Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3602
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: 17421
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3659 original size:22 final size:23
Alignment explanation
Indices: 3629--3672 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3619 TATGAGTAAG
3629 GTGTCTAA-TGGAAAATAAGGAA
1 GTGTCTAATTGGAAAATAAGGAA
*
3651 GTGTTTAATTGGAAAATAAGGA
1 GTGTCTAATTGGAAAATAAGGA
3673 CCAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.43, C:0.02, G:0.27, T:0.27
Consensus pattern (23 bp):
GTGTCTAATTGGAAAATAAGGAA
Found at i:8132 original size:22 final size:22
Alignment explanation
Indices: 8104--8225 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
8094 TTCCACATCC
8104 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
8126 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
8150 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
8173 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
8197 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
8220 ATCACA
1 ATCACA
8226 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:8139 original size:47 final size:47
Alignment explanation
Indices: 8076--8667 Score: 876
Period size: 47 Copynumber: 12.6 Consensus size: 47
8066 CCCTTCGGGA
* * *
8076 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
8123 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
8170 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
8217 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
8264 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
8311 CTTATCTC--ATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
8356 CTTATCAC--ACATACACTGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
8402 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
8451 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
8498 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
8547 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
8594 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
8641 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
8668 TATTCAAATA
Statistics
Matches: 521, Mismatches: 16, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
45 49 0.09
46 39 0.07
47 342 0.66
49 83 0.16
50 8 0.02
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:10057 original size:85 final size:85
Alignment explanation
Indices: 9928--10106 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
9918 TATTTTATTG
*
9928 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
9993 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
10013 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
10078 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
10098 CCCATGCTC
1 CCCATGCTC
10107 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:11182 original size:25 final size:25
Alignment explanation
Indices: 11145--11196 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
11135 AAGGAATTCG
11145 CACACACACAGTGC-CTCTAATCATT
1 CACACACACAGTGCTCT-TAATCATT
* *
11170 CACACACATAGTGCTCTTATTCATT
1 CACACACACAGTGCTCTTAATCATT
11195 CA
1 CA
11197 TTATTACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.29
Consensus pattern (25 bp):
CACACACACAGTGCTCTTAATCATT
Found at i:11413 original size:39 final size:40
Alignment explanation
Indices: 11361--11562 Score: 238
Period size: 39 Copynumber: 5.2 Consensus size: 40
11351 TACACGTCCC
* * *
11361 AGCATGATTGCTCTTCGGGACCTAGCCCGGTATA-A-CACC
1 AGCATGAATGCTCTTCGGGACTTAGCCCGG-ATACATCACT
* * * *
11400 AGCACGAATGCTCTTCGGG-TTTAGCACGGATATATCACT
1 AGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
* *
11439 AGCACGAATGCTCTTC-GAACTTAGCCCGGATACATCACT
1 AGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
11478 AGCATGAATGCTCTTCGGGACTTAG-CCGGATACATCACT
1 AGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
*
11517 AGCATGAATGCTCTTC-GGACTTAGCACGGA-ACAGATCACT
1 AGCATGAATGCTCTTCGGGACTTAGCCCGGATAC--ATCACT
11557 AGCATG
1 AGCATG
11563 CTGAGTGTTG
Statistics
Matches: 143, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
37 3 0.02
38 19 0.13
39 102 0.71
40 19 0.13
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
AGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACT
Found at i:14202 original size:22 final size:22
Alignment explanation
Indices: 14174--14295 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
14164 TTCCACATCC
14174 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
14196 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
14220 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
14243 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
14267 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
14290 ATCACA
1 ATCACA
14296 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:14209 original size:47 final size:47
Alignment explanation
Indices: 14146--14639 Score: 693
Period size: 47 Copynumber: 10.6 Consensus size: 47
14136 CCCTTCGGGA
* * *
14146 CTTATCACATTTATACACT-TCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
14193 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* *
14240 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
14287 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
14334 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
14381 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTC-GC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
14427 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
14474 CTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* *
14521 CTTATCACATATATATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* * *
14570 CTTATCACATATATACACT-TTCACATTCATCACATCGG-CTTTAGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
14616 CTTATCACA-ATATAC-T-TTCACATT
1 CTTATCACATATATACATGTTCACATT
14640 GTGACAGCCC
Statistics
Matches: 422, Mismatches: 20, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
43 9 0.02
45 6 0.01
46 60 0.14
47 300 0.71
48 1 0.00
49 46 0.11
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:14998 original size:56 final size:56
Alignment explanation
Indices: 14933--15107 Score: 334
Period size: 56 Copynumber: 3.1 Consensus size: 56
14923 ACAAGGGATG
14933 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
14989 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGG-AAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
15044 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
15100 ATGGGCAA
1 ATGGGCAA
15108 TAAACTAATA
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
55 55 0.47
56 62 0.53
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:16372 original size:79 final size:81
Alignment explanation
Indices: 16236--16420 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
16226 TCGAATGATG
*
16236 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
16300 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
16315 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
16377 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
16395 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
16421 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:16434 original size:40 final size:40
Alignment explanation
Indices: 16237--16420 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
16227 CGAATGATGT
* * * *
16237 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
16277 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
16317 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
16355 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
16396 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
16421 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:16442 original size:79 final size:79
Alignment explanation
Indices: 16289--16453 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
16279 GGACTAAGAT
* **
16289 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
16354 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
16368 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
16431 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
16447 CCGAAGG
1 CCGAAGG
16454 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.