Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014980.1 Kokia drynarioides strain JFW-HI SEQ_130024, 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: 191948
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:1332 original size:11 final size:11
Alignment explanation
Indices: 1318--1352 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1308 GAAAATAATT
*
1318 TTAAACTTAAA
1 TTAAATTTAAA
1329 TTAAATTTAAA
1 TTAAATTTAAA
*
1340 ATAAATTTAAA
1 TTAAATTTAAA
1351 TT
1 TT
1353 TTTAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:1335 original size:18 final size:18
Alignment explanation
Indices: 1293--1359 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 18
1283 TTTGTTTATT
*
1293 TTAAATTTTAAATTTGAAA
1 TTAAATTTTAAACTT-AAA
*
1312 AT-AATTTTAAACTTAAA
1 TTAAATTTTAAACTTAAA
*
1329 TTAAA-TTTAAA-ATAAA
1 TTAAATTTTAAACTTAAA
1345 TTTAAATTTTTAAAC
1 -TTAAA-TTTTAAAC
1360 AAATTTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 4 0.10
17 15 0.38
18 13 0.33
19 7 0.18
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (18 bp):
TTAAATTTTAAACTTAAA
Found at i:1339 original size:17 final size:16
Alignment explanation
Indices: 1293--1384 Score: 57
Period size: 17 Copynumber: 5.7 Consensus size: 16
1283 TTTGTTTATT
1293 TTAAATTTTAAATTTGAAA
1 TTAAA-TTTAAA-TT-AAA
* *
1312 ATAATTTTAAACTTAAA
1 TTAAATTTAAA-TTAAA
*
1329 TTAAATTTAAAATAAA
1 TTAAATTTAAATTAAA
1345 TTTAAATTT---TTAAA
1 -TTAAATTTAAATTAAA
* *
1359 -CAAATTTAATTTAAA
1 TTAAATTTAAATTAAA
*
1374 ATAAATTTAAA
1 TTAAATTTAAA
1385 GGGAGTATGG
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
12 6 0.10
14 4 0.07
15 5 0.09
16 12 0.21
17 20 0.34
18 8 0.14
19 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:1370 original size:34 final size:35
Alignment explanation
Indices: 1316--1384 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 35
1306 TTGAAAATAA
1316 TTTTAAACTTAAATTAAATTTAAAATAAATTTAAAT
1 TTTTAAAC-TAAATTAAATTTAAAATAAATTTAAAT
*
1352 TTTTAAAC-AAATTTAATTTAAAATAAATTTAAA
1 TTTTAAACTAAATTAAATTTAAAATAAATTTAAA
1385 GGGAGTATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 24 0.75
36 8 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (35 bp):
TTTTAAACTAAATTAAATTTAAAATAAATTTAAAT
Found at i:3643 original size:12 final size:12
Alignment explanation
Indices: 3628--3672 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
3618 ATGTTCAATT
3628 ACATGTTCGTGA
1 ACATGTTCGTGA
**
3640 ACATGTTCGTTT
1 ACATGTTCGTGA
3652 A-ATGTTCGTGA
1 ACATGTTCGTGA
3663 ACATGTTCGT
1 ACATGTTCGT
3673 TTAAGTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (12 bp):
ACATGTTCGTGA
Found at i:3660 original size:23 final size:23
Alignment explanation
Indices: 3605--3695 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 23
3595 TCATTAACTT
**
3605 TGTTCGTGAGTACATGTTCAATTACA
1 TGTTCGTGA--ACATGTTCGTTTA-A
3631 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGTTTAA
3654 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGTTTAA
**
3677 -GTTAAATGAACATGTTCGT
1 TGTT-CGTGAACATGTTCGT
3696 GAACATTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
22 3 0.05
23 37 0.62
24 11 0.18
26 9 0.15
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGTTTAA
Found at i:3704 original size:23 final size:23
Alignment explanation
Indices: 3660--3711 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3650 TTAATGTTCG
* *
3660 TGAACATGTTCGTTTAAGTTAAA
1 TGAACATGTTCGTTGAAATTAAA
3683 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGTTGAA-ATTAAA
*
3706 TAAACA
1 TGAACA
3712 AACATGAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGTTGAAATTAAA
Found at i:6026 original size:19 final size:19
Alignment explanation
Indices: 5994--6044 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
5984 AGTATTATAT
*
5994 AAAAAAT-TTTAATAAGTA
1 AAAAAATATTAAATAAGTA
*
6012 AAAAAATATTAAAT-ATTA
1 AAAAAATATTAAATAAGTA
6030 AATAAAATA-TAAATA
1 AA-AAAATATTAAATA
6045 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAAATATTAAATAAGTA
Found at i:6031 original size:18 final size:18
Alignment explanation
Indices: 6010--6045 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
6000 TTTTAATAAG
6010 TAAA-AAAATATTAAATAT
1 TAAATAAAATA-TAAATAT
6028 TAAATAAAATATAAATAT
1 TAAATAAAATATAAATAT
6046 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATAAAATATAAATAT
Found at i:7014 original size:29 final size:30
Alignment explanation
Indices: 6975--7031 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
6965 AATAATATTA
*
6975 AAAAATTAATTAATTATAAAAAT-GATAAG
1 AAAAATAAATTAATTATAAAAATAGATAAG
*
7004 AAAAATAAATTAATTATGAAAATAGATA
1 AAAAATAAATTAATTATAAAAATAGATA
7032 TTTATTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (30 bp):
AAAAATAAATTAATTATAAAAATAGATAAG
Found at i:7475 original size:20 final size:19
Alignment explanation
Indices: 7438--7475 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
7428 ATTTGAAAAC
7438 TATATATTTAACTAATAAT
1 TATATATTTAACTAATAAT
7457 TATA-ATTTATACATAATAA
1 TATATATTTA-AC-TAATAA
7476 GATTTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATATTTAACTAATAAT
Found at i:7780 original size:10 final size:9
Alignment explanation
Indices: 7726--7779 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
7716 ATTTTATATG
7726 TTATAAAGAA
1 TTATAAA-AA
7736 TT-TAAAAA
1 TTATAAAAA
*
7744 TTGTAAAAA
1 TTATAAAAA
*
7753 -TATATAAAT
1 TTATA-AAAA
7762 TTATAAAAA
1 TTATAAAAA
7771 TTATAAAAA
1 TTATAAAAA
7780 AAAGTTTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.18
9 25 0.66
10 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:9051 original size:13 final size:13
Alignment explanation
Indices: 9033--9064 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9023 AAACATTAAC
9033 AAGGAAGCAATGT
1 AAGGAAGCAATGT
*
9046 AAGGAAGCAATTT
1 AAGGAAGCAATGT
9059 AAGGAA
1 AAGGAA
9065 TCAAATGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.28, T:0.16
Consensus pattern (13 bp):
AAGGAAGCAATGT
Found at i:9284 original size:9 final size:9
Alignment explanation
Indices: 9270--9402 Score: 78
Period size: 9 Copynumber: 14.2 Consensus size: 9
9260 ATGAGTTACG
9270 ATAATTTTT
1 ATAATTTTT
9279 ATAATTTTTTT
1 ATAA--TTTTT
9290 ATGAA-TTTT
1 AT-AATTTTT
9299 AT-ATTTTT
1 ATAATTTTT
*
9307 ATATTTTTT
1 ATAATTTTT
9316 ATAATTTTT
1 ATAATTTTT
*
9325 -TTATGATTTT
1 ATAAT--TTTT
*
9335 ATAAAATTTT
1 AT-AATTTTT
9345 ATAATTTTTT
1 ATAA-TTTTT
*
9355 CTATATTTTT
1 ATA-ATTTTT
*
9365 CT-ATATTTT
1 ATAAT-TTTT
9374 AT-ATTTTT
1 ATAATTTTT
*
9382 CTAATTTTT
1 ATAATTTTT
*
9391 AAATATTTTT
1 ATA-ATTTTT
9401 AT
1 AT
9403 TAAAGTTAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 27
0.72 0.09 0.20
Matches are distributed among these distances:
7 1 0.01
8 16 0.16
9 39 0.40
10 30 0.31
11 9 0.09
12 3 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
ATAATTTTT
Found at i:9321 original size:37 final size:36
Alignment explanation
Indices: 9274--9402 Score: 145
Period size: 37 Copynumber: 3.5 Consensus size: 36
9264 GTTACGATAA
9274 TTTTTATAATTTTTTTATGAATTTTATATTTTTATAT
1 TTTTTATAATTTTTTTATG-ATTTTATATTTTTATAT
*
9311 TTTTTATAATTTTTTTATGATTTTATAAAATTTTATAAT
1 TTTTTATAATTTTTTTATGATTTTAT--ATTTTTAT-AT
* * * *
9350 TTTTTCTATATTTTTCTAT-ATTTTATATTTTTCTAA
1 TTTTTATA-ATTTTTTTATGATTTTATATTTTTATAT
*
9386 TTTTTA-AATATTTTTAT
1 TTTTTATAATTTTTTTAT
9403 TAAAGTTAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
34 8 0.10
35 1 0.01
36 13 0.16
37 25 0.32
38 7 0.09
39 16 0.20
40 9 0.11
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (36 bp):
TTTTTATAATTTTTTTATGATTTTATATTTTTATAT
Found at i:9354 original size:10 final size:10
Alignment explanation
Indices: 9270--9373 Score: 64
Period size: 10 Copynumber: 10.8 Consensus size: 10
9260 ATGAGTTACG
9270 ATAA-TTTTT
1 ATAATTTTTT
9279 ATAATTTTTTT
1 ATAA-TTTTTT
9290 ATGAA--TTTT
1 AT-AATTTTTT
9299 AT-A-TTTTT
1 ATAATTTTTT
9307 AT-ATTTTTT
1 ATAATTTTTT
9316 ATAATTTTTT
1 ATAATTTTTT
*
9326 -T-ATGATTTT
1 ATAAT-TTTTT
**
9335 ATAAAATTTT
1 ATAATTTTTT
9345 ATAATTTTTT
1 ATAATTTTTT
*
9355 CTATATTTTTCT
1 ATA-ATTTTT-T
9367 AT-ATTTT
1 ATAATTTT
9374 ATATTTTTCT
Statistics
Matches: 78, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
7 1 0.01
8 9 0.12
9 22 0.28
10 28 0.36
11 14 0.18
12 4 0.05
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:9401 original size:66 final size:66
Alignment explanation
Indices: 9275--9418 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 66
9265 TTACGATAAT
**
9275 TTTTATAATTTTTTTATGAATTTTATATTTTTATATTTTTTATAATTTTTTTATGATTTTATAAA
1 TTTTATAATTTTTTTATGAATTTTATATTTTTATATTTTTTATAATTTTTAAATGATTTTATAAA
9340 A
66 A
* * *
9341 TTTTATAATTTTTTCTAT-ATTTTTCTATATTTTATA-TTTTTCTAATTTTTAAAT-ATTTTTAT
1 TTTTATAATTTTTT-TATGAATTTTATAT-TTTTATATTTTTTATAATTTTTAAATGA-TTTTAT
*
9403 TAAA
63 AAAA
* *
9407 GTTAATAATTTT
1 TTTTATAATTTT
9419 ATAACATTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
65 1 0.01
66 56 0.84
67 10 0.15
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (66 bp):
TTTTATAATTTTTTTATGAATTTTATATTTTTATATTTTTTATAATTTTTAAATGATTTTATAAA
A
Found at i:10930 original size:17 final size:19
Alignment explanation
Indices: 10898--10932 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
10888 AATTTTATTC
10898 TTCTCTTCTCTCTTCTTTA
1 TTCTCTTCTCTCTTCTTTA
10917 TTCT-TTCTCT-TTCTTT
1 TTCTCTTCTCTCTTCTTT
10933 TTCAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (19 bp):
TTCTCTTCTCTCTTCTTTA
Found at i:17663 original size:60 final size:60
Alignment explanation
Indices: 17564--17725 Score: 217
Period size: 59 Copynumber: 2.7 Consensus size: 60
17554 TCTTTATCAC
*
17564 TTAGGTACCAAA-TAGGAAAAAA-TGGT-AAGTTCAGGTACCAAATTTGG-TCCAAAAAAAGT
1 TTAGGTACCAAATTA-GAAAAAAGT-GTCAAGTTCAGGTACCAAATTTGGAT-AAAAAAAAGT
* *
17623 TTAGGTACTAAATTAGAAAAAAGTGTCAAGTTCAGATACCAAA-TTGGATAAAAAAAAGT
1 TTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTTGGATAAAAAAAAGT
* *
17682 TTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTAGGTACCAAAT
1 TTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAAT
17726 GTTATATTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
59 72 0.79
60 19 0.21
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.25
Consensus pattern (60 bp):
TTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTTGGATAAAAAAAAGT
Found at i:17667 original size:31 final size:31
Alignment explanation
Indices: 17619--17725 Score: 123
Period size: 31 Copynumber: 3.5 Consensus size: 31
17609 GGTCCAAAAA
*
17619 AAGTTTAGGTACTAAATTAGAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAAGTGTC
* * * *
17650 AAGTTCAGATACCAAATTGGATAAAAA----A
1 AAGTTTAGGTACCAAATTAGA-AAAAAGTGTC
*
17678 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAAGTGTC
17709 AAGTTTAGGTACCAAAT
1 AAGTTTAGGTACCAAAT
17726 GTTATATTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
27 5 0.08
28 17 0.28
31 34 0.56
32 5 0.08
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAGAAAAAAGTGTC
Found at i:18322 original size:35 final size:34
Alignment explanation
Indices: 18276--18346 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 34
18266 CATTTTTTTA
* * * *
18276 AAATTTATTTTAAGGTTAAATTTATTTTAAGTTT
1 AAATTTATTTTAAAGTTAAAATTATTCTAAATTT
*
18310 AAATTTATTTTTAAATTTAAAATTATTCTAAATTT
1 AAATTTA-TTTTAAAGTTAAAATTATTCTAAATTT
18345 AA
1 AA
18347 TTAATAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
34 7 0.23
35 24 0.77
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (34 bp):
AAATTTATTTTAAAGTTAAAATTATTCTAAATTT
Found at i:18323 original size:18 final size:17
Alignment explanation
Indices: 18276--18346 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
18266 CATTTTTTTA
*
18276 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAGTTT
18293 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAGTTT
*
18310 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAGTTT
* * *
18328 AAAATTATTCTAAATTT
1 AAATTTATTTTAAGTTT
18345 AA
1 AA
18347 TTAATAATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 34 0.69
18 15 0.31
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAGTTT
Found at i:20126 original size:30 final size:29
Alignment explanation
Indices: 20087--20240 Score: 111
Period size: 30 Copynumber: 5.2 Consensus size: 29
20077 CCCTGAATTG
20087 TCCATAAATCATATTTTAACCCTTAAACTTT
1 TCCA-AAATCATATTTTAACCCTTAAAC-TT
*
20118 TCCAAAATCATATTTTAAACCTTAAACTT
1 TCCAAAATCATATTTTAACCCTTAAACTT
* **
20147 TCCTAAAATC-TCATTTTAACTCTCGAAC-T
1 TCC-AAAATCAT-ATTTTAACCCTTAAACTT
* * *
20176 TCTCAAAATTTATATTTT-GCCC-CAAACTT
1 TC-CAAAA-TCATATTTTAACCCTTAAACTT
* * * *
20205 CTCAAAAATCATATTTTGATCGTTAAAC-T
1 -TCCAAAATCATATTTTAACCCTTAAACTT
20234 TCCAAAA
1 TCCAAAA
20241 ATTACATTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 21
0.73 0.12 0.16
Matches are distributed among these distances:
28 18 0.18
29 22 0.22
30 53 0.54
31 5 0.05
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
TCCAAAATCATATTTTAACCCTTAAACTT
Found at i:20293 original size:88 final size:88
Alignment explanation
Indices: 20111--20279 Score: 209
Period size: 88 Copynumber: 1.9 Consensus size: 88
20101 TTTAACCCTT
* * * *
20111 AAACTTTTCCAAAATCATATTTTAAACCTTAAACTTTCCTAAAATCTCATTTTAACTCTCGAACT
1 AAACTTCTCAAAAATCATATTTTAAACCTTAAACTTTCCAAAAATCTCATTTTAACCCTCGAACT
* *
20176 TCTCAAAATTTATATTTTGCCCC
66 TCTCAAAAATAATATTTTGCCCC
* * * *
20199 AAACTTCTCAAAAATCATATTTTGATCGTTAAAC-TTCCAAAAAT-TACATTTT-CCCCTCGAAC
1 AAACTTCTCAAAAATCATATTTTAAACCTTAAACTTTCCAAAAATCT-CATTTTAACCCTCGAAC
*
20261 TTCTGAAAAATAATATTTT
65 TTCTCAAAAATAATATTTT
20280 TTCTCTCGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 25 0.36
87 15 0.22
88 29 0.42
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (88 bp):
AAACTTCTCAAAAATCATATTTTAAACCTTAAACTTTCCAAAAATCTCATTTTAACCCTCGAACT
TCTCAAAAATAATATTTTGCCCC
Found at i:20368 original size:59 final size:58
Alignment explanation
Indices: 20158--20427 Score: 215
Period size: 58 Copynumber: 4.6 Consensus size: 58
20148 CCTAAAATCT
* * * * * *
20158 CATTTTAACTCTCGAACTTCTCAAAATTTATA-TTTTGCCCCAAACTTCTCAAAAATCA
1 CATTTTTACTCTCGAACTTC-CAAAAATTACATTTTTACCCCAAATTTCTCAAAAATAA
* * ** * * * *
20216 TATTTTGA-TCGTTAAACTTCCAAAAATTACA-TTTTCCCCTCGAACTTCTGAAAAATAA
1 CATTTTTACTC-TCGAACTTCCAAAAATTACATTTTTACCC-CAAATTTCTCAAAAATAA
* * *
20274 TATTTTTTCTCTCGAACTTCCAAAAATTACATTTTTACCCCCTAAATTTCTCAAAAATTA
1 CATTTTTACTCTCGAACTTCCAAAAATTACATTTTTA-CCCC-AAATTTCTCAAAAATAA
* * ** * * *
20334 CATTTTTAC-CTCGAATTTCCAAAATTTATGTTTTTACCCCAAATTTTTCGAAAATGA
1 CATTTTTACTCTCGAACTTCCAAAAATTACATTTTTACCCCAAATTTCTCAAAAATAA
**
20391 CATTTTTACTCCTAAAACTTTCCAAAAATTACATTTT
1 CATTTTTACT-CTCGAAC-TTCCAAAAATTACATTTT
20428 AACCGTAAAC
Statistics
Matches: 169, Mismatches: 34, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
57 41 0.24
58 56 0.33
59 34 0.20
60 38 0.22
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (58 bp):
CATTTTTACTCTCGAACTTCCAAAAATTACATTTTTACCCCAAATTTCTCAAAAATAA
Found at i:20378 original size:28 final size:28
Alignment explanation
Indices: 20291--20427 Score: 130
Period size: 31 Copynumber: 4.6 Consensus size: 28
20281 TCTCTCGAAC
20291 TTCCAAAAATTACATTTTTACCCCCTAAAT
1 TTCCAAAAATTACATTTTTA-CCCC-AAAT
* *
20321 TTCTCAAAAATTACATTTTTACCTCGAAT
1 TTC-CAAAAATTACATTTTTACCCCAAAT
* **
20350 TTCCAAAATTTATGTTTTTACCCCAAATT
1 TTCCAAAAATTACATTTTTACCCCAAA-T
* * * *
20379 TTTCGAAAATGACATTTTTACTCCTAAAACT
1 TTCCAAAAATTACATTTTTAC-CC-CAAA-T
20410 TTCCAAAAATTACATTTT
1 TTCCAAAAATTACATTTT
20428 AACCGTAAAC
Statistics
Matches: 85, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
28 19 0.22
29 22 0.26
30 8 0.09
31 36 0.42
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (28 bp):
TTCCAAAAATTACATTTTTACCCCAAAT
Found at i:20456 original size:88 final size:87
Alignment explanation
Indices: 20296--20456 Score: 186
Period size: 88 Copynumber: 1.8 Consensus size: 87
20286 CGAACTTCCA
* * * *
20296 AAAATTACATTTTTACCCCCTAAATTTCTCAAAAATTACATTTTTACCTCGAATTTCCAAAATTT
1 AAAATGACATTTTTACCCCCTAAATTTCTCAAAAATTACATTTTAACCTCAAATCTCCAAAATTT
20361 ATGTTTTTACCCCAAATTTTTCG
66 A-GTTTTTACCCCAAATTTTTCG
*
20384 AAAATGACATTTTTA-CTCCTAAAACTTTC-CAAAAATTACATTTTAACCGT-AAACTCTCCGAA
1 AAAATGACATTTTTACCCCCT-AAA-TTTCTCAAAAATTACATTTTAACC-TCAAA-TCTCC-AA
*
20446 ACTTTA-TTTTT
61 AATTTAGTTTTT
20457 GACACTGTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
87 4 0.06
88 42 0.68
89 9 0.15
90 7 0.11
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (87 bp):
AAAATGACATTTTTACCCCCTAAATTTCTCAAAAATTACATTTTAACCTCAAATCTCCAAAATTT
AGTTTTTACCCCAAATTTTTCG
Found at i:27703 original size:16 final size:16
Alignment explanation
Indices: 27682--27713 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27672 AATCTTTTTG
27682 TAAAAGGGCCCATGGT
1 TAAAAGGGCCCATGGT
27698 TAAAAGGGCCCATGGT
1 TAAAAGGGCCCATGGT
27714 CATTATCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (16 bp):
TAAAAGGGCCCATGGT
Found at i:32955 original size:39 final size:38
Alignment explanation
Indices: 32395--32957 Score: 298
Period size: 39 Copynumber: 14.4 Consensus size: 38
32385 CAGATAAAAG
* *
32395 ATTCGATCTTTTACCCCGAGCTTGGGGCAGA-TCA-CC
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATTCAGCC
*
32431 A-TCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCC
1 ATTC-G---ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCC
* * * * *
32473 GTTCGATATTTTACCCCAAGCCTGGGGTAGA-TCA-CC
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATTCAGCC
* * *
32509 A-TCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGTAGCC
1 ATTC-G---ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCC
* *
32551 ATTTGATCTCTTACCCCGAGCTTGGGGCAGA-TCA-CC
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATTCAGCC
* * *
32587 ATTAGCAAATCTCTTACCTCGAGGCTGGGGCAGATTACAGCC
1 ATT--C-GATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCC
*
32629 ATTTGATCTCTTACCCCGAGCCTGGGGCAGA-TCA-CC
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATTCAGCC
* * * * * * *
32665 A-TCAGTAAGTTTTTTATCCCGAGACTGAGGCAAATTACAGGC
1 ATTC-G--A-TCTCTTACCCCGAGCCTGGGGCAGATT-CAGCC
* *
32707 ATTCGATCTCTTACCCC-AGGCCTGAGGCAGA-TC-CCC
1 ATTCGATCTCTTACCCCGA-GCCTGGGGCAGATTCAGCC
* ** * * *
32743 A-TCAGCCAATCTCTTACCCCAAGCCTAAGGTAGATTGCAACT
1 ATTC-G---ATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCC
* * * * *
32785 GTTTGATCTTTTACCCTGAGCCTGGGGTAGA-TCA-CC
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATTCAGCC
* * **
32821 ATCAACCAATCTCTTACCTTGAGCCTGGGGCAGATTACAGCC
1 AT---TCGATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCC
*
32863 ATTCGATCTCTTACCCCGAGCCAGGGGCAGATCATCAG-C
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGAT--TCAGCC
* * *
32902 AGTCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCC
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCC
*
32941 ATTCGATCTTTTACCCC
1 ATTCGATCTCTTACCCC
32958 AAACTTGCGG
Statistics
Matches: 401, Mismatches: 76, Indels: 97
0.70 0.13 0.17
Matches are distributed among these distances:
35 7 0.02
36 19 0.05
37 9 0.02
38 10 0.02
39 307 0.77
40 11 0.03
41 11 0.03
42 21 0.05
43 6 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.25
Consensus pattern (38 bp):
ATTCGATCTCTTACCCCGAGCCTGGGGCAGATTCAGCC
Found at i:32989 original size:78 final size:78
Alignment explanation
Indices: 32395--32957 Score: 626
Period size: 78 Copynumber: 7.2 Consensus size: 78
32385 CAGATAAAAG
* * *
32395 ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGG
32460 GCAGATTGCAGCC
66 GCAGATTGCAGCC
* * * * * * * *
32473 GTTCGATATTTTACCCCAAGCCTGGGGTAGATCACCATCAGCAAATCTCTTACCCCGATCATGGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGG
*
32538 GCAGATTGTAGCC
66 GCAGATTGCAGCC
* * * * * *
32551 ATTTGATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCAAATCTCTTACCTCGAGGCTGGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGG
*
32616 GCAGATTACAGCC
66 GCAGATTGCAGCC
* * * * * * *
32629 ATTTGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAG-TAAGTTTTTTATCCCGAGACTGA
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAA-TCTCTTACCCCGAGCCTGG
* * *
32693 GGCAAATTACAGGC
65 GGCAGATTGCAGCC
* * * **
32707 ATTCGATCTCTTACCCC-AGGCCTGAGGCAGATCCCCATCAGCCAATCTCTTACCCCAAGCCTAA
1 ATTCGATCTCTTACCCCGA-GCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGG
* * *
32771 GGTAGATTGCAACT
65 GGCAGATTGCAGCC
* * * * * * **
32785 GTTTGATCTTTTACCCTGAGCCTGGGGTAGATCACCATCAACCAATCTCTTACCTTGAGCCTGGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGG
*
32850 GCAGATTACAGCC
66 GCAGATTGCAGCC
* * * * *
32863 ATTCGATCTCTTACCCCGAGCCAGGGGCAGATCATCAGCAGTCAATCTCTTACCCCGAGCTTGGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGG
32928 GCAGATTGCAGCC
66 GCAGATTGCAGCC
*
32941 ATTCGATCTTTTACCCC
1 ATTCGATCTCTTACCCC
32958 AAACTTGCGG
Statistics
Matches: 398, Mismatches: 83, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
77 3 0.01
78 392 0.98
79 3 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.25
Consensus pattern (78 bp):
ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGG
GCAGATTGCAGCC
Found at i:33470 original size:17 final size:17
Alignment explanation
Indices: 33448--33492 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
33438 TTAAAACTTA
33448 TTTTAAATTTAAATTTG
1 TTTTAAATTTAAATTTG
*
33465 TTTTAAGTTTAAATTTG
1 TTTTAAATTTAAATTTG
33482 TTTTAAATTTA
1 TTTTAAATTTA
33493 TTTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (17 bp):
TTTTAAATTTAAATTTG
Found at i:33498 original size:29 final size:29
Alignment explanation
Indices: 33455--33521 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
33445 TTATTTTAAA
* * *
33455 TTTAAATTT-GTTTTAAGTTTAAATTTGT
1 TTTAAATTTAGTTTTAAATTTAAAATTAT
*
33483 TTTAAATTTATTTTTAAATTTAAAATTAT
1 TTTAAATTTAGTTTTAAATTTAAAATTAT
*
33512 TCTAAATTTA
1 TTTAAATTTA
33522 ATTAATAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 9 0.27
29 24 0.73
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (29 bp):
TTTAAATTTAGTTTTAAATTTAAAATTAT
Found at i:33499 original size:12 final size:12
Alignment explanation
Indices: 33472--33504 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33462 TTGTTTTAAG
33472 TTTAAATTT-GT
1 TTTAAATTTAGT
*
33483 TTTAAATTTATT
1 TTTAAATTTAGT
33495 TTTAAATTTA
1 TTTAAATTTA
33505 AAATTATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (12 bp):
TTTAAATTTAGT
Found at i:33519 original size:17 final size:17
Alignment explanation
Indices: 33422--33522 Score: 77
Period size: 17 Copynumber: 6.1 Consensus size: 17
33412 CATTTTTTTA
**
33422 AAAATTTATTTTAAGGTT
1 AAAA-TTATTTTAAATTT
33440 AAAACTTATTTTAAATTT
1 AAAA-TTATTTTAAATTT
* * *
33458 AAATTTGTTTTAAGTTT
1 AAAATTATTTTAAATTT
* *
33475 AAATTTGTTTTAAATTT
1 AAAATTATTTTAAATTT
33492 ---A-T-TTTTAAATTT
1 AAAATTATTTTAAATTT
*
33504 AAAATTATTCTAAATTT
1 AAAATTATTTTAAATTT
33521 AA
1 AA
33523 TTAATAATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
12 10 0.14
13 1 0.01
15 1 0.01
16 1 0.01
17 38 0.55
18 18 0.26
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (17 bp):
AAAATTATTTTAAATTT
Found at i:34619 original size:21 final size:21
Alignment explanation
Indices: 34589--34648 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
34579 AATAGTGAAG
*
34589 ACTTTTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* *
34610 AGTTCTACCGATATAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* *
34631 TCTTCTACCGAAACAAGT
1 ACTTCTACCGATACAAGT
34649 CTTACTTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:38916 original size:36 final size:36
Alignment explanation
Indices: 38876--39011 Score: 245
Period size: 36 Copynumber: 3.8 Consensus size: 36
38866 CGATATCTGA
*
38876 TTTACTCCTTGTTGACCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
38912 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
* *
38948 TTTACTTCTTGTTGACCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
38984 TTTACTCCCTGTTGACCCAAAGGTCATG
1 TTTACTCCCTGTTGACCCAAAGGTCATG
39012 CCTATTACCA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (36 bp):
TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
Found at i:57001 original size:17 final size:17
Alignment explanation
Indices: 56981--57023 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
56971 AACTATAATG
*
56981 AAAATG-AACTAACAAGT
1 AAAATGCAAC-AACAACT
56998 AAAATGCAACAACAACT
1 AAAATGCAACAACAACT
57015 AAAATGCAA
1 AAAATGCAA
57024 TGATAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.60, C:0.16, G:0.09, T:0.14
Consensus pattern (17 bp):
AAAATGCAACAACAACT
Found at i:68691 original size:7 final size:7
Alignment explanation
Indices: 68679--68708 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
68669 AATATTCAGT
68679 ACTCAAC
1 ACTCAAC
68686 ACTCAAC
1 ACTCAAC
*
68693 ACTCGAC
1 ACTCAAC
68700 ACTCAAC
1 ACTCAAC
68707 AC
1 AC
68709 ATTTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.40, C:0.43, G:0.03, T:0.13
Consensus pattern (7 bp):
ACTCAAC
Found at i:69651 original size:23 final size:23
Alignment explanation
Indices: 69616--69662 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
69606 TGTTTTAAGA
69616 ATTTACTCAACAAAATAACATTC
1 ATTTACTCAACAAAATAACATTC
* *
69639 ATTTGCTCGACAAAATAACATTC
1 ATTTACTCAACAAAATAACATTC
69662 A
1 A
69663 GGTCCTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (23 bp):
ATTTACTCAACAAAATAACATTC
Found at i:70057 original size:14 final size:14
Alignment explanation
Indices: 70038--70067 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
70028 TTTTTGAAAG
70038 TATGATGGGTAACA
1 TATGATGGGTAACA
70052 TATGATGGGTAACA
1 TATGATGGGTAACA
70066 TA
1 TA
70068 GAAAGTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (14 bp):
TATGATGGGTAACA
Found at i:77744 original size:164 final size:164
Alignment explanation
Indices: 77473--77802 Score: 642
Period size: 164 Copynumber: 2.0 Consensus size: 164
77463 TTATCGAATG
77473 AGCTTTCGTAAGCTTGTTTAAATCTCAAATATTATTATATAGCATATTGTTATTTTATAATAAAC
1 AGCTTTCGTAAGCTTGTTTAAATCTCAAATATTATTATATAGCATATTGTTATTTTATAATAAAC
*
77538 TTAATAACATGTATAATTTGTTTAATTAATTTGCAAATGCGATCGTATTTGTCCCGACATTGAAT
66 TTAATAACATGTATAATTTGTTTAATTAATTTGCAAATGCGATCGTATTTGTCCCAACATTGAAT
77603 GTGACATTGCATAGCTCGAACTGACGATCAAGTC
131 GTGACATTGCATAGCTCGAACTGACGATCAAGTC
77637 AGCTTTCGTAAGCTTGTTTAAATCTCAAATATTATTATATAGCATATTGTTATTTTATAATAAAC
1 AGCTTTCGTAAGCTTGTTTAAATCTCAAATATTATTATATAGCATATTGTTATTTTATAATAAAC
*
77702 TTAATAGCATGTATAATTTGTTTAATTAATTTGCAAATGCGATCGTATTTGTCCCAACATTGAAT
66 TTAATAACATGTATAATTTGTTTAATTAATTTGCAAATGCGATCGTATTTGTCCCAACATTGAAT
77767 GTGACATTGCATAGCTCGAACTGACGATCAAGTC
131 GTGACATTGCATAGCTCGAACTGACGATCAAGTC
77801 AG
1 AG
77803 GTATGGGGTG
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (164 bp):
AGCTTTCGTAAGCTTGTTTAAATCTCAAATATTATTATATAGCATATTGTTATTTTATAATAAAC
TTAATAACATGTATAATTTGTTTAATTAATTTGCAAATGCGATCGTATTTGTCCCAACATTGAAT
GTGACATTGCATAGCTCGAACTGACGATCAAGTC
Found at i:101959 original size:46 final size:46
Alignment explanation
Indices: 101872--101959 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
101862 TATTGCAATT
* *
101872 AGAGTTTTAGATTTATTTAATTTCATTATTATATAATGTTTTATTA
1 AGAGTTTTAGATTTAGTTAATTTCATTATTATATAAGGTTTTATTA
* * * *
101918 AGAGTTTTAGTTTTAGTTATTTTCTTTATTATATTAGGTTTT
1 AGAGTTTTAGATTTAGTTAATTTCATTATTATATAAGGTTTT
101960 TATTTCTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.59
Consensus pattern (46 bp):
AGAGTTTTAGATTTAGTTAATTTCATTATTATATAAGGTTTTATTA
Found at i:106326 original size:76 final size:75
Alignment explanation
Indices: 106199--106350 Score: 286
Period size: 76 Copynumber: 2.0 Consensus size: 75
106189 TTTCTTCATC
106199 TCTATCTTGTCTTGTCGGCACACAAGACAAGTCTTCACATAGGCTTCAACATCTGTGCCCATGTG
1 TCTATCTTGTCTTGTCGGCACACAAGACAAGTCTTCACATAGGCTTCAACATCTGTGCCCATGTG
106264 CGGTCAGTAA
66 CGGTCAGTAA
*
106274 TNCTATCTTGTCTTGTCGGCACACAAGACAAGTCTTCACATAGGCTTCAACATCTGTGGCCATGT
1 T-CTATCTTGTCTTGTCGGCACACAAGACAAGTCTTCACATAGGCTTCAACATCTGTGCCCATGT
106339 GCGGTCAGTAA
65 GCGGTCAGTAA
106350 T
1 T
106351 AGTTCTCTCA
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 1 0.01
76 74 0.99
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (75 bp):
TCTATCTTGTCTTGTCGGCACACAAGACAAGTCTTCACATAGGCTTCAACATCTGTGCCCATGTG
CGGTCAGTAA
Found at i:115023 original size:21 final size:21
Alignment explanation
Indices: 114999--115041 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
114989 AATTAAAATT
*
114999 TAATAATAAATAAAATTTAAA
1 TAATAATAAATAAAATATAAA
* *
115020 TAATGATATATAAAATATAAA
1 TAATAATAAATAAAATATAAA
115041 T
1 T
115042 TAATTTAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TAATAATAAATAAAATATAAA
Found at i:120019 original size:146 final size:143
Alignment explanation
Indices: 119755--120221 Score: 572
Period size: 147 Copynumber: 3.2 Consensus size: 143
119745 TGGAAAAATG
* * * * * *
119755 AGTG-TTTTTTTT-TAAAGAAAG-TTTAAATTTTAAAAAAAATAAATTGTTTCTTAGTTATTTTA
1 AGTGATTTTTTTTAAAAAGAAAGTTTTGATTTTTAAAAATAA-AAATTGTTTTTTAGTAATTTT-
* * *
119817 AAGGAAAAAGTTTAAATTTTTTAAATAAATTTTTGA-TTTTTTAACTATTTCGAAATAAAAGTTT
64 AAGGAAAAAGTTTAAA-TTTTTAAACAAA-ATTTGATTTTTTTAACTATTTCAAAATAAAAGTTT
119881 TTATTTTTAAGAAAAGT
127 TTATTTTTAAGAAAAGT
119898 AGTGATTTTTTTTAAAAAGAAAGTTTTGATTTTTAAAAATAAAAATCTGTTTTTTTAGTAATTTT
1 AGTGATTTTTTTTAAAAAGAAAGTTTTGATTTTTAAAAATAAAAAT-TG-TTTTTTAGTAATTTT
* **
119963 GAAGGAAAAAGTTTAAATTTTTAAACAAAATTTGATTTTTTTAATTATTTCAAAATAAAAACTTT
64 -AAGGAAAAAGTTTAAATTTTTAAACAAAATTTGATTTTTTTAACTATTTCAAAATAAAAGTTTT
*
120028 GATTTTTAAGAAAAGT
128 TATTTTTAAGAAAAGT
** * *
120044 AGTGATTTTTTAAGAAAAAAAGAAAGTTTAGA-TTTTAAAAATAAAAATTTGTTTTTTAGTCATT
1 AGTGATTTTTT---TTAAAAAGAAAGTTTTGATTTTTAAAAATAAAAA-TTGTTTTTTAGTAATT
* *
120108 TTAAAGAGAAAAGTTTAAATTTTTAAACAAAGTTTGATTTTTTTAACTATTTCAAAATAAAAGCT
62 TTAAGGA-AAAAGTTTAAATTTTTAAACAAAATTTGATTTTTTTAACTATTTCAAAATAAAAG-T
120173 TTTT-TTTTTAAGAAAAGT
125 TTTTATTTTTAAGAAAAGT
* *
120191 TGTGATTTTTTTTAAAAA-AAA-ATTTGATTTT
1 AGTGATTTTTTTTAAAAAGAAAGTTTTGATTTT
120222 GCAAAAAAAA
Statistics
Matches: 282, Mismatches: 29, Indels: 26
0.84 0.09 0.08
Matches are distributed among these distances:
142 4 0.01
143 10 0.04
144 13 0.05
145 17 0.06
146 83 0.29
147 119 0.42
148 20 0.07
149 16 0.06
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (143 bp):
AGTGATTTTTTTTAAAAAGAAAGTTTTGATTTTTAAAAATAAAAATTGTTTTTTAGTAATTTTAA
GGAAAAAGTTTAAATTTTTAAACAAAATTTGATTTTTTTAACTATTTCAAAATAAAAGTTTTTAT
TTTTAAGAAAAGT
Found at i:120218 original size:22 final size:23
Alignment explanation
Indices: 120173--120221 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
120163 AATAAAAGCT
* * *
120173 TTTTTTTTTAAGAAAAGTTGTGA
1 TTTTTTTTAAAAAAAAATTGTGA
120196 TTTTTTTTAAAAAAAAATT-TGA
1 TTTTTTTTAAAAAAAAATTGTGA
120218 TTTT
1 TTTT
120222 GCAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (23 bp):
TTTTTTTTAAAAAAAAATTGTGA
Found at i:120809 original size:16 final size:17
Alignment explanation
Indices: 120768--120818 Score: 70
Period size: 16 Copynumber: 3.1 Consensus size: 17
120758 TATTTATTCT
*
120768 TATTTCATCTTTATTTA
1 TATTTCATGTTTATTTA
120785 T-TTTCATGTTTATTTA
1 TATTTCATGTTTATTTA
*
120801 TATTT-ATGTTTTTTTA
1 TATTTCATGTTTATTTA
120817 TA
1 TA
120819 CATTCCCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.69
Consensus pattern (17 bp):
TATTTCATGTTTATTTA
Found at i:129747 original size:10 final size:10
Alignment explanation
Indices: 129732--129760 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
129722 TAAATCAAAT
129732 GAAACTAAAA
1 GAAACTAAAA
129742 GAAACTAAAA
1 GAAACTAAAA
129752 GAAACTAAA
1 GAAACTAAA
129761 CTAAGCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.10
Consensus pattern (10 bp):
GAAACTAAAA
Found at i:132033 original size:24 final size:24
Alignment explanation
Indices: 132002--132048 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
131992 AGAAATAATG
*
132002 TTTCAATTAAACTTTGTTTATTTA
1 TTTCAATTAAACTCTGTTTATTTA
*
132026 TTTCAATTAAGCTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
132049 GTTTGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTA
Found at i:132064 original size:24 final size:24
Alignment explanation
Indices: 132002--132064 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
131992 AGAAATAATG
* *
132002 TTTCAATTAAACTTTGTTTATTTA
1 TTTCAATCAAACTCTGTTTATTTA
* * *
132026 TTTCAATTAAGCTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTA
* *
132050 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
132065 TATTAGTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTATTTA
Found at i:145344 original size:18 final size:18
Alignment explanation
Indices: 145318--145356 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
145308 GCAGACACAT
145318 CATAATCAGATGCAGTAA
1 CATAATCAGATGCAGTAA
* *
145336 CATACTCAGATGCAGTCA
1 CATAATCAGATGCAGTAA
145354 CAT
1 CAT
145357 GCTTGTATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (18 bp):
CATAATCAGATGCAGTAA
Found at i:150909 original size:2 final size:2
Alignment explanation
Indices: 150902--150929 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
150892 TTGCAATTCC
150902 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
150930 TTTTGTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160581 original size:3 final size:3
Alignment explanation
Indices: 160575--160606 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
160565 TTTTTATTAA
160575 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
160607 AATGATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:161488 original size:17 final size:17
Alignment explanation
Indices: 161468--161500 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
161458 TGATGATTTT
161468 TAATTTT-TTGAAAATAA
1 TAATTTTATT-AAAATAA
161485 TAATTTTATTAAAATA
1 TAATTTTATTAAAATA
161501 TTTTAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TAATTTTATTAAAATAA
Found at i:163803 original size:26 final size:26
Alignment explanation
Indices: 163774--163853 Score: 115
Period size: 26 Copynumber: 3.1 Consensus size: 26
163764 AAACTCAGTG
* *
163774 TATGCTTGTATTTAATTAATCATGTT
1 TATGTTTGTATTTAATTAATTATGTT
*
163800 TATGTTTTTATTTAATTAATTATGTT
1 TATGTTTGTATTTAATTAATTATGTT
* *
163826 TATGTTTGTATTTACTAAATTATGTT
1 TATGTTTGTATTTAATTAATTATGTT
163852 TA
1 TA
163854 AAGTTTTAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.59
Consensus pattern (26 bp):
TATGTTTGTATTTAATTAATTATGTT
Found at i:166896 original size:7 final size:7
Alignment explanation
Indices: 166886--166912 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
166876 TTTTGCTGTT
166886 TGTTTTG
1 TGTTTTG
166893 TGTTTTG
1 TGTTTTG
166900 TGTTTTG
1 TGTTTTG
166907 TGTTTT
1 TGTTTT
166913 TTGGGCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (7 bp):
TGTTTTG
Found at i:167313 original size:22 final size:23
Alignment explanation
Indices: 167285--167328 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
167275 AATGTTAAAG
167285 AAAAAAAA-TTAAAACTTCTACC
1 AAAAAAAATTTAAAACTTCTACC
167307 AAAAAAAATTTAAAACTTCTAC
1 AAAAAAAATTTAAAACTTCTAC
167329 ATTTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAAAAAATTTAAAACTTCTACC
Found at i:175375 original size:26 final size:26
Alignment explanation
Indices: 175338--175423 Score: 118
Period size: 26 Copynumber: 3.3 Consensus size: 26
175328 CTAAAGGAAA
175338 ATACTGAACTAGCTTGTAAGAGCGAT
1 ATACTGAACTAGCTTGTAAGAGCGAT
* * *
175364 ATACTGAGCTAGCTCGTAAAAGCGAT
1 ATACTGAACTAGCTTGTAAGAGCGAT
* * *
175390 ATACTAAACTGGCTTTTAAGAGCGAT
1 ATACTGAACTAGCTTGTAAGAGCGAT
175416 ATACTGAA
1 ATACTGAA
175424 TTGACTCGTG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (26 bp):
ATACTGAACTAGCTTGTAAGAGCGAT
Found at i:176192 original size:55 final size:55
Alignment explanation
Indices: 176133--176246 Score: 122
Period size: 55 Copynumber: 2.1 Consensus size: 55
176123 GTGTGGCCCT
* * * *
176133 ATTTCAAAAT-CACACACGGTCTAGCACACGATCTCGTACATGAACGTGTGGGGTA
1 ATTTC-AAATGCACACACGATCTAGAACACGATCTCGTACAAGAACATGTGGGGTA
** * * **
176188 ATTTCGCATGCTCACACGATCTAGAACACGATCTTGTACAAGGGCATGTGGGGTA
1 ATTTCAAATGCACACACGATCTAGAACACGATCTCGTACAAGAACATGTGGGGTA
176243 ATTT
1 ATTT
176247 TGCATGCTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 2 0.04
55 46 0.96
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (55 bp):
ATTTCAAATGCACACACGATCTAGAACACGATCTCGTACAAGAACATGTGGGGTA
Found at i:176252 original size:55 final size:55
Alignment explanation
Indices: 176145--176261 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 55
176135 TTCAAAATCA
* * * *
176145 CACACGGTCTAGCACACGATCTCGTACATGAACGTGTGGGGTAATTTCGCATGCT
1 CACACGATCTAGAACACGATCTCGTACAAGAACATGTGGGGTAATTTCGCATGCT
* ** *
176200 CACACGATCTAGAACACGATCTTGTACAAGGGCATGTGGGGTAATTTTGCATGCT
1 CACACGATCTAGAACACGATCTCGTACAAGAACATGTGGGGTAATTTCGCATGCT
176255 CACACGA
1 CACACGA
176262 CCTGGCACAT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (55 bp):
CACACGATCTAGAACACGATCTCGTACAAGAACATGTGGGGTAATTTCGCATGCT
Found at i:179217 original size:36 final size:36
Alignment explanation
Indices: 179148--179218 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
179138 AAAGGAAGGC
* **
179148 ATATGTCTCGATTATAGCATATTGCTATGATGTTGA
1 ATATGTCTCGATTAGAGCATATTGCTACAATGTTGA
*
179184 ATATGTCTCGATTAGAGCATATTGCTGCAATGTTG
1 ATATGTCTCGATTAGAGCATATTGCTACAATGTTG
179219 CTTACGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (36 bp):
ATATGTCTCGATTAGAGCATATTGCTACAATGTTGA
Found at i:179261 original size:37 final size:37
Alignment explanation
Indices: 179218--179317 Score: 155
Period size: 37 Copynumber: 2.7 Consensus size: 37
179208 CTGCAATGTT
*
179218 GCTTACGTTTCGGTTAGAGCGTAATGTTATATGGAAG
1 GCTTACGTCTCGGTTAGAGCGTAATGTTATATGGAAG
*
179255 GCTTACGTCTCGATTAGAGCGTAATGTTATATGGAAG
1 GCTTACGTCTCGGTTAGAGCGTAATGTTATATGGAAG
* * *
179292 ACTTACGTCTCGGTTAAAGGGTAATG
1 GCTTACGTCTCGGTTAGAGCGTAATG
179318 CTATGTGATT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (37 bp):
GCTTACGTCTCGGTTAGAGCGTAATGTTATATGGAAG
Found at i:190657 original size:18 final size:18
Alignment explanation
Indices: 190583--190659 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
190573 ATTAGAATAT
190583 TGGCTCGTTAGAGCATAC
1 TGGCTCGTTAGAGCATAC
* **
190601 TGACTTATTTA-AGCATAC
1 TGGC-TCGTTAGAGCATAC
** *
190619 TATCTCGTTTGAGCATAC
1 TGGCTCGTTAGAGCATAC
*
190637 TGGCTCGTTAGAGCATGC
1 TGGCTCGTTAGAGCATAC
190655 TGGCT
1 TGGCT
190660 TATAAGAGCA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
17 3 0.07
18 38 0.84
19 4 0.09
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (18 bp):
TGGCTCGTTAGAGCATAC
Done.