Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 15 of 22
Found at i:2407222 original size:16 final size:17
Alignment explanation
Indices: 2407203--2407238 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2407193 TATATTATAA
2407203 TTATATTTA-AAATATT
1 TTATATTTATAAATATT
*
2407219 TTATATTTATATATATT
1 TTATATTTATAAATATT
2407236 TTA
1 TTA
2407239 ATACGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTATAAATATT
Found at i:2407238 original size:27 final size:26
Alignment explanation
Indices: 2407204--2407309 Score: 83
Period size: 27 Copynumber: 4.1 Consensus size: 26
2407194 ATATTATAAT
*
2407204 TATATTTAAAATATTTTATATTTATA
1 TATATTTTAAATATTTTATATTTATA
* *
2407230 TATATTTT-AATACGTTAATAATTTA-A
1 TATATTTTAAATA-TTTTAT-ATTTATA
* * * * *
2407256 T-TATATTATATAATATATATTCATA
1 TATATTTTAAATATTTTATATTTATA
*
2407281 TTATATTTTAAATATTTTATATATATA
1 -TATATTTTAAATATTTTATATTTATA
2407308 TA
1 TA
2407310 ATATACATAA
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
24 4 0.07
25 13 0.22
26 19 0.32
27 23 0.39
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (26 bp):
TATATTTTAAATATTTTATATTTATA
Found at i:2407283 original size:20 final size:21
Alignment explanation
Indices: 2407258--2407314 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2407248 TAATTTAATT
2407258 ATATTATATAATATATA-TTC
1 ATATTATATAATATATATTTC
** * *
2407278 ATATTATATTTTAAATATTTT
1 ATATTATATAATATATATTTC
2407299 ATATATATATAATATA
1 ATAT-TATATAATATA
2407315 CATAAATAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 14 0.50
21 6 0.21
22 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTATATAATATATATTTC
Found at i:2410954 original size:34 final size:33
Alignment explanation
Indices: 2410906--2411126 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 33
2410896 TGGTAAAAAC
*
2410906 CACCATTTAATCAACAATGGCAA-CTTACCAAAT
1 CACCATTTAATCAACAATGGTAAGC-TACCAAAT
* *
2410939 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
2410973 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
**
2411007 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * *
2411041 CTCCCATTTAGTCAACAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
2411075 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
2411109 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2411127 TCTCCCACTT
Statistics
Matches: 163, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
33 19 0.12
34 142 0.87
35 2 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:2411050 original size:102 final size:101
Alignment explanation
Indices: 2410906--2411126 Score: 345
Period size: 102 Copynumber: 2.2 Consensus size: 101
2410896 TGGTAAAAAC
* *
2410906 CACCATTTAATCAACAATGGCAACTTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACTTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
2410971 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
2411007 TTCTCATTTAATCAACAATGGTAAGC-TACCAAATCTCCCATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGGCAA-CTTACCAAATCTACCATTTAGTCAACAATGGCAAACCACC
2411071 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
2411109 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2411127 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
101 16 0.15
102 91 0.84
103 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACTTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:2415583 original size:34 final size:33
Alignment explanation
Indices: 2415535--2415753 Score: 278
Period size: 34 Copynumber: 6.5 Consensus size: 33
2415525 TGGTAAAAAC
*
2415535 CACCATTTAATCAACAATGGCAA-CTTACCAAAT
1 CACCATTTAATCAACAATGGTAAGC-TACCAAAT
* *
2415568 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
2415602 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
**
2415636 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * *
2415670 CTCCCATTTAATCAACAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
2415704 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
2415738 CACCATTTAATCAACA
1 CACCATTTAATCAACA
2415754 TTAAATGGTT
Statistics
Matches: 163, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
33 17 0.10
34 144 0.88
35 2 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:2415679 original size:102 final size:101
Alignment explanation
Indices: 2415535--2415753 Score: 332
Period size: 102 Copynumber: 2.2 Consensus size: 101
2415525 TGGTAAAAAC
* * *
2415535 CACCATTTAATCAACAATGGCAACTTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACTTACCAAATCTACCATTTAATCAACAATGGCAAACCACCAA
* *
2415600 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
2415636 TTCTCATTTAATCAACAATGGTAAGC-TACCAAATCTCCCATTTAATCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGGCAA-CTTACCAAATCTACCATTTAATCAACAATGGCAAACCACC
2415700 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
2415738 CACCATTTAATCAACA
1 CACCATTTAATCAACA
2415754 TTAAATGGTT
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
101 14 0.13
102 90 0.86
103 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACTTACCAAATCTACCATTTAATCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:2417055 original size:20 final size:22
Alignment explanation
Indices: 2417025--2417065 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2417015 AATTAAAAAA
*
2417025 TTTATAATTAT-TTTTTTTATT
1 TTTATAATTATAATTTTTTATT
2417046 TTTA-AATTATAATTTTTTAT
1 TTTATAATTATAATTTTTTAT
2417066 GCTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTATAATTATAATTTTTTATT
Found at i:2421334 original size:17 final size:16
Alignment explanation
Indices: 2421314--2421367 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
2421304 ATTCATGTAT
*
2421314 TTATATTATTTTTTATG
1 TTATATT-TTTTTTATA
*
2421331 TTATATTTTATTTTGTA
1 TTATATTTT-TTTTATA
* *
2421348 TTATATTTTATTTATT
1 TTATATTTTTTTTATA
2421364 TTAT
1 TTAT
2421368 CTATCTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 10 0.32
17 21 0.68
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (16 bp):
TTATATTTTTTTTATA
Found at i:2421398 original size:2 final size:2
Alignment explanation
Indices: 2421391--2421417 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2421381 GTAAGCCTCT
2421391 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2421418 TGTAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2422920 original size:2 final size:2
Alignment explanation
Indices: 2422913--2422952 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2422903 ACATTACATG
*
2422913 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2422953 GGTTTGATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2422928 original size:12 final size:12
Alignment explanation
Indices: 2422907--2422952 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
2422897 GATTCTACAT
*
2422907 TACATGTATATA
1 TACATATATATA
2422919 TACATATATATA
1 TACATATATATA
*
2422931 TATATATATATA
1 TACATATATATA
*
2422943 TATATATATA
1 TACATATATA
2422953 GGTTTGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (12 bp):
TACATATATATA
Found at i:2423221 original size:19 final size:20
Alignment explanation
Indices: 2423199--2423240 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2423189 CACACATAAG
*
2423199 TATATTTTAT-TATTTTAAA
1 TATATTTTATATATTTAAAA
2423218 TATATTTTATATATTTAAAA
1 TATATTTTATATATTTAAAA
2423238 TAT
1 TAT
2423241 TATATACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATTTTATATATTTAAAA
Found at i:2423253 original size:20 final size:19
Alignment explanation
Indices: 2423199--2423246 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2423189 CACACATAAG
*
2423199 TATATTTTAT-TATTTTAAA
1 TATATTATATATA-TTTAAA
*
2423218 TATATTTTATATATTTAAA
1 TATATTATATATATTTAAA
2423237 -ATATTATATA
1 TATATTATATA
2423247 CTTATTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 16 0.59
20 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATATATTTAAA
Found at i:2426669 original size:24 final size:22
Alignment explanation
Indices: 2426620--2426669 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2426610 TATATCAAAT
* *
2426620 TTTATATCATACTTTAATTATT
1 TTTATATCATACATTAATTATA
*
2426642 TTTATATCATGCAATTATATTATA
1 TTTATATCATAC-ATTA-ATTATA
2426666 TTTA
1 TTTA
2426670 AAATTATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
23 3 0.13
24 9 0.39
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTATATCATACATTAATTATA
Found at i:2427532 original size:3 final size:3
Alignment explanation
Indices: 2427524--2427549 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2427514 TAAATAGAGA
2427524 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2427550 ATTATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2427556 original size:3 final size:3
Alignment explanation
Indices: 2427550--2427596 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
2427540 ATAATAATAA
2427550 ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2427596 A
1 A
2427597 ATTTGCATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2430186 original size:14 final size:15
Alignment explanation
Indices: 2430169--2430219 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
2430159 TAATTATTTT
2430169 TTTATAAA-ATAATA
1 TTTATAAATATAATA
*
2430183 TTTAATAAATTTAATA
1 TTT-ATAAATATAATA
* *
2430199 TTTA-AATTTTAATA
1 TTTATAAATATAATA
2430213 TTTATAA
1 TTTATAA
2430220 TTTTTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 16 0.50
15 8 0.25
16 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTATAAATATAATA
Found at i:2434181 original size:18 final size:17
Alignment explanation
Indices: 2434160--2434202 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2434150 TTTAAATATG
2434160 TAATAAATAAAAAATAAT
1 TAATAAATAAAAAA-AAT
*
2434178 TAATAATATTAAAAAAAT
1 TAATAA-ATAAAAAAAAT
*
2434196 TATTAAA
1 TAATAAA
2434203 ATGTCAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 14 0.64
19 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATAAATAAAAAAAAT
Found at i:2441321 original size:3 final size:3
Alignment explanation
Indices: 2441313--2441337 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2441303 CAGTTTGTCC
2441313 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
2441338 GAAATCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2442259 original size:2 final size:2
Alignment explanation
Indices: 2442244--2442281 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2442234 TACACACATC
* *
2442244 TA TA TC TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2442282 AACTATAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2442843 original size:16 final size:14
Alignment explanation
Indices: 2442822--2442857 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
2442812 TATTAAAAAA
2442822 TAATATTTAATATATT
1 TAATATTTAA-AT-TT
2442838 TAATATTTAAATTT
1 TAATATTTAAATTT
2442852 TAATAT
1 TAATAT
2442858 ATACAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATATTTAAATTT
Found at i:2443329 original size:2 final size:2
Alignment explanation
Indices: 2443322--2443356 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2443312 GTTTCTTCAA
2443322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2443357 AATTGAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2444491 original size:17 final size:17
Alignment explanation
Indices: 2444466--2444513 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
2444456 ATTTAAGTAA
**
2444466 AAATATATGTTGGATAT
1 AAATATATGTTAAATAT
*
2444483 AAGTATATGTTAAATAT
1 AAATATATGTTAAATAT
2444500 AAATATAT-TTAAAT
1 AAATATATGTTAAAT
2444514 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (17 bp):
AAATATATGTTAAATAT
Found at i:2444533 original size:23 final size:24
Alignment explanation
Indices: 2444501--2444557 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
2444491 GTTAAATATA
* *
2444501 AATATATTTAAATTTTAAAATTTTT
1 AATAT-TTTAAATTTTAAAAATTAT
*
2444526 AAT-TTTTATATTTTAAAAATTAT
1 AATATTTTAAATTTTAAAAATTAT
2444549 AATATTTTA
1 AATATTTTA
2444558 TTCGTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 19 0.68
24 6 0.21
25 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
AATATTTTAAATTTTAAAAATTAT
Found at i:2448199 original size:28 final size:27
Alignment explanation
Indices: 2448137--2448218 Score: 69
Period size: 29 Copynumber: 3.0 Consensus size: 27
2448127 ATCTGAAAAT
2448137 AAAA-AATTTA-AAAATATTAATTTTA
1 AAAATAATTTATAAAATATTAATTTTA
** *
2448162 AATTTAAATTTATAAAATATTACTCTTTA
1 AAAAT-AATTTATAAAATATTAAT-TTTA
* *
2448191 AAAATAATTACATAAAATTTATAATTTT
1 AAAATAATT-TATAAAATAT-TAATTTT
2448219 TTCTTTCATA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
25 2 0.05
27 6 0.14
28 14 0.33
29 18 0.42
30 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAATAATTTATAAAATATTAATTTTA
Found at i:2456880 original size:24 final size:26
Alignment explanation
Indices: 2456843--2456894 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
2456833 TAATTATATA
* *
2456843 TATAAAAAGGTAAACTTAAAAT-TTT
1 TATAAAAAGATAAAATTAAAATCTTT
*
2456868 TATAAAAA-ATAAAATTTAAATCTTT
1 TATAAAAAGATAAAATTAAAATCTTT
2456893 TA
1 TA
2456895 ATCCGTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
TATAAAAAGATAAAATTAAAATCTTT
Found at i:2457187 original size:16 final size:15
Alignment explanation
Indices: 2457120--2457189 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 15
2457110 TATTAATTGT
*
2457120 TTTTTTATTTAAAATA
1 TTTTATATTTAAAA-A
*
2457136 TTTTATATTTTTATAAA
1 TTTTATA--TTTAAAAA
* *
2457153 TTTTAATATTTTAATA
1 TTTT-ATATTTAAAAA
2457169 TTTTATATTATAAAAA
1 TTTTATATT-TAAAAA
2457185 TTTTA
1 TTTTA
2457190 AAATAAATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.12
16 24 0.56
17 5 0.12
18 9 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTATATTTAAAAA
Found at i:2457918 original size:34 final size:34
Alignment explanation
Indices: 2457878--2457949 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
2457868 ATAATTTTCA
2457878 ATTTCACAAACATCCCACTAAATTTAATTTTGGT
1 ATTTCACAAACATCCCACTAAATTTAATTTTGGT
*
2457912 ATTTCACAAACATCCCACTAAATTTGATTTTGGT
1 ATTTCACAAACATCCCACTAAATTTAATTTTGGT
2457946 ATTT
1 ATTT
2457950 AAATAAGTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (34 bp):
ATTTCACAAACATCCCACTAAATTTAATTTTGGT
Found at i:2459475 original size:24 final size:24
Alignment explanation
Indices: 2459443--2459489 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2459433 TAGAGTCGAG
2459443 AATAGAAAATAGAAATCGAACTGA
1 AATAGAAAATAGAAATCGAACTGA
2459467 AATAGAAAATAGAAATCGAACTG
1 AATAGAAAATAGAAATCGAACTG
2459490 GGCTATTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (24 bp):
AATAGAAAATAGAAATCGAACTGA
Found at i:2461528 original size:51 final size:51
Alignment explanation
Indices: 2461452--2461557 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
2461442 TCTATAAAAG
2461452 TAACCCAACTTCTTCTACTTAAGAGAGGAACATTTCCTAGATTTCAGAATC
1 TAACCCAACTTCTTCTACTTAAGAGAGGAACATTTCCTAGATTTCAGAATC
2461503 TAACCCAACTTCTTCTACTTAAGAGAGGAACATTTCCTAGATTTCAGAATC
1 TAACCCAACTTCTTCTACTTAAGAGAGGAACATTTCCTAGATTTCAGAATC
2461554 TAAC
1 TAAC
2461558 ACACCCCATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (51 bp):
TAACCCAACTTCTTCTACTTAAGAGAGGAACATTTCCTAGATTTCAGAATC
Found at i:2462539 original size:16 final size:16
Alignment explanation
Indices: 2462518--2462556 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2462508 TCATCTATAA
*
2462518 TTTTTAATAAATTAAT
1 TTTTTAAAAAATTAAT
*
2462534 TTTTTAAAAAAATTTAT
1 TTTTT-AAAAAATTAAT
2462551 TTTTTA
1 TTTTTA
2462557 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAAAAAATTAAT
Found at i:2462802 original size:16 final size:16
Alignment explanation
Indices: 2462781--2462835 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 16
2462771 TAATCGATTT
*
2462781 TTTTATTTTAAATATG
1 TTTTATTTTAAATATA
2462797 TTTTA--TTAAATATA
1 TTTTATTTTAAATATA
2462811 TTTATATTTTATTAAATATA
1 TTT-TA--TT-TTAAATATA
2462831 TTTTA
1 TTTTA
2462836 AATATTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
14 11 0.34
15 2 0.06
16 5 0.16
19 2 0.06
20 12 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTATTTTAAATATA
Found at i:2462822 original size:20 final size:20
Alignment explanation
Indices: 2462797--2462879 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
2462787 TTTAAATATG
2462797 TTTTATTAAATATATTTATA
1 TTTTATTAAATATATTTATA
*
2462817 TTTTATTAAATATATTTTAAA
1 TTTTATTAAATATA-TTTATA
* *
2462838 TATTAATTAAGT-TATTT-TA
1 T-TTTATTAAATATATTTATA
* *
2462857 ATTTATTCAA-AT-TTTATA
1 TTTTATTAAATATATTTATA
2462875 TTTTA
1 TTTTA
2462880 ATAATAAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
17 3 0.06
18 13 0.26
19 1 0.02
20 17 0.34
21 8 0.16
22 8 0.16
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (20 bp):
TTTTATTAAATATATTTATA
Found at i:2462935 original size:22 final size:20
Alignment explanation
Indices: 2462910--2462957 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
2462900 TTGATTAATT
2462910 AAATTGAAACTCTAAATCAATC
1 AAATTGAAA-TCT-AATCAATC
* *
2462932 AAATTTTAAATCTAATTAATC
1 AAA-TTGAAATCTAATCAATC
2462953 AAATT
1 AAATT
2462958 AATTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 10 0.43
22 6 0.26
23 5 0.22
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATTGAAATCTAATCAATC
Found at i:2462970 original size:23 final size:21
Alignment explanation
Indices: 2462928--2462971 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
2462918 ACTCTAAATC
2462928 AATCAAATTTTAAATCTAATT
1 AATCAAATTTTAAATCTAATT
*
2462949 AATCAAATTAATTAAATTTAATT
1 AATCAAATT--TTAAATCTAATT
2462972 TAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
AATCAAATTTTAAATCTAATT
Found at i:2462989 original size:28 final size:28
Alignment explanation
Indices: 2462958--2463011 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2462948 TAATCAAATT
* *
2462958 AATTAAATTTAATT-TAATTTATTTTTTC
1 AATTAAA-TCAATTATAATTAATTTTTTC
2462986 AATTAAATCAATTATAATTAATTTTT
1 AATTAAATCAATTATAATTAATTTTT
2463012 ATTCTTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTAAATCAATTATAATTAATTTTTTC
Found at i:2463188 original size:16 final size:17
Alignment explanation
Indices: 2463158--2463190 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2463148 TTTGAAATCA
2463158 AAATTAAATTTATTTAT
1 AAATTAAATTTATTTAT
2463175 AAATTAAA-TTATTTAT
1 AAATTAAATTTATTTAT
2463191 CTAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATTAAATTTATTTAT
Found at i:2463203 original size:20 final size:17
Alignment explanation
Indices: 2463158--2463204 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
2463148 TTTGAAATCA
*
2463158 AAATTAAATTTATTTAT
1 AAATTAAAATTATTTAT
2463175 AAATT-AAATTATTTATCT
1 AAATTAAAATTATTTA--T
2463193 AAATTTAAAATT
1 AAA-TTAAAATT
2463205 TTATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.36
17 5 0.20
18 4 0.16
19 2 0.08
20 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTAAAATTATTTAT
Found at i:2463869 original size:10 final size:10
Alignment explanation
Indices: 2463856--2463923 Score: 55
Period size: 10 Copynumber: 6.2 Consensus size: 10
2463846 TTTTTTTAAT
2463856 ATTTTAAAAA
1 ATTTTAAAAA
2463866 ATTTTAAATAAAA
1 ATTTT--A-AAAA
*
2463879 ATATTAAAAA
1 ATTTTAAAAA
*
2463889 ATTTAAAAATTA
1 ATTTTAAAA--A
2463901 ATTTTAAAAA
1 ATTTTAAAAA
*
2463911 ATTATATAAAA
1 ATTTTA-AAAA
2463922 AT
1 AT
2463924 AAATTAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
10 22 0.47
11 7 0.15
12 10 0.21
13 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:2463889 original size:23 final size:23
Alignment explanation
Indices: 2463859--2463927 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
2463849 TTTTAATATT
2463859 TTAAAAAATTTTAAATAA-AAATA
1 TTAAAAAATTTTAAA-AATAAATA
* *
2463882 TTAAAAAA-TTTAAAAATTAATT
1 TTAAAAAATTTTAAAAATAAATA
2463904 TTAAAAAATTATATAAAAATAAAT
1 TTAAAAAATT-T-TAAAAATAAAT
2463928 TAATATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.05
22 17 0.44
23 9 0.23
24 1 0.03
25 10 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAAAAAATTTTAAAAATAAATA
Found at i:2463930 original size:23 final size:23
Alignment explanation
Indices: 2463859--2463930 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
2463849 TTTTAATATT
*
2463859 TTAAAAAATTT-TAAATAAAAATA
1 TTAAAAAATTTATAAA-AATAATA
* *
2463882 TTAAAAAATTTA-AAAATTAATT
1 TTAAAAAATTTATAAAAATAATA
2463904 TTAAAAAATTATATAAAAATAA-A
1 TTAAAAAATT-TATAAAAATAATA
2463927 TTAA
1 TTAA
2463931 TATTTTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 14 0.34
23 20 0.49
24 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAAAAAATTTATAAAAATAATA
Found at i:2464000 original size:17 final size:17
Alignment explanation
Indices: 2463980--2464024 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 17
2463970 TAATAATTTA
2463980 AATTTTTTAA-AAAAATT
1 AATTTTTTAATAAAAA-T
2463997 AATTTTTTAACTTAAAAAT
1 AATTTTTTAA--TAAAAAT
2464016 AATTTTTTA
1 AATTTTTTA
2464025 TTTTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.40
19 10 0.40
20 5 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTTTTAATAAAAAT
Found at i:2464114 original size:30 final size:32
Alignment explanation
Indices: 2464078--2464149 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
2464068 TGATTCATGT
2464078 AAATTTAAATAAT-A-ATTTTAAATAAAAATA
1 AAATTTAAATAATCATATTTTAAATAAAAATA
* * *
2464108 AAATTT-ATTATTCATATTTTAAATAAACATA
1 AAATTTAAATAATCATATTTTAAATAAAAATA
* *
2464139 AACTTAAAATA
1 AAATTTAAATA
2464150 TTAAATATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 4 0.12
30 7 0.21
31 19 0.58
32 3 0.09
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATTTAAATAATCATATTTTAAATAAAAATA
Found at i:2467557 original size:30 final size:30
Alignment explanation
Indices: 2467521--2467612 Score: 139
Period size: 30 Copynumber: 3.1 Consensus size: 30
2467511 ACTAATTTAA
*
2467521 ATCCCTTAAATTAAGGATTAGTGCACCACT
1 ATCCCTTAAATTAAGGACTAGTGCACCACT
*
2467551 ATCCCTTAGATTAAGGACTAGTGCACCACT
1 ATCCCTTAAATTAAGGACTAGTGCACCACT
* * *
2467581 ATCTCTTAAATTAAGAACTAATGCACCACT
1 ATCCCTTAAATTAAGGACTAGTGCACCACT
2467611 AT
1 AT
2467613 TTAATTTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (30 bp):
ATCCCTTAAATTAAGGACTAGTGCACCACT
Found at i:2471116 original size:31 final size:31
Alignment explanation
Indices: 2471074--2471176 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
2471064 TTATCTAACA
*
2471074 AAATCAATCAGTAATGAAGGCTGACTGAATG
1 AAATAAATCAGTAATGAAGGCTGACTGAATG
* ** * *
2471105 AAATAAATCAGTGACAAAAGCTGATCT-AATA
1 AAATAAATCAGTAATGAAGGCTGA-CTGAATG
* *
2471136 AAATCAATCAGCAATGAAGGCTGACTGAATG
1 AAATAAATCAGTAATGAAGGCTGACTGAATG
2471167 AAATAAATCA
1 AAATAAATCA
2471177 ACGATAAAAG
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
30 2 0.04
31 52 0.93
32 2 0.04
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (31 bp):
AAATAAATCAGTAATGAAGGCTGACTGAATG
Found at i:2471163 original size:62 final size:62
Alignment explanation
Indices: 2471066--2471191 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
2471056 GCAACCAATT
* **
2471066 ATCTAACAAAATCAATCAGTAATGAAGGCTGACTGAATGAAATAAATCAGTGACAAAAGCTG
1 ATCTAACAAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGACAAAAGCTG
* *
2471128 ATCTAATAAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGATAAAAGCTG
1 ATCTAACAAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGACAAAAGCTG
2471190 AT
1 AT
2471192 TCAAAGAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (62 bp):
ATCTAACAAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGACAAAAGCTG
Found at i:2471190 original size:31 final size:31
Alignment explanation
Indices: 2471093--2471190 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 31
2471083 AGTAATGAAG
* *
2471093 GCTGACTGAATGAAATAAATCAGTGACAAAA
1 GCTGACTGAATGAAATAAATCAGCGATAAAA
* * * * *
2471124 GCTGATCT-AATAAAATCAATCAGCAATGAAG
1 GCTGA-CTGAATGAAATAAATCAGCGATAAAA
*
2471155 GCTGACTGAATGAAATAAATCAACGATAAAA
1 GCTGACTGAATGAAATAAATCAGCGATAAAA
2471186 GCTGA
1 GCTGA
2471191 TTCAAAGAGA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 2 0.04
31 48 0.92
32 2 0.04
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (31 bp):
GCTGACTGAATGAAATAAATCAGCGATAAAA
Found at i:2471472 original size:30 final size:30
Alignment explanation
Indices: 2471433--2471522 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
2471423 ATTTAAATCC
*
2471433 CTTAAATTAAGGACTAGTGCACCACTATCT
1 CTTAAATTAAGGACTAATGCACCACTATCT
* * * *
2471463 CTTAGATTAAAGACTAATACACCACTATCC
1 CTTAAATTAAGGACTAATGCACCACTATCT
2471493 CTTAAATTAAGGACTAATGCACCACTATCT
1 CTTAAATTAAGGACTAATGCACCACTATCT
2471523 AATTTAAATT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (30 bp):
CTTAAATTAAGGACTAATGCACCACTATCT
Found at i:2472160 original size:14 final size:14
Alignment explanation
Indices: 2472141--2472174 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2472131 ATGCTAAATG
2472141 CCTTAACTGCCATC
1 CCTTAACTGCCATC
*
2472155 CCTTAACTGCCATG
1 CCTTAACTGCCATC
2472169 CCTTAA
1 CCTTAA
2472175 ATGCTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.38, G:0.09, T:0.29
Consensus pattern (14 bp):
CCTTAACTGCCATC
Found at i:2473645 original size:4 final size:4
Alignment explanation
Indices: 2473630--2473673 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
2473620 GAAGTTCTTC
*
2473630 ATTT ACTT ATTT ATTT ATTT ATTT A-TT A-TT A-TT A-TT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2473674 TTATTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 12 0.32
4 25 0.68
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:2473651 original size:12 final size:11
Alignment explanation
Indices: 2473636--2473679 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
2473626 CTTCATTTAC
2473636 TTATTTATTTAT
1 TTATTTA-TTAT
2473648 TTATTTATTA-
1 TTATTTATTAT
2473658 TTA-TTATTAT
1 TTATTTATTAT
2473668 TTATTT-TTAT
1 TTATTTATTAT
2473678 TT
1 TT
2473680 TTTTGCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.20
10 12 0.40
11 5 0.17
12 7 0.23
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:2473655 original size:16 final size:15
Alignment explanation
Indices: 2473630--2473679 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 15
2473620 GAAGTTCTTC
*
2473630 ATTTACTTATTTATTT
1 ATTTATTTATTTA-TT
2473646 ATTTATTTA-TTATT
1 ATTTATTTATTTATT
2473660 A-TTA-TTATTTATT
1 ATTTATTTATTTATT
2473673 -TTTATTT
1 ATTTATTT
2473680 TTTTGCAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
12 3 0.10
13 11 0.37
14 5 0.17
15 3 0.10
16 8 0.27
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTATTTATTTATT
Found at i:2475362 original size:24 final size:24
Alignment explanation
Indices: 2475312--2475362 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
2475302 AATTTTAAAC
*
2475312 ATAAAATCAAAAATTAAAATATTA
1 ATAAAATCAAAAATTAAAATATAA
2475336 ATAAATAT-AAAAA-TAAAATAATAA
1 ATAAA-ATCAAAAATTAAAAT-ATAA
2475360 ATA
1 ATA
2475363 TTTAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.25
24 16 0.67
25 2 0.08
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (24 bp):
ATAAAATCAAAAATTAAAATATAA
Found at i:2475385 original size:6 final size:6
Alignment explanation
Indices: 2475360--2475436 Score: 56
Period size: 6 Copynumber: 13.2 Consensus size: 6
2475350 AAAATAATAA
* * *
2475360 ATATTT A-ATAT ATA-TT ATATTT ATATTT AAAATTT -TA-AT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT -ATATTT ATATTT ATATTT
*
2475405 AATAATTT AT-GTT ATATTT ATATTT ATATTT A
1 -AT-ATTT ATATTT ATATTT ATATTT ATATTT A
2475437 ATAAAAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
4 1 0.02
5 15 0.27
6 26 0.47
7 9 0.16
8 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (6 bp):
ATATTT
Found at i:2475985 original size:23 final size:22
Alignment explanation
Indices: 2475949--2476011 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
2475939 TAAATTTTTT
2475949 AATTTTATAAATATATTTAAAA
1 AATTTTATAAATATATTTAAAA
* *
2475971 AATTATTATATATATCTTTAAATA
1 AATT-TTATAAATATATTTAAA-A
* *
2475995 TATTTTAAAAATATATT
1 AATTTTATAAATATATT
2476012 ATTTTATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 4 0.12
23 25 0.76
24 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTTATAAATATATTTAAAA
Found at i:2480092 original size:14 final size:14
Alignment explanation
Indices: 2480073--2480100 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2480063 ATTTTATATT
2480073 TATATAAATTTTAA
1 TATATAAATTTTAA
2480087 TATATAAATTTTAA
1 TATATAAATTTTAA
2480101 AAAATATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:2480454 original size:3 final size:3
Alignment explanation
Indices: 2480446--2480474 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2480436 AAATTTAAGG
2480446 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2480475 TGGGTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2492174 original size:2 final size:2
Alignment explanation
Indices: 2492167--2492202 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2492157 TACTATGTTC
*
2492167 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2492203 CACGCATACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2496542 original size:156 final size:155
Alignment explanation
Indices: 2496258--2496565 Score: 589
Period size: 156 Copynumber: 2.0 Consensus size: 155
2496248 AAGTTCAACA
2496258 AGTTTCTTCACTACCAACAAGAAAAGAGTTCCCATTTGTGATTCCTGACACGGCAATACCTATGT
1 AGTTTCTTCACTACCAACAAGAAAAGAGTTCCCATTTGTGATTCCTGACACGGCAATACCTATGT
*
2496323 ACTCCTGAGAAACTCCCATCACCTTATGCCTGGAGTTTTATTAGAGAAACTCATTAAGTATAAAA
66 ACTCCTGAGAAACTCCCATCACCTTATGCCTGGAGTTTCATTAGAGAAACTCATTAAGTATAAAA
2496388 TCAAAGTACAGAACAAAAACTCTACG
131 TC-AAGTACAGAACAAAAACTCTACG
*
2496414 AGTTTCTTCACTACCAACAAGAAAAGAGTTCCCATTTGTGATTCCTGACACGGCAATTCCTATGT
1 AGTTTCTTCACTACCAACAAGAAAAGAGTTCCCATTTGTGATTCCTGACACGGCAATACCTATGT
2496479 ACTCCTGAGAAACTCCCATCACCTTATGCCTGGAGTTTCATTAGAGAAACTCATTAAGTATAAAA
66 ACTCCTGAGAAACTCCCATCACCTTATGCCTGGAGTTTCATTAGAGAAACTCATTAAGTATAAAA
2496544 TCAAGTACAGAACAAAAACTCT
131 TCAAGTACAGAACAAAAACTCT
2496566 CTAAATTAAC
Statistics
Matches: 150, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
155 20 0.13
156 130 0.87
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (155 bp):
AGTTTCTTCACTACCAACAAGAAAAGAGTTCCCATTTGTGATTCCTGACACGGCAATACCTATGT
ACTCCTGAGAAACTCCCATCACCTTATGCCTGGAGTTTCATTAGAGAAACTCATTAAGTATAAAA
TCAAGTACAGAACAAAAACTCTACG
Found at i:2498043 original size:2 final size:2
Alignment explanation
Indices: 2498038--2498078 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2498028 GTATGTGGGT
* * *
2498038 GA GA GA GA GA GA GA GA GA GA AA GA GA CA GA GA GA GA CA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2498079 CCAGAGGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2498083 original size:16 final size:16
Alignment explanation
Indices: 2498038--2498084 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2498028 GTATGTGGGT
* *
2498038 GAGAGAGAGAGAGAGA
1 GAGAAAGAGACAGAGA
2498054 GAGAAAGAGACAGAGA
1 GAGAAAGAGACAGAGA
* *
2498070 GAGACAGAGCCAGAG
1 GAGAAAGAGACAGAG
2498085 GGTCACGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.49, C:0.09, G:0.43, T:0.00
Consensus pattern (16 bp):
GAGAAAGAGACAGAGA
Found at i:2498314 original size:17 final size:16
Alignment explanation
Indices: 2498287--2498331 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
2498277 AAAATATTTT
*
2498287 TTAATAATAAAATAAA
1 TTAAAAATAAAATAAA
*
2498303 TTGAAAAATAAATTAAA
1 TT-AAAAATAAAATAAA
*
2498320 TTAAAATTAAAA
1 TTAAAAATAAAA
2498332 ATTGAATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
TTAAAAATAAAATAAA
Found at i:2498343 original size:23 final size:23
Alignment explanation
Indices: 2498300--2498344 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2498290 ATAATAAAAT
*
2498300 AAATTGAAAAATAAATTAAATTA
1 AAATTGAAAAATAAATCAAATTA
*
2498323 AAATT-AAAAATTGAATCAAATT
1 AAATTGAAAAA-TAAATCAAATT
2498345 TATTATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATTGAAAAATAAATCAAATTA
Found at i:2498518 original size:28 final size:30
Alignment explanation
Indices: 2498453--2498522 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
2498443 TAAAACTTAT
*
2498453 AAATATTTAAAATTTATATGGTTAAATATAA
1 AAATATTTAAAATATATAT-GTTAAATATAA
* *
2498484 ATATATTTAAAATATATAT-TT-TATATAA
1 AAATATTTAAAATATATATGTTAAATATAA
2498512 AAATATTTAAA
1 AAATATTTAAA
2498523 TATTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.46
29 2 0.06
31 17 0.49
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATATTTAAAATATATATGTTAAATATAA
Found at i:2498530 original size:18 final size:18
Alignment explanation
Indices: 2498509--2498575 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
2498499 ATATTTTATA
2498509 TAAAAATATTTAAATATT
1 TAAAAATATTTAAATATT
* * **
2498527 TAAAATTTTTTATTTATT
1 TAAAAATATTTAAATATT
*
2498545 TAAAAA-A--TATATATT
1 TAAAAATATTTAAATATT
2498560 TAAATATATATTTAAA
1 TAAA-A-ATATTTAAA
2498576 ATAAATATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
15 11 0.31
16 1 0.03
17 1 0.03
18 20 0.56
20 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAAAATATTTAAATATT
Found at i:2498566 original size:12 final size:12
Alignment explanation
Indices: 2498549--2498587 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2498539 TTTATTTAAA
2498549 AAATATATATTT
1 AAATATATATTT
2498561 AAATATATATTT
1 AAATATATATTT
*
2498573 AAAATAAATATTT
1 -AAATATATATTT
2498586 AA
1 AA
2498588 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATATATTT
Found at i:2498583 original size:13 final size:13
Alignment explanation
Indices: 2498548--2498587 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
2498538 ATTTATTTAA
2498548 AAAATATATATTT
1 AAAATATATATTT
2498561 -AAATATATATTT
1 AAAATATATATTT
*
2498573 AAAATAAATATTT
1 AAAATATATATTT
2498586 AA
1 AA
2498588 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATATATATTT
Found at i:2499220 original size:15 final size:15
Alignment explanation
Indices: 2499200--2499240 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2499190 TTAATTCGAT
2499200 TTATTTATTTAATTA
1 TTATTTATTTAATTA
2499215 TTATTTA-TTATATTA
1 TTATTTATTTA-ATTA
*
2499230 TT-TTAATTTAA
1 TTATTTATTTAA
2499241 AAATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTTATTTAATTA
Found at i:2499272 original size:21 final size:21
Alignment explanation
Indices: 2499243--2499285 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2499233 TAATTTAAAA
*
2499243 ATATTTTTAA-AATTAATATTT
1 ATATATTTAATAATTAA-ATTT
2499264 ATATATTTAATAATTAAATTT
1 ATATATTTAATAATTAAATTT
2499285 A
1 A
2499286 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATTTAATAATTAAATTT
Found at i:2499305 original size:20 final size:21
Alignment explanation
Indices: 2499282--2499322 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2499272 AATAATTAAA
2499282 TTTAAATAAAAATA-TATTAT
1 TTTAAATAAAAATATTATTAT
*
2499302 TTTAATTAAAAATATTATTAT
1 TTTAAATAAAAATATTATTAT
2499323 AAATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAATAAAAATATTATTAT
Found at i:2499318 original size:18 final size:20
Alignment explanation
Indices: 2499284--2499330 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2499274 TAATTAAATT
*
2499284 TAAATAAAAATATATTATT-
1 TAAATTAAAATATATTATTA
*
2499303 TTAATTAAAA-ATATTATTA
1 TAAATTAAAATATATTATTA
2499322 TAAATTAAA
1 TAAATTAAA
2499331 TTAACTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATTAAAATATATTATTA
Found at i:2500426 original size:34 final size:34
Alignment explanation
Indices: 2500381--2500457 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
2500371 ATGCTGCCCC
2500381 AATAT-AAATATAACA-AAAAAAAAT-TAAATATA
1 AATATAAAATATAACATAAAAAAAATAT-AATATA
* * *
2500413 TTATATAAAATATAATATAACAAAAATATAATATA
1 -AATATAAAATATAACATAAAAAAAATATAATATA
2500448 AATATAAAAT
1 AATATAAAAT
2500458 TATATATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 18 0.49
35 14 0.38
36 1 0.03
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (34 bp):
AATATAAAATATAACATAAAAAAAATATAATATA
Found at i:2500465 original size:39 final size:38
Alignment explanation
Indices: 2500381--2500470 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 38
2500371 ATGCTGCCCC
*
2500381 AATATA-AATATAACAAAAAAAAATTAAATATATTATAT
1 AATATATAATATAACAAAAAAAAATTAAATATA-TAAAT
* *
2500419 AAAATATAATATAACAAAAATATAATATAAATATA-AAAT
1 AATATATAATATAACAAAAA-AAAAT-TAAATATATAAAT
*
2500458 TATATATAATATA
1 AATATATAATATA
2500471 TATTATTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 5 0.11
39 27 0.61
40 4 0.09
41 8 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (38 bp):
AATATATAATATAACAAAAAAAAATTAAATATATAAAT
Found at i:2500503 original size:18 final size:16
Alignment explanation
Indices: 2500443--2500502 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
2500433 CAAAAATATA
2500443 ATATAAATATAAAATT
1 ATATAAATATAAAATT
*
2500459 ATATATAATAT-ATATT
1 ATATA-AATATAAAATT
2500475 AT-TAATATATTAAAATTT
1 ATATAA-ATA-TAAAA-TT
2500493 ATATAAATAT
1 ATATAAATAT
2500503 TTTATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 5 0.14
16 12 0.33
17 8 0.22
18 7 0.19
19 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAAATATAAAATT
Found at i:2500508 original size:11 final size:11
Alignment explanation
Indices: 2500436--2500508 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 11
2500426 AATATAACAA
*
2500436 AAATATAATAT
1 AAATATATTAT
2500447 AAATATA--A-
1 AAATATATTAT
*
2500455 AATTATA-TAT
1 AAATATATTAT
2500465 AATATATATTAT
1 AA-ATATATTAT
*
2500477 TAATATATTA-
1 AAATATATTAT
*
2500487 AAATTTA-TAT
1 AAATATATTAT
*
2500497 AAATATTTTAT
1 AAATATATTAT
2500508 A
1 A
2500509 TTTTAAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.12
9 4 0.08
10 12 0.24
11 23 0.47
12 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAATATATTAT
Found at i:2500520 original size:34 final size:32
Alignment explanation
Indices: 2500438--2500507 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
2500428 TATAACAAAA
*
2500438 ATATAATA-TAAATA-TAAAATTATATATAAT
1 ATATATTATTAAATATTAAAATTATATATAAT
2500468 ATATATTATTAATATATTAAAATT-TATATAA-
1 ATATATTATTAA-ATATTAAAATTATATATAAT
*
2500499 ATATTTTAT
1 ATATATTAT
2500508 ATTTTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 7 0.20
31 11 0.31
32 10 0.29
33 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATATATTATTAAATATTAAAATTATATATAAT
Found at i:2501233 original size:12 final size:12
Alignment explanation
Indices: 2501218--2501259 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2501208 GTTAAATTTG
*
2501218 ATAATATTATAT
1 ATAATATTAAAT
2501230 ATAATA-TAAAT
1 ATAATATTAAAT
2501241 ATAAT-TTAAAAT
1 ATAATATT-AAAT
2501253 ATAATAT
1 ATAATAT
2501260 AATAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 10 0.38
12 15 0.58
13 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAATATTAAAT
Found at i:2501274 original size:26 final size:26
Alignment explanation
Indices: 2501228--2501322 Score: 68
Period size: 28 Copynumber: 3.5 Consensus size: 26
2501218 ATAATATTAT
*
2501228 ATATAATATAAATATAATTTAAAATATA
1 ATATAATA-AAATAT-TTTTAAAATATA
* *
2501256 ATATAATAAAATATTTTTATAATTTA
1 ATATAATAAAATATTTTTAAAATATA
** * *
2501282 A-ATAATTTAA-ATTATTAATATCTCATA
1 ATATAATAAAATATTTTTAA-A-AT-ATA
2501309 ATATAATAAAATAT
1 ATATAATAAAATAT
2501323 AATTTTTATG
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
24 6 0.12
25 8 0.16
26 11 0.22
27 9 0.18
28 15 0.29
29 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATAATAAAATATTTTTAAAATATA
Found at i:2501615 original size:15 final size:15
Alignment explanation
Indices: 2501577--2501615 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2501567 TTTTGAATTA
2501577 ATAAAATAATATATT
1 ATAAAATAATATATT
***
2501592 ATTTTATAATATATT
1 ATAAAATAATATATT
2501607 ATAAAATAA
1 ATAAAATAA
2501616 AAATGAGATA
Statistics
Matches: 18, Mismatches: 6, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAAATAATATATT
Found at i:2503711 original size:15 final size:14
Alignment explanation
Indices: 2503686--2503720 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2503676 TAATCAAAAT
2503686 TTTATTTTAAATTTAA
1 TTTA-TTTAAATTT-A
2503702 TTTATTTAAATTTA
1 TTTATTTAAATTTA
2503716 TTTAT
1 TTTAT
2503721 GAATTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 9 0.47
16 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTATTTAAATTTA
Found at i:2504282 original size:15 final size:15
Alignment explanation
Indices: 2504264--2504299 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2504254 ATTATTAAAA
* *
2504264 TTATATTTATATATT
1 TTATATTAAAATATT
2504279 TTATATTAAAATATT
1 TTATATTAAAATATT
2504294 TTATAT
1 TTATAT
2504300 CGAAATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATTAAAATATT
Found at i:2504305 original size:15 final size:15
Alignment explanation
Indices: 2504274--2504307 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2504264 TTATATTTAT
*
2504274 ATATTTTATATTAAA
1 ATATTTTATATCAAA
*
2504289 ATATTTTATATCGAA
1 ATATTTTATATCAAA
2504304 ATAT
1 ATAT
2504308 GAGCACTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATTTTATATCAAA
Found at i:2504506 original size:24 final size:24
Alignment explanation
Indices: 2504446--2504515 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
2504436 ATACTCCTAC
2504446 TTTTTTTATAATATATTTTATAAAT
1 TTTTTTTATAA-ATATTTTATAAAT
* *
2504471 TTATTTTT-TAAATA-TTTATTACT
1 TT-TTTTTATAAATATTTTATAAAT
* *
2504494 TTTTTATTATAAAAATATTATA
1 TTTTT-TTATAAATATTTTATA
2504516 TATTGATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
22 3 0.08
23 11 0.31
24 8 0.22
25 9 0.25
26 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTTTTATAAATATTTTATAAAT
Found at i:2510318 original size:12 final size:11
Alignment explanation
Indices: 2510292--2510333 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
2510282 TTACATTAAC
2510292 ATTTTAT-ATA
1 ATTTTATAATA
2510302 ATTTTATAATCA
1 ATTTTATAAT-A
2510314 ATTTTA-AATA
1 ATTTTATAATA
2510324 ATTTTGATAA
1 ATTTT-ATAA
2510334 AATAAGATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 13 0.46
11 6 0.21
12 9 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
ATTTTATAATA
Found at i:2513472 original size:6 final size:6
Alignment explanation
Indices: 2513463--2513492 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2513453 ATTAGTCAAT
*
2513463 TCAGAT TCAGAA TCAGAA TCAGAA TCAGAA
1 TCAGAA TCAGAA TCAGAA TCAGAA TCAGAA
2513493 GTAATCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (6 bp):
TCAGAA
Found at i:2521762 original size:17 final size:18
Alignment explanation
Indices: 2521730--2521765 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2521720 TTTGATATGA
*
2521730 TTTATAAATATTTAATTT
1 TTTAAAAATATTTAATTT
2521748 TTTAAAAAT-TTTAATTT
1 TTTAAAAATATTTAATTT
2521765 T
1 T
2521766 AAGACTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAAAATATTTAATTT
Found at i:2523189 original size:14 final size:15
Alignment explanation
Indices: 2523118--2523197 Score: 69
Period size: 14 Copynumber: 5.2 Consensus size: 15
2523108 TTACTAAATT
2523118 TATATCAATAATTTATA
1 TATATC-AT-ATTTATA
2523135 TTATAT-ATATTT-TAA
1 -TATATCATATTTAT-A
*
2523150 AATATTCATATTATATA
1 TATA-TCATATT-TATA
2523167 TATATCATATTTATA
1 TATATCATATTTATA
2523182 TA-ATCATATTTA-A
1 TATATCATATTTATA
2523195 TAT
1 TAT
2523198 TATTATATCT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
13 3 0.06
14 14 0.26
15 12 0.22
16 14 0.26
17 5 0.09
18 6 0.11
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATCATATTTATA
Found at i:2523191 original size:36 final size:32
Alignment explanation
Indices: 2523126--2523205 Score: 78
Period size: 37 Copynumber: 2.5 Consensus size: 32
2523116 TTTATATCAA
2523126 TAAT-TTATAT-TATATATATTTTAAAATA-T
1 TAATATTATATATATATATATTTTAAAATATT
*
2523155 TCATATTATATATATATCATATTTATATAATCATATT
1 TAATATTATATATATAT-ATATTT-TA-AA--ATATT
2523192 TAATATTAT-TATAT
1 TAATATTATATATAT
2523206 CTACTAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 3 0.07
30 6 0.15
31 5 0.12
32 6 0.15
33 2 0.05
34 2 0.05
36 8 0.20
37 9 0.22
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (32 bp):
TAATATTATATATATATATATTTTAAAATATT
Found at i:2528302 original size:18 final size:18
Alignment explanation
Indices: 2528279--2528486 Score: 142
Period size: 18 Copynumber: 11.6 Consensus size: 18
2528269 CTGAATCTTC
*
2528279 CTCCAATTTCAAGTTCTG
1 CTCCAAGTTCAAGTTCTG
* *
2528297 CTCCAAGTCCACGTTCTG
1 CTCCAAGTTCAAGTTCTG
2528315 CTCCAAGTTCACA-TTCTG
1 CTCCAAGTTCA-AGTTCTG
* *
2528333 CTCC-ACTGTCACGTTCTG
1 CTCCAAGT-TCAAGTTCTG
** * *
2528351 CTCCAAGCCCATGTTCTT
1 CTCCAAGTTCAAGTTCTG
2528369 CTCCAAGTTCACA-TTCTG
1 CTCCAAGTTCA-AGTTCTG
* *
2528387 CTCC-ACTGTCACGTTCTG
1 CTCCAAGT-TCAAGTTCTG
*
2528405 CTCCAAGTTCAGGTTCTG
1 CTCCAAGTTCAAGTTCTG
* * *
2528423 CTCCAAGTTCATGCTGTG
1 CTCCAAGTTCAAGTTCTG
* * *
2528441 ATTCAAGTCCAAG-TCATG
1 CTCCAAGTTCAAGTTC-TG
2528459 CTCC-AGATTC-AGATTCTG
1 CTCCAAG-TTCAAG-TTCTG
2528477 CTCCAAGTTC
1 CTCCAAGTTC
2528487 CCAGGTTGTT
Statistics
Matches: 146, Mismatches: 31, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
17 9 0.06
18 130 0.89
19 7 0.05
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (18 bp):
CTCCAAGTTCAAGTTCTG
Found at i:2528367 original size:54 final size:54
Alignment explanation
Indices: 2528291--2528433 Score: 241
Period size: 54 Copynumber: 2.6 Consensus size: 54
2528281 CCAATTTCAA
2528291 GTTCTGCTCCAAGTCCACGTTCTGCTCCAAGTTCACATTCTGCTCCACTGTCAC
1 GTTCTGCTCCAAGTCCACGTTCTGCTCCAAGTTCACATTCTGCTCCACTGTCAC
* * *
2528345 GTTCTGCTCCAAGCCCATGTTCTTCTCCAAGTTCACATTCTGCTCCACTGTCAC
1 GTTCTGCTCCAAGTCCACGTTCTGCTCCAAGTTCACATTCTGCTCCACTGTCAC
* *
2528399 GTTCTGCTCCAAGTTCAGGTTCTGCTCCAAGTTCA
1 GTTCTGCTCCAAGTCCACGTTCTGCTCCAAGTTCA
2528434 TGCTGTGATT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.17, C:0.35, G:0.15, T:0.33
Consensus pattern (54 bp):
GTTCTGCTCCAAGTCCACGTTCTGCTCCAAGTTCACATTCTGCTCCACTGTCAC
Found at i:2534024 original size:3 final size:3
Alignment explanation
Indices: 2534016--2534050 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2534006 CACCATGGAA
2534016 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2534051 AGTTTCTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2535572 original size:3 final size:3
Alignment explanation
Indices: 2535564--2535593 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2535554 TTTTTATGCA
2535564 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2535594 TGTGTGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2537712 original size:11 final size:12
Alignment explanation
Indices: 2537695--2537728 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2537685 TTTATATCTT
2537695 TTTAAATTAAAA
1 TTTAAATTAAAA
*
2537707 -TTAAATAAAAA
1 TTTAAATTAAAA
2537718 TTTAAATTAAA
1 TTTAAATTAAA
2537729 TAATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTTAAATTAAAA
Found at i:2537718 original size:17 final size:17
Alignment explanation
Indices: 2537698--2537745 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
2537688 ATATCTTTTT
*
2537698 AAATTAAAATTAAATAA
1 AAATTTAAATTAAATAA
2537715 AAATTTAAATTAAATAA
1 AAATTTAAATTAAATAA
*
2537732 TAATTTAAATTAAA
1 AAATTTAAATTAAA
2537746 AAATTATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTAAATTAAATAA
Found at i:2538337 original size:3 final size:3
Alignment explanation
Indices: 2538329--2538354 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2538319 TGAGTGAGTT
2538329 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2538355 TTACAGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2538768 original size:28 final size:26
Alignment explanation
Indices: 2538711--2538823 Score: 92
Period size: 28 Copynumber: 4.2 Consensus size: 26
2538701 TATTATGTAT
*
2538711 TTAATAAATATAAA-A-TTAATATAA
1 TTAATATATATAAATATTTAATATAA
*
2538735 TAAATATGATATAAATATTTAAATATAA
1 TTAATAT-ATATAAATATTT-AATATAA
2538763 TTAATATA-ATAATATATTTAATATATA
1 TTAATATATATAA-ATATTTAATATA-A
*
2538790 TT-ATATTCATATTAAATTTTTTAATAT-A
1 TTAATA-T-ATA-TAAA-TATTTAATATAA
2538818 TTAATA
1 TTAATA
2538824 ATTTATATTA
Statistics
Matches: 73, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
24 5 0.07
25 7 0.10
26 14 0.19
27 13 0.18
28 17 0.23
29 5 0.07
30 12 0.16
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TTAATATATATAAATATTTAATATAA
Found at i:2538770 original size:9 final size:9
Alignment explanation
Indices: 2538724--2538792 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 9
2538714 ATAAATATAA
2538724 AATTAATAT
1 AATTAATAT
*
2538733 AATAAATAT
1 AATTAATAT
*
2538742 GATATAA-AT
1 AAT-TAATAT
*
2538751 ATTTAAATAT
1 AATT-AATAT
2538761 AATTAATAT
1 AATTAATAT
2538770 AA-TAATAT
1 AATTAATAT
*
2538778 ATTTAATAT
1 AATTAATAT
2538787 ATATTA
1 A-ATTA
2538793 TATTCATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
8 8 0.17
9 29 0.62
10 10 0.21
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (9 bp):
AATTAATAT
Found at i:2538776 original size:17 final size:18
Alignment explanation
Indices: 2538712--2538787 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 18
2538702 ATTATGTATT
2538712 TAATAAATATAAAATTAATA
1 TAATAAATAT--AATTAATA
*
2538732 TAATAAATATGATATAA-A
1 TAATAAATATAAT-TAATA
*
2538750 TATTTAAATATAATTAATA
1 TA-ATAAATATAATTAATA
*
2538769 TAAT-AATATATTTAATA
1 TAATAAATATAATTAATA
2538786 TA
1 TA
2538788 TATTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 14 0.29
18 9 0.19
19 15 0.31
20 10 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (18 bp):
TAATAAATATAATTAATA
Found at i:2540388 original size:22 final size:22
Alignment explanation
Indices: 2540350--2540393 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2540340 TTATTTTACT
*
2540350 AATTTTACTTATAAAATTTAAA
1 AATTTTACTTATAAAATATAAA
*
2540372 AATTTTA-TTAATGAAATATAAA
1 AATTTTACTT-ATAAAATATAAA
2540394 GTAATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTTTACTTATAAAATATAAA
Found at i:2540468 original size:2 final size:2
Alignment explanation
Indices: 2540463--2540490 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2540453 AATAACATAA
2540463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2540491 TGTAAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2542934 original size:15 final size:16
Alignment explanation
Indices: 2542911--2542961 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
2542901 TTAAGACACT
2542911 AAAATAGAAGAGA-GAG
1 AAAA-AGAAGAGAGGAG
**
2542927 AAAAAGAAGA-ATAAG
1 AAAAAGAAGAGAGGAG
*
2542942 AAGAAGAAGAGAGGAG
1 AAAAAGAAGAGAGGAG
2542958 AAAA
1 AAAA
2542962 GGGTTTCAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 1 0.04
15 17 0.61
16 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (16 bp):
AAAAAGAAGAGAGGAG
Found at i:2543426 original size:2 final size:2
Alignment explanation
Indices: 2543419--2543448 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2543409 AAAGTCTTTT
2543419 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2543449 AATGTTTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2546979 original size:21 final size:21
Alignment explanation
Indices: 2546940--2546980 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2546930 GCTGCTGGCA
*
2546940 AGGTGAAAGGTCGAGCAAAAC
1 AGGTGAAAGGGCGAGCAAAAC
2546961 AGGTGAAAGAGGCGA-CAAAA
1 AGGTGAAAG-GGCGAGCAAAA
2546981 GCTGCTCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.12, G:0.34, T:0.07
Consensus pattern (21 bp):
AGGTGAAAGGGCGAGCAAAAC
Found at i:2547708 original size:2 final size:2
Alignment explanation
Indices: 2547703--2547733 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2547693 TCTGTGTGTG
2547703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2547734 GTCTAGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2551416 original size:18 final size:18
Alignment explanation
Indices: 2551395--2551432 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2551385 TATATTTTTT
2551395 ATTTAAATTTA-ATTTAAA
1 ATTT-AATTTATATTTAAA
2551413 ATTTAATTTATTATTTAAA
1 ATTTAATTTA-TATTTAAA
2551432 A
1 A
2551433 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAATTTATATTTAAA
Found at i:2551921 original size:3 final size:3
Alignment explanation
Indices: 2551913--2551951 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2551903 CAAAAAACAT
2551913 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2551952 ACACAGGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2554603 original size:67 final size:67
Alignment explanation
Indices: 2554529--2554673 Score: 227
Period size: 67 Copynumber: 2.2 Consensus size: 67
2554519 TTTCAATGAC
* * * *
2554529 AAAAAAAAAAAACACTGGGTATGAATTGAAATGAAACAAAAGTTTAAGTGATCAAACAACAACTT
1 AAAAAAAAAAAAAACTAGGTATGAATTGAAACGAAACAAAAGTTAAAGTGATCAAACAACAACTT
2554594 AA
66 AA
*
2554596 AAAAAAAAAAAAAACTAGGTGTGAATTGAAACGAAACAAAAGTTAAAGTGATCAAACAACAACTT
1 AAAAAAAAAAAAAACTAGGTATGAATTGAAACGAAACAAAAGTTAAAGTGATCAAACAACAACTT
*
2554661 AC
66 AA
*
2554663 CAAAAAAAAAA
1 AAAAAAAAAAA
2554674 GCTGAAATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.60, C:0.11, G:0.12, T:0.17
Consensus pattern (67 bp):
AAAAAAAAAAAAAACTAGGTATGAATTGAAACGAAACAAAAGTTAAAGTGATCAAACAACAACTT
AA
Found at i:2556784 original size:13 final size:13
Alignment explanation
Indices: 2556766--2556790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2556756 TCGGTTTTTG
2556766 TTTCATATATTTC
1 TTTCATATATTTC
2556779 TTTCATATATTT
1 TTTCATATATTT
2556791 ACAATATACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCATATATTTC
Found at i:2568231 original size:16 final size:16
Alignment explanation
Indices: 2568213--2568246 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2568203 AAATTTATGT
2568213 AAATATAATTTAAAATA
1 AAAT-TAATTTAAAATA
*
2568230 AAATTAATTTTAAATA
1 AAATTAATTTAAAATA
2568246 A
1 A
2568247 TAAAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAATTTAAAATA
Found at i:2570312 original size:19 final size:21
Alignment explanation
Indices: 2570288--2570329 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
2570278 TTGATATGAA
2570288 AATTTTAA-ATAAAATA-AAT
1 AATTTTAACATAAAATATAAT
*
2570307 AATTTTAACATTAAATATAAT
1 AATTTTAACATAAAATATAAT
2570328 AA
1 AA
2570330 ATATTTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTTAACATAAAATATAAT
Found at i:2574309 original size:35 final size:35
Alignment explanation
Indices: 2574263--2574331 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
2574253 GACGGATAAC
*
2574263 AGACAGCAAAGTGCAAACTTCCTTGGATTCGGGGA
1 AGACAGCAAAGTGCAAACTTCCTTGAATTCGGGGA
2574298 AGACAGCAAAGTGCAAACTTCCTTGAATTCGGGG
1 AGACAGCAAAGTGCAAACTTCCTTGAATTCGGGG
2574332 GAGTAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (35 bp):
AGACAGCAAAGTGCAAACTTCCTTGAATTCGGGGA
Found at i:2576439 original size:25 final size:26
Alignment explanation
Indices: 2576411--2576460 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
2576401 TATAAATTCG
*
2576411 ATAATTTTAAACATAA-ATAA-AAAAT
1 ATAATATTAAA-ATAATATAATAAAAT
2576436 ATAATATTAAAATAATATAATAAAA
1 ATAATATTAAAATAATATAATAAAA
2576461 ATATTTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 14 0.64
26 4 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAATATTAAAATAATATAATAAAAT
Found at i:2576461 original size:14 final size:15
Alignment explanation
Indices: 2576423--2576463 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
2576413 AATTTTAAAC
2576423 ATAA-ATAAAA-AAT
1 ATAATATAAAATAAT
2576436 ATAATATTAAAATAAT
1 ATAATA-TAAAATAAT
2576452 ATAATA-AAAATA
1 ATAATATAAAATA
2576464 TTTAGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.16
14 7 0.28
15 5 0.20
16 9 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATATAAAATAAT
Found at i:2576676 original size:2 final size:2
Alignment explanation
Indices: 2576669--2576702 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2576659 TCTTATACAA
2576669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2576703 TTAAGTTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2582423 original size:17 final size:18
Alignment explanation
Indices: 2582387--2582424 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2582377 TGTATTTTAA
*
2582387 TTATATTTAAAATAATTT
1 TTATATTTAAAATAAATT
*
2582405 TTATATTT-ATATAAATT
1 TTATATTTAAAATAAATT
2582422 TTA
1 TTA
2582425 ATATATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATTTAAAATAAATT
Found at i:2582436 original size:18 final size:18
Alignment explanation
Indices: 2582380--2582436 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
2582370 ATTTTGTTGT
*
2582380 ATTTTAATTATATTTAAAATA
1 ATTTTAA-TATA-TTAATA-A
*
2582401 ATTTTTATAT-TTATATAA
1 ATTTTAATATATTA-ATAA
2582419 ATTTTAATATATTAATAA
1 ATTTTAATATATTAATAA
2582437 TTTATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 17 0.55
19 5 0.16
20 3 0.10
21 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATATATTAATAA
Found at i:2582454 original size:33 final size:35
Alignment explanation
Indices: 2582397--2582461 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
2582387 TTATATTTAA
* * *
2582397 AATAATTTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATATATATATATAAATTTGAATATATT
2582432 AATAATTTATATA-ATATA-AAATTTGAATAT
1 AATAATTTATATATATATATAAATTTGAATAT
2582462 TCTGTACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 11 0.41
34 4 0.15
35 12 0.44
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (35 bp):
AATAATTTATATATATATATAAATTTGAATATATT
Found at i:2582461 original size:18 final size:16
Alignment explanation
Indices: 2582412--2582461 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2582402 TTTTTATATT
*
2582412 TATATAAATTTTAATA
1 TATATAAAATTTAATA
2582428 TAT-TAATAATTT-ATA
1 TATATAA-AATTTAATA
2582443 TAATATAAAATTTGAATA
1 T-ATATAAAATTT-AATA
2582461 T
1 T
2582462 TCTGTACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 3 0.11
18 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TATATAAAATTTAATA
Found at i:2586413 original size:14 final size:13
Alignment explanation
Indices: 2586393--2586431 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
2586383 AATAACATGG
2586393 ATATAATATAATA
1 ATATAATATAATA
2586406 ATACTAATATAAT-
1 ATA-TAATATAATA
2586419 ATA-AATATAATA
1 ATATAATATAATA
2586431 A
1 A
2586432 AATATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.33
12 1 0.04
13 6 0.25
14 9 0.38
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAATATAATA
Done.