Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 49
Found at i:3186778 original size:42 final size:43
Alignment explanation
Indices: 3186731--3186816 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
3186721 CAACTCAAAC
3186731 TTAAACC-TTAATATATGAAAATAGGTATCACCTCCTGATCTA
1 TTAAACCTTTAATATATGAAAATAGGTATCACCTCCTGATCTA
3186773 TTAAACCTTTAATATATGAAAATAGGTATCACCTCCTGATCTA
1 TTAAACCTTTAATATATGAAAATAGGTATCACCTCCTGATCTA
3186816 T
1 T
3186817 ATTTCGTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 7 0.16
43 36 0.84
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (43 bp):
TTAAACCTTTAATATATGAAAATAGGTATCACCTCCTGATCTA
Found at i:3192159 original size:2 final size:2
Alignment explanation
Indices: 3192152--3192184 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3192142 ATGGTAGTTC
3192152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3192185 ACACAACGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3194718 original size:37 final size:36
Alignment explanation
Indices: 3194659--3194778 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
3194649 ATCCCATTAT
* *
3194659 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
3194695 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
3194731 CA-TTTTCAATGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
3194766 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
3194779 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:3194734 original size:21 final size:21
Alignment explanation
Indices: 3194710--3194770 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3194700 TTCAAAGAAA
3194710 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
3194731 CATTT-TC-AA---TG-AAA-
1 CATTTACCAAACTTTGAAAAC
3194745 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
3194766 CATTT
1 CATTT
3194771 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:3194787 original size:35 final size:34
Alignment explanation
Indices: 3194669--3194808 Score: 140
Period size: 35 Copynumber: 4.0 Consensus size: 34
3194659 CATTTTTCAA
* * *
3194669 CAAACATCTACCAAACTTTGAAAAACTATTTTTCAAA
1 CAAACATTTACCAAACTTTG-AAAACCA-TTTT-AAT
*
3194706 GAAACATTTACCAAACTTTGAAAACCATTTTCAAT
1 CAAACATTTACCAAACTTTGAAAACCATTTT-AAT
* *
3194741 GAAACATTTACCAAACTTTGAAAACCATTTT-TT
1 CAAACATTTACCAAACTTTGAAAACCATTTTAAT
**
3194774 CAAAGTTGGTTACCAAAC-TTGAAAACCATTTTAAT
1 CAAACAT--TTACCAAACTTTGAAAACCATTTTAAT
3194809 AATTTCAACA
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
33 5 0.05
34 14 0.15
35 48 0.53
36 6 0.07
37 18 0.20
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (34 bp):
CAAACATTTACCAAACTTTGAAAACCATTTTAAT
Found at i:3198864 original size:16 final size:16
Alignment explanation
Indices: 3198840--3198871 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3198830 TATCGCCGAT
*
3198840 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
3198856 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
3198872 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:3199331 original size:37 final size:36
Alignment explanation
Indices: 3199268--3199386 Score: 152
Period size: 35 Copynumber: 3.3 Consensus size: 36
3199258 ATCCCATTAT
* * *
3199268 CATTTTTC-AACAAACATCTACCAAACTTTAAAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTT-GAAAAC
* *
3199304 TATTTTTCAAAAAAATATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
*
3199340 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
3199375 CATTTTTTCAAA
1 CA-TTTTTCAAA
3199387 GTTGATTACC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 33 0.46
36 13 0.18
37 26 0.36
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
Found at i:3199344 original size:21 final size:21
Alignment explanation
Indices: 3199320--3199379 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
3199310 TCAAAAAAAT
3199320 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
*
3199341 ATTT-TCAAA----G-AAA-C
1 ATTTACCAAACTTTGAAAACC
3199355 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
3199376 ATTT
1 ATTT
3199380 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAACC
Found at i:3199944 original size:21 final size:21
Alignment explanation
Indices: 3199920--3199964 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3199910 AGGATTGTGG
* *
3199920 TTCCTTTCTTCTTGCATAAAA
1 TTCCCTTCTTCTTCCATAAAA
* *
3199941 TTCCCTTCTTGTTCCATAAGA
1 TTCCCTTCTTCTTCCATAAAA
3199962 TTC
1 TTC
3199965 GATAGGGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (21 bp):
TTCCCTTCTTCTTCCATAAAA
Found at i:3200605 original size:9 final size:9
Alignment explanation
Indices: 3200593--3200617 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3200583 GAATTCGGTT
3200593 AATTAACCG
1 AATTAACCG
3200602 AATTAACCG
1 AATTAACCG
3200611 AATTAAC
1 AATTAAC
3200618 AAAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:3201017 original size:183 final size:183
Alignment explanation
Indices: 3200631--3201019 Score: 617
Period size: 183 Copynumber: 2.1 Consensus size: 183
3200621 ATTAAATTTT
* * * *
3200631 AAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTATATATATTATATATAAAATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
* *
3200696 TTTAAGATCCAATAACTTTTAAACTTAAATTAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
*
3200761 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
*
3200814 AAATATTATATATATTATATATAAAATATGGGCT-AAGCCCAAACCATTTAAAACCTAATTAATA
1 AAATATTATATATATTATATATAAAATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
* *
3200878 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAA-ATTATATAAAATT
3200943 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
*
3200998 AAATATT-TA-AT-TTTTATATAAA
1 AAATATTATATATATTATATATAAA
3201020 TTAGAAAATT
Statistics
Matches: 192, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
181 10 0.05
182 4 0.02
183 114 0.59
184 64 0.33
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTATATATATTATATATAAAATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:3205538 original size:26 final size:24
Alignment explanation
Indices: 3205476--3205538 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
3205466 CATTTTAATC
3205476 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
3205500 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
3205523 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
3205539 ATTTATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:3205540 original size:22 final size:23
Alignment explanation
Indices: 3205493--3205556 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
3205483 TAATTATTAA
* *
3205493 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
*
3205514 AATATTTCTAATAATATAATATT
1 AATATTTATAATAATATAATATT
*
3205537 -ATATTTATAATATTATAATA
1 AATATTTATAATAATATAATA
3205557 AAATAATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.28
22 22 0.61
23 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:3205697 original size:19 final size:18
Alignment explanation
Indices: 3205673--3205741 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
3205663 ATATTATTAA
3205673 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
3205692 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
3205710 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
3205732 ATT-TTAATAA
1 ATTATTAATAA
3205742 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:3205716 original size:27 final size:27
Alignment explanation
Indices: 3205636--3205721 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
3205626 AATAAAATTT
* *
3205636 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
3205663 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
3205690 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
3205719 ATA
1 ATA
3205722 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:3205762 original size:23 final size:23
Alignment explanation
Indices: 3205736--3205780 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3205726 AATAATATTT
3205736 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3205759 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3205781 ATATAGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3205859 original size:33 final size:29
Alignment explanation
Indices: 3205820--3205890 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
3205810 AATATAATTT
*
3205820 ATAATATTTTTATTTCAATAAAATATATCAATA
1 ATAATATTTTTA-TT-AATAAAAT-TAT-AAAA
*
3205853 TTAATATTTTTATTAATAAAATTATAAAA
1 ATAATATTTTTATTAATAAAATTATAAAA
3205882 ATAATATTT
1 ATAATATTT
3205891 AATAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.31
30 3 0.09
31 8 0.23
32 2 0.06
33 11 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTATAAAA
Found at i:3206771 original size:7 final size:7
Alignment explanation
Indices: 3206759--3206783 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3206749 AAAATTAATA
3206759 TAAAAAT
1 TAAAAAT
3206766 TAAAAAT
1 TAAAAAT
3206773 TAAAAAT
1 TAAAAAT
3206780 TAAA
1 TAAA
3206784 TTACTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAAAT
Found at i:3207393 original size:23 final size:23
Alignment explanation
Indices: 3207373--3207418 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3207363 TTTAATTTTC
3207373 ATTTTTAACATTTTTATATTTAT
1 ATTTTTAACATTTTTATATTTAT
* *
3207396 TTTTTTAATATTTTTATAGTTTA
1 ATTTTTAACATTTTTATA-TTTA
3207419 AATTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTTTAACATTTTTATATTTAT
Found at i:3208430 original size:20 final size:21
Alignment explanation
Indices: 3208405--3208443 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3208395 TATAAAATCC
3208405 ATCAAAGT-AGGAAACACAAT
1 ATCAAAGTCAGGAAACACAAT
*
3208425 ATCAAAGTCAGTAAACACA
1 ATCAAAGTCAGGAAACACA
3208444 TGTGTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (21 bp):
ATCAAAGTCAGGAAACACAAT
Found at i:3211286 original size:15 final size:15
Alignment explanation
Indices: 3211266--3211295 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3211256 AATCTTAAAT
*
3211266 GTTTCATGGGTTTCA
1 GTTTCATGAGTTTCA
3211281 GTTTCATGAGTTTCA
1 GTTTCATGAGTTTCA
3211296 TTTGTATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.23, T:0.47
Consensus pattern (15 bp):
GTTTCATGAGTTTCA
Found at i:3214241 original size:31 final size:31
Alignment explanation
Indices: 3214193--3214262 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
3214183 TCGTTAAAAA
***
3214193 TAGGTGTCTAACTTTTTCTTTGTTACCATTT
1 TAGGTGTCTAACTTTTTCTCCCTTACCATTT
* *
3214224 TAGGTGTTTAA-TGTTTTCTCCCTTATCATTT
1 TAGGTGTCTAACT-TTTTCTCCCTTACCATTT
3214255 TAGGTGTC
1 TAGGTGTC
3214263 CGGATGTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (31 bp):
TAGGTGTCTAACTTTTTCTCCCTTACCATTT
Found at i:3220531 original size:21 final size:20
Alignment explanation
Indices: 3220507--3220546 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3220497 CATTTTTTCA
3220507 AATTTAATTATAATTATATCT
1 AATTTAATTATAATT-TATCT
*
3220528 AATTTTATTATAATTTATC
1 AATTTAATTATAATTTATC
3220547 AACTTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTAATTATAATTTATCT
Found at i:3229644 original size:13 final size:13
Alignment explanation
Indices: 3229626--3229650 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3229616 AACCGGTAGC
3229626 GACTTTCCTTAGA
1 GACTTTCCTTAGA
3229639 GACTTTCCTTAG
1 GACTTTCCTTAG
3229651 CCATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (13 bp):
GACTTTCCTTAGA
Found at i:3229858 original size:17 final size:17
Alignment explanation
Indices: 3229830--3229882 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
3229820 AGAAATGTAA
*
3229830 GATTGCAATGTTTGGTT
1 GATTACAATGTTTGGTT
* *
3229847 GATTATAGTGTTTGGTT
1 GATTACAATGTTTGGTT
3229864 GATTACAATGTTTGGTT
1 GATTACAATGTTTGGTT
3229881 GA
1 GA
3229883 ATGAATAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.47
Consensus pattern (17 bp):
GATTACAATGTTTGGTT
Found at i:3230036 original size:16 final size:17
Alignment explanation
Indices: 3230014--3230052 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3230004 TTATTTTATT
3230014 ATTTTTAA-TATATATA
1 ATTTTTAATTATATATA
*
3230030 CTTTTTAATTATATATA
1 ATTTTTAATTATATATA
3230047 ATTTTT
1 ATTTTT
3230053 TATAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTAATTATATATA
Found at i:3234172 original size:35 final size:35
Alignment explanation
Indices: 3234121--3234188 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
3234111 CATTTTTTAG
*
3234121 ACATAATTTAAACACTTTTGTTTTAAGCTTAAATT
1 ACATAATTTAAACACTTTTATTTTAAGCTTAAATT
* *
3234156 ACATAATTTGAGCACTTTTATTTTAAGCTTAAA
1 ACATAATTTAAACACTTTTATTTTAAGCTTAAA
3234189 ATCTAACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (35 bp):
ACATAATTTAAACACTTTTATTTTAAGCTTAAATT
Found at i:3239590 original size:46 final size:46
Alignment explanation
Indices: 3239523--3239611 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
3239513 CAGCAGTGGG
3239523 ATCTGCTGGTGGATTGATGATTATGTGGAATGAAAATGATTTTTGA
1 ATCTGCTGGTGGATTGATGATTATGTGGAATGAAAATGATTTTTGA
3239569 ATCTGCTGGTGGATTGATGATTATGTGGAATGAAAATGATTTT
1 ATCTGCTGGTGGATTGATGATTATGTGGAATGAAAATGATTTT
3239612 GAAGTTTCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.28, C:0.04, G:0.28, T:0.39
Consensus pattern (46 bp):
ATCTGCTGGTGGATTGATGATTATGTGGAATGAAAATGATTTTTGA
Found at i:3247964 original size:130 final size:130
Alignment explanation
Indices: 3247718--3247965 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
3247708 TATTTATATA
*
3247718 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
3247783 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACTTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
3247848 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
3247913 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
3247966 GAAGAAATTA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:3248315 original size:28 final size:27
Alignment explanation
Indices: 3248284--3248346 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
3248274 AGTTGATACA
*
3248284 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
3248312 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
3248340 ATATTTT
1 ATATTTT
3248347 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:3248446 original size:16 final size:17
Alignment explanation
Indices: 3248425--3248457 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3248415 ATTTCTTATT
3248425 AAAAATAAAAT-ATTCA
1 AAAAATAAAATGATTCA
*
3248441 AAAAATATAATGATTCA
1 AAAAATAAAATGATTCA
3248458 TACATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAAATGATTCA
Found at i:3248601 original size:21 final size:21
Alignment explanation
Indices: 3248577--3248619 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3248567 TATTACCTTA
3248577 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
3248598 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
3248619 A
1 A
3248620 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:3248637 original size:35 final size:35
Alignment explanation
Indices: 3248588--3248673 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
3248578 ATTGAAGTAT
** * *
3248588 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
3248623 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
3248658 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
3248674 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:3251188 original size:20 final size:20
Alignment explanation
Indices: 3251163--3251225 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
3251153 TTTTCTCTTG
3251163 AAAGCAAAATTGGATTTTGA
1 AAAGCAAAATTGGATTTTGA
3251183 AAAGCAAAATTGGATTTTGA
1 AAAGCAAAATTGGATTTTGA
3251203 AAAGCAAAATTGGATTTTGA
1 AAAGCAAAATTGGATTTTGA
3251223 AAA
1 AAA
3251226 ATGATTTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.29
Consensus pattern (20 bp):
AAAGCAAAATTGGATTTTGA
Found at i:3253624 original size:122 final size:124
Alignment explanation
Indices: 3253385--3253631 Score: 444
Period size: 122 Copynumber: 2.0 Consensus size: 124
3253375 AAGTAAATGA
*
3253385 TTAAATTGATTAAAATGTTAAATATAAAAAATTAAATTTAAACTAAAACTAAATTAATATAAATA
1 TTAAATTGATTAAAATGTTAAATATAAAAAATTAAATTTAAACTAAAACTAAATTAATAGAAATA
* * *
3253450 TATAAGTTTTGATAACTAAAATTATTATTATATGAACTTTACATCTATTGATATATTTG
66 TATAAGATTTGATAACTAAAACTATTATTATATGAACTTTACATCTAATGATATATTTG
3253509 TTAAATTGATTAAAATGTTAAATAT-AAAAATTAAATTTAAACTAAAACTAAATTAATAGAAATA
1 TTAAATTGATTAAAATGTTAAATATAAAAAATTAAATTTAAACTAAAACTAAATTAATAGAAATA
3253573 TATAA-ATTTGATAACTAAAACTATTATTATATGAACTTTACATCTAATGATATATTTG
66 TATAAGATTTGATAACTAAAACTATTATTATATGAACTTTACATCTAATGATATATTTG
3253631 T
1 T
3253632 AATAACTTTT
Statistics
Matches: 119, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
122 51 0.43
123 43 0.36
124 25 0.21
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (124 bp):
TTAAATTGATTAAAATGTTAAATATAAAAAATTAAATTTAAACTAAAACTAAATTAATAGAAATA
TATAAGATTTGATAACTAAAACTATTATTATATGAACTTTACATCTAATGATATATTTG
Found at i:3253866 original size:49 final size:50
Alignment explanation
Indices: 3253809--3253907 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 50
3253799 TAGTACATAA
3253809 TTTTTCAGTTTTTTCAAAAGCATACCTTAAGTTTAGTTTTTG-TTCATTT
1 TTTTTCAGTTTTTTCAAAAGCATACCTTAAGTTTAGTTTTTGTTTCATTT
3253858 TTTTTCAGTTTTTTCAAAAGCATACCTTAAGTTTAGTTTTTGTTTCATTT
1 TTTTTCAGTTTTTTCAAAAGCATACCTTAAGTTTAGTTTTTGTTTCATTT
3253908 AGTACTCATC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 42 0.86
50 7 0.14
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (50 bp):
TTTTTCAGTTTTTTCAAAAGCATACCTTAAGTTTAGTTTTTGTTTCATTT
Found at i:3273697 original size:16 final size:16
Alignment explanation
Indices: 3273676--3273709 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3273666 TACATGATTT
3273676 TTTTTTTATTCTGAGA
1 TTTTTTTATTCTGAGA
*
3273692 TTTTTTTTTTCTGAGA
1 TTTTTTTATTCTGAGA
3273708 TT
1 TT
3273710 ATATTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (16 bp):
TTTTTTTATTCTGAGA
Found at i:3278513 original size:19 final size:19
Alignment explanation
Indices: 3278477--3278515 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3278467 ACCCAACTTG
*
3278477 ATTAAAAAATAAGGATTTA
1 ATTAAAAAATAAGAATTTA
* *
3278496 ATTAAATAATAATAATTTA
1 ATTAAAAAATAAGAATTTA
3278515 A
1 A
3278516 AAAAAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
ATTAAAAAATAAGAATTTA
Found at i:3284683 original size:23 final size:23
Alignment explanation
Indices: 3284653--3284708 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
3284643 TTTTATATGG
*
3284653 CACTTCGGT-ACAATTCTACGAGT
1 CACTTCGGTGA-AATTCTACGAGA
* *
3284676 CACTTCGGTGAAATTCTATGTGA
1 CACTTCGGTGAAATTCTACGAGA
3284699 CACTTCGGTG
1 CACTTCGGTG
3284709 CATTTATACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGAAATTCTACGAGA
Found at i:3290096 original size:23 final size:23
Alignment explanation
Indices: 3290066--3290122 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
3290056 TTTATATGGA
*
3290066 ACTTCGGTGCAATTGTACGCGGC
1 ACTTCGGTGCAATTCTACGCGGC
* *
3290089 ACTTCGGTGAAATTCTACGTGGC
1 ACTTCGGTGCAATTCTACGCGGC
*
3290112 ACATCGGTGCA
1 ACTTCGGTGCA
3290123 TTTATATGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGGC
Found at i:3293351 original size:15 final size:15
Alignment explanation
Indices: 3293341--3293371 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3293331 ATAAATATAT
3293341 TAAATTAAAATAAAA
1 TAAATTAAAATAAAA
3293356 TAAATTAAAATAAAA
1 TAAATTAAAATAAAA
3293371 T
1 T
3293372 TAGTCTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATTAAAATAAAA
Found at i:3293356 original size:20 final size:19
Alignment explanation
Indices: 3293328--3293371 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
3293318 AATTGGTGGA
* *
3293328 AAAATAAATATATTAAATT
1 AAAATAAATAAATTAAAAT
3293347 AAAATAAAATAAATTAAAAT
1 AAAAT-AAATAAATTAAAAT
3293367 AAAAT
1 AAAAT
3293372 TAGTCTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAAATAAATTAAAAT
Found at i:3293748 original size:26 final size:26
Alignment explanation
Indices: 3293711--3293771 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
3293701 TTTTTTATTA
*
3293711 AAAAAC-GGTTTTCTCCATATTAATT
1 AAAAACTGTTTTTCTCCATATTAATT
* * *
3293736 AAAAACTGTTTTTGTTCATATTATTT
1 AAAAACTGTTTTTCTCCATATTAATT
3293762 AAGAAACTGT
1 AA-AAACTGT
3293772 AAAAAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 6 0.20
26 17 0.57
27 7 0.23
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (26 bp):
AAAAACTGTTTTTCTCCATATTAATT
Found at i:3306902 original size:19 final size:20
Alignment explanation
Indices: 3306875--3306936 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 20
3306865 ATTTTGACCA
*
3306875 TTTAACCGCCCATGCATTG-
1 TTTAGCCGCCCATGCATTGT
3306894 TTTAGCCGCCC---CACTTGT
1 TTTAGCCGCCCATGCA-TTGT
3306912 TTTCAGCCGCCCATGCATTGAT
1 TTT-AGCCGCCCATGCATTG-T
3306934 TTT
1 TTT
3306937 CAACAAATCC
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
16 2 0.06
17 3 0.09
18 3 0.09
19 18 0.51
21 3 0.09
22 6 0.17
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35
Consensus pattern (20 bp):
TTTAGCCGCCCATGCATTGT
Found at i:3308295 original size:35 final size:35
Alignment explanation
Indices: 3308249--3308321 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
3308239 GGTTACGGTG
3308249 TCAACCACACCAATTTTTTTCGAATCAATCAATAT
1 TCAACCACACCAATTTTTTTCGAATCAATCAATAT
3308284 TCAACCACACCAATTTTTTTCGAATCAATCAATAT
1 TCAACCACACCAATTTTTTTCGAATCAATCAATAT
3308319 TCA
1 TCA
3308322 TTGAAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (35 bp):
TCAACCACACCAATTTTTTTCGAATCAATCAATAT
Found at i:3311388 original size:28 final size:28
Alignment explanation
Indices: 3311342--3311414 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
3311332 TAACGGAGGT
*
3311342 AGGTCG-CATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACG-CCGGCGACCAACC
3311370 AGGTCGCCATGCACGCCGGCGACCAACC
1 AGGTCGCCATGCACGCCGGCGACCAACC
3311398 AGGTCGCCATGCACGCC
1 AGGTCGCCATGCACGCC
3311415 ATATACTCAC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 36 0.84
29 7 0.16
ACGTcount: A:0.21, C:0.41, G:0.29, T:0.10
Consensus pattern (28 bp):
AGGTCGCCATGCACGCCGGCGACCAACC
Found at i:3311503 original size:28 final size:28
Alignment explanation
Indices: 3311472--3311527 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3311462 CCATATACTC
3311472 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
3311500 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
3311528 GAAATATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.32, G:0.29, T:0.04
Consensus pattern (28 bp):
ACCATGCAGACGAGCCAGCCAACGGAGA
Found at i:3311852 original size:12 final size:12
Alignment explanation
Indices: 3311818--3311858 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
3311808 TAATATACTA
*
3311818 AATAAACTTACT
1 AATAAACTAACT
3311830 AACTAAAACTAACT
1 AA-T-AAACTAACT
3311844 AATAAACTAACT
1 AATAAACTAACT
3311856 AAT
1 AAT
3311859 TTTTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 14 0.54
13 2 0.08
14 10 0.38
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAAACTAACT
Found at i:3311954 original size:42 final size:41
Alignment explanation
Indices: 3311905--3312013 Score: 100
Period size: 42 Copynumber: 2.6 Consensus size: 41
3311895 ACTATTTAAC
*
3311905 TAACAAAAACTAATTAAATAATTTTTTTA-TATAACTAACTAT
1 TAACAAAAACTAATTAAATAATTTTTTAACTAT-A-TAACTAT
3311947 TAACAAAACAAACTAATT-AAT-ATTTTTTAACTATATAACTAT
1 TAAC--AA-AAACTAATTAAATAATTTTTTAACTATATAACTAT
* * *
3311989 CAA-ACATATCTAATTAAATAATTTT
1 TAACA-AAAACTAATTAAATAATTTT
3312014 AATTTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
39 8 0.14
40 4 0.07
41 5 0.09
42 13 0.23
43 9 0.16
44 8 0.14
45 9 0.16
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (41 bp):
TAACAAAAACTAATTAAATAATTTTTTAACTATATAACTAT
Found at i:3312106 original size:16 final size:18
Alignment explanation
Indices: 3312077--3312115 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
3312067 ACTAATTAAC
*
3312077 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
3312095 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
3312111 ATTTA
1 ATTTA
3312116 CTTATCTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:3312163 original size:16 final size:16
Alignment explanation
Indices: 3312120--3312170 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3312110 AATTTACTTA
3312120 TCTCCCTTTC-TTC-T
1 TCTCCCTTTCTTTCTT
**
3312134 TCTTACTTTCCTTTCTT
1 TCTCCCTTT-CTTTCTT
3312151 TCTCCCTTTCTTTCTT
1 TCTCCCTTTCTTTCTT
3312167 TCTC
1 TCTC
3312171 GGCTGAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.23
15 1 0.03
16 14 0.47
17 8 0.27
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (16 bp):
TCTCCCTTTCTTTCTT
Found at i:3312385 original size:50 final size:46
Alignment explanation
Indices: 3312317--3312429 Score: 156
Period size: 49 Copynumber: 2.4 Consensus size: 46
3312307 CTAGGTCACA
*
3312317 TGGCATGCTGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCTGCAGGCATGCAGC-GGGAGCAGGAGC-CGTGAAGTTAT-T
3312366 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCCGTGAAGTTATT
1 TGGCATGC-TGCAGGCATGCAGCGGGAGCAGGAGCCGTGAAGTTATT
* *
3312413 TGGC-TGGTGCATGCATG
1 TGGCATGCTGCAGGCATG
3312430 GTCGGCTGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
45 9 0.15
46 2 0.03
47 5 0.08
48 11 0.18
49 20 0.33
50 13 0.22
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.21
Consensus pattern (46 bp):
TGGCATGCTGCAGGCATGCAGCGGGAGCAGGAGCCGTGAAGTTATT
Found at i:3312427 original size:49 final size:50
Alignment explanation
Indices: 3312317--3312416 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 50
3312307 CTAGGTCACA
*
3312317 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
3312366 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGC-CGTGAAGTTAT-T
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
3312413 TGGC
1 TGGC
3312417 TGGTGCATGC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
47 5 0.10
48 11 0.22
49 20 0.41
50 13 0.27
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.20
Consensus pattern (50 bp):
TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
Found at i:3312438 original size:19 final size:19
Alignment explanation
Indices: 3312414--3312450 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3312404 GAAGTTATTT
3312414 GGCTGGTGCATGCATGGTC
1 GGCTGGTGCATGCATGGTC
3312433 GGCTGGTGCATGCATGGT
1 GGCTGGTGCATGCATGGT
3312451 TCGCAGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.19, G:0.43, T:0.27
Consensus pattern (19 bp):
GGCTGGTGCATGCATGGTC
Found at i:3312513 original size:28 final size:28
Alignment explanation
Indices: 3312459--3312547 Score: 128
Period size: 27 Copynumber: 3.2 Consensus size: 28
3312449 GTTCGCAGGG
3312459 GGCGACCTACAAGGTCGCCGGGA-TACAT
1 GGCGA-CTACAAGGTCGCCGGGACTACAT
3312487 GGCGACTACAAGGTCGCCGGGACTACAT
1 GGCGACTACAAGGTCGCCGGGACTACAT
** *
3312515 GGCGACTACAAGG-CGCCCAGACTGCAT
1 GGCGACTACAAGGTCGCCGGGACTACAT
3312542 GGCGAC
1 GGCGAC
3312548 CTCTCTATTG
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
27 34 0.60
28 23 0.40
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.12
Consensus pattern (28 bp):
GGCGACTACAAGGTCGCCGGGACTACAT
Found at i:3312579 original size:29 final size:28
Alignment explanation
Indices: 3312538--3312595 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
3312528 CGCCCAGACT
*
3312538 GCATGGCGACCTCTCTATTGGCTGGCTC
1 GCATGGCGACCTCTCCATTGGCTGGCTC
*
3312566 GCATGGGCGACCTCTCCGTTGGCTGGCTC
1 GCAT-GGCGACCTCTCCATTGGCTGGCTC
3312595 G
1 G
3312596 TCTGCATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.09, C:0.33, G:0.33, T:0.26
Consensus pattern (28 bp):
GCATGGCGACCTCTCCATTGGCTGGCTC
Found at i:3312722 original size:28 final size:29
Alignment explanation
Indices: 3312690--3312764 Score: 125
Period size: 28 Copynumber: 2.6 Consensus size: 29
3312680 GTGAGTATAT
3312690 GGCGTGCATGGCGACCTGGTTGGTCG-CG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
3312718 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
*
3312747 GGTCGTACATGGCGACCT
1 GG-CGTGCATGGCGACCT
3312765 ACCTCCGTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 26 0.59
29 4 0.09
30 14 0.32
ACGTcount: A:0.09, C:0.27, G:0.43, T:0.21
Consensus pattern (29 bp):
GGCGTGCATGGCGACCTGGTTGGTCGCCG
Found at i:3314536 original size:44 final size:41
Alignment explanation
Indices: 3314439--3314547 Score: 107
Period size: 44 Copynumber: 2.6 Consensus size: 41
3314429 TTCGGTAAAA
*
3314439 CGCTACCTAAAACATTATTTGTTCTTCTGGAATGTTAATTTGG
1 CGCTACCTAAAACATTATTT-TT-TTCTGGAATGTTAATTAGG
* *
3314482 -GCGTATCT-AAACATTATTTTTTTCCTACGGAAATGTTCATTAGG
1 CGC-TACCTAAAACATTATTTTTTT-CT--GG-AATGTTAATTAGG
3314526 CGCTACCTAAAACA-TATTTTTT
1 CGCTACCTAAAACATTATTTTTT
3314548 ACCGGAAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
40 2 0.04
41 4 0.07
42 13 0.24
43 6 0.11
44 23 0.42
45 7 0.13
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (41 bp):
CGCTACCTAAAACATTATTTTTTTCTGGAATGTTAATTAGG
Found at i:3315882 original size:3 final size:3
Alignment explanation
Indices: 3315874--3315916 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3315864 TGATATATAT
* *
3315874 TTA TTA TTA TATA TTA TTA TTA TTG TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3315917 CAAAGAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3316846 original size:24 final size:22
Alignment explanation
Indices: 3316798--3316852 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
3316788 AAGTCAAATT
***
3316798 AAAAATTACAAAAAATATTTTA
1 AAAAATTACAAAAAATATGGCA
3316820 AAAAATTACTAAAAAATAATGGCA
1 AAAAATTAC-AAAAAAT-ATGGCA
3316844 AAAAATTAC
1 AAAAATTAC
3316853 CTTAAGGCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 9 0.32
23 7 0.25
24 12 0.43
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25
Consensus pattern (22 bp):
AAAAATTACAAAAAATATGGCA
Found at i:3325481 original size:17 final size:18
Alignment explanation
Indices: 3325451--3325487 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3325441 CATCAACTTC
3325451 TGATATTCCAGAAGCTGG
1 TGATATTCCAGAAGCTGG
*
3325469 TGATATT-CAGAAGGTGG
1 TGATATTCCAGAAGCTGG
3325486 TG
1 TG
3325488 GACCTCGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.30
Consensus pattern (18 bp):
TGATATTCCAGAAGCTGG
Found at i:3329993 original size:3 final size:3
Alignment explanation
Indices: 3329985--3330017 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3329975 TGCTAGCAGT
3329985 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3330018 AGAGTGAAAA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3334058 original size:4 final size:4
Alignment explanation
Indices: 3334049--3334127 Score: 63
Period size: 4 Copynumber: 19.2 Consensus size: 4
3334039 ATTGATTTAC
* * *
3334049 TATT TATT TATT TATT TATAAT TATAT AATT TA-C TATT TATT TATT TATA
1 TATT TATT TATT TATT TAT--T TAT-T TATT TATT TATT TATT TATT TATT
* *
3334099 TATT TA-C TATT TATT TATA TACTT TATT T
1 TATT TATT TATT TATT TATT TA-TT TATT T
3334128 GGAGGTCGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
3 4 0.07
4 45 0.75
5 7 0.12
6 4 0.07
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:3334080 original size:23 final size:21
Alignment explanation
Indices: 3334054--3334127 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 21
3334044 TTTACTATTT
3334054 ATTTATTTATTTATAATTATATA
1 ATTTATTTATTTAT--TTATATA
3334077 ATTTACTATTTATTTATTTATAT-
1 A-TT--TATTTATTTATTTATATA
*
3334100 ATTTA-CTATTTATTTATATA
1 ATTTATTTATTTATTTATATA
*
3334120 CTTTATTT
1 ATTTATTT
3334128 GGAGGTCGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
19 13 0.30
20 6 0.14
21 1 0.02
22 2 0.05
23 2 0.05
24 8 0.19
26 11 0.26
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTATTTATTTATTTATATA
Found at i:3334115 original size:34 final size:34
Alignment explanation
Indices: 3334037--3334115 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 34
3334027 GAAGTATATA
*
3334037 ATATTGATTTACTATTTATTTATTTATTTATAATT
1 ATATTAATTTACTATTTATTTATTTA-TTATAATT
*
3334072 ATA-TAATTTACTATTTATTTATTTA-TATATTT
1 ATATTAATTTACTATTTATTTATTTATTATAATT
*
3334104 ACTATTTATTTA
1 A-TATTAATTTA
3334116 TATACTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.18
33 2 0.05
34 27 0.69
35 3 0.08
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (34 bp):
ATATTAATTTACTATTTATTTATTTATTATAATT
Found at i:3335446 original size:2 final size:2
Alignment explanation
Indices: 3335439--3335499 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
3335429 TGATTCATTC
3335439 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3335481 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3335500 TTAGTTTTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3340343 original size:15 final size:17
Alignment explanation
Indices: 3340323--3340356 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3340313 ATTTTATATT
3340323 AAAAAT-AATTT-TAAA
1 AAAAATCAATTTATAAA
3340338 AAAAATCAATTTATAAA
1 AAAAATCAATTTATAAA
3340355 AA
1 AA
3340357 TAGAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATCAATTTATAAA
Found at i:3340391 original size:21 final size:20
Alignment explanation
Indices: 3340339--3340391 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
3340329 AATTTTAAAA
*
3340339 AAAATCAATTTATAAAAATAG
1 AAAA-CAATTAATAAAAATAG
* *
3340360 AAAAAATATTAATAAAAATAT
1 AAAACA-ATTAATAAAAATAG
3340381 AACAACAATTA
1 AA-AACAATTA
3340392 TTTTCCCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAACAATTAATAAAAATAG
Found at i:3341835 original size:32 final size:32
Alignment explanation
Indices: 3341789--3341861 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
3341779 GGTTAAATCG
* *
3341789 ATATTTTATCTAAAATTTATAGGATAAAATTA
1 ATATTTTATATAAAATTTAGAGGATAAAATTA
*
3341821 ATATTTTATATAAAATTTAGAGGTTAAAATTA
1 ATATTTTATATAAAATTTAGAGGATAAAATTA
3341853 ATATTTTAT
1 ATATTTTAT
3341862 TTTTATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (32 bp):
ATATTTTATATAAAATTTAGAGGATAAAATTA
Found at i:3346361 original size:7 final size:6
Alignment explanation
Indices: 3346329--3346360 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3346319 AATGAAAAGT
*
3346329 AATTAA AATTAA ATTTAA AATTAA AATTAA AA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AA
3346361 AAAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATTAA
Found at i:3346795 original size:2 final size:2
Alignment explanation
Indices: 3346788--3346824 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3346778 GATACTCTTC
3346788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3346825 ACTAAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3354389 original size:21 final size:21
Alignment explanation
Indices: 3354363--3354426 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3354353 TTTTGGTGCA
*
3354363 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
3354384 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
3354405 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATCCCCCCCA
3354427 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:3354433 original size:21 final size:21
Alignment explanation
Indices: 3354365--3354446 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
3354355 TTGGTGCAGA
*
3354365 GGGAATCGA-TCCCCCC-CATG
1 GGGAACCGATTCCCCCCACA-G
*
3354385 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
3354409 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
3354430 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
3354447 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
21 25 0.50
22 6 0.12
23 16 0.32
24 1 0.02
25 1 0.02
ACGTcount: A:0.23, C:0.38, G:0.24, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:3360221 original size:5 final size:5
Alignment explanation
Indices: 3360211--3360269 Score: 73
Period size: 5 Copynumber: 11.8 Consensus size: 5
3360201 TACGAGCTGA
* * * *
3360211 GCCGT GTCGT GCCGT GCCGT GCCGT GCCGT GTCGT ACCGT ACCGT GCCGT
1 GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT GCCGT
*
3360261 GCCGA GCCG
1 GCCGT GCCG
3360270 AGACGGACGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.05, C:0.37, G:0.37, T:0.20
Consensus pattern (5 bp):
GCCGT
Found at i:3361384 original size:2 final size:2
Alignment explanation
Indices: 3361379--3361412 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3361369 ACACACACAC
3361379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3361413 TATTTTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3368238 original size:20 final size:20
Alignment explanation
Indices: 3368197--3368239 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3368187 TCTTTTTCAA
*
3368197 TATCGAGATCATGGTTTTAG
1 TATCGAGATCATGGTTTGAG
*
3368217 TATCGAGATCGGTGG-TTGAG
1 TATCGAGATC-ATGGTTTGAG
3368237 TAT
1 TAT
3368240 TGATACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.37
Consensus pattern (20 bp):
TATCGAGATCATGGTTTGAG
Found at i:3376764 original size:20 final size:20
Alignment explanation
Indices: 3376739--3376810 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
3376729 TTTTCCCAAT
3376739 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
3376759 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* * ** *
3376779 TCGAAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
3376800 TCGCAATGCGA
1 TCGCAATGCGA
3376811 TACTGACTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:3376824 original size:20 final size:20
Alignment explanation
Indices: 3376799--3376933 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
3376789 AATTGGGAAA
3376799 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
3376819 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
3376839 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
3376860 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
3376880 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
3376900 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
3376920 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
3376934 TTTCTAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3376861 original size:61 final size:61
Alignment explanation
Indices: 3376796--3376933 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
3376786 GCGAATTGGG
* * *
3376796 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
3376857 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
3376918 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
3376934 TTTCTAAGCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3377457 original size:20 final size:20
Alignment explanation
Indices: 3377398--3377461 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
3377388 GCGATTTTAG
*
3377398 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
3377418 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
3377438 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
3377458 TTTC
1 TTTC
3377462 AGAAGCTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:3377652 original size:25 final size:24
Alignment explanation
Indices: 3377598--3377652 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3377588 TGTTTATTAT
* *
3377598 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
3377622 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
3377648 TGTTT
1 TGTTT
3377653 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:3378802 original size:18 final size:18
Alignment explanation
Indices: 3378781--3378825 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3378771 TCCACTTCGG
*
3378781 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3378799 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3378817 GAGCCATCA
1 GAGCCATCA
3378826 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3379338 original size:19 final size:20
Alignment explanation
Indices: 3379284--3379350 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3379274 TAGTTTACTT
* *
3379284 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
3379304 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
3379324 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
3379343 TCGCAACG
1 TCGCAACG
3379351 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:3379358 original size:14 final size:14
Alignment explanation
Indices: 3379339--3379396 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3379329 ATGCGAAATG
3379339 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3379353 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
3379369 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3379385 AAAATCGCAACG
1 AAAATCGCAACG
3379397 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3379381 original size:32 final size:33
Alignment explanation
Indices: 3379323--3379413 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3379313 GGAAATGGCT
3379323 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3379356 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3379388 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3379414 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3379449 original size:14 final size:14
Alignment explanation
Indices: 3379430--3379487 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
3379420 TTGTGTTTCG
3379430 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3379444 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
3379460 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
3379476 CGTTGCGATTTT
1 CGTTGCGATTTT
3379488 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3379499 original size:33 final size:32
Alignment explanation
Indices: 3379425--3379503 Score: 131
Period size: 32 Copynumber: 2.4 Consensus size: 32
3379415 GCGATTTGTG
*
3379425 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
*
3379457 TTTCACATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGA-TTTCA
3379490 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
3379504 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.47
Consensus pattern (32 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
Found at i:3379522 original size:20 final size:19
Alignment explanation
Indices: 3379488--3379543 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
3379478 TTGCGATTTT
*
3379488 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3379507 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
3379527 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
3379544 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3379942 original size:21 final size:20
Alignment explanation
Indices: 3379916--3379985 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
3379906 CTGTCATCCC
3379916 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
3379937 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
3379958 TCAAGAGTCCCCCCCCACCGT
1 TCAAGAGT-CCCCTCCATCGT
3379979 TCAAGAG
1 TCAAGAG
3379986 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:3380018 original size:42 final size:42
Alignment explanation
Indices: 3379909--3379997 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
3379899 GACTCACCTG
* * *
3379909 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* *
3379951 TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
3379993 TCATC
1 TCATC
3379998 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:3381434 original size:14 final size:14
Alignment explanation
Indices: 3381415--3381450 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3381405 ATTATTTAAT
3381415 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3381429 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3381443 TGATTTGT
1 TGATTTGT
3381451 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3382884 original size:33 final size:33
Alignment explanation
Indices: 3382842--3382935 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
3382832 TATCGCAATG
*
3382842 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
3382875 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
3382908 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3382936 AGTACTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:3382899 original size:19 final size:19
Alignment explanation
Indices: 3382875--3382935 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
3382865 GCGATTCCCT
3382875 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3382894 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
3382908 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3382927 CATTGCGAT
1 CGTTGCGAT
3382936 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3383061 original size:14 final size:14
Alignment explanation
Indices: 3383042--3383078 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3383032 CATCAATTAA
3383042 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3383056 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3383070 ACAAATCAA
1 ACAAATCAA
3383079 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3384497 original size:21 final size:21
Alignment explanation
Indices: 3384431--3384497 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3384421 GTGAATCGGG
*
3384431 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3384451 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3384473 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3384494 CTCT
1 CTCT
3384498 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3384878 original size:92 final size:90
Alignment explanation
Indices: 3384769--3384952 Score: 275
Period size: 91 Copynumber: 2.0 Consensus size: 90
3384759 ATTTCAAACT
*
3384769 TTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG-TTAG
1 TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAG
3384832 CA-TAATTGACAGCAACCGAATAAATTTAC
62 CAGT-ATTGACAGCAACCGAATAAATTTAC
3384861 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
1 TTCAACCAAAAGACAAAAC-AAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
*
3384926 TATTGGCAGCAACCGAATAAATTTAC
65 TATTGACAGCAACCGAATAAATTTAC
3384952 T
1 T
3384953 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
90 8 0.09
91 31 0.36
92 20 0.23
94 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAGT
ATTGACAGCAACCGAATAAATTTAC
Found at i:3386660 original size:20 final size:19
Alignment explanation
Indices: 3386629--3386783 Score: 106
Period size: 19 Copynumber: 8.8 Consensus size: 19
3386619 TCTTTTGGTT
3386629 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
3386648 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
3386669 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3386688 G--A-G--AATCGCAACGT
1 GAAATGAAAATCGCAACGA
**
3386702 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3386721 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
3386735 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3386754 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
3386768 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3386784 TGCGATTTTG
Statistics
Matches: 106, Mismatches: 13, Indels: 34
0.69 0.08 0.22
Matches are distributed among these distances:
14 31 0.29
16 6 0.06
17 6 0.06
19 32 0.30
20 29 0.27
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3386697 original size:14 final size:14
Alignment explanation
Indices: 3386678--3386766 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
3386668 GGAAATGACT
3386678 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
3386692 ATCGCAACGTGAAATGA
1 ATCGCAAC--GAGA-GA
3386709 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
3386725 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
3386744 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
3386758 ATCGCAACG
1 ATCGCAACG
3386767 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 7 0.11
17 7 0.11
18 1 0.02
19 18 0.30
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:3386711 original size:33 final size:33
Alignment explanation
Indices: 3386654--3386783 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
3386644 ACGAGATAAT
**
3386654 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGA
* **
3386688 GAGAATCGCAACGTGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
3386721 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
3386754 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
3386784 TGCGATTTTG
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 79 0.86
34 13 0.14
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:3386817 original size:17 final size:18
Alignment explanation
Indices: 3386778--3386826 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
3386768 GAAATGAAAA
*
3386778 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTT-GTT
3386797 TCGCATTGCGATTTT-TT
1 TCGCATTGCGATTTTGTT
*
3386814 TCGCGTTGCGATT
1 TCGCATTGCGATT
3386827 CTCTCGTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.50
19 14 0.50
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTTGTT
Found at i:3387417 original size:20 final size:20
Alignment explanation
Indices: 3387376--3387446 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3387366 GCTATGTAAA
* *
3387376 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
3387396 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
3387416 TCGCGTTGCGATTT-CCTAAT
1 TCGCATTGCGATTTACGT-AT
3387436 TCGCATTGCGA
1 TCGCATTGCGA
3387447 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 5 0.11
20 39 0.89
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:3387467 original size:21 final size:21
Alignment explanation
Indices: 3387443--3387498 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
3387433 AATTCGCATT
*
3387443 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
3387464 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
3387484 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
3387499 TGAATTGTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:3391133 original size:20 final size:20
Alignment explanation
Indices: 3391089--3391161 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
3391079 GTAACTCAGT
*
3391089 TTTG-AAATCGCAACACGAA
1 TTTGTAAATCGCAACGCGAA
3391108 -TTGTAAATCGCAACGCGAA
1 TTTGTAAATCGCAACGCGAA
*
3391127 TTTGTAAATCGCAACGCAAA
1 TTTGTAAATCGCAACGCGAA
3391147 TTTGTAAATCGCAAC
1 TTTGTAAATCGCAAC
3391162 ACAAAAGTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
18 3 0.06
19 14 0.28
20 33 0.66
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (20 bp):
TTTGTAAATCGCAACGCGAA
Found at i:3391355 original size:22 final size:22
Alignment explanation
Indices: 3391330--3391374 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3391320 ACTCTCTATT
* *
3391330 GCGACATCCGTCTCCATCTCCG
1 GCGACATCCGTCCCCATATCCG
3391352 GCGACATCCGTCCCCATATCCG
1 GCGACATCCGTCCCCATATCCG
3391374 G
1 G
3391375 TGACCCCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.44, G:0.20, T:0.20
Consensus pattern (22 bp):
GCGACATCCGTCCCCATATCCG
Found at i:3392122 original size:14 final size:14
Alignment explanation
Indices: 3392103--3392134 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3392093 TTTGTAGTTT
3392103 TTGGTATATCTAAC
1 TTGGTATATCTAAC
3392117 TTGGTATATCTAAC
1 TTGGTATATCTAAC
3392131 TTGG
1 TTGG
3392135 GTAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGGTATATCTAAC
Found at i:3393605 original size:21 final size:21
Alignment explanation
Indices: 3393560--3393608 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3393550 AATGGTGCTT
* * * *
3393560 TACGTGGTGAGGTATCTACTT
1 TACGTGATGAGGTAGCCACTC
3393581 TACGTGATGAGGTAGCCACTC
1 TACGTGATGAGGTAGCCACTC
3393602 TACGTGA
1 TACGTGA
3393609 GATTGTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (21 bp):
TACGTGATGAGGTAGCCACTC
Found at i:3393911 original size:21 final size:21
Alignment explanation
Indices: 3393883--3393962 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
3393873 GATTCACCTG
3393883 TCATCATTCAAGAGACCCCTCC
1 TCATCATTCAAGAG-CCCCTCC
3393905 T-ATCATTCAAGAGGCCCCT-C
1 TCATCATTCAAGA-GCCCCTCC
*
3393925 TCATCGTTCAAGATGCCCCTCC
1 TCATCATTCAAGA-GCCCCTCC
* *
3393947 -CACCGTTCAAGAGCCC
1 TCATCATTCAAGAGCCC
3393963 GATTCACATG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
20 6 0.12
21 43 0.83
22 3 0.06
ACGTcount: A:0.24, C:0.40, G:0.14, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGCCCCTCC
Found at i:3395463 original size:14 final size:14
Alignment explanation
Indices: 3395444--3395482 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3395434 CAAATTCATA
3395444 TTGCGAT-TTTCGCG
1 TTGCGATATTT-GCG
3395458 TTGCGATATTTGCG
1 TTGCGATATTTGCG
3395472 TTGCGA-ATTTG
1 TTGCGATATTTG
3395483 ATTTTCGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.21
14 16 0.67
15 3 0.12
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.44
Consensus pattern (14 bp):
TTGCGATATTTGCG
Found at i:3395498 original size:20 final size:20
Alignment explanation
Indices: 3395469--3395520 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3395459 TGCGATATTT
*
3395469 GCGTTGCGAATTTGATTTTC
1 GCGTTGCGAATTTGACTTTC
*
3395489 GCGTTACGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
*
3395509 GCTTTGCGAATT
1 GCGTTGCGAATT
3395521 CAAGGAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:3399055 original size:19 final size:20
Alignment explanation
Indices: 3399018--3399055 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3399008 TCTTTTATAT
3399018 TCATATAATTTATTATCATA
1 TCATATAATTTATTATCATA
*
3399038 TCATATGATTTA-TATCAT
1 TCATATAATTTATTATCAT
3399056 CATAACATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (20 bp):
TCATATAATTTATTATCATA
Found at i:3399064 original size:22 final size:20
Alignment explanation
Indices: 3399019--3399064 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3399009 CTTTTATATT
*
3399019 CATATAATTTATTATCATAT
1 CATATAATTTATTATCATAA
*
3399039 CATATGATTTATATCATCATAA
1 CATATAATTTAT-T-ATCATAA
3399061 CATA
1 CATA
3399065 GCACATATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 1 0.05
22 10 0.45
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.43
Consensus pattern (20 bp):
CATATAATTTATTATCATAA
Found at i:3400895 original size:3 final size:3
Alignment explanation
Indices: 3400887--3400914 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3400877 TCTTCGGGGA
3400887 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3400915 AGGGTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3401279 original size:12 final size:12
Alignment explanation
Indices: 3401258--3401291 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3401248 GGTTGTGGGT
*
3401258 TTTGAGATTGTG
1 TTTGATATTGTG
3401270 TTTGATATTGTG
1 TTTGATATTGTG
*
3401282 TTTGGTATTG
1 TTTGATATTG
3401292 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:3402103 original size:20 final size:20
Alignment explanation
Indices: 3402078--3402227 Score: 94
Period size: 20 Copynumber: 7.5 Consensus size: 20
3402068 AAATAAAAGC
3402078 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
3402098 TGTTGCGAATTTGAAAA-TCG
1 TGTTGCGAAATT-AAAATTCG
* *
3402118 AGTTGCGAAAATAAAATTCG
1 TGTTGCGAAATTAAAATTCG
* * *
3402138 TGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
* ** *
3402158 TGTTGTGAAAAGGAAACTT-G
1 TGTTGCG-AAATTAAAATTCG
3402178 TGTTGCG-AATTCATAAA-TCG
1 TGTTGCGAAATT-A-AAATTCG
* * *
3402198 AGTTGCGAATTTGAAATTCCG
1 TGTTGCGAAATTAAAATT-CG
3402219 TGTTGCGAA
1 TGTTGCGAA
3402228 TTTGGAAATC
Statistics
Matches: 95, Mismatches: 24, Indels: 21
0.68 0.17 0.15
Matches are distributed among these distances:
18 2 0.02
19 12 0.13
20 59 0.62
21 20 0.21
22 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:3402125 original size:40 final size:40
Alignment explanation
Indices: 3402079--3402246 Score: 171
Period size: 40 Copynumber: 4.2 Consensus size: 40
3402069 AATAAAAGCT
3402079 GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
* **
3402119 GTTGCGAAAATAAAATTCGTGTTGCG-ATTTAGAAAATCTT
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTT-GAAAATCGA
* ** * *
3402159 GTTGTGAAAAGGAAACTT-GTGTTGCGAA-TTCATAAATCGA
1 GTTGCG-AAATTAAAATTCGTGTTGCGAATTTGA-AAATCGA
* * * *
3402199 GTTGCGAATTTGAAATTCCGTGTTGCGAATTTGGAAATCGC
1 GTTGCGAAATTAAAATT-CGTGTTGCGAATTTGAAAATCGA
3402240 GTTGCGA
1 GTTGCGA
3402247 TTGCAGAAAC
Statistics
Matches: 102, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
39 11 0.11
40 57 0.56
41 32 0.31
42 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
Found at i:3402245 original size:20 final size:20
Alignment explanation
Indices: 3402095--3402333 Score: 118
Period size: 20 Copynumber: 11.8 Consensus size: 20
3402085 AAATTAAAAT
*
3402095 TCGTGTTGCGAATTTGAAAA
1 TCGTGTTGCGAATTTGGAAA
* ** *
3402115 TCGAGTTGCGAAAAT-AAAA
1 TCGTGTTGCGAATTTGGAAA
*
3402134 TTCGTGTTGCG-ATTTAGAAAA
1 -TCGTGTTGCGAATTT-GGAAA
* * **
3402155 TCTTGTTGTGAA-AAGGAAA
1 TCGTGTTGCGAATTTGGAAA
* ***
3402174 CTTGTGTTGCGAATTCATAAA
1 -TCGTGTTGCGAATTTGGAAA
*
3402195 TCGAGTTGCGAATTT-GAAA
1 TCGTGTTGCGAATTTGGAAA
3402214 TTCCGTGTTGCGAATTTGGAAA
1 -T-CGTGTTGCGAATTTGGAAA
*
3402236 TCGCGTTGCG-A-TTGCAGAAA
1 TCGTGTTGCGAATTTG--GAAA
*
3402256 -CTGAGTTGCGAATTTGGGAAA
1 TC-GTGTTGCGAATTT-GGAAA
*
3402277 TTCGTATTGCGAATTTGGAAA
1 -TCGTGTTGCGAATTTGGAAA
* *
3402298 -CTGTGTTGCGAAATT-GAAGT
1 TC-GTGTTGCGAATTTGGAA-A
*
3402318 TCGCGTTGCGAATTTG
1 TCGTGTTGCGAATTTG
3402334 TTGGTCATTT
Statistics
Matches: 166, Mismatches: 32, Indels: 41
0.69 0.13 0.17
Matches are distributed among these distances:
18 3 0.02
19 19 0.11
20 92 0.55
21 33 0.20
22 17 0.10
23 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (20 bp):
TCGTGTTGCGAATTTGGAAA
Found at i:3402300 original size:42 final size:39
Alignment explanation
Indices: 3402220--3402309 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 39
3402210 GAAATTCCGT
*
3402220 GTTGCGAATTTGGAAATCGCGTTGCGATTGCAGAAACTGA
1 GTTGCGAATTTGGAAATCGCATTGCGATTG-AGAAACTGA
* *
3402260 GTTGCGAATTTGGGAAATTCGTATTGCGAATTTG-GAAACTGT
1 GTTGCGAATTT-GGAAA-TCGCATTGCG-A-TTGAGAAACTGA
3402302 GTTGCGAA
1 GTTGCGAA
3402310 ATTGAAGTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
40 11 0.26
41 5 0.12
42 23 0.53
43 1 0.02
44 3 0.07
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (39 bp):
GTTGCGAATTTGGAAATCGCATTGCGATTGAGAAACTGA
Found at i:3402307 original size:62 final size:60
Alignment explanation
Indices: 3402169--3402308 Score: 169
Period size: 62 Copynumber: 2.3 Consensus size: 60
3402159 GTTGTGAAAA
* *
3402169 GGAAACTTGTGTTGCGAATTCATAAATCGAGTTGCGAATTTGAAATTCCGTGTTGCGAATTT
1 GGAAAC-TGTGTTGCG-ATTCAGAAATCGAGTTGCGAATTTGAAATTCCGTATTGCGAATTT
*
3402231 GGAAA-TCGCGTTGCGATTGCAGAAA-CTGAGTTGCGAATTTGGGAAATT-CGTATTGCGAATTT
1 GGAAACT-GTGTTGCGATT-CAGAAATC-GAGTTGCGAATTT--GAAATTCCGTATTGCGAATTT
3402293 GGAAACTGTGTTGCGA
1 GGAAACTGTGTTGCGA
3402309 AATTGAAGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
60 5 0.07
61 25 0.37
62 31 0.46
63 7 0.10
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (60 bp):
GGAAACTGTGTTGCGATTCAGAAATCGAGTTGCGAATTTGAAATTCCGTATTGCGAATTT
Found at i:3404617 original size:13 final size:13
Alignment explanation
Indices: 3404599--3404624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3404589 GTCAAATGTC
3404599 AGTCAAATTTATT
1 AGTCAAATTTATT
3404612 AGTCAAATTTATT
1 AGTCAAATTTATT
3404625 TAAAGAGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
AGTCAAATTTATT
Found at i:3404638 original size:18 final size:19
Alignment explanation
Indices: 3404612--3404647 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3404602 CAAATTTATT
3404612 AGTCAAATT-TATTTAAAG
1 AGTCAAATTCTATTTAAAG
*
3404630 AGTCCAATTCTATTTAAA
1 AGTCAAATTCTATTTAAA
3404648 CGGAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (19 bp):
AGTCAAATTCTATTTAAAG
Done.