Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009730.1 Kokia drynarioides strain JFW-HI SEQ_124449, 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: 79355
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:635 original size:19 final size:19
Alignment explanation
Indices: 579--635 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
569 ATTTCCCTTT
579 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAA--TTATTTA
* *
600 TGATTATTAAAAATATTTA
1 TTATTATTAAAATTATTTA
*
619 TTATTATTAATATTATT
1 TTATTATTAAAATTATT
636 AAAAACATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 20 0.65
21 11 0.35
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
TTATTATTAAAATTATTTA
Found at i:638 original size:28 final size:29
Alignment explanation
Indices: 593--652 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
583 TATTAAAACG
* *
593 TTATTTATGATTATTAAAAATATTTATTA
1 TTATTAATGATTATTAAAAACATTTATTA
622 TTATTAAT-ATTATTAAAAACATTTATTA
1 TTATTAATGATTATTAAAAACATTTATTA
650 TTA
1 TTA
653 ATAGTCATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
TTATTAATGATTATTAAAAACATTTATTA
Found at i:1288 original size:15 final size:15
Alignment explanation
Indices: 1268--1316 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
1258 ATTTTGAGCC
*
1268 ATTGGGTCGTTTGTA
1 ATTGGGCCGTTTGTA
*
1283 ATTGGGCCATTTGTA
1 ATTGGGCCGTTTGTA
1298 ATTGGGCCGTTTGTA
1 ATTGGGCCGTTTGTA
1313 ATTG
1 ATTG
1317 AGTCATTCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.16, C:0.10, G:0.31, T:0.43
Consensus pattern (15 bp):
ATTGGGCCGTTTGTA
Found at i:1386 original size:17 final size:16
Alignment explanation
Indices: 1364--1442 Score: 86
Period size: 17 Copynumber: 4.8 Consensus size: 16
1354 TTGGACTTTC
1364 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
1381 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
*
1398 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTTAAA
* *
1415 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
1431 TAAATTCAATTT
1 TAAATTTAATTT
1443 CCAATAGGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
16 16 0.30
17 31 0.58
18 6 0.11
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:1402 original size:34 final size:33
Alignment explanation
Indices: 1364--1442 Score: 113
Period size: 34 Copynumber: 2.4 Consensus size: 33
1354 TTGGACTTTC
* *
1364 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTT-AAA
*
1398 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTAAA
*
1431 TAAATTCAATTT
1 TAAATTTAATTT
1443 CCAATAGGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 13 0.32
34 27 0.68
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTTAAA
Found at i:1415 original size:7 final size:6
Alignment explanation
Indices: 1364--1431 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
1354 TTGGACTTTC
*
1364 TAAATT TAATTT TATAA-- TAAATT TAAATT TCAAA-- TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT
* *
1410 TAAA-A TAAACT TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAAT
1432 AAATTCAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 5 0.10
5 7 0.14
6 34 0.68
7 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:2543 original size:399 final size:394
Alignment explanation
Indices: 1882--2653 Score: 984
Period size: 399 Copynumber: 1.9 Consensus size: 394
1872 TTTGTTTTGG
* * *
1882 TCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTCAATACGCTTCTCTGTATCTCA
1 TCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTATTTCAATACACTTCTCTGTATCTCA
** * *
1947 TCAGGAAGATGAATTTGGTCCACTTCTTAGTATTTCATCAAGAAGCTAATCATTTTATTGCTTCA
66 TCAGGAAGACAAATTTGGTCCACTTCTTAGTATCTCATCAAGAAGCTAATCACTTTATTGCTTCA
* * *
2012 ACCTGCCTCTCAATCAAGAAGCTGGGGTTCGAAGATTTCGCTCATTTTGAGCCTCGTTTGAGACT
131 ACCTGCCTCTCAATCAAAAAGCTGGGGTTCGAAAATTTCGC-CACTTTGAGCCTCGTTTGAGACT
* * * *
2077 TCTTCTCAGTGCCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCACTCCTCTGTATC
195 TCTTCTCAGTGCCTCACCAGGAAGATGACCACAT--CTGTTTGTTTCAACTCACTCCTCTATATC
* *
2142 TCATCGAGAAGACGAATTTGGTT-CACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCT
258 TCATCAAAAAGACGAATTTGGTTACAC-T-TCAGTATCTCATCAGGAAGCTAACC-TTTATCGCT
* *
2206 TCGACCTGCTTCTCAATGTCTCATC-AGGAAGCTGGGGTTCGAAGATTTTGTGCACTTTGAGCCT
320 TCGACCTCCTTCTCAATGTCTCATCAAAG-AGCTGGGGTTCGAAGATTTTGTGCACTTTGAGCCT
2270 TGTTTGGGTCT
384 TGTTTGGGTCT
* *
2281 TCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTATTTCAACT-CACTTCTCTGTATCTC
1 TCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTATTTCAA-TACACTTCTCTGTATCTC
* ** * *
2345 ATCAGGAAGGCAAATTTGGTTGAC-TCTTTAGTATCTCCTCAGGAAGCTAA-C-CTTTATTGCTT
65 ATCAGGAAGACAAATTTGGTCCACTTC-TTAGTATCTCATCAAGAAGCTAATCACTTTATTGCTT
* * *
2407 CGACCTGCTTCTCGATGACTCATCAAAGAGCTGGGGTTCGAAAATTTTG-CACTTTGAGCCTCGT
129 CAACCTGCCTCTC-A--A-TCA--AAA-AGCTGGGGTTCGAAAATTTCGCCACTTTGAGCCTCGT
* * * * * *
2471 TTGGGTCTTCTTCTCAGTGTCTCACCAGGAAGATGACCGCAT-TGTTTGTTTCAACTCGCTTCTC
187 TTGAGACTTCTTCTCAGTGCCTCACCAGGAAGATGACCACATCTGTTTGTTTCAACTCACTCCTC
*
2535 TATATCTCATCAAAAAGGCGAATTTGGTTGACACTTCAGTATCTCATCAGGAAGCTAACCTTTAT
252 TATATCTCATCAAAAAGACGAATTTGGTT-ACACTTCAGTATCTCATCAGGAAGCTAACCTTTAT
* * * *
2600 TGCTTCGACCTCCTTCTCGATGTCTCCTCAAAGAGCTGGGGTTCGAAGGTTTTG
316 CGCTTCGACCTCCTTCTCAATGTCTCATCAAAGAGCTGGGGTTCGAAGATTTTG
2654 CTTGCTTTGT
Statistics
Matches: 322, Mismatches: 39, Indels: 25
0.83 0.10 0.06
Matches are distributed among these distances:
397 21 0.07
398 54 0.17
399 167 0.52
400 3 0.01
401 6 0.02
402 50 0.16
403 2 0.01
404 19 0.06
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (394 bp):
TCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTATTTCAATACACTTCTCTGTATCTCA
TCAGGAAGACAAATTTGGTCCACTTCTTAGTATCTCATCAAGAAGCTAATCACTTTATTGCTTCA
ACCTGCCTCTCAATCAAAAAGCTGGGGTTCGAAAATTTCGCCACTTTGAGCCTCGTTTGAGACTT
CTTCTCAGTGCCTCACCAGGAAGATGACCACATCTGTTTGTTTCAACTCACTCCTCTATATCTCA
TCAAAAAGACGAATTTGGTTACACTTCAGTATCTCATCAGGAAGCTAACCTTTATCGCTTCGACC
TCCTTCTCAATGTCTCATCAAAGAGCTGGGGTTCGAAGATTTTGTGCACTTTGAGCCTTGTTTGG
GTCT
Found at i:2618 original size:198 final size:197
Alignment explanation
Indices: 1882--2646 Score: 852
Period size: 198 Copynumber: 3.8 Consensus size: 197
1872 TTTGTTTTGG
* * *
1882 TCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTCAA-TACGCTTCTCTGTATCTC
1 TCTTCTCAGTATCTCATCAGGAAGATGACCGCATTGTTTGTTTCAACT-CACTTCTCTGTATCTC
* * * * * *
1946 ATCAGGAAGATGAATTTGG-TCCACTTCTTAGTATTTCATCAAGAAGCTAATCATTTTATTGCTT
65 ATCAAGAAGACGAATTTGGTTACACTTC--AGTATCTCATCAGGAAGCTAA-C-CTTTATTGCTT
* * * * *
2010 CAACCTGCC-TCTC-A--A-TCA--AGA-AGCTGGGGTTCGAAGATTTCGCTCATTTTGAGCCTC
126 CGACCT-CCTTCTCGATGACTCATCAAAGAGCTGGGGTTCGAAAATTTTG--CACTTTGAGCCTC
* *
2067 GTTTGAGACT
188 GTTTGGGTCT
** * * * *
2077 TCTTCTCAGTGCCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCACTCCTCTGTATC
1 TCTTCTCAGTATCTCATCAGGAAGATGACCGCAT---TGTTTGTTTCAACTCACTTCTCTGTATC
* *
2142 TCATCGAGAAGACGAATTTGGTT-CACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCT
63 TCATCAAGAAGACGAATTTGGTTACAC-T-TCAGTATCTCATCAGGAAGCTAACC-TTTATTGCT
* * * * *
2206 TCGACCTGCTTCTCAATGTCTCATC-AGGAAGCTGGGGTTCGAAGATTTTGTGCACTTTGAGCCT
125 TCGACCTCCTTCTCGATGACTCATCAAAG-AGCTGGGGTTCGAA-AATTT-TGCACTTTGAGCCT
*
2270 TGTTTGGGTCT
187 CGTTTGGGTCT
* *
2281 TCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTATTTCAACTCACTTCTCTGTATCTCA
1 TCTTCTCAGTATCTCATCAGGAAGATGACCGCATTGTTTGTTTCAACTCACTTCTCTGTATCTCA
* * * * * *
2346 TCAGGAAGGCAAATTTGGTTGACTCTTTAGTATCTCCTCAGGAAGCTAACCTTTATTGCTTCGAC
66 TCAAGAAGACGAATTTGGTT-ACACTTCAGTATCTCATCAGGAAGCTAACCTTTATTGCTTCGAC
*
2411 CTGCTTCTCGATGACTCATCAAAGAGCTGGGGTTCGAAAATTTTGCACTTTGAGCCTCGTTTGGG
130 CTCCTTCTCGATGACTCATCAAAGAGCTGGGGTTCGAAAATTTTGCACTTTGAGCCTCGTTTGGG
2476 TCT
195 TCT
* * * *
2479 TCTTCTCAGTGTCTCACCAGGAAGATGACCGCATTGTTTGTTTCAACTCGCTTCTCTATATCTCA
1 TCTTCTCAGTATCTCATCAGGAAGATGACCGCATTGTTTGTTTCAACTCACTTCTCTGTATCTCA
* *
2544 TCAAAAAGGCGAATTTGGTTGACACTTCAGTATCTCATCAGGAAGCTAACCTTTATTGCTTCGAC
66 TCAAGAAGACGAATTTGGTT-ACACTTCAGTATCTCATCAGGAAGCTAACCTTTATTGCTTCGAC
* *
2609 CTCCTTCTCGATGTCTCCTCAAAGAGCTGGGGTTCGAA
130 CTCCTTCTCGATGACTCATCAAAGAGCTGGGGTTCGAA
2647 GGTTTTGCTT
Statistics
Matches: 485, Mismatches: 63, Indels: 41
0.82 0.11 0.07
Matches are distributed among these distances:
195 29 0.06
196 1 0.00
197 19 0.04
198 241 0.50
199 7 0.01
200 47 0.10
201 72 0.15
202 1 0.00
203 2 0.00
204 62 0.13
205 3 0.01
206 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (197 bp):
TCTTCTCAGTATCTCATCAGGAAGATGACCGCATTGTTTGTTTCAACTCACTTCTCTGTATCTCA
TCAAGAAGACGAATTTGGTTACACTTCAGTATCTCATCAGGAAGCTAACCTTTATTGCTTCGACC
TCCTTCTCGATGACTCATCAAAGAGCTGGGGTTCGAAAATTTTGCACTTTGAGCCTCGTTTGGGT
CT
Found at i:14491 original size:30 final size:30
Alignment explanation
Indices: 14456--14540 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 30
14446 AAAAGGGTAA
14456 TTTTGAGAGTTTCGAGGTCGAAAATGG-AGT
1 TTTTGA-AGTTTCGAGGTCGAAAATGGTAGT
**
14486 TTTTGAACATTCGAGG--GTAAAATGGTAGT
1 TTTTGAAGTTTCGAGGTCG-AAAATGGTAGT
*
14515 TTTTGAAAGTTTC-AGTGTCAAAAATG
1 TTTTG-AAGTTTCGAG-GTCGAAAATG
14541 AAATTTTGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
27 1 0.02
28 7 0.16
29 18 0.41
30 12 0.27
31 6 0.14
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (30 bp):
TTTTGAAGTTTCGAGGTCGAAAATGGTAGT
Found at i:14495 original size:58 final size:59
Alignment explanation
Indices: 14428--14540 Score: 133
Period size: 58 Copynumber: 1.9 Consensus size: 59
14418 AAAAAGGAAA
* *
14428 TTTTAAACATTA-AGGGGTAAAAGGGTA-ATTTTGAGAGTTTCGAG-GTCGAAAATGGAGT
1 TTTTAAACATTAGA-GGGTAAAAGGGTAGATTTTGAAAGTTTC-AGTGTCAAAAATGGAGT
* * * *
14486 TTTTGAACATTCGAGGGTAAAATGGTAGTTTTTGAAAGTTTCAGTGTCAAAAATG
1 TTTTAAACATTAGAGGGTAAAAGGGTAGATTTTGAAAGTTTCAGTGTCAAAAATG
14541 AAATTTTGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
58 24 0.52
59 22 0.48
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.34
Consensus pattern (59 bp):
TTTTAAACATTAGAGGGTAAAAGGGTAGATTTTGAAAGTTTCAGTGTCAAAAATGGAGT
Found at i:14539 original size:59 final size:57
Alignment explanation
Indices: 14442--14869 Score: 338
Period size: 59 Copynumber: 7.3 Consensus size: 57
14432 AAACATTAAG
* * * *
14442 GGGTAAAAGGGTAA-TTTTGAGAGTTTCGAGGTCGAAAATGGAGTTTTTGAACATTCGA
1 GGGTAAAATGG-AATTTTTGAAAGTTTCGAGGTCAAAAATGGAGTTTTTGAA-GTTCGA
* * * * *
14500 GGGTAAAATGGTAGTTTTTGAAAGTTTC-AGTGTCAAAAATGAAATTTTGGAAGTTCAA
1 GGGTAAAATGG-AATTTTTGAAAGTTTCGAG-GTCAAAAATGGAGTTTTTGAAGTTCGA
*
14558 GGGTAAAAATGGAATTTTTGGAAA-TTTC-ATGGTCAAAAATGG-GATTTTTGGAAGTTCGG
1 GGGT-AAAATGGAATTTTT-GAAAGTTTCGA-GGTCAAAAATGGAG-TTTTT-GAAGTTCGA
* * *
14617 GGGTAAAATTGGAATTTTTGGAAGTTTCGAGGTCAAAAATATGA-TTTTTGGAAGTTCGG
1 GGGTAAAA-TGGAATTTTTGAAAGTTTCGAGGTCAAAAAT-GGAGTTTTT-GAAGTTCGA
* *
14676 GGGTAAAAATGGAA-ATTTGGAAGTTTCGAGGTC-AAAATGG-GATTTTTGGAAGTTCGA
1 GGGT-AAAATGGAATTTTTGAAAGTTTCGAGGTCAAAAATGGAG-TTTTT-GAAGTTCGA
* * * * *
14733 GGGGAAAAATGGAATCTTTGTAAGCTTCGGGGTCAAAAATTGGA-TTTTTGGAAGTTCGA
1 -GGGTAAAATGGAATTTTTGAAAGTTTCGAGGTCAAAAA-TGGAGTTTTT-GAAGTTCGA
** * * * * *
14792 GAATAAAAATGAAATTTTTGGAAGCTTCGAGGTCAAAAAT-AAGATTTTTGGAAGTTCGG
1 GGGT-AAAATGGAATTTTTGAAAGTTTCGAGGTCAAAAATGGAG-TTTTT-GAAGTTCGA
*
14851 GGGAAAAATGGAATTTTTG
1 GGGTAAAATGGAATTTTTG
14870 GACAGTTTAA
Statistics
Matches: 309, Mismatches: 38, Indels: 46
0.79 0.10 0.12
Matches are distributed among these distances:
56 1 0.00
57 29 0.09
58 106 0.34
59 164 0.53
60 9 0.03
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (57 bp):
GGGTAAAATGGAATTTTTGAAAGTTTCGAGGTCAAAAATGGAGTTTTTGAAGTTCGA
Found at i:14702 original size:175 final size:175
Alignment explanation
Indices: 14516--14877 Score: 487
Period size: 175 Copynumber: 2.1 Consensus size: 175
14506 AATGGTAGTT
* * *
14516 TTTGAAAGTTTC-AGTGTCAAAAAT-GAAATTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGG
1 TTTGGAAGTTTCGAG-GTC-AAAATGGAAATTTTGGAAGTTCAAGGGGAAAAATGGAATCTTTGG
* * * ** * * *
14579 AAATTTCATGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATTGGAATTTTTGGAAGTTT
64 AAACTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAAATGAAATTTTTGGAAGCTT
*
14644 CGAGGTCAAAAATATGATTTTTGGAAGTTCGGGGGTAAAAATGGAA-A
129 CGAGGTCAAAAATAAGATTTTTGGAAGTTCGGGGG-AAAAATGGAATA
* * * *
14691 TTTGGAAGTTTCGAGGTCAAAATGGGATTTTTGGAAGTTCGAGGGGAAAAATGGAATCTTTGTAA
1 TTTGGAAGTTTCGAGGTCAAAATGGAAATTTTGGAAGTTCAAGGGGAAAAATGGAATCTTTGGAA
* * *
14756 GCTTCGGGGTCAAAAATTGGATTTTTGGAAGTTCGAGAATAAAAATGAAATTTTTGGAAGCTTCG
66 ACTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAAATGAAATTTTTGGAAGCTTCG
*
14821 AGGTCAAAAATAAGATTTTTGGAAGTTCGGGGGAAAAATGGAATT
131 AGGTCAAAAATAAGATTTTTGGAAGTTCGGGGGAAAAATGGAATA
14866 TTTGGACAGTTT
1 TTTGGA-AGTTT
14878 AAGGACCCTC
Statistics
Matches: 163, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
174 15 0.09
175 141 0.87
176 7 0.04
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.33
Consensus pattern (175 bp):
TTTGGAAGTTTCGAGGTCAAAATGGAAATTTTGGAAGTTCAAGGGGAAAAATGGAATCTTTGGAA
ACTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGAGAATAAAAATGAAATTTTTGGAAGCTTCG
AGGTCAAAAATAAGATTTTTGGAAGTTCGGGGGAAAAATGGAATA
Found at i:14876 original size:29 final size:28
Alignment explanation
Indices: 14533--14876 Score: 250
Period size: 29 Copynumber: 11.8 Consensus size: 28
14523 GTTTCAGTGT
* *
14533 CAAAAAT-GAAATTTTGGAAGTTCAAGGG
1 CAAAAATGGAATTTTTGGAAGTTC-GGGG
* * * *
14561 TAAAAATGGAATTTTTGGAAATTTCATGGT
1 CAAAAATGGAATTTTTGG-AAGTTC-GGGG
*
14591 CAAAAATGGGATTTTTGGAAGTTCGGGGG
1 CAAAAATGGAATTTTTGGAAGTTC-GGGG
* * *
14620 TAAAATTGGAATTTTTGGAAGTTTCGAGGT
1 CAAAAATGGAATTTTTGGAAG-TTCG-GGG
*
14650 CAAAAATATG-ATTTTTGGAAGTTCGGGGG
1 CAAAAAT-GGAATTTTTGGAAGTTC-GGGG
* * *
14679 TAAAAATGGAA-ATTTGGAAGTTTCGAGGT
1 CAAAAATGGAATTTTTGGAAG-TTCG-GGG
*
14708 C-AAAATGGGATTTTTGGAAGTTCGAGGG
1 CAAAAATGGAATTTTTGGAAGTTCG-GGG
* * *
14736 GAAAAATGGAATCTTTGTAAGCTTCGGGG
1 CAAAAATGGAATTTTTGGAAG-TTCGGGG
**
14765 TCAAAAATTGG-ATTTTTGGAAGTTCGAGAA
1 -CAAAAA-TGGAATTTTTGGAAGTTCG-GGG
* * *
14795 TAAAAATGAAATTTTTGGAAGCTTCGAGGT
1 CAAAAATGGAATTTTTGGAAG-TTCG-GGG
*
14825 CAAAAAT-AAGATTTTTGGAAGTTCGGGG
1 CAAAAATGGA-ATTTTTGGAAGTTCGGGG
*
14853 GAAAAATGGAATTTTTGGACAGTT
1 CAAAAATGGAATTTTTGGA-AGTT
14877 TAAGGACCCT
Statistics
Matches: 252, Mismatches: 44, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
28 50 0.20
29 110 0.44
30 88 0.35
31 4 0.02
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (28 bp):
CAAAAATGGAATTTTTGGAAGTTCGGGG
Found at i:15614 original size:19 final size:20
Alignment explanation
Indices: 15575--15624 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
15565 ATTTCCCTAT
*
15575 TTATTATTAAAACGCTATTTA
1 TTATTATTAAAAC-ATATTTA
15596 TTATTATTAAAA-ATATTTA
1 TTATTATTAAAACATATTTA
15615 TTATTATTAA
1 TTATTATTAA
15625 TATTATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 16 0.57
21 12 0.43
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
TTATTATTAAAACATATTTA
Found at i:15617 original size:16 final size:16
Alignment explanation
Indices: 15596--15649 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
15586 ACGCTATTTA
15596 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
15612 TTATTATT---ATTA-
1 TTATTATTAAAAATAT
* *
15624 ATATTATTAAAAACAT
1 TTATTATTAAAAATAT
15640 TTATTATTAA
1 TTATTATTAA
15650 TAGTCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 2 0.07
16 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:15663 original size:28 final size:28
Alignment explanation
Indices: 15597--15665 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
15587 CGCTATTTAT
* * *
15597 TATTATTAAAAATATTTATTATTATTAA
1 TATTATAAAAAACATTTATTATTAATAA
* *
15625 TATTATTAAAAACATTTATTATTAATAG
1 TATTATAAAAAACATTTATTATTAATAA
15653 TCATTA-AAAAAAC
1 T-ATTATAAAAAAC
15666 GGTTCGATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 32 0.89
29 4 0.11
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (28 bp):
TATTATAAAAAACATTTATTATTAATAA
Found at i:15706 original size:3 final size:3
Alignment explanation
Indices: 15698--15742 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
15688 TTAACGTTAC
15698 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15743 ACTTATGAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16315 original size:15 final size:15
Alignment explanation
Indices: 16297--16367 Score: 88
Period size: 15 Copynumber: 4.7 Consensus size: 15
16287 TATTGGATCG
16297 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
16312 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
* *
16327 TTTGTAATTGGTCCG
1 TTTGTAATTGGGCCA
*
16342 TTTGTAGTTGGGCCA
1 TTTGTAATTGGGCCA
* *
16357 CTTGTATTTGG
1 TTTGTAATTGG
16368 ACTTTGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.14, C:0.13, G:0.28, T:0.45
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:16331 original size:30 final size:30
Alignment explanation
Indices: 16297--16367 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
16287 TATTGGATCG
*
16297 TTTGTAATTGGGCCATTTGTATTTGGGCCA
1 TTTGTAATTGGGCCATTTGTAGTTGGGCCA
* *
16327 TTTGTAATTGGTCCGTTTGTAGTTGGGCCA
1 TTTGTAATTGGGCCATTTGTAGTTGGGCCA
* *
16357 CTTGTATTTGG
1 TTTGTAATTGG
16368 ACTTTGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.14, C:0.13, G:0.28, T:0.45
Consensus pattern (30 bp):
TTTGTAATTGGGCCATTTGTAGTTGGGCCA
Found at i:16421 original size:17 final size:17
Alignment explanation
Indices: 16399--16471 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
16389 TTGGACTTTC
*
16399 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
16416 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
16433 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
16450 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
16466 TAAATT
1 TAAATT
16472 CAATATCCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.15
17 38 0.73
18 6 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:23003 original size:14 final size:14
Alignment explanation
Indices: 22984--23010 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22974 GAAAGGTTAT
22984 AATTATTCACATAC
1 AATTATTCACATAC
22998 AATTATTCACATA
1 AATTATTCACATA
23011 TATGTAGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTATTCACATAC
Found at i:24336 original size:21 final size:21
Alignment explanation
Indices: 24288--24336 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
24278 TCTGATTGAC
* *
24288 TTGGTTCAATTAGGTTTGGGT
1 TTGGTTTAATTAGGATTGGGT
24309 TTGGTTTAATT-GGATTGGGTT
1 TTGGTTTAATTAGGATTGGG-T
24330 TTGGTTT
1 TTGGTTT
24337 GGGGTTTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.12, C:0.02, G:0.33, T:0.53
Consensus pattern (21 bp):
TTGGTTTAATTAGGATTGGGT
Found at i:25773 original size:11 final size:10
Alignment explanation
Indices: 25753--25784 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
25743 ATTTCGATGG
25753 ATTATCATTT
1 ATTATCATTT
25763 ATTATTCATTT
1 ATTA-TCATTT
25774 ATTATCATTT
1 ATTATCATTT
25784 A
1 A
25785 GATGGACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTATCATTT
Found at i:28637 original size:33 final size:32
Alignment explanation
Indices: 28600--28661 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
28590 CCCAAATTTG
28600 TAACCCAAACCATG-AACCTAATACCCATGAATA
1 TAACCCAAACCATGAAACC-AA-ACCCATGAATA
* *
28633 TAACCTAAATCATGAAACCAAACCCATGA
1 TAACCCAAACCATGAAACCAAACCCATGA
28662 CACGATTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 8 0.31
33 14 0.54
34 4 0.15
ACGTcount: A:0.47, C:0.29, G:0.06, T:0.18
Consensus pattern (32 bp):
TAACCCAAACCATGAAACCAAACCCATGAATA
Found at i:29239 original size:29 final size:29
Alignment explanation
Indices: 29207--29263 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
29197 TTCCACACCT
*
29207 TGTGTGATATTATTCTATGTTGTTTTATA
1 TGTGTGATATTATTCTATGTTGTGTTATA
* *
29236 TGTGTGATTTTATTCTCTGTTGTGTTAT
1 TGTGTGATATTATTCTATGTTGTGTTAT
29264 CGCACGTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.05, G:0.19, T:0.60
Consensus pattern (29 bp):
TGTGTGATATTATTCTATGTTGTGTTATA
Found at i:31036 original size:7 final size:7
Alignment explanation
Indices: 30988--31095 Score: 51
Period size: 7 Copynumber: 15.1 Consensus size: 7
30978 AATTGTAGTC
*
30988 TTTAGGG
1 TTTAAGG
* *
30995 TTTATGA
1 TTTAAGG
31002 TTTAAGG
1 TTTAAGG
*
31009 -TTAGGG
1 TTTAAGG
31015 TTT-AGG
1 TTTAAGG
**
31021 TTCGA-G
1 TTTAAGG
31027 TTTAAGG
1 TTTAAGG
31034 TTTTAAGG
1 -TTTAAGG
**
31042 TTTATGATT
1 TTTA--AGG
31051 TTTAAGG
1 TTTAAGG
*
31058 TTTTAGG
1 TTTAAGG
*
31065 TTTTAGG
1 TTTAAGG
*
31072 TTTTAAGT
1 -TTTAAGG
31080 TTTAAGGG
1 TTTAA-GG
31088 TTTAAGG
1 TTTAAGG
31095 T
1 T
31096 GTAGAGTGGG
Statistics
Matches: 76, Mismatches: 17, Indels: 16
0.70 0.16 0.15
Matches are distributed among these distances:
6 13 0.17
7 40 0.53
8 18 0.24
9 5 0.07
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (7 bp):
TTTAAGG
Found at i:31040 original size:8 final size:8
Alignment explanation
Indices: 31027--31095 Score: 74
Period size: 7 Copynumber: 9.0 Consensus size: 8
31017 TAGGTTCGAG
31027 TTTAAGGT
1 TTTAAGGT
31035 TTTAAGG-
1 TTTAAGGT
* *
31042 TTTATGATT
1 TTTAAG-GT
31051 TTTAAGGT
1 TTTAAGGT
31059 TTT-AGGT
1 TTTAAGGT
31066 TTT-AGGT
1 TTTAAGGT
31073 TTTAA-GT
1 TTTAAGGT
*
31080 TTTAAGGG
1 TTTAAGGT
31088 TTTAAGGT
1 TTTAAGGT
31096 GTAGAGTGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
7 26 0.51
8 20 0.39
9 5 0.10
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (8 bp):
TTTAAGGT
Found at i:31093 original size:15 final size:15
Alignment explanation
Indices: 31026--31093 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
31016 TTAGGTTCGA
31026 GTTTAAGGTTTTAA-G
1 GTTTAA-GTTTTAAGG
*
31041 GTTTATGATTTTTAAGG
1 GTTTA--AGTTTTAAGG
* *
31058 TTTTAGGTTTT-AGG
1 GTTTAAGTTTTAAGG
*
31072 TTTTAAGTTTTAAGG
1 GTTTAAGTTTTAAGG
31087 GTTTAAG
1 GTTTAAG
31094 GTGTAGAGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 13 0.30
15 18 0.42
16 6 0.14
17 6 0.14
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (15 bp):
GTTTAAGTTTTAAGG
Found at i:31119 original size:25 final size:26
Alignment explanation
Indices: 31078--31127 Score: 84
Period size: 25 Copynumber: 1.9 Consensus size: 26
31068 TAGGTTTTAA
31078 GTTTTAAGGGTTTAAGGTGTAGAGTGG
1 GTTTTAA-GGTTTAAGGTGTAGAGTGG
31105 GTTTTAA-GTTTAAGGTGTAGAGT
1 GTTTTAAGGTTTAAGGTGTAGAGT
31128 TCACATGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 16 0.70
27 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (26 bp):
GTTTTAAGGTTTAAGGTGTAGAGTGG
Found at i:43050 original size:30 final size:31
Alignment explanation
Indices: 42977--43050 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
42967 GGTTCAATAT
*
42977 GATACTTAAACTTGACACTTTTTGCTAATTT
1 GATACTTAAACTTGACACTTTTTGCTAATTA
* *
43008 GATACCTAAACTTGACACTTTTT-TTAACTTA
1 GATACTTAAACTTGACACTTTTTGCTAA-TTA
43039 G-TACTTAAACTT
1 GATACTTAAACTT
43051 TTTTAGGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 13 0.34
31 25 0.66
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (31 bp):
GATACTTAAACTTGACACTTTTTGCTAATTA
Found at i:43682 original size:27 final size:26
Alignment explanation
Indices: 43652--43724 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 26
43642 GACATTCTTA
43652 ATAAAAACATTTTTAAAAAATTATA-
1 ATAAAAACATTTTTAAAAAATTATAT
*
43677 AT-ATAACATGTATTATAAAAAATTATAT
1 ATAAAAACAT-T-TT-TAAAAAATTATAT
43705 ATAATTAAA-ATTTTTAAAAA
1 ATAA--AAACATTTTTAAAAA
43725 TGGAAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
24 6 0.15
25 3 0.08
26 2 0.05
27 18 0.46
28 4 0.10
29 2 0.05
30 2 0.05
31 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (26 bp):
ATAAAAACATTTTTAAAAAATTATAT
Found at i:43913 original size:33 final size:33
Alignment explanation
Indices: 43861--43923 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
43851 TCTCATTATG
* * *
43861 TACAAAGACAAATGTAGAAATTTTTTATCATTA
1 TACAAAGACAAATGCAGAAAATTTATATCATTA
43894 TACAAAGACAAACT-CAGAAAATTTATATCA
1 TACAAAGACAAA-TGCAGAAAATTTATATCA
43924 ATATGCAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (33 bp):
TACAAAGACAAATGCAGAAAATTTATATCATTA
Found at i:44368 original size:17 final size:17
Alignment explanation
Indices: 44339--44378 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
44329 TACTAAATAA
44339 ATTTTTTTATT-AAAAT
1 ATTTTTTTATTAAAAAT
*
44355 ATTTTATTTTTTAAAAAT
1 ATTTT-TTTATTAAAAAT
44373 ATTTTT
1 ATTTTT
44379 GATTTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 10 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTTTATTAAAAAT
Found at i:44806 original size:10 final size:9
Alignment explanation
Indices: 44776--44894 Score: 55
Period size: 10 Copynumber: 12.8 Consensus size: 9
44766 TGACACGTGG
44776 AAAAAATGAT
1 AAAAAAT-AT
44786 AAAAAA-AT
1 AAAAAATAT
44794 AAAAAATATT
1 AAAAAATA-T
**
44804 AAAATTTAAT
1 AAAAAAT-AT
*
44814 AAAAACTAT
1 AAAAAATAT
*
44823 AAAAATATTT
1 AAAAA-ATAT
***
44833 AAATTTTAT
1 AAAAAATAT
**
44842 TTAAAAT-T
1 AAAAAATAT
44850 ATAAAAATCAT
1 A-AAAAAT-AT
44861 AAAAAATAT
1 AAAAAATAT
*
44870 AAAATATAT
1 AAAAAATAT
*
44879 -AGAAATAT
1 AAAAAATAT
44887 AGAAAAAT
1 A-AAAAAT
44895 TTATAAAATT
Statistics
Matches: 79, Mismatches: 21, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
8 15 0.19
9 27 0.34
10 34 0.43
11 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAAATAT
Found at i:44834 original size:29 final size:28
Alignment explanation
Indices: 44787--44857 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
44777 AAAAATGATA
44787 AAAAAATA-AAAAATATTAAAATTTAAT
1 AAAAAATATAAAAATATTAAAATTTAAT
* * *
44814 AAAAACTATAAAAATATTTAAATTTTATT
1 AAAAAATATAAAAATA-TTAAAATTTAAT
* *
44843 TAAAATTATAAAAAT
1 AAAAAATATAAAAAT
44858 CATAAAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 7 0.19
28 7 0.19
29 23 0.62
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAAAATATAAAAATATTAAAATTTAAT
Found at i:44873 original size:17 final size:17
Alignment explanation
Indices: 44843--44894 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
44833 AAATTTTATT
44843 TAAAAT-TATAAAAATCA
1 TAAAATATATAAAAAT-A
*
44860 TAAAAAATATAAAATATA
1 TAAAATATATAAAA-ATA
*
44878 TAGAAATATAGAAAAAT
1 TA-AAATATATAAAAAT
44895 TTATAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 5 0.17
18 12 0.41
19 12 0.41
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (17 bp):
TAAAATATATAAAAATA
Found at i:45013 original size:18 final size:18
Alignment explanation
Indices: 44990--45032 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
44980 CTAAAAAAGC
44990 ATTTTATAAATTTTTTAT
1 ATTTTATAAATTTTTTAT
**
45008 ATTTTATTTATTTTTTAT
1 ATTTTATAAATTTTTTAT
45026 ATTTTAT
1 ATTTTAT
45033 CATTTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTATAAATTTTTTAT
Found at i:45039 original size:18 final size:17
Alignment explanation
Indices: 44990--45039 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
44980 CTAAAAAAGC
*
44990 ATTTTATAAATTTTTTAT
1 ATTTTAT-ATTTTTTTAT
*
45008 ATTTTATTTATTTTTTAT
1 ATTTTATAT-TTTTTTAT
45026 ATTTTATCATTTTT
1 ATTTTAT-ATTTTT
45040 CGCGCACATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATATTTTTTTAT
Found at i:45259 original size:10 final size:10
Alignment explanation
Indices: 45244--45268 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
45234 AAATTTAATA
45244 ATTATTATTT
1 ATTATTATTT
45254 ATTATTATTT
1 ATTATTATTT
45264 ATTAT
1 ATTAT
45269 AGTTTTTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTATTATTT
Found at i:45544 original size:91 final size:89
Alignment explanation
Indices: 45448--45645 Score: 213
Period size: 92 Copynumber: 2.2 Consensus size: 89
45438 TTTTTTTTTT
* * *
45448 AGTTTGAGGATCTTTTTAATACA-TTTGA-AAGTTTAAGCACCCAATTGAGTGCAAAAAAAAAGG
1 AGTTTGAGG-TCTTTTTAATACATTTTGACAA-TTCAAGCACCCAATTGAATGCAAAAAAAAA-A
45511 CAAGGGATTAATTGCTTTCTTTTTTAAA
63 CAAGGGATTAATTGCTTT-TTTTTTAAA
* * * * *
45539 AGTTTGAAGGTCTTTTTGATGCATTTTGACAATTCAAGTACCTAATTGAATGCAAAAAAAAAATA
1 AGTTTG-AGGTCTTTTTAATACATTTTGACAATTCAAGCACCCAATTGAATGCAAAAAAAAAACA
* * **
45604 GGGGCTTAATTGCTTTTTTTTTTTA
65 AGGGATTAATTGCTTTTTTTTTAAA
45629 AGTTTGAGGGT-TTTTTA
1 AGTTTGA-GGTCTTTTTA
45646 CACTCTTAAG
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
89 6 0.07
90 16 0.18
91 32 0.36
92 34 0.38
93 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (89 bp):
AGTTTGAGGTCTTTTTAATACATTTTGACAATTCAAGCACCCAATTGAATGCAAAAAAAAAACAA
GGGATTAATTGCTTTTTTTTTAAA
Found at i:50667 original size:21 final size:21
Alignment explanation
Indices: 50620--50682 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
50610 TACTCACGTG
*
50620 ATTTTTATTAAAAA-AAAAGTT
1 ATTTTTAATAAAAATAAAA-TT
* *
50641 GGTTTTTAATAAAAATCAAATT
1 -ATTTTTAATAAAAATAAAATT
* *
50663 ATTTTTTATTAAAATAAAAT
1 ATTTTTAATAAAAATAAAAT
50683 ATAAAACTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 16 0.48
22 14 0.42
23 3 0.09
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTTTAATAAAAATAAAATT
Found at i:52502 original size:16 final size:16
Alignment explanation
Indices: 52477--52523 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
52467 AGATCATCTG
52477 AATTTGAAATGATTCA
1 AATTTGAAATGATTCA
*
52493 AATTTAAAATGATTCA
1 AATTTGAAATGATTCA
* *
52509 TACTTGAAATGATTC
1 AATTTGAAATGATTC
52524 GAACCTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (16 bp):
AATTTGAAATGATTCA
Found at i:61273 original size:30 final size:28
Alignment explanation
Indices: 61239--61320 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 28
61229 AGAAAGTTTA
*
61239 AGGTAAAAAATGTAATTTTTGGATATTCGG
1 AGGTAAAAAATGTAATTTTTGGA-ATGC-G
*
61269 AGGT--AAAATGGTAA-TTTTGGAATGCT
1 AGGTAAAAAAT-GTAATTTTTGGAATGCG
61295 ATGGGTAAAAAATGTAATTTTTGGAA
1 A--GGTAAAAAATGTAATTTTTGGAA
61321 GTTTTGGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
26 1 0.02
27 3 0.07
28 15 0.34
29 8 0.18
30 17 0.39
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (28 bp):
AGGTAAAAAATGTAATTTTTGGAATGCG
Found at i:61277 original size:59 final size:57
Alignment explanation
Indices: 61185--61651 Score: 201
Period size: 58 Copynumber: 7.9 Consensus size: 57
61175 CTTCGGGGGT
* ** * *
61185 AAAATGGTAATTTTTTGACATTCGGGGGTAAAATGACAATTTTTAGAAAGTTTAAGGTAA
1 AAAAT-GTAATTTTTGGA-ATTC-GGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTAA
* *
61245 AAAATGTAATTTTTGGATATTCGGAGGTAAAATGGTAA-TTTTGGAATG-CTATGGGTAA
1 AAAATGTAATTTTTGGA-ATTCGG-GGTAAAATGGTAATTTTTGGAAAGTTTA-GGGTAA
* * *
61303 AAAATGTAATTTTTGGAAGTTTTGGGGTAAAATGGTAATTTTTGGAAAATTTGGGGTAA
1 AAAATGTAATTTTTGGAA--TTCGGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTAA
* * * * * **
61362 AAAATGGAA-CTTTGGAGGTTCGGGATCAAAAATAG-AATTTTTGG-AAGTTCGGGGGT--
1 AAAATGTAATTTTTGGA-ATTCGGGGT--AAAATGGTAATTTTTGGAAAGTT-TAGGGTAA
* * * * * *
61418 AAAATGGTATTTTTTGGAAAATTTGAGGTCAAAAT-GTAATTTTT-AAAAGTTCAAGGGT-C
1 AAAAT-GTAATTTTTGG--AATTCGGGGT-AAAATGGTAATTTTTGGAAAGTT-TAGGGTAA
* * ** ** *
61477 AAAATGTAATTTTTGGAAGCTCGGGGGTCAAAAT-GTAATTATTAAAAAGATCAAGGGT-T
1 AAAATGTAATTTTTGGAA-TTC-GGGGT-AAAATGGTAATTTTTGGAAAG-TTTAGGGTAA
* * * * *
61536 AAAATATAA-TTTTGAAATGTTTAGGGGTCAAAAT-GTAATTTTTGAAAAGTTTAAGGGTTA
1 AAAATGTAATTTTTGGAA---TTCGGGGT-AAAATGGTAATTTTTGGAAAGTTT-AGGGTAA
* * * *
61596 AAAA-GTAATTTTTAAAGAGTTCGAGAGTTAAAAT-ATAATTTTTGGAAAGTTTAGGG
1 AAAATGTAATTTTT--GGAATTCG-G-GGTAAAATGGTAATTTTTGGAAAGTTTAGGG
61652 ACCTTTTGGG
Statistics
Matches: 320, Mismatches: 57, Indels: 61
0.73 0.13 0.14
Matches are distributed among these distances:
56 7 0.02
57 17 0.05
58 128 0.40
59 126 0.39
60 39 0.12
61 2 0.01
62 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAATTCGGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTAA
Found at i:61282 original size:29 final size:28
Alignment explanation
Indices: 61153--61461 Score: 115
Period size: 29 Copynumber: 10.6 Consensus size: 28
61143 GATGCTCGAG
* *
61153 GGTAAAATGGT-ACTTTTGGACACTTCGGG
1 GGTAAAATGGTAATTTTTGGA-A-TTCGGA
* *
61182 GGTAAAATGGTAATTTTTTGACATTCGGG
1 GGTAAAATGGTAATTTTTGGA-ATTCGGA
** * **
61211 GGTAAAATGACAATTTTTAGAAAGTT-TAA
1 GGTAAAATGGTAATTTTT-GGAA-TTCGGA
61240 GGTAAAAAAT-GTAATTTTTGGATATTCGGA
1 GGT--AAAATGGTAATTTTTGGA-ATTCGGA
* *
61270 GGTAAAATGGTAA-TTTTGGAATGC-TA
1 GGTAAAATGGTAATTTTTGGAATTCGGA
*
61296 TGGGTAAAAAAT-GTAATTTTTGGAAGTTTTGG-
1 --GGT--AAAATGGTAATTTTTGGAA--TTCGGA
*
61328 GGTAAAATGGTAATTTTTGGAAAATTTGG-
1 GGTAAAATGGTAATTTTTGG--AATTCGGA
* *
61357 GGTAAAAAATGG-AA-CTTTGGAGGTTCGG-
1 GGT--AAAATGGTAATTTTTGGA-ATTCGGA
* * *
61385 GATCAAAAATAG-AATTTTTGGAAGTTCGGG
1 GGT--AAAATGGTAATTTTTGGAA-TTCGGA
* *
61415 GGTAAAATGGTATTTTTTGGAAAATT-TGA
1 GGTAAAATGGTAATTTTTGG--AATTCGGA
61444 GGTCAAAAT-GTAATTTTT
1 GGT-AAAATGGTAATTTTT
61462 AAAAGTTCAA
Statistics
Matches: 218, Mismatches: 33, Indels: 58
0.71 0.11 0.19
Matches are distributed among these distances:
26 1 0.00
27 4 0.02
28 41 0.19
29 104 0.48
30 51 0.23
31 16 0.07
32 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (28 bp):
GGTAAAATGGTAATTTTTGGAATTCGGA
Found at i:61361 original size:87 final size:86
Alignment explanation
Indices: 61245--61516 Score: 247
Period size: 87 Copynumber: 3.1 Consensus size: 86
61235 TTTAAGGTAA
* *
61245 AAAAT-GTAATTTTTGG-ATATTCGGAGGT-AAAATGGTAATTTTGGAATGCTATGGGTAAAAAA
1 AAAATGGTAATTTTTGGAAAATTTGG-GGTAAAAATGGTAATTTTGGAA-GCTATGGGT-AAAAA
**
61307 TGTAATTTTTGGAAGTTTTGGGGT
63 TGTAATTTTTGGAAGTTCGGGGGT
* *
61331 AAAATGGTAATTTTTGGAAAATTTGGGGTAAAAAATGG-AACTTTGG-AGGT-TCGGGATCAAAA
1 AAAATGGTAATTTTTGGAAAATTTGGGGT-AAAAATGGTAATTTTGGAAGCTAT-GGG-T-AAAA
61393 ATAG-AATTTTTGGAAGTTCGGGGGT
62 AT-GTAATTTTTGGAAGTTCGGGGGT
* * * ** * * *
61418 AAAATGGTATTTTTTGGAAAATTTGAGGTCAAAAT-GTAATTTTTAAAAGTTCAAGGGTCAAAAT
1 AAAATGGTAATTTTTGGAAAATTTGGGGTAAAAATGGTAA-TTTTGGAAGCT-ATGGGTAAAAAT
*
61482 GTAATTTTTGGAAGCTCGGGGGT
64 GTAATTTTTGGAAGTTCGGGGGT
61505 CAAAAT-GTAATT
1 -AAAATGGTAATT
61517 ATTAAAAAGA
Statistics
Matches: 154, Mismatches: 18, Indels: 27
0.77 0.09 0.14
Matches are distributed among these distances:
85 2 0.01
86 18 0.12
87 101 0.66
88 23 0.15
89 10 0.06
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (86 bp):
AAAATGGTAATTTTTGGAAAATTTGGGGTAAAAATGGTAATTTTGGAAGCTATGGGTAAAAATGT
AATTTTTGGAAGTTCGGGGGT
Found at i:61364 original size:58 final size:59
Alignment explanation
Indices: 61128--61608 Score: 172
Period size: 58 Copynumber: 8.2 Consensus size: 59
61118 TACGAAGTCG
* * * * * * *
61128 AAAATGTGATTTTTGGATG-CTCGAGGGT-AAAATGGT-ACTTTTGGACACTTCGGGGGT-
1 AAAATGTAATTTTTGGAAGTTTCG-GGGTCAAAATGGTAATTTTTGGAAAATT-TGGGGTA
* ** * * **
61185 AAAATGGTAATTTTTTGACA--TTCGGGGGT-AAAATGACAATTTTTAGAAAGTTTAAGGTAA
1 AAAAT-GTAATTTTTGGA-AGTTTC-GGGGTCAAAATGGTAATTTTTGGAAAATTTGGGGT-A
** *
61245 AAAATGTAATTTTTGG-A-TATTCGGAGGT-AAAATGGTAA-TTTTGGAATGCTAT-GGGTAA
1 AAAATGTAATTTTTGGAAGT-TTCGG-GGTCAAAATGGTAATTTTTGGAA-AATTTGGGGT-A
*
61303 AAAATGTAATTTTTGGAAGTTTTGGGGT-AAAATGGTAATTTTTGGAAAATTTGGGGTAA
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCAAAATGGTAATTTTTGGAAAATTTGGGGT-A
* * * * * * *
61362 AAAATGGAA-CTTTGG-AGGTTCGGGATCAAAAATAG-AATTTTTGG-AAGTTCGGGGGT-
1 AAAATGTAATTTTTGGAAGTTTCGGGGTC-AAAATGGTAATTTTTGGAAAATT-TGGGGTA
* * * ** *
61418 AAAATGGTATTTTTTGGAAAATTT-GAGGTCAAAAT-GTAATTTTT--AAAAGTTCAAGGGTC
1 AAAAT-GTAATTTTTGG-AAGTTTCGGGGTCAAAATGGTAATTTTTGGAAAA-TT-TGGGGTA
* * ** *** *
61477 AAAATGTAATTTTTGGAAG-CTCGGGGGTCAAAAT-GTAATTATTAAAAAGATCAAGGGTT
1 AAAATGTAATTTTTGGAAGTTTC-GGGGTCAAAATGGTAATTTTTGGAAA-ATTTGGGGTA
* * * *
61536 AAAATATAA-TTTTGAAATGTTTAGGGGTCAAAAT-GTAATTTTT-GAAAAGTTTAAGGGTTA
1 AAAATGTAATTTTTGGAA-GTTTCGGGGTCAAAATGGTAATTTTTGGAAAA-TTT--GGGGTA
61596 AAAA-GTAATTTTT
1 AAAATGTAATTTTT
61609 AAAGAGTTCG
Statistics
Matches: 326, Mismatches: 62, Indels: 69
0.71 0.14 0.15
Matches are distributed among these distances:
56 6 0.02
57 26 0.08
58 152 0.47
59 116 0.36
60 25 0.08
61 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAGTTTCGGGGTCAAAATGGTAATTTTTGGAAAATTTGGGGTA
Found at i:61476 original size:29 final size:29
Alignment explanation
Indices: 61444--61638 Score: 183
Period size: 30 Copynumber: 6.6 Consensus size: 29
61434 GAAAATTTGA
61444 GGTCAAAATGTAATTTTTAAAAGTTCAAG
1 GGTCAAAATGTAATTTTTAAAAGTTCAAG
** * **
61473 GGTCAAAATGTAATTTTTGGAAGCTCGGG
1 GGTCAAAATGTAATTTTTAAAAGTTCAAG
* *
61502 GGTCAAAATGTAATTATTAAAAAGATCAAG
1 GGTCAAAATGTAATT-TTTAAAAGTTCAAG
* * * * * *
61532 GGTTAAAATATAATTTTGAAATGTTTAGG
1 GGTCAAAATGTAATTTTTAAAAGTTCAAG
*
61561 GGTCAAAATGTAATTTTTGAAAAGTTTAAG
1 GGTCAAAATGTAATTTTT-AAAAGTTCAAG
* * *
61591 GGTTAAAAAGTAATTTTTAAAGAGTTCGAG
1 GGTCAAAATGTAATTTTTAAA-AGTTCAAG
* * *
61621 AGTTAAAATATAATTTTT
1 GGTCAAAATGTAATTTTT
61639 GGAAAGTTTA
Statistics
Matches: 133, Mismatches: 30, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
29 66 0.50
30 67 0.50
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (29 bp):
GGTCAAAATGTAATTTTTAAAAGTTCAAG
Found at i:63153 original size:6 final size:6
Alignment explanation
Indices: 63134--63219 Score: 51
Period size: 6 Copynumber: 15.0 Consensus size: 6
63124 TTATTTTAAA
* *
63134 TAAATT TAATTT TAAATT TATAA-- TAAATT TAAATTT TCAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAA-TT TAAATT TAAATT
* * *
63180 TAAATT TAAA-A TAAACT T-AATT TAGAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT
63220 CTGTTGGACC
Statistics
Matches: 61, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
4 5 0.08
5 12 0.20
6 35 0.57
7 9 0.15
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:63166 original size:17 final size:17
Alignment explanation
Indices: 63144--63219 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
63134 TAAATTTAAT
*
63144 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
**
63161 TTTAAATTTTCAATAAA
1 TTTAAATTTAAAATAAA
63178 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
63195 CTT-AATTTAGAAATAAA
1 TTTAAATTTA-AAATAAA
63212 TTTAAATT
1 TTTAAATT
63220 CTGTTGGACC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
16 6 0.12
17 41 0.80
18 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:63183 original size:23 final size:22
Alignment explanation
Indices: 63126--63189 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
63116 ATTGGACATT
*
63126 ATTTTAAATAAATTTAATTTTAA
1 ATTTT-AATAAATTTAAATTTAA
63149 A-TTT-AT-AA--TAAATTTAA
1 ATTTTAATAAATTTAAATTTAA
63166 ATTTTCAATAAATTTAAATTTAA
1 ATTTT-AATAAATTTAAATTTAA
63189 A
1 A
63190 ATAAACTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
17 9 0.26
18 3 0.09
19 2 0.06
20 4 0.12
21 2 0.06
22 3 0.09
23 11 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTAATAAATTTAAATTTAA
Found at i:64203 original size:201 final size:200
Alignment explanation
Indices: 63574--64340 Score: 921
Period size: 201 Copynumber: 3.8 Consensus size: 200
63564 TTTCAATTTG
* *
63574 CTTCTCTGTATCTCATCAGGAAGTTAACCATTTTATTGCTTCGACCTACTTCTCTA-TATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTC-AGTATCTCAT
** *
63638 CAGGAAGCTAGGGTTCGAAGATTTGCTCACCTTGAGCC-T-AGTTTGATTTATTTGATCTTCTTC
65 CAGGAAGCT-GGGTTCGAAGATTTGCTCAAATTGAGCCTTGAG-TTG--GTA--T-A-CTTCTT-
* *
63701 TCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTGCTTCTCTATATCTCATCAGG
121 T--GTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGG
**
63766 AAGACAAATTTGGTTGA
184 AAGACAAATTTGGTCCA
*
63783 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
* * ** * * * * *
63848 AGGAAGTTGGGTTCAAAGATTTGCTCACATCGAGTATG-GTTTTGATTTGATCTTCTTCTTAGTA
66 AGGAAGCTGGGTTCGAAGATTTGCTCA-A---A-T-TGAGCCTTGAGTTGGTATACTTCTTTGTA
* * * * * *
63912 TCTCATCAGGAAGATGACCGCATCACTTGTTTCAAACCACTTCTCCGTATCTCGTCAAGAAGACG
125 TCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACA
*
63977 AATTTGGTCCG
190 AATTTGGTCCA
* * * * *
63988 CTTCTCAATATCTCATTAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
*
64053 AGGAAGCTGGGATTCGAAGATTTCCTCAAATTGAGCCTTGAGTTGGTATACTTCTTTGTATCTCA
66 AGGAAGCTGGG-TTCGAAGATTTGCTCAAATTGAGCCTTGAGTTGGTATACTTCTTTGTATCTCA
* *
64118 TCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAAACAAATTT
130 TCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACAAATTT
64183 GGTCCA
195 GGTCCA
* * * *
64189 TTTATCAGTATCTCATCAGGAAGTTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
* * * * *
64254 AGGAAGTTGGGGTTCGAAGAGTTGCTCACATTGAGCCTTGAGTTGGTATACTTCTATGTATCTCC
66 AGGAAGCT-GGGTTCGAAGATTTGCTCAAATTGAGCCTTGAGTTGGTATACTTCTTTGTATCTCA
* *
64319 TCAGGAAGATAACCGCCTCACT
130 TCAGGAAGATGACCGCATCACT
64341 ATTTGTGGAT
Statistics
Matches: 484, Mismatches: 62, Indels: 32
0.84 0.11 0.06
Matches are distributed among these distances:
200 2 0.00
201 221 0.46
202 4 0.01
205 138 0.29
206 14 0.03
208 25 0.05
209 69 0.14
210 1 0.00
212 1 0.00
213 2 0.00
214 6 0.01
215 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (200 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
AGGAAGCTGGGTTCGAAGATTTGCTCAAATTGAGCCTTGAGTTGGTATACTTCTTTGTATCTCAT
CAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACAAATTTG
GTCCA
Found at i:75654 original size:30 final size:30
Alignment explanation
Indices: 75512--75966 Score: 168
Period size: 29 Copynumber: 15.5 Consensus size: 30
75502 GCTCGAGGGC
* * *
75512 AAAATGGTAA-TTTTGGACA-CTACGGGGGC
1 AAAATGGTAATTTTTGGA-ATGTTCGGGGGT
* * *
75541 AAAATTGTAATTTTTAGACA--TTCAGGGGT
1 AAAATGGTAATTTTTGGA-ATGTTCGGGGGT
* * * * ** *
75570 AAAATGATAAATTTTAGAAAGTTCAAGGTT
1 AAAATGGTAATTTTTGGAATGTTCGGGGGT
*
75600 AGAAATGG-AATTTTTGG-ATATTCGGGGGGT
1 A-AAATGGTAATTTTTGGAATGTTC-GGGGGT
*
75630 AAAATGGTAA-TTTTGGAATGTTCGGGGTT
1 AAAATGGTAATTTTTGGAATGTTCGGGGGT
* *
75659 AAAAAT-GTATTTTTTGGAA-GTTCGAGGGT
1 -AAAATGGTAATTTTTGGAATGTTCGGGGGT
** *
75688 AAAATGGTAATTTTTGGAA-GTTTAGGAGT
1 AAAATGGTAATTTTTGGAATGTTCGGGGGT
* ** *
75717 AAAATGGTGATTTTTGGAAAATTC-GAGGT
1 AAAATGGTAATTTTTGGAATGTTCGGGGGT
* * * *
75746 CAAAAATAG-AACTTTTGG-AGGTTC-GAGGT
1 --AAAATGGTAATTTTTGGAATGTTCGGGGGT
**
75775 CAAAATGG-AATTTTTGG-ATGTTTTGGGGT
1 -AAAATGGTAATTTTTGGAATGTTCGGGGGT
** * *
75804 AAAATGGTAA-TTTTGGAAAATTTGGGGTT
1 AAAATGGTAATTTTTGGAATGTTCGGGGGT
* * ** *
75833 AAAAATGG-AGTTTTTAGAA-GTTTAAGGGTT
1 -AAAATGGTAATTTTTGGAATG-TTCGGGGGT
* *
75863 AAAAT-GTAATTTTTAG-ATGCTT-GAGGGT
1 AAAATGGTAATTTTTGGAATG-TTCGGGGGT
* * *
75891 GAAAAT-GTAATTTTTGGAAAGCTCGAGGGTT
1 -AAAATGGTAATTTTTGGAATGTTCG-GGGGT
* * * **
75922 AAAAT-ATAATTTTTGAAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAATGTTCGGGGGT
75951 CAAAAT-GTAATTTTTG
1 -AAAATGGTAATTTTTG
75967 AAAAGTTTGA
Statistics
Matches: 330, Mismatches: 70, Indels: 51
0.73 0.16 0.11
Matches are distributed among these distances:
28 42 0.13
29 161 0.49
30 113 0.34
31 14 0.04
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAATGTTCGGGGGT
Found at i:75659 original size:59 final size:58
Alignment explanation
Indices: 75512--75847 Score: 202
Period size: 59 Copynumber: 5.7 Consensus size: 58
75502 GCTCGAGGGC
* * * ** * * * *
75512 AAAATGGTAATTTTGGACACTACGGGGGCAAAATTGTAATTTTTAGACATTC-AGGGGT
1 AAAATGGTAATTTTGGAAAGTTCGGGGTTAAAA-TGGAATTTTTGGATATTCGGGGGGT
* * **
75570 AAAATGATAAATTTTAGAAAGTTCAAGGTTAGAAATGGAATTTTTGGATATTCGGGGGGT
1 AAAATGGT-AATTTTGGAAAGTTCGGGGTTA-AAATGGAATTTTTGGATATTCGGGGGGT
* * * *
75630 AAAATGGTAATTTTGGAATGTTCGGGGTTAAAAATGTATTTTTTGGA-AGTTC-GAGGGT
1 AAAATGGTAATTTTGGAAAGTTCGGGGTT-AAAATGGAATTTTTGGATA-TTCGGGGGGT
* * * * * ***
75688 AAAATGGTAATTTTTGG-AAGTTTAGGAG-TAAAATGGTGATTTTTGGAAAATTCGAGGTCA
1 AAAATGGTAA-TTTTGGAAAG-TTCGGGGTTAAAATGG-AATTTTTGG-ATATTCGGGGGGT
* * * * * **
75748 AAAATAG-AACTTTTGG-AGGTTCGAGGTCAAAATGGAATTTTTGGATGTT-TTGGGGT
1 AAAATGGTAA-TTTTGGAAAGTTCGGGGTTAAAATGGAATTTTTGGATATTCGGGGGGT
* * *
75804 AAAATGGTAATTTTGGAAAATTTGGGGTTAAAAATGGAGTTTTT
1 AAAATGGTAATTTTGGAAAGTTCGGGGTT-AAAATGGAATTTTT
75848 AGAAGTTTAA
Statistics
Matches: 209, Mismatches: 54, Indels: 30
0.71 0.18 0.10
Matches are distributed among these distances:
56 14 0.07
57 18 0.09
58 58 0.28
59 95 0.45
60 24 0.11
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTGGAAAGTTCGGGGTTAAAATGGAATTTTTGGATATTCGGGGGGT
Found at i:75933 original size:59 final size:60
Alignment explanation
Indices: 75857--75971 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
75847 TAGAAGTTTA
* * * * *
75857 AGGGTTAAAATGTAATTTTT-AGATGCTTGA-GGGTGAAAATGTAATTTTTGGAAAGCTCG
1 AGGGTTAAAATATAATTTTTGAAAAG-TTGAGGGGTCAAAATGTAATTTTTGAAAAGCTCG
*
75916 AGGGTTAAAATATAATTTTTGAAAAGTTTAGGGGTCAAAATGTAATTTTTGAAAAG
1 AGGGTTAAAATATAATTTTTGAAAAGTTGAGGGGTCAAAATGTAATTTTTGAAAAG
75972 TTTGAGAGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 22 0.46
60 26 0.54
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (60 bp):
AGGGTTAAAATATAATTTTTGAAAAGTTGAGGGGTCAAAATGTAATTTTTGAAAAGCTCG
Found at i:75967 original size:30 final size:29
Alignment explanation
Indices: 75772--76039 Score: 161
Period size: 29 Copynumber: 9.1 Consensus size: 29
75762 GGAGGTTCGA
* * *
75772 GGTCAAAATGGAATTTTTG-GATGTTTTGG
1 GGTCAAAATGTAATTTTTGAAAAG-TTTGG
*
75801 GGT-AAAATGGTAATTTTGGAAAA-TTTGG
1 GGTCAAAAT-GTAATTTTTGAAAAGTTTGG
* * * * *
75829 GGTTAAAAATGGAGTTTTT-AGAAGTTTAAG
1 GG-TCAAAATGTAATTTTTGAAAAGTTT-GG
* * * *
75859 GGTTAAAATGTAATTTTT-AGATGCTTGAG
1 GGTCAAAATGTAATTTTTGAAAAGTTTG-G
* * * *
75888 GGTGAAAATGTAATTTTTGGAAAGCTCGAG
1 GGTCAAAATGTAATTTTTGAAAAGTTTG-G
* *
75918 GGTTAAAATATAATTTTTGAAAAGTTTAGG
1 GGTCAAAATGTAATTTTTGAAAAGTTT-GG
75948 GGTCAAAATGTAATTTTTGAAAAGTTTGAG
1 GGTCAAAATGTAATTTTTGAAAAGTTTG-G
* * * *
75978 AGTC-AAATGTACTTTTTGAAGAGTTCGAG
1 GGTCAAAATGTAATTTTTGAAAAGTTTG-G
* * * * *
76007 GGTTAAAATATGATTTTTGGAAAGTTTAG
1 GGTCAAAATGTAATTTTTGAAAAGTTTGG
76036 GGTC
1 GGTC
76040 CTTTTGGGTA
Statistics
Matches: 187, Mismatches: 41, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
28 15 0.08
29 87 0.47
30 84 0.45
31 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
GGTCAAAATGTAATTTTTGAAAAGTTTGG
Found at i:75986 original size:29 final size:29
Alignment explanation
Indices: 75850--76039 Score: 134
Period size: 30 Copynumber: 6.4 Consensus size: 29
75840 GAGTTTTTAG
* * *
75850 AAGTTTAAGGGTTAAAATGTAATTTTT-AG
1 AAGTTTGAGGG-TCAAATGTAATTTTTGAA
* * * *
75879 ATGCTTGAGGGTGAAAATGTAATTTTTGGA
1 AAGTTTGAGGGT-CAAATGTAATTTTTGAA
* * * *
75909 AAGCTCGAGGGTTAAAATATAATTTTTGAA
1 AAGTTTGAGGG-TCAAATGTAATTTTTGAA
75939 AAGTTT-AGGGGTCAAAATGTAATTTTTGAA
1 AAGTTTGA-GGGTC-AAATGTAATTTTTGAA
* *
75969 AAGTTTGAGAGTCAAATGTACTTTTTGAA
1 AAGTTTGAGGGTCAAATGTAATTTTTGAA
* * * * * *
75998 GAGTTCGAGGGTTAAAATATGATTTTTGGA
1 AAGTTTGAGGG-TCAAATGTAATTTTTGAA
76028 AAGTTT-AGGGTC
1 AAGTTTGAGGGTC
76040 CTTTTGGGTA
Statistics
Matches: 128, Mismatches: 26, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
28 2 0.02
29 51 0.40
30 73 0.57
31 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
AAGTTTGAGGGTCAAATGTAATTTTTGAA
Found at i:76964 original size:3 final size:3
Alignment explanation
Indices: 76950--77030 Score: 128
Period size: 3 Copynumber: 27.3 Consensus size: 3
76940 GTATCCTTTT
* * *
76950 TTA TTA TT- TTA TTA TTA ATA TTA TTA ATG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
76997 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
77031 GCATTTATTA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:77701 original size:6 final size:6
Alignment explanation
Indices: 77682--77767 Score: 58
Period size: 6 Copynumber: 15.0 Consensus size: 6
77672 ATTATTTAAA
* *
77682 TAAATT TAATTT TAAATT TATAA-- TAAATT TAAATT TCCAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* * * *
77728 TAAATT TAAA-A TAAACT TAATTT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
77768 CTGTTGGGCC
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
4 4 0.07
5 11 0.18
6 42 0.69
7 4 0.07
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:77714 original size:17 final size:17
Alignment explanation
Indices: 77692--77767 Score: 107
Period size: 17 Copynumber: 4.5 Consensus size: 17
77682 TAAATTTAAT
*
77692 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
**
77709 TTTAAATTTCCAATAAA
1 TTTAAATTTAAAATAAA
77726 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
77743 CTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
77760 TTTAAATT
1 TTTAAATT
77768 CTGTTGGGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:78791 original size:33 final size:35
Alignment explanation
Indices: 78754--78837 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 35
78744 ATGATTATAT
*
78754 TTAAATATTTAAAATATAATTTATAT-ATT-CTAA
1 TTAAATATTTAAAATATAATTAATATAATTACTAA
* *
78787 TTAAAT-TTTATAA-ATAATTAATATAATTACTTA
1 TTAAATATTTAAAATATAATTAATATAATTACTAA
*
78820 -GAAATATTTAAAAT-TAAT
1 TTAAATATTTAAAATATAAT
78838 ATTTCATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
31 10 0.24
32 13 0.31
33 19 0.45
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTAATATAATTACTAA
Done.