Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2219
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: 30132
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4722 original size:29 final size:29
Alignment explanation
Indices: 4687--4760 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
4677 GTTGTGAGAT
* *
4687 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
4716 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
4745 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
4761 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:11468 original size:13 final size:13
Alignment explanation
Indices: 11450--11474 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11440 ATTGGAGATA
11450 AAATAAATTAAAG
1 AAATAAATTAAAG
11463 AAATAAATTAAA
1 AAATAAATTAAA
11475 AAGGAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAATAAATTAAAG
Found at i:15520 original size:15 final size:17
Alignment explanation
Indices: 15502--15533 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
15492 TAGCATAATT
15502 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
15517 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
15534 CAAGTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:18090 original size:15 final size:15
Alignment explanation
Indices: 18070--18100 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18060 CACAACATCT
18070 GCAACAATTATTATG
1 GCAACAATTATTATG
*
18085 GCAACAATTGTTATG
1 GCAACAATTATTATG
18100 G
1 G
18101 TAACTCTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (15 bp):
GCAACAATTATTATG
Found at i:21897 original size:43 final size:42
Alignment explanation
Indices: 21827--21977 Score: 137
Period size: 44 Copynumber: 3.5 Consensus size: 42
21817 TCACGCCACT
*
21827 GTCCTAGACAAGGTCTT--ACATGAAATTAAATACGATGCCAAC
1 GTCCTAGACATGGTCTTACACAT-AAATTAAAT-CGATGCCAAC
*
21869 GTCCTAGACGTGGTCTTACACATAAATTATAAGTCGATGCCAAC
1 GTCCTAGACATGGTCTTACACATAAATTA-AA-TCGATGCCAAC
* * * ** *
21913 ATCCCAAACATGGTCTTACATGTAAATCATAAGTCGATG-CAAC
1 GTCCTAGACATGGTCTTACACATAAAT--TAAATCGATGCCAAC
* *
21956 GTCGTAGACGTGGTCTTACACA
1 GTCCTAGACATGGTCTTACACA
21978 AAAACACATA
Statistics
Matches: 87, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
42 15 0.17
43 25 0.29
44 43 0.49
45 2 0.02
46 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (42 bp):
GTCCTAGACATGGTCTTACACATAAATTAAATCGATGCCAAC
Found at i:23166 original size:47 final size:47
Alignment explanation
Indices: 23088--24299 Score: 2005
Period size: 47 Copynumber: 25.6 Consensus size: 47
23078 CCCTTCGGGA
* * * * * *
23088 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23135 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23182 CTTATCACATATAT--ACTTTCACATTCATCGCATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* **
23227 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAAAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23276 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23323 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23370 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23417 CTTATCACATATATATACAATTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23466 CTGATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23513 CTTATCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23560 CTTATCACATATATATACACTTTCACATTCATCACATCAGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23609 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23656 CTTATCACATATATATACGCTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23705 CTTATCATATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
23752 CTTATCACATATATACGCTTTTACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23799 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23846 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23893 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23940 CTTATCACATATATACACTTTCACATTCATCACTTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23987 CTTATCGCATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24034 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24081 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24128 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
24177 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24226 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24273 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
24300 TATTCAAATA
Statistics
Matches: 1102, Mismatches: 51, Indels: 24
0.94 0.04 0.02
Matches are distributed among these distances:
45 37 0.03
47 801 0.73
49 264 0.24
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:25831 original size:13 final size:13
Alignment explanation
Indices: 25813--25837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25803 TACTAAATTT
25813 TCATGGATTCAAA
1 TCATGGATTCAAA
25826 TCATGGATTCAA
1 TCATGGATTCAA
25838 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:26494 original size:43 final size:43
Alignment explanation
Indices: 26446--26532 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
26436 CAAGTCCTCC
26446 CTTTTGATTACATGCACTATTAGGTCCTTGTAGATTAGCCTAT
1 CTTTTGATTACATGCACTATTAGGTCCTTGTAGATTAGCCTAT
*
26489 CTTTTGATTACATGCACTATTAGGTCTTTGTAGATTAGCCTAT
1 CTTTTGATTACATGCACTATTAGGTCCTTGTAGATTAGCCTAT
26532 C
1 C
26533 ACATTTCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (43 bp):
CTTTTGATTACATGCACTATTAGGTCCTTGTAGATTAGCCTAT
Found at i:28107 original size:40 final size:40
Alignment explanation
Indices: 28075--28649 Score: 854
Period size: 40 Copynumber: 14.5 Consensus size: 40
28065 CCAGCATGAT
* * * * **
28075 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCATAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
28115 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28155 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28195 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28235 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
28275 TGCTCTTTGGAACTTAGTCCAGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28315 TGCTCTTCGAGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28355 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28395 TGCTCTTCGAGACTTAG-CCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28434 TGCTCTTC-GGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
28473 TGCTCTTC-GGACTTAGTCC-GATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
28511 TGCTCTTC-GGACTTAGCCCGGATAACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGAT-ACATCACTAGCACGAA
*
28551 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28591 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28631 TGCTCTTCGAGATTTAGCC
1 TGCTCTTCGGGACTTAGCC
28650 GGACATTTCA
Statistics
Matches: 494, Mismatches: 37, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
38 44 0.09
39 74 0.15
40 362 0.73
41 14 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Done.