Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012074.1 Kokia drynarioides strain JFW-HI SEQ_127072, 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: 209051
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:1315 original size:24 final size:24
Alignment explanation
Indices: 1281--1331 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1271 AATTTGATTC
* *
1281 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
1305 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
1329 AAA
1 AAA
1332 GATTACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:3287 original size:24 final size:24
Alignment explanation
Indices: 3243--3334 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
3233 TAATTTAGAC
* * *
3243 TAAAAAGAATTTGACTT-AAACAAC
1 TAAAAAGAGTTT-AATTGAAACAAA
3267 TAAAAAGAGTTTAATTGAAACAAA
1 TAAAAAGAGTTTAATTGAAACAAA
* *
3291 TAAATAGAGTTTAATTGAAATAAA
1 TAAAAAGAGTTTAATTGAAACAAA
* *
3315 TAAATAGAGTTTAACTGAAA
1 TAAAAAGAGTTTAATTGAAA
3335 GATTATTTCT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 3 0.05
24 58 0.95
ACGTcount: A:0.54, C:0.05, G:0.12, T:0.28
Consensus pattern (24 bp):
TAAAAAGAGTTTAATTGAAACAAA
Found at i:3497 original size:18 final size:18
Alignment explanation
Indices: 3474--3508 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3464 GATAATTTCA
*
3474 CATTTTTTTAAAAAATAT
1 CATTTTTTGAAAAAATAT
3492 CATTTTTTGAAAAAATA
1 CATTTTTTGAAAAAATA
3509 ATAAAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
CATTTTTTGAAAAAATAT
Found at i:8011 original size:147 final size:147
Alignment explanation
Indices: 7688--8212 Score: 760
Period size: 147 Copynumber: 3.6 Consensus size: 147
7678 ACAGTCATCA
*
7688 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGGGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
* * * *
7753 GGGCCCTTTCTTTAA------ATTTTGCAAAATCC-ATCCTTTCATAATTTTAAATGTAGCAACC
66 GGGCCCTTTCTTTAATTTTTTATTTTGCCAAGTCCGATCCTTTCATAATTATATATGTAGCAACC
*
7811 TAAATTTGTATCACAATT
131 -AAACTTGTATCACAATT
7829 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
* *
7894 GGGCCCTCTCTTTAATTTTTTATTTTGCCAAGTCCGATCCTTTCATACTTATATATGTAGCAACC
66 GGGCCCTTTCTTTAATTTTTTATTTTGCCAAGTCCGATCCTTTCATAATTATATATGTAGCAACC
* *
7959 AAACTTGTATCAGATTT
131 AAACTTGTATCACAATT
*
7976 GGGTCTATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
* * *
8041 GGGCCCTTTCTTTAATTTTTTATTTTGCCAAGTCAG-TCCTTCCATAGTTATATATGTAGTTACC
66 GGGCCCTTTCTTTAATTTTTTATTTTGCCAAGTCCGATCCTTTCATAATTATATATGTAG----C
**
8105 AAAGTAAACTTGTATCACAATT
127 -AACCAAACTTGTATCACAATT
* *
8127 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGATGTCACCGGTTCAAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
**
8192 TAGCCCTTTCTTTAATTTTTT
66 GGGCCCTTTCTTTAATTTTTT
8213 TTGCCAAGCC
Statistics
Matches: 348, Mismatches: 24, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
141 78 0.22
146 21 0.06
147 124 0.36
148 26 0.07
150 1 0.00
151 98 0.28
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (147 bp):
GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
GGGCCCTTTCTTTAATTTTTTATTTTGCCAAGTCCGATCCTTTCATAATTATATATGTAGCAACC
AAACTTGTATCACAATT
Found at i:11900 original size:9 final size:9
Alignment explanation
Indices: 11874--11916 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
11864 ATTCAAGAAG
11874 TAATTAATT
1 TAATTAATT
**
11883 TAAAAAATT
1 TAATTAATT
11892 TAATTAATT
1 TAATTAATT
* *
11901 AAATTTATT
1 TAATTAATT
11910 TAATTAA
1 TAATTAA
11917 AAATATATTC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TAATTAATT
Found at i:11904 original size:14 final size:14
Alignment explanation
Indices: 11887--11917 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11877 TTAATTTAAA
11887 AAATTTAATTAATT
1 AAATTTAATTAATT
*
11901 AAATTTATTTAATT
1 AAATTTAATTAATT
11915 AAA
1 AAA
11918 AATATATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:14008 original size:21 final size:20
Alignment explanation
Indices: 13984--14023 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13974 TATACGTGTA
*
13984 AAAATAATGTATTTAAAATAC
1 AAAATAATGT-TTAAAAATAC
*
14005 AAAATCATGTTTAAAAATA
1 AAAATAATGTTTAAAAATA
14024 ACATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATAATGTTTAAAAATAC
Found at i:28020 original size:18 final size:18
Alignment explanation
Indices: 27977--28011 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27967 TACTTTTTAA
*
27977 ATATTTATTAAAATTTTC
1 ATATTTTTTAAAATTTTC
27995 ATATTTTTTAAAATTTT
1 ATATTTTTTAAAATTTT
28012 ATGGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTTTTAAAATTTTC
Found at i:28021 original size:17 final size:18
Alignment explanation
Indices: 27984--28022 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27974 TAAATATTTA
*
27984 TTAAAATTTTCATATTTT
1 TTAAAATTTTCATAGTTT
*
28002 TTAAAATTTT-ATGGTTT
1 TTAAAATTTTCATAGTTT
28019 TTAA
1 TTAA
28023 TTTTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (18 bp):
TTAAAATTTTCATAGTTT
Found at i:28046 original size:16 final size:16
Alignment explanation
Indices: 28016--28049 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28006 AATTTTATGG
**
28016 TTTTTAATTTTTTTAA
1 TTTTTAATTAATTTAA
28032 TTTTTAATTAATTTAA
1 TTTTTAATTAATTTAA
28048 TT
1 TT
28050 CAAAATGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTAATTAATTTAA
Found at i:31264 original size:2 final size:2
Alignment explanation
Indices: 31257--31282 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31247 TTGGGATTTT
31257 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
31283 GTTTTTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:41200 original size:4 final size:4
Alignment explanation
Indices: 41191--41218 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
41181 TGGACCTCAT
41191 CGAC CGAC CGAC CGAC CGAC CGAC CGAC
1 CGAC CGAC CGAC CGAC CGAC CGAC CGAC
41219 TGATCAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.50, G:0.25, T:0.00
Consensus pattern (4 bp):
CGAC
Found at i:45676 original size:24 final size:25
Alignment explanation
Indices: 45635--45686 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
45625 TAATTATAAT
**
45635 AAAAAATTATCAATAATATTTGATA
1 AAAAAATTATCAATAATAAGTGATA
* *
45660 AAAAAATTCTCTA-AATAAGTGATA
1 AAAAAATTATCAATAATAAGTGATA
45684 AAA
1 AAA
45687 TTTAAAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAAAAATTATCAATAATAAGTGATA
Found at i:46344 original size:51 final size:52
Alignment explanation
Indices: 46256--46357 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 52
46246 GGCTGGCAGG
*
46256 TGTTTGATTCTCCCTTAAAATAAAAAAAAAATTTATTTATGTTTTTTTATAAA
1 TGTTCGATTCTCCCTTAAAATAAAAAAAAAATTTATTTATG-TTTTTTATAAA
* *
46309 TGTTCGATTCT-CTTTAAAAT-AAAAAAAATTTTATTTATGTTTTTTATAA
1 TGTTCGATTCTCCCTTAAAATAAAAAAAAAATTTATTTATGTTTTTTATAA
46358 TTTATAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 10 0.22
51 18 0.39
52 8 0.17
53 10 0.22
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (52 bp):
TGTTCGATTCTCCCTTAAAATAAAAAAAAAATTTATTTATGTTTTTTATAAA
Found at i:47705 original size:20 final size:20
Alignment explanation
Indices: 47680--47717 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47670 CCATGATTTC
* *
47680 AAAAAAATAAAAATTAAAAA
1 AAAAAAAAAAAAACTAAAAA
47700 AAAAAAAAAAAAACTAAA
1 AAAAAAAAAAAAACTAAA
47718 TTACACTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAAAAAAAAAACTAAAAA
Found at i:53395 original size:17 final size:16
Alignment explanation
Indices: 53325--53399 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 16
53315 CCCAATCAGC
*
53325 TTAAATTTATTTTAAAA
1 TTAAATTTA-TTTAAAT
*
53342 TTAAGTTTATTCTAAAT
1 TTAAATTTATT-TAAAT
* * *
53359 TTAAATTTGGTTGAATT
1 TTAAATTT-ATTTAAAT
53376 TTAAATTTATTATAAAT
1 TTAAATTTATT-TAAAT
53393 TTAAATT
1 TTAAATT
53400 AAATTTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
16 4 0.09
17 40 0.87
18 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (16 bp):
TTAAATTTATTTAAAT
Found at i:55056 original size:29 final size:28
Alignment explanation
Indices: 55023--55346 Score: 226
Period size: 29 Copynumber: 11.1 Consensus size: 28
55013 CTTCTCTTAT
**
55023 TTTTAACCATGAAACTTCCAAAATTACCA
1 TTTTAACCCCGAAACTTCCAAAATT-CCA
* * *
55052 TTTTACCCCCG-AACTTTCAAAACTCTCA
1 TTTTAACCCCGAAACTTCCAAAATTC-CA
* *
55080 TTTTTTACCCCGAAACTTCCAAAAATTTCA
1 -TTTTAACCCCGAAACTTCC-AAAATTCCA
* *
55110 TTTTTAGCACCG-AACTTCCAAAATTTCCA
1 -TTTTAACCCCGAAACTTCCAAAA-TTCCA
55139 TTTTAACCCCGAAACTTCCAAAAATTACCA
1 TTTTAACCCCGAAACTTCC-AAAATT-CCA
* * *
55169 TTTT-ACCCCTAAACTTCCAAAACTCTTA
1 TTTTAACCCCGAAACTTCCAAAATTC-CA
** *
55197 TTTTTAACCCTAAAACTTCAAAAAATTCCAA
1 -TTTTAACCCCGAAACTTC-CAAAATTCC-A
* * *
55228 TTTT-ACCCCTAAACTTCTAAAAATCCCA
1 TTTTAACCCCGAAACTTC-CAAAATTCCA
* *
55256 TTTTTAACCCCAAAACTTCCAAAAATTCTA
1 -TTTTAACCCCGAAACTTCC-AAAATTCCA
* *
55286 TTTTTACCCCG-AACTTCCAAAAATGCCA
1 TTTTAACCCCGAAACTTCC-AAAATTCCA
* * * *
55314 TTTTTATCTCGAAATTTCCAAAAATTCCA
1 TTTTAACCCCGAAACTTCC-AAAATTCCA
55343 TTTT
1 TTTT
55347 GCCCCCCGGG
Statistics
Matches: 238, Mismatches: 40, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.01
28 57 0.24
29 105 0.44
30 62 0.26
31 12 0.05
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (28 bp):
TTTTAACCCCGAAACTTCCAAAATTCCA
Found at i:55112 original size:58 final size:58
Alignment explanation
Indices: 55021--55352 Score: 325
Period size: 59 Copynumber: 5.7 Consensus size: 58
55011 TCCTTCTCTT
** * *
55021 ATTTTTAACCATGAAACTTCC-AAAATTACCATTTTACCCCCGAACTTTCAAAACTCTC
1 ATTTTTAACCCCGAAACTTCCAAAAATT-CCATTTTACCCCCGAACTTCCAAAAATCTC
* * * * *
55079 ATTTTTTACCCCGAAACTTCCAAAAATTTCATTTTTAGCACCGAACTTCC-AAAATTTCC
1 ATTTTTAACCCCGAAACTTCCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATCT-C
** * *
55138 A-TTTTAACCCCGAAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAACTCTT
1 ATTTTTAACCCCGAAACTTCCAAAAATT-CCATTTTACCCCCGAACTTCCAAAAATCTC
** * ** * *
55196 ATTTTTAACCCTAAAACTTCAAAAAATTCCAATTTTACCCCTAAACTTCTAAAAATCCC
1 ATTTTTAACCCCGAAACTTCCAAAAATTCC-ATTTTACCCCCGAACTTCCAAAAATCTC
* *
55255 ATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTA-CCCCGAACTTCCAAAAATGC-C
1 ATTTTTAACCCCGAAACTTCCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAAT-CTC
* * * *
55313 ATTTTT-ATCTCGAAATTTCCAAAAATTCCATTTTGCCCCC
1 ATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTACCCCC
55353 CGGGTATCCG
Statistics
Matches: 227, Mismatches: 37, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
56 4 0.02
57 23 0.10
58 90 0.40
59 110 0.48
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (58 bp):
ATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTACCCCCGAACTTCCAAAAATCTC
Found at i:55480 original size:15 final size:15
Alignment explanation
Indices: 55454--55494 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
55444 GTATTCTGCA
*
55454 TTTTTTTGTTTTGT-
1 TTTTTTTATTTTGTC
55468 TTTTTGTTATTTTGTC
1 TTTTT-TTATTTTGTC
55484 TTTTTTTATTT
1 TTTTTTTATTT
55495 ATCTTACTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.05, C:0.02, G:0.10, T:0.83
Consensus pattern (15 bp):
TTTTTTTATTTTGTC
Found at i:57101 original size:15 final size:16
Alignment explanation
Indices: 57081--57110 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
57071 GTTAATTTTT
57081 TTTATATTTA-ATTAC
1 TTTATATTTACATTAC
57096 TTTATATTTACATTA
1 TTTATATTTACATTA
57111 TTATTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATATTTACATTAC
Found at i:58263 original size:14 final size:14
Alignment explanation
Indices: 58244--58270 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58234 TATTTTTTAT
58244 TATTAAATATTAAC
1 TATTAAATATTAAC
58258 TATTAAATATTAA
1 TATTAAATATTAA
58271 AAATATTTTC
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:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTAAATATTAAC
Found at i:63865 original size:29 final size:28
Alignment explanation
Indices: 63822--64079 Score: 166
Period size: 29 Copynumber: 8.8 Consensus size: 28
63812 TTTTTGGGGG
*
63822 AAAAATGGTAATTTTGGGAAGTTCGGGTT
1 AAAAATGG-AATTTTTGGAAGTTCGGGTT
* **
63851 AAAAACGGAATTTTTACACA-TTCGGGTGT
1 AAAAATGGAATTTTTGGA-AGTTCGGGT-T
* * * *
63880 -TAAAGGGTAA-TTTTGAAAGTTTCGAGGTC
1 AAAAATGG-AATTTTTGGAAG-TTCG-GGTT
* * *
63909 GAAAATGGAGA-TTTTGGAGGTTCGGGGGT
1 AAAAATGGA-ATTTTTGGAAGTTC-GGGTT
* *
63938 AAAAATGGGATTTTTGGAAGTTTCGGGGT
1 AAAAATGGAATTTTTGGAAG-TTCGGGTT
*
63967 AAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTCG-GGTT
* *
63996 AAAAATGGAAATTTTTTGGAAGTTTTGGGGTC
1 AAAAATGG-AA-TTTTTGGAAG--TTCGGGTT
64028 AAAAATGGAATTTTTGGAAGTTCGAGAG-T
1 AAAAATGGAATTTTTGGAAGTTCG-G-GTT
* *
64057 AAACATGGAATTTTCGGACAGTT
1 AAAAATGGAATTTTTGGA-AGTT
64080 TAGGGACCTT
Statistics
Matches: 184, Mismatches: 26, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.01
28 32 0.17
29 89 0.48
30 37 0.20
31 12 0.07
32 10 0.05
33 3 0.02
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.33
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTCGGGTT
Found at i:63965 original size:30 final size:30
Alignment explanation
Indices: 63910--64080 Score: 183
Period size: 29 Copynumber: 5.7 Consensus size: 30
63900 TTCGAGGTCG
*
63910 AAAATGGAGA-TTTTGG-AGGTTCGGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGGTA
*
63939 AAAATGGGATTTTTGGAAGTTTC-GGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGGTA
*
63968 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGGTA
*
63997 AAAATGGAAATTTTTTGGAAGTTT-TGGGGTCA
1 AAAATGG-AA-TTTTTGGAAGTTTCGGGGGT-A
* *
64029 AAAATGGAATTTTTGGAAG-TTCGAGAGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGGTA
* *
64058 AACATGGAATTTTCGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
64081 AGGGACCTTA
Statistics
Matches: 121, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
28 4 0.03
29 67 0.55
30 22 0.18
31 18 0.15
32 10 0.08
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGGTA
Found at i:65907 original size:17 final size:17
Alignment explanation
Indices: 65872--65942 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
65862 AACATTCAGT
*
65872 ATTTATAATAAATTTTAA
1 ATTTAAAATAAA-TTTAA
*
65890 ATTTAAATTAAATTTAA
1 ATTTAAAATAAATTTAA
* *
65907 ATTCAAAATCAATTT-A
1 ATTTAAAATAAATTTAA
65923 ATCTTAAAATAAATCTTAA
1 AT-TTAAAATAAAT-TTAA
65942 A
1 A
65943 ATGGGTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 3 0.07
17 26 0.60
18 12 0.28
19 2 0.05
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:68520 original size:29 final size:28
Alignment explanation
Indices: 68487--68598 Score: 73
Period size: 29 Copynumber: 3.9 Consensus size: 28
68477 TGGACAAAAA
* *
68487 AAAATCAAGTTTAGGTACCTAATTGAAT
1 AAAATAAACTTTAGGTACCTAATTGAAT
* * *
68515 CAAAATAAACTTTAGATACCAAAATGAACCTT
1 -AAAATAAACTTTAGGTACCTAATTGAA---T
* * * * * *
68547 AAAGTCAAGTTCAAGTACCTAATTGGAT
1 AAAATAAACTTTAGGTACCTAATTGAAT
68575 AAAATAAAACTTTAGGTACC-AATT
1 AAAAT-AAACTTTAGGTACCTAATT
68599 TGAACTCTAA
Statistics
Matches: 60, Mismatches: 19, Indels: 9
0.68 0.22 0.10
Matches are distributed among these distances:
28 9 0.15
29 32 0.53
31 18 0.30
32 1 0.02
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (28 bp):
AAAATAAACTTTAGGTACCTAATTGAAT
Found at i:70625 original size:2 final size:2
Alignment explanation
Indices: 70618--70643 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
70608 TCGAGAATAA
70618 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
70644 TTTTTGGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71377 original size:33 final size:33
Alignment explanation
Indices: 71335--71402 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
71325 ACTTGAGCCA
71335 TATAGATGATTCTTGAGTGTCCCATTCTCCACG
1 TATAGATGATTCTTGAGTGTCCCATTCTCCACG
71368 TATAGATGATTCTTGAGTGTCCCATTCTCCACG
1 TATAGATGATTCTTGAGTGTCCCATTCTCCACG
71401 TA
1 TA
71403 CTCATAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (33 bp):
TATAGATGATTCTTGAGTGTCCCATTCTCCACG
Found at i:80725 original size:29 final size:29
Alignment explanation
Indices: 80675--80730 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
80665 TTTTAAAGGA
80675 CCCAAAAAATTTTGAACTTTTAAAGGGGC
1 CCCAAAAAATTTTGAACTTTTAAAGGGGC
*
80704 CCCAAAAAATATTTTAAC-TTTAAAGGG
1 CCCAAAAAAT-TTTGAACTTTTAAAGGG
80731 CCAAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (29 bp):
CCCAAAAAATTTTGAACTTTTAAAGGGGC
Found at i:80731 original size:28 final size:28
Alignment explanation
Indices: 80665--80732 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
80655 ATTTTCCAAT
*
80665 TTTTAAA-GGACCCAAAAAATTTTGAAC
1 TTTTAAAGGGCCCCAAAAAATTTTGAAC
*
80692 TTTTAAAGGGGCCCCAAAAAATATTTTAAC
1 TTTTAAA-GGGCCCCAAAAAAT-TTTGAAC
80722 -TTTAAAGGGCC
1 TTTTAAAGGGCC
80733 AAAATTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 7 0.19
28 5 0.14
29 18 0.50
30 6 0.17
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (28 bp):
TTTTAAAGGGCCCCAAAAAATTTTGAAC
Found at i:83533 original size:22 final size:22
Alignment explanation
Indices: 83503--83546 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
83493 ATTTTTAAAT
* *
83503 TTATAATATTTTATGTTATTTA
1 TTATAATATATTATGTAATTTA
*
83525 TTATTATATATTATGTAATTTA
1 TTATAATATATTATGTAATTTA
83547 GAACACATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
TTATAATATATTATGTAATTTA
Found at i:83662 original size:24 final size:26
Alignment explanation
Indices: 83634--83685 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
83624 TATATAAAAA
83634 AAATTTAATAAATA-AAAAAT-ATAT
1 AAATTTAATAAATATAAAAATAATAT
* *
83658 AAATTTATTAAATATTAAAATAATAT
1 AAATTTAATAAATATAAAAATAATAT
83684 AA
1 AA
83686 TATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 5 0.21
26 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATTTAATAAATATAAAAATAATAT
Found at i:83692 original size:31 final size:33
Alignment explanation
Indices: 83631--83716 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
83621 GACTATATAA
*
83631 AAAAAATTTAATAAATAA-AAAATATATAA-ATTTAT
1 AAAAAA-TTAA-AAATAATATAATATA-AATATTT-T
* *
83666 TAAATATT-AAAATAATATAATATAAATATTTT
1 AAAAAATTAAAAATAATATAATATAAATATTTT
83698 AAAAAATTAAAAATAATAT
1 AAAAAATTAAAAATAATAT
83717 GGGCAGGCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
32 15 0.35
33 22 0.51
34 2 0.05
35 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (33 bp):
AAAAAATTAAAAATAATATAATATAAATATTTT
Found at i:88442 original size:15 final size:17
Alignment explanation
Indices: 88407--88443 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
88397 AGTAAAATAA
*
88407 ATTAATATACATTTTTT
1 ATTAATATACATTTTTC
88424 ATTAATATA-A-TTTTC
1 ATTAATATACATTTTTC
88439 ATTAA
1 ATTAA
88444 GATATGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 1 0.05
17 9 0.47
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAATATACATTTTTC
Found at i:96031 original size:16 final size:17
Alignment explanation
Indices: 96006--96042 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
95996 AGTTAAATAA
96006 ATAATAATATAAAATTT
1 ATAATAATATAAAATTT
*
96023 ATAAT-ATATAACATTT
1 ATAATAATATAAAATTT
96039 ATAA
1 ATAA
96043 AAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAATATAAAATTT
Found at i:96400 original size:22 final size:21
Alignment explanation
Indices: 96372--96412 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
96362 TATAAATTTT
*
96372 TTTATAATATATATTTTTAAGA
1 TTTATAATATA-ACTTTTAAGA
96394 TTTATAATATAACTTTTAA
1 TTTATAATATAACTTTTAA
96413 AAATTTTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTATAATATAACTTTTAAGA
Found at i:96418 original size:22 final size:22
Alignment explanation
Indices: 96372--96418 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
96362 TATAAATTTT
* *
96372 TTTATAATATATATTTTTAAGA
1 TTTATAATATATATTTTAAAAA
96394 TTTATAATATA-ACTTTTAAAAA
1 TTTATAATATATA-TTTTAAAAA
96416 TTT
1 TTT
96419 TGGCTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATAATATATATTTTAAAAA
Found at i:98682 original size:15 final size:15
Alignment explanation
Indices: 98662--98693 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
98652 TGCCAAGGTA
98662 TGATGACCGACGCGG
1 TGATGACCGACGCGG
*
98677 TGATGACCGACGTGG
1 TGATGACCGACGCGG
98692 TG
1 TG
98694 GCACTCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.19
Consensus pattern (15 bp):
TGATGACCGACGCGG
Found at i:102259 original size:6 final size:6
Alignment explanation
Indices: 102249--102286 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
102239 AAATCCCTAA
*
102249 CTGCCA CTGCCG CTGCCG CTGCCG CTGCCG CTGCCG CT
1 CTGCCG CTGCCG CTGCCG CTGCCG CTGCCG CTGCCG CT
102287 CACAACCTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.03, C:0.50, G:0.29, T:0.18
Consensus pattern (6 bp):
CTGCCG
Found at i:123138 original size:16 final size:17
Alignment explanation
Indices: 123101--123139 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
123091 GATTCGAACA
*
123101 AAAAATAGCCTGAACCT
1 AAAAATAGACTGAACCT
123118 AAAAATAGACTGAACCT
1 AAAAATAGACTGAACCT
123135 AAAAA
1 AAAAA
123140 GATCCGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.18, G:0.10, T:0.15
Consensus pattern (17 bp):
AAAAATAGACTGAACCT
Found at i:124256 original size:31 final size:31
Alignment explanation
Indices: 124221--124281 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
124211 TTATATAAAA
* *
124221 ATAATTAAATTTCAAATTTGGTTTTTATACC
1 ATAATAAAATTTCAAATTTGATTTTTATACC
* *
124252 ATAATAAAATTTGAGATTTGATTTTTATAC
1 ATAATAAAATTTCAAATTTGATTTTTATAC
124282 TTAAGGCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (31 bp):
ATAATAAAATTTCAAATTTGATTTTTATACC
Found at i:126706 original size:22 final size:22
Alignment explanation
Indices: 126673--126714 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
126663 TCAATATAAA
126673 ATTTCATAATCACTATAAATCC
1 ATTTCATAATCACTATAAATCC
*
126695 ATTTCA-ATATCACTTTAAAT
1 ATTTCATA-ATCACTATAAAT
126715 TTAACTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTCATAATCACTATAAATCC
Found at i:128404 original size:40 final size:40
Alignment explanation
Indices: 128360--128438 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
128350 ATTGTGTGAT
128360 TATTAATAATTAGGTATTAGCATATATTCCTTAAGATAAC
1 TATTAATAATTAGGTATTAGCATATATTCCTTAAGATAAC
128400 TATTAATAATTAGGTATTAGCATATATTCCTTAAGATAA
1 TATTAATAATTAGGTATTAGCATATATTCCTTAAGATAA
128439 TTAAAGATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (40 bp):
TATTAATAATTAGGTATTAGCATATATTCCTTAAGATAAC
Found at i:137807 original size:27 final size:26
Alignment explanation
Indices: 137777--137837 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
137767 AATTGATTGC
*
137777 AATTTTTATTTAGGAAATTATTT-TTTT
1 AATTTTTA-TAAGGAAATT-TTTATTTT
*
137804 AATTATTTATAAGGACATTTTTATTTT
1 AATT-TTTATAAGGAAATTTTTATTTT
137831 -ATTTTTA
1 AATTTTTA
137838 ATATATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 4 0.13
26 6 0.20
27 16 0.53
28 4 0.13
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (26 bp):
AATTTTTATAAGGAAATTTTTATTTT
Found at i:150541 original size:45 final size:45
Alignment explanation
Indices: 150477--150568 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
150467 GGAGAAAAAA
* * *
150477 CTGGGTTCTCTTCAAAATGGAATCTGAAGTTCCATGCATATTAAG
1 CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGCATATCAAG
*
150522 CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGGATATCAAG
1 CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGCATATCAAG
150567 CT
1 CT
150569 TAATTGTGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (45 bp):
CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGCATATCAAG
Found at i:151302 original size:13 final size:12
Alignment explanation
Indices: 151274--151307 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
151264 TTTTTAGATT
*
151274 TTGAAATAAGTA
1 TTGAAATAAATA
151286 TTGAAATACAATA
1 TTGAAATA-AATA
151299 TTGAAATAA
1 TTGAAATAA
151308 CTTACAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (12 bp):
TTGAAATAAATA
Found at i:152491 original size:17 final size:17
Alignment explanation
Indices: 152471--152507 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
152461 GTAAGAGGAT
152471 ATGAGAAAGCACCCGAC
1 ATGAGAAAGCACCCGAC
*
152488 AT--GAAAGCGCCCGAC
1 ATGAGAAAGCACCCGAC
152503 ATGAG
1 ATGAG
152508 TATGTTCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 4
0.77 0.05 0.18
Matches are distributed among these distances:
15 14 0.82
17 3 0.18
ACGTcount: A:0.38, C:0.27, G:0.27, T:0.08
Consensus pattern (17 bp):
ATGAGAAAGCACCCGAC
Found at i:152495 original size:15 final size:15
Alignment explanation
Indices: 152475--152506 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
152465 GAGGATATGA
152475 GAAAGCACCCGACAT
1 GAAAGCACCCGACAT
*
152490 GAAAGCGCCCGACAT
1 GAAAGCACCCGACAT
152505 GA
1 GA
152507 GTATGTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.25, T:0.06
Consensus pattern (15 bp):
GAAAGCACCCGACAT
Found at i:152610 original size:92 final size:92
Alignment explanation
Indices: 152491--152677 Score: 356
Period size: 92 Copynumber: 2.0 Consensus size: 92
152481 ACCCGACATG
152491 AAAGCGCCCGACATGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTGG
1 AAAGCGCCCGACATGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTGG
152556 AAGATCATATCCCCATATGCATGTCCA
66 AAGATCATATCCCCATATGCATGTCCA
* *
152583 AAAGTGCCCGCCATGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTGG
1 AAAGCGCCCGACATGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTGG
152648 AAGATCATATCCCCATATGCATGTCCA
66 AAGATCATATCCCCATATGCATGTCCA
152675 AAA
1 AAA
152678 ATGTGTTCGA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (92 bp):
AAAGCGCCCGACATGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTGG
AAGATCATATCCCCATATGCATGTCCA
Found at i:155365 original size:26 final size:26
Alignment explanation
Indices: 155313--155365 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
155303 GAAAATATTA
* * *
155313 AGTTTTTCATTAGCATACAGTAGATT
1 AGTTTTTAATTAGCAAACAGTAAATT
*
155339 AGTTTTTAATTAGCAAACGGTAAATT
1 AGTTTTTAATTAGCAAACAGTAAATT
155365 A
1 A
155366 TTAAACTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (26 bp):
AGTTTTTAATTAGCAAACAGTAAATT
Found at i:159095 original size:27 final size:27
Alignment explanation
Indices: 159057--159114 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
159047 GAGTGCACTG
*
159057 ATATGATCAAAAATTTACTCATAGTAT
1 ATATGATAAAAAATTTACTCATAGTAT
**
159084 ATATGATAAAAAATTTACTTGTAGTAT
1 ATATGATAAAAAATTTACTCATAGTAT
159111 ATAT
1 ATAT
159115 TTCCCATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.40
Consensus pattern (27 bp):
ATATGATAAAAAATTTACTCATAGTAT
Found at i:159543 original size:15 final size:13
Alignment explanation
Indices: 159513--159538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
159503 AACAATTTTA
159513 TGTCCATTAATAT
1 TGTCCATTAATAT
159526 TGTCCATTAATAT
1 TGTCCATTAATAT
159539 ATTGTATATA
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:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TGTCCATTAATAT
Found at i:161996 original size:33 final size:33
Alignment explanation
Indices: 161959--162023 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
161949 AAAAAACTAC
* *
161959 AATAAATATAATAAATGTTTTATTATATTAAAA
1 AATAAATAAAATAAATATTTTATTATATTAAAA
*
161992 AATAAATAAAATAAATATTTTATTGTATTAAA
1 AATAAATAAAATAAATATTTTATTATATTAAA
162024 TATAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (33 bp):
AATAAATAAAATAAATATTTTATTATATTAAAA
Found at i:162880 original size:14 final size:14
Alignment explanation
Indices: 162861--162892 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
162851 GAGAATAAAT
162861 ATTTAATTAAATAA
1 ATTTAATTAAATAA
*
162875 ATTTAATTAATTAA
1 ATTTAATTAAATAA
162889 ATTT
1 ATTT
162893 TTTAAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAATTAAATAA
Found at i:163102 original size:113 final size:113
Alignment explanation
Indices: 162968--163197 Score: 388
Period size: 113 Copynumber: 2.0 Consensus size: 113
162958 ATCTTCTTCC
*
162968 CTTTTGATTCCAATATATTTAGTGACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAAC
1 CTTTTGATTCCAATATATTTAGTGACAAATCTGTCTCAAAGCTTGAATCTATAAAACCCATTAAC
* *
163033 CAAAAGATTCAACATATTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
66 CAAAAGATTCAACATATTTCGTTCCAATATCTTCTTCCCATTAAGTTT
* * * *
163081 CTTTTGATTCCAATATCTTTAGTTACAAATTTGTCTCAAAGCTTGAATCTATAAAGCCCATTAAC
1 CTTTTGATTCCAATATATTTAGTGACAAATCTGTCTCAAAGCTTGAATCTATAAAACCCATTAAC
*
163146 CAAAAGATTCAATATATTTCGTTCCAATATCTTCTTCCCATTAAGTTT
66 CAAAAGATTCAACATATTTCGTTCCAATATCTTCTTCCCATTAAGTTT
163194 CTTT
1 CTTT
163198 GGGTTAATAG
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (113 bp):
CTTTTGATTCCAATATATTTAGTGACAAATCTGTCTCAAAGCTTGAATCTATAAAACCCATTAAC
CAAAAGATTCAACATATTTCGTTCCAATATCTTCTTCCCATTAAGTTT
Found at i:165452 original size:19 final size:19
Alignment explanation
Indices: 165424--165490 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
165414 AAAAAAATTC
165424 AAAATAAATTTAAAAATTTA
1 AAAAT-AATTTAAAAATTTA
*
165444 AAAATAATTCTAAAGAATATA
1 AAAATAATT-TAAA-AATTTA
* * * *
165465 AAGA-AAGTTAAAATTTTT
1 AAAATAATTTAAAAATTTA
165483 AAAATAAT
1 AAAATAAT
165491 AATTTTCTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
18 6 0.17
19 10 0.28
20 12 0.33
21 8 0.22
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATAATTTAAAAATTTA
Found at i:166728 original size:24 final size:26
Alignment explanation
Indices: 166703--166770 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
166693 ATTTTGTTAT
*
166703 AATTTTTATAATTTTTTAAA-ATATA
1 AATTTTAATAATTTTTTAAATATATA
* *
166728 AATTTTGA-AATTTTTATAAATATTTA
1 AATTTTAATAATTTTT-TAAATATATA
*
166754 AATTTTAATATTTTTTT
1 AATTTTAATAATTTTTT
166771 GTAATTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 7 0.19
25 11 0.31
26 12 0.33
27 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (26 bp):
AATTTTAATAATTTTTTAAATATATA
Found at i:166747 original size:18 final size:18
Alignment explanation
Indices: 166724--166759 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
166714 TTTTTTAAAA
166724 TATAAAT-TTTGAAATTTT
1 TATAAATATTT-AAATTTT
166742 TATAAATATTTAAATTTT
1 TATAAATATTTAAATTTT
166760 AATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATAAATATTTAAATTTT
Found at i:167560 original size:14 final size:15
Alignment explanation
Indices: 167543--167583 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
167533 ATTTGTTTCA
167543 TATTATATTTTA-AT
1 TATTATATTTTATAT
167557 TATTTATATTTTATAT
1 TA-TTATATTTTATAT
167573 T-TTATATTTTA
1 TATTATATTTTA
167584 GTCACTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.48
15 10 0.40
16 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTATATTTTATAT
Found at i:167571 original size:7 final size:7
Alignment explanation
Indices: 167545--167583 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
167535 TTGTTTCATA
167545 TTATATT
1 TTATATT
167552 TTA-ATTAT
1 TTATA-T-T
167560 TTATATT
1 TTATATT
167567 TTATATT
1 TTATATT
167574 TTATATT
1 TTATATT
167581 TTA
1 TTA
167584 GTCACTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 22 0.76
8 5 0.17
9 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTATATT
Found at i:167746 original size:18 final size:18
Alignment explanation
Indices: 167723--167765 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
167713 AAATAAGTTT
167723 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
167741 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
167759 TTAATTA
1 TTAATTA
167766 CACATTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:169039 original size:16 final size:15
Alignment explanation
Indices: 169012--169055 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
169002 AATGATATTT
169012 AATTATTTATTTTAAA
1 AATTA-TTATTTTAAA
169028 AATATATTA-TTT-AA
1 AAT-TATTATTTTAAA
169042 AATTATTATTTTAA
1 AATTATTATTTTAA
169056 GAAGTTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 4 0.16
16 6 0.24
17 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTATTATTTTAAA
Found at i:170021 original size:20 final size:20
Alignment explanation
Indices: 169983--170021 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
169973 TCACACACAC
* *
169983 AAAATAAAAAGATCCAAAAG
1 AAAATAAAAACATCAAAAAG
*
170003 AAAATAAAAACATTAAAAA
1 AAAATAAAAACATCAAAAA
170022 CGTTATATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAATAAAAACATCAAAAAG
Found at i:178470 original size:13 final size:13
Alignment explanation
Indices: 178428--178471 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
178418 AGTATACAAT
178428 AGAATATAGAAAA
1 AGAATATAGAAAA
* *
178441 AGAAGCATA-AAAT
1 AGAA-TATAGAAAA
178454 AGAATATAGAAAA
1 AGAATATAGAAAA
178467 AGAAT
1 AGAAT
178472 GTTAGGGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 19 0.76
14 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (13 bp):
AGAATATAGAAAA
Found at i:194313 original size:24 final size:24
Alignment explanation
Indices: 194269--194314 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
194259 ATATAATTAA
**
194269 GAATTATTAATTCTTTCAAAAAAT
1 GAATTATTAATTCAATCAAAAAAT
194293 GAATTATTAATTACAAT-AAAAA
1 GAATTATTAATT-CAATCAAAAA
194315 CAATTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (24 bp):
GAATTATTAATTCAATCAAAAAAT
Found at i:194548 original size:3 final size:3
Alignment explanation
Indices: 194540--194577 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
194530 TGGTTGAATA
194540 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
194578 AAGATATCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:197934 original size:26 final size:25
Alignment explanation
Indices: 197864--197939 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 25
197854 GGTATATAAA
*
197864 AAATTATTTGAATAGCATTTATATT
1 AAATTATTTGAATATCATTTATATT
*
197889 ---TTATAT--ATATCA-TTATATT
1 AAATTATTTGAATATCATTTATATT
197908 AAATTATTTGAATATCATTTATAATT
1 AAATTATTTGAATATCATTTAT-ATT
*
197934 ATATTA
1 AAATTA
197940 AATGATTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
19 7 0.17
20 5 0.12
22 10 0.25
24 6 0.15
25 4 0.10
26 8 0.20
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (25 bp):
AAATTATTTGAATATCATTTATATT
Found at i:197985 original size:28 final size:29
Alignment explanation
Indices: 197891--197996 Score: 79
Period size: 31 Copynumber: 3.5 Consensus size: 29
197881 TTTATATTTT
* * * *
197891 ATATATATCATTATATTAAATTATTTGAAT
1 ATATTTATTATTATATTAAATTA-TTCAAA
* *
197921 ATCATTTATAATTATATTAAATGATTCAAA
1 AT-ATTTATTATTATATTAAATTATTCAAA
* *
197951 CCTTATTTATTATTATATTTAATTATT-AAA
1 --ATATTTATTATTATATTAAATTATTCAAA
197981 ATATTTTATATATTAT
1 ATA-TTTAT-TATTAT
197997 TAATATTACA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
28 2 0.03
29 5 0.08
30 15 0.25
31 38 0.62
32 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (29 bp):
ATATTTATTATTATATTAAATTATTCAAA
Found at i:201416 original size:25 final size:26
Alignment explanation
Indices: 201388--201450 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
201378 TAAAAAACCT
201388 ATTTTTATAATTTACATA-TTATATA
1 ATTTTTATAATTTACATATTTATATA
** * *
201413 ATTTTCGTAATTTACTTATTTTTATA
1 ATTTTTATAATTTACATATTTATATA
201439 ATATTTTGATAA
1 AT-TTTT-ATAA
201451 AAAGACACGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 15 0.52
26 8 0.28
27 3 0.10
28 3 0.10
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (26 bp):
ATTTTTATAATTTACATATTTATATA
Found at i:206250 original size:23 final size:23
Alignment explanation
Indices: 206210--206254 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
206200 AAGTTTAAAT
206210 ATTAAGATTAAAAGATTAGTATAA
1 ATTAAGATTAAAAGATTA-TATAA
**
206234 ATTAAG-TTAAACTATTATATA
1 ATTAAGATTAAAAGATTATATA
206255 TATACATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTAAGATTAAAAGATTATATAA
Found at i:207034 original size:112 final size:109
Alignment explanation
Indices: 206901--207149 Score: 279
Period size: 111 Copynumber: 2.2 Consensus size: 109
206891 GGCCATTAGA
* * *
206901 TGACAAACACCAAAATATAATTTTTTTTATTTTTGGGTGTCGGCTATGAGTTGGCAATTAC-CCA
1 TGACAGACACCAAAATATAATTTTTTTTA-TTTTGGGTGTCGGCAATGAGATGGCAA--ACACCA
206965 AAAAATATATTTTTGAGTATATAGAAAAAAAG-GTGTCGA-TCATGGGT
63 AAAAA-ATATTTTTGAGTATATAGAAAAAAAGCGTGTCGACT-ATGGGT
* * * **
207012 TGACAGACACCCAAAAAATAATTTTAATTTATTTTGGGTGTTGGCAATGAGATGGCAAACACCTG
1 TGACAGACA-CCAAAATATAATTTT-TTTTATTTTGGGTGTCGGCAATGAGATGGCAAACACCAA
* * * **
207077 AAAAATATTTTTGGGTATCTGGAAAAAGGGCGTGTCGACTATGGGT
64 AAAAATATTTTTGAGTATATAGAAAAAAAGCGTGTCGACTATGGGT
*
207123 TGGCAGACACCAAAATATATATTTTTT
1 TGACAGACACCAAAATATA-ATTTTTT
207150 GGTATCTGAA
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
110 33 0.28
111 40 0.34
112 39 0.34
113 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (109 bp):
TGACAGACACCAAAATATAATTTTTTTTATTTTGGGTGTCGGCAATGAGATGGCAAACACCAAAA
AAATATTTTTGAGTATATAGAAAAAAAGCGTGTCGACTATGGGT
Done.