Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1871
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: 27029
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:892 original size:399 final size:399
Alignment explanation
Indices: 154--954 Score: 1575
Period size: 399 Copynumber: 2.0 Consensus size: 399
144 ATTACCTTGC
*
154 TTCAGCTCAAGAAACTCTTTACATTTCTGATCAATAAATCTTTCACTAATATATTTCTTCCGAAA
1 TTCAGCTCAAGAAACTCTTTACATTTCTGATCAATAAATCTTTCACTAATATATTTCTTCCAAAA
219 CTCTTCTTGAAAGAATTCCCAGGTTACCCTCTCTTTCGGTACCACCGAAATCAAAGTCTTCCACC
66 CTCTTCTTGAAAGAATTCCCAGGTTACCCTCTCTTTCGGTACCACCGAAATCAAAGTCTTCCACC
284 AATTATAGGCTGAATCTCTCAACAAAGATGTAGCACATTTCAAACATTCTTCAGGTGTACAAGAT
131 AATTATAGGCTGAATCTCTCAACAAAGATGTAGCACATTTCAAACATTCTTCAGGTGTACAAGAT
349 AATTCATCAAATACCCGGATAGAATTTTCAAGTCAGAACTCTGCTTTCTCTACATCATCATCAAT
196 AATTCATCAAATACCCGGATAGAATTTTCAAGTCAGAACTCTGCTTTCTCTACATCATCATCAAT
*
414 ATTTGCTCTAAATTCTTTAGCCCCTTGTTTACGAATTCTATCAACGGGGGTTCTATGAAATTTTA
261 ATTTGCTCTAAATTCTTCAGCCCCTTGTTTACGAATTCTATCAACGGGGGTTCTATGAAATTTTA
479 TCATATCCACTCCTTGAGGCATTGGAGGCATAGGTTGAGGAATTGGGGGAGGTGGGGGAGGTCGT
326 TCATATCCACTCCTTGAGGCATTGGAGGCATAGGTTGAGGAATTGGGGGAGGTGGGGGAGGTCGT
544 ACATTTGGG
391 ACATTTGGG
553 TTCAGCTCAAGAAACTCTTTACATTTCTGATCAATAAATCTTTCACTAATATATTTCTTCCAAAA
1 TTCAGCTCAAGAAACTCTTTACATTTCTGATCAATAAATCTTTCACTAATATATTTCTTCCAAAA
618 CTCTTCTTGAAAGAATTCCCAGGTTACCCTCTCTTTCGGTACCACCGAAATCAAAGTCTTCCACC
66 CTCTTCTTGAAAGAATTCCCAGGTTACCCTCTCTTTCGGTACCACCGAAATCAAAGTCTTCCACC
683 AATTATAGGCTGAATCTCTCAACAAAGATGTAGCACATTTCAAACATTCTTCAGGTGTACAAGAT
131 AATTATAGGCTGAATCTCTCAACAAAGATGTAGCACATTTCAAACATTCTTCAGGTGTACAAGAT
*
748 AATTCATCAAATACCCGGATAGAATTTTCAAGTCAGAACTCTGCTTTCTCTGCATCATCATCAAT
196 AATTCATCAAATACCCGGATAGAATTTTCAAGTCAGAACTCTGCTTTCTCTACATCATCATCAAT
813 ATTTGCTCTAAATTCTTCAGCCCCTTGTTTACGAATTCTATCAACGGGGGTTCTATGAAATTTTA
261 ATTTGCTCTAAATTCTTCAGCCCCTTGTTTACGAATTCTATCAACGGGGGTTCTATGAAATTTTA
878 TCATATCCACTCCTTGAGGCATTGGAGGCATAGGTTGAGGAATTGGGGGAGGTGGGGGAGGTCGT
326 TCATATCCACTCCTTGAGGCATTGGAGGCATAGGTTGAGGAATTGGGGGAGGTGGGGGAGGTCGT
943 ACATTTGGG
391 ACATTTGGG
952 TTC
1 TTC
955 GTACGAACGA
Statistics
Matches: 399, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
399 399 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (399 bp):
TTCAGCTCAAGAAACTCTTTACATTTCTGATCAATAAATCTTTCACTAATATATTTCTTCCAAAA
CTCTTCTTGAAAGAATTCCCAGGTTACCCTCTCTTTCGGTACCACCGAAATCAAAGTCTTCCACC
AATTATAGGCTGAATCTCTCAACAAAGATGTAGCACATTTCAAACATTCTTCAGGTGTACAAGAT
AATTCATCAAATACCCGGATAGAATTTTCAAGTCAGAACTCTGCTTTCTCTACATCATCATCAAT
ATTTGCTCTAAATTCTTCAGCCCCTTGTTTACGAATTCTATCAACGGGGGTTCTATGAAATTTTA
TCATATCCACTCCTTGAGGCATTGGAGGCATAGGTTGAGGAATTGGGGGAGGTGGGGGAGGTCGT
ACATTTGGG
Found at i:2645 original size:46 final size:45
Alignment explanation
Indices: 2578--2751 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 45
2568 TGTAACCCGC
*
2578 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCAT
* *
2624 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGC-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGCAT
* * * * *
2670 ACATTTCA-CGAA-TCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCAT
2716 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
2752 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
44 3 0.03
45 6 0.06
46 87 0.82
47 6 0.06
48 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGCAT
Found at i:3212 original size:30 final size:30
Alignment explanation
Indices: 3178--3237 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3168 ATTTAATACG
**
3178 AACTTTGGGAAAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
* *
3208 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
3238 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:7550 original size:44 final size:41
Alignment explanation
Indices: 7471--7624 Score: 123
Period size: 40 Copynumber: 3.7 Consensus size: 41
7461 TTCTGGTATA
* * ** *
7471 TGATTTTGTGTAAGACCACGTCTGGGATGTTGACAT-TGATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATCGACATAT-ATT
*
7512 TGAGATTTACGTGTAAGACCATGTCTGAGACATCGACATCATATT
1 T--GATTT-CGTGTAAGACCATGTCTGGGACATCGACAT-ATATT
* ** * *
7557 TGATTTCGTGTAAGACCCTGTCTGGGACAAAGGC-CATATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATCGACATATATT
* * *
7597 TGATTACATGTAAGACCACGTCTGGGAC
1 TGATTTCGTGTAAGACCATGTCTGGGAC
7625 GTTGGCATTG
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
40 29 0.32
41 1 0.01
42 23 0.25
43 10 0.11
44 24 0.26
45 4 0.04
46 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATCGACATATATT
Found at i:9496 original size:41 final size:41
Alignment explanation
Indices: 9439--9522 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
9429 ATTAGGACTC
9439 GGATTCGATTATCGGAGGAGCTCTCGAAAAAATGATTACTT
1 GGATTCGATTATCGGAGGAGCTCTCGAAAAAATGATTACTT
* * *
9480 GGATTTGATTATCGGAGGAGCTCTCGGAAAAATGATTTCTT
1 GGATTCGATTATCGGAGGAGCTCTCGAAAAAATGATTACTT
9521 GG
1 GG
9523 CTATGGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (41 bp):
GGATTCGATTATCGGAGGAGCTCTCGAAAAAATGATTACTT
Found at i:20469 original size:28 final size:27
Alignment explanation
Indices: 20405--20556 Score: 223
Period size: 27 Copynumber: 5.6 Consensus size: 27
20395 TTATTAAGTC
* *
20405 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
20432 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
20460 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
20487 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* * *
20515 CGCACACATAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
20542 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20557 GCACAATTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 65 0.56
28 51 0.44
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:20489 original size:55 final size:55
Alignment explanation
Indices: 20405--20581 Score: 237
Period size: 55 Copynumber: 3.2 Consensus size: 55
20395 TTATTAAGTC
* * *
20405 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
20460 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * * *
20515 CGCACACATAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
20571 CGCACACTTAG
1 CGCACACTTAG
20582 CGCCAATCTC
Statistics
Matches: 107, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
55 92 0.86
56 15 0.14
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Done.