Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 111 of 203
Found at i:35138782 original size:18 final size:18
Alignment explanation
Indices: 35138749--35138801 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
35138739 CAACATGGTT
*
35138749 TTTTATTGATTTTATTTTA
1 TTTTATTTA-TTTATTTTA
35138768 TTTTATTTATTTATTTTA
1 TTTTATTTATTTATTTTA
*
35138786 TCTTATCTT-TTTATTT
1 TTTTAT-TTATTTATTT
35138802 ATTACCCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 21 0.68
19 10 0.32
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTATTTATTTATTTTA
Found at i:35139532 original size:61 final size:62
Alignment explanation
Indices: 35139417--35139535 Score: 170
Period size: 62 Copynumber: 1.9 Consensus size: 62
35139407 AAAGATCGGC
* *
35139417 GGCGACTCCATTTTTATTTTTTAAAATAAAAGTCGATTTCAAAAAAAAGGTTTCGACAGCTT
1 GGCGACTCCATTTTCATTTTTTAAAATAAAAGTCGATTTAAAAAAAAAGGTTTCGACAGCTT
* **
35139479 GGCGACTCCGTTTTCATTTTTTAAAATAATAA-TTTA-TTAAAAAAAAAGGTTTCGACA
1 GGCGACTCCATTTTCATTTTTTAAAATAA-AAGTCGATTTAAAAAAAAAGGTTTCGACA
35139536 ATCTCCTTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
61 20 0.39
62 29 0.57
63 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (62 bp):
GGCGACTCCATTTTCATTTTTTAAAATAAAAGTCGATTTAAAAAAAAAGGTTTCGACAGCTT
Found at i:35151323 original size:44 final size:44
Alignment explanation
Indices: 35151268--35151354 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
35151258 GCAGAGCCCA
*
35151268 TTTATGACCAATGAAACGAGCAGCGGTGTTCCGGACAGGTTCGG
1 TTTACGACCAATGAAACGAGCAGCGGTGTTCCGGACAGGTTCGG
35151312 TTTACGACCAATGAAACGAGCAGCGGTGTTCCGGACAGGTTCG
1 TTTACGACCAATGAAACGAGCAGCGGTGTTCCGGACAGGTTCG
35151355 TACGCCGTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (44 bp):
TTTACGACCAATGAAACGAGCAGCGGTGTTCCGGACAGGTTCGG
Found at i:35155125 original size:15 final size:15
Alignment explanation
Indices: 35155105--35155135 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35155095 GCCCATATGG
35155105 ATCATCTTCATCTTC
1 ATCATCTTCATCTTC
*
35155120 ATCATCTTCTTCTTC
1 ATCATCTTCATCTTC
35155135 A
1 A
35155136 CTTTTAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCATCTTCATCTTC
Found at i:35159883 original size:24 final size:24
Alignment explanation
Indices: 35159855--35159906 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
35159845 TTAGTAAGTC
* *
35159855 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
35159879 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
35159903 AAAT
1 AAAT
35159907 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:35161781 original size:82 final size:81
Alignment explanation
Indices: 35161626--35161781 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
35161616 TGGTCTCCTT
* * * * *
35161626 AAAATGATAAAATTTTAATTTATACCTTTTATAATATATGAAATTTTAAATTAATAATGATAAAA
1 AAAATGATAAAAATTTAATTTATACCTTTTATAAAATATAAAAATATAAATTAATAATGATAAAA
*
35161691 TTATACTTTAACCTCA
66 TTACACTTTAACCTCA
35161707 AAAATGATAAAAATTTAATTTA-ACCTTTTA-AAAACTATAAAAATATAGACTATTAA-AATGAT
1 AAAATGATAAAAATTTAATTTATACCTTTTATAAAA-TATAAAAATATA-A--ATTAATAATGAT
35161769 AAAATTACACTTT
62 AAAATTACACTTT
35161782 TACTATAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
79 3 0.05
80 17 0.26
81 22 0.34
82 18 0.28
83 5 0.08
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (81 bp):
AAAATGATAAAAATTTAATTTATACCTTTTATAAAATATAAAAATATAAATTAATAATGATAAAA
TTACACTTTAACCTCA
Found at i:35167352 original size:124 final size:123
Alignment explanation
Indices: 35167128--35167376 Score: 462
Period size: 124 Copynumber: 2.0 Consensus size: 123
35167118 CCTGTCTCCA
*
35167128 AGTACTACTTCTTTCCTCGGTGTTCTTTTTTTAAATCTCTTCAATCTTTTTTTTTGTTAAAATTA
1 AGTACTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATCTTTTTTTTTGTTAAAATTA
*
35167193 TCAAGTTCTTCTCTCCAAGGACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
66 TCAAGTTCTTCTCTCCAAGCACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
*
35167251 AGTATTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATCTTTTTTTTTGGTTAAAATT
1 AGTACTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATCTTTTTTTTT-GTTAAAATT
35167316 ATCAAGTTCTTCTCTCCAAGCACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
65 ATCAAGTTCTTCTCTCCAAGCACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
35167375 AG
1 AG
35167377 CTGATGGTTC
Statistics
Matches: 122, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
123 53 0.43
124 69 0.57
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (123 bp):
AGTACTACTTCTTTCCTCGGTGTTCTTATTTTAAATCTCTTCAATCTTTTTTTTTGTTAAAATTA
TCAAGTTCTTCTCTCCAAGCACCCCGGCTAGGTAGATGGTGGCGATTGAGGACTAGTT
Found at i:35177473 original size:73 final size:73
Alignment explanation
Indices: 35177380--35177524 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
35177370 ATAACCTTTT
* * *
35177380 CATGTTATAAAACATATACAAGTAAACACATTAGACATATCATTTATTCAACATCTATTCATTTA
1 CATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATCTATTAATTTA
35177445 ACATTTCA
66 ACATTTCA
* * *
35177453 CATGTTATAAAACGTGTACAAGTAAACACATTAGATATACCATTCATTCAACATCTATTAATTTA
1 CATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATCTATTAATTTA
35177518 ACATTTC
66 ACATTTC
35177525 CCATTTCCCA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (73 bp):
CATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATCTATTAATTTA
ACATTTCA
Found at i:35177608 original size:13 final size:13
Alignment explanation
Indices: 35177577--35177648 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
35177567 TATATCTATC
35177577 CATATAAACATTT
1 CATATAAACATTT
*
35177590 CGTATAAACACTTT
1 CATATAAACA-TTT
**
35177604 -ATATAATTATTT
1 CATATAAACATTT
*
35177616 CCATATAACCGA-TT
1 -CATATAAAC-ATTT
*
35177630 CATATAATCATTT
1 CATATAAACATTT
35177643 CATATA
1 CATATA
35177649 TTCTTTTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.09
13 31 0.66
14 11 0.23
15 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (13 bp):
CATATAAACATTT
Found at i:35177735 original size:12 final size:12
Alignment explanation
Indices: 35177718--35177746 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
35177708 TTTAACACAT
35177718 AATCATTTTGTA
1 AATCATTTTGTA
35177730 AATCATTTTGTA
1 AATCATTTTGTA
35177742 AATCA
1 AATCA
35177747 CATTTCGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (12 bp):
AATCATTTTGTA
Found at i:35178095 original size:44 final size:45
Alignment explanation
Indices: 35178039--35178191 Score: 159
Period size: 45 Copynumber: 3.4 Consensus size: 45
35178029 TACCATAATG
* *
35178039 TCTTTCAACTATGGTCTTACACG-TTGAATCGTGATGCCATAGCA
1 TCTTTCAGCTATGGTCTTACACGTTTGAATCATGATGCCATAGCA
* * *
35178083 TCTTTTAGCTATGGTCTTACTCGTTTGAATCATGATGCCATAGCG
1 TCTTTCAGCTATGGTCTTACACGTTTGAATCATGATGCCATAGCA
* * * * * *
35178128 TCTTTCAGCTATGATCTTACTCATTTCCAGT-AT-AGTGCCATAGTA
1 TCTTTCAGCTATGGTCTTACACGTTT-GAATCATGA-TGCCATAGCA
*
35178173 TCTTTCAACTATGGTCTTA
1 TCTTTCAGCTATGGTCTTA
35178192 TTCACTCCCG
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
44 21 0.23
45 69 0.75
46 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (45 bp):
TCTTTCAGCTATGGTCTTACACGTTTGAATCATGATGCCATAGCA
Found at i:35178167 original size:45 final size:45
Alignment explanation
Indices: 35178073--35178243 Score: 141
Period size: 45 Copynumber: 3.8 Consensus size: 45
35178063 TGAATCGTGA
* * * * * *
35178073 TGCCATAGCATCTTTTAGCTATGGTCTTACTCGTTT-GAATCAT-G
1 TGCCATAGCATCTTTCAACTATGATCTTACTCATTTCCAGT-ATAG
* *
35178117 ATGCCATAGCGTCTTTCAGCTATGATCTTACTCATTTCCAGTATAG
1 -TGCCATAGCATCTTTCAACTATGATCTTACTCATTTCCAGTATAG
* * * * *
35178163 TGCCATAGTATCTTTCAACTATGGTCTTATTCA-CTCCCGATATAG
1 TGCCATAGCATCTTTCAACTATGATCTTACTCATTTCCAG-TATAG
* ** *
35178208 TACCATAGTGTCTTTCAACTATGATCTTATTCATTT
1 TGCCATAGCATCTTTCAACTATGATCTTACTCATTT
35178244 TTCAAGCCAA
Statistics
Matches: 105, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
44 4 0.04
45 97 0.92
46 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.40
Consensus pattern (45 bp):
TGCCATAGCATCTTTCAACTATGATCTTACTCATTTCCAGTATAG
Found at i:35179784 original size:24 final size:27
Alignment explanation
Indices: 35179757--35179806 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
35179747 CAAATACTCA
35179757 TTTATA-TA-ATTAAAATAT-TCATAT
1 TTTATACTAGATTAAAATATGTCATAT
35179781 TTTATACTAGATTAAAATATGTCATA
1 TTTATACTAGATTAAAATATGTCATA
35179807 AGTCCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 10 0.43
27 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTATACTAGATTAAAATATGTCATAT
Found at i:35180191 original size:23 final size:23
Alignment explanation
Indices: 35180148--35180233 Score: 59
Period size: 23 Copynumber: 3.6 Consensus size: 23
35180138 TACTATAAAA
* *
35180148 ATTTATTATTAATTTTGTAATAT
1 ATTTATTATTAAATATGTAATAT
35180171 ATTTATTATTAAAATAT-TAATATT
1 ATTTATTATT-AAATATGTAATA-T
* * *
35180195 AATATTGTTCATTAATATATGT-TTAA
1 -AT-TTATT-ATTAA-ATATGTAATAT
35180221 ATTTATTATTAAA
1 ATTTATTATTAAA
35180234 ATAAAATTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
22 1 0.02
23 20 0.40
24 9 0.18
25 4 0.08
26 6 0.12
27 9 0.18
28 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (23 bp):
ATTTATTATTAAATATGTAATAT
Found at i:35180376 original size:39 final size:38
Alignment explanation
Indices: 35180333--35180408 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
35180323 AATATGTATG
35180333 TTTAATA-ATATTGAAAATTACAATATTTTATT-TTAATAT
1 TTTAATATAT-TTGAAAATTA-AA-ATTTTATTATTAATAT
*
35180372 TTTAATATATTTTAAAATTAAAATTTTATTATTAATA
1 TTTAATATATTTGAAAATTAAAATTTTATTATTAATA
35180409 GAATAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 8 0.24
38 8 0.24
39 16 0.47
40 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (38 bp):
TTTAATATATTTGAAAATTAAAATTTTATTATTAATAT
Found at i:35201962 original size:16 final size:17
Alignment explanation
Indices: 35201922--35201964 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
35201912 TTCTCCACAT
35201922 AGTTATTCTCAATATAG
1 AGTTATTCTCAATATAG
35201939 AGGTTATTC-CGAATA-AG
1 A-GTTATTCTC-AATATAG
35201956 AGTTATTCT
1 AGTTATTCT
35201965 GTGATAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
18 11 0.48
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (17 bp):
AGTTATTCTCAATATAG
Found at i:35202027 original size:15 final size:16
Alignment explanation
Indices: 35202007--35202045 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35201997 AAATAATGGC
*
35202007 TCTAAATAC-ATTTGT
1 TCTAAATACAAGTTGT
35202022 TCTAAATACAAGTTGT
1 TCTAAATACAAGTTGT
*
35202038 TCCAAATA
1 TCTAAATA
35202046 ATGGTTGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (16 bp):
TCTAAATACAAGTTGT
Found at i:35206516 original size:21 final size:21
Alignment explanation
Indices: 35206490--35206529 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
35206480 CAAATGAAGT
35206490 AAGCATTTTAACTCGATTGTG
1 AAGCATTTTAACTCGATTGTG
35206511 AAGCATTTTAACTCGATTG
1 AAGCATTTTAACTCGATTG
35206530 GCGGTGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (21 bp):
AAGCATTTTAACTCGATTGTG
Found at i:35210825 original size:17 final size:17
Alignment explanation
Indices: 35210796--35210838 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
35210786 AATTAGTTAT
*
35210796 TTAAAAAATTTATAATA
1 TTAAAAAATTTATAAAA
35210813 TTAAACAAA-TTATAAAA
1 TTAAA-AAATTTATAAAA
35210830 TTACAAAAA
1 TTA-AAAAA
35210839 AGAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAAATTTATAAAA
Found at i:35210905 original size:17 final size:18
Alignment explanation
Indices: 35210874--35210909 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
35210864 TTACTATTTT
35210874 TTTTAAATATATTATAAA
1 TTTTAAATATATTATAAA
*
35210892 TTTT-AATATTTTATAAA
1 TTTTAAATATATTATAAA
35210909 T
1 T
35210910 CACATTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAATATATTATAAA
Found at i:35211199 original size:22 final size:22
Alignment explanation
Indices: 35211173--35211230 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
35211163 ATTTTCAGTA
* *
35211173 ATTTTTT-TTATTTTTATATAT
1 ATTTTTTGTAATTTTTAAATAT
35211194 ATTTTTTGTAATTTTTAAATAT
1 ATTTTTTGTAATTTTTAAATAT
* *
35211216 -GTTTTTGGAATTTTT
1 ATTTTTTGTAATTTTT
35211231 TTGTAACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
ATTTTTTGTAATTTTTAAATAT
Found at i:35211222 original size:21 final size:22
Alignment explanation
Indices: 35211182--35211252 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
35211172 AATTTTTTTT
*
35211182 ATTTTTATATATATTTTTTGTA
1 ATTTTTATATATATTTTTTGGA
35211204 ATTTTTA-A-ATATGTTTTTGGA
1 ATTTTTATATATAT-TTTTTGGA
* *
35211225 ATTTTTTTGTA-ACTTTTTTGGA
1 ATTTTTATATATA-TTTTTTGGA
*
35211247 TTTTTT
1 ATTTTT
35211253 TCATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.10
21 14 0.34
22 21 0.51
23 2 0.05
ACGTcount: A:0.23, C:0.01, G:0.10, T:0.66
Consensus pattern (22 bp):
ATTTTTATATATATTTTTTGGA
Found at i:35218389 original size:91 final size:91
Alignment explanation
Indices: 35218269--35218627 Score: 556
Period size: 91 Copynumber: 3.9 Consensus size: 91
35218259 AACTAAGAAT
* * * *
35218269 ATGCCAGATGCACATAGTGCAAACCCGTAGGCTAAATATTCTCCCTCGATAACACGCCAGATTTC
1 ATGCTAGATGCACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGC
35218334 TCATAAGAGCTATTCTAATCAATAAC
66 TCATAAGAGCTATTCTAATCAATAAC
* *
35218360 ATGCTAGATGCACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCTCGATAACACGCCAGATTTC
1 ATGCTAGATGCACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGC
35218425 TCATAAGAGCTATTCTAATCAATAAC
66 TCATAAGAGCTATTCTAATCAATAAC
* *
35218451 ATGCTAGATGCACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAATATGCCAGATTGC
1 ATGCTAGATGCACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGC
* *
35218516 TCATAAGAGCTATTCTAATCGAGAAC
66 TCATAAGAGCTATTCTAATCAATAAC
* * * * * *
35218542 ACGTTAAATGCACATAGTGCAAAGACTGTAGGCTAAATATTCTCCCCCGATAAAACGCTAGATTG
1 ATGCTAGATGCACATAGTGCAAAG-CCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTG
*
35218607 CTCATAAGAGCTATTCCAATC
65 CTCATAAGAGCTATTCTAATC
35218628 GAGAACACAC
Statistics
Matches: 251, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
91 195 0.78
92 56 0.22
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (91 bp):
ATGCTAGATGCACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGC
TCATAAGAGCTATTCTAATCAATAAC
Found at i:35223360 original size:22 final size:24
Alignment explanation
Indices: 35223335--35223383 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
35223325 CTCTTGAAAG
* *
35223335 AATACCTAAAAGAGAGT-CA-CAA
1 AATAACTAAAAGAAAGTACACCAA
*
35223357 AATAACTACAAGAAAGTACACCAA
1 AATAACTAAAAGAAAGTACACCAA
35223381 AAT
1 AAT
35223384 TGTGAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 14 0.64
23 2 0.09
24 6 0.27
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (24 bp):
AATAACTAAAAGAAAGTACACCAA
Found at i:35229159 original size:51 final size:51
Alignment explanation
Indices: 35229090--35229384 Score: 312
Period size: 51 Copynumber: 5.8 Consensus size: 51
35229080 TAAGGTATCG
* * * *
35229090 ATGAACACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA
* * * *
35229141 ATGCTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAATTT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TA
* * * * * *
35229192 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACATGTACCGATAAATG
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA
* * *
35229243 ATGAACACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TA
* * * *
35229294 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACC-ATAAA-A
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA
* *
35229343 CTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 -ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTA
35229385 TCGAATGATA
Statistics
Matches: 204, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
50 46 0.23
51 154 0.75
52 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (51 bp):
ATGATCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA
Found at i:35229179 original size:26 final size:26
Alignment explanation
Indices: 35229099--35229181 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
35229089 GATGAACACG
**
35229099 TGTGTAGTACTGTGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * *
35229125 CGTGTA-T-CGATAAAT-AATGCTCAC-A
1 TGTGTAGTAC--TAAGTGAAGGCT-ACTA
35229150 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
35229176 TGTGTA
1 TGTGTA
35229182 CCGAAAATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:35229271 original size:102 final size:102
Alignment explanation
Indices: 35229095--35229389 Score: 441
Period size: 102 Copynumber: 2.9 Consensus size: 102
35229085 TATCGATGAA
* *
35229095 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGCTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTAC
**
35229160 TAAGTGAAGGCTACTATGTGTACCGAAAATTTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * *
35229197 CACGTGTGTAGTACTGTGTGAAGGCTACTACATGTACCGATAAATGATGAACACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTAC
35229262 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * * *
35229299 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACC-ATAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATA-ATGATCACATGTGTAGTA
* * *
35229362 CTATGTGAAGGCTACTACGTGTATCGAA
65 CTAAGTGAAGGCTACTATGTGTACCGAA
35229390 TGATAAAAGT
Statistics
Matches: 175, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
101 45 0.26
102 130 0.74
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGATCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Found at i:35230539 original size:13 final size:12
Alignment explanation
Indices: 35230521--35230561 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
35230511 ATAATTTTAA
35230521 TTTTTTATAACTT
1 TTTTTTATAA-TT
35230534 TTTTTTATAAATT
1 TTTTTTAT-AATT
*
35230547 TTGTTTATAATT
1 TTTTTTATAATT
35230559 TTT
1 TTT
35230562 ATGATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.24
13 17 0.68
14 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTTTTATAATT
Found at i:35236632 original size:20 final size:18
Alignment explanation
Indices: 35236607--35236654 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
35236597 TGGCTTAAAA
35236607 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGA--GTTGTTG
35236627 TTGGTAGTGG-GTTGTTG
1 TTGGTAGTGGAGTTGTTG
*
35236644 GTGGTAGTGGA
1 TTGGTAGTGGA
35236655 ATTAACACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.46, T:0.44
Consensus pattern (18 bp):
TTGGTAGTGGAGTTGTTG
Found at i:35236811 original size:52 final size:52
Alignment explanation
Indices: 35236732--35236850 Score: 193
Period size: 52 Copynumber: 2.2 Consensus size: 52
35236722 TACTTCTGAT
*
35236732 CAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
35236785 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
35236837 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
35236851 GCTACACTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
52 44 0.71
53 18 0.29
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
Found at i:35236860 original size:37 final size:37
Alignment explanation
Indices: 35236813--35236922 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
35236803 TGATAGCTTC
*
35236813 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
35236850 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
35236887 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
35236922 G
1 G
35236923 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:35238735 original size:14 final size:13
Alignment explanation
Indices: 35238692--35238743 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 13
35238682 AGTCATCATC
35238692 TAAAAATTATAAA
1 TAAAAATTATAAA
35238705 TTAAAAATTAT-AA
1 -TAAAAATTATAAA
*
35238718 -AAAACTTATAAA
1 TAAAAATTATAAA
*
35238730 TGAAAATTA-AAA
1 TAAAAATTATAAA
35238742 TA
1 TA
35238744 TATATTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 8 0.25
12 6 0.19
13 8 0.25
14 10 0.31
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
TAAAAATTATAAA
Found at i:35238741 original size:20 final size:20
Alignment explanation
Indices: 35238724--35238765 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
35238714 ATAAAAAACT
35238724 TATAAATGAAAATTAAAATA
1 TATAAATGAAAATTAAAATA
**
35238744 TATATTTGAAAATTAAAA-A
1 TATAAATGAAAATTAAAATA
35238763 TAT
1 TAT
35238766 TAAAAAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
TATAAATGAAAATTAAAATA
Found at i:35243573 original size:17 final size:17
Alignment explanation
Indices: 35243551--35243598 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
35243541 AAATAGGAAA
35243551 GTAATTTGATAATATTT
1 GTAATTTGATAATATTT
35243568 GTAATTTGATAATATTT
1 GTAATTTGATAATATTT
*
35243585 G-ATTTTG-TAATATT
1 GTAATTTGATAATATT
35243599 GGGGATTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (17 bp):
GTAATTTGATAATATTT
Found at i:35244174 original size:123 final size:123
Alignment explanation
Indices: 35243955--35244202 Score: 496
Period size: 123 Copynumber: 2.0 Consensus size: 123
35243945 AAAAATTACT
35243955 TAAAATTATATAAATTATGAGACGAAAGATCTAATTCTGTGACACTTGTATGTACTCTAATAATA
1 TAAAATTATATAAATTATGAGACGAAAGATCTAATTCTGTGACACTTGTATGTACTCTAATAATA
35244020 AGATAATGACTATTACACTTATCAGAAATCAACATACGTCATAAATCTATAATTTGTA
66 AGATAATGACTATTACACTTATCAGAAATCAACATACGTCATAAATCTATAATTTGTA
35244078 TAAAATTATATAAATTATGAGACGAAAGATCTAATTCTGTGACACTTGTATGTACTCTAATAATA
1 TAAAATTATATAAATTATGAGACGAAAGATCTAATTCTGTGACACTTGTATGTACTCTAATAATA
35244143 AGATAATGACTATTACACTTATCAGAAATCAACATACGTCATAAATCTATAATTTGTA
66 AGATAATGACTATTACACTTATCAGAAATCAACATACGTCATAAATCTATAATTTGTA
35244201 TA
1 TA
35244203 TCGCATAGAT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 125 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34
Consensus pattern (123 bp):
TAAAATTATATAAATTATGAGACGAAAGATCTAATTCTGTGACACTTGTATGTACTCTAATAATA
AGATAATGACTATTACACTTATCAGAAATCAACATACGTCATAAATCTATAATTTGTA
Found at i:35258480 original size:26 final size:26
Alignment explanation
Indices: 35258451--35258500 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
35258441 CAAATAAACC
*
35258451 TAGCCCAATACACCACAACTCAAAAA
1 TAGCCCAATACACCACAACCCAAAAA
*
35258477 TAGCCCAATACACTACAACCCAAA
1 TAGCCCAATACACCACAACCCAAA
35258501 TCAGAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.36, G:0.04, T:0.12
Consensus pattern (26 bp):
TAGCCCAATACACCACAACCCAAAAA
Found at i:35261545 original size:12 final size:12
Alignment explanation
Indices: 35261521--35261553 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35261511 AAACTTGAAG
35261521 TATATTT-TATA
1 TATATTTATATA
35261532 TATATTTATATA
1 TATATTTATATA
*
35261544 TATACTTATA
1 TATATTTATA
35261554 AACAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATTTATATA
Found at i:35262282 original size:12 final size:12
Alignment explanation
Indices: 35262245--35262283 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35262235 GAGAACCAAT
*
35262245 AAAAGGAAAAAG
1 AAAAGGAAAAGG
*
35262257 AAAGAGGAAGAGG
1 AAA-AGGAAAAGG
35262270 AAAAGGAAAAGG
1 AAAAGGAAAAGG
35262282 AA
1 AA
35262284 GAAAATAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAAGG
Found at i:35262282 original size:18 final size:19
Alignment explanation
Indices: 35262248--35262285 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35262238 AACCAATAAA
35262248 AGGAAAAAGAAAGAGGAAG
1 AGGAAAAAGAAAGAGGAAG
*
35262267 AGGAAAAGGAAA-AGGAAG
1 AGGAAAAAGAAAGAGGAAG
35262285 A
1 A
35262286 AAATAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (19 bp):
AGGAAAAAGAAAGAGGAAG
Found at i:35264733 original size:109 final size:111
Alignment explanation
Indices: 35264615--35264823 Score: 298
Period size: 115 Copynumber: 1.9 Consensus size: 111
35264605 AAAAAAATTC
* * * * *
35264615 GTGTTAAAATAAGATATCAGTATATGAAAAAAGT-AAAAA-AAAAA-TTGGGTGCTGGCCTGTTA
1 GTGTCAAAATAAGATATCAGTATACGAAAAAAATAAAAAATAAAAATTTGGGTGCTGGCCTATCA
*
35264677 ATGGCCGGCACCGAGTACAATTTAGAAAAAAAAATTTAATTTTTTTT
66 ATGGCCGGCACCCAGTACAATTTA-AAAAAAAAATTTAATTTTTTTT
*
35264724 GTGTCAAAATCAGATATCAGTATACGAAAAAAATAAAAAAAATAAAAATTTTGGGTGCTGGCCTA
1 GTGTCAAAATAAGATATCAGTATACGAAAAAAAT--AAAAAATAAAAA-TTTGGGTGCTGGCCTA
35264789 TCAATGGCCGGCACCCAGTACAATTTAAAAAAAAA
63 TCAATGGCCGGCACCCAGTACAATTTAAAAAAAAA
35264824 TTGTGTCAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
109 30 0.34
112 5 0.06
113 5 0.06
114 8 0.09
115 39 0.45
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (111 bp):
GTGTCAAAATAAGATATCAGTATACGAAAAAAATAAAAAATAAAAATTTGGGTGCTGGCCTATCA
ATGGCCGGCACCCAGTACAATTTAAAAAAAAAATTTAATTTTTTTT
Found at i:35264939 original size:57 final size:57
Alignment explanation
Indices: 35264853--35264973 Score: 233
Period size: 57 Copynumber: 2.1 Consensus size: 57
35264843 CAGTATACGA
*
35264853 TTTTTTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAT
1 TTTTTTTTTATTTTTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAAAGAAT
35264910 TTTTTTTTTATTTTTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAAAGAAT
1 TTTTTTTTTATTTTTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAAAGAAT
35264967 TTTTTTT
1 TTTTTTT
35264974 AAATTGTACT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (57 bp):
TTTTTTTTTATTTTTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAAAGAAT
Found at i:35265726 original size:19 final size:19
Alignment explanation
Indices: 35265699--35265740 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
35265689 CATACAATTT
*
35265699 TATTACCAAAAATAAAACG
1 TATTACCAAAAAGAAAACG
* *
35265718 TATTTCCAAAAAGAAAACT
1 TATTACCAAAAAGAAAACG
35265737 TATT
1 TATT
35265741 GCCATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (19 bp):
TATTACCAAAAAGAAAACG
Found at i:35266939 original size:108 final size:106
Alignment explanation
Indices: 35266752--35266951 Score: 301
Period size: 108 Copynumber: 1.9 Consensus size: 106
35266742 TGGATTGAGA
* * *
35266752 TTTAAGAGGATATTTGACTATTTGGTCAAACGAGAAATCGAAACCCAACACATTAGGGCGCGTTT
1 TTTAAAAGGATATTTGACTATTTGATCAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTT
* *
35266817 CCTCGAATTTCCAAACGCAAAATATTATCTTACTTCGAAAT
66 CCTCAAATCTCCAAACGCAAAATATTATCTTACTTCGAAAT
* *
35266858 TTTAAAAGGATATTTGGCTATTTGATCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
1 TTTAAAAGGATATTTGACTATTTGATCAAACGAG--AAATCGAAACCCAACACATTAGGGCACGT
* *
35266923 TTTCTCAAATCTCCAAACGTAAAATATTA
64 TTCCTCAAATCTCCAAACGCAAAATATTA
35266952 CCTTTATTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 30 0.36
108 53 0.64
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (106 bp):
TTTAAAAGGATATTTGACTATTTGATCAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTT
CCTCAAATCTCCAAACGCAAAATATTATCTTACTTCGAAAT
Found at i:35267642 original size:17 final size:18
Alignment explanation
Indices: 35267620--35267656 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
35267610 ATGAAGTGTA
35267620 AAGTATATATATC-ATAT
1 AAGTATATATATCTATAT
*
35267637 AAGTATTTATATCTATAT
1 AAGTATATATATCTATAT
35267655 AA
1 AA
35267657 ATTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
AAGTATATATATCTATAT
Found at i:35274410 original size:108 final size:106
Alignment explanation
Indices: 35274223--35274426 Score: 302
Period size: 108 Copynumber: 1.9 Consensus size: 106
35274213 TGGATTAAGA
* * * *
35274223 TTTAAGAGGATATTTGGCAATTTGGTCAAACGAGAAATCGAAACCCAGCACATTAGGGCACATTT
1 TTTAAAAGGATATTTGACAATTTGATCAAACGAGAAAACGAAACCCAGCACATTAGGGCACATTT
*
35274288 TCTCGAATTTCCAAACGCAAAACATTGCCTTACTTCGAAAT
66 TCTCGAATCTCCAAACGCAAAACATTGCCTTACTTCGAAAT
* *
35274329 TTTAAAAGGATATTTGACTATTTGAT-AGAACGAGAAAAAACGAAACCCAGCACATTAGGGCACG
1 TTTAAAAGGATATTTGACAATTTGATCA-AACGAG--AAAACGAAACCCAGCACATTAGGGCACA
*
35274393 TTTTCTCGAATCTCCAAACGCAAAATATTGCCTT
63 TTTTCTCGAATCTCCAAACGCAAAACATTGCCTT
35274427 TATTATTCTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 1 0.01
106 28 0.32
108 58 0.67
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (106 bp):
TTTAAAAGGATATTTGACAATTTGATCAAACGAGAAAACGAAACCCAGCACATTAGGGCACATTT
TCTCGAATCTCCAAACGCAAAACATTGCCTTACTTCGAAAT
Found at i:35275214 original size:3 final size:3
Alignment explanation
Indices: 35275206--35275257 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
35275196 AAAATGAAAC
** * * *
35275206 TAA TAA TAA TTAA TGG TAA TAA TAA AAA TAA AAA TAA TAA TGA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35275252 TAA TAA
1 TAA TAA
35275258 AAATGATCAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:35275269 original size:15 final size:15
Alignment explanation
Indices: 35275206--35275269 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
35275196 AAAATGAAAC
* *
35275206 TAATAATAATTAATGG
1 TAATAATAA-AAATGA
35275222 TAATAATAAAAAT-A
1 TAATAATAAAAATGA
*
35275236 -AA-AATAATAATGA
1 TAATAATAAAAATGA
35275249 TAATAATAAAAATGA
1 TAATAATAAAAATGA
*
35275264 TCATAA
1 TAATAA
35275270 CACTAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.20
13 3 0.08
14 2 0.05
15 18 0.45
16 9 0.22
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (15 bp):
TAATAATAAAAATGA
Found at i:35278498 original size:15 final size:14
Alignment explanation
Indices: 35278480--35278535 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
35278470 ATTAATTTAA
35278480 TATTATTATTACCAT
1 TATTATTATTACC-T
35278495 TATTATT-TTACCCT
1 TATTATTATTA-CCT
35278509 TATTATTTATATA-CT
1 TATTA-TTAT-TACCT
35278524 TATTATTATTAC
1 TATTATTATTAC
35278536 TATATTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.06
14 13 0.36
15 18 0.50
16 1 0.03
17 2 0.06
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATTATTACCT
Found at i:35278505 original size:14 final size:14
Alignment explanation
Indices: 35278480--35278516 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
35278470 ATTAATTTAA
35278480 TATTATTATTACCAT
1 TATTATT-TTACCAT
*
35278495 TATTATTTTACCCT
1 TATTATTTTACCAT
35278509 TATTATTT
1 TATTATTT
35278517 ATATACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATTTTACCAT
Found at i:35278699 original size:15 final size:16
Alignment explanation
Indices: 35278676--35278705 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35278666 AGACTATTTA
35278676 TTTATTTTTTATTATT
1 TTTATTTTTTATTATT
35278692 TTTA-TTTTTATTAT
1 TTTATTTTTTATTAT
35278706 AACTCTAATT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTTTTATTATT
Found at i:35278777 original size:3 final size:3
Alignment explanation
Indices: 35278769--35278802 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35278759 TGTTACTACC
35278769 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35278803 CAATCTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35278944 original size:21 final size:22
Alignment explanation
Indices: 35278920--35278964 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
35278910 TAGTATGGCT
* *
35278920 TTGTTTTTTTTAATTGTT-TTA
1 TTGTTGTTATTAATTGTTATTA
*
35278941 TTGTTGTTATTCATTGTTATTA
1 TTGTTGTTATTAATTGTTATTA
35278963 TT
1 TT
35278965 TATTTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.71
Consensus pattern (22 bp):
TTGTTGTTATTAATTGTTATTA
Found at i:35279528 original size:18 final size:19
Alignment explanation
Indices: 35279494--35279529 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35279484 AGGATCATAT
35279494 TTTTAAATTTCTTTTCGAA
1 TTTTAAATTTCTTTTCGAA
35279513 TTTTAAATTT-TTTTCGA
1 TTTTAAATTTCTTTTCGA
35279530 CATTAAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTAAATTTCTTTTCGAA
Found at i:35297121 original size:10 final size:10
Alignment explanation
Indices: 35297106--35297164 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
35297096 TAAAATATTT
35297106 TTATATTAAA
1 TTATATTAAA
35297116 TTATATTAAA
1 TTATATTAAA
35297126 --ATATTCAAA
1 TTATATT-AAA
*
35297135 ATATTATTAAA
1 TTA-TATTAAA
*
35297146 TCATATTAAA
1 TTATATTAAA
*
35297156 CTAT-TTAAA
1 TTATATTAAA
35297165 AATATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
8 5 0.12
9 8 0.20
10 19 0.46
11 5 0.12
12 4 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (10 bp):
TTATATTAAA
Found at i:35297137 original size:9 final size:8
Alignment explanation
Indices: 35297077--35297140 Score: 51
Period size: 8 Copynumber: 7.9 Consensus size: 8
35297067 TCAAAATAAT
*
35297077 AATATTTA
1 AATATTAA
35297085 AATA-TAA
1 AATATTAA
35297092 AATA-TAA
1 AATATTAA
**
35297099 AATATTTT
1 AATATTAA
*
35297107 TATATTAA
1 AATATTAA
35297115 ATTATATTAA
1 A--ATATTAA
35297125 AATATTCAA
1 AATATT-AA
35297134 AATATTA
1 AATATTA
35297141 TTAAATCATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
7 13 0.29
8 16 0.36
9 8 0.18
10 8 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (8 bp):
AATATTAA
Found at i:35297145 original size:30 final size:31
Alignment explanation
Indices: 35297109--35297170 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
35297099 AATATTTTTA
* *
35297109 TATTAAATTATATTAAAATA-TTCAAAATAT
1 TATTAAATCATATTAAAATATTTAAAAATAT
*
35297139 TATTAAATCATATTAAACTATTTAAAAATAT
1 TATTAAATCATATTAAAATATTTAAAAATAT
35297170 T
1 T
35297171 TTTTTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTAAATCATATTAAAATATTTAAAAATAT
Found at i:35297238 original size:25 final size:25
Alignment explanation
Indices: 35297199--35297280 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 25
35297189 ATTAGAAATG
*
35297199 ATATTTTATTTTAAATTATATTAAA
1 ATATTTTATATTAAATTATATTAAA
* * *
35297224 ATATTTTATAATAAA-TAAATT-TA
1 ATATTTTATATTAAATTATATTAAA
35297247 ATATTTTATATTAAATTATATTAAA
1 ATATTTTATATTAAATTATATTAAA
*
35297272 ATTTTTTAT
1 ATATTTTAT
35297281 TTTTTAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
23 15 0.32
24 10 0.21
25 22 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTTTATATTAAATTATATTAAA
Found at i:35299144 original size:23 final size:23
Alignment explanation
Indices: 35299106--35299156 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
35299096 AACCCATTTA
* *
35299106 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
35299129 TGTAATACCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
35299152 AGTAA
1 TGTAA
35299157 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:35301478 original size:48 final size:48
Alignment explanation
Indices: 35301422--35301598 Score: 221
Period size: 48 Copynumber: 3.5 Consensus size: 48
35301412 CGATCTCGTA
*
35301422 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAGCCAGTG
1 TAAGACCATGTCTGAGACATGGCATCAACATCGATATGTGAGCCAGTG
* * *
35301470 TAAGACCATGTCTGAGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCA-TG
1 TAAGACCATGTCTGAGACATGGCA-T--CAACA-T-CGA-TATGTGA-G--CCAGTG
*
35301526 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAGCCAGTG
1 TAAGACCATGTCTGAGACATGGCATCAACATCGATATGTGAGCCAGTG
35301574 TAAGACCATGTCTGAGACATGGCAT
1 TAAGACCATGTCTGAGACATGGCAT
35301599 TGGCATCATT
Statistics
Matches: 110, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
47 3 0.03
48 49 0.45
49 2 0.02
50 6 0.05
51 6 0.05
52 2 0.02
53 6 0.05
54 6 0.05
55 2 0.02
56 25 0.23
57 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (48 bp):
TAAGACCATGTCTGAGACATGGCATCAACATCGATATGTGAGCCAGTG
Found at i:35301602 original size:104 final size:104
Alignment explanation
Indices: 35301422--35301753 Score: 464
Period size: 104 Copynumber: 3.2 Consensus size: 104
35301412 CGATCTCGTA
35301422 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAGCCAGTGTAAGACCATGTCTGAGA
1 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAGCCAGTGTAAGACCATGTCTGAGA
35301487 CATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
66 CATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
35301526 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAGCCAGTGTAAGACCATGTCTGAGA
1 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAGCCAGTGTAAGACCATGTCTGAGA
35301591 CATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
66 CATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
* *** * * * *
35301630 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCACA-TGTAAGA-CATGTTTG
1 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGA-G-C-CAGTGTAAGACCATGTCTG
* * * *
35301693 GGACATGACGTTGGCA-C--TGAG---ATGAGAAGTCCCATG
63 AGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
*
35301729 TAAGACCATGTTTGGGACATGGCAT
1 TAAGACCATGTCTGGGACATGGCAT
35301754 GGGCACCGAT
Statistics
Matches: 211, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
99 37 0.18
102 4 0.02
104 139 0.66
105 21 0.10
106 8 0.04
107 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (104 bp):
TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAGCCAGTGTAAGACCATGTCTGAGA
CATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
Found at i:35301695 original size:49 final size:50
Alignment explanation
Indices: 35301422--35301857 Score: 325
Period size: 50 Copynumber: 8.6 Consensus size: 50
35301412 CGATCTCGTA
*** * * *
35301422 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTG-AG--CCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCA-TG
* * *
35301470 TAAGACCATGTCTGAGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAAGTCCCATG
*** * * *
35301526 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTG-AG--CCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCA-TG
* * *
35301574 TAAGACCATGTCTGAGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAAGTCCCATG
* * *
35301630 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCACATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCATG
* * * *
35301680 TAAGA-CATGTTTGGGACATGACGTTGGCACTGAGATGAGAAGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCATG
* * * *
35301729 TAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCATG
* * * * * *
35301779 TAAGACCATATCTGGGATATGGCATTGGCA--G-TATAAGAAACATCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG-AA-GTCCCATG
* *
35301828 TAAGACCATGTCTGGGATATGGCTTTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
35301858 TGTTATTATC
Statistics
Matches: 315, Mismatches: 51, Indels: 43
0.77 0.12 0.11
Matches are distributed among these distances:
47 8 0.03
48 57 0.18
49 79 0.25
50 87 0.28
51 4 0.01
53 5 0.02
54 8 0.03
55 3 0.01
56 58 0.18
57 6 0.02
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCATG
Found at i:35301759 original size:99 final size:100
Alignment explanation
Indices: 35301422--35301808 Score: 388
Period size: 104 Copynumber: 3.8 Consensus size: 100
35301412 CGATCTCGTA
** * *
35301422 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAG-CCAGTGTAAGACCATGTCTGAG
1 TAAGACCATGTCTGGGACATGGCATCGGCACCGATATGAGAGTCCA-TGTAAGA-CATGTCTGAG
*
35301486 ACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
64 ACATGACATTGGCATCA-TGAG--TATGAGAGGTCCCATG
** * *
35301526 TAAGACCATGTCTGGGACATGGCATCAACATCGATATGTGAG-CCAGTGTAAGACCATGTCTGAG
1 TAAGACCATGTCTGGGACATGGCATCGGCACCGATATGAGAGTCCA-TGTAAGA-CATGTCTGAG
*
35301590 ACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
64 ACATGACATTGGCATCA-TGAG--TATGAGAGGTCCCATG
* * * * *
35301630 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCACATGTAAGACATGTTTGGG
1 TAAGACCATGTCTGGGACATGGCATCGGCACCGATATGAGA-GTC-CATGTAAGACATGTCTGAG
* *
35301695 ACATGACGTTGGCA-C-TGAG-ATGAGAAGTCCCATG
64 ACATGACATTGGCATCATGAGTATGAGAGGTCCCATG
* * * * *
35301729 TAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGG
1 TAAGACCATGTCTGGGACATGGCATCGGCACCGATATGAG-AGT-CCATGTAAGA-CATGTCTGA
* *
35301794 GATATGGCATTGGCA
63 GACATGACATTGGCA
35301809 GTATAAGAAA
Statistics
Matches: 255, Mismatches: 22, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
99 60 0.24
100 21 0.08
102 4 0.02
104 139 0.55
105 21 0.08
106 8 0.03
107 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (100 bp):
TAAGACCATGTCTGGGACATGGCATCGGCACCGATATGAGAGTCCATGTAAGACATGTCTGAGAC
ATGACATTGGCATCATGAGTATGAGAGGTCCCATG
Found at i:35303369 original size:23 final size:23
Alignment explanation
Indices: 35303335--35303385 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
35303325 GGGAGAGAAA
*
35303335 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
35303358 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
35303381 AGTAA
1 TGTAA
35303386 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:35305714 original size:16 final size:16
Alignment explanation
Indices: 35305693--35305732 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35305683 TAATTTGATG
*
35305693 ATTTTACTAACAATTA
1 ATTTTAATAACAATTA
*
35305709 ATTTTAATAATAATTA
1 ATTTTAATAACAATTA
*
35305725 GTTTTAAT
1 ATTTTAAT
35305733 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTAATAACAATTA
Found at i:35305733 original size:22 final size:22
Alignment explanation
Indices: 35305706--35305766 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
35305696 TTACTAACAA
* * *
35305706 TTAATTTTAATAATAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
35305728 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
35305750 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
35305767 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:35308248 original size:37 final size:37
Alignment explanation
Indices: 35308151--35308322 Score: 155
Period size: 37 Copynumber: 4.5 Consensus size: 37
35308141 ACTAGTTTGG
* ** * *
35308151 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAAATAA
1 CACCCAGTGCCTCATCGGCTAAACCGAAG---TAAATTGA
* * *
35308191 CACCTAGTGTCTCATCGGCTAAACCGAAGTAAATTGG
1 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
*
35308228 CACCCAGTGCCTCATCGGCTAAACTGAAGTAAATTGA
1 CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
** **
35308265 CACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCG-GCTAAACCG-A--AGTAAATTGA
*
35308306 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
35308323 ACTCGAAGCC
Statistics
Matches: 110, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
37 55 0.50
38 4 0.04
39 1 0.01
40 24 0.22
41 26 0.24
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTGA
Found at i:35316425 original size:17 final size:16
Alignment explanation
Indices: 35316388--35316426 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
35316378 AATAAATAAT
35316388 TAAA-TAAATTGAAAA
1 TAAATTAAATTGAAAA
35316403 TAAAATTAAATTGAGAAA
1 T-AAATTAAATTGA-AAA
35316421 TAAATT
1 TAAATT
35316427 TAGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 13 0.62
18 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGAAAA
Found at i:35319967 original size:141 final size:141
Alignment explanation
Indices: 35319786--35320060 Score: 394
Period size: 141 Copynumber: 2.0 Consensus size: 141
35319776 TACTTAGAGA
* * *
35319786 GAGAAAAACAGAAGCAGCTCTCTTCTTGCCTTTCTCTATGGCATGCTCGAGAAGAATTTGGGGCT
1 GAGAAAAACAGAAGCAGCTCTCTTCTTGCCTTTCTATATGGCATGCCCGAGAAGAATTTAGGGCT
*
35319851 AGTGGCCGAAGGCGAAGCAAGCAATAAAGGCT-GAGTGAGAAG-GACTGTCGGGTTGAGTGAGGA
66 AGTGGCCGAAGGCGAAGCAAGCAATAAAGGCTGGA-TGAGAAGAG-CTGTCGGGTTGAGTGAAGA
35319914 AGGTTTTAGAACG
129 AGGTTTTAGAACG
** *
35319927 GAGAAAAACA-AAGGTGACTCTCTTCTTGCCTTTCTATATGGCATGCCCGAGAAGAGTTTAGGGC
1 GAGAAAAACAGAAGCAG-CTCTCTTCTTGCCTTTCTATATGGCATGCCCGAGAAGAATTTAGGGC
* * ** *
35319991 TAGTGGCCGGAGGTGAAGCAAGCAATGGAGGCTGGATGAGAAGAGTTGTCGGGTTGAGTGAAGAA
65 TAGTGGCCGAAGGCGAAGCAAGCAATAAAGGCTGGATGAGAAGAGCTGTCGGGTTGAGTGAAGAA
35320056 GGTTT
130 GGTTT
35320061 CAAAATGATA
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
140 4 0.03
141 112 0.94
142 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.23
Consensus pattern (141 bp):
GAGAAAAACAGAAGCAGCTCTCTTCTTGCCTTTCTATATGGCATGCCCGAGAAGAATTTAGGGCT
AGTGGCCGAAGGCGAAGCAAGCAATAAAGGCTGGATGAGAAGAGCTGTCGGGTTGAGTGAAGAAG
GTTTTAGAACG
Found at i:35325627 original size:26 final size:28
Alignment explanation
Indices: 35325595--35325653 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
35325585 TGGGTTAATG
35325595 ATTTAATATAAATAA-AAATAT-ATATT
1 ATTTAATATAAATAATAAATATGATATT
* *
35325621 ATTTAATATATATAATTAATATGATATT
1 ATTTAATATAAATAATAAATATGATATT
*
35325649 TTTTA
1 ATTTA
35325654 TAATATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 14 0.50
27 5 0.18
28 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTTAATATAAATAATAAATATGATATT
Found at i:35325628 original size:14 final size:14
Alignment explanation
Indices: 35325611--35325653 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
35325601 TATAAATAAA
35325611 AATATATATTATTT
1 AATATATATTATTT
*
35325625 AATATATA-TAATT
1 AATATATATTATTT
*
35325638 AATATGATATTTTTT
1 AATAT-ATATTATTT
35325653 A
1 A
35325654 TAATATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.38
14 11 0.46
15 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
AATATATATTATTT
Found at i:35332088 original size:24 final size:24
Alignment explanation
Indices: 35332038--35332089 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
35332028 AATCAAAGTC
* *
35332038 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
35332062 AAATATATTATACTCATAAATATT
1 AAATATATTATACTAATAAATACT
35332086 AAAT
1 AAAT
35332090 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:35336453 original size:24 final size:24
Alignment explanation
Indices: 35336426--35336477 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
35336416 AATCAAAGTC
* *
35336426 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
35336450 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
35336474 AAAT
1 AAAT
35336478 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:35341104 original size:85 final size:83
Alignment explanation
Indices: 35340926--35341085 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 83
35340916 CAAAATTTCC
* * ** *
35340926 CTATATTTTATGCTTAGAGTTCTATTCAACTAATAAATTTATTTTAAAATTAGCACAACTTTTTT
1 CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAA--TTTTT
* *
35340991 TTTACGTCAAACTTTTTTTT
64 TTTACATCAAACTTTTTTGT
* *
35341011 CTATATTTTATACTTAGAATTCTATTCAAGTAATAAACATACTTTAAAATTAGTACAA-TTTTTT
1 CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAATTTTTTT
*
35341075 TACATTAAACT
66 TACATCAAACT
35341086 AATTATTAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
82 15 0.23
85 51 0.77
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (83 bp):
CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAATTTTTTT
TACATCAAACTTTTTTGT
Found at i:35343515 original size:163 final size:164
Alignment explanation
Indices: 35343144--35343531 Score: 625
Period size: 164 Copynumber: 2.4 Consensus size: 164
35343134 GGTTTGTAGA
*
35343144 GAAAATTGAAAAGAAATACGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
1 GAAAATTGAAAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
* *
35343209 AATTGTGCTAGGAAATGGTTTATTAGTTGGACTTTGGGAAAAAAATAAGGGTTGTTTGAAAACTA
66 AATTGTGCTAGGAAATGGTTTATTAGTTGCACTTTGGAAAAAAAATAAGGGTTGTTTGAAAACTA
* *
35343274 ACCTTTTTTGGCCGAAATTAAGGAAAAATTAAAG
131 ACCTCTTTTGGCCGAAATCAAGGAAAAATTAAAG
*
35343308 GAAAATTGATAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
1 GAAAATTGAAAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
* * * * *
35343373 ATTTGTGCTAGGGAGTGGTTTATTAGTTGCACTTTGGAAAAAAAATAAGGGTTGTTTGACAATTA
66 AATTGTGCTAGGAAATGGTTTATTAGTTGCACTTTGGAAAAAAAATAAGGGTTGTTTGAAAACTA
* * *
35343438 ACC-CTTTTGGCCGGAATCAATGAAAAATTAAGG
131 ACCTCTTTTGGCCGAAATCAAGGAAAAATTAAAG
* *
35343471 GAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAGTTTGGGTTAGAATCAAATAGGAAA
1 GAAAATTGAAAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAA
35343532 CTTTAAGAGA
Statistics
Matches: 208, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
163 84 0.40
164 124 0.60
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (164 bp):
GAAAATTGAAAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
AATTGTGCTAGGAAATGGTTTATTAGTTGCACTTTGGAAAAAAAATAAGGGTTGTTTGAAAACTA
ACCTCTTTTGGCCGAAATCAAGGAAAAATTAAAG
Found at i:35348509 original size:6 final size:6
Alignment explanation
Indices: 35348498--35348525 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35348488 GAAGTTTGGG
35348498 TTCACT TTCACT TTCACT TTCACT TTCA
1 TTCACT TTCACT TTCACT TTCACT TTCA
35348526 ACTTGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCACT
Found at i:35352415 original size:45 final size:45
Alignment explanation
Indices: 35352342--35352451 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
35352332 CCTAAACAGT
* * * *
35352342 AATCAGTAACGGTAGCAGTAACAATATTCAACACACAAAGTGTCA
1 AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
* * *
35352387 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
35352432 AATCGGTAACAGTAACAGTA
1 AATCGGTAACAGTAACAGTA
35352452 GTCGGCATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (45 bp):
AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
Found at i:35354334 original size:11 final size:11
Alignment explanation
Indices: 35354320--35354346 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35354310 AATAATGCTA
35354320 AAAATCTTAAT
1 AAAATCTTAAT
35354331 AAAATCTTAAT
1 AAAATCTTAAT
35354342 AAAAT
1 AAAAT
35354347 AACATTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATCTTAAT
Found at i:35356766 original size:3 final size:3
Alignment explanation
Indices: 35356758--35356801 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
35356748 TTGCACCATG
35356758 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35356802 GTCATTCACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35359574 original size:24 final size:24
Alignment explanation
Indices: 35359526--35359572 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
35359516 ACTGGTCATA
*
35359526 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
35359550 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
35359573 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:35359984 original size:35 final size:35
Alignment explanation
Indices: 35359938--35360008 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
35359928 CCGTTATGAG
35359938 TATGTTTCTTAGATTATTATGTAATTGTCACGACA
1 TATGTTTCTTAGATTATTATGTAATTGTCACGACA
35359973 TATGTTTCTTAGATTATTATGTAATTGTCACGACA
1 TATGTTTCTTAGATTATTATGTAATTGTCACGACA
35360008 T
1 T
35360009 TACTCATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.46
Consensus pattern (35 bp):
TATGTTTCTTAGATTATTATGTAATTGTCACGACA
Found at i:35369253 original size:27 final size:27
Alignment explanation
Indices: 35369214--35369325 Score: 161
Period size: 27 Copynumber: 4.1 Consensus size: 27
35369204 AGAGGTCGAT
* * * *
35369214 AAATGACCAAAATACCCCTACAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
35369241 AAATGATCGAAATACCCCCGTAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
35369268 AAATGATTGAAATACCCCCGTAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
35369295 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
35369322 AAAT
1 AAAT
35369326 AACTGTTATA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:35369354 original size:54 final size:54
Alignment explanation
Indices: 35369235--35369339 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
35369225 ATACCCCTAC
* * *
35369235 AGGGTAAAATGATCGAAATACCCCCGTAGGGTAAAATGATTGAAATACCCCCGT
1 AGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCGT
**
35369289 AGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACTGTTATACCCC
1 AGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACTGAAATACCCC
35369340 TAGGAGATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (54 bp):
AGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATAACTGAAATACCCCCGT
Found at i:35372338 original size:26 final size:26
Alignment explanation
Indices: 35372298--35372356 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
35372288 AGCTTGACAG
*
35372298 AATCATTTTAGACCAATCTAGTCCTT
1 AATCATTTTACACCAATCTAGTCCTT
35372324 AATCATTTTACACCAATCTAGTCCTT
1 AATCATTTTACACCAATCTAGTCCTT
35372350 AATCATT
1 AATCATT
35372357 AACATGTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (26 bp):
AATCATTTTACACCAATCTAGTCCTT
Found at i:35375966 original size:20 final size:20
Alignment explanation
Indices: 35375928--35375966 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35375918 AATCAGTTAC
**
35375928 CCGAAATCCCTTATTTTTTT
1 CCGAAATCCCTTAAATTTTT
35375948 CCGAAATCCCTTAAATTTT
1 CCGAAATCCCTTAAATTTT
35375967 CCCCGATCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (20 bp):
CCGAAATCCCTTAAATTTTT
Found at i:35375972 original size:21 final size:20
Alignment explanation
Indices: 35375927--35375972 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
35375917 AAATCAGTTA
* *
35375927 CCCGAAATCCCTTATTTTTT
1 CCCGAAATCCCTTAATTTTC
*
35375947 TCCGAAATCCCTTAAATTTTC
1 CCCGAAATCCCTT-AATTTTC
35375968 CCCGA
1 CCCGA
35375973 TCGTCTGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.37
Consensus pattern (20 bp):
CCCGAAATCCCTTAATTTTC
Found at i:35379884 original size:100 final size:103
Alignment explanation
Indices: 35379767--35380001 Score: 305
Period size: 100 Copynumber: 2.3 Consensus size: 103
35379757 CAATGTCATA
* * * *
35379767 TCCCAGATATGGTCTTACATGGGACTTCTCATATCGGTGCCCATGCCATGTCCCAAACATGGTCT
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACCAATGCCATGTCCCAAACATGGTCT
* *
35379832 TACGGGGGACCTCTC-ATCTC-GG-TGCCAACGCCATG
66 TACAGGGGACCTCTCAATCTCAGGATACCAACGCCATG
* *
35379867 TCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTACCAATGCCATGTCCCAAACATGGTCT
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACCAATGCCATGTCCCAAACATGGTCT
* * *
35379932 TACATGTGACCTCTCATGATCTCAAGGATACCAATGCCATG
66 TACAGGGGACCTCTCA--ATCTC-AGGATACCAACGCCATG
* *
35379973 TCCTAGACATGGTCTTACATGGGATCTCT
1 TCCCAGACATGGTCTTACATGGGACCTCT
35380002 TTACCCAAAT
Statistics
Matches: 116, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
100 71 0.61
103 5 0.04
105 2 0.02
106 38 0.33
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (103 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACCAATGCCATGTCCCAAACATGGTCT
TACAGGGGACCTCTCAATCTCAGGATACCAACGCCATG
Found at i:35379966 original size:56 final size:51
Alignment explanation
Indices: 35379756--35380001 Score: 273
Period size: 50 Copynumber: 4.8 Consensus size: 51
35379746 TCATGTACTG
* * * * * * *
35379756 CCAATGTCATATCCCAGATATGGTCTTACATGGGACTTCTC-ATATCGGTG
1 CCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCGATCTCGGTA
* ** *
35379806 CCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTC-ATCTCGGTG
1 CCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCGATCTCGGTA
* *
35379856 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCG-TCTCGGTA
1 CCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCGATCTCGGTA
*
35379906 CCAATGCCATGTCCCAAACATGGTCTTACATGTGACCTCTCATGATCTCAAGGATA
1 CCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTC--GATCTC--GG-TA
* * *
35379962 CCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 CCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
35380002 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
50 122 0.73
52 1 0.01
53 4 0.02
55 2 0.01
56 38 0.23
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (51 bp):
CCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCGATCTCGGTA
Found at i:35381151 original size:13 final size:13
Alignment explanation
Indices: 35381115--35381151 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
35381105 AATTAATACA
35381115 TTGTTATAATTATT
1 TTGTTATAA-TATT
35381129 TT-TTAT-ATATT
1 TTGTTATAATATT
35381140 TTGTTATAATAT
1 TTGTTATAATAT
35381152 ATGCGAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.29
12 5 0.24
13 8 0.38
14 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (13 bp):
TTGTTATAATATT
Found at i:35381493 original size:51 final size:50
Alignment explanation
Indices: 35381417--35381607 Score: 215
Period size: 51 Copynumber: 3.8 Consensus size: 50
35381407 TGTCTGCGAA
35381417 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGTAAATAAC-GGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGG-AAA-AACTGGT
* * ***
35381468 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGAATCGGAAGGCCTTGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGAAAAAC-TGGT
* * * * * *
35381519 CACGTGTGTAGTACTATGTGTAGGCTACTACGTG-AACCGAAAAGCTTGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGAAAAAC-TGGT
* *
35381569 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCG
35381608 AATGATAATA
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 45 0.38
51 74 0.62
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGAAAAACTGGT
Found at i:35384593 original size:50 final size:50
Alignment explanation
Indices: 35384492--35384606 Score: 140
Period size: 50 Copynumber: 2.3 Consensus size: 50
35384482 TACGAGCACT
* * ***
35384492 TAACGAGAAGCTCATGTGAGTTGTATAACGGGAAGCTCATGTGAGCCGTA
1 TAACGAGAAGCTCATGTGAGCTCTATAACGGGAAGCTCATCCAAGCCGTA
* * **
35384542 TAACGGGAAGCTCATGTGAGCTCTATAACGGGAAGCTTATCCAAGTTGTA
1 TAACGAGAAGCTCATGTGAGCTCTATAACGGGAAGCTCATCCAAGCCGTA
*
35384592 TAACAAGAAGCTCAT
1 TAACGAGAAGCTCAT
35384607 AAGAGCCATA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (50 bp):
TAACGAGAAGCTCATGTGAGCTCTATAACGGGAAGCTCATCCAAGCCGTA
Found at i:35384595 original size:25 final size:25
Alignment explanation
Indices: 35384492--35384578 Score: 138
Period size: 25 Copynumber: 3.5 Consensus size: 25
35384482 TACGAGCACT
* *
35384492 TAACGAGAAGCTCATGTGAGTTGTA
1 TAACGGGAAGCTCATGTGAGCTGTA
*
35384517 TAACGGGAAGCTCATGTGAGCCGTA
1 TAACGGGAAGCTCATGTGAGCTGTA
*
35384542 TAACGGGAAGCTCATGTGAGCTCTA
1 TAACGGGAAGCTCATGTGAGCTGTA
35384567 TAACGGGAAGCT
1 TAACGGGAAGCT
35384579 TATCCAAGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (25 bp):
TAACGGGAAGCTCATGTGAGCTGTA
Found at i:35385698 original size:20 final size:20
Alignment explanation
Indices: 35385670--35385712 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
35385660 TCTAAAAAAC
35385670 ATAAAAATTACAAGAAACAA
1 ATAAAAATTACAAGAAACAA
* ** *
35385690 ATAAGAATTGGACGAAACAA
1 ATAAAAATTACAAGAAACAA
35385710 ATA
1 ATA
35385713 TGCAAGACCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.12, T:0.16
Consensus pattern (20 bp):
ATAAAAATTACAAGAAACAA
Found at i:35386987 original size:18 final size:18
Alignment explanation
Indices: 35386954--35386988 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35386944 GTGAGGAGAA
* *
35386954 TGCTGATACAGGTGGTGG
1 TGCTGATAAAGATGGTGG
35386972 TGCTGATAAAGATGGTG
1 TGCTGATAAAGATGGTG
35386989 ATGGAGATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.09, G:0.40, T:0.29
Consensus pattern (18 bp):
TGCTGATAAAGATGGTGG
Found at i:35402421 original size:24 final size:24
Alignment explanation
Indices: 35402389--35402439 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
35402379 ATTGTTTGGT
*
35402389 TTGATTTGGTTTAATTGAATTAAA
1 TTGAATTGGTTTAATTGAATTAAA
*
35402413 TTGAATTGGTTTCATTGAATTAAA
1 TTGAATTGGTTTAATTGAATTAAA
35402437 TTG
1 TTG
35402440 TACGAGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (24 bp):
TTGAATTGGTTTAATTGAATTAAA
Found at i:35409628 original size:16 final size:16
Alignment explanation
Indices: 35409589--35409628 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
35409579 AGTTAATATG
35409589 GTTAAAAAAATAAAAT
1 GTTAAAAAAATAAAAT
* *
35409605 TTTAAAAAAATTAAAT
1 GTTAAAAAAATAAAAT
35409621 GTTGAAAA
1 GTT-AAAA
35409629 CTTTCATCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
GTTAAAAAAATAAAAT
Found at i:35410545 original size:296 final size:293
Alignment explanation
Indices: 35410079--35410646 Score: 682
Period size: 296 Copynumber: 1.9 Consensus size: 293
35410069 AAGTACCACG
* * *
35410079 GAATAATATAACTTATTTTAAATACGAAAGGACACTGAAGTAATTTCCCCAATCTAGTTTGGTGC
1 GAATAATATAACTTATTTTAAATACGAAAGGACACTAAAGTAATTTCCCCAAGCGAGTTTGGTGC
* ***
35410144 CTAATTAACTAGTGAGACAAACTCAATCAAACACTTAAATAGTAGTATAGATGTACAATTGATGT
66 CTAATTAACTAGTGACACAAACTCAATCAAACACTTAAATAGTAGTATAGAAAAACAATTGATGT
* **
35410209 AAATAATAAAATGTGCATATTAAAACTAAAATGCATAAAAAAATAGTAAAATAAAACTTTGATTG
131 AAATAATAAAATGTGCATATTAAAACTAAAATGCAT-AAAAAAT--CAAAATAAAACTTTGACCG
* *
35410274 AGTGTTAAATTTAA-AGTTTTAT-TAATGCAATTGGCATTG-GTTCAAATATCACCATATGT-AT
193 AGTGATAAATTTAATA-TTTT-TCTAATACAATTGGCA-TGCGTTCAAATATCACCATAT-TCAT
*
35410335 ATTTTTATTGATTTTTTAAATAAAAAGACTAAAGTACTTTT
254 ATTTTTATT-AGTTTTTAAATAAAAAGACTAAAGTACTTTT
* *
35410376 GAATAATATAACTTATTTTAAATACGAAAGGACA-TCAAAGTAATTTTCCTAAGCGAG-TTGGTG
1 GAATAATATAACTTATTTTAAATACGAAAGGACACT-AAAGTAATTTCCCCAAGCGAGTTTGGTG
* ** * * * * ** * *
35410439 CTTGGTTGATTCGTGACACCAACTCCGTCTAATACTTAAATAGTAGTATAGAAAAACAATTGATG
65 CCTAATTAACTAGTGACACAAACTCAATCAAACACTTAAATAGTAGTATAGAAAAACAATTGATG
** * * * * *
35410504 -AAAGTTTTAGAATGTGTATATTAAAACTAAAATGTATAAAAAATCAAAATAAAGCTTTGGCCGA
130 TAAA-TAATAAAATGTGCATATTAAAACTAAAATGCATAAAAAATCAAAATAAAACTTTGACCGA
* *
35410568 GTGATAAATTTAATATTTTTCTAATACAATTGGCATGCGTTCAAATATTATCATATTCATATTTT
194 GTGATAAATTTAATATTTTTCTAATACAATTGGCATGCGTTCAAATATCACCATATTCATATTTT
35410633 TATTAGTTTTTAAA
259 TATTAGTTTTTAAA
35410647 ATAGTAGGTC
Statistics
Matches: 230, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
292 13 0.06
293 71 0.31
294 1 0.00
295 10 0.04
296 85 0.37
297 50 0.22
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (293 bp):
GAATAATATAACTTATTTTAAATACGAAAGGACACTAAAGTAATTTCCCCAAGCGAGTTTGGTGC
CTAATTAACTAGTGACACAAACTCAATCAAACACTTAAATAGTAGTATAGAAAAACAATTGATGT
AAATAATAAAATGTGCATATTAAAACTAAAATGCATAAAAAATCAAAATAAAACTTTGACCGAGT
GATAAATTTAATATTTTTCTAATACAATTGGCATGCGTTCAAATATCACCATATTCATATTTTTA
TTAGTTTTTAAATAAAAAGACTAAAGTACTTTT
Found at i:35411718 original size:3 final size:3
Alignment explanation
Indices: 35411710--35411736 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35411700 CAAGAACAAA
35411710 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
35411737 GAAAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35412700 original size:19 final size:19
Alignment explanation
Indices: 35412653--35412712 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 19
35412643 AAATTAAATC
*
35412653 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
35412673 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
35412695 TCTAAGATTACATATCAT
1 TCTAAGATTACATATCAT
35412713 TGAAGATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 17 0.50
22 7 0.21
23 10 0.29
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:35412720 original size:17 final size:19
Alignment explanation
Indices: 35412679--35412721 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
35412669 CATATCTTCT
* *
35412679 AAGATTGCATATCATATCT
1 AAGATTACATATCATATCG
35412698 AAGATTACATATCAT-T-G
1 AAGATTACATATCATATCG
35412715 AAGATTA
1 AAGATTA
35412722 TGTTTCCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 14 0.64
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (19 bp):
AAGATTACATATCATATCG
Found at i:35413320 original size:44 final size:44
Alignment explanation
Indices: 35413268--35413375 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 44
35413258 GATCTATTCT
* * *
35413268 ACTGCAACTTTAGAGAGATAAGATCTATTA-TTTTAATCCGCTTC
1 ACTGCAACTTTAGAGAGATAAGAT-TACTAGCTTTAATCCGCTCC
** * * *
35413312 ACTGCAACTCCAGGGAGATAGGATTACTAGCTTTAATCTGCTCC
1 ACTGCAACTTTAGAGAGATAAGATTACTAGCTTTAATCCGCTCC
35413356 ACTGCAAC-TTAGAGAGATAA
1 ACTGCAACTTTAGAGAGATAA
35413376 AATATGTAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 12 0.24
44 39 0.76
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (44 bp):
ACTGCAACTTTAGAGAGATAAGATTACTAGCTTTAATCCGCTCC
Found at i:35413417 original size:44 final size:44
Alignment explanation
Indices: 35413369--35413596 Score: 165
Period size: 44 Copynumber: 5.2 Consensus size: 44
35413359 GCAACTTAGA
* * *
35413369 GAGATAAAATATGTAATTTTCAACCTACTCCACTGCTGCTCATG
1 GAGATAAGATATGTAATCTTCAACCTACTCCACTGCTGCTCAGG
** * * * * * *
35413413 GAGATAAGACTA-GT-GGCTTAAATCTGCTTCC-CTACTACCTTAGG
1 GAGATAAGA-TATGTAATCTTCAACCTAC-TCCACTGCT-GCTCAGG
* * ** * * * * *
35413457 AAGATAAGATTTGTCGTCTTCGATCTACTCCACTACTGCTTAAG
1 GAGATAAGATATGTAATCTTCAACCTACTCCACTGCTGCTCAGG
* * *
35413501 GAGATAAGATCTGTAATTTTCAACCTACTCCTCTGCTGCTCAGG
1 GAGATAAGATATGTAATCTTCAACCTACTCCACTGCTGCTCAGG
* * **
35413545 GAGATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGG
1 GAGATAAGATATGTAATCTTCAACCTACTCCACTGCTGCTCAGG
35413589 GAGATAAG
1 GAGATAAG
35413597 GCTAGTGGCT
Statistics
Matches: 143, Mismatches: 35, Indels: 12
0.75 0.18 0.06
Matches are distributed among these distances:
43 12 0.08
44 115 0.80
45 16 0.11
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
GAGATAAGATATGTAATCTTCAACCTACTCCACTGCTGCTCAGG
Found at i:35413485 original size:88 final size:87
Alignment explanation
Indices: 35413393--35413685 Score: 259
Period size: 88 Copynumber: 3.3 Consensus size: 87
35413383 AATTTTCAAC
* *
35413393 CTACTCCACTGCTGCTCATGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACCTTAGGA
1 CTACTCCACTACTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACCTTAGGA
*
35413458 AGATAAGATTTGTCGTCTTCGAT
66 AGATAAGATTT-ACGTCTTCGAT
* * *** * * * * * *
35413481 CTACTCCACTACTGCTTAAGGAGATAAGATCT-GTAATTTTCAACCTAC-TCCTCTGCT-GCTCA
1 CTACTCCACTACTGCTCAGGGAGATAAGA-CTAGT-GGCTTAAATCTGCTTCC-CTACTACCTTA
* * * * * *
35413543 GGGAGATAAGGTCTACAATCTTCAAC
63 GGAAGATAAGATTTAC-GTCTTCGAT
* * * * *
35413569 CTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATATGCTTCCCTATTACCTTGGGA
1 CTACTCCACTACTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACCTTAGGA
*
35413634 AGATAAGATTCACCGTCTTCGAT
66 AGATAAGATTTA-CGTCTTCGAT
* *
35413657 CTGCTCCACTACTGCTTAGGGAGATAAGA
1 CTACTCCACTACTGCTCAGGGAGATAAGA
35413686 TCTGTAATTT
Statistics
Matches: 151, Mismatches: 46, Indels: 16
0.71 0.22 0.08
Matches are distributed among these distances:
87 12 0.08
88 125 0.83
89 14 0.09
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (87 bp):
CTACTCCACTACTGCTCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACCTTAGGA
AGATAAGATTTACGTCTTCGAT
Found at i:35413577 original size:176 final size:176
Alignment explanation
Indices: 35413387--35413752 Score: 565
Period size: 176 Copynumber: 2.1 Consensus size: 176
35413377 ATATGTAATT
* *
35413387 TTCAACCTACTCCACTGCTGCTCATGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTACC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATATGCTTCCCTACTACC
***
35413452 TTAGGAAGATAAGATTTGTCGTCTTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAA
66 TTAGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAA
* * *
35413517 TTTTCAACCTACTCC-TCTGCTGCTCAGGGAGATAAGGTCT-ACAATC
131 TTTTCAACCTACCCCAT-TGCTGCTCAGAGAGAT-AGGACTCACAATC
* *
35413563 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATATGCTTCCCTATTACC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATATGCTTCCCTACTACC
* * *
35413628 TTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
66 TTAGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAA
*
35413693 TTTTTAACCTACCCCATTGCTGCTCAGAGAGATAGGACTCACAATC
131 TTTTCAACCTACCCCATTGCTGCTCAGAGAGATAGGACTCACAATC
*
35413739 TTCAACCTATTCCA
1 TTCAACCTACTCCA
35413753 TTGTTGACCA
Statistics
Matches: 173, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
175 5 0.03
176 167 0.97
177 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (176 bp):
TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTAGTGGCTTAAATATGCTTCCCTACTACC
TTAGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAA
TTTTCAACCTACCCCATTGCTGCTCAGAGAGATAGGACTCACAATC
Found at i:35413741 original size:88 final size:88
Alignment explanation
Indices: 35413473--35413741 Score: 217
Period size: 88 Copynumber: 3.1 Consensus size: 88
35413463 AGATTTGTCG
* * *
35413473 TCTTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTCAACCTACTCC-TCTGC
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACCCCAT-TGC
*
35413537 TGCTCAGGGAGATAAGGTCT-ACAA
65 TGCTCAGGGAGAT-AGGACTCACAA
* * * * * ** ** ** * *
35413561 TCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAG-GCTAGTGGCTTAAATATGCTTCCCTATT
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCT-GT-AATT-TTTAACCTACCCCATT
* * * * **
35413625 AC--CT-TGGGAAGATAAGATTCACCG
63 GCTGCTCAGGG-AGATAGGACTCACAA
*
35413649 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACCCCATTGCT
1 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACCCCATTGCT
*
35413714 GCTCAGAGAGATAGGACTCACAA
66 GCTCAGGGAGATAGGACTCACAA
35413737 TCTTC
1 TCTTC
35413742 AACCTATTCC
Statistics
Matches: 127, Mismatches: 44, Indels: 20
0.66 0.23 0.10
Matches are distributed among these distances:
86 11 0.09
87 10 0.08
88 92 0.72
89 6 0.05
90 7 0.06
91 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (88 bp):
TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACCCCATTGCT
GCTCAGGGAGATAGGACTCACAA
Found at i:35415125 original size:14 final size:15
Alignment explanation
Indices: 35415106--35415138 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
35415096 TGGCCTCTCA
*
35415106 TTTTTCCTTTTC-TT
1 TTTTTCATTTTCATT
35415120 TTTTTCATTTTCATT
1 TTTTTCATTTTCATT
35415135 TTTT
1 TTTT
35415139 AATTTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCATTTTCATT
Found at i:35415164 original size:20 final size:20
Alignment explanation
Indices: 35415121--35415158 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35415111 CCTTTTCTTT
35415121 TTTTCATTTTCATTTTTTAA
1 TTTTCATTTTCATTTTTTAA
* *
35415141 TTTTGATTTTGATTTTTT
1 TTTTCATTTTCATTTTTT
35415159 TCTTTTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTCATTTTCATTTTTTAA
Found at i:35421096 original size:23 final size:22
Alignment explanation
Indices: 35421069--35421113 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
35421059 AAATTAAGTC
35421069 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
35421092 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
35421114 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:35421116 original size:19 final size:19
Alignment explanation
Indices: 35421092--35421128 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
35421082 AATCATATCT
35421092 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
35421111 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
35421129 TGAAGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:35421136 original size:17 final size:19
Alignment explanation
Indices: 35421095--35421136 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
35421085 CATATCTTCT
*
35421095 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
35421114 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
35421131 AAGATT
1 AAGATT
35421137 ATGTTTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 1 0.05
19 15 0.68
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:35424835 original size:19 final size:19
Alignment explanation
Indices: 35424799--35424837 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
35424789 TTCCGTCTCG
*
35424799 TTTTATTTTATAGCAAATT
1 TTTTATTTTATAGAAAATT
* *
35424818 TTTTATTTTTTTGAAAATT
1 TTTTATTTTATAGAAAATT
35424837 T
1 T
35424838 AACTAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTATTTTATAGAAAATT
Found at i:35424881 original size:31 final size:31
Alignment explanation
Indices: 35424844--35424902 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
35424834 ATTTAACTAA
35424844 ATTTGTTATTATTATTTTCAATTTATATGTT
1 ATTTGTTATTATTATTTTCAATTTATATGTT
35424875 ATTTGTTATTATTATTTTCAATTTATAT
1 ATTTGTTATTATTATTTTCAATTTATAT
35424903 ATATTTTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.64
Consensus pattern (31 bp):
ATTTGTTATTATTATTTTCAATTTATATGTT
Found at i:35424900 original size:17 final size:17
Alignment explanation
Indices: 35424849--35424909 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
35424839 ACTAAATTTG
35424849 TTATTATTATTTTCAAT
1 TTATTATTATTTTCAAT
* *
35424866 TTATATGTTA-TTT---G
1 TTAT-TATTATTTTCAAT
35424880 TTATTATTATTTTCAAT
1 TTATTATTATTTTCAAT
35424897 TTA-TATATATTTT
1 TTATTAT-TATTTT
35424910 GGAGTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 4 0.12
14 7 0.21
16 3 0.09
17 16 0.47
18 4 0.12
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATTATTATTTTCAAT
Found at i:35424960 original size:22 final size:21
Alignment explanation
Indices: 35424935--35424982 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
35424925 TATATTTCTG
*
35424935 TTTAACAATTTTTTTAAAAAAT
1 TTTAA-AATTTTTTAAAAAAAT
**
35424957 TTTAAGGTTTTTTAAAAAAAT
1 TTTAAAATTTTTTAAAAAAAT
35424978 TTTAA
1 TTTAA
35424983 GAATGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (21 bp):
TTTAAAATTTTTTAAAAAAAT
Found at i:35424969 original size:21 final size:21
Alignment explanation
Indices: 35424943--35424983 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
35424933 TGTTTAACAA
*
35424943 TTTTTTTAAAAAATTTTAAGG
1 TTTTTTAAAAAAATTTTAAGG
35424964 TTTTTTAAAAAAATTTTAAG
1 TTTTTTAAAAAAATTTTAAG
35424984 AATGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTTTTAAAAAAATTTTAAGG
Found at i:35424992 original size:21 final size:21
Alignment explanation
Indices: 35424950--35424993 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
35424940 CAATTTTTTT
** **
35424950 AAAAAATTTTAAGGTTTTTTA
1 AAAAAATTTTAAGAATGATTA
35424971 AAAAAATTTTAAGAATGATTA
1 AAAAAATTTTAAGAATGATTA
35424992 AA
1 AA
35424994 GATGAATCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (21 bp):
AAAAAATTTTAAGAATGATTA
Found at i:35435331 original size:51 final size:51
Alignment explanation
Indices: 35435235--35435331 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 51
35435225 CAGTGTATAA
* * **
35435235 CGTAAGACCATAGATGAAAGATGCTATATCAGCCTGATATGAGGTACGTAG
1 CGTAAGACCATAGATGAAAGATGCTATAGCAGCATGATACAAGGTACGTAG
* * * *
35435286 CGTAAGACCATGGATGAAAGATGTTATGGCAGCATGGTACAAGGTA
1 CGTAAGACCATAGATGAAAGATGCTATAGCAGCATGATACAAGGTA
35435332 AAAGGTATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (51 bp):
CGTAAGACCATAGATGAAAGATGCTATAGCAGCATGATACAAGGTACGTAG
Found at i:35435348 original size:58 final size:58
Alignment explanation
Indices: 35435283--35435434 Score: 178
Period size: 58 Copynumber: 2.6 Consensus size: 58
35435273 ATGAGGTACG
* **
35435283 TAGCGTAAGACCATGGATGAAAGATGTTATGGCAGCATGGTACAAGGTAAAAGGTATA
1 TAGCGTAAGACCATGGATGAAAGATGCTATGGCAGCACAGTACAAGGTAAAAGGTATA
* ** * *
35435341 TAGCGTAAGACCATGGAAGAAAGACACTATGGCGGCACAGTACAAGGTATAAGGTATA
1 TAGCGTAAGACCATGGATGAAAGATGCTATGGCAGCACAGTACAAGGTAAAAGGTATA
** ** * *
35435399 CGGTATAAGACCATAGATGAAAGATGCTATGACAGC
1 TAGCGTAAGACCATGGATGAAAGATGCTATGGCAGC
35435435 CAGGCATGAT
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 76 1.00
ACGTcount: A:0.39, C:0.14, G:0.28, T:0.20
Consensus pattern (58 bp):
TAGCGTAAGACCATGGATGAAAGATGCTATGGCAGCACAGTACAAGGTAAAAGGTATA
Found at i:35435521 original size:32 final size:32
Alignment explanation
Indices: 35435484--35435545 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
35435474 GCATCCACAG
35435484 AGATAAGCCTGCTGAGACAGTAAACACAGAAT
1 AGATAAGCCTGCTGAGACAGTAAACACAGAAT
* *
35435516 AGATAAGTCTGCTGGGACAGTAAACACAGA
1 AGATAAGCCTGCTGAGACAGTAAACACAGA
35435546 TGAATTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (32 bp):
AGATAAGCCTGCTGAGACAGTAAACACAGAAT
Found at i:35449639 original size:12 final size:11
Alignment explanation
Indices: 35449620--35449649 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
35449610 CTGTGTGTTC
35449620 TTTATTTTTAT
1 TTTATTTTTAT
35449631 TTCTATTTTTAT
1 TT-TATTTTTAT
35449643 TTTATTT
1 TTTATTT
35449650 GCGATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:35451409 original size:21 final size:22
Alignment explanation
Indices: 35451382--35451435 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
35451372 AACAGCGGTG
*
35451382 GCAGTGAGATTAG-TTACTGTA
1 GCAGTGAGATTAGAATACTGTA
*
35451403 GCGGTGAGATT-GAATACTGTA
1 GCAGTGAGATTAGAATACTGTA
35451424 GCAGTGAGATTA
1 GCAGTGAGATTA
35451436 AAACAGCGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (22 bp):
GCAGTGAGATTAGAATACTGTA
Done.