Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 126 of 208
Found at i:38709955 original size:5 final size:5
Alignment explanation
Indices: 38709945--38709972 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
38709935 AAATTATTTA
38709945 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
38709973 AACATAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:38710155 original size:10 final size:10
Alignment explanation
Indices: 38710133--38710189 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
38710123 TTAAAACCCC
38710133 TTTTT-TTCTT
1 TTTTTCTTC-T
38710143 TTTTTCTTCT
1 TTTTTCTTCT
*
38710153 TTTATCTTCT
1 TTTTTCTTCT
*
38710163 TTTTTCCTCT
1 TTTTTCTTCT
38710173 CTTTTTCTT-T
1 -TTTTTCTTCT
38710183 TTTTTCT
1 TTTTTCT
38710190 GGACTGGGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 7 0.17
10 24 0.59
11 10 0.24
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:38710164 original size:21 final size:21
Alignment explanation
Indices: 38710132--38710188 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
38710122 ATTAAAACCC
*
38710132 CTTTTT-TTCTTTTTTTCT-T
1 CTTTTTCTTCTTTTTTCCTCT
38710151 CTTTTATCTTCTTTTTTCCTCT
1 CTTTT-TCTTCTTTTTTCCTCT
38710173 CTTTTTCTT-TTTTTTC
1 CTTTTTCTTCTTTTTTC
38710189 TGGACTGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.15
20 8 0.24
21 15 0.44
22 6 0.18
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (21 bp):
CTTTTTCTTCTTTTTTCCTCT
Found at i:38710238 original size:25 final size:25
Alignment explanation
Indices: 38710210--38710260 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
38710200 GGCCTGTTGG
38710210 GCTGCTG--CTAGGCCTGGGGG-CT
1 GCTGCTGCACTAGGCCTGGGGGCCT
*
38710232 GCTGCTGCACTGGGCCTGGGGGCCT
1 GCTGCTGCACTAGGCCTGGGGGCCT
38710257 GCTG
1 GCTG
38710261 GGCCTGCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
24 12 0.48
25 6 0.24
ACGTcount: A:0.04, C:0.29, G:0.45, T:0.22
Consensus pattern (25 bp):
GCTGCTGCACTAGGCCTGGGGGCCT
Found at i:38710321 original size:23 final size:23
Alignment explanation
Indices: 38710291--38710360 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
38710281 TGCATTTGGG
38710291 CTGCTTCTTTCTTCTTCTTTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
38710314 CTGCTTCTTTCTTTCTTTCTTTTTT
1 CTGCTTCTTTC-TTC-TTCTTTTTT
* * *
38710339 CTG-TTGTTTCTTTTTCTGTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
38710361 GGTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.19
23 13 0.31
24 9 0.21
25 12 0.29
ACGTcount: A:0.00, C:0.21, G:0.07, T:0.71
Consensus pattern (23 bp):
CTGCTTCTTTCTTCTTCTTTTTT
Found at i:38710327 original size:4 final size:4
Alignment explanation
Indices: 38710295--38710351 Score: 50
Period size: 4 Copynumber: 14.5 Consensus size: 4
38710285 TTTGGGCTGC
38710295 TTCT TTC- TTC- TTCT TT-T TTCT GCTTCT TTCT TTCT TTCT TT-T TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT --TTCT TTCT TTCT TTCT TTCT TTCT
*
38710341 GTTGT TTCT TT
1 -TTCT TTCT TT
38710352 TTCTGTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
3 12 0.27
4 26 0.58
5 3 0.07
6 4 0.09
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:38710352 original size:15 final size:16
Alignment explanation
Indices: 38710329--38710358 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38710319 TCTTTCTTTC
38710329 TTTCTTTTTTCTGTTG
1 TTTCTTTTTTCTGTTG
38710345 TTTC-TTTTTCTGTT
1 TTTCTTTTTTCTGTT
38710359 TTGGTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTTCTGTTG
Found at i:38710360 original size:24 final size:25
Alignment explanation
Indices: 38710291--38710351 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 25
38710281 TGCATTTGGG
38710291 CTGCTTCTTTC-TTC-TTCTTTTTT
1 CTGCTTCTTTCTTTCTTTCTTTTTT
38710314 CTGCTTCTTTCTTTCTTTCTTTTTT
1 CTGCTTCTTTCTTTCTTTCTTTTTT
*
38710339 CTG-TTGTTTCTTT
1 CTGCTTCTTTCTTT
38710352 TTCTGTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 11 0.31
24 12 0.34
25 12 0.34
ACGTcount: A:0.00, C:0.23, G:0.07, T:0.70
Consensus pattern (25 bp):
CTGCTTCTTTCTTTCTTTCTTTTTT
Found at i:38710483 original size:13 final size:13
Alignment explanation
Indices: 38710461--38710520 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 13
38710451 CTGTGATATA
*
38710461 TTTCTTTTTTTTC
1 TTTCTCTTTTTTC
38710474 TTTCTC-TTTTTC
1 TTTCTCTTTTTTC
38710486 -TTCTCTCTTTTTC
1 TTTCTCT-TTTTTC
* *
38710499 CTTCTTTCTTTTTC
1 TTTCTCT-TTTTTC
*
38710513 TTTTTCTT
1 TTTCTCTT
38710521 CTTCTTCTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 5 0.13
12 6 0.15
13 12 0.31
14 16 0.41
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTCTTTTTTC
Found at i:38710487 original size:6 final size:6
Alignment explanation
Indices: 38710468--38710526 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
38710458 ATATTTCTTT
* *
38710468 TTTTTC TTTCTC TTTTTC TTCTCTC TTTTTCC TTCTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTT-C TT-TTTC TTTTTC TTTTTC
*
38710519 TTCTTC TT
1 TTTTTC TT
38710527 CTTCGGGTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 31 0.69
7 11 0.24
8 3 0.07
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:38710497 original size:14 final size:14
Alignment explanation
Indices: 38710467--38710511 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
38710457 TATATTTCTT
38710467 TTTTTTCTT-TCTC
1 TTTTTTCTTCTCTC
38710480 -TTTTTCTTCTCTC
1 TTTTTTCTTCTCTC
* *
38710493 TTTTTCCTTCTTTC
1 TTTTTTCTTCTCTC
38710507 TTTTT
1 TTTTT
38710512 CTTTTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.29
13 4 0.14
14 16 0.57
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTCTTCTCTC
Found at i:38710683 original size:14 final size:13
Alignment explanation
Indices: 38710642--38710689 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
38710632 CTCTCTCCTT
38710642 TTTCTTCTTTGCTG
1 TTTCTT-TTTGCTG
*
38710656 TTT-TTTTTGTTG
1 TTTCTTTTTGCTG
38710668 TTTCTTGTTTGCTG
1 TTTCTT-TTTGCTG
38710682 TTT-TTTTT
1 TTTCTTTTT
38710690 TTGCTTATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 12 0.40
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (13 bp):
TTTCTTTTTGCTG
Found at i:38710692 original size:14 final size:14
Alignment explanation
Indices: 38710656--38710694 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
38710646 TTCTTTGCTG
*
38710656 TTTTTTTTGTTGTT
1 TTTTTTTTGCTGTT
* *
38710670 TCTTGTTTGCTGTT
1 TTTTTTTTGCTGTT
38710684 TTTTTTTTGCT
1 TTTTTTTTGCT
38710695 TATGCTTGCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (14 bp):
TTTTTTTTGCTGTT
Found at i:38711141 original size:29 final size:29
Alignment explanation
Indices: 38711011--38711190 Score: 145
Period size: 30 Copynumber: 6.1 Consensus size: 29
38711001 CATGGGATGC
*
38711011 AAAGTTTTTGGGG-CAAAAGAGTAATTTTAG
1 AAAG-TTTTGGGGTCAAAA-TGTAATTTTAG
* * * *
38711041 CAAA-ATAT-GGGCCAAAATGTAATTTCTTG
1 -AAAGTTTTGGGGTCAAAATGTAATTT-TAG
* * * *
38711070 AGAGTTTAGGGGTCAAAGTGCAATTTTGAG
1 AAAGTTTTGGGGTCAAAATGTAATTTT-AG
* **
38711100 AAAGTCTAAGGGTCAAAATGTAATTTTAG
1 AAAGTTTTGGGGTCAAAATGTAATTTTAG
38711129 AAAGTTTTGGGGTCAAAATGTAAATTTTAG
1 AAAGTTTTGGGGTCAAAATGT-AATTTTAG
38711159 AAAAG-TTTGGGGTCAAAATGTAAATTTT-G
1 -AAAGTTTTGGGGTCAAAATGT-AATTTTAG
38711188 AAA
1 AAA
38711191 AGTACAGGGG
Statistics
Matches: 122, Mismatches: 20, Indels: 17
0.77 0.13 0.11
Matches are distributed among these distances:
28 15 0.12
29 32 0.26
30 68 0.56
31 7 0.06
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (29 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTAG
Found at i:38711155 original size:30 final size:29
Alignment explanation
Indices: 38711053--38711208 Score: 154
Period size: 30 Copynumber: 5.2 Consensus size: 29
38711043 AAATATGGGC
* *
38711053 CAAAATGTAATTTCTTGAGAGTTTAGGGGT
1 CAAAATGTAATTT-TAGAAAGTTTAGGGGT
* * * *
38711083 CAAAGTGCAATTTTGAGAAAGTCTAAGGGT
1 CAAAATGTAATTTT-AGAAAGTTTAGGGGT
*
38711113 CAAAATGTAATTTTAGAAAGTTTTGGGGT
1 CAAAATGTAATTTTAGAAAGTTTAGGGGT
38711142 CAAAATGTAAATTTTAGAAAAGTTT-GGGGT
1 CAAAATGT-AATTTTAG-AAAGTTTAGGGGT
**
38711172 CAAAATGTAAATTTT-GAAAAGTACAGGGGT
1 CAAAATGT-AATTTTAG-AAAGTTTAGGGGT
*
38711202 TAAAATG
1 CAAAATG
38711209 CAAAAAATAG
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.26
30 73 0.68
31 7 0.06
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (29 bp):
CAAAATGTAATTTTAGAAAGTTTAGGGGT
Found at i:38712373 original size:24 final size:24
Alignment explanation
Indices: 38712346--38712392 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
38712336 TAAGAACAGG
38712346 ACAACACCAAAGTACATAATCAAA
1 ACAACACCAAAGTACATAATCAAA
** *
38712370 ACAACACGGAAGTGCATAATCAA
1 ACAACACCAAAGTACATAATCAA
38712393 GATAGCACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
ACAACACCAAAGTACATAATCAAA
Found at i:38717001 original size:37 final size:37
Alignment explanation
Indices: 38716951--38717026 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
38716941 GAATCCGTTT
*
38716951 GTGCATTAATTCACTTGTAACGTTCATGGTATGTTGG
1 GTGCATTAATTCACTTCTAACGTTCATGGTATGTTGG
* * *
38716988 GTGCATTAATTCACTTCTGACGTTCATTGTATTTTGG
1 GTGCATTAATTCACTTCTAACGTTCATGGTATGTTGG
38717025 GT
1 GT
38717027 ACCTAAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.43
Consensus pattern (37 bp):
GTGCATTAATTCACTTCTAACGTTCATGGTATGTTGG
Found at i:38718845 original size:40 final size:41
Alignment explanation
Indices: 38718796--38718899 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
38718786 AACACACCAG
* * * *
38718796 ATTGGCACCCAGTGCCTCATCGGAT-AATTCGAAGTATTAA
1 ATTGACACCCAGTGCCTCATCGAATAAATCCGAAGTAATAA
38718836 ATTGACACCCAGTGCCTCATCGAATAAATCCGAAGTAATAA
1 ATTGACACCCAGTGCCTCATCGAATAAATCCGAAGTAATAA
* *
38718877 ATTGACACCCAATGTCTCATCGA
1 ATTGACACCCAGTGCCTCATCGA
38718900 CTCGAAGTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 23 0.40
41 34 0.60
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (41 bp):
ATTGACACCCAGTGCCTCATCGAATAAATCCGAAGTAATAA
Found at i:38723856 original size:22 final size:22
Alignment explanation
Indices: 38723829--38723874 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
38723819 GAGATCAACA
38723829 AAAATA-TAAACACATACATATC
1 AAAATATTAAACACAT-CATATC
* *
38723851 AAAATATTAATCTCATCATATC
1 AAAATATTAAACACATCATATC
38723873 AA
1 AA
38723875 TCATCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATATTAAACACATCATATC
Found at i:38726050 original size:15 final size:15
Alignment explanation
Indices: 38726030--38726061 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38726020 CCACTCTCGG
38726030 TTCATTAACACAATT
1 TTCATTAACACAATT
*
38726045 TTCATTAACCCAATT
1 TTCATTAACACAATT
38726060 TT
1 TT
38726062 TGGGATGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (15 bp):
TTCATTAACACAATT
Found at i:38726342 original size:9 final size:9
Alignment explanation
Indices: 38726328--38726358 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
38726318 GATTAAGTAA
38726328 AATTAAATT
1 AATTAAATT
38726337 AATTAAATT
1 AATTAAATT
38726346 AATTAAAATT
1 AATT-AAATT
38726356 AAT
1 AAT
38726359 ATGATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:38726817 original size:25 final size:26
Alignment explanation
Indices: 38726772--38726823 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
38726762 TTTAATACAT
*
38726772 ATATTAATAGTATTTTATTAAT-TTA
1 ATATTAATAGTATTATATTAATATTA
*
38726797 ATATTAA-AGTGATTATCTTAATATTA
1 ATATTAATAGT-ATTATATTAATATTA
38726823 A
1 A
38726824 ATTTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 16 0.70
26 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (26 bp):
ATATTAATAGTATTATATTAATATTA
Found at i:38728489 original size:33 final size:35
Alignment explanation
Indices: 38728452--38728533 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 35
38728442 TTTAATATGA
*
38728452 AATTTAGTTTAATACTTAT-T-ATAGAATTTTATT
1 AATTTAATTTAATACTTATATGATAGAATTTTATT
*
38728485 AATTTAATTTAATACTTATCATGATAGTATTTTATT
1 AATTTAATTTAATACTTAT-ATGATAGAATTTTATT
38728521 AATTTAATATTAA
1 AATTTAAT-TTAA
38728534 AGTTATTATC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 18 0.42
35 1 0.02
36 20 0.47
37 4 0.09
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (35 bp):
AATTTAATTTAATACTTATATGATAGAATTTTATT
Found at i:38728541 original size:20 final size:19
Alignment explanation
Indices: 38728516--38728568 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
38728506 TGATAGTATT
38728516 TTATTAATTTAATATTAAA
1 TTATTAATTTAATATTAAA
38728535 GTTATT-ATCTTAATATTAAA
1 -TTATTAAT-TTAATATTAAA
38728555 -T-TTAATTTAATATT
1 TTATTAATTTAATATT
38728569 TATCTTATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.32
18 3 0.10
19 2 0.06
20 16 0.52
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATTAATTTAATATTAAA
Found at i:38735670 original size:20 final size:20
Alignment explanation
Indices: 38735645--38735689 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
38735635 CTTCATTTAC
38735645 CTTATTATCAAACTTAATA-T
1 CTTATTA-CAAACTTAATAGT
* *
38735665 CTTATTACATACTTACTAGT
1 CTTATTACAAACTTAATAGT
38735685 CTTAT
1 CTTAT
38735690 CATTTCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (20 bp):
CTTATTACAAACTTAATAGT
Found at i:38738517 original size:14 final size:15
Alignment explanation
Indices: 38738486--38738533 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
38738476 ATTTGAATAA
38738486 AAATAAAAACATTTATTT
1 AAATAAAAACA---ATTT
38738504 AAATAAAAAC-ATTT
1 AAATAAAAACAATTT
*
38738518 GAATAAAAACAATTT
1 AAATAAAAACAATTT
38738533 A
1 A
38738534 CAAAGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 13 0.48
15 4 0.15
18 10 0.37
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (15 bp):
AAATAAAAACAATTT
Found at i:38738524 original size:18 final size:18
Alignment explanation
Indices: 38738474--38738524 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
38738464 AAAACAATTT
38738474 ACATTTGAATAAAAATAAAA
1 ACATTTGAAT--AAATAAAA
*
38738494 ACATTT-ATTTAAATAAAA
1 ACATTTGA-ATAAATAAAA
38738512 ACATTTGAATAAA
1 ACATTTGAATAAA
38738525 AACAATTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 18 0.67
19 2 0.07
20 7 0.26
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (18 bp):
ACATTTGAATAAATAAAA
Found at i:38740749 original size:19 final size:19
Alignment explanation
Indices: 38740725--38740765 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38740715 ATCTCTTTTC
38740725 ATTCA-TTGCATTTAGATTA
1 ATTCATTTGCATTTA-ATTA
*
38740744 ATTCATTTTCATTTAATTA
1 ATTCATTTGCATTTAATTA
38740763 ATT
1 ATT
38740766 TCCTTTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTCATTTGCATTTAATTA
Found at i:38744483 original size:19 final size:19
Alignment explanation
Indices: 38744459--38744497 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
38744449 CCAAAAGGAC
*
38744459 TTTTTATTTTTATTTGTAA
1 TTTTTAATTTTATTTGTAA
38744478 TTTTTAATTTTATTTGTAA
1 TTTTTAATTTTATTTGTAA
38744497 T
1 T
38744498 AAGAAGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTTAATTTTATTTGTAA
Found at i:38752236 original size:9 final size:9
Alignment explanation
Indices: 38752225--38752300 Score: 80
Period size: 9 Copynumber: 8.4 Consensus size: 9
38752215 TTTGGTTAAA
*
38752225 AATTAACCA
1 AATTAACCG
*
38752234 AATTAACTG
1 AATTAACCG
**
38752243 AATTAACTA
1 AATTAACCG
*
38752252 AATTACCCG
1 AATTAACCG
38752261 AATTAACCG
1 AATTAACCG
**
38752270 AATTATTCG
1 AATTAACCG
38752279 AATTAACCG
1 AATTAACCG
*
38752288 AATTAACCA
1 AATTAACCG
38752297 AATT
1 AATT
38752301 GAATCACTAC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:38753657 original size:26 final size:26
Alignment explanation
Indices: 38753627--38753678 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
38753617 GTTAAATGGC
38753627 TATGGAAATGTAAATTAATGGACTTA
1 TATGGAAATGTAAATTAATGGACTTA
*
38753653 TATGGAAATGTAAATTAATGGGCTTA
1 TATGGAAATGTAAATTAATGGACTTA
38753679 AACGGTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (26 bp):
TATGGAAATGTAAATTAATGGACTTA
Found at i:38760459 original size:22 final size:22
Alignment explanation
Indices: 38760425--38760467 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
38760415 TTTGCACTCA
38760425 AATTATTAATAT-ATCAAATTTT
1 AATTATTAATATAAT-AAATTTT
**
38760447 AATTATTTTTATAATAAATTT
1 AATTATTAATATAATAAATTT
38760468 ACACAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTATTAATATAATAAATTTT
Found at i:38765257 original size:20 final size:20
Alignment explanation
Indices: 38765232--38765275 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
38765222 ACACACGCTT
*
38765232 TCTCCCTCCTTCTCTCTCTC
1 TCTCCCTCCCTCTCTCTCTC
* *
38765252 TCTCCCTCCCTCTTTCTTTC
1 TCTCCCTCCCTCTCTCTCTC
38765272 TCTC
1 TCTC
38765276 TCTTATCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (20 bp):
TCTCCCTCCCTCTCTCTCTC
Found at i:38765260 original size:24 final size:24
Alignment explanation
Indices: 38765233--38765278 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
38765223 CACACGCTTT
38765233 CTCCCTCCTTCTCTCTCTCTCTCC
1 CTCCCTCCTTCTCTCTCTCTCTCC
* *
38765257 CTCCCTCTTTCTTTCTCTCTCT
1 CTCCCTCCTTCTCTCTCTCTCT
38765279 TATCTCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (24 bp):
CTCCCTCCTTCTCTCTCTCTCTCC
Found at i:38788482 original size:42 final size:42
Alignment explanation
Indices: 38788430--38788580 Score: 135
Period size: 42 Copynumber: 3.6 Consensus size: 42
38788420 GCCCGAAGGC
* *
38788430 TGAACAGAAGCTCATGAGAGTTAAACAGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * **
38788472 TGAACGGAAGCTCGTAAGAGCTGAATGGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * * * * *
38788514 TAAACAGAAGCACAAAAGAGCTGAAC-GAAAACTCATATGAGT
1 TGAACAGAAGCTCATAAGAGCTAAACAG-AAACCCATAAGGGT
*
38788556 TAAACAGAAGCTCGA-AAGAGCTAAA
1 TGAACAGAAGCTC-ATAAGAGCTAAA
38788581 AAAAGTATAA
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 87 0.98
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:38788510 original size:21 final size:21
Alignment explanation
Indices: 38788457--38788510 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
38788447 GAGTTAAACA
* *
38788457 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGAGCTGAACG
* * * *
38788478 GAAGCTCGTAAGAGCTGAATG
1 GAAACCCATAAGAGCTGAACG
38788499 GAAACCCATAAG
1 GAAACCCATAAG
38788511 GGTTAAACAG
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.15
Consensus pattern (21 bp):
GAAACCCATAAGAGCTGAACG
Found at i:38790450 original size:25 final size:24
Alignment explanation
Indices: 38790388--38790458 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 24
38790378 GGATAGCCAT
* **
38790388 ATATCAGGAAGTTCA-AGTGAGCC
1 ATATCAGGAAGCTCACAAAGAGCC
38790411 ATATCAGGAAGCTCACAAAGAGCC
1 ATATCAGGAAGCTCACAAAGAGCC
* *
38790435 TATATCGGGATA-CTCATAAAGAGC
1 -ATATCAGGA-AGCTCACAAAGAGC
38790459 TGCAGTATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 14 0.35
24 6 0.15
25 19 0.47
26 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (24 bp):
ATATCAGGAAGCTCACAAAGAGCC
Found at i:38790766 original size:22 final size:21
Alignment explanation
Indices: 38790738--38790779 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
38790728 GACATTTATA
*
38790738 CAATTCACACATATATAATATT
1 CAATTCAAACATAT-TAATATT
38790760 CAATTCAAACATATTAATAT
1 CAATTCAAACATATTAATAT
38790780 ACATAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.36
Consensus pattern (21 bp):
CAATTCAAACATATTAATATT
Found at i:38790797 original size:19 final size:19
Alignment explanation
Indices: 38790773--38790811 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38790763 TTCAAACATA
38790773 TTAATATACATAATTTAGT
1 TTAATATACATAATTTAGT
38790792 TTAATATACATAATTTAGT
1 TTAATATACATAATTTAGT
38790811 T
1 T
38790812 ACACGAACTT
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:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
TTAATATACATAATTTAGT
Found at i:38793140 original size:21 final size:21
Alignment explanation
Indices: 38793114--38793153 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38793104 ATTGGGTGGA
*
38793114 TCAACTCTTATGAGATTCTGT
1 TCAACTCTTACGAGATTCTGT
*
38793135 TCAACTCTTACGAGCTTCT
1 TCAACTCTTACGAGATTCT
38793154 ATTAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (21 bp):
TCAACTCTTACGAGATTCTGT
Found at i:38799323 original size:21 final size:21
Alignment explanation
Indices: 38799294--38799342 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
38799284 TCTTACAAGT
*
38799294 TTCTATTCAACTCTTATGAGC
1 TTCTGTTCAACTCTTATGAGC
* *
38799315 TTTTGTTCAGCTCTTATGAGC
1 TTCTGTTCAACTCTTATGAGC
38799336 TTCTGTT
1 TTCTGTT
38799343 GACAAAGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.49
Consensus pattern (21 bp):
TTCTGTTCAACTCTTATGAGC
Found at i:38811203 original size:30 final size:31
Alignment explanation
Indices: 38811158--38811217 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
38811148 CAACCTTTTA
38811158 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAATTTTTACTCCCTTCCCAC
* * *
38811188 TTTTTCCCTAAAATTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAATTTTTACTCCCTTCCCA
38811218 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAATTTTTACTCCCTTCCCAC
Found at i:38815063 original size:16 final size:16
Alignment explanation
Indices: 38815025--38815066 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
38815015 ACTTAAATCA
38815025 TTATATATATTAAATAT
1 TTATATA-ATTAAATAT
* *
38815042 TT-TATAATTCAATTT
1 TTATATAATTAAATAT
38815057 TTATATAATT
1 TTATATAATT
38815067 TATAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 11 0.50
17 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATAATTAAATAT
Found at i:38815245 original size:18 final size:18
Alignment explanation
Indices: 38815213--38815253 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38815203 TAAAAAAAAT
*
38815213 TAATTTTAAATAATTAAA
1 TAATATTAAATAATTAAA
38815231 -AATATTAATATAATTAAA
1 TAATATTAA-ATAATTAAA
38815249 TAATA
1 TAATA
38815254 CTTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATATTAAATAATTAAA
Found at i:38815270 original size:26 final size:27
Alignment explanation
Indices: 38815241--38815291 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
38815231 AATATTAATA
38815241 TAATTAAATAATACTTA-TATTTTTGG
1 TAATTAAATAATACTTATTATTTTTGG
*
38815267 TAATTAAATAATATTTATTATTTTT
1 TAATTAAATAATACTTATTATTTTT
38815292 TTATGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (27 bp):
TAATTAAATAATACTTATTATTTTTGG
Found at i:38815438 original size:21 final size:21
Alignment explanation
Indices: 38815414--38815455 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
38815404 TTTTTAAATT
38815414 TAAA-ATAAATATTAAAATTAA
1 TAAATATAAAT-TTAAAATTAA
* *
38815435 TAAATTTAAATTTAGAATTAA
1 TAAATATAAATTTAAAATTAA
38815456 AGAAAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAATATAAATTTAAAATTAA
Found at i:38815545 original size:18 final size:17
Alignment explanation
Indices: 38815492--38815545 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 17
38815482 TTATGGATTT
*
38815492 TTATTAAAATTAAAATA
1 TTATTAAAATTAAATTA
38815509 TTATTTAAAATTGAAATTA
1 TTA-TTAAAATT-AAATTA
38815528 TTATTAAAATTAATATTA
1 TTATTAAAATTAA-ATTA
38815546 AAATATGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 5 0.15
18 20 0.61
19 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TTATTAAAATTAAATTA
Found at i:38818492 original size:5 final size:5
Alignment explanation
Indices: 38818482--38818521 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
38818472 TTTAATATAT
* *
38818482 ATAAA ATAAA ATAAG ATAAA AT-AA ATAAA ATAAA ACAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
38818522 ACACGAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:38818500 original size:10 final size:9
Alignment explanation
Indices: 38818485--38818515 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
38818475 AATATATATA
38818485 AAATAAAAT
1 AAATAAAAT
38818494 AAGATAAAAT
1 AA-ATAAAAT
38818504 AAATAAAAT
1 AAATAAAAT
38818513 AAA
1 AAA
38818516 ACAAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:38818521 original size:19 final size:19
Alignment explanation
Indices: 38818485--38818521 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38818475 AATATATATA
* *
38818485 AAATAAAATAAGATAAAAT
1 AAATAAAATAAAACAAAAT
38818504 AAATAAAATAAAACAAAA
1 AAATAAAATAAAACAAAA
38818522 ACACGAAGAA
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:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (19 bp):
AAATAAAATAAAACAAAAT
Found at i:38818856 original size:74 final size:73
Alignment explanation
Indices: 38818712--38819245 Score: 473
Period size: 74 Copynumber: 7.0 Consensus size: 73
38818702 CTCTCGAGCC
* *
38818712 ATGAGTTGATTTTTGAAAAAACAGAAACTT--AAAACACCTC-AGCGTGCAACCCGAGGCTCAAC
1 ATGAGTTGATTTTTG--AAAACATAAA-TTGAAAAATACCTCGA-CGTG--ACCCGAGGCTCAAC
38818774 TCACCTCTCGCAAT
60 TCACCTCTCGCAAT
* *
38818788 ATGAGTTGATTTTTAGAAAACATAAATTGAAAAATACATCGACGTGACTCGAGGCTCAACTCACC
1 ATGAGTTGATTTTT-GAAAACATAAATTGAAAAATACCTCGACGTGACCCGAGGCTCAACTCACC
38818853 TCTCGCAAT
65 TCTCGCAAT
* * * * *
38818862 ATGAGTTGATTTTTGAAAAGCAAAAATTAAAAAATACCTCAACATGACTCGAGGCTCAACTCACC
1 ATGAGTTGATTTTTGAAAA-CATAAATTGAAAAATACCTCGACGTGACCCGAGGCTCAACTCACC
38818927 TCTCGCAAT
65 TCTCGCAAT
* * *
38818936 ATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAGAATACCTCGGCATGCGACCCGAGGCTCAAC
1 ATGAGTTGATTTTTG--AAAACATAAATTG-AAA-AATACCTC-G-ACGTGACCCGAGGCTCAAC
*
38819001 TCACCTCTAGCAAT
60 TCACCTCTCGCAAT
**** *** * *
38819015 ATGAGTTGATTTTTTTGAGTTGATTTTTTTGAAAAATACCTCAGCATGTGACCCGAGGTTCAACT
1 ATGAGTTGA--TTTTTGAAAACA-TAAATTGAAAAATACCTC-G-ACGTGACCCGAGGCTCAACT
*
38819080 CACTTCTCGCAAT
61 CACCTCTCGCAAT
* * * * *
38819093 ATGAGTTGATTTTTGAACAACAGAAATTTAAACGAAATACCTCGGCATGACCCGAGACTCAACTC
1 ATGAGTTGATTTTTGAA-AACATAAA-TTGAA--AAATACCTCGACGTGACCCGAGGCTCAACTC
* *
38819158 ACCTCT-GTATT
62 ACCTCTCGCAAT
* * *
38819169 ATGAGTTGATTTTTGAAAAACATAAATTGAAAAGAAATACCTCGGCCTACGACCCGAGGATCAAC
1 ATGAGTTGATTTTTG-AAAACATAAATTG--AA-AAATACCTCGACGT--GACCCGAGGCTCAAC
*
38819234 TCACCCCTCGCA
60 TCACCTCTCGCA
38819246 GTNNNNNNNN
Statistics
Matches: 380, Mismatches: 54, Indels: 45
0.79 0.11 0.09
Matches are distributed among these distances:
73 5 0.01
74 107 0.28
75 18 0.05
76 79 0.21
77 40 0.11
78 69 0.18
79 53 0.14
80 3 0.01
81 6 0.02
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (73 bp):
ATGAGTTGATTTTTGAAAACATAAATTGAAAAATACCTCGACGTGACCCGAGGCTCAACTCACCT
CTCGCAAT
Found at i:38819035 original size:14 final size:14
Alignment explanation
Indices: 38819016--38819046 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
38819006 TCTAGCAATA
38819016 TGAGTTGATTTTTT
1 TGAGTTGATTTTTT
38819030 TGAGTTGATTTTTT
1 TGAGTTGATTTTTT
38819044 TGA
1 TGA
38819047 AAAATACCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.23, T:0.61
Consensus pattern (14 bp):
TGAGTTGATTTTTT
Found at i:38819237 original size:155 final size:151
Alignment explanation
Indices: 38818760--38819245 Score: 511
Period size: 155 Copynumber: 3.2 Consensus size: 151
38818750 TCAGCGTGCA
* *
38818760 ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAGAAAACATAAA-TTGAA-AAAT
1 ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAACAGAAATTTAAAGAAAT
* * * * * * *
38818823 ACATCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAAAAA
65 ACCTCGGCATGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAACATAAA
**
38818888 TT-AAAAAATACCTCAAC-ATG
130 TTGAAAAAATACCTCGCCTATG
* *
38818908 ACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAA-AGA
1 ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAAACAGAAATTTAAAGA-A
***
38818972 ATACCTCGGCATGCGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTGAGTTG
63 ATACCTCGGCAT--GACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGA--TTTTTGA-AAA
* *** * *
38819037 A-TTTTTTTG-AAAAATACCTCAGCATGTG
123 ACATAAATTGAAAAAATACCTC-GCCTATG
* *
38819065 ACCCGAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAACAACAGAAATTTAAACGAAA
1 ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA-AACAGAAATTTAAA-GAAA
* * *
38819130 TACCTCGGCATGACCCGAGACTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAACATAA
64 TACCTCGGCATGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAACATAA
*
38819194 ATTGAAAAGAAATACCTCGGCCTACG
129 ATTG-AAA-AAATACCTC-GCCTATG
* *
38819220 ACCCGAGGATCAACTCACCCCTCGCA
1 ACCCGAGGCTCAACTCACCTCTCGCA
38819246 GTNNNNNNNN
Statistics
Matches: 276, Mismatches: 43, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
147 1 0.00
148 41 0.15
149 9 0.03
150 4 0.01
151 11 0.04
152 11 0.04
153 36 0.13
154 14 0.05
155 80 0.29
156 13 0.05
157 55 0.20
158 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (151 bp):
ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTTAAAGAAATA
CCTCGGCATGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAACATAAAT
TGAAAAAATACCTCGCCTATG
Found at i:38819766 original size:77 final size:75
Alignment explanation
Indices: 38819462--38820038 Score: 924
Period size: 77 Copynumber: 7.7 Consensus size: 75
38819452 NNNNNNNNNN
38819462 TCAACTCACCTCTCGTATTATGAGTTGATTT--AAAAAAAGACATAAATTAAAAATACCTCAGCG
1 TCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCG
38819525 TGACCCGAGGC
65 TGACCCGAGGC
38819536 TCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCG
1 TCAACTCACCTCTGTATTATGAGTTGA-TTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCG
38819601 TGACCCGAGGC
65 TGACCCGAGGC
38819612 TCAACTCACCTCTGTATTATGAGTTGATTT--AAAAAAA-ACATAAATTAAAAATACCTCAGCGT
1 TCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGT
38819674 GACCCGAGGC
66 GACCCGAGGC
*
38819684 TCAACTCACCTTTGTATTATGAGTTGATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGC
1 TCAACTCACCTCTGTATTATGAGTTGA--TTTAAAAAAAAAGACATAAATTAAAAATACCTCAGC
38819749 GTGACCCGAGGC
64 GTGACCCGAGGC
*
38819761 TCAACTCACCTCTGTATTATGAGTTG-----AAAAAAAA-ACATAAATTAAAAATACTTCAGCGT
1 TCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGT
38819820 GACCCGAGGC
66 GACCCGAGGC
*
38819830 TCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAGGACATAAATTAAAAATACCTCAGCGT
1 TCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGT
38819895 GACCCGAGGC
66 GACCCGAGGC
* **
38819905 TCAACTCATCTCTGTATTATGAGTTGATTTTTTTAAAAAAAGACATAAATTAAAAATACCTCAGC
1 TCAACTCACCTCTGTATTATGAGTTGA--TTTAAAAAAAAAGACATAAATTAAAAATACCTCAGC
38819970 GTGACCCGAGGC
64 GTGACCCGAGGC
* * * *
38819982 TCAACTCATCTCTGTATTATGAGTTGATTTAAAAAAAAAAACAGAAAGTGAAAAATA
1 TCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAAGACATAAA-TTAAAAATA
38820039 TTTCTTGAAA
Statistics
Matches: 472, Mismatches: 14, Indels: 32
0.91 0.03 0.06
Matches are distributed among these distances:
69 60 0.13
70 8 0.02
72 61 0.13
73 21 0.04
74 26 0.06
75 79 0.17
76 85 0.18
77 132 0.28
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (75 bp):
TCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGT
GACCCGAGGC
Found at i:38819910 original size:221 final size:217
Alignment explanation
Indices: 38819462--38820008 Score: 902
Period size: 221 Copynumber: 2.5 Consensus size: 217
38819452 NNNNNNNNNN
*
38819462 TCAACTCACCTCTCGTATTATGAGTTGA--TTTAAAAAAAGACATAAATTAAAAATACCTCAGCG
1 TCAACTCACCT-TTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCAGCG
38819525 TGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAAGACATAAATTAAAA
65 TGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTG------AAAAAAAAGACATAAATTAAAA
38819590 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAACATAA
124 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAACATAA
38819655 ATTAAAAATACCTCAGCGTGACCCGAGGC
189 ATTAAAAATACCTCAGCGTGACCCGAGGC
38819684 TCAACTCACCTTTGTATTATGAGTTGATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGC
1 TCAACTCACCTTTGTATTATGAGTTGATTTTT--AAAAAAAGACATAAATTAAAAATACCTCAGC
*
38819749 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAAAAAAAA-ACATAAATTAAAAATACT
64 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAAAAAAAAGACATAAATTAAAAATACC
38819813 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAGGACATAAAT
129 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT-AAAAAAA--ACATAAAT
38819878 TAAAAATACCTCAGCGTGACCCGAGGC
191 TAAAAATACCTCAGCGTGACCCGAGGC
* *
38819905 TCAACTCATCTCTGTATTATGAGTTGATTTTTTTAAAAAAAGACATAAATTAAAAATACCTCAGC
1 TCAACTCACCTTTGTATTATGAGTTGA--TTTTTAAAAAAAGACATAAATTAAAAATACCTCAGC
*
38819970 GTGACCCGAGGCTCAACTCATCTCTGTATTATGAGTTGA
64 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA
38820009 TTTAAAAAAA
Statistics
Matches: 311, Mismatches: 5, Indels: 19
0.93 0.01 0.06
Matches are distributed among these distances:
218 64 0.21
219 15 0.05
221 144 0.46
222 11 0.04
223 8 0.03
225 69 0.22
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (217 bp):
TCAACTCACCTTTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCAGCGT
GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAAAAAAAAGACATAAATTAAAAATACCTC
AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAACATAAATTAAAA
ATACCTCAGCGTGACCCGAGGC
Found at i:38820904 original size:13 final size:13
Alignment explanation
Indices: 38820895--38820925 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
38820885 TGATTTTTTC
38820895 TTTTTCTTTTGTT
1 TTTTTCTTTTGTT
*
38820908 TTTTTGTTTTGTT
1 TTTTTCTTTTGTT
38820921 TTTTT
1 TTTTT
38820926 TTGTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTTGTT
Found at i:38820926 original size:15 final size:16
Alignment explanation
Indices: 38820906--38820941 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
38820896 TTTTCTTTTG
38820906 TTTTTTTG-TTTTGTT
1 TTTTTTTGTTTTTGTT
38820921 TTTTTTTGTTTTTGTT
1 TTTTTTTGTTTTTGTT
38820937 TTTTT
1 TTTTT
38820942 AGGCATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (16 bp):
TTTTTTTGTTTTTGTT
Found at i:38824905 original size:4 final size:4
Alignment explanation
Indices: 38824898--38824922 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
38824888 ATGTACATAC
38824898 AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG A
38824923 CCAATGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:38826627 original size:18 final size:18
Alignment explanation
Indices: 38826601--38826763 Score: 127
Period size: 18 Copynumber: 9.2 Consensus size: 18
38826591 CGATCAGATC
* *
38826601 AAAATACGAGAATTTTTA
1 AAAACACGAAAATTTTTA
*
38826619 AAAACACGAAGATTTTT-
1 AAAACACGAAAATTTTTA
* *** ** *
38826636 GAAACAATTAGTTTTTTG
1 AAAACACGAAAATTTTTA
38826654 AAAACACGAAAAATTTTT-
1 AAAACACG-AAAATTTTTA
*
38826672 AAAACACGAGAA-TTTTA
1 AAAACACGAAAATTTTTA
* * *
38826689 GAGACACGAAAATTCTTA
1 AAAACACGAAAATTTTTA
* *
38826707 AAAATACGAAAATTTTTG
1 AAAACACGAAAATTTTTA
*
38826725 AAAACACGGAAATTTTT-
1 AAAACACGAAAATTTTTA
*
38826742 AAAACACGAAAATTCTTA
1 AAAACACGAAAATTTTTA
38826760 AAAA
1 AAAA
38826764 TTCTTTTCTT
Statistics
Matches: 112, Mismatches: 28, Indels: 10
0.75 0.19 0.07
Matches are distributed among these distances:
16 4 0.04
17 39 0.35
18 63 0.56
19 6 0.05
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAACACGAAAATTTTTA
Found at i:38826696 original size:35 final size:35
Alignment explanation
Indices: 38826648--38826763 Score: 128
Period size: 35 Copynumber: 3.3 Consensus size: 35
38826638 AACAATTAGT
* *
38826648 TTTTTGAAAACACGAAAAATTTTTAAAACACGAGAA
1 TTTTAGAAAACACG-AAAATTTTTAAAACACGAAAA
* * *
38826684 TTTTAG-AGACACGAAAATTCTTAAAAATACGAAAA
1 TTTTAGAAAACACGAAAATT-TTTAAAACACGAAAA
* *
38826719 TTTTTGAAAACACGGAAATTTTTAAAACACGAAAA
1 TTTTAGAAAACACGAAAATTTTTAAAACACGAAAA
38826754 TTCTTA-AAAA
1 TT-TTAGAAAA
38826764 TTCTTTTCTT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
34 6 0.09
35 42 0.64
36 18 0.27
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.28
Consensus pattern (35 bp):
TTTTAGAAAACACGAAAATTTTTAAAACACGAAAA
Found at i:38826764 original size:53 final size:52
Alignment explanation
Indices: 38826649--38826753 Score: 63
Period size: 53 Copynumber: 2.0 Consensus size: 52
38826639 ACAATTAGTT
* * * *
38826649 TTTTGAAAACACGAAAAATTTTTAAAACACGAGAATT-TTAGAGACACG-AAAA
1 TTTTGAAAACACG-AAAA-TTTTAAAACACGAAAATTCCTAAAAACACGAAAAA
* * * * *
38826701 TTCTTAAAAATACGAAAATTTTTGAAAACACGGAAATT-TTTAAAACACGAAAA
1 TT-TTGAAAACACGAAAA-TTTT-AAAACACGAAAATTCCTAAAAACACGAAAA
38826754 TTCTTAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
52 11 0.26
53 29 0.67
54 3 0.07
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.27
Consensus pattern (52 bp):
TTTTGAAAACACGAAAATTTTAAAACACGAAAATTCCTAAAAACACGAAAAA
Found at i:38827274 original size:5 final size:5
Alignment explanation
Indices: 38827264--38827303 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
38827254 TTTAATATAT
* *
38827264 ATAAA ATAAA ATAAG ATAAA AT-AA ATAAA ATAAA ACAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
38827304 ACACGAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:38827282 original size:10 final size:9
Alignment explanation
Indices: 38827267--38827297 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
38827257 AATATATATA
38827267 AAATAAAAT
1 AAATAAAAT
38827276 AAGATAAAAT
1 AA-ATAAAAT
38827286 AAATAAAAT
1 AAATAAAAT
38827295 AAA
1 AAA
38827298 ACAAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:38827303 original size:19 final size:19
Alignment explanation
Indices: 38827267--38827303 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38827257 AATATATATA
* *
38827267 AAATAAAATAAGATAAAAT
1 AAATAAAATAAAACAAAAT
38827286 AAATAAAATAAAACAAAA
1 AAATAAAATAAAACAAAA
38827304 ACACGAAGAA
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:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (19 bp):
AAATAAAATAAAACAAAAT
Found at i:38828520 original size:24 final size:23
Alignment explanation
Indices: 38828476--38828520 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
38828466 TAATGATGAA
* *
38828476 AACGTGAATAAATAATTAAAAGG
1 AACGTGAAAAAATAATAAAAAGG
*
38828499 AACGTGAACAAAATTATAAAAA
1 AACGTGAA-AAAATAATAAAAA
38828521 TACAAGAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (23 bp):
AACGTGAAAAAATAATAAAAAGG
Found at i:38839607 original size:51 final size:51
Alignment explanation
Indices: 38839484--38839663 Score: 147
Period size: 51 Copynumber: 3.5 Consensus size: 51
38839474 GATGGTCAAG
* * **
38839484 TGTGTAGTACTATGTGCAGGCTACTACAT-GT-ACCGGA-A-TGATAGGTCGTA
1 TGTGTAGTACTATGTGCAGGCTACT--ATGGTAACCGGATAGTAAT-GATCACA
* * * *
38839534 TGTGTAGTACTCTGTGTAGGCTACTATGCGT-ACCGGATAGT-TTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATG-GTAACCGGATAGTAAT-GATCACA
* * * * *
38839585 TGTGTAGTACTATGTGCAGGCTACTAAGTTAATCGGATGGTAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGGTAACCGGATAGTAATGATCACA
*
38839636 TGTGTAGCACTATGTGCAGGCTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTATG
38839664 TGAACCGAAC
Statistics
Matches: 105, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
48 2 0.02
50 32 0.30
51 69 0.66
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGGTAACCGGATAGTAATGATCACA
Found at i:38839837 original size:38 final size:37
Alignment explanation
Indices: 38839791--38839863 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
38839781 AGTTGTGGAA
*
38839791 TTGAATTGAATAT-TGACTTAGAAA-TGGAAAAGTGAATT
1 TTGAATTGAAT-TGTGA-TT-GAAAGTGAAAAAGTGAATT
38839829 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
38839864 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.33
Consensus pattern (37 bp):
TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAATT
Found at i:38844393 original size:4 final size:4
Alignment explanation
Indices: 38844384--38844409 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
38844374 TGATAGCTTC
38844384 ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT AC
38844410 GTTAGATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:38849178 original size:25 final size:25
Alignment explanation
Indices: 38849120--38849170 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
38849110 CTTCAAAAAA
*
38849120 AACGCCGCTAAAGGTCATGTTCTTT
1 AACGCCGCTAAAGCTCATGTTCTTT
38849145 AACGCCGCTAAAGCTCATGTTCTTT
1 AACGCCGCTAAAGCTCATGTTCTTT
38849170 A
1 A
38849171 GCGGCGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (25 bp):
AACGCCGCTAAAGCTCATGTTCTTT
Found at i:38849195 original size:67 final size:67
Alignment explanation
Indices: 38849078--38849211 Score: 198
Period size: 67 Copynumber: 2.0 Consensus size: 67
38849068 TATAGAAATA
* * *
38849078 AACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCAAAAAAAACGCCGCTAAAGGTCATGTTCT
1 AACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTCAAAAAAAACCCCGCTAAAGGTAATGTTCT
38849143 TT
66 TT
** *
38849145 AACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTC-TCAGAAACCCCGCTAAAGGTAATGTTC
1 AACGCCGCTAAAGCTCATGTTCTTTAGCGGCGC-TTCAAAAAAAACCCCGCTAAAGGTAATGTTC
38849209 TTT
65 TTT
38849212 TAGCGGCGCC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 57 0.95
68 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (67 bp):
AACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTCAAAAAAAACCCCGCTAAAGGTAATGTTCT
TT
Found at i:38849208 original size:42 final size:43
Alignment explanation
Indices: 38849149--38849301 Score: 134
Period size: 44 Copynumber: 3.6 Consensus size: 43
38849139 TTCTTTAACG
* * *
38849149 CCGCTAAAGCTCATGTTCTTTAGCGGCG-C-TTTCTCAGAAACC
1 CCGCTAAAGGTAATGTTCTTTAGCGGCGCCTTTTC-CACAAACC
*
38849191 CCGCTAAAGGTAATGTTCTTTTAGCGGCGCCTTTTCCACAAACG
1 CCGCTAAAGGTAATGTTC-TTTAGCGGCGCCTTTTCCACAAACC
* * ** *
38849235 CCGCTACAA-GTAATGTTCTTTAACGGTGTTTTTTTCCACAAACG
1 CCGCTA-AAGGTAATGTTCTTTAGCGGCG-CCTTTTCCACAAACC
* * *
38849279 CCGCT-ATGGTCATGCTCTTTAGC
1 CCGCTAAAGGTAATGTTCTTTAGC
38849302 TTTTAGCGAC
Statistics
Matches: 93, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
42 17 0.18
43 30 0.32
44 40 0.43
45 6 0.06
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (43 bp):
CCGCTAAAGGTAATGTTCTTTAGCGGCGCCTTTTCCACAAACC
Found at i:38849248 original size:44 final size:41
Alignment explanation
Indices: 38849145--38849284 Score: 147
Period size: 44 Copynumber: 3.2 Consensus size: 41
38849135 CATGTTCTTT
* *
38849145 AACGCCGCTAAAGCTCATGTTCTTTAGCGGCGC-TTTCTCAGA
1 AACGCCGCTAAAG-TAATGTTCTTTAGCGGCGCTTTTC-CACA
*
38849187 AACCCCGCTAAAGGTAATGTTCTTTTAGCGGCGCCTTTTCCACA
1 AACGCCGCTAAA-GTAATGTTC-TTTAGCGGCG-CTTTTCCACA
* * *
38849231 AACGCCGCTACAAGTAATGTTCTTTAACGGTGTTTTTTTCCACA
1 AACGCCGCTA-AAGTAATGTTCTTTAGCGGCG--CTTTTCCACA
38849275 AACGCCGCTA
1 AACGCCGCTA
38849285 TGGTCATGCT
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
42 18 0.21
43 19 0.23
44 41 0.49
45 6 0.07
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (41 bp):
AACGCCGCTAAAGTAATGTTCTTTAGCGGCGCTTTTCCACA
Found at i:38849724 original size:21 final size:21
Alignment explanation
Indices: 38849700--38849750 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
38849690 TTCTTTTGAA
*
38849700 CCTCTGCTTCTCTCGCTG-CAG
1 CCTCTGCTTCCCTCGCTGTC-G
38849721 CCTCTGCTTCCCTCGCTGTCG
1 CCTCTGCTTCCCTCGCTGTCG
38849742 CCTCTGCTT
1 CCTCTGCTT
38849751 TAAGTTGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGTCG
Found at i:38849803 original size:87 final size:86
Alignment explanation
Indices: 38849636--38849794 Score: 219
Period size: 87 Copynumber: 1.8 Consensus size: 86
38849626 TTGTGCTTTG
* * * *
38849636 CTCTGCTTCTCTCGATGCCGCATCTGTTTTAAGTTTAGTTGGAGTTCTTCATATTTCTTTTGAAC
1 CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTTTAGCTGGAGTTCTTCATATTTCCTTTGAAC
** *
38849701 CTCTGCTTCTCTCGCTGCAGC
66 CTCAACTTCGCTCGCTGCAGC
* * *
38849722 CTCTGCTTCCCTCGCTGTCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTT-TAGCTGGAGTTCTTCATATTTCCTTTGAA
38849787 CCTCAACT
65 CCTCAACT
38849795 GTGGTCGCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
86 30 0.48
87 33 0.52
ACGTcount: A:0.13, C:0.28, G:0.17, T:0.42
Consensus pattern (86 bp):
CTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTTTAGCTGGAGTTCTTCATATTTCCTTTGAAC
CTCAACTTCGCTCGCTGCAGC
Found at i:38852578 original size:12 final size:12
Alignment explanation
Indices: 38852561--38852607 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
38852551 ATGTATGTAA
38852561 ATTATGTAAGTT
1 ATTATGTAAGTT
38852573 ATTATGTAAG--
1 ATTATGTAAGTT
38852583 -TTATGTAAGTT
1 ATTATGTAAGTT
* *
38852594 ACTATGTAGGTT
1 ATTATGTAAGTT
38852606 AT
1 AT
38852608 GTTCATTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 9 0.31
12 20 0.69
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (12 bp):
ATTATGTAAGTT
Found at i:38852606 original size:21 final size:21
Alignment explanation
Indices: 38852554--38852609 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
38852544 AATATTTATG
* *
38852554 TATGTAAATTATGTAAGTTAT
1 TATGTAAGTTATGTAAGTTAC
38852575 TATGTAAGTTATGTAAGTTAC
1 TATGTAAGTTATGTAAGTTAC
*
38852596 TATGTAGGTTATGT
1 TATGTAAGTTATGT
38852610 TCATTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (21 bp):
TATGTAAGTTATGTAAGTTAC
Found at i:38852708 original size:91 final size:88
Alignment explanation
Indices: 38852514--38852710 Score: 204
Period size: 91 Copynumber: 2.2 Consensus size: 88
38852504 ATAATTAAGC
*
38852514 TATGTAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAAGTTATTATG
1 TATGTAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAAGTTATAATG
* *
38852579 TAAGTTATGTAAGTTACTATGTAGGT
66 TAAGATATATAAG-T-CTATGTA-GT
* * * *
38852605 TATGTTCA-TTATGTAAGTTGTA-ATATGATTAATATTTATGTATGTAAATTATGATATGATTGA
1 TATG-TAAGTTATGTAAGTT-AAGATATAATTAATATTTATGTATGTAAATTATG-TAAG-TT-A
*
38852668 TAAATTTAAGATATATAAG-CTATGTA-T
61 T-AATGTAAGATATATAAGTCTATGTAGT
38852695 TATGTAAGTTTATGTA
1 TATGTAAG-TTATGTA
38852711 TGCAGGAATA
Statistics
Matches: 89, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
89 2 0.02
90 5 0.06
91 52 0.58
92 13 0.15
93 2 0.02
94 2 0.02
95 13 0.15
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.46
Consensus pattern (88 bp):
TATGTAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAAGTTATAATG
TAAGATATATAAGTCTATGTAGT
Found at i:38852799 original size:39 final size:40
Alignment explanation
Indices: 38852746--38852821 Score: 136
Period size: 39 Copynumber: 1.9 Consensus size: 40
38852736 ATGTAAGTTA
*
38852746 TGTAAGTTAAGATATAATATATATCCCGGTAAGTTATAAG
1 TGTAAGTTAAGATATAATATACATCCCGGTAAGTTATAAG
38852786 TGTAA-TTAAGATATAATATACATCCCGGTAAGTTAT
1 TGTAAGTTAAGATATAATATACATCCCGGTAAGTTAT
38852822 GTAGGTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 30 0.86
40 5 0.14
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (40 bp):
TGTAAGTTAAGATATAATATACATCCCGGTAAGTTATAAG
Found at i:38852817 original size:22 final size:21
Alignment explanation
Indices: 38852753--38852817 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
38852743 TTATGTAAGT
38852753 TAAGATATAATATATATCCCGG
1 TAAGATATAATATA-ATCCCGG
* *
38852775 TAAGTTATAAGTGTAAT-----
1 TAAGATATAA-TATAATCCCGG
38852792 TAAGATATAATATACATCCCGG
1 TAAGATATAATATA-ATCCCGG
38852814 TAAG
1 TAAG
38852818 TTATGTAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
22 15 0.47
23 3 0.09
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (21 bp):
TAAGATATAATATAATCCCGG
Found at i:38852853 original size:9 final size:9
Alignment explanation
Indices: 38852839--38852889 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
38852829 ATTAATAAGT
38852839 TATGTATTA
1 TATGTATTA
38852848 TATGTATTA
1 TATGTATTA
*
38852857 TATGTAAGT-
1 TATGT-ATTA
*
38852866 TATGTAGGT-
1 TATGTA-TTA
38852875 TATGTATTA
1 TATGTATTA
38852884 TATGTA
1 TATGTA
38852890 GGTTATGTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
8 2 0.05
9 33 0.89
10 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (9 bp):
TATGTATTA
Found at i:38852857 original size:27 final size:28
Alignment explanation
Indices: 38852817--38852904 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
38852807 ATCCCGGTAA
38852817 GTTATGTAGGTTATTA-ATAAGTTATGTA-
1 GTTATGTA--TTATTATATAAGTTATGTAG
* *
38852845 TTATATGTATTA-TATGTAAGTTATGTAG
1 GT-TATGTATTATTATATAAGTTATGTAG
* *
38852873 GTTATGTATTA-TATGTAGGTTATGTAG
1 GTTATGTATTATTATATAAGTTATGTAG
38852900 GTTAT
1 GTTAT
38852905 TATATTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.04
27 43 0.81
28 2 0.04
29 6 0.11
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (28 bp):
GTTATGTATTATTATATAAGTTATGTAG
Found at i:38852860 original size:18 final size:18
Alignment explanation
Indices: 38852837--38852898 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
38852827 TTATTAATAA
38852837 GTTATGTATTATATGTA-
1 GTTATGTATTATATGTAG
* *
38852854 TTATATGTAAGT-TATGTAG
1 GT-TATGT-ATTATATGTAG
38852873 GTTATGTATTATATGTAG
1 GTTATGTATTATATGTAG
38852891 GTTATGTA
1 GTTATGTA
38852899 GGTTATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
17 3 0.08
18 31 0.84
19 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (18 bp):
GTTATGTATTATATGTAG
Found at i:38852896 original size:9 final size:9
Alignment explanation
Indices: 38852857--38852904 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
38852847 ATATGTATTA
*
38852857 TATGTAAGT
1 TATGTAGGT
38852866 TATGTAGGT
1 TATGTAGGT
*
38852875 TATGTA-TT
1 TATGTAGGT
38852883 ATATGTAGGT
1 -TATGTAGGT
38852893 TATGTAGGT
1 TATGTAGGT
38852902 TAT
1 TAT
38852905 TATATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 1 0.03
9 32 0.94
10 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (9 bp):
TATGTAGGT
Found at i:38855882 original size:7 final size:7
Alignment explanation
Indices: 38855865--38855971 Score: 76
Period size: 7 Copynumber: 15.0 Consensus size: 7
38855855 ACATTAACTA
38855865 TAAACCCC
1 TAAA-CCC
38855873 TAAACCC
1 TAAACCC
38855880 TAAACCC
1 TAAACCC
*
38855887 TTAACCC
1 TAAACCC
38855894 T-AACCC
1 TAAACCC
*
38855900 TTAACCC
1 TAAACCC
38855907 TTAAACCC
1 -TAAACCC
*
38855915 TTAACCC
1 TAAACCC
**
38855922 TTCACCC
1 TAAACCC
38855929 TTAAACCC
1 -TAAACCC
38855937 TAAACACC
1 TAAAC-CC
38855945 --AACCC
1 TAAACCC
*
38855950 TTAAACCA
1 -TAAACCC
* *
38855958 TAATCCA
1 TAAACCC
38855965 TAAACCC
1 TAAACCC
38855972 CTAACCCATA
Statistics
Matches: 82, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
5 2 0.02
6 9 0.11
7 50 0.61
8 21 0.26
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:38855912 original size:43 final size:42
Alignment explanation
Indices: 38855865--38855997 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 42
38855855 ACATTAACTA
38855865 TAAACCCCTAAACCCTAAACCCTTAACCCTAACCCTTAACCCT
1 TAAA-CCCTAAACCCTAAACCCTTAACCCTAACCCTTAACCCT
* **
38855908 TAAACCCTTAACCCTTCACCCTTAAACCCTAAACACC--AACCCT
1 TAAACCCTAAACCCTAAACCCTT-AACCCT-AAC-CCTTAACCCT
* * * * * *
38855951 TAAACCATAATCCATAAACCCCTAACCCATATCCCTTAAACCT
1 TAAACCCTAAACCCTAAACCCTTAACCC-TAACCCTTAACCCT
38855994 TAAA
1 TAAA
38855998 TCATAGAACA
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
41 2 0.03
42 23 0.32
43 42 0.58
44 3 0.04
45 2 0.03
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (42 bp):
TAAACCCTAAACCCTAAACCCTTAACCCTAACCCTTAACCCT
Found at i:38855934 original size:57 final size:56
Alignment explanation
Indices: 38855868--38855997 Score: 138
Period size: 57 Copynumber: 2.3 Consensus size: 56
38855858 TTAACTATAA
* * * * * *
38855868 ACCCCTAAACCCTAAAC-CCTTAACCC-TAACCCTTAACCCTTAAACCCTTAACCCTT
1 ACCCTTAAACCCTAAACACC--AACCCTTAAACCATAACCCATAAACCCCTAACCCAT
*
38855924 CACCCTTAAACCCTAAACACCAACCCTTAAACCATAATCCATAAACCCCTAACCCAT
1 -ACCCTTAAACCCTAAACACCAACCCTTAAACCATAACCCATAAACCCCTAACCCAT
*
38855981 ATCCCTTAAACCTTAAA
1 A-CCCTTAAACCCTAAA
38855998 TCATAGAACA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
56 6 0.10
57 54 0.87
58 2 0.03
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.22
Consensus pattern (56 bp):
ACCCTTAAACCCTAAACACCAACCCTTAAACCATAACCCATAAACCCCTAACCCAT
Found at i:38855948 original size:28 final size:28
Alignment explanation
Indices: 38855867--38855997 Score: 115
Period size: 28 Copynumber: 4.6 Consensus size: 28
38855857 ATTAACTATA
*
38855867 AACCCCTAAACCCTAAACCCTTAACCC-T
1 AACCCTTAAACCCTAAACCC-TAACCCTT
38855895 AACCCTT-AACCCTTAAACCCTTAACCCTT
1 AACCCTTAAACCC-TAAACCC-TAACCCTT
*
38855924 CACCCTTAAACCCTAAACACC-AACCCTT
1 AACCCTTAAACCCTAAAC-CCTAACCCTT
* * * * *
38855952 AAACCATAATCCATAAACCCCTAACCCAT
1 AACCCTTAAACCCTAAA-CCCTAACCCTT
* *
38855981 ATCCCTTAAACCTTAAA
1 AACCCTTAAACCCTAAA
38855998 TCATAGAACA
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.06
28 41 0.49
29 31 0.37
30 7 0.08
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.21
Consensus pattern (28 bp):
AACCCTTAAACCCTAAACCCTAACCCTT
Found at i:38856159 original size:15 final size:15
Alignment explanation
Indices: 38856136--38856218 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 15
38856126 CTAACCCCAG
*
38856136 CCCTTAACCCTTAAC
1 CCCTAAACCCTTAAC
38856151 CCCTAAACCCTTAA-
1 CCCTAAACCCTTAAC
* *
38856165 -CCTCAACCCTTAAA
1 CCCTAAACCCTTAAC
* * * *
38856179 CCATAATCCATAAAC
1 CCCTAAACCCTTAAC
* *
38856194 CCCT-AACCCATATC
1 CCCTAAACCCTTAAC
*
38856208 CCTTAAACCCT
1 CCCTAAACCCT
38856219 AAATCATAGA
Statistics
Matches: 49, Mismatches: 16, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
13 12 0.24
14 8 0.16
15 29 0.59
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.23
Consensus pattern (15 bp):
CCCTAAACCCTTAAC
Found at i:38856160 original size:35 final size:35
Alignment explanation
Indices: 38856118--38856216 Score: 110
Period size: 35 Copynumber: 2.8 Consensus size: 35
38856108 AACATTAACT
* * *
38856118 ATAAACCCCTAACCCCAGCCCTTAACCCTTAACCC
1 ATAAACCCCTAACCCCAACCCTTAAACCATAACCC
* * * *
38856153 CTAAACCCTTAACCTCAACCCTTAAACCATAATCC
1 ATAAACCCCTAACCCCAACCCTTAAACCATAACCC
38856188 ATAAACCCCTAA-CCCATATCCCTTAAACC
1 ATAAACCCCTAACCCCA-A-CCCTTAAACC
38856217 CTAAATCATA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
34 3 0.06
35 39 0.75
36 10 0.19
ACGTcount: A:0.35, C:0.43, G:0.01, T:0.20
Consensus pattern (35 bp):
ATAAACCCCTAACCCCAACCCTTAAACCATAACCC
Found at i:38856164 original size:22 final size:22
Alignment explanation
Indices: 38856140--38856221 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 22
38856130 CCCCAGCCCT
*
38856140 TAACCCTTAACCCCTAAACCCT
1 TAACCCTTAACCCCTAAACCCA
* *
38856162 TAA-CCTCAACCCTTAAA-CCA
1 TAACCCTTAACCCCTAAACCCA
* *
38856182 TAATCCATAAACCCCT-AACCCA
1 TAA-CCCTTAACCCCTAAACCCA
* *
38856204 TATCCCTTAAACCCTAAA
1 TAACCCTTAACCCCTAAA
38856222 TCATAGAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 5 0.11
21 23 0.50
22 18 0.39
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (22 bp):
TAACCCTTAACCCCTAAACCCA
Found at i:38856265 original size:39 final size:41
Alignment explanation
Indices: 38856211--38856287 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
38856201 CCATATCCCT
38856211 TAAACCCTAAATCATAG-A-ACATATATAAACTATAAACCC
1 TAAACCCTAAATCATAGCATACATATATAAACTATAAACCC
* * *
38856250 TAAACCCTGATTCATAGCATATATATATAAACTATAAA
1 TAAACCCTAAATCATAGCATACATATATAAACTATAAA
38856288 GTGTAAACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 15 0.45
40 1 0.03
41 17 0.52
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.27
Consensus pattern (41 bp):
TAAACCCTAAATCATAGCATACATATATAAACTATAAACCC
Found at i:38856991 original size:114 final size:113
Alignment explanation
Indices: 38856869--38857196 Score: 313
Period size: 114 Copynumber: 2.9 Consensus size: 113
38856859 GTTTCTAAGA
*
38856869 AAGCGCCACTAACGTCTCTAAAACCTAAATTAAAAACGACTACGTTTTCTTAACAGTTTTGCGGC
1 AAGCGCCACTAACGTCTCTAAAACCTAAACTAAAAACGAC-ACGTTTTCTTAACAGTTTTGCGGC
* **
38856934 GCTT-TGTCTAAAGCGCCGCTAAATCTTGGCTATTACGACATTTTTT-GAT
65 GCTTATG-ATAAAGCGCCGCTAAATCTTAACTATTACGACATTTTTTAG-T
** * ** * * *
38856983 AATTGCCACTATCGTCT-TGAAAAGATAAACGAAAAACGACAATGTTTTCTTAATAGTTTTGCGG
1 AAGCGCCACTAACGTCTCT-AAAACCTAAACTAAAAACGAC-ACGTTTTCTTAACAGTTTTGCGG
* * * * * *
38857047 TGCTTATGATAAAGCGCCTCTAATTCTTAACTATTGCGGCGTTTTTTAGT
64 CGCTTATGATAAAGCGCCGCTAAATCTTAACTATTACGACATTTTTTAGT
* * * *
38857097 AAGCGCCACTAACGTCCCTAAAACCTAAACCT-AAAATGGCACCGTTTTCTTAACAGTTTTTGCT
1 AAGCGCCACTAACGTCTCTAAAACCTAAA-CTAAAAACGACA-CGTTTTCTTAACAG-TTTTGCG
* * * * *
38857161 GCGTTTATGATAAAACGCCGGTAATTCTTGACTATT
63 GCGCTTATGATAAAGCGCCGCTAAATCTTAACTATT
38857197 GCGGCGTTTC
Statistics
Matches: 170, Mismatches: 37, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
113 2 0.01
114 127 0.75
115 41 0.24
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (113 bp):
AAGCGCCACTAACGTCTCTAAAACCTAAACTAAAAACGACACGTTTTCTTAACAGTTTTGCGGCG
CTTATGATAAAGCGCCGCTAAATCTTAACTATTACGACATTTTTTAGT
Found at i:38858061 original size:17 final size:19
Alignment explanation
Indices: 38858025--38858061 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38858015 GAGAGATTTG
38858025 TTTATTTTTATATTAAATAA
1 TTTATTTTTATA-TAAATAA
38858045 TTTA-TTTTATA-AAATAA
1 TTTATTTTTATATAAATAA
38858062 CTCCTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATTTTTATATAAATAA
Found at i:38860894 original size:12 final size:12
Alignment explanation
Indices: 38860877--38860901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38860867 ATTTAATCAC
38860877 TTTAATATTAAA
1 TTTAATATTAAA
38860889 TTTAATATTAAA
1 TTTAATATTAAA
38860901 T
1 T
38860902 CTTATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:38866185 original size:27 final size:27
Alignment explanation
Indices: 38866155--38866212 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
38866145 ACGGGCATCT
* * *
38866155 TTTCATAATTCACCACAAAAGTTATTC
1 TTTCAGAATTCACCACAAAAGCTATTA
* *
38866182 TTTCAGAGTTTACCACAAAAGCTATTA
1 TTTCAGAATTCACCACAAAAGCTATTA
38866209 TTTC
1 TTTC
38866213 CTAACGTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (27 bp):
TTTCAGAATTCACCACAAAAGCTATTA
Found at i:38867482 original size:26 final size:26
Alignment explanation
Indices: 38867453--38867503 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
38867443 GTTACAAGAC
38867453 TAATTTGTAATGTAAACTG-ACTAGAT
1 TAATTTGTAATGTAAAC-GAACTAGAT
38867479 TAATTTGTAATGTAAACGAACTAGA
1 TAATTTGTAATGTAAACGAACTAGA
38867504 GAATCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (26 bp):
TAATTTGTAATGTAAACGAACTAGAT
Found at i:38876622 original size:7 final size:7
Alignment explanation
Indices: 38876610--38876634 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38876600 AGTCGATTGA
38876610 TATTTAG
1 TATTTAG
38876617 TATTTAG
1 TATTTAG
38876624 TATTTAG
1 TATTTAG
38876631 TATT
1 TATT
38876635 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:38877312 original size:18 final size:18
Alignment explanation
Indices: 38877285--38877324 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
38877275 CAGGTGCGTT
*
38877285 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
38877303 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
38877321 TCCT
1 TCCT
38877325 TTTTCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:38877650 original size:54 final size:53
Alignment explanation
Indices: 38877591--38877889 Score: 174
Period size: 54 Copynumber: 5.3 Consensus size: 53
38877581 CTGGTACTAA
38877591 CAATTAATAATTTTATATAATTCGATAATTTTACTAATCATTAATACAATTTAT
1 CAATTAATAATTTTATATAATT-GATAATTTTACTAATCATTAATACAATTTAT
* * * ** * * ** * *
38877645 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAAT-GTT-TTGACTGGTACTAA
1 CAATTAATAATTTTATA-T-A-AT--TGATA-ATTT-TACTAATCATTAAT-AC-AAT-TTAT
38877706 CAATTAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTAT
1 CAATTAATAATTTTATATAA-TTGATAATTTTACTAATCATTAATACAATTTAT
* * * ** * ** * *
38877760 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAAT-ATT-TTGACTGGTACTAA
1 CAATTAATAATTTTATA-T-A-AT--TGATA-ATTT-TACTAATCATTAAT-AC-AAT-TTAT
38877821 CAATTAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTAT
1 CAATTAATAATTTTATATAA-TTGATAATTTTACTAATCATTAATACAATTTAT
38877875 CAATTAATAATTTTA
1 CAATTAATAATTTTA
38877890 CATTCACATA
Statistics
Matches: 177, Mismatches: 42, Indels: 52
0.65 0.15 0.19
Matches are distributed among these distances:
54 51 0.29
55 12 0.07
56 20 0.11
57 13 0.07
58 11 0.06
59 22 0.12
60 12 0.07
61 36 0.20
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (53 bp):
CAATTAATAATTTTATATAATTGATAATTTTACTAATCATTAATACAATTTAT
Found at i:38877720 original size:61 final size:61
Alignment explanation
Indices: 38877645--38877950 Score: 234
Period size: 61 Copynumber: 5.2 Consensus size: 61
38877635 TACAATTTAT
*
38877645 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAA
1 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAA
* * * * ** * ** * *
38877706 CAATTAATAATTTTATA-T-A-AT-TTGATA-ATTT-TACTAATCATTAAT-AC-AAT-TTAT
1 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAAT-ATT-TTGACTGGTACTAA
38877760 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAA
1 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAA
* * * * ** * ** * *
38877821 CAATTAATAATTTTATA-T-A-AT-TTGATA-ATTT-TACTAATCATTAAT-AC-AAT-TTAT
1 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAAT-ATT-TTGACTGGTACTAA
*
38877875 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAA
1 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAA
38877936 CAATTAATAATTTTA
1 CAATTAATAATTTTA
38877951 TATAATTTGA
Statistics
Matches: 177, Mismatches: 46, Indels: 44
0.66 0.17 0.16
Matches are distributed among these distances:
54 36 0.20
55 12 0.07
56 19 0.11
57 14 0.08
58 14 0.08
59 19 0.11
60 12 0.07
61 51 0.29
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (61 bp):
CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAA
Found at i:38877740 original size:115 final size:115
Alignment explanation
Indices: 38877532--38878002 Score: 845
Period size: 115 Copynumber: 4.1 Consensus size: 115
38877522 ACATACTAAT
* * **
38877532 TTAATAATTTTACTTTCACATAATGTTAGATTTTGAAAAATGTTTTTTCCTGGTACTAACAATTA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATG-TTTTGACTGGTACTAACAATTA
*
38877597 ATAATTTTATATAATTCGATAATTTTACTAATCATTAATACAATTTATCAA
65 ATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATCAA
38877648 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
38877713 TAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATCAA
66 TAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATCAA
*
38877763 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
38877828 TAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATCAA
66 TAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATCAA
38877878 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
* *
38877943 TAATTTTATATAATTTGA-ATTTTTTACTAACCATTAATACAATTTATCAA
66 TAATTTTATATAATTTGATA-ATTTTACTAATCATTAATACAATTTATCAA
38877993 TTAATAATTT
1 TTAATAATTT
38878003 CACAAACTTA
Statistics
Matches: 345, Mismatches: 9, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
114 1 0.00
115 304 0.88
116 40 0.12
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (115 bp):
TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATCAA
Found at i:38887841 original size:18 final size:18
Alignment explanation
Indices: 38887815--38887866 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
38887805 AAAATACGAG
*
38887815 AAATAATGTTCACATTTT
1 AAATAATGTTCACATTTC
*
38887833 AAATGATGTTCACATTTC
1 AAATAATGTTCACATTTC
38887851 AAATAATGTTCACATT
1 AAATAATGTTCACATT
38887867 GATGGAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (18 bp):
AAATAATGTTCACATTTC
Found at i:38897118 original size:13 final size:13
Alignment explanation
Indices: 38897102--38897152 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
38897092 TTTAAATAAA
38897102 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
*
38897115 ACTTCTCAAAA-T
1 ACTTTTCAAAAGT
*
38897127 CACTTTTTCAAAAGC
1 -AC-TTTTCAAAAGT
*
38897142 ACGTTTCAAAA
1 ACTTTTCAAAA
38897153 ATAATGCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 1 0.03
13 20 0.65
14 10 0.32
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:38899383 original size:193 final size:193
Alignment explanation
Indices: 38899036--38899421 Score: 664
Period size: 193 Copynumber: 2.0 Consensus size: 193
38899026 CCACAAGCCT
* *
38899036 TACCTCAACCAGACCATGTGGCTTATACATCTATGTTTCTCACACGGCCCTACACACGATCATGT
1 TACCTCAACCAGACCATGTGGCTTATACATCTATGTTTCTCACACGGCCCGACACACGACCATGT
* *
38899101 AGCGTCATCAGCCTCATTTTGATTTTCACAAAATTTTAGGGTTTCCATGTTCGTTTTTAAAAATT
66 AGCGTCATCAGCCTCATTTTGATTTTCACAAAATTTCAAGGTTTCCATGTTCGTTTTTAAAAATT
*
38899166 ACGGGTTAGGTCATACAACTTATTACTTTTAGGATGTCGGCACTAAAACAGCACTCCAAGTCC
131 ACGGGTCAGGTCATACAACTTATTACTTTTAGGATGTCGGCACTAAAACAGCACTCCAAGTCC
*
38899229 TACCTCAACCAGACCATGTGGCTTATACATCTATGTTTCTCACACGGCCCGACACATGACCATGT
1 TACCTCAACCAGACCATGTGGCTTATACATCTATGTTTCTCACACGGCCCGACACACGACCATGT
* *
38899294 AGCGTCATCAGCCTCATTTTGATTTTCATAGAATTTCAAGGTTTCCATGTTCGTTTTTAAAAATT
66 AGCGTCATCAGCCTCATTTTGATTTTCACAAAATTTCAAGGTTTCCATGTTCGTTTTTAAAAATT
* * * *
38899359 ACGGGTCAGGTCGTACACCTTATTACTTTTGGGATGTCGGCACTAAAGCAGCACTCCAAGTCC
131 ACGGGTCAGGTCATACAACTTATTACTTTTAGGATGTCGGCACTAAAACAGCACTCCAAGTCC
38899422 CTGTACACGA
Statistics
Matches: 181, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
193 181 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (193 bp):
TACCTCAACCAGACCATGTGGCTTATACATCTATGTTTCTCACACGGCCCGACACACGACCATGT
AGCGTCATCAGCCTCATTTTGATTTTCACAAAATTTCAAGGTTTCCATGTTCGTTTTTAAAAATT
ACGGGTCAGGTCATACAACTTATTACTTTTAGGATGTCGGCACTAAAACAGCACTCCAAGTCC
Found at i:38901822 original size:19 final size:17
Alignment explanation
Indices: 38901798--38901837 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
38901788 ATGTTAAATT
38901798 AAATTAATTAACTAAATGC
1 AAATTAA-T-ACTAAATGC
*
38901817 AAATTAATCCTAAATGC
1 AAATTAATACTAAATGC
38901834 AAAT
1 AAAT
38901838 AAGATGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 1 0.05
19 7 0.35
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (17 bp):
AAATTAATACTAAATGC
Found at i:38911473 original size:3 final size:3
Alignment explanation
Indices: 38911465--38911535 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
38911455 ATGTCCATTG
38911465 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38911513 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
38911536 TTTGATGCTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38917462 original size:2 final size:2
Alignment explanation
Indices: 38917455--38917485 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38917445 ATCATGTGCA
38917455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38917486 CAACAGATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38937785 original size:3 final size:3
Alignment explanation
Indices: 38937777--38937817 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
38937767 GAAGAATTCA
38937777 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
38937818 AAGCCATCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:38940307 original size:11 final size:11
Alignment explanation
Indices: 38940291--38940315 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38940281 CACCCTTAAT
38940291 GAATACAAAAG
1 GAATACAAAAG
38940302 GAATACAAAAG
1 GAATACAAAAG
38940313 GAA
1 GAA
38940316 GTACGAGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (11 bp):
GAATACAAAAG
Found at i:38942415 original size:20 final size:19
Alignment explanation
Indices: 38942376--38942419 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
38942366 ATCAAATATT
**
38942376 TTTTATAAAAATTGTAAAA
1 TTTTATAAAAATCATAAAA
38942395 TTTTATAAAAATCATACAAA
1 TTTTATAAAAATCATA-AAA
38942415 TTTTA
1 TTTTA
38942420 ATGACCTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTTATAAAAATCATAAAA
Found at i:38942419 original size:39 final size:39
Alignment explanation
Indices: 38942340--38942419 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 39
38942330 TTAATAAAAA
* **
38942340 TATAAAAAATTAAAAATTTATTAAAAATCAAATATTTTT
1 TATAAAAAATTAAAAATTTATTAAAAATCAAACAAATTT
* * *
38942379 TATAAAAATTGTAAAATTTTA-TAAAAATCATACAAATTT
1 TATAAAAAAT-TAAAAATTTATTAAAAATCAAACAAATTT
38942418 TA
1 TA
38942420 ATGACCTCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 25 0.74
40 9 0.26
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (39 bp):
TATAAAAAATTAAAAATTTATTAAAAATCAAACAAATTT
Found at i:38942633 original size:9 final size:9
Alignment explanation
Indices: 38942613--38942787 Score: 62
Period size: 9 Copynumber: 19.3 Consensus size: 9
38942603 TTCTTACGAC
38942613 TTTATAAAAT
1 TTTAT-AAAT
38942623 TTTATAAAT
1 TTTATAAAT
* *
38942632 TTTTTATAT
1 TTTATAAAT
*
38942641 TTCTATATAT
1 TT-TATAAAT
38942651 TTTAT-AAT
1 TTTATAAAT
*
38942659 TTTTTAAGATT
1 TTTATAA-A-T
38942670 TTTATAAAAT
1 TTTAT-AAAT
*
38942680 TTTATAACTT
1 TTTATAA-AT
* *
38942690 TTTTTATAT
1 TTTATAAAT
*
38942699 TTT-TACGAT
1 TTTATA-AAT
**
38942708 TTTATATTT
1 TTTATAAAT
*
38942717 TTTCT-AAT
1 TTTATAAAT
38942725 TTT-T-AAT
1 TTTATAAAT
38942732 TTT-TAATAT
1 TTTATAA-AT
38942741 TTTAT---T
1 TTTATAAAT
38942747 TTTATTAAAAT
1 TTTA-T-AAAT
* *
38942758 TTAATAAAA
1 TTTATAAAT
*
38942767 TTTATAGAT
1 TTTATAAAT
*
38942776 TTTATAGAT
1 TTTATAAAT
38942785 TTT
1 TTT
38942788 TTTAATTTTT
Statistics
Matches: 128, Mismatches: 21, Indels: 33
0.70 0.12 0.18
Matches are distributed among these distances:
6 5 0.04
7 9 0.07
8 13 0.10
9 59 0.46
10 30 0.23
11 10 0.08
12 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTATAAAT
Found at i:38942691 original size:19 final size:19
Alignment explanation
Indices: 38942613--38942685 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
38942603 TTCTTACGAC
*
38942613 TTTATAAAATTTTATAAAT
1 TTTATAAAATTTTATAGAT
* * *
38942632 TTT-TTATATTTCTATATAT
1 TTTATAAAATTT-TATAGAT
**
38942651 TTTATAATTTTTTA-AGATT
1 TTTATAAAATTTTATAGA-T
38942670 TTTATAAAATTTTATA
1 TTTATAAAATTTTATA
38942686 ACTTTTTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
18 8 0.19
19 27 0.64
20 7 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTATAAAATTTTATAGAT
Found at i:38942692 original size:10 final size:10
Alignment explanation
Indices: 38942613--38942703 Score: 73
Period size: 10 Copynumber: 9.4 Consensus size: 10
38942603 TTCTTACGAC
*
38942613 TTTATAAAAT
1 TTTATAAATT
38942623 TTTATAAATT
1 TTTATAAATT
*
38942633 TTT-TATATT
1 TTTATAAATT
* *
38942642 TCTATATA-T
1 TTTATAAATT
38942651 TTTAT-AATT
1 TTTATAAATT
38942660 TTT-TAAGATT
1 TTTATAA-ATT
*
38942670 TTTATAAAAT
1 TTTATAAATT
*
38942680 TTTATAACTT
1 TTTATAAATT
* *
38942690 TTTTTATATT
1 TTTATAAATT
38942700 TTTA
1 TTTA
38942704 CGATTTTATA
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
8 2 0.03
9 17 0.27
10 42 0.66
11 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTATAAATT
Found at i:38942710 original size:28 final size:27
Alignment explanation
Indices: 38942613--38942799 Score: 111
Period size: 28 Copynumber: 6.9 Consensus size: 27
38942603 TTCTTACGAC
*
38942613 TTTATAAAATTTTATAAATTTTTTATAT
1 TTTAT-AAATTTTATAATTTTTTTATAT
* * *
38942641 TTCTATATATTTTATAATTTTTTAAGATT
1 TT-TATAAATTTTATAATTTTTTTATA-T
38942670 TTTATAAAATTTTATAACTTTTTTTATAT
1 TTTAT-AAATTTTATAA-TTTTTTTATAT
*
38942699 TTT-TACGATTTTAT-ATTTTTTCTA-AT
1 TTTATA-AATTTTATAATTTTTT-TATAT
*
38942725 TTT-T-AATTTT-TAA-TATTTTAT-T
1 TTTATAAATTTTATAATTTTTTTATAT
* ** * *
38942747 TTTATTAAAATTTAATAAAATTTATAGAT
1 TTTA-T-AAATTTTATAATTTTTTTATAT
* *
38942776 TTTATAGATTTTTTTAATTTTTTT
1 TTTATA-AATTTTATAATTTTTTT
38942800 TCTAATTTTT
Statistics
Matches: 122, Mismatches: 21, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
22 6 0.05
23 5 0.04
24 7 0.06
26 17 0.14
27 8 0.07
28 46 0.38
29 25 0.20
30 8 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTATAAATTTTATAATTTTTTTATAT
Found at i:38942710 original size:57 final size:56
Alignment explanation
Indices: 38942596--38942719 Score: 155
Period size: 57 Copynumber: 2.2 Consensus size: 56
38942586 TTACATTTTG
* *
38942596 TATAATTTTCTTACGACTTTATAAAATTTTATAAATTTTTTATATTTCTATATATTT
1 TATAATTTT-TTAAGACTTTATAAAATTTTATAAATTTTTTATATTTCTATAGATTT
* *
38942653 TATAATTTTTTAAGATTTTTATAAAATTTTATAACTTTTTTTATATTT-T-TACGATTT
1 TATAATTTTTTAAGA-CTTTATAAAATTTTATAA-ATTTTTTATATTTCTATA-GATTT
38942710 TAT-ATTTTTT
1 TATAATTTTTT
38942720 CTAATTTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
56 14 0.23
57 34 0.57
58 12 0.20
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.61
Consensus pattern (56 bp):
TATAATTTTTTAAGACTTTATAAAATTTTATAAATTTTTTATATTTCTATAGATTT
Found at i:38942759 original size:33 final size:34
Alignment explanation
Indices: 38942690--38942759 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
38942680 TTTATAACTT
* **
38942690 TTTTTATATTTTTACGATTTTATATTTTTTCTAA
1 TTTTTATATTTTTAAGATTTTATATTTTTTAAAA
*
38942724 TTTTTA-ATTTTTAATATTTTAT-TTTTATTAAAA
1 TTTTTATATTTTTAAGATTTTATATTTT-TTAAAA
38942757 TTT
1 TTT
38942760 AATAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 4 0.13
33 21 0.68
34 6 0.19
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (34 bp):
TTTTTATATTTTTAAGATTTTATATTTTTTAAAA
Found at i:38952161 original size:16 final size:16
Alignment explanation
Indices: 38952140--38952186 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
38952130 CCTATTGACT
38952140 TTCCCTCAAACTTTTA
1 TTCCCTCAAACTTTTA
38952156 TTCCCTCAAACTTTTA
1 TTCCCTCAAACTTTTA
*
38952172 TTCCCTAAAACTTTT
1 TTCCCTCAAACTTTT
38952187 TATTTAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCCCTCAAACTTTTA
Found at i:38953225 original size:15 final size:15
Alignment explanation
Indices: 38953182--38953227 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
38953172 TAAGCAAACC
*
38953182 TATTAATTATAAT-T
1 TATTAATTAAAATAT
*
38953196 TATTAAATAAAAATAT
1 TATT-AATTAAAATAT
38953212 TATTAATTAAAATAT
1 TATTAATTAAAATAT
38953227 T
1 T
38953228 GTTTCGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 18 0.67
16 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAATTAAAATAT
Found at i:38953384 original size:32 final size:32
Alignment explanation
Indices: 38953348--38953410 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
38953338 TCTTAAACTT
* * *
38953348 ATAAATTGATTATTTGAATTTAATAACTCATG
1 ATAAATTAATTAATTAAATTTAATAACTCATG
*
38953380 ATAAATTAATTAATTAAATTTGATAACTCAT
1 ATAAATTAATTAATTAAATTTAATAACTCAT
38953411 ACTGATTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTAATTAAATTTAATAACTCATG
Done.