Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 13 of 185
Found at i:3548386 original size:6 final size:6
Alignment explanation
Indices: 3548377--3548401 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3548367 TATTAATATA
3548377 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
3548402 TTATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:3548695 original size:30 final size:29
Alignment explanation
Indices: 3548632--3548695 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
3548622 TAATCTTGTT
* *
3548632 TAGTTGGATGACCAATTTAAAAAAATTCA
1 TAGTTGGATGACAAATTTAAAAAAATCCA
* * *
3548661 TAGTTGGGTGACAAATTTGAGACAAATCCA
1 TAGTTGGATGACAAATTT-AAAAAAATCCA
3548691 TAGTT
1 TAGTT
3548696 AGGTAATCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (29 bp):
TAGTTGGATGACAAATTTAAAAAAATCCA
Found at i:3549347 original size:13 final size:13
Alignment explanation
Indices: 3549329--3549354 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3549319 CATGCAAGAC
3549329 AACGTGGTTGAGA
1 AACGTGGTTGAGA
3549342 AACGTGGTTGAGA
1 AACGTGGTTGAGA
3549355 GCAAGGCAGC
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:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (13 bp):
AACGTGGTTGAGA
Found at i:3550168 original size:18 final size:18
Alignment explanation
Indices: 3550141--3550175 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3550131 AGCACCAAAG
3550141 CTTTCATCCTCCTCCTCA
1 CTTTCATCCTCCTCCTCA
* *
3550159 CTTTCTTCCTCTTCCTC
1 CTTTCATCCTCCTCCTC
3550176 TTCTTCATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTTCATCCTCCTCCTCA
Found at i:3555058 original size:14 final size:16
Alignment explanation
Indices: 3555039--3555070 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3555029 CCAATATTTT
3555039 ATTTTT-TAAAAT-TA
1 ATTTTTATAAAATATA
3555053 ATTTTTATAAAATATA
1 ATTTTTATAAAATATA
3555069 AT
1 AT
3555071 GCACTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTTATAAAATATA
Found at i:3555613 original size:21 final size:21
Alignment explanation
Indices: 3555548--3555618 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
3555538 GTTTTTAGGG
3555548 TTAAGGTTTTGTTAAAATAAT
1 TTAAGGTTTTGTTAAAATAAT
* ** *
3555569 TTAGGGTTAGGTT--TATAAGGT
1 TTAAGGTTTTGTTAAAATAA--T
3555590 TTAAGGTTTTGTTAAAATAAT
1 TTAAGGTTTTGTTAAAATAAT
*
3555611 TTAGGGTT
1 TTAAGGTT
3555619 CTTGGTTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
21 29 0.78
23 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
TTAAGGTTTTGTTAAAATAAT
Found at i:3555768 original size:34 final size:33
Alignment explanation
Indices: 3555663--3555768 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
3555653 TTTAGTGTTC
* *
3555663 TTTTTT-AAAAATTAATTAAATTAGGGTTTAGG
1 TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
** *
3555695 AGTTTTAAATTAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAAA-AAATTAATTAAATTTGGGTTTAGT
*
3555729 GTTTTTAAGAAAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAA-AAAATTAATTAAATTTGGGTTTAGT
3555763 TTTTTT
1 TTTTTT
3555769 TAAAGGCATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 4 0.06
33 2 0.03
34 55 0.89
35 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (33 bp):
TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
Found at i:3557805 original size:125 final size:127
Alignment explanation
Indices: 3557658--3558177 Score: 755
Period size: 126 Copynumber: 4.1 Consensus size: 127
3557648 GATTTTAGTT
* * * * * * *
3557658 TTTTTCTACGGTAGTTCCTGAAAAAATAATTTTGAGAAGATGATTCTCAACAAATAGTCTTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* *
3557723 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACT-AAAAAAACTCCCACGTGGA-AGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACA-CTC
* * * *
3557783 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTAAGAAGACGGTTCTAAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* *
3557848 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCTACGTGGACACTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
3557909 TTTTTCTACAGTAGTTCGTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
* * * *
3557974 ACCCTTCAAGTAGGATGCACTGTCAACAAAATTGA-AGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
3558035 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGTTTCTGAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
*
3558100 ACACTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
* *
3558161 TTTTTTTACAGCAGTTC
1 TTTTTCTACAGTAGTTC
3558178 ATGTTTGGCC
Statistics
Matches: 356, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
125 90 0.25
126 265 0.74
127 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (127 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACTGAAAAAAGCTCCCACGTGGACACTC
Found at i:3558369 original size:28 final size:28
Alignment explanation
Indices: 3558338--3558399 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
3558328 CGGCGTTATT
* *
3558338 TTTTTATCGGAGAATACAACGCGAATAA
1 TTTTTATCAGAGAACACAACGCGAATAA
*
3558366 TTTTTATCAGAGAACACAACGCGAATTA
1 TTTTTATCAGAGAACACAACGCGAATAA
3558394 TTTTTA
1 TTTTTA
3558400 ACTAGACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (28 bp):
TTTTTATCAGAGAACACAACGCGAATAA
Found at i:3560782 original size:20 final size:20
Alignment explanation
Indices: 3560757--3560794 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3560747 ACAACCTATG
3560757 GTGTACACCTGATAAATATC
1 GTGTACACCTGATAAATATC
3560777 GTGTACACCTGATAAATA
1 GTGTACACCTGATAAATA
3560795 AGACTTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
GTGTACACCTGATAAATATC
Found at i:3561710 original size:18 final size:18
Alignment explanation
Indices: 3561679--3561722 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3561669 GACTGGGAAA
* *
3561679 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
* *
3561697 ATGATACATGTAAGGGCT
1 AGGATACATATAAGGGCT
3561715 AGGATACA
1 AGGATACA
3561723 CACCTGGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:3564599 original size:20 final size:20
Alignment explanation
Indices: 3564576--3564637 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
3564566 TATTTTTCTA
3564576 GATTAGTTCAGATTTAAATT
1 GATTAGTTCAGATTTAAATT
** *** *
3564596 GATT--TTCTTATTTTTCTA
1 GATTAGTTCAGATTTAAATT
3564614 GATTAGTTCAGATTTAAATT
1 GATTAGTTCAGATTTAAATT
3564634 GATT
1 GATT
3564638 TTTATACATT
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 12 0.43
20 16 0.57
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (20 bp):
GATTAGTTCAGATTTAAATT
Found at i:3564615 original size:38 final size:38
Alignment explanation
Indices: 3564564--3564639 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3564554 ATTATATGTG
3564564 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
3564602 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
3564640 TATACATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (38 bp):
CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
Found at i:3578965 original size:49 final size:49
Alignment explanation
Indices: 3578910--3579055 Score: 222
Period size: 49 Copynumber: 3.0 Consensus size: 49
3578900 TTCGTTTTCT
* *
3578910 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGTCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* * *
3578959 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGTCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
3579008 CGATGCCATA-TCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGT-CCAGCTATGGTCTTACACGGAATCACA-AATCACAT
3579056 GTTCACATGT
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
49 81 0.93
50 6 0.07
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (49 bp):
CGATGCCATAGTCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
Found at i:3580046 original size:37 final size:37
Alignment explanation
Indices: 3579981--3580089 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
3579971 TACGTATGAT
* *
3579981 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
3580016 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
3580053 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
3580090 TAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:3580106 original size:46 final size:46
Alignment explanation
Indices: 3580053--3580307 Score: 323
Period size: 46 Copynumber: 5.3 Consensus size: 46
3580043 TAAGTGTAGC
* **
3580053 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
3580099 CACTTATCACTTT-TTATCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCA-CTTGATCAGATAAGTGTAGCCGAAGCTAT
3580145 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
3580197 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
3580243 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
3580295 CACTTATCACTTT
1 CACTTATCACTTT
3580308 CCACATAAGT
Statistics
Matches: 184, Mismatches: 11, Indels: 28
0.83 0.05 0.13
Matches are distributed among these distances:
45 1 0.01
46 94 0.51
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.45
53 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:3580176 original size:52 final size:52
Alignment explanation
Indices: 3580096--3580307 Score: 310
Period size: 52 Copynumber: 4.2 Consensus size: 52
3580086 TAGCTAAAGC
* * *
3580096 TATCACTTATCACTTTTTATCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCA-CTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
3580149 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
3580201 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* *
3580247 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
3580299 TATCACTTT
1 TATCACTTT
3580308 CCACATAAGT
Statistics
Matches: 144, Mismatches: 9, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
46 43 0.30
49 1 0.01
52 84 0.58
53 16 0.11
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:3580218 original size:98 final size:98
Alignment explanation
Indices: 3580053--3580307 Score: 422
Period size: 98 Copynumber: 2.6 Consensus size: 98
3580043 TAAGTGTAGC
* * ** *
3580053 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTTATCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCATCT
3580118 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
3580152 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCA-CT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT-TCATCT
*
3580216 TGATCAGATAAGTATAGCCGAAGCTATTACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
3580250 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
3580308 CCACATAAGT
Statistics
Matches: 148, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
98 137 0.93
99 11 0.07
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCATCTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:3583184 original size:14 final size:15
Alignment explanation
Indices: 3583158--3583189 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3583148 GAGCAACAAC
3583158 AATAAAAATAAGATA
1 AATAAAAATAAGATA
3583173 AATAAAAA-AAGATA
1 AATAAAAATAAGATA
3583187 AAT
1 AAT
3583190 CAATAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AATAAAAATAAGATA
Found at i:3583926 original size:41 final size:41
Alignment explanation
Indices: 3583864--3583983 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
3583854 TGATCGAATG
* *
3583864 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
3583905 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * * * *
3583946 CATTTCGGACTATAGGTCTAGCAGGCTAAAAGCCGGTG
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTG
3583984 TACTGAATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:3584349 original size:18 final size:18
Alignment explanation
Indices: 3584326--3584394 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
3584316 TATGATGAAT
3584326 ATGTATATATATATTCGA
1 ATGTATATATATATTCGA
3584344 ATGTATGTATTAGCTATGTATTCGAA
1 ATGTA--TA-TA--TA--TATTCG-A
3584370 TATGTATATATATATTCGA
1 -ATGTATATATATATTCGA
3584389 ATGTAT
1 ATGTAT
3584395 GTATTAGCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 18
0.70 0.00 0.30
Matches are distributed among these distances:
18 11 0.26
19 1 0.02
20 8 0.19
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 8 0.19
26 1 0.02
27 5 0.12
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (18 bp):
ATGTATATATATATTCGA
Found at i:3584368 original size:25 final size:25
Alignment explanation
Indices: 3584337--3584411 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
3584327 TGTATATATA
3584337 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
*
3584362 TATTCGAA--TATGTA-TA--TATA
1 TATTCGAATGTATGTATTAGCTATG
3584382 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
3584407 TATTC
1 TATTC
3584412 AGGTATAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
20 11 0.26
22 8 0.19
23 8 0.19
25 16 0.37
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (25 bp):
TATTCGAATGTATGTATTAGCTATG
Found at i:3584371 original size:45 final size:45
Alignment explanation
Indices: 3584322--3584411 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
3584312 TGTATATGAT
3584322 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
3584367 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
3584412 AGGTATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (45 bp):
GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
Found at i:3584387 original size:20 final size:20
Alignment explanation
Indices: 3584322--3584390 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 20
3584312 TGTATATGAT
3584322 GAATATGTATATATATATTC
1 GAATATGTATATATATATTC
*
3584342 GAATGTATGTATTAGCTATGTATTC
1 GAA--TATGTA-TA--TATATATTC
3584367 GAATATGTATATATATATTC
1 GAATATGTATATATATATTC
3584387 GAAT
1 GAAT
3584391 GTATGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 15 0.36
22 8 0.19
23 8 0.19
25 11 0.26
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43
Consensus pattern (20 bp):
GAATATGTATATATATATTC
Found at i:3588764 original size:37 final size:37
Alignment explanation
Indices: 3588714--3588787 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3588704 ATGAAAGAAA
3588714 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
1 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
3588751 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
1 AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
3588788 TAATAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (37 bp):
AGAATCCATCACATCAGGCTTGAGACAAAATGTTGGT
Found at i:3590128 original size:14 final size:14
Alignment explanation
Indices: 3590109--3590136 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3590099 ACCCTAGTAG
3590109 TAATTAACAAGAAA
1 TAATTAACAAGAAA
3590123 TAATTAACAAGAAA
1 TAATTAACAAGAAA
3590137 GTCGCTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
TAATTAACAAGAAA
Found at i:3595776 original size:17 final size:17
Alignment explanation
Indices: 3595751--3595798 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
3595741 TGATGTGTTC
*
3595751 TTCAGTAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
3595768 TTCAATAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
*
3595785 TTCGATAAAAGAAA
1 TTCAATAAAAGAAA
3595799 AGTAGGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (17 bp):
TTCAATAAAAGAAAGAA
Found at i:3602329 original size:38 final size:38
Alignment explanation
Indices: 3602276--3602352 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
3602266 AAATACTAAG
3602276 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
** **
3602314 TGATAAATTTGTTTAGCATGCTTGTTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
3602352 T
1 T
3602353 TTTGTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (38 bp):
TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
Found at i:3604292 original size:17 final size:18
Alignment explanation
Indices: 3604270--3604306 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
3604260 CAAAACTAAG
3604270 GTTCATTTGGTGTT-CAT
1 GTTCATTTGGTGTTCCAT
3604287 GTTCATTTGGTGTTCCAT
1 GTTCATTTGGTGTTCCAT
3604305 GT
1 GT
3604307 CAGGATGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.11, C:0.14, G:0.24, T:0.51
Consensus pattern (18 bp):
GTTCATTTGGTGTTCCAT
Found at i:3605589 original size:236 final size:236
Alignment explanation
Indices: 3605176--3605648 Score: 937
Period size: 236 Copynumber: 2.0 Consensus size: 236
3605166 TTTGTCTAAT
3605176 AATGCCCATAACCACACTAGTCTGCTTCAAGATTGACCTTATAAAAACCAAGTTGTACCATGCAT
1 AATGCCCATAACCACACTAGTCTGCTTCAAGATTGACCTTATAAAAACCAAGTTGTACCATGCAT
3605241 AGAGAGGGTTTAGTCTCCTTAACCTAAAATGTGAGATACTTACATATTAAGAAACACGATACTTA
66 AGAGAGGGTTTAGTCTCCTTAACCTAAAATGTGAGATACTTACATATTAAGAAACACGATACTTA
3605306 TTAGCAACATGTTCATTAGTAGTGAGTCTCTCCATAACAATCTTACATAAGATGTGTTCAGTTGC
131 TTAGCAACATGTTCATTAGTAGTGAGTCTCTCCATAACAATCTTACATAAGATGTGTTCAGTTGC
*
3605371 CATCTTGTTAGTAGTTTTTCTGTACCAAATTATGTTAAACC
196 CATCTTGTTAGTAGTTTTTCTCTACCAAATTATGTTAAACC
3605412 AATGCCCATAACCACACTAGTCTGCTTCAAGATTGACCTTATAAAAACCAAGTTGTACCATGCAT
1 AATGCCCATAACCACACTAGTCTGCTTCAAGATTGACCTTATAAAAACCAAGTTGTACCATGCAT
3605477 AGAGAGGGTTTAGTCTCCTTAACCTAAAATGTGAGATACTTACATATTAAGAAACACGATACTTA
66 AGAGAGGGTTTAGTCTCCTTAACCTAAAATGTGAGATACTTACATATTAAGAAACACGATACTTA
3605542 TTAGCAACATGTTCATTAGTAGTGAGTCTCTCCATAACAATCTTACATAAGATGTGTTCAGTTGC
131 TTAGCAACATGTTCATTAGTAGTGAGTCTCTCCATAACAATCTTACATAAGATGTGTTCAGTTGC
3605607 CATCTTGTTAGTAGTTTTTCTCTACCAAATTATGTTAAACC
196 CATCTTGTTAGTAGTTTTTCTCTACCAAATTATGTTAAACC
3605648 A
1 A
3605649 TTAGTAGCTT
Statistics
Matches: 236, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
236 236 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (236 bp):
AATGCCCATAACCACACTAGTCTGCTTCAAGATTGACCTTATAAAAACCAAGTTGTACCATGCAT
AGAGAGGGTTTAGTCTCCTTAACCTAAAATGTGAGATACTTACATATTAAGAAACACGATACTTA
TTAGCAACATGTTCATTAGTAGTGAGTCTCTCCATAACAATCTTACATAAGATGTGTTCAGTTGC
CATCTTGTTAGTAGTTTTTCTCTACCAAATTATGTTAAACC
Found at i:3615475 original size:77 final size:76
Alignment explanation
Indices: 3615348--3615569 Score: 245
Period size: 77 Copynumber: 2.9 Consensus size: 76
3615338 CAATTCTCCA
* *
3615348 CATGGTATCAAATGTTTTTGGTTCTTTCCTTATAAGTGTTTTTTTTCTGGTCGAACTCTTGCTTC
1 CATGGTATCAGATGTTTTTGGTTCTTT-CTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTC
*
3615413 TCATGTTTAGTC
65 TCATGTTCAGTC
* *
3615425 CATGGTATCAGATGTTTTTGGTT-TTT-TTCCTAAGTGTTTTCTTTTCCTGGTTGAAATCTTGCT
1 CATGGTATCAGATGTTTTTGGTTCTTTCTT-ATAAGTGTTTT-TTTT-CTGGTCGAAATCTTGCT
* *
3615488 TCTCTTGTTCATTC
63 TCTCATGTTCAGTC
* * * *
3615502 CATGGTATCAGAT-TTTTCTGGTTCCTTAC-TATGAAGAGTTTTTTTTCTTGGTCGAATTATTGC
1 CATGGTATCAGATGTTTT-TGGTT-CTTTCTTAT-AAGTGTTTTTTTTC-TGGTCGAAATCTTGC
3615565 TTCTC
62 TTCTC
3615570 CTATTCTATT
Statistics
Matches: 123, Mismatches: 13, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
74 2 0.02
75 10 0.08
76 11 0.09
77 67 0.54
78 22 0.18
79 11 0.09
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (76 bp):
CATGGTATCAGATGTTTTTGGTTCTTTCTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTCT
CATGTTCAGTC
Found at i:3617816 original size:4 final size:4
Alignment explanation
Indices: 3617807--3617840 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
3617797 AAGTTTTATT
3617807 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
3617841 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:3617848 original size:22 final size:22
Alignment explanation
Indices: 3617790--3617849 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
3617780 AAGTGGCCCA
*
3617790 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
3617814 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
3617835 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
3617850 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:3633870 original size:36 final size:30
Alignment explanation
Indices: 3633802--3633861 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3633792 GCTCAATAAG
3633802 AATCTTAAATATTAATATTGATACTAAGTT
1 AATCTTAAATATTAATATTGATACTAAGTT
*
3633832 AATCTTAAATATTAATATTGATATTAAGTT
1 AATCTTAAATATTAATATTGATACTAAGTT
3633862 TAAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (30 bp):
AATCTTAAATATTAATATTGATACTAAGTT
Found at i:3633941 original size:31 final size:27
Alignment explanation
Indices: 3633903--3633964 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 27
3633893 AAATAATCAT
3633903 TCAACTATGATAGTGTTTTTATTTTAGTCA
1 TCAACTAT-A-AGTGTTTTTA-TTTAGTCA
* *
3633933 CTCAACTATAATTTTTTTTATTTAGTCA
1 -TCAACTATAAGTGTTTTTATTTAGTCA
3633961 TCAA
1 TCAA
3633965 AGTTTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.14
28 8 0.28
29 8 0.28
30 1 0.03
31 8 0.28
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (27 bp):
TCAACTATAAGTGTTTTTATTTAGTCA
Found at i:3638452 original size:2 final size:2
Alignment explanation
Indices: 3638447--3638472 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3638437 ACACACACAG
3638447 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
3638473 GCTTAGATTA
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:3640997 original size:56 final size:56
Alignment explanation
Indices: 3640934--3641047 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
3640924 GACAAAAAGG
*
3640934 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGATGAAAACAAAAGAAAAGGGA
1 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
3640990 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
1 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
3641046 AA
1 AA
3641048 GAAGCATAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (56 bp):
AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
Found at i:3643241 original size:16 final size:16
Alignment explanation
Indices: 3643202--3643266 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
3643192 CGTTTGGTTC
*
3643202 ATTGTAATGGAATAGG
1 ATTGTAATGGAATAGA
* * *
3643218 ACTATAATGTAATAGA
1 ATTGTAATGGAATAGA
*
3643234 ATTGTAATGGAATACA
1 ATTGTAATGGAATAGA
** *
3643250 GCTGTAATAGAATAGA
1 ATTGTAATGGAATAGA
3643266 A
1 A
3643267 CTTTAATAAG
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (16 bp):
ATTGTAATGGAATAGA
Found at i:3643470 original size:26 final size:24
Alignment explanation
Indices: 3643427--3643490 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 24
3643417 TAATTATTGT
* *
3643427 TATTAAAT--TTTAATAAAATTAT
1 TATTAAATAATTTAATAAAAATAA
3643449 TATTAAATATAATTTAATAAAAATAA
1 TATT-AA-ATAATTTAATAAAAATAA
3643475 TATTAAATAATTTAAT
1 TATTAAATAATTTAAT
3643491 CATGTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.11
23 2 0.06
24 12 0.33
25 2 0.06
26 16 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTAAATAATTTAATAAAAATAA
Found at i:3644134 original size:5 final size:5
Alignment explanation
Indices: 3644124--3644148 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3644114 CGGATTTATT
3644124 TGTGA TGTGA TGTGA TGTGA TGTGA
1 TGTGA TGTGA TGTGA TGTGA TGTGA
3644149 GTAGCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TGTGA
Found at i:3644378 original size:16 final size:16
Alignment explanation
Indices: 3644357--3644398 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3644347 TTCGCTGTAT
3644357 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
3644373 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
*
3644389 TGAAATAGAG
1 TGGAATAGAG
3644399 TGTAATAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:3644403 original size:15 final size:16
Alignment explanation
Indices: 3644360--3644404 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
3644350 GCTGTATTGG
* *
3644360 AATAGAGGCGTAATGG
1 AATAGAGGTGTAATGA
3644376 AATAGAGGTGTAATGA
1 AATAGAGGTGTAATGA
3644392 AATAGA-GTGTAAT
1 AATAGAGGTGTAAT
3644405 AGCAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (16 bp):
AATAGAGGTGTAATGA
Found at i:3644651 original size:15 final size:15
Alignment explanation
Indices: 3644627--3644669 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3644617 TTTAAACATA
*
3644627 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3644642 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
3644656 A-TATAATTATAATA
1 ATTATAATTA-AATA
3644670 AAATTCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 5 0.20
15 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3644655 original size:16 final size:16
Alignment explanation
Indices: 3644618--3644659 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3644608 TTAATCATAT
*
3644618 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
3644634 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3644649 TTAAAATATAT
1 TTAAAATATAT
3644660 AATTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3644659 original size:18 final size:18
Alignment explanation
Indices: 3644638--3644673 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3644628 TTATTATTAA
3644638 ATAT-ATTATAATTAAAAT
1 ATATAATTATAA-TAAAAT
3644656 ATATAATTATAATAAAAT
1 ATATAATTATAATAAAAT
3644674 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAATTATAATAAAAT
Found at i:3644662 original size:13 final size:14
Alignment explanation
Indices: 3644627--3644669 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
3644617 TTTAAACATA
*
3644627 ATTATTATTAAATAT
1 ATTATAATTAAA-AT
3644642 ATTATAATTAAAAT
1 ATTATAATTAAAAT
*
3644656 A-TATAATTATAAT
1 ATTATAATTAAAAT
3644669 A
1 A
3644670 AAATTCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATAATTAAAAT
Found at i:3644787 original size:14 final size:15
Alignment explanation
Indices: 3644738--3644789 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3644728 ATAAAATATA
3644738 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3644753 TATTAAATATATTAT
1 AATTAAATATATTAT
3644768 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3644781 AATTTAATA
1 AATTAAATA
3644790 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3644835 original size:120 final size:121
Alignment explanation
Indices: 3644621--3644904 Score: 473
Period size: 120 Copynumber: 2.4 Consensus size: 121
3644611 ATCATATTTA
3644621 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTATAATAAAATTCTTAATAATCA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTATAATAAAATTCTTAATAATCA
* *
3644686 ATATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
*
3644742 AACATAATTATTATTAAATATATTATAATTAAAATATATAATT-TAATAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTATAATAAAATTCTTAATAATCA
*
3644806 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
* * * *
3644862 AAAATGATTAATATTAAATATAATT-TAATAAAAATATATAATT
1 AACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATT
3644905 CCCCCCACCT
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 108 0.70
121 46 0.30
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTATAATAAAATTCTTAATAATCA
ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
Found at i:3644852 original size:61 final size:61
Alignment explanation
Indices: 3644667--3644853 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
3644657 TATAATTATA
* *
3644667 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTGAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * * * *
3644728 ATAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCATAATATATGATACT
3644786 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
3644848 ATAAAA
1 ATAAAA
3644854 GATAATTTAA
Statistics
Matches: 95, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 3 0.03
58 5 0.05
59 28 0.29
60 16 0.17
61 34 0.36
62 5 0.05
63 4 0.04
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:3645573 original size:20 final size:20
Alignment explanation
Indices: 3645548--3645589 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3645538 GAGTAGAAGC
*
3645548 AAAGTAAATCATTTTACAGA
1 AAAGTAAAACATTTTACAGA
*
3645568 AAAGTAAAACATTTTCCAGA
1 AAAGTAAAACATTTTACAGA
3645588 AA
1 AA
3645590 TCATTTTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAGTAAAACATTTTACAGA
Found at i:3649628 original size:67 final size:67
Alignment explanation
Indices: 3649543--3649678 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
3649533 TACTTGTCAA
3649543 AAAACAAGATGAAACAACAAAGTATAACAGTCAAAATTTCATACAAAATCACACTGTCCAGCAGT
1 AAAACAAGATGAAACAACAAAGTATAACAGTCAAAATTTCATACAAAATCACACTGTCCAGCAGT
3649608 AC
66 AC
*
3649610 AAAACAAGATGAAACAACAAAGTATAACAGTCAAAATTTCATACAAAATCTCACTGTCCAGCAGT
1 AAAACAAGATGAAACAACAAAGTATAACAGTCAAAATTTCATACAAAATCACACTGTCCAGCAGT
3649675 AC
66 AC
3649677 AA
1 AA
3649679 TTTTTCAGTG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.51, C:0.21, G:0.10, T:0.18
Consensus pattern (67 bp):
AAAACAAGATGAAACAACAAAGTATAACAGTCAAAATTTCATACAAAATCACACTGTCCAGCAGT
AC
Found at i:3651299 original size:41 final size:41
Alignment explanation
Indices: 3651240--3651343 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
3651230 TTTAACATAT
* *
3651240 TCACCGGCACTTAGCCTGCTAGGCTAATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
* * *
3651281 TTACCGGCACTTAGCCTGCTAGGTTTACAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
*
3651322 TCACCCGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
3651344 ATTTATGGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
Found at i:3660249 original size:41 final size:41
Alignment explanation
Indices: 3660192--3660295 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
3660182 TTTAACATAT
* *
3660192 TCACCGGCACTTAGCCTGCTAGGCTTACAGCCTGATTCAGA
1 TCACCAGCACTTAGCCTGCTAGGCTTACAACCTGATTCAGA
* *
3660233 TCACCAGCACTTAGCCTGCTGGGTTTACAACCTGATTCAGA
1 TCACCAGCACTTAGCCTGCTAGGCTTACAACCTGATTCAGA
* *
3660274 TCACCCGCACTTAGCTTGCTAG
1 TCACCAGCACTTAGCCTGCTAG
3660296 ATTTATGGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (41 bp):
TCACCAGCACTTAGCCTGCTAGGCTTACAACCTGATTCAGA
Found at i:3663382 original size:41 final size:41
Alignment explanation
Indices: 3663326--3663448 Score: 169
Period size: 41 Copynumber: 3.0 Consensus size: 41
3663316 ACTAAAAATA
*
3663326 GAGCATTAGCGGCGCTTCTTCAAAAACGTCGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTCTTCAAAAACGACGCTAAAGCCCC
3663367 GAGCATTAGCGGCGCTT-TTCCAGAAAA-GACGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTCTT-CA-AAAACGACGCTAAAGCCCC
* * * *
3663408 GAGCATTAGCGACGCTTCTTGAAAAACGCCACTAAAGCCCC
1 GAGCATTAGCGGCGCTTCTTCAAAAACGACGCTAAAGCCCC
3663449 AAAAACTCAA
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
40 6 0.08
41 61 0.84
42 6 0.08
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTCTTCAAAAACGACGCTAAAGCCCC
Found at i:3663550 original size:39 final size:39
Alignment explanation
Indices: 3663507--3663605 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 39
3663497 TGGAAAACGT
3663507 CGCTAATGCTCATTTTTAGCGGCGTTTTCCAAAAAGCGC
1 CGCTAATGCTCATTTTTAGCGGCGTTTTCCAAAAAGCGC
* * **
3663546 CGCTAATACTCGATCTTTAGCGGCGTTTTTTAAAAAGCGC
1 CGCTAATGCTC-ATTTTTAGCGGCGTTTTCCAAAAAGCGC
* * *
3663586 CGGTAATGCTTATTATTAGC
1 CGCTAATGCTCATTTTTAGC
3663606 AGTGTTTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 17 0.34
40 33 0.66
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (39 bp):
CGCTAATGCTCATTTTTAGCGGCGTTTTCCAAAAAGCGC
Found at i:3664007 original size:7 final size:7
Alignment explanation
Indices: 3663995--3664021 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3663985 GATTTTCAAA
3663995 AAATTTT
1 AAATTTT
3664002 AAATTTT
1 AAATTTT
3664009 AAATTTT
1 AAATTTT
3664016 AAATTT
1 AAATTT
3664022 GAATATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AAATTTT
Found at i:3664855 original size:42 final size:42
Alignment explanation
Indices: 3664807--3664992 Score: 198
Period size: 42 Copynumber: 4.4 Consensus size: 42
3664797 TTTTAGAAAT
3664807 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCAC
* * * *
3664849 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTATCAAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCAC
* * * *
3664891 AATCGCCGCTAAAG-ACTATGACCTTTAGCAGCGCTTTTATCAC
1 AAACGCCGCTAAAGAAC-AAGACCTTTAGCGGCGCTTTT-CCAC
* * * * * *
3664934 AAACGCCGCTATAGATCAA-ACCTTTAGTGACGCTTCTTGCAA
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTT-TTCCAC
3664976 AAACGCCGCTAAA-AACA
1 AAACGCCGCTAAAGAACA
3664993 TAACTTTAAA
Statistics
Matches: 117, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
41 4 0.03
42 95 0.81
43 17 0.15
44 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCAC
Found at i:3667064 original size:17 final size:17
Alignment explanation
Indices: 3667035--3667077 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3667025 ATATTATAAT
3667035 ATTATATATTAATTTTGC
1 ATTATA-ATTAATTTTGC
3667053 ATTATAATTAATTTTGC
1 ATTATAATTAATTTTGC
3667070 ATTATAAT
1 ATTATAAT
3667078 ATTATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (17 bp):
ATTATAATTAATTTTGC
Found at i:3668312 original size:10 final size:11
Alignment explanation
Indices: 3668286--3668311 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3668276 AAAATCTGTC
3668286 AAAAATAGGAT
1 AAAAATAGGAT
3668297 AAAAATAGGAT
1 AAAAATAGGAT
3668308 AAAA
1 AAAA
3668312 TTCCTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (11 bp):
AAAAATAGGAT
Found at i:3670289 original size:7 final size:7
Alignment explanation
Indices: 3670279--3670337 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
3670269 CCTAAATCTA
*
3670279 TAACTCT
1 TAACCCT
3670286 TAACCCT
1 TAACCCT
3670293 TAA-CCT
1 TAACCCT
3670299 CTAA-CCT
1 -TAACCCT
*
3670306 CTAACCCC
1 -TAACCCT
*
3670314 TAACCCC
1 TAACCCT
3670321 TAACCCT
1 TAACCCT
*
3670328 TAAACCT
1 TAACCCT
3670335 TAA
1 TAA
3670338 ATCCCAATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
6 3 0.07
7 41 0.89
8 2 0.04
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (7 bp):
TAACCCT
Found at i:3670303 original size:21 final size:21
Alignment explanation
Indices: 3670261--3670337 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
3670251 GCCCTTGAAT
* * * *
3670261 CTCTAAACCCTAAATCTATAA
1 CTCTTAACCCTTAACCTCTAA
3670282 CTCTTAACCCTTAACCTCTAA
1 CTCTTAACCCTTAACCTCTAA
* *
3670303 C-CTCTAACCCCTAACCCCTAA
1 CTCT-TAACCCTTAACCTCTAA
* *
3670324 CCCTTAAACCTTAA
1 CTCTTAACCCTTAA
3670338 ATCCCAATCC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.27
Consensus pattern (21 bp):
CTCTTAACCCTTAACCTCTAA
Found at i:3670355 original size:34 final size:34
Alignment explanation
Indices: 3670312--3670378 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
3670302 ACCTCTAACC
3670312 CCTAACCCCTAACCCT-TAAACCTTAAATCCCAAT
1 CCTAACCCCT-ACCCTCTAAACCTTAAATCCCAAT
*
3670346 CCTAACCCCTAGCCTCTAAACCTTAAATCCCAA
1 CCTAACCCCTACCCTCTAAACCTTAAATCCCAA
3670379 CCCTTAAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.34, C:0.42, G:0.01, T:0.22
Consensus pattern (34 bp):
CCTAACCCCTACCCTCTAAACCTTAAATCCCAAT
Found at i:3670856 original size:41 final size:41
Alignment explanation
Indices: 3670799--3670951 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
3670789 AAATGTTTTT
*
3670799 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCAGAGCATTA
* *
3670840 GCGGCGCTTCTCCAAAAACGCCACTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCAGAGCATTA
* *
3670881 GCGGCGCTTCTTCAAAAATGCCGCT--AGGCCAGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCAGAGCATTA
*
3670920 GCGGTGCTTC-CTCAAAAACGCCGCTAAAGGCC
1 GCGGCGCTTCTC-CAAAAACGCCGCTAAAGGCC
3670952 CCAAAAACTC
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.34
41 65 0.66
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.17
Consensus pattern (41 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCAGAGCATTA
Found at i:3670936 original size:80 final size:81
Alignment explanation
Indices: 3670799--3670952 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 81
3670789 AAATGTTTTT
3670799 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCAC
1 GCGGCGCTTCTTCAAAAACGCCGCT-AAGGCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCAC
3670864 TAAAGGCCCGAGCATTA
65 TAAAGGCCCGAGCATTA
* * *
3670881 GCGGCGCTTCTTCAAAAATGCCGCT-AGGCCAGAGCATTAGCGGTGCTTC-CTCAAAAACGCCGC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAGGCCAGAGCATTAGCGGCGCTTCTC-CAAAAACGCCAC
3670944 TAAAGGCCC
65 TAAAGGCCC
3670953 CAAAAACTCA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
79 1 0.01
80 43 0.63
82 24 0.35
ACGTcount: A:0.27, C:0.32, G:0.24, T:0.17
Consensus pattern (81 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAGGCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCACT
AAAGGCCCGAGCATTA
Found at i:3671102 original size:12 final size:12
Alignment explanation
Indices: 3671087--3671112 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3671077 TTTTTTGTCC
3671087 AAACGCCGCTAA
1 AAACGCCGCTAA
3671099 AAACGCCGCTAA
1 AAACGCCGCTAA
3671111 AA
1 AA
3671113 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:3678014 original size:27 final size:27
Alignment explanation
Indices: 3677984--3678038 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
3677974 GGATGCTAAG
3677984 TATGATCATTTTGGATAAGTATTTTGC
1 TATGATCATTTTGGATAAGTATTTTGC
*
3678011 TATGATCGTTTTGGATAAGTATTTTGC
1 TATGATCATTTTGGATAAGTATTTTGC
3678038 T
1 T
3678039 TGGTACGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (27 bp):
TATGATCATTTTGGATAAGTATTTTGC
Found at i:3680326 original size:80 final size:80
Alignment explanation
Indices: 3680242--3680397 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 80
3680232 TTGATGTCTC
* ** *
3680242 AAATCTGTATCAAAAAAGGGTGAGAGTTTTTTTTTGGAGTTCCAATGCAATGCCATAAATAACTA
1 AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
3680307 CTCTTGATAATTTCT
66 CTCTTGATAATTTCT
* * *
3680322 AAATCTATATCAAAAACGGGTGAGAACTTTTTTTTGGAGTTCTAATGCAATGCCATCAAGAACTA
1 AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
3680387 CTCTTGATAAT
66 CTCTTGATAAT
3680398 GATGTTTGGA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (80 bp):
AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
CTCTTGATAATTTCT
Found at i:3680900 original size:14 final size:13
Alignment explanation
Indices: 3680876--3680920 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
3680866 TTTCCTTTGT
*
3680876 TTTTCTGTTTTTC
1 TTTTCTCTTTTTC
3680889 TGTTTCTCTTTTTC
1 T-TTTCTCTTTTTC
3680903 TTTTCCTCTTTATTC
1 TTTT-CTCTTT-TTC
3680918 TTT
1 TTT
3680921 ATTGTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 18 0.64
15 6 0.21
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTCTCTTTTTC
Found at i:3686547 original size:43 final size:42
Alignment explanation
Indices: 3686500--3686598 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 42
3686490 TCCCAGACGT
* *
3686500 GGTCTTACATGTAATTA-ATTATCGATGCCACTGTCCCAAACAA
1 GGTCTTACACGTAATTATA-TA-CGATGCCAATGTCCCAAACAA
* * *
3686543 GGTCTTATACGTAATTATATACGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAATTATATACGATGCCAATGTCCCAAACAA
3686585 GGTCTTACACGTAA
1 GGTCTTACACGTAA
3686599 ATCTCAAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
42 31 0.63
43 17 0.35
44 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (42 bp):
GGTCTTACACGTAATTATATACGATGCCAATGTCCCAAACAA
Found at i:3686626 original size:44 final size:41
Alignment explanation
Indices: 3686481--3686639 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 41
3686471 AGCTCATACA
* *
3686481 ATGCCAACATCCCAGACGTGGTCTTACATGTAATTAATTATCG
1 ATGCCAACATCCCAGACATGGTCTTACACGTAATTAA--ATCG
* * * * *
3686524 ATGCC-ACTGTCCCAAACAAGGTCTTATACGTAATTATATACG
1 ATGCCAAC-ATCCCAGACATGGTCTTACACGTAATTAAAT-CG
**
3686566 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAACATCCCAGACATGGTCTTACACGT-AAT-T-AAATCG
*
3686610 AGGCCAACATCCCAGACATGGTCTTACACG
1 ATGCCAACATCCCAGACATGGTCTTACACG
3686640 ATGTCACATT
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.02
42 29 0.31
43 31 0.33
44 30 0.32
45 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (41 bp):
ATGCCAACATCCCAGACATGGTCTTACACGTAATTAAATCG
Found at i:3687615 original size:15 final size:15
Alignment explanation
Indices: 3687595--3687625 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3687585 ATAAATTAAA
3687595 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
3687610 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
3687625 A
1 A
3687626 AAAGGCCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
AGGTATAATTTCAAC
Found at i:3692390 original size:106 final size:108
Alignment explanation
Indices: 3692195--3692398 Score: 324
Period size: 106 Copynumber: 1.9 Consensus size: 108
3692185 TGGATTAAGA
*
3692195 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACGT
*
3692260 TTCCTCGAATTTCCAAACGCAAAATATTGCCTTACTCTGAAAT
66 TTCCTCGAATTCCCAAACGCAAAATATTGCCTTACTCTGAAAT
* * *
3692303 TTTAA-AGGATATTTGGCTATTTGGTCGAATG-AAAAAATCGAAACCCAACACATTAGGGCACGC
1 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACG-
*
3692366 TTT-CTCGAATTCCCAAATGCAAAATATTGCCTT
65 TTTCCTCGAATTCCCAAACGCAAAATATTGCCTT
3692399 TATTATTTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
106 58 0.65
107 26 0.29
108 5 0.06
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (108 bp):
TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACGT
TTCCTCGAATTCCCAAACGCAAAATATTGCCTTACTCTGAAAT
Found at i:3693457 original size:12 final size:12
Alignment explanation
Indices: 3693419--3693457 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3693409 GAAATATATA
*
3693419 AATAATATCAAT
1 AATAATATTAAT
*
3693431 AATAATAGTAAT
1 AATAATATTAAT
*
3693443 AATAATATTATT
1 AATAATATTAAT
3693455 AAT
1 AAT
3693458 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:3699732 original size:19 final size:19
Alignment explanation
Indices: 3699708--3699746 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3699698 AAAGGAAGAG
3699708 ATAGTTAATTCATTTTCCA
1 ATAGTTAATTCATTTTCCA
3699727 ATAGTTAATTCATTTTCCA
1 ATAGTTAATTCATTTTCCA
3699746 A
1 A
3699747 AGAAGAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (19 bp):
ATAGTTAATTCATTTTCCA
Found at i:3706161 original size:13 final size:13
Alignment explanation
Indices: 3706143--3706167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3706133 ATTTCTGGTC
3706143 TTTACTCAAGTTT
1 TTTACTCAAGTTT
3706156 TTTACTCAAGTT
1 TTTACTCAAGTT
3706168 CTTAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:3710642 original size:13 final size:13
Alignment explanation
Indices: 3710624--3710648 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3710614 ATTTCTGGTC
3710624 TTTACTCAAGTTT
1 TTTACTCAAGTTT
3710637 TTTACTCAAGTT
1 TTTACTCAAGTT
3710649 CTTAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:3716534 original size:6 final size:6
Alignment explanation
Indices: 3716525--3716579 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
3716515 ATAAAACGTA
3716525 GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT
1 GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT
3716573 GGGGAT G
1 GGGGAT G
3716580 ATGCTGACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.16, C:0.00, G:0.67, T:0.16
Consensus pattern (6 bp):
GGGGAT
Found at i:3716666 original size:46 final size:46
Alignment explanation
Indices: 3716599--3716691 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
3716589 AAGAGACAAG
3716599 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATGAAAAAAATT
1 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATGAAAAAAATT
*
3716645 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
1 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATGAAAAAAATT
3716691 A
1 A
3716692 ATGCTCCAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.55, C:0.13, G:0.12, T:0.20
Consensus pattern (46 bp):
ACAAAGTCAAAAATAGATGTAGCGACAATCATACATGAAAAAAATT
Found at i:3717322 original size:22 final size:22
Alignment explanation
Indices: 3717297--3717350 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
3717287 TTGTTTTTAA
* *
3717297 AAAATTAT-TTAATTTTAATTAT
1 AAAATTATATAAATATTAA-TAT
*
3717319 AAAAGTATATAAATATTAATAT
1 AAAATTATATAAATATTAATAT
*
3717341 AACATTATAT
1 AAAATTATAT
3717351 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTATATAAATATTAATAT
Found at i:3717469 original size:29 final size:28
Alignment explanation
Indices: 3717411--3717469 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
3717401 ATGTAAAATT
* * **
3717411 ATATTAATATTAATCTTTTATTATGTTA
1 ATATTAAAATTAATATTTTATTATACTA
*
3717439 ATATTAAAATTATATATTTTATTTTACTA
1 ATATTAAAATTA-ATATTTTATTATACTA
3717468 AT
1 AT
3717470 TATCATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTAAAATTAATATTTTATTATACTA
Found at i:3722673 original size:22 final size:21
Alignment explanation
Indices: 3722648--3722690 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3722638 TTGAAAAAAA
* *
3722648 ATTTAATTTTCCTATTATTATT
1 ATTTAATTCTACTATT-TTATT
3722670 ATTTAATTCTACTATTTTATT
1 ATTTAATTCTACTATTTTATT
3722691 TTATTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTAATTCTACTATTTTATT
Found at i:3728370 original size:4 final size:4
Alignment explanation
Indices: 3728361--3728385 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3728351 TTAACTAGTT
3728361 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
3728386 ATTTCCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3734304 original size:14 final size:13
Alignment explanation
Indices: 3734269--3734306 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
3734259 AGTTTTTCTT
3734269 AAATA-TTAAAAA
1 AAATATTTAAAAA
3734281 AAATATTTTATAAAA
1 AAATA-TTTA-AAAA
3734296 AAATATTTAAA
1 AAATATTTAAA
3734307 GCAAAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.22
13 2 0.09
14 7 0.30
15 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATATTTAAAAA
Found at i:3754280 original size:7 final size:7
Alignment explanation
Indices: 3754214--3754290 Score: 55
Period size: 7 Copynumber: 11.0 Consensus size: 7
3754204 TCATTTTCAA
*
3754214 CTCAATA
1 CTCAATT
**
3754221 CTCAACC
1 CTCAATT
*
3754228 CTCAGTT
1 CTCAATT
*
3754235 CTAAATT
1 CTCAATT
* *
3754242 CTCACTC
1 CTCAATT
3754249 CTCAATT
1 CTCAATT
* *
3754256 TTCAATC
1 CTCAATT
* *
3754263 CTGAATC
1 CTCAATT
3754270 CTCAATT
1 CTCAATT
3754277 CTCAATT
1 CTCAATT
3754284 CTCAATT
1 CTCAATT
3754291 ATTATTTTTA
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.36
Consensus pattern (7 bp):
CTCAATT
Found at i:3755874 original size:42 final size:42
Alignment explanation
Indices: 3755809--3755915 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
3755799 GAAGCCCGAA
*
3755809 GGTTGAACAGAAGCTCATGAGAGCTAAAAAAAAACCCATAAG
1 GGTTGAACAGAAGCTCATAAGAGCTAAAAAAAAACCCATAAG
* * * * *
3755851 GGTTGAACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAG
1 GGTTGAACAGAAGCTCATAAGAGCTAAAAAAAAACCCATAAG
* *
3755893 GGTTAAACAGAAGCTCAAAAGAG
1 GGTTGAACAGAAGCTCATAAGAG
3755916 ATGAACGATA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.14
Consensus pattern (42 bp):
GGTTGAACAGAAGCTCATAAGAGCTAAAAAAAAACCCATAAG
Found at i:3755892 original size:21 final size:21
Alignment explanation
Indices: 3755812--3755892 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 21
3755802 GCCCGAAGGT
* * *
3755812 TGAACAGAAGCTCATGAGAGC
1 TGAACAGAAACCCATAAGAGC
* * * * *
3755833 TAAAAAAAAACCCATAAGGGT
1 TGAACAGAAACCCATAAGAGC
* * * *
3755854 TGAACGGAAGCTCGTAAGAGC
1 TGAACAGAAACCCATAAGAGC
3755875 TGAACAGAAACCCATAAG
1 TGAACAGAAACCCATAAG
3755893 GGTTAAACAG
Statistics
Matches: 39, Mismatches: 21, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (21 bp):
TGAACAGAAACCCATAAGAGC
Found at i:3755901 original size:21 final size:21
Alignment explanation
Indices: 3755840--3755904 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
3755830 AGCTAAAAAA
*
3755840 AAACCCATAAGGGTTGAACGG
1 AAACCCATAAGGGTTGAACAG
* * * * *
3755861 AAGCTCGTAAGAGCTGAACAG
1 AAACCCATAAGGGTTGAACAG
*
3755882 AAACCCATAAGGGTTAAACAG
1 AAACCCATAAGGGTTGAACAG
3755903 AA
1 AA
3755905 GCTCAAAAGA
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (21 bp):
AAACCCATAAGGGTTGAACAG
Found at i:3759358 original size:12 final size:12
Alignment explanation
Indices: 3759341--3759370 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3759331 ACAACATAAA
3759341 TAAATTGGAAAT
1 TAAATTGGAAAT
3759353 TAAATTGGAAAT
1 TAAATTGGAAAT
3759365 TAAATT
1 TAAATT
3759371 CGAATTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (12 bp):
TAAATTGGAAAT
Found at i:3761539 original size:22 final size:22
Alignment explanation
Indices: 3761514--3761575 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
3761504 ATTTGCACTG
3761514 TTGAGTGGTTTATCCACACCGT
1 TTGAGTGGTTTATCCACACCGT
*** * **
3761536 TTGAGCAATTTATCTACATTGT
1 TTGAGTGGTTTATCCACACCGT
3761558 TT-AGTGGTTTATCCACAC
1 TTGAGTGGTTTATCCACAC
3761576 TGTATTAGCA
Statistics
Matches: 29, Mismatches: 11, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (22 bp):
TTGAGTGGTTTATCCACACCGT
Found at i:3761589 original size:22 final size:21
Alignment explanation
Indices: 3761521--3761589 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
3761511 CTGTTGAGTG
*
3761521 GTTTATCCACACCGTTTGAGCA
1 GTTTATCCACACTGTTT-AGCA
* * * **
3761543 ATTTATCTACATTGTTTAGTG
1 GTTTATCCACACTGTTTAGCA
3761564 GTTTATCCACACTGTATTAGCA
1 GTTTATCCACACTGT-TTAGCA
3761586 GTTT
1 GTTT
3761590 TAATCTGCAA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (21 bp):
GTTTATCCACACTGTTTAGCA
Found at i:3766616 original size:13 final size:14
Alignment explanation
Indices: 3766598--3766626 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3766588 TAAAGACTTG
3766598 ATATG-ATTAACCA
1 ATATGAATTAACCA
3766611 ATATGAATTAACCA
1 ATATGAATTAACCA
3766625 AT
1 AT
3766627 GTCACCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (14 bp):
ATATGAATTAACCA
Found at i:3780818 original size:18 final size:18
Alignment explanation
Indices: 3780782--3780826 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
3780772 ACAAATGCCT
3780782 TTAA-AATAGTAACAAAA
1 TTAACAATAGTAACAAAA
3780799 TTAACAATAG-AACAATAA
1 TTAACAATAGTAACAA-AA
3780817 TTATACAATA
1 TTA-ACAATA
3780827 TCCAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 10 0.40
19 6 0.24
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (18 bp):
TTAACAATAGTAACAAAA
Found at i:3780849 original size:14 final size:14
Alignment explanation
Indices: 3780830--3780857 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3780820 TACAATATCC
3780830 AAATAATAACAACA
1 AAATAATAACAACA
3780844 AAATAATAACAACA
1 AAATAATAACAACA
3780858 TAATTGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:3780943 original size:20 final size:21
Alignment explanation
Indices: 3780891--3780946 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
3780881 AGTGAAAAAA
*
3780891 AAAACAACAATAAAATAGCAAG
1 AAAACAATAA-AAAATAGCAAG
*
3780913 AAAATAATAAAAAATAGCAAG
1 AAAACAATAAAAAATAGCAAG
*
3780934 -AAACAGTAAAAAA
1 AAAACAATAAAAAA
3780947 AGTAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.37
21 11 0.37
22 8 0.27
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAACAATAAAAAATAGCAAG
Found at i:3781349 original size:31 final size:31
Alignment explanation
Indices: 3781291--3781349 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
3781281 CGTGTAATTA
* **
3781291 TATACATGAAACTTTAATTGTGGTTCAAATG
1 TATACATGAAACATTAATTGTAATTCAAATG
* *
3781322 TATATATGAAACATTAATTTTAATTCAA
1 TATACATGAAACATTAATTGTAATTCAA
3781350 TTATCCACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (31 bp):
TATACATGAAACATTAATTGTAATTCAAATG
Found at i:3786517 original size:13 final size:13
Alignment explanation
Indices: 3786499--3786526 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3786489 AAAAACACTT
3786499 CTGAAATTTTTAG
1 CTGAAATTTTTAG
3786512 CTGAAATTTTTAG
1 CTGAAATTTTTAG
3786525 CT
1 CT
3786527 TTTCAGAAAT
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:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (13 bp):
CTGAAATTTTTAG
Found at i:3787057 original size:13 final size:13
Alignment explanation
Indices: 3787041--3787093 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
3787031 TTTAAACCAA
*
3787041 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
* *
3787054 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
* * *
3787067 ATTTTTCCACAGC
1 ACTTTTCAAAAGC
3787080 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
3787093 A
1 A
3787094 AAGAAGAACT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:3788258 original size:14 final size:12
Alignment explanation
Indices: 3788230--3788271 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
3788220 TAAGAAATGC
3788230 TTTTAAAAAGTA
1 TTTTAAAAAGTA
3788242 TTTTGAAAAAGTGA
1 TTTT-AAAAAGT-A
3788256 TTTTAATAAA-TA
1 TTTTAA-AAAGTA
3788268 TTTT
1 TTTT
3788272 TGAAAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 9 0.33
13 10 0.37
14 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
TTTTAAAAAGTA
Found at i:3796813 original size:18 final size:18
Alignment explanation
Indices: 3796792--3796843 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
3796782 ATAATTATAA
3796792 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
3796810 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
*
3796828 TATTATTTAATTAAAA
1 TATTAATTAA-TAAAA
3796844 AATCATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:3802279 original size:40 final size:42
Alignment explanation
Indices: 3802190--3802280 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 42
3802180 CGTTTGGATA
*
3802190 AAAAACGCCGTTAAAAATTGAGCATTAGCGGCGATTTCAGGG
1 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGGG
* **
3802232 --AAGCGCCGCTAAAAA-TGAGCATTAGCGGC-ATTTGTGGG
1 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGGG
3802270 AAAAACGCCGC
1 AAAAACGCCGC
3802281 AAATGTTAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
38 7 0.17
39 14 0.33
40 21 0.50
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (42 bp):
AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGGG
Found at i:3804138 original size:21 final size:22
Alignment explanation
Indices: 3804112--3804158 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3804102 AATAGTTGAA
*
3804112 AAAAAATCAAAACTTTT-TTTT
1 AAAAAATCAAAACTTTTCCTTT
**
3804133 AAAAAATTTAAACTTTTCCTTT
1 AAAAAATCAAAACTTTTCCTTT
3804155 AAAA
1 AAAA
3804159 TGACTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAATCAAAACTTTTCCTTT
Found at i:3804560 original size:17 final size:17
Alignment explanation
Indices: 3804538--3804570 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3804528 GTTTATGACC
3804538 AAAAAAAAAG--ATAGA
1 AAAAAAAAAGAAATAGA
3804553 AAAAAAAAAGAAATAGA
1 AAAAAAAAAGAAATAGA
3804570 A
1 A
3804571 TGCTTGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.62
17 6 0.38
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAAATAGA
Found at i:3810057 original size:23 final size:23
Alignment explanation
Indices: 3809999--3810057 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
3809989 AATTAATAAT
* *
3809999 AAAATTATATATTTTAACTTCTA
1 AAAATTATAAAATTTAACTTCTA
* * * *
3810022 AAAATAATTAAATTTAATTTTTA
1 AAAATTATAAAATTTAACTTCTA
3810045 AAAATTATAAAAT
1 AAAATTATAAAAT
3810058 AATATAAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTATAAAATTTAACTTCTA
Found at i:3813396 original size:6 final size:6
Alignment explanation
Indices: 3813385--3813417 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3813375 TAATCTAATC
3813385 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG
3813418 AATTATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (6 bp):
ATGTAT
Found at i:3822288 original size:17 final size:17
Alignment explanation
Indices: 3822268--3822301 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3822258 TAGAATTGGG
*
3822268 TTGAGAAAGTAATTTAA
1 TTGAAAAAGTAATTTAA
*
3822285 TTGAAAAATTAATTTAA
1 TTGAAAAAGTAATTTAA
3822302 ATAAAATTAA
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:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
TTGAAAAAGTAATTTAA
Found at i:3827624 original size:101 final size:101
Alignment explanation
Indices: 3827449--3827766 Score: 503
Period size: 101 Copynumber: 3.1 Consensus size: 101
3827439 AATTGATGGA
3827449 TAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTGTGGTATTCTGA
1 TAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTGTGGTATTCTGA
3827514 TGATAAGACCATAACTGGGTTATGGCACCTTGAATG
66 TGATAAGACCATAACTGGGTTATGGCACCTTGAATG
3827550 TAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTGTGGTATTCTGA
1 TAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTGTGGTATTCTGA
3827615 TGATAAGACCATAACTGGGTTATGGCACCTTGAATG
66 TGATAAGACCATAACTGGGTTATGGCACCTTGAATG
* * * * * *
3827651 TAAGACCATGGTTGGACCATGGCAGTAAATGTATACGTGTAAGACCATAGCTGGGCTATGGCATC
1 TAAGACCATGGTTGGACCATGACAGT--GTTTATA--TGTAAGACCATAGCTGGGCTGTGGTATT
* * *
3827716 CTGATAATAAGACCATAACTGGGTTATGGCA-TTATGAGTG
62 CTGATGATAAGACCATAACTGGGTTATGGCACCT-TGAATG
3827756 TAAGACCATGG
1 TAAGACCATGG
3827767 CAGGGCCATG
Statistics
Matches: 203, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
101 126 0.62
103 5 0.02
104 1 0.00
105 71 0.35
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTGTGGTATTCTGA
TGATAAGACCATAACTGGGTTATGGCACCTTGAATG
Found at i:3827732 original size:33 final size:34
Alignment explanation
Indices: 3827479--3827779 Score: 145
Period size: 33 Copynumber: 8.9 Consensus size: 34
3827469 GACAGTGTTT
* * *
3827479 ATATGTAAGACCATAGCTGGGCTGTGGTATTCTG
1 ATATGTAAGACCATAGCTGGGCTATGGCATCCTG
* *
3827513 --ATGATAAGACCATAACTGGGTTATGGCA-CCTTG
1 ATATG-TAAGACCATAGCTGGGCTATGGCATCC-TG
* * * * * ** *
3827546 A-ATGTAAGACCATGGTTGGACCATGACAGTGTTT
1 ATATGTAAGACCATAGCTGGGCTATGGCA-TCCTG
* * *
3827580 ATATGTAAGACCATAGCTGGGCTGTGGTATTCTG
1 ATATGTAAGACCATAGCTGGGCTATGGCATCCTG
* *
3827614 --ATGATAAGACCATAACTGGGTTATGGCA-CCTTG
1 ATATG-TAAGACCATAGCTGGGCTATGGCATCC-TG
* * * * **
3827647 A-ATGTAAGACCATGGTTGGACCATGGCAGTAAATG
1 ATATGTAAGACCATAGCTGGGCTATGGCA-T-CCTG
3827682 TATACGTGTAAGACCATAGCTGGGCTATGGCATCCTG
1 -ATA--TGTAAGACCATAGCTGGGCTATGGCATCCTG
* * * **
3827719 ATA-ATAAGACCATAACTGGGTTATGGCATTATG
1 ATATGTAAGACCATAGCTGGGCTATGGCATCCTG
* * * *
3827752 A-GTGTAAGACCATGGCAGGGCCATGGCA
1 ATATGTAAGACCATAGCTGGGCTATGGCA
3827780 ATTGTGTAAT
Statistics
Matches: 194, Mismatches: 56, Indels: 35
0.68 0.20 0.12
Matches are distributed among these distances:
32 8 0.04
33 124 0.64
34 10 0.05
35 22 0.11
36 4 0.02
37 3 0.02
38 1 0.01
39 22 0.11
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (34 bp):
ATATGTAAGACCATAGCTGGGCTATGGCATCCTG
Found at i:3829209 original size:5 final size:5
Alignment explanation
Indices: 3829201--3829234 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
3829191 TTTAAATTAA
3829201 AAAAT AAAAT AAAAT AAAAT -AAAT AAAACT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAA
3829235 GTAATTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3831613 original size:12 final size:12
Alignment explanation
Indices: 3831566--3831629 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
3831556 TTTTTATTTT
3831566 ATTTAATATT-A
1 ATTTAATATTAA
3831577 ATATTAATATT-A
1 AT-TTAATATTAA
3831589 ATATTAATATTAA
1 AT-TTAATATTAA
*
3831602 TATTAAAT-TTAA
1 -ATTTAATATTAA
* *
3831614 ATTTATTATTAT
1 ATTTAATATTAA
3831626 ATTT
1 ATTT
3831630 TTTGAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
11 7 0.16
12 31 0.69
13 5 0.11
14 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:3831625 original size:6 final size:6
Alignment explanation
Indices: 3831568--3831607 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
3831558 TTTATTTTAT
3831568 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
3831608 ATTTAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:3834711 original size:10 final size:10
Alignment explanation
Indices: 3834688--3834720 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3834678 CCCAGAACTT
3834688 AAATT-AAA-
1 AAATTCAAAG
3834696 AAATTCAAAG
1 AAATTCAAAG
3834706 AAATTCAAAG
1 AAATTCAAAG
3834716 AAATT
1 AAATT
3834721 GTAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.22
9 3 0.13
10 15 0.65
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (10 bp):
AAATTCAAAG
Found at i:3837415 original size:14 final size:15
Alignment explanation
Indices: 3837389--3837428 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3837379 TTAAGAATTT
*
3837389 TATTAAATT-ATATA
1 TATTTAATTAATATA
3837403 T-TTTAATTAATATA
1 TATTTAATTAATATA
3837417 TATTTAA-TAATA
1 TATTTAATTAATA
3837429 ATTATGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTAATATA
Found at i:3837418 original size:18 final size:17
Alignment explanation
Indices: 3837354--3837421 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 17
3837344 GAAATTGAGA
3837354 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
3837371 A-TTTATT--ATTA-AGA
1 ATTTTATTAAATTATA-T
3837385 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
3837402 ATTTTAATT-AA-TATAT
1 ATTTT-ATTAAATTATAT
3837418 ATTT
1 ATTT
3837422 AATAATAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 6 0.14
16 15 0.35
17 12 0.28
18 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:3838520 original size:18 final size:17
Alignment explanation
Indices: 3838492--3838526 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3838482 ATTATTAAGA
*
3838492 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3838509 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3838527 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3838531 original size:120 final size:120
Alignment explanation
Indices: 3838385--3838783 Score: 782
Period size: 120 Copynumber: 3.3 Consensus size: 120
3838375 TAATTGAAAA
*
3838385 TATATATTTT-ATTAAATTATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
3838449 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
3838504 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
3838569 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
3838624 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
3838689 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
3838744 TATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTT
3838784 TAAATATGAT
Statistics
Matches: 278, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
119 10 0.04
120 268 0.96
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATA
TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:3838640 original size:18 final size:17
Alignment explanation
Indices: 3838612--3838646 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3838602 ATTATTAAGA
*
3838612 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3838629 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3838647 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3838760 original size:18 final size:17
Alignment explanation
Indices: 3838732--3838766 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3838722 ATTATTAAGA
*
3838732 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3838749 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3838767 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3839023 original size:16 final size:16
Alignment explanation
Indices: 3839002--3839069 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
3838992 GATTTGCTAT
3839002 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3839018 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
3839034 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
3839050 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3839066 TACA
1 TACA
3839070 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3846052 original size:21 final size:21
Alignment explanation
Indices: 3845995--3846072 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
3845985 ACTTGGATTT
* * *
3845995 AAATTAAATAATTTTTATATA
1 AAATTATATAAATTTAATATA
* * * *
3846016 TATTTATTTATATTTAATTATA
1 AAATTATATAAATTTAA-TATA
3846038 AAA-TATATAAATTTAATATA
1 AAATTATATAAATTTAATATA
*
3846058 AAATTATATATATTT
1 AAATTATATAAATTT
3846073 TTTATTATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 7 0.16
21 31 0.72
22 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTATATAAATTTAATATA
Found at i:3846059 original size:20 final size:22
Alignment explanation
Indices: 3846027--3846072 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
3846017 ATTTATTTAT
3846027 ATTTAATTATAAAA-TATATAA
1 ATTTAATTATAAAATTATATAA
*
3846048 ATTTAA-TATAAAATTATATAT
1 ATTTAATTATAAAATTATATAA
3846069 ATTT
1 ATTT
3846073 TTTATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTAATTATAAAATTATATAA
Done.