Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold901
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: 11884
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:113 original size:70 final size:68
Alignment explanation
Indices: 1--174 Score: 280
Period size: 70 Copynumber: 2.5 Consensus size: 68
* *
1 GAGGCTCAACTCACCTCT-GCAATATGAGTTGATTTTGAAAAACAAATTTAAAAATACCTCAGCG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAAAATA---CAACG
65 TGTCC-
63 TGTCCT
70 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAAAATACAACGTGT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAAAATACAACGTGT
135 CCT
66 CCT
*
138 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
175 CCTTGAAAGC
Statistics
Matches: 100, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
67 9 0.09
68 36 0.36
69 18 0.18
70 37 0.37
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (68 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAAAATACAACGTGT
CCT
Found at i:3249 original size:27 final size:27
Alignment explanation
Indices: 3192--3243 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
3182 TTTCAAACAC
*
3192 GGTCAGGTACAAAATTAAGGTTTTCAG
1 GGTCAGGTACAAAATTAAGGGTTTCAG
3219 GGTCAGGTACAAAATTAAGGGTTTC
1 GGTCAGGTACAAAATTAAGGGTTTC
3244 TAGGTCGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (27 bp):
GGTCAGGTACAAAATTAAGGGTTTCAG
Found at i:7704 original size:14 final size:15
Alignment explanation
Indices: 7674--7706 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7664 AAACTAAACC
*
7674 AAAATTAAAACCATA
1 AAAATTAAAAACATA
7689 AAAATTAAAAAC-TA
1 AAAATTAAAAACATA
7703 AAAA
1 AAAA
7707 CAACCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAACATA
Found at i:8484 original size:14 final size:14
Alignment explanation
Indices: 8456--8503 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
8446 TGATGTGAAT
8456 AATA-AAATATATAA
1 AATATAAATAT-TAA
8470 AATATAAATATTAA
1 AATATAAATATTAA
*
8484 AATATCAAAATATTAG
1 AATAT--AAATATTAA
8500 AATA
1 AATA
8504 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 12 0.40
15 6 0.20
16 12 0.40
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
AATATAAATATTAA
Found at i:8484 original size:23 final size:22
Alignment explanation
Indices: 8453--8507 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
8443 TAATGATGTG
*
8453 AATAATAAAATATATAAAATATA
1 AATAATAAAATAT-CAAAATATA
*
8476 AATATTAAAATATCAAAATATTA
1 AATAATAAAATATCAAAATA-TA
8499 GAATAATAA
1 -AATAATAA
8508 TAATTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.22
23 14 0.52
24 7 0.26
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AATAATAAAATATCAAAATATA
Found at i:8488 original size:8 final size:8
Alignment explanation
Indices: 8453--8503 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
8443 TAATGATGTG
*
8453 AATAATAA
1 AATATTAA
8461 AATATATAA
1 AATAT-TAA
8470 AATA-T-A
1 AATATTAA
8476 AATATTAA
1 AATATTAA
*
8484 AATATCAA
1 AATATTAA
*
8492 AATATTAG
1 AATATTAA
8500 AATA
1 AATA
8504 ATAATAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 5 0.14
7 2 0.06
8 22 0.61
9 7 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:8494 original size:16 final size:15
Alignment explanation
Indices: 8457--8503 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
8447 GATGTGAATA
8457 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
8473 AT-AAATATTAAAAT
1 ATAAAATATTAAAAT
*
8487 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
8503 A
1 A
8504 ATAATAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 14 0.50
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:8675 original size:22 final size:24
Alignment explanation
Indices: 8617--8676 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
8607 ATACTACATC
*
8617 AATATGTACATAATATAGTGTTAAA
1 AATATATACATAATATAG-GTTAAA
*
8642 AATACATACATAATATA-GTT-AA
1 AATATATACATAATATAGGTTAAA
*
8664 GATATATACATAA
1 AATATATACATAA
8677 GATAACATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 13 0.42
23 3 0.10
25 15 0.48
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (24 bp):
AATATATACATAATATAGGTTAAA
Found at i:8722 original size:22 final size:23
Alignment explanation
Indices: 8691--8745 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
8681 ACATGTAAAA
*
8691 AATATATATAAATAATATAATAT
1 AATATATATAAATAAAATAATAT
* *
8714 AA-ATATATACATAAAATAGTAT
1 AATATATATAAATAAAATAATAT
8736 AATATATATA
1 AATATATATA
8746 TACGTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AATATATATAAATAAAATAATAT
Found at i:8730 original size:13 final size:12
Alignment explanation
Indices: 8689--8739 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 12
8679 TAACATGTAA
8689 AAAATATAT-AT
1 AAAATATATAAT
8700 -AAATAATATAAT
1 AAAAT-ATATAAT
8712 ATAAATATATACAT
1 A-AAATATATA-AT
8726 AAAATAGTATAAT
1 AAAATA-TATAAT
8739 A
1 A
8740 TATATATACG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 4 0.12
11 4 0.12
12 2 0.06
13 13 0.38
14 11 0.32
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (12 bp):
AAAATATATAAT
Found at i:8746 original size:27 final size:26
Alignment explanation
Indices: 8643--8747 Score: 90
Period size: 27 Copynumber: 4.0 Consensus size: 26
8633 AGTGTTAAAA
* *
8643 ATACATACATAATATAGT-TAAGATAT
1 ATACATAAATAATATAATATAA-ATAT
* * *
8669 ATACATAAGATAACAT-GTA-AAAAAT
1 ATACATAA-ATAATATAATATAAATAT
*
8694 ATATATAAATAATATAATATAAATAT
1 ATACATAAATAATATAATATAAATAT
* *
8720 ATACATAAAATAGTATAATATATATAT
1 ATACAT-AAATAATATAATATAAATAT
8747 A
1 A
8748 CGTAATATAG
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
24 6 0.09
25 12 0.19
26 21 0.33
27 25 0.39
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (26 bp):
ATACATAAATAATATAATATAAATAT
Found at i:8757 original size:25 final size:26
Alignment explanation
Indices: 8692--8757 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
8682 CATGTAAAAA
* *
8692 ATATATAT-AAATAATATAATATAAAT
1 ATATACATAAAATAGTATAATAT-AAT
8718 ATATACATAAAATAGTATAATAT-AT
1 ATATACATAAAATAGTATAATATAAT
* *
8743 ATATACGTAATATAG
1 ATATACATAAAATAG
8758 AATTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.43
26 7 0.20
27 13 0.37
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (26 bp):
ATATACATAAAATAGTATAATATAAT
Found at i:8820 original size:23 final size:25
Alignment explanation
Indices: 8777--8822 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
8767 TATACCTAAT
8777 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
8802 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
8823 ACAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:9340 original size:30 final size:30
Alignment explanation
Indices: 9303--9465 Score: 238
Period size: 30 Copynumber: 5.4 Consensus size: 30
9293 TAGGTACAAG
* *
9303 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* * *
9333 AGGTGGTGGAAAAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
9363 TGGTGGTGGAAAATGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
9393 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
9423 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
9453 TAGTGGTGGAAAA
1 TGGTGGTGGAAAA
9466 AGTTAAGATT
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
29 2 0.02
30 119 0.98
ACGTcount: A:0.23, C:0.03, G:0.47, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:9796 original size:18 final size:17
Alignment explanation
Indices: 9772--9819 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
9762 TCAAAATATG
*
9772 GGCCCACATGCCTGTGT
1 GGCCCACATGCCCGTGT
*
9789 GAGCCCACATTCCCGTGT
1 G-GCCCACATGCCCGTGT
*
9807 GGCCCACACGCCC
1 GGCCCACATGCCC
9820 AGATTCGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.15, C:0.44, G:0.25, T:0.17
Consensus pattern (17 bp):
GGCCCACATGCCCGTGT
Done.