Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2615
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: 10701
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Found at i:195 original size:32 final size:31
Alignment explanation
Indices: 92--273 Score: 148
Period size: 30 Copynumber: 6.0 Consensus size: 31
82 TTTTTCAGCC
*
92 CACAAGTCAGTGGCAACCT-T-TAAAAG-CC-
1 CACAAGTCGGTGGCAACCTCTCT-AAAGCCCA
** * * *
120 CACAAGTTAGTGGCACCCTTTTCAAAAG-CC-
1 CACAAGTCGGTGGCAACC-TCTCTAAAGCCCA
* **
150 CACAAGTCAGTGGCATATTTCTCTAAAGCCCA
1 CACAAGTCGGTGGCA-ACCTCTCTAAAGCCCA
* *
182 CACAAGTTGGTGGCAACCCCTC-AAAGCCCA
1 CACAAGTCGGTGGCAACCTCTCTAAAGCCCA
*
212 CACAAGTCGATGGCAACCCTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTCTCTAAAGCCCA
244 CACAAGTCGGTGGCAACC-CTTCT-AAGCCCA
1 CACAAGTCGGTGGCAACCTC-TCTAAAGCCCA
274 ATATAGCTGG
Statistics
Matches: 127, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
28 16 0.13
29 1 0.01
30 58 0.46
31 16 0.13
32 36 0.28
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.19
Consensus pattern (31 bp):
CACAAGTCGGTGGCAACCTCTCTAAAGCCCA
Found at i:196 original size:62 final size:62
Alignment explanation
Indices: 88--273 Score: 196
Period size: 62 Copynumber: 3.1 Consensus size: 62
78 TTTCTTTTTC
* * *
88 AGCCCACAAGTCAGTGGCAACCTT-T-AAAAG-CC-CACAAGTTAGTGGC-ACCCTTTTCAAA
1 AGCCCACAAGTCAGTGGCAACCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCCTTCTC-AA
*
146 AGCCCACAAGTCAGTGGCATA-TTTCTCTAAAGCCCACACAAGTTGGTGGCAACCC--CTCAA
1 AGCCCACAAGTCAGTGGCA-ACCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCCTTCTCAA
* *
206 AGCCCACACAAGTC-GATGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT--A
1 AG-CC-CACAAGTCAG-TGGCAACCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCCTTCTCAA
268 AGCCCA
1 AGCCCA
274 ATATAGCTGG
Statistics
Matches: 109, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
58 21 0.19
59 2 0.02
60 10 0.09
61 10 0.09
62 60 0.55
63 4 0.04
64 2 0.02
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.18
Consensus pattern (62 bp):
AGCCCACAAGTCAGTGGCAACCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCCTTCTCAA
Found at i:537 original size:49 final size:49
Alignment explanation
Indices: 266--1469 Score: 1449
Period size: 49 Copynumber: 24.7 Consensus size: 49
256 GCAACCCTTC
* * *
266 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-GGCACCTTCATCTT
316 TAAGTCCAATATAGCTGGCCTTGAATCAGCA-ATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
364 TAAGTCCAATGTAGCGGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
407 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* * * * *
459 TAAGTCCAATGTAGCTGGCGTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
508 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
557 TAAGACC-ATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
605 TAAGTCCAATATAGCTGGCC-TGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
652 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
695 TAAGTCCAAT-TAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* * *
746 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCA-T---CTT
* * * *
799 TAAGTACAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
848 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-CATCTT
* * *
897 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
946 TAAGACCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
995 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1043 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1086 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* * * *
1138 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1187 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * * *
1236 TAAGTCCAATGTAGCTGGCCTCGACTCAGTACATTGGCA-CTTGCACACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTT
* *
1287 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1335 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATT-GCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1383 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
1435 TAAGTTCAA-GTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
1470 ACATCATTTT
Statistics
Matches: 999, Mismatches: 109, Indels: 91
0.83 0.09 0.08
Matches are distributed among these distances:
42 26 0.03
43 91 0.09
45 3 0.00
47 25 0.03
48 225 0.23
49 347 0.35
50 68 0.07
51 51 0.05
52 122 0.12
53 41 0.04
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:715 original size:21 final size:21
Alignment explanation
Indices: 648--715 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
638 TGGCACCTCA
648 CCTTTAAGTCCAATGTAGCTGG
1 CCTTTAAGTCCAAT-TAGCTGG
* * *
670 CCTTGAA-TCAGCACATTGGC--A
1 CCTTTAAGTC--CA-ATTAGCTGG
691 CCTTTAAGTCCAATTAGCTGG
1 CCTTTAAGTCCAATTAGCTGG
712 CCTT
1 CCTT
716 GAATCAGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 13
0.64 0.11 0.25
Matches are distributed among these distances:
19 5 0.15
20 2 0.06
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (21 bp):
CCTTTAAGTCCAATTAGCTGG
Found at i:1104 original size:340 final size:339
Alignment explanation
Indices: 266--1426 Score: 1580
Period size: 340 Copynumber: 3.4 Consensus size: 339
256 GCAACCCTTC
* * *
266 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGGCACCTTTATCTTTAAGTCCAATATAGC
1 TAAGTCCAATATAGCTGGCCCTGAATCAGCATATT-GGCACCTTCATCTTTAAGTCCAATATAGC
* *
331 TGGCCTTGAATCAGCA-ATTGGCACCTTCATCTTTAAGTCCAATGTAGCGGGCCTTGAATCAGCA
65 TGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
395 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTT
130 CATCGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTT
* *
460 AAGTCCAATGTAGCTGGCGTTGACTCAGCACATTGGCACCTTCACCATTAAGCCCAATATAGCTG
195 AAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTG
*
525 GCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC-ATATAGCTGGCCCTGAATCAGCATA
260 GCCTTGAATCAGCATATTGGCA-CTTTATCTTTAAGACCAATATAGCTGGCCTTGAATCAGCATA
589 TTGGCACCTTCATCTT
324 TTGGCACCTTCATCTT
* * *
605 TAAGTCCAATATAGCTGG-CCTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCT
*
668 GGCCTTGAATCAGCACATTGG------CACCTTTAAGTCCAAT-TAGCTGGCCTTGAATCAGCAT
66 GGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
* * *
726 ATCGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
131 ATCGGCA-------C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT--
* * * * * * * * * *
791 TT-CACCATTAAGTACAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCC
185 TTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCC
* * * * * * *
855 AATGTAGCTGGCCTTGACTCAGCACATTGGCACTTGCACCATTAAGCCCAATATAGCTGGCCTTG
250 AATATAGCTGGCCTTGAATCAGCATATTGGCACTT-TATCTTTAAGACCAATATAGCTGGCCTTG
*
920 AATCAGCATATTGGCACCTTTATCTT
314 AATCAGCATATTGGCACCTTCATCTT
*
946 TAAGACCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCT
1 TAAGTCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCT
1011 GGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
66 GGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
* *
1075 ATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTA
131 ATCGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTA
1140 AGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGG
196 AGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGG
* * * * * *
1205 CCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCTGGCCTCGACTCAGTACAT
261 CCTTGAATCAGCATATTGGCAC-TTTATCTTTAAGACCAATATAGCTGGCCTTGAATCAGCATAT
* *
1270 TGGCA-CTTGCACACCAT
325 TGGCACCTT---CATCTT
* * *
1287 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* * * *
1351 GGCCTTGACTCAGCACATT-GCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
66 GGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
1415 ATCGGCACCTTT
131 ATCGGCACCTTT
1427 TCCATCTTTA
Statistics
Matches: 716, Mismatches: 78, Indels: 55
0.84 0.09 0.06
Matches are distributed among these distances:
330 25 0.03
331 15 0.02
336 35 0.05
337 12 0.02
338 19 0.03
339 186 0.26
340 251 0.35
341 67 0.09
342 22 0.03
343 42 0.06
348 16 0.02
349 26 0.04
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (339 bp):
TAAGTCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCT
GGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
ATCGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTA
AGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGG
CCTTGAATCAGCATATTGGCACTTTATCTTTAAGACCAATATAGCTGGCCTTGAATCAGCATATT
GGCACCTTCATCTT
Found at i:2353 original size:13 final size:13
Alignment explanation
Indices: 2335--2359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2325 CATAAAATGT
2335 TGTATCGATACAA
1 TGTATCGATACAA
2348 TGTATCGATACA
1 TGTATCGATACA
2360 TATTTTTTTT
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):
TGTATCGATACAA
Found at i:2441 original size:13 final size:13
Alignment explanation
Indices: 2423--2447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2413 ATTACTCAAA
2423 TGTATCGATACAT
1 TGTATCGATACAT
2436 TGTATCGATACA
1 TGTATCGATACA
2448 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2530 original size:51 final size:52
Alignment explanation
Indices: 2456--2578 Score: 214
Period size: 51 Copynumber: 2.4 Consensus size: 52
2446 CACTGATCTT
*
2456 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTA-TAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
2506 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
2558 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2579 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
50 19 0.28
51 26 0.38
52 24 0.35
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:10560 original size:9 final size:9
Alignment explanation
Indices: 10512--10564 Score: 70
Period size: 9 Copynumber: 5.8 Consensus size: 9
10502 CCTTGCACCA
*
10512 AAAAAAAAA
1 AAAAAAAAC
*
10521 AAAAAACAAA
1 AAAAAA-AAC
10531 AAAAAAAAC
1 AAAAAAAAC
10540 AAAAAAAAC
1 AAAAAAAAC
*
10549 AAAAAAAGC
1 AAAAAAAAC
10558 AAAAAAA
1 AAAAAAA
10565 TAGAAGGGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
9 32 0.78
10 9 0.22
ACGTcount: A:0.91, C:0.08, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:10564 original size:1 final size:1
Alignment explanation
Indices: 10511--10555 Score: 63
Period size: 1 Copynumber: 45.0 Consensus size: 1
10501 TCCTTGCACC
* * *
10511 AAAAAAAAAAAAAAAACAAAAAAAAAAACAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10556 GCAAAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.