Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005250.1 Hibiscus syriacus cultivar Beakdansim tig00011874_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: 190534
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:117073 original size:82 final size:80
Alignment explanation
Indices: 116984--117289 Score: 418
Period size: 82 Copynumber: 3.7 Consensus size: 80
116974 ACAACTGTAG
* *
116984 ACTATCGCAA-CGAATTTAGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAATGGAA
1 ACTATCGCAACCGAA-ATAGAAAATCGCAACG-CAA-TTTCA-ACTATCGCAACGCGAAATGGAA
117047 AATCGCAACGCGATTTTCA
62 AATCGCAACGCGATTTTCA
*
117066 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAAC-CGAAATAGAAAATCGCAACGC-AATTTCAACTATCGCAACGCGAAATGGAAAA
*
117131 TCGCAACGCGAATTTCA
64 TCGCAACGCGATTTTCA
* * *
117148 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCACAACGCGAAATGAAAAA
1 ACTATCGCAAC-CGAAATAGAAAATCGCAACGC-AATTTCAACTATCGCAACGCGAAATGGAAAA
117213 TCGCAACGCGATTTTCA
64 TCGCAACGCGATTTTCA
* * *
117230 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCTCAACGCGAAATG
1 ACTATCGCAAC-CGAAATAGAAAATCGCAACGC-AATTTCAACTATCGCAACGCGAAATG
117290 CAACGCGAAT
Statistics
Matches: 209, Mismatches: 11, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
82 188 0.90
83 17 0.08
84 4 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (80 bp):
ACTATCGCAACCGAAATAGAAAATCGCAACGCAATTTCAACTATCGCAACGCGAAATGGAAAATC
GCAACGCGATTTTCA
Found at i:117306 original size:41 final size:41
Alignment explanation
Indices: 117025--117289 Score: 476
Period size: 41 Copynumber: 6.5 Consensus size: 41
117015 ACAACTGTAG
117025 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
117066 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
117107 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
117148 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
117189 ACTATCACAACGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
117230 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
117271 ACTATCTCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
117290 CAACGCGAAT
Statistics
Matches: 215, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 215 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:120529 original size:47 final size:47
Alignment explanation
Indices: 120460--120556 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
120450 TCATCATAAA
*
120460 TGAGCATTTTAAAATGACCCACAACTTGTAAATGTTGTACACTAGTC
1 TGAGCATTTTAAAAGGACCCACAACTTGTAAATGTTGTACACTAGTC
120507 TGAGCATTTTAAAAGGACCCACAACTTGTAAATGTTGTACACTAGTC
1 TGAGCATTTTAAAAGGACCCACAACTTGTAAATGTTGTACACTAGTC
120554 TGA
1 TGA
120557 AAGTTATGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (47 bp):
TGAGCATTTTAAAAGGACCCACAACTTGTAAATGTTGTACACTAGTC
Found at i:122422 original size:21 final size:21
Alignment explanation
Indices: 122393--122445 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
122383 ATTCTGACTA
122393 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
122414 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
* *
122435 TTGCAATGCGA
1 TCGCATTGCGA
122446 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:122465 original size:20 final size:20
Alignment explanation
Indices: 122437--122577 Score: 153
Period size: 20 Copynumber: 7.0 Consensus size: 20
122427 TTCCTAATTT
122437 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* ** * *
122457 GCAACGCGAATTTGGAAAAGC
1 GCAATGCGAA-TACGTAAATC
*
122478 GCAATGCGATTACGTAAATC
1 GCAATGCGAATACGTAAATC
*
122498 GCAATGCGAAT-C-TGACTATC
1 GCAATGCGAATACGT-A-AATC
*
122518 GCAATGCGATTACGTAAATC
1 GCAATGCGAATACGTAAATC
122538 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
122558 GCAATGCGAAT-CTGTAAATC
1 GCAATGCGAATAC-GTAAATC
122578 ACAACGAGAT
Statistics
Matches: 99, Mismatches: 16, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 78 0.79
21 16 0.16
22 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:122532 original size:40 final size:40
Alignment explanation
Indices: 122437--122602 Score: 167
Period size: 40 Copynumber: 4.1 Consensus size: 40
122427 TTCCTAATTT
* * *
122437 GCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAAGC
1 GCAATGCGAATACGTAAATCGCAACGCGAATCT-GACAATC
* * *
122478 GCAATGCGATTACGTAAATCGCAATGCGAATCTGACTATC
1 GCAATGCGAATACGTAAATCGCAACGCGAATCTGACAATC
* *
122518 GCAATGCGATTACGTAAATCGCAATGCGAATAC-GTA-AATC
1 GCAATGCGAATACGTAAATCGCAACGCGAAT-CTG-ACAATC
* * * *
122558 GCAATGCGAAT-CTGTAAATCACAACGAGATTCTGACTATC
1 GCAATGCGAATAC-GTAAATCGCAACGCGAATCTGACAATC
122598 GCAAT
1 GCAAT
122603 ACTGAATTTC
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
39 3 0.03
40 72 0.67
41 32 0.30
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (40 bp):
GCAATGCGAATACGTAAATCGCAACGCGAATCTGACAATC
Found at i:125937 original size:20 final size:20
Alignment explanation
Indices: 125912--126005 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
125902 GACATTCATT
125912 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
* *
125932 TGACTATCGCAACACAGAAA
1 TGACTATCGCAACGCGGAAA
* *
125952 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
125972 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
125992 TGACTATCGCAACG
1 TGACTATCGCAACG
126006 AGAGAATCGC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 63 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:126036 original size:21 final size:19
Alignment explanation
Indices: 126010--126065 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
126000 GCAACGAGAG
126010 AATCGCAATGCGAAATGAAAA
1 AATCGCAATGCGAAATG--AA
*
126031 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
126050 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
126066 TAGTTTCGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:126053 original size:19 final size:20
Alignment explanation
Indices: 126010--126057 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
126000 GCAACGAGAG
*
126010 AATCGCAATGCGAAATGAAAA
1 AATCGCAATGCAAAATG-AAA
126031 AATCGCAATGCAAAATG-AA
1 AATCGCAATGCAAAATGAAA
126050 AATCGCAA
1 AATCGCAA
126058 CGCGAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 10 0.38
21 16 0.62
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCAAAATGAAA
Found at i:126120 original size:34 final size:34
Alignment explanation
Indices: 126077--126169 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 34
126067 AGTTTCGTGT
126077 TGCGATTTTCATTTTCGCATTGCGATTCACTCGC
1 TGCGATTTTCATTTTCGCATTGCGATTCACTCGC
* *
126111 TGCGATTTTCA-TTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTTCGCATTGCGATTCACTCGC
** * *
126144 TGCGATAGTCATTTCCGCGTTGCGAT
1 TGCGATTTTCATTTTCGCATTGCGAT
126170 AGTCTGTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.56
34 23 0.44
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (34 bp):
TGCGATTTTCATTTTCGCATTGCGATTCACTCGC
Found at i:127056 original size:29 final size:29
Alignment explanation
Indices: 127024--127081 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
127014 CCTTTAAAAT
* *
127024 ATTTAATCAAATATACTTACCTTATCGAC
1 ATTTAAACAAATATACTAACCTTATCGAC
*
127053 ATTTAAACAAATATACTAACTTTATCGAC
1 ATTTAAACAAATATACTAACCTTATCGAC
127082 CTCACACCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTTAAACAAATATACTAACCTTATCGAC
Found at i:127774 original size:42 final size:42
Alignment explanation
Indices: 127695--127787 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
127685 CCTCTTCAAC
* * *
127695 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
127737 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
127779 GATGACAGG
1 GATGACAGG
127788 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:128284 original size:20 final size:20
Alignment explanation
Indices: 128259--128335 Score: 145
Period size: 20 Copynumber: 3.9 Consensus size: 20
128249 TAGAATCTGC
128259 AAATGACTATCGCAACGCGA
1 AAATGACTATCGCAACGCGA
*
128279 AAATGACTATCGCAACGTGA
1 AAATGACTATCGCAACGCGA
128299 AAATGACTATCGCAACGCGA
1 AAATGACTATCGCAACGCGA
128319 AAATGACTATCGCAACG
1 AAATGACTATCGCAACG
128336 AGAGAATCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGA
Found at i:128399 original size:20 final size:20
Alignment explanation
Indices: 128374--128422 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
128364 CAACAACAAA
*
128374 ATCGCAACGCGAAAATGATT
1 ATCGCAACGCGAAAATGACT
* **
128394 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
128414 ATCGCAACG
1 ATCGCAACG
128423 AGAGAATCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:128492 original size:20 final size:20
Alignment explanation
Indices: 128467--128556 Score: 171
Period size: 20 Copynumber: 4.5 Consensus size: 20
128457 GATTCTTTTG
128467 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
128487 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
128507 TTGCGATAGTCATTTTCTCA
1 TTGCGATAGTCATTTTCGCA
128527 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
128547 TTGCGATAGT
1 TTGCGATAGT
128557 AAACTATTCT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:128512 original size:40 final size:40
Alignment explanation
Indices: 128429--128556 Score: 171
Period size: 40 Copynumber: 3.4 Consensus size: 40
128419 AACGAGAGAA
* **
128429 TCGCAATGCGATTTTCATTTT-GCATTGCGAT--TC-TTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
128465 T-G--TTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
128502 TCGCATTGCGATAGTCATTTTCTCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
128542 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
128557 AAACTATTCT
Statistics
Matches: 81, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
33 13 0.16
34 10 0.12
35 1 0.01
36 3 0.04
37 4 0.05
38 1 0.01
40 49 0.60
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:130489 original size:20 final size:20
Alignment explanation
Indices: 130431--130500 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
130421 GAAACTTTAA
* **
130431 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
130451 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
130471 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
130491 ATCGCAACGC
1 ATCGCAACGC
130501 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:130569 original size:20 final size:20
Alignment explanation
Indices: 130544--130590 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
130534 AATTCTCTCG
130544 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
130564 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
130584 TTGCGAT
1 TTGCGAT
130591 TCACTCATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:131346 original size:21 final size:21
Alignment explanation
Indices: 131320--131368 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
131310 TTTATGTGTG
* *
131320 TATATATATGTAAAAATATTA
1 TATATATATATAAAAATACTA
**
131341 TATATATATATAAGTATACTA
1 TATATATATATAAAAATACTA
131362 TATATAT
1 TATATAT
131369 TACAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
TATATATATATAAAAATACTA
Found at i:131423 original size:2 final size:2
Alignment explanation
Indices: 131270--131406 Score: 113
Period size: 2 Copynumber: 70.0 Consensus size: 2
131260 CTCATATAAG
*
131270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
131312 TA TG TG TG TA TA TA TA TG TA AA AA TA T- 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
* * * * *
131353 -A GTA TA CTA TA TA TA T- TA CA AA TA TA -A TG CA CA T- 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
131393 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
131407 ACATTCATAA
Statistics
Matches: 113, Mismatches: 15, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
1 5 0.04
2 105 0.93
3 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:132693 original size:21 final size:22
Alignment explanation
Indices: 132668--132718 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
132658 TAATCAAATT
132668 TATAATTCTAAATT-TAAACAA
1 TATAATTCTAAATTATAAACAA
* **
132689 TATAATTTTTTATTAATAAACAA
1 TATAATTCTAAATT-ATAAACAA
132712 TATAATT
1 TATAATT
132719 TCTTAATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.44
23 14 0.56
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
TATAATTCTAAATTATAAACAA
Found at i:140194 original size:48 final size:48
Alignment explanation
Indices: 140140--140246 Score: 178
Period size: 48 Copynumber: 2.2 Consensus size: 48
140130 TCATGTGATC
* * *
140140 GTTAATTTGGTGACCGATTGAATTAATTGAACTAATTTGATTCAGTCA
1 GTTAATTCGGTGACCGATCGAATTAATTGAACTAATTCGATTCAGTCA
*
140188 GTTAATTCGGTGACCGATCGAATTAATTGAATTAATTCGATTCAGTCA
1 GTTAATTCGGTGACCGATCGAATTAATTGAACTAATTCGATTCAGTCA
140236 GTTAATTCGGT
1 GTTAATTCGGT
140247 TAAAATCAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (48 bp):
GTTAATTCGGTGACCGATCGAATTAATTGAACTAATTCGATTCAGTCA
Found at i:140227 original size:122 final size:122
Alignment explanation
Indices: 140010--140229 Score: 352
Period size: 122 Copynumber: 1.8 Consensus size: 122
140000 CGAATTAACG
140010 ATGTGATCGCTAATTCGGTGACCGATCGAATTAATTGAACTAATTCAGTTCAGTCAGTTAATTCG
1 ATGTGATCGCTAATTCGGTGACCGATCGAATTAATTGAACTAATTCAGTTCAGTCAGTTAATTCG
*
140075 GTGACCAATTAAATTAATTGAACTAATTCGATTGAGAAAATATTGTCATTTCATGTC
66 GTGACCAATCAAATTAATTGAACTAATTCGATTGAGAAAATATTGTCATTTCATGTC
* * * *
140132 ATGTGATCGTTAATTTGGTGACCGATTGAATTAATTGAACTAATT-TGATTCAGTCAGTTAATTC
1 ATGTGATCGCTAATTCGGTGACCGATCGAATTAATTGAACTAATTCAG-TTCAGTCAGTTAATTC
* * *
140196 GGTGACCGATCGAATTAATTGAATTAATTCGATT
65 GGTGACCAATCAAATTAATTGAACTAATTCGATT
140230 CAGTCAGTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
121 1 0.01
122 88 0.99
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (122 bp):
ATGTGATCGCTAATTCGGTGACCGATCGAATTAATTGAACTAATTCAGTTCAGTCAGTTAATTCG
GTGACCAATCAAATTAATTGAACTAATTCGATTGAGAAAATATTGTCATTTCATGTC
Found at i:153470 original size:18 final size:18
Alignment explanation
Indices: 153444--153480 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
153434 AAACCATTTG
153444 ATCACTTCTTTAGATCTT
1 ATCACTTCTTTAGATCTT
* *
153462 ATCATTTCTTTTGATCTT
1 ATCACTTCTTTAGATCTT
153480 A
1 A
153481 CGAGTTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (18 bp):
ATCACTTCTTTAGATCTT
Found at i:154527 original size:24 final size:24
Alignment explanation
Indices: 154500--154597 Score: 97
Period size: 24 Copynumber: 4.1 Consensus size: 24
154490 TATAACAAAA
* *
154500 ATCAAAACAAAATCCAGGTAAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
* *
154524 ATCAGATCAAAATTCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
* * *
154548 ATCTAATCAGAATCTAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
** * *
154572 ATCCGATCAAAATCTAGGTCAGGT
1 ATCAAATCAAAATCCAGGTCAAGT
154596 AT
1 AT
154598 TATAACAGAA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAATCAAAATCCAGGTCAAGT
Found at i:154607 original size:48 final size:48
Alignment explanation
Indices: 154504--154607 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
154494 ACAAAAATCA
*
154504 AAACAAAATCCAGGTAAAGTATCAGATCAAAATTCAGGTCAAGTATCT
1 AAACAGAATCCAGGTAAAGTATCAGATCAAAATTCAGGTCAAGTATCT
* * * * *
154552 AATCAGAATCTAGGTCAAGTATCCGATCAAAA-TCTAGGTCAGGTAT-T
1 AAACAGAATCCAGGTAAAGTATCAGATCAAAATTC-AGGTCAAGTATCT
154599 ATAACAGAA
1 A-AACAGAA
154608 ATCAAATCGG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 4 0.09
48 43 0.91
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (48 bp):
AAACAGAATCCAGGTAAAGTATCAGATCAAAATTCAGGTCAAGTATCT
Found at i:155356 original size:27 final size:27
Alignment explanation
Indices: 155317--155379 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
155307 AATCCTTAGT
**
155317 GCTGAATGTGATTTAGAGTTGAGCTGA
1 GCTGAATACGATTTAGAGTTGAGCTGA
155344 GCTGAATACGATTTAGAGTTGAGCTGA
1 GCTGAATACGATTTAGAGTTGAGCTGA
155371 GCTGAATAC
1 GCTGAATAC
155380 TTCCAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (27 bp):
GCTGAATACGATTTAGAGTTGAGCTGA
Found at i:159971 original size:32 final size:32
Alignment explanation
Indices: 159893--159979 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
159883 TTAGTATTTT
* * *
159893 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTTTATATAAATATA
* *
159925 TTTATGTAAATATTATTTTTTAT-TAAA-ATAA
1 TTTATATAATTATTATTTTTTATATAAATAT-A
159956 TATTATATAATTATTATTTATTTA
1 T-TTATATAATTATTATTT-TTTA
159980 GAATTATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 2 0.04
31 5 0.11
32 34 0.76
33 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTATATAAATATA
Found at i:160141 original size:17 final size:17
Alignment explanation
Indices: 160119--160172 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
160109 AATGTTAATA
160119 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
160136 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
160153 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
160170 TTT
1 TTT
160173 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:160969 original size:128 final size:128
Alignment explanation
Indices: 160741--161241 Score: 948
Period size: 128 Copynumber: 3.9 Consensus size: 128
160731 TTACCTTATT
160741 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
160806 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
160869 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
160934 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
160997 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
161062 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
161125 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
161190 TGACGAAATAATGGAAGGCGCTCCCCCGGGAACGTGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
161242 ACTCCGATTA
Statistics
Matches: 365, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 365 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:161325 original size:8 final size:8
Alignment explanation
Indices: 161312--161352 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
161302 TCACAATCTT
161312 TCAAATTC
1 TCAAATTC
161320 TCAAATTC
1 TCAAATTC
* *
161328 CCAAACTC
1 TCAAATTC
161336 T-AAATTC
1 TCAAATTC
161343 TCAAATTC
1 TCAAATTC
161351 TC
1 TC
161353 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:166784 original size:27 final size:27
Alignment explanation
Indices: 166752--166807 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
166742 CTAAACTAAA
166752 GACTAAATTATAAATTTTAAAAGATTG
1 GACTAAATTATAAATTTTAAAAGATTG
*
166779 GACTAAATTATAAATTTTAGAAGATTG
1 GACTAAATTATAAATTTTAAAAGATTG
166806 GA
1 GA
166808 GGTAGTGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (27 bp):
GACTAAATTATAAATTTTAAAAGATTG
Found at i:166982 original size:16 final size:16
Alignment explanation
Indices: 166961--167000 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
166951 ATTTTATTTT
166961 CTCAACTCCCAACTCC
1 CTCAACTCCCAACTCC
* *
166977 CTCAACTCCCAGCTCT
1 CTCAACTCCCAACTCC
166993 CTCAACTC
1 CTCAACTC
167001 TCTCAAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.53, G:0.03, T:0.23
Consensus pattern (16 bp):
CTCAACTCCCAACTCC
Found at i:170061 original size:3 final size:3
Alignment explanation
Indices: 170053--170090 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
170043 AAACGTAGAA
170053 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
170091 AGCCCTAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:170410 original size:53 final size:53
Alignment explanation
Indices: 170352--170457 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
170342 AATGATCGGC
* * *
170352 AAGCTTCTCAAAATGGACCCAATGGTGTTTCATTTCCCAACAGTTGGCTTCAA
1 AAGCTTCTCAAAATGGACCCAATGGTGTATCATTTACCAACAGCTGGCTTCAA
* *
170405 AAGCTTCTGAAAATGGAGCCAATGGTGTATCATTTACCAACAGCTGGCTTCAA
1 AAGCTTCTCAAAATGGACCCAATGGTGTATCATTTACCAACAGCTGGCTTCAA
170458 GATGATAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (53 bp):
AAGCTTCTCAAAATGGACCCAATGGTGTATCATTTACCAACAGCTGGCTTCAA
Found at i:170540 original size:75 final size:75
Alignment explanation
Indices: 170409--170571 Score: 236
Period size: 75 Copynumber: 2.2 Consensus size: 75
170399 CTTCAAAAGC
* *
170409 TTCTGAAAATGGAGCCAATGGTGTATCATTTACCAACAGCTGGCTTCAAGATGATAATAGAATTA
1 TTCTGAAAATGGACCCAATGGTGTATCATTTACCAACAGCTGGCTTCAAGAAGATAATAGAATTA
*
170474 ACCAGCAGGA
66 ACCAGCAAGA
* * * * *
170484 TTCTGAAAATGGACCCAATGGTGTCTCATTTCCCAACAGTTGGCTTCGAGAAGATAATAGAATTG
1 TTCTGAAAATGGACCCAATGGTGTATCATTTACCAACAGCTGGCTTCAAGAAGATAATAGAATTA
*
170549 ACCAGCAAGC
66 ACCAGCAAGA
*
170559 TTCTCAAAATGGA
1 TTCTGAAAATGGA
170572 GCCATGGGTA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (75 bp):
TTCTGAAAATGGACCCAATGGTGTATCATTTACCAACAGCTGGCTTCAAGAAGATAATAGAATTA
ACCAGCAAGA
Found at i:171752 original size:32 final size:27
Alignment explanation
Indices: 171685--171748 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
171675 GGGTCGAGTT
*
171685 GGGTCGGGTTTTTTAAATGTGATATTC
1 GGGTCGGGTCTTTTAAATGTGATATTC
171712 GGGTCGGGTCTTTTAAATGTGATATTC
1 GGGTCGGGTCTTTTAAATGTGATATTC
171739 GGGTCGGGTC
1 GGGTCGGGTC
171749 GGGTTTAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.16, C:0.11, G:0.34, T:0.39
Consensus pattern (27 bp):
GGGTCGGGTCTTTTAAATGTGATATTC
Found at i:172442 original size:13 final size:13
Alignment explanation
Indices: 172426--172470 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
172416 TTTTTTGTGT
172426 GTTTATGTTGTTC
1 GTTTATGTTGTTC
172439 GTTTA---TGTTC
1 GTTTATGTTGTTC
172449 GTTTATTGTT-TTC
1 GTTTA-TGTTGTTC
172462 GTTTATGTT
1 GTTTATGTT
172471 CGTTTGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 10 0.36
12 4 0.14
13 13 0.46
14 1 0.04
ACGTcount: A:0.09, C:0.07, G:0.20, T:0.64
Consensus pattern (13 bp):
GTTTATGTTGTTC
Found at i:172449 original size:10 final size:10
Alignment explanation
Indices: 172434--172487 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
172424 GTGTTTATGT
172434 TGTTCGTTTA
1 TGTTCGTTTA
172444 TGTTCGTTTA
1 TGTTCGTTTA
172454 TTGTTTTCGTTTA
1 -TG--TTCGTTTA
*
172467 TGTTCGTTTG
1 TGTTCGTTTA
*
172477 TGTTTGTTTA
1 TGTTCGTTTA
172487 T
1 T
172488 CATTTAAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 26 0.68
11 2 0.05
12 2 0.05
13 8 0.21
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.65
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:172452 original size:23 final size:22
Alignment explanation
Indices: 172426--172481 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
172416 TTTTTTGTGT
172426 GTTTATGTTGTTCGTTTATGTTC
1 GTTTATGTT-TTCGTTTATGTTC
172449 GTTTATTGTTTTCGTTTATGTTC
1 GTTTA-TGTTTTCGTTTATGTTC
*
172472 GTTTGTGTTT
1 GTTTATGTTT
172482 GTTTATCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 5 0.16
23 22 0.71
24 4 0.13
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.64
Consensus pattern (22 bp):
GTTTATGTTTTCGTTTATGTTC
Found at i:180414 original size:24 final size:21
Alignment explanation
Indices: 180387--180444 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
180377 ATGTGAAATA
180387 ATGAAAGTGATCACATGTGTGTAT
1 ATGAAAGTGAT-ACATGT-T-TAT
180411 ATG-AAGTGAAATACATGTTTAT
1 ATGAAAGTG--ATACATGTTTAT
180433 ATGAAAAGTGAT
1 ATG-AAAGTGAT
180445 TGTAACATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 14 0.47
25 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (21 bp):
ATGAAAGTGATACATGTTTAT
Found at i:181170 original size:21 final size:21
Alignment explanation
Indices: 181144--181188 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
181134 GATTTCTGGG
* *
181144 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
181165 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
181186 CAA
1 CAA
181189 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:181815 original size:23 final size:24
Alignment explanation
Indices: 181772--181818 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
181762 ATATGGCATG
*
181772 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
181796 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
181819 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:182033 original size:31 final size:31
Alignment explanation
Indices: 181995--182150 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
181985 AGGGTCGAGG
181995 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
182026 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * *
182057 GATTACTTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
182088 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
182119 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
182150 G
1 G
182151 GTCCTTCGGG
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 110 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:182081 original size:62 final size:62
Alignment explanation
Indices: 181997--182150 Score: 247
Period size: 62 Copynumber: 2.5 Consensus size: 62
181987 GGTCGAGGGT
* *
181997 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
* *
182059 TTACTTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
182121 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
182151 GTCCTTCGGG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
62 83 0.99
63 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:185291 original size:21 final size:21
Alignment explanation
Indices: 185265--185309 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
185255 GATTTCTGGG
* *
185265 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
185286 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
185307 CAA
1 CAA
185310 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:186143 original size:31 final size:31
Alignment explanation
Indices: 186105--186260 Score: 215
Period size: 31 Copynumber: 5.0 Consensus size: 31
186095 AGGGTCGAGG
*
186105 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
186136 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * *
186167 GATTACCTATGTTTTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
186198 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
186229 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
186260 G
1 G
186261 GTCCTTCGGG
Statistics
Matches: 110, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 109 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:186259 original size:62 final size:62
Alignment explanation
Indices: 186107--186260 Score: 238
Period size: 62 Copynumber: 2.5 Consensus size: 62
186097 GGTCGAGGGT
* * *
186107 TTACCTATGTTCTTCGGGACATATGGATTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
* *
186169 TTACCTATGTTTTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
186231 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
186261 GTCCTTCGGG
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
62 82 0.99
63 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:187150 original size:22 final size:21
Alignment explanation
Indices: 187122--187238 Score: 122
Period size: 22 Copynumber: 5.8 Consensus size: 21
187112 GTTCTTAAGG
187122 AGTGGTCCTTCGGGACATATAC
1 AGTGGTCCTTCGGGACATAT-C
187144 AGTGGTCCTTCGGGACATATAC
1 AGTGGTCCTTCGGGACATAT-C
*
187166 AATGGTCCTTCGGGAC--AT-
1 AGTGGTCCTTCGGGACATATC
** *
187184 AGTGGTTTTTCGGAACA-ATC
1 AGTGGTCCTTCGGGACATATC
187204 AGTGGTCCTTCGGGACATA--
1 AGTGGTCCTTCGGGACATATC
*
187223 A-TGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
187239 AATATGCAGT
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
18 26 0.31
19 3 0.04
20 16 0.19
21 1 0.01
22 37 0.45
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
AGTGGTCCTTCGGGACATATC
Found at i:187195 original size:18 final size:18
Alignment explanation
Indices: 187168--187238 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
187158 ACATATACAA
*
187168 TGGTCCTTCGGGACATAG
1 TGGTCATTCGGGACATAG
** *
187186 TGGTTTTTCGGAACAATCAG
1 TGGTCATTCGGGAC-AT-AG
* *
187206 TGGTCCTTCGGGACATAA
1 TGGTCATTCGGGACATAG
187224 TGGTCATTCGGGACA
1 TGGTCATTCGGGACA
187239 AATATGCAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 26 0.60
19 4 0.09
20 13 0.30
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (18 bp):
TGGTCATTCGGGACATAG
Found at i:187216 original size:38 final size:40
Alignment explanation
Indices: 187122--187234 Score: 122
Period size: 38 Copynumber: 2.8 Consensus size: 40
187112 GTTCTTAAGG
*
187122 AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACATATAC
1 AGTGGTCCTTCGGGAC--AT--AGTGGTCCTTCGGAACATATAC
* **
187166 AATGGTCCTTCGGGACATAGTGGTTTTTCGGAACA-AT-C
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACATATAC
* *
187204 AGTGGTCCTTCGGGACATAATGGTCATTCGG
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGG
187235 GACAAATATG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
38 28 0.46
39 2 0.03
40 14 0.23
42 2 0.03
44 15 0.25
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACATATAC
Done.