Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_54 ID=scaffold_54-JGI_221_v2.0
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: 52030
ACGTcount: A:0.13, C:0.07, G:0.08, T:0.12
Warning! 30906 characters in sequence are not A, C, G, or T
Found at i:1160 original size:44 final size:42
Alignment explanation
Indices: 1020--1479 Score: 244
Period size: 44 Copynumber: 10.6 Consensus size: 42
1010 CCGATAATCC
* ** *
1020 TATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAAAGCA-AG-TCT
* * ** *** * *
1064 TATCTCTCTGAAGTTGCAG-AGAGCA-AATCGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAAAGCAAGTCT
1104 TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAA--AAGCAAGTCT
* * * *
1148 TATC-CTCTTGAAGTTCCAGT-GAGGCAGACTGAAAATGACAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGGCT-AAAA-G-CAAGTCT
* * * *
1193 TATCTCCCTGAAGTTGCAGTGGAGCA-GATTAAAGCCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAAAG-C-A-AGTCT
* * *
1237 TATCTCCCTGAAGTTGCAGTGGAG-TGGATTAAAATCACAGATC-
1 TATCTCCCTGAAGTTGCAGTGGAGCAGG-CTAAAAGCA-AG-TCT
* * *** * *
1280 TATTCTCTCTGAAGTTGCAG-AGAGCAGG-TCGCATCTAGTCT
1 TA-TCTCCCTGAAGTTGCAGTGGAGCAGGCTAAAAGCAAGTCT
1321 TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAA--AAGCAAGTCT
* * *
1365 TATC-CTCCTGAAGTTGCAGT-GAGGC-GGACTGAAGATGACAAATAT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGG-CT-AA-AAG-CAAGTCT
* * *
1410 TATCTCCCTGAAGTTGCAGTGGAGCA-GATAAAAGCCGACAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAAAG-C-A-AGTCT
*
1454 TATCTCCCTGAAGTTGTAGTGGAGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCA
1480 AATTACAAGA
Statistics
Matches: 325, Mismatches: 58, Indels: 66
0.72 0.13 0.15
Matches are distributed among these distances:
40 39 0.12
41 18 0.06
42 16 0.05
43 28 0.09
44 159 0.49
45 59 0.18
46 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (42 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAAAGCAAGTCT
Found at i:1387 original size:217 final size:217
Alignment explanation
Indices: 1008--1477 Score: 816
Period size: 217 Copynumber: 2.2 Consensus size: 217
998 ACAAATCCCT
1008 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAATCACAGATCTTATCTCTCT
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAATCACAGATCTTATCTCTCT
1073 GAAGTTGCAGAGAGCAAATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGT
66 GAAGTTGCAGAGAGCAAATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGT
* *
1138 AAGCAAGTCTTATCCTCTTGAAGTTCCAGTGAGGCAGACTGAAAATGACAAATCTTATCTCCCTG
131 AAGCAAGTCTTATCCTCCTGAAGTTCCAGTGAGGCAGACTGAAAATGACAAATATTATCTCCCTG
*
1203 AAGTTGCAGTGGAGCAGATTAA
196 AAGTTGCAGTGGAGCAGATAAA
**
1225 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATC-TATTCTCTC
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAATCACAGATCTTA-TCTCTC
**
1289 TGAAGTTGCAGAGAGCAGGTCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAG
65 TGAAGTTGCAGAGAGCAAATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAG
* * *
1354 TAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCGGACTGAAGATGACAAATATTATCTCCCT
130 TAAGCAAGTCTTATCCTCCTGAAGTTCCAGTGAGGCAGACTGAAAATGACAAATATTATCTCCCT
1419 GAAGTTGCAGTGGAGCAGATAAA
195 GAAGTTGCAGTGGAGCAGATAAA
* *
1442 AGCCGACAATCCTATCTCCCTGAAGTTGTAGTGGAG
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAG
1478 CAAATTACAA
Statistics
Matches: 240, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
216 2 0.01
217 238 0.99
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (217 bp):
AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAATCACAGATCTTATCTCTCT
GAAGTTGCAGAGAGCAAATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGT
AAGCAAGTCTTATCCTCCTGAAGTTCCAGTGAGGCAGACTGAAAATGACAAATATTATCTCCCTG
AAGTTGCAGTGGAGCAGATAAA
Found at i:1550 original size:31 final size:32
Alignment explanation
Indices: 1491--1551 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1481 ATTACAAGAG
*
1491 TAATTGAAACCTAATAAAAACTCTTTAAAAAT
1 TAATTGAAACCTAATAAAAACTCCTTAAAAAT
*
1523 TAATTGAATCCTAAT-AAAACTCCTTAAAA
1 TAATTGAAACCTAATAAAAACTCCTTAAAA
1552 TTATCTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (32 bp):
TAATTGAAACCTAATAAAAACTCCTTAAAAAT
Found at i:6872 original size:20 final size:21
Alignment explanation
Indices: 6814--6872 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
6804 TTTTACGGTT
*
6814 TTTTTGGCGATTTTTTTTGTGC
1 TTTTT-GCTATTTTTTTTGTGC
6836 TTTTTGCT-TCTTCTTTTT-T-C
1 TTTTTGCTAT-TT-TTTTTGTGC
6856 TTTTTGCTATTTTTTTT
1 TTTTTGCTATTTTTTTT
6873 AAAGAATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 5 0.15
20 12 0.36
21 6 0.18
22 10 0.30
ACGTcount: A:0.03, C:0.12, G:0.12, T:0.73
Consensus pattern (21 bp):
TTTTTGCTATTTTTTTTGTGC
Found at i:7470 original size:31 final size:32
Alignment explanation
Indices: 7409--7473 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
7399 GGCAAATTAC
*
7409 AAGAGTAACTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAACTAAATCCTAATAAAAACTCTTTA
* *
7441 AAGAGTAATTAAATCCTAAT-ATAACTCTTTA
1 AAGAGTAACTAAATCCTAATAAAAACTCTTTA
7472 AA
1 AA
7474 ATTATCTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.31
Consensus pattern (32 bp):
AAGAGTAACTAAATCCTAATAAAAACTCTTTA
Found at i:19549 original size:44 final size:45
Alignment explanation
Indices: 19490--19691 Score: 186
Period size: 44 Copynumber: 4.5 Consensus size: 45
19480 GATCGCACCT
*
19490 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCT-AAG-TAAGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAA-TA
*
19534 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGACA-A
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAAGAT-A-ATA
* * **
19580 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAATA
* * * * *
19625 A-TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA-ATCA-C
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAATA
*
19667 AGATCTTATCTCTCTGAAGTTGCAG
1 AG-TCTTATCTCCCTGAAGTTGCAG
19692 AGAGCAGGTC
Statistics
Matches: 133, Mismatches: 14, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
42 1 0.01
43 4 0.03
44 84 0.63
45 6 0.05
46 33 0.25
47 4 0.03
48 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAATA
Found at i:19552 original size:84 final size:89
Alignment explanation
Indices: 19406--19612 Score: 209
Period size: 84 Copynumber: 2.4 Consensus size: 89
19396 CGTAGCCGAT
* *
19406 AATCCTATCTCCCTGAAGTTGCAGTGGAGCA-AATTAACATCACAGATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAAGTAACATCACAGATCTTATCTCTCTGAAGTT
* **
19470 GCAGAGA-GCAGA-T-CG-CACCT
66 GCAGAGAGGCAGACTAAGACACAA
* *
19490 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAA-GT-A-AG-TCTTATC-CTCCTGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA-G--AAGTAACATCACAGATCTTATCTCT-CTGA
* *
19550 AGTTGCAGTGAGGCAGACTGAAGATGACAA
62 AGTTGCAGAGAGGCAGACT-AAGA-CACAA
19580 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
19613 TTAAAGCCAA
Statistics
Matches: 102, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
83 2 0.02
84 50 0.49
85 7 0.07
86 2 0.02
87 2 0.02
88 6 0.06
89 1 0.01
90 32 0.31
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (89 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAAGTAACATCACAGATCTTATCTCTCTGAAGTT
GCAGAGAGGCAGACTAAGACACAA
Found at i:19639 original size:90 final size:88
Alignment explanation
Indices: 19492--19691 Score: 228
Period size: 90 Copynumber: 2.2 Consensus size: 88
19482 TCGCACCTAG
* * *
19492 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGTAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGTAAGTCCTATCCTCCTGAAGTTGCA
* *
19557 GT-GAGGCAGACTGAAGATGACAAAA
66 GTGGA-GCAGA-TGAAAATCAC-AAA
*
19582 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-TAA-TCCTAT-CTCCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-CAAGTAAGTCCTATCCT-CCTGAAGTT
* * *
19644 GCAGTGGAGCGGATTAAAATCACAGA
63 GCAGTGGAGCAGATGAAAATCACAAA
*
19670 TCTTATCTCTCTGAAGTTGCAG
1 TCTTATCTCCCTGAAGTTGCAG
19692 AGAGCAGGTC
Statistics
Matches: 96, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
88 23 0.24
89 9 0.09
90 54 0.56
91 8 0.08
92 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGTAAGTCCTATCCTCCTGAAGTTGCA
GTGGAGCAGATGAAAATCACAAA
Found at i:48306 original size:44 final size:44
Alignment explanation
Indices: 48256--49070 Score: 451
Period size: 44 Copynumber: 18.8 Consensus size: 44
48246 GTAGCCGATA
*
48256 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * ***
48300 ATCTTATCTCTCTGAAGTTGCAG-AGAGCA-AATCGCA-C-CTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAC-AG
**
48341 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGT-A-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AA-TCACAG
* * * * *
48385 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGACAA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCACAG
** *
48429 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* *
48472 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * *** *
48516 ATCTTATC-CCTCTGAAGTTGCAG-AGAGTAG-GTCGCATC-TAG
1 ATCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
** *
48557 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACAG
* * * ** *
48601 -TCTTATC-CTCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGGCAA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCACAG
* * ** *
48645 ATCTTACCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCGATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-ACAG
* * *
48689 ATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * ** *
48733 ATCTTATCTCTCTGAAGTTGCAG-AGAGTAGATT-GCATC-TAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * *
48774 -TTTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACAG
* * ** *
48818 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCACAG
* * **
48862 ATCTTATCTTCCTGAAGTTGCACTGGAGCAGATTAAAGCCGACA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-ACAG
* * * **
48906 ATCCTATCTTCTTGAAGTTGCAGTGGAGTGGATTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * * ** *
48950 ATCTTATCTCTCTAAAGTTGTAG-AGAGCAGATT-GCATC-TAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * *
48991 -TCTTATCTCCCTGAAGTTGCAATGGAGCAGACT-AAGT-AGGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCA--CAG
* * *
49034 ATCTTATCTTCTTGAAGTTGCAATGGAGCAGATTAAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
49071 GCTGATAATC
Statistics
Matches: 576, Mismatches: 142, Indels: 105
0.70 0.17 0.13
Matches are distributed among these distances:
40 79 0.14
41 36 0.06
42 16 0.03
43 82 0.14
44 271 0.47
45 84 0.15
46 8 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
Found at i:48795 original size:84 final size:85
Alignment explanation
Indices: 48257--49021 Score: 345
Period size: 84 Copynumber: 8.9 Consensus size: 85
48247 TAGCCGATAA
* *
48257 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATCACAGATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCCCTGAAGTTGCA
* * * *
48322 G-AGAGCAAATCGCACCTAG
66 GTGGAGCAGATTGCATCTAG
**
48341 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGT-A-AG-TCTTATC-CTCCTGAAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AA-TCACAGATCTTATCTC-CCTGAAGT
* * * * *
48402 TGCAGT-GAGGTAGACTGAAGATGACAAA
62 TGCAGTGGA-GCAGATTG--CAT--CTAG
** * *
48430 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATA-ATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCCCTGAAGTTGCA
* ** *
48494 GTGGAGCGGATTAAAATCACAG
66 GTGGAGCAGATT-GCATC-TAG
* * * *** *
48516 ATCTTATC-CCTCTGAAGTTGCAG-AGAGTAG-GTCGCATC-TAG-TCTTATCTCCCTGAAGTTG
1 -TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCCCTGAAGTTG
* * * * *
48576 CAGTGGAGCAGGCTAAGTAAGCAAG
64 CAGTGGAGCA-GAT-TG-CATCTAG
* * * ** * *
48601 TCTTATC-CTCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCTTACCTCCCTGAAGTT
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCACAGATCTTATCTCCCTGAAGTT
* *** *
48664 GCAGTGGAGTAGATTAAAGCCGATAA
63 GCAGTGGAGCAGATT---GCATCTAG
* * * *
48690 TCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCCCTGAAGTTGCA
* *
48755 G-AGAGTAGATTGCATCTAG
66 GTGGAGCAGATTGCATCTAG
* * * *
48774 TTTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCA-AG-TCTTATC-CTCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACAGATCTTATCTC-CCTGAAGTT
* * * *
48836 GCAGT-GAGGCAGACTGAAGATGGCAAA
63 GCAGTGGA-GCAGATTG--CAT--CTAG
* * ** * * *
48863 TCTTATCTTCCTGAAGTTGCACTGGAGCAGATTAAAGCCGACA-ATCCTATCTTCTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-ACAGATCTTATCTCCCTGAAGTTGC
** ** *
48927 AGTGGAGTGGATTAAAATCACAG
65 AGTGGAGCAGATT-GCATC-TAG
* * * * ** *
48950 ATCTTATCTCTCTAAAGTTGTAG-AGAGCAGATT-GCATC-TAG-TCTTATCTCCCTGAAGTTGC
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCCCTGAAGTTGC
*
49011 AATGGAGCAGA
65 AGTGGAGCAGA
49022 CTAAGTAGGC
Statistics
Matches: 507, Mismatches: 121, Indels: 106
0.69 0.16 0.14
Matches are distributed among these distances:
83 2 0.00
84 183 0.36
85 25 0.05
86 20 0.04
87 50 0.10
88 76 0.15
89 145 0.29
90 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (85 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCCCTGAAGTTGCA
GTGGAGCAGATTGCATCTAG
Found at i:48812 original size:217 final size:217
Alignment explanation
Indices: 48248--49055 Score: 1294
Period size: 217 Copynumber: 3.7 Consensus size: 217
48238 ATAAATTCGT
* **
48248 AGCCGATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATCACAGATCTTATCTCTCT
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCT
* * *
48313 GAAGTTGCAGAGAGCAAATCGCACCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGT
66 GAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGT
* * *
48378 AAGTAAGTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGACAAATCTTATCTCCCTG
131 AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTG
48443 AAGTTGCAGTGGAGCAGATTAA
196 AAGTTGCAGTGGAGCAGATTAA
*
48465 AGCC-ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCCCTCT
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCT
* * *
48529 GAAGTTGCAGAGAGTAGGTCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGT
66 GAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGT
* *
48594 AAGCAAGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTACCTCCCTG
131 AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTG
*
48659 AAGTTGCAGTGGAGTAGATTAA
196 AAGTTGCAGTGGAGCAGATTAA
*
48681 AGCCGATAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCT
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCT
* * * *
48746 GAAGTTGCAGAGAGTAGATTGCATCTAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGT
66 GAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGT
*
48811 AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTG
131 AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTG
*
48876 AAGTTGCACTGGAGCAGATTAA
196 AAGTTGCAGTGGAGCAGATTAA
* * * *
48898 AGCCGACAATCCTATCTTCTTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCT
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCT
* * * *
48963 AAAGTTGTAGAGAGCAGATTGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGT
66 GAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGT
* * * *
49028 AGGCAAATCTTATCTTCTTGAAGTTGCA
131 AAGCAAGTCTTATCCTCCTGAAGTTGCA
49056 ATGGAGCAGA
Statistics
Matches: 551, Mismatches: 39, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
216 202 0.37
217 349 0.63
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCT
GAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGT
AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTG
AAGTTGCAGTGGAGCAGATTAA
Found at i:49093 original size:128 final size:128
Alignment explanation
Indices: 48863--49093 Score: 297
Period size: 128 Copynumber: 1.8 Consensus size: 128
48853 AGATGGCAAA
* * *
48863 TCTTATCTTCCTGAAGTTGCACTGGAGCAGATTAAAGCCGACAATCCTATCTTCTTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAAGCCGACAATCCTATCTTCTTGAAGTTGCA
* ** * *
48928 GTGGAGTGGATTAAAATCACAGATCTTATCTCTCTAAAGTTGTAGAGAGCAGATTGCATCTAG
66 ATGGAGCAGATTAAAATCACAGATCCTATCTCCCTAAAGTTGTAGAGAGCAGATTGCATCTAG
* *
48991 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAGGC-A-AATCTTATCTTCTTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAA--AGCCGACAATCCTATCTTCTTGAAGTTG
* * *
49054 CAATGGAGCAGATTAAAGCTGATA-ATCCTATCTCCCTAAA
64 CAATGGAGCAGATTAAA-ATCACAGATCCTATCTCCCTAAA
49094 ATTGCAGTGG
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
128 80 0.92
129 4 0.05
130 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAAGCCGACAATCCTATCTTCTTGAAGTTGCA
ATGGAGCAGATTAAAATCACAGATCCTATCTCCCTAAAGTTGTAGAGAGCAGATTGCATCTAG
Found at i:49101 original size:433 final size:433
Alignment explanation
Indices: 48248--49109 Score: 1298
Period size: 433 Copynumber: 2.0 Consensus size: 433
48238 ATAAATTCGT
*
48248 AGCCGATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATCACAGATCTTATCTCTCT
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATCACAGATCTTATCTCTCT
**
48313 GAAGTTGCAGAGAGCAAATCGCACCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGT
66 GAAGTTGCAGAGAGCAAATCGCACCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGT
* *
48378 AAGTAAGTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGACAAATCTTATCTCCCTG
131 AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTG
* *
48443 AAGTTGCAGTGGAGCAGATTAAAGCCATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
196 AAGTTGCACTGGAGCAGATTAAAGCCACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
* * *
48508 AATCACAGATCTTATCCCTCTGAAGTTGCAGAGAGTAGGTCGCATCTAGTCTTATCTCCCTGAAG
261 AATCACAGATCTTATCCCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAG
* * * * *
48573 TTGCAGTGGAGCAGGCTAAGTAAGCAAGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAG
326 TTGCAATGGAGCAGACTAAGTAAGCAAATCTTATCCTCCTAAAGTTGCAATGAGGCAGACTAAAG
* * * *
48638 ATGGCAAATCTTACCTCCCTGAAGTTGCAGTGGAGTAGATTAA
391 ATGGCAAATCCTACCTCCCTAAAATTGCAGTGGAATAGATTAA
* **
48681 AGCCGATAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCT
1 AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATCACAGATCTTATCTCTCT
* * * * *
48746 GAAGTTGCAGAGAGTAGATTGCATCTAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGT
66 GAAGTTGCAGAGAGCAAATCGCACCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGT
* *
48811 AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTG
131 AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTG
* * *
48876 AAGTTGCACTGGAGCAGATTAAAGCCGACAATCCTATCTTCTTGAAGTTGCAGTGGAGTGGATTA
196 AAGTTGCACTGGAGCAGATTAAAGCC-ACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTA
* * *
48941 AAATCACAGATCTTATCTCTCTAAAGTTGTAGAGAGCAGATTGCATCTAGTCTTATCTCCCTGAA
260 AAATCACAGATCTTATCCCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAA
* * * * *
49006 GTTGCAATGGAGCAGACTAAGTAGGCAAATCTTATCTTCTTGAAGTTGCAATG-GAGCAGATTAA
325 GTTGCAATGGAGCAGACTAAGTAAGCAAATCTTATCCTCCTAAAGTTGCAATGAG-GCAGACTAA
* *
49070 AGCT-G-ATAATCCTATCTCCCTAAAATTGCAGTGGAATAGA
389 AGATGGCA-AATCCTACCTCCCTAAAATTGCAGTGGAATAGA
49110 CTAAGATAGC
Statistics
Matches: 384, Mismatches: 42, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
432 1 0.00
433 235 0.61
434 148 0.39
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (433 bp):
AGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATCACAGATCTTATCTCTCT
GAAGTTGCAGAGAGCAAATCGCACCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGT
AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTG
AAGTTGCACTGGAGCAGATTAAAGCCACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA
AATCACAGATCTTATCCCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAG
TTGCAATGGAGCAGACTAAGTAAGCAAATCTTATCCTCCTAAAGTTGCAATGAGGCAGACTAAAG
ATGGCAAATCCTACCTCCCTAAAATTGCAGTGGAATAGATTAA
Found at i:49354 original size:15 final size:15
Alignment explanation
Indices: 49334--49365 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
49324 CGTGAAACGA
49334 CCGAGAGAGCCACCC
1 CCGAGAGAGCCACCC
49349 CCGAGAGAGCCACCC
1 CCGAGAGAGCCACCC
49364 CC
1 CC
49366 AGATTTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.50, G:0.25, T:0.00
Consensus pattern (15 bp):
CCGAGAGAGCCACCC
Found at i:51188 original size:26 final size:26
Alignment explanation
Indices: 51157--51208 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
51147 AAGCATGTGG
51157 GGCACTGTCTTTAAATTTCAAATTGC
1 GGCACTGTCTTTAAATTTCAAATTGC
51183 GGCACTGTCTTTAAATTTCAAATTGC
1 GGCACTGTCTTTAAATTTCAAATTGC
51209 ACTAGGCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (26 bp):
GGCACTGTCTTTAAATTTCAAATTGC
Done.