Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019440.1 Corchorus olitorius cultivar O-4 contig19473, 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: 66145
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1978 original size:4 final size:4
Alignment explanation
Indices: 1969--1995 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1959 AAACAAAATC
1969 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1996 TTGTGTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:4299 original size:2 final size:2
Alignment explanation
Indices: 4292--4319 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4282 ATAATTACCC
4292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4320 TGTTTAGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14470 original size:3 final size:3
Alignment explanation
Indices: 14462--14563 Score: 53
Period size: 3 Copynumber: 34.0 Consensus size: 3
14452 TTCACTTTCC
* * * * * *
14462 TCT TCT TCT TCT TCGT AC- TCC TCC TCT TCT TCT TCC TCT TCG TCG
1 TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * * * *
14507 TCT TCC TCT TCC CCT TCC CCT TCT TCC TCC TCC TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
14555 CCT TCT TCT
1 TCT TCT TCT
14564 AGTCCTTCTA
Statistics
Matches: 76, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
2 1 0.01
3 73 0.96
4 2 0.03
ACGTcount: A:0.01, C:0.45, G:0.03, T:0.51
Consensus pattern (3 bp):
TCT
Found at i:14510 original size:21 final size:21
Alignment explanation
Indices: 14458--14553 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
14448 CAGCTTCACT
* *
14458 TTCCTCTTCTTCTTCTTCGTAC
1 TTCCTCTTCTTCCTCTTCCT-C
* *
14480 -TCCTCCTCTTCTTCTTCCTC
1 TTCCTCTTCTTCCTCTTCCTC
* * *
14500 TTCGTCGTCTTCCTCTTCCCC
1 TTCCTCTTCTTCCTCTTCCTC
* *
14521 TTCCCCTTCTTCCTCCTCCTC
1 TTCCTCTTCTTCCTCTTCCTC
*
14542 TTCTTCTTCTTC
1 TTCCTCTTCTTC
14554 TCCTTCTTCT
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.02
21 59 0.98
ACGTcount: A:0.01, C:0.46, G:0.03, T:0.50
Consensus pattern (21 bp):
TTCCTCTTCTTCCTCTTCCTC
Found at i:14559 original size:27 final size:27
Alignment explanation
Indices: 14462--14550 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
14452 TTCACTTTCC
* *
14462 TCTTCTTCTTCTTCGTACTCCTCCTCT
1 TCTTCTTCCTCTTCGTCCTCCTCCTCT
* *
14489 TCTTCTTCCTCTTCGTCGTCTTCCTCT
1 TCTTCTTCCTCTTCGTCCTCCTCCTCT
** * *
14516 TCCCCTTCCCCTTCTTCCTCCTCCTCT
1 TCTTCTTCCTCTTCGTCCTCCTCCTCT
14543 TCTTCTTC
1 TCTTCTTC
14551 TTCTCCTTCT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.01, C:0.46, G:0.03, T:0.49
Consensus pattern (27 bp):
TCTTCTTCCTCTTCGTCCTCCTCCTCT
Found at i:17475 original size:2 final size:2
Alignment explanation
Indices: 17468--17496 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17458 CTTCAATTAT
17468 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 T
17497 GACATACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19595 original size:6 final size:6
Alignment explanation
Indices: 19586--19629 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
19576 ACTACTGCTG
* * * *
19586 CTCCCA CTCCCG CTCCCA CTACCA CTACCA CTACCA CTCCCA CT
1 CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CT
19630 GCTATCACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.20, C:0.59, G:0.02, T:0.18
Consensus pattern (6 bp):
CTCCCA
Found at i:19602 original size:12 final size:12
Alignment explanation
Indices: 19586--19629 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
19576 ACTACTGCTG
* *
19586 CTCCCACTCCCG
1 CTCCCACTACCA
19598 CTCCCACTACCA
1 CTCCCACTACCA
*
19610 CTACCACTACCA
1 CTCCCACTACCA
19622 CTCCCACT
1 CTCCCACT
19630 GCTATCACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.20, C:0.59, G:0.02, T:0.18
Consensus pattern (12 bp):
CTCCCACTACCA
Found at i:19643 original size:21 final size:21
Alignment explanation
Indices: 19614--19653 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19604 CTACCACTAC
19614 CACTACCACTCCCACTGCTAT
1 CACTACCACTCCCACTGCTAT
* * *
19635 CACTTCCACTGCTACTGCT
1 CACTACCACTCCCACTGCT
19654 TGAACTTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.45, G:0.07, T:0.28
Consensus pattern (21 bp):
CACTACCACTCCCACTGCTAT
Found at i:20100 original size:25 final size:25
Alignment explanation
Indices: 20066--20115 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20056 AAATTCTTAA
20066 TGGACAAAGGGGTTCAAGTATCTAC
1 TGGACAAAGGGGTTCAAGTATCTAC
20091 TGGACAAAGGGGTTCAAGTATCTAC
1 TGGACAAAGGGGTTCAAGTATCTAC
20116 AAAGTACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (25 bp):
TGGACAAAGGGGTTCAAGTATCTAC
Found at i:28490 original size:37 final size:37
Alignment explanation
Indices: 28440--28515 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
28430 TCCAATCAGT
*
28440 CTGACCTATGTACTATATTTTTGCCATACCTGCATGA
1 CTGACCTATGTACTATATTTTTACCATACCTGCATGA
28477 CTGACCTATGTACTATATTTTTACCATACCTGCATGA
1 CTGACCTATGTACTATATTTTTACCATACCTGCATGA
28514 CT
1 CT
28516 CGTCATTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (37 bp):
CTGACCTATGTACTATATTTTTACCATACCTGCATGA
Found at i:29040 original size:32 final size:32
Alignment explanation
Indices: 28999--29059 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
28989 TGTAAAACTT
*
28999 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCGACCATTATACCCTTATTTTTCTAA
29031 TTGAATCGACCATTATACCCTTATTTTTC
1 TTGAATCGACCATTATACCCTTATTTTTC
29060 AGACATATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (32 bp):
TTGAATCGACCATTATACCCTTATTTTTCTAA
Found at i:29209 original size:98 final size:97
Alignment explanation
Indices: 29092--29270 Score: 304
Period size: 98 Copynumber: 1.8 Consensus size: 97
29082 TACCTAACTA
* *
29092 ATATAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATTTAATATCTTTATAATTACT
1 ATATAGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTCAATAT-TTTATAATTACT
29157 TTACTTTTACCATTTTACTATTTTTTTCAAAAT
65 TTACTTTTACCATTTTACTATTTTTTTCAAAAT
* *
29190 ATATAGTTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTATAATTATTT
1 ATATAGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTCAATATTTTATAATTACTT
*
29255 TATTTTTACCATTTTA
66 TACTTTTACCATTTTA
29271 ATTTAAAAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
97 27 0.36
98 49 0.64
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.54
Consensus pattern (97 bp):
ATATAGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTCAATATTTTATAATTACTT
TACTTTTACCATTTTACTATTTTTTTCAAAAT
Found at i:30495 original size:31 final size:31
Alignment explanation
Indices: 30457--30518 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
30447 GAGTTTTGTA
*
30457 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
*
30488 AAACTTTTGAATCGCCTATCATATCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
30519 TTAGTCAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:30642 original size:93 final size:93
Alignment explanation
Indices: 30517--30693 Score: 291
Period size: 93 Copynumber: 1.9 Consensus size: 93
30507 CATATCCTTA
* *
30517 TTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTCTAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
* * *
30582 TTACCATTTTACTATTTTACTTTTATAG
66 TAACCATATTACTAATTTACTTTTATAG
*
30610 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATCTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
*
30675 TAACGATATTACTAATTTA
66 TAACCATATTACTAATTTA
30694 ATTAAAAAGT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (93 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
TAACCATATTACTAATTTACTTTTATAG
Found at i:44151 original size:132 final size:132
Alignment explanation
Indices: 43909--44409 Score: 588
Period size: 132 Copynumber: 3.8 Consensus size: 132
43899 CGACCGATCA
* * * **
43909 ACTTTTGTTAGTTGTTGTTTAATATATTTTACAAATTGATTTTCGAAGCGATTTTGAAAGTTGCT
1 ACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGATTTTCCAAGCGACCTTGAAAGTTGCT
* * * ** *
43974 ACAAAAAATATGATTACTTTTGAAACAACAGATTAAGTTATTGCGAAATCTTACTCTTTCCGCAA
66 ACAAAAAATATAATTACTTTTGAAGCAACAAATTAAGTCGTTGCGAAATCTTACTCTTTTCGCAA
44039 CG
131 CG
* * * * *
44041 ACTTCTGTTAGTTGTTGCTTAATATATTTTACAAATTGATTTTCCCAGTGACCTTGTAAGTTGCT
1 ACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGATTTTCCAAGCGACCTTGAAAGTTGCT
* * * *
44106 ACAAAATACATAATTACTTTTGAAGCCACAAATTAAGTCGTTGCGAAATCTTACTCTTTTTGCAA
66 ACAAAAAATATAATTACTTTTGAAGCAACAAATTAAGTCGTTGCGAAATCTTACTCTTTTCGCAA
*
44171 TG
131 CG
* * * * * *
44173 ACTATTGTTAGTCGTTGCATAATATATCTTACAAATTGATTTTCCTAGGGACCTTGAAAGTCGCT
1 ACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGATTTTCCAAGCGACCTTGAAAGTTGCT
* * * * *
44238 ACAAAAAATATTATTACTTTTGAAGCGACAAATTAAGTCGCTGCGAAATCTTACTTTTTTCGCAT
66 ACAAAAAATATAATTACTTTTGAAGCAACAAATTAAGTCGTTGCGAAATCTTACTCTTTTCGCAA
44303 CG
131 CG
* * * * * ** *
44305 ACTTTTGTTAATCGTTGCTTAATATATTTTTCAATTTGATTTTCGAAGCAATGTTGAAAGTCGCT
1 ACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGATTTTCCAAGCGACCTTGAAAGTTGCT
* * * * * *
44370 ACAATAAACATAATTACTTGTGAAACGACAGATTAAGTCG
66 ACAAAAAATATAATTACTTTTGAAGCAACAAATTAAGTCG
44410 CTGTGATCGT
Statistics
Matches: 314, Mismatches: 55, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
132 314 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (132 bp):
ACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGATTTTCCAAGCGACCTTGAAAGTTGCT
ACAAAAAATATAATTACTTTTGAAGCAACAAATTAAGTCGTTGCGAAATCTTACTCTTTTCGCAA
CG
Found at i:44449 original size:100 final size:100
Alignment explanation
Indices: 44315--44515 Score: 253
Period size: 100 Copynumber: 2.0 Consensus size: 100
44305 ACTTTTGTTA
* ** *
44315 ATCGTTGCTTAATATATTTTTCAATTTGATTTTCGAAGCAATGTTGAAAGTCGCTACAATAAACA
1 ATCGTTGCTTAATATATTTTCCAATTTGATTTTCGAAGCAACCTTGAAAGTCGCTACAAAAAACA
* * *
44380 TAATTA-CTTGTGAAACGACAGATTAAGTCGCTGTG
66 TAATCACCTT-TGAAACCACAAATTAAGTCGCTGTG
* * **
44415 ATCGTTGCTTAATATGTTTTACCAATTT-ATTTTCGCAGTGACCTTGAAAGTCGCTACAAAAAAC
1 ATCGTTGCTTAATATATTTT-CCAATTTGATTTTCGAAGCAACCTTGAAAGTCGCTACAAAAAAC
* *
44479 ATAATCACCTTTGAAGCCACAAATTAAGTCGTTGTG
65 ATAATCACCTTTGAAACCACAAATTAAGTCGCTGTG
44515 A
1 A
44516 AATCTTACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
100 77 0.90
101 9 0.10
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (100 bp):
ATCGTTGCTTAATATATTTTCCAATTTGATTTTCGAAGCAACCTTGAAAGTCGCTACAAAAAACA
TAATCACCTTTGAAACCACAAATTAAGTCGCTGTG
Found at i:46652 original size:31 final size:31
Alignment explanation
Indices: 46614--46781 Score: 129
Period size: 31 Copynumber: 5.5 Consensus size: 31
46604 AAAGGCTAAT
46614 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * **
46645 TGCTCAAATAAGGGCCCGATC-TTT-T-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGTCAAAA
*
46674 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
* **
46705 TGCTCAAATAAGGGCC---CGGTCTT-TTAATT
1 TGCTCAAATAAGGGCCTAAC-GT-TTGTCAAAA
* *
46734 TGGC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
*
46765 TGCTCAAATAAGAGCCT
1 TGCTCAAATAAGGGCCT
46782 GACATCGAAA
Statistics
Matches: 103, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
28 5 0.05
29 32 0.31
30 13 0.13
31 48 0.47
32 5 0.05
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:46711 original size:60 final size:60
Alignment explanation
Indices: 46618--46776 Score: 291
Period size: 60 Copynumber: 2.6 Consensus size: 60
46608 GCTAATTGCT
*
46618 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
46678 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
46738 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAG
46777 AGCCTGACAT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:46892 original size:29 final size:28
Alignment explanation
Indices: 46851--46952 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
46841 GGCAAATGTT
46851 AGGCCCTTATTTGGCTAAATTAAAAGATC
1 AGGCCCTTATTTGGC-AAATTAAAAGATC
* ** *
46880 AGGCCCTTATTTGAACATTTTCAATAACG-TT
1 AGGCCCTTATTTG-GCAAATT-AA-AA-GATC
46911 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
* *
46940 GGGTCCTTATTTG
1 AGGCCCTTATTTG
46953 AGCATTTTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.02
29 30 0.53
30 5 0.09
31 20 0.35
32 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (28 bp):
AGGCCCTTATTTGGCAAATTAAAAGATC
Found at i:46912 original size:60 final size:59
Alignment explanation
Indices: 46818--46983 Score: 235
Period size: 60 Copynumber: 2.8 Consensus size: 59
46808 CAAACTGATG
* *
46818 TCAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCTAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTT-GCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
*
46878 TCAGGCCCTTATTTGAACATTTT-CAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGC-A-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
* * *
46938 TCGGGTCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTG
1 TCAGGCCCTTATTTGAGCATTTT-GCAAACGTTAGGCCCTTATTTG
46984 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 91 0.96
61 1 0.01
62 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (59 bp):
TCAGGCCCTTATTTGAGCATTTTGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
Found at i:47723 original size:20 final size:20
Alignment explanation
Indices: 47698--47756 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
47688 GAGGTAGGTG
47698 AAAAAAAAATTCAATTTTAT
1 AAAAAAAAATTCAATTTTAT
47718 AAAAAAAAATTCAATTTTAT
1 AAAAAAAAATTCAATTTTAT
47738 AAAAAAAAATT-AATTTTAT
1 AAAAAAAAATTCAATTTTAT
47757 TTTAATAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAAAAATTCAATTTTAT
Found at i:53360 original size:4 final size:4
Alignment explanation
Indices: 53351--53397 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
53341 TTCTTTCAAA
*
53351 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTGT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
53398 CATGGCTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:58216 original size:115 final size:115
Alignment explanation
Indices: 58014--58244 Score: 462
Period size: 115 Copynumber: 2.0 Consensus size: 115
58004 TAAGCTAAGG
58014 TAGTTAGCAATAATTAAGCAGTTAGTTAGTAGTTAGTTATTACAGAAACTAACTCTCCTGTATAT
1 TAGTTAGCAATAATTAAGCAGTTAGTTAGTAGTTAGTTATTACAGAAACTAACTCTCCTGTATAT
58079 ATTCTCAAGTGTAATTGTAAATGAATCACGATTTCCCTTTCTTTTTCATT
66 ATTCTCAAGTGTAATTGTAAATGAATCACGATTTCCCTTTCTTTTTCATT
58129 TAGTTAGCAATAATTAAGCAGTTAGTTAGTAGTTAGTTATTACAGAAACTAACTCTCCTGTATAT
1 TAGTTAGCAATAATTAAGCAGTTAGTTAGTAGTTAGTTATTACAGAAACTAACTCTCCTGTATAT
58194 ATTCTCAAGTGTAATTGTAAATGAATCACGATTTCCCTTTCTTTTTCATT
66 ATTCTCAAGTGTAATTGTAAATGAATCACGATTTCCCTTTCTTTTTCATT
58244 T
1 T
58245 GTTTCTGATA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (115 bp):
TAGTTAGCAATAATTAAGCAGTTAGTTAGTAGTTAGTTATTACAGAAACTAACTCTCCTGTATAT
ATTCTCAAGTGTAATTGTAAATGAATCACGATTTCCCTTTCTTTTTCATT
Found at i:59467 original size:281 final size:280
Alignment explanation
Indices: 59082--59630 Score: 940
Period size: 281 Copynumber: 2.0 Consensus size: 280
59072 AAACTAATAG
* *
59082 AGCCTTCAAAGTACATGAACCTACTTATAAGTACTACTATGGCAAATAGCTACAATATTGGAAAA
1 AGCCTTCAAAGCACATGAACCCACTTATAAG-ACTACTATGGCAAATAGCTACAATATTGGAAAA
*
59147 GGGTGCTTTGTTTTTGGAGAGGCAGATTCCATCAAATCAAAATTTTTATGGGTCTAGGAGATGTG
65 AGGTGCTTTGTTTTTGGAGAGGCAGATTCCATCAAATCAAAATTTTTATGGGTCTAGGAGATGTG
* *
59212 TTGCACATTACCGATCTTTCGATTGATGGATTGCCGATCATTGCAAATTTGAAAGAAGCAAATGT
130 TTGCACATTACCAATCTTTCAATTGATGGATTGCCGATCATTGCAAATTTGAAAGAAGCAAATGT
59277 GTGCAACTTGTGTGAGAAGTGTCTTGGCACAGACAATTGCCTTGTGGGAAAAAAAAAACCGAACA
195 GTGCAACTTGTGTGAGAAGTGTCTTGGCACAGACAATTGCCTTGT-GG-AAAAAAAAA-CGAACA
*
59342 TCGATTTCTCTCTGAAGCTAACAA
257 TCAATTTCTCTCTGAAGCTAACAA
* *
59366 AGCCTTCAAAGCACATGAACCCACTT-TTA-ACTACTGTGGCAAATAGCTACAATATTGGAAAAA
1 AGCCTTCAAAGCACATGAACCCACTTATAAGACTACTATGGCAAATAGCTACAATATTGGAAAAA
*
59429 GGTGCTTTGTTTTTGGAGAGGCAGATTCCATTAAATCAAAATTTTTATGGGTCTAGGAGATGTGT
66 GGTGCTTTGTTTTTGGAGAGGCAGATTCCATCAAATCAAAATTTTTATGGGTCTAGGAGATGTGT
*
59494 TGCACATTACCAATCTTTCAATTGATGGATTGCCTATCATTGCAAATTTGAAAGAAGCAAATGTG
131 TGCACATTACCAATCTTTCAATTGATGGATTGCCGATCATTGCAAATTTGAAAGAAGCAAATGTG
* *
59559 TGCAACTTGTGTGAGAAGTGTCTTGGCATAGACAATTGCCTTGTGGAAAAAAAAACGAATATCAA
196 TGCAACTTGTGTGAGAAGTGTCTTGGCACAGACAATTGCCTTGTGGAAAAAAAAACGAACATCAA
59624 TTTCTCT
261 TTTCTCT
59631 GCCTTGGCTT
Statistics
Matches: 253, Mismatches: 12, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
278 15 0.06
279 9 0.04
280 2 0.01
281 201 0.79
283 2 0.01
284 24 0.09
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (280 bp):
AGCCTTCAAAGCACATGAACCCACTTATAAGACTACTATGGCAAATAGCTACAATATTGGAAAAA
GGTGCTTTGTTTTTGGAGAGGCAGATTCCATCAAATCAAAATTTTTATGGGTCTAGGAGATGTGT
TGCACATTACCAATCTTTCAATTGATGGATTGCCGATCATTGCAAATTTGAAAGAAGCAAATGTG
TGCAACTTGTGTGAGAAGTGTCTTGGCACAGACAATTGCCTTGTGGAAAAAAAAACGAACATCAA
TTTCTCTCTGAAGCTAACAA
Found at i:60286 original size:25 final size:25
Alignment explanation
Indices: 60258--60307 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
60248 GCTTCGTTGC
60258 GGGTTTTTCATGATTAATGAAGTGT
1 GGGTTTTTCATGATTAATGAAGTGT
*
60283 GGGTTTTTCATGGTTAATGAAGTGT
1 GGGTTTTTCATGATTAATGAAGTGT
60308 TTGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.30, T:0.44
Consensus pattern (25 bp):
GGGTTTTTCATGATTAATGAAGTGT
Found at i:64202 original size:18 final size:18
Alignment explanation
Indices: 64176--64215 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
64166 AAATTCAGAA
* *
64176 AAATGAAAATAAAACAAC
1 AAATAAAAATAAAAAAAC
64194 AAATAAAAATAAAAAAAC
1 AAATAAAAATAAAAAAAC
64212 AAAT
1 AAAT
64216 CCAAGTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (18 bp):
AAATAAAAATAAAAAAAC
Found at i:65734 original size:2 final size:2
Alignment explanation
Indices: 65727--65767 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
65717 AAAAACCTAT
* *
65727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TT 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
65768 TTAGATGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:65930 original size:40 final size:40
Alignment explanation
Indices: 65875--65956 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
65865 AACCATGACA
65875 TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT
1 TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT
65915 TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT
1 TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT
65955 TG
1 TG
65957 TCTAAGTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.35
Consensus pattern (40 bp):
TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT
Done.