Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012313.1 Kokia drynarioides strain JFW-HI SEQ_127314, 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: 121938
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--48 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48 T
1 T
49 GCTGTCGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:403 original size:8 final size:8
Alignment explanation
Indices: 392--440 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 8
382 ATATTTAAAA
392 TTTTAACTT
1 TTTTAA-TT
401 TTTTATATT
1 TTTTA-ATT
410 TTTATAATT
1 TTT-TAATT
419 TTTTAAATT
1 TTTT-AATT
428 TTTATAATT
1 TTT-TAATT
437 TTTT
1 TTTT
441 TAAATATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 2 0.06
9 30 0.83
10 4 0.11
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTAATT
Found at i:411 original size:9 final size:10
Alignment explanation
Indices: 399--440 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 10
389 AAATTTTAAC
399 TTTTTTAT-A
1 TTTTTTATAA
408 -TTTTTATAA
1 TTTTTTATAA
417 TTTTTTA-AA
1 TTTTTTATAA
426 -TTTTTATAA
1 TTTTTTATAA
435 TTTTTT
1 TTTTTT
441 TAAATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 13 0.45
9 5 0.17
10 11 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:422 original size:18 final size:18
Alignment explanation
Indices: 385--483 Score: 80
Period size: 18 Copynumber: 5.6 Consensus size: 18
375 TTAAAACATA
* *
385 TTTAAAATTTTA-ACTTT
1 TTTAAATTTTTATAATTT
*
402 TTTATATTTTTATAATTT
1 TTTAAATTTTTATAATTT
420 TTTAAATTTTTATAATTTT
1 TTTAAATTTTTATAA-TTT
* *
439 TTTAAA--TATA-AATAT
1 TTTAAATTTTTATAATTT
* *
454 TTTAAATTTTAAAAATTAT
1 TTTAAATTTTTATAATT-T
*
473 TTTGAATTTTT
1 TTTAAATTTTT
484 TAAAAGTATT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
15 8 0.12
16 2 0.03
17 15 0.23
18 21 0.32
19 19 0.29
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTAAATTTTTATAATTT
Found at i:475 original size:19 final size:19
Alignment explanation
Indices: 372--482 Score: 60
Period size: 18 Copynumber: 6.3 Consensus size: 19
362 CAAAATTATT
*
372 ATTTTAAAACA-TATTTAAA
1 ATTTTAAAA-ATTATTTTAA
* *
391 ATTTT--AACTT-TTTTAT
1 ATTTTAAAAATTATTTTAA
* *
407 ATTTTTATAATT-TTTTAA
1 ATTTTAAAAATTATTTTAA
* * *
425 ATTTTTATAATTTTTTTAA
1 ATTTTAAAAATTATTTTAA
*
444 A---TATAAA-TATTTTAA
1 ATTTTAAAAATTATTTTAA
*
459 ATTTTAAAAATTATTTTGA
1 ATTTTAAAAATTATTTTAA
478 ATTTT
1 ATTTT
483 TTAAAAGTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
15 8 0.11
16 12 0.17
17 3 0.04
18 25 0.35
19 24 0.33
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.59
Consensus pattern (19 bp):
ATTTTAAAAATTATTTTAA
Found at i:505 original size:21 final size:20
Alignment explanation
Indices: 451--503 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
441 TAAATATAAA
* * *
451 TATTTT-AAATTTTAAAAAT
1 TATTTTGAATTTTTTAAAAG
470 TATTTTGAATTTTTTAAAAG
1 TATTTTGAATTTTTTAAAAG
490 TATTTTG-ATTTTTT
1 TATTTTGAATTTTTT
504 TTTTGTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
TATTTTGAATTTTTTAAAAG
Found at i:1017 original size:22 final size:21
Alignment explanation
Indices: 961--1017 Score: 50
Period size: 22 Copynumber: 2.9 Consensus size: 21
951 ATTATTTGGG
961 TTTAG-ATTTAA-TA-AAATA
1 TTTAGAATTTAAGTATAAATA
** *
979 TTTA-AATTTCGGAATAAATA
1 TTTAGAATTTAAGTATAAATA
999 TTTTAGAATTTAAGTATAA
1 -TTTAGAATTTAAGTATAA
1018 GTTTATAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
18 8 0.29
19 1 0.04
20 5 0.18
21 4 0.14
22 10 0.36
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.44
Consensus pattern (21 bp):
TTTAGAATTTAAGTATAAATA
Found at i:4659 original size:30 final size:28
Alignment explanation
Indices: 4609--4667 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
4599 TACAAAATTA
4609 TTAAATTTAACAAGTAATTTATATTTAAT
1 TTAAATTTAACAAGTAATTTATA-TTAAT
* *
4638 TTAAATTTTAATAAGTGATTTATATTAAT
1 TTAAA-TTTAACAAGTAATTTATATTAAT
4667 T
1 T
4668 ATATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (28 bp):
TTAAATTTAACAAGTAATTTATATTAAT
Found at i:10701 original size:50 final size:51
Alignment explanation
Indices: 10603--10702 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 51
10593 ATATAATAAC
* * * * *
10603 AAATTTGGCCTTCAAAGTTTATACATTTTGTCAATTTGATCTTAATTTAAT
1 AAATTTAGCCTCCAAAGTTTATACATTCTGTCAACTTGATCCTAATTTAAT
*
10654 AAATTTAGCCTCCAATA-TTTATAC-TTCTGTCAACTTGGTCCTAATTTAA
1 AAATTTAGCCTCCAA-AGTTTATACATTCTGTCAACTTGATCCTAATTTAA
10703 CTTGTAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 21 0.50
51 20 0.48
52 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (51 bp):
AAATTTAGCCTCCAAAGTTTATACATTCTGTCAACTTGATCCTAATTTAAT
Found at i:12453 original size:48 final size:47
Alignment explanation
Indices: 12381--12472 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 47
12371 GAATAAACGG
12381 AACAGAGAGTACCAAAGTACTAAACAGAGAG-CACATAAGTACTAGGC
1 AACAGAGAGTACCAAAGTACTAAACAGAGAGACACA-AAGTACTAGGC
*
12428 AACAGAGAGTACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 AACAGAGAGTAC-CAAAGTACTAAACAGAGAG-ACACAAAGTACT
12473 GAGCACACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
47 12 0.29
48 18 0.44
49 7 0.17
50 4 0.10
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (47 bp):
AACAGAGAGTACCAAAGTACTAAACAGAGAGACACAAAGTACTAGGC
Found at i:12454 original size:23 final size:23
Alignment explanation
Indices: 12381--12568 Score: 135
Period size: 23 Copynumber: 8.4 Consensus size: 23
12371 GAATAAACGG
* *
12381 AACAGAGAGTAC-CAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
* *
12403 AACAGAGAGCACA-TAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
*
12425 GGCAACAGAGAGTACACAAAGTGCTA
1 ---AACAGAGAGCACACAAAGTGCTA
*
12451 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
12470 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
12490 ATCAAAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
12513 ATCAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
12536 ACCAGAGAGCACGA-GACGTGCTA
1 AACAGAGAGCAC-ACAAAGTGCTA
12559 AACAGAGAGC
1 AACAGAGAGC
12569 GCGCTAGTGT
Statistics
Matches: 135, Mismatches: 18, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 19 0.14
23 79 0.59
24 1 0.01
25 12 0.09
26 7 0.05
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:13640 original size:39 final size:33
Alignment explanation
Indices: 13567--13658 Score: 139
Period size: 33 Copynumber: 2.7 Consensus size: 33
13557 CTCTCTTTGA
13567 TCTTCTCTTTTCCTTTCTCTTCAATTGAGCCCTTC
1 TCTT-TCTTTT-CTTTCTCTTCAATTGAGCCCTTC
* *
13602 TCTTTCTTTTCTTTCTCTTCAATTGAGTCATTC
1 TCTTTCTTTTCTTTCTCTTCAATTGAGCCCTTC
*
13635 TCCTTCTTTTCTTTCTCTTCAATT
1 TCTTTCTTTTCTTTCTCTTCAATT
13659 TCATACAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 44 0.81
34 6 0.11
35 4 0.07
ACGTcount: A:0.10, C:0.29, G:0.04, T:0.57
Consensus pattern (33 bp):
TCTTTCTTTTCTTTCTCTTCAATTGAGCCCTTC
Found at i:20964 original size:23 final size:23
Alignment explanation
Indices: 20934--21010 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
20924 CTTATATCTT
*
20934 TGCTTAAATATTATTGTGATTTA
1 TGCTTAAATATTAATGTGATTTA
*
20957 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTA
* *
20980 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTA
21003 TGCTTAAA
1 TGCTTAAA
21011 AAATTAAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTA
Found at i:22972 original size:6 final size:6
Alignment explanation
Indices: 22961--23003 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
22951 TTTGTGATCA
* * *
22961 AAAGTG AAAGTG AAAGTG AAAGTG AAATTG GAATTG AAAGTG A
1 AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG A
23004 TATGAATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (6 bp):
AAAGTG
Found at i:23207 original size:37 final size:38
Alignment explanation
Indices: 23107--23209 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
23097 GACCTTGAGT
* * **
23107 CGATGAGACACTGGGTGTCATTATTTTACTTTGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGAGC
* * ** *
23148 CGATGAGATACTAGGTACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
23185 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
23210 TTGCTTCGAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
37 21 0.43
38 13 0.27
41 15 0.31
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
Found at i:28259 original size:44 final size:45
Alignment explanation
Indices: 28198--28285 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 45
28188 AATCCTTGAA
* *
28198 TTTTCTTAACCTTTCTTA-TTTAGACTACACATTCTAATTCTTAAT
1 TTTTCTTAACCTTTCTTATTTTA-ACCACACATTCTAACTCTTAAT
* *
28243 TTTTCTTAATC-TTCTTATTTTAACCACATATTCTAACTCTTAA
1 TTTTCTTAACCTTTCTTATTTTAACCACACATTCTAACTCTTAA
28286 CTCGACACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 24 0.63
45 14 0.37
ACGTcount: A:0.27, C:0.20, G:0.01, T:0.51
Consensus pattern (45 bp):
TTTTCTTAACCTTTCTTATTTTAACCACACATTCTAACTCTTAAT
Found at i:28725 original size:22 final size:22
Alignment explanation
Indices: 28697--28746 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
28687 TTTATTATAT
*
28697 ATATTATTATATTACTAATAAA
1 ATATTATTATATTAATAATAAA
* *
28719 ATATTATTATGTTAATTATAAA
1 ATATTATTATATTAATAATAAA
*
28741 CTATTA
1 ATATTA
28747 AATAAACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATTATTATATTAATAATAAA
Found at i:29476 original size:21 final size:21
Alignment explanation
Indices: 29419--29476 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
29409 ATATTAAAAG
*
29419 TTCAGGATTTTGAGTTTAGAA
1 TTCAAGATTTTGAGTTTAGAA
* * *** *
29440 TTCATGAGTCAAAGTTTAGGA
1 TTCAAGATTTTGAGTTTAGAA
29461 TTCAAGATTTTGAGTT
1 TTCAAGATTTTGAGTT
29477 CGAAATTTAA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (21 bp):
TTCAAGATTTTGAGTTTAGAA
Found at i:29991 original size:2 final size:2
Alignment explanation
Indices: 29984--30012 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29974 TCTTTATCTC
29984 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 T
30013 GATACTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30145 original size:13 final size:13
Alignment explanation
Indices: 30123--30154 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30113 ATACATGACA
*
30123 ATTACTTAATTTC
1 ATTACCTAATTTC
30136 ATTACCTAATTTC
1 ATTACCTAATTTC
30149 ATTACC
1 ATTACC
30155 ATGTTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTACCTAATTTC
Found at i:32187 original size:33 final size:31
Alignment explanation
Indices: 32145--32206 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
32135 TTAAAAGTTA
32145 GAGTCCCTTAAAAATTGGTAAATTTTTTTTTTG
1 GAGTCCCTTAAAAATT-G-AAATTTTTTTTTTG
* *
32178 GAGTCCCTTAAAAGTTGATATTTTTTTTT
1 GAGTCCCTTAAAAATTGAAATTTTTTTTT
32207 ACCTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 11 0.41
32 1 0.04
33 15 0.56
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.50
Consensus pattern (31 bp):
GAGTCCCTTAAAAATTGAAATTTTTTTTTTG
Found at i:34084 original size:18 final size:18
Alignment explanation
Indices: 34044--34085 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
34034 TCTTTGAGTC
*
34044 TGCCAATATTGGAGGATT
1 TGCCAATATTGGAGAATT
*
34062 CGCCAATA-TGGAGAAGTT
1 TGCCAATATTGGAGAA-TT
34080 TGCCAA
1 TGCCAA
34086 GTTCAGTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (18 bp):
TGCCAATATTGGAGAATT
Found at i:39484 original size:15 final size:15
Alignment explanation
Indices: 39464--39503 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
39454 TTTTTATTTT
39464 TATTTTATTTTTTCG
1 TATTTTATTTTTTCG
* *
39479 TATTTTATTATTTCT
1 TATTTTATTTTTTCG
*
39494 TTTTTTATTT
1 TATTTTATTT
39504 ATTTTTGGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (15 bp):
TATTTTATTTTTTCG
Found at i:51083 original size:18 final size:18
Alignment explanation
Indices: 51045--51090 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
51035 CAGTAATTTA
*
51045 TTCTTCTTTTTCTTTTCT
1 TTCTTCTTTTTCTTATCT
51063 TTCTTCTTTTTCTTAAT-T
1 TTCTTCTTTTTCTT-ATCT
51081 TTCTT-TTTTT
1 TTCTTCTTTTT
51091 TTTTCCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 20 0.77
19 1 0.04
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (18 bp):
TTCTTCTTTTTCTTATCT
Found at i:58370 original size:97 final size:97
Alignment explanation
Indices: 58204--58397 Score: 289
Period size: 97 Copynumber: 2.0 Consensus size: 97
58194 AACCTTGAAA
* * * *
58204 AAGGGTATTCGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAAATTTCA
1 AAGGGTATTCGATTATACCGATTTGAAGAAAAATCACACCTAGTAAGTTAAAGCACAAAATTTCA
* * *
58269 AAACCTGAGATAAAGGAATATTGCCTCGATTT
66 AAACCCGAAATAAAGGAATATGGCCTCGATTT
* * **
58301 AAGGGTATTCGATTATACCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAAGCACAAATTTTTG
1 AAGGGTATTCGATTATACCGATTTGAAGAAAAATCACACCTAGTAAGTTAAAGCACAAAATTTCA
58366 AAACCCGAAATAAAGGAATATGGCCTCGATTT
66 AAACCCGAAATAAAGGAATATGGCCTCGATTT
58398 TAAATATTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 86 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (97 bp):
AAGGGTATTCGATTATACCGATTTGAAGAAAAATCACACCTAGTAAGTTAAAGCACAAAATTTCA
AAACCCGAAATAAAGGAATATGGCCTCGATTT
Found at i:58813 original size:29 final size:30
Alignment explanation
Indices: 58690--59071 Score: 372
Period size: 29 Copynumber: 13.2 Consensus size: 30
58680 GGTTAAAACA
* *
58690 TAATTTTAGA-AAGTTTTAGGGGTAAAAATG
1 TAATTTTTGAGAAGTTTGA-GGGTAAAAATG
* * *
58720 TCATTTTTGAGAAGTTCGAGGGTGAAAATG
1 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
*
58750 TAA-TTTTG-G-AGTTTTG-GAGTAAAAATG
1 TAATTTTTGAGAAG-TTTGAGGGTAAAAATG
*
58777 CAATTTTTGAGAAGTTTGAGGGTAAAAATG
1 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
*
58807 TGATTTTTG-GAAGTTTGAGGGTAAAAATG
1 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
* * *
58836 TAACTTTT-AGAAGTTTAAGGGCAAAAATG
1 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
* *
58865 TAATTATTGA-AAGTTT-AGGGGCAAAAATG
1 TAATTTTTGAGAAGTTTGA-GGGTAAAAATG
* *
58894 TACTTTTTGAAAAGTTTG-GGG--AAAATG
1 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
*
58921 TAATTTTTG-GTAGTTTGAGGGTAAAAATG
1 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
58950 TAATTTTTGAGAAGTTT-AGGGGTAAAAATG
1 TAATTTTTGAGAAGTTTGA-GGGTAAAAATG
*
58980 TAA-TTTT-AAAAGTTT-AGGGGT-AAAATG
1 TAATTTTTGAGAAGTTTGA-GGGTAAAAATG
* * **
59007 TAA-TTTTAAGAAGTTTAAGGGTTTAAATG
1 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
* *
59036 TAATTTTT-AGAAGTTCGAGGGCAAAAATG
1 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
59065 TAATTTT
1 TAATTTT
59072 CAAGAGGTTT
Statistics
Matches: 299, Mismatches: 33, Indels: 41
0.80 0.09 0.11
Matches are distributed among these distances:
26 6 0.02
27 43 0.14
28 34 0.11
29 140 0.47
30 70 0.23
31 6 0.02
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TAATTTTTGAGAAGTTTGAGGGTAAAAATG
Found at i:59006 original size:86 final size:88
Alignment explanation
Indices: 58690--59050 Score: 390
Period size: 86 Copynumber: 4.2 Consensus size: 88
58680 GGTTAAAACA
* * * *
58690 TAATTTTAGA-AAGTTTTAGGGGTAAAAATGTCATTTTTGAGAAGTTCGAGGGTGAAAATGTAA-
1 TAATTTTTGAGAAG-TTTAGGGGTAAAAATGT-ATTTTTGAAAAGTTTGAGGGTAAAAATGTAAT
* *
58753 TTTT-GGAGTTT-TGGAGTAAAAATG
64 TTTTAGAAGTTTAAGG-GTAAAAATG
* * *
58777 CAATTTTTGAGAAGTTT-GAGGGTAAAAATGTGATTTTTG-GAAGTTTGAGGGTAAAAATGTAAC
1 TAATTTTTGAGAAGTTTAG-GGGTAAAAATGT-ATTTTTGAAAAGTTTGAGGGTAAAAATGTAAT
*
58840 TTTTAGAAGTTTAAGGGCAAAAATG
64 TTTTAGAAGTTTAAGGGTAAAAATG
* *
58865 TAATTATTGA-AAGTTTAGGGGCAAAAATGTACTTTTTGAAAAGTTTG-GGG--AAAATGTAATT
1 TAATTTTTGAGAAGTTTAGGGGTAAAAATGTA-TTTTTGAAAAGTTTGAGGGTAAAAATGTAATT
* * *
58926 TTTGGTAGTTTGAGGGTAAAAATG
65 TTTAGAAGTTTAAGGGTAAAAATG
*
58950 TAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTT-AAAAGTTT-AGGGGT-AAAATGTAATT
1 TAATTTTTGAGAAGTTTAGGGGTAAAAATGTATTTTTGAAAAGTTTGA-GGGTAAAAATGTAATT
* **
59012 TTAAGAAGTTTAAGGGTTTAAATG
65 TTTAGAAGTTTAAGGGTAAAAATG
59036 TAATTTTT-AGAAGTT
1 TAATTTTTGAGAAGTT
59051 CGAGGGCAAA
Statistics
Matches: 236, Mismatches: 26, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
84 8 0.03
85 53 0.22
86 80 0.34
87 60 0.25
88 33 0.14
89 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (88 bp):
TAATTTTTGAGAAGTTTAGGGGTAAAAATGTATTTTTGAAAAGTTTGAGGGTAAAAATGTAATTT
TTAGAAGTTTAAGGGTAAAAATG
Found at i:60809 original size:6 final size:6
Alignment explanation
Indices: 60798--60862 Score: 68
Period size: 6 Copynumber: 11.3 Consensus size: 6
60788 AGACATTGTT
*
60798 AATTTA AATTTA GAA--TA AATTTA AACTTA AA-TTA AATTTA AATTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
60844 GAA--TA AATTTA AATTTA AA
1 -AATTTA AATTTA AATTTA AA
60863 ATAAATCTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
4 4 0.08
5 9 0.18
6 34 0.67
7 4 0.08
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:60818 original size:11 final size:11
Alignment explanation
Indices: 60796--60858 Score: 60
Period size: 11 Copynumber: 5.6 Consensus size: 11
60786 TTAGACATTG
*
60796 TTAATTTAAAT
1 TTAAATTAAAT
60807 TTAGAA-TAAAT
1 TTA-AATTAAAT
60818 TTAAACTTAAA-
1 TTAAA-TTAAAT
60829 TTAAATTTAAAT
1 TTAAA-TTAAAT
60841 TTAGAA-TAAAT
1 TTA-AATTAAAT
60852 TTAAATT
1 TTAAATT
60859 TAAAATAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
10 4 0.09
11 30 0.68
12 8 0.18
13 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:60820 original size:17 final size:17
Alignment explanation
Indices: 60798--60873 Score: 109
Period size: 17 Copynumber: 4.5 Consensus size: 17
60788 AGACATTGTT
60798 AATTTAAATTTAGAATA
1 AATTTAAATTTAGAATA
*
60815 AATTTAAACTTA-AATTA
1 AATTTAAATTTAGAA-TA
60832 AATTTAAATTTAGAATA
1 AATTTAAATTTAGAATA
*
60849 AATTTAAATTTAAAATA
1 AATTTAAATTTAGAATA
*
60866 AATCTAAA
1 AATTTAAA
60874 AAAATGGGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
16 2 0.04
17 49 0.92
18 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAGAATA
Found at i:60836 original size:34 final size:34
Alignment explanation
Indices: 60798--60873 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
60788 AGACATTGTT
*
60798 AATTTAAATTTAGAATAAATTTAAACTTAAATTA
1 AATTTAAATTTAGAATAAATTTAAACTTAAAATA
*
60832 AATTTAAATTTAGAATAAATTTAAATTTAAAATA
1 AATTTAAATTTAGAATAAATTTAAACTTAAAATA
*
60866 AATCTAAA
1 AATTTAAA
60874 AAAATGGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (34 bp):
AATTTAAATTTAGAATAAATTTAAACTTAAAATA
Found at i:60873 original size:23 final size:23
Alignment explanation
Indices: 60813--60862 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
60803 AAATTTAGAA
*
60813 TAAATTTAAACTTAAATTAAATT
1 TAAATTTAAACATAAATTAAATT
*
60836 TAAATTTAGA-ATAAATTTAAATT
1 TAAATTTAAACATAAA-TTAAATT
60859 TAAA
1 TAAA
60863 ATAAATCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTAAACATAAATTAAATT
Found at i:61366 original size:39 final size:39
Alignment explanation
Indices: 61323--61921 Score: 206
Period size: 39 Copynumber: 15.4 Consensus size: 39
61313 GCTGATGGTG
*
61323 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGCA
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* * * * *
61362 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGGTGGTG
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* * * *
61401 ATCTACCCCAGGCT-AGGGGTAAAAGATCGAATTGCTGTA
1 ATCTGCCCCAGGCTCA-GGGTAAAAGATTGAATGGTTGTA
* * * * *
61440 ATTTGCCCCAGGCTCGGGGTAAAAGATTGAATGATGGTG
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* * * * * * *
61479 ATCTACGCCAGGCTCAGGG-AAAGAGATCGGACGATTATA
1 ATCTGCCCCAGGCTCAGGGTAAA-AGATTGAATGGTTGTA
* ** * ** * * *
61518 ATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* * * ** * * * * *
61557 ATCTACCTCAGGCTCGGGGTAAGTGATCGGACGGCTGCA
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* ** * * * * *
61596 ATCTACCCCAGGCTTGGGGTAAGAGATTGACTGATGGTG
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* * * * * * ** *
61635 ATCTGCCCTAAGCTCGGGGTAAGAGATCGGACAGCTGTA
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* * * * * * *
61674 ATCTGCCCTAGGCTCGGGGTAAGAGATTG-GTTGATGATG
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTG-TA
* * * * ** * * *
61713 ATCTGCCCTATGCTCGGGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* * *** **
61752 ATCTGCCCCAGGCTCGGGGTAAAAGATAGAATTACTACA
1 ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
* * * * * *
61791 ATCTGCCCCAAGCTCAAGG-AAAGAGATTTAATTGCTGCA
1 ATCTGCCCCAGGCTCAGGGTAAA-AGATTGAATGGTTGTA
* * * * * *
61830 ATCTACCCTAGGCTC-GGGGAAAGAGATTGAATGATGGTG
1 ATCTGCCCCAGGCTCAGGGTAAA-AGATTGAATGGTTGTA
* * *
61869 ATCTG-CCCAAGCTC-GGGTTAAAAGATCT-AATTGTTGCA
1 ATCTGCCCCAGGCTCAGGG-TAAAAGAT-TGAATGGTTGTA
*
61907 ATCTGCCTCAGGCTC
1 ATCTGCCCCAGGCTC
61922 TGGGCAAGAG
Statistics
Matches: 411, Mismatches: 138, Indels: 22
0.72 0.24 0.04
Matches are distributed among these distances:
38 35 0.09
39 372 0.91
40 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCAGGGTAAAAGATTGAATGGTTGTA
Found at i:61410 original size:78 final size:78
Alignment explanation
Indices: 61271--61968 Score: 500
Period size: 78 Copynumber: 9.0 Consensus size: 78
61261 CTTTATTGCT
* * * * * * *
61271 TCGAATGACTGCCATTTGCCCCATGATCGGAGTAATAGACTTG-CTGATGGTGATCTGCCCCAGG
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGA-TTGACTGATGGTGATCTGCCCCAGG
61335 CTCAGGGTAAAAGA
65 CTCAGGGTAAAAGA
* * * *
61349 TTGAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGGTGGTGATCTACCCCAGGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGC
61414 T-AGGGGTAAAAGA
66 TCA-GGGTAAAAGA
* * * * * * *
61427 TCGAATTGCTGTAATTTGCCCCAGGCTCGGGGTAAAAGATTGAATGATGGTGATCTACGCCAGGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGC
61492 TCAGGG-AAAGAGA
66 TCAGGGTAAA-AGA
* * ** ** * * * * *
61505 TCGGACGATTATAATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGATGGTGATCTACCTCAGGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGC
* **
61570 TCGGGGTAAGTGA
66 TCAGGGTAAAAGA
* * * * * *
61583 TCGGACGGCTGCAATCTACCCCAGGCTTGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGC
* *
61648 TCGGGGTAAGAGA
66 TCAGGGTAAAAGA
* ** * * ** * * *
61661 TCGGACAGCTGTAATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCTATGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGC
* *
61726 TCGGGGTAAGAGA
66 TCAGGGTAAAAGA
* * * * * * ***
61739 TTGGTTGATGG-TG--ATCTGCCCCAGGCTCGGGGTAAAAGATAGAATTACT-ACAATCTGCCCC
1 -TCG--AATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGA-TGGTGATCTGCCCC
* *
61800 AAGCTCAAGG-AAAGAGA
62 AGGCTCAGGGTAAA-AGA
** * * * * * *
61817 TTTAATTGCTGCAATCTACCCTAGGCTCGGGGAAAGAGATTGAATGATGGTGATCTG-CCCAAGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGC
61881 TC-GGGTTAAAAGA
66 TCAGGG-TAAAAGA
* * * * * * * * *
61894 TCTAATTGTTGCAATCTGCCTCAGGCTCTGGGCAAGAGATT-AGCTGATGATAATCTGCCCCAAG
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGA-CTGATGGTGATCTGCCCCAGG
*
61958 CTCGGGGTAAA
65 CTCAGGGTAAA
61969 GAATCAACTT
Statistics
Matches: 503, Mismatches: 98, Indels: 38
0.79 0.15 0.06
Matches are distributed among these distances:
75 3 0.01
76 5 0.01
77 68 0.14
78 413 0.82
79 9 0.02
80 2 0.00
81 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (78 bp):
TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGC
TCAGGGTAAAAGA
Found at i:61970 original size:156 final size:156
Alignment explanation
Indices: 61287--61970 Score: 562
Period size: 156 Copynumber: 4.4 Consensus size: 156
61277 GACTGCCATT
* * * * *
61287 TGCCCCATGATCGGAGTAATAGACTTG-CTGATGGTGATCTGCCCCAGGCTCAGGGTAAA-AGAT
1 TGCCCCAGGCTCGGGGTAAAAGA-TTGACTGATGGTGATCTGCCCCAAGCTCAGGGTAAAGAGAT
* * * *
61350 TGAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGGTGGTGATCTACCCCAGGCT
65 TGAATTGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT-GCCCAGGCT
* * *
61415 AGGGGTAAAAGATCGAATTGCTGTAATT
129 CGGGGTAAAAGATCGAATTGCTGCAATC
* * * *
61443 TGCCCCAGGCTCGGGGTAAAAGATTGAATGATGGTGATCTACGCCAGGCTCAGGG-AAAGAGATC
1 TGCCCCAGGCTCGGGGTAAAAGATTGACTGATGGTGATCTGCCCCAAGCTCAGGGTAAAGAGAT-
* * * * * *
61507 GGACGATT-AT--AATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGATGGTGATCTACCTCAGG
65 TGA--ATTGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCC-CAGG
** * **
61569 CTCGGGGTAAGTGATCGGACGGCTGCAATC
127 CTCGGGGTAAAAGATCGAATTGCTGCAATC
* * * * * *
61599 TACCCCAGGCTTGGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGGT-AAGAGATC
1 TGCCCCAGGCTCGGGGTAAAAGATTGACTGATGGTGATCTGCCCCAAGCTCAGGGTAAAGAGATT
* ** * * ** * *
61663 GGACAGCTGTAATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCTATGCTC
66 GAATTGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCC-AGGCTC
* * * * **
61728 GGGGTAAGAGATTG-GTTGATGGTGATC
130 GGGGTAAAAGATCGAATTGCT-GCAATC
* * * *** *
61755 TGCCCCAGGCTCGGGGTAAAAGATAGAATTACT-ACAATCTGCCCCAAGCTCAAGG-AAAGAGAT
1 TGCCCCAGGCTCGGGGTAAAAGATTGACTGA-TGGTGATCTGCCCCAAGCTCAGGGTAAAGAGAT
* * * * * *
61818 TTAATTGCTGCAATCTACCCTAGGCTCGGGGAAAGAGATTGAATGATGGTGATCTGCCCAAGCTC
65 TGAATTGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCAGGCTC
* * *
61883 GGGTTAAAAGATCTAATTGTTGCAATC
130 GGGGTAAAAGATCGAATTGCTGCAATC
* * * * * * *
61910 TGCCTCAGGCTCTGGGCAAGAGATT-AGCTGATGATAATCTGCCCCAAGCTCGGGGTAAAGA
1 TGCCCCAGGCTCGGGGTAAAAGATTGA-CTGATGGTGATCTGCCCCAAGCTCAGGGTAAAGA
61971 ATCAACTTGT
Statistics
Matches: 416, Mismatches: 94, Indels: 36
0.76 0.17 0.07
Matches are distributed among these distances:
153 1 0.00
154 3 0.01
155 72 0.17
156 334 0.80
157 3 0.01
158 1 0.00
159 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (156 bp):
TGCCCCAGGCTCGGGGTAAAAGATTGACTGATGGTGATCTGCCCCAAGCTCAGGGTAAAGAGATT
GAATTGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCAGGCTCG
GGGTAAAAGATCGAATTGCTGCAATC
Found at i:71938 original size:97 final size:97
Alignment explanation
Indices: 71772--71962 Score: 287
Period size: 97 Copynumber: 2.0 Consensus size: 97
71762 AACTTTGAAA
*
71772 AAGGGTATTTGATTATCCCGGTTTGAAGAAAAATCGAGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATGTGATTATCCCGGTTTGAAGAAAAATCGAGCCTAGTAAGTTAAGGCACAAATTTTCA
* *
71837 AAACCCGAGATAAAAG-AATATTGCCTCGACTT
66 AAACCCGAAAT-AAAGCAATATGGCCTCGACTT
* * *
71869 AAGGGTATGTGATTATCCCTGTTTGAAGAAAAAT-TACGCCTAGTAAGTTAAGGCACAAATTTTT
1 AAGGGTATGTGATTATCCCGGTTTGAAGAAAAATCGA-GCCTAGTAAGTTAAGGCACAAATTTTC
*
71933 AAAACCTGAAATAAAGCAATATGGCCTCGA
65 AAAACCCGAAATAAAGCAATATGGCCTCGA
71963 TTTTAAATAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
96 5 0.06
97 80 0.94
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (97 bp):
AAGGGTATGTGATTATCCCGGTTTGAAGAAAAATCGAGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCCGAAATAAAGCAATATGGCCTCGACTT
Found at i:72308 original size:29 final size:29
Alignment explanation
Indices: 72235--72501 Score: 149
Period size: 29 Copynumber: 9.2 Consensus size: 29
72225 GTTTGGTGTT
*
72235 AAAACGTAATTTTG-GAAAGTTTTATA-GGTA
1 AAAATGTAATTTTGAG-AAG-TTTA-AGGGTA
** *
72265 AAAATGTCTTTTTTGAGAAGTTCAAGGGTA
1 AAAATGT-AATTTTGAGAAGTTTAAGGGTA
* *
72295 AAAATGTAATTTTGA-AAG-TT-CGGGAGA
1 AAAATGTAATTTTGAGAAGTTTAAGGG-TA
* * * *
72322 AAAATGTATTTTTTAAGATGTTTGAGGGTA
1 AAAATGTA-ATTTTGAGAAGTTTAAGGGTA
* * * *
72352 AAAATGTGATTTTTGA-AAGTTTGAGAGCA
1 AAAATGT-AATTTTGAGAAGTTTAAGGGTA
* * *
72381 AAAATGTAATTTTTAGAAGTTTAGGGGCA
1 AAAATGTAATTTTGAGAAGTTTAAGGGTA
72410 AAAATGTAATTTTTG-GAAGTTT-AGTGGT-
1 AAAATGTAA-TTTTGAGAAGTTTAAG-GGTA
* * * *
72438 AAAATATAATTTTGAGTATTTTAGGGGTA
1 AAAATGTAATTTTGAGAAGTTTAAGGGTA
* * *
72467 AAAATGTGATTTT-AGAAATGTTCAAGGGTC
1 AAAATGTAATTTTGAG-AA-GTTTAAGGGTA
72497 AAAAT
1 AAAAT
72502 ATGATTTTTG
Statistics
Matches: 183, Mismatches: 37, Indels: 34
0.72 0.15 0.13
Matches are distributed among these distances:
26 3 0.02
27 15 0.08
28 33 0.18
29 67 0.37
30 52 0.28
31 12 0.07
32 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGAGAAGTTTAAGGGTA
Found at i:72415 original size:58 final size:58
Alignment explanation
Indices: 72264--72484 Score: 200
Period size: 57 Copynumber: 3.8 Consensus size: 58
72254 TTTTATAGGT
** * * * * * *
72264 AAAAATGTCTTTTTTGAGAAGTTCAAGGGTAAAAATGT-AATTTTGAAAGTTCGGGAG
1 AAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTGATTTTTGAAAGTTTGAGAG
* *
72321 AAAAATGTATTTTTTAAGATGTTT-GAGGGTAAAAATGTGATTTTTGAAAGTTTGAGAG
1 AAAAATGTAATTTTTAAGAAGTTTAG-GGGTAAAAATGTGATTTTTGAAAGTTTGAGAG
* * * *
72379 CAAAAATGTAATTTTT-AGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTTT-AGTGG
1 -AAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTGATTTTTGAAAGTTTGAG-AG
* * * * * *
72437 TAAAATATAA-TTTTGAGTATTTTAGGGGTAAAAATGTGATTTTAGAAA
1 AAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTGATTTTTGAAA
72485 TGTTCAAGGG
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
56 4 0.03
57 69 0.51
58 48 0.35
59 15 0.11
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (58 bp):
AAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTGATTTTTGAAAGTTTGAGAG
Found at i:72439 original size:87 final size:86
Alignment explanation
Indices: 72235--72441 Score: 199
Period size: 87 Copynumber: 2.4 Consensus size: 86
72225 GTTTGGTGTT
* * * *
72235 AAAACGTAA-TTTTGGAAAGTTTTA-TAGGTAAAAATGTCTTTTTTGAGAAGTTCAAGGGTAAAA
1 AAAATGTAATTTTTGG-AAG-TTTAGT-GGTAAAAATGTCATTTTTGAGAAGTTCAAGAGCAAAA
*
72298 ATGTAATTTTGAAAGTTCGGGAGA
63 ATGTAATTTTGAAAGTTAGGGAGA
* * * * **
72322 AAAATGTATTTTTTAAGATGTTTGAG-GGTAAAAATGTGATTTTTGA-AAGTTTGAGAGCAAAAA
1 AAAATGTAATTTTT-GGAAGTTT-AGTGGTAAAAATGTCATTTTTGAGAAGTTCAAGAGCAAAAA
*
72385 TGTAATTTTTAGAAGTTTAGGG-GCA
64 TGTAATTTTGA-AAG-TTAGGGAG-A
72410 AAAATGTAATTTTTGGAAGTTTAGTGGTAAAA
1 AAAATGTAATTTTTGGAAGTTTAGTGGTAAAA
72442 TATAATTTTG
Statistics
Matches: 97, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
86 25 0.26
87 45 0.46
88 26 0.27
89 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (86 bp):
AAAATGTAATTTTTGGAAGTTTAGTGGTAAAAATGTCATTTTTGAGAAGTTCAAGAGCAAAAATG
TAATTTTGAAAGTTAGGGAGA
Found at i:74194 original size:6 final size:6
Alignment explanation
Indices: 74171--74267 Score: 82
Period size: 6 Copynumber: 17.3 Consensus size: 6
74161 GGACATTATT
* * *
74171 AATTTA AATTTG AA--TA AATTTA AATTTG AA--TA AATTTA AACTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
74215 AA-TTA AATTTA AATTTA AA-ATA AATTTA AACTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
74260 AAATTA AA
1 AATTTA AA
74268 AACAAATTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
4 6 0.08
5 13 0.18
6 54 0.74
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:74223 original size:17 final size:17
Alignment explanation
Indices: 74183--74296 Score: 149
Period size: 17 Copynumber: 6.7 Consensus size: 17
74173 TTTAAATTTG
**
74183 AATAAATTTAAA-TTTG
1 AATAAATTTAAACTTAA
74199 AATAAATTTAAACTTAA
1 AATAAATTTAAACTTAA
* *
74216 ATTAAATTTAAATTTAA
1 AATAAATTTAAACTTAA
74233 AATAAATTTAAACTTAA
1 AATAAATTTAAACTTAA
*
74250 AATAAATTTAAAATTAAA
1 AATAAATTTAAACTT-AA
*
74268 AACAAATTTAAACTTAA
1 AATAAATTTAAACTTAA
*
74285 AATAAATCTAAA
1 AATAAATTTAAA
74297 AAAATGAGTT
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
16 12 0.14
17 58 0.68
18 15 0.18
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (17 bp):
AATAAATTTAAACTTAA
Found at i:74268 original size:6 final size:6
Alignment explanation
Indices: 74201--74287 Score: 54
Period size: 6 Copynumber: 15.0 Consensus size: 6
74191 TAAATTTGAA
* * * * * *
74201 TAAATT TAAACT T-AAAT TAAATT TAAATT TAAAA- TAAATT TAAACT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
* * * * *
74247 TAAAA- TAAATT TAAAAT TAAAAA CAAATT TAAACT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
74288 AAATCTAAAA
Statistics
Matches: 62, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
5 12 0.19
6 50 0.81
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAAAT
Found at i:74275 original size:35 final size:35
Alignment explanation
Indices: 74202--74297 Score: 149
Period size: 35 Copynumber: 2.8 Consensus size: 35
74192 AAATTTGAAT
* * *
74202 AAATTTAAACTTAAATTAAATTT-AAATTTAAAAT
1 AAATTTAAACTTAAAATAAATTTAAAATTAAAAAC
74236 AAATTTAAACTTAAAATAAATTTAAAATTAAAAAC
1 AAATTTAAACTTAAAATAAATTTAAAATTAAAAAC
*
74271 AAATTTAAACTTAAAATAAATCTAAAA
1 AAATTTAAACTTAAAATAAATTTAAAA
74298 AAATGAGTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 22 0.39
35 35 0.61
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.34
Consensus pattern (35 bp):
AAATTTAAACTTAAAATAAATTTAAAATTAAAAAC
Found at i:88081 original size:12 final size:12
Alignment explanation
Indices: 88064--88103 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
88054 TTTTGAGAGC
88064 ATAAAATAAAAG
1 ATAAAATAAAAG
88076 ATAAAAT-AAA-
1 ATAAAATAAAAG
88086 ATAGAAATAAAAG
1 ATA-AAATAAAAG
88099 -TAAAA
1 ATAAAA
88104 GTTTGAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 3 0.12
11 10 0.40
12 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:88086 original size:17 final size:16
Alignment explanation
Indices: 88064--88103 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
88054 TTTTGAGAGC
88064 ATAAAATAAAAGATAAA
1 ATAAAATAAAA-ATAAA
*
88081 ATAAAATAGAAATAAA
1 ATAAAATAAAAATAAA
88097 AGTAAAA
1 A-TAAAA
88104 GTTTGAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
ATAAAATAAAAATAAA
Found at i:99426 original size:17 final size:17
Alignment explanation
Indices: 99393--99455 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
99383 CATTAAATTA
*
99393 CAATGACAAATGGAAATG
1 CAATGAC-AATGAAAATG
99411 CAATGACAATGAAAATG
1 CAATGACAATGAAAATG
* *
99428 CAGTGACAATTAAAATG
1 CAATGACAATGAAAATG
* *
99445 TAATAACAATG
1 CAATGACAATG
99456 GGAATGTGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 31 0.82
18 7 0.18
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:104067 original size:59 final size:58
Alignment explanation
Indices: 103947--104138 Score: 199
Period size: 59 Copynumber: 3.2 Consensus size: 58
103937 CTCGGGGGTG
* * * * * * *
103947 AAATGGTAATTTTGGGAAAATTTGAGGTTAAAAATGGAAATTTT-AAACATTTAGGGGT-A
1 AAATGG-AATTTT-TGAAAGTTTCAGGTCAAAAATGGGAATTTTGGAA-GTTTAGGGGTAA
* *
104006 AAATGGTAATTTTTGAAAGTTTCAGTGTCAAAAATGGGAATTTTGGAAGTTCAGGGCTAA
1 AAATGG-AATTTTTGAAAGTTTCAG-GTCAAAAATGGGAATTTTGGAAGTTTAGGGGTAA
* * * *
104066 AAATGGAATTTTTGGAAGTTTCAAGGTGAAAAATAGGATTTTTGGAAGTTTAGGGGTAA
1 AAATGGAATTTTTGAAAGTTTC-AGGTCAAAAATGGGAATTTTGGAAGTTTAGGGGTAA
104125 AAATGGAATTTTTG
1 AAATGGAATTTTTG
104139 GACAGTTTAG
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
58 9 0.08
59 94 0.82
60 11 0.10
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (58 bp):
AAATGGAATTTTTGAAAGTTTCAGGTCAAAAATGGGAATTTTGGAAGTTTAGGGGTAA
Found at i:104068 original size:29 final size:28
Alignment explanation
Indices: 104001--104150 Score: 144
Period size: 29 Copynumber: 5.1 Consensus size: 28
103991 AAACATTTAG
*
104001 GGGT-AAAATGGTAATTTTTGAAAGTTTCA
1 GGGTAAAAATGG-AATTTTTGGAAG-TTCA
*
104030 GTGTCAAAAATGGGAA-TTTTGGAAGTTCA
1 GGGT-AAAAAT-GGAATTTTTGGAAGTTCA
104059 GGGCTAAAAATGGAATTTTTGGAAGTTTCA
1 GGG-TAAAAATGGAATTTTTGGAAG-TTCA
* *
104089 AGGTGAAAAATAGG-ATTTTTGGAAGTTTA
1 GGGT-AAAAAT-GGAATTTTTGGAAGTTCA
*
104118 GGGGTAAAAATGGAATTTTTGGACAGTTTA
1 -GGGTAAAAATGGAATTTTTGGA-AGTTCA
104148 GGG
1 GGG
104151 ACCCTCGAGG
Statistics
Matches: 104, Mismatches: 6, Indels: 22
0.79 0.05 0.17
Matches are distributed among these distances:
28 6 0.06
29 46 0.44
30 41 0.39
31 9 0.09
32 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTTGGAAGTTCA
Found at i:104139 original size:59 final size:59
Alignment explanation
Indices: 103996--104146 Score: 207
Period size: 59 Copynumber: 2.5 Consensus size: 59
103986 ATTTTAAACA
* *
103996 TTTAGGGGT-AAAATGGTAATTTTTGAAAGTTTCAGTGTCAAAAATGGGAATTTTGGAAG
1 TTTAGGGGTAAAAATGG-AATTTTTGGAAGTTTCAGTGTCAAAAATAGGAATTTTGGAAG
* * * *
104055 TTCAGGGCTAAAAATGGAATTTTTGGAAGTTTCAAG-GTGAAAAATAGGATTTTTGGAAG
1 TTTAGGGGTAAAAATGGAATTTTTGGAAGTTTC-AGTGTCAAAAATAGGAATTTTGGAAG
104114 TTTAGGGGTAAAAATGGAATTTTTGGACAGTTT
1 TTTAGGGGTAAAAATGGAATTTTTGGA-AGTTT
104147 AGGGACCCTC
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
59 67 0.83
60 14 0.17
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (59 bp):
TTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCAGTGTCAAAAATAGGAATTTTGGAAG
Found at i:104148 original size:30 final size:29
Alignment explanation
Indices: 103996--104150 Score: 158
Period size: 30 Copynumber: 5.2 Consensus size: 29
103986 ATTTTAAACA
*
103996 TTTAGGGGT-AAAATGGTAATTTTTGAAAG
1 TTTAGGGGTAAAAATGG-AATTTTTGGAAG
*
104025 TTTCA-GTGTCAAAAATGGGAA-TTTTGGAAG
1 TTT-AGGGGT-AAAAAT-GGAATTTTTGGAAG
* *
104055 TTCAGGGCTAAAAATGGAATTTTTGGAAG
1 TTTAGGGGTAAAAATGGAATTTTTGGAAG
*
104084 TTTCA-AGGTGAAAAATAGG-ATTTTTGGAAG
1 TTT-AGGGGT-AAAAAT-GGAATTTTTGGAAG
104114 TTTAGGGGTAAAAATGGAATTTTTGGACAG
1 TTTAGGGGTAAAAATGGAATTTTTGGA-AG
104144 TTTAGGG
1 TTTAGGG
104151 ACCCTCGAGG
Statistics
Matches: 105, Mismatches: 9, Indels: 23
0.77 0.07 0.17
Matches are distributed among these distances:
28 6 0.06
29 42 0.40
30 46 0.44
31 9 0.09
32 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTAGGGGTAAAAATGGAATTTTTGGAAG
Found at i:105087 original size:19 final size:20
Alignment explanation
Indices: 105048--105093 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
105038 TTTCCCTTTT
*
105048 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAAC-ATATTTA
105069 TTATTATTAAAA-ATATTTA
1 TTATTATTAAAACATATTTA
105088 TTATTA
1 TTATTA
105094 CTAATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.50
21 12 0.50
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATTATTAAAACATATTTA
Found at i:105090 original size:16 final size:16
Alignment explanation
Indices: 105069--105122 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
105059 ACGTTATTTA
105069 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
105085 TTATTATT---ACTA-
1 TTATTATTAAAAATAT
* *
105097 ATATTATTAAAAACAT
1 TTATTATTAAAAATAT
105113 TTATTATTAA
1 TTATTATTAA
105123 TACTCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 2 0.07
16 17 0.59
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:105104 original size:19 final size:19
Alignment explanation
Indices: 105048--105104 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
105038 TTTCCCTTTT
*
105048 TTATTATTAAAACGTTATTTA
1 TTATTACTAAAA--TTATTTA
* *
105069 TTATTATTAAAAATATTTA
1 TTATTACTAAAATTATTTA
*
105088 TTATTACTAATATTATT
1 TTATTACTAAAATTATT
105105 AAAAACATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 20 0.62
21 12 0.38
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (19 bp):
TTATTACTAAAATTATTTA
Found at i:105754 original size:15 final size:15
Alignment explanation
Indices: 105734--105782 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
105724 ACTTTGGGCC
*
105734 ATTGGGCCGTTTGTA
1 ATTGGGCCATTTGTA
*
105749 ATTGGGCCATTTGTG
1 ATTGGGCCATTTGTA
*
105764 CTTGGGCCATTTGTA
1 ATTGGGCCATTTGTA
105779 ATTG
1 ATTG
105783 TACTTTGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (15 bp):
ATTGGGCCATTTGTA
Found at i:105837 original size:17 final size:16
Alignment explanation
Indices: 105815--105893 Score: 77
Period size: 17 Copynumber: 4.8 Consensus size: 16
105805 TTGGACTTTC
105815 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
* *
105832 TAAATTCAAATTTCAAA
1 TAAATT-TAATTTTAAA
*
105849 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTTAAA
* *
105866 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
105882 TAAATTCAATTT
1 TAAATTTAATTT
105894 CCAATAGGTC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
16 16 0.32
17 28 0.56
18 6 0.12
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:105868 original size:34 final size:33
Alignment explanation
Indices: 105815--105887 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 33
105805 TTGGACTTTC
* *
105815 TAAATTTAATTTTATAATAAA-TTCAAATTTCAAA
1 TAAATTTAAATTTAAAATAAACTT-AAATTT-AAA
105849 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
1 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
105882 TAAATT
1 TAAATT
105888 CAATTTCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 9 0.25
34 25 0.69
35 2 0.06
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAATTTAAATTTAAAATAAACTTAAATTTAAA
Found at i:106963 original size:19 final size:20
Alignment explanation
Indices: 106924--106969 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
106914 TTTCCCTTTT
*
106924 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAAC-ATATTTA
106945 TTATTATTAAAA-ATATTTA
1 TTATTATTAAAACATATTTA
106964 TTATTA
1 TTATTA
106970 CTAATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.50
21 12 0.50
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATTATTAAAACATATTTA
Found at i:106966 original size:16 final size:16
Alignment explanation
Indices: 106945--106998 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
106935 ACGTTATTTA
106945 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
106961 TTATTATT---ACTA-
1 TTATTATTAAAAATAT
* *
106973 ATATTATTAAAAACAT
1 TTATTATTAAAAATAT
106989 TTATTATTAA
1 TTATTATTAA
106999 TACTCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 2 0.07
16 17 0.59
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:106980 original size:19 final size:19
Alignment explanation
Indices: 106924--106980 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
106914 TTTCCCTTTT
*
106924 TTATTATTAAAACGTTATTTA
1 TTATTACTAAAA--TTATTTA
* *
106945 TTATTATTAAAAATATTTA
1 TTATTACTAAAATTATTTA
*
106964 TTATTACTAATATTATT
1 TTATTACTAAAATTATT
106981 AAAAACATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 20 0.62
21 12 0.38
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (19 bp):
TTATTACTAAAATTATTTA
Found at i:107630 original size:15 final size:15
Alignment explanation
Indices: 107610--107658 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
107600 ACTTTGGGCC
*
107610 ATTGGGCCGTTTGTA
1 ATTGGGCCATTTGTA
*
107625 ATTGGGCCATTTGTG
1 ATTGGGCCATTTGTA
*
107640 CTTGGGCCATTTGTA
1 ATTGGGCCATTTGTA
107655 ATTG
1 ATTG
107659 TACTTTGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (15 bp):
ATTGGGCCATTTGTA
Found at i:107713 original size:17 final size:16
Alignment explanation
Indices: 107691--107769 Score: 77
Period size: 17 Copynumber: 4.8 Consensus size: 16
107681 TTGGACTTTC
107691 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
* *
107708 TAAATTCAAATTTCAAA
1 TAAATT-TAATTTTAAA
*
107725 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTTAAA
* *
107742 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
107758 TAAATTCAATTT
1 TAAATTTAATTT
107770 CCAATAGGTC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
16 16 0.32
17 28 0.56
18 6 0.12
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:107744 original size:34 final size:33
Alignment explanation
Indices: 107691--107763 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 33
107681 TTGGACTTTC
* *
107691 TAAATTTAATTTTATAATAAA-TTCAAATTTCAAA
1 TAAATTTAAATTTAAAATAAACTT-AAATTT-AAA
107725 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
1 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
107758 TAAATT
1 TAAATT
107764 CAATTTCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 9 0.25
34 25 0.69
35 2 0.06
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAATTTAAATTTAAAATAAACTTAAATTTAAA
Found at i:108785 original size:206 final size:206
Alignment explanation
Indices: 108145--108787 Score: 866
Period size: 206 Copynumber: 3.1 Consensus size: 206
108135 CTTCAACCTG
** * * * *
108145 CTTCTCAGTGCCTCATCAGGGAGATGACCACGTCGTTTGTTTCAATCCG-TTTTTCTGTATCTCA
1 CTTCTCAGTATCTCATCAGGAAGATGACCACATCGCTTGTTTCAATCCGCTTCTT-TGTATCTCA
* * * * * * *
108209 TCAGGAAGACGAATTTGGTTCACTCCTCCGTATCTCATCAGGGAGCTATCCGTTTTATTACTTC-
65 TCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCG-TTTATTGCTTCG
* * * * * * * * *
108273 AACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAG-GTTTA-T-TCATCGTGCGTAGG
129 AA-CTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGCGTGGG
* * *
108335 TTTGGTTTGGCCTT
193 CTTGATTTGGTCTT
* * *
108349 CTTCTCAATATCTCATCAAGAAGATGACCACATCGCTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCACATCGCTTGTTTCAATCCGCTTCTTTGTATCTCAT
* *
108414 CAAGAAGATGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATTGCTTCGAC
66 CAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATTGCTTCGAA
108479 CTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGCGTGGGCTT
131 CTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGCGTGGGCTT
108544 GATTTGGTCTT
196 GATTTGGTCTT
* * *
108555 CTTCTCAGTATCTTATCGGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTTTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCACATCGCTTGTTTCAATCCGCTTCTTTGTATCTCAT
108620 CAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATTGCTTCGAA
66 CAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATTGCTTCGAA
* * * *
108685 CTGCTTCTCGGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTTGCTCGCTTTGAGCATGGGCCT
131 CTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGCGTGGGCTT
*
108750 AATTTGGTCTT
196 GATTTGGTCTT
108761 CTTCTCAGTATCTCA-CTAGGAAGATGA
1 CTTCTCAGTATCTCATC-AGGAAGATGA
108788 TCGCGTCATT
Statistics
Matches: 388, Mismatches: 45, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
203 46 0.12
204 101 0.26
205 5 0.01
206 236 0.61
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.35
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCACATCGCTTGTTTCAATCCGCTTCTTTGTATCTCAT
CAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATTGCTTCGAA
CTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTACTCGCTTTGAGCGTGGGCTT
GATTTGGTCTT
Found at i:120575 original size:29 final size:28
Alignment explanation
Indices: 120543--120605 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
120533 AAAATGAGAC
*
120543 TTTTCGGATACCCGGGGGCAAAATGGTAA
1 TTTT-GGATACCCGAGGGCAAAATGGTAA
* * **
120572 TTTTGGATTCTCGAGGGTGAAATGGTAA
1 TTTTGGATACCCGAGGGCAAAATGGTAA
120600 TTTTGG
1 TTTTGG
120606 GAAAATTCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (28 bp):
TTTTGGATACCCGAGGGCAAAATGGTAA
Found at i:120720 original size:29 final size:29
Alignment explanation
Indices: 120679--120872 Score: 191
Period size: 29 Copynumber: 6.6 Consensus size: 29
120669 TTTCGAGGTC
*
120679 AAAATGGAGTTTTTGGACA-TTCGGGGCT-
1 AAAATGGAATTTTTGGA-AGTTCGGGGCTA
120707 AAAATGGTAATTTTTGGAAGTTCGGGGCTA
1 AAAATGG-AATTTTTGGAAGTTCGGGGCTA
* *
120737 AAAATGGATTTTTTTGGAAGTTTCAGGG-TCA
1 AAAATGGA-ATTTTTGGAAG-TTCGGGGCT-A
* *
120768 AAAATGGGATTTTTGGAAGTTCGGGGATA
1 AAAATGGAATTTTTGGAAGTTCGGGGCTA
* * *
120797 AAAATGGAATTTTTGGAAGTTTTGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGGGGCTA
*
120827 AAAATAGG-ATTTTTAGAAGTTCAGGGG-TA
1 AAAAT-GGAATTTTTGGAAGTTC-GGGGCTA
*
120856 CAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
120873 CAATTTAGGG
Statistics
Matches: 140, Mismatches: 15, Indels: 21
0.80 0.09 0.12
Matches are distributed among these distances:
28 10 0.07
29 60 0.43
30 54 0.39
31 16 0.11
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGGGGCTA
Found at i:120839 original size:59 final size:58
Alignment explanation
Indices: 120716--120872 Score: 208
Period size: 59 Copynumber: 2.6 Consensus size: 58
120706 TAAAATGGTA
* *
120716 ATTTTTGGAAGTTCGGGGCTAAAAATGGATTTTTTTGGAAGTTTCAGGGTCAAAAATGGG
1 ATTTTTGGAAGTTCGGGG-TAAAAATGGA-ATTTTTGGAAGTTTCAGGGTCAAAAATAGG
* *
120776 ATTTTTGGAAGTTCGGGGATAAAAATGGAATTTTTGGAAGTTT-TGAGGTTAAAAATAGG
1 ATTTTTGGAAGTTCGGGG-TAAAAATGGAATTTTTGGAAGTTTCAG-GGTCAAAAATAGG
* *
120835 ATTTTTAGAAGTTCAGGGGTACAAATGGAATTTTTGGA
1 ATTTTTGGAAGTTC-GGGGTAAAAATGGAATTTTTGGA
120873 CAATTTAGGG
Statistics
Matches: 88, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
58 1 0.01
59 55 0.62
60 32 0.36
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (58 bp):
ATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAATAGG
Found at i:121934 original size:19 final size:20
Alignment explanation
Indices: 121895--121938 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
121885 TTTCCCTTTT
*
121895 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAAC-ATATTTA
121916 TTATTATTAAAA-ATATTTA
1 TTATTATTAAAACATATTTA
121935 TTAT
1 TTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
21 12 0.55
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTATTAAAACATATTTA
Done.