Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1832
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: 5899
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Found at i:507 original size:28 final size:28
Alignment explanation
Indices: 370--511 Score: 133
Period size: 28 Copynumber: 4.9 Consensus size: 28
360 ACAGTGGTGA
* *
370 TTTGAAAAGGGTGCCATTGACTTGCATGGGC
1 TTTG-AAAGAGTGCCACTGACTTG--TGGGC
* * *
401 TTTAAAAGGGTGCGCGCTGACTTGCGTGGGC
1 TTTGAAAGAGTGC-CACTGACTT--GTGGGC
* * *
432 TTTGAAAGAATGCCACTAACTCGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGC
460 TTTGAAAG-GATGCCACTGACTTGTGGGC
1 TTTGAAAGAG-TGCCACTGACTTGTGGGC
*
488 TTTGAAAGAGTGCCAATGACTTGT
1 TTTGAAAGAGTGCCACTGACTTGT
512 TGAGACTTGG
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
28 51 0.55
29 1 0.01
30 15 0.16
31 25 0.27
33 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (28 bp):
TTTGAAAGAGTGCCACTGACTTGTGGGC
Found at i:600 original size:28 final size:28
Alignment explanation
Indices: 538--1427 Score: 1273
Period size: 28 Copynumber: 31.2 Consensus size: 28
528 AGTACATATT
*
538 AAAGGAGTGCCACTGACTTGTGTGGGCTTTA
1 AAAGG-GTGCCACTGAC-T-TGTGGGCTTTG
569 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
597 AAAGAGTGCCACTGA-TTGTGGGCTTCG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
624 CAATGGTTCCACTGACTTGTGGGCTTCG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
652 CAATGGTGCCACTGACTTGTGGGCTTCG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
680 AAAGGGTGCCACTGACTTGTGGGCTCTA
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
*
708 AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
*
736 AAAGGGTG-CACTGATTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
763 AAAAGAGTGCCGCTGACTTGTGGGCTTTG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTG
792 AAAGGAGTGCCACTGACTTGTGGGCTTGATG
1 AAAGG-GTGCCACTGACTTGTGGGCTT--TG
*
823 AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
851 AAAAGAGTGCCACTGATTTGTGGGCTTTG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
880 AAAGAGTGCCACTGGCTTGT-GGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
907 AAAGGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGG-GTGCCACTGACTTGTGGGCTTTG
*
936 AAAGGGTGCCACTGAGTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
964 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
992 AAAAGAGTGCCACTGATTTGTGGGCTTTG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1021 AAAGGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGG-GTGCCACTGACTTGTGGGCTTTG
1050 AAAGGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGG-GTGCCACTGACTTGTGGGCTTTG
1079 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
*
1107 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1135 AAAAGAGTGCCACTGATTTGTGGGCTTTG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTG
*
1164 AAAGGAGTGCCACTAACTTGTGGGCTTTG
1 AAAGG-GTGCCACTGACTTGTGGGCTTTG
1193 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
*
1221 AAAGGGTGCCACTGACTTGTGGGTTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1249 AAAAGAGTGCCACTGATTTGTAGGCTTTG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1278 AAAGGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGG-GTGCCACTGACTTGTGGGCTTTG
1307 AAAGGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGG-GTGCCACTGACTTGTGGGCTTTG
1336 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1364 AAAAGAGTGCCACTGATTTGTGGGCTTTG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTG
*
1393 AAATGAGTGCCACTGACTTGTGGGCTTTG
1 AAA-GGGTGCCACTGACTTGTGGGCTTTG
1422 AAAGGG
1 AAAGGG
1428 ATGAACATTC
Statistics
Matches: 785, Mismatches: 57, Indels: 37
0.89 0.06 0.04
Matches are distributed among these distances:
27 50 0.06
28 352 0.45
29 340 0.43
30 31 0.04
31 12 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
AAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:1082 original size:143 final size:142
Alignment explanation
Indices: 538--1424 Score: 1331
Period size: 143 Copynumber: 6.2 Consensus size: 142
528 AGTACATATT
*
538 AAAGGAGTGCCACTGACTTGTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-G
1 AAAGG-GTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* * * * * * *
601 AGTGCCACTGA-TTGTGGGCTTCGCAATGGTTCCACTGACTTGTGGGCTTCGCAATGGTGCCACT
63 AGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
*
665 GACTTGTGGGCTTCG
128 GACTTGTGGGCTTTG
* * *
680 AAAGGGTGCCACTGACTTGTGGGCTCT-AAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGG-GT
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGT
* * *
743 G-CACTGATTTGTGGGCTTTGAAAAGAGTGCCGCTGACTTGTGGGCTTTGAAAGGAGTGCCACTG
66 GCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTG
807 ACTTGTGGGCTTGATG
129 ACTTGTGGGCTT--TG
* *
823 AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAA-GAGT
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGT
*
887 GCCACTGGCTTGT-GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
66 GCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
*
951 GTTGTGGGCTTTG
130 CTTGTGGGCTTTG
*
964 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGT
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGT
1029 GCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
66 GCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
1094 CTTGTGGGCTTTG
130 CTTGTGGGCTTTG
* *
1107 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGT
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGT
*
1172 GCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAC
66 GCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAC
*
1237 TTGTGGGTTTTG
131 TTGTGGGCTTTG
* * * *
1249 AAAAGAGTGCCACTGATTTGTAGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAG
*
1314 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
65 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTG
*
1379 ATTTGTGGGCTTTG
129 ACTTGTGGGCTTTG
*
1393 AAATGAGTGCCACTGACTTGTGGGCTTTGAAA
1 AAA-GGGTGCCACTGACTTGTGGGCTTTGAAA
1425 GGGATGAACA
Statistics
Matches: 690, Mismatches: 40, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
138 6 0.01
139 54 0.08
140 27 0.04
141 93 0.13
142 71 0.10
143 313 0.45
144 117 0.17
145 9 0.01
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (142 bp):
AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGT
GCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAC
TTGTGGGCTTTG
Found at i:2655 original size:1 final size:1
Alignment explanation
Indices: 2651--2693 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
2641 TTTTTTGCTA
* * * *
2651 TTTTTTCTTTTTTTTTGTTTTGTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2694 GGGTGTAACG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:2665 original size:11 final size:11
Alignment explanation
Indices: 2641--2694 Score: 65
Period size: 11 Copynumber: 4.6 Consensus size: 11
2631 GACCCTTCTA
2641 TTTTTTGCTATTT
1 TTTTTTG-T-TTT
2654 TTTCTTT-TTTT
1 TTT-TTTGTTTT
2665 TTGTTTTGTTTT
1 TT-TTTTGTTTT
2677 TTTTTTGTTTT
1 TTTTTTGTTTT
2688 TTTTTTG
1 TTTTTTG
2695 GGTGTAACGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
11 24 0.63
12 8 0.21
13 3 0.08
14 3 0.08
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:2671 original size:16 final size:15
Alignment explanation
Indices: 2652--2693 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
2642 TTTTTGCTAT
2652 TTTTTCTTTTTTTTTG
1 TTTTT-TTTTTTTTTG
2668 TTTTGTTTTTTTTTTG
1 TTTT-TTTTTTTTTTG
2684 TTTTTTTTTT
1 TTTTTTTTTT
2694 GGGTGTAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.24
16 18 0.72
17 1 0.04
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Done.