Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013868.1 Kokia drynarioides strain JFW-HI SEQ_128896, 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: 221844
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:2730 original size:23 final size:23
Alignment explanation
Indices: 2704--2747 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2694 CAATGAGATG
*
2704 ATACAGAA-ATTGCTACAAAGGTC
1 ATACAGAATA-TGCCACAAAGGTC
2727 ATACAGAATATGCCACAAAGG
1 ATACAGAATATGCCACAAAGG
2748 CTTAGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (23 bp):
ATACAGAATATGCCACAAAGGTC
Found at i:5098 original size:10 final size:10
Alignment explanation
Indices: 5083--5112 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5073 ATTGCCGTGT
5083 GAAGAAGAAA
1 GAAGAAGAAA
5093 GAAGAAGAAA
1 GAAGAAGAAA
*
5103 TAAGAAGAAA
1 GAAGAAGAAA
5113 AATGGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:5238 original size:20 final size:21
Alignment explanation
Indices: 5202--5251 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
5192 TCATTAAGCT
*
5202 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTACA-C
5222 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCATATTTACAC
5242 TTAATATAAA
1 TTAAT-TAAA
5252 CCATGCCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTACAC
Found at i:6597 original size:2 final size:2
Alignment explanation
Indices: 6590--6632 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
6580 CAAACCAACT
*
6590 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AA AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
6632 A
1 A
6633 TATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:7226 original size:35 final size:34
Alignment explanation
Indices: 7180--7262 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
7170 GAGCTCAGCT
*
7180 CTAGTTGGATAAACCAACG-ATGTTTGCACTCAACA
1 CTAGTTGGATAAACCAACGAATGTGTGC-C-CAACA
* *
7215 CTAGTCGGATAAACCGACGAATGTGTGCCCAACA
1 CTAGTTGGATAAACCAACGAATGTGTGCCCAACA
*
7249 CTAGTTAGATAAAC
1 CTAGTTGGATAAAC
7263 TGACGATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 17 0.40
35 18 0.43
36 7 0.17
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (34 bp):
CTAGTTGGATAAACCAACGAATGTGTGCCCAACA
Found at i:7253 original size:34 final size:36
Alignment explanation
Indices: 7180--7268 Score: 112
Period size: 34 Copynumber: 2.6 Consensus size: 36
7170 GAGCTCAGCT
* *
7180 CTAGTTGGATAAACCAACG-ATGTTTGCACTCAACA
1 CTAGTTGGATAAACCGACGAATGTGTGCACTCAACA
*
7215 CTAGTCGGATAAACCGACGAATGTGTGC-C-CAACA
1 CTAGTTGGATAAACCGACGAATGTGTGCACTCAACA
* *
7249 CTAGTTAGATAAACTGACGA
1 CTAGTTGGATAAACCGACGA
7269 TATTAACAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 22 0.47
35 18 0.38
36 7 0.15
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (36 bp):
CTAGTTGGATAAACCGACGAATGTGTGCACTCAACA
Found at i:7362 original size:109 final size:108
Alignment explanation
Indices: 7136--7369 Score: 240
Period size: 109 Copynumber: 2.1 Consensus size: 108
7126 GTTTGCGCCT
* * * ** *
7136 AGCGCTAGTCTGATAAACAAACAATATTAACTATGAGCTCAGCTCTAGTTGGATAAACCAACGAT
1 AGCGCTAGT-TGATAAACAAACAATATTAACAATGAACCCAGCTCTAGTTAAATAAACCAACAAT
* * **
7201 GTTTGCACTCAACACTAGTCGGATAAACCGACGAATGTGTGCCC
65 ATGTGCACTCAACACTAGTAAGATAAACCGACGAATGTGTGCCC
* * ** *
7245 AACACTAGTTAGATAAACTGACGATATTAACAATGAACCCAGCTCTAGTTAAATAAACCAACAAA
1 AGCGCTAGTT-GATAAACAAACAATATTAACAATGAACCCAGCTCTAGTTAAATAAACCAAC-AA
* *
7310 TATGTGC-CT-AACACTAGTAAGATAAACTGATGGAA-GTTGTGCCC
64 TATGTGCACTCAACACTAGTAAGATAAACCGA-CGAATG-TGTGCCC
7354 AGCGCTAGTTGGATAA
1 AGCGCTAGTT-GATAA
7370 CCAACGAATT
Statistics
Matches: 101, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
108 20 0.20
109 75 0.74
110 6 0.06
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (108 bp):
AGCGCTAGTTGATAAACAAACAATATTAACAATGAACCCAGCTCTAGTTAAATAAACCAACAATA
TGTGCACTCAACACTAGTAAGATAAACCGACGAATGTGTGCCC
Found at i:11311 original size:58 final size:57
Alignment explanation
Indices: 11196--11622 Score: 205
Period size: 57 Copynumber: 7.5 Consensus size: 57
11186 AATGGGGTCG
* * * * * * * * *
11196 AAAATG-AAGTTTCGAAGAGTTAGGGGTAAAATGTCATTTTGGGAGAG-TTCGAGGTA
1 AAAATGTAATTTTTGAAAAGTTAGGGGAAAAATGTAATTTT-TGAAAGTTTAGGGGTA
* * * *
11252 AAAATGTGATTTTTGAGAAGTTCGGGGAAAATATGTAATTTTTGAAAGTTTGGGGGTAA
1 AAAATGTAATTTTTGAAAAGTTAGGGGAAAA-ATGTAATTTTTGAAAGTTTAGGGGT-A
* * * * * ** *
11311 AAAATGTAATTTTTG-AAAGATCGAGGGTAACAATGTGATTTTT-AGTAGTACAGGGGTT
1 AAAATGTAATTTTTGAAAAG-T-TAGGGGAAAAATGTAATTTTTGA-AAGTTTAGGGGTA
* * * * * * *
11369 AAAATGTGATTTTTG-GAAGTTTGGGGGCAAAAATATAATTTTT-AGAGGTTTAGAGGCA
1 AAAATGTAATTTTTGAAAAG-TTAGGGG-AAAAATGTAATTTTTGA-AAGTTTAGGGGTA
* * * * * * *** *
11427 AAAATGTGACTTTTG-GAAGTTTAGGGTAAAAATGTGATTTTTGGAAGTACGGGGGCA
1 AAAATGTAATTTTTGAAAAG-TTAGGGGAAAAATGTAATTTTTGAAAGTTTAGGGGTA
* * * *
11484 AAAATGTAA-TTTT-AAAACTTTAAGGGTAAAAATGTAATTTTTAAAAGTTTAAGGG-A
1 AAAATGTAATTTTTGAAAA-GTT-AGGGGAAAAATGTAATTTTTGAAAGTTTAGGGGTA
* * * *
11540 AAAATGTAATTTTGGAAAAGTTTAAGGGTAAAATGT-ATTTTTGGAAGTTT--GGGTA
1 AAAATGTAATTTTTGAAAAG-TTAGGGGAAAAATGTAATTTTTGAAAGTTTAGGGGTA
*
11595 TAAAATGTAATTTTGGAAAAGTTCAGGG
1 -AAAATGTAATTTTTGAAAAGTT-AGGG
11623 ACCTTCTGGG
Statistics
Matches: 284, Mismatches: 69, Indels: 36
0.73 0.18 0.09
Matches are distributed among these distances:
54 3 0.01
55 3 0.01
56 59 0.21
57 92 0.32
58 87 0.31
59 34 0.12
60 6 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTTGAAAAGTTAGGGGAAAAATGTAATTTTTGAAAGTTTAGGGGTA
Found at i:11470 original size:28 final size:28
Alignment explanation
Indices: 11248--11612 Score: 215
Period size: 29 Copynumber: 12.8 Consensus size: 28
11238 GAGAGTTCGA
*
11248 GGTAAAAATGTGATTTTTGAGAAG-TTCG
1 GGTAAAAATGTGATTTTTG-GAAGTTTAG
* * * *
11276 GGGAAAATATGTAATTTTTGAAAGTTTGGG
1 GGTAAAA-ATGTGATTTTTGGAAGTTT-AG
* * **
11306 GGTAAAAAATGTAATTTTTGAAAGATCGAG
1 GGT-AAAAATGTGATTTTTGGAAG-TTTAG
* * * **
11336 GGTAACAATGTGATTTTTAGTAGTACAGG
1 GGTAAAAATGTGATTTTTGGAAGTTTA-G
* *
11365 GGTTAAAATGTGATTTTTGGAAGTTTGGG
1 GGTAAAAATGTGATTTTTGGAAGTTT-AG
* * * * *
11394 GGCAAAAATATAATTTTTAGAGGTTTAG
1 GGTAAAAATGTGATTTTTGGAAGTTTAG
* *
11422 AGGCAAAAATGTGACTTTTGGAAGTTTAG
1 -GGTAAAAATGTGATTTTTGGAAGTTTAG
***
11451 GGTAAAAATGTGATTTTTGGAAGTACGGG
1 GGTAAAAATGTGATTTTTGGAAGT-TTAG
* * ** *
11480 GGCAAAAATGT-AATTTTAAAACTTTAAG
1 GGTAAAAATGTGATTTTTGGAAGTTT-AG
* **
11508 GGTAAAAATGTAATTTTTAAAAGTTTAAG
1 GGTAAAAATGTGATTTTTGGAAGTTT-AG
*
11537 GG-AAAAATGT-AATTTTGGAAAAGTTTAAG
1 GGTAAAAATGTGATTTTTGG--AAGTTT-AG
11566 GGT-AAAATGT-ATTTTTGGAAGTTT-G
1 GGTAAAAATGTGATTTTTGGAAGTTTAG
*
11591 GGTATAAAATGT-AATTTTGGAA
1 GGTA-AAAATGTGATTTTTGGAA
11613 AAGTTCAGGG
Statistics
Matches: 266, Mismatches: 55, Indels: 33
0.75 0.16 0.09
Matches are distributed among these distances:
25 4 0.02
27 27 0.10
28 61 0.23
29 146 0.55
30 23 0.09
31 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
GGTAAAAATGTGATTTTTGGAAGTTTAG
Found at i:11580 original size:56 final size:57
Alignment explanation
Indices: 11426--11617 Score: 184
Period size: 56 Copynumber: 3.4 Consensus size: 57
11416 GTTTAGAGGC
* * ** ** *
11426 AAAAATGTGACTTTTGG--AAGTTT-AGGGTAAAAATGTGATTTTTGGAAGTACGGGGGC
1 AAAAATGT-AATTTTGGAAAAGTTTAAGGGTAAAAATGTAATTTTTAAAAGT--TTGGGT
*
11483 AAAAATGTAATTTT--AAAACTTTAAGGGTAAAAATGTAATTTTTAAAAGTTTAAGGG-
1 AAAAATGTAATTTTGGAAAAGTTTAAGGGTAAAAATGTAATTTTTAAAAGTTT--GGGT
**
11539 AAAAATGTAATTTTGGAAAAGTTTAAGGGT-AAAATGT-ATTTTTGGAAGTTTGGGT
1 AAAAATGTAATTTTGGAAAAGTTTAAGGGTAAAAATGTAATTTTTAAAAGTTTGGGT
11594 ATAAAATGTAATTTTGGAAAAGTT
1 A-AAAATGTAATTTTGGAAAAGTT
11618 CAGGGACCTT
Statistics
Matches: 116, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
54 3 0.03
55 1 0.01
56 58 0.50
57 41 0.35
58 13 0.11
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (57 bp):
AAAAATGTAATTTTGGAAAAGTTTAAGGGTAAAAATGTAATTTTTAAAAGTTTGGGT
Found at i:14805 original size:16 final size:17
Alignment explanation
Indices: 14778--14809 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
14768 ATATTCTTTC
14778 CAATAGAATATTAACTT
1 CAATAGAATATTAACTT
14795 CAATA-AATATTAACT
1 CAATAGAATATTAACT
14810 ATAGGAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
CAATAGAATATTAACTT
Found at i:20527 original size:55 final size:55
Alignment explanation
Indices: 20457--20560 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
20447 ACTTGTAACT
* **
20457 TAACAATCAATTTAAACATATAAGCAATTTATTCAAAAGAAGCAATATTTCAATG
1 TAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTTCAATG
* *
20512 TAACATTCCATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATT
1 TAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATT
20561 CAACCATAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (55 bp):
TAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTTCAATG
Found at i:20571 original size:55 final size:55
Alignment explanation
Indices: 20457--20579 Score: 158
Period size: 55 Copynumber: 2.2 Consensus size: 55
20447 ACTTGTAACT
* ** **
20457 TAACAATCAATTTAAACATATAAGCAATTTATTCAAAAGAAGCAATATTTCAATG
1 TAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTTCAACA
* *
20512 TAACATTCCATTTAAACATATAAACAATCGATTCAAAAGAAGCAATA-TTCAACCA
1 TAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTTCAA-CA
*
20567 TAACAATCGATTT
1 TAACAATCAATTT
20580 CAAAGAAGCA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 5 0.09
55 53 0.91
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (55 bp):
TAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTTCAACA
Found at i:20572 original size:34 final size:34
Alignment explanation
Indices: 20534--20646 Score: 122
Period size: 34 Copynumber: 3.3 Consensus size: 34
20524 TAAACATATA
20534 AACAATCGATTCAAAAGAAGCAATA-TTCAACCAT
1 AACAATCGATTCAAAAGAAGCAATATTTCAA-CAT
20568 AACAATCGATTTC-AAAGAAGCAATATTTCAACAT
1 AACAATCGA-TTCAAAAGAAGCAATATTTCAACAT
* * * * * * *
20602 AATAATTGATTTAAAACAAACAGTATTTTAACAT
1 AACAATCGATTCAAAAGAAGCAATATTTCAACAT
*
20636 GACAATCGATT
1 AACAATCGATT
20647 TAAACATAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
33 2 0.03
34 56 0.85
35 8 0.12
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (34 bp):
AACAATCGATTCAAAAGAAGCAATATTTCAACAT
Found at i:21911 original size:3 final size:3
Alignment explanation
Indices: 21897--21953 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
21887 TCACTTGCTG
* * * * * * *
21897 CAT CAC CAT CAT CAT CAT CAT CAT CGT CGT CGT CAC CAT CCT CAT CCT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
21945 CAT CAT CAT
1 CAT CAT CAT
21954 TGGATACATC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.25, C:0.40, G:0.05, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:30648 original size:2 final size:2
Alignment explanation
Indices: 30643--30668 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30633 AAAATGCAGC
30643 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
30669 AACTGAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40204 original size:29 final size:30
Alignment explanation
Indices: 40151--40210 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
40141 AGAATTGGAT
*
40151 AAAATCAAAATTTCATGTATACAATTGCAC
1 AAAATCAAAAGTTCATGTATACAATTGCAC
40181 AAAATC-AAAGTTCATGTATACAATTGCAC
1 AAAATCAAAAGTTCATGTATACAATTGCAC
40210 A
1 A
40211 TTAAACATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (30 bp):
AAAATCAAAAGTTCATGTATACAATTGCAC
Found at i:42023 original size:25 final size:25
Alignment explanation
Indices: 41989--42198 Score: 249
Period size: 25 Copynumber: 8.4 Consensus size: 25
41979 TGACTATTGA
* * * *
41989 TTAATGTGATATATGCGTATATGAG
1 TTAACGTGATATACGCTTATATGTG
*
42014 TTAATGTGATATACGCTTATATGTG
1 TTAACGTGATATACGCTTATATGTG
*
42039 TTAACATGATATACGCTTATATGTG
1 TTAACGTGATATACGCTTATATGTG
**
42064 TTAACGTGATATACAATTATATGTG
1 TTAACGTGATATACGCTTATATGTG
* **
42089 TTAACATGATATAAACTTATATGTG
1 TTAACGTGATATACGCTTATATGTG
* * *
42114 TTAACGTGATACATGCTTATAGGTG
1 TTAACGTGATATACGCTTATATGTG
*
42139 TTAACGTGATATACACTTATATGTG
1 TTAACGTGATATACGCTTATATGTG
* * *
42164 TTAATGTGATACATGCTTATATGTG
1 TTAACGTGATATACGCTTATATGTG
*
42189 TTAATGTGAT
1 TTAACGTGAT
42199 TAATGTGTAA
Statistics
Matches: 161, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 161 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.41
Consensus pattern (25 bp):
TTAACGTGATATACGCTTATATGTG
Found at i:42037 original size:64 final size:64
Alignment explanation
Indices: 41909--42037 Score: 177
Period size: 64 Copynumber: 2.0 Consensus size: 64
41899 AAATTATCAA
* * ** *
41909 TAAATGTGACTATAGATTAATATGATTTATGCCCATATGTGTTAATGTGATATGTGCTTGTATG
1 TAAATGTGACTATAGATTAATATGATATATGCCCATATGAGTTAATGTGATATACGCTTATATG
* * **
41973 TAAATGTGACTATTGATTAATGTGATATATGCGTATATGAGTTAATGTGATATACGCTTATATG
1 TAAATGTGACTATAGATTAATATGATATATGCCCATATGAGTTAATGTGATATACGCTTATATG
42037 T
1 T
42038 GTTAACATGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (64 bp):
TAAATGTGACTATAGATTAATATGATATATGCCCATATGAGTTAATGTGATATACGCTTATATG
Found at i:42679 original size:21 final size:22
Alignment explanation
Indices: 42650--42692 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
42640 TATTGATTAT
*
42650 AAATAGGTTTAA-TAAAGGTTAA
1 AAATAGG-TTAATTAAAGCTTAA
42672 AAAT-GGTTAATTAAAGCTTAA
1 AAATAGGTTAATTAAAGCTTAA
42693 TGATGAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (22 bp):
AAATAGGTTAATTAAAGCTTAA
Found at i:43072 original size:9 final size:8
Alignment explanation
Indices: 43043--43072 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
43033 GGTTTAAGGA
43043 TGAAAATG
1 TGAAAATG
43051 TGAAAATG
1 TGAAAATG
43059 TGAAAATGG
1 TGAAAAT-G
43068 TGAAA
1 TGAAA
43073 TTACATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (8 bp):
TGAAAATG
Found at i:51257 original size:21 final size:21
Alignment explanation
Indices: 51233--51290 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
51223 GTTGCATGAT
51233 TTGTATCGGTAGAACTCATAC
1 TTGTATCGGTAGAACTCATAC
* *
51254 TTGTATCGATAGAAATCATAC
1 TTGTATCGGTAGAACTCATAC
51275 TTGTATCGGTAGAACT
1 TTGTATCGGTAGAACT
51291 AGCACAGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (21 bp):
TTGTATCGGTAGAACTCATAC
Found at i:74726 original size:24 final size:24
Alignment explanation
Indices: 74693--74738 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
74683 CAAGGCCAAT
*
74693 TATTAAAAAACCCAACATTTTGCA
1 TATTAAAAAACCCAAAATTTTGCA
*
74717 TATTAGAAAACCCAAAATTTTG
1 TATTAAAAAACCCAAAATTTTG
74739 ATTAGGGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (24 bp):
TATTAAAAAACCCAAAATTTTGCA
Found at i:83329 original size:11 final size:11
Alignment explanation
Indices: 83313--83345 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
83303 ATTTACAGCC
83313 TTTGGGAGGAA
1 TTTGGGAGGAA
83324 TTTGGGAGGAA
1 TTTGGGAGGAA
83335 TTTGGGAGGAA
1 TTTGGGAGGAA
83346 CGCTTTGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.45, T:0.27
Consensus pattern (11 bp):
TTTGGGAGGAA
Found at i:98065 original size:20 final size:19
Alignment explanation
Indices: 98027--98066 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
98017 TTGAAAAGGT
*
98027 TATATATGAAATGGATATA
1 TATATATGAAAAGGATATA
*
98046 TATATATTGAAAAGGTTATA
1 TATATA-TGAAAAGGATATA
98066 T
1 T
98067 CCAAAATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (19 bp):
TATATATGAAAAGGATATA
Found at i:98091 original size:31 final size:30
Alignment explanation
Indices: 98045--98124 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
98035 AAATGGATAT
98045 ATATATATTGAAAAGGTTATATCCAAAATGG
1 ATATATATTGAAAAGGTTATATCCAAAA-GG
* * * *
98076 ATATCTATTGGAAAGGTTGTATCCGAAAGG
1 ATATATATTGAAAAGGTTATATCCAAAAGG
*
98106 ATAT-TATACGAAAAGGTTA
1 ATATATAT-TGAAAAGGTTA
98125 AAAAGGGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 3 0.07
30 14 0.34
31 24 0.59
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (30 bp):
ATATATATTGAAAAGGTTATATCCAAAAGG
Found at i:102402 original size:23 final size:23
Alignment explanation
Indices: 102376--102421 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
102366 AAAAAGCAAC
102376 ATGTGTTAATAAAAAAATTTATT
1 ATGTGTTAATAAAAAAATTTATT
102399 ATGTGTTAATAAAAAAATTTATT
1 ATGTGTTAATAAAAAAATTTATT
102422 CTATCTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
ATGTGTTAATAAAAAAATTTATT
Found at i:102430 original size:23 final size:23
Alignment explanation
Indices: 102381--102431 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
102371 GCAACATGTG
* *
102381 TTAATAAAAAAATTTATTATGTG
1 TTAATAAAAAAATTTATTATATC
*
102404 TTAATAAAAAAATTTATTCTATC
1 TTAATAAAAAAATTTATTATATC
102427 TTAAT
1 TTAAT
102432 TTAACTACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAATAAAAAAATTTATTATATC
Found at i:107712 original size:31 final size:30
Alignment explanation
Indices: 107654--107712 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
107644 CTCTCAAACA
*
107654 TTTCCCCAAAAACTTTTACTCCTTCTCACT
1 TTTCCCCAAAAACTTTTACTCCCTCTCACT
* *
107684 TTTCCCCCAAATCTTTTACTCCCCTCTCA
1 TTTCCCCAAAAACTTTTACT-CCCTCTCA
107713 TCCCACCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTCCCCAAAAACTTTTACTCCCTCTCACT
Found at i:108362 original size:16 final size:16
Alignment explanation
Indices: 108326--108365 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
108316 CTCAAATAAA
108326 TATATTC-AATTTAAT
1 TATATTCAAATTTAAT
* *
108341 TTTATTCAAATTTCAT
1 TATATTCAAATTTAAT
108357 TATATTCAA
1 TATATTCAA
108366 CTCAATTCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTCAAATTTAAT
Found at i:111579 original size:31 final size:31
Alignment explanation
Indices: 111537--111603 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
111527 GCAATTATGT
* * *
111537 ACATGAAACTTTGGTTGTAATTCAAATGTGC
1 ACATTAAACTTTGATTGTAATTCAAATGTAC
* * *
111568 ACATTAAACTTTGATTTTGATTCAATTGTAC
1 ACATTAAACTTTGATTGTAATTCAAATGTAC
111599 ACATT
1 ACATT
111604 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (31 bp):
ACATTAAACTTTGATTGTAATTCAAATGTAC
Found at i:112785 original size:16 final size:15
Alignment explanation
Indices: 112752--112793 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
112742 TGATAAAAAA
* *
112752 TAATTTTGAATTTTT
1 TAATTTTAAATATTT
112767 TAATTTATAAATATTT
1 TAATTT-TAAATATTT
112783 TAATTTTAAAT
1 TAATTTTAAAT
112794 GCAGTAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TAATTTTAAATATTT
Found at i:115308 original size:2 final size:2
Alignment explanation
Indices: 115301--115332 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
115291 ATCTATTTAT
115301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
115333 AATACGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119059 original size:20 final size:20
Alignment explanation
Indices: 119031--119087 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
119021 TCACGTCAGC
*
119031 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
119051 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
119071 AAATTA-TTT-AAATTATT
1 AAATTATTTTAAAATTATT
119088 TTTTTGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 3 0.09
17 5 0.16
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:119083 original size:29 final size:30
Alignment explanation
Indices: 119040--119119 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
119030 CAAATGATTT
*
119040 TAAAATTATTAAAATTATTTTTTAAAAT-A
1 TAAAATTATTTAAATTATTTTTTAAAATAA
*
119069 TAAAATTATTTAAATTATTTTTTTGAAATAA
1 TAAAATTATTTAAATTA-TTTTTTAAAATAA
*
119100 TAAAATTA-TTAAATAATTTT
1 TAAAATTATTTAAATTATTTT
119120 AATTTTCAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 20 0.43
30 17 0.37
31 9 0.20
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
TAAAATTATTTAAATTATTTTTTAAAATAA
Found at i:119091 original size:30 final size:31
Alignment explanation
Indices: 119040--119119 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 31
119030 CAAATGATTT
*
119040 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
1 TAAAATTATTTAAATTATTTTTTTAAAATAA
*
119069 TAAAATTATTTAAATTATTTTTTTGAAATAA
1 TAAAATTATTTAAATTATTTTTTTAAAATAA
*
119100 TAAAATTA-TTAAATAATTTT
1 TAAAATTATTTAAATTATTTT
119120 AATTTTCAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.35
30 21 0.46
31 9 0.20
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
TAAAATTATTTAAATTATTTTTTTAAAATAA
Found at i:120248 original size:29 final size:30
Alignment explanation
Indices: 120223--120295 Score: 121
Period size: 29 Copynumber: 2.4 Consensus size: 30
120213 TTGAAAATTA
120223 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTTCAAAAAAATAAT
*
120254 TTTAATAATTTTATATTT-TAAAAAATAAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
120283 TTTAATAATTTTA
1 TTTAATAATTTTA
120296 AAAGCATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 23 0.56
30 5 0.12
31 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTAATAATTTTATATTTCAAAAAAATAAT
Found at i:120282 original size:20 final size:22
Alignment explanation
Indices: 120257--120298 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
120247 AAATAATTTT
120257 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
120277 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
120299 GCATTTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:126615 original size:4 final size:4
Alignment explanation
Indices: 126606--126639 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
126596 AATAACATTG
126606 AATT AATT AATT AATT AATT ACATT AATAT AATT
1 AATT AATT AATT AATT AATT A-ATT AAT-T AATT
126640 TTATTTTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:126623 original size:12 final size:13
Alignment explanation
Indices: 126600--126639 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
126590 GAGTAAAATA
126600 ACATTGAATTAATT
1 ACATT-AATTAATT
126614 A-ATTAATTAATT
1 ACATTAATTAATT
126626 ACATTAATATAATT
1 ACATTAAT-TAATT
126640 TTATTTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.38
13 9 0.38
14 6 0.25
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (13 bp):
ACATTAATTAATT
Found at i:127858 original size:22 final size:24
Alignment explanation
Indices: 127814--127861 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
127804 TTTTTGTAAA
*
127814 ATACAAATTTTTATAATATTAAAAT
1 ATACAAATTATTAT-ATATTAAAAT
127839 ATACAAATTATTAT-TA-TAAAAT
1 ATACAAATTATTATATATTAAAAT
127861 A
1 A
127862 AAAACATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 2 0.09
25 13 0.59
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
ATACAAATTATTATATATTAAAAT
Found at i:128132 original size:6 final size:6
Alignment explanation
Indices: 128121--128150 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
128111 AATGGATGTT
128121 CATCAA CATCAA CATCAA CATCAA CATCAA
1 CATCAA CATCAA CATCAA CATCAA CATCAA
128151 GAAAAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
CATCAA
Found at i:141831 original size:29 final size:30
Alignment explanation
Indices: 141799--141855 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
141789 TGGTTTATTG
*
141799 TGTAATTTTATAT-TTAAACTTTGATTTTA
1 TGTAATTTTATATATGAAACTTTGATTTTA
*
141828 TGTAATTTTATATATGAAATTTTGATTT
1 TGTAATTTTATATATGAAACTTTGATTT
141856 GATTCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.58
Consensus pattern (30 bp):
TGTAATTTTATATATGAAACTTTGATTTTA
Found at i:141865 original size:30 final size:29
Alignment explanation
Indices: 141799--141858 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
141789 TGGTTTATTG
* *
141799 TGTAATTTTATATTTAAACTTTGATTTTA
1 TGTAATTTTATATTGAAACTTTGATTTGA
*
141828 TGTAATTTTATATATGAAATTTTGATTTGA
1 TGTAATTTTATAT-TGAAACTTTGATTTGA
141858 T
1 T
141859 TCAATTTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.57
Consensus pattern (29 bp):
TGTAATTTTATATTGAAACTTTGATTTGA
Found at i:152552 original size:22 final size:24
Alignment explanation
Indices: 152514--152557 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
152504 TTGGTTCAGT
*
152514 CTTTTCAAGTACTTTATTTATTTG
1 CTTTTCAAGTACTTTATGTATTTG
152538 CTTTTC-AG-ACTTTATGTATT
1 CTTTTCAAGTACTTTATGTATT
152558 GAGCCAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (24 bp):
CTTTTCAAGTACTTTATGTATTTG
Found at i:153892 original size:21 final size:21
Alignment explanation
Indices: 153853--153893 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
153843 GTATGGGTTA
* *
153853 TATCGGTAGTACTTATACTTG
1 TATCGGTAGAACTCATACTTG
*
153874 TATCGGTAGAACTCCTACTT
1 TATCGGTAGAACTCATACTT
153894 CTACTAGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (21 bp):
TATCGGTAGAACTCATACTTG
Found at i:158774 original size:67 final size:68
Alignment explanation
Indices: 158690--158824 Score: 209
Period size: 67 Copynumber: 2.0 Consensus size: 68
158680 ACCAAGAGAC
* * *
158690 ATAGGATAAAATCCTAAATGTTTATTAGGCTTATTGTCTTTATATGTTTTGAATTTTCCATTTTA
1 ATAGGATAAAATCCTAAATGTTTATTAGGCTTATTGTCTCTATATGTTCTGAATATTCCATTTTA
158755 ACT
66 ACT
* * *
158758 ATAGGAT-AAATCCTAAATGTTTCTTGGGTTTATTGTCTCTATATGTTCTGAATATTCCATTTTA
1 ATAGGATAAAATCCTAAATGTTTATTAGGCTTATTGTCTCTATATGTTCTGAATATTCCATTTTA
158822 ACT
66 ACT
158825 TTATCTTCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 54 0.89
68 7 0.11
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (68 bp):
ATAGGATAAAATCCTAAATGTTTATTAGGCTTATTGTCTCTATATGTTCTGAATATTCCATTTTA
ACT
Found at i:171662 original size:3 final size:3
Alignment explanation
Indices: 171647--171691 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
171637 CTTCCCTCTG
*
171647 CTT CTT CTG CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
171692 GTTCCTCCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:171940 original size:2 final size:2
Alignment explanation
Indices: 171935--171961 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
171925 TGTGTGTTTG
171935 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
171962 ATTGTTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:177412 original size:18 final size:18
Alignment explanation
Indices: 177390--177467 Score: 120
Period size: 18 Copynumber: 4.3 Consensus size: 18
177380 CGCGCAAGGA
* *
177390 GAGCATATTGGCTCGTTA
1 GAGCATACTGGCTCGTTT
177408 GAGCATACTGGCTCGTTT
1 GAGCATACTGGCTCGTTT
*
177426 GAGTATACTGGCTCGTTT
1 GAGCATACTGGCTCGTTT
*
177444 GAGCATACTGACTCGTTT
1 GAGCATACTGGCTCGTTT
177462 GAGCAT
1 GAGCAT
177468 TTCTGGATCG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (18 bp):
GAGCATACTGGCTCGTTT
Found at i:183754 original size:9 final size:9
Alignment explanation
Indices: 183726--183818 Score: 56
Period size: 9 Copynumber: 10.9 Consensus size: 9
183716 GGTTTACAAA
183726 TTTTATAAT
1 TTTTATAAT
*
183735 TTATTA-GAT
1 TT-TTATAAT
183744 TTTTATAAT
1 TTTTATAAT
*
183753 TTTAATAAT
1 TTTTATAAT
*
183762 TTTAAT-A-
1 TTTTATAAT
*
183769 TTTTCTAAT
1 TTTTATAAT
*
183778 ATTTA-ATAT
1 TTTTATA-AT
183787 TTTT-TAAT
1 TTTTATAAT
*
183795 TTTCA-AAT
1 TTTTATAAT
*
183803 TTTT-TATT
1 TTTTATAAT
183811 TTTTATAA
1 TTTTATAA
183819 AAAATATTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
7 4 0.06
8 23 0.37
9 33 0.52
10 3 0.05
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:183764 original size:17 final size:16
Alignment explanation
Indices: 183724--183797 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 16
183714 ATGGTTTACA
*
183724 AATTTT-ATAATTTATT
1 AATTTTAATATTTTA-T
*
183740 AGATTTTTATAATTTTAAT
1 A-ATTTTAAT-ATTTT-AT
*
183759 AATTTTAATATTTTCT
1 AATTTTAATATTTTAT
*
183775 AATATTTAATATTTTTT
1 AAT-TTTAATATTTTAT
183792 AATTTT
1 AATTTT
183798 CAAATTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
16 8 0.16
17 25 0.51
18 9 0.18
19 6 0.12
20 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (16 bp):
AATTTTAATATTTTAT
Found at i:183779 original size:10 final size:9
Alignment explanation
Indices: 183742--183815 Score: 52
Period size: 8 Copynumber: 8.8 Consensus size: 9
183732 AATTTATTAG
183742 ATTTTT-AT
1 ATTTTTAAT
*
183750 AATTTTAAT
1 ATTTTTAAT
*
183759 AATTTTAAT
1 ATTTTTAAT
183768 ATTTTCTAAT
1 ATTTT-TAAT
183778 A--TTTAAT
1 ATTTTTAAT
*
183785 ATTTTTTA-
1 ATTTTTAAT
*
183793 ATTTTCAA-
1 ATTTTTAAT
*
183801 ATTTTTTAT
1 ATTTTTAAT
183810 -TTTTTA
1 ATTTTTA
183816 TAAAAAATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
7 5 0.09
8 24 0.45
9 19 0.36
10 5 0.09
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:183796 original size:25 final size:26
Alignment explanation
Indices: 183744--183817 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 26
183734 TTTATTAGAT
* * *
183744 TTTTATAAT-TTTAATAATTTTAATA
1 TTTTCTAATATTTAATATTTTTTATA
183769 TTTTCTAATATTTAATATTTTTTA-A
1 TTTTCTAATATTTAATATTTTTTATA
**
183794 TTTTC-AA-ATTTTTTATTTTTTATA
1 TTTTCTAATATTTAATATTTTTTATA
183818 AAAAATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
23 13 0.31
24 3 0.07
25 14 0.33
26 12 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTCTAATATTTAATATTTTTTATA
Found at i:185379 original size:21 final size:20
Alignment explanation
Indices: 185349--185391 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
185339 TCATGTTAAC
185349 AAATAATTTAAAAATTATAAAA
1 AAATAATTTAAAAA--ATAAAA
185371 AAAT-ATTTAAAAAATAAAA
1 AAATAATTTAAAAAATAAAA
185390 AA
1 AA
185392 TCTAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAATTTAAAAAATAAAA
Found at i:190924 original size:67 final size:67
Alignment explanation
Indices: 190806--190952 Score: 170
Period size: 67 Copynumber: 2.2 Consensus size: 67
190796 AGGTTTAAGG
* * ** * *
190806 TGTAATACCATAGCTCGGCTATGGCGACATATGGAGCCCGTCAGAAAATTAAACATGGGGTATAA
1 TGTAAAACCATAGCTCGACTATGGCGACATATGGAGCCCACCAGAAAATTAAAAAGGGGGTA-AA
190871 -TA
65 CTA
* * * *
190873 TGTAAAACCATAGCTCGACTATTGCGACATATGGAGTCCACCAGGACATTAAAAAGGGGGTAAAC
1 TGTAAAACCATAGCTCGACTATGGCGACATATGGAGCCCACCAGAAAATTAAAAAGGGGGTAAAC
*
190938 TG
66 TA
*
190940 TGTAAGACCATAG
1 TGTAAAACCATAG
190953 TTAGGCTATG
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
66 2 0.03
67 65 0.97
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (67 bp):
TGTAAAACCATAGCTCGACTATGGCGACATATGGAGCCCACCAGAAAATTAAAAAGGGGGTAAAC
TA
Found at i:201173 original size:30 final size:30
Alignment explanation
Indices: 201137--201196 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
201127 AAATTAAAGT
*
201137 TTAGATGATCCTGACTTGACATTTATGATA
1 TTAGATGATCCTGACTTGAAATTTATGATA
**
201167 TTAGATGATTGTGACTTGAAATTTATGATA
1 TTAGATGATCCTGACTTGAAATTTATGATA
201197 AAACAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (30 bp):
TTAGATGATCCTGACTTGAAATTTATGATA
Found at i:201755 original size:3 final size:3
Alignment explanation
Indices: 201749--201776 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
201739 GAAGAAATTA
201749 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
201777 GAAGCACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:205274 original size:13 final size:13
Alignment explanation
Indices: 205256--205281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
205246 TTGTATAAAA
205256 GTCCAACTTTTAG
1 GTCCAACTTTTAG
205269 GTCCAACTTTTAG
1 GTCCAACTTTTAG
205282 ACACTATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
GTCCAACTTTTAG
Found at i:216879 original size:24 final size:24
Alignment explanation
Indices: 216846--216893 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
216836 TACTAGATAG
* *
216846 CCATTTTGGGCTCGTAAGAGCTAA
1 CCATTGTGGGATCGTAAGAGCTAA
*
216870 CCATTGTGGGATCGTATGAGCTAA
1 CCATTGTGGGATCGTAAGAGCTAA
216894 TTTTGTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (24 bp):
CCATTGTGGGATCGTAAGAGCTAA
Found at i:216909 original size:25 final size:26
Alignment explanation
Indices: 216850--216918 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 26
216840 AGATAGCCAT
*
216850 TTTGGGCTCGTAAGAGCTAACCATTG
1 TTTGGGCTCGTATGAGCTAACCATTG
* **
216876 --TGGGATCGTATGAGCTAA-TTTTG
1 TTTGGGCTCGTATGAGCTAACCATTG
216899 TTTGGGCTCGTATGAGCTAA
1 TTTGGGCTCGTATGAGCTAA
216919 ATTTCTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.08
24 16 0.44
25 17 0.47
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (26 bp):
TTTGGGCTCGTATGAGCTAACCATTG
Found at i:221767 original size:26 final size:25
Alignment explanation
Indices: 221707--221767 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
221697 GTAGTTGTTA
* *
221707 AATAATAATTATTAAGTACTCAAAG
1 AATAATAATTATAAAGGACTCAAAG
* *
221732 AAGACA-AATTAGTAAAGGACTTAAAG
1 AATA-ATAATTA-TAAAGGACTCAAAG
221758 AATAATAATT
1 AATAATAATT
221768 CATTTAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (25 bp):
AATAATAATTATAAAGGACTCAAAG
Done.