Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000535.1 Hibiscus syriacus cultivar Beakdansim tig00001032_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: 63693
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:211 original size:18 final size:16
Alignment explanation
Indices: 165--214 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
155 AAAATACAAC
*
165 ATTCCC-AGTAATCCT
1 ATTCCCTAGTAATCTT
*
180 ATTCCCTGGTAATCTT
1 ATTCCCTAGTAATCTT
196 ATTCCCATTAGTAATCTT
1 ATTCCC--TAGTAATCTT
214 A
1 A
215 CATTCCGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 13 0.45
18 10 0.34
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:2289 original size:27 final size:28
Alignment explanation
Indices: 2245--2302 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
2235 TGTATCTTTC
* *
2245 CTTGCTAATTTATCTG-TTTATTGTTTA
1 CTTGCTAATATATCTGTTTTATTGATTA
* *
2272 CTTGCTACTATATTTGTTTTATTGATTA
1 CTTGCTAATATATCTGTTTTATTGATTA
2300 CTT
1 CTT
2303 TTAAATATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.59
Consensus pattern (28 bp):
CTTGCTAATATATCTGTTTTATTGATTA
Found at i:3542 original size:16 final size:16
Alignment explanation
Indices: 3521--3552 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3511 TCATCATGCT
3521 AAACAAAAGTATGGGA
1 AAACAAAAGTATGGGA
3537 AAACAAAAGTATGGGA
1 AAACAAAAGTATGGGA
3553 GGAATCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.12
Consensus pattern (16 bp):
AAACAAAAGTATGGGA
Found at i:3906 original size:26 final size:28
Alignment explanation
Indices: 3874--3948 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
3864 TTATGTTATG
* *
3874 TTATTTATTTCAAGTTAACTA-TAACTT
1 TTATTTATTGCAAGTTAACCACTAACTT
*
3901 TT-TTTATTGCATGTTAACCACTAACTT
1 TTATTTATTGCAAGTTAACCACTAACTT
**
3928 TTATTTATTGCACTTTAACCA
1 TTATTTATTGCAAGTTAACCA
3949 TTGTTATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 15 0.37
27 10 0.24
28 16 0.39
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (28 bp):
TTATTTATTGCAAGTTAACCACTAACTT
Found at i:4143 original size:117 final size:116
Alignment explanation
Indices: 3977--4291 Score: 402
Period size: 117 Copynumber: 2.7 Consensus size: 116
3967 CTGTTTCTAA
* ***** * * *
3977 TATTCAATTCGACCTTGTGGTGACCT-ATCCGGGGTATGATATGTGTTATTATCGTTCGGATTGT
1 TATTCAATTCGACCTTGTGGTGACCTAATCCAGGGTATGATCCACATTATTATGGTTCGGACTCT
4041 GCTAACCACTAACTTTTTTCATTTTATTTTATTTT-TATATATTTGTTTGAAT
66 GCTAACCACTAACTTTTTTCATTTTATTTTATTTTGT-TA-ATTTGTTTGAAT
** * * *
4093 TATTTGATTTGACTTTGTGGTGACCTAATCCAGGGTATGATCCACATTATTATGGTTCGGACCCT
1 TATTCAATTCGACCTTGTGGTGACCTAATCCAGGGTATGATCCACATTATTATGGTTCGGACTCT
*
4158 GCTAACCACTAACTTTATTTTATTTTATTTTATTTTGTTAATTTGTTTGAAT
66 GCTAACCACTAACTTT-TTTCATTTTATTTTATTTTGTTAATTTGTTTGAAT
* * *
4210 TATTCAATTCGGCCTTGTGGTGACC-ATATCCAGGATATGATCCACATTATTATGGTTTGGACTC
1 TATTCAATTCGACCTTGTGGTGACCTA-ATCCAGGGTATGATCCACATTATTATGGTTCGGACTC
*
4274 TGCTAACCGCTAACTTTT
65 TGCTAACCACTAACTTTT
4292 CTAACAACTA
Statistics
Matches: 171, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
116 24 0.14
117 126 0.74
118 20 0.12
119 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.45
Consensus pattern (116 bp):
TATTCAATTCGACCTTGTGGTGACCTAATCCAGGGTATGATCCACATTATTATGGTTCGGACTCT
GCTAACCACTAACTTTTTTCATTTTATTTTATTTTGTTAATTTGTTTGAAT
Found at i:12821 original size:16 final size:16
Alignment explanation
Indices: 12800--12830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12790 ATAAAAGTTC
*
12800 AACTTGAGCTCGAAAA
1 AACTTGAACTCGAAAA
12816 AACTTGAACTCGAAA
1 AACTTGAACTCGAAA
12831 CATTTTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (16 bp):
AACTTGAACTCGAAAA
Found at i:21182 original size:37 final size:36
Alignment explanation
Indices: 21054--21278 Score: 200
Period size: 36 Copynumber: 6.3 Consensus size: 36
21044 TTTTTTGAAA
* * *
21054 ATATATTATATAGTTTTGAAAATGATTTTTGAATATAT
1 ATATAATATATAGTTTTGAAAA-CA-TTTTGAAAATAT
* *
21092 ATAT-AT-TATAGTTTTGAAAATTATTTTTGAAAAAAT
1 ATATAATATATAGTTTTGAAAA-CA-TTTTGAAAATAT
*
21128 ATAT-ATATTATAATTTTGAAAACATTTTGAAAATAT
1 ATATAATA-TATAGTTTTGAAAACATTTTGAAAATAT
*
21164 ATATAATATATAGTTTTTGAAAACA---T--ATATAT
1 ATATAATATATAG-TTTTGAAAACATTTTGAAAATAT
* *
21196 ATATAATATATAGTTTTTGAAAAAAATTTGAAAATAT
1 ATATAATATATAG-TTTTGAAAACATTTTGAAAATAT
* * * *
21233 ATATAATGTATGGTTTTAAAAACATTTTG-GAATAT
1 ATATAATATATAGTTTTGAAAACATTTTGAAAATAT
21268 ATAT-ATATATA
1 ATATAATATATA
21279 ATATTATTTT
Statistics
Matches: 159, Mismatches: 19, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
32 29 0.18
34 6 0.04
35 10 0.06
36 65 0.41
37 32 0.20
38 17 0.11
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.45
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAAACATTTTGAAAATAT
Found at i:21185 original size:26 final size:25
Alignment explanation
Indices: 21152--21200 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
21142 TTTGAAAACA
*
21152 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAACATATAT-ATATATAGT
21178 TTTTGAAAACATATATATATATA
1 TTTTGAAAACATATATATATATA
21201 ATATATAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTGAAAACATATATATATATAGT
Found at i:21254 original size:35 final size:39
Alignment explanation
Indices: 21192--21278 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 39
21182 GAAAACATAT
*
21192 ATATATATAATATATAGTTTTTGAAAAA-AATTT-GAAA
1 ATATATATAATATATAGGTTTTGAAAAACAATTTGGAAA
* * *
21229 ATATATATAATGTAT-GGTTTT-AAAAACATTTTGGAAT
1 ATATATATAATATATAGGTTTTGAAAAACAATTTGGAAA
21266 ATATATAT-ATATA
1 ATATATATAATATA
21279 ATATTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 5 0.12
36 13 0.30
37 25 0.58
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (39 bp):
ATATATATAATATATAGGTTTTGAAAAACAATTTGGAAA
Found at i:21274 original size:69 final size:66
Alignment explanation
Indices: 21125--21276 Score: 171
Period size: 69 Copynumber: 2.2 Consensus size: 66
21115 TTTTTGAAAA
* * * *
21125 AATATATATATTATAATTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACAT
1 AATATATATA-TATAATTTTGAAAAAAATTTGAAAATATATATAATATATAGGTTTTAAAAACAT
21190 AT
65 AT
* *
21192 ATATATATAATATATAGTTTTTGAAAAAAATTTGAAAATATATATAATGTAT-GGTTTTAAAAAC
1 A-ATATAT-ATATATA-ATTTTGAAAAAAATTTGAAAATATATATAATATATAGGTTTTAAAAAC
*
21256 ATTTT
63 A-TAT
21261 GGAATATATATATATA
1 --AATATATATATATA
21277 TAATATTATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
67 1 0.01
68 21 0.29
69 43 0.60
70 6 0.08
71 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (66 bp):
AATATATATATATAATTTTGAAAAAAATTTGAAAATATATATAATATATAGGTTTTAAAAACATA
T
Found at i:21298 original size:15 final size:15
Alignment explanation
Indices: 21280--21328 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
21270 ATATATATAA
21280 TATTATTTTTATTAT
1 TATTATTTTTATTAT
*
21295 TATTATTTATATTATT
1 TATTATTTTTATTA-T
*
21311 TTTTATTTTTA-TAT
1 TATTATTTTTATTAT
21325 TATT
1 TATT
21329 GCTTATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 4 0.14
15 15 0.52
16 10 0.34
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTATTTTTATTAT
Found at i:21309 original size:18 final size:17
Alignment explanation
Indices: 21288--21328 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
21278 AATATTATTT
21288 TTATTATTATTATTTATA
1 TTATTATTATT-TTTATA
*
21306 TTATTTTTTATTTTTATA
1 TTA-TTATTATTTTTATA
21324 TTATT
1 TTATT
21329 GCTTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 12 0.57
19 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTATTATTTTTATA
Found at i:21315 original size:12 final size:12
Alignment explanation
Indices: 21279--21316 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
21269 TATATATATA
21279 ATATTA-TTTTT
1 ATATTATTTTTT
*
21290 ATTATTATTATTT
1 A-TATTATTTTTT
21303 ATATTATTTTTT
1 ATATTATTTTTT
21315 AT
1 AT
21317 TTTTATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 1 0.04
12 17 0.74
13 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:21326 original size:33 final size:32
Alignment explanation
Indices: 21285--21354 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
21275 TATAATATTA
* *
21285 TTTTTATTATT-ATTATTTATATTATTTTTTAT
1 TTTTTATTATTGATTATTTAT-TTAATTTTAAT
*
21317 TTTTATATTATTGCTTATTTATTTAATTTTAAT
1 TTTT-TATTATTGATTATTTATTTAATTTTAAT
21350 TTTTT
1 TTTTT
21355 CTTTCAGGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 5 0.15
33 20 0.61
34 8 0.24
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (32 bp):
TTTTTATTATTGATTATTTATTTAATTTTAAT
Found at i:21334 original size:18 final size:18
Alignment explanation
Indices: 21294--21336 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
21284 ATTTTTATTA
**
21294 TTATTATTTATATTATTTT
1 TTATT-TTTATATTATTGC
21313 TTATTTTTATATTATTGC
1 TTATTTTTATATTATTGC
21331 TTATTT
1 TTATTT
21337 ATTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TTATTTTTATATTATTGC
Found at i:22519 original size:15 final size:16
Alignment explanation
Indices: 22495--22524 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22485 AATATGTTTT
22495 TTATT-TTTTTATTTC
1 TTATTATTTTTATTTC
22510 TTATTATTTTTATTT
1 TTATTATTTTTATTT
22525 TATTACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATTATTTTTATTTC
Found at i:22529 original size:14 final size:15
Alignment explanation
Indices: 22492--22535 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
22482 TTTAATATGT
22492 TTTTTATT-TTTTTA
1 TTTTTATTATTTTTA
22506 TTTCTTATTATTTTTA
1 TTT-TTATTATTTTTA
*
22522 -TTTTATTACTTTTA
1 TTTTTATTATTTTTA
22536 AAATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 14 0.52
15 7 0.26
16 6 0.22
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATTATTTTTA
Found at i:22597 original size:22 final size:22
Alignment explanation
Indices: 22569--22665 Score: 83
Period size: 22 Copynumber: 4.4 Consensus size: 22
22559 TATTTTTATA
22569 TTATTTAATTTTTTCCTTTGAT
1 TTATTTAATTTTTTCCTTTGAT
* * *
22591 TTATTTAATATTTAAT-ATTT-TT
1 TTATTTAAT-TTT-TTCCTTTGAT
* *
22613 TTAATTTTATTTTTCCCTTTGAT
1 TT-ATTTAATTTTTTCCTTTGAT
* *
22636 TT-TTTTATTTTTTCCCTTGAT
1 TTATTTAATTTTTTCCTTTGAT
22657 TTATTTAAT
1 TTATTTAAT
22666 ATTTATTTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
21 19 0.33
22 23 0.40
23 15 0.26
24 1 0.02
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (22 bp):
TTATTTAATTTTTTCCTTTGAT
Found at i:22641 original size:21 final size:21
Alignment explanation
Indices: 22617--22663 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
22607 ATTTTTTTAA
22617 TTTTA-TTTTTCCCTTTGATTT
1 TTTTATTTTTTCCC-TTGATTT
22638 TTTTATTTTTTCCCTTGATTT
1 TTTTATTTTTTCCCTTGATTT
*
22659 ATTTA
1 TTTTA
22664 ATATTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTATTTTTTCCCTTGATTT
Found at i:28406 original size:85 final size:84
Alignment explanation
Indices: 28253--28484 Score: 297
Period size: 85 Copynumber: 2.7 Consensus size: 84
28243 GGAACTATTC
* *
28253 ACAGCATAGCTCAAGGCGAGAAGGGCTATCT-TCCAGCAAAAAACCTTCAAGTTCGATTACATTC
1 ACAGCATAGCTCAAGGCGAGAAGAGCTATCTGT-CAAC-AAAAACCTTC-AGTTCGATTACATTC
28317 AGCTCAAGGACATATCAAATTT
63 AGCTCAAGGACATATCAAATTT
* *
28339 ATAGCGTAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAG
1 ACAGCATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACCTTC-AGTTCGATTACATTCAG
28404 CTCAAGGACATATCAAATTT
65 CTCAAGGACATATCAAATTT
* * * * * * *
28424 ACAGCATAGCTTAAGTCGATAAAATG-TATATGTCAACAAAAACTATTCAGTTCGATGACAT
1 ACAGCATAGCTCAAGGCGAGAAGA-GCTATCTGTCAACAAAAAC-CTTCAGTTCGATTACAT
28485 ATCAACCACA
Statistics
Matches: 129, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
85 93 0.72
86 35 0.27
87 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (84 bp):
ACAGCATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACCTTCAGTTCGATTACATTCAGC
TCAAGGACATATCAAATTT
Found at i:29329 original size:2 final size:2
Alignment explanation
Indices: 29322--29381 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
29312 TGATTTTTGA
29322 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
29364 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
29382 TTTATAGTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29413 original size:65 final size:62
Alignment explanation
Indices: 29346--29554 Score: 235
Period size: 63 Copynumber: 3.3 Consensus size: 62
29336 ATATATATAT
* * * *
29346 ATATATATATATATATATATATATATATATATATATTTTATAG-TTTGAAAACATTTTGAAAAC
1 ATATATATA-ATATATATTTATA-AAATATATATAATATATAGTTTTGAAAACATTTTGAAAAC
*
29409 ATATATATAATATATAGTTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTG-AAA-
1 ATATATATAATATATA-TTTAT-AAAATATATATAATATATAG-TTTTGAAAACATTTTGAAAAC
* *
29472 ATCTATATAATATATAGTTTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATAATATATA-TTTAT--AAA-ATATATATAATATATAG-TTTTGAAAACATTTTGAAA
*
29537 AA
61 AC
29539 ATATATATAATATATA
1 ATATATATAATATATA
29555 GTTTTTGAAA
Statistics
Matches: 130, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
62 7 0.05
63 49 0.38
64 7 0.05
65 49 0.38
66 3 0.02
67 15 0.12
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (62 bp):
ATATATATAATATATATTTATAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAAC
Found at i:29425 original size:37 final size:36
Alignment explanation
Indices: 29372--29628 Score: 205
Period size: 37 Copynumber: 7.4 Consensus size: 36
29362 ATATATATAT
* *
29372 ATATATATATTTTATAGTTTGAAAACATTTTGAAAA
1 ATATATATAATATATAGTTTGAAAACATTTTGAAAA
29408 CATATATATAATATATAG--T-------TTTTG-AAA
1 -ATATATATAATATATAGTTTGAAAACATTTTGAAAA
29435 ATATATATAATATATAGTTTTTGAAAACATTTTG-AAA
1 ATATATATAATATATAG--TTTGAAAACATTTTGAAAA
*
29472 ATCTATATAATATATAG--T-------TTTTGAAAA
1 ATATATATAATATATAGTTTGAAAACATTTTGAAAA
29499 CATATATATAATATATAGTTTTTGAAAACATTTTGAAAAA
1 -ATATATATAATATATAG--TTTGAAAACATTTTG-AAAA
29539 ATATATATAATATATAGTTTTTGAAAACATTTTG-AAA
1 ATATATATAATATATAG--TTTGAAAACATTTTGAAAA
* * * *
29576 ATATATATAATGTATGGTTTTAAAAACATTTTGGAAA
1 ATATATATAATATATAG-TTTGAAAACATTTTGAAAA
*
29613 ATAAATATAATATATA
1 ATATATATAATATATA
29629 TATATATATA
Statistics
Matches: 184, Mismatches: 10, Indels: 52
0.75 0.04 0.21
Matches are distributed among these distances:
26 22 0.12
27 6 0.03
28 21 0.11
30 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 15 0.08
37 73 0.40
39 39 0.21
40 4 0.02
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (36 bp):
ATATATATAATATATAGTTTGAAAACATTTTGAAAA
Found at i:29430 original size:28 final size:28
Alignment explanation
Indices: 29399--29529 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
29389 TTTGAAAACA
29399 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATATAATATATAGT
29427 TTTTG-AAA-ATATATATAATATATAGT
1 TTTTGAAAACATATATATAATATATAGT
29453 TTTTGAAAACATTTTGAAAATCTATATAATATATAGT
1 TTTTGAAAACA---T----A--TATATAATATATAGT
29490 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATATAATATATAGT
29518 TTTTGAAAACAT
1 TTTTGAAAACAT
29530 TTTGAAAAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 22
0.81 0.00 0.19
Matches are distributed among these distances:
26 23 0.25
27 6 0.07
28 33 0.36
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
37 26 0.28
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (28 bp):
TTTTGAAAACATATATATAATATATAGT
Found at i:29432 original size:39 final size:37
Alignment explanation
Indices: 29427--29628 Score: 262
Period size: 37 Copynumber: 5.6 Consensus size: 37
29417 AATATATAGT
29427 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
29464 TTTTGAAAATCTATATAATATATAGTTTTTGAAAAC-
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
29500 --------ATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
29529 TTTTGAAAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTG--AAAATATATATAATATATAGTTTTTGAAAACA
* * *
29568 TTTTGAAAATATATATAATGTAT-GGTTTTAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
29604 TTTTGGAAAATAAATATAATATATA
1 TTTT-GAAAATATATATAATATATA
29629 TATATATATA
Statistics
Matches: 145, Mismatches: 7, Indels: 25
0.82 0.04 0.14
Matches are distributed among these distances:
28 27 0.19
36 15 0.10
37 69 0.48
39 34 0.23
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:29438 original size:26 final size:26
Alignment explanation
Indices: 29399--29461 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 26
29389 TTTGAAAACA
29399 TTTTGAAAACATATATATAATATATAGT
1 TTTTG-AAA-ATATATATAATATATAGT
29427 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
29453 TTTTGAAAA
1 TTTTGAAAA
29462 CATTTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 27 0.77
27 3 0.09
28 5 0.14
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
TTTTGAAAATATATATAATATATAGT
Found at i:29542 original size:28 final size:28
Alignment explanation
Indices: 29483--29543 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
29473 TCTATATAAT
* *
29483 ATATAGTTTTTGAAAACATATATATAAT
1 ATATAGTTTTTGAAAACATATATAAAAA
*
29511 ATATAGTTTTTGAAAACAT-TTTGAAAAA
1 ATATAGTTTTTGAAAACATATAT-AAAAA
29539 ATATA
1 ATATA
29544 TATAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (28 bp):
ATATAGTTTTTGAAAACATATATAAAAA
Found at i:29580 original size:65 final size:65
Alignment explanation
Indices: 29389--29568 Score: 292
Period size: 65 Copynumber: 2.8 Consensus size: 65
29379 TATTTTATAG
* * *
29389 TTTGAAAACATTTTGAAAACATATATATAATATATAGTTTTTGAAAATATATATAATATATAGTT
1 TTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATATTTAATATATAGTT
*
29454 TTTGAAAACATTTTG--AAAATCTATATAATATATAGTTTTTGAAAACATATATATAATATATAG
1 TTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATAT-T-TAATATATAG
29517 TT
64 TT
29519 TTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACAT
1 TTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACAT
29569 TTTGAAAATA
Statistics
Matches: 106, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
63 32 0.30
65 42 0.40
67 32 0.30
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (65 bp):
TTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATATTTAATATATAGTT
Found at i:29662 original size:9 final size:9
Alignment explanation
Indices: 29648--29689 Score: 66
Period size: 9 Copynumber: 4.6 Consensus size: 9
29638 ATAAATAATG
29648 TTATTTTTA
1 TTATTTTTA
29657 TTATTTTTA
1 TTATTTTTA
29666 TTATTTATTA
1 TTATTT-TTA
*
29676 TTATTTATA
1 TTATTTTTA
29685 TTATT
1 TTATT
29690 GCTTATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 22 0.71
10 9 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTTA
Found at i:29678 original size:19 final size:18
Alignment explanation
Indices: 29648--29689 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
29638 ATAAATAATG
*
29648 TTATTTTTATTATTTTTA
1 TTATTTTTATTATTTATA
29666 TTATTTATTATTATTTATA
1 TTATTT-TTATTATTTATA
29685 TTATT
1 TTATT
29690 GCTTATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTTATTATTTATA
Found at i:29686 original size:16 final size:16
Alignment explanation
Indices: 29648--29699 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
29638 ATAAATAATG
*
29648 TTATTTTTATTATT-T
1 TTATATTTATTATTAT
29663 TTATTATTTATTATTAT
1 TTA-TATTTATTATTAT
*
29680 TTATA-TTATTGCTTAT
1 TTATATTTATT-ATTAT
29696 TTAT
1 TTAT
29700 TTAATTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.25
16 20 0.62
17 4 0.12
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATATTTATTATTAT
Found at i:29695 original size:19 final size:19
Alignment explanation
Indices: 29654--29702 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
29644 AATGTTATTT
* *
29654 TTATTATTTTTATTATTTA
1 TTATTATTTATATTATTGA
*
29673 TTATTATTTATATTATTGC
1 TTATTATTTATATTATTGA
29692 TTATTTATTTA
1 TTA-TTATTTA
29703 ATTTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTATTATTTATATTATTGA
Found at i:30847 original size:15 final size:18
Alignment explanation
Indices: 30827--30866 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
30817 TTTAGTATGT
30827 TTTTTTTA-TT-TT-TTA
1 TTTTTTTACTTCTTATTA
30842 TTTTTTTACTTCTTATTA
1 TTTTTTTACTTCTTATTA
30860 TTTTTTT
1 TTTTTTT
30867 TATTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 2 0.09
17 2 0.09
18 10 0.45
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTACTTCTTATTA
Found at i:30858 original size:22 final size:22
Alignment explanation
Indices: 30832--30874 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30822 TATGTTTTTT
*
30832 TTATT-TTTTATTTTTTTACTTC
1 TTATTATTTT-TTTTATTACTTC
30854 TTATTATTTTTTTTATTACTT
1 TTATTATTTTTTTTATTACTT
30875 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (22 bp):
TTATTATTTTTTTTATTACTTC
Found at i:30920 original size:18 final size:18
Alignment explanation
Indices: 30899--30971 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 18
30889 TTTTATTTAT
30899 TTTATTTTTTCCCTTTGA
1 TTTATTTTTTCCCTTTGA
*
30917 TTTA-TTTTT---TAT--
1 TTTATTTTTTCCCTTTGA
30929 TTTATTTTTTCCCTTTGA
1 TTTATTTTTTCCCTTTGA
30947 TTTATTTTTTTCCC-TTGA
1 TTTA-TTTTTTCCCTTTGA
30965 TTTATTT
1 TTTATTT
30972 AATATTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
12 4 0.09
13 5 0.11
14 2 0.04
16 2 0.04
17 8 0.17
18 16 0.35
19 9 0.20
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTATTTTTTCCCTTTGA
Found at i:30930 original size:30 final size:30
Alignment explanation
Indices: 30894--30956 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
30884 AAAATTTTTA
30894 TTTATTTTATTTTTTCCCTTTGATTTATTT
1 TTTATTTTATTTTTTCCCTTTGATTTATTT
30924 TTTATTTTATTTTTTCCCTTTGATTTATTT
1 TTTATTTTATTTTTTCCCTTTGATTTATTT
30954 TTT
1 TTT
30957 TCCCTTGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.75
Consensus pattern (30 bp):
TTTATTTTATTTTTTCCCTTTGATTTATTT
Found at i:30983 original size:14 final size:14
Alignment explanation
Indices: 30966--30992 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30956 TTCCCTTGAT
30966 TTATTTAATATTTA
1 TTATTTAATATTTA
30980 TTATTTAATATTT
1 TTATTTAATATTT
30993 TTTACTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTAATATTTA
Found at i:33993 original size:18 final size:18
Alignment explanation
Indices: 33970--34004 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
33960 AGAATCCAAC
33970 TCAAATATTATAATATTT
1 TCAAATATTATAATATTT
33988 TCAAATATTATAATATT
1 TCAAATATTATAATATT
34005 AAAAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TCAAATATTATAATATTT
Found at i:37782 original size:22 final size:22
Alignment explanation
Indices: 37738--37782 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
37728 GTCACCGTTT
* *
37738 ACATATAAATTATCATGTCAAC
1 ACATATAAATCATCATATCAAC
* *
37760 ACATATAAATCATCTTATTAAC
1 ACATATAAATCATCATATCAAC
37782 A
1 A
37783 TTGTAAATCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (22 bp):
ACATATAAATCATCATATCAAC
Found at i:43180 original size:16 final size:16
Alignment explanation
Indices: 43159--43191 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
43149 TTTTCCCTCA
*
43159 TTTCTTCCTTCTTCTT
1 TTTCTTCCTTCTCCTT
43175 TTTCTTCCTTCTCCTT
1 TTTCTTCCTTCTCCTT
43191 T
1 T
43192 CCTTTTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTCTTCCTTCTCCTT
Found at i:44009 original size:9 final size:8
Alignment explanation
Indices: 43992--44020 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
43982 GTTATGTCAT
43992 AATAAAAA
1 AATAAAAA
44000 AATAAAAA
1 AATAAAAA
44008 AATAAAAA
1 AATAAAAA
44016 AATAA
1 AATAA
44021 TTCATGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AATAAAAA
Found at i:53456 original size:2 final size:2
Alignment explanation
Indices: 53451--53485 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53441 TATATTCATC
53451 TA TA 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 TA TA T
53486 CCACTCATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53958 original size:63 final size:62
Alignment explanation
Indices: 53850--53973 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
53840 AACCTCGACA
* *
53850 ACTGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* * *
53912 ACTGTCCATATGTCTCGAAAG-ACATAGGTAAAATTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTC-CCAAAGAACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
53974 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 20 0.36
63 35 0.64
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:53969 original size:32 final size:31
Alignment explanation
Indices: 53849--53976 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
53839 GAACCTCGAC
* * ** *
53849 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
53880 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
53911 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
*
53943 AATTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
53974 AAC
1 AAC
53977 CCTCGACTCT
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
30 4 0.05
31 50 0.62
32 22 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:54785 original size:63 final size:62
Alignment explanation
Indices: 54713--54874 Score: 191
Period size: 63 Copynumber: 2.6 Consensus size: 62
54703 ATCCCTAGAC
* * * * **
54713 GGGTGCATCGATGCACTATCTATGCATCGGTGCATAAATCTCATTCGATGTTTGTATTTT-AG
1 GGGTGCATCGATGCACT-CCTATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTTAAG
* *
54775 GGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATCGCATTCGATGTTTCCATTTTAAT
1 GGG-TGCATCGATGCACTCC-TATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTTAAG
* *
54839 GGGTGCATCAATGCACTCCCTATGCATCGATACACA
1 GGGTGCATCGATGCACT-CCTATGCATCGATGCACA
54875 CTGAACAATT
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
62 4 0.05
63 75 0.88
64 6 0.07
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (62 bp):
GGGTGCATCGATGCACTCCTATGCATCGATGCACAAATCGCATTCGATGTTTCCATTTTAAG
Found at i:56342 original size:31 final size:31
Alignment explanation
Indices: 56304--56397 Score: 154
Period size: 31 Copynumber: 3.0 Consensus size: 31
56294 CCCGAAAAAC
* *
56304 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
56335 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
56366 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
56397 C
1 C
56398 CCTCGACCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 59 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:59851 original size:3 final size:3
Alignment explanation
Indices: 59843--59898 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
59833 TCAACCGTTA
* *
59843 ATT ATT ATT ATT A-T ATT AGT ATAA ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
59888 ATT ATT ATT AT
1 ATT ATT ATT AT
59899 AAAACAGGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Done.