Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007976.1 Hibiscus syriacus cultivar Beakdansim tig00110413_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: 428971
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:751 original size:18 final size:17
Alignment explanation
Indices: 698--754 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
688 TCTTAAACTT
*
698 TTATTATTTTATTATAAA
1 TTATAATTTTATT-TAAA
*
716 TCTAATAATTTTA-ATAAA
1 T-T-ATAATTTTATTTAAA
734 TTATCAATTTTATTTAAA
1 TTAT-AATTTTATTTAAA
752 TTA
1 TTA
755 ATTTATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.06
17 8 0.25
18 13 0.41
19 1 0.03
20 8 0.25
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATAATTTTATTTAAA
Found at i:1253 original size:19 final size:20
Alignment explanation
Indices: 1218--1282 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
1208 AACAAATTCA
*
1218 CAACGCG-ATCTCAAATTT-G
1 CAACGCGAAT-TCCAATTTCG
1237 CAACGCGAATTCCAATTTCG
1 CAACGCGAATTCCAATTTCG
* *
1257 CAAC-CCAGTTTCCAATTTCG
1 CAACGCGA-ATTCCAATTTCG
1277 CAACGC
1 CAACGC
1283 AATATGTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 16 0.41
20 22 0.56
21 1 0.03
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (20 bp):
CAACGCGAATTCCAATTTCG
Found at i:2133 original size:12 final size:12
Alignment explanation
Indices: 2112--2146 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2102 CACCGCATTC
*
2112 CAATACCAAACA
1 CAATATCAAACA
2124 CAATATCAAACA
1 CAATATCAAACA
*
2136 CAATCTCAAAC
1 CAATATCAAAC
2147 CCACAACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.14
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:4904 original size:20 final size:20
Alignment explanation
Indices: 4879--4942 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
4869 ATGTTGCGAT
4879 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
4899 CAACGCGAAA-T--AA---G
1 CAACGCGAAAGTCAAATTCG
*
4913 CAACGCGAAAGTCAAATTCA
1 CAACGCGAAAGTCAAATTCG
4933 CAACGCGAAA
1 CAACGCGAAA
4943 TAAGCGTTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
17 4 0.11
19 1 0.03
20 20 0.54
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:4922 original size:34 final size:34
Alignment explanation
Indices: 4879--4977 Score: 153
Period size: 34 Copynumber: 2.9 Consensus size: 34
4869 ATGTTGCGAT
4879 CAACGCGAAAGTCAAATTCGCAACGCGAAATAAG
1 CAACGCGAAAGTCAAATTCGCAACGCGAAATAAG
*
4913 CAACGCGAAAGTCAAATTCACAACGCGAAATAAG
1 CAACGCGAAAGTCAAATTCGCAACGCGAAATAAG
*** *
4947 CGTTGCGATAGTCAAATTCGCAACGCGAAAT
1 CAACGCGAAAGTCAAATTCGCAACGCGAAAT
4978 CGCAAACCGA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.15
Consensus pattern (34 bp):
CAACGCGAAAGTCAAATTCGCAACGCGAAATAAG
Found at i:5055 original size:20 final size:20
Alignment explanation
Indices: 5030--5068 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5020 CAACGCTTAT
5030 TTCGCGTTGTGAATTTACCA
1 TTCGCGTTGTGAATTTACCA
5050 TTCGCGTTGTGAATTTACC
1 TTCGCGTTGTGAATTTACC
5069 TTCAACAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGTGAATTTACCA
Found at i:5158 original size:24 final size:24
Alignment explanation
Indices: 5131--5177 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5121 AAATCAATTA
*
5131 AACATTGTTGTGGGTACATTATTG
1 AACATTGTTATGGGTACATTATTG
5155 AACATTGTTATGGGTACATTATT
1 AACATTGTTATGGGTACATTATT
5178 TGGAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (24 bp):
AACATTGTTATGGGTACATTATTG
Found at i:5594 original size:39 final size:39
Alignment explanation
Indices: 5551--5637 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
5541 TCTGATGCTC
5551 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
5590 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
5629 ATCAAAATC
1 ATCAAAATC
5638 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:5904 original size:20 final size:20
Alignment explanation
Indices: 5878--5951 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
5868 CGTGAAATAA
5878 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
* * *
5898 ACGTTGCAAATTTGACTTCC
1 GCGTTGCGAATTTGACTTTC
* *
5918 GCATTGCGAATTTAACTTTC
1 GCGTTGCGAATTTGACTTTC
5938 GCGTTGCGAATTTG
1 GCGTTGCGAATTTG
5952 TACCTTCAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:6093 original size:14 final size:14
Alignment explanation
Indices: 6057--6098 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
6047 AAAATTCTTA
6057 TTTACAAATCAAAT
1 TTTACAAATCAAAT
**
6071 TAAACAAATCAAAT
1 TTTACAAATCAAAT
*
6085 TTTATAAAT-AAAT
1 TTTACAAATCAAAT
6098 T
1 T
6099 AATCAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTACAAATCAAAT
Found at i:6137 original size:59 final size:62
Alignment explanation
Indices: 6012--6141 Score: 167
Period size: 63 Copynumber: 2.1 Consensus size: 62
6002 TTAGAAACAG
* *
6012 CAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATTCTTATTTACAAATCAAATTAAA
1 CAAATCAAATTTTACAAATAAATTAAACAA-CAAAAAAATTCTTATTTACAAATCAAATTAAA
* * * **
6075 CAAATCAAATTTTATAAATAAATTAATCAA-AAAAAAA-TCTTATTTCCTCATC-AATTAAA
1 CAAATCAAATTTTACAAATAAATTAAACAACAAAAAAATTCTTATTTACAAATCAAATTAAA
6134 CAAATCAA
1 CAAATCAA
6142 CTTTCAATGT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
59 15 0.25
60 12 0.20
61 7 0.12
63 26 0.43
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (62 bp):
CAAATCAAATTTTACAAATAAATTAAACAACAAAAAAATTCTTATTTACAAATCAAATTAAA
Found at i:7610 original size:42 final size:42
Alignment explanation
Indices: 7514--7612 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 42
7504 GCAGAAAAGA
* * * * *
7514 CCTCTTGAACGATGAAAGGGGACTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAAAGAGGACTCTTGAACGATAGGAGGCG
* * * *
7556 CTTATTCG-ATGATGAGAGAGGCCTCTTGAACGATAGGAGGCG
1 CCTCTT-GAATGATGAAAGAGGACTCTTGAACGATAGGAGGCG
7598 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
7613 TAGGTGCATC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
41 1 0.02
42 42 0.95
43 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.23
Consensus pattern (42 bp):
CCTCTTGAATGATGAAAGAGGACTCTTGAACGATAGGAGGCG
Found at i:9869 original size:13 final size:13
Alignment explanation
Indices: 9847--9891 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
9837 GGGTTTCTTC
*
9847 AACAAAAAGATAA
1 AACAAAAAGACAA
*
9860 AACGAAAAGACAA
1 AACAAAAAGACAA
9873 AACAAAAAGACAA
1 AACAAAAAGACAA
9886 AACAAA
1 AACAAA
9892 GACAAATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.76, C:0.13, G:0.09, T:0.02
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:9887 original size:26 final size:24
Alignment explanation
Indices: 9847--9897 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
9837 GGGTTTCTTC
*
9847 AACAAAAAGATAAAACGAAAAGACAA
1 AACAAAAAGACAAAAC--AAAGACAA
9873 AACAAAAAGACAAAACAAAGACAA
1 AACAAAAAGACAAAACAAAGACAA
9897 A
1 A
9898 TACTAACTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.38
26 15 0.62
ACGTcount: A:0.75, C:0.14, G:0.10, T:0.02
Consensus pattern (24 bp):
AACAAAAAGACAAAACAAAGACAA
Found at i:9894 original size:11 final size:12
Alignment explanation
Indices: 9851--9897 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
9841 TTCTTCAACA
*
9851 AAAAGATAAAAC
1 AAAAGACAAAAC
9863 GAAAAGACAAAAC
1 -AAAAGACAAAAC
9876 AAAAAGACAAAAC
1 -AAAAGACAAAAC
9889 -AAAGACAAA
1 AAAAGACAAA
9898 TACTAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 9 0.28
13 23 0.72
ACGTcount: A:0.74, C:0.13, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:10144 original size:22 final size:22
Alignment explanation
Indices: 10103--10152 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
10093 ATGGAGATAA
10103 ACGGATTTCGTCGAAAATGGAG-
1 ACGGATTTCGTCGAAAATGG-GT
* *
10125 ACGGATTTCGTCGGAGATGGGT
1 ACGGATTTCGTCGAAAATGGGT
10147 ACGGAT
1 ACGGAT
10153 GTCGCCGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (22 bp):
ACGGATTTCGTCGAAAATGGGT
Found at i:10305 original size:20 final size:20
Alignment explanation
Indices: 10280--10363 Score: 109
Period size: 20 Copynumber: 4.2 Consensus size: 20
10270 GCGTAAAAAC
*
10280 ATTTGACTTTTGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
10300 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
10320 ATTTGAC-TTC-TGTGTGCGA
1 ATTTGACTTTCGCGT-TGCGA
10339 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
10359 ATTTG
1 ATTTG
10364 GAAAATCGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
18 2 0.04
19 13 0.24
20 37 0.69
21 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:10342 original size:39 final size:40
Alignment explanation
Indices: 10280--10363 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 40
10270 GCGTAAAAAC
*
10280 ATTTGACTTTTGCGTTGCGAATTTGACTATCGCGTTACGA
1 ATTTGACTTCTGCGTTGCGAATTTGACTATCGCGTTACGA
* * *
10320 ATTTGACTTCTGTG-TGCGAATTTGACTTTCGCGTTGCGA
1 ATTTGACTTCTGCGTTGCGAATTTGACTATCGCGTTACGA
10359 ATTTG
1 ATTTG
10364 GAAAATCGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 28 0.70
40 12 0.30
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (40 bp):
ATTTGACTTCTGCGTTGCGAATTTGACTATCGCGTTACGA
Found at i:10436 original size:20 final size:20
Alignment explanation
Indices: 10387--10440 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
10377 CGATTTACAT
*
10387 ATTCGTGTTGCGAAATTGGA
1 ATTCGAGTTGCGAAATTGGA
*
10407 A-ACTGAGTTGCGAAATTGGA
1 ATTC-GAGTTGCGAAATTGGA
*
10427 ATTCGCGTTGCGAA
1 ATTCGAGTTGCGAA
10441 TTTGAGATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (20 bp):
ATTCGAGTTGCGAAATTGGA
Found at i:12804 original size:43 final size:42
Alignment explanation
Indices: 12728--13005 Score: 227
Period size: 43 Copynumber: 6.5 Consensus size: 42
12718 TGAGAACAAA
* * * * *
12728 AAACGCCGTAATAGGTCAAGATATATCGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAT
* *
12771 AAACGCCGCAAAAGGTCGATATCTATAGTGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAT
* * * *
12814 AAACGCGGCAAAATGTCGAGATCTATAGCGGCGTTTTTGGAAA
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAT
* * * * ***
12857 AAACTCCGTAAAAGGTCAGT-TCTATAGCAGTGTTTTCATAAT
1 AAACGCCGCAAAAGGTCA-TATCTATAGCGGCGTTTTTGGAAT
* * * * *
12899 AAACGTCGCAAAAGGTCAGATCTATAGCGGTGTTTTGGGAAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAT
* * * *
12941 AAACGTCGCAAAAGATCATATCTATAGCGTCGTTTTTTG-AT
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAT
12982 ACAATCGCCGCAAAAAGGCTCATA
1 A-AA-CGCCGC-AAAAGG-TCATA
13006 ATAAGGAAAA
Statistics
Matches: 187, Mismatches: 42, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
41 2 0.01
42 84 0.45
43 91 0.49
44 5 0.03
45 5 0.03
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAT
Found at i:12892 original size:42 final size:42
Alignment explanation
Indices: 12755--12996 Score: 170
Period size: 42 Copynumber: 5.7 Consensus size: 42
12745 AAGATATATC
* * *
12755 GCGGCGTTTTTGGAATAAACGCCGCAAAAGGTC-GATATCTATA
1 GCGGTGTTTTTGGAACAAACTCCGCAAAAGGTCAG-T-TCTATA
* * * * * *
12798 GTGGCGTTTTTGGAACAAACGCGGCAAAATGTCGAGATCTATA
1 GCGGTGTTTTTGGAACAAACTCCGCAAAAGGTC-AGTTCTATA
* * *
12841 GCGGCGTTTTTGGAAAAAACTCCGTAAAAGGTCAGTTCTATA
1 GCGGTGTTTTTGGAACAAACTCCGCAAAAGGTCAGTTCTATA
* *** * *
12883 GCAGTGTTTTCATAATAAACGT-CGCAAAAGGTCAGATCTATA
1 GCGGTGTTTTTGGAACAAAC-TCCGCAAAAGGTCAGTTCTATA
* *
12925 GCGGTGTTTTGGGAACAAACGT-CGCAAAAGATCA-TATCTATA
1 GCGGTGTTTTTGGAACAAAC-TCCGCAAAAGGTCAGT-TCTATA
* * *
12967 GC-GTCGTTTTTTGATACAATCGCCGCAAAA
1 GCGGT-GTTTTTGGA-ACAAACTCCGCAAAA
12997 AGGCTCATAA
Statistics
Matches: 161, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.01
42 83 0.52
43 75 0.47
45 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (42 bp):
GCGGTGTTTTTGGAACAAACTCCGCAAAAGGTCAGTTCTATA
Found at i:12954 original size:84 final size:85
Alignment explanation
Indices: 12740--12976 Score: 223
Period size: 84 Copynumber: 2.8 Consensus size: 85
12730 ACGCCGTAAT
* * * * * * * * *
12740 AGGTCAAGATATATCGCGGCGTTTTTGGAATAAACGCCGCAAAAGGTCGATATCTATAGTGGCGT
1 AGGTCGAGATCTATAGCGGCGTTTTGGGAAAAAACTCCGCAAAAGATC-ATATCTATAGCGTCGT
*** *
12805 TTTTGGAACAAACG-CGGCAAA
65 TTTCATAATAAACGTC-GCAAA
* * * *
12826 ATGTCGAGATCTATAGCGGCGTTTTTGGAAAAAACTCCGTAAAAGGTCAGT-TCTATAGCAGT-G
1 AGGTCGAGATCTATAGCGGCGTTTTGGGAAAAAACTCCGCAAAAGATCA-TATCTATAGC-GTCG
12889 TTTTCATAATAAACGTCGCAAA
64 TTTTCATAATAAACGTCGCAAA
* *
12911 AGGTC-AGATCTATAGCGGTGTTTTGGGAACAAACGT-CGCAAAAGATCATATCTATAGCGTCGT
1 AGGTCGAGATCTATAGCGGCGTTTTGGGAAAAAAC-TCCGCAAAAGATCATATCTATAGCGTCGT
12974 TTT
65 TTT
12977 TTGATACAAT
Statistics
Matches: 126, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
83 3 0.02
84 49 0.39
85 30 0.24
86 44 0.35
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (85 bp):
AGGTCGAGATCTATAGCGGCGTTTTGGGAAAAAACTCCGCAAAAGATCATATCTATAGCGTCGTT
TTCATAATAAACGTCGCAAA
Found at i:15806 original size:41 final size:41
Alignment explanation
Indices: 15749--15847 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 41
15739 ACACGTTAGG
*
15749 CTATAGTGGCGTTTGTACAAAAACGCCACTAAAGTACAAGT
1 CTATAGCGGCGTTTGTACAAAAACGCCACTAAAGTACAAGT
*
15790 CTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGT
1 CTATAGCGGCGTTTGTACAAAAACGCCACTAAAGTACAAGT
* * *
15831 CTTTAACGACGTTTGTA
1 CTATAGCGGCGTTTGTA
15848 AACACAAAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (41 bp):
CTATAGCGGCGTTTGTACAAAAACGCCACTAAAGTACAAGT
Found at i:16042 original size:20 final size:20
Alignment explanation
Indices: 16019--16067 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
16009 ATTCTGGAGA
16019 AGTGTGGAACCTTATGGAAG
1 AGTGTGGAACCTTATGGAAG
16039 AGTGTGGAACCTTATGGAAG
1 AGTGTGGAACCTTATGGAAG
*
16059 AGTATGGAA
1 AGTGTGGAA
16068 GAATATGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.35, T:0.24
Consensus pattern (20 bp):
AGTGTGGAACCTTATGGAAG
Found at i:16064 original size:10 final size:10
Alignment explanation
Indices: 16031--16091 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
16021 TGTGGAACCT
16031 TATGGAAGAG
1 TATGGAAGAG
* ***
16041 TGTGGAACCT
1 TATGGAAGAG
16051 TATGGAAGAG
1 TATGGAAGAG
*
16061 TATGGAAGAA
1 TATGGAAGAG
16071 TATGGAAG-G
1 TATGGAAGAG
*
16080 GAGTGGAAGAG
1 TA-TGGAAGAG
16091 T
1 T
16092 GTAGAGCTTC
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
9 1 0.03
10 35 0.95
11 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.39, T:0.21
Consensus pattern (10 bp):
TATGGAAGAG
Found at i:16074 original size:20 final size:20
Alignment explanation
Indices: 16031--16078 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16021 TGTGGAACCT
* **
16031 TATGGAAGAGTGTGGAACCT
1 TATGGAAGAGTATGGAACAA
*
16051 TATGGAAGAGTATGGAAGAA
1 TATGGAAGAGTATGGAACAA
16071 TATGGAAG
1 TATGGAAG
16079 GGAGTGGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.35, T:0.23
Consensus pattern (20 bp):
TATGGAAGAGTATGGAACAA
Found at i:17098 original size:7 final size:7
Alignment explanation
Indices: 17086--17140 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
17076 AGATTTTTTA
*
17086 TGAATAG
1 TGAACAG
*
17093 TGAATAG
1 TGAACAG
17100 TGAACAG
1 TGAACAG
17107 T-AACAG
1 TGAACAG
17113 TGAAC-G
1 TGAACAG
*
17119 -GTACACG
1 TGAACA-G
17126 TGAACAG
1 TGAACAG
17133 TGAACAG
1 TGAACAG
17140 T
1 T
17141 ACACGTGAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 3 0.07
6 7 0.17
7 27 0.66
8 4 0.10
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (7 bp):
TGAACAG
Found at i:17131 original size:20 final size:20
Alignment explanation
Indices: 17108--17151 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
17098 AGTGAACAGT
*
17108 AACAGTGAACGGTACACGTG
1 AACAGTGAACAGTACACGTG
17128 AACAGTGAACAGTACACGTG
1 AACAGTGAACAGTACACGTG
17148 AACA
1 AACA
17152 ATATACAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (20 bp):
AACAGTGAACAGTACACGTG
Found at i:17151 original size:13 final size:13
Alignment explanation
Indices: 17098--17140 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
17088 AATAGTGAAT
17098 AGTGAACAGTAAC
1 AGTGAACAGTAAC
*
17111 AGTGAACGGT-AC
1 AGTGAACAGTAAC
17123 ACGTGAACAGTGAAC
1 A-GTGAACAGT-AAC
17138 AGT
1 AGT
17141 ACACGTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 17 0.68
14 2 0.08
15 3 0.12
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (13 bp):
AGTGAACAGTAAC
Found at i:17253 original size:11 final size:11
Alignment explanation
Indices: 17237--17261 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17227 GCATCGATGC
17237 ACTGCTACAGT
1 ACTGCTACAGT
17248 ACTGCTACAGT
1 ACTGCTACAGT
17259 ACT
1 ACT
17262 TCCAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (11 bp):
ACTGCTACAGT
Found at i:18032 original size:19 final size:21
Alignment explanation
Indices: 18008--18049 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17998 CCGTTAGACA
18008 GGGG-GAATCGGTACCCCCTG
1 GGGGAGAATCGGTACCCCCTG
*
18028 GGGGAGAATCTGTACCCCCTG
1 GGGGAGAATCGGTACCCCCTG
18049 G
1 G
18050 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.17, C:0.29, G:0.38, T:0.17
Consensus pattern (21 bp):
GGGGAGAATCGGTACCCCCTG
Found at i:19478 original size:19 final size:20
Alignment explanation
Indices: 19435--19482 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
19425 TCTAAATCCT
*
19435 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
19455 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
19474 TTTTCAAAA
1 TTTTCAAAA
19483 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:20799 original size:20 final size:20
Alignment explanation
Indices: 20762--20822 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
20752 CCGTTAGACA
*
20762 GGGGGAATCAGTACCCCCTTG
1 GGGGGAATCTGTACCCCC-TG
*
20783 GGGGGAATCTGTTCCCCCTG
1 GGGGGAATCTGTACCCCCTG
20803 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
20823 AACAATATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.15, C:0.30, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:21983 original size:20 final size:20
Alignment explanation
Indices: 21957--22049 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
21947 GCAGCCTTAG
21957 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* *
21977 AGCATCGATGCATAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
21997 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACAGCAGGA
*
22017 TGCATCGATGCACAGCATGA
1 TGCATCGATGCACAGCAGGA
22037 TGCATCGATGCAC
1 TGCATCGATGCAC
22050 TAATTGCATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:22392 original size:21 final size:21
Alignment explanation
Indices: 22368--22411 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
22358 ATGTTTAATG
22368 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
22389 AAAATGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
22410 AA
1 AA
22412 TTTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:23566 original size:19 final size:19
Alignment explanation
Indices: 23542--23591 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
23532 TTATTTTGAT
23542 TTTCAAAATCAACTTTTGC
1 TTTCAAAATCAACTTTTGC
23561 TTTCAAAATCAACTTTTGC
1 TTTCAAAATCAACTTTTGC
23580 TTTCAAAATCAA
1 TTTCAAAATCAA
23592 ATTATCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (19 bp):
TTTCAAAATCAACTTTTGC
Found at i:25534 original size:20 final size:20
Alignment explanation
Indices: 25505--25557 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
25495 GCAGCCTTGG
*
25505 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
25525 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
25545 TGCATCGATGCAC
1 TGCATCGATGCAC
25558 TAATTGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.30, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:25978 original size:46 final size:45
Alignment explanation
Indices: 25904--26048 Score: 200
Period size: 45 Copynumber: 3.2 Consensus size: 45
25894 AAAAAAAACT
*
25904 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
25949 TTTACCATTTAATACCATAATCTCATAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* * * *
25995 CTTACTATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
26040 CTTGCCATT
1 CTTACCATT
26049 ATTCTATAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
45 46 0.53
46 40 0.47
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:26079 original size:20 final size:20
Alignment explanation
Indices: 26054--26096 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
26044 CCATTATTCT
* *
26054 ATAACCATATACCATAAACA
1 ATAACCATAAACAATAAACA
*
26074 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAAACA
26094 ATA
1 ATA
26097 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAAACA
Found at i:26080 original size:13 final size:13
Alignment explanation
Indices: 26064--26089 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26054 ATAACCATAT
26064 ACCATAAACAATA
1 ACCATAAACAATA
26077 ACCATAAACAATA
1 ACCATAAACAATA
26090 GACAATAGCC
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:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
ACCATAAACAATA
Found at i:27915 original size:17 final size:17
Alignment explanation
Indices: 27893--27925 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27883 TTTTTTATTC
27893 CATTCAATAAGAAATTT
1 CATTCAATAAGAAATTT
27910 CATTCAATAAGAAATT
1 CATTCAATAAGAAATT
27926 CTATTTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (17 bp):
CATTCAATAAGAAATTT
Found at i:31237 original size:20 final size:20
Alignment explanation
Indices: 31231--31278 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
31221 TTCTGGAGAT
31231 GTGTGGAATCTTATGGACGA
1 GTGTGGAATCTTATGGACGA
* *
31251 GTGTGGAACCTTATGGAAGA
1 GTGTGGAATCTTATGGACGA
*
31271 GTATGGAA
1 GTGTGGAA
31279 GAATATGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.35, T:0.27
Consensus pattern (20 bp):
GTGTGGAATCTTATGGACGA
Found at i:36548 original size:19 final size:19
Alignment explanation
Indices: 36524--36567 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
36514 TTCACCCTAC
36524 CCAAATAGAAAATCATACA
1 CCAAATAGAAAATCATACA
36543 CCAAATAGAAAATCATACA
1 CCAAATAGAAAATCATACA
36562 CACAAA
1 C-CAAA
36568 AACCTTCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.59, C:0.23, G:0.05, T:0.14
Consensus pattern (19 bp):
CCAAATAGAAAATCATACA
Found at i:36958 original size:30 final size:30
Alignment explanation
Indices: 36924--37023 Score: 137
Period size: 30 Copynumber: 3.3 Consensus size: 30
36914 TGACTTCTAT
* * *
36924 TCTTCTTCTTTTGCTTCTGCCGCTTCTCCC
1 TCTTCTTCTTTTGCTTCTGTCGTTTCTACC
36954 TCTTCTTCTTTTGCTTCTGTCGTTTCTACC
1 TCTTCTTCTTTTGCTTCTGTCGTTTCTACC
* * **
36984 TTTTCTTCTTTTTCTTCCATCGTTTCTACC
1 TCTTCTTCTTTTGCTTCTGTCGTTTCTACC
37014 TCTTCTTCTT
1 TCTTCTTCTT
37024 CTTTGCGTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.03, C:0.33, G:0.07, T:0.57
Consensus pattern (30 bp):
TCTTCTTCTTTTGCTTCTGTCGTTTCTACC
Found at i:39126 original size:43 final size:44
Alignment explanation
Indices: 39048--39153 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 44
39038 AACGATTACA
* *
39048 CTCATTCGTACTTGAGGATACCGGAAAATGCGAGGATGATCTTG
1 CTCATTCGTACTTGAGGATACCGGAAAATACGAGGATAATCTTG
* * *
39092 CTCCTTCGTACTTG-GGATGA-CTGAAAATATGAGGATAATCTTG
1 CTCATTCGTACTTGAGGAT-ACCGGAAAATACGAGGATAATCTTG
* *
39135 CTCATTCGAATTTGAGGAT
1 CTCATTCGTACTTGAGGAT
39154 TCCAAATCTA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
43 34 0.65
44 18 0.35
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (44 bp):
CTCATTCGTACTTGAGGATACCGGAAAATACGAGGATAATCTTG
Found at i:40012 original size:19 final size:20
Alignment explanation
Indices: 39988--40026 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
39978 TATTAATTAG
39988 TTTTAATATAAT-ATAATAT
1 TTTTAATATAATAATAATAT
*
40007 TTTTAATATTATAATAATAT
1 TTTTAATATAATAATAATAT
40027 ACTCAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAATATAATAATAATAT
Found at i:40021 original size:17 final size:18
Alignment explanation
Indices: 39974--40022 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
39964 AAATATTTAA
*
39974 AATATAT-TAATTAGTTTT
1 AATATATATAA-TATTTTT
39992 AATATAATATAATATTTTT
1 AATAT-ATATAATATTTTT
40011 AATAT-TATAATA
1 AATATATATAATA
40023 ATATACTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.25
18 5 0.18
19 13 0.46
20 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATATATAATATTTTT
Found at i:40266 original size:24 final size:24
Alignment explanation
Indices: 40231--40276 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40221 GATTAATATT
*
40231 AAATAAATTATTCTATTATTTTAA
1 AAATAAATTATTCAATTATTTTAA
*
40255 AAAT-AATATATTCAATTTTTTT
1 AAATAAAT-TATTCAATTATTTT
40277 TATTAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
AAATAAATTATTCAATTATTTTAA
Found at i:41990 original size:2 final size:2
Alignment explanation
Indices: 41983--42007 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41973 CACAAAGCTT
41983 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42008 GAGAAATTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46050 original size:3 final size:3
Alignment explanation
Indices: 46044--46080 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
46034 AATAATAATA
46044 ATT ATT ATT ATT ATT ATT ATTT ATT A-T ATT A-T ATT AT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT AT
46081 ATAATGATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:47463 original size:48 final size:48
Alignment explanation
Indices: 47386--47485 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
47376 TACAACTGGC
* * * * *
47386 TTTGAGTGGTTAGAGAAAGCTATTTATGAATATGGATTTGTACTGACG
1 TTTGAGTGGTTAGAGAAAACTACTAATGAACATGGATTTATACTGACG
47434 TTTGAGTGGTTAGAGAAAACTACTAATGAACATGGATTTATACTGACG
1 TTTGAGTGGTTAGAGAAAACTACTAATGAACATGGATTTATACTGACG
47482 TTTG
1 TTTG
47486 TAAGCTTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (48 bp):
TTTGAGTGGTTAGAGAAAACTACTAATGAACATGGATTTATACTGACG
Found at i:47831 original size:31 final size:31
Alignment explanation
Indices: 47793--47855 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
47783 CGTGATCACT
47793 TCTTAATTAAATAAAAACGAAAGTGACCATA
1 TCTTAATTAAATAAAAACGAAAGTGACCATA
47824 TCTTAATTAAATAAAAACGAAAGTGACCATA
1 TCTTAATTAAATAAAAACGAAAGTGACCATA
47855 T
1 T
47856 ATTTTGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.27
Consensus pattern (31 bp):
TCTTAATTAAATAAAAACGAAAGTGACCATA
Found at i:49046 original size:31 final size:31
Alignment explanation
Indices: 49005--49064 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
48995 TGAGAGGGAC
* * *
49005 AAAATTAAAATAAACTAAAATTTGGAGGTGT
1 AAAATCAAAATAAACCAAAATTTGAAGGTGT
49036 AAAATCAAAATAAACCAAAATTTGAAGGT
1 AAAATCAAAATAAACCAAAATTTGAAGGT
49065 CTAGATACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.25
Consensus pattern (31 bp):
AAAATCAAAATAAACCAAAATTTGAAGGTGT
Found at i:51213 original size:21 final size:20
Alignment explanation
Indices: 51188--51226 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
51178 GGACAGGCTG
51188 AAAATCGGAAAAAAACCGGAA
1 AAAATCGG-AAAAAACCGGAA
*
51209 AAAATCGGGAAAAACCGG
1 AAAATCGGAAAAAACCGG
51227 GATTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.15, G:0.23, T:0.05
Consensus pattern (20 bp):
AAAATCGGAAAAAACCGGAA
Found at i:58092 original size:29 final size:29
Alignment explanation
Indices: 58051--58115 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
58041 AAGATACAAC
* *
58051 AAAAAG-AAGAAAAAAATAAAAAAGAGAG
1 AAAAAGAAAGAAAAAAAGAAAAAAGAAAG
*
58079 -AAAAGAAAGCAAAAAAGAAAAAA-AAAG
1 AAAAAGAAAGAAAAAAAGAAAAAAGAAAG
58106 AGAAAAGAAA
1 A-AAAAGAAA
58116 ATACATAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 8 0.26
28 15 0.48
29 8 0.26
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (29 bp):
AAAAAGAAAGAAAAAAAGAAAAAAGAAAG
Found at i:58106 original size:31 final size:28
Alignment explanation
Indices: 58052--58115 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
58042 AGATACAACA
*
58052 AAAAG-AAG-AAAAAAATAAAAAAGAGAG
1 AAAAGAAAGCAAAAAAA-AAAAAAAAGAG
58079 AAAAGAAAGCAAAAAAGAAAAAAAAAGAG
1 AAAAGAAAGCAAAAAA-AAAAAAAAAGAG
58108 AAAAGAAA
1 AAAAGAAA
58116 ATACATAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 5 0.15
28 3 0.09
29 24 0.73
30 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (28 bp):
AAAAGAAAGCAAAAAAAAAAAAAAAGAG
Found at i:58116 original size:17 final size:18
Alignment explanation
Indices: 58051--58114 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
58041 AAGATACAAC
*
58051 AAAAAGAAGAAAAAAATA
1 AAAAAGAAGAAAAAAAGA
58069 AAAAAGAGAGAAAAGAAAGCA
1 AAAAAGA-AGAAAA-AAAG-A
58090 AAAAAGAA-AAAAAAAGA
1 AAAAAGAAGAAAAAAAGA
*
58107 GAAAAGAA
1 AAAAAGAA
58115 AATACATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.20
18 11 0.27
19 10 0.24
20 4 0.10
21 8 0.20
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAGAAGAAAAAAAGA
Found at i:61142 original size:18 final size:18
Alignment explanation
Indices: 61119--61156 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
61109 TCAGGAAGAG
61119 AATGAAGACTGCTCTAGC
1 AATGAAGACTGCTCTAGC
*
61137 AATGAAGACTGCTCTTGC
1 AATGAAGACTGCTCTAGC
61155 AA
1 AA
61157 CCATTCCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (18 bp):
AATGAAGACTGCTCTAGC
Found at i:65351 original size:29 final size:29
Alignment explanation
Indices: 65309--65375 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
65299 ATTTTAAGTT
*
65309 AGGGGCGAACTTGAACTTATGAAATTTCA
1 AGGGGCGAACTTGAACTAATGAAATTTCA
* *
65338 AGGGGCGAACTTGAACTAATTAAATTTTA
1 AGGGGCGAACTTGAACTAATGAAATTTCA
*
65367 ATGGGCGAA
1 AGGGGCGAA
65376 AATAGATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (29 bp):
AGGGGCGAACTTGAACTAATGAAATTTCA
Found at i:78492 original size:14 final size:13
Alignment explanation
Indices: 78473--78533 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
78463 CATTCAGTAA
78473 TATGTTCGTTCATT
1 TATGTT-GTTCATT
78487 TATGTTTGTT-ATT
1 TATG-TTGTTCATT
*
78500 TATGTTAGTTCGTT
1 TATGTT-GTTCATT
*
78514 TATGTGTGTTTATT
1 TATGT-TGTTCATT
78528 TATGTT
1 TATGTT
78534 TAGCTCAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.05
13 11 0.28
14 24 0.60
15 3 0.08
ACGTcount: A:0.15, C:0.05, G:0.18, T:0.62
Consensus pattern (13 bp):
TATGTTGTTCATT
Found at i:78503 original size:27 final size:28
Alignment explanation
Indices: 78473--78533 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
78463 CATTCAGTAA
* *
78473 TATGTTCGTTCATTTATGTTTG-TTATT
1 TATGTTAGTTCATTTATGTGTGTTTATT
*
78500 TATGTTAGTTCGTTTATGTGTGTTTATT
1 TATGTTAGTTCATTTATGTGTGTTTATT
78528 TATGTT
1 TATGTT
78534 TAGCTCAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.15, C:0.05, G:0.18, T:0.62
Consensus pattern (28 bp):
TATGTTAGTTCATTTATGTGTGTTTATT
Found at i:78814 original size:10 final size:10
Alignment explanation
Indices: 78799--78828 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
78789 CGTTCACATT
*
78799 TGTTTGTTTG
1 TGTTTGTTTA
78809 TGTTTGTTTA
1 TGTTTGTTTA
78819 TGTTTGTTTA
1 TGTTTGTTTA
78829 CATCCATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (10 bp):
TGTTTGTTTA
Found at i:79980 original size:32 final size:32
Alignment explanation
Indices: 79937--80011 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
79927 GTGAGAAGAG
79937 ACTTACCTTTCTAAGCAGCACAAACCCAAGCT
1 ACTTACCTTTCTAAGCAGCACAAACCCAAGCT
* * *
79969 ACTTACATTTCTAAGCAGTACAAGCCCAAGCT
1 ACTTACCTTTCTAAGCAGCACAAACCCAAGCT
80001 ACTTACCTTTC
1 ACTTACCTTTC
80012 CAAATACTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.27
Consensus pattern (32 bp):
ACTTACCTTTCTAAGCAGCACAAACCCAAGCT
Found at i:80023 original size:32 final size:32
Alignment explanation
Indices: 79956--80033 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
79946 TCTAAGCAGC
* * * *
79956 ACAAACCCAAGCTACTTACATTTCTAAGCAGT
1 ACAAGCCCAAGCTACTTACATTTCCAAACACT
* *
79988 ACAAGCCCAAGCTACTTACCTTTCCAAATACT
1 ACAAGCCCAAGCTACTTACATTTCCAAACACT
* *
80020 ACAAGTCCGAGCTA
1 ACAAGCCCAAGCTA
80034 ATATGTCATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.23
Consensus pattern (32 bp):
ACAAGCCCAAGCTACTTACATTTCCAAACACT
Found at i:85669 original size:22 final size:22
Alignment explanation
Indices: 85641--85683 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
85631 GTGCATGTGT
85641 TGCATCCATAGCTGGGAGATTC
1 TGCATCCATAGCTGGGAGATTC
85663 TGCATCCATAGCTGGGAGATT
1 TGCATCCATAGCTGGGAGATT
85684 GTAGCCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (22 bp):
TGCATCCATAGCTGGGAGATTC
Found at i:86139 original size:28 final size:30
Alignment explanation
Indices: 86099--86160 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
86089 AATTTAGTTA
86099 ATTAGTTTGTTAGTTTAAG-T-TATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
86127 ATTAGTTTGTTAGTTTAAGTTATATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
86157 ATTA
1 ATTA
86161 TATAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
ATTAGTTTGTTAGTTTAAGTTATATATTAT
Found at i:86693 original size:20 final size:21
Alignment explanation
Indices: 86649--86693 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
86639 AAATATTGTG
**
86649 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
86670 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
86690 TTTA
1 TTTA
86694 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:89775 original size:10 final size:10
Alignment explanation
Indices: 89757--89788 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
89747 AGTAATGATA
89757 TATGTATTTC
1 TATGTATTTC
*
89767 TATGAATTTC
1 TATGTATTTC
89777 TATGTATTTC
1 TATGTATTTC
89787 TA
1 TA
89789 AGATTTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.56
Consensus pattern (10 bp):
TATGTATTTC
Found at i:89859 original size:60 final size:60
Alignment explanation
Indices: 89790--90039 Score: 411
Period size: 60 Copynumber: 4.2 Consensus size: 60
89780 GTATTTCTAA
*
89790 GATTTAGTAATGATTAGTAATAGTGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
89850 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
89910 GATTTAATAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
89970 G----AGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
90025 GATTTAGTAATGATT
1 GATTTAGTAATGATT
90040 TGATAGTAAT
Statistics
Matches: 177, Mismatches: 9, Indels: 9
0.91 0.05 0.05
Matches are distributed among these distances:
55 33 0.19
56 18 0.10
59 10 0.06
60 116 0.66
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:90010 original size:21 final size:22
Alignment explanation
Indices: 89986--90055 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
89976 TGATTAGTAA
89986 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
90007 TAATGATTTGATATTAATGATTT
1 TAATAATTTGATATTAATGA-TT
* *
90030 AGTAATGATTTGATAGTAATGATT
1 --TAATAATTTGATATTAATGATT
90054 TA
1 TA
90056 CGACTTGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 2 0.05
24 2 0.05
25 19 0.45
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:90023 original size:14 final size:14
Alignment explanation
Indices: 90007--90054 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
89997 TATTAATATT
*
90007 TAATGATTTGATAT
1 TAATGATTTGATAG
90021 TAATGA-TT--TAG
1 TAATGATTTGATAG
90032 TAATGATTTGATAG
1 TAATGATTTGATAG
90046 TAATGATTT
1 TAATGATTT
90055 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:90198 original size:10 final size:10
Alignment explanation
Indices: 90185--90211 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
90175 AATGATTTGA
90185 TAGTAATGAT
1 TAGTAATGAT
90195 TAGTAATGAT
1 TAGTAATGAT
90205 TAGTAAT
1 TAGTAAT
90212 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:90239 original size:58 final size:60
Alignment explanation
Indices: 90128--90242 Score: 180
Period size: 58 Copynumber: 1.9 Consensus size: 60
90118 GAAATTATAA
**
90128 TAATGATTTAGTAATAATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAG
1 TAATGATTTAGTAATAATTAGTAATAATGAAATTATTATTAATAGTTAATGATTTGATAG
* *
90188 TAATGA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATAGTTAATGATTTGA
1 TAATGATTTAGTAATAATTAGTAATAATGAAATTATTATTAATAGTTAATGATTTGA
90243 GATTTAATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 25 0.49
59 20 0.39
60 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (60 bp):
TAATGATTTAGTAATAATTAGTAATAATGAAATTATTATTAATAGTTAATGATTTGATAG
Found at i:91075 original size:215 final size:208
Alignment explanation
Indices: 90653--91076 Score: 767
Period size: 215 Copynumber: 2.0 Consensus size: 208
90643 GAAGTCTCAA
90653 AATTAAAGTCGTCGTCTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
1 AATTAAAGTCGTCGTCTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
*
90718 TATGAGGTTGCATGCTTCTCAACACAATTAACATTTTCTTTACGACGACCATCAAATCTGTGCAG
66 TATGAGGTTGCATGCTTCTCAACACAATTAACATTTTCTTTACGACGACCATCAAATCTGTACAG
90783 CTGGTCATGCAACCCAATCACCTGACGACGACCATCTAAGATTTGGAGGAGGTCATGATCCCATG
131 CTGGTCATGCAACCCAATCACCTGACGACGACCATCTAAGATTTGGAGGAGGTCATGATCCCATG
90848 GACTCCGCGGAAT
196 GACTCCGCGGAAT
90861 AATTAAAGTCGTCGTCTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
1 AATTAAAGTCGTCGTCTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
*
90926 TAATGTAGGTTGCATGCTTCTCAACCCAATTAACATTTTCTTTACGACGACCATCAAATCTGTAC
66 T-ATG-AGGTTGCATGCTTCTCAACACAATTAACATTTTCTTTACGACGACCATCAAATCTGTAC
90991 AGCTGGTCATGCGTCTCAACCCAATCACCTGACGACGACCATCTAAGATTTGGAGGAGGTCATGA
129 AGCTGGTCAT--G---CAACCCAATCACCTGACGACGACCATCTAAGATTTGGAGGAGGTCATGA
91056 TCCCATGGACTCCGCGGAAT
189 TCCCATGGACTCCGCGGAAT
91076 A
1 A
91077 GGTTGGTGGA
Statistics
Matches: 207, Mismatches: 2, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
208 66 0.32
209 3 0.01
210 67 0.32
212 1 0.00
215 70 0.34
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (208 bp):
AATTAAAGTCGTCGTCTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
TATGAGGTTGCATGCTTCTCAACACAATTAACATTTTCTTTACGACGACCATCAAATCTGTACAG
CTGGTCATGCAACCCAATCACCTGACGACGACCATCTAAGATTTGGAGGAGGTCATGATCCCATG
GACTCCGCGGAAT
Found at i:92606 original size:22 final size:21
Alignment explanation
Indices: 92572--92612 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
92562 TTTATGTATA
*
92572 ATATACCTTAAACTAACAATC
1 ATATACCCTAAACTAACAATC
92593 ATATAACCCTAAACTAACAA
1 ATAT-ACCCTAAACTAACAA
92613 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (21 bp):
ATATACCCTAAACTAACAATC
Found at i:92754 original size:26 final size:26
Alignment explanation
Indices: 92718--92781 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
92708 AAGAGCCTTA
*
92718 TCTCCCTTTCTTCTGCTGCAATCTCT
1 TCTCCCTTTCTTCAGCTGCAATCTCT
92744 TCTCCCTTTCTTCAGCTGCAATCTCT
1 TCTCCCTTTCTTCAGCTGCAATCTCT
92770 TCTCCCTTTCTT
1 TCTCCCTTTCTT
92782 TCTTTTATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.08, C:0.39, G:0.06, T:0.47
Consensus pattern (26 bp):
TCTCCCTTTCTTCAGCTGCAATCTCT
Found at i:93535 original size:29 final size:29
Alignment explanation
Indices: 93502--93583 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
93492 TCTGTGCAGC
* * *
93502 TCGCCGGGAAGCCATGGCGACGTAGTAGG
1 TCGCCCGGAAGGCATGGCGACCTAGTAGG
93531 TCGCCCGGAAGGCATGGCGACCTAGTAGG
1 TCGCCCGGAAGGCATGGCGACCTAGTAGG
*
93560 TCGCCCGGAAGGCATGACGACCTA
1 TCGCCCGGAAGGCATGGCGACCTA
93584 CGACCACACC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.22, C:0.28, G:0.37, T:0.13
Consensus pattern (29 bp):
TCGCCCGGAAGGCATGGCGACCTAGTAGG
Found at i:94035 original size:33 final size:33
Alignment explanation
Indices: 93993--94057 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
93983 AGGAGGACCA
* *
93993 CCTCTTGCTCCTCTGGGAGAATAGTCTTCCCTG
1 CCTCTTGCTCCTCTGGGAGAAAAGTCGTCCCTG
94026 CCTCTTGCTCCTCTGGGAGAAAAGTCGTCCCT
1 CCTCTTGCTCCTCTGGGAGAAAAGTCGTCCCT
94058 ACGAGGAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.14, C:0.34, G:0.22, T:0.31
Consensus pattern (33 bp):
CCTCTTGCTCCTCTGGGAGAAAAGTCGTCCCTG
Found at i:95017 original size:75 final size:75
Alignment explanation
Indices: 94885--95077 Score: 244
Period size: 75 Copynumber: 2.6 Consensus size: 75
94875 TAAAAACAAA
* * * * *
94885 ATTAGTAACCTTTAAACAAGCTGGTAGATATTTTAACGTAATAGGTAGCGCCTATTTTATTTTAC
1 ATTAATAACCTTTAAACAAACAGATAGATATTTTAACGTAATAGGTAGCACCTATTTTATTTTAC
*
94950 CGTTTACCTT
66 CGTTTACATT
* *
94960 ATTAATAATCTTTAAACAAACAGATAGATATTTTAATGTAATAGGTAGCACCTATTTTATTTTAC
1 ATTAATAACCTTTAAACAAACAGATAGATATTTTAACGTAATAGGTAGCACCTATTTTATTTTAC
95025 CGTTTACATT
66 CGTTTACATT
** * * * *
95035 ATTAGCAACCTTCAAACAAATC-GATAGGTAGTTTAACATAATA
1 ATTAATAACCTTTAAACAAA-CAGATAGATATTTTAACGTAATA
95078 AGCATCATTA
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
75 100 0.99
76 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (75 bp):
ATTAATAACCTTTAAACAAACAGATAGATATTTTAACGTAATAGGTAGCACCTATTTTATTTTAC
CGTTTACATT
Found at i:95115 original size:23 final size:23
Alignment explanation
Indices: 95086--95136 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
95076 TAAGCATCAT
**
95086 TATTTAACGTAATAGGTAGCGCC
1 TATTTAACAAAATAGGTAGCGCC
*
95109 TATTTAACAAAATAGGTAGCGCT
1 TATTTAACAAAATAGGTAGCGCC
95132 TATTT
1 TATTT
95137 TATTTTACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (23 bp):
TATTTAACAAAATAGGTAGCGCC
Found at i:95318 original size:74 final size:73
Alignment explanation
Indices: 95119--95346 Score: 341
Period size: 72 Copynumber: 3.1 Consensus size: 73
95109 TATTTAACAA
95119 AATAGGTAGCGCTTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGAT
1 AATAGGTAGC-C-TATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGAT
*
95184 GTTTTAACGT
64 ATTTTAACGT
* *
95194 AATAGATA-CCTATTTTATTTTACCGTTTACATTATTAGTAATCTTTAAACAAACCGGTAGATAT
1 AATAGGTAGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGATAT
*
95258 TTTAATGT
66 TTTAACGT
* * *
95266 AATAGGTAGCACTATTTTATTTTACCGTTTACATTATTAGCAACCTTCAAACAAACCGGTAGGTA
1 AATAGGTAGC-CTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGATA
* *
95331 GTTTAACAT
65 TTTTAACGT
95340 AATAGGT
1 AATAGGT
95347 GACACTTATT
Statistics
Matches: 139, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
72 66 0.47
73 2 0.01
74 64 0.46
75 7 0.05
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (73 bp):
AATAGGTAGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGATAT
TTTAACGT
Found at i:95363 original size:267 final size:268
Alignment explanation
Indices: 94885--95380 Score: 818
Period size: 267 Copynumber: 1.8 Consensus size: 268
94875 TAAAAACAAA
* * *
94885 ATTAGTAACCTTTAAACAAGCTGGTAGATATTTTAACGTAATAGGTAGCGCCTATTTTATTTTAC
1 ATTAGTAACCTTTAAACAAACCGGTAGATATTTTAACGTAATAGATA--GCCTATTTTATTTTAC
*
94950 CGTTTACCTTATTAATAATCTTTAAACAAACAGATAGATATTTTAATGTAATAGGTAGCACCTAT
64 CGTTTACATTATTAATAATCTTTAAACAAACAGATAGATATTTTAATGTAATAGGTAGCACCTAT
*
95015 TTTATTTTACCGTTTACATTATTAGCAACCTTCAAACAAATCGATAGGTAGTTTAACATAATAAG
129 TTTATTTTACCGTTTACATTATTAGCAACCTTCAAACAAACCGATAGGTAGTTTAACATAATAAG
*
95080 CATCATTATTTAACGTAATAGGTAGCGCCTATTTAACAAAATAGGTAGCGCTTATTTTATTTTAC
194 CATCATTATTTAACGTAATAGGTAGCACCTATTTAACAAAATAGGTAGCGCTTATTTTATTTTAC
95145 CGTTTACATT
259 CGTTTACATT
*
95155 ATTAGTAACCTTTAAACAAACCGGTAGATGTTTTAACGTAATAGATA-CCTATTTTATTTTACCG
1 ATTAGTAACCTTTAAACAAACCGGTAGATATTTTAACGTAATAGATAGCCTATTTTATTTTACCG
* * *
95219 TTTACATTATTAGTAATCTTTAAACAAACCGGTAGATATTTTAATGTAATAGGTAGCA-CTATTT
66 TTTACATTATTAATAATCTTTAAACAAACAGATAGATATTTTAATGTAATAGGTAGCACCTATTT
* * *
95283 TATTTTACCGTTTACATTATTAGCAACCTTCAAACAAACCGGTAGGTAGTTTAACATAATAGGTG
131 TATTTTACCGTTTACATTATTAGCAACCTTCAAACAAACCGATAGGTAGTTTAACATAATAAG-C
95348 A-CACTTATTTAACGTAATAGGTAGCACCTATTT
195 ATCA-TTATTTAACGTAATAGGTAGCACCTATTT
95381 TATTTTACCG
Statistics
Matches: 211, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
266 68 0.32
267 100 0.47
270 43 0.20
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (268 bp):
ATTAGTAACCTTTAAACAAACCGGTAGATATTTTAACGTAATAGATAGCCTATTTTATTTTACCG
TTTACATTATTAATAATCTTTAAACAAACAGATAGATATTTTAATGTAATAGGTAGCACCTATTT
TATTTTACCGTTTACATTATTAGCAACCTTCAAACAAACCGATAGGTAGTTTAACATAATAAGCA
TCATTATTTAACGTAATAGGTAGCACCTATTTAACAAAATAGGTAGCGCTTATTTTATTTTACCG
TTTACATT
Found at i:95379 original size:23 final size:23
Alignment explanation
Indices: 95332--95380 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
95322 CGGTAGGTAG
*
95332 TTTAACATAATAGGTGACACTTA
1 TTTAACATAATAGGTGACACCTA
*
95355 TTTAACGTAATAGGT-AGCACCTA
1 TTTAACATAATAGGTGA-CACCTA
95378 TTT
1 TTT
95381 TATTTTACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (23 bp):
TTTAACATAATAGGTGACACCTA
Found at i:95387 original size:172 final size:172
Alignment explanation
Indices: 95186--95553 Score: 575
Period size: 173 Copynumber: 2.1 Consensus size: 172
95176 CGGTAGATGT
* *
95186 TTTAACGTAATAG-A-TACCTATTTTATTTTACCGTTTACATTATTAGTAATC-TTTAAACAAAC
1 TTTAACGTAATAGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAA-CATTTAAACAAAA
*
95248 CGGTAGATATTTTAATGTAATAGGTAGC-ACTATTTTATTTTACCGTTTACATTATTAGCAACCT
65 CGGTAGATATTTTAATGTAATAGGTAGCGACTATTTTATTTTACCGTTTACATTATTAACAACCT
*
95312 TCAAACAAACCGGTAGGTAGTTTAACATAATAGGT-GACACTTA
130 TCAAACAAACCGGTAGGTAGTTTAACATAATAGATAG-CACTTA
*
95355 TTTAACGTAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAATCAAAA
1 TTTAACGTAATA-GTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAA
* * *
95420 TGGTAGATATTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACCT
65 CGGTAGATATTTTAATGTAATAGGTAGCGACTATTTTATTTTACCGTTTACATTATTAACAACCT
*
95485 TCAAACAAACCGGTAGGTAGTTTAACATAATAGATAGCGCTTA
130 TCAAACAAACCGGTAGGTAGTTTAACATAATAGATAGCACTTA
*
95528 TTTAACGTAATATGTAGCACTTATTT
1 TTTAACGTAATA-GTAGCACCTATTT
95554 AACGTAATAG
Statistics
Matches: 182, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
169 12 0.07
170 1 0.01
171 2 0.01
172 70 0.38
173 96 0.53
174 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (172 bp):
TTTAACGTAATAGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAAC
GGTAGATATTTTAATGTAATAGGTAGCGACTATTTTATTTTACCGTTTACATTATTAACAACCTT
CAAACAAACCGGTAGGTAGTTTAACATAATAGATAGCACTTA
Found at i:95425 original size:98 final size:97
Alignment explanation
Indices: 95258--95444 Score: 266
Period size: 98 Copynumber: 1.9 Consensus size: 97
95248 CGGTAGATAT
* * *
95258 TTTAATGTAATAGGTAGCACTATTTTATTTTACCGTTTACATTATTAGCAACCTTCAAACAAACC
1 TTTAACGTAATAGGTAGCACTATTTTATTTTACCGTTTACATTATTAGCAACATTCAAACAAAAC
*
95323 GGTAGGTAGTTTAACATAATAGGTGACACTTA
66 GGTAGATAGTTTAACATAATAGGTGACACTTA
* * *
95355 TTTAACGTAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAATCAAAA
1 TTTAACGTAATAGGTAGCA-CTATTTTATTTTACCGTTTACATTATTAGCAACATTCAAACAAAA
* * **
95420 TGGTAGATATTTTAATGTAATAGGT
65 CGGTAGATAGTTTAACATAATAGGT
95445 AGCGCCTATT
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 18 0.23
98 60 0.77
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (97 bp):
TTTAACGTAATAGGTAGCACTATTTTATTTTACCGTTTACATTATTAGCAACATTCAAACAAAAC
GGTAGATAGTTTAACATAATAGGTGACACTTA
Found at i:95500 original size:75 final size:75
Alignment explanation
Indices: 95355--95530 Score: 235
Period size: 75 Copynumber: 2.3 Consensus size: 75
95345 GTGACACTTA
* * * *
95355 TTTAACGTAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAATCAAAA
1 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACATTCAAACAAAA
* *
95420 TGGTAGATAT
66 CGGTAGATAG
* * *
95430 TTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
1 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACATTCAAACAAAA
*
95495 CGGTAGGTAG
66 CGGTAGATAG
* * *
95505 TTTAACATAATAGATAGCGCTTATTT
1 TTTAACGTAATAGGTAGCGCCTATTT
95531 AACGTAATAT
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 87 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40
Consensus pattern (75 bp):
TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACATTCAAACAAAA
CGGTAGATAG
Found at i:95538 original size:23 final size:22
Alignment explanation
Indices: 95505--95576 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 22
95495 CGGTAGGTAG
*
95505 TTTAACATAATAGATAGCGCTTA
1 TTTAACGTAATAG-TAGCGCTTA
*
95528 TTTAACGTAATATGTAGCACTTA
1 TTTAACGTAATA-GTAGCGCTTA
*
95551 TTTAACGTAATAGGTAGCGCCTA
1 TTTAACGTAATA-GTAGCGCTTA
95574 TTT
1 TTT
95577 TATTTTACCG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (22 bp):
TTTAACGTAATAGTAGCGCTTA
Found at i:95574 original size:121 final size:122
Alignment explanation
Indices: 95430--95652 Score: 358
Period size: 121 Copynumber: 1.8 Consensus size: 122
95420 TGGTAGATAT
* *
95430 TTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
1 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACATTCAAACAAAC
*
95495 CGGTAGGTA-GTTTAACATAATAGATAGCGCTTATTTAACGTAATATGTAGCACTTA
66 CGGTAGGTATGTTTAACATAATAGATAGCGCCTATTTAACGTAATATGTAGCACTTA
* * *
95551 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAT
1 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACATTCAAACAAAC
* * *
95616 CGGTAGGTATTTTTAACGTAATAGGTAGCGCCTATTT
66 CGGTAGGTATGTTTAACATAATAGATAGCGCCTATTT
95653 TATTTTACCG
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
121 69 0.75
122 23 0.25
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (122 bp):
TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAACATTCAAACAAAC
CGGTAGGTATGTTTAACATAATAGATAGCGCCTATTTAACGTAATATGTAGCACTTA
Found at i:95589 original size:196 final size:198
Alignment explanation
Indices: 95332--95729 Score: 615
Period size: 196 Copynumber: 2.0 Consensus size: 198
95322 CGGTAGGTAG
95332 TTTAACATAATAGGTGACACTTATTTAACGTAATAGGTAGCACCTATTTTATTTTACCGTTTACA
1 TTTAACATAATAGGTGACACTTATTTAACGTAATAGGTAGCACCTATTTTATTTTACCGTTTACA
* *
95397 TTATTAGTAACATTTAATCAAAAT-GGTAGATA-TTTTAATGTAATAGGTAGCGCCTATTTTATT
66 TTATTAGTAACATTTAAAC-AAATCGGTAGATATTTTTAACGTAATAGGTAGCGCCTATTTTATT
*
95460 TTACCGTTTACATTATTAATAACCTTCAAACAAACCGGTAGGTA-GTTTAACATAATAGATAGCG
130 TTACCGTTTACATTATTAATAACATTCAAACAAACCGGTAGGTATGTTTAACATAATAGATAGCG
*
95524 CTTA
195 CCTA
* * *
95528 TTTAACGTAATATGT-AGCACTTATTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTAC
1 TTTAACATAATAGGTGA-CACTTATTTAACGTAATAGGTAGCACCTATTTTATTTTACCGTTTAC
*
95592 ATTATTAGTAACATTTAAACAAATCGGTAGGTATTTTTAACGTAATAGGTAGCGCCTATTTTATT
65 ATTATTAGTAACATTTAAACAAATCGGTAGATATTTTTAACGTAATAGGTAGCGCCTATTTTATT
* * * * ** *
95657 TTACCGTTTACATTATTAGTAACATTTAAACAAATCGGTAGGTATTTTTAATGTAATAGGTAGCG
130 TTACCGTTTACATTATTAATAACATTCAAACAAACCGGTAGGTATGTTTAACATAATAGATAGCG
95722 CCTA
195 CCTA
95726 TTTA
1 TTTA
95730 TTTTACTGTT
Statistics
Matches: 183, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
195 5 0.03
196 85 0.46
197 70 0.38
198 23 0.13
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (198 bp):
TTTAACATAATAGGTGACACTTATTTAACGTAATAGGTAGCACCTATTTTATTTTACCGTTTACA
TTATTAGTAACATTTAAACAAATCGGTAGATATTTTTAACGTAATAGGTAGCGCCTATTTTATTT
TACCGTTTACATTATTAATAACATTCAAACAAACCGGTAGGTATGTTTAACATAATAGATAGCGC
CTA
Found at i:95805 original size:75 final size:76
Alignment explanation
Indices: 95551--95809 Score: 414
Period size: 76 Copynumber: 3.4 Consensus size: 76
95541 GTAGCACTTA
95551 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAT
1 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAT
95616 CGGTAGGTATT
66 CGGTAGGTATT
95627 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAT
1 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAT
95692 CGGTAGGTATT
66 CGGTAGGTATT
* * * *
95703 TTTAATGTAATAGGTAGCGCCTA-TTTATTTTACTGTTTACATTATTAGTAACATTCAAACAAAC
1 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAT
* * *
95767 CAGTAAGTA-G
66 CGGTAGGTATT
* * *
95777 TTTAACATAATAAGTAGCACCTATTTTATTTTA
1 TTTAACGTAATAGGTAGCGCCTATTTTATTTTA
95810 ACCGGTTAAG
Statistics
Matches: 171, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
74 19 0.11
75 54 0.32
76 98 0.57
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (76 bp):
TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAT
CGGTAGGTATT
Found at i:97158 original size:12 final size:12
Alignment explanation
Indices: 97143--97187 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
97133 GAAATCAAAA
97143 CAGAATTCAGAT
1 CAGAATTCAGAT
*
97155 CAG-ATATCAGAA
1 CAGAAT-TCAGAT
*
97167 CAGAATCCAGAT
1 CAGAATTCAGAT
97179 CAGAATTCA
1 CAGAATTCA
97188 AGTAATGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 2 0.07
12 23 0.85
13 2 0.07
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAT
Found at i:97163 original size:24 final size:24
Alignment explanation
Indices: 97131--97188 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
97121 AAGGAAATAC
*
97131 CAGAAATCAAAACAGAATTCAGAT
1 CAGAAATCAAAACAGAATCCAGAT
* *
97155 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATCCAGAT
*
97179 CAGAATTCAA
1 CAGAAATCAA
97189 GTAATGTATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATCCAGAT
Found at i:105149 original size:3 final size:3
Alignment explanation
Indices: 105141--105212 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
105131 ATATTTATTA
*
105141 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
**
105187 AAT TTT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
105213 AACGAAATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 52 0.87
4 6 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:106162 original size:22 final size:22
Alignment explanation
Indices: 106126--106201 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
106116 CATAAAGCTT
106126 TCATC-TTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
106147 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
106169 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
106191 TCATCTTTGAA
1 TCATCTTTGAA
106202 GAGTATAGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
21 5 0.10
22 47 0.90
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:110459 original size:9 final size:9
Alignment explanation
Indices: 110445--110508 Score: 61
Period size: 9 Copynumber: 7.9 Consensus size: 9
110435 CTTGATTCAA
110445 TTTTCCTTT
1 TTTTCCTTT
110454 TTTTCC-TT
1 TTTTCCTTT
110462 TTTT-C--T
1 TTTTCCTTT
*
110468 TTTT-ATTT
1 TTTTCCTTT
110476 TTTTCCTTT
1 TTTTCCTTT
110485 TTTTCCTTT
1 TTTTCCTTT
*
110494 TTGT--TTT
1 TTTTCCTTT
110501 TTTTCCTT
1 TTTTCCTT
110509 CTTCTTTCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
6 5 0.11
7 7 0.15
8 11 0.24
9 23 0.50
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTCCTTT
Found at i:110469 original size:16 final size:16
Alignment explanation
Indices: 110445--110508 Score: 78
Period size: 16 Copynumber: 4.1 Consensus size: 16
110435 CTTGATTCAA
110445 TTTTCCTTTTTTTCCT
1 TTTTCCTTTTTTTCCT
*
110461 TTTTTCTTTTTATT--T
1 TTTTCCTTTTT-TTCCT
110476 TTTTCCTTTTTTTCCT
1 TTTTCCTTTTTTTCCT
**
110492 TTTTGTTTTTTTTCCT
1 TTTTCCTTTTTTTCCT
110508 T
1 T
110509 CTTCTTTCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 2 0.05
15 11 0.27
16 26 0.63
17 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTCCTTTTTTTCCT
Found at i:110488 original size:25 final size:25
Alignment explanation
Indices: 110451--110519 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
110441 TCAATTTTCC
110451 TTTTTTT-C-CTTTTTTCTTTTT-A
1 TTTTTTTCCTCTTTTTTCTTTTTGA
*
110473 TTTTTTTCCT-TTTTTTCCTTTTTGT
1 TTTTTTTCCTCTTTTTT-CTTTTTGA
*
110498 TTTTTTTCCTTCTTCTTTCTTT
1 TTTTTTTCC-TCTTTTTTCTTT
110520 GCTGGATGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 7 0.18
23 7 0.18
24 6 0.15
25 9 0.23
26 5 0.13
27 5 0.13
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (25 bp):
TTTTTTTCCTCTTTTTTCTTTTTGA
Found at i:117443 original size:3 final size:3
Alignment explanation
Indices: 117435--117493 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
117425 ATGTTTATTA
**
117435 AAT AAT AAT -AT ATAT AAT ATAT AAT AAT AAT AAT -AT TTT AAT AAT
1 AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
117480 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
117494 AAGGAAATGA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:117877 original size:30 final size:31
Alignment explanation
Indices: 117818--117892 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
117808 AAGAATTAAA
117818 AGTTTA-GTTACTAAAATGGAGCAAAAACGAT
1 AGTTTATG-TACTAAAATGGAGCAAAAACGAT
117849 AGTTTATGTACTAAAATGGAGC-AAAACGAT
1 AGTTTATGTACTAAAATGGAGCAAAAACGAT
117879 AG-TTATGTACTAAA
1 AGTTTATGTACTAAA
117893 CAAGTTAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
29 12 0.28
30 10 0.23
31 20 0.47
32 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (31 bp):
AGTTTATGTACTAAAATGGAGCAAAAACGAT
Found at i:118365 original size:39 final size:40
Alignment explanation
Indices: 118268--118371 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 40
118258 ATATATTCTT
*
118268 TTTTAAAATAATTAAAATAATATATTTTATAATTATTTATTATA
1 TTTT-AAATAATT-AAAT-A-ATATTTTATAATTAATTATTATA
** *
118312 TTTTAAATGGTTAAATTAATATTTTATGA-TAATT-TTATA
1 TTTTAAATAATTAAA-TAATATTTTATAATTAATTATTATA
*
118351 TTTTAATTAATTAAATAATAT
1 TTTTAAATAATTAAATAATAT
118372 AAAATAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
38 6 0.12
39 17 0.33
40 4 0.08
41 10 0.19
42 4 0.08
43 7 0.13
44 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (40 bp):
TTTTAAATAATTAAATAATATTTTATAATTAATTATTATA
Found at i:120345 original size:19 final size:19
Alignment explanation
Indices: 120318--120360 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
120308 TTTATTCAAA
*
120318 ATAAGAAATATCTTA-AATT
1 ATAATAAATAT-TTACAATT
120337 ATAATAAATATTTACAATT
1 ATAATAAATATTTACAATT
120356 ATAAT
1 ATAAT
120361 CGTAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAATAAATATTTACAATT
Found at i:121993 original size:56 final size:56
Alignment explanation
Indices: 121883--122015 Score: 144
Period size: 56 Copynumber: 2.4 Consensus size: 56
121873 GATTTCTTAT
* * * *
121883 TAAATATATTTTATTTTTATATTAACTTATTAAATATATTTTATTCTTGTTTAACC
1 TAAATATATTTTATTCTTATATTAAATTATAAAATATATTTTATTCTTATTTAACC
* * * *
121939 TAAATATATTTTATCCTTATTTTAAATTA-AAAATATA-TTTAGTTTTTATCTTAACT
1 TAAATATATTTTATTCTTATATTAAATTATAAAATATATTTTA-TTCTTAT-TTAACC
*
121995 TAAAAAATATTTTATTCTTAT
1 T-AAATATATTTTATTCTTAT
122016 CATAACTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
54 4 0.06
55 12 0.19
56 31 0.48
57 17 0.27
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.55
Consensus pattern (56 bp):
TAAATATATTTTATTCTTATATTAAATTATAAAATATATTTTATTCTTATTTAACC
Found at i:122004 original size:28 final size:29
Alignment explanation
Indices: 121884--122023 Score: 137
Period size: 29 Copynumber: 4.9 Consensus size: 29
121874 ATTTCTTATT
* * *
121884 AAATATATTTTATTTTTATATTAACTTATT
1 AAATATATTTTATTCTTATCTTAACTTA-A
* *
121914 AAATATATTTTATTCTTGT-TTAACCT--
1 AAATATATTTTATTCTTATCTTAACTTAA
* * *
121940 AAATATATTTTATCCTTATTTTAAATTAA
1 AAATATATTTTATTCTTATCTTAACTTAA
*
121969 AAATATA-TTTAGTTTTTATCTTAACTTAA
1 AAATATATTTTA-TTCTTATCTTAACTTAA
*
121998 AAA-ATATTTTATTCTTATCATAACTT
1 AAATATATTTTATTCTTATCTTAACTT
122024 TTATATTTTG
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
26 17 0.18
27 5 0.05
28 20 0.22
29 33 0.36
30 17 0.18
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (29 bp):
AAATATATTTTATTCTTATCTTAACTTAA
Found at i:122076 original size:26 final size:25
Alignment explanation
Indices: 122039--122087 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
122029 TTTTGTTATG
* *
122039 ATAATATTTTAAATTTAAGATAAAAT
1 ATAATATATTAAA-TTAAAATAAAAT
122065 ATAATATATTAAATTAAAATAAA
1 ATAATATATTAAATTAAAATAAA
122088 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
ATAATATATTAAATTAAAATAAAAT
Found at i:122363 original size:20 final size:19
Alignment explanation
Indices: 122318--122366 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
122308 GTGTCACTGG
*
122318 TATAATTTACCTTTTATTT
1 TATAATTTACCTTTAATTT
*
122337 TAAATAATTTATCTTTAAATTT
1 T--ATAATTTACCTTT-AATTT
122359 TATAATTT
1 TATAATTT
122367 TACGTTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 7 0.28
21 12 0.48
22 5 0.20
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
TATAATTTACCTTTAATTT
Found at i:125875 original size:3 final size:3
Alignment explanation
Indices: 125867--125926 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
125857 CTGTTTGTAT
*
125867 ATA ATA ATA CTAA ATA A-A ATA ATA ATA ATA ATA ATA ATA TATA A-A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
125912 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
125927 GAAAATGGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 42 0.82
4 5 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:125902 original size:27 final size:27
Alignment explanation
Indices: 125867--125926 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
125857 CTGTTTGTAT
*
125867 ATAATAATACTAAATAAAATAATAATA
1 ATAATAATAATAAATAAAATAATAATA
*
125894 ATAATAATAATATATAAAATAATAATA
1 ATAATAATAATAAATAAAATAATAATA
125921 ATAATA
1 ATAATA
125927 GAAAATGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAATAATAATAAATAAAATAATAATA
Found at i:126421 original size:124 final size:122
Alignment explanation
Indices: 126127--126461 Score: 469
Period size: 124 Copynumber: 2.7 Consensus size: 122
126117 GGGATGATAA
* * * *
126127 TATCTCCTTCTATGA-CGTAATT-TGGAAAAGAGTTAAACAAGTTCTTCTCATTATGAACTTCTT
1 TATCTCCTTCTATGATAG-AATTATGAAAAAG-GTTGAACAAGATCTTCTCATTATGAACTTCTT
*
126190 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAAAAGTTGATGCTGATC
64 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAAAAGTTGATACTGATC
* * * *
126249 TATCTCCTTCTATGATAGAGTCATGAAAAAGGTTGAACAAAATTTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTATGATAGAATTATGAAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTTCT
*
126314 TCC-TCATTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATTTGATACTGATC
66 TCCTTC-TTCAGATGAGTTCTTCTCATTATGAAC-TT-TCTGGAAAAGTTGATACTGATC
* * * *
126373 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTCCT
1 TATCTCCTTCTATGATAGAATTATGAAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTTCT
*
126438 TCCTTCTTTAGATGAGTTCTTCTC
66 TCCTTCTTCAGATGAGTTCTTCTC
126462 TATCTGGCAA
Statistics
Matches: 188, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
121 2 0.01
122 77 0.41
123 10 0.05
124 97 0.52
125 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (122 bp):
TATCTCCTTCTATGATAGAATTATGAAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAAAAGTTGATACTGATC
Found at i:126510 original size:102 final size:101
Alignment explanation
Indices: 126397--126789 Score: 369
Period size: 113 Copynumber: 3.6 Consensus size: 101
126387 ATAGAATTAT
* * * *
126397 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTCCTTCCTTCTTTAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
126462 TATCTGGCAATGTTGATCCATAGAATGATGAATTCAA
66 TATCTGG-AATGTTGATCCATAGAATGATGAATTCAA
*
126499 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * **
126564 -AT-TATGAA-CTTGACCTGGCAATGCTGACCCATCGAATGATGAATTCA
66 TATCT-GGAATGTTGA--T--CCAT--AGA---AT-G-ATGA--ATTCAA
*
126611 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
126676 CATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAA
65 C----T--A-T----CTGG-AATGTTGATCCATAGAATGATGAATTCAA
*
126725 GCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
126790 ATTATGAACT
Statistics
Matches: 237, Mismatches: 24, Indels: 49
0.76 0.08 0.16
Matches are distributed among these distances:
99 4 0.02
100 3 0.01
101 4 0.02
102 60 0.25
103 3 0.01
105 2 0.01
108 2 0.01
109 1 0.00
110 4 0.02
112 3 0.01
113 126 0.53
114 3 0.01
116 4 0.02
117 1 0.00
118 2 0.01
120 1 0.00
121 3 0.01
123 3 0.01
125 2 0.01
126 3 0.01
127 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (101 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
TATCTGGAATGTTGATCCATAGAATGATGAATTCAA
Found at i:126663 original size:113 final size:113
Alignment explanation
Indices: 126465--126830 Score: 651
Period size: 113 Copynumber: 3.2 Consensus size: 113
126455 TCTTCTCTAT
* * *
126465 CTGGCAATGTTGATCCATAGAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATG
1 CTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
*
126530 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
*
126578 CTGGCAATGCTGACCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
1 CTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
*
126643 AACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
* *
126691 CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATG
1 CTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
126756 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
66 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
*
126804 CTGGTAATGCTGATCCATCGAATGATG
1 CTGGCAATGCTGATCCATCGAATGATG
126831 GTTTTGAACT
Statistics
Matches: 243, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 243 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (113 bp):
CTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
Found at i:127747 original size:115 final size:114
Alignment explanation
Indices: 127541--127764 Score: 376
Period size: 115 Copynumber: 2.0 Consensus size: 114
127531 GATCATGCAG
* *
127541 TTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
127606 ACACTTCCAGAAGATTCTATTAGGCCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTAGGCCTCCTTATTTCTACCATGAGCAAA
* *
127655 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTTATACCAAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACC-AAACCAGATCAGATAACTCAAAG
*
127720 AACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
65 AACACTTCCAGAAGATGCTATTAGGCCTCCTTATTTCTACCATGA
127765 TAACGTGGCA
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 37 0.36
115 65 0.64
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTAGGCCTCCTTATTTCTACCATGAGCAAA
Found at i:128517 original size:25 final size:25
Alignment explanation
Indices: 128489--128551 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
128479 CCCCCTTTTT
128489 TTCTTTTTTTATTTTC-TTCTTCTTC
1 TTCTTTTTTT-TTTTCTTTCTTCTTC
* * *
128514 TTCTCTCTTTTTTTCTTTCTTTTTC
1 TTCTTTTTTTTTTTCTTTCTTCTTC
*
128539 TTCTTTTCTTTTT
1 TTCTTTTTTTTTT
128552 CTTCAAGCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (25 bp):
TTCTTTTTTTTTTTCTTTCTTCTTC
Found at i:128524 original size:28 final size:26
Alignment explanation
Indices: 128487--128551 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 26
128477 GACCCCCTTT
*
128487 TTTTCTTTTTTTATTTTCTTCTTCTTC
1 TTTTCTTTTTTT-CTTTCTTCTTCTTC
*
128514 TTCTCTCTTTTTTTCTTTCTTTTTCTTC
1 TT-T-TCTTTTTTTCTTTCTTCTTCTTC
128542 TTTTCTTTTT
1 TTTTCTTTTT
128552 CTTCAAGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 7 0.21
27 3 0.09
28 15 0.44
29 9 0.26
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTCTTTTTTTCTTTCTTCTTCTTC
Found at i:128524 original size:37 final size:36
Alignment explanation
Indices: 128483--128553 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
128473 TCTTGACCCC
*
128483 CTTTTTTTCTTT-TTTTATTTTCTTCTTCTTCTTCTCT
1 CTTTTTTTCTTTCTTTT-TCTTCTT-TTCTTCTTCTCT
*
128520 CTTTTTTTCTTTCTTTTTCTTCTTTTCTTTTTCT
1 CTTTTTTTCTTTCTTTTTCTTCTTTTCTTCTTCT
128554 TCAAGCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 9 0.29
37 18 0.58
38 4 0.13
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (36 bp):
CTTTTTTTCTTTCTTTTTCTTCTTTTCTTCTTCTCT
Found at i:141476 original size:3 final size:3
Alignment explanation
Indices: 141468--141526 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
141458 GGCCTGTTTG
*
141468 TAA TAA TAA TAA TAC TAAA TAA -AA TAA TAA TAA TAA TATA TAA -AA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
141513 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
141527 GAAAATGGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.82
4 5 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:141500 original size:24 final size:21
Alignment explanation
Indices: 141469--141526 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
141459 GCCTGTTTGT
* *
141469 AATAATAATAATACTAAATAA
1 AATAATAATAATAATATATAA
141490 AATAATAATAATAATATATAA
1 AATAATAATAATAATATATAA
141511 AATAATAATAATAATA
1 AATAATAATAATAATA
141527 GAAAATGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AATAATAATAATAATATATAA
Found at i:144578 original size:13 final size:13
Alignment explanation
Indices: 144560--144630 Score: 85
Period size: 13 Copynumber: 5.5 Consensus size: 13
144550 CAACGGTCAA
144560 CGGGTCAACGGGT
1 CGGGTCAACGGGT
144573 CGGGTCAACGGGT
1 CGGGTCAACGGGT
144586 CGGGT---CGGGT
1 CGGGTCAACGGGT
144596 CAACGGGTCAACGGGT
1 ---CGGGTCAACGGGT
*
144612 CGGGTAAACGGGT
1 CGGGTCAACGGGT
144625 CGGGTC
1 CGGGTC
144631 GGGTTGTGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
10 5 0.10
13 40 0.80
16 5 0.10
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:144599 original size:39 final size:39
Alignment explanation
Indices: 144554--144634 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
144544 ACGGGTCAAC
*
144554 GGTCAACGGGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAACGGGTCGGGTAAACGGGTCGGGTCG
144593 GGTCAACGGGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCAACGGGTCGGGTAAACGGGTCGGGTCG
144632 GGT
1 GGT
144635 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (39 bp):
GGTCAACGGGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:144624 original size:8 final size:8
Alignment explanation
Indices: 144544--144612 Score: 74
Period size: 8 Copynumber: 8.9 Consensus size: 8
144534 CATCTGAGTC
144544 ACGGGTCA
1 ACGGGTCA
144552 AC-GGTCA
1 ACGGGTCA
144559 ACGGGTCA
1 ACGGGTCA
144567 ACGGGT--
1 ACGGGTCA
144573 -CGGGTCA
1 ACGGGTCA
*
144580 ACGGGTCGGG
1 ACGGGTC--A
*
144590 TCGGGTCA
1 ACGGGTCA
144598 ACGGGTCA
1 ACGGGTCA
144606 ACGGGTC
1 ACGGGTC
144613 GGGTAAACGG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
5 5 0.10
7 7 0.14
8 33 0.65
10 6 0.12
ACGTcount: A:0.19, C:0.25, G:0.42, T:0.14
Consensus pattern (8 bp):
ACGGGTCA
Found at i:146202 original size:24 final size:24
Alignment explanation
Indices: 146175--146231 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
146165 GTTTGCTTAT
146175 ATTCATTTACAAAAT-TATTTATTA
1 ATTCATTTACAAAATCT-TTTATTA
* *
146199 ATTCATTTATAAACTCTTTTATTA
1 ATTCATTTACAAAATCTTTTATTA
*
146223 GTTCATTTA
1 ATTCATTTA
146232 TTAAAATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTCATTTACAAAATCTTTTATTA
Done.