Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005945.1 Hibiscus syriacus cultivar Beakdansim tig00013959_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: 82036
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:24201 original size:21 final size:21
Alignment explanation
Indices: 24175--24272 Score: 78
Period size: 21 Copynumber: 4.7 Consensus size: 21
24165 ATAAGTTCCC
24175 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
24196 AGAATCGCAATGCGATTGTAT-A
1 AGAATCGCAACGCGA-T-TATGA
* ** *
24218 A-ATTCGCATTGCGATT-TTA
1 AGAATCGCAACGCGATTATGA
*
24237 CAGAATCGCAACGCGAATATGA
1 -AGAATCGCAACGCGATTATGA
*
24259 A-AATCGAAACGCGA
1 AGAATCGCAACGCGA
24273 ACATATAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
18 1 0.02
19 2 0.03
20 14 0.23
21 37 0.60
22 5 0.08
23 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:24289 original size:20 final size:20
Alignment explanation
Indices: 24240--24292 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
24230 GATTTTACAG
* *
24240 AATCGCAACGCGAATATGAA
1 AATCACAACGCGAACATGAA
24260 AATCGA-AACGCGAACAT-ATA
1 AATC-ACAACGCGAACATGA-A
24280 AATCACAACGCGA
1 AATCACAACGCGA
24293 TTCTGACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCACAACGCGAACATGAA
Found at i:24345 original size:20 final size:20
Alignment explanation
Indices: 24301--24512 Score: 181
Period size: 20 Copynumber: 10.4 Consensus size: 20
24291 GATTCTGACT
*
24301 ATCGCAACGAGTATCTGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
24322 ATCGCAACGTGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
24342 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
24363 ATCGCAACGCGTATCCATAA
1 ATCGCAACGAGTATCCGTAA
* * *
24383 ATCGCAACGAGAATACATAA
1 ATCGCAACGAGTATCCGTAA
* **
24403 ATCGCAACGCGTATCTATAA
1 ATCGCAACGAGTATCCGTAA
* **
24423 ATCGCAACGCGTATCTATAA
1 ATCGCAACGAGTATCCGTAA
* **
24443 ATCGCAACGAGAATATGTAA
1 ATCGCAACGAGTATCCGTAA
* *
24463 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
24483 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
24504 ATCGCAACG
1 ATCGCAACG
24513 CGATCGATAA
Statistics
Matches: 157, Mismatches: 32, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
20 115 0.73
21 42 0.27
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:24444 original size:60 final size:60
Alignment explanation
Indices: 24301--24491 Score: 224
Period size: 60 Copynumber: 3.1 Consensus size: 60
24291 GATTCTGACT
* * * * * *
24301 ATCGCAACGAGTATCTGTAAAATCGCAACGTGTATCCGTAAATCGCAACGAC-AATACGTA-AA
1 ATCGCAACGCGTATCTAT-AAATCGCAACGAGAATACGTAAATCGCAACG-CGTAT-C-TATAA
* *
24363 ATCGCAACGCGTATCCATAAATCGCAACGAGAATACATAAATCGCAACGCGTATCTATAA
1 ATCGCAACGCGTATCTATAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTATAA
* * **
24423 ATCGCAACGCGTATCTATAAATCGCAACGAGAATATGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCTATAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTATAA
24483 ATCGCAACG
1 ATCGCAACG
24492 ACAATACGTA
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
59 2 0.02
60 67 0.59
61 29 0.26
62 15 0.13
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (60 bp):
ATCGCAACGCGTATCTATAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTATAA
Found at i:24464 original size:40 final size:40
Alignment explanation
Indices: 24240--24534 Score: 201
Period size: 40 Copynumber: 7.3 Consensus size: 40
24230 GATTTTACAG
* * * *
24240 AATCGCAACGCGAATATGAAAATCGAAACGCG-AACATATA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGTATC-TATA
* * * * *
24280 AATCACAACGCGATTCTG-ACTATCGCAACGAGTATCTGTAA
1 AATCGCAACGCGAATCTGTA-AATCGCAACGCGTATCTAT-A
* * * *
24321 AATCGCAACGTGTATCCGTAAATCGCAACGAC-AATACGTA-A
1 AATCGCAACGCGAATCTGTAAATCGCAACG-CGTAT-C-TATA
* ** * *
24362 AATCGCAACGCGTATCCATAAATCGCAACGAGAATAC-ATA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGTAT-CTATA
* *
24402 AATCGCAACGCGTATCTATAAATCGCAACGCGTATCTATA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGTATCTATA
* * * **
24442 AATCGCAACGAGAATATGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGTATCTATA
*
24482 AATCGCAACGAC-AATAC-GTAAAATCGCAACGCG-ATCGATA
1 AATCGCAACG-CGAAT-CTGT-AAATCGCAACGCGTATCTATA
*
24522 ATTCGCAACGCGA
1 AATCGCAACGCGA
24535 TCTCCGGTAT
Statistics
Matches: 205, Mismatches: 36, Indels: 28
0.76 0.13 0.10
Matches are distributed among these distances:
39 4 0.02
40 125 0.61
41 73 0.36
42 2 0.01
43 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGAATCTGTAAATCGCAACGCGTATCTATA
Found at i:24618 original size:21 final size:21
Alignment explanation
Indices: 24589--24629 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24579 GACTATCGTA
*
24589 TTGCGATTTCCCAAATTCGCG
1 TTGCAATTTCCCAAATTCGCG
* *
24610 TTGCAATTTTCCTAATTCGC
1 TTGCAATTTCCCAAATTCGC
24630 AACGCGAATA
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:0.20, C:0.27, G:0.15, T:0.39
Consensus pattern (21 bp):
TTGCAATTTCCCAAATTCGCG
Found at i:24651 original size:20 final size:20
Alignment explanation
Indices: 24626--24672 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
24616 TTTTCCTAAT
24626 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
24646 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
24666 TCGCAAC
1 TCGCAAC
24673 AAGATTCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:24681 original size:20 final size:20
Alignment explanation
Indices: 24635--24681 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
24625 TTCGCAACGC
* **
24635 GAATATGTAAATCGCAACGC
1 GAATCTGTAAATCGCAACAA
24655 GAATCTGTAAATCGCAACAA
1 GAATCTGTAAATCGCAACAA
*
24675 GATTCTG
1 GAATCTG
24682 ACTATCGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
GAATCTGTAAATCGCAACAA
Found at i:25559 original size:24 final size:24
Alignment explanation
Indices: 25532--25585 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
25522 GTATTCGAAA
25532 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
25556 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
25580 TTTGAT
1 TTTGAT
25586 GCTTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:28024 original size:20 final size:20
Alignment explanation
Indices: 27999--28086 Score: 124
Period size: 20 Copynumber: 4.4 Consensus size: 20
27989 GACATTCATT
*
27999 TGACTATCGCAACGC-TAATA
1 TGACTATCGCAACGCGGAA-A
*
28019 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
28039 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
28059 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
28079 TGACTATC
1 TGACTATC
28087 ACAATGAGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:28125 original size:19 final size:19
Alignment explanation
Indices: 28097--28142 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
28087 ACAATGAGAG
*
28097 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATAAA
*
28116 AATCGTAATGCGAAATAAA
1 AATCGCAATGCGAAATAAA
28135 AATCGCAA
1 AATCGCAA
28143 CGAGTGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATAAA
Found at i:28213 original size:20 final size:19
Alignment explanation
Indices: 28188--28274 Score: 67
Period size: 20 Copynumber: 4.7 Consensus size: 19
28178 TCGAAATTAG
28188 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
28207 TTTTCGCATTGCGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
* *
28225 ---CTCGTTGAGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* **
28241 TTTCGCATTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
28260 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
28275 AGTCTGTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 7 0.14
16 4 0.08
18 4 0.08
19 14 0.27
20 22 0.43
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:28395 original size:14 final size:14
Alignment explanation
Indices: 28376--28412 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28366 CAGCAATTAA
28376 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
28390 ACAAATCATCTTTT
1 ACAAATCAACATTT
28404 ACAAATCAA
1 ACAAATCAA
28413 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:29864 original size:42 final size:42
Alignment explanation
Indices: 29785--29877 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
29775 CCTCTTCAAC
* * *
29785 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
29827 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
29869 GATGACAGG
1 GATGACAGG
29878 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:30382 original size:20 final size:20
Alignment explanation
Indices: 30359--30444 Score: 127
Period size: 20 Copynumber: 4.3 Consensus size: 20
30349 ACTTAAAATT
* *
30359 GCAACGCGAAAATTACTATC
1 GCAATGCGAAAATGACTATC
30379 GCAATGCGAAAATGACTATC
1 GCAATGCGAAAATGACTATC
30399 GCAATGCGAAAATGACTATC
1 GCAATGCGAAAATGACTATC
* **
30419 GCAATACGAATTTGACTATC
1 GCAATGCGAAAATGACTATC
30439 GCAATG
1 GCAATG
30445 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
GCAATGCGAAAATGACTATC
Found at i:30506 original size:19 final size:19
Alignment explanation
Indices: 30479--30553 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
30469 ATCGCAACGT
* *
30479 GATTATAGTTTCACGTTGC
1 GATTTTAGTTTCGCGTTGC
30498 GATTTTAGTTTCGCGTTGC
1 GATTTTAGTTTCGCGTTGC
*
30517 GA-TTT-G-GT--CGTTGC
1 GATTTTAGTTTCGCGTTGC
*
30531 GATTTTGGTTTCGCGTTGC
1 GATTTTAGTTTCGCGTTGC
30550 GATT
1 GATT
30554 CTCTCATTGC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.17
15 3 0.06
16 2 0.04
17 2 0.04
18 3 0.06
19 29 0.62
ACGTcount: A:0.12, C:0.15, G:0.28, T:0.45
Consensus pattern (19 bp):
GATTTTAGTTTCGCGTTGC
Found at i:30534 original size:33 final size:32
Alignment explanation
Indices: 30492--30616 Score: 155
Period size: 33 Copynumber: 3.8 Consensus size: 32
30482 TATAGTTTCA
*
30492 CGTTGCGATTTTAGTTTCGCGTTGCGATT-TGGT
1 CGTTGCGATTTTA-TTTCGCGTTGCGATTCT-CT
*
30525 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTT-ATTTCGCGTTGCGATTCTCT
* *
30558 CATTGCGATTTTCATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTT-ATTTCGCGTTGCGATTCTCT
*
30591 CGTTGCGA-TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTATTTCGCGTTGCGAT
30617 AGTCATTTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
31 14 0.17
32 2 0.02
33 64 0.79
34 1 0.01
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.45
Consensus pattern (32 bp):
CGTTGCGATTTTATTTCGCGTTGCGATTCTCT
Found at i:30582 original size:19 final size:17
Alignment explanation
Indices: 30539--30616 Score: 69
Period size: 14 Copynumber: 4.8 Consensus size: 17
30529 GCGATTTTGG
*
30539 TTTCGCGTTGCGATTC-
1 TTTCTCGTTGCGATTCA
*
30555 --TCTCATTGCGATTTTCA
1 TTTCTCGTTGCGA--TTCA
30572 TTTCTCGTTGCGATTC-
1 TTTCTCGTTGCGATTCA
30588 --TCTCGTTGCGATTCA
1 TTTCTCGTTGCGATTCA
*
30603 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
30617 AGTCATTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
14 23 0.46
16 3 0.06
17 14 0.28
19 10 0.20
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (17 bp):
TTTCTCGTTGCGATTCA
Found at i:30849 original size:94 final size:94
Alignment explanation
Indices: 30704--31082 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
30694 ATGGATTGCA
* *
30704 TTAC-TTCAACCAAAAGACAAAA-AAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
30767 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
30796 TTACTTTCAATCAAAAGACAAAACAAAGACAAATACTAACTGCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
30861 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
30890 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACTGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
30955 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
30984 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
31048 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
31078 TTACT
1 TTACT
31083 AAGCAATCTA
Statistics
Matches: 272, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
92 4 0.01
93 36 0.13
94 232 0.85
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:32823 original size:20 final size:21
Alignment explanation
Indices: 32778--32838 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
32768 TCTTTTGGTT
*
32778 GAAATGAAAATCGCAA--CGA
1 GAAATGAATATCGCAATGCGA
32797 GAGAATGAATATCGCAATGCG-
1 GA-AATGAATATCGCAATGCGA
*
32818 GAAATGACTATCGCAATGCGA
1 GAAATGAATATCGCAATGCGA
32839 TTTTGGTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 30 0.83
21 2 0.06
22 2 0.06
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (21 bp):
GAAATGAATATCGCAATGCGA
Found at i:32887 original size:33 final size:33
Alignment explanation
Indices: 32834--32914 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
32824 ACTATCGCAA
** **
32834 TGCGATTTTGGTTTCACGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTATCTAAT
* *
32867 TGCGATTTTCATTTCGCGTTGCGATTCTCTAAT
1 TGCGATTTTCATTTCACGTTGCGATTATCTAAT
32900 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
32915 TCTCGTTGCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCACGTTGCGATTATCTAAT
Found at i:32967 original size:20 final size:19
Alignment explanation
Indices: 32899--32969 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 19
32889 GATTCTCTAA
32899 TTGCGATTTTCATTTCTCTCG
1 TTGCGATTTTCATTT-TCT-G
**
32920 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCATTTTC-TG
32940 TTGCGATTTTCATTTTCATG
1 TTGCGATTTTCATTTTC-TG
32960 TTGCGATTTT
1 TTGCGATTTT
32970 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.52
Consensus pattern (19 bp):
TTGCGATTTTCATTTTCTG
Found at i:33551 original size:20 final size:20
Alignment explanation
Indices: 33526--33719 Score: 167
Period size: 20 Copynumber: 9.6 Consensus size: 20
33516 CTTTAAAAAT
*
33526 CGCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTACGGATA
33546 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33566 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
33586 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
**** * *
33607 TATATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
33627 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33647 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
33667 TGTCGTTGCGATTTATGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
33688 TGCGTTGTGATTTTACGGTTA
1 CGCGTTGCGA-TTTACGGATA
*
33709 CTCGTTGCGAT
1 CGCGTTGCGAT
33720 AGTCAGAATC
Statistics
Matches: 139, Mismatches: 28, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
20 90 0.65
21 49 0.35
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:33676 original size:61 final size:61
Alignment explanation
Indices: 33524--33719 Score: 184
Period size: 61 Copynumber: 3.2 Consensus size: 61
33514 CGCTTTAAAA
* *
33524 ATCGCGTTGCGATTTACGAATACG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 ATCGCGTTGCGATTTACGAATATGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGG
* * * * * * * *
33584 ATTGTCGTTGTGATTTACGGATATAT-ATTGCGATTTACGTATTCTCGTTGCGA-TTTACGG
1 ATCG-CGTTGCGATTTACGAATATGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGG
* * * *
33644 ATACGCGTTGCGATTTTACGTAT-TGTCGTTGCGATTTATGGATATGCGTTGTGATTTTACGG
1 AT-CGCGTTGCGA-TTTACGAATATGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGG
* *
33706 TTACTCGTTGCGAT
1 AT-CGCGTTGCGAT
33720 AGTCAGAATC
Statistics
Matches: 107, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
60 20 0.19
61 69 0.64
62 18 0.17
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (61 bp):
ATCGCGTTGCGATTTACGAATATGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGG
Found at i:33700 original size:81 final size:81
Alignment explanation
Indices: 33527--33719 Score: 280
Period size: 81 Copynumber: 2.4 Consensus size: 81
33517 TTTAAAAATC
* *
33527 GCGTTGCGATTTACGAATACGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGT
1 GCGTTGCGATTTACGTATACTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGT
*
33592 TGTGATTTACGGATAT
66 TGCGATTTACGGATAT
*** *
33608 ATATTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGT
1 GCGTTGCGATTTACGTATACTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGT
*
33673 TGCGATTTATGGATAT
66 TGCGATTTACGGATAT
*
33689 GCGTTGTGATTTTACGGT-TACTCGTTGCGAT
1 GCGTTGCGA-TTTAC-GTATACTCGTTGCGAT
33720 AGTCAGAATC
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
81 78 0.80
82 17 0.18
83 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (81 bp):
GCGTTGCGATTTACGTATACTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGT
TGCGATTTACGGATAT
Found at i:33714 original size:41 final size:41
Alignment explanation
Indices: 33526--33719 Score: 232
Period size: 41 Copynumber: 4.8 Consensus size: 41
33516 CTTTAAAAAT
* * *
33526 CGCGTTGCGA-TTTACGAATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
33566 CGCGTTGCGATTTTACGTATTGTCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
****
33607 TATATTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
33647 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* * *
33688 TGCGTTGTGATTTTACGGT-TACTCGTTGCGAT
1 CGCGTTGCGATTTTAC-GTATTCTCGTTGCGAT
33720 AGTCAGAATC
Statistics
Matches: 130, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
40 44 0.34
41 84 0.65
42 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:46820 original size:17 final size:17
Alignment explanation
Indices: 46798--46831 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
46788 TTCTTTTACC
46798 TTTTTTTACTTAACTTA
1 TTTTTTTACTTAACTTA
46815 TTTTTTTACTTAACTTA
1 TTTTTTTACTTAACTTA
46832 AATTTAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTTACTTAACTTA
Found at i:46961 original size:21 final size:21
Alignment explanation
Indices: 46935--46976 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
46925 TTTGTTTTAT
46935 TCATGAAAACTATCTATAAAA
1 TCATGAAAACTATCTATAAAA
46956 TCATGAAAACTATCTATAAAA
1 TCATGAAAACTATCTATAAAA
46977 ATAATTATAT
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:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (21 bp):
TCATGAAAACTATCTATAAAA
Found at i:51595 original size:22 final size:21
Alignment explanation
Indices: 51561--51601 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
51551 ATAATTATTT
51561 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
51582 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
51602 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:61368 original size:15 final size:15
Alignment explanation
Indices: 61344--61383 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
61334 TGGATATTTA
*
61344 GCTGGACGGGCGGAT
1 GCTGGGCGGGCGGAT
61359 GCTGGGCGGGCGGAT
1 GCTGGGCGGGCGGAT
* *
61374 ACGGGGCGGG
1 GCTGGGCGGG
61384 TAATGTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.10, C:0.20, G:0.60, T:0.10
Consensus pattern (15 bp):
GCTGGGCGGGCGGAT
Found at i:63096 original size:64 final size:64
Alignment explanation
Indices: 63020--63226 Score: 202
Period size: 64 Copynumber: 3.2 Consensus size: 64
63010 TTGATTCATT
***
63020 AGTAGTGCATCGATGAA-CTTTTTTAA-AATAAAAACATCGAATGCAATTCATGCATCGATGCAT
1 AGTAGTGCATCGATGAATC-CCATTAATAAT-AAAACATCGAATGCAATTCATGCATCGATGCAT
63083 A
64 A
* * * **
63084 AGTAGTGAATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGCATCGATGCATA
1 AGTAGTGCATCGATGAATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATGCATA
* * ** * * ** * * * *
63148 AGGAGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGCACCGATGTATC
1 AGTAGTGCATCGATGAATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATGCATA
63212 AGTAGTGCATCGATG
1 AGTAGTGCATCGATG
63227 CATACCTTCA
Statistics
Matches: 118, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
64 114 0.97
65 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (64 bp):
AGTAGTGCATCGATGAATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATGCATA
Found at i:63227 original size:64 final size:64
Alignment explanation
Indices: 63051--63229 Score: 216
Period size: 64 Copynumber: 2.8 Consensus size: 64
63041 TTTAAAATAA
* * * **
63051 AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGAATCGATGCATCCCATTAATAATG
1 AAACATCGAATACAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATG
* * *
63115 AAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAAT-
1 AAACATCGAATACAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATG
** * * * *
63178 AATACATCGAATACCTTTTATGCACCGATGTATCAGTAGTGCATCGATGCAT
1 AA-ACATCGAATACAATTGATGCATCGATGCATAAGTAGTGCATCGATGCAT
63230 ACCTTCATTA
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 2 0.02
64 97 0.98
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
AAACATCGAATACAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATG
Found at i:63555 original size:12 final size:12
Alignment explanation
Indices: 63537--63572 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
63527 TATATATGTT
63537 CATGTGATATGA
1 CATGTGATATGA
*
63549 TATGTGATATGA
1 CATGTGATATGA
63561 CATGTGATATGA
1 CATGTGATATGA
63573 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:63594 original size:23 final size:26
Alignment explanation
Indices: 63537--63605 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
63527 TATATATGTT
**
63537 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
63561 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
63586 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
63606 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:70003 original size:64 final size:64
Alignment explanation
Indices: 69935--70091 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 64
69925 TTGAAGGTGT
** *
69935 ATCGATGCATTAGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATTGAATGCAATTCATG
1 ATCGATGCATTAGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
69998 C
64 C
* **
69999 ATCGATGCA-TAGGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATTA-GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* *
70063 ATCGATGCATAAGGAGTGCATCGATGCAT
1 ATCGATGCATTAGTAGTGCATCGATGCAT
70092 ACCTTCATTA
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 2 0.02
64 74 0.91
65 5 0.06
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (64 bp):
ATCGATGCATTAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:70422 original size:12 final size:12
Alignment explanation
Indices: 70401--70434 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
70391 TATATGTTCT
* *
70401 TGTGACATGATA
1 TGTGATATGACA
70413 TGTGATATGACA
1 TGTGATATGACA
70425 TGTGATATGA
1 TGTGATATGA
70435 GAACATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (12 bp):
TGTGATATGACA
Found at i:70456 original size:23 final size:26
Alignment explanation
Indices: 70415--70467 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 26
70405 ACATGATATG
70415 TGATATGACATGTGATATGAGA-ACA
1 TGATATGACATGTGATATGAGATACA
70440 TGATATGA-A-GTGATATGAGATACA
1 TGATATGACATGTGATATGAGATACA
70464 TGAT
1 TGAT
70468 CACAAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.30
Consensus pattern (26 bp):
TGATATGACATGTGATATGAGATACA
Found at i:70597 original size:15 final size:15
Alignment explanation
Indices: 70579--70611 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
70569 GAGGGTATAA
70579 TAGTCCTTCAGGATG
1 TAGTCCTTCAGGATG
*
70594 TAGTCCTTCGGGATG
1 TAGTCCTTCAGGATG
70609 TAG
1 TAG
70612 GGGTCTTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCAGGATG
Found at i:74414 original size:12 final size:12
Alignment explanation
Indices: 74358--74415 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
74348 CACATATACC
74358 ATCATTATCAAT
1 ATCATTATCAAT
** *
74370 ATCAACATCATT
1 ATCATTATCAAT
* **
74382 ATCATGATCTCT
1 ATCATTATCAAT
*
74394 ATTATTATCAAT
1 ATCATTATCAAT
74406 ATCATTATCA
1 ATCATTATCA
74416 TGTAATATAT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (12 bp):
ATCATTATCAAT
Found at i:78909 original size:23 final size:23
Alignment explanation
Indices: 78879--78941 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
78869 AGCTCGTATA
*
78879 AATT-CACCAAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
78901 AATTGCACCGAAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
78924 AATTGCACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
78942 TATAAAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Done.