Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004347.1 Hibiscus syriacus cultivar Beakdansim tig00009527_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: 71246
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:1043 original size:60 final size:58
Alignment explanation
Indices: 966--1135 Score: 247
Period size: 58 Copynumber: 2.9 Consensus size: 58
956 AAACATATGA
966 ATAGTCGGA-GACCATTTTGTAACTTTTAATAGTCTAAGGACTCAATAAAATAACACCTT
1 ATAGTCGGATGACCATTTTGTAACTTTTAATAGTCTAAGGACTCAAT-AAA-AACACCTT
1025 ATAGTCGGATGACCATTTTGTAACTTTTAATAGTCTAAGGACTCAATAAAAACACCTT
1 ATAGTCGGATGACCATTTTGTAACTTTTAATAGTCTAAGGACTCAATAAAAACACCTT
* * *
1083 ATAGTCGGAAT-ACCA-TTTGTAACTTTTTAATAGTCGATGGACTCGAAAAAAAA
1 ATAGTCGG-ATGACCATTTTGTAAC-TTTTAATAGTCTAAGGACTC-AATAAAAA
1136 TATTTTATGT
Statistics
Matches: 104, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
57 8 0.08
58 38 0.37
59 21 0.20
60 37 0.36
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (58 bp):
ATAGTCGGATGACCATTTTGTAACTTTTAATAGTCTAAGGACTCAATAAAAACACCTT
Found at i:3405 original size:17 final size:18
Alignment explanation
Indices: 3379--3418 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3369 CCGACAAATT
*
3379 AATAAAATTTAAA-GAGAA
1 AATAAATTTTAAATGA-AA
3397 AATAAATTTTAAATGAAA
1 AATAAATTTTAAATGAAA
3415 AATA
1 AATA
3419 TAAAAATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (18 bp):
AATAAATTTTAAATGAAA
Found at i:3945 original size:2 final size:2
Alignment explanation
Indices: 3940--3964 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3930 ATTCTATTTG
3940 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3965 ATCTAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4352 original size:2 final size:2
Alignment explanation
Indices: 4345--4392 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4335 ATAAAATTAG
4345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4387 AT AT AT
1 AT AT AT
4393 TGTGTCGGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7788 original size:22 final size:22
Alignment explanation
Indices: 7760--7877 Score: 191
Period size: 22 Copynumber: 5.4 Consensus size: 22
7750 GACCACTAAT
*
7760 GTCCCGAAGGACTACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
7782 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
* *
7804 GTCCCGAAAGACTACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
7826 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAC
*
7848 ATCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
7870 GTCCCGAA
1 GTCCCGAA
7878 AGACTAATAT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.16
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:7844 original size:66 final size:66
Alignment explanation
Indices: 7760--7883 Score: 221
Period size: 66 Copynumber: 1.9 Consensus size: 66
7750 GACCACTAAT
* *
7760 GTCCCGAAGGACTACTGGATACGTCCCGAAGGACCACTGGATACGTCCCGAAAGACTACTGGATA
1 GTCCCGAAGGACCACTGGATACATCCCGAAGGACCACTGGATACGTCCCGAAAGACTACTGGATA
7825 C
66 C
*
7826 GTCCCGAAGGACCACTGGATATATCCCGAAGGACCACTGGATACGTCCCGAAAGACTA
1 GTCCCGAAGGACCACTGGATACATCCCGAAGGACCACTGGATACGTCCCGAAAGACTA
7884 ATATACCCTC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (66 bp):
GTCCCGAAGGACCACTGGATACATCCCGAAGGACCACTGGATACGTCCCGAAAGACTACTGGATA
C
Found at i:9189 original size:2 final size:2
Alignment explanation
Indices: 9182--9210 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9172 ACCCACGTGG
9182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9211 CCATTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16660 original size:23 final size:22
Alignment explanation
Indices: 16629--16673 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
16619 AGTAAAATAT
*
16629 TAAATAAAT-TAAAATACTTAAA
1 TAAATAAATACAAAATA-TTAAA
16651 TAAATTAAATACAAAATATTAAA
1 TAAA-TAAATACAAAATATTAAA
16674 AATATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 10 0.50
24 6 0.30
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAATAAATACAAAATATTAAA
Found at i:16662 original size:17 final size:18
Alignment explanation
Indices: 16621--16659 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
16611 AATATATAAG
16621 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
16638 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
16656 TAAA
1 TAAA
16660 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:16721 original size:10 final size:10
Alignment explanation
Indices: 16715--16753 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
16705 ATAAGAGTAT
16715 TTGAGAGAAG
1 TTGAGAGAAG
16725 TTGAGAGAAG
1 TTGAGAGAAG
*
16735 TTGAGAGAAA
1 TTGAGAGAAG
16745 TTGAGAGAA
1 TTGAGAGAA
16754 TTTGGTGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:16731 original size:20 final size:20
Alignment explanation
Indices: 16708--16757 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
16698 AGAGAATATA
* *
16708 AGAGTATTTGAGAGAAGTTG
1 AGAGAATTTGAGAGAAATTG
*
16728 AGAGAAGTTGAGAGAAATTG
1 AGAGAATTTGAGAGAAATTG
16748 AGAGAATTTG
1 AGAGAATTTG
16758 GTGTGATGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (20 bp):
AGAGAATTTGAGAGAAATTG
Found at i:18101 original size:15 final size:15
Alignment explanation
Indices: 18081--18116 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
18071 GAATATATTA
18081 ATATTTTA-AAATAAT
1 ATATTTTATAAA-AAT
18096 ATATTTTATAAAAAT
1 ATATTTTATAAAAAT
18111 ATATTT
1 ATATTT
18117 ATTATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTATAAAAAT
Found at i:25835 original size:20 final size:20
Alignment explanation
Indices: 25807--25878 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
25797 TAGTTGAAAA
*
25807 TCGCGTTGCGATTTTCCATT
1 TCGCATTGCGATTTTCCATT
25827 TCGCATTGCGATTTTCCATT
1 TCGCATTGCGATTTTCCATT
*
25847 TCGTATTGCGATTTTCCATT
1 TCGCATTGCGATTTTCCATT
*
25867 TCGCGTTGCGAT
1 TCGCATTGCGAT
25879 AGTCTACAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (20 bp):
TCGCATTGCGATTTTCCATT
Found at i:25928 original size:22 final size:22
Alignment explanation
Indices: 25870--25922 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
25860 TTCCATTTCG
25870 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
25892 CGTTGTGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
25914 CGTTGCGAT
1 CGTTGCGAT
25923 TTTCTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:26047 original size:5 final size:5
Alignment explanation
Indices: 26039--26065 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
26029 GACCCCGACC
26039 CGAGA CGAGA CGAGA CGAGA CGAGA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CG
26066 GCGGCGGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:26975 original size:2 final size:2
Alignment explanation
Indices: 26968--27074 Score: 214
Period size: 2 Copynumber: 53.5 Consensus size: 2
26958 TGCACCTTTC
26968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27052 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
27075 CGCATACATA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 105 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27441 original size:30 final size:30
Alignment explanation
Indices: 27340--27441 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
27330 CCCGAAGGAC
* ** *
27340 CTATCCAGAGGTCACCAAGA-CCCCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
*
27369 CTATCCATAGGCCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
*
27399 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
*
27429 CTGTCCATAGGTC
1 CTATCCATAGGTC
27442 CCGAAGAAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
29 16 0.25
30 47 0.75
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCATAGGTCATAAAGATCCTCGGTAA
Found at i:27458 original size:60 final size:59
Alignment explanation
Indices: 27340--27458 Score: 132
Period size: 60 Copynumber: 2.0 Consensus size: 59
27330 CCCGAAGGAC
* * ** *
27340 CTATCCAGAGGTCACCAAGACCCCGGTAACTATCCATAGGCCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGACCCCGGTAACTATCCATAGGCCACAAAGAAACTAGGTAA
* * * *
27399 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCC-CGAAGAAACTAGGTAA
1 CTATCCAGAGGTCACAAAGA-CCCCGGTAACTATCCATAGG-CCACAAAGAAACTAGGTAA
27459 ACTGTCCATA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
59 18 0.37
60 29 0.59
61 2 0.04
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (59 bp):
CTATCCAGAGGTCACAAAGACCCCGGTAACTATCCATAGGCCACAAAGAAACTAGGTAA
Found at i:27537 original size:63 final size:61
Alignment explanation
Indices: 27424--27552 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
27414 AAAGATCCTC
*
27424 GGTAACTGTCCATAGGTCCCGAAGAAACTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAAACTAGGTAAACTGTCCATATGTTCCGTAGAACATA
* * *
27485 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGAAAC-TAGGT-AAACTGTCCATATGTTCCGTAGAACATA
27548 GGTAA
1 GGTAA
27553 ACCCTTGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 7 0.11
62 23 0.38
63 31 0.51
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAAACTAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:27547 original size:32 final size:31
Alignment explanation
Indices: 27427--27554 Score: 145
Period size: 31 Copynumber: 4.1 Consensus size: 31
27417 GATCCTCGGT
* * *
27427 AACTGTCCATAGGTCCCGAAGAA-ACTAGGTA
1 AACTGTCCATATGTTCCGTAGAACA-TAGGTA
*
27458 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
27489 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
27521 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
27552 AAC
1 AAC
27555 CCTTGACTCT
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
30 4 0.05
31 50 0.61
32 24 0.29
33 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:28129 original size:19 final size:21
Alignment explanation
Indices: 28087--28129 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
28077 TTCATAATCA
28087 CATATTCATATAGTTTATTAT
1 CATATTCATATAGTTTATTAT
*
28108 CATA-TCATATGGTTTA-TAT
1 CATATTCATATAGTTTATTAT
28127 CAT
1 CAT
28130 CATAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (21 bp):
CATATTCATATAGTTTATTAT
Found at i:28138 original size:22 final size:20
Alignment explanation
Indices: 28093--28139 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
28083 ATCACATATT
*
28093 CATATAGTTTATTATCATAT
1 CATATAGTTTATTATCATAA
*
28113 CATATGGTTTATATCATCATAA
1 CATATAGTTTAT-T-ATCATAA
28135 CATAT
1 CATAT
28140 CACATATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATATAGTTTATTATCATAA
Found at i:28585 original size:21 final size:21
Alignment explanation
Indices: 28561--28605 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28551 TGTTGTTCGT
* *
28561 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
28582 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
28603 TTG
1 TTG
28606 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:34376 original size:30 final size:30
Alignment explanation
Indices: 34304--34402 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 30
34294 CCCGAAGGAC
** *
34304 CTATCCAGAGGTCACCAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
34333 CTATCC--A-GTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
34360 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
34390 CTGTCCATAGGTC
1 CTATCCAGAGGTC
34403 CCGAAGAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
26 8 0.14
27 14 0.24
29 7 0.12
30 30 0.51
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:34422 original size:30 final size:31
Alignment explanation
Indices: 34388--34512 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
34378 GATCCTCGGT
*
34388 AACTGTCCATAGGTCCCGAAGAA-ACTA-GTA
1 AACTGTCCATATGTCCCGAAGAACA-TAGGTA
* **
34418 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
34449 TACTGTCCATATGTCTCGAAG-ACATAGGTAA
1 AACTGTCCATATGTCCCGAAGAACATAGGT-A
* *
34480 AACTGTCCATATGTTCCGTAGAACATA-GTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
34510 AAC
1 AAC
34513 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
30 33 0.42
31 40 0.51
32 5 0.06
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:34502 original size:62 final size:60
Alignment explanation
Indices: 34385--34507 Score: 176
Period size: 62 Copynumber: 2.0 Consensus size: 60
34375 AAAGATCCTC
*
34385 GGTAACTGTCCATAGGTCCCGAAGAAACTAGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAAACTAGTAAACTGTCCATATGTTCCGTAGAACATA
* * *
34445 GGTATACTGTCCATATGTCTCGAAGACA-TAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGAAACTA-GT-AAACTGTCCATATGTTCCGTAGAACATA
34507 G
1 G
34508 TAAACCCTCG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
60 6 0.11
61 22 0.39
62 28 0.50
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (60 bp):
GGTAACTGTCCATAGGTCCCGAAGAAACTAGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:35526 original size:21 final size:21
Alignment explanation
Indices: 35502--35546 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35492 GTTTGTTCGT
* *
35502 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
35523 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
35544 TTG
1 TTG
35547 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:36483 original size:21 final size:21
Alignment explanation
Indices: 36457--36510 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
36447 GAAATGGAAA
36457 ATCTCAACGCGATTTTCAACT
1 ATCTCAACGCGATTTTCAACT
*
36478 ATCTCAATGCGATTTTCAACT
1 ATCTCAACGCGATTTTCAACT
*
36499 ATCGCAACGCGA
1 ATCTCAACGCGA
36511 AATGCAACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (21 bp):
ATCTCAACGCGATTTTCAACT
Found at i:36518 original size:21 final size:21
Alignment explanation
Indices: 36434--36518 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 21
36424 ACAACTGTAG
*
36434 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
36455 A-AATCTCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
* * ** *
36475 ACTATCTCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
36496 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
36517 AC
1 AC
36519 ACGAATTTGC
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 14 0.28
21 36 0.72
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:39116 original size:178 final size:178
Alignment explanation
Indices: 38817--39174 Score: 684
Period size: 178 Copynumber: 2.0 Consensus size: 178
38807 TTGTGAGCGG
38817 AAAAATAGACGAGCGTCGAACCAAAACTTGTAATAACAAAGAACAGCGAGCAATATAAAAGAACC
1 AAAAATAGACGAGCGTCGAACCAAAACTTGTAATAACAAAGAACAGCGAGCAATATAAAAGAACC
38882 AAGTTTTTGCTGAAAATGTTATGCCCTTATTTGAGTATATTTAAAAATTAATTCTTAGACTTGTC
66 AAGTTTTTGCTGAAAATGTTATGCCCTTATTTGAGTATATTTAAAAATTAATTCTTAGACTTGTC
38947 GTTTTCGATGGTTAAATCTAAGAGTTTTAAATAACAAGACGTTCGATA
131 GTTTTCGATGGTTAAATCTAAGAGTTTTAAATAACAAGACGTTCGATA
38995 AAAAATAGACGAGCGTCGAACCAAAACTTGTAATAAC-AAGAACAGCGAGCAATATAAAAGAACC
1 AAAAATAGACGAGCGTCGAACCAAAACTTGTAATAACAAAGAACAGCGAGCAATATAAAAGAACC
39059 AAG-TTTTGCTGAAAATGTTATGCCCTTATTTGAGTATATTTAAAAACATTAATTCTTAGACTTG
66 AAGTTTTTGCTGAAAATGTTATGCCCTTATTTGAGTATATTT-AAAA-ATTAATTCTTAGACTTG
39123 TCGTTTTCGATGGTTAAATCTAAGAGTTTTAAATAACAAGACGTTCGATA
129 TCGTTTTCGATGGTTAAATCTAAGAGTTTTAAATAACAAGACGTTCGATA
39173 AA
1 AA
39175 CTGTTCGTGA
Statistics
Matches: 178, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
176 38 0.21
177 34 0.19
178 106 0.60
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (178 bp):
AAAAATAGACGAGCGTCGAACCAAAACTTGTAATAACAAAGAACAGCGAGCAATATAAAAGAACC
AAGTTTTTGCTGAAAATGTTATGCCCTTATTTGAGTATATTTAAAAATTAATTCTTAGACTTGTC
GTTTTCGATGGTTAAATCTAAGAGTTTTAAATAACAAGACGTTCGATA
Found at i:43825 original size:14 final size:15
Alignment explanation
Indices: 43806--43834 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43796 CAAAAATCTC
43806 CCCTAAACC-CTAAA
1 CCCTAAACCACTAAA
43820 CCCTAAACCACTAAA
1 CCCTAAACCACTAAA
43835 AGCAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (15 bp):
CCCTAAACCACTAAA
Found at i:46903 original size:17 final size:16
Alignment explanation
Indices: 46877--46908 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
46867 AAAAAGCATT
46877 TTATGTATCGATACCG
1 TTATGTATCGATACCG
46893 TTATGGTATCGATACC
1 TTAT-GTATCGATACC
46909 ATATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
TTATGTATCGATACCG
Found at i:50947 original size:21 final size:21
Alignment explanation
Indices: 50904--50957 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
50894 ATATACTCAC
* *
50904 TAATTTTTCAAATTGGCCATT
1 TAATATTTCAAATTAGCCATT
* *
50925 TAATATTTCAAATTATCCTTT
1 TAATATTTCAAATTAGCCATT
50946 TAA-ATTTTCAAA
1 TAATA-TTTCAAA
50958 CTGGACATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (21 bp):
TAATATTTCAAATTAGCCATT
Found at i:51951 original size:16 final size:16
Alignment explanation
Indices: 51930--51961 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51920 ACAATTTAAT
*
51930 TTATTGGTGCTCGTCG
1 TTATTGGCGCTCGTCG
51946 TTATTGGCGCTCGTCG
1 TTATTGGCGCTCGTCG
51962 AGCGCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.22, G:0.31, T:0.41
Consensus pattern (16 bp):
TTATTGGCGCTCGTCG
Found at i:52191 original size:21 final size:21
Alignment explanation
Indices: 52165--52207 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
52155 AAGAATAATA
52165 TTTTTTATCGTTAAGACGACT
1 TTTTTTATCGTTAAGACGACT
52186 TTTTTTATCGTTAAGACGACT
1 TTTTTTATCGTTAAGACGACT
52207 T
1 T
52208 ATATTGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (21 bp):
TTTTTTATCGTTAAGACGACT
Found at i:66286 original size:21 final size:21
Alignment explanation
Indices: 66262--66313 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
66252 CGGAAATATT
** *
66262 CATTTTAGGTAGCGAAATTAA
1 CATTTTAGGTAGAAAAAATAA
66283 CATTTT-GGTAGAAAAAATAA
1 CATTTTAGGTAGAAAAAATAA
66303 CATTTTAGGTA
1 CATTTTAGGTA
66314 ACACTCTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (21 bp):
CATTTTAGGTAGAAAAAATAA
Done.