Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold855
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: 17599
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Found at i:2280 original size:28 final size:28
Alignment explanation
Indices: 2240--2311 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
2230 GAAATAAAGC
* **
2240 CGGGGTTGGAGTATCCCC-TCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAC-GAAATAA
2268 CGGGGTTGGAGTATCCCCGACGAAATAA
1 CGGGGTTGGAGTATCCCCGACGAAATAA
*
2296 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2312 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGACGAAATAA
Found at i:2281 original size:79 final size:78
Alignment explanation
Indices: 2064--2284 Score: 255
Period size: 78 Copynumber: 2.8 Consensus size: 78
2054 GATGAAATTT
* * * *
2064 AATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTTGAAAATAATGGGGTTGGAGTATCCCC
1 AATATTTTGGAAATAA-AACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCA
* **
2129 GATTGTGAAAAATC
65 AATTACGAAAAATC
* * * * *
2143 GATGA-TTAGGAAATAAATCGGGATTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCA
1 AAT-ATTTTGGAAATAAAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCA
*
2207 AATTACGAGAAATC
65 AATTACGAAAAATC
* * **
2221 AATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCC
1 AATATTTTGGAAATAAA-ACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
2285 CGACGAAATA
Statistics
Matches: 118, Mismatches: 21, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
77 1 0.01
78 65 0.55
79 51 0.43
80 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.26
Consensus pattern (78 bp):
AATATTTTGGAAATAAAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCAA
ATTACGAAAAATC
Found at i:2464 original size:52 final size:51
Alignment explanation
Indices: 2294--2948 Score: 331
Period size: 51 Copynumber: 12.6 Consensus size: 51
2284 CCGACGAAAT
* * * *
2294 AACGAGGTTGGAGTATCCTCGATTGTG-AAAATTGGTGTTTTTGGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGGAAATAAA
* * * *
2345 ATCGGAGTTGGAGTATCCCCAATTA--AAGGAAATTTGATGTTTT-GAAAT-AA
1 AACGGGGTTGGAGTATCCCCGATTATGAA--AAATTAG-TGTTTTGGAAATAAA
* *
2395 AACCGGGTTGGAGTATCCCCGATTATGAAAAATTTAGTGTTTTAGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAA-TTAGTGTTTTGGAAATAAA
* * * * *
2447 AACGGGGTTAGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAA
** * *** * * * *****
2498 GCCGGGGTTGGAGTATCCCCTCGGAGGTAATG--GGGTTGGAGTATCACCGATGAAA
1 AACGGGGTTGGAGTAT-CCC-C-GA--TTATGAAAAATTAGTGTTTTGGAAAT-AAA
* * * *
2553 TAACGAGGTTTGGAGTATCCTCGA-TGTGAAAAATTGGTGTTTTTGGAAATAAA
1 -AACG-GGGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGGAAATAAA
* * * * *
2606 ATCGGAGTTGGAGTATCCCCGATTAAAGAAAAAATTGGTGTTTTTGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATT-ATG-AAAAATTAGTGTTTTGGAAATAAA
* * * *
2659 ACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTTAGTGTTTTAGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAA
* * * * * *
2711 AACGGGG-TGGAGTATTCCCGATTGTGAGAAATCAATATTTTGGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAA
* **** * *** * * * *****
2761 AGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAA
1 A-ACGGGGTTGGAGTATCCCCGATTATG-AA--AAATTAGTGTTTTGGAAATAAA
* * * * *
2816 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTAGAAATAAA
1 -AACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGGAAATAAA
* * * * * *
2869 ATCGGAGTTGGAGTATCCCCGATTA-AAAGAAATTGGTATTTTAGAAATAAA
1 AACGGGGTTGGAGTATCCCCGATTATGAA-AAATTAGTGTTTTGGAAATAAA
*
2920 ATCGGGGTTGGAGTATCCCCGATTATGAA
1 AACGGGGTTGGAGTATCCCCGATTATGAA
2949 CAACTGGAGA
Statistics
Matches: 445, Mismatches: 126, Indels: 65
0.70 0.20 0.10
Matches are distributed among these distances:
50 53 0.12
51 138 0.31
52 124 0.28
53 55 0.12
54 26 0.06
55 29 0.07
56 9 0.02
57 11 0.02
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAA
Found at i:2857 original size:263 final size:263
Alignment explanation
Indices: 2187--2948 Score: 1245
Period size: 261 Copynumber: 2.9 Consensus size: 263
2177 CCTCGAAAAT
* *
2187 AACGGGGTTGGAGTA-TCCCAAATTACGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAG
1 AACGGGGTTGGAGTATTCCC-GATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAG
*
2251 TATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGACGAAATAACGAGGTTGGAGTATCCTCGA
65 TATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGA-TAAATAACGAGGTTGGAGTATCCTCGA
* * *
2316 TTGTG-AAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCAATTAAAG-GAAATT
129 TTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAAAT
*
2379 TGATG-TTTTGAAATAAAACC-GGGTTGGAGTATCCCCGATTATGAAAAATTTAGTGTTTTAGAA
194 TGGTGTTTTTGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATTTAGTGTTTTAGAA
2442 ATAAA
259 ATAAA
* *
2447 AACGGGGTTAGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATTCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGT
* *
2512 ATCCCCTCGGAGGTAATGGGGTTGGAGTATCACCGATGAAATAACGAGGTTTGGAGTATCCTCGA
66 ATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGAT-AAATAACGAGG-TTGGAGTATCCTCGA
2577 -TGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAAAT
129 TTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAAAT
* *
2641 TGGTGTTTTTGAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTTAGTGTTTTAGAA
194 TGGTGTTTTTGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATTTAGTGTTTTAGAA
2706 ATAAA
259 ATAAA
*
2711 AACGGGG-TGGAGTATTCCCGATTGTGAGAAATCAATATTTTGGAAATAAAAGCCGGGGTTGGAG
1 AACGGGGTTGGAGTATTCCCGATTATGAGAAATCAATATTTTGGAAAT-AAAGCCGGGGTTGGAG
2775 TATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAATAACGAGGTTGGAGTATCCTCGAT
65 TATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAATAACGAGGTTGGAGTATCCTCGAT
* *
2840 TGTGAAAAATTGGTGTTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATT-AA-AAGAAATT
130 TGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAAATT
* * *
2903 GGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAA
195 GGTGTTTTTGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAA
2949 CAACTGGAGA
Statistics
Matches: 468, Mismatches: 25, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
260 106 0.23
261 117 0.25
262 25 0.05
263 115 0.25
264 105 0.22
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (263 bp):
AACGGGGTTGGAGTATTCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGT
ATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAATAACGAGGTTGGAGTATCCTCGATT
GTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAAATTG
GTGTTTTTGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATTTAGTGTTTTAGAAAT
AAA
Done.