Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011705.1 Kokia drynarioides strain JFW-HI SEQ_126699, 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: 187767
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA 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 TA TA T
38 TGTACTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4392 original size:42 final size:41
Alignment explanation
Indices: 4337--4483 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 41
4327 TATGCTTTAT
* * *
4337 CGAGTCATAAGTCTTCCTTTAATCATATTCTCATTCTCATC
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATC
*
4378 CAGAGACATGAGTCTTCCTTTAATCATATTTTCATGCTCATTC
1 C-GAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCA-TC
* * * * * * *
4421 CGAGTCACGAGTCTTTCATTT-ATAAAAATTCTCAAGCTCAACC
1 CGAGACATGAGTC-TTCCTTTAAT-CATATTCTCATGCTC-ATC
4464 CGAGACATGAGTCTTCCTTT
1 CGAGACATGAGTCTTCCTTT
4484 TTATGCATCA
Statistics
Matches: 86, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 52 0.60
43 32 0.37
44 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (41 bp):
CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATC
Found at i:5307 original size:21 final size:20
Alignment explanation
Indices: 5283--5326 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5273 ACTTTCATCA
* *
5283 TTAAGCTTTAATTAACCCTTT
1 TTAAGC-TTAATTAAACCTAT
*
5304 TTAATCTTAATTAAACCTAT
1 TTAAGCTTAATTAAACCTAT
5324 TTA
1 TTA
5327 TACTTAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAGCTTAATTAAACCTAT
Found at i:5782 original size:99 final size:99
Alignment explanation
Indices: 5633--5819 Score: 284
Period size: 99 Copynumber: 1.9 Consensus size: 99
5623 ATTCATTTCC
* * * * *
5633 ATTCGTTTTCAATAGAATAAGTGCAGACACTTCATTGATCACACAGAATAACAAGTACACAACAT
1 ATTCATTTTCAACAGAAGAAGTGCAGACACTTCATTGATCACACAAAATAACAAATACACAACAT
* * *
5698 GGTATTTTAATACTTTCGTACCTGATTCATTCTA
66 GGTATGTTAATACATTCATACCTGATTCATTCTA
* *
5732 ATTCATTTTCAACATAAGAAGTGCAGACACTTTATTGATCACACAAAATAACAAATACACAACAT
1 ATTCATTTTCAACAGAAGAAGTGCAGACACTTCATTGATCACACAAAATAACAAATACACAACAT
5797 GGTATGTTAATACATTCATACCT
66 GGTATGTTAATACATTCATACCT
5820 TATTGTTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (99 bp):
ATTCATTTTCAACAGAAGAAGTGCAGACACTTCATTGATCACACAAAATAACAAATACACAACAT
GGTATGTTAATACATTCATACCTGATTCATTCTA
Found at i:10438 original size:27 final size:27
Alignment explanation
Indices: 10304--10429 Score: 216
Period size: 27 Copynumber: 4.7 Consensus size: 27
10294 AGGAGTAATT
10304 TGATTCTGGCTCGAAAGAGCGTTATTC
1 TGATTCTGGCTCGAAAGAGCGTTATTC
10331 TGATTCTGGCTCGAAAGAGCGTTATTC
1 TGATTCTGGCTCGAAAGAGCGTTATTC
* * *
10358 TGATTCTGGCACGAAAGAGCATTATTA
1 TGATTCTGGCTCGAAAGAGCGTTATTC
10385 TGATTCTGGCTCGAAAGAGCGTTATTC
1 TGATTCTGGCTCGAAAGAGCGTTATTC
*
10412 CGATTCTGGCTCGAAAGA
1 TGATTCTGGCTCGAAAGA
10430 AAATTATTCT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 92 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (27 bp):
TGATTCTGGCTCGAAAGAGCGTTATTC
Found at i:10481 original size:24 final size:24
Alignment explanation
Indices: 10449--10582 Score: 180
Period size: 24 Copynumber: 5.6 Consensus size: 24
10439 TTATTTTGGA
*
10449 CTCGTAAGAGATAACCATTCTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
*
10473 CTCGTAAGAGCTAATCATTCTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
* **
10497 ATAATAAGAGCTAACCATTCTGGG
1 CTCGTAAGAGCTAACCATTCTGGG
*
10521 CTCGTAAGAGCTAACCATTCTGAG
1 CTCGTAAGAGCTAACCATTCTGGG
*
10545 CTCGTAAGAGCTAACC-TATCTAGG
1 CTCGTAAGAGCTAACCAT-TCTGGG
*
10569 CTCGTATGAGCTAA
1 CTCGTAAGAGCTAA
10583 TTTTGTCTGG
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
23 1 0.01
24 95 0.99
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
CTCGTAAGAGCTAACCATTCTGGG
Found at i:12200 original size:14 final size:14
Alignment explanation
Indices: 12162--12206 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
12152 AATACATTTG
12162 TTTTTTCTTGTTGT-
1 TTTTTTCTT-TTGTC
*
12176 TTTGTTGCTTTTGTC
1 TTT-TTTCTTTTGTC
12191 TTTTTTCTTTTGTC
1 TTTTTTCTTTTGTC
12205 TT
1 TT
12207 GCAGATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (14 bp):
TTTTTTCTTTTGTC
Found at i:27476 original size:158 final size:158
Alignment explanation
Indices: 27276--27701 Score: 592
Period size: 158 Copynumber: 2.7 Consensus size: 158
27266 TTGTGGCTCT
* * * * *
27276 AGATGTTACGCTACACGATGTTGTTCACACGAGCTGTGGAGAATCCGCTACAAATATCATATCTC
1 AGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTAGAGAATCTGCTACAAATATCA-ATCTC
*
27341 AGCCATTAG-TAGGACATCTAAGACCAGCACCCATATAACCTGTAATGCTTACACGAGCTATGAA
65 AGCCATTCGATAGGACATCTAAGACCAGCACCCATATAACCTGTAATGCTTACACGAGCTATGAA
*
27405 AT-GAGCCTAATCACATGAGCTATGGGTCG
130 ATAG-GCCTAATCACACGAGCTATGGGTCG
* *
27434 AGATGTTAGGCTACGCGATGCTGCTCACACGAGCTGTAGAGAATCTGCAACAAATATCGAATCTC
1 AGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTAGAGAATCTGCTACAAATATC-AATCTC
* *
27499 AGCC-TTCGATAGGACATCTAAGATCAGCACCCATATAACCTGTAATGCTTACACGAGCTGTGAA
65 AGCCATTCGATAGGACATCTAAGACCAGCACCCATATAACCTGTAATGCTTACACGAGCTATGAA
** * *
27563 ATAGGCCTCCTCACACGAGTTATGGGTTG
130 ATAGGCCTAATCACACGAGCTATGGGTCG
* * *
27592 AGATGTTAGGCTACATGATGCTGCTCACACGAGCTGTAGGGAATCTG-TAACAAATGTCAAATCT
1 AGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTAGAGAATCTGCT-ACAAATATC-AATCT
* *
27656 CAGCCA-TCGATAAGACATTTAAGACCAGCACCCATATAACCTGTAA
64 CAGCCATTCGATAGGACATCTAAGACCAGCACCCATATAACCTGTAA
27702 ATCTCGAAAT
Statistics
Matches: 239, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
157 3 0.01
158 234 0.98
159 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (158 bp):
AGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTAGAGAATCTGCTACAAATATCAATCTCA
GCCATTCGATAGGACATCTAAGACCAGCACCCATATAACCTGTAATGCTTACACGAGCTATGAAA
TAGGCCTAATCACACGAGCTATGGGTCG
Found at i:28121 original size:17 final size:17
Alignment explanation
Indices: 28099--28131 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28089 CACTTGTACA
28099 AATTAATCCATATCCCG
1 AATTAATCCATATCCCG
28116 AATTAATCCATATCCC
1 AATTAATCCATATCCC
28132 AACACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.30
Consensus pattern (17 bp):
AATTAATCCATATCCCG
Found at i:29581 original size:20 final size:18
Alignment explanation
Indices: 29565--29619 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 18
29555 TACAAAATAA
29565 TCAAAATAATTTTAAAATTT
1 TCAAAATAATTTTAAAA--T
*
29585 TCAAAATAATTTTTAAAT
1 TCAAAATAATTTTAAAAT
29603 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTT-TAAAA
29620 ATTCTGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.12
18 12 0.38
20 16 0.50
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
TCAAAATAATTTTAAAAT
Found at i:30741 original size:37 final size:37
Alignment explanation
Indices: 30691--30766 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
30681 GGTAATGAGA
*
30691 TTGGAATGAAGATTAAGATAGGCAGTGAGGAGCCACG
1 TTGGAATGAAGATTAAGATAGGCAGCGAGGAGCCACG
30728 TTGGAATGAAGATTAAGATAGGCAGCGAGGAGCCACG
1 TTGGAATGAAGATTAAGATAGGCAGCGAGGAGCCACG
30765 TT
1 TT
30767 AAGTCCAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (37 bp):
TTGGAATGAAGATTAAGATAGGCAGCGAGGAGCCACG
Found at i:32041 original size:20 final size:20
Alignment explanation
Indices: 32016--32058 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
32006 ATATGGGAAA
32016 TAAAT-AGGATTAATTAAAGC
1 TAAATAAGGATTAATTAAA-C
*
32036 TAAATAATGATTAATTAAAC
1 TAAATAAGGATTAATTAAAC
32056 TAA
1 TAA
32059 TTATTAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (20 bp):
TAAATAAGGATTAATTAAAC
Found at i:34715 original size:18 final size:18
Alignment explanation
Indices: 34678--34719 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34668 ATAACTGATA
**
34678 TGGAGGATACATTTGAGG
1 TGGAGGATACATCGGAGG
*
34696 TGGAGGATACATCGGCGG
1 TGGAGGATACATCGGAGG
34714 TGGAGG
1 TGGAGG
34720 TGGGTGATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.45, T:0.21
Consensus pattern (18 bp):
TGGAGGATACATCGGAGG
Found at i:35695 original size:19 final size:18
Alignment explanation
Indices: 35662--35704 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
35652 TGTACAATGT
35662 AATTAAATAATATAAATTA
1 AATTAAATAATAT-AATTA
*
35681 AATTAAATTAA-ATAATTT
1 AATTAAA-TAATATAATTA
35699 AATTAA
1 AATTAA
35705 CTATTTACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTAAATAATATAATTA
Found at i:39068 original size:16 final size:17
Alignment explanation
Indices: 39047--39086 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39037 TAAATCAATA
39047 ATCATTAA-TGAAAATT
1 ATCATTAATTGAAAATT
*
39063 ATCATTAATTTAAAATT
1 ATCATTAATTGAAAATT
*
39080 AACATTA
1 ATCATTA
39087 GCATTTAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (17 bp):
ATCATTAATTGAAAATT
Found at i:40545 original size:43 final size:42
Alignment explanation
Indices: 40484--40569 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 42
40474 TATAACCTGT
*
40484 AAAATCTCTAATTAAACTCGCATATAACCTTATTAACATGCCA
1 AAAATCTCTAATTAAACTCGAATATAACCTTA-TAACATGCCA
*
40527 AAAATCTCTAATTAAACTCGAATATAACCTTATGACATGCCA
1 AAAATCTCTAATTAAACTCGAATATAACCTTATAACATGCCA
40569 A
1 A
40570 TCGTATCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 10 0.24
43 31 0.76
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (42 bp):
AAAATCTCTAATTAAACTCGAATATAACCTTATAACATGCCA
Found at i:50297 original size:18 final size:18
Alignment explanation
Indices: 50274--50363 Score: 92
Period size: 18 Copynumber: 4.9 Consensus size: 18
50264 ACGAAAGGAA
*
50274 GAGCATGCTGGCTCGTTT
1 GAGCATACTGGCTCGTTT
*
50292 GAGCATGCTGGCTTC-TTT
1 GAGCATACTGGC-TCGTTT
**
50310 GAGCATACTGGCTCGTAA
1 GAGCATACTGGCTCGTTT
* *
50328 GAGTAATTCTGGCTCGTTT
1 GAG-CATACTGGCTCGTTT
50347 GAGCAATACTGGCTCGT
1 GAGC-ATACTGGCTCGT
50364 GAGAGCATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.03
18 30 0.51
19 27 0.46
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (18 bp):
GAGCATACTGGCTCGTTT
Found at i:50341 original size:19 final size:19
Alignment explanation
Indices: 50310--50370 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
50300 TGGCTTCTTT
50310 GAGC-ATACTGGCTCGTAA
1 GAGCAATACTGGCTCGTAA
* * **
50328 GAGTAATTCTGGCTCGTTT
1 GAGCAATACTGGCTCGTAA
*
50347 GAGCAATACTGGCTCGTGA
1 GAGCAATACTGGCTCGTAA
50366 GAGCA
1 GAGCA
50371 TTAGTGGATC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 3 0.09
19 31 0.91
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (19 bp):
GAGCAATACTGGCTCGTAA
Found at i:53034 original size:19 final size:20
Alignment explanation
Indices: 52987--53035 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
52977 ACGACTGAAG
52987 GAAGGAAGAAAGAAGAAAAA
1 GAAGGAAGAAAGAAGAAAAA
*
53007 GAAAG-AGAAAGAAGAAAAA
1 GAAGGAAGAAAGAAGAAAAA
53026 -AAGGAAGAAA
1 GAAGGAAGAAA
53036 AAGGGGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
GAAGGAAGAAAGAAGAAAAA
Found at i:55521 original size:16 final size:16
Alignment explanation
Indices: 55500--55536 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
55490 GAGTTCTAAT
55500 GTAACACCCAAAAATC
1 GTAACACCCAAAAATC
55516 GTAACACCCAAAAATC
1 GTAACACCCAAAAATC
55532 GTAAC
1 GTAAC
55537 CATCTCCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.30, G:0.08, T:0.14
Consensus pattern (16 bp):
GTAACACCCAAAAATC
Found at i:57079 original size:194 final size:194
Alignment explanation
Indices: 56731--57168 Score: 456
Period size: 194 Copynumber: 2.3 Consensus size: 194
56721 TACTAGTACT
* * * * **
56731 CGATGCTGCTCACACGAGCTGTCGAGGACTCATAACATATGTGGTACCCCAACCATCGGTATGGT
1 CGATGCTACTCACACGAGCTGTCGAGGACTCACAACATATGTGGTACCTCAACCATCAGTACAGT
* * ** * * * * *
56796 GTCTATCTGTAAACTGTCTCCCTAACGATGTTGCTCACACGAGTTGTTAAGAATATGCATTTGAG
66 ATCTATCTATAAACTGTCTCCCTAACGATACTACTCACACGAGCTATCAAGAATATGCACTTGAG
* ** *
56861 CATAAATCTCAGCCATTGTAGGGCCTATAATCCATT-TAGGATTCATATCTCTT-TTT-CGACTC
131 CATAAATCCCAGCCATCATAGGGCCTATAATCCATTCTAGGATTCAT-T-TCTTATTTCCAACTC
56923 A
194 A
* * **
56924 CGATGCTACTCACACGAGCTATCGAGGACTCGCAACATATGTGGTACCTCAGTCATCAGTACAGT
1 CGATGCTACTCACACGAGCTGTCGAGGACTCACAACATATGTGGTACCTCAACCATCAGTACAGT
* * * *
56989 ATTTATAC-ATATAATTGTTTCCCTAACGATACTACTCACACGAGCTATCGAGAATATGCACTT-
66 ATCTAT-CTATA-AACTGTCTCCCTAACGATACTACTCACACGAGCTATCAAGAATATGCACTTG
* * *
57052 ATGCATAAATCCCAGCTATCATAGGGCCTGTAATCCATTCTTGGATTCATTTCTTATTTCCCAAC
129 A-GCATAAATCCCAGCCATCATAGGGCCTATAATCCATTCTAGGATTCATTTCTTATTT-CCAAC
57117 TCA
192 TCA
* * * * *
57120 TGATGCTATTCACACGAGTTGTCGAGGACACTCAACATAT-TCGGTACCT
1 CGATGCTACTCACACGAGCTGTCGAGGACTCACAACATATGT-GGTACCT
57169 TAGCCATCGC
Statistics
Matches: 201, Mismatches: 36, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
193 66 0.33
194 78 0.39
195 10 0.05
196 47 0.23
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (194 bp):
CGATGCTACTCACACGAGCTGTCGAGGACTCACAACATATGTGGTACCTCAACCATCAGTACAGT
ATCTATCTATAAACTGTCTCCCTAACGATACTACTCACACGAGCTATCAAGAATATGCACTTGAG
CATAAATCCCAGCCATCATAGGGCCTATAATCCATTCTAGGATTCATTTCTTATTTCCAACTCA
Found at i:57612 original size:22 final size:23
Alignment explanation
Indices: 57585--57630 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
57575 CCACTTTTTG
* *
57585 CAATATTTCTTTA-ACATTTATT
1 CAATATTTCCTTACAAATTTATT
57607 CAATATTTCCTTACAAATTTATT
1 CAATATTTCCTTACAAATTTATT
57630 C
1 C
57631 CTTTAACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (23 bp):
CAATATTTCCTTACAAATTTATT
Found at i:57643 original size:16 final size:16
Alignment explanation
Indices: 57624--57655 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57614 TCCTTACAAA
*
57624 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
57640 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
57656 AAAAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:60782 original size:20 final size:20
Alignment explanation
Indices: 60759--60796 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
60749 TATATTAATT
60759 ATAAATAGGT-TTAATTAAGG
1 ATAAA-AGGTGTTAATTAAGG
*
60779 ATAAAATGTGTTAATTAA
1 ATAAAAGGTGTTAATTAA
60797 AGCTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (20 bp):
ATAAAAGGTGTTAATTAAGG
Found at i:68961 original size:20 final size:21
Alignment explanation
Indices: 68922--68962 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
68912 TGTAATGCTA
*
68922 TGTTTTCTACTTGAATACATTG
1 TGTTATCTACTT-AATACATTG
68944 TGTTATCTACTT-ATACATT
1 TGTTATCTACTTAATACATT
68963 ATGGCTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (21 bp):
TGTTATCTACTTAATACATTG
Found at i:75013 original size:19 final size:19
Alignment explanation
Indices: 74989--75030 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
74979 ACCGATTGTG
74989 GTAAAGGGAAAATTTCAAA
1 GTAAAGGGAAAATTTCAAA
75008 GTAAAGGGAAAATTTCAAA
1 GTAAAGGGAAAATTTCAAA
75027 GTAA
1 GTAA
75031 TCCCTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
GTAAAGGGAAAATTTCAAA
Found at i:76138 original size:25 final size:25
Alignment explanation
Indices: 76093--76153 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
76083 TTTAGCTAAT
*
76093 ACGAGCCCAGATAAGGCTAGCTCTC
1 ACGAGCCCAGATAAAGCTAGCTCTC
* * *
76118 ACGAGCCTAGATAAAGTTAGCTCTT
1 ACGAGCCCAGATAAAGCTAGCTCTC
*
76143 ATGAGCCCAGA
1 ACGAGCCCAGA
76154 AGAGTTTAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (25 bp):
ACGAGCCCAGATAAAGCTAGCTCTC
Found at i:83446 original size:25 final size:25
Alignment explanation
Indices: 83394--83446 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
83384 CCCAAATAAG
* *
83394 GTTAGCTCTCACGAGCCTAGATAAA
1 GTTAGCTCTCACGAGCCCAGACAAA
* *
83419 GTTAGCTCTTACGAGCCCAGACAGA
1 GTTAGCTCTCACGAGCCCAGACAAA
83444 GTT
1 GTT
83447 TAACCAGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (25 bp):
GTTAGCTCTCACGAGCCCAGACAAA
Found at i:88932 original size:17 final size:18
Alignment explanation
Indices: 88900--88938 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
88890 TAAATCTAAA
88900 TAAAACTCTAAATTAACC
1 TAAAACTCTAAATTAACC
*
88918 TAAAACTCT-AATTAATC
1 TAAAACTCTAAATTAACC
88935 TAAA
1 TAAA
88939 CAAGAAGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAACTCTAAATTAACC
Found at i:90960 original size:24 final size:24
Alignment explanation
Indices: 90933--90980 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
90923 GAAATTTAGA
*
90933 ATTTATTAGCATAATATATTTGTT
1 ATTTATTAGCATAACATATTTGTT
*
90957 ATTTATTAGCATAACATCTTTGTT
1 ATTTATTAGCATAACATATTTGTT
90981 GTTACTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTATTAGCATAACATATTTGTT
Found at i:106355 original size:8 final size:8
Alignment explanation
Indices: 106322--106364 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
106312 GTACTTCTTA
106322 TTAATTTTT
1 TTAA-TTTT
106331 TTGAATTTT
1 TT-AATTTT
*
106340 TATGATTTT
1 T-TAATTTT
106349 TTAATTTT
1 TTAATTTT
106357 TTAATTTT
1 TTAATTTT
106365 AATTTTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 14 0.47
9 13 0.43
10 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (8 bp):
TTAATTTT
Found at i:106356 original size:16 final size:16
Alignment explanation
Indices: 106327--106405 Score: 51
Period size: 16 Copynumber: 4.9 Consensus size: 16
106317 TCTTATTAAT
106327 TTTTTTGAATTTTTATGA
1 TTTTTT-AA-TTTTATGA
*
106345 TTTTTTAATTTT-TTA
1 TTTTTTAATTTTATGA
*
106360 -ATTTTAA-TTT-TGA
1 TTTTTTAATTTTATGA
106373 TTTGCTTTAAATTTTA-GA
1 TTT--TTT-AATTTTATGA
106391 TTTTTATAATTTTAT
1 TTTTT-TAATTTTAT
106406 AATTGTTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
13 5 0.10
14 7 0.14
15 2 0.04
16 16 0.33
17 5 0.10
18 14 0.29
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTTTAATTTTATGA
Found at i:107494 original size:52 final size:52
Alignment explanation
Indices: 107435--107544 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 52
107425 TCTGAAATAA
* ** * *
107435 AAAATTATTTTTTAAGTTTTTTGAATTTTTTAAAT-TTTAAATTAATAAAAA-T
1 AAAATTATATTTTAA-TTTTTT-AAAATTATAAATATATAAATTAATAAAAATT
*
107487 AAAATTATATTTTAATTTTTTAAAATTATAAATATATAAATTATTAAAAATT
1 AAAATTATATTTTAATTTTTTAAAATTATAAATATATAAATTAATAAAAATT
107539 AAAATT
1 AAAATT
107545 TAATTTCAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 9 0.18
51 20 0.40
52 21 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (52 bp):
AAAATTATATTTTAATTTTTTAAAATTATAAATATATAAATTAATAAAAATT
Found at i:107498 original size:27 final size:27
Alignment explanation
Indices: 107468--107572 Score: 69
Period size: 27 Copynumber: 4.0 Consensus size: 27
107458 AATTTTTTAA
107468 ATTTTAAATTAATAAAAATAAAATTAT
1 ATTTTAAATTAATAAAAATAAAATTAT
* ** *
107495 ATTTTAATTTTTTAAAATTATAAA-TAT
1 ATTTTAAATTAATAAAAATA-AAATTAT
*
107522 A---TAAATTATTAAAAATTAAAATT-T
1 ATTTTAAATTAATAAAAA-TAAAATTAT
* * *
107546 AATTTCAATCTCATAAAAA-AAAATTAT
1 ATTTTAAAT-TAATAAAAATAAAATTAT
107573 TTCATTCTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
24 16 0.27
25 3 0.05
26 6 0.10
27 25 0.42
28 10 0.17
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
ATTTTAAATTAATAAAAATAAAATTAT
Found at i:110240 original size:17 final size:16
Alignment explanation
Indices: 110215--110252 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
110205 ATTATCAAGA
110215 TAATACAAAAATTGAGAT
1 TAATAC-AAAA-TGAGAT
110233 TAAT-CAAAATGAGAT
1 TAATACAAAATGAGAT
110248 TAATA
1 TAATA
110253 GTTAATAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.53
16 4 0.21
17 1 0.05
18 4 0.21
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (16 bp):
TAATACAAAATGAGAT
Found at i:110247 original size:15 final size:16
Alignment explanation
Indices: 110222--110251 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
110212 AGATAATACA
110222 AAAATTGAGATTAATC
1 AAAATTGAGATTAATC
110238 AAAA-TGAGATTAAT
1 AAAATTGAGATTAAT
110252 AGTTAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.30
Consensus pattern (16 bp):
AAAATTGAGATTAATC
Found at i:110565 original size:27 final size:27
Alignment explanation
Indices: 110525--110606 Score: 137
Period size: 27 Copynumber: 3.0 Consensus size: 27
110515 TTTTGTAACA
* *
110525 CTCTTATACCCGATTTAATCATCAAGT
1 CTCTTATACTCGATTTAATCATCGAGT
110552 CTCTTATACTCGATTTAATCATCGAGT
1 CTCTTATACTCGATTTAATCATCGAGT
*
110579 CTCCTATACTCGATTTAATCATCGAGT
1 CTCTTATACTCGATTTAATCATCGAGT
110606 C
1 C
110607 AAGGTATAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.38
Consensus pattern (27 bp):
CTCTTATACTCGATTTAATCATCGAGT
Found at i:113016 original size:43 final size:41
Alignment explanation
Indices: 112966--113188 Score: 180
Period size: 42 Copynumber: 5.3 Consensus size: 41
112956 ACTTGATGTA
* *
112966 TAAATGGAAGACTCATGTCTCGGATTGAGCATGAGAATTTATAT
1 TAAA-GGAAGACTCATGACTCGGAATGAGCATGAGAA--TATAT
* * * ** *
113010 GAATGGAAGACTCGTGACTCTAAACGAGCATGATG-ATATAT
1 TAAAGGAAGACTCATGACTCGGAATGAGCATGA-GAATATAT
* * *
113051 TAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGAT
1 TAAAGGAAGACTCATGACTCGGAATGAGCATGAGAATAT-AT
** * *
113093 TAAAGGAAGACTCATGACTCGGAATGAGTGTGAGATTATGTT
1 TAAAGGAAGACTCATGACTCGGAATGAGCATGAGAATAT-AT
* * * * *
113135 TAAAAAGGAAGACTTATGACTCGGTA-GAGCATAAGATTGTAT
1 T--AAAGGAAGACTCATGACTCGGAATGAGCATGAGAATATAT
113177 TAAAGGAAGACT
1 TAAAGGAAGACT
113189 TGTGAATTCG
Statistics
Matches: 144, Mismatches: 30, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
40 12 0.08
41 33 0.23
42 41 0.28
43 34 0.24
44 24 0.17
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGACTCGGAATGAGCATGAGAATATAT
Found at i:113062 original size:41 final size:41
Alignment explanation
Indices: 112966--113113 Score: 118
Period size: 41 Copynumber: 3.5 Consensus size: 41
112956 ACTTGATGTA
* * ** *
112966 TAAATGGAAGACTCATGTCTCGGATTGAGCATGAGAATTTATAT
1 TAAA-GGAAGACTCATGACTCGAAACGAGAATGAGAA--TATAT
* * * * *
113010 GAATGGAAGACTCGTGACTCTAAACGAGCATGATG-ATATAT
1 TAAAGGAAGACTCATGACTCGAAACGAGAATGA-GAATATAT
* ** *
113051 TAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGAT
1 TAAAGGAAGACTCATGACTCGAAACGAGAATGAGAATAT-AT
113093 TAAAGGAAGACTCATGACTCG
1 TAAAGGAAGACTCATGACTCG
113114 GAATGAGTGT
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
40 1 0.01
41 33 0.40
42 22 0.27
43 24 0.29
44 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGACTCGAAACGAGAATGAGAATATAT
Found at i:113138 original size:84 final size:84
Alignment explanation
Indices: 112961--113188 Score: 200
Period size: 84 Copynumber: 2.7 Consensus size: 84
112951 GAGACACTTG
* * * *
112961 ATGTATAAATGGAAGACTCATGTCTC-GGATTGAGCATGAGAATTTAT-ATGAATGGAAGACTCG
1 ATGTTTAAA-GGAAGACTCATGTCTCGGGA-TGAGCATGAGAA--TATGATTAAAGGAAGACTCA
*
113024 TGACTCTAAACGAGCATGATGAT
62 TGACTCGAAACGAGCATGATGAT
* *
113047 AT-ATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATTAAAGGAAGACTCATGAC
1 ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAATATGATTAAAGGAAGACTCATGAC
* * **
113111 TCGGAATGAGTGTGA-GATT
66 TCGAAACGAGCATGATGA-T
* * * *
113130 ATGTTTAAAAAGGAAGACTTATGACTCGGTA-GAGCATAAG-AT-TGTATTAAAGGAAGACT
1 ATGTTT--AAAGGAAGACTCATGTCTCGGGATGAGCATGAGAATATG-ATTAAAGGAAGACT
113189 TGTGAATTCG
Statistics
Matches: 118, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
82 5 0.04
83 32 0.27
84 45 0.38
85 14 0.12
86 22 0.19
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (84 bp):
ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAATATGATTAAAGGAAGACTCATGAC
TCGAAACGAGCATGATGAT
Found at i:114940 original size:24 final size:24
Alignment explanation
Indices: 114912--115006 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
114902 TGCTCATCGG
*
114912 CCACTTTACGTTTATGCTCGTCAG
1 CCACTTTACGTTTATGCTCGTCAA
* *
114936 TCACTATACGTTTATGCTCGTCAA
1 CCACTTTACGTTTATGCTCGTCAA
* * *
114960 CCACTTTATGCTTATGTTCGTCAA
1 CCACTTTACGTTTATGCTCGTCAA
*
114984 CCACTTTACGTTTATGTTCGTCA
1 CCACTTTACGTTTATGCTCGTCA
115007 GCACTCGCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (24 bp):
CCACTTTACGTTTATGCTCGTCAA
Found at i:116276 original size:18 final size:18
Alignment explanation
Indices: 116249--116294 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
116239 AAAGCAAATA
*
116249 CTAACCACACAATCCCAT
1 CTAACGACACAATCCCAT
*
116267 CTAACGACACAATCCCGT
1 CTAACGACACAATCCCAT
116285 CTAACGACAC
1 CTAACGACAC
116295 TACACATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (18 bp):
CTAACGACACAATCCCAT
Found at i:118653 original size:29 final size:27
Alignment explanation
Indices: 118602--118676 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
118592 AAACCTTTAA
* * *
118602 AAAGGAACGCCTTTGTGGCAAACCTCTC-
1 AAAGGAATGCCTTTATGGAAAACC-C-CG
118630 AAAGGAATGCCTTTATGGAAAAACCCCG
1 AAAGGAATGCCTTTATGG-AAAACCCCG
*
118658 AAAGGACATGCTTTTATGG
1 AAAGGA-ATGCCTTTATGG
118677 TGATTTCGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 23 0.57
29 16 0.40
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (27 bp):
AAAGGAATGCCTTTATGGAAAACCCCG
Found at i:118830 original size:29 final size:29
Alignment explanation
Indices: 118784--118848 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
118774 AAAGGAAGTC
*
118784 TTTGTGGCTGACTTTGTTA-AAAGAAAGCA
1 TTTGTGGCTGACTCTGTTATAAA-AAAGCA
* *
118813 TTTGTGGCTGTA-TCTGTTATAAAAAGGCC
1 TTTGTGGCTG-ACTCTGTTATAAAAAAGCA
118842 TTTGTGG
1 TTTGTGG
118849 ATAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (29 bp):
TTTGTGGCTGACTCTGTTATAAAAAAGCA
Found at i:120096 original size:21 final size:22
Alignment explanation
Indices: 120072--120120 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
120062 CATGAGAAAT
120072 ATTAGAAG-TAAA-AAATGATTA
1 ATTA-AAGTTAAACAAATGATTA
*
120093 ATTAAAGTTAAACAAGTGATTA
1 ATTAAAGTTAAACAAATGATTA
*
120115 ACTAAA
1 ATTAAA
120121 CTAATTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 8 0.33
22 13 0.54
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (22 bp):
ATTAAAGTTAAACAAATGATTA
Found at i:121122 original size:60 final size:60
Alignment explanation
Indices: 121036--121234 Score: 263
Period size: 60 Copynumber: 3.5 Consensus size: 60
121026 ACGGATTATG
121036 AGGTTCGATGACTCTGTGTCATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAA
1 AGGTTCGATGACTCTGTGTCATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAA
* ** * * *
121096 ACGTTCGATGACTCTGTGTCATCGTGAGTA-T-ATT--AAT-CTTTACAA-ATTG--T-G
1 AGGTTCGATGACTCTGTGTCATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAA
* *
121147 AGGTCCGATGACTATGTGTCATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAA
1 AGGTTCGATGACTCTGTGTCATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAA
121207 AGGTTCGATGACTCTGTGTCATCGTGAG
1 AGGTTCGATGACTCTGTGTCATCGTGAG
121235 AATCAAATGC
Statistics
Matches: 114, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
51 27 0.24
52 2 0.02
53 3 0.03
54 3 0.03
55 8 0.07
56 8 0.07
57 3 0.03
58 3 0.03
59 2 0.02
60 55 0.48
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (60 bp):
AGGTTCGATGACTCTGTGTCATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAA
Found at i:121185 original size:111 final size:112
Alignment explanation
Indices: 120990--121234 Score: 420
Period size: 111 Copynumber: 2.2 Consensus size: 112
120980 AAAAGGGTTT
* ** * *
120990 GATGACTATGTGTCATCGTGAGTATATTAATCTTTTACGGATTATGAGGTTCGATGACTCTGTGT
1 GATGACTCTGTGTCATCGTGAGTATATTAATCTTTTACAAATTATGAGGTCCGATGACTATGTGT
121055 CATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAAACGTTC
66 CATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAAACGTTC
*
121102 GATGACTCTGTGTCATCGTGAGTATATTAATC-TTTACAAATTGTGAGGTCCGATGACTATGTGT
1 GATGACTCTGTGTCATCGTGAGTATATTAATCTTTTACAAATTATGAGGTCCGATGACTATGTGT
*
121166 CATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAAAGGTTC
66 CATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAAACGTTC
121213 GATGACTCTGTGTCATCGTGAG
1 GATGACTCTGTGTCATCGTGAG
121235 AATCAAATGC
Statistics
Matches: 126, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
111 95 0.75
112 31 0.25
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (112 bp):
GATGACTCTGTGTCATCGTGAGTATATTAATCTTTTACAAATTATGAGGTCCGATGACTATGTGT
CATCGTGAGTACTAATTGAAATAAATTCCAATATGGATTAAACGTTC
Found at i:125405 original size:12 final size:12
Alignment explanation
Indices: 125384--125415 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
125374 CGAGAGGCAT
125384 AAAATAAAATAG
1 AAAATAAAATAG
*
125396 AAATTAAAATAG
1 AAAATAAAATAG
125408 AAAATAAA
1 AAAATAAA
125416 GAGTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (12 bp):
AAAATAAAATAG
Found at i:127543 original size:42 final size:41
Alignment explanation
Indices: 127392--127544 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 41
127382 TTTATAGAAG
* ** * *
127392 GGAAGACTCATGTCTCGGGTTGAGCATGAGGATTTAT-ATAAA
1 GGAAGACTCATGTCTCGAGAAGAGAATGA--AATTATGATAAA
* * *
127434 GGAAGACTCATATCTAGAGAAGAGAA-CAAGATTATGATTAAA
1 GGAAGACTCATGTCTCGAGAAGAGAATGAA-ATTATGA-TAAA
127476 GGAAGACTCATGTCTCGAGAAGAGAATGAAATTATGATCAAA
1 GGAAGACTCATGTCTCGAGAAGAGAATGAAATTATGAT-AAA
* *
127518 GGAAGACTCATGTCTCGGGATGAGAAT
1 GGAAGACTCATGTCTCGAGAAGAGAAT
127545 AAGAATACGA
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.01
40 4 0.04
41 3 0.03
42 83 0.89
43 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.24
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAGAAGAGAATGAAATTATGATAAA
Found at i:127543 original size:84 final size:83
Alignment explanation
Indices: 127392--127563 Score: 202
Period size: 84 Copynumber: 2.0 Consensus size: 83
127382 TTTATAGAAG
* ** * *
127392 GGAAGACTCATGTCTCGGGTTGAGCATGAGGATTTATATAAAGGAAGACTCATATCTAGAGAAGA
1 GGAAGACTCATGTCTCGAGAAGAGAATGA-GAATTATATAAAGGAAGACTCATATCTAGAGAAGA
* *
127457 GAACAAGATTATGATTAAA
65 GAACAAGAATACGATTAAA
* * * *
127476 GGAAGACTCATGTCTCGAGAAGAGAATGA-AATTATGATCAAAGGAAGACTCATGTCTCGGGATG
1 GGAAGACTCATGTCTCGAGAAGAGAATGAGAATTAT-AT-AAAGGAAGACTCATATCTAGAGAAG
*
127540 AGAATAAGAATACGATTAAA
64 AGAACAAGAATACGATTAAA
127560 GGAA
1 GGAA
127564 CACTTATGAC
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
82 5 0.07
83 2 0.03
84 67 0.91
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.23
Consensus pattern (83 bp):
GGAAGACTCATGTCTCGAGAAGAGAATGAGAATTATATAAAGGAAGACTCATATCTAGAGAAGAG
AACAAGAATACGATTAAA
Found at i:127561 original size:42 final size:42
Alignment explanation
Indices: 127430--127563 Score: 171
Period size: 42 Copynumber: 3.2 Consensus size: 42
127420 AGGATTTATA
* * * *
127430 TAAAGGAAGACTCATATCTAGAGAAGAGAACAAGATTATGAT
1 TAAAGGAAGACTCATGTCTCGAGAAGAGAATAAGAATATGAT
*
127472 TAAAGGAAGACTCATGTCTCGAGAAGAGAATGAA-ATTATGAT
1 TAAAGGAAGACTCATGTCTCGAGAAGAGAAT-AAGAATATGAT
* * * *
127514 CAAAGGAAGACTCATGTCTCGGGATGAGAATAAGAATACGAT
1 TAAAGGAAGACTCATGTCTCGAGAAGAGAATAAGAATATGAT
127556 TAAAGGAA
1 TAAAGGAA
127564 CACTTATGAC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 2 0.02
42 77 0.95
43 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (42 bp):
TAAAGGAAGACTCATGTCTCGAGAAGAGAATAAGAATATGAT
Found at i:133889 original size:20 final size:21
Alignment explanation
Indices: 133864--133906 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
133854 AAATGCTTGC
* *
133864 TTTGTAAGGTT-ATGGATAGA
1 TTTGTAAGCTTGATGAATAGA
133884 TTTGTAAGCTTGATGAATAGA
1 TTTGTAAGCTTGATGAATAGA
133905 TT
1 TT
133907 CATTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (21 bp):
TTTGTAAGCTTGATGAATAGA
Found at i:133996 original size:24 final size:24
Alignment explanation
Indices: 133956--134007 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
133946 TGAGGACTAG
*
133956 GTTGTGAAAATGATGAAAATGAAT
1 GTTGTGAAAATGATGAAAAGGAAT
* *
133980 GTTGTG-AAATAGTTGAATAGGAAT
1 GTTGTGAAAAT-GATGAAAAGGAAT
134004 GTTG
1 GTTG
134008 GATGAATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (24 bp):
GTTGTGAAAATGATGAAAAGGAAT
Found at i:135149 original size:21 final size:21
Alignment explanation
Indices: 135125--135202 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
135115 CTAGAGTTTT
135125 TAGTATCGATAGAAGCATAAC
1 TAGTATCGATAGAAGCATAAC
* * * *
135146 TAGTTTCGGTAGATG-TTACAC
1 TAGTATCGATAGAAGCATA-AC
* * *
135167 TTGTATCGGTAGAA-CTATCAC
1 TAGTATCGATAGAAGC-ATAAC
*
135188 AAGTATCGATAGAAG
1 TAGTATCGATAGAAG
135203 TCTACACTGT
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
20 2 0.05
21 38 0.93
22 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (21 bp):
TAGTATCGATAGAAGCATAAC
Found at i:137783 original size:22 final size:22
Alignment explanation
Indices: 137758--137815 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
137748 TAAAAAATAT
137758 TCAATTAAATTGGCGCAATCAA
1 TCAATTAAATTGGCGCAATCAA
*
137780 TCAATTAAATTGACGCAATCAA
1 TCAATTAAATTGGCGCAATCAA
*
137802 TCAATTATATTGGC
1 TCAATTAAATTGGC
137816 ATATTACATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (22 bp):
TCAATTAAATTGGCGCAATCAA
Found at i:138194 original size:14 final size:14
Alignment explanation
Indices: 138175--138209 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
138165 TGTTTGACTA
*
138175 AAAATGGTTTTCGG
1 AAAATGATTTTCGG
*
138189 AAAATGATTTTTGG
1 AAAATGATTTTCGG
138203 AAAATGA
1 AAAATGA
138210 ATTACTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (14 bp):
AAAATGATTTTCGG
Found at i:138646 original size:46 final size:46
Alignment explanation
Indices: 138579--138680 Score: 152
Period size: 46 Copynumber: 2.2 Consensus size: 46
138569 TATTACAAAT
* * **
138579 TAGTAGTACACCACATGATAACTACAATATTTTCCAAGTGCATAAC
1 TAGTATTACACCACATGATAACTACAACATCGTCCAAGTGCATAAC
138625 TAGTATTACACCACATGATAACTACAACATCGTCCAAGTGCATAAC
1 TAGTATTACACCACATGATAACTACAACATCGTCCAAGTGCATAAC
138671 T-GATATTACA
1 TAG-TATTACA
138681 AATTAGTAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 1 0.02
46 50 0.98
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (46 bp):
TAGTATTACACCACATGATAACTACAACATCGTCCAAGTGCATAAC
Found at i:143853 original size:18 final size:16
Alignment explanation
Indices: 143832--143887 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
143822 TTAAATTCCA
143832 ATTTAACCCAAAATATTT
1 ATTTAACCCAAAA-A-TT
*
143850 ATTTTACCCAAAAATT
1 ATTTAACCCAAAAATT
*
143866 ATTTAAAACCATAAAATT
1 ATTT-AACCCA-AAAATT
143884 ATTT
1 ATTT
143888 TTTCTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 6 0.18
17 5 0.15
18 22 0.67
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTAACCCAAAAATT
Found at i:144101 original size:21 final size:21
Alignment explanation
Indices: 144061--144101 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
144051 ACAACAGGTT
*
144061 TTCTTACTCATGATTGTTTTG
1 TTCTTACTCATGATTCTTTTG
**
144082 TTCTTACTCATTTTTCTTTT
1 TTCTTACTCATGATTCTTTT
144102 CTTTTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.17, G:0.07, T:0.63
Consensus pattern (21 bp):
TTCTTACTCATGATTCTTTTG
Found at i:154736 original size:21 final size:21
Alignment explanation
Indices: 154696--154736 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
154686 TTTAAGGTAC
*
154696 GGGTGTGTGAGATAGACACAA
1 GGGTGTGTGAGAGAGACACAA
* *
154717 GGGTGTGTGGGAGAGCCACA
1 GGGTGTGTGAGAGAGACACA
154737 CGGTCGTGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.44, T:0.17
Consensus pattern (21 bp):
GGGTGTGTGAGAGAGACACAA
Found at i:176666 original size:19 final size:19
Alignment explanation
Indices: 176617--176666 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
176607 TCTCCAACTT
*
176617 AATTTAACTT-TAATTAAA
1 AATTTAAATTATAATTAAA
*
176635 ATACTTAAA--ATAATTAAA
1 A-ATTTAAATTATAATTAAA
176653 AATTTAAATTATAA
1 AATTTAAATTATAA
176667 GCAATCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTAAATTATAATTAAA
Found at i:176877 original size:21 final size:22
Alignment explanation
Indices: 176842--176887 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
176832 CAAGTTTAGG
* *
176842 GTTTAATGGTTTGGGCTTACGA
1 GTTTAATGATTTGGGCTTACAA
*
176864 GTTTAA-GATTTGGGGTTACAA
1 GTTTAATGATTTGGGCTTACAA
176885 GTT
1 GTT
176888 ATGAGTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (22 bp):
GTTTAATGATTTGGGCTTACAA
Found at i:176896 original size:21 final size:20
Alignment explanation
Indices: 176850--176901 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
176840 GGGTTTAATG
* *
176850 GTTTGGGCTTACGAGTTTAA
1 GTTTGGGGTTACAAGTTTAA
*
176870 GATTTGGGGTTACAAGTTATGA
1 G-TTTGGGGTTACAAGTT-TAA
176892 GTTTGGGGTT
1 GTTTGGGGTT
176902 TAATGTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.19, C:0.06, G:0.35, T:0.40
Consensus pattern (20 bp):
GTTTGGGGTTACAAGTTTAA
Found at i:177936 original size:117 final size:117
Alignment explanation
Indices: 177502--178222 Score: 598
Period size: 117 Copynumber: 6.2 Consensus size: 117
177492 GACACCATCT
** * * * *
177502 TTTTTATTTGATAAAAAATCAATTTTTTT-GTATTGGTCATTGCATGGTCGACA-C-CCT-TTTT
1 TTTTTATCAGATAAAAAAT--ATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTATTTA
* * * * *
177563 TCTCAGATAAAAA-T--ATTTTTTTTGGTGTTGGCCATTGCATGGCCCACACCCC
64 TCTGATAAAAAAATTCAATTTTTTTT-GTGTTGGCCATTGCATGGCCGACCCCCC
* * * * *
177615 TTATTTATCTGATAAAAAATTATTTTTTTGGTATTGGCCATTGCATGGCCGATACCATCTTTTTT
1 TT-TTTATCAGATAAAAAA-TATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCA-CCTATTT
* ** *
177680 ATCTGCT-AAAAAA-TCAATTTTTTTTTGTGTTGATCATTGCATGGCCGACACCCTC
63 ATCTGATAAAAAAATTCAA-TTTTTTTTGTGTTGGCCATTGCATGGCCGAC-CCCCC
* * * * * * * * * *
177735 TTTTTGTTAGATGAAAAATATTTTTTTGGTGTTAGTCA-TGCCTTGACCGACACCGCATTTTTTA
1 TTTTTATCAGATAAAAAATATTTTTTTGGTGTTGGCCATTG-CATGGCCGACACCAC-CTATTTA
*
177799 TCT--T-AAAAAATTC-ATTTTTTTTGTGTTGGCCATTGCATAGCCGACTCCCCC
64 TCTGATAAAAAAATTCAATTTTTTTTGTGTTGGCCATTGCATGGCCGAC-CCCCC
* * * *
177850 TTTTTGTCAGATAAAAAATA-TTTTTTGGTGTTGGCAATTGCATGGCCGACACCACGTATTTATT
1 TTTTTATCAGATAAAAAATATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTATTTATC
* * * * * * *
177914 TGATAAAAAAAATCAATTTTTTTGGTGTTAGCCATTGAATGGTCGACACCACA
66 TGATAAAAAAATTCAATTTTTTTTGTGTTGGCCATTGCATGGCCGAC-CCCCC
* ** *
177967 TTTTTATCTGATAAAAAAATCAATTTTTTTGGTGTTGGTTATTGCATGGCCGACATCACCTATTT
1 TTTTTATCAGAT-AAAAAAT--ATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTATTT
* * * **
178032 ATCTGATAAAAAAATTCAA-TTTTTTGGTGTTAGCCATTGCATGGCTGA--AACC
63 ATCTGATAAAAAAATTCAATTTTTTTTGTGTTGGCCATTGCATGGCCGACCCCCC
* * *
178084 TTTTTATCCGATAAAAAATTTTAATTTTTTT-GTGTTGGCCATTGCATGGCTGACACCACCTTTT
1 TTTTTATCAGATAAAAAA---T-ATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTATT
* * **
178148 TATCTGATAAAAAAATTCAAATTTTTTTGTGTTGGCCATTGCATGGCTGACACCAAC
62 TATCTGATAAAAAAATTCAATTTTTTTTGTGTTGGCCATTGCATGGCCGAC-CCCCC
*
178205 TTTTTATCTGATAAAAAA
1 TTTTTATCAGATAAAAAA
178223 AATTAAATTT
Statistics
Matches: 503, Mismatches: 75, Indels: 52
0.80 0.12 0.08
Matches are distributed among these distances:
113 17 0.03
114 62 0.12
115 55 0.11
116 22 0.04
117 114 0.23
118 86 0.17
119 34 0.07
120 40 0.08
121 73 0.15
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (117 bp):
TTTTTATCAGATAAAAAATATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTATTTATC
TGATAAAAAAATTCAATTTTTTTTGTGTTGGCCATTGCATGGCCGACCCCCC
Found at i:178033 original size:60 final size:60
Alignment explanation
Indices: 177456--178330 Score: 718
Period size: 61 Copynumber: 14.8 Consensus size: 60
177446 TCTTTTTGTC
* * * * *
177456 AAATAAATATTTTTTGGTATTGGTCA-TGCATTGGCCGACACCATCTTTTTTATTTGAT-AAA
1 AAATCAAT-TTTTTTGGTGTTGGCCATTGCA-TGGCCGACACCA-CCTTTTTATCTGATAAAA
* * * * * *
177517 AAATCAATTTTTTT-GTATTGGTCATTGCATGGTCGACA-C-CCTTTTT-TCTCAGATAA
1 AAATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAA
* *
177573 AAAT-ATTTTTTTTGGTGTTGGCCATTGCATGGCCCACACC-CCTTATTTATCTGAT-AAA
1 AAATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTT-TTTATCTGATAAAA
* * * * *
177631 AAAT-TATTTTTTTGGTATTGGCCATTGCATGGCCGATACCATCTTTTTTATCTGCT-AAA
1 AAATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCA-CCTTTTTATCTGATAAAA
* ** * *
177690 AAATCAATTTTTTTTTGTGTTGATCATTGCATGGCCGACACC-CTCTTTTTGT-TAGAT-GAA
1 AAATCAA-TTTTTTTGGTGTTGGCCATTGCATGGCCGACACCAC-CTTTTTATCT-GATAAAA
* * * * * *
177750 AAAT--ATTTTTTTGGTGTTAGTCA-TGCCTTGACCGACACCGCATTTTTTATCT--TAAAA
1 AAATCAATTTTTTTGGTGTTGGCCATTG-CATGGCCGACACCAC-CTTTTTATCTGATAAAA
* * * * * * *
177807 AATTC-ATTTTTTTTGTGTTGGCCATTGCATAGCCGACTCCCCCTTTTTGTCAGAT-AAA
1 AAATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAA
* * * *
177865 AAAT--A-TTTTTTGGTGTTGGCAATTGCATGGCCGACACCACGTATTTATTTGATAAAAA
1 AAATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGAT-AAAA
* * * *
177923 AAATCAATTTTTTTGGTGTTAGCCATTGAATGGTCGACACCACATTTTTATCTGATAAAA
1 AAATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAA
** * *
177983 AAATCAATTTTTTTGGTGTTGGTTATTGCATGGCCGACATCACCTATTTATCTGATAAAA
1 AAATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAA
* * *
178043 AAATTCAA-TTTTTTGGTGTTAGCCATTGCATGGCTGA-A--ACCTTTTTATCCGATAAAA
1 AAA-TCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAA
* * *
178100 AATTTTAATTTTTTT-GTGTTGGCCATTGCATGGCTGACACCACCTTTTTATCTGATAAAA
1 AA-ATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAA
* *
178160 AAATTCAAATTTTTTT-GTGTTGGCCATTGCATGGCTGACACCAACTTTTTATCTGATAAAAA
1 AAA-TC-AATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGAT-AAAA
* * * * * * *
178222 AAATTAAATTTTTTGGTGTTGGTCA-TGCATTGACTGACACCA-CTATTGGTTGTCAGATAAAA
1 AAATCAATTTTTTTGGTGTTGGCCATTGCA-TGGCCGACACCACCT-TT--TTATCTGATAAAA
* * * * *
178284 AAATAAATTTTTTTGGTGTTAGTCA-TGCATTGGTCGACACCAACTTT
1 AAATCAATTTTTTTGGTGTTGGCCATTGCA-TGGCCGACACCACCTTT
178331 CCCTCCTTTC
Statistics
Matches: 670, Mismatches: 104, Indels: 79
0.79 0.12 0.09
Matches are distributed among these distances:
55 11 0.02
56 73 0.11
57 87 0.13
58 95 0.14
59 45 0.07
60 148 0.22
61 153 0.23
62 49 0.07
63 9 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (60 bp):
AAATCAATTTTTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAA
Found at i:179746 original size:30 final size:30
Alignment explanation
Indices: 179685--179795 Score: 123
Period size: 30 Copynumber: 3.7 Consensus size: 30
179675 TTTTGATTTT
* * * *
179685 TTTCGTTTATTTTTTTAATTTAATTTGTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
* *
179715 TTTCATTTACATTTTAAATTTCATTTCTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
* * * *
179745 TTTCCTGTATATTTTAATTTTAATTTGTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
*
179775 TTTCGTTTATATTTTAAATTT
1 TTTCATTTATATTTTAAATTT
179796 TCATTTCTTA
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTCATTTATATTTTAAATTTAATTTCTAA
Found at i:180739 original size:61 final size:60
Alignment explanation
Indices: 180664--180821 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 60
180654 CCAATGCATG
* *
180664 ACCAACACAAAAAAAAATTGAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATA
1 ACCAACAC--AAAAAAATTGAATTTTTTTATCAGATAAAAAGGTAGCGTCGACCATGCAATA
*** * * *
180726 GTTAACACTAAAAAAATTGAATTTTTTTATCAAAT-AAAAGGTAGCGTTGATCATGCAATA
1 ACCAACAC-AAAAAAATTGAATTTTTTTATCAGATAAAAAGGTAGCGTCGACCATGCAATA
* *
180786 ACCATCACCAAAAAATTGAA-TTTTTTATCAGATAAA
1 ACCAACACAAAAAAATTGAATTTTTTTATCAGATAAA
180822 TTGGCCAATA
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
58 12 0.15
59 13 0.16
60 25 0.31
61 25 0.31
62 5 0.06
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (60 bp):
ACCAACACAAAAAAATTGAATTTTTTTATCAGATAAAAAGGTAGCGTCGACCATGCAATA
Found at i:180852 original size:41 final size:41
Alignment explanation
Indices: 180784--180903 Score: 190
Period size: 41 Copynumber: 3.0 Consensus size: 41
180774 GATCATGCAA
*
180784 TAACCATCACC-AAAAAATTGAA-TTTTTTATCAGATAAAT
1 TAACCAACACCAAAAAAATTGAATTTTTTTATCAGATAAAT
** *
180823 TGGCCAATACCAAAAAAATTGAATTTTTTTATCAGATAAAT
1 TAACCAACACCAAAAAAATTGAATTTTTTTATCAGATAAAT
180864 TAACCAACACCAAAAAAATTGAATTTTTTTATCAGATAAA
1 TAACCAACACCAAAAAAATTGAATTTTTTTATCAGATAAA
180904 AAGGTGGTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 7 0.10
40 11 0.15
41 54 0.75
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (41 bp):
TAACCAACACCAAAAAAATTGAATTTTTTTATCAGATAAAT
Found at i:180937 original size:61 final size:59
Alignment explanation
Indices: 180866--181209 Score: 344
Period size: 60 Copynumber: 5.8 Consensus size: 59
180856 AGATAAATTA
180866 ACCAACACCAAAAAAATTGAATTTTTTTATCAGATAAAAAGGTGGTGTCGGCCATGCAATG
1 ACCAACACCAAAAAAATT--ATTTTTTTATCAGATAAAAAGGTGGTGTCGGCCATGCAATG
** * * *
180927 GTCAACACCAAAAAAATTGATTTTTTTATCAGATAAATAGGTGGTGTCAGTCATGCAATG
1 ACCAACACCAAAAAAATT-ATTTTTTTATCAGATAAAAAGGTGGTGTCGGCCATGCAATG
* *
180987 ACCAACACCAAAAAAA-TA-TTTTTTATCTGACAAAAAGG-GAGTGTCGGCCATGCAATG
1 ACCAACACCAAAAAAATTATTTTTTTATCAGATAAAAAGGTG-GTGTCGGCCATGCAATG
* * * * *
181044 GCCAACACAAAAAAAATTAATTTTTTT-TCCAAATAAAAAATGTGGTGTCGGCCAAGGC-ATG
1 ACCAACACCAAAAAAATT-ATTTTTTTAT-CAGAT-AAAAAGGTGGTGTCGGCC-ATGCAATG
** * * * ** *
181105 ACCAACACCAAAAAAA-TATATTTTTTATTTGACAAAAAAGAGGTGTCAACCATGCAATT
1 ACCAACACCAAAAAAATTAT-TTTTTTATCAGATAAAAAGGTGGTGTCGGCCATGCAATG
*
181164 ACCAACA-CAAAAAAATTGATTTTTTT-TCAAATAAAAAAGGTGGTGT
1 ACCAACACCAAAAAAATT-ATTTTTTTATCAGAT-AAAAAGGTGGTGT
181210 TTATCAAGGC
Statistics
Matches: 231, Mismatches: 38, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
56 1 0.00
57 46 0.20
58 15 0.06
59 46 0.20
60 70 0.30
61 49 0.21
62 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (59 bp):
ACCAACACCAAAAAAATTATTTTTTTATCAGATAAAAAGGTGGTGTCGGCCATGCAATG
Found at i:181033 original size:117 final size:118
Alignment explanation
Indices: 180866--181259 Score: 460
Period size: 117 Copynumber: 3.3 Consensus size: 118
180856 AGATAAATTA
* * * *
180866 ACCAACACCAAAAAAATTGAATTTTTTTATCAGATAAAAAGGTG-GTGTCGGCCATGCAATGGTC
1 ACCAACACCAAAAAAAAT--A-TTTTTTATCTGACAAAAAGG-GAGTGTCGGCCATGCAATGGCC
* * *
180930 AACACCAAAAAAATTGATTTTTTTATCAGAT-AAATAGGTGGTGTCAGTC-ATGCAATG
62 AACACCAAAAAAATTGATTTTTTT-TCAAATAAAAAAGGTGGTGTCAGTCAAGGC-ATG
180987 ACCAACACC-AAAAAAATATTTTTTATCTGACAAAAAGGGAGTGTCGGCCATGCAATGGCCAACA
1 ACCAACACCAAAAAAAATATTTTTTATCTGACAAAAAGGGAGTGTCGGCCATGCAATGGCCAACA
* * * * *
181051 CAAAAAAAATTAATTTTTTTTCCAAATAAAAAATGTGGTGTCGGCCAAGGCATG
66 CCAAAAAAATTGATTTTTTTT-CAAATAAAAAAGGTGGTGTCAGTCAAGGCATG
* * ** **
181105 ACCAACACCAAAAAAATATATTTTTTATTTGACAAAAA-AGAGGTGTCAACCATGCAATTACCAA
1 ACCAACACCAAAAAAA-ATATTTTTTATCTGACAAAAAGGGA-GTGTCGGCCATGCAATGGCCAA
*
181169 CA-CAAAAAAATTGATTTTTTTTCAAATAAAAAAGGTGGTGTTTA-TCAAGGCATG
64 CACCAAAAAAATTGATTTTTTTTCAAATAAAAAAGGTGGTG-TCAGTCAAGGCATG
* *
181223 ACCAAAACCAAAAAAAATATTTTTTATTTGACAAAAA
1 ACCAACACCAAAAAAAATATTTTTTATCTGACAAAAA
181260 ATGCATGGCC
Statistics
Matches: 240, Mismatches: 25, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
116 2 0.01
117 84 0.35
118 68 0.28
119 30 0.12
120 47 0.20
121 9 0.04
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (118 bp):
ACCAACACCAAAAAAAATATTTTTTATCTGACAAAAAGGGAGTGTCGGCCATGCAATGGCCAACA
CCAAAAAAATTGATTTTTTTTCAAATAAAAAAGGTGGTGTCAGTCAAGGCATG
Found at i:181150 original size:59 final size:60
Alignment explanation
Indices: 180866--181260 Score: 232
Period size: 60 Copynumber: 6.7 Consensus size: 60
180856 AGATAAATTA
** * * *
180866 ACCAACACCAAAAAAAT-TGAATTTTTTTATCAGA-TAAAAAGGTGGTGTCGGCCATGCAATG
1 ACCAACACCAAAAAAATAT--A-TTTTTTATTTGACAAAAAAGGTGGTGTCGACCAGGCAATG
** ** * * * *
180927 GTCAACACCAAAAAAAT-TGATTTTTTTATCAGA-TAAATAGGTGGTGTC-AGTCATGCAATG
1 ACCAACACCAAAAAAATAT-A-TTTTTTATTTGACAAAAAAGGTGGTGTCGA-CCAGGCAATG
* * *
180987 ACCAACACC-AAAAAA-ATATTTTTTATCTGAC-AAAAAGG-GAGTGTCGGCCATGCAATG
1 ACCAACACCAAAAAAATATATTTTTTATTTGACAAAAAAGGTG-GTGTCGACCAGGCAATG
* * ** * * *
181044 GCCAACACAAAAAAAAT-TAATTTTTT-TTCCAAATAAAAAATGTGGTGTCGGCCAAGGC-ATG
1 ACCAACACCAAAAAAATAT-ATTTTTTATT--TGACAAAAAAGGTGGTGTCGACC-AGGCAATG
* * * *
181105 ACCAACACCAAAAAAATATATTTTTTATTTGACAAAAAA-GAGGTGTCAACCATGCAATT
1 ACCAACACCAAAAAAATATATTTTTTATTTGACAAAAAAGGTGGTGTCGACCAGGCAATG
** * ** *
181164 ACCAACA-CAAAAAAAT-TGATTTTTT-TTCAAATAAAAAAGGTGGTGTTTATCAAGGC-ATG
1 ACCAACACCAAAAAAATAT-ATTTTTTATT-TGACAAAAAAGGTGGTGTCGA-CCAGGCAATG
*
181223 ACCAAAACCAAAAAAA-ATATTTTTTATTTGACAAAAAA
1 ACCAACACCAAAAAAATATATTTTTTATTTGACAAAAAA
181261 TGCATGGCCA
Statistics
Matches: 268, Mismatches: 43, Indels: 48
0.75 0.12 0.13
Matches are distributed among these distances:
56 1 0.00
57 41 0.15
58 35 0.13
59 61 0.23
60 67 0.25
61 56 0.21
62 7 0.03
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (60 bp):
ACCAACACCAAAAAAATATATTTTTTATTTGACAAAAAAGGTGGTGTCGACCAGGCAATG
Found at i:181260 original size:118 final size:117
Alignment explanation
Indices: 180917--181260 Score: 403
Period size: 118 Copynumber: 2.9 Consensus size: 117
180907 GTGGTGTCGG
** * *
180917 CCATGCAATGGTCAACACCAAAAAAATTGATTTTTTTATCAGAT-AAATAGGTGGTG-TCAGTC-
1 CCATGCAATGACCAACA-CAAAAAAATTGATTTTTTT-TCAAATAAAAAAGGTGGTGTTCA-TCA
* * ** **
180979 ATGCAATGACCAACACC-AAAAAAATATTTTTTATCTGACAAAAAGGGAGTGTCGG
63 AGGC-ATGACCAACACCAAAAAAAATATTTTTTATTTGACAAAAAAAGAGTGTCAA
* * * **
181034 CCATGCAATGGCCAACACAAAAAAAATTAATTTTTTTTCCAAATAAAAAATGTGGTG-TCGGCCA
1 CCATGCAATGACCAACAC-AAAAAAATTGATTTTTTTT-CAAATAAAAAAGGTGGTGTTC-ATCA
181098 AGGCATGACCAACACCAAAAAAATATATTTTTTATTTGAC-AAAAAAGAGGTGTCAA
63 AGGCATGACCAACACCAAAAAAA-ATATTTTTTATTTGACAAAAAAAGA-GTGTCAA
* *
181154 CCATGCAATTACCAACACAAAAAAATTGATTTTTTTTCAAATAAAAAAGGTGGTGTTTATCAAGG
1 CCATGCAATGACCAACACAAAAAAATTGATTTTTTTTCAAATAAAAAAGGTGGTGTTCATCAAGG
*
181219 CATGACCAAAACCAAAAAAAATATTTTTTATTTGACAAAAAA
66 CATGACCAACACCAAAAAAAATATTTTTTATTTGACAAAAAA
181261 TGCATGGCCA
Statistics
Matches: 196, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
116 2 0.01
117 53 0.27
118 71 0.36
119 34 0.17
120 36 0.18
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (117 bp):
CCATGCAATGACCAACACAAAAAAATTGATTTTTTTTCAAATAAAAAAGGTGGTGTTCATCAAGG
CATGACCAACACCAAAAAAAATATTTTTTATTTGACAAAAAAAGAGTGTCAA
Found at i:184414 original size:18 final size:19
Alignment explanation
Indices: 184383--184423 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
184373 AACTTTCGGT
*
184383 TTAAATTAAATTAA-TCGA
1 TTAAACTAAATTAATTCGA
*
184401 TTAAACTAATTTAATTCGA
1 TTAAACTAAATTAATTCGA
184420 TTAA
1 TTAA
184424 TCGATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (19 bp):
TTAAACTAAATTAATTCGA
Done.