Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003552.1 Hibiscus syriacus cultivar Beakdansim tig00007497_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: 297196
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:251231 original size:19 final size:20
Alignment explanation
Indices: 251202--251239 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
251192 AGAAATTTGT
251202 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
251222 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
251240 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:251283 original size:63 final size:62
Alignment explanation
Indices: 251207--251365 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
251197 TTTGTTGAAG
* * *
251207 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GAAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
* * ** **
251270 GTGCAACGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGAAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
251333 GTGCATCGATGCATCAGAAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGAAGTGCATCGATGCAT
251366 GCCTCCATTA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 77 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGAAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:251988 original size:149 final size:150
Alignment explanation
Indices: 251810--252115 Score: 578
Period size: 151 Copynumber: 2.0 Consensus size: 150
251800 GGGTAGAGGG
*
251810 TCTACGCGGTCCTTCGGG-ATATATATATATTCTGTAGAACATGTGTGAAGTCTTGTAAGACACA
1 TCTACGCGATCCTTCGGGAATATATATATATTCTGTAGAACATGTGTGAAGTCTTGTAAGACACA
251874 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
251939 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
251959 TCTACGCGATCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACAC
1 TCTACGCGATCCTTCGGGA-ATATATATATATTCTGTAGAACATGTGTGAAGTCTTGTAAGACAC
252024 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTAT
65 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTAT
252089 TATATGGCACTACGGTGCAAT
130 TATATGGCACTACGGTGCAAT
252110 TCTACG
1 TCTACG
252116 TGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
149 17 0.11
151 136 0.89
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (150 bp):
TCTACGCGATCCTTCGGGAATATATATATATTCTGTAGAACATGTGTGAAGTCTTGTAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
ATATGGCACTACGGTGCAAT
Found at i:252127 original size:23 final size:23
Alignment explanation
Indices: 252093--252138 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
252083 CATTATTATA
*
252093 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
252116 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
252139 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:265729 original size:18 final size:19
Alignment explanation
Indices: 265691--265733 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
265681 TTATCTGGAA
*
265691 AAAAATCCGGTTTGGGGTTT
1 AAAAATCCGG-TTGAGGTTT
265711 AAAAATCCGG-TGAGGTTT
1 AAAAATCCGGTTGAGGTTT
265729 AAAAA
1 AAAAA
265734 ATTGGATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
20 10 0.45
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (19 bp):
AAAAATCCGGTTGAGGTTT
Found at i:265734 original size:20 final size:21
Alignment explanation
Indices: 265689--265734 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
265679 TTTTATCTGG
*
265689 AAAAAAATCCGGTTTGGGGTTT
1 AAAAAAATCCGG-TTGAGGTTT
265711 --AAAAATCCGG-TGAGGTTT
1 AAAAAAATCCGGTTGAGGTTT
265729 AAAAAA
1 AAAAAA
265735 TTGGATGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (21 bp):
AAAAAAATCCGGTTGAGGTTT
Found at i:265789 original size:14 final size:15
Alignment explanation
Indices: 265760--265796 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
265750 TTTTACCGGA
*
265760 TTAAAAACTGGTTTT
1 TTAAAAACCGGTTTT
265775 TTAAAAACCGGTTTT
1 TTAAAAACCGGTTTT
265790 TTAAAAA
1 TTAAAAA
265797 AACCGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (15 bp):
TTAAAAACCGGTTTT
Found at i:266199 original size:31 final size:31
Alignment explanation
Indices: 266147--266218 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
266137 GTTAAATGAT
*
266147 TAACGGTTGAGGGGTTAAAATCGAACGGATCGA
1 TAAC-GTT-AGGGATTAAAATCGAACGGATCGA
* * *
266180 TAATGTTAGGGATTAAAATCGGATGGATCGA
1 TAACGTTAGGGATTAAAATCGAACGGATCGA
266211 TAACGTTA
1 TAACGTTA
266219 AAAACCATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 28 0.82
32 3 0.09
33 3 0.09
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.26
Consensus pattern (31 bp):
TAACGTTAGGGATTAAAATCGAACGGATCGA
Found at i:268539 original size:20 final size:18
Alignment explanation
Indices: 268500--268539 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
268490 ATCAAAAAAA
*
268500 TAAAAATTAAAAATATAT
1 TAAAAATTAAAAAAATAT
268518 TAAAAATTAGAAAGAAATAT
1 TAAAAATTA-AAA-AAATAT
268538 TA
1 TA
268540 GCTATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 3 0.16
20 7 0.37
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
TAAAAATTAAAAAAATAT
Found at i:269520 original size:29 final size:29
Alignment explanation
Indices: 269469--269661 Score: 217
Period size: 29 Copynumber: 6.6 Consensus size: 29
269459 GACCCGAACC
*
269469 GGTGACATTTTGGAAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* * *
269498 TGTGACATTTTGGGATTTTTTTTTTG-AAAA
1 GGTGACATTTTGGGA--ATTATTTTGAAAAA
* * *
269528 TGTGACATTATGGGAATTATTTTAAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* *
269557 GGTGATATTCTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* *
269586 GGTGATATGTTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* *
269615 GGTGACATTCTGAGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* * *
269644 TGAGACATTTTGGAAATT
1 GGTGACATTTTGGGAATT
269662 TTCGAATGTG
Statistics
Matches: 138, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
28 6 0.04
29 107 0.78
30 18 0.13
31 7 0.05
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.40
Consensus pattern (29 bp):
GGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:274441 original size:28 final size:28
Alignment explanation
Indices: 274409--274472 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
274399 CTGATCATAA
274409 GAGCTTAAAGTATCTTCTGACCCAGAAG
1 GAGCTTAAAGTATCTTCTGACCCAGAAG
274437 GAGCTTAAAGTATCTTCTGACCCAGAAG
1 GAGCTTAAAGTATCTTCTGACCCAGAAG
274465 GAGCTTAA
1 GAGCTTAA
274473 TTTGAGACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (28 bp):
GAGCTTAAAGTATCTTCTGACCCAGAAG
Found at i:276904 original size:19 final size:19
Alignment explanation
Indices: 276880--276964 Score: 118
Period size: 19 Copynumber: 4.5 Consensus size: 19
276870 TCCAAACCGT
276880 TCTGACCCGGTTTGATCGG
1 TCTGACCCGGTTTGATCGG
276899 TCTGACCCGGTTTGA-CTGG
1 TCTGACCCGGTTTGATC-GG
276918 TCTGACCCGGTTTGATCGG
1 TCTGACCCGGTTTGATCGG
* * *
276937 TCTGAACCGGGTTGACCGG
1 TCTGACCCGGTTTGATCGG
*
276956 TCCGACCCG
1 TCTGACCCG
276965 ACCCGTTGAC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
18 1 0.02
19 57 0.97
20 1 0.02
ACGTcount: A:0.12, C:0.29, G:0.32, T:0.27
Consensus pattern (19 bp):
TCTGACCCGGTTTGATCGG
Found at i:276914 original size:10 final size:10
Alignment explanation
Indices: 276882--276932 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
276872 CAAACCGTTC
276882 TGACCCGGTT
1 TGACCCGGTT
* *
276892 TGA-TCGGTC
1 TGACCCGGTT
276901 TGACCCGGTT
1 TGACCCGGTT
* *
276911 TGA-CTGGTC
1 TGACCCGGTT
276920 TGACCCGGTT
1 TGACCCGGTT
276930 TGA
1 TGA
276933 TCGGTCTGAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
9 14 0.45
10 17 0.55
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.31
Consensus pattern (10 bp):
TGACCCGGTT
Found at i:276922 original size:38 final size:38
Alignment explanation
Indices: 276875--276964 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 38
276865 ACCGGTCCAA
* * *
276875 ACCGTTCTGACCCGGTTTGATCGGTCTGACCCGGTTTG
1 ACCGGTCTGACCCGGTTTGATCGGTCTGAACCGGGTTG
*
276913 ACTGGTCTGACCCGGTTTGATCGGTCTGAACCGGGTTG
1 ACCGGTCTGACCCGGTTTGATCGGTCTGAACCGGGTTG
*
276951 ACCGGTCCGACCCG
1 ACCGGTCTGACCCG
276965 ACCCGTTGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.12, C:0.30, G:0.31, T:0.27
Consensus pattern (38 bp):
ACCGGTCTGACCCGGTTTGATCGGTCTGAACCGGGTTG
Found at i:276937 original size:9 final size:9
Alignment explanation
Indices: 276886--276956 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
276876 CCGTTCTGAC
276886 CCGGTTTGA
1 CCGGTTTGA
* *
276895 TCGGTCTGA
1 CCGGTTTGA
276904 CCCGGTTTGA
1 -CCGGTTTGA
* *
276914 CTGGTCTGA
1 CCGGTTTGA
276923 CCCGGTTTGA
1 -CCGGTTTGA
* *
276933 TCGGTCTGAA
1 CCGGTTTG-A
*
276943 CCGGGTTGA
1 CCGGTTTGA
276952 CCGGT
1 CCGGT
276957 CCGACCCGAC
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
9 25 0.56
10 20 0.44
ACGTcount: A:0.11, C:0.25, G:0.34, T:0.30
Consensus pattern (9 bp):
CCGGTTTGA
Found at i:277033 original size:29 final size:29
Alignment explanation
Indices: 277000--277119 Score: 190
Period size: 29 Copynumber: 4.2 Consensus size: 29
276990 GATATTTTGA
277000 GAATTATTTTGAAAAATGTGACATTCTGG
1 GAATTATTTTGAAAAATGTGACATTCTGG
* *
277029 GAATTATTTTGAAAAATGTGATATTTTGG
1 GAATTATTTTGAAAAATGTGACATTCTGG
277058 GAATTATTTTGAAAAA-GTGACATTCTGG
1 GAATTATTTTGAAAAATGTGACATTCTGG
*
277086 GAATTATTTTG-AAAATGGTGACATTTTGG
1 GAATTATTTTGAAAAAT-GTGACATTCTGG
277115 GAATT
1 GAATT
277120 TTTGAATGTG
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
27 4 0.05
28 21 0.25
29 59 0.70
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (29 bp):
GAATTATTTTGAAAAATGTGACATTCTGG
Found at i:277100 original size:57 final size:58
Alignment explanation
Indices: 276987--277119 Score: 225
Period size: 57 Copynumber: 2.3 Consensus size: 58
276977 GACCCGACCC
*
276987 GGTGATATTTTGAGAATTATTTTGAAAAATGTGACATTCTGGGAATTATTTTGAAAAAT
1 GGTGATATTTTGGGAATTATTTTGAAAAATGTGACATTCTGGGAATTATTTTG-AAAAT
277046 -GTGATATTTTGGGAATTATTTTGAAAAA-GTGACATTCTGGGAATTATTTTGAAAAT
1 GGTGATATTTTGGGAATTATTTTGAAAAATGTGACATTCTGGGAATTATTTTGAAAAT
*
277102 GGTGACATTTTGGGAATT
1 GGTGATATTTTGGGAATT
277120 TTTGAATGTG
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
56 5 0.07
57 39 0.55
58 27 0.38
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.41
Consensus pattern (58 bp):
GGTGATATTTTGGGAATTATTTTGAAAAATGTGACATTCTGGGAATTATTTTGAAAAT
Found at i:278199 original size:26 final size:26
Alignment explanation
Indices: 278146--278199 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
278136 ATGGTAACTC
* *
278146 TTTTATGGGATTTACTGCAGTATAAT
1 TTTTATGAGATTTACTGCACTATAAT
* * *
278172 TTTTATGATATTTACTGGACTATGAT
1 TTTTATGAGATTTACTGCACTATAAT
278198 TT
1 TT
278200 GTTTAGTGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCACTATAAT
Found at i:279202 original size:26 final size:26
Alignment explanation
Indices: 279168--279233 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
279158 TAAACTTATT
279168 AAATTTTAAGTGAGGACAAATATATA
1 AAATTTTAAGTGAGGACAAATATATA
279194 AAATTTTAAGTGAGGACAAATATATA
1 AAATTTTAAGTGAGGACAAATATATA
279220 AAA-TTTAAGTGAGG
1 AAATTTTAAGTGAGG
279234 CCGAACTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 11 0.28
26 29 0.73
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.30
Consensus pattern (26 bp):
AAATTTTAAGTGAGGACAAATATATA
Found at i:284370 original size:38 final size:39
Alignment explanation
Indices: 284304--284520 Score: 188
Period size: 39 Copynumber: 5.7 Consensus size: 39
284294 GTTTTTAAAA
* *
284304 AAAAATATTTTT-AAAATGTATATA--ATATATAGTTTTT
1 AAAAACATTTTTGAAAA-CTATATAATATATATAGTTTTT
**
284341 AAAAA-ACCTTTGAAAACTATAT-A-ATATATAG-TTTT
1 AAAAACATTTTTGAAAACTATATAATATATATAGTTTTT
*
284376 AAAAACATTTTTAGAAAA-TATAT-ATAATATATAATTTTT
1 AAAAACATTTTT-GAAAACTATATAAT-ATATATAGTTTTT
* *
284415 AAAATCA-TTTTGAAAACTTATATAATATATAGT-TTTTTT
1 AAAAACATTTTTGAAAAC-TATATAATATATA-TAGTTTTT
*
284454 AAAAACATTTTTGAAAACTTATATGTAATATATAT-TTTTTT
1 AAAAACATTTTTGAAAAC-TATA--TAATATATATAGTTTTT
* *
284495 AAAAATATTTTTGAAAATTATATAAT
1 AAAAACATTTTTGAAAACTATATAAT
284521 TTTTAAAACA
Statistics
Matches: 155, Mismatches: 11, Indels: 27
0.80 0.06 0.14
Matches are distributed among these distances:
35 9 0.06
36 27 0.17
37 19 0.12
38 15 0.10
39 31 0.20
40 22 0.14
41 23 0.15
42 9 0.06
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (39 bp):
AAAAACATTTTTGAAAACTATATAATATATATAGTTTTT
Found at i:284477 original size:40 final size:38
Alignment explanation
Indices: 284281--284520 Score: 249
Period size: 41 Copynumber: 6.2 Consensus size: 38
284271 TGAAAATACG
* * * *
284281 TATATAATATATGGTTTTTAAAAAAAAATATTTTTAAAAT
1 TATATAATATATAGTTTTT-TAAAAACAT-TTTTGAAAAT
** *
284321 GTATATAATATATAG-TTTTTAAAAA-ACCTTTGAAAAC
1 -TATATAATATATAGTTTTTTAAAAACATTTTTGAAAAT
284358 TATATAATATATAG--TTTTAAAAACATTTTTAGAAAAT
1 TATATAATATATAGTTTTTTAAAAACATTTTT-GAAAAT
* *
284395 ATATATAATATATA-ATTTTTAAAATCA-TTTTGAAAACT
1 -TATATAATATATAGTTTTTTAAAAACATTTTTGAAAA-T
284433 TATATAATATATAGTTTTTTTAAAAACATTTTTGAAAACT
1 TATATAATATATAG-TTTTTTAAAAACATTTTTGAAAA-T
* *
284473 TATATGTAATATATATTTTTTTAAAAATATTTTTGAAAAT
1 TATA--TAATATATAGTTTTTTAAAAACATTTTTGAAAAT
284513 TATATAAT
1 TATATAAT
284521 TTTTAAAACA
Statistics
Matches: 174, Mismatches: 14, Indels: 25
0.82 0.07 0.12
Matches are distributed among these distances:
35 9 0.05
36 18 0.10
37 30 0.17
38 23 0.13
39 26 0.15
40 24 0.14
41 35 0.20
42 9 0.05
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (38 bp):
TATATAATATATAGTTTTTTAAAAACATTTTTGAAAAT
Found at i:284524 original size:31 final size:29
Alignment explanation
Indices: 284490--284547 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
284480 AATATATATT
284490 TTTTTAAAA-ATATTTTTGAAAATTATATAA
1 TTTTTAAAACAT-TTTTT-AAAATTATATAA
284520 TTTTTAAAACATTTTTTAAAATTATATA
1 TTTTTAAAACATTTTTTAAAATTATATA
284548 GTTAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTTTAAAACATTTTTTAAAATTATATAA
Found at i:284557 original size:29 final size:29
Alignment explanation
Indices: 284495--284571 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
284485 ATATTTTTTT
* * **
284495 AAAAATATTTTTGAAAATTATATAATTTT
1 AAAAACATTTTTAAAAATTATATAATTAA
* * *
284524 TAAAACATTTTTTAAAATTATATAGTTAA
1 AAAAACATTTTTAAAAATTATATAATTAA
284553 AAAAATGCATTTTTAAAAA
1 AAAAA--CATTTTTAAAAA
284572 AAAATTATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 27 0.71
31 11 0.29
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (29 bp):
AAAAACATTTTTAAAAATTATATAATTAA
Found at i:284620 original size:3 final size:3
Alignment explanation
Indices: 284612--284658 Score: 58
Period size: 3 Copynumber: 14.7 Consensus size: 3
284602 TTTTTTATAT
*
284612 TTA TTA TTA TTA TTTA TTTA TTA TTA TTA CTTA TTA TTA TTT TTA TT
1 TTA TTA TTA TTA -TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
284659 TTTTCTCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 30 0.75
4 10 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:284631 original size:17 final size:17
Alignment explanation
Indices: 284609--284659 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
284599 ATATTTTTTA
284609 TATTTATTATTATTATT
1 TATTTATTATTATTATT
*
284626 TATTTATTATTATTACT
1 TATTTATTATTATTATT
*
284643 TA-TTATTATTTTTATT
1 TATTTATTATTATTATT
284659 T
1 T
284660 TTTCTCTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTATTATTATTATT
Found at i:286027 original size:11 final size:11
Alignment explanation
Indices: 286013--286042 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
286003 TTTAAAACAT
286013 CTTTATTTTTA
1 CTTTATTTTTA
*
286024 CTTTATTGTTA
1 CTTTATTTTTA
286035 CTTTATTT
1 CTTTATTT
286043 CTTTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.70
Consensus pattern (11 bp):
CTTTATTTTTA
Found at i:286993 original size:11 final size:11
Alignment explanation
Indices: 286977--287006 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
286967 TTTTAAACAT
286977 CTTTATTTTTA
1 CTTTATTTTTA
*
286988 CTTTATTGTTA
1 CTTTATTTTTA
286999 CTTTATTT
1 CTTTATTT
287007 CTTTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.70
Consensus pattern (11 bp):
CTTTATTTTTA
Found at i:287482 original size:967 final size:964
Alignment explanation
Indices: 285582--287509 Score: 3196
Period size: 967 Copynumber: 2.0 Consensus size: 964
285572 GGAGAGATAT
285582 CATTTTAGAGAGAGAGTGTAAAGAGTAAAATGAGAGGGTTTGGTGTTATTTCACTCTCATATGGC
1 CATTTTAGAGAGAGAGTGTAAAGAGTAAAATGAGAGGGTTTGGTGTTATTTCACTCTCATATGGC
*
285647 CTTTTATAATGCTGATGAAACGACGTAGTTTCGATGGGGGAGTGGCTCGTAATTTTGCTTAGGGG
66 CTTTTATAATGCTGATGAAACGACGTAGTTTCGATGGGGAAGTGGCTCGTAATTTTGCTTAGGGG
* *
285712 TTTATCGCAGCATGGGTCCCTCGTCCCTTGTAATGTTGCTTTCTGGCCATACATTGAACTTTTCA
131 TTTATCACAGCATGGGTCCCTCGTCCCATGTAATGTTGCTTTCTGGCCATACATTGAACTTTTCA
* *
285777 TTCATTTTATTTTGAGCATTAAATTTCCAGGATTTATATTTTATCCCTTTTTTTATATTACATGT
196 TTCATTTTATTTTGAGCATTAAATTTCCAGAATTTATATTTTAGCCC-TTTTTTATATTACATGT
* * *
285842 TTTTTTGTGTTAATATTCGAATTTGACCCTTACATTTTCATATCTTCTGTTTTGGTCACTAATTT
260 TTTTTTGTGTTAATATTCAAATTTGACCCTTACATTTTCATATATTCTGTTTTGATCACTAATTT
*
285907 GGCATGTATGCTTATGGTTAACTATATTTTTAGTCCTTCATGTTCTTACACATTTTATTTTACCA
325 GGCATGTATGCTTAGGGTTAACTATATTTTTAGTCCTTCATGTTCTTACACATTTTATTTTACCA
285972 TATTTTTTATGGGTTTTTATTATTATTATTATTTAAAACATCTTTATTTTTACTTTATTGTTACT
390 TATTTTTTATGGGTTTTTATTA-TA-TATTATTTAAAACATCTTTATTTTTACTTTATTGTTACT
* *
286037 TTATTTCTTTTTATTTATTATGATCTGTTTGTTATTTTCTATTTTTTCTTTTGATTTGTACTTTT
453 TTATTTCTTTTTATTTATTATGATATGTTTGTTATTTTCTATTTTTTCCTTTGATTTGTACTTTT
*
286102 ATTATTTCTTTATAAATATATTTTCCTTTTTTGATTTATTTAATGTTTTTTGTTTCCCTTTCAAT
518 ATTATTTATTTATAAATATATTTTCCTTTTTTGATTTATTTAATGTTTTTTGTTTCCCTTTCAAT
286167 TTATTTTATTTATTTGTTTATATATTATTGTTTTTATTATCATTTTTTCCTTTTTTTATTTTTAA
583 TTATTTTATTTA----TTTATATATTATTGTTTTTATTATCATTTTTTCCTTTTTTTATTTTTAA
286232 ATAATTTTTTCCTCTAACATTTTCGACCTATTTTTTTAGAAATTTCAAACTAATCAAAGGTAAGT
644 ATAATTTTTTCCTCTAACATTTTCGACCTATTTTTTTAGAAATTTCAAACTAATCAAAGGTAAGT
286297 AGTTGAATCGAATTCTTAAAATTTAATTTAAATTCTTAATTTTCGCAAATAAAGACAACCAGAAA
709 AGTTGAATCGAATTCTTAAAATTTAATTTAAATTCTTAATTTTCGCAAATAAAGACAACCAGAAA
*
286362 ATTAATTGGTACCAAAATGGCGGTTCAAGGGTGCTAATCCTTCATTGACCATAACCGACTCCCGA
774 ATTAATTGGTACCAAAATGGCGGTTCAAGGGTACTAATCCTTCATTGACCATAACCGACTCCCGA
*
286427 ACCCGACACATTTCCTGTACAACGCAGAACAGTTAAGATGGTATCCGACTCACCTAAATTTGTTT
839 ACCCGACACATTTCCTGTACAACGCAGAACAGTTAAGATGGTATCCGACTCACCTAAATTTATTT
*
286492 TAAAGTGGTCGGTGGCGACTCTAACCCAATCATTTCAAGTCGAAGCCCAATTTTGGGCCCAA
904 TAAAGTGGTCGGTGGCGACTCTAACCC-ATCATTTCAAGTCGAAACCCAATTTTGGGCCCAA
**
286554 CATTTTAGAGAGAGAGTGTGGAGAGTAAAATGAGAGGGTTTGGTGTTATTTCACTCTCATATGGC
1 CATTTTAGAGAGAGAGTGTAAAGAGTAAAATGAGAGGGTTTGGTGTTATTTCACTCTCATATGGC
*
286619 CTTTTTATAATGCTGATGAAACGATGTAGTTTCGATGGGGAAGTGGCTCGTAATTTTGCTTAGGG
66 C-TTTTATAATGCTGATGAAACGACGTAGTTTCGATGGGGAAGTGGCTCGTAATTTTGCTTAGGG
286684 GTTTATCACAGCATGGGTCCCTCGTCCCATGTAATGTTGCTTTCTGGCCATACATTGAACTTTTC
130 GTTTATCACAGCATGGGTCCCTCGTCCCATGTAATGTTGCTTTCTGGCCATACATTGAACTTTTC
*
286749 ATTCATTTTATTTTGAGCATTAAA-TTCCATAATTTATATTTTAGCCC-TTTTTATATTACATG-
195 ATTCATTTTATTTTGAGCATTAAATTTCCAGAATTTATATTTTAGCCCTTTTTTATATTACATGT
*
286811 TTTTTTGTGTTAATATTCAAATTTGACCCTTACATTTTCATATATTTTGTTTTGATCACTAATTT
260 TTTTTTGTGTTAATATTCAAATTTGACCCTTACATTTTCATATATTCTGTTTTGATCACTAATTT
**
286876 GGCATGTATGCTTAGGGTTAACTATATTTTTAGTCCTTCATGTTCTTACACATTTTATTTTATTA
325 GGCATGTATGCTTAGGGTTAACTATATTTTTAGTCCTTCATGTTCTTACACATTTTATTTTACCA
* *
286941 TATTTTTTCTGGGTTTTT-TTA-A-ATTATTTTAAACATCTTTATTTTTACTTTATTGTTACTTT
390 TATTTTTTATGGGTTTTTATTATATATTATTTAAAACATCTTTATTTTTACTTTATTGTTACTTT
** *
287003 ATTTCTTTTTATTTATTATTTTATGTTTGTTATTTTCTATTTTTTTCCTTTGATTTGTCCTTTTA
455 ATTTCTTTTTATTTATTATGATATGTTTGTTATTTTCTA-TTTTTTCCTTTGATTTGTACTTTTA
* *
287068 TTATTTATTTATAAATATATTTTCTTTTTTTTTTGATTTATTTAATTTTTTTTGTTTTCCCTTTC
519 TTATTTATTTATAAATATATTTTC---CTTTTTTGATTTATTTAATGTTTTTTG-TTTCCCTTTC
* *
287133 AATTTATTTTCTTTA-TT-TCT-TTATTGTTTTTATTATCAATTTTTTCCTTTTTTTATTTATTT
580 AATTTATTTTATTTATTTATATATTATTGTTTTTATTATC-ATTTTTTCCTTTTTTTA-TT-TTT
287195 AAATAATTTTTTTCCTCTAACATTTTCGACCTATTTTTTTTTAGAAATTTCAAACTAATCAAAGG
642 AAATAA-TTTTTTCCTCTAACATTTTCGACCTA--TTTTTTTAGAAATTTCAAACTAATCAAAGG
* *
287260 TAAGTAGTTGAATCGAATTCTT-AAATTTAATTTAAATTCTTAATTTTTGCAAATAAAGATAACC
704 TAAGTAGTTGAATCGAATTCTTAAAATTTAATTTAAATTCTTAATTTTCGCAAATAAAGACAACC
* * * * * *
287324 GGAAAATTAATTGGTACCGAAATGGTGGTTCAAGGGTACTAATCCTTCCTTGACCGTAACTGACT
769 AGAAAATTAATTGGTACCAAAATGGCGGTTCAAGGGTACTAATCCTTCATTGACCATAACCGACT
* * *
287389 CCCGAACCCGACACATTT-CTGGTACAATGCAGATCA-TGTAAGATGGTGTCCGACTCACCTAAA
834 CCCGAACCCGACACATTTCCT-GTACAACGCAGAACAGT-TAAGATGGTATCCGACTCACCTAAA
287452 TTTATTTTAAAGTGGTCGGTGGCGACTCTAACCCATCATTTCAAGTCGAAACCCAATT
897 TTTATTTTAAAGTGGTCGGTGGCGACTCTAACCCATCATTTCAAGTCGAAACCCAATT
287510 CCGGACCCAA
Statistics
Matches: 900, Mismatches: 42, Indels: 34
0.92 0.04 0.03
Matches are distributed among these distances:
962 17 0.02
963 19 0.02
964 79 0.09
965 55 0.06
966 53 0.06
967 186 0.21
968 80 0.09
969 164 0.18
970 15 0.02
972 84 0.09
973 148 0.16
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (964 bp):
CATTTTAGAGAGAGAGTGTAAAGAGTAAAATGAGAGGGTTTGGTGTTATTTCACTCTCATATGGC
CTTTTATAATGCTGATGAAACGACGTAGTTTCGATGGGGAAGTGGCTCGTAATTTTGCTTAGGGG
TTTATCACAGCATGGGTCCCTCGTCCCATGTAATGTTGCTTTCTGGCCATACATTGAACTTTTCA
TTCATTTTATTTTGAGCATTAAATTTCCAGAATTTATATTTTAGCCCTTTTTTATATTACATGTT
TTTTTGTGTTAATATTCAAATTTGACCCTTACATTTTCATATATTCTGTTTTGATCACTAATTTG
GCATGTATGCTTAGGGTTAACTATATTTTTAGTCCTTCATGTTCTTACACATTTTATTTTACCAT
ATTTTTTATGGGTTTTTATTATATATTATTTAAAACATCTTTATTTTTACTTTATTGTTACTTTA
TTTCTTTTTATTTATTATGATATGTTTGTTATTTTCTATTTTTTCCTTTGATTTGTACTTTTATT
ATTTATTTATAAATATATTTTCCTTTTTTGATTTATTTAATGTTTTTTGTTTCCCTTTCAATTTA
TTTTATTTATTTATATATTATTGTTTTTATTATCATTTTTTCCTTTTTTTATTTTTAAATAATTT
TTTCCTCTAACATTTTCGACCTATTTTTTTAGAAATTTCAAACTAATCAAAGGTAAGTAGTTGAA
TCGAATTCTTAAAATTTAATTTAAATTCTTAATTTTCGCAAATAAAGACAACCAGAAAATTAATT
GGTACCAAAATGGCGGTTCAAGGGTACTAATCCTTCATTGACCATAACCGACTCCCGAACCCGAC
ACATTTCCTGTACAACGCAGAACAGTTAAGATGGTATCCGACTCACCTAAATTTATTTTAAAGTG
GTCGGTGGCGACTCTAACCCATCATTTCAAGTCGAAACCCAATTTTGGGCCCAA
Found at i:288401 original size:19 final size:18
Alignment explanation
Indices: 288379--288430 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
288369 AATTAAATTC
288379 ATATTTTTATTGAATAAAA
1 ATATTTTT-TTGAATAAAA
288398 ATATTATTTTT-AATAAAA
1 ATATT-TTTTTGAATAAAA
*
288416 ATATTATTTTGAATA
1 ATATTTTTTTGAATA
288431 GGTTTCAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 16 0.53
19 7 0.23
20 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
ATATTTTTTTGAATAAAA
Found at i:288414 original size:18 final size:18
Alignment explanation
Indices: 288388--288430 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
288378 CATATTTTTA
288388 TTGAATAAAAATATTATT
1 TTGAATAAAAATATTATT
*
288406 TTTAATAAAAATATTATT
1 TTGAATAAAAATATTATT
288424 TTGAATA
1 TTGAATA
288431 GGTTTCAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
TTGAATAAAAATATTATT
Done.