Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015234.1 Corchorus olitorius cultivar O-4 contig15267, 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: 45350
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:234 original size:22 final size:22
Alignment explanation
Indices: 204--251 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
194 TTTATAATTT
* * *
204 TTTTTTTAACCTTCTTATGAAA
1 TTTTGTTAACCTCCTTAAGAAA
*
226 TTTTGTTAACCTCCTTAAGGAA
1 TTTTGTTAACCTCCTTAAGAAA
248 TTTT
1 TTTT
252 TGAAGACCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (22 bp):
TTTTGTTAACCTCCTTAAGAAA
Found at i:268 original size:45 final size:45
Alignment explanation
Indices: 219--330 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 45
209 TTAACCTTCT
* * * * *
219 TATGAAATTTTGTTAACCTCCTTAAGGAATTTTTGAAGACC-TCAC
1 TATGAAATTTTGATAACCTCC-CAAGGAAATTTTGAAAACCAACAC
* *
264 TATGAAATTTTTGATAACTTCCCAATGAAATTTTGAAAACCAACAC
1 TATGAAA-TTTTGATAACCTCCCAAGGAAATTTTGAAAACCAACAC
*
310 TATGAAATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
331 ATATGATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
45 34 0.61
46 22 0.39
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTCCCAAGGAAATTTTGAAAACCAACAC
Found at i:272 original size:23 final size:22
Alignment explanation
Indices: 246--317 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
236 CTCCTTAAGG
246 AATTTTTGAAGACCTCACTATGA
1 AATTTTTGAA-ACCTCACTATGA
* * *
269 AATTTTTGATAACTTCCCAATGA
1 AATTTTTGA-AACCTCACTATGA
*
292 AA-TTTTGAAAACCAACACTATGA
1 AATTTTTG-AAACC-TCACTATGA
315 AAT
1 AAT
318 GTTGATAACC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
22 8 0.21
23 29 0.76
24 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
AATTTTTGAAACCTCACTATGA
Found at i:350 original size:45 final size:46
Alignment explanation
Indices: 261--350 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 46
251 TTGAAGACCT
* * *
261 CACTATGAAATTTTTGATAACTTCCCAATGAAATTTTGAAAACCAA
1 CACTATGAAATTGTTGATAACCTCCCAATGAAATATTGAAAACCAA
* *
307 CACTATGAAA-TGTTGATAACCT-CCATATGATATATTGATAACCA
1 CACTATGAAATTGTTGATAACCTCCCA-ATGAAATATTGAAAACCA
351 CGTTATGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
44 3 0.08
45 25 0.66
46 10 0.26
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (46 bp):
CACTATGAAATTGTTGATAACCTCCCAATGAAATATTGAAAACCAA
Found at i:448 original size:44 final size:43
Alignment explanation
Indices: 400--1449 Score: 301
Period size: 44 Copynumber: 24.4 Consensus size: 43
390 AATCACATTC
* *
400 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTC-CTA
* * * *
444 TGAAATTTTGATAAACCTCCCTATAAAATTTTGATAATCTCCTGA
1 TGAAATTTTGAT-AACCACACTATGAAATTTTGATAACCTCCT-A
* *
489 TGAAATCTTGAT----A-ACTA-CAAATTTTGATAACCTTCCTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACC-TCCTA
** * * * * * *
527 TGATTTTTTTATAACCTCATTCTGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCT-CCTA
*** * *
571 TGAAATTTTGATCTGCATACTATGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAA-CCTCCTA
* * ** *
615 TGAAATTTTGAAAACCAAACTATGAAATTCCGATAACCTTCATA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACC-TCCTA
* * * *
659 TGAAATTTTGATATCCTC-C-CTGAAATTTTGATTA-CTCCATAA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC-T-A
* * * * * *
701 TAAAAGTTTAATAACCTTC-C--T--AA-TTTGGTAACCATACTA
1 TGAAATTTTGATAACC-ACACTATGAAATTTTGATAACC-TCCTA
* * * *
740 TGAAATTTTGATAACCTCCCCA-G-AA-----AT-ACC-ACTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCTA
* * * * * *
774 TGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTC-CTA
* * * * * *
818 TGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTC-CTA
* ** * * *
862 TAAAATTTTGATAATTACATTATGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTC-CTA
*
906 TGAAATTTTGATAA-CAGCACTATGAAATTTTGATCATA-TTCCTA
1 TGAAATTTTGATAACCA-CACTATGAAATTTTGAT-A-ACCTCCTA
* * * *
950 T-AAATTTTCG-TAATCCGATCTCTATGAAATTTCGATAATCATTCTA
1 TGAAATTTT-GATAA-CC-A-CACTATGAAATTTTGATAA-CCTCCTA
* ** * * *
996 TGAGA-TTTGATAACC-TTCTATCAAATGTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC-TA
* * * *
1036 TGAAATTGAGACTTTTATAACCATTA-TATGAAATTTTGTTAACCACACTA
1 TGAAA-T-----TTTGATAACCA-CACTATGAAATTTTGATAACCTC-CTA
** * * *
1086 AAAAATTTTGATAACCATACTATAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCT-CCTA
* * * * *
1130 TGAAATATT-AGTAACCTC-CTTATAAAATTTTGTTTAACCACACTA
1 TGAAATTTTGA-TAACCACAC-TATGAAATTTTG-ATAACCTC-CTA
* * *
1175 TGAAATTCTT-ATAACCTCGCTATGACATTTTGATAA--T-C--
1 TGAAATT-TTGATAACCACACTATGAAATTTTGATAACCTCCTA
* *** * * * *
1213 T----CTTTGATAACCTTTCTATAAAATTGTGATAATCATACTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAA-CCTCCTA
** * * **
1253 TGAAATTTCAATAACCTTC-CTAAGAAATTTCAATAACCTGATCCTA
1 TGAAATTTTGATAACC-ACACTATGAAATTTTGATAACC---TCCTA
* * *
1299 TAAAATTTTGGT-ACCACACTATGAAATTTTGATAACCTTCCCA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACC-TCCTA
* *
1342 TGAAAATTTTGATAACTTC-CA-TATGAAGTTTTGATAACCACACTA
1 TG-AAATTTTGATAAC--CACACTATGAAATTTTGATAACCTC-CTA
* * * * * *
1387 TGGAATTTTGATAACCTC-CTCATGAAATTATAATAAACATCTTA
1 TGAAATTTTGATAACCACACT-ATGAAATTTTGAT-AACCTCCTA
*
1431 TGAAATTTCGATAACCACA
1 TGAAATTTTGATAACCACA
1450 AAGAGACAAG
Statistics
Matches: 733, Mismatches: 184, Indels: 177
0.67 0.17 0.16
Matches are distributed among these distances:
33 2 0.00
34 41 0.06
35 1 0.00
36 5 0.01
37 2 0.00
38 26 0.04
39 30 0.04
40 14 0.02
41 9 0.01
42 41 0.06
43 32 0.04
44 328 0.45
45 122 0.17
46 46 0.06
47 12 0.02
48 11 0.02
49 3 0.00
50 7 0.01
51 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (43 bp):
TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCTA
Found at i:492 original size:45 final size:45
Alignment explanation
Indices: 400--502 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
390 AATCACATTC
* *
400 TGAAATTTTGAT-AATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAAACCACACTATAAAATTGTGATAACCTCGCTA
* * * *
444 TGAAATTTTGATAAACCTCCCTATAAAATTTTGATAATCTC-CTGA
1 TGAAATTTTGATAAACCACACTATAAAATTGTGATAACCTCGCT-A
*
489 TGAAATCTTGATAA
1 TGAAATTTTGATAA
503 CTACAAATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 14 0.28
45 36 0.72
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (45 bp):
TGAAATTTTGATAAACCACACTATAAAATTGTGATAACCTCGCTA
Found at i:494 original size:22 final size:22
Alignment explanation
Indices: 219--690 Score: 244
Period size: 22 Copynumber: 21.6 Consensus size: 22
209 TTAACCTTCT
*
219 TATGAAATTTTGTTAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
240 TTAAGGAATTTTTGA-AGACCTCAC
1 -T-ATGAAATTTTGATA-ACCTCAC
* *
264 TATGAAATTTTTGATAACTTCCC
1 TATGAAA-TTTTGATAACCTCAC
* * *
287 AATGAAATTTTGAAAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
*
310 TATGAAATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
331 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* * *
354 TATGAAAATTTAAAAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
* * *
376 TATG-AATTGTT-AGTAATCACAT
1 TATGAAATT-TTGA-TAACCTCAC
* * *
398 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
420 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
442 TATGAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* *
465 TATAAAATTTTGATAATCTC-C
1 TATGAAATTTTGATAACCTCAC
*
486 TGATGAAATCTTGATAA-CT-AC
1 T-ATGAAATTTTGATAACCTCAC
507 ----AAATTTTGATAACCTTC-C
1 TATGAAATTTTGATAACC-TCAC
** * *
525 TATGATTTTTTTATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * * *
547 TCTGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
569 TATGAAATTTTGATCTGCAT-AC
1 TATGAAATTTTGAT-AACCTCAC
*
591 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* **
613 TATGAAATTTTGAAAACCAAAC
1 TATGAAATTTTGATAACCTCAC
**
635 TATGAAATTCCGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
657 TATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
*
678 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
691 TACTCCATAA
Statistics
Matches: 338, Mismatches: 81, Indels: 64
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 2 0.01
20 12 0.04
21 18 0.05
22 215 0.64
23 77 0.23
24 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:821 original size:22 final size:22
Alignment explanation
Indices: 796--939 Score: 89
Period size: 22 Copynumber: 6.5 Consensus size: 22
786 AATCACATTT
*
796 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
*
818 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* * *
840 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
*
862 T-AAAATTTTGATAA-TTACAT-TA
1 TGAAAA-TTTGATAACCT-C-TCTA
* * * *
884 TGTAATTTTGATAACCTCGCTT
1 TGAAAATTTGATAACCTCTCTA
* ** *
906 TGAAATTTTGATAACAGCACTA
1 TGAAAATTTGATAACCTCTCTA
*
928 TGAAATTTTGAT
1 TGAAAATTTGAT
940 CATATTCCTA
Statistics
Matches: 96, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.03
22 89 0.93
23 4 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:934 original size:66 final size:66
Alignment explanation
Indices: 815--939 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 66
805 GATAACCTCT
* * * * *
815 TTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTATAAAATTTTGATAATTAC
1 TTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACACCACTATAAAATTTTGATAATTAC
880 A
66 A
* * * * *
881 TTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAGCACTATGAAATTTTGAT
1 TTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACACCACTATAAAATTTTGAT
940 CATATTCCTA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 49 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACACCACTATAAAATTTTGATAATTAC
A
Found at i:998 original size:22 final size:22
Alignment explanation
Indices: 925--1021 Score: 69
Period size: 22 Copynumber: 4.4 Consensus size: 22
915 GATAACAGCA
* *
925 CTATGAAATTTTGATCAT-ATT
1 CTATGAAATTTCGATAATCATT
946 CCTAT-AAATTTTCG-TAATCCGATCT
1 -CTATGAAA-TTTCGATAAT-C-AT-T
971 CTATGAAATTTCGATAATCATT
1 CTATGAAATTTCGATAATCATT
* *
993 CTATGAGATTT-GATAA-CCTT
1 CTATGAAATTTCGATAATCATT
*
1013 CTATCAAAT
1 CTATGAAAT
1022 GTTGGTACTC
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
20 10 0.16
21 11 0.18
22 19 0.31
23 2 0.03
24 12 0.19
25 8 0.13
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
CTATGAAATTTCGATAATCATT
Found at i:1078 original size:22 final size:22
Alignment explanation
Indices: 1048--1123 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
1038 AAATTGAGAC
*
1048 TTTT-ATAACCATTA-TATGAAA
1 TTTTGATAACCA-TACTATAAAA
* * *
1069 TTTTGTTAACCACACTAAAAAA
1 TTTTGATAACCATACTATAAAA
1091 TTTTGATAACCATACTATAAAA
1 TTTTGATAACCATACTATAAAA
1113 TTTTGATAACC
1 TTTTGATAACC
1124 TCCCCATGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 5 0.11
22 41 0.89
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCATACTATAAAA
Found at i:1135 original size:22 final size:22
Alignment explanation
Indices: 1062--1210 Score: 108
Period size: 22 Copynumber: 6.7 Consensus size: 22
1052 ATAACCATTA
* *
1062 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCTCAC
**
1084 TAAAAAATTTTGATAACCAT-AC
1 TATGAAATTTTGATAACC-TCAC
* *
1106 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
1128 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCTCAC
* * *
1149 TTATAAAATTTTGTTTAACCACAC
1 -TATGAAATTTTG-ATAACCTCAC
*
1173 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCAC
*
1195 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
1211 TCTCTTTGAT
Statistics
Matches: 99, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
21 5 0.05
22 77 0.78
23 14 0.14
24 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:1304 original size:24 final size:22
Alignment explanation
Indices: 1219--1306 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 22
1209 AATCTCTTTG
* *
1219 ATAACCTTTCTATAAAATTGT-G
1 ATAACCTTCCTATAAAATT-TCA
* * * *
1241 ATAATCATACTATGAAATTTCA
1 ATAACCTTCCTATAAAATTTCA
1263 ATAACCTTCCTA-AGAAATTTCA
1 ATAACCTTCCTATA-AAATTTCA
1285 ATAACCTGATCCTATAAAATTT
1 ATAACCT--TCCTATAAAATTT
1307 TGGTACCACA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 1 0.02
22 39 0.75
24 11 0.21
25 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (22 bp):
ATAACCTTCCTATAAAATTTCA
Found at i:1350 original size:23 final size:22
Alignment explanation
Indices: 1319--1415 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 22
1309 GTACCACACT
1319 ATGAAATTTTGATAACCTTCC-C
1 ATGAAATTTTGATAACC-TCCAC
* *
1341 ATGAAAATTTTGATAACTTCCAT
1 ATG-AAATTTTGATAACCTCCAC
* *
1364 ATGAAGTTTTGATAACC-ACAC
1 ATGAAATTTTGATAACCTCCAC
* *
1385 TATGGAATTTTGATAACCTCCTC
1 -ATGAAATTTTGATAACCTCCAC
1408 ATGAAATT
1 ATGAAATT
1416 ATAATAAACA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.03
22 40 0.67
23 18 0.30
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCAC
Found at i:2693 original size:10 final size:10
Alignment explanation
Indices: 2669--2715 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
2659 TTCGTACTTT
*
2669 TATATATAG-
1 TATAGATAGA
2678 TATAGATAGA
1 TATAGATAGA
2688 TATAGATAGA
1 TATAGATAGA
2698 TATAGATATAGA
1 TATAG--ATAGA
2710 TATAGA
1 TATAGA
2716 CGTATAACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 8 0.24
10 16 0.47
12 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (10 bp):
TATAGATAGA
Found at i:2694 original size:6 final size:6
Alignment explanation
Indices: 2672--2715 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
2662 GTACTTTTAT
2672 ATATAG -TATAG --ATAG ATATAG --ATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
2715 A
1 A
2716 CGTATAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 8 0.24
5 5 0.15
6 21 0.62
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (6 bp):
ATATAG
Found at i:2755 original size:18 final size:18
Alignment explanation
Indices: 2732--2767 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2722 ACATGGGCTT
2732 CTTTGCATATAAGGAATA
1 CTTTGCATATAAGGAATA
2750 CTTTGCATATAAGGAATA
1 CTTTGCATATAAGGAATA
2768 GAATTGCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
CTTTGCATATAAGGAATA
Found at i:6110 original size:7 final size:7
Alignment explanation
Indices: 6097--6135 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
6087 AGTGTTTCAA
6097 ATAATAT
1 ATAATAT
*
6104 TTAATAT
1 ATAATAT
6111 ATAATAT
1 ATAATAT
6118 AT-ATAT
1 ATAATAT
6124 ATATATAT
1 ATA-ATAT
6132 ATAA
1 ATAA
6136 CATGGGCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.21
7 15 0.54
8 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATAATAT
Found at i:8001 original size:38 final size:38
Alignment explanation
Indices: 7958--8030 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
7948 AACAAATGAG
*
7958 ATAAATTCTAATTTATAGTTAGGTTAAAGGACAAAAAA
1 ATAAATTCTAATTTATAGCTAGGTTAAAGGACAAAAAA
*
7996 ATAAATTTTAATTTATAGCTAGGTTAAAGGACAAA
1 ATAAATTCTAATTTATAGCTAGGTTAAAGGACAAA
8031 CTTATAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (38 bp):
ATAAATTCTAATTTATAGCTAGGTTAAAGGACAAAAAA
Found at i:9811 original size:99 final size:101
Alignment explanation
Indices: 9640--9832 Score: 275
Period size: 99 Copynumber: 1.9 Consensus size: 101
9630 GTCTACTATC
* **
9640 TTAAATTGACAAAAACCTACCGATCATAAATAAAGGACCCAATAAGTTTTAAAACTTGTCGGAAT
1 TTAAATTGACAAAAACCTACCGATCATAAATAAAGGACCCAATAAGCTCCAAAACTTGTCGGAAT
9705 ATATATATA-ACATT-TATAAAACATGTAAAACGCA
66 ATATATATATACATTATATAAAACATGTAAAACGCA
** * *
9739 TTAAATTGACAAGCACCTA-CGAATCATAAATAAATGACCCATTAAGCTCCAAAACTTGTCGGAA
1 TTAAATTGACAAAAACCTACCG-ATCATAAATAAAGGACCCAATAAGCTCCAAAACTTGTCGGAA
* *
9803 TATATATATATATATTATATAAGACATGTA
65 TATATATATATACATTATATAAAACATGTA
9833 CCGGGTTAGT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
98 2 0.02
99 64 0.78
100 4 0.05
101 12 0.15
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (101 bp):
TTAAATTGACAAAAACCTACCGATCATAAATAAAGGACCCAATAAGCTCCAAAACTTGTCGGAAT
ATATATATATACATTATATAAAACATGTAAAACGCA
Found at i:10675 original size:2 final size:2
Alignment explanation
Indices: 10668--10693 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10658 CCCCACAACC
10668 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
10694 TGTCGGTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10739 original size:2 final size:2
Alignment explanation
Indices: 10732--10762 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10722 TAGGTAGTAC
10732 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10763 ATGAGACAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10861 original size:22 final size:20
Alignment explanation
Indices: 10812--10864 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 20
10802 TCATTTTCAA
10812 ATAGGTAGTACCACCTTTGG
1 ATAGGTAGTACCACCTTTGG
10832 ATAGGTAGTACCACCTTTGG
1 ATAGGTAGTACCACCTTTGG
10852 ATTTAGGTAGTAC
1 A--TAGGTAGTAC
10865 TCAAAACCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 21 0.68
22 10 0.32
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (20 bp):
ATAGGTAGTACCACCTTTGG
Found at i:17674 original size:28 final size:27
Alignment explanation
Indices: 17624--17782 Score: 167
Period size: 28 Copynumber: 5.7 Consensus size: 27
17614 TATTTCTTAA
* *
17624 TTGGTCATTTGCACACTCGGGGGAATT
1 TTGGTCATTTGCACACTCAGGGGCATT
17651 TTGGTCATCTTGCA-AGCTCAGGGGCATT
1 TTGGTCAT-TTGCACA-CTCAGGGGCATT
* * *
17679 TTGATCATTTGCACACTTATGGGCATT
1 TTGGTCATTTGCACACTCAGGGGCATT
*
17706 TTGGTCATTTTGCACACTCATGGGCATT
1 TTGGTCA-TTTGCACACTCAGGGGCATT
* * *
17734 ATGGTCATTTGTACACTCCGGGAGCATT
1 TTGGTCATTTGCACACTCAGGG-GCATT
**
17762 TTGGTTGTTTTGCACACTCAG
1 TTGG-TCATTTGCACACTCAG
17783 AGTTTTTCTT
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
27 42 0.38
28 56 0.51
29 12 0.11
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (27 bp):
TTGGTCATTTGCACACTCAGGGGCATT
Found at i:17712 original size:55 final size:55
Alignment explanation
Indices: 17628--17782 Score: 159
Period size: 55 Copynumber: 2.8 Consensus size: 55
17618 TCTTAATTGG
* *
17628 TCATTTGCACACTCGGGGGAATTTTGGTCATCTTGCA-AGCTCAGGGGCATTTTGA
1 TCATTTGCACACTCAGGGGAATTTTGGTCATCTTGCACA-CTCAGGGGCATTATGA
* * * * * *
17683 TCATTTGCACACTTATGGGCATTTTGGTCATTTTGCACACTCATGGGCATTATGG
1 TCATTTGCACACTCAGGGGAATTTTGGTCATCTTGCACACTCAGGGGCATTATGA
* * * ** *
17738 TCATTTGTACACTCCGGGAGCATTTTGGTTGTTTTGCACACTCAG
1 TCATTTGCACACTCAGGG-GAATTTTGGTCATCTTGCACACTCAG
17783 AGTTTTTCTT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
55 59 0.71
56 24 0.29
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (55 bp):
TCATTTGCACACTCAGGGGAATTTTGGTCATCTTGCACACTCAGGGGCATTATGA
Found at i:19958 original size:2 final size:2
Alignment explanation
Indices: 19951--19985 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19941 ACACCTATCT
19951 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19986 ACAGGATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:21145 original size:11 final size:11
Alignment explanation
Indices: 21129--21158 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
21119 TCATGGTCCC
21129 TTTTGAGTTGA
1 TTTTGAGTTGA
21140 TTTTGAGTTGA
1 TTTTGAGTTGA
21151 TTTTGAGT
1 TTTTGAGT
21159 ATAAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.57
Consensus pattern (11 bp):
TTTTGAGTTGA
Found at i:23742 original size:18 final size:18
Alignment explanation
Indices: 23719--23753 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
23709 TAAAGATTTA
23719 TTGAAGA-TAATTGAAGAT
1 TTGAAGACT-ATTGAAGAT
23737 TTGAAGACTATTGAAGA
1 TTGAAGACTATTGAAGA
23754 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (18 bp):
TTGAAGACTATTGAAGAT
Found at i:27832 original size:38 final size:40
Alignment explanation
Indices: 27773--27858 Score: 135
Period size: 38 Copynumber: 2.2 Consensus size: 40
27763 TAGGAGGAGT
27773 AAAAA-AAAAAAACTGGACCTAAAATAGAAAGAGGTC-G-
1 AAAAAGAAAAAAACTGGACCTAAAATAGAAAGAGGTCAGA
27810 AAAAAGAAAAAAACTTGG-CCTAAAATAGAAAGAGGTCAGA
1 AAAAAGAAAAAAAC-TGGACCTAAAATAGAAAGAGGTCAGA
27850 AAAAAGAAA
1 AAAAAGAAA
27859 TAAATAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
37 5 0.11
38 27 0.60
39 4 0.09
40 9 0.20
ACGTcount: A:0.62, C:0.09, G:0.19, T:0.10
Consensus pattern (40 bp):
AAAAAGAAAAAAACTGGACCTAAAATAGAAAGAGGTCAGA
Found at i:33352 original size:21 final size:21
Alignment explanation
Indices: 33328--33382 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
33318 CCGCCCAAAG
**
33328 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
* *
33349 CCGTACCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
33370 CCGTGCCATCACC
1 CCGTGCCACCACC
33383 ATTCCAAGCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:35786 original size:12 final size:13
Alignment explanation
Indices: 35764--35793 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
35754 ACTAACAATT
35764 AAAATCAATCAAG
1 AAAATCAATCAAG
35777 AAAA-CAATCAAG
1 AAAATCAATCAAG
35789 AAAAT
1 AAAAT
35794 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:39142 original size:59 final size:59
Alignment explanation
Indices: 39058--39686 Score: 832
Period size: 59 Copynumber: 10.4 Consensus size: 59
39048 ATTCCCCTTT
* *
39058 TTGTTTCTAAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTAGTC
1 TTGTTT-TTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
* * *
39118 TTGTTTTTAAAATCCTGATCGAGGTCCCTGGTAGAGAGTTTTCAATTCAAAATCTAGCC
1 TTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
* ** *
39177 TTGTTTTTTAAAAAAATCCTTATCGAGGTCTCTGGTAGAGAGACTTCAATTCAAAATCTAGTC
1 TTG-TTTTT---AAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
* *
39240 TTGTTTTAAAAATCCTGATCGAGTTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
1 TTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
* *
39299 CTGTTTTTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
1 TTGTTTTT-AAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
** * * * * *
39359 TTGCTTTAAAAAAAAATTTCTGATCGAGGTCTCTGGTGGACAGTTTTCAATTAAAAATCTTGCC
1 TTG-TTT---TTAAAA-TCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
39423 TTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAAT-TTAGTC
1 TTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTT-GTC
*
39482 TTG-TTTTAAAATCCTGATCGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTGTC
1 TTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
* * *
39540 CTGTTTTTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCGATTCAAAATCTTGTC
1 TTGTTTTT-AAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
* * *
39600 TTGCTTTTAAAAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTATTCAATTCAAAATCTTGTC
1 TTG-TTTT---TAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
*
39663 TTG-TTTTAAAGTCCTGATCGAGGT
1 TTGTTTTTAAAATCCTGATCGAGGT
39687 TTTTGATCGA
Statistics
Matches: 507, Mismatches: 44, Indels: 38
0.86 0.07 0.06
Matches are distributed among these distances:
58 70 0.14
59 153 0.30
60 116 0.23
61 10 0.02
62 4 0.01
63 108 0.21
64 46 0.09
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (59 bp):
TTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
Found at i:39373 original size:181 final size:177
Alignment explanation
Indices: 39058--39686 Score: 882
Period size: 181 Copynumber: 3.5 Consensus size: 177
39048 ATTCCCCTTT
*
39058 TTGTTTCTAAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTAGTCTTGTT
1 TTGTTT-TAAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG-T
* * *
39123 TTTAAAATCCTGATCGAGGTCCCTGGTAGAGAGTTTTCAATTCAAAATCTAGCCTTGTTTTTTAA
64 TTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG---TTTAA
* * ** *
39188 AAAAATCCTTATCGAGGTCTCTGGTAGAGAGACTTCAATTCAAAATCTAGTC
126 AAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
* *
39240 TTGTTTTAAAAATCCTGATCGAGTTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCCTGTTT
1 TTGTTTTAAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG-TT
*
39305 TTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGCTTTAAAA
65 TT-AAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG-TTT--AA
* * * *
39370 AAAAATTTCTGATCGAGGTCTCTGGTGGACAGTTTTCAATTAAAAATCTTGCC
126 AAAAA-TTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
*
39423 TTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAAT-TTAGTCTTGTT
1 TTGTTTTAAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTT-GTCTTGTT
* * **
39487 TTAAAATCCTGATCGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTGTCCTGTTTTTAAAA
65 TTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTAAAAAA
*
39552 ATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCGATTCAAAATCTTGTC
130 ATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
* *
39600 TTGCTTTTAAAAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTATTCAATTCAAAATCTTGTCTT
1 TTG-TTTT---AAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTT
*
39665 GTTTTAAAGTCCTGATCGAGGT
62 GTTTTAAAATCCTGATCGAGGT
39687 TTTTGATCGA
Statistics
Matches: 403, Mismatches: 34, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
177 45 0.11
178 9 0.02
180 6 0.01
181 178 0.44
182 71 0.18
183 94 0.23
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (177 bp):
TTGTTTTAAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTT
TAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTAAAAAAA
TTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTC
Found at i:39498 original size:241 final size:240
Alignment explanation
Indices: 39059--39686 Score: 969
Period size: 241 Copynumber: 2.6 Consensus size: 240
39049 TTCCCCTTTT
* * *
39059 TGTTTCTAAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTAGTCTTG-TT
1 TGTTTTTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGCTT
** * * *
39123 T--TTAAAATCCTGATCGAGGTCCCTGGTAGAGAGTTTTCAATTCAAAATCTAGCCTTGTTTTTT
66 TAAAAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTG-TTTTT
*
39186 AAAAAAATCCTTATCGAGGTCTCTGGTAGAGAGACTTCAATTCAAAATCTAGTCTTGTTTTAAAA
130 ---AAAATCCTGATCGAGGTCTCTGGTAGAGAGACTTCAATTCAAAATCTAGTCTTGTTTTAAAA
* *
39251 ATCCTGATCGAGTTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCC
192 ATCCTGATCGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTGTCC
39300 TGTTTTTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGCTT
1 TGTTTTTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGCTT
* * *
39365 TAAAAAAAAATTTCTGATCGAGGTCTCTGGTGGACAGTTTTCAATTAAAAATCTTGCCTTGTTTT
66 T-AAAAAAAA-TTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTGTTTT
** *
39430 TAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATTTAGTCTTGTTTT-AAAAT
129 TAAAATCCTGATCGAGGTCTCTGGTAGAGAGACTTCAATTCAAAATCTAGTCTTGTTTTAAAAAT
39494 CCTGATCGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTGTCC
194 CCTGATCGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTGTCC
*
39541 TGTTTTTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCGATTCAAAATCTTGTCTTGCTT
1 TGTTTTTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGC-T
* *
39606 TTAAAAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTATTCAATTCAAAATCTTGTCTTG-TTTT
65 TTAAAAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTGTTTTT
*
39670 AAAGTCCTGATCGAGGT
130 AAAATCCTGATCGAGGT
39687 TTTTGATCGA
Statistics
Matches: 357, Mismatches: 24, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
239 20 0.06
240 45 0.13
241 179 0.50
242 60 0.17
245 9 0.03
246 44 0.12
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (240 bp):
TGTTTTTAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGCTT
TAAAAAAAATTCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTGTTTTTA
AAATCCTGATCGAGGTCTCTGGTAGAGAGACTTCAATTCAAAATCTAGTCTTGTTTTAAAAATCC
TGATCGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTGTCC
Found at i:40018 original size:53 final size:54
Alignment explanation
Indices: 39932--40090 Score: 158
Period size: 53 Copynumber: 2.9 Consensus size: 54
39922 TATTTCTTAA
* * ** * *
39932 TTGGTCATTTTCACACTTGGGGGCATTTTGGTCATCTTGCATGCTCATGGGTATT
1 TTGGTCATTTACACAC-TAGGGGCATTTTGGTCATCTTGCACACTCAGGGGCATT
* *
39987 TTGGTCATTTACACAC-AGGGGCATTTTGGTCATTTTGCACACTTAGGGGCATT
1 TTGGTCATTTACACACTAGGGGCATTTTGGTCATCTTGCACACTCAGGGGCATT
* * * * * *
40040 TTGGTCATTTGTACACTCCAGGAGCATTTTGATCGTTTTGCACACTCAGGG
1 TTGGTCA-TT-TACACACTAGGGGCATTTTGGTCATCTTGCACACTCAGGG
40091 TTTTTTTTTG
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
53 37 0.42
54 2 0.02
55 21 0.24
56 28 0.32
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (54 bp):
TTGGTCATTTACACACTAGGGGCATTTTGGTCATCTTGCACACTCAGGGGCATT
Found at i:40037 original size:28 final size:28
Alignment explanation
Indices: 39932--40090 Score: 157
Period size: 28 Copynumber: 5.8 Consensus size: 28
39922 TATTTCTTAA
**
39932 TTGGTCATTTT-CACACTTGGGGGCATT
1 TTGGTCATTTTGCACACTCAGGGGCATT
* ** * *
39959 TTGGTCATCTTGCATGCTCATGGGTATT
1 TTGGTCATTTTGCACACTCAGGGGCATT
*
39987 TTGGTCA-TTT--ACACACAGGGGCATT
1 TTGGTCATTTTGCACACTCAGGGGCATT
*
40012 TTGGTCATTTTGCACACTTAGGGGCATT
1 TTGGTCATTTTGCACACTCAGGGGCATT
* *
40040 TTGGTCA-TTTGTACACTCCAGGAGCATT
1 TTGGTCATTTTGCACACT-CAGGGGCATT
* *
40068 TTGATCGTTTTGCACACTCAGGG
1 TTGGTCATTTTGCACACTCAGGG
40091 TTTTTTTTTG
Statistics
Matches: 104, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
25 17 0.16
26 3 0.03
27 21 0.20
28 54 0.52
29 9 0.09
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (28 bp):
TTGGTCATTTTGCACACTCAGGGGCATT
Done.