Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006904.1 Hibiscus syriacus cultivar Beakdansim tig00017636_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: 82325
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:936 original size:3 final size:3
Alignment explanation
Indices: 928--973 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
918 GTAATTTATT
* * *
928 TAA TAA TAA TATA TAA TAA TTA TAA TAA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
974 AACAAACTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1158 original size:46 final size:45
Alignment explanation
Indices: 1081--1270 Score: 264
Period size: 46 Copynumber: 4.3 Consensus size: 45
1071 GATGGAAATG
* * *
1081 TTTGAAAACA-C-TGCA-TGATGGTCTTACAGATGACTCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-T
*
1124 TTTGAAAACATCATGCACTGAATGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-T
1170 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
1215 TTTG-AAACATCAAGCACTGAAGGACTTACAGATGAACCTAAGG-
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1258 TTTGAAAACATCA
1 TTTGAAAACATCA
1271 AAAGCTCCCG
Statistics
Matches: 135, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
43 14 0.10
44 45 0.33
45 9 0.07
46 67 0.50
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
Found at i:1242 original size:90 final size:89
Alignment explanation
Indices: 1080--1270 Score: 264
Period size: 90 Copynumber: 2.2 Consensus size: 89
1070 GGATGGAAAT
* * * *
1080 GTTTGAAAACA-C-TGCATGATGGTCTTACAGATGACTCGAAGGTTTTTGAAAACATCATGCACT
1 GTTTGAAAACATCATGCATGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACT
* *
1143 GAATGACTTACAGATGACCCGAAG
66 GAAGGACTTACAGATGAACCGAAG
1167 GTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTG-AAACATCAAGC
1 G--TTTGAAAACATCATGCA-TGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGC
*
1230 ACTGAAGGACTTACAGATGAACCTAAG
63 ACTGAAGGACTTACAGATGAACCGAAG
1257 GTTTGAAAACATCA
1 GTTTGAAAACATCA
1271 AAAGCTCCCG
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
87 1 0.01
88 13 0.14
89 10 0.11
90 36 0.39
91 9 0.10
92 23 0.25
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (89 bp):
GTTTGAAAACATCATGCATGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACT
GAAGGACTTACAGATGAACCGAAG
Found at i:1710 original size:304 final size:300
Alignment explanation
Indices: 1206--1852 Score: 1072
Period size: 304 Copynumber: 2.2 Consensus size: 300
1196 TTACAGATGA
*
1206 CCCGAAGG--TTTT-GAAACATCAAGCACTGAAGGACTTACAGATGAACCTAAGGTTTGAAAACA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAACCTAAGGTTTGAAAACA
* **
1268 TCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGC
66 TCAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTACAGGACTTACAGATGACCCTAAGGC
1333 TTTGAAACATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATG
131 TTTGAAACATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATG
*
1398 ACCCTAAGGCTTTGAAAACATCAAAAAGCT-CCGAAGGATTTTTGGAAACATCATGCACTGTAGG
196 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAA-ATCATGCACTGCAGG
1462 ACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
260 ACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
* * *
1503 -CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGAATTACAGATGACCCTAAAAGGCTTTGAAA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAACCT--AAGG-TTTGAAA
1567 ACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTACAGGACTTACAGATGACCCTA
63 ACATC-AAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTACAGGACTTACAGATGACCCTA
* * *
1632 AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTAC
127 AGGCTTTG-AAACATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTAC
*
1697 AGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAATCATGCACTG
191 AGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAAATCATGCACTG
*
1762 CAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
256 CAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1807 CCCGAAGGCTTTTTGGAAACATCATGCACT-ACAGGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGA-AGGACTTACAGATG
1853 TGGTAAATAG
Statistics
Matches: 324, Mismatches: 15, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
296 7 0.02
298 4 0.01
299 32 0.10
301 4 0.01
302 12 0.04
303 64 0.20
304 142 0.44
305 59 0.18
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (300 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAACCTAAGGTTTGAAAACA
TCAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTACAGGACTTACAGATGACCCTAAGGC
TTTGAAACATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATG
ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAAATCATGCACTGCAGGA
CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
Found at i:1878 original size:75 final size:76
Alignment explanation
Indices: 1206--1852 Score: 1078
Period size: 75 Copynumber: 8.6 Consensus size: 76
1196 TTACAGATGA
* * *
1206 CCCGAAGG--TTTT-GAAACATCAAGCACTGAAGGACTTACAGATGAACCTAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1267 ATC-AAAAGCT
66 ATCAAAAAGCT
*
1277 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTG-AAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1341 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1352 CCCAAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1417 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1428 -CCGAAGGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1492 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1503 -CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGAATTACAGATGACCCTAAAAGGCTTTGAAA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT--AAGGCTTTGAAA
1567 ACATCAAAAAGCT
64 ACATCAAAAAGCT
* *
1580 CCCGAAGGCTTTTTGAAAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1645 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1656 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1721 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1732 CCCGAAGGCTTTTTGGAAA-ATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1796 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1807 CCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1853 TGGTAAATAG
Statistics
Matches: 543, Mismatches: 23, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
71 8 0.01
73 4 0.01
74 44 0.08
75 260 0.48
76 156 0.29
77 25 0.05
78 46 0.08
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:2538 original size:22 final size:22
Alignment explanation
Indices: 2513--2580 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
2503 CATAAAGCTT
2513 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
2535 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2557 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2579 TC
1 TC
2581 TTTGAAGAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:9267 original size:12 final size:13
Alignment explanation
Indices: 9243--9271 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
9233 AAAAATGAAA
9243 AAATGCTAAATGT
1 AAATGCTAAATGT
9256 AAATGC-AAATGT
1 AAATGCTAAATGT
9268 AAAT
1 AAAT
9272 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (13 bp):
AAATGCTAAATGT
Found at i:10913 original size:21 final size:21
Alignment explanation
Indices: 10887--10927 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
10877 ATTATGAAAA
10887 TAATAAATATATAT-AATTTTT
1 TAATAAA-ATATATGAATTTTT
10908 TAATAAAATATATGAATTTT
1 TAATAAAATATATGAATTTT
10928 AAATTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TAATAAAATATATGAATTTTT
Found at i:11540 original size:12 final size:12
Alignment explanation
Indices: 11480--11536 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
11470 CTTTTCTTTG
11480 ATATTAAAAAA-
1 ATATTAAAAAAT
11491 ATATTAATAAAAT
1 ATATTAA-AAAAT
*
11504 ATTTTATAAAAAT
1 ATATTA-AAAAAT
*
11517 A-ATTAAAATAT
1 ATATTAAAAAAT
11528 ATATTAAAA
1 ATATTAAAA
11537 TATAATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 13 0.33
12 14 0.36
13 11 0.28
14 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATTAAAAAAT
Found at i:16539 original size:15 final size:15
Alignment explanation
Indices: 16519--16548 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16509 TCCTAATTAA
16519 GTAGGAGTGAGAGAC
1 GTAGGAGTGAGAGAC
16534 GTAGGAGTGAGAGAC
1 GTAGGAGTGAGAGAC
16549 TACTCCCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.47, T:0.13
Consensus pattern (15 bp):
GTAGGAGTGAGAGAC
Found at i:16987 original size:55 final size:55
Alignment explanation
Indices: 16921--17060 Score: 196
Period size: 52 Copynumber: 2.6 Consensus size: 55
16911 GACATTCAAG
*
16921 TGATTCATGAAGAAGGACGTCCGATGAATGAAGAAATTTGAACCCGATTGAAGAA
1 TGATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAACCCGATTGAAGAA
* * *
16976 TGATTCAT---GAAGGACATCCGAAGAATGAAGAAATTTGAACCTGATTGAAGAC
1 TGATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAACCCGATTGAAGAA
* * *
17028 CGATCCATGAAGAAAGACATCCGATGAATGAAG
1 TGATTCATGAAGAAGGACATCCGATGAATGAAG
17061 TTAGAAGTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
52 46 0.62
55 28 0.38
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (55 bp):
TGATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAACCCGATTGAAGAA
Found at i:23407 original size:13 final size:13
Alignment explanation
Indices: 23389--23420 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
23379 ATTTTGTGTG
23389 AATGATCTCCAAT
1 AATGATCTCCAAT
23402 AATGATCTCCAAT
1 AATGATCTCCAAT
23415 ATATGA
1 A-ATGA
23421 AGTTTCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (13 bp):
AATGATCTCCAAT
Found at i:23675 original size:10 final size:10
Alignment explanation
Indices: 23642--23675 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
23632 TTTTTTGAAA
*
23642 TTTTGGCTTT
1 TTTTGCCTTT
*
23652 TTTGGCCTTT
1 TTTTGCCTTT
23662 TTTTGCCTTT
1 TTTTGCCTTT
23672 TTTT
1 TTTT
23676 ATTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.71
Consensus pattern (10 bp):
TTTTGCCTTT
Found at i:26847 original size:124 final size:125
Alignment explanation
Indices: 26626--26857 Score: 358
Period size: 124 Copynumber: 1.9 Consensus size: 125
26616 AAGTTGTGAT
* *
26626 ATGTTGAGGCACGACTGAACCCACATCACGTTGAGATGACGAGATTAAGACCAAGGAGGCATTAA
1 ATGTTGAGGCACGACTGAACCCACATCACGTTGAGATGACAAGATTAAGACCAAGGAGGCATGAA
* *
26691 GAATGAGCCTTACAATTTGAGTTGTTGGGGCATTTTGAAGGCCTATACCAATATAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCTATACCAATATAAGATA
* * * * *
26751 ATGTTGGGGCATGACTGAACTCACATCATG-TGAGATGACAAGATTCAGACCAAGGAGGCATGAA
1 ATGTTGAGGCACGACTGAACCCACATCACGTTGAGATGACAAGATTAAGACCAAGGAGGCATGAA
**
26815 GTGTGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCC
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCC
26858 CGTACCAGAA
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
124 70 0.73
125 26 0.27
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (125 bp):
ATGTTGAGGCACGACTGAACCCACATCACGTTGAGATGACAAGATTAAGACCAAGGAGGCATGAA
GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCTATACCAATATAAGATA
Found at i:27224 original size:293 final size:291
Alignment explanation
Indices: 26639--27167 Score: 700
Period size: 293 Copynumber: 1.8 Consensus size: 291
26629 TTGAGGCACG
* * *
26639 ACTGAACCCACATCACGTTGAGATGACGAGATTAAGACCAAGGAGGCATTAAGAATGAGCCTTAC
1 ACTGAACCCACATCACGTTGAGATGACAAGATTAAGACCAACGAGGCATGAAGAATGAGCCTTAC
* * * **
26704 AATTTGAGTTGTTGGGGCATTTTGAAGGCCTATACCAATATAAGATAATGTTGGGGCATGACTGA
66 AATTTGAGGTGATGGGGCATTTTGAAGGCCTATACCAATATAAGACAATGTTGGGGCACAACTGA
* * * ** *
26769 ACTCACATCATGTGAGATGACAAGATTCAGACCAAGGAGGCATGAAGTGTGAGCCTTACAATTTG
131 ACCCACAACATGTGAGATGACAAGATTCAGACCAAGAAGGCATGAAGAATGAGCCTTACAATTGG
** * * * ***
26834 AGGTGATGGGGCATTTTGAAGGCCCGTACCAGAATGAGAACATCCCAGTTTGGAATATTTTGGGC
196 AGGTGATAAGGCATTTTGAAGGCCCGTAACAGAATAAGAACAT--CAGTTTGGAATAGTGAAGGC
26899 ATGAAGAAATCCATGAATACACATTGGGGCATA
259 ATGAAGAAATCCATGAATACACATTGGGGCATA
* *
26932 ACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAACGAGGCATGAAGAATGAGCCTTAC
1 ACTGAACCCACATCACGTTGAGATGACAAGATTAAGACCAACGAGGCATGAAGAATGAGCCTTAC
* *
26997 AATTTGAGGTGATGGGGTATTTTGAAGGCCTATACCAGTATAAGACAATGTTGGGGCACAACTGA
66 AATTTGAGGTGATGGGGCATTTTGAAGGCCTATACCAATATAAGACAATGTTGGGGCACAACTGA
** * *
27062 ACCCACAACATGTTGAGATGATGAGATTCAGACTAAGAAGGCATTG-AGAATGAGCCTTGCGAAT
131 ACCCACAACATG-TGAGATGACAAGATTCAGACCAAGAAGGCA-TGAAGAATGAGCCTTAC-AAT
* * * *
27126 TGGAGGTGTTAAGGCATTTTGAGGGCCCGTAATAGTATAAGA
193 TGGAGGTGATAAGGCATTTTGAAGGCCCGTAACAGAATAAGA
27168 TAATATTGTG
Statistics
Matches: 203, Mismatches: 30, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
293 128 0.63
294 37 0.18
295 38 0.19
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.24
Consensus pattern (291 bp):
ACTGAACCCACATCACGTTGAGATGACAAGATTAAGACCAACGAGGCATGAAGAATGAGCCTTAC
AATTTGAGGTGATGGGGCATTTTGAAGGCCTATACCAATATAAGACAATGTTGGGGCACAACTGA
ACCCACAACATGTGAGATGACAAGATTCAGACCAAGAAGGCATGAAGAATGAGCCTTACAATTGG
AGGTGATAAGGCATTTTGAAGGCCCGTAACAGAATAAGAACATCAGTTTGGAATAGTGAAGGCAT
GAAGAAATCCATGAATACACATTGGGGCATA
Found at i:28535 original size:42 final size:41
Alignment explanation
Indices: 28473--28569 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
28463 GATTTGTAAG
* * * *
28473 TCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG-ATAAA
* * *
28515 TCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAA
28556 TCCTTCGGGCCATC
1 TCCTTCGGGCCATC
28570 CATAAGACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 16 0.34
42 31 0.66
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAA
Found at i:28748 original size:42 final size:41
Alignment explanation
Indices: 28687--28783 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 41
28677 GATTTGTAAG
* * *
28687 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG-ATAAA
* * *
28729 TCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAA
28770 TCCTTCGGGCCATC
1 TCCTTCGGGCCATC
28784 CATAAGACCT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 16 0.33
42 32 0.67
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAA
Found at i:29000 original size:41 final size:42
Alignment explanation
Indices: 28898--29010 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
28888 TTCACAATTT
* * * * * *
28898 ATAAGTCCTCCAGGCCATCAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
* * * *
28940 TTAAATCTTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
*
28981 ATAAGTCCTTCGGGCCATCTATAAGACCTT
1 ATAAGTCCTTCGGGCCATCTGTAAG-CCTT
29011 CGGGTAGGAT
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
41 20 0.36
42 35 0.64
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
Found at i:29009 original size:216 final size:215
Alignment explanation
Indices: 28351--29457 Score: 1867
Period size: 216 Copynumber: 5.1 Consensus size: 215
28341 GTGAAGCAAA
*
28351 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* * *
28415 AGAAGATGGAATTTTTGAAAACAAATAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTTG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
*
28480 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
28545 AAGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
*
28565 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
28629 AGAAGATGGAATTTTTGAAAACAAATAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
*
28694 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
28759 AAGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
*
28779 CCATCCATAAGACCTTCAGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* * *
28844 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTTATAAGTCCTCC
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TTTCACGATTTGTAAGTCCTTC
* *
28909 AGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
28974 CAAGATGATAAGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
*
28995 CCATCTATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
29060 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
* * *
29125 GGCCATCAGTAAGTCCTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTAAACCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
29190 AAGATGATAAGTCCTTCAGG
196 AAGATGATAAGTCCTTCGGG
*
29210 CCATCCATAAGACTTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
*
29275 AGGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCATGATTTGTAAGTCCTTC
66 A-GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTC
* * * * * *
29340 AGGACATTAGTAAGTCTTTCCAGCATGATGCTTAAATCCTTCGGGTTATCCGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
*
29405 CAGGATGATAAGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
* * *
29426 TCATCCATAAGACCTTTTGGGCAGGATGTTTT
1 CCATCCATAAGACC-TTCGGGTAGGATGTTTT
29458 TCACCAGGAT
Statistics
Matches: 851, Mismatches: 38, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
214 260 0.31
215 220 0.26
216 356 0.42
217 15 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (215 bp):
CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGG
Found at i:29201 original size:431 final size:429
Alignment explanation
Indices: 28351--29457 Score: 1874
Period size: 431 Copynumber: 2.6 Consensus size: 429
28341 GTGAAGCAAA
*
28351 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* * **
28415 AGAAGATGGAATTTTTGAAAACAAATAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTTG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCA
*
28480 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
28545 AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAAA
196 AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAAA
*
28610 AATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACAAATAATGCGATTTTCAAAATTTC
261 AATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTC
* * *
28675 ACGATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTC
326 ACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCCTTCGAGCATGATGCTTAAATCCTTCGGGTC
** *
28740 ATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGG
391 ATCTGTAAACCTTTAGAGCAAGATGATAAGTCCTTCAGG
*
28779 CCATCCATAAGACCTTCAGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* * *
28844 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTTATAAGTCCTCC
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TTTCACGATTTGTAAGTCCTTC
*
28909 AGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTAAGCCTTTAGAG
130 AGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
* *
28974 CAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGA
195 CAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAA
*
29039 AAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATT
260 AAATG-AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATT
29104 TCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCCTTCGAGCATGATGCTTAAATCCTTCGGG
324 TCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCCTTCGAGCATGATGCTTAAATCCTTCGGG
*
29169 TTATCTGTAAACCTTTAGAGCAAGATGATAAGTCCTTCAGG
389 TCATCTGTAAACCTTTAGAGCAAGATGATAAGTCCTTCAGG
*
29210 CCATCCATAAGACTTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
*
29275 AGGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCATGATTTGTAAGTCCTTC
66 A-GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTC
* * * * *
29340 AGGACATTAGTAAGTCTTTCCAGCATGATGCTTAAATCCTTCGGGTTATCCGTAAGCCTTTAGAG
130 AGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
* * * *
29405 CAGGATGATAAGTCCTTCGGGTCATCCATAAGACCTTTTGGGCAGGATGTTTT
195 CAAGATGATAAGTCCTTCGGGCCATCCATAAGACC-TTCGGGTAGGATGTTTT
29458 TCACCAGGAT
Statistics
Matches: 635, Mismatches: 39, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
428 47 0.07
429 55 0.09
430 148 0.23
431 329 0.52
432 56 0.09
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (429 bp):
CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCA
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAAA
AATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTC
ACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCCTTCGAGCATGATGCTTAAATCCTTCGGGTC
ATCTGTAAACCTTTAGAGCAAGATGATAAGTCCTTCAGG
Found at i:29395 original size:42 final size:41
Alignment explanation
Indices: 29349--29442 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 41
29339 CAGGACATTA
* * * * *
29349 GTAAGTCTTTCCAGCATGATGCTTAAATCCTTCGGGTTATCC
1 GTAAGCCTTTACAGCAGGATG-ATAAATCCTTCGGGTCATCC
* *
29391 GTAAGCCTTTAGAGCAGGATGATAAGTCCTTCGGGTCATCC
1 GTAAGCCTTTACAGCAGGATGATAAATCCTTCGGGTCATCC
*
29432 ATAAGACCTTT
1 GTAAG-CCTTT
29443 TGGGCAGGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 21 0.49
42 22 0.51
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
GTAAGCCTTTACAGCAGGATGATAAATCCTTCGGGTCATCC
Found at i:33167 original size:3 final size:3
Alignment explanation
Indices: 33159--33222 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
33149 AATATTTATT
*
33159 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA -AA TTTA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* *
33205 TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
33223 AACTGAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 46 0.88
4 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:33199 original size:21 final size:21
Alignment explanation
Indices: 33159--33212 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
33149 AATATTTATT
33159 TAATAATAATAATATATAATAA
1 TAATAATAA-AATATATAATAA
*
33181 TAATAATAAAATTTATAATAA
1 TAATAATAAAATATATAATAA
33202 TAATAATAAAA
1 TAATAATAAAA
33213 ATAAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATAATAAAATATATAATAA
Found at i:37326 original size:60 final size:60
Alignment explanation
Indices: 37196--37424 Score: 227
Period size: 59 Copynumber: 3.9 Consensus size: 60
37186 AATTATTATC
* ** * * * *
37196 CTCATTCTAAATTGGT-CTCTAATTTTTTTAATATTCTAATTTCATCCTTAAACTAT-A-T
1 CTCATTCTAAATTAGTCCT-TAAACTTTTGAACATTCCAATTTCATCCTCAAACTATGACT
* *
37254 ACTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATTCTCAATCTATGACT
1 -CTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAACTATGACT
* * * *
37315 CTCATTCTAAATTAGTACAT-AACTTTTGAACATTCTAATTTCACCCTCAAACTATGACT
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAACTATGACT
* * * * *
37374 C-CATTCTAAATTAGTCCTCAAAATTTTAAATC-TTCCTATTTCATCCCCAAA
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAA-CATTCCAATTTCATCCTCAAA
37425 TTCATCCAAA
Statistics
Matches: 141, Mismatches: 24, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
58 15 0.11
59 103 0.73
60 22 0.16
61 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (60 bp):
CTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAACTATGACT
Found at i:39822 original size:93 final size:93
Alignment explanation
Indices: 39723--39893 Score: 236
Period size: 93 Copynumber: 1.8 Consensus size: 93
39713 TTCTTTTTTT
* * * * *
39723 ATTCGATAAAAATAAATTAGTAATTAAAAGACATA-AACAATCTATTTTAGTTTAATCCTGAATT
1 ATTCGATAAAAATAAAATAGTAATTAAAAAACATATAAAAATAT-TTTTAGTTTAATCCTAAATT
* *
39787 TAATTTAATCTAATATCATTATTTTTATA
65 CAATCTAATCTAATATCATTATTTTTATA
* * *
39816 ATTCGATGAAAATAAAATAGTAATTAAAAAATATATAAAAATATTTTTAGTTTAATCTTAAATTC
1 ATTCGATAAAAATAAAATAGTAATTAAAAAACATATAAAAATATTTTTAGTTTAATCCTAAATTC
39881 AATCTAATCTAAT
66 AATCTAATCTAAT
39894 CTAGTTTTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
93 61 0.91
94 6 0.09
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (93 bp):
ATTCGATAAAAATAAAATAGTAATTAAAAAACATATAAAAATATTTTTAGTTTAATCCTAAATTC
AATCTAATCTAATATCATTATTTTTATA
Found at i:43500 original size:30 final size:32
Alignment explanation
Indices: 43449--43514 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 32
43439 TAAAAATAAA
* *
43449 TAAATGAACACAAACATAATATTAA-A-ATTT
1 TAAATGAACACAAACAGAATATAAATACATTT
*
43479 TAAATGAATACAAATC-GAATATAAATACATTT
1 TAAATGAACACAAA-CAGAATATAAATACATTT
43511 TAAA
1 TAAA
43515 ATAAATAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 20 0.67
31 2 0.07
32 8 0.27
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (32 bp):
TAAATGAACACAAACAGAATATAAATACATTT
Found at i:52801 original size:22 final size:22
Alignment explanation
Indices: 52773--52829 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
52763 GCTTTGCATG
52773 CGCCATGCACGTCGGCGTAGGT
1 CGCCATGCACGTCGGCGTAGGT
52795 CGCCATGCACGTCGGCGTAGGT
1 CGCCATGCACGTCGGCGTAGGT
52817 CGCCATGCACGTC
1 CGCCATGCACGTC
52830 CAGCGACCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.14, C:0.35, G:0.33, T:0.18
Consensus pattern (22 bp):
CGCCATGCACGTCGGCGTAGGT
Found at i:52887 original size:29 final size:28
Alignment explanation
Indices: 52811--52944 Score: 160
Period size: 28 Copynumber: 4.7 Consensus size: 28
52801 GCACGTCGGC
* *
52811 GTAGGTCGCCATGCACGTCCAGCGACCT
1 GTAGGTCGCCATGCACGCCCAGCGACAT
* * *
52839 GTAGGTCGCCATGCAAGCCCCGGGACAT
1 GTAGGTCGCCATGCACGCCCAGCGACAT
* * *
52867 GCTAGGTCGCCATGTACGCCCAACGACCT
1 G-TAGGTCGCCATGCACGCCCAGCGACAT
* *
52896 GTAGGTCGCCATGCAAGCCCCGCGACAT
1 GTAGGTCGCCATGCACGCCCAGCGACAT
52924 GCTAGGTCGCCATGCACGCCC
1 G-TAGGTCGCCATGCACGCCC
52945 GACGACCAAG
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
28 47 0.54
29 40 0.46
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.16
Consensus pattern (28 bp):
GTAGGTCGCCATGCACGCCCAGCGACAT
Found at i:52900 original size:57 final size:57
Alignment explanation
Indices: 52812--52951 Score: 235
Period size: 57 Copynumber: 2.5 Consensus size: 57
52802 CACGTCGGCG
* * *
52812 TAGGTCGCCATGCACGTCCAGCGACCTGTAGGTCGCCATGCAAGCCCCGGGACATGC
1 TAGGTCGCCATGCACGCCCAACGACCTGTAGGTCGCCATGCAAGCCCCGCGACATGC
*
52869 TAGGTCGCCATGTACGCCCAACGACCTGTAGGTCGCCATGCAAGCCCCGCGACATGC
1 TAGGTCGCCATGCACGCCCAACGACCTGTAGGTCGCCATGCAAGCCCCGCGACATGC
*
52926 TAGGTCGCCATGCACGCCCGACGACC
1 TAGGTCGCCATGCACGCCCAACGACC
52952 AAGCCTTCAC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 77 1.00
ACGTcount: A:0.20, C:0.37, G:0.28, T:0.15
Consensus pattern (57 bp):
TAGGTCGCCATGCACGCCCAACGACCTGTAGGTCGCCATGCAAGCCCCGCGACATGC
Found at i:53181 original size:15 final size:17
Alignment explanation
Indices: 53160--53205 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 17
53150 ATAAGAAAGA
53160 AAGAAAGGGAGAA-AAG
1 AAGAAAGGGAGAAGAAG
*
53176 -AGAAAGGAAAGGAAGAAG
1 AAGAAAGG-GA-GAAGAAG
53194 AAGAAAGGGAGA
1 AAGAAAGGGAGA
53206 TAAGGCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
15 7 0.29
16 1 0.04
17 5 0.21
18 4 0.17
19 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (17 bp):
AAGAAAGGGAGAAGAAG
Found at i:53181 original size:19 final size:21
Alignment explanation
Indices: 53152--53197 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
53142 GTAGAAGCAT
*
53152 AAGAA-AGAAA-GAAAGGGAG
1 AAGAAGAGAAAGGAAAGGAAG
53171 AA-AAGAGAAAGGAAAGGAAG
1 AAGAAGAGAAAGGAAAGGAAG
53191 AAGAAGA
1 AAGAAGA
53198 AAGGGAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 7 0.30
20 10 0.43
21 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (21 bp):
AAGAAGAGAAAGGAAAGGAAG
Found at i:53198 original size:19 final size:19
Alignment explanation
Indices: 53155--53201 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
53145 GAAGCATAAG
*
53155 AAAGAAA-GAAAGGGAGAA
1 AAAGAAAGGAAAGGAAGAA
53173 AAGAGAAAGGAAAGGAAGAA
1 AA-AGAAAGGAAAGGAAGAA
*
53193 GAAGAAAGG
1 AAAGAAAGG
53202 GAGATAAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 12 0.48
20 11 0.44
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (19 bp):
AAAGAAAGGAAAGGAAGAA
Found at i:53334 original size:21 final size:21
Alignment explanation
Indices: 53309--53352 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
53299 AATTTAGTTA
53309 ATTAGTGTGTTAGTATAAATT
1 ATTAGTGTGTTAGTATAAATT
* * *
53330 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTGTGTTAGTATAAATT
53351 AT
1 AT
53353 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTGTGTTAGTATAAATT
Found at i:53362 original size:28 final size:30
Alignment explanation
Indices: 53329--53391 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
53319 TAGTATAAAT
53329 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
53357 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
53387 TATTA
1 TATTA
53392 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 20 0.61
29 1 0.03
30 12 0.36
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (30 bp):
TATTAGTTTGTTAGTTTAAGTTATATATTA
Found at i:57186 original size:11 final size:11
Alignment explanation
Indices: 57170--57211 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
57160 TTTAATTGAA
57170 TTATTTATATT
1 TTATTTATATT
57181 TTATTTATATT
1 TTATTTATATT
*
57192 TTATCTTAT-TA
1 TTAT-TTATATT
57203 TTATTTATA
1 TTATTTATA
57212 AATAGTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTTATATT
Found at i:57207 original size:16 final size:17
Alignment explanation
Indices: 57169--57211 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
57159 TTTTAATTGA
*
57169 ATTATTTATATTTTATT
1 ATTATTTATATCTTATT
57186 -TATATTT-TATCTTATT
1 AT-TATTTATATCTTATT
57202 ATTATTTATA
1 ATTATTTATA
57212 AATAGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTTATATCTTATT
Found at i:57790 original size:16 final size:16
Alignment explanation
Indices: 57769--57802 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57759 TTAATATTAT
**
57769 TAAATAGTTGAATTTA
1 TAAATAGTCAAATTTA
57785 TAAATAGTCAAATTTA
1 TAAATAGTCAAATTTA
57801 TA
1 TA
57803 TTTATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (16 bp):
TAAATAGTCAAATTTA
Found at i:57819 original size:13 final size:13
Alignment explanation
Indices: 57801--57825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57791 GTCAAATTTA
57801 TATTTATAAATAC
1 TATTTATAAATAC
57814 TATTTATAAATA
1 TATTTATAAATA
57826 ATCAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTATAAATAC
Found at i:57998 original size:15 final size:15
Alignment explanation
Indices: 57975--58015 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
57965 AATGTTTTAA
*
57975 TAATGATTTTGTATT
1 TAATGATTTTATATT
*
57990 TAATAATTTTATATT
1 TAATGATTTTATATT
58005 TAATGATTTTA
1 TAATGATTTTA
58016 GTAAAGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
TAATGATTTTATATT
Found at i:58070 original size:21 final size:22
Alignment explanation
Indices: 58046--58092 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
58036 TGATTACTAA
*
58046 TAATG-TTTTATTATTAAT-ATT
1 TAATGATTTTA-TACTAATGATT
58067 TAATGATTTTATACTAATGATT
1 TAATGATTTTATACTAATGATT
58089 TAAT
1 TAAT
58093 AATGATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (22 bp):
TAATGATTTTATACTAATGATT
Found at i:58121 original size:14 final size:14
Alignment explanation
Indices: 58089--58160 Score: 50
Period size: 14 Copynumber: 5.5 Consensus size: 14
58079 ACTAATGATT
58089 TAATAATG-ATTAG
1 TAATAATGAATTAG
58102 TAATAATGAAATTA-
1 TAATAATG-AATTAG
*
58116 TAATAATG-ATTTG
1 TAATAATGAATTAG
*
58129 ATATTAAT-AATT--
1 -TAATAATGAATTAG
*
58141 TAATAATG-ATTAC
1 TAATAATGAATTAG
58154 TAATAAT
1 TAATAAT
58161 TATTTAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
11 9 0.19
12 3 0.06
13 15 0.31
14 17 0.35
15 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (14 bp):
TAATAATGAATTAG
Found at i:58158 original size:38 final size:35
Alignment explanation
Indices: 58027--58166 Score: 115
Period size: 38 Copynumber: 3.8 Consensus size: 35
58017 TAAAGATATG
* *
58027 ATTTAGTAATGATTACTAATAATGTTTTATTATTAAT
1 ATTTAATAATGATTA-TAATAATGATTTA-TATTAAT
* * *
58064 ATTTAATGAT-TTTATACTAATGATTTA-A-TAAT
1 ATTTAATAATGATTATAATAATGATTTATATTAAT
58096 GATTAGTAATAATGAAATTATAATAATGATTTGATATTAAT
1 -ATT--TAATAATG--ATTATAATAATGATTT-ATATTAAT
*
58137 AATTTAATAATGATTACTAATAATTATTTA
1 -ATTTAATAATGATTA-TAATAATGATTTA
58167 ATAATGTTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
32 4 0.05
33 4 0.05
35 17 0.20
36 3 0.04
37 13 0.16
38 25 0.30
39 9 0.11
40 1 0.01
41 7 0.08
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (35 bp):
ATTTAATAATGATTATAATAATGATTTATATTAAT
Found at i:58234 original size:16 final size:16
Alignment explanation
Indices: 58213--58268 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
58203 TAAATCGAAG
58213 TTATAAATAGTTGAAT
1 TTATAAATAGTTGAAT
* *
58229 TTATAACTAGTCGAAT
1 TTATAAATAGTTGAAT
58245 TTATCTTAAATATGTTGAAT
1 TTA---TAAATA-GTTGAAT
58265 TTAT
1 TTAT
58269 TTTTTTTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 17 0.53
17 1 0.03
19 5 0.16
20 9 0.28
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (16 bp):
TTATAAATAGTTGAAT
Found at i:58331 original size:17 final size:15
Alignment explanation
Indices: 58297--58336 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
58287 ATAGACATGC
58297 ATATTTAATATTATA
1 ATATTTAATATTATA
*
58312 ATATTTAATTTTTAATA
1 ATATTTAA-TATT-ATA
58329 ATATTTAA
1 ATATTTAA
58337 CATATGCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTTAATATTATA
Found at i:59463 original size:18 final size:18
Alignment explanation
Indices: 59440--59474 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
59430 AATAAAATTG
59440 AGTTAAATCAAATAATAT
1 AGTTAAATCAAATAATAT
*
59458 AGTTAAATTAAATAATA
1 AGTTAAATCAAATAATA
59475 ATTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
AGTTAAATCAAATAATAT
Found at i:60766 original size:8 final size:8
Alignment explanation
Indices: 60753--60783 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
60743 AACTTAACTT
60753 AAACTAAC
1 AAACTAAC
60761 AAACTAAC
1 AAACTAAC
*
60769 AAACTAAA
1 AAACTAAC
60777 AAACTAA
1 AAACTAA
60784 TTAACTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (8 bp):
AAACTAAC
Found at i:61132 original size:11 final size:11
Alignment explanation
Indices: 61112--61177 Score: 80
Period size: 11 Copynumber: 5.9 Consensus size: 11
61102 CGTGTTACCT
*
61112 TTCTTTCTTTC
1 TTCTTCCTTTC
61123 TTCTTCCTTTC
1 TTCTTCCTTTC
*
61134 TTCTTCATTTC
1 TTCTTCCTTTC
61145 TTCTTCCTTTCC
1 TTCTTCCTTT-C
*
61157 TT-TACCTTTC
1 TTCTTCCTTTC
61167 TTTCTTCCTTT
1 -TTCTTCCTTT
61178 TTACAACCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
10 1 0.02
11 37 0.79
12 9 0.19
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (11 bp):
TTCTTCCTTTC
Found at i:61390 original size:43 final size:43
Alignment explanation
Indices: 61329--61410 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
61319 ATAGCTGCAT
* *
61329 GCAGAAGAGTAATCACACATGCATGAGGGTGCAGCAGCAGCAA
1 GCAGAAGAGGAATCACACATGCATGAGGGTGCAACAGCAGCAA
61372 GCAGAAGAGGAATCACACATGCATGAGGGTGCAACAGCA
1 GCAGAAGAGGAATCACACATGCATGAGGGTGCAACAGCA
61411 ACATACGTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.30, T:0.11
Consensus pattern (43 bp):
GCAGAAGAGGAATCACACATGCATGAGGGTGCAACAGCAGCAA
Found at i:62292 original size:18 final size:18
Alignment explanation
Indices: 62269--62303 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
62259 AAATTTGTAA
62269 AAGAAGAAGAAAAAAGAG
1 AAGAAGAAGAAAAAAGAG
*
62287 AAGAAGAAGAAGAAAGA
1 AAGAAGAAGAAAAAAGA
62304 AGTAGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAGAAGAAGAAAAAAGAG
Found at i:75736 original size:17 final size:17
Alignment explanation
Indices: 75714--75764 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
75704 TAGTATTATT
75714 TATTATTAAAATAAGAA
1 TATTATTAAAATAAGAA
*
75731 TATTA-T--AGT---AA
1 TATTATTAAAATAAGAA
75742 TATTATTAAAATAAGAA
1 TATTATTAAAATAAGAA
75759 TATTAT
1 TATTAT
75765 AGTAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
11 7 0.27
12 1 0.04
14 4 0.15
16 1 0.04
17 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TATTATTAAAATAAGAA
Found at i:75745 original size:11 final size:11
Alignment explanation
Indices: 75729--75775 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
75719 TTAAAATAAG
75729 AATATTATAGT
1 AATATTATAGT
75740 AATATTAT--T
1 AATATTATAGT
*
75749 AA-AATA-AG-
1 AATATTATAGT
75757 AATATTATAGT
1 AATATTATAGT
75768 AATATTAT
1 AATATTAT
75776 TAAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 5 0.17
9 6 0.21
10 2 0.07
11 16 0.55
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (11 bp):
AATATTATAGT
Found at i:75745 original size:28 final size:28
Alignment explanation
Indices: 75714--75782 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
75704 TAGTATTATT
75714 TATTATTAAAATAAGAATATTATAGTAA
1 TATTATTAAAATAAGAATATTATAGTAA
75742 TATTATTAAAATAAGAATATTATAGTAA
1 TATTATTAAAATAAGAATATTATAGTAA
75770 TATTATTAAAATA
1 TATTATTAAAATA
75783 TTAAATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (28 bp):
TATTATTAAAATAAGAATATTATAGTAA
Found at i:75947 original size:19 final size:19
Alignment explanation
Indices: 75923--75959 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
75913 ATGACCAACA
*
75923 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
75942 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
75960 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:76051 original size:21 final size:20
Alignment explanation
Indices: 76004--76051 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
75994 CATTTTGACC
* *
76004 ATCGCATTGCGATTTTTGAA
1 ATCGCATTACGATTTTAGAA
76024 ATCCGCATTACGATTTTAGATA
1 AT-CGCATTACGATTTTAGA-A
76046 ATCGCA
1 ATCGCA
76052 ATGCGAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.79
22 3 0.12
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (20 bp):
ATCGCATTACGATTTTAGAA
Found at i:76112 original size:20 final size:20
Alignment explanation
Indices: 76087--76194 Score: 128
Period size: 20 Copynumber: 5.2 Consensus size: 20
76077 ATAACACGTG
76087 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
76107 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
76127 ATCGCAACGCAATAATAT-ACGT
1 ATCGCAACGCGAT--TCTGAC-T
*
76149 GATCGCAACGCGATTCTAACT
1 -ATCGCAACGCGATTCTGACT
**
76170 ATCGCAACGATATTCTGACT
1 ATCGCAACGCGATTCTGACT
76190 ATCGC
1 ATCGC
76195 GTTGCGATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
20 54 0.71
21 5 0.07
22 5 0.07
23 12 0.16
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:76208 original size:63 final size:63
Alignment explanation
Indices: 76066--76194 Score: 199
Period size: 63 Copynumber: 2.1 Consensus size: 63
76056 GAATATGTAA
* * * *
76066 ATCGCAACGCGAT-A-ACACGTGATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCAATAATATACGTGATCGCAACGCGATTCTAACTATCGCAACGAGATTCTGACT
*
76127 ATCGCAACGCAATAATATACGTGATCGCAACGCGATTCTAACTATCGCAACGATATTCTGACT
1 ATCGCAACGCAATAATATACGTGATCGCAACGCGATTCTAACTATCGCAACGAGATTCTGACT
76190 ATCGC
1 ATCGC
76195 GTTGCGATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 12 0.20
62 1 0.02
63 48 0.79
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (63 bp):
ATCGCAACGCAATAATATACGTGATCGCAACGCGATTCTAACTATCGCAACGAGATTCTGACT
Found at i:76433 original size:22 final size:22
Alignment explanation
Indices: 76357--76436 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
76347 TCACTCTCTA
* *
76357 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCTGTCCCCATCTC
* *
76379 CGACGAAATCCT-TCCCCATTTC
1 CGGCGAAAT-CTGTCCCCATCTC
*
76401 CGGCAAAATCTGTCCCCATCTC
1 CGGCGAAATCTGTCCCCATCTC
76423 CGGCGAAATCTGTC
1 CGGCGAAATCTGTC
76437 TATCTCCATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.04
22 45 0.94
23 1 0.02
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CGGCGAAATCTGTCCCCATCTC
Found at i:76841 original size:20 final size:20
Alignment explanation
Indices: 76816--76864 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
76806 GCGATTATCT
*
76816 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
**
76836 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCAAATTCG
*
76856 TGTTGCGAT
1 CGTTGCGAT
76865 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:78271 original size:21 final size:20
Alignment explanation
Indices: 78200--78272 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
78190 CTCCACTTCG
78200 AGAGCCATCACCTCAC--CC
1 AGAGCCATCACCTCACAACC
*
78218 AGAGCCATCACCTGATCAACC
1 AGAGCCATCACCTCA-CAACC
* * *
78239 ACA-CTATACACCTCTACAACG
1 AGAGCCAT-CACCTC-ACAACC
78260 AGAGCCATCACCT
1 AGAGCCATCACCT
78273 ATTCTGTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 3 0.07
21 20 0.48
22 4 0.10
ACGTcount: A:0.33, C:0.41, G:0.11, T:0.15
Consensus pattern (20 bp):
AGAGCCATCACCTCACAACC
Found at i:78915 original size:20 final size:20
Alignment explanation
Indices: 78887--78975 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
78877 CAACACAAAA
*
78887 ATGATTATCGCAACGCGAAT
1 ATGACTATCGCAACGCGAAT
* * *
78907 TTGACTATCGCAATGCGAAA
1 ATGACTATCGCAACGCGAAT
*
78927 ACGACTATCGCAACGCGGAA-
1 ATGACTATCGCAACGC-GAAT
78947 ATGACTATCGCAACGCGAAT
1 ATGACTATCGCAACGCGAAT
*
78967 TTGACTATC
1 ATGACTATC
78976 ACAATGGGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
19 3 0.05
20 52 0.90
21 3 0.05
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
ATGACTATCGCAACGCGAAT
Found at i:79019 original size:20 final size:20
Alignment explanation
Indices: 78884--79016 Score: 107
Period size: 20 Copynumber: 7.0 Consensus size: 20
78874 TTGCAACACA
* *
78884 AAAATGATTATCGCAACGCG
1 AAAATGACTATCGCAATGCG
**
78904 AATTTGACTATCGCAATGCG
1 AAAATGACTATCGCAATGCG
* *
78924 AAAACGACTATCGCAACGCG
1 AAAATGACTATCGCAATGCG
* *
78944 GAAATGACTATCGCAACGCG
1 AAAATGACTATCGCAATGCG
** *
78964 AATTTGACTATCACAATG-G
1 AAAATGACTATCGCAATGCG
* *
78983 --GAT-A--ATCGCAATGCA
1 AAAATGACTATCGCAATGCG
78998 AAAATGACTATCGCAATGC
1 AAAATGACTATCGCAATGC
79017 AAATTTAGTT
Statistics
Matches: 87, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
14 8 0.09
16 1 0.01
17 3 0.03
18 1 0.01
19 1 0.01
20 73 0.84
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
AAAATGACTATCGCAATGCG
Found at i:79071 original size:20 final size:20
Alignment explanation
Indices: 79046--79112 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
79036 GATTATCTCA
79046 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
79066 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* ** *
79086 TTGCGATAATCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
79106 TTGCGAT
1 TTGCGAT
79113 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:79122 original size:20 final size:20
Alignment explanation
Indices: 79099--79142 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
79089 CGATAATCAT
79099 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
*
79119 TTTCGTGTTGTGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
79139 TTTC
1 TTTC
79143 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.09, G:0.23, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:79719 original size:42 final size:42
Alignment explanation
Indices: 79647--79729 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
79637 AATCTCCTAT
*
79647 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCACTCAAGAGGT-CCCTCCCAC
* * * *
79689 CGTTTAAGAGGCCCCTGTCATCATTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCCCA
79730 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCCCAC
Found at i:81250 original size:20 final size:20
Alignment explanation
Indices: 81225--81442 Score: 141
Period size: 20 Copynumber: 11.8 Consensus size: 20
81215 GCGATTTTCT
*
81225 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
81245 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
81265 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
* *
81284 CGTTGTGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
*
81298 CGTTTCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
81318 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
** *
81338 AATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
81352 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
81372 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
81392 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* * *
81406 CGTTGTGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
81426 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
81443 GAATGTGTAA
Statistics
Matches: 150, Mismatches: 30, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
14 27 0.18
16 3 0.02
17 1 0.01
18 2 0.01
19 16 0.11
20 101 0.67
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:81251 original size:34 final size:34
Alignment explanation
Indices: 81191--81326 Score: 121
Period size: 34 Copynumber: 3.9 Consensus size: 34
81181 ATCATATTCG
* * * *
81191 CGTTGCGATAGTCTAATACACTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
81225 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
* * *
81265 CGTTGCGATAGTC-ATTTCGCGTTGTGATTATCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
81298 CGTTTCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
81327 AGTCATTTTC
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
33 14 0.17
34 38 0.46
36 1 0.01
37 1 0.01
39 12 0.15
40 16 0.20
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:81313 original size:73 final size:74
Alignment explanation
Indices: 81181--81327 Score: 206
Period size: 73 Copynumber: 2.0 Consensus size: 74
81171 TTCAATCTGC
* * *
81181 ATCATATTCGCGTTGCGATAGTCTAATACACTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCC
1 ATCAAATTCGCGTTGCGATAGTCTAATACACGTTGCGATTATCTCGTTGCGATAGTCAAATTCCC
81246 GTTGCGATA
66 GTTGCGATA
* * * * * *
81255 ATCAAATTCGCGTTGCGATAGTC-ATTTCGCGTTGTGATTATCTCGTTTCGATAGTCAAATTCGC
1 ATCAAATTCGCGTTGCGATAGTCTAATACACGTTGCGATTATCTCGTTGCGATAGTCAAATTCCC
81319 GTTGCGATA
66 GTTGCGATA
81328 GTCATTTTCG
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
73 42 0.66
74 22 0.34
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (74 bp):
ATCAAATTCGCGTTGCGATAGTCTAATACACGTTGCGATTATCTCGTTGCGATAGTCAAATTCCC
GTTGCGATA
Found at i:81361 original size:54 final size:54
Alignment explanation
Indices: 81242--81439 Score: 308
Period size: 54 Copynumber: 3.7 Consensus size: 54
81232 ATAGTCAAAT
* * *
81242 TCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCA-TTTCGCGTTGTGATTA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* * *
81295 TCTCGTTTCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGAATTGCGATTA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
81349 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* * *
81403 TCCCGTTGTGATATTCAAATTCACGTTGCGATAGTCA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
81440 AATGAATGTG
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
53 34 0.26
54 98 0.74
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (54 bp):
TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
Done.