Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2515
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: 46455
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:2712 original size:22 final size:22
Alignment explanation
Indices: 2682--2724 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2672 TTTGGTATTT
2682 GGGAATTGGTACGAAATGGTAG
1 GGGAATTGGTACGAAATGGTAG
*
2704 GGGATTTGGTACGAAATGGTA
1 GGGAATTGGTACGAAATGGTA
2725 ATGGTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.40, T:0.26
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAG
Found at i:3914 original size:30 final size:30
Alignment explanation
Indices: 3856--3914 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3846 TTGAAAATGT
* *
3856 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
3886 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
3915 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:8811 original size:48 final size:48
Alignment explanation
Indices: 8756--8847 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
8746 TTCTTTCTTC
* * *
8756 ATTCTCAATCT-ATTTTTCAGTTCTCTTTTCTTTTTCACACTCATTTTT
1 ATTCTCAATCTCA-TTTTCAATTCTCTTTTCTATCTCACACTCATTTTT
*
8804 ATTCTCAATCTCATTTTCAATTTTCTTTTCTATCTCACACTCAT
1 ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCAT
8848 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.01, T:0.54
Consensus pattern (48 bp):
ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCATTTTT
Found at i:8869 original size:15 final size:16
Alignment explanation
Indices: 8844--8875 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
8834 TATCTCACAC
8844 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
8860 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
8875 T
1 T
8876 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:9864 original size:11 final size:11
Alignment explanation
Indices: 9848--9887 Score: 64
Period size: 12 Copynumber: 3.6 Consensus size: 11
9838 AATACAAACT
9848 TTTTTTTTGAA
1 TTTTTTTTGAA
9859 TTTTTTTTTGAA
1 -TTTTTTTTGAA
9871 TTTTTTTTG-A
1 TTTTTTTTGAA
9881 TTTTTTT
1 TTTTTTT
9888 ACAATACCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 8 0.29
11 9 0.32
12 11 0.39
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:9864 original size:12 final size:12
Alignment explanation
Indices: 9847--9887 Score: 68
Period size: 11 Copynumber: 3.6 Consensus size: 12
9837 GAATACAAAC
9847 TTTTTTTTTGAA
1 TTTTTTTTTGAA
9859 TTTTTTTTTGAA
1 TTTTTTTTTGAA
9871 -TTTTTTTTG-A
1 TTTTTTTTTGAA
9881 TTTTTTT
1 TTTTTTT
9888 ACAATACCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 1 0.04
11 15 0.54
12 12 0.43
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:26351 original size:11 final size:10
Alignment explanation
Indices: 26326--26386 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
26316 ACCAATAAAA
26326 TAAA-TGAGC
1 TAAATTGAGC
*
26335 TGAATTGTAGC
1 TAAATTG-AGC
26346 TAAATTGAGC
1 TAAATTGAGC
**
26356 TCGATTGAGC
1 TAAATTGAGC
26366 TGAAA-TGAGC
1 T-AAATTGAGC
*
26376 TCAATTGAGC
1 TAAATTGAGC
26386 T
1 T
26387 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:26387 original size:20 final size:20
Alignment explanation
Indices: 26327--26387 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
26317 CCAATAAAAT
*
26327 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
26347 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
26368 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
26388 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:28477 original size:18 final size:18
Alignment explanation
Indices: 28456--28490 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28446 TTTTTCTTTT
28456 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
28474 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
28491 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:29412 original size:15 final size:15
Alignment explanation
Indices: 29379--29432 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
29369 TTTAACTTGA
* *
29379 TTTTTTTTGCTCACCT
1 TTTTTTTTTCTCA-AT
29395 TTTTTTTTTCTCAA-
1 TTTTTTTTTCTCAAT
29409 TTTTTTTTTCAATCAAT
1 TTTTTTTTTC--TCAAT
29426 TTTTTTT
1 TTTTTTT
29433 CGAATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 10 0.30
16 16 0.48
17 7 0.21
ACGTcount: A:0.13, C:0.15, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTTTTTTCTCAAT
Found at i:29433 original size:15 final size:14
Alignment explanation
Indices: 29395--29445 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
29385 TTGCTCACCT
29395 TTTTTTTTTCTCAA
1 TTTTTTTTTCTCAA
29409 TTTTTTTTTCAATCAA
1 TTTTTTTTTC--TCAA
*
29425 -TTTTTTTTC-GAA
1 TTTTTTTTTCTCAA
29437 TTTTTTTTT
1 TTTTTTTTT
29446 TGATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 2 0.06
13 8 0.24
14 10 0.30
15 9 0.27
16 4 0.12
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCTCAA
Found at i:29451 original size:12 final size:13
Alignment explanation
Indices: 29395--29455 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 13
29385 TTGCTCACCT
*
29395 TTTTTTTTTCTCAA
1 TTTTTTTTTC-GAA
29409 TTTTTTTTTC-AA
1 TTTTTTTTTCGAA
29421 TCAATTTTTTTTCGAA
1 T---TTTTTTTTCGAA
*
29437 TTTTTTTTTTG-A
1 TTTTTTTTTCGAA
29449 TTTTTTT
1 TTTTTTT
29456 GTTACTCCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
12 11 0.26
13 9 0.21
14 10 0.24
15 9 0.21
16 3 0.07
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:30829 original size:11 final size:10
Alignment explanation
Indices: 30804--30864 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
30794 ACCAATAAAA
30804 TAAA-TGAGC
1 TAAATTGAGC
*
30813 TGAATTGTAGC
1 TAAATTG-AGC
30824 TAAATTGAGC
1 TAAATTGAGC
**
30834 TCGATTGAGC
1 TAAATTGAGC
30844 TGAAA-TGAGC
1 T-AAATTGAGC
*
30854 TCAATTGAGC
1 TAAATTGAGC
30864 T
1 T
30865 TGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:30844 original size:20 final size:19
Alignment explanation
Indices: 30804--30864 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
30794 ACCAATAAAA
30804 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
30824 TAAATTGAGCTCGATTGAGC
1 TAAA-TGAGCTCGATTGAGC
*
30844 TGAAATGAGCTCAATTGAGC
1 T-AAATGAGCTCGATTGAGC
30864 T
1 T
30865 TGTCGGAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 23 0.62
21 13 0.35
22 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:35749 original size:46 final size:46
Alignment explanation
Indices: 35696--35789 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
35686 CAAAGAAAAG
*
35696 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
35742 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
35788 AC
1 AC
35790 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:40427 original size:23 final size:22
Alignment explanation
Indices: 40375--40427 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40365 TCCACGTCTT
*
40375 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40397 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40420 TTTCTTTT
1 TTTCTTTT
40428 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42696 original size:20 final size:20
Alignment explanation
Indices: 42673--42726 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
42663 AGTTTTTCCC
*
42673 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
42693 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
42713 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
42727 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:42708 original size:30 final size:30
Alignment explanation
Indices: 42673--42746 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
42663 AGTTTTTCCC
42673 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
42703 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
42733 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
42747 TGGCTTGAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:42736 original size:20 final size:20
Alignment explanation
Indices: 42673--42737 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
42663 AGTTTTTCCC
* * * *
42673 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
42693 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
42712 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
42733 AGCTC
1 AGCTC
42738 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.