Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1753
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: 212588
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
File 2 of 2
Found at i:174589 original size:13 final size:13
Alignment explanation
Indices: 174571--174600 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
174561 ATACATTGTT
*
174571 CATTGTATTGATA
1 CATTGTATCGATA
174584 CATTGTATCGATA
1 CATTGTATCGATA
174597 CATT
1 CATT
174601 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:174640 original size:62 final size:63
Alignment explanation
Indices: 174521--174649 Score: 208
Period size: 62 Copynumber: 2.1 Consensus size: 63
174511 ATAAATTGTT
* * *
174521 CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTGTTCATTGTATTGATA
1 CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTGTGCAATGTATCGATA
174584 CATTGTATCGATACATTCTGGG-TTTACCCAGATGTATCGATACATAT-TGCAATGTATCGATA
1 CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACAT-TGTGCAATGTATCGATA
174646 CATT
1 CATT
174650 CAGGCATTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
62 39 0.63
63 23 0.37
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (63 bp):
CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTGTGCAATGTATCGATA
Found at i:176445 original size:21 final size:21
Alignment explanation
Indices: 176421--176462 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
176411 ATCCATTTCT
* *
176421 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
176442 TCATCTTCATCATCATCTTGA
1 TCATCTTCATCAACATCTTGA
176463 ACGGTTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:177594 original size:34 final size:35
Alignment explanation
Indices: 177556--177622 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
177546 CCTTACAACA
177556 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
*
177590 CTATCTTTTTCAAAGGCTCAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
177623 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:178111 original size:13 final size:13
Alignment explanation
Indices: 178093--178130 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
178083 CTATTTATAG
*
178093 TGTATCGATACAC
1 TGTATCGATACAA
*
178106 TGTATCGATATAA
1 TGTATCGATACAA
178119 TGTATCGATACA
1 TGTATCGATACA
178131 TGAATAGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:178221 original size:13 final size:13
Alignment explanation
Indices: 178203--178260 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
178193 GCCAATGCTG
178203 TGTATCGATACAA
1 TGTATCGATACAA
178216 TGTATCGATAC--
1 TGTATCGATACAA
*
178227 TG-AGC-A-A-AA
1 TGTATCGATACAA
178236 TGTATCGATACAA
1 TGTATCGATACAA
178249 TGTATCGATACA
1 TGTATCGATACA
178261 TCTGAGTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.08
10 4 0.11
11 3 0.08
12 1 0.03
13 25 0.68
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:178272 original size:33 final size:33
Alignment explanation
Indices: 178203--178282 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
178193 GCCAATGCTG
*
178203 TGTATCGATACAATGTATCGATACTGAGCAAAA
1 TGTATCGATACAATGTATCGATACTCAGCAAAA
* **
178236 TGTATCGATACAATGTATCGATACATCTG-AGTA
1 TGTATCGATACAATGTATCGATAC-TCAGCAAAA
178269 TGTATCGATACAAT
1 TGTATCGATACAAT
178283 CAAGGGTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 40 0.95
34 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACTCAGCAAAA
Found at i:178360 original size:21 final size:21
Alignment explanation
Indices: 178320--178360 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
178310 GTCAACCTTG
*
178320 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
178341 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
178361 TTTTACTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:180527 original size:51 final size:51
Alignment explanation
Indices: 180469--180588 Score: 177
Period size: 51 Copynumber: 2.4 Consensus size: 51
180459 TTATTTCCAA
* *
180469 GGGGATACTCTAACCCCGGTTTTATTTCCAAAAAATCAATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATC
* * * * *
180520 GTGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATC
180571 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
180589 TTATTTCATC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATC
Found at i:180577 original size:130 final size:130
Alignment explanation
Indices: 180409--180662 Score: 341
Period size: 130 Copynumber: 2.0 Consensus size: 130
180399 TCATTCATGT
* *
180409 TTTTATTTCCAAAACACCAATTTTTTACAATCGAGGATACTCCAACCCTGTTATTTCCA-AGGGG
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATTT-CATAGGGG
* * **
180473 ATACTCTAACCCCGGTTTTATTTCCAAAAAATCAATTTTCCACAATCG-TGGATACTCCAACTCC
65 ATACTCCAACCCCAGCCTTATTTCCAAAAAATCAATTTTCCACAATCGAT-GATACTCCAACTCC
180537 GA
129 GA
* * * *
180539 TTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCATCGGGGA
1 TTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTCATAGGGGA
* ** * *
180604 TACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTTCACAATCGATGATACTCCAA
66 TACTCCAACCCCAGCCTTATTTCCAAAAAATCAATTTTCCACAATCGATGATACTCCAA
180663 ACCCGTTATT
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
129 2 0.02
130 104 0.97
131 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (130 bp):
TTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTCATAGGGGA
TACTCCAACCCCAGCCTTATTTCCAAAAAATCAATTTTCCACAATCGATGATACTCCAACTCCGA
Found at i:180605 original size:79 final size:78
Alignment explanation
Indices: 180522--180828 Score: 323
Period size: 79 Copynumber: 3.9 Consensus size: 78
180512 CCACAATCGT
* *
180522 GGATACTCCAACTCCGA-TTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACC
1 GGATACTCCAACTCCGAGTTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACC
180586 CCGTTATTTCATCGG
66 CCGTTATTT--TCGG
* ** * * ** *
180601 GGATACTCCAAC-CCCAGCCTTATTTCTAAAGCATCGATTTTTCACAATCGATGATACTCCAAAC
1 GGATACTCCAACTCCGAGTTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACC
180665 CCGTTATTTTCGAGG
66 CCGTTATTTTC--GG
* * * * *
180680 GGATACTCCAACTCTGA-TTTTATTTTTAAAATATCGATTTTTTATAATCAGGGATACTCCAACC
1 GGATACTCCAACTCCGAGTTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACC
*
180744 CTGTTATTTTCGAG
66 CCGTTATTTTCG-G
* * * * * * * *
180758 GAAATACTCCAACCCCGATTTTTATTTCTAGAACACCGATTTTTCGTAATCGGGGATACTTCAGC
1 G-GATACTCCAACTCCGAGTTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAAC
180823 CCCGTT
65 CCCGTT
180829 GTTATCTCCA
Statistics
Matches: 184, Mismatches: 37, Indels: 13
0.79 0.16 0.06
Matches are distributed among these distances:
77 3 0.02
78 5 0.03
79 132 0.72
80 44 0.24
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (78 bp):
GGATACTCCAACTCCGAGTTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTTCGG
Found at i:193200 original size:16 final size:16
Alignment explanation
Indices: 193161--193213 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
193151 TTCTTTTTTT
*
193161 AAAAAAACAAAAAAAAC
1 AAAAAAA-AAAAAAAAG
* *
193178 AATAAAAATAAAAAAG
1 AAAAAAAAAAAAAAAG
* *
193194 AAAAAAAAGAGAAAAG
1 AAAAAAAAAAAAAAAG
193210 AAAA
1 AAAA
193214 GAACTTGCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 24 0.80
17 6 0.20
ACGTcount: A:0.85, C:0.04, G:0.08, T:0.04
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:194329 original size:55 final size:55
Alignment explanation
Indices: 194269--194457 Score: 263
Period size: 55 Copynumber: 3.3 Consensus size: 55
194259 TTCACCTTTT
* * **
194269 AGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAATTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
*
194324 AGTCCTCAAAGAGCAGGACGCCGTTT-AAAGCCCACACAAGTTTGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
194379 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCACTTCCC
194440 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
194458 TGCTCTCTCC
Statistics
Matches: 120, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
54 2 0.02
55 69 0.57
56 3 0.03
61 46 0.38
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
Found at i:194442 original size:61 final size:60
Alignment explanation
Indices: 194289--194470 Score: 248
Period size: 61 Copynumber: 3.1 Consensus size: 60
194279 GAGCAAGACG
* * **
194289 CCTTTCAAAGCCCACACAAATTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG-----
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTTCT
* *
194344 CCGTTTAAAGCCCACACAAGTTTGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACG-CTTCT
*
194405 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGATGCTCTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCT-TCT
194466 CCTTT
1 CCTTT
194471 CGCCCTTTAG
Statistics
Matches: 111, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
55 49 0.44
60 2 0.02
61 60 0.54
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (60 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTTCT
Found at i:194593 original size:27 final size:27
Alignment explanation
Indices: 194563--194648 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
194553 CGCCTTTTCC
194563 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
** * * * ** *
194590 TTTTCTAGTCCTCAAAGAGCAGGAT-GCC
1 TTTTAAAGCCCACACA-AGTTGG-TGGCA
*
194618 TTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
194645 TTTT
1 TTTT
194649 CCAGTCCTCA
Statistics
Matches: 38, Mismatches: 18, Indels: 6
0.61 0.29 0.10
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 16 0.42
29 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (27 bp):
TTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:194607 original size:156 final size:155
Alignment explanation
Indices: 194324--194616 Score: 460
Period size: 156 Copynumber: 1.9 Consensus size: 155
194314 GGCACTTTTC
* *
194324 AGTCCTCAAAGAGCAGGACGCCGTTTAAAGCCCACACAAGTTTGTGGCACTTCCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCGTTTAAAGCCCACACAAGTTGGTGGCACTTCCCACTCCTCAAA
194389 GAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGC
66 GAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGC
194454 AGGATGCTCTCTCCTTTCGCCCTTT
131 AGGATGCTCTCTCCTTTCGCCCTTT
* * * * * *
194479 AGTCCTCAAAGAGCAGGATGTCTTTTATAGCCCACACAAGTTGGTGGCACTTTTCTACTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCGTTTAAAGCCCACACAAGTTGGTGGCAC-TTCCCACTCCTCAA
* * * * *
194544 AGAGCATGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAG
65 AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAG
194609 CAGGATGC
130 CAGGATGC
194617 CTTTCAAAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
155 45 0.36
156 79 0.64
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (155 bp):
AGTCCTCAAAGAGCAGGACGCCGTTTAAAGCCCACACAAGTTGGTGGCACTTCCCACTCCTCAAA
GAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGC
AGGATGCTCTCTCCTTTCGCCCTTT
Found at i:194664 original size:211 final size:207
Alignment explanation
Indices: 194224--194681 Score: 589
Period size: 210 Copynumber: 2.2 Consensus size: 207
194214 CTTTTAAAGC
* * ** * *
194224 CTTTCTAGTCCTCAAAGAGTAGGACACTCGCTCCTTTCACCTTTTAGTCCTCAAAGAGCAAGACG
1 CTTTCCAGTCCTCAAAGAGCAGGATGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACG
*
194289 CCTTTCAAAGCCCACACAAATTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCGTTTAAAG
66 CCTTTCAAAGCCCACACAAATTGGTGGCACTTTTCACTCCTCAAAGAGCAGGACGCCGTTTAAAG
*
194354 CCCACACAAGTTTGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCA
131 CCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCC---TAAAGCCCA
194419 CACAAGTTGGTGGCA
193 CACAAGTTGGTGGCA
* * * *
194434 CTTCCCAGTCCTCAAAGAGCAGGATGCTCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGATG
1 CTTTCCAGTCCTCAAAGAGCAGGATGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACG
* * * * * *
194499 TCTTTTATAGCCCACACAAGTTGGTGGCACTTTTCTACTCCTCAAAGAGCATGACGCCTTTTCCT
66 CCTTTCAAAGCCCACACAAATTGGTGGCACTTTTC-ACTCCTCAAAGAGCAGGACG------CCG
* * * *
194564 TTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCCTT-T-C-AAAG
124 TTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTAAAG
194626 CCCACACAAGTTGGTGGCA
189 CCCACACAAGTTGGTGGCA
* *
194645 TTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCTTT
1 CTTTCCAGTCCTCAAAGAGCAGGATGCTCTCTCCTTT
194682 TAAAGACCAC
Statistics
Matches: 216, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
210 86 0.40
211 75 0.35
215 1 0.00
216 1 0.00
217 53 0.25
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (207 bp):
CTTTCCAGTCCTCAAAGAGCAGGATGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACG
CCTTTCAAAGCCCACACAAATTGGTGGCACTTTTCACTCCTCAAAGAGCAGGACGCCGTTTAAAG
CCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTAAAGCCCACAC
AAGTTGGTGGCA
Found at i:194718 original size:61 final size:60
Alignment explanation
Indices: 194479--194865 Score: 420
Period size: 61 Copynumber: 6.5 Consensus size: 60
194469 TTCGCCCTTT
* *
194479 AGTCCTCAAAGAGCAGGATG----T-CTTTTATAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGATGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCC
* * * * *
194535 ACTCCTCAAAGAGCATGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGATG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
* *
194596 AGTCCTCAAAGAGCAGGATG-----CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGATGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
* * * * *
194651 AGTCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAGACCACTCGAGTTAGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGATGCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
* * *
194712 AATCCTCAAAGAGCAGGATGC-TTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGATGCTTTTC-CTTT-TAAAGCCCACACAAGTTGGTGGCACTTTCC
* * **
194773 AGTCCTCAAAGAGCAGGACGCCTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGATG-CTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCC
*
194834 AGTCCTCAAAGAGCAGGACTCCTTTTCCTTTT
1 AGTCCTCAAAGAGCAGGA-TGCTTTTCCTTTT
194866 CTCCTTTGTC
Statistics
Matches: 280, Mismatches: 32, Indels: 32
0.81 0.09 0.09
Matches are distributed among these distances:
55 53 0.19
56 17 0.06
59 2 0.01
60 6 0.02
61 166 0.59
62 33 0.12
63 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGATGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:194781 original size:122 final size:118
Alignment explanation
Indices: 194478--194851 Score: 499
Period size: 122 Copynumber: 3.2 Consensus size: 118
194468 TTTCGCCCTT
* * *
194478 TAGTCCTCAAAGAGCAGGATGTCT-TTT-ATAGCCCACACAAGTTGGTGGCACTTTTCTACTCCT
1 TAGTCCTCAAAGAGCAGGATGTCTCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCCAGTCCT
* * *
194541 CAAAGAGCATGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTC
65 CAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACTTTC
*
194595 TAGTCCTCAAAGAGCAGGATG-C-CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1 TAGTCCTCAAAGAGCAGGATGTCTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTC
* * * * *
194658 AAAGAGCAGGATG-CTTTCTCCTTTTAAAGACCACTCGAGTTAGTGGCACCTTC
66 AAAGAGCAGGACGCCTTT-TCCTTTTAAAGCCCACACGAGTTGGTGGCACTTTC
* * *
194711 CAATCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGT
1 TAGTCCTCAAAGAGCAGGATG---TCTCTTT-CAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
*
194776 CCTCAAAGAGCAGGACGCCTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
62 CCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACGAGTTGGTGGCACTTTC
194833 TAGTCCTCAAAGAGCAGGA
1 TAGTCCTCAAAGAGCAGGA
194852 CTCCTTTTCC
Statistics
Matches: 222, Mismatches: 24, Indels: 17
0.84 0.09 0.06
Matches are distributed among these distances:
115 4 0.02
116 73 0.33
117 43 0.19
120 1 0.00
121 9 0.04
122 88 0.40
123 4 0.02
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (118 bp):
TAGTCCTCAAAGAGCAGGATGTCTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTC
AAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACTTTC
Found at i:194932 original size:45 final size:43
Alignment explanation
Indices: 194857--195130 Score: 161
Period size: 42 Copynumber: 6.7 Consensus size: 43
194847 CAGGACTCCT
* *
194857 TTTCCTT-TTCTCCTTTGTCCTCAAAGAGCAGGACACACTTCA
1 TTTCCTTCTTTTCCTTTGTCCTCAAAAAGCAGGACACACTTCA
* * * **
194899 TTCCCTTCTTTTCCCTTTTGTCCACAAAAAGCAGGACGCACTATGT
1 TTTCCTTCTTTT-CC-TTTGTCCTCAAAAAGCAGGACACACT-TCA
* * * *
194945 TTTCC-TC-TTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCA
1 TTTCCTTCTTTTCCTTTGTCCTCAAAAAGCAGGACACACTTCA
* *
194986 TTTTCCTT-TTTTCCTTTGTCCTCGAAAAGCAGGACATAC-TC-
1 -TTTCCTTCTTTTCCTTTGTCCTCAAAAAGCAGGACACACTTCA
* * * * * *
195027 TTT--TTC----ACTTTGTCCTTAAGATGCAGGACAC-TTTCC
1 TTTCCTTCTTTTCCTTTGTCCTCAAAAAGCAGGACACACTTCA
* ** * *
195063 TTTTCTT-TTTTCCTTTGTCCTCAAGGAGCAGGATC-TATTTCA
1 TTTCCTTCTTTTCCTTTGTCCTCAAAAAGCAGGA-CACACTTCA
195105 -TT-C-TCTTTTCCTTTGTCCTCAAAAAG
1 TTTCCTTCTTTTCCTTTGTCCTCAAAAAG
195131 TGGGGCACCC
Statistics
Matches: 178, Mismatches: 35, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
35 21 0.12
36 3 0.02
38 4 0.02
39 1 0.01
40 23 0.13
41 21 0.12
42 41 0.23
43 29 0.16
44 5 0.03
45 25 0.14
46 5 0.03
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.41
Consensus pattern (43 bp):
TTTCCTTCTTTTCCTTTGTCCTCAAAAAGCAGGACACACTTCA
Found at i:194972 original size:87 final size:85
Alignment explanation
Indices: 194856--195020 Score: 226
Period size: 87 Copynumber: 1.9 Consensus size: 85
194846 GCAGGACTCC
194856 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACTTCA-TTCCCTTCTTTTCCCTTTTGT
1 TTTTCCTTTTCT-CTTTGTCCTCAAAGAGCAGGACACACTTCATTTCCCTT-TTTT-CC-TTTGT
194920 CCACAAAAAGCAGGACGCACTATG
62 CCACAAAAAGCAGGACGCACTATG
* * * *
194944 TTTTCCTCTTTCT-TTTGTCCTCAAAGAGCAGGACGCATTTCATTTTCCTTTTTTCCTTTGTCCT
1 TTTTCCT-TTTCTCTTTGTCCTCAAAGAGCAGGACACACTTCATTTCCCTTTTTTCCTTTGTCCA
*
195008 CGAAAAGCAGGAC
65 CAAAAAGCAGGAC
195021 ATACTCTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
85 19 0.27
86 2 0.03
87 31 0.44
88 13 0.19
89 5 0.07
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.38
Consensus pattern (85 bp):
TTTTCCTTTTCTCTTTGTCCTCAAAGAGCAGGACACACTTCATTTCCCTTTTTTCCTTTGTCCAC
AAAAAGCAGGACGCACTATG
Found at i:195032 original size:42 final size:42
Alignment explanation
Indices: 194835--195037 Score: 159
Period size: 42 Copynumber: 4.8 Consensus size: 42
194825 GCACTTTTTA
* *
194835 GTCCTCAAAGAGCAGG----ACTCCTTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACACACTCTTTTTCCTTTTTTCCTTT
* *
194873 GTCCTCAAAGAGCAGGACACACT-TCATTCCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACACACTCT-TTTTCCTT-TTTT-CC-TTT
* * * * * *
194918 GTCCACAAAAAGCAGGACGCACTATGTTTTCC-TCTTTCTTTT
1 GTCCTCAAAGAGCAGGACACACTCT-TTTTCCTTTTTTCCTTT
* * *
194960 GTCCTCAAAGAGCAGGACGCATTTCATTTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACA-CTCTTTTTCCTTTTTTCCTTT
*
195003 GTCCTCGAAA-AGCAGGACATACTCTTTTTCACTTT
1 GTCCTC-AAAGAGCAGGACACACTCTTTTTC-CTTT
195038 GTCCTTAAGA
Statistics
Matches: 129, Mismatches: 23, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
38 16 0.12
42 44 0.34
43 32 0.25
44 8 0.06
45 24 0.19
46 5 0.04
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACACACTCTTTTTCCTTTTTTCCTTT
Found at i:195094 original size:41 final size:40
Alignment explanation
Indices: 195027--195126 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 40
195017 GGACATACTC
* *
195027 TTTTTCACTTTGTCCTTAAGATGCAGGA-C-ACTTTCCTTTTCT
1 TTTTTC-CTTTGTCCTCAAGATGCAGGATCTA-TTT-C-ATTCT
195069 TTTTTCCTTTGTCCTCAAGGA-GCAGGATCTATTTCATTCT
1 TTTTTCCTTTGTCCTCAA-GATGCAGGATCTATTTCATTCT
*
195109 CTTTTCCTTTGTCCTCAA
1 TTTTTCCTTTGTCCTCAA
195127 AAAGTGGGGC
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
40 21 0.40
41 18 0.35
42 12 0.23
43 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.12, T:0.47
Consensus pattern (40 bp):
TTTTTCCTTTGTCCTCAAGATGCAGGATCTATTTCATTCT
Found at i:195791 original size:13 final size:13
Alignment explanation
Indices: 195773--195802 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
195763 ATACATTGTT
195773 CATTGTATCGATA
1 CATTGTATCGATA
195786 CATTGTATCGATA
1 CATTGTATCGATA
195799 CATT
1 CATT
195803 CTAGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:195842 original size:62 final size:63
Alignment explanation
Indices: 195724--195851 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 63
195714 TACATTATTT
*
195724 ATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTGTTCATTGTATCGATAC
1 ATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTGTTCAATGTATCGATAC
*
195787 ATTGTATCGATACATTCTAGG-TTTACCTAGATGTATCGATACACTT-TTCAATGTATCGATAC
1 ATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACA-TTGTTCAATGTATCGATAC
195849 ATT
1 ATT
195852 CAGGCATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
62 39 0.63
63 23 0.37
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (63 bp):
ATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATACATTGTTCAATGTATCGATAC
Found at i:198334 original size:51 final size:51
Alignment explanation
Indices: 198260--198379 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
198250 TTATTTCCAA
* * *
198260 GGGGATACTCTAACCCCGGTTTTATTTTCAAAAAATCAATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATC
* * * * *
198311 GTGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATC
198362 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
198380 CTATTTCATC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATCAATTTTCCACAATC
Found at i:198395 original size:28 final size:27
Alignment explanation
Indices: 198359--198435 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 27
198349 ATTTTTCATA
198359 ATCGGGGATACTCCAACCCCGCTATTT
1 ATCGGGGATACTCCAACCCCGCTATTT
* *
198386 CATCGGGGATACTCCAACTCCGTTATTT
1 -ATCGGGGATACTCCAACCCCGCTATTT
* *
198414 TTGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
198436 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGCTATTT
Found at i:198552 original size:79 final size:78
Alignment explanation
Indices: 198469--198698 Score: 266
Period size: 79 Copynumber: 2.9 Consensus size: 78
198459 TCTCACAATT
* ** *
198469 GGAGATACTCTAACCCCAGCCTTATTTCTAAAGCATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGAGATACTCCAACCCCAGTTTTATTTCTAAA-CATCGATTTTTCATAATCGGGGATACTCCAAC
198534 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * *
198548 GGAGATACTCCAACCCC-GATTTTATTTTCAAAATATCGA-TTTTCTATAATCAGGGATACTCCA
1 GGAGATACTCCAACCCCAG-TTTTA-TTTCTAAACATCGATTTTTC-ATAATCGGGGATACTCCA
*
198611 ACCCTGTTATTTTCGA
63 ACCCCGTTATTTTCGA
* * * * * *
198627 GGGGATACTCCAACCCTGATTTTTATTTCTAGAACACCGATTTTTCATAATCGAGGATACTCCAG
1 GGAGATACTCCAACCC-CAGTTTTATTTCTA-AACATCGATTTTTCATAATCGGGGATACTCCAA
198692 CCCCGTT
64 CCCCGTT
198699 GTTATCTCCA
Statistics
Matches: 126, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
78 6 0.05
79 75 0.60
80 40 0.32
81 5 0.04
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (78 bp):
GGAGATACTCCAACCCCAGTTTTATTTCTAAACATCGATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:201807 original size:52 final size:52
Alignment explanation
Indices: 201729--201845 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
201719 TTCTGTAGCT
* *
201729 ATGTATCGATACATGCATTTGAAATTATAGTCGTTTATAGCCGTTTGAAGCA
1 ATGTATCGATACATGCATTTGAAATTATAGTCATTTATAGCCGTTCGAAGCA
*
201781 ATGTATCAATACATGCATTTGAAATTATAGTCATTTATAGCCGTTCGAAGCA
1 ATGTATCGATACATGCATTTGAAATTATAGTCATTTATAGCCGTTCGAAGCA
201833 ATGTATCGATACA
1 ATGTATCGATACA
201846 ATTCATCATG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (52 bp):
ATGTATCGATACATGCATTTGAAATTATAGTCATTTATAGCCGTTCGAAGCA
Found at i:201847 original size:13 final size:13
Alignment explanation
Indices: 201831--201882 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
201821 CCGTTCGAAG
201831 CAATGTATCGATA
1 CAATGTATCGATA
201844 CAA--T-TC-AT-
1 CAATGTATCGATA
201852 C-ATGTATCGATA
1 CAATGTATCGATA
*
201864 CATTGTATCGATA
1 CAATGTATCGATA
201877 CAATGT
1 CAATGT
201883 GCCATGTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.10
10 4 0.13
11 3 0.10
12 1 0.03
13 18 0.58
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:201876 original size:33 final size:33
Alignment explanation
Indices: 201834--201898 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
201824 TTCGAAGCAA
201834 TGTATCGATACAAT-T-CATCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
201867 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
201899 AACAATGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:201972 original size:19 final size:19
Alignment explanation
Indices: 201929--201983 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
201919 TGTCAATTTT
**
201929 ATGTATCGATACAATTGTGC
1 ATGTATCGATACAA-TGAAC
201949 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
201968 ATGTATCGATACAATG
1 ATGTATCGATACAATG
201984 TATGGATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:202614 original size:31 final size:29
Alignment explanation
Indices: 202567--202626 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 29
202557 ATAAAGGCTC
202567 TCGTTTAAAAAATTTCTCCCCCTTGATAA
1 TCGTTTAAAAAATTTCTCCCCCTTGATAA
202596 TCGTTTAAAAAAATTTTCTCCCCCTTGATAA
1 TCGTTT-AAAAAA-TTTCTCCCCCTTGATAA
202627 AAATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.21
30 6 0.21
31 17 0.59
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (29 bp):
TCGTTTAAAAAATTTCTCCCCCTTGATAA
Found at i:204315 original size:19 final size:21
Alignment explanation
Indices: 204291--204338 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
204281 TTTATTGATA
204291 ATTTTG-A-TGAAAATGAAGT
1 ATTTTGAAGTGAAAATGAAGT
*
204310 ATTTTGAAGTGAAAATGAAGA
1 ATTTTGAAGTGAAAATGAAGT
*
204331 AATTTGAA
1 ATTTTGAA
204339 AAAGATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 18 0.72
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (21 bp):
ATTTTGAAGTGAAAATGAAGT
Found at i:210656 original size:20 final size:19
Alignment explanation
Indices: 210631--210703 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
210621 ACTACCATTT
**
210631 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
210651 CATGTATCGATGCAATGAA
1 CATGTATCGATACAATGAA
*
210670 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
210691 -ATGTATCGATACA
1 CATGTATCGATACA
210704 TTTGGGTGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:210675 original size:19 final size:20
Alignment explanation
Indices: 210631--210684 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
210621 ACTACCATTT
**
210631 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
*
210651 CATGTATCGATGCAA-TGAA
1 CATGTATCGATACAATTGAA
210670 CATGTATCGATACAA
1 CATGTATCGATACAA
210685 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Done.