Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004887.1 Hibiscus syriacus cultivar Beakdansim tig00011005_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: 69022
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:6080 original size:21 final size:22
Alignment explanation
Indices: 6039--6083 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6029 TAATAATAAT
6039 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
6061 AACATATAA-AATTAAA-ATATA
1 AACA-ATAATAATTAAATATATA
6082 AA
1 AA
6084 TAAACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:7402 original size:9 final size:9
Alignment explanation
Indices: 7388--7523 Score: 125
Period size: 9 Copynumber: 15.3 Consensus size: 9
7378 GACCTGTTTG
*
7388 TAATAATAC
1 TAATAATAA
7397 TAATAATAA
1 TAATAATAA
7406 TAATAATAA
1 TAATAATAA
7415 TAATAATAA
1 TAATAATAA
*
7424 TGATAATAA
1 TAATAATAA
7433 TAATAATAA
1 TAATAATAA
*
7442 TAATAATAG
1 TAATAATAA
7451 TAATAA-AA
1 TAATAATAA
* * *
7459 TATTAAGAG
1 TAATAATAA
7468 T-ATAAATAA
1 TAAT-AATAA
* *
7477 -GATAATAT
1 TAATAATAA
*
7485 TAATATTAA
1 TAATAATAA
*
7494 TATTAATAA
1 TAATAATAA
*
7503 TAATATTAA
1 TAATAATAA
* *
7512 AAATAAAAA
1 TAATAATAA
7521 TAA
1 TAA
7524 AAAAAAACAA
Statistics
Matches: 101, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
8 11 0.11
9 90 0.89
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.34
Consensus pattern (9 bp):
TAATAATAA
Found at i:7406 original size:6 final size:6
Alignment explanation
Indices: 7388--7523 Score: 125
Period size: 6 Copynumber: 23.0 Consensus size: 6
7378 GACCTGTTTG
* *
7388 TAATAA TACTAA TAATAA TAATAA TAATAA TAATAA TGATAA TAATAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
* * * * *
7436 TAATAA TAATAA TAGTAA TAA-AA TATTAA GAGT-A TAAATAA -GATAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA T-AATAA TAATAA
* * * * * *
7482 TATTAA TATTAA TATTAA TAATAA TATTAA AAATAA AAATAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
7524 AAAAAAACAA
Statistics
Matches: 108, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
5 9 0.08
6 98 0.91
7 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.34
Consensus pattern (6 bp):
TAATAA
Found at i:8020 original size:122 final size:123
Alignment explanation
Indices: 7891--8574 Score: 859
Period size: 122 Copynumber: 5.7 Consensus size: 123
7881 GAATCAAATT
* *
7891 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCTTCTTCATATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * * * * * *
7956 GAACTCTCTCTGGAAATGCTGAGGCTGATCTATCTCTTTTTGCGATAGAGTCGAGC-A
66 GAACTCTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
* * * * *
8013 AATGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCTTTTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
*
8078 GAACTTTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
66 GAACTCTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
* * *
8136 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTTTCAGATGATTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * *
8201 GAACTTTCTCTGGAAATATTGATGCTGATCTATCTCCTTCTAGGAT-AAATCAAGCAA
66 GAACTCTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
*
8258 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT--TCCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
8321 GAACTCT-TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
66 GAACTCTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
* * * *
8378 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCTTCTTCATATGAGATCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * ** * * * *
8443 GAACTCTAC-CTGG-CA-----ATGCTGATCCA--T-C--GAGTGATGAATTCGAGCAA
66 GAACTCT-CTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
* * *
8490 AAGGTTTAACAAGTTCTTCTCATTATGAACTTC-TC-CTTTTTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* *
8553 GAACTCT-TCCGAAAATGTTGAT
66 GAACTCTCTCTGGAAATGTTGAT
8575 CCATGGAATG
Statistics
Matches: 500, Mismatches: 49, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
109 2 0.00
110 31 0.06
111 2 0.00
112 44 0.09
114 1 0.00
115 3 0.01
117 10 0.02
119 36 0.07
120 76 0.15
122 185 0.37
123 110 0.22
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
Found at i:8412 original size:242 final size:242
Alignment explanation
Indices: 7891--8574 Score: 912
Period size: 245 Copynumber: 2.9 Consensus size: 242
7881 GAATCAAATT
*
7891 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCTTCTTCATATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCATATGAGTTCTTCTCATTAT
* * * * * * *
7956 GAACTCTCTCTGGAAATGCTGAGGCTGATCTATCT-CTTTTTGCGATAGAGTCGAGC-AAATGTT
66 GAACTTTCTCTGGAAAT-ATGATGCTGATCTATCTCCTTCTAGCGATA-AATCGAGCAAAAGGTT
* * *
8019 GAACAAATTCTTCTCATTATGAACTTATTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTT
129 GAACAAGTTCTTCTCATTATGAACTTCTTCTTC--TTTCAGATGAGTTCTTCTCATTATGAACTC
8084 TCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
192 T-TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
* * * *
8136 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTTTCAGATGATTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCATATGAGTTCTTCTCATTAT
*
8201 GAACTTTCTCTGGAAATATTGATGCTGATCTATCTCCTTCTAG-GATAAATCAAGCAAAAGGTTG
66 GAACTTTCTCTGGAAATA-TGATGCTGATCTATCTCCTTCTAGCGATAAATCGAGCAAAAGGTTG
*
8265 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTCATTATGAACTCTTC
130 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCAGATGAGTTCTTCTCATTATGAACTCTTC
8330 TGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
195 TGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
* * *
8378 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCTTCTTCATATGAGATCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCATATGAGTTCTTCTCATTAT
* * * * * *
8443 GAACTCTAC-CTGG---CA--ATGCTG----A--TCCATCGAGTGATGAATTCGAGCAAAAGGTT
66 GAACT-TTCTCTGGAAATATGATGCTGATCTATCTCCTTCTAGCGAT-AAATCGAGCAAAAGGTT
* * *
8496 TAACAAGTTCTTCTCATTATGAACTTCTCCTTTTTTCAGATGAGTTCTTCTCATTATGAACTCTT
129 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCAGATGAGTTCTTCTCATTATGAACTCTT
* *
8561 CCGAAAATGTTGAT
194 CTGGAAATGTTGAT
8575 CCATGGAATG
Statistics
Matches: 397, Mismatches: 36, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
230 7 0.02
231 3 0.01
232 89 0.22
236 6 0.02
239 1 0.00
242 117 0.29
243 31 0.08
244 6 0.02
245 132 0.33
246 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (242 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCATATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAATATGATGCTGATCTATCTCCTTCTAGCGATAAATCGAGCAAAAGGTTGA
ACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
GGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCAAGCAA
Found at i:8507 original size:112 final size:109
Alignment explanation
Indices: 8253--8594 Score: 326
Period size: 112 Copynumber: 3.0 Consensus size: 109
8243 GGATAAATCA
* *
8253 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT-TCTTCCTTCAGATGAGTTCTTCTCA
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCCTT-CTTCAGATGAGATCTTCTCA
* * * *** * * *
8317 TTATGAACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGGGATAAAATCA
65 TTATGAACTCTAC-CGAAA-----ATGCTGATCCA--T-CGAAT--GATGAATTCG
* * *
8373 AGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCTTCTTCATATGAGATCTTCTT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TC-CCTTCTTCAGATGAGATCTTCTC
** *
8438 ATTATGAACTCTACCTGGCAATGCTGATCCATCGAGTGATGAATTCG
64 ATTATGAACTCTACC-GAAAATGCTGATCCATCGAATGATGAATTCG
* * * *
8485 AGCAAAAGGTTTAACAAGTTCTTCTCATTATGAACTTCTCCTTTTTTCAGATGAGTTCTTCTCAT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCCTTCTTCAGATGAGATCTTCTCAT
* * *
8550 TATGAACTCTTCCGAAAATGTTGATCCATGGAATGATGAATTCG
66 TATGAACTCTACCGAAAATGCTGATCCATCGAATGATGAATTCG
8594 A
1 A
8595 ATCTTTGCTA
Statistics
Matches: 189, Mismatches: 29, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
109 27 0.14
110 32 0.17
111 2 0.01
112 43 0.23
114 2 0.01
115 1 0.01
117 10 0.05
120 37 0.20
121 1 0.01
122 31 0.16
123 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (109 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCCTTCTTCAGATGAGATCTTCTCAT
TATGAACTCTACCGAAAATGCTGATCCATCGAATGATGAATTCG
Found at i:9013 original size:22 final size:22
Alignment explanation
Indices: 8988--9129 Score: 177
Period size: 22 Copynumber: 6.6 Consensus size: 22
8978 AATAAAGCTT
* *
8988 TCATCTTTGAAAAGATAATCTA
1 TCATCTTTGAAGAGAGAATCTA
9010 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
9032 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* * *
9054 TTATCATTAAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
9076 TCATCTTTGAAGA-ATGAATATA
1 TCATCTTTGAAGAGA-GAATCTA
9098 TCATC-TTGAAGA-ATGAATCTA
1 TCATCTTTGAAGAGA-GAATCTA
9119 TCA--TTTGAAGA
1 TCATCTTTGAAGA
9130 ATGAAGATGT
Statistics
Matches: 108, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
20 7 0.06
21 19 0.18
22 82 0.76
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:23121 original size:3 final size:3
Alignment explanation
Indices: 23113--23210 Score: 114
Period size: 3 Copynumber: 33.7 Consensus size: 3
23103 GATCTGTTTG
* * *
23113 TAA TAA TAA TAA TAT TAA TAA TAA TTA TTA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
23160 T-A TAA TAA TAA TAA TAG T-A TAAA TAA -AA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
23203 TAA TAA TA
1 TAA TAA TA
23211 TTAAAAAACA
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
2 7 0.09
3 73 0.89
4 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:25379 original size:17 final size:17
Alignment explanation
Indices: 25357--25449 Score: 59
Period size: 17 Copynumber: 5.2 Consensus size: 17
25347 AATTGAAAAA
25357 ATATAATATATATATAT
1 ATATAATATATATATAT
*
25374 ATATAATATA-AGTTTAT
1 ATATAATATATA-TATAT
*
25391 ATATAA-ACTATATTTAT
1 ATATAATA-TATATATAT
25408 ATTATAA-ACTATATA-ATT
1 A-TATAATA-TATATATA-T
*
25426 ATTATAAGCTATATATATAA
1 A-TATAA--TATATATATAT
25446 ATAT
1 ATAT
25450 GTTTATGTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
16 2 0.03
17 29 0.45
18 21 0.33
19 3 0.05
20 7 0.11
21 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:25415 original size:18 final size:18
Alignment explanation
Indices: 25386--25444 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
25376 ATAATATAAG
25386 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
25403 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
* *
25421 -TAATTATTATAAGCTATA
1 TTTA-TATTATAAACTATA
*
25439 TATATA
1 TTTATA
25445 AATATGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.23
18 26 0.74
19 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:25455 original size:25 final size:24
Alignment explanation
Indices: 25427--25493 Score: 64
Period size: 27 Copynumber: 2.6 Consensus size: 24
25417 TATATAATTA
25427 TTATAAGCTATATATATAAA-TATGT
1 TTATAA-CTATATATA-AAACTATGT
25452 TTATGTGAACTATATATAAAACTATGT
1 TTA--T-AACTATATATAAAACTATGT
*
25479 ATATAAACTATATAT
1 TTAT-AACTATATAT
25494 GTATAAACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 14 0.39
26 3 0.08
27 17 0.47
28 2 0.06
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (24 bp):
TTATAACTATATATAAAACTATGT
Found at i:25505 original size:13 final size:13
Alignment explanation
Indices: 25405--25505 Score: 64
Period size: 12 Copynumber: 7.3 Consensus size: 13
25395 AAACTATATT
25405 TATAT-TATAAAC
1 TATATATATAAAC
25417 TATATAATTATTATAAGC
1 TATAT-A-TA-TA-AA-C
25435 TATATATATAAA-
1 TATATATATAAAC
* * *
25447 TATGTTTATGTGAAC
1 TA--TATATATAAAC
25462 TATATATA-AAAC
1 TATATATATAAAC
*
25474 TATGTATATAAAC
1 TATATATATAAAC
25487 TATATATGTATAAAC
1 TATATA--TATAAAC
25502 TATA
1 TATA
25506 AAAAGTATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 21
0.70 0.08 0.21
Matches are distributed among these distances:
12 17 0.25
13 13 0.19
14 9 0.13
15 17 0.25
16 4 0.06
17 3 0.04
18 6 0.09
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:25661 original size:76 final size:75
Alignment explanation
Indices: 25491--25678 Score: 213
Period size: 76 Copynumber: 2.5 Consensus size: 75
25481 ATAAACTATA
**
25491 TATGTATAAACTATA-AAAAGTATATAGTTTATAAAATATTTTTATATTAATATAGTATATATAT
1 TATGTATAAACTATATAAAA-TATATAGTTTATAAAATATAATTATATTAATATAG-ATATATAT
25555 ATGTATATAAAC
64 ATGTATATAAAC
* * *
25567 TATGTATAAACTATATAAAATATATAGTTTATATATTATAATTATATTAATATAG-TATATGTAT
1 TATGTATAAACTATATAAAATATATAGTTTATAAAATATAATTATATTAATATAGATATATATAT
*
25631 GTATA-AATATT
66 GTATATAA-A-C
* * *
25642 TATATTAATAAAGTA-ATAAATTATATAGTTTATAAAA
1 TAT-GT-ATAAACTATATAAAATATATAGTTTATAAAA
25679 ACCTTAAACC
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
73 2 0.02
74 14 0.15
75 3 0.03
76 66 0.69
77 11 0.11
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (75 bp):
TATGTATAAACTATATAAAATATATAGTTTATAAAATATAATTATATTAATATAGATATATATAT
GTATATAAAC
Found at i:26013 original size:7 final size:7
Alignment explanation
Indices: 26003--26082 Score: 88
Period size: 7 Copynumber: 11.4 Consensus size: 7
25993 TAGTTTATAA
26003 AAACCCT
1 AAACCCT
*
26010 AAACCCC
1 AAACCCT
26017 AAACCCT
1 AAACCCT
**
26024 AAACTTT
1 AAACCCT
** *
26031 AGGCACT
1 AAACCCT
**
26038 AAATACT
1 AAACCCT
26045 AAACCCT
1 AAACCCT
26052 AAACCCT
1 AAACCCT
26059 AAACCCT
1 AAACCCT
26066 AAACCCT
1 AAACCCT
26073 AAACCCT
1 AAACCCT
26080 AAA
1 AAA
26083 ACTATACATA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.45, C:0.36, G:0.03, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:26201 original size:18 final size:18
Alignment explanation
Indices: 26171--26224 Score: 83
Period size: 18 Copynumber: 3.0 Consensus size: 18
26161 TACATGTATC
*
26171 GTATATGTATAAACTAT-
1 GTATATATATAAACTATA
26188 GTATAGTATATAAACTATA
1 GTATA-TATATAAACTATA
26207 GTATATATATAAACTATA
1 GTATATATATAAACTATA
26225 TATGTACCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 5 0.15
18 24 0.71
19 5 0.15
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (18 bp):
GTATATATATAAACTATA
Found at i:26294 original size:21 final size:21
Alignment explanation
Indices: 26268--26320 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
26258 TAGTGTACTA
* *
26268 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
26289 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
26310 TATAGTTTATA
1 TATAGTTTATA
26321 TTAATGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:26482 original size:6 final size:6
Alignment explanation
Indices: 26471--26649 Score: 75
Period size: 6 Copynumber: 28.3 Consensus size: 6
26461 ACTATATTTT
* * * *
26471 ATATTA ATATTA ATTATAA ATTATAAA ATATATT ATATTA ATA-TA A-GTTA
1 ATATTA ATATTA A-TATTA A-TAT-TA ATAT-TA ATATTA ATATTA ATATTA
* * * *
26521 ATATTA ATATTA TTA-TA ATATATA ATTATATA GTAATT- ATAATA ATAGTA
1 ATATTA ATATTA ATATTA ATAT-TA A-TAT-TA AT-ATTA ATATTA ATATTA
*
26571 TATATTTA AT-TATA TTATTA ATATTA ATAATTATA ATATTAA ATAATTA
1 -ATA-TTA ATAT-TA ATATTA ATATTA AT-A-T-TA ATATT-A AT-ATTA
*
26620 ATA-TA A-GTTA ATATTA ATATTA ATATTA AT
1 ATATTA ATATTA ATATTA ATATTA ATATTA AT
26650 TATTTTAATA
Statistics
Matches: 136, Mismatches: 17, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
5 19 0.14
6 59 0.43
7 36 0.26
8 18 0.13
9 4 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.47
Consensus pattern (6 bp):
ATATTA
Found at i:26515 original size:27 final size:27
Alignment explanation
Indices: 26470--26717 Score: 97
Period size: 27 Copynumber: 9.0 Consensus size: 27
26460 GACTATATTT
*
26470 TATATTAATATTAATTATAAATTATAAAA
1 TATATT-ATATTAA-TATAAATTATATAA
* *
26499 TATATTATATTAATATAAGTTA-ATAT
1 TATATTATATTAATATAAATTATATAA
*
26525 TAATATTAT-TATAATATATAATTATATAG
1 T-ATATTATAT-TAATATA-AATTATATAA
* * *
26554 TA-ATTATAATAATAGTATA-TATTTAA
1 TATATTATATTAATA-TAAATTATATAA
* *
26580 T-TA-TATTATTAATATTAATAATTATAA
1 TATATTA-TATTAATATAAATTA-TATAA
* *
26607 TAT-TAAATAATTAATATAAGTTAATATTAA
1 TATAT-TAT-ATTAATATAAATT-ATA-TAA
* **
26637 TAT-TAATATTAAT-TATTTTAATACTAA
1 TATATTATATTAATATAAATT-ATA-TAA
* *
26664 TTATAATATATTATTAT-AATTAATTATAA
1 -TATATTATATTAATATAAATT-A-TATAA
*
26693 -ATATT-TAATTAATAAAAATTATATA
1 TATATTAT-ATTAATATAAATTATATA
26718 GGGATGAAAT
Statistics
Matches: 168, Mismatches: 29, Indels: 47
0.69 0.12 0.19
Matches are distributed among these distances:
25 4 0.02
26 24 0.14
27 60 0.36
28 29 0.17
29 40 0.24
30 11 0.07
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TATATTATATTAATATAAATTATATAA
Found at i:26567 original size:44 final size:42
Alignment explanation
Indices: 26469--26692 Score: 126
Period size: 44 Copynumber: 5.1 Consensus size: 42
26459 AGACTATATT
* * *
26469 TTATATTAATATTAATTATAAATTATAAAATATATTATAT-TAA
1 TTATAATAATATTAA-TAT-TATTATAATATATATTATATATAA
26512 -TATAAGTTAATATTAATATTATTATAATATATAATTATATAGTAA
1 TTATAA--TAATATTAATATTATTATAATATAT-ATTATATA-TAA
*
26557 TTATAATAATAGT-ATA-TATT-TAAT-TATATTATTAATATTAA
1 TTATAATAATATTAATATTATTATAATATATATTA-T-ATA-TAA
* * *
26598 TAATTATAATATTAAATAATTAATATAAGT-TAATATTA-ATATTAA
1 TTATAATAATATT-AAT-ATTATTATAA-TAT-ATATTATATA-TAA
* * *
26643 -TATTAATTATTTTAATACTAATTATAATATATTATTATA-ATTAA
1 TTA-TAATAATATTAATA-TTATTATAATATA-TATTATATA-TAA
26687 TTATAA
1 TTATAA
26693 ATATTTAATT
Statistics
Matches: 145, Mismatches: 15, Indels: 41
0.72 0.07 0.20
Matches are distributed among these distances:
39 4 0.03
40 4 0.03
41 20 0.14
42 19 0.13
43 18 0.12
44 41 0.28
45 23 0.16
46 8 0.06
47 2 0.01
48 6 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (42 bp):
TTATAATAATATTAATATTATTATAATATATATTATATATAA
Found at i:26630 original size:10 final size:9
Alignment explanation
Indices: 26473--26706 Score: 50
Period size: 10 Copynumber: 24.8 Consensus size: 9
26463 TATATTTTAT
26473 ATTAATATTA
1 ATTAATA-TA
26483 ATT-ATA-A
1 ATTAATATA
*
26490 ATT-ATAAA
1 ATTAATATA
*
26498 ATATATTAT-
1 AT-TAATATA
26507 ATTAATATA
1 ATTAATATA
26516 AGTTAATATTAA
1 A-TTAATA-T-A
*
26528 TATTATTATA
1 -ATTAATATA
26538 A-T-ATATA
1 ATTAATATA
26545 ATTATATAGTA
1 ATTA-ATA-TA
26556 ATT-ATAATA
1 ATTAAT-ATA
26565 ATAGTATATATTTA
1 AT--TA-ATA--TA
*
26579 ATT-ATATT
1 ATTAATATA
26587 ATTAATATTA
1 ATTAATA-TA
26597 A-TAATTATAA
1 ATTAA-TAT-A
26607 TATTAA-ATA
1 -ATTAATATA
26616 ATTAATATA
1 ATTAATATA
26625 AGTTAATATTAA
1 A-TTAATA-T-A
26637 TATTAATATTA
1 -ATTAATA-TA
26648 ATT-AT-T-
1 ATTAATATA
26654 -TTAATACTA
1 ATTAATA-TA
26663 ATT-ATAATA
1 ATTAAT-ATA
*
26672 TATTATTATA
1 -ATTAATATA
26682 ATTAATTATA
1 ATTAA-TATA
* *
26692 AAT-ATTTA
1 ATTAATATA
26700 ATTAATA
1 ATTAATA
26707 AAAATTATAT
Statistics
Matches: 171, Mismatches: 13, Indels: 81
0.65 0.05 0.31
Matches are distributed among these distances:
5 2 0.01
6 2 0.01
7 13 0.08
8 25 0.15
9 39 0.23
10 50 0.29
11 12 0.07
12 20 0.12
13 4 0.02
14 4 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (9 bp):
ATTAATATA
Found at i:26641 original size:51 final size:52
Alignment explanation
Indices: 26471--26707 Score: 168
Period size: 57 Copynumber: 4.4 Consensus size: 52
26461 ACTATATTTT
* *
26471 ATATTAATATT-A-ATT-ATAAATTATAA-AATATATTATATTAATATAAGTTA
1 ATATTAATATTAATATTAAT-AATTATAATATTATAATA-ATTAATATAAGTTA
* * *
26521 ATATTAATATTATTATAATATATAATTATATAGTAATTATAATAA-TAGTATATATTTA
1 ATATTAATATTA--ATATTA-ATAATTATA-A-T-ATTATAATAATTAATATA-AGTTA
*
26579 AT-TATATTATTAATATTAATAATTATAATATTA-AATAATTAATATAAGTTA
1 ATAT-TAATATTAATATTAATAATTATAATATTATAATAATTAATATAAGTTA
* * *
26630 ATATTAATATTAATATTAATTATTTTAATACTAATTATAATATATTATTATAA-TTA
1 ATATTAATATTAATATTAA-TA-ATT-ATAAT-ATTATAATA-ATTAATATAAGTTA
* *
26686 ATTATAAATATTTA-ATTAATAA
1 A-TATTAATATTAATATTAATAA
26708 AAATTATATA
Statistics
Matches: 150, Mismatches: 16, Indels: 38
0.74 0.08 0.19
Matches are distributed among these distances:
50 11 0.07
51 25 0.17
52 13 0.09
53 4 0.03
54 7 0.05
55 22 0.15
56 21 0.14
57 26 0.17
58 14 0.09
59 7 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (52 bp):
ATATTAATATTAATATTAATAATTATAATATTATAATAATTAATATAAGTTA
Found at i:26659 original size:15 final size:14
Alignment explanation
Indices: 26469--26667 Score: 59
Period size: 15 Copynumber: 14.3 Consensus size: 14
26459 AGACTATATT
26469 TTATATTAATATTAA
1 TTAT-TTAATATTAA
* *
26484 TTA-TAAATTATAAA
1 TTATTTAA-TATTAA
*
26498 ATATATT-ATATTAA
1 TTAT-TTAATATTAA
*
26512 TATAAGTTAATATTAATA
1 T-T-ATTTAATATT-A-A
26530 TTATTATAATATATAA
1 TTATT-TAATAT-TAA
*
26546 TTA--T-ATAGTAA
1 TTATTTAATATTAA
* *
26557 TTATAATAATAGT-A
1 TTAT-TTAATATTAA
26571 TATATTT-A-ATTATA
1 T-TATTTAATATTA-A
26585 TTA-TTAATATTAA
1 TTATTTAATATTAA
*
26598 TAATTATAATATTAA
1 TTATT-TAATATTAA
* *
26613 ATAATTAATA-T-A
1 TTATTTAATATTAA
*
26625 --AGTTAATATTAA
1 TTATTTAATATTAA
26637 -TA-TTAATATTAA
1 TTATTTAATATTAA
*
26649 TTATTTTAATACTAA
1 TTA-TTTAATATTAA
26664 TTAT
1 TTAT
26668 AATATATTAT
Statistics
Matches: 140, Mismatches: 17, Indels: 55
0.66 0.08 0.26
Matches are distributed among these distances:
10 7 0.05
11 7 0.05
12 19 0.14
13 15 0.11
14 29 0.21
15 38 0.27
16 13 0.09
17 9 0.06
18 3 0.02
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (14 bp):
TTATTTAATATTAA
Found at i:26701 original size:109 final size:110
Alignment explanation
Indices: 26475--26715 Score: 275
Period size: 109 Copynumber: 2.2 Consensus size: 110
26465 TATTTTATAT
* * *
26475 TAATATTAATT-AT--AAATTATAA-AATATATTATATTAATATAAGTTAATATTAATATTATTA
1 TAATATTAATTAATAAAAATTATAATATTA-AATA-ATTAATATAAGTTAATATTAATATTAATA
* *
26536 TAATATATAATTATATAGTAATTATAATAATAGTATATATTTAATTA
64 TAATATATAATTATATACTAATTATAATAATAGTATATAATTAATTA
* * *
26583 TATTATTAA-TATTAATAATTATAATATTAAATAATTAATATAAGTTAATATTAATATTAATATT
1 TAATATTAATTAATAAAAATTATAATATTAAATAATTAATATAAGTTAATATTAATATTAATA-T
* *
26647 AAT-TAT-TTTA-ATACTAATTATAAT-ATATTATTATAATTAATTA
65 AATATATAATTATATACTAATTATAATAATAGTA-TATAATTAATTA
26690 TAAATATTTAATTAATAAAAATTATA
1 T-AATA-TTAATTAATAAAAATTATA
26716 TAGGGATGAA
Statistics
Matches: 111, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
106 5 0.05
107 26 0.23
108 15 0.14
109 35 0.32
110 27 0.24
111 3 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (110 bp):
TAATATTAATTAATAAAAATTATAATATTAAATAATTAATATAAGTTAATATTAATATTAATATA
ATATATAATTATATACTAATTATAATAATAGTATATAATTAATTA
Found at i:27418 original size:11 final size:11
Alignment explanation
Indices: 27402--27430 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
27392 CCCGAACCCA
27402 AACCCAACTCG
1 AACCCAACTCG
27413 AACCCAACTCG
1 AACCCAACTCG
27424 AACCCAA
1 AACCCAA
27431 ACCCGAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.45, G:0.07, T:0.07
Consensus pattern (11 bp):
AACCCAACTCG
Found at i:27489 original size:19 final size:19
Alignment explanation
Indices: 27448--27489 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27438 CTTGAATTTG
* *
27448 AACCTGAATCCAAAACTCA
1 AACCTGAACCCAAAACCCA
*
27467 AACCTGAACCCAAAACCCT
1 AACCTGAACCCAAAACCCA
27486 AACC
1 AACC
27490 CAATCCCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.38, G:0.05, T:0.12
Consensus pattern (19 bp):
AACCTGAACCCAAAACCCA
Found at i:27982 original size:101 final size:99
Alignment explanation
Indices: 27790--27994 Score: 331
Period size: 101 Copynumber: 2.1 Consensus size: 99
27780 TTGTTTATAT
*
27790 TGTTGATTTGTTTGTGTTGTTGGTTGTTCATTGATTGCTTTTATAATGTTATTAGCTGCCTTTTT
1 TGTTGATTTGTTTGTGTTGTTGGTTGTTCATTGATTGCTTTTATAAGGTTATTAGCTGCCTTTTT
* *
27855 TACAGTTTAAATAAACTGTTTAATTTGTAGCTAC
66 TAAAATTTAAATAAACTGTTTAATTTGTAGCTAC
*
27889 TGTTGATTTG-TTGTGTTGTTGGTTGTTCATTCAGATTGCTTTTATAAGGTTGTTAGCTGCCTTT
1 TGTTGATTTGTTTGTGTTGTTGGTTGTTCATT--GATTGCTTTTATAAGGTTATTAGCTGCCTTT
*
27953 ATTTAAAATTTAAATAAATTGTTTAATTTGTAGCTAC
64 -TTTAAAATTTAAATAAACTGTTTAATTTGTAGCTAC
27990 TGTTG
1 TGTTG
27995 GTTGTTCTTT
Statistics
Matches: 98, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
98 21 0.21
99 10 0.10
100 29 0.30
101 38 0.39
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (99 bp):
TGTTGATTTGTTTGTGTTGTTGGTTGTTCATTGATTGCTTTTATAAGGTTATTAGCTGCCTTTTT
TAAAATTTAAATAAACTGTTTAATTTGTAGCTAC
Found at i:28030 original size:31 final size:30
Alignment explanation
Indices: 27991--28061 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 30
27981 TGTAGCTACT
*
27991 GTTGGTTGTTCTTTCGAATTGCTTTTATAAG
1 GTTGGTTGTTCATTCGAATTGCTTTTAT-AG
*
28022 GTTTGTTGTTCATTCGAATTGCTTTTATAG
1 GTTGGTTGTTCATTCGAATTGCTTTTATAG
28052 GTTGGTTGTT
1 GTTGGTTGTT
28062 AACCCTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.14, C:0.08, G:0.24, T:0.54
Consensus pattern (30 bp):
GTTGGTTGTTCATTCGAATTGCTTTTATAG
Found at i:30327 original size:11 final size:11
Alignment explanation
Indices: 30311--30335 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30301 GATGATTTTG
30311 CTTATTAATTA
1 CTTATTAATTA
30322 CTTATTAATTA
1 CTTATTAATTA
30333 CTT
1 CTT
30336 TTTGTAGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (11 bp):
CTTATTAATTA
Found at i:31161 original size:23 final size:24
Alignment explanation
Indices: 31130--31179 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
31120 TTATTTTTTC
31130 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
*
31153 TTTATATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
31177 TTT
1 TTT
31180 TCCTTTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:31445 original size:16 final size:16
Alignment explanation
Indices: 31426--31456 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31416 TCAGATAAGG
31426 TCATTAACAGGTCAGA
1 TCATTAACAGGTCAGA
*
31442 TCATTTACAGGTCAG
1 TCATTAACAGGTCAG
31457 GTTAAAAATA
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:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (16 bp):
TCATTAACAGGTCAGA
Found at i:31469 original size:16 final size:16
Alignment explanation
Indices: 31450--31502 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
31440 GATCATTTAC
31450 AGGTCAGGTTAAAAAT
1 AGGTCAGGTTAAAAAT
*
31466 AGGTCAGGTTAAAAAC
1 AGGTCAGGTTAAAAAT
* *
31482 ATGTCAGGTTGAAAAT
1 AGGTCAGGTTAAAAAT
31498 AGGTC
1 AGGTC
31503 GGGTAATACC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.25
Consensus pattern (16 bp):
AGGTCAGGTTAAAAAT
Found at i:50730 original size:2 final size:2
Alignment explanation
Indices: 50717--50747 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
50707 TAACCTAAGT
*
50717 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50748 TATTTTTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54631 original size:27 final size:27
Alignment explanation
Indices: 54564--54621 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
54554 GTCTCCCTAA
54564 GATCCATTCAACAATAATTCTGAAGAT
1 GATCCATTCAACAATAATTCTGAAGAT
54591 GATCCATTCAACAATAATTCTGAAGAT
1 GATCCATTCAACAATAATTCTGAAGAT
54618 GATC
1 GATC
54622 AGTTTGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (27 bp):
GATCCATTCAACAATAATTCTGAAGAT
Found at i:55303 original size:2 final size:2
Alignment explanation
Indices: 55296--55363 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
55286 CACTCTTCAC
55296 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
55338 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
55364 GGAAAAGAAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:61346 original size:20 final size:20
Alignment explanation
Indices: 61298--61349 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
61288 TAATAAAAAA
* *
61298 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
61318 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
61338 TCGCAACGCGAT
1 TCGCAACGCGAT
61350 TTACATAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:61905 original size:19 final size:19
Alignment explanation
Indices: 61867--61933 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
61857 TTCGAGAATG
61867 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
61887 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
61906 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
61925 AAAATCGCA
1 AAAATCGCA
61934 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:61951 original size:19 final size:19
Alignment explanation
Indices: 61929--62113 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
61919 GAAACCAAAA
* *
61929 TCGCATTGCGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
61948 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
61967 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
61986 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
62006 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
62022 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
62039 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
62053 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
62072 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
62092 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
62112 TC
1 TC
62114 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:62006 original size:39 final size:38
Alignment explanation
Indices: 61929--62113 Score: 158
Period size: 33 Copynumber: 5.1 Consensus size: 38
61919 GAAACCAAAA
*
61929 TCGCATTGCGATTTTCTTTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCTTTTCGCGTTGCGATTTTCATT
61967 TCGCGTTGCGATTTT-TATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCT-TTTCGC-GTTGCGATTTTCATT
* * **
62006 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCTTTTCGCGTTGCGATTTTCATT
* **
62039 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCTTTTCGCGTTGCGATTTTCATT
* * *
62072 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTC-TTTTCGCGTTGCGATTTTCATT
62112 TC
1 TC
62114 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
37 1 0.01
38 20 0.16
39 30 0.24
40 18 0.15
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCTTTTCGCGTTGCGATTTTCATT
Found at i:62090 original size:20 final size:20
Alignment explanation
Indices: 62056--62113 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
62046 GCGATTCTCT
**
62056 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
62076 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
62096 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
62114 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:64987 original size:19 final size:18
Alignment explanation
Indices: 64955--64993 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
64945 AATAGTTTCT
64955 GAAAATGAAAATCGCACAC
1 GAAAATGAAAATCGCA-AC
**
64974 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
64992 GA
1 GA
64994 GAGAATCGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.13
Consensus pattern (18 bp):
GAAAATGAAAATCGCAAC
Found at i:65508 original size:20 final size:20
Alignment explanation
Indices: 65483--65535 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
65473 GATTATGTAT
*
65483 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
65503 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
65523 TATCTCGTTGCGA
1 TATCGCGTTGCGA
65536 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:65548 original size:41 final size:43
Alignment explanation
Indices: 65503--65638 Score: 133
Period size: 41 Copynumber: 3.3 Consensus size: 43
65493 CGAAAGTCAG
* * * *
65503 TATCGCGTTGCGAA-AGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAATAGTAAGTATCGCATTGCGATTTTCCTAA
*
65544 TATCGCATTGC-AATAGTAAGTATCGCATTGCGATTTTCCTAA
1 TATCGCGTTGCGAATAGTAAGTATCGCATTGCGATTTTCCTAA
* ** *
65586 T-TCGCGTTGCG-AT-TTACTTATTCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGAATAGTAAGTA-TCGCATTGCGATTTTCCTAA
65627 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
65639 TTTACTTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
40 6 0.08
41 71 0.89
42 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (43 bp):
TATCGCGTTGCGAATAGTAAGTATCGCATTGCGATTTTCCTAA
Found at i:65610 original size:20 final size:21
Alignment explanation
Indices: 65566--65658 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
65556 ATAGTAAGTA
*
65566 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTACTAAT
* *
65587 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACTAAT
* *
65607 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACTAAT
* *
65628 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACTAAT
*
65648 TCACATTGCGA
1 TCGCATTGCGA
65659 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTACTAAT
Found at i:65639 original size:41 final size:41
Alignment explanation
Indices: 65566--65658 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
65556 ATAGTAAGTA
*
65566 TCGCATTGCGATTTTCCTAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
65607 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
65648 TCACATTGCGA
1 TCGCATTGCGA
65659 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:66777 original size:85 final size:87
Alignment explanation
Indices: 66635--66822 Score: 258
Period size: 85 Copynumber: 2.2 Consensus size: 87
66625 GCAAAAATAC
* * **
66635 AAATG-GTATCGATACCCATTGTGTAGTATTAATATGCCTATGAAGGCGGGTACCGATACCCCA-
1 AAATGAGTACCGATACCCATTGTATAGTATTAATACCCCTATGAAGGCGGGTACCGATA-CCCAT
* *
66698 TGAGGCCCAAATTACATAATGC-
65 TAAGGCCCAAATTACAAAATGCA
* * *
66720 AAATGGGTACTGATACCCA-TGTATAGTATTAATACCCCTATGAAGGCGGGTACCGATACTCATT
1 AAATGAGTACCGATACCCATTGTATAGTATTAATACCCCTATGAAGGCGGGTACCGATACCCATT
66784 AAGGCCCAAATTACAAAATGCA
66 AAGGCCCAAATTACAAAATGCA
66806 AAATGAGTACCGATACC
1 AAATGAGTACCGATACC
66823 ATGCAAGGGT
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
84 3 0.03
85 61 0.68
86 26 0.29
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (87 bp):
AAATGAGTACCGATACCCATTGTATAGTATTAATACCCCTATGAAGGCGGGTACCGATACCCATT
AAGGCCCAAATTACAAAATGCA
Done.