Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001147.1 Hibiscus syriacus cultivar Beakdansim tig00002289_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: 85416
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1320 original size:2 final size:2
Alignment explanation
Indices: 1313--1344 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1303 ATTTATCCAC
1313 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
1345 CTTGTTGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2433 original size:32 final size:32
Alignment explanation
Indices: 2397--2478 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
2387 GGAACAATGA
*
2397 GGGCATCTTT-GAAGATTCAACATTAAATATTG
1 GGGCATCTTTAG-AGATTCAACATCAAATATTG
*
2429 GGGCAGT-TTTAGAGATTCAACATCGAATATTG
1 GGGCA-TCTTTAGAGATTCAACATCAAATATTG
*
2461 GGGCATCTTTAGGGATTC
1 GGGCATCTTTAGAGATTC
2479 TCCATCCTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 1 0.02
32 41 0.93
33 2 0.05
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (32 bp):
GGGCATCTTTAGAGATTCAACATCAAATATTG
Found at i:3561 original size:85 final size:84
Alignment explanation
Indices: 3317--3544 Score: 330
Period size: 85 Copynumber: 2.7 Consensus size: 84
3307 CTATTATAGT
3317 ATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAAAACTTCGAGTTCGATTACATTCAGCTCAAG
1 ATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAAAACTTCGAGTTCGATTACATTCAGCTCAAG
*
3382 GACATATCAAATTTACAGC
66 GACATATCAAATTTACAAC
* * * * * *
3401 ATAACTCAAGGCGATAAGGGTTATCTGTCAATAAAAACCTTCAAGTTCGATTACATTAAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAAAA-CTTCGAGTTCGATTACATTCAGCTCAA
*
3466 GGGCATATCAAATTTACAAC
65 GGACATATCAAATTTACAAC
* * * *
3486 ATAGTTCAAGGCGAGAAGGGCTATCTGTTAACAAAAACTGTCGAGTTCGATTCCATTCA
1 ATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAAAACT-TCGAGTTCGATTACATTCA
3545 TCTTGATGAT
Statistics
Matches: 125, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 35 0.28
85 90 0.72
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (84 bp):
ATAGCTCAAGGCGAGAAGGGATATCTGTCAACAAAAACTTCGAGTTCGATTACATTCAGCTCAAG
GACATATCAAATTTACAAC
Found at i:3874 original size:259 final size:259
Alignment explanation
Indices: 3398--3884 Score: 661
Period size: 259 Copynumber: 1.9 Consensus size: 259
3388 TCAAATTTAC
* *
3398 AGCATAACTCAAGGCGATAAGGGTTATCTGTCAATAAAAACCTTCAAGTTCGATTACATTAAGCT
1 AGCATAACTCAAGACGATAAGGGTTATCTGTCAACAAAAACCTTCAAGTTCGATTACATTAAGCT
* * * ** * *
3463 CAAGGGCATATCAAATTTACAACATAGTTCAAGGCGAGAAGGGCTATCTGTTAACAAAAACTGTC
66 CAAAGACATAACAAATTTACAACATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACTGTC
* ** * * *
3528 GAGTTCGATTCCATTCATCTTGATGATATATCAACTGCATGGTAGCATCGAGGAACTACTTTCCG
131 GAGTTCGATTCCATTCAGCTCAAGGACATATCAACTGCATGGTAGCAACGAGGAACTACTTTCCG
** *
3593 GTTGAAGTTTAAACCAAGGTCTTTAAGTCAAGAGGAAGATTTGGGCAATCTCTCAGCTTAGTAT
196 GTCAAAGTTCAAACCAAGGTCTTTAAGTCAAGAGGAAGATTTGGGCAATCTCTCAGCTTAGTAT
* * ** * *
3657 AGCATAACTCAAGACGATGAGGGTTATCTGTCAACAGAAACCTTTGAGTTCGATTCCATTCAGCT
1 AGCATAACTCAAGACGATAAGGGTTATCTGTCAACAAAAACCTTCAAGTTCGATTACATTAAGCT
* * ** * *
3722 CAAAGACATAACAAGTTTACAACATAACTCAAGGCAAGAAGGGTTATCTGTCAATGAAGACTTTC
66 CAAAGACATAACAAATTTACAACATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACTGTC
* *
3787 GAGTTCGATTCCATTCAGCTCAAGGGCATATCAACTGCATTGTAGCAACGGAGG-ACTACTTTCC
131 GAGTTCGATTCCATTCAGCTCAAGGACATATCAACTGCATGGTAGCAAC-GAGGAACTACTTTCC
*
3851 GGTCAAAGTTCAAACCGAGGTCTTTAAGTCAAGA
195 GGTCAAAGTTCAAACCAAGGTCTTTAAGTCAAGA
3885 ATGAGATCTG
Statistics
Matches: 194, Mismatches: 33, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
259 190 0.98
260 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (259 bp):
AGCATAACTCAAGACGATAAGGGTTATCTGTCAACAAAAACCTTCAAGTTCGATTACATTAAGCT
CAAAGACATAACAAATTTACAACATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACTGTC
GAGTTCGATTCCATTCAGCTCAAGGACATATCAACTGCATGGTAGCAACGAGGAACTACTTTCCG
GTCAAAGTTCAAACCAAGGTCTTTAAGTCAAGAGGAAGATTTGGGCAATCTCTCAGCTTAGTAT
Found at i:4356 original size:25 final size:26
Alignment explanation
Indices: 4326--4384 Score: 102
Period size: 25 Copynumber: 2.3 Consensus size: 26
4316 TAATTATTAC
*
4326 CTACCCACTAACCACCTAATCCACTA
1 CTACCCACTAACCACCTAATCCACCA
4352 C-ACCCACTAACCACCTAATCCACCA
1 CTACCCACTAACCACCTAATCCACCA
4377 CTACCCAC
1 CTACCCAC
4385 CTAATTACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 24 0.77
26 7 0.23
ACGTcount: A:0.34, C:0.51, G:0.00, T:0.15
Consensus pattern (26 bp):
CTACCCACTAACCACCTAATCCACCA
Found at i:5706 original size:5 final size:5
Alignment explanation
Indices: 5696--5728 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
5686 AATTTTAAAT
*
5696 TTTTA TTTTA TTTTA -TTCA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5729 CCCCCTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5717 original size:14 final size:14
Alignment explanation
Indices: 5700--5726 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5690 TTAAATTTTT
5700 ATTTTATTTTATTC
1 ATTTTATTTTATTC
5714 ATTTTATTTTATT
1 ATTTTATTTTATT
5727 TTCCCCCTTT
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:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTATTTTATTC
Found at i:6450 original size:44 final size:44
Alignment explanation
Indices: 6395--6481 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
6385 TATAGAAAAC
* * *
6395 GGTAAGGTCTTA-CCTTGACACATAGCAGAGGAGCCTTCAGAAAT
1 GGTAAAGTCTTACCCTTG-CACATAACAAAGGAGCCTTCAGAAAT
*
6439 GGTAAAGTCTTACCCTTGCACATAACAAATGAGCCTTCAGAAA
1 GGTAAAGTCTTACCCTTGCACATAACAAAGGAGCCTTCAGAAA
6482 CTTCCTCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 33 0.87
45 5 0.13
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (44 bp):
GGTAAAGTCTTACCCTTGCACATAACAAAGGAGCCTTCAGAAAT
Found at i:10150 original size:48 final size:49
Alignment explanation
Indices: 10071--10176 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 49
10061 TGGATATATT
* *
10071 AGAAATCA-AACTAGAATTCAGATCAAATATCATAACAGAATCCAGATC
1 AGAAATCAGAACTAGAATCCAGATCAAATATCATAACAGAATCCAAATC
* ** * *
10119 AGAAATCAGAAC-AGAATCCAGGTCAGGTATCATAACATAATTCAAATC
1 AGAAATCAGAACTAGAATCCAGATCAAATATCATAACAGAATCCAAATC
10167 AGAAATCAGA
1 AGAAATCAGA
10177 TAAAATATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 47 0.94
49 3 0.06
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (49 bp):
AGAAATCAGAACTAGAATCCAGATCAAATATCATAACAGAATCCAAATC
Found at i:10174 original size:24 final size:24
Alignment explanation
Indices: 10071--10174 Score: 104
Period size: 24 Copynumber: 4.3 Consensus size: 24
10061 TGGATATATT
*
10071 AGAAATCA-AACTAGAATTCAGATC
1 AGAAATCATAAC-AGAATCCAGATC
10095 A-AATATCATAACAGAATCCAGATC
1 AGAA-ATCATAACAGAATCCAGATC
* *
10119 AGAAATCAGAACAGAATCCAGGTC
1 AGAAATCATAACAGAATCCAGATC
** * * *
10143 AGGTATCATAACATAATTCAAATC
1 AGAAATCATAACAGAATCCAGATC
10167 AGAAATCA
1 AGAAATCA
10175 GATAAAATAT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
23 2 0.03
24 58 0.89
25 5 0.08
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.20
Consensus pattern (24 bp):
AGAAATCATAACAGAATCCAGATC
Found at i:12009 original size:17 final size:17
Alignment explanation
Indices: 11987--12028 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
11977 TTTGGTCAAA
*
11987 GTCAACGGTCAACT-GTG
1 GTCAACGGTCAA-TGGAG
12004 GTCAACGGTCAATGGAG
1 GTCAACGGTCAATGGAG
12021 GTCAACGG
1 GTCAACGG
12029 CTTGGCTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.19
Consensus pattern (17 bp):
GTCAACGGTCAATGGAG
Found at i:15571 original size:23 final size:23
Alignment explanation
Indices: 15545--15664 Score: 123
Period size: 23 Copynumber: 5.2 Consensus size: 23
15535 GAAATCATCA
15545 AAAGACAGAGGAAAACATGTCAT
1 AAAGACAGAGGAAAACATGTCAT
* * * *
15568 AAAGATAAAGAAAAACGTGTCAT
1 AAAGACAGAGGAAAACATGTCAT
* * * *
15591 AAAGATAAAGAAAAACGTGTCAT
1 AAAGACAGAGGAAAACATGTCAT
* *
15614 AAAGACAGAAGAAAACATATCAT
1 AAAGACAGAGGAAAACATGTCAT
* * *
15637 AAAGGCAGAAGAAAATATGTCAT
1 AAAGACAGAGGAAAACATGTCAT
15660 AAAGA
1 AAAGA
15665 TATAGTTATT
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.15
Consensus pattern (23 bp):
AAAGACAGAGGAAAACATGTCAT
Found at i:20342 original size:3 final size:3
Alignment explanation
Indices: 20334--20371 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
20324 AAGGAAAAGG
* *
20334 GAA GAA GAA GAA GAA GAA -AA GAA TAA CAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
20372 TGAGGTAGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.68, C:0.03, G:0.26, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:23379 original size:61 final size:61
Alignment explanation
Indices: 23274--23407 Score: 216
Period size: 61 Copynumber: 2.2 Consensus size: 61
23264 ATTTGTTGGA
*
23274 AAATCTTTAGTGTGGAGCTAAGATAATTGATATAGACTTGGTTTAGAAGTCGAACCACTAT
1 AAATCATTAGTGTGGAGCTAAGATAATTGATATAGACTTGGTTTAGAAGTCGAACCACTAT
* * *
23335 AAATCATTAGTGTGGAGCTAAGATAATTGATGTATACTTTGTTTAGAAGTCGAACCACTAT
1 AAATCATTAGTGTGGAGCTAAGATAATTGATATAGACTTGGTTTAGAAGTCGAACCACTAT
*
23396 AAATTATT-GTGT
1 AAATCATTAGTGT
23408 TATATTTTTC
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
60 4 0.06
61 64 0.94
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.35
Consensus pattern (61 bp):
AAATCATTAGTGTGGAGCTAAGATAATTGATATAGACTTGGTTTAGAAGTCGAACCACTAT
Found at i:28223 original size:25 final size:24
Alignment explanation
Indices: 28178--28264 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 24
28168 ACATTTTCAT
28178 AATATTTTATATATATTAACTTTAAAA
1 AATATTTT-T-TATATTAACTTT-AAA
28205 AATATTTTTTATATTAACTTATTAAA
1 AATATTTTTTATATTAAC-T-TTAAA
*
28231 TATATTTTTTATTAATTTAA-TTTAAA
1 AATATTTTTTA-T-A-TTAACTTTAAA
28257 AATATTTT
1 AATATTTT
28265 ATTTTTATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
25 9 0.17
26 27 0.51
27 12 0.23
28 1 0.02
29 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AATATTTTTTATATTAACTTTAAA
Found at i:28238 original size:24 final size:24
Alignment explanation
Indices: 28189--28266 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
28179 ATATTTTATA
** *
28189 TATATTAACTTTAAAAAATATTTTT
1 TATATTAAC-TTATTAAATATATTT
28214 TATATTAACTTATTAAATATATTT
1 TATATTAACTTATTAAATATATTT
* * *
28238 TTTATTAATTTAATTTAAAAATATTT
1 TATATTAACTT-A-TTAAATATATTT
28264 TAT
1 TAT
28267 TTTTATTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 21 0.48
25 10 0.23
26 13 0.30
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTAACTTATTAAATATATTT
Found at i:28539 original size:30 final size:31
Alignment explanation
Indices: 28503--28561 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
28493 GACCGCATCA
28503 TAATTAAAT-AAAACAAAA-ATGATCATATCT
1 TAATTAAATAAAAACAAAAGA-GATCATATCT
28533 TAATTAAATAAAAACAAAAGAGATCATAT
1 TAATTAAATAAAAACAAAAGAGATCATAT
28562 ATTATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 9 0.33
31 17 0.63
32 1 0.04
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (31 bp):
TAATTAAATAAAAACAAAAGAGATCATATCT
Found at i:29293 original size:42 final size:42
Alignment explanation
Indices: 29234--29315 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
29224 CCGAAATTCC
29234 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCAT
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCAT
*
29276 GTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
29316 CAATGTTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.49
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCAT
Found at i:29597 original size:29 final size:28
Alignment explanation
Indices: 29544--29599 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
29534 AAAATATTTA
* *
29544 AAATATATTTTTTAATATTTCTAATAAT
1 AAATATATTTTTAAATATTTATAATAAT
29572 AAATATTATATTTTAAATA-TTATAATAA
1 AAATA-TAT-TTTTAAATATTTATAATAA
29600 AATAATCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 11 0.46
30 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
AAATATATTTTTAAATATTTATAATAAT
Found at i:29796 original size:23 final size:23
Alignment explanation
Indices: 29749--29821 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
29739 TTTATATTTA
*
29749 ATATTAATATAATA-ATCTAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
29773 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* * *
29796 ATACTAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
29819 ATA
1 ATA
29822 ATATAACACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 29 0.69
24 13 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:29975 original size:23 final size:21
Alignment explanation
Indices: 29919--29996 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
29909 ATAAAATTAT
* **
29919 AAAATAATATTTAATAATAAA
1 AAAATAATATTAAATTTTAAA
* *
29940 AAAATTATTTTAATATTTTAAA
1 AAAATAATATTAA-ATTTTAAA
*
29962 AATAATAATATTAAATTTTATGA
1 AA-AATAATATTAAATTTTA-AA
*
29985 GAAATAATATTA
1 AAAATAATATTA
29997 TTTATTGTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
21 10 0.22
22 24 0.53
23 11 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
AAAATAATATTAAATTTTAAA
Found at i:30216 original size:14 final size:14
Alignment explanation
Indices: 30158--30216 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
30148 CCATAAATGT
* *
30158 AATTCATTTTCCAA
1 AATTCAATTTCCAG
*
30172 AATTCAATTTTCAG
1 AATTCAATTTCCAG
* *
30186 TCATTCATTTTCCAG
1 -AATTCAATTTCCAG
*
30201 AATTCAATTTCTAG
1 AATTCAATTTCCAG
30215 AA
1 AA
30217 AACTAATTAC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 24 0.69
15 11 0.31
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:35485 original size:45 final size:45
Alignment explanation
Indices: 35421--35510 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
35411 CGGTTTGCAG
*
35421 ATCTTAGTTTTAGTTTCATATCGGAGTGAAGTAGAGAGTTGAGGT
1 ATCTTAGTTTTAATTTCATATCGGAGTGAAGTAGAGAGTTGAGGT
*
35466 ATCTTAGTTTTAATTTCATATCGGAGTGATGTAGAGAGTTGAGGT
1 ATCTTAGTTTTAATTTCATATCGGAGTGAAGTAGAGAGTTGAGGT
35511 CATTTTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.07, G:0.28, T:0.39
Consensus pattern (45 bp):
ATCTTAGTTTTAATTTCATATCGGAGTGAAGTAGAGAGTTGAGGT
Found at i:38131 original size:18 final size:18
Alignment explanation
Indices: 38108--38144 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38098 GCCCTTTTCT
* *
38108 TATAATTATATTATAAAA
1 TATAATTAAAATATAAAA
38126 TATAATTAAAATATAAAA
1 TATAATTAAAATATAAAA
38144 T
1 T
38145 TAAAATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAATTAAAATATAAAA
Found at i:39344 original size:35 final size:36
Alignment explanation
Indices: 39298--39368 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
39288 ATTCTTGCTT
39298 TATGTTTCCCGCCTCTTACTATT-AGAGAGAGAGAG
1 TATGTTTCCCGCCTCTTACTATTCAGAGAGAGAGAG
*
39333 TATGTTTCCCGCCTCTTACTGTTCAGAGAGAGAGAG
1 TATGTTTCCCGCCTCTTACTATTCAGAGAGAGAGAG
39369 AGTGAGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 22 0.65
36 12 0.35
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (36 bp):
TATGTTTCCCGCCTCTTACTATTCAGAGAGAGAGAG
Found at i:41150 original size:24 final size:24
Alignment explanation
Indices: 41099--41152 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
41089 CACCACTGCT
* * * *
41099 CATATAATTTGCACCGAAGTGTCG
1 CATAGAATTTACACCGAAGTGCCA
*
41123 CATAGAATTTACACTGAAGTGCCA
1 CATAGAATTTACACCGAAGTGCCA
41147 CATAGA
1 CATAGA
41153 TTTTTCCCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (24 bp):
CATAGAATTTACACCGAAGTGCCA
Found at i:41222 original size:23 final size:23
Alignment explanation
Indices: 41189--41246 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
41179 TTTCCCCAAA
* *
41189 GACCACGTAGAATTGT-CTCGAAT
1 GACCACATAGAATTGTCCT-GAAG
*
41212 GACCACATAGATTTGTCCTGAAG
1 GACCACATAGAATTGTCCTGAAG
41235 GACCACATAGAA
1 GACCACATAGAA
41247 CTCTCGACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (23 bp):
GACCACATAGAATTGTCCTGAAG
Found at i:41461 original size:27 final size:27
Alignment explanation
Indices: 41415--41475 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
41405 TGTTTCATAG
* *
41415 AACATATTCACTTAGCACA-TATTCACAT
1 AACAT-TTCACATAGAACATTA-TCACAT
41443 AACATTTCACATAGAACATTATCACAT
1 AACATTTCACATAGAACATTATCACAT
*
41470 AGCATT
1 AACATT
41476 ATCAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (27 bp):
AACATTTCACATAGAACATTATCACAT
Found at i:41469 original size:15 final size:15
Alignment explanation
Indices: 41410--41479 Score: 55
Period size: 15 Copynumber: 5.0 Consensus size: 15
41400 ATTTATGTTT
41410 CATAGAACA-TATTCA
1 CATAGAACATTA-TCA
* *
41425 CTTAGCACA-TATTCA
1 CATAGAACATTA-TCA
41440 CAT--AACATT-TCA
1 CATAGAACATTATCA
41452 CATAGAACATTATCA
1 CATAGAACATTATCA
41467 CATAG--CATTATCA
1 CATAGAACATTATCA
41480 AATTTTATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
12 6 0.13
13 11 0.23
14 7 0.15
15 23 0.49
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30
Consensus pattern (15 bp):
CATAGAACATTATCA
Found at i:41477 original size:13 final size:13
Alignment explanation
Indices: 41437--41479 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
41427 TAGCACATAT
*
41437 TCACATAACATT-
1 TCACATAGCATTA
41449 TCACATAGAACATTA
1 TCACATAG--CATTA
41464 TCACATAGCATTA
1 TCACATAGCATTA
41477 TCA
1 TCA
41480 AATTTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.26
13 8 0.30
14 4 0.15
15 8 0.30
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (13 bp):
TCACATAGCATTA
Found at i:43400 original size:2 final size:2
Alignment explanation
Indices: 43393--43422 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43383 ATAAACAAAA
43393 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
43423 GAATTACGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43435 original size:2 final size:2
Alignment explanation
Indices: 43430--43454 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43420 TATGAATTAC
43430 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
43455 GGAAGGGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:50072 original size:15 final size:16
Alignment explanation
Indices: 50018--50080 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 16
50008 AGATTCAATC
*
50018 AAGAA-CAAAAAATAA
1 AAGAAGCAAAAAAGAA
50033 AAGAAGCAAAAAAGAAAA
1 AAGAAGCAAAAAAG--AA
*
50051 AACAAGAACAAAAAAGAA
1 AAGAAG--CAAAAAAGAA
50069 AAGAAGCAAAAA
1 AAGAAGCAAAAA
50081 TCAAAAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.12
16 13 0.32
18 14 0.35
20 8 0.20
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.02
Consensus pattern (16 bp):
AAGAAGCAAAAAAGAA
Found at i:50086 original size:22 final size:21
Alignment explanation
Indices: 50039--50102 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
50029 ATAAAAGAAG
*
50039 CAAAAAAGAAAA-AACAAGAA
1 CAAAAAAGAAAAGAACAAAAA
50059 CAAAAAAGAAAAGAAGCAAAAA
1 CAAAAAAGAAAAGAA-CAAAAA
*
50081 TC-AAAAAGAAAAGGGACAAAAA
1 -CAAAAAAGAAAA-GAACAAAAA
50103 GCTTATGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.32
21 2 0.05
22 21 0.55
23 3 0.08
ACGTcount: A:0.75, C:0.09, G:0.14, T:0.02
Consensus pattern (21 bp):
CAAAAAAGAAAAGAACAAAAA
Found at i:50087 original size:36 final size:36
Alignment explanation
Indices: 50017--50087 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
50007 AAGATTCAAT
* *
50017 CAAGAACAAAAAATAAAAGAAGCAAAAAAGAAAAAA
1 CAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAAA
*
50053 CAAGAACAAAAAAGAAAAGAAGCAAAAATCAAAAA
1 CAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAA
50088 GAAAAGGGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.76, C:0.10, G:0.11, T:0.03
Consensus pattern (36 bp):
CAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAAA
Found at i:51166 original size:18 final size:18
Alignment explanation
Indices: 51143--51178 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51133 TCAACATCAA
*
51143 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
51161 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
51179 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:51715 original size:36 final size:38
Alignment explanation
Indices: 51668--51741 Score: 116
Period size: 36 Copynumber: 2.0 Consensus size: 38
51658 CTCACCATTA
* *
51668 TCTCTTTTGAGACAGTTTCCCTT-GAAACAAA-CTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACCTTTG
51704 TCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACCTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACCTTTG
51742 AAATTGTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 22 0.65
37 7 0.21
38 5 0.15
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (38 bp):
TCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACCTTTG
Found at i:51985 original size:37 final size:37
Alignment explanation
Indices: 51915--51986 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
51905 TGGAACTAAG
* * *
51915 TTTTGTCTCTCTTGAGACAATTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAATTTCTCATAAAACAAAA
** *
51952 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAATTTCTCATAAAACAA
51987 CAGATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAATTTCTCATAAAACAAAA
Found at i:64653 original size:106 final size:106
Alignment explanation
Indices: 64465--64924 Score: 641
Period size: 106 Copynumber: 4.3 Consensus size: 106
64455 CACATCCACG
* * * *
64465 ATTTCAACTCCACAACGGAGGATATCGCGCCACCCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATATTG-G--ACTCGAGACAACACAAGTTCAACTTCACAACGAA
* * *
64530 AGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
63 GGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* * * *
64574 ATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGTTCAACTTCACAATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
64639 ATGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
** *
64680 ATTTCAACTTCACAACGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
**
64745 ATAGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* * *
64786 ATTTCAACTTTACAACGAAGGATATTGGACTCGAGATAACACAAGTTCAACGTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
64851 ACGACTGGTTGTCAACAAATAATTTCCCAATTCCATAACCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
** *
64892 ATTTCAACTTCACGGCGGAGGATATTGGACTCG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCG
64925 GAACAATACA
Statistics
Matches: 315, Mismatches: 36, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
106 292 0.93
108 1 0.00
109 22 0.07
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
Found at i:67292 original size:19 final size:18
Alignment explanation
Indices: 67249--67299 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
67239 TAAATTTAAT
*
67249 ATTATTAAAAAATATTTT
1 ATTATTAAAAAATATTTA
67267 ATT-TTAATCAAAATA-TTA
1 ATTATTAA--AAAATATTTA
67285 ATTATT-AAAAATATT
1 ATTATTAAAAAATATT
67300 AAAAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
16 6 0.21
17 5 0.18
18 9 0.32
19 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATTAAAAAATATTTA
Found at i:67339 original size:22 final size:22
Alignment explanation
Indices: 67314--67357 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
67304 ATATATTTAT
67314 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
67336 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
67358 AAAAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:67498 original size:19 final size:19
Alignment explanation
Indices: 67474--67542 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
67464 TTATTATTAA
67474 ATTATTAATAATTAATAAT
1 ATTATTAATAATTAATAAT
* *
67493 ATTATTTATGTATT--TAAT
1 ATTATTAAT-AATTAATAAT
*
67511 ATTAATATAATATTCTAATAAT
1 ATT-AT-TAATAAT-TAATAAT
67533 ATT-TTAATAA
1 ATTATTAATAA
67543 AGATATTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
18 7 0.18
19 16 0.42
20 8 0.21
22 7 0.18
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
ATTATTAATAATTAATAAT
Found at i:71561 original size:15 final size:15
Alignment explanation
Indices: 71541--71580 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
71531 TCATAACAGC
71541 TAAAAA-TAGTAACAA
1 TAAAAACTAG-AACAA
71556 TAAAAACTAGAACAA
1 TAAAAACTAGAACAA
*
71571 TAATAACTAG
1 TAAAAACTAG
71581 GATGTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (15 bp):
TAAAAACTAGAACAA
Found at i:73238 original size:19 final size:20
Alignment explanation
Indices: 73210--73249 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
73200 CAAATTCATA
73210 CCCCAACTTCAACTCC-GAT
1 CCCCAACTTCAACTCCAGAT
* *
73229 CCCCATCTTCATCTCCAGAT
1 CCCCAACTTCAACTCCAGAT
73249 C
1 C
73250 AAGGTTGCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.23, C:0.47, G:0.05, T:0.25
Consensus pattern (20 bp):
CCCCAACTTCAACTCCAGAT
Found at i:75619 original size:2 final size:2
Alignment explanation
Indices: 75612--75647 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
75602 AAATAACGTA
75612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75648 CATAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:83677 original size:158 final size:159
Alignment explanation
Indices: 83381--83712 Score: 440
Period size: 158 Copynumber: 2.1 Consensus size: 159
83371 CAAATTTGAC
*
83381 AAAAAT-GAACTTAAAATAAATCACAAATTGAAAGAATAAGGAGATTATGAAAAATTGAATGACT
1 AAAAATAG-ACTTAAAATAAATCACAAATTGAAAGAATAAGGAGATTATGAAAAACTGAATGACT
* *
83445 AAATTAAAAAATAAAAAAAATATATTATCAAAAAAAGGAATTGAAAGTACACATGTATTCTACTA
65 AAATTAAAAAATAAAAAAAATATATCATCAAAAAAAGGAATTGAAAGTACACATGTATTCTAATA
** *
83510 TGGTTTAGGATCATGTAACTCAAATTTGGT
130 TAATTTAGGATCATGTAACTCAAATTTAGT
* **
83540 AAAAAATCAGACTTAAAATAAATGATGAATTG-AAGAAATAAGGAGATTATGAAAAACTGAATGA
1 -AAAAAT-AGACTTAAAATAAATCACAAATTGAAAG-AATAAGGAGATTATGAAAAACTGAATGA
* * * * *
83604 TTAAATT-GAAAA-ACAAAAAAT-TGTCATCAAAAAGAGGAATTGAAAGTACACATGTATTCTAA
63 CTAAATTAAAAAATAAAAAAAATATATCATCAAAAAAAGGAATTGAAAGTACACATGTATTCTAA
***
83666 TATAATTTAGGATCATGTGGTTCAAATTTAGT
128 TATAATTTAGGATCATGTAACTCAAATTTAGT
83698 AAAAATAGACTTAAA
1 AAAAATAGACTTAAA
83713 TGGAGTATGA
Statistics
Matches: 152, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
156 9 0.06
157 6 0.04
158 63 0.41
159 8 0.05
160 13 0.09
161 52 0.34
162 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.27
Consensus pattern (159 bp):
AAAAATAGACTTAAAATAAATCACAAATTGAAAGAATAAGGAGATTATGAAAAACTGAATGACTA
AATTAAAAAATAAAAAAAATATATCATCAAAAAAAGGAATTGAAAGTACACATGTATTCTAATAT
AATTTAGGATCATGTAACTCAAATTTAGT
Done.