Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 81 of 106
Found at i:16166170 original size:23 final size:23
Alignment explanation
Indices: 16166144--16166190 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
16166134 TTTGAAGTCT
16166144 ATATACT-AATATATATATTTTAA
1 ATATACTGAATAT-TATATTTTAA
* *
16166167 ATATATTGAATGTTATATTTTAA
1 ATATACTGAATATTATATTTTAA
16166190 A
1 A
16166191 AATAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
ATATACTGAATATTATATTTTAA
Found at i:16166761 original size:21 final size:20
Alignment explanation
Indices: 16166706--16166762 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 20
16166696 TATTTATTTG
16166706 TTTATTATTTATAATTTTATTA
1 TTTATTATTT-T-ATTTTATTA
*
16166728 TTAAGTCT-TTTTATTTTATTA
1 TTTA-T-TATTTTATTTTATTA
16166749 TTTATTATATTTAT
1 TTTATTAT-TTTAT
16166763 GCCTTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 1 0.03
20 2 0.07
21 17 0.59
22 4 0.14
23 4 0.14
24 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTATTATTTTATTTTATTA
Found at i:16177650 original size:2 final size:2
Alignment explanation
Indices: 16177643--16177669 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16177633 GGGATTATTT
16177643 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16177670 TCAAAAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16182371 original size:31 final size:30
Alignment explanation
Indices: 16182334--16182401 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
16182324 ATTGAGCCTT
*
16182334 TTCTTTTAATGAC-GAACCCTTTATTTTTTTC
1 TTCTTTTAATGACTG-ACCCTTT-TTTTCTTC
*
16182365 TTCTTTTATTGACTTGACCCTTTTTTTCTTC
1 TTCTTTTAATGAC-TGACCCTTTTTTTCTTC
16182396 TT-TTTT
1 TTCTTTT
16182402 GCTAAAGCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 4 0.12
31 21 0.64
32 7 0.21
33 1 0.03
ACGTcount: A:0.13, C:0.19, G:0.06, T:0.62
Consensus pattern (30 bp):
TTCTTTTAATGACTGACCCTTTTTTTCTTC
Found at i:16183536 original size:23 final size:23
Alignment explanation
Indices: 16183504--16183547 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
16183494 GAAATTGTAA
* *
16183504 TATTTGATTTGGATTAAATTTTT
1 TATTTAATTTGAATTAAATTTTT
16183527 TATTTAATTTGAATTAAATTT
1 TATTTAATTTGAATTAAATTT
16183548 GAATATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (23 bp):
TATTTAATTTGAATTAAATTTTT
Found at i:16183571 original size:13 final size:12
Alignment explanation
Indices: 16183516--16183583 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 12
16183506 TTTGATTTGG
**
16183516 ATTAAATTTTTT
1 ATTAAATTTAAT
* *
16183528 ATTTAATTTGA-
1 ATTAAATTTAAT
16183539 ATTAAATTTGAAT
1 ATTAAATTT-AAT
16183552 ATT-AATTTATAT
1 ATTAAATTTA-AT
*
16183564 ATTAAATTT-AG
1 ATTAAATTTAAT
16183575 ATTAAATTT
1 ATTAAATTT
16183584 TGAATCAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
11 19 0.41
12 19 0.41
13 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (12 bp):
ATTAAATTTAAT
Found at i:16183748 original size:14 final size:13
Alignment explanation
Indices: 16183700--16183752 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
16183690 AATTTATTTA
16183700 AATATATTAAAAT
1 AATATATTAAAAT
*
16183713 AATATATAAAAATT
1 AATATATTAAAA-T
*
16183727 AA-AAATTAAAAT
1 AATATATTAAAAT
*
16183739 CAATACATTAAAAT
1 -AATATATTAAAAT
16183753 GAATCAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 20 0.61
14 12 0.36
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATATTAAAAT
Found at i:16193538 original size:28 final size:28
Alignment explanation
Indices: 16193483--16193537 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
16193473 ACGGGAAAAG
*
16193483 GTATTCTAGCACAGGTAAAATTATTTTC
1 GTATTCTAGCACAGGTAAAAGTATTTTC
16193511 GTATTCTAGCACAGGTAAAAGGTATTT
1 GTATTCTAGCACAGGTAAAA-GTATTT
16193538 CCATTTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (28 bp):
GTATTCTAGCACAGGTAAAAGTATTTTC
Found at i:16195224 original size:42 final size:42
Alignment explanation
Indices: 16195165--16195251 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
16195155 TAGGGCAGTG
16195165 CTAGGCGGCGATGGATCGAGGTGCTGACTCTGCAATATGTTA
1 CTAGGCGGCGATGGATCGAGGTGCTGACTCTGCAATATGTTA
16195207 CTAGGCGGCGATGGATCGAGGTGCTGACTCTGCAATATGTTA
1 CTAGGCGGCGATGGATCGAGGTGCTGACTCTGCAATATGTTA
16195249 CTA
1 CTA
16195252 CTTCTTTATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (42 bp):
CTAGGCGGCGATGGATCGAGGTGCTGACTCTGCAATATGTTA
Found at i:16199042 original size:5 final size:5
Alignment explanation
Indices: 16199032--16199091 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
16199022 AATAATTTAA
16199032 AATAT AATAT -A-AT AATAT AATAT AAATAT AATAT AATAT ATGATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT A--ATAT
*
16199078 AAATAT AACAT AAT
1 -AATAT AATAT AAT
16199092 TTAAAATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 29 0.62
6 9 0.19
7 4 0.09
8 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:16199212 original size:32 final size:32
Alignment explanation
Indices: 16199172--16199245 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
16199162 AAATTATAAC
* *
16199172 ATAT-AATTTTTATATATAATATAATATAAAT
1 ATATAAATTTTAACATATAATATAATATAAAT
* * * *
16199203 TTATAAATTTTAACATTTTATATGATATAAAT
1 ATATAAATTTTAACATATAATATAATATAAAT
16199235 ATATAAATTTT
1 ATATAAATTTT
16199246 CAAATCTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 3 0.09
32 32 0.91
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (32 bp):
ATATAAATTTTAACATATAATATAATATAAAT
Found at i:16201197 original size:12 final size:12
Alignment explanation
Indices: 16201180--16201230 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
16201170 ATATATAAAA
16201180 TAATTATTTATT
1 TAATTATTTATT
16201192 TAATTA--TA--
1 TAATTATTTATT
16201200 TAATTATTTATT
1 TAATTATTTATT
*
16201212 TAATTATATATT
1 TAATTATTTATT
16201224 TATATTA
1 TA-ATTA
16201231 AAAATAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
8 6 0.18
10 4 0.12
12 19 0.58
13 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TAATTATTTATT
Found at i:16201204 original size:20 final size:20
Alignment explanation
Indices: 16201179--16201226 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
16201169 TATATATAAA
16201179 ATAATTATTTATTTAATTAT
1 ATAATTATTTATTTAATTAT
16201199 ATAATTATTTATTTAATTAT
1 ATAATTATTTATTTAATTAT
*
16201219 ATATTTAT
1 ATAATTAT
16201227 ATTAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATAATTATTTATTTAATTAT
Found at i:16201358 original size:37 final size:37
Alignment explanation
Indices: 16201294--16201370 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
16201284 TATTAAATTT
***
16201294 AAATTTAAATATAAAAAATTTTTATTAAATC-AAATC
1 AAATTTAAATATAAAAAATTAAAATTAAATCGAAATC
* *
16201330 AAATTTAAATATTAAAAATATAAAATTAAATCGAATTC
1 AAATTTAAATATAAAAAAT-TAAAATTAAATCGAAATC
16201368 AAA
1 AAA
16201371 ACCTATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 18 0.53
37 9 0.26
38 7 0.21
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.35
Consensus pattern (37 bp):
AAATTTAAATATAAAAAATTAAAATTAAATCGAAATC
Found at i:16201862 original size:32 final size:32
Alignment explanation
Indices: 16201803--16201863 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
16201793 AATAATTTAT
* *
16201803 ATATTTATATTGTATAAAATATTAAAATTGAC
1 ATATTTATATTATATAAAATATAAAAATTGAC
***
16201835 ATATTTATATTATATTTTATATAAAAATT
1 ATATTTATATTATATAAAATATAAAAATT
16201864 ATTTATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (32 bp):
ATATTTATATTATATAAAATATAAAAATTGAC
Found at i:16217424 original size:11 final size:11
Alignment explanation
Indices: 16217410--16217450 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
16217400 AAAAATAATT
16217410 TTTATATTAAA
1 TTTATATTAAA
16217421 TTTAT-TTAAA
1 TTTATATTAAA
16217431 --TATATTAAA
1 TTTATATTAAA
*
16217440 ATTATATTAAA
1 TTTATATTAAA
16217451 ATAATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 3 0.11
9 5 0.19
10 5 0.19
11 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTATATTAAA
Found at i:16217451 original size:11 final size:11
Alignment explanation
Indices: 16217411--16217475 Score: 61
Period size: 10 Copynumber: 6.4 Consensus size: 11
16217401 AAAATAATTT
16217411 TTATATT-AAA
1 TTATATTAAAA
*
16217421 TT-TATTTAAA
1 TTATATTAAAA
16217431 -TATATTAAAA
1 TTATATTAAAA
16217441 TTATATTAAAA
1 TTATATTAAAA
*
16217452 TAATATATAAAA
1 TTATAT-TAAAA
16217464 --ATATT-AAA
1 TTATATTAAAA
16217472 TTAT
1 TTAT
16217476 TAAACTAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
8 3 0.06
9 6 0.13
10 18 0.38
11 15 0.32
12 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTATATTAAAA
Found at i:16217452 original size:21 final size:20
Alignment explanation
Indices: 16217412--16217479 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
16217402 AAATAATTTT
*
16217412 TATATTAAATTTAT-TTAAA
1 TATATTAAAATTATATTAAA
16217431 TATATTAAAATTATATTAAAA
1 TATATTAAAATTATATT-AAA
16217452 TAATATATAAAA--ATATTAAA
1 T-ATAT-TAAAATTATATTAAA
16217472 T-TATTAAA
1 TATATTAAA
16217480 CTAAATTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
17 4 0.09
18 3 0.07
19 13 0.30
20 6 0.14
21 9 0.20
22 4 0.09
23 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATTAAAATTATATTAAA
Found at i:16217458 original size:13 final size:13
Alignment explanation
Indices: 16217429--16217466 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
16217419 AATTTATTTA
16217429 AATATATTAAAAT
1 AATATATTAAAAT
16217442 --TATATTAAAAT
1 AATATATTAAAAT
*
16217453 AATATATAAAAAT
1 AATATATTAAAAT
16217466 A
1 A
16217467 TTAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATATTAAAAT
Found at i:16219164 original size:262 final size:261
Alignment explanation
Indices: 16218694--16219205 Score: 803
Period size: 262 Copynumber: 2.0 Consensus size: 261
16218684 AAAAACCTCT
*
16218694 ACTATCAAATAATAGATATACAAAATTCTTCTCTAACTAAAACTAGAACTAATTAACAATTAGAG
1 ACTATCAAATAATAGATATACAAAATTCTTCTCTAACTAAAACTAGAACTAATCAACAATTAGAG
* *
16218759 AGAGACAATTGAAAAAATCTCACCAAATAAGTGACTCAACAAATACACATTAAATTTGTTCTTAG
66 AAAGACAATTGAAAAAATCTCACCAAATAAGTGACTCAACAAATACACATTAAATTTATTCTTAG
* * *
16218824 AGAGCTTCAAACTCGATTTTCACCGTTCAAAATATAAAATTCTGAATCATAAACCTACTGATAAA
131 AGAGCTTCAAACTCGATCTTCACCGTTCAAAATATAAAATTCTGAATCATAAACATACTGACAAA
* * *
16218889 ATTTCAGCTCAATCGAACTATGAAGCGACTTCTATTCAATAAATTCTTCCTTCTTCTCTAATTAA
196 ATTTCAACTCAATCAAACCATGAAGCGACTTCTATTCAATAAATTCTTCCTTCTTCTCTAATTAA
16218954 A
261 A
* * *
16218955 ACTATCAAATAATATATATACAAAGTTCTTCTTTAACTAAAA-TCA-AAGCTAATCAACAATTAG
1 ACTATCAAATAATAGATATACAAAATTCTTCTCTAACTAAAACT-AGAA-CTAATCAACAATTAG
* * * *
16219018 AGAAAAGACAATTGAAAAAATCTTATCAAATAGGTGACTCAATAAATACACATTAAATTTATTCT
64 AG-AAAGACAATTGAAAAAATCTCACCAAATAAGTGACTCAACAAATACACATTAAATTTATTCT
* * *
16219083 TAGAGAGCTTCAAACTCGATCTTCACTGTTCAAAATGTAAAATTCTGAATTATAAACATACTGAC
128 TAGAGAGCTTCAAACTCGATCTTCACCGTTCAAAATATAAAATTCTGAATCATAAACATACTGAC
*
16219148 AAAATTTCAACTCAATCAAACCATGAATCGACTTCTATTCAATAAATTCTTCCTTCTT
193 AAAATTTCAACTCAATCAAACCATGAAGCGACTTCTATTCAATAAATTCTTCCTTCTT
16219206 TCTTTTCTTT
Statistics
Matches: 228, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
260 3 0.01
261 56 0.25
262 169 0.74
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (261 bp):
ACTATCAAATAATAGATATACAAAATTCTTCTCTAACTAAAACTAGAACTAATCAACAATTAGAG
AAAGACAATTGAAAAAATCTCACCAAATAAGTGACTCAACAAATACACATTAAATTTATTCTTAG
AGAGCTTCAAACTCGATCTTCACCGTTCAAAATATAAAATTCTGAATCATAAACATACTGACAAA
ATTTCAACTCAATCAAACCATGAAGCGACTTCTATTCAATAAATTCTTCCTTCTTCTCTAATTAA
A
Found at i:16221023 original size:18 final size:17
Alignment explanation
Indices: 16220991--16221024 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16220981 CCAGCCCTTA
16220991 CCCATTTCTCCTTTTTT
1 CCCATTTCTCCTTTTTT
16221008 CCCA-TTCTCTCTTTTTT
1 CCCATTTCTC-CTTTTTT
16221025 GTTAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (17 bp):
CCCATTTCTCCTTTTTT
Found at i:16222649 original size:28 final size:28
Alignment explanation
Indices: 16222617--16222671 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
16222607 TTTTTTTTAA
*
16222617 TTCTAATAATTTTAAATTTGAATCAAAG
1 TTCTAATAATTTTAAATTCGAATCAAAG
* *
16222645 TTCTAATCATTTTGAATTCGAATCAAA
1 TTCTAATAATTTTAAATTCGAATCAAA
16222672 ATTGATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (28 bp):
TTCTAATAATTTTAAATTCGAATCAAAG
Found at i:16224239 original size:2 final size:2
Alignment explanation
Indices: 16224232--16224273 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
16224222 AGAAGAGGAA
*
16224232 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16224274 CCTTTCATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16226442 original size:47 final size:47
Alignment explanation
Indices: 16226388--16226482 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
16226378 TAACAACTTT
16226388 CTTCTGAATCCTATTTCAATTAGCGTCAAACTTACTACTCTCTAATG
1 CTTCTGAATCCTATTTCAATTAGCGTCAAACTTACTACTCTCTAATG
*
16226435 CTTCTGAATCCTATTTCAATTAGCGTCAGACTTACTACTCTCTAATG
1 CTTCTGAATCCTATTTCAATTAGCGTCAAACTTACTACTCTCTAATG
16226482 C
1 C
16226483 CTGATCCAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.38
Consensus pattern (47 bp):
CTTCTGAATCCTATTTCAATTAGCGTCAAACTTACTACTCTCTAATG
Found at i:16226967 original size:18 final size:18
Alignment explanation
Indices: 16226944--16226978 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
16226934 ATCTTCAAAC
16226944 ACTGCTTCACAATCTCTT
1 ACTGCTTCACAATCTCTT
16226962 ACTGCTTCACAATCTCT
1 ACTGCTTCACAATCTCT
16226979 AATTGTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.37
Consensus pattern (18 bp):
ACTGCTTCACAATCTCTT
Found at i:16227008 original size:32 final size:32
Alignment explanation
Indices: 16226967--16227032 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
16226957 CTCTTACTGC
16226967 TTCACAATCTCTAATTGTTGGAAAACCATTTG
1 TTCACAATCTCTAATTGTTGGAAAACCATTTG
16226999 TTCACAATCTCTAATTGTTGGAAAACCATTTG
1 TTCACAATCTCTAATTGTTGGAAAACCATTTG
16227031 TT
1 TT
16227033 AAGGATTACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (32 bp):
TTCACAATCTCTAATTGTTGGAAAACCATTTG
Found at i:16227249 original size:22 final size:22
Alignment explanation
Indices: 16227214--16227258 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
16227204 ATATCGGCCC
* *
16227214 ACGAAACTTAATACTACTTGTT
1 ACGAAACCTAATACCACTTGTT
* *
16227236 ACGAAACCTGATACCATTTGTT
1 ACGAAACCTAATACCACTTGTT
16227258 A
1 A
16227259 AAAAAATCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (22 bp):
ACGAAACCTAATACCACTTGTT
Found at i:16227344 original size:42 final size:42
Alignment explanation
Indices: 16227297--16227382 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
16227287 ACATCGGCCT
*
16227297 AACTCAAAATAAACAATGCCAAATCTAATCCATTAACAAATA
1 AACTCAAAATAAACAATGCCAAATCTAATCCACTAACAAATA
* *
16227339 AACTCAAAATAAACTATGTCAAATCTAATCCACTAACAAATA
1 AACTCAAAATAAACAATGCCAAATCTAATCCACTAACAAATA
16227381 AA
1 AA
16227383 TTTTTATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.22
Consensus pattern (42 bp):
AACTCAAAATAAACAATGCCAAATCTAATCCACTAACAAATA
Found at i:16241177 original size:3 final size:3
Alignment explanation
Indices: 16241163--16241201 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
16241153 GTATACCGGT
*
16241163 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16241202 CTATCGTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16247676 original size:17 final size:17
Alignment explanation
Indices: 16247654--16247686 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16247644 TATGAGAACC
16247654 TTATATAAATATATATA
1 TTATATAAATATATATA
*
16247671 TTATATATATATATAT
1 TTATATAAATATATAT
16247687 GCTTGGGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATATAAATATATATA
Found at i:16247680 original size:15 final size:15
Alignment explanation
Indices: 16247657--16247686 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16247647 GAGAACCTTA
16247657 TATAAATATATATAT
1 TATAAATATATATAT
*
16247672 TATATATATATATAT
1 TATAAATATATATAT
16247687 GCTTGGGATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAAATATATATAT
Found at i:16257279 original size:11 final size:11
Alignment explanation
Indices: 16257263--16257287 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16257253 TCAAAAAGAT
16257263 TCAAATTAAAA
1 TCAAATTAAAA
16257274 TCAAATTAAAA
1 TCAAATTAAAA
16257285 TCA
1 TCA
16257288 GATTTGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (11 bp):
TCAAATTAAAA
Found at i:16260639 original size:20 final size:20
Alignment explanation
Indices: 16260611--16260651 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16260601 TGAGAAGAAA
*
16260611 TTTCAATGATCACTCAACAT
1 TTTCAATGATCACACAACAT
*
16260631 TTTCCATGATCACACAACAT
1 TTTCAATGATCACACAACAT
16260651 T
1 T
16260652 CGGGTCCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (20 bp):
TTTCAATGATCACACAACAT
Found at i:16273977 original size:18 final size:18
Alignment explanation
Indices: 16273956--16273992 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16273946 AATTAAATTA
16273956 TATATTT-TTATTAATTTT
1 TATATTTATT-TTAATTTT
16273974 TATATTTATTTTAATTTT
1 TATATTTATTTTAATTTT
16273992 T
1 T
16273993 TATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TATATTTATTTTAATTTT
Found at i:16274402 original size:27 final size:27
Alignment explanation
Indices: 16274364--16274419 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
16274354 TTATGATTAT
16274364 TATTTTTTGAGTTAATATCATTTACTA
1 TATTTTTTGAGTTAATATCATTTACTA
16274391 TATTTTTTGAGTTAATATCATTTACTA
1 TATTTTTTGAGTTAATATCATTTACTA
16274418 TA
1 TA
16274420 GTAGAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (27 bp):
TATTTTTTGAGTTAATATCATTTACTA
Found at i:16274491 original size:12 final size:12
Alignment explanation
Indices: 16274442--16274511 Score: 54
Period size: 13 Copynumber: 5.6 Consensus size: 12
16274432 ATATGTTATT
16274442 TAAATTTTAA-A
1 TAAATTTTAATA
*
16274453 -AAAATTTAATA
1 TAAATTTTAATA
* *
16274464 TAGTATTTAAATTA
1 TA-AATTTTAA-TA
16274478 TAAATTTTAATA
1 TAAATTTTAATA
16274490 TATAATATTTAATA
1 TA-AAT-TTTAATA
16274504 TAATATTT
1 TAA-ATTT
16274512 GAAGAGTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
10 8 0.17
11 1 0.02
12 5 0.11
13 17 0.37
14 15 0.33
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (12 bp):
TAAATTTTAATA
Found at i:16276350 original size:18 final size:18
Alignment explanation
Indices: 16276325--16276370 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
16276315 TCAAAAACTA
16276325 AAAAATTTTCAGAAATTT
1 AAAAATTTTCAGAAATTT
** *
16276343 GGAAATTTTCATAAATTT
1 AAAAATTTTCAGAAATTT
16276361 AAAAATTTTC
1 AAAAATTTTC
16276371 TAGATTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (18 bp):
AAAAATTTTCAGAAATTT
Found at i:16276651 original size:9 final size:9
Alignment explanation
Indices: 16276631--16276752 Score: 55
Period size: 8 Copynumber: 13.9 Consensus size: 9
16276621 AACACCTAAT
16276631 ATAAAA-AA
1 ATAAAATAA
16276639 ATAAAATAA
1 ATAAAATAA
16276648 ATAAAA-AA
1 ATAAAATAA
* *
16276656 ACCAAAACAA
1 A-TAAAATAA
*
16276666 CTAAAA-ACCA
1 ATAAAATA--A
*
16276676 AGAATAGATAA
1 ATAA-A-ATAA
* *
16276687 GTAAGATAA
1 ATAAAATAA
16276696 AT-A-ATAA
1 ATAAAATAA
*
16276703 ATAAACT-A
1 ATAAAATAA
16276711 ATAAAAATAA
1 AT-AAAATAA
*
16276721 AT-AGATAA
1 ATAAAATAA
16276729 ATAAAATAA
1 ATAAAATAA
16276738 A-AAAATAA
1 ATAAAATAA
16276746 A-AAAATA
1 ATAAAATA
16276753 GTTTGGCTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 26
0.69 0.10 0.20
Matches are distributed among these distances:
7 6 0.07
8 36 0.41
9 32 0.36
10 8 0.09
11 4 0.05
12 1 0.01
13 1 0.01
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (9 bp):
ATAAAATAA
Found at i:16276699 original size:4 final size:4
Alignment explanation
Indices: 16276678--16276752 Score: 53
Period size: 4 Copynumber: 18.0 Consensus size: 4
16276668 AAAAACCAAG
* * * *
16276678 AATA GATA AGTA AGATA AAT- AATA AATA AACTA ATAAA AATA AATA GATA
1 AATA AATA AATA A-ATA AATA AATA AATA AA-TA A-ATA AATA AATA AATA
* *
16276728 AATAA AATA AAAA AATA AAAA AATA
1 AAT-A AATA AATA AATA AATA AATA
16276753 GTTTGGCTAA
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
3 3 0.06
4 38 0.70
5 12 0.22
6 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:16276720 original size:25 final size:25
Alignment explanation
Indices: 16276692--16276746 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
16276682 GATAAGTAAG
*
16276692 ATAAATA-ATAAATAAACTAATAAAA
1 ATAAATAGATAAATAAAATAA-AAAA
16276717 ATAAATAGATAAATAAAATAAAAAA
1 ATAAATAGATAAATAAAATAAAAAA
16276742 ATAAA
1 ATAAA
16276747 AAAATAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
ATAAATAGATAAATAAAATAAAAAA
Found at i:16277027 original size:41 final size:41
Alignment explanation
Indices: 16276981--16277224 Score: 264
Period size: 41 Copynumber: 6.0 Consensus size: 41
16276971 AGTAAACAAA
* *
16276981 ACTCATCTAAACAGAAGCTCAACAACTTTGAAAAATAAATT
1 ACTCATCTAAACAGAAGCACCACAACTTTGAAAAATAAATT
* *
16277022 GCTCATTTAAACA-AAGGCACCACAACTTTGAAAAATAAATT
1 ACTCATCTAAACAGAA-GCACCACAACTTTGAAAAATAAATT
* * * *
16277063 ACTTC-TCTAAATAGAGGCATCACAATTTTGAAAAATAAATT
1 AC-TCATCTAAACAGAAGCACCACAACTTTGAAAAATAAATT
* *
16277104 ACTCCTTTAAACA-AAGACACCACAACTTTGAAAAAATAAATGT
1 ACTCATCTAAACAGAAG-CACCACAACTTTG-AAAAATAAAT-T
* * * *
16277147 --TCCTTTAAACAGAGGCACCACAACTTTAAAAAATAAATT
1 ACTCATCTAAACAGAAGCACCACAACTTTGAAAAATAAATT
* *
16277186 ACTCATCTAAACAGAGGTACCACAACTTTGAAAAATAAA
1 ACTCATCTAAACAGAAGCACCACAACTTTGAAAAATAAA
16277225 AGGCTCCTTG
Statistics
Matches: 172, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.01
40 16 0.09
41 139 0.81
42 15 0.09
43 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (41 bp):
ACTCATCTAAACAGAAGCACCACAACTTTGAAAAATAAATT
Found at i:16277125 original size:82 final size:81
Alignment explanation
Indices: 16276986--16277224 Score: 309
Period size: 82 Copynumber: 2.9 Consensus size: 81
16276976 ACAAAACTCA
* * * *
16276986 TCTAAACAGAAGCTCAACAACTTTGAAAAATAAATTGCTCATTTAAACAAAGGCACCACAACTTT
1 TCTAAACAGAGGCACCACAACTTTGAAAAATAAATTACTCATTTAAACAAAGGCACCACAACTTT
*
16277051 GAAAAATAAAT-TACTTC
66 GAAAAATAAATGT--TCC
* * * * *
16277068 TCTAAATAGAGGCATCACAATTTTGAAAAATAAATTACTCCTTTAAACAAAGACACCACAACTTT
1 TCTAAACAGAGGCACCACAACTTTGAAAAATAAATTACTCATTTAAACAAAGGCACCACAACTTT
16277133 GAAAAAATAAATGTTCC
66 G-AAAAATAAATGTTCC
* * * * *
16277150 TTTAAACAGAGGCACCACAACTTTAAAAAATAAATTACTCATCTAAACAGAGGTACCACAACTTT
1 TCTAAACAGAGGCACCACAACTTTGAAAAATAAATTACTCATTTAAACAAAGGCACCACAACTTT
16277215 GAAAAATAAA
66 GAAAAATAAA
16277225 AGGCTCCTTG
Statistics
Matches: 135, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
81 9 0.07
82 115 0.85
83 10 0.07
84 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (81 bp):
TCTAAACAGAGGCACCACAACTTTGAAAAATAAATTACTCATTTAAACAAAGGCACCACAACTTT
GAAAAATAAATGTTCC
Found at i:16277210 original size:123 final size:123
Alignment explanation
Indices: 16277002--16277224 Score: 342
Period size: 123 Copynumber: 1.8 Consensus size: 123
16276992 CAGAAGCTCA
*
16277002 ACAACTTTGAAAAATAAATTGCTCATTTAAACAAAGGCACCACAACTTTGAAAAATAAATTACTT
1 ACAACTTTGAAAAATAAATTGCTCATTTAAACAAAGGCACCACAACTTTAAAAAATAAATTACTT
* * *
16277067 CTCTAAATAGAGGCATCACAATTTTGAAAAATAAATTACTCCTTTAAACAAAGACACC
66 CTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTACTCCTTTAAACAAAGACACC
* * *
16277125 ACAACTTTGAAAAAATAAA-TGTTCCTTTAAACAGAGGCACCACAACTTTAAAAAATAAATTAC-
1 ACAACTTTG-AAAAATAAATTGCTCATTTAAACAAAGGCACCACAACTTTAAAAAATAAATTACT
*
16277188 TCATCTAAACAGAGGTACCACAACTTTGAAAAATAAA
65 TC-TCTAAACAGAGGCACCACAACTTTGAAAAATAAA
16277225 AGGCTCCTTG
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
122 2 0.02
123 79 0.88
124 9 0.10
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.26
Consensus pattern (123 bp):
ACAACTTTGAAAAATAAATTGCTCATTTAAACAAAGGCACCACAACTTTAAAAAATAAATTACTT
CTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTACTCCTTTAAACAAAGACACC
Found at i:16277768 original size:20 final size:21
Alignment explanation
Indices: 16277726--16277770 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
16277716 CACTTTAAAA
*
16277726 ATTCTCATTTGAAATTTGAAG
1 ATTCTCATTTGAAATTCGAAG
*
16277747 ATTCTCATTTG-AGTTCGAAG
1 ATTCTCATTTGAAATTCGAAG
16277767 ATTC
1 ATTC
16277771 ATATTCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (21 bp):
ATTCTCATTTGAAATTCGAAG
Found at i:16277830 original size:79 final size:79
Alignment explanation
Indices: 16277531--16277835 Score: 378
Period size: 79 Copynumber: 3.8 Consensus size: 79
16277521 GTCCAAAGGC
* * * *
16277531 TCACATTTGACAAATTTTAGGGTTTCACACCTCAAAGATTCTTATTTAAAATTCAAAGATTCTCG
1 TCACATTCGATAAATTTT-GGGTTTCACACCTCAAAGATTCTCATTTAAAATTCAAAGATTCTCA
*
16277596 TTTGAGTTTGAAGAC
65 TTTGAGTTTGAAGAT
* * * * * *
16277611 TCACATTTGATAAATTTTGGGTTTCACACGTCAAATATTTTCATTTGAAATTCAAATATTCTCGA
1 TCACATTCGATAAATTTTGGGTTTCACACCTCAAAGATTCTCATTTAAAATTCAAAGATTCTC-A
16277676 -TTGAGTTTGAAGAT
65 TTTGAGTTTGAAGAT
* * * * * **
16277690 TCACATTCGACAAATTTTGGGTTTCACACTTTAAAAATTCTCATTTGAAATTTGAAGATTCTCAT
1 TCACATTCGATAAATTTTGGGTTTCACACCTCAAAGATTCTCATTTAAAATTCAAAGATTCTCAT
*
16277755 TTGAGTTCGAAGAT
66 TTGAGTTTGAAGAT
* * **
16277769 TCATATTCGATAAATTTTGGGTTTCACACCTCTAAGATTCTCATTTAAAATTCAACTATTCTCAT
1 TCACATTCGATAAATTTTGGGTTTCACACCTCAAAGATTCTCATTTAAAATTCAAAGATTCTCAT
16277834 TT
66 TT
16277836 AAAATTCAAA
Statistics
Matches: 193, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
78 1 0.01
79 175 0.91
80 17 0.09
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (79 bp):
TCACATTCGATAAATTTTGGGTTTCACACCTCAAAGATTCTCATTTAAAATTCAAAGATTCTCAT
TTGAGTTTGAAGAT
Found at i:16277831 original size:21 final size:21
Alignment explanation
Indices: 16277805--16277844 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16277795 CACCTCTAAG
16277805 ATTCTCATTTAAAATTCAACT
1 ATTCTCATTTAAAATTCAACT
16277826 ATTCTCATTTAAAATTCAA
1 ATTCTCATTTAAAATTCAA
16277845 AGCTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTCTCATTTAAAATTCAACT
Found at i:16277854 original size:21 final size:22
Alignment explanation
Indices: 16277805--16277867 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 22
16277795 CACCTCTAAG
16277805 ATTCTCATTTAAAATTC-AACT
1 ATTCTCATTTAAAATTCAAACT
16277826 ATTCTCATTTAAAATTCAAAGCT
1 ATTCTCATTTAAAATTCAAA-CT
*
16277849 -TT-TCATTTGAAAACTCAAA
1 ATTCTCATTT-AAAATTCAAA
16277868 AATTCTTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 23 0.61
22 13 0.34
23 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (22 bp):
ATTCTCATTTAAAATTCAAACT
Found at i:16279172 original size:10 final size:10
Alignment explanation
Indices: 16279157--16279206 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
16279147 CATTCTTTCA
16279157 TTTTTTCATT
1 TTTTTTCATT
16279167 TTTTTTCA--
1 TTTTTTCATT
*
16279175 TTTTTTCCTCT
1 TTTTTTCAT-T
16279186 TTTTTTCATT
1 TTTTTTCATT
*
16279196 TTTTTCCATT
1 TTTTTTCATT
16279206 T
1 T
16279207 ATTAGTGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.21
10 19 0.56
11 8 0.24
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:16284561 original size:19 final size:19
Alignment explanation
Indices: 16284537--16284585 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
16284527 CTAATATAAA
*
16284537 AAAAATAAATAAGAAAACC
1 AAAAATAGATAAGAAAACC
16284556 AAAAATAGAT-A-AAAACC
1 AAAAATAGATAAGAAAACC
*
16284573 AAGAATAGATAAG
1 AAAAATAGATAAG
16284586 TAAGATTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 15 0.58
18 2 0.08
19 9 0.35
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.12
Consensus pattern (19 bp):
AAAAATAGATAAGAAAACC
Found at i:16284614 original size:4 final size:4
Alignment explanation
Indices: 16284601--16284665 Score: 52
Period size: 4 Copynumber: 17.2 Consensus size: 4
16284591 TTAACCTTAA
* *
16284601 AAAT -AAT AAAT AAAT AAAT AAACT -AAT -AAT -AAC AAAT AGAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT
16284646 AAAAT AAA- AAAT AAA- AAAT A
1 -AAAT AAAT AAAT AAAT AAAT A
16284666 GTTGGGCTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 15 0.29
4 31 0.61
5 5 0.10
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:16284618 original size:8 final size:8
Alignment explanation
Indices: 16284601--16284665 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 8
16284591 TTAACCTTAA
16284601 AAAT-AAT
1 AAATAAAT
16284608 AAATAAAT
1 AAATAAAT
16284616 AAATAAACT
1 AAATAAA-T
16284625 -AAT-AAT
1 AAATAAAT
*
16284631 -AACAAAT
1 AAATAAAT
*
16284638 AGATAAAT
1 AAATAAAT
16284646 AAAATAAA-
1 -AAATAAAT
16284654 AAATAAA-
1 AAATAAAT
16284661 AAATA
1 AAATA
16284666 GTTGGGCTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 3 0.06
7 21 0.43
8 18 0.37
9 7 0.14
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.22
Consensus pattern (8 bp):
AAATAAAT
Found at i:16286572 original size:12 final size:12
Alignment explanation
Indices: 16286555--16286586 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
16286545 AATAGATGGT
16286555 ATAAATATAATA
1 ATAAATATAATA
16286567 ATAAATATAATA
1 ATAAATATAATA
16286579 ATAAATAT
1 ATAAATAT
16286587 TAAAAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAAATATAATA
Found at i:16286812 original size:18 final size:18
Alignment explanation
Indices: 16286771--16286826 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
16286761 ATATATGAGT
*
16286771 TAATTTATTTAATTAAATTT
1 TAATTTA-TTAATT-AATTA
16286791 TAATTTATTAATTAATTA
1 TAATTTATTAATTAATTA
* * *
16286809 TAATATAATAATTCATTA
1 TAATTTATTAATTAATTA
16286827 ATTGAATTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 19 0.59
19 6 0.19
20 7 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTTATTAATTAATTA
Found at i:16295311 original size:10 final size:10
Alignment explanation
Indices: 16295296--16295323 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
16295286 CCTAGGGGTG
16295296 AACAAAATCA
1 AACAAAATCA
16295306 AACAAAATCA
1 AACAAAATCA
16295316 AACAAAAT
1 AACAAAAT
16295324 ATCATGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.18, G:0.00, T:0.11
Consensus pattern (10 bp):
AACAAAATCA
Found at i:16299811 original size:2 final size:2
Alignment explanation
Indices: 16299804--16299841 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
16299794 GCTGCAGCAA
*
16299804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16299842 TCTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:16299956 original size:8 final size:8
Alignment explanation
Indices: 16299925--16299964 Score: 53
Period size: 8 Copynumber: 4.6 Consensus size: 8
16299915 TTATTAAGTA
16299925 AATTAACAT
1 AATTAA-AT
16299934 GAATTAAATT
1 -AATTAAA-T
16299944 AATTAAAT
1 AATTAAAT
16299952 AATTAAAT
1 AATTAAAT
16299960 AATTA
1 AATTA
16299965 GTGATGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 14 0.48
9 8 0.28
10 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (8 bp):
AATTAAAT
Found at i:16300007 original size:2 final size:2
Alignment explanation
Indices: 16300000--16300024 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16299990 ATATTGAGTC
16300000 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
16300025 TGCATAACTA
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:16301062 original size:66 final size:63
Alignment explanation
Indices: 16300925--16301062 Score: 138
Period size: 70 Copynumber: 2.1 Consensus size: 63
16300915 TAGGGAAAAG
*
16300925 ATTTTG-GTTTTTGAAATCAAACAAAAATTTTTTGATTCCAACAATAGGAAAAGGATTTGGGT
1 ATTTTGAGTTTTTGAAATCAAACAAAAATTTCTTGATTCCAACAATAGGAAAAGGATTTGGGT
* * **
16300987 AAGTATTTGAGTTTTTGAAATCAAACATACAAAAATTTCTTGGTTTCAACGGTAAGGAAAA-GAT
1 -A-T-TTTGAGTTTTTGAAATC--A-A-ACAAAAATTTCTTGATTCCAACAAT-AGGAAAAGGAT
16301051 TTGGGT
58 TTGGGT
16301057 -TTTTGA
1 ATTTTGA
16301063 AATCAAACAA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
63 1 0.02
64 1 0.02
65 4 0.06
66 17 0.27
67 1 0.02
68 1 0.02
69 1 0.02
70 29 0.47
71 7 0.11
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (63 bp):
ATTTTGAGTTTTTGAAATCAAACAAAAATTTCTTGATTCCAACAATAGGAAAAGGATTTGGGT
Found at i:16308760 original size:33 final size:32
Alignment explanation
Indices: 16308698--16308761 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
16308688 TAAATCAATT
**
16308698 TCTATAATCAATTAAATCAATATTTAATATTC
1 TCTATAATCAATTAAATCAATATAGAATATTC
*
16308730 TCTA-AATCAATATAAAGTCAATCTAGAATATT
1 TCTATAATCAAT-TAAA-TCAATATAGAATATT
16308762 ACTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.26
32 8 0.30
33 12 0.44
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (32 bp):
TCTATAATCAATTAAATCAATATAGAATATTC
Found at i:16313293 original size:22 final size:21
Alignment explanation
Indices: 16313237--16313291 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
16313227 TTAATTCCTA
*
16313237 TAATCAAT-TAAATCAATATT
1 TAATCAATCTAAATCAATATC
*
16313257 TAAT-ATTCTCTAAATCAATATC
1 TAATCA--ATCTAAATCAATATC
16313279 TAATCAATCTAAA
1 TAATCAATCTAAA
16313292 ATATTATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.04
20 4 0.14
21 7 0.25
22 15 0.54
23 1 0.04
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATCAATCTAAATCAATATC
Found at i:16315028 original size:71 final size:71
Alignment explanation
Indices: 16314902--16315037 Score: 184
Period size: 71 Copynumber: 1.9 Consensus size: 71
16314892 AATTGTCAAC
* *
16314902 ATTTATTGTTCTTTGAAAAATGGAAATGTATGGCGCGGAACATAGAGACGATGATGTGAAATATT
1 ATTTATTGTTCTTTGAAAAAAGAAAATGTATGGCGCGGAACATAGAGACGATGATGTGAAATATT
16314967 GAACGT
66 GAACGT
* * * * * *
16314973 ATTTATTGTTCTTTGAAAAAAGAAAATGT-TTGCAGGGGAAGATAGGGATGGTGATGTGAAATAT
1 ATTTATTGTTCTTTGAAAAAAGAAAATGTATGGC-GCGGAACATAGAGACGATGATGTGAAATAT
16315037 T
65 T
16315038 CGCACATCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 3 0.05
71 53 0.95
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (71 bp):
ATTTATTGTTCTTTGAAAAAAGAAAATGTATGGCGCGGAACATAGAGACGATGATGTGAAATATT
GAACGT
Found at i:16330487 original size:24 final size:25
Alignment explanation
Indices: 16330453--16330508 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
16330443 CGTATATAAA
* * *
16330453 AATTATATTAAAAATTTTAAAT-AT
1 AATTATTTTAAAAAATTAAAATCAT
*
16330477 AATTATTTTAAAAAATTAAAATCCT
1 AATTATTTTAAAAAATTAAAATCAT
16330502 AATTATT
1 AATTATT
16330509 ATTTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTATTTTAAAAAATTAAAATCAT
Found at i:16330788 original size:20 final size:20
Alignment explanation
Indices: 16330759--16330806 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
16330749 ATATATTTTA
16330759 TAAT-TAATTTTAATCTTAT
1 TAATATAATTTTAATCTTAT
* *
16330778 TATTATAATTTTAATTTTAT
1 TAATATAATTTTAATCTTAT
16330798 TAATATAAT
1 TAATATAAT
16330807 AAGTAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TAATATAATTTTAATCTTAT
Found at i:16331431 original size:16 final size:19
Alignment explanation
Indices: 16331395--16331429 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
16331385 TGAAAATAGC
16331395 AAATTAAATATAATTTTTT
1 AAATTAAATATAATTTTTT
16331414 AAATT-AATAT-ATTTTT
1 AAATTAAATATAATTTTT
16331430 AATTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATTAAATATAATTTTTT
Found at i:16332164 original size:2 final size:2
Alignment explanation
Indices: 16332157--16332185 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16332147 TCCCAAATTC
16332157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16332186 TAGGCATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16332833 original size:9 final size:9
Alignment explanation
Indices: 16332808--16332847 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
16332798 ATTAATTAAT
16332808 TAAAAAAAA
1 TAAAAAAAA
*
16332817 GAAGAAAAAA
1 TAA-AAAAAA
16332827 TAAAAAAAA
1 TAAAAAAAA
16332836 TAAAAAAAA
1 TAAAAAAAA
16332845 TAA
1 TAA
16332848 TTTCAACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:16332833 original size:18 final size:18
Alignment explanation
Indices: 16332808--16332847 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
16332798 ATTAATTAAT
*
16332808 TAAAAAAAAGAAGAAAAAA
1 TAAAAAAAATAA-AAAAAA
16332827 TAAAAAAAATAAAAAAAA
1 TAAAAAAAATAAAAAAAA
16332845 TAA
1 TAA
16332848 TTTCAACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (18 bp):
TAAAAAAAATAAAAAAAA
Found at i:16333652 original size:20 final size:19
Alignment explanation
Indices: 16333620--16333664 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
16333610 CTATTTTTCT
* *
16333620 ATTTTTTATTTTGATTTTG
1 ATTTTTTAATTTGATGTTG
16333639 ATTTTATTAATTTGATGTTG
1 ATTTT-TTAATTTGATGTTG
16333659 ATTTTT
1 ATTTTT
16333665 ATTTTTGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (19 bp):
ATTTTTTAATTTGATGTTG
Found at i:16333681 original size:11 final size:12
Alignment explanation
Indices: 16333661--16333690 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16333651 TGATGTTGAT
16333661 TTTTATTTTTGG
1 TTTTATTTTTGG
*
16333673 TTTTATTTTTGT
1 TTTTATTTTTGG
16333685 TTTTAT
1 TTTTAT
16333691 GATGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTGG
Found at i:16333704 original size:3 final size:3
Alignment explanation
Indices: 16333698--16333726 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16333688 TATGATGATT
16333698 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16333727 CATTCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16333824 original size:3 final size:3
Alignment explanation
Indices: 16333816--16333853 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16333806 TAAATCTAAA
16333816 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16333854 CTATTTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16334416 original size:40 final size:40
Alignment explanation
Indices: 16334372--16334453 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
16334362 ATAATTTTAT
* * * *
16334372 TTAGGATCTCGTCAAAAAGTTAAGATGATCTTAAAATTTG
1 TTAGGATCTCATCAAAAAGTTAAGATAATCCTAAAATATG
* * *
16334412 TTAGGATTTCATCAAAGAGTTAGGATAATCCTAAAATATG
1 TTAGGATCTCATCAAAAAGTTAAGATAATCCTAAAATATG
16334452 TT
1 TT
16334454 TAATAAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (40 bp):
TTAGGATCTCATCAAAAAGTTAAGATAATCCTAAAATATG
Found at i:16346275 original size:80 final size:79
Alignment explanation
Indices: 16346144--16346377 Score: 234
Period size: 80 Copynumber: 2.9 Consensus size: 79
16346134 GCCTCTCAAA
* * *
16346144 CTTTTAAATTTAAAGTTTTGTTGCCTCTGGTCAAATGAGCTTTTTGAATTTAAAGTTTCATTGCC
1 CTTTTAAATTTAAAGTTTTGTTGCCTCTGGTCAGAGGAGCTTTTAG-ATTTAAAGTTTCATTGCC
* *
16346209 TCTGGTTGGAGAAGC
65 TCTGGTTAGAAAAGC
* * * * * * **
16346224 TTTTTGAATTTAAAATTTTGTTGCCTCTAGTTAGAGGAGACTTTTAGATTTAAAGTTTAATTATC
1 CTTTTAAATTTAAAGTTTTGTTGCCTCTGGTCAGAGGAG-CTTTTAGATTTAAAGTTTCATTGCC
* *
16346289 TTTGGTCAGAAAAGC
65 TCTGGTTAGAAAAGC
** * * * * *
16346304 CTTTTAAATTTAAAGTTTCATTGCCTTTGGTCAGAGAAGTCTTTTAACATTTAAACTTTCATAGC
1 CTTTTAAATTTAAAGTTTTGTTGCCTCTGGTCAGAGGAG-CTTTT-AGATTTAAAGTTTCATTGC
16346369 CTCTGGTTA
64 CTCTGGTTA
16346378 AATGAGCTTT
Statistics
Matches: 119, Mismatches: 33, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
80 93 0.78
81 26 0.22
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (79 bp):
CTTTTAAATTTAAAGTTTTGTTGCCTCTGGTCAGAGGAGCTTTTAGATTTAAAGTTTCATTGCCT
CTGGTTAGAAAAGC
Found at i:16346349 original size:40 final size:39
Alignment explanation
Indices: 16346144--16346375 Score: 196
Period size: 40 Copynumber: 5.8 Consensus size: 39
16346134 GCCTCTCAAA
** *
16346144 CTTTTAAATTTAAAGTTTTGTTGCCTCTGGTCAAATG-AG
1 CTTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGA-GAAG
* **
16346183 CTTTTTGAATTTAAAGTTTCATTGCCTCTGGTTGGAGAAG
1 C-TTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGAGAAG
* * ** * * *
16346223 CTTTTTGAATTTAAAATTTTGTTGCCTCTAGTTAGAGGAG
1 C-TTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGAGAAG
* * ** * *
16346263 ACTTTTAGATTTAAAGTTTAATTATCTTTGGTCAGAAAAG
1 -CTTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGAGAAG
*
16346303 CCTTTTAAATTTAAAGTTTCATTGCCTTTGGTCAGAGAAG
1 -CTTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGAGAAG
* *
16346343 TCTTTTAACATTTAAACTTTCATAGCCTCTGGT
1 -CTTTTAA-ATTTAAAGTTTCATTGCCTCTGGT
16346376 TAAATGAGCT
Statistics
Matches: 155, Mismatches: 34, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
39 2 0.01
40 131 0.85
41 22 0.14
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (39 bp):
CTTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGAGAAG
Found at i:16346708 original size:120 final size:120
Alignment explanation
Indices: 16346544--16346770 Score: 303
Period size: 120 Copynumber: 1.9 Consensus size: 120
16346534 TCATATTTAA
* * * *
16346544 AATTTAAAATTTCATTGCCTTTTATCATAGAAGCCTTTTGAATTTAAAGTTTCATTATCTCTAGT
1 AATTTAAAATTTCATTGCCTCTGATCAGAGAAGCCTTTTGAATTTAAAGATTCATTATCTCTAGT
* * * * **
16346609 CATATGAGCTTTTTTAATTTAAAGTTTTGTTGCCTTTGGTTAAAGGTACCTTTTT
66 CAGAGGAGCATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAAAGGTACCTTTTT
* * * *
16346664 AATTTAAAGTTTCATTGCCTCTGGTCAGATG-AGCCTTTTTAATTTAAAGATTCATTGTCTCTAG
1 AATTTAAAATTTCATTGCCTCTGATCAGA-GAAGCCTTTTGAATTTAAAGATTCATTATCTCTAG
*
16346728 TTAGAGGAGCATTTTAAATTTAAAGTTTCATTGCCTTTGGTTA
65 TCAGAGGAGCATTTTAAATTTAAAGTTTCATTGCCTTTGGTTA
16346771 GAGCATCCAT
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
120 90 0.99
121 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.46
Consensus pattern (120 bp):
AATTTAAAATTTCATTGCCTCTGATCAGAGAAGCCTTTTGAATTTAAAGATTCATTATCTCTAGT
CAGAGGAGCATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAAAGGTACCTTTTT
Found at i:16346748 original size:80 final size:78
Alignment explanation
Indices: 16346578--16346843 Score: 258
Period size: 80 Copynumber: 3.4 Consensus size: 78
16346568 TCATAGAAGC
* ** * * * **
16346578 CTTTTGAATTTAAAGTTTCATTATCTCTAGTCATATGAGCTTTTTTAATTTAAAGTTTTGTTGCC
1 CTTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGATGAGCCTTTTTAATTTAAAGTTTCATTG-C
* * *
16346643 TTTGGTTAAAGGTAC
65 TCTGGTTAGAGG-AG
* *
16346658 CTTTTTAATTTAAAGTTTCATTGCCTCTGGTCAGATGAGCCTTTTTAATTTAAAGATTCATTGTC
1 CTTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGATGAGCCTTTTTAATTTAAAGTTTCATTG-C
*
16346723 TCTAGTTAGAGGAG
65 TCTGGTTAGAGGAG
* * *
16346737 CATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGA-GCATCC------ATTTAAAGTTTCATTG
1 C-TTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGATG-AGCCTTTTTAATTTAAAGTTTCATTG
16346795 CTTCTGGTTAGAGGAG
64 C-TCTGGTTAGAGGAG
* *
16346811 CTCTTAAATTTAAAGTTTCATTGCCTTTGGTCA
1 CTTTTAAATTTAAAGTTTCATTGCCTCTGGTCA
16346844 AAAGAGTCAT
Statistics
Matches: 161, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
73 31 0.19
74 29 0.18
79 3 0.02
80 98 0.61
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (78 bp):
CTTTTAAATTTAAAGTTTCATTGCCTCTGGTCAGATGAGCCTTTTTAATTTAAAGTTTCATTGCT
CTGGTTAGAGGAG
Found at i:16346771 original size:40 final size:40
Alignment explanation
Indices: 16346538--16346841 Score: 212
Period size: 40 Copynumber: 7.8 Consensus size: 40
16346528 GACCTCTCAT
* * ** * * *
16346538 ATTTAAAATTTAAAATTTCATTGCCTTTTATCATAGAAGC
1 ATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAGGAGC
* * ** * * * * *
16346578 CTTTTGAATTTAAAGTTTCATTATCTCTAGTCATATGAGC
1 ATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAGGAGC
* * ** *
16346618 TTTTTTAATTTAAAGTTTTGTTGCCTTTGGTTAAAGGTA-C
1 ATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAGG-AGC
* * * * *
16346658 CTTTTTAATTTAAAGTTTCATTGCCTCTGGTCAGATGAGC
1 ATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAGGAGC
* * * * * *
16346698 CTTTTTAATTTAAAGATTCATTGTCTCTAGTTAGAGGAGC
1 ATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAGGAGC
16346738 ATTTTAAATTTAAAGTTTCATTGCCTTTGGTT--A-GAGC
1 ATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAGGAGC
**
16346775 A---TCCATTTAAAGTTTCATTG-CTTCTGGTTAGAGGAGC
1 ATTTTAAATTTAAAGTTTCATTGCCTT-TGGTTAGAGGAGC
*
16346812 -TCTTAAATTTAAAGTTTCATTGCCTTTGGT
1 ATTTTAAATTTAAAGTTTCATTGCCTTTGGT
16346842 CAAAAGAGTC
Statistics
Matches: 210, Mismatches: 44, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
33 3 0.01
34 22 0.10
36 1 0.00
37 9 0.04
38 1 0.00
39 22 0.10
40 151 0.72
41 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (40 bp):
ATTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAGGAGC
Found at i:16346784 original size:34 final size:34
Alignment explanation
Indices: 16346745--16346875 Score: 124
Period size: 34 Copynumber: 3.7 Consensus size: 34
16346735 AGCATTTTAA
16346745 ATTTAAAGTTTCATTGCCTTTGGTTAGAGCA-TCC
1 ATTTAAAGTTTCATTGCCTTTGGTTAGAG-AGTCC
*
16346779 ATTTAAAGTTTCATTG-CTTCTGGTTAGAGGAGCTCTTAA
1 ATTTAAAGTTTCATTGCCTT-TGGTTAGA-GAG-TC---C
* *
16346818 ATTTAAAGTTTCATTGCCTTTGGTCAAAAGAGT-C
1 ATTTAAAGTTTCATTGCCTTTGGT-TAGAGAGTCC
* *
16346852 ATTTAAAGTTTCATAGCCATTGGT
1 ATTTAAAGTTTCATTGCCTTTGGT
16346876 CAAAGAAGCT
Statistics
Matches: 82, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
33 3 0.04
34 47 0.57
35 1 0.01
36 2 0.02
38 1 0.01
39 23 0.28
40 5 0.06
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (34 bp):
ATTTAAAGTTTCATTGCCTTTGGTTAGAGAGTCC
Found at i:16346839 original size:73 final size:74
Alignment explanation
Indices: 16346705--16346841 Score: 224
Period size: 73 Copynumber: 1.9 Consensus size: 74
16346695 AGCCTTTTTA
*
16346705 ATTTAAAGATTCATTGTCTCTAGTTAGAGGAGCATTTTAAATTTAAAGTTTCATTGCCTTTGGTT
1 ATTTAAAGATTCATTGTCTCTAGTTAGAGGAGCATCTTAAATTTAAAGTTTCATTGCCTTTGGTT
16346770 AGAGCATCC
66 AGAGCATCC
* *
16346779 ATTTAAAGTTTCATTG-CTTCTGGTTAGAGGAGC-TCTTAAATTTAAAGTTTCATTGCCTTTGGT
1 ATTTAAAGATTCATTGTC-TCTAGTTAGAGGAGCATCTTAAATTTAAAGTTTCATTGCCTTTGGT
16346842 CAAAAGAGTC
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
73 30 0.51
74 29 0.49
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (74 bp):
ATTTAAAGATTCATTGTCTCTAGTTAGAGGAGCATCTTAAATTTAAAGTTTCATTGCCTTTGGTT
AGAGCATCC
Found at i:16346855 original size:73 final size:74
Alignment explanation
Indices: 16346705--16346865 Score: 222
Period size: 73 Copynumber: 2.2 Consensus size: 74
16346695 AGCCTTTTTA
* * *
16346705 ATTTAAAGATTCATTGTCTCTAGTTAGAGGAGCATTTTAAATTTAAAGTTTCATTGCCTTTGGTT
1 ATTTAAAGTTTCATTGTCTCTAGTTAGAGGAGCATCTTAAATTTAAAGTTTCATTGCCTTTGGTA
*
16346770 AGAGCATCC
66 AAAGCATCC
*
16346779 ATTTAAAGTTTCATTG-CTTCTGGTTAGAGGAGC-TCTTAAATTTAAAGTTTCATTGCCTTTGGT
1 ATTTAAAGTTTCATTGTC-TCTAGTTAGAGGAGCATCTTAAATTTAAAGTTTCATTGCCTTTGGT
16346842 CAAAAG-AGT-C
65 -AAAAGCA-TCC
16346852 ATTTAAAGTTTCAT
1 ATTTAAAGTTTCAT
16346866 AGCCATTGGT
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
73 46 0.58
74 33 0.42
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (74 bp):
ATTTAAAGTTTCATTGTCTCTAGTTAGAGGAGCATCTTAAATTTAAAGTTTCATTGCCTTTGGTA
AAAGCATCC
Found at i:16347134 original size:40 final size:40
Alignment explanation
Indices: 16347019--16347135 Score: 103
Period size: 39 Copynumber: 3.0 Consensus size: 40
16347009 CAGAAGAGCC
* * * * * *
16347019 ATTTAAAGTTTTATTACCTCTAGTCAGAGGAACTTTTTGG
1 ATTTAAAGTTTTATAACCTCTGGTCAAAAGAACCTTTTGA
* * * *
16347059 ATTT-AAGTTTCATTAA-TTTTGGTCAAAAGAGCCTTTTGA
1 ATTTAAAGTTTTA-TAACCTCTGGTCAAAAGAACCTTTTGA
* *
16347098 ATTTAAAGTTTTATAACCTCTGGTTAAATGAACCTTTT
1 ATTTAAAGTTTTATAACCTCTGGTCAAAAGAACCTTTT
16347136 TAAAATTTCA
Statistics
Matches: 58, Mismatches: 16, Indels: 6
0.73 0.20 0.08
Matches are distributed among these distances:
39 29 0.50
40 29 0.50
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (40 bp):
ATTTAAAGTTTTATAACCTCTGGTCAAAAGAACCTTTTGA
Found at i:16347362 original size:3 final size:3
Alignment explanation
Indices: 16347354--16347431 Score: 111
Period size: 3 Copynumber: 25.7 Consensus size: 3
16347344 TTAAATTTTA
* * * *
16347354 TAT TAT TAT TAT TAT CAT CAT CAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16347402 TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
16347432 ATTAATTAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:16348443 original size:3 final size:3
Alignment explanation
Indices: 16348370--16348432 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
16348360 ATGATGATTT
*
16348370 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16348417 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
16348433 AACGTTATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:16357514 original size:3 final size:3
Alignment explanation
Indices: 16357499--16357529 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
16357489 TAAGGAAAAT
*
16357499 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
16357530 TTTCATCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:16360857 original size:11 final size:11
Alignment explanation
Indices: 16360830--16360866 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
16360820 AAAATGATGG
16360830 TTTT-AAAATT
1 TTTTGAAAATT
16360840 TTTTG-AAATT
1 TTTTGAAAATT
16360850 TTTATGAAAATT
1 TTT-TGAAAATT
16360862 TTTTG
1 TTTTG
16360867 GGTTATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 12 0.50
11 4 0.17
12 8 0.33
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (11 bp):
TTTTGAAAATT
Found at i:16361305 original size:3 final size:3
Alignment explanation
Indices: 16361291--16361330 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
16361281 TTTTTTATGA
*
16361291 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16361331 GTTGTTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16361305 original size:9 final size:9
Alignment explanation
Indices: 16361291--16361370 Score: 70
Period size: 9 Copynumber: 8.8 Consensus size: 9
16361281 TTTTTTATGA
16361291 TATTATTGT
1 TATTATTGT
*
16361300 TATTATTAT
1 TATTATTGT
*
16361309 TATTATTAT
1 TATTATTGT
*
16361318 TATTATTAT
1 TATTATTGT
*
16361327 TATTGTTGT
1 TATTATTGT
* *
16361336 TGTTGTTGT
1 TATTATTGT
* *
16361345 TGTTGTTGT
1 TATTATTGT
*
16361354 TATTTTATGT
1 TATTAT-TGT
16361364 TATTATT
1 TATTATT
16361371 AATATTTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
9 55 0.87
10 8 0.13
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (9 bp):
TATTATTGT
Found at i:16361335 original size:3 final size:3
Alignment explanation
Indices: 16361329--16361354 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16361319 ATTATTATTA
16361329 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
16361355 ATTTTATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:16370874 original size:41 final size:41
Alignment explanation
Indices: 16370823--16370902 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
16370813 ATGAAAGAAT
* *
16370823 AAATATGGCTTTGAGGCATCAAAAACACTATCTTAAAGGAA
1 AAATATGGCTTTGAAGCATCAAAAACACTATCTAAAAGGAA
*
16370864 AAATATGGCTTTGAAGTATCAAAAACACTATCTAAAAGG
1 AAATATGGCTTTGAAGCATCAAAAACACTATCTAAAAGG
16370903 TAATTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (41 bp):
AAATATGGCTTTGAAGCATCAAAAACACTATCTAAAAGGAA
Found at i:16373352 original size:24 final size:24
Alignment explanation
Indices: 16373322--16373383 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
16373312 AATATCATTC
*
16373322 AAATATAATATTA-ATCATGCAAT
1 AAATATAATATCATATCATGCAAT
16373345 AACATATAATATCATATCATGCAAT
1 AA-ATATAATATCATATCATGCAAT
*
16373370 AAATATAAAATCAT
1 AAATATAATATCAT
16373384 GCAATTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 2 0.06
24 21 0.60
25 12 0.34
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.32
Consensus pattern (24 bp):
AAATATAATATCATATCATGCAAT
Found at i:16373585 original size:55 final size:54
Alignment explanation
Indices: 16373462--16373830 Score: 329
Period size: 55 Copynumber: 6.7 Consensus size: 54
16373452 TAAATAAATT
* * * * * *
16373462 AATAATCATGCAATTAAATATAT-ATCATACAATTAACAATGTA-AATCATGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAACATGCA
* * * * *
16373514 AATAAACATGCCATTAAATATACAATCATGCAAATAAAAATATAGAAACAATGTA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAAC-ATGCA
* * * *
16373569 AATAGATATGTAATTAAATATATAATCATGCAAATAGTAATATATAAACCATGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAA-CATGCA
* *
16373624 AACAAACATACAATTAAATATATAATCATGCAAATAATAATATATAAATCATGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAA-CATGCA
* *
16373679 AATAAAGATGCAATTAAATATATAATCATGCAAATAATAATACATAAATCATGCA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAA-CATGCA
* * ** *
16373734 ATTATGTAA-AT--AA-T-AATATATAAACCATGCAAAATATGCAATCAAATATATAATTAGGCA
1 A--AT-AAACATGCAATTAAATATAT-AATCATGC--AA-AT--AAT--AATATATAAACATGCA
*
16373794 AATAAACATGCAATTAAATATACAATCATGCAAATAA
1 AATAAACATGCAATTAAATATATAATCATGCAAATAA
16373831 ATATATTAAT
Statistics
Matches: 259, Mismatches: 38, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
52 20 0.08
53 23 0.09
54 11 0.04
55 150 0.58
56 5 0.02
57 8 0.03
58 8 0.03
59 5 0.02
60 7 0.03
61 16 0.06
62 6 0.02
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.28
Consensus pattern (54 bp):
AATAAACATGCAATTAAATATATAATCATGCAAATAATAATATATAAACATGCA
Found at i:16373677 original size:23 final size:23
Alignment explanation
Indices: 16373640--16373734 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 23
16373630 CATACAATTA
16373640 AATATAT-AATCATGCAAATAAT
1 AATATATAAATCATGCAAATAAT
16373662 AATATATAAATCATGCAAATAAAGAT
1 AATATATAAATCATGCAAAT--A-AT
*
16373688 GCAATTAAATATATAATCATGCAAATAAT
1 --AA-T-AT-ATA-AATCATGCAAATAAT
*
16373717 AATACATAAATCATGCAA
1 AATATATAAATCATGCAA
16373735 TTATGTAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
22 7 0.11
23 22 0.36
24 3 0.05
25 2 0.03
26 3 0.05
27 2 0.03
28 2 0.03
29 3 0.05
30 2 0.03
31 3 0.05
32 12 0.20
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (23 bp):
AATATATAAATCATGCAAATAAT
Found at i:16373690 original size:35 final size:32
Alignment explanation
Indices: 16373651--16373715 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 32
16373641 ATATATAATC
16373651 ATGCAAATAATAATATATAAATCATGCAAATAAAG
1 ATGC-AATAA-AATATAT-AATCATGCAAATAAAG
*
16373686 ATGCAATTAAATATATAATCATGCAAATAA
1 ATGCAATAAAATATATAATCATGCAAATAA
16373716 TAATACATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 7 0.24
34 4 0.14
35 4 0.14
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (32 bp):
ATGCAATAAAATATATAATCATGCAAATAAAG
Found at i:16373709 original size:20 final size:20
Alignment explanation
Indices: 16373634--16373737 Score: 62
Period size: 22 Copynumber: 5.3 Consensus size: 20
16373624 AACAAACATA
16373634 CAATTAAATATATAATCATG
1 CAATTAAATATATAATCATG
*
16373654 CAAATAATAATATATAAATCATG
1 C-AATTA-AATATAT-AATCATG
*
16373677 C-----AA-ATA-AA-GATG
1 CAATTAAATATATAATCATG
16373689 CAATTAAATATATAATCATG
1 CAATTAAATATATAATCATG
* *
16373709 CAAATAATAATACATAAATCATG
1 C-AATTA-AATATAT-AATCATG
16373732 CAATTA
1 CAATTA
16373738 TGTAAATAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 26
0.67 0.06 0.27
Matches are distributed among these distances:
12 4 0.06
13 2 0.03
15 3 0.05
16 2 0.03
17 2 0.03
18 3 0.05
19 2 0.03
20 5 0.08
21 8 0.12
22 17 0.27
23 16 0.25
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.30
Consensus pattern (20 bp):
CAATTAAATATATAATCATG
Found at i:16373711 original size:32 final size:31
Alignment explanation
Indices: 16373662--16373831 Score: 112
Period size: 32 Copynumber: 5.7 Consensus size: 31
16373652 TGCAAATAAT
16373662 AATATATAAATCATGCAAATAAAGATGCAATTA
1 AATATAT-AATCATGCAAATAAA-ATGCAATTA
*
16373695 AATATATAATCATGCAAATAATAATAC-A-TA
1 AATATATAATCATGCAAATAA-AATGCAATTA
** * *
16373725 AATCATGCAATTATGTAAAT--AAT--AA-T-
1 AAT-ATATAATCATGCAAATAAAATGCAATTA
* * *
16373751 -ATATA-AACCATGC-AA-AATATGCAATCA
1 AATATATAATCATGCAAATAAAATGCAATTA
* *
16373778 AATATATAATTAGGCAAATAAACATGCAATTA
1 AATATATAATCATGCAAATAAA-ATGCAATTA
*
16373810 AATATACAATCATGCAAATAAA
1 AATATATAATCATGCAAATAAA
16373832 TATATTAATA
Statistics
Matches: 104, Mismatches: 19, Indels: 29
0.68 0.12 0.19
Matches are distributed among these distances:
22 2 0.02
23 7 0.07
24 2 0.02
25 4 0.04
27 2 0.02
28 8 0.08
29 5 0.05
30 7 0.07
31 15 0.14
32 44 0.42
33 8 0.08
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (31 bp):
AATATATAATCATGCAAATAAAATGCAATTA
Found at i:16373844 original size:24 final size:24
Alignment explanation
Indices: 16373817--16373924 Score: 95
Period size: 24 Copynumber: 4.8 Consensus size: 24
16373807 TTAAATATAC
16373817 AATCATGCAAATAAATATATTAAT
1 AATCATGCAAATAAATATATTAAT
* * *
16373841 AATCAAGCAATTAAATACATTAAT
1 AATCATGCAAATAAATATATTAAT
*
16373865 AACCATGC----AAATATATTAAT
1 AATCATGCAAATAAATATATTAAT
**
16373885 AAATCACACAAATAAATATA-T--T
1 -AATCATGCAAATAAATATATTAAT
*
16373907 AATCATGCAAACAAATAT
1 AATCATGCAAATAAATAT
16373925 GTTAGGCAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
20 11 0.16
21 20 0.30
22 1 0.01
24 28 0.42
25 7 0.10
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.29
Consensus pattern (24 bp):
AATCATGCAAATAAATATATTAAT
Found at i:16373920 original size:25 final size:25
Alignment explanation
Indices: 16373873--16373923 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
16373863 ATAACCATGC
*
16373873 AAATATATTAATAAATCACACAAAT
1 AAATATATTAATAAATCAAACAAAT
*
16373898 AAATATATTAAT-CATGCAAACAAAT
1 AAATATATTAATAAAT-CAAACAAAT
16373923 A
1 A
16373924 TGTTAGGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATATATTAATAAATCAAACAAAT
Found at i:16373967 original size:20 final size:18
Alignment explanation
Indices: 16373934--16373971 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
16373924 TGTTAGGCAA
16373934 ATAAATTATCATGCAAAT
1 ATAAATTATCATGCAAAT
16373952 ATAATATTAGTCATGCAAAT
1 ATAA-ATTA-TCATGCAAAT
16373972 TCATGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (18 bp):
ATAAATTATCATGCAAAT
Found at i:16374606 original size:18 final size:18
Alignment explanation
Indices: 16374583--16374617 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
16374573 CTTTTGACTA
16374583 AAAAAATTAAAATTAAAC
1 AAAAAATTAAAATTAAAC
16374601 AAAAAATTAAAATTAAA
1 AAAAAATTAAAATTAAA
16374618 AAATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAATTAAAATTAAAC
Found at i:16374620 original size:14 final size:14
Alignment explanation
Indices: 16374601--16374627 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16374591 AAAATTAAAC
16374601 AAAAAATTAAAATT
1 AAAAAATTAAAATT
16374615 AAAAAATTAAAAT
1 AAAAAATTAAAAT
16374628 GCAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAAATTAAAATT
Found at i:16378210 original size:2 final size:2
Alignment explanation
Indices: 16378167--16378191 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16378157 ATATATATAT
16378167 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
16378192 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16394695 original size:18 final size:18
Alignment explanation
Indices: 16394669--16394703 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16394659 CTTTTTCGAT
*
16394669 AATAGAAAATATTAAAAG
1 AATAAAAAATATTAAAAG
*
16394687 AATAAAAAATTTTAAAA
1 AATAAAAAATATTAAAA
16394704 TTTTTTATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AATAAAAAATATTAAAAG
Found at i:16397824 original size:38 final size:36
Alignment explanation
Indices: 16397774--16397885 Score: 127
Period size: 37 Copynumber: 3.0 Consensus size: 36
16397764 GTTTTTGAAG
* *
16397774 TTCTTTAAGTGCATTTAGAGCCAGCATTAA-ATGCTT
1 TTCTTTAAGTGCATTTAGAACCAG-AATAAGATGCTT
*
16397810 ATTCTTTGAAGTGCACTTAGAACCAGAATAAGATGCTT
1 -TTCTTT-AAGTGCATTTAGAACCAGAATAAGATGCTT
* * *
16397848 TTTTTTAAGTCCATTTAGAACCAGAATAACAATGCTT
1 TTCTTTAAGTGCATTTAGAACCAGAATAA-GATGCTT
16397885 T
1 T
16397886 CAGCTGTCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
36 21 0.32
37 22 0.34
38 22 0.34
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (36 bp):
TTCTTTAAGTGCATTTAGAACCAGAATAAGATGCTT
Found at i:16397868 original size:36 final size:36
Alignment explanation
Indices: 16397777--16397885 Score: 121
Period size: 38 Copynumber: 2.9 Consensus size: 36
16397767 TTTGAAGTTC
* *
16397777 TTTAAGTGCATTTAGAGCCAGCATTAAATGCTTATTCT
1 TTTAAGTGCATTTAGAACCAG-AATAAATGCTT-TTCT
* *
16397815 TTGAAGTGCACTTAGAACCAGAATAAGATGCTTTT-T
1 TTTAAGTGCATTTAGAACCAGAATAA-ATGCTTTTCT
*
16397851 TTTAAGTCCATTTAGAACCAGAATAACAATGCTTT
1 TTTAAGTGCATTTAGAACCAGAAT-A-AATGCTTT
16397886 CAGCTGTCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
36 22 0.36
37 14 0.23
38 25 0.41
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (36 bp):
TTTAAGTGCATTTAGAACCAGAATAAATGCTTTTCT
Found at i:16409408 original size:20 final size:20
Alignment explanation
Indices: 16409383--16409439 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
16409373 TCTAGTATGT
16409383 CCCTCTTTTTCTCTCCCTTC
1 CCCTCTTTTTCTCTCCCTTC
*
16409403 CCCTCTCTTTTCTCT-CTTTC
1 CCCTCT-TTTTCTCTCCCTTC
*
16409423 CTCTC-TTTTCTCTCCCT
1 CCCTCTTTTTCTCTCCCT
16409440 ACCCTGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.25
19 2 0.06
20 14 0.44
21 8 0.25
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (20 bp):
CCCTCTTTTTCTCTCCCTTC
Found at i:16409419 original size:9 final size:9
Alignment explanation
Indices: 16409405--16409436 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
16409395 CTCCCTTCCC
16409405 CTCTCTTTT
1 CTCTCTTTT
*
16409414 CTCTCTTTC
1 CTCTCTTTT
16409423 CTCTCTTTT
1 CTCTCTTTT
16409432 CTCTC
1 CTCTC
16409437 CCTACCCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (9 bp):
CTCTCTTTT
Found at i:16426677 original size:3 final size:3
Alignment explanation
Indices: 16426669--16426708 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
16426659 TAACAATAAC
16426669 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16426709 TATGACTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16426951 original size:20 final size:20
Alignment explanation
Indices: 16426928--16427012 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 20
16426918 TTTTGTCTTA
16426928 TAAAA-ATAGATATAATAATT
1 TAAAATATA-ATATAATAATT
16426948 TAAAATATAATATAATAA--
1 TAAAATATAATATAATAATT
* *
16426966 TATAATATAA-A-AATAATA
1 TAAAATATAATATAATAATT
* *
16426984 TAAAAAATGAATATGATATGATT
1 TAAAATAT-AATAT-A-ATAATT
16427007 TAAAAT
1 TAAAAT
16427013 TTTTAATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
16 5 0.10
17 1 0.02
18 15 0.29
19 2 0.04
20 15 0.29
21 3 0.06
22 1 0.02
23 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAAATATAATATAATAATT
Found at i:16426969 original size:13 final size:12
Alignment explanation
Indices: 16426942--16426988 Score: 69
Period size: 13 Copynumber: 3.9 Consensus size: 12
16426932 AATAGATATA
*
16426942 ATAATTTAAAAT
1 ATAATATAAAAT
16426954 ATAATATAATAAT
1 ATAATATAA-AAT
16426967 ATAATATAAAA-
1 ATAATATAAAAT
16426978 ATAATATAAAA
1 ATAATATAAAA
16426989 AATGAATATG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 11 0.33
12 10 0.30
13 12 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:16426983 original size:11 final size:11
Alignment explanation
Indices: 16426941--16426989 Score: 62
Period size: 11 Copynumber: 4.2 Consensus size: 11
16426931 AAATAGATAT
*
16426941 AATAATTTAAA
1 AATAATATAAA
16426952 ATATAATATAATA
1 A-ATAATATAA-A
16426965 ATATAATATAAA
1 A-ATAATATAAA
16426977 AATAATATAAA
1 AATAATATAAA
16426988 AA
1 AA
16426990 ATGAATATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
11 13 0.37
12 10 0.29
13 12 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAATATAAA
Found at i:16426996 original size:13 final size:12
Alignment explanation
Indices: 16426941--16426997 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
16426931 AAATAGATAT
*
16426941 AATAATTTAAAA
1 AATAATATAAAA
*
16426953 TATAATATAATAA
1 AATAATATAA-AA
*
16426966 TATAATAT-AAA
1 AATAATATAAAA
16426977 AATAATATAAAA
1 AATAATATAAAA
16426989 AATGAATAT
1 AAT-AATAT
16426998 GATATGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 9 0.23
12 15 0.38
13 15 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAATATAAAA
Found at i:16433777 original size:20 final size:20
Alignment explanation
Indices: 16433752--16433805 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
16433742 ATTATTAAAA
*
16433752 TAATAAAATAAATTTATATT
1 TAATAAAATAAATTTAAATT
*
16433772 TAAT-AAATATATTTTAAATT
1 TAATAAAATA-AATTTAAATT
16433792 TAAAATAAAATAAA
1 T--AATAAAATAAA
16433806 AATATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
22 4 0.15
23 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATAAAATAAATTTAAATT
Found at i:16433795 original size:45 final size:46
Alignment explanation
Indices: 16433728--16433820 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 46
16433718 ATATAGTGAT
* * * *
16433728 ATAAATATTTTTTTATTATTAAAATAATAA-AATAAATTTA-TATTTA
1 ATAAATATATTTTAAATATTAAAATAA-AATAA-AAATATATTATTTA
16433774 ATAAATATATTTTAAAT-TTAAAATAAAATAAAAATATATTATTTA
1 ATAAATATATTTTAAATATTAAAATAAAATAAAAATATATTATTTA
16433819 AT
1 AT
16433821 TAGATTGAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
44 8 0.20
45 19 0.46
46 14 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (46 bp):
ATAAATATATTTTAAATATTAAAATAAAATAAAAATATATTATTTA
Found at i:16434163 original size:86 final size:86
Alignment explanation
Indices: 16434018--16434187 Score: 268
Period size: 86 Copynumber: 2.0 Consensus size: 86
16434008 TCAGTTCAAC
*
16434018 TTGTCCATAATTAGGTGGAGCAGTTAGTGTCCCTTACCCTCCCATTTTCAAAACGCTCTCTTACA
1 TTGTCCATAATTAGGTGGAGCAGTTAGTGTCCCTTACCCTCCCATTTTCAAAACGCTCTCTGACA
16434083 CTAAAGAAGCTGCTGTACGAT
66 CTAAAGAAGCTGCTGTACGAT
* * * * *
16434104 TTGTCCCTAGTTAGGTGGAGTAGTTAGTGTCCTTTCCCCTCCCATTTTCAAAACGCTCTCTGACA
1 TTGTCCATAATTAGGTGGAGCAGTTAGTGTCCCTTACCCTCCCATTTTCAAAACGCTCTCTGACA
* *
16434169 TTAAAGAAGCTGTTGTACG
66 CTAAAGAAGCTGCTGTACG
16434188 TATCTCTGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (86 bp):
TTGTCCATAATTAGGTGGAGCAGTTAGTGTCCCTTACCCTCCCATTTTCAAAACGCTCTCTGACA
CTAAAGAAGCTGCTGTACGAT
Found at i:16449992 original size:19 final size:21
Alignment explanation
Indices: 16449953--16449993 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
16449943 TGAACTATAT
*
16449953 ATATATATATTTATTTATTTG
1 ATATATATATTTAATTATTTG
16449974 ATATATA-ATTTAATT-TTTG
1 ATATATATATTTAATTATTTG
16449993 A
1 A
16449994 ACATGTTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
ATATATATATTTAATTATTTG
Found at i:16461269 original size:24 final size:24
Alignment explanation
Indices: 16461221--16461269 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
16461211 ATATCATTAT
* **
16461221 TTTATTTATTGATAATGTATAAAA
1 TTTATATATTGATAATACATAAAA
*
16461245 TTTATATATTGATAATACATTAAA
1 TTTATATATTGATAATACATAAAA
16461269 T
1 T
16461270 AAAAACTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
TTTATATATTGATAATACATAAAA
Found at i:16479734 original size:12 final size:12
Alignment explanation
Indices: 16479717--16479741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16479707 TTATAGGAAG
16479717 AAATTATTAATT
1 AAATTATTAATT
16479729 AAATTATTAATT
1 AAATTATTAATT
16479741 A
1 A
16479742 TGTGAGACGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTATTAATT
Found at i:16480315 original size:18 final size:18
Alignment explanation
Indices: 16480292--16480329 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16480282 TCTAGAATTA
*
16480292 ATTTATT-GACACATTATT
1 ATTTATTAGAC-CATGATT
16480310 ATTTATTAGACCATGATT
1 ATTTATTAGACCATGATT
16480328 AT
1 AT
16480330 GGGATCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (18 bp):
ATTTATTAGACCATGATT
Found at i:16484410 original size:2 final size:2
Alignment explanation
Indices: 16484403--16484442 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
16484393 TTATATTACT
* *
16484403 TA TA TA TA CA TA TA TA TA TA TA CA 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
16484443 AAGTTGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:16484422 original size:14 final size:14
Alignment explanation
Indices: 16484403--16484438 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
16484393 TTATATTACT
16484403 TATATATACATATA
1 TATATATACATATA
16484417 TATATATACATATA
1 TATATATACATATA
16484431 TATATATA
1 TATATATA
16484439 TATAAAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATATACATATA
Done.