Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015377.1 Kokia drynarioides strain JFW-HI SEQ_130424, 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: 212609
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 470 characters in sequence are not A, C, G, or T
Found at i:2000 original size:60 final size:60
Alignment explanation
Indices: 1875--1999 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 60
1865 GGCATGAACC
* * ** *
1875 TTTTTTGTTCAAATTAATCCTTGAACTTGACAATTGTTCTCACGGTATGGCCTGAATCTT
1 TTTTTTGTTCAAATTAATCCCTAAACTTGACAATTGTTCTCAAAGTAGGGCCTGAATCTT
* * * *
1935 TTTTTTGTTCAAATTAATCCCTAAATTTGGCAATTGTTC-CAAATTGAGGGCTTGAA-CTT
1 TTTTTTGTTCAAATTAATCCCTAAACTTGACAATTGTTCTCAAAGT-AGGGCCTGAATCTT
1994 TTTTTT
1 TTTTTT
2000 TTTATCCAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
59 12 0.22
60 43 0.78
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (60 bp):
TTTTTTGTTCAAATTAATCCCTAAACTTGACAATTGTTCTCAAAGTAGGGCCTGAATCTT
Found at i:2461 original size:15 final size:15
Alignment explanation
Indices: 2427--2485 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
2417 TAAATTTGAT
* *
2427 ACTTAAATTTTCAAT
1 ACTTAATTTTTCAAC
2442 ACTTAATTTTTCAAC
1 ACTTAATTTTTCAAC
* * ***
2457 CCTTATTTTTTTTTC
1 ACTTAATTTTTCAAC
2472 ACTTAATTTTTCAA
1 ACTTAATTTTTCAA
2486 TTTATCAAAG
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (15 bp):
ACTTAATTTTTCAAC
Found at i:5306 original size:983 final size:974
Alignment explanation
Indices: 3169--5137 Score: 2779
Period size: 983 Copynumber: 2.0 Consensus size: 974
3159 ATATTCTCAT
** * * * * * **
3169 TTTAAGTACCTAAAATTTTTGGTAAAATAAATACTTAAACTATTAATTTTGTTACATTTTACCTA
1 TTTAAGTACCTAAAATTAATGGT-AAATAAATAC---AACGATGAACTTTGTGAAATAGTACCTA
* * * * *
3234 AAAAGTGTACAATGACAATAAAACATGATACTGTGTTTTTGGTAAAATAAGATAAAATTAACCAT
62 AAAAGTGTACAATGACAATAAAACA-GATAC-GTGATTTCGCT-AAATAAGATAAAAATAACAAT
* *
3299 CTAAAAGTAATTTTTGCAAAAAAAAAAAAGAGAAAAAAAAAACTCTTAGACACCTAAGTGATAAA
124 CTAAAAGTAATCTCTGCAAAAAAAAAAAAGAGAAAAAAAAAACTCTTAGACACCTAAGTGATAAA
3364 TACGATATAGTTGGAGGGTTAATTTTGTATTTAATCCAAAAAAAAAGAAAAGAACAGATTTTACC
189 TACGATATAGTTGGAGGGTTAATTTTGTATTTAATCCAAAAAAAAAGAAAAGAACAGATTTTACC
3429 TTGTCATCTGCAAATTTGATCCAAAACAGAGCAATGGCTCTGTCATAGGGATCAACCGGCAACAA
254 TTGTCATCTGCAAATTTGATCCAAAACAGAGCAATGGCTCTGTCATAGGGATCAACCGGCAACAA
3494 GGGATTCTGCGGCCAAATTTCATCGATATATTGAAGGATGACGGTGGATTCACAAATCGGTTTTC
319 GGGATTCTGCGGCCAAATTTCATCGATATATTGAAGGATGACGGTGGATTCACAAATCGGTTTTC
3559 CGTCATGAACGAGCACCGGGACTTTCTTATGAACTGGATTATATTGAAGAAGCAAAGGACTCTTG
384 CGTCATGAACGAGCACCGGGACTTTCTTATGAACTGGATTATATTGAAGAAGCAAAGGACTCTTG
3624 TTGGGGAGATCTTCTTGGATATATTCGTAAGGTATGCCTTTCAGTTTCAGAGCCCAAATTACTCT
449 TTGGGGAGATCTTCTTGGATATATTCGTAAGGTATGCCTTTCAGTTTCAGAGCCCAAATTACTCT
*
3689 GTAAGCGTACGGACTAAACCAAGCTCCGAACAATTTCACGACTGCCATGGTTGGGAGATTAGTTT
514 GTAAGCGTACGGACTAAACCAAGCTCCGAACAATTTCACAACTGCCATGGTTGGGAGATTAGTTT
3754 AGAGATTCTGAGAGCGGTGAGTGTAAATTTATAATAGAATTGCTAGTCAAAGCTTTGACTAAGGT
579 AGAGATTCTGAGAGCGGTGAGTGTAAATTTATAATAGAATTGCTAGTCAAAGCTTTGACTAAGGT
*
3819 AATGTGTTTTTCATGGCATTACTTTTATTATATAACATATGAACAGATAATTAAAAAAAATTACC
644 AATGTGTTTTTCATGGCATTACTTTTATTATATAACATATGAACAAATAATTAAAAAAAATTACC
* *
3884 ACGAAATATGTAGATTGTCATATGAGTTGACATGTTTAAAAATTTAACGATTTAATTAATATTTC
709 ACGAAATATATAGATTGTCATATGAGTTGACATGTTTAAAAATTTAACGATTTAATCAATATTTC
*
3949 TGTTAAAAGTTCAATATTTCTATTGTGGACTACTCGGGACGCATATGGGCTAGGAGCTATCGGGA
774 TGTTAAAAGTTCAATATTTCTATTGTGGACTACTCGGGACGCATATGGGCTAGAAGCTATCGGGA
4014 CTTGGATGTGAGATTAAAGTCTATGGGAACATGGGACACATGTCGAAGTGGAAACCTCCAGATAC
839 CTTGGATGTGAGATTAAAGTCTATGGGAACATGGGACACATGTCGAAGTGGAAACCTCCAGATAC
************************************************** *
4079 TGGTTGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATCAAT
904 TGGTTGGAATCAAATTAAATTCCGATGGGGCAGTATCAAGGGATGGGAACTGGGCGTCTATCAAG
* *
4144 ATTCTC
969 AGTCGC
** * * * * * **
4150 ATTTTAAGTACCTAAAATTTTTGGTAAAATAAATACTTAAACTATTAATTTTGTTACATTTTACC
1 --TTTAAGTACCTAAAATTAATGGT-AAATAAATAC---AACGATGAACTTTGTGAAATAGTACC
* * * * *
4215 TAAAAAGTGTACAATGACAATAAAACATGATACTGTGTTTTTGGTAAAATAAGATAAAATTAACC
60 TAAAAAGTGTACAATGACAATAAAACA-GATAC-GTGATTTCGCT-AAATAAGATAAAAATAACA
* *
4280 ATCTAAAAGTAATTTTTGCAAAAAAAAAAAAGAGAAAAAAAAAACTCTTAGACACCTAAGTGATA
122 ATCTAAAAGTAATCTCTGCAAAAAAAAAAAAGAGAAAAAAAAAACTCTTAGACACCTAAGTGATA
4345 AATACGATATAGTTGGAGGGTTAATTTTGTATTTAATCCAAAAAAAAAGAAAAGAACAGATTTTA
187 AATACGATATAGTTGGAGGGTTAATTTTGTATTTAATCCAAAAAAAAAGAAAAGAACAGATTTTA
*
4410 CCTTGTCATCTGCAAATTTGATCCAAAACAGAGCAATGGCTCTGTCATAGGGATCAACCGGCAGC
252 CCTTGTCATCTGCAAATTTGATCCAAAACAGAGCAATGGCTCTGTCATAGGGATCAACCGGCAAC
*
4475 AAGGGATTCTGCGGCCAAATTTCATCGATATATTGAAGGATGACGGTGGATTCACAGATCGGTTT
317 AAGGGATTCTGCGGCCAAATTTCATCGATATATTGAAGGATGACGGTGGATTCACAAATCGGTTT
4540 TCCGTCATGAACGAGCACCGGGACTTTCTTATGAACTGGATTATATTGAAGAAGCAAAGGACTCT
382 TCCGTCATGAACGAGCACCGGGACTTTCTTATGAACTGGATTATATTGAAGAAGCAAAGGACTCT
*
4605 TGTTTGGGAGATCTTCTTGGATATATTCGTAAGGTATGCCTTTCAGTTTCAGAGCCCAAATTACT
447 TGTTGGGGAGATCTTCTTGGATATATTCGTAAGGTATGCCTTTCAGTTTCAGAGCCCAAATTACT
4670 CTGTAAGCGTACGGACTAAACCAAGCTCCGAACAATTTCACAACTGCCATGGTTGGGAGATTAGT
512 CTGTAAGCGTACGGACTAAACCAAGCTCCGAACAATTTCACAACTGCCATGGTTGGGAGATTAGT
* *
4735 TTAGAGATTCTGAGAGCGGTGAGTGTAAATTTATAATAGGATTGCTGGTCAAAGCTTTGACTAAG
577 TTAGAGATTCTGAGAGCGGTGAGTGTAAATTTATAATAGAATTGCTAGTCAAAGCTTTGACTAAG
4800 GTAATGTGTTTTTCATGGCATTACTTTTATTATATAACATATGAACAAATAATTAAAAATTATAA
642 GTAATGTGTTTTTCATGGCATTACTTTTATTATATAACATATGAAC--A-AA-T---AA-T-T--
*
4865 AAATTTAAAAAAATTACCACGAAATATATAGATTGTCATGTGAGTTGACATGTTTAAAAATTTAA
696 --A---AAAAAAATTACCACGAAATATATAGATTGTCATATGAGTTGACATGTTTAAAAATTTAA
4930 CGATTTAATCAATATTTCTGTTAAAAGTTCAATATTTCTATTGTGGACTACTCGGGACGCATATG
756 CGATTTAATCAATATTTCTGTTAAAAGTTCAATATTTCTATTGTGGACTACTCGGGACGCATATG
4995 GGCTAGAAGCTATCGGGACTTGGATGTGAGATTAAAGTCTATGGGAACATGGGACACATGTCGAA
821 GGCTAGAAGCTATCGGGACTTGGATGTGAGATTAAAGTCTATGGGAACATGGGACACATGTCGAA
5060 GTGGAAACCTCCAGATACTGGTTGG-ATCAAATTAAATTCCGATGGGGCAGTATCAAGGGATGGG
886 GTGGAAACCTCCAGATACTGGTTGGAATCAAATTAAATTCCGATGGGGCAGTATCAAGGGATGGG
5124 AACTGGGCGTCTAT
951 AACTGGGCGTCTAT
5138 AGGGGTGCTT
Statistics
Matches: 909, Mismatches: 61, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
983 688 0.76
985 1 0.00
986 1 0.00
987 1 0.00
990 2 0.00
991 1 0.00
992 1 0.00
996 1 0.00
998 3 0.00
999 210 0.23
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.30
Consensus pattern (974 bp):
TTTAAGTACCTAAAATTAATGGTAAATAAATACAACGATGAACTTTGTGAAATAGTACCTAAAAA
GTGTACAATGACAATAAAACAGATACGTGATTTCGCTAAATAAGATAAAAATAACAATCTAAAAG
TAATCTCTGCAAAAAAAAAAAAGAGAAAAAAAAAACTCTTAGACACCTAAGTGATAAATACGATA
TAGTTGGAGGGTTAATTTTGTATTTAATCCAAAAAAAAAGAAAAGAACAGATTTTACCTTGTCAT
CTGCAAATTTGATCCAAAACAGAGCAATGGCTCTGTCATAGGGATCAACCGGCAACAAGGGATTC
TGCGGCCAAATTTCATCGATATATTGAAGGATGACGGTGGATTCACAAATCGGTTTTCCGTCATG
AACGAGCACCGGGACTTTCTTATGAACTGGATTATATTGAAGAAGCAAAGGACTCTTGTTGGGGA
GATCTTCTTGGATATATTCGTAAGGTATGCCTTTCAGTTTCAGAGCCCAAATTACTCTGTAAGCG
TACGGACTAAACCAAGCTCCGAACAATTTCACAACTGCCATGGTTGGGAGATTAGTTTAGAGATT
CTGAGAGCGGTGAGTGTAAATTTATAATAGAATTGCTAGTCAAAGCTTTGACTAAGGTAATGTGT
TTTTCATGGCATTACTTTTATTATATAACATATGAACAAATAATTAAAAAAAATTACCACGAAAT
ATATAGATTGTCATATGAGTTGACATGTTTAAAAATTTAACGATTTAATCAATATTTCTGTTAAA
AGTTCAATATTTCTATTGTGGACTACTCGGGACGCATATGGGCTAGAAGCTATCGGGACTTGGAT
GTGAGATTAAAGTCTATGGGAACATGGGACACATGTCGAAGTGGAAACCTCCAGATACTGGTTGG
AATCAAATTAAATTCCGATGGGGCAGTATCAAGGGATGGGAACTGGGCGTCTATCAAGAGTCGC
Found at i:5469 original size:56 final size:57
Alignment explanation
Indices: 5318--5525 Score: 310
Period size: 57 Copynumber: 3.7 Consensus size: 57
5308 AATTGACAAA
*
5318 GAAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTTCATAATTTATTATGTCT
1 GAAATTTGAAGAAATGATTGCCTAAAATGGCCGCTGTTTTCATAATTTATTATGTCT
* * *
5375 AAAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTGCATAATTTATTATGT-T
1 GAAATTTGAAGAAATGATTGCCTAAAATGGCCGCTGTTTTCATAATTTATTATGTCT
* * * * *
5431 GAAATTTGAAGAAAAGGTTGTCTAAAATGGCAGCTGTTTTCACAATTTATTATGTCT
1 GAAATTTGAAGAAATGATTGCCTAAAATGGCCGCTGTTTTCATAATTTATTATGTCT
* *
5488 GAAATTTGAAGAAATGGTTGTCTAAAATGGCCGCTGTT
1 GAAATTTGAAGAAATGATTGCCTAAAATGGCCGCTGTT
5526 CTGTTATGGT
Statistics
Matches: 138, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
56 48 0.35
57 90 0.65
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (57 bp):
GAAATTTGAAGAAATGATTGCCTAAAATGGCCGCTGTTTTCATAATTTATTATGTCT
Found at i:5516 original size:113 final size:113
Alignment explanation
Indices: 5318--5525 Score: 326
Period size: 113 Copynumber: 1.8 Consensus size: 113
5308 AATTGACAAA
* * * *
5318 GAAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTTCATAATTTATTATGTCTAAAATTTG
1 GAAATTTGAAGAAAAGATTGCCTAAAATGGCAGCTGTTTTCACAATTTATTATGTCTAAAATTTG
*
5383 AAGAAATGATTGCCTAAAATGGCCGTTGTTTGCATAATTTATTATGTT
66 AAGAAATGATTGCCTAAAATGGCCGCTGTTTGCATAATTTATTATGTT
* * *
5431 GAAATTTGAAGAAAAGGTTGTCTAAAATGGCAGCTGTTTTCACAATTTATTATGTCTGAAATTTG
1 GAAATTTGAAGAAAAGATTGCCTAAAATGGCAGCTGTTTTCACAATTTATTATGTCTAAAATTTG
* *
5496 AAGAAATGGTTGTCTAAAATGGCCGCTGTT
66 AAGAAATGATTGCCTAAAATGGCCGCTGTT
5526 CTGTTATGGT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
113 85 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (113 bp):
GAAATTTGAAGAAAAGATTGCCTAAAATGGCAGCTGTTTTCACAATTTATTATGTCTAAAATTTG
AAGAAATGATTGCCTAAAATGGCCGCTGTTTGCATAATTTATTATGTT
Found at i:5656 original size:13 final size:14
Alignment explanation
Indices: 5640--5670 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5630 AAATTTTTTT
5640 TTAAA-ATTTTGAA
1 TTAAATATTTTGAA
5653 TTAAATATTTTGAA
1 TTAAATATTTTGAA
5667 TTAA
1 TTAA
5671 TTGAGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TTAAATATTTTGAA
Found at i:6361 original size:13 final size:15
Alignment explanation
Indices: 6343--6383 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
6333 GGTTTTTTAC
6343 AAAAATAATATA-A-
1 AAAAATAATATACAT
*
6356 AAAAATATTATACAT
1 AAAAATAATATACAT
*
6371 TAAAATAATATAC
1 AAAAATAATATAC
6384 TCCCCATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 1 0.04
15 11 0.48
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATAATATACAT
Found at i:7773 original size:57 final size:57
Alignment explanation
Indices: 7682--7894 Score: 279
Period size: 57 Copynumber: 3.9 Consensus size: 57
7672 AACGTGTTAG
*
7682 AAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTTCATAATTTATTATGTCTA
1 AAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTGCATAATTTATTATGTCTA
*
7739 AAATTTGAAGAAATGATTGCCTAAAATGGTCGTTGTTTGCATAATTTATTATGTCTA
1 AAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTGCATAATTTATTATGTCTA
7796 AAATTTGAAGAAATGATTGCCTAAAA-----------TG-ATAATTTATTATGTCTA
1 AAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTGCATAATTTATTATGTCTA
* * * * *
7841 AAATTTGAAGAAATGATTGTCTAAAATGGCAGCTGTTTTCGTAATTTATTATGT
1 AAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTGCATAATTTATTATGT
7895 AAAATGAATT
Statistics
Matches: 139, Mismatches: 5, Indels: 24
0.83 0.03 0.14
Matches are distributed among these distances:
45 42 0.30
46 2 0.01
56 1 0.01
57 94 0.68
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.40
Consensus pattern (57 bp):
AAATTTGAAGAAATGATTGCCTAAAATGGCCGTTGTTTGCATAATTTATTATGTCTA
Found at i:7819 original size:23 final size:23
Alignment explanation
Indices: 7790--7867 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
7780 TAATTTATTA
7790 TGTCTAAAATTTGAAGAAATGAT
1 TGTCTAAAATTTGAAGAAATGAT
* * * *
7813 TGCCTAAAA--TG-ATAATTTATT
1 TGTCTAAAATTTGAAGAAATGA-T
7834 ATGTCTAAAATTTGAAGAAATGAT
1 -TGTCTAAAATTTGAAGAAATGAT
7858 TGTCTAAAAT
1 TGTCTAAAAT
7868 GGCAGCTGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
20 5 0.12
21 3 0.07
22 8 0.19
23 18 0.43
24 3 0.07
25 5 0.12
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.37
Consensus pattern (23 bp):
TGTCTAAAATTTGAAGAAATGAT
Found at i:7830 original size:45 final size:45
Alignment explanation
Indices: 7779--7868 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
7769 CGTTGTTTGC
7779 ATAATTTATTATGTCTAAAATTTGAAGAAATGATTGCCTAAAATG
1 ATAATTTATTATGTCTAAAATTTGAAGAAATGATTGCCTAAAATG
*
7824 ATAATTTATTATGTCTAAAATTTGAAGAAATGATTGTCTAAAATG
1 ATAATTTATTATGTCTAAAATTTGAAGAAATGATTGCCTAAAATG
7869 GCAGCTGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (45 bp):
ATAATTTATTATGTCTAAAATTTGAAGAAATGATTGCCTAAAATG
Found at i:8200 original size:13 final size:15
Alignment explanation
Indices: 8182--8222 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
8172 GGTTTTTTAC
8182 AAAAATAATATA-A-
1 AAAAATAATATACAT
*
8195 AAAAATATTATACAT
1 AAAAATAATATACAT
*
8210 TAAAATAATATAC
1 AAAAATAATATAC
8223 TCCCCATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 1 0.04
15 11 0.48
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATAATATACAT
Found at i:16940 original size:18 final size:18
Alignment explanation
Indices: 16909--16955 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
16899 AAACATTTTA
16909 TTAAACAATA-TTTTTATT
1 TTAAA-AATATTTTTTATT
16927 TTAAAAATATTTTTTATT
1 TTAAAAATATTTTTTATT
* *
16945 TCAAAAGTATT
1 TTAAAAATATT
16956 GATTGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTAAAAATATTTTTTATT
Found at i:30521 original size:46 final size:46
Alignment explanation
Indices: 30454--30555 Score: 186
Period size: 46 Copynumber: 2.2 Consensus size: 46
30444 CTTGAAAACG
*
30454 GTTTTAAGTCTGCAATGTATTAATGACTATACATACTACTTACTCT
1 GTTTTAAGTCTGCAATATATTAATGACTATACATACTACTTACTCT
*
30500 GTTTTAAGTCTGCAATATATTAATGACTATACATACTACTTGCTCT
1 GTTTTAAGTCTGCAATATATTAATGACTATACATACTACTTACTCT
30546 GTTTTAAGTC
1 GTTTTAAGTC
30556 ACTTTGGGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (46 bp):
GTTTTAAGTCTGCAATATATTAATGACTATACATACTACTTACTCT
Found at i:30638 original size:46 final size:44
Alignment explanation
Indices: 30585--30681 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 44
30575 GTGAATATAT
30585 ATACTAGATTAAAAGTTTTGGAAGGAAAAATCCCATCAATGGTGTA
1 ATACTAGATT-AAAGTTTTGGAAGGAAAAAT-CCATCAATGGTGTA
30631 ATACTAG---AAAGTTTTGGAAGGAAAAATCCATCAATGGTGTA
1 ATACTAGATTAAAGTTTTGGAAGGAAAAATCCATCAATGGTGTA
*
30672 ATTCTAGATT
1 ATACTAGATT
30682 TAACATTCCA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
41 20 0.43
42 20 0.43
46 7 0.15
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (44 bp):
ATACTAGATTAAAGTTTTGGAAGGAAAAATCCATCAATGGTGTA
Found at i:30679 original size:41 final size:42
Alignment explanation
Indices: 30596--30679 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
30586 TACTAGATTA
30596 AAAGTTTTGGAAGGAAAAATCCCATCAATGGTGTAATACTAG
1 AAAGTTTTGGAAGGAAAAATCCCATCAATGGTGTAATACTAG
*
30638 AAAGTTTTGGAAGGAAAAAT-CCATCAATGGTGTAATTCTAG
1 AAAGTTTTGGAAGGAAAAATCCCATCAATGGTGTAATACTAG
30679 A
1 A
30680 TTTAACATTC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 21 0.51
42 20 0.49
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (42 bp):
AAAGTTTTGGAAGGAAAAATCCCATCAATGGTGTAATACTAG
Found at i:43170 original size:93 final size:93
Alignment explanation
Indices: 43058--43243 Score: 309
Period size: 93 Copynumber: 2.0 Consensus size: 93
43048 TGAATCTGAA
43058 AAAAATCCATCCCAGACCAGCAATAAAATAGAGTCAAACACCACCCACGAGGAAGAGGGTTTACC
1 AAAAATCCATCCCAGACCAGCAATAAAATAGAGTCAAACACCACCCACGAGGAAGAGGGTTTACC
43123 ATTTGGCAGTGAGAATAAAGAAAAATTT
66 ATTTGGCAGTGAGAATAAAGAAAAATTT
* * ** *
43151 AAAAATCCATCCTAGACCAGCAATGAAATAGAGTCCGACACCACCCACGATGAAGAGGGTTTACC
1 AAAAATCCATCCCAGACCAGCAATAAAATAGAGTCAAACACCACCCACGAGGAAGAGGGTTTACC
* *
43216 CTTTGGCAGTGAGAATAAAGACAAATTT
66 ATTTGGCAGTGAGAATAAAGAAAAATTT
43244 GCATTATTAG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (93 bp):
AAAAATCCATCCCAGACCAGCAATAAAATAGAGTCAAACACCACCCACGAGGAAGAGGGTTTACC
ATTTGGCAGTGAGAATAAAGAAAAATTT
Found at i:45307 original size:50 final size:50
Alignment explanation
Indices: 45232--45328 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
45222 AAAGTTCTTG
45232 GTTTGAATGCACTTGCTACGACATACCACATTATTAGAGATTTTTTTTCA
1 GTTTGAATGCACTTGCTACGACATACCACATTATTAGAGATTTTTTTTCA
*
45282 GTTTGAATGCACTTGCTACGGCATACCACATTATTAGAGATTTTTTT
1 GTTTGAATGCACTTGCTACGACATACCACATTATTAGAGATTTTTTT
45329 AAAATCGATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (50 bp):
GTTTGAATGCACTTGCTACGACATACCACATTATTAGAGATTTTTTTTCA
Found at i:49585 original size:2 final size:2
Alignment explanation
Indices: 49578--49609 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49568 GGGAAAATTA
49578 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
49610 GGGGGAAAGT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52677 original size:12 final size:13
Alignment explanation
Indices: 52646--52678 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52636 TCAACAGTAG
52646 AATTAAATATAAT
1 AATTAAATATAAT
52659 AATTAAATA-AAT
1 AATTAAATATAAT
*
52671 TATTAAAT
1 AATTAAAT
52679 TCCCTGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTAAATATAAT
Found at i:55363 original size:11 final size:10
Alignment explanation
Indices: 55344--55373 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
55334 TTTGGTCTTC
55344 TTCTTTTTTT
1 TTCTTTTTTT
55354 TTCTTTTTTT
1 TTCTTTTTTT
55364 TTCTTTTTTT
1 TTCTTTTTTT
55374 GTGGTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:58420 original size:17 final size:16
Alignment explanation
Indices: 58394--58425 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58384 TTTGCAAGAT
58394 AAAGAAAAAAATACTG
1 AAAGAAAAAAATACTG
58410 AAAGAAAAAAATACTG
1 AAAGAAAAAAATACTG
58426 TAATAATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAGAAAAAAATACTG
Found at i:68969 original size:20 final size:19
Alignment explanation
Indices: 68923--68973 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
68913 ACATACACAT
*
68923 AAAAAATATAAAAAAATGG
1 AAAAAATATAAAAAAATAG
*
68942 AAATAAATATAAAAAATTCAG
1 AAA-AAATATAAAAAAAT-AG
68963 AAAAAATATAA
1 AAAAAATATAA
68974 TTTATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 21 0.75
21 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.20
Consensus pattern (19 bp):
AAAAAATATAAAAAAATAG
Found at i:73470 original size:114 final size:117
Alignment explanation
Indices: 73317--73549 Score: 355
Period size: 114 Copynumber: 2.0 Consensus size: 117
73307 CAATGTATTG
* * * *
73317 TTACCTAATGAGCTCTGGTGTTGATCTAATCATGGATTGCATTGTTGTGGTTTGAATTTTAGTGT
1 TTACCTAATGAACCCTGGTGTTGATCTAATCATGCATTGCATTGTTGTGGTTTGAATCTTAGTGT
* * * *
73382 TTTCATGGAA-CC-CGATTAGACTTGTTCATGAGTTGATTTTGGATAAAGAT
66 TTTCATGGAACCCACAATTAAACTTGTTCAAGAGTTGAGTTTGGATAAAGAT
*
73432 TTACCTAATGAACCCT-GTGTTGATCTAATCATGCATTGCATTGTTGTGGTTTGAATCTTATTGT
1 TTACCTAATGAACCCTGGTGTTGATCTAATCATGCATTGCATTGTTGTGGTTTGAATCTTAGTGT
*
73496 TTTCATGGAACCCACAATTAAACTTGTTCAAGGGTTGAGTTTGGATAAAGAT
66 TTTCATGGAACCCACAATTAAACTTGTTCAAGAGTTGAGTTTGGATAAAGAT
73548 TT
1 TT
73550 TTACATGTTG
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
114 55 0.52
115 16 0.15
116 35 0.33
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (117 bp):
TTACCTAATGAACCCTGGTGTTGATCTAATCATGCATTGCATTGTTGTGGTTTGAATCTTAGTGT
TTTCATGGAACCCACAATTAAACTTGTTCAAGAGTTGAGTTTGGATAAAGAT
Found at i:77460 original size:1 final size:1
Alignment explanation
Indices: 77454--77481 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
77444 NNNNNNNNNN
77454 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
77482 GCATTTCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:80061 original size:28 final size:28
Alignment explanation
Indices: 80021--80087 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
80011 GGGTCCCTTG
80021 ATGTTTGGACTTAAAAACTTTGTTGTGT
1 ATGTTTGGACTTAAAAACTTTGTTGTGT
80049 ATGTTTGGACTTAAAAACTTTGTTGTGT
1 ATGTTTGGACTTAAAAACTTTGTTGTGT
80077 ATGTTTGGACT
1 ATGTTTGGACT
80088 ATTCTTTTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (28 bp):
ATGTTTGGACTTAAAAACTTTGTTGTGT
Found at i:92686 original size:159 final size:159
Alignment explanation
Indices: 92516--92834 Score: 620
Period size: 159 Copynumber: 2.0 Consensus size: 159
92506 GTCAATGGAA
*
92516 TTCAGACATCCACTGCCTTCCAGCCACGTGCCATGACATAAGTGAGCAAGTGATTTTTAAAGATT
1 TTCAGACATCCACTGCCTCCCAGCCACGTGCCATGACATAAGTGAGCAAGTGATTTTTAAAGATT
92581 TTGAGGTAAAACAGCTGGACCGTGAAATCCTAGTGTCATTCATAGCTAATCAGACAAAACCTGTG
66 TTGAGGTAAAACAGCTGGACCGTGAAATCCTAGTGTCATTCATAGCTAATCAGACAAAACCTGTG
*
92646 ACATTCCGTGGAGATAGGATGGTGACAAC
131 ACATTCCGTGGAGAGAGGATGGTGACAAC
92675 TTCAGACATCCACTGCCTCCCAGCCACGTGCCATGACATAAGTGAGCAAGTGATTTTTAAAGATT
1 TTCAGACATCCACTGCCTCCCAGCCACGTGCCATGACATAAGTGAGCAAGTGATTTTTAAAGATT
92740 TTGAGGTAAAACAGCTGGACCGTGAAATCCTAGTGTCATTCATAGCTAATCAGACAAAACCTGTG
66 TTGAGGTAAAACAGCTGGACCGTGAAATCCTAGTGTCATTCATAGCTAATCAGACAAAACCTGTG
92805 ACATTCCGTGGAGAGAGGATGGTGACAAC
131 ACATTCCGTGGAGAGAGGATGGTGACAAC
92834 T
1 T
92835 GATGTATGTT
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 158 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (159 bp):
TTCAGACATCCACTGCCTCCCAGCCACGTGCCATGACATAAGTGAGCAAGTGATTTTTAAAGATT
TTGAGGTAAAACAGCTGGACCGTGAAATCCTAGTGTCATTCATAGCTAATCAGACAAAACCTGTG
ACATTCCGTGGAGAGAGGATGGTGACAAC
Found at i:107770 original size:24 final size:24
Alignment explanation
Indices: 107684--107758 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
107674 AAAAATAATC
* * *
107684 TTTCAGTTAAACTATGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
*
107708 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
107732 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
107756 TTT
1 TTT
107759 GAGTTACACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:109725 original size:24 final size:24
Alignment explanation
Indices: 109697--109747 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
109687 AGAAATAATC
* *
109697 TTTTAGTTAAATTCTGTTTAATTG
1 TTTTAATTAAACTCTGTTTAATTG
*
109721 TTTTAATTAAACTCTGTTTATTTG
1 TTTTAATTAAACTCTGTTTAATTG
109745 TTT
1 TTT
109748 GAGTGAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.61
Consensus pattern (24 bp):
TTTTAATTAAACTCTGTTTAATTG
Found at i:109756 original size:24 final size:24
Alignment explanation
Indices: 109709--109759 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
109699 TTAGTTAAAT
* *
109709 TCTGTTTAATTGTTTTAATTAAAC
1 TCTGTTTAATTGTTTGAATGAAAC
* *
109733 TCTGTTTATTTGTTTGAGTGAAAC
1 TCTGTTTAATTGTTTGAATGAAAC
109757 TCT
1 TCT
109760 TATTAGTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (24 bp):
TCTGTTTAATTGTTTGAATGAAAC
Found at i:120207 original size:23 final size:24
Alignment explanation
Indices: 120160--120208 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
120150 ATGTTCACAA
* *
120160 ATAAGCTCGTTTATTGGCTCGTTT
1 ATAAGCTCGCTTATTGACTCGTTT
120184 ATAAGCTCGCTTA-TGACTCGTTT
1 ATAAGCTCGCTTATTGACTCGTTT
120207 AT
1 AT
120209 TTATTAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (24 bp):
ATAAGCTCGCTTATTGACTCGTTT
Found at i:120617 original size:24 final size:25
Alignment explanation
Indices: 120584--120636 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
120574 TATGAAAAGA
* *
120584 AAATAACTAAGATTATTATGCTAAT
1 AAATAACTAAAAATATTATGCTAAT
* *
120609 AAAT-ACTAAAAATATTATTCTACT
1 AAATAACTAAAAATATTATGCTAAT
120633 AAAT
1 AAAT
120637 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (25 bp):
AAATAACTAAAAATATTATGCTAAT
Found at i:120850 original size:18 final size:18
Alignment explanation
Indices: 120813--120859 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
120803 TCAAAATTAA
*
120813 TGAGTTCGTCACTTCCTG
1 TGAGCTCGTCACTTCCTG
**
120831 TGAGCTCGTCACTTTTTG
1 TGAGCTCGTCACTTCCTG
*
120849 TGAGCACGTCA
1 TGAGCTCGTCA
120860 AAATAATACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (18 bp):
TGAGCTCGTCACTTCCTG
Found at i:121306 original size:2 final size:2
Alignment explanation
Indices: 121299--121338 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
121289 TAATAGGATT
121299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
121339 TGTAATTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:121562 original size:21 final size:21
Alignment explanation
Indices: 121536--121593 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
121526 GTTTAAATTC
121536 AAGATTTAAATTTAAAGTTTA
1 AAGATTTAAATTTAAAGTTTA
* * *
121557 AAGA-TTAAGATTCAATGTTTG
1 AAGATTTAA-ATTTAAAGTTTA
121578 AA-ATTATAAATTTAAA
1 AAGATT-TAAATTTAAA
121594 ACTGAAGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.17
21 21 0.72
22 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (21 bp):
AAGATTTAAATTTAAAGTTTA
Found at i:125450 original size:13 final size:13
Alignment explanation
Indices: 125417--125457 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
125407 TCAAAAATTG
125417 TTATTTTCTTATTT
1 TTATTTT-TTATTT
*
125431 TT-GTTTTTATTT
1 TTATTTTTTATTT
125443 TTATTTTTTATTT
1 TTATTTTTTATTT
125456 TT
1 TT
125458 TTAAGTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 14 0.58
14 2 0.08
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:133251 original size:30 final size:30
Alignment explanation
Indices: 133187--133255 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
133177 TAAAAATATC
* *
133187 TTTATAATTTTTAAAAAATTAAATTAAATT
1 TTTATTATTTTTAAAAAATTAAATTAAATG
*
133217 TTTATTATTTTTAAAGAATTAAAATGT-AA-G
1 TTTATTATTTTTAAAAAATT-AAAT-TAAATG
133247 TTTATTATT
1 TTTATTATT
133256 ACTAATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 27 0.79
31 6 0.18
32 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (30 bp):
TTTATTATTTTTAAAAAATTAAATTAAATG
Found at i:141134 original size:3 final size:3
Alignment explanation
Indices: 141126--141151 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
141116 CTCAAAAGAA
141126 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
141152 CCTCAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:142518 original size:2 final size:2
Alignment explanation
Indices: 142511--142551 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
142501 GGATCCATGA
142511 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
142552 GTGTTGGCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:143614 original size:4 final size:4
Alignment explanation
Indices: 143605--143632 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
143595 AGAGGGCAGT
143605 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
143633 TATAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:146041 original size:2 final size:2
Alignment explanation
Indices: 146034--146063 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
146024 CAAAAATAAC
146034 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
146064 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146803 original size:71 final size:70
Alignment explanation
Indices: 146719--146854 Score: 263
Period size: 71 Copynumber: 1.9 Consensus size: 70
146709 AATAAATCAT
146719 CTATTTTAGATTTTAATATGAAAATAATTCTAGTGCATAAATCGATTTAGACAAAAAAAAAAAAA
1 CTATTTTAGATTTTAATATGAAAATAATTCTAGTGCATAAATCGATTTAGACAAAAAAAAAAAAA
146784 AAAAA
66 AAAAA
146789 NCTATTTTAGATTTTAATATGAAAATAATTCTAGTGCATAAATCGATTTAGACAAAAAAAAAAAA
1 -CTATTTTAGATTTTAATATGAAAATAATTCTAGTGCATAAATCGATTTAGACAAAAAAAAAAAA
146854 A
65 A
146855 TCTCAATGTG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.31
Consensus pattern (70 bp):
CTATTTTAGATTTTAATATGAAAATAATTCTAGTGCATAAATCGATTTAGACAAAAAAAAAAAAA
AAAAA
Found at i:148441 original size:25 final size:23
Alignment explanation
Indices: 148412--148464 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
148402 AATTTCACCA
* *
148412 TTTTAATAGCTTATATTTTTATAAT
1 TTTTAAAAGCTTA-AATTTTA-AAT
*
148437 TTTTAAAAGGTTAAATTTTAAAT
1 TTTTAAAAGCTTAAATTTTAAAT
148460 TTTTA
1 TTTTA
148465 TCATTTTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.32
24 6 0.24
25 11 0.44
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (23 bp):
TTTTAAAAGCTTAAATTTTAAAT
Found at i:149832 original size:18 final size:18
Alignment explanation
Indices: 149798--149836 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
149788 TCAAAAAATA
*
149798 AGTATGAATTTTTTTAAT
1 AGTATGAATTTTATTAAT
149816 AGTAT-AATTATTATTAAT
1 AGTATGAATT-TTATTAAT
149834 AGT
1 AGT
149837 TTAGAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (18 bp):
AGTATGAATTTTATTAAT
Found at i:161403 original size:21 final size:21
Alignment explanation
Indices: 161377--161419 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
161367 CCATCCATAT
161377 TATATGATAACACGTTAACAC
1 TATATGATAACACGTTAACAC
161398 TATATGATAACACGTTAACAC
1 TATATGATAACACGTTAACAC
161419 T
1 T
161420 CCCGAGGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (21 bp):
TATATGATAACACGTTAACAC
Found at i:161641 original size:2 final size:2
Alignment explanation
Indices: 161634--161668 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
161624 TAAACCTCGT
161634 TA 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 TA T
161669 CTTGGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:168199 original size:31 final size:31
Alignment explanation
Indices: 168156--168222 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
168146 GAAAATCAGG
*
168156 CTAAAGGGATGCACTAAACCTTTTGTAAAAA
1 CTAACGGGATGCACTAAACCTTTTGTAAAAA
168187 CTAACGGGATGCACTAAACCTTTTGTAAAAA
1 CTAACGGGATGCACTAAACCTTTTGTAAAAA
168218 CTAAC
1 CTAAC
168223 CTTACCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (31 bp):
CTAACGGGATGCACTAAACCTTTTGTAAAAA
Found at i:171148 original size:30 final size:29
Alignment explanation
Indices: 171112--171182 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
171102 GATCTTTTAT
* *
171112 ATAATAAAATTGTACTTTAGTTTTTTAAAA
1 ATAATAAAATT-TACTTTAATTTTTAAAAA
**
171142 ATAATAAAAATTTGGTTTAATTTTTAAAAA
1 ATAAT-AAAATTTACTTTAATTTTTAAAAA
*
171172 ATTATAAAATT
1 ATAATAAAATT
171183 ATAGATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 6 0.17
30 23 0.66
31 6 0.17
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (29 bp):
ATAATAAAATTTACTTTAATTTTTAAAAA
Found at i:173423 original size:95 final size:95
Alignment explanation
Indices: 173257--173430 Score: 260
Period size: 95 Copynumber: 1.8 Consensus size: 95
173247 ATCCGGTGAT
* * *
173257 GATGCGTTGCGTTTGCATTGAATTTATATCAAGAATAATTCGTTCTTTTGTCGTACTCGTGAATG
1 GATGCGTTGCATTTGCATTGAATTTAAATCAAGAATAATTCATTCTTTTGTCGTACTCGTGAATG
173322 GAACCGAGTGTGTTCTATGAATCTCCTGAA
66 GAACCGAGTGTGTTCTATGAATCTCCTGAA
* * *
173352 GATGCGTTGCATTTGCATTGAATTTAAAATGAAGAATAATTCATTC-TTTGTTGTAGTCGTGAAT
1 GATGCGTTGCATTTGCATTGAATTT-AAATCAAGAATAATTCATTCTTTTGTCGTACTCGTGAAT
* *
173416 GGCACCGAGTTTGTT
65 GGAACCGAGTGTGTT
173431 TATAAAAAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
95 53 0.76
96 17 0.24
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (95 bp):
GATGCGTTGCATTTGCATTGAATTTAAATCAAGAATAATTCATTCTTTTGTCGTACTCGTGAATG
GAACCGAGTGTGTTCTATGAATCTCCTGAA
Found at i:177125 original size:26 final size:26
Alignment explanation
Indices: 177089--177142 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
177079 CACTTTTAGC
177089 GAAGTTTAACTTCATAAGCAAGTTGA
1 GAAGTTTAACTTCATAAGCAAGTTGA
177115 GAAGTTTAACTTCATAAGCAAGTTGA
1 GAAGTTTAACTTCATAAGCAAGTTGA
177141 GA
1 GA
177143 GTATGATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (26 bp):
GAAGTTTAACTTCATAAGCAAGTTGA
Found at i:177208 original size:14 final size:14
Alignment explanation
Indices: 177191--177219 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
177181 TACCACACTT
177191 ATAAAAAATTCTAA
1 ATAAAAAATTCTAA
177205 ATAAAAAATTCTAA
1 ATAAAAAATTCTAA
177219 A
1 A
177220 AGAGATTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAAAATTCTAA
Found at i:180973 original size:5 final size:5
Alignment explanation
Indices: 180963--180987 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
180953 AGATAAAAGA
180963 TATGG TATGG TATGG TATGG TATGG
1 TATGG TATGG TATGG TATGG TATGG
180988 GACCAAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TATGG
Found at i:183702 original size:6 final size:6
Alignment explanation
Indices: 183691--183721 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
183681 ATCTCCCTCC
183691 ACCATA ACCATA ACCATA ACCATA ACCATA A
1 ACCATA ACCATA ACCATA ACCATA ACCATA A
183722 TTGATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCATA
Found at i:183921 original size:22 final size:23
Alignment explanation
Indices: 183891--183933 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
183881 TTTAATCTTT
*
183891 ATATCTTTTATA-AATTTAATTA
1 ATATCTTTTAAATAATTTAATTA
*
183913 ATATTTTTTAAATAATTTAAT
1 ATATCTTTTAAATAATTTAAT
183934 GATCAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATCTTTTAAATAATTTAATTA
Found at i:185195 original size:149 final size:148
Alignment explanation
Indices: 184973--185247 Score: 464
Period size: 149 Copynumber: 1.9 Consensus size: 148
184963 TACATCCATG
*
184973 TCAATTTAATGTTTTTTTATTTATCATTAATATTAAAAATAAACTATAAATTAAAACATCATAAG
1 TCAATTTAATGATTTTTTATTTATCATTAATATTAAAAATAAACTATAAATTAAAACATCATAAG
*
185038 TTTACAAATTGATTGCTTGAATTTAATAA-TTCGTGATAAATAAATAAATTTAATTTAATAATCC
66 CTTACAAATTGATTGCTTGAATTTAATAACTT--TGATAAATAAATAAATTTAATTTAATAATCC
185102 TTGTCCTATCTCGCTTTGCT
129 TTGTCCTATCTCGCTTTGCT
*
185122 TCAATTTAAT-ATTTTTTATTTATCATTAATATTAAAAAATAAACTATAAATTAGAACATCATAA
1 TCAATTTAATGATTTTTTATTTATCATTAATATT-AAAAATAAACTATAAATTAAAACATCATAA
* *
185186 GCTTACAAATTGATTGTTTGAATTTAGTAACTTTGATAAATAAATAAATTTAATTTAATAAT
65 GCTTACAAATTGATTGCTTGAATTTAATAACTTTGATAAATAAATAAATTTAATTTAATAAT
185248 TTATTCATTA
Statistics
Matches: 119, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
148 51 0.43
149 66 0.55
150 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (148 bp):
TCAATTTAATGATTTTTTATTTATCATTAATATTAAAAATAAACTATAAATTAAAACATCATAAG
CTTACAAATTGATTGCTTGAATTTAATAACTTTGATAAATAAATAAATTTAATTTAATAATCCTT
GTCCTATCTCGCTTTGCT
Found at i:185998 original size:12 final size:12
Alignment explanation
Indices: 185981--186010 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
185971 AATCAAAATA
185981 TTTTTTTTTTCT
1 TTTTTTTTTTCT
185993 TTTTTTTTTTCT
1 TTTTTTTTTTCT
186005 TCTTTT
1 T-TTTT
186011 CATCTCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:186001 original size:15 final size:15
Alignment explanation
Indices: 185981--186010 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
185971 AATCAAAATA
185981 TTTTTTTT-TTCTTT
1 TTTTTTTTCTTCTTT
185995 TTTTTTTTCTTCTTT
1 TTTTTTTTCTTCTTT
186010 T
1 T
186011 CATCTCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTCTTCTTT
Found at i:189506 original size:12 final size:14
Alignment explanation
Indices: 189478--189509 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
189468 AATTTTATGT
189478 AATTAATTATAGAA
1 AATTAATTATAGAA
189492 AATTAA-TATAG-A
1 AATTAATTATAGAA
189504 AATTAA
1 AATTAA
189510 ATGTAGCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 5 0.28
14 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (14 bp):
AATTAATTATAGAA
Found at i:189544 original size:2 final size:2
Alignment explanation
Indices: 189537--189570 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
189527 ATAATAAGAT
189537 TA 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 TA
189571 AAATATTATA
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):
TA
Found at i:194568 original size:24 final size:25
Alignment explanation
Indices: 194522--194569 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
194512 GAGTGTCTTT
*
194522 GGAAAGAATGATGGGAGAGTGGAAG
1 GGAAAGAATGATGGGAGACTGGAAG
* *
194547 GGAAAGAATTA-GGGAGTCTGGAA
1 GGAAAGAATGATGGGAGACTGGAA
194570 AGAGCCATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.44, T:0.15
Consensus pattern (25 bp):
GGAAAGAATGATGGGAGACTGGAAG
Found at i:194939 original size:22 final size:22
Alignment explanation
Indices: 194905--194953 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
194895 ATCGATATTG
*
194905 TTTTTTTATATAATTTTATCTGA
1 TTTTTTTATATAATTTTAT-TAA
194928 TTTTTTTA-ATAATTTTATTAA
1 TTTTTTTATATAATTTTATTAA
194949 TTTTT
1 TTTTT
194954 AATCATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.28
22 10 0.40
23 8 0.32
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTTATATAATTTTATTAA
Found at i:199621 original size:2 final size:2
Alignment explanation
Indices: 199614--199651 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
199604 ATTCTAACAA
199614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
199652 ATTTATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.