Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001665.1 Hibiscus syriacus cultivar Beakdansim tig00003333_pilon, 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: 94311
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1784 original size:18 final size:18
Alignment explanation
Indices: 1761--1796 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1751 AAGTAAAAGG
1761 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
1779 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
1797 CACCGGCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:3537 original size:20 final size:20
Alignment explanation
Indices: 3514--3592 Score: 115
Period size: 20 Copynumber: 3.9 Consensus size: 20
3504 ATGGTGGGAG
*
3514 GGGCCTCTTGAACAATGAGA
1 GGGCCTCTTGAACGATGAGA
3534 GGGCCTCTTGAACGATGAGA
1 GGGCCTCTTGAACGATGAGA
*
3554 GGGGACTCTTGAACGAT-AGGA
1 -GGGCCTCTTGAACGATGA-GA
3575 GGGCCTCTTGAACGATGA
1 GGGCCTCTTGAACGATGA
3593 CAGGTGAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
20 35 0.66
21 18 0.34
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.20
Consensus pattern (20 bp):
GGGCCTCTTGAACGATGAGA
Found at i:3577 original size:41 final size:41
Alignment explanation
Indices: 3511--3592 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
3501 TGAATGGTGG
*
3511 GAGGGGCCTCTTGAACAATGAGAGGGCCTCTTGAACGATGA
1 GAGGGGACTCTTGAACAATGAGAGGGCCTCTTGAACGATGA
*
3552 GAGGGGACTCTTGAACGAT-AGGAGGGCCTCTTGAACGATGA
1 GAGGGGACTCTTGAACAATGA-GAGGGCCTCTTGAACGATGA
3593 CAGGTGAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (41 bp):
GAGGGGACTCTTGAACAATGAGAGGGCCTCTTGAACGATGA
Found at i:3738 original size:4 final size:4
Alignment explanation
Indices: 3725--3761 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
3715 ATCAGGCCGC
3725 TAAA -AAA TAAA TAAA T-AA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
3762 TGCCGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:3749 original size:15 final size:15
Alignment explanation
Indices: 3729--3757 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3719 GGCCGCTAAA
3729 AAATAAATAAATAAT
1 AAATAAATAAATAAT
3744 AAATAAATAAATAA
1 AAATAAATAAATAA
3758 ATAATGCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAATAAATAAT
Found at i:3896 original size:21 final size:22
Alignment explanation
Indices: 3872--3966 Score: 74
Period size: 21 Copynumber: 4.5 Consensus size: 22
3862 GTAGAGCGGC
*
3872 TACCTCATCACGTAAAGTA-GA
1 TACCTCATCACGTAAAGTACCA
* * *
3893 TACCTCACCACGTAAAGCATCA
1 TACCTCATCACGTAAAGTACCA
* * *
3915 TTA--TCATCGCGTAAAATAGC-
1 -TACCTCATCACGTAAAGTACCA
*
3935 TACCTCACCACGTAAAG-ACCA
1 TACCTCATCACGTAAAGTACCA
3956 TACCTCATCAC
1 TACCTCATCAC
3967 ACCATGCACC
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 49 0.88
22 1 0.02
23 2 0.04
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.22
Consensus pattern (22 bp):
TACCTCATCACGTAAAGTACCA
Found at i:3964 original size:42 final size:44
Alignment explanation
Indices: 3872--3966 Score: 126
Period size: 42 Copynumber: 2.2 Consensus size: 44
3862 GTAGAGCGGC
* *
3872 TACCTCATCACGTAAAGTAGATACCTCACCACGTAAAGCATCAT
1 TACCTCATCACGTAAAATAGATACCTCACCACGTAAAGCACCAT
* *
3916 TA--TCATCGCGTAAAATAGCTACCTCACCACGTAAAG-ACCA-
1 TACCTCATCACGTAAAATAGATACCTCACCACGTAAAGCACCAT
3956 TACCTCATCAC
1 TACCTCATCAC
3967 ACCATGCACC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.05
41 3 0.07
42 37 0.84
44 2 0.05
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.22
Consensus pattern (44 bp):
TACCTCATCACGTAAAATAGATACCTCACCACGTAAAGCACCAT
Found at i:4014 original size:21 final size:21
Alignment explanation
Indices: 3990--4030 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3980 ATCGTCATGT
*
3990 AAAGTACCGACCTCATCACGC
1 AAAGCACCGACCTCATCACGC
4011 AAAGCACCGACCTCATCACG
1 AAAGCACCGACCTCATCACG
4031 TAACTCCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.39, G:0.15, T:0.12
Consensus pattern (21 bp):
AAAGCACCGACCTCATCACGC
Found at i:5736 original size:20 final size:20
Alignment explanation
Indices: 5683--5739 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
5673 TTTGAAACTT
**
5683 AAATTCGCAAAACGAAAATG
1 AAATTCGCAACGCGAAAATG
5703 AAATTCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
*
5723 AAATTCGCATCGCGAAA
1 AAATTCGCAACGCGAAA
5740 CTAAAATCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:5746 original size:20 final size:20
Alignment explanation
Indices: 5683--5746 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
5673 TTTGAAACTT
** *
5683 AAATTCGCAAAACGAAAATG
1 AAATTCGCAACGCGAAAATA
*
5703 AAATTCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATA
* *
5723 AAATTCGCATCGCGAAACTA
1 AAATTCGCAACGCGAAAATA
5743 AAAT
1 AAAT
5747 CGCGTTGCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:6144 original size:22 final size:22
Alignment explanation
Indices: 6119--6169 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
6109 GATAGAGGGG
*
6119 GTCGTCGGATATGGGGACACAT
1 GTCGTCGGAGATGGGGACACAT
**
6141 GTCGTCGGAGATGGGGACGGAT
1 GTCGTCGGAGATGGGGACACAT
6163 GTCGTCG
1 GTCGTCG
6170 TAGAGAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.43, T:0.22
Consensus pattern (22 bp):
GTCGTCGGAGATGGGGACACAT
Found at i:6295 original size:19 final size:20
Alignment explanation
Indices: 6273--6310 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6263 AATATTGTGT
6273 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
*
6292 TTCGCATTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
6311 TTTGCTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:6311 original size:19 final size:20
Alignment explanation
Indices: 6281--6323 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
6271 GTTTCGAATT
6281 CGAAAATAAAATTCGCATTG
1 CGAAAATAAAATTCGCATTG
* *
6301 CGAAAAT-AAATTTGCTTTG
1 CGAAAATAAAATTCGCATTG
6320 CGAA
1 CGAA
6324 TTTGACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (20 bp):
CGAAAATAAAATTCGCATTG
Found at i:6364 original size:20 final size:20
Alignment explanation
Indices: 6317--6367 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
6307 TAAATTTGCT
*
6317 TTGCGAATTTGACTTCTATA
1 TTGCGAATTTGACTTATATA
* * *
6337 TTGTGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATATA
6357 TTGCGAATTTG
1 TTGCGAATTTG
6368 GAAAATCGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTATATA
Found at i:7180 original size:54 final size:54
Alignment explanation
Indices: 7077--7390 Score: 472
Period size: 54 Copynumber: 5.9 Consensus size: 54
7067 CTGATACAAT
* * * **
7077 AATTCACAAACTCATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGAA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATACGAA
*
7132 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGTA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAA
* * *
7186 AATTCATAAAATTATTATGAACTTCTTAAGTTGCACACATAGTGCCAATACG-A
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAA
* * *
7239 AATTCATAAACTTATTATGAATTTCTTAGGTTG--CACATAGTGTCAATAAGGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAA
*
7291 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTTCCAATACGAA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAA
*
7345 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACATATAGTGCC
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCC
7391 TATTCGGTAA
Statistics
Matches: 236, Mismatches: 20, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
51 15 0.06
52 34 0.14
53 31 0.13
54 134 0.57
55 22 0.09
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (54 bp):
AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAA
Found at i:13622 original size:54 final size:54
Alignment explanation
Indices: 13447--13870 Score: 609
Period size: 54 Copynumber: 7.9 Consensus size: 54
13437 ACGATACAAT
* * * *
13447 AATTCATAAACTCATTATGAATTACGTGGAGTTGCACACATAGTGCCAATACGGA
1 AATTCATAAACTTATTATGAATTTCTTAG-GTTGCACACATAGTGCCAATACGGA
* * * * *
13502 AATTCATAAAATCATTATGAATTTCGTGAGGTTGAACACATAGTGCCAATATGGA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATACGGA
* *
13557 AATTCAT-AACTTATTATGAATTTCTTTGGTTGCATACATAGTGCCAATACGGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
* * * *
13610 AATTCATAAACTTATTATGAACTTCTTAAGTTGCACACACAGTGCCAATACAGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
*
13664 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
* * *
13718 AATTTAT-AACTTATTATGAATTTCTTAGGTTGCATACATAGTGCCAATATGGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
*
13771 AATTCATAAACTTATTATGAATTTCTTAGGTTACACACATAGTGCCAATACGGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
* * *
13825 AACTCATAAACTTATTATGAATTTGTTAGGTTGCACACATACTGCC
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCC
13871 CATTCGGTAT
Statistics
Matches: 329, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
53 80 0.24
54 195 0.59
55 53 0.16
56 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (54 bp):
AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
Found at i:13753 original size:161 final size:160
Alignment explanation
Indices: 13447--13870 Score: 632
Period size: 161 Copynumber: 2.6 Consensus size: 160
13437 ACGATACAAT
* **
13447 AATTCATAAACTCATTATGAATTACGTGGAGTTGCACACATAGTGCCAATACGGAAATTCATAAA
1 AATTCATAAACTTATTATGAATT-C-TTAAGTTGCACACATAGTGCCAATACGGAAATTCATAAA
* * * * * *
13512 ATCATTATGAATTTCGTGAGGTTGAACACATAGTGCCAATATGGAAATTCATAACTTATTATGAA
64 CTTATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATACGAAAATTCATAACTTATTATGAA
*
13577 TTTCTTTGGTTGCATACATAGTGCCAATACGGA
128 TTTCTTAGGTTGCATACATAGTGCCAATACGGA
* *
13610 AATTCATAAACTTATTATGAACTTCTTAAGTTGCACACACAGTGCCAATACAGAAATTCATAAAC
1 AATTCATAAACTTATTATGAA-TTCTTAAGTTGCACACATAGTGCCAATACGGAAATTCATAAAC
*
13675 TTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTTATAACTTATTATGAATT
65 TTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCATAACTTATTATGAATT
*
13740 TCTTAGGTTGCATACATAGTGCCAATATGGA
130 TCTTAGGTTGCATACATAGTGCCAATACGGA
* * *
13771 AATTCATAAACTTATTATGAATTTCTTAGGTTACACACATAGTGCCAATACGGAAACTCATAAAC
1 AATTCATAAACTTATTATGAA-TTCTTAAGTTGCACACATAGTGCCAATACGGAAATTCATAAAC
* *
13836 TTATTATGAATTTGTTAGGTTGCACACATACTGCC
65 TTATTATGAATTTCTTAGGTTGCACACATAGTGCC
13871 CATTCGGTAT
Statistics
Matches: 238, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
161 167 0.70
162 48 0.20
163 21 0.09
164 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (160 bp):
AATTCATAAACTTATTATGAATTCTTAAGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
TATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCATAACTTATTATGAATTT
CTTAGGTTGCATACATAGTGCCAATACGGA
Found at i:17391 original size:2 final size:2
Alignment explanation
Indices: 17386--17429 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
17376 TTATGAAAGA
17386 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
17428 AT
1 AT
17430 TAATAGTACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19752 original size:30 final size:30
Alignment explanation
Indices: 19592--19752 Score: 119
Period size: 30 Copynumber: 5.4 Consensus size: 30
19582 TTTAAAATTA
* *
19592 AAAGGACCAAAATGAG-AAAAACAACAACTT
1 AAAGGACTAAAATG-GTAAAAACAAAAACTT
* *** ***
19622 AAAGGACCAAAATAAAAAAAATTGAAACTT
1 AAAGGACTAAAATGGTAAAAACAAAAACTT
* * *
19652 AAAGGACTAAAATGG-AACAAATAGAAATTT
1 AAAGGACTAAAATGGTAA-AAACAAAAACTT
* *
19682 AAAGGGCTAAAATAGTAAAAACAAAAACTT
1 AAAGGACTAAAATGGTAAAAACAAAAACTT
* * ** *
19712 AAGGGTCTAAAATGGTATTAACAAAAACTA
1 AAAGGACTAAAATGGTAAAAACAAAAACTT
19742 AAAGGACTAAA
1 AAAGGACTAAA
19753 CATCAATTAC
Statistics
Matches: 104, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
29 2 0.02
30 100 0.96
31 2 0.02
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (30 bp):
AAAGGACTAAAATGGTAAAAACAAAAACTT
Found at i:21458 original size:31 final size:31
Alignment explanation
Indices: 21420--21596 Score: 122
Period size: 31 Copynumber: 5.3 Consensus size: 31
21410 AAACTACTTA
*
21420 TTTGGTCACTTATATATTATCTAATTTGTGT
1 TTTGGTCACTTATATATTATCTAATTTATGT
** ** **
21451 TTTGGTCACTTGATTATTATTTAGGGTAAACTACCT
1 TTTGGTCACTT-A-TA-TA-TTA-TCTAATTTATGT
21487 ATTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
* ** **
21519 TTTGGTCACTCTAT-TATTATTTAGGGTAGACTACCT
1 TTTGGTCACT-TATATATTATCTA----A-TTTATGT
21555 ATTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
21587 TTTGGTCACT
1 TTTGGTCACT
21597 CGACTATTAT
Statistics
Matches: 109, Mismatches: 23, Indels: 28
0.68 0.14 0.17
Matches are distributed among these distances:
31 39 0.36
32 13 0.12
33 6 0.06
34 4 0.04
35 6 0.06
36 12 0.11
37 29 0.27
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATCTAATTTATGT
Found at i:21506 original size:37 final size:37
Alignment explanation
Indices: 21451--21643 Score: 137
Period size: 37 Copynumber: 5.5 Consensus size: 37
21441 TAATTTGTGT
21451 TTTGGTCACTTGAT-TATTATTTAGGGTAAACTACCTA
1 TTTGGTCACTT-ATATATTATTTAGGGTAAACTACCTA
* ** **
21488 TTTGGTCACTTATATATTA--T---CTAATTTATGT-
1 TTTGGTCACTTATATATTATTTAGGGTAAACTACCTA
*
21519 TTTGGTCACTCTAT-TATTATTTAGGGTAGACTACCTA
1 TTTGGTCACT-TATATATTATTTAGGGTAAACTACCTA
* ** **
21556 TTTGGTCACTTATATATTA--T---CTAATTTATGT-
1 TTTGGTCACTTATATATTATTTAGGGTAAACTACCTA
* *
21587 TTTGGTCACTCGA-CTATTATTTAGGGTAAACTACCTA
1 TTTGGTCACT-TATATATTATTTAGGGTAAACTACCTA
21624 TTTGGTCACTTATATATTAT
1 TTTGGTCACTTATATATTAT
21644 CTAATATAAT
Statistics
Matches: 113, Mismatches: 26, Indels: 34
0.65 0.15 0.20
Matches are distributed among these distances:
31 30 0.27
32 15 0.13
33 2 0.02
35 2 0.02
36 17 0.15
37 47 0.42
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (37 bp):
TTTGGTCACTTATATATTATTTAGGGTAAACTACCTA
Found at i:21511 original size:68 final size:68
Alignment explanation
Indices: 21402--21739 Score: 483
Period size: 68 Copynumber: 5.0 Consensus size: 68
21392 TAGGGATTTT
* *
21402 TTTAGGGTAAACTACTTATTTGGTCACTTATATATTATCTAATTTGTGTTTTGGTCACTTGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTTGATTA
21467 TTA
66 TTA
21470 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCT-ATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACT-TGATT
21534 ATTA
65 ATTA
* * *
21538 TTTAGGGTAGACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGACTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTTGATTA
21603 TTA
66 TTA
** **
21606 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAA--TAT-AATTCAT-A-TAT-ATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACT-TGATT
*
21665 TTTA
65 ATTA
* * * *
21669 TTCAGGGCAAACTACATATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTAGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTTGATTA
21734 TTA
66 TTA
21737 TTT
1 TTT
21740 TTTTTCAAAA
Statistics
Matches: 238, Mismatches: 23, Indels: 18
0.85 0.08 0.06
Matches are distributed among these distances:
63 45 0.19
64 1 0.00
65 6 0.03
66 6 0.03
67 1 0.00
68 178 0.75
69 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTTGATTA
TTA
Found at i:25933 original size:10 final size:10
Alignment explanation
Indices: 25918--25955 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
25908 TGCACAATTC
25918 AAGAACAAAT
1 AAGAACAAAT
*
25928 AAGAAC-ACT
1 AAGAACAAAT
25937 AAGAACAAAT
1 AAGAACAAAT
25947 AAGAACAAA
1 AAGAACAAA
25956 AGAATATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.68, C:0.13, G:0.11, T:0.08
Consensus pattern (10 bp):
AAGAACAAAT
Found at i:28119 original size:18 final size:18
Alignment explanation
Indices: 28096--28130 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28086 AGAAAAAGGC
*
28096 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
28114 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
28131 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:28442 original size:140 final size:140
Alignment explanation
Indices: 28190--28459 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
28180 AAACGTTGTA
*
28190 TTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTACTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTACTA
**
28255 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGTGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
28320 TATGTGTATT
131 TATGTGTATT
*
28330 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTACTA
28395 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
28460 CACAATGCGA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTACTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCAAATTTGACTAT
TATGTGTATT
Found at i:28455 original size:20 final size:20
Alignment explanation
Indices: 28430--28639 Score: 220
Period size: 20 Copynumber: 10.8 Consensus size: 20
28420 TTACACATTC
* *
28430 ATTTGAATATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
* *
28450 ATTTGACTATCACAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
28470 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
28489 A----A-AATCGC-ACGCGA
1 ATTTGACTATCGCAACGCGA
28503 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
28523 ATTTGATTATCGCAACGTC-T
1 ATTTGACTATCGCAACG-CGA
28543 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
28563 ATTTGACTATCGCAATGTGA
1 ATTTGACTATCGCAACGCGA
*
28583 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
28603 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
28623 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
28640 AGAAAATCGC
Statistics
Matches: 157, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
13 3 0.02
14 7 0.04
15 1 0.01
18 1 0.01
19 8 0.05
20 136 0.87
21 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:28585 original size:60 final size:59
Alignment explanation
Indices: 28428--28637 Score: 254
Period size: 60 Copynumber: 3.6 Consensus size: 59
28418 TATTACACAT
* *
28428 TCATTTGAATATCGCAACGCAAATTTGACTATCACAATGCGAATTTGATTATCGCAAC-
1 TCATTTGAATATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGATTATCGCAACG
* *
28486 TCA----AAAATCGC-ACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACG
1 TCATTTGAATATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGATTATCGCAACG
* * *
28540 TCTATTTGACTATCGCAACGCGAATTTGACTATCGCAATGTGAATTTGAGTATCGCAACG
1 TC-ATTTGAATATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGATTATCGCAACG
* * *
28600 -CGAATTTGATTATCGCAACGGGTATTTGACTATCGCAA
1 TC--ATTTGAATATCGCAACGCGAATTTGACTATCGCAA
28638 CGAGAAAATC
Statistics
Matches: 131, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
53 39 0.30
54 9 0.07
55 1 0.01
58 3 0.02
59 7 0.05
60 72 0.55
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (59 bp):
TCATTTGAATATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGATTATCGCAACG
Found at i:28733 original size:20 final size:20
Alignment explanation
Indices: 28682--28735 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
28672 CGCGAATTGG
* *
28682 CTTTCGCGTTGCGATTTTGT
1 CTTTAGCGTTGCGATTTTGA
* *
28702 CTTTTGCATTGCGATTTTGA
1 CTTTAGCGTTGCGATTTTGA
*
28722 GTTTAGCGTTGCGA
1 CTTTAGCGTTGCGA
28736 AAATGTACCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.46
Consensus pattern (20 bp):
CTTTAGCGTTGCGATTTTGA
Found at i:28872 original size:29 final size:28
Alignment explanation
Indices: 28838--28893 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
28828 AATAAGAATT
*
28838 TTTTACACATCAATATTAAACAAATCAAC
1 TTTTACAAATCAAT-TTAAACAAATCAAC
* *
28867 TTTTACAAATCAATTTTAATAAATCAA
1 TTTTACAAATCAATTTAAACAAATCAA
28894 TTAAACATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (28 bp):
TTTTACAAATCAATTTAAACAAATCAAC
Found at i:28876 original size:14 final size:13
Alignment explanation
Indices: 28838--28895 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
28828 AATAAGAATT
*
28838 TTTTACACATCAA
1 TTTTACAAATCAA
*
28851 TATTAAACAAATCAA
1 T-TT-TACAAATCAA
28866 CTTTTACAAATCAA
1 -TTTTACAAATCAA
*
28880 TTTTAATAAATCAA
1 TTTT-ACAAATCAA
28894 TT
1 TT
28896 AAACATGCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.14
14 21 0.57
15 10 0.27
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTTACAAATCAA
Found at i:30387 original size:42 final size:42
Alignment explanation
Indices: 30308--30400 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
30298 CCTCTTCAAC
* * *
30308 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
30350 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
30392 GATGACAGG
1 GATGACAGG
30401 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:30909 original size:18 final size:19
Alignment explanation
Indices: 30886--30930 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
30876 GAAACTTAAA
30886 ATCGCAAAACG-AATGACT
1 ATCGCAAAACGAAATGACT
**
30904 ATCGCAACGCGAAAATGACT
1 ATCGCAAAACG-AAATGACT
30924 ATCGCAA
1 ATCGCAA
30931 CGAGAGAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
20 14 0.61
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (19 bp):
ATCGCAAAACGAAATGACT
Found at i:31041 original size:20 final size:20
Alignment explanation
Indices: 30992--31042 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
30982 ATAGTCAAAA
*
30992 TCGCGTTGCAATAGTCATTT
1 TCGCGTTGCGATAGTCATTT
*
31012 TTGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCATTT
31032 TCGCGTTGCGA
1 TCGCGTTGCGA
31043 AAGTAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATAGTCATTT
Found at i:31517 original size:22 final size:22
Alignment explanation
Indices: 31492--31535 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
31482 TGTGTTAACT
31492 TACATTATTTATTGTTGTATAC
1 TACATTATTTATTGTTGTATAC
31514 TACATTATTTATTGTTGTATAC
1 TACATTATTTATTGTTGTATAC
31536 GGTAGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (22 bp):
TACATTATTTATTGTTGTATAC
Found at i:32670 original size:20 final size:20
Alignment explanation
Indices: 32647--32687 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
32637 TCTGAAACTT
32647 AAAATAGCAACACGAAAATG
1 AAAATAGCAACACGAAAATG
*
32667 AAAATCGCAACACGAAAATG
1 AAAATAGCAACACGAAAATG
32687 A
1 A
32688 CTATCACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.17, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAATAGCAACACGAAAATG
Found at i:32697 original size:20 final size:20
Alignment explanation
Indices: 32654--32712 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
32644 CTTAAAATAG
** *
32654 CAACACGAAAATGAAAATCG
1 CAACACGAAAATGACTATCA
32674 CAACACGAAAATGACTATCA
1 CAACACGAAAATGACTATCA
* **
32694 CAACGCGAATTTGACTATC
1 CAACACGAAAATGACTATC
32713 GCAATGCGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.17
Consensus pattern (20 bp):
CAACACGAAAATGACTATCA
Found at i:32721 original size:20 final size:20
Alignment explanation
Indices: 32685--32722 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32675 AACACGAAAA
32685 TGACTATCACAACGCGAATT
1 TGACTATCACAACGCGAATT
* *
32705 TGACTATCGCAATGCGAA
1 TGACTATCACAACGCGAA
32723 ATGAAAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
TGACTATCACAACGCGAATT
Found at i:33159 original size:22 final size:22
Alignment explanation
Indices: 33128--33184 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
33118 GATGGAGATA
33128 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
33150 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
33172 GACGGATGTCGCC
1 GACGGATTTCGCC
33185 TTATAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:33388 original size:20 final size:20
Alignment explanation
Indices: 33349--33462 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
33339 GCGCTTTGAA
* *
33349 AATCGCATTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* * *
33369 CATTGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
33389 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
33409 AATCTCTTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
33429 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
33449 AATCACATTGCGAT
1 AATCGCGTTGCGAT
33463 TTACATATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:33483 original size:60 final size:60
Alignment explanation
Indices: 33349--33486 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
33339 GCGCTTTGAA
* * * *
33349 AATCGCATTACGATAGTCAGCATTGCGTTGCGACAGTCAGAATCGCGTTGCGATAGTCAG
1 AATCGCATTACGATAGTCAGAATCGCGTTGCGACAGTCAGAATCACATTGCGATAGTCAG
* * * * * * *
33409 AATCTCTTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCACATTGCGAT-TTACAT
1 AATCGCATTACGATAGTCAGAATCGCGTTGCGACAGTCAGAATCACATTGCGATAGT-CAG
*
33469 ATTCGCATTACGATAGTC
1 AATCGCATTACGATAGTC
33487 GAAAAATCGC
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
59 1 0.02
60 61 0.98
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (60 bp):
AATCGCATTACGATAGTCAGAATCGCGTTGCGACAGTCAGAATCACATTGCGATAGTCAG
Found at i:34611 original size:6 final size:6
Alignment explanation
Indices: 34600--34626 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34590 TTATTTGCGA
34600 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
34627 AATTCAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:34750 original size:8 final size:8
Alignment explanation
Indices: 34734--34773 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
34724 GAAAGGAATG
*
34734 ATAATAAA
1 ATAAAAAA
34742 ATAAAAAA
1 ATAAAAAA
*
34750 ATAAGAAA
1 ATAAAAAA
34758 ATAAAGAAA
1 ATAAA-AAA
34767 ATAAAAA
1 ATAAAAA
34774 TATTAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (8 bp):
ATAAAAAA
Found at i:34764 original size:9 final size:9
Alignment explanation
Indices: 34739--34771 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
34729 GAATGATAAT
34739 AAAATAAA-
1 AAAATAAAG
34747 AAAAT-AAG
1 AAAATAAAG
34755 AAAATAAAG
1 AAAATAAAG
34764 AAAATAAA
1 AAAATAAA
34772 AATATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 2 0.09
8 10 0.43
9 11 0.48
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (9 bp):
AAAATAAAG
Found at i:34921 original size:44 final size:44
Alignment explanation
Indices: 34873--34962 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
34863 AAAAACAAAC
* * **
34873 AAATAAATAAATAATACACTAAAATTAAAAAAAATGAATAACTA
1 AAATAAAAAAATAATAAACTAAAAAGAAAAAAAATGAATAACTA
* * **
34917 AAATAAAAAAATGATAAATTAAAAAGGGAAAAAATGAATAACTA
1 AAATAAAAAAATAATAAACTAAAAAGAAAAAAAATGAATAACTA
34961 AA
1 AA
34963 GATTTAAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (44 bp):
AAATAAAAAAATAATAAACTAAAAAGAAAAAAAATGAATAACTA
Found at i:34926 original size:21 final size:21
Alignment explanation
Indices: 34873--34962 Score: 78
Period size: 23 Copynumber: 4.1 Consensus size: 21
34863 AAAAACAAAC
*
34873 AAATAAATAAAT-AATACACTA
1 AAATAAAAAAATGAATA-ACTA
34894 AAATTAAAAAAAATGAATAACTA
1 AAA-T-AAAAAAATGAATAACTA
*
34917 AAATAAAAAAATG-ATAAATTA
1 AAATAAAAAAATGAAT-AACTA
34938 AAA-AGGGAAAAAATGAATAACTA
1 AAATA---AAAAAATGAATAACTA
34961 AA
1 AA
34963 GATTTAAAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
20 3 0.05
21 19 0.33
22 2 0.03
23 28 0.48
24 6 0.10
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (21 bp):
AAATAAAAAAATGAATAACTA
Found at i:34963 original size:21 final size:21
Alignment explanation
Indices: 34900--34963 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
34890 ACTAAAATTA
**
34900 AAAAAAATGAATAACTAAAAT
1 AAAAAAATGAATAACTAAAGG
*
34921 AAAAAAATG-ATAAATTAAAAAGG
1 AAAAAAATGAAT-AACT--AAAGG
*
34944 GAAAAAATGAATAACTAAAG
1 AAAAAAATGAATAACTAAAG
34964 ATTTAAAGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 2 0.06
21 16 0.47
23 14 0.41
24 2 0.06
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (21 bp):
AAAAAAATGAATAACTAAAGG
Found at i:36306 original size:12 final size:12
Alignment explanation
Indices: 36289--36321 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
36279 ATATGTAAAT
36289 ATAAAATAAAAA
1 ATAAAATAAAAA
36301 ATAAAAT-AAAA
1 ATAAAATAAAAA
36312 AT-AAATAAAA
1 ATAAAATAAAA
36322 TTAAGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 9 0.45
12 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:36311 original size:11 final size:11
Alignment explanation
Indices: 36284--36321 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
36274 GTGTAATATG
*
36284 TAAATATAAAA
1 TAAAAATAAAA
36295 TAAAAAATAAAA
1 T-AAAAATAAAA
36307 TAAAAAT-AAA
1 TAAAAATAAAA
36317 TAAAA
1 TAAAA
36322 TTAAGAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 8 0.32
11 7 0.28
12 10 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:37507 original size:21 final size:21
Alignment explanation
Indices: 37456--37508 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
37446 ATTATGACTA
37456 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
** *
37477 TCGCGTTGCGTTTTTCACAA-T
1 TCGCAATGCGATTTTC-CAATT
37498 TCGCAATGCGA
1 TCGCAATGCGA
37509 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:37523 original size:20 final size:21
Alignment explanation
Indices: 37498--37549 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
37488 TTTTCACAAT
*
37498 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
37518 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
37539 TCGCAATGCGA
1 TCGCAATGCGA
37550 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:37593 original size:21 final size:21
Alignment explanation
Indices: 37559--37625 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
37549 ATACTGACTA
* * *
37559 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
37580 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
37600 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
37621 TCGCA
1 TCGCA
37626 ACACGAATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:37682 original size:21 final size:21
Alignment explanation
Indices: 37629--37714 Score: 106
Period size: 20 Copynumber: 4.2 Consensus size: 21
37619 ATTCGCAACA
*
37629 CGAA-TAAGTAAATCGCAACG
1 CGAATTAAGTAAATCGCAATG
37649 CG-ATTAAGTAAATCGCAATG
1 CGAATTAAGTAAATCGCAATG
* * *
37669 CGAATTAGGAAAATCACAATG
1 CGAATTAAGTAAATCGCAATG
*
37690 CGAA-TACGTAAATCGCAATG
1 CGAATTAAGTAAATCGCAATG
37710 CGAAT
1 CGAAT
37715 CTGACTATCG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 36 0.64
21 19 0.34
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
CGAATTAAGTAAATCGCAATG
Found at i:38288 original size:20 final size:20
Alignment explanation
Indices: 38258--38317 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
38248 TAGTTTCGAG
38258 AATGAAAATCGCAACGCGAA
1 AATGAAAATCGCAACGCGAA
**
38278 AATGACTATCGCAACGCG-A
1 AATGAAAATCGCAACGCGAA
*
38297 AATGAAAATCGCAACGAGAA
1 AATGAAAATCGCAACGCGAA
38317 A
1 A
38318 CCAAAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGAA
Found at i:38301 original size:19 final size:19
Alignment explanation
Indices: 38258--38328 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
38248 TAGTTTCGAG
38258 AATGAAAATCGCAACGCGAA
1 AATGAAAATCGCAACGCG-A
**
38278 AATGACTATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
38297 AATGAAAATCGCAACGAGA
1 AATGAAAATCGCAACGCGA
**
38316 AACCAAAATCGCA
1 AATGAAAATCGCA
38329 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:38375 original size:33 final size:33
Alignment explanation
Indices: 38329--38416 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
38319 CAAAATCGCA
**
38329 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTACGATTCTCTCG
*
38362 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTACGATTCTCTCG
38395 TTGCGATAGTCATTTCCGCGTT
1 TTGCGATAGTCATTT-CGCGTT
38417 GTGATTTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 45 0.88
34 6 0.12
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTACGATTCTCTCG
Found at i:38384 original size:19 final size:19
Alignment explanation
Indices: 38360--38417 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 19
38350 ACGATTCTCT
38360 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
38379 CGTTGCGAT--TC---TCT
1 CGTTGCGATAGTCATTTCG
38393 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
38413 CGTTG
1 CGTTG
38418 TGATTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
14 11 0.35
16 2 0.06
17 2 0.06
19 10 0.32
20 6 0.19
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:40535 original size:94 final size:94
Alignment explanation
Indices: 40135--40512 Score: 597
Period size: 94 Copynumber: 4.1 Consensus size: 94
40125 TAGATTGCTT
* * *
40135 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
40196 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
40225 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTGTATTCTTTAACACTGTGAAGTTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC--TGTGTATTCTTTAACACTGTGAAGTTA
40290 GTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
64 GTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
40321 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
40386 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
40415 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
40480 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
40508 AGTAA
1 AGTAA
40513 TGCAATCCAT
Statistics
Matches: 271, Mismatches: 10, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
90 34 0.13
93 6 0.02
94 148 0.55
95 22 0.08
96 61 0.23
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:40601 original size:12 final size:12
Alignment explanation
Indices: 40584--40609 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40574 TTAGTAACAC
40584 TGTTTTGTCTTT
1 TGTTTTGTCTTT
40596 TGTTTTGTCTTT
1 TGTTTTGTCTTT
40608 TG
1 TG
40610 GTTTCGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.19, T:0.73
Consensus pattern (12 bp):
TGTTTTGTCTTT
Found at i:41124 original size:21 final size:21
Alignment explanation
Indices: 41100--41166 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
41090 TCATTCCTCG
41100 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
41121 AGAGGCCTCTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
41142 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
41163 AGAG
1 AGAG
41167 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:41124 original size:42 final size:42
Alignment explanation
Indices: 41078--41166 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
41068 CCTATCGTTG
41078 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
1 AAGAGGCCCCTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * * *
41120 AAGAGGCCTCTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCCCTATCATCCTCGAAGAGGTCCCTCCCACCATTC
41162 AAGAG
1 AAGAG
41167 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 35 0.85
43 2 0.05
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (42 bp):
AAGAGGCCCCTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:41767 original size:20 final size:20
Alignment explanation
Indices: 41746--41850 Score: 165
Period size: 20 Copynumber: 5.2 Consensus size: 20
41736 TGTATTATCT
* *
41746 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
41766 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
41786 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
41806 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
* *
41826 CGTTGCGAAAGTCAGTATCA
1 CGTTGCGAAAGTCAGAATCG
41846 CGTTG
1 CGTTG
41851 TAATTTTGTA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:41928 original size:20 final size:21
Alignment explanation
Indices: 41884--41935 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
41874 ATAGTCAGTA
*
41884 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
41905 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
41925 TCGCATTGCGA
1 TCGCATTGCGA
41936 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:41977 original size:21 final size:20
Alignment explanation
Indices: 41925--41986 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
41915 ATTTACTTAT
41925 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
41946 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
*
41967 TCGCGTTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
41987 CTGATTTGCG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.09
21 27 0.79
22 4 0.12
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:42138 original size:3 final size:3
Alignment explanation
Indices: 42130--42245 Score: 205
Period size: 3 Copynumber: 38.3 Consensus size: 3
42120 CTCTATAAAT
* *
42130 TAA TAA TAA TAC TAA TAA TAA TAA TAA GTAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
42176 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42224 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
42246 GTAATATATT
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
3 105 0.97
4 3 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43398 original size:106 final size:103
Alignment explanation
Indices: 43270--43525 Score: 304
Period size: 100 Copynumber: 2.5 Consensus size: 103
43260 GTATTGTTCT
* * * * *
43270 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATGGGAAA-T-TTTGTTGACAA
*
43335 TCAACCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCTC
63 TCAACCGCCCCTTCGTC-GTGAAGTTGAGCTTGTGCTATCTC
* * *
43376 GAGTCTAATATCATTCGTTGTGAAGTTGAAATTGACTCT-AAAT--GAAATTTTGTTGACAATCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGGAAATTTTGTTGACAATCA
* * *
43438 GCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTATCTT
66 ACCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTATCTC
* * *
43476 GGGTCCAATATCCTTCGTTGTGATGTTTAAATTGGCTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA-TGGGAA
43526 GCCCCTTCGT
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
100 78 0.61
101 5 0.04
102 5 0.04
104 6 0.05
106 33 0.26
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (103 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGGAAATTTTGTTGACAATCA
ACCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTATCTC
Found at i:47449 original size:12 final size:12
Alignment explanation
Indices: 47432--47464 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
47422 ATATGTAAAT
47432 ATAAAATAAAAA
1 ATAAAATAAAAA
47444 ATAAAAT-AAAA
1 ATAAAATAAAAA
47455 AT-AAATAAAA
1 ATAAAATAAAA
47465 TTAAGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 9 0.45
12 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:47454 original size:11 final size:11
Alignment explanation
Indices: 47427--47464 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
47417 GTGTAATATG
*
47427 TAAATATAAAA
1 TAAAAATAAAA
47438 TAAAAAATAAAA
1 T-AAAAATAAAA
47450 TAAAAAT-AAA
1 TAAAAATAAAA
47460 TAAAA
1 TAAAA
47465 TTAAGAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 8 0.32
11 7 0.28
12 10 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:48436 original size:3 final size:3
Alignment explanation
Indices: 48421--48476 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
48411 ATATATAAAT
* *
48421 TAA TAA TAC TAA TAA TAA TAA GTAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
48467 TAA T-A TAA TA
1 TAA TAA TAA TA
48477 TATTTTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:50462 original size:20 final size:20
Alignment explanation
Indices: 50437--50484 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
50427 ACGTCTCATT
50437 CGTTCATTTACGTTCGTGAA
1 CGTTCATTTACGTTCGTGAA
* * *
50457 CGTTCAGTTATGTTCGTGTA
1 CGTTCATTTACGTTCGTGAA
*
50477 TGTTCATT
1 CGTTCATT
50485 CATTTATGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (20 bp):
CGTTCATTTACGTTCGTGAA
Found at i:51428 original size:16 final size:16
Alignment explanation
Indices: 51407--51439 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
51397 CCAACGTTTA
51407 TGTTCGTTTATGATTG
1 TGTTCGTTTATGATTG
*
51423 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGATTG
51439 T
1 T
51440 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGATTG
Found at i:51990 original size:36 final size:37
Alignment explanation
Indices: 51948--52017 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
51938 AAAATTATTA
* * *
51948 AAATAATTTTAATATA-AA-TTATATATTTATTTTCAT
1 AAATAATTATAAAATAGAAGTT-TATATATATTTTCAT
51984 AAATAATTATAAAATAGAAGTTTATATATATTTT
1 AAATAATTATAAAATAGAAGTTTATATATATTTT
52018 TAAAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 14 0.48
37 13 0.45
38 2 0.07
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
AAATAATTATAAAATAGAAGTTTATATATATTTTCAT
Found at i:52420 original size:48 final size:47
Alignment explanation
Indices: 52364--52472 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 47
52354 TTTGTTTCAC
* * *
52364 TGAAAACA-TTTTCTAAAATATAAATTATGAAAAATGATTTATATTTA
1 TGAAAACATTTTTCGAAAA-ATAAATTATGAAAAATAATTTACATTTA
* *
52411 TAGAAAACATTTTTCGAAAAATGAATTCTGAAAAATAATTTACATTTA
1 T-GAAAACATTTTTCGAAAAATAAATTATGAAAAATAATTTACATTTA
52459 TGAAAA-ATATTTTC
1 TGAAAACAT-TTTTC
52473 CGTTGTTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
46 2 0.04
47 11 0.20
48 32 0.59
49 9 0.17
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (47 bp):
TGAAAACATTTTTCGAAAAATAAATTATGAAAAATAATTTACATTTA
Found at i:55469 original size:20 final size:20
Alignment explanation
Indices: 55396--55476 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
55386 TTAGATATAT
* *
55396 TTCAAAACTTTCATTTTCAGA
1 TTCATAACTTT-ACTTTCAGA
*
55417 TTCATAACTTT-C--T-AAA
1 TTCATAACTTTACTTTCAGA
55433 TTCATAA-TTTA-TTTCAGA
1 TTCATAACTTTACTTTCAGA
55451 TTCATAACTTTACTTTCAGA
1 TTCATAACTTTACTTTCAGA
55471 TTCATA
1 TTCATA
55477 GTCCAATGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.06
16 9 0.18
17 2 0.04
18 9 0.18
19 4 0.08
20 13 0.26
21 10 0.20
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (20 bp):
TTCATAACTTTACTTTCAGA
Found at i:58080 original size:31 final size:31
Alignment explanation
Indices: 58007--58090 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 31
57997 ATACCTAAAT
* *
58007 TTAA-TTTTTATTTTATTTTAGTACCCATTG
1 TTAACTTTTTATTTCATTTTAGTACACATTG
*
58037 TTAAC-TTTTATTTCATTTTAGTACATATTG
1 TTAACTTTTTATTTCATTTTAGTACACATTG
58067 TTAACTTTTTATTTCATTTTAGTA
1 TTAACTTTTTATTTCATTTTAGTA
58091 TTTAAATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
30 31 0.63
31 18 0.37
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.60
Consensus pattern (31 bp):
TTAACTTTTTATTTCATTTTAGTACACATTG
Found at i:59179 original size:7 final size:8
Alignment explanation
Indices: 59155--59181 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
59145 TAAGTGAATT
59155 AATTGAAA
1 AATTGAAA
59163 AATTGAAA
1 AATTGAAA
59171 AATTGAAA
1 AATTGAAA
59179 AAT
1 AAT
59182 ATGATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (8 bp):
AATTGAAA
Found at i:60984 original size:17 final size:19
Alignment explanation
Indices: 60942--60988 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
60932 TGTTTTACGA
*
60942 TAATTATTAATATTTTGAT
1 TAATTTTTAATATTTTGAT
60961 TAATTTTTAA-ATTTT-AT
1 TAATTTTTAATATTTTGAT
60978 T-ATTTTTAATA
1 TAATTTTTAATA
60989 AGTTTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 8 0.31
17 4 0.15
18 5 0.19
19 9 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TAATTTTTAATATTTTGAT
Found at i:64321 original size:40 final size:41
Alignment explanation
Indices: 64276--64367 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 41
64266 GTTTTTACAG
* * * *
64276 AAACGCCGCTAAATAATTTACTTTAGTGGCGCTTTTATAA-
1 AAACGCCGCTAAAGAATGTAATTTAGTGGCGCTTTTAAAAC
* *
64316 AAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTAAAAC
1 AAACGCCGCTAAAGAATGTAATTTAGTGGCGCTTTTAAAAC
64357 AAACGCCGCTA
1 AAACGCCGCTA
64368 TATACAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 34 0.76
41 11 0.24
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (41 bp):
AAACGCCGCTAAAGAATGTAATTTAGTGGCGCTTTTAAAAC
Found at i:67403 original size:2 final size:2
Alignment explanation
Indices: 67396--67429 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
67386 ACTTTTCTAA
67396 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
67430 TGCAAATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68247 original size:21 final size:21
Alignment explanation
Indices: 68223--68281 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
68213 TGATTTATTA
**
68223 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
68244 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
68265 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
68282 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:68524 original size:43 final size:43
Alignment explanation
Indices: 68485--68706 Score: 230
Period size: 44 Copynumber: 5.1 Consensus size: 43
68475 TTTTGCGGTA
*
68485 TTTTTGGGAAAAACGCCGCTAAATCTCAAGACCTATTGCGGCG
1 TTTTTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCG
* * * **
68528 TTTGTGGAAAAAAACACCATTAAATCTCAACACCTATTGCGGCG
1 TTTTTGG-GAAAAACGCCGCTAAATCTCAACACCTATTGCGGCG
* * *
68572 TTTGTGGGAAAAACACCGTTAAATCTCAACACCTATTGCGGCG
1 TTTTTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCG
* * * *
68615 TTTTTTTGGAAAAATGCCGCCAAATATCAACACCTATTGCGGCG
1 -TTTTTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCG
* * * *** *
68659 TTTGTT-GGACAAACGCCGCTATATATCGTTACCTATTGCGGCA
1 TTT-TTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCG
68702 TTTTT
1 TTTTT
68707 TGTTACCAAA
Statistics
Matches: 153, Mismatches: 23, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
42 2 0.01
43 75 0.49
44 76 0.50
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
TTTTTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCG
Found at i:68584 original size:87 final size:86
Alignment explanation
Indices: 68489--68679 Score: 242
Period size: 87 Copynumber: 2.2 Consensus size: 86
68479 GCGGTATTTT
* *
68489 TGGGAAAAACGCCGCTAAATCTCAAGACCTATTGCGGCG-TTTGTGGAAAAAAACAC-CATTAAA
1 TGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTTGTGGAAAAAAAC-CGC--CAAA
*
68552 TCTCAACACCTATTGCGGCGTTTG
63 TATCAACACCTATTGCGGCGTTTG
* * * **
68576 TGGGAAAAACACCGTTAAATCTCAACACCTATTGCGGCGTTTTTTTGGAAAAATGCCGCCAAATA
1 TGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCG-TTTTGTGGAAAAAAACCGCCAAATA
68641 TCAACACCTATTGCGGCGTTTG
65 TCAACACCTATTGCGGCGTTTG
* *
68663 TTGGACAAACGCCGCTA
1 TGGGAAAAACGCCGCTA
68680 TATATCGTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
87 75 0.84
88 1 0.01
89 13 0.15
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (86 bp):
TGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTTGTGGAAAAAAACCGCCAAATAT
CAACACCTATTGCGGCGTTTG
Found at i:68693 original size:87 final size:87
Alignment explanation
Indices: 68489--68707 Score: 219
Period size: 87 Copynumber: 2.5 Consensus size: 87
68479 GCGGTATTTT
* * * * * ** *
68489 TGGGAAAAACGCCGCTAAATCTCAAGACCTATTGCGGC--GTTTGTGGAAAAAAACAC-CATTAA
1 TGGGAAAAACACCGCTAAATATCAACACCTATTGCGGCATTTTTTTGGAAAAATGC-CGC--CAA
*
68551 ATCTCAACACCTATTGCGGCGTTTG
63 ATATCAACACCTATTGCGGCGTTTG
* * *
68576 TGGGAAAAACACCGTTAAATCTCAACACCTATTGCGGCGTTTTTTTGGAAAAATGCCGCCAAATA
1 TGGGAAAAACACCGCTAAATATCAACACCTATTGCGGCATTTTTTTGGAAAAATGCCGCCAAATA
68641 TCAACACCTATTGCGGCGTTTG
66 TCAACACCTATTGCGGCGTTTG
* * * * ***
68663 TTGGACAAACGCCGCTATATATCGTTACCTATTGCGGCATTTTTT
1 TGGGAAAAACACCGCTAAATATCAACACCTATTGCGGCATTTTTT
68708 GTTACCAAAT
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
87 96 0.87
88 1 0.01
89 13 0.12
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (87 bp):
TGGGAAAAACACCGCTAAATATCAACACCTATTGCGGCATTTTTTTGGAAAAATGCCGCCAAATA
TCAACACCTATTGCGGCGTTTG
Found at i:70716 original size:23 final size:23
Alignment explanation
Indices: 70690--70753 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
70680 CAGCTCGTAT
70690 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* *
70713 AATTGCACCGGAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACATAG
*
70736 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
70754 TATAATAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:72352 original size:21 final size:21
Alignment explanation
Indices: 72328--72370 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
72318 TCTGGTTTGT
* * *
72328 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
72349 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
72370 T
1 T
72371 AGCCCAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:75952 original size:23 final size:23
Alignment explanation
Indices: 75926--75981 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
75916 CACCACAGCT
*
75926 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
75949 CGTAGAATTGCACTGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
75972 CGTAGAATTG
1 CGTAGAATTG
75982 AATCGTAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:77615 original size:21 final size:21
Alignment explanation
Indices: 77591--77633 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
77581 TCTGGTTTGT
* * *
77591 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
77612 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
77633 T
1 T
77634 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:78359 original size:42 final size:43
Alignment explanation
Indices: 78312--78427 Score: 110
Period size: 48 Copynumber: 2.6 Consensus size: 43
78302 GGATGTTACA
* * *
78312 CTCACCCTCAGTTTTAGACTTCTCATCCTCATCATCAGCACCCTCACC
1 CTCACCCTCAGTTTTAGACTTCTCAACCTCACCAT-A--A-GC-CACC
*
78360 CTCACCCTCAGTTTTAGACTTCTCAACCTCACCCTAAG-CACC
1 CTCACCCTCAGTTTTAGACTTCTCAACCTCACCATAAGCCACC
**
78402 CTCAGTCTCAGTTTTCA-ACTTCTCAA
1 CTCACCCTCAGTTTT-AGACTTCTCAA
78428 GCTAAGTTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
42 26 0.43
43 1 0.02
45 1 0.02
47 1 0.02
48 32 0.52
ACGTcount: A:0.22, C:0.41, G:0.07, T:0.30
Consensus pattern (43 bp):
CTCACCCTCAGTTTTAGACTTCTCAACCTCACCATAAGCCACC
Found at i:78368 original size:48 final size:48
Alignment explanation
Indices: 78312--78405 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
78302 GGATGTTACA
* * *
78312 CTCACCCTCAGTTTTAGACTTCTCATCCTCATCATCAGCACCCTCACC
1 CTCACCCTCAGTTTTAGACTTCTCAACCTCACCATAAGCACCCTCACC
*
78360 CTCACCCTCAGTTTTAGACTTCTCAACCTCACCCTAAGCACCCTCA
1 CTCACCCTCAGTTTTAGACTTCTCAACCTCACCATAAGCACCCTCA
78406 GTCTCAGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.22, C:0.44, G:0.06, T:0.28
Consensus pattern (48 bp):
CTCACCCTCAGTTTTAGACTTCTCAACCTCACCATAAGCACCCTCACC
Done.