Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 9 of 26
Found at i:3174173 original size:34 final size:34
Alignment explanation
Indices: 3174084--3174178 Score: 91
Period size: 34 Copynumber: 2.8 Consensus size: 34
3174074 TGCTACACAT
* * * * ** *
3174084 CAAAACTTTAGTAGCAAATGTTACATATCAAGGT
1 CAAAGCTTTAGCAACAAATATTACACGTCAAGGC
* * *
3174118 CAAAGCTTCAGCAATAGATATTACACGTCAAGGC
1 CAAAGCTTTAGCAACAAATATTACACGTCAAGGC
*
3174152 CAAAGCTTTAGCACCAAATATTACACG
1 CAAAGCTTTAGCAACAAATATTACACG
3174179 CCAAAGCTTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (34 bp):
CAAAGCTTTAGCAACAAATATTACACGTCAAGGC
Found at i:3184601 original size:6 final size:6
Alignment explanation
Indices: 3184590--3184615 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3184580 ATTTAGAGTT
3184590 GCACAC GCACAC GCACAC GCACAC GC
1 GCACAC GCACAC GCACAC GCACAC GC
3184616 CATTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (6 bp):
GCACAC
Found at i:3186597 original size:2 final size:2
Alignment explanation
Indices: 3186590--3186625 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3186580 TTTCATTCTT
* *
3186590 TA TA TA TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3186626 GCGTTGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3187414 original size:28 final size:29
Alignment explanation
Indices: 3187369--3187443 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
3187359 ATTCTTAAAT
* *
3187369 AAAAGGTA-ATAGAAAAGA-GGTATACGTG
1 AAAAGGTACA-AGAGAAGAGGGTATACATG
*
3187397 AAAAGGTACAAGAGAAGAGGGTGTACATG
1 AAAAGGTACAAGAGAAGAGGGTATACATG
*
3187426 AATAGGTACAAGAGAAGA
1 AAAAGGTACAAGAGAAGA
3187444 AAGTGTATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 15 0.37
29 26 0.63
ACGTcount: A:0.49, C:0.05, G:0.31, T:0.15
Consensus pattern (29 bp):
AAAAGGTACAAGAGAAGAGGGTATACATG
Found at i:3187449 original size:29 final size:29
Alignment explanation
Indices: 3187395--3187460 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
3187385 GAGGTATACG
* **
3187395 TGAAAAGGTACAAGAGAAGAGGGTGTACA
1 TGAATAGGTACAAGAGAAGAAAGTGTACA
**
3187424 TGAATAGGTACAAGAGAAGAAAGTGTATG
1 TGAATAGGTACAAGAGAAGAAAGTGTACA
3187453 TGAATAGG
1 TGAATAGG
3187461 CACACAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.05, G:0.33, T:0.18
Consensus pattern (29 bp):
TGAATAGGTACAAGAGAAGAAAGTGTACA
Found at i:3192100 original size:2 final size:2
Alignment explanation
Indices: 3192093--3192120 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3192083 GTACTAAAAG
3192093 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
3192121 TCAATAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3193481 original size:19 final size:19
Alignment explanation
Indices: 3193459--3193501 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3193449 ATAGGTGGAG
3193459 AAATTTAAAAATTGAAAA-A
1 AAATTTAAAAATT-AAAATA
3193478 AAATTTAAAAATTAAAATA
1 AAATTTAAAAATTAAAATA
3193497 AAATT
1 AAATT
3193502 GAATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAATTTAAAAATTAAAATA
Found at i:3211556 original size:21 final size:21
Alignment explanation
Indices: 3211530--3211579 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
3211520 CATCAACAAC
3211530 TTCCTTCTATAAATTGGATTT
1 TTCCTTCTATAAATTGGATTT
3211551 TTCCTTCTATAAATTGGATTT
1 TTCCTTCTATAAATTGGATTT
3211572 TTCCTTCT
1 TTCCTTCT
3211580 TGTAACTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.08, T:0.54
Consensus pattern (21 bp):
TTCCTTCTATAAATTGGATTT
Found at i:3216549 original size:2 final size:2
Alignment explanation
Indices: 3216544--3216587 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3216534 GTGTGTGTGT
*
3216544 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3216586 GA
1 GA
3216588 TTGCACCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3227294 original size:17 final size:18
Alignment explanation
Indices: 3227251--3227294 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3227241 ATATTTAATC
*
3227251 TATCTAAATAACTACAGT
1 TATCTAAATAACCACAGT
*
3227269 TAGTCTAAATATCCACAGT
1 TA-TCTAAATAACCACAGT
3227288 T-TCTAAA
1 TATCTAAA
3227295 GAGGTGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 15 0.65
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (18 bp):
TATCTAAATAACCACAGT
Found at i:3229258 original size:20 final size:20
Alignment explanation
Indices: 3229233--3229271 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3229223 AGCAAAGTGG
*
3229233 TGGTGATGTATGATGGCTTC
1 TGGTGATGTATGACGGCTTC
3229253 TGGTGATGTATGACGGCTT
1 TGGTGATGTATGACGGCTT
3229272 TAGATAAGAC
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:0.15, C:0.10, G:0.36, T:0.38
Consensus pattern (20 bp):
TGGTGATGTATGACGGCTTC
Found at i:3229524 original size:23 final size:26
Alignment explanation
Indices: 3229498--3229548 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
3229488 TAATCAAGAT
*
3229498 ATTTTTTAA-TCA-ATA-AATTAATA
1 ATTTATTAATTCATATATAATTAATA
3229521 ATTTATTAATTCATATATTAATTAATA
1 ATTTATTAATTCATATA-TAATTAATA
3229548 A
1 A
3229549 AAAATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 3 0.13
25 3 0.13
27 9 0.39
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTATTAATTCATATATAATTAATA
Found at i:3232961 original size:19 final size:19
Alignment explanation
Indices: 3232924--3232961 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3232914 GCATATAGAA
*
3232924 TAGACATATACATATAAGC
1 TAGACATACACATATAAGC
3232943 TAGACATACACATATAAGC
1 TAGACATACACATATAAGC
3232962 CATACGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TAGACATACACATATAAGC
Found at i:3234697 original size:21 final size:21
Alignment explanation
Indices: 3234671--3234717 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3234661 GATCATGTAG
3234671 TTCATGACAAAGACTGATACT
1 TTCATGACAAAGACTGATACT
3234692 TTCATGACAAAGACTGATACT
1 TTCATGACAAAGACTGATACT
3234713 TTCAT
1 TTCAT
3234718 AATGAAGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (21 bp):
TTCATGACAAAGACTGATACT
Found at i:3234725 original size:21 final size:21
Alignment explanation
Indices: 3234671--3234730 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
3234661 GATCATGTAG
*
3234671 TTCATGACAAAGACTGATACT
1 TTCATAACAAAGACTGATACT
*
3234692 TTCATGACAAAGACTGATACT
1 TTCATAACAAAGACTGATACT
**
3234713 TTCATAATGAAGACTGAT
1 TTCATAACAAAGACTGAT
3234731 GCATTTATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
TTCATAACAAAGACTGATACT
Found at i:3236136 original size:10 final size:10
Alignment explanation
Indices: 3236121--3236153 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3236111 TCTAACTAAC
3236121 TTTCTTTTAT
1 TTTCTTTTAT
3236131 TTTCTTTTAT
1 TTTCTTTTAT
3236141 TTAT-TTTTAT
1 TT-TCTTTTAT
3236151 TTT
1 TTT
3236154 TTTAATTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTCTTTTAT
Found at i:3239478 original size:21 final size:20
Alignment explanation
Indices: 3239454--3239510 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
3239444 TTTGCTGATA
*
3239454 TATTAATTTTAGTTATTATTT
1 TATTAATTTTAATTATTA-TT
*
3239475 TATTAGTTTTAAATT-TTATT
1 TATTAATTTT-AATTATTATT
3239495 T-TTAATTTTAATTATT
1 TATTAATTTTAATTATT
3239511 TAGATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.13
19 9 0.29
20 3 0.10
21 12 0.39
22 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TATTAATTTTAATTATTATT
Found at i:3239511 original size:21 final size:20
Alignment explanation
Indices: 3239454--3239511 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
3239444 TTTGCTGATA
*
3239454 TATTAATTTTAGTTATTATTT
1 TATTAATTTTAATTATT-TTT
*
3239475 TATTAGTTTTAA--ATTTTAT
1 TATTAATTTTAATTATTTT-T
*
3239494 TTTTAATTTTAATTATTT
1 TATTAATTTTAATTATTT
3239512 AGATAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
21 14 0.47
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TATTAATTTTAATTATTTTT
Found at i:3241373 original size:24 final size:24
Alignment explanation
Indices: 3241340--3241385 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3241330 TTAATATTTT
3241340 AAAATATTAATGA-TTAAATTATAA
1 AAAATATTAAT-ACTTAAATTATAA
*
3241364 AAAATGTTAATACTTAAATTAT
1 AAAATATTAATACTTAAATTAT
3241386 CAATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (24 bp):
AAAATATTAATACTTAAATTATAA
Found at i:3241395 original size:39 final size:40
Alignment explanation
Indices: 3241324--3241403 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 40
3241314 AGTTTCTAAT
* *
3241324 AAAATATTAATATTTTAAAATATTAATGATTAA-ATTATAA
1 AAAATATTAATATCTTAAAATATCAATGATTAATA-TATAA
* * *
3241364 AAAATGTTAATA-CTTAAATTATCAATTATTAATATATAA
1 AAAATATTAATATCTTAAAATATCAATGATTAATATATAA
3241403 A
1 A
3241404 TTAAATTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (40 bp):
AAAATATTAATATCTTAAAATATCAATGATTAATATATAA
Found at i:3242333 original size:52 final size:49
Alignment explanation
Indices: 3242243--3242385 Score: 137
Period size: 52 Copynumber: 2.8 Consensus size: 49
3242233 ATTACCTGTT
* * * *
3242243 TTTGACTT-TGAAAATATTTTACTTTAATTTGTTGTTTATGCTTTGCTTGCA
1 TTTGACTTAAGAAAATATTTTAC-TTGATTTATTATTTATGC--TGCTTGCA
* *
3242294 TTT-AGCTTAGGAAAATATTTTAGCTTGATTTATTATTTATATGCTGTTTGCA
1 TTTGA-CTTAAGAAAATATTTTA-CTTGATTTATTA-TT-TATGCTGCTTGCA
*
3242346 TTTGACTTAAGAAAATATTTTACCTTGATTTATTCTTTAT
1 TTTGACTTAAGAAAATATTTTA-CTTGATTTATTATTTAT
3242386 TGAAAAATTG
Statistics
Matches: 78, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
50 4 0.05
51 8 0.10
52 57 0.73
53 4 0.05
54 5 0.06
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (49 bp):
TTTGACTTAAGAAAATATTTTACTTGATTTATTATTTATGCTGCTTGCA
Found at i:3257021 original size:2 final size:2
Alignment explanation
Indices: 3257014--3257047 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3257004 TCAAGGCTAA
* *
3257014 AT AT AT AT AT AT AT AT AT AT AT AC AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3257048 TTTGATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3257604 original size:18 final size:19
Alignment explanation
Indices: 3257563--3257604 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3257553 CATATGGTCA
*
3257563 TATCATTATATCACATCAT
1 TATCATTATATCACACCAT
* *
3257582 CATCATT-TATCATACCAT
1 TATCATTATATCACACCAT
3257600 TATCA
1 TATCA
3257605 ATTAAAATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (19 bp):
TATCATTATATCACACCAT
Found at i:3267246 original size:2 final size:2
Alignment explanation
Indices: 3267239--3267305 Score: 53
Period size: 2 Copynumber: 33.5 Consensus size: 2
3267229 GTTCTCTGTT
* ** * * * *
3267239 TA TA TA TA TG TA TA CG TA TA TA TA TA TA TA TA TG TA TG TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3267281 TT TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3267306 GTATTAGCAC
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3268254 original size:58 final size:58
Alignment explanation
Indices: 3268179--3268299 Score: 233
Period size: 58 Copynumber: 2.1 Consensus size: 58
3268169 TGTGGCCCGG
*
3268179 ATGAAAGAACATGAGAGATTGTTTGTCTTCAGTTGGCTATTTGGTTCAGATTCGGAGT
1 ATGACAGAACATGAGAGATTGTTTGTCTTCAGTTGGCTATTTGGTTCAGATTCGGAGT
3268237 ATGACAGAACATGAGAGATTGTTTGTCTTCAGTTGGCTATTTGGTTCAGATTCGGAGT
1 ATGACAGAACATGAGAGATTGTTTGTCTTCAGTTGGCTATTTGGTTCAGATTCGGAGT
3268295 ATGAC
1 ATGAC
3268300 GTGATTCATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.36
Consensus pattern (58 bp):
ATGACAGAACATGAGAGATTGTTTGTCTTCAGTTGGCTATTTGGTTCAGATTCGGAGT
Found at i:3279471 original size:33 final size:30
Alignment explanation
Indices: 3279402--3279476 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
3279392 TTATGCCAAA
3279402 TTAACATGTCACATCATCATCAATTATGTG
1 TTAACATGTCACATCATCATCAATTATGTG
* * *
3279432 TCAACATGTCATATTATCATCAATTATGATATG
1 TTAACATGTCACATCATCATCAATTATG---TG
3279465 TTAACATGTCAC
1 TTAACATGTCAC
3279477 GTCAGTATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 25 0.68
33 12 0.32
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (30 bp):
TTAACATGTCACATCATCATCAATTATGTG
Found at i:3285153 original size:34 final size:34
Alignment explanation
Indices: 3285115--3285182 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
3285105 GGACTCAGTT
*
3285115 TACTGTTCTGGTAGCAGTGTCATGTGAGAGGGTG
1 TACTGTTCTGGTAGCAGTGTCATGTGAAAGGGTG
3285149 TACTGTTCTGGTAGCAGTGTCATGTGAAAGGGTG
1 TACTGTTCTGGTAGCAGTGTCATGTGAAAGGGTG
3285183 ACAATTTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.19, C:0.12, G:0.37, T:0.32
Consensus pattern (34 bp):
TACTGTTCTGGTAGCAGTGTCATGTGAAAGGGTG
Found at i:3298898 original size:12 final size:12
Alignment explanation
Indices: 3298881--3298905 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3298871 GAACATATCC
3298881 AGCAATTCCACT
1 AGCAATTCCACT
3298893 AGCAATTCCACT
1 AGCAATTCCACT
3298905 A
1 A
3298906 ACAGGCTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
AGCAATTCCACT
Found at i:3300002 original size:2 final size:2
Alignment explanation
Indices: 3299995--3300028 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3299985 GAGAAAGAGC
3299995 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
3300029 TGAGAGTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3300076 original size:39 final size:39
Alignment explanation
Indices: 3300022--3300096 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
3300012 TATATATATA
*
3300022 TATATATTGAGAGTATCTTTT-TATTATAGGAAATAAAAT
1 TATATATTGAGAGTAT-TTTTGTACTATAGGAAATAAAAT
* *
3300061 TATATTTTGAGAGTATTTTTGTACTATTGGAAATAA
1 TATATATTGAGAGTATTTTTGTACTATAGGAAATAA
3300097 TTTTTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (39 bp):
TATATATTGAGAGTATTTTTGTACTATAGGAAATAAAAT
Found at i:3302379 original size:35 final size:35
Alignment explanation
Indices: 3302339--3302407 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
3302329 TGTCTTAATA
* *
3302339 GAGATTACACTTGATATTGCAACAAGCAAGTTGTT
1 GAGATTACACTTGATAGTGCAAAAAGCAAGTTGTT
*
3302374 GAGATTACATTTGATAGTGCAAAAAGCAAGTTGT
1 GAGATTACACTTGATAGTGCAAAAAGCAAGTTGT
3302408 AAAGGTTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (35 bp):
GAGATTACACTTGATAGTGCAAAAAGCAAGTTGTT
Found at i:3302417 original size:35 final size:35
Alignment explanation
Indices: 3302340--3302418 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 35
3302330 GTCTTAATAG
* * **
3302340 AGATTACACTTGATATTGCAACAAGCAAGTTGTTG
1 AGATTACACTTGATAGTGCAAAAAGCAAGTTGTAA
*
3302375 AGATTACATTTGATAGTGCAAAAAGCAAGTTGTAA
1 AGATTACACTTGATAGTGCAAAAAGCAAGTTGTAA
*
3302410 AGGTTACAC
1 AGATTACAC
3302419 CTAACTTTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (35 bp):
AGATTACACTTGATAGTGCAAAAAGCAAGTTGTAA
Found at i:3306892 original size:21 final size:21
Alignment explanation
Indices: 3306866--3306923 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
3306856 AATAATTTAT
*
3306866 AATATTATAATTAAAATAAAA
1 AATATTATAATAAAAATAAAA
* * *
3306887 AATATTAAAATAAAAATATAT
1 AATATTATAATAAAAATAAAA
*
3306908 AATATAATAATAAAAA
1 AATATTATAATAAAAA
3306924 ATTAAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATTATAATAAAAATAAAA
Found at i:3306893 original size:15 final size:15
Alignment explanation
Indices: 3306875--3306935 Score: 68
Period size: 15 Copynumber: 3.8 Consensus size: 15
3306865 TAATATTATA
3306875 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
3306890 ATTAAAATAAAAATAT
1 ATTAAAATAAAAA-AT
* *
3306906 ATAATATAATAATAAAAA
1 AT--TAAAATAA-AAAAT
3306924 ATTAAAATAAAA
1 ATTAAAATAAAA
3306936 TAAAATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 15 0.38
16 11 0.28
18 10 0.26
19 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:3306928 original size:34 final size:35
Alignment explanation
Indices: 3306866--3306935 Score: 101
Period size: 34 Copynumber: 2.0 Consensus size: 35
3306856 AATAATTTAT
3306866 AATATTATAATTAAAATAAAAAATATTAAAATAAA
1 AATATTATAATTAAAATAAAAAATATTAAAATAAA
3306901 AATA-TATAATATAATAAT-AAAAA-ATTAAAATAAA
1 AATATTATAAT-TAA-AATAAAAAATATTAAAATAAA
3306935 A
1 A
3306936 TAAAATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
34 18 0.55
35 12 0.36
36 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (35 bp):
AATATTATAATTAAAATAAAAAATATTAAAATAAA
Found at i:3306936 original size:33 final size:33
Alignment explanation
Indices: 3306866--3307067 Score: 126
Period size: 33 Copynumber: 6.2 Consensus size: 33
3306856 AATAATTTAT
*
3306866 AATATTATAAT-TAA-AATAAAAAATATTAAAATAAA
1 AATA-TATAATATAATAAT-AAAAA-ATGAAAAT-AA
3306901 AATATATAATATAATAATAAAAAAT-----TAA
1 AATATATAATATAATAATAAAAAATGAAAATAA
* *
3306929 AATA-A-AATAAAAT-ATAAAAAATTAAAAT--
1 AATATATAATATAATAATAAAAAATGAAAATAA
* * *
3306957 -TTATATAATATAGGTAA-AACAAATGAAAATAA
1 AATATATAATATA-ATAATAAAAAATGAAAATAA
3306989 AATATATAATATAAAAAATATATTAAAAAATGAAAATAA
1 AATATATAATAT----AATA-A-TAAAAAATGAAAATAA
* * *
3307028 AATATATAAAATTATAATAATAAATGAAAATAA
1 AATATATAATATAATAATAAAAAATGAAAATAA
3307061 AATATAT
1 AATATAT
3307068 GACATTAAAA
Statistics
Matches: 134, Mismatches: 12, Indels: 44
0.71 0.06 0.23
Matches are distributed among these distances:
25 9 0.07
26 7 0.05
27 3 0.02
28 7 0.05
29 6 0.04
30 13 0.10
31 1 0.01
33 32 0.24
34 9 0.07
35 15 0.11
36 5 0.04
37 2 0.01
39 25 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
AATATATAATATAATAATAAAAAATGAAAATAA
Found at i:3306986 original size:55 final size:54
Alignment explanation
Indices: 3306877--3307007 Score: 149
Period size: 55 Copynumber: 2.4 Consensus size: 54
3306867 ATATTATAAT
* * *
3306877 TAAAATAAAAAATATTAAAA-TAAAAATATATAATATAATAATAAAAAATTAAAA
1 TAAAATAAAATATA-AAAAATTAAAAATATATAATATAATAATAAAAAATGAAAA
* * *
3306931 TAAAATAAAATATAAAAAATTAAAATTTATATAATATAGGTAA-AACAAATGAAAA
1 TAAAATAAAATATAAAAAATTAAAA-ATATATAATATA-ATAATAAAAAATGAAAA
3306986 TAAAATATATAATATAAAAAAT
1 TAAAATA-A-AATATAAAAAAT
3307008 ATATTAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
53 4 0.06
54 18 0.27
55 28 0.42
56 4 0.06
57 12 0.18
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (54 bp):
TAAAATAAAATATAAAAAATTAAAAATATATAATATAATAATAAAAAATGAAAA
Found at i:3307015 original size:12 final size:14
Alignment explanation
Indices: 3306881--3307166 Score: 63
Period size: 15 Copynumber: 19.4 Consensus size: 14
3306871 TATAATTAAA
*
3306881 ATAAAAAATATTAAA
1 ATAAAAAATA-TAAT
3306896 ATAAAAATATATAAT
1 ATAAAAA-ATATAAT
*
3306911 ATAATAATAA-AAAATT
1 ATAA-AA-AATATAA-T
* *
3306927 AAAATAAAATAAAAT
1 ATAA-AAAATATAAT
*
3306942 ATAAAAAATTAAAAT
1 ATAAAAAA-TATAAT
* * * *
3306957 TTATATAATATAGGT
1 ATAAAAAATATA-AT
3306972 A-AAACAAATGA-AA-
1 ATAAA-AAAT-ATAAT
*
3306985 ATAAAATATATAAT
1 ATAAAAAATATAAT
3306999 ATAAAAAATAT-AT
1 ATAAAAAATATAAT
3307012 -TAAAAAATGA-AA-
1 ATAAAAAAT-ATAAT
*
3307024 ATAAAATATATAAAATT
1 ATAAAA-A-ATATAA-T
*
3307041 ATAATAATAA-ATGAAA
1 ATAA-AA-AATAT-AAT
* * *
3307057 ATAAAATATATGAC
1 ATAAAAAATATAAT
*
3307071 ATTAAAAATAT-AT
1 ATAAAAAATATAAT
* * * *
3307084 TTAAGAGATGATATT
1 ATAAAAAAT-ATAAT
3307099 ATTATAAAAAT-TAAT
1 A-TA-AAAAATATAAT
3307114 AATAAAAAATATAAAT
1 -ATAAAAAATAT-AAT
*
3307130 ATATTAAAAATAAAAT
1 ATA--AAAAATATAAT
*
3307146 ATATAAAATTATAAT
1 ATA-AAAAATATAAT
3307161 AATAAA
1 -ATAAA
3307167 TAAAAATAAA
Statistics
Matches: 203, Mismatches: 35, Indels: 66
0.67 0.12 0.22
Matches are distributed among these distances:
12 9 0.04
13 21 0.10
14 43 0.21
15 69 0.34
16 38 0.19
17 19 0.09
18 4 0.02
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (14 bp):
ATAAAAAATATAAT
Found at i:3307025 original size:39 final size:37
Alignment explanation
Indices: 3306977--3307084 Score: 116
Period size: 33 Copynumber: 2.9 Consensus size: 37
3306967 TAGGTAAAAC
3306977 AAATGAAAATAAAATATATAATATAAAAAATATATTAAA
1 AAATGAAAATAAAATATAT-ATAT-AAAAATATATTAAA
* * *
3307016 AAATGAAAAT--AA-A-ATATATAAAATTATAATAAT
1 AAATGAAAATAAAATATATATATAAAAATATATTAAA
*
3307049 AAATGAAAATAAAATATATGACATTAAAAATATATT
1 AAATGAAAATAAAATATAT-ATA-TAAAAATATATT
3307085 TAAGAGATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
33 21 0.37
34 4 0.07
35 4 0.07
36 2 0.04
37 4 0.07
38 2 0.04
39 20 0.35
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.30
Consensus pattern (37 bp):
AAATGAAAATAAAATATATATATAAAAATATATTAAA
Found at i:3307043 original size:8 final size:9
Alignment explanation
Indices: 3306881--3307182 Score: 54
Period size: 9 Copynumber: 35.2 Consensus size: 9
3306871 TATAATTAAA
*
3306881 ATAAAAAAT
1 ATAAAATAT
*
3306890 ATTAAA-AT
1 ATAAAATAT
3306898 A-AAAATAT
1 ATAAAATAT
*
3306906 ATAATATAAT
1 ATAAAAT-AT
*
3306916 AATAAAAAAT
1 -ATAAAATAT
*
3306926 -TAAAATAAA
1 ATAAAAT-AT
3306935 ATAAAATAT
1 ATAAAATAT
3306944 A-AAAA-AT
1 ATAAAATAT
*
3306951 -TAAAATTT
1 ATAAAATAT
*
3306959 ATATAATAT
1 ATAAAATAT
* *
3306968 AGGTAAAACAA
1 A--TAAAATAT
*
3306979 AT-GAA-A-
1 ATAAAATAT
3306985 ATAAAATAT
1 ATAAAATAT
3306994 AT--AATAT
1 ATAAAATAT
*
3307001 AAAAAATAT
1 ATAAAATAT
3307010 ATTAAAA-A-
1 A-TAAAATAT
*
3307018 AT-GAA-A-
1 ATAAAATAT
3307024 ATAAAATAT
1 ATAAAATAT
3307033 ATAAAAT-T
1 ATAAAATAT
*
3307041 ATAATAATAA
1 ATAA-AATAT
*
3307051 AT-GAA-A-
1 ATAAAATAT
3307057 ATAAAATAT
1 ATAAAATAT
* *
3307066 ATGACAT-T
1 ATAAAATAT
3307074 A-AAAATAT
1 ATAAAATAT
3307082 ATTTAAGAGATGAT
1 A--TAA-A-AT-AT
* *
3307096 AT-TATTAT
1 ATAAAATAT
3307104 A-AAAATTAAT
1 ATAAAA-T-AT
*
3307114 AATAAAAAAT
1 -ATAAAATAT
3307124 AT-AAATAT
1 ATAAAATAT
*
3307132 ATTAAA-A-
1 ATAAAATAT
3307139 ATAAAATAT
1 ATAAAATAT
3307148 ATAAAAT-T
1 ATAAAATAT
*
3307156 ATAATAATAA
1 ATAA-AATAT
3307166 AT-AAA-A-
1 ATAAAATAT
3307172 ATAAAATAT
1 ATAAAATAT
3307181 AT
1 AT
3307183 GACATCAAAA
Statistics
Matches: 213, Mismatches: 35, Indels: 90
0.63 0.10 0.27
Matches are distributed among these distances:
6 11 0.05
7 36 0.17
8 54 0.25
9 64 0.30
10 23 0.11
11 14 0.07
12 6 0.03
13 2 0.01
14 3 0.01
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (9 bp):
ATAAAATAT
Found at i:3307135 original size:24 final size:23
Alignment explanation
Indices: 3307101--3307180 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 23
3307091 ATGATATTAT
3307101 TATAAAA-ATTAATAATAAAAAA
1 TATAAAATATTAATAATAAAAAA
* *
3307123 TATAAATATATTAAAAATAAAATA
1 TATAAA-ATATTAATAATAAAAAA
3307147 TATAAAAT-TATAATAATAAATAAA
1 TATAAAATAT-TAATAATAAA-AAA
*
3307171 AATAAAATAT
1 TATAAAATAT
3307181 ATGACATCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
22 7 0.15
23 12 0.25
24 28 0.58
25 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TATAAAATATTAATAATAAAAAA
Found at i:3307152 original size:33 final size:33
Alignment explanation
Indices: 3307102--3307182 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
3307092 TGATATTATT
*
3307102 ATAAAAAT-TAATA-ATAAAAA-AT-ATAAATATA
1 ATAAAAATAAAATATATAAAAATATAAT-AATA-A
* *
3307133 TTAAAAATAAAATATATAAAATTATAATAATAA
1 ATAAAAATAAAATATATAAAAATATAATAATAA
3307166 ATAAAAATAAAATATAT
1 ATAAAAATAAAATATAT
3307183 GACATCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
31 7 0.17
32 4 0.10
33 23 0.55
34 6 0.14
35 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (33 bp):
ATAAAAATAAAATATATAAAAATATAATAATAA
Found at i:3307158 original size:115 final size:114
Alignment explanation
Indices: 3307021--3307251 Score: 417
Period size: 115 Copynumber: 2.0 Consensus size: 114
3307011 TTAAAAAATG
* *
3307021 AAAATAAAATATATAAAATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATCAAAAATATATTT
*
3307086 AAGAGATGATATTATTATAAAAATTAATAATAAAAAATATAAATATATTA
66 AAGAGATGATATTA-AATAAAAATTAATAATAAAAAATATAAATATATTA
3307136 AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATCAAAAATATATTT
1 AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATCAAAAATATATTT
*
3307201 AAGAGATGATATTAAATAAAAATTTATAATAAAAAATATAAATATATTA
66 AAGAGATGATATTAAATAAAAATTAATAATAAAAAATATAAATATATTA
3307250 AA
1 AA
3307252 CTTGTATTTT
Statistics
Matches: 112, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
114 35 0.31
115 77 0.69
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (114 bp):
AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATCAAAAATATATTT
AAGAGATGATATTAAATAAAAATTAATAATAAAAAATATAAATATATTA
Found at i:3307430 original size:15 final size:15
Alignment explanation
Indices: 3307401--3307444 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3307391 TGTTATGTTC
* *
3307401 CCTGCAATTACATTA
1 CCTGCAATCATATTA
*
3307416 CTTGCAATCATATTA
1 CCTGCAATCATATTA
*
3307431 CCTGTAATCATATT
1 CCTGCAATCATATT
3307445 GTATTGTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (15 bp):
CCTGCAATCATATTA
Found at i:3307822 original size:20 final size:20
Alignment explanation
Indices: 3307775--3307822 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3307765 TAATTAAATT
*
3307775 AATAAAAATATAAATAATAA
1 AATATAAATATAAATAATAA
* *
3307795 AATTTAAATTTAAATAATCAA
1 AATATAAATATAAATAAT-AA
3307816 AA-ATAAA
1 AATATAAA
3307823 GATCTTAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AATATAAATATAAATAATAA
Found at i:3307938 original size:14 final size:14
Alignment explanation
Indices: 3307921--3307980 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
3307911 ACATAAACTT
3307921 AAATAATTAAATAC
1 AAATAATTAAATAC
**
3307935 AAAT-ATCCAA-AC
1 AAATAATTAAATAC
*
3307947 AAATAATATAAACT-T
1 AAATAAT-TAAA-TAC
3307962 AAATAATTAAATAC
1 AAATAATTAAATAC
3307976 AAATA
1 AAATA
3307981 TCCAAACAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
12 6 0.17
13 7 0.20
14 15 0.43
15 7 0.20
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATAATTAAATAC
Found at i:3307964 original size:41 final size:41
Alignment explanation
Indices: 3307830--3308011 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 41
3307820 AAAGATCTTA
* * * * *
3307830 AACATAAACTTAAATAATTAAAAATAAATGTCCATAC-TAC
1 AACATAAACTTAAATAATTAAATACAAATATCCAAACAAAC
* ** * * *
3307870 AACATAAACTTACATAACCATATAAAAATATCCAAA-TAAC
1 AACATAAACTTAAATAATTAAATACAAATATCCAAACAAAC
*
3307910 AACATAAACTTAAATAATTAAATACAAATATCCAAACAAAT
1 AACATAAACTTAAATAATTAAATACAAATATCCAAACAAAC
*
3307951 AATATAAACTTAAATAATTAAATACAAATAT-C---CAAAC
1 AACATAAACTTAAATAATTAAATACAAATATCCAAACAAAC
*
3307988 AACATAAACTTAAATAACTAAATA
1 AACATAAACTTAAATAATTAAATA
3308012 TGCTAAAGAT
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
37 26 0.22
40 62 0.52
41 32 0.27
ACGTcount: A:0.59, C:0.15, G:0.01, T:0.25
Consensus pattern (41 bp):
AACATAAACTTAAATAATTAAATACAAATATCCAAACAAAC
Found at i:3311566 original size:22 final size:21
Alignment explanation
Indices: 3311525--3311566 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3311515 CGACACCGAC
*
3311525 AAAGCAAGTGAAATTCAAATG
1 AAAGCAAGTGAAATTAAAATG
*
3311546 AAAGCAAGATGAAGTTAAAAT
1 AAAGCAAG-TGAAATTAAAAT
3311567 TAAAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.19
Consensus pattern (21 bp):
AAAGCAAGTGAAATTAAAATG
Found at i:3314984 original size:29 final size:28
Alignment explanation
Indices: 3314926--3314983 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3314916 GATTAAAGAG
3314926 AATGCTTATTCCCTTGAAAAAACTCCAA
1 AATGCTTATTCCCTTGAAAAAACTCCAA
3314954 AATGCTTATTCCCTTGAAAAAACTCCAA
1 AATGCTTATTCCCTTGAAAAAACTCCAA
3314982 AA
1 AA
3314984 ACTCAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (28 bp):
AATGCTTATTCCCTTGAAAAAACTCCAA
Found at i:3318673 original size:10 final size:10
Alignment explanation
Indices: 3318658--3318691 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3318648 TGCCACTTCA
3318658 ACAAAAAACC
1 ACAAAAAACC
3318668 ACAAAAAACC
1 ACAAAAAACC
*
3318678 ACAACAAACC
1 ACAAAAAACC
3318688 -CAAA
1 ACAAA
3318692 CATGAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 3 0.14
10 19 0.86
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (10 bp):
ACAAAAAACC
Found at i:3319778 original size:2 final size:2
Alignment explanation
Indices: 3319773--3319810 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3319763 ATGCACACAC
3319773 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3319811 ACCAGTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3337213 original size:14 final size:14
Alignment explanation
Indices: 3337194--3337229 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3337184 TTGCTTCATT
3337194 AAAAACCTAATGGG
1 AAAAACCTAATGGG
*
3337208 AAAAACCCAATGGG
1 AAAAACCTAATGGG
3337222 AAAAACCT
1 AAAAACCT
3337230 TGACAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.19, G:0.17, T:0.11
Consensus pattern (14 bp):
AAAAACCTAATGGG
Found at i:3340795 original size:26 final size:24
Alignment explanation
Indices: 3340757--3340810 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3340747 AACATTAAAT
*
3340757 ATATAATTAAAACACATAATAAGAGC
1 ATATAATT-AAA-ACATAATAAGAAC
* *
3340783 ATATCATTTAAACATAATAAGAAC
1 ATATAATTAAAACATAATAAGAAC
3340807 ATAT
1 ATAT
3340811 TAAAACATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.64
25 2 0.08
26 7 0.28
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (24 bp):
ATATAATTAAAACATAATAAGAAC
Found at i:3341231 original size:18 final size:19
Alignment explanation
Indices: 3341195--3341232 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3341185 ACAAGTATTC
3341195 ATCCACTTCTTGATGGGTT
1 ATCCACTTCTTGATGGGTT
*
3341214 ATCCACTTC-TGGTGGGTT
1 ATCCACTTCTTGATGGGTT
3341232 A
1 A
3341233 GTGGGTTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (19 bp):
ATCCACTTCTTGATGGGTT
Found at i:3341279 original size:28 final size:28
Alignment explanation
Indices: 3341243--3341312 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
3341233 GTGGGTTACG
* *
3341243 GTATCCATCCACTTCTGGT-GCTTTGA-AA
1 GTATTCATCCACTTCTGGTAG-ATT-ACAA
* *
3341271 GTATTCATCTACTTGTGGTAGATTACAA
1 GTATTCATCCACTTCTGGTAGATTACAA
3341299 GTATTCATCCACTT
1 GTATTCATCCACTT
3341313 TTAGTGAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 33 0.94
29 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (28 bp):
GTATTCATCCACTTCTGGTAGATTACAA
Found at i:3341328 original size:18 final size:18
Alignment explanation
Indices: 3341305--3341351 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3341295 ACAAGTATTC
3341305 ATCCACTTTT-AGTGAGTA
1 ATCCACTTTTGA-TGAGTA
* * *
3341323 ATCCACATATGATGAGTT
1 ATCCACTTTTGATGAGTA
3341341 ATCCACTTTTG
1 ATCCACTTTTG
3341352 GTGGATTATC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (18 bp):
ATCCACTTTTGATGAGTA
Found at i:3341445 original size:25 final size:25
Alignment explanation
Indices: 3341427--3341485 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
3341417 TTCTGGTAGG
3341427 AAAATTATCTTTAGATTCTAATAGT
1 AAAATTATCTTTAGATTCTAATAGT
3341452 AAAATTATCTTTAGATTCTAATAGT
1 AAAATTATCTTTAGATTCTAATAGT
3341477 AAAATTATC
1 AAAATTATC
3341486 CATCCACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (25 bp):
AAAATTATCTTTAGATTCTAATAGT
Found at i:3341692 original size:59 final size:59
Alignment explanation
Indices: 3341609--3341731 Score: 174
Period size: 59 Copynumber: 2.1 Consensus size: 59
3341599 CAACATTTTC
* * * * *
3341609 CATATCCATGATCATAATTTTTAAATAATGTGACATTCACTTCAGGGAATAGATAGATT
1 CATAACCATGACCATAATTATTAAATAATGTCACATTCACTTCAGGGAATAGATAAATT
* *
3341668 CATAACCATGACCATAATTATTAAATAATGTCACATTCATTTCAGGGAATGGATAAATT
1 CATAACCATGACCATAATTATTAAATAATGTCACATTCACTTCAGGGAATAGATAAATT
*
3341727 TATAA
1 CATAA
3341732 TTTTTTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (59 bp):
CATAACCATGACCATAATTATTAAATAATGTCACATTCACTTCAGGGAATAGATAAATT
Found at i:3347123 original size:102 final size:102
Alignment explanation
Indices: 3346961--3347150 Score: 310
Period size: 102 Copynumber: 1.9 Consensus size: 102
3346951 TCAAAACCGA
*
3346961 TTCATGCATTGTAATTTCCTATAAAAACATGGTCATTAGCTTATAAATTGTTTATTCAATAATAA
1 TTCATGCATTGTAATTTCCTATAAAAACATGATCATTAGCTTATAAATTGTTTATTCAATAATAA
* * *
3347026 TTGAAAGGCTAAATATGCAAATACTCATTGAAATTGG
66 CTCAAAGGCTAAATATGAAAATACTCATTGAAATTGG
* *
3347063 TTCATGCATTGTAATTTCCTATACAAGA-ATGATTATTAGCTTATAAATTGTTTATTCAATAATA
1 TTCATGCATTGTAATTTCCTATA-AAAACATGATCATTAGCTTATAAATTGTTTATTCAATAATA
3347127 ACTCAAAGGCTAAATATGAAAATA
65 ACTCAAAGGCTAAATATGAAAATA
3347151 AGCTCTCGAC
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 78 0.96
103 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (102 bp):
TTCATGCATTGTAATTTCCTATAAAAACATGATCATTAGCTTATAAATTGTTTATTCAATAATAA
CTCAAAGGCTAAATATGAAAATACTCATTGAAATTGG
Found at i:3354127 original size:45 final size:44
Alignment explanation
Indices: 3354076--3354208 Score: 142
Period size: 45 Copynumber: 2.9 Consensus size: 44
3354066 AAAAATAGTC
3354076 AAACTTCCACTTTGATTGGCCAAATCAAAAGTACTAGAATCTCTT
1 AAACTTCCACTTTGATTGGCCAAATCAAAA-TACTAGAATCTCTT
* * *
3354121 AAACTTCCA-TTTTAGTTGGCCAAACCAAAAATACTAGAATCTTTTT
1 AAACTTCCACTTTGA-TTGGCCAAATC-AAAATACTAGAATC-TCTT
* * * * *
3354167 ACACTTTCACTTTGGTTGGCTAAATCAAATATACTAAAATCT
1 AAACTTCCACTTTGATTGGCCAAATCAAA-ATACTAGAATCT
3354209 TTTACTCTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
44 4 0.05
45 33 0.45
46 33 0.45
47 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (44 bp):
AAACTTCCACTTTGATTGGCCAAATCAAAATACTAGAATCTCTT
Found at i:3354201 original size:46 final size:45
Alignment explanation
Indices: 3354076--3354211 Score: 157
Period size: 46 Copynumber: 3.0 Consensus size: 45
3354066 AAAAATAGTC
* *
3354076 AAACTTCCACTTTGATTGGCCAAATCAAAAGTACTAGAATC-TCTT
1 AAACTTCCACTTTGGTTGGCCAAATCAAAA-TACTAGAATCTTTTT
* * *
3354121 AAACTTCCATTTTAGTTGGCCAAACCAAAAATACTAGAATCTTTTT
1 AAACTTCCACTTTGGTTGGCCAAATC-AAAATACTAGAATCTTTTT
* * * *
3354167 ACACTTTCACTTTGGTTGGCTAAATCAAATATACTAAAATCTTTT
1 AAACTTCCACTTTGGTTGGCCAAATCAAA-ATACTAGAATCTTTT
3354212 ACTCTTTTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
45 35 0.46
46 41 0.54
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (45 bp):
AAACTTCCACTTTGGTTGGCCAAATCAAAATACTAGAATCTTTTT
Found at i:3364029 original size:37 final size:35
Alignment explanation
Indices: 3363956--3364038 Score: 121
Period size: 37 Copynumber: 2.3 Consensus size: 35
3363946 GAATCATGAG
** *
3363956 AACAACTCCAACAAGTAAAGTACTACTTCATGCAA
1 AACAACTAGAACAAGTAAAGTACTACTTCATACAA
3363991 AACAACTAGAACAAGTAAACAGTACTACTTCATACAA
1 AACAACTAGAACAAGT-AA-AGTACTACTTCATACAA
3364028 AACAACTAGAA
1 AACAACTAGAA
3364039 TAAATGGAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 14 0.33
36 2 0.05
37 27 0.63
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.18
Consensus pattern (35 bp):
AACAACTAGAACAAGTAAAGTACTACTTCATACAA
Found at i:3366251 original size:102 final size:102
Alignment explanation
Indices: 3366069--3366325 Score: 290
Period size: 102 Copynumber: 2.5 Consensus size: 102
3366059 TTTATCACTT
* * * * * *
3366069 ATACTTTGGCTGCAATTATATTATACTATTGGTCGCAAGCTTTATTGCTAATTCTTTTGCCATAG
1 ATACTTTGGCTGCAATGATATTATGCTATTGGTCACAAGCTTTATCGCTCATTCTTTTGCCATAA
* * *
3366134 TTCATCACTTTTATTTCAGTC-GCAAGCTTTACT-GCTC
66 TTCATCACTTATATTTCA-ACAACAAGCTTTA-TGGCTC
* *
3366171 ATACTTTGGTTGCAATGACATTATGCTATTGGTCACAAGCTTTATCGCTCATTC-TTTGACCATA
1 ATACTTTGGCTGCAATGATATTATGCTATTGGTCACAAGCTTTATCGCTCATTCTTTTG-CCATA
*
3366235 ATTCATCA-TTCATATTTCAACAACTAGCTTTATGGCTC
65 ATTCATCACTT-ATATTTCAACAACAAGCTTTATGGCTC
* * * *
3366273 ATGA-TTTGGCTGTAATGATGTTATGTTATTGGTCATAAGCTTTATCGCTCATT
1 AT-ACTTTGGCTGCAATGATATTATGCTATTGGTCACAAGCTTTATCGCTCATT
3366326 TTCTTGGCCC
Statistics
Matches: 132, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
101 8 0.06
102 123 0.93
103 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (102 bp):
ATACTTTGGCTGCAATGATATTATGCTATTGGTCACAAGCTTTATCGCTCATTCTTTTGCCATAA
TTCATCACTTATATTTCAACAACAAGCTTTATGGCTC
Found at i:3367914 original size:34 final size:35
Alignment explanation
Indices: 3367876--3367947 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
3367866 AGAACAACTC
*
3367876 GAACAAGTGAAGTACTATTTCAC-AAAAACAATTA
1 GAACAAGTGAAGTACTACTTCACGAAAAACAATTA
* *
3367910 GAACAAGTGAAGTACTACTTCACGTAGAACAATTA
1 GAACAAGTGAAGTACTACTTCACGAAAAACAATTA
3367945 GAA
1 GAA
3367948 TAAATGGAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 22 0.65
35 12 0.35
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.22
Consensus pattern (35 bp):
GAACAAGTGAAGTACTACTTCACGAAAAACAATTA
Found at i:3371609 original size:34 final size:33
Alignment explanation
Indices: 3371571--3371647 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 33
3371561 TTTCCAAGCT
* *
3371571 CAAGCACAACCCTT-ACAATGCTTTTTTATGGGAG
1 CAAGCACAA--CTTAACAATGCTTTTTTATAGAAG
3371605 CAAGCACAACTTACACAATGCTTTTTTATAGAAG
1 CAAGCACAACTTA-ACAATGCTTTTTTATAGAAG
3371639 CAAGCACAA
1 CAAGCACAA
3371648 GCCACATAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 3 0.08
34 36 0.92
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (33 bp):
CAAGCACAACTTAACAATGCTTTTTTATAGAAG
Found at i:3372225 original size:21 final size:21
Alignment explanation
Indices: 3372173--3372252 Score: 99
Period size: 21 Copynumber: 3.9 Consensus size: 21
3372163 TATTAAGATC
*
3372173 GCCAAGTCTCTATA-CTTTGT
1 GCCAAGTCTCTATACCTTTGA
* * *
3372193 GTCAAGTATCTATACCTTCGA
1 GCCAAGTCTCTATACCTTTGA
*
3372214 GCCAAGTCTCTATACTTTTGA
1 GCCAAGTCTCTATACCTTTGA
*
3372235 GCCAAATCTCTATACCTT
1 GCCAAGTCTCTATACCTT
3372253 AAAGTGAAGT
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
20 12 0.24
21 37 0.76
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (21 bp):
GCCAAGTCTCTATACCTTTGA
Found at i:3372532 original size:21 final size:21
Alignment explanation
Indices: 3372506--3372545 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3372496 TAAAAAATCA
* *
3372506 TTCAAATAATTTCAAAGATTG
1 TTCAAACAAGTTCAAAGATTG
3372527 TTCAAACAAGTTCAAAGAT
1 TTCAAACAAGTTCAAAGAT
3372546 CATTAAAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (21 bp):
TTCAAACAAGTTCAAAGATTG
Found at i:3375668 original size:20 final size:20
Alignment explanation
Indices: 3375645--3375688 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3375635 AAAATAAAAA
3375645 AAACACAAAAGTAAAGAAAG
1 AAACACAAAAGTAAAGAAAG
*
3375665 AAACACAAAAGTAGAGAAAG
1 AAACACAAAAGTAAAGAAAG
3375685 AAAC
1 AAAC
3375689 TAAATATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.68, C:0.11, G:0.16, T:0.05
Consensus pattern (20 bp):
AAACACAAAAGTAAAGAAAG
Found at i:3380244 original size:29 final size:29
Alignment explanation
Indices: 3380211--3380268 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3380201 GAAAGATAGA
3380211 AAGGTTCCTATTATCTTTGGAAGACCTTT
1 AAGGTTCCTATTATCTTTGGAAGACCTTT
3380240 AAGGTTCCTATTATCTTTGGAAGACCTTT
1 AAGGTTCCTATTATCTTTGGAAGACCTTT
3380269 CTTATGCACA
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:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (29 bp):
AAGGTTCCTATTATCTTTGGAAGACCTTT
Found at i:3386180 original size:17 final size:17
Alignment explanation
Indices: 3386150--3386182 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3386140 CTCTTGATAA
3386150 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
3386167 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
3386183 TTATTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:3386383 original size:30 final size:29
Alignment explanation
Indices: 3386343--3386454 Score: 113
Period size: 28 Copynumber: 3.9 Consensus size: 29
3386333 TAATTAAAAT
* *
3386343 AAAAATAT-TTTATCGTGTCTAAATTGAG
1 AAAAATATATTTTTCTTGTCTAAATTGAG
* * *
3386371 AAAAATATA-TTTTCTTATCTAGATTAAG
1 AAAAATATATTTTTCTTGTCTAAATTGAG
3386399 ACAAAATATATTTTTCTTGTCTTAAATTGAG
1 A-AAAATATATTTTTCTTGTC-TAAATTGAG
* * *
3386430 ACAAACATA-TTTTCTTGTCTGAATT
1 AAAAATATATTTTTCTTGTCTAAATT
3386455 ATGATCAACT
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
28 28 0.41
29 18 0.26
30 15 0.22
31 8 0.12
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (29 bp):
AAAAATATATTTTTCTTGTCTAAATTGAG
Found at i:3386407 original size:29 final size:29
Alignment explanation
Indices: 3386344--3386548 Score: 161
Period size: 29 Copynumber: 7.1 Consensus size: 29
3386334 AATTAAAATA
* *
3386344 AAAATAT-TTTATCGTGTCTAAATTGAGA-
1 AAAATATATTT-TCTTGTCTAAATTAAGAC
* *
3386372 AAAATATATTTTCTTATCTAGATTAAGAC
1 AAAATATATTTTCTTGTCTAAATTAAGAC
*
3386401 AAAATATATTTTTCTTGTCTTAAATTGAGAC
1 AAAATATA-TTTTCTTGTC-TAAATTAAGAC
* * *
3386432 -AAACATATTTTCTTGTCTGAATTATGATC
1 AAAATATATTTTCTTGTCTAAATTAAGA-C
* *
3386461 -AACTCTGA-TTTCTTGTCTAAATTAAGAC
1 AAAATAT-ATTTTCTTGTCTAAATTAAGAC
* * * *
3386489 -AATTATGTTTTCTTATCTAAATTAACAC
1 AAAATATATTTTCTTGTCTAAATTAAGAC
* * * *
3386517 ATAACATGTTTTCTTGTTTAAATTAAGAC
1 AAAATATATTTTCTTGTCTAAATTAAGAC
3386546 AAA
1 AAA
3386549 TATGTTAAAA
Statistics
Matches: 141, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
28 50 0.35
29 66 0.47
30 16 0.11
31 9 0.06
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (29 bp):
AAAATATATTTTCTTGTCTAAATTAAGAC
Found at i:3386530 original size:57 final size:56
Alignment explanation
Indices: 3386358--3386551 Score: 174
Period size: 57 Copynumber: 3.4 Consensus size: 56
3386348 TATTTTATCG
* * * * * *
3386358 TGTCTAAATTGAGAAAAATATATTTTCTTATCTAGATTAAGACAAAATATATTTTTCT
1 TGTCTAAATTAAGACAAATATATTTTCTTATCTAAATTAA-ACATAACAT-GTTTTCT
* * * * ** * *
3386416 TGTCTTAAATTGAGACAAACATATTTTCTTGTCTGAATT-ATGATCAACTCTGATTTCT
1 TGTC-TAAATTAAGACAAATATATTTTCTTATCTAAATTAAACAT-AAC-ATGTTTTCT
* *
3386474 TGTCTAAATTAAGACAATTATGTTTTCTTATCTAAATTAACACATAACATGTTTTCT
1 TGTCTAAATTAAGACAAATATATTTTCTTATCTAAATTAA-ACATAACATGTTTTCT
*
3386531 TGTTTAAATTAAGACAAATAT
1 TGTCTAAATTAAGACAAATAT
3386552 GTTAAAACTG
Statistics
Matches: 107, Mismatches: 24, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
57 55 0.51
58 20 0.19
59 32 0.30
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (56 bp):
TGTCTAAATTAAGACAAATATATTTTCTTATCTAAATTAAACATAACATGTTTTCT
Found at i:3388333 original size:18 final size:18
Alignment explanation
Indices: 3388310--3388352 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3388300 AGCTAAATGG
3388310 TGAAAAAGG-TAGAAAAGA
1 TGAAAAAGGAT-GAAAAGA
* *
3388328 TGAAAAATGATGAAAAGT
1 TGAAAAAGGATGAAAAGA
3388346 TGAAAAA
1 TGAAAAA
3388353 AATGATTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.16
Consensus pattern (18 bp):
TGAAAAAGGATGAAAAGA
Found at i:3392132 original size:51 final size:52
Alignment explanation
Indices: 3392044--3392197 Score: 161
Period size: 51 Copynumber: 2.9 Consensus size: 52
3392034 AAACAAAACA
* *
3392044 TTTCTTGATTTTCCTAATGTTTT-GATGAAATCAAGAAATTTTAGAAGAATT-
1 TTTCTTGATTTTCCTAATGTTTTGGA-AAAATAAAGAAATTTTAGAAGAATTG
* * * *
3392095 TTTTTTTATTTTCCTAATGTTTTGGAAAAAGT-GAGAAATTTTAGGAGAAATTG
1 TTTCTTGATTTTCCTAATGTTTTGGAAAAA-TAAAGAAATTTTAGAAG-AATTG
* ** *
3392148 TTTCTTGATTTTCCCAACATTTTGGAAAAAATAAAGAAATTTTAAAAGAA
1 TTTCTTGATTTTCCTAATGTTTTGG-AAAAATAAAGAAATTTTAGAAGAA
3392198 AACATTTCTT
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
51 37 0.44
52 7 0.08
53 23 0.27
54 17 0.20
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (52 bp):
TTTCTTGATTTTCCTAATGTTTTGGAAAAATAAAGAAATTTTAGAAGAATTG
Found at i:3392171 original size:53 final size:52
Alignment explanation
Indices: 3392044--3392243 Score: 156
Period size: 53 Copynumber: 3.8 Consensus size: 52
3392034 AAACAAAACA
* * ** *
3392044 TTTCTTGATTTT-CCTAATGTTTTGATGAAATCAAGAAATTTTAGAAG-AATT
1 TTTCTTGATTTTCCCAAAT-TTTGGAAAAAATAAAGAAATTTTAGAAGAAATT
* * * * * * *
3392095 TTTTTTTATTTTCCTAATGTTTTGGAAAAAGT-GAGAAATTTTAGGAGAAATT
1 TTTCTTGATTTTCCCAA-ATTTTGGAAAAAATAAAGAAATTTTAGAAGAAATT
* **
3392147 GTTTCTTGATTTTCCCAACATTTTGGAAAAAATAAAGAAATTTTAAAAGAAAACA
1 -TTTCTTGATTTTCCCAA-ATTTTGGAAAAAATAAAGAAATTTTAGAAG-AAATT
* * *
3392202 TTTCTTGATTTTCTCAAATTTTTGACGAAAATAAA-AAATTTT
1 TTTCTTGATTTTCCCAAATTTTGGA-AAAAATAAAGAAATTTT
3392244 TAAAAAACTT
Statistics
Matches: 117, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
51 23 0.20
52 14 0.12
53 41 0.35
54 36 0.31
55 3 0.03
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.42
Consensus pattern (52 bp):
TTTCTTGATTTTCCCAAATTTTGGAAAAAATAAAGAAATTTTAGAAGAAATT
Found at i:3392198 original size:54 final size:53
Alignment explanation
Indices: 3392044--3392248 Score: 159
Period size: 54 Copynumber: 3.9 Consensus size: 53
3392034 AAACAAAACA
* * ** * *
3392044 TTTCTTGATTTTCCTAATGTTTT-GATGAAATCAAGAAATTTTAGAAG-AATT
1 TTTCTTGATTTTCCCAATATTTTGGAAAAAATAAAGAAATTTTAAAAGAAATT
* * * * * * **
3392095 TTTTTTTATTTTCCTAATGTTTTGGAAAAAGT-GAGAAATTTTAGGAGAAATT
1 TTTCTTGATTTTCCCAATATTTTGGAAAAAATAAAGAAATTTTAAAAGAAATT
* **
3392147 GTTTCTTGATTTTCCCAACATTTTGGAAAAAATAAAGAAATTTTAAAAGAAAACA
1 -TTTCTTGATTTTCCCAATATTTTGGAAAAAATAAAGAAATTTTAAAAG-AAATT
* * *
3392202 TTTCTTGATTTTCTCAA-ATTTTTGACGAAAATAAA-AAATTTTTAAAA
1 TTTCTTGATTTTCCCAATATTTTGGA-AAAAATAAAGAAA-TTTTAAAA
3392249 AACTTGATTG
Statistics
Matches: 126, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
51 34 0.27
52 9 0.07
53 36 0.29
54 44 0.35
55 3 0.02
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (53 bp):
TTTCTTGATTTTCCCAATATTTTGGAAAAAATAAAGAAATTTTAAAAGAAATT
Found at i:3398404 original size:18 final size:19
Alignment explanation
Indices: 3398374--3398410 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3398364 TGAATTTGGG
*
3398374 TATTTTTGAAAAGTTAGGA
1 TATTTTTGAAAAGCTAGGA
3398393 TATTTTTG-AAAGCTAGGA
1 TATTTTTGAAAAGCTAGGA
3398411 AATAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.41
Consensus pattern (19 bp):
TATTTTTGAAAAGCTAGGA
Found at i:3401390 original size:61 final size:61
Alignment explanation
Indices: 3401293--3401412 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 61
3401283 TCAAATGAAG
3401293 TGTTGAGGAAAATTGTAGTCTTAGGCATTTTTTGATTAATTTCTCAAGTTTAAATTGTCAT
1 TGTTGAGGAAAATTGTAGTCTTAGGCATTTTTTGATTAATTTCTCAAGTTTAAATTGTCAT
3401354 TGTTGAGGAAAATTGTAGTCTTAGGC-TTTTTCTGATTAATTTCTCAAGTTTAAATTGTC
1 TGTTGAGGAAAATTGTAGTCTTAGGCATTTTT-TGATTAATTTCTCAAGTTTAAATTGTC
3401413 GTTCTTATCA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
60 5 0.09
61 53 0.91
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (61 bp):
TGTTGAGGAAAATTGTAGTCTTAGGCATTTTTTGATTAATTTCTCAAGTTTAAATTGTCAT
Found at i:3406721 original size:15 final size:15
Alignment explanation
Indices: 3406701--3406730 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3406691 TTTGGGATGC
3406701 AAAATTTCTTCACTT
1 AAAATTTCTTCACTT
3406716 AAAATTTCTTCACTT
1 AAAATTTCTTCACTT
3406731 TTGTCCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATTTCTTCACTT
Found at i:3416570 original size:35 final size:34
Alignment explanation
Indices: 3416501--3416733 Score: 200
Period size: 35 Copynumber: 6.7 Consensus size: 34
3416491 CATTTGATTA
* * *
3416501 AAATTGTTTAATTAAGTT-GT-GCGTAATTAATT
1 AAATTATTTAATTAAGTTATTGGCCTAATTAATT
*
3416533 AAATTGTTTAATTAAGTTATTGGACCTAATTAATT
1 AAATTATTTAATTAAGTTATTGG-CCTAATTAATT
** * * *
3416568 AAATTAAATAATTAAATTATTGAGCTTAATTGATT
1 AAATTATTTAATTAAGTTATTG-GCCTAATTAATT
* * *
3416603 AAATTTGTTTAATTAAGTCATTGGGCCTAATTGATT
1 AAA-TTATTTAATTAAGTTATT-GGCCTAATTAATT
* * *
3416639 AAAATTATTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTATTTAATTAAGTTATT-GGCCTAATTAATT
* *
3416675 AAATTATTTAATTAAGTTGTTAGGCCTAATTGATT
1 AAATTATTTAATTAAGTTATT-GGCCTAATTAATT
***
3416710 AAATTAAGCAATTAAGTTAATTGG
1 AAATTATTTAATTAAGTT-ATTGG
3416734 GCTTCTTAAG
Statistics
Matches: 165, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
32 18 0.11
33 1 0.01
34 1 0.01
35 88 0.53
36 53 0.32
37 4 0.02
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (34 bp):
AAATTATTTAATTAAGTTATTGGCCTAATTAATT
Found at i:3416687 original size:107 final size:103
Alignment explanation
Indices: 3416494--3416714 Score: 264
Period size: 107 Copynumber: 2.1 Consensus size: 103
3416484 TCTCAAGCAT
* * * * *
3416494 TTGATTAAAATTGTTTAATTAAGTTGTGCGTAATTAATTAAATTGTTTAATTAAGTTATTGGACC
1 TTGATTAAATTTGTTTAATTAAGTTGGGCCTAATTAATTAAATTATTTAATTAAATTATTGGACC
*
3416559 TAATTAATTAAATTAAATAATTAAATTATT-GAGCTTAA
66 TAATTAATTAAATTAAATAATTAAATTATTAG-GCCTAA
* *
3416597 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTGTTG
1 TTGATTAAATTTGTTTAATTAAG---TTGGGCCTAATTAATT-AAATTATTTAATTAAATTATTG
* * ** * *
3416662 GGCTTAATTAATTAAATTATTTAATTAAGTTGTTAGGCCTAA
62 GACCTAATTAATTAAATTAAATAATTAAATTATTAGGCCTAA
3416704 TTGATTAAATT
1 TTGATTAAATT
3416715 AAGCAATTAA
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
103 22 0.22
106 13 0.13
107 63 0.64
108 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46
Consensus pattern (103 bp):
TTGATTAAATTTGTTTAATTAAGTTGGGCCTAATTAATTAAATTATTTAATTAAATTATTGGACC
TAATTAATTAAATTAAATAATTAAATTATTAGGCCTAA
Found at i:3416734 original size:71 final size:69
Alignment explanation
Indices: 3416524--3416737 Score: 266
Period size: 71 Copynumber: 3.0 Consensus size: 69
3416514 AAGTTGTGCG
*
3416524 TAATTAATTAAATTGTTTAATTAAGTTATTGGACCTAATTAATTAAATTAAATAATTAAATTATT
1 TAATTAATTAAATTGTTTAATTAAGTTATTGG-CCTAATTGATTAAATTAAATAATTAAATTATT
*
3416589 GAGCT
65 GGGCT
* * ** *
3416594 TAATTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTATTTAATTAAATTG
1 TAATTAATTAAA-TTGTTTAATTAAGTTATT-GGCCTAATTGATT-AAATTAAATAATTAAATTA
3416659 TTGGGCT
63 TTGGGCT
* * ** *
3416666 TAATTAATTAAATTATTTAATTAAGTTGTTAGGCCTAATTGATTAAATTAAGCAATTAAGTTAAT
1 TAATTAATTAAATTGTTTAATTAAGTTATT-GGCCTAATTGATTAAATTAAATAATTAAATT-AT
3416731 TGGGCT
64 TGGGCT
3416737 T
1 T
3416738 CTTAAGAACT
Statistics
Matches: 123, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
70 25 0.20
71 63 0.51
72 35 0.28
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (69 bp):
TAATTAATTAAATTGTTTAATTAAGTTATTGGCCTAATTGATTAAATTAAATAATTAAATTATTG
GGCT
Found at i:3418083 original size:48 final size:48
Alignment explanation
Indices: 3418007--3418107 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 48
3417997 ATTGAACACT
*
3418007 TAACCAATGTGCAGCAATTTATACTCAAGTGTCAACAAAAATAGGCAA
1 TAACTAATGTGCAGCAATTTATACTCAAGTGTCAACAAAAATAGGCAA
* *
3418055 TAACTAATGTGCAGCAATTTATACTCAAGTGTCAATAAAAATAGGCAG
1 TAACTAATGTGCAGCAATTTATACTCAAGTGTCAACAAAAATAGGCAA
3418103 TAACT
1 TAACT
3418108 TTCTCTATTC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (48 bp):
TAACTAATGTGCAGCAATTTATACTCAAGTGTCAACAAAAATAGGCAA
Found at i:3419504 original size:27 final size:27
Alignment explanation
Indices: 3419467--3419519 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3419457 TTGTCCACTC
*
3419467 GTGTGTCACTCCATATTTTGCCAACAT
1 GTGTGTCACTCCATATTTTGCAAACAT
3419494 GTGTGTCACTCCATATTTTGCAAACA
1 GTGTGTCACTCCATATTTTGCAAACA
3419520 GAGTTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (27 bp):
GTGTGTCACTCCATATTTTGCAAACAT
Found at i:3426754 original size:24 final size:24
Alignment explanation
Indices: 3426727--3426781 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
3426717 ATTCAAGTAT
3426727 TATTTTTTC-TTTT-TCTTTCTATTC
1 TATTTTTTCATTTTGT-TTTCTA-TC
3426751 TA-TTTTTCATTTTGTTTTCTATC
1 TATTTTTTCATTTTGTTTTCTATC
*
3426774 TTTTTTTT
1 TATTTTTT
3426782 TTGAATTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 9 0.33
24 17 0.63
25 1 0.04
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (24 bp):
TATTTTTTCATTTTGTTTTCTATC
Found at i:3426763 original size:23 final size:23
Alignment explanation
Indices: 3426730--3426780 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3426720 CAAGTATTAT
*
3426730 TTTTTC-TTTTTCTTTCTATTCTA
1 TTTTTCATTTTGCTTTCTA-TCTA
* *
3426753 TTTTTCATTTTGTTTTCTATCTT
1 TTTTTCATTTTGCTTTCTATCTA
3426776 TTTTT
1 TTTTT
3426781 TTTGAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.08, C:0.14, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTTCATTTTGCTTTCTATCTA
Found at i:3426928 original size:49 final size:49
Alignment explanation
Indices: 3426875--3426988 Score: 228
Period size: 49 Copynumber: 2.3 Consensus size: 49
3426865 AAATAGATAA
3426875 ATGGTTGTTGAGATAAATTAGATGAAAATTAAAATAATATTTATTGATT
1 ATGGTTGTTGAGATAAATTAGATGAAAATTAAAATAATATTTATTGATT
3426924 ATGGTTGTTGAGATAAATTAGATGAAAATTAAAATAATATTTATTGATT
1 ATGGTTGTTGAGATAAATTAGATGAAAATTAAAATAATATTTATTGATT
3426973 ATGGTTGTTGAGATAA
1 ATGGTTGTTGAGATAA
3426989 TATTGTTCAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.40
Consensus pattern (49 bp):
ATGGTTGTTGAGATAAATTAGATGAAAATTAAAATAATATTTATTGATT
Found at i:3427299 original size:21 final size:21
Alignment explanation
Indices: 3427275--3427315 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3427265 AAATTATAAA
3427275 TTTT-ATATTATATAAAAATTC
1 TTTTAATATT-TATAAAAATTC
*
3427296 TTTTAATATTTTTAAAAATT
1 TTTTAATATTTATAAAAATT
3427316 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAATATTTATAAAAATTC
Found at i:3428754 original size:73 final size:72
Alignment explanation
Indices: 3428633--3428774 Score: 189
Period size: 73 Copynumber: 1.9 Consensus size: 72
3428623 GTAGTGCTGC
* *
3428633 CTTGGCTAAGAGATGGCCGAGAGCAAGAATCAATTCTCTTTTGGTAGAGAGAAGACTGAGATGGG
1 CTTGGCTAAGAGATGGCCGAGAGCAAGAATCAATTCGCTTCT-GTAGAGAGAAGACTGAGATGGG
3428698 ATAGAAGA
65 ATAGAAGA
* * *
3428706 CTTGGCTACGAGATGGCCGAGAGCACGAATC-ATTCCGGCTTCCT-TAGAGAGAAGCCTGAGATG
1 CTTGGCTAAGAGATGGCCGAGAGCAAGAATCAATT-C-GCTT-CTGTAGAGAGAAGACTGAGATG
3428769 GGATAG
63 GGATAG
3428775 GAGCAAACGG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
72 3 0.05
73 54 0.89
74 3 0.05
75 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (72 bp):
CTTGGCTAAGAGATGGCCGAGAGCAAGAATCAATTCGCTTCTGTAGAGAGAAGACTGAGATGGGA
TAGAAGA
Found at i:3432921 original size:35 final size:35
Alignment explanation
Indices: 3432870--3432940 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
3432860 ATAGCAATAA
3432870 ATTATACCATACAACATACTTATAATGAACTTTAT
1 ATTATACCATACAACATACTTATAATGAACTTTAT
* *
3432905 ATTATACCATATAACATACTTATAATGAGCTTTAT
1 ATTATACCATACAACATACTTATAATGAACTTTAT
3432940 A
1 A
3432941 CTCTGTAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.38
Consensus pattern (35 bp):
ATTATACCATACAACATACTTATAATGAACTTTAT
Found at i:3437531 original size:19 final size:19
Alignment explanation
Indices: 3437491--3437532 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3437481 AAAATTTTGA
** *
3437491 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
3437510 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
3437529 AATA
1 AATA
3437533 CTAATGTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:3446317 original size:512 final size:513
Alignment explanation
Indices: 3445352--3446380 Score: 1790
Period size: 512 Copynumber: 2.0 Consensus size: 513
3445342 GAGATTATAA
* **
3445352 TTGAGGTGAACATTCGAGAACATATATCCAAATAGTGGTTCTTATAACATTAACATCACTTTTAA
1 TTGAGGTGAACATCCGAGAACATATATCCAAATAGTGGAGCTTATAACATTAACATCACTTTTAA
3445417 TGATTTCAAAAATATTGGTGATTAATTTGGGCCTAGTAGATTGATGAATTAGCTAGTCATCATAT
66 TGATTTCAAAAATATTGGTGATTAATTTGGGCCTAGTAGATTGATGAATTAGCTAGTCATCATAT
* * * *
3445482 CTTGATGCTTAAAAGATTAGATCTAGAGGATTAAATCACTAATTGGATGAAATATGGAACTAAGG
131 CTTGATACTTAAAAGATTAGATCTAGAGGATTAAATCAATAATTGGATGAAATATGAAACCAAGG
*
3445547 GACAAAATTGACGTAAAAGGTAAAACGGTAATTTTATCTTTTGTCATTGGATGGTTATGATGGCT
196 GACAAAATTGACGTAAAAGGTAAAACGGTAATTCTATCTTTTGTCATTGGATGGTTATGATGGCT
* * *
3445612 CACAATATAAGTTTTGTAATTAGACAACTAATAATTAATATCAAGAATTAACTCATTTCTTGTAA
261 CACAATATAAGCTTTGCAATTAGACAACTAATAATTAATATCAAGAATTAACTCATTTCTTATAA
3445677 TTATAGTTAATCCAAGAGTGCAACCAAGAATCTATAGTGGAGTGATTTCAAGGTTAATAAGCTTG
326 TTATAGTTAATCCAAGAGTGCAACCAAGAATCTATAGTGGAGTGATTTCAAGGTTAATAAGCTTG
* *
3445742 AATGATTTTAATGAGATTAAAAATAATTCTAAGTTTATTAAAGCTTGGAGTATCTATTTCCAAAT
391 AATGATTTTAATAAGATTAAAAATAATTCTAAGTTTATTAAAGCTTGGAATATCTATTTCCAAAT
*
3445807 AGACTCCCCACTTACCTTTGTAGAATTCAACTTGTTTAAGTTGGAATGCATGTTTTAT
456 AGACTCCCCACTTACCTTTGTAGAATTCAACTTGTTTAAGTTAGAATGCATGTTTTAT
3445865 TTGAGGTGAACATCCGAGAACATATATCCAAATAGTGGAGCTTATAACATTAACATCACTTTTAA
1 TTGAGGTGAACATCCGAGAACATATATCCAAATAGTGGAGCTTATAACATTAACATCACTTTTAA
* *
3445930 TGATTTCAAAAATATTGGTGATTAATTTGGGCCTAGTAGATTGATGAGTTAGCTATTCATCATAT
66 TGATTTCAAAAATATTGGTGATTAATTTGGGCCTAGTAGATTGATGAATTAGCTAGTCATCATAT
* * *
3445995 CTTGATACTTAAAAGATTAGATTTAGAGTATTAAATCAATAATTGGATGAAATCTGAAACCAAGG
131 CTTGATACTTAAAAGATTAGATCTAGAGGATTAAATCAATAATTGGATGAAATATGAAACCAAGG
* * * * *
3446060 GATAAAA-TGACTTAAAAGGTAAAATGGTAATTCTATTTTTTGTCATTGGATGGTTATGATGGTT
196 GACAAAATTGACGTAAAAGGTAAAACGGTAATTCTATCTTTTGTCATTGGATGGTTATGATGGCT
* *
3446124 CACAATATAAGCTTTGCAATTGGACAACTAATAATTAATATCAAGAATTGACTCATTTCTTATAA
261 CACAATATAAGCTTTGCAATTAGACAACTAATAATTAATATCAAGAATTAACTCATTTCTTATAA
*
3446189 TTATAGTTAATCCAAGAGTGCAACCATGAATCTATAGTGGAGTGATTTCAAGGTTAATAAGCTTG
326 TTATAGTTAATCCAAGAGTGCAACCAAGAATCTATAGTGGAGTGATTTCAAGGTTAATAAGCTTG
*
3446254 AATGATTTTAATAAGATTAAAAATAATTCTAAGTTTATTAGAGCTTGGAATATCTATTTCCAAAT
391 AATGATTTTAATAAGATTAAAAATAATTCTAAGTTTATTAAAGCTTGGAATATCTATTTCCAAAT
*
3446319 AGACTCCCCACTTAGCTTTGTAGAATTCAACTTGTTTAAGTTAGAATGCATGTTTTAT
456 AGACTCCCCACTTACCTTTGTAGAATTCAACTTGTTTAAGTTAGAATGCATGTTTTAT
3446377 TTGA
1 TTGA
3446381 TTAATTAAAT
Statistics
Matches: 487, Mismatches: 29, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
512 298 0.61
513 189 0.39
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (513 bp):
TTGAGGTGAACATCCGAGAACATATATCCAAATAGTGGAGCTTATAACATTAACATCACTTTTAA
TGATTTCAAAAATATTGGTGATTAATTTGGGCCTAGTAGATTGATGAATTAGCTAGTCATCATAT
CTTGATACTTAAAAGATTAGATCTAGAGGATTAAATCAATAATTGGATGAAATATGAAACCAAGG
GACAAAATTGACGTAAAAGGTAAAACGGTAATTCTATCTTTTGTCATTGGATGGTTATGATGGCT
CACAATATAAGCTTTGCAATTAGACAACTAATAATTAATATCAAGAATTAACTCATTTCTTATAA
TTATAGTTAATCCAAGAGTGCAACCAAGAATCTATAGTGGAGTGATTTCAAGGTTAATAAGCTTG
AATGATTTTAATAAGATTAAAAATAATTCTAAGTTTATTAAAGCTTGGAATATCTATTTCCAAAT
AGACTCCCCACTTACCTTTGTAGAATTCAACTTGTTTAAGTTAGAATGCATGTTTTAT
Found at i:3446470 original size:30 final size:29
Alignment explanation
Indices: 3446430--3446562 Score: 103
Period size: 30 Copynumber: 4.7 Consensus size: 29
3446420 TTGTCTTTAT
* *
3446430 TTAG-AAAAAAAACATGTTTTGTTTTAAA
1 TTAGAAAAAAAAACATGTTTTATCTTAAA
*
3446458 TTAGATAAAAAAAACATGTTTTATCTTAAT
1 TTAGA-AAAAAAAACATGTTTTATCTTAAA
* * * * *
3446488 TTAGAGAAGAAAACATG-TCTGTCTTAAT
1 TTAGAAAAAAAAACATGTTTTATCTTAAA
* * *
3446516 TTAG--ACAAAAACATGTTTTCTCTTAAT
1 TTAGAAAAAAAAACATGTTTTATCTTAAA
* * *
3446543 TTAGACAAGAAAACTTGTTT
1 TTAGAAAAAAAAACATGTTT
3446563 GTCTTAATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
26 9 0.10
27 13 0.15
28 17 0.20
29 21 0.24
30 26 0.30
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (29 bp):
TTAGAAAAAAAAACATGTTTTATCTTAAA
Found at i:3446540 original size:55 final size:56
Alignment explanation
Indices: 3446419--3446657 Score: 221
Period size: 57 Copynumber: 4.2 Consensus size: 56
3446409 CTTTTACAGG
* * * * * *
3446419 TTTGTCTTTATTTAGA-AAAAAAACATGTTTTGTTTTAAATTAGATAAAAAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATG-TTTGTCTTAATTTAG--ACAAGAAACATGT
* * *
3446477 TTTATCTTAATTTAGAGAAGAAAACATGTCTGTCTTAATTTAGACAA-AAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAGACAAGAAACATGT
* * * *
3446532 TTTCTCTTAATTTAGACAAGAAAACTTGTTTGTCTTAATTTAAGACAAGAAAAATAT
1 TTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTT-AGACAAGAAACATGT
* * * * * * * * *
3446589 GTTGTCATAATCTACATAAGAAAATATATTTGTCTCAATTTGGACAAGATAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAGACAAGA-AACATGT
3446646 TTTGTCTTAATT
1 TTTGTCTTAATT
3446658 AAAGATAAGA
Statistics
Matches: 148, Mismatches: 29, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
55 45 0.30
56 16 0.11
57 51 0.34
58 26 0.18
59 10 0.07
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (56 bp):
TTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAGACAAGAAACATGT
Found at i:3446577 original size:29 final size:28
Alignment explanation
Indices: 3446418--3446657 Score: 200
Period size: 28 Copynumber: 8.5 Consensus size: 28
3446408 ACTTTTACAG
* *
3446418 GTTTGTCTTTATTTAGA-AAAAAAACAT
1 GTTTGTCTTAATTTAGACAAGAAAACAT
* * * *
3446445 GTTTTGTTTTAAATTAGATAAAAAAAACAT
1 G-TTTGTCTTAATTTAGA-CAAGAAAACAT
* *
3446475 GTTTTATCTTAATTTAGAGAAGAAAACAT
1 G-TTTGTCTTAATTTAGACAAGAAAACAT
*
3446504 GTCTGTCTTAATTTAGAC-A-AAAACAT
1 GTTTGTCTTAATTTAGACAAGAAAACAT
* *
3446530 GTTTTCTCTTAATTTAGACAAGAAAACTT
1 G-TTTGTCTTAATTTAGACAAGAAAACAT
3446559 GTTTGTCTTAATTTAAGACAAGAAAA-AT
1 GTTTGTCTTAATTT-AGACAAGAAAACAT
* * * * * *
3446587 ATGTTGTCATAATCTACATAAGAAAATAT
1 GT-TTGTCTTAATTTAGACAAGAAAACAT
* * * *
3446616 ATTTGTCTCAATTTGGACAAGATAACAT
1 GTTTGTCTTAATTTAGACAAGAAAACAT
3446644 GTTTTGTCTTAATT
1 G-TTTGTCTTAATT
3446658 AAAGATAAGA
Statistics
Matches: 172, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
26 8 0.05
27 17 0.10
28 69 0.40
29 53 0.31
30 25 0.15
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (28 bp):
GTTTGTCTTAATTTAGACAAGAAAACAT
Found at i:3449409 original size:27 final size:27
Alignment explanation
Indices: 3449353--3449421 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 27
3449343 AGATAGCAAG
3449353 TTACATGCCATGTTGGAAAAAAAAAATT
1 TTACATGCCATGTT-GAAAAAAAAAATT
*
3449381 TTACATGCCATGTT-AAAAAAAAATTTT
1 TTACATGCCATGTTGAAAAAAAAA-ATT
3449408 TTACATGCCATGTT
1 TTACATGCCATGTT
3449422 TAAGGTGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 9 0.23
27 16 0.41
28 14 0.36
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
TTACATGCCATGTTGAAAAAAAAAATT
Found at i:3449424 original size:28 final size:27
Alignment explanation
Indices: 3449353--3449424 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
3449343 AGATAGCAAG
*
3449353 TTACATGCCATGTTGGAAAAAAAAAATT
1 TTACATGCCATGTT-TAAAAAAAAAATT
*
3449381 TTACATGCCATG-TTAAAAAAAAATTTT
1 TTACATGCCATGTTTAAAAAAAAA-ATT
3449408 TTACATGCCATGTTTAA
1 TTACATGCCATGTTTAA
3449425 GGTGCTTAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 9 0.22
27 15 0.38
28 16 0.40
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (27 bp):
TTACATGCCATGTTTAAAAAAAAAATT
Found at i:3449499 original size:126 final size:128
Alignment explanation
Indices: 3449262--3449500 Score: 297
Period size: 126 Copynumber: 1.9 Consensus size: 128
3449252 GTTGTATACT
* * *
3449262 ATGTTGAAAAAATAATTTTATTACACGCCATGCTTAAGGTGTTTAACTATAACAATTTATGTCCT
1 ATGTTGAAAAAAAAATTTTATTACACGCCATGCTTAAGGTGCTTAACTACAACAATTTATGTCCT
* * * *
3449327 AGTATAATACAAAAATAGATAGCAAGTTACATGCCATGTTGGAAAAAAAAAATTTTACATGCC
66 AGTATAATACAAAAATAGAGAGCAAGATACACGCCATGATGGAAAAAAAAAATTTTACATGCC
* * * * *
3449390 ATGTT-AAAAAAAAATTTT-TTACATGCCATGTTTAAGGTGCTTAACTCCAACAGTTTATGTCTT
1 ATGTTGAAAAAAAAATTTTATTACACGCCATGCTTAAGGTGCTTAACTACAACAATTTATGTCCT
* * * *
3449453 AGTGA-AATATAAAGATAGAGATCAAGATACACGTCAT-ATGGAAAAAAA
66 AGT-ATAATACAAAAATAGAGAGCAAGATACACGCCATGATGGAAAAAAA
3449501 TTTGTTACAC
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
125 10 0.11
126 66 0.70
127 13 0.14
128 5 0.05
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (128 bp):
ATGTTGAAAAAAAAATTTTATTACACGCCATGCTTAAGGTGCTTAACTACAACAATTTATGTCCT
AGTATAATACAAAAATAGAGAGCAAGATACACGCCATGATGGAAAAAAAAAATTTTACATGCC
Found at i:3450128 original size:27 final size:27
Alignment explanation
Indices: 3450095--3450167 Score: 146
Period size: 27 Copynumber: 2.7 Consensus size: 27
3450085 TTCCCACTAA
3450095 TGTTACATGCCAAGGCATGAATCACTT
1 TGTTACATGCCAAGGCATGAATCACTT
3450122 TGTTACATGCCAAGGCATGAATCACTT
1 TGTTACATGCCAAGGCATGAATCACTT
3450149 TGTTACATGCCAAGGCATG
1 TGTTACATGCCAAGGCATG
3450168 TTTTTCAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (27 bp):
TGTTACATGCCAAGGCATGAATCACTT
Found at i:3453860 original size:22 final size:22
Alignment explanation
Indices: 3453830--3453889 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
3453820 CAAATCAATA
* ***
3453830 AGTTATTAGGCATTGCAAGCTT
1 AGTTTTTAGGCATTGCAAGAGC
*
3453852 AGTTTTTAGGCATTACAAGAGC
1 AGTTTTTAGGCATTGCAAGAGC
3453874 AGTTTTTAGGCATTGC
1 AGTTTTTAGGCATTGC
3453890 TTGACTTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (22 bp):
AGTTTTTAGGCATTGCAAGAGC
Found at i:3462030 original size:59 final size:58
Alignment explanation
Indices: 3461939--3462050 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 58
3461929 CTATTAACTC
* *
3461939 GTCATGCAATGCCTAAAACCAGTTACGCAAACCCTAAGTCATGCCATGCCTAATACTT
1 GTCATGCAATGCCTAAAACCAGTTACGCAAACCCTAAGTCACGCAATGCCTAATACTT
*
3461997 GTCATGC-ATGCCCTACCAACCA-TTCACGCAAACCCTAAGTCACGCAATGCCTAA
1 GTCATGCAATG-CCTA-AAACCAGTT-ACGCAAACCCTAAGTCACGCAATGCCTAA
3462051 CCCTAACCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
57 3 0.06
58 13 0.27
59 32 0.67
ACGTcount: A:0.32, C:0.33, G:0.13, T:0.21
Consensus pattern (58 bp):
GTCATGCAATGCCTAAAACCAGTTACGCAAACCCTAAGTCACGCAATGCCTAATACTT
Found at i:3463457 original size:26 final size:26
Alignment explanation
Indices: 3463406--3463462 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
3463396 CCACTCCATT
**
3463406 TCTTA-CTCATGTGGGATTTGTCACA
1 TCTTACCTCATGTGGGATTCATCACA
* *
3463431 TCTTACCTTATGTGGGATTCATGACA
1 TCTTACCTCATGTGGGATTCATCACA
*
3463457 TTTTAC
1 TCTTAC
3463463 TCTACCCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (26 bp):
TCTTACCTCATGTGGGATTCATCACA
Found at i:3464209 original size:15 final size:15
Alignment explanation
Indices: 3464189--3464218 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3464179 ACAAAGAGAA
*
3464189 GAAGAAAAGAAAAAG
1 GAAGAAAAAAAAAAG
3464204 GAAGAAAAAAAAAAG
1 GAAGAAAAAAAAAAG
3464219 ATAAGTCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAAAAAAG
Found at i:3475968 original size:77 final size:77
Alignment explanation
Indices: 3475880--3476041 Score: 247
Period size: 77 Copynumber: 2.1 Consensus size: 77
3475870 TTTTCTTCTA
* *
3475880 TTTTTTCATCACAATTTTACACC-CACAAACTTATTTCTTTGTATTGTAAGTAGTGGGGTGATTT
1 TTTTTTCATCACAATTTTACACCAC-CAAACTTATTTCTTTGTACTGTAAGTAGTAGGGTGATTT
*
3475944 -TTTTTACTAAATT
65 GTTTTCACT-AATT
* *
3475957 TTTTTTCATCACAATTTTACACCACCAAATTTATTTCTTTGTACTGTAGGTAGTAGGGTGATTTG
1 TTTTTTCATCACAATTTTACACCACCAAACTTATTTCTTTGTACTGTAAGTAGTAGGGTGATTTG
3476022 TTTTCACTAATT
66 TTTTCACTAATT
3476034 TTTTTTCA
1 TTTTTTCA
3476042 ATAACGTCAC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
77 70 0.90
78 8 0.10
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.49
Consensus pattern (77 bp):
TTTTTTCATCACAATTTTACACCACCAAACTTATTTCTTTGTACTGTAAGTAGTAGGGTGATTTG
TTTTCACTAATT
Found at i:3483579 original size:36 final size:36
Alignment explanation
Indices: 3483495--3483613 Score: 98
Period size: 36 Copynumber: 3.3 Consensus size: 36
3483485 AAAAGCTCTC
*
3483495 ACAATAGTTTTTTAAT-GAGATCAAA-CAATAACCCTT
1 ACAATAGTTTTTTAATGGA-AT-AAAGTAATAACCCTT
* * *
3483531 AGACTAGCTTTTTAATGGAATAAAGTAATAACCCTT
1 ACAATAGTTTTTTAATGGAATAAAGTAATAACCCTT
* * * * * * *
3483567 ACAATAATTTTTTTACGGGATCAAGTGATAACCTTT
1 ACAATAGTTTTTTAATGGAATAAAGTAATAACCCTT
*
3483603 ACAATGGTTTT
1 ACAATAGTTTT
3483614 ACTAGGCTCA
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
35 3 0.05
36 60 0.92
37 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (36 bp):
ACAATAGTTTTTTAATGGAATAAAGTAATAACCCTT
Found at i:3486184 original size:35 final size:35
Alignment explanation
Indices: 3486156--3486238 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 35
3486146 GGTTGATCAC
*
3486156 AGGAAAAACCATTGTTGAAGGTTGTGGTTGAGCCT
1 AGGAAAAACCATTATTGAAGGTTGTGGTTGAGCCT
** * *
3486191 TTGAAAAACCATTATTGAAGGTTGTGGCTGAGCTT
1 AGGAAAAACCATTATTGAAGGTTGTGGTTGAGCCT
* *
3486226 ATGAAAAGCCATT
1 AGGAAAAACCATT
3486239 GTAAAAGCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (35 bp):
AGGAAAAACCATTATTGAAGGTTGTGGTTGAGCCT
Found at i:3487647 original size:73 final size:73
Alignment explanation
Indices: 3487570--3487705 Score: 191
Period size: 73 Copynumber: 1.9 Consensus size: 73
3487560 GTCATCTCTA
* * * * *
3487570 TCTTTGAACCTAGTTTCTAATAGTAGGCTCTTAGTTGACTAACAAACCTTCTTAGTCCATTAAAT
1 TCTTTGAACCTAGTTTCTAACAATAAGCTCTTAGTCGACTAACAAAACTTCTTAGTCCATTAAAT
3487635 TGTTTTTT
66 TGTTTTTT
* ** *
3487643 TCTTTGAACCTAGTTTTTGGCAATAAGCTCTTAGTCGACTAACAAAACTTCTTAGTCGATTAA
1 TCTTTGAACCTAGTTTCTAACAATAAGCTCTTAGTCGACTAACAAAACTTCTTAGTCCATTAA
3487706 GTGTTCTCTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 54 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (73 bp):
TCTTTGAACCTAGTTTCTAACAATAAGCTCTTAGTCGACTAACAAAACTTCTTAGTCCATTAAAT
TGTTTTTT
Found at i:3488302 original size:600 final size:601
Alignment explanation
Indices: 3487162--3488896 Score: 2413
Period size: 600 Copynumber: 2.9 Consensus size: 601
3487152 ATATATTCAA
* * *
3487162 AACCCAATCTTGATTAATCCCCTTAGAGTGTCTCACACACTCTAAGCAATCAAGGAGAAAAGAAA
1 AACCCAAGCTTGATTAATCCCCTTAGAGTGTCTCGCACACTCTAAGCAATCAAGGAGAAAAAAAA
* * * *
3487227 A-AAAGAAGTTCCTATGAACACTGATCTGATCTGAATGGTACAAGATGAAGTGTTTAACTCTATT
66 ATAAAGAAGTACCTATGATCACTAATCTGATCTGAATGGTACAAGATGAAGTGCTTAACTCTATT
* * * *
3487291 ACAAAGATTGAAGTGAAATGTAGAAAGTATGCAAAAAGTTTTTGCTATTTTTGAGCTCTTTTTGA
131 ACAAAGATTGGAGTGAAATGCAAAAAGTATGCAAAGAGTTTTTGCTATTTTTGAGCTCTTTTTGA
* *
3487356 TCTT-AGAAGCCTTCAAAACTAATTCATAGCCTTTGGGACTGCCTTATATACTTTGAAAATCAGC
196 TCTTGA-AAGCCTTCAAAACTAATTCATAGCCTTTGGGAGTGCCTTATATACTTTGAAAATTAGC
* * * * * * * *
3487420 TTTGATGGCTATTAGATAGATTCTGACCGTTGGAAACAATTTAGAGATAGTTCTAACAATTAATC
260 TTTGATGGCTGTTAGACAGATTCTGATCGTTGAAAATAGTTTGGAGATAGTTCTAGCAATTAATC
* * * *
3487485 TATCTTT-TAGCGTTCAAATTCAAATTTTCAAACAGAATGCTCTTAGTCGACCAACATTGTTATT
325 TGT-TTTCTAGCGTTCAAATTCAAATTTTCAAACAGAATGCTCTTAGTCGACTAACATTGCTACT
* * *
3487549 TAGTCGATTAAGTCATCTCTATCTTTGAACCTAGTTTCTAATAGTAGGCTCTTAGTTGACTAACA
389 TAGTCGATTAAGTCATCTCTGTCTTTGAACCTAGTTTCTGATAGTAGGCTCTTAGTCGACTAACA
* * * * * * * *
3487614 AACCTTCTTAGTCCATTAAATTGTTTTTTTCTTTGAACCTAGTTTTTGGCAATAAGCTCTTAGTC
454 AAACTTCTTAGTCGATTAAGTCGTTTTTATCTCTGAACCTAGTTTTTAGCAGTAAGCTCTTAGTC
* * *
3487679 GACTAACAAAACTTCTTAGTCGATTAAGTGTTCTCTGTCTCCCAATCTTAGGCTGAGTTAGAACC
519 GACTAACAAAACTTCTTAGTCGATTAAGTGTTCACTATCTCCCAATCTTAAGCTGAGTTAGAACC
3487744 TATACACTCAATCAAGCT
584 TATACACTCAATCAAGCT
* *
3487762 AACCCAAGCTTGATTAATCCCCTTAGAGTGTCTTGCACACTCTAAGCAATTAAGGAGAAAAAAAA
1 AACCCAAGCTTGATTAATCCCCTTAGAGTGTCTCGCACACTCTAAGCAATCAAGGAGAAAAAAAA
* * *
3487827 ATAAAAAAGTACCTATGATCACTAATCTGATCTAAATGGTACAAAATGAAGTGCTTAACTCTATT
66 ATAAAGAAGTACCTATGATCACTAATCTGATCTGAATGGTACAAGATGAAGTGCTTAACTCTATT
*
3487892 ACAAAGATTGGAGTGAAATGCATAAAGTATGCAAAGAGTTTTTGCTA-TTTTGAGCTCTTTTTGA
131 ACAAAGATTGGAGTGAAATGCAAAAAGTATGCAAAGAGTTTTTGCTATTTTTGAGCTCTTTTTGA
* * * * **
3487956 TCTTGAAAGTCTTTAAAACTGATTCATAGCTTTTGAAAGTGCCTTATATACTTTGAAAATTAGCT
196 TCTTGAAAGCCTTCAAAACTAATTCATAGCCTTTGGGAGTGCCTTATATACTTTGAAAATTAGCT
* * * *
3488021 CTGATGGCTGTTAGACAGATTCTGATTGTTGAAAATAGTTTGGAGACAGTTCTAGCCATTAATCT
261 TTGATGGCTGTTAGACAGATTCTGATCGTTGAAAATAGTTTGGAGATAGTTCTAGCAATTAATCT
* * * *
3488086 GTTTTCTAGCGTTCAAATTCAAATTTTCAGACAAAATGCTCTTAATGGACTAACATTGCTACTTA
326 GTTTTCTAGCGTTCAAATTCAAATTTTCAAACAGAATGCTCTTAGTCGACTAACATTGCTACTTA
* * * * * * * *
3488151 GTCAATTAAGTCATCTCTGTCTCTAAACTTAATTTCTGGTAGTAGGCTTTTAGTCGACTAATAAA
391 GTCGATTAAGTCATCTCTGTCTTTGAACCTAGTTTCTGATAGTAGGCTCTTAGTCGACTAACAAA
* * **
3488216 ACTTCTTAGTCGATTAAGTCATTTTTGTCTCTGAATCC-AGTTTCCAGCAGTAAGCTCTTAGTCG
456 ACTTCTTAGTCGATTAAGTCGTTTTTATCTCTGAA-CCTAGTTTTTAGCAGTAAGCTCTTAGTCG
* *
3488280 ACTAACAAAACTTCTTAGTCGATTAAGTGTTCACTATCTCTCAGTCTTAAGCTGAGTTAGAACCT
520 ACTAACAAAACTTCTTAGTCGATTAAGTGTTCACTATCTCCCAATCTTAAGCTGAGTTAGAACCT
3488345 ATACACTCAATCAAGCT
585 ATACACTCAATCAAGCT
* *
3488362 AACCCAAGCTTGATTAATCCCCTTAGAGTGTCTCGCACACTCTGAGCAATCAAGGAG-AAAAGAA
1 AACCCAAGCTTGATTAATCCCCTTAGAGTGTCTCGCACACTCTAAGCAATCAAGGAGAAAAAAAA
* * * * *
3488426 ATAAAGAAGTACCTGTGATCACTAACCTAATTTGAATGGTACAAGATGAAGTGCTTAACTTTATT
66 ATAAAGAAGTACCTATGATCACTAATCTGATCTGAATGGTACAAGATGAAGTGCTTAACTCTATT
* * * * * *
3488491 ATAAATATTGGAGTGAAATACAAAAAATATGCAGAGAGTTTTCGCTATTTTTGAGCTCTTTTTGA
131 ACAAAGATTGGAGTGAAATGCAAAAAGTATGCAAAGAGTTTTTGCTATTTTTGAGCTCTTTTTGA
* * *
3488556 TCTTGAAAGCCTTCAAAACAAATTCATAACCTTTGGGAGTGCCTTATATACTTTAAAAATTAGCT
196 TCTTGAAAGCCTTCAAAACTAATTCATAGCCTTTGGGAGTGCCTTATATACTTTGAAAATTAGCT
* * * * * **
3488621 TTGATAGCTGTTAAACAGATTATGATCGTTGAAAATGGTTTGGAGATAGTTTTAGCTGTTAATCT
261 TTGATGGCTGTTAGACAGATTCTGATCGTTGAAAATAGTTTGGAGATAGTTCTAGCAATTAATCT
* * * * * *
3488686 GTCTTCTAACG-TCAAATTTAAATTTTCAAACAGAATGCTCTCAGTCAACTAACACTGCTACTTA
326 GTTTTCTAGCGTTCAAATTCAAATTTTCAAACAGAATGCTCTTAGTCGACTAACATTGCTACTTA
* ** *
3488750 GTTGATTAAGTCATCTCTGTCTTTGAACCCCGTTTCTGATAGTAGGCTCTTAGTCTACTAACAAA
391 GTCGATTAAGTCATCTCTGTCTTTGAACCTAGTTTCTGATAGTAGGCTCTTAGTCGACTAACAAA
* *
3488815 ACTTCTTAGTCGATTAAGTCGTTTCTATCTCTGAACCTAGTTTTTAGCAGTAAGCGCTTAGTCGA
456 ACTTCTTAGTCGATTAAGTCGTTTTTATCTCTGAACCTAGTTTTTAGCAGTAAGCTCTTAGTCGA
*
3488880 CTAACAAAACTTTTTAG
521 CTAACAAAACTTCTTAG
3488897 ATTAGCTTTT
Statistics
Matches: 991, Mismatches: 138, Indels: 13
0.87 0.12 0.01
Matches are distributed among these distances:
598 2 0.00
599 276 0.28
600 611 0.62
601 102 0.10
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (601 bp):
AACCCAAGCTTGATTAATCCCCTTAGAGTGTCTCGCACACTCTAAGCAATCAAGGAGAAAAAAAA
ATAAAGAAGTACCTATGATCACTAATCTGATCTGAATGGTACAAGATGAAGTGCTTAACTCTATT
ACAAAGATTGGAGTGAAATGCAAAAAGTATGCAAAGAGTTTTTGCTATTTTTGAGCTCTTTTTGA
TCTTGAAAGCCTTCAAAACTAATTCATAGCCTTTGGGAGTGCCTTATATACTTTGAAAATTAGCT
TTGATGGCTGTTAGACAGATTCTGATCGTTGAAAATAGTTTGGAGATAGTTCTAGCAATTAATCT
GTTTTCTAGCGTTCAAATTCAAATTTTCAAACAGAATGCTCTTAGTCGACTAACATTGCTACTTA
GTCGATTAAGTCATCTCTGTCTTTGAACCTAGTTTCTGATAGTAGGCTCTTAGTCGACTAACAAA
ACTTCTTAGTCGATTAAGTCGTTTTTATCTCTGAACCTAGTTTTTAGCAGTAAGCTCTTAGTCGA
CTAACAAAACTTCTTAGTCGATTAAGTGTTCACTATCTCCCAATCTTAAGCTGAGTTAGAACCTA
TACACTCAATCAAGCT
Found at i:3488850 original size:73 final size:73
Alignment explanation
Indices: 3488746--3488896 Score: 169
Period size: 73 Copynumber: 2.1 Consensus size: 73
3488736 AACACTGCTA
* * * * * * * *
3488746 CTTAGTTGATTAAGTCATCTCTGTCTTTGAACCCCGTTTCTGA-TAGTAGGCTCTTAGTCTACTA
1 CTTAGTCGATTAAGTCATCTCTATCTCTGAACCCAGTTT-TGAGCAGTAAGCGCTTAGTCGACTA
3488810 ACAAAACTT
65 ACAAAACTT
* * * *
3488819 CTTAGTCGATTAAGTCGTTTCTATCTCTGAACCTAGTTTTTAGCAGTAAGCGCTTAGTCGACTAA
1 CTTAGTCGATTAAGTCATCTCTATCTCTGAACCCAGTTTTGAGCAGTAAGCGCTTAGTCGACTAA
3488884 CAAAACTT
66 CAAAACTT
*
3488892 TTTAG
1 CTTAG
3488897 ATTAGCTTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
72 2 0.03
73 62 0.97
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (73 bp):
CTTAGTCGATTAAGTCATCTCTATCTCTGAACCCAGTTTTGAGCAGTAAGCGCTTAGTCGACTAA
CAAAACTT
Found at i:3490271 original size:35 final size:35
Alignment explanation
Indices: 3490232--3490349 Score: 157
Period size: 35 Copynumber: 3.4 Consensus size: 35
3490222 TTGATCTCGG
* *
3490232 GAAAAACCATTATTGAAGGTTGTGGTAGAGCCTTT
1 GAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTT
* * **
3490267 GAAAAGCCATTGTTAAAGGTCATGGTTGAGCCTTT
1 GAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTT
*
3490302 GAAAAATCATTGTTGAAGGTTGTGGTTGAG-CTTAT
1 GAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTT-T
3490337 GAAAAACCATTGT
1 GAAAAACCATTGT
3490350 AAAAGCTTGG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
34 3 0.04
35 67 0.96
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.32
Consensus pattern (35 bp):
GAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTT
Found at i:3496205 original size:10 final size:10
Alignment explanation
Indices: 3496190--3496220 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3496180 TTATGGGAAT
3496190 ACACACGCAC
1 ACACACGCAC
3496200 ACACACGCAC
1 ACACACGCAC
*
3496210 ACACACACAC
1 ACACACGCAC
3496220 A
1 A
3496221 GGGTATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.48, G:0.06, T:0.00
Consensus pattern (10 bp):
ACACACGCAC
Found at i:3512358 original size:33 final size:34
Alignment explanation
Indices: 3512305--3512371 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
3512295 CTTAATAAAT
*
3512305 ATAACTATTTGAATAATTATATTATT-AAAGAAA
1 ATAACTATTTAAATAATTATATTATTAAAAGAAA
* *
3512338 ATAAGTATTTAAATAGTTATATTATTAAAAGAAA
1 ATAACTATTTAAATAATTATATTATTAAAAGAAA
3512372 CAAATCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.39
Consensus pattern (34 bp):
ATAACTATTTAAATAATTATATTATTAAAAGAAA
Found at i:3513182 original size:41 final size:41
Alignment explanation
Indices: 3513120--3513199 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
3513110 TTCCAACTGC
*
3513120 TTCCAGCTAATTATGAATTGCAGACTTCGTCTGCTTGATGT
1 TTCCAGCTAATTATGAATTGCAGACTTCCTCTGCTTGATGT
**
3513161 TTCCAGCTAATTATGCCTTGCAGACTTCCTCTGCTTGAT
1 TTCCAGCTAATTATGAATTGCAGACTTCCTCTGCTTGAT
3513200 TTAAAGGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (41 bp):
TTCCAGCTAATTATGAATTGCAGACTTCCTCTGCTTGATGT
Found at i:3521811 original size:2 final size:2
Alignment explanation
Indices: 3521804--3521854 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3521794 ATTTACTTTT
3521804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3521846 TA TA TA TA T
1 TA TA TA TA T
3521855 TAGACTGGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3528801 original size:18 final size:18
Alignment explanation
Indices: 3528753--3528801 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 18
3528743 CTCCACACCT
3528753 TTTTCTCCTTTCTCTTTCTC
1 TTTT-TCCTTT-TCTTTCTC
*
3528773 TTTTTCTTTTTC-TTCTC
1 TTTTTCCTTTTCTTTCTC
3528790 TTTTGTCCTTTT
1 TTTT-TCCTTTT
3528802 ATTGTTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 8 0.31
19 5 0.19
20 4 0.15
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTCCTTTTCTTTCTC
Found at i:3544289 original size:21 final size:21
Alignment explanation
Indices: 3544265--3544304 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3544255 GAATTTCTCT
*
3544265 TTTTCATGT-GATGCTTCTTCA
1 TTTTC-TGTAGATCCTTCTTCA
3544286 TTTTCTGTAGATCCTTCTT
1 TTTTCTGTAGATCCTTCTT
3544305 GGTTAAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTTCTGTAGATCCTTCTTCA
Found at i:3548677 original size:16 final size:16
Alignment explanation
Indices: 3548651--3548683 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3548641 AAAATCAATA
3548651 TTTATTTAATCAAGTTT
1 TTTATTTAATCAA-TTT
3548668 TTTA-TTAATCAATTT
1 TTTATTTAATCAATTT
3548683 T
1 T
3548684 CATACATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTATTTAATCAATTT
Found at i:3548876 original size:7 final size:7
Alignment explanation
Indices: 3548864--3548889 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3548854 TACAACATAT
3548864 TTTCTCC
1 TTTCTCC
3548871 TTTCTCC
1 TTTCTCC
3548878 TTTCTCC
1 TTTCTCC
3548885 TTTCT
1 TTTCT
3548890 TTCCTTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTCTCC
Found at i:3553086 original size:44 final size:43
Alignment explanation
Indices: 3553012--3553271 Score: 331
Period size: 43 Copynumber: 5.9 Consensus size: 43
3553002 TTTTCTATAG
* * ** *
3553012 ATATATTTTGTTATCTAGTTGAACTTAACTACACTCATTTAGGA
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTA-GT
* ** *
3553056 ATACATTTTGTTATCTAGTTGAAATCAACTAGGCTCTTTTAGT
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTAGT
* *
3553099 ATATATTTTTTTATCTAGTTGATCTCAACTAGGCTCCTTTAGT
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTAGT
* *
3553142 ATATATTTTATTATCTAGTTGATCTCAACTAGGCTTATTTAGAT
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTAG-T
*
3553186 ATATATTTTTTTATCTATAGTTGATCTCAACTAGGCTCATTTAGGT
1 ATATATTTTGTTATC--TAGTTGATCTCAACTAGGCTCATTTA-GT
* *
3553232 ATATATTTTGTTATCTAGTTGATCTTAACTAGACTCATTT
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTT
3553272 TGGGTTTTAT
Statistics
Matches: 192, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
43 78 0.41
44 73 0.38
46 40 0.21
47 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (43 bp):
ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTAGT
Done.