Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000469.1 Hibiscus syriacus cultivar Beakdansim tig00000872_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: 44315
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2610 original size:7 final size:7
Alignment explanation
Indices: 2598--2622 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2588 TAAATATATA
2598 AATTTTT
1 AATTTTT
2605 AATTTTT
1 AATTTTT
2612 AATTTTT
1 AATTTTT
2619 AATT
1 AATT
2623 AATGGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:4198 original size:6 final size:6
Alignment explanation
Indices: 4189--4268 Score: 66
Period size: 6 Copynumber: 14.2 Consensus size: 6
4179 TTTTTTTCGG
* * *
4189 CTCTGT CTCTCT CT-TTT CTCTCTGT CTCTGT CTCT-T -T-TAT CTCTGT
1 CTCTGT CTCTGT CTCTGT CTC--TGT CTCTGT CTCTGT CTCTGT CTCTGT
4235 CTCTGT CTCT-T -T-TGT CTCTGT CTCTGT CTCTGT C
1 CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT C
4269 CCTTTTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
3 2 0.03
4 4 0.07
5 8 0.13
6 42 0.69
8 5 0.08
ACGTcount: A:0.01, C:0.33, G:0.11, T:0.55
Consensus pattern (6 bp):
CTCTGT
Found at i:4243 original size:27 final size:21
Alignment explanation
Indices: 4189--4265 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
4179 TTTTTTTCGG
*
4189 CTCTGTCTC--TCTCTTTTCT
1 CTCTGTCTCTGTCTCTTTTAT
4208 CTCTGTCTCTGTCTCTTTTAT
1 CTCTGTCTCTGTCTCTTTTAT
*
4229 CTCTGTCTCTGTCTCTTTTGT
1 CTCTGTCTCTGTCTCTTTTAT
4250 CTCTGTCTCTGTCTCT
1 CTCTGTCTCTGTCTCT
4266 GTCCCTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 9 0.17
21 45 0.83
ACGTcount: A:0.01, C:0.32, G:0.10, T:0.56
Consensus pattern (21 bp):
CTCTGTCTCTGTCTCTTTTAT
Found at i:4682 original size:3 final size:3
Alignment explanation
Indices: 4666--4742 Score: 56
Period size: 3 Copynumber: 26.7 Consensus size: 3
4656 TGTAATATTA
* * * *
4666 AAT AAT -AT ATT AAT AAT AAT AAT TAT TAT AAT TAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
4712 AAT -AT TAT AAT AAAT AAT -AT AAAT AA- AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AA
4743 AAAATGAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
2 10 0.17
3 45 0.75
4 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:4721 original size:11 final size:11
Alignment explanation
Indices: 4658--4724 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
4648 TTTGGGCTTG
4658 TAATATTA-AA
1 TAATATTATAA
4668 TAATA-TATTAA
1 TAATATTA-TAA
4679 TAATA--ATAA
1 TAATATTATAA
* * *
4688 TTATTATAATTA
1 -TAATATTATAA
*
4700 TAATATAATAA
1 TAATATTATAA
4711 TAATATTATAA
1 TAATATTATAA
4722 TAA
1 TAA
4725 ATAATATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
9 5 0.11
10 10 0.21
11 29 0.62
12 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATATTATAA
Found at i:4729 original size:32 final size:31
Alignment explanation
Indices: 4667--4742 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
4657 GTAATATTAA
* *
4667 ATAATATATTAATAATAATAATTATTATAATT
1 ATAATATAATAATAATAATAATTATAATAA-T
4699 ATAATATAATAATAATATTATAA-TA-AATAAT
1 ATAATATAATAATAATA--ATAATTATAATAAT
4730 ATAA-ATAA-AATAA
1 ATAATATAATAATAA
4743 AAAATGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 5 0.12
30 4 0.10
31 5 0.12
32 20 0.50
33 2 0.05
34 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
ATAATATAATAATAATAATAATTATAATAAT
Found at i:4735 original size:9 final size:9
Alignment explanation
Indices: 4658--4743 Score: 50
Period size: 9 Copynumber: 9.0 Consensus size: 9
4648 TTTGGGCTTG
4658 TAATATTAAA
1 TAATA-TAAA
4668 TAATATATTAA
1 TAATATA--AA
*
4679 TAATAATAAT
1 TAAT-ATAAA
*
4689 TATTATAATTA
1 TAATATAA--A
4700 TAATAT-AA
1 TAATATAAA
*
4708 TAATA-ATA
1 TAATATAAA
*
4716 TTATAATAAA
1 TAAT-ATAAA
4726 TAATATAAA
1 TAATATAAA
*
4735 TAAAATAAA
1 TAATATAAA
4744 AAATGAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
8 10 0.17
9 20 0.34
10 15 0.25
11 11 0.19
12 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TAATATAAA
Found at i:4740 original size:14 final size:13
Alignment explanation
Indices: 4676--4742 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 13
4666 AATAATATAT
4676 TAATAATAATAATTA
1 TAATAA-AATAA-TA
* *
4691 TTATAATTATAATA
1 TAATAA-AATAATA
*
4705 TAATAATAATATTA
1 TAATAA-AATAATA
4719 TAAT-AAATAATA
1 TAATAAAATAATA
4731 TAAATAAAATAA
1 T-AATAAAATAA
4743 AAAATGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
12 7 0.16
13 4 0.09
14 23 0.52
15 10 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAAAATAATA
Found at i:12247 original size:23 final size:23
Alignment explanation
Indices: 12195--12248 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
12185 AAATAGCAAG
* *
12195 TATAACTATTAATATTATTATTT
1 TATAAATATTAATATTATAATTT
*
12218 T-TAAAATATTATTATTATAATTT
1 TAT-AAATATTAATATTATAATTT
12241 TATAAATA
1 TATAAATA
12249 AAAATACTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 24 0.92
24 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATAAATATTAATATTATAATTT
Found at i:25502 original size:23 final size:21
Alignment explanation
Indices: 25476--25517 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
25466 TTTTGGCTTT
25476 TTTTATTGCCTTTTTTTTTTGCC
1 TTTTATTG--TTTTTTTTTTGCC
*
25499 TTTTTTTGTTTTTTTTTTG
1 TTTTATTGTTTTTTTTTTG
25518 AAAAAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.79
Consensus pattern (21 bp):
TTTTATTGTTTTTTTTTTGCC
Found at i:25510 original size:15 final size:13
Alignment explanation
Indices: 25466--25505 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
25456 TTTTTTGAAA
*
25466 TTTTGGCTTTTTT
1 TTTTGCCTTTTTT
*
25479 TATTGCCTTTTTT
1 TTTTGCCTTTTTT
25492 TTTTGCCTTTTTT
1 TTTTGCCTTTTTT
25505 T
1 T
25506 GTTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.03, C:0.12, G:0.10, T:0.75
Consensus pattern (13 bp):
TTTTGCCTTTTTT
Found at i:29670 original size:19 final size:19
Alignment explanation
Indices: 29646--29682 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29636 ATGACCAACA
*
29646 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
29665 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
29683 CAGTATCGCA
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:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:29835 original size:20 final size:20
Alignment explanation
Indices: 29771--29882 Score: 163
Period size: 20 Copynumber: 5.5 Consensus size: 20
29761 TTTAGAAAAC
*
29771 CGCAATGCGATTCTGACTAT
1 CGCAACGCGATTCTGACTAT
* **
29791 CGCAACGCAATAAT-ACATAAT
1 CGCAACGCGATTCTGAC-T-AT
29812 CGCAACGCGATTCTGACTAT
1 CGCAACGCGATTCTGACTAT
29832 CGCAACGCGATTCTGACTAT
1 CGCAACGCGATTCTGACTAT
29852 CGCAACGCGATTCTGACTAT
1 CGCAACGCGATTCTGACTAT
29872 CGCAACGCGAT
1 CGCAACGCGAT
29883 AATACAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (20 bp):
CGCAACGCGATTCTGACTAT
Found at i:29865 original size:40 final size:41
Alignment explanation
Indices: 29771--29904 Score: 182
Period size: 41 Copynumber: 3.3 Consensus size: 41
29761 TTTAGAAAAC
* *
29771 CGCAATGCGATTCTGACTATCGCAACGCAATAATACATAAT
1 CGCAACGCGATTCTGACTATCGCAACGCGATAATACATAAT
**
29812 CGCAACGCGATTCTGACTATCGCAACGCGATTCTGAC-T-AT
1 CGCAACGCGATTCTGACTATCGCAACGCGATAAT-ACATAAT
*
29852 CGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAAT
1 CGCAACGCGATTCTGACTATCGCAACGCGATAATACATAAT
* *
29893 CTCAATGCGATT
1 CGCAACGCGATT
29905 TTCAAAGCGA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
39 2 0.02
40 34 0.42
41 43 0.53
42 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (41 bp):
CGCAACGCGATTCTGACTATCGCAACGCGATAATACATAAT
Found at i:29903 original size:61 final size:61
Alignment explanation
Indices: 29771--29904 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
29761 TTTAGAAAAC
** *
29771 CGCAATGCGATTCTGACTATCGCAACGCAATAATACATAATCGCAACGCGATTCTGACTAT
1 CGCAATGCGATTCTGACTATCGCAACGCAATAATACATAATCGCAACGCGATAATGACAAT
* * **
29832 CGCAACGCGATTCTGACTATCGCAACGCGATTCTGAC-T-ATCGCAACGCGATAAT-ACAAAAT
1 CGCAATGCGATTCTGACTATCGCAACGCAATAAT-ACATAATCGCAACGCGATAATGAC--AAT
*
29893 CTCAATGCGATT
1 CGCAATGCGATT
29905 TTCAAAGCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
59 2 0.03
60 14 0.23
61 43 0.70
62 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (61 bp):
CGCAATGCGATTCTGACTATCGCAACGCAATAATACATAATCGCAACGCGATAATGACAAT
Found at i:30551 original size:53 final size:54
Alignment explanation
Indices: 30467--30569 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 54
30457 GTCAAATTCG
*
30467 CGTTGCGATAGTCATTTTCGTGTTGCAATTTTCA-TTTCGCGTTGCGATTATCT
1 CGTTGCGATAGTCATTTTCGTATTGCAATTTTCATTTTCGCGTTGCGATTATCT
* * *
30520 CGTTGCGATAGTCATTTTTGTATTGCGATTTTCATTTTCGTGTTGCGATT
1 CGTTGCGATAGTCATTTTCGTATTGCAATTTTCATTTTCGCGTTGCGATT
30570 TTAAGTTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 31 0.69
54 14 0.31
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.48
Consensus pattern (54 bp):
CGTTGCGATAGTCATTTTCGTATTGCAATTTTCATTTTCGCGTTGCGATTATCT
Found at i:30569 original size:20 final size:20
Alignment explanation
Indices: 30463--30571 Score: 79
Period size: 20 Copynumber: 5.8 Consensus size: 20
30453 GATAGTCAAA
* **
30463 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
*
30483 TTCGTGTTGCAATTTTCA-T
1 TTCGTGTTGCGATTTTCATT
*
30502 TTCGCGTTGCGA--TT-A-T
1 TTCGTGTTGCGATTTTCATT
* **
30518 CTC--GTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
* *
30536 TTTGTATTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
30556 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
30572 AAGTTTCAGA
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
14 7 0.10
16 5 0.07
17 3 0.04
18 2 0.03
19 11 0.16
20 40 0.59
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:32562 original size:20 final size:20
Alignment explanation
Indices: 32474--32555 Score: 121
Period size: 20 Copynumber: 4.1 Consensus size: 20
32464 AAACTTAAAA
**
32474 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAATTTGACT
*
32494 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATTTGACT
32514 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
32534 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
32554 AT
1 AT
32556 TGTAACGGGA
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
19 3 0.05
20 53 0.90
21 3 0.05
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:32619 original size:20 final size:20
Alignment explanation
Indices: 32596--32633 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
32586 AATCGCAACG
*
32596 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
32616 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
32634 TTTAGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:32660 original size:19 final size:19
Alignment explanation
Indices: 32634--32719 Score: 84
Period size: 19 Copynumber: 4.5 Consensus size: 19
32624 GCAACGCGAA
*
32634 TTTAGTTTCGCGTTACGAT
1 TTTAGTTTCGCATTACGAT
*
32653 TTTGGTTTCGCATTACGATT
1 TTTAGTTTCGCATTACGA-T
*
32673 TTTA-TTTCGCATTGCGAT
1 TTTAGTTTCGCATTACGAT
* ** *
32691 TTAAGTTTCGTGTTGCGAT
1 TTTAGTTTCGCATTACGAT
32710 TTTAAGTTTC
1 TTT-AGTTTC
32720 AGAAACTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
18 4 0.07
19 42 0.75
20 10 0.18
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (19 bp):
TTTAGTTTCGCATTACGAT
Found at i:33246 original size:21 final size:22
Alignment explanation
Indices: 33222--33281 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
33212 CTCCTATCGT
33222 TCAAGAGGCCCCTATCATCC-C
1 TCAAGAGGCCCCTATCATCCGC
* *
33243 TCAAGAGTCCCCT-TCCA-CCGT
1 TCAAGAGGCCCCTAT-CATCCGC
33264 TCAAGAGGCCCCTATCAT
1 TCAAGAGGCCCCTATCAT
33282 TGTTGAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.09
21 28 0.88
22 1 0.03
ACGTcount: A:0.23, C:0.40, G:0.15, T:0.22
Consensus pattern (22 bp):
TCAAGAGGCCCCTATCATCCGC
Found at i:33291 original size:42 final size:42
Alignment explanation
Indices: 33201--33312 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
33191 CTGTCATCGT
* *
33201 TCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGTCC-CTCCCACCGTTCAAGAGGCCCCTATCATCCC
* ***
33243 TCAAGA-GTCCCCTTCCACCGTTCAAGAGGCCCCTATCATTGT
1 TCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* *
33285 TGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCAAGAGGTCCCTCCCACCGTTCAAGAG
33313 CCCGATTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
41 1 0.02
42 53 0.91
43 4 0.07
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:34745 original size:67 final size:63
Alignment explanation
Indices: 34660--34810 Score: 232
Period size: 63 Copynumber: 2.3 Consensus size: 63
34650 TTATTAGCAT
34660 TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTAATTGATGTGTAAATAATTCT
1 TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTG--T--TTAATTGATGTGTAAATAATTCT
34725 TA
62 TA
*
34727 TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
1 TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
*
34790 TTTGTT-CTTATTTAATTGATT
1 TTT-TTGCTTGTTTAATTGATT
34811 GAAATGTAAA
Statistics
Matches: 81, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
63 42 0.52
64 2 0.02
65 1 0.01
67 36 0.44
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (63 bp):
TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
Found at i:34812 original size:67 final size:63
Alignment explanation
Indices: 34660--34832 Score: 231
Period size: 67 Copynumber: 2.6 Consensus size: 63
34650 TTATTAGCAT
* *
34660 TTTTTGCTTGTTTAATTGATTTATAAAAGTTGATTTGTTTAATTAATTGATGTGTAAATAATTCT
1 TTTTTGCTTATTTAATTGATTTGTAAAAGTTGATTTG--T--TTAATTGATGTGTAAATAATTCT
34725 TA
62 TA
*
34727 TTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
1 TTTTTGCTTATTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
34790 TTTGTT-CTTATTTAATTGATTGAAATGTAAAAGTTGATTTGTT
1 TTT-TTGCTTATTTAATTGATT----TGTAAAAGTTGATTTGTT
34833 GATTTCAATC
Statistics
Matches: 99, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
63 42 0.42
64 2 0.02
65 1 0.01
67 54 0.55
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (63 bp):
TTTTTGCTTATTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
Found at i:34954 original size:20 final size:20
Alignment explanation
Indices: 34884--34957 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
34874 AGGTATACTT
*
34884 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
** * *
34904 TCGCAATACAAAAGTCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
34924 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
34944 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
34958 TCAATTCGCG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.46, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:35031 original size:34 final size:34
Alignment explanation
Indices: 34965--35059 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 34
34955 AAGTCAATTC
* * * ** *
34965 GCGTTGCGATAGTCTAATACGTTTTGCGATTTTCT
1 GCGTTGCGATAATCAAATTCGCGTTGCAATTTT-T
* *
35000 -CGTTGCGGTAGTCAAATTCGCGTTGCAATTTTT
1 GCGTTGCGATAATCAAATTCGCGTTGCAATTTTT
35033 GCGTTGCGATAATCAAATTCGCGTTGC
1 GCGTTGCGATAATCAAATTCGCGTTGC
35060 GATAATCAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
33 1 0.02
34 50 0.98
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (34 bp):
GCGTTGCGATAATCAAATTCGCGTTGCAATTTTT
Found at i:35058 original size:20 final size:20
Alignment explanation
Indices: 35033--35184 Score: 190
Period size: 20 Copynumber: 7.9 Consensus size: 20
35023 TGCAATTTTT
*
35033 GCGTTGCGATAATCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
35053 GCGTTGCGATAATCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
35073 ACGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
35093 ACGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
35113 GCGTTGCGAT--T----TTT
1 GCGTTGCGATAGTCAAATTC
*
35127 GAGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
35147 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
* *
35167 ACGTTGCGATATTCAAAT
1 GCGTTGCGATAGTCAAAT
35185 GAATGTGTAA
Statistics
Matches: 117, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
14 11 0.09
16 1 0.01
18 1 0.01
20 104 0.89
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:35117 original size:94 final size:94
Alignment explanation
Indices: 35000--35184 Score: 316
Period size: 94 Copynumber: 2.0 Consensus size: 94
34990 GCGATTTTCT
* *
35000 CGTTGCGGTAGTCAAATTCGCGTTGCAATTTTTGCGTTGCGATAATCAAATTCGCGTTGCGATAA
1 CGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGCGTTGCGATAA
35065 TCAAATTCACGTTGCGATAGTCAAATTCA
66 TCAAATTCACGTTGCGATAGTCAAATTCA
* * *
35094 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCGATAGTCAAATTCGCGTTGCGATAG
1 CGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGCGTTGCGATAA
*
35159 TCAAATTCACGTTGCGATATTCAAAT
66 TCAAATTCACGTTGCGATAGTCAAAT
35185 GAATGTGTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 85 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (94 bp):
CGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGCGTTGCGATAA
TCAAATTCACGTTGCGATAGTCAAATTCA
Found at i:35157 original size:54 final size:57
Alignment explanation
Indices: 35033--35178 Score: 199
Period size: 54 Copynumber: 2.6 Consensus size: 57
35023 TGCAATTTTT
*
35033 GCGTTGCGATAATCAAATTCGCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTCGCGTTGCGAT-AT--AATTCACGTTGCGATAGTCAAATTC
* * *
35093 ACGTTGCGATAGTCAAATTCGCGTTGCGAT-T-TTTGA-GTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATATAATTCACGTTGCGATAGTCAAATTC
*
35147 GCGTTGCGATAGTCAAATTCACGTTGCGATAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAT
35179 TCAAATGAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
54 46 0.58
55 4 0.05
58 1 0.01
60 28 0.35
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (57 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATATAATTCACGTTGCGATAGTCAAATTC
Found at i:35437 original size:140 final size:140
Alignment explanation
Indices: 35155--35430 Score: 516
Period size: 140 Copynumber: 2.0 Consensus size: 140
35145 TCGCGTTGCG
*
35155 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
35220 TAGCAATGTTCAAACTCAAGTCACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTCACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
35285 AATACACTTA
131 AATACACTTA
*
35295 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
* *
35360 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTCACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
35425 AATACA
131 AATACA
35431 TATAATACAA
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 132 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
TAGCAATGTTCAAACTCAAGTCACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
AATACACTTA
Found at i:37814 original size:24 final size:24
Alignment explanation
Indices: 37780--37833 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
37770 CTGAAACATC
37780 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
37804 ATCAAAGTCCGGGTATTGACTAAG
1 ATCAAAATCCGAGTATTGACCAAG
37828 ATCAAA
1 ATCAAA
37834 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:38677 original size:19 final size:19
Alignment explanation
Indices: 38653--38722 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
38643 GTTTTACGAT
38653 ATCGCGTTGCGATAGTCAA
1 ATCGCGTTGCGATAGTCAA
38672 ATCGCGTTGCGATTATGT--A
1 ATCGCGTTGCGA-TA-GTCAA
* * *
38691 TTAGTG-TGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCA-A
38710 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
38723 TATTATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
16 2 0.05
17 2 0.05
18 5 0.13
19 20 0.51
20 8 0.21
21 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (19 bp):
ATCGCGTTGCGATAGTCAA
Found at i:38730 original size:37 final size:37
Alignment explanation
Indices: 38660--38730 Score: 126
Period size: 38 Copynumber: 1.9 Consensus size: 37
38650 GATATCGCGT
38660 TGCGATAGTCAAATCGCGTTGCGATTATGTATTAGTG
1 TGCGATAGTCAAATCGCGTTGCGATTATGTATTAGTG
38697 TGCGATAGTCAGAATCGCGTTGCGATTAT-TATTA
1 TGCGATAGTCA-AATCGCGTTGCGATTATGTATTA
38731 TTGCGTTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (37 bp):
TGCGATAGTCAAATCGCGTTGCGATTATGTATTAGTG
Done.