Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018428.1 Corchorus olitorius cultivar O-4 contig18461, 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: 28921
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:924 original size:54 final size:54
Alignment explanation
Indices: 858--1378 Score: 640
Period size: 54 Copynumber: 9.7 Consensus size: 54
848 CTATATCAAT
* *
858 TGGAGATAAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTAGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
912 TGGAGATCAACTCTGGTCATCGAAAACTTCTTGAAACGACCGCACTGTATCAAT-
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATC-ATC
*
966 TGGAGAACAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1020 TGGAGATCAACTCTGGTCATTGAAAACTTCTTGGAACGACCGCACTGGATCAAT-
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATC-ATC
** * * * * *
1074 TAAAGATCAACTCTGATCATTGAAAACTTCTTGAAATAACCACACTAGATCATT
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1128 TGGAGATCAACCCTGATCATCGAAAACTTCTTGGAACGACCGCACTGGGTCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * *
1182 TAGAGATCAACCCTGATCATCGAGAACTTCTTGGAACGACCGCACTGGATCATT
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
1236 TGGAGATCAATTCCGATCATTGAAAACTTCTTGGAATGACTGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1290 TAG-GATCAACTCTGATCCA-AGAAAACTTCTTGGAATGACCGCACTGAATCATC
1 TGGAGATCAACTCTGAT-CATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
1343 TAGG-GATCAACTCTGATCATCG-AAACTTCTTGAAAT
1 T-GGAGATCAACTCTGATCATCGAAAACTTCTTGAAAT
1379 AAGATCAACT
Statistics
Matches: 405, Mismatches: 55, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
53 62 0.15
54 339 0.84
55 4 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
Found at i:1411 original size:35 final size:35
Alignment explanation
Indices: 1347--2129 Score: 1108
Period size: 35 Copynumber: 22.4 Consensus size: 35
1337 ATCATCTAGG
*
1347 GATCAACTCTGATCATCG-AAACTTCTTGAAATAA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
1381 GATCAACTATGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
1416 GATCAACTGTGACCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1451 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * *
1486 GATCAACTCTGATCATGGAAAACTTCTTGATAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
** *
1521 TTTCAACTCTGATCATCGAAAACTTCTTGAGATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
1556 GATCAACTCTGATCATGGAAAACTTCTTGAGATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * * **
1591 GATTAACTATGATCATCGAACACTTCTTGAAACAA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
1626 GATCAACTTTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
1661 GATCAACTCTGATTATCGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
1696 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
** * *
1731 TTTCAACTCTAATCATGGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
1766 GATCAACTCTGATCATGGAAAACTTCTTGAGATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
1801 GATCAACTCTGATCATGGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
1836 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
** *
1871 GATCAACTCTGATCAAGGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
1906 GATCAACTCTGATCATCAAAAACTTCTTG-AATCGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAT-GA
*
1941 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
** **
1976 TTTCAACTCTGATCATCGAAAACTTCTTGAAACAA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
2011 GATCAACTCTGATCATAGAAAACTTCTTGAGATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
2046 GATCAACTCTGATCATGGAAAACTTCTTGAAAT-A
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
2080 TGATCAACTCTGAT-ATTCGAAAACTTCTTGAAAT-A
1 -GATCAACTCTGATCA-TCGAAAACTTCTTGAAATGA
2115 TGATCAACTCTGATC
1 -GATCAACTCTGATC
2130 GTTGGAAAAT
Statistics
Matches: 673, Mismatches: 70, Indels: 10
0.89 0.09 0.01
Matches are distributed among these distances:
34 21 0.03
35 650 0.97
36 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
Found at i:1958 original size:19 final size:19
Alignment explanation
Indices: 1904--1959 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
1894 TTCTTGAAAG
1904 GAGATCAACTCTGATCATC
1 GAGATCAACTCTGATCATC
*
1923 -A-A-AAACTTCTTGA--ATC
1 GAGATCAAC-TC-TGATCATC
1939 GAGATCAACTCTGATCATC
1 GAGATCAACTCTGATCATC
1958 GA
1 GA
1960 AAACTTCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 7 0.25
19 8 0.29
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (19 bp):
GAGATCAACTCTGATCATC
Found at i:2226 original size:52 final size:54
Alignment explanation
Indices: 2170--2353 Score: 237
Period size: 54 Copynumber: 3.4 Consensus size: 54
2160 TCGCCTGGAG
* * *
2170 ATCAACTTAGATCTCTG-AAGCTT-TATGAAAGACTGCACAGGGTCATCTTAAA
1 ATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAA
*
2222 ATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAG
1 ATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAA
* * * * * **
2276 ATCAACTTAAATCTTTGAAAACTTCTATGAAATACCGCACAGGGCCATTTGATC
1 ATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAA
* *
2330 GTCAACTTAGATCTTTGAAAACTT
1 ATCAACTTAGATCTCTGAAAACTT
2354 TAAAAGATCG
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
52 17 0.15
53 5 0.04
54 95 0.81
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (54 bp):
ATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAA
Found at i:3740 original size:21 final size:21
Alignment explanation
Indices: 3716--3761 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3706 CTTTCCTCCG
3716 TCTTTTGCTTTTTCAACT-TTT
1 TCTTTT-CTTTTTCAACTCTTT
*
3737 TCTTTTCTTTTTCAATTCTTT
1 TCTTTTCTTTTTCAACTCTTT
3758 TCTT
1 TCTT
3762 ATTTCTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (21 bp):
TCTTTTCTTTTTCAACTCTTT
Found at i:3748 original size:20 final size:19
Alignment explanation
Indices: 3716--3781 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
3706 CTTTCCTCCG
3716 TCTTTTGCTTTTTCAACTTTT
1 TCTTTT-CTTTTTCAA-TTTT
3737 TCTTTTCTTTTTCAATTCTTT
1 TCTTTTCTTTTTCAA-T-TTT
* *
3758 TCTTAT-TTCTTCAA-TTT
1 TCTTTTCTTTTTCAATTTT
3775 TCTTTTC
1 TCTTTTC
3782 CTCTCCTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.21
20 17 0.44
21 14 0.36
ACGTcount: A:0.11, C:0.20, G:0.02, T:0.68
Consensus pattern (19 bp):
TCTTTTCTTTTTCAATTTT
Found at i:6922 original size:44 final size:45
Alignment explanation
Indices: 6866--6974 Score: 143
Period size: 44 Copynumber: 2.4 Consensus size: 45
6856 AAAAAGAAGT
6866 AGAT-AATAGTAAATAAATAGATAATAACTAAATT-TAAATA-AA
1 AGATAAATAGTAAATAAATAGATAATAACTAAATTATAAATATAA
* **
6908 AGGATAAATTGTAAATAAATAGATAATAGTTAAATTAATAAATATAA
1 A-GATAAATAGTAAATAAATAGATAATAACTAAATT-ATAAATATAA
*
6955 ATATAAATAGTAAATAAATA
1 AGATAAATAGTAAATAAATA
6975 AAAAAAATCT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.02
43 3 0.05
44 27 0.47
46 23 0.40
47 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.08, T:0.30
Consensus pattern (45 bp):
AGATAAATAGTAAATAAATAGATAATAACTAAATTATAAATATAA
Found at i:6941 original size:19 final size:19
Alignment explanation
Indices: 6865--6947 Score: 53
Period size: 19 Copynumber: 4.1 Consensus size: 19
6855 TAAAAAGAAG
6865 TAGATAATAG-TAAATAAA
1 TAGATAATAGTTAAATAAA
**
6883 TAGATAATAACTAAATTTAAA
1 TAGATAATAGTTAAA--TAAA
*
6904 TAAAAGGATAA-ATTGTAAATAAA
1 T---A-GATAATAGT-TAAATAAA
*
6927 TAGATAATAGTTAAATTAA
1 TAGATAATAGTTAAATAAA
6946 TA
1 TA
6948 AATATAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
18 9 0.18
19 18 0.35
20 3 0.06
21 5 0.10
23 5 0.10
24 2 0.04
25 9 0.18
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.31
Consensus pattern (19 bp):
TAGATAATAGTTAAATAAA
Found at i:6949 original size:27 final size:27
Alignment explanation
Indices: 6919--6976 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
6909 GGATAAATTG
*
6919 TAAATA-AATAGAT-AATAGTTAAATTAA
1 TAAATATAA-AGATAAATAG-TAAATAAA
*
6946 TAAATATAAATATAAATAGTAAATAAA
1 TAAATATAAAGATAAATAGTAAATAAA
6973 TAAA
1 TAAA
6977 AAAAATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (27 bp):
TAAATATAAAGATAAATAGTAAATAAA
Found at i:8366 original size:30 final size:30
Alignment explanation
Indices: 8332--8393 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
8322 ATTTTTATCT
8332 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
* *
8362 TGACTTTTCTCTTATACTCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
8392 TG
1 TG
8394 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.47
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:17825 original size:28 final size:28
Alignment explanation
Indices: 17785--17855 Score: 142
Period size: 28 Copynumber: 2.5 Consensus size: 28
17775 ACAAGGTCAG
17785 ATATTGGGCCTTATTGGATGAACAAAAC
1 ATATTGGGCCTTATTGGATGAACAAAAC
17813 ATATTGGGCCTTATTGGATGAACAAAAC
1 ATATTGGGCCTTATTGGATGAACAAAAC
17841 ATATTGGGCCTTATT
1 ATATTGGGCCTTATT
17856 TGCGAATGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (28 bp):
ATATTGGGCCTTATTGGATGAACAAAAC
Found at i:21506 original size:16 final size:16
Alignment explanation
Indices: 21485--21521 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
21475 AACTTAATGA
21485 TTTGATTTAAGAGTTC
1 TTTGATTTAAGAGTTC
21501 TTTGATTTAAGAGTTC
1 TTTGATTTAAGAGTTC
21517 TTTGA
1 TTTGA
21522 AGGGAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.51
Consensus pattern (16 bp):
TTTGATTTAAGAGTTC
Found at i:22988 original size:21 final size:21
Alignment explanation
Indices: 22964--23030 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
22954 GTAATATAAA
22964 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
22985 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
23005 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
23027 TAAT
1 TAAT
23031 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Found at i:23398 original size:203 final size:206
Alignment explanation
Indices: 23144--23559 Score: 664
Period size: 203 Copynumber: 2.0 Consensus size: 206
23134 TTCCTTAATA
* *
23144 ATAAATAAATCGGATCTTAATATTTTTAATTTATAATTTTGAAATTTTGTTTGACATTGATCTAA
1 ATAAATAAATCGGATCTTAATA-TTCT-ATTTATAATTTTGAAACTTTGTTTGACATTGATCTAA
* *
23209 TTTAATTT-AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATAT-AT-A
64 TTTAATTTAAAT-AATCAACCACTAATGTTCAACT-ACTTTTTTTGGTATAGTTATATATAATAA
*
23271 TAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAA-AAATTAA
127 TAATAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAGAAATTAA
*
23335 TAACATTCACCATTG
192 TAACATTCACCATTC
23350 ATAAATAAATCGGATCTTTAATA-TCT-TTTATAATTTTGAAACTTTGTTTGACATTGATCTAAT
1 ATAAATAAATCGGATC-TTAATATTCTATTTATAATTTTGAAACTTTGTTTGACATTGATCTAAT
* *
23413 TTAATTTAAATAATCAACCACTAATGTTCGACTACTTTTTTTGTTATAGTTATATATAATAATAA
65 TTAATTTAAATAATCAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTATATATAATAATAA
*
23478 TAATAATGTGTTGTATCTTATTTACTACAACTTTGTTAGTAATCTTAGACTTAAGAAATTAATAA
130 TAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAGAAATTAATAA
23543 CATTCACCATTC
195 CATTCACCATTC
23555 ATAAA
1 ATAAA
23560 GTTATTAAGC
Statistics
Matches: 196, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
202 21 0.11
203 66 0.34
204 59 0.30
205 28 0.14
206 16 0.08
207 6 0.03
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (206 bp):
ATAAATAAATCGGATCTTAATATTCTATTTATAATTTTGAAACTTTGTTTGACATTGATCTAATT
TAATTTAAATAATCAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTATATATAATAATAAT
AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAGAAATTAATAAC
ATTCACCATTC
Found at i:25481 original size:58 final size:58
Alignment explanation
Indices: 25378--25492 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
25368 ATAGCATCAT
*
25378 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
* * * *
25436 GCCTTGGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA
25493 TTTGATTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 35 0.69
59 16 0.31
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (58 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
Found at i:27266 original size:56 final size:55
Alignment explanation
Indices: 27180--27290 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 55
27170 TATCAGTTTC
*
27180 CTTTCATACAATAAATGTTATAATAAATCCTATCCTCCCTATCTCTACTTAATTAT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCC-CCCTATCTCTACTTAATTAT
27236 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTAT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTAT
27291 TCTAAAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 20 0.37
56 34 0.63
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (55 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTAT
Found at i:27418 original size:42 final size:42
Alignment explanation
Indices: 27359--27439 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
27349 TAAGGATCAG
27359 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
27401 GATTTGAGTTGAGTATTTTTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
27440 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Done.