Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1346
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: 78516
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:442 original size:6 final size:6
Alignment explanation
Indices: 431--469 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
421 TTTCTTCTCT
431 CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTC
1 CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTC
470 ACTCACTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18
Consensus pattern (6 bp):
CTCCAA
Found at i:5240 original size:2 final size:2
Alignment explanation
Indices: 5233--5268 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5223 TTTCTGTTTC
5233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5269 TCGTGTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17303 original size:2 final size:2
Alignment explanation
Indices: 17296--17323 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17286 CAAATACTGG
17296 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17324 CACACACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25661 original size:3 final size:3
Alignment explanation
Indices: 25653--25683 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
25643 CGATTCATTT
*
25653 ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
25684 ATACAGGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:30147 original size:17 final size:18
Alignment explanation
Indices: 30125--30160 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
30115 TTTATATTTG
*
30125 ATTAATTATAAATA-ATA
1 ATTAATTAAAAATATATA
30142 ATTAATTAAAAATATATA
1 ATTAATTAAAAATATATA
30160 A
1 A
30161 AATAATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTAATTAAAAATATATA
Found at i:33132 original size:2 final size:2
Alignment explanation
Indices: 33115--33159 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
33105 GTTGAATTAA
* * *
33115 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33157 AT A
1 AT A
33160 CATGTTTGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:36279 original size:6 final size:6
Alignment explanation
Indices: 36268--36292 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36258 TCTCTCAACT
36268 TTGAGA TTGAGA TTGAGA TTGAGA T
1 TTGAGA TTGAGA TTGAGA TTGAGA T
36293 AGCAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TTGAGA
Found at i:36970 original size:6 final size:6
Alignment explanation
Indices: 36959--36992 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
36949 AAGAACTTAA
*
36959 AGTGGT AGTGGT AGTGGT AGTGGT AGTGGC AGTG
1 AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTG
36993 ATAGCGGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.50, T:0.29
Consensus pattern (6 bp):
AGTGGT
Found at i:37001 original size:18 final size:18
Alignment explanation
Indices: 36962--37001 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36952 AACTTAAAGT
* * *
36962 GGTAGTGGTAGTGGTAGT
1 GGTAGTGGCAGTGATAGC
36980 GGTAGTGGCAGTGATAGC
1 GGTAGTGGCAGTGATAGC
36998 GGTA
1 GGTA
37002 AACAGTACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.47, T:0.28
Consensus pattern (18 bp):
GGTAGTGGCAGTGATAGC
Found at i:37900 original size:2 final size:2
Alignment explanation
Indices: 37893--37919 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37883 GCTGCTGATT
37893 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
37920 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:45155 original size:19 final size:17
Alignment explanation
Indices: 45123--45163 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
45113 GTTGAATCTG
45123 CCTTTACTTTGGCCTTT
1 CCTTTACTTTGGCCTTT
45140 CCTTTATCTATTGGCCTTT
1 CCTTTA-CT-TTGGCCTTT
*
45159 TCTTT
1 CCTTT
45164 TTACTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.07, C:0.27, G:0.10, T:0.56
Consensus pattern (17 bp):
CCTTTACTTTGGCCTTT
Found at i:50614 original size:2 final size:2
Alignment explanation
Indices: 50607--50644 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
50597 ATCACATCAC
50607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50645 CTAAAAGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54669 original size:2 final size:2
Alignment explanation
Indices: 54662--54701 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
54652 TAACATCTTT
* *
54662 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54702 CACATAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55075 original size:3 final size:3
Alignment explanation
Indices: 55067--55106 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
55057 ATAATTGAAA
* * *
55067 AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT TAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55107 GTAACATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:55207 original size:3 final size:3
Alignment explanation
Indices: 55199--55224 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55189 CTTAATGGAA
55199 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
55225 CGGGTCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55624 original size:2 final size:2
Alignment explanation
Indices: 55612--55649 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
55602 GATTCTTCTC
55612 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55650 GGTAACCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:56100 original size:3 final size:3
Alignment explanation
Indices: 56092--56119 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
56082 GGTCTTCCAG
56092 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56120 GATGATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:56428 original size:2 final size:2
Alignment explanation
Indices: 56421--56448 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56411 GTTTGATGAT
56421 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56449 TCTCCTTCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57628 original size:3 final size:3
Alignment explanation
Indices: 57620--57651 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
57610 ATATTCTCAA
57620 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
57652 AATGGGCGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:61377 original size:34 final size:34
Alignment explanation
Indices: 61331--61515 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
61321 GTAAAAACCA
*
61331 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
61365 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
61399 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
61433 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
61467 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
61500 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
61516 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:65608 original size:19 final size:19
Alignment explanation
Indices: 65581--65643 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
65571 TCACGTGTAC
* *
65581 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACATGAAT
65600 AGTACCCGTATACATGAAT
1 AGTACCCGTATACATGAAT
** *
65619 AGTACCTATATACGTGAAT
1 AGTACCCGTATACATGAAT
65638 AGTACC
1 AGTACC
65644 TCGACAACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACATGAAT
Found at i:65995 original size:34 final size:34
Alignment explanation
Indices: 65949--66132 Score: 246
Period size: 34 Copynumber: 5.4 Consensus size: 34
65939 GTAAAAACCA
*
65949 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
65983 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
66017 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
66051 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
66085 CCATTTAGTCAACAATGATAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
66118 CCATTTAATCAACAA
1 CCATTTAATCAACAA
66133 ATATGAGATA
Statistics
Matches: 133, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 17 0.13
34 112 0.84
35 4 0.03
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:77574 original size:2 final size:2
Alignment explanation
Indices: 77562--77601 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
77552 TCAATTACAG
77562 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
77602 ACTCCCAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.