Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1874
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: 37183
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:231 original size:38 final size:39
Alignment explanation
Indices: 181--381 Score: 177
Period size: 38 Copynumber: 5.2 Consensus size: 39
171 TGGATCTTGG
* *
181 TAACGCGGATTTAGTAACTCGCGC-ATGCCTTCGGGACT
1 TAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACT
219 TAACCCGGA-TT--T-ACTCGCACAAATGCCTTCGCGGACT
1 TAACCCGGATTTAGTAACTCGCAC-AATGCCTTCG-GGACT
256 TAACCCGGATTTAGTAACTCGCACCAATGCCTTC-GG-CT
1 TAACCCGGATTTAGTAACTCGCA-CAATGCCTTCGGGACT
* * *
294 TAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCT
1 TAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGA-CT
** * * * *
334 TAGTCCGGATAT-GTCACTTAGCACAAAGCCTTCGGGACT
1 TAACCCGGATTTAGTAAC-TCGCACAATGCCTTCGGGACT
*
373 TAGCCCGGA
1 TAACCCGGA
382 CATCATTCAA
Statistics
Matches: 137, Mismatches: 13, Indels: 25
0.78 0.07 0.14
Matches are distributed among these distances:
34 7 0.05
35 1 0.01
36 9 0.07
37 17 0.12
38 43 0.31
39 23 0.17
40 20 0.15
41 16 0.12
42 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (39 bp):
TAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACT
Found at i:272 original size:75 final size:78
Alignment explanation
Indices: 181--328 Score: 207
Period size: 75 Copynumber: 1.9 Consensus size: 78
171 TGGATCTTGG
* *
181 TAACGCGGATTTAGTAACTCGC-GC-ATGCCTTCGGGACTTAACCCGG-ATT-TA-CTCGCACAA
1 TAACCCGGATTTAGTAACTCGCACCAATGCCTTC-GG-CTTAACCCGGAATTATATCTCGCACAA
241 ATGCCTTCGCGGACT
64 ATGCCTTCGCGGACT
*
256 TAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGCTTAGCCCGGAATTAGTATCTCGCACAAA
1 TAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGCTTAACCCGGAATTA-TATCTCGCACAAA
321 TGCCTTCG
65 TGCCTTCG
329 GATCTTAGTC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
75 30 0.47
76 6 0.09
77 8 0.12
78 2 0.03
79 18 0.28
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (78 bp):
TAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGCTTAACCCGGAATTATATCTCGCACAAAT
GCCTTCGCGGACT
Found at i:375 original size:79 final size:77
Alignment explanation
Indices: 207--381 Score: 191
Period size: 79 Copynumber: 2.3 Consensus size: 77
197 ACTCGCGCAT
* *
207 GCCTTCGGGACTTAACCCGG-ATTTACTCGCACAAATGCCTTCGCGGACTTAACCCGGATTTAGT
1 GCCTTCGGGACTTAGCCCGGAATTTACTCGCACAAATGCCTTC-CGGACTTAACCCGGATATAGT
* *
271 AACTCGCACCAAT
65 AACTAGCACCAAA
**
284 GCCTTC-GG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTT-CGGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAGCCCGGAATT--TA-CTCGCACAAATGCCTTCCGGA-CTTAACCCGGATAT
*
346 -GTCACTTAGCA-CAAA
62 AGTAAC-TAGCACCAAA
361 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAGCCCGGA
382 CATCATTCAA
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
75 9 0.11
76 5 0.06
77 23 0.28
78 19 0.23
79 27 0.33
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (77 bp):
GCCTTCGGGACTTAGCCCGGAATTTACTCGCACAAATGCCTTCCGGACTTAACCCGGATATAGTA
ACTAGCACCAAA
Found at i:8191 original size:39 final size:40
Alignment explanation
Indices: 8034--8258 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
8024 GCTCCTCGTT
* *
8034 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
8074 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
8114 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
8154 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * * *
8193 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
8234 CAAA-GCCTTCGGGACTTATCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
8259 CATCATTCAA
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 118 0.72
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:8218 original size:119 final size:120
Alignment explanation
Indices: 8034--8258 Score: 296
Period size: 119 Copynumber: 1.9 Consensus size: 120
8024 GCTCCTCGTT
*
8034 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
8099 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
8154 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * * *
8216 GGATATGGTCACTTAGTACAAAGCCTTCGGGACTTATCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
8259 CATCATTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 21 0.23
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:16768 original size:16 final size:16
Alignment explanation
Indices: 16749--16784 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16739 CCAAAATACC
16749 GAAAAGCCGAAAAGCT
1 GAAAAGCCGAAAAGCT
* *
16765 GAAATGCCGAAAAGTT
1 GAAAAGCCGAAAAGCT
16781 GAAA
1 GAAA
16785 GTTTGGCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.25, T:0.11
Consensus pattern (16 bp):
GAAAAGCCGAAAAGCT
Found at i:17051 original size:29 final size:28
Alignment explanation
Indices: 16995--17118 Score: 131
Period size: 29 Copynumber: 4.4 Consensus size: 28
16985 GTGAGCATGA
* *
16995 ATATGAATGTGACTGGGCCTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
*
17023 ATATAAATGTGATTTGGGCCTAATAGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
17052 ATATACAGGTGATTTTGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
17081 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
* *
17109 AGATACATGT
1 ATATAAATGT
17119 ATGTGAAATT
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 31 0.40
29 47 0.60
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:17829 original size:5 final size:5
Alignment explanation
Indices: 17819--17844 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17809 ACTTACCCCA
17819 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
17845 TAGGTGATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:19585 original size:54 final size:54
Alignment explanation
Indices: 19449--19601 Score: 171
Period size: 54 Copynumber: 2.8 Consensus size: 54
19439 ATTATTGAAA
** * *** * * *
19449 TACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAAAAGTACCGTTT
*
19503 TACCCTCGACTTACAGAATTACCGTTTTACCCTCGATTTACAAAAGTACCGTTT
1 TACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAAAAGTACCGTTT
* * * **
19557 TACCCTTGATTTACAGAATTACTATTTTACATTCGATTTACAAAA
1 TACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAAAA
19602 TTACTAAAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (54 bp):
TACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAAAAGTACCGTTT
Found at i:19607 original size:27 final size:27
Alignment explanation
Indices: 19476--19605 Score: 161
Period size: 27 Copynumber: 4.8 Consensus size: 27
19466 ATTACCAAAG
* *
19476 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* *
19503 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
*
19530 TACCCTCGATTTACAAAAGTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* * **
19557 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACCGTTT
**
19584 TACATTCGATTTACAAAATTAC
1 TACCCTCGATTTACAAAATTAC
19606 TAAAATACCC
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCGTTT
Found at i:19656 original size:27 final size:27
Alignment explanation
Indices: 19598--19869 Score: 196
Period size: 27 Copynumber: 10.0 Consensus size: 27
19588 TTCGATTTAC
*
19598 AAAATTACTAAAATACCC-TAGTTTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
*
19624 AAAATTGCTAAAATACCCTTGGTTTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
***
19651 AAAATTAC-AGAAATACCCTCAATTTGT
1 AAAATTACTA-AAATACCCTTGGTTTGT
* * *
19678 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
* *
19705 AAAATTACCAAAATGCCAC-TGGTTTGT
1 AAAATTACTAAAATACC-CTTGGTTTGT
* * ***
19732 GAAATTA-TCGAAATACCCTCAATTTGT
1 AAAATTACT-AAAATACCCTTGGTTTGT
* * * **
19759 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTAAAATACCCTTGGTTTGT
* * *
19786 AAAGTTAC-AGAAATACCCTTGACTTTCT
1 AAAATTACTA-AAATACCCTTG-GTTTGT
* **
19814 AAAAATTA-TAGAAATACCATTGGTTTAC
1 -AAAATTACTA-AAATACCCTTGGTTTGT
*
19842 AAAATTACTGAAATACCCTTGGTTTGT
1 AAAATTACTAAAATACCCTTGGTTTGT
19869 A
1 A
19870 GATTTACCAA
Statistics
Matches: 194, Mismatches: 40, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
26 20 0.10
27 147 0.76
28 9 0.05
29 18 0.09
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTTGGTTTGT
Found at i:19728 original size:81 final size:81
Alignment explanation
Indices: 19598--19831 Score: 282
Period size: 81 Copynumber: 2.9 Consensus size: 81
19588 TTCGATTTAC
* * *
19598 AAAATTACTAAAATA-CCCTAGTTTGTAAAATTGCTAAAATACCCTTGGTTTGTAAAATTA-CAG
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTATC-G
19661 AAATACCCTCAATTTGT
65 AAATACCCTCAATTTGT
* *
19678 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATGCCAC-TGGTTTGTGAAATTATCG
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACC-CTTGGTTTGTAAAATTATCG
19742 AAATACCCTCAATTTGT
65 AAATACCCTCAATTTGT
* * *
19759 AAAATTACCAAAATACCCCT-GATT-TACAAAGTTA-CAGAAATACCCTTGACTTTCTAAAAATT
1 AAAATTACCAAAATACCCCTAGTTTGTA-AAA-TTACCA-AAATACCCTTG-GTTTGT-AAAATT
*
19821 ATAGAAATACC
61 ATCGAAATACC
19832 ATTGGTTTAC
Statistics
Matches: 134, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
79 2 0.01
80 23 0.17
81 88 0.66
82 6 0.04
83 15 0.11
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTATCGA
AATACCCTCAATTTGT
Found at i:19984 original size:27 final size:27
Alignment explanation
Indices: 19907--19984 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
19897 AAATGACTAA
* *
19907 AATACCCCTAT-TAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
19934 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
19961 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
19985 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 40 0.95
28 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:21170 original size:25 final size:25
Alignment explanation
Indices: 21141--21188 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21131 TTATAATATG
* * *
21141 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
21166 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
21189 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:21250 original size:20 final size:20
Alignment explanation
Indices: 21225--21295 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
21215 ATTTTGATAA
* *
21225 ACATGATATTTATAATATGC
1 ACATGATATGTATGATATGC
*
21245 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
21265 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
21285 ACATGAGATGT
1 ACATGATATGT
21296 TCATAAATGC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:21398 original size:25 final size:25
Alignment explanation
Indices: 21342--21484 Score: 229
Period size: 25 Copynumber: 5.8 Consensus size: 25
21332 AGGAAGTGCA
*
21342 AAAGGGCTTATACCCCAGTTAT--T
1 AAAGGGCTTATGCCCCAGTTATGAT
21365 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
21390 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
21415 GAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
21440 AAAGGGCTTATGCCCCAGTTAT-AA
1 AAAGGGCTTATGCCCCAGTTATGAT
*
21464 AAAGGGCTTTTGCCCCAGTTA
1 AAAGGGCTTATGCCCCAGTTA
21485 CTAAAAGAGG
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
23 21 0.19
24 21 0.19
25 71 0.63
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Found at i:21496 original size:25 final size:24
Alignment explanation
Indices: 21341--21510 Score: 211
Period size: 25 Copynumber: 7.0 Consensus size: 24
21331 GAGGAAGTGC
*
21341 AAAAGGGCTTATACCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATG
*
21364 TAAAGGGCTTATGCCCCAGTTATG
1 AAAAGGGCTTATGCCCCAGTTATG
21388 ATAAAGGGCTTATGCCCCAGTTATG
1 A-AAAGGGCTTATGCCCCAGTTATG
*
21413 ATGAAGGGCTTATGCCCCAGTTATG
1 A-AAAGGGCTTATGCCCCAGTTATG
*
21438 ATAAAGGGCTTATGCCCCAGTTATA
1 A-AAAGGGCTTATGCCCCAGTTATG
*
21463 AAAAGGGCTTTTGCCCCAGTTACT-
1 AAAAGGGCTTATGCCCCAGTTA-TG
*
21487 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
21511 ATGATAAAGC
Statistics
Matches: 133, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
23 21 0.16
24 30 0.23
25 82 0.62
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATG
Found at i:21739 original size:31 final size:31
Alignment explanation
Indices: 21704--21767 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
21694 CGTTTACAGT
21704 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
21735 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
21766 AA
1 AA
21768 TATGAAAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:27554 original size:43 final size:43
Alignment explanation
Indices: 27505--27674 Score: 141
Period size: 43 Copynumber: 4.0 Consensus size: 43
27495 AGGATTTCCT
*
27505 ATATGTG-TTCTCGTGTAAGACCACGTCTAGGATGTTGGCATTG
1 ATATGTGATT-TCGTGTAAGACCACGTCTAGGACGTTGGCATTG
* ** * * *
27548 ATATGTGATTACGTGTAAGACCATATCTGGGACATTGGCA-TC
1 ATATGTGATTTCGTGTAAGACCACGTCTAGGACGTTGGCATTG
* *** * *
27590 ATATTTGA-TTCGTGTAAGACTTTGTCTGGGACAG-TGGCATCG
1 ATATGTGATTTCGTGTAAGACCACGTCTAGGAC-GTTGGCATTG
** * *
27632 ATATGTGATACCATGTAAGACCACGTCTAGGACGTTGGAATTG
1 ATATGTGATTTCGTGTAAGACCACGTCTAGGACGTTGGCATTG
27675 TACGATATAT
Statistics
Matches: 97, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 25 0.26
42 16 0.16
43 54 0.56
44 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
ATATGTGATTTCGTGTAAGACCACGTCTAGGACGTTGGCATTG
Found at i:29470 original size:19 final size:20
Alignment explanation
Indices: 29446--29483 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29436 GGTACCACCA
29446 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
29465 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
29484 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:29824 original size:47 final size:49
Alignment explanation
Indices: 29708--29881 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 49
29698 AACCCACCCC
* *
29708 TAAGTGAACTCGGACTCAACTCAACGAG-TC-G--G-C-GTTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTT-ACATCCA
**
29752 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACATCCA
* * *
29800 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACATCCA
*
29845 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
29882 TCAACCATCC
Statistics
Matches: 109, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
43 6 0.06
44 29 0.27
45 4 0.04
46 30 0.28
47 29 0.27
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (49 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACATCCA
Found at i:29870 original size:93 final size:91
Alignment explanation
Indices: 29713--29881 Score: 293
Period size: 93 Copynumber: 1.8 Consensus size: 91
29703 ACCCCTAAGT
*
29713 GAACTCGGACTCAACTCAACGAGTCGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGTCGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAACG
29778 AGTTCGGATGCCTAGTTACATCTCAC
66 AGTTCGGATGCCTAGTTACATCTCAC
* *
29804 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAG-TCGG-CATTCGCATCCATAAATGAACTCGGACTCAACTCAA
29869 CGAGTTCGGATGC
64 CGAGTTCGGATGC
29882 TCAACCATCC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 23 0.32
92 4 0.05
93 46 0.63
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGTCGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:29897 original size:46 final size:46
Alignment explanation
Indices: 29707--29890 Score: 152
Period size: 44 Copynumber: 4.0 Consensus size: 46
29697 TAACCCACCC
* * * *
29707 CTAAGTGAACTCGGACTCAACTCAACGAG-TCGGCGTTCGCATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
*
29752 -TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCAT
* * * *
29799 CTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCAT
29845 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
29890 C
1 C
29891 CTAGTGACAT
Statistics
Matches: 111, Mismatches: 12, Indels: 31
0.72 0.08 0.20
Matches are distributed among these distances:
43 1 0.01
44 37 0.33
45 7 0.06
46 30 0.27
47 30 0.27
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
Done.