Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2403
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: 150165
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:545 original size:25 final size:25
Alignment explanation
Indices: 531--585 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 25
521 TTTTTATGAT
531 TAATATTTATTATAATTAATTATAA
1 TAATATTTATTATAATTAATTATAA
*
556 TAATATTTATTATATTTATAATTATAA
1 TAATATTTATTATA-AT-TAATTATAA
583 TAA
1 TAA
586 AAATAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 14 0.52
26 1 0.04
27 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TAATATTTATTATAATTAATTATAA
Found at i:1402 original size:25 final size:24
Alignment explanation
Indices: 1367--1432 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
1357 TATATGAATG
* *
1367 TAATATGAATAAAATAATTAATATA
1 TAATATAAATAAAAT-ATTAAAATA
*
1392 TAATATAAAT-ATATATTAAAATA
1 TAATATAAATAAAATATTAAAATA
*
1415 T-ATATAATATAAATTATT
1 TAATATAA-ATAAAATATT
1433 TAACATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 6 0.18
23 11 0.32
24 8 0.24
25 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TAATATAAATAAAATATTAAAATA
Found at i:1415 original size:12 final size:13
Alignment explanation
Indices: 1386--1419 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1376 TAAAATAATT
*
1386 AATATATAATATA
1 AATATATATTATA
1399 AATATATATTA-A
1 AATATATATTATA
1411 AATATATAT
1 AATATATAT
1420 AATATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATATATTATA
Found at i:1435 original size:25 final size:27
Alignment explanation
Indices: 1387--1467 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
1377 AAAATAATTA
1387 ATATATAATATAAATATATATTAAAAT
1 ATATATAATATAAATATATATTAAAAT
*
1414 ATATATAATATAAAT-TAT-TTAACAT
1 ATATATAATATAAATATATATTAAAAT
* * *
1439 AT-TAAAATTTATATATATATATAAAAT
1 ATATATAATATAAATATATAT-TAAAAT
1466 AT
1 AT
1468 CTTAAGCACG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
24 9 0.20
25 11 0.24
26 4 0.09
27 22 0.48
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
ATATATAATATAAATATATATTAAAAT
Found at i:3802 original size:32 final size:31
Alignment explanation
Indices: 3766--3858 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 31
3756 ATCATTTCGG
3766 GTTCGGGTCATTTCGGATTCGGATAATTTCAA
1 GTTCGGGTCATTTCGGATTCGGATAATTTC-A
* * **
3798 GTTCGGATCATTTC-AAGTTCGGATTGTTTCA
1 GTTCGGGTCATTTCGGA-TTCGGATAATTTCA
**
3829 GATTTAGGTCATTTCGGATTCGGATCAATT
1 G-TTCGGGTCATTTCGGATTCGGAT-AATT
3859 GGGTTTAATG
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
31 3 0.06
32 41 0.87
33 3 0.06
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.40
Consensus pattern (31 bp):
GTTCGGGTCATTTCGGATTCGGATAATTTCA
Found at i:3828 original size:16 final size:16
Alignment explanation
Indices: 3755--3821 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
3745 TTCGAGTTTA
**
3755 GATCATTTCGGGTTCG
1 GATCATTTCAAGTTCG
* *
3771 GGTCATTTC-GGATTCG
1 GATCATTTCAAG-TTCG
*
3787 GATAATTTCAAGTTCG
1 GATCATTTCAAGTTCG
3803 GATCATTTCAAGTTCG
1 GATCATTTCAAGTTCG
3819 GAT
1 GAT
3822 TGTTTCAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
15 2 0.05
16 41 0.93
17 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.37
Consensus pattern (16 bp):
GATCATTTCAAGTTCG
Found at i:3945 original size:53 final size:53
Alignment explanation
Indices: 3836--3947 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 53
3826 TCAGATTTAG
* ** * *
3836 GTCATTTCGGATTCGGATCAATTGGGTTTAATGTTCGGGTCAATTGAGTTCGA
1 GTCATTTCGGATTCGGATCAATTGGGTTGAACATTCGGGTCAAATCAGTTCGA
* *
3889 GTCA-TTCTGGATTCGGGTCAATTGGGTTGAACATTCGGGTTAAATCATGTTC-A
1 GTCATTTC-GGATTCGGATCAATTGGGTTGAACATTCGGGTCAAATCA-GTTCGA
3942 GTCATT
1 GTCATT
3948 ATAATTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
52 3 0.06
53 41 0.84
54 5 0.10
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (53 bp):
GTCATTTCGGATTCGGATCAATTGGGTTGAACATTCGGGTCAAATCAGTTCGA
Found at i:4756 original size:16 final size:16
Alignment explanation
Indices: 4697--4770 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
4687 GGTCATTTCA
*
4697 GGTTCGAATCATTTTG
1 GGTTCGGATCATTTTG
*
4713 AGTTC-GAGTCATTTTG
1 GGTTCGGA-TCATTTTG
* **
4729 AGTTATTG-TCATTTTG
1 GGTT-CGGATCATTTTG
4745 GGTTCGGATCATTTTTG
1 GGTTCGGATCA-TTTTG
4762 GGTTCGGAT
1 GGTTCGGAT
4771 AGATCGGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
15 2 0.04
16 30 0.64
17 14 0.30
18 1 0.02
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.46
Consensus pattern (16 bp):
GGTTCGGATCATTTTG
Found at i:5086 original size:22 final size:21
Alignment explanation
Indices: 5064--5151 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 21
5054 AAAAATTTAT
5064 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-ATTTATATA
*
5085 TTTTATAATTAAATTTAAATAAA
1 TTTTATAATTAAATTT--ATATA
5108 TTTT-T--TTAAA-TTAT-TA
1 TTTTATAATTAAATTTATATA
*
5124 -TTTATAATTAAATTT-GATA
1 TTTTATAATTAAATTTATATA
5143 TTTTA-AATT
1 TTTTATAATT
5152 TTATTTTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 20
0.71 0.04 0.26
Matches are distributed among these distances:
15 3 0.05
16 2 0.04
17 2 0.04
18 5 0.09
19 10 0.18
20 9 0.16
21 10 0.18
22 6 0.11
23 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (21 bp):
TTTTATAATTAAATTTATATA
Found at i:5950 original size:2 final size:2
Alignment explanation
Indices: 5901--5935 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5891 CATTTGAGGG
5901 AT AT 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 AT AT A
5936 ATCTTCATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8510 original size:13 final size:13
Alignment explanation
Indices: 8492--8549 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
8482 TTCAACGATT
8492 TGTATCGATACAA
1 TGTATCGATACAA
8505 TGTATCGATACATAA
1 TGTATCGATAC--AA
8520 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
8537 TGTATCGCTACAA
1 TGTATCGATACAA
8550 AGCTACTGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:13313 original size:103 final size:103
Alignment explanation
Indices: 13130--13335 Score: 358
Period size: 103 Copynumber: 2.0 Consensus size: 103
13120 AGGTAAAAGG
*
13130 TAATGTTGCCAAGTTTGAAATGCTCTAATCAAAGCATACACTTCTTTATCATAAGTAGGATACTT
1 TAATGTTGCCAAGTTTGAAATGCTCTAATCAAAACATACACTTCTTTATCATAAGTAGGATACTT
*
13195 CAAACTAGCCCCATTAAGTTTTTCACTAAAGTAGGCAA
66 CAAACTAGCCCCATTAAGCTTTTCACTAAAGTAGGCAA
* *
13233 TAATGTTGCCAAGTTTGAAGTGCTCTAATCAAAACATACAGTTCTTTATCATAAGTAGGATACTT
1 TAATGTTGCCAAGTTTGAAATGCTCTAATCAAAACATACACTTCTTTATCATAAGTAGGATACTT
* *
13298 TAAACTAGCCTCATTAAGCTTTTCACTAAAGTAGGCAA
66 CAAACTAGCCCCATTAAGCTTTTCACTAAAGTAGGCAA
13336 CGAGATGCCC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (103 bp):
TAATGTTGCCAAGTTTGAAATGCTCTAATCAAAACATACACTTCTTTATCATAAGTAGGATACTT
CAAACTAGCCCCATTAAGCTTTTCACTAAAGTAGGCAA
Found at i:14228 original size:20 final size:20
Alignment explanation
Indices: 14203--14256 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
14193 TATCCAGATA
*
14203 TATCGATACATTTTTCAATG
1 TATCGATACATTCTTCAATG
14223 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
* *
14243 TGTCGATATATTCT
1 TATCGATACATTCT
14257 ATCCTTTTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:15227 original size:22 final size:23
Alignment explanation
Indices: 15202--15248 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
15192 TTTTAATATG
15202 TCCATCA-TCTCATTGAATG-TTA
1 TCCATCAGT-TCATTGAATGATTA
*
15224 TCCATCAGTTCATTGTATGATTA
1 TCCATCAGTTCATTGAATGATTA
15247 TC
1 TC
15249 ACATTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (23 bp):
TCCATCAGTTCATTGAATGATTA
Found at i:27363 original size:11 final size:10
Alignment explanation
Indices: 27338--27385 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
27328 CTTTATACCT
*
27338 AAAAAAACATG
1 AAAAAAACA-A
27349 AAAAAAACAA
1 AAAAAAACAA
*
27359 CAAAAAACAA
1 AAAAAAACAA
27369 AAAAAATAGCAA
1 AAAAAA-A-CAA
27381 AAAAA
1 AAAAA
27386 TAGAAATGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 14 0.44
11 10 0.31
12 8 0.25
ACGTcount: A:0.81, C:0.10, G:0.04, T:0.04
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:28834 original size:29 final size:29
Alignment explanation
Indices: 28588--29111 Score: 554
Period size: 28 Copynumber: 18.2 Consensus size: 29
28578 AGAACGTTCA
*
28588 TCTTTTCAAAGCCCACAAGTTAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
28617 -CCTTTCAAAGCCCACAAGTTAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
28645 -CCTTTCAAAGCCCACAAGTCAATGGCA-
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
28672 TCCTTTCAAAACCCATAAGTTAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
*
28701 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
28729 CCTTTT-AAAGCCCATAAGCCTGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
28757 AC-TTTCAAAGCCTACGCAAGTCAGTAGCAC
1 TCTTTTCAAAGCC--CACAAGTCAGTGGCAC
* *
28787 -CTTTTCAAAGCCTACAAGTCAATGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
28815 TCTTTTCGTAA-CCCATAAGTTAGTGGCAC
1 TCTTTTC-AAAGCCCACAAGTCAGTGGCAC
*
28844 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
*
28872 TCTTTTCAAAGCCCACAAGTTAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
28901 -CCTTTCAAAGCTCACAAGTCAGTAGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
*
28929 TCTTTTCAAAGCCCACAAGTCAGTAGCA-
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
*
28957 TCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
28986 TC-TTTCAAAGCCCACAAGTCAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
29014 TCTTATCAAAGCCCACAAG-CTAGTGGTAAC
1 TCTTTTCAAAGCCCACAAGTC-AGTGG-CAC
*
29044 TCTTTTCAAAGCCCACACGAGTCGGTGGCAAC
1 TCTTTTCAAAGCCCACA--AGTCAGTGGC-AC
* *
29076 TCTTTTTAAAGCCCACACAAGTTAGTGGCAC
1 TCTTTTCAAAG-CC-CACAAGTCAGTGGCAC
29107 -CTTTT
1 TCTTTT
29112 TTTAAAAAAA
Statistics
Matches: 422, Mismatches: 51, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
27 5 0.01
28 238 0.56
29 98 0.23
30 46 0.11
31 2 0.00
32 26 0.06
33 3 0.01
34 4 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (29 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:28861 original size:57 final size:57
Alignment explanation
Indices: 28588--29111 Score: 594
Period size: 57 Copynumber: 9.1 Consensus size: 57
28578 AGAACGTTCA
* *
28588 TCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * * *
28645 -CCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAACCCATAAGTTAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
28701 -CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCATAAGCCTGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * * *
28757 AC-TTTCAAAGCCTACGCAAGTCAGTAGCACCTTTTCAAAGCCTACAAGTCAATGGCAC
1 TCTTTTCAAAGCC--CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
28815 TCTTTTCGTAA-CCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 TCTTTTC-AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
28872 TCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCTCACAAGTCAGTAGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
28929 TCTTTTCAAAGCCCACAAGTCAGTAGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
28986 TC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTATCAAAGCCCACAAG-CTAGTGGTAAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT-TCAAAGCCCACAAGTC-AGTGG-CAC
* * * *
29044 TCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTTAAAGCCCACACAAGTTAGTGGCAC
1 TCTTTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAG-CC-CACAAGTCAGTGGCAC
29107 -CTTTT
1 TCTTTT
29112 TTTAAAAAAA
Statistics
Matches: 400, Mismatches: 50, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
56 139 0.35
57 161 0.40
58 40 0.10
59 20 0.05
60 2 0.00
61 9 0.02
62 12 0.03
63 6 0.01
64 11 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (57 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:30049 original size:20 final size:20
Alignment explanation
Indices: 29974--30050 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
29964 AAGTACCTAG
*
29974 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* * *
29994 AAGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
30014 ATATATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
30034 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
30051 ATCCTTTTTG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:32298 original size:7 final size:7
Alignment explanation
Indices: 32286--32310 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32276 TATGGAGGAG
32286 GTTTTAT
1 GTTTTAT
32293 GTTTTAT
1 GTTTTAT
32300 GTTTTAT
1 GTTTTAT
32307 GTTT
1 GTTT
32311 AAATATCTCT
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:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (7 bp):
GTTTTAT
Found at i:38062 original size:24 final size:23
Alignment explanation
Indices: 38030--38075 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
38020 GGAGATTTTC
*
38030 AAAATATAT-ATATATAAATAAAAT
1 AAAAAATATGATA-ATAAA-AAAAT
38054 AAAAAATATGATAATAAAAAAA
1 AAAAAATATGATAATAAAAAAA
38076 CAAATGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 13 0.65
25 3 0.15
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
AAAAAATATGATAATAAAAAAAT
Found at i:38429 original size:17 final size:17
Alignment explanation
Indices: 38403--38435 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38393 TATTTTTTTT
*
38403 TTCTTTTTCTTTCTTTC
1 TTCTTCTTCTTTCTTTC
38420 TTCTTCTTCTTTCTTT
1 TTCTTCTTCTTTCTTT
38436 TCTTTCTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTCTTCTTTCTTTC
Found at i:38440 original size:9 final size:9
Alignment explanation
Indices: 38397--38443 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 9
38387 ATTTCATATT
*
38397 TTTTTTTTC
1 TTTTCTTTC
38406 TTTTTCTTTC
1 -TTTTCTTTC
38416 -TTTC-TTC
1 TTTTCTTTC
38423 TTCTTCTTTC
1 TT-TTCTTTC
38433 TTTTCTTTC
1 TTTTCTTTC
38442 TT
1 TT
38444 ACCAAACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
7 3 0.09
8 5 0.15
9 12 0.36
10 13 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:39600 original size:49 final size:45
Alignment explanation
Indices: 39547--39649 Score: 109
Period size: 45 Copynumber: 2.2 Consensus size: 45
39537 TCAAGGTTAA
*
39547 CGACATCGGGCTAAGGGCAAA-GTGGACCAATGTGCTGACTCAAGGCCAG
1 CGACATCGGGCTAA--G-AAAGGT-G-CCAATATGCTGACTCAAGGCCAG
* * *
39596 CGACATTGGGCTTAGAAAGGTGCCAATATGCTGATTCAAGGCCAG
1 CGACATCGGGCTAAGAAAGGTGCCAATATGCTGACTCAAGGCCAG
*
39641 CGATATCGG
1 CGACATCGG
39650 ACTTTAAGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
45 28 0.60
46 4 0.09
47 3 0.06
49 12 0.26
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.18
Consensus pattern (45 bp):
CGACATCGGGCTAAGAAAGGTGCCAATATGCTGACTCAAGGCCAG
Found at i:39774 original size:32 final size:32
Alignment explanation
Indices: 39729--40263 Score: 506
Period size: 32 Copynumber: 17.5 Consensus size: 32
39719 TCCATCGAAA
* * * *
39729 GTGTGGACTTTTGAAAGAGGTTCCCATCAACTT
1 GTGTGGGC-TTTGAAAGAGGTTGCCACCGACTT
* * *
39762 GTGTGGGCTTTGAAA-AGGGTTCCCATCAACTT
1 GTGTGGGCTTTGAAAGA-GGTTGCCACCGACTT
*
39794 GTGTGGGCTTTGAAATG-GGTTACCACCGACTT
1 GTGTGGGCTTTGAAA-GAGGTTGCCACCGACTT
* *
39826 GTGTGGGCTTTGAAATAGGTTGCCATCGACTT
1 GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
39858 GTGTGGGCTTTGAAA-AGGGTTGCCACCGACTT
1 GTGTGGGCTTTGAAAGA-GGTTGCCACCGACTT
* *
39890 GTATGGGCTTTGAAATG-GGTTGCGACCGACTT
1 GTGTGGGCTTTGAAA-GAGGTTGCCACCGACTT
*
39922 GTGTGGGCTTTGAAATA-G-TGCCACCGACTT
1 GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
39952 -TGTGGGCTTTGAAA-AGGGTTGCCACCGACTT
1 GTGTGGGCTTTGAAAGA-GGTTGCCACCGACTT
39983 GTGTGGGCTTTGAAATG-GGTTGCCACCGACTT
1 GTGTGGGCTTTGAAA-GAGGTTGCCACCGACTT
40015 GTGTGGGCTTTGAAATG-GGTTGCCACCGACTT
1 GTGTGGGCTTTGAAA-GAGGTTGCCACCGACTT
*
40047 GTGTGGGCTTTGAAATG-GGTTGCCACCAACTT
1 GTGTGGGCTTTGAAA-GAGGTTGCCACCGACTT
* **
40079 GTGTGGGCTTTGAAA-TGG-TGCCACTAAC-T
1 GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
* *
40108 -TGTGGGCTTTGAAA-TGG-TGCCACTGAC-T
1 GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
* *
40136 -TGTGGGCTTTG-AA-AGGATGCCACCAACTT
1 GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
* * *
40165 GTGTGGACTTTGAAA-A-GATGCCACTGAC-T
1 GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
* *
40194 -TGTGGGCTTTGAAA-A-GATGCCACTGAC-T
1 GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
* *
40222 -TGTGGGCTTTGAAA-A-GATGCCACTGAC-T
1 GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
40250 -TGTGGGCTTTGAAA
1 GTGTGGGCTTTGAAA
40264 ATGGTGCCAC
Statistics
Matches: 460, Mismatches: 23, Indels: 43
0.87 0.04 0.08
Matches are distributed among these distances:
27 4 0.01
28 116 0.25
29 17 0.04
30 41 0.09
31 20 0.04
32 255 0.55
33 7 0.02
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.31
Consensus pattern (32 bp):
GTGTGGGCTTTGAAAGAGGTTGCCACCGACTT
Found at i:39778 original size:64 final size:64
Alignment explanation
Indices: 39674--40282 Score: 601
Period size: 64 Copynumber: 9.9 Consensus size: 64
39664 AAAATGGTGA
* * * * * * * ** *
39674 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGTTTTTAAAAGGGTTTCCATCGA-AAGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * * * * *
39737 TTTTGAAA-GAGGTTCCCATCAACTTGTGTGGGCTTTGAAAAGGGTTCCCATCAACTTGTGTGGG
1 -TTTGAAATG-GGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGG
39801 C
64 C
* *
39802 TTTGAAATGGGTTACCACCGACTTGTGTGGGCTTTGAAATA-GGTTGCCATCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAA-AGGGTTGCCACCGACTTGTGTGGGC
* * * *
39866 TTTGAAAAGGGTTGCCACCGACTTGTATGGGCTTTGAAATGGGTTGCGACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
*
39930 TTTGAAAT-AG-TGCCACCGACTT-TGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
*
39991 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * **
40055 TTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTG-AAATGG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * * *
40115 TTTGAAAT-GG-TGCCACTGAC-T-TGTGGGCTTTG-AAA-GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * * * *
40173 TTTGAAA--AGATGCCACTGAC-T-TGTGGGCTTTGAAAA--GATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
* * * * **
40229 TTTGAAA--AGATGCCACTGAC-T-TGTGGGCTTTGAAAATGG-TGCCACTAACTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTG
40283 GGCTTTAGAA
Statistics
Matches: 484, Mismatches: 44, Indels: 39
0.85 0.08 0.07
Matches are distributed among these distances:
55 2 0.00
56 65 0.13
57 13 0.03
58 55 0.11
59 7 0.01
60 15 0.03
61 45 0.09
62 21 0.04
63 18 0.04
64 234 0.48
65 9 0.02
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (64 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
Found at i:40004 original size:157 final size:153
Alignment explanation
Indices: 39674--40282 Score: 607
Period size: 157 Copynumber: 4.0 Consensus size: 153
39664 AAAATGGTGA
* * * * * * * ** *
39674 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGTTTTTAAAAGGGTTTCCATCGA-AAGTGTGGACT
1 TTTG-AAATGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGT-TGGGC-
* * * * * *
39738 TTTGAAA-GAGGTTCCCATCAACTTGTGTGGGCTTTGAAAAGGGTTCCCATCAACTTGTGTGGGC
63 TTTGAAATG-GGTTGCCACCGACTTGTGTGGGCTTTGAAAA--GATGCCACCAAC-T-TGTGGGC
* *
39802 TTTGAAATGGGTTACCACCGACTTGTGTGGGC
123 TTTGAAAAGGG-TGCCACCGACTTGTGTGGGC
*
39834 TTTGAAATAGGTTGCCATCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTATGGGCT
1 TTTGAAAT-GGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGT-TGGGCT
* *
39899 TTGAAATGGGTTGCGACCGACTTGTGTGGGCTTTGAAATAG-TGCCACCGACTTTGTGGGCTTTG
64 TTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAA-AGATGCCACCAAC-TTGTGGGCTTTG
39963 AAAAGGGTTGCCACCGACTTGTGTGGGC
127 AAAAGGG-TGCCACCGACTTGTGTGGGC
*
39991 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCT
1 TTTGAAAT-GGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGT-TGGGCT
* * * *
40056 TTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGTGCCACTAACTTGTGGGCTTTG-A
64 TTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACCAACTTGTGGGCTTTGAA
* *
40120 AATGGTGCCACTGAC-T-TGTGGGC
129 AAGGGTGCCACCGACTTGTGTGGGC
* * * * *
40143 TTTGAAA-GGATGCCACCAACTTGTGTGGACTTTGAAAA--GATGCCACTGACTTG-TGGGCTTT
1 TTTGAAATGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTTGGGCTTT
* * * **
40204 GAAA--AGATGCCACTGAC-T-TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAA
66 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACCAACTTGTGGGCTTTGAAAA
* **
40265 TGGTGCCACTAACTTGTG
131 GGGTGCCACCGACTTGTG
40283 GGCTTTAGAA
Statistics
Matches: 395, Mismatches: 46, Indels: 31
0.84 0.10 0.07
Matches are distributed among these distances:
142 36 0.09
143 16 0.04
144 10 0.03
145 2 0.01
146 12 0.03
148 13 0.03
150 27 0.07
152 14 0.04
153 1 0.00
154 9 0.02
155 5 0.01
156 13 0.03
157 142 0.36
158 9 0.02
159 4 0.01
160 74 0.19
161 8 0.02
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (153 bp):
TTTGAAATGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTTGGGCTTT
GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGATGCCACCAACTTGTGGGCTTTGAAAA
GGGTGCCACCGACTTGTGTGGGC
Found at i:40323 original size:86 final size:85
Alignment explanation
Indices: 39827--40303 Score: 374
Period size: 86 Copynumber: 5.3 Consensus size: 85
39817 CACCGACTTG
* * *
39827 TGTGGGCTTTGAAATAGGTTGCCA-TCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTG
1 TGTGGGCTTTG-AA-AGGATGCCACT-GAC-T-TGTGGGCTTTGAAAA--GATGCCACCAACTTG
* **
39891 TATGGGCTTTG-AAATGGGTTGCGACCGACTT
59 --TGGGCTTTGAAAAT-GG-TGCCACTAAC-T
* * * *
39922 GTGTGGGCTTTGAAA-TAGTGCCACCGACTTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTG
1 -TGTGGGCTTTGAAAGGA-TGCCACTGAC-TTGTGGGCTTTGAAAA--GATGCCACCAAC-T-TG
**
39986 TGGGCTTTG-AAATGGGTTGCCACCGACTT
59 TGGGCTTTGAAAAT-GG-TGCCACTAAC-T
* * * *
40015 GTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAA--AGATGCCACCAAC-T-
40080 TGTGGGCTTTG-AAATGGTGCCACTAACT
57 TGTGGGCTTTGAAAATGGTGCCACTAACT
*
40108 TGTGGGCTTTGAAATGG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGA
1 TGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACCAACTTGTG-GG-
* *
40172 CTTTGAAAA-GATGCCACTGACT
63 CTTTGAAAATGGTGCCACTAACT
* **
40194 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACCAACTTGTGGGCTT
40259 TGAAAATGGTGCCACTAACT
66 TGAAAATGGTGCCACTAACT
*
40279 TGTGGGCTTTAGAAGGGAATGCCAC
1 TGTGGGCTTT-GAAAGG-ATGCCAC
40304 CGCCTTATGG
Statistics
Matches: 341, Mismatches: 23, Indels: 43
0.84 0.06 0.11
Matches are distributed among these distances:
84 13 0.04
85 27 0.08
86 86 0.25
87 10 0.03
88 14 0.04
89 1 0.00
90 9 0.03
91 2 0.01
92 14 0.04
93 73 0.21
94 20 0.06
95 18 0.05
96 54 0.16
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (85 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACCAACTTGTGGGCTT
TGAAAATGGTGCCACTAACT
Found at i:40323 original size:114 final size:114
Alignment explanation
Indices: 39859--40323 Score: 328
Period size: 114 Copynumber: 3.9 Consensus size: 114
39849 CATCGACTTG
* * * * *
39859 TGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTATGGGCTTTGAAATGGGTTGCGACCGACTTGT
1 TGTGGGCTTTGAAAA--GATGCCACTGACTTG--TGGGCTTTGAAA--GGATGCCACCAACTTGT
* * * * * **
39924 GTGGGCTTTGAAATAG-TGCCACCGACTTTGTGGGCTTTGAAAAGGGTTGCCACCGACTT
60 GTGGACTTTGAAA-AGATGCCACCGAC-TTATGGACTTT-AAAA-AGATGCCACTAAC-T
* * * * *
39983 GTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 -TGTGGGCTTTGAAA--AGATGCCACTGAC-T-TGTGGGCTTTGAAA--GGATGCCACCAACTTG
* * * * * * * * *
40048 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGTGCCACTAACT
59 TGTGGACTTTGAAA--AGATGCCACCGAC-T-TATGGACTTTAAAAAGATGCCACTAACT
* *
40108 TGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGAC
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGAC
* * * * *
40173 TTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACT
66 TTTGAAAAGATGCCACCGACTTATGGACTTTAAAAAGATGCCACTAACT
*
40222 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAATGG-TGCCACTAACTTGTG-GG
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-AAA-GGATGCCACCAACTTGTGTGG
** *
40285 -CTTTAGAAGGGAATGCCACCGCCTTATGGAC-TTAAAAAG
64 ACTTT-GAAAAG-ATGCCACCGACTTATGGACTTTAAAAAG
40324 GGTGCCACGG
Statistics
Matches: 296, Mismatches: 33, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
113 4 0.01
114 75 0.25
115 33 0.11
116 11 0.04
118 27 0.09
120 14 0.05
121 1 0.00
122 10 0.03
124 14 0.05
125 70 0.24
126 11 0.04
127 16 0.05
128 10 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (114 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGAC
TTTGAAAAGATGCCACCGACTTATGGACTTTAAAAAGATGCCACTAACT
Found at i:40392 original size:27 final size:27
Alignment explanation
Indices: 40311--41090 Score: 1130
Period size: 27 Copynumber: 28.4 Consensus size: 27
40301 CACCGCCTTA
40311 TGGACTTAAAAAGGGTGCCACGGAGTTG
1 TGGACTT-AAAAGGGTGCCACGGAGTTG
*
40339 TGAACTTAAAAGGGATGCCACGGAGTTG
1 TGGACTTAAAAGGG-TGCCACGGAGTTG
40367 TGGACTTAAAAGGGTGCCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
*
40394 TGTACTTAAAAGGGTGCCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
*
40421 TGGACTTAAAAGGGATGCCATGGAGTTG
1 TGGACTTAAAAGGG-TGCCACGGAGTTG
*
40449 TGGGCTTAAAAGGGTGCCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
*
40476 TGGACTTAAAAGGGTGCCATGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
*
40503 TGGACTTAAAAGGGTGCCACAGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
*
40530 TGGACTTAAAAGGGTGCCACGAAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
*
40557 TGGACTTTAAAAGGGTGCCACAGAGTTG
1 TGGAC-TTAAAAGGGTGCCACGGAGTTG
*
40585 TGGACTTTAAAAGGGTGCCACAGAGTTG
1 TGGAC-TTAAAAGGGTGCCACGGAGTTG
* *
40613 TGGACTTAAAAAGGATGCCACGAAGTTG
1 TGGACTT-AAAAGGGTGCCACGGAGTTG
* *
40641 TGAACTTTATAAGGGTGCCACGGAGTTG
1 TGGAC-TTAAAAGGGTGCCACGGAGTTG
40669 TGGACTTTAAAAGGGTGCCACGGAGTTG
1 TGGAC-TTAAAAGGGTGCCACGGAGTTG
40697 TGGACTTAAAAGGGTGCCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
* * *
40724 TGAACTTTAAAGGGTGTCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
* * *
40751 TGGACTTTAAAAGGGTGTCACGAAATTG
1 TGGAC-TTAAAAGGGTGCCACGGAGTTG
* *
40779 TGGACTTAAAATGATGCCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
* *
40806 TGGACTTAAAAGGATGCCACAGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
* *
40833 TGGACTTAAAAGGATGCCACGGAGTTA
1 TGGACTTAAAAGGGTGCCACGGAGTTG
*
40860 TGGACTTAAAAGGGTGCCACGGAGTGG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
*
40887 TGGACTTAAAAGGCTGCCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
40914 TGGACTTAAAAGGGTGCCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
40941 TGGACTTTAAAAGGGTGCCACGGAGTTG
1 TGGAC-TTAAAAGGGTGCCACGGAGTTG
40969 TGGACTTTAAAA-GGTGCCACGGAGTTG
1 TGGAC-TTAAAAGGGTGCCACGGAGTTG
**
40996 TGGACTTAAAAGAATGCCACGGAGTTG
1 TGGACTTAAAAGGGTGCCACGGAGTTG
* *
41023 TAGACTTTAAAAGGATGCCACGGAGTTG
1 TGGAC-TTAAAAGGGTGCCACGGAGTTG
* *
41051 TAGACTCTAAAAAGGTGCCACGGAGTTG
1 TGGACT-TAAAAGGGTGCCACGGAGTTG
*
41079 TGGACTTTAAAG
1 TGGACTTAAAAG
41091 AGGTCACAGT
Statistics
Matches: 687, Mismatches: 55, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.01
27 392 0.57
28 287 0.42
29 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (27 bp):
TGGACTTAAAAGGGTGCCACGGAGTTG
Found at i:40414 original size:82 final size:81
Alignment explanation
Indices: 40311--41090 Score: 1130
Period size: 82 Copynumber: 9.5 Consensus size: 81
40301 CACCGCCTTA
*
40311 TGGACTTAAAAAGGGTGCCACGGAGTTGTGAACTTAAAAGGGATGCCACGGAGTTGTGGACTTAA
1 TGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAA
40376 AAGGGTGCCACGGAGTTG
64 AAGGGTGCCACGGAGTTG
* * *
40394 TGTACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCATGGAGTTGTGGGCTTAAA
1 TGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAA
40459 AGGGTGCCACGGAGTTG
65 AGGGTGCCACGGAGTTG
* *
40476 TGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 TGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
40541 GGGTGCCACGAAGTTG
66 GGGTGCCACGGAGTTG
* *
40557 TGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAA
1 TGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-A
* *
40622 AAAGGATGCCACGAAGTTG
63 AAAGGGTGCCACGGAGTTG
* *
40641 TGAACTTTATAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAA
1 TGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAA
40706 AAGGGTGCCACGGAGTTG
64 AAGGGTGCCACGGAGTTG
* * * * * *
40724 TGAACTTTAAAGGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGTCACGAAATTGTGGACTTAAA
1 TGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAA
* *
40789 ATGATGCCACGGAGTTG
65 AGGGTGCCACGGAGTTG
* * * *
40806 TGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTAAAA
1 TGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
40871 GGGTGCCACGGAGTGG
66 GGGTGCCACGGAGTTG
*
40887 TGGACTTAAAAGGCTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAA
1 TGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAA
40952 AGGGTGCCACGGAGTTG
65 AGGGTGCCACGGAGTTG
** *
40969 TGGACTTTAAAA-GGTGCCACGGAGTTGTGGACTTAAAAGAATGCCACGGAGTTGTAGACTTTAA
1 TGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAA
*
41033 AAGGATGCCACGGAGTTG
64 AAGGGTGCCACGGAGTTG
* * *
41051 TAGACTCTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAG
1 TGGACT-TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
41091 AGGTCACAGT
Statistics
Matches: 638, Mismatches: 52, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
81 138 0.22
82 332 0.52
83 90 0.14
84 78 0.12
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (81 bp):
TGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
GGGTGCCACGGAGTTG
Found at i:41094 original size:28 final size:28
Alignment explanation
Indices: 40166--41094 Score: 868
Period size: 27 Copynumber: 33.6 Consensus size: 28
40156 CACCAACTTG
* * *
40166 TGTGGACTTTGAAA-AGATGCCACTGACT
1 TGTGGACTTT-AAAGAGGTGCCACGGAGT
* * * *
40194 TGTGGGCTTTGAAA-AGATGCCACTGACT
1 TGTGGACTTT-AAAGAGGTGCCACGGAGT
* * * *
40222 TGTGGGCTTTGAAA-AGATGCCACTGACT
1 TGTGGACTTT-AAAGAGGTGCCACGGAGT
* ** *
40250 TGTGGGCTTTGAAA-ATGGTGCCACTAACT
1 TGTGGACTTT-AAAGA-GGTGCCACGGAGT
* * **
40279 TGTGGGCTTTAGAAG-GGAATGCCACCGCCT
1 TGTGGACTTTA-AAGAGG--TGCCACGGAGT
* *
40309 TATGGAC-TTAAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAGA-GGTGCCACGGAGT
* *
40337 TGTGAACTTAAAAG-GGATGCCACGGAGT
1 TGTGGACTTTAAAGAGG-TGCCACGGAGT
*
40365 TGTGGACTTAAAAG-GGTGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
* *
40392 TGTGTACTTAAAAG-GGTGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
* *
40419 TGTGGACTTAAAAG-GGATGCCATGGAGT
1 TGTGGACTTTAAAGAGG-TGCCACGGAGT
* *
40447 TGTGGGCTTAAAAG-GGTGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
* *
40474 TGTGGACTTAAAAG-GGTGCCATGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
* *
40501 TGTGGACTTAAAAG-GGTGCCACAGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
* *
40528 TGTGGACTTAAAAG-GGTGCCACGAAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
*
40555 TGTGGACTTTAAA-AGGGTGCCACAGAGT
1 TGTGGACTTTAAAGA-GGTGCCACGGAGT
*
40583 TGTGGACTTTAAA-AGGGTGCCACAGAGT
1 TGTGGACTTTAAAGA-GGTGCCACGGAGT
* *
40611 TGTGGAC-TTAAAAAGGATGCCACGAAGT
1 TGTGGACTTTAAAGAGG-TGCCACGGAGT
*
40639 TGTGAACTTTATAAG-GGTGCCACGGAGT
1 TGTGGACTTTA-AAGAGGTGCCACGGAGT
40667 TGTGGACTTTAAA-AGGGTGCCACGGAGT
1 TGTGGACTTTAAAGA-GGTGCCACGGAGT
*
40695 TGTGGACTTAAAAG-GGTGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
* *
40722 TGTGAACTTTAAAG-GGTGTCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
* * *
40749 TGTGGACTTTAAA-AGGGTGTCACGAAAT
1 TGTGGACTTTAAAGA-GGTGCCACGGAGT
*
40777 TGTGGAC-TTAAA-ATGATGCCACGGAGT
1 TGTGGACTTTAAAGA-GGTGCCACGGAGT
*
40804 TGTGGAC-TTAAA-AGGATGCCACAGAGT
1 TGTGGACTTTAAAGAGG-TGCCACGGAGT
40831 TGTGGAC-TTAAA-AGGATGCCACGGAGT
1 TGTGGACTTTAAAGAGG-TGCCACGGAGT
* *
40858 TATGGACTTAAAAG-GGTGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
*
40885 GGTGGAC-TTAAA-AGGCTGCCACGGAGT
1 TGTGGACTTTAAAGAGG-TGCCACGGAGT
*
40912 TGTGGACTTAAAAG-GGTGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
40939 TGTGGACTTTAAA-AGGGTGCCACGGAGT
1 TGTGGACTTTAAAGA-GGTGCCACGGAGT
40967 TGTGGACTTTAAA-AGGTGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
* *
40994 TGTGGACTTAAAAGA-ATGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
*
41021 TGTAGACTTTAAA-AGGATGCCACGGAGT
1 TGTGGACTTTAAAGAGG-TGCCACGGAGT
* * *
41049 TGTAGACTCTAAAAAGGTGCCACGGAGT
1 TGTGGACTTTAAAGAGGTGCCACGGAGT
41077 TGTGGACTTTAAAGAGGT
1 TGTGGACTTTAAAGAGGT
41095 CACAGTACTA
Statistics
Matches: 798, Mismatches: 69, Indels: 68
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.01
27 382 0.48
28 353 0.44
29 38 0.05
30 17 0.02
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (28 bp):
TGTGGACTTTAAAGAGGTGCCACGGAGT
Found at i:52743 original size:20 final size:20
Alignment explanation
Indices: 52715--52789 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
52705 TCATACCCTG
52715 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
52735 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
52755 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
52775 ATGTATCGATACATT
1 ATGTATCGATACATT
52790 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:52782 original size:40 final size:39
Alignment explanation
Indices: 52715--52792 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
52705 TCATACCCTG
* *
52715 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
52755 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
52793 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:64752 original size:13 final size:12
Alignment explanation
Indices: 64732--64767 Score: 63
Period size: 13 Copynumber: 2.9 Consensus size: 12
64722 GTTACACCCA
64732 AAAAAAAAAAAC
1 AAAAAAAAAAAC
64744 AAAACAAAAAAAC
1 AAAA-AAAAAAAC
64757 AAAAAAAAAAA
1 AAAAAAAAAAA
64768 TAGCAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:66041 original size:29 final size:28
Alignment explanation
Indices: 65998--67134 Score: 686
Period size: 31 Copynumber: 36.4 Consensus size: 28
65988 GAATGTTCAT
*
65998 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCGGTGGCA
*
66026 CTCCTTTCAAAGCCCACAA-TCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCGGTGGCA
* *
66054 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCGGTGGCA
*
66083 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCGGTGGCA
* *
66111 CTCATTTCAAAGCCCTACAAGT-AGTGGCA
1 C-CCTTTCAAAGCCC-ACAAGTCGGTGGCA
* *
66140 CTCATTTTCAAAGCCCACAAAGTCAGTGGCA
1 C-C-CTTTCAAAGCCCAC-AAGTCGGTGGCA
*
66171 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCGGTGGCA
* *
66200 CTCATTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCGGTGGCA
**
66229 CTCCTTTCAAAGCCCACAAGTCATACAACTCATTGGCA
1 C-CCTTTCAAAGCCCACAAG---------TCGGTGGCA
* *
66267 TCCTTTCAAAGTCCACAAGTC-GTGGCA
1 CCCTTTCAAAGCCCACAAGTCGGTGGCA
* *
66294 CTCCTTTCAAAGCCCAC-AGCCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCGGTGGCA
* * **
66322 CTCTTTTCAGAGCCCACAAGTTAGTGGCAA
1 C-CCTTTCAAAGCCCACAAGTCGGTGGC-A
*
66352 CCCTTTCAGAGCCCAC-AGTCGGTGGCAA
1 CCCTTTCAAAGCCCACAAGTCGGTGGC-A
66380 CCCATTTCAAAGCCCCACACAAGTCGG-GGCAA
1 CCC-TTTCAAAG--CC-CACAAGTCGGTGGC-A
66412 CCCATTTCAAAGCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCC-CACAAGTCGGTGGC-A
* *
66443 CCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTTCAAAG-CC-CACAAGTCGGTGGC-A
*
66474 CCCATTCCAAAGCCCACACAAGTCGGTGGCA
1 CCC-TTTCAAAG-CC-CACAAGTCGGTGGCA
*
66505 CCCATTTCAAAGCCCACACAAGTCGGTGTCA
1 CCC-TTTCAAAG-CC-CACAAGTCGGTGGCA
66536 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCGGTGGC-A
*
66568 CCCATTCCAAAAGCCCCACAAGTCGGTGGCAA
1 CCC-TTTC-AAAG-CCCACAAGTCGGTGGC-A
*
66600 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCGGTGGC-A
66632 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCGGTGGC-A
*
66664 CCCATTCAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTTCAAAG-CC-CACAAGTCGGTGGC-A
* *
66695 CCATTCCAAAGCCCACACAGTCGGTGGCAA
1 CCCTTTCAAAGCCCACA-AGTCGGTGGC-A
66725 CCCATTTCAAAGCCCACACAGTCGGTGGGCAA
1 CCC-TTTCAAAGCCCACA-AGTCGGT-GGC-A
66757 CCCATTTCAAAAGCCCACACCAAGTCTGGTGGCAA
1 CCC-TTTC-AAAG-CC-CA-CAAGTC-GGTGGC-A
* * *
66792 CCCATTCCAAAGCCAAAAACAGAGTCGGGTGGAA
1 CCC-TTTCAAAGCC---CACA-AGTC-GGTGGCA
66826 CCCATGTTCAAAGCCCACAACAAGTCGGGTGGCA
1 CCC-T-TTCAAAG-CC-C-ACAAGTC-GGTGGCA
*
66860 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCGGTGGC-A
* *
66892 CCCATTCAAAACCCACAAAGTCGG-GGCAA
1 CCCTTTCAAAGCCCAC-AAGTCGGTGGC-A
* * *
66921 CCCATTCCAAGCCCCCACAAGTCGGGGGCAAA
1 CCCTTTCAAAG--CCCACAAGTCGGTGGC--A
* *
66953 CTCATTCAAACGCCCACACAAGTCGGGTGGGCCAA
1 CCCTTTCAAA-G-CC-CACAAGTC-GGT-GG-C-A
66988 CCCTTTTCAAAGCCCACCACAAAGTCGGTGGCAA
1 CCC-TTTCAAAG--C-CCAC-AAGTCGGTGGC-A
67022 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCGGTGGC-A
*
67054 CCCCAGTTCAAAAGCCCACACCAAAGTCTGGTTGGCACA
1 -CCC-TTTC-AAAG-CC-CA-C-AAGTC-GG-TGG--CA
67093 CCCCATTTCAAAGCCCACAAAGTCGGTGGCAA
1 -CCC-TTTCAAAGCCCAC-AAGTCGGTGGC-A
*
67125 CCATTTCAAA
1 CCCTTTCAAA
67135 AAAACCCTAC
Statistics
Matches: 981, Mismatches: 58, Indels: 138
0.83 0.05 0.12
Matches are distributed among these distances:
27 8 0.01
28 105 0.11
29 160 0.16
30 95 0.10
31 184 0.19
32 180 0.18
33 54 0.06
34 59 0.06
35 55 0.06
36 29 0.03
37 27 0.03
38 15 0.02
39 9 0.01
40 1 0.00
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.17
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCGGTGGCA
Found at i:66171 original size:31 final size:31
Alignment explanation
Indices: 66001--67267 Score: 1049
Period size: 32 Copynumber: 40.2 Consensus size: 31
65991 TGTTCATCCC
*
66001 TTTCAAAGCCCAC-AAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACAAAGTCGGTGGCAAC-CCA
* * *
66030 TTTCAAAGCCCAC-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
*
66058 TTTCAAAGCCCAC-AAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
* *
66086 TTTCAAAGCCCAC-AAGTCAGTGGC-ACTCA
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
* *
66115 TTTCAAAGCCCTAC-AAGT-AGTGGC-ACTCA
1 TTTCAAAGCCC-ACAAAGTCGGTGGCAACCCA
*
66144 TTTTCAAAGCCCACAAAGTCAGTGGC-ACTCC-
1 -TTTCAAAGCCCACAAAGTCGGTGGCAAC-CCA
* *
66175 TTTCAAAGCCCAC-AAGTCAGTGGC-ACTCA
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
*
66204 TTTCAAAGCCCAC-AAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACAAAGTCGGTGGCAAC-CCA
* *
66233 TTTCAAAGCCCAC-AAGTC-AT-ACAACTCATTGGCA
1 TTTCAAAGCCCACAAAGTCGGTGGCAAC-C-----CA
*
66267 TCCTTTCAAAGTCCAC-AAGTC-GTGGC-ACTCC-
1 ---TTTCAAAGCCCACAAAGTCGGTGGCAAC-CCA
* * * *
66298 TTTCAAAGCCCAC--AGCCAGTGGC-ACTCT
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
* **
66326 TTTCAGAGCCCAC-AAGTTAGTGGCAACCC-
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
*
66355 TTTCAGAGCCCAC--AGTCGGTGGCAACCCA
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
66384 TTTCAAAGCCCCACACAAGTCGG-GGCAACCCA
1 TTTCAAAG-CCCACA-AAGTCGGTGGCAACCCA
66416 TTTCAAAG-CCACACAAGTCGGTGGCAA-CCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
*
66446 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
*
66478 TTCCAAAGCCCACACAAGTCGGTGGC-ACCCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
*
66509 TTTCAAAGCCCACACAAGTCGGTGTC-ACCCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
66540 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
*
66572 TTCCAAAAGCCC-CACAAGTCGGTGGCAACCCA
1 TTTC-AAAGCCCACA-AAGTCGGTGGCAACCCA
*
66604 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
66636 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
66668 -TTCAAAGCCCACACAAGTCGGTGGCAA-CCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
* *
66698 TTCCAAAGCCCACACAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
*
66729 TTTCAAAGCCCACACAGTCGGTGGGCAACCCA
1 TTTCAAAGCCCACAAAGTCGGT-GGCAACCCA
66761 TTTCAAAAGCCCACACCAAGTCTGGTGGCAACCCA
1 TTTC-AAAGCCCACA--AAGTC-GGTGGCAACCCA
* * *
66796 TTCCAAAGCCAAAAACAGAGTCGGGTGG-AACCCA
1 TTTCAAAGCC---CACAAAGTC-GGTGGCAACCCA
66830 TGTTCAAAGCCCACAACAAGTCGGGTGGC-ACCCA
1 T-TTCAAAGCCCAC-A-AAGTC-GGTGGCAACCCA
*
66864 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
*
66896 -TTCAAAACCCACAAAGTCGG-GGCAACCCA
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
* * * *
66925 -TTCCAAGCCCCCACAAGTCGGGGGCAAACTCA
1 TTTCAAAGCCCACA-AAGTCGGTGGC-AACCCA
*
66957 -TTCAAACGCCCACACAAGTCGGGTGGGCCAACCCT
1 TTTCAAA-GCCCACA-AAGTC-GGT-GG-CAACCCA
66992 TTTCAAAGCCCACCACAAAGTCGGTGGCAACCCA
1 TTTCAAAG--C-CCACAAAGTCGGTGGCAACCCA
67026 TTTCAAAGCCCACACAAGTCGGTGGCAACCCCA
1 TTTCAAAGCCCACA-AAGTCGGTGGCAA-CCCA
*
67059 GTTCAAAAGCCCACACCAAAGTCTGGTTGGCACACCCCA
1 TTTC-AAAG-CC-CA-CAAAGTC-GG-TGGCA-A-CCCA
67098 TTTCAAAGCCCACAAAGTCGGTGGCAA-CCA
1 TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
*
67128 TTTCAAAAAAACCCTACACAAGTCTGGT-GCAACCCA
1 TTTC---AAAGCCC-ACA-AAGTC-GGTGGCAACCCA
* *
67164 TTCCAAAGCCCACACAA-TCGGTGGCTAACTCA
1 TTTCAAAGCCCACA-AAGTCGGTGGC-AACCCA
67196 TTTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 -TTTCAAAGCCCACA-AAGTCGGTGGCAACCCA
* * *
67229 TTTTAAAAGCCCATGC-AAG-CAGTGGCAACCCT
1 -TTTCAAAGCCCA--CAAAGTCGGTGGCAACCCA
67261 TTTCAAA
1 TTTCAAA
67268 TCACCATATT
Statistics
Matches: 1091, Mismatches: 63, Indels: 166
0.83 0.05 0.13
Matches are distributed among these distances:
27 6 0.01
28 102 0.09
29 154 0.14
30 105 0.10
31 196 0.18
32 205 0.19
33 108 0.10
34 62 0.06
35 61 0.06
36 31 0.03
37 37 0.03
38 15 0.01
39 9 0.01
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.17
Consensus pattern (31 bp):
TTTCAAAGCCCACAAAGTCGGTGGCAACCCA
Found at i:66275 original size:37 final size:38
Alignment explanation
Indices: 66215--66287 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
66205 TTCAAAGCCC
*
66215 ACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAT
1 ACAACTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAT
* *
66253 ACAACTCATTGGCA-TCCTTTCAAAGTCCACAAGTC
1 ACAACTCAGTGGCACTCCTTTCAAAGCCCACAAGTC
66288 GTGGCACTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 20 0.62
38 12 0.38
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.23
Consensus pattern (38 bp):
ACAACTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAT
Found at i:66304 original size:65 final size:67
Alignment explanation
Indices: 66186--66311 Score: 202
Period size: 65 Copynumber: 1.9 Consensus size: 67
66176 TTCAAAGCCC
*
66186 ACAAGTCAGTGGCACTCATTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTC
1 ACAACTCAGTGGCACTCATTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTC
66251 AT
66 AT
* * *
66253 ACAACTCATTGGCA-TCCTTTCAAAGTCCACAAGTC-GTGGCACTCCTTTCAAAGCCCACA
1 ACAACTCAGTGGCACTCATTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA
66312 GCCAGTGGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 24 0.44
66 19 0.35
67 12 0.22
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (67 bp):
ACAACTCAGTGGCACTCATTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTC
AT
Found at i:66349 original size:151 final size:155
Alignment explanation
Indices: 66097--66553 Score: 403
Period size: 151 Copynumber: 3.0 Consensus size: 155
66087 TTCAAAGCCC
* *
66097 ACAAGTCAGTGGCACTCATTTCAAAGCCCTACAAGTAGTGGCACTCATTTTCAAAGCCCACAAAG
1 ACAACTCAGTGGCACTCATTTCAAAGCCCTACAAGTAGTGGCACTCACTTTCAAAGCCCAC-AAG
*
66162 TCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGC-ACTCATTTCAAAGCCCACAAGTCAGTG
65 CCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAAC-CATTTCAAAGCCCAC-AGTCAGTG
66226 GC-ACTCC-TTTCAAAGCCCACAAGTCAT
128 GCAAC-CCATTTCAAAGCCCACAAGTCAT
* * * *
66253 ACAACTCATTGGCA-TCCTTTCAAAGTCC-ACAAGTCGTGGCACTC-CTTTCAAAGCCCAC-AGC
1 ACAACTCAGTGGCACTCATTTCAAAGCCCTACAAGTAGTGGCACTCACTTTCAAAGCCCACAAGC
* * * * * *
66314 CAGTGGCACTCTTTTCAGAGCCCACAAGTTAGTGGCAACCCTTTCAGAGCCCACAGTCGGTGGCA
66 CAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAACCATTTCAAAGCCCACAGTCAGTGGCA
66379 ACCCATTTCAAAGCCC-C-A--C--
131 ACCCATTTCAAAGCCCACAAGTCAT
* * * * *
66398 ACAAGTC-GGGGCAACCCATTTCAAAGCCAC-ACAAGTCGGTGGCAAC-CA-TTCCAAAGCCCAC
1 ACAACTCAGTGGC-ACTCATTTCAAAGCC-CTACAAGT-AGTGGC-ACTCACTTTCAAAG-CC-C
* * * * *
66459 ACAAGTCGGTGGCAAC-CCATTCCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACA
60 ACAAGCCAGTGGC-ACTCC-TTTCAAAG-CC-CACAAGTCAGTGGCAACCATTTCAAAG-CC-CA
* *
66523 CAAGTCGGTGTC-ACCCATTTCAAAGCCCACA
119 C-AGTCAGTGGCAACCCATTTCAAAGCCCACA
66554 CAAGTCGGTG
Statistics
Matches: 248, Mismatches: 32, Indels: 40
0.77 0.10 0.12
Matches are distributed among these distances:
144 3 0.01
145 7 0.03
146 10 0.04
147 8 0.03
148 13 0.05
149 5 0.02
150 15 0.06
151 70 0.28
152 10 0.04
153 15 0.06
154 37 0.15
155 14 0.06
156 31 0.12
157 10 0.04
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (155 bp):
ACAACTCAGTGGCACTCATTTCAAAGCCCTACAAGTAGTGGCACTCACTTTCAAAGCCCACAAGC
CAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAACCATTTCAAAGCCCACAGTCAGTGGCA
ACCCATTTCAAAGCCCACAAGTCAT
Found at i:66416 original size:32 final size:32
Alignment explanation
Indices: 66336--67267 Score: 1115
Period size: 32 Copynumber: 28.8 Consensus size: 32
66326 TTTCAGAGCC
** *
66336 CACAAGTTAGTGGCAACCC-TTTCAGAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
66365 CAC-AGTCGGTGGCAACCCATTTCAAAGCCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAG-CCCA
66397 CACAAGTCGG-GGCAACCCATTTCAAAG-CCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
66427 CACAAGTCGGTGGCAA-CCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
66458 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
66490 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
66521 CACAAGTCGGTGTC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
66552 CACAAGTCGGTGGCAACCCATTCCAAAAGCCC-
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
66584 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
66616 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
66648 CACAAGTCGGTGGCAACCCA-TTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
66679 CACAAGTCGGTGGCAA-CCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
66710 CAC-AGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
66741 CAC-AGTCGGTGGGCAACCCATTTCAAAAGCCCA
1 CACAAGTCGGT-GGCAACCCATTTC-AAAGCCCA
* *
66774 CACCAAGTCTGGTGGCAACCCATTCCAAAGCCAAA
1 CA-CAAGTC-GGTGGCAACCCATTTCAAAGCC-CA
*
66809 AACAGAGTCGGGTGG-AACCCATGTTCAAAGCCCA
1 CACA-AGTC-GGTGGCAACCCAT-TTCAAAGCCCA
*
66843 CAACAAGTCGGGTGGC-ACCCATTCCAAAGCCCA
1 C-ACAAGTC-GGTGGCAACCCATTTCAAAGCCCA
*
66876 CACAAGTCGGTGGCAACCCA-TTCAAAACCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
66907 CA-AAGTCGG-GGCAACCCA-TTCCAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
66936 CACAAGTCGGGGGCAAACTCA-TTCAAACGCCCA
1 CACAAGTCGGTGGC-AACCCATTTCAAA-GCCCA
*
66969 CACAAGTCGGGTGGGCCAACCCTTTTCAAAGCCCA
1 CACAAGTC-GGT-GG-CAACCCATTTCAAAGCCCA
67004 CCACAAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 -CAC-AAGTCGGTGGCAACCCATTTCAAAGCCCA
*
67038 CACAAGTCGGTGGCAACCCCAGTTCAAAAGCCCA
1 CACAAGTCGGTGGCAA-CCCATTTC-AAAGCCCA
67072 CACCAAAGTCTGGTTGGCACACCCCATTTCAAAGCCCA
1 CA-C-AAGTC-GG-TGGCA-A-CCCATTTCAAAGCCCA
*
67110 CA-AAGTCGGTGGCAA-CCATTTCAAAAAAACCCTA
1 CACAAGTCGGTGGCAACCCATTTC---AAAGCCC-A
*
67144 CACAAGTCTGGT-GCAACCCATTCCAAAGCCCA
1 CACAAGTC-GGTGGCAACCCATTTCAAAGCCCA
*
67176 CACAA-TCGGTGGCTAACTCATTTTCAAAGCCCA
1 CACAAGTCGGTGGC-AACCCA-TTTCAAAGCCCA
*
67209 CACAAGTCGGTGGCAACCCATTTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
** * *
67242 TGCAAG-CAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
67268 TCACCATATT
Statistics
Matches: 806, Mismatches: 45, Indels: 102
0.85 0.05 0.11
Matches are distributed among these distances:
28 13 0.02
29 29 0.04
30 62 0.08
31 186 0.23
32 203 0.25
33 110 0.14
34 76 0.09
35 66 0.08
36 30 0.04
37 7 0.01
38 15 0.02
39 9 0.01
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.15
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:67823 original size:20 final size:20
Alignment explanation
Indices: 67795--67869 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
67785 TCATACCCTG
67795 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
67815 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
67835 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
67855 ATGTATCGATACATT
1 ATGTATCGATACATT
67870 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:67862 original size:40 final size:39
Alignment explanation
Indices: 67795--67872 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
67785 TCATACCCTG
* *
67795 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
67835 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
67873 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:71160 original size:14 final size:14
Alignment explanation
Indices: 71143--71173 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
71133 TATTAAAAGG
71143 TTTTTAAAGAAAAT
1 TTTTTAAAGAAAAT
71157 TTTTTAAAGAAAAT
1 TTTTTAAAGAAAAT
71171 TTT
1 TTT
71174 CGTTTTAGTA
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:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TTTTTAAAGAAAAT
Found at i:81589 original size:13 final size:13
Alignment explanation
Indices: 81571--81597 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
81561 ACATTATGCT
81571 TTGTATCGATACA
1 TTGTATCGATACA
81584 TTGTATCGATACA
1 TTGTATCGATACA
81597 T
1 T
81598 GTTTATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:81631 original size:20 final size:20
Alignment explanation
Indices: 81583--81679 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 20
81573 GTATCGATAC
***
81583 ATTGTATCGATACATG-TTT
1 ATTGTATCGATACATGCACA
*
81602 ATTATATCGATACATGCACA
1 ATTGTATCGATACATGCACA
81622 ATTGTATCGATACAT-CTATCA
1 ATTGTATCGATACATGC-A-CA
*
81643 CTGTTTGTATCGATACATGGCAC-
1 ---ATTGTATCGATACAT-GCACA
81666 ATTGTATCGATACA
1 ATTGTATCGATACA
81680 ATGTATTGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
19 16 0.25
20 28 0.44
21 2 0.03
24 15 0.24
25 1 0.02
26 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATTGTATCGATACATGCACA
Found at i:81670 original size:44 final size:49
Alignment explanation
Indices: 81601--81732 Score: 150
Period size: 53 Copynumber: 2.7 Consensus size: 49
81591 GATACATGTT
*
81601 TATTATATCGATACAT-GCACAATTGTATCGATACATCTA-TCA-C-TG-
1 TATTGTATCGATACATGGCAC-ATTGTATCGATACATCTATTCAGCATGA
* *
81646 T-TTGTATCGATACATGGCACATTGTATCGATACAATGTATTGATGCATGA
1 TATTGTATCGATACATGGCACATTGTATCGATAC-ATCTATTCA-GCATGA
81696 TAAATTGTATCGATACATGGCACATTGTATCGATACA
1 T--ATTGTATCGATACATGGCACATTGTATCGATACA
81733 ATGTATTGAT
Statistics
Matches: 74, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
44 26 0.35
45 9 0.12
46 2 0.03
48 1 0.01
49 2 0.03
50 1 0.01
52 1 0.01
53 32 0.43
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (49 bp):
TATTGTATCGATACATGGCACATTGTATCGATACATCTATTCAGCATGA
Found at i:81705 original size:53 final size:53
Alignment explanation
Indices: 81647--81766 Score: 222
Period size: 53 Copynumber: 2.3 Consensus size: 53
81637 CTATCACTGT
81647 TTGTATCGATACATGGCACATTGTATCGATACAATGTATTGATGCATGATAAA
1 TTGTATCGATACATGGCACATTGTATCGATACAATGTATTGATGCATGATAAA
*
81700 TTGTATCGATACATGGCACATTGTATCGATACAATGTATTGATGTATGATAAA
1 TTGTATCGATACATGGCACATTGTATCGATACAATGTATTGATGCATGATAAA
*
81753 TTTTATCGATACAT
1 TTGTATCGATACAT
81767 TGCTTCAAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (53 bp):
TTGTATCGATACATGGCACATTGTATCGATACAATGTATTGATGCATGATAAA
Found at i:81714 original size:20 final size:20
Alignment explanation
Indices: 81674--81732 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
81664 ACATTGTATC
* * *
81674 GATACAATGTATTGATGCAT
1 GATACATTGTATCGATACAT
*
81694 GATAAATTGTATCGATACAT
1 GATACATTGTATCGATACAT
**
81714 GGCACATTGTATCGATACA
1 GATACATTGTATCGATACA
81733 ATGTATTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GATACATTGTATCGATACAT
Found at i:90409 original size:20 final size:19
Alignment explanation
Indices: 90366--90419 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
90356 AAATTATGCT
**
90366 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
*
90385 TTGTATTGATACATGCACAA
1 TTGTATCGATACATGCAC-A
**
90405 TTGTAAGGATACATG
1 TTGTATCGATACATG
90420 AAACTGGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:90493 original size:33 final size:33
Alignment explanation
Indices: 90449--90513 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
90439 GACCACTGTT
* *
90449 TGTATCGATACATGACACATTGTATCGATACAA
1 TGTATCAATACATGACAAATTGTATCGATACAA
*
90482 TGTATCAATACATGATAAATTGTATCGATACA
1 TGTATCAATACATGACAAATTGTATCGATACA
90514 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCAATACATGACAAATTGTATCGATACAA
Found at i:91982 original size:21 final size:20
Alignment explanation
Indices: 91948--91996 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
91938 TTTTATTGAT
*
91948 AATTTTG-ATGAAAATGAAG
1 AATTTTGAATGAAAAGGAAG
*
91967 TATTTTGAAGTGAAAAGGAAG
1 AATTTTGAA-TGAAAAGGAAG
*
91988 AAATTTGAA
1 AATTTTGAA
91997 AAAGATTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 17 0.71
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (20 bp):
AATTTTGAATGAAAAGGAAG
Found at i:98420 original size:20 final size:20
Alignment explanation
Indices: 98395--98449 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
98385 CTGTTAGTTT
**
98395 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
98415 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
98434 AATGTATCGATACAAT
1 CATGTATCGATACAAT
98450 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:98452 original size:13 final size:13
Alignment explanation
Indices: 98434--98461 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
98424 ATACAATGAA
98434 AATGTATCGATAC
1 AATGTATCGATAC
98447 AATGTATCGATAC
1 AATGTATCGATAC
98460 AA
1 AA
98462 AGCATAATGT
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:98457 original size:32 final size:33
Alignment explanation
Indices: 98416--98480 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
98406 ACAATTGTGC
*
98416 ATGTATCGATACAATG-AAAATGTATCGATACA
1 ATGTATCGATACAAAGCAAAATGTATCGATACA
* *
98448 ATGTATCGATACAAAGCATAATGTATTGATACA
1 ATGTATCGATACAAAGCAAAATGTATCGATACA
98481 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAAAATGTATCGATACA
Found at i:103390 original size:68 final size:68
Alignment explanation
Indices: 103307--103441 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 68
103297 AAAAGACCTT
* *
103307 TATCTATAACAATTTGATTCT-ACAATTATTATCCAAGTATCAAAAACATATATATATATATATA
1 TATCTACAACAATTTGATT-TAACAATTATTATCCAAGTATCAAAAACAAATATATATATATATA
103371 TATA
65 TATA
* * **
103375 TATCTACAATAATTTGGTTTAACAATTATTATCCAAGTATCATCAACAAATATATATATATATAT
1 TATCTACAACAATTTGATTTAACAATTATTATCCAAGTATCAAAAACAAATATATATATATATAT
103440 AT
66 AT
103442 CTCCAACAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 1 0.02
68 59 0.98
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (68 bp):
TATCTACAACAATTTGATTTAACAATTATTATCCAAGTATCAAAAACAAATATATATATATATAT
ATA
Found at i:105428 original size:144 final size:144
Alignment explanation
Indices: 105155--105429 Score: 342
Period size: 144 Copynumber: 1.9 Consensus size: 144
105145 TTTCTTTCTT
* *
105155 ACTAAACTTTTGAAGTAATTTTATTAATTTATTTTAAATAAGAAACATAATACATTCATCTCAAC
1 ACTAAACTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAACATAATACATTCATCTCAAA
* ** * ** ** * *
105220 TTTAGTATATTGGATAAAATAAGTTTAAAATATTTAGCATGTGTTTGTATTAGTACTAATTTTAA
66 GTTAAAATATTGGATAAAATAAATTTAAAATATTTAGCATGTACTTAAATTAGTAATAAATTTAA
105285 TCATTTCTTTTATC
131 TCATTTCTTTTATC
* *
105299 ACTAAA-TTTTTAAGTAATTTTATTAA-TTATTTCAAATAA-AAAGCATAATACATTTATCTCAA
1 ACTAAACTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAA-CATAATACATTCATCTCAA
* *
105361 AGTTAAAATATTTGATTAAAAATAAATTTAGAATATTTAGCATGTACTTAAATTA-TAATATAAT
65 AGTTAAAATATTGGA-T-AAAATAAATTTAAAATATTTAGCATGTACTTAAATTAGTAATA-AAT
105425 TTAAT
127 TTAAT
105430 TAGAATTTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
141 3 0.03
142 40 0.36
143 24 0.22
144 44 0.40
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (144 bp):
ACTAAACTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAACATAATACATTCATCTCAAA
GTTAAAATATTGGATAAAATAAATTTAAAATATTTAGCATGTACTTAAATTAGTAATAAATTTAA
TCATTTCTTTTATC
Found at i:107584 original size:25 final size:25
Alignment explanation
Indices: 107539--107586 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
107529 TTTGCTGGCC
107539 TTTTTGATTCTTCCTGAGGAATATA
1 TTTTTGATTCTTCCTGAGGAATATA
* *
107564 TTTTTGTTTCCTTCTTG-GGAATA
1 TTTTTGATT-CTTCCTGAGGAATA
107587 GAATATATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (25 bp):
TTTTTGATTCTTCCTGAGGAATATA
Found at i:112503 original size:19 final size:19
Alignment explanation
Indices: 112466--112503 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
112456 TTTTTGTTAT
*
112466 TTACTTTTTCTTTTCTTTA
1 TTACTTTTTCTTGTCTTTA
112485 TTACTTTTTTCTTGT-TTTA
1 TTAC-TTTTTCTTGTCTTTA
112504 AGATAGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.11, C:0.13, G:0.03, T:0.74
Consensus pattern (19 bp):
TTACTTTTTCTTGTCTTTA
Found at i:113239 original size:13 final size:13
Alignment explanation
Indices: 113221--113250 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
113211 GATACATGCG
113221 ACATTGTATCGAT
1 ACATTGTATCGAT
113234 ACATTGTATCGAT
1 ACATTGTATCGAT
113247 ACAT
1 ACAT
113251 AGTAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:114517 original size:141 final size:141
Alignment explanation
Indices: 114004--114510 Score: 682
Period size: 141 Copynumber: 3.6 Consensus size: 141
113994 TAAGCTTTAA
* ** **
114004 CTAATATTCCTATGGTTTTCTGTAGGGGTATAGAAATTTTCAAAACTTTTCATATCTTTTTTGTT
1 CTAATATTCCTATAGTTTTCTGTAGGGGTATAGAAATTTTCAAAACTTTTTGTATCTTTTCAGTT
* * * * *
114069 C-CCTATTAAGCTACGAAATGATTTTTTTGGAAATTAAAAATTAAATAAATATTATTATCTTAAT
66 CTCC-ATTAAGGTACAAAATGAATTTTTTGAAAATTAAAAATTAAATAAAAATTATTATCTTAAT
114133 TTTTCAAAATTT
130 TTTTCAAAATTT
* * *
114145 CTAATATTCCTATAGTTTTCCGTAGGGGTATAGATATTTTCAAAACTTTTAGTATCTTTTCAGTT
1 CTAATATTCCTATAGTTTTCTGTAGGGGTATAGAAATTTTCAAAACTTTTTGTATCTTTTCAGTT
* * *
114210 CTCCATTAAGATACAAAATAAATTATTTT-AAAATTACAAATTAAATAAAAATTATTATCTTAAT
66 CTCCATTAAGGTACAAAATGAATT-TTTTGAAAATTAAAAATTAAATAAAAATTATTATCTTAAT
*
114274 TTTTCAAGATTT
130 TTTTCAAAATTT
* *
114286 CTAATATTCCTATAGTTTT-TCGTAGGGATATACAAATCTTT-AAAACTTTTTGTATCTTTTCAG
1 CTAATATTCCTATAGTTTTCT-GTAGGGGTATAGAAAT-TTTCAAAACTTTTTGTATCTTTTCAG
* * *
114349 TTCTCTATTAAGGTATAAAATGAATTTTTTGAAAATTAAAAATTAAATAAAAATTATTATATTAA
64 TTCTCCATTAAGGTACAAAATGAATTTTTTGAAAATTAAAAATTAAATAAAAATTATTATCTTAA
*
114414 TTTTTCAATATTT
129 TTTTTCAAAATTT
* * * * *
114427 CTAATATTCTTATGGTTTTCTTTAGGGGTATAGAAATGTTC-AAACTTTTTGTATCTTTTTAGTT
1 CTAATATTCCTATAGTTTTCTGTAGGGGTATAGAAATTTTCAAAACTTTTTGTATCTTTTCAGTT
*
114491 CTCCATTAAGGTACGAAATG
66 CTCCATTAAGGTACAAAATG
114511 GGATTTTCGA
Statistics
Matches: 322, Mismatches: 37, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
140 45 0.14
141 267 0.83
142 10 0.03
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (141 bp):
CTAATATTCCTATAGTTTTCTGTAGGGGTATAGAAATTTTCAAAACTTTTTGTATCTTTTCAGTT
CTCCATTAAGGTACAAAATGAATTTTTTGAAAATTAAAAATTAAATAAAAATTATTATCTTAATT
TTTCAAAATTT
Found at i:116234 original size:73 final size:73
Alignment explanation
Indices: 116064--116532 Score: 531
Period size: 73 Copynumber: 6.5 Consensus size: 73
116054 TACGCTGTGA
* * * * *
116064 TAAACTTCTACAAATAAAAATAAATTATGCCATAAAAAATTTAAACTTGTATAATTATACTCAAA
1 TAAACTTCTACAAATAAAAATAAATTATACC-TTAAAAATTTAAACTCGTATAATCATACCCAAA
116129 AAA-ACATATT
65 AAATA-A-ATT
* *
116139 TAAACTTTTACAAATAAAAATAAATTATACGTTAAAAATTTAAACTCGTATAATCATACCCAAAA
1 TAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACCCAAAA
116204 AATAAATT
66 AATAAATT
* * * *
116212 TAAACTTCTACAAATAAAAATAAATAATACCCTAAAAATTTAAACTC-AATAATCA-AACCAAAA
1 TAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACCCAAAA
*
116275 AACAAATT
66 AATAAATT
* * * * ** *
116283 TAAATTTCTACAAATAAAAATAAATTACACCTTCAAAAATTTAAACTCATATAGTCATACCTTAC
1 TAAACTTCTACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCGTATAATCATACCCAAA
*
116348 AAATATATT
65 AAATAAATT
* * **
116357 TAAACTTCTATAAAGT-AAAATAAATTATACCCTT-AAAATTTAAACTCGAATAATCA-A-ATAA
1 TAAACTTCTACAAA-TAAAAATAAATTATA-CCTTAAAAATTTAAACTCGTATAATCATACCCAA
116418 AAAATAAATT
64 AAAATAAATT
* * * * * * *
116428 TAAACCTC-AAAAATAAAAATAAATTATACCTTCAAAATTTAAACTTGTGTAATCATACCCTACA
1 TAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACCCAAAA
*
116492 AATAAGTT
66 AATAAATT
*
116500 TAAACTTCTACAAATAAAAATAAATAATACCTT
1 TAAACTTCTACAAATAAAAATAAATTATACCTT
116533 TAATCAAACT
Statistics
Matches: 334, Mismatches: 49, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
69 5 0.01
70 36 0.11
71 61 0.18
72 38 0.11
73 93 0.28
74 67 0.20
75 34 0.10
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.30
Consensus pattern (73 bp):
TAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACCCAAAA
AATAAATT
Found at i:116358 original size:145 final size:144
Alignment explanation
Indices: 116064--116530 Score: 577
Period size: 145 Copynumber: 3.2 Consensus size: 144
116054 TACGCTGTGA
* * * ** * *
116064 TAAACTTCTACAAATAAAAATAAATTATGCCATAAAAAATTTAAACTTGTATAATTATACTCAAA
1 TAAACTTCTACAAATAAAAATAAATAATACCCT-AAAAATTTAAAC-TCAATAATCAAAC-C-AA
* *
116129 AAAACATATTTAAACTTT-TACAAATAAAAATAAATTATACGTT-AAAAATTTAAACTCGTATAA
62 AAAACAAATTTAAA-TTTCTACAAATAAAAATAAATTATACCTTCAAAAATTTAAACTCGTATAA
* *
116192 TCATACCCAAAAAATAAATT
126 TCATACCCTACAAAT-AATT
116212 TAAACTTCTACAAATAAAAATAAATAATACCCTAAAAATTTAAACTCAATAATCAAACCAAAAAA
1 TAAACTTCTACAAATAAAAATAAATAATACCCTAAAAATTTAAACTCAATAATCAAACCAAAAAA
* * *
116277 CAAATTTAAATTTCTACAAATAAAAATAAATTACACCTTCAAAAATTTAAACTCATATAGTCATA
66 CAAATTTAAATTTCTACAAATAAAAATAAATTATACCTTCAAAAATTTAAACTCGTATAATCATA
*
116342 CCTTACAAATATATT
131 CCCTACAAATA-ATT
* * * *
116357 TAAACTTCTATAAAGT-AAAATAAATTATACCCTTAAAATTTAAACTCGAATAATCAAA-TAAAA
1 TAAACTTCTACAAA-TAAAAATAAATAATACCCTAAAAATTTAAACTC-AATAATCAAACCAAAA
* ** * * *
116420 AATAAATTTAAACCTC-AAAAATAAAAATAAATTATACCTTC-AAAATTTAAACTTGTGTAATCA
64 AACAAATTTAAATTTCTACAAATAAAAATAAATTATACCTTCAAAAATTTAAACTCGTATAATCA
116483 TACCCTACAAATAAGTT
129 TACCCTACAAATAA-TT
116500 TAAACTTCTACAAATAAAAATAAATAATACC
1 TAAACTTCTACAAATAAAAATAAATAATACC
116531 TTTAATCAAA
Statistics
Matches: 281, Mismatches: 31, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
142 2 0.01
143 62 0.22
144 62 0.22
145 93 0.33
146 20 0.07
147 12 0.04
148 30 0.11
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.30
Consensus pattern (144 bp):
TAAACTTCTACAAATAAAAATAAATAATACCCTAAAAATTTAAACTCAATAATCAAACCAAAAAA
CAAATTTAAATTTCTACAAATAAAAATAAATTATACCTTCAAAAATTTAAACTCGTATAATCATA
CCCTACAAATAATT
Found at i:116458 original size:24 final size:27
Alignment explanation
Indices: 116412--116464 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
116402 TCGAATAATC
116412 AAATAAAAAATAAATTTAAACC-TCAA
1 AAATAAAAAATAAATTTAAACCTTCAA
*
116438 AAAT-AAAAATAAA-TTATACCTTCAA
1 AAATAAAAAATAAATTTAAACCTTCAA
116463 AA
1 AA
116465 TTTAAACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 15 0.60
26 4 0.16
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (27 bp):
AAATAAAAAATAAATTTAAACCTTCAA
Found at i:119829 original size:20 final size:19
Alignment explanation
Indices: 119787--119837 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
119777 GTTTGAAGCA
119787 ATGTATCGATACAATTCAAC
1 ATGTATCGATACAATTC-AC
119807 ATGTATCGATACAATGTTC-C
1 ATGTATCGATACAA--TTCAC
119827 ATGTATCGATA
1 ATGTATCGATA
119838 TAAACAGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 26 0.90
22 3 0.10
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATTCAC
Found at i:119913 original size:19 final size:19
Alignment explanation
Indices: 119869--119924 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
119859 CTACCAGTTT
**
119869 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
119889 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
119908 CATGTATCGATACAATG
1 CATGTATCGATACAATG
119925 TATCGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:120087 original size:22 final size:22
Alignment explanation
Indices: 120061--120117 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
120051 ATATTTTTAC
120061 TTAAAAACATTTGATTTAAGGT
1 TTAAAAACATTTGATTTAAGGT
120083 TTAAAAACATTTGATTTAAGGT
1 TTAAAAACATTTGATTTAAGGT
*
120105 TCAAAAACATTTG
1 TTAAAAACATTTG
120118 TTTTTAACTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (22 bp):
TTAAAAACATTTGATTTAAGGT
Found at i:120626 original size:68 final size:68
Alignment explanation
Indices: 120542--120688 Score: 240
Period size: 68 Copynumber: 2.2 Consensus size: 68
120532 TTTAAAAAAT
* * *
120542 TTTCTCCCCCTTGATAATCATTTAAAAAGATTTTCTCTCCCTTAATTTAAAAAATTTATTTTCAA
1 TTTCTCCCCCTCGATAATCATTTAAAAAGATTTTCTCTCCCTTAATATAAAAAATCTATTTTCAA
120607 ACA
66 ACA
* * *
120610 TTTCTCCCCCTCGATAATCGTTTAAAAAGATTTTCTCTTCCTTGATATAAAAAATCTATTTTCAA
1 TTTCTCCCCCTCGATAATCATTTAAAAAGATTTTCTCTCCCTTAATATAAAAAATCTATTTTCAA
120675 ACA
66 ACA
120678 TTTCTCCCCCT
1 TTTCTCCCCCT
120689 TTTTATTATA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (68 bp):
TTTCTCCCCCTCGATAATCATTTAAAAAGATTTTCTCTCCCTTAATATAAAAAATCTATTTTCAA
ACA
Found at i:122208 original size:18 final size:19
Alignment explanation
Indices: 122181--122216 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
122171 ATCAAACAAG
*
122181 CATAATTTAAATAACAAAA
1 CATAATTTAAACAACAAAA
122200 CATAA-TTAAACAACAAA
1 CATAATTTAAACAACAAA
122217 TTCATCCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (19 bp):
CATAATTTAAACAACAAAA
Found at i:128224 original size:20 final size:20
Alignment explanation
Indices: 128182--128235 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
128172 GTTTGAAGCA
* *
128182 ATGTATCGAAACAATTCATC
1 ATGTATCGATACAATTCACC
128202 ATGTATCGATACAATGTC-CC
1 ATGTATCGATACAAT-TCACC
*
128222 ATGTATTGATACAA
1 ATGTATCGATACAA
128236 ATAGTGGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:128308 original size:19 final size:19
Alignment explanation
Indices: 128264--128319 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
128254 CTGTTAGTTT
**
128264 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
128284 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
128303 CATGTATCGATACAATG
1 CATGTATCGATACAATG
128320 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:128322 original size:13 final size:13
Alignment explanation
Indices: 128304--128330 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
128294 TACAATGAAC
128304 ATGTATCGATACA
1 ATGTATCGATACA
128317 ATGTATCGATACA
1 ATGTATCGATACA
128330 A
1 A
128331 AGCATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:133415 original size:2 final size:2
Alignment explanation
Indices: 133408--133435 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
133398 TATCAAAAAC
133408 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133436 CTACAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133447 original size:72 final size:72
Alignment explanation
Indices: 133361--133495 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
133351 AAAAGACCTT
* *
133361 TATCTATAACAATTTGATTCT-ACAATTATTATCCAAGTATCAAAAACATATATATATATATATA
1 TATCTACAACAATTTGATT-TAACAATTATTATCCAAGTATCAAAAACAAATATATATATATATA
133425 TATATATA
65 TATATATA
* * **
133433 TATCTACAATAATTTGGTTTAACAATTATTATCCAAGTATCATCAACAAATATATATATATAT
1 TATCTACAACAATTTGATTTAACAATTATTATCCAAGTATCAAAAACAAATATATATATATAT
133496 CTCCAACAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 1 0.02
72 55 0.98
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (72 bp):
TATCTACAACAATTTGATTTAACAATTATTATCCAAGTATCAAAAACAAATATATATATATATAT
ATATATA
Found at i:135478 original size:144 final size:144
Alignment explanation
Indices: 135205--135479 Score: 351
Period size: 144 Copynumber: 1.9 Consensus size: 144
135195 TTTCTTTCTT
* *
135205 ACTAAACTTTTGAAGTAATTTTATTAATTTATTTTAAATAAGAAACATAATACATTCATCTCAAC
1 ACTAAACTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAACATAATACATTCATCTCAAA
* * * ** ** * *
135270 TTTAATATATTGGATAAAATAAGTTTAAAATATTTAGCATGTGTTTGTATTAGTACTAATTTTAA
66 GTTAAAATATTGGATAAAATAAATTTAAAATATTTAGCATGTACTTAAATTAGTAATAAATTTAA
135335 TCATTTCTTTTATC
131 TCATTTCTTTTATC
* *
135349 ACTAAA-TTTTTAAGTAATTTTATTAA-TTATTTCAAATAA-AAAGCATAATACATTTATCTCAA
1 ACTAAACTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAA-CATAATACATTCATCTCAA
* *
135411 AGTTAAAATATTTGATTAAAAATAAATTTAGAATATTTAGCATGTACTTAAATTA-TAATATAAT
65 AGTTAAAATATTGGA-T-AAAATAAATTTAAAATATTTAGCATGTACTTAAATTAGTAATA-AAT
135475 TTAAT
127 TTAAT
135480 TAGAATTTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
141 3 0.03
142 41 0.37
143 24 0.21
144 44 0.39
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (144 bp):
ACTAAACTTTTGAAGTAATTTTATTAATTTATTTCAAATAAGAAACATAATACATTCATCTCAAA
GTTAAAATATTGGATAAAATAAATTTAAAATATTTAGCATGTACTTAAATTAGTAATAAATTTAA
TCATTTCTTTTATC
Found at i:135953 original size:23 final size:21
Alignment explanation
Indices: 135926--135973 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
135916 ATCTTTATAT
135926 TATAATAATAATAATAATAAATA
1 TATAATAAT-ATAAT-ATAAATA
135949 TAT-A-AATATAATATAAATA
1 TATAATAATATAATATAAATA
135968 TATAAT
1 TATAAT
135974 TAACTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 10 0.43
20 6 0.26
21 3 0.13
22 1 0.04
23 3 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAATAATATAATATAAATA
Found at i:137644 original size:25 final size:25
Alignment explanation
Indices: 137599--137646 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
137589 TTTGCTGCCC
137599 TTTTTGATTCTTCCTGAGGAATATA
1 TTTTTGATTCTTCCTGAGGAATATA
* *
137624 TTTTTGTTTCCTTCTTG-GGAATA
1 TTTTTGATT-CTTCCTGAGGAATA
137647 GAATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (25 bp):
TTTTTGATTCTTCCTGAGGAATATA
Found at i:143063 original size:40 final size:40
Alignment explanation
Indices: 143008--143100 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
142998 ATCTTATTCA
143008 AAATGATTTTCAATATCAAAGATGTTTTAGAGTTATGTAT
1 AAATGATTTTCAATATCAAAGATGTTTTAGAGTTATGTAT
*
143048 AAATGATTTTCAATATCAAATATGTTTTAGAGTTATGTAT
1 AAATGATTTTCAATATCAAAGATGTTTTAGAGTTATGTAT
*
143088 AAATGTTTTTCAA
1 AAATGATTTTCAA
143101 GCATTAAATC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (40 bp):
AAATGATTTTCAATATCAAAGATGTTTTAGAGTTATGTAT
Found at i:143093 original size:21 final size:21
Alignment explanation
Indices: 143029--143096 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
143019 AATATCAAAG
143029 ATGTTTTAGAGTTATGTATAA
1 ATGTTTTAGAGTTATGTATAA
*
143050 ATGATTTTCA-A--TAT-CA-AA
1 ATG-TTTT-AGAGTTATGTATAA
143068 TATGTTTTAGAGTTATGTATAA
1 -ATGTTTTAGAGTTATGTATAA
143090 ATGTTTT
1 ATGTTTT
143097 TCAAGCATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 4 0.11
20 6 0.16
21 11 0.30
22 7 0.19
23 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.49
Consensus pattern (21 bp):
ATGTTTTAGAGTTATGTATAA
Found at i:143362 original size:20 final size:20
Alignment explanation
Indices: 143337--143390 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
143327 CTACTATTGC
143337 TTGTATCGATACATGCGACA
1 TTGTATCGATACATGCGACA
143357 TTGTATCGATACATGCGACA
1 TTGTATCGATACATGCGACA
143377 TTGTATCGATACAT
1 TTGTATCGATACAT
143391 TGTATCGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGCGACA
Found at i:143392 original size:13 final size:13
Alignment explanation
Indices: 143374--143403 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
143364 GATACATGCG
143374 ACATTGTATCGAT
1 ACATTGTATCGAT
143387 ACATTGTATCGAT
1 ACATTGTATCGAT
143400 ACAT
1 ACAT
143404 AGTAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:144668 original size:139 final size:140
Alignment explanation
Indices: 144159--144658 Score: 581
Period size: 139 Copynumber: 3.6 Consensus size: 140
144149 TAAGCTTTTA
* * * * * **
144159 CTAATATTCTTATGGTTTTCTGTAGGGATATAGAAAATTTCAAAAACTTTTCATATCTTTTTGGT
1 CTAATATTCATATAGTTTTCTTTAGGGATATAGAAATTTTC-AAAACTTTTCGTATCTTTTCAGT
* * * * *
144224 TC-CTTATTAAGCTACGAAATGATTTTTTTTTAAAATTAAAAATTAAAATATATATTATTATCTT
65 TCTC-CATTAAGGTACGAAATGA--ATTTTTTAAAATTAAAAATT-AAATAAAAATTATTATCTT
144288 AATTTTT-AAAATTT
126 AATTTTTCAAAATTT
* *
144302 CTAATATTCCTATAGTTTT-TTGTAGGGGTATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGT
1 CTAATATTCATATAGTTTTCTT-TAGGGATATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGT
* * *
144366 TCTCCATTAAGTTACAAAAT-AATTTTTTAAAATTAGAAATTAAATAAAAATTATTATCTTAATT
65 TCTCCATTAAGGTACGAAATGAATTTTTTAAAATTAAAAATTAAATAAAAATTATTATCTTAATT
144430 TTTCAAGAA-TT
130 TTTCAA-AATTT
* * *
144441 CTAATATTCATATAGTTTTC-ATAGGGATATACAAATCTTT-AAAAC-TTTCGTATCTTTTCAAT
1 CTAATATTCATATAGTTTTCTTTAGGGATATAGAAAT-TTTCAAAACTTTTCGTATCTTTTCAGT
* * *
144503 TCTCTATTAAGGTATGAAATGAATTTTTTGAAAATTAAAAATTAAATAAAAATTATTATATTAAT
65 TCTCCATTAAGGTACGAAATGAATTTTTT-AAAATTAAAAATTAAATAAAAATTATTATCTTAAT
*
144568 TTTTCAATATTT
129 TTTTCAAAATTT
* * * * *
144580 CTAATATTC-TATCGTTTTCTTTAGGGGTATAGAAATGTTC-AAACTTTTTGTATCTTTTTAGTT
1 CTAATATTCATATAGTTTTCTTTAGGGATATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGTT
144643 CTCCATT-AGGTACGAA
66 CTCCATTAAGGTACGAA
144659 CTGGGATTTT
Statistics
Matches: 308, Mismatches: 37, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
137 32 0.10
138 74 0.24
139 128 0.42
140 2 0.01
141 1 0.00
142 36 0.12
143 35 0.11
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (140 bp):
CTAATATTCATATAGTTTTCTTTAGGGATATAGAAATTTTCAAAACTTTTCGTATCTTTTCAGTT
CTCCATTAAGGTACGAAATGAATTTTTTAAAATTAAAAATTAAATAAAAATTATTATCTTAATTT
TTCAAAATTT
Found at i:146337 original size:73 final size:71
Alignment explanation
Indices: 146212--146679 Score: 489
Period size: 73 Copynumber: 6.5 Consensus size: 71
146202 TACGCTGTGA
* * * *
146212 TAAACTTCTACAAATAAAAATAAATTATGCCATAAAAAATTTAAACTTGTATAATTATACTCAAA
1 TAAACTTCTACAAATAAAAATAAATTATACC-TTAAAAATTTAAACTCGTATAATCATAC-CAAA
146277 AAAACATATT
64 AAAA-A-ATT
* *
146287 TAAACTTTTACAAAT-AAAATAAATTATACGTTAAAAATTTAAACTCGTATAATCATACCCAAAA
1 TAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATA-CCAAAA
146351 AATAAATT
65 AA-AAATT
* * * *
146359 TAAACTTCTACAAATAAAAATAAATAATACCCTAAAAATTTAAACTC-AATAATCAAACCAAAAA
1 TAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACCAAAAA
146423 ACAAATT
66 A-AAATT
* * * * *
146430 TAAATTTCTACAAATAAAAATAAATTACACCTTCAAAAATTTAAACTCATATAGTCATACCTTAC
1 TAAACTTCTACAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCGTATAATCATACC--AA
* *
146495 AAATATATT
63 AAAAAAATT
* * **
146504 TAAACTTCTATAAAGT-AAAATAAATTATACCCTT-AAAATTTAAACTCGAATAATCA-AATAAA
1 TAAACTTCTACAAA-TAAAAATAAATTATA-CCTTAAAAATTTAAACTCGTATAATCATACCAAA
146566 AAATAAATT
64 AAA-AAATT
* * * * * *
146575 TAAACCTC-AAAAATAAAAATAAATTATACCTTCAAAATTTAAACTTGTGTAATCATACCCTACA
1 TAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATA-CC-AAA
* *
146639 AATAAGTT
64 AAAAAATT
*
146647 TAAACTTCTACAAATAAAAATAAATAATACCTT
1 TAAACTTCTACAAATAAAAATAAATTATACCTT
146680 TAATCAAACT
Statistics
Matches: 330, Mismatches: 47, Indels: 34
0.80 0.11 0.08
Matches are distributed among these distances:
69 5 0.02
70 40 0.12
71 54 0.16
72 51 0.15
73 114 0.35
74 43 0.13
75 23 0.07
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (71 bp):
TAAACTTCTACAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATACCAAAAA
AAAATT
Found at i:146605 original size:24 final size:27
Alignment explanation
Indices: 146559--146611 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
146549 TCGAATAATC
146559 AAATAAAAAATAAATTTAAACC-TCAA
1 AAATAAAAAATAAATTTAAACCTTCAA
*
146585 AAAT-AAAAATAAA-TTATACCTTCAA
1 AAATAAAAAATAAATTTAAACCTTCAA
146610 AA
1 AA
146612 TTTAAACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 15 0.60
26 4 0.16
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (27 bp):
AAATAAAAAATAAATTTAAACCTTCAA
Found at i:147168 original size:68 final size:67
Alignment explanation
Indices: 147041--147187 Score: 161
Period size: 68 Copynumber: 2.2 Consensus size: 67
147031 ATTTAAAATT
** *
147041 TTTTATTTTATTAAAAACAATAATTAATATTTTGATTTTTCACTAAAAATATTTTAAATTAAATT
1 TTTTATTTTATTAAAAACAATAATTAATACATTGA-TTTTCAATAAAAATATTTTAAATTAAATT
*
147106 TAA
65 AAA
* ** * * * *
147109 TTTTATTTTATTAAAAATATATAATTAATACATTG-TTTTCAATTTAATTTTTTTAAAATTTAGT
1 TTTTATTTTATTAAAAACA-ATAATTAATACATTGATTTTCAATAAAAATATTTT-AAATTAAAT
147173 TAAA
64 TAAA
147177 TTTTATTTTAT
1 TTTTATTTTAT
147188 AATTTTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
67 14 0.21
68 39 0.59
69 13 0.20
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (67 bp):
TTTTATTTTATTAAAAACAATAATTAATACATTGATTTTCAATAAAAATATTTTAAATTAAATTA
AA
Found at i:149975 original size:20 final size:19
Alignment explanation
Indices: 149933--149983 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
149923 GTTTGAAGCA
149933 ATGTATCGATACAATTCAAC
1 ATGTATCGATACAATTC-AC
149953 ATGTATCGATACAATGTTC-C
1 ATGTATCGATACAA--TTCAC
149973 ATGTATCGATA
1 ATGTATCGATA
149984 TAAACAGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 26 0.90
22 3 0.10
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATTCAC
Found at i:150059 original size:19 final size:19
Alignment explanation
Indices: 150015--150070 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
150005 CTACCAGTTT
**
150015 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
150035 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
150054 CATGTATCGATACAATG
1 CATGTATCGATACAATG
150071 TATCGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Done.