Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012459.1 Corchorus olitorius cultivar O-4 contig12492, 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: 3743
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:1299 original size:47 final size:48
Alignment explanation
Indices: 1199--1365 Score: 167
Period size: 48 Copynumber: 3.5 Consensus size: 48
1189 ACCATAAGTT
* ** * * *
1199 GTGATGGTTATCCTTGGCCATTTTAACCAATTTTGACCACC-TTGCATC
1 GTGATGGTTAGCCTTGGCCATTTTGGCAAATTTTGGCCACCATCG-ATC
* * * * * *
1247 GTGATGGTTAGTCTTGGCTATTTTGTC-AATTTTTGTCACCATCGATT
1 GTGATGGTTAGCCTTGGCCATTTTGGCAAATTTTGGCCACCATCGATC
* * *
1294 GTGATGGTTAGCCTTTGCCATTTTGGCAAATTTTGGCCATCATTGATC
1 GTGATGGTTAGCCTTGGCCATTTTGGCAAATTTTGGCCACCATCGATC
*
1342 GTGATGGTTAGCCTTGGTCATTTT
1 GTGATGGTTAGCCTTGGCCATTTT
1366 TGCCACCATC
Statistics
Matches: 96, Mismatches: 21, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
47 35 0.36
48 61 0.64
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.42
Consensus pattern (48 bp):
GTGATGGTTAGCCTTGGCCATTTTGGCAAATTTTGGCCACCATCGATC
Found at i:1474 original size:93 final size:93
Alignment explanation
Indices: 1305--1483 Score: 213
Period size: 94 Copynumber: 1.9 Consensus size: 93
1295 TGATGGTTAG
* * * *
1305 CCTTTGCCATTTTGGCAAATTTTGGCCATCATTGATCGTGATGGTTAGCCTTGGTCATTTTTGCC
1 CCTTGGCCATTTTGGCAAATTTTGACCATCATTGATCATGATGATTAG-CTTGGTCATTTTTGCC
* *
1370 ACCATCGGTTGTGATGGTTAGCCTTGGGC
65 ACCATCAGTTGTGATGCTTAGCCTTGGGC
*
1399 CCTTGGCCATTTTGGCAAATTTTGACCA-CATTGGGTCATGATGATTCATG-TT-GTCA-TTTTG
1 CCTTGGCCATTTTGGCAAATTTTGACCATCATT-GATCATGATGATT-A-GCTTGGTCATTTTTG
*
1460 ACCACCATTAGTTGTGATGCTTAG
63 -CCACCATCAGTTGTGATGCTTAG
1484 TTTTGACCAT
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
92 5 0.07
93 28 0.38
94 38 0.52
95 1 0.01
96 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (93 bp):
CCTTGGCCATTTTGGCAAATTTTGACCATCATTGATCATGATGATTAGCTTGGTCATTTTTGCCA
CCATCAGTTGTGATGCTTAGCCTTGGGC
Found at i:2749 original size:21 final size:21
Alignment explanation
Indices: 2725--2833 Score: 64
Period size: 21 Copynumber: 5.2 Consensus size: 21
2715 AATTCTCTGT
2725 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
2746 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
2767 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
2788 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
2809 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
2830 AAAT
1 AAAT
2834 CCTGATCTTT
Statistics
Matches: 60, Mismatches: 20, Indels: 16
0.62 0.21 0.17
Matches are distributed among these distances:
20 12 0.20
21 36 0.60
22 12 0.20
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:2771 original size:42 final size:42
Alignment explanation
Indices: 2712--2834 Score: 237
Period size: 42 Copynumber: 2.9 Consensus size: 42
2702 GCTAAGTCTT
*
2712 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
2754 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
2796 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
2835 CTGATCTTTA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:3329 original size:109 final size:107
Alignment explanation
Indices: 3085--3344 Score: 366
Period size: 108 Copynumber: 2.4 Consensus size: 107
3075 AGTTTAGCCT
* *
3085 TAATTTCACTAGGTTTAGCCCCAAATTAAAATTTTATTTTTA--TTTTAAGGGTAAATTTCAAAA
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTTTAAGGGTAAATTCCAAAA
*
3148 TTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 TTAATAA-TTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
*
3192 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAACTTAAGGGTAAATTCCAT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTT---TTAAGGGTAAATTCCAA
* *
3257 AATTAATAA-TATTATTATAGGGTTTTAGAAATAAAATATATAAC
63 AATTAATAATTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
* * *
3301 TAA-TTCACTAAGTTTAGCCCAAATTTAAATTTAAATTTTATTTT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTT
3345 GAGGGTTAGA
Statistics
Matches: 139, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
106 23 0.17
107 17 0.12
108 40 0.29
109 35 0.25
111 24 0.17
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTTTAAGGGTAAATTCCAAAAT
TAATAATTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:3713 original size:2 final size:2
Alignment explanation
Indices: 3706--3743 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3696 GGGCGTTTAG
3706 TA TA TA TA TA TA TA TA TA TA 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 TA TA TA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.