Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 95 of 199
Found at i:29058421 original size:15 final size:15
Alignment explanation
Indices: 29058401--29058434 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
29058391 TAATTACGTA
29058401 AATTAAATAACTTTG
1 AATTAAATAACTTTG
29058416 AATTAAATAACTTTG
1 AATTAAATAACTTTG
29058431 AATT
1 AATT
29058435 CTGTCGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTAAATAACTTTG
Found at i:29060915 original size:29 final size:29
Alignment explanation
Indices: 29060883--29060957 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
29060873 CCTAAACACT
* *
29060883 AAATCCCTAACTCCTAACCCTTAAATCCC
1 AAATCCCTAACCCCTAACCCCTAAATCCC
* *
29060912 AAATCCCAAACCCCAAACCCCTAAATCCC
1 AAATCCCTAACCCCTAACCCCTAAATCCC
* *
29060941 TAACCCCTAACCCCTAA
1 AAATCCCTAACCCCTAA
29060958 ACCAATAAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.17
Consensus pattern (29 bp):
AAATCCCTAACCCCTAACCCCTAAATCCC
Found at i:29060923 original size:22 final size:22
Alignment explanation
Indices: 29060912--29060958 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
29060902 CTTAAATCCC
29060912 AAATCCCAAACCCCAAACCCCT
1 AAATCCCAAACCCCAAACCCCT
* *
29060934 AAATCCCTAACCCCTAACCCCT
1 AAATCCCAAACCCCAAACCCCT
29060956 AAA
1 AAA
29060959 CCAATAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.13
Consensus pattern (22 bp):
AAATCCCAAACCCCAAACCCCT
Found at i:29060947 original size:15 final size:15
Alignment explanation
Indices: 29060898--29060950 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
29060888 CCTAACTCCT
*
29060898 AACCCTTAAATCCCA
1 AACCCCTAAATCCCA
* *
29060913 AATCCC-AAACCCCA
1 AACCCCTAAATCCCA
*
29060927 AACCCCTAAATCCCT
1 AACCCCTAAATCCCA
29060942 AACCCCTAA
1 AACCCCTAA
29060951 CCCCTAAACC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.15
Consensus pattern (15 bp):
AACCCCTAAATCCCA
Found at i:29060948 original size:7 final size:7
Alignment explanation
Indices: 29060887--29061010 Score: 59
Period size: 7 Copynumber: 17.1 Consensus size: 7
29060877 AACACTAAAT
29060887 CCCTAAC
1 CCCTAAC
*
29060894 TCCTAAC
1 CCCTAAC
* *
29060901 CCTTAAAT
1 CCCT-AAC
* *
29060909 CCCAAAT
1 CCCTAAC
*
29060916 CCCAAAC
1 CCCTAAC
*
29060923 CCCAAAC
1 CCCTAAC
*
29060930 CCCTAAAT
1 CCCT-AAC
29060938 CCCTAAC
1 CCCTAAC
29060945 CCCTAAC
1 CCCTAAC
29060952 CCCTAAAC
1 CCCT-AAC
** *
29060960 CAATAAA
1 CCCTAAC
*
29060967 CCTTAAAC
1 CCCT-AAC
*
29060975 TCCTAAC
1 CCCTAAC
***
29060982 TTTTAAC
1 CCCTAAC
*
29060989 CTCTAAC
1 CCCTAAC
29060996 CCCTAAC
1 CCCTAAC
29061003 CCCTAAC
1 CCCTAAC
29061010 C
1 C
29061011 AATAAACTTT
Statistics
Matches: 90, Mismatches: 23, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
7 71 0.79
8 19 0.21
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.20
Consensus pattern (7 bp):
CCCTAAC
Found at i:29061640 original size:40 final size:39
Alignment explanation
Indices: 29061548--29061641 Score: 136
Period size: 39 Copynumber: 2.4 Consensus size: 39
29061538 GGGCTTAGGC
*
29061548 TTTTT-GCGGCGCTTTCCAAAAAACGCCGCTAATGCTTA
1 TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTTA
* *
29061586 TTTTTAGCGGCGTTTTCCAACAATCGCCGCTAATGCTTAA
1 TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTT-A
*
29061626 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
29061642 TTGTCCAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 5 0.10
39 29 0.58
40 16 0.32
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTTA
Found at i:29061994 original size:22 final size:22
Alignment explanation
Indices: 29061969--29062010 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29061959 TATATTCATC
29061969 TCACAAAAGAATTTGAAAATGA
1 TCACAAAAGAATTTGAAAATGA
* **
29061991 TCACCAAAGTTTTTGAAAAT
1 TCACAAAAGAATTTGAAAAT
29062011 AAATTATTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (22 bp):
TCACAAAAGAATTTGAAAATGA
Found at i:29063140 original size:29 final size:29
Alignment explanation
Indices: 29063107--29063162 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
29063097 ACCATGGACC
29063107 ATGGACTATGGACTATGGTTTCTAAGACT
1 ATGGACTATGGACTATGGTTTCTAAGACT
29063136 ATGGACTATGGACTATGGTTTCTAAGA
1 ATGGACTATGGACTATGGTTTCTAAGA
29063163 TTTTACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (29 bp):
ATGGACTATGGACTATGGTTTCTAAGACT
Found at i:29063142 original size:7 final size:7
Alignment explanation
Indices: 29063092--29063153 Score: 63
Period size: 7 Copynumber: 8.7 Consensus size: 7
29063082 AGATTTTATA
29063092 TATGGAC
1 TATGGAC
*
29063099 CATGGAC
1 TATGGAC
*
29063106 CATGGAC
1 TATGGAC
29063113 TATGGAC
1 TATGGAC
*
29063120 TATGGTTTC
1 TATGG--AC
*
29063129 TA-AGAC
1 TATGGAC
29063135 TATGGAC
1 TATGGAC
29063142 TATGGAC
1 TATGGAC
29063149 TATGG
1 TATGG
29063154 TTTCTAAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
6 3 0.07
7 39 0.85
8 1 0.02
9 3 0.07
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (7 bp):
TATGGAC
Found at i:29065164 original size:110 final size:110
Alignment explanation
Indices: 29064936--29065230 Score: 425
Period size: 110 Copynumber: 2.7 Consensus size: 110
29064926 GATAAACGAG
* * * * *
29064936 AAATCGAAACCCAGCACCTTAGGACACG-TTCCTCGAATTTCCAAACACAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* * * * *
29065000 TTG-AAATTTTTGAAGGGGTATTTAGCTATTTGGTTGAATGAGAA
66 TTGAAAATTTTAGAAGGGATATTAAGCCATTTGGTTGAACGAGAA
*
29065044 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
29065109 TTGAAAATTTTAAGAA-GGATATTAAGCCATTTGGTTGAACGAGAA
66 TTGAAAATTTT-AGAAGGGATATTAAGCCATTTGGTTGAACGAGAA
* *
29065154 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGTAAAATATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
29065219 TAGAAATATTTT
66 TTGAAA-ATTTT
29065231 CCTTTTTTGA
Statistics
Matches: 168, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
108 25 0.15
109 36 0.21
110 99 0.59
111 8 0.05
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (110 bp):
AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTGAAAATTTTAGAAGGGATATTAAGCCATTTGGTTGAACGAGAA
Found at i:29065227 original size:18 final size:17
Alignment explanation
Indices: 29065204--29065246 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
29065194 TCCAAACGTA
29065204 AAATATTGCCTTATTTAG
1 AAATATTGCCTT-TTTAG
* *
29065222 AAATATTTTCCTTTTTTG
1 AAATA-TTGCCTTTTTAG
29065240 AAATATT
1 AAATATT
29065247 AAGTGGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (17 bp):
AAATATTGCCTTTTTAG
Found at i:29065704 original size:13 final size:13
Alignment explanation
Indices: 29065685--29065715 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29065675 TATGAATCAT
29065685 AATATATAAAATA
1 AATATATAAAATA
*
29065698 CATATATAAAATA
1 AATATATAAAATA
29065711 AATAT
1 AATAT
29065716 TTTAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATATAAAATA
Found at i:29065863 original size:3 final size:3
Alignment explanation
Indices: 29065855--29065888 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
29065845 ATATAAAAGC
*
29065855 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29065889 TGAAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29071140 original size:23 final size:22
Alignment explanation
Indices: 29071111--29071160 Score: 77
Period size: 20 Copynumber: 2.3 Consensus size: 22
29071101 AATTCTAAAT
29071111 AATATTCTTCACATATTATTGAA
1 AATATT-TTCACATATTATTGAA
29071134 AATA--TTCACATATTATTGAA
1 AATATTTTCACATATTATTGAA
29071154 AATATTT
1 AATATTT
29071161 GTTAAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 20 0.80
22 1 0.04
23 4 0.16
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (22 bp):
AATATTTTCACATATTATTGAA
Found at i:29071143 original size:20 final size:20
Alignment explanation
Indices: 29071118--29071159 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
29071108 AATAATATTC
29071118 TTCACATATTATTGAAAATA
1 TTCACATATTATTGAAAATA
29071138 TTCACATATTATTGAAAATA
1 TTCACATATTATTGAAAATA
29071158 TT
1 TT
29071160 TGTTAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (20 bp):
TTCACATATTATTGAAAATA
Found at i:29072457 original size:18 final size:18
Alignment explanation
Indices: 29072426--29072476 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
29072416 TAAATGATAT
29072426 TTTTATTAAATAATAATA
1 TTTTATTAAATAATAATA
* *
29072444 TTTTAATAAGTAATAATA
1 TTTTATTAAATAATAATA
*
29072462 TTTTATTAATTAATA
1 TTTTATTAAATAATA
29072477 TTATAATACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTATTAAATAATAATA
Found at i:29077831 original size:38 final size:38
Alignment explanation
Indices: 29077775--29077925 Score: 126
Period size: 38 Copynumber: 3.9 Consensus size: 38
29077765 TAGAATAAAT
*
29077775 TGGCACATAAAGCGCATCTTGACGCACAAAGCGCATAC
1 TGGCACATAAAGTGCATCTTGACGCACAAAGCGCATAC
* * ** *
29077813 TGGCACATGAAGTACATCTTGAAACACAAAGTGCAT-C
1 TGGCACATAAAGTGCATCTTGACGCACAAAGCGCATAC
* **
29077850 ATGGCACACAAAGTGCATCTT-AGCGCATGAAGCGCATATC
1 -TGGCACATAAAGTGCATCTTGA-CGCACAAAGCGCATA-C
* * * * * *
29077890 TGGCACATGAACTGTATCTTAACACACAAAGTGCAT
1 TGGCACATAAAGTGCATCTTGACGCACAAAGCGCAT
29077926 CTTGGAGCAC
Statistics
Matches: 86, Mismatches: 22, Indels: 9
0.74 0.19 0.08
Matches are distributed among these distances:
37 2 0.02
38 56 0.65
39 26 0.30
40 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (38 bp):
TGGCACATAAAGTGCATCTTGACGCACAAAGCGCATAC
Found at i:29077849 original size:19 final size:19
Alignment explanation
Indices: 29077822--29077870 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
29077812 CTGGCACATG
*
29077822 AAGTACATCTTGAAACACA
1 AAGTGCATCTTGAAACACA
* **
29077841 AAGTGCATCATGGCACACA
1 AAGTGCATCTTGAAACACA
29077860 AAGTGCATCTT
1 AAGTGCATCTT
29077871 AGCGCATGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (19 bp):
AAGTGCATCTTGAAACACA
Found at i:29077918 original size:77 final size:76
Alignment explanation
Indices: 29077775--29077944 Score: 202
Period size: 77 Copynumber: 2.2 Consensus size: 76
29077765 TAGAATAAAT
* *
29077775 TGGCACATAAAGCGCATCTTGACGCACAAAGCGCATACTGGCACATGAAGTACATCTTGAAACAC
1 TGGCACACAAAGCGCATCTTGACGCACAAAGCGCATACTGGCACATGAACTACATCTTGAAACAC
29077840 AAAGTGCATCA
66 AAAGTGCATCA
* ** **
29077851 TGGCACACAAAGTGCATCTT-AGCGCATGAAGCGCATATCTGGCACATGAACTGTATCTT-AACA
1 TGGCACACAAAGCGCATCTTGA-CGCACAAAGCGCATA-CTGGCACATGAACTACATCTTGAA-A
*
29077914 CACAAAGTGCATCT
63 CACAAAGTGCATCA
*
29077928 TGG-AGCACGAAGCGCAT
1 TGGCA-CACAAAGCGCAT
29077945 ATATGGCAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
75 1 0.01
76 34 0.43
77 45 0.56
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (76 bp):
TGGCACACAAAGCGCATCTTGACGCACAAAGCGCATACTGGCACATGAACTACATCTTGAAACAC
AAAGTGCATCA
Found at i:29077919 original size:58 final size:58
Alignment explanation
Indices: 29077854--29078002 Score: 174
Period size: 58 Copynumber: 2.6 Consensus size: 58
29077844 TGCATCATGG
* * * * * * *
29077854 CACACAAAGTGCATCTTAGCGCATGAAGCGCATATCTGGCACATGAACTGTATCTTAA
1 CACACAAAGTGCATCTTGGAGCATGAAGCGCATATATGGCAAACGAACTGCATCCTAA
* * *
29077912 CACACAAAGTGCATCTTGGAGCACGAAGCGCATATATGGCAAACGAAGTGCATCCTAG
1 CACACAAAGTGCATCTTGGAGCATGAAGCGCATATATGGCAAACGAACTGCATCCTAA
* * *
29077970 CACACGAGGTGCATCTTGGGGCAT-AAGCGCATA
1 CACACAAAGTGCATCTTGGAGCATGAAGCGCATA
29078003 ATCCCATACA
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
57 9 0.12
58 68 0.88
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (58 bp):
CACACAAAGTGCATCTTGGAGCATGAAGCGCATATATGGCAAACGAACTGCATCCTAA
Found at i:29079396 original size:11 final size:11
Alignment explanation
Indices: 29079352--29079411 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
29079342 CTAAAAAATT
29079352 AAATTAAATTAA
1 AAATT-AATTAA
*
29079364 AAATCAA-TAA
1 AAATTAATTAA
**
29079374 AAATATTTTTAA
1 AAAT-TAATTAA
29079386 AAATTAATTAA
1 AAATTAATTAA
29079397 AAATTAA--AA
1 AAATTAATTAA
29079406 AAATTA
1 AAATTA
29079412 TAAACTAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 8 0.20
10 7 0.17
11 14 0.35
12 11 0.28
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATTAATTAA
Found at i:29079459 original size:20 final size:21
Alignment explanation
Indices: 29079420--29079459 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29079410 TATAAACTAA
*
29079420 CAAAATTACCAAAAAGTAAAT
1 CAAAATAACCAAAAAGTAAAT
29079441 CAAAATAACCAAAAA-TAAA
1 CAAAATAACCAAAAAGTAAA
29079460 CTTTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (21 bp):
CAAAATAACCAAAAAGTAAAT
Found at i:29080455 original size:17 final size:17
Alignment explanation
Indices: 29080415--29080465 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
29080405 TGGTGAAGGT
* *
29080415 ATGAAGAGAAGATGAAAA
1 ATGAAAAGAA-ATAAAAA
*
29080433 AGGAAAAGAAATAAAAA
1 ATGAAAAGAAATAAAAA
29080450 ATGAAAAGAAA-AAAAA
1 ATGAAAAGAAATAAAAA
29080466 TTAATGAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 5 0.17
17 16 0.55
18 8 0.28
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.08
Consensus pattern (17 bp):
ATGAAAAGAAATAAAAA
Found at i:29080573 original size:21 final size:22
Alignment explanation
Indices: 29080539--29080587 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
29080529 AGTTTATAAT
29080539 TTTTTATTTAATTTTAAAAATA
1 TTTTTATTTAATTTTAAAAATA
* * *
29080561 TTTTTA-TTGATTTTTAATATA
1 TTTTTATTTAATTTTAAAAATA
29080582 TTTTTA
1 TTTTTA
29080588 GATTATGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTATTTAATTTTAAAAATA
Found at i:29081961 original size:30 final size:31
Alignment explanation
Indices: 29081907--29081974 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
29081897 TAGCTTAAAT
* *
29081907 TTTTAT-AATTTTAAAAGGATTAAATCAAAA
1 TTTTATCATTTTTAAAAGGACTAAATCAAAA
* *
29081937 TTTTATCATTTTTAAAAGG-CTAAATTATAA
1 TTTTATCATTTTTAAAAGGACTAAATCAAAA
29081967 -TTTATCAT
1 TTTTATCAT
29081975 ATACTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.24
30 14 0.42
31 11 0.33
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (31 bp):
TTTTATCATTTTTAAAAGGACTAAATCAAAA
Found at i:29088764 original size:37 final size:37
Alignment explanation
Indices: 29088723--29088871 Score: 253
Period size: 37 Copynumber: 4.0 Consensus size: 37
29088713 GCTGAAGCTA
*
29088723 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
* *
29088760 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
**
29088797 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
29088834 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
29088871 C
1 C
29088872 TAAAGCTACC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:29091348 original size:57 final size:57
Alignment explanation
Indices: 29091260--29091368 Score: 218
Period size: 57 Copynumber: 1.9 Consensus size: 57
29091250 ATACTTTAAT
29091260 AACTACATTGAATGCTAAAGTCTTAGGGTTTGAACATATTAAGGAGCTATATTAAGG
1 AACTACATTGAATGCTAAAGTCTTAGGGTTTGAACATATTAAGGAGCTATATTAAGG
29091317 AACTACATTGAATGCTAAAGTCTTAGGGTTTGAACATATTAAGGAGCTATAT
1 AACTACATTGAATGCTAAAGTCTTAGGGTTTGAACATATTAAGGAGCTATAT
29091369 GATGATGATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (57 bp):
AACTACATTGAATGCTAAAGTCTTAGGGTTTGAACATATTAAGGAGCTATATTAAGG
Found at i:29094363 original size:9 final size:9
Alignment explanation
Indices: 29094336--29094374 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
29094326 TGAATTTCAC
29094336 AATTCAAAT
1 AATTCAAAT
*
29094345 AACTT-GAAT
1 AA-TTCAAAT
29094354 AATTCAAAT
1 AATTCAAAT
29094363 AATTCAAAT
1 AATTCAAAT
29094372 AAT
1 AAT
29094375 AGATTCGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (9 bp):
AATTCAAAT
Found at i:29094481 original size:20 final size:22
Alignment explanation
Indices: 29094453--29094545 Score: 86
Period size: 21 Copynumber: 4.3 Consensus size: 22
29094443 AAAAACTACC
*
29094453 AAAATAATTCAAAATAA-AT-T
1 AAAAAAATTCAAAATAATATAT
**
29094473 TCAAAAATTCAAAA-AATATAT
1 AAAAAAATTCAAAATAATATAT
* *
29094494 AAAAAAATTCAAAATTTATATTTT
1 AAAAAAATTCAAAA-TAATA-TAT
*
29094518 AAAAAAATTCTAAA-AATATAT
1 AAAAAAATTCAAAATAATATAT
29094539 AAAAAAA
1 AAAAAAA
29094546 CCTTAAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
19 2 0.03
20 13 0.22
21 22 0.38
22 3 0.05
23 3 0.05
24 15 0.26
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAAATTCAAAATAATATAT
Found at i:29099720 original size:16 final size:16
Alignment explanation
Indices: 29099699--29099731 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29099689 TTAAATATTT
29099699 TTATTAGAAAA-ATAAA
1 TTATTA-AAAATATAAA
29099715 TTATTAAAAATATAAA
1 TTATTAAAAATATAAA
29099731 T
1 T
29099732 AAGGAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TTATTAAAAATATAAA
Found at i:29102038 original size:19 final size:20
Alignment explanation
Indices: 29102022--29102063 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29102012 TTTATAAATT
29102022 TAATTTAAATATATAAACTA
1 TAATTTAAATATATAAACTA
* *
29102042 TATTTTAAATAT-TAAAATA
1 TAATTTAAATATATAAACTA
29102061 TAA
1 TAA
29102064 CCAATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATTTAAATATATAAACTA
Found at i:29107179 original size:51 final size:51
Alignment explanation
Indices: 29107055--29107235 Score: 170
Period size: 51 Copynumber: 3.6 Consensus size: 51
29107045 AAAGTGATGG
* * ** * * *
29107055 TCACGTGTGTAGTACTATGTGCAGGGTACTACGTGTACC-GA-AATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAAT-GA
* * *
29107105 TCGCATGTGTAGTACTATGTGCAGGCTACTATACGTACCAGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAAT-GA
* ** * * * *
29107156 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAATGA
29107207 TCACATGTGTAGTACTATGTGCAGGCTAC
1 TCACATGTGTAGTACTATGTGCAGGCTAC
29107236 AATGTGAACC
Statistics
Matches: 107, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
50 33 0.31
51 71 0.66
52 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAATGA
Found at i:29107718 original size:25 final size:25
Alignment explanation
Indices: 29107690--29107740 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29107680 TTAGACAGAG
29107690 TTAGAATGAGTTTGGAATCCCCTGT
1 TTAGAATGAGTTTGGAATCCCCTGT
29107715 TTAGAATGAGTTTGGAATCCCCTGT
1 TTAGAATGAGTTTGGAATCCCCTGT
29107740 T
1 T
29107741 CTGACTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (25 bp):
TTAGAATGAGTTTGGAATCCCCTGT
Found at i:29109659 original size:20 final size:20
Alignment explanation
Indices: 29109625--29109666 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29109615 AACTATTTAA
** *
29109625 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
29109645 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
29109665 AT
1 AT
29109667 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:29111356 original size:17 final size:17
Alignment explanation
Indices: 29111334--29111366 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29111324 TTTGAAAAAT
29111334 TAAAAATTAAATTAAAC
1 TAAAAATTAAATTAAAC
29111351 TAAAAATTAAATTAAA
1 TAAAAATTAAATTAAA
29111367 AGAATATATA
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:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAAATTAAATTAAAC
Found at i:29124989 original size:48 final size:48
Alignment explanation
Indices: 29124937--29125038 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
29124927 ACTATTCTAT
*
29124937 CCACTAGCAGGCCCAAGAGACTGGCCTGCATTCGGCCCAAAATACTAC
1 CCACTAGCAGGCCCAAGAGACTGACCTGCATTCGGCCCAAAATACTAC
* * * ** *
29124985 CCACTAGCAGGCCCAAGAGATTGACCTTCATTCGGTCCAAGGTACTGC
1 CCACTAGCAGGCCCAAGAGACTGACCTGCATTCGGCCCAAAATACTAC
29125033 CCACTA
1 CCACTA
29125039 TTGTACCCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.34, G:0.21, T:0.18
Consensus pattern (48 bp):
CCACTAGCAGGCCCAAGAGACTGACCTGCATTCGGCCCAAAATACTAC
Found at i:29127709 original size:19 final size:18
Alignment explanation
Indices: 29127687--29127728 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
29127677 TCAAAAAATG
29127687 AAAAAAATGGAAAATTTTT
1 AAAAAAATGGAAAA-TTTT
*
29127706 AAAAAAATGTAAAATTTT
1 AAAAAAATGGAAAATTTT
29127724 AAAAA
1 AAAAA
29127729 TTATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (18 bp):
AAAAAAATGGAAAATTTT
Found at i:29128400 original size:13 final size:14
Alignment explanation
Indices: 29128374--29128405 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
29128364 CTTTAACACA
29128374 AAAAATAATAAATT
1 AAAAATAATAAATT
29128388 AAAAATAAT-AATT
1 AAAAATAATAAATT
29128401 AAAAA
1 AAAAA
29128406 ATGACATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAATAATAAATT
Found at i:29128406 original size:14 final size:15
Alignment explanation
Indices: 29128373--29128407 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
29128363 GCTTTAACAC
29128373 AAAAAATAATAAATT
1 AAAAAATAATAAATT
29128388 -AAAAATAAT-AATT
1 AAAAAATAATAAATT
29128401 AAAAAAT
1 AAAAAAT
29128408 GACATCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAATAATAAATT
Found at i:29135277 original size:18 final size:19
Alignment explanation
Indices: 29135254--29135298 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
29135244 GTGCGAGAGC
*
29135254 AAATGAACAAG-AAAAGAA
1 AAATGAAAAAGCAAAAGAA
29135272 AAATGAAAAAGCAAAAGAA
1 AAATGAAAAAGCAAAAGAA
29135291 AAA-GAAAA
1 AAATGAAAA
29135299 GAGTTCAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (19 bp):
AAATGAAAAAGCAAAAGAA
Found at i:29135300 original size:5 final size:6
Alignment explanation
Indices: 29135265--29135298 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
29135255 AATGAACAAG
*
29135265 AAAAGA AAAATGA AAAAGC AAAAGA AAAAGA AAA
1 AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAA
29135299 GAGTTCAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:29135335 original size:26 final size:27
Alignment explanation
Indices: 29135290--29135350 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
29135280 AAGCAAAAGA
29135290 AAAAGAAAAGAGTTCAGAAAAAAAGAGAG
1 AAAAG-AAAGAGTT-AGAAAAAAAGAGAG
* * *
29135319 GAAAGAAAGAGTT-GAAAACAAGTGAG
1 AAAAGAAAGAGTTAGAAAAAAAGAGAG
29135345 AAAAGA
1 AAAAGA
29135351 GAAAACGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 16 0.57
28 8 0.29
29 4 0.14
ACGTcount: A:0.62, C:0.03, G:0.26, T:0.08
Consensus pattern (27 bp):
AAAAGAAAGAGTTAGAAAAAAAGAGAG
Found at i:29151686 original size:21 final size:21
Alignment explanation
Indices: 29151647--29151686 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29151637 AAATGACGTA
* * *
29151647 GTTTTGCCTTTTAACTTAATG
1 GTTTTGACTTTGAAATTAATG
29151668 GTTTTGACTTTGAAATTAA
1 GTTTTGACTTTGAAATTAA
29151687 GAAAAGGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (21 bp):
GTTTTGACTTTGAAATTAATG
Found at i:29153476 original size:38 final size:38
Alignment explanation
Indices: 29153395--29153502 Score: 99
Period size: 38 Copynumber: 2.8 Consensus size: 38
29153385 TATACTAAAT
* * * * * * *
29153395 ATTGTCGGATTCACCTACCAGTGCTGGCCATATATATA
1 ATTGTCAGATTCATCGACCAGTGCTGGGCACAGATACA
* *
29153433 TTTGTCAGATTCATTGACCAGTGCTGGGCACAGATACA
1 ATTGTCAGATTCATCGACCAGTGCTGGGCACAGATACA
* * * *
29153471 ATTGTCAGTTTTATCGGCCAGTGCAGGGCACA
1 ATTGTCAGATTCATCGACCAGTGCTGGGCACA
29153503 TATATTTGTC
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (38 bp):
ATTGTCAGATTCATCGACCAGTGCTGGGCACAGATACA
Found at i:29157438 original size:16 final size:17
Alignment explanation
Indices: 29157417--29157452 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
29157407 ACTTCATTTC
29157417 ATTTTTATT-TTTTTTT
1 ATTTTTATTATTTTTTT
29157433 ATTTTTATTAATTTTTTT
1 ATTTTTATT-ATTTTTTT
29157451 AT
1 AT
29157453 AAATTCCCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
ATTTTTATTATTTTTTT
Found at i:29158658 original size:12 final size:12
Alignment explanation
Indices: 29158641--29158686 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
29158631 CCACTCATCT
*
29158641 TAATAATAATAA
1 TAATAATACTAA
*
29158653 TAATAATACTAT
1 TAATAATACTAA
*
29158665 TACTAATACTAA
1 TAATAATACTAA
*
29158677 TATTAATACT
1 TAATAATACT
29158687 TACCTCACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAATACTAA
Found at i:29164114 original size:24 final size:23
Alignment explanation
Indices: 29164087--29164132 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29164077 TAACAATCTG
*
29164087 CAGAAAATTCTACCAGTAAAAATT
1 CAGAAAA-GCTACCAGTAAAAATT
* *
29164111 CAGACAAGCTACTAGTAAAAAT
1 CAGAAAAGCTACCAGTAAAAAT
29164133 GTGATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (23 bp):
CAGAAAAGCTACCAGTAAAAATT
Found at i:29167809 original size:38 final size:38
Alignment explanation
Indices: 29167767--29167882 Score: 124
Period size: 38 Copynumber: 3.0 Consensus size: 38
29167757 ATATTGAATA
*
29167767 TTGTCGGATTCACCGACTAGTGCTGGGCACACATATAT
1 TTGTCGGATTCACCGACCAGTGCTGGGCACACATATAT
* * *
29167805 TTGTCAGATTCACTGACCAGTGCTGGGCACACCTATAT
1 TTGTCGGATTCACCGACCAGTGCTGGGCACACATATAT
** ** * * *
29167843 CCGTCGGATAAACTGACCAATGCTGGGCAAACATACTAT
1 TTGTCGGATTCACCGACCAGTGCTGGGCACACATA-TAT
29167882 T
1 T
29167883 CTCAATTTTA
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
38 61 0.95
39 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (38 bp):
TTGTCGGATTCACCGACCAGTGCTGGGCACACATATAT
Found at i:29167917 original size:38 final size:36
Alignment explanation
Indices: 29167857--29167938 Score: 83
Period size: 36 Copynumber: 2.2 Consensus size: 36
29167847 CGGATAAACT
* * * *
29167857 GACCAATGCTGGGCAAACATACTATTCTCAATTTTACC
1 GACCAGTGCAGGGCAAACATAC--TTATCAATTCTACC
* * *
29167895 GACCAGTGCAGGGCAGATATACTTATCGATTCTACC
1 GACCAGTGCAGGGCAAACATACTTATCAATTCTACC
29167931 GACCAGTG
1 GACCAGTG
29167939 TTGGGCGCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
36 19 0.51
38 18 0.49
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (36 bp):
GACCAGTGCAGGGCAAACATACTTATCAATTCTACC
Found at i:29169112 original size:22 final size:22
Alignment explanation
Indices: 29169056--29169114 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
29169046 TTCAAATATA
**
29169056 TAAGCTCTCATGGCTAACGTAC
1 TAAGCTCTCATGTTTAACGTAC
*
29169078 TAAGCTCTCATGTTTCACGTAC
1 TAAGCTCTCATGTTTAACGTAC
29169100 TAAGCTCTCATGTTT
1 TAAGCTCTCATGTTT
29169115 GAACAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (22 bp):
TAAGCTCTCATGTTTAACGTAC
Found at i:29170931 original size:10 final size:9
Alignment explanation
Indices: 29170918--29170990 Score: 59
Period size: 8 Copynumber: 8.4 Consensus size: 9
29170908 TATGTTTTAA
29170918 ATATATTA-
1 ATATATTAT
29170926 ATATATTAT
1 ATATATTAT
*
29170935 -TTTATTAT
1 ATATATTAT
29170943 ATCATA-TAT
1 AT-ATATTAT
29170952 -TATATTAT
1 ATATATTAT
*
29170960 AT-TATAAT
1 ATATATTAT
29170968 AATTATATTAT
1 -A-TATATTAT
29170979 AT-TATTAT
1 ATATATTAT
29170987 ATAT
1 ATAT
29170991 TAAATAAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
7 3 0.06
8 32 0.62
9 8 0.15
10 4 0.08
11 5 0.10
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATATTAT
Found at i:29170937 original size:22 final size:20
Alignment explanation
Indices: 29170914--29170992 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 20
29170904 TTTTTATGTT
29170914 TTAAATATATTAATATATTAT-
1 TTAAAT-TA-TAATATATTATA
*
29170935 TT-TATTATATCATATATTATA
1 TTAAATTATA--ATATATTATA
*
29170956 TTATATTATAATA-ATTATA
1 TTAAATTATAATATATTATA
* *
29170975 TTATATTATTATATATTA
1 TTAAATTATAATATATTA
29170993 AATAAACTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 20 0.39
20 18 0.35
21 4 0.08
22 7 0.14
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATTATAATATATTATA
Found at i:29170955 original size:5 final size:5
Alignment explanation
Indices: 29170919--29170992 Score: 70
Period size: 5 Copynumber: 15.4 Consensus size: 5
29170909 ATGTTTTAAA
*
29170919 TATAT TA-A- TATAT TAT-T T-TAT TATAT CATATAT TATAT TATAT TATAA
1 TATAT TATAT TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT
29170967 TA-AT TATAT TATAT TAT-T ATATAT TA
1 TATAT TATAT TATAT TATAT -TATAT TA
29170993 AATAAACTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
3 3 0.05
4 10 0.17
5 39 0.67
6 1 0.02
7 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:29170974 original size:19 final size:17
Alignment explanation
Indices: 29170919--29170992 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
29170909 ATGTTTTAAA
29170919 TATATTA-A-TATATTAT
1 TATATTATATTATA-TAT
* *
29170935 TTTATTATATCATATAT
1 TATATTATATTATATAT
29170952 TATATTATATTATAATAAT
1 TATATTATATTAT-AT-AT
29170971 TATATTATATTAT-TA-
1 TATATTATATTATATAT
29170986 TATATTA
1 TATATTA
29170993 AATAAACTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
15 7 0.14
16 7 0.14
17 16 0.32
18 5 0.10
19 15 0.30
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTATATTATATAT
Found at i:29176801 original size:16 final size:16
Alignment explanation
Indices: 29176782--29176815 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29176772 GAAATTAAAA
*
29176782 TCATAAATTCATTCAT
1 TCATAAATTCAATCAT
*
29176798 TCATATATTCAATCAT
1 TCATAAATTCAATCAT
29176814 TC
1 TC
29176816 TAATCCTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (16 bp):
TCATAAATTCAATCAT
Found at i:29183267 original size:14 final size:15
Alignment explanation
Indices: 29183250--29183283 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29183240 AAAAGACTAT
*
29183250 AAATAAAA-TTATAA
1 AAATAAAATTTACAA
29183264 AAATAAAATTTACAA
1 AAATAAAATTTACAA
29183279 AAATA
1 AAATA
29183284 TGGTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAAATTTACAA
Found at i:29183508 original size:30 final size:32
Alignment explanation
Indices: 29183472--29183535 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
29183462 ATAACATTTT
* *
29183472 AATTTTTTA-TATATTATTTT-GAGTTTT-TAA
1 AATTTTTAATTATA-TATTTTAGAATTTTATAA
29183502 AATTTTTAATTATATATTTTAGAATTTTATAA
1 AATTTTTAATTATATATTTTAGAATTTTATAA
29183534 AA
1 AA
29183536 AAAATTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 14 0.48
31 10 0.34
32 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (32 bp):
AATTTTTAATTATATATTTTAGAATTTTATAA
Found at i:29184075 original size:23 final size:23
Alignment explanation
Indices: 29184026--29184075 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
29184016 TTAAATACCT
* * *
29184026 TTTTAGAATTTTATGAATATATA
1 TTTTAGAATTTTATAAAAAAATA
*
29184049 TTTTAGAATTTTATAAAAAAATG
1 TTTTAGAATTTTATAAAAAAATA
29184072 TTTT
1 TTTT
29184076 TAAACTCTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (23 bp):
TTTTAGAATTTTATAAAAAAATA
Found at i:29189044 original size:21 final size:20
Alignment explanation
Indices: 29189004--29189042 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29188994 GATACCTGAT
*
29189004 AAAAGGTAACGATATTTTTG
1 AAAAGGTAACAATATTTTTG
*
29189024 AAAAGGTATCAATATTTTT
1 AAAAGGTAACAATATTTTT
29189043 TGTGGTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (20 bp):
AAAAGGTAACAATATTTTTG
Found at i:29193168 original size:29 final size:29
Alignment explanation
Indices: 29193120--29193192 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
29193110 TATTTTTGTA
* *
29193120 TTTTTATATTTTTATAATTTATTCAATAT
1 TTTTTATATTTTTATAATTTATTAAACAT
* * * *
29193149 TTTTTGTATTTTTTTCATTTTTTAAACAT
1 TTTTTATATTTTTATAATTTATTAAACAT
* *
29193178 TTTTTTTAGTTTTAT
1 TTTTTATATTTTTAT
29193193 CCAAAAGATG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (29 bp):
TTTTTATATTTTTATAATTTATTAAACAT
Found at i:29193588 original size:3 final size:3
Alignment explanation
Indices: 29193580--29193634 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
29193570 AAATACTAAC
29193580 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29193628 TAT TAT T
1 TAT TAT T
29193635 TCAATATTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:29194040 original size:2 final size:2
Alignment explanation
Indices: 29194033--29194058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29194023 TTAAGAATTT
29194033 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
29194059 GATGATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29200350 original size:3 final size:3
Alignment explanation
Indices: 29200342--29200372 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29200332 TAATCTGATA
29200342 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29200373 TTCTAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29205956 original size:30 final size:30
Alignment explanation
Indices: 29205922--29205984 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
29205912 ACTTAATTTA
29205922 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
29205952 TTGTTAATTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
29205982 TTG
1 TTG
29205985 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:29206121 original size:11 final size:11
Alignment explanation
Indices: 29206107--29206136 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29206097 ATATATATTC
29206107 AAAAATTATAT
1 AAAAATTATAT
*
29206118 AAAAATAATAT
1 AAAAATTATAT
29206129 AAAAATTA
1 AAAAATTA
29206137 ATACGGACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:29208336 original size:25 final size:25
Alignment explanation
Indices: 29208308--29208384 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
29208298 TGGTAATTTG
29208308 ATAATTATATTAAAATAAAATAAAA
1 ATAATTATATTAAAATAAAATAAAA
* * **
29208333 ATAATTAAAATAAAATAAAACCAAA
1 ATAATTATATTAAAATAAAATAAAA
** *
29208358 ATGTTTTATCATCAAAATAAAATAAAA
1 AT-AATTAT-ATTAAAATAAAATAAAA
29208385 CCAAAATGTT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
25 23 0.59
26 3 0.08
27 13 0.33
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (25 bp):
ATAATTATATTAAAATAAAATAAAA
Found at i:29208375 original size:32 final size:32
Alignment explanation
Indices: 29208339--29208403 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29208329 AAAAATAATT
29208339 AAAATAAAATAAAACCAAAATGTTTTATCATC
1 AAAATAAAATAAAACCAAAATGTTTTATCATC
29208371 AAAATAAAATAAAACCAAAATGTTTTATCATC
1 AAAATAAAATAAAACCAAAATGTTTTATCATC
29208403 A
1 A
29208404 TCTTAATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (32 bp):
AAAATAAAATAAAACCAAAATGTTTTATCATC
Found at i:29208865 original size:13 final size:13
Alignment explanation
Indices: 29208847--29208871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29208837 GCTCAGAGAC
29208847 TAAATTGAATAAT
1 TAAATTGAATAAT
29208860 TAAATTGAATAA
1 TAAATTGAATAA
29208872 AAGTAAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TAAATTGAATAAT
Found at i:29210598 original size:15 final size:16
Alignment explanation
Indices: 29210578--29210607 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29210568 TGGTGCTTTA
29210578 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
29210593 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
29210608 AGCATATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:29219287 original size:20 final size:20
Alignment explanation
Indices: 29219259--29219307 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
29219249 GCTGACAGGA
* * *
29219259 CACCAAAGTGTATACAGAGG
1 CACCGAAGTGTAAAAAGAGG
29219279 CACCGAAGTGTAAAAAGAGG
1 CACCGAAGTGTAAAAAGAGG
*
29219299 CCCCGAAGT
1 CACCGAAGT
29219308 ACAAATCCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (20 bp):
CACCGAAGTGTAAAAAGAGG
Found at i:29222900 original size:44 final size:44
Alignment explanation
Indices: 29222850--29222939 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
29222840 GGATTATATG
*
29222850 CTTGTGTATTATAGGGAGAACCTTACTCTTATTGGATACATAGA
1 CTTGTGTATTATAGGGAGAACCTTACTCCTATTGGATACATAGA
*
29222894 CTTGTGTATTATAGGGAGAACCTTACTCCTATTGGATGCATAGA
1 CTTGTGTATTATAGGGAGAACCTTACTCCTATTGGATACATAGA
29222938 CT
1 CT
29222940 CATACTTCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (44 bp):
CTTGTGTATTATAGGGAGAACCTTACTCCTATTGGATACATAGA
Found at i:29230740 original size:30 final size:31
Alignment explanation
Indices: 29230704--29230762 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
29230694 TCTGAGCTTT
29230704 GGGGC-AAAATTGTAAATATGCAAAAGTTTA
1 GGGGCAAAAATTGTAAATATGCAAAAGTTTA
* *
29230734 GGGGCAAAAATTGTAATTATGCCAAAGTT
1 GGGGCAAAAATTGTAAATATGCAAAAGTT
29230763 CAAGTCAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (31 bp):
GGGGCAAAAATTGTAAATATGCAAAAGTTTA
Found at i:29231116 original size:51 final size:51
Alignment explanation
Indices: 29230993--29231176 Score: 176
Period size: 51 Copynumber: 3.6 Consensus size: 51
29230983 AAAGTGATGG
* * * * * * *
29230993 TCACGTGTGTAGTACTATATGCAGGCTACTACGTGTACC-GA-AATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTAAT-GA
* * * **
29231043 TCGCA-GTGTAGTACTATGTGCAGGCTACTATGCGTACCGGGTAGTTTTGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTAATGA
* * * * *
29231093 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCAGATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTAATGA
*
29231144 TCACATGTGCAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
29231177 TGAACCGAAC
Statistics
Matches: 108, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
49 30 0.28
50 8 0.07
51 70 0.65
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTAATGA
Found at i:29231249 original size:45 final size:45
Alignment explanation
Indices: 29231180--29231274 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
29231170 TACTATGTGA
* *
29231180 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
29231225 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
29231270 ACCGA
1 ACCGA
29231275 GGATCTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:29233197 original size:95 final size:95
Alignment explanation
Indices: 29233034--29233213 Score: 324
Period size: 95 Copynumber: 1.9 Consensus size: 95
29233024 GATGAAATTT
*
29233034 TACAACTCGGTATAATACGTTACAAGTGTATGTGTTCTAGTAATGCTTCGTACCCTATTCCGGCA
1 TACAACTCAGTATAATACGTTACAAGTGTATGTGTTCTAGTAATGCTTCGTACCCTATTCCGGCA
*
29233099 TCGAATACGGGTAAGGGGTAAGGGGTATAA
66 TCGAATACGGGTAAAGGGTAAGGGGTATAA
* *
29233129 TACAACTCAGTATAATATGTTACAAGTGTATGTGTTCTAGTAATGCTTCGTACCCTATTCTGGCA
1 TACAACTCAGTATAATACGTTACAAGTGTATGTGTTCTAGTAATGCTTCGTACCCTATTCCGGCA
29233194 TCGAATACGGGTAAAGGGTA
66 TCGAATACGGGTAAAGGGTA
29233214 TTACATAAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 81 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (95 bp):
TACAACTCAGTATAATACGTTACAAGTGTATGTGTTCTAGTAATGCTTCGTACCCTATTCCGGCA
TCGAATACGGGTAAAGGGTAAGGGGTATAA
Found at i:29233774 original size:26 final size:26
Alignment explanation
Indices: 29233745--29233809 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
29233735 GGTGGTAAGT
* *
29233745 TTCATTCTTGGTTTGACAGGTTTCGG
1 TTCATTCTTGGTTTAACAGGTTTCCG
29233771 TTCATTCTTGGTTTAACAGGTTTCCG
1 TTCATTCTTGGTTTAACAGGTTTCCG
29233797 TTCATTCTTGGTT
1 TTCATTCTTGGTT
29233810 GTCAATTCGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (26 bp):
TTCATTCTTGGTTTAACAGGTTTCCG
Found at i:29242190 original size:10 final size:10
Alignment explanation
Indices: 29242174--29242224 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
29242164 TAAAAAGTTA
29242174 AAATAAATTG
1 AAATAAATTG
*
29242184 GAATAAATT-
1 AAATAAATTG
*
29242193 AACA-ATATTG
1 AA-ATAAATTG
*
29242203 AAATAAGTTG
1 AAATAAATTG
29242213 AAATAAATTG
1 AAATAAATTG
29242223 AA
1 AA
29242225 GATGTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
9 6 0.19
10 26 0.81
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (10 bp):
AAATAAATTG
Found at i:29242206 original size:29 final size:28
Alignment explanation
Indices: 29242158--29242252 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 28
29242148 TATGATATCT
*
29242158 ATAAATTAAAAAGTTAAAATAAATTGGA
1 ATAAATTAAAAAGTTAAAATAAATTGAA
* *
29242186 ATAAATTAACAATA-TTGAAATAAGTTGAA
1 ATAAATTAA-AA-AGTTAAAATAAATTGAA
* * *
29242215 ATAAATTGAAGATGTTAAAAT-ATTTGAA
1 ATAAATT-AAAAAGTTAAAATAAATTGAA
*
29242243 AGAAA-TAAAA
1 ATAAATTAAAA
29242253 TATCTATATG
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
26 3 0.06
27 1 0.02
28 19 0.35
29 28 0.52
30 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.29
Consensus pattern (28 bp):
ATAAATTAAAAAGTTAAAATAAATTGAA
Found at i:29242555 original size:22 final size:22
Alignment explanation
Indices: 29242527--29242571 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
29242517 CGATGTATAT
*
29242527 AAAATAAA-GTAATGTATATAAA
1 AAAATAAACG-AATATATATAAA
29242549 AAAATAAACGAATATATATAAA
1 AAAATAAACGAATATATATAAA
29242571 A
1 A
29242572 TATAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (22 bp):
AAAATAAACGAATATATATAAA
Found at i:29242575 original size:11 final size:11
Alignment explanation
Indices: 29242559--29242596 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
29242549 AAAATAAACG
29242559 AATATATATAA-
1 AATATA-ATAAT
29242570 AATATAATAAT
1 AATATAATAAT
29242581 AATAATAATAAT
1 AAT-ATAATAAT
29242593 AATA
1 AATA
29242597 AGGATAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 10 0.40
12 11 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATATAATAAT
Found at i:29242581 original size:3 final size:3
Alignment explanation
Indices: 29242573--29242639 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
29242563 TATATAAAAT
** * * *
29242573 ATA ATA ATA ATA ATA ATA ATA ATA AGG ATA AGT- ATG ATA ATA CTG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA
* *
29242618 ATA ATA ATA ATA CTA ACA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
29242640 ATTTCTTAAT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
2 1 0.02
3 47 0.96
4 1 0.02
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:29242581 original size:19 final size:20
Alignment explanation
Indices: 29242522--29242581 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 20
29242512 AACAACGATG
* *
29242522 TATATAAAATA-AAGTAATG
1 TATATAAAATATAACTAATA
* *
29242541 TATATAAAAAAATAAACGAATA
1 TATAT-AAAATAT-AACTAATA
29242563 TATATAAAATATAA-TAATA
1 TATATAAAATATAACTAATA
29242582 ATAATAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 9 0.28
20 7 0.22
21 6 0.19
22 10 0.31
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (20 bp):
TATATAAAATATAACTAATA
Found at i:29242584 original size:22 final size:22
Alignment explanation
Indices: 29242522--29242584 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 22
29242512 AACAACGATG
*
29242522 TATATAAAATA-AAGTAAT-GTA
1 TATATAAAATATAA-TAATAATA
* **
29242543 TATA-AAAAAATAA-ACGAATA
1 TATATAAAATATAATAATAATA
29242563 TATATAAAATATAATAATAATA
1 TATATAAAATATAATAATAATA
29242585 ATAATAATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 11 0.35
21 14 0.45
22 5 0.16
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
TATATAAAATATAATAATAATA
Found at i:29244327 original size:14 final size:14
Alignment explanation
Indices: 29244282--29244332 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
29244272 GTTCATGGAA
29244282 TGAATGG-TATGGTT
1 TGAATGGTTAT-GTT
29244296 TGCTAATGGTTGATGTT
1 TG--AATGGTT-ATGTT
29244313 TGAATGGTTATGTT
1 TGAATGGTTATGTT
*
29244327 TTAATG
1 TGAATG
29244333 TTTGAATCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 12 0.38
15 7 0.22
16 5 0.16
17 6 0.19
18 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (14 bp):
TGAATGGTTATGTT
Found at i:29245578 original size:18 final size:17
Alignment explanation
Indices: 29245546--29245579 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29245536 AATGAACACA
*
29245546 AATAATCAAACAATACC
1 AATAAGCAAACAATACC
29245563 AATAAGCAATACAATAC
1 AATAAGCAA-ACAATAC
29245580 ACATGAGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (17 bp):
AATAAGCAAACAATACC
Found at i:29246064 original size:12 final size:12
Alignment explanation
Indices: 29246023--29246066 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
29246013 AACCAAATAT
*
29246023 AATAATAATATC
1 AATAATAATAAC
* *
29246035 AACAATAATAAG
1 AATAATAATAAC
*
29246047 AGTAATAATAAC
1 AATAATAATAAC
29246059 AATAATAA
1 AATAATAA
29246067 ATTAATTAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:29254538 original size:23 final size:21
Alignment explanation
Indices: 29254498--29254539 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
29254488 TATTATATAT
*
29254498 AATATATTTTTTTATATTAGC
1 AATATATTTTTTAATATTAGC
29254519 AATATATTTTTTGAACTATTA
1 AATATATTTTTT-AA-TATTA
29254540 AAAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 1 0.06
23 5 0.28
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (21 bp):
AATATATTTTTTAATATTAGC
Found at i:29262535 original size:23 final size:22
Alignment explanation
Indices: 29262482--29262540 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
29262472 TAAATATTAG
*
29262482 TTTATTAATATTTTAATTTGAT
1 TTTATTAATATATTAATTTGAT
* *
29262504 TTTTTTAATGATATT-ATTTTAT
1 TTTATTAAT-ATATTAATTTGAT
*
29262526 TGTTATTAATTTATT
1 T-TTATTAATATATT
29262541 TAGTATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTATTAATATATTAATTTGAT
Found at i:29269751 original size:14 final size:14
Alignment explanation
Indices: 29269732--29269758 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29269722 AAAAATATAA
29269732 AAAATTAAAATTAT
1 AAAATTAAAATTAT
29269746 AAAATTAAAATTA
1 AAAATTAAAATTA
29269759 AAATATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATTAAAATTAT
Found at i:29270770 original size:29 final size:29
Alignment explanation
Indices: 29270728--29270787 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
29270718 TATGTGTACC
* *
29270728 ATCAATTGCACTTATGCGATCATGAACAA
1 ATCAATTACACTTATGCAATCATGAACAA
29270757 ATCAATTACACTTATGCAATCATGAACAA
1 ATCAATTACACTTATGCAATCATGAACAA
29270786 AT
1 AT
29270788 AATCATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (29 bp):
ATCAATTACACTTATGCAATCATGAACAA
Found at i:29280096 original size:19 final size:19
Alignment explanation
Indices: 29280072--29280112 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
29280062 TCTACTATGT
*
29280072 TAAAAAATTATAAAAAACA
1 TAAAAAAATATAAAAAACA
* *
29280091 TAAAAAAATGTAAAAAAGA
1 TAAAAAAATATAAAAAACA
29280110 TAA
1 TAA
29280113 TAAACAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (19 bp):
TAAAAAAATATAAAAAACA
Found at i:29294460 original size:17 final size:16
Alignment explanation
Indices: 29294431--29294464 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29294421 CCCTTACAAG
*
29294431 TTTTCATTTCTGACCT
1 TTTTCATTACTGACCT
29294447 TTTTACATTACTGACCT
1 TTTT-CATTACTGACCT
29294464 T
1 T
29294465 GTTTTCATTT
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:0.18, C:0.24, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTTCATTACTGACCT
Found at i:29298469 original size:10 final size:9
Alignment explanation
Indices: 29298447--29298481 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
29298437 GTTTATCATC
*
29298447 TTTTTTACA
1 TTTTTTATA
29298456 TTTTTTATA
1 TTTTTTATA
29298465 TTTTTTATAA
1 TTTTTTAT-A
29298475 TTTTTTA
1 TTTTTTA
29298482 ACATAGACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTTATA
Found at i:29302958 original size:165 final size:165
Alignment explanation
Indices: 29302674--29303010 Score: 566
Period size: 165 Copynumber: 2.0 Consensus size: 165
29302664 AATCAAAGAT
* * * *
29302674 GAAAACTTACAATGAATATTACGATATTATTTCTCCAGAAAGTCGTTACACTGGTACCTCTAATA
1 GAAAACTTACAATGAATATTACGATATTATTTCTCCAGAAACTCGTTACACCGGCAACTCTAATA
*
29302739 CCAAAAGCGAGGGGGAAGGGAGAGTAGAGGGTATCTTTGAGTATGAGTGGAAGGGAATATAGACT
66 CCAAAAGCGAGGGGGAAGGGAGAGTAGAGGGTATCTTTGAGTATGAGCGGAAGGGAATATAGACT
*
29302804 CTTTTTTTAACAAAAAGGAAAGGCTTTACAAGAGA
131 CTTTTATTAACAAAAAGGAAAGGCTTTACAAGAGA
* **
29302839 GAAATCTTACAATGAATATTACGATATTATTTCTCCAGAAACTCGTTACACCGGCAACTCTGTTA
1 GAAAACTTACAATGAATATTACGATATTATTTCTCCAGAAACTCGTTACACCGGCAACTCTAATA
*
29302904 CCAAAAGTGAGGGGGAAGGGAGAGTAGAGGGTATCTTTGAGTATGAGCGGAAGGGAATATAGACT
66 CCAAAAGCGAGGGGGAAGGGAGAGTAGAGGGTATCTTTGAGTATGAGCGGAAGGGAATATAGACT
*
29302969 CTTTTATTAACAAAACGGAAAGGCTTTACAAGAGA
131 CTTTTATTAACAAAAAGGAAAGGCTTTACAAGAGA
*
29303004 AAAAACT
1 GAAAACT
29303011 AAAAAGTAAA
Statistics
Matches: 159, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
165 159 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (165 bp):
GAAAACTTACAATGAATATTACGATATTATTTCTCCAGAAACTCGTTACACCGGCAACTCTAATA
CCAAAAGCGAGGGGGAAGGGAGAGTAGAGGGTATCTTTGAGTATGAGCGGAAGGGAATATAGACT
CTTTTATTAACAAAAAGGAAAGGCTTTACAAGAGA
Found at i:29313696 original size:20 final size:20
Alignment explanation
Indices: 29313671--29313710 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29313661 CTGTTGAAAT
29313671 AATATCTTACTGTTGGTGCC
1 AATATCTTACTGTTGGTGCC
29313691 AATATCTTACTGTTGGTGCC
1 AATATCTTACTGTTGGTGCC
29313711 TTTATGAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
AATATCTTACTGTTGGTGCC
Found at i:29317127 original size:9 final size:9
Alignment explanation
Indices: 29317105--29317135 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
29317095 TCGAAAAAGT
29317105 TATTAAAAA
1 TATTAAAAA
29317114 GTATTAAAAA
1 -TATTAAAAA
29317124 TATTAAAAA
1 TATTAAAAA
29317133 TAT
1 TAT
29317136 GAAATTGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (9 bp):
TATTAAAAA
Found at i:29317274 original size:9 final size:9
Alignment explanation
Indices: 29317147--29317320 Score: 70
Period size: 9 Copynumber: 18.3 Consensus size: 9
29317137 AAATTGACAT
29317147 AAATTATAAA
1 AAATTAT-AA
29317157 AAATTTATCAA
1 AAA-TTAT-AA
*
29317168 AAATTACCAA
1 AAATTA-TAA
29317178 AAA-TATAA
1 AAATTATAA
*
29317186 AACATCTA-AT
1 AA-AT-TATAA
*
29317196 AAATTAAAA
1 AAATTATAA
*
29317205 AAATAATAA
1 AAATTATAA
* *
29317214 AACTAATAA
1 AAATTATAA
*
29317223 AATATATTTAA
1 AA-AT-TATAA
*
29317234 AATTTTATAA
1 AA-ATTATAA
*
29317244 AAACGTATTAA
1 AAA-TTA-TAA
*
29317255 AATTCTATAA
1 AAAT-TATAA
29317265 AAATTATAA
1 AAATTATAA
29317274 AAA--ATAA
1 AAATTATAA
* *
29317281 AAA-AATTA
1 AAATTATAA
29317289 AAATTAATATA
1 AAATT-ATA-A
*
29317300 AACTTATAA
1 AAATTATAA
29317309 AAATTATAA
1 AAATTATAA
29317318 AAA
1 AAA
29317321 ATCATAAAAC
Statistics
Matches: 126, Mismatches: 23, Indels: 31
0.70 0.13 0.17
Matches are distributed among these distances:
7 7 0.06
8 12 0.10
9 43 0.34
10 34 0.27
11 30 0.24
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (9 bp):
AAATTATAA
Found at i:29317307 original size:35 final size:36
Alignment explanation
Indices: 29317250--29317322 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 36
29317240 ATAAAAACGT
*
29317250 ATTAAAATTCTATAAAAATTATAAAAAATA-AAAAA
1 ATTAAAATTATATAAAAATTATAAAAAATATAAAAA
* *
29317285 ATTAAAATTA-ATATAAACTTATAAAAATTATAAAAA
1 ATTAAAATTATATA-AAAATTATAAAAAATATAAAAA
29317321 AT
1 AT
29317323 CATAAAACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 3 0.09
35 23 0.70
36 7 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (36 bp):
ATTAAAATTATATAAAAATTATAAAAAATATAAAAA
Found at i:29325787 original size:29 final size:29
Alignment explanation
Indices: 29325736--29325792 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
29325726 CATATATGTT
*
29325736 GATTTTTAAACAAAATTACCGGATTAGGTC
1 GATTTTT-AACAAAATTACCGGAATAGGTC
*
29325766 GATTTTT-ACAAAATTTATCGGAATAGG
1 GATTTTTAACAAAA-TTACCGGAATAGG
29325793 CTAATTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 11 0.46
30 7 0.29
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (29 bp):
GATTTTTAACAAAATTACCGGAATAGGTC
Found at i:29326575 original size:14 final size:14
Alignment explanation
Indices: 29326556--29326583 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29326546 AGAATAGATT
29326556 TTTAATTAAATAAA
1 TTTAATTAAATAAA
29326570 TTTAATTAAATAAA
1 TTTAATTAAATAAA
29326584 AATTTTAAAC
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:29328148 original size:32 final size:32
Alignment explanation
Indices: 29328112--29328173 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
29328102 CATAAACTTT
* *
29328112 TAAATTAATTACTTGAATTTAATAACTCATGA
1 TAAATTAATTAATTCAATTTAATAACTCATGA
*
29328144 TAAATTAATTAATTCAATTTGATAACTCAT
1 TAAATTAATTAATTCAATTTAATAACTCAT
29328174 ACCGATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.42
Consensus pattern (32 bp):
TAAATTAATTAATTCAATTTAATAACTCATGA
Found at i:29328387 original size:22 final size:23
Alignment explanation
Indices: 29328362--29328412 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
29328352 TCACTATATG
29328362 AATTCTA-ATGTAGACTTAGAAT
1 AATTCTATATGTAGACTTAGAAT
* *
29328384 AATTATCTATCTGTTGACTTAGAAT
1 AA-T-TCTATATGTAGACTTAGAAT
29328409 AATT
1 AATT
29328413 ATCTATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 2 0.08
24 5 0.21
25 15 0.62
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (23 bp):
AATTCTATATGTAGACTTAGAAT
Found at i:29333488 original size:50 final size:50
Alignment explanation
Indices: 29333359--29333605 Score: 230
Period size: 50 Copynumber: 4.8 Consensus size: 50
29333349 GATAATAACA
* ** * * *
29333359 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * * * **
29333408 TGCCAAAGTCATATCCTAGATATGGTCTTACGTGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
29333458 TGCCCATGCCATGTCCCAGACATGGTCTTACA-GGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG-GACCTCTCATATCGG
* *
29333508 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
29333564 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
29333606 TTACCCAAAT
Statistics
Matches: 162, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 77 0.48
51 2 0.01
53 2 0.01
56 41 0.25
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:29337052 original size:19 final size:19
Alignment explanation
Indices: 29337028--29337066 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29337018 CGGAGAACAA
29337028 TTAGGCCTTACAAAACCTT
1 TTAGGCCTTACAAAACCTT
29337047 TTAGGCCTTACAAAACCTT
1 TTAGGCCTTACAAAACCTT
29337066 T
1 T
29337067 ATCAGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (19 bp):
TTAGGCCTTACAAAACCTT
Found at i:29339915 original size:50 final size:50
Alignment explanation
Indices: 29339791--29340032 Score: 231
Period size: 50 Copynumber: 4.7 Consensus size: 50
29339781 GATTATAACA
* * * *
29339791 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-TGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATAT-CGG
* * * *
29339840 TTCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
* * * *
29339890 TGCCCATGCCATATCCCAGACATGGTCTTACGA-GGGACATCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACTTCTCATATCGG
* * *
29339940 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT-A--TC---GG
*
29339996 TGCCAATGCCATGTCCCATACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
29340033 TATTTACCCA
Statistics
Matches: 161, Mismatches: 21, Indels: 15
0.82 0.11 0.08
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 82 0.51
51 1 0.01
53 2 0.01
56 36 0.22
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
Found at i:29347099 original size:9 final size:9
Alignment explanation
Indices: 29347085--29347121 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
29347075 TATAGTTTGA
29347085 TATTCGAAT
1 TATTCGAAT
29347094 TATTCGAAT
1 TATTCGAAT
*
29347103 TATTCGAGT
1 TATTCGAAT
*
29347112 TATTCAAAT
1 TATTCGAAT
29347121 T
1 T
29347122 CAAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:29347191 original size:9 final size:9
Alignment explanation
Indices: 29347174--29347204 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29347164 TCGAGTTGAT
29347174 TCGAATAAC
1 TCGAATAAC
*
29347183 TCGATTAAC
1 TCGAATAAC
29347192 TCGAATAAC
1 TCGAATAAC
29347201 TCGA
1 TCGA
29347205 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:29348195 original size:27 final size:27
Alignment explanation
Indices: 29348157--29348222 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
29348147 TTATTGTTAG
29348157 TTCCCAGAGGGTCGTTGGTAGTCCCAA
1 TTCCCAGAGGGTCGTTGGTAGTCCCAA
*
29348184 TTCCTAGAGGGTCGTTGGTAGTCCCAA
1 TTCCCAGAGGGTCGTTGGTAGTCCCAA
*
29348211 TTCCCAAAGGGT
1 TTCCCAGAGGGT
29348223 TGTGGACTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (27 bp):
TTCCCAGAGGGTCGTTGGTAGTCCCAA
Found at i:29349383 original size:3 final size:3
Alignment explanation
Indices: 29349375--29349400 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29349365 ACTGATGCAA
29349375 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
29349401 TGGACTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29349469 original size:45 final size:48
Alignment explanation
Indices: 29349384--29349485 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 48
29349374 AAAGAAGAAG
*
29349384 AAGAAGAAGAAGAAGAATGGACTATGGAGGGTTTATTTTAGGGATTTTT
1 AAGAA-AAGAAGAAGAATGGACTATGGAGGGTTTAATTTAGGGATTTTT
* * *
29349433 AAGAAAAGGAGAAGAATGGA-T-TTG-GGGTTTAATTTAGGGTTTTTT
1 AAGAAAAGAAGAAGAATGGACTATGGAGGGTTTAATTTAGGGATTTTT
29349478 AGAGAAAA
1 A-AGAAAA
29349486 AGATAAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 20 0.42
46 8 0.17
47 1 0.02
48 14 0.29
49 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.30, T:0.30
Consensus pattern (48 bp):
AAGAAAAGAAGAAGAATGGACTATGGAGGGTTTAATTTAGGGATTTTT
Found at i:29352932 original size:15 final size:15
Alignment explanation
Indices: 29352912--29352950 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
29352902 TCTAGGGACG
*
29352912 TGCGGTGGTGCATAC
1 TGCGGTGGTACATAC
29352927 TGCGGTGGTACATAC
1 TGCGGTGGTACATAC
29352942 TGCGGTGGT
1 TGCGGTGGT
29352951 TGTGAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.18, G:0.41, T:0.28
Consensus pattern (15 bp):
TGCGGTGGTACATAC
Found at i:29358874 original size:51 final size:51
Alignment explanation
Indices: 29358760--29358975 Score: 326
Period size: 51 Copynumber: 4.3 Consensus size: 51
29358750 CTTACGTATG
* * *
29358760 ATCACTTATCACTAGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* * * *
29358810 ATCACTTGCCACTTGTCACTGATTAGATAAGTGTAGCTAAAGTTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
29358861 ATCACTTGTCACTTGTCACTGCTCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
29358912 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
29358963 ATCACTTGTCACT
1 ATCACTTGTCACT
29358976 GATCAGAAGT
Statistics
Matches: 148, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 33 0.22
51 115 0.78
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
Found at i:29364378 original size:39 final size:39
Alignment explanation
Indices: 29364335--29364413 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
29364325 ATGTAGTAGC
29364335 AAATATAAGAGAAAGGATCAAACAATAAAGAAAATGGTT
1 AAATATAAGAGAAAGGATCAAACAATAAAGAAAATGGTT
* * * *
29364374 AAATATAGGATAAAGGATCCAGCAATAAAGAAAATGGTT
1 AAATATAAGAGAAAGGATCAAACAATAAAGAAAATGGTT
29364413 A
1 A
29364414 GAGGGTGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (39 bp):
AAATATAAGAGAAAGGATCAAACAATAAAGAAAATGGTT
Found at i:29364736 original size:106 final size:105
Alignment explanation
Indices: 29364497--29364749 Score: 267
Period size: 106 Copynumber: 2.4 Consensus size: 105
29364487 GCAGTCATAG
* * * * **
29364497 TTGTTAAAATGTGTTTGAATATATCTAACCTGACCTACTATTTATATAGTGTGTTTTCTATAATG
1 TTGTTAGAATGTGTTTGAATATATCCAACCTGACCTACTACTTATATAGTGTGTTTTCGATAAAA
* ** ** *
29364562 GAAAAGAATTAGAGGTGGAAAAAAGCTAAGAATATTTTAG
66 AAAAAGAATTAGAGGTACAAAAAAGAAAAGAATATTTTAA
* * * *
29364602 TTGTTAGAACGGGTTTGAATATACCCAACCTGACCTACTACTTCTATAGTGTGTTTTCGATTAAA
1 TTGTTAGAATGTGTTTGAATATATCCAACCTGACCTACTACTTATATAGTGTGTTTTCGA-TAAA
* *
29364667 AAAAAAGAAATT-GAGGTACACAAAAGGAAAAGACT-TTTTAA
65 AAAAAAG-AATTAGAGGTACA-AAAAAGAAAAGAATATTTTAA
* * * *
29364708 TTGTTAGCATGTGTTTGAACATATCCAACCCGACCTATTACT
1 TTGTTAGAATGTGTTTGAATATATCCAACCTGACCTACTACT
29364750 CCTTTAGAAG
Statistics
Matches: 120, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
105 52 0.43
106 54 0.45
107 14 0.12
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (105 bp):
TTGTTAGAATGTGTTTGAATATATCCAACCTGACCTACTACTTATATAGTGTGTTTTCGATAAAA
AAAAAGAATTAGAGGTACAAAAAAGAAAAGAATATTTTAA
Found at i:29365754 original size:24 final size:24
Alignment explanation
Indices: 29365712--29365763 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
29365702 AATCAAATTC
* * *
29365712 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACCAATAAATACT
*
29365736 AAATATATTATACCCATAAATACT
1 AAATATATTATACCAATAAATACT
29365760 AAAT
1 AAAT
29365764 CTTTGAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATATATTATACCAATAAATACT
Found at i:29370158 original size:24 final size:24
Alignment explanation
Indices: 29370116--29370167 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
29370106 AATCAAATTC
** *
29370116 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
29370140 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
29370164 AAAT
1 AAAT
29370168 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:29380685 original size:22 final size:22
Alignment explanation
Indices: 29380660--29380722 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 22
29380650 AAAGTAGCTT
29380660 AATTTCTCAAAAAAATTATTAA
1 AATTTCTCAAAAAAATTATTAA
* *
29380682 AA-TT-ACAAAAAAAGTAGCTT--
1 AATTTCTCAAAAAAATTA--TTAA
29380702 AATTTCTC-AAAAAATTATTAA
1 AATTTCTCAAAAAAATTATTAA
29380723 TGCAATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 13
0.65 0.08 0.27
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 12 0.39
22 5 0.16
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (22 bp):
AATTTCTCAAAAAAATTATTAA
Found at i:29383555 original size:20 final size:20
Alignment explanation
Indices: 29383530--29383567 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29383520 ACAATTTAAA
29383530 ATATAAATTTATTAATATGT
1 ATATAAATTTATTAATATGT
29383550 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
29383568 ATGTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:29383627 original size:32 final size:32
Alignment explanation
Indices: 29383586--29383672 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 32
29383576 AAAATTTCCG
*
29383586 GAAAATATTTTCAGGAAATC-TGCCAAACAACA
1 GAAAATATTTTCAGTAAATCAT-CCAAACAACA
* *
29383618 GAAAATATTTTACA-TAGATTCATCCAAACACCA
1 GAAAATATTTT-CAGTA-AATCATCCAAACAACA
29383651 GAAAATATTTTCAGTAAATCAT
1 GAAAATATTTTCAGTAAATCAT
29383673 TTTCCAGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
32 19 0.40
33 27 0.57
34 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (32 bp):
GAAAATATTTTCAGTAAATCATCCAAACAACA
Found at i:29383690 original size:20 final size:19
Alignment explanation
Indices: 29383665--29383702 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
29383655 ATATTTTCAG
29383665 TAAATCATTTTCCAGAAAAA
1 TAAATCATTTTCCA-AAAAA
29383685 TAAATCATTTTCCAAAAA
1 TAAATCATTTTCCAAAAA
29383703 TCATTTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAATCATTTTCCAAAAAA
Done.