Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 51
Found at i:3109411 original size:55 final size:51
Alignment explanation
Indices: 3109297--3109422 Score: 135
Period size: 55 Copynumber: 2.4 Consensus size: 51
3109287 ACCCGTTTTA
* *
3109297 TTGAAGATTGTTCAATTCTTATACTCTGAAGAATAGAGAGCAGACACATTT
1 TTGAAGATTGTTCAAGTCTTATACTCTGAAGAATAGAGAGCAGACACATAT
* * * * *
3109348 TATGAAGATTGTTCGAGTCTTATACTTCCTGAAGGAATAGGGAGCAGGCTCGTCAT
1 T-TGAAGATTGTTCAAGTCTTATAC-T-CTGAA-GAATAGAGAGCAGACACAT-AT
*
3109404 TTGAAGATTTTTCAAGTCT
1 TTGAAGATTGTTCAAGTCT
3109423 CATTTATCCG
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
51 1 0.02
52 21 0.34
53 1 0.02
54 5 0.08
55 31 0.51
56 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (51 bp):
TTGAAGATTGTTCAAGTCTTATACTCTGAAGAATAGAGAGCAGACACATAT
Found at i:3119242 original size:73 final size:73
Alignment explanation
Indices: 3119165--3119301 Score: 222
Period size: 73 Copynumber: 1.9 Consensus size: 73
3119155 TAATATTACG
* *
3119165 ATAATTGTGTTTCTCGAAAGTATA-GGATTAATTTAAATTTTAGATCTCATCCCACTCTAATAGT
1 ATAATTGTGTTTCTCGAAAGTATATGG-TTAACTTAAACTTTAGATCTCATCCCACTCTAATAGT
3119229 CATATTATA
65 CATATTATA
* *
3119238 ATAATTGTGTTTCTCGAAAGTATATGGTTAGCTTAAACTTTAGATCTCATCCCACTCTACTAGT
1 ATAATTGTGTTTCTCGAAAGTATATGGTTAACTTAAACTTTAGATCTCATCCCACTCTAATAGT
3119302 AGAAAGATGG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 57 0.97
74 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (73 bp):
ATAATTGTGTTTCTCGAAAGTATATGGTTAACTTAAACTTTAGATCTCATCCCACTCTAATAGTC
ATATTATA
Found at i:3122366 original size:2 final size:2
Alignment explanation
Indices: 3122359--3122401 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3122349 AAACTTTAAT
3122359 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3122401 T
1 T
3122402 TTGTTCATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3123088 original size:2 final size:2
Alignment explanation
Indices: 3123081--3123126 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
3123071 TTAAATTCGC
3123081 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3123122 GA TA T
1 TA TA T
3123127 CGTCTAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3123218 original size:2 final size:2
Alignment explanation
Indices: 3123211--3123251 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3123201 TAGTAAATGA
3123211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3123252 CCTGTGGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3124443 original size:31 final size:31
Alignment explanation
Indices: 3124405--3124463 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3124395 TATTTTGATA
**
3124405 TCTCCCTCATTTTCTATGTTTAATTATATTT
1 TCTCCCTCATTTTCTATAATTAATTATATTT
3124436 TCTCCCTCATTTTCTATAATTAATTATA
1 TCTCCCTCATTTTCTATAATTAATTATA
3124464 CGTTGCCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.02, T:0.54
Consensus pattern (31 bp):
TCTCCCTCATTTTCTATAATTAATTATATTT
Found at i:3126115 original size:21 final size:21
Alignment explanation
Indices: 3126074--3126118 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3126064 ATACTTCACG
*
3126074 GTGCTGATGTGGTGATCCACA
1 GTGCTGATGTGGTGATACACA
3126095 GTGCTGATGTGGT-AGTACACA
1 GTGCTGATGTGGTGA-TACACA
3126116 GTG
1 GTG
3126119 GTTGGTGACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.29
Consensus pattern (21 bp):
GTGCTGATGTGGTGATACACA
Found at i:3126866 original size:22 final size:22
Alignment explanation
Indices: 3126814--3126869 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
3126804 TCTTATTTCA
*
3126814 CCTTCTCCTTTCATTTTCCTTC
1 CCTTCTTCTTTCATTTTCCTTC
3126836 CCTTCTTCTTTCATTTTCCTTC
1 CCTTCTTCTTTCATTTTCCTTC
*
3126858 CCTTTTTCTTTC
1 CCTTCTTCTTTC
3126870 TTCATTTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.04, C:0.38, G:0.00, T:0.59
Consensus pattern (22 bp):
CCTTCTTCTTTCATTTTCCTTC
Found at i:3127407 original size:42 final size:42
Alignment explanation
Indices: 3127351--3127432 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
3127341 AAAGGATCCC
*
3127351 TTTTCAAAATGATCGA-TCCATCGGGAG-AAAGGATCGATCCTT
1 TTTTCAAAAGGATCGATTCC-T-GGGAGAAAAGGATCGATCCTT
* *
3127393 TTTTCCAAAGGATCGATTCCTTGGAGAAAAGGATCGATCC
1 TTTTCAAAAGGATCGATTCCTGGGAGAAAAGGATCGATCC
3127433 CTTCTATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 4 0.11
42 28 0.80
43 3 0.09
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
TTTTCAAAAGGATCGATTCCTGGGAGAAAAGGATCGATCCTT
Found at i:3128317 original size:12 final size:13
Alignment explanation
Indices: 3128296--3128328 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3128286 TAACAAATCT
*
3128296 TAACTTTATTTAA
1 TAACTTTATTAAA
3128309 TAA-TTTATTAAA
1 TAACTTTATTAAA
3128321 TAACTTTA
1 TAACTTTA
3128329 CATTCGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (13 bp):
TAACTTTATTAAA
Found at i:3141776 original size:40 final size:40
Alignment explanation
Indices: 3141728--3141823 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
3141718 GTGATTTTCC
* * *
3141728 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGATTAT
1 GACTATCGCAACGCGAATATG-ACAATCGCAACGAGATTAT
* * * *
3141768 GACTATCGCAACGCGATTCTGACTATCGCAACGAGATTCT
1 GACTATCGCAACGCGAATATGACAATCGCAACGAGATTAT
3141808 GACTATCGCAACGCGA
1 GACTATCGCAACGCGA
3141824 TTCTGACTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 47 0.98
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGACAATCGCAACGAGATTAT
Found at i:3141864 original size:20 final size:20
Alignment explanation
Indices: 3141752--3141858 Score: 160
Period size: 20 Copynumber: 5.3 Consensus size: 20
3141742 GAATATGTAA
* *
3141752 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
3141772 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3141792 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3141812 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * *
3141832 GTCGCAACGCGATGCCGACT
1 ATCGCAACGCGATTCTGACT
3141852 ATCGCAA
1 ATCGCAA
3141859 TACGATTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3142066 original size:22 final size:22
Alignment explanation
Indices: 3142041--3142083 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3142031 CGTGACATCC
3142041 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3142063 GTCCCCATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
3142084 TGTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:3142491 original size:19 final size:19
Alignment explanation
Indices: 3142469--3142575 Score: 79
Period size: 20 Copynumber: 5.5 Consensus size: 19
3142459 AGAATCGCAA
**
3142469 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
3142488 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
** *
3142507 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTC-ATTTCGCGT
** **
3142527 TGCGATAGTCATTTTCGTAT
1 TGCGATTTTCA-TTTCGCGT
* *
3142547 TGTGATTTTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
*
3142567 TGTGATTTT
1 TGCGATTTT
3142576 AAGTTTCAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
19 26 0.35
20 48 0.65
ACGTcount: A:0.14, C:0.15, G:0.23, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:3142525 original size:20 final size:20
Alignment explanation
Indices: 3142481--3142537 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
3142471 CGATTTTGGT
** *
3142481 TTCGCGTTGCGATTTTC-AT
1 TTCGCGTTGCGATAGTCAAA
3142500 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
3142520 TTCGCGTTGCGATAGTCA
1 TTCGCGTTGCGATAGTCA
3142538 TTTTCGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.44
20 19 0.56
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:3142543 original size:20 final size:19
Alignment explanation
Indices: 3142480--3142540 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
3142470 GCGATTTTGG
**
3142480 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
3142499 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTC-A
*
3142519 ATTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
3142538 TTT
1 TTT
3142541 TCGTATTGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 19 0.51
20 18 0.49
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:3142582 original size:20 final size:20
Alignment explanation
Indices: 3142539--3142582 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3142529 CGATAGTCAT
* *
3142539 TTTCGTATTGTGATTTTCAT
1 TTTCGTATTGTGATTTTAAG
*
3142559 TTTCGTGTTGTGATTTTAAG
1 TTTCGTATTGTGATTTTAAG
3142579 TTTC
1 TTTC
3142583 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.09, G:0.18, T:0.59
Consensus pattern (20 bp):
TTTCGTATTGTGATTTTAAG
Found at i:3144141 original size:21 final size:21
Alignment explanation
Indices: 3144096--3144142 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3144086 GTTAGGGGAG
* *
3144096 TTACGTGATGAGGTCAATGCC
1 TTACGTGAGGAGGTCAATACC
* *
3144117 TTACGTGAGGAGGTCGATACT
1 TTACGTGAGGAGGTCAATACC
3144138 TTACG
1 TTACG
3144143 CAATGAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACC
Found at i:3144326 original size:18 final size:18
Alignment explanation
Indices: 3144303--3144352 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
3144293 TTTACTCGTA
3144303 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
3144321 ATTTCACTTAGATTAATC
1 ATTTCACTTAGATTAACC
3144339 ATTTCACTTAGATT
1 ATTTCACTTAGATT
3144353 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:3144547 original size:20 final size:20
Alignment explanation
Indices: 3144510--3144548 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3144500 TCGCAACGAG
**
3144510 AAAATGACTATCGTAACGCA
1 AAAATGACTATCACAACGCA
3144530 AAAATGACTATCACAACGC
1 AAAATGACTATCACAACGC
3144549 GAATTTGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (20 bp):
AAAATGACTATCACAACGCA
Found at i:3144657 original size:20 final size:20
Alignment explanation
Indices: 3144632--3144727 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
3144622 CGATTCTCTT
**
3144632 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
*
3144652 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGC
*
3144672 GTTACGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
*
3144692 GTTGCGATGGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
3144712 GTTGCGATAGTCATTT
1 GTTGCGATAGTCATTT
3144728 GTGTTGTGAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:3145315 original size:21 final size:21
Alignment explanation
Indices: 3145227--3145330 Score: 104
Period size: 21 Copynumber: 5.0 Consensus size: 21
3145217 GACTCACCAG
3145227 TCATCGTTCAAGAGGCCTCC-C
1 TCATCGTTCAAGAGGCC-CCTC
*
3145248 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
3145268 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
3145289 CCATCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
3145310 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
3145331 CCAACATTCT
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 16 0.25
21 47 0.72
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:3145323 original size:42 final size:41
Alignment explanation
Indices: 3145226--3145333 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 41
3145216 CGACTCACCA
* *
3145226 GTCATCGTTCAAGAG-GCCTCCCTATCGTTCAAGAGGCCCCT
1 GTCATCGTTCAAGAGTCCCTCCC-ATCGTTCAAGAGGCCACT
* **
3145267 ATCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCACT
1 GTCATCGTTCAAGAGT-CCCTCCCATCGTTCAAGAGGCCACT
*
3145309 GTCATCGTTGAAGAGGTCCCTCCCA
1 GTCATCGTTCAAGA-GTCCCTCCCA
3145334 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 12 0.22
42 35 0.64
43 8 0.15
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (41 bp):
GTCATCGTTCAAGAGTCCCTCCCATCGTTCAAGAGGCCACT
Found at i:3146279 original size:14 final size:14
Alignment explanation
Indices: 3146242--3146303 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
3146232 TTGGTTGTTT
*
3146242 AATTGATTTATAAA
1 AATTGATTTGTAAA
3146256 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
3146270 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
3146285 TATTGATATGTAAA
1 AATTGATTTGTAAA
3146299 TAATT
1 -AATT
3146304 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3146455 original size:20 final size:20
Alignment explanation
Indices: 3146402--3146455 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
3146392 AGGTACGCTT
* **
3146402 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
3146422 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
3146442 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
3146456 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:3146491 original size:20 final size:20
Alignment explanation
Indices: 3146449--3146823 Score: 236
Period size: 20 Copynumber: 20.6 Consensus size: 20
3146439 AAATCGCAAC
*
3146449 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
3146468 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
3146488 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
3146502 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
*
3146522 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
3146542 GCGATACTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
3146562 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
3146582 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
3146596 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
3146610 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
3146624 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
3146638 GCGATAGTCAAA-TAGCCGTT
1 GCGATAGTCAAATTCG-CGTT
* *
3146658 GCGATAATCAAATTAGCGTT
1 GCGATAGTCAAATTCGCGTT
3146678 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
3146698 GCGATAGAT-AAATTCGCGTT
1 GCGATAG-TCAAATTCGCGTT
* *
3146718 GCGATAGTCATATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
3146738 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
3146758 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
*
3146772 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
3146792 GCGATAGTCAAATTTGCG-T
1 GCGATAGTCAAATTCGCGTT
* *
3146811 ACGATATTCAAAT
1 GCGATAGTCAAAT
3146824 GAATGTGTAA
Statistics
Matches: 302, Mismatches: 31, Indels: 46
0.80 0.08 0.12
Matches are distributed among these distances:
14 75 0.25
16 3 0.01
18 3 0.01
19 22 0.07
20 195 0.65
21 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:3146597 original size:14 final size:14
Alignment explanation
Indices: 3146578--3146642 Score: 130
Period size: 14 Copynumber: 4.6 Consensus size: 14
3146568 GTCAAATTCG
3146578 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
3146592 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
3146606 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
3146620 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
3146634 CGTTGCGAT
1 CGTTGCGAT
3146643 AGTCAAATAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 51 1.00
ACGTcount: A:0.08, C:0.22, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTCT
Found at i:3149193 original size:14 final size:15
Alignment explanation
Indices: 3149174--3149210 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3149164 TCCCGTGGCA
3149174 TTTTCTTCGGGGA-C
1 TTTTCTTCGGGGATC
*
3149188 TTTTCTTCGGGGATT
1 TTTTCTTCGGGGATC
3149203 TTTTCTTC
1 TTTTCTTC
3149211 TTCTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.05, C:0.19, G:0.22, T:0.54
Consensus pattern (15 bp):
TTTTCTTCGGGGATC
Found at i:3149434 original size:24 final size:24
Alignment explanation
Indices: 3149400--3149453 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3149390 CTGAAACATC
3149400 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3149424 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3149448 ATCAAA
1 ATCAAA
3149454 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3150299 original size:20 final size:20
Alignment explanation
Indices: 3150274--3150360 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
3150264 GAAATTCAGT
3150274 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
3150294 GTTGCGACAGTCAGAATTGC
1 GTTGCGACAGTCAGAATCGC
*
3150314 GTTGCGACAGTTAGAATCGC
1 GTTGCGACAGTCAGAATCGC
* *
3150334 GTTGCGATAGTCATAATCGC
1 GTTGCGACAGTCAGAATCGC
*
3150354 ATTGCGA
1 GTTGCGA
3150361 TTTACATATT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGC
Found at i:3150361 original size:20 final size:20
Alignment explanation
Indices: 3150275--3150422 Score: 127
Period size: 20 Copynumber: 7.3 Consensus size: 20
3150265 AAATTCAGTG
* *
3150275 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* * *
3150295 TTGCGACAGTCAGAATTGCG
1 TTGCGATAGTCAGAATCGCA
* * *
3150315 TTGCGACAGTTAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
*
3150335 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
* * *
3150355 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* *
3150375 TTGCGATAGTCGAAAAATTGCA
1 TTGCGATAGTC--AGAATCGCA
*
3150397 ATGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
3150417 TTGCGA
1 TTGCGA
3150423 ATCTGGAAAC
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.01
20 89 0.83
21 1 0.01
22 16 0.15
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:3150537 original size:2 final size:2
Alignment explanation
Indices: 3150530--3150587 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
3150520 TAAAATCGTG
3150530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3150572 TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA T
3150588 CAAAACTTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3151658 original size:34 final size:33
Alignment explanation
Indices: 3151620--3151688 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 33
3151610 AAAGGTAGTG
*
3151620 GTTAGTGGCATAAAAAATAAAAATAAAATTAAAA
1 GTTAGTAGCATAAAAAATAAAAATAAAA-TAAAA
** * *
3151654 GTTAGTAGTGTTAGAAATAAAAATAAAATAAAA
1 GTTAGTAGCATAAAAAATAAAAATAAAATAAAA
3151687 GT
1 GT
3151689 CAAGTGTTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.58, C:0.01, G:0.14, T:0.26
Consensus pattern (33 bp):
GTTAGTAGCATAAAAAATAAAAATAAAATAAAA
Found at i:3153670 original size:270 final size:270
Alignment explanation
Indices: 3153189--3153724 Score: 991
Period size: 270 Copynumber: 2.0 Consensus size: 270
3153179 TTTCTTTTCT
3153189 AGACAAGTTCTTCTTATTATGAACTCCCCTACTAGAAATGTTGATATGGAGACCCACATTCTTCT
1 AGACAAGTTCTTCTTATTATGAACTCCCCTACTAGAAATGTTGATATGGAGACCCACATTCTTCT
*
3153254 GTGATGGGTTTGATCCAAAGGCTGAATAGGTCTTCCTATATGGACTTCTTCTTCCTCATCGGATG
66 GTGATGGGTTTGATCCAAAGGCTCAATAGGTCTTCCTATATGGACTTCTTCTTCCTCATCGGATG
* *
3153319 AATTCTTATCATTATGAACCCTCTATTGAAAATATTAATCCATCTCCTTCTGTGATGGATTTGAA
131 AATTCTTATCATTATGAACCCTCTATTAAAAATATTAATCCATCTCCTTCTGTGATAGATTTGAA
* *
3153384 CAAAAGGTCGAACAAGTTCTTCTCATTATGAAATTCTCATTGGAAATACTGATCCAACTCCTTAC
196 AAAAAGGTCGAACAAGTTCTTCTCATTATGAAATTCTCATTGGAAATACTAATCCAACTCCTTAC
3153449 ATGATGAACG
261 ATGATGAACG
*
3153459 AGACAAGTTCTTCTTATTATGAACTCCCCTACTAGAAATGTTGATATGGAGACCCACCTTCTTCT
1 AGACAAGTTCTTCTTATTATGAACTCCCCTACTAGAAATGTTGATATGGAGACCCACATTCTTCT
* *
3153524 GTGATGGGTTTGATCCAAAGGCTCAATAGGTTTTCCTATATGGACTTCTTCTTCCTTATCGGATG
66 GTGATGGGTTTGATCCAAAGGCTCAATAGGTCTTCCTATATGGACTTCTTCTTCCTCATCGGATG
3153589 AATTCTTATCATTATGAACCCTCTATTAAAAATATTAATCCATCTCCTTCTGTGATAGATTTGAA
131 AATTCTTATCATTATGAACCCTCTATTAAAAATATTAATCCATCTCCTTCTGTGATAGATTTGAA
*
3153654 AAAAAGGTCGAACAAGTTCTTCTCATTATGAAATTCTCATTGGAAATACTAATTCAACTCCTTAC
196 AAAAAGGTCGAACAAGTTCTTCTCATTATGAAATTCTCATTGGAAATACTAATCCAACTCCTTAC
3153719 ATGATG
261 ATGATG
3153725 GATGAGCCAC
Statistics
Matches: 257, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
270 257 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (270 bp):
AGACAAGTTCTTCTTATTATGAACTCCCCTACTAGAAATGTTGATATGGAGACCCACATTCTTCT
GTGATGGGTTTGATCCAAAGGCTCAATAGGTCTTCCTATATGGACTTCTTCTTCCTCATCGGATG
AATTCTTATCATTATGAACCCTCTATTAAAAATATTAATCCATCTCCTTCTGTGATAGATTTGAA
AAAAAGGTCGAACAAGTTCTTCTCATTATGAAATTCTCATTGGAAATACTAATCCAACTCCTTAC
ATGATGAACG
Found at i:3154502 original size:44 final size:46
Alignment explanation
Indices: 3154387--3154502 Score: 114
Period size: 46 Copynumber: 2.6 Consensus size: 46
3154377 CGAGCGAGAT
* *
3154387 ATGTTGATCCAACT-TCTTATGTGATAGAATCAAGCAAAAAAGAGTG
1 ATGTTGATCCAACTCT-TTATGTGATGGAATCAAACAAAAAAGAGTG
* * * ** *
3154433 ATGCTGATCTAACTCCTTT-TTTGATGGAATCAAACGGAACA-A-TG
1 ATGTTGATCCAACT-CTTTATGTGATGGAATCAAACAAAAAAGAGTG
3154477 ATGTTGATCCAACTCTTTATGTGATG
1 ATGTTGATCCAACTCTTTATGTGATG
3154503 AATGAGTGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
43 4 0.07
44 20 0.36
45 1 0.02
46 28 0.50
47 2 0.04
48 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (46 bp):
ATGTTGATCCAACTCTTTATGTGATGGAATCAAACAAAAAAGAGTG
Found at i:3158013 original size:30 final size:30
Alignment explanation
Indices: 3157979--3158097 Score: 175
Period size: 30 Copynumber: 4.0 Consensus size: 30
3157969 ACACGTTGGG
* *
3157979 ACAACTTGGTGGAGCATTCGGAAGACATAT
1 ACAACTTAGTGGAGCATTTGGAAGACATAT
* *
3158009 ACAACTTACTGGAGAATTTGGAAGACATAT
1 ACAACTTAGTGGAGCATTTGGAAGACATAT
*
3158039 ACAACTTAGTGGAGCATTTGGAAGACATTT
1 ACAACTTAGTGGAGCATTTGGAAGACATAT
* *
3158069 ACAGCTTAGTGGAGCATTTGGGAGACATA
1 ACAACTTAGTGGAGCATTTGGAAGACATA
3158098 AACATCTCAC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.26
Consensus pattern (30 bp):
ACAACTTAGTGGAGCATTTGGAAGACATAT
Found at i:3161464 original size:30 final size:30
Alignment explanation
Indices: 3161417--3161503 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
3161407 GGACAGCTTG
3161417 GTGGAGCATTT-GAAGACATATACAACTTA
1 GTGGAGCATTTGGAAGACATATACAACTTA
* *
3161446 GTGGAGCATTTGGAAGACATATACAGCTTG
1 GTGGAGCATTTGGAAGACATATACAACTTA
* *
3161476 GTGGAGCATTTGGGAGACATAAACAACT
1 GTGGAGCATTTGGAAGACATATACAACT
3161504 CACAAACAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
29 11 0.21
30 41 0.79
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.25
Consensus pattern (30 bp):
GTGGAGCATTTGGAAGACATATACAACTTA
Found at i:3161512 original size:11 final size:11
Alignment explanation
Indices: 3161496--3161520 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3161486 TGGGAGACAT
3161496 AAACAACTCAC
1 AAACAACTCAC
3161507 AAACAACTCAC
1 AAACAACTCAC
3161518 AAA
1 AAA
3161521 GAACATGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (11 bp):
AAACAACTCAC
Found at i:3174535 original size:13 final size:13
Alignment explanation
Indices: 3174507--3174536 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3174497 TTTCTTTTAA
3174507 TTTATTTTCAATT
1 TTTATTTTCAATT
3174520 TTTAGTTTTCAATT
1 TTTA-TTTTCAATT
3174534 TTT
1 TTT
3174537 GTTAGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTATTTTCAATT
Found at i:3175982 original size:22 final size:22
Alignment explanation
Indices: 3175954--3176000 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3175944 ACAACATCCA
3175954 AAACTGTAAGTTCCAAGTTTGT
1 AAACTGTAAGTTCCAAGTTTGT
3175976 AAACTGTAAGTTCCAAGTTTGT
1 AAACTGTAAGTTCCAAGTTTGT
3175998 AAA
1 AAA
3176001 TATATTCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (22 bp):
AAACTGTAAGTTCCAAGTTTGT
Found at i:3191238 original size:38 final size:38
Alignment explanation
Indices: 3191187--3191282 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
3191177 CTCGTATAAA
* *
3191187 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATATG
* *
3191225 TGTCCCGAAGGACCTGTCATCCCGAATGATGTAATATG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATATG
* *
3191263 TATCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
3191283 ATGTCTCATA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATATG
Found at i:3191249 original size:17 final size:17
Alignment explanation
Indices: 3191189--3191250 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
3191179 CGTATAAATG
*
3191189 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTGTCA
*
3191206 TCCCGAAGGATGTCATCTGT-G
1 TCCCGAAGGA---C--CTGTCA
3191227 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTGTCA
3191244 TCCCGAA
1 TCCCGAA
3191251 TGATGTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
16 4 0.11
17 17 0.47
18 1 0.03
20 1 0.03
21 10 0.28
22 3 0.08
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (17 bp):
TCCCGAAGGACCTGTCA
Found at i:3192984 original size:84 final size:84
Alignment explanation
Indices: 3192843--3193011 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
3192833 TAAAAATAAT
* *
3192843 CTCCAAATTATTTTTATATAATTTTTGGTGAATTTTCGAACCTACTGTCAAATTCAGAATCTAAA
1 CTCCAAATTATTTTTATATAATTTCTGGTGAATTTTCGAACCTACTGCCAAATTCAGAATCTAAA
3192908 TGTTTCTTTTAACTTCATC
66 TGTTTCTTTTAACTTCATC
*
3192927 CTCCAAATTATTTTTATATAATTTCTGGTGAATTTTCGAACCTACTGCCAAATTCAGAATCTAAC
1 CTCCAAATTATTTTTATATAATTTCTGGTGAATTTTCGAACCTACTGCCAAATTCAGAATCTAAA
3192992 TGTTTCTTTTAACTTCATC
66 TGTTTCTTTTAACTTCATC
3193011 C
1 C
3193012 CTAGATTCTT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (84 bp):
CTCCAAATTATTTTTATATAATTTCTGGTGAATTTTCGAACCTACTGCCAAATTCAGAATCTAAA
TGTTTCTTTTAACTTCATC
Found at i:3194047 original size:29 final size:30
Alignment explanation
Indices: 3194015--3194079 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3194005 ACCCATATGT
* *
3194015 AACTTTTTAAAA-TTACATTTTGGTCCCTA
1 AACTTTTTAAAAGTTACACTTTGGTCACTA
*
3194044 AAC-TTTTAAAAGTTTATACTTTGGTCACTA
1 AACTTTTTAAAAG-TTACACTTTGGTCACTA
3194074 AACTTT
1 AACTTT
3194080 ACCAAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 8 0.27
29 3 0.10
30 17 0.57
31 2 0.07
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (30 bp):
AACTTTTTAAAAGTTACACTTTGGTCACTA
Found at i:3194069 original size:30 final size:29
Alignment explanation
Indices: 3194033--3194105 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 29
3194023 AAAATTACAT
* *
3194033 TTTGGTCCCTAAACTTTTA-AAAGTTTATAC
1 TTTGGTCACTAAAC-TTTACAAA-TTTATAA
3194063 TTTGGTCACTAAACTTTACCAAATTTATAA
1 TTTGGTCACTAAACTTTA-CAAATTTATAA
3194093 TTTGGTCACTAAA
1 TTTGGTCACTAAA
3194106 TAAATCCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 32 0.82
31 3 0.08
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (29 bp):
TTTGGTCACTAAACTTTACAAATTTATAA
Found at i:3195263 original size:2 final size:2
Alignment explanation
Indices: 3195256--3195285 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3195246 GATATGTAAG
3195256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3195286 TTGGCCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3214314 original size:18 final size:18
Alignment explanation
Indices: 3214291--3214328 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3214281 GATTGACCAA
3214291 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3214309 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3214327 AC
1 AC
3214329 ATTTTGGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3214385 original size:30 final size:29
Alignment explanation
Indices: 3214325--3214506 Score: 176
Period size: 29 Copynumber: 6.3 Consensus size: 29
3214315 CCCGACCCGT
**
3214325 TGACATTTTGGGAATTATTTTACTAAAGG
1 TGACATTTTGGGAATTATTTTAAAAAAGG
*
3214354 TGACATTTTGAGAATTATTTTGAAAAAAGG
1 TGACATTTTGGGAATTATTTT-AAAAAAGG
*
3214384 TGACATTTTGGGAATT-TTTTAAAATA-G
1 TGACATTTTGGGAATTATTTTAAAAAAGG
* *
3214411 TGACATTCTGGTAATTATTTTTAAAACAA--
1 TGACATTTTGGGAATTA-TTTTAAAA-AAGG
* * *
3214440 TGAAATTTTGGGAATTA-TTTATAAAACG
1 TGACATTTTGGGAATTATTTTAAAAAAGG
* * *
3214468 TGATATTTTGGTAATTATTTTTAATAAAGG
1 TGACATTTTGGGAATTA-TTTTAAAAAAGG
*
3214498 TGATATTTT
1 TGACATTTT
3214507 TGTAATTTCG
Statistics
Matches: 128, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.02
27 21 0.16
28 20 0.16
29 46 0.36
30 39 0.30
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (29 bp):
TGACATTTTGGGAATTATTTTAAAAAAGG
Found at i:3214430 original size:57 final size:57
Alignment explanation
Indices: 3214325--3214506 Score: 210
Period size: 57 Copynumber: 3.2 Consensus size: 57
3214315 CCCGACCCGT
* *
3214325 TGACATTTTGGGAATTATTTTACTAAAGGTGACATTTTGAG-AATTATTTTGAAAAAAGG
1 TGACATTTTGGGAATTATTTTA--AAAAGTGACATTTTG-GTAATTATTTTTAAAAAAGG
*
3214384 TGACATTTTGGGAATT-TTTTAAAATAGTGACATTCTGGTAATTATTTTTAAAACAA--
1 TGACATTTTGGGAATTATTTTAAAA-AGTGACATTTTGGTAATTATTTTTAAAA-AAGG
* * * *
3214440 TGAAATTTTGGGAATTATTTATAAAACGTGATATTTTGGTAATTATTTTTAATAAAGG
1 TGACATTTTGGGAATTATTT-TAAAAAGTGACATTTTGGTAATTATTTTTAAAAAAGG
*
3214498 TGATATTTT
1 TGACATTTT
3214507 TGTAATTTCG
Statistics
Matches: 107, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
56 21 0.20
57 50 0.47
58 20 0.19
59 16 0.15
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (57 bp):
TGACATTTTGGGAATTATTTTAAAAAGTGACATTTTGGTAATTATTTTTAAAAAAGG
Found at i:3221903 original size:29 final size:28
Alignment explanation
Indices: 3221858--3221944 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
3221848 GACCCGACCT
3221858 AGTGACATTTTGGGAATTATTTTGAAAAA-
1 AGTGACATTTTGGGAATT-TTTT-AAAAAC
* **
3221887 TGTGACATTTTTTGAATTTTTTAAAAAC
1 AGTGACATTTTGGGAATTTTTTAAAAAC
* * *
3221915 AGTGACATTCTGGTAATTATTTTTAAAAC
1 AGTGACATTTTGGGAATT-TTTTAAAAAC
3221944 A
1 A
3221945 ACGGTGATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 5 0.11
28 17 0.36
29 25 0.53
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (28 bp):
AGTGACATTTTGGGAATTTTTTAAAAAC
Found at i:3221919 original size:28 final size:29
Alignment explanation
Indices: 3221858--3221969 Score: 102
Period size: 32 Copynumber: 3.8 Consensus size: 29
3221848 GACCCGACCT
3221858 AGTGACATTTTGGGAATTATTTTGAAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
* **
3221887 TGTGACATTTTTTGAATT-TTTT-AAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
* * *
3221914 CAGTGACATTCTGGTAATTATTTTTAAAACA
1 -AGTGACATTTTGGGAATTATTTTGAAAA-A
* *
3221945 ACGGTGATATTTTGGTAATTATTTT
1 A--GTGACATTTTGGGAATTATTTT
3221970 TAATAAAGGT
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.07
28 17 0.25
29 19 0.28
30 5 0.07
31 1 0.01
32 20 0.30
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (29 bp):
AGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:3221966 original size:32 final size:31
Alignment explanation
Indices: 3221902--3221994 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 31
3221892 CATTTTTTGA
* * * *
3221902 ATTTTTTAAAAACAGTGACATTCTGGTAATT
1 ATTTTTAAAAAACGGTGATATTTTGGTAATT
3221933 ATTTTTAAAACAACGGTGATATTTTGGTAATT
1 ATTTTTAAAA-AACGGTGATATTTTGGTAATT
*
3221965 ATTTTTAATAAA-GGTGATAGTTTT-GTAATT
1 ATTTTTAAAAAACGGTGATA-TTTTGGTAATT
3221995 TTTGAATGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
30 13 0.24
31 15 0.27
32 27 0.49
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (31 bp):
ATTTTTAAAAAACGGTGATATTTTGGTAATT
Found at i:3227401 original size:13 final size:14
Alignment explanation
Indices: 3227364--3227407 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
3227354 ATTTCATGAA
3227364 ATATTTTATAAATC
1 ATATTTTATAAATC
**
3227378 ATAGGTTATAAAT-
1 ATATTTTATAAATC
3227391 ATATTTTATAAATC
1 ATATTTTATAAATC
3227405 ATA
1 ATA
3227408 GGTTTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (14 bp):
ATATTTTATAAATC
Found at i:3228547 original size:31 final size:31
Alignment explanation
Indices: 3228500--3228558 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
3228490 CTGGTGATCA
*
3228500 TATCCTAACTAAATAAAAACGAAAGTGAACT
1 TATCCTAACTAAATAAAAACAAAAGTGAACT
* * *
3228531 TATCTTAATTAAATAAAAATAAAAGTGA
1 TATCCTAACTAAATAAAAACAAAAGTGA
3228559 TCATATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
TATCCTAACTAAATAAAAACAAAAGTGAACT
Found at i:3229063 original size:14 final size:14
Alignment explanation
Indices: 3229044--3229077 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3229034 ACATTAAATT
3229044 ATAAATATACAATC
1 ATAAATATACAATC
3229058 ATAAATATACAATC
1 ATAAATATACAATC
3229072 ATAAAT
1 ATAAAT
3229078 TTTTTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAAATATACAATC
Found at i:3230399 original size:18 final size:19
Alignment explanation
Indices: 3230363--3230407 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3230353 AACGAGAGAG
3230363 ATGGAAAAATTGATGGAAA
1 ATGGAAAAATTGATGGAAA
* *
3230382 ATGGAAAATTTTAT-GAAA
1 ATGGAAAAATTGATGGAAA
3230400 AT-GAAAAA
1 ATGGAAAAA
3230408 AATTAGAGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (19 bp):
ATGGAAAAATTGATGGAAA
Found at i:3230516 original size:43 final size:42
Alignment explanation
Indices: 3230400--3230737 Score: 222
Period size: 44 Copynumber: 7.9 Consensus size: 42
3230390 TTTTATGAAA
* ** *
3230400 ATGAAAAAA-ATTAGAGGCCTTGATTATAAAGGTAGAAATCGAG
1 ATGAAAAAACA-TAGGGGCCTCAATTATAAAGGTAAAAAT-GAG
* * * * *
3230443 ATTG-AAAAA-ATAGGGGTCTCTATTATAAAGGTATAATTGAT
1 A-TGAAAAAACATAGGGGCCTCAATTATAAAGGTAAAAATGAG
* *
3230484 ACTGAAAAAACATAGGGGCCTCAATTAGAAAGGTGGAAAATGAG
1 A-TGAAAAAACATAGGGGCCTCAATTATAAAGGT-AAAAATGAG
* * * *
3230528 ATTGCAAAAACTTAAGGGCCTCAATTATAAAGTTAAAAAATGAG
1 A-TGAAAAAACATAGGGGCCTCAATTATAAAGGT-AAAAATGAG
* * * * *
3230572 ATTAAAAAA-ATATGGGTCTCAATTATAAAGGTAGAAATTGAA
1 ATGAAAAAACATAGGGGCCTCAATTATAAAGGTA-AAAATGAG
* * * *
3230614 ATAGAAAAAACTTAGGGGCCTTAATTGTAAAGGTATAAAGTGAG
1 AT-GAAAAAACATAGGGGCCTCAATTATAAAGGTA-AAAATGAG
* * * * *
3230658 ATTGAAAAAACTTAAGAGCCTTAATTATAAAGTTAAAAA-GAGG
1 A-TGAAAAAACATAGGGGCCTCAATTATAAAGGTAAAAATGA-G
* *
3230701 AAAT-AAAAAA-TTTGGGGCCTCAATTATAAAGGTAAAA
1 --ATGAAAAAACATAGGGGCCTCAATTATAAAGGTAAAA
3230738 CAGAATTGAA
Statistics
Matches: 234, Mismatches: 50, Indels: 23
0.76 0.16 0.07
Matches are distributed among these distances:
41 6 0.03
42 78 0.33
43 49 0.21
44 99 0.42
45 2 0.01
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (42 bp):
ATGAAAAAACATAGGGGCCTCAATTATAAAGGTAAAAATGAG
Found at i:3230596 original size:86 final size:86
Alignment explanation
Indices: 3230488--3230737 Score: 227
Period size: 86 Copynumber: 2.9 Consensus size: 86
3230478 ATTGATACTG
* * * *
3230488 AAAAAACATAGGGGCCTCAATTAGAAAGGTGGAAAATGAGATTGCAAAAACTTAAGGGCCTCAAT
1 AAAAAA-ATAGGGGCCTCAATTAGAAAGGTAGAAAATGAAATAGAAAAAACTTAAGGGCCTCAAT
*
3230553 TATAAAGTTAAAAAATGAGATT
65 TATAAAGGTAAAAAATGAGATT
* * * * * *
3230575 AAAAAAATATGGGTCTCAATTATAAAGGTAGAAATTGAAATAGAAAAAACTTAGGGGCCTTAATT
1 AAAAAAATAGGGGCCTCAATTAGAAAGGTAGAAAATGAAATAGAAAAAACTTAAGGGCCTCAATT
* * *
3230640 GTAAAGGTATAAAGTGAGATT
66 ATAAAGGTAAAAAATGAGATT
* * * * * * * * **
3230661 GAAAAAACTTAAGAGCCTTAATTATAAAGTTAAAAAGAGGAAAT--AAAAAA-TTTGGGGCCTCA
1 -AAAAAA-ATAGGGGCCTCAATTAGAAAGGTAGAAA-ATGAAATAGAAAAAACTTAAGGGCCTCA
3230723 ATTATAAAGGTAAAA
63 ATTATAAAGGTAAAA
3230738 CAGAATTGAA
Statistics
Matches: 133, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
86 89 0.67
87 18 0.14
88 21 0.16
89 5 0.04
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (86 bp):
AAAAAAATAGGGGCCTCAATTAGAAAGGTAGAAAATGAAATAGAAAAAACTTAAGGGCCTCAATT
ATAAAGGTAAAAAATGAGATT
Found at i:3230684 original size:130 final size:127
Alignment explanation
Indices: 3230401--3230785 Score: 386
Period size: 130 Copynumber: 3.0 Consensus size: 127
3230391 TTTATGAAAA
* * * * * *
3230401 TGAAAAAAATT-AGAGGCCTTGATTATAAAGGT-AGAAATCGAGATTGAAAAAATAGGGGTCTCT
1 TGAAAAAACTTAAGA-GCCTTAATTATAAAGTTAAAAAAT-GAGATT-AAAAAATATGGGTCTCA
* * * * *
3230464 ATTATAAAGGTATAATTGATACTGAAAAAACATAGGGGCCTCAATTAG-AAAGGTGGAAAA-TGA
63 ATTATAAAGGTAAAATTGA-AATGAAAAAACTTAGGGGCCTTAATT-GTAAAGGT-AAAAAGTGA
3230527 GAT
125 GAT
* * *
3230530 TGCAAAAACTTAAGGGCCTCAATTATAAAGTTAAAAAATGAGATTAAAAAAATATGGGTCTCAAT
1 TGAAAAAACTTAAGAGCCTTAATTATAAAGTTAAAAAATGAGATT-AAAAAATATGGGTCTCAAT
*
3230595 TATAAAGGTAGAAATTGAAATAGAAAAAACTTAGGGGCCTTAATTGTAAAGGTATAAAGTGAGAT
65 TATAAAGGTA-AAATTGAAAT-GAAAAAACTTAGGGGCCTTAATTGTAAAGGTAAAAAGTGAGAT
* * * *
3230660 TGAAAAAACTTAAGAGCCTTAATTATAAAGTTAAAAAGAGGA-AATAAAAAATTTGGGGCCTCAA
1 TGAAAAAACTTAAGAGCCTTAATTATAAAGTTAAAAA-ATGAGATTAAAAAATAT-GGGTCTCAA
** * * * * * *
3230724 TTATAAAGGTAAAACAGAATTGAAAAAA-TTAGAGACTTTAATTATAAAGATAAAAAGTGAGA
64 TTATAAAGGTAAAATTGAAATGAAAAAACTTAGGGGCCTTAATTGTAAAGGTAAAAAGTGAGA
3230786 CAGAATAATA
Statistics
Matches: 216, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
127 28 0.13
128 7 0.03
129 77 0.36
130 101 0.47
131 3 0.01
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (127 bp):
TGAAAAAACTTAAGAGCCTTAATTATAAAGTTAAAAAATGAGATTAAAAAATATGGGTCTCAATT
ATAAAGGTAAAATTGAAATGAAAAAACTTAGGGGCCTTAATTGTAAAGGTAAAAAGTGAGAT
Found at i:3230778 original size:83 final size:87
Alignment explanation
Indices: 3230533--3230780 Score: 226
Period size: 86 Copynumber: 2.9 Consensus size: 87
3230523 ATGAGATTGC
* * * * * * * *
3230533 AAAAACTTAAGGGCCTCAATTATAAAGTTA-AAAAATGAGATT-AAAAAA-ATATGGGTCTCAAT
1 AAAAACTTAGGGGCCTCAATTATAAAGGTATAAACA-GAGATTGAAAAAACTTAAGAGCCTTAAT
* * **
3230595 TATAAAGGTAGAAA-TTGAAATAGA
65 TATAAAGATAAAAAGAGGAAAT--A
* * **
3230619 AAAAACTTAGGGGCCTTAATTGTAAAGGTATAAAGTGAGATTGAAAAAACTTAAGAGCCTTAATT
1 AAAAACTTAGGGGCCTCAATTATAAAGGTATAAACAGAGATTGAAAAAACTTAAGAGCCTTAATT
*
3230684 ATAAAGTTAAAAAGAGGAAATA
66 ATAAAGATAAAAAGAGGAAATA
* *
3230706 AAAAA-TTTGGGGCCTCAATTATAAAGGTA-AAACAGA-ATTGAAAAAA-TT-AGAGACTTTAAT
1 AAAAACTTAGGGGCCTCAATTATAAAGGTATAAACAGAGATTGAAAAAACTTAAGAG-CCTTAAT
3230766 TATAAAGATAAAAAG
65 TATAAAGATAAAAAG
3230781 TGAGACAGAA
Statistics
Matches: 135, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
82 4 0.03
83 22 0.16
84 10 0.07
85 5 0.04
86 53 0.39
87 15 0.11
88 21 0.16
89 5 0.04
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (87 bp):
AAAAACTTAGGGGCCTCAATTATAAAGGTATAAACAGAGATTGAAAAAACTTAAGAGCCTTAATT
ATAAAGATAAAAAGAGGAAATA
Found at i:3231165 original size:22 final size:23
Alignment explanation
Indices: 3231140--3231205 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
3231130 TTTTGAATAA
3231140 CTATG-TTTTATGTCACGTTTTT
1 CTATGCTTTTATGTCACGTTTTT
* *
3231162 CTATGTTTTTGTGTCACGTTTTT
1 CTATGCTTTTATGTCACGTTTTT
3231185 CTATGCTTTTATGTCACGTTT
1 CTATGCTTTTATGTCACGTTT
3231206 ATCTCTACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 5 0.12
23 35 0.88
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (23 bp):
CTATGCTTTTATGTCACGTTTTT
Found at i:3231176 original size:23 final size:22
Alignment explanation
Indices: 3231140--3231229 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 22
3231130 TTTTGAATAA
3231140 CTATGTTTTATGTCACGTTTTT
1 CTATGTTTTATGTCACGTTTTT
*
3231162 CTATGTTTTTGTGTCACGTTTTT
1 CTATG-TTTTATGTCACGTTTTT
3231185 CTATGCTTTTATGTCACGTTTATCT
1 CTATG-TTTTATGTCACGTTT-T-T
3231210 CTACT-TTTTA-G-CACGTTTTT
1 CTA-TGTTTTATGTCACGTTTTT
3231230 TATTATTTGA
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 12 0.20
23 36 0.59
24 6 0.10
25 4 0.07
26 1 0.02
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (22 bp):
CTATGTTTTATGTCACGTTTTT
Found at i:3232641 original size:23 final size:23
Alignment explanation
Indices: 3232601--3232646 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
3232591 TTAAACAATT
3232601 TAAAAAAATATATCAAATAAAAAA
1 TAAAAAAATATA-CAAATAAAAAA
3232625 TAAAAAAATAGTA-AAATAAAAA
1 TAAAAAAATA-TACAAATAAAAA
3232647 CAACATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 10 0.48
25 2 0.10
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (23 bp):
TAAAAAAATATACAAATAAAAAA
Found at i:3232655 original size:16 final size:16
Alignment explanation
Indices: 3232621--3232658 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3232611 TATCAAATAA
*
3232621 AAAATAAAAAAATAGT
1 AAAATAAAAAAACAGT
3232637 AAAATAAAAACAACA-T
1 AAAATAAAAA-AACAGT
3232653 AAAATA
1 AAAATA
3232659 CAAGGACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAATAAAAAAACAGT
Found at i:3232884 original size:21 final size:20
Alignment explanation
Indices: 3232849--3232901 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
3232839 CAAAATGCAA
3232849 AAATTAAAATAACAAT-AGCT
1 AAATTAAAATAACAATGA-CT
*
3232869 AAATCAAAACTAACAATGACT
1 AAATTAAAA-TAACAATGACT
3232890 AAATTAAAATAA
1 AAATTAAAATAA
3232902 AACAAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.38
21 17 0.59
22 1 0.03
ACGTcount: A:0.62, C:0.11, G:0.04, T:0.23
Consensus pattern (20 bp):
AAATTAAAATAACAATGACT
Found at i:3243367 original size:138 final size:137
Alignment explanation
Indices: 3242923--3243404 Score: 569
Period size: 137 Copynumber: 3.5 Consensus size: 137
3242913 AGTCGAGCAA
* * ** * * *
3242923 AAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * * * * *
3242988 GAAC-TCTATCTGGAAATTTTGATCCTTGAA-AGAGATGTTGTTGATTCAACTTCATATGTGATG
66 GAACTTCCA-CTGAAAATATTGGTCC-TCAAGTGAGGTCTTGTTGATTCAACTTCATATGTGATG
*
3243051 AATTAAGAC
129 AATTAACAC
* * *
3243060 AAGGTTAAACAAGTTATTCTCATTATGAAATTCTTCTTCCTCTTCAGATAAGTACTTCTCATTAT
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
3243125 GAACTTCCACTGAAAATATTGGTCCTCAAGTGCGGTGTTGTTGATTCAACTTCATATGTGATGAA
66 GAACTTCCACTGAAAATATTGGTCCTCAAGTGAGGTCTTGTTGATTCAACTTCATATGTGATGAA
*
3243190 TTAAGAC
131 TTAACAC
3243197 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * ** * *
3243262 GAACTTCC-TTGAAAATGTTGGTCCTCAAGTGAGGTTCTTCTTTTATTCATTTTCGTA-GATGCT
66 GAACTTCCACTGAAAATATTGGTCCTCAAGTGAGG-TCTT-GTTGATTCAACTTCATATG-TGAT
* *
3243325 GAA-TCACTC
128 GAATTAACAC
* *
3243334 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 -AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
3243399 TGAACT
65 TGAACT
3243405 CTTCCTCGCA
Statistics
Matches: 303, Mismatches: 36, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
136 26 0.09
137 188 0.62
138 89 0.29
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (137 bp):
AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTCCACTGAAAATATTGGTCCTCAAGTGAGGTCTTGTTGATTCAACTTCATATGTGATGAA
TTAACAC
Found at i:3244068 original size:18 final size:18
Alignment explanation
Indices: 3244045--3244081 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3244035 ATAAAAGAAT
3244045 AAATTAAATTTCAAAAAG
1 AAATTAAATTTCAAAAAG
*
3244063 AAATTAAATTTCGAAAAG
1 AAATTAAATTTCAAAAAG
3244081 A
1 A
3244082 TAAAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27
Consensus pattern (18 bp):
AAATTAAATTTCAAAAAG
Found at i:3244450 original size:4 final size:4
Alignment explanation
Indices: 3244441--3244492 Score: 56
Period size: 4 Copynumber: 13.5 Consensus size: 4
3244431 TCTATTATTA
* *
3244441 TTTC TTTC TTTC TTTC TTT- TTT- TTTT TTTCC TTT- TTTC TTTC TTTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC
3244487 TTTC TT
1 TTTC TT
3244493 CTTCAAGCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
3 9 0.21
4 30 0.71
5 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (4 bp):
TTTC
Found at i:3244456 original size:12 final size:11
Alignment explanation
Indices: 3244427--3244488 Score: 63
Period size: 12 Copynumber: 5.5 Consensus size: 11
3244417 CTTGACCCTC
*
3244427 TTTTTCTATTAT
1 TTTTTCT-TTCT
*
3244439 TATTTCTTTCT
1 TTTTTCTTTCT
3244450 TTCTTTCTTT-T
1 TT-TTTCTTTCT
*
3244461 TTTTTTTTTCCT
1 TTTTTCTTT-CT
3244473 TTTTTCTTTCT
1 TTTTTCTTTCT
3244484 TTTTT
1 TTTTT
3244489 TCTTCTTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
10 6 0.14
11 14 0.33
12 22 0.52
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:3244477 original size:11 final size:10
Alignment explanation
Indices: 3244449--3244495 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
3244439 TATTTCTTTC
*
3244449 TTTCTTTCTT
1 TTTCTTTTTT
3244459 TTT-TTTTTT
1 TTTCTTTTTT
*
3244468 TTCCTTTTTT
1 TTTCTTTTTT
3244478 CTTTCTTTTTT
1 -TTTCTTTTTT
3244489 TCTTCTT
1 T-TTCTT
3244496 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 7 0.23
10 10 0.32
11 14 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:3244489 original size:12 final size:12
Alignment explanation
Indices: 3244441--3244492 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
3244431 TCTATTATTA
*
3244441 TTTCTTTCTTTC
1 TTTCTTTCTTTT
3244453 TTTCTTT-TTTT
1 TTTCTTTCTTTT
*
3244464 TTT-TTTCCTTT
1 TTTCTTTCTTTT
3244475 TTTCTTTCTTTT
1 TTTCTTTCTTTT
3244487 TTTCTT
1 TTTCTT
3244493 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 3 0.09
11 12 0.34
12 20 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTCTTTCTTTT
Found at i:3255276 original size:2 final size:2
Alignment explanation
Indices: 3255269--3255300 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3255259 GAATATCATA
3255269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3255301 TTATGTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3263201 original size:21 final size:19
Alignment explanation
Indices: 3263168--3263209 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
3263158 GAGGCAACCC
3263168 TTTTTTTTTTTTTGCTTAT
1 TTTTTTTTTTTTTGCTTAT
*
3263187 TTTTTATTTTATTTTGTTTAT
1 TTTTT-TTTT-TTTTGCTTAT
3263208 TT
1 TT
3263210 GATTTTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.83
Consensus pattern (19 bp):
TTTTTTTTTTTTTGCTTAT
Found at i:3270253 original size:59 final size:60
Alignment explanation
Indices: 3270183--3270400 Score: 218
Period size: 59 Copynumber: 3.7 Consensus size: 60
3270173 TAGCCCTAGT
* * * *
3270183 GGTAAGACCTTATGGACCCTAAGGTACTCCCTTAGGGT-GCTCCTCTGCTGTGTGCATTG
1 GGTAAGTCCTTATGGACCCTAAGGTACTCCCTTAGGGTGGCTCCTCTACTGTCTACATTG
*
3270242 GGTAAGTCCTTATAGACCCTAAGGTACTCCCTTAGGGTGGCTCCTCTACTGTCTACATTG
1 GGTAAGTCCTTATGGACCCTAAGGTACTCCCTTAGGGTGGCTCCTCTACTGTCTACATTG
* * * * * *
3270302 GGTAAGTCCTTATGG-GCCTAAGGGCACTCCTCTCA-GGTGG-GCATCTA-TG-CTTCATCTAG
1 GGTAAGTCCTTATGGACCCTAA-GGTACTCC-CTTAGGGTGGCTCCTCTACTGTCTACAT-T-G
* *
3270361 GGTAAGAT-CTTATGGACCC-AAGGTGCTCCCTTAGGTTGGC
1 GGTAAG-TCCTTATGGACCCTAAGGTACTCCCTTAGGGTGGC
3270401 ACCTACGCCC
Statistics
Matches: 133, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
57 8 0.06
58 13 0.10
59 62 0.47
60 47 0.35
61 3 0.02
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (60 bp):
GGTAAGTCCTTATGGACCCTAAGGTACTCCCTTAGGGTGGCTCCTCTACTGTCTACATTG
Found at i:3271457 original size:16 final size:17
Alignment explanation
Indices: 3271436--3271467 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3271426 TTATCTTTGT
3271436 TTTA-TTTCTTTAGGTA
1 TTTATTTTCTTTAGGTA
3271452 TTTATTTTCTTTAGGT
1 TTTATTTTCTTTAGGT
3271468 TATCTTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.16, C:0.06, G:0.12, T:0.66
Consensus pattern (17 bp):
TTTATTTTCTTTAGGTA
Found at i:3272354 original size:32 final size:31
Alignment explanation
Indices: 3272313--3272374 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
3272303 AAACCACTAA
*
3272313 AGACTGTACTTTATTGGCATTGTTATACAAT
1 AGACTGTACTTTAGTGGCATTGTTATACAAT
* *
3272344 AGACTCGTACTTTAGTGGCGTTTTTATACAA
1 AGACT-GTACTTTAGTGGCATTGTTATACAA
3272375 ACACCTCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (31 bp):
AGACTGTACTTTAGTGGCATTGTTATACAAT
Found at i:3272440 original size:55 final size:55
Alignment explanation
Indices: 3272344--3272447 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
3272334 GTTATACAAT
* * * *
3272344 AGACTCGTACTTTAGTGGCGTTTTTATACAAACACCTCTAAAGACTCGTCGCTAA
1 AGACTCATACTTTAGTGGCATTTTTATAAAAACACCGCTAAAGACTCGTCGCTAA
*
3272399 AGACTCATACTTTAGTGGCATTTTTATAAAAACGCCGCTAAAGACTCGT
1 AGACTCATACTTTAGTGGCATTTTTATAAAAACACCGCTAAAGACTCGT
3272448 ACTTTAGTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (55 bp):
AGACTCATACTTTAGTGGCATTTTTATAAAAACACCGCTAAAGACTCGTCGCTAA
Found at i:3274080 original size:27 final size:27
Alignment explanation
Indices: 3274042--3274104 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
3274032 CACCGCTGTG
3274042 ACCGCGATAGTATCCGTTATGTCCGTA
1 ACCGCGATAGTATCCGTTATGTCCGTA
3274069 ACCGCGATAGTATCCGTTATGTCCGTA
1 ACCGCGATAGTATCCGTTATGTCCGTA
3274096 ACCGCGATA
1 ACCGCGATA
3274105 AACGCAACGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (27 bp):
ACCGCGATAGTATCCGTTATGTCCGTA
Found at i:3277206 original size:28 final size:28
Alignment explanation
Indices: 3277166--3277224 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
3277156 TGAACTTATT
3277166 CATGCATTTACCAACTATCAATGTGTAC
1 CATGCATTTACCAACTATCAATGTGTAC
3277194 CATGCATTTACCAACTATCAATGTGTAC
1 CATGCATTTACCAACTATCAATGTGTAC
3277222 CAT
1 CAT
3277225 AAAAGCATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.32
Consensus pattern (28 bp):
CATGCATTTACCAACTATCAATGTGTAC
Found at i:3280899 original size:16 final size:17
Alignment explanation
Indices: 3280861--3280902 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3280851 TTTTAAAATG
*
3280861 TGATTTTCTGAAATTTT
1 TGATTTACTGAAATTTT
* *
3280878 TTATTTACTGATA-TTT
1 TGATTTACTGAAATTTT
3280894 TGATTTACT
1 TGATTTACT
3280903 TTTAAATGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.60
Consensus pattern (17 bp):
TGATTTACTGAAATTTT
Found at i:3283910 original size:28 final size:27
Alignment explanation
Indices: 3283878--3283931 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
3283868 TAATTATTTC
*
3283878 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
*
3283906 TTTTCATAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
3283932 TTATTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:3291466 original size:22 final size:21
Alignment explanation
Indices: 3291424--3291463 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3291414 GAGTTTATTT
*
3291424 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3291445 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3291464 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3293356 original size:21 final size:21
Alignment explanation
Indices: 3293303--3293359 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3293293 TTGGAGCGTG
*
3293303 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTTCCCCCTCAT
3293324 GGGGAATCGGTTCCCCCTCAT
1 GGGGAATCGGTTCCCCCTCAT
3293345 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
3293360 TAAGTGTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.21
Consensus pattern (21 bp):
GGGGAATCGGTTCCCCCTCAT
Found at i:3302141 original size:22 final size:22
Alignment explanation
Indices: 3302115--3302172 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
3302105 TACATCTACG
*
3302115 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCC
3302137 CTCTTCAAAGATGATAGATTCC
1 CTCTTCAAAGATGATAGATTCC
*
3302159 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
3302173 AGGCTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCC
Found at i:3302693 original size:73 final size:73
Alignment explanation
Indices: 3302611--3302776 Score: 305
Period size: 73 Copynumber: 2.3 Consensus size: 73
3302601 AGAAATAAGA
* *
3302611 AGTTCATAATGAGAAAAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATCATCATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATCAGCATTG
3302676 CCAGGTAG
66 CCAGGTAG
*
3302684 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATCGGCATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATCAGCATTG
3302749 CCAGGTAG
66 CCAGGTAG
3302757 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
3302777 CATCTGAAGA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 90 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (73 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATCAGCATTG
CCAGGTAG
Found at i:3302885 original size:114 final size:112
Alignment explanation
Indices: 3302686--3303137 Score: 413
Period size: 114 Copynumber: 4.0 Consensus size: 112
3302676 CCAGGTAGAG
* * ** *
3302686 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGATGGATCGGCA-TTGC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT-ATCACTCGATGGATC-AAATTTTC
* * *
3302750 CAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAATAAA
64 CAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
* *
3302799 TTCATAATGAGAAGAATTTGTTCCAACCTTTTGTTTGAATTAGTCACTCGATGGATCAAATTTTC
1 TTCATAATGAGAAGAACTTGTT-CAACCTTTTGCTTGAATTA-TCACTCGATGGATCAAATTTTC
* * *
3302864 CAGAGAAAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAG
64 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
* * * * *
3302913 TTCATAATGATAAGAACTTGTTCAACCTTTTACATGACTCTATCACACAAAGA-GAGATATCAGC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAAT-TATCACTC---GATG-G--AT---C
3302977 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGA
56 A--AA-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-A
* * * * *
3303038 -TCATAATGAGAAGAACTTGTTTAACCTTTT--TT---TCATTACTCAATGGATC-AACTTTCCA
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTATCACTCGATGGATCAAATTTTCCA
* * * *
3303096 TAAAAAGTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAA
66 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
3303138 TTTGTTCAAC
Statistics
Matches: 285, Mismatches: 35, Indels: 46
0.78 0.10 0.13
Matches are distributed among these distances:
105 8 0.03
106 36 0.13
107 2 0.01
110 1 0.00
113 43 0.15
114 95 0.33
115 4 0.01
116 4 0.01
118 7 0.02
119 1 0.00
121 2 0.01
122 1 0.00
123 2 0.01
124 79 0.28
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (112 bp):
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTATCACTCGATGGATCAAATTTTCCA
GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
Found at i:3303357 original size:3 final size:3
Alignment explanation
Indices: 3303345--3303443 Score: 96
Period size: 3 Copynumber: 32.7 Consensus size: 3
3303335 TCGTTTTTAC
* * * * *
3303345 TAT T-T TAT TAT TAT TAAT AAT TAA TAA TAA TAA TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
3303391 TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T-AT TAT TAT
3303437 TA- TAT TA
1 TAT TAT TA
3303444 CAGGCCCAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 14
0.83 0.04 0.14
Matches are distributed among these distances:
2 6 0.07
3 68 0.80
4 11 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3303395 original size:28 final size:27
Alignment explanation
Indices: 3303350--3303439 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 27
3303340 TTTACTATTT
* * *
3303350 TATTATTATTAATAATTAATAATAATAA
1 TATTATTATTTATTATTAAT-ATATTAA
*
3303378 TATTATTATTTATTATT-AT-TATTAT
1 TATTATTATTTATTATTAATATATTAA
*
3303403 TATTATTATTTATTATTATTATTATTAA
1 TATTATTATTTATTATTAATA-TATTAA
*
3303431 TTTTATTAT
1 TATTATTAT
3303440 ATTACAGGCC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
25 21 0.40
26 1 0.02
27 2 0.04
28 28 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TATTATTATTTATTATTAATATATTAA
Found at i:3303418 original size:25 final size:25
Alignment explanation
Indices: 3303345--3303443 Score: 112
Period size: 25 Copynumber: 4.0 Consensus size: 25
3303335 TCGTTTTTAC
* * *
3303345 TATT-TTATTATTATTAATAATTAA
1 TATTATTATTATTATTATTTATTAT
* * *
3303369 TAATAATAATATTATTATTTATTAT
1 TATTATTATTATTATTATTTATTAT
3303394 TATTATTATTATTATTATTTATTAT
1 TATTATTATTATTATTATTTATTAT
3303419 TATTATTATTAATT-TTATTATATTA
1 TATTATTATT-ATTATTATT-TATTA
3303444 CAGGCCCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
24 3 0.05
25 52 0.83
26 8 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTATTATTATTATTATTTATTAT
Found at i:3304764 original size:31 final size:32
Alignment explanation
Indices: 3304729--3304788 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
3304719 ATTTTAAACC
* *
3304729 AGTTTT-ATTACTGTTTA-TATTTCAATATTAT
1 AGTTTTAATTAC-ATTTATTATTTAAATATTAT
3304760 AGTTTTAATTACATTTATTATTTAAATAT
1 AGTTTTAATTACATTTATTATTTAAATAT
3304789 ATTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (32 bp):
AGTTTTAATTACATTTATTATTTAAATATTAT
Found at i:3304857 original size:13 final size:13
Alignment explanation
Indices: 3304822--3304864 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
3304812 TTAATTATTA
*
3304822 TTATTATTATTTAG
1 TTATT-TTATTTAT
*
3304836 TCATATTTATTTAT
1 TTAT-TTTATTTAT
3304850 TTATTTTATTTAT
1 TTATTTTATTTAT
3304863 TT
1 TT
3304865 TTCTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 11 0.44
14 13 0.52
15 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:3304871 original size:17 final size:17
Alignment explanation
Indices: 3304809--3304864 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
3304799 GTTTTCAATA
*
3304809 TATTTAATTATTATTA-T
1 TATTTATTTATT-TTATT
**
3304826 TA-TTATTTAGTCATATT
1 TATTTATTTA-TTTTATT
3304843 TATTTATTTATTTTATT
1 TATTTATTTATTTTATT
3304860 TATTT
1 TATTT
3304865 TTCTATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 8 0.26
17 16 0.52
18 7 0.23
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTTATTTATTTTATT
Found at i:3306315 original size:43 final size:42
Alignment explanation
Indices: 3306220--3306315 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 42
3306210 TCATTAAAAA
3306220 AATT-ATAATTTGCTAATAGATAATAAAAATGACAAATTACT
1 AATTAATAATTTGCTAATAGATAATAAAAATGACAAATTACT
* * * * *
3306261 AATCCATTAATTTTCTAATAGATAATTAAATAT-ATTAAATTACT
1 AAT-TAATAATTTGCTAATAGATAA-TAAAAATGA-CAAATTACT
3306305 AATTAATAATT
1 AATTAATAATT
3306316 ATTATTTTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
41 3 0.07
43 24 0.55
44 17 0.39
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (42 bp):
AATTAATAATTTGCTAATAGATAATAAAAATGACAAATTACT
Found at i:3311105 original size:21 final size:18
Alignment explanation
Indices: 3311080--3311122 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3311070 TATTAATTAT
3311080 AATT-ATTAT-ATCATAAA
1 AATTAATTATAATCAT-AA
*
3311097 AATTAATTATAATCATTA
1 AATTAATTATAATCATAA
3311115 AATTAATT
1 AATTAATT
3311123 TCATTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 14 0.61
19 5 0.22
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTAATTATAATCATAA
Found at i:3311677 original size:14 final size:15
Alignment explanation
Indices: 3311658--3311686 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3311648 AATACCTTTT
3311658 AAAATAA-TTTAAAA
1 AAAATAATTTTAAAA
3311672 AAAATAATTTTAAAA
1 AAAATAATTTTAAAA
3311687 GATAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATAATTTTAAAA
Found at i:3313794 original size:12 final size:12
Alignment explanation
Indices: 3313777--3313808 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3313767 GGAGAAAGAA
3313777 ATGATTTTTAGG
1 ATGATTTTTAGG
3313789 ATGATTTTTAGG
1 ATGATTTTTAGG
3313801 ATGATTTT
1 ATGATTTT
3313809 GAAGCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (12 bp):
ATGATTTTTAGG
Found at i:3322080 original size:3 final size:3
Alignment explanation
Indices: 3322074--3322130 Score: 69
Period size: 3 Copynumber: 18.0 Consensus size: 3
3322064 GTAAAAAAAC
* *
3322074 AAT AAT AAT AATT AAT AAT AAT AAAT AAT AAT AAT AAT ATT AAAT ATT
1 AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT
3322122 AAT AAT AAT
1 AAT AAT AAT
3322131 CGGGACAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 39 0.83
4 8 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:3322092 original size:13 final size:13
Alignment explanation
Indices: 3322074--3322130 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
3322064 GTAAAAAAAC
3322074 AATAATAATAATT
1 AATAATAATAATT
*
3322087 AATAATAATAAAT
1 AATAATAATAATT
3322100 AATAATAATAA-T
1 AATAATAATAATT
*
3322112 -ATTA-AAT-ATT
1 AATAATAATAATT
3322122 AATAATAAT
1 AATAATAAT
3322131 CGGGACAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 1 0.03
10 4 0.11
11 6 0.16
12 4 0.11
13 23 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATAATAATAATT
Found at i:3322095 original size:16 final size:15
Alignment explanation
Indices: 3322074--3322130 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 15
3322064 GTAAAAAAAC
3322074 AATAATAATAATTAAT
1 AATAATAATAA-TAAT
3322090 AATAATAAATAATAAT
1 AATAAT-AATAATAAT
* *
3322106 AATAATATTAAATATT
1 AATAATAAT-AATAAT
3322122 AATAATAAT
1 AATAATAAT
3322131 CGGGACAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 2 0.06
16 29 0.81
17 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAATAATAATAAT
Found at i:3323182 original size:21 final size:21
Alignment explanation
Indices: 3323158--3323209 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3323148 GACTAGCAAC
*
3323158 GATCCGAACTGAAATTAGCTT
1 GATCCGAACTGAAATTAACTT
3323179 GATCCGAACTGAAATTAACTT
1 GATCCGAACTGAAATTAACTT
3323200 GATCCGAACT
1 GATCCGAACT
3323210 CAAACTGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (21 bp):
GATCCGAACTGAAATTAACTT
Found at i:3326337 original size:51 final size:51
Alignment explanation
Indices: 3326261--3326363 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
3326251 AGCCAGGATT
3326261 CGAACCCCTAATCTTACTTAAAAGACCTAATGCCTCATCCCACTAGACCAA
1 CGAACCCCTAATCTTACTTAAAAGACCTAATGCCTCATCCCACTAGACCAA
3326312 CGAACCCCTAATCTTACTTAAAAGACCTAATGCCTCATCCCACTAGACCAA
1 CGAACCCCTAATCTTACTTAAAAGACCTAATGCCTCATCCCACTAGACCAA
3326363 C
1 C
3326364 CCAGTTTGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.35, C:0.36, G:0.08, T:0.21
Consensus pattern (51 bp):
CGAACCCCTAATCTTACTTAAAAGACCTAATGCCTCATCCCACTAGACCAA
Found at i:3326595 original size:17 final size:17
Alignment explanation
Indices: 3326550--3326586 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3326540 TATAGTAGGG
3326550 GCAGATTCATTAAGTTT
1 GCAGATTCATTAAGTTT
3326567 GCAGATTCATTAAGTTT
1 GCAGATTCATTAAGTTT
3326584 GCA
1 GCA
3326587 TATTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (17 bp):
GCAGATTCATTAAGTTT
Found at i:3327798 original size:3 final size:3
Alignment explanation
Indices: 3327790--3327864 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
3327780 GGGTTATTTA
*
3327790 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3327838 TAT T-T TAT TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3327865 CAAGTTTATG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3330238 original size:40 final size:41
Alignment explanation
Indices: 3330122--3330243 Score: 120
Period size: 42 Copynumber: 3.0 Consensus size: 41
3330112 TCTTACTTAG
* * *
3330122 TAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTC-GGCCATCAGTAAGTCTTTCGAGTAAGATGAT
* * * *
3330164 TAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGTAAGATGA-
1 TAAGTCC-TTCGGCCATCAGTAAGTCTTTCGAGTAAGATGAT
* * * *
3330205 TAAGTCCTTCGGCCATCCGTAAGACCTTCGAGTAGGATG
1 TAAGTCCTTCGGCCATCAGTAAGTCTTTCGAGTAAGATG
3330244 TTTTCACATG
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
40 26 0.40
41 6 0.09
42 31 0.48
43 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (41 bp):
TAAGTCCTTCGGCCATCAGTAAGTCTTTCGAGTAAGATGAT
Found at i:3330443 original size:42 final size:40
Alignment explanation
Indices: 3330382--3330483 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 40
3330372 AATTGGTAAG
* *
3330382 TCCTTCGGGCATCAGTAAGTCTTTCGATC-ATGATGATTAAA
1 TCCTTCGGTCATCAGTAAGTCTTTCGAGCGA-GATGA-TAAA
* *
3330423 TCCTTCAGGTCATCTGTAAGTCTTTCGAGCGAGATGATAAG
1 TCCTTC-GGTCATCAGTAAGTCTTTCGAGCGAGATGATAAA
*
3330464 TCCTTCGGTCTATCCGTAAG
1 TCCTTCGGTC-ATCAGTAAG
3330484 ACCTTCGGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
40 4 0.08
41 23 0.43
42 25 0.47
43 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (40 bp):
TCCTTCGGTCATCAGTAAGTCTTTCGAGCGAGATGATAAA
Found at i:3330483 original size:41 final size:41
Alignment explanation
Indices: 3330378--3330483 Score: 126
Period size: 41 Copynumber: 2.6 Consensus size: 41
3330368 CCAAAATTGG
* *
3330378 TAAGTCCTTCGGGCATCAGTAAGTCTTTCGATCATGATGAT
1 TAAGTCCTTCGGTCATCAGTAAGTCTTTCGAGCATGATGAT
* *
3330419 TAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCGA-GATGA-
1 TAAGTCCTTC-GGTCATCAGTAAGTCTTTCGAGC-ATGATGAT
*
3330460 TAAGTCCTTCGGTCTATCCGTAAG
1 TAAGTCCTTCGGTC-ATCAGTAAG
3330484 ACCTTCGGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 4 0.07
41 26 0.46
42 25 0.45
43 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
TAAGTCCTTCGGTCATCAGTAAGTCTTTCGAGCATGATGAT
Found at i:3330882 original size:215 final size:215
Alignment explanation
Indices: 3330423--3330885 Score: 603
Period size: 218 Copynumber: 2.1 Consensus size: 215
3330413 GATGATTAAA
* * * * * *
3330423 TCCTTCAGGTCATCTGTAAGTCTTTCGAGCGAGATGATAAGTCCTTCGGTCTATCCGTAAGACCT
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAGCGAGATGATAAGTCATTCGGGCCATCCATAAGACCT
* * * *
3330488 TCGGGTAGGATGTTTTCACATGATTTCAAAAAAAATGAGAAAGTAATTTCCAAAGTTTCTCATTT
66 TCAGGCAGGATGTTTTCACATGATTTCAAAAAAAAAGAGAAAGTAATTTCCAAAGTTTCTCAATT
* * *
3330553 AGTATTTGTTGAAAATGAAATTTTTGAAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGC
131 AATATTTGTAGAAAATGAAATCTTTGAAAAAGTAAG-AA--GATTTCCAAAGTTTCTTACCCAGC
*
3330618 AAACTATTTCCCAAATTGGTAAG
193 AAACTATTTCCAAAATTGGTAAG
* * *
3330641 TCCTTCGGGTCATCTGTAATTCTTTCGAGCGAGATGATAAGTCATTCGGGCCATCTATAAGACCT
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAGCGAGATGATAAGTCATTCGGGCCATCCATAAGACCT
* * *
3330706 TCAGGCATGATGGTTTT-ACATGATTTTCATTAAAAAAAAGAGAAAGTGATTTCCAAAGTTTTTC
66 TCAGGCAGGAT-GTTTTCACATGA-TTTCA--AAAAAAAAGAGAAAGTAATTTCCAAAGTTTCTC
*
3330770 AATTAATATTT-TCAGAAAATGAAATCTTTG-AAAAGTAAG-A-ATTTCCAAAGTTTCTTACCTA
127 AATTAATATTTGT-AGAAAATGAAATCTTTGAAAAAGTAAGAAGATTTCCAAAGTTTCTTACCCA
*
3330831 GTAAACTATTTCCAAAATTGGTAAG
191 GCAAACTATTTCCAAAATTGGTAAG
* *
3330856 TTCTTCGGGCCATCAGTAAGTCTTTCGAGC
1 TCCTTCGGGCCATCTGTAAGTCTTTCGAGC
3330886 ATGATCATTA
Statistics
Matches: 216, Mismatches: 24, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
215 69 0.32
218 73 0.34
219 10 0.05
220 10 0.05
221 54 0.25
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (215 bp):
TCCTTCGGGCCATCTGTAAGTCTTTCGAGCGAGATGATAAGTCATTCGGGCCATCCATAAGACCT
TCAGGCAGGATGTTTTCACATGATTTCAAAAAAAAAGAGAAAGTAATTTCCAAAGTTTCTCAATT
AATATTTGTAGAAAATGAAATCTTTGAAAAAGTAAGAAGATTTCCAAAGTTTCTTACCCAGCAAA
CTATTTCCAAAATTGGTAAG
Found at i:3330931 original size:42 final size:41
Alignment explanation
Indices: 3330874--3330953 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
3330864 GCCATCAGTA
*
3330874 AGTCTTTCGAGCATGATCATTAAATCCTTTGGGTTATCTGTC
1 AGTCTTTCGAGCATGATCATTAAA-CCTTCGGGTTATCTGTC
*
3330916 AGTCTTTCGAGCATGATGATTAAACCTTCGGGTTATCT
1 AGTCTTTCGAGCATGATCATTAAACCTTCGGGTTATCT
3330954 ATTGGTCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 13 0.36
42 23 0.64
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (41 bp):
AGTCTTTCGAGCATGATCATTAAACCTTCGGGTTATCTGTC
Found at i:3334347 original size:753 final size:752
Alignment explanation
Indices: 3332598--3334780 Score: 3425
Period size: 754 Copynumber: 2.9 Consensus size: 752
3332588 TAGCGTAATT
* * * * * *
3332598 GACTCCCGATCCCTTTTCAGAATTAGTTTTTGGTTAAACGGATTTCACTTTTTATCTTTTAAAAT
1 GACTCCCGAACCCTTTTCAGAATGAATTTCTGGTTAAACGCATATCACTTTTTATCTTTTAAAAT
3332663 CATTTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAA-CC-----T--
66 CATTTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAACCCAAAGGTCG
* *
3332720 A--A-A-TCCAAATTTGTTTATTTATACATTTATTTTAAAATCCGATATTTTCTAAAATTAAGTT
131 ATGAGACTCCAAATTTGTTTATTTATGCATTTATTTTAAAACCCGATATTTTCTAAAATTAAGTT
* * *
3332781 GGATCGCTCCCTGCCATAGCCCCAAAATTATTTTGTTAAATATTATTTTGTGCAAATAATTTATA
196 GGATCTCTCCCCGTCATAGCCCCAAAATTATTTTGTTAAATATTATTTTGTGCAAATAATTTATA
* *
3332846 GAAACGCGCCTTAACTGACAATGACTATGTTTCCAAGAATTGTTCGAACAAAATAATACCTTTTA
261 GAAACGCGCCTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCGAACAAAATAATACCTTTTA
*
3332911 TATTCGAATGACTTTTTAAAATATTTAATATATTTATTTTATCTATAAGCTAAGAGAATATTATT
326 TATTCGAATGACTTTTTAAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTATT
* * * *
3332976 TTGTATGGAGAATCTATGAAAATGTGCCTTAACTGAAAAGGATCATGTTCCCAATGATTTTTCAT
391 TTGTATGGGGAATCTATGAAAATGTGTCTTAACTGACAAGGATCACGTTCCCAATGATTTTTCAT
* *
3333041 ACAAAGTAATACCTTTTTATATTCGAGTTGTCTTAAAAATTATTCTGTATATATGATTTATTAAA
456 ACAAAGTAATACCTTTTTATATTCGAGTTGTTTTAAAAATTATTATGTATATATGATTTATTAAA
* * *
3333106 ATTAGGGCAATATTATTTCGTATGGAGAATCTATGGAAATCCCCCTTAATTGACAAGAAATATAT
521 ATTAGGGCAATATTATTTCGTATGGAGAATCTATGGAAAT-CCCCTTAACTGACAAGGAAGATAT
* *
3333171 TTTCGAGAATTGTTCGTACAAAATAATATCTCTTTTTATTTTTCT-AAAAAGGATCACAATTTAA
585 TTTCGAGAATTGTTCGTACAAAATAATACCTCTTTTTATTTTTCTAAAAAATGATCACAATTTAA
* *
3333235 ATGTATATTCAAGTTTTCCAATTTCAACATCCAGATGACGTATAATCGCTTATGTACCGATTTTG
650 ATGTATATTCAAGTTTTCCAAATTCAACATCCAGATGACGTATAATCGCTTAGGTACCGATTTTG
**
3333300 GGAGTTGTGGGGGTATTAATCATTCCCCACGCGTAATC
715 GGAGTTGTGGGGGTATTAATCATTCCCCACGCAAAATC
** *
3333338 GACTCCAAAACCCTTTTCAGAATGAATTCCTGGTTAAACGCATATCACTTTTTATCTTTTAAAAT
1 GACTCCCGAACCCTTTTCAGAATGAATTTCTGGTTAAACGCATATCACTTTTTATCTTTTAAAAT
*
3333403 CATTTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGATCTACCTAACCCAAAGGTCG
66 CATTTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAACCCAAAGGTCG
*
3333468 ATGGAGACTCCAAATTTGTTTATTTATGCATTTATTTTAAAACCCGATATTTTATAAAATTAAGT
131 AT-GAGACTCCAAATTTGTTTATTTATGCATTTATTTTAAAACCCGATATTTTCTAAAATTAAGT
*
3333533 TGGATTTCTCCCCGTCATAGCCCCAAAATTATTTTGTTAAATATTATTTTGTGCAAATAATTTAT
195 TGGATCTCTCCCCGTCATAGCCCCAAAATTATTTTGTTAAATATTATTTTGTGCAAATAATTTAT
* * *
3333598 AGAAACACGCCTTAACTAACAATGAGTGTGTTTCCAAGAATTGTTCGAACAAAATAATACTTTTT
260 AGAAACGCGCCTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCGAACAAAATAATACCTTTT
*
3333663 ATATTCGAATGATTTTTTTAAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTA
325 ATATTCGAATGA-CTTTTTAAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTA
** * * *
3333728 TTTTAAATGGGGAATCTGTGTAAATGTGTCTTAACTGACAATGATCACGTTCCCAATGATTTTTC
389 TTTTGTATGGGGAATCTATGAAAATGTGTCTTAACTGACAAGGATCACGTTCCCAATGATTTTTC
*
3333793 ATACAAAGT-ATACCTTTTTATATTCGAGTTGTTTTAAAAATTATTATGTATATATGATTCATTA
454 ATACAAAGTAATACCTTTTTATATTCGAGTTGTTTTAAAAATTATTATGTATATATGATTTATTA
* * * *
3333857 AAATTAGGGCAATATTATTTCGTACGGAGAATCCATTGAAATCATCCTTAACTGACAAGGAAGAT
519 AAATTAGGGCAATATTATTTCGTATGGAGAATCTATGGAAATC-CCCTTAACTGACAAGGAAGAT
* **
3333922 ATTTTCGAGAATTATTCGTACAAAATAATACCAATTTTTATTTTTCTAAAAAATGATCACAATTT
583 ATTTTCGAGAATTGTTCGTACAAAATAATACCTCTTTTTATTTTTCTAAAAAATGATCACAATTT
*
3333987 AAATGTATATTCAAGTTTTCCAAATTCAACATCCAGATGGCGTATAATCGCTTAGGTACCGATTT
648 AAATGTATATTCAAGTTTTCCAAATTCAACATCCAGATGACGTATAATCGCTTAGGTACCGATTT
* * *
3334052 TGGGCA-TTGTGGGGGTGTTAATCCTTCCCCAGGCAAAATC
713 TGGG-AGTTGTGGGGGTATTAATCATTCCCCACGCAAAATC
* *
3334092 GACTCCCGAACCCTTTTCAAAATGAATTTCTGGTTAAACGCATATCATTTTTTATCTTTTAAAAT
1 GACTCCCGAACCCTTTTCAGAATGAATTTCTGGTTAAACGCATATCACTTTTTATCTTTTAAAAT
*
3334157 CATTTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTGCCTAACCCAAAGGTCG
66 CATTTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAACCCAAAGGTCG
* * *
3334222 ATGACGACTCCAAAATTGTTTATTTATGCATTTATTTTAAAACCCAATATTTTCTAAAATTAAGC
131 ATGA-GACTCCAAATTTGTTTATTTATGCATTTATTTTAAAACCCGATATTTTCTAAAATTAAGT
* * *
3334287 TGGATCTCTCCCCGTCATAGCCTCAAAATTA-TTTGTTAAATATTATTTTCTGCGAATAATTTAT
195 TGGATCTCTCCCCGTCATAGCCCCAAAATTATTTTGTTAAATATTATTTTGTGCAAATAATTTAT
*
3334351 AGAAACGCGACTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCGAACAAAATAATACCTTTT
260 AGAAACGCGCCTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCGAACAAAATAATACCTTTT
*
3334416 ATATTCGAATGACTTTTT-AAATATTTAATATATGTATTTTATCTATAAGCTAAGATAATATTAT
325 ATATTCGAATGACTTTTTAAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTAT
* *
3334480 TTTGTATGGGGAATCTATGGAAACGT-TCCTTAACTGACAAGGATCACGTTCCCAATGATTTTTC
390 TTTGTATGGGGAATCTATGAAAATGTGT-CTTAACTGACAAGGATCACGTTCCCAATGATTTTTC
3334544 ATACAAAGTAATACCTTTTTATATTCGAGTTGTTTTAAAAAATTATTATGTATATATGATTTATT
454 ATACAAAGTAATACCTTTTTATATTCGAGTTGTTTT-AAAAATTATTATGTATATATGATTTATT
* *
3334609 AAATATTATGACAATATTATTTCGTATGGAGAATCTATGGAAATCCCTCTTAACTGACAAGGAAG
518 AAA-ATTAGGGCAATATTATTTCGTATGGAGAATCTATGGAAATCCC-CTTAACTGACAAGGAAG
* ** *
3334674 GTATTTTCGAGAATTGTTTATACAAAATAATACCTCTTTTTATTTTT-TATTTTAAAATGATCAC
581 ATATTTTCGAGAATTGTTCGTACAAAATAATACCTCTTTTTATTTTTCTA---AAAAATGATCAC
3334738 AATTTAAATGTATATTCAAGTTTT-CAAATTTCAACATCCAGAT
643 AATTTAAATGTATATTCAAGTTTTCCAAA-TTCAACATCCAGAT
3334781 CCCGAACCCA
Statistics
Matches: 1319, Mismatches: 97, Indels: 38
0.91 0.07 0.03
Matches are distributed among these distances:
740 109 0.08
741 2 0.00
746 1 0.00
748 1 0.00
750 1 0.00
751 111 0.08
752 33 0.03
753 477 0.36
754 530 0.40
755 5 0.00
756 49 0.04
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (752 bp):
GACTCCCGAACCCTTTTCAGAATGAATTTCTGGTTAAACGCATATCACTTTTTATCTTTTAAAAT
CATTTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAACCCAAAGGTCG
ATGAGACTCCAAATTTGTTTATTTATGCATTTATTTTAAAACCCGATATTTTCTAAAATTAAGTT
GGATCTCTCCCCGTCATAGCCCCAAAATTATTTTGTTAAATATTATTTTGTGCAAATAATTTATA
GAAACGCGCCTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCGAACAAAATAATACCTTTTA
TATTCGAATGACTTTTTAAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTATT
TTGTATGGGGAATCTATGAAAATGTGTCTTAACTGACAAGGATCACGTTCCCAATGATTTTTCAT
ACAAAGTAATACCTTTTTATATTCGAGTTGTTTTAAAAATTATTATGTATATATGATTTATTAAA
ATTAGGGCAATATTATTTCGTATGGAGAATCTATGGAAATCCCCTTAACTGACAAGGAAGATATT
TTCGAGAATTGTTCGTACAAAATAATACCTCTTTTTATTTTTCTAAAAAATGATCACAATTTAAA
TGTATATTCAAGTTTTCCAAATTCAACATCCAGATGACGTATAATCGCTTAGGTACCGATTTTGG
GAGTTGTGGGGGTATTAATCATTCCCCACGCAAAATC
Found at i:3335405 original size:685 final size:682
Alignment explanation
Indices: 3334095--3335461 Score: 2251
Period size: 685 Copynumber: 2.0 Consensus size: 682
3334085 CAAAATCGAC
* *
3334095 TCCCGAACCCTTTTCAAAATGAATTTCTGGTTAAACGCATATCATTTTTTATCTTTTAAAATCAT
1 TCCCGAACCCATTTCAAAATGAATTTATGGTTAAACGCATATCATTTTTTATCTTTTAAAATCAT
*
3334160 TTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTGCCTAACCCAAAGGTCGATG
66 TTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAACCCAAAGGTCGATG
3334225 ACGACTCCAAAATTGTTTATTTATGCATTTATTTTAAAACCCAATATTTTCTAAAATTAAGCTGG
131 ACGACTCCAAAATTGTTTATTTATGCATTTATTTTAAAACCCAATATTTTCTAAAATTAAGCTGG
* *
3334290 ATCTCTCCCCGTCATAGCCTCAAAATTATTTGTTAAATATTATTTTCTGCGAATAATTTATAGAA
196 ATCGCTCCCCGTCATAGCCCCAAAATTATTTGTTAAATATTATTTTCTGCGAATAATTTATAGAA
* *
3334355 ACGCGACTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCGAACAAAATAATACCTTTTATAT
261 ACGCGACTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCAAACAAAATAATACATTTTATAT
*
3334420 TCGAATGACTTTTTAAATATTTAATATATGTATTTTATCTATAAGCTAAGATAATATTATTTTGT
326 TCGAATGACTTTTTAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTATTTTGT
*
3334485 ATGGGGAATCTATGGAAACGTTCCTTAACTGACAAGGATCACGTTCCCAATGATTTTTCATACAA
391 ATGGGGAATCTATGGAAACGTGCCTTAACTGACAAGGATCACGTTCCCAATGATTTTTCATACAA
3334550 AGTAATACCTTTTTATATTCGAGTTGTTTTAAAAAATTATTATGTATATATGATTTATTAAATAT
456 AGTAATACCTTTTTATATTCGAGTTGTTTTAAAAAATTATTATGTATATATGATTTATTAAATAT
* * * * * * *
3334615 TATGACAATATTATTTCGTATGGAGAATCTATGGAAATCCCTCTTAACTGACAAGGAAGGTATTT
521 TAGGACAATATTATTTCGTATGGAGAATCCATGAAAATCCCCCTTAACTCACAAGAAAGATATTT
* * *
3334680 TCGAGAATTGTTTATACAAAATAATACCTCTTTTTATTTTT-TATTTTAAAATGATCACAATTTA
586 TCGAGAATTGTTCATACAAAATAATACCTATTTTTATTTTTCTA----AAAAGGATCACAATTTA
3334744 AATGTATATTCAAG-TTTTCAAATTTCAACATCCAGA
647 AATGTATATTCAAGTTTTTC-AATTTCAACATCCAGA
*
3334780 TCCCGAACCCATTTCAGAATGAATTTATGGTTAAACGCATATCATTTTTTATCTTTTAAAATCAT
1 TCCCGAACCCATTTCAAAATGAATTTATGGTTAAACGCATATCATTTTTTATCTTTTAAAATCAT
*
3334845 TTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAACCCAAAGGTTGATG
66 TTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAACCCAAAGGTCGATG
** * * ** *
3334910 GTGACTCCAAATTTGTTTATTTATTCATTTATTTTAAAACCTGATATTTTCTAAAATTAAGTTGG
131 ACGACTCCAAAATTGTTTATTTATGCATTTATTTTAAAACCCAATATTTTCTAAAATTAAGCTGG
*
3334975 ATCGCTCCCAAC-T-ATAGCCCCAAAATTATTTTGTTAAATATTATTTTGTGCGAATAATTTATA
196 ATCGCTCCC--CGTCATAGCCCCAAAATTA-TTTGTTAAATATTATTTTCTGCGAATAATTTATA
*
3335038 GAAACGCTACTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCAAACAAAATAATACATTTTA
258 GAAACGCGACTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCAAACAAAATAATACATTTTA
**
3335103 TATTCGAATGTTTTTTTTAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTATT
323 TATTCGAATG-ACTTTTTAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTATT
* * * *
3335168 TTGTATGGGGAGTCTATGGAAATGTGCCTTAACTGATAAGGATCATGTTCCCAATGATTTTTCAT
387 TTGTATGGGGAATCTATGGAAACGTGCCTTAACTGACAAGGATCACGTTCCCAATGATTTTTCAT
3335233 ACAAAGTAATACCTTTTTATATTCGAGTTGTTTT-AAAAATTATTATGTATATATGATTTATTAA
452 ACAAAGTAATACCTTTTTATATTCGAGTTGTTTTAAAAAATTATTATGTATATATGATTTATTAA
*
3335297 A-ATTAGGACAATATTATTTCGTATGGAGAATCCATTAAAATCCCCCTTAACTCACAAGAAAGAT
517 ATATTAGGACAATATTATTTCGTATGGAGAATCCATGAAAATCCCCCTTAACTCACAAGAAAGAT
* * *
3335361 ATTTTTGAGAATTGTTCGTACAAAATAATACCTATTTTTATTTTTCTAAAAAGGATTACAATTTA
582 ATTTTCGAGAATTGTTCATACAAAATAATACCTATTTTTATTTTTCTAAAAAGGATCACAATTTA
3335426 AATGTATATTCAAGTTTTTCAATTTCAACATCCAGA
647 AATGTATATTCAAGTTTTTCAATTTCAACATCCAGA
3335462 CGACGTATAA
Statistics
Matches: 636, Mismatches: 40, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
682 45 0.07
683 5 0.01
685 301 0.47
686 139 0.22
687 146 0.23
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (682 bp):
TCCCGAACCCATTTCAAAATGAATTTATGGTTAAACGCATATCATTTTTTATCTTTTAAAATCAT
TTTTCTTAAAATTATTTTAAAAGATATTTTCTAGGTACTCGACCTACCTAACCCAAAGGTCGATG
ACGACTCCAAAATTGTTTATTTATGCATTTATTTTAAAACCCAATATTTTCTAAAATTAAGCTGG
ATCGCTCCCCGTCATAGCCCCAAAATTATTTGTTAAATATTATTTTCTGCGAATAATTTATAGAA
ACGCGACTTAACTGACAATGAGTGTGTTTCCAAGAATTGTTCAAACAAAATAATACATTTTATAT
TCGAATGACTTTTTAAATATTTAATATATGTATTTTATCTATAAGCTAAGAGAATATTATTTTGT
ATGGGGAATCTATGGAAACGTGCCTTAACTGACAAGGATCACGTTCCCAATGATTTTTCATACAA
AGTAATACCTTTTTATATTCGAGTTGTTTTAAAAAATTATTATGTATATATGATTTATTAAATAT
TAGGACAATATTATTTCGTATGGAGAATCCATGAAAATCCCCCTTAACTCACAAGAAAGATATTT
TCGAGAATTGTTCATACAAAATAATACCTATTTTTATTTTTCTAAAAAGGATCACAATTTAAATG
TATATTCAAGTTTTTCAATTTCAACATCCAGA
Found at i:3339786 original size:20 final size:20
Alignment explanation
Indices: 3339761--3339800 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3339751 TAGCCCACAA
3339761 GAATTTGCACTCAAGATGAC
1 GAATTTGCACTCAAGATGAC
3339781 GAATTTGCACTCAAGATGAC
1 GAATTTGCACTCAAGATGAC
3339801 TTTAAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
GAATTTGCACTCAAGATGAC
Found at i:3346753 original size:269 final size:269
Alignment explanation
Indices: 3346274--3346815 Score: 1075
Period size: 269 Copynumber: 2.0 Consensus size: 269
3346264 GCAAAATAAG
3346274 AGAGCTTGACTAGAAACTTTCTAACTTTGTTTAGCATAGACTAGATACAATCACACTGTAATATC
1 AGAGCTTGACTAGAAACTTTCTAACTTTGTTTAGCATAGACTAGATACAATCACACTGTAATATC
3346339 CCAAAATCTGAGTTAGTGACTAAAATGAGAATTTTTAGAATTTGGGGATTTATTTAGGAAAGTTG
66 CCAAAATCTGAGTTAGTGACTAAAATGAGAATTTTTAGAATTTGGGGATTTATTTAGGAAAGTTG
3346404 AAAAGTTTAAGGACTTAAATATGAATATTTTAGTATTGGATTAAATTGTAATTAGGGAAAGATTG
131 AAAAGTTTAAGGACTTAAATATGAATATTTTAGTATTGGATTAAATTGTAATTAGGGAAAGATTG
3346469 AAGGGTATTATGGTCTTTGTCCTTTCAAAGTTATTTTTCCCTCTTAAATATAAGTGAAACACGTG
196 AAGGGTATTATGGTCTTTGTCCTTTCAAAGTTATTTTTCCCTCTTAAATATAAGTGAAACACGTG
3346534 GGAGGGGGA
261 GGAGGGGGA
3346543 AGAGCTTGACTAGAAACTTTCTAACTTTGTTTAGCATAGACTAGATACAATCACACTGTAATATC
1 AGAGCTTGACTAGAAACTTTCTAACTTTGTTTAGCATAGACTAGATACAATCACACTGTAATATC
*
3346608 CCAAAATCTGAGTTAGTGACTAAAATGAGAATTTTTGGAATTTGGGGATTTATTTAGGAAAGTTG
66 CCAAAATCTGAGTTAGTGACTAAAATGAGAATTTTTAGAATTTGGGGATTTATTTAGGAAAGTTG
3346673 AAAAGTTTAAGGACTTAAATATGAATATTTTAGTATTGGATTAAATTGTAATTAGGGAAAGATTG
131 AAAAGTTTAAGGACTTAAATATGAATATTTTAGTATTGGATTAAATTGTAATTAGGGAAAGATTG
3346738 AAGGGTATTATGGTCTTTGTCCTTTCAAAGTTATTTTTCCCTCTTAAATATAAGTGAAACACGTG
196 AAGGGTATTATGGTCTTTGTCCTTTCAAAGTTATTTTTCCCTCTTAAATATAAGTGAAACACGTG
3346803 GGAGGGGGA
261 GGAGGGGGA
3346812 AGAG
1 AGAG
3346816 TTGTGTGGAA
Statistics
Matches: 272, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
269 272 1.00
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (269 bp):
AGAGCTTGACTAGAAACTTTCTAACTTTGTTTAGCATAGACTAGATACAATCACACTGTAATATC
CCAAAATCTGAGTTAGTGACTAAAATGAGAATTTTTAGAATTTGGGGATTTATTTAGGAAAGTTG
AAAAGTTTAAGGACTTAAATATGAATATTTTAGTATTGGATTAAATTGTAATTAGGGAAAGATTG
AAGGGTATTATGGTCTTTGTCCTTTCAAAGTTATTTTTCCCTCTTAAATATAAGTGAAACACGTG
GGAGGGGGA
Found at i:3347422 original size:22 final size:22
Alignment explanation
Indices: 3347395--3347446 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
3347385 GTATGAACAA
3347395 TATCGATACCCTATGAAT-GA-GG
1 TATCGATACCCTATG--TGGAGGG
3347417 TATCGATA-CCTATGTGGAGGG
1 TATCGATACCCTATGTGGAGGG
3347438 TATCGATAC
1 TATCGATAC
3347447 ATGGGGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 16 0.59
22 8 0.30
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (22 bp):
TATCGATACCCTATGTGGAGGG
Found at i:3358284 original size:20 final size:21
Alignment explanation
Indices: 3358259--3358298 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3358249 TTTATCCCAA
3358259 TTCATCC-AGTATCGATACTT
1 TTCATCCTAGTATCGATACTT
3358279 TTCATCCTAGTATCGATACT
1 TTCATCCTAGTATCGATACT
3358299 CAAACCCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (21 bp):
TTCATCCTAGTATCGATACTT
Found at i:3359739 original size:48 final size:48
Alignment explanation
Indices: 3359663--3359969 Score: 389
Period size: 48 Copynumber: 6.3 Consensus size: 48
3359653 TGGATATATA
** ** *
3359663 GATAGATAAATAGATGGATGGATGGATGGATGGATGGATGGATGCATG
1 GATAGATGGATAGATGGATATATGGATGGATGGATGGATGGATGGATG
* * *
3359711 GATGGATGGATGGATTGATATATGGATGGATGGATGGATGGATGGATG
1 GATAGATGGATAGATGGATATATGGATGGATGGATGGATGGATGGATG
* ** *
3359759 GATATATGGATGGATGGATGGATATATGGATGGATATATGGATGGATTGATG
1 G--ATA--GATGGATAGATGGATATATGGATGGATGGATGGATGGATGGATG
* *
3359811 GATATATGGATAGATAGATATATGGATGGATGGATGGATGGATGGATG
1 GATAGATGGATAGATGGATATATGGATGGATGGATGGATGGATGGATG
* * **
3359859 GATATATGGATAGATGGATATATGGATGGATGGATGGATAGATATATG
1 GATAGATGGATAGATGGATATATGGATGGATGGATGGATGGATGGATG
* *
3359907 GATAGATGGATAGATGGATATATGGATGGATGGATGGATAGATGGATA
1 GATAGATGGATAGATGGATATATGGATGGATGGATGGATGGATGGATG
*
3359955 GATGGATGGATAGAT
1 GATAGATGGATAGAT
3359970 AGATTTTGTC
Statistics
Matches: 227, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
48 181 0.80
50 5 0.02
52 41 0.18
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (48 bp):
GATAGATGGATAGATGGATATATGGATGGATGGATGGATGGATGGATG
Found at i:3359973 original size:4 final size:4
Alignment explanation
Indices: 3359675--3359965 Score: 303
Period size: 4 Copynumber: 72.8 Consensus size: 4
3359665 TAGATAAATA
*
3359675 GATG GATG GATG GATG GATG GATG GATG GATG CATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * *
3359723 GATT GATA TATG GATG GATG GATG GATG GATG GATG GATA TATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * *
3359771 GATG GATG GATA TATG GATG GATA TATG GATG GATT GATG GATA TATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * *
3359819 GATA GATA GATA TATG GATG GATG GATG GATG GATG GATG GATA TATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * *
3359867 GATA GATG GATA TATG GATG GATG GATG GATA GATA TATG GATA GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * *
3359915 GATA GATG GATA TATG GATG GATG GATG GATA GATG GATA GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
3359963 GAT
1 GAT
3359966 AGATAGATTT
Statistics
Matches: 232, Mismatches: 55, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 232 1.00
ACGTcount: A:0.31, C:0.00, G:0.39, T:0.29
Consensus pattern (4 bp):
GATG
Found at i:3360825 original size:43 final size:43
Alignment explanation
Indices: 3360764--3360849 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
3360754 TGGCTTTAGA
* * *
3360764 GAAGTTAGGAGAGAAAGTT-TTTCTCTATATGTAAATTTTTGTT
1 GAAGTTAGGACAGAAAGTTGTCTC-CTATATGTAAAGTTTTGTT
*
3360807 GAAGTTAGGACTGAAAGTTGTCTCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGACAGAAAGTTGTCTCCTATATGTAAAGTTTTGTT
3360850 TGATGCACGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 35 0.92
44 3 0.08
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (43 bp):
GAAGTTAGGACAGAAAGTTGTCTCCTATATGTAAAGTTTTGTT
Found at i:3367687 original size:54 final size:54
Alignment explanation
Indices: 3367601--3367708 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
3367591 TAACTGAAAA
* * * *
3367601 ATCTGAGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAACCACAGGAAAGAATGAATGTGTAGTCAAATATTTTACGAAC
* *
3367655 ATCTGAGCAGAAACCACAGGAAAGAATTAATGTGTAGTTAAATATTTTACGAAC
1 ATCTGAGCAGAAACCACAGGAAAGAATGAATGTGTAGTCAAATATTTTACGAAC
3367709 CAGTTATTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (54 bp):
ATCTGAGCAGAAACCACAGGAAAGAATGAATGTGTAGTCAAATATTTTACGAAC
Found at i:3368101 original size:21 final size:20
Alignment explanation
Indices: 3368075--3368128 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
3368065 TACATCTACA
3368075 CTCTTCAAAGATGATAAATT
1 CTCTTCAAAGATGATAAATT
*
3368095 CCTCTTCAAAGATGATAGATT
1 -CTCTTCAAAGATGATAAATT
3368116 CTCTTTCAAAGAT
1 CTC-TTCAAAGAT
3368129 AAAAGCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (20 bp):
CTCTTCAAAGATGATAAATT
Found at i:3368681 original size:113 final size:113
Alignment explanation
Indices: 3368484--3368936 Score: 486
Period size: 113 Copynumber: 3.9 Consensus size: 113
3368474 GCAAAGATTC
** * * *
3368484 GAATCCATCACTTAATGGATCAAC-ATGCCGGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCACTCGATGGATCAACTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
3368548 AATGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* *
3368596 GAATCCATCACTCGATGGATC-AGTATTTCTAGGTAGAGTTCATAATGAGAAGAACTCATCTGAA
1 GAATCCATCACTCGATGGATCAACT-TTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
3368660 GAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * * * *
3368709 GAATTCATCACTCGATGGATCAACTTTTCCAGAG-AAAGTTCACAATGAGAATAACTCATTTGAA
1 GAATCCATCACTCGATGGATCAACTTTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
3368773 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * * * * * * *
3368821 GACTCTATCACAGAAGGAGATAGATCAGCACCAACATTTCCAGATAAAGTTCATAATGAGAAGAA
1 GAATCCATCAC---------TCGAT--GGATCAACTTTTCCAGGTAGAGTTCATAATGAGAAGAA
* * *
3368886 CTTATCTGAA-AAGGAAGAAGAAGTTCATAATGAGAA-AAATTGTTCGACCTT
55 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
3368937 AATTTGATTC
Statistics
Matches: 287, Mismatches: 37, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
111 1 0.00
112 71 0.25
113 131 0.46
114 3 0.01
121 4 0.01
122 13 0.05
123 64 0.22
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (113 bp):
GAATCCATCACTCGATGGATCAACTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
Done.