Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2453
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: 23326
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:171 original size:42 final size:42
Alignment explanation
Indices: 35--171 Score: 125
Period size: 44 Copynumber: 3.2 Consensus size: 42
25 GAAGCAGATC
35 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGAT-GAGCTGGTT
* * * ** * * * *
78 GAAGACAAAAGATCTTG-C-CTTTCTGCATTGACAGCGAAGCAGATC
1 GAAGACACAA-ACCTTGCCTCTTTC-G-GTTGTGA-TG-AGCTGGTT
123 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGAGCTGGTT
165 GAAGACA
1 GAAGACA
172 AAAGATCTTG
Statistics
Matches: 69, Mismatches: 18, Indels: 15
0.68 0.18 0.15
Matches are distributed among these distances:
42 17 0.25
43 12 0.17
44 19 0.28
45 16 0.23
46 5 0.07
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (42 bp):
GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGAGCTGGTT
Found at i:280 original size:86 final size:88
Alignment explanation
Indices: 1--295 Score: 402
Period size: 87 Copynumber: 3.4 Consensus size: 88
*
1 ATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTG
1 ATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTG
66 ATGGAGCTGGTTGAAGACAAAAG
66 ATGGAGCTGGTTGAAGACAAAAG
* * *
89 ATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTG
1 ATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTG
154 AT-GAGCTGGTTGAAGACAAAAG
66 ATGGAGCTGGTTGAAGACAAAAG
* ** *
176 ATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCATCCATCGATTG-
1 ATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGGTTGT
* * * **
238 CAGTGGAGCTAGTTAAAGA-AGCAG
65 GA-TGGAGCTGGTTGAAGACAAAAG
* *
262 ATCTTGCCTTCCTGCATTAACAGCAAAGCAGATC
1 ATCTTGCCTTCCTACATTAACAGCGAAGCAGATC
296 AAAAAAAAAA
Statistics
Matches: 188, Mismatches: 16, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
85 6 0.03
86 51 0.27
87 66 0.35
88 65 0.35
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (88 bp):
ATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTG
ATGGAGCTGGTTGAAGACAAAAG
Found at i:517 original size:44 final size:44
Alignment explanation
Indices: 482--637 Score: 165
Period size: 44 Copynumber: 3.6 Consensus size: 44
472 TTAGAATTTC
*
482 GGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GAAGCCA
1 GGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAGAAGACA
* * *
525 GAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCGAAGACA
1 G-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAGAAGACA
** * * * * *
569 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTCA-AATAAA
1 GGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-AGAAGACA
*
613 GGATCTTATCTCTCTGAGGTTACAG
1 GGATCTTATCTCCCTGAGGTTACAG
638 CAGAGTGGAT
Statistics
Matches: 91, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
43 29 0.32
44 62 0.68
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (44 bp):
GGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAGAAGACA
Found at i:706 original size:43 final size:43
Alignment explanation
Indices: 657--813 Score: 212
Period size: 43 Copynumber: 3.7 Consensus size: 43
647 TCACATCAAG
**
657 TCTTATCTCCCTAAATAGTAGTGGAGCAGATGAAAGAAACCGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGAAACCGA
* * **
700 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAA--G-
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGAAACCGA
* *
740 TCTTATCTCCCTAAGCAGTAGTGAAGCAGACGAAAGAAACCGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGAAACCGA
*
783 TCTTATCTCCCTAAGTAGTAGTGGAGCAGAT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
814 CACATCAAGT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 33 0.34
41 1 0.01
42 1 0.01
43 61 0.64
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (43 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGAAACCGA
Found at i:755 original size:40 final size:40
Alignment explanation
Indices: 645--852 Score: 211
Period size: 40 Copynumber: 5.0 Consensus size: 40
635 CAGCAGAGTG
**
645 GATCACATCAAGTCTTATCTCCCTAAATAGTAGTGGAGCA
1 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
* * **
685 GATGAAAGAAACCGATCTTATCTCCCTAAGCAGTAGTGGAGCA
1 GATCACATCAA--G-TCTTATCTCCCTAAGCAGTAGTGGAGCA
*
728 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGAAGCA
1 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
* ** *
768 GA-CGAAAGAAACCGATCTTATCTCCCTAAGTAGTAGTGGAGCA
1 GATC-ACATCAA--G-TCTTATCTCCCTAAGCAGTAGTGGAGCA
* * * *
811 GATCACATCAAGTCTCATCTCTCTAAGCAATAGCGGAGCA
1 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
851 GA
1 GA
853 CAAAAGAAAC
Statistics
Matches: 136, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
39 1 0.01
40 65 0.48
41 2 0.01
42 2 0.01
43 65 0.48
44 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (40 bp):
GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
Found at i:873 original size:83 final size:83
Alignment explanation
Indices: 645--896 Score: 351
Period size: 83 Copynumber: 3.0 Consensus size: 83
635 CAGCAGAGTG
** *
645 GATCACATCAAGTCTTATCTCCCTAAATAGTAGTGGAGCAGATGAAAGAAACCGATCTTATCTCC
1 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCC
*
710 CTAAGCAGTAGTGGAGCA
66 CTAAGTAGTAGTGGAGCA
*
728 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGAAGCAGACGAAAGAAACCGATCTTATCTCC
1 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCC
793 CTAAGTAGTAGTGGAGCA
66 CTAAGTAGTAGTGGAGCA
* * * * * ** * *
811 GATCACATCAAGTCTCATCTCTCTAAGCAATAGCGGAGCAGACAAAAGAAACTAATCCTATCTCT
1 GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCC
* *
876 CTGAAGTTGCAGTGGAGCA
66 CT-AAGTAGTAGTGGAGCA
895 GA
1 GA
897 CTAAAACCAC
Statistics
Matches: 151, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 135 0.89
84 16 0.11
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (83 bp):
GATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCC
CTAAGTAGTAGTGGAGCA
Found at i:2288 original size:3 final size:3
Alignment explanation
Indices: 2277--2364 Score: 72
Period size: 3 Copynumber: 29.3 Consensus size: 3
2267 ATTATTTTGT
* *
2277 TTA TT- TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TCT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA
* * * * * *
2322 TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA CTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2365 ATTTATACCT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 3 0.04
3 60 0.90
4 4 0.06
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2297 original size:12 final size:12
Alignment explanation
Indices: 2282--2364 Score: 85
Period size: 12 Copynumber: 6.6 Consensus size: 12
2272 TTTGTTTATT
*
2282 TTATTATTATTA
1 TTATTATTACTA
2294 TTATTATTTACTA
1 TTATTA-TTACTA
2307 TTATTATCTTTACTA
1 TTATTA---TTACTA
* *
2322 TTATTGTTAGTA
1 TTATTATTACTA
*
2334 TTATTACTACTA
1 TTATTATTACTA
2346 TTATTATTACTA
1 TTATTATTACTA
*
2358 TCATTAT
1 TTATTAT
2365 ATTTATACCT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
12 37 0.62
13 11 0.18
15 12 0.20
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTATTACTA
Found at i:5215 original size:15 final size:17
Alignment explanation
Indices: 5194--5233 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
5184 ATAGAAATAA
5194 AAATATAATAA-A-TAG
1 AAATATAATAATAGTAG
*
5209 AATTATAATAATAGTAG
1 AAATATAATAATAGTAG
5226 AAATATAA
1 AAATATAA
5234 ATAGATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 10 0.48
16 1 0.05
17 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (17 bp):
AAATATAATAATAGTAG
Found at i:5232 original size:17 final size:15
Alignment explanation
Indices: 5188--5233 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
5178 ATATAAATAG
*
5188 AAATAAAAATATAAT
1 AAATAGAAATATAAT
*
5203 AAATAGAATTATAAT
1 AAATAGAAATATAAT
5218 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
5234 ATAGATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 15 0.58
16 1 0.04
17 10 0.38
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:5253 original size:15 final size:14
Alignment explanation
Indices: 5226--5266 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
5216 ATAATAGTAG
*
5226 AAATATAAATAGAT
1 AAATAAAAATAGAT
5240 AAATAAAAATTAGAT
1 AAATAAAAA-TAGAT
*
5255 AAATAATAATAG
1 AAATAAAAATAG
5267 TATTAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (14 bp):
AAATAAAAATAGAT
Found at i:6319 original size:44 final size:43
Alignment explanation
Indices: 6266--6611 Score: 161
Period size: 44 Copynumber: 7.9 Consensus size: 43
6256 TAAAATCTGG
* *
6266 TAATCTTCAGTCTGCTCCACTATTACTTAGGGAGATAAGATCTA
1 TAATCTTCAGTCTGTTCC-CTATTGCTTAGGGAGATAAGATCTA
* * * *
6310 TAATTTTCAGCCTATTTCCCTATTGCTTAGGG-GATAAG-GCTCA
1 TAATCTTCAGTCT-GTTCCCTATTGCTTAGGGAGATAAGATCT-A
** *
6353 CCATCTTC-GATCTGTTCCCCTATTGCTTAGGGAGATAAGATCTG
1 TAATCTTCAG-TCTGTT-CCCTATTGCTTAGGGAGATAAGATCTA
* * * * *
6397 TAATTTTC-GGCTTGTTTCCCTACTGCTTAGGGGGATAAG-GCTCA
1 TAATCTTCAGTC-TG-TTCCCTATTGCTTAGGGAGATAAGATCT-A
* * * * *
6441 CT-ATCTTCAATCTGCTCCGCTACTACTTAGGGAGATAAGATCTT
1 -TAATCTTCAGTCTGTTCC-CTATTGCTTAGGGAGATAAGATCTA
* ** * * * *
6485 TAATTTTTGGCCTGTTTCCCTACTGCTTAGGGGGATAAG-GCTCA
1 TAATCTTCAGTCTG-TTCCCTATTGCTTAGGGAGATAAGATCT-A
* * * *
6529 CT-GTCTTC-GATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTG
1 -TAATCTTCAG-TCTGTTCC-CTATTGCTTAGGGAGATAAGATCTA
* * * * * *
6573 TAATTTTTAGCCTGTTTACCTACTGCTTAGGGGGATAAG
1 TAATCTTCAGTCTG-TTCCCTATTGCTTAGGGAGATAAG
6612 GCTCACCGTC
Statistics
Matches: 225, Mismatches: 54, Indels: 46
0.69 0.17 0.14
Matches are distributed among these distances:
42 5 0.02
43 43 0.19
44 157 0.70
45 20 0.09
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (43 bp):
TAATCTTCAGTCTGTTCCCTATTGCTTAGGGAGATAAGATCTA
Found at i:6482 original size:88 final size:88
Alignment explanation
Indices: 6268--6967 Score: 893
Period size: 88 Copynumber: 8.0 Consensus size: 88
6258 AAATCTGGTA
* * * *
6268 ATCTTC-AGTCTGCTCCACTATTACTTAGGGAGATAAGATCTATAATTTTCAGCCTATTTCCCTA
1 ATCTTCGA-TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTA
*
6332 TTGCTTA-GGGGATAAGGCTCACC
65 CTGCTTAGGGGGATAAGGCTCACC
* * * * *
6355 ATCTTCGATCTGTTCCCCTATTGCTTAGGGAGATAAGATCTGTAATTTTCGGCTTGTTTCCCTAC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTAC
*
6420 TGCTTAGGGGGATAAGGCTCACT
66 TGCTTAGGGGGATAAGGCTCACC
* * * * **
6443 ATCTTCAATCTGCTCCGCTACTACTTAGGGAGATAAGATCTTTAATTTTTGGCCTGTTTCCCTAC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTAC
*
6508 TGCTTAGGGGGATAAGGCTCACT
66 TGCTTAGGGGGATAAGGCTCACC
* * * *
6531 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTTACCTAC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTAC
6596 TGCTTAGGGGGATAAGGCTCACC
66 TGCTTAGGGGGATAAGGCTCACC
* * * * *
6619 GTCTTTGATCTGCTCCACTACTGTTTAGGGAGATAAGATTTGTAATTTTCAGCCTGTTACCCTAC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTAC
* * *
6684 AGCTTAAGGGGTTAAGGCTCACC
66 TGCTTAGGGGGATAAGGCTCACC
*
6707 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTAT-CCTA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTT-TCCCTA
** * * *
6771 CAACTTAGGGGGTTAAGGTTCACT
65 CTGCTTAGGGGGATAAGGCTCACC
* * *
6795 GTCTTCGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTAC
* * *
6860 TGCTTATGGGGTTAAAGCTCACC
66 TGCTTAGGGGGATAAGGCTCACC
* * ** * * * *
6883 GTTTTTTATCTGCTCCACTACTGCTTAGGGAGATAAGATCAGTAATTTTCAGCTTGTTACTCTAC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTAC
* *
6948 TGCTTAAGGGGTTAAGGCTC
66 TGCTTAGGGGGATAAGGCTC
6968 GTATCTTCAA
Statistics
Matches: 546, Mismatches: 63, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
87 61 0.11
88 485 0.89
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (88 bp):
ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTAC
TGCTTAGGGGGATAAGGCTCACC
Found at i:6640 original size:44 final size:44
Alignment explanation
Indices: 6333--6743 Score: 175
Period size: 44 Copynumber: 9.4 Consensus size: 44
6323 ATTTCCCTAT
* * * * *
6333 TGCTTAGGG-GATAAGGCTCACCATCTTCGATCTGTTCCCCTAT
1 TGCTTAGGGAGATAAGGCTCACTATCTTTGATCTGCTCCACTAC
* ** * *
6376 TGCTTAGGGAGATAA-GATCTGTAAT-TTTCG-GCTTGTTTCC-CTAC
1 TGCTTAGGGAGATAAGGCTCACT-ATCTTT-GATC-TG-CTCCACTAC
* ** *
6420 TGCTTAGGGGGATAAGGCTCACTATCTTCAATCTGCTCCGCTAC
1 TGCTTAGGGAGATAAGGCTCACTATCTTTGATCTGCTCCACTAC
* * ** * ** *
6464 TACTTAGGGAGATAA-GATCTTTAATTTTTGGCCTGTTTCC-CTAC
1 TGCTTAGGGAGATAAGGCTCACT-ATCTTTGATCTG-CTCCACTAC
* * * *
6508 TGCTTAGGGGGATAAGGCTCACTGTCTTCGATCTGCTCCGCTAC
1 TGCTTAGGGAGATAAGGCTCACTATCTTTGATCTGCTCCACTAC
* ** * * **
6552 TGCTTAGGGAGATAA-GATCTGTAAT-TTTTAGCCTG-TTTACCTAC
1 TGCTTAGGGAGATAAGGCTCACT-ATCTTTGA-TCTGCTCCA-CTAC
* **
6596 TGCTTAGGGGGATAAGGCTCACCGTCTTTGATCTGCTCCACTAC
1 TGCTTAGGGAGATAAGGCTCACTATCTTTGATCTGCTCCACTAC
* * *** * * *
6640 TGTTTAGGGAGATAA-GATTTGTAAT-TTTCAGCCTGTTACC-CTAC
1 TGCTTAGGGAGATAAGGCTCACT-ATCTTTGA-TCTGCT-CCACTAC
* * * *
6684 AGCTTAAGGG-GTTAAGGCTCACCATCTTCGATCTGCTCCACTAC
1 TGCTT-AGGGAGATAAGGCTCACTATCTTTGATCTGCTCCACTAC
6728 TGCTTAGGGAGATAAG
1 TGCTTAGGGAGATAAG
6744 ATCTGTAATT
Statistics
Matches: 258, Mismatches: 83, Indels: 53
0.65 0.21 0.13
Matches are distributed among these distances:
43 45 0.17
44 175 0.68
45 38 0.15
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (44 bp):
TGCTTAGGGAGATAAGGCTCACTATCTTTGATCTGCTCCACTAC
Found at i:7007 original size:264 final size:262
Alignment explanation
Indices: 6276--6984 Score: 992
Period size: 264 Copynumber: 2.7 Consensus size: 262
6266 TAATCTTCAG
* * * * * *
6276 TCTGCTCCACTATTACTTAGGGAGATAAGATCTATAATTTTCAGCCTATTTCCCTATTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGG
* * * * * *
6341 GGATAAGGCTCACCATCTTCGATCTGTTCCCCTATTGCTTAGGGAGATAAGATCTGTAATTTTCG
66 GGATAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCA
* * *
6406 GCTTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACTATCTTCAATCTGCTCCGCTACTACTTAG
131 GCTTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACTATCTTCAATCTGCTCCGCTACT-CTTAG
* * **
6471 GGAGATAAGATCTTTAATTTTTGGCCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACTGTCTT
195 GGAGATAAGATCTGTAATTTTTAGCCTGTTTCCCTACAACTTAGGGGGATAAGGCTCACTGTCTT
6536 CGA
260 CGA
* *
6539 TCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTTA-CCTACTGCTTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTG-TTACCCTACTGCTTA-
* *
6603 GGGGATAAGGCTCACCGTCTTTGATCTGCTCCACTACTGTTTAGGGAGATAAGATTTGTAATTTT
64 GGGGATAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
* * * * *
6668 CAGCCTGTTACCCTACAGCTTAAGGGGTTAAGGCTCACCATCTTCGATCTGCTCCACTACTGCTT
129 CAGCTTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACTATCTTCAATCTGCTCCGCTACT-CTT
* *
6733 AGGGAGATAAGATCTGTAATTTTTAGCCTGTTAT-CCTACAACTTAGGGGGTTAAGGTTCACTGT
193 AGGGAGATAAGATCTGTAATTTTTAGCCTGTT-TCCCTACAACTTAGGGGGATAAGGCTCACTGT
6797 CTTCGA
257 CTTCGA
*
6803 TCTGCTTCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTATG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTA-G
* * * * *
6868 GGGTTAAAGCTCACCGTTTTTTATCTGCTCCACTACTGCTTAGGGAGATAAGATCAGTAATTTTC
65 GGGATAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTC
* * *
6933 AGCTTGTTACTCTACTGCTTAAGGGGTTAAGGCTC-GTATCTTCAACCTGCTC
130 AGCTTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACTATCTTCAATCTGCTC
6985 TCTTGCTACC
Statistics
Matches: 393, Mismatches: 49, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
263 68 0.17
264 324 0.82
265 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (262 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGG
GGATAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCA
GCTTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACTATCTTCAATCTGCTCCGCTACTCTTAGG
GAGATAAGATCTGTAATTTTTAGCCTGTTTCCCTACAACTTAGGGGGATAAGGCTCACTGTCTTC
GA
Found at i:7152 original size:132 final size:132
Alignment explanation
Indices: 6911--7184 Score: 422
Period size: 132 Copynumber: 2.1 Consensus size: 132
6901 TACTGCTTAG
*** * *
6911 GGAGATAAGATCAGTAATTTTCAGCTTGTTACTCTACTGCTTAAGGGGTTAAGGCTCGTATCTTC
1 GGAGATAAGATCAGTAATTTTCAGCCCATTACCCTACTGCTTAAGGGGTTAAGGCTCGCATCTTC
* *
6976 AACCTGCTCTCTTGCTACCTCCGAGAGATAAGGCCGATGGCTAAAATCTACTCCATAGCCGATAC
66 AACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGATGACTAAAATCTACTCCATAGCCGATAC
7041 AT
131 AT
* * *
7043 GGAGATAAGATCTGTAATTTTTAGCCCATTACCCTACTGCTTAGGGGGTTAAGGCTCGCATCTTC
1 GGAGATAAGATCAGTAATTTTCAGCCCATTACCCTACTGCTTAAGGGGTTAAGGCTCGCATCTTC
* * * *
7108 AACCTGTTCTCTTGTTACCTCAGAGAGATAAGGCCGGTGACTAAAATCTGCTCCATAGCCGATAC
66 AACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGATGACTAAAATCTACTCCATAGCCGATAC
7173 AT
131 AT
7175 GGAGATAAGA
1 GGAGATAAGA
7185 CTCGCCATTT
Statistics
Matches: 128, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (132 bp):
GGAGATAAGATCAGTAATTTTCAGCCCATTACCCTACTGCTTAAGGGGTTAAGGCTCGCATCTTC
AACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGATGACTAAAATCTACTCCATAGCCGATAC
AT
Found at i:7234 original size:177 final size:177
Alignment explanation
Indices: 7021--7536 Score: 782
Period size: 177 Copynumber: 2.9 Consensus size: 177
7011 GATGGCTAAA
* **
7021 ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTTAGCCCATTACCCTACTGCTTA
1 ATCTACTCCATAGCCGATACATAGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTA
* * * *
7086 GGGGGTTAAGGCTCGCATCTTCAACCTGTTCTCTTGTTACCTCAGAGAGATAAGGCCGGTGACTA
66 GGGGGTTAAGGCTCGTATCTTCAACCTGTTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTA
*
7151 AAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTAG
131 AAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCAG
* * * ** *
7198 ATCTGCTCTATAGCTGATACATAGAGATAAGATCTGT-ATTTTTCAGCCTGTTATTCTACTACTT
1 ATCTACTCCATAGCCGATACATAGAGATAAGATCTGTAATTTTT-AGCCTGTTACCCTACTGCTT
* ** *
7262 AGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAAACTGTTGGCT
65 AGGGGGTTAAGGCTCGTATCTTCAACCTGTTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCT
* *
7327 AAAATCTGCTCCATAGCTGATACATGGAGATAAGACTCGCCATTTCCG
130 AAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCAG
* * * * *
7375 ATCTACTCCATAGCCGATACATAGAGATAAGATTTGTAATTTTCAACATGTTACCCTATTGCTTA
1 ATCTACTCCATAGCCGATACATAGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTA
*
7440 GGGGGTTAAGGCTCGTATCTTCAACCTGTTCTCTTGCTACCTCAGAGAGATAAGGCTAGTGGCTA
66 GGGGGTTAAGGCTCGTATCTTCAACCTGTTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTA
7505 AAATCTGCTCCATAGCCGATACATGGAGATAA
131 AAATCTGCTCCATAGCCGATACATGGAGATAA
7537 TATCTGTAAT
Statistics
Matches: 300, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
176 6 0.02
177 289 0.96
178 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (177 bp):
ATCTACTCCATAGCCGATACATAGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTA
GGGGGTTAAGGCTCGTATCTTCAACCTGTTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTA
AAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCAG
Found at i:12094 original size:19 final size:19
Alignment explanation
Indices: 12070--12115 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
12060 TGTAAAGTTT
*
12070 AATGCACATG-ATGCAATG
1 AATGCAAATGTATGCAATG
*
12088 CAATGCAAATGTATGGAATG
1 -AATGCAAATGTATGCAATG
12108 AATGCAAA
1 AATGCAAA
12116 AGAAAGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (19 bp):
AATGCAAATGTATGCAATG
Found at i:13921 original size:18 final size:18
Alignment explanation
Indices: 13870--13922 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
13860 TAGTTACTCT
*
13870 ATAACAGTCAATTATACA
1 ATAACAGTCAATTATTCA
*
13888 ATAACAGTCATTTATTCA
1 ATAACAGTCAATTATTCA
*
13906 GTAACAGTCAATTATTC
1 ATAACAGTCAATTATTC
13923 CGTAGCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.34
Consensus pattern (18 bp):
ATAACAGTCAATTATTCA
Found at i:14076 original size:6 final size:6
Alignment explanation
Indices: 14065--14098 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
14055 CACCACAACG
*
14065 GTAACA GTAACA GTAACA GTAACA GTCACA GTAA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAA
14099 TTGTACACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:15185 original size:9 final size:9
Alignment explanation
Indices: 15173--15206 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
15163 TTGTTTTGTT
*
15173 TTTCTTTTA
1 TTTCATTTA
15182 TTTCATTTA
1 TTTCATTTA
15191 TTTC-TTTA
1 TTTCATTTA
15199 TTTCATTT
1 TTTCATTT
15207 CTTTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTCATTTA
Found at i:15200 original size:17 final size:18
Alignment explanation
Indices: 15173--15218 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
15163 TTGTTTTGTT
15173 TTTCTTTTATTTCATTTA
1 TTTCTTTTATTTCATTTA
*
15191 TTTC-TTTATTTCATTTC
1 TTTCTTTTATTTCATTTA
*
15208 TTTATTTTATT
1 TTTCTTTTATT
15219 ATTAAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTTTATTTCATTTA
Found at i:16799 original size:22 final size:23
Alignment explanation
Indices: 16752--16799 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16742 CATTCAAGAT
** *
16752 AAAATAATATATGAAACTCTTTA
1 AAAATAATATATGAAACAATTCA
16775 AAAATAATATAT-AAACAATTCA
1 AAAATAATATATGAAACAATTCA
16797 AAA
1 AAA
16800 TATATAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAATATATGAAACAATTCA
Found at i:16834 original size:51 final size:49
Alignment explanation
Indices: 16778--16875 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 49
16768 CTCTTTAAAA
* *
16778 ATAATATAT-AAACA-ATTCAAAATATATAATGTGTAAAAAAGTTTGAAATAC
1 ATAATATATGAAA-ATATT-AAAATAAATAATGTAT-AAAAA-TTTGAAATAC
*
16829 ATAATATATGAAAATATTAAAGTAAATAATGTATAAAAATTTGAAAT
1 ATAATATATGAAAATATTAAAATAAATAATGTATAAAAATTTGAAAT
16876 GAGCGTTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
49 8 0.19
50 5 0.12
51 23 0.55
52 6 0.14
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (49 bp):
ATAATATATGAAAATATTAAAATAAATAATGTATAAAAATTTGAAATAC
Found at i:17026 original size:20 final size:20
Alignment explanation
Indices: 17003--17040 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16993 ATATTAGTAT
17003 ATAAATAGAAATAAAATATA
1 ATAAATAGAAATAAAATATA
*
17023 ATAAATAGAAATATAATA
1 ATAAATAGAAATAAAATA
17041 ATAGTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
ATAAATAGAAATAAAATATA
Found at i:17036 original size:15 final size:15
Alignment explanation
Indices: 17011--17054 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
17001 ATATAAATAG
17011 AAATA-AAATATAAT
1 AAATAGAAATATAAT
17025 AAATAGAAATATAAT
1 AAATAGAAATATAAT
17040 -AATAGTAGAATATAA
1 AAATAG-A-AATATAA
17055 ATAGATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 10 0.37
15 10 0.37
16 7 0.26
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:17043 original size:14 final size:15
Alignment explanation
Indices: 17017--17072 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
17007 ATAGAAATAA
17017 AATATAATAAATAGA-
1 AATATAAT-AATAGAG
17032 AATATAATAATAGTAG
1 AATATAATAATAG-AG
*
17048 AATAT-A-AATAGAT
1 AATATAATAATAGAG
17061 AA-ATAATAATAG
1 AATATAATAATAG
17073 TATTAGAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 2 0.06
13 4 0.11
14 15 0.42
15 10 0.28
16 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (15 bp):
AATATAATAATAGAG
Found at i:21614 original size:38 final size:38
Alignment explanation
Indices: 21552--21636 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
21542 GGTCCTTAAC
* *
21552 CCGGATATTTTTCCAGCACTTAGCCTGCGGACTTTAAGT
1 CCGGAT-TTATTCCAGCACTTAGCCTGCAGACTTTAAGT
21591 CCGGATTTATTCCAGCA-TATAGCCTGCAGACTTTAAGT
1 CCGGATTTATTCCAGCACT-TAGCCTGCAGACTTTAAGT
*
21629 CCGAATTT
1 CCGGATTT
21637 CTTCTTTTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 1 0.02
38 35 0.83
39 6 0.14
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (38 bp):
CCGGATTTATTCCAGCACTTAGCCTGCAGACTTTAAGT
Done.