Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021019.1 Corchorus olitorius cultivar O-4 contig21052, 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: 43374
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1748 original size:19 final size:18
Alignment explanation
Indices: 1715--1750 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1705 TGAAAATAAT
1715 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1733 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1751 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:2929 original size:42 final size:42
Alignment explanation
Indices: 2883--2977 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
2873 TGACCTACAC
** *
2883 ATGAACATATATACAAAGGGATGGATAATGCATGATGAATGT
1 ATGAACATATATACAAAGACATGGATAATGCATGAAGAATGT
*
2925 ATGAACATATATACAAAGACATGGATAATGCATGAAGGATGT
1 ATGAACATATATACAAAGACATGGATAATGCATGAAGAATGT
2967 ATG-ACATATAT
1 ATGAACATATAT
2978 CAATGGATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 8 0.16
42 41 0.84
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.26
Consensus pattern (42 bp):
ATGAACATATATACAAAGACATGGATAATGCATGAAGAATGT
Found at i:5874 original size:41 final size:41
Alignment explanation
Indices: 5812--5889 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
5802 TAGGAGTCAA
*
5812 ATTGAACCAATTAATAAATATTAACCTCAATCAGGGATGAG
1 ATTGAACCAATTAAGAAATATTAACCTCAATCAGGGATGAG
*
5853 ATTGAACCAATTAAGACATATTAACCTCAATCAGGGA
1 ATTGAACCAATTAAGAAATATTAACCTCAATCAGGGA
5890 GCAAATGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.26
Consensus pattern (41 bp):
ATTGAACCAATTAAGAAATATTAACCTCAATCAGGGATGAG
Found at i:17004 original size:17 final size:18
Alignment explanation
Indices: 16984--17025 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
16974 TCATCCAACG
16984 TTTTCTTAA-TTTTCCTT
1 TTTTCTTAATTTTTCCTT
17001 TTTTCTTAATTTTTTCCTT
1 TTTTCTTAA-TTTTTCCTT
17020 TTTTCT
1 TTTTCT
17026 GTTGGGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.39
19 14 0.61
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCTTAATTTTTCCTT
Found at i:18123 original size:10 final size:10
Alignment explanation
Indices: 18099--18137 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
18089 TGCTTCTATG
18099 TTTCTGTTTTCT
1 TTTCT-TTTT-T
18111 TTTCTTTTTT
1 TTTCTTTTTT
18121 TTTCTTTTTT
1 TTTCTTTTTT
18131 TCTTCTT
1 T-TTCTT
18138 GAGAACATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 12 0.46
11 9 0.35
12 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:22804 original size:131 final size:131
Alignment explanation
Indices: 22579--23112 Score: 619
Period size: 131 Copynumber: 4.1 Consensus size: 131
22569 ACAATAATTA
* * * * * *
22579 AAAGTTGTTGCCTTAGTGATTTTTATGTTATTTTACCCAACAACTTTTTTAATTGTTGCCAATGC
1 AAAGTCGTTGCCTAAGTGATTTTGATGTTATTTTACACAAC-ACTTTTTTAGTTGTTGCCAATAC
* * * * *
22644 TTACAGTTTTCGTAACAACAATAAC-AAAGTCGTTGTGAAATTATAATCTATTCGTAACAA-TTT
65 TTACAATATTCGTAACAACAAAAACTAAAGTCGTTGCGAAATCATAATCTATTCGTAACAACTTT
22707 CAT
130 -AT
* * *
22710 AAAGTCGTTGCCTAAGTGATTTTGATGTTATTTTACAAAACACTTTTTTAGTCGTTGCCATTACT
1 AAAGTCGTTGCCTAAGTGATTTTGATGTTATTTTACACAACACTTTTTTAGTTGTTGCCAATACT
* * * *
22775 TACATTTTTCGTAACAACAAAAACAAAAGTCGTTGCGAAATCATAATTTATTCGTAACAACTTTA
66 TACAATATTCGTAACAACAAAAACTAAAGTCGTTGCGAAATCATAATCTATTCGTAACAACTTTA
22840 T
131 T
* * * * *
22841 AACA-TCGTTGCTTAAGTGATTTTGATGGTATTTTACACAACACATTCTTAGTTGTTGCCAATAT
1 AA-AGTCGTTGCCTAAGTGATTTTGATGTTATTTTACACAACACTTTTTTAGTTGTTGCCAATAC
** * * *
22905 TTACAATATTCGTAACAACAAATTCTTAAA-TTGTTGCGAAATCATAAACTATTTGTAACAACTT
65 TTACAATATTCGTAACAACAAAAAC-TAAAGTCGTTGCGAAATCATAATCTATTCGTAACAACTT
22969 TAT
129 TAT
** * * * **
22972 AAAAACGTTGTCTAAGTAATTTTGATGATATTTTACACAACACTTTTTTAGTTGTTGCCAATGTT
1 AAAGTCGTTGCCTAAGTGATTTTGATGTTATTTTACACAACACTTTTTTAGTTGTTGCCAATACT
** * * * *
23037 TACAATATTCGTAACAACAAATTCTTAAGTTGTTACGAAATCATAATCTATTCGTAACAAATTTA
66 TACAATATTCGTAACAACAAAAACTAAAGTCGTTGCGAAATCATAATCTATTCGTAACAACTTTA
23102 T
131 T
*
23103 -AAGTCATTGC
1 AAAGTCGTTGC
23113 GCAATCAATT
Statistics
Matches: 349, Mismatches: 48, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
130 52 0.15
131 290 0.83
132 7 0.02
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (131 bp):
AAAGTCGTTGCCTAAGTGATTTTGATGTTATTTTACACAACACTTTTTTAGTTGTTGCCAATACT
TACAATATTCGTAACAACAAAAACTAAAGTCGTTGCGAAATCATAATCTATTCGTAACAACTTTA
T
Found at i:24528 original size:136 final size:136
Alignment explanation
Indices: 24279--24541 Score: 318
Period size: 136 Copynumber: 1.9 Consensus size: 136
24269 TTCAGACATT
* *
24279 TTATCGTTATACCACATTTTTTCACAACAATACCAAACATTATTTACATTTTCTACCACAATTTC
1 TTATCGTTATACCACATTTTTTCACAACAATACCAAACATTAGTTACATTTTCTACCACAATTTA
* * * *
24344 AAAAACCATTTTTCAAAAGCACTTCTTTCAAACCAAACTTTTATAAACCGCAATCTCAATACAAT
66 AAAAAACATTTTTCAAAAGCACTTCTCTCAAACCAAACTTTTATAAACCACAACCTCAATACAAT
24409 TAGGTC
131 TAGGTC
* * * * * *
24415 TTATCTTTCTACCACA-TTTTTCTACACCAATACCAAATATTAGTTACATTTTTCTATCGCAATT
1 TTATCGTTATACCACATTTTTTC-ACAACAATACCAAACATTAGTTACA-TTTTCTACCACAATT
* * * *
24479 TAAAAAAACACTTTTT-AAAATCACTTCTCT-AAACC-GAGTTTTTTCAAACCACAACCTCAATA
64 TAAAAAAACA-TTTTTCAAAAGCACTTCTCTCAAACCAAACTTTTAT-AAACCACAACCTCAATA
24541 C
127 C
24542 CGATTACAAT
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
135 12 0.11
136 57 0.53
137 33 0.31
138 5 0.05
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (136 bp):
TTATCGTTATACCACATTTTTTCACAACAATACCAAACATTAGTTACATTTTCTACCACAATTTA
AAAAAACATTTTTCAAAAGCACTTCTCTCAAACCAAACTTTTATAAACCACAACCTCAATACAAT
TAGGTC
Found at i:25383 original size:33 final size:33
Alignment explanation
Indices: 25341--25406 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
25331 CCAAAAACAG
*
25341 CGGGTCGCGCGCGGATCGCGACCCACCATGGTC
1 CGGGTCGCGCGCGGATCACGACCCACCATGGTC
*
25374 CGGGTCGCGCGCGGATCACGACCCGCCATGGTC
1 CGGGTCGCGCGCGGATCACGACCCACCATGGTC
25407 AATGTCGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.39, G:0.36, T:0.12
Consensus pattern (33 bp):
CGGGTCGCGCGCGGATCACGACCCACCATGGTC
Found at i:25418 original size:35 final size:33
Alignment explanation
Indices: 25343--25419 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
25333 AAAAACAGCG
* **
25343 GGTCGCGCGCGGATCGCGACCCACCATGGTCCG
1 GGTCGCGCGCGGATCACGACCCACCATGGTCAA
*
25376 GGTCGCGCGCGGATCACGACCCGCCATGGTCAA
1 GGTCGCGCGCGGATCACGACCCACCATGGTCAA
*
25409 TGTCGCGCGCG
1 GGTCGCGCGCG
25420 ACCCGTGTCG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.13, C:0.38, G:0.36, T:0.13
Consensus pattern (33 bp):
GGTCGCGCGCGGATCACGACCCACCATGGTCAA
Found at i:28153 original size:73 final size:74
Alignment explanation
Indices: 28008--28251 Score: 307
Period size: 73 Copynumber: 3.3 Consensus size: 74
27998 CATTAAGTTG
* * * ** * *
28008 CGTACAAGATAATTCTTTTAACAACGATAAAATATTACTGCCAAAATATATATGTAATGACTAAA
1 CGTAAAAGATAATTCTTTTAACAACGACAAAATGTCGCTGTCAAAATATATATGTAACGACTAAA
*
28073 AAATCGTTG
66 AAATCGTTA
* * * *
28082 CGTAAAAGATAATTCTTTTAACAATGA-AAAATGTCGCTATCAAAATATATATCTAACGACTACA
1 CGTAAAAGATAATTCTTTTAACAACGACAAAATGTCGCTGTCAAAATATATATGTAACGACTAAA
*
28146 AAGTCGTTA
66 AAATCGTTA
*
28155 CGTAAAAGATAATTCTTTTAACAACGAACAAAATGTCGTTGTC-AAA-ATATATGTAACGACTAA
1 CGTAAAAGATAATTCTTTTAACAACG-ACAAAATGTCGCTGTCAAAATATATATGTAACGACTAA
*
28218 AAACTCGTTA
65 AAAATCGTTA
28228 CGTAAAAGA-ATATTCTTTTAACAA
1 CGTAAAAGATA-ATTCTTTTAACAA
28252 TGAATATATA
Statistics
Matches: 149, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
72 1 0.01
73 107 0.72
74 29 0.19
75 12 0.08
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.30
Consensus pattern (74 bp):
CGTAAAAGATAATTCTTTTAACAACGACAAAATGTCGCTGTCAAAATATATATGTAACGACTAAA
AAATCGTTA
Found at i:28206 original size:75 final size:75
Alignment explanation
Indices: 28008--28351 Score: 296
Period size: 73 Copynumber: 4.7 Consensus size: 75
27998 CATTAAGTTG
* * * *** * *
28008 CGTACAAGATAATTCTTTTAACAACG-ATAAAATATTACTGCCAAAATATATATGTAATGACTAA
1 CGTAAAAGATAATTCTTTTAACAACGAACAAAATGTCGTTGTCAAAATATATATGTAACGACTAA
* *
28072 AAAATCGTTG
66 AAAGTCGTTA
* * * * *
28082 CGTAAAAGATAATTCTTTTAACAATG-A-AAAATGTCGCTATCAAAATATATATCTAACGACTAC
1 CGTAAAAGATAATTCTTTTAACAACGAACAAAATGTCGTTGTCAAAATATATATGTAACGACTAA
28145 AAAGTCGTTA
66 AAAGTCGTTA
28155 CGTAAAAGATAATTCTTTTAACAACGAACAAAATGTCGTTGTC-AAA-ATATATGTAACGACTAA
1 CGTAAAAGATAATTCTTTTAACAACGAACAAAATGTCGTTGTCAAAATATATATGTAACGACTAA
*
28218 AAACTCGTTA
66 AAAGTCGTTA
* * * * *
28228 CGTAAAAGA-ATATTCTTTTAACAATGAATATATAT-T-GTTGTTAAAATAT-T-TTTACACAGC
1 CGTAAAAGATA-ATTCTTTTAACAACGAACA-AAATGTCGTTGTCAAAATATATATGTA-AC-G-
* ** * *
28288 AATATTAAGTTGTTG
61 ACTAAAAAGTCGTTA
* * * *
28303 CGTAAAATAAAATTCTTTTAACAAC-AACAAAATGGCGTTGTTAAAATAT
1 CGTAAAAGATAATTCTTTTAACAACGAACAAAATGTCGTTGTCAAAATAT
28352 TTTTACGCAA
Statistics
Matches: 224, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
72 9 0.04
73 121 0.54
74 38 0.17
75 55 0.25
76 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (75 bp):
CGTAAAAGATAATTCTTTTAACAACGAACAAAATGTCGTTGTCAAAATATATATGTAACGACTAA
AAAGTCGTTA
Found at i:28352 original size:75 final size:75
Alignment explanation
Indices: 28264--28404 Score: 237
Period size: 75 Copynumber: 1.9 Consensus size: 75
28254 AATATATATT
*
28264 GTTGTTAAAATATTTTTACACAGCAATATTAAGTTGTTGCGTAAAATAAAATTCTTTTAACAACA
1 GTTGTTAAAATATTTTTACACAACAATATTAAGTTGTTGCGTAAAATAAAATTCTTTTAACAACA
28329 ACAAAATGGC
66 ACAAAATGGC
* * * *
28339 GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATATAATTCTTTTAGCAACA
1 GTTGTTAAAATATTTTTACACAACAATATTAAGTTGTTGCGTAAAATAAAATTCTTTTAACAACA
28404 A
66 A
28405 TAACATGACG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (75 bp):
GTTGTTAAAATATTTTTACACAACAATATTAAGTTGTTGCGTAAAATAAAATTCTTTTAACAACA
ACAAAATGGC
Found at i:33243 original size:21 final size:21
Alignment explanation
Indices: 33217--33284 Score: 111
Period size: 21 Copynumber: 3.2 Consensus size: 21
33207 TGCTAGGAGT
33217 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
33238 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
33259 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
33280 TCATT
1 TCATT
33285 AGAATTGCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:34017 original size:26 final size:23
Alignment explanation
Indices: 33972--34018 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
33962 TCCTTCTATT
33972 CATCTATCATCAAGTTTTTCATC
1 CATCTATCATCAAGTTTTTCATC
33995 CATCTCATCGATCAAAGTTTTTCA
1 CATCT-ATC-ATC-AAGTTTTTCA
34019 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 3 0.14
26 10 0.48
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (23 bp):
CATCTATCATCAAGTTTTTCATC
Found at i:34133 original size:8 final size:8
Alignment explanation
Indices: 34117--34159 Score: 61
Period size: 8 Copynumber: 5.2 Consensus size: 8
34107 CTTGTAGTTT
34117 AATAGAAAA
1 AATA-AAAA
34126 ATATAAAAA
1 A-ATAAAAA
34135 AAT-AAAA
1 AATAAAAA
34142 AATAAAAA
1 AATAAAAA
34150 AATAAAAA
1 AATAAAAA
34158 AA
1 AA
34160 ATTCGACCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.22
8 16 0.50
9 6 0.19
10 3 0.09
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (8 bp):
AATAAAAA
Found at i:34146 original size:15 final size:15
Alignment explanation
Indices: 34122--34158 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
34112 AGTTTAATAG
34122 AAAAATATAAAAAAAT
1 AAAAA-ATAAAAAAAT
34138 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
34153 AAAAAA
1 AAAAAA
34159 AATTCGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:38634 original size:10 final size:10
Alignment explanation
Indices: 38619--38651 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
38609 TCCATTCACA
38619 TTTTTTGGAT
1 TTTTTTGGAT
*
38629 TTTTTTGTA-
1 TTTTTTGGAT
38638 TTTTTTGGAT
1 TTTTTTGGAT
38648 TTTT
1 TTTT
38652 GAACCTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (10 bp):
TTTTTTGGAT
Found at i:38641 original size:8 final size:9
Alignment explanation
Indices: 38618--38651 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
38608 TTCCATTCAC
38618 ATTTTTTGG
1 ATTTTTTGG
*
38627 ATTTTTTTGT
1 A-TTTTTTGG
38637 ATTTTTTGG
1 ATTTTTTGG
38646 ATTTTT
1 ATTTTT
38652 GAACCTAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (9 bp):
ATTTTTTGG
Found at i:38949 original size:26 final size:27
Alignment explanation
Indices: 38919--38992 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
38909 AAGTGAACCT
* **
38919 AAAATGACCAAAATGCCCTTAG-TGTA
1 AAAATGACCAAAATGCCCCTAGACATA
*
38945 AAAATGACCAAAATGCCCCTGGACATA
1 AAAATGACCAAAATGCCCCTAGACATA
*
38972 CAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
38993 TGTGACCCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 20 0.49
27 21 0.51
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAGACATA
Found at i:42564 original size:16 final size:15
Alignment explanation
Indices: 42526--42567 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
42516 ACAGAGATTG
*
42526 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
42541 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
42556 ACTAGAAAACAA
1 AC-AGAAAACAA
42568 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.