Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2993
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: 51661
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1617 original size:29 final size:29
Alignment explanation
Indices: 1578--1656 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1568 CTTAATAATC
*
1578 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
1608 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
1637 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
1657 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:9944 original size:29 final size:29
Alignment explanation
Indices: 9905--9983 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
9895 CTTAATAATC
*
9905 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
9935 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
9964 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
9984 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:13063 original size:46 final size:46
Alignment explanation
Indices: 13010--13100 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
13000 TATATATACA
* * *
13010 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
* * *
13056 CATCTCATACACATTTCGCATTAACCATTCGGCTTTCCCACATAT
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATAT
13101 ATACACTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
Found at i:13143 original size:22 final size:22
Alignment explanation
Indices: 13117--13192 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
13107 TTCCACGTTC
13117 ATCACATTGACCATTCTGCCTT
1 ATCACATTGACCATTCTGCCTT
*
13139 ATCACATAT-ATGCATGT-T-CACATTT
1 ATCACAT-TGA-CCAT-TCTGC-C--TT
*
13164 ATCACATTGGCCATTCTGCCTT
1 ATCACATTGACCATTCTGCCTT
13186 ATCACAT
1 ATCACAT
13193 ATATGCATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 18 0.43
23 7 0.17
24 7 0.17
25 10 0.24
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (22 bp):
ATCACATTGACCATTCTGCCTT
Found at i:13145 original size:47 final size:47
Alignment explanation
Indices: 13114--13452 Score: 489
Period size: 47 Copynumber: 7.2 Consensus size: 47
13104 CACTTCCACG
* *
13114 TTCATCACATTGACCATTCTGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * *
13161 TTTATCACATTGGCCATTCTGCCTTATCACATATATGCATGTTCATA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * * *
13208 TTTATCACATTGGCCATTTGGCCTTATCACATATGTGCATGTTCATA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
13255 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
13302 TTCATCACATTGGCCATTCGGCCTTATCACATATGTACATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
13349 TTCATCACATTGGCCATTCGGCCTTATCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * * * **
13396 TTCATCACATTTGCCATTCGGCCTTAGCTCATATATACACATTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
13443 TCCATCACAT
1 TTCATCACAT
13453 AAAATCCTAA
Statistics
Matches: 265, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 265 1.00
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:13237 original size:22 final size:22
Alignment explanation
Indices: 13209--13379 Score: 78
Period size: 24 Copynumber: 7.4 Consensus size: 22
13199 ATGTTCATAT
13209 TTATCACATTGGCCATTTGGCC
1 TTATCACATTGGCCATTTGGCC
****
13231 TTATCACATATGTG-CATGTTCATA
1 TTATCACAT-TG-GCCAT-TTGGCC
*
13255 TTCATCACATTGGCCATTCGGCC
1 TT-ATCACATTGGCCATTTGGCC
** *
13278 TTATCACACATAT-G-CATGTTCACA
1 TTAT--CACAT-TGGCCAT-TTGGCC
*
13302 TTCATCACATTGGCCATTCGGCC
1 TT-ATCACATTGGCCATTTGGCC
** ** *
13325 TTATCACATATGTACATGTTCACA
1 TTATCACAT-TGGCCAT-TTGGCC
*
13349 TTCATCACATTGGCCATTCGGCC
1 TT-ATCACATTGGCCATTTGGCC
13372 TTATCACA
1 TTATCACA
13380 CAAATGCATG
Statistics
Matches: 105, Mismatches: 29, Indels: 30
0.64 0.18 0.18
Matches are distributed among these distances:
22 25 0.24
23 31 0.30
24 32 0.30
25 17 0.16
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (22 bp):
TTATCACATTGGCCATTTGGCC
Found at i:15114 original size:25 final size:25
Alignment explanation
Indices: 15086--15145 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
15076 TTTATGTCAT
*
15086 TAAATAAA-AAAGTTTAAAAATATAA
1 TAAATAAATAAA-TTTAAAAACATAA
*
15111 TAAATCAAATATATTTAAAAACATAA
1 TAAAT-AAATAAATTTAAAAACATAA
15137 -AAATAAATA
1 TAAATAAATA
15146 TTAAAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 5 0.16
25 9 0.29
26 15 0.48
27 2 0.06
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAATAAATAAATTTAAAAACATAA
Found at i:15128 original size:26 final size:24
Alignment explanation
Indices: 15098--15146 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
15088 AATAAAAAAG
*
15098 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAAT-AAATATA
15124 TTTAAAAACATAAAAATAAATAT
1 TTTAAAAACATAAAAATAAATAT
15147 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
TTTAAAAACATAAAAATAAATATA
Found at i:15158 original size:22 final size:22
Alignment explanation
Indices: 15117--15175 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
15107 ATAATAAATC
* *
15117 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
15137 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
15159 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
15176 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:15252 original size:15 final size:16
Alignment explanation
Indices: 15222--15254 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
15212 AAATGGTTAT
15222 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
15239 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
15254 A
1 A
15255 AAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:20350 original size:93 final size:93
Alignment explanation
Indices: 20222--20392 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
20212 GCCCATAAGT
* *
20222 GAACTCGGACTCAACTCAATGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
20287 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
20315 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
20379 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
20393 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:20387 original size:46 final size:46
Alignment explanation
Indices: 20214--20389 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
20204 TGTAACCCGC
* * *
20214 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
*
20260 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
20310 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
20353 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
20390 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 4 0.04
46 61 0.56
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:27840 original size:93 final size:93
Alignment explanation
Indices: 27728--27899 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
27718 CGCCCATAAG
* *
27728 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
27793 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
27821 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
27886 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
27900 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:27896 original size:46 final size:46
Alignment explanation
Indices: 27721--27896 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
27711 TGTAACCCGC
* * *
27721 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
27767 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
27817 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
27860 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
27897 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:29918 original size:1 final size:1
Alignment explanation
Indices: 29912--30042 Score: 235
Period size: 1 Copynumber: 131.0 Consensus size: 1
29902 TCAATAAATT
* * *
29912 CCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCCCCACCCCCCCCCCCCCCCCCTCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
29977 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
30042 C
1 C
30043 TATATGGATC
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 124 1.00
ACGTcount: A:0.01, C:0.98, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Found at i:38209 original size:93 final size:92
Alignment explanation
Indices: 38045--38214 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 92
38035 GGATGGTTGA
*
38045 GCATCCGAACTCGTTAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
38110 GAGTCCGAGTTCGTGAAATGTAATAAG
66 GAGTCCGAGTTCGTGAAATGTAATAAG
*
38137 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCG-TGAG
1 GCATCCGAACTCGTT-AGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
38200 TTGATGTCCGAGTTC
64 TTGA-GTCCGAGTTC
38215 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
92 25 0.34
93 48 0.66
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAAATGTAATAAG
Found at i:45595 original size:45 final size:45
Alignment explanation
Indices: 45546--45716 Score: 144
Period size: 45 Copynumber: 3.8 Consensus size: 45
45536 GGTTGAGCAT
45546 TCCGAACTCG-TGAGTTGAGT-CGAGTTCACTTATGGATGCGGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGG-A-G
* * * *
45591 TCCGAAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTACTAG-GCA-
1 TCCG-AACTCGTTGAGTTGAGTCCGAGTTCACT-TATGGA-T-GCGGAG
*
45637 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-GACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGA-G
* *
45682 -CCTGAGCTC-ATGAGTTGAGTCCGAGTTCA-TTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
45717 GGCGGGTTAC
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
43 8 0.08
44 22 0.21
45 37 0.36
46 10 0.10
47 11 0.11
48 12 0.12
49 2 0.02
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGAG
Found at i:50737 original size:19 final size:19
Alignment explanation
Indices: 50704--50750 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
50694 TTTAAGAATT
*
50704 GTTTTAGTA-TTATTTTTA
1 GTTTTAATATTTATTTTTA
50722 -TTTGTAATATTTATTTTTA
1 GTTT-TAATATTTATTTTTA
50741 GTTTTAATAT
1 GTTTTAATAT
50751 ATTTGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 4 0.16
19 15 0.60
20 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (19 bp):
GTTTTAATATTTATTTTTA
Done.