Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000135.1 Hibiscus syriacus cultivar Beakdansim tig00000248_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: 73832
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:73 original size:21 final size:20
Alignment explanation
Indices: 42--84 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
32 CACTCTACGG
42 CGAAATTCGTCCCC-ATCTC
1 CGAAATTCGTCCCCAATCTC
61 CGAAGATTCCGTCCCCAATCTC
1 CGAA-ATT-CGTCCCCAATCTC
83 CG
1 CG
85 CGAAATCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 3 0.14
21 7 0.33
22 7 0.33
ACGTcount: A:0.21, C:0.42, G:0.14, T:0.23
Consensus pattern (20 bp):
CGAAATTCGTCCCCAATCTC
Found at i:471 original size:21 final size:20
Alignment explanation
Indices: 425--480 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
415 TTCTAAACTT
425 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
*
445 -ACATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
465 AAAATCGCAACGAGAA
1 AAAATCGCAACGAGAA
481 TCGCAACGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 11 0.35
20 7 0.23
21 13 0.42
ACGTcount: A:0.52, C:0.18, G:0.20, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:502 original size:30 final size:32
Alignment explanation
Indices: 459--536 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
449 CGCAACGAGA
459 GAAATGAAAATCGCAACGAG-AATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAATCGCAACGC
*
490 GAAATG-AAATCGCAACGAGATAATCGTAACGC
1 GAAATGAAAATCGCAACGAGA-AATCGCAACGC
**
522 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
537 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 14 0.34
33 8 0.20
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.12
Consensus pattern (32 bp):
GAAATGAAAATCGCAACGAGAAATCGCAACGC
Found at i:554 original size:19 final size:19
Alignment explanation
Indices: 532--615 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
522 GAAACCAAAA
*
532 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
551 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
570 TCGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
584 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
603 TCGCGTTGCGATT
1 TCGCGTTGCGATT
616 CTCTCGTTGC
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.17
16 3 0.06
17 2 0.04
19 39 0.74
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:637 original size:33 final size:33
Alignment explanation
Indices: 554--628 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
544 TTTCATTTCG
*
554 CGTTGCGATTTTAATTTCGCGTTACGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
*
587 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
620 CGTTGCGAT
1 CGTTGCGAT
629 AGTTATTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCGTTGCGATTCTCT
Found at i:2566 original size:94 final size:93
Alignment explanation
Indices: 2341--2718 Score: 596
Period size: 94 Copynumber: 4.1 Consensus size: 93
2331 TAGATTGCTT
* * * * * *
2341 AGTAAATTTATTTGGTTGCTGTCAATACTGATAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2406 ATTTGTCTTT-TGTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
*
2433 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2498 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
2527 AGTAAATTTGTTCAGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2592 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* ** * *
2621 AGTAAATTTGTTTGGTTGCTGCCAATTCTATTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2686 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
2714 AGTAA
1 AGTAA
2719 TGCAATCCAT
Statistics
Matches: 268, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
92 70 0.26
93 21 0.08
94 177 0.66
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:2859 original size:33 final size:33
Alignment explanation
Indices: 2822--2884 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2812 ACGTGAAATG
* * *
2822 AATCGCAATGAGAGAATCGCAACGCGAAACCAA
1 AATCGCAACGACAAAATCGCAACGCGAAACCAA
2855 AATCGCAACGACAAAATCGCAACGCGAAAC
1 AATCGCAACGACAAAATCGCAACGCGAAAC
2885 TATAGTCGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.08
Consensus pattern (33 bp):
AATCGCAACGACAAAATCGCAACGCGAAACCAA
Found at i:2860 original size:19 final size:19
Alignment explanation
Indices: 2836--2884 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 19
2826 GCAATGAGAG
2836 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
2855 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
2869 AATCGCAACGCGAAAC
1 AATCGCAACGCGAAAC
2885 TATAGTCGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 2 0.08
17 2 0.08
18 1 0.04
19 8 0.32
ACGTcount: A:0.47, C:0.31, G:0.16, T:0.06
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:3549 original size:21 final size:21
Alignment explanation
Indices: 3458--3562 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
3448 GACTCACCTG
3458 TCATCGTTCAAGAGGCCTCC-C
1 TCATCGTTCAAGAGGCC-CCTC
* *
3479 TTATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
3500 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
3521 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
3542 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
3563 CCAACATTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
20 2 0.03
21 61 0.97
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:3555 original size:42 final size:42
Alignment explanation
Indices: 3483--3565 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
3473 CCTCCCTTAT
*
3483 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
3525 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
3566 ACATTTTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:4937 original size:14 final size:14
Alignment explanation
Indices: 4918--4953 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4908 ATTGTTTAAT
4918 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4932 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4946 TGATTTGT
1 TGATTTGT
4954 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5111 original size:32 final size:33
Alignment explanation
Indices: 5055--5149 Score: 120
Period size: 32 Copynumber: 2.8 Consensus size: 33
5045 AAAACAGACT
* **
5055 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
5089 ATC-CAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5121 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
5150 CGAAACTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 23 0.43
33 11 0.20
34 20 0.37
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5180 original size:19 final size:19
Alignment explanation
Indices: 5158--5245 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
5148 CGCGAAACTA
*
5158 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
5177 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
5195 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
* *
5211 ATTTTGCATTGCAATTTTC
1 ATTTCGCATTGCGATTTTC
5230 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
5246 CTCTCGTTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 2 0.04
18 4 0.07
19 25 0.45
20 12 0.21
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:5265 original size:52 final size:53
Alignment explanation
Indices: 5166--5266 Score: 150
Period size: 52 Copynumber: 1.9 Consensus size: 53
5156 TAATTTCGCG
* **
5166 TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTTGCA
1 TTGCAATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTTGCA
* *
5219 TTGCAATTTTCA-TTTCGCATTGCGATTCTCTCGTTGTGATAGTCATTT
1 TTGCAATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTT
5267 CCGCGTTGCG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 32 0.74
53 11 0.26
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.48
Consensus pattern (53 bp):
TTGCAATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTTGCA
Found at i:5279 original size:20 final size:20
Alignment explanation
Indices: 5250--5343 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
5240 GCGATTCTCT
*
5250 CGTTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
5270 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
5290 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
5310 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
5330 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
5344 AATGAATGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 63 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:7774 original size:24 final size:24
Alignment explanation
Indices: 7723--7774 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
7713 ATCTGAGTAT
** *
7723 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
7747 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
7771 TGAC
1 TGAC
7775 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:8634 original size:20 final size:20
Alignment explanation
Indices: 8621--9092 Score: 190
Period size: 20 Copynumber: 23.4 Consensus size: 20
8611 CAGAATCTCA
8621 TTGCGATTTACAGATTCGCG
1 TTGCGATTTACAGATTCGCG
8641 TTGCGATTTACAGATTCGCG
1 TTGCGATTTACAGATTCGCG
8661 TTGCGATTTACAGATTCGCG
1 TTGCGATTTACAGATTCGCG
8681 TTGCGATTTAC-GTATTCGCG
1 TTGCGATTTACAG-ATTCGCG
*
8701 TTGCGATTTAC-GTAATCGCG
1 TTGCGATTTACAG-ATTCGCG
* * * * *
8721 TTGCGAATTAGGAAAATCGCA
1 TTGCGATTTA-CAGATTCGCG
** ** * *
8742 ACGCGAATTT-GGGAAATCGCA
1 TTGCG-ATTTACAG-ATTCGCG
* * *
8763 ATGCGATAGT-CAGAATCGCG
1 TTGCGAT-TTACAGATTCGCG
* ** * * ***
8783 TTGCGAATCTGGAAACT-AAT
1 TTGCG-ATTTACAGATTCGCG
8803 TTGCGA--TACCGGAGA-TCGCG
1 TTGCGATTTA-C--AGATTCGCG
*
8823 TTGCGAATTATC-GA-TCGCG
1 TTGCGATTTA-CAGATTCGCG
* *
8842 TTGCGATTTACGGATACGCG
1 TTGCGATTTACAGATTCGCG
8862 TTGCGATTTTAC-GTATT-GTCG
1 TTGCGA-TTTACAG-ATTCG-CG
* * *
8883 TTGCGATTTACGGATACGCA
1 TTGCGATTTACAGATTCGCG
*
8903 TTGCGATTTAC-GTATTCTCG
1 TTGCGATTTACAG-ATTCGCG
* *
8923 ATGCGATTTACAGATACGCG
1 TTGCGATTTACAGATTCGCG
*
8943 TTGCGATTTAC-GTATTCTCG
1 TTGCGATTTACAG-ATTCGCG
* * * *
8963 TTTCAATTTACGGATAT-GCA
1 TTGCGATTTACAGAT-TCGCG
8983 TTGCGATTTTAC-GTATT-GTCG
1 TTGCGA-TTTACAG-ATTCG-CG
* * *
9004 TTGCAATTTACGGATACGCG
1 TTGCGATTTACAGATTCGCG
* * *
9024 TTGCGATTTTACGGATACTCG
1 TTGCGA-TTTACAGATTCGCG
* *
9045 TTGCGATAGT-CAGAATCGCG
1 TTGCGAT-TTACAGATTCGCG
*
9065 TTGCGATTTATATG-TTCGCG
1 TTGCGATTTACA-GATTCGCG
9085 TTGCGATT
1 TTGCGATT
9093 CTGGAAAATC
Statistics
Matches: 354, Mismatches: 63, Indels: 70
0.73 0.13 0.14
Matches are distributed among these distances:
17 1 0.00
18 1 0.00
19 24 0.07
20 239 0.68
21 83 0.23
22 6 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATTTACAGATTCGCG
Found at i:8646 original size:40 final size:40
Alignment explanation
Indices: 8601--8726 Score: 132
Period size: 40 Copynumber: 3.1 Consensus size: 40
8591 AAATTCAGTA
*
8601 TTGCGATAGT-CAGAATCTCATTGCGATTTACAGATTCGCG
1 TTGCGAT-GTACAGAATCGCATTGCGATTTACAGATTCGCG
* * *
8641 TTGCGATTTACAGATTCGCGTTGCGATTTACAGATTCGCG
1 TTGCGATGTACAGAATCGCATTGCGATTTACAGATTCGCG
* * * *
8681 TTGCGATTTAC-GTATTCGCGTTGCGATTTAC-GTAATCGCG
1 TTGCGATGTACAG-AATCGCATTGCGATTTACAG-ATTCGCG
8721 TTGCGA
1 TTGCGA
8727 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
39 3 0.04
40 75 0.96
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (40 bp):
TTGCGATGTACAGAATCGCATTGCGATTTACAGATTCGCG
Found at i:8747 original size:21 final size:21
Alignment explanation
Indices: 8723--8768 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
8713 TAATCGCGTT
8723 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
8744 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
8765 GCGA
1 GCGA
8769 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:8928 original size:40 final size:41
Alignment explanation
Indices: 8840--9051 Score: 302
Period size: 41 Copynumber: 5.2 Consensus size: 41
8830 TTATCGATCG
*
8840 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
8881 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
8921 CGATGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * * *
8961 CGTTTCAATTTACGGATATGCATTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
9002 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
9043 CGTTGCGAT
1 CGTTGCGAT
9052 AGTCAGAATC
Statistics
Matches: 151, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 70 0.46
41 81 0.54
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:9110 original size:21 final size:21
Alignment explanation
Indices: 9086--9137 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
9076 ATGTTCGCGT
9086 TGCG-ATTCTGGAAAATCGCAA
1 TGCGAATT-TGGAAAATCGCAA
9107 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
*
9128 TACGAATTTG
1 TGCGAATTTG
9138 TACTATCACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCGAATTTGGAAAATCGCAA
Found at i:9941 original size:3 final size:3
Alignment explanation
Indices: 9933--9966 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
9923 TATGATATGA
*
9933 TAT TAT TAT TAT TAT TAT TAT TAT CAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
9967 ATAATTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:13376 original size:16 final size:16
Alignment explanation
Indices: 13357--13395 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
13347 ACGCCCTCCC
13357 TCCACAAACTCAATTT
1 TCCACAAACTCAATTT
13373 TCCACAAACTCAATTT
1 TCCACAAACTCAATTT
13389 TCCACAA
1 TCCACAA
13396 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TCCACAAACTCAATTT
Found at i:32333 original size:37 final size:37
Alignment explanation
Indices: 32283--32359 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
32273 GGTACGATAT
32283 TACGACTATATTGTATACTCTCATCAATGCAATCAAA
1 TACGACTATATTGTATACTCTCATCAATGCAATCAAA
*
32320 TACGACTATATTGTATCCTCTCATCAATGCAATCAAA
1 TACGACTATATTGTATACTCTCATCAATGCAATCAAA
32357 TAC
1 TAC
32360 AAGTCCATGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.32
Consensus pattern (37 bp):
TACGACTATATTGTATACTCTCATCAATGCAATCAAA
Found at i:33208 original size:27 final size:26
Alignment explanation
Indices: 33126--33262 Score: 82
Period size: 27 Copynumber: 4.9 Consensus size: 26
33116 ACTGAGTTTC
*
33126 TATTATTAGAATTTATAAAATAATTTT
1 TATTATTA-AAATTATAAAATAATTTT
* * *
33153 TAATTA-TAGAATATTATTTTAAAT-CTATT
1 T-ATTATTA-AA-ATTA--TAAAATAATTTT
33182 TATTATTAAAATTATAAAATAATTATT
1 TATTATTAAAATTATAAAATAATT-TT
*
33209 TATATATTTAAATATTTTAAATATATATTTT
1 TAT-TA-TTAAA-ATTATAAA-ATA-ATTTT
*
33240 T-TTATTAAAATTTTAACAATAAT
1 TATTATTAAAATTATAA-AATAAT
33263 ATGTGTTAGA
Statistics
Matches: 89, Mismatches: 8, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
25 5 0.06
26 3 0.03
27 25 0.28
28 21 0.24
29 13 0.15
30 13 0.15
31 6 0.07
32 3 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TATTATTAAAATTATAAAATAATTTT
Found at i:33238 original size:56 final size:56
Alignment explanation
Indices: 33126--33262 Score: 138
Period size: 57 Copynumber: 2.4 Consensus size: 56
33116 ACTGAGTTTC
* * *
33126 TATTATTAGAATTTATAAAATAATTTTTAATTATAGAATATTATTTTAAATCTA-TT
1 TATTATTA-AAATTATAAAATAATTTTTAATTATAGAATATTATTTAAAATATATTT
*
33182 TATTATTAAAATTATAAAATAATTATTTATATATTTA-AATA-T-TTTAAATATATATTT
1 TATTATTAAAATTATAAAATAATT-TTTA-AT-TATAGAATATTATTTAAA-ATATATTT
* *
33239 TTTTATTAAAATTTTAACAATAAT
1 TATTATTAAAATTATAA-AATAAT
33263 ATGTGTTAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
55 20 0.29
56 17 0.25
57 23 0.33
58 9 0.13
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (56 bp):
TATTATTAAAATTATAAAATAATTTTTAATTATAGAATATTATTTAAAATATATTT
Found at i:33260 original size:29 final size:27
Alignment explanation
Indices: 33178--33264 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 27
33168 ATTTTAAATC
*
33178 TATTTA-TTATTAAAATTATAAAATAA
1 TATTTATTTATTAAAATTTTAAAATAA
*
33204 TTATTTATATATTTAAATATTTT-AAATATA
1 -TATTTATTTA-TTAAA-ATTTTAAAATA-A
*
33234 TATTTTTTTATTAAAATTTTAACAATAA
1 TATTTATTTATTAAAATTTTAA-AATAA
33262 TAT
1 TAT
33265 GTGTTAGATG
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 11 0.22
28 12 0.24
29 22 0.44
30 5 0.10
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
TATTTATTTATTAAAATTTTAAAATAA
Found at i:34221 original size:29 final size:29
Alignment explanation
Indices: 34166--34221 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
34156 GTACAAAACT
* *
34166 GAAGACGCATTATGTTTCCGACGACTTTC
1 GAAGACGCACTATGTTTCCGACCACTTTC
* *
34195 GAAGTCGCACTATGTTTCCGGCCACTT
1 GAAGACGCACTATGTTTCCGACCACTT
34222 CCGACGGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (29 bp):
GAAGACGCACTATGTTTCCGACCACTTTC
Found at i:35888 original size:11 final size:11
Alignment explanation
Indices: 35872--35913 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
35862 TTGAGGCAAT
35872 ATCGAGCTTGA
1 ATCGAGCTTGA
*
35883 ATCGAGCTCAGA
1 ATCGAGCT-TGA
*
35895 ATCGAGCTTCA
1 ATCGAGCTTGA
35906 ATCGAGCT
1 ATCGAGCT
35914 CGAGTCTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (11 bp):
ATCGAGCTTGA
Found at i:35902 original size:23 final size:24
Alignment explanation
Indices: 35872--35938 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
35862 TTGAGGCAAT
*
35872 ATCGAGCTTGAATCGAGCTC-AGA
1 ATCGAGCTTCAATCGAGCTCGAGA
*
35895 ATCGAGCTTCAATCGAGCTCGAGT
1 ATCGAGCTTCAATCGAGCTCGAGA
* * *
35919 CTCGAGTTTTAATCGAGCTC
1 ATCGAGCTTCAATCGAGCTC
35939 TTAATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
ATCGAGCTTCAATCGAGCTCGAGA
Found at i:36173 original size:16 final size:16
Alignment explanation
Indices: 36152--36214 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
36142 TCCAACGTTT
36152 ATGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
*
36168 ATGTTCATTTATGTTC
1 ATGTTCGTTTATGTTC
*
36184 GTGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
*
36200 GTGTTCGTTTATGTT
1 ATGTTCGTTTATGTT
36215 AGTTTATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.57
Consensus pattern (16 bp):
ATGTTCGTTTATGTTC
Found at i:36197 original size:26 final size:26
Alignment explanation
Indices: 36149--36199 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
36139 GTCTCCAACG
*
36149 TTTATGTTCGTTTATGTTCATGTTCA
1 TTTATGTTCGTTTACGTTCATGTTCA
*
36175 TTTATGTTCGTGTT-CGTTTATGTTC
1 TTTATGTTCGT-TTACGTTCATGTTC
36200 GTGTTCGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (26 bp):
TTTATGTTCGTTTACGTTCATGTTCA
Found at i:43034 original size:27 final size:28
Alignment explanation
Indices: 43002--43077 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 28
42992 TGTTTTGATC
43002 ATTAAATTTTTAAAATTATT-AATAATT
1 ATTAAATTTTTAAAATTATTAAATAATT
**
43029 ATTAAATTAAATAAATTATTATTAAATAATT
1 ATTAAATT-TTTAAA--ATTATTAAATAATT
43060 ATTAAATTTTTTAAAATT
1 ATTAAA-TTTTTAAAATT
43078 TTATGAAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 8 0.20
28 4 0.10
29 3 0.08
30 6 0.15
31 17 0.43
32 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTAAATTTTTAAAATTATTAAATAATT
Found at i:43060 original size:11 final size:11
Alignment explanation
Indices: 43015--43066 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
43005 AAATTTTTAA
43015 AATTATT-AAT
1 AATTATTAAAT
43025 AATTATTAAATT
1 AATTATTAAA-T
43037 AA--A-TAAAT
1 AATTATTAAAT
*
43045 TATTATTAAAT
1 AATTATTAAAT
43056 AATTATTAAAT
1 AATTATTAAAT
43067 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 2 0.06
9 4 0.11
10 9 0.26
11 17 0.49
12 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTATTAAAT
Found at i:48967 original size:22 final size:22
Alignment explanation
Indices: 48942--48995 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
48932 AAACGGACGA
* *
48942 TAAACGAATAATAAATAAATGC
1 TAAACGAACAATAAATAAACGC
* * *
48964 TAAACTAACACTAAATGAACGC
1 TAAACGAACAATAAATAAACGC
48986 TAAACGAACA
1 TAAACGAACA
48996 TATTCACGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.56, C:0.17, G:0.09, T:0.19
Consensus pattern (22 bp):
TAAACGAACAATAAATAAACGC
Found at i:52914 original size:58 final size:59
Alignment explanation
Indices: 52826--52937 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 59
52816 TCGGGTGACC
* *
52826 ATTTTGTAGCTTTTAATAGTCGGGAAACTCAACAAAGCAACA-CCT-TAGTCGAAGAACT
1 ATTTTGTAACTTTTAATAGTCAGG-AACTCAACAAAGCAACACCCTATAGTCGAAGAACT
*
52884 ATTTTGTAACTTTTAATAGTCTAAGG-ACTCAACAAAGCATCACCCTATAGTCGA
1 ATTTTGTAACTTTTAATAGTC--AGGAACTCAACAAAGCAACACCCTATAGTCGA
52938 GGGTCTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
58 35 0.74
59 3 0.06
60 9 0.19
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCAGGAACTCAACAAAGCAACACCCTATAGTCGAAGAACT
Found at i:54631 original size:117 final size:116
Alignment explanation
Indices: 54426--54662 Score: 404
Period size: 117 Copynumber: 2.0 Consensus size: 116
54416 AAAGGTAATT
* * * *
54426 AAACCATAAATAAATAGAAGATTGAAGCTTAATTTCACTAATTTATAACCGTCGTGTCCTGAAAG
1 AAACCATAAAAAAATAGAAGATTGAAGCTGAATTTCACTAATTTAAAACCGTCATGTCCTGAAAG
54491 ATAATCAAACCAAAAAAAGTTAAGGACAAGACTTAATTTCATTTAATTTTG
66 ATAATCAAACCAAAAAAAGTTAAGGACAAGACTTAATTTCATTTAATTTTG
*
54542 AAACCATAAAAAAAATAGAGGATTGAAGCTGAATTTCACTAATTTTAAAACCGTCATGTCCTGAA
1 AAACCAT-AAAAAAATAGAAGATTGAAGCTGAATTTCACTAA-TTTAAAACCGTCATGTCCTGAA
54607 AGATAATCAAACCAAAAAAA-TTAAGGACAAGACTTAATTTCATTTAATTTTG
64 AGATAATCAAACCAAAAAAAGTTAAGGACAAGACTTAATTTCATTTAATTTTG
54659 AAAC
1 AAAC
54663 TGATAATGTC
Statistics
Matches: 114, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
116 7 0.06
117 67 0.59
118 40 0.35
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (116 bp):
AAACCATAAAAAAATAGAAGATTGAAGCTGAATTTCACTAATTTAAAACCGTCATGTCCTGAAAG
ATAATCAAACCAAAAAAAGTTAAGGACAAGACTTAATTTCATTTAATTTTG
Found at i:62332 original size:25 final size:24
Alignment explanation
Indices: 62285--62340 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
62275 ATTGATGATT
* *
62285 TAATTTTATATTTTTAAAATTTTTA
1 TAATTTTATATCTCT-AAATTTTTA
*
62310 TAATTTTATATCTCTAATTTTTTA
1 TAATTTTATATCTCTAAATTTTTA
*
62334 TATTTTT
1 TAATTTT
62341 CTAAATTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (24 bp):
TAATTTTATATCTCTAAATTTTTA
Found at i:64360 original size:60 final size:60
Alignment explanation
Indices: 64252--64364 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
64242 GTCAGGTGAC
* *
64252 CATTTTGTAACTTTTAATAGTCGAATGACTCAACAAAGCAACGTCCTATAGTCGGAGGAT
1 CATTTTGTAACTTTTAATAGTCGAAGGACTCAACAAAGCAACGCCCTATAGTCGGAGGAT
* *
64312 CATTTTGTAACTTTTAATAGTC-AGAGGGCTCAACAAAGTAA-GACCCTATAGTC
1 CATTTTGTAACTTTTAATAGTCGA-AGGACTCAACAAAGCAACG-CCCTATAGTC
64365 AAGGACCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGAAGGACTCAACAAAGCAACGCCCTATAGTCGGAGGAT
Found at i:66911 original size:27 final size:27
Alignment explanation
Indices: 66878--66943 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
66868 CAAAACAATA
*
66878 TTGAATGATTCAACACA-GAAGTATATT
1 TTGAATGATTCAACACATG-AGTACATT
*
66905 TTGAATGATTTAACACATGAGTACATT
1 TTGAATGATTCAACACATGAGTACATT
66932 TTGAATGATTCA
1 TTGAATGATTCA
66944 GAGTCATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (27 bp):
TTGAATGATTCAACACATGAGTACATT
Found at i:72056 original size:21 final size:21
Alignment explanation
Indices: 72032--72073 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
72022 TTACTTTTGG
72032 TTAAATT-AAAATTAATTATTT
1 TTAAATTAAAAATT-ATTATTT
72053 TTAAATTAAAAATTATTATTT
1 TTAAATTAAAAATTATTATTT
72074 AATTAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAATTAAAAATTATTATTT
Done.