Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002952.1 Hibiscus syriacus cultivar Beakdansim tig00006093_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: 45722
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1482 original size:33 final size:32
Alignment explanation
Indices: 1390--1482 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 32
1380 TATGTGTCAC
*
1390 ATGACATATTTTTAAAATATCACATAACATGTA
1 ATGACATA-TTTTAGAATATCACATAACATGTA
* * * * * *
1423 ATAATATATTCGTAGAGTATCTCATAATATGTTA
1 ATGACATATT-TTAGAATATCACATAACATG-TA
*
1457 TTGACATATTTTAGAATATCACATAA
1 ATGACATATTTTAGAATATCACATAA
1483 ATTTTCCTAT
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
32 2 0.04
33 34 0.76
34 9 0.20
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (32 bp):
ATGACATATTTTAGAATATCACATAACATGTA
Found at i:2441 original size:14 final size:15
Alignment explanation
Indices: 2422--2459 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2412 TCTTTGGGCT
2422 CTTTCCTTTAT-TTTC
1 CTTTCCTTT-TCTTTC
2437 C-TTCCTTTTCTTTC
1 CTTTCCTTTTCTTTC
2451 CTTTCCTTT
1 CTTTCCTTT
2460 CATCAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 12 0.57
15 8 0.38
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTCCTTTTCTTTC
Found at i:11704 original size:22 final size:22
Alignment explanation
Indices: 11679--11733 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
11669 AGCGTAATAT
* *
11679 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
11701 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
11723 CGGGAGTTATA
1 CAGGAGTTATA
11734 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:12149 original size:22 final size:22
Alignment explanation
Indices: 12124--12178 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
12114 CTGTTAATAT
* *
12124 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
12146 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
12168 CGGGAGTTATA
1 CAGGAGTTATA
12179 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:12502 original size:445 final size:445
Alignment explanation
Indices: 11673--12519 Score: 1676
Period size: 445 Copynumber: 1.9 Consensus size: 445
11663 TGAAGAAGCG
11673 TAATATCAGGAGTTATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAG
1 TAATATCAGGAGTTATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAG
11738 CTGAATAATGATACAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGTCATTTCAGCTGTT
66 CTGAATAATGATACAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGTCATTTCAGCTGTT
11803 ACAAATAAGAGGTTTAATCCTGAAATTTTATGGACGACTTTAACCCTATTTCTAGCCTATAAATA
131 ACAAATAAGAGGTTTAATCCTGAAATTTTATGGACGACTTTAACCCTATTTCTAGCCTATAAATA
11868 GAGAGCTATATTCAGCTTCTCAACTCACTCCAAAACATTCACAATTCACTTACCAAAGTGTTTTC
196 GAGAGCTATATTCAGCTTCTCAACTCACTCCAAAACATTCACAATTCACTTACCAAAGTGTTTTC
*
11933 TAAAGTTTTCTCTGTGAGTTCTCTCTGAGTGCTTTCCGATCAAAAGTGCAATACCACCAGCAGTC
261 TAAAGTTCTCTCTGTGAGTTCTCTCTGAGTGCTTTCCGATCAAAAGTGCAATACCACCAGCAGTC
11998 CACTCCGGTTTCAGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGGGACGGTCCGCCTAC
326 CACTCCGGTTTCAGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGGGACGGTCCGCCTAC
12063 TGCAGCGATTACCGTACACCCGATATCGTTAAGATGTACAGAGGAGACAAGCTGT
391 TGCAGCGATTACCGTACACCCGATATCGTTAAGATGTACAGAGGAGACAAGCTGT
12118 TAATATCAGGAGTTATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAG
1 TAATATCAGGAGTTATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAG
12183 CTGAATAATGATACAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGTCATTTCAGCTGTT
66 CTGAATAATGATACAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGTCATTTCAGCTGTT
12248 ACAAATAAGAGGTTTAATCCTGAAATTTTATGGACGACTTTAACCCTATTTCTAGCCTATAAATA
131 ACAAATAAGAGGTTTAATCCTGAAATTTTATGGACGACTTTAACCCTATTTCTAGCCTATAAATA
12313 GAGAGCTATATTCAGCTTCTCAACTCACTCCAAAACATTCACAATTCACTTACCAAAGTGTTTTC
196 GAGAGCTATATTCAGCTTCTCAACTCACTCCAAAACATTCACAATTCACTTACCAAAGTGTTTTC
12378 TAAAGTTCTCTCTGTGAGTTCTCTCTGAGTGCTTTCCGATCAAAAGTGCAATACCACCAGCAGTC
261 TAAAGTTCTCTCTGTGAGTTCTCTCTGAGTGCTTTCCGATCAAAAGTGCAATACCACCAGCAGTC
*
12443 CACTCCGGTTTCGGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGGGACGGTCCGCCTAC
326 CACTCCGGTTTCAGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGGGACGGTCCGCCTAC
12508 TGCAGCGATTAC
391 TGCAGCGATTAC
12520 ACACATCGAG
Statistics
Matches: 400, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
445 400 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (445 bp):
TAATATCAGGAGTTATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAG
CTGAATAATGATACAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGTCATTTCAGCTGTT
ACAAATAAGAGGTTTAATCCTGAAATTTTATGGACGACTTTAACCCTATTTCTAGCCTATAAATA
GAGAGCTATATTCAGCTTCTCAACTCACTCCAAAACATTCACAATTCACTTACCAAAGTGTTTTC
TAAAGTTCTCTCTGTGAGTTCTCTCTGAGTGCTTTCCGATCAAAAGTGCAATACCACCAGCAGTC
CACTCCGGTTTCAGGTGTACGGAATTCGGAGCGACCGTGTTAACCTCGGGGGACGGTCCGCCTAC
TGCAGCGATTACCGTACACCCGATATCGTTAAGATGTACAGAGGAGACAAGCTGT
Found at i:15599 original size:29 final size:29
Alignment explanation
Indices: 15566--15654 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
15556 AAAATTTATT
15566 TATTAATTTATTCCCATCAACCATATATA
1 TATTAATTTATTCCCATCAACCATATATA
* **
15595 TATT-ATGTTA---CCTTCAATAATATATA
1 TATTAAT-TTATTCCCATCAACCATATATA
* *
15621 AAATAATTTATTCCCATCAACCATATATA
1 TATTAATTTATTCCCATCAACCATATATA
15650 TATTA
1 TATTA
15655 TGTTACCTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
26 18 0.40
27 2 0.04
28 2 0.04
29 23 0.51
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.42
Consensus pattern (29 bp):
TATTAATTTATTCCCATCAACCATATATA
Found at i:19049 original size:11 final size:11
Alignment explanation
Indices: 19033--19095 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
19023 GCCATTACAT
19033 TATTAAAAATA
1 TATTAAAAATA
19044 TATTAAAAATA
1 TATTAAAAATA
* * ***
19055 CACTATTGATA
1 TATTAAAAATA
19066 -ATTATAAAAT-
1 TATTA-AAAATA
19076 T-TTAAAAATA
1 TATTAAAAATA
19086 TATTAAAAAT
1 TATTAAAAAT
19096 TTTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:19177 original size:14 final size:14
Alignment explanation
Indices: 19146--19200 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
19136 CAATAAACCC
*
19146 TAAATCTTAAATCT-
1 TAAACCTTAAAT-TA
19160 TAAACCTTAAATTA
1 TAAACCTTAAATTA
* *
19174 TAAACCATAAATCA
1 TAAACCTTAAATTA
*
19188 TAAACTTTAAATT
1 TAAACCTTAAATT
19201 GTACTTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 1 0.03
14 33 0.97
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAACCTTAAATTA
Found at i:19184 original size:21 final size:21
Alignment explanation
Indices: 19138--19184 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
19128 TGTCATTACA
*
19138 ATAAACCCTAAATCTTAAATC
1 ATAAACCCTAAATCTTAAACC
* *
19159 TTAAACCTTAAAT-TATAAACC
1 ATAAACCCTAAATCT-TAAACC
19180 ATAAA
1 ATAAA
19185 TCATAAACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAACCCTAAATCTTAAACC
Found at i:19275 original size:21 final size:20
Alignment explanation
Indices: 19251--19312 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
19241 ATTTTTATAA
*
19251 TAAATCTTAAACTCTAAACCT
1 TAAA-CTTAAAATCTAAACCT
* * * *
19272 TAAACCATAAATTATAAACAT
1 TAAA-CTTAAAATCTAAACCT
19293 TAAACTCTAAAATCTAAACC
1 TAAACT-TAAAATCTAAACC
19313 CGATTATGTG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAACTTAAAATCTAAACCT
Found at i:20996 original size:11 final size:11
Alignment explanation
Indices: 20980--21018 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
20970 GCACTTGAGA
20980 TTGAATCGAGT
1 TTGAATCGAGT
*
20991 TTGAATCAAGT
1 TTGAATCGAGT
*
21002 TTGAATCGAGC
1 TTGAATCGAGT
21013 TTGAAT
1 TTGAAT
21019 TGGGTTTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (11 bp):
TTGAATCGAGT
Found at i:34656 original size:36 final size:31
Alignment explanation
Indices: 34570--34635 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
34560 CTCGAAGGTC
*
34570 TTTTGTGTTTCAAGATAAACATTTTCAAAGG
1 TTTTGTGTTTCAAGAGAAACATTTTCAAAGG
34601 TTTTGTGTTTCAAGAGAAACGA-TTTCAAAGG
1 TTTTGTGTTTCAAGAGAAAC-ATTTTCAAAGG
34632 TTTT
1 TTTT
34636 TTTTTGTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (31 bp):
TTTTGTGTTTCAAGAGAAACATTTTCAAAGG
Found at i:34803 original size:102 final size:100
Alignment explanation
Indices: 34642--34880 Score: 232
Period size: 102 Copynumber: 2.4 Consensus size: 100
34632 TTTTTTTTTG
* * ** * * ** * *
34642 TGTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGT-CTCAAGGGAAACTATCTCAAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTAGTAC-CAAAAGAAAATGTCTCAAGAGA
* *
34706 GACAAAATTCATTTCAAGGGAA-ATGTTTTCAATG-TTT
65 GACAAAATTCATTTC-AGGGAAGA--TATTCAAAGATTT
* *
34743 ATGTTTCAAGAGAAACTATTTCAAGAGAGAAAAAACTTAGTACCAAAAGAAAATGTCTCAAGGGA
1 -TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTAGTACCAAAAGAAAATGTCTCAAGAGA
* * *
34808 GACGAAATTTATTTCATGGAAGATATTCAAAGATTT
65 GACAAAATTCATTTCAGGGAAGATATTCAAAGATTT
* * *
34844 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTT
34881 GGAAACTGTC
Statistics
Matches: 113, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
100 40 0.35
101 8 0.07
102 64 0.57
103 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (100 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTAGTACCAAAAGAAAATGTCTCAAGAGAG
ACAAAATTCATTTCAGGGAAGATATTCAAAGATTT
Found at i:35245 original size:106 final size:106
Alignment explanation
Indices: 35028--35505 Score: 519
Period size: 106 Copynumber: 4.5 Consensus size: 106
35018 GTATTGTTCT
* ** *
35028 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTTG-AACTGGGAAATTGTTTGTT-ACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-TTTTGAAACTGGGAAATTGTTTGTTGACA
* *
35091 ACCAGCCGTCCCTTCGCTATGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
* * *
35133 GTGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGTTTTGAAACAGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTTTGAAACTGGGAAATTGTTTGTTGACAA
* * *
35198 CCAGCAGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGCCTC
66 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
* * * * * *
35239 GAGTCCACTATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTTTGAAACTGGGAAATTGTTTGTTGACAA
* * * * * *
35304 TCAGCCGCCCCTTTGCGGTGAAGTTGAGCTTGTGCTATCTC
66 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
* * * * ** *
35345 AAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTTTGTC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG-GT-T--TTGAAACTGGGAAA-TTGTTTGTT
* * * ** * *
35410 AACAATCAGTCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTGTCTT
61 GACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
* * *
35456 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTTTGAAACTGGGAA
35506 GCCCATTCGT
Statistics
Matches: 309, Mismatches: 57, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
104 4 0.01
105 48 0.16
106 160 0.52
107 9 0.03
108 1 0.00
109 1 0.00
110 10 0.03
111 76 0.25
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTTTGAAACTGGGAAATTGTTTGTTGACAA
CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:35475 original size:217 final size:211
Alignment explanation
Indices: 35027--35505 Score: 575
Period size: 217 Copynumber: 2.2 Consensus size: 211
35017 TGTATTGTTC
* ** *
35027 TGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTTG-AACTGGGAAATTGTTTGTTACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGGGAAATTGTTTGTTACA
* * * * **
35091 ACCAGCCGTCCCTTCGCTATGAAGTTGAACTTGTGTTGTCTCGTGTCCAATATCCTTCGTTGTAA
65 ACCAGCCGCCCCTTCGCGATGAAGTTGAACTTGTGCTATCTCAAGTCCAATATCCTTCGTTGTAA
* * ** ** * *
35156 AGTTGAAATTGGTTTTGAAACAGGGAAATTGTTTGTTGACAACCAGCAGTCCCTTCGCTGTGAAG
130 AGTTGAAATTGCTTATGAAACAGAAAAATTGTTTGTCAACAACCAGCAGCCCCTTCACTGTGAAG
35221 TTGAACTTGTGTTGCCT
195 TTGAACTTGTGTTGCCT
* * *
35238 CGAGTCCACTATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTT-ACA
** * * * * *
35303 GTCAGCCGCCCCTTTGCGGTGAAGTTGAGCTTGTGCTATCTCAAGTCTAATATCCTTCGTTGTGA
65 ACCAGCCGCCCCTTCGCGATGAAGTTGAACTTGTGCTATCTCAAGTCCAATATCCTTCGTTGTAA
* * *
35368 AGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTTTGTCAACAATCAGTC-GCCCCTTCATT
130 AGTTGAAATTG-CT-T--ATGAAACAGAAAAA-TTGTTTGTCAACAACCAG-CAGCCCCTTCACT
* *
35432 GTGAAGTTGAGCTTGTGTTGTCT
189 GTGAAGTTGAACTTGTGTTGCCT
35455 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
35506 GCCCATTCGT
Statistics
Matches: 224, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
210 2 0.01
211 51 0.23
212 66 0.29
213 1 0.00
214 1 0.00
216 10 0.04
217 92 0.41
218 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (211 bp):
TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTACAA
CCAGCCGCCCCTTCGCGATGAAGTTGAACTTGTGCTATCTCAAGTCCAATATCCTTCGTTGTAAA
GTTGAAATTGCTTATGAAACAGAAAAATTGTTTGTCAACAACCAGCAGCCCCTTCACTGTGAAGT
TGAACTTGTGTTGCCT
Found at i:36266 original size:32 final size:32
Alignment explanation
Indices: 36165--36254 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
36155 ATTCCCAAAG
* ** *
36165 ATGCCCCAAAATTCGATGTTAAAAATTAAAAA
1 ATGCCCCAAAATTTGATGTTAAATCTCAAAAA
* *
36197 ATACCCCAACATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAAAATTTGATGTTAAATCTCAAAAA
*
36229 ATGCCCCAAAATTTGATGTTGAATCT
1 ATGCCCCAAAATTTGATGTTAAATCT
36255 TTAATTATGC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (32 bp):
ATGCCCCAAAATTTGATGTTAAATCTCAAAAA
Found at i:37333 original size:12 final size:12
Alignment explanation
Indices: 37316--37381 Score: 71
Period size: 12 Copynumber: 5.3 Consensus size: 12
37306 GTTTTTGTTT
37316 TTTTCTTTTTTA
1 TTTTCTTTTTTA
37328 TTTTCTTTTTTA
1 TTTTCTTTTTTA
37340 TTTTCTTTGTTT-
1 TTTTCTTT-TTTA
* *
37352 TTCTCTTTTTTC
1 TTTTCTTTTTTA
*
37364 TTCTTCTCTTTTTG
1 TT-TTCT-TTTTTA
37378 TTTT
1 TTTT
37382 TGATTGGATC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
11 3 0.06
12 29 0.62
13 8 0.17
14 7 0.15
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTCTTTTTTA
Found at i:37343 original size:24 final size:23
Alignment explanation
Indices: 37289--37381 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 23
37279 ATGCGTCTTG
* *
37289 TTTTCTTTTTTTCCTTTGTTTTTGTTT
1 TTTTCTTTTTTT--TTT-CTTTT-TTA
37316 TTTTCTTTTTTATTTTCTTTTTTA
1 TTTTCTTTTTT-TTTTCTTTTTTA
* *
37340 TTTTCTTTGTTTTTCTCTTTTTTC
1 TTTTCTTT-TTTTTTTCTTTTTTA
37364 TTCTTCTCTTTTTGTTTT
1 TT-TTCT-TTTTT-TTTT
37382 TGATTGGATC
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
24 22 0.39
25 14 0.25
26 8 0.14
27 11 0.20
28 1 0.02
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (23 bp):
TTTTCTTTTTTTTTTCTTTTTTA
Found at i:37359 original size:36 final size:38
Alignment explanation
Indices: 37309--37381 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 38
37299 TTCCTTTGTT
*
37309 TTTGTTTTTTTCTTTTTTATT-TTCT-TTTTTATTTTC
1 TTTGTTTTTCTCTTTTTTATTCTTCTCTTTTTATTTTC
* *
37345 TTTGTTTTTCTCTTTTTTCTTCTTCTCTTTTTGTTTT
1 TTTGTTTTTCTCTTTTTTATTCTTCTCTTTTTATTTT
37382 TGATTGGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 19 0.59
37 4 0.12
38 9 0.28
ACGTcount: A:0.03, C:0.12, G:0.04, T:0.81
Consensus pattern (38 bp):
TTTGTTTTTCTCTTTTTTATTCTTCTCTTTTTATTTTC
Found at i:38970 original size:52 final size:52
Alignment explanation
Indices: 38889--38992 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
38879 TGAATGAATG
* * * *
38889 CATCTCTGGATTTCATCATTTGTTGAACCTGTTCTATAACGGAAACGCCATT
1 CATCTCTGGATTTCACCATTTGCTGAACCTGTTATATAACAGAAACGCCATT
* * *
38941 CATCTCTGGCTTTTACCCTTTGCTGAACCTGTTATATAACAGAAACGCCATT
1 CATCTCTGGATTTCACCATTTGCTGAACCTGTTATATAACAGAAACGCCATT
38993 GAAATCCTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (52 bp):
CATCTCTGGATTTCACCATTTGCTGAACCTGTTATATAACAGAAACGCCATT
Found at i:40527 original size:19 final size:19
Alignment explanation
Indices: 40505--40567 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
40495 TAAATAAACC
*
40505 AAAA-AAATGAAACTAAAAA
1 AAAATAAAT-AAAATAAAAA
40524 AAAATAAATAAAATAAAAA
1 AAAATAAATAAAATAAAAA
** *
40543 AATGTTAAATAAACTAAATAA
1 AA-AATAAATAAAATAAA-AA
40564 AAAA
1 AAAA
40568 AGTGCTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 15 0.43
20 16 0.46
21 4 0.11
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAATAAATAAAATAAAAA
Found at i:40541 original size:15 final size:16
Alignment explanation
Indices: 40505--40542 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
40495 TAAATAAACC
40505 AAAAAAATGAAACTAA
1 AAAAAAATGAAACTAA
40521 AAAAAAAT-AAA-TAA
1 AAAAAAATGAAACTAA
40535 AATAAAAA
1 AA-AAAAA
40543 AATGTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAATGAAACTAA
Found at i:40576 original size:25 final size:24
Alignment explanation
Indices: 40525--40576 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
40515 AACTAAAAAA
*
40525 AAATAAATAAAATAAAAAAATGTT
1 AAATAAATAAAATAAAAAAATGCT
40549 AAATAAACT-AAATAAAAAAAGTGCT
1 AAATAAA-TAAAATAAAAAAA-TGCT
40574 AAA
1 AAA
40577 ATTTAAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
AAATAAATAAAATAAAAAAATGCT
Found at i:41868 original size:2 final size:2
Alignment explanation
Indices: 41861--41922 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
41851 TGTAAATAAC
41861 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
41903 AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
41923 ATCACATATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43081 original size:30 final size:31
Alignment explanation
Indices: 43045--43109 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
43035 CTTTTAAAAC
* *
43045 TTGCAATACAGTC-CCGAACATTTAGTCTGT
1 TTGCAATACAGTCTCCCAACATTTAGTCCGT
**
43075 TTGCAATATGGTCTCCCAACATTTAGTCCGT
1 TTGCAATACAGTCTCCCAACATTTAGTCCGT
43106 TTGC
1 TTGC
43110 GATATGGTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (31 bp):
TTGCAATACAGTCTCCCAACATTTAGTCCGT
Found at i:43099 original size:31 final size:31
Alignment explanation
Indices: 43056--43126 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
43046 TGCAATACAG
*
43056 TCCCGAACATTTAGTCTGTTTGCAATATGGTC
1 TCCC-AACATTTAGTCCGTTTGCAATATGGTC
*
43088 TCCCAACATTTAGTCCGTTTGCGATATGGTC
1 TCCCAACATTTAGTCCGTTTGCAATATGGTC
*
43119 -CCCGACAT
1 TCCCAACAT
43127 AACTATTGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 7 0.19
31 25 0.69
32 4 0.11
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (31 bp):
TCCCAACATTTAGTCCGTTTGCAATATGGTC
Found at i:44275 original size:40 final size:40
Alignment explanation
Indices: 44231--44354 Score: 124
Period size: 40 Copynumber: 3.1 Consensus size: 40
44221 AACTCCAATT
* * *
44231 TCGCAACCCAATTTCCAAATTCGCAACGCAAATATGTAAA
1 TCGCAACACAATTTCCAAATTCGCAACGCGAATCTGTAAA
**** * *
44271 TCGCATTGTGATTTTCCAAATTCGCAATGCGAATCTGTAAA
1 TCGCA-ACACAATTTCCAAATTCGCAACGCGAATCTGTAAA
**
44312 TCGCAACACAGAAGT-CAAATTCGCAACGCGAATCTGTAAA
1 TCGCAACACA-ATTTCCAAATTCGCAACGCGAATCTGTAAA
44352 TCG
1 TCG
44355 TAATATAGAA
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
40 33 0.50
41 33 0.50
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (40 bp):
TCGCAACACAATTTCCAAATTCGCAACGCGAATCTGTAAA
Found at i:44335 original size:20 final size:19
Alignment explanation
Indices: 44312--44498 Score: 162
Period size: 20 Copynumber: 9.3 Consensus size: 19
44302 AATCTGTAAA
44312 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
44332 TCGCAACGCGAA-TCTGTAAA-
1 TCGCAACACGAAGTC---AAAT
* * *
44352 TCGTAATATAGAAGTCAAAT
1 TCGCAACA-CGAAGTCAAAT
44372 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
44392 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
44412 TCGCAACACTGAATTTCAAAT
1 TCGCAACAC-GAA-GTCAAAT
*
44433 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* *
44453 TCACAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
44473 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACG-AAGTCAAAT
44493 TCGCAA
1 TCGCAA
44499 AGCTTGTTTA
Statistics
Matches: 137, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.01
19 9 0.07
20 98 0.72
21 26 0.19
22 2 0.01
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:44365 original size:40 final size:40
Alignment explanation
Indices: 44287--44498 Score: 172
Period size: 40 Copynumber: 5.3 Consensus size: 40
44277 TGTGATTTTC
*
44287 CAAATTCGCAATGCGAATCTGTAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAGAAGT
* * *
44327 CAAATTCGCAACGCGAATCTGTAAATCGTAATATAGAAGT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAGAAGT
* *
44367 CAAATTCGCAACACAGAA---GTCAAATTCGCAACGC-GATAGT
1 CAAATTCGCAACGC-GAATCTGT-AAA-TCGCAACACAGA-AGT
* *
44407 CAAATTCGCAACACTGAAT-T-TCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGC-GAATCTGT-AAA-TCGCAACACAGAAGT
* * *
44448 CAAATTCACAACGCG-AT-AGTCAAATTCGCAACGC-GAAAGT
1 CAAATTCGCAACGCGAATCTGT-AAA-TCGCAACACAG-AAGT
44488 CAAATTCGCAA
1 CAAATTCGCAA
44499 AGCTTGTTTA
Statistics
Matches: 145, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
38 2 0.01
39 7 0.05
40 103 0.71
41 32 0.22
42 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATCTGTAAATCGCAACACAGAAGT
Found at i:44385 original size:60 final size:62
Alignment explanation
Indices: 44312--44498 Score: 235
Period size: 60 Copynumber: 3.1 Consensus size: 62
44302 AATCTGTAAA
* * *
44312 TCGCAACACAGAAGTCAAATTCGCAACGCGAATCTGT-AAA-TCGTAATA-TAGAA-GTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGAAT-AGTCAAATTCGCAACACT-GAATGTCAAAT
*
44372 TCGCAACACAGAAGTCAAATTCGCAACGCG-ATAGTCAAATTCGCAACACTGAATTTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACACTGAATGTCAAAT
* * * *
44433 TCGCAACACAAAAGTCAAATTCACAACGCG-ATAGTCAAATTCGCAACGC-GAAAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACACTGAATGTCAAAT
44493 TCGCAA
1 TCGCAA
44499 AGCTTGTTTA
Statistics
Matches: 114, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
58 2 0.02
59 5 0.04
60 54 0.47
61 53 0.46
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (62 bp):
TCGCAACACAGAAGTCAAATTCGCAACGCGAATAGTCAAATTCGCAACACTGAATGTCAAAT
Found at i:44460 original size:61 final size:60
Alignment explanation
Indices: 44312--44498 Score: 218
Period size: 61 Copynumber: 3.1 Consensus size: 60
44302 AATCTGTAAA
* * * * * *
44312 TCGCAACACAGAAGTCAAATTCGCAACGCGAATCTGT-AAA-TCGTAATA-TAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCACAACGCG-AT-AGTCAAATTCGCAACACGA-AAGTCAAAT
* * **
44372 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATTTCAAAT
1 TCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGCAACAC-GAAAGTCAAAT
*
44433 TCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGCAACGCGAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGCAACACGAAAGTCAAAT
44493 TCGCAA
1 TCGCAA
44499 AGCTTGTTTA
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
58 2 0.02
59 5 0.04
60 51 0.46
61 53 0.47
62 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (60 bp):
TCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGCAACACGAAAGTCAAAT
Found at i:44530 original size:20 final size:20
Alignment explanation
Indices: 44505--44554 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
44495 GCAAAGCTTG
44505 TTTATTTTCGCAACGCGAAT
1 TTTATTTTCGCAACGCGAAT
*
44525 TTTATTTTCACAACGCGAAT
1 TTTATTTTCGCAACGCGAAT
44545 TTTATTTTCG
1 TTTATTTTCG
44555 AATTCGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (20 bp):
TTTATTTTCGCAACGCGAAT
Found at i:44698 original size:22 final size:22
Alignment explanation
Indices: 44673--44719 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
44663 CTACGGCGAC
44673 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
44695 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
44717 ATC
1 ATC
44720 ATTCTATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.45, G:0.15, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Done.