Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008672.1 Corchorus olitorius cultivar O-4 contig08699, 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: 2054
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Found at i:25 original size:2 final size:2
Alignment explanation
Indices: 18--51 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8 AATAAGTTAG
18 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
52 AATTGTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1109 original size:22 final size:22
Alignment explanation
Indices: 1084--1270 Score: 134
Period size: 22 Copynumber: 8.5 Consensus size: 22
1074 ACAATCAAAC
* * *
1084 CAAAATTACATATAAAGATTAT
1 CAAAATTTCATATAGAGGTTAT
* *
1106 CAAATTTTCATAGT-GTGGTTAT
1 CAAAATTTCATA-TAGAGGTTAT
1128 CAAAATTTCATATAGAGGTTAT
1 CAAAATTTCATATAGAGGTTAT
*
1150 CAAAACTTCATAGT-GTA-GTTAT
1 CAAAATTTCATA-TAG-AGGTTAT
* * *
1172 C-AAATTTTATACAGAGGTTAC
1 CAAAATTTCATATAGAGGTTAT
* *
1193 CAAAATTTCATAAAAAGGTTAT
1 CAAAATTTCATATAGAGGTTAT
* * * *
1215 CAAAATTTCTTAGAAATGTTAAT
1 CAAAATTTCATATAGAGGTT-AT
* *
1238 -AAAATTTCATAT-GAAAGTTAA
1 CAAAATTTCATATAG-AGGTTAT
1259 CAAAATTTCATA
1 CAAAATTTCATA
1271 GGAAGGGAGG
Statistics
Matches: 131, Mismatches: 24, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.01
21 16 0.12
22 109 0.83
23 5 0.04
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATATAGAGGTTAT
Found at i:1191 original size:43 final size:44
Alignment explanation
Indices: 1084--1270 Score: 148
Period size: 44 Copynumber: 4.3 Consensus size: 44
1074 ACAATCAAAC
* * * * * *
1084 CAAAATTACATATAAAGATTATCAAATTTTCATAGTGTGGTTAT
1 CAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTTAT
* *
1128 CAAAATTTCATATAGAGGTTATCAAAACTTCATAGTGTAGTTAT
1 CAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTTAT
* * ***
1172 C-AAATTTTATACAGAGGTTACCAAAATTTCATA-AAAAGGTTAT
1 CAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTA-GTTAT
* * * * * *
1215 CAAAATTTCTTAGAAATGTTAAT-AAAATTTCATA-TGAAAGTTAA
1 CAAAATTTCATACAGAGGTT-ATCAAAATTTCATAGTG-TAGTTAT
1259 CAAAATTTCATA
1 CAAAATTTCATA
1271 GGAAGGGAGG
Statistics
Matches: 116, Mismatches: 23, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.01
43 34 0.29
44 78 0.67
45 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (44 bp):
CAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTTAT
Found at i:1353 original size:22 final size:22
Alignment explanation
Indices: 1297--1373 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
1287 AAATTTGTGC
**
1297 TTATCAAAATTTCCTAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
*
1319 TTAACAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
* *
1341 TTATGAAAATTTTAT-GGAGAGT
1 TTATCAAAATTTTATAGG-GAGG
1363 TTATCGAAAAT
1 TTATC-AAAAT
1374 ACATAGAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 2 0.04
22 39 0.85
23 5 0.11
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGG
Found at i:1457 original size:19 final size:20
Alignment explanation
Indices: 1406--1462 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
1396 TCATTCTCAT
*
1406 ATGGAGGTTATCGAAATTTC
1 ATGGAGGTTATCAAAATTTC
*
1426 ATGGTATGGTTATCAAAATTTT
1 ATGG-A-GGTTATCAAAATTTC
1448 AT-GAGGTTATCAAAA
1 ATGGAGGTTATCAAAA
1463 CTTTGATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 11 0.33
20 5 0.15
21 2 0.06
22 15 0.45
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (20 bp):
ATGGAGGTTATCAAAATTTC
Found at i:1550 original size:22 final size:22
Alignment explanation
Indices: 1503--1653 Score: 117
Period size: 22 Copynumber: 6.9 Consensus size: 22
1493 TTTAGTGTTA
* * *
1503 TTATTAAAATTTTATAA-GCAGA
1 TTATCAAAATTTCATAATG-AGG
* *
1525 TTATCAAAATTTCACATTGAGG
1 TTATCAAAATTTCATAATGAGG
* *
1547 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAATGAGG
* * *
1569 TTACCAAATTTTCATAATGTGG
1 TTATCAAAATTTCATAATGAGG
* * *
1591 TTATCAAATTTTCAT-AGGAAAG
1 TTATCAAAATTTCATAATG-AGG
*
1613 TTATCGAAATTTCATAATGAGG
1 TTATCAAAATTTCATAATGAGG
* * *
1635 CTATCAAATTTTCAAAATG
1 TTATCAAAATTTCATAATG
1654 TATTTATCAA
Statistics
Matches: 103, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
21 2 0.02
22 98 0.95
23 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGAGG
Found at i:1595 original size:66 final size:67
Alignment explanation
Indices: 1525--1676 Score: 164
Period size: 66 Copynumber: 2.3 Consensus size: 67
1515 TATAAGCAGA
* * * * *
1525 TTATCAAAATTTCACATTG-AGGTTATCAAAATTTCATAGTGTGGTTACCAAATTTTCATAATGT
1 TTATCAAAATTTCACATTGAAAGTTATCAAAATTTCATAATGAGGCTACCAAATTTTCAAAATGT
*
1589 GG
66 AG
* * * * *
1591 TTATCAAATTTTCATA-GGAAAGTTATCGAAATTTCATAATGAGGCTATCAAATTTTCAAAATGT
1 TTATCAAAATTTCACATTGAAAGTTATCAAAATTTCATAATGAGGCTACCAAATTTTCAAAATGT
*
1655 AT
66 AG
*
1657 TTATCAATATTTCTACATTG
1 TTATCAAAATTTC-ACATTG
1677 GAGCATGAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.94
67 2 0.03
68 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (67 bp):
TTATCAAAATTTCACATTGAAAGTTATCAAAATTTCATAATGAGGCTACCAAATTTTCAAAATGT
AG
Found at i:1626 original size:44 final size:44
Alignment explanation
Indices: 1525--1648 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
1515 TATAAGCAGA
* * * **
1525 TTATCAAAATTTCACATTGAGGTTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAATGAGGTTATCAAATTTTCATAGTGAAG
* * *
1569 TTACCAAATTTTCATAATGTGGTTATCAAATTTTCATAG-GAAAG
1 TTATCAAAATTTCATAATGAGGTTATCAAATTTTCATAGTG-AAG
* *
1613 TTATCGAAATTTCATAATGAGGCTATCAAATTTTCA
1 TTATCAAAATTTCATAATGAGGTTATCAAATTTTCA
1649 AAATGTATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
43 1 0.02
44 65 0.98
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGAGGTTATCAAATTTTCATAGTGAAG
Found at i:1661 original size:44 final size:43
Alignment explanation
Indices: 1525--1669 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 43
1515 TATAAGCAGA
* * * * * *
1525 TTATCAAAATTTCACATTGAGGTTATCAAAATTTCATAGTGTGG
1 TTATC-AAATTTCATAATGAGGTTATCAAATTTTCAAAATGTAG
* * * * *
1569 TTACCAAATTTTCATAATGTGGTTATCAAATTTTC-ATAGGAAAG
1 TTATCAAA-TTTCATAATGAGGTTATCAAATTTTCAAAATG-TAG
* *
1613 TTATCGAAATTTCATAATGAGGCTATCAAATTTTCAAAATGTAT
1 TTATC-AAATTTCATAATGAGGTTATCAAATTTTCAAAATGTAG
1657 TTATCAATATTTC
1 TTATCAA-ATTTC
1670 TACATTGGAG
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
43 6 0.08
44 66 0.85
45 6 0.08
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (43 bp):
TTATCAAATTTCATAATGAGGTTATCAAATTTTCAAAATGTAG
Done.