Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014443.1 Kokia drynarioides strain JFW-HI SEQ_129482, 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: 258263
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:3246 original size:19 final size:19
Alignment explanation
Indices: 3224--3262 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3214 TGTAATATAG
3224 ATTT-AGTTTTTATATTTTA
1 ATTTCAGTTTTTAT-TTTTA
*
3243 ATTTCATTTTTTATTTTTA
1 ATTTCAGTTTTTATTTTTA
3262 A
1 A
3263 AATTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
ATTTCAGTTTTTATTTTTA
Found at i:3892 original size:21 final size:21
Alignment explanation
Indices: 3860--3899 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3850 TAAGAATGTA
*
3860 AAAAATTCTTAA-ATTTTTTT
1 AAAAATTATTAAGATTTTTTT
3880 AAAAATTAATTAAGATTTTT
1 AAAAATT-ATTAAGATTTTT
3900 GTTGTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
AAAAATTATTAAGATTTTTTT
Found at i:6013 original size:15 final size:15
Alignment explanation
Indices: 5980--6014 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5970 GCACTTATCA
**
5980 ATGTGCGAACCCTGT
1 ATGTGCGAACCCTAC
5995 ATGTGCGAACCCTAC
1 ATGTGCGAACCCTAC
6010 ATGTG
1 ATGTG
6015 AACCTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (15 bp):
ATGTGCGAACCCTAC
Found at i:6037 original size:38 final size:38
Alignment explanation
Indices: 5985--6057 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
5975 TATCAATGTG
5985 CGAACCCTGTATGTGCGAACCCTACATGTGAACCTTTA
1 CGAACCCTGTATGTGCGAACCCTACATGTGAACCTTTA
* *
6023 CGAACCCTAG-ATGTGTGAACCCTACCTGTGAACCT
1 CGAACCCT-GTATGTGCGAACCCTACATGTGAACCT
6058 GTTATGCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (38 bp):
CGAACCCTGTATGTGCGAACCCTACATGTGAACCTTTA
Found at i:13960 original size:19 final size:19
Alignment explanation
Indices: 13923--13960 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
13913 ATCTCGTTTC
*
13923 TAAAACTAAAATTACAAAA
1 TAAAACTAAAACTACAAAA
13942 TAAAACTACAAACTA-AAAA
1 TAAAACTA-AAACTACAAAA
13961 ACGGTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18
Consensus pattern (19 bp):
TAAAACTAAAACTACAAAA
Found at i:30823 original size:26 final size:26
Alignment explanation
Indices: 30788--30844 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
30778 ATTACACCCA
30788 AGAA-TGTCGCTGCACGAACATGTCC
1 AGAATTGTCGCTGCACGAACATGTCC
* *
30813 AGAATTGTCGCTGCATGAACGTGTCC
1 AGAATTGTCGCTGCACGAACATGTCC
*
30839 AAAATT
1 AGAATT
30845 ACGCCCAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (26 bp):
AGAATTGTCGCTGCACGAACATGTCC
Found at i:31664 original size:16 final size:16
Alignment explanation
Indices: 31643--31673 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31633 TTGTGAATCC
31643 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
31659 CATTTTATCTTTATT
1 CATTTTACCTTTATT
31674 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:35169 original size:26 final size:25
Alignment explanation
Indices: 35134--35183 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
35124 ATTGCACCCA
*
35134 AGAATGTCGCTGCATGAACATGTCT
1 AGAATGTCGCTACATGAACATGTCT
*
35159 AGAATTGTCGCTACATGAACGTGTC
1 AGAA-TGTCGCTACATGAACATGTC
35184 CAAAATTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (25 bp):
AGAATGTCGCTACATGAACATGTCT
Found at i:35190 original size:26 final size:26
Alignment explanation
Indices: 35138--35191 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
35128 CACCCAAGAA
* * *
35138 TGTCGCTGCATGAACATGTCTAGAAT
1 TGTCGCTACATGAACATGTCCAAAAT
*
35164 TGTCGCTACATGAACGTGTCCAAAAT
1 TGTCGCTACATGAACATGTCCAAAAT
35190 TG
1 TG
35192 CGCCCAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (26 bp):
TGTCGCTACATGAACATGTCCAAAAT
Found at i:37861 original size:11 final size:11
Alignment explanation
Indices: 37845--37878 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
37835 TGTGAAGCTC
37845 AAAGAAAAGAA
1 AAAGAAAAGAA
*
37856 AAAGAAAAAAA
1 AAAGAAAAGAA
37867 AGAAGAAAAGAA
1 A-AAGAAAAGAA
37879 CCTAATGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:43197 original size:40 final size:40
Alignment explanation
Indices: 43134--43340 Score: 234
Period size: 40 Copynumber: 5.2 Consensus size: 40
43124 TGGTTTGAGT
* * * *
43134 TTTAACACCGGCTTAGAGCCTGCTAAGTCGTAGCTTGAAC
1 TTTATCACCGGCTCATAGCCTGCTAAGCCGTAGCTTGAAC
* * *
43174 TTTATCATCGGCTCATAGTCTGCTAAGCTGTAGCTTGAAC
1 TTTATCACCGGCTCATAGCCTGCTAAGCCGTAGCTTGAAC
* * * * *
43214 TTTACCACCGGCTCATAGCGTGTTAAGTCGTAGCTTGATC
1 TTTATCACCGGCTCATAGCCTGCTAAGCCGTAGCTTGAAC
* ** *
43254 TTTATCATCAACTCATAGCCTGCTAAGCCATAGCTTGAAC
1 TTTATCACCGGCTCATAGCCTGCTAAGCCGTAGCTTGAAC
* ** *
43294 TTTATCACCGGCTCATAACCTATTAAGCCATAGCTTGAAC
1 TTTATCACCGGCTCATAGCCTGCTAAGCCGTAGCTTGAAC
43334 TTTATCA
1 TTTATCA
43341 AATGTAACTT
Statistics
Matches: 137, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 137 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (40 bp):
TTTATCACCGGCTCATAGCCTGCTAAGCCGTAGCTTGAAC
Found at i:43277 original size:80 final size:80
Alignment explanation
Indices: 43134--43340 Score: 270
Period size: 80 Copynumber: 2.6 Consensus size: 80
43124 TGGTTTGAGT
* * * ** *
43134 TTTAACACCGGCTTAGAGCCTGCTAAGTCGTAGCTTGAACTTTATCATCGGCTCATAGTCTGCTA
1 TTTAACACCGGCTCATAGCCTGTTAAGTCGTAGCTTGAACTTTATCATCAACTCATAGCCTGCTA
**
43199 AGCTGTAGCTTGAAC
66 AGCCATAGCTTGAAC
* * *
43214 TTTACCACCGGCTCATAGCGTGTTAAGTCGTAGCTTGATCTTTATCATCAACTCATAGCCTGCTA
1 TTTAACACCGGCTCATAGCCTGTTAAGTCGTAGCTTGAACTTTATCATCAACTCATAGCCTGCTA
43279 AGCCATAGCTTGAAC
66 AGCCATAGCTTGAAC
* * * * *
43294 TTTATCACCGGCTCATAACCTATTAAGCCATAGCTTGAACTTTATCA
1 TTTAACACCGGCTCATAGCCTGTTAAGTCGTAGCTTGAACTTTATCA
43341 AATGTAACTT
Statistics
Matches: 109, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 109 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (80 bp):
TTTAACACCGGCTCATAGCCTGTTAAGTCGTAGCTTGAACTTTATCATCAACTCATAGCCTGCTA
AGCCATAGCTTGAAC
Found at i:52864 original size:3 final size:3
Alignment explanation
Indices: 52856--52883 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52846 AAGAGCACAA
52856 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
52884 GGGTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:53351 original size:23 final size:23
Alignment explanation
Indices: 53325--53402 Score: 56
Period size: 23 Copynumber: 3.4 Consensus size: 23
53315 AAATAATTTC
53325 GAAATAAAAGTTTTGATTTTTAA
1 GAAATAAAAGTTTTGATTTTTAA
*
53348 GAAA-AATAGTGATTT--TCTTTTAA
1 GAAATAAAAGT--TTTGAT-TTTTAA
* * *
53371 AAAAGAGAAAGTTTAGATTTTTAA
1 GAAATA-AAAGTTTTGATTTTTAA
53395 -AAATAAAA
1 GAAATAAAA
53403 TCTATTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
22 9 0.21
23 19 0.44
24 10 0.23
25 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (23 bp):
GAAATAAAAGTTTTGATTTTTAA
Found at i:53434 original size:21 final size:20
Alignment explanation
Indices: 53408--53463 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
53398 TAAAATCTAT
53408 TTTTAATTATTTTAAAGAAAA
1 TTTTAATT-TTTTAAAGAAAA
* * *
53429 TTTTAAATTTTTAAATAAAG
1 TTTTAATTTTTTAAAGAAAA
*
53449 TTTTACTTTTTTAAA
1 TTTTAATTTTTTAAA
53464 ACTATTTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTAATTTTTTAAAGAAAA
Found at i:53604 original size:19 final size:18
Alignment explanation
Indices: 53562--53596 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53552 TTTTTTAGTC
*
53562 ATTTTAAAAAAAAGTTTA
1 ATTTTTAAAAAAAGTTTA
*
53580 ATTTTTAAACAAAGTTT
1 ATTTTTAAAAAAAGTTT
53597 TGATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (18 bp):
ATTTTTAAAAAAAGTTTA
Found at i:53635 original size:144 final size:144
Alignment explanation
Indices: 53289--53799 Score: 568
Period size: 145 Copynumber: 3.5 Consensus size: 144
53279 AATAACCTGA
* * * *
53289 TTTTAGAA-AAAGTTTTGGTTTTTTTTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAA
1 TTTTA-AACAAAGTTTT-GATTTTTTTAACT-ATTTCGAAATAAAAGTTTAGATTTTTAAGTAAA
* * * * *
53353 ATAGTGATTTTCTTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAAT-AAAATCT-ATTTTTAATT
63 ATAGTGATTTTCATTTAAAAAAGAG--AGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTC
*
53416 ATTTTAAAGAAAATTTTAAAT
126 ATTTTAAA-AAAAATTT-AAT
* * * * *
53437 TTTTAAATAAAGTTTT-ACTTTTTTAAAACTATTTTGAATTAAAA-TTTTGAATTTTTAAGTAAA
1 TTTTAAACAAAGTTTTGA-TTTTTT-TAACTATTTCGAAATAAAAGTTTAG-ATTTTTAAGTAAA
* *
53500 ATAATGATTTTC-TTTAAAAAAGAGAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTCAT
63 ATAGTGATTTTCATTTAAAAAAGAGAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCAT
53564 TTTAAAAAAAAGTTTAAT
128 TTTAAAAAAAA-TTTAAT
* * *
53582 TTTTAAACAAAGTTTTGATTTTTTTAACTATTTTGAAATCAAAGTTTAGATTTTTAAGTAAACTA
1 TTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATA
* * * * * *
53647 GTGATTTTCATTAAAAAAAGAAAGTTTAGAGTTTAAAAAATAAAAATATGTGTTTTAGTGATTTT
66 GTGATTTTCATTTAAAAAAGAGAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCA-TTT
*
53712 TAAAAAAAATTAAAT
130 TAAAAAAAATTTAAT
* * * * *
53727 TTTTAAACAAAATTTTGATTTTTTTAATTATTTCGAAATAAAAATTTTA-ATTTTCAAGTAAAGT
1 TTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAAT-AAAAGTTTAGATTTTTAAGTAAAAT
53791 AGTGATTTT
65 AGTGATTTT
53800 GTTTTCATTC
Statistics
Matches: 316, Mismatches: 35, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
144 57 0.18
145 145 0.46
146 55 0.17
147 43 0.14
148 16 0.05
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (144 bp):
TTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATA
GTGATTTTCATTTAAAAAAGAGAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTT
AAAAAAAATTTAAT
Found at i:53747 original size:19 final size:18
Alignment explanation
Indices: 53705--53749 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
53695 TGTGTTTTAG
53705 TGATTTTTAAAAAAAATT
1 TGATTTTTAAAAAAAATT
** *
53723 AAATTTTTAAACAAAATTT
1 TGATTTTTAAA-AAAAATT
53742 TGATTTTT
1 TGATTTTT
53750 TTAATTATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (18 bp):
TGATTTTTAAAAAAAATT
Found at i:55345 original size:23 final size:20
Alignment explanation
Indices: 55319--55362 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 20
55309 GTTTTTTAGC
55319 ATTTGTGCATATTAGATTTATTT
1 ATTTGTGC--ATTA-ATTTATTT
55342 ATTTGTGCATTAATTTATTT
1 ATTTGTGCATTAATTTATTT
55362 A
1 A
55363 ATTTTCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
23 8 0.38
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (20 bp):
ATTTGTGCATTAATTTATTT
Found at i:58208 original size:4 final size:4
Alignment explanation
Indices: 58199--58244 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
58189 GTGCCCCAAT
* * * *
58199 TTCA TTCA TTCA TTCA TTCA TTTA ATCA TCCA TTCA TTCA CTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
58245 TGCTCATTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (4 bp):
TTCA
Found at i:58251 original size:24 final size:24
Alignment explanation
Indices: 58200--58245 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
58190 TGCCCCAATT
* *
58200 TCATTCATTCATTCATTCATTTAA
1 TCATCCATTCATTCACTCATTTAA
58224 TCATCCATTCATTCACTCATTT
1 TCATCCATTCATTCACTCATTT
58246 GCTCATTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (24 bp):
TCATCCATTCATTCACTCATTTAA
Found at i:67283 original size:125 final size:123
Alignment explanation
Indices: 66870--67314 Score: 435
Period size: 125 Copynumber: 3.6 Consensus size: 123
66860 AAGGAAAGCA
* * * * * * *
66870 TTCATTGCATTTAAAGGTCTAGGTGCGAAGGTTCATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TTCATTGCATTTAAAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCCCAAG
*
66935 TGTGGAGGTT-ATTTACTTTTCATTGCATTCAGAGACCCAGGTGTGGAGGTCCATTTACTT
66 TGTGGA--TTCATTTACTTTTCATCGCATT-AGAGACCCAGGTGTGGAGGTCCATTTACTT
* * * * *
66995 TTCATTGCGTTTAAAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATCGTACTTAAAGGCCCATG
1 TTCATTGCATTTAAAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCCCAAG
* * * * * * *
67060 TGTGGAGGTTCATTTGCTTTTTATCGTATTTAAAGACCTAGGTGTCGAGATCCATTTACTT
66 TGTGGA--TTCATTTACTTTTCATCGCA-TTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * * * * * * *
67121 TTCATTACATTTAGAGGCCCGGGTATGCA-GACTCATTTAATTTTCATTGCATTTAAAGGTCCAA
1 TTCATTGCATTTAAAGGCCCAGGTGTGGAGGTC-CATTTACTTTTCATTGCATTTAAAGGCCCAA
* * * *
67185 GTGTGGATATCCTTTACTTTTCATCGCATCTAGAGGCCCATGTGTGGAGGTTCATTTACTT
65 GTGTGGAT-TCATTTACTTTTCATCGCAT-TAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * ** * * * *
67246 TTCATTGCATTTAGAGGTCCACATGTGGAGGTCCATTTATTTTTAATTGCATTTAGAGGCCCAAA
1 TTCATTGCATTTAAAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCCCAAG
67311 TGTG
66 TGTG
67315 AGGTCTATTT
Statistics
Matches: 258, Mismatches: 56, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
124 2 0.01
125 158 0.61
126 96 0.37
127 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (123 bp):
TTCATTGCATTTAAAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCCCAAG
TGTGGATTCATTTACTTTTCATCGCATTAGAGACCCAGGTGTGGAGGTCCATTTACTT
Found at i:67314 original size:42 final size:42
Alignment explanation
Indices: 66870--67308 Score: 434
Period size: 42 Copynumber: 10.5 Consensus size: 42
66860 AAGGAAAGCA
* * * * * *
66870 TTCATTGCATTTAAAGGTCTAGGTGCGAAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
66912 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGT-TATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
66953 TTCATTGCATTCAGAGACCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
66995 TTCATTGCGTTTAAAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * * *
67037 TTCATCGTACTTAAAGGCCCATGTGTGGAGGTTCATTTGCTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * * * *
67079 TTTATCGTATTTAAAGACCTAGGTGTCGAGATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * *
67121 TTCATTACATTTAGAGGCCCGGGTATGCA-GACTCATTTAATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
* * * **
67163 TTCATTGCATTTAAAGGTCCAAGTGTGGATATCC-TTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
67204 TTCATCGCATCTAGAGGCCCATGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* ** *
67246 TTCATTGCATTTAGAGGTCCACATGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
67288 TTAATTGCATTTAGAGGCCCA
1 TTCATTGCATTTAGAGGCCCA
67309 AATGTGAGGT
Statistics
Matches: 323, Mismatches: 70, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
41 71 0.22
42 251 0.78
43 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:67749 original size:3 final size:3
Alignment explanation
Indices: 67743--67770 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
67733 AATAATAATA
67743 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
67771 GGGTTTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:68419 original size:147 final size:148
Alignment explanation
Indices: 68173--68687 Score: 568
Period size: 147 Copynumber: 3.5 Consensus size: 148
68163 TGATTTTGGA
* * * * * *
68173 AAAATTTTG-GTTTTTTTAAACAATTTCGAAATAAAAGTTTTGATTTATAAG-AAATATAGTGAT
1 AAAATTTTGATTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAA-ATAGTGAT
* *
68236 TTTCTTTAAAAAAGAG-AAGATTTAGATTTTTAAAAATAAAAATCTGTATTTTAGTTA-TTTAAA
65 TTTCTTTAAAAAAGAGAAAG-TTTAGATTTTTAAAAATAAAAATATGT-TTTTAGTCATTTTAAA
* *
68299 GAAAATTTTAAAATTTTAAGC
128 GAAAAATTTAAAATTTTAAAC
* * ** *
68320 AAACTTTTGA-TTTTTTTTAATTATTTTGAAATAAAAATTTAGATTTTTAAGTAAAATAGTGATT
1 AAAATTTTGATTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATT
* *
68384 TTCTTTAAAAAAGAGAAAGTTTAGATTTTTGAAAATAAAAATTTGTTTTTA-TCCATTTTAAAGA
66 TTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTAGT-CATTTTAAAGA
* *
68448 AAAGTTTAAATTTTTAAAC
130 AAAATTTAAAATTTTAAAC
* * * * * *
68467 AAAGTTTTGATTTTTTTTTAACTATTCCAAAATAAAAGTTTGGATTTTTAAGCAAAGTAGTGATT
1 AAAATTTTGATTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATT
* * *
68532 TTCATT---AAA-A-AAATTTTAGATTTTTTAAAAA-ATAAAATATGTTTTTTAGTGATTTTAAA
66 TTCTTTAAAAAAGAGAAAGTTTAGA-TTTTTAAAAATA-AAAATATG-TTTTTAGTCATTTTAAA
*
68591 GAAAAAGTTAGAAATTTTAAAC
128 GAAAAATTTA-AAATTTTAAAC
* *
68613 AAAATTTTGATTTTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTGAAGTAAAGTAGTGA
1 AAAATTTTGA--TTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGA
*
68678 TTTTTTTTAA
64 TTTTCTTTAA
68688 TCAAAAGAAA
Statistics
Matches: 314, Mismatches: 39, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
143 10 0.03
144 17 0.05
145 26 0.08
146 26 0.08
147 124 0.39
148 111 0.35
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (148 bp):
AAAATTTTGATTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATT
TTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTAGTCATTTTAAAGAA
AAATTTAAAATTTTAAAC
Found at i:68629 original size:148 final size:147
Alignment explanation
Indices: 68173--68687 Score: 532
Period size: 148 Copynumber: 3.5 Consensus size: 147
68163 TGATTTTGGA
* * * * * *
68173 AAAATTTTG-GTTTTTTTAAACAATTTCGAAATAAAAGTTTTGATTTATAAG-AAATATAGTGAT
1 AAAATTTTGATTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAA-ATAGTGAT
* * *
68236 TTTCTTTAAAAAAGAGAAGATTTAGA-TTTTT-AAAAATAAAAATCTGTATTTTAGTTA-TTTAA
65 TTTCTTT-AAAAAGA-AA-ATTTAGATTTTTTAAAAAAT-AAAATATGTTTTTTAGTCATTTTAA
** *
68298 AGAAAATTTTAAAATTTTAAGC
126 AGAAAAAGTTAAAATTTTAAAC
* * ** *
68320 AAACTTTTGA-TTTTTTTTAATTATTTTGAAATAAAAATTTAGATTTTTAAGTAAAATAGTGATT
1 AAAATTTTGATTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATT
* * *
68384 TTCTTTAAAAAAGAGAAAGTTTAGATTTTTGAAAATA-AAAATTTG-TTTTTA-TCCATTTTAAA
66 TTCTTT-AAAAAGA-AAA-TTTAGATTTTTTAAAAAATAAAATATGTTTTTTAGT-CATTTTAAA
*
68446 G-AAAAGTTTAAATTTTTAAAC
127 GAAAAAG-TTAAAATTTTAAAC
* * * * * *
68467 AAAGTTTTGATTTTTTTTTAACTATTCCAAAATAAAAGTTTGGATTTTTAAGCAAAGTAGTGATT
1 AAAATTTTGATTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATT
* * *
68532 TTCATT-AAAA-AAATTTTAGATTTTTTAAAAAATAAAATATGTTTTTTAGTGATTTTAAAGAAA
66 TTCTTTAAAAAGAAAATTTAGATTTTTTAAAAAATAAAATATGTTTTTTAGTCATTTTAAAGAAA
68595 AAGTTAGAAATTTTAAAC
131 AAGTTA-AAATTTTAAAC
* *
68613 AAAATTTTGATTTTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTGAAGTAAAGTAGTGA
1 AAAATTTTGA--TTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGA
*
68678 TTTTTTTTAA
64 TTTTCTTTAA
68688 TCAAAAGAAA
Statistics
Matches: 310, Mismatches: 41, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
143 16 0.05
144 9 0.03
145 20 0.06
146 39 0.13
147 109 0.35
148 112 0.36
149 5 0.02
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (147 bp):
AAAATTTTGATTTTTTTTTAACTATTCCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATT
TTCTTTAAAAAGAAAATTTAGATTTTTTAAAAAATAAAATATGTTTTTTAGTCATTTTAAAGAAA
AAGTTAAAATTTTAAAC
Found at i:93269 original size:18 final size:18
Alignment explanation
Indices: 93231--93263 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
93221 AATTTAACTT
93231 TAATTAAATTTCTTAAAA
1 TAATTAAATTTCTTAAAA
93249 TAATT-AATTT-TTAAA
1 TAATTAAATTTCTTAAA
93264 TTATAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTAAATTTCTTAAAA
Found at i:93466 original size:27 final size:26
Alignment explanation
Indices: 93427--93479 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
93417 TTATTTTACT
93427 CTGAACCTCAAACATTAAACTCGAACC
1 CTGAACCTCAAACATTAAACTC-AACC
* * * *
93454 CTGAACTTTAAACCTTGAACTCAACC
1 CTGAACCTCAAACATTAAACTCAACC
93480 ATCAAAGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.38, C:0.32, G:0.08, T:0.23
Consensus pattern (26 bp):
CTGAACCTCAAACATTAAACTCAACC
Found at i:93532 original size:33 final size:33
Alignment explanation
Indices: 93481--93562 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
93471 AACTCAACCA
* *
93481 TCAAAGTTTAAGGTTTGGGTTCAGGATTTA-ATAT
1 TCAAGGTTTAA-GTTTGGGTTCAGGATTGAGAT-T
**
93515 TCAAGGTTTAAGTTTGGGTTTTGGATTGAGATT
1 TCAAGGTTTAAGTTTGGGTTCAGGATTGAGATT
*
93548 TTAAGGTTTAAGTTT
1 TCAAGGTTTAAGTTT
93563 AGGATTCACG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 30 0.71
34 12 0.29
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.45
Consensus pattern (33 bp):
TCAAGGTTTAAGTTTGGGTTCAGGATTGAGATT
Found at i:96255 original size:37 final size:37
Alignment explanation
Indices: 96207--96278 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
96197 AGCATTTAAC
*
96207 TTTTTGAATACTTCTATTTTTATCATTCAAATAAACT
1 TTTTTGAATACTTCTACTTTTATCATTCAAATAAACT
*
96244 TTTTTGGATACTTCTACTTTTATCATTCAAATAAA
1 TTTTTGAATACTTCTACTTTTATCATTCAAATAAA
96279 AACATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (37 bp):
TTTTTGAATACTTCTACTTTTATCATTCAAATAAACT
Found at i:100948 original size:156 final size:157
Alignment explanation
Indices: 100783--101096 Score: 621
Period size: 156 Copynumber: 2.0 Consensus size: 157
100773 ACTATTTAAT
100783 TCAAAATTTAAATTTTTTATCGAGTTTTTCGAATCGAATCGGATTTTGCTCACCCCTACTCATGA
1 TCAAAATTTAAATTTTTTATCGAGTTTTTCGAATCGAATCGGATTTTGCTCACCCCTACTCATGA
100848 CAACATCACATGATATCTCATATTATACATATTCAATCTTGAATACTAACTTTTCAAATGATCTC
66 CAACATCACATGATATCTCATATTATACATATTCAATCTTGAATACTAACTTTTCAAATGATCTC
100913 TTGAACAAATTTGTT-AAACATTTATA
131 TTGAACAAATTTGTTAAAACATTTATA
100939 TCAAAATTTAAATTTTTTATCGAGTTTTTCGAATCGAATCGGATTTTGCTCACCCCTACTCATGA
1 TCAAAATTTAAATTTTTTATCGAGTTTTTCGAATCGAATCGGATTTTGCTCACCCCTACTCATGA
101004 CAACATCACATGATATCTCATATTATACATATTCAATCTTGAATACTAACTTTTCAAATGATCTC
66 CAACATCACATGATATCTCATATTATACATATTCAATCTTGAATACTAACTTTTCAAATGATCTC
101069 TTGAACAAATTTGTTAAAACATTTATA
131 TTGAACAAATTTGTTAAAACATTTATA
101096 T
1 T
101097 AACCCTTCTT
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 145 0.92
157 12 0.08
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (157 bp):
TCAAAATTTAAATTTTTTATCGAGTTTTTCGAATCGAATCGGATTTTGCTCACCCCTACTCATGA
CAACATCACATGATATCTCATATTATACATATTCAATCTTGAATACTAACTTTTCAAATGATCTC
TTGAACAAATTTGTTAAAACATTTATA
Found at i:102589 original size:41 final size:40
Alignment explanation
Indices: 102544--102628 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
102534 GTGGCATTTT
*
102544 TAGCGGTGTTTGGACAGAAAACGCCGCAAAAGGTAAAGCAA
1 TAGCGGCGTTTGGACA-AAAACGCCGCAAAAGGTAAAGCAA
** * *
102585 TAGCGGCGTTTTTACATAAACGCCGCAAAAGGTAGAGCAA
1 TAGCGGCGTTTGGACAAAAACGCCGCAAAAGGTAAAGCAA
102625 TAGC
1 TAGC
102629 AATGCTTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 26 0.67
41 13 0.33
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (40 bp):
TAGCGGCGTTTGGACAAAAACGCCGCAAAAGGTAAAGCAA
Found at i:102679 original size:41 final size:41
Alignment explanation
Indices: 102605--102758 Score: 220
Period size: 41 Copynumber: 3.8 Consensus size: 41
102595 TTTACATAAA
* *** *
102605 CGCCGCAAAAGGT-AGAGCAATAGCAATGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAG
* *
102645 CGCCGCTAAAGGTCAGAGTAATAGTGGCGCTTATGGGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAG
* *
102686 CGCCGCTAAAGGTCAGAGCAATAGCGACACTTATGGGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAG
102727 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
102759 GTCAAAGCAA
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 12 0.12
41 88 0.88
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAG
Found at i:102767 original size:21 final size:21
Alignment explanation
Indices: 102738--102779 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
102728 GCCGCTAAAG
*
102738 GTCAGAGCAATAGCGGCGCTT
1 GTCAAAGCAATAGCGGCGCTT
102759 GTCAAAGCAATAGCGGCGCTT
1 GTCAAAGCAATAGCGGCGCTT
102780 ATGGGAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (21 bp):
GTCAAAGCAATAGCGGCGCTT
Found at i:102808 original size:61 final size:63
Alignment explanation
Indices: 102697--102820 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 63
102687 GCCGCTAAAG
* *
102697 GTCAGAGCAATAGCGACACTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAA-TAGCGGCGCTT
1 GTCAAAGCAATAGCGACACTTATGGGCAAGCGCCGCTAAAGGTCAAAGCAATTAGCGGCGCTT
* * *
102759 GTCAAAGCAATAGCGGCGCTTATGGG-AAGTGCCGCTAAAGGTCAAAGCAATTAGCGGCGCTT
1 GTCAAAGCAATAGCGACACTTATGGGCAAGCGCCGCTAAAGGTCAAAGCAATTAGCGGCGCTT
102821 ATGTGAAAGC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 22 0.39
62 34 0.61
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.18
Consensus pattern (63 bp):
GTCAAAGCAATAGCGACACTTATGGGCAAGCGCCGCTAAAGGTCAAAGCAATTAGCGGCGCTT
Found at i:102820 original size:41 final size:40
Alignment explanation
Indices: 102759--102951 Score: 226
Period size: 41 Copynumber: 4.7 Consensus size: 40
102749 AGCGGCGCTT
* * *
102759 GTCAAAGCAATAGCGGCGCTTATGGGAAGTGCCGCTAAAG
1 GTCAGAGCAATAGCGGCGCTTATGGAAAGCGCCGCTAAAG
*
102799 GTCAAAGCAATTAGCGGCGCTTATGTGAAAGCGCCGCTAAAG
1 GTCAGAGCAA-TAGCGGCGCTTATG-GAAAGCGCCGCTAAAG
*
102841 GTCAGAGCAATAGCGGCGCTTATAGGAAAGCGCCGCTAAAA
1 GTCAGAGCAATAGCGGCGCTTAT-GGAAAGCGCCGCTAAAG
* * * * *
102882 GTTAGAGCAATAGCGACACTTATGGGCAAGAC-CCACTAAAG
1 GTCAGAGCAATAGCGGCGCTTAT-GGAAAG-CGCCGCTAAAG
*
102923 GTCAGAGCATTAGCGGCGCTTATGTGAAA
1 GTCAGAGCAATAGCGGCGCTTATG-GAAA
102952 AACACCACTA
Statistics
Matches: 132, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
40 11 0.08
41 96 0.73
42 25 0.19
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.18
Consensus pattern (40 bp):
GTCAGAGCAATAGCGGCGCTTATGGAAAGCGCCGCTAAAG
Found at i:102843 original size:103 final size:103
Alignment explanation
Indices: 102664--102861 Score: 317
Period size: 103 Copynumber: 1.9 Consensus size: 103
102654 AGGTCAGAGT
* * *
102664 AATAGTGGCGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGACACTTATGGGCAAGCG
1 AATAGCGGCGCTTATGGGCAAGCGCCGCTAAAGGTCAAAGCAATAGCGACACTTATGGGAAAGCG
102729 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTGTCAAAGC
66 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTGTCAAAGC
* * * *
102767 AATAGCGGCGCTTATGGG-AAGTGCCGCTAAAGGTCAAAGCAATTAGCGGCGCTTATGTGAAAGC
1 AATAGCGGCGCTTATGGGCAAGCGCCGCTAAAGGTCAAAGCAA-TAGCGACACTTATGGGAAAGC
102831 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
65 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
102862 ATAGGAAAGC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 22 0.25
103 65 0.75
ACGTcount: A:0.29, C:0.22, G:0.31, T:0.18
Consensus pattern (103 bp):
AATAGCGGCGCTTATGGGCAAGCGCCGCTAAAGGTCAAAGCAATAGCGACACTTATGGGAAAGCG
CCGCTAAAGGTCAGAGCAATAGCGGCGCTTGTCAAAGC
Found at i:102880 original size:144 final size:144
Alignment explanation
Indices: 102632--102896 Score: 406
Period size: 144 Copynumber: 1.8 Consensus size: 144
102622 CAATAGCAAT
* * * *
102632 GCTTATGGGAAAGCGCCGCTAAAGGTCAGAGTAATAGTGGCGCTTATGGGCAAGCGCCGCTAAAG
1 GCTTATGGGAAAGCGCCGCTAAAGGTCAAAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAG
* * *
102697 GTCAGAGCAATAGCGACACTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTGTC
66 GTCAGAGCAATAGCGACACTTATAGGAAAGCGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTGTC
102762 AAAGCAATAGCGGC
131 AAAGCAATAGCGGC
* *
102776 GCTTATGGG-AAGTGCCGCTAAAGGTCAAAGCAATTAGCGGCGCTTATGTGAAAGCGCCGCTAAA
1 GCTTATGGGAAAGCGCCGCTAAAGGTCAAAGCAA-TAGCGGCGCTTATGGGAAAGCGCCGCTAAA
* * *
102840 GGTCAGAGCAATAGCGGCGCTTATAGGAAAGCGCCGCTAAAAGTTAGAGCAATAGCG
65 GGTCAGAGCAATAGCGACACTTATAGGAAAGCGCCGCTAAAAGTCAGAGCAATAGCG
102897 ACACTTATGG
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
143 21 0.19
144 87 0.81
ACGTcount: A:0.30, C:0.21, G:0.31, T:0.17
Consensus pattern (144 bp):
GCTTATGGGAAAGCGCCGCTAAAGGTCAAAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAG
GTCAGAGCAATAGCGACACTTATAGGAAAGCGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTGTC
AAAGCAATAGCGGC
Found at i:108966 original size:43 final size:43
Alignment explanation
Indices: 108913--109178 Score: 259
Period size: 43 Copynumber: 6.2 Consensus size: 43
108903 TTTGTTAATG
*
108913 TTAGTGGCGTTTGTGGGAAAA--ATGCTGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCAT-C-GCTAAAGACCATGTTCT
* ** * * *
108956 TTAGCGGCGTTTGCGGGAAAAGCGCCACTAAAGATCATGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAGACCATGTTCT
*
108999 TTAGCGGCGTTTGTGGGAAAAGCATCGTTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAGACCATGTTCT
* * * *
109042 TTAGCGGCATTTGTGAGAAAAGCATCGTTAAATACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAGACCATGTTCT
** * * * * * * *
109085 TTAGCATCATTTGTGAGATAAGCGTCGTTAAATACCATGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAGACCATGTTCT
** * *
109128 TTAGCGGCGTTTGTGCAAAAAGC-GCTGCTAAAAACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCATC-GCTAAAGACCATGTTCT
109171 TTAGCGGC
1 TTAGCGGC
109179 TTTTTTCTCA
Statistics
Matches: 188, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.01
43 186 0.99
44 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAGACCATGTTCT
Found at i:109063 original size:86 final size:86
Alignment explanation
Indices: 108913--109178 Score: 286
Period size: 86 Copynumber: 3.1 Consensus size: 86
108903 TTTGTTAATG
* * * *
108913 TTAGTGGCGTTTGTGGGAAAA--ATGCTGCTAAAGACCATGTTCTTTAGCGGCGTTTGCGGGAAA
1 TTAGCGGCGTTTGTGGGAAAAGCAT-C-GTTAAAGACCATGTTCTTTAGCGGCGTTTGTGAGAAA
* * * *
108976 AGCGCCACTAAAGATCATGGTCT
64 AGCGCCGCTAAAAACCATGTTCT
*
108999 TTAGCGGCGTTTGTGGGAAAAGCATCGTTAAAGACCATGTTCTTTAGCGGCATTTGTGAGAAAAG
1 TTAGCGGCGTTTGTGGGAAAAGCATCGTTAAAGACCATGTTCTTTAGCGGCGTTTGTGAGAAAAG
** * *
109064 CATCGTTAAATACCATGTTCT
66 CGCCGCTAAAAACCATGTTCT
** * * * * * *
109085 TTAGCATCATTTGTGAGATAAGCGTCGTTAAATACCATGGTCTTTAGCGGCGTTTGTGCA-AAAA
1 TTAGCGGCGTTTGTGGGAAAAGCATCGTTAAAGACCATGTTCTTTAGCGGCGTTTGTG-AGAAAA
*
109149 GCGCTGCTAAAAACCATGTTCT
65 GCGCCGCTAAAAACCATGTTCT
109171 TTAGCGGC
1 TTAGCGGC
109179 TTTTTTCTCA
Statistics
Matches: 149, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
86 145 0.97
87 2 0.01
88 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (86 bp):
TTAGCGGCGTTTGTGGGAAAAGCATCGTTAAAGACCATGTTCTTTAGCGGCGTTTGTGAGAAAAG
CGCCGCTAAAAACCATGTTCT
Found at i:112436 original size:3 final size:3
Alignment explanation
Indices: 112428--112455 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
112418 GACCCTCCTT
112428 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
112456 TATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:112725 original size:11 final size:11
Alignment explanation
Indices: 112696--112727 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
112686 GACCTCCTCT
*
112696 TCATCCACTCG
1 TCATCCATTCG
112707 TCATCCATTCG
1 TCATCCATTCG
112718 TCATCCATTC
1 TCATCCATTC
112728 CTTACATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.41, G:0.06, T:0.34
Consensus pattern (11 bp):
TCATCCATTCG
Found at i:116685 original size:14 final size:15
Alignment explanation
Indices: 116668--116696 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
116658 TTTTTCTATT
116668 TTCCTTCCC-TTTTC
1 TTCCTTCCCATTTTC
116682 TTCCTTCCCATTTTC
1 TTCCTTCCCATTTTC
116697 GTTTGAGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCCTTCCCATTTTC
Found at i:122275 original size:30 final size:30
Alignment explanation
Indices: 122241--122300 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
122231 TACCCTCGAG
122241 GCTCAAAATACGTATTAAAAGGGAATTGGT
1 GCTCAAAATACGTATTAAAAGGGAATTGGT
122271 GCTCAAAATACGTATTAAAAGGGAATTGGT
1 GCTCAAAATACGTATTAAAAGGGAATTGGT
122301 ACTTGTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (30 bp):
GCTCAAAATACGTATTAAAAGGGAATTGGT
Found at i:123547 original size:17 final size:18
Alignment explanation
Indices: 123515--123549 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
123505 AATTTCTATC
123515 CAATTTATACCCTAATTA
1 CAATTTATACCCTAATTA
*
123533 CAATTTA-ATCCTAATTA
1 CAATTTATACCCTAATTA
123550 ACTCATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (18 bp):
CAATTTATACCCTAATTA
Found at i:123948 original size:14 final size:15
Alignment explanation
Indices: 123931--123959 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
123921 TTTTTTCTTT
123931 TTCCTTCCC-TTTTC
1 TTCCTTCCCATTTTC
123945 TTCCTTCCCATTTTC
1 TTCCTTCCCATTTTC
123960 GTTTGAGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCCTTCCCATTTTC
Found at i:126766 original size:17 final size:17
Alignment explanation
Indices: 126744--126777 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
126734 TTAAAAAGGA
*
126744 AAATTCTTTTATAATTT
1 AAATTCTTTTAAAATTT
126761 AAATTCTTTTAAAATTT
1 AAATTCTTTTAAAATTT
126778 TTATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTCTTTTAAAATTT
Found at i:126871 original size:13 final size:13
Alignment explanation
Indices: 126845--126876 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
126835 AGTACTTCAA
126845 TAATTATTATTTT
1 TAATTATTATTTT
126858 TAATATATTATTTT
1 TAAT-TATTATTTT
126872 TAATT
1 TAATT
126877 TTTTTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TAATTATTATTTT
Found at i:134498 original size:33 final size:33
Alignment explanation
Indices: 134456--134544 Score: 178
Period size: 33 Copynumber: 2.7 Consensus size: 33
134446 ATACAAATTG
134456 AAATCCAAACTTAGAACACCCATTAGAAAAAAA
1 AAATCCAAACTTAGAACACCCATTAGAAAAAAA
134489 AAATCCAAACTTAGAACACCCATTAGAAAAAAA
1 AAATCCAAACTTAGAACACCCATTAGAAAAAAA
134522 AAATCCAAACTTAGAACACCCAT
1 AAATCCAAACTTAGAACACCCAT
134545 CAATCCATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.55, C:0.24, G:0.06, T:0.16
Consensus pattern (33 bp):
AAATCCAAACTTAGAACACCCATTAGAAAAAAA
Found at i:136870 original size:18 final size:18
Alignment explanation
Indices: 136844--136878 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
136834 ACCCGACCCG
136844 ACCCATTGACTTTGATCA
1 ACCCATTGACTTTGATCA
*
136862 ACCCGTTGACTTTGATC
1 ACCCATTGACTTTGATC
136879 TTTGACCGTT
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:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (18 bp):
ACCCATTGACTTTGATCA
Found at i:136901 original size:20 final size:20
Alignment explanation
Indices: 136864--136901 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
136854 TTTGATCAAC
*
136864 CCGTTGACTTTGATCTTTGA
1 CCGTTGACATTGATCTTTGA
136884 CCGTTGACCATTGA-CTTT
1 CCGTTGA-CATTGATCTTT
136902 TTTTAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (20 bp):
CCGTTGACATTGATCTTTGA
Found at i:140074 original size:15 final size:15
Alignment explanation
Indices: 140056--140086 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
140046 AAAAAAAAAA
140056 TAAAATAAAAGTAAT
1 TAAAATAAAAGTAAT
140071 TAAAATAAAAGTAAT
1 TAAAATAAAAGTAAT
140086 T
1 T
140087 GAATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
TAAAATAAAAGTAAT
Found at i:152688 original size:195 final size:195
Alignment explanation
Indices: 152294--152731 Score: 508
Period size: 195 Copynumber: 2.2 Consensus size: 195
152284 AACTGACGCA
* *
152294 ATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCATGAGTCGGG
1 ATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCATGACTCGGG
* * * *
152359 AAATGAGAAAAGAATCCAAGAATGAATTACAAGCCCTATGATGGCTGAGATTTATACATAAGTGC
66 AAAAGAGAAAAGAATCCAAGAATGAATTACAAGCCCTACGATAGCTGAGATCTATACATAAGTGC
* * * * * * *
152424 ATATTCTCGATAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTATATGCATAGATATCATATCG
131 ATACTCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTATATACAAACATAGCATACCG
* * * *
152489 ATGGCTGAGGTACCGCATATGTTGTGAGTCCTCGACAGTTCGTGTGAGCAACATCGTGACT-TGG
1 ATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCATGACTCGGG
* * * * * * * * * * *
152553 AAAAGAGATATGGATCCTA-AATGGATTATAGGCCCTACGATAGCTGGGA-CTATGCTTTA-TGC
66 AAAAGAGAAAAGAATCCAAGAATGAATTACAAGCCCTACGATAGCTGAGATCTATACATAAGTGC
*
152615 ATACTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTTATAGTACAAACA-AGCACCG
131 ATACTCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAG-TTATA-TACAAACATAGCA---
152679 TACCG
191 TACCG
* * *
152684 ATGGCTGGGGTATCGCATACGTTGCGAGTCCTCGACAGCTCGTGTGAG
1 ATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAG
152732 TAGCATCGAG
Statistics
Matches: 204, Mismatches: 34, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
191 42 0.21
192 14 0.07
193 29 0.14
194 16 0.08
195 103 0.50
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (195 bp):
ATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAACATCATGACTCGGG
AAAAGAGAAAAGAATCCAAGAATGAATTACAAGCCCTACGATAGCTGAGATCTATACATAAGTGC
ATACTCTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTATATACAAACATAGCATACCG
Found at i:155175 original size:41 final size:37
Alignment explanation
Indices: 155125--155212 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 37
155115 TAAAAAGTAT
*
155125 TTATATTAAAAAACACTATCACAAATATAATAAGTATTTTA
1 TTATATTAAAAAACA--A--ACAAATATAATAAATATTTTA
*
155166 TTATATTAAAAAACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAACAAACAAATATAATAAATATTTTA
*
155203 TTGTATTAAA
1 TTATATTAAA
155213 TATAATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 28 0.64
39 1 0.02
41 15 0.34
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (37 bp):
TTATATTAAAAAACAAACAAATATAATAAATATTTTA
Found at i:155774 original size:12 final size:13
Alignment explanation
Indices: 155749--155773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155739 GTTGCGGTTG
155749 AAAAGTGTTTTTT
1 AAAAGTGTTTTTT
155762 AAAAGTGTTTTT
1 AAAAGTGTTTTT
155774 AGAAAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
AAAAGTGTTTTTT
Found at i:156042 original size:31 final size:31
Alignment explanation
Indices: 155994--156101 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
155984 ATAAAATATT
* *
155994 TTTAAA-AAGTTAATATAATAATAATTAAAA
1 TTTAAATAATTTAATATAATAATAAATAAAA
* * * *
156024 TTTAAATAATTTGATATAATGATAAATGATA
1 TTTAAATAATTTAATATAATAATAAATAAAA
* *
156055 TTTAAATAATTTAATATAATGATATAT-AAA
1 TTTAAATAATTTAATATAATAATAAATAAAA
*
156085 TTATAAATTAATCTAAT
1 TT-TAAA-TAATTTAAT
156102 TTTTTATATA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 10 0.15
31 47 0.72
32 8 0.12
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.42
Consensus pattern (31 bp):
TTTAAATAATTTAATATAATAATAAATAAAA
Found at i:156787 original size:36 final size:35
Alignment explanation
Indices: 156725--156797 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
156715 TAAAAAAATA
*
156725 TTTATTTACTCAAATAATATACAAAAATTATTTAT
1 TTTATTTACTCAAATAATATACAAAAATTATTAAT
156760 TTTATTTGACT-AAAGTAATATTA-AAAAATTATTAAT
1 TTTATTT-ACTCAAA-TAATA-TACAAAAATTATTAAT
156796 TT
1 TT
156798 AATAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
35 10 0.29
36 22 0.65
37 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (35 bp):
TTTATTTACTCAAATAATATACAAAAATTATTAAT
Found at i:157200 original size:21 final size:21
Alignment explanation
Indices: 157171--157217 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
157161 AAATTGTTAT
*
157171 AATTAGTATGATATATT-TTTA
1 AATTTGTATGATAT-TTATTTA
**
157192 AATTTGTATTTTATTTATTTA
1 AATTTGTATGATATTTATTTA
157213 AATTT
1 AATTT
157218 TATTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
AATTTGTATGATATTTATTTA
Found at i:160160 original size:14 final size:14
Alignment explanation
Indices: 160123--160168 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
160113 TGGTTTCTAA
*
160123 TTTAGGGTTAAAGG
1 TTTAGGGTTCAAGG
* *
160137 TTTATGGTTCATGG
1 TTTAGGGTTCAAGG
*
160151 TTTAGGGTTCAGGG
1 TTTAGGGTTCAAGG
160165 TTTA
1 TTTA
160169 TAGGTATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.43
Consensus pattern (14 bp):
TTTAGGGTTCAAGG
Found at i:160420 original size:21 final size:21
Alignment explanation
Indices: 160396--160447 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
160386 TAGAGTCTAT
*
160396 TTGCCCCGGAGGAGTACAGTA
1 TTGCCCAGGAGGAGTACAGTA
**
160417 TTGCCCAATAGGAGTACAGTA
1 TTGCCCAGGAGGAGTACAGTA
*
160438 TT-CCCGGGAG
1 TTGCCCAGGAG
160448 CTCGTCAAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (21 bp):
TTGCCCAGGAGGAGTACAGTA
Found at i:162480 original size:16 final size:16
Alignment explanation
Indices: 162459--162507 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
162449 GGATGAGGAT
162459 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
*
162475 ATTATTTT-TTATATT-
1 ATTATTTTGGTA-ATTA
162490 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
162505 ATT
1 ATT
162508 TAGAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:163183 original size:12 final size:12
Alignment explanation
Indices: 163168--163212 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
163158 TCTTTCTCTT
163168 CTTCTTCTTCTC
1 CTTCTTCTTCTC
*
163180 CTTCTCCTTCTC
1 CTTCTTCTTCTC
*
163192 CTTTCTTTTTTCTC
1 C-TTC-TTCTTCTC
163206 CTTCTTC
1 CTTCTTC
163213 CTTTTTCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 14 0.52
13 6 0.22
14 7 0.26
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
CTTCTTCTTCTC
Found at i:163206 original size:14 final size:14
Alignment explanation
Indices: 163158--163247 Score: 73
Period size: 14 Copynumber: 6.4 Consensus size: 14
163148 AAATACATTA
163158 TCTTTCT-CTTC-T
1 TCTTTCTCCTTCTT
163170 TCTTCTTCTCCTTC--
1 TC-T-TTCTCCTTCTT
*
163184 TCCTTCTCCTTTCTT
1 TCTTTCTCC-TTCTT
163199 T-TTTCTCCTTCTT
1 TCTTTCTCCTTCTT
* *
163212 CCTTTTTCCTTCTT
1 TCTTTCTCCTTCTT
163226 TCTTTCTCTCTTTCTT
1 TCTTTCTC-C-TTCTT
163242 TCTTTC
1 TCTTTC
163248 CTTCAAACCC
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
12 8 0.13
13 9 0.14
14 29 0.46
15 6 0.10
16 11 0.17
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTTTCTCCTTCTT
Found at i:165077 original size:20 final size:20
Alignment explanation
Indices: 165040--165079 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
165030 ATAAAATAAT
*
165040 AAATAGAAATAAATAGATTA
1 AAATAGAAATAAACAGATTA
* *
165060 AAATAGAAATGACCAGATTA
1 AAATAGAAATAAACAGATTA
165080 GAACATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.23
Consensus pattern (20 bp):
AAATAGAAATAAACAGATTA
Found at i:166996 original size:30 final size:32
Alignment explanation
Indices: 166960--167027 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
166950 GGCTTCATTT
*
166960 CAGTCACCCAAC-TT-TGAAAAAGTGACAAAA
1 CAGTCACCCAACGTTATCAAAAAGTGACAAAA
*
166990 CAGTCA-CTAACGTTATCAAAAAGTGACAAAA
1 CAGTCACCCAACGTTATCAAAAAGTGACAAAA
*
167021 CAATCAC
1 CAGTCAC
167028 GGATTAACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 4 0.12
30 8 0.25
31 20 0.62
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (32 bp):
CAGTCACCCAACGTTATCAAAAAGTGACAAAA
Found at i:167611 original size:3 final size:3
Alignment explanation
Indices: 167600--167635 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
167590 TTCAGGCATC
*
167600 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
167636 AAACCCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TCT
Found at i:176815 original size:154 final size:154
Alignment explanation
Indices: 176535--177127 Score: 868
Period size: 154 Copynumber: 3.8 Consensus size: 154
176525 ACGTTCCATT
*
176535 GGTCCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCG
1 GGTCCCGTAGCTCAGTGGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCG
*
176600 CCGAGACCACCCTAAGCCCAAGAAGACTTTTTTAATTCTTAGGCTTTTTCATCAGCCCATAAAAT
66 CCGAGACCACCCTAAGCCCAAAAAGACTTTTTTAATTCTTAGGCTTTTTCATCAGCCCATAAAAT
176665 AGGCTTTGTTTTAAACAGCCGGCG
131 AGGCTTTGTTTTAAACAGCCGGCG
176689 GGTCCCGTAGCTCAGTGGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCG
1 GGTCCCGTAGCTCAGTGGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCG
*
176754 CCGAGACCACCCTAAGCCCAAAAAGACTTTTTTAATTCTTAGGCTTTTTCATCAACCCATAAAAT
66 CCGAGACCACCCTAAGCCCAAAAAGACTTTTTTAATTCTTAGGCTTTTTCATCAGCCCATAAAAT
*
176819 AGGCTTTGTTTTAAACTGCCGGCG
131 AGGCTTTGTTTTAAACAGCCGGCG
176843 GGTCCCGTAGCTCAGTGGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCG
1 GGTCCCGTAGCTCAGTGGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCG
* * *
176908 CCGGGACCACTCTAAGCCCAAAAAGAC-TTTTTAATTCTTAGGCTTTTTCATCAGCCCATAAATT
66 CCGAGACCACCCTAAGCCCAAAAAGACTTTTTTAATTCTTAGGCTTTTTCATCAGCCCATAAAAT
* *
176972 AAGCTTTGTTTTAAATAGTCGGCGGGGCTGGGATTCTTG
131 AGGCTTTGTTTT-AA-A--CAGC----C--GG---C--G
177011 TTGGTCCCGTAGCTCAGCT-GGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCC
1 --GGTCCCGTAGCTCAG-TGGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCC
* * ** * *
177075 CCGCCGGGACCACCTTAAGTTCATAAA-ACTTTTTTAATTCTTAGGCCTTTTCA
63 CCGCCGAGACCACCCTAAGCCCAAAAAGACTTTTTTAATTCTTAGGCTTTTTCA
177128 GCCCAAGCTT
Statistics
Matches: 404, Mismatches: 16, Indels: 22
0.91 0.04 0.05
Matches are distributed among these distances:
153 46 0.11
154 242 0.60
155 1 0.00
157 3 0.01
161 1 0.00
163 2 0.00
166 1 0.00
168 1 0.00
169 2 0.00
170 104 0.26
171 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (154 bp):
GGTCCCGTAGCTCAGTGGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCG
CCGAGACCACCCTAAGCCCAAAAAGACTTTTTTAATTCTTAGGCTTTTTCATCAGCCCATAAAAT
AGGCTTTGTTTTAAACAGCCGGCG
Found at i:177239 original size:160 final size:163
Alignment explanation
Indices: 176846--177246 Score: 488
Period size: 160 Copynumber: 2.4 Consensus size: 163
176836 GCCGGCGGGT
*
176846 CCCGTAGCTCAGTGGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCGCCG
1 CCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCGCCG
*
176911 GGACCACTCTAAGCCCAAAAAGACTTTTTAATTCTTAGGCTTTTTCATCAGCCCATAAATTAAGC
66 GGACCACTCTAAGCCCAAAAAGACTTTTTAATTCTTAGGCTCTTT-ATCAGCCC----A--AAGC
* **** * * *
176976 TTTGTTTTAAATAGTCGGCGGGGCTGGGATTCTTGTTGGT
124 TTTGTTTTAAATAGCCGGCGGGGCACAAACTCTCGTTGGC
*
177016 CCCGTAGCTCAGCTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCGCCG
1 CCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCGCCG
** *
177081 GGACCAC-CTTAAGTTCATAAA-ACTTTTTTAATTCTTAGGC-CTTT-TCAGCCC-AAGCTTTGT
66 GGACCACTC-TAAGCCCAAAAAGAC-TTTTTAATTCTTAGGCTCTTTATCAGCCCAAAGCTTTGT
* *
177141 TTTAATTAGCCGGCGGGGCACAAACTGTCGTTGGC
129 TTTAAATAGCCGGCGGGGCACAAACTCTCGTTGGC
* * * * *
177176 CCCGTAGCTCAGTTAGTTAGAGCGTAGGTCTTATGAGCCGAAAGTCACGGGTTCGAACCCCGCCG
1 CCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCGCCG
*
177241 AGACCA
66 GGACCA
177247 AGCTTTGTTT
Statistics
Matches: 206, Mismatches: 23, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
160 98 0.48
167 7 0.03
169 6 0.03
170 95 0.46
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.28
Consensus pattern (163 bp):
CCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCCGCCG
GGACCACTCTAAGCCCAAAAAGACTTTTTAATTCTTAGGCTCTTTATCAGCCCAAAGCTTTGTTT
TAAATAGCCGGCGGGGCACAAACTCTCGTTGGC
Found at i:178596 original size:24 final size:25
Alignment explanation
Indices: 178562--178612 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
178552 AATCTAGACT
*
178562 AATAAGAGTTTGACTCAAACAAATA
1 AATAAGAGTTTAACTCAAACAAATA
* *
178587 AATAA-AGTTTAATTGAAACAAATA
1 AATAAGAGTTTAACTCAAACAAATA
178611 AA
1 AA
178613 CAGAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (25 bp):
AATAAGAGTTTAACTCAAACAAATA
Found at i:178621 original size:24 final size:24
Alignment explanation
Indices: 178578--178628 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
178568 AGTTTGACTC
*
178578 AAACAAATAAATAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
178602 AAACAAATAAACAGAA-TTTAATTG
1 AAACAAATAAACA-AAGTTTAATTG
178626 AAA
1 AAA
178629 TATTATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:181146 original size:12 final size:12
Alignment explanation
Indices: 181132--181195 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
181122 CCAGACAATC
*
181132 AAAATAACAACC
1 AAAATAACAACA
* * *
181144 AAAACAGCAGCA
1 AAAATAACAACA
* *
181156 AAAATAATAAAA
1 AAAATAACAACA
181168 AAAATAACAACA
1 AAAATAACAACA
*
181180 AAAATAACAATA
1 AAAATAACAACA
181192 AAAA
1 AAAA
181196 CAGCACCAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.73, C:0.14, G:0.03, T:0.09
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:181160 original size:24 final size:23
Alignment explanation
Indices: 181132--181208 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 23
181122 CCAGACAATC
*
181132 AAAATAACAACCAAAACAGCAGCA
1 AAAATAACAACAAAAACAGCA-CA
* * * *
181156 AAAATAATAAAAAAAATAACAACA
1 AAAATAACAACAAAAACAGC-ACA
* *
181180 AAAATAACAATAAAAACAGCACC
1 AAAATAACAACAAAAACAGCACA
181203 AAAATA
1 AAAATA
181209 GCAGCCAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
23 8 0.19
24 33 0.79
25 1 0.02
ACGTcount: A:0.70, C:0.17, G:0.04, T:0.09
Consensus pattern (23 bp):
AAAATAACAACAAAAACAGCACA
Found at i:184000 original size:2 final size:2
Alignment explanation
Indices: 183995--184026 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
183985 AAAAAAAAAA
183995 AT 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 AT
184027 TTTCAGAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185270 original size:27 final size:27
Alignment explanation
Indices: 185220--185271 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
185210 GTTCTTTTAA
* *
185220 TTCTCTTTTTTTTTCATTCTCTTCTGC
1 TTCTCTTTTTTTTTCACTCCCTTCTGC
185247 TTCTCTTTTTGTTTTC-CTCCCTTCT
1 TTCTCTTTTT-TTTTCACTCCCTTCT
185272 TCGTTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.02, C:0.29, G:0.04, T:0.65
Consensus pattern (27 bp):
TTCTCTTTTTTTTTCACTCCCTTCTGC
Found at i:187984 original size:35 final size:36
Alignment explanation
Indices: 187944--188012 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
187934 AAGAATTATT
187944 AAATTATTACAAAA-TG-AAAATAA-TATAAATTATAA
1 AAATTATTA-AAAATTGAAAAATAATTA-AAATTATAA
187979 AAATTATTAAAAATTGAAAAATAATTAAAATTAT
1 AAATTATTAAAAATTGAAAAATAATTAAAATTAT
188013 GAATCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 4 0.13
35 11 0.35
36 14 0.45
37 2 0.06
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (36 bp):
AAATTATTAAAAATTGAAAAATAATTAAAATTATAA
Found at i:187991 original size:10 final size:9
Alignment explanation
Indices: 187960--188103 Score: 51
Period size: 9 Copynumber: 15.4 Consensus size: 9
187950 TTACAAAATG
*
187960 AAAATAATA
1 AAAATTATA
*
187969 TAAATTATA
1 AAAATTATA
187978 AAAATTATTA
1 AAAATTA-TA
*
187988 AAAATT-GA
1 AAAATTATA
* *
187996 AAAATAATT
1 AAAATTATA
188005 AAAATTATGA
1 AAAATTAT-A
*** *
188015 ATCTTTTTAA
1 AAAATTAT-A
*
188025 AAAATTGTA
1 AAAATTATA
*
188034 AAAATTTTA
1 AAAATTATA
188043 AAAA-TATA
1 AAAATTATA
*
188051 GAAAAGTGA-A
1 -AAAA-TTATA
*
188061 AAAATAAATA
1 AAAAT-TATA
**
188071 AAGTTTATA
1 AAAATTATA
188080 AAAATTTATA
1 AAAA-TTATA
*
188090 TAAAATTACA
1 -AAAATTATA
188100 AAAA
1 AAAA
188104 AAAAATTGAA
Statistics
Matches: 97, Mismatches: 28, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
8 10 0.10
9 51 0.53
10 31 0.32
11 5 0.05
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:188374 original size:20 final size:18
Alignment explanation
Indices: 188351--188403 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
188341 ATTTTAATAA
188351 TTTATATAATTTTTTGCTGT
1 TTTATATAATTTTTTG-T-T
* *
188371 TTTATATAAGTTTATGTT
1 TTTATATAATTTTTTGTT
*
188389 TTTTTATAATTTTTT
1 TTTATATAATTTTTT
188404 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 13 0.46
19 1 0.04
20 14 0.50
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.68
Consensus pattern (18 bp):
TTTATATAATTTTTTGTT
Found at i:188549 original size:17 final size:17
Alignment explanation
Indices: 188527--188560 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
188517 TGGTTGATGT
188527 TAACTTTAA-TGATTAAA
1 TAAC-TTAATTGATTAAA
188544 TAACTTAATTGATTAAA
1 TAACTTAATTGATTAAA
188561 ATTTTGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TAACTTAATTGATTAAA
Found at i:189486 original size:19 final size:19
Alignment explanation
Indices: 189462--189498 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
189452 GTCCAAGTGC
*
189462 ATAACTAGTATTACACCAT
1 ATAACTAGTACTACACCAT
189481 ATAACTAGTACTACACCA
1 ATAACTAGTACTACACCA
189499 CATTAAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAACTAGTACTACACCAT
Found at i:190493 original size:32 final size:32
Alignment explanation
Indices: 190452--190527 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
190442 TGTCAATCAT
* *
190452 TTCAATATCCAACAAGC-TTGAAATATAATAAA
1 TTCAATATCCAACAA-CTTTAAAACATAATAAA
*
190484 TTCAATATCCAACAACTTTAAAACATAATAAT
1 TTCAATATCCAACAACTTTAAAACATAATAAA
*
190516 TTCAAAATCCAA
1 TTCAATATCCAA
190528 AACAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (32 bp):
TTCAATATCCAACAACTTTAAAACATAATAAA
Found at i:198364 original size:15 final size:16
Alignment explanation
Indices: 198344--198388 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
198334 AGATCTTCCA
198344 ATCTTCATA-ATATCC
1 ATCTTCATAGATATCC
198359 ATCTTCATAGATAT-C
1 ATCTTCATAGATATCC
* *
198374 ATCGTCAGAGATATC
1 ATCTTCATAGATATC
198389 GTCATAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (16 bp):
ATCTTCATAGATATCC
Found at i:198778 original size:11 final size:11
Alignment explanation
Indices: 198762--198786 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
198752 TTATAGTACG
198762 AAAGATAATAA
1 AAAGATAATAA
198773 AAAGATAATAA
1 AAAGATAATAA
198784 AAA
1 AAA
198787 CGACTTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAGATAATAA
Found at i:202194 original size:26 final size:26
Alignment explanation
Indices: 202165--202290 Score: 130
Period size: 26 Copynumber: 4.9 Consensus size: 26
202155 GATAGAGTGT
* *
202165 AATTTTGTCTGGGCTCGTATGAGCTA
1 AATTTTGTCTAGGCTCGTAAGAGCTA
* * * *
202191 AATTTTTTTTAAGCTCATAAGAGCTA
1 AATTTTGTCTAGGCTCGTAAGAGCTA
* *
202217 AATTCTGTCTAGGCAT-GTAAGAGTTA
1 AATTTTGTCTAGGC-TCGTAAGAGCTA
* *
202243 AATTATGTCTAGGCTCGTAAAAGCTA
1 AATTTTGTCTAGGCTCGTAAGAGCTA
*
202269 AACTTTGTCTA-GCTCGTAAGAG
1 AATTTTGTCTAGGCTCGTAAGAG
202291 TTAACCTCTG
Statistics
Matches: 80, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
25 11 0.14
26 68 0.85
27 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (26 bp):
AATTTTGTCTAGGCTCGTAAGAGCTA
Found at i:204075 original size:15 final size:15
Alignment explanation
Indices: 204055--204103 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
204045 AAATCAATTT
204055 TTTATTT-GACAAAAA
1 TTTATTTAGA-AAAAA
204070 TTTATTTAGAAAAAA
1 TTTATTTAGAAAAAA
*
204085 -TTATTTATATAAAAA
1 TTTATTTAGA-AAAAA
204100 TTTA
1 TTTA
204104 ATAATTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.27
15 17 0.57
16 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (15 bp):
TTTATTTAGAAAAAA
Found at i:210918 original size:14 final size:14
Alignment explanation
Indices: 210899--210928 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
210889 TGTGTAATTC
210899 TTTTTATAATAAAT
1 TTTTTATAATAAAT
*
210913 TTTTTATCATAAAT
1 TTTTTATAATAAAT
210927 TT
1 TT
210929 GGAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTATAATAAAT
Found at i:215064 original size:14 final size:14
Alignment explanation
Indices: 215042--215075 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
215032 AATTAAATAT
*
215042 AAATAATATCTTAA
1 AAATTATATCTTAA
215056 AAATTATATCTTAA
1 AAATTATATCTTAA
215070 AAATTA
1 AAATTA
215076 ATCCTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTATATCTTAA
Found at i:215600 original size:21 final size:22
Alignment explanation
Indices: 215565--215639 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 22
215555 CACATACAAT
215565 ATATACAATATTAAAATGA-AAAA
1 ATATA-AA-ATTAAAATGATAAAA
215588 ATATCAAAA-TAAAA-GACTAAAA
1 ATAT-AAAATTAAAATGA-TAAAA
*
215610 AT-TAAAATTAAAATTATAAAA
1 ATATAAAATTAAAATGATAAAA
215631 ATATTAAAA
1 ATA-TAAAA
215640 AAAGTTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
20 6 0.14
21 18 0.41
22 8 0.18
23 11 0.25
24 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.27
Consensus pattern (22 bp):
ATATAAAATTAAAATGATAAAA
Found at i:215781 original size:12 final size:12
Alignment explanation
Indices: 215764--215788 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
215754 TAAATTATTC
215764 TTATTGTTACGT
1 TTATTGTTACGT
215776 TTATTGTTACGT
1 TTATTGTTACGT
215788 T
1 T
215789 CTCAGTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TTATTGTTACGT
Found at i:219461 original size:87 final size:87
Alignment explanation
Indices: 219315--219474 Score: 257
Period size: 87 Copynumber: 1.8 Consensus size: 87
219305 AGTGTATTTG
* *
219315 TAACACCCAAAAACCCAAAACCATCTTCGATCTAAGGTCTTAGGGTTTACTGAATTTTTCGAGCC
1 TAACACCCAAAAACCCAAAACCATCTTCGATCTAAGGTCTTAGGGTTTACTAAACTTTTCGAGCC
219380 TTTCTTTTATGACCATTAAATA
66 TTTCTTTTATGACCATTAAATA
* * * *
219402 TAACACCCAAAAACCTAAAACCATTTTCGGTCTAAGGTCTTAGGGTTTACTAAACTTTTCGAGTC
1 TAACACCCAAAAACCCAAAACCATCTTCGATCTAAGGTCTTAGGGTTTACTAAACTTTTCGAGCC
*
219467 TTTTTTTT
66 TTTCTTTT
219475 CTCTCTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (87 bp):
TAACACCCAAAAACCCAAAACCATCTTCGATCTAAGGTCTTAGGGTTTACTAAACTTTTCGAGCC
TTTCTTTTATGACCATTAAATA
Found at i:221383 original size:14 final size:14
Alignment explanation
Indices: 221364--221393 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
221354 TCTATTAAAA
221364 TAATATCATTCAAT
1 TAATATCATTCAAT
221378 TAATATCATTCAAT
1 TAATATCATTCAAT
221392 TA
1 TA
221394 TTTAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATCATTCAAT
Found at i:221631 original size:16 final size:16
Alignment explanation
Indices: 221607--221637 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
221597 TCCTTACAAA
*
221607 TTTATTCCTTTAACAG
1 TTTAGTCCTTTAACAG
221623 TTTAGTCCTTTAACA
1 TTTAGTCCTTTAACA
221638 TAAAAATCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTAGTCCTTTAACAG
Found at i:228165 original size:14 final size:14
Alignment explanation
Indices: 228146--228173 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
228136 GTAAAATAAT
228146 GAAAATATTTTACA
1 GAAAATATTTTACA
228160 GAAAATATTTTACA
1 GAAAATATTTTACA
228174 TGCAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
GAAAATATTTTACA
Found at i:228590 original size:35 final size:36
Alignment explanation
Indices: 228520--228590 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
228510 TAATAAACAA
228520 ACATCAATAAATAAATAAAGAGTAAAAAGAGAGAGC
1 ACATCAATAAATAAATAAAGAGTAAAAAGAGAGAGC
228556 ACATCAATAAATAAATAAA-ATGT-AAAAGAGAGAGC
1 ACATCAATAAATAAATAAAGA-GTAAAAAGAGAGAGC
228591 GCAAACTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 13 0.38
36 21 0.62
ACGTcount: A:0.61, C:0.08, G:0.15, T:0.15
Consensus pattern (36 bp):
ACATCAATAAATAAATAAAGAGTAAAAAGAGAGAGC
Found at i:230146 original size:72 final size:72
Alignment explanation
Indices: 230019--230163 Score: 227
Period size: 72 Copynumber: 2.0 Consensus size: 72
230009 TAGATAAAAT
* * * *
230019 ATGGTTAACATTTAAATAACCCCAAATTTCTACGAACACAGGGCACTTGCGAAAAATGTGATCAG
1 ATGGCTAACATTTAAATAACCCAAAATTTCTACGAACACAAGGCACTTGCAAAAAATGTGATCAG
230084 AGGACTC
66 AGGACTC
* * *
230091 ATGGCTAAGATTTAAATAACCCAAAATTTTTACGGACACAAGGCACTTGCAAAAAATGTGATCAG
1 ATGGCTAACATTTAAATAACCCAAAATTTCTACGAACACAAGGCACTTGCAAAAAATGTGATCAG
230156 AGGACTC
66 AGGACTC
230163 A
1 A
230164 GTACCATTGC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (72 bp):
ATGGCTAACATTTAAATAACCCAAAATTTCTACGAACACAAGGCACTTGCAAAAAATGTGATCAG
AGGACTC
Found at i:235278 original size:8 final size:7
Alignment explanation
Indices: 235267--235307 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
235257 GTCCAATCCA
235267 ATTATTT
1 ATTATTT
235274 CATTATTT
1 -ATTATTT
235282 ATTATTT
1 ATTATTT
235289 ATT-TTT
1 ATTATTT
*
235295 TTTA-TT
1 ATTATTT
235301 ATTATTT
1 ATTATTT
235308 CCCTTTTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
6 10 0.34
7 12 0.41
8 7 0.24
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTATTT
Found at i:235292 original size:19 final size:16
Alignment explanation
Indices: 235267--235308 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
235257 GTCCAATCCA
235267 ATTATTTCATTATTTATT
1 ATTATTTC-TT-TTTATT
235285 ATTTATTT-TTTTTATT
1 A-TTATTTCTTTTTATT
235301 ATTATTTC
1 ATTATTTC
235309 CCTTTTCGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.27
16 7 0.32
17 2 0.09
18 1 0.05
19 6 0.27
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTATTTCTTTTTATT
Found at i:238088 original size:87 final size:87
Alignment explanation
Indices: 237932--238193 Score: 276
Period size: 87 Copynumber: 3.0 Consensus size: 87
237922 ATAAATATGC
* * * * ** * * *
237932 AACATTAGTGGTTTATCCACGAAATTTTTGGTAGCTTTTATCTATAAATATGTTGTGCACTCACA
1 AACACTAGTAGTTTATCCACAAAATTATCAGCAGCTTTTATCTGTAAATATGTTGTGCATTCACA
237997 ACCTACTGGCAGTTTATCTACA
66 ACCTACTGGCAGTTTATCTACA
* * *
238019 AGCACTAGTAGTTTATCCACAAAATTATCAGCAGCTTTTATTTGTAAATATGTTGAGCATTCACA
1 AACACTAGTAGTTTATCCACAAAATTATCAGCAGCTTTTATCTGTAAATATGTTGTGCATTCACA
* * * *
238084 ACCTATTGGAAATTTATCTGCA
66 ACCTACTGGCAGTTTATCTACA
* * * * * * *
238106 AATATTAGTTGTTCATCCACAAACTTA-CTAGCAGCTTTTATCTGCAAATATGTTGTGCATCCAC
1 AACACTAGTAGTTTATCCACAAAATTATC-AGCAGCTTTTATCTGTAAATATGTTGTGCATTCAC
* *
238170 AACCTACTAGCAG-TTATCTGCA
65 AACCTACTGGCAGTTTATCTACA
238192 AA
1 AA
238194 TACTGGTGTT
Statistics
Matches: 144, Mismatches: 30, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
86 12 0.08
87 132 0.92
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.35
Consensus pattern (87 bp):
AACACTAGTAGTTTATCCACAAAATTATCAGCAGCTTTTATCTGTAAATATGTTGTGCATTCACA
ACCTACTGGCAGTTTATCTACA
Found at i:238149 original size:46 final size:41
Alignment explanation
Indices: 237968--238195 Score: 140
Period size: 44 Copynumber: 5.3 Consensus size: 41
237958 TTTGGTAGCT
** *
237968 TTTATCTATAAATATGTTGTGCA-CTCACAACCTACTGGCAG
1 TTTATCTGCAAATATGTTGTGCATC-CACAACCTACTAGCAG
* * ** **
238009 TTTATCTACAAGCACTA-GTAGTTTATCCACAAAATTA-TCAGCAG
1 TTTATCTGCAA--A-TATGTTGTGCATCCAC-AACCTACT-AGCAG
* * * * * * * *
238053 CTTTTATTTGTAAATATGTTGAGCATTCACAACCTATTGGAAA
1 --TTTATCTGCAAATATGTTGTGCATCCACAACCTACTAGCAG
* *
238096 TTTATCTGCAAATATTAGTTGTTCATCCACAAACTTACTAGCAG
1 TTTATCTGCAAATA-T-GTTGTGCATCCAC-AACCTACTAGCAG
238140 CTTTTATCTGCAAATATGTTGTGCATCCACAACCTACTAGCAG
1 --TTTATCTGCAAATATGTTGTGCATCCACAACCTACTAGCAG
238183 -TTATCTGCAAATA
1 TTTATCTGCAAATA
238196 CTGGTGTTTC
Statistics
Matches: 140, Mismatches: 32, Indels: 31
0.69 0.16 0.15
Matches are distributed among these distances:
40 13 0.09
41 22 0.16
42 1 0.01
43 40 0.29
44 41 0.29
45 1 0.01
46 22 0.16
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (41 bp):
TTTATCTGCAAATATGTTGTGCATCCACAACCTACTAGCAG
Found at i:242464 original size:23 final size:23
Alignment explanation
Indices: 242421--242501 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
242411 TAATGTTCAC
*
242421 GAACATGTTCATTTAAC-TTAATT
1 GAACATGTTCA-TGAACATTAATT
**
242444 GAACATGTTCATGAACATTAAAC
1 GAACATGTTCATGAACATTAATT
* *
242467 AAACATATTCATGAACATATAATT
1 GAACATGTTCATGAACAT-TAATT
242491 GAACATGTTCA
1 GAACATGTTCA
242502 CGAATAATGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 4 0.09
23 31 0.66
24 12 0.26
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (23 bp):
GAACATGTTCATGAACATTAATT
Found at i:247534 original size:12 final size:12
Alignment explanation
Indices: 247517--247542 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
247507 AAAAATTAAT
247517 ATAATTTAAAAA
1 ATAATTTAAAAA
247529 ATAATTTAAAAA
1 ATAATTTAAAAA
247541 AT
1 AT
247543 GAAAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATTTAAAAA
Found at i:250419 original size:17 final size:17
Alignment explanation
Indices: 250397--250438 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
250387 GTTTTGTTTC
250397 TCAAAAGTATTTTTAAA
1 TCAAAAGTATTTTTAAA
* *
250414 TCAAAAAATATTTTTGAA
1 TC-AAAAGTATTTTTAAA
250432 -CAAAAGT
1 TCAAAAGT
250439 TAAAATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.24
17 3 0.14
18 13 0.62
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (17 bp):
TCAAAAGTATTTTTAAA
Found at i:251890 original size:30 final size:31
Alignment explanation
Indices: 251855--251914 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
251845 GCCCAATAAA
251855 TTAAAT-AAAAACTTTGAATAATTCAGTGAC
1 TTAAATGAAAAACTTTGAATAATTCAGTGAC
*** *
251885 TTAAATGAAAGTTTTTGAATAGTTCAGTGA
1 TTAAATGAAAAACTTTGAATAATTCAGTGA
251915 TCACATTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (31 bp):
TTAAATGAAAAACTTTGAATAATTCAGTGAC
Done.