Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold503
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: 29849
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Found at i:1419 original size:54 final size:55
Alignment explanation
Indices: 1334--1485 Score: 209
Period size: 54 Copynumber: 2.7 Consensus size: 55
1324 ATATTAAGTC
*
1334 CGCACATTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTA-CTAATCAAACT
1 CGCACATT-AGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
*
1388 TGCACATTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACATTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
* * * *
1443 CGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGTGC
1 CGCACA-TTAGTGCTATATAA-TCAAACTCGCACACTTAGTGC
1486 CAATCTCATG
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
53 14 0.16
54 27 0.31
55 15 0.17
56 12 0.14
57 19 0.22
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.28
Consensus pattern (55 bp):
CGCACATTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
Found at i:1480 original size:29 final size:28
Alignment explanation
Indices: 1334--1485 Score: 204
Period size: 28 Copynumber: 5.5 Consensus size: 28
1324 ATATTAAGTC
1334 CGCACA-TTCAGTGCTATATAATC-AACT
1 CGCACACTT-AGTGCTATATAATCAAACT
*
1361 CGCACACTTAGTGCTA-CTAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
1388 TGCACA-TTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
1415 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
1443 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
1472 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1486 CAATCTCATG
Statistics
Matches: 112, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
26 14 0.12
27 37 0.33
28 42 0.38
29 19 0.17
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:1628 original size:14 final size:14
Alignment explanation
Indices: 1609--1635 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1599 TATATGCTAC
1609 ATATATATACATGT
1 ATATATATACATGT
1623 ATATATATACATG
1 ATATATATACATG
1636 CATCATTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATATATACATGT
Found at i:4660 original size:14 final size:14
Alignment explanation
Indices: 4621--4660 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4611 ATCATATCCC
4621 TTCGTTCATACCAT
1 TTCGTTCATACCAT
* *
4635 TTCATTCCTACCAT
1 TTCGTTCATACCAT
*
4649 TTCGTTCGTACC
1 TTCGTTCATACC
4661 CCTCTTTCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.33, G:0.07, T:0.42
Consensus pattern (14 bp):
TTCGTTCATACCAT
Found at i:5613 original size:9 final size:9
Alignment explanation
Indices: 5534--5614 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 9
5524 ATTTTTCACA
5534 ATTTTATTTT
1 ATTTTA-TTT
5544 ATTTTATCTT
1 ATTTTAT-TT
*
5554 ATTTTGTTT
1 ATTTTATTT
*
5563 CTTTTATTT
1 ATTTTATTT
*
5572 AATTTATTT
1 ATTTTATTT
*
5581 GA-TTGATTT
1 -ATTTTATTT
* **
5590 -TCTTCCTT
1 ATTTTATTT
5598 A-TTTATTT
1 ATTTTATTT
5606 ATTTTATTT
1 ATTTTATTT
5615 TGATTCAAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
8 8 0.15
9 30 0.57
10 15 0.28
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.72
Consensus pattern (9 bp):
ATTTTATTT
Found at i:19242 original size:39 final size:40
Alignment explanation
Indices: 19147--19408 Score: 344
Period size: 39 Copynumber: 6.7 Consensus size: 40
19137 TTGAATGATG
*
19147 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
19185 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
19226 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
19265 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
19304 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
19343 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
19382 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
19409 AACGAGGAGC
Statistics
Matches: 205, Mismatches: 10, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
39 132 0.64
40 61 0.30
41 11 0.05
42 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:22546 original size:37 final size:37
Alignment explanation
Indices: 22496--22574 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
22486 TTATTACGAA
* * *
22496 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
22533 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
22570 GTCTT
1 GTCTT
22575 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:22771 original size:47 final size:47
Alignment explanation
Indices: 22693--22899 Score: 333
Period size: 47 Copynumber: 4.4 Consensus size: 47
22683 CCCTTCGGGA
* * * * * *
22693 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
22740 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
22787 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
22834 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
22881 CTTATCACATATATACACT
1 CTTATCACATATATACACT
22900 GTCTTGGCTG
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 149 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:25724 original size:40 final size:40
Alignment explanation
Indices: 25692--25993 Score: 349
Period size: 40 Copynumber: 7.6 Consensus size: 40
25682 CCAGCATGAT
* * * *
25692 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
25732 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
25772 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
25812 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
25852 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * * * *
25892 TGCTCTTCGGGACTTAGCCTGGTTATAGTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
* ** * * *
25933 TGC-CTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
25973 TGC-CTTCGGG-CTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
25994 ATTAGTAACT
Statistics
Matches: 231, Mismatches: 30, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
39 10 0.04
40 209 0.90
41 12 0.05
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:25980 original size:80 final size:79
Alignment explanation
Indices: 25724--26035 Score: 281
Period size: 80 Copynumber: 3.9 Consensus size: 79
25714 ATATAACACC
* ** * * * *
25724 AGCACGAATGCTCTTCGGGGTTTAGCACGGATATA-TCACTAGCACGAATGCTCTTCGGAACTTA
1 AGCACCAATGCTCTTCGGGACTTAGCCCGG-TATAGTAACTCGCACAAATGC-CTTCGGAACTTA
* *
25788 GCCCGGATACATCACT
64 ACCCGGATACATAACT
** * * * *
25804 AGCATGAATGCTCTTCGGGACTTAGCCCGG-ATACATCACTAGCACGAATGCTCTTCGGAACTTA
1 AGCACCAATGCTCTTCGGGACTTAGCCCGGTATA-GTAACTCGCACAAATGC-CTTCGGAACTTA
* *
25868 GCCCGGATACATCACT
64 ACCCGGATACATAACT
** * *
25884 AGCATGAATGCTCTTCGGGACTTAGCCTGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAA
1 AGCACCAATGCTCTTCGGGACTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGAACTTAA
**
25949 CCCGGATTTAGTAACT
65 CCCGGATACA-TAACT
* * * *
25965 CGCACCAATGC-CTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAG
1 AGCACCAATGCTCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGAACTTAA
*
26028 TCCGGATA
65 CCCGGATA
26036 TGGTCACTTA
Statistics
Matches: 202, Mismatches: 24, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
78 4 0.02
79 44 0.22
80 126 0.62
81 25 0.12
82 3 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
AGCACCAATGCTCTTCGGGACTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGAACTTAAC
CCGGATACATAACT
Found at i:26003 original size:39 final size:40
Alignment explanation
Indices: 25696--26034 Score: 221
Period size: 40 Copynumber: 8.5 Consensus size: 40
25686 CATGATTGCT
* * *
25696 CTTCGGGACCTAGCCCGGA--TA-TAACACCAGCACGAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAAC-TC-GCACAAATGC
** * * * * *
25735 TCTTCGGGGTTTAGCACGGATATA-TCACTAGCACGAATGC
1 -CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* ** * * **
25775 TCTTCGGAACTTAGCCCGGATACA-TCACTAGCATGAATGC
1 -CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
** * * *
25815 TCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAATGC
1 -CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* ** * * **
25855 TCTTCGGAACTTAGCCCGGATACA-TCACTAGCATGAATGC
1 -CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
*
25895 TCTTCGGGACTTAGCCTGG-TTATAGTAACTCGCACAAATGC
1 -CTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGC
* *
25936 CTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
*
25976 CTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
*
26015 CTTC-GGATCTTAGTCCGGAT
1 CTTCGGGA-CTTAGCCCGGAT
26035 ATGGTCACTT
Statistics
Matches: 259, Mismatches: 33, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
38 2 0.01
39 34 0.13
40 204 0.79
41 14 0.05
42 5 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:27465 original size:37 final size:37
Alignment explanation
Indices: 27415--27493 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
27405 TTATTACGAA
* *
27415 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
27452 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
27489 GTCTT
1 GTCTT
27494 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:27690 original size:47 final size:47
Alignment explanation
Indices: 27612--28101 Score: 863
Period size: 47 Copynumber: 10.4 Consensus size: 47
27602 CCCTTCGGGA
* * * * * * *
27612 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
27659 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27706 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
27753 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27800 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27847 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27894 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27941 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27988 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28035 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28082 CTTATCACATATATACACTT
1 CTTATCACATATATACACTT
28102 CTTGGCTGAA
Statistics
Matches: 426, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 426 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.