Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003151.1 Hibiscus syriacus cultivar Beakdansim tig00006626_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: 69252
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2944 original size:29 final size:30
Alignment explanation
Indices: 2887--2944 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
2877 CAAATGTTAT
* *
2887 AAAATGATTATTAAAATTATCGAATATTAC
1 AAAATGATTATTAAAATTATCCAAAATTAC
* *
2917 AAAATGATTTTTAAATTTA-CCAAAATTA
1 AAAATGATTATTAAAATTATCCAAAATTA
2945 TTATTATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (30 bp):
AAAATGATTATTAAAATTATCCAAAATTAC
Found at i:5255 original size:16 final size:16
Alignment explanation
Indices: 5234--5406 Score: 79
Period size: 16 Copynumber: 10.4 Consensus size: 16
5224 GTTCATGTAT
5234 ATTTATATATAATATA
1 ATTTATATATAATATA
*
5250 ATTTATATTAACAAATTAACTA
1 ATTTATA-T-A-TAA-T-A-TA
* *
5272 GTTTATACATAATATA
1 ATTTATATATAATATA
5288 ATTTATATAGT-ATATA
1 ATTTATATA-TAATATA
*
5304 A-ATATATATACATAT-
1 ATTTATATATA-ATATA
*
5319 ATATATATAT-ATATA
1 ATTTATATATAATATA
*
5334 TATATATATATATATATA
1 -ATTTATATATA-ATATA
* *
5352 TATGTT-TTTAT-TTATA
1 -AT-TTATATATAATATA
* * *
5368 TTTTATATTTTATATA
1 ATTTATATATAATATA
* *
5384 GTTTATATATAGTATA
1 ATTTATATATAATATA
5400 ATTTATA
1 ATTTATA
5407 CATACTATAT
Statistics
Matches: 121, Mismatches: 19, Indels: 34
0.70 0.11 0.20
Matches are distributed among these distances:
14 7 0.06
15 11 0.09
16 70 0.58
17 3 0.02
18 14 0.12
19 5 0.04
20 2 0.02
21 1 0.01
22 8 0.07
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTATATATAATATA
Found at i:5303 original size:2 final size:2
Alignment explanation
Indices: 5291--5502 Score: 104
Period size: 2 Copynumber: 108.0 Consensus size: 2
5281 TAATATAATT
* *
5291 TA TA TA GTA TA TA AA TA TA TA TA CA 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
* * * * *
5334 TA TA TA TA TA TA TA TA TA TA TG TT TT TA TT TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5375 T- TT TA TA TA GTT TA TA TA TA GTA TA -A TT TA TA CA TA CTA TA
1 TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * * * *
5416 TA AA TA TA AA CTA TA TA -A TT TA TA CA TA GTT TA TA CA TA T- TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
5458 TA T- TA T- TA TA -A GTT TA CA TA TA TG TA TA TA TA T- TA -A TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5496 TA T- TA TA
1 TA TA TA TA
5503 ATTATTTCAA
Statistics
Matches: 157, Mismatches: 35, Indels: 36
0.69 0.15 0.16
Matches are distributed among these distances:
1 11 0.07
2 137 0.87
3 9 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5399 original size:18 final size:16
Alignment explanation
Indices: 5273--5439 Score: 112
Period size: 16 Copynumber: 10.4 Consensus size: 16
5263 AATTAACTAG
*
5273 TTTATACATA-ATATAA
1 TTTATATATATATAT-A
*
5289 TTTATATAGTATATAAA
1 TTTATATA-TATATATA
* *
5306 TATATATACATATATA
1 TTTATATATATATATA
*
5322 TATATATATATATATA
1 TTTATATATATATATA
*
5338 TATATATATATATATA
1 TTTATATATATATATA
* *
5354 TGTT-TTTATTTATAT-
1 T-TTATATATATATATA
*
5369 TTTATAT-TTTATATA
1 TTTATATATATATATA
5384 GTTTATATATAGTATA-A
1 -TTTATATATA-TATATA
*
5401 TTTATACATACTATATA
1 TTTATATATA-TATATA
** *
5418 AATATAAACTATATA-A
1 TTTATATA-TATATATA
5434 TTTATA
1 TTTATA
5440 CATAGTTTAT
Statistics
Matches: 123, Mismatches: 18, Indels: 20
0.76 0.11 0.12
Matches are distributed among these distances:
14 9 0.07
15 3 0.02
16 79 0.64
17 23 0.19
18 9 0.07
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTATATATATATATA
Found at i:5471 original size:25 final size:27
Alignment explanation
Indices: 5443--5492 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
5433 ATTTATACAT
*
5443 AGTTTATACATAT-TATAT-TATTATA
1 AGTTTACACATATGTATATATATTATA
*
5468 AGTTTACATATATGTATATATATTA
1 AGTTTACACATATGTATATATATTA
5493 ATATATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 5 0.24
27 5 0.24
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (27 bp):
AGTTTACACATATGTATATATATTATA
Found at i:10457 original size:8 final size:8
Alignment explanation
Indices: 10434--10468 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
10424 CTCACAATTC
*
10434 ATACATAC
1 ATACATAT
10442 ATACATAT
1 ATACATAT
10450 ATACATAT
1 ATACATAT
*
10458 ATATATAT
1 ATACATAT
10466 ATA
1 ATA
10469 TAATCTAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:19461 original size:3 final size:3
Alignment explanation
Indices: 19453--19495 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
19443 TTAACGTGTT
19453 ATA ATA 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 ATA ATA A
19496 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28108 original size:23 final size:22
Alignment explanation
Indices: 28074--28134 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 22
28064 CTCATATAAA
28074 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCG-AGTGCCACGTAGAAT
*
28097 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCG-AGTGCCACGTAGAAT
28120 TGCACCGATGTGCCA
1 TGCACCGA-GTGCCA
28135 TATAAGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (22 bp):
TGCACCGAGTGCCACGTAGAAT
Found at i:33227 original size:23 final size:23
Alignment explanation
Indices: 33193--33253 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
33183 CTCATATAAA
33193 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
33216 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
33239 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
33254 TATAAGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:38335 original size:23 final size:23
Alignment explanation
Indices: 38301--38361 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
38291 CTCATATAAA
38301 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
38324 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
38347 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
38362 TATAAGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:39524 original size:2 final size:2
Alignment explanation
Indices: 39517--39547 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39507 ATATTTCATT
39517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39548 CAAAGATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41617 original size:2 final size:2
Alignment explanation
Indices: 41612--41695 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
41602 GTGTGTGTGT
41612 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41654 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41696 CGTATGAGAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:51560 original size:19 final size:20
Alignment explanation
Indices: 51529--51573 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
51519 GGGGTACATA
51529 ATGCGGTCTGATGCGATCCG
1 ATGCGGTCTGATGCGATCCG
* *
51549 ATGCGG-CTGATGCGGTCTG
1 ATGCGGTCTGATGCGATCCG
51568 ATGCGG
1 ATGCGG
51574 GCCGATGCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (20 bp):
ATGCGGTCTGATGCGATCCG
Found at i:51568 original size:10 final size:10
Alignment explanation
Indices: 51529--51573 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
51519 GGGGTACATA
51529 ATGCGGTCTG
1 ATGCGGTCTG
* *
51539 ATGCGATCCG
1 ATGCGGTCTG
51549 ATGCGG-CTG
1 ATGCGGTCTG
51558 ATGCGGTCTG
1 ATGCGGTCTG
51568 ATGCGG
1 ATGCGG
51574 GCCGATGCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (10 bp):
ATGCGGTCTG
Found at i:51992 original size:16 final size:16
Alignment explanation
Indices: 51967--52005 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
51957 TAGATAAATT
* *
51967 CTTTTTGTTGCAATAG
1 CTTTTAGTTGCAAAAG
51983 CTTTTAGTTGCAAAAG
1 CTTTTAGTTGCAAAAG
51999 CTTTTAG
1 CTTTTAG
52006 CTTTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (16 bp):
CTTTTAGTTGCAAAAG
Found at i:52104 original size:16 final size:16
Alignment explanation
Indices: 52079--52117 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
52069 TAGATAAGTT
* *
52079 CTTTTTGTTGCAATAG
1 CTTTTAGTTGCAAAAG
52095 CTTTTAGTTGCAAAAG
1 CTTTTAGTTGCAAAAG
52111 CTTTTAG
1 CTTTTAG
52118 CTTTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (16 bp):
CTTTTAGTTGCAAAAG
Found at i:52104 original size:112 final size:112
Alignment explanation
Indices: 51907--52182 Score: 516
Period size: 112 Copynumber: 2.5 Consensus size: 112
51897 ATGTGTACTA
*
51907 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAATTGTTTTTACGTCCTATAGATAAATTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAATTCTTTT
51972 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
66 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
*
52019 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAATTCTTTT
52084 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
66 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
*
52131 AAACAAGTTGTTTTTTTGTTGCTTAAATGAATCAACTGTTTTTACGTCCTAT
1 AAACAAGTTG-TTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTAT
52183 GATTTTACTG
Statistics
Matches: 160, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
112 120 0.75
113 40 0.25
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.45
Consensus pattern (112 bp):
AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAATTCTTTT
TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
Found at i:56035 original size:171 final size:171
Alignment explanation
Indices: 55750--56085 Score: 654
Period size: 171 Copynumber: 2.0 Consensus size: 171
55740 GTAGCTACAG
*
55750 GTATATCTTTCTCAGAATTTATTTTTCAGTTTTTACTTTGTTTCATTCTTATAAGTTTTGTCGGA
1 GTATATCTTTCTCAGAATCTATTTTTCAGTTTTTACTTTGTTTCATTCTTATAAGTTTTGTCGGA
55815 ACCTACGTCCCTAAATGAATTTCAGTCCTATAGAGTTGCCGAGGGTTATTTTAGATGATAACCCA
66 ACCTACGTCCCTAAATGAATTTCAGTCCTATAGAGTTGCCGAGGGTTATTTTAGATGATAACCCA
55880 AATGAAGTTTCAACAAGTATGCATATGGCATGTTTCAACAA
131 AATGAAGTTTCAACAAGTATGCATATGGCATGTTTCAACAA
55921 GTATATCTTTCTCAGAATCTATTTTTCAGTTTTTACTTTGTTTCATTCTTATAAGTTTTGTCGGA
1 GTATATCTTTCTCAGAATCTATTTTTCAGTTTTTACTTTGTTTCATTCTTATAAGTTTTGTCGGA
*
55986 ACCTACGTCCCTAAATGAATTTCAGTCCTATAGAGTTGCTGAGGGTTATTTTAGATGATAACCCA
66 ACCTACGTCCCTAAATGAATTTCAGTCCTATAGAGTTGCCGAGGGTTATTTTAGATGATAACCCA
56051 AATGAAGTTTCAACAAGTATGCATATGGCATGTTT
131 AATGAAGTTTCAACAAGTATGCATATGGCATGTTT
56086 GGGTAAATCA
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 163 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (171 bp):
GTATATCTTTCTCAGAATCTATTTTTCAGTTTTTACTTTGTTTCATTCTTATAAGTTTTGTCGGA
ACCTACGTCCCTAAATGAATTTCAGTCCTATAGAGTTGCCGAGGGTTATTTTAGATGATAACCCA
AATGAAGTTTCAACAAGTATGCATATGGCATGTTTCAACAA
Found at i:62646 original size:15 final size:15
Alignment explanation
Indices: 62626--62676 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
62616 TTCCGAAAAA
62626 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
62641 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
62656 TGAATTACTAGAATT
1 TGAATTACTGGAATT
62671 TGAATT
1 TGAATT
62677 CTGAAAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:62656 original size:30 final size:29
Alignment explanation
Indices: 62620--62692 Score: 119
Period size: 30 Copynumber: 2.5 Consensus size: 29
62610 TTGGTTTTCC
*
62620 GAAAAATGAATTACTGGAATTTGAATTACT
1 GAAAAATGAATTACTAGAATTTGAATT-CT
*
62650 GGAAAATGAATTACTAGAATTTGAATTCT
1 GAAAAATGAATTACTAGAATTTGAATTCT
62679 GAAAAATGAATTAC
1 GAAAAATGAATTAC
62693 ATTTTTGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (29 bp):
GAAAAATGAATTACTAGAATTTGAATTCT
Found at i:62705 original size:20 final size:20
Alignment explanation
Indices: 62682--62740 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
62672 GAATTCTGAA
62682 AAATGAATTACATTTTTGGT
1 AAATGAATTACATTTTTGGT
*
62702 AAATGAATTACATTTCTGGT
1 AAATGAATTACATTTTTGGT
62722 AAATGAATTACATTTTTGG
1 AAATGAATTACATTTTTGG
62741 AAAACATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (20 bp):
AAATGAATTACATTTTTGGT
Found at i:63095 original size:22 final size:25
Alignment explanation
Indices: 63067--63114 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
63057 AATATTATTC
63067 ATTATTAAATA-TA-TAAAA-AAAA
1 ATTATTAAATATTATTAAAATAAAA
*
63089 ATTATTATATATTATTAAAATAAAA
1 ATTATTAAATATTATTAAAATAAAA
63114 A
1 A
63115 ATATAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 5 0.23
25 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTATTAAATATTATTAAAATAAAA
Found at i:63103 original size:32 final size:31
Alignment explanation
Indices: 63057--63143 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 31
63047 ATATATAAAT
63057 AATATTAT-TCATTATTAAATATATAAAAA-AA
1 AATATTATAT-ATTATTAAATATA-AAAAATAA
*
63088 AATTATTATATATTATTAAA-ATAAAAAATAT
1 AA-TATTATATATTATTAAATATAAAAAATAA
63119 AATATCT-TATATTATTATAATATAA
1 AATAT-TATATATTATTA-AATATAA
63144 TTGATTATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
30 18 0.37
31 11 0.22
32 19 0.39
33 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (31 bp):
AATATTATATATTATTAAATATAAAAAATAA
Found at i:63190 original size:22 final size:22
Alignment explanation
Indices: 63125--63194 Score: 61
Period size: 27 Copynumber: 2.9 Consensus size: 22
63115 ATATAATATC
63125 TTATATTATTATAATATAATT-GA
1 TTATATTATTATAA-AT-ATTAGA
*
63148 TTATATTATTAAACTAAAAATATTATA
1 TTATATTATT--A-T--AAATATTAGA
63175 TTATATTATTATAAATATTA
1 TTATATTATTATAAATATTA
63195 ATAAATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
22 8 0.20
23 10 0.25
24 1 0.03
25 2 0.05
26 4 0.10
27 13 0.32
28 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (22 bp):
TTATATTATTATAAATATTAGA
Found at i:63210 original size:50 final size:52
Alignment explanation
Indices: 63095--63210 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 52
63085 AAAAATTATT
* *
63095 ATATATTATTAAAATAAAAAATATAATATCTTATATTATTATAATATAATTGA
1 ATATATTATTAAAATAAAAAATAT-ATATATTATATTATTATAATATAATTAA
* *
63148 TTATATTATTAAACT-AAAAATAT-TATATTATATTATTATAAATATTAA-TAA
1 ATATATTATTAAAATAAAAAATATATATATTATATTATTAT-AATA-TAATTAA
63199 ATATATT-TTAAA
1 ATATATTATTAAA
63211 TATTTTAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
50 20 0.36
51 12 0.21
52 11 0.20
53 13 0.23
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.46
Consensus pattern (52 bp):
ATATATTATTAAAATAAAAAATATATATATTATATTATTATAATATAATTAA
Found at i:65010 original size:7 final size:7
Alignment explanation
Indices: 64998--65022 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
64988 AACAGCGAGG
64998 GAAGAGA
1 GAAGAGA
65005 GAAGAGA
1 GAAGAGA
65012 GAAGAGA
1 GAAGAGA
65019 GAAG
1 GAAG
65023 GTTGTTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
GAAGAGA
Done.