Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003378.1 Hibiscus syriacus cultivar Beakdansim tig00007099_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: 195279
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9559 original size:24 final size:24
Alignment explanation
Indices: 9527--9574 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
9517 CTAACAGGTT
9527 TACCTGCTGTCAATATGGCTGCTC
1 TACCTGCTGTCAATATGGCTGCTC
9551 TACCTGCTGTCAATATGGCTGCTC
1 TACCTGCTGTCAATATGGCTGCTC
9575 CCAAGGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (24 bp):
TACCTGCTGTCAATATGGCTGCTC
Found at i:21077 original size:20 final size:20
Alignment explanation
Indices: 21052--21090 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21042 GTTTGGTTCA
*
21052 GGGAATATAAGATTATCAGT
1 GGGAATAAAAGATTATCAGT
21072 GGGAATAAAAGATTATCAG
1 GGGAATAAAAGATTATCAG
21091 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (20 bp):
GGGAATAAAAGATTATCAGT
Found at i:21079 original size:18 final size:16
Alignment explanation
Indices: 21058--21102 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
21048 TTCAGGGAAT
21058 ATAAGATTATCAGTGGGA
1 ATAAGATTATCA--GGGA
21076 ATAAAAGATTATCAGGGA
1 AT--AAGATTATCAGGGA
21094 ATAAGATTA
1 ATAAGATTA
21103 CTGAGAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.28
18 8 0.32
20 10 0.40
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (16 bp):
ATAAGATTATCAGGGA
Found at i:22114 original size:22 final size:22
Alignment explanation
Indices: 22086--22129 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
22076 ACAGTGTATT
22086 TCTTTTGTCAGCAATTATAGCA
1 TCTTTTGTCAGCAATTATAGCA
22108 TCTTTTGTCAGCAATTATAGCA
1 TCTTTTGTCAGCAATTATAGCA
22130 GCATGTTGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (22 bp):
TCTTTTGTCAGCAATTATAGCA
Found at i:23437 original size:21 final size:21
Alignment explanation
Indices: 23386--23438 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
23376 ATTATGACTA
23386 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
23407 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
23428 TCGCAATGCGA
1 TCGCAATGCGA
23439 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:23471 original size:21 final size:21
Alignment explanation
Indices: 23428--23517 Score: 78
Period size: 20 Copynumber: 4.4 Consensus size: 21
23418 TTTTCCCAAT
** *
23428 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
23448 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
* * **
23469 TCGCAATGTG-ATACT-GACTA
1 TCGCAATGCGAAT-TTGGAAAA
23489 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
23510 CCGCAATG
1 TCGCAATG
23518 AGATACTGAC
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
20 27 0.50
21 27 0.50
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:23473 original size:41 final size:41
Alignment explanation
Indices: 23446--23540 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
23436 CGAATAAGTA
*
23446 AATCGCAATGCGAATTTGGAAAATCGCAATGTGATACTGAC
1 AATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGAC
* * *
23487 TATCGCAATGCGAATTTGGAAAACCGCAATGAGATACTGAC
1 AATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGAC
*
23528 TATCGCAATGCGA
1 AATCGCAATGCGA
23541 TTTTCCTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (41 bp):
AATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGAC
Found at i:23493 original size:20 final size:20
Alignment explanation
Indices: 23468--23537 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
23458 AATTTGGAAA
*
23468 ATCGCAATGTGATACTGACT
1 ATCGCAATGAGATACTGACT
* * **
23488 ATCGCAATGCGA-ATTTGGAAA
1 ATCGCAATGAGATA-CT-GACT
*
23509 ACCGCAATGAGATACTGACT
1 ATCGCAATGAGATACTGACT
23529 ATCGCAATG
1 ATCGCAATG
23538 CGATTTTCCT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 1 0.03
20 22 0.59
21 13 0.35
22 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAATGAGATACTGACT
Found at i:23560 original size:21 final size:21
Alignment explanation
Indices: 23530--23596 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
23520 ATACTGACTA
* *
23530 TCGCAATGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
23551 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
23571 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
23592 TCGCA
1 TCGCA
23597 ATGTGAATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:23617 original size:20 final size:20
Alignment explanation
Indices: 23592--23703 Score: 120
Period size: 20 Copynumber: 5.5 Consensus size: 20
23582 TTTTCATAAT
*
23592 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
23612 TCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAA-TACGTAAA
* * *
23632 TCGCAAAGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
23653 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
23673 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
23693 TCGCAATGCGA
1 TCGCAATGCGA
23704 TTTACATAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.75
21 17 0.21
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:24248 original size:20 final size:19
Alignment explanation
Indices: 24220--24286 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
24210 TTCGAGAATG
24220 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
24240 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
24259 AAAATCGCAACGCAAAACC
1 AAAATCGCAACGCGAAATA
24278 AAAATCGCA
1 AAAATCGCA
24287 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:24352 original size:33 final size:34
Alignment explanation
Indices: 24304--24369 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
24294 TTTCATTTCG
** *
24304 CGTTGCGATTTTCATTT-CGTGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
24337 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
24370 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:24371 original size:20 final size:19
Alignment explanation
Indices: 24282--24394 Score: 110
Period size: 19 Copynumber: 6.1 Consensus size: 19
24272 AAAACCAAAA
*
24282 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24301 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
24320 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
24334 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
24353 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
24373 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
24393 TC
1 TC
24395 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 3 0.04
19 31 0.40
20 31 0.40
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:26605 original size:21 final size:21
Alignment explanation
Indices: 26546--26606 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
26536 CTCGAGAGTC
26546 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
* ** * *
26567 CACTGTCATCGTTGAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
*
26588 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
26607 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:27966 original size:14 final size:14
Alignment explanation
Indices: 27947--27982 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
27937 ATTGTTTAAT
27947 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
27961 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
27975 TGATTTGT
1 TGATTTGT
27983 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:28140 original size:19 final size:19
Alignment explanation
Indices: 28118--28202 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
28108 CGAAATTAAA
*
28118 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
28137 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
28156 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
28170 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
28189 TTCGTATTGCGATT
1 TTCGCATTGCGATT
28203 CTCTCGTTGC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
14 12 0.22
19 43 0.78
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:28215 original size:33 final size:33
Alignment explanation
Indices: 28137--28200 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
28127 CGATTTTCAT
*
28137 TTCGCATTGCGATTTTCATTTCGCATTGCGAAA
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGAAA
*
28170 TTCGCGTTGCGATTTTCATTTCGTATTGCGA
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGA
28201 TTCTCTCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (33 bp):
TTCGCGTTGCGATTTTCATTTCGCATTGCGAAA
Found at i:30534 original size:18 final size:15
Alignment explanation
Indices: 30494--30531 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
30484 TGGCATTTTC
30494 TTTTCTTCGGGGACT
1 TTTTCTTCGGGGACT
30509 TTTTCTTCGGGGACT
1 TTTTCTTCGGGGACT
30524 TTTTCTTC
1 TTTTCTTC
30532 TTCTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.21, G:0.21, T:0.53
Consensus pattern (15 bp):
TTTTCTTCGGGGACT
Found at i:30539 original size:12 final size:12
Alignment explanation
Indices: 30522--30546 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30512 TCTTCGGGGA
30522 CTTTTTCTTCTT
1 CTTTTTCTTCTT
30534 CTTTTTCTTCTT
1 CTTTTTCTTCTT
30546 C
1 C
30547 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:31558 original size:21 final size:22
Alignment explanation
Indices: 31509--31562 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
31499 TTTTCCTAAT
*
31509 TCGCAATGCGAATATAAGTAAA
1 TCGCAATGCGAATATAAGAAAA
* **
31531 CCGCAATGCGAAT-TTGGAAAA
1 TCGCAATGCGAATATAAGAAAA
31552 TCGCAATGCGA
1 TCGCAATGCGA
31563 TACTGACTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (22 bp):
TCGCAATGCGAATATAAGAAAA
Found at i:31970 original size:14 final size:14
Alignment explanation
Indices: 31951--32004 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
31941 GAAAATCGCA
31951 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
31965 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
31982 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
*
31998 TTACGAT
1 TTGCGAT
32005 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
16 3 0.09
17 3 0.09
19 11 0.32
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:31987 original size:19 final size:16
Alignment explanation
Indices: 31946--31997 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 16
31936 AAAATGAAAA
31946 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
31962 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
31976 ATTTCGCATTGCGATTTTC
1 ---TCGCATTGCGATTTTC
31995 TCG
1 TCG
31998 TTACGATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.35
16 6 0.19
17 3 0.10
19 11 0.35
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:34092 original size:19 final size:18
Alignment explanation
Indices: 34029--34181 Score: 87
Period size: 19 Copynumber: 8.9 Consensus size: 18
34019 ATGAAACTTA
34029 AAATCGCAACGCGAAAATG
1 AAATCGCAACGCG-AAATG
*
34048 ACTATCGCAACGCGAAATGG
1 A-AATCGCAACGCGAAAT-G
** *
34068 CTATCGCAAGGCGAAATG
1 AAATCGCAACGCGAAATG
*
34086 CAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
*
34101 AAATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
34119 AAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
**
34134 AAATCGCAATACGAAATG
1 AAATCGCAACGCGAAATG
*
34152 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
34166 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
34182 CACAAATCGC
Statistics
Matches: 109, Mismatches: 11, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
14 27 0.25
16 16 0.15
17 8 0.07
18 10 0.09
19 36 0.33
20 12 0.11
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:34106 original size:14 final size:14
Alignment explanation
Indices: 34087--34176 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
34077 GGCGAAATGC
34087 AAATCGCAACGACA
1 AAATCGCAACGACA
*
34101 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
34120 AAATCGCAACGACA
1 AAATCGCAACGACA
*
34134 AAATCGCAATACGAAA
1 AAATCGC-A-ACGACA
34150 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
34166 AAATCGCAACG
1 AAATCGCAACG
34177 CGAAACACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 28 0.44
15 2 0.03
16 12 0.19
17 3 0.05
18 8 0.13
19 10 0.16
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:34115 original size:33 final size:33
Alignment explanation
Indices: 34070--34192 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 33
34060 CGAAATGGCT
*
34070 ATCGCAAGGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
*
34103 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
*
34136 ATCGCAATACGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* **
34168 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
34193 TTGCGAATTT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 28 0.34
33 54 0.66
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:34189 original size:65 final size:66
Alignment explanation
Indices: 34070--34192 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
34060 CGAAATGGCT
* * *
34070 ATCGCAAGGCGAAATGCAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAAGACGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
34135 A
66 A
*
34136 ATCGCAATACGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAAGACGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
34193 TTGCGAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 37 0.71
66 14 0.27
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (66 bp):
ATCGCAAGACGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:34229 original size:14 final size:14
Alignment explanation
Indices: 34210--34268 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
34200 TTTCATTTCG
34210 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
34224 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
34241 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
34257 CGTTGCGATTTT
1 CGTTGCGATTTT
34269 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:34237 original size:33 final size:33
Alignment explanation
Indices: 34193--34284 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
34183 ACAAATCGCA
* *
34193 TTGCGAATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
34226 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
34259 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
34285 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:34284 original size:19 final size:19
Alignment explanation
Indices: 34188--34284 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
34178 GAAACACAAA
*
34188 TCGCATTGCGAATTTCATT
1 TCGCATTGCGATTTTCATT
* *
34207 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
34223 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
34240 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
34256 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
34273 TCGCATTGCGAT
1 TCGCATTGCGAT
34285 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:34303 original size:20 final size:19
Alignment explanation
Indices: 34269--34323 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
34259 TTGCGATTTT
*
34269 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
34288 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
34308 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
34324 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:34831 original size:18 final size:18
Alignment explanation
Indices: 34805--34849 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
34795 GTCGATCAAA
*
34805 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
34823 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
34841 TGATGGCTC
1 TGATGGCTC
34850 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:36157 original size:20 final size:20
Alignment explanation
Indices: 36132--36169 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36122 TATAGTTTCT
36132 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
36152 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
36170 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:36460 original size:22 final size:22
Alignment explanation
Indices: 36433--36476 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36423 GATGGAGATA
36433 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
36455 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
36477 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:36690 original size:20 final size:20
Alignment explanation
Indices: 36665--36716 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
36655 ATTATGTATT
36665 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
36685 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
36705 ATCTCGTTGCGA
1 ATCGCGTTGCGA
36717 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:36750 original size:20 final size:20
Alignment explanation
Indices: 36725--36778 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
36715 GATTTTGTAT
36725 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
36745 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
36765 TATCGCATTGCGAT
1 TATCGCATTGCGAT
36779 TTACTTATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:36750 original size:61 final size:61
Alignment explanation
Indices: 36644--36780 Score: 184
Period size: 61 Copynumber: 2.2 Consensus size: 61
36634 CGCTTTGAAA
* * * * *
36644 ATCGCATTACGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
36705 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
36766 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
36781 ACTTATTCGC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:36831 original size:21 final size:21
Alignment explanation
Indices: 36807--36878 Score: 144
Period size: 21 Copynumber: 3.4 Consensus size: 21
36797 AATTGGGAAA
36807 ATCGCAACGACACTGTAGACC
1 ATCGCAACGACACTGTAGACC
36828 ATCGCAACGACACTGTAGACC
1 ATCGCAACGACACTGTAGACC
36849 ATCGCAACGACACTGTAGACC
1 ATCGCAACGACACTGTAGACC
36870 ATCGCAACG
1 ATCGCAACG
36879 CGATTTTCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.14
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACC
Found at i:36910 original size:21 final size:21
Alignment explanation
Indices: 36870--36910 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36860 ACTGTAGACC
** *
36870 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
36891 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
36911 GCGAATTTGC
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:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:37462 original size:60 final size:60
Alignment explanation
Indices: 37398--37528 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 60
37388 AAAGAGGGCC
** * * * *
37398 ATAGTTTAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGA-CTTATTTAGAATGAGAGTT
1 ATAGTTTAGGGATGAAATTAGAAAATTCAAAAGTTTAAGAATC-AATATAAAATGAGAGTT
* * * *
37458 ATAGTTT-GGGATGAAATTGGAAAATTTAAAAGTTTTAGAATCAATATAAAATGAGGGTT
1 ATAGTTTAGGGATGAAATTAGAAAATTCAAAAGTTTAAGAATCAATATAAAATGAGAGTT
37517 ATAGTTTAGGGA
1 ATAGTTTAGGGA
37529 CATATGATGC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 47 0.80
60 12 0.20
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAATTAGAAAATTCAAAAGTTTAAGAATCAATATAAAATGAGAGTT
Found at i:38607 original size:67 final size:67
Alignment explanation
Indices: 38527--38665 Score: 172
Period size: 67 Copynumber: 2.1 Consensus size: 67
38517 CAATAAGTCA
* * *
38527 AGCAATAGATTTTCATAACGAACTCGAGTTGAGCAAAATTTTAACGAGTTTAACGAACAACGAAT
1 AGCAATAGATTTTCATAACGAACACGAGTCGAGCAAAATTTTAACGAGCTTAACGAACAACGAAT
38592 CG
66 CG
* * * * * * *
38594 AGCAATA-ATTTTTCTTAATGAGCACGGGTCGAGCAAAATTTTAACGAGCTTAACGAATATCGAG
1 AGCAATAGA-TTTTCATAACGAACACGAGTCGAGCAAAATTTTAACGAGCTTAACGAACAACGAA
38658 TCG
65 TCG
38661 AGCAA
1 AGCAA
38666 CAAAATTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
66 1 0.02
67 60 0.98
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (67 bp):
AGCAATAGATTTTCATAACGAACACGAGTCGAGCAAAATTTTAACGAGCTTAACGAACAACGAAT
CG
Found at i:38661 original size:36 final size:36
Alignment explanation
Indices: 38542--38665 Score: 109
Period size: 36 Copynumber: 3.6 Consensus size: 36
38532 TAGATTTTCA
* *
38542 TAACGAAC-TCGAGTTGAGCAAAATTTTAACGAGTT
1 TAACGAACATCGAGTCGAGCAAAATTTTAACGAGCT
* * *
38577 TAACGAACAACGAATCGAGCAATAATTTT-----TCT
1 TAACGAACATCGAGTCGAGCAA-AATTTTAACGAGCT
* * *
38609 TAATGAGCA-CGGGTCGAGCAAAATTTTAACGAGCT
1 TAACGAACATCGAGTCGAGCAAAATTTTAACGAGCT
*
38644 TAACGAATATCGAGTCGAGCAA
1 TAACGAACATCGAGTCGAGCAA
38666 CAAAATTTTT
Statistics
Matches: 67, Mismatches: 14, Indels: 15
0.70 0.15 0.16
Matches are distributed among these distances:
30 6 0.09
31 10 0.15
32 8 0.12
35 16 0.24
36 21 0.31
37 6 0.09
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (36 bp):
TAACGAACATCGAGTCGAGCAAAATTTTAACGAGCT
Found at i:47073 original size:3 final size:3
Alignment explanation
Indices: 47065--47094 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
47055 CCACACTCTC
47065 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
47095 TCCCTCCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:51557 original size:27 final size:26
Alignment explanation
Indices: 51504--51557 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
51494 CTTAAAATCT
*
51504 AACCTAACTTAAAACTTTAATCTATA
1 AACCTAACTTAAAACTTAAATCTATA
51530 AACCTTAACTTAAAACTCTAAATC-ATA
1 AACC-TAACTTAAAACT-TAAATCTATA
51557 A
1 A
51558 TAAATATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 4 0.16
27 16 0.64
28 5 0.20
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (26 bp):
AACCTAACTTAAAACTTAAATCTATA
Found at i:58242 original size:22 final size:21
Alignment explanation
Indices: 58210--58254 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
58200 AGAAAATGTC
*
58210 TTTTAATATATATTAAATAAT
1 TTTTAATATATATTAAAGAAT
*
58231 TTTTGAATATATTTTAAAGAAT
1 TTTT-AATATATATTAAAGAAT
58253 TT
1 TT
58255 ATTTTTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTAATATATATTAAAGAAT
Found at i:63158 original size:22 final size:21
Alignment explanation
Indices: 63126--63172 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
63116 AGAAAATGTC
63126 TTTTAATATATATTAAAGAAT
1 TTTTAATATATATTAAAGAAT
*
63147 TTTTAAATATATTTTAAAGAAT
1 TTTT-AATATATATTAAAGAAT
63169 TTTT
1 TTTT
63173 TTTGGATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTAATATATATTAAAGAAT
Found at i:68336 original size:3 final size:3
Alignment explanation
Indices: 68330--68371 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
68320 TAAAAAAAAT
*
68330 TAA TAA TAA TAA TAT TAGA TAAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TA-A T-AA TAA TAA TAA TAA TAA TAA T
68372 GTATAAACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 31 0.89
4 3 0.09
5 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:78300 original size:18 final size:19
Alignment explanation
Indices: 78279--78362 Score: 79
Period size: 18 Copynumber: 4.7 Consensus size: 19
78269 AATCTACGTT
*
78279 TGATAACTGTAAAA-CATT
1 TGATAACTGTAAAATCATC
*
78297 TGATAACTG-AAAATTATC
1 TGATAACTGTAAAATCATC
* *
78315 TAATAACTAT-AAAT-ATC
1 TGATAACTGTAAAATCATC
*
78332 TGATAACTG-AAAATCATA
1 TGATAACTGTAAAATCATC
*
78350 TAATAACTGTAAA
1 TGATAACTGTAAA
78363 TATTTAGAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
17 18 0.34
18 32 0.60
19 3 0.06
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
TGATAACTGTAAAATCATC
Found at i:78337 original size:35 final size:35
Alignment explanation
Indices: 78297--78365 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
78287 GTAAAACATT
* *
78297 TGATAACTGAAAATTATCTAATAACTATAAATATC
1 TGATAACTGAAAATCATATAATAACTATAAATATC
*
78332 TGATAACTGAAAATCATATAATAACTGTAAATAT
1 TGATAACTGAAAATCATATAATAACTATAAATAT
78366 TTAGAATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.33
Consensus pattern (35 bp):
TGATAACTGAAAATCATATAATAACTATAAATATC
Found at i:78851 original size:21 final size:21
Alignment explanation
Indices: 78814--78879 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
78804 CATTATCAAC
* *
78814 CACAGTGGACTGCCATGTCAG
1 CACAGTGAACCGCCATGTCAG
78835 CATCA-TGAACCGCCATGTCAG
1 CA-CAGTGAACCGCCATGTCAG
* *
78856 TACAGTGAACTGCCATGTCAG
1 CACAGTGAACCGCCATGTCAG
78877 CAC
1 CAC
78880 TATATTAGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (21 bp):
CACAGTGAACCGCCATGTCAG
Found at i:92724 original size:55 final size:55
Alignment explanation
Indices: 92664--92776 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
92654 AGCTGGATTA
92664 CTAAGATCTAGCATTTATTTATTCATTCAGTACATATAGATAGGATACATATATG
1 CTAAGATCTAGCATTTATTTATTCATTCAGTACATATAGATAGGATACATATATG
92719 CTAAGATCTAGCATTTATTTATTCATTCAGTACATATAGATAGGATACATATATG
1 CTAAGATCTAGCATTTATTTATTCATTCAGTACATATAGATAGGATACATATATG
92774 CTA
1 CTA
92777 GGGCATTGCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (55 bp):
CTAAGATCTAGCATTTATTTATTCATTCAGTACATATAGATAGGATACATATATG
Found at i:101605 original size:47 final size:47
Alignment explanation
Indices: 101538--101646 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
101528 ATGAATGTTA
*
101538 GCATGCACATGGAGGGACCCAAACTGTGTAAAAAACAAACAATGGAT
1 GCATGCACATGGAGGGACCCAAACTGTGTAAAAAAAAAACAATGGAT
101585 GCATGCACATGGAGGGACCCAAACTGTGTAAAAAAAAAACAATGGAT
1 GCATGCACATGGAGGGACCCAAACTGTGTAAAAAAAAAACAATGGAT
* *
101632 GCATGAACATAGAGG
1 GCATGCACATGGAGG
101647 ACCACTTTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (47 bp):
GCATGCACATGGAGGGACCCAAACTGTGTAAAAAAAAAACAATGGAT
Found at i:104349 original size:29 final size:29
Alignment explanation
Indices: 104288--104373 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
104278 CCCAACCCAT
* ****
104288 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
104317 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
104346 AGGTCGCCATTCA-TGCCCGGCGACCAAG
1 AGGTCGCCATGCACT-CCCGGCGACCAAG
104374 CTTTTAACCC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 1 0.02
29 47 0.98
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAAGG
Found at i:107012 original size:47 final size:48
Alignment explanation
Indices: 106945--107054 Score: 186
Period size: 48 Copynumber: 2.3 Consensus size: 48
106935 ATGAATGTTA
106945 GCATGCACATGGAGGGACCCAAACTGTGT-AAAAAACAAACAATGGAT
1 GCATGCACATGGAGGGACCCAAACTGTGTAAAAAAACAAACAATGGAT
*
106992 GCATGCACATGGAGGGACCCAAACTGTGTAAAAAAATAAACAATGGAT
1 GCATGCACATGGAGGGACCCAAACTGTGTAAAAAAACAAACAATGGAT
* *
107040 GCATGAACATAGAGG
1 GCATGCACATGGAGG
107055 ACCACTTTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
47 29 0.49
48 30 0.51
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (48 bp):
GCATGCACATGGAGGGACCCAAACTGTGTAAAAAAACAAACAATGGAT
Found at i:113435 original size:23 final size:22
Alignment explanation
Indices: 113400--113442 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
113390 ATAATTATTT
113400 AAAAAATTAAATAAAAAATACC
1 AAAAAATTAAATAAAAAATACC
*
113422 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
113443 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACC
Found at i:118255 original size:20 final size:20
Alignment explanation
Indices: 118214--118266 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
118204 AAATAATCAA
*
118214 TAAATTCGTAACGCGATCTC
1 TAAATTCGTAACGCAATCTC
* * *
118234 TAATTTCGTAACTCAATTTC
1 TAAATTCGTAACGCAATCTC
*
118254 TAAATTCGCAACG
1 TAAATTCGTAACG
118267 TGAATATGTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (20 bp):
TAAATTCGTAACGCAATCTC
Found at i:118337 original size:20 final size:20
Alignment explanation
Indices: 118312--118392 Score: 110
Period size: 20 Copynumber: 4.0 Consensus size: 20
118302 GCGTTTTGAT
*
118312 TTTCCAAATTCGCAACGCGA
1 TTTCCAAATTCGCAACACGA
118332 TTTCCAAATTCGCAACACTGAA
1 TTTCCAAATTCGCAACAC-G-A
*
118354 TTT-CAAATTCGCAACTCGA
1 TTTCCAAATTCGCAACACGA
*
118373 TTTCTAAATTCGCAACACGA
1 TTTCCAAATTCGCAACACGA
118393 ATTTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
19 4 0.07
20 32 0.59
21 14 0.26
22 4 0.07
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.28
Consensus pattern (20 bp):
TTTCCAAATTCGCAACACGA
Found at i:118342 original size:41 final size:41
Alignment explanation
Indices: 118316--118408 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
118306 TTTGATTTTC
118316 CAAATTCGCAACGCGATTTCCAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGCGATTTCCAAATTCGCAACACTGAATTT
* *
118357 CAAATTCGCAACTCGATTTCTAAATTCGCAACAC-GAATTT
1 CAAATTCGCAACGCGATTTCCAAATTCGCAACACTGAATTT
* *
118397 TAATTTCGCAAC
1 CAAATTCGCAAC
118409 ATGTTTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
40 16 0.33
41 32 0.67
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (41 bp):
CAAATTCGCAACGCGATTTCCAAATTCGCAACACTGAATTT
Found at i:118404 original size:20 final size:19
Alignment explanation
Indices: 118317--118428 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 19
118307 TTGATTTTCC
* *
118317 AAATTCGCAACGCGATTTCC
1 AAATTCGCAACACGATTT-T
*
118337 AAATTCGCAACACTGAATTTC
1 AAATTCGCAACAC-G-ATTTT
*
118358 AAATTCGCAACTCGATTTCT
1 AAATTCGCAACACGATTT-T
118378 AAATTCGCAACACGAATTTT
1 AAATTCGCAACACG-ATTTT
* *
118398 AATTTCGCAACATG-TTTT
1 AAATTCGCAACACGATTTT
**
118416 ATTTTCGCAACAC
1 AAATTCGCAACAC
118429 AAATGTTTTG
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
18 15 0.19
19 4 0.05
20 39 0.49
21 18 0.22
22 4 0.05
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (19 bp):
AAATTCGCAACACGATTTT
Found at i:119003 original size:64 final size:64
Alignment explanation
Indices: 118902--119050 Score: 226
Period size: 64 Copynumber: 2.3 Consensus size: 64
118892 AATTTAAAAC
*
118902 AACAAATCAACTTTTACAGATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
118966 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
* *
119030 AATAAATCAATTTTTACAAAT
1 AACAAATCAACTTTTACAAAT
119051 ACATCAATTT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 77 1.00
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:120375 original size:21 final size:21
Alignment explanation
Indices: 120346--120404 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
120336 GTGAATCGGG
*
120346 CTCTCGAACGGTGGGAGAGAA
1 CTCTTGAACGGTGGGAGAGAA
* ** * **
120367 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGAGAA
120388 CTCTTGAACGGTGGGAG
1 CTCTTGAACGGTGGGAG
120405 GGGCCTCTTG
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.19
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGAGAA
Found at i:120406 original size:21 final size:21
Alignment explanation
Indices: 120367--120439 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
120357 TGGGAGAGAA
* *
120367 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGAGAGGGGC
*
120388 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGAGAGGGGC
* *
120409 CTCTTGAA-GGATGATAAGGGC
1 CTCTTGAACGG-TGAGAGGGGC
120430 CTCTTGAACG
1 CTCTTGAACG
120440 ATATGAGAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.05
21 41 0.93
22 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGC
Found at i:120413 original size:42 final size:42
Alignment explanation
Indices: 120346--120468 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 42
120336 GTGAATCGGG
* **
120346 CTCTCGAACGGTGGGAGAGAACTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGC
* * * *
120388 CTCTTGAACGGTGGGAGGGGCCTCTTGAAGGATGATAAGGGC
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGC
* ** * *
120430 CTCTTGAACGATATGAGAGGCTTCTTGAATGATGACAGG
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGG
120469 TGAATTAGGC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGC
Found at i:122171 original size:39 final size:39
Alignment explanation
Indices: 122117--122194 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
122107 GGCTAGGCTT
122117 AATTTATTCCTTAAGGTCAATGAAGCCAAAAAAAATTTC
1 AATTTATTCCTTAAGGTCAATGAAGCCAAAAAAAATTTC
*
122156 AATTTATTCCTTAAGGTCAATGAAGCCAAAAAAATTTTC
1 AATTTATTCCTTAAGGTCAATGAAGCCAAAAAAAATTTC
122195 TACAAAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (39 bp):
AATTTATTCCTTAAGGTCAATGAAGCCAAAAAAAATTTC
Found at i:122632 original size:20 final size:20
Alignment explanation
Indices: 122595--122633 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
122585 CTTAAATCGC
* * *
122595 GTTGCGATTTTCATTTTCAT
1 GTTGCGAATTTAAGTTTCAT
122615 GTTGCGAATTTAAGTTTCA
1 GTTGCGAATTTAAGTTTCA
122634 AATAGTCTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCAT
Found at i:123123 original size:19 final size:20
Alignment explanation
Indices: 123101--123138 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
123091 AATATTGTGT
123101 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
123120 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
123139 CGTGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:123227 original size:20 final size:20
Alignment explanation
Indices: 123180--123250 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
123170 AATTACAAAT
*
123180 TCGCGTTGCGAAATTGGA-A
1 TCGCGTTGCGAAATTAGAGA
* * *
123199 ACTGAGTTGCGAAATTAGAGT
1 TC-GCGTTGCGAAATTAGAGA
* *
123220 TCGTGTTGCG-AATTTGAGA
1 TCGCGTTGCGAAATTAGAGA
123239 TCGCGTTGCGAA
1 TCGCGTTGCGAA
123251 TTTGTTGGTC
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 17 0.43
20 22 0.55
21 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (20 bp):
TCGCGTTGCGAAATTAGAGA
Found at i:123246 original size:19 final size:19
Alignment explanation
Indices: 123204--123254 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
123194 TGGAAACTGA
* * *
123204 GTTGCGAAATTAGAGTTCGT
1 GTTGCG-AATTTGAGATCGC
123224 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCGC
123243 GTTGCGAATTTG
1 GTTGCGAATTTG
123255 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCGC
Found at i:124875 original size:29 final size:29
Alignment explanation
Indices: 124843--124914 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
124833 TATAAAGAAA
124843 ATTAAAAATAAAT-TAAA-ATAATTGAATAT
1 ATTAAAAATAAATATAAAGATAATT--ATAT
* * *
124872 ATTATATATGAATATAAAGATAATTATAT
1 ATTAAAAATAAATATAAAGATAATTATAT
*
124901 ATTATAAA-AAATAT
1 ATTAAAAATAAATAT
124915 CTTGAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 5 0.14
29 21 0.58
30 4 0.11
31 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTAAAAATAAATATAAAGATAATTATAT
Found at i:132143 original size:22 final size:22
Alignment explanation
Indices: 132114--132163 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
132104 TTGAAAATCG
132114 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
132136 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
132158 CGTTGC
1 CGTTGC
132164 TATTTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:132886 original size:19 final size:19
Alignment explanation
Indices: 132862--132971 Score: 69
Period size: 22 Copynumber: 5.4 Consensus size: 19
132852 CAACGAATTT
*
132862 TCGCAACGATTTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
132881 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
132903 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* *
132922 TCGCAACGACAACTGTAGAAAA
1 TCGCAACG--AA-TTTGGAAAA
*
132944 TCGCAACGCGAA-ATGGAAAA
1 TCGCAA--CGAATTTGGAAAA
132964 TCGCAACG
1 TCGCAACG
132972 CGTATCGCAA
Statistics
Matches: 70, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.03
19 21 0.30
20 14 0.20
21 3 0.04
22 28 0.40
24 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:132907 original size:41 final size:41
Alignment explanation
Indices: 132862--132971 Score: 159
Period size: 41 Copynumber: 2.7 Consensus size: 41
132852 CAACGAATTT
* **
132862 TCGCAACGATTTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGAAAA
132903 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGAAAA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGAAAA
*
132944 TCGCAACGCGAA-ATGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
132972 CGTATCGCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 44 0.70
42 15 0.24
43 4 0.06
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGAAAA
Found at i:132908 original size:22 final size:22
Alignment explanation
Indices: 132876--132971 Score: 96
Period size: 22 Copynumber: 4.6 Consensus size: 22
132866 AACGATTTTG
132876 GAAAATCGCAACGACAACTGTA
1 GAAAATCGCAACGACAACTGTA
** * *
132898 GACTATCGCAACG--AA-TTTG
1 GAAAATCGCAACGACAACTGTA
132917 GAAAATCGCAACGACAACTGTA
1 GAAAATCGCAACGACAACTGTA
*
132939 GAAAATCGCAACG-CGAAATG--
1 GAAAATCGCAACGAC-AACTGTA
132959 GAAAATCGCAACG
1 GAAAATCGCAACG
132972 CGTATCGCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
19 13 0.21
20 15 0.25
21 3 0.05
22 30 0.49
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.15
Consensus pattern (22 bp):
GAAAATCGCAACGACAACTGTA
Found at i:132964 original size:20 final size:20
Alignment explanation
Indices: 132915--132973 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
132905 GCAACGAATT
*
132915 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAA
132935 TGTAGAAAATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAA
132957 TGGAAAATCGCAACGCG
1 TGGAAAATCGCAACGCG
132974 TATCGCAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 17 0.49
21 1 0.03
22 17 0.49
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:140144 original size:21 final size:21
Alignment explanation
Indices: 140102--140162 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
140092 AGTTATCTTG
*
140102 AAAT-TTATTT-TTTATATTAA
1 AAATATTATTTATTTATA-AAA
140122 AAATATTATTTATTTATAAAA
1 AAATATTATTTATTTATAAAA
*
140143 AAATCATAATTTATTT-TAAA
1 AAAT-ATTATTTATTTATAAA
140163 TTACAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 4 0.11
21 16 0.44
22 16 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATTATTTATTTATAAAA
Found at i:140145 original size:22 final size:22
Alignment explanation
Indices: 140102--140162 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
140092 AGTTATCTTG
**
140102 AAAT-TTATTT-TTTATATTAA
1 AAATATTATTTATTTATAAAAA
140122 AAATATTATTTATTTAT-AAAA
1 AAATATTATTTATTTATAAAAA
*
140143 AAATCATAATTTATTT-TAAA
1 AAAT-ATTATTTATTTATAAA
140163 TTACAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.12
21 13 0.38
22 17 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATTATTTATTTATAAAAA
Found at i:140473 original size:19 final size:18
Alignment explanation
Indices: 140443--140487 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
140433 AAATGAAGAT
140443 TTTTAAAGTTTTTGGGTTA
1 TTTTAAA-TTTTTGGGTTA
*
140462 TTTTGAAATTTTTGTGTT-
1 TTTT-AAATTTTTGGGTTA
140480 TTTTAAAT
1 TTTTAAAT
140488 ATAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 13 0.54
20 3 0.12
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (18 bp):
TTTTAAATTTTTGGGTTA
Found at i:142665 original size:29 final size:29
Alignment explanation
Indices: 142620--142677 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
142610 GTGTTGGTCG
* *
142620 TAGGTCGCCGTGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
*
142649 TAGGTCGCCATGTCTTCCCGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
142678 AAGAGATTGT
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:0.12, C:0.38, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:142739 original size:14 final size:14
Alignment explanation
Indices: 142720--142806 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
142710 CGCTGGGCAT
142720 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
142734 CCGAGGCCATCCGAAAGAA
1 CCGAGGCCATCC----G-A
142753 TCCGAGGCCATCCGAGA
1 -CCGAGGCCATCC--GA
142770 GCATCCGAGGCCATCCGA
1 -C---CGAGGCCATCCGA
142788 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
142802 ACGAG
1 CCGAG
142807 CTATGCGAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
14 29 0.48
17 3 0.05
18 5 0.08
19 1 0.02
20 23 0.38
ACGTcount: A:0.26, C:0.37, G:0.29, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:142759 original size:20 final size:20
Alignment explanation
Indices: 142734--142787 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
142724 GGCCATCCGA
142734 CCGAGGCCATCCGAAAGAAT
1 CCGAGGCCATCCGAAAGAAT
* *
142754 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGAAT
142774 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
142788 CCGAGGCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.35, G:0.28, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGAAT
Found at i:142801 original size:10 final size:10
Alignment explanation
Indices: 142734--142787 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
142724 GGCCATCCGA
142734 CCGAGGCCAT
1 CCGAGGCCAT
* *
142744 CCGAAAG-AAT
1 CCG-AGGCCAT
142754 CCGAGGCCAT
1 CCGAGGCCAT
142764 CCGAGAG-CAT
1 CCGAG-GCCAT
142774 CCGAGGCCAT
1 CCGAGGCCAT
142784 CCGA
1 CCGA
142788 CCGAGGCCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 3 0.08
10 30 0.83
11 3 0.08
ACGTcount: A:0.28, C:0.35, G:0.28, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:142915 original size:23 final size:23
Alignment explanation
Indices: 142881--142940 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
142871 CTTGGTTGCC
142881 CTCGGATT-CCCTCGCATAGCTCG
1 CTCGG-TTGCCCTCGCATAGCTCG
142904 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGTTGCCCTCGCATAGCTCG
* * *
142927 TTCGGATGGCCTCG
1 CTCGGTTGCCCTCG
142941 GTTGGATGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (23 bp):
CTCGGTTGCCCTCGCATAGCTCG
Found at i:142957 original size:10 final size:11
Alignment explanation
Indices: 142944--142988 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
142934 GGCCTCGGTT
142944 GGATGGC-CTC
1 GGATGGCTCTC
142954 GGAT-GCTCTC
1 GGATGGCTCTC
*
142964 GGAT-GCTTTC
1 GGATGGCTCTC
142974 GGATGGC-CTC
1 GGATGGCTCTC
142984 GGATG
1 GGATG
142989 CCCAGCGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 2 0.06
10 27 0.87
11 2 0.06
ACGTcount: A:0.11, C:0.24, G:0.38, T:0.27
Consensus pattern (11 bp):
GGATGGCTCTC
Found at i:142975 original size:20 final size:20
Alignment explanation
Indices: 142952--142989 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
142942 TTGGATGGCC
142952 TCGGAT-GCTCTCGGATGCTT
1 TCGGATGGC-CTCGGATGCTT
142972 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
142990 CCAGCGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.29
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTT
Found at i:144363 original size:26 final size:26
Alignment explanation
Indices: 144332--144394 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
144322 TTTAGGGTTT
*
144332 AAATTTCATGGCCGTCATTCGATATC
1 AAATTTCATGGCAGTCATTCGATATC
**
144358 AAATTTCATGATAGTCATTCGATATC
1 AAATTTCATGGCAGTCATTCGATATC
144384 AAATTTCATGG
1 AAATTTCATGG
144395 GTCGTTTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (26 bp):
AAATTTCATGGCAGTCATTCGATATC
Found at i:167667 original size:45 final size:45
Alignment explanation
Indices: 167594--167681 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
167584 TTTCCCCTTA
* * * *
167594 ACTTATCCAGATCGACCCGCGTCGCACATATGGCTTTGGTGAGTG
1 ACTTATCCAGATCAACCCGCATCACACATATGACTTTGGTGAGTG
* *
167639 ACTTATCCAGATCAACCTGCATCACACATCTGACTTTGGTGAG
1 ACTTATCCAGATCAACCCGCATCACACATATGACTTTGGTGAG
167682 ATTTTCTACA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (45 bp):
ACTTATCCAGATCAACCCGCATCACACATATGACTTTGGTGAGTG
Found at i:167855 original size:15 final size:16
Alignment explanation
Indices: 167824--167856 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
167814 TGTATGATCT
*
167824 ATTTATAAGTTGTAAA
1 ATTTATAAGTGGTAAA
167840 ATTTATAAG-GGTAAA
1 ATTTATAAGTGGTAAA
167855 AT
1 AT
167857 GCATAAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (16 bp):
ATTTATAAGTGGTAAA
Found at i:168465 original size:2 final size:2
Alignment explanation
Indices: 168458--168484 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
168448 TTCTACCCTT
168458 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 T
168485 TAGGGATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:177784 original size:2 final size:2
Alignment explanation
Indices: 177777--177804 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
177767 TTATTCTTAA
177777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
177805 TACTTTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181680 original size:59 final size:60
Alignment explanation
Indices: 181573--181685 Score: 131
Period size: 59 Copynumber: 1.9 Consensus size: 60
181563 AATGATCATT
* * * *
181573 TTGTAATTTTTAATAGTTGGAGAAGTTAAAAAAGCAACGACTTTTAGTC-AGGGGTCAAA
1 TTGTAACTTTTAATAGTTGGAGAACTCAAAAAAGCAACGACTTATAGTCGAGGGGTCAAA
* * * *
181632 TTGTAACTTTTAATATTTGGAGGACTCAATAAAGCAA-TACGTTATAGTCGAGGG
1 TTGTAACTTTTAATAGTTGGAGAACTCAAAAAAGCAACGAC-TTATAGTCGAGGG
181686 ATCATTTGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
58 2 0.05
59 38 0.86
60 4 0.09
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (60 bp):
TTGTAACTTTTAATAGTTGGAGAACTCAAAAAAGCAACGACTTATAGTCGAGGGGTCAAA
Found at i:187289 original size:29 final size:31
Alignment explanation
Indices: 187227--187305 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 31
187217 AAATGATGTT
* * * *
187227 ATTTTAGGCATTGAACTCTAGAAATATATCA
1 ATTTTAGGCACTAAACTTTAAAAATATATCA
*
187258 ATTTT-GTCACTAAACTTTAAAAATAT-TCA
1 ATTTTAGGCACTAAACTTTAAAAATATATCA
*
187287 ATTTTAGGCATTAAACTTT
1 ATTTTAGGCACTAAACTTT
187306 TTCGACCATC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 8 0.20
30 27 0.68
31 5 0.12
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.41
Consensus pattern (31 bp):
ATTTTAGGCACTAAACTTTAAAAATATATCA
Found at i:187597 original size:493 final size:495
Alignment explanation
Indices: 186649--187640 Score: 1853
Period size: 493 Copynumber: 2.0 Consensus size: 495
186639 AATGACATAA
*
186649 TGATGTGGATGGATATCTCTGTCACTATGATGATGTGGACAAAACATCATTTTGGCGCCAGTTAT
1 TGATATGGATGGATATCTCTGTCACTATGATGATGTGGACAAAACATCATTTTGGCGCCAGTTAT
*
186714 TGATGTTTAAAATGATGTTATTTTAGGCACTGAACTCTAGAAGTATATCAATTTTGTCACTAAAC
66 TGATGTTTAAAATGATGTTATTTTAGGCACTGAACTCTAGAAATATATCAATTTTGTCACTAAAC
186779 TTAAAAAATATTCAATTTTAGGCATTAAACTTTTTCGACCAACGTTGGAAGCTAATAGTCGTCAG
131 TTAAAAAATATTCAATTTTAGGCATTAAACTTTTTCGACCAACGTTGGAAGCTAATAGTCGTCAG
186844 TCACTGATCACTTTTTGTGACAATATCAACATCAAAATGTTCATATTTCTTCTCAACGAATTAGA
196 TCACTGATCACTTTTTGTGACAATATCAACATCAAAATGTTCATATTTCTTCTCAACGAATTAGA
* *
186909 TTTTCATGAAATCCACTCAAAATTGACAAAAATCCATATTAATATTTGATGTATTAATGCTTCGA
261 TTTTCATGAAATCCACTCAAAATTGACAAAAATCCATATAAATATTTGATGTACTAATGCTTCGA
186974 TCTCCTCAAATGGTCGTCTGGTGAGGCTAGTTTTATGGTATGTTGGTCATCTTCTCAAAATAGTG
326 TCTCCTCAAATGGTCGTCTGGTGAGGCTAGTTTTATGGTATGTTGGTCATCTTCTCAAAATAGTG
*
187039 CTTCTTATCGTTCAAATTTATGAACAAATATCCAAAGTCTCAAATCTGAGAAAGCTCCAAACCCC
391 CTTCTTATCGTTCAAATTTATGAACAAACATCCAAAGTCTCAAATCTGAGAAAGCTCCAAACCCC
187104 CTAAAAATGATGGA-TTTTTTTGTTTATTCTCGTCGATTT
456 CTAAAAATGATGGACTTTTTTTGTTTATTCTCGTCGATTT
*
187143 TGATATGGATGGATATCTCTGTCACTATGATGATGTGGATAAAACATCATTTTGGCGCCAGTTAT
1 TGATATGGATGGATATCTCTGTCACTATGATGATGTGGACAAAACATCATTTTGGCGCCAGTTAT
*
187208 TGATGTTTAAAATGATGTTATTTTAGGCATTGAACTCTAGAAATATATCAATTTTGTCACTAAAC
66 TGATGTTTAAAATGATGTTATTTTAGGCACTGAACTCTAGAAATATATCAATTTTGTCACTAAAC
* *
187273 TTTAAAAATATTCAATTTTAGGCATTAAACTTTTTCGACCATCGTTGGAAGCTAATAGTCGTCAG
131 TTAAAAAATATTCAATTTTAGGCATTAAACTTTTTCGACCAACGTTGGAAGCTAATAGTCGTCAG
187338 TCACTGATCACTTTTTGTGACAATATCAACATC-AAATGTTCATATTTCTTCTCAACGAATTAGA
196 TCACTGATCACTTTTTGTGACAATATCAACATCAAAATGTTCATATTTCTTCTCAACGAATTAGA
187402 TTTTCATGAAATCCACTCAAAATTGACAAAAATCCATATAAATATTTGATGTACTAATGCTTCGA
261 TTTTCATGAAATCCACTCAAAATTGACAAAAATCCATATAAATATTTGATGTACTAATGCTTCGA
* *
187467 TCTCCTCAAATGGTCGTCTGGTGAGGCTAGTTTTGTGGTATGTTGTTCATCTTCTCAAAATAGTG
326 TCTCCTCAAATGGTCGTCTGGTGAGGCTAGTTTTATGGTATGTTGGTCATCTTCTCAAAATAGTG
*
187532 CTTCTTATCGTTCGAATTTATGAACAAACATCCAAAGTCTCAAATCTGAGAAAGCTCCAAACCCC
391 CTTCTTATCGTTCAAATTTATGAACAAACATCCAAAGTCTCAAATCTGAGAAAGCTCCAAACCCC
187597 CTAAAAATGATGGATCTTTTTTTGTTTATTCTCGTCGATTT
456 CTAAAAATGATGGA-CTTTTTTTGTTTATTCTCGTCGATTT
187638 TGA
1 TGA
187641 GTGTGTTCGT
Statistics
Matches: 484, Mismatches: 12, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
493 234 0.48
494 222 0.46
495 28 0.06
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (495 bp):
TGATATGGATGGATATCTCTGTCACTATGATGATGTGGACAAAACATCATTTTGGCGCCAGTTAT
TGATGTTTAAAATGATGTTATTTTAGGCACTGAACTCTAGAAATATATCAATTTTGTCACTAAAC
TTAAAAAATATTCAATTTTAGGCATTAAACTTTTTCGACCAACGTTGGAAGCTAATAGTCGTCAG
TCACTGATCACTTTTTGTGACAATATCAACATCAAAATGTTCATATTTCTTCTCAACGAATTAGA
TTTTCATGAAATCCACTCAAAATTGACAAAAATCCATATAAATATTTGATGTACTAATGCTTCGA
TCTCCTCAAATGGTCGTCTGGTGAGGCTAGTTTTATGGTATGTTGGTCATCTTCTCAAAATAGTG
CTTCTTATCGTTCAAATTTATGAACAAACATCCAAAGTCTCAAATCTGAGAAAGCTCCAAACCCC
CTAAAAATGATGGACTTTTTTTGTTTATTCTCGTCGATTT
Found at i:188272 original size:21 final size:20
Alignment explanation
Indices: 188186--188343 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
188176 AAATGACCAA
**
188186 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
188205 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
188225 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
188245 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
188266 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
188287 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
188307 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
188328 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
188344 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:188334 original size:20 final size:20
Alignment explanation
Indices: 188310--188519 Score: 217
Period size: 20 Copynumber: 10.5 Consensus size: 20
188300 CGATTTTCCA
* ** *
188310 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
188330 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
188350 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
188370 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
188390 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
188410 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
188430 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
188450 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
188470 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
188490 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
188510 AAATCACAAC
1 AAATCGCAAC
188520 ACTGAAATTT
Statistics
Matches: 159, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 156 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:189436 original size:12 final size:12
Alignment explanation
Indices: 189419--189443 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
189409 ATATAATCCT
189419 GAAGAAGAAAAA
1 GAAGAAGAAAAA
189431 GAAGAAGAAAAA
1 GAAGAAGAAAAA
189443 G
1 G
189444 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:191762 original size:33 final size:34
Alignment explanation
Indices: 191711--191911 Score: 195
Period size: 33 Copynumber: 5.9 Consensus size: 34
191701 CGGAAATTAC
*
191711 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
191744 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
191778 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* *
191811 AATCGCAATGCGAAATTAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
*
191844 AATCGCCATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCG-CA-ACG--ATGAAAATCGCAATGCGAAATGAA
*
191882 AATCGCAACGA-GAGAATCGCAATGCGAAAT
1 AATCGCAACGATGAAAATCGCAATGCGAAAT
191912 TATAAACGCA
Statistics
Matches: 141, Mismatches: 12, Indels: 30
0.77 0.07 0.16
Matches are distributed among these distances:
32 1 0.01
33 78 0.55
34 33 0.23
35 5 0.04
36 4 0.03
37 4 0.03
38 16 0.11
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:191816 original size:19 final size:19
Alignment explanation
Indices: 191725--191889 Score: 171
Period size: 19 Copynumber: 9.4 Consensus size: 19
191715 GCAACGAGAG
191725 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
191744 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
191758 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
191778 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
191792 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
191811 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
191830 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
191844 AATCGCCATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
191863 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
191882 AATCGCAA
1 AATCGCAA
191890 CGAGAGAATC
Statistics
Matches: 120, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
14 30 0.25
15 2 0.02
16 5 0.04
17 4 0.03
18 3 0.03
19 63 0.52
20 13 0.11
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:191927 original size:52 final size:52
Alignment explanation
Indices: 191753--191911 Score: 291
Period size: 52 Copynumber: 3.0 Consensus size: 52
191743 AAATCCCAAC
191753 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
191806 ATGAAAATCGCAATGCGAAATTAAAATCGCAACGAGAGAATCGCCATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
191858 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
191910 AT
1 AT
191912 TATAAACGCA
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 86 0.84
53 16 0.16
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:192020 original size:52 final size:52
Alignment explanation
Indices: 191918--192021 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
191908 AAATTATAAA
*
191918 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATGTCATTT
191970 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATAGTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAT-GTCATTT
192022 TTGCCTTCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 11 0.22
52 39 0.78
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (52 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATGTCATTT
Found at i:192021 original size:19 final size:18
Alignment explanation
Indices: 191936--192013 Score: 92
Period size: 19 Copynumber: 4.4 Consensus size: 18
191926 GATTCTCTCG
191936 TTGCGATTTTCATTTCCGCA
1 TTGCGA-TTTCATTT-CGCA
191956 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
191974 TTGCGA-TTC-TCTCG--
1 TTGCGATTTCATTTCGCA
191988 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
192007 TTGCGAT
1 TTGCGAT
192014 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
14 6 0.12
16 7 0.14
17 7 0.14
18 11 0.22
19 14 0.27
20 6 0.12
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:192136 original size:14 final size:13
Alignment explanation
Indices: 192108--192165 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
192098 TTATGTTCGC
*
192108 ATCAATTACACAA
1 ATCAATTATACAA
192121 ATCAACTTATACAA
1 ATCAA-TTATACAA
* *
192135 ATCATCTTTTACAA
1 ATCA-ATTATACAA
*
192149 ATCAATTAAAC-A
1 ATCAATTATACAA
192161 ATCAA
1 ATCAA
192166 AAATAAGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 6 0.16
13 9 0.24
14 22 0.59
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (13 bp):
ATCAATTATACAA
Found at i:194091 original size:19 final size:19
Alignment explanation
Indices: 194046--194159 Score: 97
Period size: 19 Copynumber: 6.6 Consensus size: 19
194036 ATAGTTACTT
* **
194046 TCGCAACACGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
194065 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
194084 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
194098 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
194117 TCGCAA--CG-AA-G--AA
1 TCGCAACGCGAAATGAAAA
194130 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
194149 TCGCAATGCGA
1 TCGCAACGCGA
194160 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
13 8 0.10
14 8 0.10
15 3 0.04
16 9 0.12
17 8 0.10
19 42 0.54
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:194135 original size:32 final size:33
Alignment explanation
Indices: 194063--194154 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
194053 ACGAAACCAA
194063 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
194096 AATCGCAATGCGAAATGAAAATCGCAACGA-AG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
194128 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
194155 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 28 0.49
33 29 0.51
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:194177 original size:19 final size:19
Alignment explanation
Indices: 194155--194283 Score: 109
Period size: 19 Copynumber: 7.3 Consensus size: 19
194145 AAAATCGCAA
194155 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
194174 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
194188 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
194207 TGCGATTCT-G-TT--C-T
1 TGCGATTTTGGTTTCGCGT
**
194221 AT-CGATTTTCATTTCGCGT
1 -TGCGATTTTGGTTTCGCGT
194240 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
194259 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
194279 TGCGA
1 TGCGA
194284 AGTAAACTAT
Statistics
Matches: 88, Mismatches: 9, Indels: 25
0.72 0.07 0.20
Matches are distributed among these distances:
14 18 0.20
15 3 0.03
16 3 0.03
17 3 0.03
18 4 0.05
19 44 0.50
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:194197 original size:33 final size:34
Alignment explanation
Indices: 194154--194246 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 34
194144 GAAAATCGCA
194154 ATGCGATTTTGGTTTCGCGTTGCGA-TCT-TGTCGT
1 ATGCGATTTTGGTTTCGCGTTGCGATTCTGT-TC-T
194188 -TGCGATTTTGGTTTCGCGTTGCGATTCTGTTCT
1 ATGCGATTTTGGTTTCGCGTTGCGATTCTGTTCT
**
194221 AT-CGATTTTCATTTCGCGTTGCGATT
1 ATGCGATTTTGGTTTCGCGTTGCGATT
194247 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
33 47 0.87
34 6 0.11
35 1 0.02
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (34 bp):
ATGCGATTTTGGTTTCGCGTTGCGATTCTGTTCT
Found at i:194474 original size:91 final size:93
Alignment explanation
Indices: 194330--194878 Score: 927
Period size: 91 Copynumber: 6.1 Consensus size: 93
194320 ATGGATTGCA
194330 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-AAGAATACAC-G-T
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
194391 TAGCAGAATTGGCAGCAA-CGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
194418 TTACTTTCAACAACAAAAGACAAAACAAAGACAAA-ACTATTTCACAGTGTTAAAGAATACACAG
1 TTACTTTCAAC--CAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
194482 TTTAGCAGAA-TGGCAGCAACCGAACAAAT
64 TTTAGCAGAATTGGCAGCAACCGAACAAAT
194511 TTACTTTCAACCAAAAGACAAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA--
1 TTACTTTCAACCAAAAGAC-AAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGT
194574 TTAGCAGAATTGGCA--AACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
194601 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAAT--ACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
194663 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
194691 TTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTTAAAGAATACACAG-
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTG-TTAAAGAATACACAGT
194754 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
194783 TTACTTTCAACC-AAA-ACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
194846 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
194874 TTACT
1 TTACT
194879 AAGCAATCTA
Statistics
Matches: 441, Mismatches: 1, Indels: 35
0.92 0.00 0.07
Matches are distributed among these distances:
86 3 0.01
88 37 0.08
89 50 0.11
90 95 0.22
91 122 0.28
92 73 0.17
93 61 0.14
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Done.