Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004129.1 Kokia drynarioides strain JFW-HI SEQ_117322, 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: 214019
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 233 characters in sequence are not A, C, G, or T
Found at i:7807 original size:2 final size:2
Alignment explanation
Indices: 7800--7824 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7790 ATTATTATTT
7800 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7825 TGGATTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14277 original size:13 final size:13
Alignment explanation
Indices: 14259--14283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14249 TTTTAACACA
14259 AAAAAATATTTTG
1 AAAAAATATTTTG
14272 AAAAAATATTTT
1 AAAAAATATTTT
14284 TTTGACCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AAAAAATATTTTG
Found at i:19732 original size:23 final size:23
Alignment explanation
Indices: 19706--19796 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
19696 GCTCTCCGTT
*
19706 ATTAGCACTTCATGTGCTCTCCA
1 ATTAGCACTTCGTGTGCTCTCCA
*
19729 ATTAGCACTTCGTGTGCTCTCCG
1 ATTAGCACTTCGTGTGCTCTCCA
* * *
19752 ATTA-CACTTCGTGTACTTTCCG
1 ATTAGCACTTCGTGTGCTCTCCA
*
19774 TTTAGCACTTCGTGTGCTCTCCA
1 ATTAGCACTTCGTGTGCTCTCCA
19797 TTATCCAGCA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
22 19 0.32
23 40 0.68
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.37
Consensus pattern (23 bp):
ATTAGCACTTCGTGTGCTCTCCA
Found at i:19844 original size:70 final size:68
Alignment explanation
Indices: 19697--19846 Score: 151
Period size: 70 Copynumber: 2.1 Consensus size: 68
19687 ACGTTTCATG
*
19697 CTCTCCGTTATTAGCACTTCATGTGCTCTCCAATTAGCACTTCGTGTGCTCTCCGATTACACTTC
1 CTCTCCG-T-TTAGCACTTCATGTGCTCTCCAATCAGCACTTCGTGTGCTCTCCGATTACACTTC
**
19762 GTGTA
64 GAATA
* * ** * *
19767 CTTTCCGTTTAGCACTTCGTGTGCTCTCCATTATCCAGCA-TTTTTGTGCTCTCCGTTTAGTACT
1 CTCTCCGTTTAGCACTTCATGTGCTCTCCA--AT-CAGCACTTCGTGTGCTCTCCGATTA-CACT
19831 TC-AATA
62 TCGAATA
19837 CTCTCCGTTT
1 CTCTCCGTTT
19847 TTGTTCCATA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
68 21 0.32
69 1 0.02
70 35 0.53
71 9 0.14
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (68 bp):
CTCTCCGTTTAGCACTTCATGTGCTCTCCAATCAGCACTTCGTGTGCTCTCCGATTACACTTCGA
ATA
Found at i:19994 original size:15 final size:15
Alignment explanation
Indices: 19970--19999 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19960 CGTAAATACT
*
19970 ATATGTGTATGAAAG
1 ATATGAGTATGAAAG
19985 ATATGAGTATGAAAG
1 ATATGAGTATGAAAG
20000 CTAAAGTGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (15 bp):
ATATGAGTATGAAAG
Found at i:22937 original size:1 final size:1
Alignment explanation
Indices: 22931--22959 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
22921 NNNNNNNNNN
22931 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22960 ATAGATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25966 original size:6 final size:6
Alignment explanation
Indices: 25911--25959 Score: 71
Period size: 6 Copynumber: 7.7 Consensus size: 6
25901 GCATGTTCTT
25911 GGAGAA GGAAGGAA GGGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAG
1 GGAGAA GG-A-GAA -GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAG
25960 GGAGAGGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 30 0.75
7 4 0.10
8 4 0.10
9 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
GGAGAA
Found at i:27762 original size:198 final size:198
Alignment explanation
Indices: 27424--27820 Score: 776
Period size: 198 Copynumber: 2.0 Consensus size: 198
27414 CAACAAAGAG
*
27424 AAAGATCATATATGAGCATAAAAATATCCAATCAAGACCCTATTCGTTAAAGAAATCTATGAAAC
1 AAAGATCATATATGAGCATAAAAATATCCAAGCAAGACCCTATTCGTTAAAGAAATCTATGAAAC
27489 ATGTATCATGAACTAAGAAAATATATAAATTTGATGTCACTTGCCTTGATTTTCATATATAGGTT
66 ATGTATCATGAACTAAGAAAATATATAAATTTGATGTCACTTGCCTTGATTTTCATATATAGGTT
27554 AGGAAAGTTATCAGCCTCGAAAGGAAGGGTGCCACAAAGAAGGGCATACGATATAACACCACAGC
131 AGGAAAGTTATCAGCCTCGAAAGGAAGGGTGCCACAAAGAAGGGCATACGATATAACACCACAGC
27619 TCC
196 TCC
27622 AAAGATCATATATGAGCATAAAAATATCCAAGCAAGACCCTATTCGTTAAAGAAATCTATGAAAC
1 AAAGATCATATATGAGCATAAAAATATCCAAGCAAGACCCTATTCGTTAAAGAAATCTATGAAAC
27687 ATGTATCATGAACTAAGAAAATATATAAATTTGATGTCACTTGCCTTGATTTTCATATATAGGTT
66 ATGTATCATGAACTAAGAAAATATATAAATTTGATGTCACTTGCCTTGATTTTCATATATAGGTT
*
27752 AGGAAAGTTATCAGCCTCGAAAGGAAGGGTGCCGCAAAGAAGGGCATACGATATAACACCACAGC
131 AGGAAAGTTATCAGCCTCGAAAGGAAGGGTGCCACAAAGAAGGGCATACGATATAACACCACAGC
27817 TCC
196 TCC
27820 A
1 A
27821 TATATCCACT
Statistics
Matches: 197, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
198 197 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (198 bp):
AAAGATCATATATGAGCATAAAAATATCCAAGCAAGACCCTATTCGTTAAAGAAATCTATGAAAC
ATGTATCATGAACTAAGAAAATATATAAATTTGATGTCACTTGCCTTGATTTTCATATATAGGTT
AGGAAAGTTATCAGCCTCGAAAGGAAGGGTGCCACAAAGAAGGGCATACGATATAACACCACAGC
TCC
Found at i:30637 original size:18 final size:18
Alignment explanation
Indices: 30607--30653 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 18
30597 ATTTCACCTC
30607 ATAAA-AAACTAAAATATT
1 ATAAATAAA-TAAAATATT
30625 ATAAATAAAT-AAATATT
1 ATAAATAAATAAAATATT
30642 -T-AAT-AATAAAAT
1 ATAAATAAATAAAAT
30654 GTATTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.11
15 7 0.26
16 1 0.04
17 7 0.26
18 6 0.22
19 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAAATAAAATATT
Found at i:34831 original size:24 final size:25
Alignment explanation
Indices: 34781--34836 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
34771 ACCATAACCC
* *
34781 GATAGAGCTCCGTATGAAGCCGGTG
1 GATAGAGCTCCATATGAAGCCGATG
* *
34806 GATAG-GCTCCATATGGAGTCGATG
1 GATAGAGCTCCATATGAAGCCGATG
34830 GAT-GAGC
1 GATAGAGC
34837 CCCGTAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.04
24 20 0.77
25 5 0.19
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (25 bp):
GATAGAGCTCCATATGAAGCCGATG
Found at i:34889 original size:24 final size:23
Alignment explanation
Indices: 34837--34890 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
34827 ATGGATGAGC
* * *
34837 CCCGTAAGGTGCCGGTTGAGGGG
1 CCCGTAAGGAGCCGATTGAGGGA
34860 CTCCGTAAGGAGCCGATTGAGGGTA
1 C-CCGTAAGGAGCCGATTGAGGG-A
34885 CCCGTA
1 CCCGTA
34891 TGAAGGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.19, C:0.24, G:0.39, T:0.19
Consensus pattern (23 bp):
CCCGTAAGGAGCCGATTGAGGGA
Found at i:36603 original size:24 final size:24
Alignment explanation
Indices: 36576--36621 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
36566 CTGAACTTGA
36576 TGGAGAAGCCCCAT-CTGGTGCCGG
1 TGGAGAAGCCCCATAC-GGTGCCGG
*
36600 TGGAGCAGCCCCATACGGTGCC
1 TGGAGAAGCCCCATACGGTGCC
36622 AATGAAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.17, C:0.33, G:0.35, T:0.15
Consensus pattern (24 bp):
TGGAGAAGCCCCATACGGTGCCGG
Found at i:37446 original size:14 final size:14
Alignment explanation
Indices: 37403--37449 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
37393 AGATAATATA
37403 TATATTATTTTTAATT
1 TATA-TATTTTT-ATT
*
37419 TA-ATATTTAATATT
1 TATATATTT-TTATT
37433 TATATATTTTTATT
1 TATATATTTTTATT
37447 TAT
1 TAT
37450 TAAATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 17 0.63
15 8 0.30
16 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATATATTTTTATT
Found at i:37499 original size:18 final size:17
Alignment explanation
Indices: 37472--37505 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
37462 TATATGTTAT
37472 AATTCATAATACATAAG
1 AATTCATAATACATAAG
*
37489 AATTACATAATATATAA
1 AATT-CATAATACATAA
37506 AACATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (17 bp):
AATTCATAATACATAAG
Found at i:39578 original size:218 final size:219
Alignment explanation
Indices: 39200--39598 Score: 701
Period size: 218 Copynumber: 1.8 Consensus size: 219
39190 GTTGCTTGCC
*
39200 TGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATGTGCATATGATGAACTCAACTCAGATTCCCC
1 TGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATATGCATATGATGAACTCAACTCAGATTCCCC
* *
39265 TTCAAGACTTCATGGGTGATGCTAGCTTGAGTTTCTGATGCAAACATCAAGTGATCAATTTTACA
66 TTCAAGACTTCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACATCAAGTGATCAATTTTACA
*
39330 TAGTTCACAAATTTGGTTTGTATGAAAGTAT-AAGAAATGTGTTTCTTCATTCTTTCTTCAATTC
131 TAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAAATGTGTTTCTTCATTCTTTCTTCAATTC
39394 GGTTTGTTAATTTGCTTTCCTATT
196 GGTTTGTTAATTTGCTTTCCTATT
* **
39418 TGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATATGCATATGATGAACTCTACTTGGATTCCCC
1 TGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATATGCATATGATGAACTCAACTCAGATTCCCC
*
39483 TTCAAGACTTCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACATTAAGTGATCAATTTTACA
66 TTCAAGACTTCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACATCAAGTGATCAATTTTACA
*
39548 TGGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAAAATGTGTTTCTTCA
131 TAGTTCACAAATTTGGTTTGTATGAAAGTAT-AAAAAAATGTGTTTCTTCA
39599 ATCCTCTAAT
Statistics
Matches: 170, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
218 153 0.90
220 17 0.10
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (219 bp):
TGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATATGCATATGATGAACTCAACTCAGATTCCCC
TTCAAGACTTCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACATCAAGTGATCAATTTTACA
TAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAAATGTGTTTCTTCATTCTTTCTTCAATTC
GGTTTGTTAATTTGCTTTCCTATT
Found at i:41178 original size:2 final size:2
Alignment explanation
Indices: 41171--41197 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41161 TCACTTTTGA
41171 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
41198 GGTTTAAGTT
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:42916 original size:19 final size:19
Alignment explanation
Indices: 42892--42932 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42882 CTCCCATCTT
*
42892 TTTTAT-TATTTAAAATATA
1 TTTTATATATTAAAAATA-A
42911 TTTTATATATTAAAAATAA
1 TTTTATATATTAAAAATAA
42930 TTT
1 TTT
42933 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTATATATTAAAAATAA
Found at i:48100 original size:12 final size:12
Alignment explanation
Indices: 48083--48131 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
48073 TCATTAGCAT
48083 TGTTCATGAACA
1 TGTTCATGAACA
* *
48095 TGTTCAAT-TATA
1 TGTTC-ATGAACA
48107 TGTTCATGAACA
1 TGTTCATGAACA
*
48119 TGTTCGTGAACA
1 TGTTCATGAACA
48131 T
1 T
48132 TAAACAAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 2 0.07
12 26 0.87
13 2 0.07
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (12 bp):
TGTTCATGAACA
Found at i:53805 original size:12 final size:12
Alignment explanation
Indices: 53790--53876 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
53780 ACTGTTTTAG
*
53790 TGTTGTTTTTGT
1 TGTTATTTTTGT
53802 TGTTATTTTTGT
1 TGTTATTTTTGT
* *
53814 TGCTATTTTTAT
1 TGTTATTTTTGT
*
53826 TGTTA-TTTTGA
1 TGTTATTTTTGT
*
53837 TGTTATTTTTGC
1 TGTTATTTTTGT
* * *
53849 TGCTGTTTTGGT
1 TGTTATTTTTGT
53861 TGTTATTTTTGT
1 TGTTATTTTTGT
53873 TGTT
1 TGTT
53877 TGGATTTTTT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
11 9 0.15
12 51 0.85
ACGTcount: A:0.08, C:0.03, G:0.20, T:0.69
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:53805 original size:20 final size:20
Alignment explanation
Indices: 53760--53805 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
53750 TATTTTGGTC
*
53760 GTTGTTTTAGTGTTTTTTTT
1 GTTGTTTTAGTGTTGTTTTT
**
53780 ACTGTTTTAGTGTTGTTTTT
1 GTTGTTTTAGTGTTGTTTTT
53800 GTTGTT
1 GTTGTT
53806 ATTTTTGTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.02, G:0.22, T:0.70
Consensus pattern (20 bp):
GTTGTTTTAGTGTTGTTTTT
Found at i:53811 original size:35 final size:34
Alignment explanation
Indices: 53772--53876 Score: 102
Period size: 35 Copynumber: 3.0 Consensus size: 34
53762 TGTTTTAGTG
* *
53772 TTTTTTTTACTGTTTTAGTGTTGTTTTTGTTGTTA
1 TTTTTGTTGCTGTTTTAGTGTT-TTTTTGTTGTTA
* * * *
53807 TTTTTGTTGCTATTTTTATTGTTATTTTGATGTTA
1 TTTTTGTTGCT-GTTTTAGTGTTTTTTTGTTGTTA
* *
53842 TTTTTGCTGCTGTTTTGGTTGTTATTTTTGTTGTT
1 TTTTTGTTGCTGTTTTAG-TGTT-TTTTTGTTGTT
53877 TGGATTTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
34 4 0.07
35 33 0.60
36 18 0.33
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.70
Consensus pattern (34 bp):
TTTTTGTTGCTGTTTTAGTGTTTTTTTGTTGTTA
Found at i:60823 original size:2 final size:2
Alignment explanation
Indices: 60777--60807 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
60767 TTTTTTTACT
60777 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
60808 ATAATTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:86626 original size:33 final size:33
Alignment explanation
Indices: 86584--86647 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
86574 AATGAAGGAC
*
86584 AGATTTGGTTGGTTAAGTTCTTTTGTTTAGGGT
1 AGATTTGGTTGGTTAAGTACTTTTGTTTAGGGT
86617 AGATTTGGTTGGTTAAGTACTTTTGTTTAGG
1 AGATTTGGTTGGTTAAGTACTTTTGTTTAGG
86648 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.17, C:0.03, G:0.30, T:0.50
Consensus pattern (33 bp):
AGATTTGGTTGGTTAAGTACTTTTGTTTAGGGT
Found at i:86651 original size:19 final size:19
Alignment explanation
Indices: 86594--86651 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
86584 AGATTTGGTT
*
86594 GGTTAAGTTCTTTTGTTTA
1 GGTTAAGTACTTTTGTTTA
* *
86613 GGGT-AG-A--TTTGGTT-
1 GGTTAAGTACTTTTGTTTA
86627 GGTTAAGTACTTTTGTTTA
1 GGTTAAGTACTTTTGTTTA
86646 GGTTAA
1 GGTTAA
86652 AATTTATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 10
0.66 0.11 0.23
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 1 0.03
18 8 0.28
19 9 0.31
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (19 bp):
GGTTAAGTACTTTTGTTTA
Found at i:86746 original size:22 final size:22
Alignment explanation
Indices: 86718--86761 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
86708 GAATATTTTG
*
86718 GAAAATAAATTGATTTTGAAGA
1 GAAAATAAATCGATTTTGAAGA
*
86740 GAAAATAAGTCGATTTTGAAGA
1 GAAAATAAATCGATTTTGAAGA
86762 TGTGCATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (22 bp):
GAAAATAAATCGATTTTGAAGA
Found at i:86980 original size:12 final size:12
Alignment explanation
Indices: 86963--86993 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
86953 CGAAAACGTA
86963 GGTTTACAACTT
1 GGTTTACAACTT
86975 GGTTTACAACTT
1 GGTTTACAACTT
86987 GGTTTAC
1 GGTTTAC
86994 CGGTGGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (12 bp):
GGTTTACAACTT
Found at i:96980 original size:21 final size:21
Alignment explanation
Indices: 96956--97000 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
96946 GCATATACAT
*
96956 TTTAAACTGTAATATTTAAAA
1 TTTAAACTGTAATATATAAAA
* * *
96977 TTTAAATTTTATTATATAAAA
1 TTTAAACTGTAATATATAAAA
96998 TTT
1 TTT
97001 TCACAACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTAAACTGTAATATATAAAA
Found at i:97761 original size:15 final size:16
Alignment explanation
Indices: 97741--97770 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
97731 TCGTCAATTA
97741 AATT-AATTTTTAACC
1 AATTAAATTTTTAACC
97756 AATTAAATTTTTAAC
1 AATTAAATTTTTAAC
97771 AAAAGAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAATTTTTAACC
Found at i:122253 original size:10 final size:9
Alignment explanation
Indices: 122211--122352 Score: 51
Period size: 9 Copynumber: 15.2 Consensus size: 9
122201 TTAAATTTTA
122211 ATAAAAATT
1 ATAAAAATT
122220 ATTAACAAA-T
1 A-TAA-AAATT
122230 ATAAAAATT
1 ATAAAAATT
*
122239 GTAAAAACTT
1 ATAAAAA-TT
122249 AT-AAAATAT
1 ATAAAAAT-T
*
122258 ATAGAAA-T
1 ATAAAAATT
*
122266 ATAAAATTTT
1 ATAAAA-ATT
**
122276 ATAAATTTT
1 ATAAAAATT
*
122285 TTATAAAATCGT
1 ATA-AAAAT--T
*
122297 ATGAAAATT
1 ATAAAAATT
122306 ATATAAAA-T
1 ATA-AAAATT
*
122315 ATAAAGAAAT
1 ATAAA-AATT
***
122325 AT-AATGGT
1 ATAAAAATT
*
122333 AAAAAAATT
1 ATAAAAATT
122342 ATAAAAATT
1 ATAAAAATT
122351 AT
1 AT
122353 CGTACAAAAA
Statistics
Matches: 98, Mismatches: 20, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
8 14 0.14
9 47 0.48
10 27 0.28
11 8 0.08
12 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:125562 original size:16 final size:16
Alignment explanation
Indices: 125543--125596 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
125533 AATATGATTA
125543 AATTTATTTTTATGTT
1 AATTTATTTTTATGTT
* * *
125559 AATTT-TTATATAATATA
1 AATTTATT-T-TTATGTT
125576 AATTTATTTTTATGTT
1 AATTTATTTTTATGTT
125592 AATTT
1 AATTT
125597 TTATATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.07
16 15 0.52
17 10 0.34
18 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
AATTTATTTTTATGTT
Found at i:125565 original size:12 final size:11
Alignment explanation
Indices: 125544--125625 Score: 51
Period size: 11 Copynumber: 7.5 Consensus size: 11
125534 ATATGATTAA
125544 ATTT-ATTTTT
1 ATTTAATTTTT
125554 ATGTTAATTTTT
1 AT-TTAATTTTT
* * **
125566 ATATAATATAA
1 ATTTAATTTTT
125577 ATTT-ATTTTT
1 ATTTAATTTTT
125587 ATGTTAATTTTT
1 AT-TTAATTTTT
* * **
125599 ATATAATATAA
1 ATTTAATTTTT
*
125610 ATTTATTTTTT
1 ATTTAATTTTT
125621 ATTTA
1 ATTTA
125626 TATAATTTTT
Statistics
Matches: 51, Mismatches: 17, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
10 7 0.14
11 28 0.55
12 16 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:125579 original size:17 final size:17
Alignment explanation
Indices: 125559--125613 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
125549 TTTTTATGTT
125559 AATTTTTATATAATATA
1 AATTTTTATATAATATA
* * *
125576 AATTTATT-T-TTATGTT
1 AATTT-TTATATAATATA
125592 AATTTTTATATAATATA
1 AATTTTTATATAATATA
125609 AATTT
1 AATTT
125614 ATTTTTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.07
16 10 0.34
17 15 0.52
18 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTTTATATAATATA
Found at i:125579 original size:33 final size:33
Alignment explanation
Indices: 125541--125619 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
125531 TAAATATGAT
125541 TAAATTTATTTTTATGTTAATTTTTATATAATA
1 TAAATTTATTTTTATGTTAATTTTTATATAATA
125574 TAAATTTATTTTTATGTTAATTTTTATATAATA
1 TAAATTTATTTTTATGTTAATTTTTATATAATA
125607 TAAATTTATTTTT
1 TAAATTTATTTTT
125620 TATTTATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (33 bp):
TAAATTTATTTTTATGTTAATTTTTATATAATA
Found at i:125608 original size:38 final size:35
Alignment explanation
Indices: 125528--125619 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 35
125518 ATATTATCAA
*
125528 ATATAAATATGATTAAATTTATTTTTATGTTAATTT
1 ATAT-AATATAATTAAATTTATTTTTATGTTAATTT
125564 -T-T-ATATAATATAAATTTATTTTTATGTTAATTT
1 ATATAATATAAT-TAAATTTATTTTTATGTTAATTT
125597 -T-T-ATATAATATAAATTTATTTTT
1 ATATAATATAAT-TAAATTTATTTTT
125620 TATTTATATA
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
32 6 0.11
33 46 0.85
34 1 0.02
35 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (35 bp):
ATATAATATAATTAAATTTATTTTTATGTTAATTT
Found at i:133004 original size:30 final size:29
Alignment explanation
Indices: 132968--133026 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 29
132958 TTTATGAAAG
132968 AATGTTGTATTTCTATCCTCATTCTTTAGC
1 AATGTTGTATTTCTATCC-CATTCTTTAGC
132998 AATGTTGTATTTCTATCCCATTCTTTAGC
1 AATGTTGTATTTCTATCCCATTCTTTAGC
133027 CAATTCACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.49
Consensus pattern (29 bp):
AATGTTGTATTTCTATCCCATTCTTTAGC
Found at i:135874 original size:17 final size:18
Alignment explanation
Indices: 135843--135876 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
135833 ATCCACGTGT
*
135843 ATTTTATTTTTTAATTTG
1 ATTTTATTTTATAATTTG
135861 ATTTT-TTTTATAATTT
1 ATTTTATTTTATAATTT
135877 TTTAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTATTTTATAATTTG
Found at i:136151 original size:23 final size:23
Alignment explanation
Indices: 136125--136176 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
136115 TTCATTTAAC
136125 TTAATCAAACATGTTCACGAACA
1 TTAATCAAACATGTTCACGAACA
* * * *
136148 TTAAACGAACATGTTTATGAACA
1 TTAATCAAACATGTTCACGAACA
136171 TATAAT
1 T-TAAT
136177 TGAACATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (23 bp):
TTAATCAAACATGTTCACGAACA
Found at i:144395 original size:24 final size:27
Alignment explanation
Indices: 144364--144414 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
144354 ATTAAATAAA
144364 TTTTTTTA-AGT-T-AAATTTGATCAT
1 TTTTTTTATAGTGTCAAATTTGATCAT
144388 TTTTTTTATAGTGTCAAATTTGATCAT
1 TTTTTTTATAGTGTCAAATTTGATCAT
144415 CAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 8 0.33
25 3 0.12
26 1 0.04
27 12 0.50
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (27 bp):
TTTTTTTATAGTGTCAAATTTGATCAT
Found at i:144636 original size:29 final size:29
Alignment explanation
Indices: 144566--144641 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
144556 TCTCTATATT
* *
144566 TTTTTTGTAAATTT-GAAATTTAATTTTTA
1 TTTTTT-TAATTTTAGAAATGTAATTTTTA
** **
144595 TACTTTTGTTTTTAGAAATGTAATTTTTA
1 TTTTTTTAATTTTAGAAATGTAATTTTTA
144624 TTTTTTTAATTTTA-AAAT
1 TTTTTTTAATTTTAGAAAT
144642 TCAAGTCTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
28 8 0.22
29 28 0.78
ACGTcount: A:0.30, C:0.01, G:0.07, T:0.62
Consensus pattern (29 bp):
TTTTTTTAATTTTAGAAATGTAATTTTTA
Found at i:144698 original size:59 final size:59
Alignment explanation
Indices: 144631--144748 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
144621 TTATTTTTTT
144631 AATTTTAAAATTCAAGTCTAATTATTAATATAGTTAAGATGTTAAATTCAAGTTCATTA
1 AATTTTAAAATTCAAGTCTAATTATTAATATAGTTAAGATGTTAAATTCAAGTTCATTA
144690 AATTTTAAAATTCAAGTCTAATTATTAATATAGTTAAGATGTTAAATTCAAGTTCATTA
1 AATTTTAAAATTCAAGTCTAATTATTAATATAGTTAAGATGTTAAATTCAAGTTCATTA
144749 CAATATTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (59 bp):
AATTTTAAAATTCAAGTCTAATTATTAATATAGTTAAGATGTTAAATTCAAGTTCATTA
Found at i:150250 original size:2 final size:2
Alignment explanation
Indices: 150243--150275 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
150233 AGTTATATTT
150243 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
150276 TGGATTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:152351 original size:11 final size:11
Alignment explanation
Indices: 152335--152359 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
152325 ACAACGGATT
152335 TTTATGGAAGC
1 TTTATGGAAGC
152346 TTTATGGAAGC
1 TTTATGGAAGC
152357 TTT
1 TTT
152360 TATATTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (11 bp):
TTTATGGAAGC
Found at i:153768 original size:134 final size:134
Alignment explanation
Indices: 153528--153798 Score: 506
Period size: 134 Copynumber: 2.0 Consensus size: 134
153518 CTAGACATGA
153528 TAAATTTGAATTTATTGCACCATCTTTGTATTTAAAATTATTTACTTGTTTTACTCAAAGGTTTT
1 TAAATTTGAATTTATTGCACCATCTTTGTATTTAAAATTATTTACTTGTTTTACTCAAAGGTTTT
*
153593 TAAAATTGATCAATGGTCAAATCGATTAGATCACCGGTTTGATCAGATTGACCTATTTGATTAAA
66 TAAAATTGACCAATGGTCAAATCGATTAGATCACCGGTTTGATCAGATTGACCTATTTGATTAAA
153658 TAAT
131 TAAT
*
153662 TAAATTTGAATTTATTGCACCATCTTTGTATTTAAAATTGTTTACTTGTTTTACTCAAAGGTTTT
1 TAAATTTGAATTTATTGCACCATCTTTGTATTTAAAATTATTTACTTGTTTTACTCAAAGGTTTT
* *
153727 TAAAATTGACCAATGGTCAAATCGATTAGATCACTGGTTTGATCAGATTGACTTATTTGATTAAA
66 TAAAATTGACCAATGGTCAAATCGATTAGATCACCGGTTTGATCAGATTGACCTATTTGATTAAA
153792 TAAT
131 TAAT
153796 TAA
1 TAA
153799 TTAAAAATTC
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (134 bp):
TAAATTTGAATTTATTGCACCATCTTTGTATTTAAAATTATTTACTTGTTTTACTCAAAGGTTTT
TAAAATTGACCAATGGTCAAATCGATTAGATCACCGGTTTGATCAGATTGACCTATTTGATTAAA
TAAT
Found at i:161024 original size:17 final size:17
Alignment explanation
Indices: 161004--161039 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
160994 TAAAACTAAA
*
161004 TTATAATTTTCATAATT
1 TTATAATTTTAATAATT
*
161021 TTATTATTTTAATAATT
1 TTATAATTTTAATAATT
161038 TT
1 TT
161040 TAAAGAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATAATTTTAATAATT
Found at i:168281 original size:25 final size:25
Alignment explanation
Indices: 168248--168296 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
168238 ATTGTGTTCA
*
168248 TTTGGATTTTAATTTT-TTACTTTAT
1 TTTGGATTTCAATTTTATTA-TTTAT
*
168273 TTTGTATTTCAATTTTATTATTTA
1 TTTGGATTTCAATTTTATTATTTA
168297 AGTTTGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.67
Consensus pattern (25 bp):
TTTGGATTTCAATTTTATTATTTAT
Found at i:170174 original size:34 final size:35
Alignment explanation
Indices: 170107--170176 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
170097 TAAAAAATCA
* * *
170107 ATTTACTCTTTAATTTAACATATAAAAATTAATTT
1 ATTTACTCTTTAATATAAAAAATAAAAATTAATTT
170142 ATTTACTCTTTAA-ATAAAAAAT-AAAATATAATTT
1 ATTTACTCTTTAATATAAAAAATAAAAAT-TAATTT
170176 A
1 A
170177 ACTCTTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 5 0.16
34 13 0.42
35 13 0.42
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (35 bp):
ATTTACTCTTTAATATAAAAAATAAAAATTAATTT
Found at i:178718 original size:60 final size:59
Alignment explanation
Indices: 178567--178760 Score: 198
Period size: 59 Copynumber: 3.3 Consensus size: 59
178557 TTAATATAAC
* *
178567 ATTTGATACCTAAATTTGATAT-TTTTCTTAAATTGGTACCTAAACTTATTTTT-ACCCA
1 ATTTGATACCTAAATTTGACATCTTTTCTTAATTTGGTACCTAAACTT-TTTTTGACCCA
* * * *
178625 ATTTGATACTTGAACTTGACA-CTTTTTCTTAATTTGATACCTAAACTTTTTTTGGACCCA
1 ATTTGATACCTAAATTTGACATC-TTTTCTTAATTTGGTACCTAAACTTTTTTT-GACCCA
* * * * * * *
178685 ATTTGGTACCTGAATTTGGCATCTTTTCCTAATTTGGTACCT-AATTTTTTTTAGATCCG
1 ATTTGATACCTAAATTTGACATCTTTTCTTAATTTGGTACCTAAACTTTTTTT-GACCCA
*
178744 ATTTGGTACCTAAATTT
1 ATTTGATACCTAAATTT
178761 ATTAAATATT
Statistics
Matches: 114, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
58 22 0.19
59 52 0.46
60 39 0.34
61 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (59 bp):
ATTTGATACCTAAATTTGACATCTTTTCTTAATTTGGTACCTAAACTTTTTTTGACCCA
Found at i:178978 original size:58 final size:59
Alignment explanation
Indices: 178916--179059 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 59
178906 CCAAATTACG
* * **
178916 AAAAAGAGTCAAATTCAGGTACCAAATTAGATC-CCAAAAAGTTTAAGTACTAAC-TT-AA
1 AAAAAGTGTCAAGTTCAGGTACCAAATTAGA-CAAAAAAAAGTTTAAGTAC-AACATTAAA
* * * *
178974 AAAAAGTGTCAAGTT-TGAGTACTAAATTAGACAAAAAAAAGTTTATGTACCACATTAAA
1 AAAAAGTGTCAAGTTCAG-GTACCAAATTAGACAAAAAAAAGTTTAAGTACAACATTAAA
*
179033 AAAAAGTGTCAAGTTCAAGTACCAAAT
1 AAAAAGTGTCAAGTTCAGGTACCAAAT
179060 GTTATATTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
57 4 0.06
58 41 0.59
59 25 0.36
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (59 bp):
AAAAAGTGTCAAGTTCAGGTACCAAATTAGACAAAAAAAAGTTTAAGTACAACATTAAA
Found at i:183298 original size:30 final size:31
Alignment explanation
Indices: 183235--183299 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
183225 TTATAAGATG
* * *
183235 GTCATTAAATTAATCAAAAGTTTTTATTTAA
1 GTCATTAAACTAATCAAAAGTTTTTACTAAA
* *
183266 GTCATTAAACTATTCGAAAG-TTTTACTAAA
1 GTCATTAAACTAATCAAAAGTTTTTACTAAA
183296 GTCA
1 GTCA
183300 CTGAATTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (31 bp):
GTCATTAAACTAATCAAAAGTTTTTACTAAA
Found at i:212697 original size:50 final size:51
Alignment explanation
Indices: 212606--212703 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
212596 GGTTTTCCCC
* **
212606 ACAAACGCCGCTTAAAGAACATAGTATTTAGCGGCTTTTTTCTAACAACTT
1 ACAAACGCCGCTTAAAGAACATAGTATTTAACGGCGCTTTTCTAACAACTT
* * *
212657 ACAAACGCCGC-TAAAGAACATAGTCTTTAACGGGGCTTTTCTTACAA
1 ACAAACGCCGCTTAAAGAACATAGTATTTAACGGCGCTTTTCTAACAA
212704 ACGCTGCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
50 30 0.73
51 11 0.27
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (51 bp):
ACAAACGCCGCTTAAAGAACATAGTATTTAACGGCGCTTTTCTAACAACTT
Found at i:212747 original size:43 final size:43
Alignment explanation
Indices: 212523--212800 Score: 152
Period size: 43 Copynumber: 6.3 Consensus size: 43
212513 TTATGAGTAA
* * * ** *
212523 AAACGCCGCTATAGAACATGGTCTTTAGTGGC-ACTTTT-CATT
1 AAACGCCGCTAAATAACATGGTCTTTAGCGGCTTTTTTTCCA-C
* * * * * **
212565 AAACACCGCTAAAGAAAAAGGTCTTTAGCGAG-GTTTTCCCCAC
1 AAACGCCGCTAAATAACATGGTCTTTAGCG-GCTTTTTTTCCAC
* * *
212608 AAACGCCGCTTAAAGAACATAGTATTTAGCGGCTTTTTTCTAACAACTTAC
1 AAACGCCGC-TAAATAACATGGTCTTTAGCGGCTTTTTT-T--C--C--AC
* * * *
212659 AAACGCCGCTAAAGAACATAGTCTTTAACGGGGCTTTTCTT--AC
1 AAACGCCGCTAAATAACATGGTCTTT-A-GCGGCTTTTTTTCCAC
* *
212702 AAACGCTGCTAAATAACATGGTCTTTAGCGGTTTTTTTTCCAC
1 AAACGCCGCTAAATAACATGGTCTTTAGCGGCTTTTTTTCCAC
* * * * **
212745 AAATGTCACTAAATAACATGGTCTTTAGTGGCGCTTTTTCCAC
1 AAACGCCGCTAAATAACATGGTCTTTAGCGGCTTTTTTTCCAC
*
212788 AAACACCGCTAAA
1 AAACGCCGCTAAA
212801 ATTAACAAAT
Statistics
Matches: 181, Mismatches: 39, Indels: 31
0.72 0.16 0.12
Matches are distributed among these distances:
41 9 0.05
42 26 0.14
43 83 0.46
44 23 0.13
47 1 0.01
49 1 0.01
50 16 0.09
51 13 0.07
52 9 0.05
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTAAATAACATGGTCTTTAGCGGCTTTTTTTCCAC
Found at i:213420 original size:26 final size:26
Alignment explanation
Indices: 213362--213420 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
213352 GGTGGTAGCT
* *
213362 AAATAAATCATGGTTAAATAGCATGC
1 AAATAAACCATGGTTAAATAGAATGC
*
213388 AACTAAACCATGGTTAAATAGAAAT-C
1 AAATAAACCATGGTTAAATAG-AATGC
213414 AAATAAA
1 AAATAAA
213421 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (26 bp):
AAATAAACCATGGTTAAATAGAATGC
Done.