Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003753.1 Hibiscus syriacus cultivar Beakdansim tig00008032_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: 97658
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:754 original size:41 final size:40
Alignment explanation
Indices: 707--806 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 40
697 ATTCGCGTTG
707 CATTTCGCTTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGC-TTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
748 CATTTCGCGTTGTGATAGTTGAAAATCGCGTTGTGATTTTC
1 CATTTCGC-TTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
789 CAAATTCG-TTGCGATAGT
1 C-ATTTCGCTTGCGATAGT
807 CTACAGTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
40 9 0.17
41 39 0.74
42 5 0.09
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (40 bp):
CATTTCGCTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:784 original size:21 final size:21
Alignment explanation
Indices: 711--780 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
701 GCGTTGCATT
*
711 TCGCTTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
732 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
752 TCGCGTTGTGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
773 TCGCGTTG
1 TCGCGTTG
781 TGATTTTCCA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1588 original size:19 final size:19
Alignment explanation
Indices: 1564--1651 Score: 95
Period size: 19 Copynumber: 4.5 Consensus size: 19
1554 CAACGAATTT
1564 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
1583 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
*
1605 TCGCAACAAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
*
1624 TCGCAACGAATTTGAAAAA
1 TCGCAACGAATTTGGAAAA
1643 TCGCAACGA
1 TCGCAACGA
1652 CAACTGTAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
19 39 0.71
20 2 0.04
21 2 0.04
22 12 0.22
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:1686 original size:42 final size:41
Alignment explanation
Indices: 1636--1720 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
1626 GCAACGAATT
1636 TGAAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGAAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * * *
1678 TGAAAAATCGCAATGCGATTTTCAACTATCGCAACGCGAAA
1 TGAAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
1719 TG
1 TG
1721 CAATGCGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 23 0.61
42 15 0.39
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (41 bp):
TGAAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:2524 original size:42 final size:42
Alignment explanation
Indices: 2477--2599 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
2467 ATGAATCGGG
* **
2477 CTCTTGAATGGTAGGAGGGACCTCTTCAATTATGACAGGGGC
1 CTCTTGAACGGTAGGAGGGACCTCTTCAAGGATGACAGGGGC
* * * *
2519 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTAGGA-GGGACCTCTTCAAGGATGACAGGGGC
* * *
2561 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGGTAGGAG-GGACCTCTTCAAGGATGACAGG
2600 TGAGTCGGTC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 61 0.92
43 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTAGGAGGGACCTCTTCAAGGATGACAGGGGC
Found at i:2537 original size:21 final size:21
Alignment explanation
Indices: 2513--2591 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
2503 CAATTATGAC
2513 AGGGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGGTGGG
* * **
2534 AGGGGACTCTTG-AGGGATGAT
1 AGGGGCCTCTTGAACGG-TGGG
* *
2555 AGGGGCCTCTTGAACGATAGG
1 AGGGGCCTCTTGAACGGTGGG
*
2576 AGAGGCCTCTTGAACG
1 AGGGGCCTCTTGAACG
2592 ATGACAGGTG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 3 0.07
21 40 0.89
22 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.41, T:0.20
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGGTGGG
Found at i:3097 original size:20 final size:19
Alignment explanation
Indices: 3072--3114 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3062 AATAGTTTCT
3072 GAAACTTAAAATCGCAACAC
1 GAAAC-TAAAATCGCAACAC
* *
3092 GAAACTCAAATCGCAACGC
1 GAAACTAAAATCGCAACAC
3111 GAAA
1 GAAA
3115 ATGACTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.49, C:0.26, G:0.14, T:0.12
Consensus pattern (19 bp):
GAAACTAAAATCGCAACAC
Found at i:3126 original size:20 final size:20
Alignment explanation
Indices: 3101--3167 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
3091 CGAAACTCAA
3101 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
3121 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
3141 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3161 ATCGCAA
1 ATCGCAA
3168 TGGGATAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3207 original size:19 final size:20
Alignment explanation
Indices: 3174--3212 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3164 GCAATGGGAT
*
3174 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
*
3193 AATCGCAACGTGAAACTAAA
1 AATCGCAACGCGAAACTAAA
3213 TTTATGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:3309 original size:20 final size:20
Alignment explanation
Indices: 3284--3350 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 20
3274 GCGATTATCC
*
3284 CGTTGCGATAGTCAACTTCG
1 CGTTGCGATAGTCAATTTCG
3304 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAATTTCG
* *
3323 CGTTACGATA-TCATTTTCG
1 CGTTGCGATAGTCAATTTCG
3342 CGTTGCGAT
1 CGTTGCGAT
3351 TTAAGTTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 2 0.05
19 27 0.64
20 13 0.31
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:5269 original size:20 final size:20
Alignment explanation
Indices: 5244--5287 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5234 AAAACTTAAA
5244 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
5264 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
5284 ATCG
1 ATCG
5288 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:5545 original size:26 final size:26
Alignment explanation
Indices: 5507--5562 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
5497 AATTACCAGT
5507 AAACTTATCATCAATTTCAATATGAA
1 AAACTTATCATCAATTTCAATATGAA
*
5533 AAACTTATTATCAATTTCAATATGAA
1 AAACTTATCATCAATTTCAATATGAA
5559 AAAC
1 AAAC
5563 CTAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (26 bp):
AAACTTATCATCAATTTCAATATGAA
Found at i:5706 original size:22 final size:22
Alignment explanation
Indices: 5679--5736 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
5669 GATGGAGATA
5679 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
5701 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
5723 GACGGATGTCGCCG
1 GACGGATTTCGCCG
5737 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:5898 original size:21 final size:21
Alignment explanation
Indices: 5880--5928 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5870 GAAAATCGTA
*
5880 TTGCGATTTTGTATTATCGCG
1 TTGCGATTATGTATTATCGCG
*
5901 TTGCGATTATGTTTTATCGCG
1 TTGCGATTATGTATTATCGCG
5922 TTGCGAT
1 TTGCGAT
5929 AGTCAGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.47
Consensus pattern (21 bp):
TTGCGATTATGTATTATCGCG
Found at i:5987 original size:20 final size:20
Alignment explanation
Indices: 5916--5987 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
5906 ATTATGTTTT
*
5916 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
* * *
5936 ATCGTGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAAA
* * *
5956 TTCGCATAGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
5976 ATCGCGTTGCGA
1 ATCGCGTTGCGA
5988 ATCTGGAAAC
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:8168 original size:15 final size:15
Alignment explanation
Indices: 8127--8168 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
8117 CTAAGAAAGT
8127 ATATTATTTTCAAATA
1 ATATTATTTT-AAATA
*
8143 AT-TTGAATTTAAATA
1 ATATT-ATTTTAAATA
8158 ATATTATTTTA
1 ATATTATTTTA
8169 TAAAATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTATTTTAAATA
Found at i:8712 original size:28 final size:27
Alignment explanation
Indices: 8681--8734 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
8671 TAAAAAAATG
* *
8681 TATTATTGAATATATTAGTATTTTTTAA
1 TATTATTG-ATAAAATAGTATTTTTTAA
* *
8709 TATTTTTGATAAAATATTATTTTTTA
1 TATTATTGATAAAATAGTATTTTTTA
8735 TCGGAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (27 bp):
TATTATTGATAAAATAGTATTTTTTAA
Found at i:15367 original size:2 final size:2
Alignment explanation
Indices: 15362--15391 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15352 AAAAAATTAG
15362 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
15392 GAAAGTGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15604 original size:21 final size:21
Alignment explanation
Indices: 15578--15622 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
15568 TTTTTTTTAA
15578 TTTTTGTGAGAACAAATGAAT
1 TTTTTGTGAGAACAAATGAAT
15599 TTTTTGTGAGAACAAATGAAT
1 TTTTTGTGAGAACAAATGAAT
15620 TTT
1 TTT
15623 AAGGATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (21 bp):
TTTTTGTGAGAACAAATGAAT
Found at i:17611 original size:2 final size:2
Alignment explanation
Indices: 17604--17666 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
17594 GGTAAAATAC
17604 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
17646 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
17667 ACCTATTAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20483 original size:17 final size:17
Alignment explanation
Indices: 20442--20484 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
20432 CAAAAATGTA
*
20442 ATAATAATATTAATGAT
1 ATAATAATAATAATGAT
*
20459 ATACTAATAATAAT-AT
1 ATAATAATAATAATGAT
20475 ATAATTAATA
1 ATAA-TAATA
20485 TTTATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAATAATAATAATGAT
Found at i:21722 original size:18 final size:21
Alignment explanation
Indices: 21677--21725 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
21667 TCCCTATTGG
21677 GAGTATCGATACTCTACCATC
1 GAGTATCGATACTCTACCATC
*
21698 G-GTATCGATACT-T-TCAT-
1 GAGTATCGATACTCTACCATC
21715 GAGTATCGATA
1 GAGTATCGATA
21726 TCAAAATAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 1 0.04
20 11 0.42
21 1 0.04
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (21 bp):
GAGTATCGATACTCTACCATC
Found at i:21782 original size:20 final size:20
Alignment explanation
Indices: 21757--21857 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 20
21747 TGATCAAGTC
21757 CCCGAGTATCGATACTAGGT
1 CCCGAGTATCGATACTAGGT
*
21777 CCCGAGTATCGATACCAAAATAGCT
1 CCCGAGTATCGATA-C----TAGGT
** * * *
21802 TACTAGAATCTGAT-C-AAGT
1 CCCGAGTATC-GATACTAGGT
21821 CCCCGAGTATCGATACTAGGT
1 C-CCGAGTATCGATACTAGGT
21842 CCCGAGTATCGATACT
1 CCCGAGTATCGATACT
21858 CATTGATGTG
Statistics
Matches: 60, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
19 5 0.08
20 36 0.60
21 5 0.08
24 1 0.02
25 10 0.17
26 3 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (20 bp):
CCCGAGTATCGATACTAGGT
Found at i:21801 original size:65 final size:65
Alignment explanation
Indices: 21715--21856 Score: 275
Period size: 65 Copynumber: 2.2 Consensus size: 65
21705 ATACTTTCAT
*
21715 GAGTATCGATATCAAAATAGCTTACTAGAATCTGATCAAGTCCCCGAGTATCGATACTAGGTCCC
1 GAGTATCGATACCAAAATAGCTTACTAGAATCTGATCAAGTCCCCGAGTATCGATACTAGGTCCC
21780 GAGTATCGATACCAAAATAGCTTACTAGAATCTGATCAAGTCCCCGAGTATCGATACTAGGTCCC
1 GAGTATCGATACCAAAATAGCTTACTAGAATCTGATCAAGTCCCCGAGTATCGATACTAGGTCCC
21845 GAGTATCGATAC
1 GAGTATCGATAC
21857 TCATTGATGT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 76 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (65 bp):
GAGTATCGATACCAAAATAGCTTACTAGAATCTGATCAAGTCCCCGAGTATCGATACTAGGTCCC
Found at i:27152 original size:16 final size:16
Alignment explanation
Indices: 27131--27336 Score: 87
Period size: 16 Copynumber: 12.8 Consensus size: 16
27121 AATAAGATTT
27131 TTACTTTCGGTTCGGG
1 TTACTTTCGGTTCGGG
27147 TTACTTTCGGTTCGGG
1 TTACTTTCGGTTCGGG
* *
27163 TTAATTTTC-GTTCGGA
1 TT-ACTTTCGGTTCGGG
* * *
27179 TTGCTTTCAGG-TCCGA
1 TTACTTTC-GGTTCGGG
** **
27195 TTAAATTCACTTCGGG
1 TTACTTTCGGTTCGGG
* ***
27211 TTACTTTCGGATCTAA
1 TTACTTTCGGTTCGGG
* *
27227 TTAAAATTT-GGTTCGGA
1 TT--ACTTTCGGTTCGGG
* *
27244 TTTCTTTC-GATCTGGG
1 TTACTTTCGGTTC-GGG
**
27260 TTAAATTCGGTTCGGG
1 TTACTTTCGGTTCGGG
* **
27276 TTTGCTTTCGGTTCATG
1 -TTACTTTCGGTTCGGG
* *
27293 TTGCTTTCAGTTCGGG
1 TTACTTTCGGTTCGGG
* *
27309 TTAATTTCGGTTCAGG
1 TTACTTTCGGTTCGGG
*
27325 TTGCTTTCGGTT
1 TTACTTTCGGTT
27337 TCGCTAAATT
Statistics
Matches: 134, Mismatches: 46, Indels: 20
0.67 0.23 0.10
Matches are distributed among these distances:
15 10 0.07
16 93 0.69
17 27 0.20
18 4 0.03
ACGTcount: A:0.14, C:0.17, G:0.25, T:0.45
Consensus pattern (16 bp):
TTACTTTCGGTTCGGG
Found at i:27347 original size:32 final size:32
Alignment explanation
Indices: 27281--27347 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
27271 TCGGGTTTGC
* * *
27281 TTTCGGTTCATGTTGCTTTCAGTTCGGGTTAA
1 TTTCGGTTCAGGTTGCTTTCAGTTCGGCTAAA
*
27313 TTTCGGTTCAGGTTGCTTTCGGTTTC-GCTAAA
1 TTTCGGTTCAGGTTGCTTTCAG-TTCGGCTAAA
27345 TTT
1 TTT
27348 TGGATCGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 27 0.90
33 3 0.10
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (32 bp):
TTTCGGTTCAGGTTGCTTTCAGTTCGGCTAAA
Found at i:36698 original size:20 final size:19
Alignment explanation
Indices: 36660--36704 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
36650 TAGTTTTTAC
36660 TAAATATTTAAATAATTAT
1 TAAATATTTAAATAATTAT
* **
36679 TCAATATATTAAATTGTTAT
1 TAAATAT-TTAAATAATTAT
36699 TAAATA
1 TAAATA
36705 ATTGTTGTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATATTTAAATAATTAT
Found at i:36762 original size:11 final size:11
Alignment explanation
Indices: 36733--36773 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
36723 ATAATCTTAA
36733 AATTTAAT-A-
1 AATTTAATAAT
36742 AATTTAATAAT
1 AATTTAATAAT
* *
36753 TATTTTATAAT
1 AATTTAATAAT
36764 AATTTAATAA
1 AATTTAATAA
36774 AGTTAATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 8 0.31
10 1 0.04
11 17 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:37207 original size:5 final size:5
Alignment explanation
Indices: 37197--37224 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
37187 AAATCAAACT
37197 ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATA
37225 GTTAAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:42437 original size:2 final size:2
Alignment explanation
Indices: 42430--42457 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42420 GCATTGAGAT
42430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42458 ATTCGAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51119 original size:14 final size:14
Alignment explanation
Indices: 51100--51133 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
51090 ATCATATCAA
51100 TCATATAATACAAT
1 TCATATAATACAAT
51114 TCATATAATACAAT
1 TCATATAATACAAT
51128 TCATAT
1 TCATAT
51134 CACAAAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
TCATATAATACAAT
Found at i:52165 original size:64 final size:63
Alignment explanation
Indices: 52090--52230 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
52080 TCTTTAACAT
* * *
52090 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
52153 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
52217 GTGCATCGATGCAC
1 GTGCATCGATGCAC
52231 ATTGAATATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:54223 original size:123 final size:123
Alignment explanation
Indices: 54004--54376 Score: 665
Period size: 123 Copynumber: 3.0 Consensus size: 123
53994 ATACAACATT
* * * * * *
54004 GTTCAGTTTTGGCAGTAAAACCGGCTGTGATGGGCTAAAATTTGTGTCGCCACAGATTGGCGCGA
1 GTTCAGTTTCGACAGTAGAACCGGCTGTGATGGGCTGAAATTTGCGTCGCCACAGATTGGCACGA
* * *
54069 ATAGTTACCTGGGTTAGCCCAGTGCTAACATTCCCCATTTGATTTTCCAGCTCCAGCA
66 ATAGTTGCCTGGGTTAGCCCAGTGGTAACATTCCCCAATTGATTTTCCAGCTCCAGCA
54127 GTTCAGTTTCGACAGTAGAACCGGCTGTGATGGGCTGAAATTTGCGTCGCCACAGATTGGCACGA
1 GTTCAGTTTCGACAGTAGAACCGGCTGTGATGGGCTGAAATTTGCGTCGCCACAGATTGGCACGA
54192 ATAGTTGCCTGGGTTAGCCCAGTGGTAACATTCCCCAATTGATTTTCCAGCTCCAGCA
66 ATAGTTGCCTGGGTTAGCCCAGTGGTAACATTCCCCAATTGATTTTCCAGCTCCAGCA
54250 GTTCAGTTTCGACAGTAGAACCGGCTGTGATGGGCTGAAATTTGCGTCGCCACAGATTGGCACGA
1 GTTCAGTTTCGACAGTAGAACCGGCTGTGATGGGCTGAAATTTGCGTCGCCACAGATTGGCACGA
54315 ATAGTTGCCTGGGTTAGCCCAGTGGTAACATTCCCCAATTGATTTTCCAGCTCCAGCA
66 ATAGTTGCCTGGGTTAGCCCAGTGGTAACATTCCCCAATTGATTTTCCAGCTCCAGCA
54373 GTTC
1 GTTC
54377 CTAAACCCAA
Statistics
Matches: 241, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 241 1.00
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (123 bp):
GTTCAGTTTCGACAGTAGAACCGGCTGTGATGGGCTGAAATTTGCGTCGCCACAGATTGGCACGA
ATAGTTGCCTGGGTTAGCCCAGTGGTAACATTCCCCAATTGATTTTCCAGCTCCAGCA
Found at i:56660 original size:20 final size:21
Alignment explanation
Indices: 56637--56675 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56627 ATGTCTTTTT
56637 TTTC-TTTTTCTTTCGAACAA
1 TTTCTTTTTTCTTTCGAACAA
*
56657 TTTCTTTTTTTTTTCGAAC
1 TTTCTTTTTTCTTTCGAAC
56676 TGTTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.18, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTCTTTTTTCTTTCGAACAA
Found at i:63454 original size:15 final size:15
Alignment explanation
Indices: 63434--63465 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
63424 TGGCAGATCC
63434 AAATCCAGAACGGGA
1 AAATCCAGAACGGGA
63449 AAATCCAGAACGGGA
1 AAATCCAGAACGGGA
63464 AA
1 AA
63466 GAAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCCAGAACGGGA
Found at i:67192 original size:33 final size:33
Alignment explanation
Indices: 67122--67194 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
67112 TTCTGCTGCT
* * *
67122 GCTGCTGCAAATGACTAGGGATTCCTCCAGTAA
1 GCTGCTGCAAATGACTAGAGACTCCTACAGTAA
* * **
67155 GCTGCTGCAACTGATTAGAGACTCCTACAGTTG
1 GCTGCTGCAAATGACTAGAGACTCCTACAGTAA
67188 GCTGCTG
1 GCTGCTG
67195 TTGGTGGTGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (33 bp):
GCTGCTGCAAATGACTAGAGACTCCTACAGTAA
Found at i:89165 original size:2 final size:2
Alignment explanation
Indices: 89158--89190 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
89148 AAGTACTCAA
89158 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
89191 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:97181 original size:9 final size:9
Alignment explanation
Indices: 97163--97194 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
97153 GATGTTAGTA
*
97163 TTTTCGCAG
1 TTTTCACAG
97172 TTTTCACAG
1 TTTTCACAG
97181 TTTTCACAG
1 TTTTCACAG
97190 TTTTC
1 TTTTC
97195 TATGAGCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (9 bp):
TTTTCACAG
Done.