Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004020.1 Hibiscus syriacus cultivar Beakdansim tig00008781_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: 70976
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6385 original size:21 final size:24
Alignment explanation
Indices: 6331--6380 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
6321 ATAAACATCA
*
6331 AATACAATAAATAAAATTATTTATT
1 AATAAAAT-AATAAAATTATTTATT
*
6356 AATAAAATAATAATATTATTT-TT
1 AATAAAATAATAAAATTATTTATT
6379 AA
1 AA
6381 AAATATTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATAAAATAATAAAATTATTTATT
Found at i:6489 original size:30 final size:29
Alignment explanation
Indices: 6433--6507 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
6423 ATTCTTAAAT
*
6433 TATTATATAT-ATAATTTTATAAATAAAAA
1 TATTATAAATAAT-ATTTTATAAATAAAAA
*
6462 TATTA-AAATAATATTTTATTAAAATAAAAT
1 TATTATAAATAATATTTTA-T-AAATAAAAA
*
6492 TATTATAAATTATATT
1 TATTATAAATAATATT
6508 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 9 0.23
29 8 0.21
30 13 0.33
31 9 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TATTATAAATAATATTTTATAAATAAAAA
Found at i:6500 original size:16 final size:16
Alignment explanation
Indices: 6429--6500 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 16
6419 TATTATTCTT
*
6429 AAATTATTAT-ATATA
1 AAATTATTATAAAATA
*
6444 TAATT-TTAT-AAATA
1 AAATTATTATAAAATA
*
6458 AAAATA-T-TAAAATA
1 AAATTATTATAAAATA
*
6472 ATATT-TTATTAAAATA
1 AAATTATTA-TAAAATA
6488 AAATTATTATAAA
1 AAATTATTATAAA
6501 TTATATTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
13 1 0.02
14 21 0.48
15 4 0.09
16 15 0.34
17 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTATTATAAAATA
Found at i:6964 original size:18 final size:17
Alignment explanation
Indices: 6941--6974 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
6931 TTTATTAAAA
6941 TAATATTAAATAATATAT
1 TAATATTAAA-AATATAT
6959 TAATATTAAAAATATA
1 TAATATTAAAAATATA
6975 AAGTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATTAAAAATATAT
Found at i:8191 original size:15 final size:15
Alignment explanation
Indices: 8171--8202 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8161 CGAAACATAC
*
8171 ATATATATATGTATT
1 ATATATATATATATT
8186 ATATATATATATATT
1 ATATATATATATATT
8201 AT
1 AT
8203 GTATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:9559 original size:15 final size:15
Alignment explanation
Indices: 9537--9632 Score: 67
Period size: 15 Copynumber: 6.4 Consensus size: 15
9527 TATTTTTACC
9537 TTATTTGTTTTATTT
1 TTATTTGTTTTATTT
9552 TT-TGTTGTTGTT-TTT
1 TTAT-TTGTT-TTATTT
9567 TTATTTGTTTTA-TT
1 TTATTTGTTTTATTT
* **
9581 TAATTCCATTTT-TTT
1 TTATT-TGTTTTATTT
*
9596 ATT-GTTGTTTTATTT
1 -TTATTTGTTTTATTT
*
9611 TTATTTTGTTTTATCT
1 TTA-TTTGTTTTATTT
9627 TTATTT
1 TTATTT
9633 ATGTTCTCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 15 0.24
15 30 0.48
16 17 0.27
ACGTcount: A:0.12, C:0.03, G:0.08, T:0.76
Consensus pattern (15 bp):
TTATTTGTTTTATTT
Found at i:9564 original size:18 final size:18
Alignment explanation
Indices: 9541--9575 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9531 TTTACCTTAT
9541 TTGTTTTATTT-TTTGTTG
1 TTGTTTT-TTTATTTGTTG
9559 TTGTTTTTTTATTTGTT
1 TTGTTTTTTTATTTGTT
9576 TTATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.06, C:0.00, G:0.14, T:0.80
Consensus pattern (18 bp):
TTGTTTTTTTATTTGTTG
Found at i:9632 original size:16 final size:16
Alignment explanation
Indices: 9593--9637 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
9583 ATTCCATTTT
*
9593 TTTATTGTTGTTTTATT
1 TTTATT-TTGTTTTATC
9610 TTTATTTTGTTTTATC
1 TTTATTTTGTTTTATC
9626 TTTATTTATGTT
1 TTTATTT-TGTT
9638 CTCATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTATTTTGTTTTATC
Found at i:9646 original size:17 final size:16
Alignment explanation
Indices: 9609--9650 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
9599 GTTGTTTTAT
*
9609 TTTTATTT-TGTTTTA
1 TTTTATTTATGTTTCA
9624 TCTTTATTTATGTTCTCA
1 T-TTTATTTATGTT-TCA
9642 TTTTATTTA
1 TTTTATTTA
9651 ATTTGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 1 0.04
16 7 0.30
17 12 0.52
18 3 0.13
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTTATTTATGTTTCA
Found at i:13526 original size:15 final size:15
Alignment explanation
Indices: 13506--13536 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13496 AAGACCAGAT
13506 GAATATGGTCAAAGG
1 GAATATGGTCAAAGG
13521 GAATATGGTCAAAGG
1 GAATATGGTCAAAGG
13536 G
1 G
13537 GACCATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.35, T:0.19
Consensus pattern (15 bp):
GAATATGGTCAAAGG
Found at i:14577 original size:54 final size:54
Alignment explanation
Indices: 14495--14602 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
14485 TTGGATCCAT
14495 TTCAACTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
1 TTCAACTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
*
14549 TTCAATTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
1 TTCAACTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
14603 CTATAATTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (54 bp):
TTCAACTCTAGAACACCGAACGCTGCCCAGATCCCTTTCCTAATCATCAGGAGA
Found at i:22103 original size:2 final size:2
Alignment explanation
Indices: 22096--22137 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
22086 TGACCGAATC
*
22096 AT AT AT AT AT AT AT AT AT AT AT GT AT -T AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22136 AT
1 AT
22138 GTATTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:23459 original size:2 final size:2
Alignment explanation
Indices: 23447--23507 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
23437 ACCATTGAAT
* *
23447 TA TA CA TA TA TA TA TA TA TG 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 TA TA TA TA TA TA TA
23489 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
23508 TTTTACCTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23526 original size:18 final size:18
Alignment explanation
Indices: 23505--23541 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
23495 TATATATATA
23505 TATTTTTACCTTATTTGT
1 TATTTTTACCTTATTTGT
23523 TATTTTTACCTTATTTGT
1 TATTTTTACCTTATTTGT
23541 T
1 T
23542 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (18 bp):
TATTTTTACCTTATTTGT
Found at i:23547 original size:9 final size:9
Alignment explanation
Indices: 23533--23602 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
23523 TATTTTTACC
23533 TTATTTGTT
1 TTATTTGTT
23542 TTATTT-TT
1 TTATTTGTT
*
23550 TT-TTGTTTT
1 TTATT-TGTT
23559 TTATTTGTT
1 TTATTTGTT
*
23568 TTATTTAATT
1 TTATTT-GTT
*
23578 TAATTT-TT
1 TTATTTGTT
23586 TTATTTTTGTT
1 TTA--TTTGTT
23597 TTATTT
1 TTATTT
23603 TTATTTCGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
7 2 0.04
8 9 0.18
9 22 0.44
10 12 0.24
11 5 0.10
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (9 bp):
TTATTTGTT
Found at i:23566 original size:44 final size:44
Alignment explanation
Indices: 23515--23616 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
23505 TATTTTTACC
* *
23515 TTATTTGTTATT-TTTACCTT-ATTTGTTTTATTTTT-TTTTGTTTT
1 TTATTTGTT-TTATTTAACTTAATTT-TTTTATTTTTGTTTT-ATTT
*
23559 TTATTTGTTTTATTTAATTTAATTTTTTTATTTTTGTTTTATTT
1 TTATTTGTTTTATTTAACTTAATTTTTTTATTTTTGTTTTATTT
23603 TTATTTCGTTTTAT
1 TTATTT-GTTTTAT
23617 CTTTATTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
43 2 0.04
44 34 0.67
45 15 0.29
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (44 bp):
TTATTTGTTTTATTTAACTTAATTTTTTTATTTTTGTTTTATTT
Found at i:29809 original size:117 final size:117
Alignment explanation
Indices: 29603--29837 Score: 470
Period size: 117 Copynumber: 2.0 Consensus size: 117
29593 TCTGATCCCT
29603 TTGTTCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGC
1 TTGTTCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGC
29668 TTGCCCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTA
66 TTGCCCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTA
29720 TTGTTCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGC
1 TTGTTCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGC
29785 TTGCCCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTA
66 TTGCCCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTA
29837 T
1 T
29838 GTACCAAATG
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (117 bp):
TTGTTCACCTCACGTGCACGACCATATACACTGTTATACATGTTCAAGCTATATATCAAGATAGC
TTGCCCTGATCCCTTCGAACTACATTTTGCAGAGGGGTGGGCAAGCTAAGTA
Found at i:31236 original size:17 final size:17
Alignment explanation
Indices: 31185--31237 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
31175 AATATGATAA
*
31185 AAAAT-AATTATTTATGT
1 AAAATAAATTA-TTATTT
**
31202 AAAATCAAATTAAGATTT
1 AAAAT-AAATTATTATTT
31220 AAAATAAATTATTATTT
1 AAAATAAATTATTATTT
31237 A
1 A
31238 TTATATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 16 0.55
18 8 0.28
19 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
AAAATAAATTATTATTT
Found at i:32683 original size:3 final size:3
Alignment explanation
Indices: 32657--32754 Score: 119
Period size: 3 Copynumber: 31.7 Consensus size: 3
32647 TTGTAATATT
* *
32657 TAA TAAA TAA TATA TAA TAT TAA TAA TAG TAA TAA TAAA TAA -AA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
32704 TAA TAA TAA TAA TATA TAA -AA TAA TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
32750 TAA TA
1 TAA TA
32755 GAAAATGAAG
Statistics
Matches: 84, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
2 4 0.05
3 65 0.77
4 15 0.18
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:33133 original size:121 final size:123
Alignment explanation
Indices: 32977--33286 Score: 453
Period size: 124 Copynumber: 2.5 Consensus size: 123
32967 ATGTAATTTG
* * ** *
32977 GAAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 GAAAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* *
33042 TTATGAAC-TT-TCTGGAAAAGTTGATGCTGATCTATCTCCTTTTATGATAGAGTCAT
66 TTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAATCAT
* *
33098 GAAAAAGGTTGAACAAAATTTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATGGGTTCTTCTC
1 GAAAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCT-CTTCAGATGAGTTCTTCTC
* * *
33163 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATTTCCTTCTGTGATAGAATTAT
65 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAATCAT
* **
33222 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GAAAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
33287 TATCTGGAAA
Statistics
Matches: 168, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
121 40 0.24
122 26 0.15
123 2 0.01
124 99 0.59
125 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
GAAAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAATCAT
Found at i:33346 original size:102 final size:107
Alignment explanation
Indices: 33224--33718 Score: 699
Period size: 113 Copynumber: 4.6 Consensus size: 107
33214 AGAATTATGC
* *
33224 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC-T
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
33288 -A-T-CTGGAAATGTTGATCCATAGAATGATGAATTCAAG-A
66 AACTCCTGGAAATGTTGATCCATAGAATGATGAATTCAAGCG
*
33326 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC-T
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
33390 -A-T-CTGGAAATGTTGATCCATAGAATGATGAATTCAAGC-
66 AACTCCTGGAAATGTTGATCCATAGAATGATGAATTCAAGCG
33428 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC--
* * *
33493 TATGAACTCGACCTGGTAATGTTGATCCATCGAATTATGAATTCAAGCG
64 -AT-AACT---CCTGGAAATGTTGATCCATAGAATGATGAATTCAAGCG
33542 AAAAA-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC--
* *
33606 TATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCG
64 -AT-AACT---CCTGGAAATGTTGATCCATAGAATGATGAATTCAAGCG
33655 AAAAA-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
33719 TATGAACTCG
Statistics
Matches: 372, Mismatches: 8, Indels: 18
0.93 0.02 0.05
Matches are distributed among these distances:
102 160 0.43
106 1 0.00
108 1 0.00
109 1 0.00
110 2 0.01
113 202 0.54
114 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (107 bp):
AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
AACTCCTGGAAATGTTGATCCATAGAATGATGAATTCAAGCG
Found at i:33595 original size:113 final size:113
Alignment explanation
Indices: 33392--33757 Score: 662
Period size: 113 Copynumber: 3.2 Consensus size: 113
33382 TCTTCTCTAT
* *
33392 CTGGAAATGTTGATCCATAGAATGATGAATTCAAGC-AAAAAGTTGAACAAGTTCTTCTCATTAT
1 CTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAA-TTGAACAAGTTCTTCTCATTAT
33456 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
65 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
*
33505 CTGGTAATGTTGATCCATCGAATTATGAATTCAAGCGAAAAATTGAACAAGTTCTTCTCATTATG
1 CTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAATTGAACAAGTTCTTCTCATTATG
33570 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
33618 CTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAATTGAACAAGTTCTTCTCATTATG
1 CTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAATTGAACAAGTTCTTCTCATTATG
33683 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
* * *
33731 ATGGTAATGCTGATCCATTGAATGATG
1 CTGGTAATGTTGATCCATCGAATGATG
33758 GATTTGAACT
Statistics
Matches: 245, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
113 240 0.98
114 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (113 bp):
CTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAATTGAACAAGTTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
Found at i:35281 original size:20 final size:17
Alignment explanation
Indices: 35265--35347 Score: 107
Period size: 17 Copynumber: 4.8 Consensus size: 17
35255 TTTTTTTCTC
35265 TCTTTTTTTCTTCTTTTT
1 TCTTTTTTTCTT-TTTTT
*
35283 TCTTTTTTT-TTCTTTT
1 TCTTTTTTTCTTTTTTT
35299 TCTTTTTTTTCTTTTTCTT
1 TC-TTTTTTTCTTTTT-TT
*
35318 T-TCTTTTTCTTTTTTT
1 TCTTTTTTTCTTTTTTT
35334 TCTTTTTTTCTTTT
1 TCTTTTTTTCTTTT
35348 CATTTTTTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
16 9 0.16
17 32 0.56
18 13 0.23
19 3 0.05
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TCTTTTTTTCTTTTTTT
Found at i:35305 original size:32 final size:30
Alignment explanation
Indices: 35255--35347 Score: 111
Period size: 32 Copynumber: 3.1 Consensus size: 30
35245 TCTTGACCCC
*
35255 TTTTTTTCTCTCTTTTTTTCTTCTTTTTTCTT
1 TTTTTTTCT-TTTTTTTTTCTTC-TTTTTCTT
*
35287 TTTTTTTCTTTTTCTTTTTTTTCTTTTTCTT
1 TTTTTTTCTTTTT-TTTTTCTTCTTTTTCTT
35318 TTCTTTTTC--TTTTTTTTCTT-TTTTTCTT
1 TT-TTTTTCTTTTTTTTTTCTTCTTTTTCTT
35346 TT
1 TT
35348 CATTTTTTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
28 10 0.18
29 7 0.12
30 3 0.05
31 13 0.23
32 23 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (30 bp):
TTTTTTTCTTTTTTTTTTCTTCTTTTTCTT
Found at i:35307 original size:26 final size:25
Alignment explanation
Indices: 35269--35342 Score: 130
Period size: 26 Copynumber: 2.9 Consensus size: 25
35259 TTTCTCTCTT
35269 TTTTTCTTCTTTTTTCTTTTTTTTTC
1 TTTTTCTT-TTTTTTCTTTTTTTTTC
35295 TTTTTCTTTTTTTTCTTTTTCTTTTC
1 TTTTTCTTTTTTTTCTTTTT-TTTTC
35321 TTTTTCTTTTTTTTCTTTTTTT
1 TTTTTCTTTTTTTTCTTTTTTT
35343 CTTTTCATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
25 14 0.30
26 33 0.70
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (25 bp):
TTTTTCTTTTTTTTCTTTTTTTTTC
Found at i:35353 original size:6 final size:5
Alignment explanation
Indices: 35270--35353 Score: 79
Period size: 5 Copynumber: 16.8 Consensus size: 5
35260 TTCTCTCTTT
*
35270 TTTTC TTCTT- TTTTC TTTTT TTTTC TTTTTC TTTT- TTTTC TTTTTC
1 TTTTC TT-TTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC -TTTTC
35316 TTTTC TTTTTC TTTT- TTTTC -TTT- TTTTC TTTTC ATTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTT
35354 TTCTTCAAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
4 16 0.24
5 30 0.45
6 21 0.31
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:35355 original size:1 final size:1
Alignment explanation
Indices: 35267--35347 Score: 63
Period size: 1 Copynumber: 81.0 Consensus size: 1
35257 TTTTTCTCTC
* * * * * * * * *
35267 TTTTTTTCTTCTTTTTTCTTTTTTTTTCTTTTTCTTTTTTTTCTTTTTCTTTTCTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
35332 TTTCTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTT
35348 CATTTTTTCT
Statistics
Matches: 58, Mismatches: 22, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:35360 original size:11 final size:10
Alignment explanation
Indices: 35256--35359 Score: 84
Period size: 9 Copynumber: 11.0 Consensus size: 10
35246 CTTGACCCCT
35256 TTTTTTCTCTC
1 TTTTTTCT-TC
35267 TTTTTTTCTTC
1 -TTTTTTCTTC
35278 TTTTTTC-T-
1 TTTTTTCTTC
35286 TTTTTT-TTC
1 TTTTTTCTTC
35295 -TTTTTCTT-
1 TTTTTTCTTC
35303 TTTTTTCTT-
1 TTTTTTCTTC
*
35312 TTTCTT-TTC
1 TTTTTTCTTC
35321 -TTTTTCTT-
1 TTTTTTCTTC
35329 TTTTTTCTT-
1 TTTTTTCTTC
*
35338 TTTTTCTTTTC
1 TTTTT-TCTTC
35349 ATTTTTTCTTC
1 -TTTTTTCTTC
35360 AAGCATAATA
Statistics
Matches: 78, Mismatches: 4, Indels: 21
0.76 0.04 0.20
Matches are distributed among these distances:
8 18 0.23
9 31 0.40
10 10 0.13
11 6 0.08
12 13 0.17
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:42705 original size:15 final size:15
Alignment explanation
Indices: 42682--42713 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42672 TGCAATGAAT
42682 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
42697 AATGCATGTATGCAA
1 AATGAATGTATGCAA
42712 AA
1 AA
42714 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:45928 original size:20 final size:20
Alignment explanation
Indices: 45903--45946 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
45893 AGCTTTATGT
*
45903 TGTGCAATGCAAGTGTTGTG
1 TGTGCAATGCAAGTATTGTG
45923 TGTGCAATGCAAGTATTGTG
1 TGTGCAATGCAAGTATTGTG
45943 TGTG
1 TGTG
45947 AGGAGAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.09, G:0.34, T:0.36
Consensus pattern (20 bp):
TGTGCAATGCAAGTATTGTG
Found at i:46852 original size:17 final size:18
Alignment explanation
Indices: 46812--46853 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
46802 AAATAATAAT
*
46812 TTATGTAAAATCAAATTA
1 TTATTTAAAATCAAATTA
**
46830 AGATTTAAAAT-AAATTA
1 TTATTTAAAATCAAATTA
46847 TTATTTA
1 TTATTTA
46854 TTATATATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
TTATTTAAAATCAAATTA
Found at i:48298 original size:3 final size:3
Alignment explanation
Indices: 48271--48357 Score: 97
Period size: 3 Copynumber: 27.7 Consensus size: 3
48261 TTGTAATATT
*
48271 TAA TAAA TAA TATA TAAA TAT TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA T-AA TAA TA-A T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
48319 TAA TATA TAA -AA TAA TAA TAA TAA TAAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
48358 GAAAATGGAG
Statistics
Matches: 74, Mismatches: 2, Indels: 16
0.80 0.02 0.17
Matches are distributed among these distances:
2 4 0.05
3 53 0.72
4 16 0.22
5 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48316 original size:18 final size:18
Alignment explanation
Indices: 48276--48357 Score: 114
Period size: 18 Copynumber: 4.6 Consensus size: 18
48266 ATATTTAATA
*
48276 AATAATATATAAATATTAAT
1 AATAATA-ATAAATA-AAAT
48296 AATAATAATAAATAAAAT
1 AATAATAATAAATAAAAT
*
48314 AATAATAATATATAAAAT
1 AATAATAATAAATAAAAT
48332 AATAATAAT-AAT-AAAT
1 AATAATAATAAATAAAAT
48348 AATAATAATA
1 AATAATAATA
48358 GAAAATGGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
16 13 0.22
17 2 0.03
18 29 0.50
19 7 0.12
20 7 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATAATAAATAAAAT
Found at i:52122 original size:3 final size:3
Alignment explanation
Indices: 52114--52163 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
52104 AAGAGAAAGA
* *
52114 AAG AAG AAG AA- AAG -TG AAG AAG AAG AAG AAG AAG AAG -AG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
52159 AAG AA
1 AAG AA
52164 TGTGGGGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.12
3 36 0.88
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:52125 original size:26 final size:26
Alignment explanation
Indices: 52086--52163 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 26
52076 GCATGATAAG
*
52086 AGAAA-AAGAAGAAAAGTTAAG-AGAA
1 AGAAAGAAGAAGAAAAGTGAAGAAG-A
52111 AGAAAGAAGAAGAAAAGTGAAGAAGA
1 AGAAAGAAGAAGAAAAGTGAAGAAGA
*
52137 AG-AAGAAGAAGAAGAG-G-AGAAGA
1 AGAAAGAAGAAGAAAAGTGAAGAAGA
52160 AGAA
1 AGAA
52164 TGTGGGGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.17
24 2 0.04
25 18 0.38
26 18 0.38
27 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (26 bp):
AGAAAGAAGAAGAAAAGTGAAGAAGA
Found at i:54463 original size:3 final size:3
Alignment explanation
Indices: 54450--54493 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
54440 TATTTTAATA
54450 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54494 GTAACGCCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:65514 original size:26 final size:26
Alignment explanation
Indices: 65485--65552 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
65475 AGATTCGATC
65485 CTTAAATAATTTTTAAAAAATTAATT
1 CTTAAATAATTTTTAAAAAATTAATT
65511 CTTAAATAATTTTTAAAAAATTAATT
1 CTTAAATAATTTTTAAAAAATTAATT
65537 CTTAAATAATTTTTAA
1 CTTAAATAATTTTTAA
65553 TTTTTAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
CTTAAATAATTTTTAAAAAATTAATT
Found at i:65515 original size:15 final size:15
Alignment explanation
Indices: 65491--65547 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 15
65481 GATCCTTAAA
*
65491 TAATTTTTAAAAAAT
1 TAATTCTTAAAAAAT
65506 TAATTCTT---AAA-
1 TAATTCTTAAAAAAT
*
65517 TAATTTTTAAAAAAT
1 TAATTCTTAAAAAAT
*
65532 TAATTCTTAAATAAT
1 TAATTCTTAAAAAAT
65547 T
1 T
65548 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
11 7 0.21
12 3 0.09
14 3 0.09
15 21 0.62
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTCTTAAAAAAT
Found at i:66811 original size:17 final size:16
Alignment explanation
Indices: 66789--66832 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
66779 CACTGTTTTA
66789 TTATTTTATTTTTATGT
1 TTATTTT-TTTTTATGT
*
66806 TTATTTGTTTTTTATTT
1 TTATTT-TTTTTTATGT
66823 TCTATTTTTT
1 T-TATTTTTT
66833 ATTAACCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (16 bp):
TTATTTTTTTTTATGT
Found at i:66828 original size:7 final size:7
Alignment explanation
Indices: 66784--66835 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
66774 CTATGCACTG
66784 TTTTATT
1 TTTTATT
66791 ATTTTATT
1 -TTTTATT
*
66799 TTTATGTT
1 TTT-TATT
*
66807 TATTTGTT
1 T-TTTATT
66815 TTTTATT
1 TTTTATT
*
66822 TTCTATT
1 TTTTATT
66829 TTTTATT
1 TTTTATT
66836 AACCACTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
7 20 0.53
8 16 0.42
9 2 0.05
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (7 bp):
TTTTATT
Found at i:67990 original size:27 final size:27
Alignment explanation
Indices: 67952--68004 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
67942 TGGAGGTGCT
67952 GACTTGAATAAGGATCCATTGAGAGAA
1 GACTTGAATAAGGATCCATTGAGAGAA
*
67979 GACTTGAATAAGGGTCCATTGAGAGA
1 GACTTGAATAAGGATCCATTGAGAGA
68005 CCCGACCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (27 bp):
GACTTGAATAAGGATCCATTGAGAGAA
Found at i:69656 original size:31 final size:31
Alignment explanation
Indices: 69614--69672 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
69604 AACGGTCGGA
69614 GACCATATTGCAAACAAACTAAATGTTGGGG
1 GACCATATTGCAAACAAACTAAATGTTGGGG
* ***
69645 GACCATTTTGCAAATGGACTAAATGTTG
1 GACCATATTGCAAACAAACTAAATGTTG
69673 AGGAATTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (31 bp):
GACCATATTGCAAACAAACTAAATGTTGGGG
Done.