Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3112
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: 38317
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:2975 original size:29 final size:29
Alignment explanation
Indices: 2936--3014 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
2926 CTTAATAATC
*
2936 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
2966 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
2995 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
3015 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:3057 original size:43 final size:43
Alignment explanation
Indices: 2996--3098 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
2986 TGCATTTCAA
2996 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
3039 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
3082 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
3099 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:6358 original size:40 final size:40
Alignment explanation
Indices: 6274--6498 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
6264 TTGAATGATG
* * * *
6274 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
6314 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6354 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6393 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
6433 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
6474 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6499 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.21
40 119 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:7992 original size:47 final size:47
Alignment explanation
Indices: 7914--8693 Score: 1281
Period size: 47 Copynumber: 16.5 Consensus size: 47
7904 CCCTTCGGGA
* * * * * *
7914 CTTATCACATTTATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7961 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8008 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8055 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8102 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8149 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8196 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8243 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8290 CTTACCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8337 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8386 CTTATCACATATATATACACTTTCACATTCATCACATCGGCAATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8435 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8482 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8529 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGCC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8578 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8625 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8672 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
8694 TTGGCTGAAT
Statistics
Matches: 700, Mismatches: 29, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
47 561 0.80
49 139 0.20
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20731 original size:17 final size:17
Alignment explanation
Indices: 20709--20741 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20699 GTATGCATGT
20709 AATGAT-ATGTCTTGTTG
1 AATGATGATGT-TTGTTG
20726 AATGATGATGTTTGTT
1 AATGATGATGTTTGTT
20742 AAATTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.48
Consensus pattern (17 bp):
AATGATGATGTTTGTTG
Found at i:30257 original size:14 final size:13
Alignment explanation
Indices: 30234--30265 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
30224 GGGATATCAA
30234 AACAATAATTAAG
1 AACAATAATTAAG
30247 AACACATAATTAAG
1 AACA-ATAATTAAG
30261 AACAA
1 AACAA
30266 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:31917 original size:40 final size:40
Alignment explanation
Indices: 31880--32142 Score: 324
Period size: 40 Copynumber: 6.6 Consensus size: 40
31870 GCTACTCGTT
*
31880 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
31920 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
31960 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * *
32000 CCAATGCCTTCGGG-CTTAGCCCAG-AATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
*
32039 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TTATAGTAACTCGCA
* * * * *
32079 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
32120 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
32143 ACATCATTCA
Statistics
Matches: 198, Mismatches: 15, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 31 0.16
40 152 0.77
41 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:32104 original size:119 final size:120
Alignment explanation
Indices: 31882--32143 Score: 338
Period size: 119 Copynumber: 2.2 Consensus size: 120
31872 TACTCGTTCA
* **
31882 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
* *
31947 ATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCACC
66 ATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTTAGCA-C
*
32002 AATGCCTTCGGG-CTTAGCCCAGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
** * *
32064 ATT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC
64 -TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAACTTAGCAC
*
32121 AAAGCCTTCGGGACTTAGCCCGA
1 AATGCCTTCGGGACTTAGCCCGA
32144 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
118 6 0.05
119 91 0.73
120 28 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
ATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTTAGCAC
Done.