Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 29
Found at i:2687682 original size:28 final size:27
Alignment explanation
Indices: 2687651--2687726 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 27
2687641 TATACAAAAT
*
2687651 ATATGTAATATATAATATATGACATGTG
1 ATATGTAATATATAATATATAACATG-G
* * *
2687679 ATATATGATATATGATATATAACATGG
1 ATATGTAATATATAATATATAACATGG
2687706 -TATGTAATATATATATATATA
1 ATATGTAATATATA-ATATATA
2687727 CACACGTATG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 10 0.25
27 8 0.20
28 22 0.55
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.41
Consensus pattern (27 bp):
ATATGTAATATATAATATATAACATGG
Found at i:2687743 original size:27 final size:28
Alignment explanation
Indices: 2687652--2687736 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
2687642 ATACAAAATA
*
2687652 TATGTAATATATA--ATATATGACAT-G
1 TATGTAATATATATGATATATAACATCG
* *
2687677 TGATAT-ATGATATATGATATATAACATGG
1 T-ATGTAAT-ATATATGATATATAACATCG
2687706 TATGTAATATATAT-ATATATACACA-CG
1 TATGTAATATATATGATATATA-ACATCG
2687733 TATG
1 TATG
2687737 ACATATAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
25 3 0.06
26 8 0.16
27 12 0.24
28 22 0.45
29 4 0.08
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (28 bp):
TATGTAATATATATGATATATAACATCG
Found at i:2687867 original size:14 final size:14
Alignment explanation
Indices: 2687779--2687891 Score: 59
Period size: 13 Copynumber: 8.6 Consensus size: 14
2687769 TAATTATAAT
2687779 ATATAAT-ATATATA
1 ATATAATAATAT-TA
*
2687793 A-ATAATACTATGT-
1 ATATAATAATAT-TA
2687806 A-ATAATAATATTTA
1 ATATAATAATA-TTA
* *
2687820 A-AAAATAATGTTA
1 ATATAATAATATTA
2687833 A-ATAATAA-A-TA
1 ATATAATAATATTA
2687844 ATA-AGA-AATATTA
1 ATATA-ATAATATTA
2687857 ATATAATAATATTA
1 ATATAATAATATTA
* * *
2687871 ATACACTAATACT-
1 ATATAATAATATTA
2687884 ATATAATA
1 ATATAATA
2687892 TATAGTATAA
Statistics
Matches: 78, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
11 6 0.08
12 3 0.04
13 37 0.47
14 32 0.41
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (14 bp):
ATATAATAATATTA
Found at i:2688422 original size:117 final size:117
Alignment explanation
Indices: 2688219--2688471 Score: 294
Period size: 117 Copynumber: 2.2 Consensus size: 117
2688209 GATTATTCTA
* **
2688219 ATTATGTACTTCTTCTCCTTCCATGGACAAGTTCTTCTCAGTATGAACTCCCCAATAAAATGTTA
1 ATTATGAACTTCTTCTCCCACCATGGACAAGTTCTTCTCAGTATGAACTCCCCAATAAAATGTTA
2688284 ATCCACCTCATTCTATAATGGACTTGAGAAAAAAGTCAAACAAGTTCTTATC
66 ATCCACCTCATTCTATAATGGACTTGAGAAAAAAGTCAAACAAGTTCTTATC
** * * *
2688336 ATTATGAACTTCTTCTCCCACTGTGGACGAGTTCTTCTC-GTTATGATCT-CCTAATTAAAATGT
1 ATTATGAACTTCTTCTCCCACCATGGACAAGTTCTTCTCAG-TATGAACTCCCCAA-TAAAATGT
* * * * * ** * ** *
2688399 TAATTCACCTCTTTCTGTTATGGATTTGAGTGAAATGTTGAACAAGTTCTTCTC
64 TAATCCACCTCATTCTATAATGGACTTGAGAAAAAAGTCAAACAAGTTCTTATC
*
2688453 ATTATGAACTTTTTCTCCC
1 ATTATGAACTTCTTCTCCC
2688472 CCCCCCCCCC
Statistics
Matches: 114, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
116 5 0.04
117 109 0.96
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (117 bp):
ATTATGAACTTCTTCTCCCACCATGGACAAGTTCTTCTCAGTATGAACTCCCCAATAAAATGTTA
ATCCACCTCATTCTATAATGGACTTGAGAAAAAAGTCAAACAAGTTCTTATC
Found at i:2690718 original size:90 final size:90
Alignment explanation
Indices: 2690601--2690778 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
2690591 TAATCCCGAA
* * *
2690601 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
2690666 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
2690691 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATTAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
2690756 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
2690779 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:2696457 original size:90 final size:89
Alignment explanation
Indices: 2696344--2696518 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
2696334 TCCCAAATAT
* * * *
2696344 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTAA
2696409 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
*
2696433 TTAAATTCTAATTAATTAATTATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTA
*
2696498 AGGTAACTTGGCTATAAAAGG
65 AGGTAACTTGGATATAAAAGG
2696519 GTGTGTTATG
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTAA
GGTAACTTGGATATAAAAGGATTA
Found at i:2701566 original size:14 final size:14
Alignment explanation
Indices: 2701547--2701579 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2701537 TACACTTTGG
2701547 TTTTTCTTTCT-TTT
1 TTTTTC-TTCTATTT
2701561 TTTTTCTTCTATTT
1 TTTTTCTTCTATTT
2701575 TTTTT
1 TTTTT
2701580 GTTTTTCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTCTTCTATTT
Found at i:2702257 original size:16 final size:17
Alignment explanation
Indices: 2702236--2702272 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2702226 TAAACCCTCG
*
2702236 TTTTATTT-ATTTTCTT
1 TTTTATTTAATTTTATT
2702252 TTTTATTTAATTTTATT
1 TTTTATTTAATTTTATT
2702269 TTTT
1 TTTT
2702273 CCTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATTTAATTTTATT
Found at i:2707930 original size:19 final size:17
Alignment explanation
Indices: 2707899--2707935 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
2707889 TACACTTGAT
2707899 TTTTTATTGCATTTTCA
1 TTTTTATTGCATTTTCA
2707916 TTTTTATTTGTCATTTTCA
1 TTTTTA-TTG-CATTTTCA
2707935 T
1 T
2707936 GCAAAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTATTGCATTTTCA
Found at i:2711578 original size:13 final size:13
Alignment explanation
Indices: 2711560--2711614 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
2711550 TGCGTCATGA
*
2711560 ATTTATGACGTGC
1 ATTTATGACGCGC
*
2711573 ATTTATGACACGC
1 ATTTATGACGCGC
*
2711586 ATTTATGACGCGT
1 ATTTATGACGCGC
*
2711599 ATTTATGACGCTC
1 ATTTATGACGCGC
2711612 ATT
1 ATT
2711615 GCGCGTCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:2711738 original size:85 final size:84
Alignment explanation
Indices: 2711586--2711751 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 84
2711576 TATGACACGC
* * * * *
2711586 ATTTATGACGCGTATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCATCATAAATGAAGACGA
1 ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCACACACCATAAA-GAAGACGA
*
2711651 CACACATTTGTGTGTCATAA
65 CACACATTCGTGTGTCATAA
* * *
2711671 ATTTATGACACGCATTTATGAC-TTACATTGCGTGTCATTGAAGCACACACCATTAGAA-AAGAT
1 ATTTATGACACGCATTTATGACGCT-CATTGCGCGTCATTGAAGCACACACCA-TA-AAGAAGAC
2711734 GACACACATTCGTGTGTC
63 GACACACATTCGTGTGTC
2711752 GTGATTGTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 64 0.93
86 2 0.03
87 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (84 bp):
ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCACACACCATAAAGAAGACGAC
ACACATTCGTGTGTCATAA
Found at i:2721251 original size:19 final size:19
Alignment explanation
Indices: 2721227--2721265 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2721217 GGAGTGAGGT
2721227 AGAGGAAATAATCACAGGC
1 AGAGGAAATAATCACAGGC
2721246 AGAGGAAATAATCACAGGC
1 AGAGGAAATAATCACAGGC
2721265 A
1 A
2721266 AAGTTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.26, T:0.10
Consensus pattern (19 bp):
AGAGGAAATAATCACAGGC
Found at i:2732252 original size:61 final size:61
Alignment explanation
Indices: 2732142--2732296 Score: 195
Period size: 61 Copynumber: 2.5 Consensus size: 61
2732132 TAAGGACACT
* * *
2732142 TAGTGCAAGTGGTGGGCACGACCTTATGTCTCATATACGGATCAACACTAGAGTGTAAACC
1 TAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATACAGATCAACACTAGAGTGTAAACC
* * * * * *
2732203 TGGTGCAGGTGGTGGGCACAACTTTATGTGTCATA-ACCAGATTAGCACTAGAGTGTAAACT
1 TAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATA-CAGATCAACACTAGAGTGTAAACC
* *
2732264 TACTGCAGGCGGTGGGCACGACCTTATGTGTCA
1 TAGTGCAGGTGGTGGGCACGACCTTATGTGTCA
2732297 CAACACTACG
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 1 0.01
61 78 0.99
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (61 bp):
TAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATACAGATCAACACTAGAGTGTAAACC
Found at i:2736765 original size:19 final size:17
Alignment explanation
Indices: 2736732--2736769 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
2736722 ATCCTAGCCT
2736732 TTCTTCCCTCTTCTTTC
1 TTCTTCCCTCTTCTTTC
2736749 TTCTTCCACTCCTTCTTTC
1 TTCTTCC-CT-CTTCTTTC
2736768 TT
1 TT
2736770 TGCTAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCTTCCCTCTTCTTTC
Found at i:2743341 original size:20 final size:22
Alignment explanation
Indices: 2743298--2743494 Score: 81
Period size: 21 Copynumber: 9.3 Consensus size: 22
2743288 ATAAAATTAA
*
2743298 ATAAAT-TAATATAATAAGTAT
1 ATAAATATACTATAATAAGTAT
*
2743319 ATATATA-AC-ATAATAATGT-T
1 ATAAATATACTATAATAA-GTAT
*
2743339 ATAAATATACTATAAT-A-TAA
1 ATAAATATACTATAATAAGTAT
2743359 ATATAATATA-TATAAACTAA-TAT
1 ATA-AATATACTAT-AA-TAAGTAT
* *
2743382 AT-AATATAATATACAT-A-TAC
1 ATAAATATACTATA-ATAAGTAT
* *
2743402 ATATATATACTAT-A-AACTAT
1 ATAAATATACTATAATAAGTAT
*
2743422 ATACTATATACTAT-AT-A-TAT
1 ATA-AATATACTATAATAAGTAT
*
2743442 ATATATATAACTA-ATATAA-TAT
1 ATAAATAT-ACTATA-ATAAGTAT
2743464 ATAAATATAGACTATAATAA-TAT
1 ATAAATAT--ACTATAATAAGTAT
2743487 AATAAATA
1 -ATAAATA
2743495 ATAATAATAA
Statistics
Matches: 142, Mismatches: 11, Indels: 43
0.72 0.06 0.22
Matches are distributed among these distances:
19 8 0.06
20 40 0.28
21 49 0.35
22 21 0.15
23 16 0.11
24 8 0.06
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAAATATACTATAATAAGTAT
Found at i:2743346 original size:22 final size:20
Alignment explanation
Indices: 2743298--2743364 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
2743288 ATAAAATTAA
*
2743298 ATAAAT-TAATATAATAAGT
1 ATAAATATAACATAATAAGT
*
2743317 ATATATATAACATAATAATGTT
1 ATAAATATAACATAATAA-G-T
2743339 ATAAATAT-AC-T-ATAA-T
1 ATAAATATAACATAATAAGT
2743355 ATAAATATAA
1 ATAAATATAA
2743365 TATATATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
16 9 0.22
17 1 0.02
19 9 0.22
20 11 0.27
21 3 0.07
22 8 0.20
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
ATAAATATAACATAATAAGT
Found at i:2743356 original size:47 final size:47
Alignment explanation
Indices: 2743304--2743608 Score: 157
Period size: 47 Copynumber: 6.1 Consensus size: 47
2743294 TTAAATAAAT
* **
2743304 TAATATAATA-AGTATATATATAACATAATA-ATGTTATAAATATAC-TA
1 TAATATAATATAATATATATA-AAC-TAATATATAATAT-AATATACATA
2743351 TAATATAAATATAATATATATAAACTAATATATAATATAATATACATA
1 TAATAT-AATATAATATATATAAACTAATATATAATATAATATACATA
* * *
2743399 TACATAT-ATATACTATAAACTATATACT-ATATACTATATATATATATATATAA
1 TA-ATATAATATA--ATATA-TATAAACTAATATA-TA-ATATA-ATATACAT-A
* *
2743452 CTAATATAATAT-ATAAATATAGACTATAATAATATAATA-AATAATA-ATAA
1 -TAATATAATATAATATATATAAAC--TAAT-ATATAATATAAT-ATACAT-A
* *
2743502 TAATATACTGAATATATATATATATATACTATTATAT-ATATATATATAC-TA
1 T-A-ATA-T-AATATA-ATATATATAAACTAATATATAATATA-ATATACATA
*
2743553 T-ATATAATAATAATATACTATACTA-TATATATATATATATAATATACTATA
1 TAATATAAT-ATAATATA-TATA-AACTA-ATATATA-ATATAATATAC-ATA
2743604 TAATA
1 TAATA
2743609 ATGCACCATA
Statistics
Matches: 210, Mismatches: 11, Indels: 69
0.72 0.04 0.24
Matches are distributed among these distances:
46 8 0.04
47 33 0.16
48 26 0.12
49 29 0.14
50 27 0.13
51 25 0.12
52 24 0.11
53 19 0.09
54 9 0.04
55 10 0.05
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (47 bp):
TAATATAATATAATATATATAAACTAATATATAATATAATATACATA
Found at i:2743371 original size:2 final size:2
Alignment explanation
Indices: 2743338--2743671 Score: 175
Period size: 2 Copynumber: 172.0 Consensus size: 2
2743328 ATAATAATGT
* * *
2743338 TA TA AA TA TA CTA TA -A TA TA AA TA TA -A TA TA TA TA AA CTA -A
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
2743379 TA TA TA -A TA TA -A TA TA CA TA TA CA TA TA TA TA CTA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
2743421 TA TA CTA TA TA CTA TA TA TA TA TA TA TA TA -A CTA -A TA TA -A
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
2743461 TA TA TA AA TA TA GA CTA TA -A TA -A TA TA -A TA AA TA -A TA -A
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2743499 TA -A TA -A TA TA CTGA -A TA TA TA TA TA TA TA TA CTA T- TA TA
1 TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA -TA TA TA TA
2743538 TA TA TA TA TA TA CTA TA TA TA -A TA -A TA -A TA TA CTA TA CTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA
* * *
2743578 TA TA TA TA TA TA TA TA -A TA TA CTA TA TA -A TA -A TG CA CCA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* *
2743619 -A TA TA -A TA CA TA CTA TA TA T- TA TA TA T- TA TA TA TGG TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
2743659 TA -A AA TA TA TA TA
1 TA TA TA TA TA TA TA
2743672 GTATTAATCC
Statistics
Matches: 259, Mismatches: 27, Indels: 92
0.69 0.07 0.24
Matches are distributed among these distances:
1 28 0.11
2 202 0.78
3 28 0.11
4 1 0.00
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (2 bp):
TA
Found at i:2743381 original size:14 final size:14
Alignment explanation
Indices: 2743338--2743610 Score: 151
Period size: 13 Copynumber: 20.1 Consensus size: 14
2743328 ATAATAATGT
*
2743338 TATAAATATACT-A
1 TATATATATACTAA
*
2743351 TAATATAAATA-TAA
1 T-ATATATATACTAA
*
2743365 TATATATAAACTAA
1 TATATATATACTAA
2743379 TATATA-ATA-TAA
1 TATATATATACTAA
*
2743391 TATACATATAC--A
1 TATATATATACTAA
2743403 TATATATACTA-TAA
1 TATATATA-TACTAA
*
2743417 -A-CTATATACT-A
1 TATATATATACTAA
2743428 TATACTATATA-T-A
1 TATA-TATATACTAA
2743441 TATATATATAACTAA
1 TATATATAT-ACTAA
2743456 TATA-ATATA-TAAA
1 TATATATATACT-AA
* *
2743469 TATAGACTATAATAA
1 TATATA-TATACTAA
* *
2743484 TATAATAAATAATAA
1 TAT-ATATATACTAA
2743499 TA-ATAATATACTGAA
1 TATAT-ATATACT-AA
2743514 TATATATATA-T-A
1 TATATATATACTAA
2743526 TATACTAT-TA-TATA
1 TATA-TATATACTA-A
2743540 TATATATATACT-A
1 TATATATATACTAA
*
2743553 TATATA-ATAATAA
1 TATATATATACTAA
2743566 TATACTATACTA-TATA
1 TATA-TATA-TACTA-A
2743582 TATATATATA-TAA
1 TATATATATACTAA
*
2743595 TATACTATATAATAA
1 TATA-TATATACTAA
2743610 T
1 T
2743611 GCACCATAAT
Statistics
Matches: 211, Mismatches: 14, Indels: 68
0.72 0.05 0.23
Matches are distributed among these distances:
11 3 0.01
12 40 0.19
13 56 0.27
14 56 0.27
15 44 0.21
16 12 0.06
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (14 bp):
TATATATATACTAA
Found at i:2743383 original size:12 final size:12
Alignment explanation
Indices: 2743304--2743608 Score: 166
Period size: 12 Copynumber: 24.0 Consensus size: 12
2743294 TTAAATAAAT
2743304 TAATATAATAAGTA
1 TAATAT-ATAA-TA
*
2743318 T-ATATATAACA
1 TAATATATAATA
**
2743329 TAATA-ATGTTA
1 TAATATATAATA
*
2743340 TAA-ATATACTA
1 TAATATATAATA
2743351 TAATATA-AATA
1 TAATATATAATA
*
2743362 TAATATATATAAA
1 TAATATATA-ATA
2743375 CTAATATATAATA
1 -TAATATATAATA
*
2743388 TAATATA-CATA
1 TAATATATAATA
2743399 TACATATATATACTA
1 TA-ATATATA-A-TA
2743414 TAAACTATATACTATA
1 T-AA-TATATA--ATA
*
2743430 TACTATATATATA
1 TAATATATA-ATA
2743443 TATATATAACTAATA
1 TA-ATAT-A-TAATA
2743458 TAATATATAAATA
1 TAATATAT-AATA
2743471 TAGACTATAATAATA
1 TA-A-TAT-ATAATA
*
2743486 TAATAAATAATAA
1 TAATATATAAT-A
2743499 TAATA-AT-ATA
1 TAATATATAATA
2743509 CTGAATATAT-ATA
1 -T-AATATATAATA
*
2743522 T-ATATATACTA
1 TAATATATAATA
*
2743533 TTATATAT-ATA
1 TAATATATAATA
2743544 T-ATATACTATATA
1 TAATATA-TA-ATA
2743557 TAATA-ATAATA
1 TAATATATAATA
2743568 TACTATACTATATATA
1 TA--ATA-TATA-ATA
2743584 TATATATATAATA
1 TA-ATATATAATA
*
2743597 TACTATATAATA
1 TAATATATAATA
2743609 ATGCACCATA
Statistics
Matches: 239, Mismatches: 17, Indels: 72
0.73 0.05 0.22
Matches are distributed among these distances:
10 13 0.05
11 45 0.19
12 53 0.22
13 47 0.20
14 33 0.14
15 27 0.11
16 19 0.08
17 2 0.01
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (12 bp):
TAATATATAATA
Found at i:2743400 original size:79 final size:77
Alignment explanation
Indices: 2743304--2743603 Score: 211
Period size: 77 Copynumber: 3.9 Consensus size: 77
2743294 TTAAATAAAT
* *
2743304 TAATATAATA-AGTATATATATAACATAATAATGTTATAAATATACTATA-ATA-TAAATATAAT
1 TAATATAATATA-CATATATAT-ATATAATAA--TTAT-AATATACTATATATACTAAATATAAT
2743366 ATATATAAACTAATATA
61 ATATATAAACTAATATA
* * *
2743383 TAATATAATATACATATACATATAT-AT-ACTATAAACTATA-TACTATATACTATATAT-ATAT
1 TAATATAATATACATATATATATATAATAATTAT-AA-TATACTA-TATATACTAAATATAATAT
2743444 ATATATAACTAATATA
63 ATATA-AACTAATATA
* * *
2743460 -ATATATAAATATAGACTATA-ATAATATAATAA--ATAATAATAATA-ATATACTGAATATATA
1 TA-ATAT-AATATACA-TATATAT-ATATAATAATTATAAT-ATACTATATATACTAAATATA-A
* *
2743520 TATATATATACTATTATA
60 TATATATAAACTAATATA
*
2743538 T-ATATATATATAC-TATATATA-ATAATAA-TATACTATACTATATATA-TATATATATAATAT
1 TAATATA-ATATACATATATATATATAATAATTATAATATACTATATATACTA-A-ATATAATAT
2743598 ACTATA
63 A-TATA
2743604 TAATAATGCA
Statistics
Matches: 183, Mismatches: 14, Indels: 51
0.74 0.06 0.21
Matches are distributed among these distances:
74 21 0.11
75 26 0.14
76 26 0.14
77 43 0.23
78 25 0.14
79 38 0.21
80 3 0.02
81 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (77 bp):
TAATATAATATACATATATATATATAATAATTATAATATACTATATATACTAAATATAATATATA
TAAACTAATATA
Found at i:2743456 original size:77 final size:75
Alignment explanation
Indices: 2743343--2743610 Score: 236
Period size: 77 Copynumber: 3.5 Consensus size: 75
2743333 AATGTTATAA
*
2743343 ATATACTATA-ATATAAATATAATATATATAAACTAATATATAATATAATATACATATACATATA
1 ATATACTATATATATATATAT-ATATATAT-AACTAATATATAATATAATATACATATA-ATATA
2743407 TATACTATAAACT
63 TATACTATAAACT
*
2743420 ATATACTATATACTATATATATATATATATAACTAATATA-ATATATAAATATAGACTATAATA-
1 ATATACTATATA-TATATATATATATATATAACTAATATATA-ATAT-AATATACA-TATAATAT
2743483 ATATA--ATAAA-T
62 ATATACTATAAACT
* * *
2743494 A-ATAATAATAATATACTGAATATATATATATATATACTATTATATATATATATATACTATATAT
1 ATATACT-AT-ATATA-T--ATATATATATATATA-ACTAATATATA-ATATA-ATA-TACATAT
2743558 AATAATAATATACTAT--ACT
57 AAT-AT-ATATACTATAAACT
2743577 ATATA-TATATATATATA-ATATACTATATAA-TAAT
1 ATATACTATATATATATATATATA-TATATAACTAAT
2743611 GCACCATAAT
Statistics
Matches: 163, Mismatches: 6, Indels: 45
0.76 0.03 0.21
Matches are distributed among these distances:
73 4 0.02
74 6 0.04
75 9 0.06
76 4 0.02
77 50 0.31
78 37 0.23
79 27 0.17
80 5 0.03
81 5 0.03
82 8 0.05
83 3 0.02
84 5 0.03
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (75 bp):
ATATACTATATATATATATATATATATATAACTAATATATAATATAATATACATATAATATATAT
ACTATAAACT
Found at i:2755526 original size:20 final size:20
Alignment explanation
Indices: 2755503--2755556 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
2755493 CTATTGAAGC
*
2755503 AGTATCGATACTATGC-TAGT
1 AGTATCGATACTA-GCAGAGT
2755523 AGTATCGATACCTAGCAAGAGT
1 AGTATCGATA-CTAGC-AGAGT
2755545 AGTATCGATACT
1 AGTATCGATACT
2755557 GGGTGACCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.40
21 5 0.17
22 13 0.43
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTAGCAGAGT
Found at i:2763089 original size:2 final size:2
Alignment explanation
Indices: 2763084--2763283 Score: 78
Period size: 2 Copynumber: 100.5 Consensus size: 2
2763074 AAAAATCTAA
* *
2763084 AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT AGT AT AT GGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT
* * * * * *
2763126 TT AA AT AA AT AT AT AGT AT AT AGT TT TT AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * *
2763170 AT A- AT AT AGT AT TT A- AA AT AC AT AT AT AT AT AG AT AT AT A-
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
2763210 AT AT AGT AT AC A- AGT -T TT GA- AA AT CT AT GT AA AT AT AT -T
1 AT AT A-T AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT
*
2763249 AT A- AT AT GAT AT AA 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
2763284 ATTTTATACA
Statistics
Matches: 150, Mismatches: 29, Indels: 38
0.69 0.13 0.18
Matches are distributed among these distances:
1 10 0.07
2 128 0.85
3 12 0.08
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2763308 original size:30 final size:30
Alignment explanation
Indices: 2763242--2763339 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
2763232 ATCTATGTAA
* * *
2763242 ATATATTATAA-TATGATATAAATATATATAT
1 ATATATTATAATTAT--TATACATTTTTATAT
2763273 ATATATATATAATT-TTATACATTTTTATAT
1 ATATAT-TATAATTATTATACATTTTTATAT
* * *
2763303 TTATATTATTATTATTATTCA-TTTTAT-T
1 ATATATTATAATTATTATACATTTTTATAT
2763331 -TATATTATA
1 ATATATTATA
2763340 GGTTCAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
27 8 0.14
28 1 0.02
29 12 0.21
30 23 0.40
31 6 0.11
32 6 0.11
33 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (30 bp):
ATATATTATAATTATTATACATTTTTATAT
Found at i:2769852 original size:22 final size:22
Alignment explanation
Indices: 2769824--2769874 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
2769814 TATTCGGTTC
*
2769824 GTTTATGTTCATGAACAAGTTT
1 GTTTATGTTCATGAACAAGCTT
2769846 GTTTATGTTCATGAACAAGCTT
1 GTTTATGTTCATGAACAAGCTT
2769868 GTTTATG
1 GTTTATG
2769875 AGTTCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (22 bp):
GTTTATGTTCATGAACAAGCTT
Found at i:2776673 original size:13 final size:13
Alignment explanation
Indices: 2776655--2776688 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2776645 ATAATATGAT
* *
2776655 TTTTCAAACATTG
1 TTTTCAAAAATAG
2776668 TTTTCAAAAATAG
1 TTTTCAAAAATAG
2776681 TTTTCAAA
1 TTTTCAAA
2776689 TTTTACCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:2778434 original size:13 final size:13
Alignment explanation
Indices: 2778412--2778445 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2778402 AGATGGAGTA
*
2778412 ATTTTCAAAATTG
1 ATTTTCAAAAATG
2778425 A-TTTCAAAAATG
1 ATTTTCAAAAATG
2778437 ATTTTCAAA
1 ATTTTCAAA
2778446 GAAAATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:2779768 original size:30 final size:32
Alignment explanation
Indices: 2779734--2779793 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 32
2779724 CGTGAACAAT
2779734 AATAAACGAACAC-AA-AC-ACTTTTAAAAATA
1 AATAAACGAACACGAATACGA-TTTTAAAAATA
2779764 AATAAACGAACACGAATACGATTTTAAAAA
1 AATAAACGAACACGAATACGATTTTAAAAA
2779794 CTTAAACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 13 0.48
31 2 0.07
32 11 0.41
33 1 0.04
ACGTcount: A:0.58, C:0.15, G:0.07, T:0.20
Consensus pattern (32 bp):
AATAAACGAACACGAATACGATTTTAAAAATA
Found at i:2781754 original size:17 final size:17
Alignment explanation
Indices: 2781732--2781782 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
2781722 AATATTGGTT
2781732 TAATAA-AATAATAATAG
1 TAATAATAAT-ATAATAG
2781749 TAATAATAATATAATAATG
1 TAATAATAATATAAT-A-G
*
2781768 T-ATAATGATATAATA
1 TAATAATAATATAATA
2781783 TATGTACTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 12 0.40
18 16 0.53
19 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
TAATAATAATATAATAG
Found at i:2781755 original size:12 final size:11
Alignment explanation
Indices: 2781732--2781784 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
2781722 AATATTGGTT
*
2781732 TAATAAAATAA
1 TAATATAATAA
2781743 TAATAGTAATAA
1 TAATA-TAATAA
2781755 TAATATAATAA
1 TAATATAATAA
*
2781766 T-GTATAATGATA
1 TAATATAAT-A-A
2781778 TAATATA
1 TAATATA
2781785 TGTACTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 6 0.17
11 13 0.37
12 12 0.34
13 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (11 bp):
TAATATAATAA
Found at i:2781906 original size:25 final size:23
Alignment explanation
Indices: 2781854--2781910 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 23
2781844 ATATACAACT
*
2781854 ATATAATAATGTATGTACTATATA
1 ATATAAT-ATATATGTACTATATA
*
2781878 ATATAATATATATGTATCCTATATC
1 ATATAATATATATGTA--CTATATA
2781903 ATATAATA
1 ATATAATA
2781911 AATGCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 8 0.28
24 7 0.24
25 14 0.48
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (23 bp):
ATATAATATATATGTACTATATA
Found at i:2781966 original size:18 final size:19
Alignment explanation
Indices: 2781934--2781972 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2781924 ATAGTACGTT
2781934 TATACTATATAATATA-AA
1 TATACTATATAATATATAA
2781952 TATACTATA-AGATATATAA
1 TATACTATATA-ATATATAA
2781971 TA
1 TA
2781973 ATGTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 14 0.74
19 4 0.21
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
TATACTATATAATATATAA
Found at i:2783800 original size:37 final size:36
Alignment explanation
Indices: 2783749--2783818 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
2783739 CTTTTCGTGT
* *
2783749 AAAAAATTAGTCACAAAAACCATAAATAATTGTCTC
1 AAAAAATTAATCACAAAAAACATAAATAATTGTCTC
* *
2783785 AAAAAATATAATCACAAAAAATATAAGTAATTGT
1 AAAAAAT-TAATCACAAAAAACATAAATAATTGT
2783819 GACAAAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 7 0.24
37 22 0.76
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (36 bp):
AAAAAATTAATCACAAAAAACATAAATAATTGTCTC
Found at i:2797072 original size:23 final size:21
Alignment explanation
Indices: 2797027--2797107 Score: 94
Period size: 23 Copynumber: 3.8 Consensus size: 21
2797017 ATAGGGCAGA
2797027 GGGAATCGATACCCCCTTAAAG
1 GGGAATCGATACCCCCTT-AAG
*
2797049 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TT-AAG
* *
2797072 GGGAACCGATTCCCCC-T-AG
1 GGGAATCGATACCCCCTTAAG
2797091 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
2797108 GGGGTTCTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
19 16 0.31
21 1 0.02
22 15 0.29
23 20 0.38
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (21 bp):
GGGAATCGATACCCCCTTAAG
Found at i:2797111 original size:18 final size:19
Alignment explanation
Indices: 2797070--2797111 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2797060 CCCCCTTTGA
*
2797070 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCT
*
2797089 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATACCCCCT
2797108 -GGGG
1 AGGGG
2797112 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:2853370 original size:16 final size:16
Alignment explanation
Indices: 2853349--2853379 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2853339 TAATAAATAG
2853349 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2853365 ACGAACATAAACGAA
1 ACGAACATAAACGAA
2853380 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2853469 original size:16 final size:16
Alignment explanation
Indices: 2853448--2853508 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
2853438 TAATAAATAA
2853448 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2853464 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2853480 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2853496 ACGAACATAAACG
1 ACGAACATAAACG
2853509 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2854271 original size:14 final size:14
Alignment explanation
Indices: 2854254--2854309 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
2854244 AATGAACATA
2854254 AACGAACATAATCG
1 AACGAACATAATCG
2854268 AACGAACAT-A---
1 AACGAACATAATCG
* *
2854278 AACAAACATAACCG
1 AACGAACATAATCG
2854292 AACGAACATAATCG
1 AACGAACATAATCG
2854306 AACG
1 AACG
2854310 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:2854274 original size:24 final size:24
Alignment explanation
Indices: 2854234--2854308 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
2854224 GATTGAGTTA
*
2854234 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
2854258 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
2854282 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
2854306 AAC
1 AAC
2854309 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:2854655 original size:18 final size:18
Alignment explanation
Indices: 2854632--2854676 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2854622 CCGATTGTTT
*
2854632 ACCATTGACCCACCATTG
1 ACCATTGACCAACCATTG
*
2854650 ACCATTGACCAACCGTTG
1 ACCATTGACCAACCATTG
2854668 ACCATTGAC
1 ACCATTGAC
2854677 TTTGACTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.36, G:0.13, T:0.22
Consensus pattern (18 bp):
ACCATTGACCAACCATTG
Found at i:2855502 original size:39 final size:39
Alignment explanation
Indices: 2855448--2855557 Score: 166
Period size: 39 Copynumber: 2.8 Consensus size: 39
2855438 CGCTTTCCGC
* *
2855448 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCATATTGT
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCATACTAT
* *
2855487 AGGCTCATCGGCTTTGTACTCAGGGTAAGTCCATACTAT
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCATACTAT
* *
2855526 AGGCTCCTTGGCTTTATGCTCAGGGTAAGTCC
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCC
2855558 TTACCGCAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (39 bp):
AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCATACTAT
Found at i:2857943 original size:18 final size:18
Alignment explanation
Indices: 2857920--2857963 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2857910 TAGTTTGATT
*
2857920 AATGAATTAACATTATTC
1 AATGAACTAACATTATTC
*
2857938 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
2857956 AATGAACT
1 AATGAACT
2857964 CGATGCATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:2861387 original size:57 final size:57
Alignment explanation
Indices: 2861316--2861426 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
2861306 GATGATCTTG
* *
2861316 GAGAGGAAGAAGTTGTGCAAGCCTCACCTAATCTTGCTACATCAAATAATGATGCAC
1 GAGAGAAAGAAGTTGTGCAAGCCTCACCTAATCTAGCTACATCAAATAATGATGCAC
* * *
2861373 GAGAGAAAGTAGTTGTGCACGTCTCACCTAATCTAGCTACATCAAATAATGATG
1 GAGAGAAAGAAGTTGTGCAAGCCTCACCTAATCTAGCTACATCAAATAATGATG
2861427 TTATCCCGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (57 bp):
GAGAGAAAGAAGTTGTGCAAGCCTCACCTAATCTAGCTACATCAAATAATGATGCAC
Found at i:2868071 original size:3 final size:3
Alignment explanation
Indices: 2868063--2868095 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2868053 AAAGAATAAT
2868063 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2868096 ATTTTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2868512 original size:24 final size:24
Alignment explanation
Indices: 2868484--2868529 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2868474 AAGAAAATTA
2868484 ATAAATAAATTA-TTTTTATAATAT
1 ATAAAT-AATTATTTTTTATAATAT
*
2868508 ATAAATATTTATTTTTTATAAT
1 ATAAATAATTATTTTTTATAAT
2868530 TTAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATAAATAATTATTTTTTATAATAT
Found at i:2869626 original size:7 final size:7
Alignment explanation
Indices: 2869616--2869651 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
2869606 GGAAAAAATG
2869616 AATAATA
1 AATAATA
2869623 AATAATAA
1 AATAAT-A
2869631 AATAAATA
1 AAT-AATA
2869639 AATAATA
1 AATAATA
2869646 AATAAT
1 AATAAT
2869652 GTATTATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 16 0.59
8 8 0.30
9 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:2870178 original size:33 final size:33
Alignment explanation
Indices: 2870137--2870203 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2870127 AAATGATTCG
* *
2870137 GGTTTTAGTATTTTAATATGACTCAAATACGTT
1 GGTTTTAGTATTTCAATAAGACTCAAATACGTT
*
2870170 GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
1 GGTTTTAGTATTTCAATAAGACTCAAATACGTT
2870203 G
1 G
2870204 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (33 bp):
GGTTTTAGTATTTCAATAAGACTCAAATACGTT
Found at i:2870270 original size:3 final size:3
Alignment explanation
Indices: 2870257--2870297 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
2870247 GGCTTGCAAA
2870257 AAT AAT AAAT AAT AAT AAT AAT AAT AA- ATAT AAT -AT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
2870298 AATGTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 3 0.09
3 27 0.79
4 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2871165 original size:110 final size:108
Alignment explanation
Indices: 2870962--2871220 Score: 362
Period size: 110 Copynumber: 2.4 Consensus size: 108
2870952 GTATTGCTCC
* * *
2870962 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTTGCTCTG---GAACTGGGAAATTATTTGTTGA
1 GAGTCCAATATCCTTCGCCGTGAAGTTGAAA-TTGCTCTGAAAGAAATGGAAAATTATTTGTTGA
*
2871024 CAATCAGCCGCCCCTTCGTCTTGAAGTTGAGCTTCTGTTGTCTT
65 CAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTCTGTTGTCTT
** * *
2871068 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAAGAAATTGAAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTG-CTCTGAAAGAAATGGAAAA-TTATTTGTTG
* *
2871133 ACAATTAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
64 ACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTCTGTTGTCTT
*
2871178 GGGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAA
1 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATT-GCTCTGAAA
2871221 TTAGGAAGCC
Statistics
Matches: 134, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
105 3 0.02
106 33 0.25
109 8 0.06
110 89 0.66
111 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (108 bp):
GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGCTCTGAAAGAAATGGAAAATTATTTGTTGAC
AATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTCTGTTGTCTT
Found at i:2875249 original size:10 final size:10
Alignment explanation
Indices: 2875234--2875283 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
2875224 AGGAAAAAAT
2875234 TAATAATAAA
1 TAATAATAAA
2875244 TAAT-A-AAA
1 TAATAATAAA
2875252 T-A-AATAAA
1 TAATAATAAA
2875260 -AATAAATAAA
1 TAAT-AATAAA
2875270 TAATAATAAA
1 TAATAATAAA
2875280 TAAT
1 TAAT
2875284 GTATTATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 2 0.06
8 8 0.24
9 1 0.03
10 20 0.59
11 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAATAATAAA
Found at i:2875792 original size:33 final size:33
Alignment explanation
Indices: 2875755--2875836 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
2875745 AGTCCTACTT
*
2875755 GGACTCAAATGC-TTCGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTT-GGTTTTAGTGTTTCAATA
2875788 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
*
2875821 AGACTCAAATACGTTG
1 GGACTCAAATACGTTG
2875837 ATTTATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 44 0.96
34 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (33 bp):
GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
Found at i:2875901 original size:8 final size:8
Alignment explanation
Indices: 2875888--2875947 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
2875878 GGAGCCTACA
2875888 AAAATAAT
1 AAAATAAT
2875896 AAAATAAT
1 AAAATAAT
2875904 AATAATAAT
1 AA-AATAAT
*
2875913 AATA-AAT
1 AAAATAAT
2875920 -AAATAA-
1 AAAATAAT
2875926 ATAAAT-AT
1 A-AAATAAT
*
2875934 AATATAAT
1 AAAATAAT
2875942 AAAATA
1 AAAATA
2875948 TTTTTGTAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
6 2 0.05
7 9 0.21
8 23 0.55
9 8 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:2875904 original size:3 final size:3
Alignment explanation
Indices: 2875890--2875947 Score: 52
Period size: 3 Copynumber: 19.3 Consensus size: 3
2875880 AGCCTACAAA
2875890 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAAT AAAT AAAT AA- ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT AAT A-AT AAT
2875937 -AT AAT AA- AAT A
1 AAT AAT AAT AAT A
2875948 TTTTTGTAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
2 7 0.14
3 30 0.61
4 12 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2875946 original size:27 final size:29
Alignment explanation
Indices: 2875888--2875947 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
2875878 GGAGCCTACA
2875888 AAAAT-AATAAAATAATAATAATAATAAT
1 AAAATAAATAAAATAATAATAATAATAAT
2875916 -AAATAAAT-AAATAA-ATATAAT-ATAAT
1 AAAATAAATAAAATAATA-ATAATAATAAT
2875942 AAAATA
1 AAAATA
2875948 TTTTTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 6 0.21
27 20 0.69
28 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAATAAATAAAATAATAATAATAATAAT
Found at i:2876274 original size:16 final size:16
Alignment explanation
Indices: 2876253--2876285 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2876243 TGAATCAAAT
2876253 CTCAAACTAAAATAAC
1 CTCAAACTAAAATAAC
2876269 CTCAAACTAAAATAAC
1 CTCAAACTAAAATAAC
2876285 C
1 C
2876286 CAACCCGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (16 bp):
CTCAAACTAAAATAAC
Found at i:2876468 original size:17 final size:18
Alignment explanation
Indices: 2876446--2876481 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2876436 CGGTTCTCCC
*
2876446 ATAAATATT-TTTATATT
1 ATAAATATTATTAATATT
2876463 ATAAATATTATTAATATT
1 ATAAATATTATTAATATT
2876481 A
1 A
2876482 GTTGAAACAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAAATATTATTAATATT
Found at i:2878835 original size:101 final size:103
Alignment explanation
Indices: 2878547--2879218 Score: 499
Period size: 101 Copynumber: 6.3 Consensus size: 103
2878537 TTTTATTTGA
* * * * ** ** *
2878547 AATATAAATTAATTAGATTATTTATATTGATTTTATAGATTAAGCTGTATTCAAGTGGTCTGGTA
1 AATATAAATT-ATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGAGTGGTTTGGTA
* ** *
2878612 AGTTTA-TTTAAATTTTCGTGTAATT-TTTGTTT-TTAATTT
65 AGTTTAGTTTAAAATTTATTGT-ATTATTT-TTTATTAA-GT
* ***
2878651 AA-ATTATAATTATTAGA-TATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAAAACTTG
1 AATA-TA-AATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGAGT--GGTTTG
*
2878714 GTAAGTGTAGTTT-AAA-TTATTAG-ATTA-TTTTTATTAAGT
62 GTAAGTTTAGTTTAAAATTTATT-GTATTATTTTTTATTAAGT
* * *
2878753 AATATAAATTATTAGACTAATTATTTT-ATTTTACAGATTAAATCGTATTTGAGTGGTTTGGTAA
1 AATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGAGTGGTTTGGTAA
* * *
2878817 GTTTAGTTTAAAATTTATTGTTTTATTTTTTTCTTTTATTGT
66 GTTTAGTTTAAAATTTATTGTATTA--TTTTT-TATTA-AGT
* * * * *
2878859 AAATATAAATTATTTACACTATTTATTATGATTTTACATATTAAACTCTATTTGAGTGGTTTGAT
1 -AATATAAATTA-TTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGAGTGGTTTGGT
* * * * * *
2878924 AAGTTAAATTTAAATTTTCGTGTAATTTTTAGTATAATTTTTTTTTAAATTT
64 AAGTTTAGTTTAAA--AT--T-T-A---TT-GTATTATTTTTTATT-AA-GT
* *
2878976 AA-ATTATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTTGGT
1 AATA-TA-AATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGAGTGGTTTGGT
*
2879040 AAGTTTAGTTT-AAATTATATT-T-TTATTTTTTATTGAGT
64 AAGTTTAGTTTAAAATT-TATTGTATTATTTTTTATTAAGT
* * *
2879078 AATATAAATTATTGGACTATTTATTTTGATTTTACATACTAAATTGTATTTGAGTGGTTTAGTAA
1 AATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGAGTGGTTTGGTAA
* * * * *
2879143 GTTTAGTTTAAATTTTATTGTTTTGTTTTTTGTTTTTATTGT
66 GTTTAGTTTAAAATTTATTG-TAT-TATTTT-TTATTA-AGT
*
2879185 AAATGTAAATTAATTAGACTATTTATTTTGATTT
1 -AATATAAATT-ATTAGACTATTTATTTTGATTT
2879219 AACAAATTTT
Statistics
Matches: 455, Mismatches: 68, Indels: 85
0.75 0.11 0.14
Matches are distributed among these distances:
99 15 0.03
100 4 0.01
101 109 0.24
102 26 0.06
103 46 0.10
104 28 0.06
105 27 0.06
106 9 0.02
107 15 0.03
108 22 0.05
109 63 0.14
110 1 0.00
111 3 0.01
113 2 0.00
114 1 0.00
115 4 0.01
116 62 0.14
117 12 0.03
118 2 0.00
119 4 0.01
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (103 bp):
AATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGAGTGGTTTGGTAA
GTTTAGTTTAAAATTTATTGTATTATTTTTTATTAAGT
Found at i:2879072 original size:325 final size:326
Alignment explanation
Indices: 2878632--2879218 Score: 923
Period size: 326 Copynumber: 1.8 Consensus size: 326
2878622 AATTTTCGTG
*
2878632 TAATTTTTGTTTTTAATTTAAATTATAATTATTAGATATTTATTTTGATTTTACATATTAAGTTG
1 TAATTTTTGTTTTAAATTTAAATTATAATTATTAGATATTTATTTTGATTTTACATATTAAGTTG
2878697 TATTTGAGTAAAACTTGGTAAGTGTAGTTTAAATTATTAGATTATTTTTATTAAGTAATATAAAT
66 TATTTGAGT-AAACTTGGTAAGTGTAGTTTAAATTATTAGATTATTTTTATTAAGTAATATAAAT
* *
2878762 TATTAGACTAATTATTTT-ATTTTACAGATTAAATCGTATTTGAGTGGTTTGGTAAGTTTAGTTT
130 TATTAGACTAATTATTTTGATTTTACAGACTAAATCGTATTTGAGTGGTTTAGTAAGTTTAGTTT
*
2878826 AAAATTTATTGTTTTATTTTTT-TCTTTTATTGTAAATATAAATTATTTACACTATTTATTATGA
195 AAAATTTATTGTTTTATTTTTTGT-TTTTATTGTAAATATAAATTAATTACACTATTTATTATGA
2878890 TTTTACATATTAAACTCTATTTGAGTGGTTTGATAAGTTAAATTTAAATTTTCGTGTAATTTTTA
259 TTTTACATATTAAACTCTATTTGAGTGGTTTGATAAGTTAAATTTAAATTTTCGTGTAATTTTTA
2878955 GTA
324 GTA
2878958 TAATTTTT-TTTTAAATTTAAATTATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTT
1 TAATTTTTGTTTTAAATTTAAATTATAATTATTAGA-TATTTATTTTGATTTTACATATTAAGTT
** * ** *
2879022 GTATTTGAGT-AGTTTGGTAAGTTTAGTTTAAATTA-TATTTTTATTTTTTATTGAGTAATATAA
65 GTATTTGAGTAAACTTGGTAAGTGTAGTTTAAATTATTA-GATTA-TTTTTATTAAGTAATATAA
* * * *
2879085 ATTATTGGACTATTTATTTTGATTTTACATACTAAATTGTATTTGAGTGGTTTAGTAAGTTTAGT
128 ATTATTAGACTAATTATTTTGATTTTACAGACTAAATCGTATTTGAGTGGTTTAGTAAGTTTAGT
* * * * *
2879150 TTAAATTTTATTGTTTTGTTTTTTGTTTTTATTGTAAATGTAAATTAATTAGACTATTTATTTTG
193 TTAAAATTTATTGTTTTATTTTTTGTTTTTATTGTAAATATAAATTAATTACACTATTTATTATG
2879215 ATTT
258 ATTT
2879219 AACAAATTTT
Statistics
Matches: 237, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
323 2 0.01
324 25 0.11
325 62 0.26
326 147 0.62
327 1 0.00
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (326 bp):
TAATTTTTGTTTTAAATTTAAATTATAATTATTAGATATTTATTTTGATTTTACATATTAAGTTG
TATTTGAGTAAACTTGGTAAGTGTAGTTTAAATTATTAGATTATTTTTATTAAGTAATATAAATT
ATTAGACTAATTATTTTGATTTTACAGACTAAATCGTATTTGAGTGGTTTAGTAAGTTTAGTTTA
AAATTTATTGTTTTATTTTTTGTTTTTATTGTAAATATAAATTAATTACACTATTTATTATGATT
TTACATATTAAACTCTATTTGAGTGGTTTGATAAGTTAAATTTAAATTTTCGTGTAATTTTTAGT
A
Found at i:2879130 original size:217 final size:223
Alignment explanation
Indices: 2878759--2879158 Score: 566
Period size: 217 Copynumber: 1.8 Consensus size: 223
2878749 AAGTAATATA
*
2878759 AATTATTAGACTAATTATTTTATTTTACAGATTAAATCGTATTTGAGTGGTTTGGTAAGTTTAGT
1 AATTATTAGACTAATTATTTTATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGTTTAGT
* *
2878824 TTAAAATTTATTGTTTTATTTTTTTCTTTTATTGTAAATATAAATTATTTACACTATTTATTATG
66 TTAAAATTTATTGTTTTATTTTTTTCATTGA-TGTAAATATAAATTATTTACACTATTTATTATG
*
2878889 ATTTTACATATTAAACTCTATTTGAGTGGTTT-GATAAGTTAAATTTAAATTTTCGTGTAATTTT
130 ATTTTACATACTAAACTCTATTTGAGTGGTTTAG-TAAGTTAAATTTAAATTTTCGTGTAATTTT
2878953 TAGTATAATTTTTTTTTAAATTTAAATTAT
194 TAGTATAATTTTTTTTTAAATTTAAATTAT
* * * *
2878983 AATTATTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTTGGTAAGTTTAG
1 AATTATTAGACTAATTATTTT-ATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGTTTAG
** *
2879048 TTT-AAA-TTATAT-TTTTA-TTTTTT-ATTGA-GT-AATATAAATTA-TTGGACTATTTATTTT
65 TTTAAAATTTAT-TGTTTTATTTTTTTCATTGATGTAAATATAAATTATTTACACTATTTATTAT
* * * *
2879105 GATTTTACATACTAAATTGTATTTGAGTGGTTTAGTAAGTTTAGTTTAAATTTT
129 GATTTTACATACTAAACTCTATTTGAGTGGTTTAGTAAGTTAAATTTAAATTTT
2879159 ATTGTTTTGT
Statistics
Matches: 158, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
217 60 0.38
218 12 0.08
219 2 0.01
221 3 0.02
222 6 0.04
223 9 0.06
224 24 0.15
225 42 0.27
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.54
Consensus pattern (223 bp):
AATTATTAGACTAATTATTTTATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGTTTAGT
TTAAAATTTATTGTTTTATTTTTTTCATTGATGTAAATATAAATTATTTACACTATTTATTATGA
TTTTACATACTAAACTCTATTTGAGTGGTTTAGTAAGTTAAATTTAAATTTTCGTGTAATTTTTA
GTATAATTTTTTTTTAAATTTAAATTAT
Found at i:2883736 original size:85 final size:85
Alignment explanation
Indices: 2883635--2883800 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 85
2883625 ATACAATCAC
* * * * *
2883635 GACACACGAATGTGTGTCATCTT-TTTTAATGATGTGTGCTTCAATGACACTCAATGTAA-GTCA
1 GACACACAAATGTGTGTCATCTTAATTT-ATGACGGGGGCTTCAATGACACTCAATG-AATGTCA
* *
2883698 TACATGCGTGTCATAAATTTAT
64 TAAATGCGCGTCATAAATTTAT
*
2883720 GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACGCTCAATGAATGTCATA
1 GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACTCAATGAATGTCATA
2883785 AATGCGCGTCATAAAT
66 AATGCGCGTCATAAAT
2883801 GTGTGTCATA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
84 2 0.03
85 66 0.93
86 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACTCAATGAATGTCATA
AATGCGCGTCATAAATTTAT
Found at i:2883795 original size:13 final size:13
Alignment explanation
Indices: 2883779--2883823 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
2883769 CTCAATGAAT
*
2883779 GTCATAAATGCGC
1 GTCATAAATGTGC
*
2883792 GTCATAAATGTGT
1 GTCATAAATGTGC
2883805 GTCATAAATGTGC
1 GTCATAAATGTGC
2883818 GTCATA
1 GTCATA
2883824 GATTTATGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (13 bp):
GTCATAAATGTGC
Found at i:2883801 original size:26 final size:26
Alignment explanation
Indices: 2883772--2883823 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2883762 AATGACGCTC
2883772 AATGAATGTCATAAATGCGCGTCATA
1 AATGAATGTCATAAATGCGCGTCATA
** *
2883798 AATGTGTGTCATAAATGTGCGTCATA
1 AATGAATGTCATAAATGCGCGTCATA
2883824 GATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (26 bp):
AATGAATGTCATAAATGCGCGTCATA
Found at i:2884443 original size:18 final size:18
Alignment explanation
Indices: 2884420--2884474 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
2884410 TTTGAATCAT
2884420 CTCATATGCAACCATGTG
1 CTCATATGCAACCATGTG
2884438 CTCATATTG----C-T-T-
1 CTCATA-TGCAACCATGTG
2884450 CTCATATGCAACCATGTG
1 CTCATATGCAACCATGTG
2884468 CTCATAT
1 CTCATAT
2884475 TACTTTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 2 0.07
12 6 0.21
13 1 0.03
14 1 0.03
15 2 0.07
16 1 0.03
17 1 0.03
18 13 0.45
19 2 0.07
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (18 bp):
CTCATATGCAACCATGTG
Found at i:2884453 original size:30 final size:30
Alignment explanation
Indices: 2884419--2884475 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
2884409 TTTTGAATCA
2884419 TCTCATATGCAACCATGTGCTCATATTGCT
1 TCTCATATGCAACCATGTGCTCATATTGCT
2884449 TCTCATATGCAACCATGTGCTCATATT
1 TCTCATATGCAACCATGTGCTCATATT
2884476 ACTTTCGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (30 bp):
TCTCATATGCAACCATGTGCTCATATTGCT
Found at i:2896086 original size:12 final size:12
Alignment explanation
Indices: 2896065--2896094 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2896055 AATGATATGT
2896065 GAAAAATAGAGA
1 GAAAAATAGAGA
*
2896077 GAAAACTAGAGA
1 GAAAAATAGAGA
2896089 GAAAAA
1 GAAAAA
2896095 GAAGATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:2896283 original size:12 final size:13
Alignment explanation
Indices: 2896266--2896294 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2896256 AAAGATAAAA
2896266 TAAAATAATATT-
1 TAAAATAATATTC
2896278 TAAAATAATATTC
1 TAAAATAATATTC
2896291 TAAA
1 TAAA
2896295 TCCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATTC
Found at i:2896328 original size:85 final size:85
Alignment explanation
Indices: 2896181--2896352 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
2896171 AATTACAAGC
* * *
2896181 TAAAGATAATTTTAAAATAATATCTTAAATCCTAATTAAAACATTTAAAATTATTTAAACTAAAA
1 TAAAGATAATTTTAAAATAATATCTTAAATCCTAATTAAAACATCTAAAACTATTCAAACTAAAA
2896246 TA-TCTAAAACAAAGATAAAA
66 TACT-TAAAACAAAGATAAAA
* *
2896266 TAAA-ATAATATTTAAAATAATAT-TCTAAATCCTAATTGAAATA-CTAAAACCTATTCAAACTA
1 TAAAGATAAT-TTTAAAATAATATCT-TAAATCCTAATTAAAACATCTAAAA-CTATTCAAACTA
2896328 AAATACTTAAAACAAAGATAAAA
63 AAATACTTAAAACAAAGATAAAA
2896351 TA
1 TA
2896353 TAATGTTTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
84 11 0.14
85 66 0.85
86 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (85 bp):
TAAAGATAATTTTAAAATAATATCTTAAATCCTAATTAAAACATCTAAAACTATTCAAACTAAAA
TACTTAAAACAAAGATAAAA
Found at i:2897703 original size:17 final size:17
Alignment explanation
Indices: 2897659--2897695 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2897649 AATCTCTTTA
2897659 ATTATTTATTTAATTATT
1 ATTATTTA-TTAATTATT
*
2897677 ATTATTTATTAATTCTT
1 ATTATTTATTAATTATT
2897694 AT
1 AT
2897696 CTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTATTTATTAATTATT
Found at i:2902453 original size:5 final size:5
Alignment explanation
Indices: 2902440--2902502 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
2902430 GAGGCAACCC
* * * *
2902440 ATTTC ATTTT ATTTTT ATTTT ATTTT ATTTC ATTTTT TTTTT ATTTC ATTTT
1 ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT
2902492 ATTTTT ATTTT
1 A-TTTT ATTTT
2902503 TAACAAACCT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 35 0.73
6 13 0.27
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:2902464 original size:16 final size:16
Alignment explanation
Indices: 2902446--2902501 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
2902436 ACCCATTTCA
*
2902446 TTTTATTTTTATTTTA-
1 TTTTA-TTTCATTTTAT
*
2902462 TTTTATTTCATTTTTT
1 TTTTATTTCATTTTAT
2902478 TTTTATTTCATTTTAT
1 TTTTATTTCATTTTAT
2902494 TTTTATTT
1 TTTTATTT
2902502 TTAACAAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 8 0.22
16 28 0.78
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTTCATTTTAT
Found at i:2902480 original size:26 final size:26
Alignment explanation
Indices: 2902440--2902495 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
2902430 GAGGCAACCC
*
2902440 ATTTCATTTTATTTTTATTTTATTTT
1 ATTTCATTTTATTTTTATTTCATTTT
*
2902466 ATTTCATTTTTTTTTTATTTCATTTT
1 ATTTCATTTTATTTTTATTTCATTTT
2902492 ATTT
1 ATTT
2902496 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (26 bp):
ATTTCATTTTATTTTTATTTCATTTT
Found at i:2913895 original size:26 final size:25
Alignment explanation
Indices: 2913845--2913904 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
2913835 ATAAAATAAC
*
2913845 TAAATTAAATATATAAAAATTAAAT
1 TAAATTAAATATATAAAAATCAAAT
*
2913870 TAAATTACAATGTAATAAAAA-CAAAT
1 TAAATTA-AATAT-ATAAAAATCAAAT
*
2913896 AAAATTAAA
1 TAAATTAAA
2913905 ATTACATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.30
26 14 0.47
27 7 0.23
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (25 bp):
TAAATTAAATATATAAAAATCAAAT
Found at i:2915069 original size:3 final size:3
Alignment explanation
Indices: 2915061--2915148 Score: 124
Period size: 3 Copynumber: 29.3 Consensus size: 3
2915051 GCCTGTAATT
*
2915061 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* **
2915106 TAT TAA TAA TAA TAA TAA TAA TAA TTG TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2915149 TTTAAAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.03
3 71 0.95
4 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2915479 original size:79 final size:78
Alignment explanation
Indices: 2915365--2915512 Score: 228
Period size: 79 Copynumber: 1.9 Consensus size: 78
2915355 AAAACATCTT
2915365 AATCCTAATTAAAACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGAT-AATATAATATTT
1 AATCCTAATTAAAACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAATATAATATTT
2915429 AAATTATATCATA
66 AAATTATATCATA
*
2915442 AATCCTAATTGAAATAC-TAAAACCTATTTAAACTAAAATACTTAAAACAAAGATAAAATATAAT
1 AATCCTAATT-AAA-ACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGAT-AAATATAAT
*
2915506 GTTTAAA
62 ATTTAAA
2915513 ATATTGTCCT
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
77 10 0.16
78 8 0.12
79 32 0.50
81 14 0.22
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (78 bp):
AATCCTAATTAAAACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAATATAATATTT
AAATTATATCATA
Found at i:2916638 original size:18 final size:18
Alignment explanation
Indices: 2916604--2916641 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2916594 TTGTTTCATG
**
2916604 TAAAAAAATATTTAAATT
1 TAAAAAAATATAAAAATT
2916622 TAAAAAAATATAAAAATT
1 TAAAAAAATATAAAAATT
2916640 TA
1 TA
2916642 TTAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAAAATATAAAAATT
Found at i:2918544 original size:42 final size:42
Alignment explanation
Indices: 2918309--2918548 Score: 210
Period size: 42 Copynumber: 5.6 Consensus size: 42
2918299 CCGCTAAAGT
* * ** **
2918309 TAGCGGCGTTTGTGGAAAAAAAACGATGCAAAAGGTCATATCTA
1 TAGCGGCGTTTTTGG--AACAAACGCCGCAAAAGGTCGGATCTA
* ** *
2918353 TAGCGGCGTTTTTGTAACAAAAACTGCAAAAGGTCGGATCTA
1 TAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGGATCTA
* * * * *
2918395 TAGCGGCATTTTTTGAACAAACTCCGCAATAGGTTGAGATCTA
1 TAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCG-GATCTA
* * * * * * * **
2918438 TAGCAGCATTTTCGAAAAAAACACCACAAAAGGTTAGATCTA
1 TAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGGATCTA
* * *
2918480 TTGCGGCGTTTTTGTAATAAACGCCGCAAAAGGTCGGATCTA
1 TAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGGATCTA
2918522 TAGCGGCGTTTTTGGAACAAACGCCGC
1 TAGCGGCGTTTTTGGAACAAACGCCGC
2918549 TAATTACCGT
Statistics
Matches: 157, Mismatches: 38, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
42 111 0.71
43 33 0.21
44 13 0.08
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGGATCTA
Found at i:2918681 original size:22 final size:21
Alignment explanation
Indices: 2918656--2918704 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
2918646 ACATCAACCA
2918656 TAAATTTAAACAACAACAAAAT
1 TAAATTTAAA-AACAACAAAAT
* **
2918678 TAAAATTTATAAACATTAAAAT
1 T-AAATTTAAAAACAACAAAAT
2918700 TAAAT
1 TAAAT
2918705 GTAATGTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 11 0.48
23 8 0.35
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATTTAAAAACAACAAAAT
Found at i:2922441 original size:20 final size:19
Alignment explanation
Indices: 2922391--2922437 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
2922381 TATCTATCAG
2922391 TATTTTTCCAATTATCTTT
1 TATTTTTCCAATTATCTTT
2922410 TATTTTTCCAATTATCTTT
1 TATTTTTCCAATTATCTTT
2922429 TATTTTTCC
1 TATTTTTCC
2922438 CAATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTTCCAATTATCTTT
Found at i:2923910 original size:15 final size:16
Alignment explanation
Indices: 2923873--2923909 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2923863 TAAACTAAAT
2923873 GAAAAACCAACTTGAA
1 GAAAAACCAACTTGAA
2923889 GAAAAACCAACTTGAA
1 GAAAAACCAACTTGAA
2923905 GAAAA
1 GAAAA
2923910 CTTACCTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.11
Consensus pattern (16 bp):
GAAAAACCAACTTGAA
Found at i:2930123 original size:546 final size:543
Alignment explanation
Indices: 2929094--2930177 Score: 2132
Period size: 546 Copynumber: 2.0 Consensus size: 543
2929084 TAATGTTCAA
*
2929094 TTATGTCTTATTTTAACTAGCATTATTAAAAAGAAATTTCTTACATACTATTATCTTTCCTTTTA
1 TTATGTCTTATTTTAACTAGCATTAGTAAAAAGAAATTTCTTACATACTATTATCTTTCCTTTTA
2929159 TATTTAGATTTTTGCATCACAAATAACTATCAATTAATTTCTTATGGCCTTATGTTTATTGCACA
66 TATTTAGATTTTTGCATCACAAATAACTATCAATTAATTTCTTATGGCCTTATGTTTATTGCACA
2929224 CGTTTAAAGAGAAGATATTATATAGCATTTTTTGAGTCAATCGAACCAAAGAAATGACCAAGAGG
131 CGTTTAAAGAGAAGATATTATATAGCATTTTTTGAGTCAATCGAACCAAAGAAATGACCAAGAGG
2929289 GGTAAATTGACAATAATAAGATTAATAGAAGCCTTTGCAAGAAAATAAAATTTTAACCTTCATTA
196 GGTAAATTGACAATAATAAGATTAATAGAAGCCTTTGCAAGAAAATAAAATTTTAACCTTCATTA
2929354 ATTTTAGAGTGTTCAACTTCTTCAATGAAGTATACATTCATTACCTTAGCTTCCACACTAAGGAT
261 ATTTTAGAGTGTTCAACTTCTTCAATGAAGTATACATTCATTACCTTAGCTTCCACACTAAGGAT
2929419 TCCAACAAATTCACTAACTTTTTCAAACCTTTTAAGTCAAGGTGTAACCTTATAACACACTTAGA
326 TCCAACAAATTCACTAACTTTTTCAAACCTTTTAAGTCAAGGTGTAACCTTATAACACACTTAGA
2929484 CTTGTACCCCCAAAGTGTAAAACCCTTTCTAAAAAGAAATTAATATATATCTAATTAACTATCCA
391 CTTGTACCCCCAAAGTGTAAAACCCTTTCTAAAAAGAAATTAATATATATCTAATTAACTATCCA
2929549 TAATTTCTTATGTTCTTAAATCAGAATATATTCAAGCTTATAATCTTCGAGGGACAATAATTAAT
456 TAATTTCTTATGTTCTTAAATCAGAATATATTCAAGCTTATAATCTTCGAGGGACAATAATTAAT
2929614 TTAAGATCCAATCATAAACTTTC
521 TTAAGATCCAATCATAAACTTTC
2929637 TTATGTCTTATTTTAACTAGCATTAGTAAAAAGAAATTTCTTACATACTATTATCTTTCCTTTTA
1 TTATGTCTTATTTTAACTAGCATTAGTAAAAAGAAATTTCTTACATACTATTATCTTTCCTTTTA
2929702 TATTTAGATTTTTGCATCACAAATAACTATCAATTAATTTCTTATGGCCTTATGTTTATTGCACA
66 TATTTAGATTTTTGCATCACAAATAACTATCAATTAATTTCTTATGGCCTTATGTTTATTGCACA
2929767 CGTTTAAAGAGAAGATATTATATAGCATTTTTTGAGTCAATCGAACCAAAGAAATGACCAAGAGG
131 CGTTTAAAGAGAAGATATTATATAGCATTTTTTGAGTCAATCGAACCAAAGAAATGACCAAGA-G
2929832 GGGTAAATTGACAATAATAAGATTAATAGAAGCCTTTTGCAAGAAAATAAAAATTTTAACCTTCA
195 GGGTAAATTGACAATAATAAGATTAATAGAAGCC-TTTGCAAGAAAAT-AAAATTTTAACCTTCA
2929897 TTAATTTTAGAGTGTTCAACTTCTTCAATGAAGTATACATTCATTACCTTAGCTTCCACACTAAG
258 TTAATTTTAGAGTGTTCAACTTCTTCAATGAAGTATACATTCATTACCTTAGCTTCCACACTAAG
2929962 GATTCCAACAAATTCACTAACTTTTTCAAACCTTTTAAGTCAAGGTGTAACCTTATAACACACTT
323 GATTCCAACAAATTCACTAACTTTTTCAAACCTTTTAAGTCAAGGTGTAACCTTATAACACACTT
2930027 AGACTTGTACCCCCAAAGTGTAAAACCCTTTCTAAAAAGAAATTAATATATATCTAATTAACTAT
388 AGACTTGTACCCCCAAAGTGTAAAACCCTTTCTAAAAAGAAATTAATATATATCTAATTAACTAT
2930092 CCATAATTTCTTATGTTCTTAAATCAGAATATATTCAAGCTTATAATCTTCGAGGGACAATAATT
453 CCATAATTTCTTATGTTCTTAAATCAGAATATATTCAAGCTTATAATCTTCGAGGGACAATAATT
2930157 AATTTAAGATCCAATCATAAA
518 AATTTAAGATCCAATCATAAA
2930178 ATTTAAAGTG
Statistics
Matches: 537, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
543 192 0.36
544 35 0.07
545 13 0.02
546 297 0.55
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (543 bp):
TTATGTCTTATTTTAACTAGCATTAGTAAAAAGAAATTTCTTACATACTATTATCTTTCCTTTTA
TATTTAGATTTTTGCATCACAAATAACTATCAATTAATTTCTTATGGCCTTATGTTTATTGCACA
CGTTTAAAGAGAAGATATTATATAGCATTTTTTGAGTCAATCGAACCAAAGAAATGACCAAGAGG
GGTAAATTGACAATAATAAGATTAATAGAAGCCTTTGCAAGAAAATAAAATTTTAACCTTCATTA
ATTTTAGAGTGTTCAACTTCTTCAATGAAGTATACATTCATTACCTTAGCTTCCACACTAAGGAT
TCCAACAAATTCACTAACTTTTTCAAACCTTTTAAGTCAAGGTGTAACCTTATAACACACTTAGA
CTTGTACCCCCAAAGTGTAAAACCCTTTCTAAAAAGAAATTAATATATATCTAATTAACTATCCA
TAATTTCTTATGTTCTTAAATCAGAATATATTCAAGCTTATAATCTTCGAGGGACAATAATTAAT
TTAAGATCCAATCATAAACTTTC
Found at i:2931271 original size:21 final size:23
Alignment explanation
Indices: 2931245--2931286 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2931235 AATTAAGTAT
2931245 AAATGAATTT-TAAG-ATTTTAC
1 AAATGAATTTCTAAGTATTTTAC
*
2931266 AAATGATTTTCTAAGTATTTT
1 AAATGAATTTCTAAGTATTTT
2931287 CGATTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (23 bp):
AAATGAATTTCTAAGTATTTTAC
Found at i:2931645 original size:64 final size:63
Alignment explanation
Indices: 2931439--2931646 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
2931429 TTTCAGAGTG
* **
2931439 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTCA-GG--TATTTTGAAACATCGAATGCATT
2931502 TC
62 TC
* * *
2931504 ATGCATCGATGCA-CATACTATGCATCGATACACTTAGAGT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCAG-GTATTT-TG-AAACATCGAATGCATT
*
2931567 TG
62 TC
* * *
2931569 ATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATTGAATGCATTTT
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCAGG-TATTTTGAAACATCGAATGCATTTC
2931633 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2931647 TCTTAGTGAA
Statistics
Matches: 121, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 48 0.40
65 64 0.53
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCAGGTATTTTGAAACATCGAATGCATTTC
Found at i:2937068 original size:23 final size:22
Alignment explanation
Indices: 2936997--2937078 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
2936987 ACACTTAACA
2936997 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
2937021 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
2937042 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
2937065 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2937079 AAGGCCATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:2939832 original size:60 final size:59
Alignment explanation
Indices: 2939751--2939905 Score: 154
Period size: 64 Copynumber: 2.5 Consensus size: 59
2939741 GAATAAATTG
* * *
2939751 AACATAGAATGCATTTCATGCATCGATGCA-TATGCATCAATGCACTCAGAG-T-TTTATGAA
1 AACATCGAATGC-TTTTATGCATCGATGCACCATGCATCAATGCACTCAG-GCTATTT-TG-A
* *
2939811 AACATCGAATGCTTTTGATGCATCGATGCACCAGCCATGCCTCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCTTTT-ATGCATCGATG---CA-CCATGCATCAATGCACTCAGGCTATTTTGA
2939875 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGC-TTTTATGCATCGATGCAC
2939906 TCTTAGTGCA
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
59 3 0.04
60 23 0.28
61 2 0.02
63 2 0.02
64 25 0.31
65 23 0.28
66 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (59 bp):
AACATCGAATGCTTTTATGCATCGATGCACCATGCATCAATGCACTCAGGCTATTTTGA
Found at i:2941301 original size:21 final size:21
Alignment explanation
Indices: 2941261--2941301 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2941251 TTTCTTAAAA
* * *
2941261 TCATTTACTCAACATTTGAAC
1 TCATTTACACAAAATATGAAC
2941282 TCATTTACACAAAATATGAA
1 TCATTTACACAAAATATGAA
2941302 AACATTAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
TCATTTACACAAAATATGAAC
Found at i:2942163 original size:35 final size:35
Alignment explanation
Indices: 2942078--2942164 Score: 147
Period size: 35 Copynumber: 2.5 Consensus size: 35
2942068 TTGAAAAGTG
* *
2942078 ACTTTTAAAAGTATTGTAGAAATGAACTTTTAAAA
1 ACTTTTAAAAGTGTTGTAGAAACGAACTTTTAAAA
2942113 ACTTTTAAAAGTGTTGTAGAAACGAACTTTTAAAA
1 ACTTTTAAAAGTGTTGTAGAAACGAACTTTTAAAA
*
2942148 ACTTTTAAAAATGTTGT
1 ACTTTTAAAAGTGTTGT
2942165 GCAAAAAGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.38
Consensus pattern (35 bp):
ACTTTTAAAAGTGTTGTAGAAACGAACTTTTAAAA
Found at i:2942408 original size:7 final size:6
Alignment explanation
Indices: 2942382--2942415 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2942372 TTTAAATTAT
*
2942382 AATATA AATATAA AATAAA AATAAA AATAAA AAT
1 AATAAA AATA-AA AATAAA AATAAA AATAAA AAT
2942416 TACAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
AATAAA
Found at i:2942451 original size:6 final size:6
Alignment explanation
Indices: 2942413--2942451 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
2942403 TAAAAATAAA
*
2942413 AATTAC AATTAT AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AAT
2942452 AAAAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTAT
Found at i:2944024 original size:29 final size:30
Alignment explanation
Indices: 2943992--2944056 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
2943982 GGATTATTAT
* * *
2943992 TATTTAT-ATAAAAAGAATAATCATATAAA
1 TATTTATAATAAAAAGAAAAATAAAATAAA
2944021 TATTT-TAATAAAAAGAAAAATAAAATAAA
1 TATTTATAATAAAAAGAAAAATAAAATAAA
*
2944050 TAATTAT
1 TATTTAT
2944057 TTATTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (30 bp):
TATTTATAATAAAAAGAAAAATAAAATAAA
Found at i:2945417 original size:3 final size:3
Alignment explanation
Indices: 2945409--2945440 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2945399 TATTTATTTT
2945409 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2945441 TAAATGAAAA
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:2945896 original size:113 final size:113
Alignment explanation
Indices: 2945763--2946322 Score: 954
Period size: 113 Copynumber: 5.0 Consensus size: 113
2945753 ATAGGGACAT
*
2945763 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
2945828 ATTATGAACTTTCTCTGGAAACGTTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
2945876 GCAAAAGATTCAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2945941 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
2945989 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
2946054 ATTATTAACTTTCTCTGGAAAAGC-GATCCATCAAGTGATGGA-TTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
2946100 GCAAAAGG-TGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2946164 ATTATGAAC-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
2946211 GCAAATGGTTGAACCAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAA-CAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
2946276 CATTATGAACTCTT-TCTGGAAATGTTGATCCAT--TGTGATGGATTTGA
65 CATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
2946323 ATCTTTGCTA
Statistics
Matches: 427, Mismatches: 14, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
109 14 0.03
110 82 0.19
111 23 0.05
112 35 0.08
113 254 0.59
114 17 0.04
115 2 0.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:2946231 original size:223 final size:226
Alignment explanation
Indices: 2945763--2946322 Score: 954
Period size: 223 Copynumber: 2.5 Consensus size: 226
2945753 ATAGGGACAT
*
2945763 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
2945828 ATTATGAACTTTCTCTGGAAACGTTGATCCATCGAGTGATGGATTTGAGCAAAAGATTCAACAAG
66 ATTATGAACTTTCTCTGGAAAAGTCGATCCATCAAGTGATGGATTTGAGCAAAAGAGTCAACAAG
2945893 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
131 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
2945958 GAAAAGCTGATCCATCAAGTGATGGATTTGA
196 GAAAAGCTGATCCATCAAGTGATGGATTTGA
2945989 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
2946054 ATTATTAACTTTCTCTGGAAAAG-CGATCCATCAAGTGATGGA-TTGAGCAAAAG-GTGAACAAG
66 ATTATGAACTTTCTCTGGAAAAGTCGATCCATCAAGTGATGGATTTGAGCAAAAGAGTCAACAAG
2946116 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
131 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
2946180 GAAAAGCTGATCCATCAAGTGATGGATTTGA
196 GAAAAGCTGATCCATCAAGTGATGGATTTGA
*
2946211 GCAAATGGTTGAACCAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAA-CAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
2946276 CATTATGAACTCTT-TCTGGAAATGTTGATCCAT--TGTGATGGATTTGA
65 CATTATGAACT-TTCTCTGGAAAAGTCGATCCATCAAGTGATGGATTTGA
2946323 ATCTTTGCTA
Statistics
Matches: 318, Mismatches: 12, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
222 58 0.18
223 138 0.43
224 20 0.06
225 17 0.05
226 85 0.27
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (226 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGTCGATCCATCAAGTGATGGATTTGAGCAAAAGAGTCAACAAG
CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:2947488 original size:18 final size:17
Alignment explanation
Indices: 2947465--2947511 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 17
2947455 AAAAAAAAAG
2947465 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTC-AA
2947483 AATAAATTGAA--TCAA
1 AATAAATTGAATTTCAA
*
2947498 AAAAAATTGAATTT
1 AATAAATTGAATTT
2947512 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.46
16 2 0.08
17 1 0.04
18 11 0.42
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (17 bp):
AATAAATTGAATTTCAA
Found at i:2947519 original size:18 final size:17
Alignment explanation
Indices: 2947468--2947519 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 17
2947458 AAAAAAGAAT
*
2947468 AAATTGAATTTCGAAAA
1 AAATTGAATTTAGAAAA
*
2947485 TAAATTGAA-TCA-AAAA
1 -AAATTGAATTTAGAAAA
*
2947501 AAATTGAATTTAGAGAA
1 AAATTGAATTTAGAAAA
2947518 AA
1 AA
2947520 TAAACTTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 6 0.21
18 8 0.29
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.27
Consensus pattern (17 bp):
AAATTGAATTTAGAAAA
Found at i:2947879 original size:10 final size:10
Alignment explanation
Indices: 2947864--2947910 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
2947854 CTTGACCCTC
*
2947864 TTTTTTTA-A
1 TTTTTTTATT
2947873 TTTTTTTATT
1 TTTTTTTATT
*
2947883 TTCTTTTTCTT
1 TT-TTTTTATT
*
2947894 TTTTTTTCTT
1 TTTTTTTATT
2947904 TTTTTTT
1 TTTTTTT
2947911 CTTCAAGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 8 0.24
10 17 0.50
11 9 0.26
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:2947895 original size:16 final size:15
Alignment explanation
Indices: 2947873--2947910 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
2947863 CTTTTTTTAA
2947873 TTTTTTTATTTTCTT
1 TTTTTTTATTTTCTT
*
2947888 TTTCTTTTTTTTTCTT
1 TTT-TTTTATTTTCTT
2947904 TTTTTTT
1 TTTTTTT
2947911 CTTCAAGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTATTTTCTT
Found at i:2947911 original size:10 final size:10
Alignment explanation
Indices: 2947873--2947913 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
2947863 CTTTTTTTAA
*
2947873 TTTTTTTATT
1 TTTTTTTCTT
2947883 TTCTTTTTCTT
1 TT-TTTTTCTT
2947894 TTTTTTTCTT
1 TTTTTTTCTT
2947904 TTTTTTTCTT
1 TTTTTTTCTT
2947914 CAAGCATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:2951462 original size:9 final size:9
Alignment explanation
Indices: 2951439--2951469 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2951429 GAAAAATAAT
2951439 GAATGTAAA
1 GAATGTAAA
2951448 -AATGTAAA
1 GAATGTAAA
2951456 GAATGTAAA
1 GAATGTAAA
2951465 GAATG
1 GAATG
2951470 ATTGCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:2961987 original size:5 final size:5
Alignment explanation
Indices: 2961979--2962366 Score: 688
Period size: 5 Copynumber: 79.4 Consensus size: 5
2961969 TGATAAGATA
2961979 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
2962029 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
2962079 AACAT AACAT -ACA- AACAT AACAT AACAT AACAT AAC-- AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
2962125 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT -A-AT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
2962173 AACAT AACAT AACAT AACAT AACAT AACAT AACAT -ACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
*
2962222 AACAT AACAT AACAT AACAT AACAT AA-AT -ACAA ACACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT A-ACAT AACAT AACAT
2962271 -ACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
2962320 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AA
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AA
2962367 TATACTATCT
Statistics
Matches: 370, Mismatches: 2, Indels: 22
0.94 0.01 0.06
Matches are distributed among these distances:
3 6 0.02
4 19 0.05
5 341 0.92
6 4 0.01
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AACAT
Found at i:2971650 original size:14 final size:14
Alignment explanation
Indices: 2971633--2971662 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2971623 GCTTTACATT
*
2971633 TTTCAATATTTTAA
1 TTTCAATACTTTAA
2971647 TTTCAATACTTTAA
1 TTTCAATACTTTAA
2971661 TT
1 TT
2971663 ATTACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTCAATACTTTAA
Found at i:2971866 original size:2 final size:2
Alignment explanation
Indices: 2971859--2971883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2971849 ATCTTAGTCT
2971859 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 T
2971884 TGTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2972748 original size:28 final size:28
Alignment explanation
Indices: 2972677--2972742 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
2972667 TAATCCTTTC
* *
2972677 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATACTTATTA
2972705 TTTTCATAATATTTATATATA-TTATT-
1 TTTTCATAATATTTATATATACTTATTA
2972731 TTTT-ATTAATAT
1 TTTTCA-TAATAT
2972743 CTTTATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 1 0.03
26 10 0.29
27 5 0.14
28 19 0.54
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTCATAATATTTATATATACTTATTA
Found at i:2974363 original size:26 final size:26
Alignment explanation
Indices: 2974323--2974382 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
2974313 CATCCTTTGT
2974323 TTTGCATTGTCGTATTTGCATTTGCA
1 TTTGCATTGTCGTATTTGCATTTGCA
*
2974349 TTTGCATTGTTGTATTTGCATTTGCA
1 TTTGCATTGTCGTATTTGCATTTGCA
*
2974375 TTTTCATT
1 TTTGCATT
2974383 TGCATCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.55
Consensus pattern (26 bp):
TTTGCATTGTCGTATTTGCATTTGCA
Found at i:2974394 original size:14 final size:12
Alignment explanation
Indices: 2974336--2974397 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
2974326 GCATTGTCGT
*
2974336 ATTTGCATTTGC
1 ATTTTCATTTGC
* *
2974348 ATTTGCATTGTTGT
1 ATTTTCA-T-TTGC
*
2974362 ATTTGCATTTGC
1 ATTTTCATTTGC
2974374 ATTTTCATTTGC
1 ATTTTCATTTGC
2974386 ATCTTTTCATTT
1 A--TTTTCATTT
2974398 TTACGTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
12 22 0.51
13 2 0.05
14 19 0.44
ACGTcount: A:0.16, C:0.15, G:0.13, T:0.56
Consensus pattern (12 bp):
ATTTTCATTTGC
Found at i:2974398 original size:6 final size:6
Alignment explanation
Indices: 2974336--2974387 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
2974326 GCATTGTCGT
* *
2974336 ATTTGC ATTTGC ATTTGC ATTGTTGT ATTTGC ATTTGC ATTTTC ATTTGC
1 ATTTGC ATTTGC ATTTGC A-T-TTGC ATTTGC ATTTGC ATTTGC ATTTGC
2974386 AT
1 AT
2974388 CTTTTCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
6 34 0.85
7 2 0.05
8 4 0.10
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.54
Consensus pattern (6 bp):
ATTTGC
Found at i:2977682 original size:18 final size:19
Alignment explanation
Indices: 2977651--2977689 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2977641 AAAAAAAGTG
2977651 AAAAAAGTG-AAAAAGAAA
1 AAAAAAGTGAAAAAAGAAA
2977669 AAAAAAG-GAAAAAAAGAAA
1 AAAAAAGTG-AAAAAAGAAA
2977688 AA
1 AA
2977690 TTGAGTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 7 0.37
19 11 0.58
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAAAAGTGAAAAAAGAAA
Found at i:2980927 original size:75 final size:74
Alignment explanation
Indices: 2980802--2981001 Score: 210
Period size: 75 Copynumber: 2.7 Consensus size: 74
2980792 ATGAACAAGA
* * * * *
2980802 AGCAAATA-CTGGGGTATGATGAAAACCCATTTCAATCA-TAATCAGGAATATTGACGTATTTTG
1 AGCAAATATC-GGGGCATGCTGAAAACCCATTTCAATCAGAAAT-TGGAATATTGACGCATTTTG
*
2980865 AATGTTCACGTCA-
64 AACG-TC-CGT-AT
* **
2980878 A-CAAATATCGGGGCATGCTGAAAACCTATTTCAATCAGAAATTGGAATATTGGTGCATTTTGAA
1 AGCAAATATCGGGGCATGCTGAAAACCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
*
2980942 CGTCTGTATT
66 CGTCCGTA-T
* *
2980952 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAAATTGGAATA
1 AGCAAATATCGGGGCATGCTGAAAACCCATTTCAATCAGAAATTGGAATA
2981002 ACATTTTGAA
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
72 1 0.01
73 2 0.02
74 3 0.03
75 95 0.90
76 5 0.05
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (74 bp):
AGCAAATATCGGGGCATGCTGAAAACCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
CGTCCGTAT
Found at i:2982435 original size:22 final size:22
Alignment explanation
Indices: 2982364--2982439 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
2982354 TCTACATTCC
*
2982364 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTTT
* *
2982386 TAAAAAATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTTT
*
2982408 CCAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTTT
2982430 TCAAAGATGA
1 TCAAAGATGA
2982440 AAGCTTTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTTT
Found at i:2983485 original size:29 final size:29
Alignment explanation
Indices: 2983443--2983608 Score: 206
Period size: 29 Copynumber: 5.7 Consensus size: 29
2983433 ACCGTTGATC
*
2983443 GGTGCTATTCTGGTAAATAATTTGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
2983472 GGTGCTATTCTGGTAAATAATTCGGTTTTTT
1 GGTGCTATTCTGGTAAATAATTCGG--TTTT
*
2983503 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2983532 GGTGCTATTCTGGTAAATAATTAGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
* * * * *** *
2983561 GGTTCTATTCTAGTAATTTATTCGAAATG
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2983590 GGTGCTATTTTGGTAAATA
1 GGTGCTATTCTGGTAAATA
2983609 TTTTAAAAAG
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
29 89 0.76
31 28 0.24
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:2983536 original size:60 final size:60
Alignment explanation
Indices: 2983443--2983608 Score: 210
Period size: 60 Copynumber: 2.8 Consensus size: 60
2983433 ACCGTTGATC
* *
2983443 GGTGCTATTCTGGTAAATAATTTGGTTTTGGTGCTATTCTGGTAAATAATTCGGTTTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTTGGTGCTATTCTGGTAAATAATTAGGTTTTTT
*
2983503 GGTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTCTGGTAAATAATTAGG--TTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTTGGTGCTATTCTGGTAAATAATTAGGTTTTTT
* * * * *** * *
2983561 GGTTCTATTCTAGTAATTTATTCGAAATGGGTGCTATTTTGGTAAATA
1 GGTGCTATTCTGGTAAATAATTCGGTTTTGGTGCTATTCTGGTAAATA
2983609 TTTTAAAAAG
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 42 0.45
60 51 0.55
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (60 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTTGGTGCTATTCTGGTAAATAATTAGGTTTTTT
Found at i:2990858 original size:13 final size:13
Alignment explanation
Indices: 2990857--2990890 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
2990847 CCGTTTACCC
2990857 GACCCGACCCGTT
1 GACCCGACCCGTT
2990870 GACCCGACCCGTT
1 GACCCGACCCGTT
2990883 GACCCGAC
1 GACCCGAC
2990891 TCGATCGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2990862 original size:18 final size:18
Alignment explanation
Indices: 2990839--2990880 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2990829 TACCGGTCAT
*
2990839 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
2990857 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
2990875 GACCCG
1 GACCCG
2990881 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:2990876 original size:31 final size:30
Alignment explanation
Indices: 2990838--2990903 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
2990828 TTACCGGTCA
*
2990838 TGACCCGACCCGTTTACCCGACCCGACCCGT
1 TGACCCGACCCGTTGACCCGACCCGA-CCGT
* *
2990869 TGACCCGACCCGTTGACCCGACTCGATCGT
1 TGACCCGACCCGTTGACCCGACCCGACCGT
2990899 TGACC
1 TGACC
2990904 GTTGACCGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.17, C:0.44, G:0.21, T:0.18
Consensus pattern (30 bp):
TGACCCGACCCGTTGACCCGACCCGACCGT
Found at i:2990953 original size:29 final size:29
Alignment explanation
Indices: 2990911--2991022 Score: 161
Period size: 29 Copynumber: 3.8 Consensus size: 29
2990901 ACCGTTGACC
2990911 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
*
2990940 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
* *
2990969 GGTGTTATTCTGGTAAATAATTCGGTTTTT
1 GGTGCTATTCTGGTAAATAATTCAG-TTTT
* * *
2990999 TGTGCTATTCTAGTAATTAATTCA
1 GGTGCTATTCTGGTAAATAATTCA
2991023 AAATGGGTGC
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
29 52 0.69
30 23 0.31
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:2991041 original size:29 final size:29
Alignment explanation
Indices: 2991000--2991066 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
2990990 TCGGTTTTTT
* * * *
2991000 GTGCTATTCTAGTAATTAATTCAAAATGG
1 GTGCTATTTTAGTAAATAATTCAAAAAGA
* *
2991029 GTGCTATTTTAGTAAATATTTTAAAAAGA
1 GTGCTATTTTAGTAAATAATTCAAAAAGA
2991058 GTGCTATTT
1 GTGCTATTT
2991067 GTGTAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.42
Consensus pattern (29 bp):
GTGCTATTTTAGTAAATAATTCAAAAAGA
Found at i:2991044 original size:59 final size:58
Alignment explanation
Indices: 2990911--2991046 Score: 155
Period size: 59 Copynumber: 2.3 Consensus size: 58
2990901 ACCGTTGACC
* **** *
2990911 GGTGCTATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTAGTAAATAATTCAAAATG
* * * *
2990969 GGTGTTATTCTGGTAAATAATTCGGTTTTTTGTGCTATTCTAGTAATTAATTCAAAATG
1 GGTGCTATTCTGGTAAATAATTCAG-TTTTGGTGCTATTCTAGTAAATAATTCAAAATG
* *
2991028 GGTGCTATTTTAGTAAATA
1 GGTGCTATTCTGGTAAATA
2991047 TTTTAAAAAG
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
58 23 0.36
59 41 0.64
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.45
Consensus pattern (58 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTAGTAAATAATTCAAAATG
Found at i:2993225 original size:36 final size:36
Alignment explanation
Indices: 2993185--2993324 Score: 131
Period size: 37 Copynumber: 3.8 Consensus size: 36
2993175 GTTTTTCTTA
** *
2993185 AAACAAAATGCATCTCTCTTGAGACAGTTTCACTCG
1 AAACAAAATTTATCTCTCTTGAGATAGTTTCACTCG
* * ** **
2993221 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAA-AATTTATCTCTCTTGAGATAGTTTCACTCG
*
2993258 AAACAAAATTTGTCT-TGCTTGAGATAGTTTCACTCG
1 AAACAAAATTTATCTCT-CTTGAGATAGTTTCACTCG
*
2993294 AAACAACAATTTATCT-TACTTGAGATTGTTT
1 AAACAA-AATTTATCTCT-CTTGAGATAGTTT
2993325 TTCTTAAAAT
Statistics
Matches: 82, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
36 34 0.41
37 48 0.59
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (36 bp):
AAACAAAATTTATCTCTCTTGAGATAGTTTCACTCG
Found at i:2993244 original size:37 final size:37
Alignment explanation
Indices: 2993152--2993324 Score: 152
Period size: 36 Copynumber: 4.7 Consensus size: 37
2993142 GTTTTCAAAT
* * ** *
2993152 AACAATTTATATCACTTGAGATTGTTTTTCTTAAAAC
1 AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
** * * *
2993189 AA-AATGCATCTCTCTTGAGACAGTTTCACTCGAAAC
1 AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
* ** *
2993225 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
* ** *
2993262 AA-AATTTGTCTTGCTTGAGATAGTTTCACTCGAAAC
1 AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
* *
2993298 AACAATTTATCTTACTTGAGATTGTTT
1 AACAATTTATCTCACTTGAGATAGTTT
2993325 TTCTTAAAAT
Statistics
Matches: 104, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
36 54 0.52
37 50 0.48
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (37 bp):
AACAATTTATCTCACTTGAGATAGTTTCACTCAAAAC
Found at i:2993378 original size:73 final size:73
Alignment explanation
Indices: 2993152--2993370 Score: 330
Period size: 73 Copynumber: 3.0 Consensus size: 73
2993142 GTTTTCAAAT
* * * *
2993152 AACAATTTATATCACTTGAGATTGTTTTTCTTAAAACAAAATGCATCTCTCTTGAGACAGTTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
2993217 CTCGAAAC
66 CTCGAAAC
* * *
2993225 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTTGCTTGAGATAGTTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
2993290 CTCGAAAC
66 CTCGAAAC
* * * *
2993298 AACAATTTATCTTACTTGAGATTGTTTTTCTTAAAATAAGATTCGTCTCGCTTGAGACAATTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
*
2993363 CTAGAAAC
66 CTCGAAAC
2993371 TGAAATTTCC
Statistics
Matches: 131, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 131 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (73 bp):
AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
CTCGAAAC
Done.