Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008381.1 Hibiscus syriacus cultivar Beakdansim tig00111141_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: 100594
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:162 original size:30 final size:28
Alignment explanation
Indices: 128--191 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 28
118 AATAAGAGTG
128 ATTTGTTTAATTGATGTGT-AAATAATTCTT
1 ATTTGTTTAATTGATGT-TAAAAT-A-TCTT
158 ATTTGTTTAATTGATGTTAAAATATCTT
1 ATTTGTTTAATTGATGTTAAAATATCTT
186 ATTTGT
1 ATTTGT
192 GCTTGTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 10 0.30
29 2 0.06
30 21 0.64
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (28 bp):
ATTTGTTTAATTGATGTTAAAATATCTT
Found at i:362 original size:20 final size:21
Alignment explanation
Indices: 332--498 Score: 132
Period size: 20 Copynumber: 8.7 Consensus size: 21
322 ACTTTACAAT
*
332 TTTCTCGTTGCGATAGTCAAA
1 TTTCGCGTTGCGATAGTCAAA
*
353 TTTC-CGTTGCGATAATCAAA
1 TTTCGCGTTGCGATAGTCAAA
*
373 -TTCACGTTGC-ATTAGTC--A
1 TTTCGCGTTGCGA-TAGTCAAA
391 TTTCGCGTTGCGAT--T---A
1 TTTCGCGTTGCGATAGTCAAA
* *
407 --TCTCGTTACGATAGTCAAA
1 TTTCGCGTTGCGATAGTCAAA
*
426 TTT-GCGTTGCGATAGTTAAA
1 TTTCGCGTTGCGATAGTCAAA
*
446 -TTCGCGTTGCGATAGTC-AT
1 TTTCGCGTTGCGATAGTCAAA
*
465 TTTCGCGTTGCGATAGTC-AT
1 TTTCGCGTTGCGATAGTCAAA
*
485 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
499 TATCCCGTTA
Statistics
Matches: 122, Mismatches: 11, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
14 10 0.08
16 2 0.02
17 1 0.01
18 1 0.01
19 18 0.15
20 85 0.70
21 5 0.04
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (21 bp):
TTTCGCGTTGCGATAGTCAAA
Found at i:419 original size:73 final size:74
Alignment explanation
Indices: 334--478 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 74
324 TTTACAATTT
*
334 TCTCGTTGCGATAGTCAAATTTCCGTTGCGATAATCAAATTCACGTTGC-ATTAGTCA-TTTCGC
1 TCTCGTTACGATAGTCAAATTTCCGTTGCGATAATCAAATTCACGTTGCGA-TAGTCATTTTCGC
397 GTTGCGATTA
65 GTTGCGATTA
* * * *
407 TCTCGTTACGATAGTCAAATTTGCGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCG
1 TCTCGTTACGATAGTCAAATTTCCGTTGCGATAATCAAATTCACGTTGCGATAGTCATTTTCGCG
472 TTGCGAT
66 TTGCGAT
479 AGTCATTTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 50 0.77
74 15 0.23
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (74 bp):
TCTCGTTACGATAGTCAAATTTCCGTTGCGATAATCAAATTCACGTTGCGATAGTCATTTTCGCG
TTGCGATTA
Found at i:490 original size:40 final size:41
Alignment explanation
Indices: 337--498 Score: 150
Period size: 40 Copynumber: 4.2 Consensus size: 41
327 ACAATTTTCT
* *
337 CGTTGCGATAGTCAAATTTC-CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTTCGCGTTGCGATAGTCAAATTCG
*
377 CGTTGC-ATTAGTC--ATTTCGCGTTGCGAT--T---A-TCT
1 CGTTGCGA-TAGTCAAATTTCGCGTTGCGATAGTCAAATTCG
* *
410 CGTTACGATAGTCAAATTT-GCGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTTCGCGTTGCGATAGTCAAATTCG
* **
450 CGTTGCGATAGTC-ATTTTCGCGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTTCGCGTTGCGATAGTCAAATTCG
*
490 CATTGCGAT
1 CGTTGCGAT
499 TATCCCGTTA
Statistics
Matches: 101, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
33 12 0.12
34 12 0.12
35 4 0.04
36 1 0.01
37 1 0.01
38 5 0.05
39 15 0.15
40 51 0.50
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCAAATTTCGCGTTGCGATAGTCAAATTCG
Found at i:530 original size:93 final size:93
Alignment explanation
Indices: 340--531 Score: 246
Period size: 93 Copynumber: 2.1 Consensus size: 93
330 ATTTTCTCGT
*
340 TGCGATAGTCAAATTTCCGTTGCGATAATCAAATTCACGTTGCATTAGTCATTTCGCGTTGCGAT
1 TGCGATAGTCAAATTTCCGTTGCGATAATCAAATTCACGTTGCATTAGTCATTTCGCATTGCGAT
* *
405 TATCTCGTTACGATAGTCAAATTTGCGT
66 TATCCCGTTACGATAGTCAAATTTGCGA
* * ** *
433 TGCGATAGTTAAA-TTCGCGTTGCGATAGTCATTTTCGCGTTGCGA-TAGTCATTTTCGCATTGC
1 TGCGATAGTCAAATTTC-CGTTGCGATAATCAAATTCACGTTGC-ATTAGTCA-TTTCGCATTGC
**
496 GATTATCCCGTTACGATAGTCATTTTTGC-A
63 GATTATCCCGTTACGATAGTCAAATTTGCGA
526 TGCGAT
1 TGCGAT
532 TATCCGTTGT
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
92 3 0.03
93 46 0.53
94 37 0.43
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (93 bp):
TGCGATAGTCAAATTTCCGTTGCGATAATCAAATTCACGTTGCATTAGTCATTTCGCATTGCGAT
TATCCCGTTACGATAGTCAAATTTGCGA
Found at i:535 original size:33 final size:34
Alignment explanation
Indices: 470--536 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
460 GTCATTTTCG
*
470 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTACGATAGTCATTTTCGCATTGCGATTATCC
*
504 CGTTACGATAGTCATTTTTGCA-TGCGATTATCC
1 CGTTACGATAGTCATTTTCGCATTGCGATTATCC
537 GTTGTGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (34 bp):
CGTTACGATAGTCATTTTCGCATTGCGATTATCC
Found at i:581 original size:19 final size:20
Alignment explanation
Indices: 536--606 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
526 TGCGATTATC
* * * *
536 CGTTGTGATATTCAAATTCA
1 CGTTGCGATAGTCATATTCG
556 CGTTGCGATAGTCATA-TCG
1 CGTTGCGATAGTCATATTCG
*
575 TGTTGCGAT--TCATATTCG
1 CGTTGCGATAGTCATATTCG
593 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
607 AATGAATGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.12
18 11 0.26
19 10 0.24
20 16 0.38
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCG
Found at i:599 original size:18 final size:18
Alignment explanation
Indices: 545--601 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
535 CCGTTGTGAT
* *
545 ATTCAAATTCACGTTGCG
1 ATTCATATTCGCGTTGCG
*
563 ATAGTCATA-TCGTGTTGCG
1 AT--TCATATTCGCGTTGCG
582 ATTCATATTCGCGTTGCG
1 ATTCATATTCGCGTTGCG
600 AT
1 AT
602 AGTCAAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 5 0.16
18 13 0.41
19 10 0.31
20 4 0.12
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (18 bp):
ATTCATATTCGCGTTGCG
Found at i:2854 original size:14 final size:14
Alignment explanation
Indices: 2835--2871 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2825 TCCCGTGGCA
2835 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
2849 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
2863 TTCTTCTTC
1 TT-TTCTTC
2872 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:9185 original size:21 final size:21
Alignment explanation
Indices: 9161--9200 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9151 TCCCCTTTGA
*
9161 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
9182 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
9201 TTGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:13558 original size:20 final size:20
Alignment explanation
Indices: 13530--13636 Score: 153
Period size: 20 Copynumber: 5.3 Consensus size: 20
13520 AATTCAGTGA
*
13530 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
13550 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
13570 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
*
13591 TGCGATAGTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGT
13611 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
13631 TGCGAT
1 TGCGAT
13637 CATGTATTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.75
21 15 0.19
22 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:13588 original size:41 final size:41
Alignment explanation
Indices: 13543--13678 Score: 143
Period size: 41 Copynumber: 3.3 Consensus size: 41
13533 GTTAGTCAGA
13543 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
* **
13584 ATCGCGTTGCGATAGTCAGAATCTCGTTGCGAT-A-GTCAGA
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGT-ATT
** * * *
13624 ATCGCGTTGCGATCATGT-ATTATTGCGTTGCGATCACATGTT
1 ATCGCGTTGCGAT-A-GTCAGAATCGCGTTGCGATCACGTATT
*
13666 ATCGCGTTACGAT
1 ATCGCGTTGCGAT
13679 TTACATATTC
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.03
40 15 0.19
41 45 0.58
42 15 0.19
43 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
Found at i:13589 original size:21 final size:20
Alignment explanation
Indices: 13543--13678 Score: 98
Period size: 20 Copynumber: 6.7 Consensus size: 20
13533 GTTAGTCAGA
**
13543 ATCGCGTTGCGAT-AGTCAGA
1 ATCGCGTTGCGATCAGT-ATT
13563 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCA-GTATT
**
13584 ATCGCGTTGCGAT-AGTCAGA
1 ATCGCGTTGCGATCAGT-ATT
* **
13604 ATCTCGTTGCGAT-AGTCAGA
1 ATCGCGTTGCGATCAGT-ATT
13624 ATCGCGTTGCGATCATGTATT
1 ATCGCGTTGCGATCA-GTATT
* * *
13645 ATTGCGTTGCGATCACATGTT
1 ATCGCGTTGCGATCA-GTATT
*
13666 ATCGCGTTACGAT
1 ATCGCGTTGCGAT
13679 TTACATATTC
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.02
20 46 0.47
21 45 0.46
22 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATCAGTATT
Found at i:13603 original size:61 final size:61
Alignment explanation
Indices: 13530--13657 Score: 220
Period size: 61 Copynumber: 2.1 Consensus size: 61
13520 AATTCAGTGA
*
13530 TGCGTTAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
* * *
13591 TGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGCGTTGCGATCATGTATTATTGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
13652 TGCGAT
1 TGCGAT
13658 CACATGTTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (61 bp):
TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
Found at i:13696 original size:82 final size:81
Alignment explanation
Indices: 13530--13717 Score: 209
Period size: 82 Copynumber: 2.3 Consensus size: 81
13520 AATTCAGTGA
* * *
13530 TGCGTTAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGTTGCG
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACATATTATCGCGTTACG
* *
13595 ATAGTCAGAATCTCGT
66 ATAGTCAGAATCGCAT
** * *
13611 TGCGATAGTCAGAATCGCGTTGCGATCATGT-ATTATTGCGTTGCGATCACATGTTATCGCGTTA
1 TGCGATAGTCAGAATCGCGTTGCGAT-A-GTCAGAATCGCGTTGCGATCACATATTATCGCGTTA
* * *
13675 CGAT-TTACATATTCGCAT
64 CGATAGT-CAGAATCGCAT
* *
13693 TGCGATGGTCAAAATCGCGTTGCGA
1 TGCGATAGTCAGAATCGCGTTGCGA
13718 ATCTGGAAAC
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
81 26 0.29
82 62 0.69
83 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (81 bp):
TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACATATTATCGCGTTACG
ATAGTCAGAATCGCAT
Found at i:13755 original size:20 final size:19
Alignment explanation
Indices: 13731--13777 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13721 TGGAAACTGA
*
13731 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
13751 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
13770 ATTGCGAT
1 ATTGCGAT
13778 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:13767 original size:19 final size:19
Alignment explanation
Indices: 13743--13779 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13733 TGCGATAATG
*
13743 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
13762 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
13780 TGTTGGTCAT
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:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:14357 original size:56 final size:56
Alignment explanation
Indices: 14295--14442 Score: 260
Period size: 56 Copynumber: 2.6 Consensus size: 56
14285 TAATCATATA
** *
14295 TCGTACATAAGCATTATAGATCTTATGTCATGTCAAGATTAAAGTCTTAAATTAAT
1 TCGTACATAAGTGTTATAGATCTTATGTCATGTCAAGATTAAAATCTTAAATTAAT
*
14351 TCGTACATAAGTGTTATAGATCTTATGTCATGTCAAGATTAAAATCTTCAATTAAT
1 TCGTACATAAGTGTTATAGATCTTATGTCATGTCAAGATTAAAATCTTAAATTAAT
14407 TCGTACATAAGTGTTATAGATCTTATGTCATGTCAA
1 TCGTACATAAGTGTTATAGATCTTATGTCATGTCAA
14443 CTGTACCCGA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 88 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.39
Consensus pattern (56 bp):
TCGTACATAAGTGTTATAGATCTTATGTCATGTCAAGATTAAAATCTTAAATTAAT
Found at i:29374 original size:43 final size:43
Alignment explanation
Indices: 29307--29617 Score: 267
Period size: 42 Copynumber: 7.2 Consensus size: 43
29297 TGAGAACCAA
* * * * * *
29307 AAACGCCGCTATAGGTCAAGATCTATGGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * *
29350 AAACGCCGCAAAATGTCGATATCTATAGCGGCGTTTTTAGAAAAAAA
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTT-G---GAAC
* * * *
29397 AAACGCCACAAAATGTCGAGATCTATAGCGGCGTTTATGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * * * *
29440 AAGCGACGCAAAAGGTTAGACAT-T-TAGCGGTGTTTTTGGAAC
1 AAACGCCGCAAAAGG-TCGATATCTATAGCGGCGTTTTTGGAAC
* *
29482 AAACACCGTAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * * *
29524 AAACACCGCAAAAGGTTAGAT-T-AATAGCGGTGTTTTT-GATAC
1 AAACGCCGCAAAAGG-TCGATATCTATAGCGGCGTTTTTGGA-AC
* *
29566 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTTGATAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-AC
29609 AAACGCCGC
1 AAACGCCGC
29618 TAATTACCAT
Statistics
Matches: 217, Mismatches: 38, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
40 4 0.02
41 6 0.03
42 100 0.46
43 61 0.28
44 8 0.04
46 1 0.00
47 37 0.17
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
Found at i:31396 original size:19 final size:19
Alignment explanation
Indices: 31372--31410 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31362 TATTGATCAT
31372 AACCAGCGCGTAGAACTAC
1 AACCAGCGCGTAGAACTAC
*
31391 AACCAGTGCGTAGAACTAC
1 AACCAGCGCGTAGAACTAC
31410 A
1 A
31411 GCCAAATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.13
Consensus pattern (19 bp):
AACCAGCGCGTAGAACTAC
Found at i:32936 original size:24 final size:24
Alignment explanation
Indices: 32904--32959 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
32894 TACATTCTTC
32904 TTTTCTCTCTAGTTTTTATAAAAG
1 TTTTCTCTCTAGTTTTTATAAAAG
32928 TTTTCTCTCTAGTTTTTATAAAAG
1 TTTTCTCTCTAGTTTTTATAAAAG
32952 TTTTCTCT
1 TTTTCTCT
32960 TTTCCTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (24 bp):
TTTTCTCTCTAGTTTTTATAAAAG
Found at i:32968 original size:24 final size:24
Alignment explanation
Indices: 32904--32968 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
32894 TACATTCTTC
**
32904 TTTTCTCTCTAGTTTTTATAAAAG
1 TTTTCTCTCTACCTTTTATAAAAG
**
32928 TTTTCTCTCTAGTTTTTATAAAAG
1 TTTTCTCTCTACCTTTTATAAAAG
* *
32952 TTTTCTCTTTTCCTTTT
1 TTTTCTCTCTACCTTTT
32969 CAAGTTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTCTCTCTACCTTTTATAAAAG
Found at i:42133 original size:22 final size:22
Alignment explanation
Indices: 42104--42148 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42094 AAAAAATGTT
*
42104 GAAAAAAATAGCAGTTCGAAAAA
1 GAAAAAAA-AACAGTTCGAAAAA
*
42127 GAAAAAAAAACTGTTCGAAAAA
1 GAAAAAAAAACAGTTCGAAAAA
42149 AAAGACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (22 bp):
GAAAAAAAAACAGTTCGAAAAA
Found at i:45298 original size:80 final size:82
Alignment explanation
Indices: 45153--45327 Score: 237
Period size: 80 Copynumber: 2.2 Consensus size: 82
45143 TTAGCGGCAG
* * * * * * * *
45153 AAACGCCATTAAAGTATGAGCATTTAGCGGCGTTTGTGCTTATAACGCCACTAAAGTACATTATT
1 AAACACCACTAAAGTATGAGCATTTAGCGGCGTTTATGATAAAAACGCCACTAAAGCACAGTATT
*
45218 TAGCGGCTTTTATATAA
66 TAGCGGCGTTTATATAA
*
45235 AAACACCACTAAAGTAT-AGTATTTAGCGGCGTTTAT-ATAAAAACGCCACTAAAGCACAGTATT
1 AAACACCACTAAAGTATGAGCATTTAGCGGCGTTTATGATAAAAACGCCACTAAAGCACAGTATT
*
45298 TAGTGGCGTTTATATAA
66 TAGCGGCGTTTATATAA
45315 AAACACCACTAAA
1 AAACACCACTAAA
45328 ACACAAGTAT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 50 0.61
81 17 0.21
82 15 0.18
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (82 bp):
AAACACCACTAAAGTATGAGCATTTAGCGGCGTTTATGATAAAAACGCCACTAAAGCACAGTATT
TAGCGGCGTTTATATAA
Found at i:45358 original size:42 final size:40
Alignment explanation
Indices: 45200--45359 Score: 203
Period size: 40 Copynumber: 4.0 Consensus size: 40
45190 GCTTATAACG
* * *
45200 CCACTAAAGTACATTATTTAGCGGCTTTTATATAAAAACA
1 CCACTAAAGCACAGTATTTAGCGGCGTTTATATAAAAACA
* * *
45240 CCACTAAAGTATAGTATTTAGCGGCGTTTATATAAAAACG
1 CCACTAAAGCACAGTATTTAGCGGCGTTTATATAAAAACA
*
45280 CCACTAAAGCACAGTATTTAGTGGCGTTTATATAAAAACA
1 CCACTAAAGCACAGTATTTAGCGGCGTTTATATAAAAACA
* * * *
45320 CCACTAAAACACAAGTATTTTACCGGCGTTTGTTTAAAAA
1 CCACTAAAGCAC-AGTA-TTTAGCGGCGTTTATATAAAAA
45360 ACGCCGCTAA
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
40 83 0.79
41 4 0.04
42 18 0.17
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (40 bp):
CCACTAAAGCACAGTATTTAGCGGCGTTTATATAAAAACA
Found at i:56653 original size:17 final size:18
Alignment explanation
Indices: 56625--56658 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
56615 CCCTACTATT
56625 ATTATATATTATATTTTC
1 ATTATATATTATATTTTC
56643 ATTAT-TATTATATTTT
1 ATTATATATTATATTTT
56659 ACTCCCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATATATTATATTTTC
Found at i:56723 original size:2 final size:2
Alignment explanation
Indices: 56710--56743 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
56700 TTTATTTTAT
* *
56710 TA TA TT TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56744 CATAACCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67458 original size:1 final size:1
Alignment explanation
Indices: 67452--67486 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
67442 TCCTAAGTTG
* *
67452 AAAAAAAAAACAAAAAAACAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
67487 CGTTTAGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:67476 original size:17 final size:17
Alignment explanation
Indices: 67453--67487 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
67443 CCTAAGTTGA
67453 AAAAAAAAACAAAAAAAC
1 AAAAAAAAA-AAAAAAAC
67471 AAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAC
67488 GTTTAGGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAC
Found at i:68493 original size:105 final size:105
Alignment explanation
Indices: 68308--69139 Score: 1366
Period size: 105 Copynumber: 7.9 Consensus size: 105
68298 AGGTTTTACC
*
68308 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
68373 ACGAAGGGACCGCTGGCTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGCTGTCAATAAACATTTCTCAATTT
* * *
68413 CAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACATCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
68478 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGCTGTCAATAAACATTTCTCAATTT
* *
68518 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
68583 ACGAAGGGACCGCTGGCTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGCTGTCAATAAACATTTCTCAATTT
* *
68623 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
68688 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGCTGTCAATAAACATTTCTCAATTT
* *
68728 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
68793 ATGAAGGGACCGCT-GCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGC-TGTCAATAAACATTTCTCAATTT
*
68833 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
68898 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGCTGTCAATAAACATTTCTCAATTT
*
68938 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
69003 ACGGAGGGACCGCT-GCTTGTCAAT-AACAACTTCCCAATCT
66 ACGAAGGGACCGCTGGC-TGTCAATAAAC-ATTTCTCAATTT
69043 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
69108 ACGAAGGGACCGCTGGTTGTCAACAAA-ATTTC
66 ACGAAGGGACCGCTGGCTGTCAATAAACATTTC
69140 AGTCAGATTC
Statistics
Matches: 676, Mismatches: 45, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
104 9 0.01
105 663 0.98
106 4 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGCTGTCAATAAACATTTCTCAATTT
Found at i:70400 original size:17 final size:18
Alignment explanation
Indices: 70372--70405 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
70362 CCCTACTACT
70372 ATTATATATTATATTTTC
1 ATTATATATTATATTTTC
70390 ATTAT-TATTATATTTT
1 ATTATATATTATATTTT
70406 ACTCCCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATATATTATATTTTC
Found at i:70470 original size:2 final size:2
Alignment explanation
Indices: 70457--70498 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
70447 TTTATTTTAT
* *
70457 TA TA TT TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70499 CATAACCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72536 original size:13 final size:13
Alignment explanation
Indices: 72536--72610 Score: 78
Period size: 13 Copynumber: 5.3 Consensus size: 13
72526 CCGTTGACCC
72536 GACCCGACCCGTT
1 GACCCGACCCGTT
*
72549 TACCCGACCCGTT
1 GACCCGACCCGTT
72562 GACCCGACCGACCCGTT
1 GA--C--CCGACCCGTT
72579 GACCCGACCCGTT
1 GACCCGACCCGTT
*
72592 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
72607 GACC
1 GACC
72611 GTTGACCGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
13 27 0.51
15 14 0.26
17 12 0.23
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:72537 original size:18 final size:18
Alignment explanation
Indices: 72514--72589 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
72504 ACCGGTCACA
72514 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
72532 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
72549 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
72563 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
72580 ACCCGACCCG
1 ACCCGACCCG
72590 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
13 12 0.24
17 17 0.34
18 21 0.42
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:72565 original size:8 final size:8
Alignment explanation
Indices: 72554--72617 Score: 66
Period size: 8 Copynumber: 8.5 Consensus size: 8
72544 CCGTTTACCC
72554 GACCCGTT
1 GACCCGTT
**
72562 GACCCGACC
1 GACCCG-TT
72571 GACCCGTT
1 GACCCGTT
72579 GACCC---
1 GACCCGTT
72584 GACCCGTT
1 GACCCGTT
72592 GA-CCGTT
1 GACCCGTT
72599 GACCCGTT
1 GACCCGTT
72607 GA-CCGTT
1 GACCCGTT
72614 GACC
1 GACC
72618 GGAGTTGACC
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
5 5 0.11
7 14 0.30
8 21 0.46
9 6 0.13
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.19
Consensus pattern (8 bp):
GACCCGTT
Found at i:72575 original size:30 final size:31
Alignment explanation
Indices: 72518--72595 Score: 140
Period size: 30 Copynumber: 2.5 Consensus size: 31
72508 GTCACAACCC
72518 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
72549 TACCCGACCCGTTGACCCGA-CCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
72579 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
72596 GTTGACCCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 26 0.58
31 19 0.42
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:72599 original size:7 final size:7
Alignment explanation
Indices: 72587--72618 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
72577 TTGACCCGAC
72587 CCGTTGA
1 CCGTTGA
72594 CCGTTGA
1 CCGTTGA
72601 CCCGTTGA
1 -CCGTTGA
72609 CCGTTGA
1 CCGTTGA
72616 CCG
1 CCG
72619 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:72604 original size:15 final size:15
Alignment explanation
Indices: 72571--72617 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
72561 TGACCCGACC
*
72571 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
72584 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
72599 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
72614 GACC
1 GACC
72618 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:73956 original size:18 final size:18
Alignment explanation
Indices: 73930--73965 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
73920 TCGAAAGGAC
*
73930 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
73948 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
73966 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:75196 original size:24 final size:24
Alignment explanation
Indices: 75092--75198 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
75082 ATATTTTATC
*
75092 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
75116 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
75140 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
* *
75164 TGATATCTGATCTGAATTATATTT
1 TGATTTCTGATCTGAATTATGTTT
75188 TGATTTCTGAT
1 TGATTTCTGAT
75199 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:76288 original size:29 final size:28
Alignment explanation
Indices: 76233--76288 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
76223 CACCATAAGC
* * *
76233 TTCAGCTTCATGCTGCTCATGTGTTCAG
1 TTCAGCTCCATGCTGCTCATATATTCAG
*
76261 TTCATGCTCCATGCTGCTCGTATATTCA
1 TTCA-GCTCCATGCTGCTCATATATTCA
76289 TTTTTAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (28 bp):
TTCAGCTCCATGCTGCTCATATATTCAG
Found at i:85059 original size:26 final size:26
Alignment explanation
Indices: 85030--85102 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
85020 AATTTAAAAT
85030 ATCAAACCATAATCCTCAAATCATAA
1 ATCAAACCATAATCCTCAAATCATAA
* *
85056 ATCAAACTATAGTCCTCAAATCATAA
1 ATCAAACCATAATCCTCAAATCATAA
*
85082 ACCAAACCATAAATCCT-AAAT
1 ATCAAACCAT-AATCCTCAAAT
85103 TACAACCCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 36 0.88
27 5 0.12
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.23
Consensus pattern (26 bp):
ATCAAACCATAATCCTCAAATCATAA
Found at i:85835 original size:23 final size:23
Alignment explanation
Indices: 85805--85856 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
85795 TATCTAAAGC
85805 GATGATGTGATTATTAAATAAGT
1 GATGATGTGATTATTAAATAAGT
*
85828 GATGATGTGATTATTAGATAAGT
1 GATGATGTGATTATTAAATAAGT
85851 GATGAT
1 GATGAT
85857 ATGACATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.25, T:0.38
Consensus pattern (23 bp):
GATGATGTGATTATTAAATAAGT
Found at i:85881 original size:32 final size:32
Alignment explanation
Indices: 85845--85978 Score: 128
Period size: 32 Copynumber: 4.2 Consensus size: 32
85835 TGATTATTAG
*
85845 ATAAGTGATGATATGACATATGTAATATGTAC
1 ATAAGTGATGATATGACATATGTAATATGTAT
* * **
85877 ATAAGTGATGATAT-ATCACATACTACGA-GTAT
1 ATAAGTGATGATATGA-CATAT-GTAATATGTAT
* * * *
85909 ATTAGTGATGATATGACATGTGTTACATGTAT
1 ATAAGTGATGATATGACATATGTAATATGTAT
* * *
85941 ATAAGTGATGACATGACATATATTATATGTAT
1 ATAAGTGATGATATGACATATGTAATATGTAT
85973 ATAAGT
1 ATAAGT
85979 AATAACGTAA
Statistics
Matches: 81, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
31 3 0.04
32 74 0.91
33 4 0.05
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (32 bp):
ATAAGTGATGATATGACATATGTAATATGTAT
Found at i:86414 original size:37 final size:37
Alignment explanation
Indices: 86373--86483 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
86363 AACATAGCGT
*
86373 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
86410 TAGAGTTTTACTAGGATTCAAACTCCTACAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
86447 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
86484 CCCAGAAGCA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:86943 original size:3 final size:3
Alignment explanation
Indices: 86935--86994 Score: 61
Period size: 3 Copynumber: 19.7 Consensus size: 3
86925 AATAGTATAT
*
86935 TTA TTA TTA TATA TTT TTA TTA TCTA TTA TTA TTA TTA TT- TTA CTT-
1 TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA -TTA
*
86981 TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TT
86995 TATTCTTTCG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
2 4 0.08
3 37 0.76
4 8 0.16
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:86956 original size:13 final size:13
Alignment explanation
Indices: 86930--86976 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
86920 ATTCCAATAG
86930 TATATTTATTATTA
1 TATATTT-TTATTA
86944 TATATTTTTATTA
1 TATATTTTTATTA
* *
86957 TCTATTATTATTA
1 TATATTTTTATTA
86970 T-TATTTT
1 TATATTTT
86977 ACTTTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 5 0.17
13 18 0.60
14 7 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATTTTTATTA
Found at i:86987 original size:23 final size:25
Alignment explanation
Indices: 86934--86994 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
86924 CAATAGTATA
86934 TTTATTATTATATATTTTTATTATCT
1 TTTATTATTAT-TATTTTTATTATCT
*
86960 ATTATTATTATTA-TTTTACTT-T-T
1 TTTATTATTATTATTTTTA-TTATCT
86983 TTTATTATTATT
1 TTTATTATTATT
86995 TATTCTTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 12 0.38
24 6 0.19
25 4 0.12
26 10 0.31
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTATTATTATTATTTTTATTATCT
Found at i:87048 original size:26 final size:28
Alignment explanation
Indices: 87016--87076 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 28
87006 CATTTTAATC
87016 TATATATATA-TATATATTATCACTAT-
1 TATATATATACTATATATTATCACTATG
*
87042 TATATAT-TACTATATTTTATCACTATG
1 TATATATATACTATATATTATCACTATG
87069 TATATATA
1 TATATATA
87077 CTTTTGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 2 0.06
26 22 0.71
27 7 0.23
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (28 bp):
TATATATATACTATATATTATCACTATG
Found at i:87380 original size:30 final size:30
Alignment explanation
Indices: 87323--87380 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
87313 TGAATCCCTA
* **
87323 TTTCTTTTTTTCTCTCTCAATTGTATTTGT
1 TTTCATTTTTTCTCTCTCAATCATATTTGT
87353 TTTCATTTTTTCTCTCTCTAA-CATATTT
1 TTTCATTTTTTCTCTCTC-AATCATATTT
87381 CTTGACTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.14, C:0.19, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTCATTTTTTCTCTCTCAATCATATTTGT
Found at i:90448 original size:14 final size:14
Alignment explanation
Indices: 90422--90472 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
90412 AATCAGAAAA
90422 AAAGAGAAAAAAAGC
1 AAAGAG-AAAAAAGC
90437 AAAGAGAAAAAAGC
1 AAAGAGAAAAAAGC
90451 AAAGAGAAAAAA-C
1 AAAGAGAAAAAAGC
90464 AAAG-GAAAA
1 AAAGAGAAAA
90473 TTGAAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 20 0.56
15 6 0.17
ACGTcount: A:0.75, C:0.06, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAGAGAAAAAAGC
Found at i:90669 original size:21 final size:21
Alignment explanation
Indices: 90643--90684 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
90633 CTGATTTGTC
90643 TCAAACACAAAGCTCATGCTT
1 TCAAACACAAAGCTCATGCTT
90664 TCAAACACAAAGCTCATGCTT
1 TCAAACACAAAGCTCATGCTT
90685 AGAATAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.24
Consensus pattern (21 bp):
TCAAACACAAAGCTCATGCTT
Found at i:92125 original size:37 final size:36
Alignment explanation
Indices: 92055--92171 Score: 139
Period size: 36 Copynumber: 3.2 Consensus size: 36
92045 TATTTTTTCC
* *
92055 TTGAAACAAATTTCT-TCTCCCTTGAGATAGTTTCTT
1 TTGAAACAAATTT-TGTCTCTCTTGAGACAGTTTCTT
*
92091 TT-AGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* * *
92128 TTGAAACAAATTTTGTCCCTATTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
92164 TTGAAACA
1 TTGAAACA
92172 CAAGAAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
35 1 0.01
36 39 0.56
37 29 0.41
38 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:92390 original size:83 final size:83
Alignment explanation
Indices: 92234--92492 Score: 288
Period size: 83 Copynumber: 3.1 Consensus size: 83
92224 TTTCTCTTGA
* * *
92234 AACACAAGGCCTTCGAGTTCGATTACACTCAACTTC-GAGGGCACATCATTTGCAGCATAACTCA
1 AACA-AAGACCTTCGAGTTTGACTACACTCAAC-TCAGA-GGCACATCATTTGCAGCATAACTCA
* *
92298 AGCCTAGAAGGGTTATCTGTC
63 AGGCAAGAAGGGTTATCTGTC
* **
92319 AACAAAGACCTTCGAGTTTGACTACGCTCAGTTCCA-AGGCACATCATTTGCAGCATAACTCAAG
1 AACAAAGACCTTCGAGTTTGACTACACTCAACT-CAGAGGCACATCATTTGCAGCATAACTCAAG
*
92383 GCAAGAAGGGTTATCAGTC
65 GCAAGAAGGGTTATCTGTC
* * * * * *
92402 ATCAAAGACCTTCGAGTTTGATTACATTCAACTCAGAGGCAAATCAAATTTACAGCATAGCTCAA
1 AACAAAGACCTTCGAGTTTGACTACACTCAACTCAGAGGCACATC--ATTTGCAGCATAACTCAA
* * *
92467 GGCAAGAAGAGCTATCTGCC
64 GGCAAGAAGGGTTATCTGTC
92487 AACAAA
1 AACAAA
92493 ATTGTCGAGT
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
82 2 0.01
83 79 0.54
84 24 0.16
85 41 0.28
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (83 bp):
AACAAAGACCTTCGAGTTTGACTACACTCAACTCAGAGGCACATCATTTGCAGCATAACTCAAGG
CAAGAAGGGTTATCTGTC
Found at i:92532 original size:84 final size:85
Alignment explanation
Indices: 92234--92532 Score: 202
Period size: 83 Copynumber: 3.6 Consensus size: 85
92224 TTTCTCTTGA
* * * * *
92234 AACACAAGGCCTTCGAGTTCGATTACACTCAACTTC-GAGGGCACATC--ATTTGCAGCATAACT
1 AACA-AAGACCTTCGAGTTCGATTACATTCAAC-TCAGA-GACAAATCAAATTTACAGCATAACT
* * * * * *
92296 CAAGCCTAGAAGGGTTATCTGTC
63 CAAGGCAAGAAGAGCTATCAGCC
* * ** ** * * *
92319 AACAAAGACCTTCGAGTTTGACTACGCTCAGTTCCA-AGGCACATC--ATTTGCAGCATAACTCA
1 AACAAAGACCTTCGAGTTCGATTACATTCAACT-CAGAGACAAATCAAATTTACAGCATAACTCA
* * *
92381 AGGCAAGAAGGGTTATCAGTC
65 AGGCAAGAAGAGCTATCAGCC
* * * *
92402 ATCAAAGACCTTCGAGTTTGATTACATTCAACTCAGAGGCAAATCAAATTTACAGCATAGCTCAA
1 AACAAAGACCTTCGAGTTCGATTACATTCAACTCAGAGACAAATCAAATTTACAGCATAACTCAA
*
92467 GGCAAGAAGAGCTATCTGCC
66 GGCAAGAAGAGCTATCAGCC
* * *
92487 AACAAA-A-TTGTCGAGTTCGATTCCATTCAGCTC-GATGACAAATCAA
1 AACAAAGACCT-TCGAGTTCGATTACATTCAACTCAGA-GACAAATCAA
92533 TCACACTACT
Statistics
Matches: 179, Mismatches: 28, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
82 2 0.01
83 82 0.46
84 54 0.30
85 41 0.23
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (85 bp):
AACAAAGACCTTCGAGTTCGATTACATTCAACTCAGAGACAAATCAAATTTACAGCATAACTCAA
GGCAAGAAGAGCTATCAGCC
Found at i:93099 original size:37 final size:37
Alignment explanation
Indices: 92993--93100 Score: 189
Period size: 37 Copynumber: 2.9 Consensus size: 37
92983 AACATAGCGT
*
92993 TAGAGTTTTACTAGGATTCAAACTCCTAAAAACAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
93030 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
93067 TAGAGTTCTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATA
93101 AGATCCGGAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:93563 original size:3 final size:3
Alignment explanation
Indices: 93555--93616 Score: 63
Period size: 3 Copynumber: 19.7 Consensus size: 3
93545 AATAGTATAT
* *
93555 TTA TTA TTA TATA TTT TTA TTA TCTA TTA TCTA TTA TTA TT- TTA CTTT
1 TTA TTA TTA T-TA TTA TTA TTA T-TA TTA T-TA TTA TTA TTA TTA -TTA
93603 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
93617 TATTCTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 2 0.04
3 37 0.74
4 11 0.22
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:93692 original size:26 final size:25
Alignment explanation
Indices: 93635--93692 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
93625 TTTCATTTTA
93635 ATATA-TATATATTATCACTATTAT
1 ATATACTATATATTATCACTATTAT
*
93659 ATATTACTATATTTTATCACTATGTAT
1 ATA-TACTATATATTATCACTAT-TAT
93686 ATATACT
1 ATATACT
93693 TTTGATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 3 0.10
25 2 0.07
26 19 0.63
27 6 0.20
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (25 bp):
ATATACTATATATTATCACTATTAT
Found at i:93801 original size:16 final size:18
Alignment explanation
Indices: 93770--93802 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
93760 CTTTTTTTTT
93770 CATTTTCTACTTTATTTC
1 CATTTTCTACTTTATTTC
93788 CATTTT-TA-TTTATTT
1 CATTTTCTACTTTATTT
93803 TATATTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (18 bp):
CATTTTCTACTTTATTTC
Found at i:94756 original size:4 final size:4
Alignment explanation
Indices: 94747--94782 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
94737 AACTAATGAA
94747 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
94783 TTTAATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:95688 original size:17 final size:18
Alignment explanation
Indices: 95663--95716 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
95653 TTATGTTTTA
95663 TATATTTTTTAAAAAAA-
1 TATATTTTTTAAAAAAAT
95680 TATTATTTTTTAAAAAAAT
1 TA-TATTTTTTAAAAAAAT
95699 TATA-TTTTTAAAAAAAT
1 TATATTTTTTAAAAAAAT
95716 T
1 T
95717 GAAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.46
18 17 0.49
19 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATTTTTTAAAAAAAT
Found at i:99456 original size:16 final size:16
Alignment explanation
Indices: 99427--99483 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
99417 CGTTCATTTA
99427 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
99441 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
99457 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
99473 ATAAATGAACA
1 ATAAATGAACA
99484 TAAACGTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 32 0.82
ACGTcount: A:0.60, C:0.18, G:0.11, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Done.