Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, 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: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 24 of 402
Found at i:5506769 original size:15 final size:16
Alignment explanation
Indices: 5506732--5506813 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 16
5506722 TTATTAAAGT
*
5506732 ATATTGAAATTATTTA
1 ATATTAAAATTATTTA
*
5506748 TTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
* *
5506763 ATATTAAAGAATAATTA
1 ATATTAAA-ATTATTTA
*
5506780 TATTTTAATAATAATATTTA
1 -ATATTAA-AAT--TATTTA
5506800 ATATTAAATATTAT
1 ATATTAAA-ATTAT
5506814 ATCAATATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
15 10 0.20
16 13 0.25
17 6 0.12
18 8 0.16
19 9 0.18
20 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:5506966 original size:17 final size:15
Alignment explanation
Indices: 5506927--5506969 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
5506917 TTAAATTAGT
5506927 AATATTTAT-TATTA
1 AATATTTATATATTA
5506941 AATATTTTATACTATTTA
1 AATA-TTTATA-TA-TTA
5506959 AATATTTATAT
1 AATATTTATAT
5506970 TTTATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.16
15 5 0.20
16 1 0.04
17 8 0.32
18 7 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATTTATATATTA
Found at i:5507281 original size:15 final size:15
Alignment explanation
Indices: 5507252--5507291 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
5507242 ATATTTATGT
5507252 TTAATAATATATAAAA
1 TTAA-AATATATAAAA
*
5507268 TTAAAATATTTAAAA
1 TTAAAATATATAAAA
5507283 TTAAAATAT
1 TTAAAATAT
5507292 GAAAAGACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAATATATAAAA
Found at i:5507751 original size:15 final size:14
Alignment explanation
Indices: 5507724--5507750 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5507714 TTAAAAATGT
5507724 AAAAATCATTTTTC
1 AAAAATCATTTTTC
5507738 AAAAATCATTTTT
1 AAAAATCATTTTT
5507751 TGTGAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAATCATTTTTC
Found at i:5510095 original size:24 final size:24
Alignment explanation
Indices: 5510068--5510115 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5510058 AAAAAAATAA
5510068 AATTTAAACAATGAAACCAATTTT
1 AATTTAAACAATGAAACCAATTTT
5510092 AATTTAAACAATGAAACCAATTTT
1 AATTTAAACAATGAAACCAATTTT
5510116 CCCCCTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
AATTTAAACAATGAAACCAATTTT
Found at i:5513924 original size:17 final size:17
Alignment explanation
Indices: 5513902--5513937 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
5513892 TTAAATTTTG
5513902 ATAAATTTT-ATATAATT
1 ATAAATTTTAAT-TAATT
5513919 ATAAATTTTAATTAATT
1 ATAAATTTTAATTAATT
5513936 AT
1 AT
5513938 TTATACTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAAATTTTAATTAATT
Found at i:5515056 original size:24 final size:23
Alignment explanation
Indices: 5514998--5515056 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
5514988 ACGATGATAT
*
5514998 ATTATAAATAAAATATAAAAATA
1 ATTATATATAAAATATAAAAATA
* **
5515021 A-TATAATTTAAAATTATAATTATA
1 ATTAT-ATATAAAA-TATAAAAATA
5515045 ATTATATATAAA
1 ATTATATATAAA
5515057 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 3 0.11
23 7 0.25
24 15 0.54
25 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTATATATAAAATATAAAAATA
Found at i:5516157 original size:16 final size:16
Alignment explanation
Indices: 5516128--5516162 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5516118 TATTCATCAT
* *
5516128 AATCATATTTAAAATA
1 AATCACATTAAAAATA
5516144 AATCACATTAAAAATA
1 AATCACATTAAAAATA
5516160 AAT
1 AAT
5516163 AATATATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
AATCACATTAAAAATA
Found at i:5517058 original size:13 final size:13
Alignment explanation
Indices: 5517035--5517067 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5517025 TTTGCTTTTC
5517035 TATTTTATTT-AA
1 TATTTTATTTAAA
5517047 TATTTATATTTAAA
1 TATTT-TATTTAAA
5517061 TATTTTA
1 TATTTTA
5517068 AAACATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 7 0.37
14 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTATTTAAA
Found at i:5517159 original size:2 final size:2
Alignment explanation
Indices: 5517152--5517177 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5517142 AATCACTAGG
5517152 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
5517178 GTGTATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5520474 original size:42 final size:42
Alignment explanation
Indices: 5520420--5520507 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
5520410 AAATAAACTA
* * *
5520420 TAAACATGTTTTTTGTTAAGGTGAGGAAGCGTTACAAATAAG
1 TAAACATATTTTTTGTTAAGGTGAGGAAGCATTACAAACAAG
* *
5520462 TAAACATATTTTTTGTTGAGGTGAGGAAGTATTACAAACAAG
1 TAAACATATTTTTTGTTAAGGTGAGGAAGCATTACAAACAAG
5520504 TAAA
1 TAAA
5520508 ACAGAATGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (42 bp):
TAAACATATTTTTTGTTAAGGTGAGGAAGCATTACAAACAAG
Found at i:5521906 original size:48 final size:48
Alignment explanation
Indices: 5521848--5522021 Score: 210
Period size: 48 Copynumber: 3.6 Consensus size: 48
5521838 AATAAAAGTG
* * * * *
5521848 TTTCCCTAAAAAATAGGAGAATTATTAAAAGGAATAGGTAAGAGACTA
1 TTTCCTTAAAAAATAAGAAAATTATTAAAAGGAATAGGTAAGGGAGTA
* * *
5521896 TTTCCTTAAAAAATAAGAAAATTATTAAAA-AAAAAGGTAATGGGAGTG
1 TTTCCTTAAAAAATAAGAAAATTATTAAAAGGAATAGGTAA-GGGAGTA
* *
5521944 TTT-CTCTAAAAAAT-AGAAAAACTATTAAAAGGAATAAGTAAGGGAGTA
1 TTTCCT-TAAAAAATAAG-AAAATTATTAAAAGGAATAGGTAAGGGAGTA
5521992 TTTCCTTAAAAAATAAGAAAATTATTAAAA
1 TTTCCTTAAAAAATAAGAAAATTATTAAAA
5522022 ATAATAGATA
Statistics
Matches: 106, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
47 12 0.11
48 83 0.78
49 11 0.10
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (48 bp):
TTTCCTTAAAAAATAAGAAAATTATTAAAAGGAATAGGTAAGGGAGTA
Found at i:5521953 original size:96 final size:96
Alignment explanation
Indices: 5521844--5522022 Score: 295
Period size: 96 Copynumber: 1.9 Consensus size: 96
5521834 AAGTAATAAA
* * * *
5521844 AGTGTTTCCCTAAAAAATAGGAGAATTATTAAAAGGAATAGGTAAGAGACTATTTCCTTAAAAAA
1 AGTGTTTCCCTAAAAAATAGAAAAACTATTAAAAGGAATAAGTAAGAGACTATTTCCTTAAAAAA
5521909 TAAGAAAATTATTAAAAAAAAAGGTAATGGG
66 TAAGAAAATTATTAAAAAAAAAGGTAATGGG
* * *
5521940 AGTGTTTCTCTAAAAAATAGAAAAACTATTAAAAGGAATAAGTAAGGGAGTATTTCCTTAAAAAA
1 AGTGTTTCCCTAAAAAATAGAAAAACTATTAAAAGGAATAAGTAAGAGACTATTTCCTTAAAAAA
5522005 TAAGAAAATTATTAAAAA
66 TAAGAAAATTATTAAAAA
5522023 TAATAGATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 76 1.00
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (96 bp):
AGTGTTTCCCTAAAAAATAGAAAAACTATTAAAAGGAATAAGTAAGAGACTATTTCCTTAAAAAA
TAAGAAAATTATTAAAAAAAAAGGTAATGGG
Found at i:5522197 original size:24 final size:24
Alignment explanation
Indices: 5522165--5522214 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5522155 ATACGAAATC
5522165 AATGTAGGTAATTATTATATGTTT
1 AATGTAGGTAATTATTATATGTTT
5522189 AATGTAGGTAATTATTATATGTTT
1 AATGTAGGTAATTATTATATGTTT
5522213 AA
1 AA
5522215 GTCAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (24 bp):
AATGTAGGTAATTATTATATGTTT
Found at i:5522375 original size:3 final size:3
Alignment explanation
Indices: 5522367--5522398 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
5522357 TTGCTTTTAT
5522367 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T
5522399 AATTGATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5522599 original size:21 final size:23
Alignment explanation
Indices: 5522556--5522604 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
5522546 AAAATTTTTT
*
5522556 AAGAATAAAATCTAATGAAATTTG
1 AAGAATAAAATCTAA-GAAATTTA
5522580 AAGAATAAAAT-TAA-AAATTTA
1 AAGAATAAAATCTAAGAAATTTA
5522601 AAGA
1 AAGA
5522605 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 10 0.42
23 3 0.12
24 11 0.46
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (23 bp):
AAGAATAAAATCTAAGAAATTTA
Found at i:5532585 original size:11 final size:11
Alignment explanation
Indices: 5532569--5532599 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5532559 CTCTAAACTT
5532569 TTATTTGAAGA
1 TTATTTGAAGA
5532580 TTATTTGAAGA
1 TTATTTGAAGA
*
5532591 ATATTTGAA
1 TTATTTGAA
5532600 TTTGGTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (11 bp):
TTATTTGAAGA
Found at i:5533351 original size:20 final size:19
Alignment explanation
Indices: 5533297--5533355 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
5533287 TTGTGAAAGA
5533297 TATTTTGTGAAATATACTTAT
1 TATTTTGTGAAATAT--TTAT
*
5533318 T-TTTGTGCTTAAATATTTAT
1 TATTT-TG-TGAAATATTTAT
5533338 TAATTTTGTGAAATATTT
1 T-ATTTTGTGAAATATTT
5533356 TAGATTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 17 0.53
21 5 0.16
22 10 0.31
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TATTTTGTGAAATATTTAT
Found at i:5535834 original size:23 final size:24
Alignment explanation
Indices: 5535777--5535835 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
5535767 ATATCAAATG
* *
5535777 GATAAATTTGCTTGTGCTTGACAT
1 GATATATTTGATTGTGCTTGACAT
* *
5535801 GCATATGTTTGATTGTGCTT-ATAT
1 G-ATATATTTGATTGTGCTTGACAT
5535825 GATATATTTGA
1 GATATATTTGA
5535836 CTAACATATG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 9 0.31
24 5 0.17
25 15 0.52
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (24 bp):
GATATATTTGATTGTGCTTGACAT
Found at i:5538416 original size:8 final size:7
Alignment explanation
Indices: 5538369--5538415 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
5538359 CAATCAAAAA
5538369 TTTTATTT
1 TTTTA-TT
5538377 TTTTATT
1 TTTTATT
*
5538384 TTTTGGTT
1 TTTT-ATT
5538392 TTTTA-T
1 TTTTATT
5538398 TTTTATT
1 TTTTATT
5538405 TTTTATT
1 TTTTATT
5538412 TTTT
1 TTTT
5538416 TGAAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 6 0.17
7 18 0.51
8 11 0.31
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:5538957 original size:16 final size:16
Alignment explanation
Indices: 5538936--5538974 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
5538926 TTCCCCTCCC
5538936 CTTTC-TCTCTTCTCTT
1 CTTTCTTCTC-TCTCTT
5538952 CTTTCTTCTCTCTCTT
1 CTTTCTTCTCTCTCTT
5538968 CTTTCTT
1 CTTTCTT
5538975 TACACCCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
CTTTCTTCTCTCTCTT
Found at i:5539984 original size:45 final size:44
Alignment explanation
Indices: 5539746--5539976 Score: 262
Period size: 44 Copynumber: 5.4 Consensus size: 44
5539736 ATTTTTAGAG
* * *
5539746 AATAAACAAAGCTCCTCAAAACAGAGGCTCAACGACTTTTGAAA
1 AATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTAGAAA
* *
5539790 AACAAACAAAGCTCCTCTAATCAGAAGCTCAACGACTTTAGAAAA
1 AATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTAG-AAA
** * *
5539835 AATAAACAAAGCTTTTCTAATTAAAGGCTCAACGACTTT-GAAAA
1 AATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTAG-AAA
*
5539879 AATAAACAAAGCTCCTCTAATCAGAGGTTCAACG-----A-AAA
1 AATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTAGAAA
* * *
5539917 AATAACCAAAACTCCTCTAATCAGAGGCTCAGCGACTTTAGAAA
1 AATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTAGAAA
*
5539961 AATAAA-TAAGCTCCTC
1 AATAAACAAAGCTCCTC
5539977 GATAATCACA
Statistics
Matches: 156, Mismatches: 23, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
38 33 0.21
43 9 0.06
44 78 0.50
45 36 0.23
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.21
Consensus pattern (44 bp):
AATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTAGAAA
Found at i:5541010 original size:10 final size:11
Alignment explanation
Indices: 5540985--5541023 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5540975 TACCTAAGTC
*
5540985 CTTTTTTTCAT
1 CTTTTTTTTAT
5540996 CTTTTTTTTAT
1 CTTTTTTTTAT
*
5541007 TTTTTTTTTAT
1 CTTTTTTTTAT
*
5541018 GTTTTT
1 CTTTTT
5541024 AAGTGTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (11 bp):
CTTTTTTTTAT
Found at i:5551657 original size:8 final size:8
Alignment explanation
Indices: 5551639--5551686 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
5551629 TCAATCAAAA
5551639 TTTTTATT
1 TTTTTATT
*
5551647 TTTTT-TA
1 TTTTTATT
*
5551654 TTTTT-TG
1 TTTTTATT
*
5551661 GTTTTATT
1 TTTTTATT
5551669 TTTTTATT
1 TTTTTATT
5551677 TTTTTATT
1 TTTTTATT
5551685 TT
1 TT
5551687 GTTGGAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 11 0.32
8 23 0.68
ACGTcount: A:0.10, C:0.00, G:0.04, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:5551681 original size:22 final size:22
Alignment explanation
Indices: 5551640--5551680 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
5551630 CAATCAAAAT
5551640 TTTTATTTTTTTTATTTTTTGG
1 TTTTATTTTTTTTATTTTTTGG
5551662 TTTTA-TTTTTTTATTTTTT
1 TTTTATTTTTTTTATTTTTT
5551681 TATTTTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.10, C:0.00, G:0.05, T:0.85
Consensus pattern (22 bp):
TTTTATTTTTTTTATTTTTTGG
Found at i:5551686 original size:21 final size:22
Alignment explanation
Indices: 5551640--5551686 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
5551630 CAATCAAAAT
*
5551640 TTTTATTTTTTTTATTTTTTGG
1 TTTTATTTTTTTTATTTTTTGA
*
5551662 TTTTA-TTTTTTTATTTTTTTA
1 TTTTATTTTTTTTATTTTTTGA
5551683 TTTT
1 TTTT
5551687 GTTGGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.85
Consensus pattern (22 bp):
TTTTATTTTTTTTATTTTTTGA
Found at i:5552762 original size:16 final size:16
Alignment explanation
Indices: 5552729--5552778 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5552719 ATAGAAAATT
*
5552729 AATCAAAAACAAATAA
1 AATCAAAAACAAAAAA
5552745 AATCTAAAAA-AAAAAA
1 AATC-AAAAACAAAAAA
* *
5552761 AA-CAAAAATAAAATA
1 AATCAAAAACAAAAAA
5552776 AAT
1 AAT
5552779 AACTATTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 11 0.38
17 5 0.17
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (16 bp):
AATCAAAAACAAAAAA
Found at i:5558266 original size:22 final size:22
Alignment explanation
Indices: 5558241--5558290 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
5558231 AAAAGTTTTT
* *
5558241 AAAAAAATTTTTAAAAATTCTA
1 AAAAAAAATTTCAAAAATTCTA
*
5558263 AAAAAAAATTTCAAAAGTTCTA
1 AAAAAAAATTTCAAAAATTCTA
5558285 AAAAAA
1 AAAAAA
5558291 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAAAAATTTCAAAAATTCTA
Found at i:5558289 original size:19 final size:19
Alignment explanation
Indices: 5558240--5558304 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
5558230 AAAAAGTTTT
*
5558240 TAAAAAAATTTTTAAAAATTC
1 TAAAAAAA--TTTAAAAGTTC
5558261 TAAAAAAAAATTTCAAAAGTTC
1 T--AAAAAAATTT-AAAAGTTC
*
5558283 TAAAAAAATTTAAAATTTC
1 TAAAAAAATTTAAAAGTTC
5558302 TAA
1 TAA
5558305 TAATTATCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 10 0.26
20 10 0.26
21 4 0.10
22 8 0.21
23 7 0.18
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAAAAATTTAAAAGTTC
Found at i:5558595 original size:20 final size:20
Alignment explanation
Indices: 5558566--5558612 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5558556 TGAAAGAATA
*
5558566 TGAAATTTTTAAAAAAATTT
1 TGAAAATTTTAAAAAAATTT
* *
5558586 TGAAAATTTTTAAAAACTTT
1 TGAAAATTTTAAAAAAATTT
5558606 TGAAAAT
1 TGAAAAT
5558613 GTAAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (20 bp):
TGAAAATTTTAAAAAAATTT
Found at i:5558906 original size:17 final size:18
Alignment explanation
Indices: 5558886--5558922 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5558876 TTTTTTTAAG
5558886 TTTATGAAAATTTT-ATT
1 TTTATGAAAATTTTCATT
*
5558903 TTTATTAAAATTTTCATT
1 TTTATGAAAATTTTCATT
5558921 TT
1 TT
5558923 GTTGAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATGAAAATTTTCATT
Found at i:5559097 original size:9 final size:9
Alignment explanation
Indices: 5559013--5559148 Score: 51
Period size: 9 Copynumber: 14.3 Consensus size: 9
5559003 TAATTTTTTT
5559013 ATTTTTCAAA
1 ATTTTT-AAA
* *
5559023 ATATTTCAA
1 ATTTTTAAA
*
5559032 ATTTGT-AA
1 ATTTTTAAA
* *
5559040 TTTTTTATA
1 ATTTTTAAA
*
5559049 AGTTTTAAA
1 ATTTTTAAA
*
5559058 ATATTTTAGA
1 AT-TTTTAAA
*
5559068 TTTTTTAAAAA
1 ATTTTT--AAA
** *
5559079 AAATTCAAA
1 ATTTTTAAA
5559088 ATTTTTAAAA
1 ATTTTT-AAA
* *
5559098 AATTTT-GA
1 ATTTTTAAA
5559106 ATATTTTAAA
1 AT-TTTTAAA
5559116 ATTTTTAAAAAA
1 ATTTTT---AAA
*
5559128 ATTTTTAGA
1 ATTTTTAAA
5559137 ATTTTTAAA
1 ATTTTTAAA
5559146 ATT
1 ATT
5559149 ATTTCTTTTA
Statistics
Matches: 89, Mismatches: 27, Indels: 21
0.65 0.20 0.15
Matches are distributed among these distances:
8 8 0.09
9 45 0.51
10 23 0.26
11 4 0.04
12 9 0.10
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:5559111 original size:20 final size:19
Alignment explanation
Indices: 5559051--5559116 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
5559041 TTTTTATAAG
*
5559051 TTTTAAAATATTTTAGAT-T
1 TTTTAAAAAATTTTA-ATAT
* * *
5559070 TTTTAAAAAAAATTCAAAAT
1 TTTT-AAAAAATTTTAATAT
5559090 TTTTAAAAAATTTTGAATA-
1 TTTTAAAAAATTTT-AATAT
5559109 TTTTAAAA
1 TTTTAAAA
5559117 TTTTTAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (19 bp):
TTTTAAAAAATTTTAATAT
Found at i:5559121 original size:29 final size:30
Alignment explanation
Indices: 5559085--5559148 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
5559075 AAAAAAATTC
5559085 AAAATTTTT-AAAAAA-TTTT-GAATATTTT
1 AAAATTTTTAAAAAAATTTTTAGAAT-TTTT
5559113 AAAATTTTTAAAAAAATTTTTAGAATTTTT
1 AAAATTTTTAAAAAAATTTTTAGAATTTTT
5559143 AAAATT
1 AAAATT
5559149 ATTTCTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 9 0.27
29 6 0.18
30 14 0.42
31 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AAAATTTTTAAAAAAATTTTTAGAATTTTT
Found at i:5560125 original size:19 final size:19
Alignment explanation
Indices: 5560078--5560126 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5560068 AGATTAACTT
* *
5560078 AATAAAGTTGTTTTGTAAT
1 AATAAAGTTTTTTTGTAAG
5560097 AATAAAGTTTTTTTGTAAG
1 AATAAAGTTTTTTTGTAAG
5560116 AATAAAGTTTT
1 AATAAAGTTTT
5560127 CCAACATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (19 bp):
AATAAAGTTTTTTTGTAAG
Found at i:5562226 original size:17 final size:17
Alignment explanation
Indices: 5562185--5562229 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5562175 AGTTGAATTT
5562185 CTTTATTTTTTATTATA
1 CTTTATTTTTTATTATA
* *
5562202 ATTGATTTTCTT-TTATA
1 CTTTATTTT-TTATTATA
5562219 CTTTATTTTTT
1 CTTTATTTTTT
5562230 CAAGTCAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (17 bp):
CTTTATTTTTTATTATA
Found at i:5562279 original size:35 final size:35
Alignment explanation
Indices: 5562212--5562281 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
5562202 ATTGATTTTC
** *
5562212 TTTTATACTTTATTTTTTCAAGTCAAAGTTTATAA
1 TTTTATACTTTATTTTTTCAAAACAAAATTTATAA
5562247 TTTTATACTTTATTTTTT-AAAACAAAAATTTATAA
1 TTTTATACTTTATTTTTTCAAAAC-AAAATTTATAA
5562282 CTATGCAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 3 0.10
35 28 0.90
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTTATACTTTATTTTTTCAAAACAAAATTTATAA
Found at i:5564139 original size:15 final size:17
Alignment explanation
Indices: 5564121--5564154 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
5564111 AAATTATATA
5564121 AATTTTGA-AAA-AAAT
1 AATTTTGATAAATAAAT
5564136 AATTTTGATAAATAAAT
1 AATTTTGATAAATAAAT
5564153 AA
1 AA
5564155 ATTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
AATTTTGATAAATAAAT
Found at i:5564665 original size:15 final size:16
Alignment explanation
Indices: 5564591--5564668 Score: 56
Period size: 16 Copynumber: 4.8 Consensus size: 16
5564581 AACAACTTAA
* *
5564591 TTTT-TTATTTTATGT
1 TTTTATTATTATATTT
5564606 TTTTA-TACTTATATTT
1 TTTTATTA-TTATATTT
*
5564622 GTCATTATTATTATATTT
1 -T-TTTATTATTATATTT
5564640 TTTTATATATTA-ATTT
1 TTTTAT-TATTATATTT
5564656 TTATT-TTATTATA
1 TT-TTATTATTATA
5564669 GATAATAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
15 11 0.22
16 18 0.35
17 9 0.18
18 11 0.22
19 2 0.04
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTATTATTATATTT
Found at i:5564665 original size:32 final size:33
Alignment explanation
Indices: 5564593--5564668 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 33
5564583 CAACTTAATT
* *
5564593 TTTTATTTTATGTTTTTATACTTATATTTGTCA
1 TTTTATTATATGTTTTTATAATTATATTTGTCA
* *
5564626 TTATTATTATATTTTTTTATATATTA-ATTT-TTA
1 TT-TTATTATATGTTTTTATA-ATTATATTTGTCA
5564659 TTTTATTATA
1 TTTTATTATA
5564669 GATAATAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 8 0.22
33 6 0.16
34 20 0.54
35 3 0.08
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (33 bp):
TTTTATTATATGTTTTTATAATTATATTTGTCA
Found at i:5564980 original size:10 final size:11
Alignment explanation
Indices: 5564950--5564992 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
5564940 TTTTTATTAG
5564950 AATATTTTAAA
1 AATATTTTAAA
5564961 AATATTTTAAA
1 AATATTTTAAA
* *
5564972 CAT-TTTTAAT
1 AATATTTTAAA
5564982 AA-ATTTTAAA
1 AATATTTTAAA
5564992 A
1 A
5564993 TCTCAGCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
AATATTTTAAA
Found at i:5565222 original size:16 final size:17
Alignment explanation
Indices: 5565201--5565284 Score: 68
Period size: 18 Copynumber: 4.9 Consensus size: 17
5565191 ATGTAAATGA
*
5565201 AAATAAACAAAT-CAAT
1 AAATAAACAAATAAAAT
*
5565217 AAATAAA-AACTAAAAT
1 AAATAAACAAATAAAAT
5565233 AAATAGAACAAATAAAA-
1 AAATA-AACAAATAAAAT
*
5565250 ACAA-AAATAAAATAAAAT
1 A-AATAAA-CAAATAAAAT
*
5565268 AAAATAAAAAAATAAAA
1 -AAATAAACAAATAAAA
5565285 ATAGAAAGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
15 3 0.05
16 17 0.30
17 12 0.21
18 20 0.36
19 4 0.07
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.15
Consensus pattern (17 bp):
AAATAAACAAATAAAAT
Found at i:5565254 original size:10 final size:9
Alignment explanation
Indices: 5565200--5565285 Score: 59
Period size: 9 Copynumber: 9.1 Consensus size: 9
5565190 TATGTAAATG
5565200 AAAATAAACA
1 AAAATAAA-A
5565210 AATCAATAAATA
1 AA--AATAAA-A
5565222 AAAACTAAAA
1 AAAA-TAAAA
* *
5565232 TAAATAGAA
1 AAAATAAAA
*
5565241 CAAATAAAA
1 AAAATAAAA
* *
5565250 ACAA-AAAT
1 AAAATAAAA
5565258 AAAATAAAA
1 AAAATAAAA
5565267 TAAAAT-AAA
1 -AAAATAAAA
5565276 AAAATAAAA
1 AAAATAAAA
5565285 A
1 A
5565286 TAGAAAGAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
8 11 0.18
9 23 0.38
10 13 0.22
11 4 0.07
12 9 0.15
ACGTcount: A:0.78, C:0.06, G:0.01, T:0.15
Consensus pattern (9 bp):
AAAATAAAA
Found at i:5565261 original size:5 final size:5
Alignment explanation
Indices: 5565253--5565284 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
5565243 AATAAAAACA
5565253 AAAAT AAAAT AAAAT AAAAT -AAA- AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
5565285 ATAGAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:5565281 original size:35 final size:37
Alignment explanation
Indices: 5565217--5565285 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
5565207 ACAAATCAAT
*
5565217 AAATAAAAACTAAAATAAATAGAACAAATAAAAACAA
1 AAATAAAAACTAAAATAAATAGAAAAAATAAAAACAA
5565254 AAAT-AAAA-TAAAATAAAATA-AAAAAATAAAAA
1 AAATAAAAACTAAAAT-AAATAGAAAAAATAAAAA
5565286 TAGAAAGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 17 0.57
36 9 0.30
37 4 0.13
ACGTcount: A:0.80, C:0.04, G:0.01, T:0.14
Consensus pattern (37 bp):
AAATAAAAACTAAAATAAATAGAAAAAATAAAAACAA
Found at i:5565539 original size:3 final size:3
Alignment explanation
Indices: 5565531--5565564 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5565521 ATTCATCTTT
5565531 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5565565 AATTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5565873 original size:25 final size:25
Alignment explanation
Indices: 5565839--5565886 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5565829 TTTATCTTTT
*
5565839 AAATTTCTAAAGAAAATT-TATTTAA
1 AAATTCCTAAA-AAAATTATATTTAA
5565864 AAATTCCTAAAAAAATTATATTT
1 AAATTCCTAAAAAAATTATATTT
5565887 TGACACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATTCCTAAAAAAATTATATTTAA
Found at i:5565980 original size:16 final size:17
Alignment explanation
Indices: 5565961--5565994 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
5565951 TTATCATTTA
5565961 ATTAAAATA-AAATAAT
1 ATTAAAATATAAATAAT
5565977 ATTAAAATATAAATAAT
1 ATTAAAATATAAATAAT
5565994 A
1 A
5565995 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTAAAATATAAATAAT
Found at i:5566008 original size:14 final size:16
Alignment explanation
Indices: 5565964--5566008 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5565954 TCATTTAATT
*
5565964 AAAATA-AAATAATATT
1 AAAATATAAATAATA-A
5565980 AAAATATAAATAATAA
1 AAAATATAAATAATAA
5565996 AAAAT-TAAA-AATA
1 AAAATATAAATAATA
5566009 TATGCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 4 0.15
15 4 0.15
16 11 0.41
17 8 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATATAAATAATAA
Found at i:5566086 original size:3 final size:3
Alignment explanation
Indices: 5566078--5566106 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5566068 AAAATTTTAA
5566078 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5566107 AAGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5566278 original size:3 final size:3
Alignment explanation
Indices: 5566270--5566300 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5566260 CACTGTCCGT
5566270 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA C
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA C
5566301 CCTTTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CTA
Found at i:5573113 original size:23 final size:22
Alignment explanation
Indices: 5573087--5573134 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
5573077 TCAAAATAGA
5573087 ATTAATTAAATTA-AATTATTTTT
1 ATTAATTAAA-TAGAATT-TTTTT
*
5573110 ATTAATTGAATAGAATTTTTTT
1 ATTAATTAAATAGAATTTTTTT
5573132 ATT
1 ATT
5573135 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
ATTAATTAAATAGAATTTTTTT
Found at i:5573477 original size:23 final size:22
Alignment explanation
Indices: 5573443--5573485 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
5573433 AATTCTTTTA
5573443 AAATTATCTTGAATAATTGATTG
1 AAATTATCTTG-ATAATTGATTG
5573466 AAATTAAT-TTGATAATTGAT
1 AAATT-ATCTTGATAATTGAT
5573486 CGATTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 8 0.42
24 2 0.11
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (22 bp):
AAATTATCTTGATAATTGATTG
Found at i:5577858 original size:30 final size:30
Alignment explanation
Indices: 5577809--5577885 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
5577799 AATTACATTA
* *
5577809 AAATATAATTTTAACATTTAATTTATACCC
1 AAATAAAATTTTAATATTTAATTTATACCC
* **
5577839 AAA-AAAATTTTTAATATTTAATTTGTACTT
1 AAATAAAA-TTTTAATATTTAATTTATACCC
5577869 AAATAAAATTTTAATAT
1 AAATAAAATTTTAATAT
5577886 AAATTAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.08
30 33 0.82
31 4 0.10
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.45
Consensus pattern (30 bp):
AAATAAAATTTTAATATTTAATTTATACCC
Found at i:5577888 original size:17 final size:17
Alignment explanation
Indices: 5577868--5577918 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
5577858 AATTTGTACT
5577868 TAAATAAAATTTTAATA
1 TAAATAAAATTTTAATA
* * *
5577885 TAAAT-TAATATTTCATT
1 TAAATAAAAT-TTTAATA
5577902 TGAAATAAAATTTTAAT
1 T-AAATAAAATTTTAAT
5577919 TGGATACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
16 3 0.12
17 11 0.42
18 9 0.35
19 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATAAAATTTTAATA
Found at i:5577938 original size:30 final size:28
Alignment explanation
Indices: 5577904--5577975 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
5577894 ATTTCATTTG
*
5577904 AAATAAAATTTTAATTGGATACAAATAAAA
1 AAATAAAA-TTTAATTAGATA-AAATAAAA
* *
5577934 AAATAACAATTTATTTAGATATAATAAAA
1 AAATAA-AATTTAATTAGATAAAATAAAA
*
5577963 ATATAAAAATTTA
1 AAAT-AAAATTTA
5577976 TTTAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 16 0.44
30 18 0.50
31 2 0.06
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (28 bp):
AAATAAAATTTAATTAGATAAAATAAAA
Found at i:5577986 original size:29 final size:29
Alignment explanation
Indices: 5577927--5577986 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
5577917 ATTGGATACA
* * *
5577927 AATAAAAAAATAACAATTTATTTAGATAT
1 AATAAAAAAATAAAAATTTATTTAAAAAT
*
5577956 AATAAAAATATAAAAATTTATTTAAAAAT
1 AATAAAAAAATAAAAATTTATTTAAAAAT
5577985 AA
1 AA
5577987 AATAGTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
AATAAAAAAATAAAAATTTATTTAAAAAT
Found at i:5582424 original size:15 final size:14
Alignment explanation
Indices: 5582384--5582427 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
5582374 AATATATTAA
5582384 AATCACATTATTATT
1 AATCA-ATTATTATT
* *
5582399 TATCTATTATTATAT
1 AATCAATTATTAT-T
5582414 AATCAATTATTATT
1 AATCAATTATTATT
5582428 TACAAATTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (14 bp):
AATCAATTATTATT
Found at i:5584016 original size:30 final size:30
Alignment explanation
Indices: 5583982--5584042 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5583972 GTGAATAATA
5583982 ATATCTATTGTTTTGCCATATTGTAATTTT
1 ATATCTATTGTTTTGCCATATTGTAATTTT
*
5584012 ATATCTATTGTTTTGCCATGTTGTAATTTT
1 ATATCTATTGTTTTGCCATATTGTAATTTT
5584042 A
1 A
5584043 AGATGAGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.56
Consensus pattern (30 bp):
ATATCTATTGTTTTGCCATATTGTAATTTT
Found at i:5585059 original size:50 final size:50
Alignment explanation
Indices: 5584927--5585214 Score: 304
Period size: 50 Copynumber: 5.9 Consensus size: 50
5584917 AGACCTATAG
* * * *
5584927 TTAATCTTTATAATTAAATGTTAATTCATAAAATAA-T-TATTATAATAT
1 TTAATTTTTATAATTAAATGCTAATTTATAAAACAATTATATTATAATAT
* * * * * * *
5584975 TTAATTTGTATAATTAAAAGCAAATTAATCAAACAATTACATTATAACAT
1 TTAATTTTTATAATTAAATGCTAATTTATAAAACAATTATATTATAATAT
*
5585025 TT-ATTTTTATAATTAATTGCTAATTTATAAAAACAATTATATTATAATAT
1 TTAATTTTTATAATTAAATGCTAATTTAT-AAAACAATTATATTATAATAT
* * * * *
5585075 TTAATTTGTATGATTAAATGCTAATTAATAAAACAATTATATTGTAACAT
1 TTAATTTTTATAATTAAATGCTAATTTATAAAACAATTATATTATAATAT
* *
5585125 TTAATCTTTATAATTAAATGCT-AGTT-T-AAA-AA-TATATTATAATAT
1 TTAATTTTTATAATTAAATGCTAATTTATAAAACAATTATATTATAATAT
* * *
5585170 TTAATCTTTATAATTAAATGCTAATCTAAAAATACAATTATATTA
1 TTAATTTTTATAATTAAATGCTAATTTATAAA-ACAATTATATTA
5585215 ATTTTTATTT
Statistics
Matches: 196, Mismatches: 34, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
45 33 0.17
46 4 0.02
47 3 0.02
48 31 0.16
49 25 0.13
50 71 0.36
51 29 0.15
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (50 bp):
TTAATTTTTATAATTAAATGCTAATTTATAAAACAATTATATTATAATAT
Found at i:5585079 original size:100 final size:98
Alignment explanation
Indices: 5584927--5585214 Score: 338
Period size: 100 Copynumber: 2.9 Consensus size: 98
5584917 AGACCTATAG
* *
5584927 TTAATCTTTATAATTAAATGTTAATTCATAAAATAAT-TATTATAATATTTAATTTGTATAATTA
1 TTAATCTTTATAATTAAATGCTAATTTATAAAA-AATATATTATAATATTTAATTTGTATAATTA
*
5584991 AAAGCAAATTAATCAAACAATTACATTATAACAT
65 AAAGCAAATTAATAAAACAATTACATTATAACAT
* * *
5585025 TT-ATTTTTATAATTAATTGCTAATTTATAAAAACAATTATATTATAATATTTAATTTGTATGAT
1 TTAATCTTTATAATTAAATGCTAATTTAT-AAAA-AA-TATATTATAATATTTAATTTGTATAAT
* * * *
5585089 TAAATGCTAATTAATAAAACAATTATATTGTAACAT
63 TAAAAGCAAATTAATAAAACAATTACATTATAACAT
*
5585125 TTAATCTTTATAATTAAATGCT-AGTT-T-AAAAATATATTATAATATTTAATCTT-TATAATTA
1 TTAATCTTTATAATTAAATGCTAATTTATAAAAAATATATTATAATATTTAAT-TTGTATAATTA
* * *
5585186 AATGCTAATCTAA-AAATACAATTATATTA
65 AAAGCAAAT-TAATAAA-ACAATTACATTA
5585215 ATTTTTATTT
Statistics
Matches: 167, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
95 37 0.22
96 18 0.11
97 25 0.15
98 8 0.05
99 2 0.01
100 60 0.36
101 17 0.10
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (98 bp):
TTAATCTTTATAATTAAATGCTAATTTATAAAAAATATATTATAATATTTAATTTGTATAATTAA
AAGCAAATTAATAAAACAATTACATTATAACAT
Found at i:5586880 original size:15 final size:15
Alignment explanation
Indices: 5586860--5586888 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5586850 TGTATTATTA
5586860 TAGTATAGTACATTG
1 TAGTATAGTACATTG
5586875 TAGTATAGTACATT
1 TAGTATAGTACATT
5586889 ATATCGCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (15 bp):
TAGTATAGTACATTG
Found at i:5586936 original size:3 final size:3
Alignment explanation
Indices: 5586924--5587044 Score: 133
Period size: 3 Copynumber: 40.7 Consensus size: 3
5586914 GTTGTTGTTG
* * *
5586924 TTA TTG TTA TTA TTA TTA TTA TTA TTA -TA TTA -TA GTA TTA CTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5586969 TTA CTGTA TTA -TG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5587015 TTA TTA TTA CTA TTA TTA TTTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
5587045 TTCTTTCCTT
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
2 7 0.07
3 87 0.86
4 5 0.05
5 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5587855 original size:17 final size:17
Alignment explanation
Indices: 5587824--5587885 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 17
5587814 CAGGTTTTGC
*
5587824 TTATTTTATTT-TATTT
1 TTATTTTTTTTATATTT
5587840 TTATTTTTTTTATATTT
1 TTATTTTTTTTATATTT
* * *
5587857 TGAATTTTTTTAAATTT
1 TTATTTTTTTTATATTT
*
5587874 TTATTTATTTTA
1 TTATTTTTTTTA
5587886 CCGACTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
16 10 0.26
17 28 0.74
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.76
Consensus pattern (17 bp):
TTATTTTTTTTATATTT
Found at i:5587996 original size:14 final size:13
Alignment explanation
Indices: 5587961--5588000 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5587951 ATATTTTTAT
*
5587961 TAAAAAAACAAAA
1 TAAAAAAATAAAA
*
5587974 CAAAAAAATAAAA
1 TAAAAAAATAAAA
5587987 TAAAAGAAATAAAA
1 TAAAA-AAATAAAA
5588001 AAATCTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:5591111 original size:218 final size:218
Alignment explanation
Indices: 5590733--5591156 Score: 767
Period size: 218 Copynumber: 1.9 Consensus size: 218
5590723 TCTTATTACA
*
5590733 TACGTCACAATATATTATCGTAAGATGGTGGCACATGTCAGCAACGAAAAATTGCTCATGCATGT
1 TACGTCACAATATATTATCGTAAGATGGTGGCACATGTCAGCAACGAAAAACTGCTCATGCATGT
* *
5590798 TTTTTAGAATAGCTTAATCGGGTCCACTGCAAGGTGGTCTGTTTAGTTGGATAAGACTCATATAA
66 TTTTTAGAATAGCTAAATCGGGTCCACTGCAAGGTGGTCTGTTTAGTTAGATAAGACTCATATAA
* *
5590863 GATCGTGGAAGGATTTGACTCAATCTTTCATTAACCAATATTGCTACATCATAGATATGGCTCAT
131 GATCGTGAAAGGATTTAACTCAATCTTTCATTAACCAATATTGCTACATCATAGATATGGCTCAT
5590928 AATAATCTTTTAACCAATATTGC
196 AATAATCTTTTAACCAATATTGC
*
5590951 TACGTCACAATATATTATCGTAAGATGGTGGCACATGTCAGCAACGAAAAACTGCTTATGCATGT
1 TACGTCACAATATATTATCGTAAGATGGTGGCACATGTCAGCAACGAAAAACTGCTCATGCATGT
*
5591016 TTTTTAGAATAGCTAAATCGGGTCCACTGCAAGGTGGTCTGTTTAGTTAGATAGGACTCATATAA
66 TTTTTAGAATAGCTAAATCGGGTCCACTGCAAGGTGGTCTGTTTAGTTAGATAAGACTCATATAA
*
5591081 GATCGTGAAAGGATTTAACTCAATCTTTCATTAACCAATATTGCTACATCATATATATGGCTCAT
131 GATCGTGAAAGGATTTAACTCAATCTTTCATTAACCAATATTGCTACATCATAGATATGGCTCAT
*
5591146 AATCATCTTTT
196 AATAATCTTTT
5591157 GTTATAAGGT
Statistics
Matches: 197, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 197 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (218 bp):
TACGTCACAATATATTATCGTAAGATGGTGGCACATGTCAGCAACGAAAAACTGCTCATGCATGT
TTTTTAGAATAGCTAAATCGGGTCCACTGCAAGGTGGTCTGTTTAGTTAGATAAGACTCATATAA
GATCGTGAAAGGATTTAACTCAATCTTTCATTAACCAATATTGCTACATCATAGATATGGCTCAT
AATAATCTTTTAACCAATATTGC
Found at i:5592910 original size:14 final size:14
Alignment explanation
Indices: 5592901--5592937 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
5592891 CCAAAAAAAT
5592901 AATTAAAAAAGTAAA
1 AATTAAAAAAG-AAA
5592916 AA-TAAAAAAGAAA
1 AATTAAAAAAGAAA
5592929 AATTAAAAA
1 AATTAAAAA
5592938 GCAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 14 0.67
15 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (14 bp):
AATTAAAAAAGAAA
Found at i:5592938 original size:13 final size:14
Alignment explanation
Indices: 5592901--5592938 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5592891 CCAAAAAAAT
5592901 AATTAAAAAAGTAAA
1 AATT-AAAAAGTAAA
*
5592916 AATAAAAAAG-AAA
1 AATTAAAAAGTAAA
5592929 AATTAAAAAG
1 AATTAAAAAG
5592939 CAAGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 6 0.29
15 3 0.14
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
AATTAAAAAGTAAA
Found at i:5593941 original size:55 final size:55
Alignment explanation
Indices: 5593677--5594207 Score: 320
Period size: 55 Copynumber: 9.7 Consensus size: 55
5593667 TCAATTTCGG
* * * * * * * * * *
5593677 CTCAGTCCAAATCATTTTTCAAACTTGTGGTTCCATCTCGATCATCTAATTTTGG
1 CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTCGGTCATCTGATCTTGA
* * * * * * * * *
5593732 CTCAGTCCAGATAATTTTCCTAACCTATGGCTTAGTCTTGGTTATCCGATCTTG-
1 CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTCGGTCATCTGATCTTGA
* * * * *
5593786 CTCAGTCTAGATCATTTTCTTAACTTATGGCTCAATTTTGGTCATTTGATCTT-A
1 CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTCGGTCATCTGATCTTGA
* * * * * ** *** *
5593840 GTTCAGTCCAGATTATTTTCTTGACTTGTGATTTTGTC-CTGGTCATCTAATCTTGA
1 -CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTC-GGTCATCTGATCTTGA
* ** * * *
5593896 CTCAGTCTAAATCATTTTTTTAACTTGTGGCTCAATCTCGATCATCCGATCTTGG
1 CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTCGGTCATCTGATCTTGA
* * *
5593951 CTCAGTCTAGATCATTTTCCTAACTTATGGCTCAATCTTGGTCATTTGATCTTTG-
1 CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTCGGTCATCTGATC-TTGA
* * * * * ** * * *
5594006 CTCAGTCTAAATAATTTTCTTGACTTGTGGTTCCGTCTCAGTCATCCGATCTTAA
1 CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTCGGTCATCTGATCTTGA
* ** * * * * * *
5594061 CTCAGTCTAGATTATTTTTTTGACTTATGGCTCAGTCACGATCATCTGATCTTGG
1 CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTCGGTCATCTGATCTTGA
* * * * * *
5594116 CTCAGTCTAGATCATGTT-CTAGACTTGAGGTTCCATCTCGGTCAT-TCAATCTTGC
1 CTCAGTCTAGATCATTTTCCTA-ACTTGTGGCTCAATCTCGGTCATCT-GATCTTGA
* *
5594171 CTTAGTCTAGATCATTTT-CTAGACTTGTGGTTCAATC
1 CTCAGTCTAGATCATTTTCCTA-ACTTGTGGCTCAATC
5594208 CTAGTCGCTT
Statistics
Matches: 362, Mismatches: 105, Indels: 18
0.75 0.22 0.04
Matches are distributed among these distances:
54 47 0.13
55 310 0.86
56 5 0.01
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.42
Consensus pattern (55 bp):
CTCAGTCTAGATCATTTTCCTAACTTGTGGCTCAATCTCGGTCATCTGATCTTGA
Found at i:5593947 original size:110 final size:109
Alignment explanation
Indices: 5593676--5594135 Score: 402
Period size: 110 Copynumber: 4.2 Consensus size: 109
5593666 TTCAATTTCG
* * * * ** * *
5593676 GCTCAGTCCAAATCATTTT-TCAAACTTGTGGTTCCATCTCGATCATCTAATTTTGGCTCAGTCC
1 GCTCAGTCTAAATCATTTTCT-TAACTTGTGGCTCAATCTCGATCATCCGATCTTAGCTCAGTCC
* * * *
5593740 AGATAATTTTCCTAACCTATGGCTTAGTCTTGGTTATCCGATCTT
65 AGATTATTTTCCTAACTTATGGCTTAGTCTTGGTCATCTGATCTT
* * * * * ** *
5593785 GCTCAGTCTAGATCATTTTCTTAACTTATGGCTCAATTTTGGTCATTTGATCTTAGTTCAGTCCA
1 GCTCAGTCTAAATCATTTTCTTAACTTGTGGCTCAATCTCGATCATCCGATCTTAGCTCAGTCCA
* * * ** * * *
5593850 GATTATTTTCTTGACTTGTGATTTTGTCCTGGTCATCTAATCTT
66 GATTATTTTCCTAACTTATGGCTTAGTCTTGGTCATCTGATCTT
* * *
5593894 GACTCAGTCTAAATCATTTTTTTAACTTGTGGCTCAATCTCGATCATCCGATCTTGGCTCAGTCT
1 G-CTCAGTCTAAATCATTTTCTTAACTTGTGGCTCAATCTCGATCATCCGATCTTAGCTCAGTCC
* * * *
5593959 AGATCATTTTCCTAACTTATGGCTCAATCTTGGTCATTTGATCTTT
65 AGATTATTTTCCTAACTTATGGCTTAGTCTTGGTCATCTGATC-TT
* * * ** * *
5594005 GCTCAGTCTAAATAATTTTCTTGACTTGTGGTTCCGTCTC-AGTCATCCGATCTTAACTCAGTCT
1 GCTCAGTCTAAATCATTTTCTTAACTTGTGGCTCAATCTCGA-TCATCCGATCTTAGCTCAGTCC
** * * ** *
5594069 AGATTATTTTTTTGACTTATGGCTCAGTCACGATCATCTGATCTT
65 AGATTATTTTCCTAACTTATGGCTTAGTCTTGGTCATCTGATCTT
* *
5594114 GGCTCAGTCTAGATCATGTTCT
1 -GCTCAGTCTAAATCATTTTCT
5594136 AGACTTGAGG
Statistics
Matches: 277, Mismatches: 69, Indels: 9
0.78 0.19 0.03
Matches are distributed among these distances:
109 85 0.31
110 189 0.68
111 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (109 bp):
GCTCAGTCTAAATCATTTTCTTAACTTGTGGCTCAATCTCGATCATCCGATCTTAGCTCAGTCCA
GATTATTTTCCTAACTTATGGCTTAGTCTTGGTCATCTGATCTT
Found at i:5594161 original size:165 final size:164
Alignment explanation
Indices: 5593775--5594213 Score: 517
Period size: 165 Copynumber: 2.7 Consensus size: 164
5593765 AGTCTTGGTT
*
5593775 ATCCGATCTT-GCTCAGTCTAGATCATTTTCTTAACTTATGGCTCAATTTTGGTCATTTGATCTT
1 ATCCGATCTTGGCTCAGTCTAGATCATTTTC-TAACTTATGGCTCAATCTTGGTCATTTGATCTT
* * * * * ** * * *
5593839 AGTTCAGTCCAGATTATTTTCTTGACTTGTGATTTTGTCCTGGTCATCTAATCTTGACTCAGTCT
65 TGCTCAGTCTAGATAATTTTCTTGACTTGTGGTTCCGTCCTAGTCATCCAATCTTAACTCAGTCT
* *
5593904 AAATCATTTTTTTAACTTGTGGCTCAATCTCGATC
130 AAATCATTTTTTTAACTTATGGCTCAATCACGATC
5593939 ATCCGATCTTGGCTCAGTCTAGATCATTTTCCTAACTTATGGCTCAATCTTGGTCATTTGATCTT
1 ATCCGATCTTGGCTCAGTCTAGATCATTTT-CTAACTTATGGCTCAATCTTGGTCATTTGATCTT
* *
5594004 TGCTCAGTCTAAATAATTTTCTTGACTTGTGGTTCCGT-CTCAGTCATCCGATCTTAACTCAGTC
65 TGCTCAGTCTAGATAATTTTCTTGACTTGTGGTTCCGTCCT-AGTCATCCAATCTTAACTCAGTC
* * * *
5594068 TAGATTATTTTTTTGACTTATGGCTCAGTCACGATC
129 TAAATCATTTTTTTAACTTATGGCTCAATCACGATC
* * * * * **
5594104 ATCTGATCTTGGCTCAGTCTAGATCATGTTCTAGACTTGA-GGTTCCATCTCGGTCATTCAATC-
1 ATCCGATCTTGGCTCAGTCTAGATCATTTTCTA-ACTT-ATGGCTCAATCTTGGTCATTTGATCT
* * * **
5594167 TTGCCTTAGTCTAGATCATTTTCTAGACTTGTGGTTCAATCCTAGTC
64 TTG-CTCAGTCTAGATAATTTTCTTGACTTGTGGTTCCGTCCTAGTC
5594214 GCTTGATCTT
Statistics
Matches: 236, Mismatches: 32, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
164 18 0.08
165 214 0.91
166 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.42
Consensus pattern (164 bp):
ATCCGATCTTGGCTCAGTCTAGATCATTTTCTAACTTATGGCTCAATCTTGGTCATTTGATCTTT
GCTCAGTCTAGATAATTTTCTTGACTTGTGGTTCCGTCCTAGTCATCCAATCTTAACTCAGTCTA
AATCATTTTTTTAACTTATGGCTCAATCACGATC
Found at i:5594221 original size:110 final size:109
Alignment explanation
Indices: 5593675--5594227 Score: 357
Period size: 110 Copynumber: 5.0 Consensus size: 109
5593665 TTTCAATTTC
* * * ** * *
5593675 GGCTCAGTCCAAATCATTTT-TCAAACTTGTGGTTCCATCTCGATCATCTAATTTTGGCTCAGTC
1 GGCTCAGTCTAAATCATTTTCT-AGACTTGTGGTTCCATCTCGGTCATCCGATCTTGACTCAGTC
* * * * * * * * *
5593739 CAGATAATTTTCCTA-ACCTATGGCTTAGTCTTGGTTATCCGATCTT
65 TAGATCATTTT-CTAGACTTATGGCTCAATCCTAGTCAT-TGATCTT
* * * * * * ** *
5593785 -GCTCAGTCTAGATCATTTTCTTA-ACTTATGGCTCAATTTTGGTCATTTGATCTT-AGTTCAGT
1 GGCTCAGTCTAAATCATTTTC-TAGACTTGTGGTTCCATCTCGGTCATCCGATCTTGA-CTCAGT
* * * * ** *** * *
5593847 CCAGATTATTTTCTTGACTTGTGATTTTGTCCTGGTCATCTAATCTT
64 CTAGATCATTTTCTAGACTTATGGCTCAATCCTAGTCAT-TGATCTT
* * * * * *
5593894 GACTCAGTCTAAATCATTTTTTTA-ACTTGTGGCTCAATCTCGATCATCCGATCTTGGCTCAGTC
1 GGCTCAGTCTAAATCA-TTTTCTAGACTTGTGGTTCCATCTCGGTCATCCGATCTTGACTCAGTC
* *
5593958 TAGATCATTTTCCTA-ACTTATGGCTCAATCTTGGTCATTTGATCTT
65 TAGATCATTTT-CTAGACTTATGGCTCAATCCTAGTCA-TTGATCTT
* * * * * *
5594004 TGCTCAGTCTAAATAATTTTCTTGACTTGTGGTTCCGTCTCAGTCATCCGATCTTAACTCAGTCT
1 GGCTCAGTCTAAATCATTTTCTAGACTTGTGGTTCCATCTCGGTCATCCGATCTTGACTCAGTCT
* * * * *
5594069 AGATTATTTTTTTGACTTATGGCTCAGTCACGA-TCATCTGATCTT
66 AGATCATTTTCTAGACTTATGGCTCAATC-CTAGTCAT-TGATCTT
* * * * * * *
5594114 GGCTCAGTCTAGATCATGTTCTAGACTTGAGGTTCCATCTCGGTCATTCAATCTTGCCTTAGTCT
1 GGCTCAGTCTAAATCATTTTCTAGACTTGTGGTTCCATCTCGGTCATCCGATCTTGACTCAGTCT
* * *
5594179 AGATCATTTTCTAGACTTGTGGTTCAATCCTAGTCGCTTGATCTT
66 AGATCATTTTCTAGACTTATGGCTCAATCCTAGTC-ATTGATCTT
5594224 GGCT
1 GGCT
5594228 TAATCCAGAT
Statistics
Matches: 342, Mismatches: 86, Indels: 30
0.75 0.19 0.07
Matches are distributed among these distances:
108 2 0.01
109 86 0.25
110 245 0.72
111 9 0.03
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (109 bp):
GGCTCAGTCTAAATCATTTTCTAGACTTGTGGTTCCATCTCGGTCATCCGATCTTGACTCAGTCT
AGATCATTTTCTAGACTTATGGCTCAATCCTAGTCATTGATCTT
Found at i:5594223 original size:55 final size:54
Alignment explanation
Indices: 5593889--5594251 Score: 191
Period size: 55 Copynumber: 6.6 Consensus size: 54
5593879 TGGTCATCTA
* * * * * * *
5593889 ATCTTGACTCAGTCTAAATCATTTTTTTA-ACTTGTGGCTCAATCTC-GATCATCCG
1 ATCTTGGCTTAGTCTAGATCA-TTTTCTAGACTTGAGGTTCAATCTCAG-TCAT-TG
* * **
5593944 ATCTTGGCTCAGTCTAGATCATTTTCCTA-ACTT-ATGGCTCAATCTTGGTCATTTG
1 ATCTTGGCTTAGTCTAGATCATTTT-CTAGACTTGA-GGTTCAATCTCAGTCA-TTG
* * * * * * ** *
5593999 ATCTTTGCTCAGTCTAAATAATTTTCTTGACTTGTGGTTCCGTCTCAGTCATCCG
1 ATCTTGGCTTAGTCTAGATCATTTTCTAGACTTGAGGTTCAATCTCAGTCAT-TG
** * * * * * * *
5594054 ATCTTAACTCAGTCTAGATTATTTTTTTGACTT-ATGGCTCAGTCAC-GATCATCTG
1 ATCTTGGCTTAGTCTAGATCATTTTCTAGACTTGA-GGTTCAATCTCAG-TCAT-TG
* * * * *
5594109 ATCTTGGCTCAGTCTAGATCATGTTCTAGACTTGAGGTTCCATCTCGGTCATTCA
1 ATCTTGGCTTAGTCTAGATCATTTTCTAGACTTGAGGTTCAATCTCAGTCATT-G
* * *
5594164 ATCTTGCCTTAGTCTAGATCATTTTCTAGACTTGTGGTTCAATC-CTAGTCGCTTG
1 ATCTTGGCTTAGTCTAGATCATTTTCTAGACTTGAGGTTCAATCTC-AGTC-ATTG
* * * *
5594219 ATCTTGGCTTAATCCAGATTATTTTCTTGACTT
1 ATCTTGGCTTAGTCTAGATCATTTTCTAGACTT
5594252 ACAGTTTAGT
Statistics
Matches: 243, Mismatches: 51, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
54 10 0.04
55 227 0.93
56 6 0.02
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (54 bp):
ATCTTGGCTTAGTCTAGATCATTTTCTAGACTTGAGGTTCAATCTCAGTCATTG
Found at i:5594586 original size:28 final size:27
Alignment explanation
Indices: 5594555--5594634 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
5594545 GTTATATTAC
5594555 TATAGTATATTATCTTGTATTATTATAG
1 TATAGTATATTAT-TTGTATTATTATAG
* *
5594583 TATAGTACATTATATCGTATATATTATAG
1 TATAGTATATTAT-TTGTAT-TATTATAG
* *
5594612 TTTA-TATGTTA-TTGTATTATTAT
1 TATAGTATATTATTTGTATTATTAT
5594635 TATTATTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 6 0.14
26 5 0.11
28 22 0.50
29 11 0.25
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (27 bp):
TATAGTATATTATTTGTATTATTATAG
Found at i:5594617 original size:14 final size:15
Alignment explanation
Indices: 5594600--5594663 Score: 50
Period size: 14 Copynumber: 4.7 Consensus size: 15
5594590 CATTATATCG
5594600 TATATATTATAGT-T
1 TATATATTATAGTAT
* *
5594614 TATATGTTATTGTAT
1 TATATATTATAGTAT
5594629 TAT-TATTAT--TAT
1 TATATATTATAGTAT
**
5594641 TAT-TATTATACCAT
1 TATATATTATAGTAT
5594655 TAT-TATTAT
1 TATATATTAT
5594664 TATTTATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
12 12 0.28
14 27 0.63
15 4 0.09
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (15 bp):
TATATATTATAGTAT
Found at i:5594634 original size:3 final size:3
Alignment explanation
Indices: 5594626--5594677 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
5594616 TATGTTATTG
* *
5594626 TAT TAT TAT TAT TAT TAT TAT TA- TAC CAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
5594671 TAT TAT T
1 TAT TAT T
5594678 TTCTTTCATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5595514 original size:11 final size:11
Alignment explanation
Indices: 5595485--5595584 Score: 53
Period size: 12 Copynumber: 8.4 Consensus size: 11
5595475 TTTTCTTTTC
5595485 TTTATTTTCATT
1 TTTATTTT-ATT
*
5595497 TTCATTTTATT
1 TTTATTTTATT
5595508 TTTA-TTTATT
1 TTTATTTTATT
*
5595518 TTATATTTTAAAAT
1 TT-TATTTT--ATT
5595532 TTT-TTTTAGTT
1 TTTATTTTA-TT
*
5595543 TTTTTATTTATT
1 TTTAT-TTTATT
5595555 TTACTAACTTTTATT
1 TT--T-A-TTTTATT
5595570 ATTTA-TTTATT
1 -TTTATTTTATT
5595581 TTTA
1 TTTA
5595585 CTAAGAAATT
Statistics
Matches: 71, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
10 13 0.18
11 18 0.25
12 19 0.27
13 6 0.08
14 6 0.08
15 6 0.08
16 3 0.04
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:5595579 original size:30 final size:29
Alignment explanation
Indices: 5595509--5595581 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 29
5595499 CATTTTATTT
* * *
5595509 TTATTTATTT-TATATTTTAAAATTTTTT
1 TTATTTATTTATTTATTTTAAAACTTTTA
* *
5595537 TTAGTTTTTTTATTTATTTTACTAACTTTTA
1 TTA-TTTATTTATTTATTTTA-AAACTTTTA
5595568 TTATTTATTTATTT
1 TTATTTATTTATTT
5595582 TTACTAAGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.08
29 6 0.17
30 18 0.50
31 9 0.25
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (29 bp):
TTATTTATTTATTTATTTTAAAACTTTTA
Found at i:5599299 original size:38 final size:38
Alignment explanation
Indices: 5599245--5599327 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
5599235 CCAAGAATAC
5599245 TTCTAAGAATCCAAGAATACCCACCAAAGGTTCAAACT
1 TTCTAAGAATCCAAGAATACCCACCAAAGGTTCAAACT
* * *
5599283 TTTTAAGAATCCAAGAATACCCATCAAAGGTTCAAGCT
1 TTCTAAGAATCCAAGAATACCCACCAAAGGTTCAAACT
5599321 TTCTAAG
1 TTCTAAG
5599328 GACTCAGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (38 bp):
TTCTAAGAATCCAAGAATACCCACCAAAGGTTCAAACT
Found at i:5599361 original size:19 final size:19
Alignment explanation
Indices: 5599337--5599386 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
5599327 GGACTCAGAG
5599337 AGTAGTTTTTACTGGAATA
1 AGTAGTTTTTACTGGAATA
5599356 AGTAGTTTTTACTGGAATA
1 AGTAGTTTTTACTGGAATA
5599375 AGTAGTTTTTAC
1 AGTAGTTTTTAC
5599387 CCAGATGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (19 bp):
AGTAGTTTTTACTGGAATA
Found at i:5613548 original size:16 final size:19
Alignment explanation
Indices: 5613506--5613548 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5613496 ATCATTTTTC
5613506 ATTATTATTATTGTTATTA
1 ATTATTATTATTGTTATTA
*
5613525 GTTATTATTATT-TTA-TA
1 ATTATTATTATTGTTATTA
5613542 ATT-TTAT
1 ATTATTAT
5613549 AAGGTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 3 0.14
19 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATTATTATTATTGTTATTA
Found at i:5614910 original size:16 final size:17
Alignment explanation
Indices: 5614876--5614913 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5614866 TTTTTTTTCC
*
5614876 TTTTTGTTTTTAGCCTT
1 TTTTTGTTTTTAGCATT
*
5614893 TTTTTGTTTTT-GTATT
1 TTTTTGTTTTTAGCATT
5614909 TTTTT
1 TTTTT
5614914 TGTTAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.79
Consensus pattern (17 bp):
TTTTTGTTTTTAGCATT
Found at i:5615880 original size:80 final size:80
Alignment explanation
Indices: 5615791--5615942 Score: 232
Period size: 80 Copynumber: 1.9 Consensus size: 80
5615781 AATTGAACCG
* *
5615791 AATTTATTAATTTCAAAGAAAATCTAATTGATTGGAATTTAATTTGATTAATTCAGTTAATTTTT
1 AATTTATTAATTTCAAAGAAAATCTAATTGATTGGAATTTAACTTGATTAATTCAGATAATTTTT
5615856 GAATTAACTCAATCA
66 GAATTAACTCAATCA
** * * * *
5615871 AATTTATTAATTTTGAAGAACATCTAATTGATTGGAATTTAACTTGTTTAATTTAGATATTTTTT
1 AATTTATTAATTTCAAAGAAAATCTAATTGATTGGAATTTAACTTGATTAATTCAGATAATTTTT
5615936 GAATTAA
66 GAATTAA
5615943 TTTAATAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (80 bp):
AATTTATTAATTTCAAAGAAAATCTAATTGATTGGAATTTAACTTGATTAATTCAGATAATTTTT
GAATTAACTCAATCA
Found at i:5621102 original size:29 final size:29
Alignment explanation
Indices: 5621047--5621146 Score: 98
Period size: 30 Copynumber: 3.3 Consensus size: 29
5621037 AAAAAAAAAC
5621047 TTATATATTTTATTATTTTATTTAAATAAATTT
1 TTATAT-TTTTATTATTTTA---AAATAAATTT
*
5621080 TTATATTTTTATTATTTTAAAATAAATTC
1 TTATATTTTTATTATTTTAAAATAAATTT
*
5621109 ATA-ATTTTTAATTTATATTT-AAATAAATTT
1 TTATATTTTT-A-TTAT-TTTAAAATAAATTT
5621139 TTAT-TTTT
1 TTATATTTT
5621147 AATTTGTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
28 6 0.10
29 12 0.20
30 19 0.32
31 3 0.05
32 13 0.22
33 6 0.10
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (29 bp):
TTATATTTTTATTATTTTAAAATAAATTT
Found at i:5621149 original size:29 final size:29
Alignment explanation
Indices: 5621052--5621164 Score: 115
Period size: 29 Copynumber: 3.9 Consensus size: 29
5621042 AAAACTTATA
*
5621052 TATTTTATTATTT-TATTTAAATAAATTTT
1 TATTTT-TAATTTATATTTAAATAAATTTT
* *
5621081 TATATTTTTA-TTAT-TTTAAAATAAATTCAT
1 TAT-TTTTAATTTATATTT-AAATAAATT-TT
*
5621111 AATTTTTAATTTATATTTAAATAAATTTT
1 TATTTTTAATTTATATTTAAATAAATTTT
* *
5621140 TATTTTTAATTTGTATTTATATAAA
1 TATTTTTAATTTATATTTAAATAAA
5621165 ATGTTAACAT
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
28 5 0.07
29 44 0.62
30 19 0.27
31 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
TATTTTTAATTTATATTTAAATAAATTTT
Found at i:5623863 original size:3 final size:3
Alignment explanation
Indices: 5623855--5623902 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
5623845 TTAGGTTAAG
5623855 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5623903 CTTGAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5624580 original size:30 final size:30
Alignment explanation
Indices: 5624507--5624580 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
5624497 ATTGAATTCG
* *
5624507 AATAAATTTTTAATTTTTAATTTACATATA
1 AATAAAATTTTAATTTTTAAATTACATATA
**
5624537 AAT-AGGTTATTAATTTTTAAATTACA-ATTA
1 AATAAAATT-TTAATTTTTAAATTACATA-TA
5624567 AATAAAATTTTAAT
1 AATAAAATTTTAAT
5624581 ATAAATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
29 4 0.11
30 29 0.81
31 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (30 bp):
AATAAAATTTTAATTTTTAAATTACATATA
Found at i:5624665 original size:29 final size:30
Alignment explanation
Indices: 5624600--5624677 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
5624590 TATTTTATTT
* ** *
5624600 AACAAAAAAATTTATTTCGATACAAATCAA
1 AACATAAAAATTTATTTAAATACAAATAAA
*
5624630 AACATAAAAATTTATTTAAATA-TAATAAA
1 AACATAAAAATTTATTTAAATACAAATAAA
*
5624659 AATATAAAAATTTATTTAA
1 AACATAAAAATTTATTTAA
5624678 GAAAAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.33
Consensus pattern (30 bp):
AACATAAAAATTTATTTAAATACAAATAAA
Found at i:5625741 original size:2 final size:2
Alignment explanation
Indices: 5625734--5625761 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5625724 GTCCGATTTT
5625734 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
5625762 CAAAATGCAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5625960 original size:24 final size:24
Alignment explanation
Indices: 5625928--5625990 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
5625918 AAGGTTTTTT
5625928 TTTTTTTTTTTTAACT-TATTTCTG
1 TTTTTTTTTTTTAACTAT-TTTCTG
**
5625952 TTTTTTTTTTAAAACTATTTTCTG
1 TTTTTTTTTTTTAACTATTTTCTG
5625976 TTTTTTATTTCTTTA
1 TTTTTT-TTT-TTTA
5625991 TTTTATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 26 0.81
25 4 0.12
26 2 0.06
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (24 bp):
TTTTTTTTTTTTAACTATTTTCTG
Found at i:5626998 original size:19 final size:17
Alignment explanation
Indices: 5626974--5627014 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 17
5626964 AAAAAAATCA
5626974 ATTTATTTACAATTATTTT
1 ATTTATTTACAA--ATTTT
5626993 ATTTATTTACAAATTTT
1 ATTTATTTACAAATTTT
5627010 ATTTA
1 ATTTA
5627015 CAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.45
19 12 0.55
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATTTACAAATTTT
Found at i:5627012 original size:13 final size:13
Alignment explanation
Indices: 5626994--5627019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5626984 AATTATTTTA
5626994 TTTATTTACAAAT
1 TTTATTTACAAAT
5627007 TTTATTTACAAAT
1 TTTATTTACAAAT
5627020 AATAAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTATTTACAAAT
Found at i:5628929 original size:66 final size:64
Alignment explanation
Indices: 5628849--5629091 Score: 177
Period size: 66 Copynumber: 3.7 Consensus size: 64
5628839 TGGAAAGAAT
* * *
5628849 ATAAAACTTTTTAATCTTTTGAAAAAAATTTATGAATTAATTTTCAAAATTTTAAATTTTAAATA
1 ATAAAATTTTTTAAT-TTTTGATAAAATTTTATGAATTAATTTTCAAAA-TTTAAATTTTAAATA
5628914 A
64 A
* * * * * ** *
5628915 ATAAAATTTTTTAATATCTTGATAAGATTTTTTGAATGAAATTTTTAAAAAATTTAAATTCCATA
1 ATAAAATTTTTTAAT-TTTTGATAAAATTTTATGAAT-TAA-TTTT-CAAAATTTAAATTTTAAA
*
5628980 TCA
62 TAA
* * ** * * * *
5628983 ATAAAAATCTTTAATAGTGGATAAAATTTTATGAATTAATTTTCAAAAATT-AATTTTTAATCTA
1 ATAAAATTTTTTAATTTTTGATAAAATTTTATGAATTAATTTTCAAAATTTAAATTTTAAAT-AA
* * ** *
5629047 ATAAAATCTTTTAA--TATGGCAAAACTTTATGAATTAATTTTCAAA
1 ATAAAATTTTTTAATTTTTGATAAAATTTTATGAATTAATTTTCAAA
5629092 TTCATAAAAA
Statistics
Matches: 136, Mismatches: 37, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
62 25 0.18
63 6 0.04
64 18 0.13
65 4 0.03
66 32 0.24
67 18 0.13
68 29 0.21
69 4 0.03
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (64 bp):
ATAAAATTTTTTAATTTTTGATAAAATTTTATGAATTAATTTTCAAAATTTAAATTTTAAATAA
Found at i:5631389 original size:3 final size:3
Alignment explanation
Indices: 5631383--5631415 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5631373 TTTTTTAATT
5631383 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5631416 CTTTAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5634127 original size:13 final size:13
Alignment explanation
Indices: 5634109--5634143 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
5634099 AAAATATCTT
5634109 TTCTTCCAACCTC
1 TTCTTCCAACCTC
5634122 TTCTTCCAACCTC
1 TTCTTCCAACCTC
5634135 TTCTTCCAA
1 TTCTTCCAA
5634144 AAAGCTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCTTCCAACCTC
Found at i:5634651 original size:12 final size:13
Alignment explanation
Indices: 5634634--5634662 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5634624 TATAATACCC
5634634 TTTTTTTTTTA-A
1 TTTTTTTTTTACA
5634646 TTTTTTTTTTACA
1 TTTTTTTTTTACA
5634659 TTTT
1 TTTT
5634663 GACATCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTACA
Found at i:5634914 original size:2 final size:2
Alignment explanation
Indices: 5634907--5634934 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5634897 ATAAAACGTA
5634907 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
5634935 GAAAATAGCT
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:5641677 original size:12 final size:12
Alignment explanation
Indices: 5641660--5641689 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5641650 TTATCCCTTA
5641660 AAGCTTTTGAAG
1 AAGCTTTTGAAG
*
5641672 AAGCTTTTGTAG
1 AAGCTTTTGAAG
5641684 AAGCTT
1 AAGCTT
5641690 CCTCTATAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (12 bp):
AAGCTTTTGAAG
Found at i:5641844 original size:20 final size:20
Alignment explanation
Indices: 5641819--5641856 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5641809 TGGGGGTTAG
*
5641819 GGAAACTACTGTAAAGAAGA
1 GGAAACAACTGTAAAGAAGA
*
5641839 GGAAACAACTGTATAGAA
1 GGAAACAACTGTAAAGAA
5641857 TTTTTGATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.16
Consensus pattern (20 bp):
GGAAACAACTGTAAAGAAGA
Found at i:5644189 original size:20 final size:20
Alignment explanation
Indices: 5644164--5644212 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5644154 CATATTCTTT
5644164 GTAAAATGACTAAATGAGAA
1 GTAAAATGACTAAATGAGAA
5644184 GTAAAATGACTAAATGAGAA
1 GTAAAATGACTAAATGAGAA
*
5644204 GTACAATGA
1 GTAAAATGA
5644213 TATGCTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.20
Consensus pattern (20 bp):
GTAAAATGACTAAATGAGAA
Found at i:5646695 original size:17 final size:18
Alignment explanation
Indices: 5646669--5646702 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5646659 CAATCCCATT
5646669 TAATACATTA-TATTATG
1 TAATACATTATTATTATG
*
5646686 TAATAGATTATTATTAT
1 TAATACATTATTATTAT
5646703 TATGCACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (18 bp):
TAATACATTATTATTATG
Found at i:5649665 original size:92 final size:94
Alignment explanation
Indices: 5649569--5649752 Score: 300
Period size: 94 Copynumber: 2.0 Consensus size: 94
5649559 ATTTTCCATA
* *
5649569 ATTTGAGCTTATTTAGAAATTTTATTTTTT-TATTTT-TTAAGAAAATAATATGACAATTACTTT
1 ATTTGAGCATATTTAAAAATTTTATTTTTTGTATTTTCTTAAGAAAATAATATGACAATTACTTT
5649632 TCTCGAGATTTCATTTAAATTTTTTCACC
66 TCTCGAGATTTCATTTAAATTTTTTCACC
* * *
5649661 ATTTGGGCATATTTAAAAATTTTATTTTTTGTTTTTTCTTAAGAAAGTAATATGACAATTACTTT
1 ATTTGAGCATATTTAAAAATTTTATTTTTTGTATTTTCTTAAGAAAATAATATGACAATTACTTT
*
5649726 TCTTGAGATTTCATTTAAATTTTTTCA
66 TCTCGAGATTTCATTTAAATTTTTTCA
5649753 TAATTACTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 27 0.32
93 5 0.06
94 52 0.62
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.52
Consensus pattern (94 bp):
ATTTGAGCATATTTAAAAATTTTATTTTTTGTATTTTCTTAAGAAAATAATATGACAATTACTTT
TCTCGAGATTTCATTTAAATTTTTTCACC
Found at i:5650344 original size:11 final size:11
Alignment explanation
Indices: 5650306--5650367 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 11
5650296 AAATACTCAT
*
5650306 AAAATAAACAA
1 AAAATAAATAA
*
5650317 ACATATAAATAAA
1 A-AAATAAAT-AA
*
5650330 AAAATAATTAA
1 AAAATAAATAA
5650341 AAAATAAAATAA
1 AAAAT-AAATAA
*
5650353 AAAAT-ACTAA
1 AAAATAAATAA
5650363 AAAAT
1 AAAAT
5650368 CGAAACGGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
10 9 0.21
11 8 0.19
12 22 0.52
13 3 0.07
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:5650357 original size:12 final size:13
Alignment explanation
Indices: 5650319--5650363 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
5650309 ATAAACAAAC
5650319 ATATAAATAAAAA
1 ATATAAATAAAAA
*
5650332 A-ATAATTAAAAA
1 ATATAAATAAAAA
5650344 ATA-AAATAAAAA
1 ATATAAATAAAAA
5650356 ATACTAAA
1 ATA-TAAA
5650364 AAATCGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 22 0.81
13 2 0.07
14 3 0.11
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (13 bp):
ATATAAATAAAAA
Found at i:5650357 original size:23 final size:23
Alignment explanation
Indices: 5650323--5650367 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5650313 ACAAACATAT
*
5650323 AAATAAAAAAATAATTAAAAAATA
1 AAATAAAAAAAT-ACTAAAAAATA
5650347 AAAT-AAAAAATACTAAAAAAT
1 AAATAAAAAAATACTAAAAAAT
5650368 CGAAACGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 7 0.35
24 4 0.20
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAAAAAAATACTAAAAAATA
Found at i:5651367 original size:41 final size:41
Alignment explanation
Indices: 5651318--5651601 Score: 327
Period size: 41 Copynumber: 6.9 Consensus size: 41
5651308 AACAAAGCTT
* * * *
5651318 CTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAATACTC
1 CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAATGCTC
* * *
5651359 CTCTAAACAGAGGCACCACAACTTTGGAAAGTAAATTGCTC
1 CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAATGCTC
* * *
5651400 CTCTAAATAGAGGCACCATAACTTTGAAAAATAAATTGCTC
1 CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAATGCTC
* *
5651441 CTTTAAACAGATGCACCACAACTTTGGAAAAATAAAATGCTC
1 CTCTAAACAGAGGCACCACAACTTT-GAAAAATAAAATGCTC
* * * * * *
5651483 TTCTAAA-AGGAAGTACCACAACTTTGAAAAATAAACTACTT
1 CTCTAAACA-GAGGCACCACAACTTTGAAAAATAAAATGCTC
* * * *
5651524 TTTTAAACAGAGGCACCATAACTTTGAAAAATAAATTGCTC
1 CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAATGCTC
* *
5651565 CTCTAAACAGAGGCACCATATCTTTGAAAAATAAAAT
1 CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
5651602 TACTCCTTGA
Statistics
Matches: 206, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
41 171 0.83
42 35 0.17
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (41 bp):
CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAATGCTC
Found at i:5651540 original size:124 final size:123
Alignment explanation
Indices: 5651318--5651608 Score: 377
Period size: 124 Copynumber: 2.3 Consensus size: 123
5651308 AACAAAGCTT
* * * *
5651318 CTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAATACTCCTCTAAACAGAGGCACCACAACTT
1 CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAATACTCCTCTAAACAGAAGCACCACAACTT
* * * * *
5651383 TGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCATAACTTTGAAAAATAAATTGCTC
66 TGAAAAATAAACTACTCCTCTAAACAGAGGCACCATAACTTTGAAAAATAAATTGCTC
* * * * *
5651441 CTTTAAACAGATGCACCACAACTTTGGAAAAATAAAATGCTCTTCTAAA-AGGAAGTACCACAAC
1 CTCTAAACAGAGGCACCACAACTTT-GAAAAATAAAATACTCCTCTAAACA-GAAGCACCACAAC
** *
5651505 TTTGAAAAATAAACTACTTTTTTAAACAGAGGCACCATAACTTTGAAAAATAAATTGCTC
64 TTTGAAAAATAAACTACTCCTCTAAACAGAGGCACCATAACTTTGAAAAATAAATTGCTC
* *
5651565 CTCTAAACAGAGGCACCATATCTTTGAAAAATAAAATTACTCCT
1 CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAA-TACTCCT
5651609 TGACAATCAT
Statistics
Matches: 142, Mismatches: 23, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
123 32 0.23
124 110 0.77
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (123 bp):
CTCTAAACAGAGGCACCACAACTTTGAAAAATAAAATACTCCTCTAAACAGAAGCACCACAACTT
TGAAAAATAAACTACTCCTCTAAACAGAGGCACCATAACTTTGAAAAATAAATTGCTC
Found at i:5651972 original size:80 final size:79
Alignment explanation
Indices: 5651861--5652052 Score: 215
Period size: 79 Copynumber: 2.4 Consensus size: 79
5651851 TGAATTTTGG
* * * ** * * *
5651861 AGATTCACATCTAAAAGTTCAAAGCTTCTCATTCGAGTCCAAAGGCTCACATTTGATAAAT-TTT
1 AGATTCACATTTGAAA-TTCAAAGATTCTCATTCGAGTCCAAAAACTCACATTCGACAAATATTG
5651925 AAGGTTTCACAACTCAA
65 AA--TTTCACAACTCAA
* * * *
5651942 AGATTCACATTTGAAATTCAAATATTCTCATTTGAGTTCAAAAATTCACATTCGACAAATATTGA
1 AGATTCACATTTGAAATTCAAAGATTCTCATTCGAGTCCAAAAACTCACATTCGACAAATATTGA
* *
5652007 ATTTCATACCTCAA
66 ATTTCACAACTCAA
*
5652021 AGATTCTCATTTGAAATTCAAAGATTCTCATT
1 AGATTCACATTTGAAATTCAAAGATTCTCATT
5652053 TGAGAACTCA
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 41 0.44
80 35 0.37
81 18 0.19
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (79 bp):
AGATTCACATTTGAAATTCAAAGATTCTCATTCGAGTCCAAAAACTCACATTCGACAAATATTGA
ATTTCACAACTCAA
Found at i:5651983 original size:20 final size:21
Alignment explanation
Indices: 5651938--5651993 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
5651928 GTTTCACAAC
*
5651938 TCAAAGATTCACATTTGAAAT
1 TCAAAAATTCACATTTGAAAT
* * *
5651959 TCAAATATTCTCATTTG-AGT
1 TCAAAAATTCACATTTGAAAT
5651979 TCAAAAATTCACATT
1 TCAAAAATTCACATT
5651994 CGACAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (21 bp):
TCAAAAATTCACATTTGAAAT
Found at i:5652069 original size:22 final size:22
Alignment explanation
Indices: 5652016--5652078 Score: 85
Period size: 21 Copynumber: 2.9 Consensus size: 22
5652006 AATTTCATAC
5652016 CTCAAAGATTCTCATTTGA-AA
1 CTCAAAGATTCTCATTTGAGAA
*
5652037 TTCAAAGATTCTCATTTGAGAA
1 CTCAAAGATTCTCATTTGAGAA
*
5652059 CTC-AAGAATTCTCTTTTGAG
1 CTCAAAG-ATTCTCATTTGAG
5652079 GATTCATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.57
22 16 0.43
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (22 bp):
CTCAAAGATTCTCATTTGAGAA
Found at i:5652980 original size:10 final size:9
Alignment explanation
Indices: 5652960--5652990 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5652950 TCCTTTTTCA
5652960 TTTTTTATT
1 TTTTTTATT
5652969 TTTTTTATT
1 TTTTTTATT
*
5652978 TTTTTTCTT
1 TTTTTTATT
5652987 TTTT
1 TTTT
5652991 CAAGCATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTATT
Found at i:5657890 original size:145 final size:145
Alignment explanation
Indices: 5657627--5657915 Score: 542
Period size: 145 Copynumber: 2.0 Consensus size: 145
5657617 AACAGAAACA
5657627 TTATGTGCCACACATGCCTAATTTAGTATTTTTAGCAAAGCATTCTGATGTGGTTTTAAATTCAA
1 TTATGTGCCACACATGCCTAATTTAGTATTTTTAGCAAAGCATTCTGATGTGGTTTTAAATTCAA
5657692 TAGCAGTGATAATAATGAGATTCATGTCGGTATCTTATTTAACTGTTCAACCATAGAATATTCAT
66 TAGCAGTGATAATAATGAGATTCATGTCGGTATCTTATTTAACTGTTCAACCATAGAATATTCAT
*
5657757 TGTGTTTTATCAACT
131 TATGTTTTATCAACT
*
5657772 TTATGTGCCACACATGCCTAATTTAGTATTTTTAGCAAAGCATTCTGATGTGGTTTTGAATTCAA
1 TTATGTGCCACACATGCCTAATTTAGTATTTTTAGCAAAGCATTCTGATGTGGTTTTAAATTCAA
* *
5657837 TAGCAGTGATAATAATGAGATTCATGTTGGTATCTTATTTAATTGTTCAACCATAGAATATTCAT
66 TAGCAGTGATAATAATGAGATTCATGTCGGTATCTTATTTAACTGTTCAACCATAGAATATTCAT
5657902 TATGTTTTATCAAC
131 TATGTTTTATCAAC
5657916 CATAGCAAAG
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 140 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (145 bp):
TTATGTGCCACACATGCCTAATTTAGTATTTTTAGCAAAGCATTCTGATGTGGTTTTAAATTCAA
TAGCAGTGATAATAATGAGATTCATGTCGGTATCTTATTTAACTGTTCAACCATAGAATATTCAT
TATGTTTTATCAACT
Found at i:5664016 original size:149 final size:151
Alignment explanation
Indices: 5663836--5664116 Score: 464
Period size: 151 Copynumber: 1.9 Consensus size: 151
5663826 TTTTTTTAAC
*
5663836 TTCTAAATTTTTCACCATTTAGGTCTATTTAG-AATTCTCTTTT-TTTGGTTT-TTTTTTTAAGA
1 TTCTAAATTTTTCACCATTTAGGCCTATTTAGAAATTCTCTTTTGTTT-GTTTGTTTTTTTAAGA
*
5663898 AAATAATATGATAATTACTTTTCTTGATATTTCATTTAAATTCTTCCATC-ATTTGAGATAAATT
65 AAATAATATGATAATTACTTTTCTTGAGATTTCATTTAAATTCTTCCA-CAATTTGAGATAAATT
5663962 TAAAATATTCTCATTTTTGGAAT
129 TAAAATATTCTCATTTTTGGAAT
*
5663985 TTCTAAATTTTTCACCATTTGGGCC-ATTTTAGAAATTCTCTTTTGTTTGTTTGTTTTTTTAAGA
1 TTCTAAATTTTTCACCATTTAGGCCTA-TTTAGAAATTCTCTTTTGTTTGTTTGTTTTTTTAAGA
*
5664049 AAATAATATGATAATTACTTTTCTTGAGATTTCATTTAAATTCTTCCACAATTTGGGATAAATTT
65 AAATAATATGATAATTACTTTTCTTGAGATTTCATTTAAATTCTTCCACAATTTGAGATAAATTT
5664114 AAA
130 AAA
5664117 TAACTTTCTC
Statistics
Matches: 123, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
148 1 0.01
149 28 0.23
150 16 0.13
151 78 0.63
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (151 bp):
TTCTAAATTTTTCACCATTTAGGCCTATTTAGAAATTCTCTTTTGTTTGTTTGTTTTTTTAAGAA
AATAATATGATAATTACTTTTCTTGAGATTTCATTTAAATTCTTCCACAATTTGAGATAAATTTA
AAATATTCTCATTTTTGGAAT
Found at i:5664589 original size:201 final size:200
Alignment explanation
Indices: 5664212--5664590 Score: 466
Period size: 201 Copynumber: 1.9 Consensus size: 200
5664202 CAACCAAAAT
* *
5664212 TTTTTATTTGAAAAAGAATACAATTACTTTTATTGAAATTTCATCTAAATTATTCCACCATTTGG
1 TTTTTATTTGAAAAAGAATACAATTACTTTTATTGAAACTTCATCTAAATTATTCCACAATTTGG
**
5664277 GACAAATTTAAACAAAATTCTCACCTAAAGCCTTCTTAGAAAATTCACAATTTAAAATTTCTAAA
66 GACAAATTTAAACAAAATTCTCACCTAAAGAATTCTTAGAAAATTCACAATTTAAAATTTCTAAA
* * **
5664342 AATCTCATCCTTGGGTAATTTGTATTTAATTCCAAAATTTTTATTTTTATTTGTTTTTCTTTTCC
131 AATCTCATCATTGGATAATTAATATTTAATTCCAAAATTTTTATTTTTATTTGTTTTTCTTTTCC
5664407 AATTC
196 AATTC
* *
5664412 TTTTTGTTTGAAAATA-AATATTAATTA-TTATTATTGAAAGCTT-ATCTAAATTATTCCACAAT
1 TTTTTATTTGAAAA-AGAATA-CAATTACTT-TTATTGAAA-CTTCATCTAAATTATTCCACAAT
* * * * * *
5664474 TTGGGACAAATTTAGACAAAATATCTCACCT-AGGAATT-TTATAATAATTTACCATTTGAAATT
62 TTGGGACAAATTTAAACAAAAT-TCTCACCTAAAGAATTCTTAGAA-AATTCACAATTTAAAATT
* * *
5664537 TCTATAAAT-TCCATCATTGGATAATTAAT-TTTTATTCTAAAATTTATTATTTTT
125 TCTAAAAATCT-CATCATTGGATAATTAATATTTAATTCCAAAATTT-TTATTTTT
5664591 TTATTTCATT
Statistics
Matches: 152, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
200 39 0.26
201 103 0.68
202 10 0.07
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (200 bp):
TTTTTATTTGAAAAAGAATACAATTACTTTTATTGAAACTTCATCTAAATTATTCCACAATTTGG
GACAAATTTAAACAAAATTCTCACCTAAAGAATTCTTAGAAAATTCACAATTTAAAATTTCTAAA
AATCTCATCATTGGATAATTAATATTTAATTCCAAAATTTTTATTTTTATTTGTTTTTCTTTTCC
AATTC
Found at i:5669468 original size:15 final size:15
Alignment explanation
Indices: 5669446--5669482 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
5669436 TTAATGTTTT
5669446 TCTTTTAAAAAATTA
1 TCTTTTAAAAAATTA
*
5669461 TTTTTTAAAAAATTA
1 TCTTTTAAAAAATTA
5669476 TCTTTTA
1 TCTTTTA
5669483 TATAGGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
TCTTTTAAAAAATTA
Found at i:5675873 original size:3 final size:3
Alignment explanation
Indices: 5675865--5675910 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5675855 AAGGTTAAGG
5675865 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5675911 ATTGTAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5677523 original size:10 final size:10
Alignment explanation
Indices: 5677508--5677535 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5677498 TAGTTTTGAA
5677508 TTTTCAATAC
1 TTTTCAATAC
5677518 TTTTCAATAC
1 TTTTCAATAC
5677528 TTTTCAAT
1 TTTTCAAT
5677536 GAAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTCAATAC
Found at i:5677807 original size:69 final size:69
Alignment explanation
Indices: 5677686--5677822 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 69
5677676 TTATTCTTTT
* * * * * *
5677686 ATAAACGTAATGATTGTAAATTTTTTTAATCAAAGATTATGATTTTACTTTTATGAACTTAGTGA
1 ATAAACGTAATGATTATAAATTTTTTTAATAAAAAATTATGATTTTACTTTTATAAACATAATGA
5677751 TTGC
66 TTGC
* *
5677755 ATAAATGTAATGATTAT-AATTTTTTTAATAAAAAATTATGTTTTTACTTTTTATAAACATAATG
1 ATAAACGTAATGATTATAAATTTTTTTAATAAAAAATTATGATTTTAC-TTTTATAAACATAATG
5677819 ATTG
65 ATTG
5677823 TAAAAAATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
68 27 0.46
69 32 0.54
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (69 bp):
ATAAACGTAATGATTATAAATTTTTTTAATAAAAAATTATGATTTTACTTTTATAAACATAATGA
TTGC
Found at i:5677950 original size:21 final size:22
Alignment explanation
Indices: 5677926--5677968 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5677916 CTATATCCAA
5677926 TAAAATATAGTCTTT-ACTTAT
1 TAAAATATAGTCTTTGACTTAT
* *
5677947 TAAAATGTTGTCTTTGACTTAT
1 TAAAATATAGTCTTTGACTTAT
5677969 ATTTTTATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (22 bp):
TAAAATATAGTCTTTGACTTAT
Found at i:5679569 original size:30 final size:30
Alignment explanation
Indices: 5679512--5679571 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5679502 TAATTATGTA
** *
5679512 AAAATAAATATTTAAAGGCTCATTTAATTG
1 AAAATAAATATTTAAAAACTCAATTAATTG
*
5679542 AAAATAAATATTTAAAAATTCAATTAATTG
1 AAAATAAATATTTAAAAACTCAATTAATTG
5679572 CAATAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.37
Consensus pattern (30 bp):
AAAATAAATATTTAAAAACTCAATTAATTG
Done.