Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3750
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: 40585
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:1404 original size:102 final size:101
Alignment explanation
Indices: 1209--1468 Score: 364
Period size: 102 Copynumber: 2.6 Consensus size: 101
1199 AACCGTTATT
* * * *
1209 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCTTCGGGGA
* *
1274 ATCAGCACATAGCAACCCCCTTTTATTTCAGAGATAC
65 ATCAGCACATAGCAACCCCCTTTCATTTCAAAGATAC
1311 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGTGGGAATCAGCACTTAGCAACCC-TCGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-G-GGGAATCAGCACTTAGCAACCCTTCGGGG
1374 AATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATAC
64 AATCAGCACATAGCAACCCCCTTT--CATTTCAAAGATAC
* * **
1413 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAACACACAGCAACCC
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCC
1469 CTTTATGTAC
Statistics
Matches: 143, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
100 7 0.05
101 41 0.29
102 75 0.52
103 20 0.14
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (101 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCTTCGGGGAA
TCAGCACATAGCAACCCCCTTTCATTTCAAAGATAC
Found at i:7634 original size:26 final size:26
Alignment explanation
Indices: 7599--7648 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
7589 AATGTGAAAG
*
7599 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
7625 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
7649 AGTTCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.24, G:0.34, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:7655 original size:103 final size:103
Alignment explanation
Indices: 7521--7784 Score: 399
Period size: 103 Copynumber: 2.6 Consensus size: 103
7511 GTTGTACATA
** *
7521 AAGGGGTTGCTGTGTG-TGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
7585 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCC
66 CTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
7623 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
7687 TCTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
7726 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
7785 AATAACGGTT
Statistics
Matches: 147, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
102 38 0.26
103 108 0.73
104 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:9136 original size:79 final size:79
Alignment explanation
Indices: 9005--9171 Score: 235
Period size: 79 Copynumber: 2.1 Consensus size: 79
8995 GTTACAACCA
** * * *
9005 AACTCCCTCAAGTCTTCTTTTAGTTTGCCCATTCCTCCATCACGTCAAATTTTCCTATCTTCATC
1 AACTCCCTCAAGTCCCCTTTCAGTTCGCCCATTCCTCCATCACGCCAAATTTTCCTATCTTCATC
*
9070 TAACCCGTTAAAGT
66 TAACCCGTCAAAGT
* * * *
9084 AACTCCCTCGAGTCCCCTTTCAGTTCGTCCATTCCTCCATTATGCCAAATTTTCCTATCTTCATC
1 AACTCCCTCAAGTCCCCTTTCAGTTCGCCCATTCCTCCATCACGCCAAATTTTCCTATCTTCATC
*
9149 TAACCTGTCAAAGT
66 TAACCCGTCAAAGT
9163 AACTCCCTC
1 AACTCCCTC
9172 TGTACTCCGC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.22, C:0.34, G:0.08, T:0.36
Consensus pattern (79 bp):
AACTCCCTCAAGTCCCCTTTCAGTTCGCCCATTCCTCCATCACGCCAAATTTTCCTATCTTCATC
TAACCCGTCAAAGT
Found at i:22778 original size:24 final size:24
Alignment explanation
Indices: 22743--22794 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
22733 CTGAATTGAT
*
22743 TTTTACAATTTTATAATATTTTAA
1 TTTTACAATTTTATAATAATTTAA
* *
22767 TTTTA-AATTTTTTTAGTAATTTAA
1 TTTTACAA-TTTTATAATAATTTAA
22791 TTTT
1 TTTT
22795 TTAAACCGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTACAATTTTATAATAATTTAA
Found at i:28065 original size:13 final size:11
Alignment explanation
Indices: 28031--28058 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28021 TATATATATT
28031 TAAAAATAATA
1 TAAAAATAATA
28042 TAAAAATAATA
1 TAAAAATAATA
28053 TAAAAA
1 TAAAAA
28059 ATTAATACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:28809 original size:16 final size:15
Alignment explanation
Indices: 28788--28835 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
28778 GATGTGAATA
28788 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
28804 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
28819 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
28835 A
1 A
28836 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:28811 original size:24 final size:24
Alignment explanation
Indices: 28784--28839 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
28774 TAATGATGTG
*
28784 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
28808 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
28832 AATAATAA
1 AATAATAA
28840 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:28818 original size:8 final size:8
Alignment explanation
Indices: 28784--28835 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
28774 TAATGATGTG
*
28784 AATAATAA
1 AATATTAA
28792 AATATATAA
1 AATAT-TAA
28801 AATA-TAA
1 AATATTAA
28808 AATATTAA
1 AATATTAA
*
28816 AATATCAA
1 AATATTAA
*
28824 AATATTAG
1 AATATTAA
28832 AATA
1 AATA
28836 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:29007 original size:22 final size:23
Alignment explanation
Indices: 28966--29051 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 23
28956 TGTACATATA
* * *
28966 TAAAAATAAATACGTGATATA-T
1 TAAAAATATATACATAATATAGT
*
28988 TAAAAATATGTACATAATATAGTGT
1 TAAAAATATATACATAATATA--GT
*
29013 TAAAAATACATACATAATATAGT
1 TAAAAATATATACATAATATAGT
*
29036 T-AAGATATATACATAA
1 TAAAAATATATACATAA
29052 GATAACATGT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
22 30 0.57
23 3 0.06
25 20 0.38
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (23 bp):
TAAAAATATATACATAATATAGT
Found at i:29017 original size:25 final size:25
Alignment explanation
Indices: 28987--29035 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28977 ACGTGATATA
**
28987 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATACATACATAATATAGTG
29012 TTAAAAATACATACATAATATAGT
1 TTAAAAATACATACATAATATAGT
29036 TAAGATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGTG
Found at i:30469 original size:13 final size:13
Alignment explanation
Indices: 30453--30487 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
30443 TGAAAAATAT
30453 AAATTGAAAACAG
1 AAATTGAAAACAG
*
30466 AAATTGAAAGCAG
1 AAATTGAAAACAG
30479 AAATT-AAAA
1 AAATTGAAAA
30488 GACCTCAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (13 bp):
AAATTGAAAACAG
Found at i:30612 original size:70 final size:71
Alignment explanation
Indices: 30469--30780 Score: 328
Period size: 70 Copynumber: 4.2 Consensus size: 71
30459 AAAACAGAAA
* ** *
30469 TTGAAAGCAGAAATT-AAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAACAGAAATTGAAATTACCTCAGC--GTG-TCCGAGGCTCAACTCACCTCTCGCAATATG
*
30533 AGTTAATTT
63 AGTTGATTT
*
30542 TTGACAACAGAAATTGAAATTACCTCAGCGTGTCCGAGGCTCAACTCACCT-TCGCAATATGAGT
1 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGT
30606 TGATTT
66 TGATTT
* *
30612 TTGAAAAAAGAAATT-AAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAG
30676 TTGATTT
65 TTGATTT
** *
30683 TT-TTAACAGAAATTGAAAACAGAAATTGAAAAACCTCAGCATGTGCCGAGGCTCAACTCACCTC
1 TTGAAAACAGAAATT-------GAAATT-----ACCTCAGCGTGT-CCGAGGCTCAACTCACCTC
30747 TCGCAATATGAGTTGA-TT
53 TCGCAATATGAGTTGATTT
30765 TTGAAAAACAGAAATT
1 TTG-AAAACAGAAATT
30781 AAAAGCTTCA
Statistics
Matches: 204, Mismatches: 16, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
69 18 0.09
70 56 0.27
71 39 0.19
72 3 0.01
73 13 0.06
74 11 0.05
78 4 0.02
82 4 0.02
83 44 0.22
84 12 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (71 bp):
TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTT
Found at i:30705 original size:13 final size:13
Alignment explanation
Indices: 30687--30714 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30677 TGATTTTTTT
30687 AACAGAAATTGAA
1 AACAGAAATTGAA
30700 AACAGAAATTGAA
1 AACAGAAATTGAA
30713 AA
1 AA
30715 ACCTCAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.14
Consensus pattern (13 bp):
AACAGAAATTGAA
Found at i:30751 original size:83 final size:83
Alignment explanation
Indices: 30612--30766 Score: 260
Period size: 83 Copynumber: 1.9 Consensus size: 83
30602 GAGTTGATTT
*
30612 TTGAAAAAAGAAATTAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TTGAAAAAAGAAATTAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
30677 TGATTTTTTTAACAGAAA
66 TGATTTTTTTAACAGAAA
*
30695 TTGAAAACAGAAATTGAAAA-ACCTCAGCATGTGCC-GAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAAAGAAATT-AAAATACCTCAGCATGT-CCTGAGGCTCAACTCACCTCTCGCAATATGA
30758 GTTGATTTT
64 GTTGATTTT
30767 GAAAAACAGA
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
83 62 0.91
84 6 0.09
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (83 bp):
TTGAAAAAAGAAATTAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTAACAGAAA
Found at i:30804 original size:52 final size:52
Alignment explanation
Indices: 30735--30835 Score: 170
Period size: 52 Copynumber: 1.9 Consensus size: 52
30725 GTGCCGAGGC
30735 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATTAAAAGCT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACA-AAATTAAAAGCT
30788 TCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAACAAAATTAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAATTAAAA
30836 TACCTCAGCG
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
51 9 0.19
52 25 0.53
53 13 0.28
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.30
Consensus pattern (52 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAATTAAAAGCT
Found at i:30991 original size:67 final size:68
Alignment explanation
Indices: 30915--31075 Score: 254
Period size: 67 Copynumber: 2.4 Consensus size: 68
30905 GTTCAACTCA
* *
30915 CCTCTCGCAATATGAGTTGATTTTG-AAAACAGAAATTGAAATACCTCAGCGTGTC-CGAGGCTC
1 CCTCTCGCAATATGAGTTGATTTTGAAAAACA-AAATTAAAATACCTCAACGTGTCTCGAGGCTC
30978 AACT
65 AACT
*
30982 CCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAAATACCTCAACGTGTCTTGAGGCTCA
1 CCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAAATACCTCAACGTGTCTCGAGGCTCA
31047 ACT
66 ACT
31050 CATCTCTCGCAATATGAGTTGATTTT
1 C--CTCTCGCAATATGAGTTGATTTT
31076 CCTTGAAAAG
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
67 46 0.53
68 18 0.21
70 23 0.26
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (68 bp):
CCTCTCGCAATATGAGTTGATTTTGAAAAACAAAATTAAAATACCTCAACGTGTCTCGAGGCTCA
ACT
Found at i:31031 original size:120 final size:120
Alignment explanation
Indices: 30695--31022 Score: 522
Period size: 120 Copynumber: 2.7 Consensus size: 120
30685 TTAACAGAAA
* *
30695 TTGAAAACAGAAATTGAAAAACCTCAGCATGTGCCGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TTGAAAACAGAAATTGAAATACCTCAGCGTGT-CCGAGGCTCAACT-ACCTCTCGCAATATGAGT
30760 TGATTTTGAAAAACAGAAATTAAAAGCTTCAACTCACTCTCGCAATATGAGTTGATTT
64 TGATTTTGAAAAACA-AAATTAAAAGCTTCAACTCACTCTCGCAATATGAGTTGATTT
*
30818 TTGAAAACA-AAATTAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TTGAAAACAGAAATTGAAATACCTCAGCGTGTCC-GAGGCTCAACT-ACCTCTCGCAATATGAGT
* *
30881 TGATTTTGAAAAA-GAAATTAAAAGGTTCAACTCACCTCTCGCAATATGAGTTGA-TT
64 TGATTTTGAAAAACAAAATTAAAAGCTTCAACTCA-CTCTCGCAATATGAGTTGATTT
30937 TTGAAAACAGAAATTGAAATACCTCAGCGTGTCCGAGGCTCAACT-CCTCTCGCAATATGAGTTG
1 TTGAAAACAGAAATTGAAATACCTCAGCGTGTCCGAGGCTCAACTACCTCTCGCAATATGAGTTG
31001 ATTTTGAAAAACAAAATTAAAA
66 ATTTTGAAAAACAAAATTAAAA
31023 TACCTCAACG
Statistics
Matches: 193, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
118 30 0.16
119 39 0.20
120 52 0.27
121 45 0.23
122 18 0.09
123 9 0.05
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (120 bp):
TTGAAAACAGAAATTGAAATACCTCAGCGTGTCCGAGGCTCAACTACCTCTCGCAATATGAGTTG
ATTTTGAAAAACAAAATTAAAAGCTTCAACTCACTCTCGCAATATGAGTTGATTT
Found at i:39317 original size:12 final size:12
Alignment explanation
Indices: 39285--39320 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
39275 TGGGATATGC
39285 AATGTATGAATG
1 AATGTATGAATG
**
39297 AATACATGAATG
1 AATGTATGAATG
39309 AATGTATGAATG
1 AATGTATGAATG
39321 TCAAATGTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (12 bp):
AATGTATGAATG
Done.