Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 93 of 106
Found at i:35533942 original size:31 final size:31
Alignment explanation
Indices: 35533907--35534067 Score: 111
Period size: 31 Copynumber: 5.2 Consensus size: 31
35533897 TGGATGCCAA
* *
35533907 TTTAAGTCTAGTTATGTTGGCATAAAAAGAC
1 TTTAAGTCAAGTTATGTTGGCATAAAAAGAG
* **
35533938 TTTAAGCGCAA-TGTA-GTTGGCAT-TCAAGATG
1 TTTAAG-TCAAGT-TATGTTGGCATAAAAAGA-G
35533969 TTTAAGTCAAGTTATGTTGGCATGAAAAA-AG
1 TTTAAGTCAAGTTATGTTGGCAT-AAAAAGAG
* **
35534000 TTTAAGCTCAATTTA-GTTGGCAT-TCAAGATG
1 TTTAAG-TCAAGTTATGTTGGCATAAAAAGA-G
* * *
35534031 TTTAAGTTC-AGTTGTGTTGGCAGAAAAAGAC
1 TTTAAG-TCAAGTTATGTTGGCATAAAAAGAG
35534062 TTTAAG
1 TTTAAG
35534068 CCCAATTTAG
Statistics
Matches: 100, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
29 2 0.02
30 13 0.13
31 67 0.67
32 16 0.16
33 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTAAGTCAAGTTATGTTGGCATAAAAAGAG
Found at i:35534004 original size:62 final size:63
Alignment explanation
Indices: 35533907--35534112 Score: 271
Period size: 62 Copynumber: 3.3 Consensus size: 63
35533897 TGGATGCCAA
* * *
35533907 TTTAAGTCTAGTTATGTTGGCAT-AAAAAGACTTTAAGCGCAATGTAGTTGGCATTCAAGATG
1 TTTAAGTCAAGTTATGTTGGCATGAAAAAGACTTTAAGCCCAATTTAGTTGGCATTCAAGATG
* *
35533969 TTTAAGTCAAGTTATGTTGGCATGAAAAA-AGTTTAAGCTCAATTTAGTTGGCATTCAAGATG
1 TTTAAGTCAAGTTATGTTGGCATGAAAAAGACTTTAAGCCCAATTTAGTTGGCATTCAAGATG
* * *
35534031 TTTAAGTTC-AGTTGTGTTGGCA-GAAAAAGACTTTAAGCCCAATTTAGCTGGC-TTCTAAGATA
1 TTTAAG-TCAAGTTATGTTGGCATGAAAAAGACTTTAAGCCCAATTTAGTTGGCATTC-AAGATG
35534093 TTTAAGT-ATAGTTATGTTGG
1 TTTAAGTCA-AGTTATGTTGG
35534113 AACTAGAGAA
Statistics
Matches: 128, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
61 10 0.08
62 111 0.87
63 7 0.05
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (63 bp):
TTTAAGTCAAGTTATGTTGGCATGAAAAAGACTTTAAGCCCAATTTAGTTGGCATTCAAGATG
Found at i:35535299 original size:16 final size:17
Alignment explanation
Indices: 35535277--35535316 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
35535267 TTAGAAAGAG
*
35535277 AAAAAAGGTTGA-AGAA
1 AAAAAAGGTGGAGAGAA
*
35535293 AATAAAGGTGGAGAGAA
1 AAAAAAGGTGGAGAGAA
35535310 AAAAAAG
1 AAAAAAG
35535317 TTTAAACAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (17 bp):
AAAAAAGGTGGAGAGAA
Found at i:35535311 original size:17 final size:16
Alignment explanation
Indices: 35535272--35535316 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
35535262 GATAGTTAGA
* *
35535272 AAGAGAAAAAAGGTTG
1 AAGAAAAAAAAGGTGG
*
35535288 AAGAAAATAAAGGTGG
1 AAGAAAAAAAAGGTGG
35535304 AGAGAAAAAAAAG
1 A-AGAAAAAAAAG
35535317 TTTAAACAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.09
Consensus pattern (16 bp):
AAGAAAAAAAAGGTGG
Found at i:35537048 original size:13 final size:13
Alignment explanation
Indices: 35537030--35537055 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35537020 AGACTTGCAC
35537030 ATTATGACAGAGA
1 ATTATGACAGAGA
35537043 ATTATGACAGAGA
1 ATTATGACAGAGA
35537056 GTAGGAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
ATTATGACAGAGA
Found at i:35539551 original size:28 final size:29
Alignment explanation
Indices: 35539519--35539574 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
35539509 TAAGAAGTGA
* *
35539519 ATTTCCAACG-AAATTTCATTGGAAAACC
1 ATTTCCAACGAAAATTCCAATGGAAAACC
*
35539547 ATTTCTAACGTAAAATTCCAATGGAAAA
1 ATTTCCAACG-AAAATTCCAATGGAAAA
35539575 GTGTTGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.39
30 14 0.61
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (29 bp):
ATTTCCAACGAAAATTCCAATGGAAAACC
Found at i:35539756 original size:21 final size:21
Alignment explanation
Indices: 35539709--35539775 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
35539699 TTAATTTAAT
35539709 CTAAACAATTAAAATTAAGAAA
1 CTAAA-AATTAAAATTAAGAAA
* * *
35539731 -GAAAAATTTAAATTAATAAA
1 CTAAAAATTAAAATTAAGAAA
* *
35539751 CTAAAAACTAAAACT-A-AAA
1 CTAAAAATTAAAATTAAGAAA
35539770 CTAAAA
1 CTAAAA
35539776 CTAAAACTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 9 0.24
20 15 0.41
21 13 0.35
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.22
Consensus pattern (21 bp):
CTAAAAATTAAAATTAAGAAA
Found at i:35539763 original size:6 final size:6
Alignment explanation
Indices: 35539748--35539793 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
35539738 TTAAATTAAT
* *
35539748 AAACTAA AAACTA AAACTA AAACTA AAACTA AAACTC AATCTA AAA
1 AAACT-A AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA AAA
35539794 TCTATTAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
6 30 0.86
7 5 0.14
ACGTcount: A:0.65, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
AAACTA
Found at i:35546368 original size:6 final size:6
Alignment explanation
Indices: 35546345--35546387 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
35546335 AGTTTTTTTG
* ** *
35546345 TCTTCG TCTTCA AGTTCA TCTTCA TCTTCA TCTTCA TTTTCA T
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA T
35546388 GTCCTTCCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.28, G:0.05, T:0.51
Consensus pattern (6 bp):
TCTTCA
Found at i:35546411 original size:30 final size:30
Alignment explanation
Indices: 35546375--35546439 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
35546365 TTCATCTTCA
* *
35546375 TCTTCATTTTCATGTCCTTCCATGTCACCT
1 TCTTCATCTTCATCTCCTTCCATGTCACCT
* * *
35546405 TCTTCATCTTCATCTCTTTGCATGTCATCT
1 TCTTCATCTTCATCTCCTTCCATGTCACCT
35546435 TCTTC
1 TCTTC
35546440 TTCCTCAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.12, C:0.32, G:0.06, T:0.49
Consensus pattern (30 bp):
TCTTCATCTTCATCTCCTTCCATGTCACCT
Found at i:35559531 original size:2 final size:2
Alignment explanation
Indices: 35559524--35559643 Score: 90
Period size: 2 Copynumber: 61.0 Consensus size: 2
35559514 CAAGTAGAAT
*
35559524 TA TA TA TA TA TA TA TA AA TA -A TA TA CTA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
35559565 TA TA T- TA TA TG TT TA NTA GA TA -A GTA GA -A TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
35559606 TA TA TA TA CTT TA TA TA TA TA TA TA TA TA -A TC TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35559644 GTGTTTAAAC
Statistics
Matches: 94, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
1 6 0.06
2 82 0.87
3 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:35566860 original size:22 final size:20
Alignment explanation
Indices: 35566832--35566877 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
35566822 GAGGAGGTTT
* *
35566832 TATAATTTATTAATAATTATAA
1 TATAATTAATT-AT-ATTAAAA
35566854 TATAATTAATTATATTAAAA
1 TATAATTAATTATATTAAAA
35566874 TATA
1 TATA
35566878 TAAAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATAATTAATTATATTAAAA
Found at i:35567268 original size:23 final size:24
Alignment explanation
Indices: 35567241--35567287 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
35567231 TTTTTTCTTG
35567241 TATAAA-AAA-AAACAACAAAAAAA
1 TATAAAGAAAGAAACAA-AAAAAAA
35567264 TATAAAGAAAGGAAACAAAAAAAA
1 TATAAAGAAA-GAAACAAAAAAAA
35567288 TGAAAACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 3 0.14
25 6 0.29
26 6 0.29
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (24 bp):
TATAAAGAAAGAAACAAAAAAAAA
Found at i:35567339 original size:11 final size:12
Alignment explanation
Indices: 35567323--35567351 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
35567313 TCTTCTCAAA
35567323 AAAAAAAAAG-G
1 AAAAAAAAAGAG
35567334 AAAAAAAAAGAG
1 AAAAAAAAAGAG
35567346 AAAAAA
1 AAAAAA
35567352 TATTTAGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:35574580 original size:17 final size:16
Alignment explanation
Indices: 35574546--35574615 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
35574536 TGAAGGCATG
* *
35574546 AAAACAAAAAAAATAA
1 AAAAAAAAAAAAAGAA
*
35574562 AAAATAAAAAAAAGAA
1 AAAAAAAAAAAAAGAA
*
35574578 AAAAAAAAGAGAAAGATA
1 AAAAAAAA-AAAAAGA-A
* **
35574596 AAAAGAAAATGAAGAA
1 AAAAAAAAAAAAAGAA
35574612 AAAA
1 AAAA
35574616 GAAAGAATGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
16 26 0.58
17 11 0.24
18 8 0.18
ACGTcount: A:0.83, C:0.01, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:35574619 original size:7 final size:7
Alignment explanation
Indices: 35574553--35574619 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
35574543 ATGAAAACAA
*
35574553 AAAAAAT
1 AAAAAAG
*
35574560 AAAAAAT
1 AAAAAAG
35574567 AAAAAA-
1 AAAAAAG
35574573 AAGAAAA-
1 AA-AAAAG
35574580 AAAAAAG
1 AAAAAAG
*
35574587 -AGAAAG
1 AAAAAAG
35574593 ATAAAAAG
1 A-AAAAAG
35574601 AAAATGAAG
1 AAAA--AAG
35574610 AAAAAAG
1 AAAAAAG
35574617 AAA
1 AAA
35574620 GAATGGTGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
6 11 0.21
7 28 0.54
8 6 0.12
9 7 0.13
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:35574622 original size:11 final size:11
Alignment explanation
Indices: 35574552--35574604 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 11
35574542 CATGAAAACA
*
35574552 AAAAAAATAAAA
1 AAAAAAA-AAAG
35574564 AATAAAAAAAAG
1 AA-AAAAAAAAG
35574576 AAAAAAAAAAG
1 AAAAAAAAAAG
35574587 AGAAAGATAAAAAG
1 A-AAA-A-AAAAAG
35574601 AAAA
1 AAAA
35574605 TGAAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 10 0.28
12 10 0.28
13 9 0.25
14 7 0.19
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:35576766 original size:31 final size:31
Alignment explanation
Indices: 35576731--35577068 Score: 155
Period size: 31 Copynumber: 10.9 Consensus size: 31
35576721 CGAAAAGATA
*
35576731 TTAAGCCCAATTTAGTTGGCATCTAAGATGT
1 TTAAGCCCAATTTAGTTGGCATCAAAGATGT
* *
35576762 TTAAGTCC--TGTTATGTTGGCATGAAAAGAT-T
1 TTAAGCCCAAT-TTA-GTTGGCAT-CAAAGATGT
* **
35576793 TTAAGCCCAATTTAGTTGGCGTCCTAGATGT
1 TTAAGCCCAATTTAGTTGGCATCAAAGATGT
* *
35576824 TTAAGTCTAA-TTATGTTGGCA-CGAAAAGA-GT
1 TTAAGCCCAATTTA-GTTGGCATC--AAAGATGT
* * * * *
35576855 TTAAACACAATTTAGCTAGCATCCAAGATGT
1 TTAAGCCCAATTTAGTTGGCATCAAAGATGT
* * * *
35576886 TTAAGTCC-A-TTATGTTGGTATGAAA-ATATT
1 TTAAGCCCAATTTA-GTTGGCATCAAAGAT-GT
* * *
35576916 TTAAGCCTAATTTAGCTGGCATCCAAGATGT
1 TTAAGCCCAATTTAGTTGGCATCAAAGATGT
* * *
35576947 TTAAG-TCTAGTTATGTTGGCA-CAAAAAGA-GT
1 TTAAGCCCAATTTA-GTTGGCATC--AAAGATGT
* * *
35576978 TTAAGCCTAATTTAGATGGCATCCAAGATGT
1 TTAAGCCCAATTTAGTTGGCATCAAAGATGT
* * * * *
35577009 ATAAG-TCTAGTTATGTTGGCATGAAAAGA-GT
1 TTAAGCCCAATTTA-GTTGGCAT-CAAAGATGT
* * *
35577040 TTAAGCCCAATTTAGCTAGCATCCAAGAT
1 TTAAGCCCAATTTAGTTGGCATCAAAGAT
35577069 TTGTAAGTCT
Statistics
Matches: 216, Mismatches: 64, Indels: 54
0.65 0.19 0.16
Matches are distributed among these distances:
29 6 0.03
30 47 0.22
31 124 0.57
32 38 0.18
33 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (31 bp):
TTAAGCCCAATTTAGTTGGCATCAAAGATGT
Found at i:35576822 original size:62 final size:61
Alignment explanation
Indices: 35576722--35577583 Score: 720
Period size: 62 Copynumber: 13.9 Consensus size: 61
35576712 AACCAAACAC
* * *
35576722 GAAAAGA-TATTAAGCCCAATTTAGTTGGCATCTAAGATGTTTAAGTCCTGTTATGTTGGCAT
1 GAAAAGAGT-TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGT-CAGTTATGTTGGCAT
* * * * * *
35576784 GAAAAGATTTTAAGCCCAATTTAGTTGGCGTCCTAGATGTTTAAGTCTAATTATGTTGGCAC
1 GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGTC-AGTTATGTTGGCAT
* * * *
35576846 GAAAAGAGTTTAAACACAATTTAGCTAGCATCCAAGATGTTTAAGTCCA-TTATGTTGGTAT
1 GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGT-CAGTTATGTTGGCAT
* * * *
35576907 GAAAATATTTTAAGCCTAATTTAGCTGGCATCCAAGATGTTTAAGTCTAGTTATGTTGGCAC
1 GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGTC-AGTTATGTTGGCAT
* * * *
35576969 AAAAAGAGTTTAAGCCTAATTTAGATGGCATCCAAGATGTATAAGTCTAGTTATGTTGGCAT
1 GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGTC-AGTTATGTTGGCAT
* * *
35577031 GAAAAGAGTTTAAGCCCAATTTAGCTAGCATCCAAGAT-TTGTAAGTCTAGTTATTTTGG-TT
1 GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTT-TAAGTC-AGTTATGTTGGCAT
* * * * ** ** * *
35577092 TAATAAGATGTTTAGGCTCAA-TCAAATGAGCATGTAAGATGTGTAAGTTCAATTATGTTGGC-T
1 GAA-AAGA-GTTTAAGCCCAATTTAGCTG-GCATCCAAGATGTTTAAG-TCAGTTATGTTGGCAT
* * ** * * *
35577155 CGAAAAGATCTTTAAGCCTAATCAAACTGGCATCCAAGATGTTTAAGTCCAATTACT-TTGGCAC
1 -GAAAAGA-GTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGT-CAGTTA-TGTTGGCAT
** * ** **
35577219 GAAAAGAGTTTAAGCCCAATCCAACTGGCATCCAAGATGTGCAAGTTCAACTATGTTGGTCCA-
1 GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAG-TCAGTTATGTTGG--CAT
* *
35577282 -AAAAGACGTTTAAG-CCAATTTAGCTGGCATTCAAGATGTTTAAGTCTAGTTATATTGGCAT
1 GAAAAGA-GTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGTC-AGTTATGTTGGCAT
* * * ** **
35577343 AAAAAAGAGTTTGAGCCCAATCTAATTGGCATCCAAGATGTTTAAGTCCAGTTATGTTGGTTT
1 -GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGT-CAGTTATGTTGGCAT
* ** * * * * * *
35577406 GAAAAGATGTTTAAGCCTAATGAAACTAGCATCCAAGATATTTAAGTCCAATTATGTTGGTAC
1 GAAAAGA-GTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGT-CAGTTATGTTGGCAT
* * ** * *
35577469 AAAAAGAGTTTAAGCCAAATTTATTTAGCATCCAAGATGTTTAAGTCAGTTATGTTGGGAT
1 GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGTCAGTTATGTTGGCAT
* * * *
35577530 GAATAGATGTTTAAGACCAATTTAACTAGCATCCAAGAT-TTTAAGTCCAGTTAT
1 GAAAAGA-GTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGT-CAGTTAT
35577584 CTTAGCACAA
Statistics
Matches: 659, Mismatches: 110, Indels: 62
0.79 0.13 0.07
Matches are distributed among these distances:
60 3 0.00
61 83 0.13
62 376 0.57
63 184 0.28
64 13 0.02
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (61 bp):
GAAAAGAGTTTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGTCAGTTATGTTGGCAT
Found at i:35577250 original size:250 final size:248
Alignment explanation
Indices: 35576723--35577583 Score: 892
Period size: 250 Copynumber: 3.5 Consensus size: 248
35576713 ACCAAACACG
* *
35576723 AAAAGA-TATTAAGCCCAATTTAGTTGGCATCTAAGATGTTTAAGTCCT-GTTATGTTGGCATGA
1 AAAAGAGT-TTAAGCCCAATTTAATTGGCATCCAAGATGTTTAAGT-CTAGTTATGTTGGCATGA
* * * * * * * **
35576786 AAAGA-TTTTAAGCCCAATTTAGTTGGCGTCCTAGATGTTTAAGTCTAATTATGTTGGCACGAAA
64 AAAGACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGTTATATTGGCATAAAA
** * ** * *
35576850 AGAGTTTAAACACAATTTAGCT-AGCATCCAAGATGTTTAAG-TCCATTATGTTGGTATGAAAAT
129 AGAGTTTAGGCACAA-TCAAATGAGCATCCAAGATGTTTAAGTTCAATTATGTTGGT-TGAAAAG
** * * *
35576913 ATTTTAAGCCTAATTTAGCTGGCATCCAAGATGTTTAAGTCTAGTTATGTTGGCACA
192 ATTTTAAGCCTAATCAAACTGGCATCCAAGATGTTTAAGTCCAATTATGTTGGCACA
* *
35576970 AAAAGAGTTTAAGCCTAATTTAGA-TGGCATCCAAGATGTATAAGTCTAGTTATGTTGGCATGAA
1 AAAAGAGTTTAAGCCCAATTTA-ATTGGCATCCAAGATGTTTAAGTCTAGTTATGTTGGCATGAA
* ** *
35577034 AAGA-GTTTAAGCCCAATTTAGCTAGCATCCAAGAT-TTGTAAGTCTAGTTATTTTGGTTTAATA
65 AAGACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTT-TAAGTCTAGTTATATTGGCATAAAA
* ** * *
35577097 AGATGTTTAGGCTCAATCAAATGAGCATGTAAGATGTGTAAGTTCAATTATGTTGGCTCGAAAAG
129 AGA-GTTTAGGCACAATCAAATGAGCATCCAAGATGTTTAAGTTCAATTATGTTGG-TTGAAAAG
*
35577162 ATCTTTAAGCCTAATCAAACTGGCATCCAAGATGTTTAAGTCCAATTACT-TTGGCACG
192 AT-TTTAAGCCTAATCAAACTGGCATCCAAGATGTTTAAGTCCAATTA-TGTTGGCACA
** * ** **
35577220 AAAAGAGTTTAAGCCCAATCCAACTGGCATCCAAGATGTGCAAGT-TCAACTATGTTGGTCCA--
1 AAAAGAGTTTAAGCCCAATTTAATTGGCATCCAAGATGTTTAAGTCT-AGTTATGTTGG--CATG
* *
35577282 AAAAGACGTTTAAG-CCAATTTAGCTGGCATTCAAGATGTTTAAGTCTAGTTATATTGGCATAAA
63 AAAAGACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGTTATATTGGCAT-AA
* * * *
35577346 AAAGAGTTT-GAGCCCAATCTAATTG-GCATCCAAGATGTTTAAGTCCAGTTATGTTGGTTTGAA
127 AAAGAGTTTAG-GCACAATC-AAATGAGCATCCAAGATGTTTAAGTTCAATTATGTTGG-TTGAA
* * * *
35577409 AAGATGTTTAAGCCTAATGAAACTAGCATCCAAGATATTTAAGTCCAATTATGTTGGTACA
189 AAGAT-TTTAAGCCTAATCAAACTGGCATCCAAGATGTTTAAGTCCAATTATGTTGGCACA
* * * * *
35577470 AAAAGAGTTTAAGCCAAATTTATTTAGCATCCAAGATGTTTAAGTC-AGTTATGTTGGGATGAAT
1 AAAAGAGTTTAAGCCCAATTTAATTGGCATCCAAGATGTTTAAGTCTAGTTATGTTGGCATGAAA
* * * *
35577534 AGATGTTTAAGACCAATTTAACTAGCATCCAAGAT-TTTAAGTCCAGTTAT
66 AGACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGTTAT
35577584 CTTAGCACAA
Statistics
Matches: 511, Mismatches: 79, Indels: 46
0.80 0.12 0.07
Matches are distributed among these distances:
246 4 0.01
247 109 0.21
248 26 0.05
249 58 0.11
250 292 0.57
251 20 0.04
252 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (248 bp):
AAAAGAGTTTAAGCCCAATTTAATTGGCATCCAAGATGTTTAAGTCTAGTTATGTTGGCATGAAA
AGACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGTTATATTGGCATAAAAAG
AGTTTAGGCACAATCAAATGAGCATCCAAGATGTTTAAGTTCAATTATGTTGGTTGAAAAGATTT
TAAGCCTAATCAAACTGGCATCCAAGATGTTTAAGTCCAATTATGTTGGCACA
Found at i:35577590 original size:30 final size:31
Alignment explanation
Indices: 35577489--35577590 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 31
35577479 TAAGCCAAAT
35577489 TTAT-TTAGCATCCAAGATGTTTAAGT-CAG
1 TTATCTTAGCATCCAAGATGTTTAAGTCCAG
* * * ** * *
35577518 TTATGTTGGGATGAATAGATGTTTAAGACCAAT
1 TTATCTTAGCATCCA-AGATGTTTAAGTCC-AG
*
35577551 TTAAC-TAGCATCCAAGAT-TTTAAGTCCAG
1 TTATCTTAGCATCCAAGATGTTTAAGTCCAG
35577580 TTATCTTAGCA
1 TTATCTTAGCA
35577591 CAAGAGAATT
Statistics
Matches: 53, Mismatches: 15, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
29 9 0.17
30 19 0.36
31 15 0.28
32 6 0.11
33 4 0.08
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (31 bp):
TTATCTTAGCATCCAAGATGTTTAAGTCCAG
Found at i:35582415 original size:34 final size:34
Alignment explanation
Indices: 35582348--35582415 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
35582338 GTTTTGTTTA
*
35582348 ACTATCATTTTTATGTCTTTTGAGAAAATTTGTT
1 ACTATCATTTTTATGTCTTTTGAGAAAACTTGTT
35582382 ACTATCATTTTTATGTCTTTTGA-AGAAACTTGTT
1 ACTATCATTTTTATGTCTTTTGAGA-AAACTTGTT
35582416 CTCCTAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.51
Consensus pattern (34 bp):
ACTATCATTTTTATGTCTTTTGAGAAAACTTGTT
Found at i:35584453 original size:31 final size:31
Alignment explanation
Indices: 35584388--35584453 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
35584378 AAAAGGAATC
* * * *
35584388 AAAATAATGAAGGGCTGCAGAAGTATCTAGG
1 AAAATAATGAACGGCTGCAGAAGTACCCAAG
* *
35584419 AAAATAATGAACTGTTGCAGAAGTACCCAAG
1 AAAATAATGAACGGCTGCAGAAGTACCCAAG
35584450 AAAA
1 AAAA
35584454 ACACACCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.18
Consensus pattern (31 bp):
AAAATAATGAACGGCTGCAGAAGTACCCAAG
Found at i:35584878 original size:2 final size:2
Alignment explanation
Indices: 35584871--35584955 Score: 68
Period size: 2 Copynumber: 42.5 Consensus size: 2
35584861 CGATGGAAAC
* * *
35584871 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CT- TA TA TA CA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
35584913 TA TA CA TA TA TA TA CA TA CA CT- TA T- TA TNA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T-A TA TA TA TA TA TA
35584955 T
1 T
35584956 CTAAAGCTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
1 3 0.04
2 62 0.93
3 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:35586036 original size:2 final size:2
Alignment explanation
Indices: 35586031--35586056 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35586021 TCTGTGTGTG
35586031 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
35586057 CTTTGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35588511 original size:41 final size:41
Alignment explanation
Indices: 35588466--35588547 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
35588456 GGACTTGTTG
35588466 CAACAACCTAATAGTGGCTTGATTATTGGATTCAATCTCAC
1 CAACAACCTAATAGTGGCTTGATTATTGGATTCAATCTCAC
35588507 CAACAACCTAATAGTGGCTTGATTATTGGATTCAATCTCAC
1 CAACAACCTAATAGTGGCTTGATTATTGGATTCAATCTCAC
35588548 TACCTATAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (41 bp):
CAACAACCTAATAGTGGCTTGATTATTGGATTCAATCTCAC
Found at i:35591064 original size:80 final size:80
Alignment explanation
Indices: 35590942--35591189 Score: 333
Period size: 80 Copynumber: 3.1 Consensus size: 80
35590932 CATGAGTTCC
* * *
35590942 ATTTATGAGATTGT-AACATGTATGCCATGTGACGTATGTGTTAAGGATA-TCATGTACACTATG
1 ATTTATGAGATTATGAA-ATGTATGCCATGAGATGTATGTGTTAA-GATAGTCATGTACACTATG
35591005 GGCTAAGCATGTGAATG
64 GGCTAAGCATGTGAATG
* * *
35591022 ATTTATGAGATTATGAAATGTATGCCATGAGATGTATGTGTTAAGATAGT-AGTATACATTATTG
1 ATTTATGAGATTATGAAATGTATGCCATGAGATGTATGTGTTAAGATAGTCA-TGTACACTATGG
*
35591086 GCTAAGCATGTGAGTG
65 GCTAAGCATGTGAATG
* * * *
35591102 ATTTATGAGGTTATGAAATATATGCCATGAGATGTTTGTGTTGAGATAGTCATGTACACTATGGG
1 ATTTATGAGATTATGAAATGTATGCCATGAGATGTATGTGTTAAGATAGTCATGTACACTATGGG
35591167 CTAAGCATGATG-ATG
66 CTAAGCATG-TGAATG
35591182 ATTTATGA
1 ATTTATGA
35591190 AAATGTTATA
Statistics
Matches: 148, Mismatches: 15, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
79 5 0.03
80 138 0.93
81 5 0.03
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (80 bp):
ATTTATGAGATTATGAAATGTATGCCATGAGATGTATGTGTTAAGATAGTCATGTACACTATGGG
CTAAGCATGTGAATG
Found at i:35596859 original size:21 final size:21
Alignment explanation
Indices: 35596829--35596869 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35596819 AGGTGTCATA
35596829 AGAATATACCCAAAGGTTTTG
1 AGAATATACCCAAAGGTTTTG
* **
35596850 AGAATGTACCCGGAGGTTTT
1 AGAATATACCCAAAGGTTTT
35596870 TAAAAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (21 bp):
AGAATATACCCAAAGGTTTTG
Found at i:35596939 original size:125 final size:125
Alignment explanation
Indices: 35596718--35596999 Score: 334
Period size: 125 Copynumber: 2.3 Consensus size: 125
35596708 TCCACATCAG
* * * * * *
35596718 AGGTTTTGAAAATGTACTCGAAGG-TTTTATAAGAAAAGGTTACTCTTCATCTCTAAATGAGGTT
1 AGGTTTTGAAAATGTACCCGGAGGTTTTTAAAAGAAAAAGTTACTCTTCATCTCTAAATAAGGCT
*
35596782 ACGTACCTTTAAAGAAATATTAATTCTAGTTACCTAAAGGTGTCATAAGAATATACCCAA
66 ACGTAACTTTAAAGAAATATTAATTCTAGTTACCTAAAGGTGTCATAAGAATATACCCAA
* * * *
35596842 AGGTTTTGAGAATGTACCCGGAGGTTTTTAAAAGAAAAAGTTGCTCTTTATCTTTAAATAAGGCT
1 AGGTTTTGAAAATGTACCCGGAGGTTTTTAAAAGAAAAAGTTACTCTTCATCTCTAAATAAGGCT
* * * ** * * * *
35596907 ACGTAATTTTAAAGAAATATTAGTGT-TAGTTACTTGGAGGTTTCTTAAGAATGTACCCAG
66 ACGTAACTTTAAAGAAATATTAAT-TCTAGTTACCTAAAGGTGTCATAAGAATATACCCAA
* * *
35596967 AGATTTTGAAAATGTATCCGGAGGTTTTAAAAA
1 AGGTTTTGAAAATGTACCCGGAGGTTTTTAAAA
35597000 ATGTATTTAG
Statistics
Matches: 132, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
124 21 0.16
125 110 0.83
126 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (125 bp):
AGGTTTTGAAAATGTACCCGGAGGTTTTTAAAAGAAAAAGTTACTCTTCATCTCTAAATAAGGCT
ACGTAACTTTAAAGAAATATTAATTCTAGTTACCTAAAGGTGTCATAAGAATATACCCAA
Found at i:35596994 original size:21 final size:21
Alignment explanation
Indices: 35596942--35597005 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
35596932 TTAGTTACTT
* *
35596942 GGAGGTTTCTTAAGAATGTACCC
1 GGAGG-TT-TTAAAAATGTATCC
* * *
35596965 AGAGATTTTGAAAATGTATCC
1 GGAGGTTTTAAAAATGTATCC
35596986 GGAGGTTTTAAAAAATGTAT
1 GGAGGTTTT-AAAAATGTAT
35597006 TTAGAGGTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 18 0.56
22 11 0.34
23 3 0.09
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.33
Consensus pattern (21 bp):
GGAGGTTTTAAAAATGTATCC
Found at i:35617895 original size:18 final size:18
Alignment explanation
Indices: 35617872--35617907 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35617862 TTCCTTTTTG
*
35617872 TATTTATTATTATTATTA
1 TATTTATTATTATCATTA
*
35617890 TATTTATTGTTATCATTA
1 TATTTATTATTATCATTA
35617908 CTTCTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTTATTATTATCATTA
Found at i:35622186 original size:38 final size:38
Alignment explanation
Indices: 35622088--35622193 Score: 117
Period size: 38 Copynumber: 2.7 Consensus size: 38
35622078 CTCACCCAGC
*
35622088 TCATGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCA
1 TCATGTGCATCCCCCCACATCGTGCACATAGCT-G-GCCA
* *
35622128 TCGTGTGCATCCCTCCACATCGTGCACAGTCAG-T-GCCA
1 TCATGTGCATCCCCCCACATCGTGCACA-T-AGCTGGCCA
* *
35622166 TCATGTACATCCCCCCACATCATGCACA
1 TCATGTGCATCCCCCCACATCGTGCACA
35622194 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
38 27 0.47
40 26 0.46
41 2 0.04
42 2 0.04
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (38 bp):
TCATGTGCATCCCCCCACATCGTGCACATAGCTGGCCA
Found at i:35622317 original size:2 final size:2
Alignment explanation
Indices: 35622310--35622335 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35622300 AATGCACAAC
35622310 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
35622336 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35648735 original size:39 final size:40
Alignment explanation
Indices: 35648692--35648774 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
35648682 TGTTGTGAAA
* *
35648692 AACACCAAT-TGTGGCAAAGTT-GGAAACCCTACTAAGGTG
1 AACACCAATCT-TGGCAAAGTTAGAAAACCCCACTAAGGTG
*
35648731 AACACCAATCTTGGCAAGGTTAGAAAACCCCACTAAGGTG
1 AACACCAATCTTGGCAAAGTTAGAAAACCCCACTAAGGTG
35648771 AACA
1 AACA
35648775 ACGACCAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 18 0.46
40 21 0.54
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (40 bp):
AACACCAATCTTGGCAAAGTTAGAAAACCCCACTAAGGTG
Found at i:35653865 original size:65 final size:65
Alignment explanation
Indices: 35653784--35653914 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
35653774 TAAGTGAAGA
35653784 AACCTTCCCAAAACCAAATTGGTGAAAGTGCCAAAAGGTTCATTTATGCCCATTAACCTCTAAGG
1 AACCTTCCCAAAACCAAATTGGTGAAAGTGCCAAAAGGTTCATTTATGCCCATTAACCTCTAAGG
* *
35653849 AACCTTCCCAAAACCAAATTGGTGAAGGTGCCCAAAGGTTCATTTATGCCCATTAACCTCTAAGG
1 AACCTTCCCAAAACCAAATTGGTGAAAGTGCCAAAAGGTTCATTTATGCCCATTAACCTCTAAGG
35653914 A
1 A
35653915 CCCATCAAAG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (65 bp):
AACCTTCCCAAAACCAAATTGGTGAAAGTGCCAAAAGGTTCATTTATGCCCATTAACCTCTAAGG
Found at i:35658141 original size:11 final size:11
Alignment explanation
Indices: 35658125--35658152 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
35658115 AACTTTTGGG
35658125 TTTAAAGTTGT
1 TTTAAAGTTGT
35658136 TTTAAAGTTGT
1 TTTAAAGTTGT
35658147 TTTAAA
1 TTTAAA
35658153 AACTACAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (11 bp):
TTTAAAGTTGT
Found at i:35667899 original size:6 final size:6
Alignment explanation
Indices: 35667839--35667881 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
35667829 CCTTTCCCTC
* * *
35667839 TCTTTT TCTTTT TCTTTT CCTTTCT TCTCTC TCTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTT-T TCTTTT TCTTTT TCTTTT
35667882 GTTTCCTCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TCTTTT
Found at i:35675864 original size:23 final size:24
Alignment explanation
Indices: 35675838--35675895 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
35675828 ATGAACAAAT
*
35675838 TAAATAGAAATGAA-AAAAATAA-A
1 TAAATAAAAAT-AATAAAAATAATA
*
35675861 TAAATAAAAATAATAATAATAATA
1 TAAATAAAAATAATAAAAATAATA
35675885 TAAATTAAAAA
1 TAAA-TAAAAA
35675896 ATTTTAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 2 0.07
23 17 0.57
24 5 0.17
25 6 0.20
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (24 bp):
TAAATAAAAATAATAAAAATAATA
Found at i:35676914 original size:2 final size:2
Alignment explanation
Indices: 35676907--35676952 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
35676897 TTGACCAAAG
35676907 CA CA CA CA TCA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA -CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35676949 CA CA
1 CA CA
35676953 TATATATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:35676957 original size:2 final size:2
Alignment explanation
Indices: 35676952--35676999 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
35676942 ACACACACAC
35676952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
35676995 AT AT A
1 AT AT A
35677000 NACACACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35677006 original size:2 final size:2
Alignment explanation
Indices: 35677001--35677037 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35676991 ATATATATAN
35677001 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
35677038 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:35677042 original size:2 final size:2
Alignment explanation
Indices: 35677037--35677103 Score: 100
Period size: 2 Copynumber: 33.5 Consensus size: 2
35677027 ACACACACAC
*
35677037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
35677079 AT AT GT AT AT AT AT -T CAT AT AT AT A
1 AT AT AT AT AT AT AT AT -AT AT AT AT A
35677104 GTTGTTCTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 57 0.97
3 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35681946 original size:29 final size:28
Alignment explanation
Indices: 35681904--35681962 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 28
35681894 ATATACCTTA
35681904 AACATAACGTGTAATAACTTCTTTTTTTC
1 AACATAACGTGTAATAA-TTCTTTTTTTC
*
35681933 AACATAACGTGTAATAATTTTTTTTTTC
1 AACATAACGTGTAATAATTCTTTTTTTC
35681961 AA
1 AA
35681963 TATGACATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.46
Consensus pattern (28 bp):
AACATAACGTGTAATAATTCTTTTTTTC
Found at i:35681973 original size:28 final size:29
Alignment explanation
Indices: 35681904--35681974 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 29
35681894 ATATACCTTA
*
35681904 AACATAACGTGTAATAACTTCTTTTTTTC
1 AACATAACATGTAATAACTTCTTTTTTTC
* *
35681933 AACATAACGTGTAATAA-TTTTTTTTTTC
1 AACATAACATGTAATAACTTCTTTTTTTC
* *
35681961 AATATGACATGTAA
1 AACATAACATGTAA
35681975 CTTAGTTCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (29 bp):
AACATAACATGTAATAACTTCTTTTTTTC
Found at i:35682055 original size:26 final size:27
Alignment explanation
Indices: 35682026--35682084 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
35682016 AAGCACCTTA
35682026 AACATGAC-GTGTAAT-AATTTTTTTTC
1 AACATGACGGT-TAATAAATTTTTTTTC
* *
35682052 AACATAATGGTTAATAAATTTTTTTTC
1 AACATGACGGTTAATAAATTTTTTTTC
35682079 AACATG
1 AACATG
35682085 GCGTATAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (27 bp):
AACATGACGGTTAATAAATTTTTTTTC
Found at i:35682298 original size:25 final size:26
Alignment explanation
Indices: 35682264--35682320 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
35682254 AAACACGTGA
* *
35682264 AACATGACGTGTAAT-ATTTTTTTTT
1 AACATAACGTGTAATAATATTTTTTT
35682289 AACATAACGTGTAATAATATTTTTTT
1 AACATAACGTGTAATAATATTTTTTT
35682315 AACATA
1 AACATA
35682321 GTATATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (26 bp):
AACATAACGTGTAATAATATTTTTTT
Found at i:35692151 original size:17 final size:17
Alignment explanation
Indices: 35692101--35692152 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
35692091 CATTTTTGTT
* *
35692101 TATTTTTTAACATTTTCT
1 TATTTTTT-ACTTTTTCA
*
35692119 TACTTTTTTA-TATTTCA
1 TA-TTTTTTACTTTTTCA
35692136 TATTTTTTACTTTTTCA
1 TATTTTTTACTTTTTCA
35692153 CATAAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 7 0.25
17 12 0.43
18 3 0.11
19 6 0.21
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTTTACTTTTTCA
Found at i:35695489 original size:12 final size:12
Alignment explanation
Indices: 35695472--35695516 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
35695462 ATAATAAAAT
35695472 ATAAAAAAATAA
1 ATAAAAAAATAA
35695484 ATAAAAAAATATA
1 ATAAAAAAATA-A
*
35695497 ATAATAATAAT-A
1 ATAA-AAAAATAA
35695509 ATAAAAAA
1 ATAAAAAA
35695517 GAGGTATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 3 0.10
12 16 0.55
13 5 0.17
14 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
ATAAAAAAATAA
Found at i:35695492 original size:22 final size:25
Alignment explanation
Indices: 35695462--35695516 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 25
35695452 AATTTAAATT
*
35695462 ATAATAAAATATAA-AAAAAT-A-A
1 ATAAAAAAATATAATAAAAATAATA
*
35695484 ATAAAAAAATATAATAATAATAATA
1 ATAAAAAAATATAATAAAAATAATA
35695509 ATAAAAAA
1 ATAAAAAA
35695517 GAGGTATGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.46
23 5 0.18
24 1 0.04
25 9 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (25 bp):
ATAAAAAAATATAATAAAAATAATA
Found at i:35695998 original size:21 final size:20
Alignment explanation
Indices: 35695973--35696013 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
35695963 GGAAACCCGC
*
35695973 AAGGAGAAAGGAGAGAAAGAG
1 AAGGAGAAA-GAAAGAAAGAG
35695994 AAGGAGAAAGAAAGAAAGAG
1 AAGGAGAAAGAAAGAAAGAG
35696014 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (20 bp):
AAGGAGAAAGAAAGAAAGAG
Found at i:35696020 original size:17 final size:16
Alignment explanation
Indices: 35695986--35696026 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
35695976 GAGAAAGGAG
* *
35695986 AGAAAGAGAAGGAGAA
1 AGAAAGAAAAGGAAAA
35696002 AGAAAGAAAGAGGAAAA
1 AGAAAGAAA-AGGAAAA
35696019 AGAAAGAA
1 AGAAAGAA
35696027 GAAGCCAGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAGGAAAA
Found at i:35696058 original size:9 final size:9
Alignment explanation
Indices: 35696046--35696099 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 9
35696036 GGGGAGAGAG
35696046 AAGAGAAGA
1 AAGAGAAGA
35696055 AAGAGAA-A
1 AAGAGAAGA
*
35696063 AA-AGAAAA
1 AAGAGAAGA
35696071 AAGAGAAGA
1 AAGAGAAGA
35696080 AAG-GAAAGA
1 AAGAG-AAGA
*
35696089 AAGGGAAGA
1 AAGAGAAGA
35696098 AA
1 AA
35696100 AAAAAAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 4 0.10
8 7 0.17
9 28 0.70
10 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (9 bp):
AAGAGAAGA
Found at i:35696096 original size:18 final size:18
Alignment explanation
Indices: 35696046--35696116 Score: 78
Period size: 16 Copynumber: 4.1 Consensus size: 18
35696036 GGGGAGAGAG
35696046 AAGAGAAGAAAGAGAA-AA
1 AAGA-AAGAAAGAGAAGAA
35696064 AAGAAA-AAAGAGAAGAA
1 AAGAAAGAAAGAGAAGAA
* *
35696081 AGGAAAGAAAGGGAAGAA
1 AAGAAAGAAAGAGAAGAA
*
35696099 AA-AAA-AAAGAAAAGAA
1 AAGAAAGAAAGAGAAGAA
35696115 AA
1 AA
35696117 AACAAGACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
16 19 0.41
17 12 0.26
18 15 0.33
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAAGAGAAGAA
Found at i:35696105 original size:34 final size:34
Alignment explanation
Indices: 35696051--35696115 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
35696041 GAGAGAAGAG
*
35696051 AAGAAAGAGAAAAAAGAAAAAAGAGAAGAAAGGA
1 AAGAAAGAGAAAAAAGAAAAAAGAAAAGAAAGGA
*
35696085 AAGAAAGGGAAGAAAA-AAAAAAGAAAAGAAA
1 AAGAAAGAGAA-AAAAGAAAAAAGAAAAGAAA
35696116 AAACAAGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (34 bp):
AAGAAAGAGAAAAAAGAAAAAAGAAAAGAAAGGA
Found at i:35696511 original size:12 final size:11
Alignment explanation
Indices: 35696486--35696521 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
35696476 TACATGATAC
35696486 AAATATAAAAA
1 AAATATAAAAA
*
35696497 AAATATAATAA
1 AAATATAAAAA
35696508 AAA-ATAAAAA
1 AAATATAAAAA
35696518 AAAT
1 AAAT
35696522 GAATGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATATAAAAA
Found at i:35696530 original size:21 final size:21
Alignment explanation
Indices: 35696490--35696533 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35696480 TGATACAAAT
*
35696490 ATAAAAAAAATATAATAAAAA
1 ATAAAAAAAATAGAATAAAAA
35696511 ATAAAAAAAAT-GAATGAAAAA
1 ATAAAAAAAATAGAAT-AAAAA
35696532 AT
1 AT
35696534 GAAATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (21 bp):
ATAAAAAAAATAGAATAAAAA
Found at i:35709407 original size:2 final size:2
Alignment explanation
Indices: 35709400--35709424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35709390 AAAGATGAAA
35709400 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
35709425 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:35709429 original size:2 final size:2
Alignment explanation
Indices: 35709424--35709499 Score: 72
Period size: 2 Copynumber: 40.0 Consensus size: 2
35709414 ACACACACAC
* *
35709424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
35709464 NAT A- AT GT AT AT -T AT AA AT AT AT -T AT AT AT AT AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35709500 TCTTTTCATT
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
1 5 0.08
2 57 0.90
3 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35718840 original size:18 final size:19
Alignment explanation
Indices: 35718801--35718841 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
35718791 AGTCTGAAGC
*
35718801 CTTGATGAAAACAAATAACT
1 CTTGATGAAAAC-AACAACT
35718821 CTTGATGAAAAC-ACAACT
1 CTTGATGAAAACAACAACT
35718839 CTT
1 CTT
35718842 AAATGCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (19 bp):
CTTGATGAAAACAACAACT
Found at i:35722371 original size:19 final size:19
Alignment explanation
Indices: 35722347--35722383 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
35722337 CCATTTGACT
35722347 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
35722366 TATTGGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
35722384 AGTTTAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:35723664 original size:13 final size:13
Alignment explanation
Indices: 35723646--35723670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35723636 NNNNNNNNNG
35723646 ATTTTATAAAATA
1 ATTTTATAAAATA
35723659 ATTTTATAAAAT
1 ATTTTATAAAAT
35723671 TTTTAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:35740487 original size:110 final size:110
Alignment explanation
Indices: 35740326--35740662 Score: 611
Period size: 110 Copynumber: 3.1 Consensus size: 110
35740316 GGCCTGCGTC
* *
35740326 GCCGACGTGAATACCAGCTGCAGATCGGCGCCAAGGATCTGCTGCCGGCACAAGAGGAAGAAGAG
1 GCCGACGTGAATACCAGCTGCAGATCGGCGCCAAGGATCTGCTACCAGCACAAGAGGAAGAAGAG
*
35740391 CTGAGCTGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCA
66 CTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCA
35740436 GCCGACGTGAATACCAGCTGCAGATCGGCGCCAAGGATCTGCTACCAGCACAAGAGGAAGAAGAG
1 GCCGACGTGAATACCAGCTGCAGATCGGCGCCAAGGATCTGCTACCAGCACAAGAGGAAGAAGAG
* *
35740501 CTGAGCGGAGGAATAGAGAAGGAGAGAGGTGGAGCCGCGGTACCA
66 CTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCA
*
35740546 ACCGACGTGAATACCAGCTGCAGATCGGCGCCAAGGATCTGCTACCAGCACAAGAGGAAGAAGAG
1 GCCGACGTGAATACCAGCTGCAGATCGGCGCCAAGGATCTGCTACCAGCACAAGAGGAAGAAGAG
*
35740611 CTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCAGTACCA
66 CTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCA
35740656 GCCGACG
1 GCCGACG
35740663 GAAAAGGGGG
Statistics
Matches: 218, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 218 1.00
ACGTcount: A:0.32, C:0.23, G:0.36, T:0.09
Consensus pattern (110 bp):
GCCGACGTGAATACCAGCTGCAGATCGGCGCCAAGGATCTGCTACCAGCACAAGAGGAAGAAGAG
CTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCA
Found at i:35740742 original size:12 final size:12
Alignment explanation
Indices: 35740705--35740736 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
35740695 ACGAGAAGAT
35740705 AGAGAGAGAAAG
1 AGAGAGAGAAAG
35740717 AGAGAGAGAAAG
1 AGAGAGAGAAAG
35740729 AGAGAGAG
1 AGAGAGAG
35740737 GCAGAGCCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAAAG
Found at i:35741660 original size:18 final size:19
Alignment explanation
Indices: 35741620--35741661 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
35741610 TAAATAAATA
* * *
35741620 AATAAAATAAGTAAATAAT
1 AATAAAATAAATAAAAAAC
35741639 AATAAAA-AAATAAAAAAC
1 AATAAAATAAATAAAAAAC
35741657 AATAA
1 AATAA
35741662 CTAATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
AATAAAATAAATAAAAAAC
Found at i:35743933 original size:30 final size:30
Alignment explanation
Indices: 35743867--35743934 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
35743857 TTCAATCAAG
*
35743867 TTCTTATATTTTTATTTTGAACCAAATAAA
1 TTCTTATACTTTTATTTTGAACCAAATAAA
** **
35743897 CCCTTATACTTTTATTTTGAGTCAAATAAA
1 TTCTTATACTTTTATTTTGAACCAAATAAA
35743927 TTCTTATA
1 TTCTTATA
35743935 ACTAATGATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (30 bp):
TTCTTATACTTTTATTTTGAACCAAATAAA
Found at i:35745419 original size:33 final size:33
Alignment explanation
Indices: 35745377--35745440 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
35745367 GACCAAACTT
35745377 TTTTTAAATAAACATTTATGACTTAATCAATAA
1 TTTTTAAATAAACATTTATGACTTAATCAATAA
35745410 TTTTTAAATAAACATTTATGACTTAATCAAT
1 TTTTTAAATAAACATTTATGACTTAATCAAT
35745441 GACGTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (33 bp):
TTTTTAAATAAACATTTATGACTTAATCAATAA
Found at i:35745618 original size:2 final size:2
Alignment explanation
Indices: 35745611--35745651 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
35745601 TTTTATAATT
35745611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35745652 AAAAAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35746630 original size:2 final size:2
Alignment explanation
Indices: 35746623--35746647 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35746613 TAAAAATTAC
35746623 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35746648 AATTCTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35748035 original size:26 final size:26
Alignment explanation
Indices: 35747967--35748037 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
35747957 TATATATCAA
* * *
35747967 GTTACACATCATGTTGAAAAAAAGTT
1 GTTACACGTCATGTTTAAAAAAAATT
*
35747993 ATTACACGTCATGTTTAAAAAAAATT
1 GTTACACGTCATGTTTAAAAAAAATT
*
35748019 GTTACACGTCATATTTAAA
1 GTTACACGTCATGTTTAAA
35748038 GTGTTCAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (26 bp):
GTTACACGTCATGTTTAAAAAAAATT
Found at i:35748157 original size:26 final size:27
Alignment explanation
Indices: 35748117--35748183 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
35748107 AAAAATATTA
* *
35748117 TTGTTACACACCATATT-CAAAAAAAG
1 TTGTTACACATCATATTAAAAAAAAAG
35748143 TTGTTACACATCATATTAAAAAAAAAG
1 TTGTTACACATCATATTAAAAAAAAAG
* *
35748170 TTATTACACGTCAT
1 TTGTTACACATCAT
35748184 TTTTGAGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 16 0.44
27 20 0.56
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (27 bp):
TTGTTACACATCATATTAAAAAAAAAG
Found at i:35748172 original size:24 final size:26
Alignment explanation
Indices: 35748119--35748172 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
35748109 AAATATTATT
**
35748119 GTTACACACCATATTCAAAAAAAGTT
1 GTTACACACCATATTCAAAAAAAGAA
*
35748145 GTTACACATCATATT-AAAAAAA-AA
1 GTTACACACCATATTCAAAAAAAGAA
35748169 GTTA
1 GTTA
35748173 TTACACGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 7 0.28
26 14 0.56
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (26 bp):
GTTACACACCATATTCAAAAAAAGAA
Found at i:35748245 original size:153 final size:150
Alignment explanation
Indices: 35747967--35748258 Score: 320
Period size: 153 Copynumber: 1.9 Consensus size: 150
35747957 TATATATCAA
* * * * * * *
35747967 GTTACACATCATGTTGAAAAAAAGTTATTACACGTCATGTTTAAAAAAAATTGTTACACGTCATA
1 GTTACACACCATATTCAAAAAAAGTTATTACACATCATATTAAAAAAAAATTATTACACGTCATA
* * ** *
35748032 TTTAAAGTGTTCAACTCTAAAAGTTTATGTTCCAATGAAATAAAATAATATAAATTAAGTTACAT
66 TTTAAAGTGTTCAACTCCAAAAGTTTATATTCCAATGAAATAAAATAATATAAACCAAGTTAAAT
35748097 GCCATATTTAAAAAATATTATT
131 G-C-TATTTAAAAAATATTATT
*
35748119 GTTACACACCATATTCAAAAAAAGTTGTTACACATCATATTAAAAAAAAAGTTATTACACGTCAT
1 GTTACACACCATATTCAAAAAAAGTTATTACACATCATATTAAAAAAAAA-TTATTACACGTCAT
* * * * * * * *
35748184 TTTTGAGGTGTTTAACTCCAAAAGTTTATA-TCTTAGTGAAATATGAA-GATA-AAGACCAAGTT
65 ATTTAAAGTGTTCAACTCCAAAAGTTTATATTC-CAATGAAATA-AAATAATATAA-ACCAAGTT
35748246 AAATGCTATTTAA
127 AAATGCTATTTAA
35748259 GGTGTTTAAA
Statistics
Matches: 115, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
151 7 0.06
152 48 0.42
153 58 0.50
154 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (150 bp):
GTTACACACCATATTCAAAAAAAGTTATTACACATCATATTAAAAAAAAATTATTACACGTCATA
TTTAAAGTGTTCAACTCCAAAAGTTTATATTCCAATGAAATAAAATAATATAAACCAAGTTAAAT
GCTATTTAAAAAATATTATT
Found at i:35761663 original size:16 final size:16
Alignment explanation
Indices: 35761627--35761664 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
35761617 TTCTTAAAGT
*
35761627 AAATTAAATCAAAATA
1 AAATAAAATCAAAATA
35761643 AAATAAAAT-AAAACTA
1 AAATAAAATCAAAA-TA
35761659 AAATAA
1 AAATAA
35761665 CTTAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAAATCAAAATA
Found at i:35762287 original size:4 final size:4
Alignment explanation
Indices: 35762278--35762303 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35762268 AGAAAATAAG
35762278 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
35762304 TATATCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:35763055 original size:20 final size:20
Alignment explanation
Indices: 35763032--35763076 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
35763022 GTAAAAATAA
*
35763032 AAAGACAAAAG-AGAAGAAAG
1 AAAGA-AAAAGAAAAAGAAAG
*
35763052 AAAGAAAAAGAAAAAGAGAG
1 AAAGAAAAAGAAAAAGAAAG
35763072 AAAGA
1 AAAGA
35763077 GAATTTGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAGAAAG
Found at i:35764304 original size:49 final size:49
Alignment explanation
Indices: 35764248--35764404 Score: 251
Period size: 49 Copynumber: 3.2 Consensus size: 49
35764238 TAGCTGGATA
** *
35764248 ATCATCATCATCGGCCTATGCGCACTCCCTACTCATACATAATCGGGTC
1 ATCATCATCATCGGCCTATGCGCACTCCCTACTCGCACATAGTCGGGTC
* *
35764297 ATTATCATCATCGGCCTATGCGCACTCCCTACTCGCACATAGTAGGGTC
1 ATCATCATCATCGGCCTATGCGCACTCCCTACTCGCACATAGTCGGGTC
* *
35764346 ATCATCATCATCGGCCTATGCGCTCTCCCTACTCGCACATAGCCGGGTC
1 ATCATCATCATCGGCCTATGCGCACTCCCTACTCGCACATAGTCGGGTC
35764395 ATCATCATCA
1 ATCATCATCA
35764405 CACAAGATTA
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 99 1.00
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (49 bp):
ATCATCATCATCGGCCTATGCGCACTCCCTACTCGCACATAGTCGGGTC
Found at i:35766935 original size:42 final size:42
Alignment explanation
Indices: 35766841--35766936 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
35766831 TCAACATCAC
*
35766841 CATCGGCTTATGTGCACTCCCATTAGCACATAGCCGGGTCAG
1 CATCGGCTTATGTGCACTCCCACTAGCACATAGCCGGGTCAG
* * * * *
35766883 CATCGACTTATGTGCACTCTCACTGGTACATAGTCGGGTCAG
1 CATCGGCTTATGTGCACTCCCACTAGCACATAGCCGGGTCAG
* *
35766925 TATTGGCTTATG
1 CATCGGCTTATG
35766937 CACACTTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (42 bp):
CATCGGCTTATGTGCACTCCCACTAGCACATAGCCGGGTCAG
Found at i:35780016 original size:30 final size:30
Alignment explanation
Indices: 35779981--35780069 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
35779971 CATCCAAGAT
35779981 GTTTAAGTCTAGTTATGTTGGCATGAAAAA
1 GTTTAAGTCTAGTTATGTTGGCATGAAAAA
* * * * * *
35780011 GTTTAAGCCCAATT-TAGTTGGCATCCAAGAT
1 GTTTAAGTCTAGTTAT-GTTGGCAT-GAAAAA
* *
35780042 GTTTAAGTCTAGTTATTTTGGCACGAAA
1 GTTTAAGTCTAGTTATGTTGGCATGAAA
35780070 TTGTTTTAAG
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
29 1 0.02
30 21 0.49
31 20 0.47
32 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (30 bp):
GTTTAAGTCTAGTTATGTTGGCATGAAAAA
Found at i:35780044 original size:61 final size:61
Alignment explanation
Indices: 35779852--35780069 Score: 267
Period size: 62 Copynumber: 3.5 Consensus size: 61
35779842 ACTCAGATTA
* * * *
35779852 AAGATATTTAAGT-TCAGTTATGTTGGCACGAAAAAAGTTTCAGCCTAATTTAGCTGATATCT
1 AAGATGTTTAAGTCT-AGTTATGTTGGCACG-AAAAAGTTTAAGCCTAATTTAGCTGACATCC
* * ** * *
35779914 AAGATGTTTAAGTCCAGTTATGTTGGCACAAAAAGAGTTTAAATCTAATTTAACTAACATCC
1 AAGATGTTTAAGTCTAGTTATGTTGGCACGAAAA-AGTTTAAGCCTAATTTAGCTGACATCC
* * * *
35779976 AAGATGTTTAAGTCTAGTTATGTTGGCATGAAAAAGTTTAAGCCCAATTTAGTTGGCATCC
1 AAGATGTTTAAGTCTAGTTATGTTGGCACGAAAAAGTTTAAGCCTAATTTAGCTGACATCC
*
35780037 AAGATGTTTAAGTCTAGTTATTTTGGCACGAAA
1 AAGATGTTTAAGTCTAGTTATGTTGGCACGAAA
35780070 TTGTTTTAAG
Statistics
Matches: 132, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
61 55 0.42
62 77 0.58
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (61 bp):
AAGATGTTTAAGTCTAGTTATGTTGGCACGAAAAAGTTTAAGCCTAATTTAGCTGACATCC
Found at i:35780063 original size:31 final size:31
Alignment explanation
Indices: 35779971--35780064 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
35779961 ATTTAACTAA
35779971 CATCCAAGATGTTTAAGTCTAGTTATGTTGG
1 CATCCAAGATGTTTAAGTCTAGTTATGTTGG
* * * * * *
35780002 CAT-GAAAAAGTTTAAGCCCAATT-TAGTTGG
1 CATCCAAGATGTTTAAGTCTAGTTAT-GTTGG
*
35780032 CATCCAAGATGTTTAAGTCTAGTTATTTTGG
1 CATCCAAGATGTTTAAGTCTAGTTATGTTGG
35780063 CA
1 CA
35780065 CGAAATTGTT
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 1 0.02
30 22 0.47
31 23 0.49
32 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (31 bp):
CATCCAAGATGTTTAAGTCTAGTTATGTTGG
Found at i:35780100 original size:61 final size:61
Alignment explanation
Indices: 35779852--35780103 Score: 215
Period size: 62 Copynumber: 4.1 Consensus size: 61
35779842 ACTCAGATTA
* * * * * ** *
35779852 AAGATATTTAAGT-TCAGTTATGTTGGCACGAAAAAAGTTTCAGCCTAATTTAGCTGATATCT
1 AAGATGTTTAAGTCT-AGTTATGTTGGCACG-AAAAAGTTTAAGCCCAATTAACCTGGCATCC
* * ** * **
35779914 AAGATGTTTAAGTCCAGTTATGTTGGCACAAAAAGAGTTTAAATCTAATTTAA-CTAACATCC
1 AAGATGTTTAAGTCTAGTTATGTTGGCACGAAAA-AGTTTAAGCCCAA-TTAACCTGGCATCC
* * **
35779976 AAGATGTTTAAGTCTAGTTATGTTGGCATGAAAAAGTTTAAGCCCAATTTAGTTGGCATCC
1 AAGATGTTTAAGTCTAGTTATGTTGGCACGAAAAAGTTTAAGCCCAATTAACCTGGCATCC
* ** *
35780037 AAGATGTTTAAGTCTAGTTATTTTGGCACGAAATTGTTTTAAGTCCAATATAACCT-GCA-CC
1 AAGATGTTTAAGTCTAGTTATGTTGGCACGAAAAAG-TTTAAGCCCAAT-TAACCTGGCATCC
35780098 AAGATG
1 AAGATG
35780104 CGTAAACCTA
Statistics
Matches: 156, Mismatches: 28, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
60 3 0.02
61 60 0.38
62 87 0.56
63 6 0.04
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (61 bp):
AAGATGTTTAAGTCTAGTTATGTTGGCACGAAAAAGTTTAAGCCCAATTAACCTGGCATCC
Found at i:35780175 original size:61 final size:59
Alignment explanation
Indices: 35779914--35780201 Score: 204
Period size: 61 Copynumber: 4.7 Consensus size: 59
35779904 GCTGATATCT
* * * * ** **
35779914 AAGATGTTTAAGTCC-AGTTATGTTGGCACAAAAAGAGTTTAAATCTAATTTAACTAACATCC
1 AAGATGTTTAAG-CCTAGTTATGTTGGCAC-GAAAGA-TTTAAGTCCAATATAGTTGGCA-CC
* * * * *
35779976 AAGATGTTTAAGTCTAGTTATGTTGGCATGAAAAAGTTTAAGCCCAATTTAGTTGGCATCC
1 AAGATGTTTAAGCCTAGTTATGTTGGCACGAAAGA-TTTAAGTCCAATATAGTTGGCA-CC
* * * **
35780037 AAGATGTTTAAGTCTAGTTATTTTGGCACGAAATTGTTTTAAGTCCAATATAACCT-GCACC
1 AAGATGTTTAAGCCTAGTTATGTTGGCACGAAA--GATTTAAGTCCAATAT-AGTTGGCACC
** * * *
35780098 AAGATGCGTAAACCTAGTTGA-GTTGGCACGATACGATTTAAGTCTAATATAGTTGGCACC
1 AAGATGTTTAAGCCTAGTT-ATGTTGGCACGA-AAGATTTAAGTCCAATATAGTTGGCACC
* * *
35780158 AAGATGTTTTAAGCCTAGTTAAGTTGGCATGAGAAGATTGAAGT
1 AAGATG-TTTAAGCCTAGTTATGTTGGCACGA-AAGATTTAAGT
35780202 TACATAACCT
Statistics
Matches: 181, Mismatches: 36, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
59 2 0.01
60 26 0.14
61 109 0.60
62 42 0.23
63 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (59 bp):
AAGATGTTTAAGCCTAGTTATGTTGGCACGAAAGATTTAAGTCCAATATAGTTGGCACC
Found at i:35780615 original size:19 final size:19
Alignment explanation
Indices: 35780586--35780630 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
35780576 AGATCCAAAA
35780586 AAATCAAACAAAAAATAAAT
1 AAAT-AAACAAAAAATAAAT
* *
35780606 AAATAAACAACAAATATAT
1 AAATAAACAAAAAATAAAT
35780625 -AATAAA
1 AAATAAA
35780631 ATAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 13 0.57
20 4 0.17
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (19 bp):
AAATAAACAAAAAATAAAT
Found at i:35785474 original size:17 final size:19
Alignment explanation
Indices: 35785449--35785486 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
35785439 GAGGCACAAG
*
35785449 AGCCGCCATCA-A-CATCA
1 AGCCACCATCACAGCATCA
35785466 AGCCACCATCACAGCATCA
1 AGCCACCATCACAGCATCA
35785485 AG
1 AG
35785487 GAGGATGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.37, C:0.39, G:0.13, T:0.11
Consensus pattern (19 bp):
AGCCACCATCACAGCATCA
Found at i:35789205 original size:17 final size:17
Alignment explanation
Indices: 35789191--35789223 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35789181 GGAGAAAATG
35789191 TGAAAAAAAGAAAAAAC
1 TGAAAAAAAGAAAAAAC
*
35789208 TGAAAAAAATAAAAAA
1 TGAAAAAAAGAAAAAA
35789224 AAAAGTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
TGAAAAAAAGAAAAAAC
Found at i:35791663 original size:9 final size:9
Alignment explanation
Indices: 35791649--35791674 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35791639 ATCAAACTTA
35791649 TTTAATAGT
1 TTTAATAGT
35791658 TTTAATAGT
1 TTTAATAGT
35791667 TTTAATAG
1 TTTAATAG
35791675 CTTATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (9 bp):
TTTAATAGT
Found at i:35793831 original size:8 final size:7
Alignment explanation
Indices: 35793810--35793892 Score: 62
Period size: 7 Copynumber: 11.3 Consensus size: 7
35793800 GCAAATATTC
35793810 TTCTTTT
1 TTCTTTT
35793817 TT-TTTT
1 TTCTTTT
*
35793823 TACTTTT
1 TTCTTTT
35793830 TTCTTTT
1 TTCTTTT
*
35793837 TTGCTTTC
1 TT-CTTTT
35793845 TTCTTTT
1 TTCTTTT
*
35793852 CCTTTTTTT
1 --TTCTTTT
35793861 ATTACTTTT
1 -TT-CTTTT
*
35793870 TT-TCTT
1 TTCTTTT
35793876 TTCTTTCT
1 TTCTTT-T
35793884 TTCTTTT
1 TTCTTTT
35793891 TT
1 TT
35793893 TTATTATCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
6 10 0.17
7 23 0.38
8 17 0.28
9 10 0.17
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.80
Consensus pattern (7 bp):
TTCTTTT
Found at i:35793836 original size:15 final size:15
Alignment explanation
Indices: 35793813--35793851 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
35793803 AATATTCTTC
35793813 TTTTT-TTTTTTACT
1 TTTTTCTTTTTTACT
*
35793827 TTTTTCTTTTTTGCT
1 TTTTTCTTTTTTACT
*
35793842 TTCTTCTTTT
1 TTTTTCTTTT
35793852 CCTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTTTTACT
Found at i:35793851 original size:21 final size:20
Alignment explanation
Indices: 35793810--35793893 Score: 89
Period size: 21 Copynumber: 4.1 Consensus size: 20
35793800 GCAAATATTC
*
35793810 TTCTTTTTTTTTTTAC-TTTT
1 TTCTTTTTTTCTTT-CTTTTT
*
35793830 TTCTTTTTTGCTTTCTTCTTT
1 TTCTTTTTTTCTTTCTT-TTT
* * *
35793851 TCCTTTTTTTATTACTTTTT
1 TTCTTTTTTTCTTTCTTTTT
35793871 TTCTTTTCTTTCTTTCTTTTT
1 TTCTTTT-TTTCTTTCTTTTT
35793892 TT
1 TT
35793894 TATTATCTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
19 1 0.02
20 22 0.42
21 29 0.56
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.80
Consensus pattern (20 bp):
TTCTTTTTTTCTTTCTTTTT
Found at i:35793872 original size:35 final size:34
Alignment explanation
Indices: 35793807--35793907 Score: 84
Period size: 34 Copynumber: 2.9 Consensus size: 34
35793797 CATGCAAATA
**
35793807 TTCTTCTTTT-TTTTTTTACTTTTTTCTTTTTTGC-T
1 TTCTTCTTTTCTTTTTTTA-TTACTT-TTTTTT-CTT
35793842 TTCTTCTTTTCCTTTTTTTATTAC-TTTTTTTCTT
1 TTCTTCTTTT-CTTTTTTTATTACTTTTTTTTCTT
*
35793876 TTCTT-TCTTTCTTTTTTTTATTATCTTCTTTT
1 TTCTTCT-TTTC-TTTTTTTATTA-CTTTTTTT
35793908 AATCTATTCG
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
33 3 0.05
34 26 0.46
35 12 0.21
36 7 0.12
37 8 0.14
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.78
Consensus pattern (34 bp):
TTCTTCTTTTCTTTTTTTATTACTTTTTTTTCTT
Found at i:35793879 original size:34 final size:34
Alignment explanation
Indices: 35793831--35793907 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
35793821 TTTACTTTTT
*
35793831 TCTTTTTTGCTTTC-TTCTTTTCCTTTTTTTATTA
1 TCTTTTTTTCTTTCTTTC-TTTCCTTTTTTTATTA
*
35793865 -CTTTTTTTCTTTTCTTTCTTTCTTTTTTTTATTA
1 TCTTTTTTTC-TTTCTTTCTTTCCTTTTTTTATTA
*
35793899 TCTTCTTTT
1 TCTTTTTTT
35793908 AATCTATTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 8 0.22
34 19 0.51
35 10 0.27
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.77
Consensus pattern (34 bp):
TCTTTTTTTCTTTCTTTCTTTCCTTTTTTTATTA
Found at i:35793904 original size:17 final size:17
Alignment explanation
Indices: 35793854--35793907 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
35793844 CTTCTTTTCC
*
35793854 TTTTTTTATTA-CTTTT
1 TTTTTTTATTATCTTCT
*
35793870 TTTCTTTTCTT-TCTTTCT
1 TTT-TTTTATTATC-TTCT
35793888 TTTTTTTATTATCTTCT
1 TTTTTTTATTATCTTCT
35793905 TTT
1 TTT
35793908 AATCTATTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.10
17 20 0.65
18 8 0.26
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTATTATCTTCT
Found at i:35793904 original size:21 final size:22
Alignment explanation
Indices: 35793866--35793906 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35793856 TTTTTATTAC
* *
35793866 TTTTTTTCTTTTCTTTCTTTCT
1 TTTTTTTATTATCTTTCTTTCT
35793888 TTTTTTTATTATC-TTCTTT
1 TTTTTTTATTATCTTTCTTT
35793907 TAATCTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTATTATCTTTCTTTCT
Found at i:35794508 original size:24 final size:23
Alignment explanation
Indices: 35794481--35794563 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 23
35794471 TTTCTTTACC
35794481 TCTCTATTTTTTTATCATCTTTTT
1 TCTCTATTTTTTTAT-ATCTTTTT
*
35794505 TCTCT-TTTTCTTT-TAT-TTTCT
1 TCTCTATTTT-TTTATATCTTTTT
* *
35794526 T-TC-ATTCTTTTATTTTCTTTTT
1 TCTCTATTTTTTTA-TATCTTTTT
*
35794548 TCTCTTTTTTTTTATA
1 TCTCTATTTTTTTATA
35794564 ATTGCCTCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 15
0.67 0.10 0.22
Matches are distributed among these distances:
19 3 0.07
20 5 0.11
21 7 0.16
22 7 0.16
23 8 0.18
24 15 0.33
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (23 bp):
TCTCTATTTTTTTATATCTTTTT
Found at i:35794526 original size:25 final size:26
Alignment explanation
Indices: 35794461--35794527 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
35794451 TTCATTTAAA
35794461 TTTTCTTTT-TTTTCTTTACCTCTCT
1 TTTTCTTTTATTTTCTTTACCTCTCT
* ** **
35794486 ATTT-TTTTATCATCTTT-TTTCTCT
1 TTTTCTTTTATTTTCTTTACCTCTCT
35794510 TTTTCTTTTATTTTCTTT
1 TTTTCTTTTATTTTCTTT
35794528 CATTCTTTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
24 12 0.38
25 20 0.62
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTCTTTTATTTTCTTTACCTCTCT
Found at i:35794559 original size:18 final size:17
Alignment explanation
Indices: 35794502--35794550 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
35794492 TTATCATCTT
35794502 TTTTCTCTTTTTCTTTTA
1 TTTTCT-TTTTTCTTTTA
*
35794520 TTTTCTTTCATTCTTTTA
1 TTTTCTTT-TTTCTTTTA
35794538 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
35794551 CTTTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTTA
Found at i:35801911 original size:57 final size:58
Alignment explanation
Indices: 35801806--35801917 Score: 156
Period size: 57 Copynumber: 1.9 Consensus size: 58
35801796 GGAAAGCAAG
* * *
35801806 TTTGGTGCAGATATAGTTGATGAGTCAATATATGAGTTTAATATACAAATCTTTGAAA
1 TTTGATGCAGATATAGTTGATGAGTCAATATATGAGCTTAATAGACAAATCTTTGAAA
* *
35801864 TTTGATGCAGATAGTAGTTGATGAGT-TA-ATATGAGCTTAATCGACAAATCTTTG
1 TTTGATGCAGATA-TAGTTGATGAGTCAATATATGAGCTTAATAGACAAATCTTTG
35801918 TAGGGCATAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 23 0.48
58 13 0.27
59 12 0.25
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.38
Consensus pattern (58 bp):
TTTGATGCAGATATAGTTGATGAGTCAATATATGAGCTTAATAGACAAATCTTTGAAA
Found at i:35803234 original size:18 final size:19
Alignment explanation
Indices: 35803211--35803248 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
35803201 TTTAGATACT
35803211 TAAAAACTTAAAATT-AAA
1 TAAAAACTTAAAATTCAAA
* *
35803229 TAAAAATTTTAAATTCAAA
1 TAAAAACTTAAAATTCAAA
35803248 T
1 T
35803249 CGCATCCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAACTTAAAATTCAAA
Found at i:35804075 original size:9 final size:9
Alignment explanation
Indices: 35804057--35804088 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
35804047 AATTCATTCT
35804057 TTCTTTTTC
1 TTCTTTTTC
*
35804066 TTCTTCTTC
1 TTCTTTTTC
35804075 TTCTTTTTC
1 TTCTTTTTC
35804084 TTCTT
1 TTCTT
35804089 GGGTTGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:35812718 original size:21 final size:21
Alignment explanation
Indices: 35812682--35812723 Score: 52
Period size: 19 Copynumber: 2.0 Consensus size: 21
35812672 TTTACTATCC
35812682 TCTTGTGTTTTGCC-TTGATT
1 TCTTGTGTTTTGCCTTTGATT
35812702 TCTT-TGTTTTGATCCTTTGATT
1 TCTTGTGTTTTG--CCTTTGATT
35812724 AGCTGGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 2 0.11
22 6 0.32
ACGTcount: A:0.07, C:0.14, G:0.17, T:0.62
Consensus pattern (21 bp):
TCTTGTGTTTTGCCTTTGATT
Found at i:35822824 original size:13 final size:13
Alignment explanation
Indices: 35822806--35822830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35822796 GGAAAATGAG
35822806 ATTTTATAAAATA
1 ATTTTATAAAATA
35822819 ATTTTATAAAAT
1 ATTTTATAAAAT
35822831 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:35825193 original size:18 final size:17
Alignment explanation
Indices: 35825155--35825187 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35825145 ATCGATCAAC
35825155 ATTATAATTTAATTGAA
1 ATTATAATTTAATTGAA
35825172 ATTATCAATTT-ATTGA
1 ATTAT-AATTTAATTGA
35825188 GTATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTATAATTTAATTGAA
Found at i:35846304 original size:15 final size:16
Alignment explanation
Indices: 35846278--35846307 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35846268 TTATGAAATT
35846278 TTTTTTATATTATATA
1 TTTTTTATATTATATA
35846294 TTTTTTA-ATTATAT
1 TTTTTTATATTATAT
35846308 TTAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTATATTATATA
Found at i:35846326 original size:22 final size:20
Alignment explanation
Indices: 35846274--35846326 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
35846264 AAATTTATGA
*
35846274 AATTTTTT-TTATATTATAT
1 AATTTTTTATTATATTAAAT
35846293 -ATTTTTTAATTATATTTAAAAT
1 AATTTTTT-ATTATA-TT-AAAT
35846315 AATTTTTTATTA
1 AATTTTTTATTA
35846327 AATAATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.25
20 5 0.18
21 2 0.07
22 7 0.25
23 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTTTTTATTATATTAAAT
Found at i:35846688 original size:16 final size:15
Alignment explanation
Indices: 35846661--35846701 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
35846651 CTGTTATGTA
35846661 GATTTTATTTTTAAT
1 GATTTTATTTTTAAT
35846676 GATTTTAATTTTTAA-
1 GATTTT-ATTTTTAAT
35846691 -ATTTT-TTTTTA
1 GATTTTATTTTTA
35846702 TAATTAGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.24
14 5 0.20
15 6 0.24
16 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
GATTTTATTTTTAAT
Found at i:35848246 original size:18 final size:18
Alignment explanation
Indices: 35848223--35848261 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
35848213 CAGCTTATTT
35848223 CTGTTCACAATATCGCTG
1 CTGTTCACAATATCGCTG
35848241 CTGTTCACAATATCGCTG
1 CTGTTCACAATATCGCTG
35848259 CTG
1 CTG
35848262 GTCAAAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (18 bp):
CTGTTCACAATATCGCTG
Found at i:35849662 original size:22 final size:22
Alignment explanation
Indices: 35849634--35849681 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
35849624 GTTATTAAAA
** *
35849634 ATATTTTTAGTAATATTTTTTT
1 ATATTTTTAAAAATATTTTTAT
35849656 ATATTTTTAAAAATATTTTTAT
1 ATATTTTTAAAAATATTTTTAT
35849678 ATAT
1 ATAT
35849682 GTGATTTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATATTTTTAAAAATATTTTTAT
Found at i:35850028 original size:62 final size:61
Alignment explanation
Indices: 35849931--35850049 Score: 202
Period size: 62 Copynumber: 1.9 Consensus size: 61
35849921 TCTTAACTAG
* * *
35849931 GTTTTGGTGTTTTACATTAAGTTTGATAGGAACGTATTTATAATGATGCAGGTTTTTTTTAA
1 GTTTTGGTGTTTTACATTAAATTTGATAGGAACGTATCTACAATGATGCA-GTTTTTTTTAA
35849993 GTTTTGGTGTTTTACATTAAATTTGATAGGAACGTATCTACAATGATGCAGTTTTTT
1 GTTTTGGTGTTTTACATTAAATTTGATAGGAACGTATCTACAATGATGCAGTTTTTT
35850050 ATTTTTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 7 0.13
62 47 0.87
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.47
Consensus pattern (61 bp):
GTTTTGGTGTTTTACATTAAATTTGATAGGAACGTATCTACAATGATGCAGTTTTTTTTAA
Found at i:35853904 original size:2 final size:2
Alignment explanation
Indices: 35853897--35853924 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35853887 ACCATCAGAN
35853897 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
35853925 CTGTGTGTGT
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:35853931 original size:2 final size:2
Alignment explanation
Indices: 35853926--35853966 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35853916 TATATATATC
35853926 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
35853967 ATAGAAGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:35861132 original size:10 final size:11
Alignment explanation
Indices: 35861106--35861160 Score: 53
Period size: 10 Copynumber: 5.0 Consensus size: 11
35861096 GGAAAGGATG
35861106 GAGAAAGAAGCAA
1 GAGAAAG-AG-AA
35861119 G-GAAAGAGAA
1 GAGAAAGAGAA
35861129 G-GAAAGAGGAA
1 GAGAAAGA-GAA
35861140 GAGAAA-AGAA
1 GAGAAAGAGAA
*
35861150 GAGAGAGAGAA
1 GAGAAAGAGAA
35861161 AGGAGAGCGG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 17 0.45
11 11 0.29
12 9 0.24
13 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (11 bp):
GAGAAAGAGAA
Found at i:35861229 original size:14 final size:14
Alignment explanation
Indices: 35861207--35861242 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
35861197 GGGAGAAAAG
* *
35861207 GAAGGAGAAAGAGA
1 GAAGAAGAAAGAAA
35861221 GAAGAAGAAAGAAA
1 GAAGAAGAAAGAAA
35861235 GAAGAAGA
1 GAAGAAGA
35861243 GGTAAGTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAAGAAA
Found at i:35861661 original size:2 final size:2
Alignment explanation
Indices: 35861654--35861686 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35861644 AATTAGTGTA
35861654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35861687 AGTAGGNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35862496 original size:14 final size:15
Alignment explanation
Indices: 35862477--35862537 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 15
35862467 ACGACTGGGA
35862477 GAGAAA-AAAAGAAG
1 GAGAAAGAAAAGAAG
35862491 GAGAAAGAAAAGAA-
1 GAGAAAGAAAAGAAG
*
35862505 GA-AAGAGAAAAGAAA
1 GAGAA-AGAAAAGAAG
*
35862520 AAGAAAGAGAGAAGAAG
1 GAGAAAGA-A-AAGAAG
35862537 G
1 G
35862538 GGGGAGCGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.05
14 17 0.45
15 11 0.29
16 3 0.08
17 5 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
GAGAAAGAAAAGAAG
Found at i:35862501 original size:18 final size:18
Alignment explanation
Indices: 35862478--35862535 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
35862468 CGACTGGGAG
*
35862478 AGAAAAAAAGAAGGAGAA
1 AGAAAAAAAGAAAGAGAA
*
35862496 AGAAAAGAAGAAAGAGAA
1 AGAAAAAAAGAAAGAGAA
*
35862514 A-AGAAAAAGAAAGAGAGA
1 AGAAAAAAAGAAAGAGA-A
35862532 AGAA
1 AGAA
35862536 GGGGGGAGCG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 13 0.39
18 19 0.58
19 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAGAAAGAGAA
Found at i:35862525 original size:17 final size:17
Alignment explanation
Indices: 35862482--35862535 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
35862472 TGGGAGAGAA
*
35862482 AAAAAGAAGGAG-AAAG
1 AAAAAGAAAGAGAAAAG
35862498 AAAAGAAGAAAGAGAAAAG
1 -AAA-AAGAAAGAGAAAAG
*
35862517 AAAAAGAAAGAGAGAAG
1 AAAAAGAAAGAGAAAAG
35862534 AA
1 AA
35862536 GGGGGGAGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 18 0.55
18 11 0.33
19 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAGAAAAG
Found at i:35864500 original size:31 final size:31
Alignment explanation
Indices: 35864425--35864634 Score: 178
Period size: 31 Copynumber: 6.8 Consensus size: 31
35864415 TTTGTCCTTA
* * *
35864425 TTGGCATCCAAGATGTATAAGTCC-AGTTATG
1 TTGGCATCCAAGATGTTTAAGCCCAATTTA-G
* *
35864456 TTGGTA-CAAAAGATGTTTAAGCCCAATTTAG
1 TTGGCATC-CAAGATGTTTAAGCCCAATTTAG
* * * *
35864487 CTAGCATCCAAGATGTTTAAGCCCCAGTTATG
1 TTGGCATCCAAGATGTTTAAGCCCAATTTA-G
* * *
35864519 TTGGCA-CCGAGATATTTAAACCCAATTTAG
1 TTGGCATCCAAGATGTTTAAGCCCAATTTAG
35864549 TTGGCATCCAAGATGTTTAAGCCCAATTATA-
1 TTGGCATCCAAGATGTTTAAGCCCAATT-TAG
* ** *
35864580 TTGGCA-CAAAGATAATTAAGCCCAATTTAA
1 TTGGCATCCAAGATGTTTAAGCCCAATTTAG
* * *
35864610 ATGGCATCTAAGATGTTTAAACCCA
1 TTGGCATCCAAGATGTTTAAGCCCA
35864635 GTTATCTTGG
Statistics
Matches: 142, Mismatches: 29, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
29 2 0.01
30 31 0.22
31 97 0.68
32 12 0.08
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (31 bp):
TTGGCATCCAAGATGTTTAAGCCCAATTTAG
Found at i:35864615 original size:61 final size:61
Alignment explanation
Indices: 35864426--35864646 Score: 271
Period size: 61 Copynumber: 3.6 Consensus size: 61
35864416 TTGTCCTTAT
* * * * *
35864426 TGGCATCCAAGATGTATAAGTCCAGTTATGTTGGTACAAAAGATGTTTAAGCCCAATTTAGC
1 TGGCATCCAAGATGTTTAAGCCCAGTTATGTTGGCAC-AAAGATATTTAAGCCCAATTTAGA
* ** * *
35864488 TAGCATCCAAGATGTTTAAGCCCCAGTTATGTTGGCACCGAGATATTTAAACCCAATTTAGT
1 TGGCATCCAAGATGTTTAAG-CCCAGTTATGTTGGCACAAAGATATTTAAGCCCAATTTAGA
* * * *
35864550 TGGCATCCAAGATGTTTAAGCCCAATTATATTGGCACAAAGATAATTAAGCCCAATTTAAA
1 TGGCATCCAAGATGTTTAAGCCCAGTTATGTTGGCACAAAGATATTTAAGCCCAATTTAGA
* * *
35864611 TGGCATCTAAGATGTTTAAACCCAGTTATCTTGGCA
1 TGGCATCCAAGATGTTTAAGCCCAGTTATGTTGGCA
35864647 TGAGAGAATT
Statistics
Matches: 136, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
61 65 0.48
62 56 0.41
63 15 0.11
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (61 bp):
TGGCATCCAAGATGTTTAAGCCCAGTTATGTTGGCACAAAGATATTTAAGCCCAATTTAGA
Found at i:35864760 original size:22 final size:22
Alignment explanation
Indices: 35864703--35864891 Score: 157
Period size: 22 Copynumber: 8.6 Consensus size: 22
35864693 CTTTTCTTCG
* *
35864703 AAAACCTCCGGGTACA-TCTTTC
1 AAAACCTCCGGGTATATTC-TCC
35864725 -AAACCTCCGGGTATATTCTCC
1 AAAACCTCCGGGTATATTCTCC
* * * *
35864746 AAAATCTCCGAGTATATTCGCT
1 AAAACCTCCGGGTATATTCTCC
** * * *
35864768 AAAACCTCCTAGTATCTGCTTC
1 AAAACCTCCGGGTATATTCTCC
35864790 AAAACCTCCGGGTATATTCTCC
1 AAAACCTCCGGGTATATTCTCC
* *
35864812 AAAACCTCCGGGTATGTTCTCT
1 AAAACCTCCGGGTATATTCTCC
* ** * *
35864834 AAAACCTCCGGATACCTGCTTC
1 AAAACCTCCGGGTATATTCTCC
* * **
35864856 AAAACCTCCAGGCATATTCTTT
1 AAAACCTCCGGGTATATTCTCC
35864878 AAAACCTCCGGGTA
1 AAAACCTCCGGGTA
35864892 CCTGCTTCAA
Statistics
Matches: 130, Mismatches: 35, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
21 16 0.12
22 114 0.88
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (22 bp):
AAAACCTCCGGGTATATTCTCC
Found at i:35864844 original size:44 final size:44
Alignment explanation
Indices: 35864703--35864913 Score: 167
Period size: 44 Copynumber: 4.8 Consensus size: 44
35864693 CTTTTCTTCG
* *
35864703 AAAACCTCCGGGTACA-TCTTTC-AAACCTCCGGGTATATTCTCC
1 AAAACCTCCGGGTACATTC-TCCAAAACCTCCGGGTATATTCTCT
* * * * * ** * *
35864746 AAAATCTCCGAGTATATTCGCTAAAACCTCCTAGTATCTGCT-T
1 AAAACCTCCGGGTACATTCTCCAAAACCTCCGGGTATATTCTCT
* *
35864789 CAAAACCTCCGGGTATATTCTCCAAAACCTCCGGGTATGTTCTCT
1 -AAAACCTCCGGGTACATTCTCCAAAACCTCCGGGTATATTCTCT
* * * * * * *
35864834 AAAACCTCCGGATACCTGCTTCAAAACCTCCAGGCATATTCTTT
1 AAAACCTCCGGGTACATTCTCCAAAACCTCCGGGTATATTCTCT
* * * *
35864878 AAAACCTCCGGGTACCTGCTTCAAAACCTCAGGGTA
1 AAAACCTCCGGGTACATTCTCCAAAACCTCCGGGTA
35864914 ATTAGTTTCA
Statistics
Matches: 132, Mismatches: 32, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
43 13 0.10
44 118 0.89
45 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.27
Consensus pattern (44 bp):
AAAACCTCCGGGTACATTCTCCAAAACCTCCGGGTATATTCTCT
Done.