Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_124 ID=scaffold_124-JGI_221_v2.0
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: 13540
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.28
Warning! 1635 characters in sequence are not A, C, G, or T
Found at i:29 original size:15 final size:15
Alignment explanation
Indices: 9--37 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1 ACACGGAA
9 GAAATACAGAAATTT
1 GAAATACAGAAATTT
24 GAAATACAGAAATT
1 GAAATACAGAAATT
38 ATTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (15 bp):
GAAATACAGAAATTT
Found at i:628 original size:13 final size:13
Alignment explanation
Indices: 610--634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
600 ATTCGGGCCT
610 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
623 TTTTTGTTTTTT
1 TTTTTGTTTTTT
635 TTCTTTTTTC
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:785 original size:18 final size:20
Alignment explanation
Indices: 762--798 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
752 TGGGCCTGGC
762 CTGCTGCT-TTT-TTTTTTG
1 CTGCTGCTATTTCTTTTTTG
780 CTGCTGCTATTTCTTTTTT
1 CTGCTGCTATTTCTTTTTT
799 TTCTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.03, C:0.19, G:0.14, T:0.65
Consensus pattern (20 bp):
CTGCTGCTATTTCTTTTTTG
Found at i:918 original size:15 final size:14
Alignment explanation
Indices: 887--940 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
877 AATGTATTTC
887 TTTT-TTTCTTC-T
1 TTTTCTTTCTTCTT
899 TTTTCTTTCTCTCTT
1 TTTTCTTTCT-TCTT
914 TTTTCTTTCTTTCTT
1 TTTTCTTTC-TTCTT
* *
929 TCTTCTTCCTTC
1 TTTTCTTTCTTC
941 CCTTCGACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 4 0.11
13 5 0.14
14 5 0.14
15 21 0.58
16 1 0.03
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTTTCTTCTT
Found at i:922 original size:4 final size:4
Alignment explanation
Indices: 883--932 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
873 CTGTAATGTA
* * *
883 TTTC TTTT TTTC TTCTT TTTC TTTC TCTC TTT- TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
931 TT
1 TT
933 CTTCCTTCCC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:1238 original size:23 final size:23
Alignment explanation
Indices: 1194--1238 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1184 GCCCTTTGGC
* *
1194 TTGCTGCTTTTTGTTTGATTTTT
1 TTGCTGCTTTTTCTTAGATTTTT
1217 TTGCTGCTGTTTTCTTAG-TTTT
1 TTGCTGCT-TTTTCTTAGATTTT
1239 CTTTCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.04, C:0.11, G:0.18, T:0.67
Consensus pattern (23 bp):
TTGCTGCTTTTTCTTAGATTTTT
Found at i:1553 original size:30 final size:29
Alignment explanation
Indices: 1500--1637 Score: 129
Period size: 30 Copynumber: 4.7 Consensus size: 29
1490 AAATATGGGC
* * *
1500 CAAAATGTAATTTCTTGAGAGTTTAGGGGT
1 CAAAATGAAATTT-TAGAAAGTTTAGGGGT
* * *
1530 CAAAGTGCAATTTTGAGAAAGTTTAAGGGT
1 CAAAATGAAATTTT-AGAAAGTTTAGGGGT
*
1560 CAAAATGTAATTTTAGAAAGTTTTA-GGGT
1 CAAAATGAAATTTTAGAAAG-TTTAGGGGT
1589 CAAAATGTAAATTTTAGAAAAGTTTA-GGGT
1 CAAAATG-AAATTTTAG-AAAGTTTAGGGGT
*
1619 TAAAATGTAAATTTT-GAAA
1 CAAAATG-AAATTTTAGAAA
1638 AGTACAGGGT
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
28 3 0.03
29 19 0.20
30 69 0.73
31 4 0.04
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (29 bp):
CAAAATGAAATTTTAGAAAGTTTAGGGGT
Found at i:1567 original size:60 final size:59
Alignment explanation
Indices: 1500--1637 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 59
1490 AAATATGGGC
* * * *
1500 CAAAATGTAATTTCTTGAGAG-TTTAGGGGTCAAAGTG-CAATTTT-GAGAAAGTTTAAGGGT
1 CAAAATGTAATTT-TAGAAAGTTTTA-GGGTCAAAATGTAAATTTTAGA-AAAGTTT-AGGGT
1560 CAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATGTAAATTTTAGAAAAGTTTAGGGT
1 CAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATGTAAATTTTAGAAAAGTTTAGGGT
*
1619 TAAAATGTAAATTTT-GAAA
1 CAAAATGT-AATTTTAGAAA
1638 AGTACAGGGT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
59 31 0.45
60 36 0.52
61 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (59 bp):
CAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATGTAAATTTTAGAAAAGTTTAGGGT
Found at i:1618 original size:59 final size:58
Alignment explanation
Indices: 1500--1637 Score: 156
Period size: 59 Copynumber: 2.3 Consensus size: 58
1490 AAATATGGGC
* * *
1500 CAAAATGTAATTTCTTGAGAGTTTAGGGGTCAAAGTGCAATTTTGAGAAAGTTTAAGGGT
1 CAAAATGTAA-TT-TTGAAAGTTTAGGGGTCAAAATGAAATTTTGAGAAAGTTTAAGGGT
1560 CAAAATGTAATTTTAGAAAGTTTTA-GGGTCAAAATGTAAATTTT-AGAAAAGTTT-AGGGT
1 CAAAATGTAATTTT-GAAAG-TTTAGGGGTCAAAATG-AAATTTTGAG-AAAGTTTAAGGGT
*
1619 TAAAATGTAAATTTTGAAA
1 CAAAATGT-AATTTTGAAA
1638 AGTACAGGGT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
58 2 0.03
59 34 0.49
60 33 0.48
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (58 bp):
CAAAATGTAATTTTGAAAGTTTAGGGGTCAAAATGAAATTTTGAGAAAGTTTAAGGGT
Found at i:1647 original size:29 final size:30
Alignment explanation
Indices: 1555--1654 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 30
1545 AGAAAGTTTA
* **
1555 AGGGTCAAAATGT-AATTTTAG-AAAGTTTT
1 AGGGTTAAAATGTAAATTTTAGAAAAG-TAC
* **
1584 AGGGTCAAAATGTAAATTTTAGAAAAGTTT
1 AGGGTTAAAATGTAAATTTTAGAAAAGTAC
1614 AGGGTTAAAATGTAAATTTT-GAAAAGTAC
1 AGGGTTAAAATGTAAATTTTAGAAAAGTAC
1643 AGGGTTAAAATG
1 AGGGTTAAAATG
1655 CAAAAAATAA
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
29 32 0.48
30 30 0.45
31 4 0.06
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (30 bp):
AGGGTTAAAATGTAAATTTTAGAAAAGTAC
Found at i:1647 original size:59 final size:60
Alignment explanation
Indices: 1538--1654 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 60
1528 GTCAAAGTGC
**
1538 AATTTTGAGAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATGTA
1 AATTTTGAGAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAGTTACAGGGTCAAAATGTA
* *
1598 AATTTT-AGAAAAGTTT-AGGGTTAAAATGTAAATTTT-GAAAAG-TACAGGGTTAAAATG
1 AATTTTGAG-AAAGTTTAAGGGTCAAAATGT-AATTTTAG-AAAGTTACAGGGTCAAAATG
1655 CAAAAAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
59 27 0.54
60 23 0.46
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (60 bp):
AATTTTGAGAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAGTTACAGGGTCAAAATGTA
Found at i:1942 original size:75 final size:73
Alignment explanation
Indices: 1851--2664 Score: 889
Period size: 75 Copynumber: 10.6 Consensus size: 73
1841 CTCGGCGTGC
* * * * **
1851 GACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGATCTTCGAAAAACA-AAAATCGAAAATA
1 GACCCGAGGCTCAACTCACCTC-TGTATTATGAGTTGATTTTTGAAAAACACAAAATAAAAAATA
*
1915 CCTCAACATGT
65 CCTCAGC--GT
* * * *
1926 GCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTCAAAAA-ACATAAATTTAAAAG
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAACACA-AAA--T-AAA-
* *
1990 AAATACCTCGGCAT
60 AAATACCTCAGCGT
** ** *
2004 GGTCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACGGAAATTTAAAAGAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACACAAA-AT-AAA-AAA
* *
2069 TACCTCGGCAT
63 TACCTCAGCGT
* *
2080 GACCCGAGACTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACAGACATAAATTAAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAC--ACA-AAATAAAAAA
*
2145 TACTTCAGCGT
63 TACCTCAGCGT
* *
2156 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAACGACATAAATTAAAAAT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAC-ACA-AAATAAAAAAT
2221 ACCTCAGCGT
64 ACCTCAGCGT
2231 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA-AGCAGAAATTTAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAACA-CA-AAA--TAAAA
2295 AATACCTCAGCGT
61 AATACCTCAGCGT
* ** * *
2308 GACCCAAGGCTCAACTCACCTCTGTATTATGAGTTGATTTATAAAAAAAGACATAAATTAAAAAT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT-TTGAAAAACACA-AAATAAAAAAT
2373 ACCTCAGCGT
64 ACCTCAGCGT
2383 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA-AGCAGAAATTTAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAACA-CA-AAA--TAAAA
*
2447 AATACCTCAGCAT
61 AATACCTCAGCGT
*
2460 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTATGAAAAAACAGAAATTAAATTAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT-TG-AAAAAC--ACA--AAA-T--
2525 AAAAAATACCTCAGCGT
57 AAAAAATACCTCAGCGT
*
2542 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAATTAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTG-AAAAAC--ACA--AAA-T-A
2607 AAAAATACCTCAGCGT
58 AAAAATACCTCAGCGT
2623 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT
2665 TTGAAAAAAA
Statistics
Matches: 658, Mismatches: 50, Indels: 57
0.86 0.07 0.07
Matches are distributed among these distances:
74 4 0.01
75 172 0.26
76 147 0.22
77 145 0.22
78 32 0.05
79 3 0.00
80 18 0.03
81 59 0.09
82 74 0.11
83 4 0.01
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (73 bp):
GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAACACAAAATAAAAAATAC
CTCAGCGT
Found at i:2559 original size:82 final size:79
Alignment explanation
Indices: 1909--2673 Score: 1015
Period size: 76 Copynumber: 9.8 Consensus size: 79
1899 ACAAAAATCG
* * * * *
1909 AAAATACCTCAACATGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTCAAA
1 AAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAA
*
1973 AAACATAAAT---TTAAA
63 AAACAGAAATAAATT-AA
* * **
1988 AGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTG-AAAA
1 A-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
*
2051 ACGGAAAT---TTAAA
65 ACAGAAATAAATT-AA
* * *
2064 AGAAATACCTCGGCATGACCCGAGACTCAACTCACCTCTGTATTATGAGTTGA-TTTTTG-AAAA
1 A-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAA
*
2127 ACAGACATAAATT-A
65 ACAGAAATAAATTAA
*
2141 AAAATACTTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTT-AAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
*
2204 C-GACATAAATT-A
66 CAGAAATAAATTAA
2216 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
2281 GCAGAAAT---TTAA
66 -CAGAAATAAATTAA
* *
2293 AAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTAT-AAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
*
2356 -AGACATAAATT-A
66 CAGAAATAAATTAA
2368 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
2433 GCAGAAAT---TTAA
66 -CAGAAATAAATTAA
* *
2445 AAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTATGAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
2510 CAGAAATTAAATTAAAA
66 CAGAAA-TAAATT--AA
2527 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
2592 CAGAAATTAAATTAAA
66 CAGAAA-TAAATT-AA
2608 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTTGAAAAA
2673 A
65 A
2674 ATAGAATTTT
Statistics
Matches: 630, Mismatches: 31, Indels: 47
0.89 0.04 0.07
Matches are distributed among these distances:
73 5 0.01
75 120 0.19
76 164 0.26
77 148 0.23
78 23 0.04
79 12 0.02
80 12 0.02
81 55 0.09
82 91 0.14
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (79 bp):
AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
CAGAAATAAATTAA
Done.