Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008661.1 Hibiscus syriacus cultivar Beakdansim tig00111659_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1762280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:5980 original size:20 final size:20
Alignment explanation
Indices: 5915--5983 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
5905 TTTAAAACTT
*
5915 AAATTCGCAACTCGAAAATG
1 AAATTCGCAACGCGAAAATG
**
5935 AAATTCGCAATACG---A--
1 AAATTCGCAACGCGAAAATG
5950 AAA-TCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
5969 AAATTCGCAACGCGA
1 AAATTCGCAACGCGA
5984 TTTTAGTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
14 8 0.21
15 3 0.08
17 2 0.05
19 3 0.08
20 23 0.59
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:6013 original size:20 final size:20
Alignment explanation
Indices: 5990--6027 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5980 GCGATTTTAG
*
5990 TTTTCGCGTTGCAAATTTCA
1 TTTTCGCGTTACAAATTTCA
6010 TTTTCGCGTTACAAATTT
1 TTTTCGCGTTACAAATTT
6028 TGCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.47
Consensus pattern (20 bp):
TTTTCGCGTTACAAATTTCA
Found at i:7633 original size:42 final size:42
Alignment explanation
Indices: 7573--7683 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
7563 TAACCACCCC
* * * ** *
7573 CCACTTTGACACCAAGATCCATAACCTCATCGAGCCTCTTTT
1 CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
*
7615 CCACTTCGACACCGAGATCCATCACCTGATCGAGCCGATTCT
1 CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
* * *
7657 ACACCTCGTCACCGAGATCCATCACCT
1 CCACTTCGACACCGAGATCCATCACCT
7684 ATTCCATCAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.25, C:0.39, G:0.13, T:0.23
Consensus pattern (42 bp):
CCACTTCGACACCGAGATCCATCACCTCATCGAGCCGATTCT
Found at i:7682 original size:21 final size:21
Alignment explanation
Indices: 7624--7683 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
7614 TCCACTTCGA
7624 CACCGAGATCCATCACCTGAT
1 CACCGAGATCCATCACCTGAT
* *
7645 CGAGCCGA-TTCTA-CACCTCG-T
1 C-A-CCGAGATCCATCACCT-GAT
7666 CACCGAGATCCATCACCT
1 CACCGAGATCCATCACCT
7684 ATTCCATCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 13 0.43
22 5 0.17
23 4 0.13
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.20
Consensus pattern (21 bp):
CACCGAGATCCATCACCTGAT
Found at i:7888 original size:21 final size:21
Alignment explanation
Indices: 7798--7913 Score: 67
Period size: 21 Copynumber: 5.5 Consensus size: 21
7788 GTTAGGGGAG
*
7798 TTACGTGATGAGGTCAGTG-CT
1 TTACGTGATGAGGT-AGGGTCT
* *
7819 TTACGTGATGAGGTTGGTTCT
1 TTACGTGATGAGGTAGGGTCT
* * ** * *
7840 CTACGTGACGA-CAATGGTGCA
1 TTACGTGATGAGGTAGGGT-CT
**
7861 TGGCGTGATGAGGTAGGGTCT
1 TTACGTGATGAGGTAGGGTCT
* *
7882 TTACGTGGTGAGGTAGCTGT-T
1 TTACGTGATGAGGTAG-GGTCT
7903 TTACGTGATGA
1 TTACGTGATGA
7914 CAATTGTGCT
Statistics
Matches: 67, Mismatches: 24, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
20 3 0.04
21 58 0.87
22 6 0.09
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.33
Consensus pattern (21 bp):
TTACGTGATGAGGTAGGGTCT
Found at i:7908 original size:63 final size:63
Alignment explanation
Indices: 7801--7922 Score: 151
Period size: 63 Copynumber: 1.9 Consensus size: 63
7791 AGGGGAGTTA
* *
7801 CGTGATGAGGTCAGTGCTTTACGTGATGAGGTTGGTTCTCTACGTGACGACAATGGTGCATGG
1 CGTGATGAGGTCAGGGCTTTACGTGATGAGGTAGGTTCTCTACGTGACGACAATGGTGCATGG
* * *
7864 CGTGATGAGGT-AGGGTCTTTACGTGGTGAGGTAGCTGTT-T-TACGTGATGACAATTGTGC
1 CGTGATGAGGTCAGGG-CTTTACGTGATGAGGTAG--GTTCTCTACGTGACGACAATGGTGC
7923 TTTACGTGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 3 0.06
63 44 0.86
64 1 0.02
65 3 0.06
ACGTcount: A:0.19, C:0.14, G:0.35, T:0.32
Consensus pattern (63 bp):
CGTGATGAGGTCAGGGCTTTACGTGATGAGGTAGGTTCTCTACGTGACGACAATGGTGCATGG
Found at i:7910 original size:42 final size:43
Alignment explanation
Indices: 7864--7960 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 43
7854 TGGTGCATGG
* **
7864 CGTGATGAGGTAGGGT-CTTTACGTGGTGAGGTAGCTGTTTTA
1 CGTGATGAGGTAGGGTGCTTTACGTGGTGACGTAGCTACTTTA
** ** *
7906 CGTGATGA-CAATTGTGCTTTACGTGGTGACGTATCTACTTTA
1 CGTGATGAGGTAGGGTGCTTTACGTGGTGACGTAGCTACTTTA
7948 CGTGATGAGGTAG
1 CGTGATGAGGTAG
7961 CTGTTCTGCG
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
41 3 0.07
42 38 0.90
43 1 0.02
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (43 bp):
CGTGATGAGGTAGGGTGCTTTACGTGGTGACGTAGCTACTTTA
Found at i:8292 original size:21 final size:21
Alignment explanation
Indices: 8266--8398 Score: 130
Period size: 21 Copynumber: 6.3 Consensus size: 21
8256 AAAGAATCCC
*
8266 GATCCACCTACCATTGTTCAG
1 GATCCACCTACCATCGTTCAG
*
8287 GATCCACCTACCATTGTTCAG
1 GATCCACCTACCATCGTTCAG
*
8308 GATCCACCT-CCTATTGTTCAG
1 GATCCACCTACC-ATCGTTCAG
* *
8329 GATTCACCTGA-CATCGTTCAA
1 GATCCACCT-ACCATCGTTCAG
* *
8350 GAGGCC-CCTCCCATCGTTCAG
1 GA-TCCACCTACCATCGTTCAG
*
8371 GATCCACCT-CTCACCGTTCAG
1 GATCCACCTAC-CATCGTTCAG
8392 GATCCAC
1 GATCCAC
8399 ATGCCATACT
Statistics
Matches: 96, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
20 5 0.05
21 89 0.93
22 2 0.02
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (21 bp):
GATCCACCTACCATCGTTCAG
Found at i:10176 original size:6 final size:6
Alignment explanation
Indices: 10167--10201 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10157 TTGTGATTGG
**
10167 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
10202 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:10183 original size:18 final size:18
Alignment explanation
Indices: 10160--10200 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
10150 AAGGCGGTTG
*
10160 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
10178 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
10196 TGATT
1 TGATT
10201 TCCTTTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:12513 original size:24 final size:24
Alignment explanation
Indices: 12475--12528 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12465 CTGAAACATC
*
12475 ATCAAAATCCAAGTATTGACCAAT
1 ATCAAAATCCAAGTATTGACCAAG
* *
12499 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
12523 ATCAAA
1 ATCAAA
12529 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCAAGTATTGACCAAG
Found at i:12542 original size:24 final size:24
Alignment explanation
Indices: 12491--12542 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
12481 ATCCAAGTAT
* * *
12491 TGACCAATATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
12515 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
12539 TGAC
1 TGAC
12543 TAGTACTTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:12675 original size:12 final size:12
Alignment explanation
Indices: 12654--12687 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12644 GGTTGTGGGT
*
12654 TTTGAGATTGTG
1 TTTGATATTGTG
12666 TTTGATATTGTG
1 TTTGATATTGTG
*
12678 TTTGGTATTG
1 TTTGATATTG
12688 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:13498 original size:20 final size:19
Alignment explanation
Indices: 13454--13562 Score: 87
Period size: 20 Copynumber: 5.6 Consensus size: 19
13444 CAAAACATTT
* *
13454 GTGTTGCGAAAATAAAAGC
1 GTGTTGCGAAATTAAAATC
13473 -TGTTGCGAAATTAAAATCC
1 GTGTTGCGAAATTAAAAT-C
* *
13492 GTGTTGCGAATTTGAAAATT
1 GTGTTGCGAAATT-AAAATC
* **
13512 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAA-TC
13532 GTGTTGCG-AATTAGGAAATC
1 GTGTTGCGAAATTA--AAATC
*
13552 TTGTTGCGAAA
1 GTGTTGCGAAA
13563 AGGAAACTTG
Statistics
Matches: 70, Mismatches: 13, Indels: 12
0.74 0.14 0.13
Matches are distributed among these distances:
18 15 0.21
19 8 0.11
20 37 0.53
21 10 0.14
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:13558 original size:40 final size:40
Alignment explanation
Indices: 13473--13689 Score: 147
Period size: 40 Copynumber: 5.4 Consensus size: 40
13463 AAATAAAAGC
** * * *
13473 TGTTGCGAAATTAAAATCCGTGTTGCGAATTTGAAAATTG
1 TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
* * *
13513 AGTTGCGAAAACAAAATTCGTGTTGCGAATTAGGAAATCT
1 TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
* * *
13553 TGTTGCGAAAAGGAAACTT-GTGTTGTGAATTTA-AAAATCG
1 TGTTGCGAAAA-CAAAATTCGTGTTGCGAA-TTAGAAAATCG
* * * **
13593 CGTTGCTAAAA-ATTAATTCGCATTGCGAATTCAG-AAATCG
1 TGTTGCGAAAACA-AAATTCGTGTTGCGAATT-AGAAAATCG
* * * * *
13633 AGTTGC-AAAAAAGAAATTCGCGTTGCGAATTTGAAAATCCA
1 TGTTGCGAAAACA-AAATTCGTGTTGCGAATTAGAAAAT-CG
13674 TGTTGCGAATAACAAA
1 TGTTGCGAA-AACAAA
13690 TTTGCAACAC
Statistics
Matches: 137, Mismatches: 29, Indels: 20
0.74 0.16 0.11
Matches are distributed among these distances:
38 1 0.01
39 10 0.07
40 105 0.77
41 14 0.10
42 4 0.03
43 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (40 bp):
TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
Found at i:13576 original size:20 final size:19
Alignment explanation
Indices: 13507--13577 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
13497 GCGAATTTGA
* **
13507 AAATTGAGTTGCGAAAACA
1 AAATTGTGTTGCGAAAAGG
*
13526 AAATTCGTGTTGCGAATTAGG
1 AAATT-GTGTTGCGAA-AAGG
13547 AAATCT-TGTTGCGAAAAGG
1 AAAT-TGTGTTGCGAAAAGG
13566 AAACTTGTGTTG
1 AAA-TTGTGTTG
13578 TGAATTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 12 0.29
20 24 0.57
21 5 0.12
22 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (19 bp):
AAATTGTGTTGCGAAAAGG
Found at i:13577 original size:80 final size:80
Alignment explanation
Indices: 13486--13689 Score: 207
Period size: 80 Copynumber: 2.5 Consensus size: 80
13476 TGCGAAATTA
* * **
13486 AAATCCGTGTTGCGAATTTGAAAATTGAGTTGCGAAAACAAAATTCGTGTTGCGAATT-AGGAAA
1 AAATTCGTGTTGCGAATTTGAAAATCGAGTTGCGAAAACAAAATTCGCATTGCGAATTCA-GAAA
** * *
13550 TCTTGTTGCGAAAAGG
65 TCGAGTTGCAAAAAAG
* * * * *
13566 AAACTT-GTGTTGTGAATTTAAAAATCGCGTTGCTAAAA-ATTAATTCGCATTGCGAATTCAGAA
1 AAA-TTCGTGTTGCGAATTTGAAAATCGAGTTGCGAAAACA-AAATTCGCATTGCGAATTCAGAA
13629 ATCGAGTTGCAAAAAAG
64 ATCGAGTTGCAAAAAAG
* *
13646 AAATTCGCGTTGCGAATTTGAAAATCCATGTTGCGAATAACAAA
1 AAATTCGTGTTGCGAATTTGAAAATCGA-GTTGCGAA-AACAAA
13690 TTTGCAACAC
Statistics
Matches: 97, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
79 3 0.03
80 81 0.84
81 9 0.09
82 3 0.03
83 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (80 bp):
AAATTCGTGTTGCGAATTTGAAAATCGAGTTGCGAAAACAAAATTCGCATTGCGAATTCAGAAAT
CGAGTTGCAAAAAAG
Found at i:13770 original size:20 final size:20
Alignment explanation
Indices: 13747--13785 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13737 TGCGAAAAAG
13747 AAAATCAAGTTGCGAATTTC
1 AAAATCAAGTTGCGAATTTC
** *
13767 AAAATTGAGTTGTGAATTT
1 AAAATCAAGTTGCGAATTT
13786 GGAAACTGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (20 bp):
AAAATCAAGTTGCGAATTTC
Found at i:17408 original size:2 final size:2
Alignment explanation
Indices: 17401--17445 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
17391 TTATTTAAGT
17401 TA TA TA TA TA 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 TA TA TA TA TA
17443 TA T
1 TA T
17446 TTGACATTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21524 original size:21 final size:21
Alignment explanation
Indices: 21498--21537 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21488 TCGAGTTACG
*
21498 CGCGACGGCCGCAATAGCGTC
1 CGCGACAGCCGCAATAGCGTC
21519 CGCGACAGCCGCAATAGCG
1 CGCGACAGCCGCAATAGCG
21538 CCCCCGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.33, T:0.07
Consensus pattern (21 bp):
CGCGACAGCCGCAATAGCGTC
Found at i:28773 original size:709 final size:711
Alignment explanation
Indices: 26193--28974 Score: 3940
Period size: 711 Copynumber: 3.9 Consensus size: 711
26183 AATTAAGAAC
* *
26193 CCCCTATTTTAAGTTATGTTACGTGAACCACTCCCCCTTATCCCTCACCAAACGCTCTTCTTCTT
1 CCCCTATTTTATGTTATGTTACGTGAACCACTCCCCCTTATCCCTCACCAAACACTCTTCTTCTT
*
26258 CCTTCTACATTTTCTTTCTTCTTCCTCATTTCCAAAGTAGA-GATTTTAA-AGATTTCAAGTGTA
66 CCTTCTACCTTTTCTTTCTTCTTCCTCATTTCCAAAGTAGATGATTTTAAGA-ATTTCAAGTGTA
26321 AGTTGGTTAACCAAGGTAAGAATATTAATCCCCATCCTTCAAGCTTCAATTTAAGTC-CAATTTC
130 AGTTGGTTAACCAAGGTAAGAATATTAATCCCCATCCTTCAAGCTTCAATTTAAGTCTC-ATTTC
* * *
26385 TCAAGTTTTACCCTTTGATTCCAAAAATGGGGTTTTAGGAGGTTAAAAGAATCTATGGATTCTAG
194 TCAAGTTTTACCCTTTGGTTCCAAAAATGGGTTTTTGGGAGGTTAAAAGAATCTATGGATTCTAG
* * * *
26450 TTT-TTTTTATAAATTCAAGTTCTAGGAAATATCTTTATCTCTAATACAACCACCTAGTTAAGTT
259 TTTGTTTTTATAGATTCAAGTTCTAGGAAGTGTCTTTATCTCTAATCCAACCACCTAGTTAAGTT
* *
26514 AGTAATTCATTTTTCTTACCTTTGATTAGTGAAAGAAGTGGGAGAAAGCTCAAAAGCAAGAGGAA
324 AGTAATTCATTTTTCTTACCTTTGATTAGTGAAAGAAGTGGGAGAAAGCTCAAGAGCAAAAGGAA
*
26579 AAAAGAAGTTATTCCTTGGGTGATTTGAGGACTTTTAGCAGCCAAGAATTCAAGGTTACACACTT
389 AAAAGAAGTTATTCCTTGGGTGATTTGAGGACTTTTAGCAGCCAAGAATTCAAGGTAACACACTT
* * * *
26644 ATAACTTCTTTATACCATTTGGGGTCATTAGAAATACAATGTATCTTAAGAGTTAGTTTGAAGCA
454 ATAACTTCTTAAGACCATTTGGGGTCATTAGAAATACAATGTAGCTTAAGATTTAGTTTGAAGCA
* * *
26709 TGTTGAGTGGATTTTATGGTAACTTCTATGTTTAGGGTTATAACATGTTTTTAAGCCTTAATTAT
519 TGTTGAGTGAATTTCATGGTAACTTCTATGTTTAGGGTTATAACATGTTTCTAAGCCTTAATTAT
* ** * * * *
26774 GACCCTTTTATATCACATAAAACTCTAATAATGGTTGGGATATTATTATGGAATTTTTGGGTGGT
584 GACCCCTTTATATCACATAAAACTCTAATAATGGTTGGGACCTCAGTAGGGTATTTTTGGGTGGT
* *
26839 TTAGGGTGTTACATTTAGTACCAAAAGTTTAAATTT-CCCTTGTTCAAATTAAGAGCTAAAAA
649 TTAGGGTGTTACATTTAGTACCAAAAGTGTAAATTTCCCCTTGTTCAAATTAGGAGCTAAAAA
* * * * *
26901 TCCCT-TGATTTATGTTGTGTTACGTGAACCACTCGCCTTTAT-CCTGACCAAACACTCTTCTTC
1 CCCCTAT--TTTATGTTATGTTACGTGAACCACTCCCCCTTATCCCTCACCAAACACTCTTCTTC
* * * * *
26964 TTCCTTATACCTTTTCTTTATTCTTCCTCATTTCCAAAGTAG-GGATTTTAAGTATTTTAAGTGT
64 TTCCTTCTACCTTTTCTTTCTTCTTCCTCATTTCCAAAGTAGATGATTTTAAGAATTTCAAGTGT
* * *
27028 AAGTTGGTTAACCAATGTAAGAATATTAATCCCCGTCCTTCAAGGTTCAATTTAAGTCTCATTTC
129 AAGTTGGTTAACCAAGGTAAGAATATTAATCCCCATCCTTCAAGCTTCAATTTAAGTCTCATTTC
* * *
27093 TTAAGTTTTACCCTTTGGTTCCAAAAATGGGTTTTTTGGGAGGTTAAGAGAATCAATGGATTCTA
194 TCAAGTTTTACCCTTTGGTTCCAAAAATGGG-TTTTTGGGAGGTTAAAAGAATCTATGGATTCTA
27158 GTTTGTTCTTTATAGATTCAAGTTCTAGGAAGTGTCTTTATCTCTAATCCAACCACCTAGTTAAG
258 GTTTGTT-TTTATAGATTCAAGTTCTAGGAAGTGTCTTTATCTCTAATCCAACCACCTAGTTAAG
* * * * * * *
27223 TTATTAAATTC-GTTTTCTTACTTTTAATTAATGAAAGAAGTGGGAGAACGCTCAAG-GATAAAA
322 TTAGT-AATTCATTTTTCTTACCTTTGATTAGTGAAAGAAGTGGGAGAAAGCTCAAGAG-CAAAA
* * *
27286 GGAAAACAGAAGTTA-TCCTTTGGGTAATTTGAGGACTTTTAGCAGCCATGAATTCAAGGTAACA
385 GGAAAAAAGAAGTTATTCC-TTGGGTGATTTGAGGACTTTTAGCAGCCAAGAATTCAAGGTAACA
* * * * **
27350 CACTTATAACTTGTTCATG-CCATTTGGGGTCATTAGAAATGCAATATATTTTAAAGATTTAGTT
449 CACTTATAACTTCTT-AAGACCATTTGGGGTCATTAGAAATACAATGTAGCTT-AAGATTTAGTT
* * *
27414 TGAAGCATGTTTAGTGGAA-TTCATGGTAACTTCTATGTTTAGTGTTATAGCATGTTTCTAAGCC
512 TGAAGCATGTTGAGT-GAATTTCATGGTAACTTCTATGTTTAGGGTTATAACATGTTTCTAAGCC
* * * *
27478 TTAATTATGACCCCTTTATATCATATAAAATTCTAATAATGGTTAGAGACCTCAGTAGGGCATTT
576 TTAATTATGACCCCTTTATATCACATAAAACTCTAATAATGGTT-GGGACCTCAGTAGGGTATTT
* * *
27543 TTTGGTGGTTTATGGTGTTACATTTAGTACCAAAAGTGTAAATTTCCCATTGTTCAAATTAGGAG
640 TTGGGTGGTTTAGGGTGTTACATTTAGTACCAAAAGTGTAAATTTCCCCTTGTTCAAATTAGGAG
27608 -TCAAAAA
705 CT-AAAAA
* * **
27615 -CCCTATTTTATGTTATGTTACGTAAACCACTCCCCCTTATCCGTCACCAAACACTCTTCCGCAT
1 CCCCTATTTTATGTTATGTTACGTGAACCACTCCCCCTTATCCCTCACCAAACACTCTTCTTC-T
* * ** * * *
27679 T-TTTCTACCTTTT-GTTCTTCTTATTTATTTCCAAAGTAGAT-ATTTTAAGGATTTCAAGTTTA
65 TCCTTCTACCTTTTCTTTCTTCTTCCTCATTTCCAAAGTAGATGATTTTAAGAATTTCAAGTGTA
* * * * * *
27741 ATTTGGTTAACCAAGGTAATAATATTAATCTCCATCCTTCAAACATCAATTTAAGTCTCATTTAT
130 AGTTGGTTAACCAAGGTAAGAATATTAATCCCCATCCTTCAAGCTTCAATTTAAGTCTCATTTCT
* * *
27806 CAAGTTTTACCATTTGGTTCCAAAAATGGGTTTTTGGGAGGCTAAAAGAATATATGGATTCTAGT
195 CAAGTTTTACCCTTTGGTTCCAAAAATGGGTTTTTGGGAGGTTAAAAGAATCTATGGATTCTAGT
27871 TTGTTTTTGATAGATTCAAGTTCTAGGAAGTGTCTTTATCTCTAATCCAACCACCTAGTTAAGTT
260 TTGTTTTT-ATAGATTCAAGTTCTAGGAAGTGTCTTTATCTCTAATCCAACCACCTAGTTAAGTT
* * *
27936 AGTAATTCATTTTTCTTACCTTTGATTAGTGAAAGAAATGGGAGAAAGCTCAAGGGAAAAAGGAA
324 AGTAATTCATTTTTCTTACCTTTGATTAGTGAAAGAAGTGGGAGAAAGCTCAAGAGCAAAAGGAA
* *
28001 AAAAGAAGCTATTCCTTGGGTGATTTGAGGACTTTTAGCAGCCAAGAATTCAAGGTCACACACTT
389 AAAAGAAGTTATTCCTTGGGTGATTTGAGGACTTTTAGCAGCCAAGAATTCAAGGTAACACACTT
* * * * * *
28066 ACAATTTATTAAGACCATTTGGGGTCATTATAAATACAATGTAGCTTAAGCTTTAGTTTAAAGCA
454 ATAACTTCTTAAGACCATTTGGGGTCATTAGAAATACAATGTAGCTTAAGATTTAGTTTGAAGCA
28131 TGTTGAGTGAATTTCATGGTAACTTCTATGTTTAGGGTTATAACATGTTTCTAAGCCTTAATTAT
519 TGTTGAGTGAATTTCATGGTAACTTCTATGTTTAGGGTTATAACATGTTTCTAAGCCTTAATTAT
* * * *
28196 GACCCTTTTATATAACATAAAACTCTAATAATGGTTGGGACCTTATTAGGGTATTTTTGGGTGGT
584 GACCCCTTTATATCACATAAAACTCTAATAATGGTTGGGACCTCAGTAGGGTATTTTTGGGTGGT
28261 TTAGGGTGTTACATTTAGTACCAAAAGTGTAAATTTCCCCTTGTTCAAATTAGGAGCTGAAAAA
649 TTAGGGTGTTACATTTAGTACCAAAAGTGTAAATTTCCCCTTGTTCAAATTAGGAGCT-AAAAA
* * *
28325 CCCCTATTTTATGTTATGTTACGTGAACCACT-CCCCTTATCCCTCAGCAAACAGTGTTCTTCTT
1 CCCCTATTTTATGTTATGTTACGTGAACCACTCCCCCTTATCCCTCACCAAACACTCTTCTTCTT
* * *
28389 CCTTCCACCTTTAT-TTTCTTCTTCCTCATTTCCAAAATA-ATGATTTTAAGAATTTCAAGTGCA
66 CCTTCTACCTTT-TCTTTCTTCTTCCTCATTTCCAAAGTAGATGATTTTAAGAATTTCAAGTGTA
* *
28452 AGTTGGTTAACCAAGGTAAGAATATTAATCTCCATCCTTCAAGCTTCAATTTAACTCTCATTTCT
130 AGTTGGTTAACCAAGGTAAGAATATTAATCCCCATCCTTCAAGCTTCAATTTAAGTCTCATTTCT
* *
28517 CAAGTTTTACCCTTTGGTTCCAAAAATGGGTTTTGGGGAGGTTAAGAGAATCTATGGATTCTAGT
195 CAAGTTTTACCCTTTGGTTCCAAAAATGGGTTTTTGGGAGGTTAAAAGAATCTATGGATTCTAGT
*
28582 TT-TTTTTATAGATTCAAGTTCTAGGAAGTGTTTTTATCTCTAATCCAACCACCTAGTTAA-TAT
260 TTGTTTTTATAGATTCAAGTTCTAGGAAGTGTCTTTATCTCTAATCCAACCACCTAGTTAAGT-T
* * * * *
28645 AGTAATTCATTTTTCTTACTTTTGATTAGTGAAAGAAGTTGGAGAAAACTTAAGAGCAAGAGGAA
324 AGTAATTCATTTTTCTTACCTTTGATTAGTGAAAGAAGTGGGAGAAAGCTCAAGAGCAAAAGGAA
*
28710 AATAGAA-TCTA-TCCTTTGGGTGATTTGAGGACTTTTAGCAGCCAAGAATTCAAGGTAACACAC
389 AAAAGAAGT-TATTCC-TTGGGTGATTTGAGGACTTTTAGCAGCCAAGAATTCAAGGTAACACAC
* * * * ** * *
28773 TTATAACTTCTTCATACAATTTGGGGTCACTAGAAATGTAATGTAGTTTAAGAATTAGTTTGAAG
452 TTATAACTTCTTAAGACCATTTGGGGTCATTAGAAATACAATGTAGCTTAAGATTTAGTTTGAAG
* * * * *
28838 CATGTTGATTAAATTTCATGTTAACTTGTATGTTTAGTGTTATAACATGTTTCTAAGCCTTAATT
517 CATGTTGAGTGAATTTCATGGTAACTTCTATGTTTAGGGTTATAACATGTTTCTAAGCCTTAATT
* * *
28903 ATGACCCCTTTATATCACATAAAACTCTATTAATGGTTGAGGACCTCAGTAGAGTATTTTTGGTT
582 ATGACCCCTTTATATCACATAAAACTCTAATAATGGTTG-GGACCTCAGTAGGGTATTTTTGGGT
28968 GGTTTAG
646 GGTTTAG
28975 AGAGTCATTT
Statistics
Matches: 1832, Mismatches: 206, Indels: 70
0.87 0.10 0.03
Matches are distributed among these distances:
707 1 0.00
708 173 0.09
709 459 0.25
710 196 0.11
711 621 0.34
712 268 0.15
713 89 0.05
714 25 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (711 bp):
CCCCTATTTTATGTTATGTTACGTGAACCACTCCCCCTTATCCCTCACCAAACACTCTTCTTCTT
CCTTCTACCTTTTCTTTCTTCTTCCTCATTTCCAAAGTAGATGATTTTAAGAATTTCAAGTGTAA
GTTGGTTAACCAAGGTAAGAATATTAATCCCCATCCTTCAAGCTTCAATTTAAGTCTCATTTCTC
AAGTTTTACCCTTTGGTTCCAAAAATGGGTTTTTGGGAGGTTAAAAGAATCTATGGATTCTAGTT
TGTTTTTATAGATTCAAGTTCTAGGAAGTGTCTTTATCTCTAATCCAACCACCTAGTTAAGTTAG
TAATTCATTTTTCTTACCTTTGATTAGTGAAAGAAGTGGGAGAAAGCTCAAGAGCAAAAGGAAAA
AAGAAGTTATTCCTTGGGTGATTTGAGGACTTTTAGCAGCCAAGAATTCAAGGTAACACACTTAT
AACTTCTTAAGACCATTTGGGGTCATTAGAAATACAATGTAGCTTAAGATTTAGTTTGAAGCATG
TTGAGTGAATTTCATGGTAACTTCTATGTTTAGGGTTATAACATGTTTCTAAGCCTTAATTATGA
CCCCTTTATATCACATAAAACTCTAATAATGGTTGGGACCTCAGTAGGGTATTTTTGGGTGGTTT
AGGGTGTTACATTTAGTACCAAAAGTGTAAATTTCCCCTTGTTCAAATTAGGAGCTAAAAA
Found at i:39247 original size:44 final size:44
Alignment explanation
Indices: 39184--39289 Score: 149
Period size: 44 Copynumber: 2.4 Consensus size: 44
39174 AAATGGTAAT
**
39184 TTATGCATTTTCATTTATGGCACATTTCTTCCAATAATGAACCA
1 TTATGCATTTTCATTTATGGCACATTTCAGCCAATAATGAACCA
* * *
39228 TTATGCATTTTCATTTATGGCACCTTTCAGCCAATAATGCACCG
1 TTATGCATTTTCATTTATGGCACATTTCAGCCAATAATGAACCA
* *
39272 TTATGCAATTTCGTTTAT
1 TTATGCATTTTCATTTAT
39290 CCATTCATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (44 bp):
TTATGCATTTTCATTTATGGCACATTTCAGCCAATAATGAACCA
Found at i:41866 original size:3 final size:3
Alignment explanation
Indices: 41806--41857 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
41796 TATTCAGGTT
41806 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
41855 TTA
1 TTA
41858 GCATTATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42765 original size:28 final size:28
Alignment explanation
Indices: 42725--42781 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
42715 GGTTGTTCAC
*
42725 AGGAAACTGGATTTTTCTCTATAACCGA
1 AGGAAACTGGATTTTTCTCTAGAACCGA
42753 AGGAAACTGGATTTTTCTCTAGAACCGA
1 AGGAAACTGGATTTTTCTCTAGAACCGA
42781 A
1 A
42782 TGAACACGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (28 bp):
AGGAAACTGGATTTTTCTCTAGAACCGA
Found at i:43314 original size:2 final size:2
Alignment explanation
Indices: 43307--43360 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
43297 TCTAACCATA
43307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43349 AT AT AT AT AT AT
1 AT AT AT AT AT AT
43361 TCATATTATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43881 original size:157 final size:159
Alignment explanation
Indices: 43592--43995 Score: 589
Period size: 157 Copynumber: 2.5 Consensus size: 159
43582 AATTAAAGTT
* * * * * *
43592 ACATGTATTCTATTGTGGTATATGAGCATGTGGTTCAAATTTTGTAAAAACAAAGTGACTTAAAA
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAA-AATG-GACTTAAAA
* * * *
43657 TAAATCACAAATTGAAGGAATAAGGAGATTATGAAAATTTGAAGTACTAAATTGAAAAATAAAAA
64 TAAATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGTACTAAATTGAAAAATAAAAA
43722 ATTTGTTATC-AAAAGAGGAATTGAAAGTAC
129 ATTTGTTATCAAAAAGAGGAATTGAAAGTAC
*
43752 ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGT-AAAAAATGGACTTAAAATA
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAATGGACTTAAAATA
* *
43816 AATGATGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAAG-ATTAAATTGAAAAATAAAAAA
66 AATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTG-AAGTACTAAATTGAAAAATAAAAAA
43880 TTTGTTATCAAAAAGAGGAATTGAAAGTAC
130 TTTGTTATCAAAAAGAGGAATTGAAAGTAC
* * * * *
43910 ACATGTTTTCTACTATGGTTTAGGAGTATGTGGTTCAAAATTGGTAAAAAAATAGACTTAAAATG
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAATGGACTTAAAATA
*
43975 AATGAGGAATTGAAGAAATAA
66 AATGACGAATTGAAGAAATAA
43996 TGAAATCAAG
Statistics
Matches: 221, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
157 74 0.33
158 67 0.30
159 41 0.19
160 39 0.18
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (159 bp):
ACATGTATTCTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAATGGACTTAAAATA
AATGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGTACTAAATTGAAAAATAAAAAAT
TTGTTATCAAAAAGAGGAATTGAAAGTAC
Found at i:44630 original size:2 final size:2
Alignment explanation
Indices: 44623--44656 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
44613 AGTATTCCCT
44623 TA 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 TA
44657 GTGTTTCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45424 original size:13 final size:13
Alignment explanation
Indices: 45408--45432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45398 GCGAATGTAT
45408 ATGCAAAATGTGA
1 ATGCAAAATGTGA
45421 ATGCAAAATGTG
1 ATGCAAAATGTG
45433 TTAATTCCAT
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:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (13 bp):
ATGCAAAATGTGA
Found at i:47833 original size:29 final size:30
Alignment explanation
Indices: 47791--47903 Score: 93
Period size: 30 Copynumber: 3.8 Consensus size: 30
47781 CCCGAATGAC
*
47791 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGAAA
* *
47820 CTATCCAGAGGTCAGAAAGAACCTCGGAAA
1 CTATCCAGAGGTCACAAAGAACCCCGGAAA
* * * * * **
47850 CTGTCCATAGGTCCCGACGAACCTAGGTAAA
1 CTATCCAGAGGTCACAAAGAACCCCGG-AAA
* * *
47881 CTATCCATAGGTCCCGAAGAACC
1 CTATCCAGAGGTCACAAAGAACC
47904 TAGGTAAACT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
29 18 0.26
30 28 0.40
31 24 0.34
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGAAA
Found at i:47862 original size:30 final size:31
Alignment explanation
Indices: 47818--47920 Score: 120
Period size: 31 Copynumber: 3.4 Consensus size: 31
47808 AGACCCCGGT
* *
47818 AACTATCCAGAGGT-CAGAAAGAACCTCGG-A
1 AACTATCCATAGGTCCAG-AAGAACCTAGGTA
* * *
47848 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTATCCATAGGTCCAGAAGAACCTAGGTA
*
47879 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATAGGTCCAGAAGAACCTAGGTA
*
47910 AACTGTCCATA
1 AACTATCCATA
47921 TGTCTCGAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
30 21 0.33
31 42 0.67
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.18
Consensus pattern (31 bp):
AACTATCCATAGGTCCAGAAGAACCTAGGTA
Found at i:47888 original size:31 final size:31
Alignment explanation
Indices: 47836--47943 Score: 139
Period size: 31 Copynumber: 3.5 Consensus size: 31
47826 AGAGGTCAGA
*
47836 AAGAACCTCGG-AAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
* *
47866 ACGAACCTAGGTAAACTATCCATAGGTCCCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
* *
47897 AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
*
47928 AA-AGACATAGGTAAAC
1 AAGA-ACCTAGGTAAAC
47944 CCTCGACTCT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
30 10 0.15
31 58 0.85
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (31 bp):
AAGAACCTAGGTAAACTGTCCATAGGTCCCG
Found at i:50512 original size:131 final size:131
Alignment explanation
Indices: 50119--50513 Score: 567
Period size: 131 Copynumber: 3.0 Consensus size: 131
50109 TGAATTTTAA
* *
50119 GAGAGAAAACTATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTCATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * ** *
50184 TTCATTTATTGCTCCAATTGAAATGAAGAGATACTACTATTTTTTCCTAAAGTTCAATATTGATT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCATCCTAAAATTCAATATTGATT
50249 C
131 C
* * * * *
50250 AAGGGAAAAAGATAATATCTCATTATTTCCAATCGAGAATAATTGACCTCTTATGCCTTAAAGC-
1 GAGAGAAAACGATAATATCTCATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
50314 ATCCATTTATTACTCCAATCGAATTGAAAATATATTACTATTTCGTCCTAAAATTCAATATTGAT
66 AT-CATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCATCCTAAAATTCAATATTGAT
50379 TC
130 TC
*
50381 GAGAGAAAACGATAATATCTCATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTCATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
50446 ATAATTTATTACTCCAATCAAAATGAAGAGATATTACTATTTCATCCTAAAATTTAATATTAATT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCATCCTAAAATTCAATATTGATT
50511 C
131 C
50512 GA
1 GA
50514 CTGTTATTTG
Statistics
Matches: 231, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
130 1 0.00
131 228 0.99
132 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTCATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCATCCTAAAATTCAATATTGATT
C
Found at i:51201 original size:24 final size:25
Alignment explanation
Indices: 51157--51239 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 25
51147 AAATGTAATC
* *
51157 AAATAAAAAACATGGCCAAAT-CAT
1 AAATAAAAAACATGACAAAATGCAT
51181 AAATAAAAAA-ATGACTAAAATGCAT
1 AAATAAAAAACATGAC-AAAATGCAT
** *
51206 AAATTAAAAATACAACACAAAATTCAT
1 AAA-TAAAAA-ACATGACAAAATGCAT
*
51233 GAATAAA
1 AAATAAA
51240 TAATAAAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 4 0.08
24 14 0.29
25 6 0.12
26 10 0.21
27 11 0.23
28 3 0.06
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.19
Consensus pattern (25 bp):
AAATAAAAAACATGACAAAATGCAT
Found at i:52375 original size:11 final size:11
Alignment explanation
Indices: 52359--52396 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
52349 TTTGGGCCCA
52359 GGTTTGGGTTT
1 GGTTTGGGTTT
**
52370 GGTTTGGGCCT
1 GGTTTGGGTTT
52381 GGTTTGGGTTT
1 GGTTTGGGTTT
52392 GGTTT
1 GGTTT
52397 AAGTCTGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.05, G:0.45, T:0.50
Consensus pattern (11 bp):
GGTTTGGGTTT
Found at i:52387 original size:22 final size:23
Alignment explanation
Indices: 52349--52396 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
52339 TGAGTTTCAA
52349 TTTGGGCCCAGGTTTGGGTTTGG
1 TTTGGGCCCAGGTTTGGGTTTGG
*
52372 TTTGGG-CCTGGTTTGGGTTTGG
1 TTTGGGCCCAGGTTTGGGTTTGG
52394 TTT
1 TTT
52397 AAGTCTGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.02, C:0.10, G:0.42, T:0.46
Consensus pattern (23 bp):
TTTGGGCCCAGGTTTGGGTTTGG
Found at i:52404 original size:22 final size:22
Alignment explanation
Indices: 52359--52408 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
52349 TTTGGGCCCA
**
52359 GGTTTGGGTTTGGTTTGGGCCT
1 GGTTTGGGTTTGGTTTAAGCCT
*
52381 GGTTTGGGTTTGGTTTAAGTCT
1 GGTTTGGGTTTGGTTTAAGCCT
52403 GGTTTG
1 GGTTTG
52409 TAAATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.04, C:0.06, G:0.42, T:0.48
Consensus pattern (22 bp):
GGTTTGGGTTTGGTTTAAGCCT
Found at i:52427 original size:12 final size:11
Alignment explanation
Indices: 52410--52452 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
52400 TCTGGTTTGT
52410 AAATAAAATAA
1 AAATAAAATAA
52421 GAAATAAAATAA
1 -AAATAAAATAA
*
52433 AAATAACAACAA
1 AAATAA-AATAA
*
52445 AAACAAAA
1 AAATAAAA
52453 ACAAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:52471 original size:6 final size:6
Alignment explanation
Indices: 52426--52468 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
52416 AATAAGAAAT
* * * *
52426 AAAATA AAAATA ACAACA AAAACA AAAACA AAAACA ACAACA A
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA A
52469 CAATAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.79, C:0.16, G:0.00, T:0.05
Consensus pattern (6 bp):
AAAACA
Found at i:52554 original size:21 final size:21
Alignment explanation
Indices: 52529--52585 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
52519 TAGCTTCCTT
52529 TTATATAATTC-TTTCGTTTAA
1 TTATATAATTCATTT-GTTTAA
52550 TTATATAATTCATTTGTTTAA
1 TTATATAATTCATTTGTTTAA
* *
52571 TGATAAATATTCATT
1 TTATATA-ATTCATT
52586 CAAATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.54
Consensus pattern (21 bp):
TTATATAATTCATTTGTTTAA
Found at i:54510 original size:22 final size:23
Alignment explanation
Indices: 54475--54518 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
54465 TTTTAATCCT
*
54475 TTAAAATTACTAAAATAATTTAA
1 TTAAAATTAATAAAATAATTTAA
54498 TTAAAA-TAATAAAATAATTTA
1 TTAAAATTAATAAAATAATTTA
54519 TATCTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTAAAATTAATAAAATAATTTAA
Found at i:56020 original size:72 final size:73
Alignment explanation
Indices: 55944--56109 Score: 192
Period size: 72 Copynumber: 2.3 Consensus size: 73
55934 CCTTAAAACT
* * *
55944 AAGTTCGGCTCGACTTGAAAATTCACGAGCTTAAAATTGTC-TGGTTTGACACGAACTCGAAAT-
1 AAGTTCGGCTCGACTTGAAAATTCACGAGCTTAAAACTGTCAT-GTTTGACACAAACACGAAATA
*
56007 AAAAAGTTG
65 AAAAAATTG
* * * * * * *
56016 AAGTTTGACTCCACTCGAAATTTCGCGAGCTTAAAACTGTCATGTTTGACTCAAACACGAAATAA
1 AAGTTCGGCTCGACTTGAAAATTCACGAGCTTAAAACTGTCATGTTTGACACAAACACGAAAT-A
56081 AAAAAATTG
65 AAAAAATTG
*
56090 AAGTTCGGCTCGAATTGAAA
1 AAGTTCGGCTCGACTTGAAA
56110 GCTTGCGAGC
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
72 51 0.68
73 1 0.01
74 23 0.31
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (73 bp):
AAGTTCGGCTCGACTTGAAAATTCACGAGCTTAAAACTGTCATGTTTGACACAAACACGAAATAA
AAAAATTG
Found at i:58616 original size:35 final size:34
Alignment explanation
Indices: 58550--58672 Score: 106
Period size: 35 Copynumber: 3.5 Consensus size: 34
58540 ACTAAAAAGA
*
58550 TAATATCTTTTAAGT-TGAAAATATTTAAAAAGATATT
1 TAATATCTTTTAA-TAT-TAAA-ATTTAAAAAGATA-T
* * *
58587 TCATATTTTTTAATATTTAAATTTAAAAAGATAAT
1 TAATATCTTTTAATATTAAAATTTAAAAAGAT-AT
* *
58622 AAATATCTTTTAGT-TTAAAATATTCAAAAAGATAT
1 TAATATCTTTTAATATTAAAAT-TT-AAAAAGATAT
*
58657 TGATATCTTTTAATAT
1 TAATATCTTTTAATAT
58673 CTTTTGATAT
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
34 6 0.09
35 38 0.55
36 13 0.19
37 12 0.17
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (34 bp):
TAATATCTTTTAATATTAAAATTTAAAAAGATAT
Found at i:58674 original size:10 final size:10
Alignment explanation
Indices: 58659--58693 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
58649 AAAGATATTG
58659 ATATCTTTTA
1 ATATCTTTTA
*
58669 ATATCTTTTG
1 ATATCTTTTA
58679 ATATCTTTTTA
1 ATATC-TTTTA
58690 ATAT
1 ATAT
58694 TCAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.60
Consensus pattern (10 bp):
ATATCTTTTA
Found at i:58763 original size:91 final size:89
Alignment explanation
Indices: 58589--58763 Score: 210
Period size: 91 Copynumber: 1.9 Consensus size: 89
58579 AAGATATTTC
* * * * *
58589 ATATTTTTTAATATTTAAATTTAAAAAGATAATAAATATCTTTTAGTTTAAAATATTCAAAAAGA
1 ATATTTTTTAATATTCAAATTTAAAAAAATAATAAATATCTCTTACTTTAAAATATTCAAAAACA
* *
58654 TATTGATATCTTTTAATATCTTTTG
66 TATT-ATATCTATCAATATCTTTTG
*
58679 ATATCTTTTTAATATTCAAATTTAAAAAAATAAT-AATATCTCTTACTTTAAAATATTTAAAAGT
1 ATAT-TTTTTAATATTCAAATTTAAAAAAATAATAAATATCTCTTACTTTAAAATATTCAAAA--
*
58743 ACATAATT-TTTCTATCAATAT
63 ACAT-ATTATATCTATCAATAT
58764 TCAAATGTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
90 29 0.40
91 37 0.51
92 3 0.04
93 3 0.04
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (89 bp):
ATATTTTTTAATATTCAAATTTAAAAAAATAATAAATATCTCTTACTTTAAAATATTCAAAAACA
TATTATATCTATCAATATCTTTTG
Found at i:64677 original size:2 final size:2
Alignment explanation
Indices: 64636--64662 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64626 GAGAGCAACA
64636 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 A
64663 AAATAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64970 original size:17 final size:16
Alignment explanation
Indices: 64932--64980 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
64922 AATAATGAAG
64932 AATTTATATATAAATC
1 AATTTATATATAAATC
* *
64948 ATATTTATATATAGATTT
1 A-ATTTATATATA-AATC
*
64966 AATTTTTATATAAAT
1 AATTTATATATAAAT
64981 GGTATTTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
AATTTATATATAAATC
Found at i:66089 original size:28 final size:28
Alignment explanation
Indices: 66057--66129 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
66047 TTATAAATAA
66057 TAGGTACCTAAACTATTTTTGGTTAAAT
1 TAGGTACCTAAACTATTTTTGGTTAAAT
*
66085 TAGGTACTTAAACTATTTTTGGTTAAAT
1 TAGGTACCTAAACTATTTTTGGTTAAAT
66113 TAGGTACCTAAACTATT
1 TAGGTACCTAAACTATT
66130 ATATCTAACC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (28 bp):
TAGGTACCTAAACTATTTTTGGTTAAAT
Found at i:66295 original size:39 final size:37
Alignment explanation
Indices: 66240--66314 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 37
66230 AAAACAAATA
66240 CCTAATTTTTACATGGCACGTCAAAATAATTTCACAAGTG
1 CCTAATTTTTACATGGCACGTC--AAT-ATTTCACAAGTG
66280 CCTAA-TTTTACATGGCACGTCAATATTTCACAAGT
1 CCTAATTTTTACATGGCACGTCAATATTTCACAAGT
66315 ACTTATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 11 0.31
37 3 0.09
39 16 0.46
40 5 0.14
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (37 bp):
CCTAATTTTTACATGGCACGTCAATATTTCACAAGTG
Found at i:66325 original size:36 final size:38
Alignment explanation
Indices: 66233--66326 Score: 120
Period size: 36 Copynumber: 2.5 Consensus size: 38
66223 TTTGGTCAAA
*
66233 ACAAATACCTAATTTTTACATGGCACGTCAAAATAATTTC
1 ACAAGTACCT-ATTTTTACATGGCACGTC-AAATAATTTC
* *
66273 ACAAGTGCCTAATTTTACATGGCACGTC-AAT-ATTTC
1 ACAAGTACCTATTTTTACATGGCACGTCAAATAATTTC
*
66309 ACAAGTACTTATTTTTAC
1 ACAAGTACCTATTTTTAC
66327 TTTAAACCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 20 0.42
37 3 0.06
39 17 0.35
40 8 0.17
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (38 bp):
ACAAGTACCTATTTTTACATGGCACGTCAAATAATTTC
Found at i:69829 original size:21 final size:21
Alignment explanation
Indices: 69786--69830 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
69776 TATCGCATTA
**
69786 CGATTTTCCAAATTCGCGTTG
1 CGATTTTCCAAATTCGCAATG
*
69807 CGATTTTCCTAATTCGCAATG
1 CGATTTTCCAAATTCGCAATG
69828 CGA
1 CGA
69831 ATATGTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (21 bp):
CGATTTTCCAAATTCGCAATG
Found at i:69852 original size:20 final size:20
Alignment explanation
Indices: 69820--69913 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
69810 TTTTCCTAAT
* *
69820 TCGCAATGCGAATATGTAAA
1 TCGCAACGCGAATACGTAAA
* ** *
69840 TCGTAACGCGAATTTGGAAAA
1 TCGCAACGCGAA-TACGTAAA
*
69861 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
69881 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
69901 TCGCAACGCGAAT
1 TCGCAACGCGAAT
69914 CTGACTATCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:70135 original size:22 final size:22
Alignment explanation
Indices: 70110--70175 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
70100 GGCGACATCC
70110 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
70132 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
70154 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
70176 TTCATGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:70599 original size:20 final size:20
Alignment explanation
Indices: 70512--70601 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
70502 CGATTCTGTC
*
70512 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
** **
70531 GTTGCGATAGTCAAATTCGAT
1 GTTGCGATTTTCATTTTCG-T
**
70552 -TTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
70571 ATTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
70591 GTTGCGATTTT
1 GTTGCGATTTT
70602 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
19 12 0.20
20 47 0.80
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:70608 original size:20 final size:20
Alignment explanation
Indices: 70565--70608 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
70555 CGATAGTCAT
* *
70565 TTTCGTATTGCGATTTTCAT
1 TTTCGTATTGCGATTTTAAG
*
70585 TTTCGTGTTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
70605 TTTC
1 TTTC
70609 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTATTGCGATTTTAAG
Found at i:72645 original size:40 final size:40
Alignment explanation
Indices: 72471--72649 Score: 145
Period size: 40 Copynumber: 4.8 Consensus size: 40
72461 AGAATAGTTT
* *
72471 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACCATCGCAACGCGAAAATG
* *
72511 ACTATCGCAAT--GAGAA--A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACCATCGCAACGCGAAAATG
**
72544 AAAATCGCAA--C-AACAA--A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAA-AATGACCATCGCAACGCGAAAATG
* * *
72578 ACTATCGCAATTCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACCATCGCAACGCGAAAATG
*
72618 ACTATCGCAATGC-AAATTTGACCATCGCAACG
1 ACTATCGCAATGCGAAA-ATGACCATCGCAACG
72650 AAAGAATCTC
Statistics
Matches: 116, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
32 1 0.01
33 26 0.22
34 24 0.21
36 4 0.03
37 2 0.02
38 5 0.04
39 3 0.03
40 51 0.44
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACCATCGCAACGCGAAAATG
Found at i:72647 original size:20 final size:20
Alignment explanation
Indices: 72471--72630 Score: 168
Period size: 20 Copynumber: 8.7 Consensus size: 20
72461 AGAATAGTTT
72471 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
72491 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
72511 ACTATCGCAAT--GAGAA--
1 ACTATCGCAATGCGAAAATG
72527 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
72544 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
72560 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
72578 ACTATCGCAATTCGAAAATG
1 ACTATCGCAATGCGAAAATG
72598 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
72618 ACTATCGCAATGC
1 ACTATCGCAATGC
72631 AAATTTGACC
Statistics
Matches: 120, Mismatches: 5, Indels: 30
0.77 0.03 0.19
Matches are distributed among these distances:
14 15 0.12
15 2 0.02
16 6 0.05
17 5 0.04
18 7 0.06
19 7 0.06
20 78 0.65
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:72721 original size:20 final size:20
Alignment explanation
Indices: 72692--72760 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
72682 TCGATTCTCT
* **
72692 CATTGTGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
72712 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
72732 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
72752 CGTTGCGAT
1 CATTGCGAT
72761 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:73127 original size:18 final size:19
Alignment explanation
Indices: 73088--73129 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
73078 CTCACCTGTC
73088 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
73109 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
73127 ATC
1 ATC
73130 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:74792 original size:34 final size:33
Alignment explanation
Indices: 74704--74799 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
74694 AAAACAGACT
* ** *
74704 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
74738 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
74771 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
74800 CAAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:74839 original size:20 final size:19
Alignment explanation
Indices: 74810--74876 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
74800 CAAAACTAAA
*
74810 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
74830 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
74846 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
74863 TTCGCATTGCGATT
1 TTCGCATTGCGATT
74877 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 3 0.08
18 4 0.10
19 8 0.21
20 11 0.28
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:74857 original size:34 final size:34
Alignment explanation
Indices: 74814--74909 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
74804 ACTAAATTCG
74814 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
74848 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
74881 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
74910 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:74906 original size:20 final size:20
Alignment explanation
Indices: 74881--74974 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
74871 GCGATTCTCT
74881 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
74901 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
74921 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
74941 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
74961 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
74975 AATGAATGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 67 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:77399 original size:24 final size:24
Alignment explanation
Indices: 77365--77418 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
77355 CTGAAACATC
77365 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
77389 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
77413 ATCAAA
1 ATCAAA
77419 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:78301 original size:20 final size:22
Alignment explanation
Indices: 78255--78304 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
78245 TTGAAATTCA
78255 GTATTGCGATAGTCAGAATCTC
1 GTATTGCGATAGTCAGAATCTC
78277 G--TTGCGATAGTCAG-ATC-C
1 GTATTGCGATAGTCAGAATCTC
78295 GTATTGCGAT
1 GTATTGCGAT
78305 TTATGTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 20 0.77
22 1 0.04
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (22 bp):
GTATTGCGATAGTCAGAATCTC
Found at i:78320 original size:20 final size:20
Alignment explanation
Indices: 78297--78505 Score: 274
Period size: 20 Copynumber: 10.3 Consensus size: 20
78287 TCAGATCCGT
* *
78297 ATTGCGATTTATGTATTCTC
1 ATTGCGATTTACGTATTCGC
* *
78317 ATTGCGATTTACATATCCGC
1 ATTGCGATTTACGTATTCGC
*
78337 ATTGCGATTTACGTATTCTC
1 ATTGCGATTTACGTATTCGC
78357 ATTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
*
78377 ATTGCGATTTACGTATTCTC
1 ATTGCGATTTACGTATTCGC
78397 ATTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
* **
78417 ATTGCGATTTTTCAAATTCGC
1 ATTGCGA-TTTACGTATTCGC
*
78438 GTTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
* **
78458 ATTGCGATTTTTCAAATTCGC
1 ATTGCGA-TTTACGTATTCGC
*
78479 GTTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
78499 ATTGCGA
1 ATTGCGA
78506 ATTAGGAAAA
Statistics
Matches: 161, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 129 0.80
21 32 0.20
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTGCGATTTACGTATTCGC
Found at i:78322 original size:40 final size:38
Alignment explanation
Indices: 78273--78426 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 38
78263 ATAGTCAGAA
* * *
78273 TCTCGTTGCGATAGTCAGATCCGTATTGCGATTTATGTAT
1 TCTCATTGCGAT--TCAGATCCGCATTGCGATTTACGTAT
*
78313 TCTCATTGCGATTTACATATCCGCATTGCGATTTACGTAT
1 TCTCATTGCGA-TT-CAGATCCGCATTGCGATTTACGTAT
* *
78353 TCTCATTGCGATTTACGTATTCGCATTGCGATTTACGTAT
1 TCTCATTGCGATTCA-G-ATCCGCATTGCGATTTACGTAT
* *
78393 TCTCATTGCGATTTACGTATTCGCATTGCGATTT
1 TCTCATTGCGATTCA-G-ATCCGCATTGCGATTT
78427 TTCAAATTCG
Statistics
Matches: 103, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
38 1 0.01
39 3 0.03
40 98 0.95
41 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (38 bp):
TCTCATTGCGATTCAGATCCGCATTGCGATTTACGTAT
Found at i:78526 original size:21 final size:21
Alignment explanation
Indices: 78502--78547 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
78492 TATTCGCATT
78502 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
78523 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
78544 GCGA
1 GCGA
78548 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:86662 original size:21 final size:21
Alignment explanation
Indices: 86636--86675 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
86626 TCAATTGTGT
86636 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTGCTACAGTGC
86657 ATCGATGCACTGCTACAGT
1 ATCGATGCACTGCTACAGT
86676 AATGCTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
ATCGATGCACTGCTACAGTGC
Found at i:87418 original size:32 final size:32
Alignment explanation
Indices: 87367--87630 Score: 367
Period size: 32 Copynumber: 8.3 Consensus size: 32
87357 GTTACTAAGA
87367 ACATAGGT-A-ACTGTCCATATGTCCCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
* *
87397 ACATAAGTAATTCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
*
87429 ACATAGGTAATACTGTCCATATGTCCCGAAAA
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
** *
87461 ACATAACTAATATTGTCCATATGTCCCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
*
87493 ACATAGGTAATACTGTCCATATGTCTCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
*
87525 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
87557 ACATAGGTAATACTGTCCATATGTCCCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
* * *
87589 AC--AGGTAAAATCTATCCATATGTCTC-AAAGG
1 ACATAGGTAATA-CTGTCCATATGTCCCGAAA-G
*
87620 ACATCGGTAAT
1 ACATAGGTAAT
87631 CATCGAATCA
Statistics
Matches: 207, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
30 17 0.08
31 17 0.08
32 168 0.81
33 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (32 bp):
ACATAGGTAATACTGTCCATATGTCCCGAAAG
Found at i:95348 original size:18 final size:19
Alignment explanation
Indices: 95325--95363 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
95315 ATAATGATGT
*
95325 AATTTTTTTAT-TTTTTAA
1 AATTTTTATATATTTTTAA
95343 AATTTTTATATCATTTTTAA
1 AATTTTTATAT-ATTTTTAA
95363 A
1 A
95364 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTTTTATATATTTTTAA
Found at i:96071 original size:23 final size:23
Alignment explanation
Indices: 96043--96090 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
96033 TCCTAACAAC
*
96043 ACTGTAACAATTGTTATATTTCA
1 ACTGTAACAATCGTTATATTTCA
*
96066 ACTGTAACAATCGTTCTATTTCA
1 ACTGTAACAATCGTTATATTTCA
96089 AC
1 AC
96091 AAATAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (23 bp):
ACTGTAACAATCGTTATATTTCA
Found at i:96449 original size:31 final size:31
Alignment explanation
Indices: 96423--96497 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
96413 ATTTATACAC
* *
96423 TTTTGGTCACTTATGTTATTGTTTTATTAAG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
*
96454 TTTTGGTTACTTACGTTATCGTTTTATTAAG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
96485 TTTTGGTCACTTA
1 TTTTGGTCACTTA
96498 GGCATTGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.56
Consensus pattern (31 bp):
TTTTGGTCACTTACGTTATCGTTTTATTAAG
Found at i:97051 original size:29 final size:29
Alignment explanation
Indices: 96982--97049 Score: 129
Period size: 28 Copynumber: 2.4 Consensus size: 29
96972 TTGGAAAGGT
96982 TCAAATTCAAACCGGAAAAAAAATTAAAG
1 TCAAATTCAAACCGGAAAAAAAATTAAAG
97011 TCAAATTCAAACCGG-AAAAAAATTAAAG
1 TCAAATTCAAACCGGAAAAAAAATTAAAG
97039 TCAAATTCAAA
1 TCAAATTCAAA
97050 ACAAAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
28 24 0.62
29 15 0.38
ACGTcount: A:0.57, C:0.15, G:0.09, T:0.19
Consensus pattern (29 bp):
TCAAATTCAAACCGGAAAAAAAATTAAAG
Found at i:101177 original size:13 final size:13
Alignment explanation
Indices: 101159--101202 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
101149 TGATAAATAA
*
101159 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
101172 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
101185 AAACAACTACAAT
1 AAAAAACTACAAT
101198 AAAAA
1 AAAAA
101203 GTATTAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:103274 original size:9 final size:9
Alignment explanation
Indices: 103260--103293 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
103250 TAAGTAAAAT
103260 ATTAAATAA
1 ATTAAATAA
103269 ATTAAA-AA
1 ATTAAATAA
*
103277 CTTAAATAA
1 ATTAAATAA
103286 ATTAAATA
1 ATTAAATA
103294 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAAATAA
Found at i:104402 original size:20 final size:20
Alignment explanation
Indices: 104366--104403 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
104356 TTATTCATAA
*
104366 TATTATAATTTAAAATTTCT
1 TATTATAATTAAAAATTTCT
104386 TATTAT-ATTAAATAATTT
1 TATTATAATTAAA-AATTT
104404 AACGTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATAATTAAAAATTTCT
Found at i:105362 original size:21 final size:21
Alignment explanation
Indices: 105336--105380 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
105326 CTGATTGCGA
105336 TTTGTCGGTGGTC-TTCAGTAG
1 TTTGTCGGT-GTCATTCAGTAG
105357 TTTGTCGGTGTCATTCAGTAG
1 TTTGTCGGTGTCATTCAGTAG
105378 TTT
1 TTT
105381 TCATCTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.11, C:0.13, G:0.29, T:0.47
Consensus pattern (21 bp):
TTTGTCGGTGTCATTCAGTAG
Found at i:117986 original size:15 final size:16
Alignment explanation
Indices: 117961--117993 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
117951 ATCTTATAAA
117961 ATAAAATTTAAAAGTT
1 ATAAAATTTAAAAGTT
*
117977 ATAAAA-TTAAAATTT
1 ATAAAATTTAAAAGTT
117992 AT
1 AT
117994 TTATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATAAAATTTAAAAGTT
Found at i:118412 original size:20 final size:21
Alignment explanation
Indices: 118389--118432 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
118379 CTAATTTAAT
* *
118389 TTTATTTTTGAT-TTTTTATA
1 TTTATTTTTAATATTGTTATA
118409 TTTATTTTTAATATTGTTATA
1 TTTATTTTTAATATTGTTATA
118430 TTT
1 TTT
118433 TAAATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTATTTTTAATATTGTTATA
Found at i:118460 original size:24 final size:24
Alignment explanation
Indices: 118412--118455 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
118402 TTTTATATTT
*
118412 ATTTTTAATATTGTTATATTTTAA
1 ATTTATAATATTGTTATATTTTAA
118436 ATTTATAATATT-TTAT-TTTT
1 ATTTATAATATTGTTATATTTT
118456 CTAAAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 4 0.21
24 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
ATTTATAATATTGTTATATTTTAA
Found at i:119722 original size:40 final size:40
Alignment explanation
Indices: 119667--119778 Score: 179
Period size: 40 Copynumber: 2.8 Consensus size: 40
119657 AAGCGTTGCA
** *
119667 CCAGAATATTGAATAACATGCATCATACATATAAATTAAG
1 CCAGAATATCAAATAACATGCATCATGCATATAAATTAAG
* *
119707 CCAGAATATCAAATAATATGCATCATGCATGTAAATTAAG
1 CCAGAATATCAAATAACATGCATCATGCATATAAATTAAG
119747 CCAGAATATCAAATAACATGCATCATGCATAT
1 CCAGAATATCAAATAACATGCATCATGCATAT
119779 GAACTTGTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.27
Consensus pattern (40 bp):
CCAGAATATCAAATAACATGCATCATGCATATAAATTAAG
Found at i:125332 original size:60 final size:59
Alignment explanation
Indices: 125221--125357 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 59
125211 ATAGTCGAGT
* * * *
125221 GACCAATTTGTAACTTTTGATAGTCGAAGAACTCAACAAAGTAACACCCTATAGTCAG-A
1 GACC-ATTTATAACTTTTAATAGTCGAAGAACGCAACAAAGTAACACCCTATAATCAGAA
* * * ***
125280 GAACCATTTTATAACTTTTAATAGTTGATGGACGCAACAAAGTAATGTCCTATAATCAGAA
1 G-ACCA-TTTATAACTTTTAATAGTCGAAGAACGCAACAAAGTAACACCCTATAATCAGAA
125341 GACCATTTATATACTTT
1 GACCATTTATA-ACTTT
125358 ACCCTATTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
59 8 0.12
60 54 0.84
61 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (59 bp):
GACCATTTATAACTTTTAATAGTCGAAGAACGCAACAAAGTAACACCCTATAATCAGAA
Found at i:125762 original size:31 final size:30
Alignment explanation
Indices: 125599--125754 Score: 124
Period size: 31 Copynumber: 5.2 Consensus size: 30
125589 GTTATAAAAT
*
125599 AGTCCTCGACTATGGGACATTACTTT-TTCG
1 AGTCCTCGACTATAGGACATTACTTTATT-G
* *
125629 AGTCCCTCGACTATAGGGCATTACTTTGTTG
1 AGT-CCTCGACTATAGGACATTACTTTATTG
* * *
125660 AGTCCCCCCACTATAAGG-CATTACTTTTTTG
1 AGT-CCTCGACTAT-AGGACATTACTTTATTG
* * * **
125691 AGTCCTCAACTACTA-AAAATTAC-AAATTG
1 AGTCCTCGACTA-TAGGACATTACTTTATTG
*
125720 -GTCCCCGACTATAGGACATTACTTTATTG
1 AGTCCTCGACTATAGGACATTACTTTATTG
125749 AGTCCT
1 AGTCCT
125755 TTGACTATTA
Statistics
Matches: 99, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
27 2 0.02
28 15 0.15
29 7 0.07
30 20 0.20
31 50 0.51
32 5 0.05
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (30 bp):
AGTCCTCGACTATAGGACATTACTTTATTG
Found at i:126065 original size:59 final size:60
Alignment explanation
Indices: 125999--126133 Score: 186
Period size: 59 Copynumber: 2.3 Consensus size: 60
125989 TAGTTGAGTA
* *
125999 ACCATTTTGTAACTTTTAATAATCAAGAGACTCAACAAA-TCAACATCATATAGTTGA-AG
1 ACCATTTTGTAACTTTTAATAATCAAGAGACTCAAAAAAGT-AACATCATATAATTGAGAG
* *
126058 ACCATTTTGTAACTTTTAATAATCAAGTGACTCAAAAAAGTAACATCTTATAATTGAGAG
1 ACCATTTTGTAACTTTTAATAATCAAGAGACTCAAAAAAGTAACATCATATAATTGAGAG
*
126118 ATCATTTTTGT-ACTTT
1 ACCA-TTTTGTAACTTT
126134 ACCCGAAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
59 51 0.75
60 11 0.16
61 6 0.09
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (60 bp):
ACCATTTTGTAACTTTTAATAATCAAGAGACTCAAAAAAGTAACATCATATAATTGAGAG
Found at i:127213 original size:17 final size:17
Alignment explanation
Indices: 127188--127221 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
127178 TTATTATTAC
127188 ATTAAATTATAAAATAA
1 ATTAAATTATAAAATAA
* *
127205 ATTATATTATAATATAA
1 ATTAAATTATAAAATAA
127222 GTATATGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATTATAAAATAA
Found at i:131209 original size:15 final size:15
Alignment explanation
Indices: 131189--131229 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
131179 GTACAAACAT
131189 CACATGCTCCAC-TA
1 CACATGCTCCACTTA
131203 GCACATGCTCCACTTA
1 -CACATGCTCCACTTA
*
131219 CACCTGCTCCA
1 CACATGCTCCA
131230 TCAACTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.24, C:0.44, G:0.10, T:0.22
Consensus pattern (15 bp):
CACATGCTCCACTTA
Found at i:142168 original size:19 final size:20
Alignment explanation
Indices: 142137--142175 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
142127 ACCCCACTTA
142137 CTTTTTACTTTTCACTTTCT
1 CTTTTTACTTTTCACTTTCT
142157 CTTTTTAC-TTTCACTTTCT
1 CTTTTTACTTTTCACTTTCT
142176 AAGTTTCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTTACTTTTCACTTTCT
Found at i:146326 original size:17 final size:19
Alignment explanation
Indices: 146304--146338 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
146294 TCCACTACGC
146304 CATTCCAT-T-TTGCCACA
1 CATTCCATCTGTTGCCACA
146321 CATTCCATCTGTTGCCAC
1 CATTCCATCTGTTGCCAC
146339 CATAACTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.20, C:0.37, G:0.09, T:0.34
Consensus pattern (19 bp):
CATTCCATCTGTTGCCACA
Found at i:147255 original size:17 final size:17
Alignment explanation
Indices: 147230--147293 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
147220 ACCTATTCAT
*
147230 AATACAAAATAATATAA
1 AATAAAAAATAATATAA
*
147247 AATAAAAAATACATGTAA
1 AATAAAAAATA-ATATAA
* *
147265 ATAAAAAAAATAATATTA
1 A-ATAAAAAATAATATAA
*
147283 TA-AAAAAATAA
1 AATAAAAAATAA
147294 AAAAAATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 9 0.23
17 11 0.28
18 10 0.26
19 9 0.23
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (17 bp):
AATAAAAAATAATATAA
Found at i:147295 original size:22 final size:21
Alignment explanation
Indices: 147262--147302 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
147252 AAAATACATG
* *
147262 TAAATAAAAAAAATAATATTA
1 TAAAAAAAAAAAAAAATATTA
147283 TAAAAAAATAAAAAAAATAT
1 TAAAAAAA-AAAAAAAATAT
147303 AATTCTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAAAAAAAAAAAATATTA
Found at i:147616 original size:203 final size:200
Alignment explanation
Indices: 147337--147745 Score: 633
Period size: 203 Copynumber: 2.0 Consensus size: 200
147327 CCAAAAAAAG
** * * * *
147337 GTGTAAGTAAAAGTAGTAAAACATGTAGTAGATGATGTAGGTGTGTAAGAAATTACTAAAGCAAA
1 GTGTAAGTAAAAGTAGTAAAACAAATAGTAGAAGATGTAGGCGCGTAAGAAAGTACTAAAGCAAA
* * *
147402 TAGTAGAGAATTTTTTTTTGAAGTGTT-AAAATAATTGGAAAAAATGAATTTAAAAATCAAAATA
66 TAGTAGAGAA-TTTGTTTGGAAGTGTTAAAAATAATT-AAAAAAATGAATTTAAAAATCAAAATA
* *
147466 TTAAAAAAAAATTCACAATCAAAG-TAAGAAGTAAAGAAGGCAACGGGAGGAAGCATAAAAACTC
129 TT--AAAAAAATTCACAATCAAAGTTAA-AAGTAAAGAAGGCAACGGGAGGAAACAGAAAAACTC
147530 TAGTTTCAAA
191 TAGTTTCAAA
*
147540 GTGTAAGTAAATGTAGTAAAACAAATAGTAGAAGATGTAGGCGCGTAAGAAAGTACTAAAGCAAA
1 GTGTAAGTAAAAGTAGTAAAACAAATAGTAGAAGATGTAGGCGCGTAAGAAAGTACTAAAGCAAA
147605 TAGTAGAGAATTTGTTTGGAAGTGTTAAAAATAATTAAAAAAATGAATTTAAAAATCAAAATATT
66 TAGTAGAGAATTTGTTTGGAAGTGTTAAAAATAATTAAAAAAATGAATTTAAAAATCAAAATATT
* *
147670 AAAAAAATTCACAATCAAAGTTAAAAGTAAAGAAGGCAACGGGAGGAAACAGAGAAACTTTAGTT
131 AAAAAAATTCACAATCAAAGTTAAAAGTAAAGAAGGCAACGGGAGGAAACAGAAAAACTCTAGTT
147735 TCAAA
196 TCAAA
147740 GTGTAA
1 GTGTAA
147746 ACCTTTCATC
Statistics
Matches: 190, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
200 68 0.36
201 3 0.02
202 42 0.22
203 77 0.41
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (200 bp):
GTGTAAGTAAAAGTAGTAAAACAAATAGTAGAAGATGTAGGCGCGTAAGAAAGTACTAAAGCAAA
TAGTAGAGAATTTGTTTGGAAGTGTTAAAAATAATTAAAAAAATGAATTTAAAAATCAAAATATT
AAAAAAATTCACAATCAAAGTTAAAAGTAAAGAAGGCAACGGGAGGAAACAGAAAAACTCTAGTT
TCAAA
Found at i:149534 original size:23 final size:23
Alignment explanation
Indices: 149470--149538 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
149460 CACCACAGCT
*
149470 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * * *
149493 CGTAGAATTACATCTAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
149516 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
149539 TATAAGATGT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:150956 original size:20 final size:22
Alignment explanation
Indices: 150931--150988 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
150921 TTCCCCTTGA
150931 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
150951 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
150974 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
150989 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:151082 original size:61 final size:62
Alignment explanation
Indices: 150978--151133 Score: 206
Period size: 62 Copynumber: 2.5 Consensus size: 62
150968 TTTAACATGT
* *
150978 GCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTT-CATTTTAAGGGGA
1 GCATCGATGCACT-CCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGGGA
* * * * * *
151040 GCATCGATGCACTCCTTTGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAAGGTGT
1 GCATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGGGA
*
151102 GCATCGATGCACTTCCTGTGCATCGATACACA
1 GCATCGATGCAC-TCCTATGCATCGATACACA
151134 CTGAACAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
61 29 0.36
62 36 0.44
63 16 0.20
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (62 bp):
GCATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGGGA
Found at i:156228 original size:22 final size:21
Alignment explanation
Indices: 156178--156242 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
156168 GATTCCCCTG
156178 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTT-CCC-TCA
** *
156201 AAGGGGTAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
* *
156222 TGGGGGGGGATCGATTCCCTC
1 T-GGGGGGAATCGGTTCCCTC
156243 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
21 3 0.09
22 18 0.55
23 12 0.36
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:167213 original size:19 final size:19
Alignment explanation
Indices: 167191--167228 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
167181 CTTTTTTTTC
167191 TTTTTCTTTT-TT-TTCGAA
1 TTTTT-TTTTGTTGTTCGAA
167209 TTTTTTTTTGTTGTTCGAA
1 TTTTTTTTTGTTGTTCGAA
167228 T
1 T
167229 CAAACTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 7 0.39
19 7 0.39
ACGTcount: A:0.11, C:0.08, G:0.11, T:0.71
Consensus pattern (19 bp):
TTTTTTTTTGTTGTTCGAA
Found at i:175983 original size:140 final size:139
Alignment explanation
Indices: 175757--176040 Score: 493
Period size: 142 Copynumber: 2.0 Consensus size: 139
175747 CTAATATATC
175757 TATACAAAGAAAAACAAGTAATTTAGGAGAGTAAAGATTATTAGCATAATTTTTAAAATTAAGAT
1 TATACAAAGAAAAACAAGTAATTTAGGAGAGTAAAGATTATTAGCATAATTTTTAAAATTAAGAT
*
175822 TTAAATTTATTGAATTGTTTTGAAA-AGAACCAA-TTGATAAAATGTGTAACTTTTGGAAACTGA
66 TTAAATTTATTGAATTGTTTTGAAATAGAACCAATTTGATAAAATGTGTAACTTTTGGAAACTAA
*
175885 ATTTATTAT
131 ATTTACTAT
175894 TATACAAAAGAAAAACAAGTAATTTAGGAGAGT-AAGATTATATTAGCATAATTTTTAAAATTTA
1 TATAC-AAAGAAAAACAAGTAATTTAGGAGAGTAAAGA-T-TATTAGCATAATTTTTAAAA-TTA
175958 AGATTTAAATTTATTGAATTGTTTTGAAATAGAACCAATTTGATAAAATGTGTAACTTTTGGAAA
62 AGATTTAAATTTATTGAATTGTTTTGAAATAGAACCAATTTGATAAAATGTGTAACTTTTGGAAA
176023 CTAAATTTACTAT
127 CTAAATTTACTAT
176036 TATAC
1 TATAC
176041 TAGGCCAAGT
Statistics
Matches: 139, Mismatches: 2, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
137 9 0.06
138 28 0.20
139 20 0.14
140 32 0.23
141 8 0.06
142 42 0.30
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (139 bp):
TATACAAAGAAAAACAAGTAATTTAGGAGAGTAAAGATTATTAGCATAATTTTTAAAATTAAGAT
TTAAATTTATTGAATTGTTTTGAAATAGAACCAATTTGATAAAATGTGTAACTTTTGGAAACTAA
ATTTACTAT
Found at i:176668 original size:2 final size:2
Alignment explanation
Indices: 176661--176712 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
176651 AAACCCTAAC
176661 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176701 AT AT AT AT AT AT
1 AT AT AT AT AT AT
176713 TGGGTTGAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176710 original size:17 final size:17
Alignment explanation
Indices: 176661--176710 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
176651 AAACCCTAAC
*
176661 ATATATATATATATAAT
1 ATATATATATATATATT
176678 ATATATATATATATATT
1 ATATATATATATATATT
176695 ATATATATATATATAT
1 ATATATATATATATAT
176711 ATTGGGTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:176713 original size:19 final size:19
Alignment explanation
Indices: 176661--176713 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
176651 AAACCCTAAC
*
176661 ATATATATATATATAATAT
1 ATATATATATATATTATAT
176680 ATATATATATATATTATAT
1 ATATATATATATATTATAT
176699 ATATATATATATATT
1 ATATATATATATATT
176714 GGGTTGAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATATATATATTATAT
Found at i:179576 original size:207 final size:201
Alignment explanation
Indices: 179194--179601 Score: 701
Period size: 207 Copynumber: 2.0 Consensus size: 201
179184 AGCCATGCTC
*
179194 GATATAGACAGCGTGCGCGTCGAAAGGGGCTTTTGATTGGGTCTTATGCGCGATTCTGACACCCG
1 GATATAGACAGCGTGCGCGTCGAAAGGGGCTTTTGATTGGGTCTTATGCGCGATTCCGACACCCG
179259 TAGCCAAAGTTAGGCTAAAAGACTGAAACGCACTCAAACGGCCCCAATGAGTAAATATCACACTC
66 TAGCCAAAGTTAGGCTAAAAGACTGAAACGCACTCAAACGGCCCCAATGAGTAAATATCACACTC
*
179324 AACTCCGCCTTTGCGCTGATATGCCAACTCATGGTATCTCAGCGCCATC-ATGTGCAATCTGACA
131 AACTCCGCCTTTGCGCTAATATGCCAACTCATGGTATCTCAGCGCCATCAATGTGCAATCTGACA
179388 GCTCAG
196 GCTCAG
* *
179394 GATATGGACAGCGTGTGCGTCGAAAGGGGCTTTTTGAATTGGGGTCTTATGCGCGATTCCGACAC
1 GATATAGACAGCGTGCGCGTCGAAAGGGGC-TTTTG-ATT-GGGTCTTATGCGCGATTCCGACAC
179459 CCGTAGCCAAAGTTATGGCTAAAAGACTGAAACGCACTCAAAACGGCCCCAATGAGTAACATATC
63 CCGTAGCCAAAGTTA-GGCTAAAAGACTGAAACGCACTC-AAACGGCCCCAATGAGTAA-ATATC
*
179524 ACACTCAACTCCCGCCTTTGCGCTAATCTGCCAACTCATGGTATCTCAGCGCCATCAATGTGCAA
125 ACACTCAACT-CCGCCTTTGCGCTAATATGCCAACTCATGGTATCTCAGCGCCATCAATGTGCAA
179589 TCTGACAGCTCAG
189 TCTGACAGCTCAG
179602 CATCATCTAT
Statistics
Matches: 195, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
200 28 0.14
201 5 0.03
202 3 0.02
203 38 0.19
204 23 0.12
205 19 0.10
206 15 0.08
207 43 0.22
208 21 0.11
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (201 bp):
GATATAGACAGCGTGCGCGTCGAAAGGGGCTTTTGATTGGGTCTTATGCGCGATTCCGACACCCG
TAGCCAAAGTTAGGCTAAAAGACTGAAACGCACTCAAACGGCCCCAATGAGTAAATATCACACTC
AACTCCGCCTTTGCGCTAATATGCCAACTCATGGTATCTCAGCGCCATCAATGTGCAATCTGACA
GCTCAG
Found at i:191672 original size:24 final size:24
Alignment explanation
Indices: 191645--191722 Score: 147
Period size: 24 Copynumber: 3.2 Consensus size: 24
191635 TTATTTTTAT
191645 GGTGTTGTTTAGATTTGAACATAA
1 GGTGTTGTTTAGATTTGAACATAA
*
191669 GGTGTTGTTTAGATTTAAACATAA
1 GGTGTTGTTTAGATTTGAACATAA
191693 GGTGTTGTTTAGATTTGAACATAA
1 GGTGTTGTTTAGATTTGAACATAA
191717 GGTGTT
1 GGTGTT
191723 TGATGAAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (24 bp):
GGTGTTGTTTAGATTTGAACATAA
Found at i:195525 original size:20 final size:21
Alignment explanation
Indices: 195500--195539 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
195490 AAATTCACAT
195500 TCTAACATCAATTT-CAGCAC
1 TCTAACATCAATTTCCAGCAC
*
195520 TCTAACATTAATTTCCAGCA
1 TCTAACATCAATTTCCAGCA
195540 TAATACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (21 bp):
TCTAACATCAATTTCCAGCAC
Found at i:196547 original size:25 final size:25
Alignment explanation
Indices: 196519--196566 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
196509 GCTTAATTTA
196519 ATACCATTCCAATTTTCTCAAATAT
1 ATACCATTCCAATTTTCTCAAATAT
196544 ATACCATTCCAATTTTCTCAAAT
1 ATACCATTCCAATTTTCTCAAAT
196567 TTTTATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (25 bp):
ATACCATTCCAATTTTCTCAAATAT
Found at i:196744 original size:30 final size:29
Alignment explanation
Indices: 196708--196772 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
196698 CAAAATACAT
196708 AACTTTTAAAAACTAAACTTTTGGTCCCTA
1 AACTTTTAAAAACTAAACTTTTGGT-CCTA
* * * **
196738 AACTTTTGAGAATTACCCTTTTGGTCCTA
1 AACTTTTAAAAACTAAACTTTTGGTCCTA
196767 AACTTT
1 AACTTT
196773 ATACTTTGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (29 bp):
AACTTTTAAAAACTAAACTTTTGGTCCTA
Found at i:198015 original size:51 final size:49
Alignment explanation
Indices: 197931--198031 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 49
197921 CATGACAACA
*
197931 CAAGCTTATATGAGACAGGGTAGTGAGTTCACTCAACTTCTTCATAAGG
1 CAAGCTTATATGAGACAGGGTAGTGAGTTCACTCAACTTCTTCACAAGG
*
197980 CAAGCTTATATGAGACAAAGGGTTGTGAGTTCACTCAACTTCTTCACAAGG
1 CAAGCTTATATGAGAC--AGGGTAGTGAGTTCACTCAACTTCTTCACAAGG
198031 C
1 C
198032 CTTTCTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 16 0.33
51 32 0.67
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (49 bp):
CAAGCTTATATGAGACAGGGTAGTGAGTTCACTCAACTTCTTCACAAGG
Found at i:198147 original size:28 final size:22
Alignment explanation
Indices: 198092--198142 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
198082 CGAGAGACGA
198092 TTTTGGAAGACCAAGACATAAT
1 TTTTGGAAGACCAAGACATAAT
198114 TTTTGGAAGACCAAGACATAAT
1 TTTTGGAAGACCAAGACATAAT
198136 TTTTGGA
1 TTTTGGA
198143 TTTGGTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (22 bp):
TTTTGGAAGACCAAGACATAAT
Found at i:199282 original size:15 final size:15
Alignment explanation
Indices: 199264--199294 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
199254 AAATTCTAAA
199264 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
199279 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
199294 T
1 T
199295 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:203417 original size:2 final size:2
Alignment explanation
Indices: 203410--203440 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
203400 TTTACATCCT
203410 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 T
203441 TAATGACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:212517 original size:18 final size:18
Alignment explanation
Indices: 212494--212533 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
212484 ACTTTCTGGA
*
212494 TTAACCTATTCTGTTTCC
1 TTAACCTATTCTATTTCC
*
212512 TTAACCTCTTCTATTTCC
1 TTAACCTATTCTATTTCC
212530 TTAA
1 TTAA
212534 ATGGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.50
Consensus pattern (18 bp):
TTAACCTATTCTATTTCC
Found at i:217707 original size:22 final size:22
Alignment explanation
Indices: 217647--217707 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 22
217637 ATCGAGGCTG
* *
217647 AAAGAACGATATCGGTACTTGAT
1 AAAGAACAATATCGGTAC-TGAC
* *
217670 AAACAA-AAT-T-GATACTGAC
1 AAAGAACAATATCGGTACTGAC
217689 AAAGAACAATATCGGTACT
1 AAAGAACAATATCGGTACT
217708 ATATGAAGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
19 8 0.28
20 7 0.24
21 2 0.07
22 7 0.24
23 5 0.17
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (22 bp):
AAAGAACAATATCGGTACTGAC
Found at i:221562 original size:17 final size:17
Alignment explanation
Indices: 221540--221572 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
221530 AACGATCAAC
221540 GGTCAACGATCGGGTCG
1 GGTCAACGATCGGGTCG
*
221557 GGTCAACGGTCGGGTC
1 GGTCAACGATCGGGTC
221573 AGACCGGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.24, G:0.42, T:0.18
Consensus pattern (17 bp):
GGTCAACGATCGGGTCG
Found at i:228590 original size:17 final size:17
Alignment explanation
Indices: 228570--228622 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
228560 GAAAGTCAAC
*
228570 GGTCAACGTTCAGGTCG
1 GGTCAACGGTCAGGTCG
*
228587 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCAGGTCG
228604 GGTC-A-GGTC-GGTCG
1 GGTCAACGGTCAGGTCG
228618 GGTCA
1 GGTCA
228623 GACCGGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 9 0.27
15 4 0.12
16 1 0.03
17 19 0.58
ACGTcount: A:0.13, C:0.23, G:0.43, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCAGGTCG
Found at i:228618 original size:14 final size:15
Alignment explanation
Indices: 228582--228623 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 15
228572 TCAACGTTCA
228582 GGTCGGGTCAACGGTCG
1 GGTCGGGTC-A-GGTCG
228599 GGTCGGGTCAGGTC-
1 GGTCGGGTCAGGTCG
228613 GGTCGGGTCAG
1 GGTCGGGTCAG
228624 ACCGGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.44
15 4 0.16
16 1 0.04
17 9 0.36
ACGTcount: A:0.10, C:0.21, G:0.50, T:0.19
Consensus pattern (15 bp):
GGTCGGGTCAGGTCG
Found at i:229467 original size:69 final size:70
Alignment explanation
Indices: 229390--229582 Score: 257
Period size: 69 Copynumber: 2.8 Consensus size: 70
229380 AAATGAGATT
* ** * **
229390 ATGA-TTTAAATATATTAAATTTTATGAACAAAAAATAGTGCTATTATAAAAAAA-TTGAAAGTG
1 ATGATTTTAAATATAATATTTTTTATTAACAAAAGTTAGTGCTATTATAAAAAAACTTGAAAGTG
229453 GACAC
66 GACAC
*
229458 ATGATTTTAAATATAGTATTTTTTATTAACAAAAGTTAGTGCTATTA-AAAAAAACTTGAAAGTG
1 ATGATTTTAAATATAATATTTTTTATTAACAAAAGTTAGTGCTATTATAAAAAAACTTGAAAGTG
*
229522 GAGAC
66 GACAC
* *
229527 ATGAGATTTTAAATATAATATTTTTTATTACCAAAAGTTAGTGCTTTTATAAAAAA
1 AT--GATTTTAAATATAATATTTTTTATTAACAAAAGTTAGTGCTATTATAAAAAA
229583 TAAAAATTAA
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
68 11 0.10
69 51 0.46
71 42 0.38
72 6 0.05
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (70 bp):
ATGATTTTAAATATAATATTTTTTATTAACAAAAGTTAGTGCTATTATAAAAAAACTTGAAAGTG
GACAC
Found at i:229596 original size:18 final size:17
Alignment explanation
Indices: 229575--229617 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
229565 TAGTGCTTTT
229575 ATAAAAAATAAAAATTAA
1 ATAAAAAAT-AAAATTAA
*
229593 ATAAAATAATATAATTAA
1 ATAAAA-AATAAAATTAA
*
229611 TTAAAAA
1 ATAAAAA
229618 CGTGATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAAATAAAATTAA
Found at i:229849 original size:2 final size:2
Alignment explanation
Indices: 229834--229865 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
229824 AAAATTCGAA
229834 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
229866 TAATAATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231053 original size:123 final size:123
Alignment explanation
Indices: 230911--231490 Score: 952
Period size: 123 Copynumber: 4.7 Consensus size: 123
230901 GAATCAATCT
* *
230911 AAGGTTGAACGAGTTCTTCTTCA-GATTAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTC-TCATGATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTA
*
230975 CGAACTTCTTATGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
65 CGAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
* *
231034 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAC
1 AAGGTTGAACAAGTTCTTCTCATGATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTAC
231099 GAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
66 GAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
* * *
231157 AAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAC
1 AAGGTTGAACAAGTTCTTCTCATGATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTAC
* **
231222 AAACTTCTTCTGGAAATGTTGATGTTGATCTGGCTCCTTCTGTGATAGAATCAAGCGA
66 GAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
*
231280 AAGGTTGAACAAGTTCTTCTTCA-GATTAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTC-TCATGATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTA
*
231344 CGAACTTCTTCTGGAAATGTTGATGTTGATTTATCTCCTTCTGTGATAGAATCAAGCGA
65 CGAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
* *
231403 AAGGTTGAACAAGTTCTTCTCATTG-TGAACTTCTTCTTCCTCTTT-AGATAAGTTCTTCTTATT
1 AAGGTTGAACAAGTTCTTCTCA-TGATGAACTTCTTCTTCCT-TTTCAGATGAGTTCTTCTCATT
*
231466 ACGAACTTCTTCTGGAAATATTGAT
64 ACGAACTTCTTCTGGAAATGTTGAT
231491 CCATCGAGTG
Statistics
Matches: 431, Mismatches: 21, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
122 6 0.01
123 418 0.97
124 7 0.02
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATGATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTAC
GAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCGA
Found at i:232004 original size:22 final size:22
Alignment explanation
Indices: 231961--232006 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
231951 TTATAAAATA
**
231961 TTTATAAAAGAATAAATTGAAT
1 TTTATAAAAGAATAAACGGAAT
231983 TTTA-AAAAGAATAAAACGGAAT
1 TTTATAAAAGAAT-AAACGGAAT
232005 TT
1 TT
232007 GGGAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (22 bp):
TTTATAAAAGAATAAACGGAAT
Found at i:232391 original size:20 final size:21
Alignment explanation
Indices: 232362--232401 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
232352 TTGACCCTCT
232362 TTTTTATTTTCT-ATTTTTTTG
1 TTTTTATTTT-TAATTTTTTTG
232383 TTTTT-TTTTTAATTTTTTT
1 TTTTTATTTTTAATTTTTTT
232402 TCTTCAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 12 0.67
21 5 0.28
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (21 bp):
TTTTTATTTTTAATTTTTTTG
Done.