Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold422
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: 33998
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:2392 original size:22 final size:22
Alignment explanation
Indices: 2367--2419 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2357 CAATCCTCTT
* * * *
2367 TCAATTTTCTCCTATTTTTCTC
1 TCAATTTTCTCATAATTCTCGC
*
2389 TCAATTCTCTCATAATTCTCGC
1 TCAATTTTCTCATAATTCTCGC
2411 TCAATTTTC
1 TCAATTTTC
2420 AATCCTCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.02, T:0.51
Consensus pattern (22 bp):
TCAATTTTCTCATAATTCTCGC
Found at i:2399 original size:11 final size:11
Alignment explanation
Indices: 2324--2416 Score: 50
Period size: 11 Copynumber: 8.5 Consensus size: 11
2314 CATTTCCTTT
*
2324 TCAATTCACTC
1 TCAATTCTCTC
* *
2335 TTACTTCTCTC
1 TCAATTCTCTC
2346 T-AATTCAT-TC
1 TCAATTC-TCTC
* *
2356 TCAATCCTCTT
1 TCAATTCTCTC
*
2367 TCAATTTTCTC
1 TCAATTCTCTC
* *
2378 -CTATTTTTCTC
1 TC-AATTCTCTC
2389 TCAATTCTCTC
1 TCAATTCTCTC
*
2400 AT-AATTCTCGC
1 -TCAATTCTCTC
2411 TCAATT
1 TCAATT
2417 TTCAATCCTC
Statistics
Matches: 62, Mismatches: 13, Indels: 14
0.70 0.15 0.16
Matches are distributed among these distances:
10 10 0.16
11 50 0.81
12 2 0.03
ACGTcount: A:0.20, C:0.30, G:0.01, T:0.48
Consensus pattern (11 bp):
TCAATTCTCTC
Found at i:2482 original size:26 final size:24
Alignment explanation
Indices: 2437--2496 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
2427 TTTCAACTCT
2437 CATTTTTTTATTAAAATTGTATTAA
1 CATTTTTTTATTAAAATTGT-TTAA
** *
2462 CATTTTTTTAATTAATTTTGTTTTA
1 CATTTTTTT-ATTAAAATTGTTTAA
2487 CGATTTTTTT
1 C-ATTTTTTT
2497 CGTATTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (24 bp):
CATTTTTTTATTAAAATTGTTTAA
Found at i:3092 original size:15 final size:16
Alignment explanation
Indices: 3066--3101 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3056 TGGAGTGGGG
*
3066 ATTTAGTTTATTTTTT
1 ATTTAGTTTATTTTTA
3082 ATTTA-TTTATTTTTA
1 ATTTAGTTTATTTTTA
3097 ATTTA
1 ATTTA
3102 AATTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
ATTTAGTTTATTTTTA
Found at i:8650 original size:3 final size:3
Alignment explanation
Indices: 8644--8676 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
8634 TTGTTGTTTT
8644 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8677 GGATTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12741 original size:19 final size:18
Alignment explanation
Indices: 12717--12797 Score: 81
Period size: 20 Copynumber: 4.2 Consensus size: 18
12707 TATAATTCAC
12717 TGCCCTGTTTGCACTTCGG
1 TGCCCTGTTTGCACTT-GG
12736 TGCCCTGTTTGCACTTTGG
1 TGCCCTGTTTGCAC-TTGG
* * *
12755 TGCTTCTGTATGCACATTTG
1 TGC-CCTGTTTGCAC-TTGG
12775 TGCCCTGTTTAGCACCTTGG
1 TGCCCTGTTT-GCA-CTTGG
12795 TGC
1 TGC
12798 TCCTTGATAC
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 24 0.47
20 26 0.51
21 1 0.02
ACGTcount: A:0.09, C:0.27, G:0.25, T:0.40
Consensus pattern (18 bp):
TGCCCTGTTTGCACTTGG
Found at i:12768 original size:20 final size:19
Alignment explanation
Indices: 12717--12797 Score: 92
Period size: 19 Copynumber: 4.2 Consensus size: 19
12707 TATAATTCAC
*
12717 TGCCCTGTTTGCACTTCGG
1 TGCCCTGTTTGCACTTTGG
12736 TGCCCTGTTTGCACTTTGG
1 TGCCCTGTTTGCACTTTGG
* *
12755 TGCTTCTGTATGCACATTT-G
1 TGC-CCTGTTTGCAC-TTTGG
*
12775 TGCCCTGTTTAGCACCTTGG
1 TGCCCTGTTT-GCACTTTGG
12795 TGC
1 TGC
12798 TCCTTGATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
19 28 0.54
20 21 0.40
21 3 0.06
ACGTcount: A:0.09, C:0.27, G:0.25, T:0.40
Consensus pattern (19 bp):
TGCCCTGTTTGCACTTTGG
Found at i:12769 original size:39 final size:40
Alignment explanation
Indices: 12721--12798 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
12711 ATTCACTGCC
* *
12721 CTGTTTGCAC-TTCGGTGCCCTGTTT-GCACTTTGGTGCTT
1 CTGTATGCACATT-GGTGCCCTGTTTAGCACCTTGGTGCTT
*
12760 CTGTATGCACATTTGTGCCCTGTTTAGCACCTTGGTGCT
1 CTGTATGCACATTGGTGCCCTGTTTAGCACCTTGGTGCT
12799 CCTTGATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 20 0.59
40 14 0.41
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (40 bp):
CTGTATGCACATTGGTGCCCTGTTTAGCACCTTGGTGCTT
Found at i:15151 original size:21 final size:21
Alignment explanation
Indices: 15125--15190 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
15115 AGAACCCAGC
15125 ACTTTCCCATAGAGTTCAAAG
1 ACTTTCCCATAGAGTTCAAAG
** * **
15146 ACTTT-CC--AGA-ACCCACC
1 ACTTTCCCATAGAGTTCAAAG
15163 ACTTTCCCATAGAGTTCAAAG
1 ACTTTCCCATAGAGTTCAAAG
15184 ACTTTCC
1 ACTTTCC
15191 ACAATCCTTT
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
17 7 0.23
18 5 0.16
20 5 0.16
21 14 0.45
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (21 bp):
ACTTTCCCATAGAGTTCAAAG
Found at i:15157 original size:38 final size:38
Alignment explanation
Indices: 15115--15191 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
15105 TTGGATTGAA
*
15115 AGAACCCAGCACTTTCCCATAGAGTTCAAAGACTTTCC
1 AGAACCCACCACTTTCCCATAGAGTTCAAAGACTTTCC
15153 AGAACCCACCACTTTCCCATAGAGTTCAAAGACTTTCC
1 AGAACCCACCACTTTCCCATAGAGTTCAAAGACTTTCC
15191 A
1 A
15192 CAATCCTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.23
Consensus pattern (38 bp):
AGAACCCACCACTTTCCCATAGAGTTCAAAGACTTTCC
Found at i:19341 original size:2 final size:2
Alignment explanation
Indices: 19334--19370 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19324 CTCCATCATT
19334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19371 CCAGAGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22370 original size:69 final size:69
Alignment explanation
Indices: 22271--22506 Score: 251
Period size: 69 Copynumber: 3.4 Consensus size: 69
22261 GTGTAATGCT
* ** * * *
22271 ATAGCTTGGCTATGGTAACCAATAGAGTCCATCTAGATAGTAAACACGAGGATTTCAAGGTGAAA
1 ATAGCTTAGCTATGACAACCAATAGAGTCCATCCAGACAGTAAACACGAGGATTTCAAGGTGTAA
22336 GACC
66 GACC
* * * *
22340 ATAGTTTGGCTATGACAACCAATAGAGTCCA-CCAGGACAGTAAACACAAAGATTTCAAGGTGTA
1 ATAGCTTAGCTATGACAACCAATAGAGTCCATCCA-GACAGTAAACACGAGGATTTCAAGGTGTA
***
22404 ATTTC
65 AGACC
* * ** * * * *
22409 ATAGCTCAGCTATGGA-AACCAATAGAGTTCATCGGGACAATAAACACGGGGATTTTAATGTGTA
1 ATAGCTTAGCTAT-GACAACCAATAGAGTCCATCCAGACAGTAAACACGAGGATTTCAAGGTGTA
22473 AGACC
65 AGACC
22478 ATAGCTTAGCTATGACAACCAATAGAGTC
1 ATAGCTTAGCTATGACAACCAATAGAGTC
22507 TGTCAAAACA
Statistics
Matches: 135, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
68 4 0.03
69 128 0.95
70 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (69 bp):
ATAGCTTAGCTATGACAACCAATAGAGTCCATCCAGACAGTAAACACGAGGATTTCAAGGTGTAA
GACC
Found at i:27021 original size:50 final size:50
Alignment explanation
Indices: 26897--27145 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
26887 GATAATAACA
* * ** * *
26897 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
26948 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
26998 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
27048 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
27103 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
27146 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:27075 original size:100 final size:104
Alignment explanation
Indices: 26896--27145 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
26886 TGATAATAAC
**
26896 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
26961 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
26998 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
27061 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
27103 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27146 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:27261 original size:13 final size:13
Alignment explanation
Indices: 27240--27271 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27230 GCTTGGATCA
*
27240 TCATCAAATAAAT
1 TCATAAAATAAAT
27253 TCATAAAATAAAT
1 TCATAAAATAAAT
27266 TCATAA
1 TCATAA
27272 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:27518 original size:30 final size:30
Alignment explanation
Indices: 27483--27540 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
27473 CCTCGACTCT
*
27483 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
27513 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
27541 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Done.