Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_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: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 18
Found at i:3388320 original size:20 final size:20
Alignment explanation
Indices: 3388292--3388329 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3388282 TTTTGTAGAA
*
3388292 AAATTATCCCCAACGGCTCC
1 AAATCATCCCCAACGGCTCC
3388312 AAATCATCCCCAACGGCT
1 AAATCATCCCCAACGGCT
3388330 AAAAACAACC
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:0.32, C:0.39, G:0.11, T:0.18
Consensus pattern (20 bp):
AAATCATCCCCAACGGCTCC
Found at i:3390272 original size:34 final size:30
Alignment explanation
Indices: 3390234--3390302 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
3390224 TTGATATAAC
3390234 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
* *
3390268 AATTT-ACAATATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
3390297 AATTTA
1 AATTTA
3390303 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 12 0.38
31 5 0.16
33 1 0.03
34 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:3390414 original size:19 final size:19
Alignment explanation
Indices: 3390392--3390466 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
3390382 TTCAAGATTG
3390392 CCCAGGGGTACAGATTCCC
1 CCCAGGGGTACAGATTCCC
*
3390411 CCCAGGGGGTACAGA-T--A
1 CCCA-GGGGTACAGATTCCC
*
3390428 CCC--GGGTACAGATACCC
1 CCCAGGGGTACAGATTCCC
*
3390445 CCCAGGGGTACCGATTCCC
1 CCCAGGGGTACAGATTCCC
3390464 CCC
1 CCC
3390467 TGTCTAAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.20
17 6 0.13
19 20 0.44
20 10 0.22
ACGTcount: A:0.21, C:0.39, G:0.27, T:0.13
Consensus pattern (19 bp):
CCCAGGGGTACAGATTCCC
Found at i:3390436 original size:14 final size:14
Alignment explanation
Indices: 3390417--3390444 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3390407 TCCCCCCAGG
3390417 GGGTACAGATACCC
1 GGGTACAGATACCC
3390431 GGGTACAGATACCC
1 GGGTACAGATACCC
3390445 CCCAGGGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (14 bp):
GGGTACAGATACCC
Found at i:3390532 original size:20 final size:21
Alignment explanation
Indices: 3390492--3390533 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3390482 AAAAGAATGT
3390492 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
3390513 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
3390534 TGTTCAACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:3390595 original size:21 final size:21
Alignment explanation
Indices: 3390569--3390611 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3390559 ATTTGAATAT
*
3390569 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3390590 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3390611 T
1 T
3390612 CTATTTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3390677 original size:20 final size:22
Alignment explanation
Indices: 3390639--3390678 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3390629 TTTGAGTATA
3390639 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
3390661 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
3390679 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:3390932 original size:34 final size:32
Alignment explanation
Indices: 3390893--3390962 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
3390883 TTTTGTAAAG
*
3390893 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3390927 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3390959 GGGA
1 GGGA
3390963 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3392945 original size:22 final size:22
Alignment explanation
Indices: 3392919--3392965 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3392909 GTTTGGTTTG
3392919 AAAAATTCAATTTCTTAATAAA
1 AAAAATTCAATTTCTTAATAAA
*
3392941 AAAAATTCAATTTCTTAATGAA
1 AAAAATTCAATTTCTTAATAAA
3392963 AAA
1 AAA
3392966 GGGGGAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATTCAATTTCTTAATAAA
Found at i:3393292 original size:20 final size:20
Alignment explanation
Indices: 3393269--3393346 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
3393259 TTCAAGATTG
3393269 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
* *
3393289 CCCAGGTGGTACAGA-T-AC
1 CCCAGGGGGTACAGATTCCC
* *
3393307 CCC---GGGTACATATACCCC
1 CCCAGGGGGTACAGAT-TCCC
*
3393325 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
3393345 CC
1 CC
3393347 TGTCTAAAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
15 7 0.16
18 8 0.19
19 1 0.02
20 19 0.44
21 8 0.19
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:3393325 original size:35 final size:36
Alignment explanation
Indices: 3393275--3393345 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
3393265 ATTGCCCAGG
* *
3393275 GGGTACAGAT-TCCCCCCAGGTGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
* * *
3393310 GGGTACATATACCCCCCCAGGGGGTACCGATTCCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
3393346 CTGTCTAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 9 0.30
36 21 0.70
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:3393528 original size:20 final size:21
Alignment explanation
Indices: 3393493--3393531 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3393483 TTTTGAGTAT
3393493 AAAAAATCCCCAAACGGCTCC
1 AAAAAATCCCCAAACGGCTCC
*
3393514 AAAACATCCCC-AACGGCT
1 AAAAAATCCCCAAACGGCT
3393532 ATATAACGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.38, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAAATCCCCAAACGGCTCC
Found at i:3393784 original size:34 final size:32
Alignment explanation
Indices: 3393745--3393814 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
3393735 TTTTGTAAAG
*
3393745 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3393779 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3393811 GGGA
1 GGGA
3393815 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3394757 original size:11 final size:12
Alignment explanation
Indices: 3394738--3394768 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
3394728 CAAATATCCC
3394738 TATTATTATTAA
1 TATTATTATTAA
3394750 TA-TATTATTAA
1 TATTATTATTAA
3394761 TATTATTA
1 TATTATTA
3394769 CAAACCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:3401408 original size:2 final size:2
Alignment explanation
Indices: 3401396--3401462 Score: 104
Period size: 2 Copynumber: 35.0 Consensus size: 2
3401386 TCCTTTCAAA
*
3401396 AT AT GT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3401437 AT AT AT A- AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3401463 CCCTTGTTGC
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.95
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3401736 original size:9 final size:9
Alignment explanation
Indices: 3401732--3401889 Score: 85
Period size: 9 Copynumber: 17.7 Consensus size: 9
3401722 AGAAAGGAAA
*
3401732 AAAAGAAAGC
1 AAAA-AAAGG
*
3401742 AAAAAAAGC
1 AAAAAAAGG
**
3401751 AAAAAACAAC
1 AAAAAA-AGG
*
3401761 AAAAAAAGA
1 AAAAAAAGG
*
3401770 AAGAAAAAAG
1 AA-AAAAAGG
*
3401780 ACAAAAAGG
1 AAAAAAAGG
*
3401789 GAAAAAAGG
1 AAAAAAAGG
3401798 -AAAAAAGG
1 AAAAAAAGG
3401806 -AAAAAAGG
1 AAAAAAAGG
3401814 AAAAAAAAAGG
1 --AAAAAAAGG
3401825 AAAAAAA--
1 AAAAAAAGG
3401832 AAAAAAA--
1 AAAAAAAGG
**
3401839 AAAAAAAAA
1 AAAAAAAGG
**
3401848 AAAAAAAAA
1 AAAAAAAGG
**
3401857 AAAAAAAAA
1 AAAAAAAGG
**
3401866 AAAAAAAAA
1 AAAAAAAGG
3401875 AAAAAAAGG
1 AAAAAAAGG
3401884 AAAAAA
1 AAAAAA
3401890 GAGAAGAAAT
Statistics
Matches: 130, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
7 14 0.11
8 16 0.12
9 74 0.57
10 18 0.14
11 8 0.06
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:3401754 original size:8 final size:8
Alignment explanation
Indices: 3401737--3401819 Score: 57
Period size: 8 Copynumber: 10.4 Consensus size: 8
3401727 GGAAAAAAAG
3401737 AAAGCAAAA
1 AAAGC-AAA
3401746 AAAGCAAA
1 AAAGCAAA
3401754 AAA-CAACA
1 AAAGCAA-A
3401762 AAA--AAA
1 AAAGCAAA
3401768 GAAAG-AAA
1 -AAAGCAAA
3401776 AAAGACAAA
1 AAAG-CAAA
* *
3401785 AAGGGAAA
1 AAAGCAAA
*
3401793 AAAGGAAA
1 AAAGCAAA
*
3401801 AAAGGAAA
1 AAAGCAAA
*
3401809 AAAGGAAA
1 AAAGCAAA
3401817 AAA
1 AAA
3401820 AAAGGAAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
6 1 0.02
7 12 0.18
8 42 0.64
9 11 0.17
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAGCAAA
Found at i:3401754 original size:21 final size:19
Alignment explanation
Indices: 3401730--3401889 Score: 111
Period size: 16 Copynumber: 8.3 Consensus size: 19
3401720 GAAGAAAGGA
3401730 AAAAAAGAAAGCAAAAAAAG
1 AAAAAA-AAAGCAAAAAAAG
*
3401750 CAAAAAACAA-CAAAAAAAG
1 -AAAAAAAAAGCAAAAAAAG
*
3401769 AAAGAAAAAAGACAAAAAGGGAAA
1 AAA-AAAAAAG-CAAAAA---AAG
* *
3401793 AAAGGAAAAAAGGAAAAAAGG
1 AAA--AAAAAAGCAAAAAAAG
*
3401814 AAAAAAAAAGGAAAAAAA-
1 AAAAAAAAAGCAAAAAAAG
3401832 AAAAAAAAA--AAAAAAA-
1 AAAAAAAAAGCAAAAAAAG
3401848 AAAAAAAAA--AAAAAAA-
1 AAAAAAAAAGCAAAAAAAG
**
3401864 AAAAAAAAAAAAAAAAAAGG
1 AAAAAAAAAGCAAAAAAA-G
3401884 AAAAAA
1 AAAAAA
3401890 GAGAAGAAAT
Statistics
Matches: 121, Mismatches: 7, Indels: 23
0.80 0.05 0.15
Matches are distributed among these distances:
16 32 0.26
18 19 0.16
19 28 0.23
20 8 0.07
21 16 0.13
24 10 0.08
25 8 0.07
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGCAAAAAAAG
Found at i:3401785 original size:7 final size:7
Alignment explanation
Indices: 3401730--3401891 Score: 108
Period size: 7 Copynumber: 23.1 Consensus size: 7
3401720 GAAGAAAGGA
3401730 AAAAAAG
1 AAAAAAG
**
3401737 AAAGCA-
1 AAAAAAG
3401743 AAAAAAG
1 AAAAAAG
*
3401750 CAAAAAAC
1 -AAAAAAG
3401758 AACAAAA-
1 AA-AAAAG
3401765 AAAGAAAG
1 AAA-AAAG
3401773 AAAAAAG
1 AAAAAAG
3401780 ACAAAAAGGG
1 A-AAAAA--G
3401790 AAAAAAGG
1 AAAAAA-G
3401798 AAAAAAGG
1 AAAAAA-G
3401806 AAAAAAG
1 AAAAAAG
*
3401813 -GAAAA-
1 AAAAAAG
*
3401818 AAAAAGG
1 AAAAAAG
3401825 AAAAAA-
1 AAAAAAG
3401831 AAAAAA-
1 AAAAAAG
3401837 AAAAAA-
1 AAAAAAG
3401843 AAAAAA-
1 AAAAAAG
3401849 AAAAAA-
1 AAAAAAG
*
3401855 AAAAAAA
1 AAAAAAG
*
3401862 AAAAAAA
1 AAAAAAG
*
3401869 AAAAAAA
1 AAAAAAG
3401876 AAAAAAGG
1 AAAAAA-G
3401884 AAAAAAG
1 AAAAAAG
3401891 A
1 A
3401892 GAAGAAATAA
Statistics
Matches: 133, Mismatches: 10, Indels: 24
0.80 0.06 0.14
Matches are distributed among these distances:
6 42 0.32
7 44 0.33
8 40 0.30
9 5 0.04
10 2 0.02
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3401794 original size:17 final size:15
Alignment explanation
Indices: 3401743--3401891 Score: 90
Period size: 15 Copynumber: 9.5 Consensus size: 15
3401733 AAAGAAAGCA
*
3401743 AAAAAAGCAAAAAA-C
1 AAAAAAG-AAAAAAGG
3401758 AACAAAA-AAAGAAA-G
1 AA-AAAAGAAA-AAAGG
3401773 AAAAAAGACAAAAAGGG
1 AAAAAAGA-AAAAA-GG
3401790 AAAAAAGGAAAAAAGG
1 AAAAAA-GAAAAAAGG
3401806 AAAAAAGGAAAAAAAAAGG
1 AAAAAA-G---AAAAAAGG
**
3401825 AAAAAA-AAAAAAAA
1 AAAAAAGAAAAAAGG
* **
3401839 AAAAAAAAAAAAAAA
1 AAAAAAGAAAAAAGG
* **
3401854 AAAAAAAAAAAAAAA
1 AAAAAAGAAAAAAGG
*
3401869 AAAAAAAAAAAAAGG
1 AAAAAAGAAAAAAGG
3401884 AAAAAAGA
1 AAAAAAGA
3401892 GAAGAAATAA
Statistics
Matches: 117, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
14 19 0.16
15 54 0.46
16 16 0.14
17 12 0.10
18 2 0.02
19 14 0.12
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAGG
Found at i:3401830 original size:8 final size:8
Alignment explanation
Indices: 3401772--3401819 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
3401762 AAAAAAGAAA
3401772 GAAAAAA-
1 GAAAAAAG
3401779 GACAAAAAGG
1 GA-AAAAA-G
3401789 GAAAAAAG
1 GAAAAAAG
3401797 GAAAAAAG
1 GAAAAAAG
3401805 GAAAAAAG
1 GAAAAAAG
3401813 GAAAAAA
1 GAAAAAA
3401820 AAAGGAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 2 0.05
8 29 0.76
9 5 0.13
10 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (8 bp):
GAAAAAAG
Found at i:3401889 original size:1 final size:1
Alignment explanation
Indices: 3401814--3401881 Score: 118
Period size: 1 Copynumber: 68.0 Consensus size: 1
3401804 GGAAAAAAGG
**
3401814 AAAAAAAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3401879 AAA
1 AAA
3401882 GGAAAAAAGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:3403815 original size:55 final size:54
Alignment explanation
Indices: 3403705--3403837 Score: 169
Period size: 55 Copynumber: 2.5 Consensus size: 54
3403695 GATTTTCGGA
* * *
3403705 GGTTTCTTGATGACAACGAAGAAA-AAGCTCAAGGGACCAACGTGATATGTAGG
1 GGTTCCTTGATGACAACAAAGAAACAAACTCAAGGGACCAACGTGATATGTAGG
* ** * *
3403758 GGTTCCTTGATGACAACAAAGAAACCAAACTCGAGGGAGGAATGTGATATGTTGG
1 GGTTCCTTGATGACAACAAAGAAA-CAAACTCAAGGGACCAACGTGATATGTAGG
*
3403813 GGTTCCTTGATGACAACTAAGAAAC
1 GGTTCCTTGATGACAACAAAGAAAC
3403838 TAATCTTGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
53 22 0.32
54 1 0.01
55 46 0.67
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (54 bp):
GGTTCCTTGATGACAACAAAGAAACAAACTCAAGGGACCAACGTGATATGTAGG
Found at i:3403892 original size:20 final size:19
Alignment explanation
Indices: 3403867--3403946 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 19
3403857 TTTCTTGATG
3403867 AGTAAGTCTTTCGGGCCATC
1 AGTAAGTCTTTCGGG-CATC
* *
3403887 AGTAAGTCTTTCGAGCATG
1 AGTAAGTCTTTCGGGCATC
*
3403906 ATGCGTAAGTCCTTCGGGACATC
1 A---GTAAGTCTTTCGGG-CATC
* *
3403929 AATAAGTCTTTCGAGCAT
1 AGTAAGTCTTTCGGGCAT
3403947 GATGTGTAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
19 7 0.15
20 25 0.52
22 12 0.25
23 4 0.08
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (19 bp):
AGTAAGTCTTTCGGGCATC
Found at i:3403908 original size:42 final size:42
Alignment explanation
Indices: 3403862--3403976 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 42
3403852 AAGGGTTTCT
*
3403862 TGATGAGTAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCTTTCGGGCCATCAATAAGTCTTTCGAGCA
* * *
3403904 TGATGCGTAAGTCCTTCGGGACATCAATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCTTTCGGGCCATCAATAAGTCTTTCGAGCA
* * *
3403946 TGATGTGTAAGACCTTT-GGGCCATCCATAAG
1 TGATGAGTAAG-TCTTTCGGGCCATCAATAAG
3403977 ACCTTCGGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 60 0.95
43 3 0.05
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (42 bp):
TGATGAGTAAGTCTTTCGGGCCATCAATAAGTCTTTCGAGCA
Found at i:3403916 original size:22 final size:22
Alignment explanation
Indices: 3403888--3403956 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
3403878 CGGGCCATCA
3403888 GTAAGTCTTTCGAGCATGATGC
1 GTAAGTCTTTCGAGCATGATGC
* * *
3403910 GTAAGTCCTTCG-GGA-CAT-C
1 GTAAGTCTTTCGAGCATGATGC
* *
3403929 AATAAGTCTTTCGAGCATGATGT
1 -GTAAGTCTTTCGAGCATGATGC
3403952 GTAAG
1 GTAAG
3403957 ACCTTTGGGC
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
19 1 0.03
20 12 0.35
21 4 0.12
22 17 0.50
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (22 bp):
GTAAGTCTTTCGAGCATGATGC
Found at i:3404180 original size:42 final size:42
Alignment explanation
Indices: 3404132--3404222 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
3404122 AAGTCTTTAA
* * *
3404132 GGCCATCAGTTAGTCTTTTGAGCATGATACATAAGTCCTTCG
1 GGCCATCAGTAAGTCTTTCGAGCATGATACATAAGACCTTCG
***
3404174 GGCCATCAGTAAGTCTTTCGAGCATGATGTGTAAGACCTTCG
1 GGCCATCAGTAAGTCTTTCGAGCATGATACATAAGACCTTCG
3404216 GGCCATC
1 GGCCATC
3404223 CATAAGACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (42 bp):
GGCCATCAGTAAGTCTTTCGAGCATGATACATAAGACCTTCG
Found at i:3404188 original size:20 final size:20
Alignment explanation
Indices: 3404163--3404238 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
3404153 GCATGATACA
*
3404163 TAAGTCCTTCGGGCCATCAG
1 TAAGACCTTCGGGCCATCAG
* * * *
3404183 TAAGTCTTTCGAG-CATGATGTG
1 TAAGACCTTCGGGCCATCA---G
3404205 TAAGACCTTCGGGCCATCCA-
1 TAAGACCTTCGGGCCAT-CAG
3404225 TAAGACCTTCGGGC
1 TAAGACCTTCGGGC
3404239 ATGATGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
19 4 0.09
20 25 0.57
22 11 0.25
23 3 0.07
24 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.26
Consensus pattern (20 bp):
TAAGACCTTCGGGCCATCAG
Found at i:3404241 original size:42 final size:42
Alignment explanation
Indices: 3404163--3404245 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
3404153 GCATGATACA
* * *
3404163 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTG
1 TAAGACCTTCGGGCCATCAGTAAGACCTTCGAGCATGATGTG
*
3404205 TAAGACCTTCGGGCCATCCA-TAAGACCTTCGGGCATGATGT
1 TAAGACCTTCGGGCCAT-CAGTAAGACCTTCGAGCATGATGT
3404246 TTTCAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (42 bp):
TAAGACCTTCGGGCCATCAGTAAGACCTTCGAGCATGATGTG
Found at i:3404264 original size:252 final size:253
Alignment explanation
Indices: 3403812--3404513 Score: 971
Period size: 252 Copynumber: 2.8 Consensus size: 253
3403802 TGATATGTTG
*
3403812 GGGTTCCTTGATGACAACTAAGAAACTAATCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCTT
1 GGGTTCCTTGATGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCTT
* * *
3403877 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAGTCCTTCGGGACATCAATAAGTCTTTCG
66 TCAGGCCATCAGTAAGTCTTTTGAGCATGATGCGTAAGTCCTTCGGGCCATC-ATAAGTCTTTCG
* *
3403942 AGCATGATGTGTAAGACCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAATATTTCT
130 AGCATGATGTGTAAGACCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAATATTTAT
* * *
3404007 GATTCATCACAAACGGGGTTGAATTAACAACACTAAGCTCAAGGGACCAACGTGATA-T
195 GATTCATCACAAACGGAGTTGAATCAACAACACTAAGCTCAAGGGACCAACATGATAGT
** *
3404065 -GGTTCCTTGATGACGGCCAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCTT
1 GGGTTCCTTGATGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCTT
* * * *
3404129 TAAGGCCATCAGTTAGTCTTTTGAGCATGATACATAAGTCCTTCGGGCCATCAGTAAGTCTTTCG
66 TCAGGCCATCAGTAAGTCTTTTGAGCATGATGCGTAAGTCCTTCGGGCCATCA-TAAGTCTTTCG
* * *
3404194 AGCATGATGTGTAAGACCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTTTTCAAAATTTAT
130 AGCATGATGTGTAAGACCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAATATTTAT
* * * *
3404259 GATTCATCACAAATGGATTTGAATCAATAACACTAAGCTCGAGGGACCAACATGATATGT
195 GATTCATCACAAACGGAGTTGAATCAACAACACTAAGCTCAAGGGACCAACATGATA-GT
**
3404319 AGGGGTTCCTTGATGACAACTAAGAAACTGGGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTC
1 --GGGTTCCTTGATGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTC
* * ** * * *
3404384 CTTCAGCCCATCAGTGGGTTTTTTCGAACATGATGCGTAAGTCCTTCGGGCCATTTATAAGAT-T
64 TTTCAGGCCATCAGTAAGTCTTTT-GAGCATGATGCGTAAGTCCTTCGGGCCA-TCATAAG-TCT
* ** * *
3404448 TTCGAGTAAAATG-ATAAGACCTTCGGGCCATCCATAAGACCTTTGGGTAGGATGTTTTCAATAT
126 TTCGAGCATGATGTGTAAGACCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAATAT
3404512 TT
191 TT
3404514 CACGTACTCA
Statistics
Matches: 394, Mismatches: 46, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
251 1 0.00
252 226 0.57
254 1 0.00
257 123 0.31
258 40 0.10
259 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (253 bp):
GGGTTCCTTGATGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCTT
TCAGGCCATCAGTAAGTCTTTTGAGCATGATGCGTAAGTCCTTCGGGCCATCATAAGTCTTTCGA
GCATGATGTGTAAGACCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAATATTTATG
ATTCATCACAAACGGAGTTGAATCAACAACACTAAGCTCAAGGGACCAACATGATAGT
Found at i:3404957 original size:11 final size:11
Alignment explanation
Indices: 3404930--3404958 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3404920 TAAGCCCATT
3404930 AACCCAAACAA
1 AACCCAAACAA
3404941 AA-CCAAACAA
1 AACCCAAACAA
3404951 AACCCAAA
1 AACCCAAA
3404959 TAATTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (11 bp):
AACCCAAACAA
Found at i:3409173 original size:45 final size:43
Alignment explanation
Indices: 3409109--3409507 Score: 235
Period size: 45 Copynumber: 9.8 Consensus size: 43
3409099 ATAAAAGAAT
*
3409109 AATGCATATGGGTGTATTATTGGCATGAAAAGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATG-CATAGCT-A
***
3409154 AATGCATATGGGTGCATTATCAACAT--AAA-A-G-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCATAGCTA
* *
3409188 AATGCATATGGGTGGATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATG-CATAGCT-A
*
3409233 AATGCATATGGGTGCATTATCGGCAT--AAA-A-G-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCATAGCTA
* *
3409267 AATGCAAATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATG-CATAGCT-A
*
3409312 AATGCATATGGGTGCATTATCGGCAT--AAA-A-G-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCATAGCTA
* *
3409346 AATGCATATGGGTGCATTATTTGCATGAAAGGATGACATAGCTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATG-CATAGCT-A
*
3409391 AATGCATATGGGTGCATTA-T--CA-GAATAA-AAG-A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAA-AAGATGCATAGCTA
* * **
3409425 AATGCATATGGTTGCATTATTGGCATGAAAGGATGCCATAAATAA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATG-CATAGCT-A
* *
3409470 AATGCATGAAAT-GATGCATTATTGGCATGAAAGGATGC
1 AATGCAT---ATGGGTGCATTATTGGCATGAAAAGATGC
3409508 CATAAATAAA
Statistics
Matches: 278, Mismatches: 27, Indels: 97
0.69 0.07 0.24
Matches are distributed among these distances:
34 88 0.32
35 1 0.00
36 10 0.04
37 6 0.02
38 12 0.04
39 4 0.01
40 4 0.01
41 12 0.04
42 6 0.02
43 11 0.04
44 1 0.00
45 96 0.35
46 1 0.00
47 24 0.09
48 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (43 bp):
AATGCATATGGGTGCATTATTGGCATGAAAAGATGCATAGCTA
Found at i:3409197 original size:34 final size:34
Alignment explanation
Indices: 3409154--3409455 Score: 190
Period size: 34 Copynumber: 7.9 Consensus size: 34
3409144 TCATAGCTGA
**
3409154 AATGCATATGGGTGCATTATCAACATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
3409188 AATGCATATGGGTGGATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
3409231 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
3409267 AATGCAAATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
3409310 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
**
3409346 AATGCATATGGGTGCATTATTTGCATGAAAGGATGACATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
* *
3409389 AAAATGCATATGGGTGCATTATCAGAATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
3409425 AATGCATATGGTTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAG
3409456 GATGCCATAA
Statistics
Matches: 215, Mismatches: 20, Indels: 66
0.71 0.07 0.22
Matches are distributed among these distances:
34 96 0.45
35 9 0.04
36 3 0.01
37 3 0.01
38 6 0.03
39 3 0.01
40 3 0.01
41 6 0.03
42 3 0.01
43 3 0.01
44 9 0.04
45 71 0.33
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:3409476 original size:79 final size:79
Alignment explanation
Indices: 3409097--3409464 Score: 603
Period size: 79 Copynumber: 4.7 Consensus size: 79
3409087 TAGAACAAAT
* * *
3409097 GAATAAAAGAATAATGCATATGGGTGTATTATTGGCATGAAAAGATGTCATAGCTGAAATGCATA
1 GAATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATA
3409162 TGGGTGCATTATCA
66 TGGGTGCATTATCA
*
3409176 -ACATAAAAGAATAATGCATATGGGTGGATTATTGGCATGAAAGGATGCCATAGCTGAAATGCAT
1 GA-ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCAT
*
3409240 ATGGGTGCATTATCG
65 ATGGGTGCATTATCA
* *
3409255 GCATAAAAGAATAATGCAAATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATA
1 GAATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATA
*
3409320 TGGGTGCATTATCG
66 TGGGTGCATTATCA
* * * *
3409334 GCATAAAAGAATAATGCATATGGGTGCATTATTTGCATGAAAGGATGACATAGCTAAAATGCATA
1 GAATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATA
3409399 TGGGTGCATTATCA
66 TGGGTGCATTATCA
*
3409413 GAATAAAAGAATAATGCATATGGTTGCATTATTGGCATGAAAGGATGCCATA
1 GAATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA
3409465 AATAAAATGC
Statistics
Matches: 271, Mismatches: 16, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
78 1 0.00
79 270 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (79 bp):
GAATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATA
TGGGTGCATTATCA
Found at i:3409550 original size:93 final size:93
Alignment explanation
Indices: 3409437--3409612 Score: 255
Period size: 93 Copynumber: 1.9 Consensus size: 93
3409427 TGCATATGGT
* * * *
3409437 TGCATTATTGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTATTGGCATGAAA
1 TGCATTATAGGCATGAAAGGATGCCATAAATAAAATACATGAAAGGATGCATTA-AGGCATGAAA
*
3409502 GGATGCCATAAATAAAATGCATGAAATGA
65 GAATGCCATAAATAAAATGCATGAAATGA
* *
3409531 TGCATTA-AGGCATGAAAGGATGTCATAAATAAAATACATGAAAGGATGCGTTAAGGCATGAAAG
1 TGCATTATAGGCATGAAAGGATGCCATAAATAAAATACATGAAAGGATGCATTAAGGCATGAAAG
* *
3409595 AATGCCTTAATTAAAATG
66 AATGCCATAAATAAAATG
3409613 AAATTTAATG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 25 0.34
93 41 0.56
94 7 0.10
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (93 bp):
TGCATTATAGGCATGAAAGGATGCCATAAATAAAATACATGAAAGGATGCATTAAGGCATGAAAG
AATGCCATAAATAAAATGCATGAAATGA
Found at i:3409560 original size:46 final size:47
Alignment explanation
Indices: 3409437--3409612 Score: 257
Period size: 46 Copynumber: 3.8 Consensus size: 47
3409427 TGCATATGGT
*
3409437 TGCATTATTGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
1 TGCATTATAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
*
3409484 TGCATTATTGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
1 TGCATTATAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
* * *
3409531 TGCATTA-AGGCATGAAAGGATGTCATAAATAAAATACATGAAAGGA
1 TGCATTATAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
* * * *
3409577 TGCGTTA-AGGCATGAAAGAATGCCTTAATTAAAATG
1 TGCATTATAGGCATGAAAGGATGCCATAAATAAAATG
3409613 AAATTTAATG
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
46 65 0.55
47 54 0.45
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (47 bp):
TGCATTATAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
Found at i:3409592 original size:20 final size:20
Alignment explanation
Indices: 3409567--3409604 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3409557 AAATAAAATA
* *
3409567 CATGAAAGGATGCGTTAAGG
1 CATGAAAGAATGCCTTAAGG
3409587 CATGAAAGAATGCCTTAA
1 CATGAAAGAATGCCTTAA
3409605 TTAAAATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.21
Consensus pattern (20 bp):
CATGAAAGAATGCCTTAAGG
Found at i:3410110 original size:2 final size:2
Alignment explanation
Indices: 3410103--3410142 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3410093 GTATAAAAGG
3410103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3410143 TAAATGTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3412491 original size:3 final size:3
Alignment explanation
Indices: 3412483--3412521 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
3412473 AAATATTATC
* *
3412483 TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3412522 AATTACATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3413325 original size:37 final size:36
Alignment explanation
Indices: 3413284--3413399 Score: 126
Period size: 38 Copynumber: 3.1 Consensus size: 36
3413274 TTTTTGATTT
*
3413284 TGTTTAACTTGAAACAAAACAAAGAAATCTTTGAGTC
1 TGTTTAACTTGAAACAAAACAAA-ACATCTTTGAGTC
*
3413321 TGTTTCAA-TTGAAACAAAACAAAACTCATCTTTGAGTT
1 TGTTT-AACTTGAAACAAAACAAAA--CATCTTTGAGTC
** * *
3413359 TGTTTCCCTTTAAACAAAACAAATCATCTTTGAGTC
1 TGTTTAACTTGAAACAAAACAAAACATCTTTGAGTC
*
3413395 GGTTT
1 TGTTT
3413400 CCCTTAAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
36 16 0.24
37 20 0.30
38 31 0.46
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (36 bp):
TGTTTAACTTGAAACAAAACAAAACATCTTTGAGTC
Found at i:3413363 original size:38 final size:37
Alignment explanation
Indices: 3413276--3413393 Score: 134
Period size: 37 Copynumber: 3.2 Consensus size: 37
3413266 TTGAGAATTT
* *
3413276 TTTGATTTTGTTT-AACTTGAAACAAAACAAAGA-AATC
1 TTTGAGTTTGTTTCAA-TTGAAACAAAACAAA-ATCATC
*
3413313 TTTGAGTCTGTTTCAATTGAAACAAAACAAAACTCATC
1 TTTGAGTTTGTTTCAATTGAAACAAAACAAAA-TCATC
** *
3413351 TTTGAGTTTGTTTCCCTTTAAACAAAAC-AAATCATC
1 TTTGAGTTTGTTTCAATTGAAACAAAACAAAATCATC
3413387 TTTGAGT
1 TTTGAGT
3413394 CGGTTTCCCT
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
36 13 0.18
37 29 0.41
38 29 0.41
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (37 bp):
TTTGAGTTTGTTTCAATTGAAACAAAACAAAATCATC
Found at i:3413609 original size:131 final size:130
Alignment explanation
Indices: 3413435--3413672 Score: 331
Period size: 131 Copynumber: 1.8 Consensus size: 130
3413425 TGGCATGCCG
* *
3413435 TCCTCATCACGTAGAACCGTGTAATCCCCTGACCAGACATCCTCATCATGT-AGAAGCCATGTCA
1 TCCTCATCACGTAGAACCGTGTAATCCCCTGACCAGACATCCTCATCACGTAAG-AGCCACGTCA
*
3413499 CCCTTAGATAACCA-GTCA-TCCTCATCACGTAGGAACTGTGTTACTATCCCTAAAGATGGCCTA
65 ACCTTAGATAA-CATG-CAGTCCTCATCACGTAGGAACTGTGTTACTATCCCTAAAGATGGCCTA
3413562 TCA
128 TCA
* * * *
3413565 TCCTCATCACGTAGGAATCGTGTCATCCACC-GACCAGACCTCCTCATCACGTAAGAGTCACGTC
1 TCCTCATCACGTA-GAACCGTGTAATCC-CCTGACCAGACATCCTCATCACGTAAGAGCCACGTC
*
3413629 AACCTTAGATAACATGCAGTCCTCATCACGTAGGAATTGTGTTA
64 AACCTTAGATAACATGCAGTCCTCATCACGTAGGAACTGTGTTA
3413673 TCACCCTTCC
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
130 17 0.18
131 74 0.78
132 4 0.04
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.25
Consensus pattern (130 bp):
TCCTCATCACGTAGAACCGTGTAATCCCCTGACCAGACATCCTCATCACGTAAGAGCCACGTCAA
CCTTAGATAACATGCAGTCCTCATCACGTAGGAACTGTGTTACTATCCCTAAAGATGGCCTATCA
Found at i:3413962 original size:3 final size:3
Alignment explanation
Indices: 3413954--3414055 Score: 176
Period size: 3 Copynumber: 35.3 Consensus size: 3
3413944 GGTCTATAAA
3413954 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3414002 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT -TT -TT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3414046 ATT ATT ATT A
1 ATT ATT ATT A
3414056 AATTACATTT
Statistics
Matches: 96, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
2 8 0.08
3 88 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3415566 original size:30 final size:31
Alignment explanation
Indices: 3415532--3415658 Score: 111
Period size: 30 Copynumber: 4.3 Consensus size: 31
3415522 TTAATACTAG
*
3415532 TTTAGTCCCT-TAACTTTCTATTTTTGTTAT
1 TTTAGTCCCTGTAACTTTCTATTTTTGCTAT
* * * *
3415562 TTTAGT-TCTGTAACTTTTTGTTTTTACTAT
1 TTTAGTCCCTGTAACTTTCTATTTTTGCTAT
* * * * *
3415592 TTTAAT-CCTTTAAGTTTCTATTTTTGTTGT
1 TTTAGTCCCTGTAACTTTCTATTTTTGCTAT
* *
3415622 TTTAGT-ACTGTAAATTTCTATTTTTGCTA-
1 TTTAGTCCCTGTAACTTTCTATTTTTGCTAT
3415651 TTTAGTCC
1 TTTAGTCC
3415659 TTTATTTTAC
Statistics
Matches: 74, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
29 8 0.11
30 66 0.89
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (31 bp):
TTTAGTCCCTGTAACTTTCTATTTTTGCTAT
Found at i:3415590 original size:60 final size:59
Alignment explanation
Indices: 3415526--3415658 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 59
3415516 TTTCTGTTAA
* * * *
3415526 TACTAGTTTAGTCCCTTAACTTTCTATTTTTGTTATTTTAGTTCTGTAACTTTTTGTTTT
1 TACTA-TTTAGTCCCTTAACTTTCTATTTTTGTTATTTTAGTACTGTAAATTTCTATTTT
* * * *
3415586 TACTATTTTAATCCTTTAAGTTTCTATTTTTGTTGTTTTAGTACTGTAAATTTCTATTTT
1 TACTA-TTTAGTCCCTTAACTTTCTATTTTTGTTATTTTAGTACTGTAAATTTCTATTTT
*
3415646 TGCTATTTAGTCC
1 TACTATTTAGTCC
3415659 TTTATTTTAC
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 7 0.11
60 55 0.89
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.59
Consensus pattern (59 bp):
TACTATTTAGTCCCTTAACTTTCTATTTTTGTTATTTTAGTACTGTAAATTTCTATTTT
Found at i:3417345 original size:16 final size:16
Alignment explanation
Indices: 3417324--3417384 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 16
3417314 TCTCTTGTAA
3417324 AGATGAAAATTCTTTT
1 AGATGAAAATTCTTTT
*
3417340 AGATGAATGGAACTCTTTTT
1 AGATGAA---AATTC-TTTT
3417360 AAAGATGAAAATTCTTTT
1 --AGATGAAAATTCTTTT
*
3417378 GGATGAA
1 AGATGAA
3417385 TGGAACTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
16 13 0.36
18 4 0.11
19 8 0.22
20 4 0.11
22 7 0.19
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (16 bp):
AGATGAAAATTCTTTT
Found at i:3417358 original size:19 final size:19
Alignment explanation
Indices: 3417334--3417396 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
3417324 AGATGAAAAT
3417334 TCTTTTAGATGAATGGAAC
1 TCTTTTAGATGAATGGAAC
*
3417353 TCTTTTTAAAGATGAA---AAT
1 TC-TTTT--AGATGAATGGAAC
*
3417372 TCTTTTGGATGAATGGAAC
1 TCTTTTAGATGAATGGAAC
3417391 TCTTTT
1 TCTTTT
3417397 TAAAGATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
16 6 0.17
18 4 0.11
19 14 0.40
20 4 0.11
22 7 0.20
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (19 bp):
TCTTTTAGATGAATGGAAC
Found at i:3417365 original size:38 final size:38
Alignment explanation
Indices: 3417321--3417403 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
3417311 ATCTCTCTTG
3417321 TAAAGATGAAAATTCTTTTAGATGAATGGAACTCTTTT
1 TAAAGATGAAAATTCTTTTAGATGAATGGAACTCTTTT
*
3417359 TAAAGATGAAAATTCTTTTGGATGAATGGAACTCTTTT
1 TAAAGATGAAAATTCTTTTAGATGAATGGAACTCTTTT
3417397 TAAAGAT
1 TAAAGAT
3417404 TATTACTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (38 bp):
TAAAGATGAAAATTCTTTTAGATGAATGGAACTCTTTT
Found at i:3417367 original size:22 final size:22
Alignment explanation
Indices: 3417340--3417403 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
3417330 AAATTCTTTT
3417340 AGATGAATGGAACTCTTTTTAA
1 AGATGAATGGAACTCTTTTTAA
*
3417362 AGATGAA---AATTC-TTTT--
1 AGATGAATGGAACTCTTTTTAA
*
3417378 GGATGAATGGAACTCTTTTTAA
1 AGATGAATGGAACTCTTTTTAA
3417400 AGAT
1 AGAT
3417404 TATTACTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 6 0.19
18 4 0.12
19 8 0.25
20 4 0.12
22 10 0.31
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (22 bp):
AGATGAATGGAACTCTTTTTAA
Found at i:3420200 original size:21 final size:21
Alignment explanation
Indices: 3420162--3420202 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3420152 CAAGGTGATC
*
3420162 GAATTGAGGAAACTAACCTTA
1 GAATTGAGGAAACCAACCTTA
* *
3420183 GAATTTAGGTAACCAACCTT
1 GAATTGAGGAAACCAACCTT
3420203 TCGATCTTGA
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:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (21 bp):
GAATTGAGGAAACCAACCTTA
Found at i:3420644 original size:16 final size:15
Alignment explanation
Indices: 3420623--3420663 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
3420613 AAATCGAGAA
*
3420623 AACATACATCAATAC
1 AACATACATCAACAC
3420638 TAACATACATCAACAC
1 -AACATACATCAACAC
3420654 ATACATACAT
1 A-ACATACAT
3420664 GACACATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (15 bp):
AACATACATCAACAC
Found at i:3421398 original size:67 final size:66
Alignment explanation
Indices: 3421327--3421480 Score: 177
Period size: 67 Copynumber: 2.3 Consensus size: 66
3421317 CAAAATAATA
* * *
3421327 TTGAGTCAGTTTCCCTTGAAACACTAATCTTAGAATATGTTT-CTTTGGAAACAAAATTTTGTCT
1 TTGAGACAGTTTCTCTTGAAACACTAATCTTAGAATATGTTTCCCTT-GAAAC-AAATTTTGTCT
3421391 CTC
64 CTC
* * * ** * *
3421394 TTGAGACAGTTTCTATTGAAAACACTTATCTTTGTGTTTGTTTCCCTTGAAACAAGTTTTGTCTC
1 TTGAGACAGTTTCTCTTG-AAACACTAATCTTAGAATATGTTTCCCTTGAAACAAATTTTGTCTC
3421459 TC
65 TC
3421461 TTGAGACAGTTT-TCTTGAAA
1 TTGAGACAGTTTCTCTTGAAA
3421481 AATCTTTGGT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
65 3 0.04
66 4 0.05
67 40 0.54
68 24 0.32
69 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (66 bp):
TTGAGACAGTTTCTCTTGAAACACTAATCTTAGAATATGTTTCCCTTGAAACAAATTTTGTCTCT
C
Found at i:3421454 original size:21 final size:20
Alignment explanation
Indices: 3421430--3421473 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3421420 TATCTTTGTG
*
3421430 TTTGTTTCCCTTGAAACAAGT
1 TTTGTCTCCCTTGAAAC-AGT
* *
3421451 TTTGTCTCTCTTGAGACAGT
1 TTTGTCTCCCTTGAAACAGT
3421471 TTT
1 TTT
3421474 CTTGAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (20 bp):
TTTGTCTCCCTTGAAACAGT
Found at i:3421495 original size:60 final size:65
Alignment explanation
Indices: 3421374--3421509 Score: 183
Period size: 67 Copynumber: 2.1 Consensus size: 65
3421364 TGTTTCTTTG
*
3421374 GAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAAACACTTATCTTTGTGTTTGTTTCC
1 GAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAAACA--TATCTTTGTGTTTGTTTCA
3421439 CTT
63 CTT
* *
3421442 GAAACAAGTTTTGTCTCTCTTGAGACAGTTT-TCTTG-AAA-A-ATCTTTG-GTTTGTTTCACTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAAACATATCTTTGTGTTTGTTTCACTT
3421502 GAAACAAA
1 GAAACAAA
3421510 ACAAAGAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
60 19 0.30
61 7 0.11
64 1 0.02
65 3 0.05
66 4 0.06
67 25 0.39
68 5 0.08
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (65 bp):
GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAAACATATCTTTGTGTTTGTTTCACTT
Found at i:3421571 original size:38 final size:38
Alignment explanation
Indices: 3421482--3421617 Score: 174
Period size: 36 Copynumber: 3.7 Consensus size: 38
3421472 TTCTTGAAAA
3421482 ATCTTTG-GTTTGTTTCACTTGAAACAAAACAAAGAA--
1 ATCTTTGAGTTTGTTTCACTTGAAACAAAACAAA-AATC
* *
3421518 ATCTTTGAGTCTGTTTCAATTGAAACAAAACAAAAATC
1 ATCTTTGAGTTTGTTTCACTTGAAACAAAACAAAAATC
*
3421556 ATCTTTGAGTTTGTTTCCCTTGAAACAAAAC--AAATC
1 ATCTTTGAGTTTGTTTCACTTGAAACAAAACAAAAATC
* * *
3421592 ATCTTTAAGTTAGTTTCCCTTGAAAC
1 ATCTTTGAGTTTGTTTCACTTGAAAC
3421618 CATTATCCCT
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
36 38 0.42
37 24 0.27
38 28 0.31
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (38 bp):
ATCTTTGAGTTTGTTTCACTTGAAACAAAACAAAAATC
Found at i:3422047 original size:3 final size:3
Alignment explanation
Indices: 3422039--3422109 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
3422029 AAATATTATC
3422039 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3422087 TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
3422110 CATTTACATT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3429343 original size:160 final size:161
Alignment explanation
Indices: 3429079--3429401 Score: 614
Period size: 160 Copynumber: 2.0 Consensus size: 161
3429069 CAAGGCCTAT
3429079 TTCCTTAACGAATAATTATCAAGGCTACTTTAGAATTGGAGTCTTATCCAACAAATTTTAAAAGC
1 TTCCTTAACGAATAATTATCAAGGCTACTTTAGAATTGGAGTCTTATCCAACAAATTTTAAAAGC
3429144 CTAGATCTTGAATCCCAAAATAGAGGAGTTAAAGTAGATATTAAACTTAAAA-TTAGCATGTTTT
66 CTAGATCTTGAATCCCAAAATAGAGGAGTTAAAGTAGATATTAAACTTAAAATTTAGCATG-TTT
*
3429208 ATATAGGTTCGGATTCGCTTGCAGT-AAACTC
130 ATATAGGTTAGGATTCGCTTGCAGTAAAACTC
3429239 TTCCTTAACGAATAATTATCAAGGCTACTTTAGAATTGGAGTCTTATCCAACAAATTTTAAAAGC
1 TTCCTTAACGAATAATTATCAAGGCTACTTTAGAATTGGAGTCTTATCCAACAAATTTTAAAAGC
3429304 CTAGATCTTGAATCCCAAAATAGAGGAGTTAAAGTAGATATTAAACTTAAAATTTAGCATGTTTA
66 CTAGATCTTGAATCCCAAAATAGAGGAGTTAAAGTAGATATTAAACTTAAAATTTAGCATGTTTA
3429369 TATAGGTTAGGATTCGCTTGCAGTAAAACTC
131 TATAGGTTAGGATTCGCTTGCAGTAAAACTC
3429400 TT
1 TT
3429402 TTAGGTTTAC
Statistics
Matches: 160, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
160 144 0.90
161 16 0.10
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (161 bp):
TTCCTTAACGAATAATTATCAAGGCTACTTTAGAATTGGAGTCTTATCCAACAAATTTTAAAAGC
CTAGATCTTGAATCCCAAAATAGAGGAGTTAAAGTAGATATTAAACTTAAAATTTAGCATGTTTA
TATAGGTTAGGATTCGCTTGCAGTAAAACTC
Found at i:3429624 original size:16 final size:17
Alignment explanation
Indices: 3429603--3429634 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3429593 TCTCCAGCCC
3429603 TCATCTCTA-CTCTACA
1 TCATCTCTATCTCTACA
3429619 TCATCTCTATCTCTAC
1 TCATCTCTATCTCTAC
3429635 TCTAAAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.41
Consensus pattern (17 bp):
TCATCTCTATCTCTACA
Found at i:3429886 original size:23 final size:21
Alignment explanation
Indices: 3429860--3429921 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 21
3429850 GAAAATAATG
3429860 TAACAAAGAAAAGAAAAAGAAAA
1 TAACAAA-AAAAGAAAAAG-AAA
*
3429883 TAACAAAAGAAAGTAAAAGAAA
1 TAACAAAA-AAAGAAAAAGAAA
3429905 TAA-AAAAAATAGAAAAA
1 TAACAAAAAA-AGAAAAA
3429922 TTAACAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 2 0.06
21 10 0.29
22 7 0.20
23 16 0.46
ACGTcount: A:0.77, C:0.03, G:0.11, T:0.08
Consensus pattern (21 bp):
TAACAAAAAAAGAAAAAGAAA
Found at i:3429895 original size:28 final size:29
Alignment explanation
Indices: 3429846--3429904 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
3429836 AAGATAGAAT
***
3429846 AAAAGAAAATAATGTAACAAAG-AAAAGA
1 AAAAGAAAATAACAAAACAAAGTAAAAGA
*
3429874 AAAAGAAAATAACAAAAGAAAGTAAAAGA
1 AAAAGAAAATAACAAAACAAAGTAAAAGA
3429903 AA
1 AA
3429905 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08
Consensus pattern (29 bp):
AAAAGAAAATAACAAAACAAAGTAAAAGA
Found at i:3438601 original size:23 final size:24
Alignment explanation
Indices: 3438565--3438610 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
3438555 ATTCCCTTGT
3438565 GGGAGGAATCGGTTCCCCTTCAAA
1 GGGAGGAATCGGTTCCCCTTCAAA
*
3438589 GGGA-GAATTGGTTCCCCTTCAA
1 GGGAGGAATCGGTTCCCCTTCAA
3438611 GGGGGTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (24 bp):
GGGAGGAATCGGTTCCCCTTCAAA
Found at i:3438625 original size:22 final size:22
Alignment explanation
Indices: 3438569--3438625 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
3438559 CCTTGTGGGA
*
3438569 GGAATCGGTTCCCCTTCAAAGGG
1 GGAATCGATTCCCCTTC-AAGGG
* * *
3438592 AGAATTGGTTCCCCTTCAAGGG
1 GGAATCGATTCCCCTTCAAGGG
*
3438614 GGTATCGATTCC
1 GGAATCGATTCC
3438626 ATCTGCACTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (22 bp):
GGAATCGATTCCCCTTCAAGGG
Found at i:3442115 original size:18 final size:18
Alignment explanation
Indices: 3442092--3442134 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
3442082 GACAACCTTA
3442092 TCTTTAGTAGTAATGAAT
1 TCTTTAGTAGTAATGAAT
3442110 TCTTTAGTAGTAATGAAT
1 TCTTTAGTAGTAATGAAT
3442128 TCTTTAG
1 TCTTTAG
3442135 GAACCCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (18 bp):
TCTTTAGTAGTAATGAAT
Found at i:3444422 original size:22 final size:21
Alignment explanation
Indices: 3444396--3444450 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3444386 TCGTTGATCA
3444396 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTA-CCCCTTGG
3444418 GGGGGAATCGGTACCCCTTGG
1 GGGGGAATCGGTACCCCTTGG
3444439 GGGGGAATCGGT
1 GGGGGAATCGGT
3444451 TCCCTCTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCTTGG
Found at i:3447243 original size:21 final size:21
Alignment explanation
Indices: 3447219--3447278 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
3447209 CTGAAGCGAA
3447219 AGAAGCAAAGAGAGAAACGAG
1 AGAAGCAAAGAGAGAAACGAG
* * *
3447240 AGAAGCAGAA-AGAGTAGCGAT
1 AGAAGCA-AAGAGAGAAACGAG
* *
3447261 AGAAGCAGAGAGGGAAAC
1 AGAAGCAAAGAGAGAAAC
3447279 AACATTTTAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 27 0.90
22 2 0.07
ACGTcount: A:0.52, C:0.10, G:0.35, T:0.03
Consensus pattern (21 bp):
AGAAGCAAAGAGAGAAACGAG
Found at i:3451476 original size:15 final size:16
Alignment explanation
Indices: 3451446--3451480 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3451436 TTTTTTATAT
*
3451446 AATATTTAGTTATTTA
1 AATATTTAATTATTTA
3451462 AATATTTAATT-TTTA
1 AATATTTAATTATTTA
3451477 AATA
1 AATA
3451481 AAAACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
AATATTTAATTATTTA
Found at i:3452868 original size:21 final size:21
Alignment explanation
Indices: 3452844--3452886 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3452834 CATTCTCACG
3452844 CCTTTAATTAATTCGGACTAA
1 CCTTTAATTAATTCGGACTAA
3452865 CCTTTAATTAATTCGGACTAA
1 CCTTTAATTAATTCGGACTAA
3452886 C
1 C
3452887 TTATATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (21 bp):
CCTTTAATTAATTCGGACTAA
Found at i:3453996 original size:13 final size:13
Alignment explanation
Indices: 3453978--3454010 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3453968 CGTATAGTTC
3453978 AAATTTTCCAGGA
1 AAATTTTCCAGGA
*
3453991 AAA-TTTCCTGGA
1 AAATTTTCCAGGA
3454003 AAATTTTC
1 AAATTTTC
3454011 TAGTTGCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (13 bp):
AAATTTTCCAGGA
Found at i:3456711 original size:18 final size:19
Alignment explanation
Indices: 3456688--3456735 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
3456678 TTTTTTGGGG
3456688 TTATTATTAATAAT-AATA
1 TTATTATTAATAATCAATA
*
3456706 TTATTATT-ATAATCATTA
1 TTATTATTAATAATCAATA
*
3456724 TTATTTTTAATA
1 TTATTATTAATA
3456736 CAGTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 5 0.19
18 18 0.69
19 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTATTAATAATCAATA
Found at i:3456727 original size:15 final size:14
Alignment explanation
Indices: 3456689--3456728 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
3456679 TTTTTGGGGT
*
3456689 TATTATTAATAATAA
1 TATTATT-ATTATAA
3456704 TATTATTATTATAA
1 TATTATTATTATAA
3456718 TCATTATTATT
1 T-ATTATTATT
3456729 TTTAATACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTATTATTATAA
Found at i:3458225 original size:2 final size:2
Alignment explanation
Indices: 3458218--3458249 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3458208 ATTATCTTAT
3458218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3458250 CACACACGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3464882 original size:259 final size:258
Alignment explanation
Indices: 3464298--3464884 Score: 840
Period size: 259 Copynumber: 2.3 Consensus size: 258
3464288 TTCTTATTTA
* *
3464298 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGGTGATTAAAT-CTTTCAGGTCATCTGT
1 GTAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTT-AGGTCATCTGT
* *
3464362 CAGTCTTTCGAGCGAGATGATAAGCCCTTCGGGCTGTCTATAAGACCTTCAGGCATGATGTTTTC
65 CAGTCTTTCGAGCGAGATGATAAGCCCTTCGGGCTGTCTATAAGACCTTCAGGCAAGATGCTTTC
* **
3464427 ACATGAATTTTGAAAAATGAGAAAGCGGTTTCCAAAGTTTCTCATTTAATATTTTCAAAAAATGA
130 ACATGAATTTTAAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAATATTTTCAAAAAATGA
* * *
3464492 AATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGCAAACTATTTCGAGAATTG
195 AATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGCAAACTATTTCCAAAATTG
* ** ** * *
3464556 GTAAGTCTTTCACACCATCAGTAAGTCTTTCGAGCATGACAATTAAATCCTTCAAGTCATCTGTC
1 GTAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTAGGTCATCTGTC
* * * *
3464621 AGTCTTTCGAGCGAGATGATAAGTCCTTTGGGTTGTCCCTA-AAG-CCTTCGGGCAAGATGCTTT
66 AGTCTTTCGAGCGAGATGATAAGCCCTTCGGGCTGT--CTATAAGACCTTCAGGCAAGATGCTTT
* * *
3464684 CACATGATTTTTCAAAAAATGA-AGAAGCAATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAA
129 CACATGAATTTT-AAAAAATGAGA-AAGCAATTTCCAAAGTTTCTCATTTAATATTTTCAAAAAA
*
3464748 TGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAT
192 TGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGCAAACTATTTCCAAAAT
3464813 TG
257 TG
* * * *
3464815 GTAAGTCCTTCGGACCATCAGTAAGTTTTTCGAGCATGATGATTAAATCCTTTGGGTTATTTGTC
1 GTAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTAGGTCATCTGTC
3464880 AGTCT
66 AGTCT
3464885 CACTTGAGAC
Statistics
Matches: 288, Mismatches: 36, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
258 113 0.39
259 172 0.60
260 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (258 bp):
GTAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTAGGTCATCTGTC
AGTCTTTCGAGCGAGATGATAAGCCCTTCGGGCTGTCTATAAGACCTTCAGGCAAGATGCTTTCA
CATGAATTTTAAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAATATTTTCAAAAAATGAA
ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGCAAACTATTTCCAAAATTG
Found at i:3465014 original size:3 final size:3
Alignment explanation
Indices: 3465006--3465057 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
3464996 TTTTTCCGGG
*
3465006 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
3465052 TTA TTA
1 TTA TTA
3465058 CAGTTTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3465667 original size:33 final size:33
Alignment explanation
Indices: 3465607--3465673 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
3465597 GAGAGAAAAA
3465607 AAAGGAGACTTTTTCGAAAACAAAAAA-GAAAC
1 AAAGGAGACTTTTTCGAAAACAAAAAAGGAAAC
**
3465639 AAAGAGAGA-TTTTTCGAAAAACCCAAAAGGAAAC
1 AAAG-GAGACTTTTTCG-AAAACAAAAAAGGAAAC
3465673 A
1 A
3465674 TAAAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 11 0.37
33 13 0.43
34 6 0.20
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.15
Consensus pattern (33 bp):
AAAGGAGACTTTTTCGAAAACAAAAAAGGAAAC
Found at i:3469148 original size:98 final size:96
Alignment explanation
Indices: 3468984--3469340 Score: 425
Period size: 98 Copynumber: 3.7 Consensus size: 96
3468974 CATTTCTGGA
* *
3468984 AGAAAGGTGTCATTAATGCAAGTTAGATGAAAAAT-GATGCATTTTTGGCAGAAAGATGCCATTA
1 AGAAAGGTGTCATTAATGCAAGTTAGATGAAAAATGGA-GCATTTTTGGCAGAAAGGTGCCACTA
3469048 ATGCAAGTTAAGTGCCTAACGATGCATTTTTAGC
65 ATGCAAGTTAAGTGCCTAACG-TGCATTTTT-GC
* * *
3469082 AAAAAGGTGTCATTAATGCAAGTTAGATGAAAAATGGAGCATTTTTGGCATAAAGGTGTCACTAA
1 AGAAAGGTGTCATTAATGCAAGTTAGATGAAAAATGGAGCATTTTTGGCAGAAAGGTGCCACTAA
*
3469147 TGCAAGTTAAGTGCCTAACTGTGCATTTTTGGG
66 TGCAAGTTAAGTGCCTAAC-GTGCATTTTT-GC
* * * * *
3469180 AGAAATGTGACATTAATGCAAGTTAGATGAAAAATGGTGCATTTTTTGCAGAACA-GTACCACTA
1 AGAAAGGTGTCATTAATGCAAGTTAGATGAAAAATGGAGCATTTTTGGCAGAA-AGGTGCCACTA
3469244 ATGCAAGTTAAGTGCCTAACGGTGCATTTTTGAC
65 ATGCAAGTTAAGTGCCTAAC-GTGCATTTTTG-C
* * * * * * * *
3469278 AGAAAGGTGCCACTAATG-ACAGTTAAATGCATAATGGTGCA-TTTCGGCATAAAAGGTGCCACT
1 AGAAAGGTGTCATTAATGCA-AGTTAGATGAAAAATGGAGCATTTTTGGCA-GAAAGGTGCCACT
3469341 CATGGTAATT
Statistics
Matches: 225, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
97 9 0.04
98 212 0.94
99 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (96 bp):
AGAAAGGTGTCATTAATGCAAGTTAGATGAAAAATGGAGCATTTTTGGCAGAAAGGTGCCACTAA
TGCAAGTTAAGTGCCTAACGTGCATTTTTGC
Found at i:3469246 original size:49 final size:48
Alignment explanation
Indices: 3468959--3469340 Score: 295
Period size: 49 Copynumber: 7.8 Consensus size: 48
3468949 AACTGCTCTA
* * * * * *
3468959 TAATGTAAAACGGTGCATTTCTGGAAGAAAGGTGTCATTAATGCAAGT
1 TAATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * * *
3469007 TAGATGAAAAATGATGCATTTTTGGCAGAAAGATGCCATTAATGCAAGT
1 TA-ATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
** * * * * * *
3469056 TAAGTGCCTAACGATGCATTTTTAGCAAAAAGGTGTCATTAATGCAAGT
1 TAA-TGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * * *
3469105 TAGATGAAAAATGGAGCATTTTTGGCATAAAGGTGTCACTAATGCAAGT
1 TA-ATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * * * * *
3469154 TAAGTGCCTAACT-GTGCATTTTTGGGAGAAATGTGACATTAATGCAAGT
1 TAA-TG-CAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * *
3469203 TAGATGAAAAATGGTGCATTTTTTGCAGAACA-GTACCACTAATGCAAGT
1 TA-ATGCAAAATGGTGCATTTTTGGCAGAA-AGGTGCCACTAATGCAAGT
** * *
3469252 TAAGTGCCTAACGGTGCATTTTTGACAGAAAGGTGCCACTAATG-ACAGT
1 TAA-TGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCA-AGT
* * *
3469301 TAAATGCATAATGGTGCA-TTTCGGCATAAAAGGTGCCACT
1 T-AATGCAAAATGGTGCATTTTTGGCA-GAAAGGTGCCACT
3469341 CATGGTAATT
Statistics
Matches: 268, Mismatches: 53, Indels: 25
0.77 0.15 0.07
Matches are distributed among these distances:
48 16 0.06
49 244 0.91
50 8 0.03
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (48 bp):
TAATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
Found at i:3471175 original size:24 final size:24
Alignment explanation
Indices: 3471122--3471168 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3471112 TAAAGTTATA
*
3471122 TACTTTTAATCAAACAATGTTTAC
1 TACTTTTAATCAAACAAGGTTTAC
**
3471146 TACTTTTAATCAAAGTAGGTTTA
1 TACTTTTAATCAAACAAGGTTTA
3471169 TTGCTTTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (24 bp):
TACTTTTAATCAAACAAGGTTTAC
Found at i:3471601 original size:2 final size:2
Alignment explanation
Indices: 3471594--3471661 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
3471584 TAAATTAATA
*
3471594 AT AT AT AT -T AT AT AT AT AT AT AT AT A- AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3471634 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
3471662 TTTGTCAACC
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3473043 original size:34 final size:34
Alignment explanation
Indices: 3473005--3473075 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
3472995 TCCTCTAAAT
3473005 AAGTCAAAATAAGGGTTATAAAAAAGACCTGTAA
1 AAGTCAAAATAAGGGTTATAAAAAAGACCTGTAA
* * *
3473039 AAGTCAAAATAAGGGTTATTAAAAGGACTTGTAA
1 AAGTCAAAATAAGGGTTATAAAAAAGACCTGTAA
3473073 AAG
1 AAG
3473076 AGGTGTAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.23
Consensus pattern (34 bp):
AAGTCAAAATAAGGGTTATAAAAAAGACCTGTAA
Found at i:3477026 original size:23 final size:23
Alignment explanation
Indices: 3476999--3477043 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3476989 AAATCAATGC
*
3476999 ATTAAATTTAGTGAGAAAATTGT
1 ATTAAATTTAGTAAGAAAATTGT
*
3477022 ATTAAGTTTAGTAAGAAAATTG
1 ATTAAATTTAGTAAGAAAATTG
3477044 AAAAGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (23 bp):
ATTAAATTTAGTAAGAAAATTGT
Found at i:3477835 original size:19 final size:20
Alignment explanation
Indices: 3477788--3477835 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
3477778 GGGTTGCCGT
*
3477788 TTCATTTAGTTGTATGACTTTTT
1 TTCATTTAGTTGTATGA---TTA
3477811 TTCATTTAGTTGTATGA-TA
1 TTCATTTAGTTGTATGATTA
3477830 TTCATT
1 TTCATT
3477836 GCTATTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
23 17 0.71
ACGTcount: A:0.21, C:0.08, G:0.12, T:0.58
Consensus pattern (20 bp):
TTCATTTAGTTGTATGATTA
Found at i:3479457 original size:22 final size:20
Alignment explanation
Indices: 3479411--3479483 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
3479401 GACCCGAATC
3479411 AAAATAATATATTTATTCTA
1 AAAATAATATATTTATTCTA
* *
3479431 AAAATATTATTTTTATTCAATA
1 AAAATAATATATTTATTC--TA
* *
3479453 AAAATAATGAT-TTAATT-GA
1 AAAATAAT-ATATTTATTCTA
3479472 AAAATAATATAT
1 AAAATAATATAT
3479484 AGAGAGACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 2 0.05
19 10 0.23
20 16 0.36
22 14 0.32
23 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATAATATATTTATTCTA
Found at i:3480526 original size:51 final size:51
Alignment explanation
Indices: 3480447--3480556 Score: 139
Period size: 51 Copynumber: 2.2 Consensus size: 51
3480437 CCTCTGTAGA
* * * * * *
3480447 AAGGCGCGACCCATGTACCGCGCTTTACGCTGATGTGGCACAACGTAGGGT
1 AAGGCGCGACACATGCACCGCACCTTACGCTGACGTGGCACAACGCAGGGT
* * *
3480498 AAGGCGCGACACATGCACCGCACCTTACGTTGACGTGGCGCCACGCAGGGT
1 AAGGCGCGACACATGCACCGCACCTTACGCTGACGTGGCACAACGCAGGGT
3480549 AAGGCGCG
1 AAGGCGCG
3480557 GTTCATGGGC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.22, C:0.30, G:0.33, T:0.15
Consensus pattern (51 bp):
AAGGCGCGACACATGCACCGCACCTTACGCTGACGTGGCACAACGCAGGGT
Found at i:3480592 original size:40 final size:40
Alignment explanation
Indices: 3480537--3480614 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
3480527 TTGACGTGGC
**
3480537 GCCACGCAGGGTAAGGCGCGGTTCATGGG-CTGCGCCTTAT
1 GCCACGCAGGGTAAGGCGCAATTCATGGGTC-GCGCCTTAT
*
3480577 GCCACGTAGGGTAAGGCGCAATTCATGGGTCGCGCCTT
1 GCCACGCAGGGTAAGGCGCAATTCATGGGTCGCGCCTT
3480615 CTGCTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.21
Consensus pattern (40 bp):
GCCACGCAGGGTAAGGCGCAATTCATGGGTCGCGCCTTAT
Found at i:3480788 original size:23 final size:24
Alignment explanation
Indices: 3480762--3480807 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3480752 AGGTATATTT
*
3480762 TATTCTATTTAA-TATTTTATTAG
1 TATTCTATTTAATTATTTAATTAG
*
3480785 TATTTTATTTAATTATTTAATTA
1 TATTCTATTTAATTATTTAATTA
3480808 TTTTATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TATTCTATTTAATTATTTAATTAG
Found at i:3486737 original size:30 final size:30
Alignment explanation
Indices: 3486660--3486729 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
3486650 ATCAAATATA
*
3486660 AGAGGATTGTCGGGTAATATTTACGGGTTG
1 AGAGGATTGTCGGGTGATATTTACGGGTTG
3486690 AGAGGATTGTCGGGTGATATTTACGGGTTG
1 AGAGGATTGTCGGGTGATATTTACGGGTTG
3486720 AGAGGATTGT
1 AGAGGATTGT
3486730 TGTGTGATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.23, C:0.06, G:0.39, T:0.33
Consensus pattern (30 bp):
AGAGGATTGTCGGGTGATATTTACGGGTTG
Found at i:3500894 original size:17 final size:17
Alignment explanation
Indices: 3500860--3500893 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3500850 TGAACAACAC
*
3500860 TCAAATTTATATACTTT
1 TCAAATATATATACTTT
3500877 TCAAATATATATA-TTT
1 TCAAATATATATACTTT
3500893 T
1 T
3500894 TATAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TCAAATATATATACTTT
Found at i:3501841 original size:31 final size:32
Alignment explanation
Indices: 3501806--3501906 Score: 107
Period size: 31 Copynumber: 3.2 Consensus size: 32
3501796 TGCTCAATCT
**
3501806 GATATTGACCCGA-CCTGAAATCAATCGATCC
1 GATATTGACCCGACCCAAAAATCAATCGATCC
* * *
3501837 GATATTGACCCAACCCAAAAACCAAACCGATCC
1 GATATTGACCCGACCCAAAAATC-AATCGATCC
**
3501870 GATATT-AATCGACCCAAAAATCAATCGATCC
1 GATATTGACCCGACCCAAAAATCAATCGATCC
*
3501901 AATATT
1 GATATT
3501907 AATCCGACTG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
31 25 0.44
32 18 0.32
33 14 0.25
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.21
Consensus pattern (32 bp):
GATATTGACCCGACCCAAAAATCAATCGATCC
Found at i:3502650 original size:20 final size:21
Alignment explanation
Indices: 3502625--3502676 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3502615 TTTTCCCAAT
*
3502625 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
3502645 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
3502666 TCGCAATGCGA
1 TCGCAATGCGA
3502677 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:3503330 original size:19 final size:19
Alignment explanation
Indices: 3503294--3503335 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3503284 ATGAGAGAAT
*
3503294 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
3503313 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
3503332 CGCA
1 CGCA
3503336 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:3503353 original size:19 final size:19
Alignment explanation
Indices: 3503331--3503474 Score: 148
Period size: 19 Copynumber: 8.1 Consensus size: 19
3503321 GAAACCAAAA
*
3503331 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3503350 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3503364 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3503383 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3503402 TCGCGTTGCGA-TTTC---
1 TCGCGTTGCGATTTTCATT
**
3503417 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
3503434 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
3503453 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3503473 TC
1 TC
3503475 AACCAAAAGA
Statistics
Matches: 104, Mismatches: 9, Indels: 24
0.76 0.07 0.18
Matches are distributed among these distances:
13 8 0.08
14 12 0.12
15 1 0.01
16 3 0.03
17 4 0.04
18 4 0.04
19 55 0.53
20 17 0.16
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3503422 original size:32 final size:32
Alignment explanation
Indices: 3503380--3503446 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
3503370 TGCGATTTTC
**
3503380 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCG
1 ATTTCGCGTTGCGATAGTCATTTCGCGTTGCG
*
3503412 ATTTCTCGTTGCGATAGTCATTTCGCGTTGCG
1 ATTTCGCGTTGCGATAGTCATTTCGCGTTGCG
3503444 ATT
1 ATT
3503447 CTCATTATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (32 bp):
ATTTCGCGTTGCGATAGTCATTTCGCGTTGCG
Found at i:3503440 original size:51 final size:51
Alignment explanation
Indices: 3503331--3503467 Score: 211
Period size: 52 Copynumber: 2.6 Consensus size: 51
3503321 GAAACCAAAA
* **
3503331 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATT-TCTCGTTGCGATAGTCATT
3503383 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCTCGTTGCGATAGTCATT
* *
3503434 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTT
3503468 TCATTTCAAC
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 35 0.44
52 44 0.56
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (51 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCTCGTTGCGATAGTCATT
Found at i:3505025 original size:63 final size:63
Alignment explanation
Indices: 3504926--3505056 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
3504916 GTTACGTGAT
*
3504926 GAGGTCAATGCCTTGCGTGAGTAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
3504989 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
3505052 GAGGT
1 GAGGT
3505057 GTCTACTTTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (63 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:3505704 original size:21 final size:21
Alignment explanation
Indices: 3505680--3505746 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3505670 TCATTCCTCG
3505680 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3505701 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3505722 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3505743 AGAG
1 AGAG
3505747 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3505704 original size:42 final size:42
Alignment explanation
Indices: 3505628--3505746 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
3505618 GACTCGCCTG
* * * * * * *
3505628 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
3505670 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
3505712 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
3505747 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:3507122 original size:14 final size:14
Alignment explanation
Indices: 3507102--3507138 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
3507092 GATTGTTTAA
3507102 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
3507115 TGTGATTTGTAAAAG
1 T-TGATTTGTAAAAG
3507130 TTGATTTGT
1 TTGATTTGT
3507139 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:3507269 original size:19 final size:19
Alignment explanation
Indices: 3507245--3507291 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3507235 AAAAAGTACT
*
3507245 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
3507264 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
3507283 ATCGCAACG
1 ATCGCAACG
3507292 AGAGAAACGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:3507362 original size:33 final size:32
Alignment explanation
Indices: 3507320--3507446 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
3507310 ATTAAATTCG
*
3507320 CGTTGCGATTTTCATTTTGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
3507353 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
3507386 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
3507419 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3507447 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:3507377 original size:19 final size:19
Alignment explanation
Indices: 3507316--3507446 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
3507306 CGAAATTAAA
*
3507316 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
3507335 TTTGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
3507351 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
3507368 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
3507382 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3507401 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
3507417 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3507434 TTCGCATTGCGAT
1 TTCGCATTGCGAT
3507447 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 23 0.28
16 12 0.15
17 13 0.16
19 34 0.41
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3507393 original size:66 final size:66
Alignment explanation
Indices: 3507313--3507445 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
3507303 ACGCGAAATT
* *
3507313 AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
3507378 G
66 G
*
3507379 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
3507444 G
66 G
3507445 A
1 A
3507446 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:3509755 original size:12 final size:12
Alignment explanation
Indices: 3509738--3509762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3509728 TCTTCGGGGA
3509738 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3509750 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3509762 C
1 C
3509763 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3509895 original size:24 final size:24
Alignment explanation
Indices: 3509868--3509921 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3509858 GTGTTTCATC
* *
3509868 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
3509892 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
3509916 ATCAAA
1 ATCAAA
3509922 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:3511001 original size:20 final size:20
Alignment explanation
Indices: 3510976--3511013 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3510966 ATTCATTTGA
*
3510976 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
3510996 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
3511014 CGCAATGCGA
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:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:3511073 original size:19 final size:19
Alignment explanation
Indices: 3511032--3511098 Score: 99
Period size: 19 Copynumber: 3.8 Consensus size: 19
3511022 GAAATGAAAA
3511032 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
3511048 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3511065 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3511084 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
3511099 GTCGTTGCGA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3511075 original size:52 final size:52
Alignment explanation
Indices: 3511013--3511127 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 52
3511003 AACGAGAAAA
* ***
3511013 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** ** *
3511065 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
3511117 TCGCGTTGCGA
1 TCGCATTGCGA
3511128 TAGTCTGTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:3511235 original size:14 final size:14
Alignment explanation
Indices: 3511216--3511252 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3511206 CATCAATTAA
3511216 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3511230 ACAAATCATCTTTT
1 ACAAATCAACATTT
3511244 ACAAATCAA
1 ACAAATCAA
3511253 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3513155 original size:18 final size:19
Alignment explanation
Indices: 3513122--3513186 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
3513112 GAAACTTAAA
3513122 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3513141 ATCGCAACG-GAAATGGCT
1 ATCGCAACGCGAAATGACT
* **
3513159 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3513178 ATCGCAACG
1 ATCGCAACG
3513187 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 16 0.41
19 23 0.59
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3513194 original size:14 final size:14
Alignment explanation
Indices: 3513175--3513232 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3513165 ATGCGAAATG
3513175 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3513189 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3513205 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3513221 AAAATCGCAACG
1 AAAATCGCAACG
3513233 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3513217 original size:32 final size:32
Alignment explanation
Indices: 3513119--3513237 Score: 141
Period size: 32 Copynumber: 3.5 Consensus size: 32
3513109 CACGAAACTT
*
3513119 AAAATCGCAACGCGAAATGACTATCGCAACGGA-
1 AAAATCGCAACGCGAAATGA-AATCGCAAC-GAC
* *
3513152 AATGGCTATCGCAATGCGAAATGAAAATCGCAACGAC
1 AA----AATCGCAACGCGAAATG-AAATCGCAACGAC
3513189 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACGAC
3513221 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
3513238 CACAAATCAC
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
32 30 0.40
33 17 0.23
36 2 0.03
37 25 0.33
38 1 0.01
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.12
Consensus pattern (32 bp):
AAAATCGCAACGCGAAATGAAATCGCAACGAC
Found at i:3513283 original size:14 final size:14
Alignment explanation
Indices: 3513260--3513323 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
3513250 TGCGATTTTC
3513260 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
3513273 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
3513287 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
3513305 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
3513319 ATTTT
1 ATTTT
3513324 CATTTCGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
16 8 0.18
18 9 0.20
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:3513330 original size:33 final size:33
Alignment explanation
Indices: 3513249--3513339 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
3513239 ACAAATCACA
* *
3513249 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3513282 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3513314 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
3513340 AGCCATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:3513351 original size:20 final size:20
Alignment explanation
Indices: 3513326--3513396 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
3513316 GCGATTTTCA
*
3513326 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
3513346 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
3513366 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
3513386 TTTCGTGTTGC
1 TTTCGCGTTGC
3513397 AAAAGTAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:3513905 original size:18 final size:18
Alignment explanation
Indices: 3513879--3513923 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3513869 GTCGATCAGA
*
3513879 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
3513897 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
3513915 TGATGGCTC
1 TGATGGCTC
3513924 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:3515266 original size:20 final size:20
Alignment explanation
Indices: 3515241--3515278 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3515231 AATAGTTTCT
3515241 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
3515261 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
3515279 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3515569 original size:22 final size:22
Alignment explanation
Indices: 3515542--3515585 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3515532 GATGGAGATA
*
3515542 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
3515564 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
3515586 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:3515849 original size:41 final size:41
Alignment explanation
Indices: 3515753--3515850 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
3515743 CGCTTTGAAA
* *
3515753 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
* * * * *
3515794 ATCTCGTTGTGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
3515835 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
3515851 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.40
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
Found at i:3515865 original size:21 final size:21
Alignment explanation
Indices: 3515836--3515928 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
3515826 ATAGTCAGTA
3515836 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3515857 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3515877 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3515898 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3515918 TCGCATTGCGA
1 TCGCATTGCGA
3515929 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:3515866 original size:41 final size:41
Alignment explanation
Indices: 3515836--3515928 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
3515826 ATAGTCAGTA
* *
3515836 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
3515877 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
3515918 TCGCATTGCGA
1 TCGCATTGCGA
3515929 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:3516726 original size:68 final size:68
Alignment explanation
Indices: 3516617--3516752 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
3516607 ATTCATTTAC
3516617 CCAATGTTTCTTTTCCTTTTATTTTTTTCATGTTAAATATTAGTGAAGATAAGGATTAAATTAAA
1 CCAATGTTTCTTTTCCTTTTATTTTTTTCATGTTAAATATTAGTGAAGATAAGGATTAAATTAAA
3516682 CAA
66 CAA
3516685 CCAATGTTTCTTTTCCTTTTATTTTTTTCATGTTAAATATTAGTGAAGATAAGGATTAAATTAAA
1 CCAATGTTTCTTTTCCTTTTATTTTTTTCATGTTAAATATTAGTGAAGATAAGGATTAAATTAAA
3516750 CAA
66 CAA
3516753 ATGGTGAACT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (68 bp):
CCAATGTTTCTTTTCCTTTTATTTTTTTCATGTTAAATATTAGTGAAGATAAGGATTAAATTAAA
CAA
Done.