAAATAAGAAGACCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
3481898 TGATTCGGTATAAACCCCAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTCGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATT
* *
3481947 TTCTCATAGTAGAAATACGAAGACCCAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
3482012 TGATTCGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATAAATT
66 TGATTCGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATT
* * * * * * *
3482061 TGCTCATAGTAGACATAAGAAGACCCAATAGAATCTTCTAGAAGTTTTCTTTGAGTCATCTGATA
1 TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * *
3482126 TGGTTCGGTAGGAACCACAGAACCAATCATTGGAATTAAAAGATGAA
66 TGATTCGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAA
3482173 CTGCATGATC
Statistics
Matches: 204, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 204 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (114 bp):
TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATT
Found at i:3483422 original size:113 final size:113
Alignment explanation
Indices: 3482865--3483420 Score: 941
Period size: 113 Copynumber: 4.9 Consensus size: 113
3482855 GATTAAAATC
** * *
3482865 CATCATTCAATGGATCAACATTTTCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1 CATCATTCAATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
3482930 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * *
3482978 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAATAACTCATTTGAAGAAGGA
1 CATCATTCAATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
3483043 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
*
3483091 CATCATTCAATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAATGA
1 CATCATTCAATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
3483156 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* *
3483204 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
* * *
3483269 AGAAGAAATTCATAATGAAAAGAATTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * *
3483317 CATCATTCAATTGATCAGCATTACCTGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
3483382 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
3483421 GCATGATTCT
Statistics
Matches: 424, Mismatches: 18, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
113 419 0.99
114 5 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
CATCATTCAATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
Found at i:3483697 original size:3 final size:3
Alignment explanation
Indices: 3483689--3483740 Score: 68
Period size: 3 Copynumber: 16.0 Consensus size: 3
3483679 ACTTATTTAT
3483689 TTA TTA TTA TTA TTA TTA TTA TTA TATA TATA TATA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA T-TA TTA TTA TTA
3483738 TTA
1 TTA
3483741 AAAAATAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 33 0.69
4 15 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3487693 original size:16 final size:17
Alignment explanation
Indices: 3487672--3487712 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
3487662 TTTTGTAGGA
3487672 TAAAATTTAAA-AAAAT
1 TAAAATTTAAAGAAAAT
*
3487688 TAAAATTAAAAGAAAAT
1 TAAAATTTAAAGAAAAT
3487705 T-AAATTTA
1 TAAAATTTA
3487713 TTTATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAAATTTAAAGAAAAT
Found at i:3488843 original size:19 final size:16
Alignment explanation
Indices: 3488808--3488872 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
3488798 GACGCCATCT
3488808 AAAATATTTAAAAATA
1 AAAATATTTAAAAATA
3488824 AAAATATTATAAACAAATAA
1 AAAATATT-T-AA-AAAT-A
* **
3488844 AAAATAATTAAATTTA
1 AAAATATTTAAAAATA
3488860 AAAA-ATTTAAAAA
1 AAAATATTTAAAAA
3488873 AAGTTAAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 6 0.15
16 13 0.33
17 3 0.08
18 4 0.10
19 5 0.13
20 8 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATTTAAAAATA
Found at i:3493559 original size:70 final size:70
Alignment explanation
Indices: 3493445--3493587 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
3493435 TTAACTACAA
*
3493445 CAAATTATAAAAGTATGACCAACAAGACTTGCCTCCAAATCCAAGTGGATTTTCCATAAACCATT
1 CAAATTATAAAAGTATGACCAACAAGACTTGCCTCCAAACCCAAGTGGATTTTCCATAAACCATT
3493510 ATTTG
66 ATTTG
3493515 CAAATTATAAAAGTATGACCAACAAGACTTGCCTCCAAACCCAAGTGGATTTTCCATAAACCATT
1 CAAATTATAAAAGTATGACCAACAAGACTTGCCTCCAAACCCAAGTGGATTTTCCATAAACCATT
3493580 ATTTG
66 ATTTG
3493585 CAA
1 CAA
3493588 TATCACAAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.27
Consensus pattern (70 bp):
CAAATTATAAAAGTATGACCAACAAGACTTGCCTCCAAACCCAAGTGGATTTTCCATAAACCATT
ATTTG
Found at i:3497687 original size:30 final size:29
Alignment explanation
Indices: 3497653--3497737 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
3497643 AAATTAAGAA
*
3497653 ACTTAATTGTTACAATCTATAAATT-GAGTG
1 ACTTAATTGTTACAAT-GATAAATTGGA-TG
* * *
3497683 ACTTAGTTATTATAAATGATAAATTGGATG
1 ACTTAATTGTTA-CAATGATAAATTGGATG
*
3497713 ACTTAACTGTTACATATGATAAATT
1 ACTTAATTGTTACA-ATGATAAATT
3497738 AACTTGATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 1 0.02
30 38 0.86
31 5 0.11
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (29 bp):
ACTTAATTGTTACAATGATAAATTGGATG
Found at i:3498154 original size:16 final size:15
Alignment explanation
Indices: 3498133--3498171 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
3498123 GAAAAAGTGT
3498133 AATATATAATTTTGAA
1 AATATAT-ATTTTGAA
3498149 AATATAT-TTTTGAA
1 AATATATATTTTGAA
*
3498163 AACATATAT
1 AATATATAT
3498172 AATATATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.62
15 1 0.05
16 7 0.33
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (15 bp):
AATATATATTTTGAA
Found at i:3498202 original size:78 final size:75
Alignment explanation
Indices: 3498118--3498265 Score: 215
Period size: 78 Copynumber: 1.9 Consensus size: 75
3498108 TTGAAAATAA
* * * *
3498118 TTTTGGAAAAAGTGTAATATATAATTTTGAAAATATATTTTTGAAAACATATATAATATATAGTT
1 TTTTGGAAAAACTATAATATATAATTTTGAAAACACATTTTTGAAAAC--ATATAATATATAG-T
3498183 TTTTAAAAATTGG
63 TTTTAAAAATTGG
* *
3498196 TTTTGGAAAACCTATAATATATAGTTTTGAAAACACATTTTTGAAAACATATAATATATAGTTTT
1 TTTTGGAAAAACTATAATATATAATTTTGAAAACACATTTTTGAAAACATATAATATATAGTTTT
3498261 TAAAA
66 TAAAA
3498266 TATTTCTGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 9 0.14
76 13 0.20
78 42 0.66
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (75 bp):
TTTTGGAAAAACTATAATATATAATTTTGAAAACACATTTTTGAAAACATATAATATATAGTTTT
TAAAAATTGG
Found at i:3498212 original size:39 final size:37
Alignment explanation
Indices: 3498132--3498305 Score: 149
Period size: 37 Copynumber: 4.6 Consensus size: 37
3498122 GGAAAAAGTG
* * * *
3498132 TAATATATAATTTTGAAAATATATTTTTGAAAACATATA
1 TAATATATAGTTTTTAAAACACATTTTTGAAAAC--ATA
* *
3498171 TAATATATAGTTTTTTAAAA-A-TTGGTTTTGGAAAACCTA
1 TAATATATAG-TTTTTAAAACACAT--TTTT-GAAAACATA
*
3498210 TAATATATAGTTTTGAAAACACATTTTTGAAAACATA
1 TAATATATAGTTTTTAAAACACATTTTTGAAAACATA
* *
3498247 TAATATATAGTTTTT-AAA-ATATTTCTGAAAACATA
1 TAATATATAGTTTTTAAAACACATTTTTGAAAACATA
*
3498282 TATATAATATAATTTTTGAAAACA
1 TA-AT-ATATAGTTTTT-AAAACA
3498306 TATAATATAT
Statistics
Matches: 113, Mismatches: 11, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
35 17 0.15
36 5 0.04
37 32 0.28
38 13 0.12
39 26 0.23
40 14 0.12
41 6 0.05
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (37 bp):
TAATATATAGTTTTTAAAACACATTTTTGAAAACATA
Found at i:3498302 original size:61 final size:61
Alignment explanation
Indices: 3498232--3498365 Score: 232
Period size: 61 Copynumber: 2.2 Consensus size: 61
3498222 TTGAAAACAC
*
3498232 ATTTTTGAAAACATATAATATATAGTTTTTAAAATATTTCTGAAAACATATATATAATATA
1 ATTTTTGAAAACATATAATATATAGTTTTTAAAATATTTCTGAAAACATATATATAATACA
* *
3498293 ATTTTTGAAAACATATAATATATAGTTTTTAAAATATTTTTGAAAACGTATATATAATACA
1 ATTTTTGAAAACATATAATATATAGTTTTTAAAATATTTCTGAAAACATATATATAATACA
*
3498354 GTTTTTGAAAAC
1 ATTTTTGAAAAC
3498366 GTATTTTTGA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (61 bp):
ATTTTTGAAAACATATAATATATAGTTTTTAAAATATTTCTGAAAACATATATATAATACA
Found at i:3498315 original size:24 final size:26
Alignment explanation
Indices: 3498267--3498326 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
3498257 TTTTTAAAAT
*
3498267 ATTTCTGAAAACATATATATAATATA
1 ATTTTTGAAAACATATATATAATATA
3498293 ATTTTTGAAAACATATA-AT-ATATA
1 ATTTTTGAAAACATATATATAATATA
*
3498317 GTTTTT-AAAA
1 ATTTTTGAAAA
3498327 TATTTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 4 0.12
24 10 0.31
25 2 0.06
26 16 0.50
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (26 bp):
ATTTTTGAAAACATATATATAATATA
Found at i:3498392 original size:13 final size:14
Alignment explanation
Indices: 3498355--3498391 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
3498345 TATAATACAG
3498355 TTTTTGAAAACGTA
1 TTTTTGAAAACGTA
3498369 TTTTTGAAAACGTA
1 TTTTTGAAAACGTA
3498383 TTTTTGAAA
1 TTTTTGAAA
3498392 CATATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (14 bp):
TTTTTGAAAACGTA
Found at i:3498482 original size:13 final size:13
Alignment explanation
Indices: 3498461--3498525 Score: 57
Period size: 12 Copynumber: 5.2 Consensus size: 13
3498451 ATAAATATAG
*
3498461 TATACATATTATT
1 TATATATATTATT
3498474 TATATATATTATT
1 TATATATATTATT
3498487 TAT-TATATT-TAT
1 TATATATATTAT-T
*
3498499 TATAT-TGTTATT
1 TATATATATTATT
* *
3498511 AATAT-TATTTTT
1 TATATATATTATT
3498523 TAT
1 TAT
3498526 TTTTTTAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
11 1 0.02
12 25 0.58
13 17 0.40
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (13 bp):
TATATATATTATT
Found at i:3498515 original size:21 final size:22
Alignment explanation
Indices: 3498470--3498516 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
3498460 GTATACATAT
*
3498470 TATTTATATATATTATTTATTA
1 TATTTATATATATTAGTTATTA
3498492 TATTTAT-TATATT-GTTATTAA
1 TATTTATATATATTAGTTATT-A
3498513 TATT
1 TATT
3498517 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTATATATATTAGTTATTA
Found at i:3499782 original size:18 final size:19
Alignment explanation
Indices: 3499761--3499804 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3499751 TAAATTTTTA
*
3499761 TTTATTTCTTTA-TTTCTT
1 TTTATTTATTTATTTTCTT
3499779 TTTATTTATTTATTTTCTT
1 TTTATTTATTTATTTTCTT
*
3499798 TTAATTT
1 TTTATTT
3499805 TAACATGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTATTTATTTATTTTCTT
Found at i:3499898 original size:34 final size:32
Alignment explanation
Indices: 3499843--3499949 Score: 90
Period size: 36 Copynumber: 3.2 Consensus size: 32
3499833 TTAAACATTT
* *
3499843 TTTTTATCTTTT-TTTTATTTTCTCTTTTAAC
1 TTTTTATATTTTATTTTTTTTTCTCTTTTAAC
*
3499874 TTTTTATATATATTATTTTTTTTTCCTTCTTTTAAA
1 TTTTTATAT-T-TTATTTTTTTTT-C-TCTTTTAAC
* * *
3499910 ATTTGATATTTTCTTCATTTTTTTCTCTTTTAAC
1 TTTTTATATTTTATT--TTTTTTTCTCTTTTAAC
3499944 ATTTTT
1 -TTTTT
3499950 TTAACTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
31 8 0.14
32 1 0.02
33 2 0.03
34 20 0.34
35 6 0.10
36 22 0.37
ACGTcount: A:0.18, C:0.11, G:0.01, T:0.70
Consensus pattern (32 bp):
TTTTTATATTTTATTTTTTTTTCTCTTTTAAC
Found at i:3501166 original size:20 final size:20
Alignment explanation
Indices: 3501108--3501181 Score: 60
Period size: 22 Copynumber: 3.5 Consensus size: 20
3501098 ATTCAATATT
*
3501108 TTTTTATCTTTATTTTATAAG
1 TTTTTATC-TTATATTATAAG
* *
3501129 TTTTTTTTCTTA-AGTATAAG
1 -TTTTTATCTTATATTATAAG
*
3501149 TTTTTATCTTATCTTATACAG
1 TTTTTATCTTATATTATA-AG
*
3501170 ATTTTAGTCTTA
1 TTTTTA-TCTTA
3501182 CTTTTATTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 10 0.24
20 10 0.24
21 10 0.24
22 12 0.29
ACGTcount: A:0.24, C:0.08, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTTATCTTATATTATAAG
Found at i:3503602 original size:26 final size:26
Alignment explanation
Indices: 3503568--3503619 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3503558 CATTAAGAAT
* *
3503568 TTTATAATTATGT-TCGTGTTTATTTA
1 TTTAAAATTATGTGTC-TGTTCATTTA
3503594 TTTAAAATTATGTGTCTGTTCATTTA
1 TTTAAAATTATGTGTCTGTTCATTTA
3503620 ATCTTTGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTAAAATTATGTGTCTGTTCATTTA
Found at i:3503654 original size:23 final size:23
Alignment explanation
Indices: 3503610--3503654 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3503600 ATTATGTGTC
* * *
3503610 TGTTCATTTAATCTTTGGGAACT
1 TGTTCATTTAATATCTAGGAACT
*
3503633 TGTTCATTTAATATCTATGAAC
1 TGTTCATTTAATATCTAGGAAC
3503655 ATATTTGTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (23 bp):
TGTTCATTTAATATCTAGGAACT
Found at i:3505214 original size:21 final size:21
Alignment explanation
Indices: 3505190--3505290 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
3505180 TTATTAATAA
3505190 TATTTTGTGACATGGTAATTT
1 TATTTTGTGACATGGTAATTT
**
3505211 TATTATT-T--CAT--TAATAA
1 TATT-TTGTGACATGGTAATTT
3505228 TATTTTGTGACATGGTAATTT
1 TATTTTGTGACATGGTAATTT
**
3505249 TATTATT-T--CAT--TAATAA
1 TATT-TTGTGACATGGTAATTT
3505266 TATTTTGTGACATGGTAATTT
1 TATTTTGTGACATGGTAATTT
3505287 TATT
1 TATT
3505291 ATTTCATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 24
0.65 0.09 0.26
Matches are distributed among these distances:
16 4 0.07
17 18 0.30
19 12 0.20
21 22 0.37
22 4 0.07
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (21 bp):
TATTTTGTGACATGGTAATTT
Found at i:3505218 original size:38 final size:38
Alignment explanation
Indices: 3505175--3505340 Score: 289
Period size: 38 Copynumber: 4.4 Consensus size: 38
3505165 TCACTCTAAT
*
3505175 TTATTTTATTAATAATATTTTGTGACATGGTAATTTTA
1 TTATTTCATTAATAATATTTTGTGACATGGTAATTTTA
3505213 TTATTTCATTAATAATATTTTGTGACATGGTAATTTTA
1 TTATTTCATTAATAATATTTTGTGACATGGTAATTTTA
3505251 TTATTTCATTAATAATATTTTGTGACATGGTAATTTTA
1 TTATTTCATTAATAATATTTTGTGACATGGTAATTTTA
*
3505289 TTATTTCATTAATAATATTTTGTGACATGAT-ATTTTAA
1 TTATTTCATTAATAATATTTTGTGACATGGTAATTTT-A
*
3505327 TTATTTTATTAATA
1 TTATTTCATTAATA
3505341 TATAATTAAA
Statistics
Matches: 124, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
37 5 0.04
38 119 0.96
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (38 bp):
TTATTTCATTAATAATATTTTGTGACATGGTAATTTTA
Found at i:3511475 original size:13 final size:15
Alignment explanation
Indices: 3511457--3511488 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3511447 ACGTGTGACA
3511457 ATTTAAAAA-A-TTT
1 ATTTAAAAATATTTT
3511470 ATTTAAAAATATTTT
1 ATTTAAAAATATTTT
3511485 ATTT
1 ATTT
3511489 TCGAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 1 0.06
15 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAAAATATTTT
Found at i:3511851 original size:20 final size:20
Alignment explanation
Indices: 3511826--3511866 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3511816 AGTGTAGTGC
3511826 TGGTTCGTGGGTAATCCAAT
1 TGGTTCGTGGGTAATCCAAT
3511846 TGGTTCGTGGGTAATCCAAT
1 TGGTTCGTGGGTAATCCAAT
3511866 T
1 T
3511867 ATTTGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.37
Consensus pattern (20 bp):
TGGTTCGTGGGTAATCCAAT
Found at i:3513619 original size:18 final size:18
Alignment explanation
Indices: 3513576--3513628 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3513566 TACAGATCCG
* *
3513576 CCTACAACCAC-GAATCCG
1 CCTACAACCACAG-ACCCC
*
3513594 CCTGCAACCACAGACCCC
1 CCTACAACCACAGACCCC
*
3513612 CCTACAACTACAGACCC
1 CCTACAACCACAGACCC
3513629 ACCAGCAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.32, C:0.49, G:0.09, T:0.09
Consensus pattern (18 bp):
CCTACAACCACAGACCCC
Found at i:3520752 original size:21 final size:20
Alignment explanation
Indices: 3520726--3520823 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
3520716 ATCAGTTTCC
3520726 AAAATCGCAACGCGATTCTTA
1 AAAATCGCAACGCGATT-TTA
* **
3520747 AAAATCGCAATGCGATAGTA
1 AAAATCGCAACGCGATTTTA
* ** *
3520767 CAAATTCGCATTGCGATTTTCC
1 -AAAATCGCAACGCGATTTT-A
* * *
3520789 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTA
3520809 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
3520824 ACACATAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTA
Found at i:3520852 original size:20 final size:20
Alignment explanation
Indices: 3520790--3520984 Score: 216
Period size: 20 Copynumber: 9.8 Consensus size: 20
3520780 CGATTTTCCA
* ** *
3520790 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3520810 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3520830 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3520850 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3520870 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3520890 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3520910 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3520930 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
3520950 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
3520970 AAATCGCAACG-GTAT
1 AAATCGCAACGCGTAT
3520985 ATAACACTGA
Statistics
Matches: 149, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
19 5 0.03
20 142 0.95
21 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3521680 original size:24 final size:24
Alignment explanation
Indices: 3521641--3521687 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3521631 AAATTTGGTC
3521641 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3521665 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3521688 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3522034 original size:19 final size:19
Alignment explanation
Indices: 3521992--3522150 Score: 175
Period size: 19 Copynumber: 8.6 Consensus size: 19
3521982 TAGTTTACTT
* *
3521992 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
3522012 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
3522031 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
3522050 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3522069 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3522088 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3522102 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3522121 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3522140 TCGCAATGCGA
1 TCGCAACGCGA
3522151 TTTTGGTTTC
Statistics
Matches: 120, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
14 8 0.07
16 5 0.04
17 5 0.04
19 90 0.75
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3522126 original size:52 final size:55
Alignment explanation
Indices: 3521992--3522145 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 55
3521982 TAGTTTACTT
* * *
3521992 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGATAATCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGAAAATCGCAAC-AG-AACCAAAA
*
3522050 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAAC-G-A-CAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
* **
3522102 TCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAA
3522146 TGCGATTTTG
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
52 45 0.51
53 1 0.01
55 1 0.01
57 29 0.33
58 13 0.15
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (55 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
Found at i:3522168 original size:19 final size:18
Alignment explanation
Indices: 3522146--3522274 Score: 94
Period size: 19 Copynumber: 7.3 Consensus size: 18
3522136 AAAATCGCAA
3522146 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3522165 TGCGA--TTCTTT--CGT
1 TGCGATTTTGTTTCGCGT
*
3522179 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3522198 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
3522212 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3522231 TGCGCTTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3522250 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
3522270 TGCGA
1 TGCGA
3522275 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.22
16 6 0.07
17 6 0.07
19 43 0.49
20 13 0.15
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:3522181 original size:14 final size:14
Alignment explanation
Indices: 3522162--3522218 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3522152 TTTGGTTTCG
3522162 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3522176 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3522193 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
3522209 CGTTGCGATT
1 CGTTGCGATT
3522219 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3522194 original size:33 final size:33
Alignment explanation
Indices: 3522146--3522234 Score: 151
Period size: 33 Copynumber: 2.7 Consensus size: 33
3522136 AAAATCGCAA
** *
3522146 TGCGATTTTGGTTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
3522179 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
3522212 TGCGATTTTCATTTCGCGTTGCG
1 TGCGATTTTCATTTCGCGTTGCG
3522235 CTTTTGGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.08, C:0.20, G:0.26, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:3522438 original size:93 final size:93
Alignment explanation
Indices: 3522322--3522882 Score: 1099
Period size: 93 Copynumber: 6.1 Consensus size: 93
3522312 ATGGATTGCA
3522322 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3522386 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3522414 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3522479 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3522507 TTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3522571 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3522599 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3522664 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3522692 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3522757 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3522785 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
3522850 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3522878 TTACT
1 TTACT
3522883 AAGCAATCTA
Statistics
Matches: 466, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 96 0.21
93 370 0.79
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3522639 original size:185 final size:186
Alignment explanation
Indices: 3522322--3522882 Score: 1099
Period size: 185 Copynumber: 3.0 Consensus size: 186
3522312 ATGGATTGCA
3522322 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3522386 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
3522451 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
3522507 TTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3522571 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
3522636 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
3522692 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3522757 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
3522822 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
3522878 TTACT
1 TTACT
3522883 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 189 0.51
186 184 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3524627 original size:21 final size:21
Alignment explanation
Indices: 3524571--3524635 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
3524561 TCTTTTGGTT
*
3524571 GAAATGAAAATCGCAACGAGA
1 GAAATTAAAATCGCAACGAGA
***
3524592 G-AA-TAGCTGTCGCAACGAGA
1 GAAATTA-AAATCGCAACGAGA
3524612 GAAATTAAAATCGCAACGAGA
1 GAAATTAAAATCGCAACGAGA
3524633 GAA
1 GAA
3524636 TCGCAACGCG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.03
20 14 0.41
21 17 0.50
22 2 0.06
ACGTcount: A:0.48, C:0.15, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAATTAAAATCGCAACGAGA
Found at i:3524639 original size:14 final size:14
Alignment explanation
Indices: 3524620--3524676 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3524610 GAGAAATTAA
3524620 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3524634 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3524653 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3524667 AATCGCAACG
1 AATCGCAACG
3524677 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3524655 original size:33 final size:33
Alignment explanation
Indices: 3524571--3524692 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
3524561 TCTTTTGGTT
*
3524571 GAAATGAAAATCGCAACGAGAGAATAGCTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A-A----TCGCAAC--GC
*
3524612 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3524645 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3524678 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
3524693 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
32 9 0.12
33 39 0.50
35 7 0.09
39 1 0.01
40 1 0.01
41 21 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3524658 original size:19 final size:19
Alignment explanation
Indices: 3524634--3524697 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 19
3524624 GCAACGAGAG
3524634 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3524653 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3524667 AATCGCAACGCGAAATG-A
1 AATCGCAACGCGAAATGAA
*
3524685 AATCGCAATGCGA
1 AATCGCAACGCGA
3524698 TTTTGGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
14 10 0.27
15 1 0.03
16 2 0.05
17 2 0.05
18 13 0.35
19 9 0.24
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3524747 original size:19 final size:19
Alignment explanation
Indices: 3524723--3524759 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3524713 GCGATTCTCT
3524723 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
3524742 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
3524760 TCTCGTTGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3524782 original size:20 final size:20
Alignment explanation
Indices: 3524716--3524811 Score: 113
Period size: 21 Copynumber: 4.8 Consensus size: 20
3524706 TCGCGTTGCG
3524716 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3524736 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
3524755 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
*
3524776 ATTCTCTCGTTGCGATTTTT
1 ATTCTCTCGTTGCGATTTTC
*
3524796 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
3524812 CTCTTCTGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.25
20 21 0.33
21 26 0.41
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3524805 original size:41 final size:40
Alignment explanation
Indices: 3524720--3524812 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
3524710 GTTGCGATTC
*** *
3524720 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTC
1 TCTCGTTGCGACAGTCATTTCGCGTTGCGATTTTCATTTA
* *
3524760 TCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTTATTTA
1 TCTCGTTGCGACAGTCATT-TCGCGTTGCGATTTTCATTTA
3524801 TCTCGTTGCGAC
1 TCTCGTTGCGAC
3524813 TCTTCTGCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 16 0.35
41 30 0.65
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (40 bp):
TCTCGTTGCGACAGTCATTTCGCGTTGCGATTTTCATTTA
Found at i:3524933 original size:33 final size:33
Alignment explanation
Indices: 3524891--3524961 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3524881 AATACTAACT
*
3524891 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3524924 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3524957 TGAAA
1 TGAAA
3524962 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3525195 original size:22 final size:22
Alignment explanation
Indices: 3525143--3525197 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3525133 TGGTTGTGAG
**
3525143 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
* **
3525165 GAAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3525187 GGATTTCTTCG
1 GGATTTCTTCG
3525198 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3525531 original size:60 final size:60
Alignment explanation
Indices: 3525344--3525537 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3525334 CTTTAAATAT
* **
3525344 CGCGTTGCGATTTATGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* *** *
3525405 CGCGTTGCGATATACGGATACGCGTTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3525465 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3525525 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3525538 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 85 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3525538 original size:20 final size:20
Alignment explanation
Indices: 3525344--3525537 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3525334 CTTTAAATAT
*
3525344 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
* *
3525364 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3525386 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3525405 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
**
3525425 CGCGTTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3525445 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3525465 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3525485 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3525505 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3525525 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3525538 TGGAAAATCG
Statistics
Matches: 150, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 130 0.87
21 16 0.11
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3525554 original size:21 final size:21
Alignment explanation
Indices: 3525524--3525606 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
3525514 ATTTTCATAT
*
3525524 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3525545 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3525566 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
**
3525587 TCGTGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3525607 CTGATTTGCG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3526837 original size:27 final size:27
Alignment explanation
Indices: 3526786--3526848 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3526776 ATGTTTTTAC
*
3526786 CCTCTATAATTTTATATATTTAAGTTCA
1 CCTCTA-AATTTTATATATTCAAGTTCA
*
3526814 CCTCTAAATTTTATA-AGTTCAAGTTTA
1 CCTCTAAATTTTATATA-TTCAAGTTCA
3526841 CCTTCTAA
1 CC-TCTAA
3526849 CATAAAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.03
27 19 0.61
28 11 0.35
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (27 bp):
CCTCTAAATTTTATATATTCAAGTTCA
Found at i:3526934 original size:27 final size:28
Alignment explanation
Indices: 3526886--3526940 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
3526876 ATCGTTAATA
3526886 TGATAATGTAAAATTATTTTATTATTAAG
1 TGATAATGT-AAATTATTTTATTATTAAG
*
3526915 TGATAATGT-AATTATTTTATTCTTAA
1 TGATAATGTAAATTATTTTATTATTAA
3526941 TAATGTAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 16 0.64
29 9 0.36
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (28 bp):
TGATAATGTAAATTATTTTATTATTAAG
Found at i:3533840 original size:2 final size:2
Alignment explanation
Indices: 3533833--3533880 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3533823 ACGTCTTCTA
3533833 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
3533875 AT AT AT
1 AT AT AT
3533881 TTCCGAAGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3538391 original size:138 final size:138
Alignment explanation
Indices: 3538143--3538418 Score: 525
Period size: 138 Copynumber: 2.0 Consensus size: 138
3538133 GTGCAACCCG
* *
3538143 GGTCGGTCCAGATTAGTCAGGGCAAAACCTTGAAACTAGAAGACAACCAAAAGAGAGAAAAAAGA
1 GGTCGGTCCAGATTAATCAGGACAAAACCTTGAAACTAGAAGACAACCAAAAGAGAGAAAAAAGA
3538208 AGAAGAAAAAAACCAATCACTTAAGTTCACAGGGACCATACAAAGAAAATATTGAAAACTCTAAC
66 AGAAGAAAAAAACCAATCACTTAAGTTCACAGGGACCATACAAAGAAAATATTGAAAACTCTAAC
3538273 CAAATAAA
131 CAAATAAA
3538281 GGTCGGTCCAGATTAATCAGGACAAAACCTTGAAACTAGAAGACAACCAAAAGAGAGAAAAAAGA
1 GGTCGGTCCAGATTAATCAGGACAAAACCTTGAAACTAGAAGACAACCAAAAGAGAGAAAAAAGA
*
3538346 ATAAGAAAAAAACCAATCACTTAAGTTCACAGGGACCATACAAAGAAAATATTGAAAACTCTAAC
66 AGAAGAAAAAAACCAATCACTTAAGTTCACAGGGACCATACAAAGAAAATATTGAAAACTCTAAC
3538411 CAAATAAA
131 CAAATAAA
3538419 TCACGTATCA
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.15
Consensus pattern (138 bp):
GGTCGGTCCAGATTAATCAGGACAAAACCTTGAAACTAGAAGACAACCAAAAGAGAGAAAAAAGA
AGAAGAAAAAAACCAATCACTTAAGTTCACAGGGACCATACAAAGAAAATATTGAAAACTCTAAC
CAAATAAA
Found at i:3538711 original size:20 final size:20
Alignment explanation
Indices: 3538672--3538712 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3538662 TTATTAAAAT
*
3538672 TAAAAAAAATAAAGATATAA
1 TAAAAAAAATAAAGAAATAA
3538692 TAAAATAAAATAAA-AAATAA
1 TAAAA-AAAATAAAGAAATAA
3538712 T
1 T
3538713 CAGATGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAAAAAAATAAAGAAATAA
Found at i:3540002 original size:30 final size:30
Alignment explanation
Indices: 3539793--3539985 Score: 377
Period size: 30 Copynumber: 6.4 Consensus size: 30
3539783 TCCGAAGGAC
3539793 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3539823 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3539853 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3539883 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3539913 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3539943 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3539973 CTATCCATAGGTC
1 CTATCCAGAGGTC
3539986 CCGAAGAACC
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 162 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3540002 original size:90 final size:90
Alignment explanation
Indices: 3539793--3540010 Score: 364
Period size: 90 Copynumber: 2.4 Consensus size: 90
3539783 TCCGAAGGAC
*
3539793 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
3539858 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
*
3539883 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
3539948 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * * * *
3539973 CTATCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
3540011 TATGTTCCTT
Statistics
Matches: 121, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
90 112 0.93
91 9 0.07
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (90 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCATAAAGATCCTCGGTAA
Found at i:3540025 original size:31 final size:31
Alignment explanation
Indices: 3539971--3540063 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
3539961 GATCCTCGGT
* *
3539971 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
3540002 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
3540033 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
3540064 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:3540247 original size:4 final size:4
Alignment explanation
Indices: 3540238--3540262 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3540228 ATATAACTAT
3540238 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
3540263 GTAATCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:3542262 original size:2 final size:2
Alignment explanation
Indices: 3542255--3542316 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3542245 AATCATTTTC
3542255 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
3542297 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3542317 GGGGGGTAAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3544921 original size:32 final size:32
Alignment explanation
Indices: 3544872--3544969 Score: 135
Period size: 32 Copynumber: 3.1 Consensus size: 32
3544862 GTATGAGTCG
*
3544872 CAACAGAGTC-ATCATTGCATTCATATAATGCA
1 CAACAGAATCAAT-ATTGCATTCATATAATGCA
*
3544904 CAACAGAATCAATATTGCATTCAGATAATGCA
1 CAACAGAATCAATATTGCATTCATATAATGCA
** *
3544936 CAGTAGAATCAATATTGCATTGATATAATGCA
1 CAACAGAATCAATATTGCATTCATATAATGCA
3544968 CA
1 CA
3544970 TTAGAGCCAG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 57 0.97
33 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (32 bp):
CAACAGAATCAATATTGCATTCATATAATGCA
Found at i:3548453 original size:2 final size:2
Alignment explanation
Indices: 3548446--3548474 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3548436 CCTATCTAGT
3548446 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
3548475 GATTAATATA
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:3548612 original size:2 final size:2
Alignment explanation
Indices: 3548605--3548641 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3548595 TTTATTTACC
3548605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3548642 GCTTAATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3555562 original size:43 final size:43
Alignment explanation
Indices: 3555506--3555611 Score: 185
Period size: 43 Copynumber: 2.5 Consensus size: 43
3555496 TTTCATACTC
3555506 CAACATTCACCCTACTCAATTACTCTTGAAGAATTGCATTCAT
1 CAACATTCACCCTACTCAATTACTCTTGAAGAATTGCATTCAT
* *
3555549 CAACATTCACCCTACTCAGTTACTCTTGAAGAATTGCATTCGT
1 CAACATTCACCCTACTCAATTACTCTTGAAGAATTGCATTCAT
*
3555592 CAACATTCACCCTGCTCAAT
1 CAACATTCACCCTACTCAAT
3555612 GATTTTGCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (43 bp):
CAACATTCACCCTACTCAATTACTCTTGAAGAATTGCATTCAT
Found at i:3565039 original size:21 final size:21
Alignment explanation
Indices: 3564999--3565037 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3564989 TTCGATTAGG
*
3564999 ATTTAAGGGTTTAGGATTTGA
1 ATTTAAAGGTTTAGGATTTGA
3565020 ATTTAAAGGTTT-GGATTT
1 ATTTAAAGGTTTAGGATTT
3565038 TGGGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
ATTTAAAGGTTTAGGATTTGA
Found at i:3572814 original size:33 final size:33
Alignment explanation
Indices: 3572768--3572865 Score: 117
Period size: 33 Copynumber: 2.9 Consensus size: 33
3572758 CGGGTGAGAT
3572768 TTCGATTGTTGTCTTTGTGTTGTTTCATGGACA
1 TTCGATTGTTGTCTTTGTGTTGTTTCATGGACA
* * * *
3572801 TTCGATTGCTGTCTTTGTATTGCTTCACTGG-CT
1 TTCGATTGTTGTCTTTGTGTTGTTTCA-TGGACA
* *
3572834 TTCGATTGTTGCCTTTGGGTTGTTTCAATGGA
1 TTCGATTGTTGTCTTTGTGTTGTTTC-ATGGA
3572866 TCTCGATCGT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
33 49 0.92
34 4 0.08
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.49
Consensus pattern (33 bp):
TTCGATTGTTGTCTTTGTGTTGTTTCATGGACA
Found at i:3572872 original size:33 final size:33
Alignment explanation
Indices: 3572769--3572878 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 33
3572759 GGGTGAGATT
3572769 TCGATTGTTGTCTTTGTGTTGTTTC-ATGGA-C
1 TCGATTGTTGTCTTTGTGTTGTTTCAATGGATC
* * * * * *
3572800 ATTCGATTGCTGTCTTTGTATTGCTTCACTGGCTT
1 --TCGATTGTTGTCTTTGTGTTGTTTCAATGGATC
* *
3572835 TCGATTGTTGCCTTTGGGTTGTTTCAATGGATC
1 TCGATTGTTGTCTTTGTGTTGTTTCAATGGATC
*
3572868 TCGATCGTTGT
1 TCGATTGTTGT
3572879 TCCATCTTCA
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
33 56 0.95
34 3 0.05
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (33 bp):
TCGATTGTTGTCTTTGTGTTGTTTCAATGGATC
Found at i:3576988 original size:22 final size:22
Alignment explanation
Indices: 3576963--3577008 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3576953 AATATACTTG
* *
3576963 TCTTAATTCTCAAGTGGATTAA
1 TCTTAAATCCCAAGTGGATTAA
3576985 TCTTAAATCCCAAGTGGATTAA
1 TCTTAAATCCCAAGTGGATTAA
3577007 TC
1 TC
3577009 GTTCTGCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (22 bp):
TCTTAAATCCCAAGTGGATTAA
Found at i:3578210 original size:30 final size:29
Alignment explanation
Indices: 3578176--3578238 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
3578166 TGGAAAATGG
*
3578176 ATTACCTGAAAATTATTTTAC-ATAAAATAA
1 ATTACCT-AAAACTATTTTACGATAAAA-AA
*
3578206 ATTACCTAAAACTGTTTTACGTATAAAAAA
1 ATTACCTAAAACTATTTTACG-ATAAAAAA
3578236 ATT
1 ATT
3578239 CATTTTCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (29 bp):
ATTACCTAAAACTATTTTACGATAAAAAA
Found at i:3578543 original size:19 final size:19
Alignment explanation
Indices: 3578521--3578563 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3578511 TTTATAAACA
*
3578521 TAATACTAAAT-TATTATAT
1 TAATACTAAATATA-TAAAT
*
3578540 TAATATTAAATATATAAAT
1 TAATACTAAATATATAAAT
3578559 TAATA
1 TAATA
3578564 TTATTCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATACTAAATATATAAAT
Found at i:3578759 original size:15 final size:15
Alignment explanation
Indices: 3578701--3578790 Score: 62
Period size: 15 Copynumber: 5.9 Consensus size: 15
3578691 AAGTACATGT
3578701 TAATATAATATTATTAA
1 TAAT-TAATATT-TTAA
*
3578718 -AATT-ATATTATATA
1 TAATTAATATTTTA-A
3578732 TATATTAAATATTTTAA
1 TA-ATT-AATATTTTAA
*
3578749 TAATTAATATTTTCA
1 TAATTAATATTTTAA
* *
3578764 T-ATTAAAATATT-A
1 TAATTAATATTTTAA
3578777 TATATTAATATTTT
1 TA-ATTAATATTTT
3578791 TTTGGATGTC
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
13 4 0.07
14 15 0.25
15 21 0.36
16 9 0.15
17 3 0.05
18 7 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTAATATTTTAA
Found at i:3578787 original size:29 final size:30
Alignment explanation
Indices: 3578733--3578790 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
3578723 TATTATATAT
*
3578733 ATATTAAATATTTTAATAATTAATATTTTC
1 ATATTAAATATTATAATAATTAATATTTTC
3578763 ATATTAAAATATTAT-AT-ATTAATATTTT
1 ATATT-AAATATTATAATAATTAATATTTT
3578791 TTTGGATGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 7 0.27
31 8 0.31
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATTAAATATTATAATAATTAATATTTTC
Found at i:3584652 original size:21 final size:20
Alignment explanation
Indices: 3584623--3584661 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3584613 CTTTATTCTT
3584623 AAAGCTTAAACATCTCAAAG
1 AAAGCTTAAACATCTCAAAG
*
3584643 AAAGCCTTAATCATCTCAA
1 AAAG-CTTAAACATCTCAA
3584662 TAAAGACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (20 bp):
AAAGCTTAAACATCTCAAAG
Found at i:3584666 original size:20 final size:20
Alignment explanation
Indices: 3584622--3584666 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3584612 TCTTTATTCT
3584622 TAAAGCTTAAACATCTCAAA
1 TAAAGCTTAAACATCTCAAA
* *
3584642 GAAAGCCTTAATCATCTC-AA
1 TAAAG-CTTAAACATCTCAAA
3584662 TAAAG
1 TAAAG
3584667 ACTATTTCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (20 bp):
TAAAGCTTAAACATCTCAAA
Found at i:3584842 original size:21 final size:20
Alignment explanation
Indices: 3584813--3584851 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3584803 CTTTATTCTT
3584813 AAAGCTTAAACATCTCAAAG
1 AAAGCTTAAACATCTCAAAG
*
3584833 AAAGCCTTAATCATCTCAA
1 AAAG-CTTAAACATCTCAA
3584852 TAAAGACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (20 bp):
AAAGCTTAAACATCTCAAAG
Found at i:3584856 original size:20 final size:20
Alignment explanation
Indices: 3584812--3584856 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3584802 TCTTTATTCT
3584812 TAAAGCTTAAACATCTCAAA
1 TAAAGCTTAAACATCTCAAA
* *
3584832 GAAAGCCTTAATCATCTC-AA
1 TAAAG-CTTAAACATCTCAAA
3584852 TAAAG
1 TAAAG
3584857 ACTATTTCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (20 bp):
TAAAGCTTAAACATCTCAAA
Found at i:3584896 original size:190 final size:190
Alignment explanation
Indices: 3584573--3584952 Score: 760
Period size: 190 Copynumber: 2.0 Consensus size: 190
3584563 CATTGTTAGT
3584573 CAATCATGGAATATGGCAGTGCAAGGCAACCCAATGAAGTCTTTATTCTTAAAGCTTAAACATCT
1 CAATCATGGAATATGGCAGTGCAAGGCAACCCAATGAAGTCTTTATTCTTAAAGCTTAAACATCT
3584638 CAAAGAAAGCCTTAATCATCTCAATAAAGACTATTTCAGTGACATCTCGGCTTGAACTAGACTAA
66 CAAAGAAAGCCTTAATCATCTCAATAAAGACTATTTCAGTGACATCTCGGCTTGAACTAGACTAA
3584703 AAAGAGAAGAACTTGATAGGTAGCAAATTCTTACCTTAAGAGGTGATGATTCCTTGGAGA
131 AAAGAGAAGAACTTGATAGGTAGCAAATTCTTACCTTAAGAGGTGATGATTCCTTGGAGA
3584763 CAATCATGGAATATGGCAGTGCAAGGCAACCCAATGAAGTCTTTATTCTTAAAGCTTAAACATCT
1 CAATCATGGAATATGGCAGTGCAAGGCAACCCAATGAAGTCTTTATTCTTAAAGCTTAAACATCT
3584828 CAAAGAAAGCCTTAATCATCTCAATAAAGACTATTTCAGTGACATCTCGGCTTGAACTAGACTAA
66 CAAAGAAAGCCTTAATCATCTCAATAAAGACTATTTCAGTGACATCTCGGCTTGAACTAGACTAA
3584893 AAAGAGAAGAACTTGATAGGTAGCAAATTCTTACCTTAAGAGGTGATGATTCCTTGGAGA
131 AAAGAGAAGAACTTGATAGGTAGCAAATTCTTACCTTAAGAGGTGATGATTCCTTGGAGA
3584953 AAGAACTCGA
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 190 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (190 bp):
CAATCATGGAATATGGCAGTGCAAGGCAACCCAATGAAGTCTTTATTCTTAAAGCTTAAACATCT
CAAAGAAAGCCTTAATCATCTCAATAAAGACTATTTCAGTGACATCTCGGCTTGAACTAGACTAA
AAAGAGAAGAACTTGATAGGTAGCAAATTCTTACCTTAAGAGGTGATGATTCCTTGGAGA
Found at i:3597286 original size:20 final size:20
Alignment explanation
Indices: 3597244--3597286 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3597234 CGGCCTATCA
*
3597244 TTTATTTTTTCAAAGATTAT
1 TTTATTTTTTCAAAGAATAT
3597264 TTTACTTTTTTCAAAGAAT-T
1 TTTA-TTTTTTCAAAGAATAT
3597284 TTT
1 TTT
3597287 TTTAAAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTATTTTTTCAAAGAATAT
Found at i:3601957 original size:50 final size:47
Alignment explanation
Indices: 3601898--3602016 Score: 127
Period size: 50 Copynumber: 2.5 Consensus size: 47
3601888 CTCTACGTAT
*
3601898 AATAAAAAAATCAAAAAAAAAAAAACCTTC-AATATTCAAATCAGAAAAAA
1 AATAAAAAAATCAAAAAAAAAAAAA-CTTCTAACATTCAAAT---AAAAAA
* * *
3601948 AATAAAAAAAT-AAGAAGAAAAAAATTTCTTAACATTCAAATAAAAAA
1 AATAAAAAAATCAAAAAAAAAAAAACTTC-TAACATTCAAATAAAAAA
*
3601995 AAT-CAAAAATCAAAAAAAAAAA
1 AATAAAAAAATCAAAAAAAAAAA
3602017 TAATTATAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
46 6 0.10
47 18 0.31
48 3 0.05
49 11 0.19
50 21 0.36
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (47 bp):
AATAAAAAAATCAAAAAAAAAAAAACTTCTAACATTCAAATAAAAAA
Found at i:3609558 original size:42 final size:42
Alignment explanation
Indices: 3609511--3609596 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
3609501 TCTGCATGTG
3609511 CCATGCACGTCCCCAACACCCCAACACAGGTCGCCATGCACT
1 CCATGCACGTCCCCAACACCCCAACACAGGTCGCCATGCACT
* *
3609553 CCATGCACGTCCCCAACACCCCAACATAGGTTGCCATGCACT
1 CCATGCACGTCCCCAACACCCCAACACAGGTCGCCATGCACT
3609595 CC
1 CC
3609597 CAGCGACCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.47, G:0.14, T:0.14
Consensus pattern (42 bp):
CCATGCACGTCCCCAACACCCCAACACAGGTCGCCATGCACT
Found at i:3609622 original size:29 final size:29
Alignment explanation
Indices: 3609580--3609662 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
3609570 ACCCCAACAT
*
3609580 AGGTTGCCATGCACTCCCAGCGACC-TACA
1 AGGTCGCCATGCACTCCCAGCGACCTTA-A
* *
3609609 AGGTCGCCATGCACTCCCAACGACCTTAT
1 AGGTCGCCATGCACTCCCAGCGACCTTAA
* * *
3609638 AGGTCGCCAAGCAGTCCCGGCGACC
1 AGGTCGCCATGCACTCCCAGCGACC
3609663 AAGCTGGCGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
29 44 0.96
30 2 0.04
ACGTcount: A:0.23, C:0.39, G:0.23, T:0.16
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTTAA
Found at i:3609746 original size:24 final size:24
Alignment explanation
Indices: 3609705--3609764 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
3609695 GTGCATGCAT
3609705 TGCATCCAT-AGCTGGGAGATTCC
1 TGCATCCATAAGCTGGGAGATTCC
3609728 TGCATCCATAAGCTGGGAGATTCC
1 TGCATCCATAAGCTGGGAGATTCC
3609752 TGCATCCATAAGC
1 TGCATCCATAAGC
3609765 GTTAATTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 9 0.25
24 27 0.75
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (24 bp):
TGCATCCATAAGCTGGGAGATTCC
Found at i:3610661 original size:17 final size:17
Alignment explanation
Indices: 3610619--3610662 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3610609 TGTGCGAGAT
3610619 AATTTA-TGTTTAAAAA
1 AATTTAGTGTTTAAAAA
3610635 AATATT-GTGTTTAAAAA
1 AAT-TTAGTGTTTAAAAA
*
3610652 TATTTAGTGTT
1 AATTTAGTGTT
3610663 GTTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (17 bp):
AATTTAGTGTTTAAAAA
Found at i:3610688 original size:20 final size:21
Alignment explanation
Indices: 3610644--3610688 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3610634 AAATATTGTG
**
3610644 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
3610665 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
3610685 TTTA
1 TTTA
3610689 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:3613752 original size:10 final size:10
Alignment explanation
Indices: 3613734--3613765 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3613724 AGTAATGATA
3613734 TATGTATTTC
1 TATGTATTTC
*
3613744 TATGAATTTC
1 TATGTATTTC
3613754 TATGTATTTC
1 TATGTATTTC
3613764 TA
1 TA
3613766 AGATTTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.56
Consensus pattern (10 bp):
TATGTATTTC
Found at i:3613803 original size:21 final size:21
Alignment explanation
Indices: 3613776--3613863 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
3613766 AGATTTAGTA
3613776 ATGATTAGTAATAATGAAATT
1 ATGATTAGTAATAATGAAATT
* * *
3613797 ATTATTAATATTTAATG--ATT
1 ATGATTAGTA-ATAATGAAATT
* ** * *
3613817 -TGA-TAGTAATGATTTAGTA
1 ATGATTAGTAATAATGAAATT
3613836 ATGATTAGTAATAATGAAATT
1 ATGATTAGTAATAATGAAATT
*
3613857 ATTATTA
1 ATGATTA
3613864 ATATTTAATG
Statistics
Matches: 46, Mismatches: 16, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
17 3 0.07
18 4 0.09
19 3 0.07
20 6 0.13
21 25 0.54
22 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.44
Consensus pattern (21 bp):
ATGATTAGTAATAATGAAATT
Found at i:3613835 original size:60 final size:60
Alignment explanation
Indices: 3613767--3614019 Score: 456
Period size: 60 Copynumber: 4.2 Consensus size: 60
3613757 GTATTTCTAA
*
3613767 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
3613827 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
* *
3613887 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAATAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
*
3613947 GA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
3614005 GATTTAGTAATGATT
1 GATTTAGTAATGATT
3614020 TGATAGTAAT
Statistics
Matches: 186, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
58 34 0.18
59 33 0.18
60 119 0.64
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
Found at i:3613995 original size:21 final size:22
Alignment explanation
Indices: 3613966--3614043 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 22
3613956 TGATTAGTAA
3613966 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
3613987 TAATGATTTGATATTAATGATTT
1 TAATAATTTGATATTAATGA-TT
* *
3614010 AGTAATGATTTGATAGTAATGATT
1 --TAATAATTTGATATTAATGATT
*
3614034 T-ACAATTTGA
1 TAATAATTTGA
3614044 ACAATGAACA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
21 22 0.46
22 3 0.06
23 2 0.04
24 2 0.04
25 19 0.40
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.49
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:3614003 original size:14 final size:14
Alignment explanation
Indices: 3613987--3614034 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
3613977 TATTAATATT
*
3613987 TAATGATTTGATAT
1 TAATGATTTGATAG
3614001 TAATGA-TT--TAG
1 TAATGATTTGATAG
3614012 TAATGATTTGATAG
1 TAATGATTTGATAG
3614026 TAATGATTT
1 TAATGATTT
3614035 ACAATTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:3614132 original size:21 final size:20
Alignment explanation
Indices: 3614108--3614299 Score: 65
Period size: 21 Copynumber: 9.2 Consensus size: 20
3614098 GAAATTATAA
3614108 TAATGATTTAATAATGATTAG
1 TAAT-ATTTAATAATGATTAG
* * * *
3614129 TAATA-ATGA-AATTATTAT
1 TAATATTTAATAATGATTAG
* *
3614147 TAATATTTAATGATTTGA-TAT
1 TAATATTTAAT-A-ATGATTAG
*
3614168 TAATGATTTAGTAATGATTAG
1 TAAT-ATTTAATAATGATTAG
* * *
3614189 TAATAATT-A-AATTATTAT
1 TAATATTTAATAATGATTAG
*
3614207 TAATATTTAATGATTTGA-TAG
1 TAATATTTAAT-A-ATGATTAG
* *
3614228 TAATAATTAGTAATGAAATTATTAT
1 TAAT-ATT--TAAT--AATGATTAG
* *
3614253 TAATATTTAATGATTTGA-TAT
1 TAATATTTAAT-A-ATGATTAG
*
3614274 TAATCATTTAGTAATGATTAG
1 TAAT-ATTTAATAATGATTAG
3614295 TAATA
1 TAATA
3614300 ATAAAATTAT
Statistics
Matches: 124, Mismatches: 29, Indels: 37
0.65 0.15 0.19
Matches are distributed among these distances:
18 26 0.21
19 5 0.04
20 11 0.09
21 41 0.33
22 25 0.20
24 9 0.07
25 7 0.06
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (20 bp):
TAATATTTAATAATGATTAG
Found at i:3614134 original size:13 final size:12
Alignment explanation
Indices: 3614101--3614137 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
3614091 TAGTAATGAA
3614101 ATTATAATAATG
1 ATTATAATAATG
3614113 ATT-TAATAATG
1 ATTATAATAATG
3614124 ATTAGTAATAATG
1 ATTA-TAATAATG
3614137 A
1 A
3614138 AATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 3 0.13
13 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:3614158 original size:35 final size:34
Alignment explanation
Indices: 3614119--3614221 Score: 89
Period size: 35 Copynumber: 3.2 Consensus size: 34
3614109 AATGATTTAA
3614119 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAAT-AAATTATTATTAATATT
* * * *
3614154 TAATGATT--TGAT-AT---TAATGATT--TA-G
1 TAATGATTAGTAATAATAAATTATTATTAATATT
3614179 TAATGATTAGTAATAATTAAATTATTATTAATATT
1 TAATGATTAGTAATAA-TAAATTATTATTAATATT
3614214 TAATGATT
1 TAATGATT
3614222 TGATAGTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
25 8 0.16
26 2 0.04
27 3 0.06
28 7 0.14
29 1 0.02
32 8 0.16
33 3 0.06
34 2 0.04
35 16 0.32
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (34 bp):
TAATGATTAGTAATAATAAATTATTATTAATATT
Found at i:3614175 original size:60 final size:60
Alignment explanation
Indices: 3614108--3614400 Score: 239
Period size: 60 Copynumber: 5.2 Consensus size: 60
3614098 GAAATTATAA
*
3614108 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* *
3614168 TAATGATTTAGTAATGATTAGTAATAATTAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* * * * * * * *
3614228 TAAT-AATTAGTAATGAAATTATTATTAAT--ATTTAATGATTTGATA-TTAATCA-TT--TAG
1 TAATGATTTAATAATG--ATTAGTAATAATGAAATT-ATTA-TTAATATTTAATGATTTGATAG
* *
3614285 TAATGA-TTA----------GTAATAATAAAATTATTATTAATTTTTAATGATTTGATAG
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* * * * * *
3614334 TAGTGA-TTAGTAATGATTAGTAATAAT-AATTTACTATTAATATTTAATAATTTGATAT
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
3614392 TAATGATTT
1 TAATGATTT
3614401 GATAGTAATG
Statistics
Matches: 187, Mismatches: 24, Indels: 45
0.73 0.09 0.18
Matches are distributed among these distances:
45 10 0.05
46 9 0.05
47 5 0.03
49 11 0.06
57 10 0.05
58 32 0.17
59 25 0.13
60 70 0.37
61 15 0.08
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (60 bp):
TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
Found at i:3614247 original size:46 final size:47
Alignment explanation
Indices: 3614192--3614290 Score: 164
Period size: 46 Copynumber: 2.1 Consensus size: 47
3614182 TGATTAGTAA
*
3614192 TAATTAAATTATTATTAATATTTAATGATTTGATAGTAAT-AATTAG
1 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATCAATTAG
* *
3614238 TAATGAAATTATTATTAATATTTAATGATTTGATATTAATCATTTAG
1 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATCAATTAG
3614285 TAATGA
1 TAATGA
3614291 TTAGTAATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 38 0.78
47 11 0.22
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.47
Consensus pattern (47 bp):
TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATCAATTAG
Found at i:3614264 original size:22 final size:22
Alignment explanation
Indices: 3614192--3614265 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
3614182 TGATTAGTAA
*
3614192 TAATTAAATTATTATTAATATT
1 TAATGAAATTATTATTAATATT
* *
3614214 TAATG-ATTTGA-TAGTAATAATT
1 TAATGAAATT-ATTATTAAT-ATT
3614236 AGTAATGAAATTATTATTAATATT
1 --TAATGAAATTATTATTAATATT
3614260 TAATGA
1 TAATGA
3614266 TTTGATATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
21 9 0.22
22 14 0.34
24 9 0.22
25 9 0.22
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (22 bp):
TAATGAAATTATTATTAATATT
Found at i:3614289 original size:25 final size:23
Alignment explanation
Indices: 3614204--3614292 Score: 80
Period size: 25 Copynumber: 3.9 Consensus size: 23
3614194 ATTAAATTAT
3614204 TATTAATATT--TAATGATTTGA
1 TATTAATATTAGTAATGATTTGA
* *
3614225 TAGTAATAATTAGTAATGAAATT-A
1 TATTAAT-ATTAGTAATG-ATTTGA
3614249 TTATTAATATT--TAATGATTTGA
1 -TATTAATATTAGTAATGATTTGA
3614271 TATTAATCATTTAGTAATGATT
1 TATTAAT-A-TTAGTAATGATT
3614293 AGTAATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
21 16 0.30
22 10 0.19
23 2 0.04
24 9 0.17
25 17 0.31
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.48
Consensus pattern (23 bp):
TATTAATATTAGTAATGATTTGA
Found at i:3614381 original size:21 final size:22
Alignment explanation
Indices: 3614357--3614400 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
3614347 TGATTAGTAA
3614357 TAATAATTT-ACTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
3614378 TAATAATTTGATATTAATGATT
1 TAATAATTTGATATTAATGATT
3614400 T
1 T
3614401 GATAGTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:3614394 original size:14 final size:14
Alignment explanation
Indices: 3614377--3614414 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
3614367 CTATTAATAT
*
3614377 TTAATAATTTGATA
1 TTAATGATTTGATA
3614391 TTAATGATTTGATA
1 TTAATGATTTGATA
*
3614405 GTAATGATTT
1 TTAATGATTT
3614415 ACGACTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TTAATGATTTGATA
Found at i:3616649 original size:15 final size:14
Alignment explanation
Indices: 3616626--3616656 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3616616 TACAACACTA
3616626 AACTTTAATATAAT
1 AACTTTAATATAAT
3616640 AACTTATAATATAAT
1 AACTT-TAATATAAT
3616655 AA
1 AA
3616657 ACTAACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:3616885 original size:43 final size:41
Alignment explanation
Indices: 3616836--3616964 Score: 102
Period size: 43 Copynumber: 3.1 Consensus size: 41
3616826 CAAATATAAC
*
3616836 TTAACTATTTAACTACCACAAACTAATTAAATAATTTTTTT
1 TTAACTATATAACTACCACAAACTAATTAAATAATTTTTTT
* * * * * *
3616877 ATATAACTA-ACT-ATTAACA-AAACAAACTAATTAATTATTTT
1 -T-TAACTATA-TAACTACCACAAACTAATTAAATAATTTTTTT
* *
3616918 TTAACTATATAACTATCAAACATACTAATTAAATAATTTTTTAT
1 TTAACTATATAACTA-C-CACAAACTAATTAAATAATTTTTT-T
3616962 TTA
1 TTA
3616965 TGTATAATAT
Statistics
Matches: 64, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
39 7 0.11
40 5 0.08
41 18 0.28
42 7 0.11
43 23 0.36
44 4 0.06
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (41 bp):
TTAACTATATAACTACCACAAACTAATTAAATAATTTTTTT
Found at i:3616932 original size:47 final size:47
Alignment explanation
Indices: 3616829--3616919 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 47
3616819 CAACAAACAA
**
3616829 ATATAACTTAACTATTTAACTACCACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTT
*
3616877 ATATAACTAACTA-TTAAC-AAAACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTT
3616920 AACTATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 10 0.25
45 12 0.30
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTT
Found at i:3617150 original size:13 final size:13
Alignment explanation
Indices: 3617111--3617157 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3617101 CTCACAAGAG
3617111 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
3617125 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
3617139 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
3617152 -CTTTCT
1 CCTTTCT
3617158 TTCTCGGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:3617186 original size:29 final size:27
Alignment explanation
Indices: 3617154--3617235 Score: 100
Period size: 26 Copynumber: 3.1 Consensus size: 27
3617144 CTCCCTTTCT
*
3617154 TTCTTTCTCGGCTGCAATTTCTTCTCCC
1 TTCTTTCTC-GCTGCAATCTCTTCTCCC
3617182 ATTC-TTCT-GCTGCAATCTCTTCTCCC
1 -TTCTTTCTCGCTGCAATCTCTTCTCCC
3617208 TT-TTT-TCAGCTGCAATCTCTTCTCCC
1 TTCTTTCTC-GCTGCAATCTCTTCTCCC
3617234 TT
1 TT
3617236 TATTTCTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
24 1 0.02
25 4 0.08
26 37 0.76
28 4 0.08
29 3 0.06
ACGTcount: A:0.10, C:0.35, G:0.09, T:0.46
Consensus pattern (27 bp):
TTCTTTCTCGCTGCAATCTCTTCTCCC
Found at i:3617234 original size:26 final size:26
Alignment explanation
Indices: 3617164--3617241 Score: 111
Period size: 26 Copynumber: 3.0 Consensus size: 26
3617154 TTCTTTCTCG
* * * *
3617164 GCTGCAATTTCTTCTCCCATTCTTCT
1 GCTGCAATCTCTTCTCCCTTTTTTCA
3617190 GCTGCAATCTCTTCTCCCTTTTTTCA
1 GCTGCAATCTCTTCTCCCTTTTTTCA
3617216 GCTGCAATCTCTTCTCCCTTTATTTC
1 GCTGCAATCTCTTCTCCCTTT-TTTC
3617242 TTTTATGTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 43 0.91
27 4 0.09
ACGTcount: A:0.12, C:0.35, G:0.08, T:0.46
Consensus pattern (26 bp):
GCTGCAATCTCTTCTCCCTTTTTTCA
Done.