Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023928.1 Corchorus olitorius cultivar O-4 contig23961, 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: 7748
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Found at i:3319 original size:163 final size:164
Alignment explanation
Indices: 3012--3336 Score: 433
Period size: 163 Copynumber: 2.0 Consensus size: 164
3002 TAAAAGTACG
*
3012 AATAATGGAAAACTTTACGTTTTCCGATTATACCCTTTTTTCAAATATATTTCTAAACTGACATT
1 AATAATGGAAAACTGTACGTTTTCCGATTATACCCTTTTTTCAAATATATTTCTAAACTGACATT
* *
3077 ATTAAAATTTATTATTTAAAAATTAATCATAAAATTTCAATTTGGACCGAATTTTAAGTTTGTAA
66 ATTAAAATTTATTATTT--AAATTAATCATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAA
3142 AATTGATTTTCATTGATGAACATGCAAATTTCTATT
129 AATTGATTTTCATTGATGAACATGCAAATTTCTATT
* * * * * * **
3178 AATAATGGGAAACTGTATGTTTT-TGATTGTACCC-TTTTTCAATTATATTTCTAAATTTCCATT
1 AATAATGGAAAACTGTACGTTTTCCGATTATACCCTTTTTTCAAATATATTTCTAAACTGACATT
* * * *
3241 ATTAAAATTTAGTATAATTT-TATTATTTA-AAAATTTCAATTTAGACCGAATTATAAGTTTGTC
66 ATTAAAATTTA-T-T-ATTTAAATTAATCATAAAATTTCAATTTAGACCGAATTATAAGTTTGTA
*
3304 AAATTGATTTTCATTGATGAATATGCAAATTTC
128 AAATTGATTTTCATTGATGAACATGCAAATTTC
3337 CTTACTATTA
Statistics
Matches: 140, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
163 63 0.45
164 42 0.30
165 10 0.07
166 21 0.15
167 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.44
Consensus pattern (164 bp):
AATAATGGAAAACTGTACGTTTTCCGATTATACCCTTTTTTCAAATATATTTCTAAACTGACATT
ATTAAAATTTATTATTTAAATTAATCATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAA
TTGATTTTCATTGATGAACATGCAAATTTCTATT
Found at i:3386 original size:20 final size:20
Alignment explanation
Indices: 3349--3387 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3339 TACTATTATT
3349 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
3369 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
3388 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:3577 original size:22 final size:22
Alignment explanation
Indices: 3552--3678 Score: 100
Period size: 22 Copynumber: 5.9 Consensus size: 22
3542 TGTCTCTGTG
3552 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
3574 TGGTTATTATAA--TCATGAGG
1 TGGTTATCAAAATTTCATAAGA
* *
3594 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
3617 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
3638 AGGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
3660 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
3679 GGATCAGGTT
Statistics
Matches: 81, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
20 15 0.19
21 4 0.05
22 61 0.75
23 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:3719 original size:68 final size:66
Alignment explanation
Indices: 3554--3732 Score: 186
Period size: 68 Copynumber: 2.7 Consensus size: 66
3544 TCTCTGTGTG
* * * *
3554 GTTATCAAAATTTCATAAGATGGTTATTATAA--TCATGAG-GTGGTTACCAAAATTTCATATGG
1 GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATATGG
3616 AA
65 AA
*
3618 GTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GGA
1 GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
3682 TCA
66 --A
* * ** ** *
3685 GGTTATTAAATTTTTTTAGGAAGGTTATTGAAATTTCATAGTATGGTT
1 -GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTT
3733 TTCACAATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 27 0.28
65 5 0.05
66 24 0.25
67 1 0.01
68 39 0.41
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (66 bp):
GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
A
Found at i:3732 original size:22 final size:21
Alignment explanation
Indices: 3552--3732 Score: 75
Period size: 22 Copynumber: 8.2 Consensus size: 21
3542 TGTCTCTGTG
* *
3552 TGGTTATCAAAATTTCATAAGA
1 TGGTTAT-TAAATTTCATAGGA
3574 TGGTTATTATAA--TCATGAGG-
1 TGGTTATTA-AATTTCAT-AGGA
**
3594 TGGTTACCAAAATTTCATATGGA
1 TGGTTA-TTAAATTTCATA-GGA
* * *
3617 -AGTTATCAAAATTTCATGGGA
1 TGGTTAT-TAAATTTCATAGGA
* *
3638 AGGTTATCAAAATTTCATAGTG-
1 TGGTTAT-TAAATTTCATAG-GA
**
3660 TGGTTACCAAAATTTCATAGGA
1 TGGTTA-TTAAATTTCATAGGA
**
3682 TCAGGTTATTAAATTTTTTTAGGA
1 T--GGTTATTAAA-TTTCATAGGA
* *
3706 AGGTTATTGAAATTTCATAGTA
1 TGGTTATT-AAATTTCATAGGA
3728 TGGTT
1 TGGTT
3733 TTCACAATTT
Statistics
Matches: 123, Mismatches: 20, Indels: 32
0.70 0.11 0.18
Matches are distributed among these distances:
20 12 0.10
21 9 0.07
22 82 0.67
23 7 0.06
24 13 0.11
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (21 bp):
TGGTTATTAAATTTCATAGGA
Found at i:3821 original size:44 final size:43
Alignment explanation
Indices: 3768--3929 Score: 157
Period size: 44 Copynumber: 3.7 Consensus size: 43
3758 ATCAAAGAGA
*
3768 TTATCAAAATGTCATAGCGAGGTTA-TAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTACTAA-AATTTCATAGTGTGG
* * * *
3812 TTAACAAAATTTCATAAGGAGGTTACTAATATTTCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTACTAAAATTTCATAGTGTGG
* * * ** *
3856 TTATCAAAATTTAATAGTGTGGTTATTAAAATTTTTTAGTGTGC
1 TTATCAAAATTTCATAG-GAGGTTACTAAAATTTCATAGTGTGG
*
3900 TTATCAAAATTTCATATGAAGGTTA-TAAAA
1 TTATCAAAATTTCATA-GGAGGTTACTAAAA
3930 GTCTTAATTT
Statistics
Matches: 96, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
43 7 0.07
44 83 0.86
45 6 0.06
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGAGGTTACTAAAATTTCATAGTGTGG
Found at i:3893 original size:149 final size:147
Alignment explanation
Indices: 3619--3890 Score: 338
Period size: 149 Copynumber: 1.8 Consensus size: 147
3609 CATATGGAAG
* * *
3619 TTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATC
1 TTATCAAAATGTCATGCGAAGGTTATCAAAATTTCATAGTGTGGTTAACAAAATTTCATAGGA--
* ** ** * *
3684 AGGTTATTAAATTTTTTTAGGAAGGTTATTGAAATTTCATAGTATGGTTTTCACAATTTTATAAA
64 AGGTTACTAAATTTTCATAGGAAGGTTATCAAAATTTAATAGTATGGTTTTCAAAATTTTATAAA
3749 AATTAGGTTATCAAAGAGA
129 AATTAGGTTATCAAAGAGA
3768 TTATCAAAATGTCATAGCG-AGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGG
1 TTATCAAAATGTCAT-GCGAAGGTTATCAA-AATTTCATAGTGTGGTTAACAAAATTTCAT-AGG
* *
3831 -AGGTTACT-AATATTTCATAGGGAGGTTATCAAAATTTAATAGTGTGGTTATT-AAAATTTT
63 AAGGTTACTAAAT-TTTCATAGGAAGGTTATCAAAATTTAATAGTATGGTT-TTCAAAATTTT
3891 TTAGTGTGCT
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
146 3 0.03
147 44 0.42
148 4 0.04
149 50 0.47
150 5 0.05
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (147 bp):
TTATCAAAATGTCATGCGAAGGTTATCAAAATTTCATAGTGTGGTTAACAAAATTTCATAGGAAG
GTTACTAAATTTTCATAGGAAGGTTATCAAAATTTAATAGTATGGTTTTCAAAATTTTATAAAAA
TTAGGTTATCAAAGAGA
Found at i:3912 original size:66 final size:65
Alignment explanation
Indices: 3768--3929 Score: 166
Period size: 66 Copynumber: 2.5 Consensus size: 65
3758 ATCAAAGAGA
* * *
3768 TTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
1 TTATCAAAATTTCATAGGGAGGTTATAA-AATTTAATAGTGTGGTTAACAAAATTTCATAAGGAG
*
3833 G
65 C
* ** * *
3834 TTA-CTAATATTTCATAGGGAGGTTATCAAAATTTAATAGTGTGGTTATTAAAATTT-TTTAGTG
1 TTATC-AAAATTTCATAGGGAGGTTAT-AAAATTTAATAGTGTGGTTAACAAAATTTCATAAG-G
*
3897 TGC
63 AGC
* *
3900 TTATCAAAATTTCATATGAAGGTTATAAAA
1 TTATCAAAATTTCATAGGGAGGTTATAAAA
3930 GTCTTAATTT
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
65 8 0.10
66 68 0.86
67 3 0.04
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (65 bp):
TTATCAAAATTTCATAGGGAGGTTATAAAATTTAATAGTGTGGTTAACAAAATTTCATAAGGAGC
Found at i:4037 original size:21 final size:24
Alignment explanation
Indices: 3969--4052 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 24
3959 TGATAGAAGG
* *
3969 TTATC-AAATCTCATAGAG-TA-A
1 TTATCGAAATTTCATAGAGACAGA
*
3990 TTATCGAAATTTCATAGAGATCGGA
1 TTATCGAAATTTCATAGAGA-CAGA
4015 TTATCGAAATTT-ATAG-GA-AGA
1 TTATCGAAATTTCATAGAGACAGA
* *
4036 TTAGCAAAATTTCATAG
1 TTATCGAAATTTCATAG
4053 TGTTGTTATC
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
21 17 0.33
22 16 0.31
23 2 0.04
24 4 0.08
25 13 0.25
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (24 bp):
TTATCGAAATTTCATAGAGACAGA
Found at i:4065 original size:22 final size:22
Alignment explanation
Indices: 3768--4159 Score: 121
Period size: 22 Copynumber: 17.6 Consensus size: 22
3758 ATCAAAGAGA
* * *
3768 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGAGAAG
* **
3790 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGAGAAG
* *
3812 TTAACAAAATTTCATA-AGGAGG
1 TTATCAAAATTTCATAGA-GAAG
* * *
3834 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATAGAGAAG
* * **
3856 TTATCAAAATTTAATAGTGTGG
1 TTATCAAAATTTCATAGAGAAG
* ** * *
3878 TTATTAAAATTTTTTAGTG-TG
1 TTATCAAAATTTCATAGAGAAG
*
3899 CTTATCAAAATTTCATATGA-AGG
1 -TTATCAAAATTTCATA-GAGAAG
* *
3922 TTATAAAAGTCTTAATTTCATA-AGGAG
1 TTAT-CAA-----AATTTCATAGAGAAG
* * *
3949 -TACCAAAATTTGATAGA-AGG
1 TTATCAAAATTTCATAGAGAAG
*
3969 TTATC-AAATCTCATAGAGTAA-
1 TTATCAAAATTTCATAGAG-AAG
* *
3990 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGAGA--AG
*
4014 ATTATCGAAATTT-ATAG-GAAG
1 -TTATCAAAATTTCATAGAGAAG
* * **
4035 ATTAGCAAAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGAGAAG
*
4058 TTATCAAAATTACATA-ATGACA-
1 TTATCAAAATTTCATAGA-GA-AG
* **
4080 ATATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGAGAAG
* * *
4102 TCAACAAAATTTTATAGAGAAG
1 TTATCAAAATTTCATAGAGAAG
*
4124 TTATCAAAATTTCATAAAG-AG
1 TTATCAAAATTTCATAGAGAAG
*
4145 ATTATCAAATTTTCA
1 -TTATCAAAATTTCA
4160 AAATGTGATT
Statistics
Matches: 278, Mismatches: 60, Indels: 64
0.69 0.15 0.16
Matches are distributed among these distances:
20 19 0.07
21 28 0.10
22 188 0.68
23 12 0.04
24 4 0.01
25 14 0.05
26 3 0.01
27 1 0.00
28 9 0.03
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGAAG
Found at i:4400 original size:22 final size:22
Alignment explanation
Indices: 4265--4721 Score: 229
Period size: 22 Copynumber: 21.0 Consensus size: 22
4255 CTATGGAGTA
*
4265 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
4285 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
4307 ATTAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
4329 TTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
** * *
4351 ATCAAAATTTCATA-CTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
4373 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
4395 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
4417 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
4439 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
4455 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
4477 ATCAAAATTTTATAGCAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* ** * *
4499 ATCACAATTTCATAATGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
4521 ATTAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * *
4543 A-CTAACAA-TTGAAATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * * ** *
4565 CTTAGATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
4587 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
4609 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
** *
4632 ATCAAAATTTCATTCGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
4654 ATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
4676 TTCAAAATTCCTTAGGTAGGTT
1 ATCAAAATTTCATAGGGAGGTT
4698 ATCAAAAATTTCATAGGGAGGTT
1 ATC-AAAATTTCATAGGGAGGTT
4721 A
1 A
4722 AAAAAAATTT
Statistics
Matches: 318, Mismatches: 100, Indels: 35
0.70 0.22 0.08
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 12 0.04
21 6 0.02
22 247 0.78
23 38 0.12
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:4789 original size:22 final size:22
Alignment explanation
Indices: 4764--4815 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
4754 ATAGTATCGC
*
4764 TATTAAAGTTTCAT-AGGAAGGT
1 TATTAAAATTTCATAAGG-AGGT
*
4786 TATTAAAATTTGATAAGGAGGT
1 TATTAAAATTTCATAAGGAGGT
*
4808 TATCAAAA
1 TATTAAAA
4816 ATAGTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (22 bp):
TATTAAAATTTCATAAGGAGGT
Done.