Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007891.1 Hibiscus syriacus cultivar Beakdansim tig00110273_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: 893409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:477495 original size:9 final size:9
Alignment explanation
Indices: 477450--477501 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
477440 AAGATGGAGG
477450 AAAAAAAGA
1 AAAAAAAGA
477459 AAAATAAAG-
1 AAAA-AAAGA
*
477468 AAAGAAAGA
1 AAAAAAAGA
477477 AGAAAAAAGA
1 A-AAAAAAGA
*
477487 AATAAAAGA
1 AAAAAAAGA
477496 AAAAAA
1 AAAAAA
477502 TAAGAAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 4 0.11
9 20 0.56
10 12 0.33
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:477509 original size:14 final size:14
Alignment explanation
Indices: 477465--477510 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
477455 AAGAAAAATA
* *
477465 AAGAAAGAAAGAAG
1 AAGAAAAAAATAAG
477479 AA-AAAAGAAATAA-
1 AAGAAAA-AAATAAG
477492 AAGAAAAAAATAAG
1 AAGAAAAAAATAAG
477506 AAGAA
1 AAGAA
477511 TAAGAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAATAAG
Found at i:480394 original size:11 final size:11
Alignment explanation
Indices: 480372--480427 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
480362 TATTTTTTTC
480372 AAAAAAAC--A
1 AAAAAAACAAA
480381 AAAAAAACAAA
1 AAAAAAACAAA
*
480392 AAAAAAGGC--A
1 AAAAAA-ACAAA
480402 AAAAAAACAAA
1 AAAAAAACAAA
480413 AAAAAAACAAA
1 AAAAAAACAAA
480424 AAAA
1 AAAA
480428 GAGCCAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 9 0.22
10 7 0.17
11 23 0.57
12 1 0.03
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:480408 original size:30 final size:31
Alignment explanation
Indices: 480372--480438 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
480362 TATTTTTTTC
480372 AAAAAAACAAAAAAAACAA-AAAAAAAG-GCA
1 AAAAAAACAAAAAAAA-AACAAAAAAAGAGCA
*
480402 AAAAAAACAAAAAAAAAACAAAAAAAGAGCC
1 AAAAAAACAAAAAAAAAACAAAAAAAGAGCA
480433 AAAAAA
1 AAAAAA
480439 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 2 0.06
30 24 0.71
31 8 0.24
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (31 bp):
AAAAAAACAAAAAAAAAACAAAAAAAGAGCA
Found at i:480427 original size:9 final size:9
Alignment explanation
Indices: 480372--480426 Score: 67
Period size: 9 Copynumber: 5.8 Consensus size: 9
480362 TATTTTTTTC
480372 AAAAAAACA
1 AAAAAAACA
480381 AAAAAAACAA
1 AAAAAAAC-A
480391 AAAAAAAGGCA
1 AAAAAAA--CA
480402 AAAAAAACA
1 AAAAAAACA
480411 AAAAAAA-A
1 AAAAAAACA
480419 ACAAAAAA
1 A-AAAAAA
480427 AGAGCCAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.05
9 23 0.55
10 8 0.19
11 8 0.19
12 1 0.02
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:480438 original size:21 final size:19
Alignment explanation
Indices: 480372--480427 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
480362 TATTTTTTTC
480372 AAAAAAACAAAAAAAACAA
1 AAAAAAACAAAAAAAACAA
480391 AAAAAAAGGCAAAAAAAACAAA
1 AAAAAAA--CAAAAAAAAC-AA
480413 AAAAAAACAAAAAAA
1 AAAAAAACAAAAAAA
480428 GAGCCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.21
20 8 0.24
21 10 0.29
22 9 0.26
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAACAA
Found at i:484547 original size:48 final size:48
Alignment explanation
Indices: 484455--484547 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
484445 CACACTCCAA
* * * *
484455 TTTGCCTTTTCATCACGACTAGGAGGGTTGTTAGAGCCATTTATCGTG
1 TTTGCCTTTTCATCACGACTAGGAGGGTCGATAGAGACACTTATCGTG
**
484503 TTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACACTTATC
1 TTTGCCTTTTCATCACGACTAGGAGGG-TCGATAGAGACACTTATC
484548 CATCTATTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 33 0.87
49 5 0.13
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (48 bp):
TTTGCCTTTTCATCACGACTAGGAGGGTCGATAGAGACACTTATCGTG
Found at i:484829 original size:143 final size:141
Alignment explanation
Indices: 484558--484836 Score: 540
Period size: 143 Copynumber: 2.0 Consensus size: 141
484548 CATCTATTCC
484558 CAAATCCATTCGCACCATCAATCGTCTTTACCGTTCACCTTCATAAGGGAGATATTTTGATTTCT
1 CAAATCCATTCGCACCATCAATCGTCTTTACCGTTCACCTTCATAAGGGAGATATTTTGATTTCT
484623 ATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTATTGCCTTGA
66 ATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTATTGCCTTGA
484688 TTCCAGATCCA
131 TTCCAGATCCA
484699 CAAATCCATTCGCACCATCAATCGTCTTTACCGTTCACCTTCATAAGGGAGATATTTTGATTTCT
1 CAAATCCATTCGCACCATCAATCGTCTTTACCGTTCACCTTCATAAGGGAGATATTTTGATTTC-
484764 TTATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTATTGCCTT
65 -TATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTATTGCCTT
484829 GATTCCAG
129 GATTCCAG
484837 CATAAAAGAA
Statistics
Matches: 136, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
141 64 0.47
143 72 0.53
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (141 bp):
CAAATCCATTCGCACCATCAATCGTCTTTACCGTTCACCTTCATAAGGGAGATATTTTGATTTCT
ATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTATTGCCTTGA
TTCCAGATCCA
Found at i:485464 original size:91 final size:92
Alignment explanation
Indices: 485355--485530 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 92
485345 TTGAGGATTG
*
485355 ACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATTTGACA-AGGGAGAACAAGTTCATAAT
1 ACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCTGACAGAGGGAGAACAAGTTCATAAT
485419 AAGAAGAACTTGTTCAACCTTGGATCA
66 AAGAAGAACTTGTTCAACCTTGGATCA
** * *
485446 ACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCTGACAGAGGGAGAACAAGTTCATAAT
* * *
485511 GAGAAGAGCTTGTTCGACCT
66 AAGAAGAACTTGTTCAACCT
485531 ATCACTCGAT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
91 40 0.53
92 36 0.47
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (92 bp):
ACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCTGACAGAGGGAGAACAAGTTCATAAT
AAGAAGAACTTGTTCAACCTTGGATCA
Found at i:485680 original size:227 final size:225
Alignment explanation
Indices: 485216--485754 Score: 782
Period size: 227 Copynumber: 2.4 Consensus size: 225
485206 AAGATAAATT
* * * *
485216 GATCAACATTT-CTGATGGAGAGTT-ATAATAAGAAGAACTCATCCGACAGAGGGAGAAAAAGTT
1 GATCAACATTTCCAG-TGGGGAGTTCATAATGAGAAGAACTCAT-CGACAGAGGGAGAAGAAGTT
* * **
485279 CATAATTAGAAGAGCTTGCTCGACCTATCACTCAATTCATGGCATTAAGAATCAGTGATGCCTCG
64 CATAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACAGCATTAAGAATCAGTGATGCCTCG
**
485344 CTTGAGGATTGACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATTTGACAAGGGAGAACA
129 CTTGAGGATTGACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCCGACAAGGGAGAACA
485409 AGTTCATAATAAGAAGAACTTGTTCAACCTTG
194 AGTTCATAATAAGAAGAACTTGTTCAACCTTG
485441 GATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTC
1 GATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATC-GACAGAGGGAGAAGAAGTTC
* **
485506 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGCATTTTGAATCAGTGATGCCTCGC
65 ATAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACAGCATTAAGAATCAGTGATGCCTCGC
* * * * *
485571 TTGAGGGGTTGACATTTCTAGTGAAGAGTTCATAATGAA-AATAACTCATCCGACGAGGGAGAAG
130 TTGA-GGATTGACATTTCCAGTGAAGAGTTCATAAT-AAGAAGAACTCATCCGACAAGGGAGAAC
*
485635 AAGTTCATAATGAGAAGAACTTGTTCAACCTTG
193 AAGTTCATAATAAGAAGAACTTGTTCAACCTTG
* * *
485668 GATCATCATTTCCAGTGGGGAGTTCATAATGAGAAGAACCCATC--CAAAGGGAGAAGAAGTTCA
1 GATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCGACAGAGGGAGAAGAAGTTCA
* *
485731 TAATGAGAAGAACTTGTTCAACCT
66 TAATGAGAAGAGCTTGTTCGACCT
485755 TGGCTCAACA
Statistics
Matches: 285, Mismatches: 24, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
224 40 0.14
225 20 0.07
226 100 0.35
227 123 0.43
228 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (225 bp):
GATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCGACAGAGGGAGAAGAAGTTCA
TAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCACAGCATTAAGAATCAGTGATGCCTCGCT
TGAGGATTGACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCCGACAAGGGAGAACAAG
TTCATAATAAGAAGAACTTGTTCAACCTTG
Found at i:485738 original size:89 final size:89
Alignment explanation
Indices: 485582--485843 Score: 357
Period size: 89 Copynumber: 2.9 Consensus size: 89
485572 TGAGGGGTTG
* * *
485582 ACATTTCTAGTGAAGAGTTCATAATGA-AAATAACTCATCCGACGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAGTGGAGAGTTCATAATGAGAAA-AACTCATCC-A-AAGGGAGAAGAAGTTCATAAT
485646 GAGAAGAACTTGTTCAACCTTGGATCA
63 GAGAAGAACTTGTTCAACCTTGGATCA
* * * *
485673 TCATTTCCAGTGGGGAGTTCATAATGAGAAGAACCCATCCAAAGGGAGAAGAAGTTCATAATGAG
1 ACATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAAAGGGAGAAGAAGTTCATAATGAG
*
485738 AAGAACTTGTTCAACCTTGGCTCA
66 AAGAACTTGTTCAACCTTGGATCA
* * * * * *
485762 ACATTTCTAGTGGAGAGTTCATAATGAGAAAAACTCATCCTATGAG-GCAGAAGTTCATAATAAG
1 ACATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAAAGGGAGAAGAAGTTCATAATGAG
485826 AAGAACTTGTTCAACCTT
66 AAGAACTTGTTCAACCTT
485844 AGCTTGTTTC
Statistics
Matches: 152, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
88 34 0.22
89 84 0.55
90 1 0.01
91 31 0.20
92 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (89 bp):
ACATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAAAGGGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTGGATCA
Found at i:486153 original size:39 final size:42
Alignment explanation
Indices: 486056--486155 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
486046 TAGCTACATT
* * *
486056 CCATCGCATAAGGAGTTGGATCAGCATCATCATTTCGCTCAT
1 CCATCGCATAAGGAGTTGGATCAGCATCATCATTTAGATCAA
* *
486098 CCATCACATATGGAGTTGGATCAGCATCA-C-TTTAGATCAA
1 CCATCGCATAAGGAGTTGGATCAGCATCATCATTTAGATCAA
*
486138 CCATCGCA-AAAGAGTTGG
1 CCATCGCATAAGGAGTTGG
486156 GTCAACGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 8 0.16
40 14 0.28
41 1 0.02
42 27 0.54
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (42 bp):
CCATCGCATAAGGAGTTGGATCAGCATCATCATTTAGATCAA
Found at i:486417 original size:13 final size:14
Alignment explanation
Indices: 486391--486426 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
486381 AATTTTACCC
486391 ATAAAAATAATAATAA
1 ATAAAAATAAT-A-AA
486407 ATAAAAATAATAAA
1 ATAAAAATAATAAA
486421 ATAAAA
1 ATAAAA
486427 TAAAATAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 11 0.55
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAAAAATAATAAA
Found at i:486425 original size:5 final size:5
Alignment explanation
Indices: 486394--486434 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
486384 TTTACCCATA
*
486394 AAAAT AATAAT -AAAT AAAA- ATAAT AAAAT AAAAT AAAAT AA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
486435 GGGAGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 6 0.19
5 22 0.71
6 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:488244 original size:91 final size:92
Alignment explanation
Indices: 488135--488310 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 92
488125 TGAGGGATTG
488135 ACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCCGACA-AGGGAGAACAAGTTCATAAT
1 ACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAACAAGTTCATAAT
488199 AAGAAGAACTTGTTCAACCTTGGATCA
66 AAGAAGAACTTGTTCAACCTTGGATCA
** * * *
488226 ACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAACAAGTTCATAAT
* * *
488291 GAGAAGATCTTGTTCGACCT
66 AAGAAGAACTTGTTCAACCT
488311 ATCACTCGAT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
91 40 0.53
92 36 0.47
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (92 bp):
ACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAACAAGTTCATAAT
AAGAAGAACTTGTTCAACCTTGGATCA
Found at i:488412 original size:227 final size:223
Alignment explanation
Indices: 487998--488533 Score: 769
Period size: 223 Copynumber: 2.4 Consensus size: 223
487988 AAGATAAATT
* * * * *
487998 GATCAACATTT-CTGATGGAGAGTTTATAATAAGAATAACTCATCCGACAGAGGGAGAAGAAGTT
1 GATCAACATTTCCAG-TGGGGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
* * *** *
488062 CATAATTAGAAGAGCTTGTTCGACCTATCACTCAATTCATGGCAAAATCAGTGATGCCTCGCTTG
65 CATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACAACAAAATCAGTGACGCCTCGCTTG
*
488127 AGGGATTGACATTTCCAGTGAAGAGTTCATAATAAGAAGAACTCATCCGACAAGGGAGAACAAGT
130 AGGGATTGACATTTCCAGTGAAGAGTTCATAATAAGAACAACTCATCCGACAAGGGAGAACAAGT
488192 TCATAATAAGAAGAACTTGTTCAACCTTG
195 TCATAATAAGAAGAACTTGTTCAACCTTG
*
488221 GATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTC
1 GATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
* * *
488286 ATAATGAGAAGATCTTGTTCGACCTATCACTCGATTCACAACATTTTGAATCAGTGACGCCTCGC
66 ATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACAACA----AAATCAGTGACGCCTCGC
* * *
488351 TTGAGGGATTGACATTTCTAGTGAAGAGTTCATAATGAA-AACAACTCATCCGACGAGGGAGAAG
127 TTGAGGGATTGACATTTCCAGTGAAGAGTTCATAAT-AAGAACAACTCATCCGACAAGGGAGAAC
*
488415 AAGTTCATAATGAGAAGAACTTGTTCAACCTTG
191 AAGTTCATAATAAGAAGAACTTGTTCAACCTTG
* *
488448 GATCAACATTTCCA--GGGGAGTTCATAATGAGAAGAACCCATCCAAC-GA-GGAGAAGAAGTTC
1 GATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
*
488509 ATAATGAGAAGAACTTGTTCAACCT
66 ATAATGAGAAGAACTTGTTCGACCT
488534 TGGCTCAACA
Statistics
Matches: 283, Mismatches: 24, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
223 129 0.46
224 4 0.01
225 29 0.10
227 119 0.42
228 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (223 bp):
GATCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACAACAAAATCAGTGACGCCTCGCTTGA
GGGATTGACATTTCCAGTGAAGAGTTCATAATAAGAACAACTCATCCGACAAGGGAGAACAAGTT
CATAATAAGAAGAACTTGTTCAACCTTG
Found at i:488624 original size:91 final size:90
Alignment explanation
Indices: 488362--488630 Score: 400
Period size: 88 Copynumber: 3.0 Consensus size: 90
488352 TGAGGGATTG
* *
488362 ACATTTCTAGTGAAGAGTTCATAATGA-AAACAACTCATCCGACGAGGGAGAAGAAGTTCATAAT
1 ACATTTCTAGTGGAGAGTTCATAATGAGAAA-AACTCATCCAACGA-GGAGAAGAAGTTCATAAT
*
488426 GAGAAGAACTTGTTCAACCTTGGATCA
64 GAGAAGAACTTGTTCAACCTTGGCTCA
* * *
488453 ACATTTCCAG-GG-GAGTTCATAATGAGAAGAACCCATCCAACGAGGAGAAGAAGTTCATAATGA
1 ACATTTCTAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGAGAAGAAGTTCATAATGA
488516 GAAGAACTTGTTCAACCTTGGCTCA
66 GAAGAACTTGTTCAACCTTGGCTCA
* * *
488541 ACATTTCTAGTGGAGAGTTCATAATGAGAAAAACTCATCCTATGAGGCAGAAGAAGTTCATAATA
1 ACATTTCTAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGG-AGAAGAAGTTCATAATG
*
488606 AGAAGAACTTGTTCAACCTTAGCTC
65 AGAAGAACTTGTTCAACCTTGGCTC
488631 GTTTCCATCT
Statistics
Matches: 161, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
88 53 0.33
89 27 0.17
90 32 0.20
91 49 0.30
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (90 bp):
ACATTTCTAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTGGCTCA
Found at i:488935 original size:39 final size:42
Alignment explanation
Indices: 488838--488937 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
488828 TAGCTACATT
* * *
488838 CCATCGCATAAGGAGTTGGATCAGCATCATCATTTCGCTCAT
1 CCATCGCATAAGGAGTTGGATCAGCATCATCATTTAGATCAA
* *
488880 CCATCACATATGGAGTTGGATCAGCATCA-C-TTTAGATCAA
1 CCATCGCATAAGGAGTTGGATCAGCATCATCATTTAGATCAA
*
488920 CCATCGCA-AAAGAGTTGG
1 CCATCGCATAAGGAGTTGG
488938 GTCAACGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 8 0.16
40 14 0.28
41 1 0.02
42 27 0.54
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (42 bp):
CCATCGCATAAGGAGTTGGATCAGCATCATCATTTAGATCAA
Found at i:490333 original size:26 final size:27
Alignment explanation
Indices: 490290--490372 Score: 64
Period size: 27 Copynumber: 3.0 Consensus size: 27
490280 ATTAGTGTAG
490290 TTGTGTTTATTTTA-TTTTA-TATGTTTT
1 TTGT-TTTATTTTATTTTTACTAT-TTTT
* *
490317 TTGTTTTGTTTTGTTTTTACTATTTTT
1 TTGTTTTATTTTATTTTTACTATTTTT
* * *
490344 TTATTTTTTTATTATTGTTT-TTATTTTT
1 TTGTTTTATT-TTATT-TTTACTATTTTT
490372 T
1 T
490373 AAAATTTGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
26 7 0.15
27 21 0.46
28 15 0.33
29 3 0.07
ACGTcount: A:0.12, C:0.01, G:0.08, T:0.78
Consensus pattern (27 bp):
TTGTTTTATTTTATTTTTACTATTTTT
Found at i:490353 original size:20 final size:20
Alignment explanation
Indices: 490330--490372 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
490320 TTTTGTTTTG
490330 TTTTTACTATT-TTTTTATT
1 TTTTTACTATTGTTTTTATT
*
490349 TTTTTATTATTGTTTTTATT
1 TTTTTACTATTGTTTTTATT
490369 TTTT
1 TTTT
490373 AAAATTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTTACTATTGTTTTTATT
Found at i:490826 original size:23 final size:22
Alignment explanation
Indices: 490797--490868 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
490787 GTCCTTGTAC
490797 TTTTTTTTATTTTTTATTTTAT
1 TTTTTTTTATTTTTTATTTTAT
490819 TTTGTTTTTACTGTTTTT-TTTTAT
1 TTT-TTTTTA-T-TTTTTATTTTAT
* * *
490843 TTTTTATTA-TTGTTACTTTAT
1 TTTTTTTTATTTTTTATTTTAT
490864 TTTTT
1 TTTTT
490869 AAATTAGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
20 4 0.09
21 10 0.23
22 3 0.07
23 11 0.26
24 10 0.23
25 5 0.12
ACGTcount: A:0.12, C:0.03, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTTTTTATTTTTTATTTTAT
Found at i:490826 original size:24 final size:24
Alignment explanation
Indices: 490800--490845 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
490790 CTTGTACTTT
490800 TTTTTA-T-TTTTTATTTTATTTTG
1 TTTTTACTGTTTTT-TTTTATTTTG
490823 TTTTTACTGTTTTTTTTTATTTT
1 TTTTTACTGTTTTTTTTTATTTT
490846 TTATTATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.83
Consensus pattern (24 bp):
TTTTTACTGTTTTTTTTTATTTTG
Found at i:490858 original size:29 final size:28
Alignment explanation
Indices: 490802--490869 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
490792 TGTACTTTTT
* *
490802 TTTATTTTTTATTTTATTTTGTTTTTAC
1 TTTATTTTTTATTTTATTTTATTGTTAC
*
490830 TGTTTTTTTTTATTTT-TTATTATTGTTAC
1 T-TTATTTTTTATTTTATT-TTATTGTTAC
490859 TTTATTTTTTA
1 TTTATTTTTTA
490870 AATTAGGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 12 0.35
29 22 0.65
ACGTcount: A:0.15, C:0.03, G:0.04, T:0.78
Consensus pattern (28 bp):
TTTATTTTTTATTTTATTTTATTGTTAC
Found at i:490869 original size:7 final size:7
Alignment explanation
Indices: 490799--490850 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
490789 CCTTGTACTT
490799 TTTTTTA
1 TTTTTTA
490806 TTTTTTA
1 TTTTTTA
*
490813 TTTTATTT
1 TTTT-TTA
490821 TGTTTTTA
1 T-TTTTTA
* *
490829 CTGTTT-
1 TTTTTTA
490835 TTTTTTA
1 TTTTTTA
490842 TTTTTTA
1 TTTTTTA
490849 TT
1 TT
490851 ATTGTTACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
6 4 0.11
7 24 0.67
8 5 0.14
9 3 0.08
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.83
Consensus pattern (7 bp):
TTTTTTA
Found at i:494897 original size:129 final size:130
Alignment explanation
Indices: 494667--494921 Score: 494
Period size: 129 Copynumber: 2.0 Consensus size: 130
494657 TTACGTCTAA
*
494667 TCTAAAATATTATATTTTTTAATCATTTTCACTATTTTCAAATTTTAAATTAAGCTGCTTCTTTT
1 TCTAAAATATTATAATTTTTAATCATTTTCACTATTTTCAAATTTTAAATTAAGCTGCTTCTTTT
494732 GATTGCTATACTAATTTATACTAATTTTTAAGGGTTCG-CCCTACTAATTTGATATTTAATCATT
66 GATTGCTATACTAATTTATACTAATTTTTAAGGGTTCGCCCCTACTAATTTGATATTTAATCATT
494796 TCTAAAATATTATAATTTTTAATCATTTTCACTATTTTCAAATTTTAAATTAAGCTGCTTCTTTT
1 TCTAAAATATTATAATTTTTAATCATTTTCACTATTTTCAAATTTTAAATTAAGCTGCTTCTTTT
494861 GATTGCTATACTAATTTATACTAATTTTTAAGGGTTCGCCCCTACTAATTTGATATTTAAT
66 GATTGCTATACTAATTTATACTAATTTTTAAGGGTTCGCCCCTACTAATTTGATATTTAAT
494922 TTTAATAGAT
Statistics
Matches: 124, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
129 102 0.82
130 22 0.18
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (130 bp):
TCTAAAATATTATAATTTTTAATCATTTTCACTATTTTCAAATTTTAAATTAAGCTGCTTCTTTT
GATTGCTATACTAATTTATACTAATTTTTAAGGGTTCGCCCCTACTAATTTGATATTTAATCATT
Found at i:501714 original size:32 final size:32
Alignment explanation
Indices: 501675--501736 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
501665 TATTATTTTA
*
501675 TTAGGAATTAAGATAGAGTCAAAACATTATCT
1 TTAGGAATTAAGATAGAATCAAAACATTATCT
*
501707 TTAGGAATTAAGATAGAATTAAAACATTAT
1 TTAGGAATTAAGATAGAATCAAAACATTAT
501737 ATTTTAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (32 bp):
TTAGGAATTAAGATAGAATCAAAACATTATCT
Found at i:503018 original size:27 final size:29
Alignment explanation
Indices: 502988--503050 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 29
502978 TTTTTATTAT
* *
502988 TTAATTTA-AATTTTAATAAGAA-TATAA
1 TTAATTTATAATTTTAACAAAAATTATAA
* *
503015 TTAAATTATATTTTTAACAAAAATTATAA
1 TTAATTTATAATTTTAACAAAAATTATAA
503044 TT-ATTTA
1 TTAATTTA
503051 GAAAAACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 7 0.24
28 15 0.52
29 7 0.24
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TTAATTTATAATTTTAACAAAAATTATAA
Found at i:510254 original size:16 final size:16
Alignment explanation
Indices: 510235--510268 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
510225 CAATATACGA
510235 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
510251 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
510267 AT
1 AT
510269 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:510342 original size:16 final size:18
Alignment explanation
Indices: 510310--510343 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
510300 TATTAATTTA
510310 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
510328 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
510344 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:511014 original size:130 final size:130
Alignment explanation
Indices: 510810--511057 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
510800 AATTTTCTTC
* * *
510810 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACAGGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
510875 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
510940 TAATTAGGTGGTGACAGGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCATAT
1 TAATTAGGTGGTGACAGGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
511005 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
511058 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACAGGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:511506 original size:35 final size:35
Alignment explanation
Indices: 511456--511531 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
511446 AATTGAATTT
* *
511456 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
511491 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
511526 AATTGA
1 AATTGA
511532 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:512386 original size:16 final size:16
Alignment explanation
Indices: 512361--512394 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
512351 ATTAAAACTC
* *
512361 AACTCGAACTTAAAAA
1 AACTCAAACTCAAAAA
512377 AACTCAAACTCAAAAA
1 AACTCAAACTCAAAAA
512393 AA
1 AA
512395 TATTAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.21, G:0.03, T:0.15
Consensus pattern (16 bp):
AACTCAAACTCAAAAA
Found at i:512417 original size:46 final size:46
Alignment explanation
Indices: 512330--512417 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
512320 TAAAATTTTC
* *
512330 AAACTCACCTCAAAATATAATATTAAAACTCAACTCGAACTTAAAA
1 AAACTCAACTCAAAATATAATATTAAAACTCAACTCAAACTTAAAA
* *
512376 AAACTCAAACTCAAAA-A-AATATTAAAAACTCGATTCAAACTT
1 AAACTC-AACTCAAAATATAATATT-AAAACTCAACTCAAACTT
512418 GATATTGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 6 0.17
46 22 0.61
47 8 0.22
ACGTcount: A:0.53, C:0.20, G:0.02, T:0.24
Consensus pattern (46 bp):
AAACTCAACTCAAAATATAATATTAAAACTCAACTCAAACTTAAAA
Found at i:512434 original size:23 final size:23
Alignment explanation
Indices: 512402--512459 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
512392 AAATATTAAA
* *
512402 AACTCGATTCAAACTTGATATTG
1 AACTCAATTCAAACTCGATATTG
*
512425 AACTTAATTCAAACTCGATATTG
1 AACTCAATTCAAACTCGATATTG
*
512448 AGCTCAATTCAA
1 AACTCAATTCAA
512460 GCCACTAGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (23 bp):
AACTCAATTCAAACTCGATATTG
Found at i:514069 original size:17 final size:18
Alignment explanation
Indices: 514036--514069 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
514026 CCGCTACTAA
514036 TGAACCAGTTAAAACCGT
1 TGAACCAGTTAAAACCGT
*
514054 TGAACCA-TTCAAACCG
1 TGAACCAGTTAAAACCG
514070 GACCGGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (18 bp):
TGAACCAGTTAAAACCGT
Found at i:516003 original size:10 final size:10
Alignment explanation
Indices: 515988--516022 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
515978 TTCATCACAC
515988 CAAATTCTCT
1 CAAATTCTCT
*
515998 CAAATTTTCT
1 CAAATTCTCT
*
516008 CAATTTCTCT
1 CAAATTCTCT
516018 CAAAT
1 CAAAT
516023 ACCCTATATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:516107 original size:17 final size:18
Alignment explanation
Indices: 516070--516110 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
516060 ATATTATGTA
*
516070 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
516088 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
516105 TTTACT
1 TTTACT
516111 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:522170 original size:51 final size:50
Alignment explanation
Indices: 522070--522175 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 50
522060 CTACGTGGCG
* ** *
522070 TATATCGCGGATAAGGGGGCGCGCTATACACACGTGTAACCCATGTCAGCT
1 TATAGCGCGGATAAGGGGGCGCGCTATACACACGTG-AACCCAAATCAGCA
*
522121 TATAGCGCGG-TACAGGGGGCGCGCTATACCCCACGTG-ACGCCAAATCAGCA
1 TATAGCGCGGATA-AGGGGGCGCGCTATA-CACACGTGAAC-CCAAATCAGCA
522172 TATA
1 TATA
522176 ACGTAGCGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
50 4 0.09
51 36 0.77
52 7 0.15
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.19
Consensus pattern (50 bp):
TATAGCGCGGATAAGGGGGCGCGCTATACACACGTGAACCCAAATCAGCA
Found at i:526392 original size:56 final size:56
Alignment explanation
Indices: 526325--526436 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
526315 AGCTCGATAA
526325 AAGGTGAGTAGGCTTAAACCCGAATCTCTCATCTCTCTCTTTCTTATCTATATTTT
1 AAGGTGAGTAGGCTTAAACCCGAATCTCTCATCTCTCTCTTTCTTATCTATATTTT
526381 AAGGTGAGTAGGCTTAAACCCGAATCTCTCATCTCTCTCTTTCTTATCTATATTTT
1 AAGGTGAGTAGGCTTAAACCCGAATCTCTCATCTCTCTCTTTCTTATCTATATTTT
526437 CTTTTTTCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (56 bp):
AAGGTGAGTAGGCTTAAACCCGAATCTCTCATCTCTCTCTTTCTTATCTATATTTT
Found at i:526956 original size:24 final size:24
Alignment explanation
Indices: 526928--526981 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
526918 ATGTTGTAGT
526928 TGGGCTTGTAACCCGGGCTCCTAG
1 TGGGCTTGTAACCCGGGCTCCTAG
526952 TGGGCTTGTAACCCGGGCTCCTAG
1 TGGGCTTGTAACCCGGGCTCCTAG
526976 TGGGCT
1 TGGGCT
526982 GTTGTAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.11, C:0.28, G:0.35, T:0.26
Consensus pattern (24 bp):
TGGGCTTGTAACCCGGGCTCCTAG
Found at i:527047 original size:3 final size:3
Alignment explanation
Indices: 527020--527095 Score: 91
Period size: 3 Copynumber: 24.7 Consensus size: 3
527010 CAAAAAAATG
* * *
527020 TAA TAT TAA TAA AAA TAA CAA TAA TAA TAA TAA TAA TAA TATA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A
527067 TAA TAA TAA TAA TAA TAA T-A TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA
527096 TTTTTGTAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 52 0.81
4 10 0.16
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:527477 original size:129 final size:129
Alignment explanation
Indices: 527294--527537 Score: 350
Period size: 131 Copynumber: 1.9 Consensus size: 129
527284 ATCTTTAGGA
* *
527294 AGGGTGATAACATGGTTCCTACGCGATGATGACAGCTGGTTATCTAGGGGTGACACGA-CCTACG
1 AGGGTGATAACACGGTTCCTACGCGATGAGGACAGCTGGTTATCTAGGGGTGACACGACCCTACG
*
527358 TGATGAGGAGGTCTA-GTCGGGGGATGACACAGTGCCTACACAATGAGGATAGTAGGCCATCTTT
66 TGATGAGGAGGTC-AGGTAGGGGGATGACACAGTGCCTACACAATGAGGATAGTAGGCCATCTTT
* * *
527422 AGGGATGATTACACGGTTCCTACGTGATGAGGA-TGACTGGTTATCTAGGGGTGACACGACTCCT
1 AGGG-TGATAACACGGTTCCTACGCGATGAGGACAG-CTGGTTATCTAGGGGTGACACGAC-CCT
* * *
527486 ACGTGATGAGGAGGTCAGGTAGGGGGATGACACGGTTCCTACACGATGAGGA
63 ACGTGATGAGGAGGTCAGGTAGGGGGATGACACAGTGCCTACACAATGAGGA
527538 CGGCAAGTCA
Statistics
Matches: 102, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
128 5 0.05
129 47 0.46
130 1 0.01
131 49 0.48
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (129 bp):
AGGGTGATAACACGGTTCCTACGCGATGAGGACAGCTGGTTATCTAGGGGTGACACGACCCTACG
TGATGAGGAGGTCAGGTAGGGGGATGACACAGTGCCTACACAATGAGGATAGTAGGCCATCTTT
Found at i:527837 original size:61 final size:62
Alignment explanation
Indices: 527695--527915 Score: 211
Period size: 61 Copynumber: 3.5 Consensus size: 62
527685 GATGGTTTTA
* * *
527695 TTTCAAAAGAAACATACTCAAAGATTTTGTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAAAT
1 TTTCAAGAGAAACAAACTCAAAGA-TTT-TTT-T-AAAAGAAATTGTCT-AAGAGATAC-AAAAT
*
527760 ATG
60 TTG
* *
527763 TTTTC-AGAGAAACAAACTCAAATATTTTTTTAAAAGAAATTGTCT-TGAGATACAAAATTTG
1 -TTTCAAGAGAAACAAACTCAAAGATTTTTTTAAAAGAAATTGTCTAAGAGATACAAAATTTG
* * *
527824 ATTCAAGAGAAAC-AACTCAAAGGA-TTTTTCAAAAGAAATTGTCTCAAGAGATA-AAACTTTG
1 TTTCAAGAGAAACAAACTCAAA-GATTTTTTTAAAAGAAATTGTCT-AAGAGATACAAAATTTG
* *
527885 TTTCAAG-GAAACAGACTCAAAGTTTATTTTT
1 TTTCAAGAGAAACAAACTCAAAGATT-TTTTT
527916 CAAGTGAAAC
Statistics
Matches: 130, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
60 36 0.28
61 37 0.28
62 16 0.12
64 14 0.11
65 1 0.01
66 3 0.02
67 3 0.02
68 16 0.12
69 4 0.03
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (62 bp):
TTTCAAGAGAAACAAACTCAAAGATTTTTTTAAAAGAAATTGTCTAAGAGATACAAAATTTG
Found at i:527948 original size:24 final size:27
Alignment explanation
Indices: 527887--527950 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
527877 AAACTTTGTT
*
527887 TCAAGGAAACAGACTCAAAGTTTATTTT
1 TCAAGGAAACAGACTCAAAG-TTATTTC
527915 TCAAGTGAAACAGACTCAAAG-T-TTTC
1 TCAAG-GAAACAGACTCAAAGTTATTTC
*
527941 TCAAGAAAAC
1 TCAAGGAAAC
527951 TATCTTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 4 0.12
26 8 0.24
27 1 0.03
28 5 0.15
29 15 0.45
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (27 bp):
TCAAGGAAACAGACTCAAAGTTATTTC
Found at i:528232 original size:36 final size:38
Alignment explanation
Indices: 528141--528236 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 38
528131 TATCTCAAAG
*
528141 GAAAATTGTCTCAAGCGAAACGAAATTTGTTTTTAAGA
1 GAAAATTGTCTCAAGCGAGACGAAATTTGTTTTTAAGA
* *
528179 GAAAACTATCTCAAGCGAGAC-AACATTTGTTTTT-A-A
1 GAAAATTGTCTCAAGCGAGACGAA-ATTTGTTTTTAAGA
*
528215 GAAAATTGTCTCTAGCGAGACG
1 GAAAATTGTCTCAAGCGAGACG
528237 GCACTTTGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
36 19 0.38
37 3 0.06
38 28 0.56
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (38 bp):
GAAAATTGTCTCAAGCGAGACGAAATTTGTTTTTAAGA
Found at i:529411 original size:16 final size:17
Alignment explanation
Indices: 529375--529418 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
529365 TTTAGGTTGT
529375 TTTTAGGGTTTTAAAGG
1 TTTTAGGGTTTTAAAGG
529392 -TTTAGGGTTTT-AAGG
1 TTTTAGGGTTTTAAAGG
*
529407 TTTTATGGTTTT
1 TTTTAGGGTTTT
529419 GATAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (17 bp):
TTTTAGGGTTTTAAAGG
Found at i:529606 original size:26 final size:26
Alignment explanation
Indices: 529574--529651 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
529564 GGGTATTGTG
529574 TTTTTTAAGTTAAAATGGTTTAGAGT
1 TTTTTTAAGTTAAAATGGTTTAGAGT
* *
529600 TTTTTTAGGTTTAAATGGTTTAG-G-
1 TTTTTTAAGTTAAAATGGTTTAGAGT
* *
529624 GTTTTTAAGATTAAAGTGGTTTAGAGT
1 TTTTTTAAG-TTAAAATGGTTTAGAGT
529651 T
1 T
529652 GATTTTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
24 7 0.17
25 13 0.31
26 22 0.52
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (26 bp):
TTTTTTAAGTTAAAATGGTTTAGAGT
Found at i:529992 original size:53 final size:52
Alignment explanation
Indices: 529894--530059 Score: 212
Period size: 53 Copynumber: 3.2 Consensus size: 52
529884 ACCGAAAAAA
*
529894 ATTAGAAAATACACATACATTGAAATATATTAGAAAATAAAATTACATTGAAAT
1 ATTAGAAAAAACACATACATT-AAA-ATATTAGAAAATAAAATTACATTGAAAT
* *
529948 ATTAGAAACAAACACAAACATTAAAATATTAGAAAATAATATTACATTGAAAT
1 ATTAGAAA-AAACACATACATTAAAATATTAGAAAATAAAATTACATTGAAAT
* * *
530001 ATTAG-AAAAACACATACATTGAAATATTATAAAAGT-ACA-TACATTGAAAT
1 ATTAGAAAAAACACATACATTAAAATATTAGAAAA-TAAAATTACATTGAAAT
*
530051 AATAGAAAA
1 ATTAGAAAA
530060 TACAATTACA
Statistics
Matches: 101, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
50 15 0.15
51 29 0.29
52 3 0.03
53 32 0.32
54 11 0.11
55 11 0.11
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.27
Consensus pattern (52 bp):
ATTAGAAAAAACACATACATTAAAATATTAGAAAATAAAATTACATTGAAAT
Found at i:530024 original size:25 final size:26
Alignment explanation
Indices: 529894--530063 Score: 188
Period size: 25 Copynumber: 6.5 Consensus size: 26
529884 ACCGAAAAAA
529894 ATTAGAAAATACACATACATTGAAATAT
1 ATTAGAAAATACACATACATTG-AA-AT
*
529922 ATTAGAAAATA-AAATTACATTGAAAT
1 ATTAGAAAATACACA-TACATTGAAAT
* * *
529948 ATTAGAAACAAACACAAACATTAAAAT
1 ATTAGAAA-ATACACATACATTGAAAT
*
529975 ATTAGAAAATA-ATATTACATTGAAAT
1 ATTAGAAAATACACA-TACATTGAAAT
530001 ATTAGAAAA-ACACATACATTGAAAT
1 ATTAGAAAATACACATACATTGAAAT
*
530026 ATTATAAAAGT--ACATACATTGAAAT
1 ATTAGAAAA-TACACATACATTGAAAT
*
530051 AATAGAAAATACA
1 ATTAGAAAATACA
530064 ATTACATAAG
Statistics
Matches: 120, Mismatches: 13, Indels: 20
0.78 0.08 0.13
Matches are distributed among these distances:
24 1 0.01
25 43 0.36
26 33 0.28
27 23 0.19
28 20 0.17
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (26 bp):
ATTAGAAAATACACATACATTGAAAT
Found at i:534588 original size:57 final size:57
Alignment explanation
Indices: 534500--534618 Score: 193
Period size: 57 Copynumber: 2.1 Consensus size: 57
534490 CACGACACAC
* *
534500 AAATGTGTGCCATTTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCAT
1 AAATGTGTGCCATCTTCATTTATGAAGGGGGCTTCAATGACACGCAATGTAAGTCAT
* * *
534557 AAATGTGTGTCATCTTCATTTATGAAGGGGGCTTCAATGACGCTCAATGTAAGTCAT
1 AAATGTGTGCCATCTTCATTTATGAAGGGGGCTTCAATGACACGCAATGTAAGTCAT
534614 AAATG
1 AAATG
534619 CGCGTCATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (57 bp):
AAATGTGTGCCATCTTCATTTATGAAGGGGGCTTCAATGACACGCAATGTAAGTCAT
Found at i:534625 original size:13 final size:13
Alignment explanation
Indices: 534609--534656 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
534599 CTCAATGTAA
534609 GTCATAAATGCGC
1 GTCATAAATGCGC
*
534622 GTCATAAATGCGT
1 GTCATAAATGCGC
*
534635 GTCATAAATGTGC
1 GTCATAAATGCGC
534648 GTCATAAAT
1 GTCATAAAT
534657 TCATGACGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:534631 original size:26 final size:26
Alignment explanation
Indices: 534602--534656 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
534592 AATGACGCTC
*
534602 AATGTAAGTCATAAATGCGCGTCATA
1 AATGCAAGTCATAAATGCGCGTCATA
** *
534628 AATGCGTGTCATAAATGTGCGTCATA
1 AATGCAAGTCATAAATGCGCGTCATA
534654 AAT
1 AAT
534657 TCATGACGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (26 bp):
AATGCAAGTCATAAATGCGCGTCATA
Found at i:541937 original size:15 final size:15
Alignment explanation
Indices: 541875--541934 Score: 102
Period size: 15 Copynumber: 4.0 Consensus size: 15
541865 CATCTTCCAT
541875 ACAACATCAACACCA
1 ACAACATCAACACCA
541890 ACAACATCAACACCA
1 ACAACATCAACACCA
541905 ACAACATCAACACCA
1 ACAACATCAACACCA
* *
541920 GCAACATAAACACCA
1 ACAACATCAACACCA
541935 GCATACTTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.53, C:0.38, G:0.02, T:0.07
Consensus pattern (15 bp):
ACAACATCAACACCA
Found at i:545356 original size:23 final size:23
Alignment explanation
Indices: 545310--545357 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
545300 CGAGTTTGAG
* * *
545310 ATACAACATCATCACCATCTTCC
1 ATACAACATCAACACCAACATCC
545333 ATACAACATCAACACCAACATCC
1 ATACAACATCAACACCAACATCC
545356 AT
1 AT
545358 TTTCCATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.21
Consensus pattern (23 bp):
ATACAACATCAACACCAACATCC
Found at i:554210 original size:19 final size:19
Alignment explanation
Indices: 554178--554215 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
554168 ACTATTGAAT
* *
554178 TTTAAGATTTTATATTCGA
1 TTTAAAATTATATATTCGA
554197 TTTAAAATTATATATTCGA
1 TTTAAAATTATATATTCGA
554216 GTAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTTAAAATTATATATTCGA
Found at i:560987 original size:55 final size:54
Alignment explanation
Indices: 560924--561434 Score: 221
Period size: 53 Copynumber: 9.5 Consensus size: 54
560914 CAATGGGTTA
*
560924 GCTCCCTCTTGCTTCAGGGTGTGTAGAACTCAAACAATCTACTGCCAACAAGTTC
1 GCTCCCTCTTGCTTCAGGG-GAGTAGAACTCAAACAATCTACTGCCAACAAGTTC
* * ** * *
560979 GCTCCCTCTTGCTTCA-GGGAGTAGAACTCGAACAATCTTCTGCGTACGAGTTT
1 GCTCCCTCTTGCTTCAGGGGAGTAGAACTCAAACAATCTACTGCCAACAAGTTC
* ** * ** ***
561032 GCTCCCTCTTGCTTTA-GGGAGTAGAACTTGAACAATCTTCTGCTTATGGGTTC
1 GCTCCCTCTTGCTTCAGGGGAGTAGAACTCAAACAATCTACTGCCAACAAGTTC
* * * * * * * * **
561085 ACTCCCTCTTTCTTTA-GGGAGTATATCTCGAACAATCTTCTGACAACGGGTTC
1 GCTCCCTCTTGCTTCAGGGGAGTAGAACTCAAACAATCTACTGCCAACAAGTTC
** * * * * * * **
561138 ATTCCCTCTTTCTTTTA-GGGTGTAGGAACTCAAACAATCTTCTACCCACGGGTTC
1 GCTCCCTCTTGC-TTCAGGGGAGTA-GAACTCAAACAATCTACTGCCAACAAGTTC
* * ** * * * * **
561193 ACTCCATCTTTTTTTCA-GGGAGTAGAAAATCGAACAATATTCTGCCAACGGGTTC
1 GCTCCCTC-TTGCTTCAGGGGAGTAG-AACTCAAACAATCTACTGCCAACAAGTTC
* * * * * * **
561248 CCTCCCTCTTTCTTTTA-GGGAGTAGGAACTCAAAAAATCTTCTGCCTACGGGTTC
1 GCTCCCTCTTGC-TTCAGGGGAGTA-GAACTCAAACAATCTACTGCCAACAAGTTC
* * * * * * **
561303 ACTCCCTCTTTCTTTA-GGGAGTAAGAACTCAAACAATCTTCTCCCTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGGAGT-AGAACTCAAACAATCTACTGCCAACAAGTTC
** * * * * ** *
561357 GCTCCCTCTTTTTTTA-GGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTT
1 GCTCCCTCTTGCTTCAGGGGAGTA-GAACTCAAACAATCTACTGCCAACAAGTTC
* *
561411 GCTCCCTCTTTCTTTA-GGGAGTAG
1 GCTCCCTCTTGCTTCAGGGGAGTAG
561435 GAATTTGAAC
Statistics
Matches: 390, Mismatches: 58, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
53 132 0.34
54 123 0.32
55 131 0.34
56 4 0.01
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (54 bp):
GCTCCCTCTTGCTTCAGGGGAGTAGAACTCAAACAATCTACTGCCAACAAGTTC
Found at i:561176 original size:161 final size:161
Alignment explanation
Indices: 560900--561770 Score: 880
Period size: 161 Copynumber: 5.4 Consensus size: 161
560890 CCTCTTCTTT
* * * * * * *
560900 GAACAATCTTC-GACCAATGGGTTAGCTCCCTCTTGCTTCAGGGTGT-GTAGAACTCAAACAATC
1 GAACAATCTTCTG-CCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAG--GAACTCGAACAATC
* * * ** * * * * * *
560963 TACTGCCAACAAGTTCGCTCCCTCTTGCTTCAGGGAGTA-GAACTCGAACAATCTTCTGCGTACG
63 TTCTGACTACGGGTTCACTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTACCTACG
* * * *
561027 AGTTTGCTCCCTCTTGCTTTAGGGAGTAGAACTT
128 GGTTCGCTCCCTCTTTCTTTAGGGAGTAGAACTC
* * * * *
561061 GAACAATCTTCTGCTTATGGGTTCACTCCCTCTTTCTTTAGGGAGTA-TATCTCGAACAATCTTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
* * * *
561125 TGACAACGGGTTCATTCCCTCTTTCTTTTAGGGTGTAGGAACTCAAACAATCTTCTACCCACGGG
66 TGACTACGGGTTCACTCCCTCTTTC-TTTAGGGAGTAGGAACTCAAACAATCTTCTACCTACGGG
* * * *
561190 TTCACTCCATCTTTTTTTCAGGGAGTAGAAAATC
130 TTCGCTCCCTCTTTCTTT-AGGGAGTAG-AACTC
* * * * *
561224 GAACAATATTCTGCCAACGGGTTCCCTCCCTCTTTCTTTTAGGGAGTAGGAACTCAAAAAATCTT
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTC-TTTAGGGAGTAGGAACTCGAACAATCTT
* * *
561289 CTGCCTACGGGTTCACTCCCTCTTTCTTTAGGGAGTAAGAACTCAAACAATCTTCTCCCTACGGG
65 CTGACTACGGGTTCACTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTACCTACGGG
*
561354 TTCGCTCCCTCTTTTTTTAGGGAGTAGGAACTC
130 TTCGCTCCCTCTTTCTTTAGGGAGTA-GAACTC
* * *
561387 GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTTCTTTAGGGAGTAGGAATTTGAACAATC-TC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
* ** ** ** *
561451 TGCCTATTGGTTTGCTCCCTCTTTCTTTAGGGAGTAGGAACTTGAACAATCTTCTACCTACGAGT
66 TGACTACGGGTTCACTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTACCTACGGGT
** *
561516 TCGCTTTCTCTTTCTTTAGGGAGTAGGAACTT
131 TCGCTCCCTCTTTCTTTAGGGAGTA-GAACTC
* * * * *
561548 GAACATTCTTCGGCCTACGGGTTGGCTCCCTCTTTCTTTAGGGAGTAAGAACTTGAACAATCTTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
* * * * ** * * **
561613 T-ACCTACGTGTTCGCTCTCTTTTTCTTTAGGGACCAGGAACTCAAATAATCTACTGTCTACGGG
66 TGA-CTACGGGTTCACTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTACCTACGGG
* *
561677 TTCACTCCCTCTTTCTTTCGGGAGTAGAAACTC
130 TTCGCTCCCTCTTTCTTTAGGGAGTAG-AACTC
* *
561710 GAATAATCTTCTGCCTACGGGTT---TGCC-CTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
561771 CGGTGTGATT
Statistics
Matches: 595, Mismatches: 103, Indels: 27
0.82 0.14 0.04
Matches are distributed among these distances:
158 32 0.05
159 35 0.06
160 9 0.02
161 216 0.36
162 127 0.21
163 78 0.13
164 63 0.11
165 35 0.06
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (161 bp):
GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
TGACTACGGGTTCACTCCCTCTTTCTTTAGGGAGTAGGAACTCAAACAATCTTCTACCTACGGGT
TCGCTCCCTCTTTCTTTAGGGAGTAGAACTC
Found at i:561333 original size:54 final size:54
Alignment explanation
Indices: 560900--561770 Score: 855
Period size: 54 Copynumber: 16.2 Consensus size: 54
560890 CCTCTTCTTT
* * * * * * *
560900 GAACAATCTTC-GACCAATGGGTTAGCTCCCTCTTGCTTCAGGGTGTGTAGAACTC
1 GAACAATCTTCTG-CCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGT-AAGAACTC
* * * ** * *
560955 AAACAATCTACTGCCAACAAGTTCGCTCCCTCTTGCTTCAGGGAGT-AGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * * * *
561008 GAACAATCTTCTGCGTACGAGTTTGCTCCCTCTTGCTTTAGGGAGT-AGAACTT
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * * * *
561061 GAACAATCTTCTGCTTATGGGTTCACTCCCTCTTTCTTTAGGGAGT-ATATCTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * ** * *
561114 GAACAATCTTCTGACAACGGGTTCATTCCCTCTTTCTTTTAGGGTGTAGGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTC-TTTAGGGAGTAAGAACTC
* * * * * * *
561169 AAACAATCTTCTACCCACGGGTTCACTCCATCTTTTTTTCAGGGAGT-AGAAAATC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTT-AGGGAGTAAG-AACTC
* * * *
561224 GAACAATATTCTGCCAACGGGTTCCCTCCCTCTTTCTTTTAGGGAGTAGGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTC-TTTAGGGAGTAAGAACTC
* * *
561279 AAAAAATCTTCTGCCTACGGGTTCACTCCCTCTTTCTTTAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * * *
561333 AAACAATCTTCTCCCTACGGGTTCGCTCCCTCTTTTTTTAGGGAGTAGGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * * *
561387 GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTTCTTTAGGGAGTAGGAATTT
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
** * * *
561441 GAACAATC-TCTGCCTATTGGTTTGCTCCCTCTTTCTTTAGGGAGTAGGAACTT
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * ** * *
561494 GAACAATCTTCTACCTACGAGTTCGCTTTCTCTTTCTTTAGGGAGTAGGAACTT
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * * *
561548 GAACATTCTTCGGCCTACGGGTTGGCTCCCTCTTTCTTTAGGGAGTAAGAACTT
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * * * ** *
561602 GAACAATCTTCTACCTACGTGTTCGCTCTCTTTTTCTTTAGGGACCAGGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
* * * * * *
561656 AAATAATCTACTGTCTACGGGTTCACTCCCTCTTTCTTTCGGGAGT-AGAAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAG-AACTC
* * *
561710 GAATAATCTTCTGCCTACGGGTT---TGCC-CTTTCTTTAGGGAGTAGGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
561760 GAACAATCTTC
1 GAACAATCTTC
561771 CGGTGTGATT
Statistics
Matches: 688, Mismatches: 118, Indels: 25
0.83 0.14 0.03
Matches are distributed among these distances:
50 29 0.04
51 4 0.01
53 178 0.26
54 321 0.47
55 151 0.22
56 5 0.01
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (54 bp):
GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTC
Found at i:561598 original size:269 final size:270
Alignment explanation
Indices: 560900--561770 Score: 972
Period size: 269 Copynumber: 3.2 Consensus size: 270
560890 CCTCTTCTTT
* * * * * * *
560900 GAACAATCTTC-GACCAATGGGTTAGCTCCCTCTTGCTTCAGGGTGT-GTAGAACTCAAACAATC
1 GAACAATCTTCTG-CCTACGGGTTTGCTCCCTCTTTCTTTAGGGAGTAG--GAACTCGAACAATC
* * * * *
560963 TACTGCCAACAAGTTCGCTCCCTCTTGCTTCAGGGAGTA-GAACTCGAACAATCTTCTGCGTACG
63 TTCTGCCAACGAGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCTACG
* * * * * * *
561027 AGTTTGCTCCCTCTTGCTTTAGGGAGT-AGAACTTGAACAATCTTCTGCTTATGGGTTCACTCCC
128 GGTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTTGAACAATCTTCTACCTACGGGTTCGCTCCC
* * * * *
561091 TCTTTCTTTAGGGAGTA-TATCTCGAACAATCTTCTGACAACGGGTTCATTCCCTCTTTCTTTTA
193 TCTTTTTTTAGGGAGTAGGAACTCGAACAATCTTCTGACTACGGGTTCACTCCCTCTTTC-TTTA
*
561155 GGGTGTAGGAACTC
257 GGGAGTAGGAACTC
* * * ** * * * * *
561169 AAACAATCTTCTACCCACGGGTTCACTCCATCTTTTTTTCAGGGAGTAGAAAATCGAACAATATT
1 GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTTCTTT-AGGGAGTAGGAACTCGAACAATCTT
* * * *
561234 CTGCCAACGGGTTCCCTCCCTCTTTCTTTTAGGGAGTAGGAACTCAAAAAATCTTCTGCCTACGG
65 CTGCCAACGAGTTCGCTCCCTCTTTC-TTTAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGG
* ** *
561299 GTTCACTCCCTCTTTCTTTAGGGAGTAAGAACTCAAACAATCTTCTCCCTACGGGTTCGCTCCCT
129 GTTCGCTCCCTCTTTCTTTAGGGAGTAAGAACTTGAACAATCTTCTACCTACGGGTTCGCTCCCT
* **
561364 CTTTTTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTTCTTTAGG
194 CTTTTTTTAGGGAGTAGGAACTCGAACAATCTTCTGACTACGGGTTCACTCCCTCTTTCTTTAGG
* *
561429 GAGTAGGAATTT
259 GAGTAGGAACTC
** *
561441 GAACAATC-TCTGCCTATTGGTTTGCTCCCTCTTTCTTTAGGGAGTAGGAACTTGAACAATCTTC
1 GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
* * ** * * *
561505 TACCTACGAGTTCGCTTTCTCTTTCTTTAGGGAGTAGGAACTTGAACATTCTTCGGCCTACGGGT
66 TGCCAACGAGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGT
* * *
561570 TGGCTCCCTCTTTCTTTAGGGAGTAAGAACTTGAACAATCTTCTACCTACGTGTTCGCTCTCT-T
131 TCGCTCCCTCTTTCTTTAGGGAGTAAGAACTTGAACAATCTTCTACCTACGGGTTCGCTCCCTCT
** * * * * *
561634 TTTCTTTAGGGACCAGGAACTCAAATAATCTACTGTCTACGGGTTCACTCCCTCTTTCTTTCGGG
196 TTT-TTTAGGGAGTAGGAACTCGAACAATCTTCTGACTACGGGTTCACTCCCTCTTTCTTTAGGG
*
561699 AGTAGAAACTC
260 AGTAGGAACTC
*
561710 GAATAATCTTCTGCCTACGGGTTTG---CC-CTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
1 GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
561771 CGGTGTGATT
Statistics
Matches: 501, Mismatches: 92, Indels: 21
0.82 0.15 0.03
Matches are distributed among these distances:
266 33 0.07
267 2 0.00
268 4 0.01
269 219 0.44
270 71 0.14
271 68 0.14
272 69 0.14
273 35 0.07
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (270 bp):
GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTC
TGCCAACGAGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGT
TCGCTCCCTCTTTCTTTAGGGAGTAAGAACTTGAACAATCTTCTACCTACGGGTTCGCTCCCTCT
TTTTTTAGGGAGTAGGAACTCGAACAATCTTCTGACTACGGGTTCACTCCCTCTTTCTTTAGGGA
GTAGGAACTC
Found at i:562224 original size:42 final size:42
Alignment explanation
Indices: 562176--562351 Score: 128
Period size: 42 Copynumber: 4.3 Consensus size: 42
562166 ATCATATTGT
*
562176 TTGAAAGACTTACAAATGACCTGAAGGATTTAATCATCATGC
1 TTGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGC
* *** **** * * *
562218 TTGAAAGACTTACTAATGATTTGCTTCA-CTACTCTTC-TG-
1 TTGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGC
* * *
562257 -TG-AAGACTTATAAATTACCCGAAGGATTTAATCATCACGC
1 TTGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGC
* ** * *
562297 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGC
1 TTGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGC
*
562339 TCGAAAGACTTAC
1 TTGAAAGACTTAC
562352 TGATGGAACT
Statistics
Matches: 97, Mismatches: 32, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
37 14 0.14
38 8 0.08
39 1 0.01
40 2 0.02
41 7 0.07
42 65 0.67
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (42 bp):
TTGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGC
Found at i:562333 original size:121 final size:121
Alignment explanation
Indices: 562177--562522 Score: 424
Period size: 121 Copynumber: 2.8 Consensus size: 121
562167 TCATATTGTT
** * * * *
562177 TGAAAGACTTACAAATGACCTGAAGGATTTAATCATCATGCTTGAAAGACTTACTAAT-GATTTG
1 TGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATAGATTTG
* * * **
562241 CTTCACTACTCTTCTGTGAAGACTTATAAATTACCCGAAGGATTTAATCATCACGC
66 CTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCAAAC
562297 TCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGAACT
1 T-GAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTAC---T---A--
562362 TATTAATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCAT
57 -A-T-A--GATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCAT
562427 CAAAC
117 CAAAC
* *
562432 TGAAAGACTTACTGATGGCCCGAAAGATTTCATCATCATGCTCGAAAGACTTACTGATAGATTTG
1 TGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATAGATTTG
* *
562497 CTTCACTAATCTTCGGTGAAGGCTTA
66 CTTCACTACTCTTCCGTGAAGGCTTA
562523 AGATGTATTT
Statistics
Matches: 196, Mismatches: 15, Indels: 29
0.82 0.06 0.12
Matches are distributed among these distances:
120 1 0.01
121 77 0.39
123 1 0.01
124 2 0.01
125 1 0.01
127 1 0.01
130 1 0.01
131 2 0.01
134 52 0.27
135 58 0.30
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (121 bp):
TGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTAATAGATTTG
CTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCAAAC
Found at i:562352 original size:42 final size:42
Alignment explanation
Indices: 562274--562489 Score: 168
Period size: 42 Copynumber: 5.0 Consensus size: 42
562264 TTATAAATTA
* *
562274 CCCGAAGGATTTAATCATCACGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGG
562316 CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGG
*** * * * ** **
562358 AACTTATTAATGGATTTGCTTCA-CTACT-CTTCCGTGAAGGCTTACAAATTA
1 --C--CCGAA-GGATTT-CATCATC-A-TGC-T-CG-AAAGACTTACTGATGG
* **
562409 CCCGAAGGATTTAATCATCAAACT-GAAAGACTTACTGATGG
1 CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGG
*
562450 CCCGAAAGATTTCATCATCATGCTCGAAAGACTTACTGAT
1 CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGAT
562490 AGATTTGCTT
Statistics
Matches: 132, Mismatches: 28, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
41 30 0.23
42 56 0.42
44 2 0.02
45 5 0.04
46 9 0.07
47 9 0.07
48 6 0.05
49 3 0.02
50 2 0.02
51 10 0.08
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (42 bp):
CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGG
Found at i:562455 original size:41 final size:42
Alignment explanation
Indices: 562409--562489 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 42
562399 TTACAAATTA
*
562409 CCCGAAGGATTTAATCATCAAACT-GAAAGACTTACTGATGG
1 CCCGAAAGATTTAATCATCAAACTCGAAAGACTTACTGATGG
* **
562450 CCCGAAAGATTTCATCATCATGCTCGAAAGACTTACTGAT
1 CCCGAAAGATTTAATCATCAAACTCGAAAGACTTACTGAT
562490 AGATTTGCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (42 bp):
CCCGAAAGATTTAATCATCAAACTCGAAAGACTTACTGATGG
Found at i:562458 original size:20 final size:19
Alignment explanation
Indices: 562433--562489 Score: 51
Period size: 22 Copynumber: 2.8 Consensus size: 19
562423 TCATCAAACT
562433 GAAAGACTTACTGATGGCCC
1 GAAAGACTTACTGAT-GCCC
* * *
562453 GAAAGATTTCATCATCATGCTC
1 GAAAGACTT-A-C-TGATGCCC
562475 GAAAGACTTACTGAT
1 GAAAGACTTACTGAT
562490 AGATTTGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.10
20 9 0.31
21 2 0.07
22 12 0.41
23 3 0.10
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (19 bp):
GAAAGACTTACTGATGCCC
Found at i:562475 original size:134 final size:134
Alignment explanation
Indices: 562225--562489 Score: 451
Period size: 134 Copynumber: 2.0 Consensus size: 134
562215 TGCTTGAAAG
* *
562225 ACTTACTAATGATTTGCTTCACTACTCTTCTGTGAAGACTTATAAATTACCCGAAGGATTTAATC
1 ACTTACTAATGATTTGCTTCACTACTCTTCCGTGAAGACTTACAAATTACCCGAAGGATTTAATC
** *
562290 ATCACGCTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGA
66 ATCAAACTCGAAAGACTTACTGATGGCCCGAAAGATTTCATCATCATGCTCGAAAGACTTACTGA
562355 TGGA
131 TGGA
* *
562359 ACTTATTAATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTAAT-GATTTGCTTCACTACTCTTCCGTGAAGACTTACAAATTACCCGAAGGATTTAAT
562424 CATCAAACT-GAAAGACTTACTGATGGCCCGAAAGATTTCATCATCATGCTCGAAAGACTTACTG
65 CATCAAACTCGAAAGACTTACTGATGGCCCGAAAGATTTCATCATCATGCTCGAAAGACTTACTG
562488 AT
130 AT
562490 AGATTTGCTT
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
134 65 0.53
135 58 0.47
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (134 bp):
ACTTACTAATGATTTGCTTCACTACTCTTCCGTGAAGACTTACAAATTACCCGAAGGATTTAATC
ATCAAACTCGAAAGACTTACTGATGGCCCGAAAGATTTCATCATCATGCTCGAAAGACTTACTGA
TGGA
Found at i:562548 original size:37 final size:37
Alignment explanation
Indices: 562491--562605 Score: 160
Period size: 37 Copynumber: 3.1 Consensus size: 37
562481 CTTACTGATA
*
562491 GATTTGCTTCACTAATCTTCGGTGAAGGCTTAAGATG
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
* *
562528 TATTTGCTTCACTACCCTTCGGTGAAGGCTT-AGAATG
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAG-ATG
* * *
562565 GATTTGCTTCACTACTTTTTGGTGAAGGCTTAAGATC
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
562602 GATT
1 GATT
562606 CACTTCTTCG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
36 2 0.03
37 64 0.94
38 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (37 bp):
GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
Found at i:563797 original size:17 final size:15
Alignment explanation
Indices: 563786--563893 Score: 96
Period size: 17 Copynumber: 6.9 Consensus size: 15
563776 ATTTTCTCTC
563786 TTTTTTCTTTTTTT-
1 TTTTTTCTTTTTTTA
563800 TTTTTT-TTTTTTTA
1 TTTTTTCTTTTTTTA
*
563814 TTTTTT-ATTTTTTA
1 TTTTTTCTTTTTTTA
*
563828 TTTTTTTTTATTTTTTA
1 -TTTTTTCT-TTTTTTA
563845 TTTTTTCCTTTTTCTTTA
1 TTTTTT-C-TTTT-TTTA
563863 TTTTTTCTTTTCTTTTCA
1 TTTTTTC-TTT-TTTT-A
*
563881 TTTTTCCTTTTTT
1 TTTTTTCTTTTTT
563894 CCTTTTCTTC
Statistics
Matches: 81, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
13 7 0.09
14 19 0.23
15 6 0.07
16 9 0.11
17 21 0.26
18 19 0.23
ACGTcount: A:0.06, C:0.08, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTTTTTTA
Found at i:563804 original size:24 final size:22
Alignment explanation
Indices: 563784--563878 Score: 95
Period size: 22 Copynumber: 4.3 Consensus size: 22
563774 TTATTTTCTC
*
563784 TCTTTTTTCTTTTTTTTTTTTT
1 TCTTTTTTATTTTTTTTTTTTT
563806 T-TTTTTTATTTTTTATTTTTTAT
1 TCTTTTTTATTTTTT-TTTTTT-T
* *
563829 TTTTTTTTATTTTTTATTTTTT
1 TCTTTTTTATTTTTTTTTTTTT
* * *
563851 CCTTTTTCT-TTATTTTTTCTTT
1 TCTTTTT-TATTTTTTTTTTTTT
563873 TCTTTT
1 TCTTTT
563879 CATTTTTCCT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
21 12 0.20
22 28 0.46
23 8 0.13
24 13 0.21
ACGTcount: A:0.06, C:0.07, G:0.00, T:0.86
Consensus pattern (22 bp):
TCTTTTTTATTTTTTTTTTTTT
Found at i:563808 original size:28 final size:28
Alignment explanation
Indices: 563771--563850 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 28
563761 TGAGACCTAC
* * *
563771 TTTTTATTTTCTCTCTTTTTTCTTTTTT
1 TTTTTTTTTTCTCTATTTTTTATTTTTT
* *
563799 TTTTTTTTTTTTTTATTTTTTA--TTTT
1 TTTTTTTTTTCTCTATTTTTTATTTTTT
*
563825 TTATTTTTTT-T-TATTTTTTATTTTTT
1 TTTTTTTTTTCTCTATTTTTTATTTTTT
563851 CCTTTTTCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 9 0.20
25 1 0.02
26 17 0.39
28 17 0.39
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (28 bp):
TTTTTTTTTTCTCTATTTTTTATTTTTT
Found at i:563893 original size:1 final size:1
Alignment explanation
Indices: 563786--563878 Score: 78
Period size: 1 Copynumber: 93.0 Consensus size: 1
563776 ATTTTCTCTC
* * * * * *
563786 TTTTTTCTTTTTTTTTTTTTTTTTTTTATTTTTTATTTTTTATTTTTTTTTATTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * * *
563851 CCTTTTTCTTTATTTTTTCTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
563879 CATTTTTCCT
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:563902 original size:42 final size:42
Alignment explanation
Indices: 563817--563899 Score: 121
Period size: 43 Copynumber: 2.0 Consensus size: 42
563807 TTTTTTATTT
* *
563817 TTTATTTTTTATTTTTTTTTATTTTTTATTTTTTCCTTTTTC
1 TTTATTTTTTATTTTTTTTCATTTTTCATTTTTTCCTTTTTC
* *
563859 TTTATTTTTTCTTTTCTTTTCATTTTTCCTTTTTTCCTTTT
1 TTTATTTTTTATTTT-TTTTCATTTTTCATTTTTTCCTTTT
563900 CTTCTTCAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 14 0.39
43 22 0.61
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (42 bp):
TTTATTTTTTATTTTTTTTCATTTTTCATTTTTTCCTTTTTC
Found at i:568622 original size:55 final size:55
Alignment explanation
Indices: 568550--568705 Score: 224
Period size: 55 Copynumber: 2.8 Consensus size: 55
568540 TTTGAAAAAA
* * *
568550 GTCTTCAATCAACTTCAAACTTC-TCTATTCATCAAATGTCTTTCTTAATGGATCG
1 GTCTTCAATCAATTTCAAATTTCTTC-ATTCATCAAATGTCTTTCTTAACGGATCG
* * *
568605 GTCTTCAATCAATTTCAAATTTCTTCCTTCATCATATGTCTTTCTTCACGGATCG
1 GTCTTCAATCAATTTCAAATTTCTTCATTCATCAAATGTCTTTCTTAACGGATCG
* *
568660 GTCTTCAATCAATTTTAAATTTCTTCATTCATCGAATGTCTTTCTT
1 GTCTTCAATCAATTTCAAATTTCTTCATTCATCAAATGTCTTTCTT
568706 CATGAATCCT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 88 0.98
56 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.44
Consensus pattern (55 bp):
GTCTTCAATCAATTTCAAATTTCTTCATTCATCAAATGTCTTTCTTAACGGATCG
Found at i:581756 original size:55 final size:55
Alignment explanation
Indices: 581672--581874 Score: 309
Period size: 55 Copynumber: 3.7 Consensus size: 55
581662 CAACGAGAAT
*
581672 TTCATAAACTTATTATGAATTTCTTAGTTTTGCACACGCAGTGCTCATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCTCATACGGAAA
* *
581727 TTCATAAAATTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCTCATACGGAAA
* * * * *
581782 TTCATAAACTTATTATGATTTTTTTAGTTTTACACACACAGTG-TCCATATGAAAA
1 TTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCT-CATACGGAAA
*
581837 TTCATAAACTTATTATGAATTTATTAGTTTTGCACACA
1 TTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
581875 TATAGTGCCA
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
55 134 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (55 bp):
TTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCTCATACGGAAA
Found at i:584914 original size:24 final size:24
Alignment explanation
Indices: 584882--584930 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
584872 TGAAAAATTG
584882 CATCCTTTTG-TTGTTCAATAGACA
1 CATCCTTTTGATT-TTCAATAGACA
* *
584906 CATCTTTTTGATTTTCAATGGACA
1 CATCCTTTTGATTTTCAATAGACA
584930 C
1 C
584931 GTCTCCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.43
Consensus pattern (24 bp):
CATCCTTTTGATTTTCAATAGACA
Found at i:591080 original size:2 final size:2
Alignment explanation
Indices: 591073--591100 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
591063 ATAAAATAAA
591073 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
591101 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:593498 original size:18 final size:17
Alignment explanation
Indices: 593475--593508 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
593465 TAATAAATTA
593475 ATAATAAAATTATATAAT
1 ATAATAAAATTA-ATAAT
593493 ATAATAAAATTAATAA
1 ATAATAAAATTAATAA
593509 AATTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAAAATTAATAAT
Found at i:593519 original size:27 final size:29
Alignment explanation
Indices: 593455--593529 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 29
593445 ATATTCTTAT
*
593455 TTTAATAATATAAT-AAATTAATAATAAA
1 TTTATTAATATAATAAAATTAATAATAAA
*
593483 ATTATATAATATAATAAAATTAAT-A-AAA
1 TTTAT-TAATATAATAAAATTAATAATAAA
* *
593511 TTTATTAATTTTATAAAAT
1 TTTATTAATATAATAAAAT
593530 ATTATTATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 12 0.30
28 10 0.25
29 10 0.25
30 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTATTAATATAATAAAATTAATAATAAA
Found at i:601041 original size:15 final size:14
Alignment explanation
Indices: 601021--601095 Score: 93
Period size: 14 Copynumber: 5.4 Consensus size: 14
601011 TCCATTATAG
601021 AGAAAAAAAGAGAAA
1 AGAAAAAAA-AGAAA
601036 AGAAAATAAAAGAAA
1 AGAAAA-AAAAGAAA
*
601051 A-AAAGAAAA-AAA
1 AGAAAAAAAAGAAA
601063 AGAAAAAAAAGAAA
1 AGAAAAAAAAGAAA
601077 A-AGAAAAAAAGAAA
1 AGA-AAAAAAAGAAA
601091 AGAAA
1 AGAAA
601096 TTAAATCAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.08
13 12 0.23
14 21 0.40
15 13 0.25
16 3 0.06
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (14 bp):
AGAAAAAAAAGAAA
Found at i:601054 original size:8 final size:8
Alignment explanation
Indices: 601021--601091 Score: 83
Period size: 8 Copynumber: 8.8 Consensus size: 8
601011 TCCATTATAG
601021 AGAAAAAA
1 AGAAAAAA
601029 AGAGAAAAGA
1 AGA-AAAA-A
*
601039 A-AATAAA
1 AGAAAAAA
601046 AGAAAAAA
1 AGAAAAAA
601054 AGAAAAAAA
1 AG-AAAAAA
601063 AGAAAAAA
1 AGAAAAAA
*
601071 A-AGAAAA
1 AGAAAAAA
601078 AGAAAAAA
1 AGAAAAAA
601086 AGAAAA
1 AGAAAA
601092 GAAATTAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
7 8 0.15
8 31 0.57
9 13 0.24
10 2 0.04
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (8 bp):
AGAAAAAA
Found at i:601057 original size:23 final size:22
Alignment explanation
Indices: 601024--601095 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 22
601014 ATTATAGAGA
*
601024 AAAAAAGAGAAAAGAAAATAAAAG
1 AAAAAA-AGAAAA-AAAAGAAAAG
601048 AAAAAAAGAAAAAAAAGAAAA-
1 AAAAAAAGAAAAAAAAGAAAAG
*
601069 AAAAGAAAAAGAAAAAAAGAAAAG
1 AAAA-AAAGA-AAAAAAAGAAAAG
601093 AAA
1 AAA
601096 TTAAATCAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.09
22 12 0.28
23 18 0.42
24 9 0.21
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAAGAAAAG
Found at i:601062 original size:9 final size:9
Alignment explanation
Indices: 601033--601095 Score: 85
Period size: 9 Copynumber: 6.9 Consensus size: 9
601023 AAAAAAAGAG
601033 AAAAGAAAA
1 AAAAGAAAA
601042 TAAAAG-AAA
1 -AAAAGAAAA
601051 AAAAGAAAA
1 AAAAGAAAA
601060 AAAAGAAAA
1 AAAAGAAAA
601069 AAAAGAAAA
1 AAAAGAAAA
601078 AGAAA-AAAA
1 A-AAAGAAAA
601087 GAAAAGAAA
1 -AAAAGAAA
601096 TTAAATCAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
8 5 0.10
9 32 0.65
10 12 0.24
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:601067 original size:32 final size:33
Alignment explanation
Indices: 601021--601091 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 33
601011 TCCATTATAG
*
601021 AGAAAAAAAGAGAAAAGAAAA-TAAAAGAAAAAA
1 AGAAAAAAAGAGAAAA-AAAAGAAAAAGAAAAAA
601054 AGAAAAAAA-AGAAAAAAAAGAAAAAGAAAAAA
1 AGAAAAAAAGAGAAAAAAAAGAAAAAGAAAAAA
601086 AGAAAA
1 AGAAAA
601092 GAAATTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 4 0.11
32 23 0.64
33 9 0.25
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (33 bp):
AGAAAAAAAGAGAAAAAAAAGAAAAAGAAAAAA
Found at i:603368 original size:149 final size:148
Alignment explanation
Indices: 603060--603449 Score: 577
Period size: 149 Copynumber: 2.6 Consensus size: 148
603050 AAAAAATGAA
* *
603060 ATGATAAAGGTTTCTCATTCCAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
1 ATGA-AAAGGTTTCTTATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
603125 CCTAGTAAAATATTTCCAAAATTTATAAGTCATTCGGACCATCCATAAGACCTTTGGGCAGGATG
65 CCTAGTAAAATATTTCCAAAATTTAT-AGTCATTCGGACCATCCATAAGACCTTTGGGCAGGATG
603190 ATTTCAAATGTCTATAAAAT
129 ATTTCAAATGTCTATAAAAT
* **
603210 ATGATAAGGTTTCTTATTCAAATTTGAAATTTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAAAAGGTTTCTTATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* * * *
603275 CTAGTAAAGTATTTCCAAAATTTAT-GTCCTTCGGTCCATCCATAAGACCTTTGGGCAGTATG-T
66 CTAGTAAAATATTTCCAAAATTTATAGTCATTCGGACCATCCATAAGACCTTTGGGCAGGATGAT
* *
603338 TTTATATTGTCTATCAAAAT
131 TTCA-AATGTCTAT-AAAAT
* * * *
603358 ATGAGAAAGGTTTATTATTCGAATTTGAAAAATTGAAATTTTTAAAAAGTAAGAAATGTTTCTTA
1 ATGA-AAAGGTTTCTTATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
*
603423 CCTAGTAAACTATTTCCAAAATTTATA
65 CCTAGTAAAATATTTCCAAAATTTATA
603450 AGTCCTTTGG
Statistics
Matches: 217, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
146 4 0.02
147 42 0.19
148 9 0.04
149 158 0.73
150 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (148 bp):
ATGAAAAGGTTTCTTATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
CTAGTAAAATATTTCCAAAATTTATAGTCATTCGGACCATCCATAAGACCTTTGGGCAGGATGAT
TTCAAATGTCTATAAAAT
Found at i:603544 original size:41 final size:41
Alignment explanation
Indices: 603445--603560 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 41
603435 TTTCCAAAAT
* * * * * *
603445 TTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGA
1 TTATAAGTCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
*
603486 TGCT-TAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
1 T--TATAAGTCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
*
603528 TTATAAGTCCTTCGGGTCATCTATAAGACCTTT
1 TTATAAGTCCTTCGGGTCATCTGTAAG-CCTTT
603561 GGCCAGGATG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 1 0.02
41 23 0.37
42 37 0.60
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (41 bp):
TTATAAGTCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
Found at i:603772 original size:42 final size:42
Alignment explanation
Indices: 603679--603775 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
603669 TCCAAAATTT
* * * *
603679 ATAAGTCCTTCGGTTCATCAGTAAGTCTTTCGAGCACGATGG
1 ATAAGTCCTTCGGCTCATCAGTAAGCCTTTAGAGCAAGATGG
* *
603721 TTAAATCCTTCGGCTCATCTA-TAAAGCCTTTAGAGCAAGAT-G
1 ATAAGTCCTTCGGCTCATC-AGT-AAGCCTTTAGAGCAAGATGG
603763 ATAAGTCCTTCGG
1 ATAAGTCCTTCGG
603776 GTTATTCATA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
42 29 0.64
43 16 0.36
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
ATAAGTCCTTCGGCTCATCAGTAAGCCTTTAGAGCAAGATGG
Found at i:604047 original size:235 final size:233
Alignment explanation
Indices: 603300--604106 Score: 1151
Period size: 235 Copynumber: 3.5 Consensus size: 233
603290 CAAAATTTAT
* * **
603300 GTCCTTC-GGTCCATCCATAAGACCTTTGGGC-AGTATGTTTT-ATATTGTCTATCAAAATATGA
1 GTCCTTCGGGT-CATCCATAAGACCTTTGGGCAAG-ATGTTTTCACA-TGTCTTTTGAAATATGA
* * * * *
603362 GAAAGGTTTAT--TATTCGAATTTGAAAAATTGAAATTTTTAAAAAGTAAGAAATGTTTCTTACC
63 GAAAGGTTTCTCATATT-AAATCTG-AAAATTGAAA-TTTTGAAAAGTAAGAAAGGTTTCTTACC
** *
603425 TAGTAAACTATTTCCAAAATTTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
125 TAGTAAACTATTTCCAAAATTTATAAGTCCTTTGGTTCATCAGTAAGTCTTTCGAGCACGATGCT
* *
603490 TAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATTATAA
190 TAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* * *
603534 GTCCTTCGGGTCATCTATAAGACCTTTGGCCAGGATGTTTTCACATGTCTTTTGAAATATGAGAA
1 GTCCTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTTTTCACATGTCTTTTGAAATATGAGAA
**
603599 AGG-TTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTACTAAAGGTTTCTTACCTAGTAA
66 AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAA
* *
603663 ACTATTTCCAAAATTTATAAGTCCTTCGGTTCATCAGTAAGTCTTTCGAGCACGATGGTTAAATC
131 ACTATTTCCAAAATTTATAAGTCCTTTGGTTCATCAGTAAGTCTTTCGAGCACGATGCTTAAATC
* * *
603728 CTTCGGCTCATCTATAAAGCCTTTAGAGCAAGATGATAA
196 CTTCGGGTCATCTGT-AAGCCTTTCGAGCAAGATGATAA
* * * * *
603767 GTCCTTCGGGTTATTCATAAGACCTTCGGGCAGGATGTTTTCACATGCCTTTTGAAATATGAGAA
1 GTCCTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTTTTCACATGTCTTTTGAAATATGAGAA
603832 AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAA
66 AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAA
* *
603897 GA-TAATTTCCAAAATTTTATAAGTCATTTGGTTCATCAGTAAGTCTTTCAAGCACGATGCTTAA
131 -ACT-ATTTCCAAAA-TTTATAAGTCCTTTGGTTCATCAGTAAGTCTTTCGAGCACGATGCTTAA
*
603961 ATTCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
193 ATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* *
604002 GTCTTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTCTTCACATGTCTTTTGAAATATGAGAA
1 GTCCTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTTTTCACATGTCTTTTGAAATATGAGAA
* *
604067 AGTTTTCTCATATTAAATTTGAAAATTGAAATTTTGAAAA
66 AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAA
604107 ATCTAATATT
Statistics
Matches: 514, Mismatches: 49, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
232 103 0.20
233 95 0.18
234 117 0.23
235 139 0.27
236 60 0.12
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (233 bp):
GTCCTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTTTTCACATGTCTTTTGAAATATGAGAA
AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAA
ACTATTTCCAAAATTTATAAGTCCTTTGGTTCATCAGTAAGTCTTTCGAGCACGATGCTTAAATC
CTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
Found at i:604559 original size:15 final size:14
Alignment explanation
Indices: 604539--604573 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
604529 TTTCATTATA
604539 ATTATTATTAATATT
1 ATTATTATTAA-ATT
604554 ATTATTATTAAATT
1 ATTATTATTAAATT
*
604568 TTTATT
1 ATTATT
604574 TTATTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTATTAAATT
Found at i:614917 original size:15 final size:15
Alignment explanation
Indices: 614899--614949 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
614889 TTTCATTTTC
614899 TTTCATCCTTTCTTA
1 TTTCATCCTTTCTTA
*
614914 TTTCATTACC-TT-TTC
1 TTTCA-T-CCTTTCTTA
614929 TTTCATCCTTTCTTA
1 TTTCATCCTTTCTTA
614944 TTTCAT
1 TTTCAT
614950 TACCTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 20 0.67
16 3 0.10
17 2 0.07
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCATCCTTTCTTA
Found at i:614918 original size:30 final size:30
Alignment explanation
Indices: 614882--614962 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
614872 TTTTTCTCTC
*
614882 TATTTCATTTCATTTTCTTTCATCCTTTCT
1 TATTTCATTACATTTTCTTTCATCCTTTCT
*
614912 TATTTCATTACCTTTTCTTTCATCCTTTCT
1 TATTTCATTACATTTTCTTTCATCCTTTCT
* *
614942 TATTTCATTACCTTATCTTTC
1 TATTTCATTACATTTTCTTTC
614963 TTAACCATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTTCATTACATTTTCTTTCATCCTTTCT
Found at i:614928 original size:18 final size:18
Alignment explanation
Indices: 614907--614960 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 18
614897 TCTTTCATCC
614907 TTTCTTATTTCATTACCT
1 TTTCTTATTTCATTACCT
614925 TTTC---TTTCA-T-CC-
1 TTTCTTATTTCATTACCT
614937 TTTCTTATTTCATTACCT
1 TTTCTTATTTCATTACCT
*
614955 TATCTT
1 TTTCTT
614961 TCTTAACCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
12 4 0.14
13 2 0.07
14 1 0.03
15 10 0.34
16 1 0.03
17 2 0.07
18 9 0.31
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTCTTATTTCATTACCT
Found at i:618837 original size:19 final size:21
Alignment explanation
Indices: 618813--618864 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
618803 CGGCCAAGAG
*
618813 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
618832 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
618853 CATGTATTTTCA
1 CATGTATTTTCA
618865 AAGGGGTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:619514 original size:17 final size:17
Alignment explanation
Indices: 619494--619529 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
619484 GAGAAAAATC
* *
619494 AGAAAAGAAGAAAGAAA
1 AGAAAAGAAAAAAAAAA
619511 AGAAAAGAAAAAAAAAA
1 AGAAAAGAAAAAAAAAA
619528 AG
1 AG
619530 TTCAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAAAAAAAAA
Found at i:621955 original size:16 final size:18
Alignment explanation
Indices: 621934--621969 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
621924 ACCTATAGTT
621934 CACATC-TTATA-ATATG
1 CACATCATTATATATATG
621950 CACATCATTATATATATG
1 CACATCATTATATATATG
621968 CA
1 CA
621970 TTATATAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (18 bp):
CACATCATTATATATATG
Found at i:622796 original size:19 final size:21
Alignment explanation
Indices: 622772--622823 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
622762 CGGCCAAGAG
*
622772 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
622791 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
622812 CATGTATTTTCA
1 CATGTATTTTCA
622824 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:638773 original size:28 final size:28
Alignment explanation
Indices: 638741--638875 Score: 109
Period size: 28 Copynumber: 4.9 Consensus size: 28
638731 TGAATTAACT
*
638741 AAACAAATGATGAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
*
638769 AAACAAATGATGAACATGTTGTTATG--
1 AAACAAATGATGAACATGCTGTTATGCA
** ** * * * *
638795 TGA-ATGTGAGTGCACGTGAAT-TTA-ACA
1 AAACAAATGA-TGAACATG-CTGTTATGCA
* *
638822 AAACAAATGATAAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
638850 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
638876 AACCCCACGA
Statistics
Matches: 78, Mismatches: 22, Indels: 14
0.68 0.19 0.12
Matches are distributed among these distances:
25 4 0.05
26 11 0.14
27 9 0.12
28 54 0.69
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:638854 original size:81 final size:80
Alignment explanation
Indices: 638701--638875 Score: 287
Period size: 81 Copynumber: 2.2 Consensus size: 80
638691 GATAATGAAA
* * * * *
638701 AACATGTTGTAAAGTGAATGTGGGTGCACGTGAATTAACTAAACAAATGATGAATATGCTGTTAT
1 AACATGTTGTTATGTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATAAATATGCTGTTAT
638766 GCAAAACAAATGATG
66 GCAAAACAAATGATG
638781 AACATGTTGTTATGTGAATGTGAGTGCACGTGAATTTAACAAAACAAATGATAAATATGCTGTTA
1 AACATGTTGTTATGTGAATGTGAGTGCACGTGAA-TTAACAAAACAAATGATAAATATGCTGTTA
638846 TGCAAAACAAATGATG
65 TGCAAAACAAATGATG
*
638862 AACATGCTGTTATG
1 AACATGTTGTTATG
638876 AACCCCACGA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 31 0.35
81 57 0.65
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.29
Consensus pattern (80 bp):
AACATGTTGTTATGTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATAAATATGCTGTTAT
GCAAAACAAATGATG
Found at i:640141 original size:13 final size:13
Alignment explanation
Indices: 640119--640148 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
640109 ACTAGACACC
640119 TTTC-ACATACCT
1 TTTCAACATACCT
640131 TTTCAACATACCT
1 TTTCAACATACCT
640144 TTTCA
1 TTTCA
640149 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:644056 original size:23 final size:24
Alignment explanation
Indices: 644002--644056 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
643992 TTTTCTTTTC
*
644002 TTTTCTTTTTTTAATTTTCAGAAT
1 TTTTTTTTTTTTAATTTTCAGAAT
**
644026 TTGGTTTTTTTTAATTTTCAG-AT
1 TTTTTTTTTTTTAATTTTCAGAAT
644049 TTTTTTTT
1 TTTTTTTT
644057 CAAAATGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.71
Consensus pattern (24 bp):
TTTTTTTTTTTTAATTTTCAGAAT
Found at i:645347 original size:28 final size:28
Alignment explanation
Indices: 645315--645368 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
645305 TGAATTAACT
*
645315 AAACAAATGATGAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
*
645343 AAACAAATGATGAACATGTTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
645369 TGAGTGTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:645419 original size:81 final size:80
Alignment explanation
Indices: 645275--645449 Score: 269
Period size: 81 Copynumber: 2.2 Consensus size: 80
645265 GATAATGAAA
* * * * * *
645275 AACATGTTGTAAAGTGAATGTGGGTGCACGTGAATTAACTAAACAAATGATGAATATGCTGTTAT
1 AACATGTTGTTATGTGAATGTGAGTACACGTGAATTAACAAAACAAATGATAAATATGCTGTTAT
645340 GCAAAACAAATGATG
66 GCAAAACAAATGATG
* *
645355 AACATGTTGTTATGTGAGTGTGAGTACACGTGAATTTAACAAAACAAATGATAAATATGTTGTTA
1 AACATGTTGTTATGTGAATGTGAGTACACGTGAA-TTAACAAAACAAATGATAAATATGCTGTTA
645420 TGCAAAACAAATGATG
65 TGCAAAACAAATGATG
645436 AACATGTTGTTATG
1 AACATGTTGTTATG
645450 AACCCCACGA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 29 0.34
81 57 0.66
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (80 bp):
AACATGTTGTTATGTGAATGTGAGTACACGTGAATTAACAAAACAAATGATAAATATGCTGTTAT
GCAAAACAAATGATG
Found at i:645434 original size:28 final size:28
Alignment explanation
Indices: 645394--645449 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
645384 GTGAATTTAA
*
645394 CAAAACAAATGATAAATATGTTGTTATG
1 CAAAACAAATGATAAACATGTTGTTATG
*
645422 CAAAACAAATGATGAACATGTTGTTATG
1 CAAAACAAATGATAAACATGTTGTTATG
645450 AACCCCACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (28 bp):
CAAAACAAATGATAAACATGTTGTTATG
Found at i:646982 original size:15 final size:15
Alignment explanation
Indices: 646959--646993 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
646949 CTGGTCATGA
*
646959 GGCACTCACATGGGC
1 GGCATTCACATGGGC
646974 GGCATTCACATGGGC
1 GGCATTCACATGGGC
646989 GGCAT
1 GGCAT
646994 AGGGAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.29, G:0.34, T:0.17
Consensus pattern (15 bp):
GGCATTCACATGGGC
Found at i:651402 original size:17 final size:16
Alignment explanation
Indices: 651381--651436 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
651371 AGGATAAAGT
651381 AATGAAAAATAAGAAA
1 AATGAAAAATAAGAAA
*
651397 AGATGAATGAATAAG-AA
1 A-ATGAA-AAATAAGAAA
*
651414 AATGAAATAGTAAGAAA
1 AATGAAA-AATAAGAAA
651431 AATGAA
1 AATGAA
651437 GATAACTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 11 0.33
17 16 0.48
18 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (16 bp):
AATGAAAAATAAGAAA
Found at i:651672 original size:21 final size:19
Alignment explanation
Indices: 651637--651683 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
651627 GATGTATGAG
651637 TCTTTTTCTTTTCTTTTTC
1 TCTTTTTCTTTTCTTTTTC
*
651656 TGTTTTTCTTCTTTCTTTTTC
1 TCTTTTTC-T-TTTCTTTTTC
651677 TCTTTTT
1 TCTTTTT
651684 GTTGCTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 1 0.04
21 16 0.67
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (19 bp):
TCTTTTTCTTTTCTTTTTC
Found at i:660577 original size:36 final size:36
Alignment explanation
Indices: 660504--660608 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
660494 ATTTATAAGT
* * * *
660504 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
*
660539 TGGTGATGATATAGGCCTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
660575 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCATGATAATGGTGATGGAC
660609 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 18 0.28
36 46 0.72
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGATAATGGTGATGGACTA
Found at i:664282 original size:12 final size:13
Alignment explanation
Indices: 664265--664294 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
664255 GTTGTAGGAG
664265 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
664277 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
664290 TCTTT
1 TCTTT
664295 CTTGTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:664722 original size:22 final size:23
Alignment explanation
Indices: 664694--664745 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
664684 AATTATAAGT
*
664694 TGGTGATAATATGGGCATGAT-A
1 TGGTGATAATATAGGCATGATAA
* *
664716 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCATGATAA
664739 TGGTGAT
1 TGGTGAT
664746 GGACTATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCATGATAA
Found at i:664737 original size:36 final size:38
Alignment explanation
Indices: 664696--664785 Score: 122
Period size: 36 Copynumber: 2.5 Consensus size: 38
664686 TTATAAGTTG
664696 GTGATAATATGG-GCAT-GA-TATGGTGATGATATAGGC
1 GTGATAATATGGTG-ATGGACTATGGTGATGATATAGGC
664732 GTGAT-A-ATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATGGTGATGGACTATGGTGATGATATAGGC
664768 GTGAT-A-ATGGTGATGGAC
1 GTGATAATATGGTGATGGAC
664786 AGCTTGTATC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
34 6 0.12
35 4 0.08
36 41 0.80
ACGTcount: A:0.29, C:0.06, G:0.36, T:0.30
Consensus pattern (38 bp):
GTGATAATATGGTGATGGACTATGGTGATGATATAGGC
Found at i:667826 original size:8 final size:8
Alignment explanation
Indices: 667813--667851 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
667803 AAATCTTTTT
667813 TTTTCTTC
1 TTTTCTTC
667821 TTTTCTTC
1 TTTTCTTC
667829 TTTTCTTC
1 TTTTCTTC
667837 TTTT-TGTC
1 TTTTCT-TC
667845 TTTTCTT
1 TTTTCTT
667852 TCGTTTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 27 0.93
9 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (8 bp):
TTTTCTTC
Found at i:667858 original size:17 final size:16
Alignment explanation
Indices: 667813--667859 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
667803 AAATCTTTTT
*
667813 TTTTCTTC-TTTTCTTC
1 TTTTCTTCGTTTT-GTC
*
667829 TTTTCTTCTTTTTGTC
1 TTTTCTTCGTTTTGTC
667845 TTTTCTTTCGTTTTG
1 TTTTC-TTCGTTTTG
667860 CACTCCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTCTTCGTTTTGTC
Found at i:672776 original size:20 final size:20
Alignment explanation
Indices: 672753--672790 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
672743 CAACCTAAGG
*
672753 CATGAATCTTCATCAAAAGT
1 CATGAAACTTCATCAAAAGT
672773 CATGAAACTTCATCAAAA
1 CATGAAACTTCATCAAAA
672791 AATGCATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (20 bp):
CATGAAACTTCATCAAAAGT
Found at i:673539 original size:21 final size:22
Alignment explanation
Indices: 673488--673539 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
673478 TGTCATCATG
*
673488 TATTAGCTCATGTCATGTTTAC
1 TATTAGCTCATATCATGTTTAC
* *
673510 T-TTAACTCATATTATGTTTA-
1 TATTAGCTCATATCATGTTTAC
673530 TATTAGCTCA
1 TATTAGCTCA
673540 CTTGATTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (22 bp):
TATTAGCTCATATCATGTTTAC
Found at i:682387 original size:19 final size:19
Alignment explanation
Indices: 682345--682408 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
682335 CTATTTTTTT
*
682345 CAAAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAGA
* *
682364 AAAAAAAAAAAAAAAAAGG
1 CAAAAAAAAAAAAAAAAGA
* * *
682383 CAAAAAACAAAAAAAGAGC
1 CAAAAAAAAAAAAAAAAGA
682402 CAAAAAA
1 CAAAAAA
682409 GCCAAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAAAAAGA
Found at i:682397 original size:1 final size:1
Alignment explanation
Indices: 682346--682380 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
682336 TATTTTTTTC
682346 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
682381 GGCAAAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:687033 original size:21 final size:20
Alignment explanation
Indices: 687005--687044 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
686995 TTTGATAACA
687005 TTTCTTTCCATTTCAATTCT
1 TTTCTTTCCATTTCAATTCT
* *
687025 TTTCATTTCTATTTCCATTC
1 TTTC-TTTCCATTTCAATTC
687045 CTAATTATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCTTTCCATTTCAATTCT
Found at i:688131 original size:15 final size:15
Alignment explanation
Indices: 688106--688142 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
688096 ATATCAATCC
688106 GATATTGGGATCTCAA
1 GATA-TGGGATCTCAA
688122 GATATGGGATCTCAA
1 GATATGGGATCTCAA
688137 GATATG
1 GATATG
688143 CCCAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (15 bp):
GATATGGGATCTCAA
Found at i:696458 original size:36 final size:36
Alignment explanation
Indices: 696410--696514 Score: 133
Period size: 35 Copynumber: 2.9 Consensus size: 36
696400 ACTACGTAAA
696410 CATCACCATCTTCCATCACCATTTTCACGCCTATAAT
1 CATCACCATCTTCCATCACCA-TTTCACGCCTATAAT
* *
696447 -ATCACCATCTTCCATTACCATTGCACGCCTAT-AT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAAT
* * * *
696481 CATTACCATATTCTATCACCATTTCATGCCTATA
1 CATCACCATCTTCCATCACCATTTCACGCCTATA
696515 TAACCACCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
34 2 0.03
35 37 0.64
36 19 0.33
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.34
Consensus pattern (36 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAAT
Found at i:703585 original size:90 final size:90
Alignment explanation
Indices: 703407--703589 Score: 269
Period size: 90 Copynumber: 2.0 Consensus size: 90
703397 GGGAAATGAT
* *
703407 GCTTGGTCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
703472 GGGCTGTTCACATACAAAACACATG
66 GGGCTGGTCACATACAAAACACATG
* *
703497 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTT-GCGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
* * **
703561 GGGGCTGGTCATATGCAAGGCACATG
65 GGGGCTGGTCACATACAAAACACATG
703587 GCT
1 GCT
703590 ATTCTAGGAA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 28 0.34
90 55 0.66
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.21
Consensus pattern (90 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGCTGGTCACATACAAAACACATG
Found at i:704913 original size:26 final size:26
Alignment explanation
Indices: 704859--704910 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
704849 CCTTGGCTTG
*
704859 CTTTC-TCTTTTTTATTTTCTTTTTC
1 CTTTCTTCTTTTTTATTTTCTTCTTC
704884 CTTTCTTCTTTTTTGAATTTT-TTCTTC
1 CTTTCTTCTTTTTT--ATTTTCTTCTTC
704911 TTTTTGTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.22
26 8 0.35
27 5 0.22
28 5 0.22
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (26 bp):
CTTTCTTCTTTTTTATTTTCTTCTTC
Found at i:704916 original size:18 final size:18
Alignment explanation
Indices: 704885--704934 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
704875 TTCTTTTTCC
704885 TTTCTTCTTTTTTGAATTT
1 TTTCTTC-TTTTTGAATTT
**
704904 TTTCTTCTTTTTGTCTTT
1 TTTCTTCTTTTTGAATTT
704922 TCTT-TTCTTTTTG
1 T-TTCTTCTTTTTG
704935 CACTCCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 19 0.68
19 9 0.32
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTCTTCTTTTTGAATTT
Done.