Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 8 of 213
Found at i:2377570 original size:20 final size:19
Alignment explanation
Indices: 2377547--2377596 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2377537 TTGTCTACAT
2377547 TTTTTTTTCTGAATTTTCAC
1 TTTTTTTT-TGAATTTTCAC
* *
2377567 TTTTTCCTTTGAATTTTCTC
1 TTTTT-TTTTGAATTTTCAC
2377587 TTCTTTTTTT
1 TT-TTTTTTT
2377597 TTATCTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.10, C:0.16, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTTTTTTGAATTTTCAC
Found at i:2379704 original size:16 final size:15
Alignment explanation
Indices: 2379674--2379712 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2379664 TGTTTAGTCA
*
2379674 TTAGGGTTTTTGGGT
1 TTAGGGTTTTAGGGT
2379689 TTAGGGATTTTAGGGT
1 TTAGGG-TTTTAGGGT
*
2379705 TTAAGGTT
1 TTAGGGTT
2379713 AGGATTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (15 bp):
TTAGGGTTTTAGGGT
Found at i:2380104 original size:14 final size:14
Alignment explanation
Indices: 2380085--2380115 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2380075 TAACCGCTAT
*
2380085 TGTTAACTGCTAAC
1 TGTTAACTACTAAC
2380099 TGTTAACTACTAAC
1 TGTTAACTACTAAC
2380113 TGT
1 TGT
2380116 CATAACAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (14 bp):
TGTTAACTACTAAC
Found at i:2383088 original size:24 final size:25
Alignment explanation
Indices: 2383046--2383111 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 25
2383036 CAGTAAAATT
* *
2383046 TATTTTTAT-ATTATGTTTTGAT-A
1 TATTTTTATCATTTTATTTTGATCA
*
2383069 TGTTTTTATCATTTTATTTTGATCA
1 TATTTTTATCATTTTATTTTGATCA
*
2383094 TAATTTT-TCATTTTATTT
1 TATTTTTATCATTTTATTT
2383112 GTTCCATTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.22
24 22 0.61
25 6 0.17
ACGTcount: A:0.23, C:0.05, G:0.06, T:0.67
Consensus pattern (25 bp):
TATTTTTATCATTTTATTTTGATCA
Found at i:2388843 original size:29 final size:29
Alignment explanation
Indices: 2388800--2388855 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2388790 GAGGGCATGC
*
2388800 AAAAAGAAAAGGAAGAAGAAAGAAAAAAAT
1 AAAAAGAAAAAGAAGAA-AAAGAAAAAAAT
*
2388830 AAAAA-AAAAAGAAGAAAAAGGAAAAA
1 AAAAAGAAAAAGAAGAAAAAGAAAAAA
2388856 TTATGACACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 10 0.42
30 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (29 bp):
AAAAAGAAAAAGAAGAAAAAGAAAAAAAT
Found at i:2392763 original size:22 final size:20
Alignment explanation
Indices: 2392725--2392764 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2392715 AAAATAAATT
*
2392725 TTTATATTTTTATATTTAAC
1 TTTAAATTTTTATATTTAAC
2392745 TTTAAATTATTTATTATTTA
1 TTTAAATT-TTTA-TATTTA
2392765 TTCTTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAAATTTTTATATTTAAC
Found at i:2395892 original size:21 final size:20
Alignment explanation
Indices: 2395864--2395902 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2395854 TTTTTTTTTG
*
2395864 AATTGAGTCAAGTGAAATGA
1 AATTGAGTCAAGTCAAATGA
2395884 AATTCGAGTCAAGTCAAAT
1 AATT-GAGTCAAGTCAAAT
2395903 CGAATCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (20 bp):
AATTGAGTCAAGTCAAATGA
Found at i:2395959 original size:20 final size:19
Alignment explanation
Indices: 2395932--2395984 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
2395922 CAAGTTAAAT
2395932 TTTTAAAAAAAAATAAACA
1 TTTTAAAAAAAAATAAACA
*
2395951 TTTTAAAAAAAATTAAACA
1 TTTTAAAAAAAAATAAACA
* *
2395970 TTTCAAATAAAAATA
1 TTTTAAAAAAAAATA
2395985 TTATTAAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (19 bp):
TTTTAAAAAAAAATAAACA
Found at i:2396217 original size:26 final size:26
Alignment explanation
Indices: 2396165--2396218 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2396155 TTTTATAATT
**
2396165 TTTTTAAAAATATATAATTTTTGAAA
1 TTTTTAAAAATATATAATTTTAAAAA
*
2396191 TTTTTATAAATAT-TGAATTTTAAAAA
1 TTTTTAAAAATATAT-AATTTTAAAAA
2396217 TT
1 TT
2396219 ATTTTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
TTTTTAAAAATATATAATTTTAAAAA
Found at i:2399962 original size:16 final size:17
Alignment explanation
Indices: 2399933--2399966 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2399923 TGAATTGTAT
2399933 ATATGTATACATATATA
1 ATATGTATACATATATA
*
2399950 ATATGT-TATATATATA
1 ATATGTATACATATATA
2399966 A
1 A
2399967 GTAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGTATACATATATA
Found at i:2400195 original size:19 final size:19
Alignment explanation
Indices: 2400148--2400195 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
2400138 GTTGTCTACA
*
2400148 TTTTTTCTGAATTTTCACT
1 TTTTTTTTGAATTTTCACT
*
2400167 TTTTCCTTTGAATTTTCACT
1 TTTT-TTTTGAATTTTCACT
2400187 TTTTTTTTG
1 TTTTTTTTG
2400196 TTTTTATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.12, C:0.15, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTTTTTGAATTTTCACT
Found at i:2407173 original size:52 final size:52
Alignment explanation
Indices: 2407091--2407195 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
2407081 TTCTCGTCGG
* *
2407091 ATTTGTGGTCCCAAAACCACTGTTCTGACTAGACCCAAAATCGGGCTGTTAC
1 ATTTGTGGTCCCAAAACCACTGTTCGGACTAGACCCAAAATCAGGCTGTTAC
* *
2407143 ATTTGTGGTTCCAAAACTACTGTTCGGACTAGACCCAAAATCAGGCTGTTAC
1 ATTTGTGGTCCCAAAACCACTGTTCGGACTAGACCCAAAATCAGGCTGTTAC
2407195 A
1 A
2407196 ATTTCAAAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (52 bp):
ATTTGTGGTCCCAAAACCACTGTTCGGACTAGACCCAAAATCAGGCTGTTAC
Found at i:2407330 original size:31 final size:31
Alignment explanation
Indices: 2407292--2407353 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2407282 TAAAGATAGG
2407292 CCTACTATATGTCTACTATTGTTTCAATGCT
1 CCTACTATATGTCTACTATTGTTTCAATGCT
2407323 CCTACTATATGTCTACTATTGTTTCAATGCT
1 CCTACTATATGTCTACTATTGTTTCAATGCT
2407354 TAACAGTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (31 bp):
CCTACTATATGTCTACTATTGTTTCAATGCT
Found at i:2409008 original size:15 final size:15
Alignment explanation
Indices: 2408985--2409014 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2408975 ATTGTATAAC
2408985 ACTTGTTTTATTATT
1 ACTTGTTTTATTATT
*
2409000 ACTTTTTTTATTATT
1 ACTTGTTTTATTATT
2409015 TTAGAGGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (15 bp):
ACTTGTTTTATTATT
Found at i:2409629 original size:20 final size:20
Alignment explanation
Indices: 2409606--2409655 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2409596 AATATATAAT
*
2409606 TTTTGAAGTTTTTATAAA-TA
1 TTTTGAA-TTTTTAAAAATTA
2409626 TTTTGAA-TTTTAAAAATTA
1 TTTTGAATTTTTAAAAATTA
2409645 TTTTGAATTTT
1 TTTTGAATTTT
2409656 ATTTGTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 8 0.30
19 9 0.33
20 10 0.37
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTTGAATTTTTAAAAATTA
Found at i:2409636 original size:28 final size:27
Alignment explanation
Indices: 2409572--2409626 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
2409562 TAACTCTTTT
*
2409572 TATAT-ATTTTTAGAATTTTTTAAAAA
1 TATATAATTTTTAGAAGTTTTTAAAAA
*
2409598 TATATAATTTTT-GAAGTTTTTATAAA
1 TATATAATTTTTAGAAGTTTTTAAAAA
2409624 TAT
1 TAT
2409627 TTTGAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (27 bp):
TATATAATTTTTAGAAGTTTTTAAAAA
Found at i:2409646 original size:19 final size:18
Alignment explanation
Indices: 2409615--2409656 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
2409605 TTTTTGAAGT
*
2409615 TTTTATAAATATTTTGAA
1 TTTTAAAAATATTTTGAA
2409633 TTTTAAAAATTATTTTGAA
1 TTTTAAAAA-TATTTTGAA
2409652 TTTTA
1 TTTTA
2409657 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTTAAAAATATTTTGAA
Found at i:2411430 original size:19 final size:19
Alignment explanation
Indices: 2411371--2411445 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
2411361 TTTAGTCATA
2411371 TAATAAATTA-TTAATATAAT
1 TAATAAATTATTTAATAT--T
*
2411391 TAATATAATT-TATT-ATTTT
1 TAATA-AATTAT-TTAATATT
2411410 TAATAAATTATTTAATATT
1 TAATAAATTATTTAATATT
*
2411429 TAA-AATTTATTTTAATA
1 TAATAAATTA-TTTAATA
2411446 GAAAGTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
18 11 0.24
19 21 0.46
20 5 0.11
21 7 0.15
22 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATAAATTATTTAATATT
Found at i:2412051 original size:14 final size:14
Alignment explanation
Indices: 2412032--2412067 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2412022 GAAAAGTAAG
2412032 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
* *
2412046 TCATTTTCCGGAAG
1 TCATTTTCCAGAAA
2412060 TCATTTTC
1 TCATTTTC
2412068 AGTAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:2413616 original size:21 final size:21
Alignment explanation
Indices: 2413592--2413632 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2413582 ATATTAACTC
2413592 TTTTTAT-ATATTTTTTAAAAT
1 TTTTTATAAT-TTTTTTAAAAT
2413613 TTTTTATAATTTTTTTAAAA
1 TTTTTATAATTTTTTTAAAA
2413633 AATATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTATAATTTTTTTAAAAT
Found at i:2413672 original size:19 final size:19
Alignment explanation
Indices: 2413643--2413692 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2413633 AATATATAAT
2413643 TTTTGGAATTTTTATAAA-TA
1 TTTT-GAATTTTTA-AAATTA
2413663 TTTTGAA-TTTTAAAATTTA
1 TTTTGAATTTTTAAAA-TTA
2413682 TTTTGAATTTT
1 TTTTGAATTTT
2413693 ATTTGTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.11
18 5 0.19
19 12 0.44
20 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (19 bp):
TTTTGAATTTTTAAAATTA
Found at i:2414213 original size:9 final size:9
Alignment explanation
Indices: 2414196--2414232 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2414186 TGAGTTTTCG
2414196 AATTCGAAT
1 AATTCGAAT
*
2414205 AACTCGAAT
1 AATTCGAAT
*
2414214 AATTTGAAT
1 AATTCGAAT
2414223 AATTCGAAT
1 AATTCGAAT
2414232 A
1 A
2414233 TCAAATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2414353 original size:30 final size:30
Alignment explanation
Indices: 2414291--2414353 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
2414281 ACTTTTCCCT
* *
2414291 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCCTCCCACTTCCCCCC
2414321 CAAAACTTTTACTCCCCTCCC-C-TCCCCTCC
1 CAAAACTTTTACT-CCCTCCCACTTCCCC-CC
2414351 CAA
1 CAA
2414354 CCCCCCATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 19 0.66
31 6 0.21
ACGTcount: A:0.21, C:0.51, G:0.00, T:0.29
Consensus pattern (30 bp):
CAAAACTTTTACTCCCTCCCACTTCCCCCC
Found at i:2417294 original size:5 final size:5
Alignment explanation
Indices: 2417284--2417313 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2417274 ATGAAGCAAC
2417284 ATAAA ATAAA ATAAA ATAAA ATGAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA AT-AAA ATAA
2417314 GAACCACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2417410 original size:3 final size:3
Alignment explanation
Indices: 2417402--2417443 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
2417392 AAACAAGCAA
2417402 AAT AAT AAT AAT AAT AAT AAT AAT AGAT ACA- AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT
2417444 CTATTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
2 3 0.09
3 28 0.80
4 4 0.11
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2418547 original size:20 final size:19
Alignment explanation
Indices: 2418512--2418566 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
2418502 TTTGTTTTGT
*
2418512 TTTCTTT-TGTTTGCTTCTG
1 TTTCTTTCT-TTTGCTTATG
2418531 TTTCTTTCTTTTCGCTTATG
1 TTTCTTTCTTTT-GCTTATG
2418551 TTGTC-TTCTTTTGCTT
1 TT-TCTTTCTTTTGCTT
2418567 GCGTGTTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 14 0.44
20 16 0.50
21 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.13, T:0.67
Consensus pattern (19 bp):
TTTCTTTCTTTTGCTTATG
Found at i:2419510 original size:44 final size:45
Alignment explanation
Indices: 2419448--2419656 Score: 111
Period size: 44 Copynumber: 4.5 Consensus size: 45
2419438 GTTTGCTCTG
*
2419448 CTGCAACTTTA-GAGAGATAAG-GCTGGTGGCTTCAATCTGCTCCA
1 CTGCAACTTCAGGA-AGATAAGAGCTGGTGGCTTCAATCTGCTCCA
* * * * *
2419492 CTGCAACTTCAGGAAGATAAGATCCATCATAATTTGTAGCTTTAATCTGTTCCA
1 CTGCAACTTCAGGAAGATAAG----AGC-----TGGTGGCTTCAATCTGCTCCA
* ** ** * * * * **
2419546 CTGTAACGCCAGGGAA-ATAAGATTTGTTGTCTTCAGTCTGTTCTG
1 CTGCAACTTCA-GGAAGATAAGAGCTGGTGGCTTCAATCTGCTCCA
* *
2419591 CTGCAACTTCAGGGAGATAAG-GCTGGTGGCTTCAATCTACTCCA
1 CTGCAACTTCAGGAAGATAAGAGCTGGTGGCTTCAATCTGCTCCA
*
2419635 CTGCAACTTCAGAAAGATAAGA
1 CTGCAACTTCAGGAAGATAAGA
2419657 TCCGCCATAA
Statistics
Matches: 118, Mismatches: 33, Indels: 27
0.66 0.19 0.15
Matches are distributed among these distances:
44 53 0.45
45 28 0.24
49 1 0.01
50 2 0.02
54 30 0.25
55 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (45 bp):
CTGCAACTTCAGGAAGATAAGAGCTGGTGGCTTCAATCTGCTCCA
Found at i:2419754 original size:45 final size:45
Alignment explanation
Indices: 2419699--2419843 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 45
2419689 TTGTAACACT
*
2419699 AGGGAAATAAGATTTGCTGTCTTCAGTCTGCTCTACTGCAACTTC
1 AGGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCACTGCAACTTC
* ** * * * * * *
2419744 AGGGAGATAAG-GCTCCTGGCTTCAATTTGATCCACTGCAA-TGCC
1 AGGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCACTGCAACT-TC
* * * * *
2419788 AAGGAAATAAGATTTGCTGTCTTTAGTCTGCTCCGCTACAACTTT
1 AGGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCACTGCAACTTC
*
2419833 AGGGAGATAAG
1 AGGGAAATAAG
2419844 GCTGGTGGCT
Statistics
Matches: 71, Mismatches: 26, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
43 1 0.01
44 31 0.44
45 38 0.54
46 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (45 bp):
AGGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCACTGCAACTTC
Found at i:2419800 original size:143 final size:143
Alignment explanation
Indices: 2419165--2419783 Score: 864
Period size: 143 Copynumber: 4.3 Consensus size: 143
2419155 CGCTCCACTA
** * * ** * **
2419165 CAACTTCAGGGAGAT-AGAATCGATGGCTTCAATCTGCTTGACTGCAACTTTAAAAAGATAAGAT
1 CAACTTCAGGGAGATAAGGCT-GGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGAT
* * * * *
2419229 CTGCCATAATTTGTATCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGATATCTTC
65 CCGCCATAATTTGTAGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTTGATGTCTTC
*
2419294 AGTCTGCTCCGCTG
130 AGTCTGCTCTGCTG
* *
2419308 TAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAGGATC
1 CAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATC
* * * *
2419373 TGCCATAATTTGTAGCTTTAACCTGTTCCACTGTAATGCCAGGGAAATAAGATTTGGTGTCTTCA
66 CGCCATAATTTGTAGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTTGATGTCTTCA
*
2419438 GTTTGCTCTGCTG
131 GTCTGCTCTGCTG
* * *
2419451 CAACTTTAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATC
1 CAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATC
** *
2419516 CATCATAATTTGTAGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTTGTTGTCTTCA
66 CGCCATAATTTGTAGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTTGATGTCTTCA
*
2419581 GTCTGTTCTGCTG
131 GTCTGCTCTGCTG
*
2419594 CAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGAAAGATAAGATC
1 CAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATC
* * * *
2419659 CGCCATAATTTGTAGCTTTAATCTGTTCCATTGTAACACTAGGGAAATAAGATTTGCTGTCTTCA
66 CGCCATAATTTGTAGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTTGATGTCTTCA
*
2419724 GTCTGCTCTACTG
131 GTCTGCTCTGCTG
** *
2419737 CAACTTCAGGGAGATAAGGCTCCTGGCTTCAATTTGA-TCCACTGCAA
1 CAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCT-ACTCCACTGCAA
2419784 TGCCAAGGAA
Statistics
Matches: 426, Mismatches: 48, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
143 422 0.99
144 4 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (143 bp):
CAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATC
CGCCATAATTTGTAGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTTGATGTCTTCA
GTCTGCTCTGCTG
Found at i:2419839 original size:232 final size:232
Alignment explanation
Indices: 2419530--2420016 Score: 661
Period size: 232 Copynumber: 2.1 Consensus size: 232
2419520 ATAATTTGTA
* * * * * * * *
2419530 GCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTTGTTGTCTTCAGTCTGTTCTGCTGC
1 GCTTCAATCTGATCCACTGCAACGCCAAGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCGCTAC
* * * *
2419595 AACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTC-AGAAAGATAAGATC
66 AACTTCAGGGAGATAAGGCTGGTGGCTTCAATATACCCCACTACAAATTCAAG-AAGATAAGATC
* * * ** *
2419659 CGCCATAATTTGTAGCTTTAATCTGTTCCATTGTAACACTAGGGAAATAAGATTTGCTGTCTTCA
130 CGCCATAATTTGTAGCTTTAATCTATTCCACTGTAACACTAGGGAAATAAAATTCACTATCTTCA
* *
2419724 GTCTGCTCTACTGCAACTTCAGGGAGATAAGGCTCCTG
195 GTCTGCTCCACTGCAACTTCAGGGAAATAAGGCTCCTG
* * *
2419762 GCTTCAATTTGATCCACTGCAATGCCAAGGAAATAAGATTTGCTGTCTTTAGTCTGCTCCGCTAC
1 GCTTCAATCTGATCCACTGCAACGCCAAGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCGCTAC
* * *
2419827 AACTTTAGGGAGATAAGGCTGGTGGCTTGAATATGCCCCACTACAAATTCAAGAAGATAAGATCC
66 AACTTCAGGGAGATAAGGCTGGTGGCTTCAATATACCCCACTACAAATTCAAGAAGATAAGATCC
** *
2419892 GCCATAATTTGTAGCTTTAATCTATTCCACTGTAATGCTAGGGAAATAAAATTCACTATCTTTAG
131 GCCATAATTTGTAGCTTTAATCTATTCCACTGTAACACTAGGGAAATAAAATTCACTATCTTCAG
* **
2419957 TCTGCTCCGCTGCAACTTCAGGGAAATAAGGCTGGTG
196 TCTGCTCCACTGCAACTTCAGGGAAATAAGGCTCCTG
*
2419994 GCTTCAATCTGCTCCACTGCAAC
1 GCTTCAATCTGATCCACTGCAAC
2420017 TTCAGGAAGA
Statistics
Matches: 219, Mismatches: 35, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
232 217 0.99
233 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (232 bp):
GCTTCAATCTGATCCACTGCAACGCCAAGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCGCTAC
AACTTCAGGGAGATAAGGCTGGTGGCTTCAATATACCCCACTACAAATTCAAGAAGATAAGATCC
GCCATAATTTGTAGCTTTAATCTATTCCACTGTAACACTAGGGAAATAAAATTCACTATCTTCAG
TCTGCTCCACTGCAACTTCAGGGAAATAAGGCTCCTG
Found at i:2419868 original size:89 final size:89
Alignment explanation
Indices: 2419701--2419868 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 89
2419691 GTAACACTAG
* *
2419701 GGAAATAAGATTTGCTGTCTTCAGTCTGCTCTACTGCAACTTCAGGGAGATAAGGCTCCTGGCTT
1 GGAAATAAGATTTGCTGTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGGCTCCTGGCTT
* *
2419766 CAATTTGATCCACTGCAATGCCAA
66 CAATATGACCCACTGCAATGCCAA
* * * **
2419790 GGAAATAAGATTTGCTGTCTTTAGTCTGCTCCGCTACAACTTTAGGGAGATAAGGCTGGTGGCTT
1 GGAAATAAGATTTGCTGTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGGCTCCTGGCTT
* *
2419855 GAATATGCCCCACT
66 CAATATGACCCACT
2419869 ACAAATTCAA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 68 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (89 bp):
GGAAATAAGATTTGCTGTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGGCTCCTGGCTT
CAATATGACCCACTGCAATGCCAA
Found at i:2419971 original size:375 final size:375
Alignment explanation
Indices: 2419399--2420142 Score: 1110
Period size: 375 Copynumber: 2.0 Consensus size: 375
2419389 TTTAACCTGT
* * * * * *
2419399 TCCACTGTAATGCCAGGGAAATAAGATTTGGTGTCTTCAGTTTGCTCTGCTGCAACTTTAGAGAG
1 TCCACTGCAATGCCAAGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCGCTACAACTTTAGAGAG
* * * * * *
2419464 ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCATCATAATTTGT
66 ATAAGGCTGGTGGCTTCAATATGCCCCACTACAAATTCAAGAAGATAAGATCCACCATAATTTGT
* * *** * * *
2419529 AGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGATTTGTTGTCTTCAGTCTGTTCTGCTG
131 AGCTTTAATCTATTCCACTGTAACGCCAGGGAAATAAAATTCACTATCTTCAGTCTGCTCCGCTG
*
2419594 CAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGAAAGATAAGATC
196 CAACTTCAGGGAAATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGAAAGATAAGATC
* ** * *
2419659 CGCCATAATTTGTAGCTTTAATCTGTTCCATTGTAACACTAGGGAAATAAGATTTGCTGTCTTCA
261 CACCATAATTTGTAGCTTTAATCTGTTCCACCGTAACACTAAGGAAATAAGATTCGCTGTCTTCA
* *
2419724 GTCTGCTCTACTGCAACTTCAGGGAGATAAGGCTCCTGGCTTCAATTTGA
326 GTCTGCTCCACTGCAACTTCAGAGAGATAAGGCTCCTGGCTTCAATTTGA
* *
2419774 TCCACTGCAATGCCAAGGAAATAAGATTTGCTGTCTTTAGTCTGCTCCGCTACAACTTTAGGGAG
1 TCCACTGCAATGCCAAGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCGCTACAACTTTAGAGAG
* *
2419839 ATAAGGCTGGTGGCTTGAATATGCCCCACTACAAATTCAAGAAGATAAGATCCGCCATAATTTGT
66 ATAAGGCTGGTGGCTTCAATATGCCCCACTACAAATTCAAGAAGATAAGATCCACCATAATTTGT
* * *
2419904 AGCTTTAATCTATTCCACTGTAATGCTAGGGAAATAAAATTCACTATCTTTAGTCTGCTCCGCTG
131 AGCTTTAATCTATTCCACTGTAACGCCAGGGAAATAAAATTCACTATCTTCAGTCTGCTCCGCTG
* *
2419969 CAACTTCAGGGAAATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATC
196 CAACTTCAGGGAAATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGAAAGATAAGATC
*
2420034 CACCATAATTTGTAGCTTTAATCTGTTCCACCGTAACGCTAAGGAAATAAGATTCGCTGTCTTCA
261 CACCATAATTTGTAGCTTTAATCTGTTCCACCGTAACACTAAGGAAATAAGATTCGCTGTCTTCA
* * **
2420099 GTTTGTTCCACTGCAACTTCAGAGAGATAAGGCTGGTGGCTTCA
326 GTCTGCTCCACTGCAACTTCAGAGAGATAAGGCTCCTGGCTTCA
2420143 GTCTGCTCCA
Statistics
Matches: 327, Mismatches: 42, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
375 327 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (375 bp):
TCCACTGCAATGCCAAGGAAATAAGATTTGCTGTCTTCAGTCTGCTCCGCTACAACTTTAGAGAG
ATAAGGCTGGTGGCTTCAATATGCCCCACTACAAATTCAAGAAGATAAGATCCACCATAATTTGT
AGCTTTAATCTATTCCACTGTAACGCCAGGGAAATAAAATTCACTATCTTCAGTCTGCTCCGCTG
CAACTTCAGGGAAATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGAAAGATAAGATC
CACCATAATTTGTAGCTTTAATCTGTTCCACCGTAACACTAAGGAAATAAGATTCGCTGTCTTCA
GTCTGCTCCACTGCAACTTCAGAGAGATAAGGCTCCTGGCTTCAATTTGA
Found at i:2420032 original size:143 final size:143
Alignment explanation
Indices: 2419774--2420185 Score: 581
Period size: 143 Copynumber: 2.9 Consensus size: 143
2419764 TTCAATTTGA
* * * * *
2419774 TCCACTGCAATGCCAAGGAAATAAGATTTGCTGTCTTTAGTCTGCTCCGCTACAACTTTAGGGAG
1 TCCACTGTAATGCTAAGGAAATAAGATTCGCTGTCTTTAGTCTGCTCCGCTGCAACTTCAGGGAG
* * * * * *
2419839 ATAAGGCTGGTGGCTTGAATATGCCCCACTACAAATTCAAGAAGATAAGATCCGCCATAATTTGT
66 ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGT
2419904 AGCTTTAATCTAT
131 AGCTTTAATCTAT
* * * * *
2419917 TCCACTGTAATGCTAGGGAAATAAAATTCACTATCTTTAGTCTGCTCCGCTGCAACTTCAGGGAA
1 TCCACTGTAATGCTAAGGAAATAAGATTCGCTGTCTTTAGTCTGCTCCGCTGCAACTTCAGGGAG
*
2419982 ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCACCATAATTTGT
66 ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGT
*
2420047 AGCTTTAATCTGT
131 AGCTTTAATCTAT
* * * * * * *
2420060 TCCACCGTAACGCTAAGGAAATAAGATTCGCTGTCTTCAGTTTGTTCCACTGCAACTTCAGAGAG
1 TCCACTGTAATGCTAAGGAAATAAGATTCGCTGTCTTTAGTCTGCTCCGCTGCAACTTCAGGGAG
* *
2420125 ATAAGGCTGGTGGCTTCAGTCTGCTCCACTGTAACTTCAGGAAGATAAGATCCGCCATAAT
66 ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAAT
2420186 GACTTCAATA
Statistics
Matches: 236, Mismatches: 33, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
143 236 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (143 bp):
TCCACTGTAATGCTAAGGAAATAAGATTCGCTGTCTTTAGTCTGCTCCGCTGCAACTTCAGGGAG
ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGT
AGCTTTAATCTAT
Found at i:2421074 original size:17 final size:16
Alignment explanation
Indices: 2421052--2421083 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2421042 GCCTCTCCTT
2421052 TTTTTTCTTTTCTTTTC
1 TTTTTTCTTTT-TTTTC
2421069 TTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTTT
2421084 AAGTGAAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTC
Found at i:2422608 original size:13 final size:13
Alignment explanation
Indices: 2422590--2422652 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
2422580 TTTTCATTGT
2422590 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
* *
2422603 TTTTGAAAAATTC
1 TTTTGAAAAGTGC
* * *
2422616 TGTGGAAAAGTAC
1 TTTTGAAAAGTGC
*
2422629 TTTTGAAGAGTGC
1 TTTTGAAAAGTGC
*
2422642 TTTTAAAAAGT
1 TTTTGAAAAGT
2422653 TTGGTTTAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:2426030 original size:23 final size:23
Alignment explanation
Indices: 2426001--2426097 Score: 167
Period size: 23 Copynumber: 4.2 Consensus size: 23
2425991 GCTATGTCGA
2426001 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
2426024 TTAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
2426047 TCAGGCACTTTATGTGTCGTATA
1 TCAGGCACTTTATGTGTCGTATT
*
2426070 CCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
2426093 TCAGG
1 TCAGG
2426098 TACCTCGTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:2426107 original size:16 final size:16
Alignment explanation
Indices: 2426086--2426121 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2426076 ACTTTATGTG
*
2426086 TCGTATTTCAGGTACC
1 TCGTATTTCAGGCACC
*
2426102 TCGTATTTTAGGCACC
1 TCGTATTTCAGGCACC
2426118 TCGT
1 TCGT
2426122 GTGTCGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (16 bp):
TCGTATTTCAGGCACC
Found at i:2426137 original size:21 final size:20
Alignment explanation
Indices: 2426111--2426150 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2426101 CTCGTATTTT
*
2426111 AGGCACCTCGTGTGTCGTATC
1 AGGCA-CTCATGTGTCGTATC
*
2426132 AGGCACTTATGTGTCGTAT
1 AGGCACTCATGTGTCGTAT
2426151 ACTGATCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.33
Consensus pattern (20 bp):
AGGCACTCATGTGTCGTATC
Found at i:2426940 original size:47 final size:47
Alignment explanation
Indices: 2426889--2426985 Score: 115
Period size: 47 Copynumber: 2.1 Consensus size: 47
2426879 TGGTTGGACC
* * *
2426889 ATGGCAAC-ATGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCT
1 ATGGCAACGATGTAATATGTG-CTACCGTATAAGACCATAGCTGGGCT
* * * *
2426936 ATGGCATCGGTGTAATATGTGCTACTGTGTAAGACCATAGCTGGGCT
1 ATGGCAACGATGTAATATGTGCTACCGTATAAGACCATAGCTGGGCT
2426983 ATG
1 ATG
2426986 ACATCAGTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 32 0.76
48 10 0.24
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (47 bp):
ATGGCAACGATGTAATATGTGCTACCGTATAAGACCATAGCTGGGCT
Found at i:2427378 original size:29 final size:30
Alignment explanation
Indices: 2427285--2427392 Score: 130
Period size: 29 Copynumber: 3.7 Consensus size: 30
2427275 AAAAAAACTG
* *
2427285 CATTTTGACCCCT-AACTTTTTTGAAATTA
1 CATTTTGACCCCTAAAATTTCTTGAAATTA
** * *
2427314 CATTTCAACCCCTAAACTTTCTTAAAATTA
1 CATTTTGACCCCTAAAATTTCTTGAAATTA
2427344 CATTTTGA-CCCTAAAATTTCTTGAAATTA
1 CATTTTGACCCCTAAAATTTCTTGAAATTA
* *
2427373 CATTTTGGCCCCAAAAATTT
1 CATTTTGACCCCTAAAATTT
2427393 TACTGCGTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 37 0.55
30 30 0.45
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (30 bp):
CATTTTGACCCCTAAAATTTCTTGAAATTA
Found at i:2427998 original size:16 final size:16
Alignment explanation
Indices: 2427977--2428014 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2427967 GTATTTATAT
2427977 TTTTAATTTAATTTAA
1 TTTTAATTTAATTTAA
* *
2427993 TTTTAATTTTATTTTA
1 TTTTAATTTAATTTAA
2428009 TTTTAA
1 TTTTAA
2428015 ATAATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATTTAATTTAA
Found at i:2428218 original size:20 final size:20
Alignment explanation
Indices: 2428190--2428237 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
2428180 TTTTTGTTTC
*
2428190 TTCAAAAATTTTTCTCGTGTT
1 TTCAAAAATTTAT-TCGTGTT
2428211 TT-AAAAA-TTATTCGTGTT
1 TTCAAAAATTTATTCGTGTT
2428229 TTCAAAAAT
1 TTCAAAAAT
2428238 AAGGCAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 5 0.21
21 2 0.08
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (20 bp):
TTCAAAAATTTATTCGTGTT
Found at i:2428458 original size:17 final size:18
Alignment explanation
Indices: 2428417--2428475 Score: 75
Period size: 17 Copynumber: 3.2 Consensus size: 18
2428407 TCCGTTATTC
*
2428417 AAAATTTTTCATGTTTTCAA
1 AAAATTTTT-GTGTTTTC-A
2428437 AAAATTTTTGTGTTTT-A
1 AAAATTTTTGTGTTTTCA
*
2428454 AAAATTTTCGTGTTTTCA
1 AAAATTTTTGTGTTTTCA
2428472 AAAA
1 AAAA
2428476 AAATAATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 16 0.44
18 5 0.14
19 6 0.17
20 9 0.25
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (18 bp):
AAAATTTTTGTGTTTTCA
Found at i:2436606 original size:5 final size:5
Alignment explanation
Indices: 2436596--2436625 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2436586 ATGAAGCAAC
2436596 ATAAA ATAAA ATAAA ATAAA ATGAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA AT-AAA ATAA
2436626 GAACCACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2436722 original size:3 final size:3
Alignment explanation
Indices: 2436714--2436747 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2436704 AAACAAGCAA
2436714 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2436748 GAGACAATAA
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):
AAT
Found at i:2437878 original size:5 final size:5
Alignment explanation
Indices: 2437868--2437900 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
2437858 CAATATTCGT
2437868 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTT
2437901 CTTAGTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:2438290 original size:13 final size:13
Alignment explanation
Indices: 2438251--2438303 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
2438241 AGTTTGGCAA
2438251 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
2438264 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
2438277 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
2438290 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
2438303 T
1 T
2438304 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 28 0.82
14 3 0.09
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:2438501 original size:21 final size:21
Alignment explanation
Indices: 2438477--2438519 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2438467 CTTGTTGCTA
2438477 ATATTTT-AATATATGAAATAT
1 ATATTTTAAATAT-TGAAATAT
*
2438498 ATATTTTAAATATTTAAATAT
1 ATATTTTAAATATTGAAATAT
2438519 A
1 A
2438520 ACCATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATTTTAAATATTGAAATAT
Found at i:2441657 original size:16 final size:17
Alignment explanation
Indices: 2441620--2441661 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2441610 CTAAGCTAGG
2441620 TACA-ATAT-ATATGTA
1 TACATATATAATATGTA
2441635 TACATATATAATATGT-
1 TACATATATAATATGTA
*
2441651 TATATATATAA
1 TACATATATAA
2441662 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 14 0.58
17 6 0.25
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (17 bp):
TACATATATAATATGTA
Found at i:2444122 original size:34 final size:33
Alignment explanation
Indices: 2444066--2444155 Score: 101
Period size: 34 Copynumber: 2.7 Consensus size: 33
2444056 TTAGAGTTTT
**
2444066 TTTTAAAAAAATT-ATTAAATTAGATTTTAGAGG
1 TTTT-AAAAAATTAATTAAATTAGAGCTTAGAGG
* *
2444099 TTTTAAATAAATTAATTAAATTAGGGCTTAGAGT
1 TTTTAAA-AAATTAATTAAATTAGAGCTTAGAGG
*
2444133 TTTTAAGAAAATTAACTAAATTA
1 TTTTAA-AAAATTAATTAAATTA
2444156 TGGTTTAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
32 3 0.06
33 9 0.18
34 36 0.73
35 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (33 bp):
TTTTAAAAAATTAATTAAATTAGAGCTTAGAGG
Found at i:2448366 original size:21 final size:21
Alignment explanation
Indices: 2448337--2448393 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2448327 ATTTTCGAGG
2448337 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
2448358 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
2448379 ATATACAATATTAGA
1 ATATACAATCTTAGA
2448394 AGATATGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:2452869 original size:28 final size:30
Alignment explanation
Indices: 2452829--2452886 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
2452819 AGACCCTAAG
2452829 AGTCAATTTC-T-GTAGAAGGTCCTTTAAT
1 AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
2452857 AGTCAATTTCTGTAGTAGAAGGTCCTTTAA
1 AGTCAATTTC-GTAGTAGAAGGTCCTTTAA
2452887 CTTCTCCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (30 bp):
AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
Found at i:2458235 original size:34 final size:33
Alignment explanation
Indices: 2458130--2458238 Score: 103
Period size: 34 Copynumber: 3.2 Consensus size: 33
2458120 GTTTAGAGTT
* *
2458130 TTTTTTAAAAAA-TAATTAAATTAGGTTTTAGGG
1 TTTTTAAAAAAATTAATTAAATTAGG-TTTAGTG
* * * * *
2458163 GTTTTAAATAAATGAATTAAATTAGGGATTAGAG
1 TTTTTAAAAAAATTAATTAAATTA-GGTTTAGTG
* *
2458197 TTTTTAAAAAAATTAACTAAATTATGGTTTAGTT
1 TTTTTAAAAAAATTAATTAAATTA-GGTTTAGTG
2458231 TTTTTAAA
1 TTTTTAAA
2458239 TAATTTTGTC
Statistics
Matches: 60, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
33 9 0.15
34 49 0.82
35 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (33 bp):
TTTTTAAAAAAATTAATTAAATTAGGTTTAGTG
Found at i:2459420 original size:16 final size:16
Alignment explanation
Indices: 2459396--2459433 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2459386 ATCTAAACTC
* *
2459396 AAATGATTCAAACTTG
1 AAATAATTCAAACTTA
2459412 AAATAATTCAAACTTA
1 AAATAATTCAAACTTA
2459428 AAATAA
1 AAATAA
2459434 GTTGAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (16 bp):
AAATAATTCAAACTTA
Found at i:2461447 original size:16 final size:16
Alignment explanation
Indices: 2461414--2461447 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2461404 AGGTAATGTT
* *
2461414 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2461430 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2461446 AA
1 AA
2461448 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2466226 original size:16 final size:16
Alignment explanation
Indices: 2466193--2466226 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2466183 GGAGATTGTT
* *
2466193 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2466209 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2466225 AA
1 AA
2466227 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2469567 original size:12 final size:12
Alignment explanation
Indices: 2469552--2469576 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2469542 CAATATTTTA
2469552 TATACATATTAT
1 TATACATATTAT
2469564 TATACATATTAT
1 TATACATATTAT
2469576 T
1 T
2469577 CTCATTGAGT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TATACATATTAT
Found at i:2482898 original size:22 final size:22
Alignment explanation
Indices: 2482848--2482898 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2482838 TTTGTTGCAT
* * *
2482848 TATAAATAAAAATTTTAAACTC
1 TATAAATAAAAATTATAAAATA
2482870 TATAAATAAAAAATTATAAAATA
1 TATAAAT-AAAAATTATAAAATA
2482893 TA-AAAT
1 TATAAAT
2482899 GAGTATGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
TATAAATAAAAATTATAAAATA
Found at i:2484597 original size:12 final size:12
Alignment explanation
Indices: 2484582--2484606 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2484572 AATATTTTTA
2484582 TATACATATTAT
1 TATACATATTAT
2484594 TATACATATTAT
1 TATACATATTAT
2484606 T
1 T
2484607 CTTGTAACAG
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TATACATATTAT
Found at i:2485021 original size:5 final size:5
Alignment explanation
Indices: 2485011--2485081 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
2485001 AAAGAAATAT
* *
2485011 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
2485057 -A-TA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
2485082 ACATAAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 4 0.07
4 8 0.15
5 31 0.56
6 11 0.20
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:2485063 original size:19 final size:19
Alignment explanation
Indices: 2485039--2485081 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2485029 ATTATGTTTT
2485039 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
2485058 TATATTATATTATATTATA
1 TATATTATATTATATTATA
2485077 TATAT
1 TATAT
2485082 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:2485112 original size:16 final size:16
Alignment explanation
Indices: 2485091--2485123 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2485081 TACATAAAAC
*
2485091 AAAAGAAAGAATAGAA
1 AAAAGAAAGAAAAGAA
2485107 AAAAGAAAGAAAAGAA
1 AAAAGAAAGAAAAGAA
2485123 A
1 A
2485124 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAA
Found at i:2486143 original size:46 final size:44
Alignment explanation
Indices: 2486084--2486198 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2486074 ACAGGACAGA
* *
2486084 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2486130 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2486174 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2486199 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2486179 original size:44 final size:45
Alignment explanation
Indices: 2486084--2486217 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2486074 ACAGGACAGA
* *
2486084 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2486130 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2486174 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2486218 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2488612 original size:13 final size:13
Alignment explanation
Indices: 2488596--2488623 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2488586 CGATTTCTTC
2488596 TGGGTATTCTATA
1 TGGGTATTCTATA
2488609 TGGGTATTCTATA
1 TGGGTATTCTATA
2488622 TG
1 TG
2488624 CTCTTTTATC
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:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:2488970 original size:24 final size:24
Alignment explanation
Indices: 2488920--2488991 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
2488910 AGTGATATTC
*
2488920 TTCTTGTGGATTTTCTCT-GGATA
1 TTCTTTTGGATTTTCTCTGGGATA
*
2488943 TTCTTTTGGACTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
2488967 TTCTTTTGGATTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
2488991 T
1 T
2488992 CATCGATCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 16 0.36
24 29 0.64
ACGTcount: A:0.12, C:0.14, G:0.21, T:0.53
Consensus pattern (24 bp):
TTCTTTTGGATTTTCTCTGGGATA
Found at i:2488989 original size:12 final size:12
Alignment explanation
Indices: 2488927--2488989 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
2488917 TTCTTCTTGT
2488927 GGATTTTCTCT-
1 GGATTTTCTCTG
* * *
2488938 GGATATTCTTTT
1 GGATTTTCTCTG
*
2488950 GGACTTTCTCTG
1 GGATTTTCTCTG
* * *
2488962 GGATATTCTTTT
1 GGATTTTCTCTG
2488974 GGATTTTCTCTG
1 GGATTTTCTCTG
2488986 GGAT
1 GGAT
2488990 ATCATCGATC
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.13, C:0.14, G:0.22, T:0.51
Consensus pattern (12 bp):
GGATTTTCTCTG
Found at i:2490612 original size:14 final size:14
Alignment explanation
Indices: 2490587--2490625 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2490577 TGATTATGTT
2490587 TTATATTATATTATTA
1 TTATA-TATATTA-TA
2490603 TTA-ATATATTATA
1 TTATATATATTATA
2490616 TTATATATAT
1 TTATATATAT
2490626 ATACATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 1 0.05
16 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATATATTATA
Found at i:2490614 original size:24 final size:24
Alignment explanation
Indices: 2490556--2490622 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
2490546 GTGTTAAAGA
2490556 AATATTATTATATTATAGTAATGATT
1 AATA-TATTATATTATA-TAATGATT
* * * *
2490582 -ATGTTTTATATTATATTATTATT
1 AATATATTATATTATATAATGATT
2490605 AATATATTATATTATATA
1 AATATATTATATTATATA
2490623 TATATACATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
23 6 0.18
24 25 0.76
25 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
AATATATTATATTATATAATGATT
Found at i:2490658 original size:16 final size:16
Alignment explanation
Indices: 2490637--2490669 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2490627 TACATAAAAC
*
2490637 AAAAGAAAGAATAGAA
1 AAAAGAAAGAAAAGAA
2490653 AAAAGAAAGAAAAGAA
1 AAAAGAAAGAAAAGAA
2490669 A
1 A
2490670 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAA
Found at i:2490736 original size:4 final size:4
Alignment explanation
Indices: 2490729--2490762 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
2490719 GAGAAGGAAG
2490729 GAAA GAAA GAAA GAAA GAAA GAAA -AAA -AAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
2490763 AAGGGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2491692 original size:46 final size:44
Alignment explanation
Indices: 2491633--2491747 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2491623 ACAGGACAGA
* *
2491633 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2491679 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2491723 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2491748 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2491728 original size:44 final size:45
Alignment explanation
Indices: 2491633--2491766 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2491623 ACAGGACAGA
* *
2491633 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2491679 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2491723 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2491767 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2501074 original size:44 final size:45
Alignment explanation
Indices: 2501004--2501815 Score: 707
Period size: 44 Copynumber: 18.5 Consensus size: 45
2500994 GGATGGATTG
* * *
2501004 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * *
2501048 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * * * * *
2501092 GGATCGACGA-CGCA-ATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * * *
2501135 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * *
2501179 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * * *
2501223 GGATCGAAGAT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * * * *
2501267 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTAG-CGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * *
2501311 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * * *
2501355 GGATCGAAGA-CGCAGATCTTGTCTTCCCATACTGGT-GCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * * *
2501398 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * *
2501442 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * * *
2501486 GGATCGAATAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * *
2501530 AGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGG-CGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * *
2501574 AGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * *
2501618 GGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * *
2501662 AGATC-ACAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
1 AGATCGA-AGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * * *
2501706 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* * * *
2501750 GGATC-AAGATA-CAGATCTTGTCTTCCCATACT-GTGGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
* *
2501792 AGATCGAAGAAAGCAGATATTGTC
1 AGATCGAAGATAGCAGATCTTGTC
2501816 CCTGTATTTG
Statistics
Matches: 600, Mismatches: 145, Indels: 46
0.76 0.18 0.06
Matches are distributed among these distances:
41 2 0.00
42 43 0.07
43 126 0.21
44 347 0.58
45 82 0.14
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (45 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGT
Found at i:2501320 original size:132 final size:132
Alignment explanation
Indices: 2501004--2501815 Score: 1407
Period size: 132 Copynumber: 6.2 Consensus size: 132
2500994 GGATGGATTG
*
2501004 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* *
2501069 ATCTTCCTATATTGGTAGGAAGTGGATCGACGACGCA-ATCTTGTCTTCCCATACTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
2501133 GT
131 GT
*
2501135 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
2501200 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
2501265 GT
131 GT
* *
2501267 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
*
2501332 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATACTGGT-GCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
2501396 GT
131 GT
*
2501398 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* *
2501463 ATCTTCCTATATTGGTAGGAAGTGGATCGAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
2501528 GT
131 GT
* * * *
2501530 AGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
*
2501595 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
2501660 GT
131 GT
*
2501662 AGATCACAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* * *
2501727 ATCTTCCTATATTGATAGGAAGTGGATC-AAGATACAGATCTTGTCTTCCCATACT-GTGGTGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
2501790 GT
131 GT
* *
2501792 AGATCGAAGAAAGCAGATATTGTC
1 AGATCGCAGAAAGCAGATCTTGTC
2501816 CCTGTATTTG
Statistics
Matches: 651, Mismatches: 28, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
130 30 0.05
131 250 0.38
132 371 0.57
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (132 bp):
AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAA
GT
Found at i:2501484 original size:263 final size:264
Alignment explanation
Indices: 2501004--2501815 Score: 1443
Period size: 263 Copynumber: 3.1 Consensus size: 264
2500994 GGATGGATTG
2501004 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
*
2501069 ATCTTCCTATATTGGTAGGAAGTGGATCGACGACGCA-ATCTTGTCTTCCCATACTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATACTGGTGGCGAA
2501133 GTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTC
131 GTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTC
2501198 CTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCG
196 CTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCG
2501263 AAGT
261 AAGT
* * *
2501267 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
2501332 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATACTGGT-GCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATACTGGTGGCGAA
2501396 GTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTC
131 GTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTC
* *
2501461 CTATCTTCCTATATTGGTAGGAAGTGGATCGAATATGCAGATCTTGTCTTCCCATATTGGTGGCG
196 CTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCG
2501526 AAGT
261 AAGT
* * *
2501530 AGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCT
1 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* *
2501595 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATACTGGTGGCGAA
* *
2501660 GTAGATCACAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTC
131 GTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTC
* * *
2501725 CTATCTTCCTATATTGATAGGAAGTGGATC-AAGATACAGATCTTGTCTTCCCATACT-GTGGTG
196 CTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCG
2501788 AAGT
261 AAGT
*
2501792 AGATCGAAGAAAGCAGATATTGTC
1 AGATCGAAGAAAGCAGATCTTGTC
2501816 CCTGTATTTG
Statistics
Matches: 524, Mismatches: 23, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
262 31 0.06
263 375 0.72
264 118 0.23
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (264 bp):
AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
ATCTTCCTATATTGGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATACTGGTGGCGAA
GTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTC
CTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCG
AAGT
Found at i:2501990 original size:42 final size:42
Alignment explanation
Indices: 2501944--2502108 Score: 187
Period size: 42 Copynumber: 4.0 Consensus size: 42
2501934 CCGATAACTC
2501944 ATCTCCCTAAGCAGTAGTGGAGCAGACAAAACCACAGATCTT
1 ATCTCCCTAAGCAGTAGTGGAGCAGACAAAACCACAGATCTT
** *
2501986 ATCTCCCTAA-CAGTAGTGGAGCAGATC-GCATCA-AG-TCTT
1 ATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAACCACAGATCTT
* *
2502025 ATCTCCTTAAGCAGTAGCGGAGCAGA-AGAAACCACAGATCTT
1 ATCTCCCTAAGCAGTAGTGGAGCAGACA-AAACCACAGATCTT
** * *
2502067 ATCTCCCTAAATAGTAGTGGAGCAGACTAAAAACACAAATCT
1 ATCTCCCTAAGCAGTAGTGGAGCAGAC-AAAACCACAGATCT
2502109 CATCCCCATG
Statistics
Matches: 101, Mismatches: 14, Indels: 15
0.78 0.11 0.12
Matches are distributed among these distances:
39 13 0.13
40 19 0.19
41 20 0.20
42 37 0.37
43 11 0.11
44 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
ATCTCCCTAAGCAGTAGTGGAGCAGACAAAACCACAGATCTT
Found at i:2503830 original size:12 final size:12
Alignment explanation
Indices: 2503815--2503839 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2503805 AATATTTTTA
2503815 TATACATATTAT
1 TATACATATTAT
2503827 TATACATATTAT
1 TATACATATTAT
2503839 T
1 T
2503840 CTCATTGAGT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TATACATATTAT
Found at i:2507450 original size:17 final size:17
Alignment explanation
Indices: 2507417--2507450 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2507407 AATGGAATTT
*
2507417 TAAATTTTGAGATATAA
1 TAAATTTTGAGAGATAA
*
2507434 TAAATTTTGTGAGATAA
1 TAAATTTTGAGAGATAA
2507451 GGTTAGAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
TAAATTTTGAGAGATAA
Found at i:2508185 original size:15 final size:16
Alignment explanation
Indices: 2508150--2508192 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2508140 ACCAAAAATT
2508150 TATTTTAAAAATAAAA
1 TATTTTAAAAATAAAA
* *
2508166 AATTTTAAAAA-AAAG
1 TATTTTAAAAATAAAA
2508181 TA-TTTAAAAATA
1 TATTTTAAAAATA
2508193 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
16 10 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
TATTTTAAAAATAAAA
Found at i:2508212 original size:24 final size:22
Alignment explanation
Indices: 2508156--2508217 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 22
2508146 AATTTATTTT
2508156 AAAAATAAAAA-ATTTTAAAAA
1 AAAAATAAAAATATTTTAAAAA
*
2508177 AAAGTATTTAAAAATATTTTAAAATTA
1 AAA--A-ATAAAAATATTTTAAAA--A
2508204 AAAAATAAAAATAT
1 AAAAATAAAAATAT
2508218 ATATTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 3 0.09
23 1 0.03
24 15 0.45
25 10 0.30
27 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAATAAAAATATTTTAAAAA
Found at i:2514709 original size:18 final size:18
Alignment explanation
Indices: 2514686--2514723 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2514676 ATCGTGTTTG
2514686 ATTTTT-ATTTCTAAATTT
1 ATTTTTGATTT-TAAATTT
*
2514704 ATTTTTGATTTTAGATTT
1 ATTTTTGATTTTAAATTT
2514722 AT
1 AT
2514724 CCTTAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
ATTTTTGATTTTAAATTT
Found at i:2519413 original size:23 final size:25
Alignment explanation
Indices: 2519370--2519431 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
2519360 TTAACAATAC
2519370 TGAAGTTTATTTTTATATTTTGT-TT
1 TGAA-TTTATTTTTATATTTTGTATT
* * *
2519395 TG-ATTTATTTTTGTCTTTTTTATT
1 TGAATTTATTTTTATATTTTGTATT
*
2519419 TGAATTTTTTTTT
1 TGAATTTATTTTT
2519432 CATTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 15 0.48
24 5 0.16
25 11 0.35
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.73
Consensus pattern (25 bp):
TGAATTTATTTTTATATTTTGTATT
Found at i:2521305 original size:30 final size:30
Alignment explanation
Indices: 2521250--2521307 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2521240 TAATATCAAC
** *
2521250 AATAAATTAAAAATTGGTATGAACAATAAT
1 AATAAATTAAAAATTAATATCAACAATAAT
*
2521280 AATAAATTAAAGATTAATATCAACAATA
1 AATAAATTAAAAATTAATATCAACAATA
2521308 TTTTATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAAATTAAAAATTAATATCAACAATAAT
Found at i:2524287 original size:18 final size:18
Alignment explanation
Indices: 2524266--2524307 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2524256 GAAAATGAAC
* *
2524266 TTTTAAATTTTTTTTATT
1 TTTTAAAGTTTTTATATT
2524284 TTTTAAAGTTTTTATATT
1 TTTTAAAGTTTTTATATT
2524302 TTTTAA
1 TTTTAA
2524308 GAATTAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTAAAGTTTTTATATT
Found at i:2526885 original size:20 final size:20
Alignment explanation
Indices: 2526860--2526909 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2526850 TGGCTTAAAA
2526860 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2526880 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2526897 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2526910 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2531524 original size:20 final size:20
Alignment explanation
Indices: 2531499--2531548 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2531489 TGGCTTAAAA
2531499 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2531519 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2531536 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2531549 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2538566 original size:51 final size:52
Alignment explanation
Indices: 2538477--2538575 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 52
2538467 GATAAAAGTT
2538477 CAAATTAATTACTTTTAGTTTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
1 CAAATTAATTACTTTTAG-TTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
** *
2538530 CAAATTAATTGTTTTTAG-TTTAGAAATAAAATTGTAAGTATTGAAA
1 CAAATTAATTACTTTTAGTTTTAGAAATAAAATTGTAAATATTGAAA
2538576 CTTTTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 27 0.63
53 16 0.37
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.40
Consensus pattern (52 bp):
CAAATTAATTACTTTTAGTTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
Found at i:2542988 original size:92 final size:91
Alignment explanation
Indices: 2542831--2543040 Score: 271
Period size: 92 Copynumber: 2.3 Consensus size: 91
2542821 ATTGATTTTA
* * * *
2542831 ATAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTGTTAAATTA
1 ATAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTA
* *
2542896 TATTTAAT-ATTAATTATTTTAAATTGT
65 TATGTAATAATT-ATTATTTTAAATTAT
*
2542923 ATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATT
1 ATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATT
2542987 ATATGTAATAATTATTATTTTAAATTAT
64 ATATGTAATAATTATTATTTTAAATTAT
* * * *
2543015 ACAAATTCATAAAATATAATTTATTA
1 ATAAATTCATATAAGAAAATTTATTA
2543041 GTTATAATTA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
ATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTAT
Found at i:2543003 original size:24 final size:25
Alignment explanation
Indices: 2542968--2543015 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2542958 TTATGAAATT
2542968 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
2542992 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
2543016 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:2543217 original size:15 final size:15
Alignment explanation
Indices: 2543182--2543233 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2543172 TAAGAAATTT
*
2543182 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2543196 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2543210 TATTTAATAATAAT-
1 TATTTAATTATAATA
2543224 TATGTTAATT
1 TAT-TTAATT
2543234 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2543332 original size:16 final size:16
Alignment explanation
Indices: 2543311--2543352 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2543301 TTATTAAATT
*
2543311 ATATATTTTAATTATA
1 ATATATTTTAATAATA
2543327 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
2543342 AT-TATGTTTAA
1 ATATAT-TTTAA
2543353 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:2543337 original size:15 final size:15
Alignment explanation
Indices: 2543302--2543343 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2543292 TTAAGAATTT
*
2543302 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2543316 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2543330 TATTTAATAATAAT
1 TATTTAATTATAAT
2543344 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2543340 original size:120 final size:121
Alignment explanation
Indices: 2543055--2543354 Score: 491
Period size: 121 Copynumber: 2.5 Consensus size: 121
2543045 TAATTATTTT
* * * *
2543055 AAATTTTATTAAATCATATATTTTAAATAAAATATATTTAATATTAATTAT-TTCAAATTTTCAT
1 AAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTTTCAT
*
2543119 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
2543176 AAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTAT-AT
1 AAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTT-TCA-
2543239 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
2543297 -AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
2543355 ATGATTAAAT
Statistics
Matches: 169, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
120 57 0.34
121 107 0.63
122 5 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (121 bp):
AAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTTTCATT
TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:2543463 original size:153 final size:156
Alignment explanation
Indices: 2543286--2543598 Score: 524
Period size: 153 Copynumber: 2.0 Consensus size: 156
2543276 ATAAGAATAT
* * *
2543286 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
* *
2543351 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
2543416 T-A-A-TTACCAAAACAAATTTCTGC
131 TAACATTTACCAAAACAAATTTATGC
* *
2543439 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGGGTTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
2543504 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
2543569 TAATCATTTACCAAAACAAATTTATGC
131 TAA-CATTTACCAAAACAAATTTATGC
2543596 TAA
1 TAA
2543599 GGGTATTCTA
Statistics
Matches: 148, Mismatches: 8, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
153 124 0.84
154 1 0.01
156 1 0.01
157 22 0.15
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAACATTTACCAAAACAAATTTATGC
Found at i:2543742 original size:16 final size:16
Alignment explanation
Indices: 2543721--2543772 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
2543711 GATTTGTTAT
2543721 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2543737 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
2543753 TACACATCTAATCCAA
1 TACACCTCTAATCCAA
2543769 TACA
1 TACA
2543773 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2545005 original size:28 final size:28
Alignment explanation
Indices: 2544953--2545008 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2544943 TATAACTTTT
*
2544953 TTTTATTTACCAAAATATTATAAAAAAA
1 TTTTATTTACCAAAATATTACAAAAAAA
2544981 TTTTATTTACCAAAATA-TACCAAAAAAA
1 TTTTATTTACCAAAATATTA-CAAAAAAA
2545009 AAACCTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.36
Consensus pattern (28 bp):
TTTTATTTACCAAAATATTACAAAAAAA
Found at i:2545070 original size:27 final size:27
Alignment explanation
Indices: 2545031--2545116 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
2545021 GCCTGATCAG
* * *
2545031 GCCAATCACATTGGAGGCACCAAAGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
2545058 GCCAATGAGATTGGAGGCACCAATGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
* *
2545085 GCCAAAGAGATTGGCGGCACCAATGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
2545112 GCCAA
1 GCCAA
2545117 AGGACTAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.31, C:0.23, G:0.30, T:0.15
Consensus pattern (27 bp):
GCCAATGAGATTGGAGGCACCAATGGT
Found at i:2545117 original size:27 final size:27
Alignment explanation
Indices: 2545040--2545118 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
2545030 GGCCAATCAC
* *
2545040 ATTGGAGGCACCAAAGGTGCCAATGAG
1 ATTGGAGGCACCAATGGTGCCAAAGAG
2545067 ATTGGAGGCACCAATGGTGCCAAAGAG
1 ATTGGAGGCACCAATGGTGCCAAAGAG
*
2545094 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGAGGCACCAATGGTGCCAAAG
2545119 GACTAAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.32, C:0.20, G:0.33, T:0.15
Consensus pattern (27 bp):
ATTGGAGGCACCAATGGTGCCAAAGAG
Found at i:2545693 original size:18 final size:18
Alignment explanation
Indices: 2545670--2545733 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 18
2545660 TAAGATAGAG
2545670 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
* * *
2545688 TTATTAAATTAAAATAGAG
1 TTATTAAATGAGAATAG-T
*
2545707 TTATTAAATGAGAATTGT
1 TTATTAAATGAGAATAGT
2545725 TTATTAAAT
1 TTATTAAAT
2545734 TAAAATAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 24 0.63
19 14 0.37
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTATTAAATGAGAATAGT
Found at i:2545705 original size:37 final size:37
Alignment explanation
Indices: 2545657--2545752 Score: 165
Period size: 37 Copynumber: 2.6 Consensus size: 37
2545647 GTTAAGTGAT
*
2545657 AATTAAGATAGAGTTATTAAATGAGAATAGTTTATTA
1 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
*
2545694 AATTAAAATAGAGTTATTAAATGAGAATTGTTTATTA
1 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
*
2545731 AATTAAAATAAAGTTATTAAAT
1 AATTAAAATAGAGTTATTAAAT
2545753 AAACTATTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (37 bp):
AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
Found at i:2545712 original size:19 final size:19
Alignment explanation
Indices: 2545657--2545752 Score: 97
Period size: 19 Copynumber: 5.2 Consensus size: 19
2545647 GTTAAGTGAT
*
2545657 AATTAAGATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * *
2545676 AATGAGAATAG-TTTATTA
1 AATTAAAATAGAGTTATTA
2545694 AATTAAAATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * * *
2545713 AATGAGAATTG-TTTATTA
1 AATTAAAATAGAGTTATTA
*
2545731 AATTAAAATAAAGTTATTA
1 AATTAAAATAGAGTTATTA
2545750 AAT
1 AAT
2545753 AAACTATTCT
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
18 28 0.47
19 31 0.53
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
AATTAAAATAGAGTTATTA
Found at i:2545771 original size:37 final size:37
Alignment explanation
Indices: 2545657--2545772 Score: 121
Period size: 37 Copynumber: 3.1 Consensus size: 37
2545647 GTTAAGTGAT
* * *
2545657 AATTAAGATAGAGTTATTAAATGAGAA-TAGTTTATTA
1 AATTAAAATAAAGTTATTAAATGAGAACTA-TTTATCA
* * * *
2545694 AATTAAAATAGAGTTATTAAATGAGAATTGTTTATTA
1 AATTAAAATAAAGTTATTAAATGAGAACTATTTATCA
2545731 AATTAAAATAAAGTTATTAAAT-A-AACTATTCTCATCA
1 AATTAAAATAAAGTTATTAAATGAGAACTATT-T-ATCA
2545768 AATTA
1 AATTA
2545773 CCAAAATAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
35 5 0.07
36 2 0.03
37 62 0.89
38 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (37 bp):
AATTAAAATAAAGTTATTAAATGAGAACTATTTATCA
Found at i:2545926 original size:27 final size:27
Alignment explanation
Indices: 2545865--2545926 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
2545855 TTTTTTTTGT
* **
2545865 ATATTTTAATAAATAAAAAATTTTATA
1 ATATTTTGATAAATAAAAAAAGTTATA
2545892 ATATTTTGATAAATAAAAAAAGTTATA
1 ATATTTTGATAAATAAAAAAAGTTATA
2545919 ATATTTTG
1 ATATTTTG
2545927 GTTATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAAAGTTATA
Found at i:2549996 original size:15 final size:17
Alignment explanation
Indices: 2549960--2549993 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2549950 TGTAATGGTG
*
2549960 GGTTTTTTTTTTGTAAT
1 GGTTATTTTTTTGTAAT
2549977 GGTTATTTTTTT-TAAT
1 GGTTATTTTTTTGTAAT
2549993 G
1 G
2549994 TTAAAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.68
Consensus pattern (17 bp):
GGTTATTTTTTTGTAAT
Found at i:2550196 original size:22 final size:22
Alignment explanation
Indices: 2550171--2550240 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
2550161 TTTATAAGAT
2550171 AATTAGAAACGTTGGTAGATCG
1 AATTAGAAACGTTGGTAGATCG
** **
2550193 AATTAGGGA-GTTTATAAGAT--
1 AATTAGAAACGTTGGT-AGATCG
2550213 AATTAGAAACGTTGGTAGATCG
1 AATTAGAAACGTTGGTAGATCG
2550235 AATTAG
1 AATTAG
2550241 GGGTGTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 11 0.31
21 8 0.22
22 17 0.47
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.30
Consensus pattern (22 bp):
AATTAGAAACGTTGGTAGATCG
Found at i:2550218 original size:42 final size:42
Alignment explanation
Indices: 2550159--2550242 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
2550149 GGGATATGTA
2550159 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
1 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
2550201 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
1 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
2550243 GTGTATTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (42 bp):
AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
Found at i:2550232 original size:20 final size:20
Alignment explanation
Indices: 2550167--2550232 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
2550157 TAAGTTTATA
2550167 AGATAATTAGAAACGTTGGT
1 AGATAATTAGAAACGTTGGT
** **
2550187 AGATCGAATTAGGGA-GTTTAT
1 AGAT--AATTAGAAACGTTGGT
2550208 AAGATAATTAGAAACGTTGGT
1 -AGATAATTAGAAACGTTGGT
2550229 AGAT
1 AGAT
2550233 CGAATTAGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 15 0.44
21 8 0.24
22 11 0.32
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (20 bp):
AGATAATTAGAAACGTTGGT
Found at i:2551091 original size:28 final size:29
Alignment explanation
Indices: 2551041--2551097 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
2551031 TTTCCACACG
*
2551041 GGCTGGACACACAGTCGTGTGTGCCAAACA
1 GGCTGGACACACAGTCG-ATGTGCCAAACA
*
2551071 GGCTGGACACACGGTC-ATGTGCCAAAC
1 GGCTGGACACACAGTCGATGTGCCAAAC
2551098 CATGTCGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
30 15 0.60
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (29 bp):
GGCTGGACACACAGTCGATGTGCCAAACA
Found at i:2552490 original size:45 final size:45
Alignment explanation
Indices: 2552421--2552507 Score: 158
Period size: 45 Copynumber: 1.9 Consensus size: 45
2552411 GTGTATAACT
2552421 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
1 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
2552466 TATCTCATCTATTGAAT-CTGATAAGTATGATTTATCTTCCTT
1 TATCTCATCTATTGAATCCT-ATAAGTATGATTTATCTTCCTT
2552508 AATAAGGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.47
Consensus pattern (45 bp):
TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
Found at i:2553088 original size:8 final size:8
Alignment explanation
Indices: 2553042--2553104 Score: 64
Period size: 8 Copynumber: 8.2 Consensus size: 8
2553032 GGCATAAGTG
2553042 TATATATAT
1 TATA-ATAT
2553051 TATAAATAT
1 TAT-AATAT
2553060 T-TAA-AT
1 TATAATAT
*
2553066 T-TAA-AA
1 TATAATAT
2553072 TAT-ATAT
1 TATAATAT
2553079 TATAATAT
1 TATAATAT
2553087 TATAATAT
1 TATAATAT
2553095 TATAATAT
1 TATAATAT
2553103 TA
1 TA
2553105 AAACTTAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
6 9 0.19
7 7 0.15
8 23 0.48
9 8 0.17
10 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TATAATAT
Found at i:2553132 original size:43 final size:43
Alignment explanation
Indices: 2553042--2553143 Score: 109
Period size: 43 Copynumber: 2.3 Consensus size: 43
2553032 GGCATAAGTG
* * * *
2553042 TATATATATTATAAATATTTAAATTTAAAATATATATTATAATAT
1 TATA-ATATTAT-AATATTAAAACTTAAAATATATAGTATAACAT
2553087 TATAATATTATAATATTAAAACTTAAAAGT-TA-AGTATATACAT
1 TATAATATTATAATATTAAAACTTAAAA-TATATAGTATA-ACAT
*
2553130 TATTATATTATAAT
1 TATAATATTATAAT
2553144 GATAAAGTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
42 5 0.10
43 33 0.66
44 8 0.16
45 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATATTATAATATTAAAACTTAAAATATATAGTATAACAT
Found at i:2553209 original size:4 final size:4
Alignment explanation
Indices: 2553195--2553240 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
2553185 AACTGCACAG
*
2553195 AGAA GGAA AGAA AGAAA AGAA A-AA A-AA AGAA AGAA AGAA AGAA AGA
1 AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA
2553241 GAAAAATTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 6 0.16
4 28 0.74
5 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2555087 original size:17 final size:18
Alignment explanation
Indices: 2555067--2555100 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2555057 TATATGAATA
*
2555067 TATTTTTTATA-ACATAC
1 TATTTTATATATACATAC
2555084 TATTTTATATATACATA
1 TATTTTATATATACATA
2555101 TATAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTATATATACATAC
Found at i:2555327 original size:3 final size:3
Alignment explanation
Indices: 2555319--2555373 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
2555309 ATATATTGAT
2555319 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2555367 TTA TTA T
1 TTA TTA T
2555374 CTTGGTGAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2557715 original size:51 final size:51
Alignment explanation
Indices: 2557568--2557753 Score: 200
Period size: 51 Copynumber: 3.7 Consensus size: 51
2557558 AGTGAAAGTG
* * * *
2557568 ATGGTCACGTGTGTAGTACTATGTGCAGGGTACTACGTGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTTCGTGTACCGGATAGTA
* * *
2557617 ATGGGTCGCATGTGTAGTACTATGTGCAGGGTACTAT-GCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACT-TCGTGTACCGGATAGTA
* * * * * *
2557668 TTCGATCACGTGTGTAGTACTATGTGCAAGCTACTTCGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTTCGTGTACCGGATAGTA
2557720 ATGGTCACATGTGTAGTACTATGTGCAGGCTACT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACT
2557754 ATGTGAACCG
Statistics
Matches: 113, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.02
50 40 0.35
51 69 0.61
52 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTTCGTGTACCGGATAGTA
Found at i:2557756 original size:102 final size:101
Alignment explanation
Indices: 2557572--2557756 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 101
2557562 AAAGTGATGG
* * *
2557572 TCACGTGTGTAGTACTATGTGCAGGGTACTACGTGTACCGGAATGATGGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAATGATGGGTCACATGTGTAGTAC
*
2557637 TATGTGCAGGGTACTATGCGTACCGGATAGTTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* *
2557673 TCACGTGTGTAGTACTATGTGCAAGCTACTTCGTGTATCGG-ATGGTAAT-GGTCACATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAAT-G--ATGGGTCACATGTGTAG
2557736 TACTATGTGCAGGCTACTATG
63 TACTATGTGCAGGCTACTATG
2557757 TGAACCGAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 2 0.03
101 38 0.51
102 33 0.44
103 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAATGATGGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:2572855 original size:103 final size:103
Alignment explanation
Indices: 2572675--2573044 Score: 521
Period size: 103 Copynumber: 3.6 Consensus size: 103
2572665 TAACCGTTAT
* * * * *
2572675 CGGTGGATTCCGCACTTAGCAACCACCAAT-GAATCGAGGAATCAGCACACAGCAACCCCTTGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATAG-GTAGGGGAATCAGCACACAGCAACCCCTTGGG
* * *
2572739 GGAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATG
65 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * * **
2572777 CAGTGGAATCAGCACTTAGCAACCACCAA-ATGAGTCGGGGAGTCAGCACTTAGCAACCCCTTGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATA-G-GTAGGGGAATCAGCACACAGCAACCCCTTGG
2572841 GGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
64 GGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* ** *
2572881 CGGTGGGATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCTTGGGG
2572946 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* *
2572984 TGGTGGGATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCTT
2573045 TATATGCAAT
Statistics
Matches: 244, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
102 26 0.11
103 177 0.73
104 40 0.16
105 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:2572930 original size:33 final size:33
Alignment explanation
Indices: 2572888--2573040 Score: 111
Period size: 33 Copynumber: 4.5 Consensus size: 33
2572878 ATACGGTGGG
2572888 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
1 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
*
2572921 ATCAGCACTTAGCAACC-CC--T-CG--GGGGA
1 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
* ** *
2572948 ATCAGCACTTAGCAACCCCCTTTCACATTTAAAATATGGTGGG
1 ATCAGCACTTAGCAA-CCAC---CA-A--T-AGGTA-GG-GGA
2572991 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
1 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
**
2573024 ATCAGCACACAGCAACC
1 ATCAGCACTTAGCAACC
2573041 CCTTTATATG
Statistics
Matches: 94, Mismatches: 10, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
27 20 0.21
28 2 0.02
29 2 0.02
30 1 0.01
32 3 0.03
33 34 0.36
34 2 0.02
35 3 0.03
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
42 5 0.05
43 17 0.18
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
Found at i:2581008 original size:45 final size:45
Alignment explanation
Indices: 2580939--2581025 Score: 158
Period size: 45 Copynumber: 1.9 Consensus size: 45
2580929 GTGTATAACT
2580939 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
1 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
2580984 TATCTCATCTATTGAAT-CTGATAAGTATGATTTATCTTCCTT
1 TATCTCATCTATTGAATCCT-ATAAGTATGATTTATCTTCCTT
2581026 AATAAGGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.47
Consensus pattern (45 bp):
TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
Done.