Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012192.1 Corchorus capsularis cultivar CVL-1 contig12213, 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: 98362
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:290 original size:23 final size:23
Alignment explanation
Indices: 259--343 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
249 GATAACCTCG
*
259 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
282 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
305 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
327 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
344 CCTCCCTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:401 original size:23 final size:22
Alignment explanation
Indices: 31--481 Score: 236
Period size: 22 Copynumber: 20.5 Consensus size: 22
21 AAATTTTTTT
* * * *
31 TAACCTTCTTATGAAATTTGGT
1 TAACCTCCCTATGAAATTTTGA
* *
53 TAACC-CCCTAAGGAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
** *
74 -AGACCTCAATATAAAATTTTGA
1 TA-ACCTCCCTATGAAATTTTGA
* *
96 TAACTTCCCAATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * * *
118 TAACCAACACTATGAGATATTGA
1 TAACC-TCCCTATGAAATTTTGA
* * *
141 TAACCTCCATATGATATATTGA
1 TAACCTCCCTATGAAATTTTGA
** * *
163 TAA-CTACATTATGAAAATTTAA
1 TAACCT-CCCTATGAAATTTTGA
* *
185 AAACCTCCGTATG-AATTGTT-A
1 TAACCTCCCTATGAAATT-TTGA
* * * *
206 GTAATCACACTCTGAAATTTTGA
1 -TAACCTCCCTATGAAATTTTGA
* * * *
229 TAATCACACTATGAAATTGTGA
1 TAACCTCCCTATGAAATTTTGA
*
251 TAACCTCGCTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
273 TAAATCTTCCTATAAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
*
296 TAAACCTCCCTATAAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
* * * *
319 TAACTTTCTTATGAAATCTTGA
1 TAACCTCCCTATGAAATTTTGA
**
341 TAACCTCCCTATGATTTTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
363 TAACCT-CATATGAATTTTTGT
1 TAACCTCCCTATGAAATTTTGA
*
384 TAATCTCCCTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * * *
406 TCTACAT-ACTATGAAATTTTTA
1 T-AACCTCCCTATGAAATTTTGA
* *
428 TAACC-CTCTTGTGAAATTTTGA
1 TAACCTC-CCTATGAAATTTTGA
* **
450 -AAACTAAACTATGAAATTTTGA
1 TAACCT-CCCTATGAAATTTTGA
*
472 TATCCTCCCT
1 TAACCTCCCT
482 GAATTCTGAT
Statistics
Matches: 319, Mismatches: 92, Indels: 36
0.71 0.21 0.08
Matches are distributed among these distances:
20 1 0.00
21 41 0.13
22 208 0.65
23 69 0.22
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCCCTATGAAATTTTGA
Found at i:511 original size:20 final size:20
Alignment explanation
Indices: 461--511 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
451 AACTAAACTA
461 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* * *
481 TG-AATTCTGATATCCTTCT
1 TGAAATTTTGATATCCTCCC
500 TGAAATTTTGAT
1 TGAAATTTTGAT
512 TACTCCATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:670 original size:22 final size:22
Alignment explanation
Indices: 620--784 Score: 86
Period size: 22 Copynumber: 7.6 Consensus size: 22
610 TCACATTTTG
620 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* *
641 GAAATTTTGATAGCCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* * * *
663 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTTTAT
* * * * *
685 GAAATTCTGATAATCACATTAT
1 AAAATTTTGATAACCTCTTTAT
** * *
707 GTAATTTTAATAACCTCGCTT-T
1 AAAATTTTGATAACCTC-TTTAT
* ** *
729 GAAATTTTGATAACAACATTAT
1 AAAATTTTGATAACCTCTTTAT
* * *
751 GAGATTTTGATAA--TCTTTCT
1 AAAATTTTGATAACCTCTTTAT
771 ATAAATTTTGATAA
1 A-AAATTTTGATAA
785 TTCTATCTAT
Statistics
Matches: 107, Mismatches: 33, Indels: 8
0.72 0.22 0.05
Matches are distributed among these distances:
20 4 0.04
21 16 0.15
22 85 0.79
23 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:758 original size:88 final size:88
Alignment explanation
Indices: 593--759 Score: 194
Period size: 88 Copynumber: 1.9 Consensus size: 88
583 AGAAATACCA
* * * * * **
593 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAGCCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTAATAACCTCCTTATGAAATTTTGATAACAAC
*
658 TTTATAAAATTTTGTTGACCCCT
66 ATTATAAAATTTTGTTGACCCCT
* *
681 CTATGAAA-TTCTGATAATCACATTATGTAATTTTAATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTAATAACCTC-CTTATGAAATTTTGATAACA
* *
744 ACATTATGAGATTTTG
64 ACATTATAAAATTTTG
760 ATAATCTTTC
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
87 4 0.06
88 59 0.91
89 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTAATAACCTCCTTATGAAATTTTGATAACAAC
ATTATAAAATTTTGTTGACCCCT
Found at i:899 original size:22 final size:22
Alignment explanation
Indices: 728--921 Score: 73
Period size: 22 Copynumber: 8.6 Consensus size: 22
718 AACCTCGCTT
**
728 TGAAATTTTGATAA-CAACATTA
1 TGAAATTTTGATAATCTTCA-TA
*
750 TGAGATTTTGATAATCTTTC-TA
1 TGAAATTTTGATAATC-TTCATA
772 T-AAATTTTGATAATTCTATCTATA
1 TGAAATTTTGATAA-TCT-TC-ATA
* *
796 TGAAATTTCGATAATCACTC-TA
1 TGAAATTTTGATAATC-TTCATA
* * *
818 TTAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAATCTTCATA
* * *
838 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATAAT-CTTCAT---A
*
863 TTGAGACTTTT-ATAATCTTCATA
1 -TGA-AATTTTGATAATCTTCATA
**
886 TGAAATTTTGATAA-CCACACTA
1 TGAAATTTTGATAATCTTCA-TA
*
908 TAAAATTTTGATAA
1 TGAAATTTTGATAA
922 CCTCCCCATG
Statistics
Matches: 129, Mismatches: 24, Indels: 38
0.68 0.13 0.20
Matches are distributed among these distances:
20 7 0.05
21 34 0.26
22 51 0.40
23 2 0.02
24 8 0.06
25 15 0.12
26 7 0.05
27 5 0.04
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAATCTTCATA
Found at i:935 original size:22 final size:22
Alignment explanation
Indices: 885--935 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
875 TAATCTTCAT
*
885 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
907 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
929 ATGAAAT
1 ATGAAAT
936 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:1099 original size:24 final size:22
Alignment explanation
Indices: 1035--1235 Score: 139
Period size: 22 Copynumber: 9.3 Consensus size: 22
1025 TTGTGATAAT
*
1035 TAACCATCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTAA
* * *
1057 TAACCAACCTAAGAGATTTTAA
1 TAACCATCCTATGAAATTTTAA
**
1079 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTAA
* **
1103 TAACCATACTATGAAATTTTGG
1 TAACCATCCTATGAAATTTTAA
* **
1125 TAACCA-CACTATGGAATTTTGG
1 TAACCATC-CTATGAAATTTTAA
**
1147 T-A--A-CC-ATGAAATTTTGG
1 TAACCATCCTATGAAATTTTAA
*
1164 TAACCA-CACTATGAAATTTTGA
1 TAACCATC-CTATGAAATTTTAA
*
1186 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTAA
* *
1208 TAACCATCGTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTAA
1230 TAACCA
1 TAACCA
1236 CATAGAGACA
Statistics
Matches: 149, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
17 12 0.08
18 2 0.01
19 2 0.01
20 2 0.01
21 4 0.03
22 107 0.72
23 3 0.02
24 17 0.11
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTAA
Found at i:1167 original size:39 final size:39
Alignment explanation
Indices: 1113--1190 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
1103 TAACCATACT
* *
1113 ATGAAATTTTGGTAACCACACTATGGAATTTTGGTAACC
1 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
1152 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
1 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
1191 TCCTCATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (39 bp):
ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
Found at i:1212 original size:61 final size:61
Alignment explanation
Indices: 1091--1214 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 61
1081 ACCTGATCCT
* * * * **
1091 ATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACCACACTATGGAATTTTGGTAACC
1 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCACACTATGAAATTATAATAACC
*
1152 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTC-CTCATGAAATTATAATAACC
1 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCACACT-ATGAAATTATAATAACC
1213 AT
1 AT
1215 CGTATGAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 2 0.04
61 53 0.96
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (61 bp):
ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCACACTATGAAATTATAATAACC
Found at i:1432 original size:19 final size:20
Alignment explanation
Indices: 1401--1438 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1391 TATTGACATT
1401 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
1420 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
1439 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:1800 original size:31 final size:31
Alignment explanation
Indices: 1735--1800 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1725 TGACAATTTT
* * *
1735 GAAATATGTTTTAAAGAAAATGGTATAATTG
1 GAAATATGTTTTAAAGAAAAGGGTACAATCG
1766 GAAATATGTTTTAAA-AATAAGGGTACAATCG
1 GAAATATGTTTTAAAGAA-AAGGGTACAATCG
1797 GAAA
1 GAAA
1801 ATATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (31 bp):
GAAATATGTTTTAAAGAAAAGGGTACAATCG
Found at i:1923 original size:22 final size:22
Alignment explanation
Indices: 1868--1923 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1858 CCTCCTAATT
*
1868 AAATTTTGTTAACCACACTATG
1 AAATTTTGATAACCACACTATG
* *
1890 AAATTCTT-ATAACCTCGCTATG
1 AAATT-TTGATAACCACACTATG
*
1912 ACATTTTGATAA
1 AAATTTTGATAA
1924 TCTCTTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:2023 original size:24 final size:22
Alignment explanation
Indices: 1959--2074 Score: 83
Period size: 22 Copynumber: 5.2 Consensus size: 22
1949 TTGTGATAAT
* *
1959 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
1981 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
2003 TAACCTGAGCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
* *
2027 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
2049 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
2071 TAAC
1 TAAC
2075 TATTCGTAGA
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
21 3 0.04
22 54 0.73
24 17 0.23
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:3204 original size:38 final size:35
Alignment explanation
Indices: 3143--3220 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 35
3133 GACGTTGAAG
3143 ACAAAGACAAAACAAAATTAAATACAATGATTGGAA
1 ACAAAGACAAAACAAAATTAAATACAATG-TTGGAA
*
3179 ACAAAGACAAAAGGCAAAATTAAATAGAATGTTGGAA
1 ACAAAGACAAAA--CAAAATTAAATACAATGTTGGAA
3216 ACAAA
1 ACAAA
3221 AGCCATTGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
36 12 0.31
37 11 0.28
38 16 0.41
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.15
Consensus pattern (35 bp):
ACAAAGACAAAACAAAATTAAATACAATGTTGGAA
Found at i:3366 original size:30 final size:31
Alignment explanation
Indices: 3332--3396 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3322 TAGCAATTTA
* * *
3332 GAAATATGTTTTTAAAAA-AGTG-TACAATTG
1 GAAATAT-ATTTTAAAAATAATGATACAATCG
3362 GAAATATATTTTAAAAATAATGATACAATCG
1 GAAATATATTTTAAAAATAATGATACAATCG
3393 GAAA
1 GAAA
3397 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 9 0.30
30 10 0.33
31 11 0.37
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAATGATACAATCG
Found at i:7277 original size:21 final size:21
Alignment explanation
Indices: 7251--7292 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
7241 GATCAAGTGT
7251 CTGGTAATGATCATTTGGTTG
1 CTGGTAATGATCATTTGGTTG
7272 CTGGTAATGATCATTTGGTTG
1 CTGGTAATGATCATTTGGTTG
7293 GTAATGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.43
Consensus pattern (21 bp):
CTGGTAATGATCATTTGGTTG
Found at i:7296 original size:18 final size:20
Alignment explanation
Indices: 7250--7301 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
7240 TGATCAAGTG
7250 TCTGGTAATGATCATTTGGT
1 TCTGGTAATGATCATTTGGT
7270 TGCTGGTAATGATCATTTGG-
1 T-CTGGTAATGATCATTTGGT
7290 T-TGGTAATGATC
1 TCTGGTAATGATC
7302 CAGTACATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.35
20 2 0.06
21 18 0.58
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (20 bp):
TCTGGTAATGATCATTTGGT
Found at i:9994 original size:21 final size:21
Alignment explanation
Indices: 9965--10013 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
9955 CCCACCTCTG
9965 TCCA-GCCTGCAAATTCAACC
1 TCCAGGCCTGCAAATTCAACC
*
9985 TCCAGGCCTGCAAGTTCAACC
1 TCCAGGCCTGCAAATTCAACC
*
10006 TCTAGGCC
1 TCCAGGCC
10014 ACTCCCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.20
Consensus pattern (21 bp):
TCCAGGCCTGCAAATTCAACC
Found at i:28550 original size:43 final size:42
Alignment explanation
Indices: 28501--28596 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 42
28491 GCATACTGCT
* * * *
28501 TATTTAAATATTGA-ATAAGTTTTACTCTTCATTGCAAGAGTTG
1 TATTTAAATA-TCATATAAG-TTTACTCTTCATCGAAAGAGTTA
*
28544 TATTTAAATGATCATCTAAGTTTACTCTTCATCGAAAGAGTTA
1 TATTTAAAT-ATCATATAAGTTTACTCTTCATCGAAAGAGTTA
*
28587 TATTTGAATA
1 TATTTAAATA
28597 ATATCCAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.02
43 39 0.87
44 5 0.11
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (42 bp):
TATTTAAATATCATATAAGTTTACTCTTCATCGAAAGAGTTA
Found at i:32883 original size:1 final size:1
Alignment explanation
Indices: 32877--32904 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
32867 GGGCTTCTTC
32877 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
32905 AAATATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33982 original size:14 final size:14
Alignment explanation
Indices: 33965--33997 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33955 ACAAGAACTA
33965 GAGAGGGAGAAGGG
1 GAGAGGGAGAAGGG
33979 GAGAGGGAGAAGGG
1 GAGAGGGAGAAGGG
33993 GAGAG
1 GAGAG
33998 AGCGGCTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (14 bp):
GAGAGGGAGAAGGG
Found at i:34446 original size:39 final size:39
Alignment explanation
Indices: 34403--34517 Score: 94
Period size: 38 Copynumber: 3.0 Consensus size: 39
34393 TACGTATAAT
34403 TTATTTTGAAGTTCAATGTAATATACTTGAAATAAAAAA
1 TTATTTTGAAGTTCAATGTAATATACTTGAAATAAAAAA
** * ** * **
34442 TTATTTTTTA--TCAATATTTTGA-AATAAAAAATAAAAAA
1 TTATTTTGAAGTTCAATGTAAT-ATACT-TGAAATAAAAAA
* *
34480 ATA-CTTGAAGTTCAATGTAATATACTTGAAATAAAAAA
1 TTATTTTGAAGTTCAATGTAATATACTTGAAATAAAAAA
34518 AACATACCTG
Statistics
Matches: 53, Mismatches: 18, Indels: 11
0.65 0.22 0.13
Matches are distributed among these distances:
37 12 0.23
38 24 0.45
39 17 0.32
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (39 bp):
TTATTTTGAAGTTCAATGTAATATACTTGAAATAAAAAA
Found at i:35569 original size:21 final size:20
Alignment explanation
Indices: 35543--35596 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
35533 TTGTTTAAGG
35543 GTGAAATCGAACAAACCCACT
1 GTGAAATCGAACAAACCCA-T
* *
35564 GTGAAATCGAAGCTAATCCAT
1 GTGAAATCGAA-CAAACCCAT
35585 GTGAAATCGAAC
1 GTGAAATCGAAC
35597 GGGTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 23 0.77
22 6 0.20
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
GTGAAATCGAACAAACCCAT
Found at i:36793 original size:99 final size:95
Alignment explanation
Indices: 36623--36803 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 95
36613 TGAGAACTTG
* * *
36623 ATTTGATTTGATTCAAGGGTCGAATGACTTGGTCTTGAATTTAATAATTTAATTCAAGGGTCTTG
1 ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTTAATAAATTAATTCAAGGGTCTTG
36688 ACGACTTGATCTTGAATTGATGACTTGGGA
66 ACGACTTGATCTTGAATTGATGACTTGGGA
* * *
36718 ATTTGATTTGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGATGATAAATTGATTCAAGGG
1 ATTTGATTTGATTCAAGGGTC---GAATGACTTGATCTCGAATT--TAATAAATTAATTCAAGGG
*
36782 TCTTGGCGACTTGATCTTGAAT
61 TCTTGACGACTTGATCTTGAAT
36804 AAACAAAATT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
95 20 0.27
97 16 0.22
98 1 0.01
99 37 0.50
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (95 bp):
ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTTAATAAATTAATTCAAGGGTCTTG
ACGACTTGATCTTGAATTGATGACTTGGGA
Found at i:37037 original size:16 final size:16
Alignment explanation
Indices: 37013--37046 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
37003 TCTGAAATAT
*
37013 TTCAGAGCTTTTCTGC
1 TTCAAAGCTTTTCTGC
37029 TTCAAAGCTTTTCTGC
1 TTCAAAGCTTTTCTGC
37045 TT
1 TT
37047 TCTGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (16 bp):
TTCAAAGCTTTTCTGC
Found at i:37865 original size:24 final size:25
Alignment explanation
Indices: 37829--37876 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
37819 GCCCATATTT
37829 ATTTTTTAAAATAAAATAAT-AATTAA
1 ATTTTTT-AAATAAAA-AATGAATTAA
37855 ATTTTTT-AATAAAAAATGAATT
1 ATTTTTTAAATAAAAAATGAATT
37877 TTAAACATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 11 0.52
26 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTTTTTAAATAAAAAATGAATTAA
Found at i:39381 original size:21 final size:21
Alignment explanation
Indices: 39356--39410 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
39346 CCCGATTAAC
39356 TAGGGTTAGGGTATTGAATAA
1 TAGGGTTAGGGTATTGAATAA
39377 TAGGGTTAGGGTATTGAATAA
1 TAGGGTTAGGGTATTGAATAA
39398 TAGGGTTAGGGTA
1 TAGGGTTAGGGTA
39411 GGGTACGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (21 bp):
TAGGGTTAGGGTATTGAATAA
Found at i:39709 original size:19 final size:20
Alignment explanation
Indices: 39691--39726 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
39681 AATTAATTAT
39691 TTTA-ATATTA-ATTTTTTA
1 TTTATATATTATATTTTTTA
39709 TTTATATATTATATTTTT
1 TTTATATATTATATTTTT
39727 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATATTATATTTTTTA
Found at i:40274 original size:82 final size:84
Alignment explanation
Indices: 40113--40276 Score: 253
Period size: 82 Copynumber: 2.0 Consensus size: 84
40103 CAATTTGGGA
* *
40113 TTAATCCTAATTCCAGTTCTTTCCCAACTTCTCTCTCCTATTACCCTCTCTCAAGAGTTCATTTC
1 TTAATCCTAATTCCAGTTCTTTCCCAACATCTCTCTCCGATTACCCTCTCTCAAGAGTTCATTTC
40178 TTGAAGGTCATTCTTGTAC
66 TTGAAGGTCATTCTTGTAC
* **
40197 TTAATCCTAATTCCAGTTCTTTCCCAA-AT-TCTCTCCGGTTACTTTCTCTCAAGAGTTCATTTC
1 TTAATCCTAATTCCAGTTCTTTCCCAACATCTCTCTCCGATTACCCTCTCTCAAGAGTTCATTTC
40260 TTGAAGG-CTATTCTTGT
66 TTGAAGGTC-ATTCTTGT
40277 TCATCGGCTT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
81 1 0.01
82 45 0.61
83 1 0.01
84 27 0.36
ACGTcount: A:0.20, C:0.27, G:0.10, T:0.43
Consensus pattern (84 bp):
TTAATCCTAATTCCAGTTCTTTCCCAACATCTCTCTCCGATTACCCTCTCTCAAGAGTTCATTTC
TTGAAGGTCATTCTTGTAC
Found at i:45448 original size:45 final size:45
Alignment explanation
Indices: 45380--45488 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
45370 TGAGCTTGTT
** * **
45380 TGGTTGTAATTGTTGCCATAAGAAATTGATTAAGAGGCTAAATAA
1 TGGTTGTAATTCCTGCCACAAGAAATAAATTAAGAGGCTAAATAA
* * * *
45425 TGGTTGTAATTCCTGCCGCAAGAAATAAATTAAGTGGTTGAATAA
1 TGGTTGTAATTCCTGCCACAAGAAATAAATTAAGAGGCTAAATAA
* **
45470 TGATCCTAATTCCTGCCAC
1 TGGTTGTAATTCCTGCCAC
45489 TAAGGTTTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (45 bp):
TGGTTGTAATTCCTGCCACAAGAAATAAATTAAGAGGCTAAATAA
Found at i:54286 original size:13 final size:14
Alignment explanation
Indices: 54268--54296 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54258 TGTTGTTATT
54268 TTGTAGATCTA-AA
1 TTGTAGATCTAGAA
54281 TTGTAGATCTAGAA
1 TTGTAGATCTAGAA
54295 TT
1 TT
54297 ATGTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (14 bp):
TTGTAGATCTAGAA
Found at i:54564 original size:31 final size:33
Alignment explanation
Indices: 54505--54570 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 33
54495 ATGTGCCGCC
*
54505 CACCGTGGCTGATGCCGCCCTCCTGGGGCGGCA
1 CACCGTGGCTCATGCCGCCCTCCTGGGGCGGCA
54538 CACCGTGG-TCATGCCGCCC-CCTGGGGCGGCA
1 CACCGTGGCTCATGCCGCCCTCCTGGGGCGGCA
54569 CA
1 CA
54571 TGTAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 14 0.44
32 10 0.31
33 8 0.25
ACGTcount: A:0.11, C:0.41, G:0.35, T:0.14
Consensus pattern (33 bp):
CACCGTGGCTCATGCCGCCCTCCTGGGGCGGCA
Found at i:55208 original size:20 final size:20
Alignment explanation
Indices: 55185--55222 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55175 GGACTAAATT
55185 GACC-CAAATTGGAATATAGG
1 GACCACAAATT-GAATATAGG
*
55205 GACCATAAATTGAATATA
1 GACCACAAATTGAATATA
55223 TTAATTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (20 bp):
GACCACAAATTGAATATAGG
Found at i:57234 original size:72 final size:77
Alignment explanation
Indices: 57146--57313 Score: 220
Period size: 77 Copynumber: 2.2 Consensus size: 77
57136 TCCATCCTGG
* * * *
57146 GGTAAAATGATCATTTTATCAATCTATGAGACTGA-T-A-AA-T-CTTATATACTCACTTTTCTT
1 GGTAAAATGATCATTTTATCAATCTATGAGACTAATTAATAAGTACTCACATACTCACTTTTCTC
57206 ATTCATTCTAAA
66 ATTCATTCTAAA
** * * *
57218 GGTAAAATGATCATTTTATCTCTTTGTGAGACTAATTAATAAGTACTCCCATACTCACTTTTCTC
1 GGTAAAATGATCATTTTATCAATCTATGAGACTAATTAATAAGTACTCACATACTCACTTTTCTC
57283 ATTCATTCTAAA
66 ATTCATTCTAAA
57295 GGTAAAATGATCATTTTAT
1 GGTAAAATGATCATTTTAT
57314 ACATCTGTGT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
72 30 0.37
73 1 0.01
74 1 0.01
75 2 0.02
76 1 0.01
77 47 0.57
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (77 bp):
GGTAAAATGATCATTTTATCAATCTATGAGACTAATTAATAAGTACTCACATACTCACTTTTCTC
ATTCATTCTAAA
Found at i:63837 original size:30 final size:29
Alignment explanation
Indices: 63772--63839 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
63762 TCATGCATGC
* *
63772 AATGGCTATTTTGAAAGTTTAAGGGCTAA
1 AATGTCTATTTTGAAAGTTTAAGGGCCAA
** * *
63801 TTTGTCTATTTTTACAAGTTTAAGTGCCAA
1 AATGTCTATTTTGA-AAGTTTAAGGGCCAA
63831 AATGTCTAT
1 AATGTCTAT
63840 GAAACTTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (29 bp):
AATGTCTATTTTGAAAGTTTAAGGGCCAA
Found at i:65340 original size:29 final size:29
Alignment explanation
Indices: 65307--65366 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
65297 ATTCCAAAAC
*
65307 ACGTCACCCAGGAGTGATTGCAATTTTCA
1 ACGTCACCCAGGAGTGATTGCAATTTCCA
* *
65336 ACGTCACCTAGGGGTGATTGCAATTTCCA
1 ACGTCACCCAGGAGTGATTGCAATTTCCA
65365 AC
1 AC
65367 AGCGTTACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (29 bp):
ACGTCACCCAGGAGTGATTGCAATTTCCA
Found at i:76310 original size:22 final size:22
Alignment explanation
Indices: 76282--76326 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
76272 CTTCAGTCTC
76282 TCGGTTTCTTTTCTAAAATTCT
1 TCGGTTTCTTTTCTAAAATTCT
76304 TCGGTTTCTTTTCTAAAATTCT
1 TCGGTTTCTTTTCTAAAATTCT
76326 T
1 T
76327 TGTGATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.56
Consensus pattern (22 bp):
TCGGTTTCTTTTCTAAAATTCT
Found at i:78018 original size:12 final size:12
Alignment explanation
Indices: 78001--78025 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
77991 CTCGTATCAT
78001 ATCAAATTGTTA
1 ATCAAATTGTTA
78013 ATCAAATTGTTA
1 ATCAAATTGTTA
78025 A
1 A
78026 GCATCCAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCAAATTGTTA
Found at i:78426 original size:2 final size:2
Alignment explanation
Indices: 78414--78449 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
78404 GTCGGATACA
*
78414 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78450 AGTTATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:82055 original size:2 final size:2
Alignment explanation
Indices: 82048--82087 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
82038 TATTTTCTTG
82048 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
82088 ATCATACATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:91195 original size:6 final size:7
Alignment explanation
Indices: 91168--91194 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
91158 AATCAAATTG
91168 GAAAAAA
1 GAAAAAA
91175 GAAAAAA
1 GAAAAAA
91182 GAAAAAA
1 GAAAAAA
91189 GAAAAA
1 GAAAAA
91195 GCAAATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Done.