Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013837.1 Kokia drynarioides strain JFW-HI SEQ_128865, 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: 267015
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:160 original size:25 final size:23
Alignment explanation
Indices: 116--165 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
106 ACACTAGCGC
*
116 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGAACTGTGTGT
* *
139 GCTCTCTGTTTAGAACTTTGTGT
1 GCTCTCTGATTAGAACTGTGTGT
162 GCTC
1 GCTC
166 AGTACTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGAACTGTGTGT
Found at i:1128 original size:20 final size:17
Alignment explanation
Indices: 1092--1130 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
1082 TCTATTTTTA
1092 TTTCATTATTTTTTAAT
1 TTTCATTATTTTTTAAT
1109 TTTCATTTATGTTATTTAAT
1 TTTCA-TTAT-TT-TTTAAT
1129 TT
1 TT
1131 CATACATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 2 0.11
20 8 0.42
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTCATTATTTTTTAAT
Found at i:2356 original size:19 final size:19
Alignment explanation
Indices: 2320--2360 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2310 AACTAAGTTT
*
2320 TTTTATTTAGTTGGTTTTG
1 TTTTATTTAATTGGTTTTG
**
2339 TTTTATTTAATTTTTTTTG
1 TTTTATTTAATTGGTTTTG
2358 TTT
1 TTT
2361 GTTTGGTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (19 bp):
TTTTATTTAATTGGTTTTG
Found at i:2402 original size:24 final size:24
Alignment explanation
Indices: 2375--2460 Score: 131
Period size: 24 Copynumber: 3.6 Consensus size: 24
2365 GGTTAGTTAA
*
2375 CATAAACGAACATGTTCGCGAATG
1 CATAAACGAACATATTCGCGAATG
2399 CATAAACGAACATATTCGCGAATG
1 CATAAACGAACATATTCGCGAATG
*
2423 TATAAACGAACATATTCGCGAA--
1 CATAAACGAACATATTCGCGAATG
2445 CATTAAACGAACATAT
1 CA-TAAACGAACATAT
2461 AAACGAACAT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
22 1 0.02
23 13 0.22
24 44 0.76
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
CATAAACGAACATATTCGCGAATG
Found at i:2463 original size:12 final size:12
Alignment explanation
Indices: 2400--2494 Score: 75
Period size: 12 Copynumber: 8.0 Consensus size: 12
2390 TCGCGAATGC
2400 ATAAACGAACAT
1 ATAAACGAACAT
*** **
2412 ATTCGCGAATGT
1 ATAAACGAACAT
2424 ATAAACGAACAT
1 ATAAACGAACAT
***
2436 ATTCGCGAACAT
1 ATAAACGAACAT
2448 -TAAACGAACAT
1 ATAAACGAACAT
2459 ATAAACGAACAT
1 ATAAACGAACAT
* **
2471 GTTCACGAACAT
1 ATAAACGAACAT
*
2483 ATAAACAAACAT
1 ATAAACGAACAT
2495 GTTCACGAGC
Statistics
Matches: 59, Mismatches: 23, Indels: 2
0.70 0.27 0.02
Matches are distributed among these distances:
11 8 0.14
12 51 0.86
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (12 bp):
ATAAACGAACAT
Found at i:2464 original size:35 final size:36
Alignment explanation
Indices: 2423--2494 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
2413 TTCGCGAATG
* *
2423 TATAAACGAACATATTCGCGAACAT-TAAACGAACA
1 TATAAACGAACATATTCACGAACATATAAACAAACA
*
2458 TATAAACGAACATGTTCACGAACATATAAACAAACA
1 TATAAACGAACATATTCACGAACATATAAACAAACA
2494 T
1 T
2495 GTTCACGAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (36 bp):
TATAAACGAACATATTCACGAACATATAAACAAACA
Found at i:2467 original size:23 final size:24
Alignment explanation
Indices: 2425--2565 Score: 101
Period size: 23 Copynumber: 6.0 Consensus size: 24
2415 CGCGAATGTA
***
2425 TAAACGAACATATTCGCGAACAT-
1 TAAACGAACATATAAACGAACATG
2448 TAAACGAACATATAAACGAACATG
1 TAAACGAACATATAAACGAACATG
** *
2472 TTCACGAACATATAAACAAACATG
1 TAAACGAACATATAAACGAACATG
** * *
2496 TTCACGAGCGT-TAAACGAACATG
1 TAAACGAACATATAAACGAACATG
** *
2519 TTCACGAACGT-TAAACGAACATG
1 TAAACGAACATATAAACGAACATG
*** *
2542 TTTGCGAACGT-TAAACGAACATG
1 TAAACGAACATATAAACGAACATG
2565 T
1 T
2566 TTGTGAACGA
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
23 75 0.71
24 30 0.29
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (24 bp):
TAAACGAACATATAAACGAACATG
Found at i:2527 original size:12 final size:12
Alignment explanation
Indices: 2463--2527 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
2453 GAACATATAA
2463 ACGAACATGTTC
1 ACGAACATGTTC
* **
2475 ACGAACATATAA
1 ACGAACATGTTC
*
2487 ACAAACATGTTC
1 ACGAACATGTTC
* *
2499 ACGAGC--GTTAA
1 ACGAACATGTT-C
2510 ACGAACATGTTC
1 ACGAACATGTTC
2522 ACGAAC
1 ACGAAC
2528 GTTAAACGAA
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
10 3 0.08
11 5 0.13
12 27 0.71
13 3 0.08
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (12 bp):
ACGAACATGTTC
Found at i:2527 original size:59 final size:59
Alignment explanation
Indices: 2400--2517 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
2390 TCGCGAATGC
* ** * *
2400 ATAAACGAACATATTCGCGAATGTATAAACGAACATATTCGCGAACATTAAACGAACAT
1 ATAAACGAACATATTCACGAACATATAAACAAACATATTCACGAACATTAAACGAACAT
* * * *
2459 ATAAACGAACATGTTCACGAACATATAAACAAACATGTTCACGAGCGTTAAACGAACAT
1 ATAAACGAACATATTCACGAACATATAAACAAACATATTCACGAACATTAAACGAACAT
2518 GTTCACGAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (59 bp):
ATAAACGAACATATTCACGAACATATAAACAAACATATTCACGAACATTAAACGAACAT
Found at i:2568 original size:23 final size:23
Alignment explanation
Indices: 2451--2566 Score: 160
Period size: 23 Copynumber: 5.0 Consensus size: 23
2441 CGAACATTAA
*
2451 ACGAACATATAAACGAACATGTTC
1 ACGAACGT-TAAACGAACATGTTC
* *
2475 ACGAACATATAAACAAACATGTTC
1 ACGAACGT-TAAACGAACATGTTC
*
2499 ACGAGCGTTAAACGAACATGTTC
1 ACGAACGTTAAACGAACATGTTC
*
2522 ACGAACGTTAAACGAACATGTTT
1 ACGAACGTTAAACGAACATGTTC
*
2545 GCGAACGTTAAACGAACATGTT
1 ACGAACGTTAAACGAACATGTT
2567 TGTGAACGAT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
23 56 0.66
24 29 0.34
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.22
Consensus pattern (23 bp):
ACGAACGTTAAACGAACATGTTC
Found at i:2573 original size:23 final size:23
Alignment explanation
Indices: 2460--2584 Score: 133
Period size: 23 Copynumber: 5.4 Consensus size: 23
2450 AACGAACATA
** *
2460 TAAACGAACATGTTCACGAACAT
1 TAAACGAACATGTTTGCGAACGT
* ** *
2483 ATAAACAAACATGTTCACGAGCGT
1 -TAAACGAACATGTTTGCGAACGT
**
2507 TAAACGAACATGTTCACGAACGT
1 TAAACGAACATGTTTGCGAACGT
2530 TAAACGAACATGTTTGCGAACGT
1 TAAACGAACATGTTTGCGAACGT
* *
2553 TAAACGAACATGTTTGTGAACGA
1 TAAACGAACATGTTTGCGAACGT
*
2576 TAAATGAAC
1 TAAACGAAC
2585 GAGCACGAAC
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
23 71 0.78
24 20 0.22
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (23 bp):
TAAACGAACATGTTTGCGAACGT
Found at i:9383 original size:15 final size:14
Alignment explanation
Indices: 9356--9382 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9346 GGGTATTGTA
9356 AAATATTAAAAAAT
1 AAATATTAAAAAAT
9370 AAATATTAAAAAA
1 AAATATTAAAAAA
9383 AAAAAAGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:14262 original size:18 final size:20
Alignment explanation
Indices: 14220--14279 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 20
14210 CTTTCATTAA
**
14220 ATTTTAATCCATTATTTTAGT
1 ATTTTAATCC-TTATTTTTTT
14241 -TTTTAA-CCTT-TTTTTTT
1 ATTTTAATCCTTATTTTTTT
14258 ATTTTAATCCTTAATTTTTTT
1 ATTTTAATCCTT-ATTTTTTT
14279 A
1 A
14280 CTTCGACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 5 0.15
18 8 0.24
19 6 0.18
20 6 0.18
21 8 0.24
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTTAATCCTTATTTTTTT
Found at i:14269 original size:19 final size:19
Alignment explanation
Indices: 14241--14279 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
14231 TTATTTTAGT
14241 TTTTAACCTT-TTTTTTTA
1 TTTTAACCTTATTTTTTTA
14259 TTTTAATCCTTAATTTTTTTA
1 TTTTAA-CCTT-ATTTTTTTA
14280 CTTCGACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
21 8 0.44
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAACCTTATTTTTTTA
Found at i:16235 original size:6 final size:6
Alignment explanation
Indices: 16226--16263 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
16216 TTATACGTCA
*
16226 TCCCTT TCCCTT TCCCTT TCCCTT TCCTTT TCCCTT TC
1 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TC
16264 ATACAATCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
TCCCTT
Found at i:16844 original size:2 final size:2
Alignment explanation
Indices: 16837--16863 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16827 TATCTCTTTA
16837 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16864 AAGCGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28314 original size:2 final size:2
Alignment explanation
Indices: 28307--28336 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28297 GTTGTATACA
28307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28337 GTGCGCGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31850 original size:68 final size:69
Alignment explanation
Indices: 31724--31855 Score: 167
Period size: 68 Copynumber: 1.9 Consensus size: 69
31714 ATGCTCCATC
* * * *
31724 AACTCCTCCTTCAGCTTATCCAAGCTTGTTTGGGAGTCTTACAGGGCTGAGCTACTGCTGCCTTA
1 AACTCCTCCTTCAGCTTAT-C-AGCTTGTTTGGGAATCTCACAGAGCTGAGCTACTGCTACCTTA
31789 CCTTAA
64 CCTTAA
* * * *
31795 AACTCCTCCTTCAGCTTAT-AGCTTGTTTGGGAATCTCATAGAGTTGAGTTGCTGCTACCTT
1 AACTCCTCCTTCAGCTTATCAGCTTGTTTGGGAATCTCACAGAGCTGAGCTACTGCTACCTT
31856 CTCAACAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
68 34 0.64
71 19 0.36
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (69 bp):
AACTCCTCCTTCAGCTTATCAGCTTGTTTGGGAATCTCACAGAGCTGAGCTACTGCTACCTTACC
TTAA
Found at i:51818 original size:26 final size:26
Alignment explanation
Indices: 51675--51812 Score: 125
Period size: 26 Copynumber: 5.3 Consensus size: 26
51665 AAACTACTGA
51675 ACTAGCTCGAAAGAGCGATATATTGT
1 ACTAGCTCGAAAGAGCGATATATTGT
* * * * *
51701 ACTGGCTCAAAAGAGCAATTTATTGA
1 ACTAGCTCGAAAGAGCGATATATTGT
* * *
51727 ACTAGCTCGAAAGAGCGATTTACTCT
1 ACTAGCTCGAAAGAGCGATATATTGT
* * * **
51753 ACTATCTCGAAAGAGTGATATAATAA
1 ACTAGCTCGAAAGAGCGATATATTGT
* *
51779 ACT-GACTCGTAAGAGTGATATATTGT
1 ACTAG-CTCGAAAGAGCGATATATTGT
51805 ACTAGCTC
1 ACTAGCTC
51813 ATAAGAACAA
Statistics
Matches: 88, Mismatches: 22, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
26 87 0.99
27 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (26 bp):
ACTAGCTCGAAAGAGCGATATATTGT
Found at i:54243 original size:25 final size:24
Alignment explanation
Indices: 54162--54251 Score: 69
Period size: 24 Copynumber: 3.8 Consensus size: 24
54152 CTAGGCTTAA
* * *
54162 ATGAGCTAACTTATCTAGGCTCAT
1 ATGAGCTAACTTTTCTGGGCTCGT
*
54186 -TGGAGCTAACCTATT-TGGGCTCGT
1 AT-GAGCTAA-CTTTTCTGGGCTCGT
* *
54210 ATTAACTAATCTTTTCTGGGCTCGT
1 ATGAGCTAA-CTTTTCTGGGCTCGT
*
54235 ATGAGCTAA-ATTTCTGG
1 ATGAGCTAACTTTTCTGG
54252 AAGATTTAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
23 8 0.16
24 23 0.45
25 20 0.39
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (24 bp):
ATGAGCTAACTTTTCTGGGCTCGT
Found at i:56827 original size:20 final size:20
Alignment explanation
Indices: 56804--56849 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
56794 GTTAAAATGT
56804 TTTTAAACAAGTCAAAATAA
1 TTTTAAACAAGTCAAAATAA
** *
56824 TTTTAGCCAAGTCAAAATCA
1 TTTTAAACAAGTCAAAATAA
56844 TTTTAA
1 TTTTAA
56850 CCATGTAGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (20 bp):
TTTTAAACAAGTCAAAATAA
Found at i:66007 original size:182 final size:183
Alignment explanation
Indices: 65702--66062 Score: 661
Period size: 182 Copynumber: 2.0 Consensus size: 183
65692 TGAATAATTA
*
65702 TATATATATATATATATAATTGACCACTTAATTTAAAAAAAAAATTGGATTTGAGGTTAACTGTG
1 TATATATATATATATATAATTGACCACTTAATTTAAAAAAAAAATTAGATTTGAGGTTAACTGTG
* *
65767 TATCATTTACCAATGGGTATTTTGATCAAATTCCTGGAAGATTTTTGGGATTTTTGCCTAAACCC
66 TACCATTTACCAATGGGTATTTTGATCAAATTCCTGAAAGATTTTTGGGATTTTTGCCTAAACCC
*
65832 GATAATGAAGTAAATTCAAGATATAGAATAAAAATCTTATATCTCATACCAAT
131 GATAATGAAATAAATTCAAGATATAGAATAAAAATCTTATATCTCATACCAAT
*
65885 TATATATATATATATATAATTGACCACTTAATTT-TAAAAAAAATTAGATTTGAGGTTAACTGTG
1 TATATATATATATATATAATTGACCACTTAATTTAAAAAAAAAATTAGATTTGAGGTTAACTGTG
65949 TACCATTTACCAATGGGTATTTTGATCAAATTCCTGAAAGATTTTTGGGATTTTTGCCTAAACCC
66 TACCATTTACCAATGGGTATTTTGATCAAATTCCTGAAAGATTTTTGGGATTTTTGCCTAAACCC
*
66014 GATAATGAAATAAATTTAAGATATAGAATAAAAATCTTATATCTCATAC
131 GATAATGAAATAAATTCAAGATATAGAATAAAAATCTTATATCTCATAC
66063 AGAAGACTTG
Statistics
Matches: 172, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
182 138 0.80
183 34 0.20
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (183 bp):
TATATATATATATATATAATTGACCACTTAATTTAAAAAAAAAATTAGATTTGAGGTTAACTGTG
TACCATTTACCAATGGGTATTTTGATCAAATTCCTGAAAGATTTTTGGGATTTTTGCCTAAACCC
GATAATGAAATAAATTCAAGATATAGAATAAAAATCTTATATCTCATACCAAT
Found at i:69387 original size:55 final size:55
Alignment explanation
Indices: 69324--69434 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
69314 GTGAGAAATG
*
69324 TATGATAGGCTATGTGTGAGAAATAATTTACGTGAAAATTATCAACGGTGAGTTT
1 TATGATAGGCTATGTGTGAGAAATAATTTACGTGAAAATTATCAACGGCGAGTTT
69379 TATGATAGGCTATGTGTGAGAAATAATTTACGTGAAAATTATCAACGGCGAGTTT
1 TATGATAGGCTATGTGTGAGAAATAATTTACGTGAAAATTATCAACGGCGAGTTT
69434 T
1 T
69435 GGTTCAGTGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.34
Consensus pattern (55 bp):
TATGATAGGCTATGTGTGAGAAATAATTTACGTGAAAATTATCAACGGCGAGTTT
Found at i:74915 original size:29 final size:29
Alignment explanation
Indices: 74866--74923 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
74856 CGTTTAGATA
* *
74866 CCTTATTAGTTTGGCAGTATGAAAAGCTT
1 CCTTATTAGTTTGACAATATGAAAAGCTT
74895 CCTTATTAGTTTGACAATATGAAAAGCTT
1 CCTTATTAGTTTGACAATATGAAAAGCTT
74924 TGCATGCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (29 bp):
CCTTATTAGTTTGACAATATGAAAAGCTT
Found at i:77092 original size:38 final size:38
Alignment explanation
Indices: 77011--77093 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
77001 TAATTTTTTG
* * * * *
77011 TAAAGAATTTCATTAAAATTTTTAAATTAATTATTTTTT
1 TAAA-AATTTCATTAAAATTTTTAAATAAACTAATATTA
77050 TAAAAATTTCATTAAAATATTTTAAA-AAACTAATATTA
1 TAAAAATTTCATTAAAAT-TTTTAAATAAACTAATATTA
77088 TAAAAA
1 TAAAAA
77094 ATATTACAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (38 bp):
TAAAAATTTCATTAAAATTTTTAAATAAACTAATATTA
Found at i:85555 original size:30 final size:30
Alignment explanation
Indices: 85521--85590 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
85511 GCCCAAGGTG
85521 CCAAAGAAGAAACCAAAAAAGCCTAAAGAA
1 CCAAAGAAGAAACCAAAAAAGCCTAAAGAA
* **
85551 CCAAAGAAGAAACCCAGCAAGCCTAAAGAA
1 CCAAAGAAGAAACCAAAAAAGCCTAAAGAA
* *
85581 GCTAAGAAGA
1 CCAAAGAAGA
85591 GATCGGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.57, C:0.21, G:0.17, T:0.04
Consensus pattern (30 bp):
CCAAAGAAGAAACCAAAAAAGCCTAAAGAA
Found at i:88658 original size:18 final size:18
Alignment explanation
Indices: 88637--88681 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
88627 TATTCAAATT
88637 CAACCACAATCACGACTA
1 CAACCACAATCACGACTA
88655 CAACCACAATCACGACTA
1 CAACCACAATCACGACTA
88673 CAACCACAA
1 CAACCACAA
88682 CCATCTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.47, C:0.40, G:0.04, T:0.09
Consensus pattern (18 bp):
CAACCACAATCACGACTA
Found at i:92639 original size:21 final size:21
Alignment explanation
Indices: 92600--92639 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
92590 GAGGATGAAC
* *
92600 ATCATGTGGAAGAGGAAGCCA
1 ATCATGTAGAAGAGCAAGCCA
*
92621 ATCATGTAGATGAGCAAGC
1 ATCATGTAGAAGAGCAAGC
92640 GAAGAAGGAA
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:0.38, C:0.15, G:0.30, T:0.17
Consensus pattern (21 bp):
ATCATGTAGAAGAGCAAGCCA
Found at i:96153 original size:21 final size:21
Alignment explanation
Indices: 96115--96154 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
96105 ACATACAGTA
*
96115 TTTAAATATCAATTTAATTTC
1 TTTAAATATCAATGTAATTTC
96136 TTTAAAT-TCAGATGTAATT
1 TTTAAATATCA-ATGTAATT
96155 ATAACTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTAAATATCAATGTAATTTC
Found at i:97187 original size:27 final size:27
Alignment explanation
Indices: 97130--97308 Score: 164
Period size: 27 Copynumber: 6.6 Consensus size: 27
97120 ATATAACTCA
* *
97130 TTCGAGCCAGATTCAGAA-ATTGGCT-T
1 TTCGAGCCAGATACAGAATAAT-GCTCT
* * *
97156 ATTCAAGCCAAACACAGAATAATGCTCT
1 -TTCGAGCCAGATACAGAATAATGCTCT
* *
97184 TTCAAGCCAGATATAGAATAATGCTCT
1 TTCGAGCCAGATACAGAATAATGCTCT
* *
97211 TTCGATCCAGATATAGAATAATGCTCT
1 TTCGAGCCAGATACAGAATAATGCTCT
* * *
97238 TTTGACCCAGATACAAAATAATGCTCT
1 TTCGAGCCAGATACAGAATAATGCTCT
* * *
97265 TTCGAGCTAGATACAGAATGATGCTCC
1 TTCGAGCCAGATACAGAATAATGCTCT
* * *
97292 CTCGATCCAGCTACAGA
1 TTCGAGCCAGATACAGA
97309 GTATTTCTTA
Statistics
Matches: 126, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
27 123 0.98
28 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (27 bp):
TTCGAGCCAGATACAGAATAATGCTCT
Found at i:100581 original size:12 final size:12
Alignment explanation
Indices: 100559--100592 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
100549 TCAAATCTTG
100559 CTTTCATTTTCTA
1 CTTT-ATTTTCTA
*
100572 TTTTATTTTCTA
1 CTTTATTTTCTA
100584 CTTTATTTT
1 CTTTATTTT
100593 ATGTTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (12 bp):
CTTTATTTTCTA
Found at i:100943 original size:14 final size:13
Alignment explanation
Indices: 100926--100970 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
100916 TAGATACGAT
100926 TTTATTTTATTTTA
1 TTTATTTT-TTTTA
*
100940 TTTATTTTTTGTA
1 TTTATTTTTTTTA
*
100953 TTTCATTTTCTTTA
1 TTT-ATTTTTTTTA
100967 TTTA
1 TTTA
100971 ATTAATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATTTTTTTTA
Found at i:107196 original size:22 final size:24
Alignment explanation
Indices: 107162--107210 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
107152 AGAGAGAAAA
*
107162 AAAGGAGAAG-AAA-TGTTTTTTT
1 AAAGGAGAAGAAAATTGATTTTTT
107184 AAAGGA-AAGGAAAATTGATTTTTT
1 AAAGGAGAA-GAAAATTGATTTTTT
107208 AAA
1 AAA
107211 TTTTTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 2 0.09
22 7 0.30
23 3 0.13
24 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (24 bp):
AAAGGAGAAGAAAATTGATTTTTT
Found at i:107429 original size:18 final size:19
Alignment explanation
Indices: 107400--107443 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
107390 AATATCGTCC
107400 TTTTAA-TTT-CCCATTTA
1 TTTTAATTTTCCCCATTTA
*
107417 TTTTAATTTTCCCCGTTTA
1 TTTTAATTTTCCCCATTTA
107436 TTTTAATT
1 TTTTAATT
107444 ATGATGCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 3 0.12
19 15 0.62
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTAATTTTCCCCATTTA
Found at i:107745 original size:21 final size:19
Alignment explanation
Indices: 107680--107748 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 19
107670 TTTGTCTCCT
107680 TTATTATTATTTTTTATTA
1 TTATTATTATTTTTTATTA
*
107699 TTTTTGAATTTATTTTATATATTA
1 TTATT--A-TTATTTT-T-TATTA
107723 TTATTATTATTTGTTTATCTA
1 TTATTATTATTT-TTTAT-TA
107744 TTATT
1 TTATT
107749 TATTTCTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
19 4 0.10
20 3 0.07
21 15 0.37
22 9 0.22
23 1 0.02
24 9 0.22
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (19 bp):
TTATTATTATTTTTTATTA
Found at i:110598 original size:79 final size:79
Alignment explanation
Indices: 110463--110614 Score: 207
Period size: 79 Copynumber: 1.9 Consensus size: 79
110453 TTCAACCATT
* * ** * *
110463 TTGTCAACTCTTGGCACCCGATGCCTAGCAGATAAACAGTGATTAATGAGCTCAGCTCTAGTTGG
1 TTGTCAACTCATGGCACCCAATGCCTAGCAGATAAACAGCAATAAATGAGCCCAGCTCTAGTTGG
110528 ATTAACCATCAAAC
66 ATTAACCATCAAAC
* * *
110542 TTGTCAATTCATGGCACCTAATGCCTAGCGGATAAATC-GCAATAAATGAGCCCAGCTCTAGTTG
1 TTGTCAACTCATGGCACCCAATGCCTAGCAGATAAA-CAGCAATAAATGAGCCCAGCTCTAGTTG
110606 GATTAACCA
65 GATTAACCA
110615 ATGGATTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 62 0.98
80 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (79 bp):
TTGTCAACTCATGGCACCCAATGCCTAGCAGATAAACAGCAATAAATGAGCCCAGCTCTAGTTGG
ATTAACCATCAAAC
Found at i:117366 original size:21 final size:21
Alignment explanation
Indices: 117335--117393 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
117325 TAGATGTATG
*
117335 ACTTATTTCGGTAGAAGAGTC
1 ACTTATATCGGTAGAAGAGTC
* * * *
117356 TCTTGTATCGGTAAAACAGTC
1 ACTTATATCGGTAGAAGAGTC
117377 ACTTATATCGGTAGAAG
1 ACTTATATCGGTAGAAG
117394 TCTGCATTGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTTATATCGGTAGAAGAGTC
Found at i:124339 original size:32 final size:32
Alignment explanation
Indices: 124279--124339 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
124269 TAAATTAGTA
* *
124279 TATTACTAATAGATAAAAAAATAATATAAAAC
1 TATTACTAATACATAAAAAAACAATATAAAAC
* * *
124311 TATTAGTAATACATAAAATAACATTATAA
1 TATTACTAATACATAAAAAAACAATATAA
124340 TATGTAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (32 bp):
TATTACTAATACATAAAAAAACAATATAAAAC
Found at i:127222 original size:7 final size:7
Alignment explanation
Indices: 127210--127237 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
127200 CCAAGTCAGA
127210 ATCAAAT
1 ATCAAAT
127217 ATCAAAT
1 ATCAAAT
127224 ATCAAAT
1 ATCAAAT
127231 ATCAAAT
1 ATCAAAT
127238 CTCACATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCAAAT
Found at i:142108 original size:17 final size:17
Alignment explanation
Indices: 142088--142127 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
142078 TAGATGCAGC
*
142088 GACAATAAAAATGCAAT
1 GACAATAAAAATGCAAG
* *
142105 GACATTAATAATGCAAG
1 GACAATAAAAATGCAAG
142122 GACAAT
1 GACAAT
142128 TATACAACAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (17 bp):
GACAATAAAAATGCAAG
Found at i:146119 original size:45 final size:44
Alignment explanation
Indices: 146067--146151 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
146057 AATATTAATT
* *
146067 AAATTGTGATAATTATTCATTTAAAAAATAATTATAGTTTAATAA
1 AAATTGTGATAACTATTCATTT-AAAAATAATTATAATTTAATAA
*
146112 AAATTGTGATAACTATTCATTTAAAAATAGTTATAATTTA
1 AAATTGTGATAACTATTCATTTAAAAATAATTATAATTTA
146152 TCGATTAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 16 0.43
45 21 0.57
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (44 bp):
AAATTGTGATAACTATTCATTTAAAAATAATTATAATTTAATAA
Found at i:146912 original size:21 final size:21
Alignment explanation
Indices: 146867--146912 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
146857 AAAATGGCTT
*
146867 TTAAATTTTTTTTTTGAAAAA
1 TTAATTTTTTTTTTTGAAAAA
*
146888 -TAATTTTTTTTTTTTAAAAA
1 TTAATTTTTTTTTTTGAAAAA
146908 TTAAT
1 TTAAT
146913 AATTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTAATTTTTTTTTTTGAAAAA
Found at i:146918 original size:21 final size:21
Alignment explanation
Indices: 146873--146920 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
146863 GCTTTTAAAT
*
146873 TTTTTTTTTGAAAAATAAT-T
1 TTTTTTTTTGAAAAATAATAA
*
146893 TTTTTTTTTTAAAAATTAATAA
1 TTTTTTTTTGAAAAA-TAATAA
146915 TTTTTT
1 TTTTTT
146921 ATGTTTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.58
21 4 0.17
22 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTTTTTGAAAAATAATAA
Found at i:149036 original size:28 final size:27
Alignment explanation
Indices: 149004--149085 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
148994 ATATATTTAT
149004 AATTTTTATAAATTTTTAAATAAATTAA
1 AATTTTTA-AAATTTTTAAATAAATTAA
* **
149032 AA-TTTTAAATATTTTTATAATAATTTTT
1 AATTTTTAAA-ATTTTTA-AATAAATTAA
* *
149060 TATTTTTAAAACTTTTAAA-AAATTAA
1 AATTTTTAAAATTTTTAAATAAATTAA
149086 TTAATTATTG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
26 6 0.14
27 14 0.33
28 16 0.37
29 7 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (27 bp):
AATTTTTAAAATTTTTAAATAAATTAA
Found at i:149066 original size:46 final size:51
Alignment explanation
Indices: 148972--149069 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 51
148962 TTGATTTTTT
*
148972 TAAATTAAAAATTATTAAATATATATATTTATAATTTTTATAAATTTTTAAA
1 TAAATTAAAAATTATTAAATATATATATTAATAATTTTTAT-AATTTTTAAA
* *
149024 TAAATT-AAAATT-TTAAATATTTTTA-TAATAATTTTT-T-ATTTTTAAA
1 TAAATTAAAAATTATTAAATATATATATTAATAATTTTTATAATTTTTAAA
149070 ACTTTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
46 9 0.21
48 1 0.02
49 10 0.23
50 11 0.26
51 6 0.14
52 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (51 bp):
TAAATTAAAAATTATTAAATATATATATTAATAATTTTTATAATTTTTAAA
Found at i:155123 original size:18 final size:18
Alignment explanation
Indices: 155102--155162 Score: 122
Period size: 18 Copynumber: 3.4 Consensus size: 18
155092 AAGGACTCTT
155102 TGGTAATAGAAGTAAAAG
1 TGGTAATAGAAGTAAAAG
155120 TGGTAATAGAAGTAAAAG
1 TGGTAATAGAAGTAAAAG
155138 TGGTAATAGAAGTAAAAG
1 TGGTAATAGAAGTAAAAG
155156 TGGTAAT
1 TGGTAAT
155163 TATTAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.25
Consensus pattern (18 bp):
TGGTAATAGAAGTAAAAG
Found at i:155696 original size:21 final size:21
Alignment explanation
Indices: 155646--155696 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
155636 GTTATGTAAA
*
155646 GCCCTTGTATTGCACTCCGGT
1 GCCCTTGTATCGCACTCCGGT
* *
155667 GCTCTTGTATCGCACTTCGGT
1 GCCCTTGTATCGCACTCCGGT
*
155688 GCCCCTGTA
1 GCCCTTGTA
155697 ATGTACCTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.10, C:0.33, G:0.24, T:0.33
Consensus pattern (21 bp):
GCCCTTGTATCGCACTCCGGT
Found at i:156800 original size:15 final size:15
Alignment explanation
Indices: 156780--156809 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
156770 GAATGAGTGA
156780 TAATTAAAATAAATG
1 TAATTAAAATAAATG
*
156795 TAATTAAACTAAATG
1 TAATTAAAATAAATG
156810 CAAATGATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (15 bp):
TAATTAAAATAAATG
Found at i:157384 original size:19 final size:19
Alignment explanation
Indices: 157330--157387 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
157320 TATTTAATTG
*
157330 TTTATTCTGACATTTAATTTA
1 TTTATT-TGTCATTT-ATTTA
* * **
157351 TTGATTTTTTGTTTATTTA
1 TTTATTTGTCATTTATTTA
157370 TTTATTTGTCATTTATTT
1 TTTATTTGTCATTTATTT
157388 TCATGCCTAA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 19 0.68
20 4 0.14
21 5 0.18
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTATTTGTCATTTATTTA
Found at i:159992 original size:24 final size:24
Alignment explanation
Indices: 159956--160001 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
159946 ACATTCATCC
* *
159956 AATTCATGCATTA-GCATTCAAAAG
1 AATTCAAGAATTACGCA-TCAAAAG
159980 AATTCAAGAATTACGCATCAAA
1 AATTCAAGAATTACGCATCAAA
160002 TGAAAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
AATTCAAGAATTACGCATCAAAAG
Found at i:161891 original size:17 final size:17
Alignment explanation
Indices: 161869--161904 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
161859 TTCCCAACGC
161869 AGTCGAGAAATTGTTCT
1 AGTCGAGAAATTGTTCT
161886 AGTCGAGAAATTGTTCT
1 AGTCGAGAAATTGTTCT
161903 AG
1 AG
161905 CGACTTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (17 bp):
AGTCGAGAAATTGTTCT
Found at i:166730 original size:18 final size:18
Alignment explanation
Indices: 166709--166748 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
166699 TTATATGACT
* *
166709 GCATCTGATTTTGTGATC
1 GCATCCGATCTTGTGATC
*
166727 GCATCCGGTCTTGTGATC
1 GCATCCGATCTTGTGATC
166745 GCAT
1 GCAT
166749 TTTATTTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (18 bp):
GCATCCGATCTTGTGATC
Found at i:175987 original size:6 final size:6
Alignment explanation
Indices: 175971--176059 Score: 98
Period size: 6 Copynumber: 15.3 Consensus size: 6
175961 TCAAACTAGC
* *
175971 AAAAAG AAAAA- AGAAAAG -AAAAG AAAAAG --AGAG AAGAAAG AAAAAT
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG
*
176017 AAAAAG AAAAAG AAAAAG AAAAA- AAGAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
176060 GAGGTCGAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
4 3 0.04
5 10 0.14
6 52 0.74
7 5 0.07
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:175994 original size:17 final size:17
Alignment explanation
Indices: 175972--176055 Score: 86
Period size: 17 Copynumber: 4.9 Consensus size: 17
175962 CAAACTAGCA
175972 AAAAGAAAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
*
175989 AAAAGAAAAAGAGAGAAG
1 AAAAGAAAAA-AGAAAAG
176007 -AAAGAAAAATA-AAAAG
1 AAAAGAAAAA-AGAAAAG
*
176023 AAAA-AGAAAAAGAAAAA
1 AAAAGA-AAAAAGAAAAG
176040 AAGAAG-AAAAAGAAAA
1 AA-AAGAAAAAAGAAAA
176056 AGAAGAGGTC
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
16 6 0.11
17 43 0.75
18 8 0.14
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:176035 original size:35 final size:33
Alignment explanation
Indices: 175971--176059 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 33
175961 TCAAACTAGC
*
175971 AAAAAGAAAAAAGAAAAG-AAAAGAAAAAGAGAGA
1 AAAAAGAAAAAA-AAAAGAAAAAGAAAAAGA-AAA
*
176005 AGAAAGAAAAATAAAAAGAAAAAGAAAAAGAAAA
1 AAAAAGAAAAA-AAAAAGAAAAAGAAAAAGAAAA
176039 AAAGAAGAAAAAGAAAAAGAA
1 AAA-AAGAAAAA-AAAAAGAA
176060 GAGGTCGAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 19 0.40
35 29 0.60
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (33 bp):
AAAAAGAAAAAAAAAAGAAAAAGAAAAAGAAAA
Found at i:176056 original size:23 final size:23
Alignment explanation
Indices: 175971--176059 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 23
175961 TCAAACTAGC
175971 AAAAAGAAAAAAGAAAAGAAAAGAA-
1 AAAAAG-AAAAAG-AAA-AAAAGAAG
*
175996 AAAGAGAGAAGAAAGAAAAATAAAAAG
1 AAA-A-AGAA-AAAGAAAAA-AAGAAG
176023 AAAAAGAAAAAGAAAAAAAGAAG
1 AAAAAGAAAAAGAAAAAAAGAAG
176046 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
176060 GAGGTCGAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
23 19 0.33
24 9 0.16
25 9 0.16
26 11 0.19
27 9 0.16
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (23 bp):
AAAAAGAAAAAGAAAAAAAGAAG
Found at i:179451 original size:49 final size:49
Alignment explanation
Indices: 178691--179445 Score: 473
Period size: 49 Copynumber: 15.4 Consensus size: 49
178681 ATAGAGTTTA
* * * * *
178691 AAGAGGAATAGGTTGAAGCCGCAAC-AGCGGACCTAACATCCTAAAACCA
1 AAGAGGGATAGATTGAAGCCGCAACGA-CGGACCTAACACCCTAAAATCG
* * *** * * *
178740 AAAAGGGATAGGTTGAAATTGTAACAATGGACCTAACATCCC-AAAATCG
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACA-CCCTAAAATCG
* * ** ** * *
178789 AAGAGGGATAGATTCAAGTCGCAACGACAAATTTAACACCCTAAAACCA
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
* * * * * * * *
178838 AAAAGGGAAAGATTGAATCCACAACGACGGATCTTACACCTTAAAATTG
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
* * * *
178887 AAGAGAGATAGGTTGAAGCCGCAACGGCGGACCTAACATCCTAAAATCG
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
* * * *
178936 AAGAGGGATAGATTGAAGTCGTAACGACAGATCTAACACCCTAAAA-CTG
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATC-G
* * * * * * * * *
178985 AAGAGGGAAAAATTGAAGCAGTAACGGCGGATCTTACACCTTAAAATTG
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
* * ** * *
179034 AAGAGGGATAGGTTGAAGCCGTAACGACAAACCTAACACCC-AAAAACTA
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATC-G
* * * * * * * *
179083 AAGAGGGAAAGATTAAAGTCACAACGACAGATCTTACACCTTAAAATCG
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
* * * * * *
179132 AAGAGGGATAGGTTGAAGTCGTAATGATGGACCTAACACCCTAAAA-CTA
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATC-G
* * * * * *
179181 AAAAGGGATAGATTGAAGCCGTAAC-AGTGGATCTAACACCCTAAAACCA
1 AAGAGGGATAGATTGAAGCCGCAACGA-CGGACCTAACACCCTAAAATCG
* * * * * * * * *
179230 AAAAGGGAAAGGTTGAAGCCGTAATGGCGGACCTTACACCTTAAAATTG
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
* * * *
179279 AAGAGGGATATG-TTGAAGCCGTAATGGCAGACCTAACACCCTAAAATCG
1 AAGAGGGATA-GATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
* ** * * * * * * *
179328 AAGAGGGAAAGATTGAAATCACAACGATGGATCTTACATCTTAAAATTG
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
* * * * * *
179377 AAGAGGGATAGGTTCAAGCTGCGACGACAGACCTAACACCCTAAAA-CC
1 AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
179425 AAGGAGGGATAGATTGAAGCC
1 AA-GAGGGATAGATTGAAGCC
179446 ACGACGGTGG
Statistics
Matches: 533, Mismatches: 159, Indels: 28
0.74 0.22 0.04
Matches are distributed among these distances:
48 13 0.02
49 510 0.96
50 10 0.02
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (49 bp):
AAGAGGGATAGATTGAAGCCGCAACGACGGACCTAACACCCTAAAATCG
Found at i:179482 original size:98 final size:98
Alignment explanation
Indices: 179306--179482 Score: 223
Period size: 98 Copynumber: 1.8 Consensus size: 98
179296 GCCGTAATGG
* * *
179306 CAGACCTAACACCCTAAAATCGAAGAGGGAAAGATTGAAATCACAACGATGGATCTTACATCTTA
1 CAGACCTAACACCCTAAAATCCAAGAGGGAAAGATTGAAACCACAACGATGGATCTTACACCTTA
*** *
179371 AAATTGAAGAGGGATAGGTTCAAGCTGCGACGA
66 AAACCAAAAAGGGATAGGTTCAAGCTGCGACGA
* * * *
179404 CAGACCTAACACCCTAAAA-CCAAGGAGGGATAGATTGAAGCCACGACGGTGGATC-TATCACCT
1 CAGACCTAACACCCTAAAATCCAA-GAGGGAAAGATTGAAACCACAACGATGGATCTTA-CACCT
179467 TAAAACCAAAAAGGGA
64 TAAAACCAAAAAGGGA
179483 ACAAATTGAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
97 5 0.08
98 61 0.92
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (98 bp):
CAGACCTAACACCCTAAAATCCAAGAGGGAAAGATTGAAACCACAACGATGGATCTTACACCTTA
AAACCAAAAAGGGATAGGTTCAAGCTGCGACGA
Found at i:180522 original size:6 final size:6
Alignment explanation
Indices: 180511--180544 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
180501 TTAGCATTTA
180511 ATTTTT ATTTTT ATTTTT ATTTTT -TTGTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATT-TTT ATTT
180545 ATCTTGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.08
6 22 0.85
7 2 0.08
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:180597 original size:23 final size:23
Alignment explanation
Indices: 180538--180598 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 23
180528 TATTTTTTTG
* *
180538 TTTATTTATCTTGTTGTTATTTAT
1 TTTA-TTATTTTGTTGTTATCTAT
*
180562 TTTCATGTCATTTTGTTGTTATCTCT
1 TTT-AT-T-ATTTTGTTGTTATCTAT
180588 TTTATTATTTT
1 TTTATTATTTT
180599 TATTTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 5 0.16
24 5 0.16
25 4 0.13
26 17 0.55
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (23 bp):
TTTATTATTTTGTTGTTATCTAT
Found at i:181994 original size:24 final size:24
Alignment explanation
Indices: 181955--182006 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
181945 TTTTGCTGAT
* *
181955 GGCTCTCCAAGTTGGCTGACCAAG
1 GGCTCTCCAAGATGGCCGACCAAG
*
181979 GGCTCTCCGAGATGGCCGACCAAG
1 GGCTCTCCAAGATGGCCGACCAAG
182003 GGCT
1 GGCT
182007 TTTTAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (24 bp):
GGCTCTCCAAGATGGCCGACCAAG
Found at i:187826 original size:13 final size:13
Alignment explanation
Indices: 187808--187833 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
187798 GTAGCAACAT
187808 TAAAAAATTTGGA
1 TAAAAAATTTGGA
187821 TAAAAAATTTGGA
1 TAAAAAATTTGGA
187834 AAACCAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
TAAAAAATTTGGA
Found at i:189119 original size:111 final size:111
Alignment explanation
Indices: 188915--189121 Score: 324
Period size: 111 Copynumber: 1.9 Consensus size: 111
188905 GGAGAATGCC
* * * * *
188915 TTAGAGTTTAACTCTTTAGAGGATGGAGAAGGTGAAGAAAACATGGTTTTGATGGAAGCCAATCC
1 TTAGAGTTTAACCCTTTAGAGGATGAAAAAGGTGAAGAAAACATGGGTTTGATGGAAGCAAATCC
* *
188980 GAGAAATTTTATTCAATCCGCATGGTTTGAACCATTAGAGGGAGCT
66 GAGAAATTTTATTCAATCCACATAGTTTGAACCATTAGAGGGAGCT
* *
189026 TTAGAGTTTGACCCTTTAGAGGATGAAAAAGGTGAAGAAAACATGGGTTTGATGGAAGCAAATCT
1 TTAGAGTTTAACCCTTTAGAGGATGAAAAAGGTGAAGAAAACATGGGTTTGATGGAAGCAAATCC
*
189091 GAGAAATTTTATTCAATCCATATAGTTTGAA
66 GAGAAATTTTATTCAATCCACATAGTTTGAA
189122 TCGTTGGAGT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 86 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (111 bp):
TTAGAGTTTAACCCTTTAGAGGATGAAAAAGGTGAAGAAAACATGGGTTTGATGGAAGCAAATCC
GAGAAATTTTATTCAATCCACATAGTTTGAACCATTAGAGGGAGCT
Found at i:211941 original size:141 final size:141
Alignment explanation
Indices: 211687--211969 Score: 476
Period size: 141 Copynumber: 2.0 Consensus size: 141
211677 AGACAAGGTC
* * * *
211687 ATGGAGAAACTCAGTACTCACTGGAAGTGATTCATCAGTATGTCATAATAAAATTCTATCTTGAA
1 ATGGAGAAACTCAATACTCACCGGAAGTGATTCATAAGTAAGTCATAATAAAATTCTATCTTGAA
*
211752 TATGACTTGTGTAATTAAGTTATTAAAAAGAAAGTTAGGCAAGGAAATGGATATATGTTAGCTTA
66 TATGACTTGTGTAATTAAGTTATTAAAAAGAAAGTTAGGCAAGGAAATGGATATATGTTAGCTGA
*
211817 ATTGTAGTATA
131 ATTCTAGTATA
* *
211828 ATGGAGAAACTCAATACTCACCGGAAGTGATTCATAAGTAAGTCATAGTAAAATTTTATCTTGAA
1 ATGGAGAAACTCAATACTCACCGGAAGTGATTCATAAGTAAGTCATAATAAAATTCTATCTTGAA
* *
211893 TATGACTTGTGTAATTAAGTTATTAAATAGAAAGTTAGGTAAGGAAATGGATATATGTTAGCTGA
66 TATGACTTGTGTAATTAAGTTATTAAAAAGAAAGTTAGGCAAGGAAATGGATATATGTTAGCTGA
211958 ATTCTAGTATA
131 ATTCTAGTATA
211969 A
1 A
211970 ATATTGGTAT
Statistics
Matches: 132, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
141 132 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (141 bp):
ATGGAGAAACTCAATACTCACCGGAAGTGATTCATAAGTAAGTCATAATAAAATTCTATCTTGAA
TATGACTTGTGTAATTAAGTTATTAAAAAGAAAGTTAGGCAAGGAAATGGATATATGTTAGCTGA
ATTCTAGTATA
Found at i:212060 original size:21 final size:21
Alignment explanation
Indices: 212015--212060 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
212005 ATTCTACTCC
* *
212015 GATGCCCCTATATCGCACTTC
1 GATGCCCCTATATCGCACCTA
212036 GATGCCCCTATAAT-GCACCTA
1 GATGCCCCTAT-ATCGCACCTA
212057 GATG
1 GATG
212061 TTTCTATGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (21 bp):
GATGCCCCTATATCGCACCTA
Found at i:219892 original size:12 final size:12
Alignment explanation
Indices: 219875--219905 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
219865 GAGGAGCAAG
219875 AGAAGAAAAGAA
1 AGAAGAAAAGAA
*
219887 AGAAGAAAAGGA
1 AGAAGAAAAGAA
219899 AGAAGAA
1 AGAAGAA
219906 GAAAGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAGAA
Found at i:222181 original size:24 final size:24
Alignment explanation
Indices: 222148--222247 Score: 85
Period size: 24 Copynumber: 4.1 Consensus size: 24
222138 ATACTAGTTA
222148 AACTCTATCTGGGCTCGAATGAGCT
1 AACT-TATCTGGGCTCGAATGAGCT
*
222173 AACTTATCTAGGCTCGTAA-GAGCT
1 AACTTATCTGGGCTCG-AATGAGCT
* * * *
222197 AACCTATCTGGGCTTGTATGAACT
1 AACTTATCTGGGCTCGAATGAGCT
* * * *
222221 AATTTTGTCTGGGCTTGTATGAGCT
1 AA-CTTATCTGGGCTCGAATGAGCT
222246 AA
1 AA
222248 ATTTCTAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
23 1 0.02
24 35 0.56
25 26 0.42
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (24 bp):
AACTTATCTGGGCTCGAATGAGCT
Found at i:229434 original size:33 final size:33
Alignment explanation
Indices: 229358--229434 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
229348 CCTATTTATT
* * * ** *
229358 TAAAATAAATAATTTTAGTCAAAATGAAATTAG
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
229391 GAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
229423 TAAAATAAACAA
1 TAAAATAAACAA
229435 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.26
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:232261 original size:24 final size:24
Alignment explanation
Indices: 232234--232288 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
232224 ACAATCAATT
* *
232234 CATTTTATATTTCAGTTGCACTGA
1 CATTTTATATTACAATTGCACTGA
* *
232258 CATTTTGTATTACAATTGCATTGA
1 CATTTTATATTACAATTGCACTGA
232282 CAATTTT
1 C-ATTTT
232289 TACTCTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (24 bp):
CATTTTATATTACAATTGCACTGA
Found at i:234444 original size:42 final size:42
Alignment explanation
Indices: 234378--234961 Score: 691
Period size: 42 Copynumber: 13.9 Consensus size: 42
234368 AAGGAAAGCA
* * * * *
234378 TTCATTGCATTTAAAGGTCTAGGTGTGGAGGTTCATTTACTT
1 TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
234420 TTCATCGCATTTAGAGGCCAAGGTGTGGAGG-CCTATTTACTT
1 TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCC-ATTTACTT
* * *
234462 TTCATCCCATTTAGAGGCGC-AGGTGTGGAGGCCCTTTTACTT
1 TTCATCGCATTTAGAGGC-CAAGGTGTGGAGGTCCATTTACTT
* *
234504 TTCATCGTATTTAGAGG-CACAGGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCA-AGGTGTGGAGGTCCATTTACTT
* * *
234546 TTCATTGCATTTAGAGGCTC-GGGTGTGGA-GACTCATTTACTT
1 TTCATCGCATTTAGAGGC-CAAGGTGTGGAGGTC-CATTTACTT
* ** * *
234588 TTCATTGCATTTAGAGGCTTAGGTGTGAAGGTCCATTTATTT
1 TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
234630 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
*
234672 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
234714 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTATTT
1 TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
234756 TTCATCGCATGTAGAGGCCTAA-GTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCC-AAGGTGTGGAGGTCCATTTACTT
*
234798 TTCTTCGCATTTAGAGGCTC-AGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGC-CAAGGTGTGGAGGTCCATTTACTT
** *
234840 TTCATCATATTTAGAGGCCCAA-GT-TGGAGGTTCATTTACTT
1 TTCATCGCATTTAGAGG-CCAAGGTGTGGAGGTCCATTTACTT
* ** *
234881 TTCATCGCATTTAGAGACTTAGGTGTGGAGGTCCATTTAATT
1 TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* * * * *
234923 TTCATTGCATTTAGAGTCCCAGGTATGGAGTTCCATTTA
1 TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTA
234962 GAGGACCAAG
Statistics
Matches: 473, Mismatches: 52, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
40 3 0.01
41 36 0.08
42 424 0.90
43 9 0.02
44 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
TTCATCGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
Found at i:235383 original size:3 final size:3
Alignment explanation
Indices: 235375--235401 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
235365 AAGGGCCCAA
235375 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
235402 TTTAGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:236207 original size:3 final size:3
Alignment explanation
Indices: 236199--236227 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
236189 TTTCATTTAA
236199 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
236228 ATTTCCGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:241753 original size:52 final size:51
Alignment explanation
Indices: 241697--241846 Score: 133
Period size: 52 Copynumber: 2.9 Consensus size: 51
241687 TACTTTTTTT
* *
241697 CAAACCCCAAAACTTTTTTCCTTTTATTTTCTCCCCAAAATTTTTACTTTCC-
1 CAAACCCCAAAAC-TTTTTCCTTTAATTTTCTCCCCAAAATTTTTAC-CTCCA
* * * * * * *
241749 CAAACCCCTAAACCTTTTT-CTTTCCACTTCCTCTCCAAGACTTTTACCTCCA
1 CAAACCCC-AAAACTTTTTCCTTT-AATTTTCTCCCCAAAATTTTTACCTCCA
* * *
241801 TCAAACTCCAAAACTTTTTCCTTTAATTTTCACCCTAAAATTTTTA
1 -CAAACCCCAAAACTTTTTCCTTTAATTTTCTCCCCAAAATTTTTA
241847 ATCCCCTACA
Statistics
Matches: 75, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
51 7 0.09
52 53 0.71
53 15 0.20
ACGTcount: A:0.27, C:0.32, G:0.01, T:0.41
Consensus pattern (51 bp):
CAAACCCCAAAACTTTTTCCTTTAATTTTCTCCCCAAAATTTTTACCTCCA
Found at i:252430 original size:19 final size:18
Alignment explanation
Indices: 252406--252443 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
252396 ATTGCGTGTT
*
252406 TGAATAGAAATAAACGAAA
1 TGAATAGAAA-AAAAGAAA
252425 TGAATAGAAAAAAAGAAA
1 TGAATAGAAAAAAAGAAA
252443 T
1 T
252444 AAGAAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.66, C:0.03, G:0.16, T:0.16
Consensus pattern (18 bp):
TGAATAGAAAAAAAGAAA
Found at i:255391 original size:25 final size:25
Alignment explanation
Indices: 255363--255429 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 25
255353 GCATTACAGA
* * *
255363 ATTTGCTATACAGGCTTTCCAAATG
1 ATTTGCCACACAGGCTTCCCAAATG
* *
255388 ATTTGCCACAGAGGCTTCCCAAATA
1 ATTTGCCACACAGGCTTCCCAAATG
***
255413 ATACACCACACAGGCTT
1 ATTTGCCACACAGGCTT
255430 TACAGATAAC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (25 bp):
ATTTGCCACACAGGCTTCCCAAATG
Found at i:262635 original size:24 final size:24
Alignment explanation
Indices: 262602--262656 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
262592 GTTAAGAGTA
* *
262602 AAAATTGTCAGTGCAATTGTAATAC
1 AAAA-TGTCAGTGCAACTGAAATAC
*
262627 AAAATGTCAGTGCAACTGAAATAT
1 AAAATGTCAGTGCAACTGAAATAC
262651 AAAATG
1 AAAATG
262657 AATTGATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAATGTCAGTGCAACTGAAATAC
Done.