Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008028.1 Hibiscus syriacus cultivar Beakdansim tig00110504_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: 72062
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Found at i:2447 original size:20 final size:19
Alignment explanation
Indices: 2422--2576 Score: 204
Period size: 20 Copynumber: 7.9 Consensus size: 19
2412 TTGGTTTACG
2422 GAATGTAAGATTACCAGTA
1 GAATGTAAGATTACCAGTA
* *
2441 TGAATGTAAAATTAACAGTGA
1 -GAATGTAAGATTACCAGT-A
*
2462 GAATGTAAGATTAACAGT-
1 GAATGTAAGATTACCAGTA
2480 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGT-A
*
2500 GAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAGT-A
*
2520 GAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAGT-A
2540 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGT-A
2560 GAATGTAAGATTACCAG
1 GAATGTAAGATTACCAG
2577 GGAATAAGAT
Statistics
Matches: 126, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.13
20 108 0.86
21 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.26
Consensus pattern (19 bp):
GAATGTAAGATTACCAGTA
Found at i:2535 original size:40 final size:39
Alignment explanation
Indices: 2422--2576 Score: 231
Period size: 40 Copynumber: 3.9 Consensus size: 39
2412 TTGGTTTACG
* * *
2422 GAATGTAAGATTACCAGTATGAATGTAAAATTAACAGTGA
1 GAATGTAAGATTACCAGT-GGAATGTAAGATTACCAGTGA
*
2462 GAATGTAAGATTAACAGT-GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGTGGAATGTAAGATTACCAGTGA
*
2500 GAATGTAAGATTACCAGTGGGAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAGT-GGAATGTAAGATTACCAGTGA
2540 GAATGTAAGATTACCAGTGAGAATGTAAGATTACCAG
1 GAATGTAAGATTACCAGTG-GAATGTAAGATTACCAG
2577 GGAATAAGAT
Statistics
Matches: 107, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
38 35 0.33
39 1 0.01
40 71 0.66
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.26
Consensus pattern (39 bp):
GAATGTAAGATTACCAGTGGAATGTAAGATTACCAGTGA
Found at i:2596 original size:15 final size:16
Alignment explanation
Indices: 2485--2589 Score: 66
Period size: 20 Copynumber: 5.6 Consensus size: 16
2475 ACAGTGAATG
2485 TAAGATTACCAGTGAGAA
1 TAAGATTACCAG-G-GAA
2503 TGTAAGATTACCAGTGGGAA
1 --TAAGATTACCA--GGGAA
2523 TGTAAGATTACCAGTGGGAA
1 --TAAGATTACCA--GGGAA
2543 TGTAAGATTACCAGTGAGAA
1 --TAAGATTACCAG-G-GAA
2563 TGTAAGATTACCAGGGAA
1 --TAAGATTACCAGGGAA
2581 TAAGATTAC
1 TAAGATTAC
2590 TGGGAATGTT
Statistics
Matches: 81, Mismatches: 0, Indels: 12
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.11
18 4 0.05
19 2 0.02
20 64 0.79
21 1 0.01
22 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.25
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:2695 original size:71 final size:71
Alignment explanation
Indices: 2604--2746 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
2594 AATGTTGTAT
*
2604 TTTGTGTTTGGTTGGTTTAGCAGGAATGTAAGATTACCGTGTTGGGTTAAAGGAATAAAAGATTA
1 TTTGTGTTTGGTTGGTTTAGCAAGAATGTAAGATTACCGTGTTGGGTTAAAGGAATAAAAGATTA
2669 TTGGAA
66 TTGGAA
* *
2675 TTTGTGTTTGGTTGGTTTAGCAAGAATGTAAGATTACCGTGTTTGGTTAAATGAATAAAAGATTA
1 TTTGTGTTTGGTTGGTTTAGCAAGAATGTAAGATTACCGTGTTGGGTTAAAGGAATAAAAGATTA
2740 TTGGAA
66 TTGGAA
2746 T
1 T
2747 GTATATTTGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.30, C:0.04, G:0.27, T:0.38
Consensus pattern (71 bp):
TTTGTGTTTGGTTGGTTTAGCAAGAATGTAAGATTACCGTGTTGGGTTAAAGGAATAAAAGATTA
TTGGAA
Found at i:10773 original size:13 final size:13
Alignment explanation
Indices: 10755--10780 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10745 TACTTTTAGA
10755 GCACTTGTAATAC
1 GCACTTGTAATAC
10768 GCACTTGTAATAC
1 GCACTTGTAATAC
10781 TTGCTTCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
GCACTTGTAATAC
Found at i:10837 original size:21 final size:21
Alignment explanation
Indices: 10803--10864 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
10793 TTATCATGTG
*
10803 TGTGTATATATATATATATAA
1 TGTGTGTATATATATATATAA
* *
10824 TGTGTGTGTGTATATATATAA
1 TGTGTGTATATATATATATAA
10845 TGTGTGTATATATATATATA
1 TGTGTGTATATATATATATA
10865 TATATATTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (21 bp):
TGTGTGTATATATATATATAA
Found at i:10839 original size:17 final size:19
Alignment explanation
Indices: 10811--10862 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 19
10801 TGTGTGTATA
10811 TATATATATATAATGTGTGTG
1 TATATATATATAA--TGTGTG
*
10832 TGTATATATATAATGTGTG
1 TATATATATATAATGTGTG
10851 TATATATATATA
1 TATATATATATA
10863 TATATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
21 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (19 bp):
TATATATATATAATGTGTG
Found at i:18858 original size:15 final size:15
Alignment explanation
Indices: 18838--18882 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
18828 TAATAAGGTT
18838 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
18853 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
18868 AATTATTATAAAATA
1 ATTTATTTTAAAATA
18883 TGGATTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:18895 original size:22 final size:22
Alignment explanation
Indices: 18870--19018 Score: 113
Period size: 22 Copynumber: 6.5 Consensus size: 22
18860 TTAAAATAAA
*
18870 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
* *
18892 TTATTTTAAAATAT--ATTTTAA
1 TTATTTTAAAATATGGA-TTGAT
* * * *
18913 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGAT
18936 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
*
18958 TTATTAATAATTTATTAGTATGGATTGAT
1 TTATT-TTAA---A--A-TATGGATTGAT
* *
18987 TTATTTTAAAATATGAATTTAT
1 TTATTTTAAAATATGGATTGAT
19009 TTATTTTAAA
1 TTATTTTAAA
19019 TAATTTATTA
Statistics
Matches: 99, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.01
21 9 0.09
22 53 0.54
23 13 0.13
24 1 0.01
25 1 0.01
26 1 0.01
28 4 0.04
29 16 0.16
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:19045 original size:54 final size:54
Alignment explanation
Indices: 18905--19315 Score: 413
Period size: 54 Copynumber: 7.7 Consensus size: 54
18895 TTTTAAAATA
18905 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
1 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
* *
18959 TA--TT-AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTTATT
1 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
*
19010 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTTATT
1 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
* * ** * * * * *
19060 TGTATGGATTGATTTATTTTAAAATATTGATTAATTTATTTTAAAATATGGATTGATT
1 TATTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTTAAAATATGGATTGATT
*
19118 TA-TTTAAATAA--T-TTAGTATGAATTGATTTATTTT-AAATATGGATTGATT
1 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
19167 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
1 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
* * * * * *
19221 TATTATT--ATAGTTCTA-T-GGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
1 TATT-TTAAATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTGATT
* *
19279 TATTTTAAATAATTTATTTGTATAGATTGATTTATTT
1 TATTTTAAATAATTTATTAGTATGGATTGATTTATTT
19316 ATTTTAAATA
Statistics
Matches: 296, Mismatches: 33, Indels: 55
0.77 0.09 0.14
Matches are distributed among these distances:
49 17 0.06
50 42 0.14
51 47 0.16
52 15 0.05
53 37 0.12
54 71 0.24
55 12 0.04
57 12 0.04
58 26 0.09
59 9 0.03
60 8 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
Found at i:19048 original size:32 final size:32
Alignment explanation
Indices: 18998--19082 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
18988 TATTTTAAAA
* *
18998 TATGAATTTATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
19030 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
19062 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
19083 ATATTGATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:19074 original size:18 final size:18
Alignment explanation
Indices: 19021--19078 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
19011 ATTTTAAATA
*
19021 ATTTATTAGTATGGATTG
1 ATTTATTTGTATGGATTG
* *
19039 ATTTATTT-TA---AATA
1 ATTTATTTGTATGGATTG
19053 ATTTATTTGTATGGATTG
1 ATTTATTTGTATGGATTG
19071 ATTTATTT
1 ATTTATTT
19079 TAAAATATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 10 0.32
15 2 0.06
17 2 0.06
18 17 0.55
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTTATTTGTATGGATTG
Found at i:19091 original size:22 final size:22
Alignment explanation
Indices: 19062--19175 Score: 131
Period size: 22 Copynumber: 5.0 Consensus size: 22
19052 AATTTATTTG
19062 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
* *
19084 TATTGATTAATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
19106 TATGGATTGATTTATTTAAATAATTTAG
1 TATGGATTGATTTATTT---TAA---AA
*
19134 TATGAATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAAA
19155 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
19176 TAATTTATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
21 18 0.23
22 37 0.48
24 1 0.01
25 4 0.05
28 17 0.22
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:19099 original size:72 final size:68
Alignment explanation
Indices: 19019--19170 Score: 189
Period size: 72 Copynumber: 2.1 Consensus size: 68
19009 TTATTTTAAA
* *
19019 TAATTTATT-AGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAA
1 TAATTTATTAAATATGGATTGATTTA-TTTAAATAATTTA---GTATGAATTGATTTATTTT-AA
*
19083 ATATTGAT
61 ATATGGAT
19091 TAATTTATTTTAAAATATGGATTGATTTATTTAAATAATTTAGTATGAATTGATTTATTTTAAAT
1 TAATTTA--TT-AAATATGGATTGATTTATTTAAATAATTTAGTATGAATTGATTTATTTTAAAT
19156 ATGGAT
63 ATGGAT
*
19162 TGATTTATT
1 TAATTTATT
19171 TTAAATAATT
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
69 2 0.03
71 15 0.21
72 25 0.35
74 2 0.03
75 13 0.18
76 15 0.21
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (68 bp):
TAATTTATTAAATATGGATTGATTTATTTAAATAATTTAGTATGAATTGATTTATTTTAAATATG
GAT
Found at i:19201 original size:18 final size:18
Alignment explanation
Indices: 19178--19225 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
19168 ATTTTAAATA
*
19178 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
19196 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
19218 ATTTATTA
1 ATTTATTA
19226 TTATAGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:19212 original size:22 final size:22
Alignment explanation
Indices: 19187--19255 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
19177 AATTTATTAG
19187 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
**
19209 TATGGATTGATTTATTATTATAGTTC
1 TATGGATTGATTTATT-TTA-A--AA
19235 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
19256 TAATTTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 16 0.40
23 3 0.08
24 2 0.05
25 3 0.08
26 16 0.40
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:19319 original size:26 final size:26
Alignment explanation
Indices: 19290--19367 Score: 61
Period size: 26 Copynumber: 3.0 Consensus size: 26
19280 ATTTTAAATA
*
19290 ATTTATTTGTATAGATTGATTTATTT
1 ATTTAATTGTATAGATTGATTTATTT
* * **
19316 ATTTTAAAT-AATTTATTGATTTA-TT
1 A-TTTAATTGTATAGATTGATTTATTT
* *
19341 ATTGTAGTTGTATGGATTGATTTATTT
1 ATT-TAATTGTATAGATTGATTTATTT
19368 TAAATAATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 7
0.69 0.18 0.13
Matches are distributed among these distances:
24 2 0.05
25 6 0.16
26 23 0.61
27 7 0.18
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (26 bp):
ATTTAATTGTATAGATTGATTTATTT
Found at i:19332 original size:36 final size:32
Alignment explanation
Indices: 19235--19315 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
19225 ATTATAGTTC
19235 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
19267 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
19299 TATAGATTGATTTATTT
1 TATGGATTGATTTATTT
19316 ATTTTAAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:19408 original size:22 final size:22
Alignment explanation
Indices: 19383--19425 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
19373 AATTTATTAG
19383 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
19405 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
19426 TAATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:25399 original size:24 final size:24
Alignment explanation
Indices: 25372--25427 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
25362 TTACTTGAAT
* *
25372 TCTGATCTGGATTCTGTTATGATA
1 TCTGATATGAATTCTGTTATGATA
* *
25396 TCTGATATGAATTCTGTTTTGATT
1 TCTGATATGAATTCTGTTATGATA
25420 TCTGATAT
1 TCTGATAT
25428 CTCCATTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (24 bp):
TCTGATATGAATTCTGTTATGATA
Found at i:26449 original size:2 final size:2
Alignment explanation
Indices: 26442--26483 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
26432 ATAAAAATAA
26442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26484 GGTCGGGTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27364 original size:18 final size:16
Alignment explanation
Indices: 27328--27359 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27318 GTTCATTTTA
27328 ATATTTTTTTAATATT
1 ATATTTTTTTAATATT
*
27344 ATATTTTTTTATTATT
1 ATATTTTTTTAATATT
27360 CTATACATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATATTTTTTTAATATT
Found at i:27771 original size:31 final size:31
Alignment explanation
Indices: 27736--27810 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
27726 AAATTGAAAA
27736 TTTAAGTATTAAAACATATCAAAATTAATAG
1 TTTAAGTATTAAAACATATCAAAATTAATAG
27767 TTTAAGTATTAAAACATATCAAAATTAATAG
1 TTTAAGTATTAAAACATATCAAAATTAATAG
*
27798 TTTATGTATTAAA
1 TTTAAGTATTAAA
27811 TATGTAGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (31 bp):
TTTAAGTATTAAAACATATCAAAATTAATAG
Found at i:42822 original size:14 final size:14
Alignment explanation
Indices: 42794--42834 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
42784 ATGCTTGAAG
42794 AAAAAAATGAA-AA
1 AAAAAAATGAAGAA
42807 AATAAAAA-GAAGAA
1 AA-AAAAATGAAGAA
42821 AAAAAAATGAAGAA
1 AAAAAAATGAAGAA
42835 GGAGGGTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (14 bp):
AAAAAAATGAAGAA
Found at i:44196 original size:271 final size:270
Alignment explanation
Indices: 43794--44284 Score: 788
Period size: 271 Copynumber: 1.8 Consensus size: 270
43784 AAAAAGAGAT
* *
43794 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
* *
43859 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
** * * *
43924 CTTGAGGAATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAA
131 CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCC--AAAAGAGAGAA
*
43989 GAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
194 GAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
44054 ACCTCGCTTGAG
259 ACCTCGCTTGAG
44066 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
* * *
44130 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAG-CATTTCGAGTTAGGGACGCCTC
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-AGACATTTCGAATCAGGGACACCTC
* * *
44194 GCTTGAGGGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
130 GCTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
*
44259 AAGTTCATAATGCGAAGAACTTGTTC
195 AAGTTCATAATGAGAAGAACTTGTTC
44285 AATCTAACAA
Statistics
Matches: 201, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
269 35 0.17
271 118 0.59
272 48 0.24
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (270 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAGA
AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACAC
CTCGCTTGAG
Found at i:44202 original size:135 final size:135
Alignment explanation
Indices: 43794--44284 Score: 770
Period size: 136 Copynumber: 3.6 Consensus size: 135
43784 AAAAAGAGAT
* *
43794 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACA-AGGGAGAAGAAGTT
43859 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
43924 CTTGAG
130 CTTGAG
* ** * *
43930 GAATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACAAGGGAGAAGAAGTT
43995 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
44060 CTTGAG
130 CTTGAG
*
44066 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* * * * *
44131 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-CAGCATTTCGAGTTAGGGACGCCTCG
66 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGA-CATTTCGAATCAGTGACACCTCG
44195 CTTGAG
130 CTTGAG
* * * *
44201 GGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAA-AAGAGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* *
44265 ATAATGCGAAGAACTTGTTC
66 ATAATGAGAAGAGCTTGTTC
44285 AATCTAACAA
Statistics
Matches: 328, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
134 33 0.10
135 125 0.38
136 168 0.51
137 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (135 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGC
TTGAG
Found at i:54283 original size:23 final size:22
Alignment explanation
Indices: 54256--54326 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
54246 GAATATCTTC
54256 TCATTTTCTACTATTAATCTCAG
1 TCATTTTCTACTA-TAATCTCAG
*
54279 TCATTTAT-T-TTA-ATATCTTC--
1 TCATTT-TCTACTATA-ATC-TCAG
54299 TCATTTTCTACTATAATCTCAG
1 TCATTTTCTACTATAATCTCAG
54321 TCATTT
1 TCATTT
54327 ATTTTTACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 17
0.67 0.04 0.30
Matches are distributed among these distances:
19 1 0.03
20 10 0.26
21 8 0.21
22 11 0.29
23 7 0.18
24 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.52
Consensus pattern (22 bp):
TCATTTTCTACTATAATCTCAG
Found at i:54333 original size:43 final size:43
Alignment explanation
Indices: 54247--54331 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
54237 TTCCCAAGTG
54247 AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
1 AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
54290 AATATCTTCTCATTTTCTACTA-TAATCTCAGTCATTTATTTT
1 AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
54332 TACTCATTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 20 0.48
43 22 0.52
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (43 bp):
AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
Found at i:58322 original size:13 final size:12
Alignment explanation
Indices: 58292--58325 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58282 TTTATGTATT
*
58292 ATTTTTTAATTA
1 ATTTTTTAAATA
58304 ATTTTTTAAATA
1 ATTTTTTAAATA
*
58316 ATATTTTAAA
1 ATTTTTTAAA
58326 AATAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTTTAAATA
Found at i:60383 original size:42 final size:43
Alignment explanation
Indices: 60324--60417 Score: 154
Period size: 42 Copynumber: 2.2 Consensus size: 43
60314 ATGTAGCATT
60324 TGGCCTGGGAGTTTGATTCAGCAATCC-TTGTTGCACAGCCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCCTTTGTTGCACAGCCTG
*
60366 TGGCCTGGGAGTTTGATTCAGTAATCCTTGTTGTTGCACAGCCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCC-T-TTGTTGCACAGCCTG
60411 TGGCCTG
1 TGGCCTG
60418 TACGTACAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 26 0.54
45 22 0.46
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (43 bp):
TGGCCTGGGAGTTTGATTCAGCAATCCTTTGTTGCACAGCCTG
Found at i:60531 original size:57 final size:56
Alignment explanation
Indices: 60443--60556 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 56
60433 ATTATAAATC
* *
60443 AAATACCAAGAGGAATATAATTTATTTAAGTATTTAATGCGTTTCCTTAATGGTTTG
1 AAATACCAAAAGGAATAGAATTTATTTAAGTATTTAATG-GTTTCCTTAATGGTTTG
*
60500 AAATACCAAAAGGAATAGAATTTATTTAAGTATTTAATGTTTTCCTTAATGGTTTG
1 AAATACCAAAAGGAATAGAATTTATTTAAGTATTTAATGGTTTCCTTAATGGTTTG
60556 A
1 A
60557 TGAGATAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 17 0.31
57 37 0.69
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (56 bp):
AAATACCAAAAGGAATAGAATTTATTTAAGTATTTAATGGTTTCCTTAATGGTTTG
Found at i:62475 original size:14 final size:14
Alignment explanation
Indices: 62456--62483 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
62446 CCGAGAACAT
62456 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
62470 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
62484 GGGCAACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:62485 original size:10 final size:10
Alignment explanation
Indices: 62433--62469 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
62423 ACACGTTGGG
62433 CATCCGAGGC
1 CATCCGAGGC
**
62443 CATCCGAGAA
1 CATCCGAGGC
62453 CATCCGAGGC
1 CATCCGAGGC
62463 CATCCGA
1 CATCCGA
62470 CCGAGGCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.27, C:0.38, G:0.24, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:62493 original size:24 final size:24
Alignment explanation
Indices: 62453--62498 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
62443 CATCCGAGAA
*
62453 CATCCGAGGCCATCCGACCGAGGC
1 CATCCGAGGCCAACCGACCGAGGC
* *
62477 CATCCGAGGGCAACCGAGCGAG
1 CATCCGAGGCCAACCGACCGAG
62499 CTATGCGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.37, G:0.33, T:0.07
Consensus pattern (24 bp):
CATCCGAGGCCAACCGACCGAGGC
Found at i:62568 original size:29 final size:29
Alignment explanation
Indices: 62535--62707 Score: 206
Period size: 29 Copynumber: 5.9 Consensus size: 29
62525 GAGCGAGGGT
62535 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
62564 AGGTCGCCCGGA--GCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* * * **
62591 AAGTCGTCCGGAGGGCATGGCGACCTATGTGGGT
1 AGGTCGCCCGGAGTGCATGGCGACCTA-----CA
* *
62625 AGGTCGCCCTGAGTACATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
62654 AGATCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
62683 AGGTCGCCCGGAGTGCCTGGCGACC
1 AGGTCGCCCGGAGTGCATGGCGACC
62708 AACGGCCAAC
Statistics
Matches: 121, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
27 25 0.21
29 74 0.61
34 22 0.18
ACGTcount: A:0.20, C:0.30, G:0.35, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:62665 original size:63 final size:61
Alignment explanation
Indices: 62564--62680 Score: 173
Period size: 63 Copynumber: 1.9 Consensus size: 61
62554 GCGACCTACA
*
62564 AGGTCGCCCGGAGCATGGCGACCTACAAAGTCGTCCGGAGGGCATGGCGACCTATGTGGGT
1 AGGTCGCCCGGAGCATGGCGACCTACAAAGTCGCCCGGAGGGCATGGCGACCTATGTGGGT
* *
62625 AGGTCGCCCTGAGTACATGGCGACCTAC-AAGATCGCCCGGAGTGCATGGCGACCTA
1 AGGTCGCCCGGAG--CATGGCGACCTACAAAG-TCGCCCGGAGGGCATGGCGACCTA
62681 CAAGGTCGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
61 12 0.24
62 3 0.06
63 35 0.70
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.16
Consensus pattern (61 bp):
AGGTCGCCCGGAGCATGGCGACCTACAAAGTCGCCCGGAGGGCATGGCGACCTATGTGGGT
Found at i:67084 original size:2 final size:2
Alignment explanation
Indices: 67077--67108 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
67067 TTACATTATG
67077 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
67109 ACAGTTATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.