Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021904.1 Corchorus olitorius cultivar O-4 contig21937, 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: 11444
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:908 original size:132 final size:132
Alignment explanation
Indices: 717--968 Score: 504
Period size: 132 Copynumber: 1.9 Consensus size: 132
707 TTAGAAATTG
717 AATAAATGTATTTAGCATAGAAATACAAGTGGATTTTTTCTTGACATCATACAAAGTGGATTTTG
1 AATAAATGTATTTAGCATAGAAATACAAGTGGATTTTTTCTTGACATCATACAAAGTGGATTTTG
782 TTAGCTTTTAGTCTTTTCATCATTAATTGTTTATATGATATATCTGATAAGGTTTAGTCTTTTCA
66 TTAGCTTTTAGTCTTTTCATCATTAATTGTTTATATGATATATCTGATAAGGTTTAGTCTTTTCA
847 TC
131 TC
849 AATAAATGTATTTAGCATAGAAATACAAGTGGATTTTTTCTTGACATCATACAAAGTGGATTTTG
1 AATAAATGTATTTAGCATAGAAATACAAGTGGATTTTTTCTTGACATCATACAAAGTGGATTTTG
914 TTAGCTTTTAGTCTTTTCATCATTAATTGTTTATATGATATATCTGATAAGGTTT
66 TTAGCTTTTAGTCTTTTCATCATTAATTGTTTATATGATATATCTGATAAGGTTT
969 TCGATCAAGT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 120 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (132 bp):
AATAAATGTATTTAGCATAGAAATACAAGTGGATTTTTTCTTGACATCATACAAAGTGGATTTTG
TTAGCTTTTAGTCTTTTCATCATTAATTGTTTATATGATATATCTGATAAGGTTTAGTCTTTTCA
TC
Found at i:1170 original size:25 final size:26
Alignment explanation
Indices: 1120--1170 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1110 TAACCTGAAT
1120 AATAATTTCTGGGTCTTTATAGCAAA
1 AATAATTTCTGGGTCTTTATAGCAAA
1146 AATAATTTCT-GGTCTTATATA-CAAA
1 AATAATTTCTGGGTCTT-TATAGCAAA
1171 TTAGGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (26 bp):
AATAATTTCTGGGTCTTTATAGCAAA
Found at i:8009 original size:201 final size:204
Alignment explanation
Indices: 7638--8047 Score: 729
Period size: 201 Copynumber: 2.0 Consensus size: 204
7628 TTCCTTAATA
7638 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
* * *
7703 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATATAATAG
66 ATTTAATAAATCAACCACTAATGTTCAACTAACTTTTTTTTGGTATAGTTATATATATATAATAA
* *
7768 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
131 TAATATGTTGTATCTTATTCACTACAACCTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
7833 TCACCATTG
196 TCACCATTG
*
7842 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAATTTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
7907 AATTTAATAAATCAA-C-C-AATGTTCAACT-ACTTTTTTTTGGTATAGTTATATATATATAATA
65 AATTTAATAAATCAACCACTAATGTTCAACTAACTTTTTTTTGGTATAGTTATATATATATAATA
7968 ATAATATGTTGTATCTTATTCACTACAACCTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
130 ATAATATGTTGTATCTTATTCACTACAACCTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
8033 TTCACCATTG
195 TTCACCATTG
8043 ATAAA
1 ATAAA
8048 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
201 108 0.54
202 11 0.06
203 1 0.01
204 17 0.09
205 62 0.31
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (204 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAACTTTTTTTTGGTATAGTTATATATATATAATAA
TAATATGTTGTATCTTATTCACTACAACCTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
TCACCATTG
Found at i:8312 original size:60 final size:59
Alignment explanation
Indices: 8176--8337 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 59
8166 GCTAATTGCT
*
8176 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGG-CGGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATG--AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
8235 CAAATAAGGACCTAACGTTATAGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-GAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
8295 CAAATAAGGGCCCAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTAT-GAAAATGCTCAAATAAGGGCC
8338 TGGCATCAGT
Statistics
Matches: 95, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
59 36 0.38
60 58 0.61
61 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:8333 original size:31 final size:29
Alignment explanation
Indices: 8172--8337 Score: 106
Period size: 31 Copynumber: 5.6 Consensus size: 29
8162 ATTGGCTAAT
*
8172 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCCAACGTTTG--AAAA
** * * **
8203 TGCTCAAATAAGGGCGGATC-TTTTAATT
1 TGCTCAAATAAGGGCCCAACGTTTGAAAA
* *
8231 TGGC-CAAATAAGGACCTAACGTTATAGAAAA
1 T-GCTCAAATAAGGGCCCAACGTT-T-GAAAA
* * **
8262 TGCTCAAATAAGGGCCCGATC-TTTTAATT
1 TGCTCAAATAAGGGCCC-AACGTTTGAAAA
8291 TGGC-CAAATAAGGGCCCAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCCAACGTT-T-GAAAA
8322 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
8338 TGGCATCAGT
Statistics
Matches: 101, Mismatches: 23, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
28 17 0.17
29 22 0.22
30 12 0.12
31 48 0.48
32 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCCAACGTTTGAAAA
Found at i:8415 original size:31 final size:30
Alignment explanation
Indices: 8380--8544 Score: 135
Period size: 31 Copynumber: 5.5 Consensus size: 30
8370 CGACACCAGA
*
8380 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** * **
8411 CCCTTATTTG-GCCAAATT--AAAAGATCGGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
8440 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** * *
8471 CCCTTATTTG-GTCAAATT--AAAAGATCAGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
8500 CCCTTATTTGAGCATTTTTGCAAACGTTAGG
1 CCCTTATTTGAGCA-TTTTGCAAACGTTAGG
8531 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
8545 ATTAGCCTAT
Statistics
Matches: 103, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 8 0.08
29 32 0.31
30 6 0.06
31 49 0.48
32 8 0.08
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGG
Found at i:8453 original size:60 final size:60
Alignment explanation
Indices: 8380--8540 Score: 286
Period size: 60 Copynumber: 2.7 Consensus size: 60
8370 CGACACCAGA
* *
8380 CCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
*
8440 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCAGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
*
8500 CCCTTATTTGAGCATTTTTGCAAACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
8541 AGCAATTAGC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
Found at i:8508 original size:29 final size:28
Alignment explanation
Indices: 8411--8509 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
8401 AAACGTTAGA
*
8411 CCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGG-CAAATTAAAAGATCAGG
** * *
8440 CCCTTATTTGAGCATTTTGGCAAACG-TTAGG
1 CCCTTATTTG-GCAAATT---AAAAGATCAGG
8471 CCCTTATTTGGTCAAATTAAAAGATCAGG
1 CCCTTATTTGG-CAAATTAAAAGATCAGG
8500 CCCTTATTTG
1 CCCTTATTTG
8510 AGCATTTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 4 0.07
29 28 0.51
30 2 0.04
31 17 0.31
32 4 0.07
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (28 bp):
CCCTTATTTGGCAAATTAAAAGATCAGG
Found at i:8998 original size:36 final size:36
Alignment explanation
Indices: 8944--9013 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
8934 GAGATTTTGG
* *
8944 AGAAATATAATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAATA
* *
8980 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAA
9014 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (36 bp):
AGAAATATAATAACCAAAATCACAAAAAATGTAATA
Found at i:10374 original size:58 final size:58
Alignment explanation
Indices: 10276--10385 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
10266 ATCATGCCTC
*
10276 GGTCCTAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCGAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGTCTT
* *
10334 GGTCCGAAAACGTCTTTTTTTATG-CATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTA-GCCATCTAATAAAAAAACATGTCACTCGATA
10386 TTTGATTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
58 31 0.66
59 15 0.32
60 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGTCTT
Done.