Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000628.1 Hibiscus syriacus cultivar Beakdansim tig00001221_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: 75248
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:553 original size:18 final size:18
Alignment explanation
Indices: 530--575 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
520 TTTAGGTTGA
530 CTCTTCCTCTACCACTAC
1 CTCTTCCTCTACCACTAC
548 CTCTTCCTCTACCACTAC
1 CTCTTCCTCTACCACTAC
*
566 CCCTTCCTCT
1 CTCTTCCTCT
576 CTGAGTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.52, G:0.00, T:0.35
Consensus pattern (18 bp):
CTCTTCCTCTACCACTAC
Found at i:2484 original size:21 final size:20
Alignment explanation
Indices: 2392--2485 Score: 57
Period size: 21 Copynumber: 4.6 Consensus size: 20
2382 GGACAACCTT
*
2392 AAGGATCACATATATT-CCA
1 AAGGACCACATATATTCCCA
* * * *
2411 AAGGACCAAATATGTGTTCCG
1 AAGGACCACATATAT-TCCCA
* *
2432 AAGAACCGCATATATGTTCCC-
1 AAGGACCACATATA--TTCCCA
**
2453 AAGGATTACATATATATCCCA
1 AAGGACCACATATAT-TCCCA
2474 AAGGACCACATA
1 AAGGACCACATA
2486 GAACCCTCGA
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
19 13 0.24
20 5 0.09
21 32 0.59
22 3 0.06
23 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.23
Consensus pattern (20 bp):
AAGGACCACATATATTCCCA
Found at i:8261 original size:20 final size:20
Alignment explanation
Indices: 8236--8287 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
8226 GATGTAAGCA
*
8236 GTATCGATACCAAAAGGGAG
1 GTATCGATACCAAAAGGAAG
* **
8256 GTATCGATACTATGAGGAAG
1 GTATCGATACCAAAAGGAAG
8276 GTATCGATACCA
1 GTATCGATACCA
8288 TTGTTAACAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (20 bp):
GTATCGATACCAAAAGGAAG
Found at i:8334 original size:19 final size:21
Alignment explanation
Indices: 8310--8358 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
8300 TGCAAAAATG
*
8310 GTATCGATACCGTA-ATAG-A
1 GTATCGATACCATAGATAGTA
*
8329 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
8351 GTATCGAT
1 GTATCGAT
8359 GAAGCTCCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.50
21 4 0.17
22 8 0.33
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:8618 original size:54 final size:54
Alignment explanation
Indices: 8533--9033 Score: 759
Period size: 54 Copynumber: 9.3 Consensus size: 54
8523 ACCAAATAGG
8533 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* *
8587 GGTACTAAGTGTGCAATTCACGGAATTCATCATATATTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
8641 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCATCTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* *
8695 GACACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAATCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
8749 GGCACTAAGTGTCCAATTCACAGAATTCATCATATGTTGATGAATAGCTGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* *
8803 GGCACTAAGTGTACAATTCACGTAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * *
8857 GACACTAAGAGTGCAATTCACGGAATTCATCATATGTTGATGAATAATCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
**
8911 AACACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * * * * * *
8965 GGCACTAAGTGTGCAATTCACGAAATTCATAATATGTTTATGAATGATCGTATA
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
*
9019 GGCACTATGTGTGCA
1 GGCACTAAGTGTGCA
9034 TCGTAACGAA
Statistics
Matches: 406, Mismatches: 41, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 406 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:12523 original size:46 final size:46
Alignment explanation
Indices: 12456--12643 Score: 238
Period size: 46 Copynumber: 4.1 Consensus size: 46
12446 TAAGTTTTTC
* * * *
12456 AAAAAAGA-GTGTTTAGAGTGAAAACCCGAAAGGGCACTCGAAATCG
1 AAAAAA-ATGTGTTTAGAGTGAAAACCCAAAAGGGCGCTCTAAATCT
*
12502 AAAAAAATGTGTTTAGAGTGAAAACCCAAAAGGCCGCTCTAAAT-T
1 AAAAAAATGTGTTTAGAGTGAAAACCCAAAAGGGCGCTCTAAATCT
* * * *
12547 AAAAAAATATGTTTAGAGTAAAAAACCAAAAGGGCGCTCTAAATAT
1 AAAAAAATGTGTTTAGAGTGAAAACCCAAAAGGGCGCTCTAAATCT
* * *
12593 AAAAAAATGTGTTTATAGTGAAAACCCGAAATGGCGCTCTAAATC-
1 AAAAAAATGTGTTTAGAGTGAAAACCCAAAAGGGCGCTCTAAATCT
12638 AAAAAA
1 AAAAAA
12644 CAAAAAAACA
Statistics
Matches: 124, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
45 47 0.38
46 77 0.62
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (46 bp):
AAAAAAATGTGTTTAGAGTGAAAACCCAAAAGGGCGCTCTAAATCT
Found at i:12562 original size:91 final size:92
Alignment explanation
Indices: 12456--12643 Score: 254
Period size: 91 Copynumber: 2.1 Consensus size: 92
12446 TAAGTTTTTC
* * * *
12456 AAAAAAGAGTGTTTAGAGTGAAAACCCGAAAGGGCACTCGAAATCGAAAAAAATGTGTTTAGAGT
1 AAAAAAGAGTGTTTAGAGTAAAAAACCAAAAGGGCACTCGAAATAGAAAAAAATGTGTTTAGAGT
*
12521 GAAAACCC-AAAAGGCCGCTCTAAATTA
66 GAAAACCCGAAAAGG-CGCTCTAAATCA
* * * * *
12548 AAAAAATA-TGTTTAGAGTAAAAAACCAAAAGGGCGCTCTAAATATAAAAAAATGTGTTTATAGT
1 AAAAAAGAGTGTTTAGAGTAAAAAACCAAAAGGGCACTCGAAATAGAAAAAAATGTGTTTAGAGT
*
12612 GAAAACCCGAAATGGCGCTCTAAATCA
66 GAAAACCCGAAAAGGCGCTCTAAATCA
12639 AAAAA
1 AAAAA
12644 CAAAAAAACA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
91 72 0.86
92 12 0.14
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (92 bp):
AAAAAAGAGTGTTTAGAGTAAAAAACCAAAAGGGCACTCGAAATAGAAAAAAATGTGTTTAGAGT
GAAAACCCGAAAAGGCGCTCTAAATCA
Found at i:14487 original size:23 final size:22
Alignment explanation
Indices: 14449--14533 Score: 91
Period size: 23 Copynumber: 3.8 Consensus size: 22
14439 TATATAATAT
14449 ATATAGTTTTTGAAAACATAAA
1 ATATAGTTTTTGAAAACATAAA
**
14471 ATATAGTTTTTGAAAAACATATT
1 ATATAGTTTTTG-AAAACATAAA
**
14494 ATATA-AATTTGAAAACATATAA
1 ATATAGTTTTTGAAAACATA-AA
*
14516 TATATAGTTTTTTAAAAC
1 -ATATAGTTTTTGAAAAC
14534 GGTTTTTTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 8 0.16
22 16 0.32
23 18 0.36
24 8 0.16
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
ATATAGTTTTTGAAAACATAAA
Found at i:14508 original size:21 final size:22
Alignment explanation
Indices: 14457--14519 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
14447 ATATATAGTT
* **
14457 TTTG-AAAACATAAAATATAGTT
1 TTTGAAAAACATATAATATA-AA
*
14479 TTTGAAAAACATATTATATAAA
1 TTTGAAAAACATATAATATAAA
14501 TTTG-AAAACATATAATATA
1 TTTGAAAAACATATAATATA
14520 TAGTTTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 14 0.40
22 8 0.23
23 13 0.37
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (22 bp):
TTTGAAAAACATATAATATAAA
Found at i:14543 original size:38 final size:39
Alignment explanation
Indices: 14501--14639 Score: 176
Period size: 38 Copynumber: 3.6 Consensus size: 39
14491 ATTATATAAA
14501 TTTGAAAACATATA-ATATATAGTTTTTTAAAACGGTTT
1 TTTGAAAACATATATATATATAGTTTTTTAAAACGGTTT
* **
14539 TTTGAAAACATATATA-ATATAGTTTTTGAAAACATATTAT
1 TTTGAAAACATATATATATATAGTTTTTTAAAAC-GGTT-T
* *
14579 TTTGAAAATATATATATATATAGTTTTTTAAAACGG-AT
1 TTTGAAAACATATATATATATAGTTTTTTAAAACGGTTT
*
14617 TTCGAAAACATATATAGTATATA
1 TTTGAAAACATATATA-TATATA
14640 TAATCTTTGA
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
38 45 0.52
39 9 0.10
40 16 0.19
41 16 0.19
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (39 bp):
TTTGAAAACATATATATATATAGTTTTTTAAAACGGTTT
Found at i:14686 original size:23 final size:23
Alignment explanation
Indices: 14654--14716 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
14644 CTTTGAAAAC
14654 ATAT-TATATTATT-TTTTAAAT
1 ATATATATATTATTATTTTAAAT
*
14675 ATAATATATATTATATAGTTTTTAAT
1 AT-ATATATATTAT-TA-TTTTAAAT
*
14701 ATATACATATTATTAT
1 ATATATATATTATTAT
14717 ATATTATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 9 0.26
24 3 0.09
25 10 0.29
26 9 0.26
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATATATATTATTATTTTAAAT
Found at i:14686 original size:28 final size:30
Alignment explanation
Indices: 14654--14718 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 30
14644 CTTTGAAAAC
*
14654 ATATTATATTATTTTTTAA-ATATA-ATAT
1 ATATTATATTAGTTTTTAATATATACATAT
14682 ATATTATA-TAGTTTTTAATATATACATAT
1 ATATTATATTAGTTTTTAATATATACATAT
14711 -TATTATAT
1 ATATTATAT
14719 ATTATTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 9 0.27
28 20 0.61
29 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (30 bp):
ATATTATATTAGTTTTTAATATATACATAT
Found at i:15322 original size:20 final size:20
Alignment explanation
Indices: 15297--15346 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
15287 GGTCATTTCT
15297 AGCCGTTGGAAGTGTTTTGG
1 AGCCGTTGGAAGTGTTTTGG
15317 AGCCGTTGGAAGTGTTTTGG
1 AGCCGTTGGAAGTGTTTTGG
15337 AGCCGTTGGA
1 AGCCGTTGGA
15347 GCCATTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.32
Consensus pattern (20 bp):
AGCCGTTGGAAGTGTTTTGG
Found at i:20121 original size:3 final size:3
Alignment explanation
Indices: 20108--20148 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
20098 ATTTATTGAC
20108 ATT ATTT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
20149 GAAGAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:20127 original size:16 final size:16
Alignment explanation
Indices: 20116--20148 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20106 ACATTATTTA
20116 TTATTATTATTATTAT
1 TTATTATTATTATTAT
20132 TTATTATTATTATTAT
1 TTATTATTATTATTAT
20148 T
1 T
20149 GAAGAAAAAA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:20130 original size:19 final size:19
Alignment explanation
Indices: 20108--20148 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
20098 ATTTATTGAC
20108 ATTATTTATTATTATTATT
1 ATTATTTATTATTATTATT
20127 ATTATTTATTATTATTATT
1 ATTATTTATTATTATTATT
20146 ATT
1 ATT
20149 GAAGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTATTTATTATTATTATT
Found at i:24313 original size:39 final size:39
Alignment explanation
Indices: 24259--24356 Score: 169
Period size: 39 Copynumber: 2.5 Consensus size: 39
24249 AATGGCATAT
* *
24259 CAAGAGCAGAATGCACTTGTCCCTTACGCTATCAGATAC
1 CAAGAGCACAATGCACTTGTCCCTTACACTATCAGATAC
*
24298 CAAGAGCACAATGCACTTGTCCCTTATACTATCAGATAC
1 CAAGAGCACAATGCACTTGTCCCTTACACTATCAGATAC
24337 CAAGAGCACAATGCACTTGT
1 CAAGAGCACAATGCACTTGT
24357 TGTTCATAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (39 bp):
CAAGAGCACAATGCACTTGTCCCTTACACTATCAGATAC
Found at i:35677 original size:74 final size:74
Alignment explanation
Indices: 35551--35699 Score: 280
Period size: 74 Copynumber: 2.0 Consensus size: 74
35541 TACCAGCAAG
*
35551 ATTCGTTCAGGTGATAAATAATTTGATATTGCTCAAGTAATATTTCGAGTTTTAGTCATTGTGTA
1 ATTCATTCAGGTGATAAATAATTTGATATTGCTCAAGTAATATTTCGAGTTTTAGTCATTGTGTA
*
35616 TATAAAAAA
66 TACAAAAAA
35625 ATTCATTCAGGTGATAAATAATTTGATATTGCTCAAGTAATATTTCGAGTTTTAGTCATTGTGTA
1 ATTCATTCAGGTGATAAATAATTTGATATTGCTCAAGTAATATTTCGAGTTTTAGTCATTGTGTA
35690 TACAAAAAA
66 TACAAAAAA
35699 A
1 A
35700 AATTATTATG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (74 bp):
ATTCATTCAGGTGATAAATAATTTGATATTGCTCAAGTAATATTTCGAGTTTTAGTCATTGTGTA
TACAAAAAA
Found at i:36787 original size:60 final size:60
Alignment explanation
Indices: 36694--36809 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
36684 ATTGTCGATT
* **** * *
36694 GACTATTTTGTAACTTTTAATAGTTGGGAGACTCAATAAAGTAAT-TCTATATAGTCAATA
1 GACTATTTTATAACTTTTAATAGCCAAGAGACTCAACAAAATAATATCT-TATAGTCAATA
36754 GACTATTTTATAACTTTTAATAGCCAAGAGACTCAACAAAATAATATCTTATAGTC
1 GACTATTTTATAACTTTTAATAGCCAAGAGACTCAACAAAATAATATCTTATAGTC
36810 GAGAGACCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 45 0.94
61 3 0.06
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (60 bp):
GACTATTTTATAACTTTTAATAGCCAAGAGACTCAACAAAATAATATCTTATAGTCAATA
Found at i:39295 original size:20 final size:20
Alignment explanation
Indices: 39270--39313 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39260 CTAAATATAT
*
39270 AATTTA-AAAATTTTAATTAA
1 AATTTATAAAA-TTAAATTAA
*
39290 AATTTATTAAATTAAATTAA
1 AATTTATAAAATTAAATTAA
39310 AATT
1 AATT
39314 ACAACAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTATAAAATTAAATTAA
Found at i:41416 original size:30 final size:30
Alignment explanation
Indices: 41370--41429 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
41360 ATTGCATAAA
*
41370 ATTAATTGAACTGTAAGAAATAGATAAAAT
1 ATTAATTGAACCGTAAGAAATAGATAAAAT
*
41400 ATTAGTTGAACCGTAAGAAATAGATAAAAT
1 ATTAATTGAACCGTAAGAAATAGATAAAAT
41430 CAGGACAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.15, T:0.28
Consensus pattern (30 bp):
ATTAATTGAACCGTAAGAAATAGATAAAAT
Found at i:43926 original size:20 final size:21
Alignment explanation
Indices: 43901--43941 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
43891 GAATTCAACA
*
43901 ATGAAAAGTT-AAGCATTGAT
1 ATGAAAAATTAAAGCATTGAT
43921 ATGAAAAATTAGAAGCATTGA
1 ATGAAAAATTA-AAGCATTGA
43942 ATTTATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.27
Consensus pattern (21 bp):
ATGAAAAATTAAAGCATTGAT
Found at i:44405 original size:21 final size:21
Alignment explanation
Indices: 44384--44423 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44374 ATTAAAATTA
*
44384 AAATAAT-ACATAATATATTT
1 AAATAATCAAATAATATATTT
*
44404 AAATACTCAAATAATATATT
1 AAATAATCAAATAATATATT
44424 ATCAACATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATCAAATAATATATTT
Found at i:46788 original size:18 final size:17
Alignment explanation
Indices: 46763--46806 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
46753 ATCTTTGTGT
46763 TTTA-ATTTATCCAAAAA
1 TTTATATTTAT-CAAAAA
*
46780 TTTATATTTTATCAAGAA
1 TTTATA-TTTATCAAAAA
46798 TTTATATTT
1 TTTATATTT
46807 TGTAAGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 12 0.50
19 5 0.21
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTATATTTATCAAAAA
Found at i:46807 original size:18 final size:19
Alignment explanation
Indices: 46768--46807 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
46758 TGTGTTTTAA
46768 TTTATCCAAAAATTTATAT
1 TTTATCCAAAAATTTATAT
*
46787 TTTAT-CAAGAATTTATAT
1 TTTATCCAAAAATTTATAT
46805 TTT
1 TTT
46808 GTAAGTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTATCCAAAAATTTATAT
Found at i:48309 original size:2 final size:2
Alignment explanation
Indices: 48302--48327 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48292 GAGAGCAACA
48302 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
48328 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50212 original size:53 final size:53
Alignment explanation
Indices: 50132--50345 Score: 365
Period size: 53 Copynumber: 4.0 Consensus size: 53
50122 GTTATTTTGA
* *
50132 AAGTATACGAAAGTATGCAACAAAATCACTCCACTAAACCATATAATAATCAT
1 AAGTATATGAAAGTAAGCAACAAAATCACTCCACTAAACCATATAATAATCAT
50185 AAGTATATGAAAGTAAGCAACAAAATCACTCCACTAAACCATATAATAATCAT
1 AAGTATATGAAAGTAAGCAACAAAATCACTCCACTAAACCATATAATAATCAT
50238 AAGTATATGAAAGTAAGCAACAAAATCACTCCACTAAACCATATAATAATCAT
1 AAGTATATGAAAGTAAGCAACAAAATCACTCCACTAAACCATATAATAATCAT
* * * * *
50291 AAGTATATGAAAGTATGCAACTAAATCACTCCACTAAACTATATTATAATAAT
1 AAGTATATGAAAGTAAGCAACAAAATCACTCCACTAAACCATATAATAATCAT
50344 AA
1 AA
50346 TAATAATAAT
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 154 1.00
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.24
Consensus pattern (53 bp):
AAGTATATGAAAGTAAGCAACAAAATCACTCCACTAAACCATATAATAATCAT
Found at i:50344 original size:3 final size:3
Alignment explanation
Indices: 50336--50372 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
50326 AAACTATATT
50336 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
50373 CAAAATGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:57468 original size:7 final size:8
Alignment explanation
Indices: 57452--57476 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
57442 CACGGAGAAG
57452 AAAATAAA
1 AAAATAAA
57460 AAAATAAA
1 AAAATAAA
57468 AAAATAAA
1 AAAATAAA
57476 A
1 A
57477 CATATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:61233 original size:23 final size:24
Alignment explanation
Indices: 61192--61236 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
61182 CCAATTTTTT
*
61192 TCGGTTAATCGATCGATTATTTGA
1 TCGGTTAATCGATCAATTATTTGA
*
61216 TCGGTTAA-CGATTAATTATTT
1 TCGGTTAATCGATCAATTATTT
61237 TTTTCAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (24 bp):
TCGGTTAATCGATCAATTATTTGA
Found at i:65620 original size:19 final size:19
Alignment explanation
Indices: 65596--65640 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
65586 ATTTAAAATT
*
65596 CATTTTAATACAAAATGTA
1 CATTTTAACACAAAATGTA
* *
65615 CATTTTACCACAAAATGTC
1 CATTTTAACACAAAATGTA
65634 CATTTTA
1 CATTTTA
65641 CCCTTGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (19 bp):
CATTTTAACACAAAATGTA
Found at i:65641 original size:19 final size:19
Alignment explanation
Indices: 65605--65642 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
65595 TCATTTTAAT
65605 ACAAAATGTACATTTTACC
1 ACAAAATGTACATTTTACC
*
65624 ACAAAATGTCCATTTTACC
1 ACAAAATGTACATTTTACC
65643 CTTGAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (19 bp):
ACAAAATGTACATTTTACC
Found at i:66793 original size:313 final size:313
Alignment explanation
Indices: 66100--66894 Score: 986
Period size: 313 Copynumber: 2.5 Consensus size: 313
66090 ACACCAAACC
* * * *
66100 TTCATTATTCATTCTCTGGTTACTAACTGAATTTTTAGGGTATTACAACGATGTTAAGTTAAGGT
1 TTCATTATTCA-T-TCTGATTACTAACTGAATTTTTAGGGTATTACAACGAGGTTACGTTAAGAT
* * * * * * * * *
66165 TAACATTGATGATGTTTTTGGAGTGGCTTTTGGAGGTGTTGTAGTGAACAA-TAGGGTGATTTGT
64 TAACGTTGATGATGTTTTTGAAGTGGCTATTGGTGGTGGTGAAATGAAGAAGTAGGGTGATTTGC
* * * *
66229 ATGACATAGTAATAGACTAGTTCTAACAAGCCATGTAAAGGTTTTACGTCGCATGCATAAACCGA
129 ATGAGATAGTAAAAGACTAGTTCTAACAAGTCATGCAAAGGTTTTACGTCGCATGCATAAACCGA
* *
66294 GTGTGGTTGAGGTGAATGCTCTCACTACTGAAGGTTTACATGTTGCACTTGATAATGGTTGGAGT
194 GCGTGGTTGAGGTGAATGCTCTCACTACTGAAGGTTTACATGTTGCACTTGATAATGGTTGGAAT
* **
66359 GTTTTTGTAAAAAGGGACGCCACCAACTTGGTTAATAAGCTTTTGCATCATGGCC
259 GTTTTTGTAAAAAGGGACGCCACCAACTTGGTTAATAAGCTTATGCATCATGGAA
* * *
66414 TTCATTATTCATTTTGATTACTAACTGAATTTTTAGGGTATTATAATG-GCGTTACGTTAAGATT
1 TTCATTATTCATTCTGATTACTAACTGAATTTTTAGGGTATTACAACGAG-GTTACGTTAAGATT
* * * * *
66478 AACGTTGATGATGATTTTGAAGTGGATATCGGTGGTGGTGAAATGTAGAAGTAAGGTGATTTGCA
65 AACGTTGATGATGTTTTTGAAGTGGCTATTGGTGGTGGTGAAATGAAGAAGTAGGGTGATTTGCA
* * * * *
66543 TAAGATATTAAAAGACTAGTTCTAAAAAGTCATGCAAAGGTTTTACGTCGTATGCAT-GACCTGA
130 TGAGATAGTAAAAGACTAGTTCTAACAAGTCATGCAAAGGTTTTACGTCGCATGCATAAACC-GA
* ** *
66607 GCGTTGTTGAGGTGTGTGCTCTCACTATTGAAGGTTTACATGTTGCACTTGATAATGGTTGGAAT
194 GCGTGGTTGAGGTGAATGCTCTCACTACTGAAGGTTTACATGTTGCACTTGATAATGGTTGGAAT
* * * *
66672 G-TTTTGTAAAAAGGGCCGCCGCCAACTTTGTTAATAAGCTTATGCCTCATGGAA
259 GTTTTTGTAAAAAGGGACGCCACCAACTTGGTTAATAAGCTTATGCATCATGGAA
* ** * *
66726 TTCATTATTCATTCTGATTACTAACTTAATTTTTTAATGTATTACAACGAGGTTACTTTATGATT
1 TTCATTATTCATTCTGATTACTAACTGAA-TTTTTAGGGTATTACAACGAGGTTACGTTAAGATT
* * * ** *
66791 AACGTTGATAATGTTTTTTGAAGTGGCTATTGGTGGTGGTGGTGCAATGCAGCGGTAGGGCGATT
65 AACGTTGATGATG-TTTTTGAAGTGGCTA-T--TGGTGGTGGTGAAATGAAGAAGTAGGGTGATT
*
66856 TGCATGAGATAGTAAGAGACTAGTTCTAACAAGTCATGC
126 TGCATGAGATAGTAAAAGACTAGTTCTAACAAGTCATGC
66895 TATAATATCC
Statistics
Matches: 407, Mismatches: 65, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
312 158 0.39
313 163 0.40
314 25 0.06
315 1 0.00
317 60 0.15
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (313 bp):
TTCATTATTCATTCTGATTACTAACTGAATTTTTAGGGTATTACAACGAGGTTACGTTAAGATTA
ACGTTGATGATGTTTTTGAAGTGGCTATTGGTGGTGGTGAAATGAAGAAGTAGGGTGATTTGCAT
GAGATAGTAAAAGACTAGTTCTAACAAGTCATGCAAAGGTTTTACGTCGCATGCATAAACCGAGC
GTGGTTGAGGTGAATGCTCTCACTACTGAAGGTTTACATGTTGCACTTGATAATGGTTGGAATGT
TTTTGTAAAAAGGGACGCCACCAACTTGGTTAATAAGCTTATGCATCATGGAA
Found at i:72546 original size:24 final size:24
Alignment explanation
Indices: 72519--72568 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
72509 GACCTGACAT
72519 TATGTTTAGTGTTTGCTTATGTGC
1 TATGTTTAGTGTTTGCTTATGTGC
72543 TATGTTTAGTGTTTGCTTATGTGC
1 TATGTTTAGTGTTTGCTTATGTGC
72567 TA
1 TA
72569 GATTTCAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.08, G:0.24, T:0.54
Consensus pattern (24 bp):
TATGTTTAGTGTTTGCTTATGTGC
Done.