Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 30 of 190
Found at i:5170962 original size:2 final size:2
Alignment explanation
Indices: 5170955--5170998 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5170945 TAGAGGATGA
*
5170955 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5170997 AG
1 AG
5170999 TAACGGAAAG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5171628 original size:24 final size:24
Alignment explanation
Indices: 5171586--5171708 Score: 111
Period size: 24 Copynumber: 5.0 Consensus size: 24
5171576 CGGCCCAATA
* *
5171586 TATCTATAAATTATGATTTATAATC
1 TATCTAT-ATTTATAATTTATAATC
* *
5171611 TATCTGTATTTATAATTTATAATT
1 TATCTATATTTATAATTTATAATC
* *
5171635 TATCTATGATATATATTATCTATAATC
1 TATCTAT-AT-T-TATAATTTATAATC
* * *
5171662 TATCCATATCTATAATTTAAAATC
1 TATCTATATTTATAATTTATAATC
**
5171686 TATCTATATTTATGTTTTATAAT
1 TATCTATATTTATAATTTATAAT
5171709 ATATTTAATA
Statistics
Matches: 77, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
24 49 0.64
25 8 0.10
26 3 0.04
27 17 0.22
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (24 bp):
TATCTATATTTATAATTTATAATC
Found at i:5172017 original size:22 final size:21
Alignment explanation
Indices: 5171984--5172036 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 21
5171974 TTTTTTATTT
5171984 ATATATTTATATTTTAAAAAATA
1 ATAT-TTTATATTTT-AAAAATA
*
5172007 ATATTTTATATTTTAAAATTA
1 ATATTTTATATTTTAAAAATA
5172028 ATATTTTAT
1 ATATTTTAT
5172037 TAATTTCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 15 0.52
22 10 0.34
23 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTTTATATTTTAAAAATA
Found at i:5180690 original size:19 final size:18
Alignment explanation
Indices: 5180643--5180683 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 18
5180633 ATGTTTATAG
5180643 AATAAATTAAATAATTAATT
1 AATAAATT--ATAATTAATT
5180663 AATAAATTATAACTTAATT
1 AATAAATTATAA-TTAATT
5180682 AA
1 AA
5180684 ATAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATTATAATTAATT
Found at i:5181075 original size:20 final size:19
Alignment explanation
Indices: 5181050--5181089 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5181040 AAAATTTTTT
5181050 ATAATAA-ATAATTAAAATTA
1 ATAATAATAT-ATT-AAATTA
5181070 ATAATAATATATTAAATTA
1 ATAATAATATATTAAATTA
5181089 A
1 A
5181090 GAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 10 0.53
21 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATAATATATTAAATTA
Found at i:5181078 original size:19 final size:20
Alignment explanation
Indices: 5181050--5181089 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
5181040 AAAATTTTTT
5181050 ATAATAAATA-ATTAAAATTA
1 ATAATAAATATATT-AAATTA
5181070 ATAAT-AATATATTAAATTA
1 ATAATAAATATATTAAATTA
5181089 A
1 A
5181090 GAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAATAAATATATTAAATTA
Found at i:5182766 original size:15 final size:17
Alignment explanation
Indices: 5182721--5182769 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
5182711 CTGTATATGA
*
5182721 AATTTTAAGTAGTAT-T
1 AATTTTCAGTAGTATAT
*
5182737 -TTTTTCAGTAGTATAT
1 AATTTTCAGTAGTATAT
5182753 AATTTTC-GTA-TATAT
1 AATTTTCAGTAGTATAT
5182768 AA
1 AA
5182770 AGAATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 19 0.68
16 4 0.14
17 5 0.18
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (17 bp):
AATTTTCAGTAGTATAT
Found at i:5186274 original size:24 final size:24
Alignment explanation
Indices: 5186217--5186294 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
5186207 AAAAATTAAT
* * **
5186217 ATTTATTTATTAATAAAATAATATT
1 ATTTATATATTAATAATAT-ATAAA
5186242 ATTTAATATATTAATAATATATAAA
1 ATTT-ATATATTAATAATATATAAA
* **
5186267 ATTTATATACTAATAATGCATAAA
1 ATTTATATATTAATAATATATAAA
5186291 ATTT
1 ATTT
5186295 TAACTCAGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
24 21 0.47
25 11 0.24
26 13 0.29
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (24 bp):
ATTTATATATTAATAATATATAAA
Found at i:5187482 original size:13 final size:13
Alignment explanation
Indices: 5187456--5187508 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
5187446 TTAAAGAATA
* *
5187456 AAAATTAATTTTT
1 AAAATAAATATTT
5187469 AAAATAAATATTT
1 AAAATAAATATTT
*
5187482 AAAAATTAATATTT
1 -AAAATAAATATTT
5187496 AAAA-AAATTATTT
1 AAAATAAA-TATTT
5187509 GTTAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 20 0.59
14 12 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:5187488 original size:27 final size:27
Alignment explanation
Indices: 5187454--5187508 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
5187444 CATTAAAGAA
*
5187454 TAAAAATTAATTTTTAAAATAAA-TATT
1 TAAAAATTAATATTTAAAA-AAATTATT
5187481 TAAAAATTAATATTTAAAAAAATTATT
1 TAAAAATTAATATTTAAAAAAATTATT
5187508 T
1 T
5187509 GTTAATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAAAATTAATATTTAAAAAAATTATT
Found at i:5187505 original size:16 final size:14
Alignment explanation
Indices: 5187454--5187500 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
5187444 CATTAAAGAA
5187454 TAAAAATTAAT-TT
1 TAAAAATTAATATT
* *
5187467 TTAAAATAAATATT
1 TAAAAATTAATATT
5187481 TAAAAATTAATATT
1 TAAAAATTAATATT
5187495 TAAAAA
1 TAAAAA
5187501 AATTATTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 9 0.31
14 20 0.69
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAAATTAATATT
Found at i:5188152 original size:47 final size:47
Alignment explanation
Indices: 5188101--5188193 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
5188091 ACATAAAATA
* *
5188101 ATTAAATTAATCTTT-AAATTCAATCACCTGTTTATTTAATAATCAAT
1 ATTAAATTAAT-TTTCAAATTCAATCACCTGCTTATTCAATAATCAAT
*
5188148 ATTAAATTAATTTTCGAATTCAATCACCTGCTTATTCAATAATCAA
1 ATTAAATTAATTTTCAAATTCAATCACCTGCTTATTCAATAATCAA
5188194 CTTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
46 3 0.07
47 39 0.93
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (47 bp):
ATTAAATTAATTTTCAAATTCAATCACCTGCTTATTCAATAATCAAT
Found at i:5189336 original size:30 final size:31
Alignment explanation
Indices: 5189283--5189378 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 31
5189273 AATCAAAAGC
* * * *
5189283 TTAATTTGAATGAAAATATATATTTATAGAT
1 TTAATTTGAATAAAAATAAATATTTAAAAAT
5189314 TTAATTTG-ATAAAAATAAATATTTAAAAAT
1 TTAATTTGAATAAAAATAAATATTTAAAAAT
* * *
5189344 TTAA-TT-AATTCAAATTAAA-AATTAAAAAT
1 TTAATTTGAA-TAAAAATAAATATTTAAAAAT
5189373 TTAATT
1 TTAATT
5189379 AATTATAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
29 16 0.29
30 31 0.56
31 8 0.15
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (31 bp):
TTAATTTGAATAAAAATAAATATTTAAAAAT
Found at i:5189399 original size:29 final size:29
Alignment explanation
Indices: 5189338--5189413 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
5189328 ATAAATATTT
*
5189338 AAAAATTTAATTAATTCA-AATTAAAAATT
1 AAAAATTTAATTAATT-ATAATTAAAAATC
5189367 AAAAATTTAATTAATTATAA-TAAAATATC
1 AAAAATTTAATTAATTATAATTAAAA-ATC
* *
5189396 AAAAACTTAAATAATTAT
1 AAAAATTTAATTAATTAT
5189414 TAAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 6 0.14
29 36 0.86
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAAATTTAATTAATTATAATTAAAAATC
Found at i:5190520 original size:38 final size:37
Alignment explanation
Indices: 5190475--5190549 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
5190465 TCAAATATAA
*
5190475 AAATTTAATTTAATTGATGAATTAAATT-ATTTAAATTT
1 AAATTTAATTTAA-TAAT-AATTAAATTAATTTAAATTT
5190513 AAATTTAATTTAATAATAATTAAATTAAATTTAAATT
1 AAATTTAATTTAATAATAATTAAATT-AATTTAAATT
5190550 ATATTCTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 9 0.26
37 3 0.09
38 22 0.65
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (37 bp):
AAATTTAATTTAATAATAATTAAATTAATTTAAATTT
Found at i:5190535 original size:21 final size:21
Alignment explanation
Indices: 5190475--5190546 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
5190465 TCAAATATAA
*
5190475 AAATTTAATTTAATTGATGAATT
1 AAATTTAATTTAA-TAAT-AATT
5190498 AAA-TT-ATTT-A-AAT--TT
1 AAATTTAATTTAATAATAATT
5190513 AAATTTAATTTAATAATAATT
1 AAATTTAATTTAATAATAATT
*
5190534 AAATTAAATTTAA
1 AAATTTAATTTAA
5190547 ATTATATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
15 5 0.12
16 2 0.05
17 4 0.10
18 3 0.07
19 3 0.07
20 1 0.02
21 18 0.44
22 2 0.05
23 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AAATTTAATTTAATAATAATT
Found at i:5190550 original size:11 final size:11
Alignment explanation
Indices: 5190505--5190550 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
5190495 ATTAAATTAT
5190505 TTAAATTTAAA
1 TTAAATTTAAA
*
5190516 TTTAATTT-AA
1 TTAAATTTAAA
*
5190526 -TAATAATTAAA
1 TTAA-ATTTAAA
5190537 TTAAATTTAAA
1 TTAAATTTAAA
5190548 TTA
1 TTA
5190551 TATTCTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
9 2 0.07
10 5 0.18
11 18 0.64
12 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:5197095 original size:22 final size:22
Alignment explanation
Indices: 5197064--5197113 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5197054 TTTATTTAGT
* *
5197064 AAAA-AATTTATTAATCAATGA
1 AAAATAATTTACTAATCAATCA
*
5197085 AAAATAATTTACTAATCAATCT
1 AAAATAATTTACTAATCAATCA
5197107 AAAATAA
1 AAAATAA
5197114 GGTCTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATAATTTACTAATCAATCA
Found at i:5197358 original size:36 final size:37
Alignment explanation
Indices: 5197298--5197367 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
5197288 TAACATAATA
*
5197298 TTTTAATCTTAAATATTATTATTAA-AATATAATTATT
1 TTTTAATATTAAATATTATTATTAATAA-ATAATTATT
5197335 TTTTAATATT-AATAATT-TTATTAATAAATAATT
1 TTTTAATATTAAAT-ATTATTATTAATAAATAATT
5197368 TTAATATGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (37 bp):
TTTTAATATTAAATATTATTATTAATAAATAATTATT
Found at i:5197366 original size:25 final size:25
Alignment explanation
Indices: 5197338--5197420 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
5197328 AATTATTTTT
5197338 TAATATTAATAATTTTATTAATAAA
1 TAATATTAATAATTTTATTAATAAA
* *
5197363 TAATTTTAAT-ATGCTTTAATAATAAA
1 TAATATTAATAAT--TTTATTAATAAA
* *
5197389 T-ATATT-CTAATATT-TTAAT-AA
1 TAATATTAATAATTTTATTAATAAA
*
5197410 TTATATTAATA
1 TAATATTAATA
5197421 TTATTTGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
21 3 0.07
22 9 0.20
23 4 0.09
24 3 0.07
25 15 0.33
26 12 0.26
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (25 bp):
TAATATTAATAATTTTATTAATAAA
Found at i:5197370 original size:16 final size:17
Alignment explanation
Indices: 5197323--5197370 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
5197313 TTATTATTAA
*
5197323 AATATAATTATTTT-TT
1 AATATAATAATTTTATT
5197339 AATATTAATAATTTTATT
1 AATA-TAATAATTTTATT
5197357 AATA-AATAATTTTA
1 AATATAATAATTTTA
5197371 ATATGCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.48
17 9 0.31
18 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATAATAATTTTATT
Found at i:5197387 original size:26 final size:25
Alignment explanation
Indices: 5197344--5197410 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
5197334 TTTTTAATAT
* *
5197344 TAATAATTTTATTAATAAATA-ATTT
1 TAAT-ATTTTAATAATAAATATATTC
5197369 TAATATGCTTTAATAATAAATATATTC
1 TAATAT--TTTAATAATAAATATATTC
5197396 TAATATTTTAATAAT
1 TAATATTTTAATAAT
5197411 TATATTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 2 0.05
25 13 0.35
26 13 0.35
27 9 0.24
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (25 bp):
TAATATTTTAATAATAAATATATTC
Found at i:5198487 original size:21 final size:21
Alignment explanation
Indices: 5198436--5198487 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
5198426 AACAATTATT
5198436 ATTTATATTTATTAAAATATAA
1 ATTTA-ATTTATTAAAATATAA
*
5198458 ATATT-ATTTATTAATATAT-A
1 AT-TTAATTTATTAAAATATAA
5198478 ATTTACATTT
1 ATTTA-ATTT
5198488 TATTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 17 0.65
22 2 0.08
23 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAATTTATTAAAATATAA
Found at i:5198527 original size:15 final size:16
Alignment explanation
Indices: 5198484--5198529 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
5198474 TATAATTTAC
* *
5198484 ATTTTATTTTTTATTA
1 ATTTTATATATTATTA
5198500 ATTTTATATATTATTA
1 ATTTTATATATTATTA
*
5198516 TTTTTATA-ATTATT
1 ATTTTATATATTATT
5198530 TTAATTATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTATATATTATTA
Found at i:5202940 original size:284 final size:284
Alignment explanation
Indices: 5202430--5202972 Score: 1059
Period size: 284 Copynumber: 1.9 Consensus size: 284
5202420 TCCTCCTACC
5202430 AAATATATGTTCCCTCCTGGAGACTAACATTGGTTCCTTAAGAGATGGCCTGCAACCTGTCTTTC
1 AAATATATGTTCCCTCCTGGAGACTAACATTGGTTCCTTAAGAGATGGCCTGCAACCTGTCTTTC
*
5202495 TATAAGCGTCTTTCTTTTGATCACCCAGAAGTAATACAACCTCATATTCACAAACGATGGCAACA
66 TATAAGCGTCTTTCTTTTGATCACCCAGAAGCAATACAACCTCATATTCACAAACGATGGCAACA
5202560 CAGTAATCTGATTGCGGCTCGGTCTCACCATTGAATTTTGCAGCCTTGAGGTCCCAAACCACATC
131 CAGTAATCTGATTGCGGCTCGGTCTCACCATTGAATTTTGCAGCCTTGAGGTCCCAAACCACATC
5202625 AACAGTCGTACCATCAACAATAAAATGCTTGGACCCTTGTTTTCTCCAGAAATACCAGGACTTCT
196 AACAGTCGTACCATCAACAATAAAATGCTTGGACCCTTGTTTTCTCCAGAAATACCAGGACTTCT
5202690 GGAGACTAACATTGGTTCCTTAAG
261 GGAGACTAACATTGGTTCCTTAAG
5202714 AAATATATGTTCCCTCCTGGAGACTAACATTGGTTCCTTAAGAGATGGCCTGCAACCTGTCTTTC
1 AAATATATGTTCCCTCCTGGAGACTAACATTGGTTCCTTAAGAGATGGCCTGCAACCTGTCTTTC
*
5202779 TATAAGCGTCTTTCTTTTGATCACCCAGAAGCAATACAACCTCATCTTCACAAACGATGGCAACA
66 TATAAGCGTCTTTCTTTTGATCACCCAGAAGCAATACAACCTCATATTCACAAACGATGGCAACA
*
5202844 TAGTAATCTGATTGCGGCTCGGTCTCACCATTGAATTTTGCAGCCTTGAGGTCCCAAACCACATC
131 CAGTAATCTGATTGCGGCTCGGTCTCACCATTGAATTTTGCAGCCTTGAGGTCCCAAACCACATC
5202909 AACAGTCGTACCATCAACAATAAAATGCTTGGACCCTTGTTTTCTCCAGAAATACCAGGACTTC
196 AACAGTCGTACCATCAACAATAAAATGCTTGGACCCTTGTTTTCTCCAGAAATACCAGGACTTC
5202973 AGTTCAATTT
Statistics
Matches: 256, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
284 256 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (284 bp):
AAATATATGTTCCCTCCTGGAGACTAACATTGGTTCCTTAAGAGATGGCCTGCAACCTGTCTTTC
TATAAGCGTCTTTCTTTTGATCACCCAGAAGCAATACAACCTCATATTCACAAACGATGGCAACA
CAGTAATCTGATTGCGGCTCGGTCTCACCATTGAATTTTGCAGCCTTGAGGTCCCAAACCACATC
AACAGTCGTACCATCAACAATAAAATGCTTGGACCCTTGTTTTCTCCAGAAATACCAGGACTTCT
GGAGACTAACATTGGTTCCTTAAG
Found at i:5215223 original size:3 final size:3
Alignment explanation
Indices: 5215215--5215265 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
5215205 AAATTTATGC
5215215 ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA AT- ATA ATA AT-
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
5215259 ATA ATA A
1 ATA ATA A
5215266 ATATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5215238 original size:16 final size:16
Alignment explanation
Indices: 5215217--5215268 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
5215207 ATTTATGCAT
5215217 AATAATAATAATAATA
1 AATAATAATAATAATA
5215233 AATAATAATAATAATA
1 AATAATAATAATAATA
5215249 ATATAATAAT-ATAATA
1 A-ATAATAATAATAATA
5215265 AATA
1 AATA
5215269 TATATATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 3 0.09
16 24 0.69
17 8 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:5215239 original size:19 final size:20
Alignment explanation
Indices: 5215215--5215265 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
5215205 AAATTTATGC
5215215 ATAATAATAATAATAATA-A
1 ATAATAATAATAATAATATA
5215234 ATAATAATAATAATAATATA
1 ATAATAATAATAATAATATA
5215254 ATAAT-ATAATAA
1 ATAATAATAATAA
5215266 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAATAATAATAATATA
Found at i:5215575 original size:12 final size:13
Alignment explanation
Indices: 5215558--5215586 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5215548 ATTTTGTTAA
5215558 AAAAATAAAT-AT
1 AAAAATAAATAAT
5215570 AAAAATAAATAAT
1 AAAAATAAATAAT
5215583 AAAA
1 AAAA
5215587 TAATAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAATAAATAAT
Found at i:5218976 original size:23 final size:24
Alignment explanation
Indices: 5218925--5218973 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5218915 TATTTGGATT
* * *
5218925 TTAATTTTAATTTTTAATTTTTTG
1 TTAATTTCAATTTTCAATATTTTG
5218949 TTAATTTCAATTTTCAATATTTTG
1 TTAATTTCAATTTTCAATATTTTG
5218973 T
1 T
5218974 AATATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TTAATTTCAATTTTCAATATTTTG
Found at i:5219035 original size:18 final size:16
Alignment explanation
Indices: 5218977--5219040 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 16
5218967 ATTTTGTAAT
*
5218977 ATAAAAAATAAAAAATAG
1 ATAAAAAAT-AAAAA-AC
5218995 ATAAAAAATAAAAAAC
1 ATAAAAAATAAAAAAC
* *
5219011 TTTAAAAATGACAAAAAC
1 ATAAAAAAT-A-AAAAAC
*
5219029 ATAAAAATTAAA
1 ATAAAAAATAAA
5219041 TTAAGTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 10 0.26
17 7 0.18
18 21 0.55
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (16 bp):
ATAAAAAATAAAAAAC
Found at i:5219489 original size:16 final size:16
Alignment explanation
Indices: 5219470--5219542 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 16
5219460 TAAATTGTAA
*
5219470 GAAAATTAAAATACAT
1 GAAAAGTAAAATACAT
*
5219486 GAAAAGCAAAATACAT
1 GAAAAGTAAAATACAT
** * *
5219502 -AAATTTAAAGTGCAT
1 GAAAAGTAAAATACAT
* *
5219517 GAAAAATAAATTACAT
1 GAAAAGTAAAATACAT
*
5219533 TAAAAGTAAA
1 GAAAAGTAAA
5219543 TAAAAGTATG
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
15 10 0.23
16 33 0.77
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (16 bp):
GAAAAGTAAAATACAT
Found at i:5223573 original size:24 final size:24
Alignment explanation
Indices: 5223545--5223608 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
5223535 CTACATACAT
* *
5223545 AACTATCTATTTTTAATAGATAGA
1 AACTATCTATTTTTAATAGACAAA
* *
5223569 AACTATCTGTTTTGAATAGACAAA
1 AACTATCTATTTTTAATAGACAAA
*
5223593 AATTATCTATTTTTAA
1 AACTATCTATTTTTAA
5223609 ACAATTAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (24 bp):
AACTATCTATTTTTAATAGACAAA
Found at i:5226256 original size:61 final size:61
Alignment explanation
Indices: 5226190--5226313 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
5226180 ATATTTTTAC
* *
5226190 AAAAAATTACATTTCTTGATTTAATAATAGTGTTAACTGAAATTAAATCATTTGGTTCAAT
1 AAAAAATTACATCTCTTGATTTAATAACAGTGTTAACTGAAATTAAATCATTTGGTTCAAT
*
5226251 AAAAAATTACATCTCTTGATTTAATAACAGTGTTAACTGAAATTGAATCATTTGGTTCAAT
1 AAAAAATTACATCTCTTGATTTAATAACAGTGTTAACTGAAATTAAATCATTTGGTTCAAT
5226312 AA
1 AA
5226314 CCATGAACCT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (61 bp):
AAAAAATTACATCTCTTGATTTAATAACAGTGTTAACTGAAATTAAATCATTTGGTTCAAT
Found at i:5228849 original size:25 final size:24
Alignment explanation
Indices: 5228806--5228873 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
5228796 CTATAGATAT
*
5228806 AATTGTCTATTTTGAATAAATAAA
1 AATTATCTATTTTGAATAAATAAA
*
5228830 AATTATCTATTTTTGAATAATTAAA
1 AATTATCTA-TTTTGAATAAATAAA
*
5228855 ACTGT-T-TATTTTGAATAAA
1 AAT-TATCTATTTTGAATAAA
5228874 CTTATCTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 10 0.26
24 10 0.26
25 17 0.45
26 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (24 bp):
AATTATCTATTTTGAATAAATAAA
Found at i:5229829 original size:13 final size:12
Alignment explanation
Indices: 5229806--5229830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5229796 TTGAATTATA
5229806 AACAATTTTTTT
1 AACAATTTTTTT
5229818 AACAATTTTTTT
1 AACAATTTTTTT
5229830 A
1 A
5229831 CATAATATTG
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:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
AACAATTTTTTT
Found at i:5232284 original size:22 final size:22
Alignment explanation
Indices: 5232259--5232303 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5232249 GCAATGGTAG
5232259 ACACAATAAGCCTTTCTATATT
1 ACACAATAAGCCTTTCTATATT
5232281 ACACAATAAGCCTTTCTATATT
1 ACACAATAAGCCTTTCTATATT
5232303 A
1 A
5232304 TCTTAATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (22 bp):
ACACAATAAGCCTTTCTATATT
Found at i:5238654 original size:29 final size:29
Alignment explanation
Indices: 5238605--5238666 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
5238595 AGTTCTTATT
* * *
5238605 TTATTTTTTTGTTTTGTTTTTTATATATA
1 TTATTTTTATGTTTTATTTTTAATATATA
5238634 TTATTTTTAT-TTTTATATTTTAATATATA
1 TTATTTTTATGTTTTAT-TTTTAATATATA
5238663 TTAT
1 TTAT
5238667 GGTTGTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (29 bp):
TTATTTTTATGTTTTATTTTTAATATATA
Found at i:5238738 original size:20 final size:20
Alignment explanation
Indices: 5238713--5238751 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5238703 AAAAAATAGT
5238713 TTATTTTAGCATGAATTTAC
1 TTATTTTAGCATGAATTTAC
5238733 TTATTTTAGCATGAATTTA
1 TTATTTTAGCATGAATTTA
5238752 ATATATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (20 bp):
TTATTTTAGCATGAATTTAC
Found at i:5238887 original size:21 final size:23
Alignment explanation
Indices: 5238849--5238916 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 23
5238839 TATTTAATCA
5238849 CATGATA-ATTA-A-TATTATTG
1 CATGATATATTATATTATTATTG
* *
5238869 CATGATA-GTT-TATTATTATTA
1 CATGATATATTATATTATTATTG
*
5238890 CCTGATATATTATATTATTATTG
1 CATGATATATTATATTATTATTG
5238913 CATG
1 CATG
5238917 GTATTATTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 10 0.26
21 13 0.34
22 2 0.05
23 13 0.34
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (23 bp):
CATGATATATTATATTATTATTG
Found at i:5241201 original size:12 final size:12
Alignment explanation
Indices: 5241186--5241211 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5241176 AATAATGAAA
5241186 AAAAAAAAAGAG
1 AAAAAAAAAGAG
5241198 AAAAAAAAAGAG
1 AAAAAAAAAGAG
5241210 AA
1 AA
5241212 TGAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:5241568 original size:15 final size:15
Alignment explanation
Indices: 5241517--5241579 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
5241507 AAAAAGATAT
5241517 GAAAAAAATGAAAAAA
1 GAAAAAAA-GAAAAAA
*
5241533 TG-AAAAAAGCAAAAA
1 -GAAAAAAAGAAAAAA
* * *
5241548 G--TAAAATAACAAA
1 GAAAAAAAGAAAAAA
5241561 GAAAAAAAGAAAAAA
1 GAAAAAAAGAAAAAA
5241576 GAAA
1 GAAA
5241580 GACTCAAACT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
13 9 0.25
14 1 0.03
15 19 0.53
16 6 0.17
17 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.06
Consensus pattern (15 bp):
GAAAAAAAGAAAAAA
Found at i:5241575 original size:7 final size:7
Alignment explanation
Indices: 5241519--5241579 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
5241509 AAAGATATGA
5241519 AAAAAATG
1 AAAAAA-G
5241527 AAAAAATG
1 AAAAAA-G
5241535 AAAAAAG
1 AAAAAAG
*
5241542 CAAAAAG
1 AAAAAAG
* *
5241549 -TAAAAT
1 AAAAAAG
*
5241555 AACAAAG
1 AAAAAAG
5241562 AAAAAAAG
1 -AAAAAAG
5241570 AAAAAAG
1 AAAAAAG
5241577 AAA
1 AAA
5241580 GACTCAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
6 4 0.09
7 20 0.45
8 20 0.45
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.07
Consensus pattern (7 bp):
AAAAAAG
Found at i:5243247 original size:20 final size:20
Alignment explanation
Indices: 5243222--5243260 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5243212 AAAGAATAGT
* *
5243222 TTATTTTTGCATGATTTTAC
1 TTATTTTAGCATGAATTTAC
5243242 TTATTTTAGCATGAATTTA
1 TTATTTTAGCATGAATTTA
5243261 ATATATTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (20 bp):
TTATTTTAGCATGAATTTAC
Found at i:5243267 original size:21 final size:20
Alignment explanation
Indices: 5243222--5243268 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5243212 AAAGAATAGT
* * *
5243222 TTATTTTTGCATGATTTTAC
1 TTATTTTAGCATGAATTTAA
5243242 TTATTTTAGCATGAATTTAA
1 TTATTTTAGCATGAATTTAA
5243262 TATATTT
1 T-TATTT
5243269 GCATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (20 bp):
TTATTTTAGCATGAATTTAA
Found at i:5243396 original size:21 final size:23
Alignment explanation
Indices: 5243370--5243425 Score: 80
Period size: 21 Copynumber: 2.5 Consensus size: 23
5243360 TAATAATTAA
*
5243370 TATTATTACATGATA-GT-TTAT
1 TATTATTACATGATATGTACTAT
5243391 TATTATTACATGATATGTACTAT
1 TATTATTACATGATATGTACTAT
*
5243414 TATTATTGCATG
1 TATTATTACATG
5243426 GTATTATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 15 0.48
22 2 0.06
23 14 0.45
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (23 bp):
TATTATTACATGATATGTACTAT
Found at i:5244173 original size:3 final size:3
Alignment explanation
Indices: 5244165--5244200 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
5244155 TAAACACCAT
5244165 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT
5244201 TATTTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5245773 original size:13 final size:13
Alignment explanation
Indices: 5245757--5245784 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5245747 AAATTTTTTC
5245757 AAAAATTTAAATT
1 AAAAATTTAAATT
5245770 AAAAATTTAAATT
1 AAAAATTTAAATT
5245783 AA
1 AA
5245785 TAAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATTTAAATT
Found at i:5248255 original size:50 final size:51
Alignment explanation
Indices: 5248173--5248277 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 51
5248163 GGTGAGTTCT
* * *
5248173 TAAAATTTATTAAACAAAATTTAAAATTATCCCGACTCTTC-AACGAAATCC
1 TAAAAGTTATTAAACAAAATTTAAAATCATCCCAACT-TTCTAACGAAATCC
** * *
5248224 TAAAAGTT-TTAAACAAGTTTTAAGATCATCCCAACTTTCTAACGAGATCC
1 TAAAAGTTATTAAACAAAATTTAAAATCATCCCAACTTTCTAACGAAATCC
5248274 TAAA
1 TAAA
5248278 TAATTTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
49 3 0.07
50 36 0.78
51 7 0.15
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (51 bp):
TAAAAGTTATTAAACAAAATTTAAAATCATCCCAACTTTCTAACGAAATCC
Found at i:5248368 original size:24 final size:23
Alignment explanation
Indices: 5248301--5248369 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
5248291 AATTAAAAGA
*
5248301 ATTAATTAATTAATTTTTATTATG
1 ATTATTTAATT-ATTTTTATTATG
* * *
5248325 GTTATTTAA-AATTTTGTATTATTT
1 ATTATTTAATTATTTT-TATTA-TG
5248349 ATTATTTAATTATTTTTATTA
1 ATTATTTAATTATTTTTATTA
5248370 AAAAATTTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 5 0.14
23 5 0.14
24 21 0.58
25 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
ATTATTTAATTATTTTTATTATG
Found at i:5248699 original size:19 final size:21
Alignment explanation
Indices: 5248677--5248719 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5248667 CATTTAAATA
5248677 ATTTATCA-TTTT-TTATTTT
1 ATTTATCATTTTTCTTATTTT
5248696 ATTTATCATTTTTCTTATTTT
1 ATTTATCATTTTTCTTATTTT
5248717 ATT
1 ATT
5248720 ATTTTTTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.36
20 4 0.18
21 10 0.45
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTATCATTTTTCTTATTTT
Found at i:5248715 original size:16 final size:17
Alignment explanation
Indices: 5248678--5248725 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
5248668 ATTTAAATAA
* *
5248678 TTTATCATTTTTTATTTT
1 TTTATCA-TTTTTCTTAT
5248696 ATTTATCATTTTTCTTAT
1 -TTTATCATTTTTCTTAT
*
5248714 TTTATTATTTTT
1 TTTATCATTTTT
5248726 TAGCAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 8 0.31
19 7 0.27
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATCATTTTTCTTAT
Found at i:5249804 original size:3 final size:3
Alignment explanation
Indices: 5249789--5249830 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
5249779 TTTTTTAGAT
*
5249789 TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5249831 ACAAAATTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5258080 original size:2 final size:2
Alignment explanation
Indices: 5258073--5258101 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5258063 TCTTTCTCTT
5258073 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
5258102 TTATGTGTGT
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:5264090 original size:25 final size:21
Alignment explanation
Indices: 5264052--5264109 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 21
5264042 TGATTATAAT
5264052 ATAAAAGATAATTATATTTTTA
1 ATAAAAGATAATTAT-TTTTTA
5264074 TATTAAAAGAATAATTATTTTTTA
1 -A-TAAAAG-ATAATTATTTTTTA
5264098 ATAAAAGATAAT
1 ATAAAAGATAAT
5264110 AATAATCGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.15
22 6 0.18
23 2 0.06
24 12 0.36
25 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
ATAAAAGATAATTATTTTTTA
Found at i:5264110 original size:24 final size:25
Alignment explanation
Indices: 5264052--5264112 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 25
5264042 TGATTATAAT
*
5264052 ATAAAAGATAATTA-TATTTTTATA
1 ATAAAAGATAATAATTATTTTTATA
*
5264076 TTAAAAG--AATAATTATTTTT-TA
1 ATAAAAGATAATAATTATTTTTATA
5264098 ATAAAAGATAATAAT
1 ATAAAAGATAATAAT
5264113 AATCGCACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 12 0.39
23 7 0.23
24 12 0.39
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (25 bp):
ATAAAAGATAATAATTATTTTTATA
Found at i:5264448 original size:20 final size:21
Alignment explanation
Indices: 5264412--5264463 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5264402 CTCGAAATTA
5264412 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
5264434 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
5264455 AT-AAATATT
1 ATAAAATATT
5264464 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:5264454 original size:21 final size:22
Alignment explanation
Indices: 5264412--5264463 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5264402 CTCGAAATTA
5264412 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
5264434 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
5264455 AT-AAATATT
1 ATAAAATATT
5264464 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:5264471 original size:30 final size:30
Alignment explanation
Indices: 5264436--5264496 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5264426 TTTAAAATAT
* * * *
5264436 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATAATTA
*
5264466 AAAATATCATTATATAAATATATATAATTA
1 AAAATATCATTATATAAATATAAATAATTA
5264496 A
1 A
5264497 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATAATTA
Found at i:5269339 original size:39 final size:39
Alignment explanation
Indices: 5269285--5269361 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
5269275 CAACATAGGG
* **
5269285 AAAATCACAGTAACCTCGTACTAATGTATTAGAGAATCT
1 AAAATCACAGGAACCTCAAACTAATGTATTAGAGAATCT
5269324 AAAATCACAGGAACCTCAAACTAATGTATTAGAGAATC
1 AAAATCACAGGAACCTCAAACTAATGTATTAGAGAATC
5269362 CAAGTAATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (39 bp):
AAAATCACAGGAACCTCAAACTAATGTATTAGAGAATCT
Found at i:5271867 original size:17 final size:17
Alignment explanation
Indices: 5271845--5271908 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
5271835 GTTTAATACC
5271845 AAAAAAAATAATAAAAT
1 AAAAAAAATAATAAAAT
* *
5271862 AAAAAAGATAAGAGAAA-
1 AAAAAAAATAATA-AAAT
5271879 AATAAATAAA-AATAAAAAT
1 AA-AAA-AAATAAT-AAAAT
*
5271898 AAAATAAATAA
1 AAAAAAAATAA
5271909 AGAGCTGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
17 16 0.44
18 15 0.42
19 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAAAAATAATAAAAT
Found at i:5271901 original size:21 final size:21
Alignment explanation
Indices: 5271845--5271909 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
5271835 GTTTAATACC
5271845 AAAAA-AAATAATAAAATAAA-
1 AAAAATAAA-AATAAAATAAAT
* *
5271865 AAAGATAAGAGA-AAAATAAAT
1 AAAAATAA-AAATAAAATAAAT
5271886 AAAAATAAAAATAAAATAAAT
1 AAAAATAAAAATAAAATAAAT
5271907 AAA
1 AAA
5271910 GAGCTGGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 14 0.38
21 22 0.59
22 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAAATAAAAATAAAATAAAT
Found at i:5282275 original size:2 final size:2
Alignment explanation
Indices: 5282268--5282316 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
5282258 TATTTAAATA
* * * *
5282268 AT AT AT AT GT AT AT AT AT AT AT GT GT GT 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
5282310 AT AT AT A
1 AT AT AT A
5282317 CACATATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5282287 original size:14 final size:14
Alignment explanation
Indices: 5282268--5282316 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
5282258 TATTTAAATA
5282268 ATATATATGTATAT
1 ATATATATGTATAT
* *
5282282 ATATATATGTGTGT
1 ATATATATGTATAT
*
5282296 ATATATATATATAT
1 ATATATATGTATAT
5282310 ATATATA
1 ATATATA
5282317 CACATATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:5287659 original size:19 final size:17
Alignment explanation
Indices: 5287637--5287671 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
5287627 TTTTTATTAC
5287637 TAAATTTATTTAATAAAAA
1 TAAATTT-TTTAA-AAAAA
5287656 TAAATTTTTTAAAAAA
1 TAAATTTTTTAAAAAA
5287672 TTCCCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTTTTAAAAAAA
Found at i:5287916 original size:22 final size:22
Alignment explanation
Indices: 5287891--5287961 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
5287881 ATTTTTTTAC
*
5287891 AAAAATTTATTTAATAAAAATA
1 AAAAATTAATTTAATAAAAATA
* * *
5287913 AAAAAATAATTTATTAACAAACA
1 AAAAATTAATTTAATAA-AAATA
* *
5287936 ACAAATAAATTTAATAAAAAATA
1 AAAAATTAATTTAAT-AAAAATA
5287959 AAA
1 AAA
5287962 TAAAACAACC
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
22 14 0.38
23 21 0.57
24 2 0.05
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAAATTAATTTAATAAAAATA
Found at i:5287945 original size:26 final size:26
Alignment explanation
Indices: 5287894--5287945 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
5287884 TTTTTACAAA
* *
5287894 AATTTATTTAATAAAAATAAAAAAAT
1 AATTTATTTAACAAAAACAAAAAAAT
*
5287920 AATTTA-TTAACAAACAACAAATAAAT
1 AATTTATTTAACAAA-AACAAAAAAAT
5287946 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (26 bp):
AATTTATTTAACAAAAACAAAAAAAT
Found at i:5288817 original size:2 final size:2
Alignment explanation
Indices: 5288810--5288836 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5288800 CTCCTTAACA
5288810 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 A
5288837 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5290750 original size:16 final size:16
Alignment explanation
Indices: 5290725--5290768 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5290715 ATAAAAACAT
*
5290725 TTTTTAATATTTATTTA
1 TTTTT-ATATTTATATA
5290742 TTTTTATATTTATATA
1 TTTTTATATTTATATA
*
5290758 TGTATTATATT
1 T-TTTTATATT
5290769 AATAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTTTATATTTATATA
Found at i:5291376 original size:13 final size:15
Alignment explanation
Indices: 5291350--5291415 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
5291340 GATATATATA
5291350 ATATATTTATTATTT
1 ATATATTTATTATTT
*
5291365 ATATA-TTA-TATTA
1 ATATATTTATTATTT
5291378 ATA-AGTTTATTATTT
1 ATATA-TTTATTATTT
*
5291393 AATAAAATATTA-TATTT
1 -AT-ATAT-TTATTATTT
5291410 ATATAT
1 ATATAT
5291416 AATTGAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
12 1 0.02
13 7 0.17
14 6 0.15
15 12 0.29
16 4 0.10
17 7 0.17
18 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATATATTTATTATTT
Found at i:5291919 original size:2 final size:2
Alignment explanation
Indices: 5291914--5291940 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5291904 TGTTACTAAC
5291914 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 A
5291941 AATTCAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5292250 original size:17 final size:18
Alignment explanation
Indices: 5292230--5292267 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5292220 AATTATCTTT
* *
5292230 TTTAAA-TATTTATTTAA
1 TTTAAATTATTAATATAA
5292247 TTTAAATTATTAATATAA
1 TTTAAATTATTAATATAA
5292265 TTT
1 TTT
5292268 TTGAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATTATTAATATAA
Found at i:5298935 original size:29 final size:29
Alignment explanation
Indices: 5298893--5298949 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
5298883 GAAAAACCAC
5298893 AGATTTAAATAAACAAGGATATCTTCTTT
1 AGATTTAAATAAACAAGGATATCTTCTTT
5298922 AGATTTAAATAAACAAGGATATCTTCTT
1 AGATTTAAATAAACAAGGATATCTTCTT
5298950 CTCCCTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (29 bp):
AGATTTAAATAAACAAGGATATCTTCTTT
Found at i:5300253 original size:15 final size:16
Alignment explanation
Indices: 5300222--5300263 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
5300212 ATTTTTTTTA
5300222 TTTGAATTTTGAGGTT
1 TTTGAATTTTGAGGTT
*
5300238 TTTGGATTTT-AGG-T
1 TTTGAATTTTGAGGTT
5300252 TTTGACATTTTG
1 TTTGA-ATTTTG
5300264 GATTTTAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 9 0.41
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.57
Consensus pattern (16 bp):
TTTGAATTTTGAGGTT
Found at i:5300613 original size:3 final size:3
Alignment explanation
Indices: 5300605--5300660 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
5300595 TAATGAAGAT
* * *
5300605 TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTT TTA TTTA TTA ATC TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA
5300651 TTA TTA TTA T
1 TTA TTA TTA T
5300661 ATTTTGATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
2 2 0.04
3 37 0.82
4 6 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5300642 original size:16 final size:15
Alignment explanation
Indices: 5300605--5300665 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
5300595 TAATGAAGAT
5300605 TTATTA-TTATTATTA
1 TTATTATTTATT-TTA
*
5300620 TTATTATTTATTTTT
1 TTATTATTTATTTTA
* *
5300635 TTATTTATTAATCTTA
1 TTA-TTATTTATTTTA
5300651 TTATTATTATATTTT
1 TTATTATT-TATTTT
5300666 GATAATATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 16 0.43
16 21 0.57
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTATTTATTTTA
Found at i:5302700 original size:106 final size:106
Alignment explanation
Indices: 5302489--5302743 Score: 343
Period size: 106 Copynumber: 2.4 Consensus size: 106
5302479 TAAATCAAAA
* *
5302489 AAATAATGAGGATCGGGATTAAA-CAGCGAGTCAAAGATT-AAGATGACTGGGACTAAACCATAA
1 AAATAATGAGGATCGGGATTAAATC-GCGAGTCAAAGATTAAAGATGACTAGGACTAAACCACAA
* * *
5302552 ATTAAAAAATAAAAACGATTGAGATTAAAGAGCAAGTCAGAG
65 ATTAAAAAATAAAAACGATCGAAATTAAACAGCAAGTCAGAG
** * * * *
5302594 AAATAATGAGGATCGGGATTAAATCGTAAGTCAAAGATTAAATATGACTAGGACTAAATCGCAAG
1 AAATAATGAGGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACTAGGACTAAACCACAAA
* * * *
5302659 TTAAAAAATAGAAACGATCGAAATTAAACCGTAAGTTAGAG
66 TTAAAAAATAAAAACGATCGAAATTAAACAGCAAGTCAGAG
*
5302700 AAATAATGAGGATCAGGATTAAATCGCGAGTCAAAGATTAAAGA
1 AAATAATGAGGATCGGGATTAAATCGCGAGTCAAAGATTAAAGA
5302744 GGATCGAGAT
Statistics
Matches: 129, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
105 35 0.27
106 94 0.73
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (106 bp):
AAATAATGAGGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACTAGGACTAAACCACAAA
TTAAAAAATAAAAACGATCGAAATTAAACAGCAAGTCAGAG
Found at i:5302740 original size:19 final size:19
Alignment explanation
Indices: 5302716--5302776 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
5302706 TGAGGATCAG
5302716 GATTAAATCGCGAGTCAAA
1 GATTAAATCGCGAGTCAAA
** *
5302735 GATTAAAGAG-GA-TC-GA
1 GATTAAATCGCGAGTCAAA
5302751 GATTAAATCGCGAGTCAAA
1 GATTAAATCGCGAGTCAAA
*
5302770 AATTAAA
1 GATTAAA
5302777 GACGATTGGG
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.28
17 4 0.12
18 4 0.12
19 15 0.47
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.21
Consensus pattern (19 bp):
GATTAAATCGCGAGTCAAA
Found at i:5302755 original size:35 final size:35
Alignment explanation
Indices: 5302707--5302778 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
5302697 GAGAAATAAT
*
5302707 GAGGATCAGGATTAAATCGCGAGTCAAAGATTAAA
1 GAGGATCAGGATTAAATCGCGAGTCAAAAATTAAA
5302742 GAGGATC-GAGATTAAATCGCGAGTCAAAAATTAAA
1 GAGGATCAG-GATTAAATCGCGAGTCAAAAATTAAA
5302777 GA
1 GA
5302779 CGATTGGGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.19
Consensus pattern (35 bp):
GAGGATCAGGATTAAATCGCGAGTCAAAAATTAAA
Found at i:5302793 original size:106 final size:104
Alignment explanation
Indices: 5302489--5302804 Score: 339
Period size: 106 Copynumber: 3.0 Consensus size: 104
5302479 TAAATCAAAA
* * **
5302489 AAATAATGAGGATCGGGATTAAA-CAGCGAGTCAAAGATT-AAGATGACTGGGACTAAACCATAA
1 AAATAATGAGGATCGGGATTAAATC-GCGAGTCAAAGATTAAAGATGAC-GAGACTAAATCGCAA
* *
5302552 ATTAAAAAATAAAAACGATTGAGATTAAAGAGCAAGTCAGAG
64 GTTAAAAAAT-AAAACGATTGAGATTAAACAGCAAGTCAGAG
** * *
5302594 AAATAATGAGGATCGGGATTAAATCGTAAGTCAAAGATTAAATATGACTAGGACTAAATCGCAAG
1 AAATAATGAGGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACGA-GACTAAATCGCAAG
* * * * *
5302659 TTAAAAAATAGAAACGATCGAAATTAAACCGTAAGTTAGAG
65 TTAAAAAATA-AAACGATTGAGATTAAACAGCAAGTCAGAG
* * * *
5302700 AAATAATGAGGATCAGGATTAAATCGCGAGTCAAAGATTAAAGAGGATCGAGATTAAATCGCGAG
1 AAATAATGAGGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGA-CGAGACTAAATCGCAAG
* * * * *
5302765 TCAAAAATTAAAGACGATTGGGACTAAACTGCAAGTCAGA
65 TTAAAAAATAAA-ACGATTGAGATTAAACAGCAAGTCAGA
5302805 AAGCAAAATT
Statistics
Matches: 173, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
105 38 0.22
106 133 0.77
107 2 0.01
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.21
Consensus pattern (104 bp):
AAATAATGAGGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACGAGACTAAATCGCAAGT
TAAAAAATAAAACGATTGAGATTAAACAGCAAGTCAGAG
Found at i:5302802 original size:35 final size:35
Alignment explanation
Indices: 5302555--5302802 Score: 94
Period size: 35 Copynumber: 7.0 Consensus size: 35
5302545 ACCATAAATT
* * * * **
5302555 AAAAAATAAAAACGATTGAGATTAAAGAGCAAGTC
1 AAAAATTAAAGACGATCGAGACTAAATCGCAAGTC
* * * * *
5302590 AGAGAAA-TAATGAGGATCGGGATTAAATCGTAAGTC
1 A-A-AAATTAAAGACGATCGAGACTAAATCGCAAGTC
* * * * *
5302626 AAAGATTAAATATGA-CTAGGACTAAATCGCAAGTT
1 AAAAATTAAAGACGATCGA-GACTAAATCGCAAGTC
* * * * * *
5302661 AAAAAATAGAA-ACGATCGAAATTAAACCGTAAGTT
1 AAAAATTA-AAGACGATCGAGACTAAATCGCAAGTC
* * * *
5302696 AGAGAAA-TAATGAGGATC-AGGATTAAATCGCGAGTC
1 A-A-AAATTAAAGACGATCGA-GACTAAATCGCAAGTC
* * * *
5302732 AAAGATTAAAGAGGATCGAGATTAAATCGCGAGTC
1 AAAAATTAAAGACGATCGAGACTAAATCGCAAGTC
* *
5302767 AAAAATTAAAGACGATTGGGACTAAA-CTGCAAGTC
1 AAAAATTAAAGACGATCGAGACTAAATC-GCAAGTC
5302802 A
1 A
5302803 GAAAGCAAAA
Statistics
Matches: 160, Mismatches: 40, Indels: 26
0.71 0.18 0.12
Matches are distributed among these distances:
34 6 0.04
35 100 0.62
36 48 0.30
37 6 0.04
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (35 bp):
AAAAATTAAAGACGATCGAGACTAAATCGCAAGTC
Found at i:5303946 original size:10 final size:10
Alignment explanation
Indices: 5303931--5303970 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
5303921 TCACTTTCCC
5303931 TTTTTTTTCT
1 TTTTTTTTCT
5303941 TTTTTTTTACT
1 TTTTTTTT-CT
*
5303952 TATTTTTTCT
1 TTTTTTTTCT
5303962 TCTTTTTTT
1 T-TTTTTTT
5303971 TAAGCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 11 0.42
11 15 0.58
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:5303957 original size:13 final size:12
Alignment explanation
Indices: 5303931--5303971 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
5303921 TCACTTTCCC
5303931 TTTTTT-TTCTT
1 TTTTTTCTTCTT
*
5303942 TTTTTT-TACTT
1 TTTTTTCTTCTT
5303953 ATTTTTTCTTCTT
1 -TTTTTTCTTCTT
5303966 TTTTTT
1 TTTTTT
5303972 AAGCAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 10 0.38
12 12 0.46
13 4 0.15
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTCTT
Found at i:5314669 original size:13 final size:14
Alignment explanation
Indices: 5314639--5314668 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5314629 TTCCCCTTCA
5314639 TTTAAAAAATTTTT
1 TTTAAAAAATTTTT
5314653 TTTAAAAAATTTTT
1 TTTAAAAAATTTTT
5314667 TT
1 TT
5314669 ATTTAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAAAAAATTTTT
Found at i:5315594 original size:49 final size:48
Alignment explanation
Indices: 5315467--5315596 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 48
5315457 CAGATTTTGG
* *
5315467 GATTTAGGATTTCGATTTTAAGGTTTAGGATCAATGGTTTTGATTTTAA
1 GATTT-GGATTTCGATTTTAAGGTTTAGGGTTAATGGTTTTGATTTTAA
* * *
5315516 GGTTTGGAATTTCGATTTTACGGTTTAGGGTTAGTGGGTTTT-ATTTTAA
1 GATTTGG-ATTTCGATTTTAAGGTTTAGGGTTAAT-GGTTTTGATTTTAA
* *
5315565 GATTTGAGATTTAGATTTTAGGGTTTAGGGTT
1 GATTTG-GATTTCGATTTTAAGGTTTAGGGTT
5315597 TTAAGGTTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
48 2 0.03
49 61 0.87
50 7 0.10
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.48
Consensus pattern (48 bp):
GATTTGGATTTCGATTTTAAGGTTTAGGGTTAATGGTTTTGATTTTAA
Found at i:5315729 original size:3 final size:3
Alignment explanation
Indices: 5315721--5315774 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
5315711 TTTAATGAGG
* * *
5315721 ATT ATT ATT ATT ATT ATCT ATT -TT TTT ATTT ATT AAT CTT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT A-TT ATT ATT ATT ATT ATT
5315767 ATT ATT AT
1 ATT ATT AT
5315775 ATTTTGATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5317015 original size:20 final size:20
Alignment explanation
Indices: 5316992--5317032 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5316982 GTAGTGGTAT
5316992 GATGGCTAGGCAGGGGCGTG
1 GATGGCTAGGCAGGGGCGTG
* * *
5317012 GATGGTTGGGCAGGGGTGTG
1 GATGGCTAGGCAGGGGCGTG
5317032 G
1 G
5317033 GCGGCCATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.59, T:0.20
Consensus pattern (20 bp):
GATGGCTAGGCAGGGGCGTG
Found at i:5322718 original size:14 final size:14
Alignment explanation
Indices: 5322699--5322726 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5322689 AATTAATTAA
5322699 TTACGATGGCGTTT
1 TTACGATGGCGTTT
5322713 TTACGATGGCGTTT
1 TTACGATGGCGTTT
5322727 GGTGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (14 bp):
TTACGATGGCGTTT
Found at i:5322874 original size:23 final size:24
Alignment explanation
Indices: 5322820--5322874 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5322810 TTAAATCATC
*
5322820 AAAAATGATTAAATTATTATTTTA
1 AAAAATAATTAAATTATTATTTTA
* * *
5322844 AAATATAATTTAATTTTTA-TTTA
1 AAAAATAATTAAATTATTATTTTA
5322867 AAAAATAA
1 AAAAATAA
5322875 ATATATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AAAAATAATTAAATTATTATTTTA
Found at i:5323457 original size:17 final size:17
Alignment explanation
Indices: 5323424--5323458 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5323414 AAATAACGAG
* *
5323424 TAATAAAATTACTTTGA
1 TAATAAAATCACCTTGA
5323441 TAATAAAATCACCTTGA
1 TAATAAAATCACCTTGA
5323458 T
1 T
5323459 GATTATGTTA
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:0.11, G:0.06, T:0.37
Consensus pattern (17 bp):
TAATAAAATCACCTTGA
Found at i:5323548 original size:13 final size:12
Alignment explanation
Indices: 5323525--5323577 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 12
5323515 GATTTATCAA
5323525 AATTTTATTTAT
1 AATTTTATTTAT
5323537 AATTTATATTTAT
1 AATTT-TATTTAT
5323550 GAATATTTAATTTAT
1 -AAT-TTT-ATTTAT
*
5323565 ATATTTTTTTTAT
1 A-ATTTTATTTAT
5323578 TACTATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 5 0.14
13 12 0.34
14 8 0.23
15 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
AATTTTATTTAT
Found at i:5323557 original size:28 final size:29
Alignment explanation
Indices: 5323516--5323570 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
5323506 AGGAAGTATG
*
5323516 ATTTATCAAAATTTTATTTATA-ATTTAT
1 ATTTATCAAAATTTAATTTATATATTTAT
* *
5323544 ATTTATGAATATTTAATTTATATATTT
1 ATTTATCAAAATTTAATTTATATATTT
5323571 TTTTTATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTTATCAAAATTTAATTTATATATTTAT
Found at i:5331208 original size:25 final size:25
Alignment explanation
Indices: 5331159--5331210 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5331149 GTATAAAAGT
*
5331159 AAAACTTTATATTTTATTTTCAACA
1 AAAACTTTATATTTTATTATCAACA
*
5331184 AAAATTTTATATTTTATCTAT-AACA
1 AAAACTTTATATTTTAT-TATCAACA
5331209 AA
1 AA
5331211 TTTTTAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAACTTTATATTTTATTATCAACA
Found at i:5331514 original size:27 final size:26
Alignment explanation
Indices: 5331484--5331544 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
5331474 TAAATTAAGA
* *
5331484 TAAATATAAAAAATATTTTTAATGTGT
1 TAAATATAAAAAATATGTTTAA-CTGT
* **
5331511 TAAATGTATCAAATATGTTTAACTGT
1 TAAATATAAAAAATATGTTTAACTGT
5331537 TAAATATA
1 TAAATATA
5331545 TTAAACATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (26 bp):
TAAATATAAAAAATATGTTTAACTGT
Found at i:5333311 original size:14 final size:14
Alignment explanation
Indices: 5333287--5333330 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
5333277 AAAAAATCAT
*
5333287 AATTTAAAAATAAAA
1 AATTTAAATAT-AAA
*
5333302 AATTTCAAATATTAA
1 AATTT-AAATATAAA
5333317 AATTTAAATATAAA
1 AATTTAAATATAAA
5333331 CTTTTTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.32
15 12 0.48
16 5 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTTAAATATAAA
Found at i:5333711 original size:16 final size:17
Alignment explanation
Indices: 5333677--5333711 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5333667 AAGATGCACA
*
5333677 CTCCTCCACTCTTCTTC
1 CTCCTCCACTCTACTTC
5333694 CTCCTCCAC-CTACTTC
1 CTCCTCCACTCTACTTC
5333710 CT
1 CT
5333712 TTTCTCTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.09, C:0.54, G:0.00, T:0.37
Consensus pattern (17 bp):
CTCCTCCACTCTACTTC
Found at i:5348124 original size:290 final size:291
Alignment explanation
Indices: 5347603--5348182 Score: 1117
Period size: 290 Copynumber: 2.0 Consensus size: 291
5347593 TGTGCAACTA
5347603 TTAACCTTAAATCAATTTTTCTGTTCATTTAGTAAGAAATATTGCACAATGTTAAGCCTGTAGTT
1 TTAACCTTAAATCAATTTTTCTGTTCATTTAGTAAGAAATATTGCACAATGTTAAGCCTGTAGTT
*
5347668 TGGTAACTTATAGAAAATTAAGCAGCAAAAATAGAACAAACCCACTAAAGTATCTAAGAGCTCAA
66 TGGTAACTTATAGAAAACTAAGCAGCAAAAATAGAACAAACCCACTAAAGTATCTAAGAGCTCAA
5347733 CAAGTAGTTCAACTAACTTCCAAATGTTGTCAGTGCCCTTTTTAGTTTTGTCATGCATTTGTAGA
131 CAAGTAGTTCAACTAACTTCCAAATGTTGTCAGTGCCCTTTTTAGTTTTGTCATGCATTTGTAGA
*
5347798 ACATAATCTTGTTTCCTCCAGAACAGAACAAGCTACAGCAAGTATCGTGTTTACAAGTCTGTTAA
196 ACATAATCTTGTTTCCTCCAGAACAGAACAAGCTACAGCAAGTATCATGTTTACAAGTCTGTTAA
5347863 CAATTATAAATGCCATTTCCAGGAAATTCTG
261 CAATTATAAATGCCATTTCCAGGAAATTCTG
*
5347894 TTAACCTTAAATCAATTTTTCTGTTCATTTAGTAAGACATATTGCACAATGTTAAGCCTGTAGTT
1 TTAACCTTAAATCAATTTTTCTGTTCATTTAGTAAGAAATATTGCACAATGTTAAGCCTGTAGTT
5347959 TGGTAAC-TATAGAAAACTAAGCAGCAAAAATAGAACAAACCCACTAAAGTATCTAAGAGCTCAA
66 TGGTAACTTATAGAAAACTAAGCAGCAAAAATAGAACAAACCCACTAAAGTATCTAAGAGCTCAA
5348023 CAAGTAGTTCAACTAACTTCCAAATGTTGTCAGTGCCCTTTTTAGTTTTGTCATGCATTTGTAGA
131 CAAGTAGTTCAACTAACTTCCAAATGTTGTCAGTGCCCTTTTTAGTTTTGTCATGCATTTGTAGA
*
5348088 ACATAATCTTGTTTCCTCCAGAACAGAGCAAGCTACAGCAAGTATCATGTTTACAAGTCTGTTAA
196 ACATAATCTTGTTTCCTCCAGAACAGAACAAGCTACAGCAAGTATCATGTTTACAAGTCTGTTAA
5348153 CAATTATAAATGCCATTTCCAGGAAATTCT
261 CAATTATAAATGCCATTTCCAGGAAATTCT
5348183 AATTATTTCG
Statistics
Matches: 285, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
290 214 0.75
291 71 0.25
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (291 bp):
TTAACCTTAAATCAATTTTTCTGTTCATTTAGTAAGAAATATTGCACAATGTTAAGCCTGTAGTT
TGGTAACTTATAGAAAACTAAGCAGCAAAAATAGAACAAACCCACTAAAGTATCTAAGAGCTCAA
CAAGTAGTTCAACTAACTTCCAAATGTTGTCAGTGCCCTTTTTAGTTTTGTCATGCATTTGTAGA
ACATAATCTTGTTTCCTCCAGAACAGAACAAGCTACAGCAAGTATCATGTTTACAAGTCTGTTAA
CAATTATAAATGCCATTTCCAGGAAATTCTG
Found at i:5349085 original size:2 final size:2
Alignment explanation
Indices: 5349078--5349110 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5349068 TTTCAGATTT
5349078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5349111 TCCAGTCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5358466 original size:21 final size:21
Alignment explanation
Indices: 5358441--5358482 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5358431 AGGAGATGAG
* *
5358441 GGAGTTGGAGAGGAAAGCGGA
1 GGAGTTGCAGAGCAAAGCGGA
*
5358462 GGAGTTGCAGAGCAAGGCGGA
1 GGAGTTGCAGAGCAAAGCGGA
5358483 AGCAGAGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.50, T:0.10
Consensus pattern (21 bp):
GGAGTTGCAGAGCAAAGCGGA
Found at i:5361617 original size:15 final size:16
Alignment explanation
Indices: 5361599--5361632 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5361589 ATTGAAAAAG
5361599 TTTAAATTCAAATA-A
1 TTTAAATTCAAATAGA
*
5361614 TTTAAATTTAAATAGA
1 TTTAAATTCAAATAGA
5361630 TTT
1 TTT
5361633 GATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTAAATTCAAATAGA
Found at i:5364402 original size:2 final size:2
Alignment explanation
Indices: 5364390--5364431 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5364380 TCCTTAAGAC
*
5364390 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5364432 TCTCATCACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5371600 original size:2 final size:2
Alignment explanation
Indices: 5371593--5371622 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5371583 TGATTTCAAT
5371593 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5371623 GCAAAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5372530 original size:2 final size:2
Alignment explanation
Indices: 5372523--5372550 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5372513 CTTCTGAGTG
5372523 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
5372551 GCAACACAGA
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:5374952 original size:27 final size:25
Alignment explanation
Indices: 5374911--5374962 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
5374901 GTTGATTTAG
*
5374911 AAAATATAAAATTTTTATGTATGATTA
1 AAAAAATAAAATTTTTAT-TAT-ATTA
*
5374938 AAAAAATAAATTTTTTATTATATTA
1 AAAAAATAAAATTTTTATTATATTA
5374963 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
AAAAAATAAAATTTTTATTATATTA
Found at i:5375094 original size:21 final size:23
Alignment explanation
Indices: 5375070--5375121 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5375060 ATTAAATAAT
*
5375070 TTTTTAA-AAA-ATATTTTTATA
1 TTTTTAATAAATATAATTTTATA
5375091 TTTTTAATAAATATAATTTTATA
1 TTTTTAATAAATATAATTTTATA
*
5375114 ATTTTAAT
1 TTTTTAAT
5375122 TATTATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 7 0.26
22 3 0.11
23 17 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTAATAAATATAATTTTATA
Found at i:5376473 original size:15 final size:16
Alignment explanation
Indices: 5376446--5376475 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5376436 TTATGTAATC
5376446 TAAAAATATAATTAAG
1 TAAAAATATAATTAAG
5376462 TAAAAATA-AATTAA
1 TAAAAATATAATTAA
5376476 AAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAAAAATATAATTAAG
Found at i:5381591 original size:19 final size:20
Alignment explanation
Indices: 5381567--5381604 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5381557 TATTATTATT
5381567 ATTATTA-TTATTTAAAAAA
1 ATTATTATTTATTTAAAAAA
*
5381586 ATTATTATTTTTTTAAAAA
1 ATTATTATTTATTTAAAAA
5381605 TGTAGATCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATTATTTATTTAAAAAA
Found at i:5381592 original size:22 final size:20
Alignment explanation
Indices: 5381564--5381604 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
5381554 TATTATTATT
5381564 ATTATTATTATTATTTAAAAAA
1 ATTATTATT-TT-TTTAAAAAA
5381586 ATTATTATTTTTTTAAAAA
1 ATTATTATTTTTTTAAAAA
5381605 TGTAGATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTATTATTTTTTTAAAAAA
Found at i:5381594 original size:3 final size:3
Alignment explanation
Indices: 5381551--5381578 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5381541 ATTAAACCAA
5381551 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5381579 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5381844 original size:38 final size:38
Alignment explanation
Indices: 5381765--5381844 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
5381755 AGTCAAATGA
* *
5381765 TAAAAAAAATGATCGAGACAACATCGTCAATCAAGACG
1 TAAAAAAAATGATCGAGACAACATCGACAATCAAGAAG
* * * * * *
5381803 TAAACAAAATGATCGGGACAACATTGAGAGTCGAGAAG
1 TAAAAAAAATGATCGAGACAACATCGACAATCAAGAAG
5381841 TAAA
1 TAAA
5381845 GAATCGATCG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.49, C:0.15, G:0.20, T:0.16
Consensus pattern (38 bp):
TAAAAAAAATGATCGAGACAACATCGACAATCAAGAAG
Found at i:5381863 original size:37 final size:37
Alignment explanation
Indices: 5381768--5381886 Score: 98
Period size: 37 Copynumber: 3.2 Consensus size: 37
5381758 CAAATGATAA
* ** * **
5381768 AAAAAAT-GATCGAGACAACATCGTCAATCAAGACGT
1 AAAAAATCGATCGGGACAACATCGAGAATCGAGAAAT
* * *
5381804 AAACAAAAT-GATCGGGACAACATTGAGAGTCGAGAAGT
1 -AA-AAAATCGATCGGGACAACATCGAGAATCGAGAAAT
* * *
5381842 AAAGAATCGATCGGGATAACATCGTGAATCGAGAAAT
1 AAAAAATCGATCGGGACAACATCGAGAATCGAGAAAT
5381879 AAAAAATC
1 AAAAAATC
5381887 AATTGAGACA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
36 4 0.06
37 35 0.53
38 27 0.41
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (37 bp):
AAAAAATCGATCGGGACAACATCGAGAATCGAGAAAT
Found at i:5381939 original size:24 final size:24
Alignment explanation
Indices: 5381909--5381956 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5381899 ACCGCGAATC
5381909 AAAATCATGCTC-GAAGGTCTTACA
1 AAAATCATGC-CAGAAGGTCTTACA
5381933 AAAATCATGCCAGAAGGTCTTACA
1 AAAATCATGCCAGAAGGTCTTACA
5381957 GAATGACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
AAAATCATGCCAGAAGGTCTTACA
Found at i:5382040 original size:37 final size:37
Alignment explanation
Indices: 5381972--5382114 Score: 148
Period size: 37 Copynumber: 3.9 Consensus size: 37
5381962 ACAACACCAT
* * * *
5381972 AAGTCGAG-AATAATAAATCGATCGGGGCAACACTGC
1 AAGTCGAGAAATAAAAAATCAATTGGGACAACACTGC
* * * *
5382008 AAGTCGAGAAATAAAGAATCAATTAGGACAACACCGT
1 AAGTCGAGAAATAAAAAATCAATTGGGACAACACTGC
* * *
5382045 AACTCGAG-AATAATAAAAT-GATTGGGATAACACTGC
1 AAGTCGAGAAATAA-AAAATCAATTGGGACAACACTGC
*
5382081 AAGTCGAGAAATAAAAAATCAATTGGGATAACAC
1 AAGTCGAGAAATAAAAAATCAATTGGGACAACAC
5382115 CGCGAATCAA
Statistics
Matches: 86, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
36 37 0.43
37 49 0.57
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.18
Consensus pattern (37 bp):
AAGTCGAGAAATAAAAAATCAATTGGGACAACACTGC
Found at i:5382061 original size:73 final size:73
Alignment explanation
Indices: 5381961--5382116 Score: 224
Period size: 73 Copynumber: 2.1 Consensus size: 73
5381951 CTTACAGAAT
* * * *
5381961 GACAACACCATAAGTCGAGAATAAT-AAATCGATCGGGGCAACACTGCAAGTCGAGAAATAAAGA
1 GACAACACCGTAACTCGAGAATAATAAAAT-GATCGGGACAACACTGCAAGTCGAGAAATAAAAA
5382025 ATCAATTAG
65 ATCAATTAG
* *
5382034 GACAACACCGTAACTCGAGAATAATAAAATGATTGGGATAACACTGCAAGTCGAGAAATAAAAAA
1 GACAACACCGTAACTCGAGAATAATAAAATGATCGGGACAACACTGCAAGTCGAGAAATAAAAAA
*
5382099 TCAATTGG
66 TCAATTAG
*
5382107 GATAACACCG
1 GACAACACCG
5382117 CGAATCAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 70 0.95
74 4 0.05
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (73 bp):
GACAACACCGTAACTCGAGAATAATAAAATGATCGGGACAACACTGCAAGTCGAGAAATAAAAAA
TCAATTAG
Found at i:5382196 original size:36 final size:37
Alignment explanation
Indices: 5382146--5382237 Score: 141
Period size: 36 Copynumber: 2.5 Consensus size: 37
5382136 GAGGTCTTAC
*
5382146 AGAATCGATTGGGACAACACCGTAAGTCGA-AAATAA
1 AGAATCGATCGGGACAACACCGTAAGTCGAGAAATAA
* *
5382182 TGAATCGATCGGGACAACACTGTAAGTCGAGAAATAA
1 AGAATCGATCGGGACAACACCGTAAGTCGAGAAATAA
*
5382219 AGAATCGATCGGGATAACA
1 AGAATCGATCGGGACAACA
5382238 TCGCGAATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 27 0.54
37 23 0.46
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (37 bp):
AGAATCGATCGGGACAACACCGTAAGTCGAGAAATAA
Found at i:5382263 original size:124 final size:123
Alignment explanation
Indices: 5382022--5382427 Score: 380
Period size: 124 Copynumber: 3.4 Consensus size: 123
5382012 CGAGAAATAA
* * * * * *
5382022 AGAATCAATTAGGACAACACCGTAACTCGAGAATAATAAAAT-GATTGGGATAACACTGCAAGTC
1 AGAATCGATTGGGACAACACCGTAAGTCGAGAATAAT-GAATCGATTGGGACAACACTGTAAGTC
* * **** *
5382086 GAGAAATAAAAAATCAATTGGGATAACACCGCGAATCAAAATCATATTTAGAGGTCTTAC
65 GAGAAATAAAGAATC-ATCGGGATAACACCGCGAATCAAAATCATGCCCAGAGGTCTTAG
* *
5382146 AGAATCGATTGGGACAACACCGTAAGTCGAAAATAATGAATCGATCGGGACAACACTGTAAGTCG
1 AGAATCGATTGGGACAACACCGTAAGTCGAGAATAATGAATCGATTGGGACAACACTGTAAGTCG
* *
5382211 AGAAATAAAGAATCGATCGGGATAACATCGCGAATCAAAATTATGCCCAGAGGTCTTAG
66 AGAAATAAAGAATC-ATCGGGATAACACCGCGAATCAAAATCATGCCCAGAGGTCTTAG
* ** * *
5382270 A-AATC-A-T--G----C-CCG-AAGATC----TTACA-GAATCGATTGAAACAATACCGTAAGT
1 AGAATCGATTGGGACAACACCGTAAG-TCGAGAATA-ATGAATCGATTGGGACAACACTGTAAGT
* * *
5382319 CGA-AATTAAAGAATCATCGGGATAATACCGCGAATCGAAATCATGCCCAGAGGTCTTAG
64 CGAGAAATAAAGAATCATCGGGATAACACCGCGAATCAAAATCATGCCCAGAGGTCTTAG
** * *
5382378 AGAATCGATTGGGACAACATTGCATGTCGAGAATAATGAATCGATTGGGA
1 AGAATCGATTGGGACAACACCGTAAGTCGAGAATAATGAATCGATTGGGA
5382428 TAATACCGTG
Statistics
Matches: 228, Mismatches: 35, Indels: 40
0.75 0.12 0.13
Matches are distributed among these distances:
108 41 0.18
109 15 0.07
110 27 0.12
111 2 0.01
113 4 0.02
114 5 0.02
115 1 0.00
117 1 0.00
118 3 0.01
119 3 0.01
121 2 0.01
122 14 0.06
123 7 0.03
124 103 0.45
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (123 bp):
AGAATCGATTGGGACAACACCGTAAGTCGAGAATAATGAATCGATTGGGACAACACTGTAAGTCG
AGAAATAAAGAATCATCGGGATAACACCGCGAATCAAAATCATGCCCAGAGGTCTTAG
Found at i:5382463 original size:87 final size:86
Alignment explanation
Indices: 5382269--5382469 Score: 226
Period size: 86 Copynumber: 2.3 Consensus size: 86
5382259 AGAGGTCTTA
* * * *
5382269 GAAATCATGCCCGAAGATCTTACAGAATCGATTGAAACAATACCGTAAGTCGAAATTAAAGAATC
1 GAAATCATGCCCGGAGATCTTAGAGAATCGATTGAAACAACACCGCAAGTCGAAATTAAAGAATC
*
5382334 ATCGGGATAATACCGCGAATC
66 ATCGGGATAATACCGCGAACC
* * ** ** * *
5382355 GAAATCATGCCCAGAGGTCTTAGAGAATCGATTGGGACAACATTGCATGTCGAGAA-TAATGAAT
1 GAAATCATGCCCGGAGATCTTAGAGAATCGATTGAAACAACACCGCAAGTCGA-AATTAAAGAAT
* *
5382419 CGATTGGGATAATACCGTGAACC
65 C-ATCGGGATAATACCGCGAACC
*
5382442 GAAATCATGTCCGGAGATCTTAGA-AATC
1 GAAATCATGCCCGGAGATCTTAGAGAATC
5382470 AAGATCTTTA
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
86 54 0.57
87 41 0.43
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (86 bp):
GAAATCATGCCCGGAGATCTTAGAGAATCGATTGAAACAACACCGCAAGTCGAAATTAAAGAATC
ATCGGGATAATACCGCGAACC
Found at i:5383089 original size:32 final size:32
Alignment explanation
Indices: 5383047--5383357 Score: 256
Period size: 32 Copynumber: 9.6 Consensus size: 32
5383037 TTGGGACCAA
* *
5383047 ATAAACTGGGCTTAAATTTTATTGAAGGCTAG
1 ATAAACTGGGCTTAAATTTCATTGAAGGCCAG
* * ** *
5383079 TTAAATTGGGCTTAAAACCTCATTTGAA-GTCAG
1 ATAAACTGGGCTT-AAATTTCA-TTGAAGGCCAG
* *
5383112 ATAAACTGGGCTTAAAACTTCATTGATGGCCAG
1 ATAAACTGGGCTT-AAATTTCATTGAAGGCCAG
* * *
5383145 ATAAATTGGGCTTAAATGTCATTGATGGCCAG
1 ATAAACTGGGCTTAAATTTCATTGAAGGCCAG
* *
5383177 ATAAACTAGGCTTAAATTTTATT-AATGGCCAG
1 ATAAACTGGGCTTAAATTTCATTGAA-GGCCAG
* * *
5383209 ATAAACTGGGCTCAAATGTCATTGATGGCCAG
1 ATAAACTGGGCTTAAATTTCATTGAAGGCCAG
* * *
5383241 ATAAATTGAGCTTAAAACTTT-ATTG-AGACCAG
1 ATAAACTGGGCTT-AAA-TTTCATTGAAGGCCAG
* * *
5383273 ATAAACTGGGTTTAAAGCTTT-ATTGATGGCCAA
1 ATAAACTGGGCTTAAA--TTTCATTGAAGGCCAG
* * *
5383306 ATAAACTGAGCTTAAAGCTTCATT-AATGGTCAG
1 ATAAACTGGGCTTAAA-TTTCATTGAA-GGCCAG
5383339 ATAAACTGGGCTTAAATTT
1 ATAAACTGGGCTTAAATTT
5383358 TATTTCTTTC
Statistics
Matches: 222, Mismatches: 46, Indels: 22
0.77 0.16 0.08
Matches are distributed among these distances:
31 4 0.02
32 120 0.54
33 91 0.41
34 7 0.03
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (32 bp):
ATAAACTGGGCTTAAATTTCATTGAAGGCCAG
Found at i:5383095 original size:65 final size:66
Alignment explanation
Indices: 5383043--5383354 Score: 203
Period size: 65 Copynumber: 4.8 Consensus size: 66
5383033 TCTTTTGGGA
* * * *
5383043 CCAAATAAACTGGGCTT-AAATTTTATTGAAGGCTAGTTAAATTGGGCTTAAAACCTCATTTGAA
1 CCAAATAAACTGGGCTTAAAACTTCATTGAAGGCCAGATAAATTGGGCTTAAAACCTCATTTGAA
5383107 G
66 G
* * * **
5383108 TCAGATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAATTGGGCTT-AAATGTCA-TTGAT
1 CCAAATAAACTGGGCTTAAAACTTCATTGAAGGCCAGATAAATTGGGCTTAAAACCTCATTTGA-
*
5383171 GG
65 AG
* * * * * * **
5383173 CCAGATAAACTAGGCTT-AAATTTTATT-AATGGCCAGATAAACTGGGC-TCAAATGTCA-TTGA
1 CCAAATAAACTGGGCTTAAAACTTCATTGAA-GGCCAGATAAATTGGGCTTAAAACCTCATTTGA
*
5383234 TGG
65 -AG
* * * * * * * * * *
5383237 CCAGATAAATTGAGCTTAAAACTTTATTG-AGACCAGATAAACTGGGTTTAAAGCTTTA-TTGAT
1 CCAAATAAACTGGGCTTAAAACTTCATTGAAGGCCAGATAAATTGGGCTTAAAACCTCATTTGA-
*
5383300 GG
65 AG
* * * *
5383302 CCAAATAAACTGAGCTTAAAGCTTCATT-AATGGTCAGATAAACTGGGCTTAAA
1 CCAAATAAACTGGGCTTAAAACTTCATTGAA-GGCCAGATAAATTGGGCTTAAA
5383355 TTTTATTTCT
Statistics
Matches: 204, Mismatches: 34, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
63 2 0.01
64 72 0.35
65 84 0.41
66 46 0.23
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (66 bp):
CCAAATAAACTGGGCTTAAAACTTCATTGAAGGCCAGATAAATTGGGCTTAAAACCTCATTTGAA
G
Found at i:5383361 original size:65 final size:65
Alignment explanation
Indices: 5383109--5383355 Score: 304
Period size: 64 Copynumber: 3.8 Consensus size: 65
5383099 CATTTGAAGT
* * *
5383109 CAGATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAATTGGGCTTAAATGTCATTGATGGC
1 CAGATAAACTGAGCTTAAAACTTCATTAATGGCCAGATAAACTGGGCTTAAATGTCATTGATGGC
* * *
5383174 CAGATAAACT-AGGCTT-AAATTTTATTAATGGCCAGATAAACTGGGCTCAAATGTCATTGATGG
1 CAGATAAACTGA-GCTTAAAACTTCATTAATGGCCAGATAAACTGGGCTTAAATGTCATTGATGG
5383237 C
65 C
* * * * * *
5383238 CAGATAAATTGAGCTTAAAACTTTATTGA-GACCAGATAAACTGGGTTTAAA-GCTTTATTGATG
1 CAGATAAACTGAGCTTAAAACTTCATTAATGGCCAGATAAACTGGGCTTAAATG--TCATTGATG
5383301 GC
64 GC
* * *
5383303 CAAATAAACTGAGCTTAAAGCTTCATTAATGGTCAGATAAACTGGGCTTAAAT
1 CAGATAAACTGAGCTTAAAACTTCATTAATGGCCAGATAAACTGGGCTTAAAT
5383356 TTTATTTCTT
Statistics
Matches: 154, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 75 0.49
65 59 0.38
66 19 0.12
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (65 bp):
CAGATAAACTGAGCTTAAAACTTCATTAATGGCCAGATAAACTGGGCTTAAATGTCATTGATGGC
Done.