Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold504
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: 246700
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 2
Found at i:1397 original size:19 final size:19
Alignment explanation
Indices: 1373--1458 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
1363 AGCGTTACAT
1373 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
1392 TGTATCAATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1405 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
1424 TGTATCGATACAGTTACTGTT
1 TGTATCGATACA-AAACT-TA
1445 TGTATCGATACAAA
1 TGTATCGATACAAA
1459 TTATTGAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
13 10 0.19
14 1 0.02
16 2 0.04
18 1 0.02
19 22 0.42
20 3 0.06
21 13 0.25
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1409 original size:32 final size:32
Alignment explanation
Indices: 1368--1435 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1358 TTCGTAGCGT
1368 TACATTGTATCGATACAAAACTTATGTATCAA
1 TACATTGTATCGATACAAAACTTATGTATCAA
* *
1400 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCAA
1432 TACA
1 TACA
1436 GTTACTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCAA
Found at i:1520 original size:21 final size:20
Alignment explanation
Indices: 1494--1532 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1484 GTTGGGACCT
1494 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
1515 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
1533 CAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:2931 original size:20 final size:20
Alignment explanation
Indices: 2906--2959 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2896 ATTTGGGACA
* * **
2906 ATGTATCGATATAATTTTTC
1 ATGTATCGATACAATGTGCC
2926 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
2946 ATGTATCGATACAA
1 ATGTATCGATACAA
2960 ATAGTGGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:3125 original size:20 final size:20
Alignment explanation
Indices: 3100--3151 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3090 GTCAACCTTA
3100 ATGTATCGATACAAATACCT
1 ATGTATCGATACAAATACCT
3120 ATGTATCGATACAAATACCT
1 ATGTATCGATACAAATACCT
3140 ATGTATCGATAC
1 ATGTATCGATAC
3152 TTTAGTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAATACCT
Found at i:5627 original size:20 final size:21
Alignment explanation
Indices: 5596--5635 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
5586 ATCTAAGTTT
5596 TTTCAGATGTATCGATACATC
1 TTTCAGATGTATCGATACATC
5617 TTTCA-ATGTATCGATACAT
1 TTTCAGATGTATCGATACAT
5636 TTTGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTCAGATGTATCGATACATC
Found at i:7006 original size:16 final size:15
Alignment explanation
Indices: 6985--7015 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
6975 CAATATTTCC
6985 TCTATTAAAACATTTT
1 TCTATTAAAA-ATTTT
7001 TCTATTAAAAATTTT
1 TCTATTAAAAATTTT
7016 GAAAGCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (15 bp):
TCTATTAAAAATTTT
Found at i:9527 original size:15 final size:15
Alignment explanation
Indices: 9509--9546 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
9499 CAAGTCAACT
9509 TCATCATTATCATCA
1 TCATCATTATCATCA
* *
9524 TCATCATTATCTTTA
1 TCATCATTATCATCA
9539 TCATCATT
1 TCATCATT
9547 GATGGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:12213 original size:79 final size:78
Alignment explanation
Indices: 12081--12409 Score: 315
Period size: 79 Copynumber: 4.2 Consensus size: 78
12071 ACAACGAGGC
* * ** *
12081 TGGAGTATCCCTTGACTATGGAAAATCGGTGTTTT-GAAAATAAAATCCGGGTTGGAGTATCCCC
1 TGGAGTATCCC-CGATTAT-GAAAATCAATGTTTTAG-AAATAAAATCGGGGTTGGAGTATCCCC
*
12145 TAGGAAATAACAGGGT
63 TAGAAAATAACAGGGT
* * *
12161 TGGAGTATCCCTGATTATAGAAAACCAATGTTTT-GAAAATAAAATCGGGGTTGGAGTATCTCCT
1 TGGAGTATCCCCGATTAT-GAAAATCAATGTTTTAG-AAATAAAATCGGGGTTGGAGTATCCCCT
* *
12225 TGAAAATAATAGGGT
64 AGAAAATAACAGGGT
* * * ** * *
12240 TGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAAT-AAGGCTGGGGTTGGAGTATTCTC-
1 TGGAGTATCCCCGATTATG-AAAATCAATGTTTTAGAAATAAAATC-GGGGTTGGAGTATCCCCT
12303 ATGAAAATAACAGGGT
64 A-GAAAATAACAGGGT
* * * * *
12319 TGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCTCCTC
1 TGGAGTATCCCCGATTATGA-AAATCAATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTA
*
12384 GAAAATAACGGGGT
65 GAAAATAACAGGGT
* *
12398 TAGAGTGTCCCC
1 TGGAGTATCCCC
12410 AATGAAATAA
Statistics
Matches: 208, Mismatches: 34, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
78 5 0.02
79 188 0.90
80 15 0.07
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (78 bp):
TGGAGTATCCCCGATTATGAAAATCAATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTAG
AAAATAACAGGGT
Found at i:14968 original size:49 final size:50
Alignment explanation
Indices: 14913--15045 Score: 169
Period size: 50 Copynumber: 2.7 Consensus size: 50
14903 AAAATGCCTG
* * *
14913 AATGTATCGATACATTGAAAAATATATCGATACATCTGGGT-AAACCCAA
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTGGATAAAACCCAA
* * * *
14962 AATGTATCGATACAATGAACAATGTATCGATAGATTTGGATAAAACCCAG
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTGGATAAAACCCAA
* * *
15012 AATGTATCGATGCAATGAAGAATGCATCGATACA
1 AATGTATCGATACAATGAAAAATGTATCGATACA
15046 AATTATAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 35 0.49
50 37 0.51
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (50 bp):
AATGTATCGATACAATGAAAAATGTATCGATACATCTGGATAAAACCCAA
Found at i:15798 original size:61 final size:61
Alignment explanation
Indices: 15728--16121 Score: 476
Period size: 61 Copynumber: 6.7 Consensus size: 61
15718 GGCAAAGGAG
* * *
15728 AAAAGGAAAAGGAGTCCTGCTTTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
15789 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
15849 AAAAGGAAAAGGTGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
15910 ------AAAAGGCGTCCTGCTCTTTGAGGCCT-AGAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTT
** *
15965 AAAAGGAAAAAACGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAATTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
16027 AAAA-G---A--CGTCCTGCTCTTTGAGGACTAGGAAA-TGCTACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
16082 AAAAGGAATAGGCATCTTGCTCTTTGAAGACTAAAAAGTG
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTG
16122 AAAGGAGAAA
Statistics
Matches: 289, Mismatches: 27, Indels: 34
0.83 0.08 0.10
Matches are distributed among these distances:
55 74 0.26
56 26 0.09
58 1 0.00
59 1 0.00
60 59 0.20
61 98 0.34
62 29 0.10
63 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (61 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:15927 original size:55 final size:55
Alignment explanation
Indices: 15734--16087 Score: 379
Period size: 55 Copynumber: 6.1 Consensus size: 55
15724 GGAGAAAAGG
* * * *
15734 AAAAGGAGTCCTGCTTTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
15789 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTT
1 ------AAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
15849 AAAAGGAAAAGGTGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
1 ------AAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
15910 AAAAGGCGTCCTGCTCTTTGAGGCCTAGAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
15965 AAAAGGAAAAAACGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAATTTGTGTGGGCTTT
1 AAAAGG------CGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
16027 AAAAGACGTCCTGCTCTTTGAGGACTAGGAAA-TGCTACCAACTTGTGTGGGCTTT
1 AAAAGGCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
16082 AAAAGG
1 AAAAGG
16088 AATAGGCATC
Statistics
Matches: 260, Mismatches: 25, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
55 82 0.32
56 25 0.10
60 55 0.21
61 68 0.26
62 30 0.12
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (55 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:16067 original size:117 final size:116
Alignment explanation
Indices: 15728--16121 Score: 515
Period size: 117 Copynumber: 3.3 Consensus size: 116
15718 GGCAAAGGAG
* *
15728 AAAAGGAAAAGGA-GTCCTGCTTTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAA
1 AAAAGGAAAA-GACGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAA
*
15792 AGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTT
65 A-G---A--CGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
15849 AAAAGGAAAAGGTGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* *
15914 GGCGTCCTGCTCTTTGAGGCCTAGAAGGTGCCACCAACTTGTGTGGGCTTT
66 GACGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT
* *
15965 AAAAGGAAAAAACGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAATTTGTGTGGGCTTTAAA
1 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAA
* *
16030 AGACGTCCTGCTCTTTGAGGACTAGGAA-ATGCTACCAACTTGTGTGGGCTTT
65 AGACGTCCTGCTCTTTGAGGACTA-GAAGGTGCCACCAACTTGTGTGGGCTTT
* * * * * *
16082 AAAAGGAATAGGCATCTTGCTCTTTGAAGACTAAAAAGTG
1 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACTGAAAAGTG
16122 AAAGGAGAAA
Statistics
Matches: 244, Mismatches: 25, Indels: 13
0.87 0.09 0.05
Matches are distributed among these distances:
115 19 0.08
116 62 0.25
117 100 0.41
118 3 0.01
120 2 0.01
121 58 0.24
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (116 bp):
AAAAGGAAAAGACGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
GACGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:26723 original size:20 final size:20
Alignment explanation
Indices: 26698--26807 Score: 144
Period size: 20 Copynumber: 5.8 Consensus size: 20
26688 ATTTTTCGAT
26698 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
26718 ACAATGTATCGATACAATTA
1 ACAATGTATCGATACAATGA
26738 ACAATGTATCGATAC-AT--
1 ACAATGTATCGATACAATGA
*
26755 ----TGTATCAATACAATGA
1 ACAATGTATCGATACAATGA
26771 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
26791 ACAATGCATCGATACAA
1 ACAATGTATCGATACAA
26808 ATTGTAAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 14
0.81 0.04 0.14
Matches are distributed among these distances:
13 10 0.13
14 2 0.03
19 2 0.03
20 65 0.82
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:26735 original size:33 final size:33
Alignment explanation
Indices: 26693--26807 Score: 90
Period size: 33 Copynumber: 3.3 Consensus size: 33
26683 CCAAAATTTT
26693 TCGATACAATGTATCGATACAATGAACAATGTATCGA
1 TCGATACAATGTATCGATACAATGAACAATG-A---A
* * * *
26730 TACAATTAACAATGTATCGATACATTGTATCAATACAA
1 T-CGA-T-ACAATGTATCGATACAATG-AACAAT-GAA
*
26768 T-GA-ACAATGTATCGATACAATGAACAATGCA
1 TCGATACAATGTATCGATACAATGAACAATGAA
26799 TCGATACAA
1 TCGATACAA
26808 ATTGTAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
31 2 0.03
32 7 0.11
33 22 0.35
36 1 0.02
37 1 0.02
38 4 0.06
39 1 0.02
40 18 0.29
41 6 0.10
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (33 bp):
TCGATACAATGTATCGATACAATGAACAATGAA
Found at i:26773 original size:53 final size:53
Alignment explanation
Indices: 26693--26807 Score: 194
Period size: 53 Copynumber: 2.2 Consensus size: 53
26683 CCAAAATTTT
* * *
26693 TCGATACAATGTATCGATACAATGAACAATGTATCGATACAATTAACAATGTA
1 TCGATACAATGTATCAATACAATGAACAATGTATCGATACAATGAACAATGCA
*
26746 TCGATACATTGTATCAATACAATGAACAATGTATCGATACAATGAACAATGCA
1 TCGATACAATGTATCAATACAATGAACAATGTATCGATACAATGAACAATGCA
26799 TCGATACAA
1 TCGATACAA
26808 ATTGTAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (53 bp):
TCGATACAATGTATCAATACAATGAACAATGTATCGATACAATGAACAATGCA
Found at i:26789 original size:13 final size:13
Alignment explanation
Indices: 26693--26769 Score: 52
Period size: 13 Copynumber: 6.8 Consensus size: 13
26683 CCAAAATTTT
26693 TCGATACAATGTA
1 TCGATACAATGTA
26706 TCGATAC-A---A
1 TCGATACAATGTA
26715 T-GA-ACAATGTA
1 TCGATACAATGTA
26726 TCGATACAA--T-
1 TCGATACAATGTA
26736 T--A-ACAATGTA
1 TCGATACAATGTA
*
26746 TCGATACATTGTA
1 TCGATACAATGTA
*
26759 TCAATACAATG
1 TCGATACAATG
26770 AACAATGTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 24
0.64 0.04 0.32
Matches are distributed among these distances:
7 6 0.12
8 4 0.08
9 3 0.06
10 2 0.04
11 3 0.06
12 4 0.08
13 27 0.55
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (13 bp):
TCGATACAATGTA
Found at i:27528 original size:42 final size:43
Alignment explanation
Indices: 27421--27623 Score: 159
Period size: 42 Copynumber: 4.7 Consensus size: 43
27411 AAATGGGTCC
* * * * *
27421 TGCTCCTTGGGGACTAAGGAAAAAAGG-AAATAAAATGCATCA
1 TGCTCTTTGAGGACAAAGGAAAAAAGGAAAATAAAGTGCATCT
* * *
27463 TGCCCTTTGAAGAC-AAGGGAAAAAGGAAAATAAA-TGTC-TCT
1 TGCTCTTTGAGGACAAAGGAAAAAAGGAAAATAAAGTG-CATCT
* *
27504 TGCTTTTTGAGGACAAAGGAAAAAA--AAGAATAAAGTGCGTCT
1 TGCTCTTTGAGGACAAAGGAAAAAAGGAA-AATAAAGTGCATCT
* * * * *
27546 TACTTTTTGAGAACTAGAAGGGAAAAGAAGG-AAATGAAGTGCATCC
1 TGCTCTTTGAGGAC-A-AA-GGAAAA-AAGGAAAATAAAGTGCATCT
*
27592 TGCTCTTTGAGGACAAAGGAAAAAAAGAAAAT
1 TGCTCTTTGAGGACAAAGGAAAAAAGGAAAAT
27624 GCGTCCTACT
Statistics
Matches: 129, Mismatches: 19, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
40 2 0.02
41 33 0.26
42 47 0.36
43 11 0.09
44 4 0.03
45 7 0.05
46 24 0.19
47 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (43 bp):
TGCTCTTTGAGGACAAAGGAAAAAAGGAAAATAAAGTGCATCT
Found at i:27536 original size:41 final size:42
Alignment explanation
Indices: 27431--27617 Score: 130
Period size: 41 Copynumber: 4.4 Consensus size: 42
27421 TGCTCCTTGG
* * * * **
27431 GGACTAAGG-AAAAAAGGAAATAAAATGCATCATGCCCTTTGA
1 GGACAAAGGAAAAAAAAG-AATAAAGTGCATCTTGCTTTTTGA
* * *
27473 AGACAAGGGAAAAAGGAA-AATAAA-TGTC-TCTTGCTTTTTGA
1 GGACAAAGGAAAAA-AAAGAATAAAGTG-CATCTTGCTTTTTGA
* *
27514 GGACAAAGGAAAAAAAAGAATAAAGTGCGTCTTACTTTTTGA
1 GGACAAAGGAAAAAAAAGAATAAAGTGCATCTTGCTTTTTGA
* * * * * *
27556 GAACTAGAAGGGAAAAGAAGGAAATGAAGTGCATCCTGCTCTTTGA
1 GGAC-A-AA-GGAAAAAAAAG-AATAAAGTGCATCTTGCTTTTTGA
27602 GGACAAAGGAAAAAAA
1 GGACAAAGGAAAAAAA
27618 GAAAATGCGT
Statistics
Matches: 113, Mismatches: 22, Indels: 19
0.73 0.14 0.12
Matches are distributed among these distances:
40 2 0.02
41 31 0.27
42 30 0.27
43 13 0.12
44 5 0.04
45 10 0.09
46 22 0.19
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.20
Consensus pattern (42 bp):
GGACAAAGGAAAAAAAAGAATAAAGTGCATCTTGCTTTTTGA
Found at i:27831 original size:61 final size:61
Alignment explanation
Indices: 27650--28095 Score: 537
Period size: 61 Copynumber: 7.5 Consensus size: 61
27640 GGCAAAGGAG
* *
27650 AAAAGGAAAAGGCGGCCTGCTCTTTGAGGACTGAAAAGTGCCA-CAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
27710 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCAACAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
27770 AAAAAGAAAAGGCCTCCTGCTCTTTGAGGACTGGAAAGTGCTACCAACTTGTGTGGACTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
27831 ------AAAAGGCATCCTGCTCTTTGA-GACCTGGAAAATCCCACCAACTTGTGTGGGCTAT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGA-CTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* ** * * * *
27886 AAAAGGAAAAGGTGTTTTGCTCTTTGAGGACTAGAAGGTGCCACCAACCTGTGTGAGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
27947 AAAAGGAAAAAGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
*
28009 ------AAAAGGCGTCCTGCTCTTTGAGGATTGGGAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
28064 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT
28096 TAAAAGTGAA
Statistics
Matches: 325, Mismatches: 44, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
54 2 0.01
55 69 0.21
56 26 0.08
59 8 0.02
60 78 0.24
61 116 0.36
62 26 0.08
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (61 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:27859 original size:55 final size:55
Alignment explanation
Indices: 27656--28069 Score: 350
Period size: 55 Copynumber: 7.1 Consensus size: 55
27646 GGAGAAAAGG
** *
27656 AAAAGGCGGCCTGCTCTTTGAGGACTGAAAAGTGCCA-CAACTTGTGTGGGCTTT
1 AAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
27710 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCAACAACTTGTGTGGGCTTT
1 ------AAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
27770 AAAAAGAAAAGGCCTCCTGCTCTTTGAGGACTGGAAAGTGCTACCAACTTGTGTGGACTTT
1 ------AAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
27831 AAAAGGCATCCTGCTCTTTGA-GACCTGGAAAATCCCACCAACTTGTGTGGGCTAT
1 AAAAGGCATCCTGCTCTTTGAGGA-CTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* ** * * * *
27886 AAAAGGAAAAGGTGTTTTGCTCTTTGAGGACTAGAAGGTGCCACCAACCTGTGTGAGCTTT
1 AAAAGG--CA----TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
27947 AAAAGGAAAAAGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAA-G-----GCATCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
28009 AAAAGGCGTCCTGCTCTTTGAGGATTGGGAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAAGGCATCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
28064 AAAAGG
1 AAAAGG
28070 AAAAGGCGTC
Statistics
Matches: 298, Mismatches: 39, Indels: 39
0.79 0.10 0.10
Matches are distributed among these distances:
54 2 0.01
55 81 0.27
56 22 0.07
57 1 0.00
59 8 0.03
60 72 0.24
61 79 0.27
62 31 0.10
65 1 0.00
67 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (55 bp):
AAAAGGCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:27907 original size:116 final size:115
Alignment explanation
Indices: 27650--28069 Score: 401
Period size: 116 Copynumber: 3.6 Consensus size: 115
27640 GGCAAAGGAG
** * *
27650 AAAAGGAAAAGGCGGCCTGCTCTTTGAGGACTGAAAAGTGCCA-CAACTTGTGTGGGCTTTAAAA
1 AAAAGGAAAAGGCCTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGACTTT----
* ** *
27714 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCAACAACTTGTGTGGGCTTT
62 --AAAAGGCATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT
* *
27770 AAAAAGAAAAGGCCTCCTGCTCTTTGAGGACTGGAAAGTGCTACCAACTTGTGTGGACTTTAAAA
1 AAAAGGAAAAGGCCTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGACTTTAAAA
* *
27835 GGCATCCTGCTCTTTGA-GACCTGGAAAATCCCACCAACTTGTGTGGGCTAT
66 GGCATCCTGCTCTTTGAGGA-CT-GAAAATGCCACCAACTTGTGTGGGCTTT
** ** * * *
27886 AAAAGGAAAAGGTGTTTTGCTCTTTGAGGACTAGAAGGTGCCACCAACCTGTGT-GAGCTTTAAA
1 AAAAGGAAAAGGCCTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGA-CTTTAAA
*
27950 AGGAAAAAGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
65 A-G-----GCATCCTGCTCTTTGAGGACT-GAAAA-TGCCACCAACTTGTGTGGGCTTT
* * *
28009 ------AAAAGGCGTCCTGCTCTTTGAGGATTGGGAAA-TGCCACCAACTTGTGTGGGCTTTAAA
1 AAAAGGAAAAGGCCTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGACTTTAAA
28067 AGG
65 AGG
28070 AAAAGGCGTC
Statistics
Matches: 253, Mismatches: 33, Indels: 37
0.78 0.10 0.11
Matches are distributed among these distances:
111 1 0.00
114 2 0.01
115 24 0.09
116 77 0.30
117 46 0.18
118 4 0.02
120 38 0.15
121 16 0.06
122 22 0.09
123 23 0.09
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (115 bp):
AAAAGGAAAAGGCCTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGACTTTAAAA
GGCATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:28027 original size:178 final size:176
Alignment explanation
Indices: 27656--28095 Score: 652
Period size: 178 Copynumber: 2.5 Consensus size: 176
27646 GGAGAAAAGG
*
27656 AAAAGGCGGCCTGCTCTTTGAGGACT-GAAAAGTGCCA-CAACTTGTGTGGGCTTTAAAAGGAAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* * * *
27719 AGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCAACAACTTGTGTGGGCTTTAAAAAGAAAAGGCC
65 AGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCAACAACCTGTGTGAGCTTTAAAAAGAAAAAGCA
* * *
27784 TCCTGCTCTTTGAGGACTGGAAAGTGCTACCAACTTGTGTGGACTTT
130 TCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGACTTT
* * *
27831 AAAAGGCATCCTGCTCTTTGA-GACCTGGAAAATCCCACCAACTTGTGTGGGCTATAAAAGGAAA
1 AAAAGGCGTCCTGCTCTTTGAGGA-CTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* ** * *
27895 AGGTGTTTTGCTCTTTGAGGACTAGAAGGTGCCACCAACCTGTGTGAGCTTTAAAAGGAAAAAGC
65 AGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCAACAACCTGTGTGAGCTTTAAAAAGAAAAAGC
*
27960 ATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
129 ATCCTACTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGACTTT
* *
28009 AAAAGGCGTCCTGCTCTTTGAGGATTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
28074 GGCGTCCTGCTCTTTGAGGACT
66 GGCGTCCTGCTCTTTGAGGACT
28096 TAAAAGTGAA
Statistics
Matches: 234, Mismatches: 25, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
174 2 0.01
175 25 0.11
176 50 0.21
177 53 0.23
178 102 0.44
179 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (176 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
GGCGTCCTGCTCTTTGAGGACTGAAGGTGCCAACAACCTGTGTGAGCTTTAAAAAGAAAAAGCAT
CCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGACTTT
Found at i:35869 original size:17 final size:17
Alignment explanation
Indices: 35843--35880 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
35833 TATCGATACA
*
35843 TCACTGTTCATAACTGT
1 TCACTATTCATAACTGT
35860 TCACTATTCATAACTGT
1 TCACTATTCATAACTGT
35877 TCAC
1 TCAC
35881 ATATCACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.39
Consensus pattern (17 bp):
TCACTATTCATAACTGT
Found at i:36472 original size:34 final size:35
Alignment explanation
Indices: 36409--36475 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
36399 CTAAGTGATT
36409 GAGAGGTTCTATCTTAGCCTCTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTCTG-AAAAGATAGAGA
36445 GAGAGGTTTCTATCTTAGCCT-TG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTCTGAAAAGATAG
36476 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 8 0.27
37 14 0.47
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTCTGAAAAGATAGAGA
Found at i:37117 original size:21 final size:21
Alignment explanation
Indices: 37091--37153 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
37081 TCGATTTAGA
37091 AATCTATATTTCTATATTATT
1 AATCTATATTTCTATATTATT
37112 AATCTATATTTCTATATTATT
1 AATCTATATTTCTATATTATT
*
37133 AATCTATATATCTATATTATT
1 AATCTATATTTCTATATTATT
37154 TATATTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.56
Consensus pattern (21 bp):
AATCTATATTTCTATATTATT
Found at i:37177 original size:19 final size:19
Alignment explanation
Indices: 37149--37209 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 19
37139 TATATCTATA
*
37149 TTATTTATATTATTTATTT
1 TTATTAATATTATTTATTT
*
37168 TTATTAATATATAATATATTAT
1 TTATTAATAT-T-ATTTATT-T
* *
37190 TTAAATATTATTATTTATTT
1 TT-ATTAATATTATTTATTT
37210 AAATGTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 9 0.27
20 2 0.06
21 12 0.36
22 4 0.12
23 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTAATATTATTTATTT
Found at i:37197 original size:18 final size:18
Alignment explanation
Indices: 37149--37228 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
37139 TATATCTATA
* *
37149 TTATTTATAT-TATTTAT
1 TTATTTAAATATAATTAT
*
37166 TTTTATTAATATATAA-TAT
1 TTAT-TTAA-ATATAATTAT
*
37185 ATTATTTAAATATTATTAT
1 -TTATTTAAATATAATTAT
* *
37204 TTATTTAAATGTTATTATT
1 TTATTTAAATATAATTA-T
37223 TTATTT
1 TTATTT
37229 TTATTTAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 3 0.06
18 24 0.47
19 19 0.37
20 5 0.10
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
TTATTTAAATATAATTAT
Found at i:37263 original size:19 final size:16
Alignment explanation
Indices: 37228--37286 Score: 61
Period size: 15 Copynumber: 3.7 Consensus size: 16
37218 TTATTTTATT
*
37228 TTTATTTAATT-TTAA
1 TTTAATTAATTATTAA
37243 TTTAAGTTAAATATATTAA
1 TTTAA-TT-AAT-TATTAA
37262 TTT-ATTAATTATTAA
1 TTTAATTAATTATTAA
37277 TTTAA-TAATT
1 TTTAATTAATT
37287 TAGAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 18 0.47
16 6 0.16
17 5 0.13
18 2 0.05
19 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTAATTAATTATTAA
Found at i:38812 original size:14 final size:14
Alignment explanation
Indices: 38795--38823 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38785 CATTTTAATA
38795 ATTTAATAATATTT
1 ATTTAATAATATTT
38809 ATTTAATAATATTT
1 ATTTAATAATATTT
38823 A
1 A
38824 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTAATAATATTT
Found at i:39441 original size:14 final size:14
Alignment explanation
Indices: 39424--39454 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39414 AATGGATATA
39424 TATCGTATAATTCT
1 TATCGTATAATTCT
39438 TATCGTATAATTCT
1 TATCGTATAATTCT
39452 TAT
1 TAT
39455 ATATATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:47061 original size:32 final size:32
Alignment explanation
Indices: 47020--47080 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
47010 ATCTATTTTC
47020 ATTGTTCAACTCTTTGACAACACGAAAAACCT
1 ATTGTTCAACTCTTTGACAACACGAAAAACCT
*
47052 ATTGTTCAACTCTTTGACAACATGAAAAA
1 ATTGTTCAACTCTTTGACAACACGAAAAA
47081 ACCAAAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (32 bp):
ATTGTTCAACTCTTTGACAACACGAAAAACCT
Found at i:47481 original size:13 final size:14
Alignment explanation
Indices: 47462--47495 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
47452 TACTAAAACT
*
47462 AATAAAATTAATAC
1 AATAAAATAAATAC
47476 -ATAAAATAAATAC
1 AATAAAATAAATAC
47489 AATAAAA
1 AATAAAA
47496 GATAAGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAATAAATAC
Found at i:48379 original size:13 final size:13
Alignment explanation
Indices: 48361--48423 Score: 66
Period size: 13 Copynumber: 5.3 Consensus size: 13
48351 GTAAACTTAG
48361 AATGTATCGATAC
1 AATGTATCGATAC
48374 AATGTATCGATAC
1 AATGTATCGATAC
48387 AATG-A---AT--
1 AATGTATCGATAC
*
48394 AACGTATCGATAC
1 AATGTATCGATAC
*
48407 ATTGTATCGATAC
1 AATGTATCGATAC
48420 AATG
1 AATG
48424 AACAATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
7 3 0.08
8 1 0.03
9 2 0.05
11 2 0.05
12 1 0.03
13 31 0.77
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:48441 original size:33 final size:33
Alignment explanation
Indices: 48365--48441 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
48355 ACTTAGAATG
* * *
48365 TATCGATACAATGTATCGATACAATGAATAACG
1 TATCGATACATTGTATCGATACAATGAACAACA
*
48398 TATCGATACATTGTATCGATACAATGAACAATA
1 TATCGATACATTGTATCGATACAATGAACAACA
48431 TATCGATACAT
1 TATCGATACAT
48442 CTAGGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (33 bp):
TATCGATACATTGTATCGATACAATGAACAACA
Found at i:49133 original size:42 final size:41
Alignment explanation
Indices: 49083--49267 Score: 154
Period size: 41 Copynumber: 4.4 Consensus size: 41
49073 CTTGGGGACT
* * * *
49083 AAAGAAAAAAGGAAATAAAATGCATCATGCCCTTTAAAAAC
1 AAAGGAAAAAGGAAATAAAATGCATCCTGCTCTTTAAGAAC
* ** * * *
49124 AAAGGAAAAAGGAAATTAAATGTGTCCTACTTTTTAAGGAC
1 AAAGGAAAAAGGAAATAAAATGCATCCTGCTCTTTAAGAAC
* *
49165 AAAGGAAAAAGGAGAATAAAATACATCCTGCTCTTTGAGAAC
1 AAAGGAAAAAGGA-AATAAAATGCATCCTGCTCTTTAAGAAC
* * * * *
49207 TATAAGGGAAAAGAAGGAAATGAAATGCGTCCTGCTCTTTGAGGAT
1 -A-AA-GG-AAA-AAGGAAATAAAATGCATCCTGCTCTTTAAGAAC
*
49253 AAAGGAAAAAAGAAA
1 AAAGGAAAAAGGAAA
49268 AAGGTGTCCT
Statistics
Matches: 114, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
41 50 0.44
42 23 0.20
43 3 0.03
44 4 0.04
45 3 0.03
46 26 0.23
47 5 0.04
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (41 bp):
AAAGGAAAAAGGAAATAAAATGCATCCTGCTCTTTAAGAAC
Found at i:49173 original size:83 final size:89
Alignment explanation
Indices: 49078--49264 Score: 210
Period size: 88 Copynumber: 2.2 Consensus size: 89
49068 TGCTCCTTGG
*
49078 GGACTAAA-GAAAAAAGGA-AATAAAATGCATCATGCCCTTTAAAAAC-A-AA-GG-AAA-AAGG
1 GGAC-AAAGGAAAAAAGGAGAATAAAATACATCATGCCCTTTAAAAACTATAAGGGAAAAGAAGG
* * *
49136 AAATTAAATGTGTCCTACTTTTTAA
65 AAATGAAATGCGTCCTACTCTTTAA
* * * *
49161 GGACAAAGG-AAAAAGGAGAATAAAATACATCCTGCTCTTTGAGAACTATAAGGGAAAAGAAGGA
1 GGACAAAGGAAAAAAGGAGAATAAAATACATCATGCCCTTTAAAAACTATAAGGGAAAAGAAGGA
* *
49225 AATGAAATGCGTCCTGCTCTTTGA
66 AATGAAATGCGTCCTACTCTTTAA
*
49249 GGATAAAGGAAAAAAG
1 GGACAAAGGAAAAAAG
49265 AAAAAGGTGT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
82 11 0.13
83 28 0.33
84 1 0.01
85 2 0.02
86 2 0.02
87 3 0.04
88 32 0.38
89 6 0.07
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.20
Consensus pattern (89 bp):
GGACAAAGGAAAAAAGGAGAATAAAATACATCATGCCCTTTAAAAACTATAAGGGAAAAGAAGGA
AATGAAATGCGTCCTACTCTTTAA
Found at i:49379 original size:61 final size:61
Alignment explanation
Indices: 49297--49867 Score: 587
Period size: 61 Copynumber: 9.7 Consensus size: 61
49287 GGCAAAGGAG
* * *
49297 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
**** * * * *
49358 AAAAAGAAAAAATATCTTACTCTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
49418 AAAAGGAAAAGGCGTCCTTCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTAGG-TTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
49478 -----TAAAAGGCGTCCTTCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
49534 ------AAAAGGCGTCCTGCTCTTTGAGGCCTGGGAAA-TGCCACTAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
49589 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTT
* * *
49650 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
49711 AAAAGGAAAATGCATCCTCCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
49773 ------AAAAGGTGTCCTGCTCTTTGAGGACTGGGAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
49828 AAAAGGAATAA-GCGTCCTACTCTTTGAGAATTGAAAAGTG
1 AAAAAGAA-AAGGCGTCCTGCTCTTTGAGGACTGAAAAGTG
49868 AAAGGAGGAA
Statistics
Matches: 444, Mismatches: 45, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
55 119 0.27
56 34 0.08
60 59 0.13
61 203 0.46
62 28 0.06
63 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (61 bp):
AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:49510 original size:27 final size:27
Alignment explanation
Indices: 49425--49510 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
49415 TTTAAAAGGA
49425 AAAGGCGTCCTTCTCTTTGAGGACTGG
1 AAAGGCGTCCTTCTCTTTGAGGACTGG
** ** * ** **
49452 AAAGTGCCACCAACT-TGTGTAGGTTTTA
1 AAAG-GCGTCCTTCTCTTTG-AGGACTGG
49480 AAAGGCGTCCTTCTCTTTGAGGACTGG
1 AAAGGCGTCCTTCTCTTTGAGGACTGG
49507 AAAG
1 AAAG
49511 TGCCACCAAC
Statistics
Matches: 38, Mismatches: 18, Indels: 6
0.61 0.29 0.10
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (27 bp):
AAAGGCGTCCTTCTCTTTGAGGACTGG
Found at i:49825 original size:239 final size:231
Alignment explanation
Indices: 49303--49855 Score: 820
Period size: 239 Copynumber: 2.4 Consensus size: 231
49293 GGAGAAAAGG
* ** *
49303 AAAAGGCGTCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* ** * * *
49368 AATATCTTACTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGCGT
66 GACGTCCTACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGT
* * * * *
49433 CCTTCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTAGGTTTTAAAAGGCGTCCTTCTCTTT
131 CCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGCATCCTCCTCTTT
*
49498 GAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
196 GAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
49534 AAAAGGCGTCCTGCTCTTTGAGGCCTGGGAAATGCCACTAACTTGTGTGGGCTTTAAAAGGAAAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
*
49599 GACGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACG
66 GACGTCCTACTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACG
* *
49664 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGCATCCT
130 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTAGGCTTTAAAA-G-----GCATCCT
49729 CCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
189 CCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
*
49773 AAAAGGTGTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAATA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAA-A
49838 AG-CGTCCTACTCTTTGAG
65 AGACGTCCTACTCTTTGAG
49856 AATTGAAAAG
Statistics
Matches: 288, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
231 76 0.26
232 86 0.30
233 1 0.00
238 19 0.07
239 103 0.36
240 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (231 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
GACGTCCTACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGT
CCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGCATCCTCCTCTTT
GAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:63105 original size:80 final size:79
Alignment explanation
Indices: 62966--63281 Score: 323
Period size: 79 Copynumber: 4.0 Consensus size: 79
62956 ACAACGGGGC
* * * * * * *
62966 TGGAGTATCCCCTGACTATGGAAAATCGGTGTTCTGGAAATAGAATCGAGATTGGAGTATCCCCT
1 TGGAGTATCCCC-GATTATGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCT
*
63031 C-AGAAATAACAGGAT
65 CGA-AAATAACGGGAT
* * * * * *
63046 TGGAGTATCCCTGATTATAGAAAATCGATGTTTTGAAAAATAAAATCGGGGTTGTAGTATCCCCT
1 TGGAGTATCCCCGATTATGGAAAATCGATGTTTT-AGAAATAAAACCGAGGTTGGAGTATCCCCT
* *
63111 CGAAAATAATGGGGT
65 CGAAAATAACGGGAT
* * * * * *
63126 TGGAGCATCCCCGATTGTGGAAAATCGATGCTTTAGAAATAAAGCCAAGGTTGGAGTATCCTCAT
1 TGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCC-CCT
63191 -GAAAATAACGGGAT
65 CGAAAATAACGGGAT
* * * * *
63205 TGGAGTATCCCCGATTGT-GAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCACT
1 TGGAGTATCCCCGATTATGGA-AAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCT
63269 CGAAAATAACGGG
65 CGAAAATAACGGG
63282 GTTCGAGTGT
Statistics
Matches: 194, Mismatches: 37, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
78 3 0.02
79 114 0.59
80 76 0.39
81 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTC
GAAAATAACGGGAT
Found at i:63283 original size:28 final size:29
Alignment explanation
Indices: 63250--63321 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
63240 GAAATAAAAC
63250 CGGGGTTGGAGTATCCACTCGA-AAATAA
1 CGGGGTTGGAGTATCCACTCGAGAAATAA
* * *
63278 CGGGGTTCGAGTGT--TCTCGATGAAATAA
1 CGGGGTTGGAGTATCCACTCGA-GAAATAA
*
63306 CGGTGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
63322 CCAATTATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.15
28 29 0.85
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCACTCGAGAAATAA
Found at i:63421 original size:51 final size:51
Alignment explanation
Indices: 63310--63425 Score: 124
Period size: 51 Copynumber: 2.3 Consensus size: 51
63300 AAATAACGGT
* **
63310 GTTGGAGTATCCCCAATTATGAAAAATAGGTGCTTTGGAAATAAAATTGGA
1 GTTGGAGTATCCCCAATTATGAAAAATAGGTGCTTTAGAAATAAAACCGGA
** * * * ** * *
63361 GTTAAAGTATCCCCGATTGTGGAAAATTTGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCAATTATGAAAAATAGGTGCTTTAGAAATAAAACCGGA
63412 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
63426 TCGGAAATAA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTATGAAAAATAGGTGCTTTAGAAATAAAACCGGA
Found at i:65885 original size:20 final size:20
Alignment explanation
Indices: 65860--65898 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
65850 AAACCTAGAA
65860 GAACAATGTATCGATACAAT
1 GAACAATGTATCGATACAAT
65880 GAACAATGTATCGATACAA
1 GAACAATGTATCGATACAA
65899 ATTGTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (20 bp):
GAACAATGTATCGATACAAT
Found at i:66338 original size:13 final size:13
Alignment explanation
Indices: 66320--66344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66310 CAATTGTGCA
66320 TGTATCGATACAT
1 TGTATCGATACAT
66333 TGTATCGATACA
1 TGTATCGATACA
66345 ATGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:68287 original size:32 final size:33
Alignment explanation
Indices: 68246--68325 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 33
68236 AACGCGATCG
* * *
68246 TATGCTAACTATTATTACTCATTAGTAAGG-CC
1 TATGCTAACTATTATAACCCATTAGTAAGGTCA
* *
68278 TATGCTAACTATAATAACCCGTTAGTAAGGTCA
1 TATGCTAACTATTATAACCCATTAGTAAGGTCA
68311 TATGCTAACTATTAT
1 TATGCTAACTATTAT
68326 CATATGTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 26 0.63
33 15 0.37
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (33 bp):
TATGCTAACTATTATAACCCATTAGTAAGGTCA
Found at i:68356 original size:21 final size:22
Alignment explanation
Indices: 68332--68374 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
68322 TTATCATATG
68332 TTAATGAGGCC-TATGCTAACT
1 TTAATGAGGCCGTATGCTAACT
68353 TTAATGAGGCCGTATGCTAACT
1 TTAATGAGGCCGTATGCTAACT
68375 ATTATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (22 bp):
TTAATGAGGCCGTATGCTAACT
Found at i:68437 original size:32 final size:31
Alignment explanation
Indices: 68386--68445 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
68376 TTATTTTCAA
68386 TTAATAGGCCTATGCTAACTATTGTAACTAG
1 TTAATAGGCCTATGCTAACTATTGTAACTAG
*
68417 TTAATAGGGCTTATGCTAACTATTGTAAC
1 TTAATA-GGCCTATGCTAACTATTGTAAC
68446 CTGTTGGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (31 bp):
TTAATAGGCCTATGCTAACTATTGTAACTAG
Found at i:74128 original size:21 final size:21
Alignment explanation
Indices: 74096--74135 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
74086 AACTATCATA
*
74096 TCTATTTTTAAT-TTATTTTT
1 TCTATTTATAATCTTATTTTT
74116 TCTAGTTTATAATCTTATTT
1 TCTA-TTTATAATCTTATTT
74136 CCCTAATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (21 bp):
TCTATTTATAATCTTATTTTT
Found at i:74308 original size:21 final size:21
Alignment explanation
Indices: 74276--74315 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
74266 AACTATCATA
*
74276 TCTATTTTTAAT-TTATTTTT
1 TCTATTTATAATCTTATTTTT
74296 TCTAGTTTATAATCTTATTT
1 TCTA-TTTATAATCTTATTT
74316 CCCTAATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (21 bp):
TCTATTTATAATCTTATTTTT
Found at i:74337 original size:180 final size:180
Alignment explanation
Indices: 73934--74482 Score: 900
Period size: 184 Copynumber: 3.0 Consensus size: 180
73924 TAAAGAGAGA
*
73934 TAGTTTATAATCTTATTTTCCTAATTAGAGTACTTTAAAACTTTATTCTAAAAAAGAGGTAGTTT
1 TAGTTTATAATCTTATTTCCCTAATTAGAGTACTTTAAAACTTTATTCTAAAAAAGAGGTAGTTT
* * *
73999 CATATAGTTGGATTCCACGTCAACGTAAGAATTCCAAGCCATTTTCCTTCTTCTATCTTCCTTTT
66 CGTATAGTTGGATTCCACGTCAACGTAAGAATTCCAAGTCATTTTCCTTCCTCTATCTT-C---T
*
74064 TTCTTTATCCCTATAAATCTATAACTATCATATCTATTTTTAATTTATTTTTTC
127 TTCTTTATCCCTATAAATCTGTAACTATCATATCTATTTTTAATTTATTTTTTC
*
74118 TAGTTTATAATCTTATTTCCCTAATTAGAGTACTTTAAAACTTTATTCTAAAAAAGAGGTAATTT
1 TAGTTTATAATCTTATTTCCCTAATTAGAGTACTTTAAAACTTTATTCTAAAAAAGAGGTAGTTT
* *
74183 CGTATAGTTGGATTCCACGTCAACATAAAAATTCCAAGTCATTTTCCTTCCTCTATCTTCTTTCT
66 CGTATAGTTGGATTCCACGTCAACGTAAGAATTCCAAGTCATTTTCCTTCCTCTATCTTCTTTCT
74248 TTATCCCTATAAATCTGTAACTATCATATCTATTTTTAATTTATTTTTTC
131 TTATCCCTATAAATCTGTAACTATCATATCTATTTTTAATTTATTTTTTC
* * *
74298 TAGTTTATAATCTTATTTCCCTAATTAGGGTACTTTAAAACTTTATTTTAAAAAATAGGTAGTTT
1 TAGTTTATAATCTTATTTCCCTAATTAGAGTACTTTAAAACTTTATTCTAAAAAAGAGGTAGTTT
*
74363 CGTATAGTTGGATTCCATGTCAACGTAAGAATTCCAAGTCATTTTCCTTCCTCTATCTTCCTTCT
66 CGTATAGTTGGATTCCACGTCAACGTAAGAATTCCAAGTCATTTTCCTTCCTCTA---T-CTTCT
* *
74428 TTCTTTATCCTTATAAATCTGTAACTATCATATCTTTTTTTAATTTATTTTTTC
127 TTCTTTATCCCTATAAATCTGTAACTATCATATCTATTTTTAATTTATTTTTTC
74482 T
1 T
74483 TTTACCAATA
Statistics
Matches: 344, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
180 167 0.49
183 2 0.01
184 175 0.51
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.46
Consensus pattern (180 bp):
TAGTTTATAATCTTATTTCCCTAATTAGAGTACTTTAAAACTTTATTCTAAAAAAGAGGTAGTTT
CGTATAGTTGGATTCCACGTCAACGTAAGAATTCCAAGTCATTTTCCTTCCTCTATCTTCTTTCT
TTATCCCTATAAATCTGTAACTATCATATCTATTTTTAATTTATTTTTTC
Found at i:76505 original size:24 final size:25
Alignment explanation
Indices: 76478--76534 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
76468 TCAAAAATTA
*
76478 TATAAAAATAAAATTA-AAAAAAAT
1 TATAAAAATAAAAATAGAAAAAAAT
* * *
76502 TAT-AATATAAAAATAGCAAAAAGT
1 TATAAAAATAAAAATAGAAAAAAAT
76526 TATAAAAAT
1 TATAAAAAT
76535 TAATATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 10 0.38
24 12 0.46
25 4 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (25 bp):
TATAAAAATAAAAATAGAAAAAAAT
Found at i:77412 original size:39 final size:39
Alignment explanation
Indices: 77349--77424 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
77339 GGGTAGTTTT
* *
77349 AGGTATAGCATGAAGTATACAAAGATGGATGAGTGATCA
1 AGGTATAGCATGAAATATACAAAGATGGATAAGTGATCA
* **
77388 AGGTATGGCATGAAATATTTAAAGATGGATAAGTGAT
1 AGGTATAGCATGAAATATACAAAGATGGATAAGTGAT
77425 TTAGTAGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.41, C:0.05, G:0.28, T:0.26
Consensus pattern (39 bp):
AGGTATAGCATGAAATATACAAAGATGGATAAGTGATCA
Found at i:80728 original size:11 final size:11
Alignment explanation
Indices: 80711--80744 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
80701 TGGAAAATTA
80711 AATAATTATTT
1 AATAATTATTT
*
80722 GATAATTATTT
1 AATAATTATTT
*
80733 AATAAATATTT
1 AATAATTATTT
80744 A
1 A
80745 CATGAAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
AATAATTATTT
Found at i:82239 original size:23 final size:23
Alignment explanation
Indices: 82191--82240 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
82181 TTTTAAATCT
*
82191 TTTGAATTTTTAATTTTTTTTTAA
1 TTTGAATTTTTAA-TTTTTTTAAA
82215 TTTGAATTTTATAA-TTTTTTAAA
1 TTTGAATTTT-TAATTTTTTTAAA
82238 TTT
1 TTT
82241 ATTATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 11 0.46
24 10 0.42
25 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTGAATTTTTAATTTTTTTAAA
Found at i:82905 original size:28 final size:29
Alignment explanation
Indices: 82861--82920 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
82851 TTTAAAAGTT
82861 AATGAAAAGTTATAA-TTACATTGAAGGA
1 AATGAAAAGTTATAATTTACATTGAAGGA
* *
82889 AATGAAAACTT-TAAATTTTACATTTAAGGA
1 AATGAAAAGTTAT-AA-TTTACATTGAAGGA
82919 AA
1 AA
82921 CTGTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 12 0.44
30 14 0.52
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (29 bp):
AATGAAAAGTTATAATTTACATTGAAGGA
Found at i:84334 original size:20 final size:21
Alignment explanation
Indices: 84309--84347 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
84299 TCTAATTAGT
84309 TTTGAAGTTTAATT-TTTTGG
1 TTTGAAGTTTAATTATTTTGG
84329 TTTGAAGTTTAATTATTTT
1 TTTGAAGTTTAATTATTTT
84348 TGAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (21 bp):
TTTGAAGTTTAATTATTTTGG
Found at i:84738 original size:16 final size:16
Alignment explanation
Indices: 84705--84745 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
84695 AATAAAATTG
*
84705 AAATAAATTATTTCATA
1 AAATAAA-TATTTAATA
84722 AAATAAATATTTAATA
1 AAATAAATATTTAATA
*
84738 AATTAAAT
1 AAATAAAT
84746 TTAACTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAAATATTTAATA
Found at i:86113 original size:36 final size:36
Alignment explanation
Indices: 86073--86145 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
86063 TCGGATCTTG
86073 GCTAACCTCATGCTTTGTATATGTTTCTTCTTGTTA
1 GCTAACCTCATGCTTTGTATATGTTTCTTCTTGTTA
*
86109 GCTAACCTCATGTTTTGTATATGTTTCTTCTTGTTA
1 GCTAACCTCATGCTTTGTATATGTTTCTTCTTGTTA
86145 G
1 G
86146 TCCAACATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.16, C:0.18, G:0.15, T:0.51
Consensus pattern (36 bp):
GCTAACCTCATGCTTTGTATATGTTTCTTCTTGTTA
Found at i:90659 original size:18 final size:19
Alignment explanation
Indices: 90636--90682 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
90626 AACCCCAAAT
90636 TAAATTAAAAACAAAAAA-
1 TAAATTAAAAACAAAAAAC
* *
90654 TAAATTATAATATAAAAAAC
1 TAAATTA-AAAACAAAAAAC
90674 T-AATTAAAA
1 TAAATTAAAA
90683 GAGTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 9 0.38
19 14 0.58
20 1 0.04
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAATTAAAAACAAAAAAC
Found at i:96622 original size:2 final size:2
Alignment explanation
Indices: 96610--96674 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
96600 CTGGGTTATG
* * * *
96610 TA TA TA CA TA TA TA TA TA TG TA TA TA CA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
96652 TA TA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
96675 GATGTGCTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:96631 original size:20 final size:20
Alignment explanation
Indices: 96606--96670 Score: 112
Period size: 20 Copynumber: 3.1 Consensus size: 20
96596 TTTTCTGGGT
96606 TATGTATATACATATATATA
1 TATGTATATACATATATATA
96626 TATGTATATACATATATATATA
1 TATGTATATAC--ATATATATA
96648 TATGTATATACATATATATA
1 TATGTATATACATATATATA
96668 TAT
1 TAT
96671 ATATGATGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
20 23 0.53
22 20 0.47
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
TATGTATATACATATATATA
Found at i:96642 original size:22 final size:22
Alignment explanation
Indices: 96606--96672 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
96596 TTTTCTGGGT
96606 TATGTATATAC--ATATATATA
1 TATGTATATACATATATATATA
96626 TATGTATATACATATATATATA
1 TATGTATATACATATATATATA
96648 TATGTATATACATATATATATA
1 TATGTATATACATATATATATA
96670 TAT
1 TAT
96673 ATGATGTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.24
22 34 0.76
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
TATGTATATACATATATATATA
Found at i:97145 original size:2 final size:2
Alignment explanation
Indices: 97138--97170 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
97128 TATCAAAATT
97138 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
97171 GGTTTTATAT
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:99438 original size:30 final size:31
Alignment explanation
Indices: 99365--99446 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 31
99355 ATAAAATCAA
* *
99365 TAAATAATTAAAAAATTTTACATATTATCTTAT
1 TAAATAATGATAAAATTTTACATATTA--TTAT
*
99398 TATATAATGATAAAATTTTACATATTA-TAT
1 TAAATAATGATAAAATTTTACATATTATTAT
*
99428 TAAATTATGAT-AAATTTTA
1 TAAATAATGATAAAATTTTA
99447 TAAATTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 8 0.18
30 12 0.27
33 24 0.55
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (31 bp):
TAAATAATGATAAAATTTTACATATTATTAT
Found at i:99453 original size:29 final size:30
Alignment explanation
Indices: 99365--99459 Score: 84
Period size: 33 Copynumber: 3.1 Consensus size: 30
99355 ATAAAATCAA
* * *
99365 TAAATAATTAAAAAATTTTACATATTATCTTAT
1 TAAATAATGATAAAATTTTACAAATTA---TAT
* *
99398 TATATAATGATAAAATTTTACATATTATAT
1 TAAATAATGATAAAATTTTACAAATTATAT
* * *
99428 TAAATTATGAT-AAATTTTATAAATTAAAT
1 TAAATAATGATAAAATTTTACAAATTATAT
99457 TAA
1 TAA
99460 TAAAATTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.33
30 12 0.22
33 24 0.44
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (30 bp):
TAAATAATGATAAAATTTTACAAATTATAT
Found at i:101046 original size:18 final size:18
Alignment explanation
Indices: 101023--101080 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
101013 TTTAAAATAT
101023 TATATTTATAAATTTTAA
1 TATATTTATAAATTTTAA
* *
101041 TATATTAAT-AA--TTCA
1 TATATTTATAAATTTTAA
*
101056 TAT-TATATAAATTTTAA
1 TATATTTATAAATTTTAA
101073 TATATTTA
1 TATATTTA
101081 AATTTTCGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 3 0.10
15 8 0.27
17 8 0.27
18 11 0.37
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTTATAAATTTTAA
Found at i:101046 original size:32 final size:32
Alignment explanation
Indices: 101005--101096 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 32
100995 TTTATGTCAG
*
101005 TAATCATATTTAAAATATTATATT-TATAAATTT
1 TAAT-ATATTTAAAAT-TCATATTATATAAATTT
101038 TAATATA-TTAATAATTCATATTATATAAATTT
1 TAATATATTTAA-AATTCATATTATATAAATTT
* *
101070 TAATATATTTAAATTTTCGTATTATAT
1 TAATATATTTAAA-ATTCATATTATAT
101097 TTTAATTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
31 10 0.19
32 23 0.44
33 19 0.37
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (32 bp):
TAATATATTTAAAATTCATATTATATAAATTT
Found at i:102057 original size:86 final size:85
Alignment explanation
Indices: 101949--102118 Score: 225
Period size: 86 Copynumber: 2.0 Consensus size: 85
101939 ATTTATTATA
* * *
101949 TTTAATATTTGTTTAAAATTAAAATAACTTTTAAATATTTAAAATTTTATTTAAATGAACT-AGC
1 TTTAATATTTATTTAAAATTAAAATAACTTTTAAATACTTAAAATTTTATTT-AATAAACTGAGC
*
102013 AAGTTGAATTGAAAATCAAAAG
65 AA-TTGAATTGAAAATAAAAAG
* * * * * *
102035 TTTAATATTTATTTGACATTAAAATTACTTTTAAATACTTAAACTTTTATTTAATAAACTGATCG
1 TTTAATATTTATTTAAAATTAAAATAACTTTTAAATACTTAAAATTTTATTTAATAAACTGAGCA
102100 ATTGAATTGAAAATAAAAA
66 ATTGAATTGAAAATAAAAA
102119 TCTATTGATT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
85 24 0.33
86 49 0.67
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (85 bp):
TTTAATATTTATTTAAAATTAAAATAACTTTTAAATACTTAAAATTTTATTTAATAAACTGAGCA
ATTGAATTGAAAATAAAAAG
Found at i:106194 original size:19 final size:20
Alignment explanation
Indices: 106167--106205 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
106157 ATATATACAA
*
106167 AAATATAAAACTTATAAAAT
1 AAATATAAAAATTATAAAAT
*
106187 AAAT-TAAAAATTTTAAAAT
1 AAATATAAAAATTATAAAAT
106206 TGATTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAAAAATTATAAAAT
Found at i:109412 original size:11 final size:11
Alignment explanation
Indices: 109398--109422 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
109388 AATTTTTAAT
109398 ATTAAATCAAA
1 ATTAAATCAAA
109409 ATTAAATCAAA
1 ATTAAATCAAA
109420 ATT
1 ATT
109423 TGAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTAAATCAAA
Found at i:109571 original size:31 final size:31
Alignment explanation
Indices: 109493--109572 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
109483 AACCACAATC
*
109493 GCATAAGTGTAGAGACTAAAGTCACATTTTG
1 GCATAAGTATAGAGACTAAAGTCACATTTTG
* * *
109524 GCATAAGCATAGAGACTAAATTCTCATTTTG
1 GCATAAGTATAGAGACTAAAGTCACATTTTG
** *
109555 GTGTAAGTATAAAGACTA
1 GCATAAGTATAGAGACTA
109573 GTAAAATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (31 bp):
GCATAAGTATAGAGACTAAAGTCACATTTTG
Found at i:111270 original size:20 final size:20
Alignment explanation
Indices: 111224--111262 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
111214 ATGAGTAATT
*
111224 TAATGAATTGATAAAAAATA
1 TAATTAATTGATAAAAAATA
*
111244 TATTTAATTGATAAAAAAT
1 TAATTAATTGATAAAAAAT
111263 TACATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (20 bp):
TAATTAATTGATAAAAAATA
Found at i:111308 original size:19 final size:20
Alignment explanation
Indices: 111281--111322 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
111271 ATATGTTAAA
*
111281 ATTAGTTTTATATTAATTTT
1 ATTAGTTTTATATTAATTAT
*
111301 ATTA-TTTTTTATTAATTAT
1 ATTAGTTTTATATTAATTAT
111320 ATT
1 ATT
111323 TTTATAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTAGTTTTATATTAATTAT
Found at i:111812 original size:17 final size:18
Alignment explanation
Indices: 111767--111841 Score: 57
Period size: 19 Copynumber: 4.1 Consensus size: 18
111757 ATATTAACGT
*
111767 TATAAATATTAATATCATAA
1 TATAATTATTAATAT--TAA
*
111787 T-GAATTATTAATATTAA
1 TATAATTATTAATATTAA
* *
111804 TTTAA-TATTTATA-TATA
1 TATAATTATTAATATTA-A
111821 TATAATTATTTAATATTAA
1 TATAATTA-TTAATATTAA
111840 TA
1 TA
111842 ACATATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
16 2 0.05
17 16 0.36
18 4 0.09
19 19 0.43
20 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TATAATTATTAATATTAA
Found at i:111832 original size:25 final size:26
Alignment explanation
Indices: 111803--111851 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
111793 ATTAATATTA
* *
111803 ATTTAATATTTAT-ATATATATAATT
1 ATTTAATATTAATAACATATATAATT
111828 ATTTAATATTAATAACATATATAA
1 ATTTAATATTAATAACATATATAA
111852 CCTATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAATATTAATAACATATATAATT
Found at i:111834 original size:36 final size:36
Alignment explanation
Indices: 111771--111840 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
111761 TAACGTTATA
111771 AATATTAATATCATAATGAATTATTAATATTAATTT
1 AATATTAATATCATAATGAATTATTAATATTAATTT
*
111807 AATATTTATAT-ATATAT-AATTATTTAATATTAAT
1 AATATTAATATCATA-ATGAATTA-TTAATATTAAT
111841 AACATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 8 0.26
36 23 0.74
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (36 bp):
AATATTAATATCATAATGAATTATTAATATTAATTT
Found at i:111842 original size:17 final size:17
Alignment explanation
Indices: 111784--111842 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
111774 ATTAATATCA
111784 TAATGAATTA-TTAATAT
1 TAAT-AATTATTTAATAT
111801 TAATTTAA-TATTT-ATAT
1 TAA--TAATTATTTAATAT
111818 ATATATAATTATTTAATAT
1 -TA-ATAATTATTTAATAT
111837 TAATAA
1 TAATAA
111843 CATATATAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
17 16 0.46
18 13 0.37
19 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAATAATTATTTAATAT
Found at i:111956 original size:12 final size:13
Alignment explanation
Indices: 111939--112001 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 13
111929 AATATGATAT
111939 TATTAAATA-AAA
1 TATTAAATATAAA
111951 TATTAAA-ATAAA
1 TATTAAATATAAA
*
111963 TAATAAATATCGAATA
1 TATTAAATAT--AA-A
111979 TATTAAATAATAAA
1 TATTAAAT-ATAAA
*
111993 TAATAAATA
1 TATTAAATA
112002 ATTAATAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
11 1 0.02
12 16 0.38
13 3 0.07
14 8 0.19
15 4 0.10
16 8 0.19
17 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:111957 original size:28 final size:28
Alignment explanation
Indices: 111907--111960 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
111897 TATAATTAAT
*
111907 ATATTATTATAATATAAGATAAAATATG
1 ATATTATTATAATAAAAGATAAAATATG
*
111935 ATATTATTA-AATAAAATATTAAAATA
1 ATATTATTATAATAAAAGA-TAAAATA
111961 AATAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (28 bp):
ATATTATTATAATAAAAGATAAAATATG
Found at i:111969 original size:7 final size:7
Alignment explanation
Indices: 111957--112017 Score: 61
Period size: 7 Copynumber: 8.3 Consensus size: 7
111947 AAAATATTAA
111957 AATAAAT
1 AATAAAT
111964 AATAAAT
1 AATAAAT
111971 -ATCGAATAT
1 AAT--AA-AT
*
111980 ATTAAAT
1 AATAAAT
111987 AATAAAT
1 AATAAAT
111994 AATAAAT
1 AATAAAT
*
112001 AATTAAT
1 AATAAAT
112008 AACTAAAT
1 AA-TAAAT
112016 AA
1 AA
112018 ATATATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
6 2 0.04
7 30 0.67
8 10 0.22
9 2 0.04
10 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (7 bp):
AATAAAT
Found at i:112048 original size:41 final size:41
Alignment explanation
Indices: 112003--112087 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
111993 TAATAAATAA
*
112003 TTAATAACTAAATAA-A-TATATTTATTAAT-TATTTATTATAT
1 TTAAT-ACTAAA-AATATTATATTTAATAATATATTTATT-TAT
* *
112044 TTAATATTAAAAATATTATATTTAATATTATATTTATTTAT
1 TTAATACTAAAAATATTATATTTAATAATATATTTATTTAT
112085 TTA
1 TTA
112088 TTAATTAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
39 2 0.05
40 6 0.16
41 22 0.58
42 8 0.21
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (41 bp):
TTAATACTAAAAATATTATATTTAATAATATATTTATTTAT
Found at i:112070 original size:12 final size:12
Alignment explanation
Indices: 112036--112079 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
112026 ATTAATTATT
112036 TATTATATTTAA
1 TATTATATTTAA
*
112048 TATTA-A--AAA
1 TATTATATTTAA
112057 TATTATATTTAA
1 TATTATATTTAA
112069 TATTATATTTA
1 TATTATATTTA
112080 TTTATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.26
10 1 0.04
11 1 0.04
12 18 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTATATTTAA
Found at i:112094 original size:21 final size:21
Alignment explanation
Indices: 112019--112087 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
112009 ACTAAATAAA
* *
112019 TATATTTATTAAT-TATTTAT
1 TATATTTAATATTATATTTAT
* **
112039 TATATTTAATATTAAAAATAT
1 TATATTTAATATTATATTTAT
112060 TATATTTAATATTATATTTAT
1 TATATTTAATATTATATTTAT
112081 T-TATTTA
1 TATATTTA
112088 TTAATTAACC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATTTAATATTATATTTAT
Found at i:112467 original size:17 final size:18
Alignment explanation
Indices: 112430--112528 Score: 66
Period size: 17 Copynumber: 5.4 Consensus size: 18
112420 TATTTAAGAA
112430 ATATTAATTAATAAAATT
1 ATATTAATTAATAAAATT
112448 ATATT-ATTAATAATAA-T
1 ATATTAATTAATAA-AATT
*
112465 ATATAAATTTAAATATAAATAAT
1 ATATTAA-TT-AATA-AAAT--T
*
112488 ATATTAAAT-ATAAATATT
1 ATATTAATTAATAAA-ATT
112506 ATATT-A-TAATTAAAATT
1 ATATTAATTAA-TAAAATT
112523 -TATTAA
1 ATATTAA
112529 ATATATTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 25
0.70 0.03 0.27
Matches are distributed among these distances:
16 5 0.08
17 19 0.29
18 18 0.27
19 4 0.06
20 11 0.17
21 1 0.02
22 1 0.02
23 7 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAATTAATAAAATT
Found at i:112519 original size:24 final size:24
Alignment explanation
Indices: 112459--112504 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
112449 TATTATTAAT
*
112459 AATAATATA-TAAATTTAAATATA
1 AATAATATATTAAATATAAATATA
112482 AATAATATATTAAATATAAATAT
1 AATAATATATTAAATATAAATAT
112505 TATATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAATATATTAAATATAAATATA
Found at i:112803 original size:6 final size:6
Alignment explanation
Indices: 112792--112816 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
112782 AGAGAAAATT
112792 GACATG GACATG GACATG GACATG G
1 GACATG GACATG GACATG GACATG G
112817 TCTTGAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GACATG
Found at i:122777 original size:10 final size:10
Alignment explanation
Indices: 122762--122791 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
122752 TATATGTGTG
122762 TGTATATATA
1 TGTATATATA
*
122772 TGTATATGTA
1 TGTATATATA
122782 TGTATATATA
1 TGTATATATA
122792 GTCAGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TGTATATATA
Found at i:124948 original size:34 final size:34
Alignment explanation
Indices: 124910--124999 Score: 83
Period size: 35 Copynumber: 2.6 Consensus size: 34
124900 AATTCATACA
*
124910 GAAAGGAATAGAATATAGATTAGTACTTC-TAGCT
1 GAAAGGAATAGAATATAGATTAGCACTTCAT-GCT
* * *
124944 GAAAGGGATTAGAACATATATTAGCACTTCATGCT
1 GAAA-GGAATAGAATATAGATTAGCACTTCATGCT
* * * *
124979 GAATGGGATTGAATCTAGATT
1 GAAAGGAATAGAATATAGATT
125000 TGAGTCCATG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
34 15 0.35
35 27 0.63
36 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (34 bp):
GAAAGGAATAGAATATAGATTAGCACTTCATGCT
Found at i:124987 original size:35 final size:35
Alignment explanation
Indices: 124910--124988 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
124900 AATTCATACA
* * *
124910 GAAA-GGAATAGAATATAGATTAGTACTTCTAGCT
1 GAAAGGGATTAGAACATAGATTAGCACTTCTAGCT
*
124944 GAAAGGGATTAGAACATATATTAGCACTTC-ATGCT
1 GAAAGGGATTAGAACATAGATTAGCACTTCTA-GCT
*
124979 GAATGGGATT
1 GAAAGGGATT
124989 GAATCTAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (35 bp):
GAAAGGGATTAGAACATAGATTAGCACTTCTAGCT
Found at i:127849 original size:2 final size:2
Alignment explanation
Indices: 127842--127873 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127832 GAGAGCATGT
127842 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
127874 ATTTCTCTTT
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):
TA
Found at i:128486 original size:20 final size:20
Alignment explanation
Indices: 128458--128503 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
128448 TTTAAATTAT
* *
128458 AATATTTTTAAATTTTAAA-A
1 AATAATTTT-AATATTAAATA
128478 AATAATTTTAATATTAAATA
1 AATAATTTTAATATTAAATA
128498 AATAAT
1 AATAAT
128504 AAATATAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATTTTAATATTAAATA
Found at i:133818 original size:16 final size:17
Alignment explanation
Indices: 133797--133843 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
133787 ATTAGCTGAA
133797 AAAATTAAATATAT-TT
1 AAAATTAAATATATATT
133813 AAAATTAAAATTATATATT
1 AAAATT-AAA-TATATATT
133832 ATAAA-TAAATAT
1 A-AAATTAAATAT
133844 TATAAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.22
17 6 0.22
18 8 0.30
19 4 0.15
20 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTAAATATATATT
Found at i:133837 original size:20 final size:18
Alignment explanation
Indices: 133797--133847 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
133787 ATTAGCTGAA
133797 AAAATT-AAA-TATATTT
1 AAAATTAAAATTATATTT
133813 AAAATTAAAATTATATATT
1 AAAATTAAAATTATAT-TT
133832 ATAAA-TAAATATTATA
1 A-AAATTAAA-ATTATA
133848 AATGTTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.20
17 3 0.10
18 5 0.17
19 7 0.23
20 9 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTAAAATTATATTT
Found at i:133888 original size:14 final size:14
Alignment explanation
Indices: 133871--133912 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
133861 ATGATTTTAA
*
133871 ATATTAAATATTAT
1 ATATTAAATATAAT
* *
133885 ATATAAAATAAAAT
1 ATATTAAATATAAT
133899 ATATTAAATATAAT
1 ATATTAAATATAAT
133913 TTTTATATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATTAAATATAAT
Found at i:134775 original size:74 final size:76
Alignment explanation
Indices: 134688--134835 Score: 237
Period size: 77 Copynumber: 2.0 Consensus size: 76
134678 ACTTATTGAC
* *
134688 TAATTTGATCAAAATA-ATTATATATACATGAAATA-TAATTTTAAAATTTAATAAATAACACAT
1 TAATTTGATCAAAATATATTATATATACATAAAAAATTAATTTTAAAATTTAATAAATAACACAT
134751 AATAAATATCT
66 AATAAATATCT
* *
134762 TAATTTGATCAAAATATTTTTATATATACATAAAAAATTAATTTTAAAATTTAATAAATAACATA
1 TAATTTGATCAAAATA-TATTATATATACATAAAAAATTAATTTTAAAATTTAATAAATAACACA
134827 TAATAAATA
65 TAATAAATA
134836 ATTAATATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
74 16 0.24
76 16 0.24
77 35 0.52
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.39
Consensus pattern (76 bp):
TAATTTGATCAAAATATATTATATATACATAAAAAATTAATTTTAAAATTTAATAAATAACACAT
AATAAATATCT
Found at i:134826 original size:33 final size:35
Alignment explanation
Indices: 134718--134833 Score: 90
Period size: 42 Copynumber: 3.1 Consensus size: 35
134708 TATATACATG
134718 AAATATAATTTTAAAATTTAATAAATAACACATAATA
1 AAAT-TAATTTTAAAATTTAATAAAT-ACACATAATA
** * *
134755 AATATCTTAATTTGATCAAAATATTTTTATATATACATAA-A
1 AA-A--TTAATTT--T-AAAAT-TTAATAAATACACATAATA
*
134796 AAATTAATTTTAAAATTTAATAAATAACATATAATA
1 AAATTAATTTTAAAATTTAATAAAT-ACACATAATA
134832 AA
1 AA
134834 TAATTAATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
34 6 0.10
35 11 0.18
36 4 0.07
37 2 0.03
38 8 0.13
39 6 0.10
40 2 0.03
41 4 0.07
42 12 0.20
43 6 0.10
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (35 bp):
AAATTAATTTTAAAATTTAATAAATACACATAATA
Found at i:134845 original size:23 final size:23
Alignment explanation
Indices: 134819--134871 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
134809 AATTTAATAA
134819 ATAACATATA-ATAAATAATTAAT
1 ATAA-ATATATATAAATAATTAAT
* * *
134842 ATAAGTATATATTAATATTTAAT
1 ATAAATATATATAAATAATTAAT
134865 ATAAATA
1 ATAAATA
134872 CAAGAAATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
ATAAATATATATAAATAATTAAT
Found at i:136952 original size:16 final size:16
Alignment explanation
Indices: 136931--136965 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
136921 ATTTGAATTT
*
136931 TAATTATTTATACAAA
1 TAATTAGTTATACAAA
*
136947 TAATTAGTTATACTAA
1 TAATTAGTTATACAAA
136963 TAA
1 TAA
136966 ATTTTAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (16 bp):
TAATTAGTTATACAAA
Found at i:142050 original size:58 final size:60
Alignment explanation
Indices: 141961--142073 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 60
141951 TACCACTATG
*
141961 TTTTCATGCATATTAAGGAAAATTATATAAATTCATTCATTTTAGGACCATTTTAATCAT
1 TTTTCATGCATATTAAGGAAAATTATATAAATTCATGCATTTTAGGACCATTTTAATCAT
** * **
142021 TTTTCATG-AT-TTAAGGACTATTATGTAAATTCATGCATTTTAGGGTCATTTTA
1 TTTTCATGCATATTAAGGAAAATTATATAAATTCATGCATTTTAGGACCATTTTA
142074 GTTATTTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 37 0.79
59 2 0.04
60 8 0.17
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (60 bp):
TTTTCATGCATATTAAGGAAAATTATATAAATTCATGCATTTTAGGACCATTTTAATCAT
Found at i:142131 original size:17 final size:18
Alignment explanation
Indices: 142099--142132 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
142089 TTAAGGTTGT
*
142099 TTTAGTCATTTTTTATGA
1 TTTAGTCATTTATTATGA
142117 TTTAGT-ATTTATTATG
1 TTTAGTCATTTATTATG
142133 CAATTTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.62
Consensus pattern (18 bp):
TTTAGTCATTTATTATGA
Found at i:142190 original size:59 final size:58
Alignment explanation
Indices: 142098--142375 Score: 198
Period size: 54 Copynumber: 4.9 Consensus size: 58
142088 TTTAAGGTTG
** * ** *
142098 TTTTAGTCATTTTTTATGATTTAGTATTTATTATGCAATTTTATGCATTTTAGGA-CTA
1 TTTTAGTCATTTTCCATGATTTAGGAACTATTATGCAATTTCATGCATTTTAGGATC-A
* * * *
142156 TTTTAGTCATTTTTTCATGATTTAGGAACTATTATGTAATTTCATGTATTTTAGAATCA
1 TTTTAGTCA-TTTTCCATGATTTAGGAACTATTATGCAATTTCATGCATTTTAGGATCA
* * * * * *
142215 ATTTATTCATTTTCCATGGTTTAGG---GA-TATGTAATTTCATGCTTTTTAGGATCA
1 TTTTAGTCATTTTCCATGATTTAGGAACTATTATGCAATTTCATGCATTTTAGGATCA
* * * * * *
142269 TTTTATTCATTTTCCATGATTTAGGGACCATTATGC-ATAATCATG-ATTTTA-TAGTCT
1 TTTTAGTCATTTTCCATGATTTAGGAACTATTATGCAAT-TTCATGCATTTTAGGA-TCA
* * * *
142326 TTTTAATCATGTTT-CATAATTTA-GAGACTATTATGTAATTTAATGCATTT
1 TTTTAGTCAT-TTTCCATGATTTAGGA-ACTATTATGCAATTTCATGCATTT
142376 AAGTCTTGTA
Statistics
Matches: 177, Mismatches: 31, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
54 47 0.27
55 1 0.01
56 2 0.01
57 39 0.22
58 41 0.23
59 46 0.26
60 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (58 bp):
TTTTAGTCATTTTCCATGATTTAGGAACTATTATGCAATTTCATGCATTTTAGGATCA
Found at i:145021 original size:34 final size:34
Alignment explanation
Indices: 144975--145056 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 34
144965 GTAAAAACCA
*
144975 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAACTACCAAATTTC
*
145009 CCATTTAGTCAACAATGGTAAACTACCAAA--TC
1 CCATTTAATCAACAATGGTAAACTACCAAATTTC
145041 ACCA-TTAATCAACAAT
1 -CCATTTAATCAACAAT
145057 TCTCCCACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 13 0.30
33 3 0.07
34 28 0.64
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATTTC
Found at i:149149 original size:19 final size:19
Alignment explanation
Indices: 149122--149184 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
149112 TCACGTGTAC
* *
149122 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
149141 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
149160 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
149179 AGTACC
1 AGTACC
149185 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:149568 original size:33 final size:34
Alignment explanation
Indices: 149487--149569 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
149477 TGGTAAAAAC
*
149487 CACCATTTAATCAACAATGGTAAGCTACCAAATTT
1 CACCATTTAATCAACAATGGTAAACTACCAAA-TT
*
149522 C-CCATTTAGTCAACAATGGTAAACTACCAAA-T
1 CACCATTTAATCAACAATGGTAAACTACCAAATT
149554 CACCATTTAATCAACA
1 CACCATTTAATCAACA
149570 GTATAATTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 2 0.05
33 13 0.30
34 28 0.64
35 1 0.02
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (34 bp):
CACCATTTAATCAACAATGGTAAACTACCAAATT
Found at i:155083 original size:46 final size:46
Alignment explanation
Indices: 155016--155106 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
155006 AAATAGAACC
*
155016 TTAATAGATAAATGGGTCTAAATATAGAGATATAGATATAATATGA
1 TTAATACATAAATGGGTCTAAATATAGAGATATAGATATAATATGA
155062 TTAATACATAAATGGGTCTAAATATAGAGATATAGATATAATATG
1 TTAATACATAAATGGGTCTAAATATAGAGATATAGATATAATATG
155107 GTATTCTTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.33
Consensus pattern (46 bp):
TTAATACATAAATGGGTCTAAATATAGAGATATAGATATAATATGA
Found at i:155357 original size:21 final size:20
Alignment explanation
Indices: 155333--155371 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
155323 ATTAAAATAT
155333 TATTCTTAT-ATTAATATTTTA
1 TATT-TTATAATTAA-ATTTTA
155354 TATTTTATAATTAAATTT
1 TATTTTATAATTAAATTT
155372 AAATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTATAATTAAATTTTA
Found at i:157268 original size:2 final size:2
Alignment explanation
Indices: 157261--157293 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
157251 AATGAATTTA
157261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
157294 AAAGAAGATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:158750 original size:23 final size:22
Alignment explanation
Indices: 158708--158750 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
158698 ATATAAATTA
**
158708 TAAAATTATAAATATTAATATC
1 TAAAATTATAAATACAAATATC
158730 TAAAATTATTAAATACAAATA
1 TAAAATTA-TAAATACAAATA
158751 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATTATAAATACAAATATC
Found at i:159611 original size:121 final size:111
Alignment explanation
Indices: 159414--159700 Score: 335
Period size: 121 Copynumber: 2.5 Consensus size: 111
159404 TATTATTTTT
159414 AATAAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATGATTT
1 AATAAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATGATTT
*
159479 TTTAAAAATAAAAAATTTAAATAAAAAAGGGT-TTTATTATTATCATTTTTTAATAA
66 TTT-AAAAT----AA---AAAT-AAAAA--GTATATATTATTATCATTTTTTAATAA
* * *
159535 ACTTAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTA
1 AATAAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATGATT-
** * *
159600 TGTTT-TTATAAACATAAAAAGTATATATTATTATTATTTTTTAATAA
65 T-TTTAAAATAAAAATAAAAAGTATATATTATTATCATTTTTTAATAA
* * *
159647 AATAAAAAATAATATTTAATTAAATTTTAAAAAATTTATATTAACAAATTAAAA
1 AATAAAAAATAATATTTAATT-AAGTTTAAAAAAATTACATTAACAAATTAAAA
159701 AATAATATTT
Statistics
Matches: 149, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
111 2 0.01
112 41 0.28
113 34 0.23
114 3 0.02
117 2 0.01
121 63 0.42
122 1 0.01
123 3 0.02
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (111 bp):
AATAAAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATGATTT
TTTAAAATAAAAATAAAAAGTATATATTATTATCATTTTTTAATAA
Found at i:159636 original size:36 final size:35
Alignment explanation
Indices: 159586--159668 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 35
159576 AACAAATTAA
*
159586 AATATTAATTATTATGTTTTT-ATAAACATAAAAAGT
1 AATATTAATTATTAT-TTTTTAATAAA-ATAAAAAAT
159622 ATATATT-ATTATTATTTTTTAATAAAATAAAAAAT
1 A-ATATTAATTATTATTTTTTAATAAAATAAAAAAT
159657 AATATTTAATTA
1 AATA-TTAATTA
159669 AATTTTAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
34 3 0.07
35 16 0.38
36 18 0.43
37 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (35 bp):
AATATTAATTATTATTTTTTAATAAAATAAAAAAT
Found at i:159665 original size:22 final size:22
Alignment explanation
Indices: 159639--159724 Score: 93
Period size: 22 Copynumber: 3.8 Consensus size: 22
159629 ATTATTATTT
*
159639 TTTAATAAAATAAAAAATAATA
1 TTTAATAAATTAAAAAATAATA
*
159661 TTTAATTAAATTTTAAAAAAT-TTA
1 TTTAA-TAAA--TTAAAAAATAATA
*
159685 TATTAACAAATTAAAAAATAATA
1 T-TTAATAAATTAAAAAATAATA
*
159708 TTTAAGAAATTAAAAAA
1 TTTAATAAATTAAAAAA
159725 ATTAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
22 29 0.54
23 7 0.13
24 6 0.11
25 12 0.22
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (22 bp):
TTTAATAAATTAAAAAATAATA
Found at i:159674 original size:35 final size:35
Alignment explanation
Indices: 159587--159662 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 35
159577 ACAAATTAAA
* *
159587 ATATTAATTATTATGTTTTTATAAACATAAAAAGTAT
1 ATATT-ATTATAAT-TTTTTATAAACATAAAAAATAT
*
159624 ATATTATTATTATTTTTTAATAAA-ATAAAAAATA-
1 ATATTATTATAATTTTTT-ATAAACATAAAAAATAT
159658 ATATT
1 ATATT
159663 TAATTAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
34 5 0.14
35 14 0.38
36 13 0.35
37 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (35 bp):
ATATTATTATAATTTTTTATAAACATAAAAAATAT
Found at i:159735 original size:46 final size:47
Alignment explanation
Indices: 159640--159735 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 47
159630 TTATTATTTT
* * * *
159640 TTAATAAAATAAAAAATAATATTTAATTAAATTTTAAAAAATTTATA
1 TTAACAAAATAAAAAATAATATTTAATGAAATTTAAAAAAATTAATA
*
159687 TTAACAAATTAAAAAATAATATTTAA-GAAA-TTAAAAAAATTAATTA
1 TTAACAAAATAAAAAATAATATTTAATGAAATTTAAAAAAATTAA-TA
159733 TTA
1 TTA
159736 TTCAAGTCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 11 0.26
46 8 0.19
47 24 0.56
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (47 bp):
TTAACAAAATAAAAAATAATATTTAATGAAATTTAAAAAAATTAATA
Found at i:162615 original size:82 final size:82
Alignment explanation
Indices: 162478--162640 Score: 308
Period size: 82 Copynumber: 2.0 Consensus size: 82
162468 TGGTTCAATA
*
162478 TCGTTGTTGTCATCACTGTCATCAGATTCAGCACATTTTTTAGGCTTAGTAAAGTCACCAATATC
1 TCGTTGTTGTCATCACTGTCATCAGATTCAACACATTTTTTAGGCTTAGTAAAGTCACCAATATC
162543 ACAACGTGGCTCGACTG
66 ACAACGTGGCTCGACTG
162560 TCGTTGTTGTCATCACTGTCATCAGATTCAACACATTTTTTAGGCTTAGTAAAGTCACCAATATC
1 TCGTTGTTGTCATCACTGTCATCAGATTCAACACATTTTTTAGGCTTAGTAAAGTCACCAATATC
*
162625 ACAATGTGGCTCGACT
66 ACAACGTGGCTCGACT
162641 TTTACGAGTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (82 bp):
TCGTTGTTGTCATCACTGTCATCAGATTCAACACATTTTTTAGGCTTAGTAAAGTCACCAATATC
ACAACGTGGCTCGACTG
Found at i:163732 original size:79 final size:77
Alignment explanation
Indices: 163588--163847 Score: 304
Period size: 79 Copynumber: 3.3 Consensus size: 77
163578 TGGGGATAAC
* * * * * * ** *
163588 AACGGGGATAGAGTATCCCCGATTATGGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTAGAGT
1 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTT-TAAAAATAAAGCCGGGGTTGGAGT
*
163653 ATCCCTTCGGAAAT
65 ATCCC-TCGAAAAT
* * *
163667 AACGGGGTTGAAGTATCCCCGATTGTGAAAAATCGATGCTTTAAAAATAAGGCCGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATG-TTTAAAAATAAAGCCGGGGTTGGAGT
*
163732 ATCTCCGCGAAAAT
65 ATC-CCTCGAAAAT
* * * *
163746 AACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGAT-GTTTAAAAATAAAGCCGGGGTTGGAGT
163811 ATTCCCTCGAAAAT
65 A-TCCCTCGAAAAT
163825 AACGGGGTTGGAGTATCCCCGAT
1 AACGGGGTTGGAGTATCCCCGAT
163848 AAAATAACGG
Statistics
Matches: 155, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
79 149 0.96
80 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (77 bp):
AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTAAAAATAAAGCCGGGGTTGGAGTA
TCCCTCGAAAAT
Found at i:163875 original size:28 final size:28
Alignment explanation
Indices: 163799--163875 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
163789 GAAATAAAGC
163799 CGGGGTTGGAGTATTCCCTCG--AAAATAA
1 CGGGGTTGGAGTA-TCCC-CGATAAAATAA
163827 CGGGGTTGGAGTATCCCCGATAAAATAA
1 CGGGGTTGGAGTATCCCCGATAAAATAA
*
163855 CGGGGTTAGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
163876 TATGAAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 40 0.87
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATAAAATAA
Found at i:163919 original size:107 final size:107
Alignment explanation
Indices: 163723--163919 Score: 268
Period size: 107 Copynumber: 1.8 Consensus size: 107
163713 ATAAGGCCGA
* * * * *
163723 GGTTGGAGTATCTCCGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTT
1 GGTTGGAGTATCCCCGAGAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTT
* * * *
163788 AGAAATAAAGCCGGGGTTGGAGTATTCCCTCGAAAATAACGG
66 AAAAATAAAACCGGAGTTGAAGTATTCCCTCGAAAATAACGG
* * *
163830 GGTTGGAGTATCCCCGATAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATTAATGTTTT
1 GGTTGGAGTATCCCCGAGAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTT
* *
163895 AAAAATAAAATCTGAGTTGAAGTAT
66 AAAAATAAAACCGGAGTTGAAGTAT
163920 ACCCGATTAT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
107 76 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (107 bp):
GGTTGGAGTATCCCCGAGAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTT
AAAAATAAAACCGGAGTTGAAGTATTCCCTCGAAAATAACGG
Found at i:163970 original size:51 final size:52
Alignment explanation
Indices: 163856--163970 Score: 146
Period size: 51 Copynumber: 2.2 Consensus size: 52
163846 ATAAAATAAC
* *
163856 GGGGTTAGAGTATCCCCGATTATGAAAAATTAATGTTTTAAAAATAAAATCT
1 GGGGTTTGAGTATACCCGATTATGAAAAATTAATGTTTTAAAAATAAAATCT
* ** *
163908 -GAG-TTGAAGTATACCCGATTATGAAAAATTTGTGTTTTAGAAATAAAA-CT
1 GGGGTTTG-AGTATACCCGATTATGAAAAATTAATGTTTTAAAAATAAAATCT
163958 GGGGTTTGAGTAT
1 GGGGTTTGAGTAT
163971 CTCTTCGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
50 4 0.08
51 46 0.87
52 3 0.06
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (52 bp):
GGGGTTTGAGTATACCCGATTATGAAAAATTAATGTTTTAAAAATAAAATCT
Found at i:168020 original size:93 final size:87
Alignment explanation
Indices: 167688--168122 Score: 382
Period size: 87 Copynumber: 4.9 Consensus size: 87
167678 TAACATGTAA
* * * * * * *
167688 AATCAATCAAATTTTCTACT-TATAAAAAGAAATTTGATTTTCCA-ATATAATTTATGTATTAGT
1 AATCAATCAACTTTTTTTCTATA-AAAAAG-AATCTGATTCT-CAGATATAATTCATGCATTAGT
* *
167751 CTAATCTTTACAGTCTGATATTTAC
63 CTAATCTTTGCAGTCTGACATTTAC
* *
167776 AATCAATCAACTTTTTTTCTATAAAAAAGAATGC-AATTCTCTGATATAATTCATGCATTAGTCT
1 AATCAATCAACTTTTTTTCTATAAAAAAGAAT-CTGATTCTCAGATATAATTCATGCATTAGTCT
167840 AAT-TCTTGCAGTCTGACATTTAC
65 AATCT-TTGCAGTCTGACATTTAC
* * * *
167863 AATCAATCAACTTTTTTTTTAT-AAAAAGAATCTGATTCTCAAATATAATTCACGCATTAATCTA
1 AATCAATCAACTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTA
* * *
167927 ATCTTTGCAGTTTGATATTTAT
66 ATCTTTGCAGTCTGACATTTAC
* * * *
167949 ACTCAATCAACTTTTCTTTTTTTTCTATAAAAAAGAATCTGATTCTCTGATATAACTCATGCATC
1 AATCAATCAA-----C-TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATT
* * * *
168014 AGTCTAATCCTTGCAGTATAACATTTGC
60 AGTCTAATCTTTGCAGTCTGACATTTAC
* * * *
168042 ACTTAATCAACTTTTCTTTTTTTATTAAAAAAGAAT-TCGATT-TCAGATATAATTCATGTATTA
1 AATCAATCAAC--TT-TTTTTCTA-TAAAAAAGAATCT-GATTCTCAGATATAATTCATGCATTA
*
168105 GTCTCATAC-TTGCAGTCT
61 GTCTAAT-CTTTGCAGTCT
168123 TTCTTTTTTT
Statistics
Matches: 287, Mismatches: 42, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
85 1 0.00
86 63 0.22
87 67 0.23
88 24 0.08
89 5 0.02
90 39 0.14
91 17 0.06
92 10 0.03
93 61 0.21
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (87 bp):
AATCAATCAACTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTA
ATCTTTGCAGTCTGACATTTAC
Done.