Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 15
Found at i:2704025 original size:2 final size:2
Alignment explanation
Indices: 2703839--2704012 Score: 56
Period size: 2 Copynumber: 86.0 Consensus size: 2
2703829 TTATATAGTT
* * * * * *
2703839 TA TA CA TA TA TA GTT TA TA TA CA TA CA TA CA TA CA 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
* * * *
2703882 TA CTA TA T- TA -A TA TA AA T- TA TA T- TT TA TA AA CTA TA TA TT
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
2703922 TT TA TA GTT TA TA TA AA TA -A TA TA AA T- TA TA GTA TA TA AA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
2703964 TA TA GTA TA TA AA TA TA AA CTA TA -A TT TA TA TA TA GTA TA TA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
2704006 CTA TA TA
1 -TA TA TA
2704013 AATAGTTTAT
Statistics
Matches: 123, Mismatches: 33, Indels: 32
0.65 0.18 0.17
Matches are distributed among these distances:
1 7 0.06
2 102 0.83
3 14 0.11
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2704045 original size:22 final size:22
Alignment explanation
Indices: 2704020--2704067 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2704010 ATAAATAGTT
*
2704020 TATATAGTTCACTA-ATAAACTA
1 TATATAGGTCA-TATATAAACTA
*
2704042 TATATAGGTCATATGTAAACTA
1 TATATAGGTCATATATAAACTA
2704064 TATA
1 TATA
2704068 GTTTACATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (22 bp):
TATATAGGTCATATATAAACTA
Found at i:2704076 original size:22 final size:22
Alignment explanation
Indices: 2704051--2704100 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2704041 ATATATAGGT
2704051 CATA-TGTAAACTATATAGTTTA
1 CATAGTGTAAA-TATATAGTTTA
* *
2704073 CATAGTTTATATATATAGTTTA
1 CATAGTGTAAATATATAGTTTA
*
2704095 TATAGT
1 CATAGT
2704101 TTATACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (22 bp):
CATAGTGTAAATATATAGTTTA
Found at i:2704092 original size:13 final size:13
Alignment explanation
Indices: 2704074--2704098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2704064 TATAGTTTAC
2704074 ATAGTTTATATAT
1 ATAGTTTATATAT
2704087 ATAGTTTATATA
1 ATAGTTTATATA
2704099 GTTTATACAT
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
ATAGTTTATATAT
Found at i:2704101 original size:22 final size:22
Alignment explanation
Indices: 2704062--2704113 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2704052 ATATGTAAAC
2704062 TATATAGTTTACATAGTTTATA
1 TATATAGTTTACATAGTTTATA
*
2704084 TATATAGTTTATATAGTTTATA
1 TATATAGTTTACATAGTTTATA
*
2704106 CATATAGT
1 TATATAGT
2704114 ATAAGTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (22 bp):
TATATAGTTTACATAGTTTATA
Found at i:2704110 original size:13 final size:12
Alignment explanation
Indices: 2704074--2704150 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 12
2704064 TATAGTTTAC
2704074 ATAGTTTATATAT
1 ATAGTTTATA-AT
2704087 ATAG-TT-T-AT
1 ATAGTTTATAAT
2704096 ATAGTTTATACAT
1 ATAGTTTATA-AT
2704109 ATAG--TATAAGT
1 ATAGTTTATAA-T
2704120 -TAGTTTAT-AT
1 ATAGTTTATAAT
2704130 -T-GTTTAT-AT
1 ATAGTTTATAAT
2704139 ATAGTTTA-AAT
1 ATAGTTTATAAT
2704150 A
1 A
2704151 CTACTATCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
9 14 0.26
10 9 0.17
11 16 0.30
12 5 0.09
13 10 0.19
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (12 bp):
ATAGTTTATAAT
Found at i:2704170 original size:30 final size:28
Alignment explanation
Indices: 2704136--2704192 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
2704126 ATATTGTTTA
* *
2704136 TATATAGTTTAAATACTACTATCTATAAAC
1 TATATAATTTAAATA-TAAT-TCTATAAAC
*
2704166 TATATAATTTATATATAATTCTATAAA
1 TATATAATTTAAATATAATTCTATAAA
2704193 TTAACCCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 3 0.12
30 13 0.54
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (28 bp):
TATATAATTTAAATATAATTCTATAAAC
Found at i:2704348 original size:11 final size:11
Alignment explanation
Indices: 2704329--2704408 Score: 114
Period size: 11 Copynumber: 7.5 Consensus size: 11
2704319 ATATAAATTG
*
2704329 TATAGTTTATA
1 TATAATTTATA
2704340 TATAATTTATA
1 TATAATTTATA
2704351 TATAATTTATA
1 TATAATTTATA
2704362 TATAATTTATA
1 TATAATTTATA
2704373 TATAATTTATA
1 TATAATTTATA
2704384 TATAA---ACTA
1 TATAATTTA-TA
2704393 TATAATTTATA
1 TATAATTTATA
2704404 T-TAAT
1 TATAAT
2704409 AAACTATGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
8 1 0.02
9 7 0.11
10 4 0.06
11 51 0.80
12 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
TATAATTTATA
Found at i:2704371 original size:33 final size:31
Alignment explanation
Indices: 2704349--2704429 Score: 65
Period size: 31 Copynumber: 2.5 Consensus size: 31
2704339 ATATAATTTA
**
2704349 TATATAATTTATATATAATTTATATATAATT
1 TATATAATTTATATATAATTTATATATAAAC
**
2704380 TATAT-ATAAACTATATAATTTATATTAATAAAC
1 TATATAATTTA-TATATAATTTATA-T-ATAAAC
* * *
2704413 TATGTAGTTTCTATATA
1 TATATAATTTATATATA
2704430 GTTAAATAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
30 3 0.08
31 18 0.49
32 1 0.03
33 14 0.38
34 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (31 bp):
TATATAATTTATATATAATTTATATATAAAC
Found at i:2704485 original size:2 final size:2
Alignment explanation
Indices: 2704478--2704619 Score: 91
Period size: 2 Copynumber: 71.0 Consensus size: 2
2704468 TTATACATGG
* *
2704478 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2704519 GTA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TT TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * *
2704560 TA -A TA TA TA TA CTT TA TA TA TA AA CTA TA TA GTT TA TA T- TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
2704601 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
2704620 GTTGTTTTAT
Statistics
Matches: 110, Mismatches: 16, Indels: 28
0.71 0.10 0.18
Matches are distributed among these distances:
1 7 0.06
2 95 0.86
3 8 0.07
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2704506 original size:22 final size:22
Alignment explanation
Indices: 2704329--2704614 Score: 154
Period size: 22 Copynumber: 13.2 Consensus size: 22
2704319 ATATAAATTG
*
2704329 TATAGTTTATATATAATTTATA
1 TATAGTTTATATATAATATATA
* *
2704351 TATAATTTATATATAATTTATA
1 TATAGTTTATATATAATATATA
*
2704373 TATAATTTATATATAA-ACTATA
1 TATAGTTTATATATAATA-TATA
*
2704395 TA-A-TTTATAT-TAATAAACTA
1 TATAGTTTATATATAATATA-TA
* * *
2704415 TGTAGTTTCTATATAGT-TA-A
1 TATAGTTTATATATAATATATA
*
2704435 -ATAGTTCATATATAAACTATATGGTA
1 TATAGTTTATATAT-AA-TATA---TA
* **
2704461 TTATAGTTTATACAT--GGTATA
1 -TATAGTTTATATATAATATATA
*
2704482 TATAGTTTATACATAATATATA
1 TATAGTTTATATATAATATATA
* *
2704504 TATA-TATATAATATAGTATATA
1 TATAGTTTAT-ATATAATATATA
* * * *
2704526 -ATAATATAAATATAA-A-CTA
1 TATAGTTTATATATAATATATA
*
2704545 TATAGTTTTTATAT-ATAATATA
1 TATAGTTTATATATAAT-ATATA
* *
2704567 TATACTTTATATATAA-A-CTA
1 TATAGTTTATATATAATATATA
2704587 TATAGTTTATATTATATATATATA
1 TATAGTTTATA-TATA-ATATATA
2704611 TATA
1 TATA
2704615 TTATAGTTGT
Statistics
Matches: 203, Mismatches: 33, Indels: 54
0.70 0.11 0.19
Matches are distributed among these distances:
19 17 0.08
20 49 0.24
21 23 0.11
22 89 0.44
23 5 0.02
24 8 0.04
26 1 0.00
28 11 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (22 bp):
TATAGTTTATATATAATATATA
Found at i:2704566 original size:9 final size:9
Alignment explanation
Indices: 2704489--2704615 Score: 68
Period size: 9 Copynumber: 13.8 Consensus size: 9
2704479 ATATATAGTT
*
2704489 TATACATAA
1 TATATATAA
2704498 TATATAT-A
1 TATATATAA
2704506 TATATATAA
1 TATATATAA
2704515 TATAGTAT-A
1 TATA-TATAA
2704524 TAATAATATAA
1 T-AT-ATATAA
2704535 -ATATA-AA
1 TATATATAA
**
2704542 CTATATAGTTTT
1 -TATATA--TAA
2704554 TATATATAA
1 TATATATAA
*
2704563 TATATATACTT
1 TATATATA--A
2704574 TATATATAA
1 TATATATAA
*
2704583 -ACTATATAG
1 TA-TATATAA
* *
2704592 TTTATATTA
1 TATATATAA
2704601 TATATAT-A
1 TATATATAA
2704609 TATATAT
1 TATATAT
2704616 TATAGTTGTT
Statistics
Matches: 92, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
7 2 0.02
8 20 0.22
9 46 0.50
10 8 0.09
11 16 0.17
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (9 bp):
TATATATAA
Found at i:2704568 original size:11 final size:11
Alignment explanation
Indices: 2704227--2704619 Score: 94
Period size: 11 Copynumber: 36.1 Consensus size: 11
2704217 ACCCTAAACC
*
2704227 ATATATATTAT
1 ATATATAATAT
2704238 ATATATAA-A-
1 ATATATAATAT
* * *
2704247 CTATATAGTTT
1 ATATATAATAT
*
2704258 ATAT-TAATAA
1 ATATATAATAT
*
2704268 ACTATATAATTT
1 A-TATATAATAT
*
2704280 ATACAATATATATT
1 ATA-TATA-ATA-T
*
2704294 ATTTATAAT-T
1 ATATATAATAT
**
2704304 ATACGTAATAT
1 ATATATAATAT
2704315 ATAAATATAA-AT
1 AT--ATATAATAT
* * *
2704327 -TGTATAGTTT
1 ATATATAATAT
*
2704337 ATATATAATTT
1 ATATATAATAT
*
2704348 ATATATAATTT
1 ATATATAATAT
*
2704359 ATATATAATTT
1 ATATATAATAT
*
2704370 ATATATAATTT
1 ATATATAATAT
2704381 ATATATAA-A-
1 ATATATAATAT
* *
2704390 CTATATAATTT
1 ATATATAATAT
*
2704401 ATAT-TAATAA
1 ATATATAATAT
* * *
2704411 ACTATGTAGTTT
1 A-TATATAATAT
* *
2704423 CTATATAGT-T
1 ATATATAATAT
*
2704433 A-A-ATAGT-T
1 ATATATAATAT
2704441 CATATATAA-ACT
1 -ATATATAATA-T
* *
2704453 ATATGGTATTAT
1 ATAT-ATAATAT
* *
2704465 AGTTTATACATGGT
1 A-TATATA-AT-AT
* *
2704479 ATATATAGTTT
1 ATATATAATAT
*
2704490 ATACATAATAT
1 ATATATAATAT
2704501 ATATAT-ATAT
1 ATATATAATAT
*
2704511 ATAATATAGTAT
1 AT-ATATAATAT
2704523 ATA-ATAATAT
1 ATATATAATAT
*
2704533 AAATATAA-ACT
1 ATATATAATA-T
* *
2704544 ATATAGT-TTTT
1 ATATA-TAATAT
2704555 ATATATAATAT
1 ATATATAATAT
*
2704566 ATATACT-TTAT
1 ATATA-TAATAT
2704577 ATATA-AACTAT
1 ATATATAA-TAT
*
2704588 ATAGT-TTATAT
1 ATA-TATAATAT
2704599 -TATAT-ATAT
1 ATATATAATAT
*
2704608 ATATATATTAT
1 ATATATAATAT
2704619 A
1 A
2704620 GTTGTTTTAT
Statistics
Matches: 279, Mismatches: 62, Indels: 82
0.66 0.15 0.19
Matches are distributed among these distances:
8 6 0.02
9 24 0.09
10 44 0.16
11 150 0.54
12 32 0.11
13 18 0.06
14 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (11 bp):
ATATATAATAT
Found at i:2705370 original size:216 final size:214
Alignment explanation
Indices: 2704715--2705407 Score: 1064
Period size: 208 Copynumber: 3.3 Consensus size: 214
2704705 TTGATCCCTT
** * * **
2704715 TGTGTTGTTTAATTTATTTAAATTTAAATTTGTAATTTCATATTTATCCAATTTAGTCCTTAAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* *
2704780 TTATATTTGCTTCTGAAATTGACCCATACTTATTACTTATTCATATTTTTTAATTGGCCCAT-AG
66 TTATATTTGCATCTGAAATTGACCCATACTTATTACTTATTC-TATTTTTTAATTGGCCCATAAC
2704844 TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTA-TT
130 TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTT
2704908 CTGATTTGATCCCT--T----
195 C-GATTTGATCCCTCATCAAG
*
2704923 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTTAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* *
2704988 TTATATTTGCATCTGAAATTGACCCATACTTATAACTTATT-TATATCTTTAATTGGCCCATAAC
66 TTATATTTGCATCTGAAATTGACCCATACTTATTACTTATTCTAT-TTTTTAATTGGCCCATAAC
*
2705052 TTTTTAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTT
130 TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTT
2705116 CGATTTGATCCCTCATCAATG
195 CGATTTGATCCCTCATCAA-G
* **
2705137 TGTGTTGTTTAATTTATTTAAATTTTTATTTTTAATTTCATATTTGTTCAATTTAGTCCTCCATT
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * * * *
2705202 TTTTATCTGCATATGAAATTGATCCATAATTATTACTTAATTCTATTTTTTAATTGGCCCATAAC
66 TTATATTTGCATCTGAAATTGACCCATACTTATTACTT-ATTCTATTTTTTAATTGGCCCATAAC
* *
2705267 TTTTTAAATGGGTATTATTTAGTACTTTTTTGTATTAATTTAAACCTTACAATTTAAAATTATTT
130 TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTT
2705332 CGATTTGATCCCTCATCAACG
195 CGATTTGATCCCTCATCAA-G
2705353 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
2705408 ATTCTTAAAT
Statistics
Matches: 444, Mismatches: 28, Indels: 18
0.91 0.06 0.04
Matches are distributed among these distances:
206 3 0.01
207 62 0.14
208 126 0.28
209 1 0.00
214 93 0.21
215 45 0.10
216 114 0.26
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.51
Consensus pattern (214 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
TTATATTTGCATCTGAAATTGACCCATACTTATTACTTATTCTATTTTTTAATTGGCCCATAACT
TTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTC
GATTTGATCCCTCATCAAG
Found at i:2713653 original size:38 final size:38
Alignment explanation
Indices: 2713602--2713677 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2713592 TGGAAGTTAG
2713602 CTTAGCTGTTGGTCATGGTGATTAGCATGGTTGTATAT
1 CTTAGCTGTTGGTCATGGTGATTAGCATGGTTGTATAT
2713640 CTTAGCTGTTGGTCATGGTGATTAGCATGGTTGTATAT
1 CTTAGCTGTTGGTCATGGTGATTAGCATGGTTGTATAT
2713678 ATACAATAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (38 bp):
CTTAGCTGTTGGTCATGGTGATTAGCATGGTTGTATAT
Found at i:2713664 original size:20 final size:20
Alignment explanation
Indices: 2713603--2713665 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
2713593 GGAAGTTAGC
2713603 TTAGCTGTTGGTCATGGTGA
1 TTAGCTGTTGGTCATGGTGA
* *
2713623 TTAGCATGGTT-GT-AT-AT-C
1 TTAGC-T-GTTGGTCATGGTGA
2713641 TTAGCTGTTGGTCATGGTGA
1 TTAGCTGTTGGTCATGGTGA
2713661 TTAGC
1 TTAGC
2713666 ATGGTTGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
16 3 0.09
17 3 0.09
18 7 0.21
19 2 0.06
20 12 0.36
21 3 0.09
22 3 0.09
ACGTcount: A:0.17, C:0.11, G:0.30, T:0.41
Consensus pattern (20 bp):
TTAGCTGTTGGTCATGGTGA
Found at i:2714772 original size:51 final size:51
Alignment explanation
Indices: 2714673--2714772 Score: 114
Period size: 51 Copynumber: 2.0 Consensus size: 51
2714663 TACGAGTTCG
* ** **
2714673 AATAAAATAATTTTTTTTATTAAAATCTATCACATCGAGTTAAAAAGTTAA
1 AATAAAAAAATTAATTTTATTAAAATCTATCACATCGACATAAAAAGTTAA
*
2714724 AATAAAAAAATTAATTTTATTAAAA-CTTATCATC-TCGACATAATAAGTT
1 AATAAAAAAATTAATTTTATTAAAATC-TATCA-CATCGACATAAAAAGTT
2714773 TCATGTCATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
50 1 0.02
51 39 0.95
52 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (51 bp):
AATAAAAAAATTAATTTTATTAAAATCTATCACATCGACATAAAAAGTTAA
Found at i:2724170 original size:15 final size:18
Alignment explanation
Indices: 2724135--2724167 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2724125 AGTTAACATA
2724135 AAAAACTATTATAAAATT
1 AAAAACTATTATAAAATT
2724153 AAAAA-TATTA-AAAAT
1 AAAAACTATTATAAAAT
2724168 AAATTTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAACTATTATAAAATT
Found at i:2724334 original size:3 final size:3
Alignment explanation
Indices: 2724326--2724365 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2724316 AAAGAAATCA
2724326 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
2724366 GAAATGAATA
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:2724929 original size:15 final size:15
Alignment explanation
Indices: 2724908--2724990 Score: 76
Period size: 15 Copynumber: 5.5 Consensus size: 15
2724898 TATCATCATC
2724908 AATTATTTAAACATG
1 AATTATTTAAACATG
* *
2724923 TATTATTTAATCATG
1 AATTATTTAAACATG
* * *
2724938 AATTATTCAAAATATC
1 AATTATT-TAAACATG
*
2724954 AATTATTTAAATATG
1 AATTATTTAAACATG
* * *
2724969 AATAATGTAAACATT
1 AATTATTTAAACATG
2724984 AATTATT
1 AATTATT
2724991 GAAATGAAAT
Statistics
Matches: 52, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
15 41 0.79
16 11 0.21
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (15 bp):
AATTATTTAAACATG
Found at i:2726035 original size:38 final size:38
Alignment explanation
Indices: 2725984--2726061 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
2725974 GTAAAGAACT
*
2725984 CAGAGAACCATTAGGGTTCCCACTCTTCCCCAAAGCGC
1 CAGAGAACCATTAGGGTTCCCACTCTTCCCCAAAACGC
2726022 CAGAGAACCATTAGGGTTCCCACTCTTCCCCAAAACGC
1 CAGAGAACCATTAGGGTTCCCACTCTTCCCCAAAACGC
2726060 CA
1 CA
2726062 CTAAACATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.18
Consensus pattern (38 bp):
CAGAGAACCATTAGGGTTCCCACTCTTCCCCAAAACGC
Found at i:2728307 original size:108 final size:106
Alignment explanation
Indices: 2728104--2728307 Score: 236
Period size: 108 Copynumber: 1.9 Consensus size: 106
2728094 TACCCGAGGG
* *
2728104 TCCATTTTAGGCTTATTTTCTTTAGTCCTTTAATGTAGGGAATTCGATTTGGCCACCGCCTTAAT
1 TCCATTTTAGGATTATTTTCTTTAGTCCTTTAATGTAGGGAATTCGATTTGGACACCGCCTTAAT
* ***
2728169 GCTCGAGGGTTTATCTCGACTATTCAATTCACATTAGAGCC
66 GCTCAAGGGCCCATCTCGACTATTCAATTCACATTAGAGCC
* *
2728210 TCCATTTTAGGATTATTTTCACTTTAGT-CTTTAATTTAGGGAATATTTGATTT-GACACTCGCC
1 TCCATTTTAGGATTATTTT--CTTTAGTCCTTTAATGTAGGG-A-ATTCGATTTGGACAC-CGCC
* *
2728273 TT-ATGC-CTAAGGGCCCATTTCGACTATTCGATTCA
61 TTAATGCTC-AAGGGCCCATCTCGACTATTCAATTCA
2728308 ATAATTGGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
106 18 0.22
107 13 0.16
108 37 0.45
109 14 0.17
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (106 bp):
TCCATTTTAGGATTATTTTCTTTAGTCCTTTAATGTAGGGAATTCGATTTGGACACCGCCTTAAT
GCTCAAGGGCCCATCTCGACTATTCAATTCACATTAGAGCC
Found at i:2746282 original size:23 final size:24
Alignment explanation
Indices: 2746235--2746326 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 24
2746225 CCACTAGAGG
*
2746235 CACATAGAATTTGTCCCGAAGGAC
1 CACATAGAATATGTCCCGAAGGAC
* * *
2746259 CGCATAGAA-ATGTCCTGAATGAC
1 CACATAGAATATGTCCCGAAGGAC
*
2746282 CACAT---ATAAGTCCCGAAGGAC
1 CACATAGAATATGTCCCGAAGGAC
*
2746303 CACATAG---ATGTCCAGAAGGAC
1 CACATAGAATATGTCCCGAAGGAC
2746324 CAC
1 CAC
2746327 TCCTTAAGGA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.02
21 31 0.56
23 15 0.27
24 8 0.15
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (24 bp):
CACATAGAATATGTCCCGAAGGAC
Found at i:2751552 original size:18 final size:17
Alignment explanation
Indices: 2751519--2751551 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2751509 TGACTTCGAT
2751519 TAAAAAGTCAAATTTTC
1 TAAAAAGTCAAATTTTC
*
2751536 TAAAAAGTCACATTTT
1 TAAAAAGTCAAATTTT
2751552 TATTGTTTAT
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:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAAAAAGTCAAATTTTC
Found at i:2758190 original size:15 final size:15
Alignment explanation
Indices: 2758134--2758193 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
2758124 TTAGAATAAG
2758134 AAAAA-TGAAAATGA
1 AAAAATTGAAAATGA
* *
2758148 AAAAATAGGGAAAT-A
1 AAAAAT-TGAAAATGA
2758163 AAAATTGATTGAAAATGA
1 AAAA---ATTGAAAATGA
2758181 AAAAATTGAAAAT
1 AAAAATTGAAAAT
2758194 AAGGTTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
14 5 0.14
15 14 0.39
16 5 0.14
17 5 0.14
18 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (15 bp):
AAAAATTGAAAATGA
Found at i:2759510 original size:116 final size:116
Alignment explanation
Indices: 2759361--2759792 Score: 494
Period size: 116 Copynumber: 3.7 Consensus size: 116
2759351 TAGATAAAAT
* * * * *
2759361 ATTTCCAGTGGAAGGGTTCATAATAATAAGAACTCGTCTGATCAGGGAAAAGAAGTTTCAAATGA
1 ATTTTCAGTAGAAGGGTTCATAATAAGAAGAACTCGTCCGATCAGGGAAAAGAAGTTTCTAATGA
* * *
2759426 TAAGAACTTGTTCAACCTTGGTTCATCCATCATAGAAGGAGGTGGATCAAC
66 GAAGAACTTGTTCAACCTTGGCTCATTCATCATAGAAGGAGGTGGATCAAC
* * *
2759477 ATTTTCAATAGAAGGGTTCATAATAAGAAGAACTCGTCCGATCAAGGAAAATAA-TTTCCTAATG
1 ATTTTCAGTAGAAGGGTTCATAATAAGAAGAACTCGTCCGATCAGGGAAAAGAAGTTT-CTAATG
* * * * * *
2759541 AGAAAAACTTGTTCGACCTTGGCTCATTCATCACAAAATGATGTGGATCAAC
65 AGAAGAACTTGTTCAACCTTGGCTCATTCATCATAGAAGGAGGTGGATCAAC
* * * *
2759593 ATTTCCAGTAG-AGAGGTTCATAATGAGAAGAACTCGTCCGATCATGGAGAAGAAG-TTCTTAAT
1 ATTTTCAGTAGAAG-GGTTCATAATAAGAAGAACTCGTCCGATCAGGGAAAAGAAGTTTC-TAAT
* * *
2759656 GAGAAG-ACTTTGTTCAACCTTGGCTCATTCATCATAGAAGGAGTTGGTTCAGC
64 GAGAAGAAC-TTGTTCAACCTTGGCTCATTCATCATAGAAGGAGGTGGATCAAC
* * * * * * * * * *
2759709 ATTTTTAGTGGAAGGGGTCCTAATGAGAATAACTCGTCCAATAAGGGAGAAGAAGTTCCTAATGA
1 ATTTTCAGTAGAAGGGTTCATAATAAGAAGAACTCGTCCGATCAGGGAAAAGAAGTTTCTAATGA
2759774 GAAGAACTTGTTCAACCTT
66 GAAGAACTTGTTCAACCTT
2759793 TTTTTCCAGA
Statistics
Matches: 266, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
115 8 0.03
116 252 0.95
117 6 0.02
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (116 bp):
ATTTTCAGTAGAAGGGTTCATAATAAGAAGAACTCGTCCGATCAGGGAAAAGAAGTTTCTAATGA
GAAGAACTTGTTCAACCTTGGCTCATTCATCATAGAAGGAGGTGGATCAAC
Found at i:2759770 original size:232 final size:232
Alignment explanation
Indices: 2759361--2759792 Score: 566
Period size: 232 Copynumber: 1.9 Consensus size: 232
2759351 TAGATAAAAT
* * *
2759361 ATTTCCAGTGGAAGGGTTCATAATAATAAGAACTCGTCTGATCAGGGAAAAGAAGTTTCAAATGA
1 ATTTCCAGTAGAAGGGTTCATAATAAGAAGAACTCGTCCGATCAGGGAAAAGAAGTTTCAAATGA
* *
2759426 TAAGAACTTGTTCAACCTTGGTTCATCCATCATAGAAGGAGGTGGATCAACATTTTCAATAGAAG
66 GAAGAACTTGTTCAACCTTGGCTCATCCATCATAGAAGGAGGTGGATCAACATTTTCAATAGAAG
* * * * *
2759491 GGTTCATAATAAGAAGAACTCGTCCGATCAAGGAAAATAATTTCCTAATGAGAAAAACTTGTTCG
131 GGGTCATAATAAGAAGAACTCGTCCAATCAAGGAAAAGAAGTTCCTAATGAGAAAAACTTGTTCA
2759556 ACCTTGGCTCATTCATCACAAAATGATGTGGATCAAC
196 ACCTTGGCTCATTCATCACAAAATGATGTGGATCAAC
* * * *
2759593 ATTTCCAGTAG-AGAGGTTCATAATGAGAAGAACTCGTCCGATCATGGAGAAGAAG-TTCTTAAT
1 ATTTCCAGTAGAAG-GGTTCATAATAAGAAGAACTCGTCCGATCAGGGAAAAGAAGTTTC-AAAT
* * * * * * *
2759656 GAGAAG-ACTTTGTTCAACCTTGGCTCATTCATCATAGAAGGAGTTGGTTCAGCATTTTTAGTGG
64 GAGAAGAAC-TTGTTCAACCTTGGCTCATCCATCATAGAAGGAGGTGGATCAACATTTTCAATAG
* * * * *
2759720 AAGGGGTCCTAATGAGAATAACTCGTCCAAT-AAGGGAGAAGAAGTTCCTAATGAGAAGAACTTG
128 AAGGGGTCATAATAAGAAGAACTCGTCCAATCAA-GGAAAAGAAGTTCCTAATGAGAAAAACTTG
2759784 TTCAACCTT
192 TTCAACCTT
2759793 TTTTTCCAGA
Statistics
Matches: 170, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
231 9 0.05
232 161 0.95
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (232 bp):
ATTTCCAGTAGAAGGGTTCATAATAAGAAGAACTCGTCCGATCAGGGAAAAGAAGTTTCAAATGA
GAAGAACTTGTTCAACCTTGGCTCATCCATCATAGAAGGAGGTGGATCAACATTTTCAATAGAAG
GGGTCATAATAAGAAGAACTCGTCCAATCAAGGAAAAGAAGTTCCTAATGAGAAAAACTTGTTCA
ACCTTGGCTCATTCATCACAAAATGATGTGGATCAAC
Found at i:2771288 original size:18 final size:19
Alignment explanation
Indices: 2771260--2771295 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2771250 AAAAATATCA
2771260 AATCACTAACCCTAACCTT
1 AATCACTAACCCTAACCTT
2771279 AATC-CTAACCCTAACCT
1 AATCACTAACCCTAACCT
2771296 CCATTGCCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.25
Consensus pattern (19 bp):
AATCACTAACCCTAACCTT
Found at i:2776427 original size:19 final size:20
Alignment explanation
Indices: 2776337--2776427 Score: 116
Period size: 19 Copynumber: 4.7 Consensus size: 20
2776327 ATGCGTTTGC
2776337 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
*
2776358 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
*
2776377 CAAATTCGCAACTCG-ATTT
1 CAAATTCGCAACACGAATTT
*
2776396 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
2776416 -AATTTCGCAACA
1 CAAATTCGCAACA
2776428 AGTTTTAGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 45 0.73
20 5 0.08
21 12 0.19
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:2776602 original size:14 final size:15
Alignment explanation
Indices: 2776583--2776620 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2776573 TCCCCATCTC
2776583 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
2776597 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
2776613 TAATTTTT
1 TAATTTTT
2776621 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:2777388 original size:24 final size:24
Alignment explanation
Indices: 2777361--2777414 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2777351 GTATTCAAAA
2777361 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2777385 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2777409 TTTGAT
1 TTTGAT
2777415 GATGTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2779696 original size:18 final size:18
Alignment explanation
Indices: 2779673--2779708 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2779663 AAGCAAAAGG
*
2779673 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
2779691 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
2779709 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2779968 original size:20 final size:20
Alignment explanation
Indices: 2779904--2779967 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
2779894 TACGATTGAT
2779904 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
** **
2779924 GCGAAAGTCAAATTTTCATT
1 GCGAAAGTCAAATTCGCAAC
*
2779944 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
2779964 GCGA
1 GCGA
2779968 TTATCACGTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:2780057 original size:20 final size:20
Alignment explanation
Indices: 2780034--2780118 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
2780024 AAATCGCAAC
*
2780034 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCACGTT
*
2780054 GCGAATTTGACTTTAACGTT
1 GCGAATTTGACTTTCACGTT
* ***
2780074 GCGAATTTGACTATCACAAC
1 GCGAATTTGACTTTCACGTT
* *
2780094 GCGAATTTAACTTTCGCGTT
1 GCGAATTTGACTTTCACGTT
2780114 GCGAA
1 GCGAA
2780119 AATGTACCTT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (20 bp):
GCGAATTTGACTTTCACGTT
Found at i:2780260 original size:27 final size:27
Alignment explanation
Indices: 2780222--2780324 Score: 100
Period size: 27 Copynumber: 3.6 Consensus size: 27
2780212 ATAATTCTTA
*
2780222 TTTACACATCAATTAAACAAATCAACT
1 TTTACAAATCAATTAAACAAATCAACT
*
2780249 TTTACAAATCAATTAAAC-AAGCAAATTCTT
1 TTTACAAATCAATTAAACAAATC-AA--C-T
* **
2780279 ATTTCCTCATCAATTAAACAAATCAACT
1 -TTTACAAATCAATTAAACAAATCAACT
2780307 TTTACAAATCAATGTAAA
1 TTTACAAATCAAT-TAAA
2780325 ATTCAATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
26 3 0.05
27 29 0.48
28 5 0.08
29 2 0.03
30 1 0.02
31 17 0.28
32 3 0.05
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (27 bp):
TTTACAAATCAATTAAACAAATCAACT
Found at i:2780304 original size:58 final size:60
Alignment explanation
Indices: 2780173--2780324 Score: 218
Period size: 58 Copynumber: 2.5 Consensus size: 60
2780163 TTGAATAAAC
*
2780173 AACAAATGAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGC----AATAATTCTTATTTACACATCAATTA
* *
2780237 AACAAATCAACTTTTACAAATCAATTAAACAAGC-A-AATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAATAATTCTTATTTACACATCAATTA
2780295 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
2780325 ATTCAATTAA
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
58 46 0.55
59 5 0.06
64 33 0.39
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAATAATTCTTATTTACACATCAATTA
Found at i:2781707 original size:21 final size:21
Alignment explanation
Indices: 2781681--2781799 Score: 132
Period size: 21 Copynumber: 5.7 Consensus size: 21
2781671 GTGAATCGGG
* * *
2781681 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGGC
* *
2781702 CTCTTGAATGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
2781723 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
2781744 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
2781765 CTCTTGAATGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
*
2781786 CTCTTGAATGATGA
1 CTCTTGAACGATGA
2781800 CAGGTGCATC
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
20 1 0.01
21 81 0.98
22 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:2781740 original size:42 final size:41
Alignment explanation
Indices: 2781681--2781803 Score: 174
Period size: 42 Copynumber: 2.9 Consensus size: 41
2781671 GTGAATCGGG
2781681 CTCTTGAACGGTGGGAGGGACCTCTTGAATGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAATGATGACAGGGGC
* *
2781723 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAATGATGACAGGGGC
* * *
2781765 CTCTTGAATGATAGGAGGCGCCTCTTGAATGATGACAGG
1 CTCTTGAACGGTGGGAGG-GCCTCTTGAATGATGACAGG
2781804 TGCATCGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.03
42 67 0.93
43 3 0.04
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAATGATGACAGGGGC
Found at i:2784315 original size:31 final size:31
Alignment explanation
Indices: 2784217--2784341 Score: 99
Period size: 31 Copynumber: 4.0 Consensus size: 31
2784207 GTCGAGGGTA
* *
2784217 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTAAGGAACATATGGACAG-TT
* *** * *
2784249 TACGTATG-TCTTTCGAGACATATGGATAGTA
1 TACCTATGTTCTAAGGA-ACATATGGACAGTT
*
2784280 TACCTATGTTCTAAGGAACATGTGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTT
* ** * *
2784311 TACCTAGGTTCTTCGAAACCTATGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTT
2784342 GCCAAGGATC
Statistics
Matches: 71, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
31 48 0.68
32 23 0.32
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTT
Found at i:2784382 original size:30 final size:30
Alignment explanation
Indices: 2784328--2784399 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
2784318 GTTCTTCGAA
* * *
2784328 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
2784358 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
2784388 ACCTCTGGATAG
1 ACCTCTGGATAG
2784400 GTTCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:2786779 original size:20 final size:20
Alignment explanation
Indices: 2786756--2786828 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2786746 AAACTTAAAT
*
2786756 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
**
2786776 TCGCAACGTAAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
2786796 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
2786816 TCGCAACGTGAAA
1 TCGCAACGCGAAA
2786829 CTAAATTCGC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:2787384 original size:20 final size:20
Alignment explanation
Indices: 2787359--2787442 Score: 150
Period size: 20 Copynumber: 4.2 Consensus size: 20
2787349 ATAAACGCGC
2787359 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
2787379 TTTGACTTATGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
2787399 TTTGACTTCTGTATTGCGAA
1 TTTGACTTCTGTGTTGCGAA
2787419 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
2787439 TTTG
1 TTTG
2787443 GAAAATCGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.17, C:0.13, G:0.24, T:0.46
Consensus pattern (20 bp):
TTTGACTTCTGTGTTGCGAA
Found at i:2787460 original size:21 final size:21
Alignment explanation
Indices: 2787434--2787495 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
2787424 CTTCTGTGTT
* *
2787434 GCGAATTTGGAAAATCGTAAC
1 GCGAATTTAGAAAATCGCAAC
2787455 GCGAATTTAGAAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
2787476 GCGAATTTAGAAAATCGCAA
1 GCGAATTTAGAAAATCGCAA
2787496 TGTGATTCAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:2787572 original size:19 final size:19
Alignment explanation
Indices: 2787510--2787584 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
2787500 ATTCACATAT
2787510 TCGCGTTGCGAATTTG-GAA
1 TCGCGTTGCGAATTTGAG-A
* * * * *
2787529 ACTGGGTTGTGAAATTGGAGT
1 TC-GCGTTGCG-AATTTGAGA
2787550 TCGCGTTGCGAATTTGAGA
1 TCGCGTTGCGAATTTGAGA
*
2787569 TCGCGTTACGAATTTG
1 TCGCGTTGCGAATTTG
2787585 TTGGTCATTT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 23 0.55
20 12 0.29
21 6 0.14
22 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.33
Consensus pattern (19 bp):
TCGCGTTGCGAATTTGAGA
Found at i:2789015 original size:27 final size:27
Alignment explanation
Indices: 2788980--2789043 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
2788970 GTCGGTTTGA
*
2788980 TTTTAAAAAATA-TTTTCTATTTTT-AT
1 TTTTTAAAAATAGTTTTC-ATTTTTAAT
2789006 TTTTTAAAAATAGTTTTCATTTTTAAT
1 TTTTTAAAAATAGTTTTCATTTTTAAT
*
2789033 TTTTTGAAAAT
1 TTTTTAAAAAT
2789044 TAAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 17 0.50
27 17 0.50
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTTTAAAAATAGTTTTCATTTTTAAT
Found at i:2789594 original size:21 final size:21
Alignment explanation
Indices: 2789551--2789594 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2789541 ACAATATATA
*
2789551 ATATTAATGTGATAGTTCACG
1 ATATTAATGTGATAGTACACG
* * *
2789572 ATATTATTGTGGTAGTACTCG
1 ATATTAATGTGATAGTACACG
2789593 AT
1 AT
2789595 GGACAATGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (21 bp):
ATATTAATGTGATAGTACACG
Found at i:2794513 original size:21 final size:22
Alignment explanation
Indices: 2794489--2794530 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2794479 ATAAAAATTG
* *
2794489 ACTATACCCAT-ACTGAACACA
1 ACTATAACCATAACCGAACACA
2794510 ACTATAACCATAACCGAACAC
1 ACTATAACCATAACCGAACAC
2794531 TCACCCCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.45, C:0.33, G:0.05, T:0.17
Consensus pattern (22 bp):
ACTATAACCATAACCGAACACA
Found at i:2797782 original size:18 final size:18
Alignment explanation
Indices: 2797759--2797796 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2797749 CAAAACATGC
*
2797759 AAAGAACCATTGCCTTCT
1 AAAGAACCAGTGCCTTCT
2797777 AAAGAACCAGTGCCTTCT
1 AAAGAACCAGTGCCTTCT
2797795 AA
1 AA
2797797 TCTTATCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (18 bp):
AAAGAACCAGTGCCTTCT
Found at i:2802578 original size:18 final size:19
Alignment explanation
Indices: 2802555--2802591 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2802545 TTTATTGAAA
*
2802555 AACCGATAAA-CCAAACCG
1 AACCGAAAAACCCAAACCG
2802573 AACCGAAAAACCCAAACCG
1 AACCGAAAAACCCAAACCG
2802592 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.35, G:0.11, T:0.03
Consensus pattern (19 bp):
AACCGAAAAACCCAAACCG
Found at i:2805011 original size:43 final size:43
Alignment explanation
Indices: 2804963--2805048 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
2804953 ACATTGACTC
2804963 GTCAATTTACATACAATCATAGCATAGTTCACTTATACCAAAA
1 GTCAATTTACATACAATCATAGCATAGTTCACTTATACCAAAA
*
2805006 GTCAATTTGCATACAATCATAGCATAGTTCACTTATACCAAAA
1 GTCAATTTACATACAATCATAGCATAGTTCACTTATACCAAAA
2805049 ATAACAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (43 bp):
GTCAATTTACATACAATCATAGCATAGTTCACTTATACCAAAA
Found at i:2808501 original size:17 final size:17
Alignment explanation
Indices: 2808479--2808516 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2808469 CAACGGTCAC
*
2808479 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCAGGTCG
2808496 GGTCAACGGTCAGGTCG
1 GGTCAACGGTCAGGTCG
2808513 GGTC
1 GGTC
2808517 GGTCGGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCAGGTCG
Found at i:2808514 original size:22 final size:23
Alignment explanation
Indices: 2808473--2808518 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
2808463 AGAGGTCAAC
2808473 GGTCACGGTCAACGGTCGGGTCG
1 GGTCACGGTCAACGGTCGGGTCG
2808496 GGTCAACGGTC-A-GGTCGGGTCG
1 GGTC-ACGGTCAACGGTCGGGTCG
2808518 G
1 G
2808519 TCGGGTCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.50
23 5 0.23
24 6 0.27
ACGTcount: A:0.13, C:0.24, G:0.46, T:0.17
Consensus pattern (23 bp):
GGTCACGGTCAACGGTCGGGTCG
Found at i:2808546 original size:19 final size:19
Alignment explanation
Indices: 2808524--2808582 Score: 93
Period size: 19 Copynumber: 3.1 Consensus size: 19
2808514 GTCGGTCGGG
2808524 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2808543 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2808562 TC-GAACCGGTCAAAACCGGT
1 TCAG-ACCGGTC-AAACCGGT
2808582 T
1 T
2808583 TTCCAACTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 1 0.03
19 28 0.74
20 9 0.24
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2808552 original size:10 final size:9
Alignment explanation
Indices: 2808522--2808581 Score: 66
Period size: 10 Copynumber: 6.3 Consensus size: 9
2808512 GGGTCGGTCG
*
2808522 GGTCAGACC
1 GGTCAAACC
2808531 GGTCAAACC
1 GGTCAAACC
*
2808540 GGTTCAGACC
1 GG-TCAAACC
2808550 GGTCAAACC
1 GGTCAAACC
*
2808559 GGTTCGAACC
1 GG-TCAAACC
2808569 GGTCAAAACC
1 GGTC-AAACC
2808579 GGT
1 GGT
2808582 TTTCCAACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
9 20 0.47
10 23 0.53
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2815793 original size:5 final size:5
Alignment explanation
Indices: 2815783--2815832 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
2815773 AACGATCAAC
* *
2815783 GGTCG GGTCG GGTCAAC GGTCG GGTCG TGTCG GGTC- GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
2815833 AGATCGGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 4 0.11
5 30 0.79
7 4 0.11
ACGTcount: A:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:2815800 original size:17 final size:17
Alignment explanation
Indices: 2815778--2815833 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
2815768 CGGTTAACGA
2815778 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
*
2815795 TCAACGGTCGGGTCGTG
1 TCAACGGTCGGGTCGGG
**
2815812 TCGGGTCGGTCGGGTCGGG
1 TC--AACGGTCGGGTCGGG
2815831 TCA
1 TCA
2815834 GATCGGTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 18 0.56
19 14 0.44
ACGTcount: A:0.09, C:0.23, G:0.46, T:0.21
Consensus pattern (17 bp):
TCAACGGTCGGGTCGGG
Found at i:2815825 original size:9 final size:9
Alignment explanation
Indices: 2815799--2815829 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
2815789 GTCGGGTCAA
2815799 CGGTCGGGT
1 CGGTCGGGT
2815808 CGTGTCGGGT
1 CG-GTCGGGT
2815818 CGGTCGGGT
1 CGGTCGGGT
2815827 CGG
1 CGG
2815830 GTCAGATCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.00, C:0.23, G:0.55, T:0.23
Consensus pattern (9 bp):
CGGTCGGGT
Found at i:2815828 original size:14 final size:15
Alignment explanation
Indices: 2815783--2815832 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
2815773 AACGATCAAC
*
2815783 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTC--G
*
2815800 GGTCGGGTCGTGTCG
1 GGTCGGGTCGGGTCG
2815815 GGTC-GGTCGGGTCG
1 GGTCGGGTCGGGTCG
2815829 GGTC
1 GGTC
2815833 AGATCGGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.43
15 4 0.13
17 13 0.43
ACGTcount: A:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (15 bp):
GGTCGGGTCGGGTCG
Found at i:2815839 original size:19 final size:19
Alignment explanation
Indices: 2815782--2815841 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 19
2815772 TAACGATCAA
2815782 CGGTCGGGTCGGGTCA-A-
1 CGGTCGGGTCGGGTCAGAT
* * *
2815799 CGGTCGGGTCGTGTCGGGT
1 CGGTCGGGTCGGGTCAGAT
2815818 CGGTCGGGTCGGGTCAGAT
1 CGGTCGGGTCGGGTCAGAT
2815837 CGGTC
1 CGGTC
2815842 AAACCGGTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 14 0.40
19 21 0.60
ACGTcount: A:0.07, C:0.23, G:0.48, T:0.22
Consensus pattern (19 bp):
CGGTCGGGTCGGGTCAGAT
Found at i:2831308 original size:22 final size:22
Alignment explanation
Indices: 2831268--2831310 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2831258 CATTACGTAA
**
2831268 CACCGCAACATGCTATAAATTG
1 CACCGCAACAAACTATAAATTG
*
2831290 CACCGCAACAAACTCTAAATT
1 CACCGCAACAAACTATAAATT
2831311 ATCTGAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (22 bp):
CACCGCAACAAACTATAAATTG
Found at i:2833341 original size:19 final size:20
Alignment explanation
Indices: 2833297--2833341 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2833287 ATTTGTTTTT
*
2833297 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
2833317 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
2833336 AATAAA
1 AATAAA
2833342 ATATTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:2834949 original size:12 final size:12
Alignment explanation
Indices: 2834932--2834956 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2834922 TTTCTTGTCC
2834932 CCGTATCTGTAT
1 CCGTATCTGTAT
2834944 CCGTATCTGTAT
1 CCGTATCTGTAT
2834956 C
1 C
2834957 GGTGCAACAT
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:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (12 bp):
CCGTATCTGTAT
Found at i:2835236 original size:3 final size:3
Alignment explanation
Indices: 2835228--2835310 Score: 103
Period size: 3 Copynumber: 27.0 Consensus size: 3
2835218 AAATTTAAAT
**
2835228 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
2835276 TTA TTA TTA ATA TTA ATA ATA TATA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA
2835311 AATATTACAA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
3 64 0.91
4 6 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2835369 original size:20 final size:20
Alignment explanation
Indices: 2835333--2835370 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2835323 CCAAGACCCG
*
2835333 GAGGCCCGTTTTACAAATAT
1 GAGGCCCGTTATACAAATAT
2835353 GAGGCCCAGTTAT-CAAAT
1 GAGGCCC-GTTATACAAAT
2835371 TCCAGACCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
GAGGCCCGTTATACAAATAT
Found at i:2838118 original size:24 final size:22
Alignment explanation
Indices: 2838091--2838142 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 22
2838081 ATACACTTAT
2838091 TATTTTTATAATATTTATTATGTA
1 TATTTTTATAATATTT-TTAT-TA
*
2838115 TATTTTTATAATATTTTTATTT
1 TATTTTTATAATATTTTTATTA
2838137 TATTTT
1 TATTTT
2838143 CAAGTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 7 0.26
23 4 0.15
24 16 0.59
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTTTATAATATTTTTATTA
Found at i:2838142 original size:11 final size:11
Alignment explanation
Indices: 2838091--2838134 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
2838081 ATACACTTAT
2838091 TATTTTTATAA
1 TATTTTTATAA
*
2838102 TATTTATTATGTA
1 TATTT-TTAT-AA
2838115 TATTTTTATAA
1 TATTTTTATAA
2838126 TATTTTTAT
1 TATTTTTAT
2838135 TTTATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 15 0.52
12 8 0.28
13 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (11 bp):
TATTTTTATAA
Found at i:2844874 original size:114 final size:114
Alignment explanation
Indices: 2844673--2844896 Score: 394
Period size: 114 Copynumber: 2.0 Consensus size: 114
2844663 GTGCCACATT
2844673 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
2844738 GTTTGGTATAAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTG
66 GTTCGGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
2844787 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
2844852 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GTTCGGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
2844897 CTCCATGATC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTCGGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
Found at i:2847570 original size:22 final size:22
Alignment explanation
Indices: 2847541--2847595 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2847531 ATCTACACTC
2847541 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2847563 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2847585 TTCAAAGATGA
1 TTCAAAGATGA
2847596 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2848424 original size:75 final size:75
Alignment explanation
Indices: 2848276--2849057 Score: 1341
Period size: 75 Copynumber: 10.4 Consensus size: 75
2848266 ATTTCCCACG
*
2848276 TCTGTAAGTCCTGCAATGCATGATGTTTCCAAAAAGCCTTCGGGAG-TTTTTGATGTTTTCAAAG
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA-
2848340 CCTTAGGGTCA
65 CCTTAGGGTCA
2848351 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
*
2848416 CTTCGGGTCA
66 CTTAGGGTCA
* *
2848426 TCTGTAAGTCCTGCAGTGCATTATGTTTCCAAAATGCCTTCGGGAGCTTTTTGATGTTTTTCAAA
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTTCAAA
*
2848491 GACTTAGGGTCA
65 -CCTTAGGGTCA
2848503 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
*
2848568 CTTCGGGTCA
66 CTTAGGGTCA
2848578 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAG
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA-
2848643 CCTTAGGGTCA
65 CCTTAGGGTCA
* *
2848654 TCTGTAAGTCCTGCAGTGCATTATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
*
2848719 CTTCGGGTCA
66 CTTAGGGTCA
* *
2848729 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAAAC
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
* *
2848794 CTTCGAGTCA
66 CTTAGGGTCA
*
2848804 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
*
2848869 CTTCGGGTCA
66 CTTAGGGTCA
*
2848879 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
2848944 CTTAGGGTCA
66 CTTAGGGTCA
* *
2848954 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAG
1 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA-
2849019 CCTTAGGGTCA
65 CCTTAGGGTCA
*
2849030 TCTGTAAGTCCTTCAGTGCATGATGTTT
1 TCTGTAAGTCCTGCAGTGCATGATGTTT
2849058 TTAAAACCTT
Statistics
Matches: 678, Mismatches: 24, Indels: 9
0.95 0.03 0.01
Matches are distributed among these distances:
75 472 0.70
76 143 0.21
77 63 0.09
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (75 bp):
TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
CTTAGGGTCA
Found at i:2849058 original size:45 final size:45
Alignment explanation
Indices: 2849005--2849106 Score: 161
Period size: 45 Copynumber: 2.3 Consensus size: 45
2848995 AGGAGCTTTT
*
2849005 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCC-TTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAG-CCATTCAGTGCA
* *
2849050 TGATGTTTTTAAAACCTTCGGGTCATCTGTAAGCCATTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCATTCAGTGCA
2849095 TGATGTTTTCAA
1 TGATGTTTTCAA
2849107 CATTTCCATC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 2 0.04
45 50 0.96
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCATTCAGTGCA
Found at i:2849249 original size:3 final size:3
Alignment explanation
Indices: 2849241--2849311 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
2849231 CATTTTAAAT
** *
2849241 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2849289 TTA ATA ATA TATA TTA TTTA TTA
1 TTA TTA TTA T-TA TTA -TTA TTA
2849312 AATATTACAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2858101 original size:288 final size:286
Alignment explanation
Indices: 2857336--2858952 Score: 1488
Period size: 288 Copynumber: 5.7 Consensus size: 286
2857326 ATCTCAAAAA
* * ** *
2857336 TCGGATCGGGTGGAAGATTTAAAATTTTTGGGTCA-ACCTAGGTAGACCAAAAATCCGACCCGAC
1 TCGGATCAGGTGGAAGATTTAAAATTTTCGGGTCAGGTC-AGGTGGACCAAAAATCCGACCCGAC
* * *
2857400 TCGACCCATGCCCATCCTTAGTTGTGATAAAGTTAATTATATCACACGTCATAAACTGCCATCCT
65 T-----CATGCCCATCCCTAGTTGTGATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCT
* * *
2857465 TGGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTCTATTTCAAACTAGTCTTTTCATAT
125 TAGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATAT
* * * *
2857530 AAATTATTTCAGGTCGAGTTC-GGTCGGGCTCGGATTTTACCT-AAAAAATT--GT---GTT---
190 AAATTATTTCAGGTCGA-ATCGGGTCAGGTTCGGATTTTATCTCAAAAAATTGGGTCAGGTTCAA
* *
2857585 T--GGTGGAAGGGGTATATTTTTCTGG-TCGTGT
254 TCGGGTGGAAGGGATATATTTTTC-GGATCGAGT
* * * * * * *
2857616 TTGGATCTGGCGGAGGATTTAAAATTTTCGAGTCAGGT-TGAGTGGACCAAAAATCTGACCCGAC
1 TCGGATCAGGTGGAAGATTTAAAATTTTCGGGTCAGGTCAG-GTGGACCAAAAATCCGACCCGAC
* * * * * * * * * *
2857680 CCATGGCCATCTCTAATTGTGATAAAGTTAATTATGTCAAACGTCATAAACTGGCATCTTTAGAC
65 TCATGCCCATCCCTAGTTGTGATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGAC
* * * *
2857745 TTTTGAACGTTTCAATTTCATATAAATTATGAATTTTGTTTCAAATTAGTCTTTTCATATAAATT
130 TTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATATAAATT
* * * * **
2857810 ATTTCAGGTTGAACCGGGTCAGGTTCGAATTTTGTCTCAAAAAATTGGGTCAAATTCGAATCGGG
195 ATTTCAGGTCGAATCGGGTCAGGTTCGGATTTTATCTCAAAAAATTGGGTCAGGTTC-AATCGGG
2857875 TGGAAGGGATATATTTTTCGGATCGAGT
259 TGGAAGGGATATATTTTTCGGATCGAGT
* * * *
2857903 TCGAATCAGGTGGAAAATTTAAAATTTTTGGGGTCAGGTCGGGTGGACCAAAAATCCGACCCGAC
1 TCGGATCAGGTGGAAGATTTAAAA-TTTTCGGGTCAGGTCAGGTGGACCAAAAATCCGACCCGAC
* * * *
2857968 TCATGTCCATCCCTAGCTGTGATAGAGGTAATTATATCATACGTCCTAAACTGCCATCCTTAGAC
65 TCATGCCCATCCCTAGTTGTGATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGAC
* *
2858033 TTTTGAATGTTTC-AGTTTCATATAAATTATGAGTTTTATTTCAAATTAATCTTTTCATATAAAT
130 TTTTGAATGTTTCGA-TTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATATAAAT
* ** * * * * *
2858097 TATTTCAGGTCGAGTAAGGTTAAGTTCGGATTTTATCT-AAAAAATTGGGTCGGGTTCAGGTTGG
194 TATTTCAGGTCGAATCGGGTCAGGTTCGGATTTTATCTCAAAAAATTGGGTCAGGTTCA-ATCGG
* * *
2858161 ATGGAAGAGATATATTTTTCGGGTC-ATGT
258 GTGGAAGGGATATATTTTTCGGATCGA-GT
** * ** **
2858190 TCTAATCGGGTGGAAGATTTAAAATTTTCGGGTCAGGTCAAATGGACTGAAAATCCGA--C--C-
1 TCGGATCAGGTGGAAGATTTAAAATTTTCGGGTCAGGTCAGGTGGACCAAAAATCCGACCCGACT
* * * *
2858250 CATGCTCATCCTTAGTTGTGATAGAGTTAATTTTATCACAC-TCCTAAACT---A---TTAGACA
66 CATGCCCATCCCTAGTTGTGATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGACT
*
2858308 TTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTATTTTCATATAAATTA
131 TTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATATAAATTA
* * * * * ** ** * *
2858373 TTTTAGGTCGAATTGGATCAGGTTTGGATTTTATTTC-AAAAATTGAATCAGACTCGGATCGAGT
196 TTTCAGGTCGAATCGGGTCAGGTTCGGATTTTATCTCAAAAAATTGGGTCAGGTTC-AATCGGGT
* * * *
2858437 AGAAGGG-TATATTTTTTGGATTGGGT
260 GGAAGGGATATATTTTTCGGATCGAGT
* * * * * * * * * *
2858463 TCGGATCAAGTCGAGGTTTTAAAATTTTTGGGTCAAGTCTGGTGGACCGAAAATCCAATCCGAAC
1 TCGGATCAGGTGGAAGATTTAAAATTTTCGGGTCAGGTCAGGTGGACCAAAAATCCGACCCG-AC
* * * *
2858528 TCATGCCCATCCCTTGTTGTTTTAATAGAGTTAATAATATTACACGTCCTAAACTGCCATCCTTA
65 TCATGCCCATCCCTAGTTG---TGATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTA
* * *
2858593 GACTTTTGAATG-TTCGGATTTCGTATAAATTATTACTTTTATTTCAAATTAATCTTTTCATATA
127 GACTTTTGAATGTTTC-GATTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATATA
** ** * * * ** ** *
2858657 AATTATTTCAAATATAGTTGGGTCGGGTTCATATTTTATCTC-AAAAATCAGGTCGGGTTCCAAT
191 AATTATTTCAGGTCGAATCGGGTCAGGTTCGGATTTTATCTCAAAAAATTGGGTCAGGTT-CAAT
* * * * * * *
2858721 CAGGTAGAAGGGGTATTTTTTTCGGGTCTAAT
255 CGGGTGGAAGGGATATATTTTTCGGATCGAGT
* * * * * * * *
2858753 TCGGATTAGGTTGAGGATTTACAATTTTCGGGTCAGATTAGATGGACCGAAAATCCGACCCGAAC
1 TCGGATCAGGTGGAAGATTTAAAATTTTCGGGTCAGGTCAGGTGGACCAAAAATCCGACCCG-AC
* * ** *
2858818 -CATG-TCATCCCTAGTTGTGATAGAGTTAATTATATGACACGTGTTAAACTGTCATCCTTAGAC
65 TCATGCCCATCCCTAGTTGTGATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGAC
* * *
2858881 TTTTGAATGTTTGGATTTCATATAAAATATGACTTTTATTTCAAATTAGTCTTTTCATATAGATT
130 TTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATATAAATT
2858946 ATTTCAG
195 ATTTCAG
2858953 ATTTTATCTA
Statistics
Matches: 1083, Mismatches: 209, Indels: 85
0.79 0.15 0.06
Matches are distributed among these distances:
273 58 0.05
274 115 0.11
275 143 0.13
276 8 0.01
277 1 0.00
278 3 0.00
279 16 0.01
280 59 0.05
281 36 0.03
282 20 0.02
283 9 0.01
284 1 0.00
285 103 0.10
286 35 0.03
287 108 0.10
288 188 0.17
289 115 0.11
290 65 0.06
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (286 bp):
TCGGATCAGGTGGAAGATTTAAAATTTTCGGGTCAGGTCAGGTGGACCAAAAATCCGACCCGACT
CATGCCCATCCCTAGTTGTGATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGACT
TTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATATAAATTA
TTTCAGGTCGAATCGGGTCAGGTTCGGATTTTATCTCAAAAAATTGGGTCAGGTTCAATCGGGTG
GAAGGGATATATTTTTCGGATCGAGT
Found at i:2858370 original size:18 final size:19
Alignment explanation
Indices: 2858322--2858373 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
2858312 AATGTTTCGA
2858322 TTTCATATAAATTATGACT
1 TTTCATATAAATTATGACT
*
2858341 TTT-ATTTCAAATTA-GTA-T
1 TTTCATAT-AAATTATG-ACT
2858359 TTTCATATAAATTAT
1 TTTCATATAAATTAT
2858374 TTTAGGTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTCATATAAATTATGACT
Found at i:2858577 original size:563 final size:560
Alignment explanation
Indices: 2857352--2858952 Score: 1642
Period size: 563 Copynumber: 2.8 Consensus size: 560
2857342 CGGGTGGAAG
* * * *
2857352 ATTTAAAATTTTT-GGGTCAA-CCTAGGTAGACCAAAAATCCGACCCGACTCGACCCATGCCCAT
1 ATTTAAAATTTTTGGGGTCAAGTC-GGGTGGACCAAAAATCCAACCCGACT-----CATGCCCAT
* * * * * *
2857415 CCTTAGTTGTGATAAAGTTAATTATATCACACGTCATAAACTGCCATCCTTGGACTTTTGAATGT
60 CCCTAGCTGTAATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGACTTTTGAATGT
* * *
2857480 TTCGATTTCATATAAATTATGACTTCTATTTCAAACTAGTCTTTTCATATAAATTATTTCAGGTC
125 TTCGATTTCATATAAATTATGACTTTTATTTCAAATTAATCTTTTCATATAAATTATTTCAGGTC
* * *
2857545 GAGTTCGGTCGGGCTCGGATTTTACCTAAAAAATT-GT---G-T--TTGGTGGAAGGGGTATATT
190 GAGTTAGGTCGGGTTCGGATTTTATCTAAAAAATTGGTCGGGTTCATTGGTGGAAGGGGTATATT
* * * * * * *
2857603 TTTCTGGTCGTGTT-TGGATCTGGCGGAGGATTTAAAATTTTCGAGTCAGGTTGAGTGGACCAAA
255 TTTCGGGTC-TGTTCT-GATCAGGTGGAGGATTTAAAATTTTCGGGTCAGGTTAAATGGACCGAA
* * * *
2857667 AATCTGACCCGACCCATGGC-CAT-CTCTAATTGTGATAAAGTTAATTATGTCAAACGTCATAAA
318 AA--T---CCGACCCAT-GCTCATCCT-TAGTTGTGATAGAGTTAATTATATCACACGTCATAAA
* * * *
2857730 CTGGCATCTTTAGACTTTTGAACGTTTCAATTTCATATAAATTATGAATTTTGTTTCAAATTAGT
376 CT--CA-C-TTAGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGT
* * * **
2857795 CTTTTCATATAAATTATTTCAGGTTGAACCGGGTCAGGTTCGAATTTTGTCTCAAAAAATTGGGT
437 CTTTTCATATAAATTATTTCAGGTCGAACCGGATCAGGTTCGAATTTTATCTCAAAAAATTGAAT
* * * * *
2857860 CAAATTCGAATCGGGTGGAAGGGATATATTTTTCGGATCGAGTTCGAATCAGGTGGAAA
502 CAAACTCGAATCGAGTAGAAGGGATATATTTTTCGGATCGAGTTCGAATCAAGTCGAAA
* * *
2857919 ATTTAAAATTTTTGGGGTCAGGTCGGGTGGACCAAAAATCCGACCCGACTCATGTCCATCCCTAG
1 ATTTAAAATTTTTGGGGTCAAGTCGGGTGGACCAAAAATCCAACCCGACTCATGCCCATCCCTAG
* * *
2857984 CTGTGATAGAGGTAATTATATCATACGTCCTAAACTGCCATCCTTAGACTTTTGAATGTTTC-AG
66 CTGTAATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGACTTTTGAATGTTTCGA-
* *
2858048 TTTCATATAAATTATGAGTTTTATTTCAAATTAATCTTTTCATATAAATTATTTCAGGTCGAGTA
130 TTTCATATAAATTATGACTTTTATTTCAAATTAATCTTTTCATATAAATTATTTCAGGTCGAGTT
*** * *
2858113 AGGTTAAGTTCGGATTTTATCTAAAAAATTGGGTCGGGTTCAGGTTGGATGGAAGAGATATATTT
195 AGGTCGGGTTCGGATTTTATCTAAAAAATT-GGTCGGGTTCA--TTGG-TGGAAGGGGTATATTT
* * * * *
2858178 TTCGGGTCATGTTCTAATCGGGTGGAAGATTTAAAATTTTCGGGTCAGGTCAAATGGACTGAAAA
256 TTCGGGTC-TGTTCTGATCAGGTGGAGGATTTAAAATTTTCGGGTCAGGTTAAATGGACCGAAAA
* *
2858243 TCCGACCCATGCTCATCCTTAGTTGTGATAGAGTTAATTTTATCACAC-TCCTAAACT-A-TTAG
320 TCCGACCCATGCTCATCCTTAGTTGTGATAGAGTTAATTATATCACACGTCATAAACTCACTTAG
* *
2858305 ACATTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTATTTTCATATAAA
385 ACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATATAAA
* ** * * * * *
2858370 TTATTTTAGGTCGAATTGGATCAGGTTTGGATTTTATTTC-AAAAATTGAATCAGACTCGGATCG
450 TTATTTCAGGTCGAACCGGATCAGGTTCGAATTTTATCTCAAAAAATTGAATCAAACTCGAATCG
* * * * **
2858434 AGTAGAAGGG-TATATTTTTTGGATTGGGTTCGGATCAAGTCGAGG
515 AGTAGAAGGGATATATTTTTCGGATCGAGTTCGAATCAAGTCGAAA
* * * * *
2858479 TTTTAAAATTTTT-GGGTCAAGTCTGGTGGACCGAAAATCCAATCCGAACTCATGCCCATCCCTT
1 ATTTAAAATTTTTGGGGTCAAGTCGGGTGGACCAAAAATCCAACCCG-ACTCATGCCCATCCCTA
* * *
2858543 GTTGTTTTAATAGAGTTAATAATATTACACGTCCTAAACTGCCATCCTTAGACTTTTGAATG-TT
65 GCTG---TAATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGACTTTTGAATGTTT
* * ** **
2858607 CGGATTTCGTATAAATTATTACTTTTATTTCAAATTAATCTTTTCATATAAATTATTTCAAATAT
127 C-GATTTCATATAAATTATGACTTTTATTTCAAATTAATCTTTTCATATAAATTATTTCAGGTCG
* ** * * * *
2858672 AGTTGGGTCGGGTTCATATTTTATCTCAAAAATCAGGTCGGGTTCCAATCAGGTAGAAGGGGTAT
191 AGTTAGGTCGGGTTCGGATTTTATCTAAAAAAT-TGGTCGGGTT-C-AT-TGGTGGAAGGGGTAT
* * * * * * * *
2858737 TTTTTTCGGGTCTAATTCGGATTAGGTTGAGGATTTACAATTTTCGGGTCAGATTAGATGGACCG
252 ATTTTTCGGGTCT-GTTCTGATCAGGTGGAGGATTTAAAATTTTCGGGTCAGGTTAAATGGACCG
* * **
2858802 AAAATCCGACCCGAACCATG-TCATCCCTAGTTGTGATAGAGTTAATTATATGACACGTGTTAAA
316 AAAATCCGA--C---CCATGCTCATCCTTAGTTGTGATAGAGTTAATTATATCACACGTCATAAA
* *
2858866 CTGTCATCCTTAGACTTTTGAATGTTTGGATTTCATATAAAATATGACTTTTATTTCAAATTAGT
376 C--TCA--CTTAGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGT
*
2858931 CTTTTCATATAGATTATTTCAG
437 CTTTTCATATAAATTATTTCAG
2858953 ATTTTATCTA
Statistics
Matches: 863, Mismatches: 131, Indels: 73
0.81 0.12 0.07
Matches are distributed among these distances:
559 28 0.03
560 57 0.07
561 27 0.03
562 99 0.11
563 360 0.42
564 4 0.00
565 5 0.01
567 46 0.05
568 52 0.06
569 38 0.04
570 3 0.00
571 1 0.00
572 1 0.00
573 4 0.00
574 137 0.16
575 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (560 bp):
ATTTAAAATTTTTGGGGTCAAGTCGGGTGGACCAAAAATCCAACCCGACTCATGCCCATCCCTAG
CTGTAATAGAGTTAATTATATCACACGTCCTAAACTGCCATCCTTAGACTTTTGAATGTTTCGAT
TTCATATAAATTATGACTTTTATTTCAAATTAATCTTTTCATATAAATTATTTCAGGTCGAGTTA
GGTCGGGTTCGGATTTTATCTAAAAAATTGGTCGGGTTCATTGGTGGAAGGGGTATATTTTTCGG
GTCTGTTCTGATCAGGTGGAGGATTTAAAATTTTCGGGTCAGGTTAAATGGACCGAAAATCCGAC
CCATGCTCATCCTTAGTTGTGATAGAGTTAATTATATCACACGTCATAAACTCACTTAGACTTTT
GAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATTAGTCTTTTCATATAAATTATTT
CAGGTCGAACCGGATCAGGTTCGAATTTTATCTCAAAAAATTGAATCAAACTCGAATCGAGTAGA
AGGGATATATTTTTCGGATCGAGTTCGAATCAAGTCGAAA
Found at i:2858659 original size:18 final size:19
Alignment explanation
Indices: 2858611--2858661 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
2858601 AATGTTCGGA
* *
2858611 TTTCGTATAAATTATTACT
1 TTTCATATAAATTAATACT
*
2858630 TTT-ATTTCAAATTAAT-CT
1 TTTCATAT-AAATTAATACT
2858648 TTTCATATAAATTA
1 TTTCATATAAATTA
2858662 TTTCAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTCATATAAATTAATACT
Found at i:2859144 original size:268 final size:255
Alignment explanation
Indices: 2858802--2859472 Score: 711
Period size: 268 Copynumber: 2.6 Consensus size: 255
2858792 AGATGGACCG
* * * * *
2858802 AAAATCCGACCCGAACCATG----TCATCCCTAGTTGTGATAGAGTTAATTATATGACACGTGT-
1 AAAATCCGACCCGACCCATGACTATCCTCCCTAATTGTGATAGAGTTAATTATATCACACAT-TC
* * *
2858862 TAAACTGTCATCCTTAGACTTTTGAATGTTTGGATTTCATATAAAATATGACTTTTATTTCAAAT
65 TAAACTGACATCCTTAGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAAT
* * * *
2858927 TAGTCTTTTCATATAGATTATTTCAGATTTTATCTAAAAAAAATAA-ACAAATTAGGATCGTGAG
130 TAGTCTTTTCATATAAATTATTTCAG--GTTATCT--AAAAAATAAGAC-AAGT-GGA-AG-GAG
*
2858991 TATATTTTTTGAAATC-GAGTTCGGA-TAAG-GCATAGGATTAAAAATTTTAGGTCAGATCGAGT
187 TATA-TTTTTCAAATCAG-GTTCGGATTAAGTGCAT-GGATTAAAAATTTTAGGTCAGATCGAGT
2859053 GGA-CCA
249 GGATCCA
2859059 AAAATCCGACCCGACCCGACCTGACTCATGCCCGTCCCTAATTGTGATAGAGTTAATTATATCAC
1 AAAATCCGACCCGACCC-A--TGACT-AT--CC-TCCCTAATTGTGATAGAGTTAATTATATCAC
* * *
2859124 ACATTCTAAACTGCCATCCTTAGACTTTTGAATGTTTCGATTTCATGTAAATTATGACTTTTATC
59 ACATTCTAAACTGACATCCTTAGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATT
* * * * ** *
2859189 TCAAATTAATATTTTCCTATAAAATTATTTCAGGTTATCTAAAAAATAAGTCGGGTGGAAGGGGT
124 TCAAATTAGTCTTTTCATAT-AAATTATTTCAGGTTATCTAAAAAATAAGACAAGTGGAAGGAGT
** ** * * * * * *
2859254 ATATTTTTCAGGTCAGGTTCGGATTGGGTGGATGGTTTAAAATTTTTGGGTCAGGTCGGGTGGAT
188 ATATTTTTCAAATCAGGTTCGGATTAAGTGCATGGATTAAAAATTTTAGGTCAGATCGAGTGGAT
*
2859319 CGA
253 CCA
* * * * *
2859322 AAAATTCGACCCGACCCATGCCTATCCT---TATTTATGATAGAGTTAATTATATCACACATCCT
1 AAAATCCGACCCGACCCATGACTATCCTCCCTAATTGTGATAGAGTTAATTATATCACACATTCT
*
2859384 AAATTGACATCCTTAGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATT
66 AAACTGACATCCTTAGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATT
2859449 AGTCTTTTCATATAAATTATTTCA
131 AGTCTTTTCATATAAATTATTTCA
2859473 TGTCGAATAG
Statistics
Matches: 351, Mismatches: 45, Indels: 41
0.80 0.10 0.09
Matches are distributed among these distances:
252 11 0.03
253 102 0.29
256 1 0.00
257 18 0.05
258 1 0.00
259 2 0.01
260 6 0.02
261 15 0.04
262 36 0.10
263 22 0.06
264 3 0.01
265 11 0.03
266 1 0.00
267 8 0.02
268 103 0.29
269 11 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (255 bp):
AAAATCCGACCCGACCCATGACTATCCTCCCTAATTGTGATAGAGTTAATTATATCACACATTCT
AAACTGACATCCTTAGACTTTTGAATGTTTCGATTTCATATAAATTATGACTTTTATTTCAAATT
AGTCTTTTCATATAAATTATTTCAGGTTATCTAAAAAATAAGACAAGTGGAAGGAGTATATTTTT
CAAATCAGGTTCGGATTAAGTGCATGGATTAAAAATTTTAGGTCAGATCGAGTGGATCCA
Found at i:2859465 original size:18 final size:19
Alignment explanation
Indices: 2859417--2859468 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
2859407 AATGTTTCGA
2859417 TTTCATATAAATTATGACT
1 TTTCATATAAATTATGACT
* *
2859436 TTT-ATTTCAAATTA-GTCT
1 TTTCATAT-AAATTATGACT
2859454 TTTCATATAAATTAT
1 TTTCATATAAATTAT
2859469 TTCATGTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTCATATAAATTATGACT
Found at i:2859746 original size:18 final size:20
Alignment explanation
Indices: 2859698--2859748 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
2859688 AATGCTTCAA
2859698 TTTCATATAAATT-ATGCAT
1 TTTCATATAAATTAATGCAT
*
2859717 TTT-ATTTCAAATTAAT-C-T
1 TTTCATAT-AAATTAATGCAT
2859735 TTTCATATAAATTA
1 TTTCATATAAATTA
2859749 TTTCAGGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 13 0.48
19 12 0.44
20 2 0.07
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTCATATAAATTAATGCAT
Found at i:2860510 original size:20 final size:20
Alignment explanation
Indices: 2860485--2860933 Score: 496
Period size: 20 Copynumber: 22.2 Consensus size: 20
2860475 AATGACCAAC
*
2860485 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
2860505 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
2860525 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
2860545 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
2860566 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
2860587 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
2860608 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
2860629 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
2860651 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
2860669 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2860689 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2860709 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
2860731 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
2860749 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2860769 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2860791 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2860809 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2860831 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2860849 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2860871 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2860891 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2860909 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2860929 AAAAT
1 AAAAT
2860934 GAGTAAATTC
Statistics
Matches: 376, Mismatches: 24, Indels: 58
0.82 0.05 0.13
Matches are distributed among these distances:
18 14 0.04
20 306 0.81
21 13 0.03
22 43 0.11
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:2861040 original size:6 final size:6
Alignment explanation
Indices: 2861029--2861073 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
2861019 GACACGTATT
2861029 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2861074 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2861432 original size:6 final size:6
Alignment explanation
Indices: 2861421--2861531 Score: 222
Period size: 6 Copynumber: 18.5 Consensus size: 6
2861411 TCTCGTCTCG
2861421 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2861469 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2861517 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
2861532 AATACGTGTC
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 105 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2861652 original size:20 final size:20
Alignment explanation
Indices: 2861627--2861914 Score: 261
Period size: 20 Copynumber: 14.2 Consensus size: 20
2861617 GAATTTACTC
2861627 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
2861647 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
2861667 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
*
2861687 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
2861707 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
2861727 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
*
2861747 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
2861767 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* *
2861789 ATTCTCTTAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
2861809 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
*
2861831 ATTTTCTT--TTGACCGTTGCG
1 ATTTTCTTAATCG--CGTTGCG
* *
2861851 ATTTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
*
2861871 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
2861891 A-TTT-TTATTTCGCGTTGCG
1 ATTTTCTTA-ATCGCGTTGCG
2861910 ATTTT
1 ATTTT
2861915 GTTGGTCATT
Statistics
Matches: 222, Mismatches: 27, Indels: 38
0.77 0.09 0.13
Matches are distributed among these distances:
18 13 0.06
19 14 0.06
20 148 0.67
21 12 0.05
22 35 0.16
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:2864564 original size:21 final size:21
Alignment explanation
Indices: 2864538--2864579 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2864528 CCAGAATGGG
*
2864538 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2864559 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2864580 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2864718 original size:20 final size:20
Alignment explanation
Indices: 2864693--2864769 Score: 94
Period size: 20 Copynumber: 4.1 Consensus size: 20
2864683 AAACCATACA
2864693 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
2864713 GGGGGGAATCTGT--TCCC-
1 GGGGGGAATCTGTACCCCCT
2864730 --GGGGAATC-GATACCCCCT
1 GGGGGGAATCTG-TACCCCCT
2864748 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
2864768 GG
1 GG
2864770 ACAATCTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
14 1 0.02
15 9 0.19
17 3 0.06
18 3 0.06
20 31 0.65
21 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.19
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:2867607 original size:35 final size:35
Alignment explanation
Indices: 2867567--2867652 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
2867557 AAAACAGTCA
* * *
2867567 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
2867602 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
2867637 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
2867653 ATACTTCAAT
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:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:2867646 original size:21 final size:21
Alignment explanation
Indices: 2867621--2867663 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2867611 TTCTAAACCC
2867621 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
2867642 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
2867663 T
1 T
2867664 TAAGGTAATA
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:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:2867818 original size:16 final size:18
Alignment explanation
Indices: 2867786--2867819 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2867776 TATTAATGTA
2867786 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
2867804 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
2867820 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:2868490 original size:130 final size:130
Alignment explanation
Indices: 2868287--2868534 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
2868277 AATTTTCTTC
* * *
2868287 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
2868352 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
2868417 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
2868482 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
2868535 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:2869476 original size:31 final size:31
Alignment explanation
Indices: 2869441--2869504 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
2869431 GAGTATATGA
* * *
2869441 TCTCTAATATTATTAATTTGTTCGATTTTAG
1 TCTCTAACATTATTAATATATTCGATTTTAG
*
2869472 TCTCTAACATTATTGATATATTCGATTTTAG
1 TCTCTAACATTATTAATATATTCGATTTTAG
2869503 TC
1 TC
2869505 ATTCAACCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (31 bp):
TCTCTAACATTATTAATATATTCGATTTTAG
Found at i:2870344 original size:17 final size:16
Alignment explanation
Indices: 2870307--2870378 Score: 92
Period size: 16 Copynumber: 4.4 Consensus size: 16
2870297 TTTGAAATTG
*
2870307 AAAT-TAATAACAAAT
1 AAATATAATAATAAAT
*
2870322 AAATATAATAATAATT
1 AAATATAATAATAAAT
2870338 AAAATATAATAATAAAT
1 -AAATATAATAATAAAT
2870355 AAATATAATAATTAAAAT
1 AAATATAATAA-T-AAAT
2870373 AAATAT
1 AAATAT
2870379 TTTATAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.08
16 20 0.40
17 16 0.32
18 10 0.20
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATAATAATAAAT
Found at i:2870355 original size:33 final size:32
Alignment explanation
Indices: 2870302--2870366 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
2870292 GAACCTTTGA
*
2870302 AATTGAAATTAATAACAAATAAATATAATAAT
1 AATTAAAATTAATAACAAATAAATATAATAAT
*
2870334 AATTAAAATATAATAATAAATAAATATAATAAT
1 AATTAAAAT-TAATAACAAATAAATATAATAAT
2870367 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (32 bp):
AATTAAAATTAATAACAAATAAATATAATAAT
Found at i:2870386 original size:33 final size:29
Alignment explanation
Indices: 2870319--2870402 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
2870309 ATTAATAACA
*
2870319 AATAAATATAATAATAATTAAAATATAAT
1 AATAAATAAAATAATAATTAAAATATAAT
2870348 AATAAATAAATATAATAATTAAAATA-AAT
1 AATAAATAAA-ATAATAATTAAAATATAAT
* ** *
2870377 ATTTTAT-AAATAATAATTATAATATA
1 AATAAATAAAATAATAATTAAAATATA
2870403 TTTTGTAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
27 14 0.29
28 3 0.06
29 16 0.33
30 15 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AATAAATAAAATAATAATTAAAATATAAT
Found at i:2870392 original size:36 final size:33
Alignment explanation
Indices: 2870307--2870375 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2870297 TTTGAAATTG
* *
2870307 AAAT-TAATAACAAATAAATATAATAATAATTA
1 AAATATAATAATAAATAAATATAATAATAAATA
2870339 AAATATAATAATAAATAAATATAATAATTAAAATA
1 AAATATAATAATAAATAAATATAATAA-T-AAATA
2870374 AA
1 AA
2870376 TATTTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 4 0.12
33 21 0.66
34 1 0.03
35 6 0.19
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (33 bp):
AAATATAATAATAAATAAATATAATAATAAATA
Found at i:2870795 original size:20 final size:19
Alignment explanation
Indices: 2870770--2870835 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
2870760 TTAATTAATA
2870770 TTATTTTATATTTTTAGTAT
1 TTATTTTAT-TTTTTAGTAT
*
2870790 TTA-TTTATTTGTTTTGGTAT
1 TTATTTTA-TT-TTTTAGTAT
** * *
2870810 TTAAATAATTTTTTAATAT
1 TTATTTTATTTTTTAGTAT
2870829 TTATTTT
1 TTATTTT
2870836 GTAGCAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
19 16 0.46
20 17 0.49
21 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (19 bp):
TTATTTTATTTTTTAGTAT
Found at i:2873621 original size:64 final size:64
Alignment explanation
Indices: 2873488--2873644 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
2873478 TAATGAAGGT
* * * ** *
2873488 ATGCATCGATGCACCACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
* * *
2873552 ATGCATCGATGCACTACTTATGCATCGATGCATTAATTGCATTCGATGTT-T-TTATCTTAAA-A
1 ATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTA--TTAAAGA
2873614 G
64 G
*
2873615 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTAATGCATCGAT
2873645 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 74 0.93
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
Found at i:2875850 original size:23 final size:23
Alignment explanation
Indices: 2875820--2875870 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2875810 TTACTATATT
2875820 TAATTATT-TATTATATTTAATAA
1 TAATTATTATATT-TATTTAATAA
* *
2875843 TAATTATTATATTTATTTATTAT
1 TAATTATTATATTTATTTAATAA
2875866 TAATT
1 TAATT
2875871 TCAATTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TAATTATTATATTTATTTAATAA
Found at i:2875851 original size:19 final size:17
Alignment explanation
Indices: 2875806--2875876 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 17
2875796 AATATATATT
*
2875806 TTAATTACTATATTTAA
1 TTAATTATTATATTTAA
*
2875823 TTATTTATTATATTTAA
1 TTAATTATTATATTTAA
2875840 TAATAATTATTATATTT-A
1 T--TAATTATTATATTTAA
*
2875858 TTTATTATTA-ATTTCAA
1 TTAATTATTATATTT-AA
2875875 TT
1 TT
2875877 TCAAAGGTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.09
16 8 0.17
17 19 0.41
18 2 0.04
19 13 0.28
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATTATTATATTTAA
Found at i:2876547 original size:24 final size:25
Alignment explanation
Indices: 2876495--2876547 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
2876485 GAGTAAAAGT
* *
2876495 TAAAACAACAAATTTAATTAAATAT
1 TAAAACAAAAAATTTAATTAAATAA
* *
2876520 TAAAATAAAAAATTT-ATTAATTAA
1 TAAAACAAAAAATTTAATTAAATAA
2876544 TAAA
1 TAAA
2876548 CTAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
TAAAACAAAAAATTTAATTAAATAA
Found at i:2880255 original size:12 final size:12
Alignment explanation
Indices: 2880238--2880262 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2880228 GCTATCACTT
2880238 GACTTCAAAACC
1 GACTTCAAAACC
2880250 GACTTCAAAACC
1 GACTTCAAAACC
2880262 G
1 G
2880263 TATTTCCGAT
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:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (12 bp):
GACTTCAAAACC
Found at i:2885291 original size:13 final size:13
Alignment explanation
Indices: 2885273--2885315 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2885263 TCAAAAAAAC
2885273 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
*
2885286 AAAAAAAGGTAAA
1 AAAAAAAGGCAAA
*
2885299 AAAACAAA-ACAAA
1 AAAA-AAAGGCAAA
2885312 AAAA
1 AAAA
2885316 CCAAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 23 0.88
14 3 0.12
ACGTcount: A:0.81, C:0.07, G:0.09, T:0.02
Consensus pattern (13 bp):
AAAAAAAGGCAAA
Found at i:2891397 original size:32 final size:30
Alignment explanation
Indices: 2891333--2891397 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
2891323 TCAAACTGAC
* * *
2891333 ATTTTATCAAAATTTAGGAACTAAATAAAT
1 ATTTTATCAAAACTTAAGAACCAAATAAAT
*
2891363 ATTTTATCTAAAACTTAATAACCAAATTAAAT
1 ATTTTATC-AAAACTTAAGAACCAAA-TAAAT
2891395 ATT
1 ATT
2891398 AATCTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 8 0.28
31 13 0.45
32 8 0.28
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (30 bp):
ATTTTATCAAAACTTAAGAACCAAATAAAT
Found at i:2892051 original size:4 final size:4
Alignment explanation
Indices: 2892042--2892144 Score: 55
Period size: 4 Copynumber: 24.5 Consensus size: 4
2892032 ATATCCCTTC
* * * * * * *
2892042 AAAT AAAT AAAT AAAT AAAT TACT AATT TATT CGAAAT AAAT GAAT AAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAAT
* * *
2892092 AAAT AAAT AAAT GATT CGAAAT AAAT AAAT AATTT AAAAT AAAT -AAT
1 AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AA-AT -AAAT AAAT AAAT
2892139 AAAT AA
1 AAAT AA
2892145 TCAAACACAT
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
3 3 0.04
4 64 0.85
5 2 0.03
6 6 0.08
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:2892089 original size:34 final size:34
Alignment explanation
Indices: 2892042--2892123 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
2892032 ATATCCCTTC
* * * * *
2892042 AAATAAATAAATAAATAAATTACTAATTTATTCG
1 AAATAAATAAATAAAGAAATAAATAAATGATTCG
*
2892076 AAATAAATGAATAAAGAAATAAATAAATGATTCG
1 AAATAAATAAATAAAGAAATAAATAAATGATTCG
2892110 AAATAAATAAATAA
1 AAATAAATAAATAA
2892124 TTTAAAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (34 bp):
AAATAAATAAATAAAGAAATAAATAAATGATTCG
Found at i:2892114 original size:18 final size:18
Alignment explanation
Indices: 2892071--2892137 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
2892061 TTACTAATTT
*
2892071 ATTCGAAATAAATGAATA
1 ATTCGAAATAAATAAATA
* *
2892089 A--AGAAATAAATAAATG
1 ATTCGAAATAAATAAATA
2892105 ATTCGAAATAAATAAATA
1 ATTCGAAATAAATAAATA
**
2892123 ATTTAAAATAAATAA
1 ATTCGAAATAAATAA
2892138 TAAATAATCA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 13 0.32
18 27 0.68
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (18 bp):
ATTCGAAATAAATAAATA
Found at i:2897287 original size:24 final size:24
Alignment explanation
Indices: 2897211--2897294 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
2897201 TGAATTTTGT
* *
2897211 TATGGTACCTGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
* *
2897235 TATGATA-TTGGCATGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
* *
2897258 TATGATACATGACCTGGATTGTGA
1 TATGATACTTGACCTGGATTCTGA
*
2897282 TCTGATACTTGAC
1 TATGATACTTGAC
2897295 TTGAATTATA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
23 20 0.41
24 29 0.59
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTGA
Found at i:2897418 original size:35 final size:35
Alignment explanation
Indices: 2897372--2897445 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
2897362 GGAGGAAGAA
*
2897372 TACTTGGAGGCTCATCGACTTTGTGCTCAGGGCCT
1 TACTTGCAGGCTCATCGACTTTGTGCTCAGGGCCT
* *
2897407 TACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCCT
1 TACTTGCAGGCTCATCGACTTTGTGCTCAGGGCCT
2897442 TACT
1 TACT
2897446 GTTCGTGACG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.12, C:0.28, G:0.27, T:0.32
Consensus pattern (35 bp):
TACTTGCAGGCTCATCGACTTTGTGCTCAGGGCCT
Found at i:2902789 original size:24 final size:23
Alignment explanation
Indices: 2902770--2902840 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
2902760 GTTATGGTAC
2902770 CAGACCTGGATTCTGATATGATA
1 CAGACCTGGATTCTGATATGATA
** * *
2902793 TTGGCATGGATTCTGATATGATA
1 CAGACCTGGATTCTGATATGATA
*
2902816 CATGACCTGGATTCTGATCTGATA
1 CA-GACCTGGATTCTGATATGATA
2902840 C
1 C
2902841 TTGACTTGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (23 bp):
CAGACCTGGATTCTGATATGATA
Found at i:2902845 original size:24 final size:24
Alignment explanation
Indices: 2902772--2902845 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
2902762 TATGGTACCA
2902772 GACCTGGATTCTGATATGATA-TT
1 GACCTGGATTCTGATATGATACTT
* * *
2902795 GGCATGGATTCTGATATGATACAT
1 GACCTGGATTCTGATATGATACTT
*
2902819 GACCTGGATTCTGATCTGATACTT
1 GACCTGGATTCTGATATGATACTT
2902843 GAC
1 GAC
2902846 TTGAATTATG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 19 0.44
24 24 0.56
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (24 bp):
GACCTGGATTCTGATATGATACTT
Found at i:2902970 original size:35 final size:35
Alignment explanation
Indices: 2902924--2902997 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
2902914 GGAGGAAGAA
*
2902924 TACTTGGAGGCTCATCGAATTTGTGCTCAGGGCCT
1 TACTTGCAGGCTCATCGAATTTGTGCTCAGGGCCT
**
2902959 TACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCCT
1 TACTTGCAGGCTCATCGAATTTGTGCTCAGGGCCT
2902994 TACT
1 TACT
2902998 GTTCGTGACG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.15, C:0.26, G:0.27, T:0.32
Consensus pattern (35 bp):
TACTTGCAGGCTCATCGAATTTGTGCTCAGGGCCT
Found at i:2908100 original size:20 final size:20
Alignment explanation
Indices: 2908075--2908112 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2908065 TTCCACTTGA
2908075 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
2908095 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
2908113 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:2908128 original size:24 final size:20
Alignment explanation
Indices: 2908075--2908132 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
2908065 TTCCACTTGA
*
2908075 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAC
2908095 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
2908118 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2908133 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2908198 original size:64 final size:63
Alignment explanation
Indices: 2908120--2908260 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 63
2908110 TCTTTAACAT
* *
2908120 GTGCATCGATGCACTACC-CATGCATCGATACA-CAAATTACCTTCGATGTTTTCAT-TTTAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACATC-AATTACATTCGATG-TTTCATCTTTAAAG
*
2908182 G
63 A
* * *
2908183 GATGCATCGATGCACTCCTTATGCATCGATGCATCAATTACATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
2908247 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2908261 ATTGAATATG
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
63 21 0.31
64 46 0.68
65 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:2911770 original size:18 final size:18
Alignment explanation
Indices: 2911749--2911800 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
2911739 TCTTCTTCTT
*
2911749 CCTTCATCCTTCCTTCAC
1 CCTTCATTCTTCCTTCAC
*
2911767 CCTTCATTCTTACTTCAC
1 CCTTCATTCTTCCTTCAC
2911785 CCTTCATTCTTCCTTC
1 CCTTCATTCTTCCTTC
2911801 TCACACTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (18 bp):
CCTTCATTCTTCCTTCAC
Found at i:2919279 original size:20 final size:20
Alignment explanation
Indices: 2919251--2919342 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
2919241 GGGCATAATA
2919251 GTATCGATACTATAGATATG
1 GTATCGATACTATAGATATG
* * * *
2919271 GTATTGATATTGTAGATGTG
1 GTATCGATACTATAGATATG
* *
2919291 GTATCAATACTCATACA-ATGG
1 GTATCGATACT-ATAGATAT-G
* * *
2919312 GTATCGATATTGTAGATGTG
1 GTATCGATACTATAGATATG
*
2919332 GTATTGATACT
1 GTATCGATACT
2919343 CGTAGGGTGG
Statistics
Matches: 52, Mismatches: 17, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (20 bp):
GTATCGATACTATAGATATG
Found at i:2919607 original size:20 final size:20
Alignment explanation
Indices: 2919582--2919632 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2919572 TAGTTAGTTA
*
2919582 GTATCGGTACTAAAAGGTGG
1 GTATCGATACTAAAAGGTGG
2919602 GTATCGATACTAAAAGGTGG
1 GTATCGATACTAAAAGGTGG
2919622 GTATCGATACT
1 GTATCGATACT
2919633 TAGGGGTCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.27
Consensus pattern (20 bp):
GTATCGATACTAAAAGGTGG
Found at i:2920649 original size:21 final size:22
Alignment explanation
Indices: 2920616--2920657 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2920606 TAAAACTGTC
2920616 AAATATTATAAAA-TAATATTT
1 AAATATTATAAAATTAATATTT
2920637 AAAT-TTATCAAAATTAATATT
1 AAATATTAT-AAAATTAATATT
2920658 ATTTTATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATTATAAAATTAATATTT
Found at i:2921115 original size:3 final size:3
Alignment explanation
Indices: 2921107--2921174 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
2921097 AGTTTCTTCA
2921107 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2921155 AAT AAT GAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AA
2921175 ATCGCAGCGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2922057 original size:89 final size:89
Alignment explanation
Indices: 2921906--2922073 Score: 241
Period size: 89 Copynumber: 1.9 Consensus size: 89
2921896 CAATGCATGC
* * *
2921906 AATTTGAATTCGGTTTATGTATATTTTTAATTGCTTTGATTCATTTTAAATTGTCATTTTTTATG
1 AATTTGAATTCGGTTAATGTAGATTTTTAATTGCTTTAATTCATTTTAAATTGTCATTTTTTATG
2921971 AACTTATTTGGTGACGGTGAACGA
66 AACTTATTTGGTGACGGTGAACGA
* ** *
2921995 AATTTGAATTTGGTTAATGTAGATTTTTAATTGCTTTTAATTTGTTTTAAAATT-TTA-TTTTTA
1 AATTTGAATTCGGTTAATGTAGATTTTTAATTGC-TTTAATTCATTTT-AAATTGTCATTTTTTA
2922058 TGAACTTATTTGGTGA
64 TGAACTTATTTGGTGA
2922074 ACATTCTCCT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
89 53 0.76
90 12 0.17
91 5 0.07
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.52
Consensus pattern (89 bp):
AATTTGAATTCGGTTAATGTAGATTTTTAATTGCTTTAATTCATTTTAAATTGTCATTTTTTATG
AACTTATTTGGTGACGGTGAACGA
Found at i:2930718 original size:21 final size:20
Alignment explanation
Indices: 2930670--2930716 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
2930660 AATATGTAAA
2930670 GTAATATCCTACATTAACTAT
1 GTAATATCCTACATTAAC-AT
*
2930691 GTAATATCTTACATTAA-AT
1 GTAATATCCTACATTAACAT
*
2930710 GTCATAT
1 GTAATAT
2930717 ATATTAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
21 16 0.67
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (20 bp):
GTAATATCCTACATTAACAT
Found at i:2939260 original size:16 final size:18
Alignment explanation
Indices: 2939224--2939260 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2939214 TTTGTATGTG
2939224 TTTTTATAATATTAAATT
1 TTTTTATAATATTAAATT
*
2939242 TTTTTATTATA-TAAATT
1 TTTTTATAATATTAAATT
2939259 TT
1 TT
2939261 GAGACTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTATAATATTAAATT
Done.