Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 61 of 160
Found at i:12770172 original size:237 final size:234
Alignment explanation
Indices: 12769694--12770292 Score: 681
Period size: 237 Copynumber: 2.5 Consensus size: 234
12769684 ATGTTTTATT
* * * * * *
12769694 ATTTTATGTGACATTATTAATTTTTATCATAATTTGAATATTTTAGTTAACTATTAATAACATAG
1 ATTTTA-GTGACGTTATTAATTTTTATCATAAATTGAACACTTTAATTAACTATTAATAACATTG
* * * *
12769759 TAATTTCGTCACGT-CAGT-TAATGGTGTTATATGACGATAACATAAATATCACAAACTTTTATT
65 AAATTTCGTCACGTCCA-TAT-ATGGTGTTATATGATGATAACATAAATGTCACAAACTTTTAAT
* *
12769822 GCTAAATTTATTTGGTGAAAAAATTTTTTGTCATGTTTTTATTTTAGGTGACATTATAATTTTGT
128 GCTAAATTCATTTGGTGAAAAAATTTTTTGTCATGTTTTTATTTTAGGTAACATTATAATTTTGT
* *
12769887 TACCAATTTAAAATTTTATCTATGATGAATTTTTTCTTATAG
193 CACCAATTTAAAATTTTATCTATGATGAATTTTTTCTTATAA
* **
12769929 ATTTTAGATGACGTTATTAATTTTTTTCATAAATTGAACACTTTAATTAAGC-ATTAATGTCATT
1 ATTTTAG-TGACGTTATTAATTTTTATCATAAATTGAACACTTTAATTAA-CTATTAATAACATT
* * * *
12769993 GCAATTTTGTCACGTCCATATATGGTGTTGTATGATGATAACATAAATGTCATAAACTTTTACCA
64 GAAATTTCGTCACGTCCATATATGGTGTTATATGATGATAACATAAATGTCACAAACTTTTA--A
* ** * **
12770058 T-C-AAATTCATTTGGTGGGAAATTTTTTTTGTGACAT-TTTTTGTTTTAGGTAATGTTATAATT
127 TGCTAAATTCATTTGGT-GAAAAAATTTTTTGT--CATGTTTTTATTTTAGGTAACATTATAATT
* *
12770120 TTGTCATCAATTTAAAATTTTATCTGTGATGAATTTTTT-TTAGTAA
189 TTGTCACCAATTTAAAATTTTATCTATGATGAATTTTTTCTTA-TAA
* * * *
12770166 ATTTTAGGTGACGTTATTAATTTTTGTCACAAATTAAACACTTTAATTAACTATTAATAACATTA
1 ATTTTA-GTGACGTTATTAATTTTTATCATAAATTGAACACTTTAATTAACTATTAATAACATTG
* * * * * * *
12770231 AAATTTCATAACTTCGATATATGATGTTATATGATTATAAAATAAATGTCACAAACTTTTAA
65 AAATTTCGTCACGTCCATATATGGTGTTATATGATGATAACATAAATGTCACAAACTTTTAA
12770293 ATGAAGTTAT
Statistics
Matches: 307, Mismatches: 45, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
234 1 0.00
235 115 0.37
236 21 0.07
237 166 0.54
238 4 0.01
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (234 bp):
ATTTTAGTGACGTTATTAATTTTTATCATAAATTGAACACTTTAATTAACTATTAATAACATTGA
AATTTCGTCACGTCCATATATGGTGTTATATGATGATAACATAAATGTCACAAACTTTTAATGCT
AAATTCATTTGGTGAAAAAATTTTTTGTCATGTTTTTATTTTAGGTAACATTATAATTTTGTCAC
CAATTTAAAATTTTATCTATGATGAATTTTTTCTTATAA
Found at i:12770546 original size:17 final size:17
Alignment explanation
Indices: 12770508--12770563 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
12770498 ACATAATTTG
*
12770508 TTTAGAATTTTAAAATAAA
1 TTTAAAATTTT-AAA-AAA
12770527 TTTAAAATTTTAAAAAA
1 TTTAAAATTTTAAAAAA
** *
12770544 TTTCTAATTTAAAAAAA
1 TTTAAAATTTTAAAAAA
12770561 TTT
1 TTT
12770564 TTAAAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 20 0.61
18 3 0.09
19 10 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAAATTTTAAAAAA
Found at i:12778906 original size:32 final size:32
Alignment explanation
Indices: 12778850--12778958 Score: 166
Period size: 32 Copynumber: 3.4 Consensus size: 32
12778840 TGCATGTCCC
* *
12778850 TTACATTGTTATAACATTTTTGTTATAAGCTT
1 TTACATTGTTATAAAATTTCTGTTATAAGCTT
* *
12778882 TTATAATGTTATAAAATTTCTGTTATAAGCTT
1 TTACATTGTTATAAAATTTCTGTTATAAGCTT
*
12778914 TTACATTGTTATAAAA-TTCTATTATAAGCTT
1 TTACATTGTTATAAAATTTCTGTTATAAGCTT
12778945 TTACATTGTTATAA
1 TTACATTGTTATAA
12778959 CCAAAGGTCT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 28 0.40
32 42 0.60
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (32 bp):
TTACATTGTTATAAAATTTCTGTTATAAGCTT
Found at i:12779308 original size:32 final size:32
Alignment explanation
Indices: 12779264--12779344 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
12779254 GTGTGTATAT
* *
12779264 CTCTTATATTGTTATAATATTTATGTTATAAA
1 CTCTTATATTGTTATAAAATTTATATTATAAA
* * *
12779296 CTCTTATTTTGTTATAAAATTTTTATTATAAG
1 CTCTTATATTGTTATAAAATTTATATTATAAA
* * *
12779328 CTTTTACATCGTTATAA
1 CTCTTATATTGTTATAA
12779345 CTAAGGGTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (32 bp):
CTCTTATATTGTTATAAAATTTATATTATAAA
Found at i:12780121 original size:42 final size:42
Alignment explanation
Indices: 12780075--12780159 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
12780065 AACTTCAGTA
* * *
12780075 AAAAAACATTAAACCA-AAATATGCCTAACTATGGATAACAAC
1 AAAAAACATTAAACCACAAA-ATGACTAACTATGAAGAACAAC
* * *
12780117 AAAAAGCCTTCAACCACAAAATGACTAACTATGAAGAACAAC
1 AAAAAACATTAAACCACAAAATGACTAACTATGAAGAACAAC
12780159 A
1 A
12780160 TAACCTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
42 33 0.92
43 3 0.08
ACGTcount: A:0.54, C:0.21, G:0.08, T:0.16
Consensus pattern (42 bp):
AAAAAACATTAAACCACAAAATGACTAACTATGAAGAACAAC
Found at i:12780570 original size:20 final size:20
Alignment explanation
Indices: 12780523--12780570 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
12780513 AAAAAATCCA
*
12780523 AATTAGCATGAAATTTGTCT
1 AATTAGCTTGAAATTTGTCT
12780543 AATTAGCTTGAAATTTGTCT
1 AATTAGCTTGAAATTTGTCT
12780563 AATTAGCT
1 AATTAGCT
12780571 GATTCGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (20 bp):
AATTAGCTTGAAATTTGTCT
Found at i:12784033 original size:197 final size:198
Alignment explanation
Indices: 12783275--12784204 Score: 898
Period size: 197 Copynumber: 4.7 Consensus size: 198
12783265 TTAATGAAGT
* * * ** * * * *
12783275 TAATTGTGTCA-TCAATACTATGACAATTTATCTTTTGTTATTAATATATTAGATTTTATCATTT
1 TAATTATGTCACT-AATACTATGATAATTTACCTTTCATCACTAATATATCAAATTTTATCATTT
* * * * *
12783339 ATTTTGTGATGATTATAACATTTAATGACTTTTTTTCCATATATAGTTGATGAAATCTAATGTCA
65 ATTTTGTGACGATTATAGCCTTTAATGA-TTTTTTT-CATAAATAGTTGATGAAAACTAATGTCA
* ** *
12783404 TAAGAAAAAAGCATAAAGTGACATTTGATTTTATTGTCACAATTGATATTATCTTAC-AATCATT
128 -AA-AAAAAAGCATAAGGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAAATCA-T
***
12783468 TGTT-ATGT
190 TGTTGACAA
* * * *
12783476 TAATTTTGTCA-TCAATA-TAGTGATGATTTATCTTTCATCACTAATACATCAAATTTTATCATT
1 TAATTATGTCACT-AATACTA-TGATAATTTACCTTTCATCACTAATATATCAAATTTTATCATT
* * * ** * * * *
12783539 TATTATGTGACGATTTTAACCTTTAATGATAATTTTCAAAAATAGCTAAAGAAAACTAATGTCAC
64 TATTTTGTGACGATTATAGCCTTTAATGATTTTTTTCATAAATAGTTGATGAAAACTAATGT--C
* * **
12783604 AAAAAAAAAGCATAAGGTTACATTTGATTTTATTGTCAAGTTTGACATTATCTTA-TTATCATTG
127 AAAAAAAAAGCATAAGGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAAATCATTG
* **
12783668 GTGATGA
192 TTGACAA
* ** *
12783675 TAATTATGTCACTAATACTATGATAATTTA-TTTTTGTTACTAATATATCAAATTTTATCATTTA
1 TAATTATGTCACTAATACTATGATAATTTACCTTTCATCACTAATATATCAAATTTTATCATTTA
* * ** * *
12783739 TTTTATGACAATTATAG-CTTTAATGACATTTTTCATAAATAGATGATGAAAACTACTGTCACAA
66 TTTTGTGACGATTATAGCCTTTAATGATTTTTTTCATAAATAGTTGATGAAAACTAATGTCA-AA
* **
12783803 AAAAAAGCATAAGATGATGTTTGATTTTATTGTCACGTTTGACATTATCTTACAAAT-ATTGTTG
130 AAAAAAGCATAAGGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAAATCATTGTTG
12783867 ACAA
195 ACAA
*
12783871 TAATTATGTCA-TCAATACTATGATGATTTACCTTTCATCACTAAT-TGATCAAATTTTATCATT
1 TAATTATGTCACT-AATACTATGATAATTTACCTTTCATCACTAATAT-ATCAAATTTTATCATT
** * * ** *
12783934 T-TTTAATGATGATTATAGCTTTTAATGATGTTTTTTTGTAAATAGTTGATGAAAACTAATTTCA
64 TATTTTGTGACGATTATAGCCTTTAATGAT-TTTTTTCATAAATAGTTGATGAAAACTAATGTCA
* ** * ** *
12783998 TAAAAAAATTATAAGGTAATGTTTGATTTTATTGTCACGTTTGACATTATCTTACAAA-CATTGC
128 AAAAAAAAGCATAAGGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAAATCATTGT
12784062 TGACAA
193 TGACAA
* * * * * * * *
12784068 TAAATATGTCACTAACACTGTGACAATTTACTTTTCGTCACTAATATATCAAAATTTATAATTTA
1 TAATTATGTCACTAATACTATGATAATTTACCTTTCATCACTAATATATCAAATTTTATCATTTA
* *
12784133 TTTTGTGACAATTATAGCCTTTAATGATTTTTTTTCATAAATAGTT-AGTGAAAACTAACGTCAC
66 TTTTGTGACGATTATAGCCTTTAATGA-TTTTTTTCATAAATAGTTGA-TGAAAACTAATGTCA-
12784197 AAAAAAAA
128 AAAAAAAA
12784205 AAAAAAAACA
Statistics
Matches: 607, Mismatches: 101, Indels: 44
0.81 0.13 0.06
Matches are distributed among these distances:
195 3 0.00
196 99 0.16
197 187 0.31
198 125 0.21
199 104 0.17
200 12 0.02
201 77 0.13
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (198 bp):
TAATTATGTCACTAATACTATGATAATTTACCTTTCATCACTAATATATCAAATTTTATCATTTA
TTTTGTGACGATTATAGCCTTTAATGATTTTTTTCATAAATAGTTGATGAAAACTAATGTCAAAA
AAAAAGCATAAGGTGACATTTGATTTTATTGTCACGTTTGACATTATCTTACAAATCATTGTTGA
CAA
Found at i:12784157 original size:395 final size:395
Alignment explanation
Indices: 12783291--12784204 Score: 1063
Period size: 395 Copynumber: 2.3 Consensus size: 395
12783281 TGTCATCAAT
* * * **
12783291 ACTATGACAATTTATCTTTTGTTATTAATATATTAGATTTTATCATTTATTTTGTGATGATTATA
1 ACTATGACAATTTA-CTTTTGTTACTAATATATCAAATTTTATCATTTATTTTGTGACAATTATA
* * * * * *
12783356 ACATTTAATGACTTTTTTTCCATATATAGTTGATGAAATCTAATGTCATAAGAAAAAAGCATAAA
65 GCCTTTAATGAC-TTTTTT-CATAAATAG-TGATGAAAACTACTGTCACAA-AAAAAAGCATAAA
* *** *
12783421 GTGACATTTGATTTTATTGTCACAATTGATATTATCTTACAATCATTTGTTATGTTAATTTTGTC
126 GTGACATTTGATTTTATTGTCACAATTGACATTATCTTACAATCATTTGTTACAATAATTATGTC
* *
12783486 ATCAATATAGTGATGATTTATCTTTCATCACTAATACATCAAATTTTATCATTTATTATGTGACG
191 ATCAATATAGTGATGATTTACCTTTCATCACTAATACATCAAATTTTATCATTTATTATATGACG
*
12783551 ATTTTAACCTTTAATGATAATTTTCAAAAATAGCTAAAGAAAACTAATGTCACAAAAAAAAAGCA
256 ATTATAACCTTTAATGATAATTTTCAAAAATAGCTAAAGAAAACTAATGTCACAAAAAAAAAGCA
* ** * * ** *
12783616 TAAGGTTACATTTGATTTTATTGTCAAGTTTGACATTATCTTATTATCATTGGTGATGATAATTA
321 TAAGGTAACATTTGATTTTATTGTCAAGTTTGACATTATCTTACAAACATTGCTGACAATAAATA
*
12783681 TGTCACTAAT
386 TGTCACTAAC
* * *
12783691 ACTATGATAATTTATTTTTGTTACTAATATATCAAATTTTATCATTTATTTTATGACAATTATAG
1 ACTATGACAATTTACTTTTGTTACTAATATATCAAATTTTATCATTTATTTTGTGACAATTATAG
*
12783756 -CTTTAATGACATTTTTCATAAATAGATGATGAAAACTACTGTCACAAAAAAAAGCAT-AAGATG
66 CCTTTAATGACTTTTTTCATAAATAG-TGATGAAAACTACTGTCACAAAAAAAAGCATAAAG-TG
** **
12783819 ATGTTTGATTTTATTGTCACGTTTGACATTATCTTACAA--ATATTGTTGACAATAATTATGTCA
129 ACATTTGATTTTATTGTCACAATTGACATTATCTTACAATCAT-TTGTT-ACAATAATTATGTCA
** * *
12783882 TCAATACTA-TGATGATTTACCTTTCATCACTAATTGATCAAATTTTATCATTTTTTA-ATGATG
192 TCAATA-TAGTGATGATTTACCTTTCATCACTAATACATCAAATTTTATCATTTATTATATGACG
* * ** *** * * * * * **
12783945 ATTATAGCTTTTAATGATGTTTTTTTGTAAATAGTTGATGAAAACTAAT-T-TCATAAAAAAATT
256 ATTATAACCTTTAATGAT-AATTTTCAAAAATAGCTAAAGAAAACTAATGTCACAAAAAAAAAGC
** *
12784008 ATAAGGTAATGTTTGATTTTATTGTCACGTTTGACATTATCTTACAAACATTGCTGACAATAAAT
320 ATAAGGTAACATTTGATTTTATTGTCAAGTTTGACATTATCTTACAAACATTGCTGACAATAAAT
12784073 ATGTCACTAAC
385 ATGTCACTAAC
* * * *
12784084 ACTGTGACAATTTACTTTTCGTCACTAATATATCAAAATTTATAATTTATTTTGTGACAATTATA
1 ACTATGACAATTTACTTTT-GTTACTAATATATCAAATTTTATCATTTATTTTGTGACAATTATA
* *
12784149 GCCTTTAATGATTTTTTTTCATAAATAGTTAGTGAAAACTAAC-GTCACAAAAAAAA
65 GCCTTTAATGA-CTTTTTTCATAAATAGTGA-TGAAAACT-ACTGTCACAAAAAAAA
12784205 AAAAAAAACA
Statistics
Matches: 436, Mismatches: 68, Indels: 24
0.83 0.13 0.05
Matches are distributed among these distances:
393 91 0.21
394 70 0.16
395 140 0.32
396 63 0.14
397 7 0.02
398 9 0.02
399 43 0.10
400 13 0.03
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (395 bp):
ACTATGACAATTTACTTTTGTTACTAATATATCAAATTTTATCATTTATTTTGTGACAATTATAG
CCTTTAATGACTTTTTTCATAAATAGTGATGAAAACTACTGTCACAAAAAAAAGCATAAAGTGAC
ATTTGATTTTATTGTCACAATTGACATTATCTTACAATCATTTGTTACAATAATTATGTCATCAA
TATAGTGATGATTTACCTTTCATCACTAATACATCAAATTTTATCATTTATTATATGACGATTAT
AACCTTTAATGATAATTTTCAAAAATAGCTAAAGAAAACTAATGTCACAAAAAAAAAGCATAAGG
TAACATTTGATTTTATTGTCAAGTTTGACATTATCTTACAAACATTGCTGACAATAAATATGTCA
CTAAC
Found at i:12788640 original size:49 final size:48
Alignment explanation
Indices: 12788512--12788674 Score: 168
Period size: 49 Copynumber: 3.4 Consensus size: 48
12788502 AAAAAAATTA
* * * * * *
12788512 AATTTTTAAAGTTTCGATGCCTCTGTTGAGAAGGAACTTTTTGGTTGAG
1 AATTTTTAAAGTTTCAACGCCTCTATTAAGGAGGAAC-TTTTGGTTGTG
* * *
12788561 AATTTTTAAAATTGCAACGCTTCTATTAAGGA-GAAGCCTTTTGGTTGTG
1 AATTTTTAAAGTTTCAACGCCTCTATTAAGGAGGAA--CTTTTGGTTGTG
* *
12788610 AATTTTTAAAGTTTCAACGCCTCTATTAAGGATGATA-TTTTGGTTATG
1 AATTTTTAAAGTTTCAACGCCTCTATTAAGGAGGA-ACTTTTGGTTGTG
*
12788658 AATATTTAAAGTTTCAA
1 AATTTTTAAAGTTTCAA
12788675 AACCTCTTTT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
48 29 0.30
49 63 0.66
50 3 0.03
51 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (48 bp):
AATTTTTAAAGTTTCAACGCCTCTATTAAGGAGGAACTTTTGGTTGTG
Found at i:12788743 original size:43 final size:43
Alignment explanation
Indices: 12788662--12788761 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
12788652 GTTATGAATA
** * *
12788662 TTTAAAGTTTCAAAACCTCTTTTGAGGGGGAGCATTTTAAATT
1 TTTAAAGTTTCAAAACCTCTGCTGAAGGGAAGCATTTTAAATT
* * *
12788705 TTTAAAGTTTCAAAACTTCTGCTGAAGTGAAGCCTTTTAAATT
1 TTTAAAGTTTCAAAACCTCTGCTGAAGGGAAGCATTTTAAATT
* *
12788748 TTAAAATTTTCAAA
1 TTTAAAGTTTCAAA
12788762 GCTTTTGAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (43 bp):
TTTAAAGTTTCAAAACCTCTGCTGAAGGGAAGCATTTTAAATT
Found at i:12789034 original size:7 final size:7
Alignment explanation
Indices: 12789022--12789080 Score: 63
Period size: 7 Copynumber: 8.7 Consensus size: 7
12789012 CCCAAAAGTA
12789022 TATTTTT
1 TATTTTT
12789029 TA--TTT
1 TATTTTT
12789034 TATTTTAT
1 TATTTT-T
12789042 TATTTATT
1 TATTT-TT
12789050 TATTTTT
1 TATTTTT
*
12789057 TAGTTTT
1 TATTTTT
12789064 TA-TTTT
1 TATTTTT
12789070 TA-TTTT
1 TATTTTT
12789076 TATTT
1 TATTT
12789081 ATTTTATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
5 5 0.11
6 12 0.26
7 16 0.35
8 12 0.26
9 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.80
Consensus pattern (7 bp):
TATTTTT
Found at i:12789039 original size:12 final size:12
Alignment explanation
Indices: 12789022--12789091 Score: 67
Period size: 12 Copynumber: 5.9 Consensus size: 12
12789012 CCCAAAAGTA
12789022 TATTTTTTATTT
1 TATTTTTTATTT
12789034 TATTTTATTA-TT
1 TATTTT-TTATTT
*
12789046 TATTTATT-TTT
1 TATTTTTTATTT
*
12789057 TAGTTTTTATTT
1 TATTTTTTATTT
12789069 T-TATTTTTA-TT
1 TAT-TTTTTATTT
12789080 TATTTTATTATT
1 TATTTT-TTATT
12789092 CAGTAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
11 16 0.34
12 27 0.57
13 4 0.09
ACGTcount: A:0.20, C:0.00, G:0.01, T:0.79
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:12789067 original size:30 final size:28
Alignment explanation
Indices: 12789022--12789091 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 28
12789012 CCCAAAAGTA
12789022 TATTTTTTATTTTA-TTTTATTATTTATT
1 TATTTTTTATTTTATTTTTATT-TTTATT
12789050 TATTTTTTAGTTTTTATTTTTATTTTTATT
1 TATTTTTTA--TTTTATTTTTATTTTTATT
12789080 TATTTTATTATT
1 TATTTT-TTATT
12789092 CAGTAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
28 9 0.24
29 2 0.05
30 17 0.45
31 10 0.26
ACGTcount: A:0.20, C:0.00, G:0.01, T:0.79
Consensus pattern (28 bp):
TATTTTTTATTTTATTTTTATTTTTATT
Found at i:12789069 original size:6 final size:6
Alignment explanation
Indices: 12789025--12789080 Score: 64
Period size: 6 Copynumber: 9.5 Consensus size: 6
12789015 AAAAGTATAT
*
12789025 TTTTTA -TTTTA -TTTTA TTATTTA TTTAT- TTTTTA GTTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA -TTTTTA TTTTTA
12789072 TTTTTA TTT
1 TTTTTA TTT
12789081 ATTTTATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 14 0.32
6 18 0.41
7 12 0.27
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:12790042 original size:36 final size:38
Alignment explanation
Indices: 12789971--12790047 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 38
12789961 TTACTCTTTT
*
12789971 TTTTTATTAATTTTGATTGAATTGAAAATAATGAAAATAA
1 TTTTGATTAATTTTGATTGAATTG-AAAT-ATGAAAATAA
12790011 TTTTGATTCAATTTTGATTG-ATTG-AAT-TGAAAATAA
1 TTTTGATT-AATTTTGATTGAATTGAAATATGAAAATAA
12790047 T
1 T
12790048 GAGAAAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 10 0.29
38 3 0.09
40 11 0.31
41 11 0.31
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (38 bp):
TTTTGATTAATTTTGATTGAATTGAAATATGAAAATAA
Found at i:12790177 original size:31 final size:31
Alignment explanation
Indices: 12790138--12790204 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
12790128 TATATTATGA
* * * *
12790138 CATTTATTTGCATGATTTTTTTTATGGATTT
1 CATTTATTTGCATAATATATTGTATGGATTT
*
12790169 TATTTATTTGCATAATATATTGTATGGATTT
1 CATTTATTTGCATAATATATTGTATGGATTT
12790200 CATTT
1 CATTT
12790205 GCATTATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (31 bp):
CATTTATTTGCATAATATATTGTATGGATTT
Found at i:12792460 original size:24 final size:24
Alignment explanation
Indices: 12792403--12792462 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
12792393 TATATATATA
* *
12792403 TATGTATGTATGTGTGTGTGTGTG
1 TATGTATGTGTGAGTGTGTGTGTG
** * *
12792427 TATGCGTGTGTGAGTTTGTGTGTT
1 TATGTATGTGTGAGTGTGTGTGTG
12792451 TATGTATGTGTG
1 TATGTATGTGTG
12792463 TGCATTAGAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.02, G:0.37, T:0.50
Consensus pattern (24 bp):
TATGTATGTGTGAGTGTGTGTGTG
Found at i:12810092 original size:13 final size:13
Alignment explanation
Indices: 12810074--12810100 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12810064 CTTGTTGGAG
12810074 GTAAATTTTGAAT
1 GTAAATTTTGAAT
12810087 GTAAATTTTGAAT
1 GTAAATTTTGAAT
12810100 G
1 G
12810101 ATTGTCTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (13 bp):
GTAAATTTTGAAT
Found at i:12810573 original size:24 final size:24
Alignment explanation
Indices: 12810541--12810589 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
12810531 TTTATTAAAT
*
12810541 TGGCTCTTAAGGTAAAGGAGAACC
1 TGGCCCTTAAGGTAAAGGAGAACC
12810565 TGGCCCTTAAGGTAAAGGAGAACC
1 TGGCCCTTAAGGTAAAGGAGAACC
12810589 T
1 T
12810590 TGGAGAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (24 bp):
TGGCCCTTAAGGTAAAGGAGAACC
Found at i:12822378 original size:61 final size:62
Alignment explanation
Indices: 12822283--12822406 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 62
12822273 CAACGCTCAT
12822283 ATCTTTTTCCTTTTCTTACTCAGAGTCTACCATCTCCAAGTGTCATCCCTTCGTGCCTTCAC
1 ATCTTTTTCCTTTTCTTACTCAGAGTCTACCATCTCCAAGTGTCATCCCTTCGTGCCTTCAC
12822345 ATCTTTTTCCTTTTCTT-CTCAGAGTCTACCATCTCCAAGTGTCATCCCTTCGTGCCTTCAC
1 ATCTTTTTCCTTTTCTTACTCAGAGTCTACCATCTCCAAGTGTCATCCCTTCGTGCCTTCAC
12822406 A
1 A
12822407 ATCTCGCTCC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 45 0.73
62 17 0.27
ACGTcount: A:0.16, C:0.34, G:0.10, T:0.40
Consensus pattern (62 bp):
ATCTTTTTCCTTTTCTTACTCAGAGTCTACCATCTCCAAGTGTCATCCCTTCGTGCCTTCAC
Found at i:12839121 original size:22 final size:20
Alignment explanation
Indices: 12839076--12839122 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
12839066 AGATGAAGAA
*
12839076 TTATGGGAGATTCGTGTGTT
1 TTATGGGAGATTCGTGGGTT
*
12839096 TTATGGGAGATATATGTGGGTT
1 TTATGGGAGAT-T-CGTGGGTT
12839118 TTATG
1 TTATG
12839123 ATGGTTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.45
Consensus pattern (20 bp):
TTATGGGAGATTCGTGGGTT
Found at i:12842618 original size:8 final size:8
Alignment explanation
Indices: 12842605--12842705 Score: 67
Period size: 8 Copynumber: 13.5 Consensus size: 8
12842595 TTATTACTTT
12842605 TATATTAA
1 TATATTAA
12842613 TATATTAA
1 TATATTAA
12842621 TATATTAA
1 TATATTAA
*
12842629 TATGTT-A
1 TATATTAA
*
12842636 TTTATTAGA
1 TATATTA-A
12842645 T-TA-T-A
1 TATATTAA
12842650 -ATATT-A
1 TATATTAA
* *
12842656 TTTACTAA
1 TATATTAA
12842664 TATATT-A
1 TATATTAA
12842671 TAATATT-A
1 T-ATATTAA
*
12842679 TTTATTAA
1 TATATTAA
12842687 TATATT-A
1 TATATTAA
*
12842694 TTTATTAA
1 TATATTAA
12842702 TATA
1 TATA
12842706 ATATAATATT
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
5 3 0.04
6 2 0.03
7 21 0.29
8 45 0.62
9 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (8 bp):
TATATTAA
Found at i:12842652 original size:38 final size:37
Alignment explanation
Indices: 12842605--12842721 Score: 87
Period size: 43 Copynumber: 2.9 Consensus size: 37
12842595 TTATTACTTT
12842605 TATATTAATATATTAATATATTAATATGTTATTTATTAGA
1 TATA-TAATATATTAATATATTAATAT-TTATTTATTA-A
12842645 T-TATAATATTATTTACTAATATATT-ATAATATTATTTATTAA
1 TATATAATA-TA--T--TAATATATTAAT-AT-TTATTTATTAA
* *
12842687 TATATTATTTATTAATATAATATAATA-TTATTTAT
1 TATATAATATATTAATAT-AT-TAATATTTATTTAT
12842722 AAGTAAAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
38 19 0.30
39 6 0.09
40 4 0.06
41 3 0.05
42 6 0.09
43 26 0.41
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (37 bp):
TATATAATATATTAATATATTAATATTTATTTATTAA
Found at i:12842670 original size:15 final size:15
Alignment explanation
Indices: 12842607--12842705 Score: 75
Period size: 15 Copynumber: 6.7 Consensus size: 15
12842597 ATTACTTTTA
*
12842607 TATTAATATATTAATA
1 TATTAATATATT-ATT
*
12842623 TATTAATATGTTATT
1 TATTAATATATTATT
*
12842638 TATTAGAT-TATAATAT
1 TATTA-ATATATTAT-T
*
12842654 TATT--TACTA--ATA
1 TATTAATA-TATTATT
12842666 TATT-ATAATATTATT
1 TATTAAT-ATATTATT
12842681 TATTAATATATTATT
1 TATTAATATATTATT
12842696 TATTAATATA
1 TATTAATATA
12842706 ATATAATATT
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
12 4 0.06
13 6 0.09
14 1 0.01
15 37 0.54
16 20 0.29
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (15 bp):
TATTAATATATTATT
Found at i:12842694 original size:23 final size:23
Alignment explanation
Indices: 12842607--12842694 Score: 95
Period size: 23 Copynumber: 3.6 Consensus size: 23
12842597 ATTACTTTTA
*
12842607 TATTAATATATTAATATATTAATATGT
1 TATTAATATATT-ATA-A-TATTAT-T
* *
12842634 TATTTATTAGATTATAATATTATT
1 TA-TTAATATATTATAATATTATT
*
12842658 TACTAATATATTATAATATTATT
1 TATTAATATATTATAATATTATT
12842681 TATTAATATATTAT
1 TATTAATATATTAT
12842695 TTATTAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 31 0.58
24 3 0.06
25 5 0.09
26 1 0.02
27 5 0.09
28 8 0.15
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (23 bp):
TATTAATATATTATAATATTATT
Found at i:12842708 original size:43 final size:43
Alignment explanation
Indices: 12842618--12842721 Score: 114
Period size: 38 Copynumber: 2.5 Consensus size: 43
12842608 ATTAATATAT
*
12842618 TAATATATTAATATGTTATTTATTAGATTATAATATTATTTAC
1 TAATATATTAATATATTATTTATTAGATTATAATATTATTTAC
*
12842661 TAATATATT-ATAATATTATTTATT--A--AT-ATATTATTTAT
1 TAATATATTAAT-ATATTATTTATTAGATTATAATATTATTTAC
*
12842699 TAATATAAT-ATAATATTATTTAT
1 TAATATATTAAT-ATATTATTTAT
12842722 AAGTAAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
38 32 0.56
39 2 0.04
41 1 0.02
42 2 0.04
43 20 0.35
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (43 bp):
TAATATATTAATATATTATTTATTAGATTATAATATTATTTAC
Found at i:12846398 original size:15 final size:14
Alignment explanation
Indices: 12846375--12846433 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
12846365 ATGAAAATGT
12846375 AAAAA-AAGAAAAA
1 AAAAAGAAGAAAAA
12846388 AAAAGAGAAGAAAAA
1 AAAA-AGAAGAAAAA
* *
12846403 AAACATGAATAGAAAA
1 AAA-AAGAAGA-AAAA
*
12846419 AAATAGAAGAAAAA
1 AAAAAGAAGAAAAA
12846433 A
1 A
12846434 GAGAGAAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 4 0.11
14 6 0.16
15 19 0.51
16 8 0.22
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (14 bp):
AAAAAGAAGAAAAA
Found at i:12846403 original size:14 final size:14
Alignment explanation
Indices: 12846384--12846440 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
12846374 TAAAAAAAGA
12846384 AAAAAAAAGAGAAG
1 AAAAAAAAGAGAAG
* *
12846398 AAAAAAAACATGAAT
1 AAAAAAAAGA-GAAG
*
12846413 AGAAAAAAATAGAAG
1 A-AAAAAAAGAGAAG
*
12846428 AAAAAAGAGAGAA
1 AAAAAAAAGAGAA
12846441 AGTAAAGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 19 0.54
15 8 0.23
16 8 0.23
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (14 bp):
AAAAAAAAGAGAAG
Found at i:12849111 original size:17 final size:17
Alignment explanation
Indices: 12849091--12849123 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12849081 AAAGAATAAG
12849091 AAAAAAAACATTCTTTC
1 AAAAAAAACATTCTTTC
*
12849108 AAAAAAAATATTCTTT
1 AAAAAAAACATTCTTT
12849124 TGACTTACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAAAACATTCTTTC
Found at i:12849319 original size:13 final size:12
Alignment explanation
Indices: 12849301--12849340 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
12849291 TAGGCTAAAT
12849301 AAGAAAGCAAAAA
1 AAGAAAG-AAAAA
12849314 AAGAAA-AAAAA
1 AAGAAAGAAAAA
12849325 AAGAAATGAAAAA
1 AAGAAA-GAAAAA
12849338 AAG
1 AAG
12849341 GAAAAATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.44
13 14 0.56
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (12 bp):
AAGAAAGAAAAA
Found at i:12849336 original size:24 final size:24
Alignment explanation
Indices: 12849301--12849346 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12849291 TAGGCTAAAT
12849301 AAGAAAGCAAAAAAAGAAAAAAAA
1 AAGAAAGCAAAAAAAGAAAAAAAA
*
12849325 AAGAAATG-AAAAAAAGGAAAAA
1 AAGAAA-GCAAAAAAAGAAAAAA
12849347 TCTTTGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (24 bp):
AAGAAAGCAAAAAAAGAAAAAAAA
Found at i:12849854 original size:37 final size:37
Alignment explanation
Indices: 12849495--12849864 Score: 248
Period size: 37 Copynumber: 10.0 Consensus size: 37
12849485 AAGTTAGAAA
* * *
12849495 TAATAAGATGATACGTGCATTCCATTTTATGCACATCT
1 TAAT-AGATAATACATGCATTCCATCTTATGCACATCT
* * ** *
12849533 TAATA-AGTAGTACATGCACTCCAT-TTCATGCTTATTT
1 TAATAGA-TAATACATGCATTCCATCTT-ATGCACATCT
* * * *
12849570 TAGTAGGTAATACATGCATTCCAT-TTCATACATATCT
1 TAATAGATAATACATGCATTCCATCTT-ATGCACATCT
* * * *
12849607 TAATAAATAATACATGTATTCTATTTTATGCACATCT
1 TAATAGATAATACATGCATTCCATCTTATGCACATCT
* * ** * * * *
12849644 AAATAAATAATACATAAAGTCCATCTCATGCATATCA
1 TAATAGATAATACATGCATTCCATCTTATGCACATCT
* * * * *
12849681 TAATAGATAATACATGTAGTCTATCCTATGTACAT-T
1 TAATAGATAATACATGCATTCCATCTTATGCACATCT
* * *
12849717 ATAATGGA-CATACATGCATTCCATCTTATACACATCT
1 -TAATAGATAATACATGCATTCCATCTTATGCACATCT
** * * * *
12849754 TAATAGATAGCACATGCGTTCAATCTCATACACAGT-T
1 TAATAGATAATACATGCATTCCATCTTATGCACA-TCT
* **
12849791 TAATAGATAATACATGTATTTAATCTTATGCACATCT
1 TAATAGATAATACATGCATTCCATCTTATGCACATCT
* * *
12849828 TAATAGATAGTACATGCATTCCATCTTAGGCATATCT
1 TAATAGATAATACATGCATTCCATCTTATGCACATCT
12849865 CAAATAATAG
Statistics
Matches: 255, Mismatches: 68, Indels: 19
0.75 0.20 0.06
Matches are distributed among these distances:
36 30 0.12
37 218 0.85
38 7 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (37 bp):
TAATAGATAATACATGCATTCCATCTTATGCACATCT
Found at i:12852877 original size:10 final size:10
Alignment explanation
Indices: 12852864--12852971 Score: 51
Period size: 10 Copynumber: 11.0 Consensus size: 10
12852854 AAAGAATGAG
12852864 AAGAAAAAAA
1 AAGAAAAAAA
12852874 AAGAGAAAAAA
1 AAGA-AAAAAA
* * *
12852885 ATGTAAGAAA
1 AAGAAAAAAA
* * *
12852895 AGGGAAATAA
1 AAGAAAAAAA
* **
12852905 ACGAAGGAAA
1 AAGAAAAAAA
*
12852915 AACAAAAAAA
1 AAGAAAAAAA
*
12852925 ATGAAAAAAA
1 AAGAAAAAAA
*
12852935 AA-AAAGAAA
1 AAGAAAAAAA
* *
12852944 AA-AATAGAA
1 AAGAAAAAAA
*
12852953 GA-AAAAAAA
1 AAGAAAAAAA
12852962 AAGAAAAAAA
1 AAGAAAAAAA
12852972 TGAATGATTG
Statistics
Matches: 69, Mismatches: 27, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
9 19 0.28
10 42 0.61
11 8 0.12
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.05
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:12852936 original size:13 final size:12
Alignment explanation
Indices: 12852918--12852971 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
12852908 AAGGAAAAAC
*
12852918 AAAAAAAATGAAA
1 AAAAAAAAAG-AA
12852931 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
12852943 AAAAATAGAAG-A
1 AAAAA-AAAAGAA
12852955 AAAAAAAAAGAA
1 AAAAAAAAAGAA
12852967 AAAAA
1 AAAAA
12852972 TGAATGATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.11
12 19 0.53
13 13 0.36
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:12852939 original size:24 final size:23
Alignment explanation
Indices: 12852919--12852975 Score: 89
Period size: 24 Copynumber: 2.5 Consensus size: 23
12852909 AGGAAAAACA
12852919 AAAAAAATG-AAAAAAAAAAAAG
1 AAAAAAATGAAAAAAAAAAAAAG
*
12852941 AAAAAAATAGAAGAAAAAAAAAAG
1 AAAAAAAT-GAAAAAAAAAAAAAG
12852965 AAAAAAATGAA
1 AAAAAAATGAA
12852976 TGATTGAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 8 0.25
23 4 0.12
24 20 0.62
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (23 bp):
AAAAAAATGAAAAAAAAAAAAAG
Found at i:12855064 original size:10 final size:10
Alignment explanation
Indices: 12855049--12855092 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
12855039 TAGATGGAGT
12855049 AAAAAAAAAG
1 AAAAAAAAAG
12855059 AAAAAAAAA-
1 AAAAAAAAAG
12855068 ACAACAAAAAAG
1 A-AA-AAAAAAG
12855080 AAAAAAAAAG
1 AAAAAAAAAG
12855090 AAA
1 AAA
12855093 TTAAGAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.03
10 21 0.68
11 8 0.26
12 1 0.03
ACGTcount: A:0.89, C:0.05, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:12855517 original size:43 final size:43
Alignment explanation
Indices: 12855410--12855517 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 43
12855400 TTAGATTTCA
* * * *
12855410 TTCAAATCTCGATAGTGATATCTAAGTGTTCAAAGTCTAAGTT
1 TTCAAATCTTGATAGTGATATTTAAGTGTTCAAAGTCAAAATT
* ** *
12855453 TTCAAATCTTAACGGTAATATTTAAGTGTTCAAAGTCAAAATT
1 TTCAAATCTTGATAGTGATATTTAAGTGTTCAAAGTCAAAATT
*
12855496 TTTAAATCTTGATAGTGATATT
1 TTCAAATCTTGATAGTGATATT
12855518 CGAGTCTTTG
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (43 bp):
TTCAAATCTTGATAGTGATATTTAAGTGTTCAAAGTCAAAATT
Found at i:12855714 original size:35 final size:37
Alignment explanation
Indices: 12855627--12855718 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 37
12855617 TAAGTTTGAA
* *
12855627 TTTCATTAAAATTTTCTTTGTGGCGAAATCTAACCTC
1 TTTCATTAAAATTTTCTTGGTCGCGAAATCTAACCTC
* *
12855664 TTT-GTTAAAATTTTCTTGGTCGCGAAATCTGA-CT-
1 TTTCATTAAAATTTTCTTGGTCGCGAAATCTAACCTC
*
12855698 TTTCATTAAAACTTTCTTGGT
1 TTTCATTAAAATTTTCTTGGT
12855719 GGTGATATCC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
34 3 0.06
35 17 0.35
36 25 0.52
37 3 0.06
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (37 bp):
TTTCATTAAAATTTTCTTGGTCGCGAAATCTAACCTC
Found at i:12856061 original size:47 final size:48
Alignment explanation
Indices: 12856010--12856120 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
12856000 TCATGTCTAC
* *
12856010 ATTTCTTTAAAATTTTTTGA-TCATGATATCCGAGTATTCAGGTTAGA
1 ATTTCTTTAAAATTTTTTCAGTCATGATATCCGAATATTCAGGTTAGA
* * ** *
12856057 ATTTCTTAAAAAATTTTTCAGTGGTGATATTCGAATATTCAGGTTAGA
1 ATTTCTTTAAAATTTTTTCAGTCATGATATCCGAATATTCAGGTTAGA
* *
12856105 ATTTTTTTTAAATTTT
1 ATTTCTTTAAAATTTT
12856121 AAAAAAATTC
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
47 17 0.33
48 35 0.67
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.48
Consensus pattern (48 bp):
ATTTCTTTAAAATTTTTTCAGTCATGATATCCGAATATTCAGGTTAGA
Found at i:12857678 original size:52 final size:53
Alignment explanation
Indices: 12857497--12857743 Score: 222
Period size: 54 Copynumber: 4.7 Consensus size: 53
12857487 TTTAAGTTCA
* ** * *
12857497 TTGCCTATCTTCATA-AAAACCATTTTCAAATTGAGATTTTTTTTAAAAAGTTTG
1 TTGCCTATCTTCATAGGAGTCC-TTTTCAAATTAAGA-TTTTTTTAAAAAGCTTG
* * * * * *
12857551 TTGTCTATCTTCATAAGAGCCCTTTCCAAATTGAA-A--TTTTT--AAAGTTTA
1 TTGCCTATCTTCATAGGAGTCCTTTTCAAATT-AAGATTTTTTTAAAAAGCTTG
* * **
12857600 TTACCTATTTTTGTAGGAGTCCTTTTCAAATTAAGATTTTTTT-AAAAGCTTG
1 TTGCCTATCTTCATAGGAGTCCTTTTCAAATTAAGATTTTTTTAAAAAGCTTG
*
12857652 TTGCCTATCTTCATAGGAGTCTTTTTCAAATTAAGATTTTTTTAAAAAAGCTTG
1 TTGCCTATCTTCATAGGAGTCCTTTTCAAATTAAGATTTTTTT-AAAAAGCTTG
* * * *
12857706 TTGCCTATCTTCATAGCA-TCTTTTTCAAAATGAGATTT
1 TTGCCTATCTTCATAGGAGTCCTTTTCAAATTAAGATTT
12857744 AAAAAAAAAA
Statistics
Matches: 160, Mismatches: 25, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
48 2 0.01
49 32 0.20
51 10 0.06
52 44 0.28
53 18 0.11
54 50 0.31
55 4 0.03
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (53 bp):
TTGCCTATCTTCATAGGAGTCCTTTTCAAATTAAGATTTTTTTAAAAAGCTTG
Found at i:12857733 original size:53 final size:52
Alignment explanation
Indices: 12857519--12857743 Score: 201
Period size: 52 Copynumber: 4.3 Consensus size: 52
12857509 ATAAAAACCA
* * * * *
12857519 TTTTCAAATTGAGATTTTTTTTAAAAAGTTTGTTGTCTATCTTCATAAG-AGCCC
1 TTTTCAAATTAAGA-TTTTTTT-AAAAGCTTGTTGCCTATCTTCAT-AGCAGTCT
* * * * * ** * *
12857573 TTTCCAAATTGAA-A--TTTTT-AAAGTTTATTACCTATTTTTGTAGGAGTCC
1 TTTTCAAATT-AAGATTTTTTTAAAAGCTTGTTGCCTATCTTCATAGCAGTCT
*
12857622 TTTTCAAATTAAGATTTTTTTAAAAGCTTGTTGCCTATCTTCATAGGAGTCT
1 TTTTCAAATTAAGATTTTTTTAAAAGCTTGTTGCCTATCTTCATAGCAGTCT
12857674 TTTTCAAATTAAGATTTTTTTAAAAAAGCTTGTTGCCTATCTTCATAGCA-TCT
1 TTTTCAAATTAAGATTTTTTT--AAAAGCTTGTTGCCTATCTTCATAGCAGTCT
* *
12857727 TTTTCAAAATGAGATTT
1 TTTTCAAATTAAGATTT
12857744 AAAAAAAAAA
Statistics
Matches: 143, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
48 4 0.03
49 30 0.21
51 10 0.07
52 44 0.31
53 18 0.13
54 36 0.25
55 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (52 bp):
TTTTCAAATTAAGATTTTTTTAAAAGCTTGTTGCCTATCTTCATAGCAGTCT
Found at i:12858486 original size:143 final size:145
Alignment explanation
Indices: 12858307--12858573 Score: 344
Period size: 143 Copynumber: 1.9 Consensus size: 145
12858297 TAGATCATGA
* * * * * * * *
12858307 TTTAATATTATTTGATGATTTTTGAAATATTGAAAATCTTAATC-GTACCTCG-AAGGTGTGAAA
1 TTTAAAATTATTTGATAATTTTTGAAACATTAAAAATCTT-AGCAATACCTCGAAAAGTATGAAA
* * * *
12858370 TTACTAAAATACT-CTTTTAGGGT-ATTTTGTAATTTGACATTCCCAAAGTCAATTTTTCATGAA
65 TTACTAAAATACTCCTTGTA-CGTAATTTTATAATTTGACATTCCCAAAGTCAAATTTTCATGAA
12858433 ACATTTCAAATAATTTT
129 ACATTTCAAATAATTTT
***
12858450 TTTAAAATTATTTGATAATTTTTGGTGCATTAAAAATCTTAGCAATACCTCGAAAAGTATGAAAT
1 TTTAAAATTATTTGATAATTTTTGAAACATTAAAAATCTTAGCAATACCTCGAAAAGTATGAAAT
*
12858515 TACTAAAATATTCCTTGTACGTAATTTTATAATTTGACATTCCCAAAGTCAAATTTTCA
66 TACTAAAATACTCCTTGTACGTAATTTTATAATTTGACATTCCCAAAGTCAAATTTTCA
12858574 CCAAAATTTT
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
142 2 0.02
143 40 0.38
144 23 0.22
145 39 0.38
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (145 bp):
TTTAAAATTATTTGATAATTTTTGAAACATTAAAAATCTTAGCAATACCTCGAAAAGTATGAAAT
TACTAAAATACTCCTTGTACGTAATTTTATAATTTGACATTCCCAAAGTCAAATTTTCATGAAAC
ATTTCAAATAATTTT
Found at i:12858987 original size:19 final size:19
Alignment explanation
Indices: 12858963--12859011 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
12858953 CTAGAAATGT
*
12858963 AGAAAAAATAAGGGAAAAA
1 AGAAAAAAAAAGGGAAAAA
*
12858982 AGAAAAAAAAAGTGAAAAA
1 AGAAAAAAAAAGGGAAAAA
12859001 A-AAAAGAAAAA
1 AGAAAA-AAAAA
12859012 AAAAAGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (19 bp):
AGAAAAAAAAAGGGAAAAA
Found at i:12858991 original size:11 final size:11
Alignment explanation
Indices: 12858977--12859018 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
12858967 AAAATAAGGG
12858977 AAAAAAGAAAA
1 AAAAAAGAAAA
*
12858988 AAAAAGTGAAAA
1 AAAAA-AGAAAA
12859000 AAAAAAGAAAA
1 AAAAAAGAAAA
12859011 AAAAAAGA
1 AAAAAAGA
12859019 GAGAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:12859000 original size:13 final size:13
Alignment explanation
Indices: 12858984--12859031 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
12858974 GGGAAAAAAG
12858984 AAAAAAAAAGTGA
1 AAAAAAAAAGTGA
12858997 AAAAAAAAA--GA
1 AAAAAAAAAGTGA
*
12859008 AAAAAAAAAGAGA
1 AAAAAAAAAGTGA
* *
12859021 GAAAGAAAAGT
1 AAAAAAAAAGT
12859032 TGGAGAAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 11 0.37
13 19 0.63
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAGTGA
Found at i:12859029 original size:24 final size:23
Alignment explanation
Indices: 12858977--12859030 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
12858967 AAAATAAGGG
*
12858977 AAAAAAGAAAAAAAAAGTGAAAA
1 AAAAAAGAAAAAAAAAGAGAAAA
*
12859000 AAAAAAGAAAAAAAAAAGAGAGAA
1 AAAAAAG-AAAAAAAAAGAGAAAA
*
12859024 AGAAAAG
1 AAAAAAG
12859031 TTGGAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAAAAAAAGAGAAAA
Found at i:12860039 original size:7 final size:7
Alignment explanation
Indices: 12860029--12860181 Score: 64
Period size: 7 Copynumber: 22.4 Consensus size: 7
12860019 TTTAAAATCT
12860029 TAAACTC
1 TAAACTC
*
12860036 TAAACCC
1 TAAACTC
12860043 TAAAC-C
1 TAAACTC
*
12860049 TTAAA-TAT
1 -TAAACT-C
12860057 TAAA-TC
1 TAAACTC
12860063 ATAAACAT-
1 -TAAAC-TC
12860071 TAAAC-C
1 TAAACTC
12860077 TAAACAT-
1 TAAAC-TC
12860084 TAAA-TC
1 TAAACTC
12860090 TTAAA-TC
1 -TAAACTC
12860097 CTAAA-TC
1 -TAAACTC
12860104 TTAAACTC
1 T-AAACTC
12860112 TAAACTC
1 TAAACTC
12860119 T-AACT-
1 TAAACTC
12860124 TAAAC-C
1 TAAACTC
*
12860130 TAAAATC
1 TAAACTC
*
12860137 TAAACAC
1 TAAACTC
12860144 TAAA-TC
1 TAAACTC
*
12860150 TTAAACAC
1 -TAAACTC
12860158 TAAA-TC
1 TAAACTC
*
12860164 TTAAACTT
1 -TAAACTC
12860172 TAAACTC
1 TAAACTC
12860179 TAA
1 TAA
12860182 CCTAGACCCA
Statistics
Matches: 114, Mismatches: 12, Indels: 40
0.69 0.07 0.24
Matches are distributed among these distances:
5 2 0.02
6 20 0.18
7 86 0.75
8 5 0.04
9 1 0.01
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAACTC
Found at i:12860051 original size:21 final size:21
Alignment explanation
Indices: 12860027--12860181 Score: 101
Period size: 21 Copynumber: 7.6 Consensus size: 21
12860017 AATTTAAAAT
*
12860027 CTTAAACTCTAAACCCTAAAC
1 CTTAAACTCTAAACCTTAAAC
* * *
12860048 CTTAAA-TATTAAATCATAAAC
1 CTTAAACT-CTAAACCTTAAAC
* * *
12860069 ATTAAAC-CTAAACATTAAAT
1 CTTAAACTCTAAACCTTAAAC
*
12860089 CTTAAA-TCCTAAATCTTAAA-
1 CTTAAACT-CTAAACCTTAAAC
12860109 CTCTAAACTCT-AA-CTTAAAC
1 CT-TAAACTCTAAACCTTAAAC
* *
12860129 C-TAAAATCTAAACAC-TAAAT
1 CTTAAACTCTAAAC-CTTAAAC
* *
12860149 CTTAAACACTAAATCTTAAAC
1 CTTAAACTCTAAACCTTAAAC
*
12860170 TTTAAACTCTAA
1 CTTAAACTCTAA
12860182 CCTAGACCCA
Statistics
Matches: 102, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
18 7 0.07
19 8 0.08
20 25 0.25
21 61 0.60
22 1 0.01
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (21 bp):
CTTAAACTCTAAACCTTAAAC
Found at i:12860138 original size:18 final size:19
Alignment explanation
Indices: 12860103--12860139 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12860093 AATCCTAAAT
*
12860103 CTTAAACTCTAAACTCTAA
1 CTTAAACTCTAAAATCTAA
12860122 CTTAAAC-CTAAAATCTAA
1 CTTAAACTCTAAAATCTAA
12860140 ACACTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (19 bp):
CTTAAACTCTAAAATCTAA
Found at i:12860162 original size:27 final size:24
Alignment explanation
Indices: 12860105--12860169 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 24
12860095 TCCTAAATCT
*
12860105 TAAACTCTAAACTCTAACTTAAACC
1 TAAA-TCTAAACACTAACTTAAACC
12860130 TAAAATCTAAACACTAAATCTTAAACAC
1 T-AAATCTAAACACT-AA-CTTAAAC-C
12860158 TAAATCTTAAAC
1 TAAATC-TAAAC
12860170 TTTAAACTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
25 10 0.29
26 5 0.15
27 12 0.35
28 7 0.21
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAATCTAAACACTAACTTAAACC
Found at i:12860175 original size:14 final size:14
Alignment explanation
Indices: 12860043--12860175 Score: 85
Period size: 14 Copynumber: 9.3 Consensus size: 14
12860033 CTCTAAACCC
* *
12860043 TAAACCTTAAATAT
1 TAAATCTTAAACAT
*
12860057 TAAATCATAAACAT
1 TAAATCTTAAACAT
*
12860071 TAAA-CCTAAACAT
1 TAAATCTTAAACAT
*
12860084 TAAATCTTAAATC-C
1 TAAATCTTAAA-CAT
12860098 TAAATCTTAAAC-T
1 TAAATCTTAAACAT
*
12860111 CTAAACTCTAACTTAAACCT
1 -TAAA---T--CTTAAACAT
* *
12860131 AAAATC-TAAACAC
1 TAAATCTTAAACAT
*
12860144 TAAATCTTAAACAC
1 TAAATCTTAAACAT
*
12860158 TAAATCTTAAACTT
1 TAAATCTTAAACAT
12860172 TAAA
1 TAAA
12860176 CTCTAACCTA
Statistics
Matches: 96, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
13 23 0.24
14 59 0.61
15 1 0.01
16 1 0.01
17 1 0.01
19 10 0.10
20 1 0.01
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATCTTAAACAT
Found at i:12860314 original size:14 final size:13
Alignment explanation
Indices: 12860295--12860324 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
12860285 GTCCTACATC
12860295 CATATCATGTCATT
1 CATATCATGT-ATT
12860309 CATATCATGTATT
1 CATATCATGTATT
12860322 CAT
1 CAT
12860325 TATACATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
CATATCATGTATT
Found at i:12860378 original size:16 final size:16
Alignment explanation
Indices: 12860357--12860404 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
12860347 CATGCATTTG
12860357 TTTTAAA-AAAATAAGT
1 TTTTAAATAAAATAA-T
12860373 TTTTAAAGTAAAAT-AT
1 TTTTAAA-TAAAATAAT
12860389 TTTTAAATAAAATAAT
1 TTTTAAATAAAATAAT
12860405 ATCTTGAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.21
16 17 0.59
17 1 0.03
18 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
TTTTAAATAAAATAAT
Found at i:12860716 original size:33 final size:33
Alignment explanation
Indices: 12860678--12860745 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
12860668 TAGAATCATT
* *
12860678 TTTAACCAAAGTTTAAAAATAACATGCAATTAA
1 TTTAACCAAAATTTAAAAATAACATACAATTAA
* * * *
12860711 TTTAACTAAAATTTCAAGATAACATATAATTAA
1 TTTAACCAAAATTTAAAAATAACATACAATTAA
12860744 TT
1 TT
12860746 GATATCATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.35
Consensus pattern (33 bp):
TTTAACCAAAATTTAAAAATAACATACAATTAA
Found at i:12866182 original size:41 final size:41
Alignment explanation
Indices: 12866137--12866222 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
12866127 TTTTTATTTT
12866137 TTAAAAAATAAAATCTATTATATTTCATCTTAAGAGTTATA
1 TTAAAAAATAAAATCTATTATATTTCATCTTAAGAGTTATA
12866178 TTAAAAAATAAAATCTATTATATTTCATCTTAAGAGTTATA
1 TTAAAAAATAAAATCTATTATATTTCATCTTAAGAGTTATA
12866219 TTAA
1 TTAA
12866223 TATTTATCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (41 bp):
TTAAAAAATAAAATCTATTATATTTCATCTTAAGAGTTATA
Found at i:12866484 original size:21 final size:20
Alignment explanation
Indices: 12866460--12866524 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
12866450 ATTTTTGAAG
*
12866460 TTGTTTGCTATTAATTAAGAA
1 TTGTTTGTTATTAATTAA-AA
* *
12866481 TTGTTCGTTA-TATTTTAAAA
1 TTGTTTGTTATTA-ATTAAAA
12866501 GTTGTTTGTTATTAATTAAAA
1 -TTGTTTGTTATTAATTAAAA
12866522 TTG
1 TTG
12866525 AATTTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
20 7 0.19
21 27 0.75
22 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (20 bp):
TTGTTTGTTATTAATTAAAA
Found at i:12866606 original size:16 final size:16
Alignment explanation
Indices: 12866587--12866618 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12866577 TAATTGAGTA
12866587 TTTAAGAGATTCGAAT
1 TTTAAGAGATTCGAAT
*
12866603 TTTAAGAGATTTGAAT
1 TTTAAGAGATTCGAAT
12866619 ATTATAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.41
Consensus pattern (16 bp):
TTTAAGAGATTCGAAT
Found at i:12871735 original size:24 final size:24
Alignment explanation
Indices: 12871708--12871753 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12871698 ATTTTTGTGC
*
12871708 TTGGTTT-AGTTTTAGGGTTTGGGG
1 TTGGTTTAAGGTTTA-GGTTTGGGG
12871732 TTGGTTTAAGGTTTAGGTTTGG
1 TTGGTTTAAGGTTTAGGTTTGG
12871754 TTTAAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.11, C:0.00, G:0.39, T:0.50
Consensus pattern (24 bp):
TTGGTTTAAGGTTTAGGTTTGGGG
Found at i:12871739 original size:18 final size:18
Alignment explanation
Indices: 12871718--12871764 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
12871708 TTGGTTTAGT
*
12871718 TTTAGGGTTTGGGGTTGG
1 TTTAAGGTTTGGGGTTGG
* *
12871736 TTTAAGGTTTAGGTTTGG
1 TTTAAGGTTTGGGGTTGG
12871754 TTTAAGGTTTG
1 TTTAAGGTTTG
12871765 AGGTGAGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.49
Consensus pattern (18 bp):
TTTAAGGTTTGGGGTTGG
Found at i:12871842 original size:11 final size:11
Alignment explanation
Indices: 12871822--12871863 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
12871812 GGTTTAAGGG
12871822 TTAGGAATTGGT
1 TTAGG-ATTGGT
12871834 TTAGGATTGG-
1 TTAGGATTGGT
*
12871844 GT-GGATTGGT
1 TTAGGATTGGT
12871854 TTAGGATTGG
1 TTAGGATTGG
12871864 GTAATTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 12 0.46
12 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (11 bp):
TTAGGATTGGT
Found at i:12871872 original size:20 final size:20
Alignment explanation
Indices: 12871826--12871876 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
12871816 TAAGGGTTAG
12871826 GAATTGGTTTAGGATTGGGT
1 GAATTGGTTTAGGATTGGGT
*
12871846 GGATTGGTTTAGGATTGGGT
1 GAATTGGTTTAGGATTGGGT
12871866 -AATTTGGTTTA
1 GAA-TTGGTTTA
12871877 AGGTTTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (20 bp):
GAATTGGTTTAGGATTGGGT
Found at i:12871910 original size:20 final size:20
Alignment explanation
Indices: 12871885--12871931 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
12871875 TAAGGTTTAT
*
12871885 GTTTAGGAGTTTCATTTAGG
1 GTTTAGGAATTTCATTTAGG
*
12871905 GTTTAGGAATTTCATTTATG
1 GTTTAGGAATTTCATTTAGG
12871925 GTTTAGG
1 GTTTAGG
12871932 GATTAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.47
Consensus pattern (20 bp):
GTTTAGGAATTTCATTTAGG
Found at i:12871975 original size:19 final size:19
Alignment explanation
Indices: 12871951--12872161 Score: 115
Period size: 19 Copynumber: 10.5 Consensus size: 19
12871941 AGGTTTAAGC
12871951 TAGGGTTTGAGATTTGGTT
1 TAGGGTTTGAGATTTGGTT
*
12871970 TAGGGTTTAGGGA-TTGGTT
1 TAGGGTTT-GAGATTTGGTT
* * *
12871989 TAAGGTTTAGGGA-TTGGTC
1 TAGGGTTT-GAGATTTGGTT
* *
12872008 TAAGGTTTTAGGA-TTGGCTT
1 TAGGGTTTGA-GATTTGG-TT
* *
12872028 TAGGGTTTAAGGGTTTGGTT
1 TAGGGTTTGA-GATTTGGTT
* *
12872048 TAGAGTTTGAAAATTTGGTT
1 TAGGGTTTG-AGATTTGGTT
*
12872068 TAGGGTTCTATGATTGGTTTAGGATT
1 TAGGG-T-T-TGA--GATTT-GG-TT
* *
12872094 TATGGTTTAAGAGTTTGGTT
1 TAGGGTTTGAGA-TTTGGTT
* *
12872114 TAAGGTTTGATTATTTGGTT
1 TAGGGTTTGA-GATTTGGTT
12872134 TAGGGTTTAGAGA-TTGGTT
1 TAGGGTTT-GAGATTTGGTT
12872153 TAGGGTTTG
1 TAGGGTTTG
12872162 GTCTCGATTT
Statistics
Matches: 153, Mismatches: 24, Indels: 31
0.74 0.12 0.15
Matches are distributed among these distances:
18 1 0.01
19 59 0.39
20 59 0.39
21 12 0.08
22 5 0.03
23 4 0.03
24 4 0.03
25 3 0.02
26 6 0.04
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.45
Consensus pattern (19 bp):
TAGGGTTTGAGATTTGGTT
Found at i:12872049 original size:20 final size:20
Alignment explanation
Indices: 12871963--12872160 Score: 109
Period size: 20 Copynumber: 9.8 Consensus size: 20
12871953 GGGTTTGAGA
12871963 TTTGGTTTAGGGTTT-AGGG
1 TTTGGTTTAGGGTTTAAGGG
* *
12871982 ATTGGTTTAAGGTTT-AGGG
1 TTTGGTTTAGGGTTTAAGGG
* * * *
12872001 ATTGGTCTAAGGTTTTA-GG
1 TTTGGTTTAGGGTTTAAGGG
*
12872020 ATTGGCTTTAGGGTTTAAGGG
1 TTTGG-TTTAGGGTTTAAGGG
* **
12872041 TTTGGTTTAGAGTTTGAA-AA
1 TTTGGTTTAGGGTTT-AAGGG
*
12872061 TTTGGTTTAGGGTTCTATGATTGG
1 TTTGGTTTAGGGTT-TA--A-GGG
* *
12872085 TTTAGGATTTATGGTTTAAGAG
1 TTT-GG-TTTAGGGTTTAAGGG
* * ***
12872107 TTTGGTTTAAGGTTTGATTA
1 TTTGGTTTAGGGTTTAAGGG
*
12872127 TTTGGTTTAGGGTTT-AGAG
1 TTTGGTTTAGGGTTTAAGGG
*
12872146 ATTGGTTTAGGGTTT
1 TTTGGTTTAGGGTTT
12872161 GGTCTCGATT
Statistics
Matches: 142, Mismatches: 26, Indels: 22
0.75 0.14 0.12
Matches are distributed among these distances:
19 53 0.37
20 57 0.40
21 11 0.08
22 5 0.04
23 1 0.01
24 3 0.02
25 4 0.03
26 8 0.06
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (20 bp):
TTTGGTTTAGGGTTTAAGGG
Found at i:12872113 original size:66 final size:66
Alignment explanation
Indices: 12872026--12872156 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
12872016 TAGGATTGGC
* *
12872026 TTTAGGGTTTAAGGGTTTGGTTT-AGAGTTTGAAAATTTGGTTTAGGGTTCTA-TGATTGGTTTA
1 TTTAGGGTTTAAGAGTTTGGTTTAAG-GTTTGAAAATTTGGTTTAGGGTT-TAGAGATTGGTTTA
12872089 GGA
64 GGA
* **
12872092 TTTATGGTTTAAGAGTTTGGTTTAAGGTTTGATTATTTGGTTTAGGGTTTAGAGATTGGTTTAGG
1 TTTAGGGTTTAAGAGTTTGGTTTAAGGTTTGAAAATTTGGTTTAGGGTTTAGAGATTGGTTTAGG
12872157 GTTTGGTCTC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
65 2 0.03
66 54 0.93
67 2 0.03
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (66 bp):
TTTAGGGTTTAAGAGTTTGGTTTAAGGTTTGAAAATTTGGTTTAGGGTTTAGAGATTGGTTTAGG
A
Found at i:12872114 original size:13 final size:13
Alignment explanation
Indices: 12872081--12872122 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
12872071 GGTTCTATGA
* *
12872081 TTGGTTTAGGATT
1 TTGGTTTAAGAGT
12872094 TATGGTTTAAGAGT
1 T-TGGTTTAAGAGT
12872108 TTGGTTTAAG-GT
1 TTGGTTTAAGAGT
12872120 TTG
1 TTG
12872123 ATTATTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 11 0.42
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (13 bp):
TTGGTTTAAGAGT
Found at i:12872305 original size:26 final size:28
Alignment explanation
Indices: 12872240--12872305 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 28
12872230 GCTTAGTTTG
12872240 AGGTTTGAGGGTTTATGTTAGGGGTTTAA
1 AGGTTT-AGGGTTTATGTTAGGGGTTTAA
*
12872269 AGGTTTA--GTTT-TGGTTTGGGGTTT-A
1 AGGTTTAGGGTTTAT-GTTAGGGGTTTAA
12872294 A-GTTTAGGGTTT
1 AGGTTTAGGGTTT
12872306 GAAGATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
24 5 0.15
25 3 0.09
26 18 0.55
28 1 0.03
29 6 0.18
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (28 bp):
AGGTTTAGGGTTTATGTTAGGGGTTTAA
Found at i:12872325 original size:40 final size:40
Alignment explanation
Indices: 12872232--12872330 Score: 94
Period size: 39 Copynumber: 2.5 Consensus size: 40
12872222 TGATTAAGGC
* * *
12872232 TTAGTTTGAGGTTTGAGGGTTTATGTTAGGGGTTTAAAGGT
1 TTAG-TTGGGGTTTGAGGGTTTAAGTTAGGGGTTTAAAGAT
** *
12872273 TTAGTTTTGGTTTG-GGGTTTAAGTTTA-GGGTTTGAAGAT
1 TTAGTTGGGGTTTGAGGGTTTAAG-TTAGGGGTTTAAAGAT
*
12872312 TTAAGTTGGGGTTTAAGGG
1 TT-AGTTGGGGTTTGAGGG
12872331 CTTGGCTTAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
39 20 0.43
40 20 0.43
41 7 0.15
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.44
Consensus pattern (40 bp):
TTAGTTGGGGTTTGAGGGTTTAAGTTAGGGGTTTAAAGAT
Found at i:12876777 original size:144 final size:143
Alignment explanation
Indices: 12876512--12876920 Score: 392
Period size: 145 Copynumber: 2.8 Consensus size: 143
12876502 AGATTTTAAA
* * * * * * **
12876512 GCACTAAAAATCATGAAATATTATGAGATTAAGATATGAAAAGTTTCGTGAAAATC-CAAGCTTG
1 GCACAAAAAATCATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATCTGAA-CTAA
* * * * * *
12876576 GAAAGGCCAAATTATGAAAATACCCCTATATGAGTATTTTGGTAATTTTACACTTTTCGA-GTAC
65 AAAAAGCTAAATTATAAAAATA-CCCTATAAG-GTATTTTGGTAATTTTACCCTTTTCGACGTAC
** *
12876640 TGCTGTGATCTCAGAT
128 TAATGTGATCTCAAAT
* * * * * *
12876656 GCACCAAAAATCATGAAATATTATAAAATTATGATCTGAAAAGTTTCATGAAATTTTGATCTCAA
1 GCACAAAAAATCATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATCTGAACTAAA
*
12876721 AAAAGCTAAATTATAAAAATACCCTTATAAGGCTATTTTGGTAATTTCACCCTTTTCGACGTACT
66 AAAAGCTAAATTATAAAAATACCC-TATAAGG-TATTTTGGTAATTTTACCCTTTTCGACGTACT
* *
12876786 AATGTGATTTTAAAT
129 AATGTGATCTCAAAT
* * * * * * **
12876801 GTATAAAAAATTAT-AGAATATTATAAAGTTAAAATCTAAAAAGTTTCACAAAAATCTGAACTAA
1 GCACAAAAAATCATGA-AATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATCTGAACTAA
* **
12876865 AAAAAGCTAAATTACAAAAATAATACTATAAGGGTATTTTGGTAATTTTACCCTTT
65 AAAAAGCTAAATTATAAAAAT-ACCCTATAA-GGTATTTTGGTAATTTTACCCTTT
12876921 CTAAGGCCCA
Statistics
Matches: 216, Mismatches: 42, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
143 4 0.02
144 98 0.45
145 110 0.51
146 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (143 bp):
GCACAAAAAATCATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATCTGAACTAAA
AAAAGCTAAATTATAAAAATACCCTATAAGGTATTTTGGTAATTTTACCCTTTTCGACGTACTAA
TGTGATCTCAAAT
Found at i:12878949 original size:20 final size:20
Alignment explanation
Indices: 12878890--12878941 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 20
12878880 AAGCCCAAAC
*
12878890 TTTTTTAATTGTAAT-TTGA
1 TTTTTTAATTTTAATCTTGA
12878909 --TTTTAATTTTAATCTTGA
1 TTTTTTAATTTTAATCTTGA
*
12878927 TTTTTTTATTTTAAT
1 TTTTTTAATTTTAAT
12878942 TTAGATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 12 0.43
18 4 0.14
20 12 0.43
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTTTTAATTTTAATCTTGA
Found at i:12879972 original size:6 final size:6
Alignment explanation
Indices: 12879963--12879990 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12879953 TGACTTTTTT
12879963 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
12879991 CTAATTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:12880166 original size:24 final size:24
Alignment explanation
Indices: 12880139--12880199 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
12880129 TATTTTTTTC
12880139 ATGATTTTATA-TTATTTACATGAT
1 ATGATTTTATATTTA-TTACATGAT
*
12880163 ATGATTTTATATTTATTGCATGAT
1 ATGATTTTATATTTATTACATGAT
12880187 ATGA--TTATATTTA
1 ATGATTTTATATTTA
12880200 ATTTAACTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
22 9 0.26
24 23 0.66
25 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (24 bp):
ATGATTTTATATTTATTACATGAT
Found at i:12880250 original size:24 final size:24
Alignment explanation
Indices: 12880139--12880251 Score: 78
Period size: 24 Copynumber: 4.8 Consensus size: 24
12880129 TATTTTTTTC
12880139 ATGATT-TTATA-TTATTTACATGA
1 ATGATTATTATATTTATTTA-ATGA
**
12880162 TATGATT-TTATATTTATTGCATGA
1 -ATGATTATTATATTTATTTAATGA
* *
12880186 TATGATTA-TAT-TTAATTTAACTGC
1 -ATGATTATTATATTTATTTAA-TGA
* *
12880210 ATGGTTATTA-ATATATTTAATTG-
1 ATGATTATTATATTTATTTAA-TGA
12880233 ATGATTATTATATTTATTT
1 ATGATTATTATATTTATTT
12880252 GTGTGATTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
23 21 0.30
24 45 0.63
25 5 0.07
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (24 bp):
ATGATTATTATATTTATTTAATGA
Found at i:12880347 original size:19 final size:18
Alignment explanation
Indices: 12880300--12880360 Score: 77
Period size: 19 Copynumber: 3.3 Consensus size: 18
12880290 ATTTATGTGA
*
12880300 TTTATATTTGCATGATTAA
1 TTTATATTTGCATGA-TAT
*
12880319 TTAATATTTGCATGATAT
1 TTTATATTTGCATGATAT
*
12880337 TTTATATTTTGCTTGATAT
1 TTTATA-TTTGCATGATAT
12880356 TTTAT
1 TTTAT
12880361 TGCATGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.19
19 30 0.81
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTATATTTGCATGATAT
Found at i:12880430 original size:19 final size:20
Alignment explanation
Indices: 12880390--12880442 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
12880380 TTATTGCATG
* *
12880390 ATTATTGTATCATATATTAT
1 ATTATTGCATGATATATTAT
12880410 ATTATTGCATGATAT-TTAT
1 ATTATTGCATGATATATTAT
*
12880429 ATTAATGCATGATA
1 ATTATTGCATGATA
12880443 ATTTTTGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (20 bp):
ATTATTGCATGATATATTAT
Found at i:12882806 original size:18 final size:19
Alignment explanation
Indices: 12882785--12882820 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
12882775 ATTTAAAATC
12882785 TTATTTTATTTT-TTATTT
1 TTATTTTATTTTATTATTT
12882803 TTATTTTATTTTATTATT
1 TTATTTTATTTTATTATT
12882821 ATTAGATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTATTTTATTTTATTATTT
Found at i:12883030 original size:18 final size:19
Alignment explanation
Indices: 12882973--12883030 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 19
12882963 GTTCTTATTA
**
12882973 TAGGGTTTCAACTAGGCGTT
1 TAGGGTTTCATTTAGG-GTT
*
12882993 TAGGGTTTCATTTAGAGTT
1 TAGGGTTTCATTTAGGGTT
*
12883012 TAGGG-TTCTTTTAGGGTT
1 TAGGGTTTCATTTAGGGTT
12883030 T
1 T
12883031 TGTTTCACCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 12 0.36
19 8 0.24
20 13 0.39
ACGTcount: A:0.17, C:0.09, G:0.29, T:0.45
Consensus pattern (19 bp):
TAGGGTTTCATTTAGGGTT
Found at i:12883119 original size:19 final size:19
Alignment explanation
Indices: 12883095--12883133 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12883085 TAAAGTTTTT
*
12883095 ACCTAGGATTTAGGGTTTC
1 ACCTAGGATTTAAGGTTTC
*
12883114 ACCTAGGGTTTAAGGTTTC
1 ACCTAGGATTTAAGGTTTC
12883133 A
1 A
12883134 TTTGAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (19 bp):
ACCTAGGATTTAAGGTTTC
Found at i:12883529 original size:15 final size:16
Alignment explanation
Indices: 12883509--12883547 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
12883499 CATCAAAGAT
12883509 AAATTAAAGCATAT-A
1 AAATTAAAGCATATGA
*
12883524 AAATTAAATCATATGA
1 AAATTAAAGCATATGA
12883540 AAATTAAA
1 AAATTAAA
12883548 ATAATCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (16 bp):
AAATTAAAGCATATGA
Found at i:12884611 original size:13 final size:14
Alignment explanation
Indices: 12884587--12884614 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12884577 ATGATTACAA
12884587 TTTTTGGTTTTTTT
1 TTTTTGGTTTTTTT
12884601 TTTTTGGTTTTTTT
1 TTTTTGGTTTTTTT
12884615 CTTCCTTTTT
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:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTTGGTTTTTTT
Found at i:12885536 original size:18 final size:19
Alignment explanation
Indices: 12885515--12885554 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
12885505 TTGATGATCG
12885515 AAACTC-AATTACAAAA-AT
1 AAACTCAAATTA-AAAAGAT
12885533 AAACTCAAATTAAAAAGAT
1 AAACTCAAATTAAAAAGAT
12885552 AAA
1 AAA
12885555 ATATTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.20
Consensus pattern (19 bp):
AAACTCAAATTAAAAAGAT
Found at i:12893441 original size:34 final size:34
Alignment explanation
Indices: 12893414--12893479 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
12893404 TTACATTCTT
*
12893414 TCTAATAAAATTTTTAGGTGAAGATTACTATCTC
1 TCTAACAAAATTTTTAGGTGAAGATTACTATCTC
* *
12893448 TCTAACAAAATTTTTATGTGAAGATTGCTATC
1 TCTAACAAAATTTTTAGGTGAAGATTACTATC
12893480 ATATTATGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (34 bp):
TCTAACAAAATTTTTAGGTGAAGATTACTATCTC
Found at i:12897265 original size:2 final size:2
Alignment explanation
Indices: 12897260--12897284 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12897250 GTGCAATAGG
12897260 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12897285 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12897289 original size:2 final size:2
Alignment explanation
Indices: 12897284--12897308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12897274 ATATATATAT
12897284 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12897309 ACAACAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12898032 original size:2 final size:2
Alignment explanation
Indices: 12898025--12898071 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
12898015 ATGGAATCTA
12898025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12898067 A- AT AT
1 AT AT AT
12898072 TACAAAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12901259 original size:19 final size:20
Alignment explanation
Indices: 12901216--12901260 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
12901206 AATATTTGAA
* *
12901216 TTATATATTTTTATTAATTTT
1 TTATATATTTTTA-TAAATTC
12901237 TTATATATTTTTA-AAATTC
1 TTATATATTTTTATAAATTC
12901256 TTATA
1 TTATA
12901261 AAATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATATTTTTATAAATTC
Found at i:12901380 original size:20 final size:20
Alignment explanation
Indices: 12901355--12901423 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
12901345 ATAAACCAAA
12901355 TCAAATTAATAAAATTCAAT
1 TCAAATTAATAAAATTCAAT
* * * *
12901375 TCAAATCATTAAATTTTTTCAAA
1 TCAAATTAATAAA---ATTCAAT
12901398 TCAAATTAATAAAATTCAAT
1 TCAAATTAATAAAATTCAAT
12901418 TCAAAT
1 TCAAAT
12901424 CATTAAATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 22 0.58
23 16 0.42
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
TCAAATTAATAAAATTCAAT
Found at i:12901395 original size:23 final size:23
Alignment explanation
Indices: 12901369--12901436 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
12901359 ATTAATAAAA
12901369 TTCAATTCAAATCATTAAATTTT
1 TTCAATTCAAATCATTAAATTTT
* * * *
12901392 TTCAAATCAAATTAATAAA---A
1 TTCAATTCAAATCATTAAATTTT
12901412 TTCAATTCAAATCATTAAATTTT
1 TTCAATTCAAATCATTAAATTTT
12901435 TT
1 TT
12901437 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 16 0.47
23 18 0.53
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (23 bp):
TTCAATTCAAATCATTAAATTTT
Found at i:12901398 original size:43 final size:43
Alignment explanation
Indices: 12901351--12901436 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
12901341 ATTAATAAAC
12901351 CAAATCAAATTAATAAAATTCAATTCAAATCATTAAATTTTTT
1 CAAATCAAATTAATAAAATTCAATTCAAATCATTAAATTTTTT
12901394 CAAATCAAATTAATAAAATTCAATTCAAATCATTAAATTTTTT
1 CAAATCAAATTAATAAAATTCAATTCAAATCATTAAATTTTTT
12901437 TTTTTTAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (43 bp):
CAAATCAAATTAATAAAATTCAATTCAAATCATTAAATTTTTT
Found at i:12901430 original size:20 final size:20
Alignment explanation
Indices: 12901364--12901430 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
12901354 ATCAAATTAA
12901364 TAAAATTCAATTCAAATCAT
1 TAAAATTCAATTCAAATCAT
* * * *
12901384 TAAATTTTTTCAAATCAAATTAA
1 TAAA---ATTCAATTCAAATCAT
12901407 TAAAATTCAATTCAAATCAT
1 TAAAATTCAATTCAAATCAT
12901427 TAAA
1 TAAA
12901431 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
20 20 0.56
23 16 0.44
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAATTCAATTCAAATCAT
Found at i:12906788 original size:5 final size:5
Alignment explanation
Indices: 12906764--12906801 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
12906754 AAATTTAATC
*
12906764 TAAAA T-AAC TAAAA TAAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAA
12906802 CTTTTAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.10
5 21 0.72
6 5 0.17
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:12910473 original size:2 final size:2
Alignment explanation
Indices: 12910466--12910497 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12910456 ATTCAAAAGG
*
12910466 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12910498 TTAGATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12910649 original size:27 final size:29
Alignment explanation
Indices: 12910608--12910661 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
12910598 TTAAAAAAGA
12910608 TAATATATTTAAATTA-TATT-TTATTGT
1 TAATATATTTAAATTATTATTATTATTGT
12910635 TAATAATATTT-AATTATTATTATTATT
1 TAAT-ATATTTAAATTATTATTATTATT
12910662 TACAGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.38
28 10 0.42
29 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TAATATATTTAAATTATTATTATTATTGT
Found at i:12910963 original size:34 final size:34
Alignment explanation
Indices: 12910900--12910966 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
12910890 TTAAGTTTTT
*
12910900 AAAAATTTATATTTTAATTATTTAATTTTTTTAA
1 AAAAATTTATATTTTAAGTATTTAATTTTTTTAA
* *
12910934 AAAAATTTTTATTTTAAAGT-TTTATTTTTTTTA
1 AAAAATTTATATTTT-AAGTATTTAATTTTTTTA
12910967 TTAATAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
AAAAATTTATATTTTAAGTATTTAATTTTTTTAA
Found at i:12911069 original size:2 final size:2
Alignment explanation
Indices: 12911062--12911089 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12911052 TTAAATCATT
12911062 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12911090 AAAAACTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12911375 original size:14 final size:15
Alignment explanation
Indices: 12911344--12911376 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12911334 AATCTAAATG
12911344 AATTTTTTTATTACT
1 AATTTTTTTATTACT
*
12911359 AATTTTTTTTTTA-T
1 AATTTTTTTATTACT
12911373 AATT
1 AATT
12911377 AGACTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
AATTTTTTTATTACT
Found at i:12912215 original size:20 final size:22
Alignment explanation
Indices: 12912180--12912234 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
12912170 ATTTTGTTGG
12912180 ATTTATTTTTAGTATTGCTGAGAA
1 ATTTATTTTTA-T-TTGCTGAGAA
* *
12912204 ATTT-TTTTTATTTGTTGAGTA
1 ATTTATTTTTATTTGCTGAGAA
12912225 ATTTATTTTT
1 ATTTATTTTT
12912235 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 12 0.43
22 6 0.21
23 6 0.21
24 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.62
Consensus pattern (22 bp):
ATTTATTTTTATTTGCTGAGAA
Found at i:12914817 original size:36 final size:36
Alignment explanation
Indices: 12914777--12914852 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
12914767 CAATGTGTTT
12914777 AACACAATAATGAATATTAAAGGTAAAACCAAAGAC
1 AACACAATAATGAATATTAAAGGTAAAACCAAAGAC
* * *
12914813 AACACAATGATGGATATTAAAGGTAAAACCAAAGAT
1 AACACAATAATGAATATTAAAGGTAAAACCAAAGAC
12914849 AACA
1 AACA
12914853 TAAAGGCTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (36 bp):
AACACAATAATGAATATTAAAGGTAAAACCAAAGAC
Found at i:12916313 original size:62 final size:60
Alignment explanation
Indices: 12916122--12916403 Score: 435
Period size: 62 Copynumber: 4.7 Consensus size: 60
12916112 TCTTGTGTAG
* * *
12916122 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-TATTTTTTTGAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTTATTTTCAA
** * *
12916180 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAT-CCTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTTATTTTCAA
*
12916239 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTT-GAAATTTT-ATTTTCAA
12916301 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTT-GAAATTTT-ATTTTCAA
12916363 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
12916404 AAGGAGAATT
Statistics
Matches: 211, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
58 44 0.21
59 44 0.21
60 7 0.03
61 7 0.03
62 109 0.52
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTTATTTTCAA
Found at i:12916438 original size:28 final size:28
Alignment explanation
Indices: 12916398--12916485 Score: 176
Period size: 28 Copynumber: 3.1 Consensus size: 28
12916388 CCTAAAAATA
12916398 TTTTTTAAGGAGAATTGATACTTCCAAC
1 TTTTTTAAGGAGAATTGATACTTCCAAC
12916426 TTTTTTAAGGAGAATTGATACTTCCAAC
1 TTTTTTAAGGAGAATTGATACTTCCAAC
12916454 TTTTTTAAGGAGAATTGATACTTCCAAC
1 TTTTTTAAGGAGAATTGATACTTCCAAC
12916482 TTTT
1 TTTT
12916486 CCCTAAAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (28 bp):
TTTTTTAAGGAGAATTGATACTTCCAAC
Found at i:12916590 original size:343 final size:333
Alignment explanation
Indices: 12916126--12916740 Score: 889
Period size: 343 Copynumber: 1.8 Consensus size: 333
12916116 GTGTAGGGAA
* *
12916126 AATTGATACTTTCAACTTTTCCCCAAAAATTATTTTTTTGAAATTTATTTTTAAGGAAAATTGAT
1 AATTGATACTTCCAACTTTTCCCCAAAAATTATTTTTTGGAAATTTATTTTTAAGGAAAATTGAT
* * *
12916191 ACTTTCAACTTTTCCCTAAAAATCCTTTTTTTGAAAATTTATTTTTAAGAAAAATTGATACTTTC
66 ACTTTCAACTTTTCCCTAAAAAT-CATTTCTTGAAAATTTATTTTCAAGAAAAATTGATACTTTC
* *
12916256 AACTTTTCCCTAAAAATATTTTTTTTTGGAAA-TT-TTGAT-TTTCAAGGAAAATTGATACTTTC
130 AACTTTTCCCCAAAAATA---TTTTTTGAAAATTTATTGATCTTTCAAGGAAAATTGATACTTTC
*** *
12916318 AACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTCAAGGAAAATTGATACTTTCAAC
192 AACTTTT-CCTAAAAA-A-CCCTTTTT-GAAA-TTT-ATTTTCAAGAAAAATTGATACTTTCAAC
12916383 TTTTCCCTAAAAATATTTTTTAAGGAGAATTGATACTTCCAACTTTTTTAAGGAGAATTGATACT
251 TTTTCCCTAAAAATATTTTTTAAGGAGAATTGATACTTCCAACTTTTTTAAGGAGAATTGATACT
12916448 TCCAACTTTTTTAAGGAG
316 TCCAACTTTTTTAAGGAG
* *
12916466 AATTGATACTTCCAACTTTTCCCTAAAAA-TATTTTTTGGAATTTATTTTTCTTTTAAGGAAAAT
1 AATTGATACTTCCAACTTTTCCCCAAAAATTATTTTTTGGAA---ATTTAT-TTTTAAGGAAAAT
*
12916530 TGATACTTTCAACTTTTCCCTAAAAAT-ATTTCTTGAAAATTTTGATTTTCAAGGAAAATTGATA
62 TGATACTTTCAACTTTTCCCTAAAAATCATTTCTTGAAAA-TTT-ATTTTCAAGAAAAATTGATA
**
12916594 CTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTCTTTCAAGGAAAATTGATACTT
125 CTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTGATCTTTCAAGGAAAATTGATACTT
* *
12916659 TCAACTTTTCCTCAAAAACCCTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTT
190 TCAACTTTTCCTAAAAAACCCTTTTTGAAATTTATTTTCAAGAAAAATTGATACTTTCAACTTTT
12916724 CCCTAAAAATATTTTTT
255 CCCTAAAAATATTTTTT
12916741 TTGGAATTTT
Statistics
Matches: 248, Mismatches: 18, Indels: 21
0.86 0.06 0.07
Matches are distributed among these distances:
337 47 0.19
338 3 0.01
339 15 0.06
340 42 0.17
341 13 0.05
342 18 0.07
343 110 0.44
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (333 bp):
AATTGATACTTCCAACTTTTCCCCAAAAATTATTTTTTGGAAATTTATTTTTAAGGAAAATTGAT
ACTTTCAACTTTTCCCTAAAAATCATTTCTTGAAAATTTATTTTCAAGAAAAATTGATACTTTCA
ACTTTTCCCCAAAAATATTTTTTGAAAATTTATTGATCTTTCAAGGAAAATTGATACTTTCAACT
TTTCCTAAAAAACCCTTTTTGAAATTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCCTAA
AAATATTTTTTAAGGAGAATTGATACTTCCAACTTTTTTAAGGAGAATTGATACTTCCAACTTTT
TTAAGGAG
Found at i:12916742 original size:121 final size:120
Alignment explanation
Indices: 12916455--12916740 Score: 429
Period size: 120 Copynumber: 2.4 Consensus size: 120
12916445 ACTTCCAACT
* * *
12916455 TTTTTAAGGAGAATTGATACTTCCAACTTTTCCCTAAAAATATTTTTTGGAATTTATTTTTCTTT
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAATTTATTTTTCTTT
* *
12916520 TAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTCTTGAAAATTTTGA
66 CAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAACATTTCTTGAAAATTTTGA
* *
12916575 TTTTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTCTT
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTG-AAATTTATTTTTCTT
*
12916640 TCAAGGAAAATTGATACTTTCAACTTTT-CCTCAAAAACCCTTT-TTG-AAA-TTT-A
65 TCAAGGAAAATTGATACTTTCAACTTTTCCCT-AAAAA-CATTTCTTGAAAATTTTGA
*
12916693 TTTTTAAGAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
12916741 TTGGAATTTT
Statistics
Matches: 152, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
118 46 0.30
119 3 0.02
120 51 0.34
121 49 0.32
122 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (120 bp):
TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAATTTATTTTTCTTT
CAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAACATTTCTTGAAAATTTTGA
Found at i:12916754 original size:61 final size:59
Alignment explanation
Indices: 12916455--12916759 Score: 359
Period size: 61 Copynumber: 5.1 Consensus size: 59
12916445 ACTTCCAACT
* * *
12916455 TTTTTAAGGAGAATTGATACTTCCAACTTTTCCCTAAAAATATTTTTTGGAATTTATTTT
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAATTT-TTTA
* * * *
12916515 TCTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTCTTGAAAATTTTGA
1 T-TTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAATTTTTTA
* * *
12916575 TTTTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTT-
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTG-GAATTT-TTTA
*** *
12916635 TTCTTTCAAGGAAAATTGATACTTTCAACTTTT-CCTCAAAAACCCTTTTT-GAA--ATTTA
1 TT-TTT-AAGGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTGGAATTTTTTA
*
12916693 TTTTTAAGAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAATTTTTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAATTTTTTA
12916754 TTTTTA
1 TTTTTA
12916760 TTTAAAGAAA
Statistics
Matches: 208, Mismatches: 24, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
56 30 0.14
57 9 0.04
58 7 0.03
59 48 0.23
60 13 0.06
61 65 0.31
62 36 0.17
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.47
Consensus pattern (59 bp):
TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAATTTTTTA
Found at i:12916782 original size:8 final size:8
Alignment explanation
Indices: 12916769--12916847 Score: 60
Period size: 8 Copynumber: 10.2 Consensus size: 8
12916759 ATTTAAAGAA
12916769 AATAAAAT
1 AATAAAAT
12916777 AATAAAA-
1 AATAAAAT
*
12916784 AA-AATAAA
1 AATAA-AAT
12916792 AATAAAAT
1 AATAAAAT
*
12916800 AAAAAAAT
1 AATAAAAT
12916808 AA-AGAAA-
1 AATA-AAAT
* *
12916815 AGTAAAAA
1 AATAAAAT
*
12916823 AATAAAAA
1 AATAAAAT
12916831 AATAAAA-
1 AATAAAAT
12916838 AATAAAAT
1 AATAAAAT
12916846 AA
1 AA
12916848 AGATAAAAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
6 2 0.03
7 16 0.27
8 40 0.67
9 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (8 bp):
AATAAAAT
Found at i:12916795 original size:18 final size:17
Alignment explanation
Indices: 12916762--12916861 Score: 89
Period size: 18 Copynumber: 5.6 Consensus size: 17
12916752 TATTTTTATT
*
12916762 TAAAGAAAAT-AAAATAA
1 TAAA-AAAATAAAAAAAA
12916779 TAAAAAAAATAAAAATAAAA
1 T-AAAAAAAT-AAAA-AAAA
*
12916799 TAAAAAAATAAAGAAAAG
1 TAAAAAAATAAA-AAAAA
12916817 TAAAAAAAT-AAAAAAA
1 TAAAAAAATAAAAAAAA
12916833 T-AAAAAATAAAATAAAGA
1 TAAAAAAATAAAA-AAA-A
12916851 TAAAAAGAATA
1 TAAAAA-AATA
12916862 TTAAATAAAC
Statistics
Matches: 70, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
15 7 0.10
16 8 0.11
17 11 0.16
18 20 0.29
19 16 0.23
20 8 0.11
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (17 bp):
TAAAAAAATAAAAAAAA
Found at i:12916812 original size:45 final size:46
Alignment explanation
Indices: 12916762--12916848 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
12916752 TATTTTTATT
*
12916762 TAAAGAAAA-TAAAATAATAAAAAAA-ATAAAAATAAAATAAAAAAA
1 TAAAGAAAAGTAAAAAAATAAAAAAATA-AAAAATAAAATAAAAAAA
12916807 TAAAGAAAAGTAAAAAAATAAAAAAATAAAAAATAAAATAAA
1 TAAAGAAAAGTAAAAAAATAAAAAAATAAAAAATAAAATAAA
12916849 GATAAAAAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 9 0.23
46 29 0.74
47 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (46 bp):
TAAAGAAAAGTAAAAAAATAAAAAAATAAAAAATAAAATAAAAAAA
Found at i:12916855 original size:23 final size:22
Alignment explanation
Indices: 12916767--12916848 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 22
12916757 TTATTTAAAG
12916767 AAAATAAAATAATAAAAAAAATA
1 AAAATAAAATAA-AAAAAAAATA
*
12916790 AAAATAAAATAAAAAAATAAAGA
1 AAAATAAAATAAAAAAA-AAATA
*
12916813 AAAGTAAAA-AAATAAAAAAATAA
1 AAAATAAAATAAA-AAAAAAAT-A
12916836 AAAATAAAATAAA
1 AAAATAAAATAAA
12916849 GATAAAAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
22 11 0.22
23 37 0.73
24 3 0.06
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (22 bp):
AAAATAAAATAAAAAAAAAATA
Found at i:12916870 original size:34 final size:33
Alignment explanation
Indices: 12916762--12916861 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
12916752 TATTTTTATT
*
12916762 TAAAGAAAATAAAATAATAAA-AAAA--ATAAAAA
1 TAAA-AAAATAAAA-AATAAAGAAAAGTAAAAAAA
*
12916794 T-AAAATA-AAAAAATAAAGAAAAGTAAAAAAA
1 TAAAAAAATAAAAAATAAAGAAAAGTAAAAAAA
12916825 TAAAAAAATAAAAAATAAA-ATAAAGATAAAAAGAA
1 TAAAAAAATAAAAAATAAAGA-AAAG-TAAAAA-AA
12916860 TA
1 TA
12916862 TTAAATAAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
28 6 0.11
29 8 0.14
30 3 0.05
31 9 0.16
32 7 0.12
33 14 0.25
34 6 0.11
35 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (33 bp):
TAAAAAAATAAAAAATAAAGAAAAGTAAAAAAA
Found at i:12917889 original size:16 final size:16
Alignment explanation
Indices: 12917862--12917912 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
12917852 AAATATTATA
12917862 ATATAA-TA-ATAAAT
1 ATATAACTATATAAAT
12917876 ATATAACTATATAAAT
1 ATATAACTATATAAAT
* *
12917892 ATATTAC-ATATAGAT
1 ATATAACTATATAAAT
12917907 AT-TAAC
1 ATATAAC
12917913 AGAGAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 9 0.28
15 11 0.34
16 12 0.38
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (16 bp):
ATATAACTATATAAAT
Found at i:12918204 original size:1 final size:1
Alignment explanation
Indices: 12918198--12918245 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
12918188 AACATTGTCA
* * * * *
12918198 TTTTTTTATTTTTTTTTTGTGTTTTTTTTGTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12918246 GACCAATGCT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:12918223 original size:22 final size:22
Alignment explanation
Indices: 12918198--12918245 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
12918188 AACATTGTCA
12918198 TTTTTTTATTTTTTTTTTGTGT
1 TTTTTTTATTTTTTTTTTGTGT
* *
12918220 TTTTTTTGTTTTTTTTTTTTGT
1 TTTTTTTATTTTTTTTTTGTGT
12918242 TTTT
1 TTTT
12918246 GACCAATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.02, C:0.00, G:0.08, T:0.90
Consensus pattern (22 bp):
TTTTTTTATTTTTTTTTTGTGT
Found at i:12918245 original size:11 final size:11
Alignment explanation
Indices: 12918198--12918237 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
12918188 AACATTGTCA
*
12918198 TTTTTTTATTT
1 TTTTTTTGTTT
*
12918209 TTTTTTTGTGT
1 TTTTTTTGTTT
12918220 TTTTTTTGTTT
1 TTTTTTTGTTT
12918231 TTTTTTT
1 TTTTTTT
12918238 TTGTTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:12918346 original size:41 final size:40
Alignment explanation
Indices: 12918252--12918628 Score: 549
Period size: 41 Copynumber: 9.2 Consensus size: 40
12918242 TTTTGACCAA
* *
12918252 TGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAAGTAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-TAAAT
*
12918294 TGCTCCTCTAAACAGAGGCACCATGACTTTTGAAAATAAAT
1 TGCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAATAAAT
*
12918335 TGCTCCTCTAAACAGAGGCCCCACGACTTTGAAAAATAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAATAAAT
*
12918376 TGCTCCTCTAAAGAGAGGCACCACGACTTTGAAAATAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAATAAAT
12918416 TGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAATAAAT
1 TGCTCCTCTAAACAGAGGCACCACGAC-TTTG-AAAATAAAT
*
12918458 TGCTTCTCTAAACAGAGGCACCACGACTTTGAAAAATAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAATAAAT
12918499 TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAA-TAAAT
* *
12918541 TGCTCCTCTAAACAGAGGCACCACAACTTTAAAAAGTAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA-TAAAT
* * *
12918582 TGCTCCTCTAAATAGAGGCAACA-GACTTTGGAAAGTAAAT
1 TGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAATAAAT
12918622 TGCTCCT
1 TGCTCCT
12918629 TGACAATCAT
Statistics
Matches: 312, Mismatches: 17, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
40 56 0.18
41 155 0.50
42 96 0.31
43 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (40 bp):
TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAATAAAT
Found at i:12918347 original size:83 final size:81
Alignment explanation
Indices: 12918252--12918628 Score: 576
Period size: 83 Copynumber: 4.6 Consensus size: 81
12918242 TTTTGACCAA
* *
12918252 TGCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 TGCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGGCACCA
*
12918317 TGACTTTTGAAAATAAAT
65 CGAC-TTTGAAAATAAAT
* * *
12918335 TGCTCCTCTAAACAGAGGCCCCACGACTTTGAAAAATAAATTGCTCCTCTAAAGAGAGGCACCAC
1 TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
12918400 GACTTTGAAAATAAAT
66 GACTTTGAAAATAAAT
* *
12918416 TGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAATAAATTGCTTCTCTAAACAGAGGCACCA
1 TGCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
12918481 CGACTTTGAAAAATAAAT
65 CGACTTTG-AAAATAAAT
12918499 TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 TGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
* *
12918564 CAACTTTAAAAAGTAAAT
65 CGACTTTGAAAA-TAAAT
* * *
12918582 TGCTCCTCTAAATAGAGGCAACA-GACTTTGGAAAGTAAATTGCTCCT
1 TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCT
12918629 TGACAATCAT
Statistics
Matches: 275, Mismatches: 15, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
81 55 0.20
82 91 0.33
83 129 0.47
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (81 bp):
TGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
GACTTTGAAAATAAAT
Found at i:12919838 original size:24 final size:25
Alignment explanation
Indices: 12919802--12919890 Score: 109
Period size: 24 Copynumber: 3.7 Consensus size: 25
12919792 TTTGAATCTC
12919802 TTTTTTCATTTTTTTCATTTTTTCA
1 TTTTTTCATTTTTTTCATTTTTTCA
12919827 TTTTTTCA-TTTTTTCATTTTTTCA
1 TTTTTTCATTTTTTTCATTTTTTCA
*
12919851 TTTTTTCTTCTTTCTTTC-TTTTTT--
1 TTTTTTCAT-TTT-TTTCATTTTTTCA
12919875 TTTTTT--TTTTTTTCAT
1 TTTTTTCATTTTTTTCAT
12919891 CATCTTCTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
20 4 0.07
21 4 0.07
22 1 0.02
24 29 0.49
25 8 0.14
26 9 0.15
27 4 0.07
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTTTCATTTTTTTCATTTTTTCA
Found at i:12919871 original size:8 final size:8
Alignment explanation
Indices: 12919802--12919857 Score: 103
Period size: 8 Copynumber: 6.9 Consensus size: 8
12919792 TTTGAATCTC
12919802 TTTTTTCA
1 TTTTTTCA
12919810 TTTTTTTCA
1 -TTTTTTCA
12919819 TTTTTTCA
1 TTTTTTCA
12919827 TTTTTTCA
1 TTTTTTCA
12919835 TTTTTTCA
1 TTTTTTCA
12919843 TTTTTTCA
1 TTTTTTCA
12919851 TTTTTTC
1 TTTTTTC
12919858 TTCTTTCTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
8 39 0.83
9 8 0.17
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:12919903 original size:18 final size:18
Alignment explanation
Indices: 12919880--12919915 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
12919870 TTTTTTTTTT
12919880 TTTTTTTTCATCA-TCTTC
1 TTTTTTTTC-TCATTCTTC
12919898 TTTTTTTTCTCATTCTTC
1 TTTTTTTTCTCATTCTTC
12919916 ACCTATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTTTCTCATTCTTC
Found at i:12925938 original size:61 final size:60
Alignment explanation
Indices: 12925796--12926095 Score: 387
Period size: 61 Copynumber: 5.0 Consensus size: 60
12925786 TCTTGTGTAG
*
12925796 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-TATTTTTTT-GAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTTGGAAATTTTATTTTTAA
*
12925854 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTT-ATTTTTAA
** *
12925915 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATCCTTTTTTT-GAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTATTTTTAA
* * * * *
12925974 GGAGAATTGATACTTCCAACTTTTTCCTAAAAATA--TTTTTTGTAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAA--T-TTTAT-TTTTAA
* *
12926036 AGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAATTTTTTATTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAA-ATTTTATTTTTA
12926096 TTTAAAGAAA
Statistics
Matches: 210, Mismatches: 20, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
57 6 0.03
58 43 0.20
59 43 0.20
60 10 0.05
61 57 0.27
62 41 0.20
63 1 0.00
64 9 0.04
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTATTTTTAA
Found at i:12926003 original size:120 final size:120
Alignment explanation
Indices: 12925796--12926085 Score: 406
Period size: 120 Copynumber: 2.4 Consensus size: 120
12925786 TCTTGTGTAG
* *
12925796 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTATTTTTTTGAAATTTATTTTTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTTGAAATTTATTTTTAAGGAAAAT
*
12925861 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAA-TT-TTGAT-TTTCAA
66 TGATACTTCCAACTTTTCCCTAAAAATA--TTTTTTGGAAATTTATTGATCTTTCAA
** *
12925915 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATCCTTTTTTTGAAAATTTATTTTTAAGGAGAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTTG-AAATTTATTTTTAAGGAAAA
* * ** *
12925980 TTGATACTTCCAACTTTTTCCTAAAAATATTTTTTGTAAATTTATTTTTCTTTTAA
65 TTGATACTTCCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTGATCTTTCAA
* * *
12926036 AGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAATTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTTGAAATTT
12926086 TTTATTTTTA
Statistics
Matches: 153, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
118 10 0.07
119 43 0.28
120 54 0.35
121 46 0.30
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (120 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTTGAAATTTATTTTTAAGGAAAAT
TGATACTTCCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTGATCTTTCAA
Found at i:12926128 original size:10 final size:10
Alignment explanation
Indices: 12926113--12926183 Score: 69
Period size: 10 Copynumber: 7.2 Consensus size: 10
12926103 AAAATAGAAT
12926113 AATAAAAATA
1 AATAAAAATA
12926123 AATAAAAATAA
1 AATAAAAAT-A
12926134 AATAAAAA-A
1 AATAAAAATA
12926143 AATAAAAA-A
1 AATAAAAATA
*
12926152 AGT-AAAA-A
1 AATAAAAATA
12926160 AATAAAAAATAA
1 AAT-AAAAAT-A
*
12926172 AATAAAGATA
1 AATAAAAATA
12926182 AA
1 AA
12926184 AAGAATATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
8 7 0.13
9 12 0.23
10 16 0.30
11 14 0.26
12 4 0.08
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (10 bp):
AATAAAAATA
Done.