Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005394.1 Hibiscus syriacus cultivar Beakdansim tig00012361_pilon, 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: 127775
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1386 original size:18 final size:19
Alignment explanation
Indices: 1365--1407 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1355 AATTTTGATA
*
1365 TTTATTATAAAGT-TTATT
1 TTTATTATAAAGTCTAATT
* *
1383 TTTATTTTAGAGTCTAATT
1 TTTATTATAAAGTCTAATT
1402 TTTATT
1 TTTATT
1408 TTTTGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTATTATAAAGTCTAATT
Found at i:2627 original size:189 final size:187
Alignment explanation
Indices: 2302--2687 Score: 460
Period size: 191 Copynumber: 2.1 Consensus size: 187
2292 ATTCTATATG
*
2302 GTGACGTTATGCATAATCATCATTCATAATATTATTAGGTACGATATTATGTCACTAAATGTGAC
1 GTGACGTTATGCATAAACATCATTCATAATATTATTAGGTACGATATTATGTCACTAAATGTGAC
* * * *
2367 AGTATCTTTTTCGTCATATATAAGTTGATTTTAATGCATTATTGTGACAATATAAGCTATCAATA
66 AATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTATGACAATATAAGCTATCAATA
** *
2432 ACGAAATCTTATTTAATTTAGTGACGTAACCAACTGTCATAGAATA-TAATTATAAA
131 ACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATTAATTATAAA
*
2488 GTGACGTTATGC-TAAACATCATTCATAATATTATTAGGTAACATTTATATTATGTCACTAAAAA
1 GTGACGTTATGCATAAACATCATTCATAATATTATTAGGT-AC---GATATTATGTCACT--AAA
* * * * *
2552 TTTGACAATATCTCTTTCGTCACATATATGTTGATTTTAATG-TTTATTCATGACGATATAA-AT
60 TGTGACAATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATT-ATGACAATATAAGCT
* ** ** * *
2615 CATC-A-AACGAAATTTTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATA
124 -ATCAATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATTAATTATAAA
*
2678 GTGATGTTAT
1 GTGACGTTAT
2688 ATATAAATGT
Statistics
Matches: 169, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
185 26 0.15
186 14 0.08
189 51 0.30
190 25 0.15
191 53 0.31
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (187 bp):
GTGACGTTATGCATAAACATCATTCATAATATTATTAGGTACGATATTATGTCACTAAATGTGAC
AATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTATGACAATATAAGCTATCAATA
ACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATTAATTATAAA
Found at i:10221 original size:14 final size:16
Alignment explanation
Indices: 10202--10239 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
10192 AAGTTCTATT
10202 AATAATA-TAT-ATAA
1 AATAATAGTATAATAA
10216 AATAATAGTATCAATAA
1 AATAATAGTAT-AATAA
10233 AATAATA
1 AATAATA
10240 ACAGTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 3 0.14
17 11 0.52
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
AATAATAGTATAATAA
Found at i:17977 original size:21 final size:21
Alignment explanation
Indices: 17953--18040 Score: 63
Period size: 21 Copynumber: 4.1 Consensus size: 21
17943 CCACAGCTCG
*
17953 TAATTTTCACGAAGTACCACA
1 TAATTGTCACGAAGTACCACA
* *
17974 TAATTGTCCCGAA-TGAGCACA
1 TAATTGTCACGAAGT-ACCACA
* *
17995 TAGGTT-TGCACCGAAGTGCCACA
1 TA-ATTGT-CA-CGAAGTACCACA
* *
18018 TAATTGTCCCGAAGAACCACA
1 TAATTGTCACGAAGTACCACA
18039 TA
1 TA
18041 GAACCCTCAA
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
20 1 0.02
21 31 0.62
22 6 0.12
23 11 0.22
24 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (21 bp):
TAATTGTCACGAAGTACCACA
Found at i:28574 original size:105 final size:105
Alignment explanation
Indices: 28456--28665 Score: 321
Period size: 105 Copynumber: 2.0 Consensus size: 105
28446 ACATTTTTAC
* *
28456 CTAAGTACACTTAATTTTTAGCTACAAAAGGAGGTTATCTCCTTCATTTTCAACTCACTCATTTC
1 CTAAGTACACTTAATTTTTAACTACAAAAGGAGGCTATCTCCTTCATTTTCAACTCACTCATTTC
* *
28521 TTCATTCTCCTCTCTTCTTCTGTGTTTTCTATATTCACAA
66 TTCATTCTCCTCTCTTCTTCTATATTTTCTATATTCACAA
* * * * *
28561 CTAAGTACCCTTAATTTTTAACTATAAAAGGAGGCTCTCTCCTTCATTTTTAACTTACTCATTTC
1 CTAAGTACACTTAATTTTTAACTACAAAAGGAGGCTATCTCCTTCATTTTCAACTCACTCATTTC
* *
28626 TTCATTCTCCTCTCTTCTTCTATATTTTCTCTCTTCACAA
66 TTCATTCTCCTCTCTTCTTCTATATTTTCTATATTCACAA
28666 GCATAGTGAA
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 94 1.00
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (105 bp):
CTAAGTACACTTAATTTTTAACTACAAAAGGAGGCTATCTCCTTCATTTTCAACTCACTCATTTC
TTCATTCTCCTCTCTTCTTCTATATTTTCTATATTCACAA
Found at i:32021 original size:2 final size:2
Alignment explanation
Indices: 32014--32048 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
32004 ATGGATTGCT
32014 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
32049 TTAGTATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:32109 original size:2 final size:2
Alignment explanation
Indices: 32102--32130 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32092 TCAATCTACA
32102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32131 ATTTACGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32308 original size:13 final size:13
Alignment explanation
Indices: 32287--32351 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
32277 AATGACGCTC
*
32287 AATGCGCGTCATA
1 AATGAGCGTCATA
*
32300 AATGAGCGTTATA
1 AATGAGCGTCATA
* *
32313 AATGTGTGTCATA
1 AATGAGCGTCATA
* *
32326 AATGCGTGTCATA
1 AATGAGCGTCATA
32339 AATGCA-CGTCATA
1 AATG-AGCGTCATA
32352 GATTTATGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:32349 original size:26 final size:26
Alignment explanation
Indices: 32287--32351 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
32277 AATGACGCTC
*
32287 AATGCGCGTCATAAATGAGCGTTATA
1 AATGCGCGTCATAAATGAGCGTCATA
* * * *
32313 AATGTGTGTCATAAATGCGTGTCATA
1 AATGCGCGTCATAAATGAGCGTCATA
*
32339 AATGCACGTCATA
1 AATGCGCGTCATA
32352 GATTTATGAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (26 bp):
AATGCGCGTCATAAATGAGCGTCATA
Found at i:33252 original size:24 final size:24
Alignment explanation
Indices: 33220--33278 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
33210 CTATTCTTTC
*
33220 GCTTCAATTGAGCTCAAATTTTTG
1 GCTTCAATTGAGCTCAAATTTTAG
33244 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
33268 GCTTCAATTGA
1 GCTTCAATTGA
33279 ACTTCTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:34209 original size:23 final size:23
Alignment explanation
Indices: 34183--34230 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
34173 ATAAAGTACA
*
34183 ATAACATACTAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
** *
34206 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
34229 AT
1 AT
34231 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:34683 original size:23 final size:23
Alignment explanation
Indices: 34648--34721 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
34638 ATACTTTACA
34648 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
34671 ATATAAACTCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
34694 ATATAAGCGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATT
34717 ATATA
1 ATATA
34722 TTTACCTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:37723 original size:183 final size:183
Alignment explanation
Indices: 37198--37688 Score: 858
Period size: 183 Copynumber: 2.7 Consensus size: 183
37188 TTAAAATTAC
* *
37198 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAGGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* * *
37263 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTTGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
37328 ATATTACAAAATTATCTATTACATTATAAATCTAGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATAGGTTCCGATGTGTAAATGT
37381 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
37446 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCAGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
37511 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATAGGTTCCGATGTGTAAATGT
*
37564 CGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* *
37628 TATTAAAAAGTGACGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATAC
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATAC
37689 TGATAGCATT
Statistics
Matches: 294, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 291 0.99
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATAGGTTCCGATGTGTAAATGT
Found at i:38107 original size:22 final size:23
Alignment explanation
Indices: 38069--38119 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
38059 ATACTTTACA
*
38069 ATATAACCACTACCTATTATATT
1 ATATAACCACTACCTATTACATT
*
38092 ATATAACGA-TACCTATTACATT
1 ATATAACCACTACCTATTACATT
38114 ATATAA
1 ATATAA
38120 GTGCTACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:38528 original size:23 final size:23
Alignment explanation
Indices: 38499--38556 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
38489 ATATAACCAC
38499 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
38522 TATCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
38545 TACCTATTACAT
1 TACCTATTACAT
38557 CACATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:38714 original size:421 final size:425
Alignment explanation
Indices: 37727--38761 Score: 1797
Period size: 426 Copynumber: 2.4 Consensus size: 425
37717 TTATAATATG
37727 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
37792 TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
37857 C-AAAAATTATTTGATTGTTTTGATATTTATAAAATAATATTAAGAATTTTTAATTTAATAATAA
130 CAAAAAATTATTTGATTGTTTTGATATTTATAAAAT-ATATTTAGAATTTTTAATTTAATAATAA
37921 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
194 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
*
37986 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
259 TCACTCAAAAGATAACCTTAAATTAATGATTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
*
38051 AAGGATAGATACTTTACAATATAACCACTACCTATTATATTATATAACGATACCTATTACATTAT
324 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAACGATACCTATTACATTAT
* *
38116 ATAAGTGCTACCTTACATCATATTTTTACCTATTATA
389 ATAAGCGCTACCTTACATCACATTTTTACCTATTATA
38153 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
38218 TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
38283 CAAAAAATTATTTGATT-ATTTGATATTTATAAAATATATTTAGAATTTTTAATTTAATAAT-A-
130 CAAAAAATTATTTGATTGTTTTGATATTTATAAAATATATTTAGAATTTTTAATTTAATAATAAT
38345 ATATATCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAA-TAATATCTTAAAACT
195 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
38408 CACTCAAAAGATAACCTTAAATTAAT-ATTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAA
260 CACTCAAAAGATAACCTTAAATTAATGATTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAA
*
38472 AGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATATCTATTACATTAT
325 AGGATAGATACTTTACAATATAACCACTACCTATTACATTATAT-AACGATACCTATTACATTAT
38537 ATAAGCGCTACCTATTACATCACATTTTTACCTATTATA
389 ATAAGCGCTACC--TTACATCACATTTTTACCTATTATA
* *
38576 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAAGTTA-GTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT-AAAGATATGTAATTTATGT
*
38640 TTCAA-TTTTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTCAATTTTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
*
38703 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATA-ATTTTAGAA-TTTAAATTTAA
129 ACAAAAAATTATTTGATTGTTTTGATA-TTTATAAAATATA-TTTAGAATTTTTAATTTAA
38762 CAACATTAAC
Statistics
Matches: 588, Mismatches: 12, Indels: 22
0.95 0.02 0.04
Matches are distributed among these distances:
420 82 0.14
421 143 0.24
422 52 0.09
423 116 0.20
424 7 0.01
425 25 0.04
426 148 0.25
427 15 0.03
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (425 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
TCAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTATAAAATATATTTAGAATTTTTAATTTAATAATAATA
TATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTC
ACTCAAAAGATAACCTTAAATTAATGATTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAA
GGATAGATACTTTACAATATAACCACTACCTATTACATTATATAACGATACCTATTACATTATAT
AAGCGCTACCTTACATCACATTTTTACCTATTATA
Found at i:40147 original size:3 final size:3
Alignment explanation
Indices: 40139--40222 Score: 69
Period size: 3 Copynumber: 28.0 Consensus size: 3
40129 ACTTGTTTGG
* * * * *
40139 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC GTC GTC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
40187 GTC AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
40223 GTCAGCTTCA
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:40156 original size:12 final size:12
Alignment explanation
Indices: 40139--40234 Score: 81
Period size: 12 Copynumber: 8.2 Consensus size: 12
40129 ACTTGTTTGG
40139 ATCATCATCTTC
1 ATCATCATCTTC
40151 ATCATCA---TC
1 ATCATCATCTTC
* *
40160 ATCATCGTCGTC
1 ATCATCATCTTC
*
40172 GTCATCATCTTC
1 ATCATCATCTTC
* *
40184 ATCGTCAGCTTC
1 ATCATCATCTTC
* *
40196 ATCGTCATCATC
1 ATCATCATCTTC
*
40208 ATCGTCATCTTC
1 ATCATCATCTTC
* *
40220 ATCGTCAGCTTC
1 ATCATCATCTTC
40232 ATC
1 ATC
40235 TTCTGCGACC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
9 8 0.11
12 62 0.89
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.36
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:40162 original size:18 final size:18
Alignment explanation
Indices: 40139--40237 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
40129 ACTTGTTTGG
40139 ATCATCATCTTCA---TC
1 ATCATCATCTTCATCGTC
* *
40154 ATCATCATCATCGTCGTC
1 ATCATCATCTTCATCGTC
*
40172 GTCATCATCTTCATCGTC
1 ATCATCATCTTCATCGTC
* * * *
40190 AGCTTCATCGTCATCATC
1 ATCATCATCTTCATCGTC
*
40208 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCGTC
* *
40226 AGCTTCATCTTC
1 ATCATCATCTTC
40238 TGCGACCGCT
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
15 11 0.17
18 54 0.83
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.37
Consensus pattern (18 bp):
ATCATCATCTTCATCGTC
Found at i:40237 original size:6 final size:6
Alignment explanation
Indices: 40143--40237 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
40133 GTTTGGATCA
* * * * * *
40143 TCATCT TCATCA TCATCA TCATCGT CGTCGTCA TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATC-T --TCATCT TCATCT TCATCT TCATCT
* * * * *
40194 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
40238 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
6 64 0.94
9 4 0.06
ACGTcount: A:0.19, C:0.34, G:0.09, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:42040 original size:198 final size:198
Alignment explanation
Indices: 41702--42472 Score: 1373
Period size: 198 Copynumber: 3.9 Consensus size: 198
41692 TTTAAATTAG
41702 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
* *
41767 TTGTACCGGTTAGATTGAAAAATTACATATTACGTTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGTTTTTGGGATC
* * * *
41832 GACACTTTTTATATACGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTAATTCTTGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
41897 AAA
196 AAA
*
41900 TATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
41965 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGTTTTTGGGATC
* *
42030 GACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTTCTATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
42095 AAA
196 AAA
*
42098 TATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
42163 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATAATTTTGGGTT-AGATGTTTTTGGGAT
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCA-ATGTTTTTGGGAT
*
42227 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
42292 AAAA
195 AAAA
*
42296 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAATCCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
42361 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCAATGTTTTTGGGA
42426 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
129 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
42473 GGCCATATTG
Statistics
Matches: 551, Mismatches: 18, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
197 1 0.00
198 398 0.72
199 91 0.17
200 61 0.11
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
AAA
Found at i:42617 original size:18 final size:18
Alignment explanation
Indices: 42591--42638 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
42581 TTATATTCAC
*
42591 ATACAAAAATATAAATCGT
1 ATACAAAATTAT-AATCGT
*
42610 ATACAAAATTATAATCTT
1 ATACAAAATTATAATCGT
42628 ATACAAAATTA
1 ATACAAAATTA
42639 ACCCTACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:44465 original size:33 final size:33
Alignment explanation
Indices: 44428--44493 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
44418 CATCTTAATA
*
44428 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
44461 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
44494 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:44551 original size:19 final size:19
Alignment explanation
Indices: 44527--44568 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
44517 CCCCTTATGC
44527 CTCTCAAGTGTATCTTCGA
1 CTCTCAAGTGTATCTTCGA
* *
44546 CTCTCAAGTTTCTCTTCGA
1 CTCTCAAGTGTATCTTCGA
44565 CTCT
1 CTCT
44569 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (19 bp):
CTCTCAAGTGTATCTTCGA
Found at i:46804 original size:17 final size:18
Alignment explanation
Indices: 46782--46824 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
46772 ATATATCCAG
46782 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
46799 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
46819 TATCAT
1 TATCAT
46825 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:46842 original size:20 final size:19
Alignment explanation
Indices: 46787--46833 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
46777 TCCAGTATCA
46787 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
46806 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
46827 TTTTACC
1 TTTTACC
46834 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:47168 original size:182 final size:182
Alignment explanation
Indices: 46754--47227 Score: 697
Period size: 182 Copynumber: 2.6 Consensus size: 182
46744 CGTACTTACG
* * *
46754 AAAGTATCGACACTTTCAATATATCCAGTATCATTTTACCGGTTTTATCATTTTG-ATACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTATACCGGTT
* * *
46818 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTA
66 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
*
46882 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
46934 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTA-ACTGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTATACCGGTT
* *
46998 TTATCATATTTTTACCTAG-TATATCGTTTTGGATCGATACATTTTTTAAAAGTATCTACACTTT
66 TTATCATATTTTTACCT-GTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATT
** *
47062 ATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 ATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * *
47116 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCA-TTTCTATACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTATACCGGTT
* * *
47180 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTTA
66 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTA
47228 TTTGGATCGA
Statistics
Matches: 265, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
180 94 0.35
181 76 0.29
182 95 0.36
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTATACCGGTT
TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:49207 original size:14 final size:14
Alignment explanation
Indices: 49190--49230 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
49180 GTTCGGTTAT
49190 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
49204 GTTCGGTTATGTTC
1 GTTCGTTTATGTTC
*
49218 GTTCATTTATGTT
1 GTTCGTTTATGTT
49231 TAACTCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:50258 original size:16 final size:16
Alignment explanation
Indices: 50237--50303 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
50227 GTCTCTAACG
50237 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
50253 TTTATGTCCGTGTTCG
1 TTTATGTTCGTGTTCA
* * *
50269 TTTATATTCGTATTCG
1 TTTATGTTCGTGTTCA
50285 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
50299 TTTAT
1 TTTAT
50304 TAAATGAACG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.05
16 37 0.84
ACGTcount: A:0.13, C:0.12, G:0.16, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:54360 original size:28 final size:28
Alignment explanation
Indices: 54325--54380 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
54315 GGCTAAACTA
54325 CTAAAAGGGCCCTTGAGGTAGTTTACTT
1 CTAAAAGGGCCCTTGAGGTAGTTTACTT
54353 CTAAAAGGGCCCTTGAGGTAGTTTACTT
1 CTAAAAGGGCCCTTGAGGTAGTTTACTT
54381 TTGTTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (28 bp):
CTAAAAGGGCCCTTGAGGTAGTTTACTT
Found at i:58082 original size:22 final size:22
Alignment explanation
Indices: 58001--58309 Score: 225
Period size: 22 Copynumber: 13.3 Consensus size: 22
57991 TATATATTAC
* *
58001 ATATGTTTTTCAAAAACTATATAT
1 ATATATTTTT-AAAAACTATA-CT
* *
58025 ATTATATGTTTTCAAAACTATATAACA
1 A-TATAT-TTTTAAAAAC--TAT-ACT
*
58052 ATATGTTTTTAAAAACTATACT
1 ATATATTTTTAAAAACTATACT
* * *
58074 ATATATTTTCAAATACTATATATT
1 ATATATTTTTAAAAAC--TATACT
* *
58098 ATATATTTTTTAAAGCTATA-T
1 ATATATTTTTAAAAACTATACT
58119 A-ATATGTTTTCAAAAACTATACT
1 ATATAT-TTTT-AAAAACTATACT
*
58142 ATATGTTTTTAAAAACTATACT
1 ATATATTTTTAAAAACTATACT
58164 ATATATTTTTAAAAACTATA-T
1 ATATATTTTTAAAAACTATACT
*
58185 ATTATATTTTTTTTAAAACTATA-T
1 A-TATA--TTTTTAAAAACTATACT
*
58209 A-ATATGTTTTCAAAAACTATATT
1 ATATAT-TTTT-AAAAACTATACT
*
58232 ATATGTTTTTTTAAAAACTATACT
1 ATA--TATTTTTAAAAACTATACT
*
58256 ATATATTTTCAAAAACTATA-T
1 ATATATTTTTAAAAACTATACT
* *
58277 ATTATATGTTTTTAAAACTGTATAAT
1 A-TATAT-TTTTAAAAAC--TATACT
58303 ATATATT
1 ATATATT
58310 ATCATAAATT
Statistics
Matches: 233, Mismatches: 27, Indels: 50
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.02
21 14 0.06
22 94 0.40
23 19 0.08
24 53 0.23
25 31 0.13
26 12 0.05
27 4 0.02
28 1 0.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (22 bp):
ATATATTTTTAAAAACTATACT
Found at i:58107 original size:46 final size:46
Alignment explanation
Indices: 57991--58293 Score: 332
Period size: 46 Copynumber: 6.5 Consensus size: 46
57981 TATATATATA
*
57991 TATATATTACATATGTTTTTCAAAAACTATATATATTATATGTTTTC-AAAAC
1 TATATATT--ATATGTTTTT-AAAAACTATA-CTA-TATA--TTTTCAAAAAC
** *
58043 TATATAACAATATGTTTTTAAAAACTATACTATATATTTTCAAATAC
1 TATAT-ATTATATGTTTTTAAAAACTATACTATATATTTTCAAAAAC
* * * *
58090 TATATATTATATATTTTTTAAAGCTATA-TAATATGTTTTCAAAAAC
1 TATATATTATATGTTTTTAAAAACTATACT-ATATATTTTCAAAAAC
* *
58136 --TATACTATATGTTTTTAAAAACTATACTATATATTTTTAAAAAC
1 TATATATTATATGTTTTTAAAAACTATACTATATATTTTCAAAAAC
* * *
58180 TATATATTATATTTTTTTTAAAACTATA-TAATATGTTTTCAAAAAC
1 TATATATTATATGTTTTTAAAAACTATACT-ATATATTTTCAAAAAC
58226 --TATATTATATGTTTTTTTAAAAACTATACTATATATTTTCAAAAAC
1 TATATATTATATG--TTTTTAAAAACTATACTATATATTTTCAAAAAC
58272 TATATATTATATGTTTTTAAAA
1 TATATATTATATGTTTTTAAAA
58294 CTGTATAATA
Statistics
Matches: 214, Mismatches: 25, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
44 46 0.21
45 3 0.01
46 112 0.52
47 10 0.05
48 15 0.07
49 2 0.01
50 10 0.05
51 10 0.05
52 5 0.02
53 1 0.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (46 bp):
TATATATTATATGTTTTTAAAAACTATACTATATATTTTCAAAAAC
Found at i:58160 original size:90 final size:89
Alignment explanation
Indices: 58022--58304 Score: 424
Period size: 90 Copynumber: 3.1 Consensus size: 89
58012 AAAAACTATA
* *
58022 TATATTATATGTTTTC-AAAACTATATAACAATATGTTTTTAAAAACTATACTATATATTTTCAA
1 TATATAATATGTTTTCAAAAAC--TAT-ACTATATGTTTTTAAAAACTATACTATATATTTTCAA
* *
58086 ATACTATATATTATATATTTTTTAAAGC
63 AAACTATATATTATAT-TTTTTTAAAAC
*
58114 TATATAATATGTTTTCAAAAACTATACTATATGTTTTTAAAAACTATACTATATATTTTTAAAAA
1 TATATAATATGTTTTCAAAAACTATACTATATGTTTTTAAAAACTATACTATATATTTTCAAAAA
58179 CTATATATTATATTTTTTTTAAAAC
66 CTATATATTATA-TTTTTTTAAAAC
*
58204 TATATAATATGTTTTCAAAAACTATATTATATGTTTTTTTAAAAACTATACTATATATTTTCAAA
1 TATATAATATGTTTTCAAAAACTATACTATATG--TTTTTAAAAACTATACTATATATTTTCAAA
*
58269 AACTATATATTATATGTTTTTAAAAC
64 AACTATATATTATATTTTTTTAAAAC
*
58295 TGTATAATAT
1 TATATAATAT
58305 ATATTATCAT
Statistics
Matches: 178, Mismatches: 9, Indels: 9
0.91 0.05 0.05
Matches are distributed among these distances:
90 91 0.51
91 24 0.13
92 58 0.33
93 5 0.03
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (89 bp):
TATATAATATGTTTTCAAAAACTATACTATATGTTTTTAAAAACTATACTATATATTTTCAAAAA
CTATATATTATATTTTTTTAAAAC
Found at i:61891 original size:12 final size:13
Alignment explanation
Indices: 61863--61893 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
61853 TGTTTTTATA
61863 AATTTTAAAAATG
1 AATTTTAAAAATG
61876 AATTTTAAAAAT-
1 AATTTTAAAAATG
61888 AATTTT
1 AATTTT
61894 CAGATTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
AATTTTAAAAATG
Found at i:64164 original size:3 final size:3
Alignment explanation
Indices: 64158--64183 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
64148 TATTATAAAT
64158 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
64184 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:64637 original size:24 final size:22
Alignment explanation
Indices: 64610--64666 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
64600 AAACCTGCGA
64610 AAGAGAAAAACACGAACAACCACC
1 AAGAGAAAAACAC-AACAA-CACC
*
64634 AAGAGAAAAGCACAACAACACC
1 AAGAGAAAAACACAACAACACC
*
64656 AA-ACAAAAACA
1 AAGAGAAAAACA
64667 GAGCAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.23
22 6 0.20
23 5 0.17
24 12 0.40
ACGTcount: A:0.63, C:0.26, G:0.11, T:0.00
Consensus pattern (22 bp):
AAGAGAAAAACACAACAACACC
Found at i:65416 original size:58 final size:58
Alignment explanation
Indices: 65353--65462 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 58
65343 TAGAGCCTTT
*
65353 AATTTT-GATATTTTACATTTTAATCTCTGATA-TTTTAA-TTATTTTCATTTTGACCATG
1 AATTTTAGATATTTTACAATTTAAT-TCT-ATACTTTTAATTTATTTT-ATTTTGACCATG
* *
65411 AATTTTATATATTTTTCAATTTAATTCTATACTTTTAATTTATTTTATTTTG
1 AATTTTAGATATTTTACAATTTAATTCTATACTTTTAATTTATTTTATTTTG
65463 GTCATTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
57 3 0.07
58 21 0.46
59 22 0.48
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (58 bp):
AATTTTAGATATTTTACAATTTAATTCTATACTTTTAATTTATTTTATTTTGACCATG
Found at i:67453 original size:19 final size:19
Alignment explanation
Indices: 67409--67446 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
67399 TCAATTGTCC
67409 CTATAAATATATCATTTTG
1 CTATAAATATATCATTTTG
67428 CTATAAATATATCATTTTG
1 CTATAAATATATCATTTTG
67447 TGGTAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (19 bp):
CTATAAATATATCATTTTG
Found at i:69816 original size:33 final size:34
Alignment explanation
Indices: 69745--69819 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
69735 TAAAATTTGG
*
69745 AATT-GAAAGTTTAAAAAATCGAATTATAAATAA
1 AATTAGAAAGTTTAAAAAATCGAATCATAAATAA
* *
69778 AATTAGAAAGTTTAAAAGATTGAA-CATAAATAA
1 AATTAGAAAGTTTAAAAAATCGAATCATAAATAA
*
69811 TATTAGAAA
1 AATTAGAAA
69820 TGATAATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.29
Consensus pattern (34 bp):
AATTAGAAAGTTTAAAAAATCGAATCATAAATAA
Found at i:70502 original size:2 final size:2
Alignment explanation
Indices: 70495--70522 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70485 ACATTATGAA
70495 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
70523 CACATGCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76807 original size:26 final size:26
Alignment explanation
Indices: 76777--76853 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 26
76767 TAATGCACCG
*
76777 AAAGTGCATTAGTTGACAGTAATGAT
1 AAAGTGCATTAGTTGGCAGTAATGAT
*
76803 AAAGTGCATTAGTTGGCAGCAATGAT
1 AAAGTGCATTAGTTGGCAGTAATGAT
76829 AAAGTGCATTAGTTGGCA-TAATGAT
1 AAAGTGCATTAGTTGGCAGTAATGAT
76854 TCATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
25 6 0.12
26 42 0.88
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (26 bp):
AAAGTGCATTAGTTGGCAGTAATGAT
Found at i:80036 original size:23 final size:25
Alignment explanation
Indices: 80010--80070 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 25
80000 GTATATATAT
*
80010 ATTTTAAT-TTTTCATTTTTTAA-A
1 ATTTTAATATTTTCATTTTCTAATA
*
80033 A-TTTAATAATTT-ATTTTCTAATA
1 ATTTTAATATTTTCATTTTCTAATA
*
80056 ATTTAAATATTTTCA
1 ATTTTAATATTTTCA
80071 AATGTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 14 0.47
23 6 0.20
24 9 0.30
25 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTAATATTTTCATTTTCTAATA
Found at i:80196 original size:20 final size:20
Alignment explanation
Indices: 80171--80222 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
80161 AAATGACTAA
80171 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * *
80191 CAAATTTGTAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
80211 CAAATTCGCAAC
1 CAAATTCGCAAC
80223 AGGTTTTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:81000 original size:12 final size:12
Alignment explanation
Indices: 80979--81012 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
80969 ACCACATTTC
*
80979 CAATACCAAACA
1 CAATATCAAACA
80991 CAATATCAAACA
1 CAATATCAAACA
*
81003 CAATCTCAAA
1 CAATATCAAA
81013 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:81382 original size:12 final size:12
Alignment explanation
Indices: 81365--81389 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
81355 ATATAACCCT
81365 GAAGAAGAAAAA
1 GAAGAAGAAAAA
81377 GAAGAAGAAAAA
1 GAAGAAGAAAAA
81389 G
1 G
81390 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:83464 original size:18 final size:18
Alignment explanation
Indices: 83441--83476 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
83431 AAGCAAAAGG
*
83441 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
83459 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
83477 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:83823 original size:20 final size:20
Alignment explanation
Indices: 83800--83866 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
83790 AATCGCAAAC
83800 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* * *
83820 CGAATTTAACTATCGCGTAG
1 CGAATTTGACTTTCGCGTTG
*
83840 CGAATTTGACTTTCGTGTTG
1 CGAATTTGACTTTCGCGTTG
83860 CGAATTT
1 CGAATTT
83867 ACCTTCAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:83972 original size:25 final size:25
Alignment explanation
Indices: 83934--83983 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
83924 AAATCAATTA
*
83934 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
83959 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
83984 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:84391 original size:18 final size:18
Alignment explanation
Indices: 84370--84406 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
84360 GTAATTGGAG
84370 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
84388 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
84406 T
1 T
84407 ATAAATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:84413 original size:24 final size:24
Alignment explanation
Indices: 84362--84414 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
84352 TTTCATATGT
* * *
84362 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
84386 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
84410 AATTT
1 AATTT
84415 CAGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:84758 original size:39 final size:39
Alignment explanation
Indices: 84715--84801 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
84705 TCCGATGCTC
*
84715 ATCAAAATCCAAAGCTCATATGGTTCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
84754 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
84793 ATCAAAATC
1 ATCAAAATC
84802 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:85003 original size:20 final size:20
Alignment explanation
Indices: 84978--85050 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 20
84968 TGTTACGATC
84978 AACGCGAAAGTCAAATTCGT
1 AACGCGAAAGTCAAATTCGT
*
84998 AACGCGAAA-T--AA-GCGT
1 AACGCGAAAGTCAAATTCGT
* * * *
85014 --TGTGATAGTCAAATTCGC
1 AACGCGAAAGTCAAATTCGT
85032 AACGCGAAAGTCAAATTCG
1 AACGCGAAAGTCAAATTCG
85051 CAAACCGAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 12
0.64 0.15 0.20
Matches are distributed among these distances:
14 4 0.11
15 1 0.03
16 3 0.08
17 4 0.11
18 2 0.05
19 1 0.03
20 23 0.61
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (20 bp):
AACGCGAAAGTCAAATTCGT
Found at i:85087 original size:20 final size:20
Alignment explanation
Indices: 85062--85117 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
85052 AAACCGAAAA
85062 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
* *
85082 TCGCGTTGTGAATTTAACTT
1 TCGCGTTGCGAATTTGACTT
85102 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
85118 TACCTTCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:85258 original size:14 final size:14
Alignment explanation
Indices: 85224--85277 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
85214 ATAATTCTTA
*
85224 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
85238 TAAACAAATCAACT
1 TTTACAAATCAACT
* *
85252 TTTACAATTCATCT
1 TTTACAAATCAACT
85266 TTTACAAATCAA
1 TTTACAAATCAA
85278 TTAATCAAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:85325 original size:74 final size:76
Alignment explanation
Indices: 85176--85327 Score: 200
Period size: 79 Copynumber: 2.0 Consensus size: 76
85166 TTTAGAAAAA
*
85176 ACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACAAATCAAATTAA
1 ACAAATCAACTTTTACAAATCAATTAAAC---AAAAAAATAAATCTTATTTACAAATCAAATTAA
85241 ACAAATCAACTTTT
63 ACAAATCAACTTTT
* * * * **
85255 ACAATTCATCTTTTACAAATCAATTAATC-AAAAAATAAATCTTATTTCCTCATC-AATTAAACA
1 ACAAATCAACTTTTACAAATCAATTAAACAAAAAAATAAATCTTATTTACAAATCAAATTAAACA
85318 AATCAACTTT
66 AATCAACTTT
85328 CAATTAAACA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 19 0.29
75 21 0.32
79 26 0.39
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (76 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAAAAAATAAATCTTATTTACAAATCAAATTAAACA
AATCAACTTTT
Found at i:90886 original size:21 final size:21
Alignment explanation
Indices: 90860--90899 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
90850 CCCCCTTTGA
*
90860 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
90881 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
90900 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:95586 original size:21 final size:21
Alignment explanation
Indices: 95542--95616 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
95532 GGCGAGACCA
* *
95542 CTTGAACGATGACAG-GAGCCT
1 CTTGAATGATGAGAGAG-GCCT
* * * *
95563 CTTGAATGGTGGGAGGGGCTT
1 CTTGAATGATGAGAGAGGCCT
*
95584 CTTCAATGATGAGAGAGGCCT
1 CTTGAATGATGAGAGAGGCCT
95605 CTTGAATGATGA
1 CTTGAATGATGA
95617 TAGGTGCATC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.25
Consensus pattern (21 bp):
CTTGAATGATGAGAGAGGCCT
Found at i:97809 original size:19 final size:20
Alignment explanation
Indices: 97787--97827 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
97777 AATTCGCAAC
97787 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
97806 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
97826 GC
1 GC
97828 AAATTTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:98115 original size:22 final size:22
Alignment explanation
Indices: 98087--98129 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
98077 TGGAGATAGA
*
98087 CGGATTTTGTCGGAAATGGGGT
1 CGGATTTCGTCGGAAATGGGGT
*
98109 CGGATTTCGTCGGAGATGGGG
1 CGGATTTCGTCGGAAATGGGG
98130 ACGGGTGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.12, G:0.44, T:0.28
Consensus pattern (22 bp):
CGGATTTCGTCGGAAATGGGGT
Found at i:98288 original size:20 final size:20
Alignment explanation
Indices: 98263--98388 Score: 132
Period size: 20 Copynumber: 6.2 Consensus size: 20
98253 GCGTAAAAAC
98263 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
98283 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
98303 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
*
98322 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
*
98343 ATTTGACTTTCGCATTGCGA
1 ATTTGACTTTCGCGTTGCGA
***
98363 ATTTGGAAAATCGCGTTGCGA
1 ATTT-GACTTTCGCGTTGCGA
98384 ATTTG
1 ATTTG
98389 GAAACTGAGT
Statistics
Matches: 89, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 56 0.63
21 23 0.26
22 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:98308 original size:40 final size:40
Alignment explanation
Indices: 98263--98465 Score: 175
Period size: 40 Copynumber: 5.1 Consensus size: 40
98253 GCGTAAAAAC
**
98263 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGAATTTGAAAATCGCGTTGCGA
*
98303 ATTTGAC-TTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTTTC-GCGTTGCGAATTTGA-AAA-TCGCGTTGCGA
*
98343 ATTTGACTTTCGCATTGCGAATTTGGAAAATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGAATTT-GAAAATCGCGTTGCGA
*** * * * *
98384 ATTTGGAAACT-GAGTTGCGAAATTGGAATTCGCGTTGCGA
1 ATTT-GACTTTCGCGTTGCGAATTTGAAAATCGCGTTGCGA
** * * *
98424 ATTTGA-GATCACGTTGCGAATTTG-AGATCGCGTTGCGG
1 ATTTGACTTTCGCGTTGCGAATTTGAAAATCGCGTTGCGA
98462 ATTT
1 ATTT
98466 CTTGGTCATT
Statistics
Matches: 133, Mismatches: 21, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
38 17 0.13
39 21 0.16
40 56 0.42
41 32 0.24
42 6 0.05
43 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.35
Consensus pattern (40 bp):
ATTTGACTTTCGCGTTGCGAATTTGAAAATCGCGTTGCGA
Found at i:98401 original size:81 final size:80
Alignment explanation
Indices: 98263--98465 Score: 216
Period size: 81 Copynumber: 2.5 Consensus size: 80
98253 GCGTAAAAAC
* ** ** * *
98263 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTTA
1 ATTTGACTTTCGCATTGCGAATTTGAAAATCGCGTTGCGAATTTGACAACTGAGTTGCGAAATT-
98327 CAAATTCGCGTTGCGA
65 CAAATTCGCGTTGCGA
98343 ATTTGACTTTCGCATTGCGAATTTGGAAAATCGCGTTGCGAATTTGGA-AACTGAGTTGCGAAAT
1 ATTTGACTTTCGCATTGCGAATTT-GAAAATCGCGTTGCGAATTT-GACAACTGAGTTGCGAAAT
**
98407 TGGAATTCGCGTTGCGA
64 TCAAATTCGCGTTGCGA
** * * * *
98424 ATTTGA-GATCACGTTGCGAATTTG-AGATCGCGTTGCGGATTT
1 ATTTGACTTTCGCATTGCGAATTTGAAAATCGCGTTGCGAATTT
98466 CTTGGTCATT
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
78 16 0.15
79 1 0.01
80 36 0.34
81 47 0.45
82 5 0.05
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.35
Consensus pattern (80 bp):
ATTTGACTTTCGCATTGCGAATTTGAAAATCGCGTTGCGAATTTGACAACTGAGTTGCGAAATTC
AAATTCGCGTTGCGA
Found at i:98402 original size:20 final size:21
Alignment explanation
Indices: 98357--98428 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 21
98347 GACTTTCGCA
*
98357 TTGCGAATTTGGAAAATCGCG
1 TTGCGAATTTGGAAAATCGAG
*
98378 TTGCGAATTTGGAAACT-GAG
1 TTGCGAATTTGGAAAATCGAG
* * *
98398 TTGCGAAATTGG-AATTCGCG
1 TTGCGAATTTGGAAAATCGAG
98418 TTGCGAATTTG
1 TTGCGAATTTG
98429 AGATCACGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.07
20 25 0.57
21 16 0.36
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (21 bp):
TTGCGAATTTGGAAAATCGAG
Found at i:98438 original size:19 final size:19
Alignment explanation
Indices: 98416--98465 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
98406 TTGGAATTCG
98416 CGTTGCGAATTTGAGATCA
1 CGTTGCGAATTTGAGATCA
*
98435 CGTTGCGAATTTGAGATCG
1 CGTTGCGAATTTGAGATCA
*
98454 CGTTGCGGATTT
1 CGTTGCGAATTT
98466 CTTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (19 bp):
CGTTGCGAATTTGAGATCA
Found at i:99483 original size:17 final size:17
Alignment explanation
Indices: 99461--99501 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
99451 TACCAAAATA
99461 AAACATAAATAATTTTG
1 AAACATAAATAATTTTG
99478 AAACATAAATAATTTTG
1 AAACATAAATAATTTTG
99495 AAACATA
1 AAACATA
99502 TGAAAGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (17 bp):
AAACATAAATAATTTTG
Found at i:107440 original size:24 final size:23
Alignment explanation
Indices: 107366--107471 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
107356 ATAATTTGCA
107366 CCAAAGTG-CCACATAA--TTGTC
1 CCAAAG-GACCACATAAGTTTGTC
107387 CCAAAGGACCACATAAGTTTGTC
1 CCAAAGGACCACATAAGTTTGTC
* * *
107410 CCGAAGGACCACGTAGGTTTTGTC
1 CCAAAGGACCACATAAG-TTTGTC
* *
107434 CCAAAGGACCACATAATTTTTTC
1 CCAAAGGACCACATAAGTTTGTC
107457 CCGAAA-GACCACATA
1 CC-AAAGGACCACATA
107472 GAACCCTCGA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.01
21 14 0.19
23 35 0.49
24 22 0.31
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (23 bp):
CCAAAGGACCACATAAGTTTGTC
Found at i:114335 original size:24 final size:23
Alignment explanation
Indices: 114277--114344 Score: 91
Period size: 24 Copynumber: 2.9 Consensus size: 23
114267 TGCCACATAA
* *
114277 TTGTCCCAAAGGACCATATAAGT
1 TTGTCCCAAAGGACCACATAGGT
**
114300 TTGTCCTGAAGGACCACATAGGTT
1 TTGTCCCAAAGGACCACATAGG-T
114324 TTGTCCCAAAGGACCACATAG
1 TTGTCCCAAAGGACCACATAG
114345 AACCCTCGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (23 bp):
TTGTCCCAAAGGACCACATAGGT
Found at i:115863 original size:3 final size:3
Alignment explanation
Indices: 115855--115895 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
115845 TAGTAAAAAT
115855 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
115896 AAACGGGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:116340 original size:42 final size:41
Alignment explanation
Indices: 116243--116343 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 41
116233 AAGGTCTTAT
*
116243 AGATGGCCCGAAGGACTTTTCACCTTACTCGAAAGACTAAC
1 AGATGGCCCGAAGGACTTTTCACCATACTCGAAAGACTAAC
* ** * * *
116284 AGATGACCTAAAGGA-TTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTTT--TCACCATACTCGAAAGACTAAC
*
116326 TGATGGCCCGAAGGACTT
1 AGATGGCCCGAAGGACTT
116344 ACAAATTTTG
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
40 3 0.07
41 12 0.26
42 29 0.63
43 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTTTCACCATACTCGAAAGACTAAC
Found at i:116509 original size:258 final size:258
Alignment explanation
Indices: 116036--116538 Score: 774
Period size: 258 Copynumber: 1.9 Consensus size: 258
116026 ATATACCCCG
* * * * *
116036 AAGGGTTTTATCATCATGCTCGAAAGATTTACTGATATCCCGAAGGACTTACCAATTTTGGAAAT
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTACAAATTTTGGAAAT
* * *
116101 AATTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
66 AATTTACTAGGTAAGAAAATTTGGAAATCACTTTCTTACATTTCAAAAATTTCATCTTCTGAAAA
*
116166 CACTAAATGAGAAACTTTGGAAATCGCTTTCTCATGTTTGAAAATCATGTGAAAACATCCTTGCC
131 CACTAAATGAGAAACTTTGGAAATCACTTTCTCATGTTTGAAAATCATGTGAAAACATCCTTGCC
* * * *
116231 CAAAGGTCTTATAGATGGCCCGAAGGACTTTTCACCTTACTCGAAAGACTAACAGATGACCTA
196 CAAAGGTCTTACAAATGGCCCGAAAGACTTATCACCTTACTCGAAAGACTAACAGATGACCTA
*
116294 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAAT
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTACAAATTTTGGAAAT
* ** *
116359 AATTTACTAGGTAATAAAATTTGGAAATTGCTTTCTTACATTTCAAATATTTCATCTTCTGAAAA
66 AATTTACTAGGTAAGAAAATTTGGAAATCACTTTCTTACATTTCAAAAATTTCATCTTCTGAAAA
* * *
116424 TATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCC-TGC
131 CACTAAATGAGAAACTTTGGAAATCACTTTCTCATGTTT-GAAAATCATGTGAAAACATCCTTGC
* * *
116488 CCGAAGGTCTTACAAATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACT
195 CCAAAGGTCTTACAAATGGCCCGAAAGACTTATCACCTTACTCGAAAGACT
116539 TATCATCTTG
Statistics
Matches: 220, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
258 199 0.90
259 21 0.10
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (258 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTACAAATTTTGGAAAT
AATTTACTAGGTAAGAAAATTTGGAAATCACTTTCTTACATTTCAAAAATTTCATCTTCTGAAAA
CACTAAATGAGAAACTTTGGAAATCACTTTCTCATGTTTGAAAATCATGTGAAAACATCCTTGCC
CAAAGGTCTTACAAATGGCCCGAAAGACTTATCACCTTACTCGAAAGACTAACAGATGACCTA
Found at i:116533 original size:21 final size:21
Alignment explanation
Indices: 116509--116559 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
116499 ACAAATGGCC
116509 CGAAAGACTTATCATCTTGCT
1 CGAAAGACTTATCATCTTGCT
116530 CGAAAGACTTATCATCTTGCT
1 CGAAAGACTTATCATCTTGCT
116551 CGAAAGACT
1 CGAAAGACT
116560 AACTGATGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (21 bp):
CGAAAGACTTATCATCTTGCT
Found at i:116642 original size:258 final size:258
Alignment explanation
Indices: 116045--116726 Score: 630
Period size: 258 Copynumber: 2.6 Consensus size: 258
116035 GAAGGGTTTT
* * * * * **** * *
116045 ATCATCATGCTCGAAAGATTTACTGAT-ATCCCGAAGGACTTACCAATTTTGGAAATAATTTACT
1 ATCATCATGCCCGAAAGACTTACTCATGA-CCCAAAGGACTTACAAATGCCCGAAAGAACTTACT
* * *
116109 AGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACACTAAAT
65 AGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCA-TTTCTGAAAATATTAAAT
*
116174 GAGAAACTTTGGAAATCGCTTTCTCATGTTT-GAAAATCATGTGAAAACATCCTTGCCCAAAGGT
129 GAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTTGCCCAAAGGT
* * * * * * *
116238 CTTATAGATGGCCCGAAGGACTTTTCACCTTACTCGAAAGACTAACAGATGACCTAAAGGATTTA
194 CTTACAAATGGCCCGAAAGACTTATCACCTTACTCGAAAGACTAACACATGACCGAAAGGATCTA
* * * * **** * *
116303 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAATTTACTA
1 ATCATCATGCCCGAAAGACTTACTCATGACCCAAAGGACTTACAAATGCCCGAAAGAACTTACTA
* * * * *
116368 GGTAATAAAATTTGGAAATTGCTTTCTTACATTTCAAATATTTCATCTTCTGAAAATATTAAATG
66 GGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAT-TTCTGAAAATATTAAATG
* *
116433 AGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCC-TGCCCGAAGGTC
130 AGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTTGCCCAAAGGTC
* * * *
116497 TTACAAATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACTTATCATCTTG-CTCGAAA-GA-C
195 TTACAAATGGCCCGAAAGACTTATCACCTTACTCGAAAGAC-TAACA-CATGAC-CGAAAGGATC
116559 TA
257 TA
* * * * * * **
116561 A-C-TGATGACCCGAAGGATTTAATTTCAT-ACTCAAATGACTTACTGATGGCCCG-AAGAACTT
1 ATCATCATG-CCCGAAAGACTT-A-CTCATGACCCAAAGGACTTACAAAT-GCCCGAAAGAACTT
* * * * * *
116622 ACTATGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTAAAAAATTTCGTTTTTAGCAAATATTT
62 ACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTCT-GAAAATA-TT
* * * *
116687 AAATGAGATACATTGGAAATTGCTTTTTCATTTTTC-AAAA
125 AAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAA
116727 CAACTTAATG
Statistics
Matches: 353, Mismatches: 59, Indels: 24
0.81 0.14 0.06
Matches are distributed among these distances:
256 4 0.01
257 14 0.04
258 264 0.75
259 65 0.18
260 6 0.02
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (258 bp):
ATCATCATGCCCGAAAGACTTACTCATGACCCAAAGGACTTACAAATGCCCGAAAGAACTTACTA
GGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTCTGAAAATATTAAATGA
GAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTTGCCCAAAGGTCT
TACAAATGGCCCGAAAGACTTATCACCTTACTCGAAAGACTAACACATGACCGAAAGGATCTA
Found at i:125073 original size:22 final size:22
Alignment explanation
Indices: 125032--125082 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
125022 TCCCGAAGGA
125032 CCACATAGGTTACACTGAAGTG
1 CCACATAGGTTACACTGAAGTG
*
125054 CCACATAGGTTTGCAC-GAAGTG
1 CCACATAGG-TTACACTGAAGTG
125076 CCACATA
1 CCACATA
125083 TTTGTCCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (22 bp):
CCACATAGGTTACACTGAAGTG
Found at i:125100 original size:21 final size:21
Alignment explanation
Indices: 125076--125186 Score: 172
Period size: 21 Copynumber: 5.4 Consensus size: 21
125066 GCACGAAGTG
* *
125076 CCACATATTTGTCCCGAATGA
1 CCACATAATTATCCCGAATGA
125097 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAATGA
125118 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAATGA
125139 CCACATAA-T-TCCCGAATGA
1 CCACATAATTATCCCGAATGA
* *
125158 CCACATAATTATCCTGAAGGA
1 CCACATAATTATCCCGAATGA
125179 CCACATAA
1 CCACATAA
125187 AACCCTCGAC
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
19 18 0.21
20 2 0.02
21 64 0.76
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (21 bp):
CCACATAATTATCCCGAATGA
Found at i:125163 original size:40 final size:42
Alignment explanation
Indices: 125076--125186 Score: 172
Period size: 40 Copynumber: 2.7 Consensus size: 42
125066 GCACGAAGTG
* *
125076 CCACATATTTGTCCCGAATGACCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAATGACCACATAATTATCCCGAATGA
125118 CCACATAATTATCCCGAATGACCACATAA-T-TCCCGAATGA
1 CCACATAATTATCCCGAATGACCACATAATTATCCCGAATGA
* *
125158 CCACATAATTATCCTGAAGGACCACATAA
1 CCACATAATTATCCCGAATGACCACATAA
125187 AACCCTCGAC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
40 37 0.57
41 1 0.02
42 27 0.42
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (42 bp):
CCACATAATTATCCCGAATGACCACATAATTATCCCGAATGA
Done.