Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3243
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: 19559
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:2158 original size:32 final size:33
Alignment explanation
Indices: 2116--2193 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
2106 GACTTTAGCT
*
2116 CAGACGAAACTCCACACAAGT-ATCGGTCTACC
1 CAGACAAAACTCCACACAAGTCATCGGTCTACC
**
2148 CAGACAAAACTCC-CAGTAGTCATCGGTCTACC
1 CAGACAAAACTCCACACAAGTCATCGGTCTACC
* *
2180 CGGACAAATCTCCA
1 CAGACAAAACTCCA
2194 ACGTATCATC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 5 0.13
32 34 0.87
ACGTcount: A:0.33, C:0.35, G:0.15, T:0.17
Consensus pattern (33 bp):
CAGACAAAACTCCACACAAGTCATCGGTCTACC
Found at i:2203 original size:32 final size:32
Alignment explanation
Indices: 2137--2204 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
2127 CCACACAAGT
*
2137 ATCGGTCTACCCAGACAAAACTCCCAGTAGTC
1 ATCGGTCTACCCAGACAAAACTCCAAGTAGTC
* *
2169 ATCGGTCTACCCGGACAAATCTCCAACGTA-TC
1 ATCGGTCTACCCAGACAAAACTCCAA-GTAGTC
2201 ATCG
1 ATCG
2205 AGCTTAGAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 29 0.91
33 3 0.09
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (32 bp):
ATCGGTCTACCCAGACAAAACTCCAAGTAGTC
Found at i:2454 original size:45 final size:46
Alignment explanation
Indices: 2404--3311 Score: 914
Period size: 45 Copynumber: 19.4 Consensus size: 46
2394 TTGTGCCACA
2404 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
2450 ATATATATACACTTTCACATTCATCACATTGGCCATT-GGCCTTATCAC
1 ---TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
2498 ATATATATACACTTTCACATTCATC-CCTC-GCCATT-GATCCATTATACAC
1 ---TATATACACTTTCACATTCATCACATCGGCCATTAG-GCC-TTAT-CAC
* *** **
2547 TAATTATAAAAAATCACAATAATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 T-A-TATACACTTTCAC-AT--T-CA---TCACA-TCGGC-CATT----A---GGCCTTATCAC
*
2611 -ATATACACATTCACATTCATCA-ATC-GCCATTA-GCC-TATCAC
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
2652 ATATATATATACACTTTCACATTC-TCACATCGGCCATTAGGCCTTATCAC
1 -----TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
2702 TATATACACTTTCACATTCATCACATCGGCCATTAGG------C-C
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
2741 TATATAC-CTTTCACATTCATCACATCGGCCATTAGGCC-TATCAC
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
2785 ATATATACA-TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 -TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
2831 ATATATACAC-TTCACATTCATCACATC-GCTATTAGGCC-TATCAC
1 -TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
2875 ATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTTATCAC
1 -TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
2921 ATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 ---TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
2970 ATATATACACTTTCACATTCATCATATC-GCCATT-GGCCTTATACAT
1 -TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-CAC
* *
3016 TATATA-ACTTTCACA-TCATCACATTGGCCATTCGGCCTTATCAC
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
3060 -ATATACACACTTCACATTCATCACATCGGCCATTA-GCC-TATACATATA
1 TATATACAC-TTTCACATTCATCACATCGGCCATTAGGCCTTAT-C--A-C
3108 TATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTA-CAC
1 TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
3152 ATATATACAC-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 -TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
3198 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 -TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
3245 ATATATATACACTTTCACATTCATCACATCGGCTATTAGG-CTTATCAC
1 ---TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
3293 ATATATACACTTTCACATT
1 -TATATACACTTTCACATT
3312 TATTCAAATA
Statistics
Matches: 754, Mismatches: 36, Indels: 141
0.81 0.04 0.15
Matches are distributed among these distances:
38 29 0.04
39 8 0.01
40 1 0.00
41 6 0.01
42 3 0.00
43 14 0.02
44 39 0.05
45 158 0.21
46 129 0.17
47 112 0.15
48 101 0.13
49 98 0.13
50 10 0.01
51 2 0.00
52 4 0.01
53 1 0.00
54 3 0.00
55 2 0.00
56 1 0.00
57 4 0.01
58 2 0.00
59 4 0.01
60 2 0.00
61 10 0.01
62 1 0.00
64 3 0.00
65 4 0.01
66 2 0.00
67 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (46 bp):
TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:2671 original size:47 final size:46
Alignment explanation
Indices: 2559--3311 Score: 936
Period size: 45 Copynumber: 16.5 Consensus size: 46
2549 ATTATAAAAA
* *
2559 ATCACA-ATAATACACTTTCACATTCATCACATTGGCCATTCGGCCTT
1 ATCACATAT-ATACACTTTCACATTCATCACATCGGCCATT-AGCCTT
*
2606 ATCAC--ATATACACATTCACATTCATCA-ATC-GCCATTAGCC-T
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTT
2647 ATCACATATATATATACACTTTCACATTC-TCACATCGGCCATTAGGCCTT
1 ATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTT
2697 ATCAC-TATATACACTTTCACATTCATCACATCGGCCATTAG----
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTT
*
2738 -GC-C-TATATAC-CTTTCACATTCATCACATCGGCCATTAGGCC-T
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTT
2780 ATCACATATATACA-TTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTT
*
2826 ATCACATATATACAC-TTCACATTCATCACATC-GCTATTAGGCC-T
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTT
2870 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTT
* *
2916 ATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTT
1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATT-AGCCTT
* *
2965 ATCACATATATACACTTTCACATTCATCATATC-GCCATTGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTT
* *
3010 AT-ACATTATATA-ACTTTCACA-TCATCACATTGGCCATTCGGCCTT
1 ATCACA-TATATACACTTTCACATTCATCACATCGGCCATT-AGCCTT
*
3055 ATCACATATACACAC-TTCACATTCATCACATCGGCCATTAGCC-T
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTT
*
3099 ATACATATATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTT
1 AT-C--ACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTT
* *
3148 A-CACATATATACAC-TTCACATTCATCACATTGGCCATTCGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATT-AGCCTT
3193 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTT
* *
3240 ATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGCTT
1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGCCTT
3288 ATCACATATATACACTTTCACATT
1 ATCACATATATACACTTTCACATT
3312 TATTCAAATA
Statistics
Matches: 636, Mismatches: 26, Indels: 89
0.85 0.03 0.12
Matches are distributed among these distances:
38 27 0.04
39 9 0.01
40 1 0.00
41 6 0.01
42 3 0.00
43 15 0.02
44 40 0.06
45 183 0.29
46 123 0.19
47 120 0.19
48 53 0.08
49 50 0.08
50 6 0.01
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (46 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTT
Found at i:3093 original size:275 final size:271
Alignment explanation
Indices: 2559--3310 Score: 1027
Period size: 275 Copynumber: 2.8 Consensus size: 271
2549 ATTATAAAAA
* * *
2559 ATCACA-ATAATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACA-TT
1 ATCACATAT-ATACAC-TTCACATTCATCACA-TCGCCATTAGGCC-TATCACATATATACACTT
2622 CACATTCATCA-ATC-GCCATTAGCC-TATCACATATATATATACACTTTCACATTC-TCACATC
62 CACATTCATCACATCGGCCATTAGCCTTATCAC--ATATATATACACTTTCACATTCATCACATC
2683 GGCCATTAGGCCTTATCAC-TATATACACTTTCACATTCATCACATCGGCCATTAGGC-----C-
125 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCTTATACA
* * *
2741 TATATACCTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACATTTCACATTCAT
190 TATATAACTTTCACA-TCATCACATCGGCCATTAGGCCTATCACATATACACACTTCACATTCAT
2806 CACATCGGCCATTAGGCCTT
254 CACATCGGCCATTA-GCC-T
*
2826 ATCACATATATACACTTCACATTCATCACATCGCTATTAGGCCTATCACATATATACACTTTCAC
1 ATCACATATATACACTTCACATTCATCACATCGCCATTAGGCCTATCACATATATACAC-TTCAC
*
2891 ATTCATCACATCGGCCATTAGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCA
65 ATTCATCACATCGGCCATTAGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCA
* *
2956 TTCGGCCTTATCACATATATACACTTTCACATTCATCATATC-GCCATT-GGCCTTATACATTAT
130 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CTTATACA-TAT
* *
3019 ATAACTTTCACATCATCACATTGGCCATTCGGCCTTATCACATATACACACTTCACATTCATCAC
193 ATAACTTTCACATCATCACATCGGCCATTAGGCC-TATCACATATACACACTTCACATTCATCAC
3084 ATCGGCCATTAGCCT
257 ATCGGCCATTAGCCT
*
3099 ATACATATATATATACACTTCACATTCATCACATCGGCCATTAGGCCT-TACACATATATACACT
1 AT-C--ACATATATACACTTCACATTCATCACATC-GCCATTAGGCCTAT-CACATATATACACT
* *
3163 TCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCACATC
61 TCACATTCATCACATCGGCCATT-AGCCTTATCACATATATATACACTTTCACATTCATCACATC
*
3226 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGCTTATC
125 GGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCTTAT-
3291 ACATATATACACTTTCACAT
187 ACATATATA-ACTTTCACAT
3311 TTATTCAAAT
Statistics
Matches: 436, Mismatches: 20, Indels: 46
0.87 0.04 0.09
Matches are distributed among these distances:
264 14 0.03
265 10 0.02
266 28 0.06
267 39 0.09
268 43 0.10
269 32 0.07
273 4 0.01
274 24 0.06
275 98 0.22
276 52 0.12
277 61 0.14
278 16 0.04
279 15 0.03
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (271 bp):
ATCACATATATACACTTCACATTCATCACATCGCCATTAGGCCTATCACATATATACACTTCACA
TTCATCACATCGGCCATTAGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCAT
TAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCTTATACATATATA
ACTTTCACATCATCACATCGGCCATTAGGCCTATCACATATACACACTTCACATTCATCACATCG
GCCATTAGCCT
Found at i:5747 original size:18 final size:19
Alignment explanation
Indices: 5724--5760 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5714 GCTATTTTGC
5724 ATAAGT-TGCAAAATAGTG
1 ATAAGTGTGCAAAATAGTG
*
5742 ATAAGTGTGCGAAATAGTG
1 ATAAGTGTGCAAAATAGTG
5761 GATTTTGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (19 bp):
ATAAGTGTGCAAAATAGTG
Found at i:12840 original size:15 final size:15
Alignment explanation
Indices: 12810--12852 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
12800 TTAATTTTAT
12810 ATTATCTTTTTAATATA
1 ATTAT-TTTTT-ATATA
12827 ATTATTTTTTATATA
1 ATTATTTTTTATATA
*
12842 ATTATTCTTTA
1 ATTATTTTTTA
12853 ATTCATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 15 0.60
16 5 0.20
17 5 0.20
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTTTTTATATA
Found at i:14073 original size:23 final size:23
Alignment explanation
Indices: 14043--14113 Score: 101
Period size: 23 Copynumber: 3.1 Consensus size: 23
14033 AAATTGTTTA
*
14043 GGGCTGTCAAATTTGGGGATTTT
1 GGGCTGTCGAATTTGGGGATTTT
14066 GGGCTGTCGAATTTGGGGA-TTT
1 GGGCTGTCGAATTTGGGGATTTT
*
14088 GGG-TGGTTGAATTTGGGGATTTT
1 GGGCT-GTCGAATTTGGGGATTTT
14111 GGG
1 GGG
14114 TAAGGGTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.02
22 19 0.43
23 24 0.55
ACGTcount: A:0.14, C:0.06, G:0.42, T:0.38
Consensus pattern (23 bp):
GGGCTGTCGAATTTGGGGATTTT
Found at i:14126 original size:29 final size:29
Alignment explanation
Indices: 14094--14172 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 29
14084 ATTTGGGTGG
14094 TTGAATTTGGGGATTTTGGGTAAGGGTTT
1 TTGAATTTGGGGATTTTGGGTAAGGGTTT
* * ** *
14123 TTGACTTTGGGAATTTTTGTTTAAGGTTTT
1 TTGAATTTGGGGA-TTTTGGGTAAGGGTTT
* * *
14153 TTGATTTTTGAGATTTTGGG
1 TTGAATTTGGGGATTTTGGG
14173 GATTGCTCAC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
29 16 0.42
30 22 0.58
ACGTcount: A:0.16, C:0.01, G:0.30, T:0.52
Consensus pattern (29 bp):
TTGAATTTGGGGATTTTGGGTAAGGGTTT
Found at i:14785 original size:11 final size:11
Alignment explanation
Indices: 14769--14835 Score: 72
Period size: 11 Copynumber: 6.5 Consensus size: 11
14759 GTTTAGGCTT
14769 TTTTAAAATAA
1 TTTTAAAATAA
*
14780 TTTT--AATTA
1 TTTTAAAATAA
*
14789 TTTTAAAATCA
1 TTTTAAAATAA
14800 TTTT--AATAA
1 TTTTAAAATAA
*
14809 TTTT-AAATTA
1 TTTTAAAATAA
14819 TTTTAAAATAA
1 TTTTAAAATAA
14830 TTTTAA
1 TTTTAA
14836 TAATTTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
9 16 0.34
10 8 0.17
11 23 0.49
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAA
Found at i:14794 original size:20 final size:20
Alignment explanation
Indices: 14769--14835 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
14759 GTTTAGGCTT
*
14769 TTTTAAAATAATTTTAATTA
1 TTTTAAAATAATTTTAATAA
*
14789 TTTTAAAATCATTTTAATAA
1 TTTTAAAATAATTTTAATAA
*
14809 TTTT-AAATTATTTTAAAATAA
1 TTTTAAAATAATTTT--AATAA
14830 TTTTAA
1 TTTTAA
14836 TAATTTCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 9 0.22
20 22 0.54
21 9 0.22
22 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAAAATAATTTTAATAA
Found at i:14820 original size:30 final size:30
Alignment explanation
Indices: 14775--14852 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
14765 GCTTTTTTAA
*
14775 AATAATTTT-AATTATTTTAAAATCATTTT
1 AATAATTTTAAATTATTTTAAAATAATTTT
14804 AATAATTTTAAATTATTTTAAAATAATTTT
1 AATAATTTTAAATTATTTTAAAATAATTTT
*
14834 AATAATTTCAAATTCATTT
1 AATAATTTTAAATT-ATTT
14853 GTTGATGTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 9 0.20
30 32 0.71
31 4 0.09
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (30 bp):
AATAATTTTAAATTATTTTAAAATAATTTT
Found at i:14839 original size:9 final size:10
Alignment explanation
Indices: 14769--14846 Score: 72
Period size: 9 Copynumber: 7.8 Consensus size: 10
14759 GTTTAGGCTT
14769 TTTTAAAATAA
1 TTTT-AAATAA
*
14780 TTTT-AATTA
1 TTTTAAATAA
*
14789 TTTTAAAATCA
1 TTTT-AAATAA
14800 TTTT-AATAA
1 TTTTAAATAA
*
14809 TTTTAAATTA
1 TTTTAAATAA
14819 TTTTAAAATAA
1 TTTT-AAATAA
14830 TTTT-AATAA
1 TTTTAAATAA
*
14839 TTTCAAAT
1 TTTTAAAT
14847 TCATTTGTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
9 24 0.43
10 11 0.20
11 21 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:17761 original size:31 final size:31
Alignment explanation
Indices: 17726--17787 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
17716 ATATGTGTTA
*
17726 GGCTTTTGGATTCAAATTGAGTTGCATTATG
1 GGCTTTTAGATTCAAATTGAGTTGCATTATG
17757 GGCTTTTAGATTCAAATTGAGTTGCATTATG
1 GGCTTTTAGATTCAAATTGAGTTGCATTATG
17788 CTATGTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (31 bp):
GGCTTTTAGATTCAAATTGAGTTGCATTATG
Done.