Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1814
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: 30419
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:78 original size:41 final size:43
Alignment explanation
Indices: 7--444 Score: 405
Period size: 41 Copynumber: 9.9 Consensus size: 43
1 TCATCT
7 TTAAGTCCAATGTAGGCTGGGCCTTGACTCAGCACATT-GCCCCA
1 TTAAGTCCAATGTA-GCT-GGCCTTGACTCAGCACATTGGCCCCA
51 TTAAGTCCAATG-AGCTGGCCTTGACTCAGCACATTGG-CCCA
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCCCCA
* *
92 TTAAGTCCAATATAGCT-GCCTTGA-TCAG--CATTGGCATCTTCATCT
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGC--C--C--CA
*
137 TTAAGT-CAATGTAGTTGGCCTTGACTCAGCACATTGGCCCTTCA
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCCC--CA
* *
181 TCTTTAAGTCC-ATGTAGCTGGCCTTGAATCAGCACATTGGCACTCA
1 ---TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGC-CCCA
227 TCCTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTCA
1 T--TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGC-CC-CA
* *
274 CTTTTAGTCCAATGTAGCTGGCCTTGACTCAGCAC-TTGGCACCA
1 --TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCCCCA
* * * *
318 -TAAGTCCAATATAGCTGGCCTTGAATCAGCATA-TGGCATCTTCATCT
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGC--C--C--CA
* * *
365 TTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCCCCA
* * *
408 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTG
445 CACATTTTCC
Statistics
Matches: 337, Mismatches: 24, Indels: 67
0.79 0.06 0.16
Matches are distributed among these distances:
38 6 0.02
40 4 0.01
41 74 0.22
42 8 0.02
43 40 0.12
44 25 0.07
45 24 0.07
46 43 0.13
47 68 0.20
48 40 0.12
49 5 0.01
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (43 bp):
TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCCCCA
Found at i:188 original size:47 final size:47
Alignment explanation
Indices: 1--492 Score: 461
Period size: 47 Copynumber: 10.8 Consensus size: 47
*
1 TCATCTTTAAGTCCAATGTAGGCTGGGCCTTGACTCAGCACATT-GCCC
1 TCATCTTTAAGTCCAATGTA-GCT-GGCCTTGAATCAGCACATTGGCCC
*
49 -CA---TTAAGTCCAATG-AGCTGGCCTTGACTCAGCACATTGG-CC
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCCC
* *
90 -CA---TTAAGTCCAATATAGCT-GCCTTG-ATCAG--CATTGGCATCT
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC--CC
* *
131 TCATCTTTAAGT-CAATGTAGTTGGCCTTGACTCAGCACATTGGCCC
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCCC
*
177 TTCATCTTTAAGTCC-ATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 -TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCCC
* *
224 TCATC-CTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC-CC
* * *
271 TCA-CTTTTAGTCCAATGTAGCTGGCCTTGACTCAGCAC-TTGGCAC
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCCC
* * *
316 -CA----TAAGTCCAATATAGCTGGCCTTGAATCAGCATA-TGGCATCT
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC--CC
359 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG---
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCCC
* * * *
403 -CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-GCACATTT
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC-C---C
*
452 TCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAAGCAC
1 T-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATC-AGCAC
493 GTTGACATCC
Statistics
Matches: 376, Mismatches: 31, Indels: 70
0.79 0.06 0.15
Matches are distributed among these distances:
38 6 0.02
40 4 0.01
41 73 0.19
42 11 0.03
43 39 0.10
44 24 0.06
45 20 0.05
46 45 0.12
47 78 0.21
48 39 0.10
49 3 0.01
51 30 0.08
52 4 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (47 bp):
TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCCC
Found at i:249 original size:93 final size:92
Alignment explanation
Indices: 137--492 Score: 469
Period size: 93 Copynumber: 3.9 Consensus size: 92
127 ATCTTCATCT
*
137 TTAAGT-CAATGTAGTTGGCCTTGACTCAGCACATTGGC-CCTTCATCTTTAAGTCC-ATGTAGC
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
199 TGGCCTTGAATCAGCACATTGGCACTCA
66 TGGCCTTGAATCAGCACATTGGCAC-CA
*
227 TCCTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TCA-CTTTTAGTCCAATGTA
1 T--TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
*
290 GCTGGCCTTGACTCAGCAC-TTGGCACCA
64 GCTGGCCTTGAATCAGCACATTGGCACCA
* * * *
318 -TAAGTCCAATATAGCTGGCCTTGAATCAGCATA-TGGCATCTTCATCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
*
381 TGGCCTTGAATCAGCACATTGGCACCT
66 TGGCCTTGAATCAGCACATTGGCACCA
* * * * *
408 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-GCACATTTTCCATCTTTAAGTTCAATGT
1 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC--CTT-CATCTTTAAGTCCAATGT
472 AGCTGGCCTTGAATCAAGCAC
63 AGCTGGCCTTGAATC-AGCAC
493 GTTGACATCC
Statistics
Matches: 239, Mismatches: 13, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
87 6 0.03
88 33 0.14
89 33 0.14
90 9 0.04
91 38 0.16
92 22 0.09
93 59 0.25
94 34 0.14
95 5 0.02
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (92 bp):
TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGGCACCA
Found at i:743 original size:170 final size:173
Alignment explanation
Indices: 406--801 Score: 656
Period size: 170 Copynumber: 2.3 Consensus size: 173
396 ACATTGGCAC
* *
406 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGCACATTTTCCATCTTTAAGTTCAATG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG-GCATCTT-CATCTTTAAGTTCAATG
471 TAGCTGGCCTTGAATCAAGCACGTTGACATCCTTTTTCTCATCTCTTTAAGCCCAATATCGTTGG
64 TAGCTGGCCTTGAATCAAGCACGTTGACATCCTTTTTCTCA-CTCTTTAAGCCCAATATCGTTGG
536 CCATGAATCAACATATGGCATCTTTATCACGTTTTCTCATCATCAT
128 CCATGAATCAACATATGGCATCTTTATCACGTTTTCTCATCATCAT
* *
582 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA-TGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
*
646 GCTGGCCTTGAATC-AGCACGTTGACATCCTTTTTCTCA-TCTTTAGGCCCAATATCGTTGGCCA
66 GCTGGCCTTGAATCAAGCACGTTGACATCCTTTTTCTCACTCTTTAAGCCCAATATCGTTGGCCA
*
709 TGAATCAACATATTGGCATCTTTATCAC-TTTTCTCATCTTCAT
131 TGAATCAACATA-TGGCATCTTTATCACGTTTTCTCATCATCAT
* *
752 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
802 ATCTCTAAAA
Statistics
Matches: 209, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
170 84 0.40
171 27 0.13
172 24 0.11
173 33 0.16
174 5 0.02
175 2 0.01
176 34 0.16
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (173 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAAGCACGTTGACATCCTTTTTCTCACTCTTTAAGCCCAATATCGTTGGCCA
TGAATCAACATATGGCATCTTTATCACGTTTTCTCATCATCAT
Found at i:1608 original size:13 final size:13
Alignment explanation
Indices: 1590--1614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1580 CATAAAGTGT
1590 TGTATCGATACAA
1 TGTATCGATACAA
1603 TGTATCGATACA
1 TGTATCGATACA
1615 TATTTTTTTG
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:1612 original size:33 final size:33
Alignment explanation
Indices: 1570--1636 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1560 TTCAACGATT
1570 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1603 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1636 T
1 T
1637 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1695 original size:13 final size:13
Alignment explanation
Indices: 1677--1701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1667 ATTACTCAAA
1677 TGTATCGATACAT
1 TGTATCGATACAT
1690 TGTATCGATACA
1 TGTATCGATACA
1702 CCGATCTTTG
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:1766 original size:52 final size:52
Alignment explanation
Indices: 1710--1829 Score: 204
Period size: 52 Copynumber: 2.3 Consensus size: 52
1700 CACCGATCTT
* *
1710 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
* *
1762 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTTTCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
1814 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1830 AGTAACTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
Found at i:5814 original size:18 final size:16
Alignment explanation
Indices: 5767--5808 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
5757 ACAAGAAATT
*
5767 TAAAAATAAACCTAAA
1 TAAAAAAAAACCTAAA
5783 TAAAAAAAAACCTAAA
1 TAAAAAAAAACCTAAA
5799 TAAAAAAAAA
1 TAAAAAAAAA
5809 AACCTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (16 bp):
TAAAAAAAAACCTAAA
Found at i:5824 original size:18 final size:17
Alignment explanation
Indices: 5768--5828 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
5758 CAAGAAATTT
* *
5768 AAAAATAAACCTAA-AT
1 AAAAAAAAACCTAATAA
5784 AAAAAAAAACCTAAATAA
1 AAAAAAAAACCT-AATAA
5802 AAAAAAAAACCT-ATCAA
1 AAAAAAAAACCTAAT-AA
5819 ACAAAAAAAA
1 A-AAAAAAAA
5829 ATAGCAAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
16 13 0.33
17 5 0.13
18 21 0.54
ACGTcount: A:0.75, C:0.13, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAAAAACCTAATAA
Found at i:6844 original size:13 final size:13
Alignment explanation
Indices: 6826--6851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6816 TACAGCAAGT
6826 ATGTATCGATACA
1 ATGTATCGATACA
6839 ATGTATCGATACA
1 ATGTATCGATACA
6852 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9357 original size:154 final size:155
Alignment explanation
Indices: 9019--9398 Score: 417
Period size: 154 Copynumber: 2.5 Consensus size: 155
9009 CTAAGTTCAA
* * * *
9019 AAAAAATTATGAAAATGCCCCTAGGGGATACCTTTGACGTAGAAGTACATGATACCCCTAAAAGA
1 AAAAAATTATGAAAATGACCATAGGGGATACTTTTGACGTAGAAGTACACGATACCCCTAAAAGA
*
9084 CTTAAAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGAGGACT
66 CTTAAAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGAGGACC
*
9149 CGGTGACAACTTAAGACTTGGTTCT
131 CGGTGACAACCTAAGACTTGGTTCT
* * ** * * * * *
9174 AAAAAATTATGAAAA-CATCCTTAAAGGATACTTTTGATGTCGAAGTGCCCGATACCCCTAAAGG
1 AAAAAATTATGAAAATGA-CCATAGGGGATACTTTTGACGTAGAAGTACACGATACCCCTAAAAG
* * * ** * * *
9238 AC-T-GAAAGGATTTTAGAATTTGATGAACCTATCCTAAATACCCATCTTT-AGCATAACAGCGG
65 ACTTAAAAAAGATTATAG-ATGGGATGAACCTATCCTAAATACCCACCTTTGA-CATAAAAGAGG
* *
9300 ACCCGGTGACGACCTAAGAGTTGGTTCT
128 ACCCGGTGACAACCTAAGACTTGGTTCT
* * * * * * *
9328 AAAAAATTACGAAAATGACCATAGGGGATACTTTCGACGTAAAAGTACTCAATACCTCTAAATGA
1 AAAAAATTATGAAAATGACCATAGGGGATACTTTTGACGTAGAAGTACACGATACCCCTAAAAGA
9393 CTTAAA
66 CTTAAA
9399 GATGATAATC
Statistics
Matches: 180, Mismatches: 39, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
153 11 0.06
154 113 0.63
155 55 0.31
156 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (155 bp):
AAAAAATTATGAAAATGACCATAGGGGATACTTTTGACGTAGAAGTACACGATACCCCTAAAAGA
CTTAAAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGAGGACC
CGGTGACAACCTAAGACTTGGTTCT
Found at i:11621 original size:23 final size:23
Alignment explanation
Indices: 11595--11640 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11585 AATTTCAAGG
11595 AAAAAATTCAAAACTCATGCAAA
1 AAAAAATTCAAAACTCATGCAAA
11618 AAAAAATTCAAAACTCATGCAAA
1 AAAAAATTCAAAACTCATGCAAA
11641 TAAATGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.17
Consensus pattern (23 bp):
AAAAAATTCAAAACTCATGCAAA
Found at i:18278 original size:20 final size:20
Alignment explanation
Indices: 18255--18306 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
18245 TATTTAGGGA
*
18255 TGTATCAATACATTGTGTAT-
1 TGTATCGATACATT-TGTATG
*
18275 TGTATCGATACATTTTTATG
1 TGTATCGATACATTTGTATG
18295 TGTATCGATACA
1 TGTATCGATACA
18307 AAAAGGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTTGTATG
Found at i:21246 original size:49 final size:49
Alignment explanation
Indices: 21095--21260 Score: 196
Period size: 48 Copynumber: 3.4 Consensus size: 49
21085 AATACCGTGT
* * * * * *
21095 ATGTATCGATACATTAGTGAATGTATCGATACAATCTGG--AAACTTAG
1 ATGTATCGATACATTATTCATTATATCGATACATTCTGGAAAAACCTAG
* * *
21142 ATGTATCGATATATTATTCATTGTATTGATACATTCT-GAAAAACCTAG
1 ATGTATCGATACATTATTCATTATATCGATACATTCTGGAAAAACCTAG
*
21190 ATGTATCGCTACATT-TTACATTATATCGATACATTCTGGAAAAACCTAG
1 ATGTATCGATACATTATT-CATTATATCGATACATTCTGGAAAAACCTAG
*
21239 ATATATCGATACATTATTCATT
1 ATGTATCGATACATTATTCATT
21261 GTACTAATAC
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
46 1 0.01
47 33 0.33
48 37 0.37
49 28 0.28
50 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (49 bp):
ATGTATCGATACATTATTCATTATATCGATACATTCTGGAAAAACCTAG
Found at i:28835 original size:21 final size:21
Alignment explanation
Indices: 28806--28879 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
28796 AGTTAATTCA
**
28806 TTATTTTCTTTTGTAACTCAT
1 TTATTTTCTTTTCCAACTCAT
*
28827 TTCTTTTCTTTTCCAACTCAT
1 TTATTTTCTTTTCCAACTCAT
* * * *
28848 TTATTTTCTCTTCTAATTCAC
1 TTATTTTCTTTTCCAACTCAT
*
28869 TTACTTTCTTT
1 TTATTTTCTTT
28880 CGAGATATTT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.16, C:0.22, G:0.01, T:0.61
Consensus pattern (21 bp):
TTATTTTCTTTTCCAACTCAT
Done.