Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 24 of 31
Found at i:4936079 original size:3 final size:3
Alignment explanation
Indices: 4936071--4936102 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4936061 TATATCTCTT
4936071 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4936103 TTCTATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4937034 original size:2 final size:2
Alignment explanation
Indices: 4937027--4937074 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
4937017 ATTGTAGAAC
*
4937027 AT AT AT AT AT AT AT AT AT GT AT CAT AT CAT 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 AT AT AT AT
4937071 AT AT
1 AT AT
4937075 TGATCAATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 38 0.90
3 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4937326 original size:10 final size:12
Alignment explanation
Indices: 4937281--4937488 Score: 108
Period size: 11 Copynumber: 17.9 Consensus size: 12
4937271 ATAATATTAA
4937281 ATAAAATATAATT
1 ATAAAATATAA-T
*
4937294 ATATAATAATAACAT
1 ATAAAAT-AT-A-AT
4937309 GATAAAAT-TAAT
1 -ATAAAATATAAT
4937321 -TAAAATATAAT
1 ATAAAATATAAT
*
4937332 ATAAAAAATAAT
1 ATAAAATATAAT
4937344 A-AAAATA-ATAT
1 ATAAAATATA-AT
4937355 ATAAAA-A-AAT
1 ATAAAATATAAT
4937365 AT--AATATAAT
1 ATAAAATATAAT
*
4937375 GTAAAAT-TAAT
1 ATAAAATATAAT
4937386 AT-AAATATAAT
1 ATAAAATATAAT
*
4937397 ATATTAAA-AT-TT
1 ATA--AAATATAAT
*
4937409 ATATAATATAAT
1 ATAAAATATAAT
*
4937421 A-AATATATAAAT
1 ATAAAATAT-AAT
4937433 ATAAAATAT--T
1 ATAAAATATAAT
*
4937443 -TTAAATATAAT
1 ATAAAATATAAT
*
4937454 -TATAATATAAT
1 ATAAAATATAAT
* **
4937465 AAAAAATATACG
1 ATAAAATATAAT
4937477 ATAATAATATAA
1 ATAA-AATATAA
4937489 GAAGTGCAGA
Statistics
Matches: 150, Mismatches: 21, Indels: 48
0.68 0.10 0.22
Matches are distributed among these distances:
8 2 0.01
9 8 0.05
10 22 0.15
11 42 0.28
12 40 0.27
13 21 0.14
14 6 0.04
15 2 0.01
16 7 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:4937336 original size:22 final size:21
Alignment explanation
Indices: 4937310--4937399 Score: 92
Period size: 21 Copynumber: 4.1 Consensus size: 21
4937300 TAATAACATG
4937310 ATAAAATTAATTAAAATATAAT
1 ATAAAATTAA-TAAAATATAAT
*
4937332 ATAAAAAATAATAAAA-ATAAT
1 AT-AAAATTAATAAAATATAAT
** *
4937353 ATATAAAAAAATATAATATAAT
1 ATA-AAATTAATAAAATATAAT
*
4937375 GTAAAATTAATATAAATATAAT
1 ATAAAATTAATA-AAATATAAT
4937397 ATA
1 ATA
4937400 TTAAAATTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 24 0.43
22 24 0.43
23 7 0.12
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (21 bp):
ATAAAATTAATAAAATATAAT
Found at i:4937342 original size:12 final size:12
Alignment explanation
Indices: 4937312--4937373 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
4937302 ATAACATGAT
*
4937312 AAAATTAAT-TA
1 AAAAATAATATA
*
4937323 AAATATAATATA
1 AAAAATAATATA
4937335 AAAAATAATA-A
1 AAAAATAATATA
*
4937346 AAATAATATATAAA
1 AAA-AATA-ATATA
4937360 AAAATATAATATA
1 AAAA-ATAATATA
4937373 A
1 A
4937374 TGTAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 11 0.26
12 15 0.36
13 9 0.21
14 7 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:4937358 original size:16 final size:16
Alignment explanation
Indices: 4937339--4937392 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
4937329 AATATAAAAA
4937339 ATAATAAAAATAATAT
1 ATAATAAAAATAATAT
4937355 ATAA-AAAAAT-ATAAT
1 ATAATAAAAATAAT-AT
*
4937370 ATAATGTAAAATTAATAT
1 ATAA--TAAAAATAATAT
4937388 A-AATA
1 ATAATA
4937393 TAATATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
14 2 0.06
15 14 0.44
16 4 0.12
17 2 0.06
18 8 0.25
19 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
ATAATAAAAATAATAT
Found at i:4937393 original size:27 final size:25
Alignment explanation
Indices: 4937361--4937421 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
4937351 ATATATAAAA
4937361 AAATATAATATAATGTAAAATTAATAT
1 AAATATAATAT-AT-TAAAATTAATAT
*
4937388 AAATATAATATATTAAAATTTATAT
1 AAATATAATATATTAAAATTAATAT
4937413 -AATATAATA
1 AAATATAATA
4937422 AATATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 9 0.27
25 11 0.33
26 2 0.06
27 11 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
AAATATAATATATTAAAATTAATAT
Found at i:4937412 original size:19 final size:18
Alignment explanation
Indices: 4937325--4937436 Score: 62
Period size: 17 Copynumber: 6.6 Consensus size: 18
4937315 ATTAATTAAA
*
4937325 ATATAATATAAAAAATA-
1 ATATAATATAATAAATAT
* *
4937342 ATA-AAAATAATATATA-
1 ATATAATATAATAAATAT
* * *
4937358 AAAAAATATAATATAATGT
1 ATATAATATAATA-AATAT
*
4937377 A-A-AAT-TAAT--ATAA
1 ATATAATATAATAAATAT
* *
4937390 ATATAATATATTAAAATTT
1 ATATAATATAAT-AAATAT
4937409 ATATAATATAATAAATAT
1 ATATAATATAATAAATAT
4937427 ATA-AATATAA
1 ATATAATATAA
4937437 AATATTTTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 18
0.69 0.13 0.17
Matches are distributed among these distances:
13 3 0.04
14 1 0.01
15 3 0.04
16 19 0.26
17 21 0.29
18 11 0.15
19 14 0.19
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (18 bp):
ATATAATATAATAAATAT
Found at i:4937413 original size:41 final size:41
Alignment explanation
Indices: 4937274--4937463 Score: 137
Period size: 41 Copynumber: 4.6 Consensus size: 41
4937264 TATATTGATA
* * * *
4937274 ATATT-AAATAAAATATAATTATATAATAATA-ACATGATAAA
1 ATATTAAAATATAATATAA-TATAAAATAATATAAAT-ATAAT
4937315 ATTAATTAAAATATAATAT-A-A-AAAATAATA-AAA-ATAAT
1 A-T-ATTAAAATATAATATAATATAAAATAATATAAATATAAT
* *
4937353 ATATAAAAAAATATAATATAATGTAAAATTAATATAAATATAAT
1 ATAT--TAAAATATAATATAATATAAAA-TAATATAAATATAAT
* *
4937397 ATATTAAAAT-TTATATAATATAATAA-ATATATAAATATAAA
1 ATATTAAAATATAATATAATATAA-AATA-ATATAAATATAAT
*
4937438 ATATTTTAAATATAATTATAATATAA
1 ATA-TTAAAATATAA-TATAATATAA
4937464 TAAAAAATAT
Statistics
Matches: 121, Mismatches: 12, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
36 2 0.02
37 1 0.01
38 17 0.14
39 1 0.01
40 11 0.09
41 32 0.26
42 19 0.16
43 9 0.07
44 29 0.24
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (41 bp):
ATATTAAAATATAATATAATATAAAATAATATAAATATAAT
Found at i:4937461 original size:68 final size:65
Alignment explanation
Indices: 4937313--4937470 Score: 153
Period size: 68 Copynumber: 2.4 Consensus size: 65
4937303 TAACATGATA
* * *
4937313 AAAT-TAATTAAAATATAATATAAAAAATAATAAAAATAATATATAAAAAAATATAATATAATGT
1 AAATATAATTATAATATAATATAAAAAATAATAAAAATAATAAATAAAAAAATATAAAATAATGT
* * * * *
4937377 AAA-ATTAA-TATAAATATAATATATTAAAATTTATATAATATAATAAATATATAAATATAAAAT
1 AAATA-TAATTAT-AATATAATATA--AAAAATAATA-AAAATAATAAATAAAAAAATATAAAAT
* *
4937440 ATTTT
61 AATGT
4937445 AAATATAATTATAATATAATA-AAAAA
1 AAATATAATTATAATATAATATAAAAA
4937471 TATACGATAA
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
64 5 0.07
65 18 0.24
67 9 0.12
68 40 0.53
69 4 0.05
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (65 bp):
AAATATAATTATAATATAATATAAAAAATAATAAAAATAATAAATAAAAAAATATAAAATAATGT
Found at i:4939093 original size:2 final size:2
Alignment explanation
Indices: 4939086--4939120 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4939076 TAATATTAAC
4939086 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
4939121 AATTCTAGAC
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:4939375 original size:3 final size:3
Alignment explanation
Indices: 4939367--4939395 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4939357 AAGAAAAAAT
4939367 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4939396 TTGTAAATGT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4944258 original size:187 final size:187
Alignment explanation
Indices: 4943943--4944316 Score: 615
Period size: 187 Copynumber: 2.0 Consensus size: 187
4943933 CAACTGGGGC
* *
4943943 CTCTGTTACTCCAGTTTTCTTCTTTAAACACTCTAATGGTGTGGAGAACTTAAGTAAACCCTAAT
1 CTCTGTTACTCCAGTTTTCTTCTTTAAACACTCTAATGGTGTAGAGAACTTAAGCAAACCCTAAT
*
4944008 ATTTGTCATGCTGGCTAGTTGGTTGCCTTCTGTCCTGCTTGTGTTTATGAGTGATCAGGCAGGTT
66 ATTTGTCATGCTGGCTAGTTGGTTGCCTTCTGTCCTGCTTGTGTTTATGAGTGATAAGGCAGGTT
* *
4944073 ACCTATTGGTATGTTGTAGTCATATTCTGTTCTGCTTGGCTATTTGAATTTAGCATT
131 ACCTACTGGTATCTTGTAGTCATATTCTGTTCTGCTTGGCTATTTGAATTTAGCATT
** * *
4944130 CTCTGTTACTTTAGTTTTCTTCTTTATACACTTTAATGGTGTAGAGAACTTAAGCAAACCCTAAT
1 CTCTGTTACTCCAGTTTTCTTCTTTAAACACTCTAATGGTGTAGAGAACTTAAGCAAACCCTAAT
* *
4944195 ATTTTTCATGCTGGCTAGTTGGTTGCCTTCTGTCCTGCTTGTTTTTATGA-TGGATAAGGCAGGT
66 ATTTGTCATGCTGGCTAGTTGGTTGCCTTCTGTCCTGCTTGTGTTTATGAGT-GATAAGGCAGGT
**
4944259 TTTCTACTGGTATCTTGTAGTCATATTCTGTTCTGCTTGGCTATTTGAATTTAGCATT
130 TACCTACTGGTATCTTGTAGTCATATTCTGTTCTGCTTGGCTATTTGAATTTAGCATT
4944317 TGTTGAGCAT
Statistics
Matches: 173, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
186 1 0.01
187 172 0.99
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (187 bp):
CTCTGTTACTCCAGTTTTCTTCTTTAAACACTCTAATGGTGTAGAGAACTTAAGCAAACCCTAAT
ATTTGTCATGCTGGCTAGTTGGTTGCCTTCTGTCCTGCTTGTGTTTATGAGTGATAAGGCAGGTT
ACCTACTGGTATCTTGTAGTCATATTCTGTTCTGCTTGGCTATTTGAATTTAGCATT
Found at i:4945845 original size:21 final size:21
Alignment explanation
Indices: 4945819--4945886 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
4945809 GGCTAGGTTA
4945819 TCAGCAGATAGCAAATTTTTC
1 TCAGCAGATAGCAAATTTTTC
* ** * *
4945840 TCAGCAG--AGGAGGTTAGGTTA
1 TCAGCAGATAGCAAATT--TTTC
4945861 TCAGCAGATAGCAAATTTTTC
1 TCAGCAGATAGCAAATTTTTC
4945882 TCAGC
1 TCAGC
4945887 GATGTTGTAA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 5 0.15
21 23 0.70
23 5 0.15
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (21 bp):
TCAGCAGATAGCAAATTTTTC
Found at i:4945862 original size:42 final size:42
Alignment explanation
Indices: 4945803--4945886 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
4945793 CTGATAGTTT
4945803 AGAGGAGGCTAGGTTATCAGCAGATAGCAAATTTTTCTCAGC
1 AGAGGAGGCTAGGTTATCAGCAGATAGCAAATTTTTCTCAGC
*
4945845 AGAGGAGGTTAGGTTATCAGCAGATAGCAAATTTTTCTCAGC
1 AGAGGAGGCTAGGTTATCAGCAGATAGCAAATTTTTCTCAGC
4945887 GATGTTGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (42 bp):
AGAGGAGGCTAGGTTATCAGCAGATAGCAAATTTTTCTCAGC
Found at i:4952356 original size:22 final size:21
Alignment explanation
Indices: 4952331--4952372 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
4952321 AGAAAATATA
4952331 TTAAAATAAAAATTTAAATTAT
1 TTAAAATAAAAA-TTAAATTAT
*
4952353 TTAAAATTAAAATTAAATTA
1 TTAAAATAAAAATTAAATTA
4952373 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAAATAAAAATTAAATTAT
Found at i:4956175 original size:20 final size:21
Alignment explanation
Indices: 4956133--4956177 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4956123 TTAAAGTGTG
* * *
4956133 ATTTTTTTTTCATAAATATTA
1 ATTTTTTATTCATAAAGAATA
4956154 ATTTTTTATTCA-AAAGAATA
1 ATTTTTTATTCATAAAGAATA
4956174 ATTT
1 ATTT
4956178 ATGATTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTTATTCATAAAGAATA
Found at i:4958955 original size:2 final size:2
Alignment explanation
Indices: 4958948--4958974 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4958938 GAAATCATAC
4958948 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
4958975 GTGCATATAG
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:4960360 original size:27 final size:29
Alignment explanation
Indices: 4960330--4960389 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
4960320 TTTTTATATA
* *
4960330 TTATTATGTTTTAA-TT-TTTTAAATTTT
1 TTATTATATCTTAACTTATTTTAAATTTT
*
4960357 TTATTATATCTTAACTTATTTTATATTTT
1 TTATTATATCTTAACTTATTTTAAATTTT
4960386 TTAT
1 TTAT
4960390 AATTTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 12 0.43
28 2 0.07
29 14 0.50
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (29 bp):
TTATTATATCTTAACTTATTTTAAATTTT
Found at i:4960498 original size:19 final size:20
Alignment explanation
Indices: 4960454--4960499 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
4960444 AATATAAAAA
4960454 ATTATTTAAATAATTTATTAT
1 ATTA-TTAAATAATTTATTAT
*
4960475 ATTATTAATTAATTT-TTAT
1 ATTATTAAATAATTTATTAT
*
4960494 TTTATT
1 ATTATT
4960500 TTTAATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 10 0.43
21 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTATTAAATAATTTATTAT
Found at i:4961360 original size:16 final size:17
Alignment explanation
Indices: 4961339--4961375 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
4961329 TATACACTTT
4961339 AAAATATAAAAA-AA-TA
1 AAAATA-AAAAATAATTA
4961355 AAAATAAAAAATAATTA
1 AAAATAAAAAATAATTA
4961372 AAAA
1 AAAA
4961376 ATAGTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 8 0.42
17 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATAAAAAATAATTA
Found at i:4961519 original size:15 final size:15
Alignment explanation
Indices: 4961499--4961528 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4961489 CTTTTTTAAA
4961499 AATTAAATTAAAAAT
1 AATTAAATTAAAAAT
*
4961514 AATTAATTTAAAAAT
1 AATTAAATTAAAAAT
4961529 TTAAATATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAAATTAAAAAT
Found at i:4961975 original size:2 final size:2
Alignment explanation
Indices: 4961970--4962001 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4961960 ACATACATAT
4961970 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4962002 GATGATCTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4962445 original size:15 final size:14
Alignment explanation
Indices: 4962425--4962474 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
4962415 ATATTTAAAT
4962425 ATTATAAATAATTAA
1 ATTATAAATAATT-A
*
4962440 ATTATAACA-ATTTTA
1 ATTATAA-ATA-ATTA
4962455 ATTATAAATAA-TA
1 ATTATAAATAATTA
4962468 ATTATAA
1 ATTATAA
4962475 TCATCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 9 0.30
14 1 0.03
15 17 0.57
16 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTATAAATAATTA
Found at i:4963411 original size:7 final size:7
Alignment explanation
Indices: 4963401--4963435 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
4963391 TAGTTGGCTT
4963401 TTGGAAC
1 TTGGAAC
4963408 TTGGAAC
1 TTGGAAC
4963415 TTGGAAC
1 TTGGAAC
4963422 TTGGAAC
1 TTGGAAC
4963429 TTGGAAC
1 TTGGAAC
4963436 AAGAACATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
TTGGAAC
Found at i:4965532 original size:15 final size:14
Alignment explanation
Indices: 4965512--4965564 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
4965502 AATCGATTTA
4965512 AAATTAATTAAATCT
1 AAATTAATTAAAT-T
* *
4965527 AAATTAATCAACTT
1 AAATTAATTAAATT
* *
4965541 AATTTATATAAAATT
1 AAATTA-ATTAAATT
4965556 AAATTAATT
1 AAATTAATT
4965565 TTTTTATAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTAATTAAATT
Found at i:4965842 original size:2 final size:2
Alignment explanation
Indices: 4965835--4965867 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4965825 TCTTGTCTAG
4965835 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 A
4965868 ATTATGGCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4969444 original size:2 final size:2
Alignment explanation
Indices: 4969437--4969532 Score: 60
Period size: 2 Copynumber: 51.0 Consensus size: 2
4969427 ATAAAATAAA
* *
4969437 AT AT AT AT -T A- AT AT AT A- AT AT AA AT AT AT AA AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
4969475 A- AA AT TT AT AT AA AT AT A- AT AT AT AT AT AT AT AA AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
4969515 AA AA AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT
4969533 GTATTGTGGG
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
1 6 0.08
2 65 0.92
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:4969449 original size:31 final size:30
Alignment explanation
Indices: 4969414--4969502 Score: 96
Period size: 29 Copynumber: 3.0 Consensus size: 30
4969404 ACCAAAAAAA
4969414 TAATAATTTATGTATAAA-ATAAAATATATAT
1 TAATAATTTA--TATAAATATAAAATATATAT
* *
4969445 TAAT-ATATAATATAAATATATAA-ATATAT
1 TAATAAT-TTATATAAATATAAAATATATAT
*
4969474 TAA-AATTTATATAAATATAATATATATAT
1 TAATAATTTATATAAATATAAAATATATAT
4969503 ATATAAATAC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
28 13 0.27
29 23 0.47
30 7 0.14
31 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (30 bp):
TAATAATTTATATAAATATAAAATATATAT
Found at i:4969479 original size:41 final size:42
Alignment explanation
Indices: 4969432--4969532 Score: 131
Period size: 41 Copynumber: 2.5 Consensus size: 42
4969422 TATGTATAAA
*
4969432 ATAAAATATATATTAATATATAATATA-A-ATATATAAATAT
1 ATAAAATATATATTAATATATAATATATATATATATAAATAC
*
4969472 ATTAAAATTTATA-TAA-ATATAATATATATATATATAAATAC
1 A-TAAAATATATATTAATATATAATATATATATATATAAATAC
*
4969513 ATAAAA-ATATATAAATATAT
1 ATAAAATATATATTAATATAT
4969533 GTATTGTGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
39 14 0.27
40 12 0.23
41 26 0.50
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (42 bp):
ATAAAATATATATTAATATATAATATATATATATATAAATAC
Found at i:4969503 original size:39 final size:40
Alignment explanation
Indices: 4969432--4969531 Score: 125
Period size: 39 Copynumber: 2.5 Consensus size: 40
4969422 TATGTATAAA
4969432 ATAAAATATATATTAATATATAATATAAATATATA-AATATA-
1 ATAAAATATATA-TAA-ATATAATATAAATATATATAA-ATAC
* * *
4969473 TTAAAATTTATATAAATATAATATATATATATATAAATAC
1 ATAAAATATATATAAATATAATATAAATATATATAAATAC
4969513 ATAAAA-ATATATAAATATA
1 ATAAAATATATATAAATATA
4969532 TGTATTGTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
39 32 0.62
40 10 0.19
41 10 0.19
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (40 bp):
ATAAAATATATATAAATATAATATAAATATATATAAATAC
Found at i:4970208 original size:20 final size:19
Alignment explanation
Indices: 4970166--4970212 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
4970156 TATATAAGTG
* **
4970166 TAAATATATATGATAATTT
1 TAAATATATATGAAAATAA
4970185 TAAATATGATATGAAAATAA
1 TAAATAT-ATATGAAAATAA
4970205 TAAATATA
1 TAAATATA
4970213 ATAATATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (19 bp):
TAAATATATATGAAAATAA
Found at i:4970247 original size:35 final size:35
Alignment explanation
Indices: 4970168--4970248 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
4970158 TATAAGTGTA
* *
4970168 AATATATATGATAATTTTAAATATGATATGAAAAT
1 AATATATATAATAATTATAAATATGATATGAAAAT
* *
4970203 AATAAATATAATAA-TATAAATATGAATATG-ATAT
1 AATATATATAATAATTATAAATATG-ATATGAAAAT
4970237 AATGATATATAA
1 AAT-ATATATAA
4970249 ATATGTATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
34 15 0.38
35 24 0.62
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (35 bp):
AATATATATAATAATTATAAATATGATATGAAAAT
Found at i:4973627 original size:20 final size:21
Alignment explanation
Indices: 4973580--4973621 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4973570 TTTAAATAAA
4973580 AAAATTAAAATATAAATTTTT
1 AAAATTAAAATATAAATTTTT
*
4973601 AAAATTAAAATA-AATTTTTT
1 AAAATTAAAATATAAATTTTT
4973621 A
1 A
4973622 TTATTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTAAAATATAAATTTTT
Found at i:4973980 original size:22 final size:22
Alignment explanation
Indices: 4973949--4974003 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
4973939 TAATTTTATT
*
4973949 TATTTATTTAAAGTTTAAAATA
1 TATTTATTTAAAATTTAAAATA
* *
4973971 TATTTTTTTAAAATTTAATATA
1 TATTTATTTAAAATTTAAAATA
*
4973993 TAATATATTTA
1 T-ATTTATTTA
4974004 TTTTTATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTATTTAAAATTTAAAATA
Found at i:4975045 original size:2 final size:2
Alignment explanation
Indices: 4975040--4975079 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4975030 TATATAAGAA
4975040 AT AT AT 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 AT AT AT
4975080 TCAGTTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4976488 original size:27 final size:30
Alignment explanation
Indices: 4976459--4976526 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 30
4976449 TTATTCTAGA
*
4976459 TTTAATA-ATTTAATAAT-TTAT-ATTTTA
1 TTTAATATATTTAATAATATTATAATTATA
*
4976486 TTT-ATATATTTTATAATATTATAATTATA
1 TTTAATATATTTAATAATATTATAATTATA
*
4976515 TTTAAAATATTT
1 TTTAATATATTT
4976527 TATATTTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 3 0.09
27 12 0.35
28 4 0.12
29 8 0.24
30 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTAATATATTTAATAATATTATAATTATA
Found at i:4976531 original size:16 final size:16
Alignment explanation
Indices: 4976510--4976612 Score: 52
Period size: 16 Copynumber: 6.4 Consensus size: 16
4976500 AATATTATAA
4976510 TTATATTTAAAATATT
1 TTATATTTAAAATATT
4976526 TTATATTTTACTAAAT-TT
1 TTATA-TTTA--AAATATT
* * *
4976544 TGATACGTT--AATAAT
1 TTATA-TTTAAAATATT
*
4976559 TTATATTATATAA-ATT
1 TTATATT-TAAAATATT
* * *
4976575 TTATATTTATATTATA
1 TTATATTTAAAATATT
* *
4976591 TCATATTTTAAATATT
1 TTATATTTAAAATATT
4976607 TTATAT
1 TTATAT
4976613 GTGTTTTATT
Statistics
Matches: 64, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
14 4 0.06
15 10 0.16
16 32 0.50
17 6 0.09
18 8 0.12
19 4 0.06
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:4976585 original size:22 final size:23
Alignment explanation
Indices: 4976557--4976600 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
4976547 TACGTTAATA
4976557 ATTTATATTATAT-AAATTTTAT
1 ATTTATATTATATCAAATTTTAT
*
4976579 ATTTATATTATATCATATTTTA
1 ATTTATATTATATCAAATTTTA
4976601 AATATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTATATTATATCAAATTTTAT
Found at i:4976586 original size:17 final size:17
Alignment explanation
Indices: 4976510--4976586 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 17
4976500 AATATTATAA
4976510 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
4976526 TTATATTT-TACTAAATT
1 TTATATTTATA-TAAATT
*
4976543 TTGATACGTTA-AT-AA-T
1 TT-ATA-TTTATATAAATT
4976559 TTATA-TTATATAAATT
1 TTATATTTATATAAATT
4976575 TTATATTTATAT
1 TTATATTTATAT
4976587 TATATCATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 19
0.71 0.01 0.27
Matches are distributed among these distances:
13 3 0.06
14 2 0.04
15 5 0.10
16 18 0.36
17 13 0.26
18 6 0.12
19 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:4978405 original size:2 final size:2
Alignment explanation
Indices: 4978398--4978423 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4978388 TGATTGGCTC
4978398 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
4978424 GCTTTTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4979607 original size:16 final size:15
Alignment explanation
Indices: 4979586--4979646 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
4979576 TACTCAAATC
4979586 TAAATTTTAAATAATA
1 TAAA-TTTAAATAATA
*
4979602 TAAATTTAATATGATA
1 TAAATTTAA-ATAATA
*
4979618 TAAATTTGAAATAATT
1 TAAATTT-AAATAATA
*
4979634 TGAATTTAAATAA
1 TAAATTTAAATAA
4979647 CTATTATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
15 11 0.28
16 26 0.67
17 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (15 bp):
TAAATTTAAATAATA
Found at i:4981214 original size:4 final size:4
Alignment explanation
Indices: 4981195--4981253 Score: 75
Period size: 4 Copynumber: 14.8 Consensus size: 4
4981185 TATTCTAATA
* * *
4981195 AAAT AAAG AAAG AAAT AAAT AAAAT AAA- ATAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
4981243 AAAT AAAT AAA
1 AAAT AAAT AAA
4981254 AATACATATG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 2 0.04
4 43 0.88
5 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:4982145 original size:29 final size:30
Alignment explanation
Indices: 4982113--4982177 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
4982103 TAAAAAGTTA
*
4982113 TTATATTTTTA-TTATACTC-AAATAAGTCT
1 TTATATTTTAATTTATA-TCAAAATAAGTCT
* * *
4982142 TTATACTTTAATTTGTATCAAAATAAGTTT
1 TTATATTTTAATTTATATCAAAATAAGTCT
4982172 TTATAT
1 TTATAT
4982178 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (30 bp):
TTATATTTTAATTTATATCAAAATAAGTCT
Found at i:4982287 original size:30 final size:28
Alignment explanation
Indices: 4982253--4982340 Score: 77
Period size: 30 Copynumber: 3.0 Consensus size: 28
4982243 GAACGATTGC
4982253 TAAAAATTAAAAATTTATTTGAGTATAAAA
1 TAAAAATTAAAAATTTATTTGA--ATAAAA
* * * *
4982283 TAAAAGTTAAGAACTTATTTGAATATAA
1 TAAAAATTAAAAATTTATTTGAATAAAA
* * * *
4982311 TAAAATTTTAAAGATTTATTTTAAAAAAA
1 TAAAA-ATTAAAAATTTATTTGAATAAAA
4982340 T
1 T
4982341 TGCAAAGTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 10 0.22
29 17 0.37
30 19 0.41
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (28 bp):
TAAAAATTAAAAATTTATTTGAATAAAA
Found at i:4987466 original size:2 final size:2
Alignment explanation
Indices: 4987459--4987486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4987449 AATACATAAA
4987459 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
4987487 TTTTCATTTT
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:4990392 original size:58 final size:58
Alignment explanation
Indices: 4990322--4990438 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
4990312 GTTCAAGCTC
4990322 TGGCTATCAGATTCCGTAGCTGCTATATTTTTATGTGTGAAATTGCAAGACCATGGAA
1 TGGCTATCAGATTCCGTAGCTGCTATATTTTTATGTGTGAAATTGCAAGACCATGGAA
*
4990380 TGGCTATCAGATTCCGTAGCTGCTATTTTTTTATGTGTGAAATTGCAAGACCATGGAA
1 TGGCTATCAGATTCCGTAGCTGCTATATTTTTATGTGTGAAATTGCAAGACCATGGAA
4990438 T
1 T
4990439 AATTCGAAGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (58 bp):
TGGCTATCAGATTCCGTAGCTGCTATATTTTTATGTGTGAAATTGCAAGACCATGGAA
Found at i:4990903 original size:20 final size:23
Alignment explanation
Indices: 4990878--4990922 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
4990868 TATATCTGTT
4990878 ATAAAAATA-A-ATATAA-TATA
1 ATAAAAATACATATATAATTATA
4990898 ATAAAAATACATATATAATTATA
1 ATAAAAATACATATATAATTATA
4990921 AT
1 AT
4990923 TTAAATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 6 0.27
23 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAAAATACATATATAATTATA
Found at i:4991710 original size:121 final size:120
Alignment explanation
Indices: 4991439--4991750 Score: 401
Period size: 121 Copynumber: 2.6 Consensus size: 120
4991429 ATCTAATACT
* * *
4991439 TAAATAATTAAAATTATCCATTTAAATAATTAAATTTTAAGATTTGAAG-TCAAACTACATTATC
1 TAAATAATTATAATTATCTATTTAAATAATTAAATTTTAAGA-TTCAAGATCAAACTACATTA--
* * *
4991503 TACCTTTGTTATCCAATAATTAAATAATTAAGCATATGTAACTGGAATCCTTCCTAAAC
63 T-CCTTTGTTATCCAATAATTAAATAATTAAGCATATCTAACTAGAATCCTTCATAAAC
* *
4991562 TAAATAATTATAATTATCTATTTAAATAATTAAATTTCAAGATTCAAGATCAAACCACATTATCC
1 TAAATAATTATAATTATCTATTTAAATAATTAAATTTTAAGATTCAAGATCAAACTACATTATCC
* * * * * *
4991627 TTTGTTATCTAGTAATTAAATAATTAAGCTTTATCTCAGTAGATTCCTTCATAAAC
66 TTTGTTATCCAATAATTAAATAATTAAGC-ATATCTAACTAGAATCCTTCATAAAC
* * * * *
4991683 TCAATAATTATAATTATCTATTTAAATAGTTAAATTTTAAGATTTAAAAACAAACTACATTATCC
1 TAAATAATTATAATTATCTATTTAAATAATTAAATTTTAAGATTCAAGATCAAACTACATTATCC
4991748 TTT
66 TTT
4991751 TTTGTTATTA
Statistics
Matches: 166, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
120 29 0.17
121 81 0.49
122 5 0.03
123 51 0.31
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (120 bp):
TAAATAATTATAATTATCTATTTAAATAATTAAATTTTAAGATTCAAGATCAAACTACATTATCC
TTTGTTATCCAATAATTAAATAATTAAGCATATCTAACTAGAATCCTTCATAAAC
Found at i:4994024 original size:20 final size:20
Alignment explanation
Indices: 4993999--4994042 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4993989 GTTAAACGTT
*
4993999 ACATTAGAATGGTCAAAGCC
1 ACATTAGAATGATCAAAGCC
* *
4994019 ACATTAGAATTATCAAAGTC
1 ACATTAGAATGATCAAAGCC
4994039 ACAT
1 ACAT
4994043 CGTTAGCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (20 bp):
ACATTAGAATGATCAAAGCC
Found at i:4994275 original size:25 final size:25
Alignment explanation
Indices: 4994241--4994315 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
4994231 GAAAGGGAAG
4994241 GAAAGGGAAAGGGGAAGTAGAAACA
1 GAAAGGGAAAGGGGAAGTAGAAACA
* * *
4994266 GAAAGGGAAAGAGGAAAG-AAAAAGA
1 GAAAGGGAAAG-GGGAAGTAGAAACA
* *
4994291 GAAAGAGAAA-AGGAGAGTAGAAACA
1 GAAAGGGAAAGGGGA-AGTAGAAACA
4994316 ACTATTTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 30 0.77
26 5 0.13
ACGTcount: A:0.59, C:0.03, G:0.36, T:0.03
Consensus pattern (25 bp):
GAAAGGGAAAGGGGAAGTAGAAACA
Found at i:4994282 original size:19 final size:19
Alignment explanation
Indices: 4994247--4994297 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
4994237 GAAGGAAAGG
*
4994247 GAAAGGGGAAGTA-GAAACA
1 GAAAGGGAAAG-AGGAAACA
*
4994266 GAAAGGGAAAGAGGAAAGA
1 GAAAGGGAAAGAGGAAACA
* *
4994285 AAAAGAGAAAGAG
1 GAAAGGGAAAGAG
4994298 AAAAGGAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.59, C:0.02, G:0.37, T:0.02
Consensus pattern (19 bp):
GAAAGGGAAAGAGGAAACA
Found at i:4994537 original size:21 final size:20
Alignment explanation
Indices: 4994496--4994543 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
4994486 TTTCATAATA
*
4994496 AAATATATATTATATACATAT
1 AAATATAT-TTAAATACATAT
*
4994517 AAATATATTTAAAT-TATAT
1 AAATATATTTAAATACATAT
*
4994536 ATATATAT
1 AAATATAT
4994544 GTTTATATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATATTTAAATACATAT
Found at i:4995181 original size:2 final size:2
Alignment explanation
Indices: 4995174--4995199 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4995164 CTGAATATGC
4995174 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
4995200 ACTCCCACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4997903 original size:6 final size:6
Alignment explanation
Indices: 4997892--4997926 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4997882 TCTTTTACCT
4997892 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
4997927 TATAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:4998105 original size:2 final size:2
Alignment explanation
Indices: 4998100--4998129 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4998090 GTGTGTTTTA
4998100 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
4998130 TTAAGGTCCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5000828 original size:15 final size:16
Alignment explanation
Indices: 5000801--5000830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5000791 ATTTAATAAG
5000801 AAAATTATCAATTAAA
1 AAAATTATCAATTAAA
5000817 AAAATTAT-AATTAA
1 AAAATTATCAATTAA
5000831 TGATTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTATCAATTAAA
Found at i:5001119 original size:20 final size:21
Alignment explanation
Indices: 5001058--5001131 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
5001048 TAAATAAAAG
5001058 AATTT-TAAAT-TTAATTATAAA
1 AATTTATAAATATTAA-TAT-AA
5001079 AATTTATAAATATTAATATAA
1 AATTTATAAATATTAATATAA
5001100 AATTTAT-AATATT-ATAATAA
1 AATTTATAAATATTAAT-ATAA
* *
5001120 ATTTTAAAAATA
1 AATTTATAAATA
5001132 AAATAGATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.04
20 15 0.32
21 18 0.38
22 8 0.17
23 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTATAAATATTAATATAA
Found at i:5003284 original size:26 final size:27
Alignment explanation
Indices: 5003248--5003303 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
5003238 TGGAAGGTTT
* *
5003248 TTAATATTTATA-AATATTTAATTTA-A
1 TTAATAATTATATAA-ATTTAAATTATA
5003274 TTAATAATTATATAAATTTAAATTATA
1 TTAATAATTATATAAATTTAAATTATA
5003301 TTA
1 TTA
5003304 TATTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAATAATTATATAAATTTAAATTATA
Found at i:5003293 original size:21 final size:21
Alignment explanation
Indices: 5003261--5003311 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
5003251 ATATTTATAA
*
5003261 ATATTTAATTT-AATTAATAATT
1 ATATTAAATTTAAATT-AT-ATT
5003283 ATA-TAAATTTAAATTATATT
1 ATATTAAATTTAAATTATATT
5003303 ATATTAAAT
1 ATATTAAAT
5003312 AATAATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 13 0.50
22 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTAAATTTAAATTATATT
Found at i:5003358 original size:17 final size:19
Alignment explanation
Indices: 5003323--5003365 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
5003313 ATAATTATTT
*
5003323 ATTTAAATATTTTTTTATA
1 ATTTAAATATTTTTATATA
5003342 ATTTAAA-A-TTTTATATA
1 ATTTAAATATTTTTATATA
5003359 A-TTAAAT
1 ATTTAAAT
5003366 TTGAAGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.23
17 9 0.41
18 1 0.05
19 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAATATTTTTATATA
Found at i:5004118 original size:12 final size:12
Alignment explanation
Indices: 5004079--5004119 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
5004069 ATAACACAAT
5004079 ATAA-ATAAAAA
1 ATAATATAAAAA
*
5004090 ATAAT-TAAAAC
1 ATAATATAAAAA
*
5004101 ACAATATAAAAA
1 ATAATATAAAAA
5004113 ATAATAT
1 ATAATAT
5004120 GAATATGACA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:5004644 original size:130 final size:133
Alignment explanation
Indices: 5004399--5004648 Score: 407
Period size: 130 Copynumber: 1.9 Consensus size: 133
5004389 TATGTAAATC
5004399 ATTTTATATATATTTTAAAAATATTTATTTATTAATTATATCCAAGTGGCTGGAATAAAATTTTT
1 ATTTTATATATATTTTAAAAATATTTATTTATTAATTATATCCAAGTGGCTGGAAT-AAATTTTT
* * * *
5004464 TTTACGTGTTCAGATGTACTATATATTAATATTTATTAATAGTCTAAGCTGAAATTAATGATTTG
65 TTCACGTGTTCAGATGTACGATATATTAATACTTATTAAAAGTCTAAGCTGAAATTAATGATTTG
5004529 AATT
130 AATT
*
5004533 ATTTTATATATA-TTT-AAAATATTTATTTATTAATTATATCTAAGTGGCTGGAAT-AATTTTTT
1 ATTTTATATATATTTTAAAAATATTTATTTATTAATTATATCCAAGTGGCTGGAATAAATTTTTT
* *
5004595 TCACGTGTTCCGATGTACGATATATTAATACTTATTAAAAGTCTCAGCTGAAAT
66 TCACGTGTTCAGATGTACGATATATTAATACTTATTAAAAGTCTAAGCTGAAAT
5004649 CTTCTCAGCA
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
130 56 0.51
132 38 0.35
133 3 0.03
134 12 0.11
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (133 bp):
ATTTTATATATATTTTAAAAATATTTATTTATTAATTATATCCAAGTGGCTGGAATAAATTTTTT
TCACGTGTTCAGATGTACGATATATTAATACTTATTAAAAGTCTAAGCTGAAATTAATGATTTGA
ATT
Found at i:5005836 original size:16 final size:15
Alignment explanation
Indices: 5005811--5005840 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5005801 TATGTTATAA
5005811 ATTTTTTTATTATCG
1 ATTTTTTTATTATCG
5005826 ATTTTTATTATTATC
1 ATTTTT-TTATTATC
5005841 AATTATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (15 bp):
ATTTTTTTATTATCG
Found at i:5010716 original size:2 final size:2
Alignment explanation
Indices: 5010709--5010743 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5010699 ACTTATCCAA
5010709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5010744 GAGCATCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5014232 original size:16 final size:16
Alignment explanation
Indices: 5014211--5014251 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5014201 CTATAGTTAT
5014211 TTTATTCTACTCCAAC
1 TTTATTCTACTCCAAC
* * *
5014227 TTTATTCTATTCTAAT
1 TTTATTCTACTCCAAC
5014243 TTTATTCTA
1 TTTATTCTA
5014252 GTTTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATTCTACTCCAAC
Found at i:5014665 original size:24 final size:24
Alignment explanation
Indices: 5014630--5014706 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 24
5014620 ATAAAAATTT
*
5014630 GCCACCAA-TTTTGACAAACAACAA
1 GCCA-CAATTTTTGACAAACAAAAA
*
5014654 GCCACAATTTTTGATAAACAAAAAA
1 GCCACAATTTTTGACAAAC-AAAAA
* *
5014679 GAATCCACCATTTTTGACAAACACAAA
1 G---CCACAATTTTTGACAAACAAAAA
5014706 G
1 G
5014707 GGTGGCTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
23 3 0.07
24 14 0.33
25 5 0.12
27 5 0.12
28 16 0.37
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (24 bp):
GCCACAATTTTTGACAAACAAAAA
Found at i:5019201 original size:23 final size:25
Alignment explanation
Indices: 5019167--5019212 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
5019157 AATAAAAATT
5019167 AGCCACCAA-TTTTGACAAACAACA
1 AGCCACCAATTTTTGACAAACAACA
5019191 AGCCA-CAATTTTTGACAAACAA
1 AGCCACCAATTTTTGACAAACAA
5019213 AAAAGGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.20
Consensus pattern (25 bp):
AGCCACCAATTTTTGACAAACAACA
Found at i:5021898 original size:20 final size:20
Alignment explanation
Indices: 5021873--5021910 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5021863 TATACATATA
5021873 AATAAAAATAAAA-AAATGAT
1 AATAAAAA-AAAACAAATGAT
5021893 AATAAAAAAAAACAAATG
1 AATAAAAAAAAACAAATG
5021911 CAAACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (20 bp):
AATAAAAAAAAACAAATGAT
Found at i:5022979 original size:25 final size:25
Alignment explanation
Indices: 5022913--5022966 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
5022903 AGCCACTCAT
* *
5022913 TTTCCTCCCTTTTTTTTACTTTTTG
1 TTTCCTTCTTTTTTTTTACTTTTTG
*
5022938 TTTCCTTCTTTTTTTTTGCTTTTTG
1 TTTCCTTCTTTTTTTTTACTTTTTG
5022963 TTTC
1 TTTC
5022967 TTTTTTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.02, C:0.20, G:0.06, T:0.72
Consensus pattern (25 bp):
TTTCCTTCTTTTTTTTTACTTTTTG
Found at i:5023548 original size:19 final size:19
Alignment explanation
Indices: 5023513--5023563 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
5023503 CAAAGAAAGG
5023513 GAAAGGGAAAGCA-GAAACA
1 GAAAGGGAAAG-AGGAAACA
*
5023532 GAAAGGGAAAGAGGAAAGA
1 GAAAGGGAAAGAGGAAACA
* *
5023551 AAAAGAGAAAGAG
1 GAAAGGGAAAGAG
5023564 AAAAGGAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.61, C:0.04, G:0.35, T:0.00
Consensus pattern (19 bp):
GAAAGGGAAAGAGGAAACA
Found at i:5024069 original size:20 final size:20
Alignment explanation
Indices: 5024041--5024115 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
5024031 TCATACCCTG
5024041 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
5024061 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
5024081 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
5024101 ATGTATCGATACATT
1 ATGTATCGATACATT
5024116 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:5024108 original size:40 final size:39
Alignment explanation
Indices: 5024041--5024118 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
5024031 TCATACCCTG
* *
5024041 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
5024081 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
5024119 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:5040197 original size:32 final size:32
Alignment explanation
Indices: 5039947--5041399 Score: 2205
Period size: 32 Copynumber: 46.2 Consensus size: 32
5039937 TGTTCATCCC
*
5039947 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * *
5039976 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
5040005 TTTCAAAG-CC-TACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
5040033 TTTCAAA-ACC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* ** * *
5040062 TTTCAAAG-CC-TACAAGTTAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
** * *
5040091 TTTCAAAGCCCACA-AA-TTAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
5040120 TTTTAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040148 TTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040180 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040212 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040244 TTCCAAAG-CCACACAAGTCGGTGGCAA-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040274 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040305 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040337 TTTCAAAGCCCACACTAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACAC-AAGTCGGTGGCAACCCA
5040370 -TTCAAAG-CCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040400 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040432 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040464 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040496 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040528 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040560 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040592 TTCCAAAGCCCACACAAGTC-GTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040623 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040654 TTTCAAAGGCCCACAACAAAGTCGGTGGCAACCCA
1 TTTCAAA-GCCCAC-AC-AAGTCGGTGGCAACCCA
* *
5040689 TTCCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040721 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040753 TTTCATAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5040785 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040817 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040849 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040881 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040913 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
5040945 TTCCAAAACCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5040977 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5041009 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5041041 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5041073 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5041105 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
5041137 TTCCAAAGCCCACACAAGTCGATGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5041169 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
5041201 TTCCAAAGCCCACACAAGTCGATGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5041233 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5041265 TTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
5041297 TTCCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5041329 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** * *
5041361 TTTAAAAGCCCATGCAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5041393 TTTCAAA
1 TTTCAAA
5041400 TCACCATATT
Statistics
Matches: 1341, Mismatches: 55, Indels: 53
0.93 0.04 0.04
Matches are distributed among these distances:
27 3 0.00
28 40 0.03
29 108 0.08
30 78 0.06
31 63 0.05
32 994 0.74
33 25 0.02
34 7 0.01
35 23 0.02
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.16
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:5041955 original size:20 final size:20
Alignment explanation
Indices: 5041927--5042001 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
5041917 TCATACCCTG
5041927 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
5041947 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
5041967 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
5041987 ATGTATCGATACATT
1 ATGTATCGATACATT
5042002 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:5041994 original size:40 final size:39
Alignment explanation
Indices: 5041927--5042004 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
5041917 TCATACCCTG
* *
5041927 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
5041967 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
5042005 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:5045432 original size:2 final size:2
Alignment explanation
Indices: 5045425--5045450 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5045415 CTGAATATGC
5045425 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
5045451 ACTCCCACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5045535 original size:16 final size:17
Alignment explanation
Indices: 5045499--5045538 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
5045489 AATTTAAAAA
*
5045499 TAATAATATTAATAATC
1 TAATAATATTAAGAATC
*
5045516 TAATAA-ATTAAGAATT
1 TAATAATATTAAGAATC
5045532 TAATAAT
1 TAATAAT
5045539 TACCTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (17 bp):
TAATAATATTAAGAATC
Found at i:5046052 original size:15 final size:15
Alignment explanation
Indices: 5046032--5046061 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5046022 ACAATATGCC
5046032 CGTGCATATCGTTGA
1 CGTGCATATCGTTGA
5046047 CGTGCATATCGTTGA
1 CGTGCATATCGTTGA
5046062 AGTGTAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (15 bp):
CGTGCATATCGTTGA
Found at i:5050143 original size:50 final size:50
Alignment explanation
Indices: 5050068--5050177 Score: 184
Period size: 50 Copynumber: 2.2 Consensus size: 50
5050058 CTGGACGCGA
*
5050068 ATCCTACGTGAATACGCTAACCACTCTAGCGCATCCACGTAGGATTCACG
1 ATCCTACGTGAATACGCTAACCACTCTAGCGCATCCACATAGGATTCACG
* *
5050118 ATCCTACGTGAATGCGCTAATCACTCTAGCGCATCCACATAGGATTCACG
1 ATCCTACGTGAATACGCTAACCACTCTAGCGCATCCACATAGGATTCACG
*
5050168 ATCTTACGTG
1 ATCCTACGTG
5050178 GCATTGACAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (50 bp):
ATCCTACGTGAATACGCTAACCACTCTAGCGCATCCACATAGGATTCACG
Found at i:5051647 original size:18 final size:18
Alignment explanation
Indices: 5051624--5051669 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5051614 GCTATACCGC
*
5051624 TATATATTTATATGTGTA
1 TATATATTTATATATGTA
*
5051642 TATATATATATATATGTA
1 TATATATTTATATATGTA
*
5051660 TGTATATTTA
1 TATATATTTA
5051670 ATTAGCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (18 bp):
TATATATTTATATATGTA
Found at i:5052372 original size:33 final size:33
Alignment explanation
Indices: 5052329--5052394 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
5052319 TTGTGCTTAA
*
5052329 ATAAATTTTTTGCGCTAAATCATGGTCAAATTC
1 ATAAACTTTTTGCGCTAAATCATGGTCAAATTC
5052362 ATAAACTTTTTGCGCTAAATCATGGTCAAATTC
1 ATAAACTTTTTGCGCTAAATCATGGTCAAATTC
5052395 TTTTATGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (33 bp):
ATAAACTTTTTGCGCTAAATCATGGTCAAATTC
Found at i:5053053 original size:6 final size:6
Alignment explanation
Indices: 5053042--5053100 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
5053032 TCTTTTACCT
5053042 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5053090 ATATAA ATATA
1 ATATAA ATATA
5053101 TATAATTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:5055109 original size:20 final size:19
Alignment explanation
Indices: 5055068--5055113 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5055058 TTTATTCTTA
5055068 AAAAATTATCCACTTTACT
1 AAAAATTATCCACTTTACT
*
5055087 AAATAATTATCTACTTT-CGT
1 AAA-AATTATCCACTTTAC-T
5055107 AAAAATT
1 AAAAATT
5055114 CTGCTCGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAAATTATCCACTTTACT
Found at i:5055362 original size:14 final size:15
Alignment explanation
Indices: 5055343--5055371 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5055333 GATAATTAAT
5055343 AATTATC-TTAAAAA
1 AATTATCTTTAAAAA
5055357 AATTATCTTTAAAAA
1 AATTATCTTTAAAAA
5055372 TTTTAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATCTTTAAAAA
Found at i:5055999 original size:37 final size:38
Alignment explanation
Indices: 5055920--5056006 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 38
5055910 GACAAATAAT
* * *
5055920 ATTTGAGTGGC-TTGGTCAATCTACTAATGATTGTTAGT
1 ATTTGAGTGGCAGT-GTCAATCTACTAATGATTATTAGA
*
5055958 ATTTGGGTGGCAGTGTCAATCTACT-ATGATTATTAGA
1 ATTTGAGTGGCAGTGTCAATCTACTAATGATTATTAGA
5055995 ATTTGAGTGGCA
1 ATTTGAGTGGCA
5056007 ATACCAATCC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 21 0.49
38 21 0.49
39 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (38 bp):
ATTTGAGTGGCAGTGTCAATCTACTAATGATTATTAGA
Found at i:5056015 original size:37 final size:38
Alignment explanation
Indices: 5055936--5056015 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
5055926 GTGGCTTGGT
* * * * **
5055936 CAATCTACTAATGATTGTTAGTATTTGGGTGGCAGTGT
1 CAATCTACTAATGATTATTAGAATTTGAGTGGCAATAC
5055974 CAATCTACT-ATGATTATTAGAATTTGAGTGGCAATAC
1 CAATCTACTAATGATTATTAGAATTTGAGTGGCAATAC
5056011 CAATC
1 CAATC
5056016 CATGAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 27 0.75
38 9 0.25
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (38 bp):
CAATCTACTAATGATTATTAGAATTTGAGTGGCAATAC
Found at i:5060338 original size:52 final size:52
Alignment explanation
Indices: 5060260--5060388 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
5060250 CAAAATATGA
* *
5060260 AAATTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
5060312 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
5060364 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
5060389 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:5060401 original size:52 final size:51
Alignment explanation
Indices: 5060260--5060408 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
5060250 CAAAATATGA
*
5060260 AAATTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
5060312 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
5060364 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
5060409 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:5060415 original size:13 final size:13
Alignment explanation
Indices: 5060397--5060421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5060387 CAAAGATCAG
5060397 TGTATCGATACAA
1 TGTATCGATACAA
5060410 TGTATCGATACA
1 TGTATCGATACA
5060422 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5060505 original size:13 final size:13
Alignment explanation
Indices: 5060487--5060511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5060477 CAAAAAAATA
5060487 TGTATCGATACAT
1 TGTATCGATACAT
5060500 TGTATCGATACA
1 TGTATCGATACA
5060512 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5064363 original size:37 final size:37
Alignment explanation
Indices: 5064282--5064365 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
5064272 GGGTGGCTTG
* ** *
5064282 GCCAATCAACTATGATTGTTAGTATTTGGGTGGCAGT
1 GCCAATCCACTATGATTGTTAAAATTTGGATGGCAGT
*
5064319 ACCAATCCACTATGATTGTTAAAATTTGGATGGCAGT
1 GCCAATCCACTATGATTGTTAAAATTTGGATGGCAGT
5064356 GCCAATCCAC
1 GCCAATCCAC
5064366 GAAAAATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (37 bp):
GCCAATCCACTATGATTGTTAAAATTTGGATGGCAGT
Found at i:5066084 original size:14 final size:14
Alignment explanation
Indices: 5066062--5066098 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5066052 GAAGGTTAGG
*
5066062 AGTTTGAATTTAAA
1 AGTTTGAATATAAA
*
5066076 AGTTGGAATATAAA
1 AGTTTGAATATAAA
5066090 AGTTTGAAT
1 AGTTTGAAT
5066099 CTCTCTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (14 bp):
AGTTTGAATATAAA
Found at i:5073683 original size:6 final size:6
Alignment explanation
Indices: 5073668--5073697 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5073658 AAATTTATCT
5073668 TATT-A TATTAA TATTAA TATTAA TATTAA T
1 TATTAA TATTAA TATTAA TATTAA TATTAA T
5073698 TTATATGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAA
Found at i:5074722 original size:29 final size:27
Alignment explanation
Indices: 5074669--5074722 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
5074659 TATTAATATT
**
5074669 TATATATTTTATAATTTAATTTAAAAA
1 TATATATTTTATAATTTAAAATAAAAA
*
5074696 TATATATTATTTTAATTTAAAAATAAA
1 TATATATT-TTATAATTT-AAAATAAA
5074723 TTTTAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 8 0.36
29 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATATTTTATAATTTAAAATAAAAA
Found at i:5075779 original size:21 final size:20
Alignment explanation
Indices: 5075758--5075794 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5075748 CATGGAATTA
5075758 TATTT-TTTTAAAAATTAAT
1 TATTTATTTTAAAAATTAAT
5075777 TATTTATTTTAAAAATTA
1 TATTTATTTTAAAAATTA
5075795 TTAAATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTATTTTAAAAATTAAT
Found at i:5075797 original size:19 final size:18
Alignment explanation
Indices: 5075753--5075797 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
5075743 TAAATCATGG
5075753 AATTA-TATTTTTTTAAA
1 AATTATTATTTTTTTAAA
5075770 AATTAATTATTTATTTTAAA
1 AATT-ATTATTT-TTTTAAA
5075790 AATTATTA
1 AATTATTA
5075798 AATAAAGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.16
18 1 0.04
19 9 0.36
20 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTATTATTTTTTTAAA
Found at i:5081571 original size:22 final size:22
Alignment explanation
Indices: 5081544--5081600 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
5081534 TTATTAATAT
5081544 GTGTGTTAGGTGAGTATATTAA
1 GTGTGTTAGGTGAGTATATTAA
*
5081566 GTGTGTTAGGTGAGTATATTAG
1 GTGTGTTAGGTGAGTATATTAA
5081588 GTGTGTTAGGTGA
1 GTGTGTTAGGTGA
5081601 TGTGTTAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (22 bp):
GTGTGTTAGGTGAGTATATTAA
Found at i:5085876 original size:35 final size:35
Alignment explanation
Indices: 5085821--5085903 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
5085811 AAACATATTA
** *
5085821 GGTGTGTTAGGTG-AGTATATTAGGTGCGTTAGGT
1 GGTGTGTTAGGTGAAACATATTAGGTGCATTAGGT
*
5085855 GGTGTGTTAGGTGAAACATATTAGGTGTATTAGGT
1 GGTGTGTTAGGTGAAACATATTAGGTGCATTAGGT
**
5085890 AATGTGTTAGGTGA
1 GGTGTGTTAGGTGA
5085904 GCAAAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 13 0.31
35 29 0.69
ACGTcount: A:0.23, C:0.02, G:0.37, T:0.37
Consensus pattern (35 bp):
GGTGTGTTAGGTGAAACATATTAGGTGCATTAGGT
Found at i:5094259 original size:29 final size:29
Alignment explanation
Indices: 5094217--5094280 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
5094207 CAGGTCTAAT
* * *
5094217 TAAAATTATATTAAAAGTTATCAAGATGA
1 TAAAATCATATTAAAAGTTATCAAAATCA
*
5094246 TAAAATCATATTAAAGGTTATCAAAATCA
1 TAAAATCATATTAAAAGTTATCAAAATCA
5094275 TAAAAT
1 TAAAAT
5094281 TAAGGCTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (29 bp):
TAAAATCATATTAAAAGTTATCAAAATCA
Found at i:5094426 original size:21 final size:21
Alignment explanation
Indices: 5094400--5094535 Score: 103
Period size: 21 Copynumber: 6.3 Consensus size: 21
5094390 TGTTGGCTAC
5094400 CAAAATTATTTCAAAGGTTAT
1 CAAAATTATTTCAAAGGTTAT
* *
5094421 CAAAATTATATTAAAAGAAAGGTAT
1 CAAAATTAT-TTCAAAG---GTTAT
*
5094446 CAAAATTATATCAAAGGTTAT
1 CAAAATTATTTCAAAGGTTAT
* * ** *
5094467 TAAAATTATATCAAATATTTT
1 CAAAATTATTTCAAAGGTTAT
* * * *
5094488 TAAAATCATTTCAGAGGTTAC
1 CAAAATTATTTCAAAGGTTAT
*
5094509 CAAAATTATATT-AAAGATTAT
1 CAAAATTAT-TTCAAAGGTTAT
5094530 CAAAAT
1 CAAAAT
5094536 CAAAATTAAA
Statistics
Matches: 89, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
21 63 0.71
22 8 0.09
24 5 0.06
25 13 0.15
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (21 bp):
CAAAATTATTTCAAAGGTTAT
Found at i:5096444 original size:17 final size:16
Alignment explanation
Indices: 5096419--5096452 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5096409 TTAACTGAAT
5096419 AAAACCAAAACAAAAAA
1 AAAACCAAAA-AAAAAA
*
5096436 AAAATCAAAAAAAAAA
1 AAAACCAAAAAAAAAA
5096452 A
1 A
5096453 TTAAACACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAACCAAAAAAAAAA
Found at i:5096830 original size:21 final size:21
Alignment explanation
Indices: 5096804--5096923 Score: 116
Period size: 21 Copynumber: 5.7 Consensus size: 21
5096794 ATAGCAAAGG
*
5096804 TCAAATATTATTAAAATTATA
1 TCAAATATTATCAAAATTATA
5096825 TCAAATATTATCAAAATTATA
1 TCAAATATTATCAAAATTATA
* * *
5096846 TCCAAA-GTTAACAAAATCATA
1 T-CAAATATTATCAAAATTATA
** *
5096867 TCAAAGGTTATAAAAGATTATA
1 TCAAATATTATCAAA-ATTATA
* *
5096889 TTAAATTTTATCAAAATTATA
1 TCAAATATTATCAAAATTATA
**
5096910 AAAAATATTATCAA
1 TCAAATATTATCAA
5096924 GTTGTATTAA
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
20 4 0.05
21 58 0.71
22 20 0.24
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (21 bp):
TCAAATATTATCAAAATTATA
Found at i:5096851 original size:12 final size:11
Alignment explanation
Indices: 5096804--5096909 Score: 59
Period size: 10 Copynumber: 10.0 Consensus size: 11
5096794 ATAGCAAAGG
5096804 TCAAATATTAT-
1 TCAAA-ATTATA
5096815 T-AAAATTATA
1 TCAAAATTATA
5096825 TC-AAA-TATTA
1 TCAAAATTA-TA
5096835 TCAAAATTATA
1 TCAAAATTATA
*
5096846 TCCAAAGTTA-A
1 T-CAAAATTATA
*
5096857 -CAAAATCATA
1 TCAAAATTATA
*
5096867 TCAAAGGTTATA
1 TCAAA-ATTATA
5096879 --AAAGATTATA
1 TCAAA-ATTATA
* *
5096889 T-TAAATTTTA
1 TCAAAATTATA
5096899 TCAAAATTATA
1 TCAAAATTATA
5096910 AAAAATATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
9 13 0.18
10 27 0.36
11 21 0.28
12 13 0.18
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (11 bp):
TCAAAATTATA
Found at i:5097864 original size:34 final size:34
Alignment explanation
Indices: 5097821--5097955 Score: 225
Period size: 34 Copynumber: 4.0 Consensus size: 34
5097811 TTCGAATATG
*
5097821 GCAGTACAAAACAGTGATGGTTGTGGAAACTATT
1 GCAGTACAAAACAGTGATGGTTGTGGAAATTATT
5097855 GCAGTACAAAACAGTGATGGTTGTGGAAATTATT
1 GCAGTACAAAACAGTGATGGTTGTGGAAATTATT
* *
5097889 ACAGTTCAAAACAGTGATGGTTGTGGAAATTATT
1 GCAGTACAAAACAGTGATGGTTGTGGAAATTATT
* *
5097923 GCAGTACAAAACAGTGATGGCTATGGAAATTAT
1 GCAGTACAAAACAGTGATGGTTGTGGAAATTAT
5097956 CATCATCGAC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 94 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.28
Consensus pattern (34 bp):
GCAGTACAAAACAGTGATGGTTGTGGAAATTATT
Found at i:5098914 original size:11 final size:11
Alignment explanation
Indices: 5098898--5098930 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5098888 GTGTATTTTA
5098898 TATAATAATTT
1 TATAATAATTT
*
5098909 TATAATAAGTT
1 TATAATAATTT
5098920 T-TAATAATTT
1 TATAATAATTT
5098930 T
1 T
5098931 CATGTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TATAATAATTT
Found at i:5101698 original size:2 final size:2
Alignment explanation
Indices: 5101693--5101726 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5101683 ATATCTTGTA
5101693 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
5101727 GATTCTATTT
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:5104233 original size:12 final size:12
Alignment explanation
Indices: 5104204--5104255 Score: 60
Period size: 11 Copynumber: 4.7 Consensus size: 12
5104194 ATTTTGGTAT
5104204 AAAATTA-TATC
1 AAAATTATTATC
5104215 -AAA-TATTATC
1 AAAATTATTATC
5104225 AAAATTATTAT-
1 AAAATTATTATC
5104236 AAAATTA-TATC
1 AAAATTATTATC
5104247 AAATATTAT
1 AAA-ATTAT
5104256 AAAGCTTACC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.06
10 10 0.29
11 13 0.37
12 10 0.29
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTATTATC
Found at i:5104253 original size:20 final size:20
Alignment explanation
Indices: 5104230--5104370 Score: 71
Period size: 20 Copynumber: 7.0 Consensus size: 20
5104220 TTATCAAAAT
5104230 TATTATAAAATTATATCAAA
1 TATTATAAAATTATATCAAA
* **
5104250 TATTATAAAGCTTACCTAAAAAA
1 TATTATAAA-ATTA--TATCAAA
*
5104273 CTAATA-AAAATTATATCAAA
1 -TATTATAAAATTATATCAAA
* ** *
5104293 AATTA-CCAA-GAT-TCAAA
1 TATTATAAAATTATATCAAA
*
5104310 -GTTATTAAAATTATATC-AA
1 TATTA-TAAAATTATATCAAA
*
5104329 GATTACTAAAATTATATC-AA
1 TATTA-TAAAATTATATCAAA
5104349 TAATTATTAAAATTATATCAAA
1 T-ATTA-TAAAATTATATCAAA
5104371 GGTTGCTAAA
Statistics
Matches: 90, Mismatches: 20, Indels: 20
0.69 0.15 0.15
Matches are distributed among these distances:
16 3 0.03
17 5 0.06
18 4 0.04
19 9 0.10
20 33 0.37
21 19 0.21
22 5 0.06
23 8 0.09
24 4 0.04
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (20 bp):
TATTATAAAATTATATCAAA
Found at i:5104355 original size:12 final size:11
Alignment explanation
Indices: 5104316--5104370 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 11
5104306 CAAAGTTATT
5104316 AAAATTATATC
1 AAAATTATATC
* *
5104327 AAGATTA-CT-
1 AAAATTATATC
5104336 AAAATTATATC
1 AAAATTATATC
5104347 AATAATTAT-T-
1 AA-AATTATATC
5104357 AAAATTATATC
1 AAAATTATATC
5104368 AAA
1 AAA
5104371 GGTTGCTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
9 12 0.34
10 5 0.14
11 12 0.34
12 6 0.17
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (11 bp):
AAAATTATATC
Found at i:5104359 original size:21 final size:20
Alignment explanation
Indices: 5104305--5104370 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
5104295 TTACCAAGAT
*
5104305 TCAAAGTTATTAAAATTATA
1 TCAAAATTATTAAAATTATA
* *
5104325 TCAAGATTACTAAAATTATA
1 TCAAAATTATTAAAATTATA
5104345 TCAATAATTATTAAAATTATA
1 TCAA-AATTATTAAAATTATA
5104366 TCAAA
1 TCAAA
5104371 GGTTGCTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 22 0.55
21 18 0.45
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.38
Consensus pattern (20 bp):
TCAAAATTATTAAAATTATA
Found at i:5104380 original size:21 final size:21
Alignment explanation
Indices: 5104305--5104388 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
5104295 TTACCAAGAT
*
5104305 TCAAAG-TTATTAAAATTATA
1 TCAAAGATTACTAAAATTATA
5104325 TC-AAGATTACTAAAATTATA
1 TCAAAGATTACTAAAATTATA
*
5104345 TCAATA-ATTATTAAAATTATA
1 TCAA-AGATTACTAAAATTATA
* *
5104366 TCAAAGGTTGCTAAAATTATA
1 TCAAAGATTACTAAAATTATA
5104387 TC
1 TC
5104389 GATGTTACCA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
19 3 0.05
20 18 0.33
21 33 0.60
22 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (21 bp):
TCAAAGATTACTAAAATTATA
Found at i:5104404 original size:41 final size:41
Alignment explanation
Indices: 5104316--5104407 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
5104306 CAAAGTTATT
**
5104316 AAAATTATATCAAGATTACTAAAATTATATCAATAATTATT
1 AAAATTATATCAAGATTACTAAAATTATATCAATAATTACC
* * * *
5104357 AAAATTATATCAAAGGTTGCTAAAATTATATCGAT-GTTACC
1 AAAATTATATC-AAGATTACTAAAATTATATCAATAATTACC
*
5104398 ATAATTATAT
1 AAAATTATAT
5104408 TGATTGTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (41 bp):
AAAATTATATCAAGATTACTAAAATTATATCAATAATTACC
Found at i:5104405 original size:20 final size:21
Alignment explanation
Indices: 5104378--5104428 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
5104368 AAAGGTTGCT
*
5104378 AAAATTATATCGA-TGTTACC
1 AAAATTATATCGATTGTTAAC
* *
5104398 ATAATTATATTGATTGTTAAC
1 AAAATTATATCGATTGTTAAC
5104419 AAAATTATAT
1 AAAATTATAT
5104429 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (21 bp):
AAAATTATATCGATTGTTAAC
Found at i:5104641 original size:21 final size:21
Alignment explanation
Indices: 5104616--5104656 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5104606 TCAAAGACTA
**
5104616 TTACAAATGTTATCAAAATTC
1 TTACAAAAATTATCAAAATTC
5104637 TTACAAAAATTATCAAAATT
1 TTACAAAAATTATCAAAATT
5104657 AGATTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (21 bp):
TTACAAAAATTATCAAAATTC
Found at i:5104759 original size:21 final size:21
Alignment explanation
Indices: 5104624--5104823 Score: 131
Period size: 21 Copynumber: 9.6 Consensus size: 21
5104614 TATTACAAAT
*
5104624 GTTATCAAAATTCT-TACAAAA
1 GTTATCAAAATTATATA-AAAA
* *
5104645 ATTATCAAAATTAGATTAAAAA
1 GTTATCAAAATTATA-TAAAAA
** * *
5104667 -TTATCAAAAACATATCAAGA
1 GTTATCAAAATTATATAAAAA
* * *
5104687 GCTACCTAAAATTATATAATAA
1 GTTATC-AAAATTATATAAAAA
* *
5104709 -TTATCACAATTAT-TTAAAA
1 GTTATCAAAATTATATAAAAA
**
5104728 GTTATTGAAATTATATAAAAA
1 GTTATCAAAATTATATAAAAA
* **
5104749 GTTACCAAAATTATATCTAAA
1 GTTATCAAAATTATATAAAAA
* *
5104770 GTTATCAAAAGTATCACAAAAA
1 GTTATCAAAATTAT-ATAAAAA
*
5104792 -TTATCAAAATTATATCAAAA
1 GTTATCAAAATTATATAAAAA
* *
5104812 GTCATAAAAATT
1 GTTATCAAAATT
5104824 TTGTTAATAG
Statistics
Matches: 132, Mismatches: 39, Indels: 16
0.71 0.21 0.09
Matches are distributed among these distances:
19 4 0.03
20 26 0.20
21 82 0.62
22 18 0.14
23 2 0.02
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (21 bp):
GTTATCAAAATTATATAAAAA
Found at i:5104807 original size:11 final size:11
Alignment explanation
Indices: 5104739--5104813 Score: 59
Period size: 11 Copynumber: 7.1 Consensus size: 11
5104729 TTATTGAAAT
*
5104739 TATATAAAAAG
1 TATATCAAAAG
* *
5104750 T-TACCAAAAT
1 TATATCAAAAG
*
5104760 TATATCTAAAG
1 TATATCAAAAG
5104771 T-TATCAAAAG
1 TATATCAAAAG
*
5104781 TATCA-CAAAAA
1 TAT-ATCAAAAG
*
5104792 T-TATCAAAAT
1 TATATCAAAAG
5104802 TATATCAAAAG
1 TATATCAAAAG
5104813 T
1 T
5104814 CATAAAAATT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
9 1 0.02
10 23 0.47
11 24 0.49
12 1 0.02
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (11 bp):
TATATCAAAAG
Found at i:5105041 original size:21 final size:20
Alignment explanation
Indices: 5105029--5105066 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5105019 AAATCATATG
5105029 AAAGATTATC-AAATATATAA
1 AAAG-TTATCAAAATATATAA
5105049 AAAGTTATCAAAAT-TATA
1 AAAGTTATCAAAATATATA
5105067 TTAAATGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAGTTATCAAAATATATAA
Found at i:5105323 original size:21 final size:21
Alignment explanation
Indices: 5105208--5105373 Score: 156
Period size: 21 Copynumber: 7.9 Consensus size: 21
5105198 GTATCCAAGT
*
5105208 TTATCAAAA-TATTTACAAAAG
1 TTATCAAAATTATAT-CAAAAG
* *
5105229 TTATCAAAATTATATAAAAAT
1 TTATCAAAATTATATCAAAAG
* *
5105250 TTATCAAAACTATATTAAATA-
1 TTATCAAAATTATATCAAA-AG
5105271 TTATCAAAATTATATCAAAAG
1 TTATCAAAATTATATCAAAAG
* * *
5105292 TTATTAAAATTTTATTAAAAG
1 TTATCAAAATTATATCAAAAG
* * *
5105313 ATATCAAAATTCTATCAAAGG
1 TTATCAAAATTATATCAAAAG
* * *
5105334 TTATAAAAATTGTATTAAAAG
1 TTATCAAAATTATATCAAAAG
*
5105355 TTATAAAAAATTATATCAA
1 TTAT-CAAAATTATATCAA
5105374 TGATTACCAA
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
20 1 0.01
21 101 0.85
22 17 0.14
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTATATCAAAAG
Found at i:5105329 original size:42 final size:42
Alignment explanation
Indices: 5105224--5105562 Score: 189
Period size: 42 Copynumber: 8.0 Consensus size: 42
5105214 AAATATTTAC
* * * *
5105224 AAAAGTTATCAAAATTATATAAAAATTTATCAAAACTATATT
1 AAAAGTTATCAAAATTATATCAAAAGTTATAAAAATTATATT
* *
5105266 AAATA-TTATCAAAATTATATCAAAAGTTATTAAAATTTTATT
1 AAA-AGTTATCAAAATTATATCAAAAGTTATAAAAATTATATT
* * * *
5105308 AAAAGATATCAAAATTCTATCAAAGGTTATAAAAATTGTATT
1 AAAAGTTATCAAAATTATATCAAAAGTTATAAAAATTATATT
* * * * *
5105350 AAAAGTTATAAAAAATTATATC-AATGATTACCAAAAGA-AAAACTGT
1 AAAAGTTAT-CAAAATTATATCAAAAG-TTA-TAAAA-ATTATA-T-T
* * * **
5105396 ACCAAAGGTTAACAAAATCATAT-AAAAATTATATGAA--A-A-T
1 A--AAA-GTTATCAAAATTATATCAAAAGTTATAAAAATTATATT
* * *
5105436 AAAGGTTATCATAATTATATCAAAAATTATAAAAATTATATT
1 AAAAGTTATCAAAATTATATCAAAAGTTATAAAAATTATATT
* * * *
5105478 AAATA-TTA-CTAAAATTTACATCAAAAGTT-TTAAAATAATATA
1 AAA-AGTTATC-AAAA-TTATATCAAAAGTTATAAAAATTATATT
* * * * *
5105520 AAAAATTATCAAAATTATATTAATA-TTATCACAATTATATT
1 AAAAGTTATCAAAATTATATCAAAAGTTATAAAAATTATATT
5105561 AA
1 AA
5105563 TATTATTGCA
Statistics
Matches: 228, Mismatches: 46, Indels: 47
0.71 0.14 0.15
Matches are distributed among these distances:
37 13 0.06
38 14 0.06
40 5 0.02
41 23 0.10
42 111 0.49
43 28 0.12
44 6 0.03
45 3 0.01
46 4 0.02
47 3 0.01
48 14 0.06
49 4 0.02
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.35
Consensus pattern (42 bp):
AAAAGTTATCAAAATTATATCAAAAGTTATAAAAATTATATT
Done.