Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012059.1 Kokia drynarioides strain JFW-HI SEQ_127057, 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: 132307
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:353 original size:59 final size:59
Alignment explanation
Indices: 288--722 Score: 370
Period size: 59 Copynumber: 7.3 Consensus size: 59
278 GCTAGGGGGC
* *
288 AAATGGTAATTTTTGGAAGGCTCGAGGTCAAAAATGGAATTTTTGGACATTCGGGGGTA
1 AAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTA
* * *
347 AAATGGTAATTTTTGGAAGGTTTCG-GATCAAAAATGGAGTTTTTAGACATTCGAGGGTA
1 AAATGGTAATTTTTGGAAGG-TTCGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTA
* * * ** * * *
406 AAATGGTAAATTTTGGAAGGTTCGAGATAAAAAAAACAGAGTTTTTAGACATCCG-GGAGTA
1 AAATGGTAATTTTTGGAAGGTTCGAGGT--CAAAAATGGAATTTTTGGACATTCGAGG-GTA
* * * * *
467 AAATGATAATTTTTGAAAGTTTCGAGGTCAAAAATGGATTTTTTGGA-AGTTTG-GGGTTA
1 AAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTGGACA-TTCGAGGG-TA
* * * * *
526 AAATAGTAA-TTTTGGAAGGTTCG-GGATAAAAAAAAAATCGAGTTTTTAGACATTCGAGGGTA
1 AAATGGTAATTTTTGGAAGGTTCGAGG-T----CAAAAATGGAATTTTTGGACATTCGAGGGTA
* * *
588 AAATGGTAATTTTTGAAAGTTTCGAGGTC-AAAATGGAA-TTTTGGAAAGTTCGAGGGTAA
1 AAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTGGACA-TTCGAGGGT-A
* * * * * *
647 AAAT-GTAATTTATGAAAAGATCGAGGTCAAAAATGGAA-TTTTGAAAAGTTCGAGGGTAA
1 AAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTGGACA-TTCGAGGGT-A
706 AAAT-GTAATTTTTGGAA
1 AAATGGTAATTTTTGGAA
723 AAAAATAGGG
Statistics
Matches: 311, Mismatches: 46, Indels: 38
0.79 0.12 0.10
Matches are distributed among these distances:
57 9 0.03
58 55 0.18
59 148 0.48
60 5 0.02
61 47 0.15
62 28 0.09
63 17 0.05
64 2 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (59 bp):
AAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTA
Found at i:357 original size:29 final size:28
Alignment explanation
Indices: 318--422 Score: 86
Period size: 28 Copynumber: 3.6 Consensus size: 28
308 CTCGAGGTCA
318 AAAATGGAATTTTTGGACATTCGGGGGT
1 AAAATGGAATTTTTGGACATTCGGGGGT
****
346 AAAATGGTAATTTTTGGA-AGGTTTCGGATCA
1 AAAATGG-AATTTTTGGACA---TTCGGGGGT
* * *
377 AAAATGGAGTTTTTAGACATTCGAGGGT
1 AAAATGGAATTTTTGGACATTCGGGGGT
*
405 AAAATGGTAAATTTTGGA
1 AAAATGG-AATTTTTGGA
423 AGGTTCGAGA
Statistics
Matches: 57, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
28 19 0.33
29 17 0.30
30 8 0.14
31 13 0.23
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTTGGACATTCGGGGGT
Found at i:436 original size:29 final size:29
Alignment explanation
Indices: 288--722 Score: 122
Period size: 30 Copynumber: 14.6 Consensus size: 29
278 GCTAGGGGGC
*
288 AAATGGTAATTTTTGGAAGGCTCGAGGTCAA
1 AAATGGTAATTTTTGGAAGGTTCGAGGT--A
*
319 AAATGG-AATTTTTGGACA--TTCGGGGGTA
1 AAATGGTAATTTTTGGA-AGGTTC-GAGGTA
*
347 AAATGGTAATTTTTGGAAGGTTTCG-GATCAA
1 AAATGGTAATTTTTGGAAGG-TTCGAGGT--A
* *
378 AAATGG-AGTTTTTAGACA--TTCGAGGGTA
1 AAATGGTAATTTTTGGA-AGGTTCGA-GGTA
* *
406 AAATGGTAAATTTTGGAAGGTTCGAGATAA
1 AAATGGTAATTTTTGGAAGGTTCGAGGT-A
**** * * *
436 AAAAAACAGAGTTTTTAGACA--TCCGGGAGTA
1 AAATGGTA-A-TTTTTGGA-AGGTTCGAG-GTA
* * *
467 AAATGATAATTTTTGAAAGTTTCGAGGTCAA
1 AAATGGTAATTTTTGGAAGGTTCGAGGT--A
* * *
498 AAATGG-ATTTTTTGGAA-GTTTGGGGTTA
1 AAATGGTAATTTTTGGAAGGTTCGAGG-TA
*
526 AAATAGTAA-TTTTGGAAGGTTCG-GGATAAAAAAA
1 AAATGGTAATTTTTGGAAGGTTCGAGG-T------A
* * *
560 AAATCG-AGTTTTTAGACA--TTCGAGGGTA
1 AAATGGTAATTTTTGGA-AGGTTCGA-GGTA
* *
588 AAATGGTAATTTTTGAAAGTTTCGAGGTCA
1 AAATGGTAATTTTTGGAAGGTTCGAGGT-A
*
618 AAATGG-AA-TTTTGGAAAGTTCGAGGGTAA
1 AAATGGTAATTTTTGGAAGGTTCGA-GGT-A
* * * *
647 AAAT-GTAATTTATGAAAAGATCGAGGTCAA
1 AAATGGTAATTTTTGGAAGGTTCGAGGT--A
* *
677 AAATGG-AA-TTTTGAAAAGTTCGAGGGTAA
1 AAATGGTAATTTTTGGAAGGTTCGA-GGT-A
706 AAAT-GTAATTTTTGGAA
1 AAATGGTAATTTTTGGAA
723 AAAAATAGGG
Statistics
Matches: 303, Mismatches: 53, Indels: 97
0.67 0.12 0.21
Matches are distributed among these distances:
28 59 0.19
29 87 0.29
30 92 0.30
31 36 0.12
32 7 0.02
33 6 0.02
34 13 0.04
35 3 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (29 bp):
AAATGGTAATTTTTGGAAGGTTCGAGGTA
Found at i:601 original size:121 final size:118
Alignment explanation
Indices: 317--657 Score: 415
Period size: 120 Copynumber: 2.8 Consensus size: 118
307 GCTCGAGGTC
* * * *
317 AAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTTCG-GATCAAAAA
1 AAAAAT-GAGTTTTTAGACATTC-GGGGTAAAATGGTAATTTTT-GAAAGTTTCGAGGTCAAAAA
*
381 TGGAGTTTTTAGACA-TTCGAGGG-TAAAATGGTAAATTTTGGAAGGTTCGAGATAAAAA
63 TGGA-TTTTTGGA-AGTTCGAGGGTTAAAAT-GT-AATTTTGGAAGGTTCGAGATAAAAA
* * *
439 AAACA-GAGTTTTTAGACATCCGGGAGTAAAATGATAATTTTTGAAAGTTTCGAGGTCAAAAATG
1 AAAAATGAGTTTTTAGACATTCGGG-GTAAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATG
* *
503 GATTTTTTGGAAGTTTG-GGGTTAAAATAGTAATTTTGGAAGGTTCGGGATAAAAA
65 GA-TTTTTGGAAGTTCGAGGGTTAAAAT-GTAATTTTGGAAGGTTCGAGATAAAAA
558 AAAAATCGAGTTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTC-AAAAT
1 AAAAAT-GAGTTTTTAGACATTCG-GGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAAT
* *
622 GGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTT
64 GGATTTTTGG-AAGTTCGAGGGTTAAAATGTAATTT
658 ATGAAAAGAT
Statistics
Matches: 192, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
119 50 0.26
120 80 0.42
121 56 0.29
122 6 0.03
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (118 bp):
AAAAATGAGTTTTTAGACATTCGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGG
ATTTTTGGAAGTTCGAGGGTTAAAATGTAATTTTGGAAGGTTCGAGATAAAAA
Found at i:614 original size:30 final size:31
Alignment explanation
Indices: 578--724 Score: 161
Period size: 29 Copynumber: 5.0 Consensus size: 31
568 TTTTTAGACA
578 TTCGAGGGT-AAAATGGTAATTTTTG-AAAG
1 TTCGAGGGTAAAAATGGTAATTTTTGAAAAG
* *
607 TTTCGA-GGTCAAAATGG-AA-TTTTGGAAAG
1 -TTCGAGGGTAAAAATGGTAATTTTTGAAAAG
*
636 TTCGAGGGTAAAAAT-GTAATTTATGAAAAG
1 TTCGAGGGTAAAAATGGTAATTTTTGAAAAG
*
666 ATCGA-GGTCAAAAATGG-AA-TTTTGAAAAG
1 TTCGAGGGT-AAAAATGGTAATTTTTGAAAAG
695 TTCGAGGGTAAAAAT-GTAATTTTTGGAAAA
1 TTCGAGGGTAAAAATGGTAATTTTT-GAAAA
725 AAATAGGGTT
Statistics
Matches: 100, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
28 12 0.12
29 43 0.43
30 39 0.39
31 6 0.06
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (31 bp):
TTCGAGGGTAAAAATGGTAATTTTTGAAAAG
Found at i:739 original size:59 final size:59
Alignment explanation
Indices: 578--757 Score: 195
Period size: 59 Copynumber: 3.0 Consensus size: 59
568 TTTTTAGACA
* *** * *
578 TTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTC-AAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAAAT-GTAATTTATGAAAAAATAGAGGTCAAAAATGGAATTTTGAAAAG
* *
636 TTCGAGGGTAAAAATGTAATTTATGAAAAGATCGAGGTCAAAAATGGAATTTTGAAAAG
1 TTCGAGGGTAAAAATGTAATTTATGAAAAAATAGAGGTCAAAAATGGAATTTTGAAAAG
* * * *
695 TTCGAGGGTAAAAATGTAATTTTTGGAAAAAAATAG-GGTTAAAATTGGAATTTTAGAGAAG
1 TTCGAGGGTAAAAATGTAATTTAT-G-AAAAAATAGAGGTCAAAAATGGAATTTT-GAAAAG
756 TT
1 TT
758 TAGGGGTCAA
Statistics
Matches: 106, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
58 29 0.27
59 46 0.43
60 17 0.16
61 14 0.13
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (59 bp):
TTCGAGGGTAAAAATGTAATTTATGAAAAAATAGAGGTCAAAAATGGAATTTTGAAAAG
Found at i:1887 original size:21 final size:21
Alignment explanation
Indices: 1861--1901 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1851 TAATATTACC
1861 AAAAA-TATTTATTATTATTAA
1 AAAAATTA-TTATTATTATTAA
1882 AAAAATTATTATTATTATTA
1 AAAAATTATTATTATTATTA
1902 TTATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAAATTATTATTATTATTAA
Found at i:1892 original size:3 final size:3
Alignment explanation
Indices: 1886--1910 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1876 TATTAAAAAA
1886 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1911 ATGATTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2626 original size:17 final size:17
Alignment explanation
Indices: 2606--2680 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
2596 ATTTATTTAT
* *
2606 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
2623 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
2641 TTTAAACTTAAACTAAA
1 TTTAAATTTAAAATAAA
2658 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
2675 TTTAAA
1 TTTAAA
2681 ATGAGTTTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
17 37 0.73
18 14 0.27
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:2632 original size:6 final size:6
Alignment explanation
Indices: 2606--2680 Score: 59
Period size: 6 Copynumber: 13.0 Consensus size: 6
2596 ATTTATTTAT
* ** *
2606 TTTAAA TTTATAA --TAAT TTTAAA TTTAAA AATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
2653 -CTAAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2681 ATGAGTTTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
4 1 0.02
5 10 0.19
6 40 0.75
7 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:2662 original size:11 final size:11
Alignment explanation
Indices: 2625--2682 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
2615 ATAATAATTT
2625 TAAATTTAAAAA
1 TAAATTT-AAAA
*
2637 TAAATTTAAACT
1 TAAATTTAAA-A
* *
2649 TAAA-CTAAATT
1 TAAATTTAAA-A
2660 TAAATTTAAAA
1 TAAATTTAAAA
2671 TAAATTTAAAA
1 TAAATTTAAAA
2682 T
1 T
2683 GAGTTTGGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.62
12 15 0.38
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:12369 original size:23 final size:23
Alignment explanation
Indices: 12314--12372 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
12304 TTATCTTCCT
*
12314 TTGTGACACGTTTTTTCTCTACC
1 TTGTGACACGCTTTTTCTCTACC
*
12337 TTCTGACACGCTTTTTCTCTGA-C
1 TTGTGACACGCTTTTTCTCT-ACC
*
12360 TTGTGGCACGCTT
1 TTGTGACACGCTT
12373 CTATCTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.44
Consensus pattern (23 bp):
TTGTGACACGCTTTTTCTCTACC
Found at i:18823 original size:22 final size:21
Alignment explanation
Indices: 18785--18826 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18775 TCTAATTATA
*
18785 AAAAAAAATAATCTTAAAATT
1 AAAAAAAATAATATTAAAATT
*
18806 AAAAAAAGTAGATATTAAAAT
1 AAAAAAAATA-ATATTAAAAT
18827 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAAAAATAATATTAAAATT
Found at i:19894 original size:16 final size:17
Alignment explanation
Indices: 19873--19905 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19863 TTAAATTAAT
19873 TAATG-ATTTGAAAAAA
1 TAATGAATTTGAAAAAA
19889 TAATGATATTTGAAAAA
1 TAATGA-ATTTGAAAAA
19906 TAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (17 bp):
TAATGAATTTGAAAAAA
Found at i:20132 original size:17 final size:18
Alignment explanation
Indices: 20110--20148 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
20100 ACATTTGGGC
20110 ATAATATAGCAAACAAA-
1 ATAATATAGCAAACAAAT
*
20127 ATAATATAGCAATCAAAT
1 ATAATATAGCAAACAAAT
20145 ATAA
1 ATAA
20149 ATATTTCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (18 bp):
ATAATATAGCAAACAAAT
Found at i:20204 original size:90 final size:90
Alignment explanation
Indices: 20029--20206 Score: 234
Period size: 90 Copynumber: 2.0 Consensus size: 90
20019 TAAAATTAAT
* *
20029 CAAACAAAATAATATAACAGTCAAATATGAATATTCCATTTTCCTTATATTTACAAAATGAATAT
1 CAAACAAAATAATATAACAATCAAATATAAATATTCCATTTTCCTTATATTTACAAAATGAATAT
** ***
20094 AGTAATACATTTGGGCATAATATAG
66 AACAATACATTTGAAAATAATATAG
* *
20119 CAAACAAAATAATATAGCAATCAAATATAAATATTTCAGTTTT-CTTATATTTACAAAATGAATA
1 CAAACAAAATAATATAACAATCAAATATAAATATTCCA-TTTTCCTTATATTTACAAAATGAATA
*
20183 TAACAAT-CTTTTTGAAAATAATAT
65 TAACAATAC-ATTTGAAAATAATAT
20207 TTCATTTTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
89 1 0.01
90 71 0.93
91 4 0.05
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (90 bp):
CAAACAAAATAATATAACAATCAAATATAAATATTCCATTTTCCTTATATTTACAAAATGAATAT
AACAATACATTTGAAAATAATATAG
Found at i:22688 original size:98 final size:98
Alignment explanation
Indices: 22519--22716 Score: 360
Period size: 98 Copynumber: 2.0 Consensus size: 98
22509 AGACCGACGT
*
22519 TCAACCACTAGTTATTGTTTCTTTCTAGGTGATTCTCTCATTTCTTGGCGAAGTAAAAAGCAAAC
1 TCAACCACTAGTTATTGTTTCTTTCTAGGTGATTCTCTCATTACTTGGCGAAGTAAAAAGCAAAC
22584 TATTATCGCTCACTCTAGCACCAAATCTGAATA
66 TATTATCGCTCACTCTAGCACCAAATCTGAATA
* *
22617 TCAACTACTAGTTATTGTTTCTTTCTAGGTGATTCTCTCATTACTTGGCGAAGTAAAAAGCAAAT
1 TCAACCACTAGTTATTGTTTCTTTCTAGGTGATTCTCTCATTACTTGGCGAAGTAAAAAGCAAAC
*
22682 TATTATCGCTCACTCTAGCACCGAATCTGAATA
66 TATTATCGCTCACTCTAGCACCAAATCTGAATA
22715 TC
1 TC
22717 GTGCTCTTAT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
TCAACCACTAGTTATTGTTTCTTTCTAGGTGATTCTCTCATTACTTGGCGAAGTAAAAAGCAAAC
TATTATCGCTCACTCTAGCACCAAATCTGAATA
Found at i:23236 original size:19 final size:19
Alignment explanation
Indices: 23212--23249 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23202 TGATTCTAGC
* *
23212 ATGATTTTAGCATGTAAAT
1 ATGATTCTAGCATGCAAAT
23231 ATGATTCTAGCATGCAAAT
1 ATGATTCTAGCATGCAAAT
23250 TAGGCTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
ATGATTCTAGCATGCAAAT
Found at i:26198 original size:3 final size:3
Alignment explanation
Indices: 26190--26219 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
26180 CCTTTTCTGC
26190 AGA AGA AGA AGA AGA AGA AGA AGA ATGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AG
26220 CCAGTTCTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:28376 original size:28 final size:26
Alignment explanation
Indices: 28319--28370 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
28309 AGTTATAAAT
* *
28319 TAAAATTAAAATTTTATTTAATACAA
1 TAAAATTAAAAATTTATTTAAAACAA
28345 TAAAATCTAAATAATTTATTTAAAAC
1 TAAAAT-TAAA-AATTTATTTAAAAC
28371 CCTAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 4 0.18
28 12 0.55
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAAATTAAAAATTTATTTAAAACAA
Found at i:37186 original size:36 final size:36
Alignment explanation
Indices: 37111--37179 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
37101 CTCTGGAATC
* *
37111 AACACAACCTAAACTTGATACAAAAGAGAATCCCAA
1 AACACAACCTAAACCTGACACAAAAGAGAATCCCAA
*
37147 AACAGAACCTAAACCTGACACAAAAGAGAATCC
1 AACACAACCTAAACCTGACACAAAAGAGAATCC
37180 TGAAACATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.12
Consensus pattern (36 bp):
AACACAACCTAAACCTGACACAAAAGAGAATCCCAA
Found at i:38247 original size:42 final size:42
Alignment explanation
Indices: 38184--38283 Score: 182
Period size: 42 Copynumber: 2.4 Consensus size: 42
38174 ATAGATTATG
*
38184 TATATATATATATATAGTCTAATTTTTTAGTTTCTTAACAAAT
1 TATATAT-TATTTATAGTCTAATTTTTTAGTTTCTTAACAAAT
38227 TATATATTATTTATAGTCTAATTTTTTAGTTTCTTAACAAAT
1 TATATATTATTTATAGTCTAATTTTTTAGTTTCTTAACAAAT
38269 TATATATTATTTATA
1 TATATATTATTTATA
38284 TATATACATG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 49 0.88
43 7 0.12
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (42 bp):
TATATATTATTTATAGTCTAATTTTTTAGTTTCTTAACAAAT
Found at i:39770 original size:11 final size:11
Alignment explanation
Indices: 39754--39783 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
39744 GATTACATGT
39754 AATAAAAAAGA
1 AATAAAAAAGA
39765 AAT-AAAAAGA
1 AATAAAAAAGA
39775 AATAAAAAA
1 AATAAAAAA
39784 AAAAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (11 bp):
AATAAAAAAGA
Found at i:47095 original size:31 final size:31
Alignment explanation
Indices: 47054--47126 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
47044 ATAAGAAAGT
*
47054 TTGGATAAAAATATAAG-TCTGAAAAATAGGA
1 TTGGACAAAAATATAAGTTC-GAAAAATAGGA
* * *
47085 TTGGACAAAAATATATGTTCGAAAAATGGGT
1 TTGGACAAAAATATAAGTTCGAAAAATAGGA
*
47116 TTAGACAAAAA
1 TTGGACAAAAA
47127 AATGAGACTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (31 bp):
TTGGACAAAAATATAAGTTCGAAAAATAGGA
Found at i:47260 original size:21 final size:21
Alignment explanation
Indices: 47234--47317 Score: 87
Period size: 22 Copynumber: 3.9 Consensus size: 21
47224 AATTATATTG
*
47234 TTGTTTTGGTGCTGTTTTTTA
1 TTGTTTTGGTGTTGTTTTTTA
*
47255 TTGTTTTGATTGTTGTTTTTTA
1 TTGTTTTG-GTGTTGTTTTTTA
* *
47277 TTGTTTTAGTGTTTTTTTTTTA
1 TTGTTTTGGTG-TTGTTTTTTA
* *
47299 CTGTTTTGGTTATTGTTTT
1 TTGTTTTGG-TGTTGTTTT
47318 GGTGTTGTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 10 0.20
22 40 0.78
23 1 0.02
ACGTcount: A:0.07, C:0.02, G:0.19, T:0.71
Consensus pattern (21 bp):
TTGTTTTGGTGTTGTTTTTTA
Found at i:47315 original size:12 final size:12
Alignment explanation
Indices: 47252--47340 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
47242 GTGCTGTTTT
*
47252 TTATTGTTTTGA
1 TTATTGTTTTGG
*
47264 TTGTTGTTTT--
1 TTATTGTTTTGG
47274 TTATTGTTTTAGTG
1 TTATTGTTTT-G-G
47288 TT-TT-TTTT--
1 TTATTGTTTTGG
*
47296 TTACTGTTTTGG
1 TTATTGTTTTGG
47308 TTATTGTTTTGG
1 TTATTGTTTTGG
* *
47320 -TGTTGTTTTTG
1 TTATTGTTTTGG
*
47331 CTATTGTTTT
1 TTATTGTTTT
47341 TATTGCTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
8 2 0.03
9 1 0.02
10 13 0.21
11 9 0.15
12 32 0.52
13 2 0.03
14 2 0.03
ACGTcount: A:0.08, C:0.02, G:0.19, T:0.71
Consensus pattern (12 bp):
TTATTGTTTTGG
Found at i:47346 original size:15 final size:16
Alignment explanation
Indices: 47322--47367 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
47312 TGTTTTGGTG
*
47322 TTGTTTTTGCTATTGT
1 TTGTTATTGCTATTGT
47338 TT-TTATTGCTATT-T
1 TTGTTATTGCTATTGT
*
47352 TTGTTGTTG-TATTGT
1 TTGTTATTGCTATTGT
47367 T
1 T
47368 ACTACTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.27
15 17 0.65
16 2 0.08
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (16 bp):
TTGTTATTGCTATTGT
Found at i:48095 original size:19 final size:19
Alignment explanation
Indices: 48073--48118 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
48063 ATTTTTTTGA
*
48073 ATTTTTATGAACTTTT-TAT
1 ATTTTTATGAA-TTTTAAAT
48092 ATTTTCT-TGAATTTTAAAT
1 ATTTT-TATGAATTTTAAAT
48111 ATTTTTAT
1 ATTTTTAT
48119 TTTTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (19 bp):
ATTTTTATGAATTTTAAAT
Found at i:67126 original size:31 final size:28
Alignment explanation
Indices: 67088--67166 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 28
67078 TTCCGGATAA
67088 ATATATAAATTATAATTTAATATGTAATTGT
1 ATATATAAATT-TAATTT--TATGTAATTGT
* *
67119 ATATATAAACTTTAAATTTATGTAATTTT
1 ATATATAAA-TTTAATTTTATGTAATTGT
*
67148 ATACATGAAATTGTAATTT
1 ATATAT-AAATT-TAATTT
67167 GATCAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 17 0.41
30 8 0.20
31 14 0.34
32 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (28 bp):
ATATATAAATTTAATTTTATGTAATTGT
Found at i:74556 original size:15 final size:15
Alignment explanation
Indices: 74538--74569 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
74528 AGTTCATCAT
*
74538 ATATTTCATTTTTTA
1 ATATTTCATATTTTA
74553 ATATTTCATATTTTA
1 ATATTTCATATTTTA
74568 AT
1 AT
74570 TTCTTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTCATATTTTA
Found at i:85192 original size:27 final size:26
Alignment explanation
Indices: 85162--85222 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 26
85152 TTGACAAGAA
85162 ATAATAATATATAA-ATTTT-AAAAATAT
1 ATAA-AATATA-AATATTTTCAAAAA-AT
85189 ATAAAA-ATAAATATTTTCAAAAAAT
1 ATAAAATATAAATATTTTCAAAAAAT
85214 ATAACAATA
1 ATAA-AATA
85223 AATCTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
24 2 0.07
25 14 0.47
26 9 0.30
27 5 0.17
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAAAATATAAATATTTTCAAAAAAT
Found at i:85210 original size:25 final size:25
Alignment explanation
Indices: 85176--85225 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
85166 TAATATATAA
*
85176 ATTTTAAAAATATATAAAAATAAAT
1 ATTTTAAAAAAATATAAAAATAAAT
* *
85201 ATTTTCAAAAAATATAACAATAAAT
1 ATTTTAAAAAAATATAAAAATAAAT
85226 CTAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
ATTTTAAAAAAATATAAAAATAAAT
Found at i:86823 original size:21 final size:21
Alignment explanation
Indices: 86793--86832 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
86783 TTTTATTTAA
86793 TATTAATATAAATTTTAAATT
1 TATTAATATAAATTTTAAATT
* **
86814 TATTATTATATTTTTTAAA
1 TATTAATATAAATTTTAAA
86833 ATATTTATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATATAAATTTTAAATT
Found at i:88339 original size:4 final size:4
Alignment explanation
Indices: 88330--88354 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
88320 ATGTAAATCA
88330 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
88355 TATATATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:90922 original size:21 final size:22
Alignment explanation
Indices: 90890--90930 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
90880 TCTTTAATAC
90890 TTTAATTTTTTAAAATAAAAAA
1 TTTAATTTTTTAAAATAAAAAA
*
90912 TTTAA-TTTTTATAATAAAA
1 TTTAATTTTTTAAAATAAAA
90931 CTTCAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAATTTTTTAAAATAAAAAA
Found at i:97982 original size:21 final size:20
Alignment explanation
Indices: 97928--97982 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
97918 ATGATGATGA
97928 TTATAATTTT-AAAATAATT
1 TTATAATTTTAAAAATAATT
*
97947 TTAT-ATTTAAAAAAAATAATT
1 TTATAATTT--TAAAAATAATT
97968 TTAATAATTTTAAAA
1 TT-ATAATTTTAAAA
97983 TCATTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
21 15 0.52
22 2 0.07
23 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATAATTTTAAAAATAATT
Found at i:102067 original size:15 final size:17
Alignment explanation
Indices: 102049--102081 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
102039 GAATAAGAAC
102049 TGGAATC-GGA-AGAGA
1 TGGAATCTGGAGAGAGA
102064 TGGAATCTGGAGAGAGA
1 TGGAATCTGGAGAGAGA
102081 T
1 T
102082 AAGGATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.39, T:0.18
Consensus pattern (17 bp):
TGGAATCTGGAGAGAGA
Found at i:104729 original size:25 final size:25
Alignment explanation
Indices: 104678--104737 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
104668 TTAGAAAATA
* * *
104678 AAAAATTAAAATTTTAATTTTTATAT
1 AAAAATT-AAATTTCAAATTTCATAT
*
104704 AAAAATTAAATTTCAAATTTCGTAT
1 AAAAATTAAATTTCAAATTTCATAT
*
104729 AAATATTAA
1 AAAAATTAA
104738 TAATATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAAATTAAATTTCAAATTTCATAT
Found at i:104771 original size:4 final size:4
Alignment explanation
Indices: 104762--104786 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
104752 TTACTGATAT
104762 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
104787 CATGGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:116014 original size:23 final size:23
Alignment explanation
Indices: 115969--116014 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
115959 TTAACTTAAT
* *
115969 CGAATATTAATCGAACATATTCA
1 CGAATATTAAACGAAAATATTCA
*
115992 CGAATATTAAACGAAAATGTTCA
1 CGAATATTAAACGAAAATATTCA
116015 TGAACATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (23 bp):
CGAATATTAAACGAAAATATTCA
Found at i:116167 original size:12 final size:12
Alignment explanation
Indices: 116130--116176 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
116120 ATCATTAATA
116130 AATAAACGAGCT
1 AATAAACGAGCT
* *
116142 -ATAAAGGAGTT
1 AATAAACGAGCT
116153 AATAAACGAGCT
1 AATAAACGAGCT
116165 AATAAACGAGCT
1 AATAAACGAGCT
116177 TGTTCGTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (12 bp):
AATAAACGAGCT
Found at i:116964 original size:13 final size:13
Alignment explanation
Indices: 116928--116977 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
116918 TTAAATCAAA
*
116928 TTTTTCAAAAATAC
1 TTTTT-AAAAGTAC
116942 TTTTTAAAAGTAC
1 TTTTTAAAAGTAC
*
116955 TTTTTAAAAGCAC
1 TTTTTAAAAGTAC
*
116968 TTCTTAAAAG
1 TTTTTAAAAG
116978 CAATACTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 28 0.85
14 5 0.15
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (13 bp):
TTTTTAAAAGTAC
Found at i:127417 original size:94 final size:95
Alignment explanation
Indices: 127305--127487 Score: 289
Period size: 94 Copynumber: 1.9 Consensus size: 95
127295 GATATCCCTT
*
127305 TCTCGAGAAAAAAATTTCAAAATTTTTTTGTGTTGACCATCAAATGGCCGACACC-CTTTTTTCT
1 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGACCATCAAATGGCCGACACCTCTTTTTT-T
*
127369 CAAAAAAAAATGCATTTTTGGGTGTTGGCCA
65 CAAAAAAAAATACATTTTTGGGTGTTGGCCA
* *
127400 TCTCGAG-AAAAATTTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCTTTTTTTC
1 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGACCATCAAATGGCCGACACCTCTTTTTTTC
* *
127464 GAAAAAAATTACATTTTTGGGTGT
66 AAAAAAAAATACATTTTTGGGTGT
127488 AGGCGATTGC
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
94 67 0.83
95 14 0.17
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (95 bp):
TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGACCATCAAATGGCCGACACCTCTTTTTTTC
AAAAAAAAATACATTTTTGGGTGTTGGCCA
Found at i:127470 original size:59 final size:58
Alignment explanation
Indices: 127400--127990 Score: 419
Period size: 59 Copynumber: 9.9 Consensus size: 58
127390 GTGTTGGCCA
*
127400 TCTCGAGAAAAATTTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCTTTT
1 TCTCGA-AAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACC-CTTTT
* * * * * *** *
127460 TTTCGAAAAAAA-TT--ACATTTTTGGGTGTAGGCGATTGCATGGCCGACAACCCTTTC
1 TCTCGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGAC-ACCCTTTT
** * *
127516 TCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGACCATCAAATGGTCGACACCCCTTTT
1 TCTCGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCCTTTT
*** **** * ** *
127575 TCTCG-AAATTTTTTTTTCATTTTTGGGTGTTGGCTTTGC--ATGGCCGACATCCCCTTT
1 TCTCGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT-CAAATGGCCGACA-CCCTTTT
** ***
127632 TCTCGAGAAAAAATTTCAAAATTTTTTGGTGTTGATCATTGCATGGCCGACACCCTCTTT
1 TCTCGA-AAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCT-TTT
* * * *
127692 TCTCGAGAAAAAAATTTTAAAATTTTTTGGTATTGCCCATCAAATGGTCGACACCCTCTTT
1 TCTC--GAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCT-TTT
* * *
127753 TCTAGAAAAAAATTGCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTT
1 TCTCGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCT-TTT
* * * *
127812 T-TGAGAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGC-AATGGCCGACACCCCCTGT
1 TCT---CGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT-CAAATGGCCGACA-CCCTTTT
* * ***
127873 TCTCGAATAAAAAAATTGCAAAATTTTTTTGTGTTGGCCATGC-AATGTTTGACACCCCTTTT
1 TCTCG---AAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT-CAAATGGCCGACA-CCCTTTT
* * * **
127935 TCTTGGATAAAAAAATTGC-AATTTTTTTGTGTGTTGGCCATGTAATGGCCGACACC
1 TC-TCG--AAAAAAATTTCAAAATTTTTTG-GTGTTGGCCATCAAATGGCCGACACC
127991 AACTTCCCCT
Statistics
Matches: 419, Mismatches: 87, Indels: 49
0.75 0.16 0.09
Matches are distributed among these distances:
56 39 0.09
57 25 0.06
58 25 0.06
59 113 0.27
60 22 0.05
61 106 0.25
62 87 0.21
63 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (58 bp):
TCTCGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTTTT
Found at i:127714 original size:61 final size:61
Alignment explanation
Indices: 127400--127990 Score: 476
Period size: 61 Copynumber: 9.9 Consensus size: 61
127390 GTGTTGGCCA
*
127400 TCTCGAG-AAAAATTTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCTCTTTT
1 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTC-TTT
* * * * * *** *
127460 TTTC--GAAAAAAA-TT--ACATTTTTGGGTGTAGGCGATTGCATGGCCGACAACC-C-TT
1 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTT
* *
127514 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGACCATCAAATGGTCGACACCC-CTTTT
1 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTC-TTT
***** * **
127575 TCTCGA-AATTTTTTTTTC---ATTTTTGGGTGTTGGCTTTGC--ATGGCCGACATCCC-CTTT
1 TCTCGAGAA-AAAAATTTCAAAATTTTTTGGTGTTGGCCAT-CAAATGGCCGACA-CCCTCTTT
** ***
127632 TCTCGAG-AAAAAATTTCAAAATTTTTTGGTGTTGATCATTGCATGGCCGACACCCTCTTT
1 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTT
* * * *
127692 TCTCGAGAAAAAAATTTTAAAATTTTTTGGTATTGCCCATCAAATGGTCGACACCCTCTTT
1 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTT
* *
127753 TCT--AGAAAAAAATTGCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTT
1 TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTT
* * * *
127812 T-TGAGAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGC-AATGGCCGACACCCCCTGT
1 TCT-CGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT-CAAATGGCCGACACCCTCTTT
* * * ***
127873 TCTCGAATAAAAAAATTGCAAAATTTTTTTGTGTTGGCCATGC-AATGTTTGACACCC-CTTTT
1 TCTCG-AGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCAT-CAAATGGCCGACACCCTC-TTT
* * * * **
127935 TCTTGGATAAAAAAATTGC-AATTTTTTTGTGTGTTGGCCATGTAATGGCCGACACC
1 TC-TCGAGAAAAAAATTTCAAAATTTTTTG-GTGTTGGCCATCAAATGGCCGACACC
127991 AACTTCCCCT
Statistics
Matches: 427, Mismatches: 74, Indels: 58
0.76 0.13 0.10
Matches are distributed among these distances:
54 5 0.01
56 40 0.09
57 23 0.05
58 23 0.05
59 102 0.24
60 26 0.06
61 122 0.29
62 84 0.20
63 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (61 bp):
TCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTT
Found at i:127984 original size:124 final size:123
Alignment explanation
Indices: 127407--127990 Score: 415
Period size: 120 Copynumber: 4.9 Consensus size: 123
127397 CCATCTCGAG
* * * ***
127407 AAAAATTTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCTCTTTTT-TTCGAAAAA
1 AAAAAATTGCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTTGAGAGAAAAA
* * * * * *
127470 AATT--ACA-TTTTTGGGTGTAGGCGATTGC-ATGGCCGACA-ACCCT-TTCTCG-AGA
66 AATTGCAAATTTTTTTGGTGTTGGCCA-TGCAATGGCCGACACCCCCTGTTCTCGAATA
* * * * *** **
127522 AAAAAATTTCAAAATTTTTTGGTGTTGACCATCAAATGGTCGACACCC-CTTTTT-CTCGAAATT
1 AAAAAATTGCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTTGAGAGAAAAA
** **** * ** * * *
127585 TTTTTTTCA-TTTTTGGGTGTTGGCTTTGC-ATGGCCGACATCCCCTTTTCTCG-A-G
66 AATTGCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGAATA
* * ** *** *
127639 AAAAAATTTCAAAATTTTTTGGTGTTGATCATTGCATGGCCGACACCCTCTTTTCT-CGAGAAAA
1 AAAAAATTGCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTT-TGAGAGAAAA
** * * * * * * *
127703 AAATTTTAAAATTTTTTGGTATTGCCCAT-CAAATGGTCGACACCCTCT-TT-TC-TAGA
65 AAATTGCAAATTTTTTTGGTGTTGGCCATGC-AATGGCCGACACCCCCTGTTCTCGAATA
127759 AAAAAATTGCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTTGAGAGAAAAA
1 AAAAAATTGCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTTGAGAGAAAAA
*
127824 AATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGAATA
66 AATTGCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGAATA
*** * *
127882 AAAAAATTGCAAAATTTTTTT-GTGTTGGCCATGC-AATGTTTGACACCCCTTTTTCTTG-GATA
1 AAAAAATTGC-AAATTTTTTTGGTGTTGGCCAT-CAAATGGCCGACA-CCCTCTTT-TTGAGAGA
*
127944 AAAAAATTGC-AATTTTTTTGTGTGTTGGCCATGTAATGGCCGACACC
62 AAAAAATTGCAAATTTTTTTG-GTGTTGGCCATGCAATGGCCGACACC
127991 AACTTCCCCT
Statistics
Matches: 388, Mismatches: 59, Indels: 35
0.80 0.12 0.07
Matches are distributed among these distances:
115 56 0.14
116 15 0.04
117 63 0.16
118 12 0.03
119 16 0.04
120 109 0.28
121 16 0.04
122 2 0.01
123 41 0.11
124 55 0.14
125 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.36
Consensus pattern (123 bp):
AAAAAATTGCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTTGAGAGAAAAA
AATTGCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGAATA
Found at i:131722 original size:12 final size:12
Alignment explanation
Indices: 131705--131753 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
131695 TATTTGTGTA
131705 AAAATTAATTTG
1 AAAATTAATTTG
131717 AAAATTAATTTAAG
1 AAAATTAATTT--G
131731 TTAAAATTAATTTG
1 --AAAATTAATTTG
*
131745 GAAATTAAT
1 AAAATTAAT
131754 GAACACGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 19 0.59
14 2 0.06
16 11 0.34
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:131813 original size:22 final size:21
Alignment explanation
Indices: 131761--131813 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
131751 AATGAACACG
*
131761 TTTAAATTTAAATAATTTAAA
1 TTTAAAATTAAATAATTTAAA
* * *
131782 CTTAATAATTATATAAGTTTGAA
1 TTTAA-AATTAAATAA-TTTAAA
131805 TTTAAAATT
1 TTTAAAATT
131814 CTACTTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.16
22 12 0.48
23 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTAAAATTAAATAATTTAAA
Found at i:131955 original size:84 final size:83
Alignment explanation
Indices: 131867--132145 Score: 380
Period size: 84 Copynumber: 3.3 Consensus size: 83
131857 AATTTAACAT
* * *
131867 TATTTAAATAAAAAATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATAC
1 TATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* *
131932 ATTATTTATCAAATTTT-CA
65 ATTATTTAT-TAATTTTATA
* *
131951 TATTTAAAGTACAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
1 TATTTAAA-TAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
132016 ATTATTTATTAATTTTATA
65 ATTATTTATTAATTTTATA
* * * *
132035 TATTTAAATAAAAATTATTATTATTATATTAAAATTTTTATCATATAATATGTTGATTTGATAAT
1 TATTTAAAT-AAAA--ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
*
132100 AGATTATTTATTAATTTTATA
63 ACATTATTTATTAATTTTATA
132121 TATTTAAATAAAAATTATTACTTAT
1 TATTTAAATAAAAATTATTA-TTAT
132146 TTATTAATTT
Statistics
Matches: 175, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
83 14 0.08
84 83 0.47
85 5 0.03
86 73 0.42
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (83 bp):
TATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACA
TTATTTATTAATTTTATA
Found at i:132066 original size:39 final size:38
Alignment explanation
Indices: 132016--132183 Score: 176
Period size: 39 Copynumber: 4.1 Consensus size: 38
132006 TTGACAATAC
132016 ATTATTTATTAATTTTATATATTTAAATAAAAATTATT
1 ATTATTTATTAATTTTATATATTTAAATAAAAATTATT
* *** *
132054 ATTATTATATTAAAATTTT-TATCATATAATATGTTGATTTGATAAT
1 ATTATT-TATT--AATTTTATAT-ATTTAA-AT-AAAAATT-AT--T
132100 AGATTATTTATTAATTTTATATATTTAAATAAAAATTATT
1 --ATTATTTATTAATTTTATATATTTAAATAAAAATTATT
132140 ACTTATTTATTAATTTTATATATTTAAATAAAAATTATT
1 A-TTATTTATTAATTTTATATATTTAAATAAAAATTATT
132179 ATTAT
1 ATTAT
132184 ATTACAATTT
Statistics
Matches: 107, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
38 11 0.10
39 42 0.39
40 4 0.04
41 11 0.10
42 4 0.04
43 6 0.06
44 4 0.04
45 11 0.10
46 4 0.04
47 4 0.04
48 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (38 bp):
ATTATTTATTAATTTTATATATTTAAATAAAAATTATT
Found at i:132151 original size:86 final size:86
Alignment explanation
Indices: 131867--132152 Score: 379
Period size: 86 Copynumber: 3.4 Consensus size: 86
131857 AATTTAACAT
* * * *
131867 TATTTAAATAAAAA--ATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAAT
1 TATTTAAATAAAAATTATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTTGACAAT
* *
131930 ACATTATTTATCAAATTTT-CA
66 ACATTATTTAT-TAATTTTATA
* * *
131951 TATTTAAAGT-ACAA--ACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAA
1 TATTTAAA-TAAAAATTATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTTGACAA
132013 TACATTATTTATTAATTTTATA
65 TACATTATTTATTAATTTTATA
* * *
132035 TATTTAAATAAAAATTATTATTATTATATTAAAATTTTTATCATATAATATGTTGATTTGATAAT
1 TATTTAAATAAAAATTATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTTGACAAT
*
132100 AGATTATTTATTAATTTTATA
66 ACATTATTTATTAATTTTATA
132121 TATTTAAATAAAAATTATTACTTATT-TATTAA
1 TATTTAAATAAAAATTATTA-TTATTATATTAA
132153 TTTTATATAT
Statistics
Matches: 182, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
83 7 0.04
84 79 0.43
85 1 0.01
86 90 0.49
87 5 0.03
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (86 bp):
TATTTAAATAAAAATTATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTTGACAAT
ACATTATTTATTAATTTTATA
Found at i:132197 original size:39 final size:39
Alignment explanation
Indices: 132103--132194 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
132093 TGATAATAGA
*
132103 TTATTTATTAATTTTATATATTTAAATAAAAATTATTAC
1 TTATTTATCAATTTTATATATTTAAATAAAAATTATTAC
*
132142 TTATTTATTAATTTTATATATTTAAATAAAAATTATTA-
1 TTATTTATCAATTTTATATATTTAAATAAAAATTATTAC
132180 TTATATTA-CAATTTT
1 TTAT-TTATCAATTTT
132195 TATTAAATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
38 10 0.20
39 41 0.80
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (39 bp):
TTATTTATCAATTTTATATATTTAAATAAAAATTATTAC
Found at i:132231 original size:83 final size:85
Alignment explanation
Indices: 132142--132303 Score: 274
Period size: 86 Copynumber: 1.9 Consensus size: 85
132132 AAATTATTAC
* *
132142 TTATTTATTAATTTTATATATTTAAAT-AAAA-ATTATTATTATATTACAATTTTTATTAAATAA
1 TTATTTATTAATTTTAAATATTTAAATAAAAATATTATTATTATATTACAATTTTTATCAAATAA
132205 TATGTTGATTTGAGAATAAA
66 TATGTTGATTTGAGAATAAA
132225 TTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATA
1 TTATTTATTAATTTTAAATATTTAAATAAAAA-TATTATTATTATATTACAATTTTTATCAAATA
*
132290 ATGTGTTGATTTGA
65 ATATGTTGATTTGA
132304 CAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 26 0.36
84 4 0.05
86 43 0.59
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (85 bp):
TTATTTATTAATTTTAAATATTTAAATAAAAATATTATTATTATATTACAATTTTTATCAAATAA
TATGTTGATTTGAGAATAAA
Found at i:132237 original size:122 final size:123
Alignment explanation
Indices: 132016--132273 Score: 421
Period size: 122 Copynumber: 2.1 Consensus size: 123
132006 TTGACAATAC
*
132016 ATTATTTATTAATTTTATATATTTAAATAAAAATTATTATTATTATATTAAAATTTTTATCATAT
1 ATTATTTATTAATTTTATATATTTAAATAAAAA-TATTATTATTATATTAAAATTTTTATCAAAT
* * *
132081 AATATGTTGATTTGATAATAGATTATTTATTAATTTTATATATTTAAATAAAAATTATT
65 AATATGTTGATTTGAGAATAAATTATTTATTAATTTTAAATATTTAAATAAAAATTATT
* *
132140 ACTTATTTATTAATTTTATATATTTAAAT-AAAA-ATTATTATTATATTACAATTTTTATTAAAT
1 A-TTATTTATTAATTTTATATATTTAAATAAAAATATTATTATTATATTAAAATTTTTATCAAAT
132203 AATATGTTGATTTGAGAATAAATTATTTATTAATTTTAAATATTTAAATAAAAATTATT
65 AATATGTTGATTTGAGAATAAATTATTTATTAATTTTAAATATTTAAATAAAAATTATT
132262 ATTATTATATTA
1 ATTATT-TATTA
132274 CAATTTTTAT
Statistics
Matches: 126, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
121 5 0.04
122 89 0.71
124 5 0.04
125 27 0.21
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (123 bp):
ATTATTTATTAATTTTATATATTTAAATAAAAATATTATTATTATATTAAAATTTTTATCAAATA
ATATGTTGATTTGAGAATAAATTATTTATTAATTTTAAATATTTAAATAAAAATTATT
Done.