Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3820
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: 17112
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Found at i:1784 original size:40 final size:40
Alignment explanation
Indices: 1729--1869 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
1719 TATTCGAATG
*
1729 ATATCCGGGCTAAGTCCCGAAGGCATTTCTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1769 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
1809 ATATCCGGGCTAAGTCCCGCAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
1849 ATATCC-GGCTAAAT-CCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
1870 ACTTGGGTTT
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
38 6 0.06
39 7 0.07
40 80 0.84
41 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:5461 original size:45 final size:45
Alignment explanation
Indices: 5411--5496 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
5401 CAAAACATGT
5411 GTCACATATATCACGAAC-CTAGACCACAACTCAATGAGTTCGGAC
1 GTCACATATATCACGAACTC-AGACCACAACTCAATGAGTTCGGAC
* *
5456 GTCACATATATCATGAACTCAGACCACAACTTAATGAGTTC
1 GTCACATATATCACGAACTCAGACCACAACTCAATGAGTTC
5497 ATATTCATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (45 bp):
GTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGAC
Found at i:8534 original size:40 final size:41
Alignment explanation
Indices: 8466--8600 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 41
8456 TTGATATCTA
* * *
8466 GCACACTAAGTGCCGTACATAG-TCGAAGCTAT-CTCAAGTT
1 GCACACTAAGTGCCATATATAGCTCGAAGCTATGCTCAA-TC
* * *
8506 GCACACTAAGTGCCATATATAGCT-GAAGCTCTGTTGAATC
1 GCACACTAAGTGCCATATATAGCTCGAAGCTATGCTCAATC
* * * * **
8546 GTACACTAAGTGCCATATATAGC-CGACGATATGTTGTATC
1 GCACACTAAGTGCCATATATAGCTCGAAGCTATGCTCAATC
8586 GCACACTAAGTGCCA
1 GCACACTAAGTGCCA
8601 CAAATAACTG
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 76 0.95
41 4 0.05
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (41 bp):
GCACACTAAGTGCCATATATAGCTCGAAGCTATGCTCAATC
Found at i:14708 original size:27 final size:28
Alignment explanation
Indices: 14670--14728 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
14660 AGCATACATT
*
14670 ATCAAACATAAAACATTTA-TCTCATAA
1 ATCAAACATAAAACATTCATTCTCATAA
* *
14697 ATCAAACATAAAGCATTCATTCTTATAA
1 ATCAAACATAAAACATTCATTCTCATAA
14725 ATCA
1 ATCA
14729 TTCAACACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.31
Consensus pattern (28 bp):
ATCAAACATAAAACATTCATTCTCATAA
Found at i:16268 original size:37 final size:37
Alignment explanation
Indices: 16205--16350 Score: 213
Period size: 37 Copynumber: 3.9 Consensus size: 37
16195 AGTTCAGATG
* * *
16205 AAATCTCCATACGA-AGTTATCAGGTCTTACCCGGACA
1 AAATCTCCACAC-ATAGTCATCGGGTCTTACCCGGACA
16242 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
* *
16279 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
* *
16316 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGA
16351 ATATATTTCC
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
36 1 0.01
37 102 0.99
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
Found at i:16307 original size:74 final size:74
Alignment explanation
Indices: 16206--16350 Score: 236
Period size: 74 Copynumber: 2.0 Consensus size: 74
16196 GTTCAGATGA
* *
16206 AATCTCCATACGAAGTTATCAGGTCTTACCCGGACAAAATCTCCACACATAGTCATCGGGTCTTA
1 AATCTCCACACGAAGTCATCAGGTCTTACCCGGACAAAATCTCCACACATAGTCATCGGGTCTTA
16271 CCCGGACAT
66 CCCGGACAT
* * * *
16280 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTA
1 AATCTCCACACGAAGTCATCAGGTCTTACCCGGACAAAATCTCCACACATAGTCATCGGGTCTTA
16345 CCCGGA
66 CCCGGA
16351 ATATATTTCC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (74 bp):
AATCTCCACACGAAGTCATCAGGTCTTACCCGGACAAAATCTCCACACATAGTCATCGGGTCTTA
CCCGGACAT
Found at i:16618 original size:47 final size:48
Alignment explanation
Indices: 16492--16973 Score: 690
Period size: 47 Copynumber: 10.0 Consensus size: 48
16482 ACACATCGCC
*
16492 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* **
16542 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGTATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
16590 TACATA-TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
16639 TATATATTTTCACATTAACCATTCAGC-TTACCACATATACATATCTCA
1 TACATA-TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
16687 TATATATATTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATAT-TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
16736 TAC-TATTTCACATTAGCCATTCGGATTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
16783 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
16831 TGCATATTTCACA-TAGCCAGTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
16878 TACATATTTCACATTAGCCAGCCAGTCGGC-TTACCACATATACATATCTCA
1 TACATATTTCACATT----AGCCATTCGGCTTTACCACATATACATATCTCA
16929 TACATATTTCACATTAGCCATTCGGC-TTACCACATATACATATCT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
16974 TATGCATCAA
Statistics
Matches: 395, Mismatches: 23, Indels: 31
0.88 0.05 0.07
Matches are distributed among these distances:
47 152 0.38
48 88 0.22
49 30 0.08
50 61 0.15
51 53 0.13
52 11 0.03
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:16753 original size:146 final size:144
Alignment explanation
Indices: 16492--16973 Score: 699
Period size: 146 Copynumber: 3.3 Consensus size: 144
16482 ACACATCGCC
*
16492 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATA-TTCACATT
**
16557 -GACCATTCGGCTTTACCACATATGTATATCTCATAC-ATATTCACATTAGCCATTCGGCTTTAC
65 AG-CCATTCGGCTTTACCACATATACATATCTCATACTAT-TTCACATTAGCCATTCGGCTTTAC
16620 CACATATACATATCTCATA
128 CACATATACATATCTC--A
* * * *
16639 TATATATTTTCACATTAACCATTCAGC-TTACCACATATACATATCTCATATATATATTCGCATT
1 TACATA-TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTCACATT
*
16703 AGCCATTCGGCTTTACCACATATACATATCTCATACTATTTCACATTAGCCATTCGGATTTACCA
65 AGCCATTCGGCTTTACCACATATACATATCTCATACTATTTCACATTAGCCATTCGGCTTTACCA
16768 CATATACATATCTCA
130 CATATACATATCTCA
* **
16783 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTATGCATAT-TTCACA-TA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTCACATTA
* *
16846 GCCAGTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCAGCCAGTCGGC-TT
66 GCCATTCGGCTTTACCACATATACATATCTCATAC-TATTTCACATT----AGCCATTCGGCTTT
16910 ACCACATATACATATCTCA
126 ACCACATATACATATCTCA
16929 TACATATTTCACATTAGCCATTCGGC-TTACCACATATACATATCT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
16974 TATGCATCAA
Statistics
Matches: 308, Mismatches: 18, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
142 36 0.12
143 34 0.11
144 31 0.10
145 19 0.06
146 125 0.41
147 46 0.15
148 17 0.06
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (144 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTCACATTA
GCCATTCGGCTTTACCACATATACATATCTCATACTATTTCACATTAGCCATTCGGCTTTACCAC
ATATACATATCTCA
Found at i:16813 original size:95 final size:94
Alignment explanation
Indices: 16492--16973 Score: 639
Period size: 95 Copynumber: 5.0 Consensus size: 94
16482 ACACATCGCC
* *
16492 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATA-CTATTTCACATT
**
16557 -GACCATTCGGCTTTACCACATATGTATATCTCA
63 AG-CCATTCGG-TTTACCACATATACATATCTCA
*
16590 TACATA-TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTTCACAT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATA-CTA-TTTCACAT
* * *
16654 TAACCATTCAGCTTACCACATATACATATCTCA
62 TAGCCATTCGGTTTACCACATATACATATCTCA
* *
16687 TATATATATTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCATACTATTTCACATTAG
1 TACATAT-TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACTATTTCACATTAG
16752 CCATTCGGATTTACCACATATACATATCTCA
65 CCATTCGG-TTTACCACATATACATATCTCA
* *
16783 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTATGCATATTTCACA-TAG
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAC-TATTTCACATTAG
*
16847 CCAGTCGGCTTTACCACATATACATATCTCA
65 CCATTCGG-TTTACCACATATACATATCTCA
*
16878 TACATATTTCACATTAGCCAGCCAGTCGGC-TTACCACATATACATATCTCATACATATTTCACA
1 TACATATTTCACATT----AGCCATTCGGCTTTACCACATATACATATCTCATAC-TATTTCACA
*
16942 TTAGCCATTCGGCTTACCACATATACATATCT
61 TTAGCCATTCGGTTTACCACATATACATATCT
16974 TATGCATCAA
Statistics
Matches: 350, Mismatches: 23, Indels: 22
0.89 0.06 0.06
Matches are distributed among these distances:
95 105 0.30
96 38 0.11
97 75 0.21
98 73 0.21
99 59 0.17
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (94 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACTATTTCACATTAGC
CATTCGGTTTACCACATATACATATCTCA
Done.