Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005197.1 Hibiscus syriacus cultivar Beakdansim tig00011742_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: 89045
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1175 original size:42 final size:41
Alignment explanation
Indices: 1057--1265 Score: 182
Period size: 43 Copynumber: 5.1 Consensus size: 41
1047 GTCCTCATTT
* *
1057 TTTTTATCTTTATAATTAAGT-TCTTAATTTTTAAATCTTA-
1 TTTTTATCTTTATAATTAAGTCTC-TAATTTTTCAATCTCAC
* *
1097 TTTTTACCTTTATAATTGATGT-TCTAATTTTATTCAATCTCAC
1 TTTTTATCTTTATAATT-AAGTCTCTAA-TTT-TTCAATCTCAC
*
1140 TTGTTATCTTTATAATTACAGTCTCTAATTTTTCAAT-T---
1 TTTTTATCTTTATAATTA-AGTCTCTAATTTTTCAATCTCAC
* * *
1178 TTTTTAAT-TTTATAATTGAGGACTCTAATTTTTTAATCTCAC
1 TTTTT-ATCTTTATAATT-AAGTCTCTAATTTTTCAATCTCAC
* * *
1220 TTTTTAACTTTATAATTGAGGCTCTTAAGTTTTTCAATCTCAC
1 TTTTTATCTTTATAATTAAGTCTC-TAA-TTTTTCAATCTCAC
1263 TTT
1 TTT
1266 CTACCTTTTC
Statistics
Matches: 138, Mismatches: 16, Indels: 27
0.76 0.09 0.15
Matches are distributed among these distances:
38 28 0.20
39 4 0.03
40 19 0.14
41 14 0.10
42 32 0.23
43 36 0.26
44 5 0.04
ACGTcount: A:0.27, C:0.13, G:0.06, T:0.55
Consensus pattern (41 bp):
TTTTTATCTTTATAATTAAGTCTCTAATTTTTCAATCTCAC
Found at i:1231 original size:80 final size:82
Alignment explanation
Indices: 1057--1236 Score: 226
Period size: 80 Copynumber: 2.2 Consensus size: 82
1047 GTCCTCATTT
* * *
1057 TTTTTATCTTTATAATTAAGTTCTTAATTTTTAAATCTTATTTTTACCTTTATAATTGATGTTCT
1 TTTTTATCTTTATAATTAAGTTCTTAATTTTTAAA-CTTATTTTTAACTTTATAATTGAGGCTCT
1122 AATTTTATTCAATCTCAC
65 AATTTTATTCAATCTCAC
* * *
1140 TTGTTATCTTTATAATTACAG-TCTCTAATTTTTCAA-TT-TTTTTAATTTTATAATTGAGGACT
1 TTTTTATCTTTATAATTA-AGTTCT-TAATTTTTAAACTTATTTTTAACTTTATAATTGAGG-CT
1202 CTAATTTT-TT-AATCTCAC
63 CTAATTTTATTCAATCTCAC
*
1220 TTTTTAACTTTATAATT
1 TTTTTATCTTTATAATT
1237 GAGGCTCTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
80 23 0.27
81 20 0.23
82 11 0.13
83 20 0.23
84 12 0.14
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (82 bp):
TTTTTATCTTTATAATTAAGTTCTTAATTTTTAAACTTATTTTTAACTTTATAATTGAGGCTCTA
ATTTTATTCAATCTCAC
Found at i:1274 original size:51 final size:51
Alignment explanation
Indices: 1219--1316 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 51
1209 TTTAATCTCA
* * * * *
1219 CTTTT-TAACTTTATAATTGAGGCTCTTAAGTTTTTCAATCTCACTTTCTAC
1 CTTTTCTAACATTATAATTAAGGCCCCTAA-TTTTTCAATCCCACTTTCTAC
* *
1270 CTTTTCTACCATTATAATTAAGGCCCCTAATTTTTTAATCCCACTTT
1 CTTTTCTAACATTATAATTAAGGCCCCTAATTTTTCAATCCCACTTT
1317 TTTACTTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 20 0.51
52 19 0.49
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.47
Consensus pattern (51 bp):
CTTTTCTAACATTATAATTAAGGCCCCTAATTTTTCAATCCCACTTTCTAC
Found at i:1393 original size:73 final size:73
Alignment explanation
Indices: 1311--1465 Score: 213
Period size: 73 Copynumber: 2.1 Consensus size: 73
1301 TTTTTAATCC
* * **
1311 CACTTTTTT-ACTTTATAATTGAGTTCCTTAAGTTTTTTTCAATCTCAATTTCTACCTTTATAAT
1 CACTTTTTTAACTTTATAATTGAG-ACCCTAAAATTTTTTCAATCTCAATTTCTACCTTTATAAT
*
1375 TGAGGCCCT
65 TGAGACCCT
* *
1384 CACTTTTTTAAGTTTATAATTGAGACCCTAAAATTTTTTCAATCTCACTTTCTACCTTTATAATT
1 CACTTTTTTAACTTTATAATTGAGACCCTAAAATTTTTTCAATCTCAATTTCTACCTTTATAATT
1449 GAGACCCT
66 GAGACCCT
* *
1457 AAGTTTTTT
1 CACTTTTTT
1466 CAATCTCAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
73 59 0.82
74 13 0.18
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.48
Consensus pattern (73 bp):
CACTTTTTTAACTTTATAATTGAGACCCTAAAATTTTTTCAATCTCAATTTCTACCTTTATAATT
GAGACCCT
Found at i:1447 original size:44 final size:43
Alignment explanation
Indices: 1396--1534 Score: 165
Period size: 43 Copynumber: 3.2 Consensus size: 43
1386 CTTTTTTAAG
1396 TTTATAATTGAGACCCTAAAATTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGACCCTAAAATTTTTTCAATCTCA-TTTCTACC
* * *
1440 TTTATAATTGAGACCCT-AAGTTTTTTCAATCTCAATTATACC
1 TTTATAATTGAGACCCTAAAATTTTTTCAATCTCATTTCTACC
** * * *
1482 TTTATAA-TGAGATCCCTAATTTTTTTTCGATCTCAATTTCGATC
1 TTTATAATTGAGA-CCCTAAAATTTTTTCAATCTC-ATTTCTACC
1526 TTTATAATT
1 TTTATAATT
1535 AAAGCCTCTA
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
41 5 0.06
42 17 0.21
43 29 0.36
44 29 0.36
45 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (43 bp):
TTTATAATTGAGACCCTAAAATTTTTTCAATCTCATTTCTACC
Found at i:14470 original size:14 final size:14
Alignment explanation
Indices: 14441--14496 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
14431 CGTTCGTGAA
14441 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
14457 CGTTCATTTA---T
1 CGTTCATTTATGTT
14468 -GTTCATTTATGTT
1 CGTTCATTTATGTT
14481 CGTTCATTTATGTT
1 CGTTCATTTATGTT
14495 CG
1 CG
14497 AACAGAGGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 17 0.47
15 3 0.08
16 5 0.14
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:14483 original size:24 final size:26
Alignment explanation
Indices: 14442--14497 Score: 98
Period size: 24 Copynumber: 2.2 Consensus size: 26
14432 GTTCGTGAAC
14442 GTTCGATTATATGTTCGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
14468 GTTC-ATT-TATGTTCGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
14492 GTTCGA
1 GTTCGA
14498 ACAGAGGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 21 0.72
25 4 0.14
26 4 0.14
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.54
Consensus pattern (26 bp):
GTTCGATTATATGTTCGTTCATTTAT
Found at i:14758 original size:14 final size:14
Alignment explanation
Indices: 14730--14769 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
14720 TTTTTTGTGT
14730 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
14743 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
*
14757 GTTCGTGTTCGTT
1 GTTTGTGTTCGTT
14770 TATTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.03, C:0.12, G:0.28, T:0.57
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:14848 original size:16 final size:16
Alignment explanation
Indices: 14827--14859 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
14817 AAAAAAAATT
14827 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
14843 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
14859 T
1 T
14860 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:23710 original size:143 final size:143
Alignment explanation
Indices: 23452--24093 Score: 819
Period size: 142 Copynumber: 4.5 Consensus size: 143
23442 GGTTTCGACA
* * * *
23452 GAGTTGATATATCACTAGAAAGTTGCTGAAGATGCTTAATTGTGTACTAAAAAGTTTCTGCCAAG
1 GAGTTGATATATCACTAAAAAGTTGCTGAAGATGATTAATTGTGTACTAGAAAGTTTCTGCCATG
* * * * *
23517 GTGCATTATTTGGTCAATGAGAAATACATGTTTTTTTTATATGAAGTGATAATACACCACTAAAA
66 GTGCATTATTTGGCCTATGAGAAATACACGTTTTTCTAATATGAAGTGATAATACACCACTAAAA
**
23582 TGTTTTCTGATTT
131 AATTTTCTGATTT
*
23595 GAGTTGATATATCACTAAAAAGTTGCTGAAGATGATTAATTGTGTACTGGAAAGTTTCTGCCATG
1 GAGTTGATATATCACTAAAAAGTTGCTGAAGATGATTAATTGTGTACTAGAAAGTTTCTGCCATG
* * * **
23660 GTTCATTATTTGGCCTATGAGAAATACACGTATTTC-ATATATGAAGTGATAATGCACCA-TTGA
66 GTGCATTATTTGGCCTATGAGAAATACACGTTTTTCTA-ATATGAAGTGATAATACACCACTAAA
*
23723 ATATTTTCTGATTT
130 AAATTTTCTGATTT
* * ** * *
23737 GAGTTGATATATCAGTGAAAAGTTAATGAAGATGATTAATTATGTACT-GAAAAGTTTCTTCCAT
1 GAGTTGATATATCACTAAAAAGTTGCTGAAGATGATTAATTGTGTACTAG-AAAGTTTCTGCCAT
* * * * *
23801 GTTACATTATTTGGCCTATGAGAAATACACATTTTTCTAATATGAAGTGATGATGCACCACTAAA
65 GGTGCATTATTTGGCCTATGAGAAATACACGTTTTTCTAATATGAAGTGATAATACACCACTAAA
*
23866 AAAATTTCTGATTT
130 AAATTTTCTGATTT
* * * *
23880 GAATTGATATATC-CCACAAAAGTTGTTGAAGATGATTAATTGTGTACTAGAAAGTTTCTACCAT
1 GAGTTGATATATCACTA-AAAAGTTGCTGAAGATGATTAATTGTGTACTAGAAAGTTTCTGCCAT
* * *
23944 GGTGCATTA-TTGGCCTATGAAAAATAAACGTTTTTCTAATATGAAGTGATAACACACCACTAAA
65 GGTGCATTATTTGGCCTATGAGAAATACACGTTTTTCTAATATGAAGTGATAATACACCACTAAA
*
24008 AAGTTTTCTGATTT
130 AAATTTTCTGATTT
* * * **
24022 GAGTTGATATGTCCCAAAAAAGTTGC-GAAAGATGATTAATTGTGCGCTAGAAAGTTTCTGCCAT
1 GAGTTGATATATCACTAAAAAGTTGCTG-AAGATGATTAATTGTGTACTAGAAAGTTTCTGCCAT
24086 GGTGCATT
65 GGTGCATT
24094 TGTTTGGCAT
Statistics
Matches: 435, Mismatches: 56, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
141 2 0.00
142 245 0.56
143 187 0.43
144 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (143 bp):
GAGTTGATATATCACTAAAAAGTTGCTGAAGATGATTAATTGTGTACTAGAAAGTTTCTGCCATG
GTGCATTATTTGGCCTATGAGAAATACACGTTTTTCTAATATGAAGTGATAATACACCACTAAAA
AATTTTCTGATTT
Found at i:24017 original size:285 final size:285
Alignment explanation
Indices: 23452--24093 Score: 781
Period size: 285 Copynumber: 2.3 Consensus size: 285
23442 GGTTTCGACA
** * *
23452 GAGTTGATATATCACTAGAAAGTTGCTGAAGATGCTTAATTGTGTACTAAAAAGTTTCTGCCAAG
1 GAGTTGATATATCACTAGAAAGTTAATGAAGATGATTAATTATGTACTAAAAAGTTTCTGCCAAG
* * ** * *
23517 GTGCATTATTTGGTCAATGAGAAATACATGTTTTTTTTATATGAAGTGATAATACACCACTAAAA
66 GTACATTATTTGGCCAATGAGAAATACACATTTTTCTAATATGAAGTGATAATACACCACTAAAA
*** * * *
23582 TGTTTTCTGATTTGAGTTGATATATCACTAAAAAGTTGCTGAAGATGATTAATTGTGTACTGGAA
131 AAATTTCTGATTTGAATTGATATATCACCAAAAAGTTGCTGAAGATGATTAATTGTGTACTAGAA
* * * *
23647 AGTTTCTGCCATGGTTCATTATTTGGCCTATGAGAAATACACGTATTTCATATATGAAGTGATAA
196 AGTTTCTACCATGGTGCATTATTTGGCCTATGAAAAATAAACGTATTTCATATATGAAGTGATAA
** * * *
23712 TGCACCATTGAATATTTTCTGATTT
261 CACACCACTAAAAATTTTCTGATTT
* * * *
23737 GAGTTGATATATCAGT-GAAAAGTTAATGAAGATGATTAATTATGTACTGAAAAGTTTCTTCCAT
1 GAGTTGATATATCACTAG-AAAGTTAATGAAGATGATTAATTATGTACTAAAAAGTTTCTGCCAA
* * * *
23801 GTTACATTATTTGGCCTATGAGAAATACACATTTTTCTAATATGAAGTGATGATGCACCACTAAA
65 GGTACATTATTTGGCCAATGAGAAATACACATTTTTCTAATATGAAGTGATAATACACCACTAAA
*
23866 AAAATTTCTGATTTGAATTGATATATC-CCACAAAAGTTGTTGAAGATGATTAATTGTGTACTAG
130 AAAATTTCTGATTTGAATTGATATATCACCA-AAAAGTTGCTGAAGATGATTAATTGTGTACTAG
*
23930 AAAGTTTCTACCATGGTGCATTA-TTGGCCTATGAAAAATAAACGTTTTTC-TAATATGAAGTGA
194 AAAGTTTCTACCATGGTGCATTATTTGGCCTATGAAAAATAAACGTATTTCAT-ATATGAAGTGA
23993 TAACACACCACTAAAAAGTTTTCTGATTT
258 TAACACACCACTAAAAA-TTTTCTGATTT
* * * * ** * ** * *
24022 GAGTTGATATGTCCCAAAAAAGTT-GCGAAAGATGATTAATTGTGCGCTAGAAAGTTTCTGCCAT
1 GAGTTGATATATCACTAGAAAGTTAATG-AAGATGATTAATTATGTACTAAAAAGTTTCTGCCAA
*
24086 GGTGCATT
65 GGTACATT
24094 TGTTTGGCAT
Statistics
Matches: 301, Mismatches: 50, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
283 1 0.00
284 51 0.17
285 249 0.83
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (285 bp):
GAGTTGATATATCACTAGAAAGTTAATGAAGATGATTAATTATGTACTAAAAAGTTTCTGCCAAG
GTACATTATTTGGCCAATGAGAAATACACATTTTTCTAATATGAAGTGATAATACACCACTAAAA
AAATTTCTGATTTGAATTGATATATCACCAAAAAGTTGCTGAAGATGATTAATTGTGTACTAGAA
AGTTTCTACCATGGTGCATTATTTGGCCTATGAAAAATAAACGTATTTCATATATGAAGTGATAA
CACACCACTAAAAATTTTCTGATTT
Found at i:29447 original size:23 final size:21
Alignment explanation
Indices: 29400--29479 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
29390 AGAACCCTAG
* ***
29400 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTCAA
29421 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC-AA
*
29444 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGATTCCCCTCAA
*
29464 GGGGGGATCGATTCCC
1 GGGGGAATCGATTCCC
29480 TCTACACCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 13 0.27
21 20 0.41
22 4 0.08
23 12 0.24
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAA
Found at i:29467 original size:20 final size:21
Alignment explanation
Indices: 29421--29481 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
29411 TTCCCCTGTG
29421 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TCAAA
*
29444 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGATTCCCTCAAA
*
29464 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
29482 TACACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAA
Found at i:33334 original size:22 final size:21
Alignment explanation
Indices: 33292--33331 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33282 GAGTTTGTTT
*
33292 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
33313 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
33332 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:36567 original size:21 final size:21
Alignment explanation
Indices: 36538--36579 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
36528 CCATGAGCAG
*
36538 TGCTTCAGTGTACCGATGCAC
1 TGCTACAGTGTACCGATGCAC
*
36559 TGCTACAGTGTATCGATGCAC
1 TGCTACAGTGTACCGATGCAC
36580 AAAAACATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAC
Found at i:36626 original size:21 final size:21
Alignment explanation
Indices: 36601--36660 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
36591 ATATAAATTG
36601 TGTATCGATGCACTGCTACAA
1 TGTATCGATGCACTGCTACAA
*
36622 TGTATCGATGCACTGCTACAG
1 TGTATCGATGCACTGCTACAA
* *
36643 TATACCGATGCACTGCTA
1 TGTATCGATGCACTGCTA
36661 TAGTCTACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (21 bp):
TGTATCGATGCACTGCTACAA
Found at i:36909 original size:29 final size:30
Alignment explanation
Indices: 36861--36917 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
36851 GTGAGCATAA
36861 TAATAATGACAATAAAATATAATGAAATTG
1 TAATAATGACAATAAAATATAATGAAATTG
* *
36891 TAATAATGA-AATACAATATCATGAAAT
1 TAATAATGACAATAAAATATAATGAAAT
36918 CATATATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (30 bp):
TAATAATGACAATAAAATATAATGAAATTG
Found at i:39478 original size:16 final size:17
Alignment explanation
Indices: 39457--39502 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
39447 ATAGCAAATT
39457 CAAACATTCAAAC-ATC
1 CAAACATTCAAACAATC
*
39473 CAAACA-TAAAACAATC
1 CAAACATTCAAACAATC
39489 CATAATCATTCAAA
1 CA-AA-CATTCAAA
39503 ATGTTTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 2 0.08
18 2 0.08
19 4 0.17
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (17 bp):
CAAACATTCAAACAATC
Found at i:40951 original size:18 final size:18
Alignment explanation
Indices: 40916--40971 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
40906 TATAGTTTTC
*
40916 ATCAAAACAACATAATTAA
1 ATCAAAA-AACTTAATTAA
40935 ATCAAAAAACTTAATTAA
1 ATCAAAAAACTTAATTAA
40953 ATCAAAAAACTTAATTAA
1 ATCAAAAAACTTAATTAA
40971 A
1 A
40972 ACAATACTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 29 0.81
19 7 0.19
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (18 bp):
ATCAAAAAACTTAATTAA
Found at i:41461 original size:21 final size:22
Alignment explanation
Indices: 41406--41485 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
41396 CATAGTAGCG
41406 TGCATCGATGCACCTTCAAGGAA
1 TGCATCGATGCACCTTCAAGG-A
* *
41429 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACCTTCAAGGA
* *
41450 TGTATCGATGCACATTCAAGGGA
1 TGCATCGATGCACCTTCAA-GGA
*
41473 TGCATTGATGCAC
1 TGCATCGATGCAC
41486 TGTATAGTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 30 0.64
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACCTTCAAGGA
Found at i:41476 original size:44 final size:43
Alignment explanation
Indices: 41409--41504 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
41399 AGTAGCGTGC
* * *
41409 ATCGATGCACCTTCAAGGAATGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGGAATGCATCGATGCA-CTGT-ATAGTGT
* *
41453 ATCGATGCACATTCAAGGGATGCATTGATGCACTGTATAGTGT
1 ATCGATGCACATTCAAGGAATGCATCGATGCACTGTATAGTGT
41496 ATCGATGCA
1 ATCGATGCA
41505 TAGTGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 17 0.37
44 29 0.63
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (43 bp):
ATCGATGCACATTCAAGGAATGCATCGATGCACTGTATAGTGT
Found at i:46802 original size:2 final size:2
Alignment explanation
Indices: 46795--46835 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
46785 GATCGAAAAC
46795 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46836 TATGTTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47096 original size:21 final size:21
Alignment explanation
Indices: 47067--47124 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
47057 AGTTGAGGGT
*
47067 TTATATGGTCATTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
47088 TTATGTGGTCATAT-GGGACAA
1 TTATGTGGTCAT-TCGGGACAA
*
47109 ATATGTGG-CACTTCGG
1 TTATGTGGTCA-TTCGG
47125 TGCAACCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 3 0.09
21 28 0.88
22 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:47167 original size:22 final size:23
Alignment explanation
Indices: 47110--47161 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
47100 ATGGGACAAA
47110 TATGTGGCACTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
*
47133 TTTGTGGCACTTCGGTGCAA-CC
1 TATGTGGCACTTCGGTGCAACCC
47155 TATGTGG
1 TATGTGG
47162 TCCTTCAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAACCC
Found at i:48161 original size:17 final size:18
Alignment explanation
Indices: 48128--48161 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48118 TGCTATTTTG
*
48128 GTATCGGTACTCTAGGGA
1 GTATCGATACTCTAGGGA
48146 GTATCGATAC-CTAGGG
1 GTATCGATACTCTAGGG
48162 TCTCAGTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (18 bp):
GTATCGATACTCTAGGGA
Found at i:48408 original size:65 final size:65
Alignment explanation
Indices: 48304--48433 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
48294 TCGATACCAA
*
48304 GATTAAGAATTGGGCTTTAATTCAAAGGAAATTATAGAAACAAATGAGGTTTCCTAAAATCTTAT
1 GATTAAGAATTGGGCTTTAATTCAAAGGAAATTATAGAAACAAATAAGGTTTCCTAAAATCTTAT
*
48369 GATTAAGAATTGGGCTTTAATTCAAAGGGAATTATAGAAACAAATAAGGTTTCCTAAAATCTTAT
1 GATTAAGAATTGGGCTTTAATTCAAAGGAAATTATAGAAACAAATAAGGTTTCCTAAAATCTTAT
48434 AAGAACAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (65 bp):
GATTAAGAATTGGGCTTTAATTCAAAGGAAATTATAGAAACAAATAAGGTTTCCTAAAATCTTAT
Found at i:48459 original size:65 final size:65
Alignment explanation
Indices: 48316--48459 Score: 184
Period size: 65 Copynumber: 2.2 Consensus size: 65
48306 TTAAGAATTG
* ** **
48316 GGCTTTAATTCAAAGGAAATTATAGAAACAAATGAGGTTTCCTAAAATCTTATGATTAAGAATTG
1 GGCTTTAATTCAAAGGAAATTATAGAAACAAATAAGGTTTCCTAAAATCTTATGAACAAGAATAA
* *
48381 GGCTTTAATTCAAAGGGAATTATAGAAACAAATAAGGTTTCCTAAAATCTTATAAGAACAATAAT
1 GGCTTTAATTCAAAGGAAATTATAGAAACAAATAAGGTTTCCTAAAATCTTAT--GAACAAGAAT
48446 AA
64 AA
*
48448 TGC-TTAA-TCAAA
1 GGCTTTAATTCAAA
48460 CATAGAAATG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
65 56 0.81
66 4 0.06
67 9 0.13
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (65 bp):
GGCTTTAATTCAAAGGAAATTATAGAAACAAATAAGGTTTCCTAAAATCTTATGAACAAGAATAA
Found at i:52634 original size:18 final size:18
Alignment explanation
Indices: 52608--52643 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52598 ATATGCAAAT
*
52608 TACAATTCTTTTAGTTTC
1 TACAATTCTTTAAGTTTC
*
52626 TACATTTCTTTAAGTTTC
1 TACAATTCTTTAAGTTTC
52644 CATATTCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (18 bp):
TACAATTCTTTAAGTTTC
Found at i:52651 original size:17 final size:18
Alignment explanation
Indices: 52612--52653 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
52602 GCAAATTACA
*
52612 ATTCTTTTAGTTTCTACAT
1 ATTCTTTAAGTTTC-ACAT
52631 -TTCTTTAAGTTTC-CAT
1 ATTCTTTAAGTTTCACAT
52647 ATTCTTT
1 ATTCTTT
52654 CCTAATGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 6 0.29
18 12 0.57
ACGTcount: A:0.19, C:0.17, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTCTTTAAGTTTCACAT
Found at i:58053 original size:21 final size:21
Alignment explanation
Indices: 58028--58104 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
58018 GAATATCTCA
58028 AAGGACCACATATATGTCCCG
1 AAGGACCACATATATGTCCCG
* * * * * *
58049 AAGGACCTCGTAGAATTATCTCA
1 AAGGACCACATA-TA-TGTCCCG
58072 AAGGACCACATATATGTCCCG
1 AAGGACCACATATATGTCCCG
*
58093 AAGGACCGCATA
1 AAGGACCACATA
58105 AAACCCTCAA
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 25 0.61
22 2 0.05
23 14 0.34
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
AAGGACCACATATATGTCCCG
Found at i:58078 original size:44 final size:43
Alignment explanation
Indices: 58016--58099 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 43
58006 GAGTGTAACA
58016 TAGAATATCTCAAAGGACCACATATATGTCCCGAAGGACCTCG
1 TAGAATATCTCAAAGGACCACATATATGTCCCGAAGGACCTCG
58059 TAGAATTATCTCAAAGGACCACATATATGTCCCGAAGGACC
1 TAGAA-TATCTCAAAGGACCACATATATGTCCCGAAGGACC
58100 GCATAAAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 5 0.12
44 35 0.88
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (43 bp):
TAGAATATCTCAAAGGACCACATATATGTCCCGAAGGACCTCG
Found at i:60276 original size:81 final size:81
Alignment explanation
Indices: 60141--60690 Score: 695
Period size: 81 Copynumber: 6.8 Consensus size: 81
60131 TAAATAAAAA
* * * * *
60141 ATTAATTGCCTAGCTATACATTTGACAGAAATGTGTCAATCATGGC-AGTTAGATGAAATGTTAA
1 ATTAATTGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTAT-GCTAGTTAGATGAAAGGTTAA
*
60205 ATACCTTTGTGTTAAAG
65 ATACCTTTGAGTTAAAG
* *
60222 ATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAAA
1 ATTAATTGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCTAGTTAGATGAAAGGTTAAA
*
60287 TACCTCTGAG-TAAAG
66 TACCTTTGAGTTAAAG
* * * * *
60302 ATTAATTACCTAGTTATTCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAA
1 ATTAATTGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCTAGTTAGATGAAAGGTTAAA
60367 TACCTTTGAGTTAAAG
66 TACCTTTGAGTTAAAG
* * * *
60383 ATTAATTACCTAGTTGTGCATTTGATAGAAA-GATATCAATTATGCCAGTTAGATGAAAGGTTAA
1 ATTAATTGCCTAGTTGTGCATTTGACAGAAATG-TGTCAATTATGCTAGTTAGATGAAAGGTTAA
*
60447 ATACCTTTGAGTAAAAG
65 ATACCTTTGAGTTAAAG
* * * * *
60464 ATTAATTGCCTAGCTGTGCATTTGAAAAAAAATGTGTTAATTATGCTAGTTAGATCAAAGGTTAA
1 ATTAATTGCCTAGTTGTGCATTTG-ACAGAAATGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
60529 ATACCTTTGA-TTAAAAG
65 ATACCTTTGAGTT-AAAG
*
60546 ATTAATTGCCTAGTTGTGCATTTGACATAAATGTGTCAATTATG-TCAGTTAGATGAAAGGTTAA
1 ATTAATTGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCT-AGTTAGATGAAAGGTTAA
*
60610 ATACCTTTGAGTTAAAT
65 ATACCTTTGAGTTAAAG
* * * * *
60627 ATTAAATT-CCTAGTTGTGC--TTGGCA-AAAAGATGTCAATCATGCAAGTTAGATGAAAGGCTA
1 ATT-AATTGCCTAGTTGTGCATTTGACAGAAATG-TGTCAATTATGCTAGTTAGATGAAAGGTTA
60688 AAT
64 AAT
60691 GACTTTGGGT
Statistics
Matches: 416, Mismatches: 42, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
78 4 0.01
79 34 0.08
80 76 0.18
81 226 0.54
82 75 0.18
83 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (81 bp):
ATTAATTGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCTAGTTAGATGAAAGGTTAAA
TACCTTTGAGTTAAAG
Found at i:60406 original size:161 final size:161
Alignment explanation
Indices: 60141--60690 Score: 725
Period size: 161 Copynumber: 3.4 Consensus size: 161
60131 TAAATAAAAA
* * *
60141 ATTAATTGCCTAGCTATACATTTGACAGAAATGTGTCAATCATGGCAGTTAGATGAAATGTTAAA
1 ATTAATTGCCTAGCTATGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAA
* *
60206 TACCTTTGTGTTAAAGATTAATTGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCTAGT
66 TACCTTTGAGTTAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGT
*
60271 TAGATGAAAGGTTAAATACCTCTGAGTAAAG
131 TAGATGAAAGGTTAAATACCTTTGAGTAAAG
* * *
60302 ATTAATTACCTAGTTATTCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAA
1 ATTAATTGCCTAGCTATGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAA
* * * * *
60367 TACCTTTGAGTTAAAGATTAATTACCTAGTTGTGCATTTGATAGAAAGATATCAATTATGCCAGT
66 TACCTTTGAGTTAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGT
60432 TAGATGAAAGGTTAAATACCTTTGAGTAAAAG
131 TAGATGAAAGGTTAAATACCTTTGAGT-AAAG
* * * * * * *
60464 ATTAATTGCCTAGCTGTGCATTTGAAAAAAAATGTGTTAATTATGCTAGTTAGATCAAAGGTTAA
1 ATTAATTGCCTAGCTATGCATTTG-ACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAA
* *
60529 ATACCTTTGA-TTAAAAGATTAATTGCCTAGTTGTGCATTTGACATAAATGTGTCAATTATG-TC
65 ATACCTTTGAGTT-AAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCT-
*
60592 AGTTAGATGAAAGGTTAAATACCTTTGAGTTAAAT
128 AGTTAGATGAAAGGTTAAATACCTTTGAG-TAAAG
* * * * * *
60627 ATTAAATT-CCTAGTTGTGC--TTGGCA-AAAAGATGTCAATCATGCAAGTTAGATGAAAGGCTA
1 ATT-AATTGCCTAGCTATGCATTTGACAGAAATG-TGTCAATCATGCCAGTTAGATGAAAGGTTA
60688 AAT
64 AAT
60691 GACTTTGGGT
Statistics
Matches: 342, Mismatches: 40, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
159 4 0.01
160 29 0.08
161 147 0.43
162 26 0.08
163 131 0.38
164 5 0.01
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (161 bp):
ATTAATTGCCTAGCTATGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAA
TACCTTTGAGTTAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGT
TAGATGAAAGGTTAAATACCTTTGAGTAAAG
Found at i:61276 original size:22 final size:22
Alignment explanation
Indices: 61246--61288 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
61236 ATCGGTACTC
*
61246 ATACCATGGGATCGATACTTCT
1 ATACCATGGGACCGATACTTCT
* *
61268 ATACTATGGTACCGATACTTC
1 ATACCATGGGACCGATACTTC
61289 CTTTAAGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (22 bp):
ATACCATGGGACCGATACTTCT
Found at i:63480 original size:47 final size:46
Alignment explanation
Indices: 63401--63617 Score: 221
Period size: 47 Copynumber: 4.8 Consensus size: 46
63391 TATAAAATCT
* * * *
63401 CTTACCATTT-ATCCCATAAGCTTGTAATCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
63446 CTAACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
63493 TTTACCATTT-GTTCCGTAAGCTC-TAAGCTTATTTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTA-TTTTACCAATATA
* * * *
63538 TTTACCATTTAATACCATAAGCTCATAAGCTTATTTTTCCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
63584 CTTGA-CA-TT-ATTTCGTAAGCTCATAAGCTTATTT
1 CTT-ACCATTTAATTCCATAAGCTCGTAAGCTTATTT
63618 GCATGGTTAC
Statistics
Matches: 147, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
44 30 0.20
45 44 0.30
46 26 0.18
47 47 0.32
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:63581 original size:91 final size:92
Alignment explanation
Indices: 63402--63617 Score: 246
Period size: 91 Copynumber: 2.3 Consensus size: 92
63392 ATAAAATCTC
* * * * *
63402 TTACCATTTATCCCATAAGCTTGTAATCTTA-TTTTACCAAAATACTAACCATTTAAATTCCATA
1 TTACCATTT-TTCCGTAAGC-TCTAAGCTTATTTTTACCAAAATACTAACCATTTAAATACCATA
*
63466 AGCTCGTAAGCTTATTTTATCAATATA-T
64 AGCTCATAAGCTTATTTTATCAATATACT
* * *
63494 TTACCATTTGTTCCGTAAGCTCTAAGCTTATTTTTACCAATATATTTACCATTT-AATACCATAA
1 TTACCATTT-TTCCGTAAGCTCTAAGCTTATTTTTACCAAAATACTAACCATTTAAATACCATAA
63558 GCTCATAAGCTTATTTT-TCCAATATACT
65 GCTCATAAGCTTATTTTAT-CAATATACT
*
63586 TGA-CATTATTT-CGTAAGCTCATAAGCTTATTT
1 TTACCATT-TTTCCGTAAGCTC-TAAGCTTATTT
63618 GCATGGTTAC
Statistics
Matches: 108, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
90 10 0.09
91 57 0.53
92 41 0.38
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (92 bp):
TTACCATTTTTCCGTAAGCTCTAAGCTTATTTTTACCAAAATACTAACCATTTAAATACCATAAG
CTCATAAGCTTATTTTATCAATATACT
Found at i:63611 original size:44 final size:44
Alignment explanation
Indices: 63464--63617 Score: 172
Period size: 44 Copynumber: 3.4 Consensus size: 44
63454 TTAAATTCCA
*
63464 TAAGCTCGTAAGCTTATTTTAT-CAATATATTTACCATT-TGTTCCG
1 TAAGCTCATAAGCTTATTTT-TCCAATATATTTACCATTAT-TT-CG
** *
63509 TAAGCTC-TAAGCTTATTTTTACCAATATATTTACCATTTAATACCA
1 TAAGCTCATAAGCTTATTTTT-CCAATATATTTACCA-TT-ATTTCG
*
63555 TAAGCTCATAAGCTTATTTTTCCAATATACTTGA-CATTATTTCG
1 TAAGCTCATAAGCTTATTTTTCCAATATA-TTTACCATTATTTCG
63599 TAAGCTCATAAGCTTATTT
1 TAAGCTCATAAGCTTATTT
63618 GCATGGTTAC
Statistics
Matches: 95, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
43 1 0.01
44 34 0.36
45 23 0.24
46 20 0.21
47 16 0.17
48 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (44 bp):
TAAGCTCATAAGCTTATTTTTCCAATATATTTACCATTATTTCG
Found at i:66057 original size:16 final size:16
Alignment explanation
Indices: 66036--66068 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
66026 CTAGCCCTCT
66036 TGGTCAGAATCTGAGA
1 TGGTCAGAATCTGAGA
66052 TGGTCAGAATCTGAGA
1 TGGTCAGAATCTGAGA
66068 T
1 T
66069 AGGCTCTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (16 bp):
TGGTCAGAATCTGAGA
Found at i:74358 original size:18 final size:17
Alignment explanation
Indices: 74322--74364 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
74312 ACTCGTTACA
* *
74322 AATTCTTTCTTCCCATC
1 AATTCTTTATTCACATC
74339 AATTCTTATATTCACATC
1 AATTCTT-TATTCACATC
74357 AATTCTTT
1 AATTCTTT
74365 GTCTTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTCTTTATTCACATC
Found at i:83477 original size:14 final size:14
Alignment explanation
Indices: 83414--83488 Score: 55
Period size: 14 Copynumber: 5.2 Consensus size: 14
83404 TAATAAAAAT
83414 ATTA-ATTATTA-A
1 ATTATATTATTATA
83426 ATTATATTTATTGATA
1 ATTATA-TTATT-ATA
* * * *
83442 TTTTTAATAATATAA
1 ATTATATTATTAT-A
*
83457 TATTATATTGTTATA
1 -ATTATATTATTATA
83472 ATTATATTATTATA
1 ATTATATTATTATA
83486 ATT
1 ATT
83489 GACAAAGTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
12 4 0.09
13 1 0.02
14 23 0.49
15 6 0.13
16 13 0.28
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
ATTATATTATTATA
Found at i:85362 original size:64 final size:63
Alignment explanation
Indices: 85271--85408 Score: 145
Period size: 64 Copynumber: 2.2 Consensus size: 63
85261 ATTGAATTTA
* * * *
85271 CATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAAATGGTGCATCGATGCATAAGG-AGTG
1 CATCGATGCACCCTTTAAAGAAGAAACAACAAAGGCAAATGGTGCATCGATGCAT-AGGTAGTG
* * * * * *
85334 CATCGATGCATCCCTTTAAA-ATGAAAACAACAAAGGTAATTTGTGTATCGATGCATGGGTAGTG
1 CATCGATGCA-CCCTTTAAAGAAG-AAACAACAAAGGCAAATGGTGCATCGATGCATAGGTAGTG
85398 CATCGATGCAC
1 CATCGATGCAC
85409 ATGTTAAAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
63 15 0.24
64 47 0.76
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (63 bp):
CATCGATGCACCCTTTAAAGAAGAAACAACAAAGGCAAATGGTGCATCGATGCATAGGTAGTG
Found at i:85444 original size:20 final size:20
Alignment explanation
Indices: 85419--85471 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
85409 ATGTTAAAGA
85419 ATGCATCGATGCATTGTAGC
1 ATGCATCGATGCATTGTAGC
85439 ATGCATCGATGCATTGTAGC
1 ATGCATCGATGCATTGTAGC
*
85459 ATGCATCAATGCA
1 ATGCATCGATGCA
85472 CTTCATGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (20 bp):
ATGCATCGATGCATTGTAGC
Done.