Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004449.1 Hibiscus syriacus cultivar Beakdansim tig00009771_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: 87568
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7613 original size:5 final size:6
Alignment explanation
Indices: 7581--7622 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
7571 GACACGTATT
7581 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
7623 TGAGACGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:8237 original size:21 final size:21
Alignment explanation
Indices: 8211--8301 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 21
8201 CACCAGTCGT
*
8211 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTCGACTATCGCAA
** *
8232 TGCGATAGTCGACTATCGCAT
1 TGCGATTTTCGACTATCGCAA
* * *
8253 TGCAATTTAC-A-TATTCGCAT
1 TGCGATTTTCGACTA-TCGCAA
** *
8273 TGCGATAGTCGACTATCGCAT
1 TGCGATTTTCGACTATCGCAA
8294 TGCGATTT
1 TGCGATTT
8302 ACATATTCGC
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.04
20 13 0.25
21 36 0.68
22 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (21 bp):
TGCGATTTTCGACTATCGCAA
Found at i:8271 original size:41 final size:41
Alignment explanation
Indices: 8226--8367 Score: 180
Period size: 41 Copynumber: 3.4 Consensus size: 41
8216 TTTTGGACTA
*
8226 TCGCAATGCGATAGTCGACTATCGCATTGCAATTTACATAT
1 TCGCATTGCGATAGTCGACTATCGCATTGCAATTTACATAT
*
8267 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCGACTATCGCATTGCAATTTACATAT
* * * * *
8308 TCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCCA-AGT
1 TCGCATTGCGATAGT-CGACTATCGCATTGCAAT-TTACATA-T
8350 TCGCATTGCGATAGTCGA
1 TCGCATTGCGATAGTCGA
8368 AGTTTGCGTT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
41 69 0.76
42 22 0.24
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (41 bp):
TCGCATTGCGATAGTCGACTATCGCATTGCAATTTACATAT
Found at i:8272 original size:20 final size:20
Alignment explanation
Indices: 8247--8319 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
8237 TAGTCGACTA
*
8247 TCGCATTGCAATTTACATAT
1 TCGCATTGCGATTTACATAT
*
8267 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
8288 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
8308 TCGCATTGCGAT
1 TCGCATTGCGAT
8320 AGTCCAAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 2 0.04
20 26 0.58
21 15 0.33
22 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:8333 original size:21 final size:21
Alignment explanation
Indices: 8266--8381 Score: 130
Period size: 21 Copynumber: 5.6 Consensus size: 21
8256 AATTTACATA
* *
8266 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
8286 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
8307 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
8328 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
8349 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* *
8370 TTTGCGTTGCGA
1 TTCGCATTGCGA
8382 ATCTGGAAAC
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
20 15 0.18
21 68 0.81
22 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:8364 original size:42 final size:41
Alignment explanation
Indices: 8247--8381 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
8237 TAGTCGACTA
* * * *
8247 TCGCATTGCAATTTACATATTCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGT
*
8287 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 -TCGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGT
* *
8329 TCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGAT-GTACATA-TTCGCATTGCGATAGTCCAAGT
* *
8371 TTGCGTTGCGA
1 TCGCATTGCGA
8382 ATCTGGAAAC
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
41 47 0.57
42 36 0.43
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
TCGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGT
Found at i:9414 original size:12 final size:12
Alignment explanation
Indices: 9378--9422 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
9368 TTATTTATTA
*
9378 CAAACCCAATACC
1 CAAACCCAA-ATC
*
9391 CAACATCCAAATC
1 CAA-ACCCAAATC
9404 CAAACCCAAATC
1 CAAACCCAAATC
9416 CAAACCC
1 CAAACCC
9423 GGACTCAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 15 0.54
13 8 0.29
14 5 0.18
ACGTcount: A:0.47, C:0.44, G:0.00, T:0.09
Consensus pattern (12 bp):
CAAACCCAAATC
Found at i:15915 original size:45 final size:45
Alignment explanation
Indices: 15862--15985 Score: 176
Period size: 45 Copynumber: 2.7 Consensus size: 45
15852 TAAATGCTTG
*
15862 CGAACTAGATATCATGCGATTAGGTTTATTTTTCGAACAAGCATA
1 CGAACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATA
* * *
15907 CGAACTAGATATCATGCGGTTAGGTTTATTTTTTGAATAAGCATG
1 CGAACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATA
* * *
15952 CGAATTAGATATCATGTGGTTAGGATTTCTTTTT
1 CGAACTAGATATCATGCGGTTAGG-TTTATTTTT
15986 GTGGATAACA
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 63 0.89
46 8 0.11
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (45 bp):
CGAACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATA
Found at i:25390 original size:30 final size:30
Alignment explanation
Indices: 25354--25546 Score: 350
Period size: 30 Copynumber: 6.4 Consensus size: 30
25344 TCCGAAGGAC
25354 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
25384 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
25414 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
25444 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
25474 CTGTCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
25504 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
25534 CTGTCCATAGGTC
1 CTATCCAGAGGTC
25547 CCGAAGAACC
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 157 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:25563 original size:30 final size:30
Alignment explanation
Indices: 25357--25573 Score: 245
Period size: 30 Copynumber: 7.2 Consensus size: 30
25347 GAAGGACCTA
* * *
25357 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* * *
25387 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* * *
25417 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* *
25447 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* *
25477 TCCATAGGTCATAAAGATCCTCGGTAACTA
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* *
25507 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* * * * *
25537 TCCATAGGTCCCGAAGAACCTAGGTAAACTA
1 TCCATAGGTCACAAAGATCCTCGGT-AACTG
25568 TCCATA
1 TCCATA
25574 TGTTCCTTAG
Statistics
Matches: 174, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 164 0.94
31 10 0.06
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
TCCATAGGTCACAAAGATCCTCGGTAACTG
Found at i:25563 original size:90 final size:90
Alignment explanation
Indices: 25354--25573 Score: 341
Period size: 90 Copynumber: 2.4 Consensus size: 90
25344 TCCGAAGGAC
* *
25354 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCATAGGTCATAAAGATCCTCGGTAACTATC
25419 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* *
25444 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCATAGGTCATAAAGATCCTCGGTAACTATC
25509 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * * * * *
25534 CTGTCCATAGGTCCCGAAGAACCTAGGTAAACTATCCATA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCATA
25574 TGTTCCTTAG
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
90 109 0.92
91 10 0.08
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (90 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCATAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCATAAAGATCCTCGGTAA
Found at i:25620 original size:31 final size:30
Alignment explanation
Indices: 25529--25624 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
25519 AAAGATCCTC
* * *
25529 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
25559 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
25590 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
25621 GGTA
1 GGTA
25625 GTTCTTCGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:25807 original size:4 final size:4
Alignment explanation
Indices: 25798--25826 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
25788 ATATAACCAT
25798 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
25827 GTCATCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:28412 original size:9 final size:8
Alignment explanation
Indices: 28398--28583 Score: 54
Period size: 9 Copynumber: 21.4 Consensus size: 8
28388 TCGCTTGAAG
28398 AAGAAATAA
1 AAGAAA-AA
28407 AAGAAAAA
1 AAGAAAAA
*
28415 ATGAAAAA
1 AAGAAAAA
28423 AATGAAAAA
1 AA-GAAAAA
* *
28432 AATAATAA
1 AAGAAAAA
* *
28440 TA-AAAAT
1 AAGAAAAA
* *
28447 GAGAAGAA
1 AAGAAAAA
28455 AAG-AAAA
1 AAGAAAAA
* *
28462 ATGAGGAAA
1 AAGA-AAAA
28471 AAGAAAAA
1 AAGAAAAA
*
28479 TGATGGAAAAA
1 --A-AGAAAAA
*
28490 ACGAAAAGAAA
1 A--AGAA-AAA
*
28501 AAGAAAAG
1 AAGAAAAA
28509 AAGAAAAA
1 AAGAAAAA
*
28517 ATAGAAAATGG
1 A-AGAAAA--A
28528 AAGAAAAA
1 AAGAAAAA
*
28536 ATGAAAGAGA
1 AAGAAA-A-A
28546 AA-AACAAA
1 AAGAA-AAA
28554 AAGAGAAAA
1 AAGA-AAAA
*
28563 ATGAAAAA
1 AAGAAAAA
28571 AGAGAAATAA
1 A-AGAAA-AA
28581 AAG
1 AAG
28584 GAGGGTTCAA
Statistics
Matches: 129, Mismatches: 29, Indels: 38
0.66 0.15 0.19
Matches are distributed among these distances:
7 9 0.07
8 46 0.36
9 47 0.36
10 16 0.12
11 11 0.09
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (8 bp):
AAGAAAAA
Found at i:28425 original size:21 final size:22
Alignment explanation
Indices: 28401--28456 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
28391 CTTGAAGAAG
28401 AAAT-AAAAGAAAAAATGAA-AA
1 AAATGAAAAGAAAAAAT-AATAA
*
28422 AAATGAAAA-AAATAATAATAA
1 AAATGAAAAGAAAAAATAATAA
*
28443 AAATGAGAAGAAAA
1 AAATGAAAAGAAAA
28457 GAAAAATGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (22 bp):
AAATGAAAAGAAAAAATAATAA
Found at i:28429 original size:17 final size:17
Alignment explanation
Indices: 28400--28432 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28390 GCTTGAAGAA
28400 GAAATAAAAGAAAAAAT
1 GAAATAAAAGAAAAAAT
28417 GAAA-AAAATGAAAAAA
1 GAAATAAAA-GAAAAAA
28433 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (17 bp):
GAAATAAAAGAAAAAAT
Found at i:28435 original size:30 final size:31
Alignment explanation
Indices: 28401--28462 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 31
28391 CTTGAAGAAG
28401 AAATAA-AAGAAAAAATGA-AA-AAAATGAAAA
1 AAATAATAA-AAAAAATGAGAAGAAAA-GAAAA
*
28431 AAATAATAATAAAAATGAGAAGAAAAGAAAA
1 AAATAATAAAAAAAATGAGAAGAAAAGAAAA
28462 A
1 A
28463 TGAGGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 14 0.50
31 10 0.36
32 4 0.14
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (31 bp):
AAATAATAAAAAAAATGAGAAGAAAAGAAAA
Found at i:28463 original size:17 final size:16
Alignment explanation
Indices: 28441--28577 Score: 71
Period size: 19 Copynumber: 7.8 Consensus size: 16
28431 AAATAATAAT
28441 AAAAATGAGAAGAAAAG
1 AAAAATGAGAA-AAAAG
*
28458 AAAAATGAGGAAAAAG
1 AAAAATGAGAAAAAAG
28474 AAAAATGATGGAAAAAACG
1 AAAAATGA--GAAAAAA-G
**
28493 AAAAGAAAAAGAAAAGAAG
1 -AAA-AATGAGAAAA-AAG
28512 AAAAAAT-AGAAAATGGAAG
1 -AAAAATGAGAAAA---AAG
*
28531 AAAAAATGAAAGAGAAAAAC
1 -AAAAATG--AGA-AAAAAG
*
28551 AAAAA-GAGAAAAATG
1 AAAAATGAGAAAAAAG
*
28566 AAAAAAGAGAAA
1 AAAAATGAGAAA
28578 TAAAAGGAGG
Statistics
Matches: 99, Mismatches: 8, Indels: 27
0.74 0.06 0.20
Matches are distributed among these distances:
15 9 0.09
16 22 0.22
17 16 0.16
18 9 0.09
19 27 0.27
20 7 0.07
21 3 0.03
22 3 0.03
23 3 0.03
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.06
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:28472 original size:16 final size:16
Alignment explanation
Indices: 28441--28489 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 16
28431 AAATAATAAT
*
28441 AAAAATGAGAAGAAAAG
1 AAAAATGAGGA-AAAAG
28458 AAAAATGAGGAAAAAG
1 AAAAATGAGGAAAAAG
28474 AAAAATGATGGAAAAA
1 AAAAATGA-GGAAAAA
28490 ACGAAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (16 bp):
AAAAATGAGGAAAAAG
Found at i:28506 original size:46 final size:46
Alignment explanation
Indices: 28453--28570 Score: 118
Period size: 46 Copynumber: 2.5 Consensus size: 46
28443 AAATGAGAAG
*
28453 AAAAGAAAAATGAGGAAAAAGAAAAAT-GATGGAAAAAACGAAA-AGA
1 AAAAGAAAAA-GAGGAAAAAGAAAAATGGA-AGAAAAAACGAAAGAGA
* * *
28499 AAAAG-AAAAGAAGAAAAAATAGAAAATGGAAGAAAAAATGAAAGAGA
1 AAAAGAAAAAG-AGGAAAAAGA-AAAATGGAAGAAAAAACGAAAGAGA
*
28546 AAAACAAAAAGA-GAAAAATGAAAAA
1 AAAAGAAAAAGAGGAAAAA-GAAAAA
28571 AGAGAAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
44 1 0.02
45 12 0.20
46 30 0.51
47 11 0.19
48 5 0.08
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (46 bp):
AAAAGAAAAAGAGGAAAAAGAAAAATGGAAGAAAAAACGAAAGAGA
Found at i:28536 original size:12 final size:13
Alignment explanation
Indices: 28467--28568 Score: 58
Period size: 12 Copynumber: 8.3 Consensus size: 13
28457 GAAAAATGAG
*
28467 GAAAAAGAAAAAT
1 GAAAGAGAAAAAT
** *
28480 GATGGA-AAAAAC
1 GAAAGAGAAAAAT
28492 GAAA-AGAAAAA-
1 GAAAGAGAAAAAT
28503 GAAA-AGAAGAAA-
1 GAAAGAGAA-AAAT
*
28515 -AAATAG-AAAAT
1 GAAAGAGAAAAAT
*
28526 GGAAGA-AAAAAT
1 GAAAGAGAAAAAT
*
28538 GAAAGAGAAAAACA
1 GAAAGAGAAAAA-T
*
28552 AAAAGAGAAAAAT
1 GAAAGAGAAAAAT
28565 GAAA
1 GAAA
28569 AAAGAGAAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
10 3 0.04
11 13 0.19
12 30 0.44
13 11 0.16
14 11 0.16
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.06
Consensus pattern (13 bp):
GAAAGAGAAAAAT
Found at i:28569 original size:14 final size:14
Alignment explanation
Indices: 28496--28583 Score: 56
Period size: 14 Copynumber: 6.0 Consensus size: 14
28486 AAAAACGAAA
28496 AGAAAAA-GAAAAG
1 AGAAAAATGAAAAG
28509 AAGAAAAAATAGAAAATGG
1 -AG-AAAAAT-GAAAA--G
28528 AAGAAAAAATG-AAAG
1 -AG-AAAAATGAAAAG
**
28543 AGAAAAACAAAAAG
1 AGAAAAATGAAAAG
*
28557 AGAAAAATGAAAAA
1 AGAAAAATGAAAAG
*
28571 AGAGAAAT-AAAAG
1 AGAAAAATGAAAAG
28584 GAGGGTTCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
13 9 0.15
14 26 0.43
15 6 0.10
17 8 0.13
18 1 0.02
19 11 0.18
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (14 bp):
AGAAAAATGAAAAG
Found at i:28582 original size:27 final size:27
Alignment explanation
Indices: 28484--28583 Score: 64
Period size: 27 Copynumber: 3.7 Consensus size: 27
28474 AAAAATGATG
* *
28484 GAAAAAACGA-AAAGAAAA-AGAAAAGAA
1 GAAAAAA-GAGAAATAAAAGAGAAAA-AT
* **
28511 GAAAAAATAGAAAATGGAAGA-AAAAAT
1 GAAAAAAGAG-AAATAAAAGAGAAAAAT
* * *
28538 G-AAAGAGAAAAACAAAAAGAGAAAAAT
1 GAAAAAAGAGAAA-TAAAAGAGAAAAAT
28565 GAAAAAAGAGAAATAAAAG
1 GAAAAAAGAGAAATAAAAG
28584 GAGGGTTCAA
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
25 3 0.06
26 10 0.19
27 21 0.40
28 18 0.34
29 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (27 bp):
GAAAAAAGAGAAATAAAAGAGAAAAAT
Found at i:30013 original size:55 final size:55
Alignment explanation
Indices: 29944--30587 Score: 598
Period size: 55 Copynumber: 11.7 Consensus size: 55
29934 TTTATGAAGA
* * *
29944 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCAGACTCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* *
29999 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACTCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
*
30054 TCGAGTTCTATACTCTCTGAAGAAATAGAGAGCGGACCCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* * * * *
30109 TCGAGTTCTATACTCCCTGAATGACTAGGGAGTGGACCCGTTTGT-TGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGT
* *
30164 TCGATTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGCTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* * *
30219 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGT
* * * * * *
30274 TTGAGTTCTATACTCCCTAAACGAATAGGGAGCGGACCCG-TTTATTGAAGATTGA
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGT
* * *
30329 TCGAG-TCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT-TGAAGA----
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGT
* * * * * *
30380 TCAAGTCCTATACTCTCTGAAGAAATA-AGGAGCGGACACATTTGT-TAAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGA-GAGCGGACCCGTTT-TATGAAGATTGT
** * * * ** * *
30435 TTAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACGCATTTTTTTTTAAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC-C--CGTTTTATGAAGATTGT
* ** * ** * *
30493 TCGAG-TCTTATACTCCCTGACTGAATAGGGAGCATACACG-TTTACCGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGT
* * *
30548 TCGAG-TCTTATACTC-CTTGAAAGAATAGGGAGCAGACCCG
1 TCGAGTTC-TATACTCTC-TGAAGGAATAGAGAGCGGACCCG
30588 CCATTTGAAG
Statistics
Matches: 505, Mismatches: 62, Indels: 44
0.83 0.10 0.07
Matches are distributed among these distances:
51 41 0.08
52 1 0.00
53 1 0.00
54 9 0.02
55 407 0.81
56 4 0.01
57 3 0.01
58 39 0.08
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
Found at i:30418 original size:51 final size:51
Alignment explanation
Indices: 30327--30477 Score: 185
Period size: 51 Copynumber: 2.9 Consensus size: 51
30317 ATTGAAGATT
* * * * * *
30327 GATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAA
1 GATCAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACATTTGTTAAA
*
30378 GATCAAGTCCTATACTCTCTGAAGAAATAAGGAGCGGACACATTTGTTAAA
1 GATCAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACATTTGTTAAA
* *
30429 GATTGTTTAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACGCATTT
1 GA----TCAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACATTT
30478 TTTTTTAAAG
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 46 0.53
55 40 0.47
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (51 bp):
GATCAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACATTTGTTAAA
Found at i:33418 original size:61 final size:58
Alignment explanation
Indices: 33297--33418 Score: 127
Period size: 58 Copynumber: 2.1 Consensus size: 58
33287 GTCCCCTAAC
* * * * * * *
33297 TATAAGGTGTTGCTTTATTGATTCCTCTGACTTAAAAGTTACAAAATAGTCCCCCGAT
1 TATAAGATGTTGCTTTATTAATTCCACTAACTTAAAAGTTACAAAATAGTCACACAAT
* * *
33355 TATAAGATGTTGCTTTTTTAATTCCACTAACAATTAAAAAGTTACAAAATGGTTACACAAT
1 TATAAGATGTTGCTTTATTAATTCCACTAAC--TT-AAAAGTTACAAAATAGTCACACAAT
33416 TAT
1 TAT
33419 TCATTGTGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
58 26 0.51
60 2 0.04
61 23 0.45
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (58 bp):
TATAAGATGTTGCTTTATTAATTCCACTAACTTAAAAGTTACAAAATAGTCACACAAT
Found at i:39583 original size:116 final size:115
Alignment explanation
Indices: 39380--39608 Score: 431
Period size: 116 Copynumber: 2.0 Consensus size: 115
39370 TTCATATTAT
39380 TCTAATTGAGAAAATAATTTTTCTTTCCCCATGTGAGCAATTCTTTTTTTTTTCCATGATATTAT
1 TCTAATTGAGAAAATAATTTTTCTTTCCCCATGTGAGCAATTCTTTTTTTTTTCCATGATATTAT
39445 CTATGGAAAATTGCCCATCTTTCCTACTCATTACACCTACATTTGACAAC
66 CTATGGAAAATTGCCCATCTTTCCTACTCATTACACCTACATTTGACAAC
*
39495 TCTAATTGAGAAAATAATTTTTCTTTACCCCATGTGAGCAATTCTTTTTTTTTTTCATGATATTA
1 TCTAATTGAGAAAATAATTTTTCTTT-CCCCATGTGAGCAATTCTTTTTTTTTTCCATGATATTA
*
39560 TCTATGGAGAATTGCCCATCTTTCCTACTCATTACACCTACATTTGACA
65 TCTATGGAAAATTGCCCATCTTTCCTACTCATTACACCTACATTTGACA
39609 TACCTTTGGT
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
115 26 0.23
116 85 0.77
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (115 bp):
TCTAATTGAGAAAATAATTTTTCTTTCCCCATGTGAGCAATTCTTTTTTTTTTCCATGATATTAT
CTATGGAAAATTGCCCATCTTTCCTACTCATTACACCTACATTTGACAAC
Found at i:40613 original size:18 final size:19
Alignment explanation
Indices: 40568--40613 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
40558 GAAAATAAGA
*
40568 TAATATTTATTTAAAGAAT
1 TAATATTTATTTAAACAAT
* *
40587 T-TTAATTATTT-AACAAT
1 TAATATTTATTTAAACAAT
40604 TAATATTTAT
1 TAATATTTAT
40614 ATTCATGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
17 6 0.29
18 14 0.67
19 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATTTATTTAAACAAT
Found at i:54394 original size:20 final size:20
Alignment explanation
Indices: 54369--54738 Score: 370
Period size: 20 Copynumber: 18.5 Consensus size: 20
54359 GATTTTCCAT
* * *
54369 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATACGTA
* * *
54389 AATCGCAACGCGAACACATA
1 AATCGCAACGCGTATACGTA
*
54409 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* *
54429 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATACGTA
**
54449 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATACGTA
**
54469 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATACGTA
* *
54489 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* *
54509 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
*
54529 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* * *
54549 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATACGTA
*
54569 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* *
54589 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
*
54609 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* *
54629 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATACGTA
*
54649 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATACGTA
* *
54669 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATACGTA
* *
54689 AATCGCAACGAGAAT-CTGTA
1 AATCGCAACGCGTATAC-GTA
* *
54709 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATACGTA
54729 AATCGCAACG
1 AATCGCAACG
54739 AGAATCTGTA
Statistics
Matches: 312, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.01
20 307 0.98
21 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATACGTA
Found at i:54739 original size:20 final size:19
Alignment explanation
Indices: 54407--54757 Score: 405
Period size: 20 Copynumber: 17.6 Consensus size: 19
54397 CGCGAACACA
54407 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
54427 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
54447 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
**
54467 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
54487 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
54507 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
54527 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
54547 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
54567 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
54587 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
54607 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
54627 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
54647 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
54667 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
54687 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
54707 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
54727 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
54747 TAAATCACAAC
1 TAAATCGCAAC
54758 ACTGAAATTT
Statistics
Matches: 296, Mismatches: 29, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
19 2 0.01
20 293 0.99
21 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:55469 original size:24 final size:23
Alignment explanation
Indices: 55430--55475 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
55420 AAATTTGGTC
55430 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
55454 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
55476 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:55667 original size:12 final size:12
Alignment explanation
Indices: 55650--55674 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55640 ATATAATCCT
55650 GAAGAAGAAAAA
1 GAAGAAGAAAAA
55662 GAAGAAGAAAAA
1 GAAGAAGAAAAA
55674 G
1 G
55675 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:57999 original size:19 final size:19
Alignment explanation
Indices: 57977--58283 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
57967 CGGAAAATAC
*
57977 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57996 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
58010 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
58030 AATCGCAA--CG---TGAG
1 AATCGCAATGCGAAATGAA
58044 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58063 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
58082 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
58096 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58115 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
58134 AATCG-AA--CAGACAT---
1 AATCGCAATGC-GAAATGAA
*
58148 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
58167 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
58186 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58205 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58224 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
58238 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58257 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58276 AATCGCAA
1 AATCGCAA
58284 CGAGATAATC
Statistics
Matches: 249, Mismatches: 11, Indels: 56
0.79 0.03 0.18
Matches are distributed among these distances:
14 46 0.18
15 3 0.01
16 16 0.06
17 15 0.06
18 4 0.02
19 152 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:58097 original size:52 final size:52
Alignment explanation
Indices: 58005--58283 Score: 347
Period size: 52 Copynumber: 5.2 Consensus size: 52
57995 AAATCCCAAC
* *
58005 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGTGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
*
58058 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
58110 ATGAAAATCGCAATGCGAAATGAAAATCG-AAC-AGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA-A-AATCGCAATGCGAA
* *
58162 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
58219 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
58271 ATGAAAATCGCAA
1 ATGAAAATCGCAA
58284 CGAGATAATC
Statistics
Matches: 212, Mismatches: 5, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
50 3 0.01
51 3 0.01
52 151 0.71
53 18 0.08
54 1 0.00
55 6 0.03
57 26 0.12
58 2 0.01
59 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:58128 original size:71 final size:71
Alignment explanation
Indices: 58044--58283 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 71
58034 GCAACGTGAG
*
58044 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
58109 AATGAA
66 AATGAA
* *
58115 AATCGCAATGCGAAATGAAAATCG-AA--CAGACAT---AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAA--CG-AA--AGAATCGCA
*
58174 ATACGAAATGAA
60 ATGCGAAATGAA
58186 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
58251 AATGAA
66 AATGAA
58257 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
58284 CGAGATAATC
Statistics
Matches: 150, Mismatches: 7, Indels: 24
0.83 0.04 0.13
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
70 2 0.01
71 113 0.75
72 2 0.01
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:58229 original size:142 final size:137
Alignment explanation
Indices: 57977--58315 Score: 506
Period size: 142 Copynumber: 2.4 Consensus size: 137
57967 CGGAAAATAC
* * *
57977 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAACA-GAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
58040 TGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
58105 GCGAAATGAA
128 GCGAAATGAA
58115 AATCGCAATGCGAAATGAAAATCGAACAGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACAGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
58180 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 --TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
58245 ATGCGAAATGAA
126 ATGCGAAATGAA
58257 AATCGCAATGCGAAATGAAAATCGCAAC-GAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACAGA-ATAATCGCAATGCGAAATTA-AAATCGCA
58316 TTGCGATTTT
Statistics
Matches: 186, Mismatches: 6, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 19 0.10
138 33 0.18
139 3 0.02
142 123 0.66
143 6 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACAGAATAATCGCAATGCGAAATTAAAATCGCAAACGTGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:58421 original size:19 final size:19
Alignment explanation
Indices: 58312--58413 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
58302 AAATTATAAA
58312 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
58331 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
58351 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
58367 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
58384 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
58403 CGCATTGCGAT
1 CGCATTGCGAT
58414 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:58552 original size:13 final size:14
Alignment explanation
Indices: 58525--58560 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
58515 CATCAATTAC
58525 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
58539 ACAAATCATC-TTT
1 ACAAATCAACTTTT
58552 ACAAATCAA
1 ACAAATCAA
58561 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:58572 original size:12 final size:12
Alignment explanation
Indices: 58555--58627 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
58545 CATCTTTACA
58555 AATCAATTAAAC
1 AATCAATTAAAC
*
58567 AATCAA--AAATTG
1 AATCAATTAAA--C
**
58579 AATCAACTTTTAC
1 AATCAA-TTAAAC
58592 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
58605 AATCAA-AAAAC
1 AATCAATTAAAC
58616 AATCAATTAAAC
1 AATCAATTAAAC
58628 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:60509 original size:33 final size:33
Alignment explanation
Indices: 60463--60555 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
60453 GCGAAACCAA
*
60463 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
60496 AATCGCAATGCGAAATGAAAATCACAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
60529 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
60556 TGCGATTTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:60537 original size:14 final size:14
Alignment explanation
Indices: 60482--60538 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
60472 GCGAAATGAA
*
60482 AATCGCAACGACAG
1 AATCGCAACGAAAG
60496 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
60513 AAAATCACAACGAAAG
1 --AATCGCAACGAAAG
60529 AATCGCAACG
1 AATCGCAACG
60539 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:60553 original size:19 final size:19
Alignment explanation
Indices: 60426--60560 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
60416 TAGTTTACTT
* *
60426 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
60446 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
60465 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
60484 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
60498 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
60517 TCACAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
60531 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
60550 TCGCAATGCGA
1 TCGCAACGCGA
60561 TTTGGTTTCG
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:60610 original size:33 final size:33
Alignment explanation
Indices: 60566--60646 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
60556 TGCGATTTGG
60566 TTTCGCGTTGCGA-TCTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTC-TGTCGTTGCGATTTTCA
*
60599 TTTCGCATTGCGATTCTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
60632 TTTCGCGTTGCGATT
1 TTTCGCGTTGCGATT
60647 TTGGTTTCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
Found at i:60611 original size:19 final size:19
Alignment explanation
Indices: 60585--60683 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
60575 GCGATCTTGT
60585 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
60604 CATTGCGA--TTC-TGT--
1 CGTTGCGATTTTCATTTCG
60618 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
60637 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTCATTTCG
*
60656 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
60676 TGTTGCGA
1 CGTTGCGA
60684 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 7 0.11
16 5 0.08
17 5 0.08
19 36 0.55
20 12 0.18
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:61111 original size:91 final size:93
Alignment explanation
Indices: 60727--61196 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
60717 TTGAATGGAT
60727 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
60792 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
60820 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
60885 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
60913 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
60978 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
61006 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
61069 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
61097 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAA-AATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
61161 AGTTTAGCAGAA-TGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
61188 AAATTTACT
1 AAATTTACT
61197 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
91 113 0.30
92 23 0.06
93 239 0.64
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:62923 original size:14 final size:14
Alignment explanation
Indices: 62904--62993 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
62894 TTGAAATGAA
62904 AATCGCAACGAGAG
1 AATCGCAACGAGAG
62918 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
62935 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
62951 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
62970 AATCGCAACGAGAG
1 AATCGCAACGAGAG
62984 AATCGCAACG
1 AATCGCAACG
62994 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:62941 original size:33 final size:33
Alignment explanation
Indices: 62896--63010 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
62886 TCTTTTGGTT
62896 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
62929 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
62962 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
62995 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
63011 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:62942 original size:19 final size:18
Alignment explanation
Indices: 62903--63015 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
62893 GTTGAAATGA
62903 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
62918 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
62935 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
62951 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
62968 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
62984 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
63001 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
63016 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:63046 original size:14 final size:14
Alignment explanation
Indices: 63027--63083 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
63017 TTTGGTTTCG
63027 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
63041 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
*
63060 CGTTGCGATTCTAT
1 CGTTGCGATTCTCT
63074 CGTTGCGATT
1 CGTTGCGATT
63084 GTCATCTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:63059 original size:33 final size:33
Alignment explanation
Indices: 63022--63102 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
63012 GCGATTTTGG
*
63022 TTTCGCGTTGCGATTCTCTCGTTGCGATT-TCCA
1 TTTCGCGTTGCGATTCTATCGTTGCGATTGT-CA
63055 TTTCGCGTTGCGATTCTATCGTTGCGATTGTCA
1 TTTCGCGTTGCGATTCTATCGTTGCGATTGTCA
*
63088 TCTCGCGTTGCGATT
1 TTTCGCGTTGCGATT
63103 TTCATTTATC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 44 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTATCGTTGCGATTGTCA
Found at i:63065 original size:19 final size:18
Alignment explanation
Indices: 63022--63109 Score: 66
Period size: 19 Copynumber: 5.2 Consensus size: 18
63012 GCGATTTTGG
63022 TTTCGCGTTGCGA-TTC-
1 TTTCGCGTTGCGATTTCA
*
63038 --TCTCGTTGCGATTTCCA
1 TTTCGCGTTGCGATTT-CA
63055 TTTCGCGTTGCGA-TTC-
1 TTTCGCGTTGCGATTTCA
*
63071 TAT--CGTTGCGATTGTCA
1 TTTCGCGTTGCGATT-TCA
*
63088 TCTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
63107 TTT
1 TTT
63110 ATCTCGTTGC
Statistics
Matches: 56, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
14 18 0.32
15 3 0.05
16 5 0.09
17 3 0.05
18 2 0.04
19 23 0.41
20 2 0.04
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:63243 original size:33 final size:33
Alignment explanation
Indices: 63201--63271 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
63191 AATACTAACT
*
63201 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
63234 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
63267 TGAAA
1 TGAAA
63272 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:63505 original size:22 final size:22
Alignment explanation
Indices: 63453--63507 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
63443 TGGTTGTGAG
**
63453 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
63475 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
63497 GGATTTCTTCG
1 GGATTTCTTCG
63508 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:63678 original size:20 final size:20
Alignment explanation
Indices: 63653--63846 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
63643 CTTTAAATAT
63653 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
63673 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
63695 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
63714 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
63734 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
63754 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
63774 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
63794 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
63814 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
63834 CGCGTTGCGATTT
1 CGCGTTGCGATTT
63847 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:63840 original size:60 final size:60
Alignment explanation
Indices: 63653--63846 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
63643 CTTTAAATAT
**
63653 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
63714 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
63774 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
63834 CGCGTTGCGATTT
1 CGCGTTGCGATTT
63847 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:63863 original size:21 final size:20
Alignment explanation
Indices: 63839--63915 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
63829 ATATTCGCGT
63839 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
63860 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
63880 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
63902 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
63916 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:63926 original size:20 final size:20
Alignment explanation
Indices: 63901--63952 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
63891 AAGAATCGCG
*
63901 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
63921 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
63941 TTGCGATTCTGG
1 TTGCGATTCTGG
63953 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:75356 original size:59 final size:59
Alignment explanation
Indices: 75266--75377 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
75256 ACATACATAG
* * *
75266 AGTTTGGGATGAAATCGGAATGTTCAAAAAGTTTG-GGAACCAATTTAGAATGAACTCAT
1 AGTTTGGGATGAAATCGAAAAGTTCAAAAAGTTTGAGG-ACCAATTTAAAATGAACTCAT
* *
75325 AGTTTGGGAATGAAATTGAAAAGTTC-AAAAGTTTGAGGACTAATTTAAAATGA
1 AGTTTGGG-ATGAAATCGAAAAGTTCAAAAAGTTTGAGGACCAATTTAAAATGA
75378 TAGTTATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 30 0.65
60 16 0.35
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.29
Consensus pattern (59 bp):
AGTTTGGGATGAAATCGAAAAGTTCAAAAAGTTTGAGGACCAATTTAAAATGAACTCAT
Found at i:79564 original size:18 final size:19
Alignment explanation
Indices: 79519--79565 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
79509 GAAATTTTAT
*
79519 AAAATTATATTAAAATTAA
1 AAAAATATATTAAAATTAA
*
79538 AAAACATATA-TAAAATTAC
1 AAAA-ATATATTAAAATTAA
79557 AAAAATATA
1 AAAAATATA
79566 GGTGGTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 16 0.64
20 4 0.16
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATATATTAAAATTAA
Found at i:80229 original size:21 final size:21
Alignment explanation
Indices: 80137--80229 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 21
80127 TCGCATTACG
* ** *
80137 ATTTTTCAAATTCGCGTTGCG
1 ATTTTTCAAAATCGCAATGCA
**
80158 ATTTTAGAAAATCGCAATGCAA
1 ATTTTTCAAAATCGCAATGC-A
* * *
80180 ATATGT--AAATCGCAAGGCA
1 ATTTTTCAAAATCGCAATGCA
** *
80199 ATAATACAAAATCGCAATGCA
1 ATTTTTCAAAATCGCAATGCA
80220 ATTTTTCAAA
1 ATTTTTCAAA
80230 TTTACGTTAG
Statistics
Matches: 52, Mismatches: 17, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
19 4 0.08
20 11 0.21
21 34 0.65
22 3 0.06
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (21 bp):
ATTTTTCAAAATCGCAATGCA
Found at i:80685 original size:19 final size:19
Alignment explanation
Indices: 80661--80697 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
80651 TTATTTTGGA
80661 TTTTTCACTATCACAACAC
1 TTTTTCACTATCACAACAC
*
80680 TTTTTCACTATCGCAACA
1 TTTTTCACTATCACAACA
80698 ACACGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCACAACAC
Found at i:80701 original size:22 final size:20
Alignment explanation
Indices: 80661--80709 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
80651 TTATTTTGGA
80661 TTTTTCACTATCACAACAC-
1 TTTTTCACTATCACAACACG
80680 TTTTTCACTATCGCAACAACACG
1 TTTTTCACTAT--C-ACAACACG
80703 TTTTTCA
1 TTTTTCA
80710 AACTCTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.42
21 1 0.04
22 7 0.27
23 7 0.27
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.39
Consensus pattern (20 bp):
TTTTTCACTATCACAACACG
Found at i:80759 original size:20 final size:20
Alignment explanation
Indices: 80731--80787 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
80721 CATTTTTCAA
* *
80731 AATCGCGTTACGAATCTTAC
1 AATCACGTTGCGAATCTTAC
80751 AATCACGTTGCGAATCTTAC
1 AATCACGTTGCGAATCTTAC
80771 AATCACGTTGCGAATCT
1 AATCACGTTGCGAATCT
80788 GGATATTCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (20 bp):
AATCACGTTGCGAATCTTAC
Found at i:81353 original size:60 final size:60
Alignment explanation
Indices: 81235--81409 Score: 160
Period size: 60 Copynumber: 2.9 Consensus size: 60
81225 AAGCAATAAT
* ** * *
81235 TCTCATTTTAAATTGGTCCTTAACCTTTTGAATATTCCAATTTCATCCTCAAATTATGAC
1 TCTCATTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAATTATGAC
** *
81295 TCTCATTCTAAATTAATCCTTAAACTTTTGAACATTTTAATTTCATCCT-TAATATATGAC
1 TCTCATTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAAT-TATGAC
* ** * * *
81355 -CAT-ATTTCTAAATGAATCCCCAAACTTTTTAATATTCCAATTCCATGCC-CAAATT
1 TC-TCA-TTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCAT-CCTCAAATT
81410 CATCCAAATA
Statistics
Matches: 93, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
59 5 0.05
60 83 0.89
61 5 0.05
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (60 bp):
TCTCATTCTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAATTATGAC
Found at i:81665 original size:60 final size:60
Alignment explanation
Indices: 81557--81708 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
81547 ATTAGAATGT
* * * *
81557 TTAAAAAGTTTGAGGGACTAATTTAAAAT-AAAGGTTATAATTTGGGGATGAAATT-GAAGTG
1 TTAAAAAGTTTGA-GGACTAATTTAAAATGAAA-GTCATAATTTAGGGATAAAATTGGAA-TA
* * *
81618 TTCAAAAGTTTGAGAACTAATTTAAAATGATAA-TCATAGTTTAGGGATAAAATTGGAATA
1 TTAAAAAGTTTGAGGACTAATTTAAAATGA-AAGTCATAATTTAGGGATAAAATTGGAATA
* *
81678 TTAAAAAGTTTAAGGACCAATTTAAAATGAA
1 TTAAAAAGTTTGAGGACTAATTTAAAATGAA
81709 TGTTATACTT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
59 1 0.01
60 58 0.75
61 16 0.21
62 2 0.03
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (60 bp):
TTAAAAAGTTTGAGGACTAATTTAAAATGAAAGTCATAATTTAGGGATAAAATTGGAATA
Done.