Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006159.1 Hibiscus syriacus cultivar Beakdansim tig00014632_pilon, whole genome shotgun sequence
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: 201630
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2524 original size:20 final size:20
Alignment explanation
Indices: 2499--2548 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2489 AGAGAGTAAG
2499 GCAGCTTTGTTGCGTTGAGA
1 GCAGCTTTGTTGCGTTGAGA
2519 GCAGCTTTGTTGCGTTGAGA
1 GCAGCTTTGTTGCGTTGAGA
2539 GCAGCTTTGT
1 GCAGCTTTGT
2549 CTCTAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.16, G:0.34, T:0.36
Consensus pattern (20 bp):
GCAGCTTTGTTGCGTTGAGA
Found at i:3140 original size:200 final size:204
Alignment explanation
Indices: 2761--3147 Score: 665
Period size: 200 Copynumber: 1.9 Consensus size: 204
2751 AATTAATATT
2761 AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTAATG
1 AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTAATG
2826 TTTTTTTTTATAAAATAGTTTAATCCCTTAATCACTCAGATTTGAATGTATTATACTTCTTTTAC
66 -TTTTTTTTATAAAATAGTTTAATCCCTTAATCACTCAGATTTGAATGTATTATACTTCTTTTAC
*
2891 AAGTTACATTTTCGCTGTCATTTTTTCATCTACCAAAGTCTTTAAAATTCTTTAAAACATTTGAT
130 AAGTTACATTTTCGCTGTCATTTTTTCATATACCAAAGTCTTTAAAATTCTTTAAAACATTTGAT
2956 TTATAATTTA
195 TTATAATTTA
*
2966 AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTCATG
1 AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTAATG
* * * *
3031 -TTTTTTT-T-AAATTGTTTAAT-CCTTGATCACTTAGATTTGAATGTATTATATTTCTTTTACA
66 TTTTTTTTATAAAATAGTTTAATCCCTTAATCACTCAGATTTGAATGTATTATACTTCTTTTACA
* *
3092 AGTTACATTTTTGCTGTCATTTTTTCATATATCAAAGTCTTTAAAATTCTTTAAAA
131 AGTTACATTTTCGCTGTCATTTTTTCATATACCAAAGTCTTTAAAATTCTTTAAAA
3148 GTGTAACGAT
Statistics
Matches: 174, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
200 91 0.52
201 11 0.06
202 1 0.01
203 7 0.04
205 64 0.37
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (204 bp):
AATTAATTTAATTATTTAAATGTTTGTTAATATTTTAATAAAATAAAGAATTTAATCCCTTAATG
TTTTTTTTATAAAATAGTTTAATCCCTTAATCACTCAGATTTGAATGTATTATACTTCTTTTACA
AGTTACATTTTCGCTGTCATTTTTTCATATACCAAAGTCTTTAAAATTCTTTAAAACATTTGATT
TATAATTTA
Found at i:14434 original size:34 final size:34
Alignment explanation
Indices: 14373--14439 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 34
14363 TTCTTGAGAG
14373 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTTATC-AGAGAGAAGTTGTTA
14407 TTGTTTTCTCCTTGTTATATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-TATCAGAGAGAAGTTGT
14440 AATTCCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 20 0.67
35 6 0.20
36 4 0.13
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTTATCAGAGAGAAGTTGTTA
Found at i:17736 original size:27 final size:27
Alignment explanation
Indices: 17695--17818 Score: 221
Period size: 27 Copynumber: 4.6 Consensus size: 27
17685 AAATGGTCTT
*
17695 TTTATCTAAAAGATAACTATCTTATCTC
1 TTTAT-TAAGAGATAACTATCTTATCTC
17723 TTTATTAAGAGATAACTATCTTATCTC
1 TTTATTAAGAGATAACTATCTTATCTC
*
17750 TTTATTAAGAGATAACTATCTTATCTA
1 TTTATTAAGAGATAACTATCTTATCTC
17777 TTTATTAAGAGATAACTATCTTATCTC
1 TTTATTAAGAGATAACTATCTTATCTC
17804 TTTATTAAGAGATAA
1 TTTATTAAGAGATAA
17819 GCAGGTGAGG
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 88 0.95
28 5 0.05
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (27 bp):
TTTATTAAGAGATAACTATCTTATCTC
Found at i:19683 original size:22 final size:22
Alignment explanation
Indices: 19653--19703 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
19643 CGGGACATAT
* *
19653 ACAATATACAGAGGTCCTTCAGG
1 ACAA-ATACAGAAGTCATTCAGG
* *
19676 ACAAATACATAAGTCATTCGGG
1 ACAAATACAGAAGTCATTCAGG
19698 ACAAAT
1 ACAAAT
19704 TTCACATGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (22 bp):
ACAAATACAGAAGTCATTCAGG
Found at i:20438 original size:21 final size:21
Alignment explanation
Indices: 20412--20552 Score: 219
Period size: 21 Copynumber: 6.7 Consensus size: 21
20402 AGATGAAGTT
*
20412 ACTGTAGCAGTACATCGATAC
1 ACTGTAGCAGTGCATCGATAC
*
20433 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
*
20454 ACTGTAGCAGTGCATTGATAC
1 ACTGTAGCAGTGCATCGATAC
* *
20475 ACTGTAGCAGTGTATCAATAC
1 ACTGTAGCAGTGCATCGATAC
*
20496 ACTGTAGCAGTGCATCAATAC
1 ACTGTAGCAGTGCATCGATAC
*
20517 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
20538 ACTGTAGCAGTGCAT
1 ACTGTAGCAGTGCAT
20553 TAGTACACTA
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 110 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:26883 original size:23 final size:23
Alignment explanation
Indices: 26857--26926 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
26847 GTCACCACAG
*
26857 CTCGTATAATTGCACCGAAGTGC
1 CTCGTAGAATTGCACCGAAGTGC
26880 CTCGTAGAATTGCACC-AGAGTGC
1 CTCGTAGAATTGCACCGA-AGTGC
* *
26903 CGCGTAGAATTGCACCGTAGTGC
1 CTCGTAGAATTGCACCGAAGTGC
26926 C
1 C
26927 ATATAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 1 0.02
23 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.23
Consensus pattern (23 bp):
CTCGTAGAATTGCACCGAAGTGC
Found at i:27114 original size:103 final size:103
Alignment explanation
Indices: 26943--27160 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
26933 TAATGTCCAT
*
26943 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
27008 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
27046 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
27111 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
27149 AAGGACCACATA
1 AAGGACCACATA
27161 GACCCTCGAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:28826 original size:12 final size:12
Alignment explanation
Indices: 28809--28852 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
28799 TTGACAAGTC
28809 AAATTCAACTTA
1 AAATTCAACTTA
28821 AAATTCAACTT-
1 AAATTCAACTTA
*
28832 --A-TCAACTTT
1 AAATTCAACTTA
28841 AAATTCAACTTA
1 AAATTCAACTTA
28853 TCAACTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
8 7 0.26
9 1 0.04
11 1 0.04
12 18 0.67
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTCAACTTA
Found at i:28860 original size:20 final size:20
Alignment explanation
Indices: 28813--28861 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
28803 CAAGTCAAAT
*
28813 TCAACTTAAAATTCAACTTA
1 TCAACTTTAAATTCAACTTA
28833 TCAACTTTAAATTCAACTTA
1 TCAACTTTAAATTCAACTTA
28853 TCAACTTTA
1 TCAACTTTA
28862 TTTCAAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAACTTTAAATTCAACTTA
Found at i:31857 original size:23 final size:23
Alignment explanation
Indices: 31830--31883 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
31820 TGTGAGTCTA
*
31830 TAGTGCCTCGTAGAATTGCACCAG
1 TAGTGCCACGTAGAATTGCACC-G
31854 -AGTGCCACGTAGAATTGCACCG
1 TAGTGCCACGTAGAATTGCACCG
31876 TAGTGCCA
1 TAGTGCCA
31884 TATAATAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (23 bp):
TAGTGCCACGTAGAATTGCACCG
Found at i:32070 original size:103 final size:103
Alignment explanation
Indices: 31903--32116 Score: 374
Period size: 103 Copynumber: 2.1 Consensus size: 103
31893 GTCCATAAGA
* *
31903 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
*
31968 TCACACATGTTCCAAAGAATACATATATGTCCCGAATG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
* * *
32006 ACCACATATCATTCTTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
32071 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
32109 ACCACATA
1 ACCACATA
32117 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
Found at i:32257 original size:24 final size:24
Alignment explanation
Indices: 32229--32281 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
32219 TGTAGTTCTT
* * *
32229 TCACATAGCTCATCGTCATATAAA
1 TCACATAGCCCATAGACATATAAA
*
32253 TCACATATCCCATAGACATATAAA
1 TCACATAGCCCATAGACATATAAA
32277 -CACAT
1 TCACAT
32282 GGTTCACTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (24 bp):
TCACATAGCCCATAGACATATAAA
Found at i:36639 original size:16 final size:17
Alignment explanation
Indices: 36618--36659 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
36608 ATTATATATA
36618 TATATATATAATATT-T
1 TATATATATAATATTAT
* *
36634 TATATATTTTATATTAAT
1 TATATATATAATATT-AT
36652 TATATATA
1 TATATATA
36660 ATACAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
18 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATATATAATATTAT
Found at i:47423 original size:3 final size:3
Alignment explanation
Indices: 47415--47447 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
47405 TTTGAGACTT
47415 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
47448 TTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:47977 original size:17 final size:17
Alignment explanation
Indices: 47955--47991 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
47945 CTAATGTTGT
47955 AGTTTGGTTGTTGATGC
1 AGTTTGGTTGTTGATGC
47972 AGTTTGGTTGTTGATGC
1 AGTTTGGTTGTTGATGC
47989 AGT
1 AGT
47992 CAGCTCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.14, C:0.05, G:0.35, T:0.46
Consensus pattern (17 bp):
AGTTTGGTTGTTGATGC
Found at i:49792 original size:87 final size:87
Alignment explanation
Indices: 49646--49809 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 87
49636 TGGAAATATT
* * **
49646 TTTCAGAAAATATAATTTAATATTAGGTTAAACGACCTCACATTATACGACAAGCGAGGTACACT
1 TTTCAGAAAATACAAATTAATATTAAATTAAACGACCTCACATTATACGACAAGCGAGGTACA-T
*
49711 -AGAACCTGAAACGCTTCACCAA
65 GAGAAACTGAAACGCTTCACCAA
* ** *
49733 TTTCAGATAATACAAATTAATATTAAATTAAACGACCTTGCATTATCCGACACA-CGAGGTACAT
1 TTTCAGAAAATACAAATTAATATTAAATTAAACGACCTCACATTATACGACA-AGCGAGGTACAT
49797 GAGAAACTGAAAC
65 GAGAAACTGAAAC
49810 ATCCACCAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.02
87 64 0.97
88 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (87 bp):
TTTCAGAAAATACAAATTAATATTAAATTAAACGACCTCACATTATACGACAAGCGAGGTACATG
AGAAACTGAAACGCTTCACCAA
Found at i:52103 original size:20 final size:20
Alignment explanation
Indices: 52056--52383 Score: 289
Period size: 20 Copynumber: 16.2 Consensus size: 20
52046 AATGACCAAC
52056 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
52075 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
52095 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
52115 AAGATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
52135 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
52157 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
52177 GAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
52197 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
52217 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
52237 AGAATCGCAACGCGATCCAG
1 AAAATCGCAACGCGATTCAG
52257 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
52277 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
52299 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
52319 AAAATCGCAACGAGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
52339 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
52359 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
52379 AAAAT
1 AAAAT
52384 GAGTAAATTC
Statistics
Matches: 258, Mismatches: 33, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
18 1 0.00
19 24 0.09
20 187 0.72
21 8 0.03
22 36 0.14
23 2 0.01
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:52207 original size:40 final size:40
Alignment explanation
Indices: 52056--52383 Score: 371
Period size: 40 Copynumber: 8.1 Consensus size: 40
52046 AATGACCAAC
* *
52056 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTAAG
* * **** *
52095 AAAAGCGCAACGTTGAAAAGAAG-ATCGCAACGCGATTCAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGATTAAG
52135 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG
* *
52177 GAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
**
52217 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
***
52257 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGAT-TAAG
* *
52298 AAGAATCGCAACGCGATT-CAGAAAATCGCAACGAGATTCCAAG
1 AA-AATCGCAACGCGATTCCA-AGAATCGCAACGCGATT--AAG
52341 --AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
52379 AAAAT
1 AAAAT
52384 GAGTAAATTC
Statistics
Matches: 245, Mismatches: 30, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
38 3 0.01
39 13 0.05
40 160 0.65
41 10 0.04
42 59 0.24
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:52233 original size:102 final size:101
Alignment explanation
Indices: 52113--52383 Score: 390
Period size: 102 Copynumber: 2.7 Consensus size: 101
52103 AACGTTGAAA
* *
52113 AGAAGATCGCAACGCGATT-CAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AGAAAATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG
*
52177 GAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATTT
63 GAAATCGCAACGCGACTTCCAAGAATCGCAACGCGATTC
*
52215 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGA-TCCAGAAAATCGCAACGCGATTCCAA-
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCA-AGAATCGCAACGCGATT--AAG
52278 G-AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
63 GAAATCGCAACGCGA-CTTCCAAGAATCGCAACGCGATTC
* *
52317 AGAAAATCGCAACGAGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAA
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGGAA
52382 AT
66 AT
52384 GAGTAAATTC
Statistics
Matches: 153, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
99 4 0.03
100 31 0.20
101 1 0.01
102 111 0.73
103 6 0.04
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.15
Consensus pattern (101 bp):
AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGGAA
ATCGCAACGCGACTTCCAAGAATCGCAACGCGATTC
Found at i:52490 original size:6 final size:6
Alignment explanation
Indices: 52479--52510 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
52469 GACACGTATT
52479 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
52511 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:53038 original size:6 final size:6
Alignment explanation
Indices: 53007--53089 Score: 138
Period size: 6 Copynumber: 14.5 Consensus size: 6
52997 TCTCGTCTCG
53007 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
53051 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
53090 AATACGTGTC
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 20 0.26
6 57 0.74
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:53241 original size:20 final size:20
Alignment explanation
Indices: 53193--53538 Score: 285
Period size: 20 Copynumber: 16.9 Consensus size: 20
53183 TCATTTTCTT
*
53193 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCGA
**
53214 AGATCGCGTTGCGATTTTATA
1 A-ATCGCGTTGCGATTTTCGA
*
53235 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCGA
*
53256 AGATCGCGTTGCGATTCTT-GG
1 A-ATCGCGTTGCGATT-TTCGA
53277 AATCGCGTTGCGATTTTCTG-
1 AATCGCGTTGCGATTTTC-GA
* *
53297 GATCGCGTTGCGATTCTT-GG
1 AATCGCGTTGCGATT-TTCGA
*
53317 AATCGCGTTGCGATTTTCTA
1 AATCGCGTTGCGATTTTCGA
*
53337 AATCGCGTTGCGATTCTT-GG
1 AATCGCGTTGCGATT-TTCGA
*
53357 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCGA
53378 AGATCGCGTTGCGATTTTCTG-
1 A-ATCGCGTTGCGATTTTC-GA
*
53399 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCGA
*
53420 AGATCGCGTTGCGATTTTATG-
1 A-ATCGCGTTGCGATTTT-CGA
* *
53441 AATCGCATTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCGA
*
53462 AGATCGCGTTGCGATTTTC-T
1 A-ATCGCGTTGCGATTTTCGA
** * * *
53482 TTTCAACGTTGCGCTTTTCTA
1 AATC-GCGTTGCGATTTTCGA
*
53503 AATCGCGTTGCGGTTTT-GA
1 AATCGCGTTGCGATTTTCGA
*
53522 TATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
53539 GTTGGTCATT
Statistics
Matches: 272, Mismatches: 32, Indels: 44
0.78 0.09 0.13
Matches are distributed among these distances:
19 23 0.08
20 141 0.52
21 34 0.12
22 74 0.27
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTTTCGA
Found at i:53244 original size:42 final size:41
Alignment explanation
Indices: 53193--53479 Score: 404
Period size: 42 Copynumber: 7.0 Consensus size: 41
53183 TCATTTTCTT
**
53193 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATA
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTT-GG
53235 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTGG
*
53277 AATCGCGTTGCGATT-TTCTG--GATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATT-TTGG
**
53317 AATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTGG
*
53357 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTG
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTT-GG
*
53399 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATG
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTT-GG
*
53441 AATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTT
53480 CTTTTCAACG
Statistics
Matches: 228, Mismatches: 10, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
40 71 0.31
41 8 0.04
42 147 0.64
43 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (41 bp):
AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTGG
Found at i:53302 original size:62 final size:61
Alignment explanation
Indices: 53194--53479 Score: 325
Period size: 62 Copynumber: 4.6 Consensus size: 61
53184 CATTTTCTTA
**
53194 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATAAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTT-TGGATCGCGTTGCGATTCTTGGAAG
53258 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGGATCGCGTTGCGATTCTTGG-A-
1 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTT-TGGATCGCGTTGCGATTCTTGGAAG
** *
53318 ATCGCGTTGCGATT-TTCTAAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTTGG-ATCGCGTTGCGATTCTTGGAAG
* * *
53380 ATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TT--ATG
1 ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATT-TTTG--GATCGCGTTGCGATTCTTGGAAG
*
53441 AATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTT
1 -ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTT
53480 CTTTTCAACG
Statistics
Matches: 199, Mismatches: 12, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
59 5 0.03
60 49 0.25
61 4 0.02
62 83 0.42
63 10 0.05
64 47 0.24
65 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (61 bp):
ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTTGGATCGCGTTGCGATTCTTGGAAG
Found at i:53494 original size:42 final size:41
Alignment explanation
Indices: 53192--53536 Score: 391
Period size: 42 Copynumber: 8.4 Consensus size: 41
53182 CTCATTTTCT
*
53192 TAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTA
1 TAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTG
53233 TAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTG
1 T-AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTG
* *
53276 GAATCGCGTTGCGATT-TTCTG--GATCGCGTTGCGATTCTTG
1 TAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATT-TTG
* **
53316 GAATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTTG
1 TAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTG
* *
53356 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTC
1 TAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTG
*
53397 TGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTA
1 T-AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTG
* *
53439 TGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTC
1 T-AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTG
** * * ** *
53481 TTTTCAACGTTGCGCTT-TTCTAA-ATCGCGTTGCGGTTTTG
1 TAATC-GCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTG
53521 -ATATCGCGTTGCGATT
1 TA-ATCGCGTTGCGATT
53537 TTGTTGGTCA
Statistics
Matches: 269, Mismatches: 25, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
39 9 0.03
40 88 0.33
41 15 0.06
42 155 0.58
43 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (41 bp):
TAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTG
Found at i:53494 original size:62 final size:58
Alignment explanation
Indices: 53193--53538 Score: 302
Period size: 62 Copynumber: 5.6 Consensus size: 58
53183 TCATTTTCTT
*
53193 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATAAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATT-TTGG-A-ATCGCGTTGCGATTTTCT-AATCGCGTTGCGATTCTTGG
*
53255 AAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGGATCGCGTTGCGATTCTTGG
1 -A-ATCGCGTTGCGATT-TTGGAATCGCGTTGCGATTTTCT-AATCGCGTTGCGATTCTTGG
** **
53317 AATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTT-GGAATCGCGTTGCGATT-TTCTAATCGCGTTGCGATTCTTGG
* ** *
53377 AAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTATG
1 -A-ATCGCGTTGCGATTTT-GGAATCGCGTTGCGATT-TT-CTA-ATCGCGTTGCGATTCTT-GG
* ** * * **
53441 AATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTTTCAACGTTGCGCTT-TTCTA
1 AATCGCGTTGCGATT-TTGG-A-ATCGCGTTGCGATTTTCTAATC-GCGTTGCGATTCTT-GG
*
53503 AATCGCGTTGCGGTTTT-GATATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTTGGA-ATCGCGTTGCGATTTT
53539 GTTGGTCATT
Statistics
Matches: 247, Mismatches: 24, Indels: 28
0.83 0.08 0.09
Matches are distributed among these distances:
59 19 0.08
60 49 0.20
61 8 0.03
62 111 0.45
63 12 0.05
64 48 0.19
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (58 bp):
AATCGCGTTGCGATTTTGGAATCGCGTTGCGATTTTCTAATCGCGTTGCGATTCTTGG
Found at i:55141 original size:202 final size:202
Alignment explanation
Indices: 54744--55150 Score: 477
Period size: 202 Copynumber: 2.0 Consensus size: 202
54734 ACAAGTGTTT
* * * *
54744 ATAGGCACATTCGAGAGGTATTTCCATGTAGTTAATTTAAAAATTTTCGTAATTTATATATGATT
1 ATAGGCACAATCGAGAGGTATTTCCAGGTAGTTAATTAAAAAAATTTCGTAATTTATATATGATT
* **
54809 AGAGGCGTAGTATTGAAATTTATTTTTCAATTAAGGCCAATATCAACACATACAAGATATTGTAA
66 AGAGGCGTAGTATTGAAACTTATTTTTCAACCAAGGCCAATATCAACACATACAAGATATTGTAA
* *
54874 GCATGTTAAAAATCGCATTGAAAATGGTTCCAAAGTTTATTTTGTGCTTGAAGAAAAAACTAAAA
131 GCAGGTTAAAAATCGCATTGAAAATGGTTCCAAAGTTGATTTTGTGCTTGAAGAAAAAACTAAAA
54939 -TGATTTG
196 TTGA-TTG
* *
54946 ATAGGCACAATCGAGAGGT-TTCTTCGGGTAGTTAATCTAAAAAAATTT-GTAATTTATA-A-GA
1 ATAGGCACAATCGAGAGGTATT-TCCAGGTAGTTAAT-TAAAAAAATTTCGTAATTTATATATGA
* * ** * *
55007 TTAGGGGCGTAGTATT-ATAACTTATTTTTCAACCGAGGGTAATATCGATACATACAAGATATTG
64 TTAGAGGCGTAGTATTGA-AACTTATTTTTCAACCAAGGCCAATATCAACACATACAAGATATTG
* * ** * * **
55071 TAAGCGGGTTAAAAAAT-GACGTTGAAAATGGTTCTGAAGCTTGGTTTTGTTCTTGAAGAAAATG
128 TAAGCAGGTT-AAAAATCG-CATTGAAAATGGTTCCAAAG-TTGATTTTGTGCTTGAAGAAAAAA
55135 CTAAAATTGATTG
190 CTAAAATTGATTG
55148 ATA
1 ATA
55151 AACATGTTCG
Statistics
Matches: 173, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
199 1 0.01
200 64 0.37
201 26 0.15
202 70 0.40
203 12 0.07
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (202 bp):
ATAGGCACAATCGAGAGGTATTTCCAGGTAGTTAATTAAAAAAATTTCGTAATTTATATATGATT
AGAGGCGTAGTATTGAAACTTATTTTTCAACCAAGGCCAATATCAACACATACAAGATATTGTAA
GCAGGTTAAAAATCGCATTGAAAATGGTTCCAAAGTTGATTTTGTGCTTGAAGAAAAAACTAAAA
TTGATTG
Found at i:56149 original size:2 final size:2
Alignment explanation
Indices: 56142--56173 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
56132 CCGCCCCGAT
56142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56174 TTTATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56180 original size:32 final size:32
Alignment explanation
Indices: 56141--56208 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
56131 CCCGCCCCGA
56141 TTATA-TATATATATATATATATATATATAATATT
1 TTATATTATATATAT-TA-AT-TATATATAATATT
* *
56175 TTATATTTTTTATATTAATTATATATAATATT
1 TTATATTATATATATTAATTATATATAATATT
56207 TT
1 TT
56209 CGAGTTCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 15 0.48
33 2 0.06
34 7 0.23
35 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TTATATTATATATATTAATTATATATAATATT
Found at i:58196 original size:21 final size:21
Alignment explanation
Indices: 58167--58219 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
58157 ATTCTGACTA
58167 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
58188 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
58209 TCGCAATGCGA
1 TCGCATTGCGA
58220 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:58251 original size:20 final size:20
Alignment explanation
Indices: 58228--58294 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
58218 GAATACGTAA
* *
58228 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
58248 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
* *
58268 ATCGTAATGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
58288 ATCGCAA
1 ATCGCAA
58295 TACTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:59384 original size:15 final size:15
Alignment explanation
Indices: 59364--59394 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59354 ATATAACCCT
59364 AAAGAAGAAAAAGAA
1 AAAGAAGAAAAAGAA
*
59379 AAAGAAGAAGAAGAA
1 AAAGAAGAAAAAGAA
59394 A
1 A
59395 TCCCCAAAGA
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAAAAGAA
Found at i:61654 original size:20 final size:19
Alignment explanation
Indices: 61629--61697 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 19
61619 CAACGCGGAA
61629 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
* *
61649 ATCGCAATAGGGAAATGACT
1 ATCGCAA-CGCGAAATGACT
61669 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
61689 ATCGCAACG
1 ATCGCAACG
61698 AGAGAATTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 38 0.88
21 4 0.09
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:61803 original size:19 final size:20
Alignment explanation
Indices: 61790--61830 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
61780 GTTGCGATTT
61790 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCATTGCGATAG
*
61809 TCATTTCCGCGTTGCGATAG
1 TCATTTCCGCATTGCGATAG
61829 TC
1 TC
61831 TGTTTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (20 bp):
TCATTTCCGCATTGCGATAG
Found at i:61825 original size:20 final size:19
Alignment explanation
Indices: 61779--61830 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
61769 GCAATTCTCT
**
61779 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
61798 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
61818 CGTTGCGATAGTC
1 CGTTGCGATAGTC
61831 TGTTTTGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:61951 original size:14 final size:14
Alignment explanation
Indices: 61932--61968 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
61922 CATCAATTAA
61932 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
61946 ACAAATCATCTTTT
1 ACAAATCAACATTT
61960 ACAAATCAA
1 ACAAATCAA
61969 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:63456 original size:42 final size:42
Alignment explanation
Indices: 63358--63460 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 42
63348 TTCGGAGGGA
* * * *
63358 CCTCTTCAACGATGACAGTGGCCTCTTGAACAGTGGGAGGGG
1 CCTCTTAAACGATGATAGGGGCCTCTTGAACAGTGGGAGAGG
* * **
63400 ACTCTTGAGGGATGATAGGGGCCTCTTGAAC-GATAGGG-GAGG
1 CCTCTTAAACGATGATAGGGGCCTCTTGAACAG-T-GGGAGAGG
63442 CCTCTTAAACGATGATAGG
1 CCTCTTAAACGATGATAGG
63461 TGAGTCGGGC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
41 1 0.02
42 44 0.92
43 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.22
Consensus pattern (42 bp):
CCTCTTAAACGATGATAGGGGCCTCTTGAACAGTGGGAGAGG
Found at i:63964 original size:20 final size:20
Alignment explanation
Indices: 63941--64009 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
63931 GAAACTTAAA
63941 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
63961 ATCGCAACGC-AAAAGTGACT
1 ATCGCAACGCGAAAA-TGACT
* **
63981 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
64001 ATCGCAACG
1 ATCGCAACG
64010 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.09
20 37 0.86
21 2 0.05
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:64079 original size:20 final size:20
Alignment explanation
Indices: 64054--64100 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
64044 GATTCTTTCG
64054 TTGCGATAGTCATTTTCCCA
1 TTGCGATAGTCATTTTCCCA
* *
64074 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCCCA
64094 TTGCGAT
1 TTGCGAT
64101 TTTGTTGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCCCA
Found at i:64131 original size:33 final size:34
Alignment explanation
Indices: 64074--64167 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
64064 CATTTTCCCA
* * *
64074 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
** *
64108 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
64141 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
64168 AGTTATTTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:64164 original size:20 final size:20
Alignment explanation
Indices: 64139--64190 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
64129 GCGATTCTCT
64139 CGTTGCGATAGTCATTT-TCG
1 CGTTGCGATAGTCATTTGT-G
*
64159 CGTTGCGATAGTTATTTGTG
1 CGTTGCGATAGTCATTTGTG
*
64179 CATTGCGATAGT
1 CGTTGCGATAGT
64191 AAACTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTGTG
Found at i:64185 original size:87 final size:87
Alignment explanation
Indices: 64022--64187 Score: 262
Period size: 87 Copynumber: 1.9 Consensus size: 87
64012 AGAATCGCAA
*
64022 TGCGATTTTCATTTCGCATTACGATTCTTTCGTTGCGATAGTCATTTTCCCATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTTTCCCATTGCGATAGTCAT
*
64087 TTTCGCGTTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
* * * *
64109 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTTAT
1 TGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTTTCCCATTGCGATAGTCAT
64174 TTGT-GCATTGCGAT
66 TT-TCGCATTGCGAT
64188 AGTAAACTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
87 71 0.99
88 1 0.01
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTTTCCCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:65881 original size:20 final size:20
Alignment explanation
Indices: 65858--65961 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 20
65848 CTGAAACTTT
*
65858 AAATCGCAACACGAAAATGA
1 AAATCGCAACGCGAAAATGA
* * *
65878 AAATCGCAACACAAAAATTA
1 AAATCGCAACGCGAAAATGA
** **
65898 CTATCGCAACGCGAATTTGA
1 AAATCGCAACGCGAAAATGA
** **
65918 CTATCGCAACGCGAATTTGA
1 AAATCGCAACGCGAAAATGA
*
65938 ATATCGCAACGCG-AAATGA
1 AAATCGCAACGCGAAAATGA
65957 AAATC
1 AAATC
65962 ATAACGACAG
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 8 0.11
20 63 0.89
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGAAAATGA
Found at i:66278 original size:22 final size:22
Alignment explanation
Indices: 66253--66314 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
66243 TGACCGTGAA
*
66253 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
* *
66275 TGATATCGTTGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
66297 TGATTTCGTCGGAGATGG
1 TGATTTCGTCGGAGATGG
66315 GGATGGATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.23, C:0.13, G:0.37, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:66540 original size:20 final size:20
Alignment explanation
Indices: 66516--66584 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
66506 CGATAGTCAG
* *
66516 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTACGATTTACGT
*
66536 CTTCGCATTACGATTTACGT
1 ATTCGCATTACGATTTACGT
*
66556 ATTCGCATTACGATTTACTT
1 ATTCGCATTACGATTTACGT
66576 ATTCGCATT
1 ATTCGCATT
66585 GCGAAATAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (20 bp):
ATTCGCATTACGATTTACGT
Found at i:66951 original size:11 final size:11
Alignment explanation
Indices: 66911--66975 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
66901 AAAATTTAGG
66911 AGCTCGATTGA
1 AGCTCGATTGA
*
66922 AGCTCTAGACTCG-
1 AGCTC--GA-TTGA
66935 AGCTCGATTGA
1 AGCTCGATTGA
66946 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
66958 AGCTCGATTCA
1 AGCTCGATTGA
66969 AGCTCGA
1 AGCTCGA
66976 ACTCAAAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 4 0.09
11 21 0.48
12 7 0.16
13 10 0.23
14 2 0.05
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:66964 original size:23 final size:22
Alignment explanation
Indices: 66910--66975 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
66900 AAAAATTTAG
66910 GAGCTCGATTGAAGCTCTAGACTC
1 GAGCTCGATTGAAGCTC--GACTC
* *
66934 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGA-CTC
*
66957 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTGAAGCTCGA
66976 ACTCAAAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.05
23 19 0.50
24 17 0.45
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (22 bp):
GAGCTCGATTGAAGCTCGACTC
Found at i:69121 original size:16 final size:17
Alignment explanation
Indices: 69100--69135 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
69090 AGATGATAGT
69100 TTTAGTTAAT-ATTAGG
1 TTTAGTTAATAATTAGG
*
69116 TTTAGTTTATAATTAGG
1 TTTAGTTAATAATTAGG
69133 TTT
1 TTT
69136 TTATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (17 bp):
TTTAGTTAATAATTAGG
Found at i:77932 original size:21 final size:21
Alignment explanation
Indices: 77906--77950 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
77896 GATTTCTGGG
* *
77906 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
77927 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
77948 CAA
1 CAA
77951 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:79324 original size:32 final size:31
Alignment explanation
Indices: 79282--79409 Score: 136
Period size: 31 Copynumber: 4.1 Consensus size: 31
79272 AGAGTCGAGG
79282 GTTTACCTATGTTCTACAGAACATATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
*
79313 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACAGA-ACATATGGACA
*
79345 GTATACCTATGTTCTA-AGGAACATATGGACA
1 GTTTACCTATGTTCTACA-GAACATATGGACA
* * * * *
79376 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
79407 GTT
1 GTT
79410 ACCGAGGATC
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
31 53 0.65
32 28 0.35
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACAGAACATATGGACA
Found at i:79429 original size:30 final size:30
Alignment explanation
Indices: 79368--79464 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
79358 CTAAGGAACA
* * ***
79368 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
79399 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * *
79429 TCTGGATAGTTACCGAGGATCTTTATAACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
79459 TCTGGA
1 TATGGA
79465 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 49 0.84
31 9 0.16
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:79465 original size:30 final size:30
Alignment explanation
Indices: 79396--79467 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
79386 GTTCTTCGGG
* * *
79396 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
79426 ACCTCTGGATAGTTACCGAGGATCTTTATA
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
79456 ACCTCTGGATAG
1 ACCTCTGGATAG
79468 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATA
Found at i:82781 original size:21 final size:21
Alignment explanation
Indices: 82755--82799 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
82745 GATTTCTGGG
* *
82755 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
82776 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
82797 CAA
1 CAA
82800 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:84174 original size:32 final size:31
Alignment explanation
Indices: 84132--84259 Score: 136
Period size: 31 Copynumber: 4.1 Consensus size: 31
84122 AGAGTCGAGG
84132 GTTTACCTATGTTCTACAGAACATATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
*
84163 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACAGA-ACATATGGACA
*
84195 GTATACCTATGTTCTA-AGGAACATATGGACA
1 GTTTACCTATGTTCTACA-GAACATATGGACA
* * * * *
84226 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
84257 GTT
1 GTT
84260 ACCGAGGATC
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
31 53 0.65
32 28 0.35
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACAGAACATATGGACA
Found at i:84279 original size:30 final size:30
Alignment explanation
Indices: 84218--84314 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
84208 CTAAGGAACA
* * ***
84218 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
84249 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * *
84279 TCTGGATAGTTACCGAGGATCTTTATAACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
84309 TCTGGA
1 TATGGA
84315 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 49 0.84
31 9 0.16
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:84315 original size:30 final size:30
Alignment explanation
Indices: 84246--84317 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
84236 GTTCTTCGGG
* * *
84246 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
84276 ACCTCTGGATAGTTACCGAGGATCTTTATA
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
84306 ACCTCTGGATAG
1 ACCTCTGGATAG
84318 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATA
Found at i:99147 original size:22 final size:25
Alignment explanation
Indices: 99120--99170 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
99110 ATTTATTTTA
* *
99120 ATTTTTTTTTAAAAATAAA-A-AAT
1 ATTTTTATTAAAAAATAAATATAAT
99143 ATTTTTATTAAAAAATAAATATAAT
1 ATTTTTATTAAAAAATAAATATAAT
99168 ATT
1 ATT
99171 GAAAAAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.71
24 1 0.04
25 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTTTATTAAAAAATAAATATAAT
Found at i:99657 original size:22 final size:23
Alignment explanation
Indices: 99631--99678 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
99621 CCAAAAATTG
99631 AAAAATATAAC-GATAGAAAC-TT
1 AAAAATATAACTGATA-AAACGTT
99653 AAAAATATAACTGATAAAACGTT
1 AAAAATATAACTGATAAAACGTT
99676 AAA
1 AAA
99679 CACTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (23 bp):
AAAAATATAACTGATAAAACGTT
Found at i:100160 original size:24 final size:26
Alignment explanation
Indices: 100133--100180 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
100123 CATAGAATTA
100133 TAAATTAATTAAAA-AAAT-TAAAGG
1 TAAATTAATTAAAATAAATGTAAAGG
*
100157 TAAATTATTTAAAATAAATGTAAA
1 TAAATTAATTAAAATAAATGTAAA
100181 TTATACCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 4 0.19
26 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (26 bp):
TAAATTAATTAAAATAAATGTAAAGG
Found at i:100174 original size:20 final size:21
Alignment explanation
Indices: 100146--100184 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
100136 ATTAATTAAA
100146 AAAATTAAAGGTAAATTATTT
1 AAAATTAAAGGTAAATTATTT
*
100167 AAAA-TAAATGTAAATTAT
1 AAAATTAAAGGTAAATTAT
100185 ACCAGTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (21 bp):
AAAATTAAAGGTAAATTATTT
Found at i:101619 original size:2 final size:2
Alignment explanation
Indices: 101612--101658 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
101602 ATAATACTCC
101612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
101653 AT AT AT
1 AT AT AT
101659 GATAGAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:101961 original size:30 final size:28
Alignment explanation
Indices: 101927--101991 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 28
101917 TTTATTTTAA
* * *
101927 ATAATTTACCTTTAATTTTTTTAATAATTT
1 ATAATTTACATTT-ATTCTTTT-AGAATTT
101957 ATAATTATACATTTATTCTTTTAGAATTT
1 ATAATT-TACATTTATTCTTTTAGAATTT
101986 -TAATTT
1 ATAATTT
101992 TTTATGAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.03
28 5 0.16
29 6 0.19
30 13 0.42
31 6 0.19
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (28 bp):
ATAATTTACATTTATTCTTTTAGAATTT
Found at i:102224 original size:13 final size:13
Alignment explanation
Indices: 102199--102243 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
102189 AAATATTATA
102199 AAAAAATATAAAT
1 AAAAAATATAAAT
*
102212 AAAATATATAAAT
1 AAAAAATATAAAT
102225 AACCAAAATATAATAT
1 AA--AAAATATAA-AT
102241 AAA
1 AAA
102244 CTATGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 14 0.52
14 1 0.04
15 8 0.30
16 4 0.15
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATATAAAT
Found at i:111313 original size:21 final size:21
Alignment explanation
Indices: 111278--111332 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
111268 AAATAATAAT
*
111278 AAAATAT-TATTTTTATTCAATA
1 AAAATATATA-TTTAATTCAA-A
*
111300 AAAATATATATTTAATTGAAA
1 AAAATATATATTTAATTCAAA
111321 AAAATAATATAT
1 AAAAT-ATATAT
111333 AGAGGAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 21 0.72
23 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAATATATATTTAATTCAAA
Found at i:111638 original size:7 final size:7
Alignment explanation
Indices: 111626--111658 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
111616 CTTAATTGCG
111626 AAAATTA
1 AAAATTA
111633 AAAATTA
1 AAAATTA
111640 AAAATTA
1 AAAATTA
*
111647 AAATTTA
1 AAAATTA
111654 AAAAT
1 AAAAT
111659 CCAATTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATTA
Found at i:113828 original size:106 final size:106
Alignment explanation
Indices: 113643--114371 Score: 1111
Period size: 106 Copynumber: 6.9 Consensus size: 106
113633 GTACTGTTCC
* ** * * * * *
113643 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* ** * *
113708 CCAGCGGCCCCTTCGTTATGAAGATGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
113749 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
113814 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
113855 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * * * *
113920 TCAGTC-GCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCTT
66 CCAG-CGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTG
* *
113961 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
114026 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
114067 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
114132 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTGTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
114173 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
114238 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
114279 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
** *
114344 CCAGCCATCCCTTCGTTGTGAAGTTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAA
114372 ATCCACTCTC
Statistics
Matches: 576, Mismatches: 43, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
105 2 0.00
106 572 0.99
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:115142 original size:22 final size:22
Alignment explanation
Indices: 115116--115166 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
115106 TTGTGTTTGG
115116 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
115138 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
115160 TCAAAGG
1 TCAAAGG
115167 ATTGATGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:115812 original size:11 final size:10
Alignment explanation
Indices: 115790--115862 Score: 65
Period size: 11 Copynumber: 6.8 Consensus size: 10
115780 TTCTTTTTGA
*
115790 TTTTTGTTCT
1 TTTTTTTTCT
115800 TTCTTTTTTCT
1 TT-TTTTTTCT
*
115811 TTTGTTCTTCT
1 TTT-TTTTTCT
115822 TTTTTTCTTCT
1 TTTTTT-TTCT
*
115833 TTTTTTTGCT
1 TTTTTTTTCT
*
115843 TTTTTGCTTCT
1 TTTTT-TTTCT
115854 TTTCTTTTT
1 TTT-TTTTT
115863 TGTTCTTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
10 13 0.25
11 36 0.71
12 2 0.04
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:115814 original size:26 final size:26
Alignment explanation
Indices: 115777--115873 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 26
115767 TTTTTGTCCC
115777 TTTTTCTTTTTGATTTTTGTTCTTTCT
1 TTTTTC-TTTTGATTTTTGTTCTTTCT
*
115804 TTTTTCTTTTG-TTCTTCT-TTTTTTCT
1 TTTTTCTTTTGATT-TT-TGTTCTTTCT
*
115830 TCTTTT-TTTTGCTTTTTTGCTTCTTTTCT
1 T-TTTTCTTTTG-ATTTTTG-TTC-TTTCT
*
115859 TTTTTGTTCTTGATT
1 TTTTTCTT-TTGATT
115874 AGATCTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
25 2 0.04
26 21 0.37
27 13 0.23
28 8 0.14
29 10 0.18
30 3 0.05
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.77
Consensus pattern (26 bp):
TTTTTCTTTTGATTTTTGTTCTTTCT
Found at i:115832 original size:22 final size:20
Alignment explanation
Indices: 115790--115861 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 20
115780 TTCTTTTTGA
*
115790 TTTTTGTTCTTTCTTTT-TTC
1 TTTTTTTTCTTT-TTTTCTTC
115810 TTTTGTTCTTCTTTTTTTCTTC
1 TTTT-TT-TTCTTTTTTTCTTC
*
115832 TTTTTTTTGCTTTTTTGCTTC
1 TTTTTTTT-CTTTTTTTCTTC
115853 TTTTCTTTT
1 TTTT-TTTT
115862 TTGTTCTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
20 6 0.13
21 22 0.49
22 17 0.38
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTTCTTC
Found at i:116700 original size:105 final size:105
Alignment explanation
Indices: 116518--116724 Score: 414
Period size: 105 Copynumber: 2.0 Consensus size: 105
116508 AGGTCTAATC
116518 TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
1 TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
116583 GAAGAACTAAAGATTAAAATTTGTTCAATTGCTCCACCTT
66 GAAGAACTAAAGATTAAAATTTGTTCAATTGCTCCACCTT
116623 TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
1 TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
116688 GAAGAACTAAAGATTAAAATTTGTTCAATTGCTCCAC
66 GAAGAACTAAAGATTAAAATTTGTTCAATTGCTCCAC
116725 TTTAGAAAGT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (105 bp):
TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
GAAGAACTAAAGATTAAAATTTGTTCAATTGCTCCACCTT
Found at i:118862 original size:7 final size:7
Alignment explanation
Indices: 118850--118888 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
118840 CTTAATTGCG
118850 AAAATTA
1 AAAATTA
118857 AAAATTA
1 AAAATTA
118864 AAAATT-
1 AAAATTA
118870 AAAATTA
1 AAAATTA
*
118877 AAATTTA
1 AAAATTA
118884 AAAAT
1 AAAAT
118889 CCAATTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AAAATTA
Found at i:118866 original size:13 final size:13
Alignment explanation
Indices: 118850--118886 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
118840 CTTAATTGCG
118850 AAAATTAAAAATTA
1 AAAATT-AAAATTA
118864 AAAATTAAAATTA
1 AAAATTAAAATTA
*
118877 AAATTTAAAA
1 AAAATTAAAA
118887 ATCCAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAATTA
Found at i:118873 original size:20 final size:20
Alignment explanation
Indices: 118850--118888 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
118840 CTTAATTGCG
118850 AAAATTAAAAATTAAAAATT
1 AAAATTAAAAATTAAAAATT
*
118870 AAAATTAAAATTTAAAAAT
1 AAAATTAAAAATTAAAAAT
118889 CCAATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTAAAAATTAAAAATT
Found at i:120794 original size:21 final size:20
Alignment explanation
Indices: 120747--120785 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
120737 CCCAAAATCC
**
120747 CTATAATTTTAAATTTTCAA
1 CTATAATTTTAAAAATTCAA
120767 CTATAATTTTAAAAATTCA
1 CTATAATTTTAAAAATTCA
120786 TATTATAATC
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:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
CTATAATTTTAAAAATTCAA
Found at i:127045 original size:105 final size:105
Alignment explanation
Indices: 126863--127175 Score: 563
Period size: 105 Copynumber: 3.0 Consensus size: 105
126853 CAAATCCTGG
* * *
126863 TTGAACCGGCCTTTCTTTTGTCTTTGTGCCAGACATGGTCTTCAAGTCTGCTATCAATAACCAAA
1 TTGAACCGGCCTTTCTTTTGTCTTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
126928 AATATATCTTTTCGATGTGATCAAGTCATCAAACATGGTC
66 AATATATCTTTTCGATGTGATCAAGTCATCAAACATGGTC
*
126968 TTGAACCGGCCTTTCTTTTGTATTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
1 TTGAACCGGCCTTTCTTTTGTCTTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
127033 AATATATCTTTTCGATGTGATCAAGTCATCAAACATGGTC
66 AATATATCTTTTCGATGTGATCAAGTCATCAAACATGGTC
*
127073 TTGAACCGGCCTTTCTTTCGTCTTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
1 TTGAACCGGCCTTTCTTTTGTCTTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
* *
127138 AATATATCTTTTCGATGTGATCGATTCATCAAACATGG
66 AATATATCTTTTCGATGTGATCAAGTCATCAAACATGG
127176 ACAATCTATT
Statistics
Matches: 200, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 200 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (105 bp):
TTGAACCGGCCTTTCTTTTGTCTTTGGGCCAGACATGGTCTTGAAATCTGCTATCAATAACCAAA
AATATATCTTTTCGATGTGATCAAGTCATCAAACATGGTC
Found at i:128630 original size:21 final size:24
Alignment explanation
Indices: 128606--128648 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
128596 TCAAGAGTAA
128606 ATTTATT-TT-TA-AATAATATTT
1 ATTTATTATTATAGAATAATATTT
128627 ATTTATTATTATAGAATAATAT
1 ATTTATTATTATAGAATAATAT
128649 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 2 0.11
24 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTATTATTATAGAATAATATTT
Found at i:128652 original size:2 final size:2
Alignment explanation
Indices: 128645--128680 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
128635 TTATAGAATA
128645 AT AT AT AT 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 AT AT AT AT
128681 TAGGTGGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130021 original size:22 final size:22
Alignment explanation
Indices: 129979--130028 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
129969 TATTTCTTTA
* *
129979 TTATGTATTTGAATCTTATTTT
1 TTATGTATTTGAATCTAATTTG
*
130001 TTATGTATTTTGTATC-AATTTG
1 TTATGTA-TTTGAATCTAATTTG
130023 TTATGT
1 TTATGT
130029 TTCTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (22 bp):
TTATGTATTTGAATCTAATTTG
Found at i:132001 original size:83 final size:82
Alignment explanation
Indices: 131914--132230 Score: 347
Period size: 83 Copynumber: 3.8 Consensus size: 82
131904 AATAGTGATA
* * *
131914 CATCCCATCTGAAATGAAAGGCGTGTTT-TGAGATAATCATTTTCAATTATTATTCAGAGAATAT
1 CATCCCATCTGAAATGAAAGGCGCGTTTCTGGGA-AATCATTTTC-ATTATTATTCAGAGAATCT
*
131978 CTACCGTGTCAGAGTGTTC
64 CTACCATGTCAGAGTGTTC
* * *
131997 CATCCTATCTGAAAT-AAAGACGCGTTTC-GGGAAAGCATTTTCCATTATTATTCAGAGAATCTC
1 CATCCCATCTGAAATGAAAGGCGCGTTTCTGGGAAATCATTTT-CATTATTATTCAGAGAATCTC
** * *
132060 TGTCATGTCATAGTGTCC
65 TACCATGTCAGAGTGTTC
** * * * * *
132078 CATCCCATCT-AAATTGAAAGGCGTATTTCGGGGAAAACTTTTTTCATTATTATTTAAAGAATCT
1 CATCCCATCTGAAA-TGAAAGGCGCGTTTCTGGGAAATC-ATTTTCATTATTATTCAGAGAATCT
*
132142 CTGCCATGTCAGAGTGTTC
64 CTACCATGTCAGAGTGTTC
* *
132161 CATCCCATCTGAAATGAAAGGTGCGTTTCAT-GGAAATCCTTTTCTATTATTATTCAGAGAATCT
1 CATCCCATCTGAAATGAAAGGCGCGTTTC-TGGGAAATCATTTTC-ATTATTATTCAGAGAATCT
132225 CTACCA
64 CTACCA
132231 CTTTACATAA
Statistics
Matches: 194, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
80 3 0.02
81 50 0.26
82 29 0.15
83 105 0.54
84 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (82 bp):
CATCCCATCTGAAATGAAAGGCGCGTTTCTGGGAAATCATTTTCATTATTATTCAGAGAATCTCT
ACCATGTCAGAGTGTTC
Found at i:132098 original size:164 final size:166
Alignment explanation
Indices: 131870--132226 Score: 413
Period size: 164 Copynumber: 2.2 Consensus size: 166
131860 AAGGAACTGT
* * *
131870 TTTTCCATTATTATTCAAAGAATATCTGGATTATAATAGTGATACATCCCATCTGAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCATTATAATAGTGATACATCCCATCTGAAATGAAAGG
* * * * *
131935 CGTGTTT-TGAGATAA-TCATTTTCAATTATTATTCAGAGAATATCTACCGTGTCAGAGTGTTCC
66 CGTATTTCGGAGAAAACT-ATTTTC-ATTATTATTCAAAGAATATCTACCATGTCAGAGTGTTCC
*
131998 ATCCTATCTGAAAT-AAAGACGCGTTTC-GGGAAAGCA
129 ATCCCATCTGAAATGAAAGACGCGTTTCAGGGAAAGCA
* * *
132034 TTTTCCATTATTATTCAGAGAATCTCTGTCA-TGTCATAGTG-TCCCATCCCATCT-AAATTGAA
1 TTTTCCATTATTATTCAGAGAATCTCTG-CATTATAATAGTGAT-ACATCCCATCTGAAA-TGAA
* * * * *
132096 AGGCGTATTTCGGGGAAAACTTTTTTCATTATTATTTAAAGAATCTCTGCCATGTCAGAGTGTTC
63 AGGCGTATTTCGGAGAAAACTATTTTCATTATTATTCAAAGAATATCTACCATGTCAGAGTGTTC
** * * *
132161 CATCCCATCTGAAATGAAAGGTGCGTTTCATGGAAATCC
128 CATCCCATCTGAAATGAAAGACGCGTTTCAGGGAAAGCA
*
132200 TTTTCTATTATTATTCAGAGAATCTCT
1 TTTTCCATTATTATTCAGAGAATCTCT
132227 ACCACTTTAC
Statistics
Matches: 163, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
163 4 0.02
164 104 0.64
165 22 0.13
166 33 0.20
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (166 bp):
TTTTCCATTATTATTCAGAGAATCTCTGCATTATAATAGTGATACATCCCATCTGAAATGAAAGG
CGTATTTCGGAGAAAACTATTTTCATTATTATTCAAAGAATATCTACCATGTCAGAGTGTTCCAT
CCCATCTGAAATGAAAGACGCGTTTCAGGGAAAGCA
Found at i:134066 original size:24 final size:24
Alignment explanation
Indices: 134039--134113 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
134029 TTAATTATAT
134039 TTGTATTTATTTTATTTTGTTTAA
1 TTGTATTTATTTTATTTTGTTTAA
* *
134063 TTGTAATT-TTTTATTATT-TCTTAT
1 TTGTATTTATTTTATT-TTGT-TTAA
* * *
134087 TTAATATTTACTTTATTTTGTTAAA
1 TT-GTATTTATTTTATTTTGTTTAA
134112 TT
1 TT
134114 TGTTAGACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
23 8 0.21
24 14 0.36
25 10 0.26
26 7 0.18
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (24 bp):
TTGTATTTATTTTATTTTGTTTAA
Found at i:148001 original size:42 final size:41
Alignment explanation
Indices: 147955--148280 Score: 293
Period size: 42 Copynumber: 7.7 Consensus size: 41
147945 GAAAATGATT
* *
147955 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGT-ATTATTGAA
1 AAATTA-GGGCTTCAATTATAAAAGTAAAAAGTGA-GATTGAA
* *
147997 AAATTAGGGATCTCAATTAT-AAAGTTAAAAAGTGAGATTAAA
1 AAATTAGGGCT-TCAATTATAAAAG-TAAAAAGTGAGATTGAA
*
148039 AAATTCAGGGTCTT-AATT-TTAAAGTAAAAAGTGAGATTGAA
1 AAATT-AGGG-CTTCAATTATAAAAGTAAAAAGTGAGATTGAA
* * *
148080 AATATTTAAGGGCTTAAATTATATAAGTAAAAAGTGAGATCGAA
1 AA-A-TT-AGGGCTTCAATTATAAAAGTAAAAAGTGAGATTGAA
* * *
148124 AAATTAGGGCCTCAATTATAAAAGTAAAAGGTGATATTGAAA
1 AAATTAGGGCTTCAATTATAAAAGTAAAAAGTGAGATTG-AA
* * *
148166 AAATTAGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAA
1 AAATTAGGGCTTCAATTATAAAAGTAAAAAGTGAGATTG-AA
* * * *
148208 AAAATAGGAAC-TCAATTATAAAAGTACAAAGTGGGATTGAA
1 AAATTAGG-GCTTCAATTATAAAAGTAAAAAGTGAGATTGAA
** * *
148249 AAACTTAGTATCATCAATTATAAATGTAAAAA
1 AAA-TTAG-GGCTTCAATTATAAAAGTAAAAA
148281 AAAGTAGGAG
Statistics
Matches: 239, Mismatches: 30, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
41 60 0.25
42 121 0.51
43 35 0.15
44 23 0.10
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (41 bp):
AAATTAGGGCTTCAATTATAAAAGTAAAAAGTGAGATTGAA
Found at i:148112 original size:127 final size:127
Alignment explanation
Indices: 147962--148208 Score: 340
Period size: 127 Copynumber: 1.9 Consensus size: 127
147952 ATTAAATTAG
* * *
147962 GGGCTTAAATTATAAAAGTAAAAAGT-ATTATTGAAAAATTAGGGATCTCAATTAT-AAAGTTAA
1 GGGCTTAAATTATAAAAGTAAAAAGTGA-GATCGAAAAATTAGGG-CCTCAATTATAAAAG-TAA
* * *
148025 AAAGTGAGATT-AAAAAATTCAGGGTCTTAATTTTAAA-GTAAAAAGTGAGATTGAAAATATTTA
63 AAAGTGAGATTGAAAAAATT-AGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAATATTTA
148088 A
127 A
* *
148089 GGGCTTAAATTATATAAGTAAAAAGTGAGATCGAAAAATTAGGGCCTCAATTATAAAAGTAAAAG
1 GGGCTTAAATTATAAAAGTAAAAAGTGAGATCGAAAAATTAGGGCCTCAATTATAAAAGTAAAAA
* *
148154 GTGATATTGAAAAAATTAGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAA
66 GTGAGATTGAAAAAATTAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
148209 AAATAGGAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
126 35 0.33
127 70 0.66
128 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.28
Consensus pattern (127 bp):
GGGCTTAAATTATAAAAGTAAAAAGTGAGATCGAAAAATTAGGGCCTCAATTATAAAAGTAAAAA
GTGAGATTGAAAAAATTAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAATATTTAA
Found at i:148249 original size:84 final size:84
Alignment explanation
Indices: 147955--148280 Score: 313
Period size: 85 Copynumber: 3.9 Consensus size: 84
147945 GAAAATGATT
* * * *
147955 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGT-ATTATTG-AAAAATTAGGGATCTCAATTATA
1 AAATTAGGGAC-TCAATTATAAAAGTAAAAAGTGA-GATTGAAAAAATTAGGG-CCTCAATTATA
*
148018 AAGTTAAAAAGTGAGATT-AAA
63 AAGGTAAAAAGTGAGATTGAAA
* * * * * *
148039 AAATTCAGGGTCTTAATT-TTAAAGTAAAAAGTGAGATTGAAAATATTTAAGGGCTTAAATTATA
1 AAATT-AGGGACTCAATTATAAAAGTAAAAAGTGAGATTGAAAA-AATT-AGGGCCTCAATTATA
*
148103 TAA-GTAAAAAGTGAGATCG-AA
63 -AAGGTAAAAAGTGAGATTGAAA
* * *
148124 AAATTAGGGCCTCAATTATAAAAGTAAAAGGTGATATTGAAAAAATTAGGGCCTCAATTATAAAG
1 AAATTAGGGACTCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGCCTCAATTATAAAG
*
148189 GTAGAAAGTGAGATTGAAA
66 GTAAAAAGTGAGATTGAAA
* * * * * ** *
148208 AAAATAGGAACTCAATTATAAAAGTACAAAGTGGGATTGAAAAACTTAGTATCATCAATTATAAA
1 AAATTAGGGACTCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAG-GGCCTCAATTATAAA
*
148273 TGTAAAAA
65 GGTAAAAA
148281 AAAGTAGGAG
Statistics
Matches: 198, Mismatches: 33, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
82 2 0.01
83 44 0.22
84 70 0.35
85 76 0.38
86 6 0.03
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (84 bp):
AAATTAGGGACTCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGCCTCAATTATAAAG
GTAAAAAGTGAGATTGAAA
Found at i:148266 original size:127 final size:125
Alignment explanation
Indices: 147965--148280 Score: 329
Period size: 127 Copynumber: 2.5 Consensus size: 125
147955 AAATTAGGGG
*
147965 CTTAAATTATAAAAGTAAAAAGT-ATTATTGAAAAATTAGGGATCTCAATTAT-AAAGTTAAAAA
1 CTTAAATTATAAAAGTAAAAAGTGA-GATTGAAAAATTA--GATCTCAATTATAAAAG-TAAAAA
* * * ** *
148028 GTGAGATTAAAAAATTCAGGGTCTTAATTTTAAAGTAAAAAGTGAGATTGAAAATATTTAAGGG
62 GTGAGATTAAAAAATTCAGGGCCTCAATTATAAAGTAAAAAGTGAGATTGAAAATAAATAAGGA
* * ** *
148092 CTTAAATTATATAAGTAAAAAGTGAGATCGAAAAATTAGGGCCTCAATTATAAAAGTAAAAGGTG
1 CTTAAATTATAAAAGTAAAAAGTGAGATTGAAAAATTA-GATCTCAATTATAAAAGTAAAAAGTG
* *
148157 ATATTGAAAAAATT-AGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAA-AAAT-AGGAA
65 AGATT-AAAAAATTCAGGGCCTCAATTATAAA-GTAAAAAGTGAGATTGAAAATAAATAAGG-A
* * * *
148218 C-TCAATTATAAAAGTACAAAGTGGGATTGAAAAACTTAGTATCATCAATTATAAATGTAAAAA
1 CTTAAATTATAAAAGTAAAAAGTGAGATTGAAAAA-TTAG-ATC-TCAATTATAAAAGTAAAAA
148281 AAAGTAGGAG
Statistics
Matches: 158, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
125 32 0.20
126 44 0.28
127 81 0.51
128 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (125 bp):
CTTAAATTATAAAAGTAAAAAGTGAGATTGAAAAATTAGATCTCAATTATAAAAGTAAAAAGTGA
GATTAAAAAATTCAGGGCCTCAATTATAAAGTAAAAAGTGAGATTGAAAATAAATAAGGA
Found at i:148270 original size:168 final size:169
Alignment explanation
Indices: 147955--148280 Score: 387
Period size: 168 Copynumber: 1.9 Consensus size: 169
147945 GAAAATGATT
* *
147955 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGTATTATTGAAAAATTAGGGATCTCAATTATAAA
1 AAATTAGGGGCCTAAATTATAAAAGTAAAAAGTATTATTGAAAAATTAGGGACCTCAATTATAAA
* * ** * * *
148020 GTTAAAAAGTGAGATTAAAAAATTCAGGGTCTTAATTTTAAAGTAAAAAGTGAGATTGAAAATAT
66 GGTAAAAAGTGAGATTAAAAAAATCAGGAACTCAATTTAAAAGTAAAAAGTGAGATTGAAAATAC
* *
148085 TTAAGGGCTTAAATTATATAA-GTAAAAAGTGAGATCGAA
131 TTAAGAGCATAAATTATA-AATGTAAAAAGTGAGATCGAA
* *
148124 AAATTA-GGGCCTCAATTATAAAAGTAAAAGGTGA-TATTGAAAAAATTAGGG-CCTCAATTATA
1 AAATTAGGGGCCTAAATTATAAAAGTAAAAAGT-ATTATTG-AAAAATTAGGGACCTCAATTATA
* * *
148186 AAGGTAGAAAGTGAGATTGAAAAAAAT-AGGAACTCAATTATAAAAGTACAAAGTGGGATTGAAA
64 AAGGTAAAAAGTGAGATT-AAAAAAATCAGGAACTCAATT-TAAAAGTAAAAAGTGAGATTGAAA
* *
148250 A-ACTT-AGTATCATCAATTATAAATGTAAAAA
127 ATACTTAAG-AGCATAAATTATAAATGTAAAAA
148281 AAAGTAGGAG
Statistics
Matches: 133, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
167 4 0.03
168 82 0.62
169 47 0.35
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (169 bp):
AAATTAGGGGCCTAAATTATAAAAGTAAAAAGTATTATTGAAAAATTAGGGACCTCAATTATAAA
GGTAAAAAGTGAGATTAAAAAAATCAGGAACTCAATTTAAAAGTAAAAAGTGAGATTGAAAATAC
TTAAGAGCATAAATTATAAATGTAAAAAGTGAGATCGAA
Found at i:154511 original size:23 final size:23
Alignment explanation
Indices: 154485--154529 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
154475 CACCACAGCT
*
154485 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
154508 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
154530 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:154747 original size:149 final size:149
Alignment explanation
Indices: 154497--154960 Score: 858
Period size: 149 Copynumber: 3.1 Consensus size: 149
154487 TATAATTGCA
154497 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
*
154561 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
154626 CCACAGAATATATATATATC
130 CCACAGAATATATATATATC
154646 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
154711 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
154776 CACAGAATATATATATATC
131 CACAGAATATATATATATC
154795 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
* *
154860 TCCTTAATAATCATATATATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* * *
154925 CAAAGAATATACATATGTC
131 CACAGAATATATATATATC
154944 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
154961 CCCTCGACTC
Statistics
Matches: 308, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.00
149 307 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:156462 original size:63 final size:63
Alignment explanation
Indices: 156356--156495 Score: 199
Period size: 63 Copynumber: 2.2 Consensus size: 63
156346 TAATGGAGGC
* * * **
156356 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTATTATAA
1 ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAATAA
* ** *
156419 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTAAAATTA
1 ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAATAA
156482 ATGCATCGATGCAC
1 ATGCATCGATGCAC
156496 CTTCAACAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAATAA
Found at i:159614 original size:23 final size:23
Alignment explanation
Indices: 159588--159632 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
159578 CACCACAGCT
*
159588 CGTATAATTACACCGAAGTGCCG
1 CGTAGAATTACACCGAAGTGCCG
* *
159611 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTACACCGAAGTGCC
159633 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCG
Found at i:159850 original size:149 final size:149
Alignment explanation
Indices: 159600--159948 Score: 655
Period size: 149 Copynumber: 2.3 Consensus size: 149
159590 TATAATTACA
159600 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
159664 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
159729 CCACAAAATATATATATATC
130 CCACAAAATATATATATATC
*
159749 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
159814 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
159879 CACAGAATATATATATATC
131 CACAAAATATATATATATC
*
159898 CCAAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAA
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAA
159949 TAATTATATA
Statistics
Matches: 195, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 194 0.99
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAAAATATATATATATC
Found at i:161546 original size:44 final size:44
Alignment explanation
Indices: 161455--161556 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
161445 TGCACTCCTG
* * **
161455 ATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTAGTAGAA
1 ATGCATCGATGCACTGAGGACATTCGATGTTCATATTAAAAGAA
* ** **
161499 ATGCATCGATGCACTGATGACATTCGATGTTTGTATTAAAATTA
1 ATGCATCGATGCACTGAGGACATTCGATGTTCATATTAAAAGAA
161543 ATGCATCGATGCAC
1 ATGCATCGATGCAC
161557 CTTCAACAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (44 bp):
ATGCATCGATGCACTGAGGACATTCGATGTTCATATTAAAAGAA
Found at i:167810 original size:21 final size:21
Alignment explanation
Indices: 167784--167824 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
167774 CCGAAATTAC
* *
167784 TGTAGCAGTGCATCGGTACAT
1 TGTAGCAGTACATCGATACAT
167805 TGTAGCAGTACATCGATACA
1 TGTAGCAGTACATCGATACA
167825 CAATTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (21 bp):
TGTAGCAGTACATCGATACAT
Found at i:168404 original size:183 final size:184
Alignment explanation
Indices: 168084--168470 Score: 643
Period size: 183 Copynumber: 2.1 Consensus size: 184
168074 TTTTTTAATT
* * * * * * *
168084 TATATAA-AAATTAAATATTTTTTAATTCAAAAAGAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAACAATTTACAAATAATTTAAATAATATATAAT
*
168148 TATAAAATAAAAATTTTAGATAATTTTTTAAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAATTTTTTAAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* * *
168213 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTTAGTCCATAAGTTA
131 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATAAGTTA
168267 TATATAATATATTTAATATTTTTTAATTAAAAAACAATTTACAAATAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAACAATTTACAAATAATTTAAATAATATATAAT
*
168332 TATAAAATAAAAAATTTATATAATTTTTT-AATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAATTTTTTAAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
*
168396 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
131 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATAAGTTA
168450 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
168471 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
183 113 0.59
184 77 0.41
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAACAATTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAATTTTTTAAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATAAGTTA
Found at i:168495 original size:9 final size:9
Alignment explanation
Indices: 168476--168509 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
168466 TATTTAAAAT
168476 TTAATTTCGG
1 TTAA-TTCGG
168486 TTAATTCGG
1 TTAATTCGG
*
168495 TTAATTCAG
1 TTAATTCGG
168504 TTAATT
1 TTAATT
168510 AACCGAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:171645 original size:2 final size:2
Alignment explanation
Indices: 171638--171663 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
171628 TTGTTCATCA
171638 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
171664 CAAACCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:171749 original size:25 final size:24
Alignment explanation
Indices: 171721--171767 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
171711 CATCAAGTTC
*
171721 AAACTCTAATAAAGCCTCATTTAAA
1 AAACTCTAATAAAACCTC-TTTAAA
*
171746 AAACTCTGATAAAACCTCTTTA
1 AAACTCTAATAAAACCTCTTTA
171768 TGTACGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (24 bp):
AAACTCTAATAAAACCTCTTTAAA
Found at i:173108 original size:17 final size:18
Alignment explanation
Indices: 173082--173115 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
173072 TTTCATATAT
*
173082 TTTTTAAAAATTTATTGA
1 TTTTTAAAAATTAATTGA
173100 TTTTT-AAAATTAATTG
1 TTTTTAAAAATTAATTG
173116 TTTAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTTTAAAAATTAATTGA
Found at i:173288 original size:30 final size:30
Alignment explanation
Indices: 173252--173333 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
173242 ATAATAATTC
* * *
173252 ATTTGATCCCACAATTGTAATTAAAAGTTT
1 ATTTGATCCCGCAATTCTAATTAAAAGTAT
* *
173282 ATTTGATCCCGCAGTTTTAATTAAAAGTAT
1 ATTTGATCCCGCAATTCTAATTAAAAGTAT
173312 ATTTGATCCCGCAATTCTAATT
1 ATTTGATCCCGCAATTCTAATT
173334 TTATTAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (30 bp):
ATTTGATCCCGCAATTCTAATTAAAAGTAT
Found at i:177354 original size:21 final size:21
Alignment explanation
Indices: 177303--177355 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
177293 GCGATGGTAC
*
177303 TGATACTAAGCCCTTTAGTAT
1 TGATACTAATCCCTTTAGTAT
177324 TGATACTAATCCCTTTAGTAT
1 TGATACTAATCCCTTTAGTAT
177345 TGATACTAATC
1 TGATACTAATC
177356 TATCAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (21 bp):
TGATACTAATCCCTTTAGTAT
Found at i:178902 original size:32 final size:34
Alignment explanation
Indices: 178850--178913 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
178840 TTTCTTTCAA
178850 AAAACTAGTTTTTAACAAAAAA-AAA-TACTTAT
1 AAAACTAGTTTTTAACAAAAAATAAATTACTTAT
* **
178882 AAAATTAGTTTTTATTAAAAAATAAATTACTT
1 AAAACTAGTTTTTAACAAAAAATAAATTACTT
178914 GAAACTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 19 0.70
33 3 0.11
34 5 0.19
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAACTAGTTTTTAACAAAAAATAAATTACTTAT
Found at i:189759 original size:81 final size:81
Alignment explanation
Indices: 189616--189857 Score: 430
Period size: 81 Copynumber: 3.0 Consensus size: 81
189606 ATTTTTTGGA
* *
189616 CTCCCGTTCGGTTGCTTGTCTTAAATTCTCTGTTTCAAACATCTAATACATACAGTACACTTATT
1 CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTACACTTATT
189681 CACTTTCATTAGTAAC
66 CACTTTCATTAGTAAC
*
189697 CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTATACTTATT
1 CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTACACTTATT
189762 CACTTTCATTAGTAAC
66 CACTTTCATTAGTAAC
* *
189778 CTCCCGTTCGGTTGCTTGCCTTAAACTCTCTGTTTCAAACTTCTAATACATACACTACACTTATT
1 CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTACACTTATT
*
189843 CACTTTCACTAGTAA
66 CACTTTCATTAGTAA
189858 GGAGTGACAT
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 154 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (81 bp):
CTCCCGTTCGGTTGCTTGTCTTAAACTCTCTGTTTCAAACATCTAATACATACACTACACTTATT
CACTTTCATTAGTAAC
Found at i:193332 original size:20 final size:20
Alignment explanation
Indices: 193284--193338 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
193274 CAACATGAAA
*
193284 TTTCAAATTCGCAACTCGAT
1 TTTCAAATTCGCAACGCGAT
**
193304 TTTTGAATTCGCAACGCGAT
1 TTTCAAATTCGCAACGCGAT
*
193324 TTTCAAATTTGCAAC
1 TTTCAAATTCGCAAC
193339 ACGAACTCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTCAAATTCGCAACGCGAT
Found at i:194135 original size:24 final size:24
Alignment explanation
Indices: 194108--194161 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
194098 GTATTCAAAA
* *
194108 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGCTCAATACTCAGAC
*
194132 TTTGATCTTGCTCAATACTCAGAT
1 TTTGATCTTGCTCAATACTCAGAC
194156 TTTGAT
1 TTTGAT
194162 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGCTCAATACTCAGAC
Found at i:196399 original size:18 final size:18
Alignment explanation
Indices: 196373--196408 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
196363 AAGCAAAAAG
*
196373 AAATAAAAATCGCAATCA
1 AAATAAAAATCCCAATCA
*
196391 AAATCAAAATCCCAATCA
1 AAATAAAAATCCCAATCA
196409 CAACCGCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.22, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATAAAAATCCCAATCA
Found at i:196720 original size:20 final size:20
Alignment explanation
Indices: 196697--196739 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
196687 GAAAATCGAA
196697 TTCGCAACGCGAATTTGATT
1 TTCGCAACGCGAATTTGATT
***
196717 TTCGCGTTGCGAATTTGATT
1 TTCGCAACGCGAATTTGATT
196737 TTC
1 TTC
196740 TTAAAGGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
TTCGCAACGCGAATTTGATT
Found at i:198277 original size:20 final size:21
Alignment explanation
Indices: 198237--198286 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
198227 AGGTGGATCA
198237 TGAACGATGGGAAGGGCCTCT
1 TGAACGATGGGAAGGGCCTCT
* *
198258 TGAACGATGGG-TGTGCCTCT
1 TGAACGATGGGAAGGGCCTCT
198278 TGAACGATG
1 TGAACGATG
198287 ACAAGTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (21 bp):
TGAACGATGGGAAGGGCCTCT
Found at i:198320 original size:21 final size:21
Alignment explanation
Indices: 198296--198339 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
198286 GACAAGTGAT
198296 TCCTGAACAATGGAAGGTGGA
1 TCCTGAACAATGGAAGGTGGA
*
198317 TCCTGAACAATGGTAGGTGGA
1 TCCTGAACAATGGAAGGTGGA
198338 TC
1 TC
198340 GGGCTTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (21 bp):
TCCTGAACAATGGAAGGTGGA
Found at i:198644 original size:21 final size:21
Alignment explanation
Indices: 198620--198670 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
198610 TAAAACAATC
* *
198620 TCACGTAGAGCAGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
198641 TCACGTAAAGCATATACCTCA
1 TCACGTAAAGCAGATACCTCA
*
198662 CCACGTAAA
1 TCACGTAAA
198671 TCACCATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:198725 original size:41 final size:43
Alignment explanation
Indices: 198633--198728 Score: 119
Period size: 41 Copynumber: 2.3 Consensus size: 43
198623 CGTAGAGCAG
198633 CTACCTCATCACGTAAAGCATATACCTCACCACGTAAATCACC
1 CTACCTCATCACGTAAAGCATATACCTCACCACGTAAATCACC
* ** *
198676 AT-TGTCATCACGTAAA-CA-ACTACCTCACCATGTAAAT-ACC
1 CTACCTCATCACGTAAAGCATA-TACCTCACCACGTAAATCACC
198716 CTACCTCATCACG
1 CTACCTCATCACG
198729 CATGCACCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
40 5 0.11
41 26 0.59
42 12 0.27
43 1 0.02
ACGTcount: A:0.34, C:0.35, G:0.07, T:0.23
Consensus pattern (43 bp):
CTACCTCATCACGTAAAGCATATACCTCACCACGTAAATCACC
Found at i:198941 original size:42 final size:41
Alignment explanation
Indices: 198881--199024 Score: 150
Period size: 42 Copynumber: 3.5 Consensus size: 41
198871 ATTATGGAAT
* ** *
198881 AGTGATGGCTCTTAGTGTCGAGGTGTAGAATCGACTCGATT
1 AGTGATGGATCTCGGTGTCGAGGTGTAGAATCGACTCGATC
* * *
198922 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCGTCTTGATC
1 A-GTGATGGATCTCGGTGTCGAGGTGTAGAATCGACTCGATC
* * *
198964 ATGTGATGGATCTCGGTGTCGAAGTG--GAA-AGAGCTCGATG
1 A-GTGATGGATCTCGGTGTCGAGGTGTAGAATCGA-CTCGATC
199004 AGTGATGGATCTCGGTGTCGA
1 AGTGATGGATCTCGGTGTCGA
199025 AGTGGGGGTG
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 21 0.24
40 9 0.10
41 1 0.01
42 58 0.65
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (41 bp):
AGTGATGGATCTCGGTGTCGAGGTGTAGAATCGACTCGATC
Found at i:199028 original size:21 final size:21
Alignment explanation
Indices: 198966--199028 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 21
198956 TCTTGATCAT
198966 GTGATGGATCTCGGTGTCGAA
1 GTGATGGATCTCGGTGTCGAA
** * *
198987 GTGGAAAGAGCTC-G-AT-G-A
1 GT-GATGGATCTCGGTGTCGAA
199005 GTGATGGATCTCGGTGTCGAA
1 GTGATGGATCTCGGTGTCGAA
199026 GTG
1 GTG
199029 GGGGTGTTCA
Statistics
Matches: 29, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 7 0.24
18 4 0.14
19 2 0.07
20 2 0.07
21 7 0.24
22 7 0.24
ACGTcount: A:0.22, C:0.13, G:0.40, T:0.25
Consensus pattern (21 bp):
GTGATGGATCTCGGTGTCGAA
Found at i:200540 original size:14 final size:14
Alignment explanation
Indices: 200523--200554 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
200513 ACTCGAAAAT
200523 GAAATTCGCAACAC
1 GAAATTCGCAACAC
*
200537 GAAATTCGCAACGC
1 GAAATTCGCAACAC
200551 GAAA
1 GAAA
200555 ACTAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (14 bp):
GAAATTCGCAACAC
Found at i:200554 original size:34 final size:34
Alignment explanation
Indices: 200490--200555 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
200480 CTTGAAACTT
* * *
200490 AAATTTGCAACATGAAAATCCTAACTCGAAAATG
1 AAATTCGCAACACGAAAATCCTAACGCGAAAATG
*
200524 AAATTCGCAACACGAAATTCGC-AACGCGAAAA
1 AAATTCGCAACACGAAAATC-CTAACGCGAAAA
200556 CTAAAATCGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.18
Consensus pattern (34 bp):
AAATTCGCAACACGAAAATCCTAACGCGAAAATG
Found at i:200988 original size:22 final size:21
Alignment explanation
Indices: 200932--200990 Score: 93
Period size: 20 Copynumber: 2.8 Consensus size: 21
200922 GGTCGCGGAT
*
200932 ATGGGACGGATGTCGCCAGAG
1 ATGGGACGAATGTCGCCAGAG
200953 ATGGGAC-AATGTCGCCAGAG
1 ATGGGACGAATGTCGCCAGAG
200973 ATGGGGACGAATGTCGCC
1 AT-GGGACGAATGTCGCC
200991 GTAGAGAGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 14 0.40
21 12 0.34
22 9 0.26
ACGTcount: A:0.25, C:0.20, G:0.39, T:0.15
Consensus pattern (21 bp):
ATGGGACGAATGTCGCCAGAG
Found at i:201056 original size:26 final size:27
Alignment explanation
Indices: 201018--201084 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
201008 AAGATGAGAC
201018 TGAGTTGCGATTT-GAGTTTTAGGTTA
1 TGAGTTGCGATTTAGAGTTTTAGGTTA
* *
201044 TGAGTTGCTATTTAGGGTTTTAGGTTA
1 TGAGTTGCGATTTAGAGTTTTAGGTTA
*
201071 TGAGTTGTGATTTA
1 TGAGTTGCGATTTA
201085 CGGGATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 12 0.33
27 24 0.67
ACGTcount: A:0.19, C:0.03, G:0.30, T:0.48
Consensus pattern (27 bp):
TGAGTTGCGATTTAGAGTTTTAGGTTA
Found at i:201256 original size:20 final size:21
Alignment explanation
Indices: 201223--201261 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
201213 TGCGAAAAAG
*
201223 AAATTCGAGTTGCGAATTTCA
1 AAATTCGAGATGCGAATTTCA
201244 AAATT-GAGATGCGAATTT
1 AAATTCGAGATGCGAATTT
201262 TGGAACTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (21 bp):
AAATTCGAGATGCGAATTTCA
Found at i:201276 original size:20 final size:21
Alignment explanation
Indices: 201253--201301 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
201243 AAAATTGAGA
201253 TGCGAATTTTGGAACT-GTGT
1 TGCGAATTTTGGAACTCGTGT
* *
201273 TGCGAA-ATTGGAGCTCGTGT
1 TGCGAATTTTGGAACTCGTGT
*
201293 TGCAAATTT
1 TGCGAATTT
201302 ATTGGTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.30
20 15 0.65
21 1 0.04
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (21 bp):
TGCGAATTTTGGAACTCGTGT
Done.