Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2674
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: 35847
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Found at i:3154 original size:27 final size:27
Alignment explanation
Indices: 3124--3321 Score: 159
Period size: 27 Copynumber: 7.4 Consensus size: 27
3114 GAGAAAAATG
* *
3124 GTAATTATACCCAACAAGGGTATCTCA
1 GTAATTCTACCCTACAAGGGTATCTCA
* * *
3151 GTAATTCTACCCTACATGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATCTCA
* * **
3178 GTATTTCTACCCTACAAGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATCTCA
* * * *
3205 GTAATTCTATCCTATAGGGGTATTTC-
1 GTAATTCTACCCTACAAGGGTATCTCA
* * *
3231 GTAATTCTACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATCTCA
* * *
3258 ATAATTCTACCCTACAGGGGTATTTC-
1 GTAATTCTACCCTACAAGGGTATCTCA
* * *
3284 GATAATTCTACCATACAGGGGTATTTC-
1 G-TAATTCTACCCTACAAGGGTATCTCA
3311 GATAATTCTAC
1 G-TAATTCTAC
3322 AACTTATCCA
Statistics
Matches: 149, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 23 0.15
27 126 0.85
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATCTCA
Found at i:3195 original size:54 final size:54
Alignment explanation
Indices: 3123--3321 Score: 240
Period size: 54 Copynumber: 3.7 Consensus size: 54
3113 CGAGAAAAAT
* * * *
3123 GGTAATTATACCCAACAAGGGTATCTCAGTAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* ** * *
3177 GGTATTTCTACCCTACAAGGGTATTTTGGTAATTCTATCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* * *
3231 -GTAATTCTACCCTACAGGGGTATTTTAATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* * *
3284 GATAATTCTACCATACAGGGGTATTTC-GATAATTCTAC
1 GGTAATTCTACCCTACAAGGGTATTTCAG-TAATTCTAC
3322 AACTTATCCA
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
53 47 0.38
54 77 0.62
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
Found at i:3244 original size:80 final size:80
Alignment explanation
Indices: 3141--3321 Score: 238
Period size: 80 Copynumber: 2.2 Consensus size: 80
3131 TACCCAACAA
* * ** * * *
3141 GGGTATCTCAGTAATTCTACCCTACATGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTGG
1 GGGTATTTC-GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGA
*
3206 TAATTCTATCC-TATAG
65 TAATTCTA-CCATACAG
* *
3222 GGGTATTTCGTAATTCTACCCTACAGGGGTATTTTAATAATTCTACCCTACAGGGGTATTTCGAT
1 GGGTATTTCGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGAT
3287 AATTCTACCATACAG
66 AATTCTACCATACAG
3302 GGGTATTTCGATAATTCTAC
1 GGGTATTTCG-TAATTCTAC
3322 AACTTATCCA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
79 2 0.02
80 69 0.78
81 17 0.19
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (80 bp):
GGGTATTTCGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGAT
AATTCTACCATACAG
Found at i:3317 original size:107 final size:107
Alignment explanation
Indices: 3124--3320 Score: 277
Period size: 107 Copynumber: 1.8 Consensus size: 107
3114 GAGAAAAATG
* * * *
3124 GTAATTATACCCAACAAGGGTATCTCAGTAATTCTACCCTACATGGGTATTTCGGTATTTCTACC
1 GTAATTATACCCAACAAGGGTATCTCAATAATTCTACCCTACAGGGGTATTTCGATAATTCTACC
* * *
3189 CTACAAGGGTATTTTGGTAATTCTATCCTATAGGGGTATTTC
66 ATACAAGGGTATTTCGATAATTCTATCCTATAGGGGTATTTC
* * * * *
3231 GTAATTCTACCCTACAGGGGTATTTTAATAATTCTACCCTACAGGGGTATTTCGATAATTCTACC
1 GTAATTATACCCAACAAGGGTATCTCAATAATTCTACCCTACAGGGGTATTTCGATAATTCTACC
*
3296 ATACAGGGGTATTTCGATAATTCTA
66 ATACAAGGGTATTTCGATAATTCTA
3321 CAACTTATCC
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
107 77 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.36
Consensus pattern (107 bp):
GTAATTATACCCAACAAGGGTATCTCAATAATTCTACCCTACAGGGGTATTTCGATAATTCTACC
ATACAAGGGTATTTCGATAATTCTATCCTATAGGGGTATTTC
Found at i:9383 original size:27 final size:26
Alignment explanation
Indices: 9335--9386 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
9325 GCGAGGCTGC
*
9335 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
9361 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
9387 TTACAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:10068 original size:27 final size:27
Alignment explanation
Indices: 10039--10236 Score: 254
Period size: 27 Copynumber: 7.3 Consensus size: 27
10029 GGGCAAAATG
* * * * *
10039 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
10066 GTAATTCTACCCTGCAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
10093 GTATTTCTACTCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
10120 GTAATTCTATCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
10147 GTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
10174 ATAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
10201 GTAATTCTACCTTACAGGGGTATTTC-
1 GTAATTCTACCCTACAGGGGTATTTCA
10227 GATAATTCTA
1 G-TAATTCTA
10237 GAACTTATCC
Statistics
Matches: 149, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.01
27 148 0.99
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:13451 original size:37 final size:37
Alignment explanation
Indices: 13372--13444 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
13362 CTTATTACGA
* *
13372 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATCTCCACACGAAGTCATCG
*
13409 AGTCTTACCCGGACAAAATCTCCACACGTAGTCATC
1 AGTCTTACCCGGACAAAATCTCCACACGAAGTCATC
13445 AGGTCTTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATCTCCACACGAAGTCATCG
Found at i:13644 original size:49 final size:49
Alignment explanation
Indices: 13570--14105 Score: 876
Period size: 49 Copynumber: 11.1 Consensus size: 49
13560 CCCTTCGGGA
* * * * *
13570 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
13617 CCTGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13666 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13713 CCTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13760 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
13807 CCTATCACATGTATATACACTTTCACATTCAGCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13856 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
13905 CCTATCACATATATATACACTTTTACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13954 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14001 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14050 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14099 CTTATCA
1 CTTATCA
14106 TCATTTCATA
Statistics
Matches: 460, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
47 191 0.42
48 1 0.00
49 268 0.58
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:13774 original size:96 final size:95
Alignment explanation
Indices: 13570--14105 Score: 876
Period size: 96 Copynumber: 5.6 Consensus size: 95
13560 CCCTTCGGGA
* * * * * * *
13570 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATATAC
*
13635 ACTTCCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
13666 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATACA
13730 CTTTCACATTCATCACATCGGCCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
*
13760 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATGTATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATATAC
*
13825 ACTTTCACATTCAGCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
13856 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATAT
*
13921 ACACTTTTACATTCATCACATCGGCCATTAGGC
63 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
13954 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATATAC
14019 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
*
14050 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCA
14106 TCATTTCATA
Statistics
Matches: 419, Mismatches: 15, Indels: 10
0.94 0.03 0.02
Matches are distributed among these distances:
94 93 0.22
96 187 0.45
98 139 0.33
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATACA
CTTTCACATTCATCACATCGGCCATTAGGC
Found at i:26101 original size:27 final size:27
Alignment explanation
Indices: 26071--26270 Score: 213
Period size: 27 Copynumber: 7.4 Consensus size: 27
26061 CGGGAAAAAT
* * *
26071 GGTAATTATACCCAACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
26098 GGTAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
26125 GGTATTTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* ** *
26152 GGTAATTCTATCCTGTAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
26179 -GTAAGTTCTACCCTACAGGGGTATTTT
1 GGTAA-TTCTACCCTACAAGGGTATTTC
** *
26206 AATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
26233 GATAATTCTACCATACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
26260 GATAATTCTAC
1 GGTAATTCTAC
26271 AACTTATCCA
Statistics
Matches: 150, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 4 0.03
27 143 0.95
28 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:32350 original size:27 final size:26
Alignment explanation
Indices: 32302--32353 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
32292 GCGAGGCTGC
*
32302 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
32328 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
32354 TTGCAACGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:33050 original size:27 final size:27
Alignment explanation
Indices: 33010--33199 Score: 249
Period size: 27 Copynumber: 7.1 Consensus size: 27
33000 ATGGTAGTTT
* * * *
33010 TACCCCACAAGGGTATCTCGGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
* *
33037 TACCCTGCAGGGGTATTTCAGTATTTC
1 TACCCTACAGGGGTATTTCAGTAATTC
* *
33064 TACTCTACAAGGGTATTTCAGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
33091 TA-TCTACAGGGGTATTTCAGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
33117 TACCCTACAGGGGTATTTCAATAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
33144 TACCCTACAGGGGTATTTCGGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
33171 TACCTTACAGGGGTATTTC-GATAATTC
1 TACCCTACAGGGGTATTTCAG-TAATTC
33198 TA
1 TA
33200 GAACTTATCC
Statistics
Matches: 145, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 26 0.18
27 119 0.82
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
TACCCTACAGGGGTATTTCAGTAATTC
Found at i:33122 original size:80 final size:80
Alignment explanation
Indices: 33020--33199 Score: 254
Period size: 80 Copynumber: 2.2 Consensus size: 80
33010 TACCCCACAA
* * * * *
33020 GGGTATCTCGGTAATTCTACCCTGCAGGGGTATTTCAGTATTTCTACTCTACAAGGGTATTTCAG
1 GGGTATTTC-GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCAG
*
33085 TAATTCTATC-TACAG
65 TAATTCTACCTTACAG
* *
33100 GGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCGG
1 GGGTATTTC-GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCAG
33165 TAATTCTACCTTACAG
65 TAATTCTACCTTACAG
33181 GGGTATTTCGATAATTCTA
1 GGGTATTTCG-TAATTCTA
33200 GAACTTATCC
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 67 0.75
81 22 0.25
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (80 bp):
GGGTATTTCGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCAGT
AATTCTACCTTACAG
Done.