Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3371
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: 27893
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:6432 original size:26 final size:24
Alignment explanation
Indices: 6405--6452 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
6395 TAAAACTACT
6405 TTTAAAAAAACTCAAGAGAGAATTC
1 TTTAAAAAAACTCAA-AGAGAATTC
* *
6430 TTTGAGAAAACTCAAAGAGAATT
1 TTTAAAAAAACTCAAAGAGAATT
6453 TTTCACTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (24 bp):
TTTAAAAAAACTCAAAGAGAATTC
Found at i:9291 original size:11 final size:10
Alignment explanation
Indices: 9266--9326 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
9256 ACCAATAAAA
9266 TAAA-TGAGC
1 TAAATTGAGC
*
9275 TGAATTGTAGC
1 TAAATTG-AGC
9286 TAAATTGAGC
1 TAAATTGAGC
**
9296 TCGATTGAGC
1 TAAATTGAGC
9306 TGAAA-TGAGC
1 T-AAATTGAGC
*
9316 TCAATTGAGC
1 TAAATTGAGC
9326 T
1 T
9327 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:9327 original size:20 final size:20
Alignment explanation
Indices: 9267--9327 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
9257 CCAATAAAAT
*
9267 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
9287 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
9308 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
9328 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:11416 original size:17 final size:18
Alignment explanation
Indices: 11394--11427 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11384 TTTTTCTTTT
11394 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
11411 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
11428 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:11531 original size:6 final size:6
Alignment explanation
Indices: 11465--11518 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
11455 ACTATTTTGA
* ** * *
11465 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
11512 TTTCTT T
1 TTTCTT T
11519 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:14066 original size:28 final size:28
Alignment explanation
Indices: 14003--14173 Score: 308
Period size: 28 Copynumber: 6.1 Consensus size: 28
13993 ATATTAAGTC
* *
14003 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
14030 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
14058 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
14086 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
14114 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
14142 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
14170 CGCA
1 CGCA
14174 ATAATCAAAC
Statistics
Matches: 141, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
27 22 0.16
28 119 0.84
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:14143 original size:84 final size:83
Alignment explanation
Indices: 14003--14326 Score: 417
Period size: 71 Copynumber: 4.2 Consensus size: 83
13993 ATATTAAGTC
* *
14003 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTATATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
14068 GTGCTACATAATCAAACT
66 GTGCTACATAATCAAACT
*
14086 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
1 CGCACACTCAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
14151 AGTGCTACATAATCAAACT
65 AGTGCTACATAATCAAACT
*
14170 CG--CA---A----TA-ATCA--AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
14223 GTGCTACATAATCAAACT
66 GTGCTACATAATCAAACT
*
14241 CG--CA---A----TA-ATCA--AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
14294 GTGCTACATAATCAAACT
66 GTGCTACATAATCAAACT
*
14312 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
14327 GTACAATTTA
Statistics
Matches: 227, Mismatches: 4, Indels: 23
0.89 0.02 0.09
Matches are distributed among these distances:
71 133 0.59
73 2 0.01
74 3 0.01
75 2 0.01
76 1 0.00
79 1 0.00
80 1 0.00
82 2 0.01
83 21 0.09
84 61 0.27
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (83 bp):
CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAATCAAACT
Found at i:14179 original size:15 final size:15
Alignment explanation
Indices: 14159--14188 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14149 TTAGTGCTAC
14159 ATAATCAAACTCGCA
1 ATAATCAAACTCGCA
14174 ATAATCAAACTCGCA
1 ATAATCAAACTCGCA
14189 CACTTAGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
ATAATCAAACTCGCA
Found at i:14192 original size:43 final size:43
Alignment explanation
Indices: 14131--14216 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
14121 TTAGTGCTAC
14131 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
14174 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
14217 CACTTAGTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (43 bp):
ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
Found at i:14214 original size:28 final size:28
Alignment explanation
Indices: 14174--14244 Score: 142
Period size: 28 Copynumber: 2.5 Consensus size: 28
14164 CAAACTCGCA
14174 ATAATCAAACTCGCACACTTAGTGCTAC
1 ATAATCAAACTCGCACACTTAGTGCTAC
14202 ATAATCAAACTCGCACACTTAGTGCTAC
1 ATAATCAAACTCGCACACTTAGTGCTAC
14230 ATAATCAAACTCGCA
1 ATAATCAAACTCGCA
14245 ATAATCAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (28 bp):
ATAATCAAACTCGCACACTTAGTGCTAC
Found at i:14219 original size:71 final size:71
Alignment explanation
Indices: 14103--14315 Score: 426
Period size: 71 Copynumber: 3.0 Consensus size: 71
14093 TTAGTGCTAC
14103 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
14168 CTCGCA
66 CTCGCA
14174 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
14239 CTCGCA
66 CTCGCA
14245 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
14310 CTCGCA
66 CTCGCA
14316 CACTTAGTGC
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 142 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (71 bp):
ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
CTCGCA
Found at i:14249 original size:43 final size:43
Alignment explanation
Indices: 14202--14287 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
14192 TTAGTGCTAC
14202 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
14245 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
14288 CACTTAGTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (43 bp):
ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA
Found at i:14250 original size:15 final size:15
Alignment explanation
Indices: 14230--14259 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14220 TTAGTGCTAC
14230 ATAATCAAACTCGCA
1 ATAATCAAACTCGCA
14245 ATAATCAAACTCGCA
1 ATAATCAAACTCGCA
14260 CACTTAGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
ATAATCAAACTCGCA
Found at i:14277 original size:99 final size:100
Alignment explanation
Indices: 14047--14326 Score: 414
Period size: 99 Copynumber: 2.8 Consensus size: 100
14037 TTAGTGCTAT
14047 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
14112 CTCGCACACTTAGTGCTACATAATCAAACTCGCAC
66 CTCGCACACTTAGTGCTACATAATCAAACTCGCAC
* * * *
14147 ACTTAGTGCTACATAAT--CAAAC-T--CGC-A-ATAATCAAACTCGCACACTTAGTGCTACATA
1 A--TAAT-C-A-A-ACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATA
14205 ATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCA-
60 ATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCAC
14245 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
1 ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
14310 CTCGCACACTTAGTGCT
66 CTCGCACACTTAGTGCT
14327 GTACAATTTA
Statistics
Matches: 159, Mismatches: 8, Indels: 27
0.82 0.04 0.14
Matches are distributed among these distances:
92 2 0.01
93 1 0.01
94 5 0.03
95 2 0.01
96 3 0.02
97 2 0.01
98 2 0.01
99 125 0.79
100 2 0.01
101 2 0.01
102 3 0.02
103 2 0.01
104 5 0.03
105 1 0.01
106 2 0.01
ACGTcount: A:0.37, C:0.28, G:0.10, T:0.25
Consensus pattern (100 bp):
ATAATCAAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAA
CTCGCACACTTAGTGCTACATAATCAAACTCGCAC
Found at i:14285 original size:28 final size:28
Alignment explanation
Indices: 14245--14326 Score: 164
Period size: 28 Copynumber: 2.9 Consensus size: 28
14235 CAAACTCGCA
14245 ATAATCAAACTCGCACACTTAGTGCTAC
1 ATAATCAAACTCGCACACTTAGTGCTAC
14273 ATAATCAAACTCGCACACTTAGTGCTAC
1 ATAATCAAACTCGCACACTTAGTGCTAC
14301 ATAATCAAACTCGCACACTTAGTGCT
1 ATAATCAAACTCGCACACTTAGTGCT
14327 GTACAATTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (28 bp):
ATAATCAAACTCGCACACTTAGTGCTAC
Found at i:22392 original size:28 final size:28
Alignment explanation
Indices: 22333--22457 Score: 227
Period size: 28 Copynumber: 4.5 Consensus size: 28
22323 ATATTAAGTC
*
22333 CGCACACTCAGTGCTA-ATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
22359 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
22387 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
22415 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
22443 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
22458 GTACAATTTA
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
26 15 0.16
27 6 0.06
28 75 0.78
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:24302 original size:21 final size:23
Alignment explanation
Indices: 24289--24331 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
24279 TTTTCTTTTC
24289 TTTTTTTTG-ATTTTT-TTTGAA
1 TTTTTTTTGAATTTTTCTTTGAA
24310 TTTTTTTTGAATTTCTTCTTTG
1 TTTTTTTTGAATTT-TTCTTTG
24332 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 2 0.11
24 4 0.21
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.74
Consensus pattern (23 bp):
TTTTTTTTGAATTTTTCTTTGAA
Done.