Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007175.1 Hibiscus syriacus cultivar Beakdansim tig00018833_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: 129687
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1032 original size:24 final size:24
Alignment explanation
Indices: 978--1032 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
968 GCTGACTTCC
*
978 GCAGCTGTCGCAATAGCAGCAGCA
1 GCAGCTGTAGCAATAGCAGCAGCA
* * *
1002 GCTGCTGTAGCAA-AGGCTGCAGCT
1 GCAGCTGTAGCAATA-GCAGCAGCA
1026 GCAGCTG
1 GCAGCTG
1033 CCATGTTGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.16
Consensus pattern (24 bp):
GCAGCTGTAGCAATAGCAGCAGCA
Found at i:5000 original size:31 final size:32
Alignment explanation
Indices: 4941--5003 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
4931 CCGTTCTTAA
* *
4941 CTATTTTAATATGTTTTGAAATAGAATATTTT
1 CTATTTCAATATGTTTTGAAATAAAATATTTT
*
4973 CTATTTCAATATG-TTTGAATTAAAATATTTT
1 CTATTTCAATATGTTTTGAAATAAAATATTTT
5004 GAAATATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (32 bp):
CTATTTCAATATGTTTTGAAATAAAATATTTT
Found at i:6855 original size:31 final size:31
Alignment explanation
Indices: 6815--6891 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
6805 ATTTTTAAAT
* *
6815 GATTTTTAAATTTTTTAA-ATTATTAT-AAAA
1 GATTATTAAATTTATTAACA-TATTATAAAAA
6845 GATTCATTAAATTTATTAACATATTATAAAAA
1 GATT-ATTAAATTTATTAACATATTATAAAAA
*
6877 GATTATTAAACTTAT
1 GATTATTAAATTTAT
6892 CAAAATTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.10
31 28 0.68
32 9 0.22
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (31 bp):
GATTATTAAATTTATTAACATATTATAAAAA
Found at i:21487 original size:9 final size:9
Alignment explanation
Indices: 21473--21499 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
21463 ATTAATGGAT
21473 TCAAAATGA
1 TCAAAATGA
21482 TCAAAATGA
1 TCAAAATGA
21491 TCAAAATGA
1 TCAAAATGA
21500 ACTAACATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
TCAAAATGA
Found at i:22446 original size:26 final size:24
Alignment explanation
Indices: 22401--22470 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
22391 TTAAATTCAT
22401 AATATTTTTTATATATTAACTTTAAGA
1 AATA-TTTTT-TATATTAAC-TTAAGA
**
22428 AATATGTTTTTATATTAACTTATTA
1 AATAT-TTTTTATATTAACTTAAGA
*
22453 AATATTTTTTTTATTAAC
1 AATATTTTTTATATTAAC
22471 CTAATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
24 12 0.31
25 9 0.23
26 10 0.26
27 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (24 bp):
AATATTTTTTATATTAACTTAAGA
Found at i:24528 original size:23 final size:23
Alignment explanation
Indices: 24484--24528 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
24474 ACTTAAATCA
*
24484 TTAAAATTAATATAATAGTTTAT
1 TTAAAATTAATATAAGAGTTTAT
* * *
24507 TTAAAATTGATTTAAGATTTTA
1 TTAAAATTAATATAAGAGTTTA
24529 ATATTTTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (23 bp):
TTAAAATTAATATAAGAGTTTAT
Found at i:24667 original size:28 final size:25
Alignment explanation
Indices: 24603--24680 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
24593 TAAAAATAAT
24603 TTAATATTCAAATT-ATAATATACA
1 TTAATATTCAAATTAATAATATACA
*
24627 TT-ATATT-ATAATTAATGATATATATA
1 TTAATATTCA-AATTAAT-A-ATATACA
24653 TATAATATTCAAATT-ATAATCATACA
1 T-TAATATTCAAATTAATAAT-ATACA
24679 TT
1 TT
24681 TGTAACATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
22 1 0.02
23 9 0.20
24 4 0.09
25 4 0.09
26 13 0.30
27 3 0.07
28 9 0.20
29 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.45
Consensus pattern (25 bp):
TTAATATTCAAATTAATAATATACA
Found at i:28424 original size:19 final size:19
Alignment explanation
Indices: 28400--28437 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28390 CATATACTCA
28400 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
28419 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
28438 AAGCCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CCATGCAGACGAGCCATAC
Found at i:28496 original size:32 final size:32
Alignment explanation
Indices: 28452--28522 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
28442 CATATACTCA
* *
28452 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
*
28484 CCATGCAAACGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
28516 CCATGCA
1 CCATGCA
28523 GTCTGGGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.30, T:0.08
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:28613 original size:29 final size:29
Alignment explanation
Indices: 28510--28604 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
28500 GCCAATAGAG
* **
28510 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
28539 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
28568 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
28597 AGGTCGCC
1 AGGTCGCC
28605 CCGGCGTCCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:28703 original size:49 final size:48
Alignment explanation
Indices: 28639--28734 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 48
28629 CATGCATGCA
28639 CATGCAGCCAAATAACTTCACGTGCTCCTGCT-CCCGCTGCATGCCTG
1 CATGCAGCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTG
28686 CATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCT
1 CATGCA-GCCAA-ATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCT
28735 ACAACATGCC
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 6 0.13
48 5 0.11
49 21 0.46
50 14 0.30
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.24
Consensus pattern (48 bp):
CATGCAGCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTG
Found at i:28743 original size:49 final size:48
Alignment explanation
Indices: 28645--28745 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 48
28635 TGCACATGCA
* *
28645 GCCAAATAACTTCACGTGCTCCTGCTCCCGCTGCATGCCTGCATGCAT
1 GCCAAATAACTTCACGTGCTCCTGCTCCCGCTGCATGCCTACATACAT
28693 GCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACA-ACAT
1 GCCAA-ATAACTTCACGTGCTCCTGCT-CCCGCTGCATGCCTACATACAT
28742 GCCA
1 GCCA
28746 TGTGATCCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
48 5 0.10
49 28 0.57
50 16 0.33
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.23
Consensus pattern (48 bp):
GCCAAATAACTTCACGTGCTCCTGCTCCCGCTGCATGCCTACATACAT
Found at i:28980 original size:16 final size:18
Alignment explanation
Indices: 28956--28992 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
28946 GAGATAAGGT
*
28956 AATTTGTTTA-TATT-TA
1 AATTAGTTTATTATTATA
28972 AATTAGTTTATTATTATA
1 AATTAGTTTATTATTATA
28990 AAT
1 AAT
28993 GTTAATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
AATTAGTTTATTATTATA
Found at i:29099 original size:41 final size:41
Alignment explanation
Indices: 29053--29158 Score: 108
Period size: 41 Copynumber: 2.5 Consensus size: 41
29043 GTATACATAA
*
29053 ATTAAAAATTATTTAATTAGTATATGT-TTGATAGTTA-TAT
1 ATTAAAAATTATTTAATTAGT-TATGTGTTAATAGTTAGTAT
* * * *
29093 AGTTAAAAAATAATTAATTAGTTTTTTGTTAATAGTTAGTTAT
1 A-TTAAAAATTATTTAATTAGTTATGTGTTAATAGTTAG-TAT
*
29136 ATAAAAAAATTATTTAATTAGTT
1 AT-TAAAAATTATTTAATTAGTT
29159 TTTGTTAGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
40 4 0.08
41 27 0.51
42 1 0.02
43 21 0.40
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (41 bp):
ATTAAAAATTATTTAATTAGTTATGTGTTAATAGTTAGTAT
Found at i:29397 original size:14 final size:14
Alignment explanation
Indices: 29378--29407 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29368 GTTTATTAGT
29378 TTATTATATTAAAG
1 TTATTATATTAAAG
29392 TTATTATATTAAAG
1 TTATTATATTAAAG
29406 TT
1 TT
29408 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:31567 original size:17 final size:17
Alignment explanation
Indices: 31545--31577 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31535 ACAATGATGT
31545 TAGTATCAAATAATTAC
1 TAGTATCAAATAATTAC
31562 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
31578 GTATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:31581 original size:14 final size:14
Alignment explanation
Indices: 31544--31594 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
31534 AACAATGATG
31544 TTAGTATCAAATAA
1 TTAGTATCAAATAA
31558 TTACTAGTATCAAATAA
1 -T--TAGTATCAAATAA
* *
31575 TTAGTATTAAATCA
1 TTAGTATCAAATAA
31589 TTAGTA
1 TTAGTA
31595 ATAATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 17 0.53
15 1 0.03
16 1 0.03
17 13 0.41
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (14 bp):
TTAGTATCAAATAA
Found at i:31596 original size:21 final size:21
Alignment explanation
Indices: 31572--31615 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
31562 TAGTATCAAA
* *
31572 TAATTAGTATTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
*
31593 TAATAATTAGTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
31614 TA
1 TA
31616 TCAAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
TAATAAGTAGTAAATCATTAG
Found at i:31614 original size:11 final size:11
Alignment explanation
Indices: 31582--31615 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31572 TAATTAGTAT
31582 TAAATCATTAG
1 TAAATCATTAG
*
31593 T-AATAATTAG
1 TAAATCATTAG
31603 TAAATCATTAG
1 TAAATCATTAG
31614 TA
1 TA
31616 TCAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (11 bp):
TAAATCATTAG
Found at i:31623 original size:14 final size:13
Alignment explanation
Indices: 31562--31626 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
31552 AAATAATTAC
*
31562 TAGTATCAAATAAT
1 TAGTAT-AAATCAT
31576 TAGTATTAAATCAT
1 TAGTA-TAAATCAT
*
31590 TAG--T-AATAAT
1 TAGTATAAATCAT
31600 TAG--TAAATCAT
1 TAGTATAAATCAT
31611 TAGTATCAAATCAT
1 TAGTAT-AAATCAT
31625 TA
1 TA
31627 AATATTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.21
11 9 0.21
13 1 0.02
14 23 0.53
15 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TAGTATAAATCAT
Found at i:31730 original size:13 final size:12
Alignment explanation
Indices: 31712--31807 Score: 81
Period size: 11 Copynumber: 7.9 Consensus size: 12
31702 TTAGTATTCT
31712 ATAATTATTAGTA
1 ATAATTATTA-TA
31725 ATAATTATTA-A
1 ATAATTATTATA
*
31736 ATCATTATTATAA
1 ATAATTATTAT-A
*
31749 ATAATTACTA-A
1 ATAATTATTATA
**
31760 ATAA-TAACATA
1 ATAATTATTATA
31771 ATAATTATTATAAA
1 ATAATTATTAT--A
*
31785 ATCATTATTATA
1 ATAATTATTATA
*
31797 ATGATTATTAT
1 ATAATTATTAT
31808 CAAATCATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.04
11 20 0.29
12 15 0.22
13 19 0.28
14 11 0.16
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (12 bp):
ATAATTATTATA
Found at i:31793 original size:14 final size:13
Alignment explanation
Indices: 31774--31986 Score: 82
Period size: 12 Copynumber: 15.2 Consensus size: 13
31764 TAACATAATA
31774 ATTATTATAAAATC
1 ATTATTAT-AAATC
*
31788 ATTATTAT-AATG
1 ATTATTATAAATC
31800 ATTATTATCAAATC
1 ATTATTAT-AAATC
31814 ATTACTAAATCATCAAATC
1 ATTA-T---T-AT-AAATC
*
31833 ATTAAATATTTAAATC
1 ATT--AT-TATAAATC
31849 ATTA-T-TAAATC
1 ATTATTATAAATC
* *
31860 ATTTTTAT-AATG
1 ATTATTATAAATC
31872 ATTATTACTAAATC
1 ATTATTA-TAAATC
* *
31886 ATTACTAT-AATG
1 ATTATTATAAATC
31898 ATTATTATCAAATC
1 ATTATTAT-AAATC
31912 ATTACTAAATCATCAAATC
1 ATTA-T---T-AT-AAATC
*
31931 ATTAAATATTTAAATC
1 ATT--AT-TATAAATC
31947 ATTA-T-TAAATC
1 ATTATTATAAATC
* *
31958 ATTTTTAT-AATG
1 ATTATTATAAATC
31970 ATTATTACTAAATC
1 ATTATTA-TAAATC
31984 ATT
1 ATT
31987 GTTCATTGTT
Statistics
Matches: 157, Mismatches: 16, Indels: 52
0.70 0.07 0.23
Matches are distributed among these distances:
11 18 0.11
12 43 0.27
13 5 0.03
14 39 0.25
15 2 0.01
16 16 0.10
17 2 0.01
18 6 0.04
19 22 0.14
20 2 0.01
21 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTATTATAAATC
Found at i:31797 original size:26 final size:25
Alignment explanation
Indices: 31715--31915 Score: 111
Period size: 26 Copynumber: 8.2 Consensus size: 25
31705 GTATTCTATA
31715 ATTATTAGTAATAATTA-T-TAAATC
1 ATTATTA-TAATAATTATTATAAATC
*
31739 ATTATTATAAATAATTA--CTAAAT-
1 ATTATTAT-AATAATTATTATAAATC
* **
31762 AATAACATAATAATTATTATAAAATC
1 ATTATTATAATAATTATTAT-AAATC
*
31788 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATAATTATTAT-AAATC
* * * *
31814 ATTACTA-AATCATCAAATCATTAAAT-
1 ATTATTATAATAAT--TATTA-TAAATC
*
31840 A-T-TTA-AATCATTA-T-TAAATC
1 ATTATTATAATAATTATTATAAATC
* *
31860 ATTTTTATAATGATTATTACTAAATC
1 ATTATTATAATAATTATTA-TAAATC
* *
31886 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATAATTATTAT-AAATC
31912 ATTA
1 ATTA
31916 CTAAATCATC
Statistics
Matches: 141, Mismatches: 19, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
19 5 0.04
20 1 0.01
21 1 0.01
22 12 0.09
23 13 0.09
24 30 0.21
25 11 0.08
26 60 0.43
27 7 0.05
28 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTATTATAATAATTATTATAAATC
Found at i:31937 original size:98 final size:98
Alignment explanation
Indices: 31768--31986 Score: 404
Period size: 98 Copynumber: 2.2 Consensus size: 98
31758 AAATAATAAC
* *
31768 ATAATAATTATTA-TAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAAT
1 ATAATGATTATTACT-AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAAT
31832 CATTAAATATTTAAATCATTATTAAATCATTTTT
65 CATTAAATATTTAAATCATTATTAAATCATTTTT
31866 ATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
31931 ATTAAATATTTAAATCATTATTAAATCATTTTT
66 ATTAAATATTTAAATCATTATTAAATCATTTTT
31964 ATAATGATTATTACTAAATCATT
1 ATAATGATTATTACTAAATCATT
31987 GTTCATTGTT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 117 0.99
99 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (98 bp):
ATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
ATTAAATATTTAAATCATTATTAAATCATTTTT
Found at i:31994 original size:7 final size:7
Alignment explanation
Indices: 31982--32008 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
31972 TATTACTAAA
31982 TCATTGT
1 TCATTGT
31989 TCATTGT
1 TCATTGT
31996 TCATTGT
1 TCATTGT
32003 TCATTG
1 TCATTG
32009 AACCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TCATTGT
Found at i:32100 original size:14 final size:14
Alignment explanation
Indices: 32081--32128 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
32071 TTCAAGTCGT
32081 AAATCATTACTATC
1 AAATCATTACTATC
32095 AAATCATTAC--T-
1 AAATCATTACTATC
*
32106 AAATCATTAATATC
1 AAATCATTACTATC
32120 AAATCATTA
1 AAATCATTA
32129 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:32108 original size:25 final size:25
Alignment explanation
Indices: 32080--32128 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
32070 GTTCAAGTCG
*
32080 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
32105 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
32129 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:32144 original size:21 final size:22
Alignment explanation
Indices: 32080--32138 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 22
32070 GTTCAAGTCG
*
32080 TAAATCATTACTATCAAATCATT
1 TAAATCATTAATATCAAATCA-T
32103 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
32127 TAAAT-ATTAATA
1 TAAATCATTAATA
32139 ATAAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
24 1 0.03
25 20 0.61
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:32149 original size:21 final size:22
Alignment explanation
Indices: 32080--32149 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
32070 GTTCAAGTCG
* *
32080 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATC-AA--ATTAT
*
32105 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATTAT
32127 TAAAT-ATTAATAAT-AAATTAT
1 TAAATCATTAAT-ATCAAATTAT
32148 TA
1 TA
32150 TTAAAACACG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 14 0.35
22 10 0.25
24 2 0.05
25 14 0.35
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATTAT
Found at i:34418 original size:45 final size:42
Alignment explanation
Indices: 34329--34429 Score: 130
Period size: 45 Copynumber: 2.3 Consensus size: 42
34319 GTTTAAACAC
*
34329 ACTAACAAATTAATTAAATATTTTTTACATTTAATAACTTAA
1 ACTAACAAATTAATTAAATATTTTTTACATATAATAACTTAA
* * * *
34371 ACTAAGAAACTAATTAACTAATTTTTTATATAATATATAACTTAA
1 ACTAACAAATTAATTAAAT-ATTTTTTACAT-ATA-ATAACTTAA
34416 ACTAACAAATTAAT
1 ACTAACAAATTAAT
34430 ATAATATAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 16 0.33
43 10 0.20
44 2 0.04
45 21 0.43
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.40
Consensus pattern (42 bp):
ACTAACAAATTAATTAAATATTTTTTACATATAATAACTTAA
Found at i:34436 original size:28 final size:28
Alignment explanation
Indices: 34405--34458 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
34395 TTTATATAAT
*
34405 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
34433 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
34459 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:34465 original size:28 final size:28
Alignment explanation
Indices: 34400--34465 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
34390 AATTTTTTAT
*
34400 ATAATATATAACTTAAACTAACAAATTA
1 ATAATATATAACTTAAACTAACAAACTA
34428 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
34456 ATAATTTATA
1 ATAATATATA
34466 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:34468 original size:21 final size:21
Alignment explanation
Indices: 34435--34483 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
34425 TTAATATAAT
34435 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
34456 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
34477 ATTAACT
1 A-TAACT
34484 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:35135 original size:30 final size:30
Alignment explanation
Indices: 35095--35204 Score: 184
Period size: 30 Copynumber: 3.7 Consensus size: 30
35085 TTTGGCGAGC
35095 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * *
35125 TGGCCGTGCATGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
35155 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
35185 TGGGCGTGCATGGAGGTCGT
1 TGGGCGTGCATGGAGGTCGT
35205 GGGGTAGGTC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.11, C:0.18, G:0.47, T:0.24
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:35252 original size:29 final size:29
Alignment explanation
Indices: 35211--35293 Score: 157
Period size: 29 Copynumber: 2.9 Consensus size: 29
35201 TCGTGGGGTA
*
35211 GGTCGCAGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
35240 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
35269 GGTCGCCGGGCGTGCATGGCGACCT
1 GGTCGCCGGGCGTGCATGGCGACCT
35294 ACCCCCGGTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.08, C:0.28, G:0.45, T:0.19
Consensus pattern (29 bp):
GGTCGCCGGGCGTGCATGGCGACCTGGTT
Found at i:39997 original size:17 final size:16
Alignment explanation
Indices: 39971--40023 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
39961 TTATACAAAA
*
39971 AAGTATTTAAATCATTT
1 AAGTACTTAAAT-ATTT
39988 AAGTACTTAAAATATTT
1 AAGTACTT-AAATATTT
*
40005 AAGTACTTATATGATTT
1 AAGTACTTAAAT-ATTT
40022 AA
1 AA
40024 ATATTTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 3 0.09
17 25 0.78
18 4 0.12
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (16 bp):
AAGTACTTAAATATTT
Found at i:40031 original size:25 final size:25
Alignment explanation
Indices: 39997--40054 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
39987 TAAGTACTTA
39997 AAATATTTAAGTACTTATATGATTT
1 AAATATTTAAGTACTTATATGATTT
40022 AAATATTTAAGTACTTATATGATTT
1 AAATATTTAAGTACTTATATGATTT
40047 AAATATTT
1 AAATATTT
40055 TTTATAGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (25 bp):
AAATATTTAAGTACTTATATGATTT
Found at i:40074 original size:17 final size:17
Alignment explanation
Indices: 40052--40084 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40042 GATTTAAATA
*
40052 TTTTTTATAGACATATT
1 TTTTTTATAGAAATATT
40069 TTTTTTATAGAAATAT
1 TTTTTTATAGAAATAT
40085 GGGTCTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTTTTATAGAAATATT
Found at i:41915 original size:16 final size:17
Alignment explanation
Indices: 41875--41916 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
41865 TATAAGATAT
41875 ATATTATTTTAAATTAA
1 ATATTATTTTAAATTAA
*
41892 A-ATAATTTTAAA-TAA
1 ATATTATTTTAAATTAA
41907 ATATTATTTT
1 ATATTATTTT
41917 GTAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 4 0.18
16 17 0.77
17 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTATTTTAAATTAA
Found at i:44452 original size:16 final size:16
Alignment explanation
Indices: 44431--44461 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44421 TTAAGCGATG
44431 AATGATTCAAATGCTA
1 AATGATTCAAATGCTA
*
44447 AATGATTCAGATGCT
1 AATGATTCAAATGCT
44462 CTGTATGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (16 bp):
AATGATTCAAATGCTA
Found at i:47392 original size:22 final size:21
Alignment explanation
Indices: 47346--47392 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
47336 AAAAAGGTCA
*
47346 AATT-TTTTAAATTTTGACAT
1 AATTATTTTAAATTTTGAAAT
* *
47366 GATTATTTTAAATATTTTAAAT
1 AATTATTTTAAAT-TTTGAAAT
47388 AATTA
1 AATTA
47393 AAATTTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
AATTATTTTAAATTTTGAAAT
Found at i:49752 original size:20 final size:20
Alignment explanation
Indices: 49708--49753 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
49698 TTGTGCAAAG
* *
49708 TCATTTAATAAATTTAATGA
1 TCATTTTATAAATGTAATGA
49728 T-ATTTTATAAGATGTAAT-A
1 TCATTTTATAA-ATGTAATGA
49747 TCATTTT
1 TCATTTT
49754 TAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (20 bp):
TCATTTTATAAATGTAATGA
Found at i:50616 original size:2 final size:2
Alignment explanation
Indices: 50609--50659 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
50599 TTTTATGTTT
50609 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
*
50651 TG TA TA TA T
1 TA TA TA TA T
50660 GTTTATCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57174 original size:58 final size:60
Alignment explanation
Indices: 57066--57182 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 60
57056 AAGAATAAAT
57066 TAATCATTTACATAAAAAAAATTAAGGAGAATTTAAAATAAAAATATGAAAA-TGAAAAA
1 TAATCATTTACATAAAAAAAATTAAGGAGAATTTAAAATAAAAATATGAAAATTGAAAAA
* *
57125 TAATCATTTCCGTAAAAAAAATTAAGGAGAATTTAAAAT-AAAATATGAAAATTGAAAA
1 TAATCATTTACATAAAAAAAATTAAGGAGAATTTAAAATAAAAATATGAAAATTGAAAA
57183 GATATTTACC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
58 12 0.22
59 43 0.78
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.26
Consensus pattern (60 bp):
TAATCATTTACATAAAAAAAATTAAGGAGAATTTAAAATAAAAATATGAAAATTGAAAAA
Found at i:58230 original size:20 final size:21
Alignment explanation
Indices: 58197--58235 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
58187 CTAAACTTTC
58197 AAAATCTATAAAATAATTATT
1 AAAATCTATAAAATAATTATT
* *
58218 AAAA-CTATCAAATTATTA
1 AAAATCTATAAAATAATTA
58236 CAAAATGATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATCTATAAAATAATTATT
Found at i:60905 original size:24 final size:24
Alignment explanation
Indices: 60878--60950 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
60868 CGTTCATTTA
60878 CGTTC-GTGAACGTTCGATTATGTT
1 CGTTCGGT-AACGTTCGATTATGTT
* * *
60902 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGATTATGTT
* *
60926 CGTTCGGTTATGTTC-ATTTATGTT
1 CGTTCGGTAACGTTCGA-TTATGTT
60950 C
1 C
60951 ATTCATTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 41 0.95
25 2 0.05
ACGTcount: A:0.12, C:0.15, G:0.23, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGATTATGTT
Found at i:60907 original size:14 final size:14
Alignment explanation
Indices: 60888--60940 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
60878 CGTTCGTGAA
*
60888 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
60902 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
60916 CG-T---TTATGTT
1 CGTTCGGTTATGTT
60926 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
60940 C
1 C
60941 ATTTATGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:60963 original size:24 final size:24
Alignment explanation
Indices: 60895--60950 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
60885 GAACGTTCGA
*
60895 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCAT
60919 TTATGTTCGTTCGGTTATGTTCAT
1 TTATGTTCGTTCGGTTATGTTCAT
60943 TTATGTTC
1 TTATGTTC
60951 ATTCATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.55
Consensus pattern (24 bp):
TTATGTTCGTTCGGTTATGTTCAT
Found at i:62071 original size:16 final size:16
Alignment explanation
Indices: 62046--62112 Score: 89
Period size: 16 Copynumber: 4.1 Consensus size: 16
62036 CCAACGTTTA
62046 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
62062 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
62078 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCG
*
62094 TGGTCGTTTTTATGTTCG
1 TGTTCG--TTTATGTTCG
62112 T
1 T
62113 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
16 34 0.77
18 10 0.23
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:62203 original size:16 final size:16
Alignment explanation
Indices: 62182--62214 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
62172 AAAAAAAATT
62182 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
62198 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
62214 T
1 T
62215 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:63525 original size:29 final size:29
Alignment explanation
Indices: 63492--63549 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
63482 GCAGAAATAA
*
63492 GATTTATATGTTTAATTATAGTAATTATT
1 GATTTATATGTTCAATTATAGTAATTATT
*
63521 GATTTATATGTTCAATTATGGTAATTATT
1 GATTTATATGTTCAATTATAGTAATTATT
63550 TCAATTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (29 bp):
GATTTATATGTTCAATTATAGTAATTATT
Found at i:64634 original size:3 final size:3
Alignment explanation
Indices: 64621--64679 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
64611 CGGGTCTTTT
** **
64621 TTA TATA TTA TTA TTA TCG TTA TT- TTAA TTA TTA TTA GCA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
64667 TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TT
64680 TACATATTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 35 0.80
4 5 0.11
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:66776 original size:22 final size:22
Alignment explanation
Indices: 66751--66794 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
66741 TCAAACGATG
*
66751 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
66773 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
66795 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:71823 original size:14 final size:15
Alignment explanation
Indices: 71804--71834 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
71794 AAGAGAAGAC
71804 AAATTTG-TGGGGCA
1 AAATTTGATGGGGCA
71818 AAATTTGATGGGGCA
1 AAATTTGATGGGGCA
71833 AA
1 AA
71835 TAAAACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (15 bp):
AAATTTGATGGGGCA
Found at i:72464 original size:35 final size:35
Alignment explanation
Indices: 72419--72517 Score: 112
Period size: 35 Copynumber: 2.8 Consensus size: 35
72409 GTTTCCTTCG
*
72419 AAAACAAATTTTGTCTCGCTTGAGACA-GT-TCTT
1 AAAACAAATTTTGTCTCACTTGAGACATGTATCTT
* *
72452 GAAAAACAAATTTTGTCTCACTTAAGACAATTTATCTT
1 --AAAACAAATTTTGTCTCACTTGAGAC-ATGTATCTT
* *
72490 AAAACAAATTTCGTCTCTCTTGAGACAT
1 AAAACAAATTTTGTCTCACTTGAGACAT
72518 TTTGCCTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
35 26 0.47
36 24 0.44
37 1 0.02
38 4 0.07
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (35 bp):
AAAACAAATTTTGTCTCACTTGAGACATGTATCTT
Found at i:72656 original size:107 final size:108
Alignment explanation
Indices: 72482--72794 Score: 473
Period size: 107 Copynumber: 3.0 Consensus size: 108
72472 CTTAAGACAA
*
72482 TTTATCTT-AAAACAAATTTCGTCTCTCTTGAGACA---TTTTGCCTTTGAGATACAAATTTTGA
1 TTTAT-TTAAAAACAAATTTCGTCTCGCTTGAGACATTTTTTTGCCTTTGAGATACAAATTTTGA
72543 ATTTGCTTCACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
65 ATTTGCTTCACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
* *
72587 TTT-TTTAAAAACAAATTTCGTCTCGCTTGGGACATTTTTTTGCCTTTGAGAAACAAATTTTGAA
1 TTTATTTAAAAACAAATTTCGTCTCGCTTGAGACATTTTTTTGCCTTTGAGATACAAATTTTGAA
72651 TTTGCTTCACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
66 TTTGCTTCACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
* * *
72694 TTTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTTT--CTCTGAGATACAAA-TTTAAA
1 TTTATTTAAAAACAAATTTCGTCTCGCTTGAGACATTTTTTTGCCTTTGAGATACAAATTTTGAA
* *
72756 TTTG-TTGTACTTGAAACAAAATTAATATCACTTGAGATT
66 TTTGCTT-CACTTGAAACAAAATTAATCTCACTTGAGATT
72795 TTCAAAGCTG
Statistics
Matches: 192, Mismatches: 10, Indels: 12
0.90 0.05 0.06
Matches are distributed among these distances:
103 2 0.01
104 28 0.15
105 42 0.22
106 12 0.06
107 72 0.38
108 36 0.19
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (108 bp):
TTTATTTAAAAACAAATTTCGTCTCGCTTGAGACATTTTTTTGCCTTTGAGATACAAATTTTGAA
TTTGCTTCACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
Found at i:72992 original size:28 final size:30
Alignment explanation
Indices: 72961--73036 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
72951 TTGTGAGACA
*
72961 GTTTCTCTTG-AA-ATAAATCTTTGAGTCT
1 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
*
72989 GTTTCTTTTGAAACAAAAATCTTTGAGTCT
1 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
*
73019 ATTTCT-TTGGAAACAAAA
1 GTTTCTCTT-GAAACAAAA
73037 TTTTGTCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 9 0.21
29 4 0.10
30 29 0.69
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (30 bp):
GTTTCTCTTGAAACAAAAATCTTTGAGTCT
Found at i:73037 original size:29 final size:30
Alignment explanation
Indices: 72975--73036 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
72965 CTCTTGAAAT
* *
72975 AAATCTTTGAGTCTGTTTCTTTTGAAACAA
1 AAATCTTTGAGTCTATTTCTTTGGAAACAA
73005 AAATCTTTGAGTCTATTTCTTTGGAAACAA
1 AAATCTTTGAGTCTATTTCTTTGGAAACAA
73035 AA
1 AA
73037 TTTTGTCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (30 bp):
AAATCTTTGAGTCTATTTCTTTGGAAACAA
Found at i:73095 original size:26 final size:27
Alignment explanation
Indices: 73057--73199 Score: 81
Period size: 26 Copynumber: 5.5 Consensus size: 27
73047 CTTAAGACAA
*
73057 TTTCTTTTGAAAAAATCTTTGAGTCTG
1 TTTCTCTTGAAAAAATCTTTGAGTCTG
* *
73084 TTTCTCTT---AAAA----TGAGACAG
1 TTTCTCTTGAAAAAATCTTTGAGTCTG
* *
73104 TTTCTCTTGAAATAAATCTTTGAATATG
1 TTTCTCTTGAAA-AAATCTTTGAGTCTG
* * *
73132 TTCCTTTTG-AAAAATCTTTGAGTTTG
1 TTTCTCTTGAAAAAATCTTTGAGTCTG
* * *
73158 CTTCTCTTAACAAAATCATCTTTGAGTCTA
1 TTTCTCTTGA-AAAA--ATCTTTGAGTCTG
73188 TTTCT-TT-AAAAA
1 TTTCTCTTGAAAAA
73200 CAAATGTTGT
Statistics
Matches: 86, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
20 14 0.16
23 1 0.01
24 7 0.08
26 18 0.21
27 13 0.15
28 16 0.19
29 2 0.02
30 15 0.17
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (27 bp):
TTTCTCTTGAAAAAATCTTTGAGTCTG
Found at i:73607 original size:28 final size:28
Alignment explanation
Indices: 73575--73638 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
73565 GCTTGTTTTA
* *
73575 CTTGAAACAAAACTTTGAGTCTATTTCT
1 CTTGAAACAAAACTTTGAATCGATTTCT
* *
73603 TTTGAAACAAATCTTTGAATCGATTTCT
1 CTTGAAACAAAACTTTGAATCGATTTCT
73631 CTTGAAAC
1 CTTGAAAC
73639 CATGATCCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (28 bp):
CTTGAAACAAAACTTTGAATCGATTTCT
Found at i:73860 original size:40 final size:40
Alignment explanation
Indices: 73805--74024 Score: 124
Period size: 40 Copynumber: 5.2 Consensus size: 40
73795 CCGTCCTCAA
* * *
73805 CACGTAGGAACCGTGTCATCCCTCGACTAGATCTCTTCAT
1 CACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCTTCAT
* * * *
73845 CACGTAGGAGCCGTGTCACCCCTAGATAACTAGCTGT-TCTCAT
1 CACGTAGGAGCCGTGTCATCCCTAG---ACCAGATCTCT-TCAT
** * * *
73888 TGCGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCAT
1 CACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCTTCAT
* * *
73934 CATGTATGAGCCGTGTCATTCCC-CGACCAGATCTCTTCAT
1 CACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCTTCAT
* *
73974 CACGTATGAGCCGTGTCA-CCCTAGATAACCAG-TCGTCCTCAT
1 CACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCTTCAT
74016 CACGTAGGA
1 CACGTAGGA
74025 ACTGAGTTAT
Statistics
Matches: 137, Mismatches: 26, Indels: 32
0.70 0.13 0.16
Matches are distributed among these distances:
38 3 0.02
39 1 0.01
40 52 0.38
41 2 0.01
42 20 0.15
43 29 0.21
44 2 0.01
46 25 0.18
47 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (40 bp):
CACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCTTCAT
Found at i:73887 original size:134 final size:133
Alignment explanation
Indices: 73646--74036 Score: 546
Period size: 134 Copynumber: 3.0 Consensus size: 133
73636 AACCATGATC
*
73646 CCTAAAGATGGCCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCTCTTCAT
1 CCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCTCTTCAT
*
73711 CACGTAGGAGTCGTGTCACCCCTAGATAACTAGTCGTCCTCATTGCGTAGGAACCGAGTTATCAC
66 CACGTAGGAGCCGTGTCACCCCTAGATAACTAGTCGTCCTCATTGCGTAGGAACCGAGTTATCAC
73776 CATT
131 C-TT
* * *
73780 CCTAAAGATGGCCAGCCGTCCTCAACACGTAGGAACCGTGTCATCCCTCGACTAGATCTCTTCAT
1 CCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCTCTTCAT
* *
73845 CACGTAGGAGCCGTGTCACCCCTAGATAACTAG-CTGTTCTCATTGCGTAGGAACCGTGTTATCA
66 CACGTAGGAGCCGTGTCACCCCTAGATAACTAGTC-GTCCTCATTGCGTAGGAACCGAGTTATCA
73909 CCTT
130 CCTT
* * * *
73913 --T--AGATGGCCAGAAC-TCTTCATCATGTATGAGCCGTGTCATTCCC-CGACCAGATCTCTTC
1 CCTAAAGATGGCCAG-ACGTCCTCATCACGTAGGAACCGTGTCA-TCCCTCGACCAGATCTCTTC
* * ** *
73972 ATCACGTATGAGCCGTGTCA-CCCTAGATAACCAGTCGTCCTCATCACGTAGGAACTGAGTTATC
64 ATCACGTAGGAGCCGTGTCACCCCTAGATAACTAGTCGTCCTCATTGCGTAGGAACCGAGTTATC
74036 A
129 A
74037 TCCACCCTTA
Statistics
Matches: 233, Mismatches: 20, Indels: 14
0.87 0.07 0.05
Matches are distributed among these distances:
128 37 0.16
129 64 0.27
130 5 0.02
131 1 0.00
133 3 0.01
134 123 0.53
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (133 bp):
CCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCTCTTCAT
CACGTAGGAGCCGTGTCACCCCTAGATAACTAGTCGTCCTCATTGCGTAGGAACCGAGTTATCAC
CTT
Found at i:74242 original size:3 final size:3
Alignment explanation
Indices: 74231--74287 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
74221 CCGGGTTTTT
** **
74231 TTA TATA TTA TTA TTA TCG TTA TT- TTAA TTA TTA TTA GCA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
74277 TTA TTA TTA TT
1 TTA TTA TTA TT
74288 TACATATTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.84
4 5 0.12
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:80506 original size:23 final size:25
Alignment explanation
Indices: 80479--80537 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 25
80469 TATAATATTT
80479 TTATATTTTTAATAAT-TAAAAA-A
1 TTATATTTTTAATAATATAAAAATA
80502 TTATATATTTTAATAATATAAAAATA
1 TTATAT-TTTTAATAATATAAAAATA
80528 TT-T-TTTTTAA
1 TTATATTTTTAA
80538 ATATTAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.36
24 11 0.33
25 7 0.21
26 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATATTTTTAATAATATAAAAATA
Found at i:87496 original size:23 final size:22
Alignment explanation
Indices: 87466--87511 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
87456 CAATGAAACG
87466 TTGGATGAATATGGATGCTTTTT
1 TTGGATGAATATGGATG-TTTTT
*
87489 TTGGATGAATTTGGATGTTTTT
1 TTGGATGAATATGGATGTTTTT
87511 T
1 T
87512 CAGGTGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.20, C:0.02, G:0.26, T:0.52
Consensus pattern (22 bp):
TTGGATGAATATGGATGTTTTT
Found at i:89569 original size:21 final size:21
Alignment explanation
Indices: 89544--89586 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
89534 ATTCAAAGAG
*
89544 TTTGACTGATAAAATGACACT
1 TTTGACTGATAAAATGAAACT
89565 TTTGACTGATAAAATGAAACT
1 TTTGACTGATAAAATGAAACT
89586 T
1 T
89587 CTAAACTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
TTTGACTGATAAAATGAAACT
Found at i:90577 original size:57 final size:58
Alignment explanation
Indices: 90472--90616 Score: 195
Period size: 57 Copynumber: 2.5 Consensus size: 58
90462 GTAAAGATAT
* * *
90472 GATAAGGTGACATGAATATAAAATATAATCTTATTCATATTTGATGATACGAAAATAA
1 GATAAGGTGACATGAATATAAGATATGATCTTATTCATATTTGATGATACAAAAATAA
* **
90530 GATAAGGTGACATGATTATGTGATATGATC-TATTCATATTTTG-TGATACAAAAATAA
1 GATAAGGTGACATGAATATAAGATATGATCTTATTCATA-TTTGATGATACAAAAATAA
* *
90587 GATAAAGTGACGTGAATATAAGATATGATC
1 GATAAGGTGACATGAATATAAGATATGATC
90617 AAGTGACTCG
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
57 46 0.61
58 29 0.39
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (58 bp):
GATAAGGTGACATGAATATAAGATATGATCTTATTCATATTTGATGATACAAAAATAA
Found at i:96111 original size:2 final size:2
Alignment explanation
Indices: 96104--96136 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
96094 ACAGACACCT
96104 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
96137 CATTTTGTTC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:103596 original size:32 final size:32
Alignment explanation
Indices: 103559--103651 Score: 88
Period size: 31 Copynumber: 3.0 Consensus size: 32
103549 AGAATGAGGT
*
103559 ATAAAATTTTATTTTTTTTAAATAATGAGTAC
1 ATAAAATTTTATTTTTTTTAAATAATGAGAAC
* * *
103591 ATAAAATTTT-TTTATCTTAAA-AATTA-AAC
1 ATAAAATTTTATTTTTTTTAAATAATGAGAAC
103620 -T-AAATTAAATTATTTTTTTTAAATAATGAGAA
1 ATAAAATT---TTATTTTTTTTAAATAATGAGAA
103652 TGTACTTGAC
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
27 5 0.10
28 1 0.02
29 2 0.04
30 6 0.12
31 18 0.38
32 14 0.29
33 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (32 bp):
ATAAAATTTTATTTTTTTTAAATAATGAGAAC
Found at i:122132 original size:21 final size:21
Alignment explanation
Indices: 122093--122132 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
122083 TGCGCTACAT
*
122093 TTTTTATTTTCTGATTTTTGG
1 TTTTTATTTTCTGACTTTTGG
* *
122114 TTTTTATTTTTTTACTTTT
1 TTTTTATTTTCTGACTTTT
122133 TTATTTTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTATTTTCTGACTTTTGG
Done.