Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2081
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: 60807
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1932 original size:249 final size:247
Alignment explanation
Indices: 1481--1981 Score: 828
Period size: 249 Copynumber: 2.0 Consensus size: 247
1471 AAGAAGGAAG
* *
1481 GGTTGATGAAACCAAGGATGGTCCTTGAAGACAACGACCTGAAGGCGTTGGGAAGGTTTCAAGGA
1 GGTTGATGAAACCAAGGAAGGTCCTTGAAGACAAAGACCTGAAGGCGTTGGGAAGGTTTCAAGGA
* *
1546 CCAATGACGAGGGCAAAGGCAAAGAGGATAATGGAAGACCTAGAGAAGACGGTTGCTGCCCTATT
66 CCAATAACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGACGGTTGCTGCCCTATT
*
1611 TGAAAGTAAACCCAATTGGAGCTAGAAGAGCCCAAGCTGGTCAATTGCATATATTTGGAAGATAT
131 TGAAAGTAAACCCAATTGGAGCTAGAAGAGCCCAAGCTAGTCAATTGCATATATTTGGAAGATAT
*
1676 GGGCTCCAATGGATTGAATTAGGACTTGGGTTTTTTTGTAATAAAGGGCCTGCT
196 GGGCTCCAATGGATTGAATTAGGACTTGGGTTATTTT-TAAT-AAGGGCCTGCT
1730 GGTTGATGAAACCAAGGAAGGTCCATTGAAGACAAAGACCTGAAGGCGTT-GGAAGGATTTCAAG
1 GGTTGATGAAACCAAGGAAGGTCC-TTGAAGACAAAGACCTGAAGGCGTTGGGAAGG-TTTCAAG
* * *
1794 GTCCAATAACGA-GGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGATGGTTGCTGGCCTA
64 GACCAATAACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGACGGTTGCTGCCCTA
* * *
1858 TTTGAAAGTAGACCCAATTTGGAGTTAGAAGAGCCCAAGCTAGTTAATTGCATATATTTGGAAGA
129 TTTGAAAGTAAACCCAA-TTGGAGCTAGAAGAGCCCAAGCTAGTCAATTGCATATATTTGGAAGA
1923 TAT-GGCTCCAATGGATTGAATTAGGACTTGGGTTATTTTTAATAAGGGCCTGCT
193 TATGGGCTCCAATGGATTGAATTAGGACTTGGGTTATTTTTAATAAGGGCCTGCT
1977 GGTTG
1 GGTTG
1982 TGACTTGCTT
Statistics
Matches: 237, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
247 16 0.07
248 4 0.02
249 129 0.54
250 88 0.37
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.24
Consensus pattern (247 bp):
GGTTGATGAAACCAAGGAAGGTCCTTGAAGACAAAGACCTGAAGGCGTTGGGAAGGTTTCAAGGA
CCAATAACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGACGGTTGCTGCCCTATT
TGAAAGTAAACCCAATTGGAGCTAGAAGAGCCCAAGCTAGTCAATTGCATATATTTGGAAGATAT
GGGCTCCAATGGATTGAATTAGGACTTGGGTTATTTTTAATAAGGGCCTGCT
Found at i:3409 original size:30 final size:30
Alignment explanation
Indices: 3373--3437 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3363 AGAGAATAGT
* * *
3373 AGAGATAGGAGGGATAGGAGGAGA-GACAGG
1 AGAGATAAGAGAGAGAGGAGG-GATGACAGG
*
3403 AGAGATAATAGAGAGAGGAGGGATGACAGG
1 AGAGATAAGAGAGAGAGGAGGGATGACAGG
3433 AGAGA
1 AGAGA
3438 GAGAAGAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (30 bp):
AGAGATAAGAGAGAGAGGAGGGATGACAGG
Found at i:13933 original size:148 final size:149
Alignment explanation
Indices: 13691--13977 Score: 336
Period size: 148 Copynumber: 1.9 Consensus size: 149
13681 AGTTCGTTCA
* * *
13691 TCAAATGAGACAAACATAGATTCTTGTAATAATCTCCACTTTTTTGTGATAGGCCCTATAAACAT
1 TCAAATGAGACAAACATAGATTCTTATAATAATCTCCACTTTTTTATGATAGG-CCTAAAAACAT
* * * * * * *
13756 TTTTTCCTCATTGGGATACATAATATGATGCTTTGGTCTTC-CAAGAAAAGCTTTT-TTTC-ACC
65 GTTCTCCTAATTAGGATACACAATATGATGCTTTAGT-TTCACAAAAAAAGCTTTTCTTTCTACC
*
13818 ATTTTTCTTAAAATTTGTCTC
129 ATTTTCCTTAAAATTTGTCTC
*
13839 TCAAATGAGACAAACATGGATTCTTAT-ATAAATCTCCA-TTTTTTCATGATTAGG-CTAAAAAA
1 TCAAATGAGACAAACATAGATTCTTATAAT-AATCTCCACTTTTTT-ATGA-TAGGCCT-AAAAA
* *
13901 CATGTTCTCC-AATTAGGATATACAATATTGATGTTTTAGTTTCACAAAAAAAGCTTTTCTTTCT
62 CATGTTCTCCTAATTAGGATACACAATA-TGATGCTTTAGTTTCACAAAAAAAGCTTTTCTTTCT
13965 ACCATTTTCCTTA
126 ACCATTTTCCTTA
13978 TAATCAAAGT
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
147 26 0.22
148 71 0.61
149 8 0.07
150 12 0.10
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (149 bp):
TCAAATGAGACAAACATAGATTCTTATAATAATCTCCACTTTTTTATGATAGGCCTAAAAACATG
TTCTCCTAATTAGGATACACAATATGATGCTTTAGTTTCACAAAAAAAGCTTTTCTTTCTACCAT
TTTCCTTAAAATTTGTCTC
Found at i:14102 original size:159 final size:157
Alignment explanation
Indices: 13841--14211 Score: 437
Period size: 160 Copynumber: 2.3 Consensus size: 157
13831 TTTGTCTCTC
* * * * *
13841 AAATGAGACAAACATGGATTCT-TATATAAATCTCCATT-TTTTCATGATTAGGCTAAAAAACAT
1 AAATGAGAGAAACATGGATTCTGTA-AT-AATCTCCATTCTTTTCAAGATTTGGCAAAAAAAAAT
* ** *
13904 GTTCTCCAATTAGGATATACAATATTGATGTTTTAGTTTCACAAAAAAA-GCTTTTCTTTCTACC
64 GTTCTCCAATTAGGATAAACAATATTGATACTTTAGTTTCACAAAAAAAGGCTTTTCTTTCCACC
* *
13968 ATTTTCCTTATAATCAAAGTTCATCACTT
129 ATTTTCCTTAGAATCAAAGTTAATCACTT
**
13997 AAATGAGAGAAACATGGATTCATGTAATAATCTGAATTCTTTTCAAGATTTGGCAACAAAAAAAT
1 AAATGAGAGAAACATGGATTC-TGTAATAATCTCCATTCTTTTCAAGATTTGGCAA-AAAAAAAT
* * * * *
14062 GTTTTCCTAATTGGGATAAACAGTATTGATACTTTGGTTTCACAAAAAAAGGCTTTTCTTTCCAT
64 GTTCTCC-AATTAGGATAAACAATATTGATACTTTAGTTTCACAAAAAAAGGCTTTTCTTTCCAC
* * *
14127 TATTTTCCTTAGAATCATAGTTAATCCCTT
128 CATTTTCCTTAGAATCAAAGTTAATCACTT
*
14157 AAATGAG-GCAAAGATGGATTCTTGTAATAATCTCCATTCTTTT-ATAGATTTGGCA
1 AAATGAGAG-AAACATGGATTC-TGTAATAATCTCCATTCTTTTCA-AGATTTGGCA
14212 CTGCAAAAGT
Statistics
Matches: 182, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
156 28 0.15
157 17 0.09
158 15 0.08
159 38 0.21
160 84 0.46
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (157 bp):
AAATGAGAGAAACATGGATTCTGTAATAATCTCCATTCTTTTCAAGATTTGGCAAAAAAAAATGT
TCTCCAATTAGGATAAACAATATTGATACTTTAGTTTCACAAAAAAAGGCTTTTCTTTCCACCAT
TTTCCTTAGAATCAAAGTTAATCACTT
Found at i:14598 original size:159 final size:158
Alignment explanation
Indices: 13632--15440 Score: 723
Period size: 159 Copynumber: 11.5 Consensus size: 158
13622 CTGATATGCC
* * * * * * * *
13632 TTGGTTTTGCAAGAAAAACTTTTCTTTT-CACCATTTTCCTTGGAGTCAAAGTTCGTTCATCAAA
1 TTGGTTTCGCAAGAAAAGCTTTT-TTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAAA
* * * ** * * *
13696 TGAGACAAACATAGATTCTTGTAATAATCTCCACT-TTTTTGTGA-TAGGC-CCTATAA-ACATT
65 TGAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCATGATTTGGCAAC-AAAAGACA-T
* * * *
13757 TTTTCCTCATTGGGATACATAATA-TGATGCT
128 TCTT-CTCATTTGGATACATGATATTGATACT
* ** * *
13788 TTGGTCTTC-CAAGAAAAGC-TTTTTTT-CACCATTTTTCTT---A--AAA-TTTGTCTCTCAAA
1 TTGGT-TTCGCAAGAAAAGCTTTTTTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAAA
* * * * *
13844 TGAGACAAACATGGATTCTTAT-ATAAATCTCCA-TTTTTTCATGATTAGGCTA-AAAA-ACA-T
65 TGAGACAAACATGGATTCTTGTAAT-AATCTCTAGTCTTTTCATGATTTGGCAACAAAAGACATT
* * * ** **
13904 GTTCTCCAATTAGGATATACAATATTGATGTT
129 CTTCT-C-ATTTGGATACATGATATTGATACT
* * * * * * *
13936 TTAGTTTCACAAAAAAAGCTTTTCTTTCTACCATTTTCCTTATAATCAAAGTTCATCACTTAAAT
1 TTGGTTTCGCAAGAAAAGCTTTTTTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAAAT
* * ** * * * *
14001 GAGAGAAACATGGATTCATGTAATAATCTGAATTCTTTTCAAGATTTGGCAACAAAA-AAATGTT
66 GAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCATGATTTGGCAACAAAAGACAT-TC
* *
14065 TTCCTAATTGGGATAAACA-G-TATTGATACT
130 TT-CTCATTTGGAT--ACATGATATTGATACT
* * * ** * *
14095 TTGGTTTCACAAAAAAAGGCTTTTCTTTCCATTATTTTCCTTAGAATCATAGTTAATCCCTTAAA
1 TTGGTTTCGCAAGAAAA-GCTTTTTTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAAA
* * * * * **
14160 TGAGGCAAAGATGGATTCTTGTAATAATCTCCATTCTTTT-ATAGATTTGGCACTGCAAAAG-TG
65 TGAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCAT-GATTTGGCA--ACAAAAGACA
* * *
14223 TTCTTGTCA-TTGAGATACATGATAATGATGCT
127 TTCTTCTCATTTG-GATACATGATATTGATACT
** * * * * * * * * *
14255 TTAATTTCCCAAGAAATGATTTTGTTTT-CACTATTTTTCTAAG-ATGTAAA-TTCATGCCTCAA
1 TTGGTTTCGCAAGAAAAGCTTTT-TTTTCCACCATTTTCCTTAGAAT-CAAAGTTCATCCCTTAA
* * ** * * *
14317 ATGAGACAAATATGGTTTCTCATAATAATCTCTAGTCTTTTCATAATTGGGCAA-AAAAAATGCA
64 ATGAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCATGATTTGGCAACAAAAGA--CA
** * * *
14381 TTCCCCTTATTAGGATACACGATATTGATACT
127 TTCTTCTCATTTGGATACATGATATTGATACT
* * * * * *
14413 TTGCTTTTGCAAGAAAACCATCTTTTTCCACCATATTCCTTAGAATCAAAGTTCATCCCTTAAAT
1 TTGGTTTCGCAAGAAAAGCTTTTTTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAAAT
* * * * * * *
14478 AAGACAAACATGGATTCTTGTAGTAATCTCTAGTCTATTCATGGTTAGGCAGCAAAAGCACATTT
66 GAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCATGATTTGGCAACAAAAG-ACATTC
* *
14543 TTCTCATTTGGATACATGATATTAATGCT
130 TTCTCATTTGGATACATGATATTGATACT
* * * *
14572 TTGGTTTTGCAAGAAAAGCTTTTTTTTCCAACATTTTCCTTAGAATAAAAATTCATCCCTTAAAT
1 TTGGTTTCGCAAGAAAAGCTTTTTTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAAAT
** ** * ** * * * * ** ** *
14637 GAGATGAATGTGTATTCTCATAATAATCTCCATTCTTATCAAGATTCAGCCCCATAAACACATT-
66 GAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCATGATTTGGCAACA-AAAGACATTC
* *
14701 GTC-CATATTGGGATACATGATATTGATGCT
130 TTCTCAT-TT-GGATACATGATATTGATACT
* * ** * ** * * * ** *
14731 TTGATTCCATAAGAAAA-ATTTTTCTTTCCATTATTTTCTTTAGAATTATAGTTCAT-TTTTCGA
1 TTGGTTTCGCAAGAAAAGCTTTTT-TTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTT-AA
* * ** * ** * * **
14794 ATAAGATAAACATGGATTCTCATAATAATCCCTA-T-TTTTTGTGA-TTGGGAAAAAAACTCATT
64 ATGAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCATGATTTGGCAACAAAAGACATT
* * *
14856 CTCCTCA-TTGAGACACAAT-ATATT-AAAGCT
129 CTTCTCATTTG-GATAC-ATGATATTGATA-CT
* * * * *
14886 TTAGTTTCACAAGAAAAG-TTTTTATCTCCACCATTTTCCTTAGAATCAAAAATTCATCCCTCAA
1 TTGGTTTCGCAAGAAAAGCTTTTT-TTTCCACCATTTTCCTTAGAATC-AAAGTTCATCCCTTAA
* ** * * * * * * *
14950 ATGAGATAAACATGGATT-TTAAAAACAATCGCCACTTTTTTCATGA-TTGGTCACCATAA-ACA
64 ATGAGACAAACATGGATTCTT-GTAATAATCTCTAGTCTTTTCATGATTTGG-CAACAAAAGACA
* * * *
15012 TGTTCTCCTTATTAGGATACAAT-ATATTGATATT
127 --TTCTTCTCATTTGGATAC-ATGATATTGATACT
* * * *
15046 TTGGTTTCCCAAGAAATGC-TTTTTTTCCACCATTTT--TATAAAATCAAAGTTCATCCCTAAAA
1 TTGGTTTCGCAAGAAAAGCTTTTTTTTCCACCATTTTCCT-TAGAATCAAAGTTCATCCCTTAAA
* * * * * * * * **
15108 TAAGACAAATAAGGATTCTCGTAATAATTTCTA-TCTTTTTCATGAATAGGCAACAAGAAAATGT
65 TGAGACAAACATGGATTCTTGTAATAATCTCTAGTC-TTTTCATGATTTGGCAACAA-AAGACAT
* ** *
15172 TCTCCTCA-TTGAGATACACAATATTGGTGA-T
128 TCTTCTCATTTG-GATACATGATATTGAT-ACT
* * * * ** ** *
15203 CTAGTTTC-CTAAGAAAAGCTTTTCTTTT-CACCTTTTTCCTTAAAATCAAAGTTTGTCTGTCAA
1 TTGGTTTCGC-AAGAAAAGCTTTT-TTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAA
** ** * * * * * * *
15266 ATGAGACAAACATATATTCTCATAAAAATCTTTATTCTTTTCTTAAATAGGCAA-AAAA-ACA-T
64 ATGAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCATGATTTGGCAACAAAAGACATT
* * * * **
15328 CTTCTCCACCTTGG---GAGGACATTGATGTTT
129 CTTCT-CA-TTTGGATACATGATATTGAT-ACT
* * *
15358 TTGGTTT-GCAAGAAAAGCTTTTTATTTCCACCATTTTCATTAGAAACAAAGTTCATCCCTCAAA
1 TTGGTTTCGCAAGAAAAGCTTTTT-TTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAAA
* * *
15422 TGAGGCAAATATAGATTCT
65 TGAGACAAACATGGATTCT
15441 AGTAGACAAA
Statistics
Matches: 1251, Mismatches: 313, Indels: 179
0.72 0.18 0.10
Matches are distributed among these distances:
145 2 0.00
146 4 0.00
147 19 0.02
148 69 0.06
149 14 0.01
150 11 0.01
153 2 0.00
154 42 0.03
155 124 0.10
156 96 0.08
157 122 0.10
158 164 0.13
159 400 0.32
160 164 0.13
161 12 0.01
162 6 0.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (158 bp):
TTGGTTTCGCAAGAAAAGCTTTTTTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCCTTAAAT
GAGACAAACATGGATTCTTGTAATAATCTCTAGTCTTTTCATGATTTGGCAACAAAAGACATTCT
TCTCATTTGGATACATGATATTGATACT
Found at i:15966 original size:156 final size:157
Alignment explanation
Indices: 15806--16091 Score: 349
Period size: 157 Copynumber: 1.8 Consensus size: 157
15796 TGGGCACCAT
* ** * * *
15806 AAACACATTATCCTTGTTAGGATACTTGATATTGATGC-TTGGTTTCCCAAGAAGAGCTTTTCTT
1 AAACACATTATCCCTGTTAGGATACAAGATATTGATGCATTGGTATCACAAGAAAAGCTTTTCTT
* * * *
15870 TTCACCATTTTACATAGAATCAAAATTCATCTATCAAATGAGATAAACATGCATTCTAGTAATAA
66 TTCACCATTTCACATAGAATCAAAATTCATCTACCAAATGAGACAAACATGAATTCTAGTAATAA
15935 ACTATTGTTTTTGTGATTAGGCTACAA
131 ACTATTGTTTTTGTGATTAGGCTACAA
** * * ***
15962 AAACATGTTCTCCCTGTTTGGATACAAGATATTGATGCATTGGTATCATTGGAAAAGCTTTTCTT
1 AAACACATTATCCCTGTTAGGATACAAGATATTGATGCATTGGTATCACAAGAAAAGCTTTTCTT
* * * * * * *
16027 TTCTCCATTTCCCTTAGAATCAAAGTTCGTCTACCAAATGAGACATACATGAATTCTCGTAATAA
66 TTCACCATTTCACATAGAATCAAAATTCATCTACCAAATGAGACAAACATGAATTCTAGTAATAA
16092 TTCTGGTCTT
Statistics
Matches: 105, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
156 31 0.30
157 74 0.70
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (157 bp):
AAACACATTATCCCTGTTAGGATACAAGATATTGATGCATTGGTATCACAAGAAAAGCTTTTCTT
TTCACCATTTCACATAGAATCAAAATTCATCTACCAAATGAGACAAACATGAATTCTAGTAATAA
ACTATTGTTTTTGTGATTAGGCTACAA
Found at i:21331 original size:15 final size:14
Alignment explanation
Indices: 21294--21332 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
21284 AGAATACAAA
21294 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
21308 AATACAAAAAGAAAGG
1 AA-AAAAAAAGAAA-G
21324 AAAAAAAAA
1 AAAAAAAAA
21333 CCAGTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:22100 original size:12 final size:11
Alignment explanation
Indices: 22078--22153 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
22068 AGAGAAAGAA
*
22078 GAGAGAGGAGG
1 GAGATAGGAGG
22089 GATGATAGGAGG
1 GA-GATAGGAGG
*
22101 AGAGACAGGA--
1 -GAGATAGGAGG
*
22111 GAGATAGTA--
1 GAGATAGGAGG
22120 GAGATAGGAGG
1 GAGATAGGAGG
22131 GATGATAGGAGG
1 GA-GATAGGAGG
*
22143 AGAGACAGGAG
1 -GAGATAGGAG
22154 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:22129 original size:42 final size:42
Alignment explanation
Indices: 22068--22186 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
22058 TAGCCCTCAA
* *
22068 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
22110 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
22152 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
22187 GAGAGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:22170 original size:18 final size:18
Alignment explanation
Indices: 22143--22192 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
22133 TGATAGGAGG
*
22143 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
22161 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
22179 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
22193 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:30024 original size:27 final size:28
Alignment explanation
Indices: 29981--30033 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
29971 TTGATTAATA
*
29981 AATAAGAAAGATCAA-GGAAGTGAAATC
1 AATAAGAAAGATCAAGGGAAATGAAATC
* *
30008 AATAAGAAATATGAAGGGAAATGAAA
1 AATAAGAAAGATCAAGGGAAATGAAA
30034 AAAGCAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (28 bp):
AATAAGAAAGATCAAGGGAAATGAAATC
Found at i:31479 original size:66 final size:64
Alignment explanation
Indices: 31365--31490 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 64
31355 TATTATGCTT
* *
31365 AGCTGCTCTTATTTTCATTGGTTCTGCCATGCATAGTGGTGCAAAAACTCCAGGTACTATACTG
1 AGCTGCTCTTATTTTCATTGGTTCTACCATGCATAGTGGTGCAAAAACTCCAGGCACTATACTG
* * * *
31429 AGCTGCTCTT-TTTTTATTGGTTCTACCATGTAGAGTAGTGGTGCAGAAACTCTAGGCACTAT
1 AGCTGCTCTTATTTTCATTGGTTCTACCATG--CA-TAGTGGTGCAAAAACTCCAGGCACTAT
31491 GTTGGACATC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 18 0.34
64 10 0.19
65 1 0.02
66 24 0.45
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (64 bp):
AGCTGCTCTTATTTTCATTGGTTCTACCATGCATAGTGGTGCAAAAACTCCAGGCACTATACTG
Found at i:35996 original size:103 final size:101
Alignment explanation
Indices: 35792--36012 Score: 247
Period size: 103 Copynumber: 2.2 Consensus size: 101
35782 TGAAAGGTGG
* *
35792 GGTTGGAGTATCCCCTCAGAAAGATGGGGTTAGAGTATCCCCATGGATGACAAATAATTTTGACA
1 GGTTGGAGTATCCCCTCAGAAAGATGGGGTTAGAGTATCCCCACGGACGACAAATAATTTTGACA
*
35857 AAGGAAGAGTTTTAAATCTTGACAATTTTGAATGGCGC
66 AAGGAAGAGATTTAAATCTTGACAATTTTGAAT-G-GC
* * * *
35895 GGTTGGAGTATCCCCTCAGAAGGTTGGGGTTGGAGTATCCCCACGGACGATAAA-AGA-TTTGAC
1 GGTTGGAGTATCCCCTCAGAAAGATGGGGTTAGAGTATCCCCACGGACGACAAATA-ATTTTGA-
* **
35958 CAAAGGAA-A-ATTTAATTC-TGATGATTTTGGAAAGTGGC
64 CAAAGGAAGAGATTTAAATCTTGACAATTTT-G-AA-TGGC
35996 -GTTGGAGTATCCCCTCA
1 GGTTGGAGTATCCCCTCA
36013 AGGTGGTGGC
Statistics
Matches: 103, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
100 25 0.24
101 10 0.10
102 10 0.10
103 58 0.56
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (101 bp):
GGTTGGAGTATCCCCTCAGAAAGATGGGGTTAGAGTATCCCCACGGACGACAAATAATTTTGACA
AAGGAAGAGATTTAAATCTTGACAATTTTGAATGGC
Found at i:39248 original size:20 final size:20
Alignment explanation
Indices: 39211--39260 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
39201 ATGGTCGAGC
* ** *
39211 ATCGATACATGAGTTCATTT
1 ATCGATACATAAACTCATGT
39231 ATCGATACATAAACTCATGT
1 ATCGATACATAAACTCATGT
*
39251 ATTGATACAT
1 ATCGATACAT
39261 TTTCACACTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCGATACATAAACTCATGT
Found at i:39833 original size:38 final size:37
Alignment explanation
Indices: 39791--39869 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 37
39781 TGCCGCTAGC
* * * *
39791 TTGTGCAAGCTTTGACTCAGACTTGGGTTGCCACCAAT
1 TTGTGCAAGATTTGACTCAAAC-TAGATTGCCACCAAT
* * *
39829 TTGTGTAGGATTTGACTCAAACTAGATTGCCACCAGT
1 TTGTGCAAGATTTGACTCAAACTAGATTGCCACCAAT
39866 TTGT
1 TTGT
39870 AAAGGCTTCG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 16 0.47
38 18 0.53
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (37 bp):
TTGTGCAAGATTTGACTCAAACTAGATTGCCACCAAT
Found at i:40391 original size:13 final size:13
Alignment explanation
Indices: 40369--40474 Score: 85
Period size: 13 Copynumber: 8.2 Consensus size: 13
40359 ACACAATTTT
40369 TTCTTGACAAAAG
1 TTCTTGACAAAAG
*
40382 TTCATGACAAAAG
1 TTCTTGACAAAAG
* * *
40395 TTTCCTGATGAAAGGG
1 -TTCTTGA-CAAA-AG
*
40411 TT-TTGACATAAG
1 TTCTTGACAAAAG
40423 TTCTTGACAAAA-
1 TTCTTGACAAAAG
40435 TTCTTGAC-AAAG
1 TTCTTGACAAAAG
*
40447 TT-TCTGACAAATG
1 TTCT-TGACAAAAG
*
40460 TTCTTGACAATAG
1 TTCTTGACAAAAG
40473 TT
1 TT
40475 TCTTAACAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
11 4 0.05
12 17 0.23
13 36 0.49
14 10 0.14
15 5 0.07
16 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (13 bp):
TTCTTGACAAAAG
Found at i:40440 original size:12 final size:12
Alignment explanation
Indices: 40413--40474 Score: 72
Period size: 12 Copynumber: 4.9 Consensus size: 12
40403 TGAAAGGGTT
40413 TTGACATAAGTTC
1 TTGACA-AAGTTC
*
40426 TTGACAAAATTC
1 TTGACAAAGTTC
40438 TTGACAAAGTT-
1 TTGACAAAGTTC
40449 TCTGACAAATGTTC
1 T-TGACAAA-GTTC
40463 TTGACAATAGTT
1 TTGACAA-AGTT
40475 TCTTAACAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 1 0.02
12 22 0.51
13 18 0.42
14 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (12 bp):
TTGACAAAGTTC
Found at i:40522 original size:14 final size:14
Alignment explanation
Indices: 40423--40522 Score: 63
Period size: 14 Copynumber: 7.5 Consensus size: 14
40413 TTGACATAAG
*
40423 TTCTTGACAA-A-A
1 TTCTTGACAATAGT
40435 TTCTTGACAA-AGT
1 TTCTTGACAATAGT
40448 TTC-TGACAA-A-T
1 TTCTTGACAATAGT
40459 GTTCTTGACAATAGT
1 -TTCTTGACAATAGT
*
40474 TTCTTAACAAT-GAT
1 TTCTTGACAATAG-T
* *
40488 TTCTTGATAAT-GG
1 TTCTTGACAATAGT
**
40501 CACTTTGACAATAGT
1 TTC-TTGACAATAGT
40516 TTCTTGA
1 TTCTTGA
40523 TAAAAAGGGT
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
11 1 0.01
12 21 0.30
13 11 0.16
14 33 0.48
15 3 0.04
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (14 bp):
TTCTTGACAATAGT
Found at i:40811 original size:28 final size:27
Alignment explanation
Indices: 40779--40842 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
40769 GACTCTAATG
40779 GGGATTGTAATTCATTCTAG-TTCCACTA
1 GGGATTGTAA--CATTCTAGATTCCACTA
* * *
40807 GGGATTGGAACTTTCTTGATTCCACTA
1 GGGATTGTAACATTCTAGATTCCACTA
40834 GGGATTGTA
1 GGGATTGTA
40843 GGTTGTCAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 6 0.19
27 16 0.52
28 9 0.29
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (27 bp):
GGGATTGTAACATTCTAGATTCCACTA
Found at i:40867 original size:28 final size:28
Alignment explanation
Indices: 40834--40894 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
40824 GATTCCACTA
* * *
40834 GGGATTGTAGGTTGTCAAGGCTCCATTG
1 GGGATTGCAGGTTATCAAGACTCCATTG
*
40862 GGGATTGCAGGTTATCCAGACTCCATTG
1 GGGATTGCAGGTTATCAAGACTCCATTG
40890 GGGAT
1 GGGAT
40895 ATGACATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (28 bp):
GGGATTGCAGGTTATCAAGACTCCATTG
Found at i:41746 original size:11 final size:10
Alignment explanation
Indices: 41732--41792 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 10
41722 TTATTTTCTT
41732 TTTTTTCTTGA
1 TTTTTT-TTGA
41743 TTTTTTTCAT-A
1 TTTTTTT--TGA
41754 TATTTTTTTGA
1 T-TTTTTTTGA
41765 CTTTTTTTT-A
1 -TTTTTTTTGA
*
41775 TTCTTTTTGA
1 TTTTTTTTGA
41785 TTTTTTTT
1 TTTTTTTT
41793 CTTTTTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
9 7 0.17
10 11 0.26
11 16 0.38
12 8 0.19
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:41769 original size:10 final size:9
Alignment explanation
Indices: 41755--41808 Score: 51
Period size: 10 Copynumber: 6.1 Consensus size: 9
41745 TTTTTCATAT
41755 ATTTTTTTG
1 ATTTTTTTG
*
41764 ACTTTTTTTT
1 A-TTTTTTTG
41774 ATTCTTTTTG
1 ATT-TTTTTG
41784 ATTTTTTT-
1 ATTTTTTTG
*
41792 -TCTTTTT-
1 ATTTTTTTG
41799 ATTTTTTTG
1 ATTTTTTTG
41808 A
1 A
41809 CCCCTCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 6 0.16
8 6 0.16
9 9 0.24
10 16 0.43
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.78
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:41781 original size:19 final size:19
Alignment explanation
Indices: 41739--41792 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 19
41729 CTTTTTTTTC
*
41739 TTGATTTTTTTCATATATTTTT
1 TTGATTTTTTT--TAT-TCTTT
41761 TTGACTTTTTTTTATTCTTT
1 TTGA-TTTTTTTTATTCTTT
41781 TTGATTTTTTTT
1 TTGATTTTTTTT
41793 CTTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 8 0.27
20 8 0.27
21 3 0.10
22 4 0.13
23 7 0.23
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.76
Consensus pattern (19 bp):
TTGATTTTTTTTATTCTTT
Found at i:41794 original size:16 final size:15
Alignment explanation
Indices: 41768--41806 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
41758 TTTTTGACTT
41768 TTTTTTATTCTTTTTGA
1 TTTTTT-TTCTTTTT-A
41785 TTTTTTTTCTTTTTA
1 TTTTTTTTCTTTTTA
41800 TTTTTTT
1 TTTTTTT
41807 GACCCCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
16 8 0.36
17 6 0.27
ACGTcount: A:0.08, C:0.05, G:0.03, T:0.85
Consensus pattern (15 bp):
TTTTTTTTCTTTTTA
Found at i:41806 original size:9 final size:9
Alignment explanation
Indices: 41720--41798 Score: 52
Period size: 9 Copynumber: 8.1 Consensus size: 9
41710 TTTCTGGACC
41720 TTTTATTTT
1 TTTTATTTT
41729 CTTTT-TTTT
1 -TTTTATTTT
* *
41738 CTTGATTTT
1 TTTTATTTT
41747 TTTCATATATTT
1 TTT--TAT-TTT
41759 TTTTGACTTTT
1 TTTT-A-TTTT
41770 TTTTATTCTT
1 TTTTATT-TT
*
41780 TTTGATTTT
1 TTTTATTTT
*
41789 TTTTCTTTT
1 TTTTATTTT
41798 T
1 T
41799 ATTTTTTTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
8 2 0.04
9 22 0.40
10 14 0.25
11 10 0.18
12 7 0.13
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (9 bp):
TTTTATTTT
Found at i:46375 original size:20 final size:19
Alignment explanation
Indices: 46328--46381 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
46318 ACATTATACT
* **
46328 TTGTATCGATACACGTTCA
1 TTGTATCGATACATGCACA
*
46347 TTATATCGATACATGCACAA
1 TTGTATCGATACATGCAC-A
46367 TTGTATCGATACATG
1 TTGTATCGATACATG
46382 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:51833 original size:42 final size:42
Alignment explanation
Indices: 51778--51896 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
51768 TTATTCTCTC
* *
51778 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
51820 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
51862 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
51897 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:51837 original size:12 final size:11
Alignment explanation
Indices: 51811--51886 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
51801 TCTATTATCT
*
51811 CTCCTGTCTCTC
1 CTCCTATCTC-C
51823 CTCCTATCATCC
1 CTCCTATC-TCC
51835 CTCCTATCT--
1 CTCCTATCTCC
*
51844 CTACTATCT--
1 CTCCTATCTCC
*
51853 CTCCTGTCTCTC
1 CTCCTATCTC-C
51865 CTCCTATCATCC
1 CTCCTATC-TCC
*
51877 CTCCTCTCTC
1 CTCCTATCTC
51887 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:51838 original size:24 final size:24
Alignment explanation
Indices: 51802--51887 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
51792 CCTCCTCTCT
* *
51802 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
51826 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
51847 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
51868 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
51888 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:51862 original size:18 final size:18
Alignment explanation
Indices: 51793--51863 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
51783 CCTGTCATCC
* *
51793 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
51811 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
51833 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
51853 CTCCTGTCTCT
1 CTCCTGTCTCT
51864 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:58858 original size:20 final size:19
Alignment explanation
Indices: 58812--58860 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
58802 CACATCTAGA
**
58812 TGTATCGATACATGTTCAT
1 TGTATCGATACATGCACAT
*
58831 TATATCGATACATGCACAAT
1 TGTATCGATACATGCAC-AT
58851 TGTATCGATA
1 TGTATCGATA
58861 TATGAAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGCACAT
Found at i:58918 original size:20 final size:20
Alignment explanation
Indices: 58893--58946 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
58883 CTACCACTGT
* *
58893 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGACAAA
*
58913 TTGTATCGATACATGATAAA
1 TTGTATCGATACATGACAAA
58933 TTGTATCGATACAT
1 TTGTATCGATACAT
58947 TGCTTCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:60803 original size:12 final size:12
Alignment explanation
Indices: 60774--60803 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
60764 GATTTTAGTG
60774 TTTTTTATTTTC
1 TTTTTTATTTTC
*
60786 TCTTTTATTTTC
1 TTTTTTATTTTC
60798 TTTTTT
1 TTTTTT
60804 TCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTATTTTC
Done.