Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2809
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: 24468
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Found at i:1038 original size:40 final size:40
Alignment explanation
Indices: 917--1000 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
907 GGTTTAGCAC
*
917 GATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCG
1 GATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCG
957 GATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCG
1 GATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCG
997 GATA
1 GATA
1001 TGGTCACTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (40 bp):
GATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCG
Found at i:1383 original size:29 final size:29
Alignment explanation
Indices: 1344--1422 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1334 CTTAATAATC
*
1344 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
1374 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
1403 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
1423 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:1465 original size:43 final size:43
Alignment explanation
Indices: 1404--1506 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
1394 TGCATTTCAA
1404 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1447 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1490 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
1507 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:3417 original size:37 final size:37
Alignment explanation
Indices: 3367--3445 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
3357 TTATTACGAA
* *
3367 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
3404 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
3441 GTCTT
1 GTCTT
3446 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:3642 original size:47 final size:47
Alignment explanation
Indices: 3564--4050 Score: 861
Period size: 47 Copynumber: 10.4 Consensus size: 47
3554 CCCTTCGGGA
* * * * * * *
3564 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
3611 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3658 CTTA-CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3704 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3750 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3797 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3844 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3891 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3938 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3985 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4032 CTTATCACATATATACACT
1 CTTATCACATATATACACT
4051 GTCTTGGCTG
Statistics
Matches: 424, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
46 92 0.22
47 332 0.78
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:6683 original size:50 final size:50
Alignment explanation
Indices: 6616--6807 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
6606 TTTCTTGTAC
* * * ** *
6616 TGCCAATGCCATATCCCAGATATGGTATTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
6666 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
6716 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
6766 TGCCAACT-CCATGTCCTAGACATGGTCTTACATGGGACCTCT
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
6808 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
50 123 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:6808 original size:50 final size:50
Alignment explanation
Indices: 6569--6808 Score: 245
Period size: 50 Copynumber: 4.8 Consensus size: 50
6559 TAATAACATA
* * * * * *
6569 CCAAAGCCATGTCCTAGACATGGTCTTACATGAGA--TGTT-TCTTGTACTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG--GTG
* * * ** * *
6618 CCAATGCCATATCCCAGATATGGTATTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
* ** * *
6668 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
*
6718 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
*
6768 CCAACT-CCATGTCCTAGACATGGTCTTACATGGGACCTCTT
1 CCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
6809 TACCCAAATG
Statistics
Matches: 158, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
49 29 0.18
50 124 0.78
51 2 0.01
52 3 0.02
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
Found at i:14780 original size:40 final size:40
Alignment explanation
Indices: 14743--14875 Score: 232
Period size: 40 Copynumber: 3.3 Consensus size: 40
14733 GCTACTCGTT
* *
14743 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
14783 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
14823 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
14863 CAAATGCCTTCGG
1 CAAATGCCTTCGG
14876 TCCGGATTAG
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
40 88 0.98
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:14898 original size:29 final size:32
Alignment explanation
Indices: 14844--14904 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 32
14834 GGGACTTAAC
14844 CCGGATTTAGTAACTCGCACAAATGCCTTCGGT
1 CCGGATTTAGTAACTCG-ACAAATGCCTTCGGT
14877 CCGGA-TTAGT-ACTCG-CAAATGCCTTCGG
1 CCGGATTTAGTAACTCGACAAATGCCTTCGG
14905 ATCTTAGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 13 0.46
31 5 0.18
32 5 0.18
33 5 0.18
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (32 bp):
CCGGATTTAGTAACTCGACAAATGCCTTCGGT
Found at i:22844 original size:39 final size:39
Alignment explanation
Indices: 22701--22923 Score: 283
Period size: 40 Copynumber: 5.7 Consensus size: 39
22691 GCTACTCGTT
* *
22701 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
22741 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
22781 CAAATGCCTTCGGG-CTTAACCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
*
22819 CAAATGCCTTC-GGATCTTAGTCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAGTAACTCGCA
* * * *
22858 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
22899 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
22924 CATCATTCAA
Statistics
Matches: 168, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
37 2 0.01
38 24 0.14
39 60 0.36
40 70 0.42
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:22883 original size:117 final size:119
Alignment explanation
Indices: 22701--22923 Score: 294
Period size: 117 Copynumber: 1.9 Consensus size: 119
22691 GCTACTCGTT
*
22701 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
22766 ATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAACCCGGATTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
* * **
22819 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
22881 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
22924 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
116 3 0.03
117 50 0.55
118 38 0.42
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
Done.