Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 18 of 135
Found at i:4869117 original size:19 final size:19
Alignment explanation
Indices: 4869093--4869129 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4869083 TAGGGAAGTG
*
4869093 TCCTTTTTGCTTTTTATTT
1 TCCTTTTTGATTTTTATTT
*
4869112 TCCTTTTTTATTTTTATT
1 TCCTTTTTGATTTTTATT
4869130 AAAATATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.76
Consensus pattern (19 bp):
TCCTTTTTGATTTTTATTT
Found at i:4870053 original size:17 final size:17
Alignment explanation
Indices: 4869984--4870056 Score: 94
Period size: 17 Copynumber: 4.3 Consensus size: 17
4869974 GGACATTTTA
*
4869984 TTAAATTTACAAT-AAT
1 TTAAATTTAAAATAAAT
*
4870000 ATTAAACTTAAAATAAAT
1 -TTAAATTTAAAATAAAT
4870018 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
4870035 TTAATTTTAAAGTAAAT
1 TTAAATTTAAAATAAAT
4870052 TTAAA
1 TTAAA
4870057 ATAGTTTGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
17 46 0.94
18 3 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:4871011 original size:17 final size:17
Alignment explanation
Indices: 4870988--4871078 Score: 121
Period size: 17 Copynumber: 5.4 Consensus size: 17
4870978 TCAAGATCCC
4870988 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
4871006 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
4871022 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
4871039 TTTGAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
4871056 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
4871073 TTTAAA
1 TTTAAA
4871079 ATAAATAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
16 1 0.02
17 61 0.98
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:4871025 original size:6 final size:6
Alignment explanation
Indices: 4871016--4871078 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
4871006 TTAAATTTGT
* * * *
4871016 TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
4871062 TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
4871079 ATAAATAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
5 12 0.27
6 33 0.73
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:4871036 original size:11 final size:11
Alignment explanation
Indices: 4871022--4871076 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
4871012 TTGTTTTAAA
*
4871022 TTTAGATTTAT
1 TTTAAATTTAT
*
4871033 TTTAAATTTGAA
1 TTTAAATTT-AT
*
4871045 TTT-AATTTAAG
1 TTTAAATTT-AT
4871056 TTTAAATTTAT
1 TTTAAATTTAT
4871067 TTTAAATTTA
1 TTTAAATTTA
4871077 AAATAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:4871046 original size:23 final size:23
Alignment explanation
Indices: 4871020--4871077 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
4871010 ATTTGTTTTA
*
4871020 AATTTAGATTT-ATTTTAAATTTG
1 AATTTA-ATTTAAGTTTAAATTTG
4871043 AATTTAATTTAAGTTTAAATTT-
1 AATTTAATTTAAGTTTAAATTTG
*
4871065 ATTTTAAATTTAA
1 AATTT-AATTTAA
4871078 AATAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
AATTTAATTTAAGTTTAAATTTG
Found at i:4872918 original size:29 final size:29
Alignment explanation
Indices: 4872884--4873102 Score: 110
Period size: 29 Copynumber: 7.5 Consensus size: 29
4872874 AAACTATTTG
*
4872884 AAAATTACATTTTTACCCCCAAACTACCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* *** **
4872913 AAAATTTTAC-TTTTAACCTTAAAACTTTTA
1 AAAA--TTACATTTTTACCCCCAAACTTCCA
* *
4872943 AAAATTACATTTTTACCCTCGAACATT-CA
1 AAAATTACATTTTTACCCCCAAAC-TTCCA
** * *
4872972 AAAATT-CTATTTTTAACCCTAAAATTTCTA
1 AAAATTAC-ATTTTT-ACCCCCAAACTTCCA
*
4873002 AAAATTCCA-TTTTACCCCCAAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
** * * **
4873030 AAACCT-CATTTTTAACCTCAAAACTTTTTA
1 AAAATTACATTTTT-ACCCCCAAAC-TTCCA
*
4873060 AAAATTACCA-TTTTACCCCCGAA-TATCCA
1 AAAATTA-CATTTTTACCCCCAAACT-TCCA
*
4873089 AAAATTCCATTTTT
1 AAAATTACATTTTT
4873103 GATCTCAATT
Statistics
Matches: 141, Mismatches: 34, Indels: 30
0.69 0.17 0.15
Matches are distributed among these distances:
27 2 0.01
28 27 0.19
29 54 0.38
30 47 0.33
31 9 0.06
32 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCCAAACTTCCA
Found at i:4873077 original size:117 final size:117
Alignment explanation
Indices: 4872884--4873138 Score: 300
Period size: 117 Copynumber: 2.2 Consensus size: 117
4872874 AAACTATTTG
* ** * *
4872884 AAAATTACATTTTTACCCCCAAACTACCAAAAATTTTACTTTTAACCTTAAAACTTTTAAAAATT
1 AAAATTCCA-TTTTACCCCCAAACTACCAAAAACCTCACTTTTAACCTCAAAACTTTTAAAAATT
* * *
4872949 ACATTTTTACCCTCGAACATTCAAAAATTCTATTTTTAACC-CTAAAATTTCTA
65 ACATTTTTACCCCCGAACATCCAAAAATTCCATTTTTAACCTC-AAAATTTCTA
* *
4873002 AAAATTCCATTTTACCCCCAAACTTCC-AAAACCTCATTTTTAACCTCAAAACTTTTTAAAAATT
1 AAAATTCCATTTTACCCCCAAACTACCAAAAACCTCACTTTTAACCTCAAAAC-TTTTAAAAATT
* * * **
4873066 ACCA-TTTTACCCCCGAATATCCAAAAATTCCATTTTTGATCTCAATTTTTCTA
65 A-CATTTTTACCCCCGAACATCCAAAAATTCCATTTTTAACCTCAAAATTTCTA
*
4873119 AAAATTACCATTTTGCCCCC
1 AAAATT-CCATTTTACCCCC
4873139 GAGTATCCAA
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
116 20 0.17
117 74 0.63
118 23 0.20
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (117 bp):
AAAATTCCATTTTACCCCCAAACTACCAAAAACCTCACTTTTAACCTCAAAACTTTTAAAAATTA
CATTTTTACCCCCGAACATCCAAAAATTCCATTTTTAACCTCAAAATTTCTA
Found at i:4873121 original size:59 final size:59
Alignment explanation
Indices: 4872884--4873151 Score: 223
Period size: 59 Copynumber: 4.6 Consensus size: 59
4872874 AAACTATTTG
* ** * * *
4872884 AAAATTA-CATTTTTACCCCCAAACTA-CCAAAAATTTTACTTTTAACCTTAAAACTTT-TA
1 AAAATTACCA-TTTTACCCCCGAA-TATCCAAAAATTCCATTTTTAA-CTCAAAATTTTCTA
* * * * *
4872943 AAAATTA-CATTTTTACCCTCGAACATTCAAAAATTCTATTTTTAACCCTAAAA-TTTCTA
1 AAAATTACCA-TTTTACCCCCGAATATCCAAAAATTCCATTTTTAACTC-AAAATTTTCTA
* **
4873002 AAAATT-CCATTTTACCCCCAAACT-TCCAAAACCT-CATTTTTAACCTCAAAACTTTT-TA
1 AAAATTACCATTTTACCCCCGAA-TATCCAAAAATTCCATTTTTAA-CTCAAAA-TTTTCTA
* *
4873060 AAAATTACCATTTTACCCCCGAATATCCAAAAATTCCATTTTTGATCTC-AATTTTTCTA
1 AAAATTACCATTTTACCCCCGAATATCCAAAAATTCCATTTTT-AACTCAAAATTTTCTA
* *
4873119 AAAATTACCATTTTGCCCCCGAGTATCCAAAAA
1 AAAATTACCATTTTACCCCCGAATATCCAAAAA
4873152 GTCTTATTTT
Statistics
Matches: 173, Mismatches: 23, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
57 12 0.07
58 38 0.22
59 112 0.65
60 10 0.06
61 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATATCCAAAAATTCCATTTTTAACTCAAAATTTTCTA
Found at i:4876207 original size:18 final size:18
Alignment explanation
Indices: 4876184--4876220 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4876174 TTTGTGATCA
4876184 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
4876202 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
4876220 A
1 A
4876221 TATGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:4876209 original size:12 final size:12
Alignment explanation
Indices: 4876184--4876220 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
4876174 TTTGTGATCA
4876184 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
4876196 AAAGTGAAATTG
1 AAATTGAAAGTG
4876208 AAATTGAAAGTG
1 AAATTGAAAGTG
4876220 A
1 A
4876221 TATGAATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:4877612 original size:33 final size:33
Alignment explanation
Indices: 4877573--4877645 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
4877563 TCACACAAGC
4877573 TGCATTTACAA-GAGCTGCAGTCACATAAACTGT
1 TGCATTTACAAGGA-CTGCAGTCACATAAACTGT
* * *
4877606 TGCATTTACATGGATTGCAGTCATATAAACTGT
1 TGCATTTACAAGGACTGCAGTCACATAAACTGT
4877639 TGCATTT
1 TGCATTT
4877646 GCACAAACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 34 0.94
34 2 0.06
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (33 bp):
TGCATTTACAAGGACTGCAGTCACATAAACTGT
Found at i:4880198 original size:13 final size:14
Alignment explanation
Indices: 4880148--4880202 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
4880138 TTAAATCAAG
*
4880148 CTTTTT-AAAAGTA
1 CTTTTTCAAAAGCA
*
4880161 -TTTTTCAAAATCA
1 CTTTTTCAAAAGCA
*
4880174 -TTTTTCCAAAGCA
1 CTTTTTCAAAAGCA
4880187 CTTTTT-AAAAGCA
1 CTTTTTCAAAAGCA
4880200 CTT
1 CTT
4880203 CCTAAAAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 5 0.14
13 25 0.71
14 5 0.14
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (14 bp):
CTTTTTCAAAAGCA
Found at i:4882338 original size:17 final size:16
Alignment explanation
Indices: 4882315--4882373 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
4882305 TTAATAAGAT
*
4882315 TTAATATTAATTTTAA
1 TTAATATTAATATTAA
* *
4882331 TCTAATATTTATCTTAA
1 T-TAATATTAATATTAA
4882348 -TAAGTATT-ATATTAA
1 TTAA-TATTAATATTAA
4882363 TTTAATATTAA
1 -TTAATATTAA
4882374 AGTGATTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 9 0.26
16 9 0.26
17 17 0.49
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (16 bp):
TTAATATTAATATTAA
Found at i:4883732 original size:16 final size:17
Alignment explanation
Indices: 4883713--4883745 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4883703 ATGTCTTATA
4883713 AAATATATTAA-AAATT
1 AAATATATTAATAAATT
4883729 AAATATATTAATAAATT
1 AAATATATTAATAAATT
4883746 CAACACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATATTAATAAATT
Found at i:4885608 original size:19 final size:18
Alignment explanation
Indices: 4885584--4885636 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
4885574 TTAAATCCTA
*
4885584 TTTTATTTTATTTTTCTTT
1 TTTTATTTTATTTTT-TCT
**
4885603 TTTTATTGGATTTATTTCT
1 TTTTATTTTATTT-TTTCT
4885622 TTTTATATTTATTTT
1 TTTTAT-TTTATTTT
4885637 GAGGTCTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTATTTTATTTTTTCT
Found at i:4885841 original size:14 final size:14
Alignment explanation
Indices: 4885807--4885842 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4885797 TAAAATTTTA
* *
4885807 AAATTTCAAATCTT
1 AAATTTTAAAACTT
4885821 AAATTTTAAAACTT
1 AAATTTTAAAACTT
4885835 AAATTTTA
1 AAATTTTA
4885843 TAGTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTTAAAACTT
Found at i:4885877 original size:39 final size:41
Alignment explanation
Indices: 4885807--4885904 Score: 101
Period size: 39 Copynumber: 2.4 Consensus size: 41
4885797 TAAAATTTTA
* * * * * *
4885807 AAATTTCAAATCTTAAATTTTAAAACTTAAAT-TTTATAGT
1 AAATTTTAAATATTAAATGTTAAAACCTAAATATTAATACT
*
4885847 -AATTTTAAATATTAAATGTTAAACCCTAAATATTAATACT
1 AAATTTTAAATATTAAATGTTAAAACCTAAATATTAATACT
* *
4885887 AAATCTTAAAAATTAAAT
1 AAATTTTAAATATTAAAT
4885905 CCTAATCTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 26 0.55
40 6 0.13
41 15 0.32
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (41 bp):
AAATTTTAAATATTAAATGTTAAAACCTAAATATTAATACT
Found at i:4887394 original size:17 final size:18
Alignment explanation
Indices: 4887372--4887407 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4887362 AATTTGTATT
4887372 ATTAATTAT-TAAATTCG
1 ATTAATTATCTAAATTCG
*
4887389 ATTAATTATCTAATTTCG
1 ATTAATTATCTAAATTCG
4887407 A
1 A
4887408 ACCGAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (18 bp):
ATTAATTATCTAAATTCG
Found at i:4890777 original size:43 final size:43
Alignment explanation
Indices: 4890729--4890826 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
4890719 GGAAGGTACG
* * *
4890729 TGTTCTTTAGCGATGTTTGTG-GAGAAAGCGCCGCTAAAGACCA
1 TGTTCTTTAGCGACGTTTGTGAGA-AAAGCACCGCTAAAGAACA
* *
4890772 TGTTCTTTAGCGGCGTTTGTGAGAAAAGCATCGCTAAAGAACA
1 TGTTCTTTAGCGACGTTTGTGAGAAAAGCACCGCTAAAGAACA
*
4890815 TGGTCTTTAGCG
1 TGTTCTTTAGCG
4890827 GCACTTTTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 46 0.96
44 2 0.04
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
TGTTCTTTAGCGACGTTTGTGAGAAAAGCACCGCTAAAGAACA
Found at i:4894205 original size:19 final size:20
Alignment explanation
Indices: 4894181--4894225 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
4894171 TAATTAATTA
*
4894181 TTTATATATAAA-ATATAAT
1 TTTATATATAAATACATAAT
*
4894200 TTTATATTTAAATACATAAT
1 TTTATATATAAATACATAAT
*
4894220 TGTATA
1 TTTATA
4894226 CTAGATCTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTATATATAAATACATAAT
Found at i:4897506 original size:23 final size:23
Alignment explanation
Indices: 4897480--4897547 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
4897470 TTCATTTAAC
*
4897480 TTAATCGAACGTGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* * *
4897503 TTAAACAAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAACA
* *
4897526 TATAATTGAACATGTCCACGAA
1 T-TAATCGAACATGTTCACGAA
4897548 TAATGTTAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:4899191 original size:5 final size:5
Alignment explanation
Indices: 4899154--4899190 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
4899144 CGCAACGCCA
4899154 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT- TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
4899191 TGTGCTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:4900113 original size:22 final size:24
Alignment explanation
Indices: 4900083--4900127 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
4900073 AGATAACATA
4900083 ACAATATTTAATAT-AAATAATTT
1 ACAATATTTAATATCAAATAATTT
*
4900106 ACAA-ATTTAATATCACATAATT
1 ACAATATTTAATATCAAATAATT
4900128 AAGTTATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (24 bp):
ACAATATTTAATATCAAATAATTT
Found at i:4901831 original size:31 final size:33
Alignment explanation
Indices: 4901760--4901832 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 33
4901750 AAATTTTAAA
*
4901760 TTAAAAAAATTAAAAACCTAAGTTTTAATTTTT
1 TTAAAATAATTAAAAACCTAAGTTTTAATTTTT
* * *
4901793 TT--TATAATTATAAA-CTAA-TTTTAGTTTTT
1 TTAAAATAATTAAAAACCTAAGTTTTAATTTTT
4901822 TTAAAATAATT
1 TTAAAATAATT
4901833 GAGGAATATG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
29 12 0.36
30 4 0.12
31 15 0.45
33 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (33 bp):
TTAAAATAATTAAAAACCTAAGTTTTAATTTTT
Found at i:4903868 original size:23 final size:23
Alignment explanation
Indices: 4903824--4903869 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4903814 ACAATTCCTT
* *
4903824 AAAATTTTGGCCTCCTCTTGTGG
1 AAAAATTTGGCCTCCTCATGTGG
4903847 AAAAATTTGGCCT-CTGCATGTGG
1 AAAAATTTGGCCTCCT-CATGTGG
4903870 CTTTGATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (23 bp):
AAAAATTTGGCCTCCTCATGTGG
Found at i:4912561 original size:20 final size:19
Alignment explanation
Indices: 4912538--4912586 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
4912528 TTGTTAAATT
*
4912538 TTAATTTTAAATCATCAAAA
1 TTAATATTAAATCAT-AAAA
* *
4912558 TTAATATTAAGTGATAAAA
1 TTAATATTAAATCATAAAA
4912577 TTAA-ATTAAA
1 TTAATATTAAA
4912587 AATAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 12 0.48
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (19 bp):
TTAATATTAAATCATAAAA
Found at i:4917037 original size:3 final size:3
Alignment explanation
Indices: 4917029--4917062 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4917019 ATATATAATA
4917029 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4917063 TTAAACACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4917389 original size:31 final size:31
Alignment explanation
Indices: 4917332--4917395 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
4917322 GTATACTAAT
*
4917332 AATGTATTTTTTTATTATTTAAATAGTCTTA
1 AATGTATTTTTTTATTATTCAAATAGTCTTA
4917363 AATGTATTTTTTTATTATTCAAATAGTCTTA
1 AATGTATTTTTTTATTATTCAAATAGTCTTA
4917394 AA
1 AA
4917396 AAATTATCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (31 bp):
AATGTATTTTTTTATTATTCAAATAGTCTTA
Found at i:4929750 original size:2 final size:2
Alignment explanation
Indices: 4929743--4929767 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4929733 GATTACACGA
4929743 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4929768 AAGGGAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4934601 original size:23 final size:23
Alignment explanation
Indices: 4934531--4934589 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
4934521 AATGGACAAA
*
4934531 TAAACGGAGAGCACA-AACGTGC
1 TAAACAGAGAGCACACAACGTGC
*
4934553 TAAACAGAGAGCACACAAAGTGC
1 TAAACAGAGAGCACACAACGTGC
4934576 TAAACAGAGAGCAC
1 TAAACAGAGAGCAC
4934590 TTTACGTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.46, C:0.22, G:0.24, T:0.08
Consensus pattern (23 bp):
TAAACAGAGAGCACACAACGTGC
Found at i:4937558 original size:15 final size:14
Alignment explanation
Indices: 4937540--4937573 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
4937530 AAATAATAAA
4937540 ATATTATTATTTATT
1 ATATTATTA-TTATT
4937555 ATATTATTATTATT
1 ATATTATTATTATT
4937569 A-ATTA
1 ATATTA
4937574 ATATATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 6 0.32
15 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTATTATTATT
Found at i:4940801 original size:32 final size:31
Alignment explanation
Indices: 4940748--4940814 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
4940738 GTTTTTAATG
* *
4940748 TTTATTTTTTTATAAAATTGATCTTTATTTT
1 TTTATTTTTTTATAAAATTGATCATTAATTT
*
4940779 TTTA-TTTTTTAGTTAAATTTGATCATTAATTT
1 TTTATTTTTTTA--TAAAATTGATCATTAATTT
4940811 TTTA
1 TTTA
4940815 AAAAAGAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 4 0.13
32 20 0.65
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (31 bp):
TTTATTTTTTTATAAAATTGATCATTAATTT
Found at i:4943665 original size:13 final size:15
Alignment explanation
Indices: 4943645--4943677 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4943635 TTATCCCGAT
*
4943645 AAATTTTTTATT-TA
1 AAATTTTTAATTATA
4943659 AAATTTTTAATTATA
1 AAATTTTTAATTATA
4943674 AAAT
1 AAAT
4943678 ATATAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTTTTAATTATA
Found at i:4948105 original size:22 final size:21
Alignment explanation
Indices: 4948080--4948120 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4948070 AATATAATAA
*
4948080 CAAACTGACAACAAAACAACAT
1 CAAAATGACAAC-AAACAACAT
*
4948102 CAAAATGATAACAAACAAC
1 CAAAATGACAACAAACAAC
4948121 GGTAAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.61, C:0.24, G:0.05, T:0.10
Consensus pattern (21 bp):
CAAAATGACAACAAACAACAT
Found at i:4952019 original size:21 final size:21
Alignment explanation
Indices: 4952002--4952052 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
4951992 GAATTTCAGC
*
4952002 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
4952023 AGCAAACTGTAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
4952044 AGAAAACTA
1 AGCAAACTA
4952053 AGGCATCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (21 bp):
AGCAAACTATAGATTTTCAAA
Found at i:4955924 original size:3 final size:3
Alignment explanation
Indices: 4955918--4955976 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
4955908 TTAATTTTTT
* * *
4955918 TTA TTA TTA TTA TTA -TA TTA TTA -TA TTA TTA TTT TTA TTT TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4955964 TTAA TTAA TTA TT
1 TT-A TT-A TTA TT
4955977 TTTTATTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.09
3 36 0.77
4 7 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4955932 original size:22 final size:21
Alignment explanation
Indices: 4955911--4955980 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 21
4955901 AACCCAATTA
4955911 ATTTTTTTTATTATTATTATT
1 ATTTTTTTTATTATTATTATT
* *
4955932 A-TATTATTA-TATTATTATT
1 ATTTTTTTTATTATTATTATT
*
4955951 -TTTATTTTTATAATTAATTAATT
1 ATTT-TTTTTATTATT-ATT-ATT
4955974 ATTTTTT
1 ATTTTTT
4955981 ATTTGTCCAG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 11 0.29
20 11 0.29
21 4 0.11
22 3 0.08
23 6 0.16
24 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTTTTTATTATTATTATT
Found at i:4955938 original size:8 final size:8
Alignment explanation
Indices: 4955918--4955976 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
4955908 TTAATTTTTT
4955918 TTATTATTA
1 TTATTA-TA
4955927 TTATTATA
1 TTATTATA
4955935 TTATTATA
1 TTATTATA
4955943 TTATTAT-
1 TTATTATA
4955950 TT-TTAT-
1 TTATTATA
4955956 TT-TTATAA
1 TTATTAT-A
4955964 TTAATTA-A
1 TT-ATTATA
4955972 TTATT
1 TTATT
4955977 TTTTATTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
6 10 0.22
7 5 0.11
8 22 0.48
9 6 0.13
10 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATTATA
Found at i:4958374 original size:19 final size:21
Alignment explanation
Indices: 4958331--4958377 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
4958321 ATTTTTGTTA
4958331 GGATTTAATATTTAAGATATT
1 GGATTTAATATTTAAGATATT
*
4958352 --ATTTATTATTTAA-AT-TT
1 GGATTTAATATTTAAGATATT
4958369 GGATTTAAT
1 GGATTTAAT
4958378 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (21 bp):
GGATTTAATATTTAAGATATT
Found at i:4959410 original size:13 final size:14
Alignment explanation
Indices: 4959380--4959418 Score: 62
Period size: 13 Copynumber: 2.8 Consensus size: 14
4959370 AACTAATTTC
4959380 TTTTTAATTTTAGCT
1 TTTTTAATTTTA-CT
4959395 TTTTTAATTTTA-T
1 TTTTTAATTTTACT
4959408 TTTTTAATTTT
1 TTTTTAATTTT
4959419 TTATAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTAATTTTACT
Found at i:4959991 original size:44 final size:44
Alignment explanation
Indices: 4959943--4960038 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
4959933 GTAAAATGCA
* *
4959943 TAAAAATAACATCCAAA-CAACCAAAATAACAACCAAAACAACAG
1 TAAAAATAACA-CCAAAGCAACAAAAATAACAACAAAAACAACAG
* * *
4959987 TAAAAATAACAGCAAAGCAACAAAAATAGCAACAAAAATAACAG
1 TAAAAATAACACCAAAGCAACAAAAATAACAACAAAAACAACAG
*
4960031 CAAAAATA
1 TAAAAATA
4960039 GCAACAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 4 0.09
44 41 0.91
ACGTcount: A:0.66, C:0.20, G:0.05, T:0.09
Consensus pattern (44 bp):
TAAAAATAACACCAAAGCAACAAAAATAACAACAAAAACAACAG
Found at i:4959992 original size:24 final size:23
Alignment explanation
Indices: 4959944--4960047 Score: 69
Period size: 20 Copynumber: 4.7 Consensus size: 23
4959934 TAAAATGCAT
*
4959944 AAAAATAACATCC-AAACAAC--
1 AAAAATAACAACCAAAACAACAG
*
4959964 CAAAATAACAACCAAAACAACAG
1 AAAAATAACAACCAAAACAACAG
* *
4959987 TAAAAATAAC-AGCAAAGCAAC--
1 -AAAAATAACAACCAAAACAACAG
* * *
4960008 AAAAATAGCAACAAAAATAACAG
1 AAAAATAACAACCAAAACAACAG
*
4960031 CAAAAATAGCAA-CAAAA
1 -AAAAATAACAACCAAAA
4960048 TTAGCAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
20 19 0.29
21 14 0.22
23 13 0.20
24 19 0.29
ACGTcount: A:0.66, C:0.20, G:0.06, T:0.08
Consensus pattern (23 bp):
AAAAATAACAACCAAAACAACAG
Found at i:4960017 original size:12 final size:12
Alignment explanation
Indices: 4960002--4960062 Score: 86
Period size: 12 Copynumber: 5.1 Consensus size: 12
4959992 ATAACAGCAA
4960002 AGCAACAAAAAT
1 AGCAACAAAAAT
4960014 AGCAACAAAAAT
1 AGCAACAAAAAT
* *
4960026 AACAGCAAAAAT
1 AGCAACAAAAAT
*
4960038 AGCAACAAAATT
1 AGCAACAAAAAT
*
4960050 AGCAAAAAAAAT
1 AGCAACAAAAAT
4960062 A
1 A
4960063 AAAGCATCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.67, C:0.15, G:0.08, T:0.10
Consensus pattern (12 bp):
AGCAACAAAAAT
Found at i:4960053 original size:36 final size:33
Alignment explanation
Indices: 4959988--4960068 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 33
4959978 AAACAACAGT
*
4959988 AAAAATAACAGC-AAAGCAACAAAAATAGCAAC
1 AAAAATAACAGCAAAAGCAACAAAAATAGCAAA
*
4960020 AAAAATAACAGCAAAAATAGCAACAAAATTAGCAAA
1 AAAAATAACAGC--AAA-AGCAACAAAAATAGCAAA
*
4960056 AAAAATAAAAGCA
1 AAAAATAACAGCA
4960069 TCAAAACAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 12 0.29
34 1 0.02
35 2 0.05
36 27 0.64
ACGTcount: A:0.68, C:0.15, G:0.09, T:0.09
Consensus pattern (33 bp):
AAAAATAACAGCAAAAGCAACAAAAATAGCAAA
Found at i:4960140 original size:17 final size:17
Alignment explanation
Indices: 4960112--4960151 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4960102 TAAAACAATA
*
4960112 AAAAAACACAAAAATAGT
1 AAAAAACAC-AAAACAGT
4960130 AAAAAAC-CAAAACAGT
1 AAAAAACACAAAACAGT
4960146 AAAAAA
1 AAAAAA
4960152 AGCAACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.75, C:0.12, G:0.05, T:0.07
Consensus pattern (17 bp):
AAAAAACACAAAACAGT
Found at i:4960163 original size:37 final size:35
Alignment explanation
Indices: 4960103--4960172 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 35
4960093 AACAGCAACT
4960103 AAAACAATAAAAAAACACAAAAATAGTAAAAAACC
1 AAAACAATAAAAAAACACAAAAATAGTAAAAAACC
* *
4960138 AAAACAGTAAAAAAAGCAACTAAAATAGTAAAAAA
1 AAAACAATAAAAAAA-C-ACAAAAATAGTAAAAAA
4960173 ATAACACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 14 0.45
36 1 0.03
37 16 0.52
ACGTcount: A:0.73, C:0.11, G:0.06, T:0.10
Consensus pattern (35 bp):
AAAACAATAAAAAAACACAAAAATAGTAAAAAACC
Found at i:4963337 original size:3 final size:3
Alignment explanation
Indices: 4963329--4963363 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4963319 GAAACTTTGC
4963329 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
4963364 ATTAACATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:4965580 original size:2 final size:2
Alignment explanation
Indices: 4965573--4965604 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4965563 TTTTGTGTTT
4965573 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4965605 ATACGTACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4967698 original size:15 final size:15
Alignment explanation
Indices: 4967678--4967714 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
4967668 TAACTTAAAA
4967678 TATAAATTTTAAATT
1 TATAAATTTTAAATT
4967693 TATAAATTTTAAATT
1 TATAAATTTTAAATT
4967708 TATAAAT
1 TATAAAT
4967715 GGTTGTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATAAATTTTAAATT
Found at i:4967700 original size:8 final size:8
Alignment explanation
Indices: 4967678--4967714 Score: 60
Period size: 7 Copynumber: 4.9 Consensus size: 8
4967668 TAACTTAAAA
4967678 TATAAATT
1 TATAAATT
4967686 T-TAAATT
1 TATAAATT
4967693 TATAAATT
1 TATAAATT
4967701 T-TAAATT
1 TATAAATT
4967708 TATAAAT
1 TATAAAT
4967715 GGTTGTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 14 0.52
8 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TATAAATT
Found at i:4972298 original size:15 final size:14
Alignment explanation
Indices: 4972270--4972308 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
4972260 TTTATTTTAA
4972270 TATTTAATAATTTT
1 TATTTAATAATTTT
*
4972284 TATTTAATAAATTT
1 TATTTAATAATTTT
4972298 T-TTTATATAAT
1 TATTTA-ATAAT
4972309 CATCTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTAATAATTTT
Found at i:4986041 original size:160 final size:160
Alignment explanation
Indices: 4985777--4986071 Score: 439
Period size: 160 Copynumber: 1.8 Consensus size: 160
4985767 CACCAGAGAA
* * *
4985777 CTTAAGGTGGTGGCCCATATAATTTCAAACTGTATCGTGATTGCTAAGTGATACCCTAATTACCC
1 CTTAAGGTGGTGGCCCATATAATTCCAAAATATATCGTGATTGCTAAGTGATACCCTAATTACCC
** * * *
4985842 AAAGAGTCTTTATATGATAAAGGCATCAGATTTAAATCATATTGCACTTTTCAACGCAACATCAT
66 AAAGAACCTCTATATGACAAAGGCATCAGATTTAAATCATATTGCACTTTTCAACGCAACACCAT
4985907 GCACTTTTAAGATTCTAACTTTGAAAAGAG
131 GCACTTTTAAGATTCTAACTTTGAAAAGAG
* * * * *
4985937 CTTAAGGTGGTGGCCCATGTAATTCCAAAATATATCGTGGTTGTTAAGTGATACTCTAATTGCCC
1 CTTAAGGTGGTGGCCCATATAATTCCAAAATATATCGTGATTGCTAAGTGATACCCTAATTACCC
* *
4986002 AAAGAACCTCTATATGACAATGGCATTAG-TTTCAAATCATATTGCACTTTTCAACGCAACACCA
66 AAAGAACCTCTATATGACAAAGGCATCAGATTT-AAATCATATTGCACTTTTCAACGCAACACCA
4986066 TGCACT
130 TGCACT
4986072 CTTACTCTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
159 3 0.03
160 116 0.97
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (160 bp):
CTTAAGGTGGTGGCCCATATAATTCCAAAATATATCGTGATTGCTAAGTGATACCCTAATTACCC
AAAGAACCTCTATATGACAAAGGCATCAGATTTAAATCATATTGCACTTTTCAACGCAACACCAT
GCACTTTTAAGATTCTAACTTTGAAAAGAG
Found at i:4991142 original size:24 final size:23
Alignment explanation
Indices: 4991107--4991168 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
4991097 CTATATAAAA
4991107 AAAATTTATAAATA-AAAAATATAT
1 AAAA-TTATAAATATAAAAATAT-T
*
4991131 AAAATTACTAAATATTAAAATATT
1 AAAATTA-TAAATATAAAAATATT
4991155 AAAA-TATAAATATA
1 AAAATTATAAATATA
4991169 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 7 0.21
23 5 0.15
24 15 0.44
25 7 0.21
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATTATAAATATAAAAATATT
Found at i:4991151 original size:8 final size:8
Alignment explanation
Indices: 4991122--4991183 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
4991112 TTATAAATAA
4991122 AAAATATAT
1 AAAATAT-T
*
4991131 AAAATTACT
1 AAAA-TATT
4991140 -AAATATT
1 AAAATATT
4991147 AAAATATT
1 AAAATATT
4991155 AAAATA-T
1 AAAATATT
4991162 AAATATATTT
1 AAA-ATA-TT
*
4991172 AAAAAATT
1 AAAATATT
4991180 AAAA
1 AAAA
4991184 ATAATATCAG
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
7 7 0.16
8 25 0.56
9 7 0.16
10 6 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:4997130 original size:17 final size:17
Alignment explanation
Indices: 4997108--4997183 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
4997098 TTCAATGAGA
4997108 TAAATTTAATTTTAAA-T
1 TAAATTT-ATTTTAAATT
4997125 TAAATTTATTTTAAATT
1 TAAATTTATTTTAAATT
*** *
4997142 TAAATTTGCATAAAATT
1 TAAATTTATTTTAAATT
*
4997159 TAAATTTATTATAAATT
1 TAAATTTATTTTAAATT
4997176 TAAATTTA
1 TAAATTTA
4997184 AAATTAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
16 8 0.16
17 41 0.84
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:4997145 original size:6 final size:6
Alignment explanation
Indices: 4997108--4997193 Score: 74
Period size: 6 Copynumber: 15.0 Consensus size: 6
4997098 TTCAATGAGA
* * **
4997108 TAAATT TAATTT TAAA-T TAAATT T-ATTT TAAATT TAAATT TGCA-T
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
4997153 AAAATT TAAATT T--ATT ATAAATT TAAATT TAAAAT TAAATT
1 TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT TAAATT
4997194 GGATAAAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
4 3 0.05
5 12 0.19
6 44 0.71
7 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:4997160 original size:45 final size:45
Alignment explanation
Indices: 4997109--4997203 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
4997099 TCAATGAGAT
* * *
4997109 AAATTTAATTTTAA-ATTAAATTT-ATTTTAAATTTAAATTTGCATA
1 AAATTTAAATTTAATA-TAAATTTAAATTTAAAATTAAA-TTGCATA
* *
4997154 AAATTTAAATTTATTATAAATTTAAATTTAAAATTAAATTGGATA
1 AAATTTAAATTTAATATAAATTTAAATTTAAAATTAAATTGCATA
4997199 AAATT
1 AAATT
4997204 AATGTCTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
45 30 0.70
46 13 0.30
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (45 bp):
AAATTTAAATTTAATATAAATTTAAATTTAAAATTAAATTGCATA
Found at i:4998597 original size:2 final size:2
Alignment explanation
Indices: 4998590--4998631 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4998580 AGAAGAGGGT
4998590 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4998632 TTTTAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4998810 original size:32 final size:33
Alignment explanation
Indices: 4998761--4998824 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
4998751 TACGTGTTTG
*
4998761 GTCCTTTCATATTTTTTAATT-GTTTTAATTTA
1 GTCCTTTCATATCTTTTAATTAGTTTTAATTTA
*
4998793 GTCCTTTTCATA-CTTTTAATTATTTTTAATTT
1 GTCC-TTTCATATCTTTTAATTAGTTTTAATTT
4998825 GGCCCAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (33 bp):
GTCCTTTCATATCTTTTAATTAGTTTTAATTTA
Found at i:4999152 original size:29 final size:28
Alignment explanation
Indices: 4999098--4999210 Score: 111
Period size: 29 Copynumber: 3.8 Consensus size: 28
4999088 CCGTAAAGTG
* *
4999098 TTCAAAAATTATATTTGTGATCCCAAAAC
1 TTCAAAAATTATATTT-TAACCCCAAAAC
4999127 TTCAGAAAATTATATTTTAACCCCAAAAC
1 TTCA-AAAATTATATTTTAACCCCAAAAC
* *
4999156 TTCTAAAAATTACCATTTT-ACCCCTAAAC
1 TTC-AAAAATTA-TATTTTAACCCCAAAAC
*
4999185 TTTCCAAAATTCCATATTTTAACCCC
1 -TTCAAAAATT--ATATTTTAACCCC
4999211 GATTTCACCC
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
29 39 0.55
30 26 0.37
31 6 0.08
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.35
Consensus pattern (28 bp):
TTCAAAAATTATATTTTAACCCCAAAAC
Found at i:4999209 original size:60 final size:57
Alignment explanation
Indices: 4999138--4999292 Score: 154
Period size: 58 Copynumber: 2.6 Consensus size: 57
4999128 TCAGAAAATT
4999138 ATATTTTAACCCCAAAACTTCTA-AAAATTACCATTTTACCCCTAAACTTTCCAAAAT-TCC
1 ATATTTTAACCCC--AACTTC-ACAAAATTACCATTTTACCCC-AAACTTTCCAAAATCT-C
* * * *
4999198 ATATTTTAACCCCGATTTCACCCAAAATTACCATTTTGCGCCAAACTTTCCAAAATCTC
1 ATATTTTAACCCCAACTTCA--CAAAATTACCATTTTACCCCAAACTTTCCAAAATCTC
* *
4999257 AT-TTTTAACCCCGATTTCACCAAAAATTACCATTTT
1 ATATTTTAACCCCAACTTCA-C-AAAATTACCATTTT
4999293 TAACCTCGAA
Statistics
Matches: 86, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
57 3 0.03
58 35 0.41
59 17 0.20
60 31 0.36
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (57 bp):
ATATTTTAACCCCAACTTCACAAAATTACCATTTTACCCCAAACTTTCCAAAATCTC
Found at i:4999272 original size:58 final size:60
Alignment explanation
Indices: 4999160--4999292 Score: 209
Period size: 58 Copynumber: 2.2 Consensus size: 60
4999150 CAAAACTTCT
4999160 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATATTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATATTTTAACCCCGATTTCACC
* * *
4999220 CAAAATTACCATTTTGCGCC-AAACTTTCCAAAA-TCTCAT-TTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTC-CATATTTTAACCCCGATTTCACC
4999278 AAAAATTACCATTTT
1 AAAAATTACCATTTT
4999293 TAACCTCGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
58 35 0.51
59 16 0.24
60 17 0.25
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (60 bp):
AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATATTTTAACCCCGATTTCACC
Found at i:4999292 original size:31 final size:29
Alignment explanation
Indices: 4999188--4999297 Score: 86
Period size: 31 Copynumber: 3.7 Consensus size: 29
4999178 CCTAAACTTT
4999188 CCAAAATTCCATATTTTAACCCCGATTTCA
1 CCAAAATTCCAT-TTTTAACCCCGATTTCA
* **
4999218 CCCAAAATTACCA-TTTT-GCGCCAAACTTT--
1 -CCAAAATT-CCATTTTTAAC-CCCGA-TTTCA
4999247 CCAAAA-TCTCATTTTTAACCCCGATTTCA
1 CCAAAATTC-CATTTTTAACCCCGATTTCA
4999276 CCAAAAATTACCATTTTTAACC
1 CC-AAAATT-CCATTTTTAACC
4999298 TCGAATTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
26 1 0.02
27 6 0.10
28 13 0.21
29 4 0.06
30 11 0.18
31 23 0.37
32 4 0.06
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
CCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:5002152 original size:13 final size:13
Alignment explanation
Indices: 5002110--5002152 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5002100 ATTTTCATTT
5002110 AATTATCATTAAA
1 AATTATCATTAAA
* *
5002123 AATTCTCA-AAAA
1 AATTATCATTAAA
5002135 GAATTATCATTAAA
1 -AATTATCATTAAA
5002149 AATT
1 AATT
5002153 TATAAATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 18 0.75
14 3 0.12
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (13 bp):
AATTATCATTAAA
Found at i:5010683 original size:24 final size:24
Alignment explanation
Indices: 5010648--5010697 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5010638 GAGTTATAAT
*
5010648 TTAATAATAAATTATTA-TGTTTTA
1 TTAATAATAAATT-TTATTATTTTA
5010672 TTAAT-ATAAAATTTTATTATTTTA
1 TTAATAAT-AAATTTTATTATTTTA
5010696 TT
1 TT
5010698 TTTTAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAATAATAAATTTTATTATTTTA
Found at i:5014920 original size:18 final size:19
Alignment explanation
Indices: 5014899--5014937 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5014889 TCTTTTTATT
*
5014899 TTATTTTTATTTAA-TAAA
1 TTATTGTTATTTAATTAAA
*
5014917 TTATTGTTCTTTAATTAAA
1 TTATTGTTATTTAATTAAA
5014936 TT
1 TT
5014938 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATTGTTATTTAATTAAA
Found at i:5031915 original size:15 final size:15
Alignment explanation
Indices: 5031897--5031930 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5031887 AATATGTTTA
5031897 TTTATAATATTTATT
1 TTTATAATATTTATT
* *
5031912 TTTATATTTTTTATT
1 TTTATAATATTTATT
5031927 TTTA
1 TTTA
5031931 AAATTACCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATAATATTTATT
Found at i:5033275 original size:18 final size:17
Alignment explanation
Indices: 5033248--5033281 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5033238 CTTTAAAAAT
5033248 TATAAAAATATAAATTAA
1 TATAAAAATA-AAATTAA
*
5033266 TATAATAATAAAATTA
1 TATAAAAATAAAATTA
5033282 CATTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TATAAAAATAAAATTAA
Found at i:5037427 original size:58 final size:59
Alignment explanation
Indices: 5037377--5037528 Score: 218
Period size: 60 Copynumber: 2.6 Consensus size: 59
5037367 GTAAAAATGA
5037377 AATTTTGGTGAAATCGGGGTCAAAAATGGAATTTT-GAAACATTCGGGGGTAAAATGGT
1 AATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAACATTCGGGGGTAAAATGGT
* * ** *
5037435 AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTGGCAAGTTTGGGGGGTAAAATGGT
1 AATTTTGGTGAAATCGGGGTCAAAAATGGAA-TTTTGGAAACATTCGGGGGTAAAATGGT
* *
5037495 AATTTTGGTGAAATCGAGGTC-AAAATGTAATTTT
1 AATTTTGGTGAAATCGGGGTCAAAAATGGAATTTT
5037529 CGGATAGTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
58 34 0.40
59 12 0.14
60 38 0.45
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (59 bp):
AATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAACATTCGGGGGTAAAATGGT
Found at i:5037463 original size:30 final size:29
Alignment explanation
Indices: 5037337--5037528 Score: 129
Period size: 29 Copynumber: 6.7 Consensus size: 29
5037327 GGATACCCGA
*
5037337 GGGT-AAAATGGTAATTTT--TGACTATCG
1 GGGTAAAAATGGTAATTTTGGTGA-AATCG
*
5037364 AGGGTAAAAAT-GAAATTTTGGTGAAATCG
1 -GGGTAAAAATGGTAATTTTGGTGAAATCG
*
5037393 GGGTCAAAAATGG-AATTTT-G-AAACATTCGG
1 GGGT-AAAAATGGTAATTTTGGTGAA-A-TC-G
5037423 GGGT-AAAATGGTAATTTTGGTGAAATCG
1 GGGTAAAAATGGTAATTTTGGTGAAATCG
* * *
5037451 GGGTTAAAAATGG-AATTTTTGG-CAAGTTTGGG
1 GGG-TAAAAATGGTAA-TTTTGGTGAA--AT-CG
5037483 GGGT-AAAATGGTAATTTTGGTGAAATCG
1 GGGTAAAAATGGTAATTTTGGTGAAATCG
* *
5037511 AGGTCAAAAT-GTAATTTT
1 GGGTAAAAATGGTAATTTT
5037529 CGGATAGTTT
Statistics
Matches: 133, Mismatches: 11, Indels: 40
0.72 0.06 0.22
Matches are distributed among these distances:
27 2 0.02
28 40 0.30
29 42 0.32
30 37 0.28
31 8 0.06
32 4 0.03
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGGTAATTTTGGTGAAATCG
Found at i:5038686 original size:21 final size:21
Alignment explanation
Indices: 5038662--5038712 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
5038652 TAATATTTAC
*
5038662 TTATTATTAAAACATTTCTTA
1 TTATTATTAAAACATTTATTA
*
5038683 TTATTATTAAAGCATTTATTA
1 TTATTATTAAAACATTTATTA
*
5038704 TAATTATTA
1 TTATTATTA
5038713 TTAATATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (21 bp):
TTATTATTAAAACATTTATTA
Found at i:5038701 original size:18 final size:18
Alignment explanation
Indices: 5038656--5038709 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
5038646 AATAAATAAT
5038656 ATTTACTTATTATTAAAAC
1 ATTTA-TTATTATTAAAAC
*
5038675 ATTTCTTATTATTATTAAAGC
1 A--T-TTATTATTATTAAAAC
*
5038696 ATTTATTATAATTA
1 ATTTATTATTATTA
5038710 TTATTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 11 0.37
19 2 0.07
21 14 0.47
22 3 0.10
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTTATTATTATTAAAAC
Found at i:5039433 original size:20 final size:20
Alignment explanation
Indices: 5039404--5039450 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5039394 AACTTTGGAC
* *
5039404 TTGTAATTGGACTTTTAATT
1 TTGTATTTGGACATTTAATT
5039424 TTGTATTTGGACATTTAATT
1 TTGTATTTGGACATTTAATT
5039444 TT-TATTT
1 TTGTATTT
5039451 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.23, C:0.04, G:0.13, T:0.60
Consensus pattern (20 bp):
TTGTATTTGGACATTTAATT
Found at i:5039470 original size:17 final size:17
Alignment explanation
Indices: 5039444--5039480 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5039434 ACATTTAATT
*
5039444 TTTATTTTAAATTTAAA
1 TTTATATTAAATTTAAA
*
5039461 TTTATATTAAGTTTAAA
1 TTTATATTAAATTTAAA
5039478 TTT
1 TTT
5039481 TAGAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATATTAAATTTAAA
Found at i:5040214 original size:200 final size:200
Alignment explanation
Indices: 5039865--5041164 Score: 1887
Period size: 200 Copynumber: 6.6 Consensus size: 200
5039855 GTTTCGTTGA
* * * ** *
5039865 CTTCGATCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTCGCTTGCATT-AG-TTT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGTT
* * * * * * * * * *
5039928 GATTTGGTCTTCTTCTCAGTGTATCATCAGAAAGATGACCGCCTTGATTGTCTTAATTCACTTCT
66 GAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCT
* *
5039993 CTGGATCTCCTCAGGAAGACGAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGCTAACCGTTT
131 CTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTT
5040058 TATTG
196 TATTG
*
5040063 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAAATTGGCTCGTGTTGAGCGTT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGTT
5040128 GAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCT
66 GAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCT
* *
5040193 CTGGATCTCCTTAGAAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTT
131 CTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTT
5040258 TATTG
196 TATTG
* * * * *
5040263 CTCCGACCTACTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAAATTGGGTCGTGTTAAGCGTT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGTT
* *
5040328 GAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGCTTGTTTTAATTTGCTTCT
66 GAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCT
* *
5040393 CTAGATCTCCTCAGGAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTT
131 CTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTT
5040458 TATTG
196 TATTG
* *
5040463 CTTCGACCTGC-T-T-A-----TCA--A-GAAGCTGGGTTCGAAAATTAGG-TCGTGTTGAGCAT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATT-GGCTCGTGTTGAGCGT
* * **
5040516 TGAGTTAGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGTCTCGCTTGTTTTAATTTACTTC
65 TGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTC
* * * *
5040581 TCTAGATCTCCTCAGGAAGACTAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGCTAACTATT
130 TCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATT
5040646 TTATTG
195 TTATTG
* * ** *
5040652 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTTCGAAGATTTGCTCGCATTAAGCGTT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGTT
* *
5040717 GAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGATTGTTTTAATTCGCTTCT
66 GAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCT
* *
5040782 CTGGATCTCCTCAGGAAGACAAATTTAGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTT
131 CTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTT
*
5040847 AATTG
196 TATTG
* * * *
5040852 TTTCGACCTGCTTCTCAGTGTCTCATCAGGAAACTGGGTACGAAGATTTGCTCGCT-TTGAGCGT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCG-TGTTGAGCGT
5040916 TGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTG-TTGTTTTAATTCGCTT
65 TGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTC-GCTTGTTTTAATTCGCTT
* * *
5040980 CTCTGGATCTCCTTAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAGCTAACCAT
129 CTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCAT
5041045 TTTATTG
194 TTTATTG
* * * *
5041052 TTTCGACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCT-TTGAGCGT
1 CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCG-TGTTGAGCGT
*
5041116 TGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGCT
65 TGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCT
5041165 GTCTTGTTGA
Statistics
Matches: 1008, Mismatches: 76, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
189 169 0.17
190 4 0.00
191 1 0.00
192 4 0.00
197 4 0.00
198 53 0.05
199 6 0.01
200 766 0.76
201 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (200 bp):
CTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGTT
GAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCT
CTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTT
TATTG
Found at i:5040772 original size:589 final size:595
Alignment explanation
Indices: 5039937--5041169 Score: 1847
Period size: 589 Copynumber: 2.1 Consensus size: 595
5039927 TGATTTGGTC
* * * * * * *
5039937 TTCTTCTCAGTGTATCATCAGAAAGATGACCGCCTTGATTGTCTTAATTCACTTCTCTGGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTCTTAATTCACTTCTCTAGATCTC
* *
5040002 CTCAGGAAGACGAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGCTAACCGTTTTATTGCTTC
66 CTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* ** *
5040067 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAAATTGGCTCGTGTTGAGCGTTGAGT
131 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTTCGAAAATTGGCTCGCATTAAGCGTTGAGT
* *
5040132 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGG
196 TGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGATTGTTTTAATTCGCTTCTCTGG
* * * *
5040197 ATCTCCTTAGAAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
261 ATCTCCTCAGAAAGACAAATTTAGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTAATT
* * *
5040262 GCTCCGACCTACTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAAATTGGGTCG-TGTTAAGCG
326 GCTCCGACCTACTTCTCAGTGTCTCATCAGGAAACTGGGTACGAAAATTGGCTCGCT-TTAAGCG
*
5040326 TTGAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTC-GCTTGTTTTAATTTGCT
390 TTGAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCTG-TTGTTTTAATTCGCT
* * *
5040390 TCTCTAGATCTCCTCAGGAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCA
454 TCTCTAGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAGCTAACCA
* *
5040455 TTTTATTGCTTCGACCTGC-T-T-A-TCA-A-GAAGCTGGGTTCGAAAATTAGGTCG-TGTTGAG
519 TTTTATTGCTTCGACCTGCTTCTCAGTCACAGGAAGCTGGGTACGAAAATTAGCTCGCT-TTGAG
5040513 CATTGAGTTAGTA
583 CATTGAGTTAGTA
* * *
5040526 TTCTTCTCTGTATCTCATCAGGAAGATGACCGTCTCGCTTGTTTTAATTTACTTCTCTAGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTCTTAATTCACTTCTCTAGATCTC
* * *
5040591 CTCAGGAAGACTAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGCTAACTATTTTATTGCTTC
66 CTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* *
5040656 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTTCGAAGATTTGCTCGCATTAAGCGTTGAGT
131 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTTCGAAAATTGGCTCGCATTAAGCGTTGAGT
5040721 TGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGATTGTTTTAATTCGCTTCTCTGG
196 TGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGATTGTTTTAATTCGCTTCTCTGG
*
5040786 ATCTCCTCAGGAAGACAAATTTAGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTAATT
261 ATCTCCTCAGAAAGACAAATTTAGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTAATT
* * * * * *
5040851 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAACTGGGTACGAAGATTTGCTCGCTTTGAGCGT
326 GCTCCGACCTACTTCTCAGTGTCTCATCAGGAAACTGGGTACGAAAATTGGCTCGCTTTAAGCGT
*
5040916 TGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTC
391 TGAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTC
* *
5040981 TCTGGATCTCCTTAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAGCTAACCATT
456 TCTAGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAGCTAACCATT
* * * *
5041046 TTATTGTTTCGACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTG
521 TTATTGCTTCGACCTGCTTCTCA--G--TCA-CAGGAAGCTGGGTACGAAAATTAGCTCGCTTTG
* *
5041111 AGCGTTGAGTTGGTA
581 AGCATTGAGTTAGTA
*
5041126 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCGC-TGTCTT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTCTT
5041170 GTTGAACTAC
Statistics
Matches: 575, Mismatches: 55, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
589 487 0.85
590 3 0.01
591 1 0.00
592 1 0.00
597 3 0.01
599 6 0.01
600 73 0.13
601 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (595 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTCTTAATTCACTTCTCTAGATCTC
CTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
GACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTTCGAAAATTGGCTCGCATTAAGCGTTGAGT
TGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGATTGTTTTAATTCGCTTCTCTGG
ATCTCCTCAGAAAGACAAATTTAGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTAATT
GCTCCGACCTACTTCTCAGTGTCTCATCAGGAAACTGGGTACGAAAATTGGCTCGCTTTAAGCGT
TGAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTC
TCTAGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAGGAAGCTAACCATT
TTATTGCTTCGACCTGCTTCTCAGTCACAGGAAGCTGGGTACGAAAATTAGCTCGCTTTGAGCAT
TGAGTTAGTA
Found at i:5052722 original size:30 final size:27
Alignment explanation
Indices: 5052688--5052926 Score: 96
Period size: 30 Copynumber: 8.1 Consensus size: 27
5052678 AAAAATGGGA
5052688 TTTTGGAAGGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAA--TTCG-GGGTAAAATGGTAAT
* *
5052718 TTTTGGTGAAATCGAGGTTAAAAATGG-AAT
1 TTTT-G-GAATTCG-GGGT-AAAATGGTAAT
*** *
5052748 TTTAAAAAGTTTAGGGGTAAAATGGTAAT
1 TTTTGGAA--TTCGGGGTAAAATGGTAAT
5052777 TTTTGGTGAAATT-GGGGTCAAAAATGG-AA-
1 TTTT-G-G-AATTCGGGGT--AAAATGGTAAT
*
5052806 TTTTGAAACATTCGGGGGTAAAATGGTAAT
1 TTTTG-GA-ATTC-GGGGTAAAATGGTAAT
5052836 TTTGGTGGAA-TCGGGGTTAAAAATGG-AAT
1 TTT--TGGAATTCGGGG-T-AAAATGGTAAT
* *
5052865 TTTTGGCAAGTTTAGAGGTAAAATGGTAAT
1 TTTTGG-AA--TTCGGGGTAAAATGGTAAT
* *
5052895 TTTGGTGAAATCGGGGTCAAAAT-GTAAT
1 TTTTG-GAATTCGGGGT-AAAATGGTAAT
5052923 TTTT
1 TTTT
5052927 AGATAGTTTA
Statistics
Matches: 161, Mismatches: 21, Indels: 56
0.68 0.09 0.24
Matches are distributed among these distances:
27 4 0.02
28 39 0.24
29 41 0.25
30 49 0.30
31 21 0.13
32 7 0.04
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (27 bp):
TTTTGGAATTCGGGGTAAAATGGTAAT
Found at i:5052737 original size:59 final size:58
Alignment explanation
Indices: 5052673--5052925 Score: 287
Period size: 59 Copynumber: 4.3 Consensus size: 58
5052663 GGGAAATTCA
* *
5052673 GGGTTAAAAATGGGATTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGTTAAAAATGGAATTTTGAAAGGTTCGAGGGTAAAATGGTAA-TTTTGGTGAAATCG
* * * * *
5052732 AGGTTAAAAATGGAATTTTAAAAAGTT-TAGGGGTAAAATGGTAATTTTTGGTGAAATTG
1 GGGTTAAAAATGGAATTTTGAAAGGTTCGA-GGGTAAAATGGTAA-TTTTGGTGAAATCG
* ** * *
5052791 GGGTCAAAAATGGAATTTTGAAACATTCGGGGGTAAAATGGTAATTTTGGTGGAATCG
1 GGGTTAAAAATGGAATTTTGAAAGGTTCGAGGGTAAAATGGTAATTTTGGTGAAATCG
* * *
5052849 GGGTTAAAAATGGAATTTTTGGCAAGTTTAGA-GGTAAAATGGTAATTTTGGTGAAATCG
1 GGGTTAAAAATGGAA-TTTT-GAAAGGTTCGAGGGTAAAATGGTAATTTTGGTGAAATCG
* *
5052908 GGG-TCAAAATGTAATTTT
1 GGGTTAAAAATGGAATTTT
5052926 TAGATAGTTT
Statistics
Matches: 165, Mismatches: 25, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
57 4 0.02
58 36 0.22
59 119 0.72
60 6 0.04
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (58 bp):
GGGTTAAAAATGGAATTTTGAAAGGTTCGAGGGTAAAATGGTAATTTTGGTGAAATCG
Found at i:5052825 original size:118 final size:117
Alignment explanation
Indices: 5052673--5052925 Score: 348
Period size: 118 Copynumber: 2.2 Consensus size: 117
5052663 GGGAAATTCA
* * * **
5052673 GGGTTAAAAATGGGATTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTA
1 GGGTCAAAAATGGAATTTTGAAACATTCGAGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTA
* *
5052738 AAAATGGAA-TTTTAAAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATTG
65 AAAATGGAATTTTTAAAAAGTTTAGAGGTAAAATGGTAA-TTTTGGTGAAATCG
* * *
5052791 GGGTCAAAAATGGAATTTTGAAACATTCGGGGGTAAAATGGTAATTTTGGTGGAATCGGGGTTAA
1 GGGTCAAAAATGGAATTTTGAAACATTCGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAA
***
5052856 AAATGGAATTTTTGGCAAGTTTAGAGGTAAAATGGTAATTTTGGTGAAATCG
66 AAATGGAATTTTTAAAAAGTTTAGAGGTAAAATGGTAATTTTGGTGAAATCG
*
5052908 GGGTC-AAAATGTAATTTT
1 GGGTCAAAAATGGAATTTT
5052926 TAGATAGTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
116 12 0.10
117 45 0.38
118 63 0.52
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (117 bp):
GGGTCAAAAATGGAATTTTGAAACATTCGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAA
AAATGGAATTTTTAAAAAGTTTAGAGGTAAAATGGTAATTTTGGTGAAATCG
Found at i:5052926 original size:29 final size:28
Alignment explanation
Indices: 5052703--5052925 Score: 122
Period size: 29 Copynumber: 7.6 Consensus size: 28
5052693 GAAGGTTCGA
5052703 GGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGTAAAATGGTAA-TTTTGGTGAAATCG
* ** *
5052732 AGGTTAAAAATGG-AATTTT--AAAAAGTTTAG
1 -GGGT-AAAATGGTAATTTTGGTGAAA---TCG
*
5052762 GGGTAAAATGGTAATTTTTGGTGAAATTG
1 GGGTAAAATGGTAA-TTTTGGTGAAATCG
*
5052791 GGGTCAAAAATGG-AATTTT-G-AAACATTCGG
1 GGGT--AAAATGGTAATTTTGGTGAA-A-TC-G
*
5052821 GGGTAAAATGGTAATTTTGGTGGAATCG
1 GGGTAAAATGGTAATTTTGGTGAAATCG
* * *
5052849 GGGTTAAAAATGG-AATTTTTGG-CAAGTTTAG
1 GGG-T-AAAATGGTAA-TTTTGGTGAA--ATCG
*
5052880 AGGTAAAATGGTAATTTTGGTGAAATCG
1 GGGTAAAATGGTAATTTTGGTGAAATCG
5052908 GGGTCAAAAT-GTAATTTT
1 GGGT-AAAATGGTAATTTT
5052926 TAGATAGTTT
Statistics
Matches: 148, Mismatches: 21, Indels: 50
0.68 0.10 0.23
Matches are distributed among these distances:
27 5 0.03
28 33 0.22
29 50 0.34
30 38 0.26
31 19 0.13
32 3 0.02
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGTGAAATCG
Found at i:5054026 original size:21 final size:21
Alignment explanation
Indices: 5054002--5054052 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
5053992 TAATATTTAC
*
5054002 TTATTATTAAAACATTTCTTA
1 TTATTATTAAAACATTTATTA
*
5054023 TTATTATTAAAGCATTTATTA
1 TTATTATTAAAACATTTATTA
*
5054044 TAATTATTA
1 TTATTATTA
5054053 TTAATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (21 bp):
TTATTATTAAAACATTTATTA
Found at i:5054041 original size:18 final size:18
Alignment explanation
Indices: 5053996--5054049 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
5053986 AATAAATAAT
5053996 ATTTACTTATTATTAAAAC
1 ATTTA-TTATTATTAAAAC
*
5054015 ATTTCTTATTATTATTAAAGC
1 A--T-TTATTATTATTAAAAC
*
5054036 ATTTATTATAATTA
1 ATTTATTATTATTA
5054050 TTATTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 11 0.37
19 2 0.07
21 14 0.47
22 3 0.10
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTTATTATTATTAAAAC
Found at i:5054780 original size:20 final size:19
Alignment explanation
Indices: 5054755--5054795 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
5054745 GGACTTATAA
5054755 TTGGACTTTTAATTTTGTAT
1 TTGGACTTTTAATTTT-TAT
5054775 TTGGACTTTTAATTTTTAT
1 TTGGACTTTTAATTTTTAT
5054794 TT
1 TT
5054796 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.05, G:0.12, T:0.63
Consensus pattern (19 bp):
TTGGACTTTTAATTTTTAT
Found at i:5054815 original size:17 final size:17
Alignment explanation
Indices: 5054789--5054825 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5054779 ACTTTTAATT
*
5054789 TTTATTTTAAATTTAAA
1 TTTATATTAAATTTAAA
*
5054806 TTTATATTAAGTTTAAA
1 TTTATATTAAATTTAAA
5054823 TTT
1 TTT
5054826 TAGAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATATTAAATTTAAA
Found at i:5059384 original size:32 final size:33
Alignment explanation
Indices: 5059339--5059400 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
5059329 ATGAATGAAA
5059339 TTTTTGATAAATTTAATATTTAATGTTTTTATT
1 TTTTTGATAAATTTAATATTTAATGTTTTTATT
* * * *
5059372 TTTTTG-TCAATTTGATTTTTAATTTTTTT
1 TTTTTGATAAATTTAATATTTAATGTTTTT
5059401 TACAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 19 0.76
33 6 0.24
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (33 bp):
TTTTTGATAAATTTAATATTTAATGTTTTTATT
Found at i:5059557 original size:47 final size:46
Alignment explanation
Indices: 5059473--5059566 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 46
5059463 AATATTTACA
* * *
5059473 AAAATATTAATTTTTTAATAATATTGGCGTGGCTGCCCATGTGACT
1 AAAACATTAATTTTTTAATAATATTGACGTGACTGCCCATGTGACT
*
5059519 AAAACATTAATTTTTTTAATAATATTGACGTGATTGCCCATGTGACT
1 AAAACATTAA-TTTTTTAATAATATTGACGTGACTGCCCATGTGACT
5059566 A
1 A
5059567 CGTGTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 9 0.21
47 34 0.79
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (46 bp):
AAAACATTAATTTTTTAATAATATTGACGTGACTGCCCATGTGACT
Found at i:5061179 original size:830 final size:830
Alignment explanation
Indices: 5059581--5061236 Score: 3258
Period size: 830 Copynumber: 2.0 Consensus size: 830
5059571 TATTTTATGA
5059581 TAATATGGTACTATTTATCTTATATATTAAGTAAAAAATAATTACAAAATTATAAAACATTCAAA
1 TAATATGGTACTATTTATCTTATATATTAAGTAAAAAATAATTACAAAATTATAAAACATTCAAA
*
5059646 AAATAAAAATAGTTCATAAAATTCAAAAAATTATTATAAAGTAGACGTGGATTAGTTACTATGTT
66 AAATAAAAATAGTTCATAAAATTCAAAAAATTATTATAAAGTAGACGTGGATTAGTTACTATGAT
5059711 TAAAAAATTAATCAAAATAAATAAGAAAAGAGAAATAGGATTCTTTGCTTTAGGGTAGATTTGGA
131 TAAAAAATTAATCAAAATAAATAAGAAAAGAGAAATAGGATTCTTTGCTTTAGGGTAGATTTGGA
5059776 TAGGCGGTACGTTTATCTGAGATTAGTGTAAAAATAACGGTCATAATAAAATTAGATATTATAAC
196 TAGGCGGTACGTTTATCTGAGATTAGTGTAAAAATAACGGTCATAATAAAATTAGATATTATAAC
5059841 GATACTGTAACGTAAGACAAAAAGTAAATCAAATATACCGTACCATAACTCACTAAAATCTCATC
261 GATACTGTAACGTAAGACAAAAAGTAAATCAAATATACCGTACCATAACTCACTAAAATCTCATC
5059906 GAGTTCCTTTTCAAGAGATTTTAATTCCTCCTTCCGACTTTGAATTATCGCTCTGTTTTGGAGTG
326 GAGTTCCTTTTCAAGAGATTTTAATTCCTCCTTCCGACTTTGAATTATCGCTCTGTTTTGGAGTG
5059971 ACTTTATTTTTCAATAAGATCTCAACATCCTATCTAATGTTCCTCTTAGCAGCATGATTACAACG
391 ACTTTATTTTTCAATAAGATCTCAACATCCTATCTAATGTTCCTCTTAGCAGCATGATTACAACG
5060036 AGAGAGAGCATTCTTAGGACTCTTGATTTTGTCTGTGAAGTTCCCATTAGATTCATTATTACCAA
456 AGAGAGAGCATTCTTAGGACTCTTGATTTTGTCTGTGAAGTTCCCATTAGATTCATTATTACCAA
5060101 TTTCAACGCAACCCTCAGTAACTATATCTTTACAGTCAACCAGCCATTTTGACTCAAATTTGAAA
521 TTTCAACGCAACCCTCAGTAACTATATCTTTACAGTCAACCAGCCATTTTGACTCAAATTTGAAA
5060166 GATTTTCGAACATGTCTATCCCTTTTCTGGGGACACAATAAGAAAGGCTTATGATCCGAGCCAAT
586 GATTTTCGAACATGTCTATCCCTTTTCTGGGGACACAATAAGAAAGGCTTATGATCCGAGCCAAT
*
5060231 AGCGATATCGGTGGACCCAAATATAATGATTCAACTTTTTTTAATGTCGAAAAATAATATTTTGG
651 AGCGATATCGGTGGACCCAAATATAATGATTCAACTTTTTTCAATGTCGAAAAATAATATTTTGG
5060296 AACATTATTTCTGTAAATTGAATTTGTAAAGATGAATTAAAAATAATTATGAAGTTAATGTGTTA
716 AACATTATTTCTGTAAATTGAATTTGTAAAGATGAATTAAAAATAATTATGAAGTTAATGTGTTA
* *
5060361 ATATTTTAAAAATCGATTAAATAATTTAATCAAGAAAATTGTTAATGTGT
781 ATATATTAAAAATCGATTAAATAATTTAATCAAGAAAATAGTTAATGTGT
5060411 TAATATGGTACTATTTATCTTATATATTAAGTAAAAAATAATTACAAAATTATAAAACATTCAAA
1 TAATATGGTACTATTTATCTTATATATTAAGTAAAAAATAATTACAAAATTATAAAACATTCAAA
5060476 AAATAAAAATAGTTCATAAAATTCAAAAAATTATTATAAAGTAGACGTGGATTAGTTACTATGAT
66 AAATAAAAATAGTTCATAAAATTCAAAAAATTATTATAAAGTAGACGTGGATTAGTTACTATGAT
5060541 TAAAAAATTAATCAAAATAAATAAGAAAAGAGAAATAGGATTCTTTGCTTTAGGGTAGATTTGGA
131 TAAAAAATTAATCAAAATAAATAAGAAAAGAGAAATAGGATTCTTTGCTTTAGGGTAGATTTGGA
5060606 TAGGCGGTACGTTTATCTGAGATTAGTGTAAAAATAACGGTCATAATAAAATTAGATATTATAAC
196 TAGGCGGTACGTTTATCTGAGATTAGTGTAAAAATAACGGTCATAATAAAATTAGATATTATAAC
5060671 GATACTGTAACGTAAGACAAAAAGTAAATCAAATATACCGTACCATAACTCACTAAAATCTCATC
261 GATACTGTAACGTAAGACAAAAAGTAAATCAAATATACCGTACCATAACTCACTAAAATCTCATC
5060736 GAGTTCCTTTTCAAGAGATTTTAATTCCTCCTTCCGACTTTGAATTATCGCTCTGTTTTGGAGTG
326 GAGTTCCTTTTCAAGAGATTTTAATTCCTCCTTCCGACTTTGAATTATCGCTCTGTTTTGGAGTG
*
5060801 ACTTTATTTTTCAATAAGATCTCAACATCCTGTCTAATGTTCCTCTTAGCAGCATGATTACAACG
391 ACTTTATTTTTCAATAAGATCTCAACATCCTATCTAATGTTCCTCTTAGCAGCATGATTACAACG
*
5060866 AGAGAGAGCATTCTTAGGACTCTTGATTTTGTCTGTGAAGTTCCCATTAGATTCCTTATTACCAA
456 AGAGAGAGCATTCTTAGGACTCTTGATTTTGTCTGTGAAGTTCCCATTAGATTCATTATTACCAA
5060931 TTTCAACGCAACCCTCAGTAACTATATCTTTACAGTCAACCAGCCATTTTGACTCAAATTTGAAA
521 TTTCAACGCAACCCTCAGTAACTATATCTTTACAGTCAACCAGCCATTTTGACTCAAATTTGAAA
5060996 GATTTTCGAACATGTCTATCCCTTTTCTGGGGACACAATAAGAAAGGCTTATGATCCGAGCCAAT
586 GATTTTCGAACATGTCTATCCCTTTTCTGGGGACACAATAAGAAAGGCTTATGATCCGAGCCAAT
5061061 AGCGATATCGGTGGACCCAAATATAATGATTCAACTTTTTTCAATGTCGAAAAATAATATTTTGG
651 AGCGATATCGGTGGACCCAAATATAATGATTCAACTTTTTTCAATGTCGAAAAATAATATTTTGG
5061126 AACATTATTTCTGTAAATTGAATTTGTAAAGATGAATTAAAAATAATTATGAAGTTAATGTGTTA
716 AACATTATTTCTGTAAATTGAATTTGTAAAGATGAATTAAAAATAATTATGAAGTTAATGTGTTA
5061191 ATATATTAAAAATCGATTAAATAATTTAATCAAGAAAATAGTTAAT
781 ATATATTAAAAATCGATTAAATAATTTAATCAAGAAAATAGTTAAT
5061237 TAAAACTTAA
Statistics
Matches: 820, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
830 820 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (830 bp):
TAATATGGTACTATTTATCTTATATATTAAGTAAAAAATAATTACAAAATTATAAAACATTCAAA
AAATAAAAATAGTTCATAAAATTCAAAAAATTATTATAAAGTAGACGTGGATTAGTTACTATGAT
TAAAAAATTAATCAAAATAAATAAGAAAAGAGAAATAGGATTCTTTGCTTTAGGGTAGATTTGGA
TAGGCGGTACGTTTATCTGAGATTAGTGTAAAAATAACGGTCATAATAAAATTAGATATTATAAC
GATACTGTAACGTAAGACAAAAAGTAAATCAAATATACCGTACCATAACTCACTAAAATCTCATC
GAGTTCCTTTTCAAGAGATTTTAATTCCTCCTTCCGACTTTGAATTATCGCTCTGTTTTGGAGTG
ACTTTATTTTTCAATAAGATCTCAACATCCTATCTAATGTTCCTCTTAGCAGCATGATTACAACG
AGAGAGAGCATTCTTAGGACTCTTGATTTTGTCTGTGAAGTTCCCATTAGATTCATTATTACCAA
TTTCAACGCAACCCTCAGTAACTATATCTTTACAGTCAACCAGCCATTTTGACTCAAATTTGAAA
GATTTTCGAACATGTCTATCCCTTTTCTGGGGACACAATAAGAAAGGCTTATGATCCGAGCCAAT
AGCGATATCGGTGGACCCAAATATAATGATTCAACTTTTTTCAATGTCGAAAAATAATATTTTGG
AACATTATTTCTGTAAATTGAATTTGTAAAGATGAATTAAAAATAATTATGAAGTTAATGTGTTA
ATATATTAAAAATCGATTAAATAATTTAATCAAGAAAATAGTTAATGTGT
Found at i:5061966 original size:49 final size:48
Alignment explanation
Indices: 5061894--5062061 Score: 201
Period size: 49 Copynumber: 3.4 Consensus size: 48
5061884 GATTATTGAT
* *
5061894 ATAGTGAAAATCATCATTGTCGGGTCATCCGGGATGGTAGAATATGTAA
1 ATAGTGAAAATCATCGTTGTCGGGTCA-CCGGGATGGTAGAATATGCAA
* * *
5061943 ATAGTGAAGATCATCGTTGTCGGGCCACTTGGGATGGTAGAATATGCAA
1 ATAGTGAAAATCATCGTTGTCGGGTCAC-CGGGATGGTAGAATATGCAA
* * * *
5061992 ATAGTGAAAACCATCGTTGTCGGGTCACCCGAGATTGTAGAATACGCAA
1 ATAGTGAAAATCATCGTTGTCGGGTCA-CCGGGATGGTAGAATATGCAA
* * *
5062041 ATATTGAAAGTCATTGTTGTC
1 ATAGTGAAAATCATCGTTGTC
5062062 AAGCCGCTCG
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
48 1 0.01
49 99 0.98
50 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (48 bp):
ATAGTGAAAATCATCGTTGTCGGGTCACCGGGATGGTAGAATATGCAA
Found at i:5062077 original size:98 final size:98
Alignment explanation
Indices: 5061894--5062083 Score: 229
Period size: 98 Copynumber: 1.9 Consensus size: 98
5061884 GATTATTGAT
* * * * *
5061894 ATAGTGAAAATCATCATTGTCGGGTCATCCGGGATGGTAGAATATGTAAATAGTGAAGATCATCG
1 ATAGTGAAAACCATCATTGTCGGGTCACCCGAGATGGTAGAATACGCAAATAGTGAAGATCATCG
** * *
5061959 TTGTCGGGCCACTTGGGATGGTAGAATATGCAA
66 TTGTCAAGCCACTCGAGATGGTAGAATATGCAA
* * * *
5061992 ATAGTGAAAACCATCGTTGTCGGGTCACCCGAGATTGTAGAATACGCAAATATTGAA-AGTCATT
1 ATAGTGAAAACCATCATTGTCGGGTCACCCGAGATGGTAGAATACGCAAATAGTGAAGA-TCATC
* *
5062056 GTTGTCAAGCCGCTCGAGATGGTTGAAT
65 GTTGTCAAGCCACTCGAGATGGTAGAAT
5062084 GTACAAGTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
97 1 0.01
98 75 0.99
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (98 bp):
ATAGTGAAAACCATCATTGTCGGGTCACCCGAGATGGTAGAATACGCAAATAGTGAAGATCATCG
TTGTCAAGCCACTCGAGATGGTAGAATATGCAA
Found at i:5062779 original size:18 final size:18
Alignment explanation
Indices: 5062752--5062788 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5062742 TAAGTATTGG
5062752 TTTGGGTGGCAATTAGGT
1 TTTGGGTGGCAATTAGGT
*
5062770 TTTGGTTGGCAATTAGGT
1 TTTGGGTGGCAATTAGGT
5062788 T
1 T
5062789 AATATAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.05, G:0.35, T:0.43
Consensus pattern (18 bp):
TTTGGGTGGCAATTAGGT
Found at i:5066647 original size:16 final size:17
Alignment explanation
Indices: 5066616--5066648 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5066606 TAATTTTTAA
5066616 TGAAATTTAAAAAAAAC
1 TGAAATTTAAAAAAAAC
5066633 TGAAA-TTAAATAAAAA
1 TGAAATTTAAA-AAAAA
5066649 AACTTCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (17 bp):
TGAAATTTAAAAAAAAC
Found at i:5076403 original size:20 final size:22
Alignment explanation
Indices: 5076359--5076409 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
5076349 AAAAACAACG
*
5076359 AATAAGAGATTTTAAAGGGAGA
1 AATAAGAGATTTTAAAGGAAGA
*
5076381 AATAAGAGA-TTTAGA-GAAGA
1 AATAAGAGATTTTAAAGGAAGA
*
5076401 AATTAGAGA
1 AATAAGAGA
5076410 GAAAGCAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 12 0.46
21 5 0.19
22 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (22 bp):
AATAAGAGATTTTAAAGGAAGA
Found at i:5080616 original size:3 final size:3
Alignment explanation
Indices: 5080608--5080633 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5080598 ATAGTGGTAT
5080608 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
5080634 ATGGTGCTTT
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:5083721 original size:25 final size:25
Alignment explanation
Indices: 5083692--5083742 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5083682 TTAAAATATA
*
5083692 TATTTTTATAAT-TTTTAATCATTTT
1 TATTTTTAGAATATTTTAAT-ATTTT
*
5083717 TATTTTTAGAATATTTTTATATTTT
1 TATTTTTAGAATATTTTAATATTTT
5083742 T
1 T
5083743 TTGAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (25 bp):
TATTTTTAGAATATTTTAATATTTT
Found at i:5083741 original size:19 final size:17
Alignment explanation
Indices: 5083691--5083742 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
5083681 TTTAAAATAT
5083691 ATATTTTTATAATTTTTA
1 ATATTTTTAT-ATTTTTA
*
5083709 ATCATTTTTAT-TTTTAGA
1 AT-ATTTTTATATTTT-TA
5083727 ATATTTTTATATTTTT
1 ATATTTTTATATTTTT
5083743 TTGAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 12 0.41
18 9 0.31
19 8 0.28
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
ATATTTTTATATTTTTA
Found at i:5086122 original size:6 final size:6
Alignment explanation
Indices: 5086111--5086135 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5086101 TGTAATATTT
5086111 CCATTG CCATTG CCATTG CCATTG C
1 CCATTG CCATTG CCATTG CCATTG C
5086136 TGTTGTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (6 bp):
CCATTG
Found at i:5088533 original size:27 final size:26
Alignment explanation
Indices: 5088495--5088577 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 26
5088485 GTATAAATGG
5088495 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTG-CAGGCGGCACCA
*
5088522 GTGGTGCCTACCT------GGCACTA
1 GTGGTGCCTACCTGCAGGCGGCACCA
5088542 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTG-CAGGCGGCACCA
*
5088569 ATGGTGCCT
1 GTGGTGCCT
5088578 TTCTATCAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
20 19 0.41
27 27 0.59
ACGTcount: A:0.16, C:0.31, G:0.33, T:0.20
Consensus pattern (26 bp):
GTGGTGCCTACCTGCAGGCGGCACCA
Found at i:5088544 original size:20 final size:20
Alignment explanation
Indices: 5088515--5088555 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5088505 CCTGACAGGC
5088515 GGCACCAGTGGTGCCTACCT
1 GGCACCAGTGGTGCCTACCT
*
5088535 GGCACTAGTGGTGCCTACCT
1 GGCACCAGTGGTGCCTACCT
5088555 G
1 G
5088556 TCAGGCGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.22
Consensus pattern (20 bp):
GGCACCAGTGGTGCCTACCT
Found at i:5088661 original size:15 final size:15
Alignment explanation
Indices: 5088618--5088661 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5088608 ATTACAAAAC
5088618 TAATACAAAAAAAATA
1 TAATAC-AAAAAAATA
* **
5088634 TTATACACCAAAATA
1 TAATACAAAAAAATA
5088649 TAATACAAAAAAA
1 TAATACAAAAAAA
5088662 ATTAGTAACT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (15 bp):
TAATACAAAAAAATA
Found at i:5088875 original size:58 final size:57
Alignment explanation
Indices: 5088748--5088879 Score: 135
Period size: 58 Copynumber: 2.3 Consensus size: 57
5088738 AAAAATTAAA
* * *
5088748 TTAAATAT-TAAATAAGAATAACTCAATATTTTTAAATGAATAATATAAAAAAATAT
1 TTAAATATAAAAATAATAATAACTCAAGATTTTTAAATGAATAATATAAAAAAATAT
** * * * *
5088804 TTATTTATCAAAATAATAATAATCTCTAGATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATATAAAAATAATAATAA-CTCAAGATTTTTA-AATGAATAATATAAAAAAATAT
5088861 TTAAATATAAAAAATAATA
1 TTAAATAT-AAAAATAATA
5088880 CACTTTTATA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
56 6 0.10
57 19 0.31
58 33 0.54
59 3 0.05
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (57 bp):
TTAAATATAAAAATAATAATAACTCAAGATTTTTAAATGAATAATATAAAAAAATAT
Found at i:5088937 original size:16 final size:15
Alignment explanation
Indices: 5088895--5088928 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
5088885 TTATATATTT
5088895 TTAAATTAAA-AAAA
1 TTAAATTAAATAAAA
5088909 TTAAATTAAATAAAA
1 TTAAATTAAATAAAA
5088924 TTAAA
1 TTAAA
5088929 ATTTGATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAATTAAATAAAA
Found at i:5088983 original size:27 final size:27
Alignment explanation
Indices: 5088940--5089000 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
5088930 TTTGATAAGA
5088940 GGTGCCTACTAGATAGGCGACACTAGT
1 GGTGCCTACTAGATAGGCGACACTAGT
* * *
5088967 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACTAGATAGGCGACACTAGT
5088994 GGTGCCT
1 GGTGCCT
5089001 TTGTCAATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.18, C:0.23, G:0.36, T:0.23
Consensus pattern (27 bp):
GGTGCCTACTAGATAGGCGACACTAGT
Found at i:5092053 original size:6 final size:6
Alignment explanation
Indices: 5092042--5092094 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
5092032 ATATTTGCAT
*
5092042 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATAA ACATAA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATAA
5092090 ACATA
1 ACATA
5092095 TTTAATGGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 1 0.02
6 41 0.95
7 1 0.02
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:5094493 original size:13 final size:13
Alignment explanation
Indices: 5094477--5094504 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5094467 TAATTTTTCA
5094477 TTTTAAAAAATAT
1 TTTTAAAAAATAT
5094490 TTTTAAAAAATAT
1 TTTTAAAAAATAT
5094503 TT
1 TT
5094505 AATATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:5094525 original size:17 final size:17
Alignment explanation
Indices: 5094496--5094543 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
5094486 ATATTTTTAA
5094496 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
5094512 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
* *
5094529 CAAATGAATTAAATA
1 AAAAT-ATTTAAATA
5094544 AAATAATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 11 0.39
18 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:5095513 original size:27 final size:27
Alignment explanation
Indices: 5095483--5095571 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
5095473 CTGGTAGGTT
*
5095483 GGCACCACTGATGCCGTCTACCAGACA
1 GGCACCACTGGTGCCGTCTACCAGACA
*
5095510 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGTCTACCAGACA
5095537 GGCACCACTGGTGCC-TCCTACCAGACA
1 GGCACCACTGGTGCCGT-CTACCAGACA
5095564 GGCACCAC
1 GGCACCAC
5095572 CCAAAAATAC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (27 bp):
GGCACCACTGGTGCCGTCTACCAGACA
Found at i:5095805 original size:14 final size:15
Alignment explanation
Indices: 5095769--5095809 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
5095759 AACGGGAAGA
5095769 ATATATTATTTTGGT
1 ATATATTATTTTGGT
**
5095784 ATATATTATTTTTTT
1 ATATATTATTTTGGT
5095799 A-ATATTATTTT
1 ATATATTATTTT
5095810 AGTAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
ATATATTATTTTGGT
Found at i:5095819 original size:14 final size:14
Alignment explanation
Indices: 5095771--5095819 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5095761 CGGGAAGAAT
*
5095771 ATATTATTTTGGTA
1 ATATTATTTTAGTA
**
5095785 TATATTATTTTTTTA
1 -ATATTATTTTAGTA
5095800 ATATTATTTTAGTA
1 ATATTATTTTAGTA
*
5095814 AAATTA
1 ATATTA
5095820 CCCCAGCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (14 bp):
ATATTATTTTAGTA
Found at i:5107514 original size:9 final size:9
Alignment explanation
Indices: 5107495--5107538 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
5107485 AGACCTTCCC
5107495 TTATGAAAAA
1 TTAT-AAAAA
5107505 TTATAAAAA
1 TTATAAAAA
5107514 TTATAGAAAA
1 TTATA-AAAA
5107524 -TATGAAAAA
1 TTAT-AAAAA
5107533 TTATAA
1 TTATAA
5107539 CTTTTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 19 0.61
10 12 0.39
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:5107545 original size:28 final size:27
Alignment explanation
Indices: 5107496--5107558 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
5107486 GACCTTCCCT
5107496 TATGAAAAATTATAAAAATTATAGAAAA
1 TATGAAAAATTATAAAAATTATA-AAAA
***
5107524 TATGAAAAATTATAACTTTTATAAAAA
1 TATGAAAAATTATAAAAATTATAAAAA
*
5107551 TATTAAAA
1 TATGAAAA
5107559 GTTACCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 11 0.35
28 20 0.65
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (27 bp):
TATGAAAAATTATAAAAATTATAAAAA
Found at i:5107571 original size:28 final size:27
Alignment explanation
Indices: 5107496--5107575 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
5107486 GACCTTCCCT
* **
5107496 TATGAAAAATTATAAAAATTATAGAAAA
1 TATGAAAAATTACAAATTTTATA-AAAA
* *
5107524 TATGAAAAATTATAACTTTTATAAAAA
1 TATGAAAAATTACAAATTTTATAAAAA
* *
5107551 TATTAAAAGTTACCAAATTTTATAA
1 TATGAAAAATTA-CAAATTTTATAA
5107576 CCCACGACGT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 14 0.32
28 30 0.68
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (27 bp):
TATGAAAAATTACAAATTTTATAAAAA
Found at i:5108593 original size:16 final size:18
Alignment explanation
Indices: 5108554--5108587 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5108544 TAAGTTTATA
5108554 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
5108571 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
5108588 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:5108869 original size:21 final size:21
Alignment explanation
Indices: 5108838--5108919 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
5108828 TTTTGGTACT
5108838 TTTTCTTTTACTGTTTTGGTTG
1 TTTT-TTTTACTGTTTTGGTTG
*
5108860 TTTTTTTTACTGTTTTTGTAT-
1 TTTTTTTTACTGTTTTGGT-TG
*
5108881 TGTTTTTTACTGTTTT-G--G
1 TTTTTTTTACTGTTTTGGTTG
5108899 TTTTTTTTACTGTTTTGGTTG
1 TTTTTTTTACTGTTTTGGTTG
5108920 ATGTTTTCGT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 15 0.29
19 1 0.02
20 1 0.02
21 30 0.58
22 5 0.10
ACGTcount: A:0.06, C:0.06, G:0.17, T:0.71
Consensus pattern (21 bp):
TTTTTTTTACTGTTTTGGTTG
Found at i:5108914 original size:10 final size:10
Alignment explanation
Indices: 5108862--5108896 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5108852 TTTGGTTGTT
5108862 TTTTTTACTG
1 TTTTTTACTG
*
5108872 TTTTTGTATTG
1 TTTTT-TACTG
5108883 TTTTTTACTG
1 TTTTTTACTG
5108893 TTTT
1 TTTT
5108897 GGTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.09, C:0.06, G:0.11, T:0.74
Consensus pattern (10 bp):
TTTTTTACTG
Found at i:5108981 original size:56 final size:55
Alignment explanation
Indices: 5108929--5109049 Score: 136
Period size: 56 Copynumber: 2.2 Consensus size: 55
5108919 GATGTTTTCG
* *
5108929 TGTTGTTTTTGTTATTATTTTTATTGCTATTTTTG-TTGCTAATTTTGTTGTTTTTAA
1 TGTTG-TTTTGCTATTATTTTTATTGCT-GTTTTGATTGCTAATTTTGTTG-TTTTAA
* * * * *
5108986 TGTTGTTTTGCTGTTATTTTTGTTGCTGTTTTGATTGTTATTTTTGTTGTTTGAA
1 TGTTGTTTTGCTATTATTTTTATTGCTGTTTTGATTGCTAATTTTGTTGTTTTAA
*
5109041 TGTTATTTT
1 TGTTGTTTT
5109050 TTATGTGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
55 18 0.33
56 32 0.58
57 5 0.09
ACGTcount: A:0.12, C:0.03, G:0.17, T:0.68
Consensus pattern (55 bp):
TGTTGTTTTGCTATTATTTTTATTGCTGTTTTGATTGCTAATTTTGTTGTTTTAA
Found at i:5109005 original size:23 final size:24
Alignment explanation
Indices: 5108974--5109030 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
5108964 TTGCTAATTT
* *
5108974 TGTTGTTTTTAATGTTGTTTTG-C
1 TGTTATTTTTAATGCTGTTTTGAC
** *
5108997 TGTTATTTTTGTTGCTGTTTTGAT
1 TGTTATTTTTAATGCTGTTTTGAC
5109021 TGTTATTTTT
1 TGTTATTTTT
5109031 GTTGTTTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.68
Consensus pattern (24 bp):
TGTTATTTTTAATGCTGTTTTGAC
Found at i:5109009 original size:20 final size:21
Alignment explanation
Indices: 5108986--5109050 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 21
5108976 TTGTTTTTAA
*
5108986 TGTTGTTTTG-CTGTTATTTT
1 TGTTGTTTTGAATGTTATTTT
*
5109006 TGTTGCTGTTTTGATTGTTATTTT
1 TG-T--TGTTTTGAATGTTATTTT
5109030 TGTTG-TTTGAATGTTATTTT
1 TGTTGTTTTGAATGTTATTTT
5109050 T
1 T
5109051 TATGTGCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 17 0.44
21 3 0.08
23 8 0.21
24 11 0.28
ACGTcount: A:0.09, C:0.03, G:0.20, T:0.68
Consensus pattern (21 bp):
TGTTGTTTTGAATGTTATTTT
Found at i:5109009 original size:44 final size:44
Alignment explanation
Indices: 5108956--5109050 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
5108946 TTTTTATTGC
*
5108956 TATTTTTGTTGCTAATTTTG-TTGTT-TTTAATGTTGTTTTG-CTGT
1 TATTTTTGTTGCT-ATTTTGATTGTTATTT-ATGTTG-TTTGAATGT
* *
5109000 TATTTTTGTTGCTGTTTTGATTGTTATTTTTGTTGTTTGAATGT
1 TATTTTTGTTGCTATTTTGATTGTTATTTATGTTGTTTGAATGT
5109044 TATTTTT
1 TATTTTT
5109051 TATGTGCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
43 9 0.20
44 33 0.73
45 3 0.07
ACGTcount: A:0.12, C:0.03, G:0.18, T:0.67
Consensus pattern (44 bp):
TATTTTTGTTGCTATTTTGATTGTTATTTATGTTGTTTGAATGT
Found at i:5109035 original size:12 final size:12
Alignment explanation
Indices: 5108929--5109036 Score: 66
Period size: 12 Copynumber: 9.3 Consensus size: 12
5108919 GATGTTTTCG
*
5108929 TGTTGTTTTTGT
1 TGTTATTTTTGT
* *
5108941 TATTATTTTTAT
1 TGTTATTTTTGT
*
5108953 TGCTATTTTTGT
1 TGTTATTTTTGT
* *
5108965 TGCTAATTTTGT
1 TGTTATTTTTGT
*
5108977 TGTT-TTTAATGT
1 TGTTATTT-TTGT
*
5108989 TG----TTTTGC
1 TGTTATTTTTGT
5108997 TGTTATTTTTGT
1 TGTTATTTTTGT
* *
5109009 TGCT-GTTTTGAT
1 TGTTATTTTTG-T
5109021 TGTTATTTTTGT
1 TGTTATTTTTGT
5109033 TGTT
1 TGTT
5109037 TGAATGTTAT
Statistics
Matches: 72, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
8 4 0.06
9 2 0.03
11 7 0.10
12 54 0.75
13 5 0.07
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.69
Consensus pattern (12 bp):
TGTTATTTTTGT
Done.