Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga02g00816.F1
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: 6219
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Found at i:67 original size:18 final size:18
Alignment explanation
Indices: 46--101 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
36 AGCTTCAGGC
*
46 TCATCTTCACATTCCAGT
1 TCATCTTCACATTCAAGT
* *
64 TCATATTCACATTCTAGT
1 TCATCTTCACATTCAAGT
*
82 TCTTCTTCACATTCAAGT
1 TCATCTTCACATTCAAGT
100 TC
1 TC
102 TTTTAAGCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.29, G:0.05, T:0.43
Consensus pattern (18 bp):
TCATCTTCACATTCAAGT
Found at i:112 original size:18 final size:18
Alignment explanation
Indices: 49--120 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 18
39 TTCAGGCTCA
* * *
49 TCTTCACATTCCAGTTCA
1 TCTTAACATTCAAGTTCT
* * *
67 TATTCACATTCTAGTTCT
1 TCTTAACATTCAAGTTCT
*
85 TCTTCACATTCAAGTTCT
1 TCTTAACATTCAAGTTCT
*
103 T-TTAAGCATTCAAATTCT
1 TCTTAA-CATTCAAGTTCT
121 GGTTCTTCTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
17 3 0.07
18 43 0.93
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (18 bp):
TCTTAACATTCAAGTTCT
Found at i:677 original size:192 final size:192
Alignment explanation
Indices: 310--1143 Score: 760
Period size: 192 Copynumber: 4.2 Consensus size: 192
300 TTCAAGTTCA
* * * * * * * *
310 GCTTCTGGATCATCCTCAAAATCTAGTTTATCTCCACATTCCGGTTCTAGTGCTACTAACTCATC
1 GCTTCAGGCTCATCCTCAAATTCCAGTTCATCTTCACATTCTGGTTCTAGTGCTGCTAACTCATC
* * * * * *
375 CACATACTTGGGTTCTGACAATTCTAAGGATACTGATTCTACTACAACTTCTCAGTCTTCATTAA
66 CAAAAACTTAGGTTCTAACAATTCTAAGGATTCTGATTCTACTACAGCTTCTCAGTCTTCATTAA
* ** * *
440 ATCATAAGGCTTCTAGTTCCTCTGCAAGTTCT-AGTTCTCTATCAGGTACTAGCAATTATAAG
131 ATCATAAGGCTTCTAATTCCTCCACAAGTTCTGA-TTCTTTATCAGGTTCTAGCAATTATAAG
* **
502 GCTTCAGGCTTATCCAAAAATTCCAGTTCATCTTCACATTCTGGTTCTAGTGCTGCTAACTCATC
1 GCTTCAGGCTCATCCTCAAATTCCAGTTCATCTTCACATTCTGGTTCTAGTGCTGCTAACTCATC
* * *
567 CAAAAACTCAGGTTCTAACCATTCTAAGGATTCTTATTCTAC-AGCAGCTTCTCAGTCTTCATTA
66 CAAAAACTTAGGTTCTAACAATTCTAAGGATTCTGATTCTACTA-CAGCTTCTCAGTCTTCATTA
** * * ** *
631 AATCATGGGGCTTCTAGTTCCTCCATAAGTTCTGATTCTTTATCAGGTTCTAATAATTCTAAG
130 AATCATAAGGCTTCTAATTCCTCCACAAGTTCTGATTCTTTATCAGGTTCTAGCAATTATAAG
** * * * * * * * *
694 GCTTTTGGCTCATCTTCAGACTCCAGTTC-TTTTAAGCATTCTGGTTCTGGTGCTTCTAACTCTT
1 GCTTCAGGCTCATCCTCAAATTCCAGTTCATCTTCA-CATTCTGGTTCTAGTGCTGCTAACTCAT
* * * * * *** *
758 CCACAAA-TATAGGTTCCAACAATTCTAATGATTCTGCTCCTACTGTGGCTTCTCAGTCTACATT
65 CCAAAAACT-TAGGTTCTAACAATTCTAAGGATTCTGATTCTACTACAGCTTCTCAGTCTTCATT
*** ** *
822 AAATCACGGGGCTTCTAATTCCTCTTCAAGTTCTGGTTCTTTATCAGGTTCTAGCAATTATAAG
129 AAATCATAAGGCTTCTAATTCCTCCACAAGTTCTGATTCTTTATCAGGTTCTAGCAATTATAAG
* * * *
886 GCTTCCGGGTCATCCTCAAATTCTATTTCATCTTCACATTCTGGTTCTTTTAATCACTTTGGTCC
1 GCTTCAGGCTCATCCTCAAATTCCAGTTCATCTTCACATTCTGGTTC------T-A-----G---
* * * * * * *
951 TATTGCTGGTAACTCCTCCACAAACTTAGGTTCTAACAGTTCTAAGGGTTCTAATTCTACTACGG
51 ---TGCTGCTAACTCATCCAAAAACTTAGGTTCTAACAATTCTAAGGATTCTGATTCTACTACAG
* * *
1016 CTTCTCAGTCTTCATTAAA-CTATAAGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAAG
113 CTTCTCAGTCTTCATTAAATC-ATAAGGCTTCTAATTCCTCCACAAGTTCTGATTCTTTATCAGG
*
1080 TTCTAGAAATTATAAG
177 TTCTAGCAATTATAAG
* *
1096 GCTTCGGGCTCATCCTCAAATTCTAGTTCATCTTCACATTCTGGTTCT
1 GCTTCAGGCTCATCCTCAAATTCCAGTTCATCTTCACATTCTGGTTCT
1144 TTTAAGCATT
Statistics
Matches: 519, Mismatches: 97, Indels: 40
0.79 0.15 0.06
Matches are distributed among these distances:
191 6 0.01
192 340 0.66
193 5 0.01
198 1 0.00
204 2 0.00
209 1 0.00
210 163 0.31
211 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (192 bp):
GCTTCAGGCTCATCCTCAAATTCCAGTTCATCTTCACATTCTGGTTCTAGTGCTGCTAACTCATC
CAAAAACTTAGGTTCTAACAATTCTAAGGATTCTGATTCTACTACAGCTTCTCAGTCTTCATTAA
ATCATAAGGCTTCTAATTCCTCCACAAGTTCTGATTCTTTATCAGGTTCTAGCAATTATAAG
Found at i:1065 original size:210 final size:210
Alignment explanation
Indices: 719--1310 Score: 719
Period size: 210 Copynumber: 2.8 Consensus size: 210
709 TCAGACTCCA
* ** * * * *
719 GTTCTTTTAAGCATTCTGGTTCTGGTGCTTCTAACTCTTCCACAAATATAGGTTCCAACAATTCT
1 GTTCTTTTAAGCATTCTGGTCCTACTACTGCTAACTCATCCACAAAT-TAGGTTCTAACAATTCT
* ** ** * * * *
784 AATGATTCTGCTCCTACTGTGGCTTCTCAGTCTACATTAAA-TCACGGGGCTTCTAATTCCTCTT
65 AAGGATTCTAATCCTACTACGGCTTCTCAGTCTTCATTAAACT-ATGAGGCTTCTAATTCCTCTA
* *
848 CAAGTTCTGGTTCTTTATCAGGTTCTAGCAATTATAAGGCTTCCGGG-TCATCCTCAAATTCTAT
129 CAAGTTCTGGTTCTTTATCAGGTTCTAGAAATTATAAGGCTTCCGGGCTCATCCTCAAATTCTAG
912 TTCATCTTCACATTCTG
194 TTCATCTTCACATTCTG
* * * * * *
929 GTTCTTTTAATCACTT-TGGTCCTATTGCTGGTAACTCCTCCACAAACTTAGGTTCTAACAGTTC
1 GTTCTTTTAAGCA-TTCTGGTCCTACTACTGCTAACTCATCCACAAA-TTAGGTTCTAACAATTC
* * *
993 TAAGGGTTCTAATTCTACTACGGCTTCTCAGTCTTCATTAAACTATAAGGCTTCTAATTCCTCTA
64 TAAGGATTCTAATCCTACTACGGCTTCTCAGTCTTCATTAAACTATGAGGCTTCTAATTCCTCTA
*
1058 CAAGTTCTGGTTCTTTATCAAGTTCTAGAAATTATAAGGCTT-CGGGCTCATCCTCAAATTCTAG
129 CAAGTTCTGGTTCTTTATCAGGTTCTAGAAATTATAAGGCTTCCGGGCTCATCCTCAAATTCTAG
1122 TTCATCTTCACATTCTG
194 TTCATCTTCACATTCTG
* * *
1139 GTTCTTTTAAGCATTCTGGTTCTACTACTGCTAACTTATCCACAAATTCTGGTT-TGAACAATTC
1 GTTCTTTTAAGCATTCTGGTCCTACTACTGCTAACTCATCCACAAATT-AGGTTCT-AACAATTC
* * * **
1203 TAAGGATTCTAGTCCTACTACGGCTTCTAAGTCTTCTTTAGAAC-ATGAGGCTTCTGGTTCCTCT
64 TAAGGATTCTAATCCTACTACGGCTTCTCAGTCTTCATTA-AACTATGAGGCTTCTAATTCCTCT
* ** *
1267 ACAAGTTCTGGTTCTTTGTCAGGTTCTAGTGATTCTAAGGCTTC
128 ACAAGTTCTGGTTCTTTATCAGGTTCTAGAAATTATAAGGCTTC
1311 TGGCTTGTCA
Statistics
Matches: 327, Mismatches: 46, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
209 9 0.03
210 311 0.95
211 7 0.02
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (210 bp):
GTTCTTTTAAGCATTCTGGTCCTACTACTGCTAACTCATCCACAAATTAGGTTCTAACAATTCTA
AGGATTCTAATCCTACTACGGCTTCTCAGTCTTCATTAAACTATGAGGCTTCTAATTCCTCTACA
AGTTCTGGTTCTTTATCAGGTTCTAGAAATTATAAGGCTTCCGGGCTCATCCTCAAATTCTAGTT
CATCTTCACATTCTG
Found at i:1927 original size:18 final size:18
Alignment explanation
Indices: 1904--1939 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1894 AAAGGATTTG
1904 GTTCTGATAATTCTCAAA
1 GTTCTGATAATTCTCAAA
**
1922 GTTCTGATTCTTCTCAAA
1 GTTCTGATAATTCTCAAA
1940 CTTCACAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (18 bp):
GTTCTGATAATTCTCAAA
Found at i:3098 original size:312 final size:312
Alignment explanation
Indices: 2533--3160 Score: 1033
Period size: 312 Copynumber: 2.0 Consensus size: 312
2523 TGGTTCGTTT
* *
2533 ACAGCTTCTGGTCACTCTTCCGCAAGTCATAGTTCTGGTTTTAAAGCTTTAGGCTCCTCATCAGG
1 ACAGCTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTTTTAAAGCTTCAGGCTCCTCATCAGG
* *
2598 TTCTGAAGGGTCTAAGACCGCTACAAGTGACTCTTCGGTTTCTGGTAATTCAAAGGCTTCAAGTA
66 TTCTGAAGGATCTAAGACCGCTACAAGTGACTCTTCAGTTTCTGGTAATTCAAAGGCTTCAAGTA
* *
2663 CTAAAAATGAAAGTGCTTCCATGGGTTCCAATGCTTCAGCGACTAATGGTTCTACGACTTTTATT
131 CTAAAAATGAAAGTGCTTCCATGGGTACCAATGCTTCAACGACTAATGGTTCTACGACTTTTATT
* *
2728 CCTACGAACCCTTCCACAGGTTCTGACGGATCTATGTCTTCAATAAGTAACCCTTCAGGCACTAG
196 CCTACGAACCCTTCCACAGGTTCTGACGGATCTAAGTCTTCAACAAGTAACCCTTCAGGCACTAG
* * *
2793 TACTTCAGTGACAAATGGTCCTACAGCTTCTACTCCTTCTTCAAGCCCTTCC
261 TACTTCAATAACAAATGGTCCTACAGCTTCTACTCCTCCTTCAAGCCCTTCC
* * * *
2845 ACAGCTTTTGGTCGCTCTTCCGCAAGTCATGGTTCTAGTTTTAAAGCTTCAGGCTCCTCATTAGG
1 ACAGCTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTTTTAAAGCTTCAGGCTCCTCATCAGG
* ** *
2910 TTCTGAAGGATCTAAGTCTTCTACGAA-TGACTCTTCAGTTTCTGGTAATTCCAAGGCTTCAAGT
66 TTCTGAAGGATCTAAGACCGCTAC-AAGTGACTCTTCAGTTTCTGGTAATTCAAAGGCTTCAAGT
2974 ACTAAAAATGAAAGTGCTTCCATGGGTACCAATGCTTCAACGACTAATGGTTCTACGACTTTTAT
130 ACTAAAAATGAAAGTGCTTCCATGGGTACCAATGCTTCAACGACTAATGGTTCTACGACTTTTAT
* *
3039 TCTTACGAACCCTTCCACAGGTTCTGACGGATCTAAGTCTTCTACAAGTAACCCTTCAGGCACTA
195 TCCTACGAACCCTTCCACAGGTTCTGACGGATCTAAGTCTTCAACAAGTAACCCTTCAGGCACTA
* *
3104 GTACTTCAATAACAAATGGTCCTACAGCTTTTACTCCTCCTTCGAGCCCTTCC
260 GTACTTCAATAACAAATGGTCCTACAGCTTCTACTCCTCCTTCAAGCCCTTCC
3157 ACAG
1 ACAG
3161 GCGTTAGTTA
Statistics
Matches: 292, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
312 290 0.99
313 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (312 bp):
ACAGCTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTTTTAAAGCTTCAGGCTCCTCATCAGG
TTCTGAAGGATCTAAGACCGCTACAAGTGACTCTTCAGTTTCTGGTAATTCAAAGGCTTCAAGTA
CTAAAAATGAAAGTGCTTCCATGGGTACCAATGCTTCAACGACTAATGGTTCTACGACTTTTATT
CCTACGAACCCTTCCACAGGTTCTGACGGATCTAAGTCTTCAACAAGTAACCCTTCAGGCACTAG
TACTTCAATAACAAATGGTCCTACAGCTTCTACTCCTCCTTCAAGCCCTTCC
Found at i:4080 original size:198 final size:197
Alignment explanation
Indices: 3618--4083 Score: 657
Period size: 198 Copynumber: 2.4 Consensus size: 197
3608 GCAATAGTTT
* *
3618 TGGTTCCAAAACTTCAAGCTCTTCCACAAACATTGGTTCTACTTCGACTGATGGCCATACAACTA
1 TGGTTCCAAAACTTCAAGCTCTTCCAC-AACACTGGTTCTACTACGACTGATGGCCATACAACTA
* * *
3683 CCGGTTCTACTTTGAGTGCCTCTTCAGGTTCTAGTTCTCGTAAGACTAATAGTCACATGACTTCT
65 CTGGTTCTACTTTGAGTCCCTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACATGACTTCT
* * * * *
3748 AGTCATACAAAATCTAGTTCTTCCACACACACCGATTCTTCCAATCACGCTGGTTCTTTGACAAC
130 AGTCATACAAAATCTAGCTCTTCCACACACACAGATTCTTCCAAACACACTGGTTCTTTCACAAC
3813 ATC
195 ATC
* * ** *
3816 TGGTTCCAAAACTTCAGGCTCTTCTACTAACACTGGTTCCGCTACGACTGATGGCAATACAACTA
1 TGGTTCCAAAACTTCAAGCTCTTCCAC-AACACTGGTTCTACTACGACTGATGGCCATACAACTA
* * *
3881 CTGGTTCTATTTTGAG-CCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACATGAGTTT
65 CTGGTTCTACTTTGAGTCC-CTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACATGACTTC
* * *
3945 TGGTCATACAAAATC-AGGCTCTTCTACACACACAGGTTCTTCCAAACACACTGGTTCTTTCACA
129 TAGTCATACAAAATCTA-GCTCTTCCACACACACAGATTCTTCCAAACACACTGGTTCTTTCACA
4009 ACATC
193 ACATC
* * *
4014 TGGTTCCAAAACTTCAAGCTCTTCCACAAGCCCTGGTTCTACTACGACTAATGGCCATGCAACTA
1 TGGTTCCAAAACTTCAAGCTCTTCCACAA-CACTGGTTCTACTACGACTGATGGCCATACAACTA
4079 CTGGT
65 CTGGT
4084 CCTGCTATGA
Statistics
Matches: 235, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
197 4 0.02
198 231 0.98
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (197 bp):
TGGTTCCAAAACTTCAAGCTCTTCCACAACACTGGTTCTACTACGACTGATGGCCATACAACTAC
TGGTTCTACTTTGAGTCCCTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACATGACTTCTA
GTCATACAAAATCTAGCTCTTCCACACACACAGATTCTTCCAAACACACTGGTTCTTTCACAACA
TC
Found at i:4556 original size:198 final size:198
Alignment explanation
Indices: 4229--4599 Score: 589
Period size: 198 Copynumber: 1.9 Consensus size: 198
4219 TCTTCCAATC
* *
4229 ACACTGGTTCTGCTACAACTGATGGCCATACAACTACTGGTTCTATTTCGAGCTACTCTTCAGGT
1 ACACTGGTGCTGCTACAACTGATGGCCATACAACTACTGGTTCTATTTCGAGCCACTCTTCAGGT
* * *
4294 TCTAGTTCTCATAAGACTAATAGTCACACGACATCTGCTCATACAAAATCTGGCTCTTCTACACA
66 TCTACTTCTCATAACACTAATAGTCACACGACATCTACTCATACAAAATCTGGCTCTTCTACACA
* *
4359 CACAAGTTCCTCTAAATACACAGGTTCTTTCACAACCTCTGGTTCTAAAATTTCGGGCTCTTCCA
131 CACAAGTTCCTCCAAACACACAGGTTCTTTCACAACCTCTGGTTCTAAAATTTCGGGCTCTTCCA
4424 CAA
196 CAA
* * * *
4427 ACACTGGTGCTGCTACGATTGGTGGCCATACAACTACTGGTTCTATTTCGAGCCACTCTTTAGGT
1 ACACTGGTGCTGCTACAACTGATGGCCATACAACTACTGGTTCTATTTCGAGCCACTCTTCAGGT
* * *
4492 TCTACTTCTCATAACAGTAATAGTCACACGACTTCTACTCATACAAAATTTGGCTCTTCTACACA
66 TCTACTTCTCATAACACTAATAGTCACACGACATCTACTCATACAAAATCTGGCTCTTCTACACA
* * *
4557 CACAGGTTCTTCCAAACACACTGGTTCTTTCACAACCTCTGGT
131 CACAAGTTCCTCCAAACACACAGGTTCTTTCACAACCTCTGGT
4600 CACTCTTCCA
Statistics
Matches: 156, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
198 156 1.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (198 bp):
ACACTGGTGCTGCTACAACTGATGGCCATACAACTACTGGTTCTATTTCGAGCCACTCTTCAGGT
TCTACTTCTCATAACACTAATAGTCACACGACATCTACTCATACAAAATCTGGCTCTTCTACACA
CACAAGTTCCTCCAAACACACAGGTTCTTTCACAACCTCTGGTTCTAAAATTTCGGGCTCTTCCA
CAA
Done.