Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021023.1 Corchorus olitorius cultivar O-4 contig21056, 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: 170671
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:21 original size:2 final size:2
Alignment explanation
Indices: 16--47 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6 ACACACACAC
16 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
48 GACATTTCAT
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:1252 original size:20 final size:20
Alignment explanation
Indices: 1215--1252 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1205 TGGCCTAAGG
*
1215 CATCATACAATAAGCATTTT
1 CATCATACAATAAACATTTT
1235 CATCAT-CAATAAAACATT
1 CATCATACAAT-AAACATT
1253 AAAGCGCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (20 bp):
CATCATACAATAAACATTTT
Found at i:2117 original size:39 final size:39
Alignment explanation
Indices: 2068--2199 Score: 185
Period size: 39 Copynumber: 3.4 Consensus size: 39
2058 TAGTACCCCA
*
2068 GAAGGTGTTGTTTTTATTCCTGTTTGCCCTTCCCCATCG
1 GAAGGTGTTGTTTTTATTCCTGTTTGCCCTTCCCCACCG
* *
2107 GAAGAG-GTTGTTTTTATTCCTGTTTGCCCTTCCTCGCCG
1 GAAG-GTGTTGTTTTTATTCCTGTTTGCCCTTCCCCACCG
**
2146 GAAGGTGTTGTTTTTATTCCCAATTTGCCCTTCCCCACCG
1 GAAGGTGTTGTTTTTATT-CCTGTTTGCCCTTCCCCACCG
*
2186 GAAGGTTTTGTTTT
1 GAAGGTGTTGTTTT
2200 ATTTCCAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
38 1 0.01
39 50 0.61
40 31 0.38
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.42
Consensus pattern (39 bp):
GAAGGTGTTGTTTTTATTCCTGTTTGCCCTTCCCCACCG
Found at i:2198 original size:79 final size:78
Alignment explanation
Indices: 2068--2238 Score: 204
Period size: 79 Copynumber: 2.2 Consensus size: 78
2058 TAGTACCCCA
** * **
2068 GAAGGTGTTGTTTTTATTCCTGTTTGCCCTTCCCCATCGGAAGAGGTTGTTTT-TATTCCTGT-T
1 GAAGGTGTTGTTTTTATTCCAATTTGCCCTTCCCCACCGGAAGAGGTTGTTTTAT-TTCCAATAT
2131 TGCCCTTCCTCGCCG
65 TGCCCTTCC-CGCCG
*
2146 GAAGGTGTTGTTTTTATTCCCAATTTGCCCTTCCCCACCGGAAG-GTTTTGTTTTATTTCCAATA
1 GAAGGTGTTGTTTTTATT-CCAATTTGCCCTTCCCCACCGGAAGAG-GTTGTTTTATTTCCAATA
* *
2210 TTGCCCTTCCGGTCG
64 TTGCCCTTCCCGCCG
*
2225 GAAGGCGTTGTTTT
1 GAAGGTGTTGTTTT
2239 GTCATATTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
78 19 0.24
79 50 0.62
80 11 0.14
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.42
Consensus pattern (78 bp):
GAAGGTGTTGTTTTTATTCCAATTTGCCCTTCCCCACCGGAAGAGGTTGTTTTATTTCCAATATT
GCCCTTCCCGCCG
Found at i:2200 original size:39 final size:39
Alignment explanation
Indices: 2068--2219 Score: 182
Period size: 39 Copynumber: 3.8 Consensus size: 39
2058 TAGTACCCCA
** *
2068 GAAGGTGTTGTTTTTATTCCTGTTTGCCCTTCCCCATCG
1 GAAGGTGTTGTTTTTATTCCAATTTGCCCTTCCCCACCG
** * *
2107 GAAGAG-GTTGTTTTTATTCCTGTTTGCCCTTCCTCGCCG
1 GAAG-GTGTTGTTTTTATTCCAATTTGCCCTTCCCCACCG
2146 GAAGGTGTTGTTTTTATTCCCAATTTGCCCTTCCCCACCG
1 GAAGGTGTTGTTTTTATT-CCAATTTGCCCTTCCCCACCG
*
2186 GAAGGTTTTG-TTTTATTTCCAATATTGCCCTTCC
1 GAAGGTGTTGTTTTTA-TTCCAAT-TTGCCCTTCC
2220 GGTCGGAAGG
Statistics
Matches: 100, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
38 1 0.01
39 60 0.60
40 39 0.39
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.42
Consensus pattern (39 bp):
GAAGGTGTTGTTTTTATTCCAATTTGCCCTTCCCCACCG
Found at i:2227 original size:39 final size:38
Alignment explanation
Indices: 2068--2238 Score: 143
Period size: 39 Copynumber: 4.4 Consensus size: 38
2058 TAGTACCCCA
**
2068 GAAGGTGTTGTTTTTATT-CCTGTTTGCCCTTCCC-CATCG
1 GAAGGTGTTG-TTTTATTCCCAATTTGCCCTTCCCGC--CG
**
2107 GAAGAG-GTTGTTTTTATT-CCTGTTTGCCCTTCCTCGCCG
1 GAAG-GTGTTG-TTTTATTCCCAATTTGCCCTTCC-CGCCG
*
2146 GAAGGTGTTGTTTTTATTCCCAATTTGCCCTTCCCCACCG
1 GAAGGTGTTG-TTTTATTCCCAATTTGCCCTT-CCCGCCG
* * * *
2186 GAAGGTTTTGTTTTATTTCCAATATTGCCCTTCCGGTCG
1 GAAGGTGTTGTTTTATTCCCAAT-TTGCCCTTCCCGCCG
*
2225 GAAGGCGTTGTTTT
1 GAAGGTGTTGTTTT
2239 GTCATATTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
38 1 0.01
39 77 0.67
40 34 0.30
41 3 0.03
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.42
Consensus pattern (38 bp):
GAAGGTGTTGTTTTATTCCCAATTTGCCCTTCCCGCCG
Found at i:5600 original size:2 final size:2
Alignment explanation
Indices: 5593--5630 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5583 TTTATTGCAA
*
5593 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5631 CATAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5923 original size:15 final size:14
Alignment explanation
Indices: 5903--5940 Score: 53
Period size: 12 Copynumber: 2.8 Consensus size: 14
5893 AGTTTTAGAA
5903 AATTATCAACAAATT
1 AATTAT-AACAAATT
5918 AATTAT-A-AAATT
1 AATTATAACAAATT
5930 AATTATAACAA
1 AATTATAACAA
5941 GCAGGCTGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.52
13 2 0.10
14 2 0.10
15 6 0.29
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTATAACAAATT
Found at i:8504 original size:35 final size:35
Alignment explanation
Indices: 8440--8506 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
8430 GCAACTTCCT
* * * **
8440 TTGAAGCTATCAAATAAGTCTGCTGTTATGCTAAA
1 TTGAAGCAATCAAACAAGTCTACCATTATGCTAAA
8475 TTGAAGCAATCAAACAAGTCTACCATTATGCT
1 TTGAAGCAATCAAACAAGTCTACCATTATGCT
8507 TAACTTTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (35 bp):
TTGAAGCAATCAAACAAGTCTACCATTATGCTAAA
Found at i:9125 original size:2 final size:2
Alignment explanation
Indices: 9118--9170 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
9108 TAATTAATTT
* *
9118 CA CA CA CA CA CA CA CA GA CA CA CA CA CA GA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
9160 CA CA CA CA CA C
1 CA CA CA CA CA C
9171 TCAGGTCTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.47, G:0.04, T:0.00
Consensus pattern (2 bp):
CA
Found at i:15745 original size:35 final size:35
Alignment explanation
Indices: 15694--15762 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
15684 ATTTCCTTTA
* **
15694 AAGCTATCAAATAAGTCTGTCGTTATGCTAAATTG
1 AAGCTATCAAACAAGTCTCCCGTTATGCTAAATTG
15729 AAGCTATCAAACAAGTCTCCCGTTATGCTAAATT
1 AAGCTATCAAACAAGTCTCCCGTTATGCTAAATT
15763 TTTGAAAGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (35 bp):
AAGCTATCAAACAAGTCTCCCGTTATGCTAAATTG
Found at i:18703 original size:22 final size:22
Alignment explanation
Indices: 18678--18723 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
18668 GTTCAAATAC
18678 AATCCATCAATACC-AAAGTTCA
1 AATCCATCAATACCGAAA-TTCA
18700 AATCCATCAATACCGAAATTCA
1 AATCCATCAATACCGAAATTCA
18722 AA
1 AA
18724 GCTCAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.48, C:0.26, G:0.04, T:0.22
Consensus pattern (22 bp):
AATCCATCAATACCGAAATTCA
Found at i:18809 original size:69 final size:69
Alignment explanation
Indices: 18720--18856 Score: 170
Period size: 69 Copynumber: 2.0 Consensus size: 69
18710 TACCGAAATT
* * * *
18720 CAAAGCTCAATCTTCAAAGTTTAAAATTCTAACTTCTAAGAC-A-ATATATAAATTAAACATCAA
1 CAAAGCTCAAACTTAAAAGTTTAAAATTCTAAC-T-AAAGACAATATATATAAACTAAACATCAA
18783 GTCCAC
64 GTCCAC
* * * *
18789 CAAAGTTCAAACTTAAAAGTTTAGAATTCTAACTAAAGGCAATATATATAAACTAAAGATCAAGT
1 CAAAGCTCAAACTTAAAAGTTTAAAATTCTAACTAAAGACAATATATATAAACTAAACATCAAGT
18854 CCA
66 CCA
18857 TCTTCTCCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 4 0.07
68 2 0.03
69 52 0.90
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.28
Consensus pattern (69 bp):
CAAAGCTCAAACTTAAAAGTTTAAAATTCTAACTAAAGACAATATATATAAACTAAACATCAAGT
CCAC
Found at i:21976 original size:35 final size:36
Alignment explanation
Indices: 21937--22009 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 36
21927 CCAACTTCCT
*
21937 TTGAAGCTATCAAATAAGTCTACCGTTATGCTA-AA
1 TTGAAGCTATCAAACAAGTCTACCGTTATGCTACAA
*
21972 TTGAAGCTATCAAACAAGTCTCCCGTTATGCTACAA
1 TTGAAGCTATCAAACAAGTCTACCGTTATGCTACAA
22008 TT
1 TT
22010 TTGAAAGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 31 0.89
36 4 0.11
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (36 bp):
TTGAAGCTATCAAACAAGTCTACCGTTATGCTACAA
Found at i:22635 original size:2 final size:2
Alignment explanation
Indices: 22630--22665 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22620 ACACACACAC
22630 AT AT 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 AT AT
22666 TAATAGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23548 original size:35 final size:35
Alignment explanation
Indices: 23509--23577 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
23499 ACTTCCTTTA
*
23509 AAGCTATCAAATAAGTCTACCGTTATACTAAATTG
1 AAGCTATCAAACAAGTCTACCGTTATACTAAATTG
* *
23544 AAGCTATCAAACAAGTCTCCCGTTATGCTAAATT
1 AAGCTATCAAACAAGTCTACCGTTATACTAAATT
23578 TTGAAAGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (35 bp):
AAGCTATCAAACAAGTCTACCGTTATACTAAATTG
Found at i:24967 original size:972 final size:971
Alignment explanation
Indices: 23046--24978 Score: 2709
Period size: 971 Copynumber: 2.0 Consensus size: 971
23036 TTTATATTGA
*
23046 TGTTTTATTTTTTTATAATTATCCTTAAAAACATCAGAATATTATTATATTTTGTTTCAGCTAAG
1 TGTTTTATTATTTTATAATTATCCTTAAAAACATCAGAATATTATTATATTTTGTTTCAGCTAAG
* * * *
23111 AATTGTCTATGCTTAATTTTTGGCGGAAATGCTGCAGTCTTACATGAAAATATTGCAAAGAATGA
66 AATTGTCTATGCTAAATTTTTGACGGAAATGCAGCAGGCTTACATGAAAATATTGCAAAGAATGA
* * * * * * *
23176 TGCCTGGTGCTATCATTTATTATGTTTGTAGGGTGAAATGGGGCTTGGACGTGCAACTATTGCCT
131 TGCATGGTGCTATCACTTATTATATGTGAAGGGTGAAATGGGGCTTGGACGGGCAACTATTGACT
* * *
23241 TATGTTTCTTTTACTCGAACATATCGCTCCTCTTATGCGAGGTCTTGCTTATTGCTTGGATGTGA
196 TATGTTTCTTTGACCCGAACATATCGCTCCTCTTATGCGAGGTCTTGCTTATTGCTTGGATGTAA
* * * *
23306 TGTAGTGTTTATATAATCTCATCTCGACAAAAGCTTTAAAACAAATAACATCTTAAGGTATGAAC
261 TGTAGTCTTTATACAATCTCATCTCGACAAAAGCTATAAAACAAATAACATCTTAAGGTATAAAC
* * *
23371 ATTCTTACTTGACACTCTTGGTTTATTTAAGCATAAAAAATATATCTAGCTTTATTGATGTATTC
326 ATTCTTACTTGACACTCCTGATTCATTTAAGCATAAAAAATATATCTAGCTTTATTGATGTATTC
*
23436 AAATAATTATTGATTTCAGAAAATATAGATTATTGATTTAAGTTTGTCCAAATTTAATTTGCAAC
391 AAATAATTATTGATTTCAGAAAATATAGATTATTAATTTAAGTTTGTCCAAATTTAATTTGCAAC
* *
23501 TTCCTTTAAAGCTATCAAATAAGTCTACCGTTATACTAAATTGAAGCTATCAAACAAGTCTCCCG
456 TTCCTTTAAAGCTATCAAATAAGTCTACCGTTATACTAAATTGAAACTATCAAACAAGTCTCCCA
*
23566 TTATGCTAAATTTTGAAAGTATAAGTGAATGAAAGAGTAAGTTTAAATGAGAATTGTTCTACTAT
521 TTAGGCTAAATTTTGAAAGTATAAGTGAATGAAAGAGTAAGTTTAAATGAGAATTGTTCTACTAT
* * * *
23631 CCTTGAAAGGTAGTTGCCAGTTTACTGCAAAAATAAAGTTTCGTTTTCCATTCCCTGTATAATTG
586 CCTTGAAAAGTAGTTGCCAATTAACTGCAAAAAGAAAGTTTCGTTTTCCATTCCCTGTATAATTG
* * * *
23696 GAGATAAAAAATTTGAGAAGGCTATGATACTCGCTCCAATGGCTCTGATACTAATTCCAAAATTT
651 AAGATAAAAAATTTGAGAAGACTATGATACTAGCTCCAATGGCTCTGATACCAATTCCAAAATTT
* * * *
23761 ATTTTTAAGAGTTATGTTTCCTATCCTTGTGATATTCAAGAGGGTTATATTGAGATCTCACATGA
716 ATTCTTAAGAGTTATGTTTCCTATCCTTGTGATATTCAAAAGGGTTATATTGAGATCACAAATGA
* * * *
23826 CAAAATCCATCATTAAGATATCTATCAACTCCCCTTTTTTTAATTTTTCGAACTACGAGTTAGAT
781 CAAAATCCATCATTAAGATATCTATCAACTCCCCTATTTTTAATATTTCGAAATACGAGTTAAAT
* *
23891 TAATATTGCACCTCAACAAATCTATACTTAAGATTGATAATGTTAAAAATTGTTACGATTATTAT
846 TAATATTGCACCTCAACAAATCTATACTTAAGATTAATAATGTTAAAAATTGTTAAGATTATTAT
* * *
23956 ATAAGTTTACAACGTTAAATTCTATGACTCATCTTTCGAGCAAAAAATTACATGTCACTGT
911 AAAAGTTTACAACGTTAAAGTCTACGACTCATCTTTCGAGCAAAAAATTACATGTCACTGT
* * * * *
24017 TGTTTTATTATTTTATAATTATCCTTAAAAACGTCATAATATTTTTCTATTTTGTTTCAGGTAAG
1 TGTTTTATTATTTTATAATTATCCTTAAAAACATCAGAATATTATTATATTTTGTTTCAGCTAAG
* *
24082 AATTAT-TCATGGTAAATTTTTGACGGAAATGCAGCAGGCTTACATGAAAATATTGCAAAGAATG
66 AATTGTCT-ATGCTAAATTTTTGACGGAAATGCAGCAGGCTTACATGAAAATATTGCAAAGAATG
* * * * *
24146 ATGGATGCG-GCTGTTACTTATTATATGTGAAGGGTGGAATGGGGCTTGGACGGGCAACTCTTGA
130 ATGCATG-GTGCTATCACTTATTATATGTGAAGGGTGAAATGGGGCTTGGACGGGCAACTATTGA
* * * * *
24210 CTTATGTTTCTTTGACCCGAACATATCGTTCCT-TCTGTGCGAGGTCTTGCTTGTTGTTTGGGTG
194 CTTATGTTTCTTTGACCCGAACATATCGCTCCTCT-TATGCGAGGTCTTGCTTATTGCTTGGATG
*
24274 TAATGTCGTCTTTATACAATCTCATCTCGACAAAAGCTATAAAACAAATAACATCTTAAGGTATA
258 TAATGTAGTCTTTATACAATCTCATCTCGACAAAAGCTATAAAACAAATAACATCTTAAGGTATA
* * * *
24339 AACTTTCTTACTTGACACTCCTGATTCATTTGATCATAAAAAAATATATCTAGCTTTATTTATGT
323 AACATTCTTACTTGACACTCCTGATTCATTTAAGCAT-AAAAAATATATCTAGCTTTATTGATGT
* * *
24404 ATTTAAATAATTATTGATTTCAGAAAATATAGATTATTAATTTAAGTTTGTCCAATTTTAATTTT
387 ATTCAAATAATTATTGATTTCAGAAAATATAGATTATTAATTTAAGTTTGTCCAAATTTAATTTG
*** ** * *
24469 CAACTTCCTTTCCTGCTATCAAATAAGTCTGTCGTTATGCTAAATTGAAACTATTAAACAAGTCT
452 CAACTTCCTTTAAAGCTATCAAATAAGTCTACCGTTATACTAAATTGAAACTATCAAACAAGTCT
*
24534 CCCATTAGGCTAAATTTTTTAAAGTATAAGGTGAATGAAA-AGGTAAGTTTAAA-GAAGAATTGT
517 CCCATTAGGCTAAA-TTTTGAAAGTATAA-GTGAATGAAAGA-GTAAGTTTAAATG-AGAATTGT
* *
24597 TTTGCTATCCTTGAAAAGTAGTTGCCAATTAACTGCAAAAAGAAAGTATT-GTTTTCCA-TCCCT
578 TCTACTATCCTTGAAAAGTAGTTGCCAATTAACTGCAAAAAGAAAGT-TTCGTTTTCCATTCCCT
* * **
24660 -TATAAAATTGAAGGTAAGAAATTTGAGAAGACTATGATACTAGCTCCCCTGGCTCTGATACCAA
642 GTAT--AATTGAAGATAAAAAATTTGAGAAGACTATGATACTAGCTCCAATGGCTCTGATACCAA
* * * * * *
24724 TTCCAAAATTTCTTCTTAAGAGTTATGTTTGCTATTCTTTTGATTTTCAAAAGGGTTATATTGAT
705 TTCCAAAATTTATTCTTAAGAGTTATGTTTCCTATCCTTGTGATATTCAAAAGGGTTATATTGAG
* ** * * *
24789 ATCACAAATGACGAAATCCATTTTTAAGATGTCT-TTACACT-CCC-ATTTTTCATATTTCGAAA
770 ATCACAAATGACAAAATCCATCATTAAGATATCTATCA-ACTCCCCTATTTTTAATATTTCGAAA
* * *
24851 TACGGGTTAAATTAATATTGCATCTTAACAAATCTATACTTAAGATTAATAATGTTAAAAATTGT
834 TACGAGTTAAATTAATATTGCACCTCAACAAATCTATACTTAAGATTAATAATGTTAAAAATTGT
* ** * * * *
24916 TAAGATTATTGTAAAAGTTTATGATGTTAAAGTCTGCGACTTATCTTTCGAGCTAAAAATTAC
899 TAAGATTATTATAAAAGTTTACAACGTTAAAGTCTACGACTCATCTTTCGAGCAAAAAATTAC
24979 GTGTTGTTGC
Statistics
Matches: 842, Mismatches: 108, Indels: 23
0.87 0.11 0.02
Matches are distributed among these distances:
970 2 0.00
971 310 0.37
972 286 0.34
973 25 0.03
974 217 0.26
975 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (971 bp):
TGTTTTATTATTTTATAATTATCCTTAAAAACATCAGAATATTATTATATTTTGTTTCAGCTAAG
AATTGTCTATGCTAAATTTTTGACGGAAATGCAGCAGGCTTACATGAAAATATTGCAAAGAATGA
TGCATGGTGCTATCACTTATTATATGTGAAGGGTGAAATGGGGCTTGGACGGGCAACTATTGACT
TATGTTTCTTTGACCCGAACATATCGCTCCTCTTATGCGAGGTCTTGCTTATTGCTTGGATGTAA
TGTAGTCTTTATACAATCTCATCTCGACAAAAGCTATAAAACAAATAACATCTTAAGGTATAAAC
ATTCTTACTTGACACTCCTGATTCATTTAAGCATAAAAAATATATCTAGCTTTATTGATGTATTC
AAATAATTATTGATTTCAGAAAATATAGATTATTAATTTAAGTTTGTCCAAATTTAATTTGCAAC
TTCCTTTAAAGCTATCAAATAAGTCTACCGTTATACTAAATTGAAACTATCAAACAAGTCTCCCA
TTAGGCTAAATTTTGAAAGTATAAGTGAATGAAAGAGTAAGTTTAAATGAGAATTGTTCTACTAT
CCTTGAAAAGTAGTTGCCAATTAACTGCAAAAAGAAAGTTTCGTTTTCCATTCCCTGTATAATTG
AAGATAAAAAATTTGAGAAGACTATGATACTAGCTCCAATGGCTCTGATACCAATTCCAAAATTT
ATTCTTAAGAGTTATGTTTCCTATCCTTGTGATATTCAAAAGGGTTATATTGAGATCACAAATGA
CAAAATCCATCATTAAGATATCTATCAACTCCCCTATTTTTAATATTTCGAAATACGAGTTAAAT
TAATATTGCACCTCAACAAATCTATACTTAAGATTAATAATGTTAAAAATTGTTAAGATTATTAT
AAAAGTTTACAACGTTAAAGTCTACGACTCATCTTTCGAGCAAAAAATTACATGTCACTGT
Found at i:28542 original size:14 final size:15
Alignment explanation
Indices: 28516--28545 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28506 GTTATGGGGA
28516 AGGGAGAGGAAGAAG
1 AGGGAGAGGAAGAAG
28531 AGGGAG-GGAAGAAG
1 AGGGAGAGGAAGAAG
28545 A
1 A
28546 AAAGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (15 bp):
AGGGAGAGGAAGAAG
Found at i:29448 original size:52 final size:52
Alignment explanation
Indices: 29392--29539 Score: 224
Period size: 52 Copynumber: 2.8 Consensus size: 52
29382 TCCTTCAAAG
* * * * *
29392 TTTTCAAATTGGGAAAGTTCCCAACAAGTTTTCAAAGTGTTTAATTTAGATC
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTATTCAATTTAGATC
* *
29444 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTATTCGATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTATTCAATTTAGATC
*
29496 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGCATTCAA
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTATTCAA
29540 ACAACATTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 87 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (52 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTATTCAATTTAGATC
Found at i:33412 original size:53 final size:53
Alignment explanation
Indices: 33327--33479 Score: 198
Period size: 53 Copynumber: 2.9 Consensus size: 53
33317 AATTGCAAGT
* * * *
33327 ACTATAAACAGAAGATTTTGGTGAAACATTGTTCAATTCACCAAGTACTATAA
1 ACTAGAAACAAAAGACTTTGGTGAAACATTGTTCCATTCACCAAGTACTATAA
* *
33380 ACTAGATACAAAAGACTTTGGTGAAACATTGTTCCATTCACCATGTACTATAA
1 ACTAGAAACAAAAGACTTTGGTGAAACATTGTTCCATTCACCAAGTACTATAA
* * * * * *
33433 ACTATAAACAGAAGACTTTGTTAAAATATTGTTCCATTCACCGAGTA
1 ACTAGAAACAAAAGACTTTGGTGAAACATTGTTCCATTCACCAAGTA
33480 ATAATATATA
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 86 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (53 bp):
ACTAGAAACAAAAGACTTTGGTGAAACATTGTTCCATTCACCAAGTACTATAA
Found at i:35435 original size:21 final size:21
Alignment explanation
Indices: 35411--35462 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
35401 TCATCATCCA
35411 TCTCCATCTCATGGTCTTCAT
1 TCTCCATCTCATGGTCTTCAT
*
35432 TCTCCATCTCGTGGTCTTCAT
1 TCTCCATCTCATGGTCTTCAT
*
35453 CCTCCATCTC
1 TCTCCATCTC
35463 TTGATGTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.12, C:0.38, G:0.10, T:0.40
Consensus pattern (21 bp):
TCTCCATCTCATGGTCTTCAT
Found at i:36203 original size:32 final size:32
Alignment explanation
Indices: 36167--36232 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
36157 AATTATCCTC
36167 CTCATTTAATGGTATGGAAAATCTACTCCTAG
1 CTCATTTAATGGTATGGAAAATCTACTCCTAG
36199 CTCATTTAATGGTATGGAAAATCTACTCCTAG
1 CTCATTTAATGGTATGGAAAATCTACTCCTAG
36231 CT
1 CT
36233 TTAACCTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (32 bp):
CTCATTTAATGGTATGGAAAATCTACTCCTAG
Found at i:39956 original size:37 final size:38
Alignment explanation
Indices: 39902--40011 Score: 123
Period size: 38 Copynumber: 2.9 Consensus size: 38
39892 TTTTTATTTA
* * * * *
39902 TTTCTTTTTCTGACCTCTCTCTGTTTTAGGACCAG-TT
1 TTTCATTTTCCGACCTCTTTCTATTTTAGGTCCAGTTT
* *
39939 TTTCCTTTTCCGACCTCTTTCTATTTTAGGTCTAGTTT
1 TTTCATTTTCCGACCTCTTTCTATTTTAGGTCCAGTTT
* * *
39977 TTTTATTTTTCGACCTCTTTCTTTTTTAGGTCCAG
1 TTTCATTTTCCGACCTCTTTCTATTTTAGGTCCAG
40012 CTCTTTTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
37 29 0.48
38 32 0.52
ACGTcount: A:0.11, C:0.23, G:0.12, T:0.55
Consensus pattern (38 bp):
TTTCATTTTCCGACCTCTTTCTATTTTAGGTCCAGTTT
Found at i:40024 original size:38 final size:36
Alignment explanation
Indices: 39906--40024 Score: 121
Period size: 38 Copynumber: 3.1 Consensus size: 36
39896 TATTTATTTC
* * * *
39906 TTTTTCTGACCTCTCTCTGTTTTAGGACCAGTTTTTCC
1 TTTTTC-GACCTCTTTCTATTTTAGGTCCAGTTTTT-T
* *
39944 TTTTCCGACCTCTTTCTATTTTAGGTCTAGTTTTTTT
1 TTTTTCGACCTCTTTCTATTTTAGGTCCAG-TTTTTT
*
39981 ATTTTTCGACCTCTTTCTTTTTTAGGTCCAGCTCTTTTT
1 -TTTTTCGACCTCTTTCTATTTTAGGTCCAG-T-TTTTT
40020 TTTTT
1 TTTTT
40025 AGCTCCTTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
37 20 0.29
38 43 0.63
39 5 0.07
ACGTcount: A:0.10, C:0.22, G:0.11, T:0.57
Consensus pattern (36 bp):
TTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTT
Found at i:48531 original size:76 final size:76
Alignment explanation
Indices: 48394--48545 Score: 186
Period size: 76 Copynumber: 2.0 Consensus size: 76
48384 ACAAGGACCC
* *
48394 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
48459 GGG-TAGTGTCA
66 GGGCT-GTGTCA
* * **
48470 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGTGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
48532 GATGGGCTGTGTCA
63 GATGGGCTGTGTCA
48546 TAGCTCATCA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
75 4 0.06
76 55 0.83
77 7 0.11
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (76 bp):
CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCTGTGTCA
Found at i:49517 original size:26 final size:25
Alignment explanation
Indices: 49469--49527 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
49459 GTGTTCATGA
* *
49469 TTTAGGGGTTACTAACTCCCTTTTT
1 TTTAGAGGTTACTAACGCCCTTTTT
* *
49494 CTTTTGAGGTTACTAACGCTCTTTTT
1 -TTTAGAGGTTACTAACGCCCTTTTT
49520 TTTAGAGG
1 TTTAGAGG
49528 GACAATACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (25 bp):
TTTAGAGGTTACTAACGCCCTTTTT
Found at i:51916 original size:21 final size:21
Alignment explanation
Indices: 51892--51936 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
51882 GTAAGTGATG
*
51892 AAGT-AGTGAAATTGATGATCA
1 AAGTGAGTGAAATTG-TGAACA
*
51913 AAGTGAGTGAATTTGTGAACA
1 AAGTGAGTGAAATTGTGAACA
51934 AAG
1 AAG
51937 GTAATAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.42, C:0.04, G:0.27, T:0.27
Consensus pattern (21 bp):
AAGTGAGTGAAATTGTGAACA
Found at i:55664 original size:27 final size:28
Alignment explanation
Indices: 55634--55686 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
55624 AAAAGTAACT
55634 AAGAAAAATAAAC-AAAAATA-AAAGAAA
1 AAGAAAAAT-AACGAAAAATACAAAGAAA
55661 AAGAAAAATAACGAAAAATACAAAGA
1 AAGAAAAATAACGAAAAATACAAAGA
55687 TAAGGGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 3 0.12
27 16 0.67
28 5 0.21
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.08
Consensus pattern (28 bp):
AAGAAAAATAACGAAAAATACAAAGAAA
Found at i:67028 original size:13 final size:13
Alignment explanation
Indices: 67010--67039 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
67000 AACCGTTAAT
67010 ATCAAAATCATAA
1 ATCAAAATCATAA
*
67023 ATCAAAGTCATAA
1 ATCAAAATCATAA
67036 ATCA
1 ATCA
67040 GAGTAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (13 bp):
ATCAAAATCATAA
Found at i:68284 original size:29 final size:29
Alignment explanation
Indices: 68242--68299 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
68232 GCCACGCTAC
68242 ATGTGCAAAAATGACCATAATGCCCCTGG
1 ATGTGCAAAAATGACCATAATGCCCCTGG
68271 ATGTGCAAAAATGACCATAATGCCCCTGG
1 ATGTGCAAAAATGACCATAATGCCCCTGG
68300 GCGTGCGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (29 bp):
ATGTGCAAAAATGACCATAATGCCCCTGG
Found at i:68819 original size:7 final size:7
Alignment explanation
Indices: 68807--68855 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
68797 TTCTGTTCTT
68807 CTTTTTC
1 CTTTTTC
68814 CTTTTTC
1 CTTTTTC
*
68821 CCTTTTC
1 CTTTTTC
*
68828 ATTTTT-
1 CTTTTTC
*
68834 CATTTTC
1 CTTTTTC
68841 C-TTTTC
1 CTTTTTC
68847 C-TTTTC
1 CTTTTTC
68853 CTT
1 CTT
68856 CCTTTCTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 16 0.46
7 19 0.54
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (7 bp):
CTTTTTC
Found at i:68873 original size:23 final size:23
Alignment explanation
Indices: 68843--68886 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
68833 TCATTTTCCT
68843 TTTCCTTTTCCTT-CCTTTCTTTC
1 TTTCC-TTTCCTTCCCTTTCTTTC
68866 TTTCCTTTCCTTCCCTTTCTT
1 TTTCCTTTCCTTCCCTTTCTT
68887 ATTGGGCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTCCTTTCCTTCCCTTTCTTTC
Found at i:84130 original size:35 final size:35
Alignment explanation
Indices: 84070--84141 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
84060 GCAACTTTAT
* * * *
84070 TTGAAACTATCAAACCATTCTCCCGTTATGATAAA
1 TTGAAACTATCAAACAAGTCACCCGTTACGATAAA
* *
84105 TTGAAACTATCAAATAAGTCACCCGTTACGCTAAA
1 TTGAAACTATCAAACAAGTCACCCGTTACGATAAA
84140 TT
1 TT
84142 TTTTTTAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.31
Consensus pattern (35 bp):
TTGAAACTATCAAACAAGTCACCCGTTACGATAAA
Found at i:85848 original size:40 final size:40
Alignment explanation
Indices: 85797--85940 Score: 161
Period size: 40 Copynumber: 3.6 Consensus size: 40
85787 ACTTTTTGAT
* *
85797 GGGAACTTTCCCTACATTGAAAACTAAAACCAAAGCCGAC
1 GGGAACTTTCCCTATATTGAAAACTAAAACCAAAGCTGAC
* *
85837 GGGATCTTTCCCTATATTGAAAACTTTGAAA--AAA-CTTGAC
1 GGGAACTTTCCCTATATTGAAAAC--TAAAACCAAAGC-TGAC
* * *
85877 GGGATCTTTCCC-ATGTTGAAAACTAAAACCAGAGCTGAC
1 GGGAACTTTCCCTATATTGAAAACTAAAACCAAAGCTGAC
*
85916 GGGAACTTTCCCTAAATTGAAAACT
1 GGGAACTTTCCCTATATTGAAAACT
85941 TTTAAAACTT
Statistics
Matches: 87, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
37 4 0.05
39 28 0.32
40 51 0.59
42 4 0.05
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (40 bp):
GGGAACTTTCCCTATATTGAAAACTAAAACCAAAGCTGAC
Found at i:85987 original size:52 final size:52
Alignment explanation
Indices: 85926--86233 Score: 442
Period size: 52 Copynumber: 6.0 Consensus size: 52
85916 GGGAACTTTC
* * *
85926 CCTAAATTGAAAACTTTTAAAACTTGATGGGAACATTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
*
85978 CCTAAATTGAACGCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
86030 GCTAAATTGAACA-TTTGGAAAACTTGATTGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTT-GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* * ** * *
86082 GCTAAATCGAACAAATTGAAAACTTGATAGGAACTTTCCCACTTTGATAAGA
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
86134 CCTAAATTGAACACTTTGAAAACTTGATGGGAGCATTCCCACTTTG-AAA-A
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
86184 CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCGCACTTTGAAAA
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
86234 CCTTGAAGGA
Statistics
Matches: 230, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 43 0.19
51 8 0.03
52 177 0.77
53 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
Found at i:86217 original size:22 final size:22
Alignment explanation
Indices: 86142--86217 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
86132 GACCTAAATT
86142 GAACACTTTGAAAACTTGATGG
1 GAACACTTTGAAAACTTGATGG
** *
86164 GAGCATTCCCACTTTGAAAACCTAAAT-C
1 GA--A----CACTTTGAAAA-CTTGATGG
86192 GAACACTTTGAAAACTTGATGG
1 GAACACTTTGAAAACTTGATGG
86214 GAAC
1 GAAC
86218 TTTCGCACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
21 4 0.10
22 17 0.43
24 1 0.03
26 1 0.03
28 13 0.32
29 4 0.10
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (22 bp):
GAACACTTTGAAAACTTGATGG
Found at i:87244 original size:6 final size:6
Alignment explanation
Indices: 87233--87267 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
87223 GTCGTTTACC
*
87233 CTTTTT CTTTTT CTTTTT CTTTTT C-TCTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
87268 TCTCCTCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:87256 original size:18 final size:17
Alignment explanation
Indices: 87233--87267 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
87223 GTCGTTTACC
*
87233 CTTTTTCTTTTTCTTTTT
1 CTTTTTC-TCTTCTTTTT
87251 CTTTTTCTCTTCTTTTT
1 CTTTTTCTCTTCTTTTT
87268 TCTCCTCTTC
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTTTCTCTTCTTTTT
Found at i:92589 original size:26 final size:28
Alignment explanation
Indices: 92555--92622 Score: 95
Period size: 26 Copynumber: 2.5 Consensus size: 28
92545 AAATTACCAA
**
92555 GGGCATTTTGGTCA-TTTTTGCCTCA-G
1 GGGCATTTTGGTCACTTTCCGCCTCATG
92581 GGGCATTTTGGTCACTTTCCGCCTCATG
1 GGGCATTTTGGTCACTTTCCGCCTCATG
*
92609 GGGCATTTAGGTCA
1 GGGCATTTTGGTCA
92623 AGATTACTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 14 0.38
27 9 0.24
28 14 0.38
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (28 bp):
GGGCATTTTGGTCACTTTCCGCCTCATG
Found at i:96040 original size:47 final size:47
Alignment explanation
Indices: 95973--96489 Score: 836
Period size: 47 Copynumber: 10.9 Consensus size: 47
95963 TTTAAACTAA
* *
95973 AAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAGCTAAGTAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
* *
96020 AAAAAAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
*
96067 AAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
** *
96114 AAAAGTGGAAGAGATTAGTTTAATTCTAGGTAATTAAAGTAAGTAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
96161 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
*
96208 AAAAGAGGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
* * *
96255 AAAAGGAGAAGAGATTAGTTTAATTCTAGATAATTAAACTAAATAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
*
96302 AAAAGAGGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
96349 AAAAGAAGAAGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 --AA-AAG-A-AGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
* *
96401 AAAAGAAGAAGAGATTAGTTTAATTCCAGGTAAGTAAACTAAGTAGT
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
* *
96448 AAAAGAAGAAGAGATTAGTTTAATACCAGGTAATTAAACTAA
1 AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAA
96490 AGAAGATGTT
Statistics
Matches: 437, Mismatches: 28, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
47 385 0.88
48 1 0.00
49 5 0.01
50 5 0.01
51 1 0.00
52 40 0.09
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (47 bp):
AAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
Found at i:96502 original size:36 final size:36
Alignment explanation
Indices: 96453--96525 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
96443 GTAGTAAAAG
* *
96453 AAGAAGAGATTAGTTTAATACCAGGTAATTAAACTA
1 AAGAAGAGATTAGTTTAATACCAGGAAAGTAAACTA
* *
96489 AAGAAGATG-TTAGTTTAATTCTAGGAAAGTAAACTA
1 AAGAAGA-GATTAGTTTAATACCAGGAAAGTAAACTA
96525 A
1 A
96526 GTAGCAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.29
Consensus pattern (36 bp):
AAGAAGAGATTAGTTTAATACCAGGAAAGTAAACTA
Found at i:96569 original size:86 final size:82
Alignment explanation
Indices: 96406--96578 Score: 215
Period size: 83 Copynumber: 2.0 Consensus size: 82
96396 GTAGTAAAAG
* * *
96406 AAGAAGAGATTAGTTTAATTCCAGGTAAGTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAA
1 AAGAAGAGATTAGTTTAATTCCAGGAAAGTAAACTAAGTAGCAAAAGAAGAAAAGATTAGTTTAA
96471 TACCAGGTAATTAAACTA
66 TA-CAGGTAATTAAACTA
* *
96489 AAGAAGATG-TTAGTTTAATTCTAGGAAAGTAAACTAAGTAGCAAATGAAGAACAAGCAATTAGT
1 AAGAAGA-GATTAGTTTAATTCCAGGAAAGTAAACTAAGTAGCAAAAGAAGAA-AAG--ATTAGT
*
96553 TTAAT-CATGGGTAATTAAATTA
62 TTAATACA--GGTAATTAAACTA
96575 AAGA
1 AAGA
96579 GGAATAGAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
83 46 0.59
84 5 0.06
86 27 0.35
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (82 bp):
AAGAAGAGATTAGTTTAATTCCAGGAAAGTAAACTAAGTAGCAAAAGAAGAAAAGATTAGTTTAA
TACAGGTAATTAAACTA
Found at i:102024 original size:40 final size:40
Alignment explanation
Indices: 101924--102414 Score: 501
Period size: 40 Copynumber: 12.0 Consensus size: 40
101914 AAAACATTGA
* * *
101924 AAACAACACCTTCCGACCGA-GAAGGGCGAAAC-AGGAA-TG
1 AAACAACACCTTCCGA-TGAGGAAGGGC-AAACTGGGAATTT
* *
101963 AAATCAACACCTTCCGATGGGGAAGGGCAAAAC-GGGAA-TG
1 AAA-CAACACCTTCCGATGAGGAAGGGC-AAACTGGGAATTT
* * *
102003 AAATCAACACCTTCCGGTGGGGAAGGGAAAACTGGAAAGAATGGGCTTT
1 AAA-CAACACCTTCCGATGAGGAAGGGCAAACTGG---GAA-----TTT
* * *
102052 AAACAATACCTTCCGATGAGGAAGGGCAAACTGGAAATCT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
* * *
102092 AAACAACACCTTCCGGTGAGGAAGGACAAACTGGTGAACTT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAATTT
* *
102133 AAACAATACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-TT
* * *
102174 -GACAACACCTTCCGATGAGGAAGGGAAAACTAGGAATTT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
** * *
102213 ACAATGACACCTTCCGATGAGGAAGGACAAAATGGGAATTTT
1 A-AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-TTT
102255 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
** *
102295 AAACAACACCTTATGATGAGGTAGGGCAAACT-GGAATTT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
*
102334 AAAACAACACCTTCTGATGAGGAAGGGCAAACTTGGGAATTT
1 -AAACAACACCTTCCGATGAGGAAGGGCAAAC-TGGGAATTT
* *
102376 AAACAACATCTTCCGATGAGAAAGGGCAAACTGGGAATT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATT
102415 ATCGAAGGAA
Statistics
Matches: 384, Mismatches: 48, Indels: 39
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.04
40 196 0.51
41 125 0.33
42 11 0.03
43 3 0.01
45 2 0.01
48 27 0.07
49 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (40 bp):
AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
Found at i:102185 original size:81 final size:80
Alignment explanation
Indices: 102049--102413 Score: 457
Period size: 81 Copynumber: 4.5 Consensus size: 80
102039 AAGAATGGGC
* * *
102049 TTTAAACAATACCTTCCGATGAGGAAGGGCAAACTGGAAATCTAAACAACACCTTCCGGTGAGGA
1 TTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATCTAAACAACACCTTCCGATGAGGA
102114 AGGACAAACTGGTGAA
66 AGGACAAACTGG-GAA
* * *
102130 CTTAAACAATACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT-GACAACACCTTCCGATGAGG
1 TTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-CTAAACAACACCTTCCGATGAGG
*
102194 AAGGGA-AAACTAGGAA
65 AA-GGACAAACTGGGAA
** * * *
102210 TTTACAATGACACCTTCCGATGAGGAAGGACAAAATGGGAATTTTAAACAACACCTTCCGATGAG
1 TTTA-AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-TCTAAACAACACCTTCCGATGAG
*
102275 GAAGGGCAAACTGGGAA
64 GAAGGACAAACTGGGAA
** * * *
102292 TTTAAACAACACCTTATGATGAGGTAGGGCAAACT-GGAATTTAAAACAACACCTTCTGATGAGG
1 TTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATCT-AAACAACACCTTCCGATGAGG
*
102356 AAGGGCAAACTTGGGAA
65 AAGGACAAAC-TGGGAA
* *
102373 TTTAAACAACATCTTCCGATGAGAAAGGGCAAACTGGGAAT
1 TTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT
102414 TATCGAAGGA
Statistics
Matches: 247, Mismatches: 28, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
79 3 0.01
80 40 0.16
81 159 0.64
82 45 0.18
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (80 bp):
TTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATCTAAACAACACCTTCCGATGAGGA
AGGACAAACTGGGAA
Found at i:102642 original size:42 final size:43
Alignment explanation
Indices: 102430--102683 Score: 379
Period size: 43 Copynumber: 6.0 Consensus size: 43
102420 AGGAAAAATG
* * * * *
102430 GGACCTTCCGA-CTGGAAGGTGCATTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAATAA
* *
102472 GGACCTTCCAACCAGGAAGGGGCATTTTCGGAAATGAAAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAATAA
102515 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAATAA
* * *
102558 GCACCTTCCAACCAGGTAGGCGCATTTTTGGAAAAGAAAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAATAA
102601 GGACCTTCCAACCAGGAAGGGGCA-TTTTGGAAAAGAAAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAATAA
*
102643 GGACCTTCCAACCAAGAAGGGGCATTTTT-GAAAACGAAAAT
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAA-GAAAAT
102684 CGATCAGGAA
Statistics
Matches: 195, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
42 56 0.29
43 139 0.71
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (43 bp):
GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAATAA
Found at i:104444 original size:42 final size:44
Alignment explanation
Indices: 104397--104486 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 44
104387 CATTATTAAA
*
104397 ATTCTACT-TC-ATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCTCTATCTCTAGATAATTCATCAAAATAAAGCTAAT
*
104439 ATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAGGTAAT
1 ATTCTACT-CTCTATCTCTAGATAATTCATCAAAATAAAGCTAAT
104484 ATT
1 ATT
104487 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 8 0.19
44 2 0.05
45 33 0.77
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.37
Consensus pattern (44 bp):
ATTCTACTCTCTATCTCTAGATAATTCATCAAAATAAAGCTAAT
Found at i:109882 original size:2 final size:2
Alignment explanation
Indices: 109875--109910 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
109865 CACTCTGATA
109875 AT AT 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 AT AT
109911 TTGTTTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110889 original size:27 final size:27
Alignment explanation
Indices: 110849--110900 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
110839 TCATTAATGC
110849 TTATATATAATATATATTATTTTTAGT
1 TTATATATAATATATATTATTTTTAGT
**
110876 TTATATATGTTATATATTATTTTTA
1 TTATATATAATATATATTATTTTTA
110901 TTGATTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TTATATATAATATATATTATTTTTAGT
Found at i:114142 original size:30 final size:30
Alignment explanation
Indices: 114108--114203 Score: 122
Period size: 29 Copynumber: 3.2 Consensus size: 30
114098 AAGTACCTAA
* *
114108 TTAGTCCCTATATTATAGAAAAAAATCAAT
1 TTAGTCCCTCTATTATAGAAAAATATCAAT
* **
114138 TTAGTCCCTCCATTATA-AAATCTATCAAT
1 TTAGTCCCTCTATTATAGAAAAATATCAAT
*
114167 TTAGTCCCTCTATTATTGAAAAGATATCAAT
1 TTAGTCCCTCTATTATAGAAAA-ATATCAAT
114198 TTAGTC
1 TTAGTC
114204 TCTCCATGAC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
29 24 0.44
30 18 0.33
31 13 0.24
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (30 bp):
TTAGTCCCTCTATTATAGAAAAATATCAAT
Found at i:114165 original size:29 final size:31
Alignment explanation
Indices: 114108--114210 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 31
114098 AAGTACCTAA
** * *
114108 TTAGTCCCTATATTATAGAAAA-AAATCAAT
1 TTAGTCCCTCCATTATTGAAAAGATATCAAT
**
114138 TTAGTCCCTCCATTA-T-AAAATCTATCAAT
1 TTAGTCCCTCCATTATTGAAAAGATATCAAT
*
114167 TTAGTCCCTCTATTATTGAAAAGATATCAAT
1 TTAGTCCCTCCATTATTGAAAAGATATCAAT
*
114198 TTAGTCTCTCCAT
1 TTAGTCCCTCCAT
114211 GACGGGACCA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.07
29 20 0.33
30 14 0.23
31 22 0.37
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (31 bp):
TTAGTCCCTCCATTATTGAAAAGATATCAAT
Found at i:114487 original size:13 final size:13
Alignment explanation
Indices: 114466--114496 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
114456 TTCCCTCTCT
*
114466 TTCTTCTTCCTTC
1 TTCTCCTTCCTTC
114479 TTCTCCTTCCTTC
1 TTCTCCTTCCTTC
114492 TTCTC
1 TTCTC
114497 TGCTTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (13 bp):
TTCTCCTTCCTTC
Found at i:123851 original size:43 final size:41
Alignment explanation
Indices: 123752--124119 Score: 398
Period size: 43 Copynumber: 8.7 Consensus size: 41
123742 AAATTGACCT
* *
123752 TGTGTTATAAATGTGTTT-AGGGAC-TTTAGTATAGATGCCTC
1 TGTGTTATAAATGTGTTTGA-GGACTTTTAG-AGAGATGCCCC
*
123793 TATGTTATAAATGTGTTTGAGGACTTTTAGAGAGGATTGCCCC
1 TGTGTTATAAATGTGTTTGAGGACTTTTAGAGA-GA-TGCCCC
* * * *
123836 TGTGTTATAATTGTGTTTGGGGACTTTGATATAGAGATGCCTC
1 TGTGTTATAAATGTGTTTGAGGACTTT--TAGAGAGATGCCCC
123879 TGTGTTATAAATGTGTTTGAGGACTTTTAGAGAGGATTGCCCC
1 TGTGTTATAAATGTGTTTGAGGACTTTTAGAGA-GA-TGCCCC
* * * *
123922 TGTGTTATAATTGTGTTTGGGGACTTTGATATAGAGATGCCTC
1 TGTGTTATAAATGTGTTTGAGGACTTT--TAGAGAGATGCCCC
* *
123965 TGTGTTATAAATGTGCTTGAGGACTTTTAAAGAGAATTGCCCC
1 TGTGTTATAAATGTGTTTGAGGACTTTTAGAGAG-A-TGCCCC
* * * * * *
124008 TGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTC
1 TGTGTTATAAATGTGTTTGAGGACTTTTAGAGAGATGCCCC
*
124049 TGTGTTATAAATGTGTTTGAGGACTTTAGAGAGAGAATTGCCCC
1 TGTGTTATAAATGTGTTTGAGGACTTT-TAGAGAG-A-TGCCCC
*
124093 TGTGTTATAAATGTGTTTGGGGACTTT
1 TGTGTTATAAATGTGTTTGAGGACTTT
124120 GGGGAGGGAG
Statistics
Matches: 278, Mismatches: 34, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
41 64 0.23
42 17 0.06
43 152 0.55
44 35 0.13
45 10 0.04
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (41 bp):
TGTGTTATAAATGTGTTTGAGGACTTTTAGAGAGATGCCCC
Found at i:123901 original size:86 final size:84
Alignment explanation
Indices: 123752--124120 Score: 598
Period size: 86 Copynumber: 4.3 Consensus size: 84
123742 AAATTGACCT
* * *
123752 TGTGTTATAAATGTGTTTAGGGACTTT-AGTATAGATGCCTCTATGTTATAAATGTGTTTGAGGA
1 TGTGTTATAATTGTGTTTGGGGACTTTGA-TATAGATGCCTCTGTGTTATAAATGTGTTTGAGGA
123816 CTTTTAGAGAGGATTGCCCC
65 CTTTTAGAGAGGATTGCCCC
123836 TGTGTTATAATTGTGTTTGGGGACTTTGATATAGAGATGCCTCTGTGTTATAAATGTGTTTGAGG
1 TGTGTTATAATTGTGTTTGGGGACTTTGATAT--AGATGCCTCTGTGTTATAAATGTGTTTGAGG
123901 ACTTTTAGAGAGGATTGCCCC
64 ACTTTTAGAGAGGATTGCCCC
*
123922 TGTGTTATAATTGTGTTTGGGGACTTTGATATAGAGATGCCTCTGTGTTATAAATGTGCTTGAGG
1 TGTGTTATAATTGTGTTTGGGGACTTTGATAT--AGATGCCTCTGTGTTATAAATGTGTTTGAGG
* *
123987 ACTTTTAAAGAGAATTGCCCC
64 ACTTTTAGAGAGGATTGCCCC
124008 TGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGAC
1 TGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGAC
124073 -TTTAGAGAGAGAATTGCCCC
66 TTTTAGAGAG-G-ATTGCCCC
*
124093 TGTGTTATAAATGTGTTTGGGGACTTTG
1 TGTGTTATAATTGTGTTTGGGGACTTTG
124121 GGGAGGGAGA
Statistics
Matches: 270, Mismatches: 10, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
83 8 0.03
84 60 0.22
85 36 0.13
86 166 0.61
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (84 bp):
TGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGAC
TTTTAGAGAGGATTGCCCC
Found at i:126717 original size:16 final size:16
Alignment explanation
Indices: 126696--126727 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
126686 TGTATACTCC
*
126696 GCTGCGGTGACATTCT
1 GCTGCGGTAACATTCT
126712 GCTGCGGTAACATTCT
1 GCTGCGGTAACATTCT
126728 ACTACAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.31
Consensus pattern (16 bp):
GCTGCGGTAACATTCT
Found at i:127801 original size:35 final size:34
Alignment explanation
Indices: 127718--127804 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 34
127708 TGACATATAT
*
127718 AGCCCCAAGTGTTGAATGATGAAGGAATTGCTGG
1 AGCCCCAAGTGTTGAATGATGAAGGAATTGCTGC
* ** *
127752 AGTCCCCAAATGTTGAATGATGAAGGGGTTGTTGC
1 AG-CCCCAAGTGTTGAATGATGAAGGAATTGCTGC
127787 AGCCCCTAAGTGTTGAAT
1 AGCCCC-AAGTGTTGAAT
127805 CTGATGATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
34 6 0.13
35 39 0.87
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (34 bp):
AGCCCCAAGTGTTGAATGATGAAGGAATTGCTGC
Found at i:134270 original size:41 final size:41
Alignment explanation
Indices: 134225--134325 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 41
134215 TAAAATCTTT
* * * * *
134225 AATCAGGGACGAAATTGAGTCAATAAATAAATAT-TACTCTA
1 AATCAGGGACAAAATTGAATCAATAAACAAACATAAAC-CTA
* *
134266 AATCAGGGATAAAATTGAATCAATTAACAAACATAAACCTA
1 AATCAGGGACAAAATTGAATCAATAAACAAACATAAACCTA
* *
134307 AATCAGGGACTATATTGAA
1 AATCAGGGACAAAATTGAA
134326 AACGAAAAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
41 47 0.96
42 2 0.04
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.25
Consensus pattern (41 bp):
AATCAGGGACAAAATTGAATCAATAAACAAACATAAACCTA
Found at i:138036 original size:69 final size:69
Alignment explanation
Indices: 137944--138365 Score: 596
Period size: 69 Copynumber: 6.1 Consensus size: 69
137934 ACTTGGCCTA
* * * * * * *
137944 TGGAAAAGCCTCTGTTG-TATGGATGGACCCAATGTTTAAACTGACTCGCACGGAAACGAGTTTG
1 TGGAAAAGCCTATGTGGCT-TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTG
* *
138008 ACTTA
65 GCTTG
* * * *
138013 TGGAAAAGTCTATATGGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGG
1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
138078 CTTG
66 CTTG
* * *
138082 TGGAAAAGCCTATGTGGCTTGGAAGGAACCAAGGCTTGAACTGACTCGTATGGAAACAAGTTTGG
1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
138147 CTTG
66 CTTG
* *
138151 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTAAC-CTGTATGGAAACGAGTTTC
1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTC-GTATGGAAACGAGTTTG
138215 GCTTG
65 GCTTG
* * *
138220 TGGAAAAGCCTACGTGGCTTGGATGGAACCAAGGCTTAAACTAACTTGTATGGAAACGAGTTTGG
1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
138285 CTTG
66 CTTG
* *
138289 TGGAAAAGCCTACGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGA
1 TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
*
138354 CTTA
66 CTTG
138358 TGGAAAAG
1 TGGAAAAG
138366 TCAAAGCATT
Statistics
Matches: 320, Mismatches: 30, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
68 1 0.00
69 318 0.99
70 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (69 bp):
TGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
CTTG
Found at i:139430 original size:20 final size:20
Alignment explanation
Indices: 139401--139443 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
139391 AGCTTTATAT
* *
139401 TATATGGTTATGGTTAAGCG
1 TATATAGTTATGGTTAAACG
139421 TATATAGTTATGGTTAAACG
1 TATATAGTTATGGTTAAACG
139441 TAT
1 TAT
139444 CCTTGGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (20 bp):
TATATAGTTATGGTTAAACG
Found at i:139886 original size:2 final size:2
Alignment explanation
Indices: 139881--139916 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
139871 CAAACAATCC
139881 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
139917 AAAACCTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:140544 original size:12 final size:11
Alignment explanation
Indices: 140516--140634 Score: 84
Period size: 10 Copynumber: 10.9 Consensus size: 11
140506 GGCCCAATGG
*
140516 GAAAAGGAAAA
1 GAAAAAGAAAA
140527 -AAAAAGAACAA
1 GAAAAAGAA-AA
140538 GAAAAAGAAAAA
1 GAAAAAG-AAAA
* *
140550 TAAAAAGGAAA
1 GAAAAAGAAAA
*
140561 G-GAAAGAAAA
1 GAAAAAGAAAA
140571 GAAAAAGGAAAA
1 GAAAAA-GAAAA
* *
140583 AAAAAAGAAAG
1 GAAAAAGAAAA
*
140594 GGAAAAGAAAA
1 GAAAAAGAAAA
*
140605 -AAAAATAAAA
1 GAAAAAGAAAA
*
140615 -AAAAGGAAAA
1 GAAAAAGAAAA
* *
140625 TAAAGAGAAA
1 GAAAAAGAAA
140635 TTTCGGGAAT
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
10 31 0.37
11 27 0.32
12 24 0.29
13 2 0.02
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:140548 original size:5 final size:5
Alignment explanation
Indices: 140516--140634 Score: 51
Period size: 5 Copynumber: 21.8 Consensus size: 5
140506 GGCCCAATGG
* * * *
140516 GAAAA GGAAAA AAAAA GAACAA GAAAAA GAAAAA TAAAAA GGAAA GGAAA
1 GAAAA -GAAAA GAAAA GAA-AA G-AAAA G-AAAA -GAAAA GAAAA GAAAA
* * * *
140566 GAAAA GAAAAA GGAAAAA AAAAA GAAAGG GAAAA GAAAA AAAAA TAAAA
1 GAAAA G-AAAA -G-AAAA GAAAA GAAA-A GAAAA GAAAA GAAAA GAAAA
*
140615 -AAAA GGAAAA TAAAGA GAAA
1 GAAAA -GAAAA GAAA-A GAAA
140635 TTTCGGGAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.04
5 42 0.47
6 36 0.40
7 8 0.09
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (5 bp):
GAAAA
Found at i:140577 original size:16 final size:15
Alignment explanation
Indices: 140558--140609 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
140548 AATAAAAAGG
140558 AAAGGAAAGAAAAGAA
1 AAAGGAAAGAAAA-AA
*
140574 AAAGGAAAAAAAAAA
1 AAAGGAAAGAAAAAA
140589 GAAAGGGAAAAGAAAAAA
1 -AAA-GG-AAAGAAAAAA
140607 AAA
1 AAA
140610 TAAAAAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 2 0.06
16 15 0.48
17 5 0.16
18 9 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGGAAAGAAAAAA
Found at i:140588 original size:33 final size:32
Alignment explanation
Indices: 140529--140618 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 32
140519 AAGGAAAAAA
140529 AAAGAACAAGAAAAAGAAAAATAAAAAGGAAAGG
1 AAAGAA-AAGAAAAAGAAAAA-AAAAAGGAAAGG
140563 AAAGAAAAGAAAAAGGAAAAAAAAAA-GAAAGGG
1 AAAGAAAAGAAAAA-GAAAAAAAAAAGGAAA-GG
*
140596 AAAAGAAAA-AAAAATAAAAAAAA
1 -AAAGAAAAGAAAAAGAAAAAAAA
140619 GGAAAATAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
32 12 0.23
33 20 0.38
34 20 0.38
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (32 bp):
AAAGAAAAGAAAAAGAAAAAAAAAAGGAAAGG
Found at i:140605 original size:6 final size:6
Alignment explanation
Indices: 140517--140634 Score: 68
Period size: 6 Copynumber: 20.3 Consensus size: 6
140507 GCCCAATGGG
* * * *
140517 AAAAGG AAAA-A AAAAGA ACAAGA AAAAGA AAAATA AAAAG- GAAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * *
140562 GAAAG- AAAAGA AAAAGGA AAAA-A AAAAG- AAAGGG AAAAGA AAAAAA
1 AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * *
140608 AATAAAA AAAAGG AAAATA AAGAGA AA
1 AA-AAGA AAAAGA AAAAGA AAAAGA AA
140635 TTTCGGGAAT
Statistics
Matches: 89, Mismatches: 17, Indels: 12
0.75 0.14 0.10
Matches are distributed among these distances:
5 26 0.29
6 51 0.57
7 12 0.13
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:140635 original size:25 final size:27
Alignment explanation
Indices: 140540--140624 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 27
140530 AAGAACAAGA
140540 AAAAGAAAAATAAAAAGGAAAGGAAAGAAAAG
1 AAAA-AAAAATAAAAA-GAAAGG---GAAAAG
*
140572 AAAAAGGAAAAAAAAAAGAAAGGGAAAAG
1 AAAAA--AAAATAAAAAGAAAGGGAAAAG
140601 AAAAAAAAATAAAAA-AAA-GGAAAA
1 AAAAAAAAATAAAAAGAAAGGGAAAA
140625 TAAAGAGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
25 6 0.12
26 3 0.06
27 9 0.18
29 11 0.22
31 1 0.02
32 10 0.20
33 9 0.18
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (27 bp):
AAAAAAAAATAAAAAGAAAGGGAAAAG
Found at i:143620 original size:158 final size:158
Alignment explanation
Indices: 143332--143649 Score: 627
Period size: 158 Copynumber: 2.0 Consensus size: 158
143322 CTTTTTTTAT
143332 AATGGGTGGAACAGATAATAGCAACAATTTTTTTACAGAGATAATATGTCTATTGGAGGAGATGA
1 AATGGGTGGAACAGATAATAGCAACAATTTTTTTACAGAGATAATATGTCTATTGGAGGAGATGA
*
143397 TGCCTTTAGCAGTGATAGCTTTTTGCAAGATGCAATAGGCAATGATGTTCAACATATACATGAGG
66 TGCCTTTAGCAGTGATAGCTTTTTGCAAGATGAAATAGGCAATGATGTTCAACATATACATGAGG
143462 AGAATGAAGCCCATTCAATCGGGGACGC
131 AGAATGAAGCCCATTCAATCGGGGACGC
143490 AATGGGTGGAACAGATAATAGCAACAATTTTTTTACAGAGATAATATGTCTATTGGAGGAGATGA
1 AATGGGTGGAACAGATAATAGCAACAATTTTTTTACAGAGATAATATGTCTATTGGAGGAGATGA
143555 TGCCTTTAGCAGTGATAGCTTTTTGCAAGATGAAATAGGCAATGATGTTCAACATATACATGAGG
66 TGCCTTTAGCAGTGATAGCTTTTTGCAAGATGAAATAGGCAATGATGTTCAACATATACATGAGG
143620 AGAATGAAGCCCATTCAATCGGGGACGC
131 AGAATGAAGCCCATTCAATCGGGGACGC
143648 AA
1 AA
143650 ATGGAAAGTC
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 159 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.27
Consensus pattern (158 bp):
AATGGGTGGAACAGATAATAGCAACAATTTTTTTACAGAGATAATATGTCTATTGGAGGAGATGA
TGCCTTTAGCAGTGATAGCTTTTTGCAAGATGAAATAGGCAATGATGTTCAACATATACATGAGG
AGAATGAAGCCCATTCAATCGGGGACGC
Found at i:149008 original size:25 final size:25
Alignment explanation
Indices: 148970--149035 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
148960 ACGACTCATG
* * *
148970 TGCGTTGGGTAAACGCTCATGTGCT
1 TGCGTTTGGAAAACGCGCATGTGCT
* *
148995 TGCGTTTGGAAAACGAGCCTGTGCT
1 TGCGTTTGGAAAACGCGCATGTGCT
149020 TGCGTTTGGAAAACGC
1 TGCGTTTGGAAAACGC
149036 ATGGGTTGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.29
Consensus pattern (25 bp):
TGCGTTTGGAAAACGCGCATGTGCT
Found at i:157491 original size:15 final size:15
Alignment explanation
Indices: 157453--157492 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
157443 ATTTTCTGTA
*
157453 TCTTCTTTCAAAGCT
1 TCTTCTTTGAAAGCT
157468 TCTTCTTTGAAAGCT
1 TCTTCTTTGAAAGCT
157483 TCTTCTTTGA
1 TCTTCTTTGA
157493 TTTCATAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (15 bp):
TCTTCTTTGAAAGCT
Found at i:164453 original size:2 final size:2
Alignment explanation
Indices: 164446--164478 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
164436 TAATTTCATT
164446 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
164479 GAAAAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:166292 original size:14 final size:14
Alignment explanation
Indices: 166270--166320 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
166260 AGATGGCACT
*
166270 ATCCTCAAAAACCA
1 ATCCCCAAAAACCA
*
166284 ATCCCCAAATTACC-
1 ATCCCCAAA-AACCA
166298 A-CCCTCAAAAACCA
1 ATCCC-CAAAAACCA
166312 ATCCCCAAA
1 ATCCCCAAA
166321 GTCTTTCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 6 0.20
14 18 0.60
15 6 0.20
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (14 bp):
ATCCCCAAAAACCA
Found at i:170276 original size:31 final size:31
Alignment explanation
Indices: 170241--170312 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
170231 TAAATTATTG
*
170241 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATAAAAGTC-TTAAATTAAA
*
170272 CAAA-TAATTAAAATAAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATAAAAGTCTTAAATTAAA
170303 CAAATTAAAA
1 CAAATTAAAA
170313 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATAAAAGTCTTAAATTAAA
Done.