Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 51
Found at i:1646552 original size:3 final size:3
Alignment explanation
Indices: 1646544--1646624 Score: 103
Period size: 3 Copynumber: 26.7 Consensus size: 3
1646534 GGCCTGTTTG
**
1646544 TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1646589 TATA TAA -AA TAA TAA TAA TAA TAAA TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
1646625 GAAAATGGAG
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 56 0.81
4 9 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1646972 original size:114 final size:119
Alignment explanation
Indices: 1646823--1647174 Score: 312
Period size: 124 Copynumber: 2.9 Consensus size: 119
1646813 GGGGATGATA
* * * * * *
1646823 ATATCTCATTCTGTGAT-GTAAT-TTGGAAAAGGGTTGAACAAGTTCTTCTTATTATAAAATTTT
1 ATATCTCCTTCTGTGATAG-AATCATGCAAAA-GGTTGAACAAGCTCTTCTCATTATAAAATTCT
*
1646886 TCTTCCTTCTTC-A-GA-T-T-ATTATGAACTTTCCCTGGAAAAGTTGATGTTGAC
64 TCTTCCTTCTTCAATGATTCTCATTATGAACTTTCCCTGGAAAAGTTGATGCTGAC
* * * * * * *
1646937 CTATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTC
1 ATATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATAAAATTCTTC
* * *
1647002 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGAT
66 TTCCTTCTTCA-ATGA----TTCTCATTATGAACTTTCCCTGGAAAAGTTGATGCTGAC
* * *
1647061 ATATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGT-GAA--CTTC
1 ATATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATAAAATTCTTC
* * *
1647123 TT-ATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGAT
66 TTCCTTCTTCA-ATGA----TTCTCATTATGAACTTTCCCTGGAAAAGTTGAT
1647175 CTATCAAGTG
Statistics
Matches: 198, Mismatches: 28, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
114 53 0.27
115 6 0.03
116 1 0.01
117 2 0.01
120 48 0.24
121 6 0.03
122 1 0.01
123 2 0.01
124 79 0.40
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (119 bp):
ATATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATAAAATTCTTC
TTCCTTCTTCAATGATTCTCATTATGAACTTTCCCTGGAAAAGTTGATGCTGAC
Found at i:1647054 original size:124 final size:120
Alignment explanation
Indices: 1646903--1647174 Score: 400
Period size: 124 Copynumber: 2.2 Consensus size: 120
1646893 TCTTCAGATT
* * * * * *
1646903 ATTATGAACTTTCCCTGGAAAAGTTGATGTTGACCTATTTCCTTCTGTGATAGAGTCATTCAAAA
1 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGACATATCTCCTTCTGTGATAGAATCATGCAAAA
* *
1646968 GGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
66 GGTTGAACAAGCTCTTCTCATTATGAA---CTTC-TTATTCTTCAGATGAGTTCTTCTC
* *
1647027 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATATATCTCCTTCTGTGATAGAATTATGCAAAA
1 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGACATATCTCCTTCTGTGATAGAATCATGCAAAA
*
1647092 GGTTGAACAAGCTCTTCTCATTGTGAACTTCTTATTCTTCAGATGAGTTCTTCTC
66 GGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCTTCAGATGAGTTCTTCTC
*
1647147 ATTATGAACTTTCTCTGGAAAAGCTGAT
1 ATTATGAACTTTCTCTGGAAAAGTTGAT
1647175 CTATCAAGTG
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
120 50 0.37
121 4 0.03
124 82 0.60
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (120 bp):
ATTATGAACTTTCTCTGGAAAAGTTGATGCTGACATATCTCCTTCTGTGATAGAATCATGCAAAA
GGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCTTCAGATGAGTTCTTCTC
Found at i:1647385 original size:225 final size:228
Alignment explanation
Indices: 1647087--1647612 Score: 904
Period size: 229 Copynumber: 2.3 Consensus size: 228
1647077 TAGAATTATG
* * * *
1647087 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTT-ATTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
1647148 TTATGAACTTTCTCTGGAAAAGCTGATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
1647213 TCTTCTCATTATGAA-T-TTC-TTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
131 TCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
1647275 GGCAATGTTGATCCATCAAATGATGAATTCAAA
196 GGCAATGTTGATCCATCAAATGATGAATTCAAA
*
1647308 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1647373 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
1647438 TCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
131 TCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
*
1647503 TGGCAATGTTGATCCATCAAATGATGAATTTAAA
195 TGGCAATGTTGATCCATCAAATGATGAATTCAAA
*
1647537 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCTTTCTTCAGATGAGTTTTTCT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-C-TTCTTCAGATGAGTTCTTCT
1647602 CATTATGAACT
64 CATTATGAACT
1647613 CTAACTGGCA
Statistics
Matches: 286, Mismatches: 9, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
221 28 0.10
224 6 0.02
225 101 0.35
227 1 0.00
228 3 0.01
229 116 0.41
230 1 0.00
231 30 0.10
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (228 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
TCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT
GGCAATGTTGATCCATCAAATGATGAATTCAAA
Found at i:1647541 original size:116 final size:112
Alignment explanation
Indices: 1647087--1647651 Score: 687
Period size: 113 Copynumber: 5.0 Consensus size: 112
1647077 TAGAATTATG
** * *
1647087 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAA--CTTC-TTATTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * * *
1647149 TATGAACT-TTCTCTGGAAAAGCTGATCTATCAAGTGATGGATTTGAG
66 TATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGGATTTAAA
1647196 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-T-TTC-TTCTTCTTCAGATGACGAGTTCTTCT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGAT---GAGTTCTTCT
* *
1647258 CATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
63 CATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGGATTTAAA
* *
1647308 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
* * * * * * *
1647373 TTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
65 TTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGGATTTAAA
1647421 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGAT---GAGTTCTTC
*
1647486 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
62 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGGATTTAAA
* * *
1647537 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCTTTCTTCAGATGAGTTTTTCT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTT-TC-TTCTTCAGATGAGTTCTTCT
* * *
1647602 CATTATGAACTCTAACTGGCACTGTTGATCCATTAAATGATGGATTTAAA
63 CATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGGATTTAAA
1647652 TCTTTGCTAA
Statistics
Matches: 396, Mismatches: 44, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
109 44 0.11
112 80 0.20
113 100 0.25
114 1 0.00
115 58 0.15
116 99 0.25
117 4 0.01
118 10 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGGATTTAAA
Found at i:1648551 original size:114 final size:114
Alignment explanation
Indices: 1648346--1648564 Score: 332
Period size: 114 Copynumber: 1.9 Consensus size: 114
1648336 ATGCAGTTCA
* * * ** *
1648346 TCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCGATTCAGATCAGATAACTCAAAGAACAC
1 TCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAAGAACAC
*
1648411 TTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCC
66 TTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCAAATTCC
* * *
1648460 TCTTTCAAATCTAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAAATAACTCAAAGAATAC
1 TCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAAGAACAC
1648525 TTCCAGAAGATGCTATTGGG-CTTCCTTATTTCTACCATGA
66 TTCCAGAAGATGCTATTGGGTC-TCCTTATTTCTACCATGA
1648565 TAACGTGGCA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 1 0.01
114 93 0.99
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (114 bp):
TCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAAGAACAC
TTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCAAATTCC
Found at i:1649263 original size:3 final size:3
Alignment explanation
Indices: 1649257--1649333 Score: 69
Period size: 3 Copynumber: 27.7 Consensus size: 3
1649247 CTCTTTTTTT
* *
1649257 TTC TTC TTC TTC -TC TT- TTT TTC TTC TTTC TTC TT- TT- TTC TTT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC
*
1649299 TTC TTC TTC TTC TTC TT- TT- TTT TTC TT- TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1649334 TTCATTTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 14 0.22
3 47 0.73
4 3 0.05
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (3 bp):
TTC
Found at i:1649276 original size:19 final size:20
Alignment explanation
Indices: 1649248--1649335 Score: 112
Period size: 19 Copynumber: 4.5 Consensus size: 20
1649238 CCCTTTTTTC
1649248 TCTT-TTTTTTTCTTCTTCT
1 TCTTCTTTTTTTCTTCTTCT
1649267 TC-TCTTTTTTTCTTCTTTCT
1 TCTTCTTTTTTTCTTC-TTCT
*
1649287 TCTTTTTTCTTTTTCTTCTTCT
1 TC-TTCTT-TTTTTCTTCTTCT
1649309 TCTTCTTTTTTT-TTCTT-T
1 TCTTCTTTTTTTCTTCTTCT
1649327 TCTTCTTTT
1 TCTTCTTTT
1649336 CATTTTTTCT
Statistics
Matches: 62, Mismatches: 2, Indels: 11
0.83 0.03 0.15
Matches are distributed among these distances:
18 11 0.18
19 18 0.29
20 11 0.18
21 4 0.06
22 9 0.15
23 9 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
TCTTCTTTTTTTCTTCTTCT
Found at i:1649318 original size:42 final size:41
Alignment explanation
Indices: 1649240--1649347 Score: 146
Period size: 43 Copynumber: 2.6 Consensus size: 41
1649230 TCTTGACCCC
* *
1649240 CTTTTTTCTCTTTTTTTTTCTTCTTCTTCTCTTTTTTTCTT
1 CTTTCTTCTTTTTTTTTTTCTTCTTCTTCTCTTTTTTTCTT
1649281 CTTTCTTCTTTTTTCTTTTTCTTCTTCTTCTTCTTTTTTT-TT
1 CTTTCTTCTTTTTT-TTTTTCTTCTTCTTC-TCTTTTTTTCTT
*
1649323 CTTTTCTTCTTTTCATTTTTTCTTC
1 C-TTTCTTCTTTT-TTTTTTTCTTC
1649348 AAGCATAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
41 12 0.20
42 18 0.30
43 29 0.48
44 1 0.02
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (41 bp):
CTTTCTTCTTTTTTTTTTTCTTCTTCTTCTCTTTTTTTCTT
Found at i:1649674 original size:15 final size:15
Alignment explanation
Indices: 1649654--1649685 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1649644 AATTGATCAA
1649654 ATCTAGCTTGGATCC
1 ATCTAGCTTGGATCC
1649669 ATCTAGCTTGGATCC
1 ATCTAGCTTGGATCC
1649684 AT
1 AT
1649686 TCAGATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (15 bp):
ATCTAGCTTGGATCC
Found at i:1658433 original size:15 final size:15
Alignment explanation
Indices: 1658413--1658442 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1658403 CACATATCTT
1658413 TCGTAATTTCTTTCG
1 TCGTAATTTCTTTCG
1658428 TCGTAATTTCTTTCG
1 TCGTAATTTCTTTCG
1658443 GCCATTCTTG
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:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (15 bp):
TCGTAATTTCTTTCG
Found at i:1662577 original size:20 final size:19
Alignment explanation
Indices: 1662538--1662589 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1662528 TTTCTTTGAT
1662538 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1662557 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1662577 ATTTATAAAATAA
1 A-TTAAAAAATAA
1662590 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1662690 original size:120 final size:120
Alignment explanation
Indices: 1662447--1662681 Score: 300
Period size: 120 Copynumber: 2.0 Consensus size: 120
1662437 AATATATATT
* * * *
1662447 AATTTATATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAG
* * *
1662510 ATGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 ATACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
*
1662565 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCA
* ** * **
1662630 GTTATTTTAAGACTGC-CCTTTC-TTAATATTGGAAAATAAATAAAT-ATTAAAA
65 GATACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAA
1662682 TAGGATTAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 17 0.17
119 26 0.26
120 39 0.39
121 18 0.18
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAG
ATACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:1664086 original size:3 final size:3
Alignment explanation
Indices: 1664078--1664158 Score: 103
Period size: 3 Copynumber: 26.7 Consensus size: 3
1664068 GGCCTGTTTG
**
1664078 TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1664123 TATA TAA -AA TAA TAA TAA TAA TAAA TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
1664159 GAAAATGGAG
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 56 0.81
4 9 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1669863 original size:102 final size:102
Alignment explanation
Indices: 1669687--1669896 Score: 402
Period size: 102 Copynumber: 2.1 Consensus size: 102
1669677 TTAAACATGC
1669687 ATTTAATTCACAACTTCATAAATTATTAAAGACAATTTGAACTCAAAACAATAAACATTTAACCA
1 ATTTAATTCACAACTTCATAAATTATTAAAGACAATTTGAACTCAAAACAATAAACATTTAACCA
1669752 AAAGTCAAGATCAAAGTAGATTCTAATGAATAACTTT
66 AAAGTCAAGATCAAAGTAGATTCTAATGAATAACTTT
*
1669789 ATTTAATTCACAACTTCATAAATTATTAAAGACAATTTGAACTCAAAACAATAATCATTTAACCA
1 ATTTAATTCACAACTTCATAAATTATTAAAGACAATTTGAACTCAAAACAATAAACATTTAACCA
1669854 AAAGTCAAGATCAAAGTAGATTCTAATGAATAACTTT
66 AAAGTCAAGATCAAAGTAGATTCTAATGAATAACTTT
*
1669891 TTTTAA
1 ATTTAA
1669897 ACAAACCGAA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 106 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (102 bp):
ATTTAATTCACAACTTCATAAATTATTAAAGACAATTTGAACTCAAAACAATAAACATTTAACCA
AAAGTCAAGATCAAAGTAGATTCTAATGAATAACTTT
Found at i:1670184 original size:18 final size:19
Alignment explanation
Indices: 1670163--1670202 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1670153 ATATAACTGA
*
1670163 TTATAAAAC-AAATAAATT
1 TTATAAAACAAAACAAATT
*
1670181 TTATAAATCAAAACAAATT
1 TTATAAAACAAAACAAATT
1670200 TTA
1 TTA
1670203 ACATCTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
TTATAAAACAAAACAAATT
Found at i:1672362 original size:22 final size:22
Alignment explanation
Indices: 1672336--1672377 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1672326 TATATTTAAG
*
1672336 AAAAATGGTAAATTTTCTGTAA
1 AAAAATGGTAAACTTTCTGTAA
1672358 AAAAATGGTAAACTTTCTGT
1 AAAAATGGTAAACTTTCTGT
1672378 TTCGTTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (22 bp):
AAAAATGGTAAACTTTCTGTAA
Found at i:1674040 original size:17 final size:17
Alignment explanation
Indices: 1674018--1674074 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 17
1674008 AATAATATAA
*
1674018 TATAATATTTTTATTAT
1 TATAATATTTATATTAT
1674035 TAT-A-A-TTATATTAT
1 TATAATATTTATATTAT
*
1674049 TATAATATCTA-ATT-T
1 TATAATATTTATATTAT
1674064 TATAAT-TTTAT
1 TATAATATTTAT
1674075 TTAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 14 0.42
15 9 0.27
16 5 0.15
17 5 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TATAATATTTATATTAT
Found at i:1674222 original size:23 final size:23
Alignment explanation
Indices: 1674180--1674278 Score: 59
Period size: 23 Copynumber: 4.5 Consensus size: 23
1674170 TAATATTATA
1674180 ATTTTTAAT-AGTTTAA-TAATATT
1 ATTTTTAATAAG--TAATTAATATT
1674203 ATTTTTAATAAGTAATTAATA-T
1 ATTTTTAATAAGTAATTAATATT
* * *
1674225 A--ATTAATAA-TATATTATTCTT
1 ATTTTTAATAAGTA-ATTAATATT
* * *
1674246 A-TTTTAATAAATAATTAAGATA
1 ATTTTTAATAAGTAATTAATATT
*
1674268 ATTTATAATAA
1 ATTTTTAATAA
1674279 TTTTATTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
19 2 0.03
20 12 0.20
21 2 0.03
22 18 0.30
23 24 0.40
24 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (23 bp):
ATTTTTAATAAGTAATTAATATT
Found at i:1674229 original size:26 final size:23
Alignment explanation
Indices: 1674168--1674229 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
1674158 ATATTTGTAT
* *
1674168 TTTAATATTATAATTTTTAATAG
1 TTTAATATAATTATTTTTAATAG
1674191 TTTAATA-ATATTATTTTTAATAAG
1 TTTAATATA-ATTATTTTTAAT-AG
1674215 TAATTAATATAATTA
1 T--TTAATATAATTA
1674230 ATAATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 18 0.56
24 3 0.09
26 10 0.31
27 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTAATATAATTATTTTTAATAG
Found at i:1674239 original size:37 final size:38
Alignment explanation
Indices: 1674193--1674293 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 38
1674183 TTTAATAGTT
* *
1674193 TAATAATATTAT-TTTTAATAAGTAATTAATATAATTAA
1 TAAT-ATATTATATTTTAATAAATAATTAAGATAATTAA
*
1674231 TAATATATTATTCTTATTTTAATAAATAATTAAGATAATTTA
1 TAATATATTA----TATTTTAATAAATAATTAAGATAATTAA
*
1674273 TAATA-ATTTTATTTTAATAAA
1 TAATATATTATATTTTAATAAA
1674294 ATATAATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
37 18 0.33
38 4 0.07
41 4 0.07
42 28 0.52
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (38 bp):
TAATATATTATATTTTAATAAATAATTAAGATAATTAA
Found at i:1674422 original size:17 final size:16
Alignment explanation
Indices: 1674398--1674431 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1674388 ATTTTAAAAA
*
1674398 TAATAATATTATTTTT
1 TAATAATAATATTTTT
1674414 TAATAAATAATATTTTT
1 TAAT-AATAATATTTTT
1674431 T
1 T
1674432 TTGTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATAATAATATTTTT
Found at i:1674735 original size:22 final size:21
Alignment explanation
Indices: 1674701--1674774 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 21
1674691 ATAATTAAAT
1674701 AATTATTTATAAAATTTATATTA
1 AATTA-TTATAAAA-TTATATTA
1674724 AATTATTATAAAAATTATATTTA
1 AATTATTAT-AAAATTATA-TTA
* *
1674747 TAA-TATTATGAAATTATTTTA
1 -AATTATTATAAAATTATATTA
*
1674768 AAATATT
1 AATTATT
1674775 TATTTAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
20 2 0.04
21 7 0.16
22 16 0.36
23 18 0.40
24 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (21 bp):
AATTATTATAAAATTATATTA
Found at i:1674777 original size:22 final size:21
Alignment explanation
Indices: 1674707--1674774 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
1674697 AAATAATTAT
* *
1674707 TTATAAAATTTATATTAAATTA
1 TTATAAAA-TTATTTTAAAATA
*
1674729 TTATAAAAATTATATTTATAATA
1 TTAT-AAAATTAT-TTTAAAATA
*
1674752 TTATGAAATTATTTTAAAATA
1 TTATAAAATTATTTTAAAATA
1674773 TT
1 TT
1674775 TATTTAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.26
22 15 0.38
23 14 0.36
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (21 bp):
TTATAAAATTATTTTAAAATA
Found at i:1674783 original size:22 final size:22
Alignment explanation
Indices: 1674736--1674853 Score: 59
Period size: 20 Copynumber: 5.4 Consensus size: 22
1674726 TTATTATAAA
* **
1674736 AATTATATTTATAATA-TTATGA
1 AATTAT-TTTAAAATATTTATTT
1674758 AATTATTTTAAAATATTTATTT
1 AATTATTTTAAAATATTTATTT
1674780 AA-T-TTTTAAAATCA--TA-TT
1 AATTATTTTAAAAT-ATTTATTT
* * * *
1674798 ATTTATTTGAAATTATATTAATT
1 AATTATTTTAAAATAT-TTATTT
* *
1674821 ATTTATTTTAAATAATATTATTTTT
1 AATTATTTT-AA-AATATT-TATTT
1674846 AATTATTT
1 AATTATTT
1674854 ATTTAATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 16 0.22
21 10 0.14
22 14 0.19
23 10 0.14
24 3 0.04
25 14 0.19
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTATTTTAAAATATTTATTT
Found at i:1674788 original size:20 final size:22
Alignment explanation
Indices: 1674763--1674802 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1674753 TATGAAATTA
1674763 TTTTAAAAT-AT-TTATTTAAT
1 TTTTAAAATCATATTATTTAAT
1674783 TTTTAAAATCATATTATTTA
1 TTTTAAAATCATATTATTTA
1674803 TTTGAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATCATATTATTTAAT
Found at i:1674810 original size:19 final size:19
Alignment explanation
Indices: 1674778--1674824 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1674768 AAATATTTAT
*
1674778 TTAATT-TTTAAAATCATA
1 TTAATTATTTGAAATCATA
* *
1674796 TTATTTATTTGAAATTATA
1 TTAATTATTTGAAATCATA
1674815 TTAATTATTT
1 TTAATTATTT
1674825 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTAATTATTTGAAATCATA
Found at i:1674825 original size:23 final size:23
Alignment explanation
Indices: 1674795--1674840 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1674785 TTAAAATCAT
*
1674795 ATTATTTATTTGAAATTATATTA
1 ATTATTTATTTGAAATAATATTA
*
1674818 ATTATTTATTTTAAATAATATTA
1 ATTATTTATTTGAAATAATATTA
1674841 TTTTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTATTTATTTGAAATAATATTA
Found at i:1674840 original size:19 final size:19
Alignment explanation
Indices: 1674760--1674843 Score: 64
Period size: 23 Copynumber: 4.1 Consensus size: 19
1674750 TATTATGAAA
1674760 TTATTTT-AA-AATATTTAT
1 TTATTTTAAATAATA-TTAT
*
1674778 TTAATTTTTAAAATCATATTAT
1 TT-A-TTTT-AAATAATATTAT
*
1674800 TTATTTGAAATTATATTAATTAT
1 TTATTTTAAA-TA-A-T-ATTAT
1674823 TTATTTTAAATAATATTAT
1 TTATTTTAAATAATATTAT
1674842 TT
1 TT
1674844 TTAATTATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
18 2 0.04
19 11 0.21
20 9 0.17
21 3 0.06
22 11 0.21
23 17 0.32
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (19 bp):
TTATTTTAAATAATATTAT
Found at i:1675461 original size:42 final size:47
Alignment explanation
Indices: 1675415--1675506 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 47
1675405 ATTAATATAT
* *
1675415 TATTTTAGT-ATCATTTTAATAA-A-AGTA-TTAATTATTA-AATTA
1 TATTTTAGTGATAATTTTAATAATATAATATTTAATTATTATAATTA
* *
1675457 TA-TTTATTGATAATTTTAATAATATAATATTTTATTATTATAATTA
1 TATTTTAGTGATAATTTTAATAATATAATATTTAATTATTATAATTA
1675503 TATT
1 TATT
1675507 ATTAAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
41 5 0.12
42 14 0.35
43 1 0.03
44 3 0.08
45 9 0.22
46 7 0.17
47 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (47 bp):
TATTTTAGTGATAATTTTAATAATATAATATTTAATTATTATAATTA
Found at i:1675508 original size:14 final size:14
Alignment explanation
Indices: 1675441--1675510 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
1675431 TAATAAAAGT
1675441 ATTA-ATTATTA-A
1 ATTATATTATTATA
1675453 ATTATATTTATTGATA
1 ATTATA-TTATT-ATA
* * *
1675469 ATTTTAATAATATAA
1 ATTATATTATTAT-A
*
1675484 TATTTTATTATTATA
1 -ATTATATTATTATA
1675499 ATTATATTATTA
1 ATTATATTATTA
1675511 AAATATCTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 4 0.09
13 1 0.02
14 18 0.39
15 6 0.13
16 17 0.37
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (14 bp):
ATTATATTATTATA
Found at i:1675535 original size:29 final size:29
Alignment explanation
Indices: 1675495--1675551 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1675485 ATTTTATTAT
1675495 TATAATTATATTATTAA-AATATCTAATAC
1 TATAATTATATT-TTAATAATATCTAATAC
* *
1675524 TATAATTTTATTTTAATAATATTTAATA
1 TATAATTATATTTTAATAATATCTAATA
1675552 AATTAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
TATAATTATATTTTAATAATATCTAATAC
Found at i:1675670 original size:14 final size:14
Alignment explanation
Indices: 1675651--1675700 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1675641 ATAATTTTTT
1675651 ATTTTAATATTATA
1 ATTTTAATATTATA
*
1675665 ATTTTAATATTTTA
1 ATTTTAATATTATA
* *
1675679 ATATTATTATTAT-
1 ATTTTAATATTATA
*
1675692 TTTTTAATA
1 ATTTTAATA
1675701 AGTAATTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 6 0.21
14 23 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTAATATTATA
Found at i:1675678 original size:22 final size:21
Alignment explanation
Indices: 1675640--1675685 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
1675630 TAAAATATAA
*
1675640 TATAATTTTTTATTTTAATAT
1 TATAATTTTATATTTTAATAT
1675661 TATAATTTTAATATTTTAATAT
1 TATAATTTT-ATATTTTAATAT
1675683 TAT
1 TAT
1675686 TATTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATAATTTTATATTTTAATAT
Found at i:1675739 original size:42 final size:39
Alignment explanation
Indices: 1675637--1675783 Score: 144
Period size: 42 Copynumber: 3.7 Consensus size: 39
1675627 CCTTAAAATA
*
1675637 TAATATAATT-TTTTATTTTAATATTATAATTTTAATAT--TT
1 TAATAT-ATTATTTTATTTTAATA-AATAA--TTAATATAATT
*
1675677 TAATATTATTATTATT-TTTTAATAAGTAATTAATATAATT
1 TAATA-TATTATT-TTATTTTAATAAATAATTAATATAATT
*
1675717 CATAATATATTATTCTTATTTTAATAAATAATTACTATAATT
1 --TAATATATTATT-TTATTTTAATAAATAATTAATATAATT
1675759 T-ATA-ATTATTTTATTTTAATAAATA
1 TAATATATTATTTTATTTTAATAAATA
1675784 TAATAATCTT
Statistics
Matches: 94, Mismatches: 5, Indels: 19
0.80 0.04 0.16
Matches are distributed among these distances:
37 15 0.16
38 13 0.14
39 3 0.03
40 14 0.15
41 20 0.21
42 29 0.31
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (39 bp):
TAATATATTATTTTATTTTAATAAATAATTAATATAATT
Found at i:1675894 original size:18 final size:20
Alignment explanation
Indices: 1675871--1675919 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
1675861 TAAATTAATC
1675871 TAATATTTTA-ATTAA-AAA
1 TAATATTTTATATTAATAAA
*
1675889 TAATATTATTATTTTTAATAAA
1 TAATATT-TTA-TATTAATAAA
1675911 TAATATTTT
1 TAATATTTT
1675920 TTTATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.27
19 3 0.12
21 6 0.23
22 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATATTTTATATTAATAAA
Found at i:1675927 original size:22 final size:23
Alignment explanation
Indices: 1675876--1675929 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1675866 TAATCTAATA
*
1675876 TTTTAATTAA-AAATAATATTAT
1 TTTTATTTAATAAATAATATTAT
*
1675898 TATT-TTTAATAAATAATATT-T
1 TTTTATTTAATAAATAATATTAT
1675919 TTTTATTTAAT
1 TTTTATTTAAT
1675930 GTTTATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATTTAATAAATAATATTAT
Found at i:1676279 original size:23 final size:22
Alignment explanation
Indices: 1676227--1676288 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
1676217 TAAAAAATAA
* *
1676227 TTAAATATTTATTTATATATAT
1 TTAAAAATTTATTTAAATATAT
1676249 TTATAAAATTTATATTAAAT-TAT
1 TTA-AAAATTTAT-TTAAATATAT
*
1676272 TCTAAAAAGTATATTTA
1 T-TAAAAA-TTTATTTA
1676289 TCATATTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 3 0.09
23 19 0.58
24 11 0.33
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAAAAATTTATTTAAATATAT
Found at i:1676336 original size:44 final size:46
Alignment explanation
Indices: 1676288--1676387 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 46
1676278 AAGTATATTT
*
1676288 ATCATATTATGAAATTATTTTAAAATAT-TTATTTAATT-TTTAAA
1 ATCATATTATGAAATTATTTGAAAATATATTATTTAATTATTTAAA
** * * * *
1676332 ATCATATTATTTATTTATTTGAAATTATATTATTTATTTATTTTAA
1 ATCATATTATGAAATTATTTGAAAATATATTATTTAATTATTTAAA
*
1676378 ATAATATTAT
1 ATCATATTAT
1676388 TTTTAAATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 23 0.50
45 9 0.20
46 14 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (46 bp):
ATCATATTATGAAATTATTTGAAAATATATTATTTAATTATTTAAA
Found at i:1676356 original size:23 final size:23
Alignment explanation
Indices: 1676306--1676389 Score: 102
Period size: 23 Copynumber: 3.8 Consensus size: 23
1676296 ATGAAATTAT
*
1676306 TTTAAAAT-AT-TTATTTAATT-
1 TTTAAAATAATATTATTTATTTA
*
1676326 TTTAAAATCATATTATTTATTTA
1 TTTAAAATAATATTATTTATTTA
* *
1676349 TTTGAAATTATATTATTTATTTA
1 TTTAAAATAATATTATTTATTTA
*
1676372 TTTTAAATAATATTATTT
1 TTTAAAATAATATTATTT
1676390 TTAAATTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
20 8 0.14
21 2 0.04
22 9 0.16
23 37 0.66
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (23 bp):
TTTAAAATAATATTATTTATTTA
Found at i:1676387 original size:19 final size:19
Alignment explanation
Indices: 1676342--1676450 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 19
1676332 ATCATATTAT
*
1676342 TTATTTATTTGAAATTATATTA
1 TTATTTATTTTAAA-TA-A-TA
1676364 TTTATTTATTTTAAATAATA
1 -TTATTTATTTTAAATAATA
*
1676384 TTA--T-TTTTAAATTAT-
1 TTATTTATTTTAAATAATA
1676399 TTATTTAATTTTAAATAATA
1 TTATTT-ATTTTAAATAATA
*
1676419 TTA--T-TTTTAAATTAT-
1 TTATTTATTTTAAATAATA
1676434 TTATTTAATTTTAAATA
1 TTATTT-ATTTTAAATA
1676451 TTTTTTAAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
15 6 0.08
16 20 0.28
17 3 0.04
18 1 0.01
19 21 0.29
20 5 0.07
21 1 0.01
22 2 0.03
23 13 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
TTATTTATTTTAAATAATA
Found at i:1676391 original size:16 final size:16
Alignment explanation
Indices: 1676372--1676439 Score: 75
Period size: 16 Copynumber: 4.1 Consensus size: 16
1676362 TATTTATTTA
1676372 TTTTAAATAATATTAT
1 TTTTAAATAATATTAT
* *
1676388 TTTTAAATTATTTATTTAA
1 TTTTAAA-TA-ATA-TTAT
1676407 TTTTAAATAATATTAT
1 TTTTAAATAATATTAT
*
1676423 TTTTAAATTAT-TTAT
1 TTTTAAATAATATTAT
1676438 TT
1 TT
1676440 AATTTTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
15 6 0.14
16 20 0.45
17 4 0.09
18 4 0.09
19 10 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAATAATATTAT
Found at i:1676399 original size:49 final size:45
Alignment explanation
Indices: 1676291--1676400 Score: 107
Period size: 44 Copynumber: 2.4 Consensus size: 45
1676281 TATATTTATC
* * *
1676291 ATATTA-TGAAATTATTTTAAAATATTTATTTAATTTTTAAAATC
1 ATATTATTTAAATTATTTGAAAATATTTATTTAATTTTTAAAATA
* * * *
1676335 ATATTATTT-ATTTATTTGAAATTATATTATTTATTTATTTTAAATA
1 ATATTATTTAAATTATTTGAAAATAT-TTATTTAATT-TTTAAAATA
1676381 ATATTATTTTTAAATTATTT
1 ATATTA--TTTAAATTATTT
1676401 ATTTAATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
44 19 0.37
45 10 0.19
46 13 0.25
48 3 0.06
49 7 0.13
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (45 bp):
ATATTATTTAAATTATTTGAAAATATTTATTTAATTTTTAAAATA
Found at i:1676400 original size:26 final size:23
Alignment explanation
Indices: 1676291--1676389 Score: 96
Period size: 23 Copynumber: 4.4 Consensus size: 23
1676281 TATATTTATC
**
1676291 ATATTATGAAATTATTTT-AA-A
1 ATATTATTTAATTATTTTAAATA
* *
1676312 ATATTTATTTAATT-TTTAAAATC
1 ATA-TTATTTAATTATTTTAAATA
* * *
1676335 ATATTATTTATTTATTTGAAATT
1 ATATTATTTAATTATTTTAAATA
*
1676358 ATATTATTTATTTATTTTAAATA
1 ATATTATTTAATTATTTTAAATA
1676381 ATATTATTT
1 ATATTATTT
1676390 TTAAATTATT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.09
22 19 0.29
23 40 0.62
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (23 bp):
ATATTATTTAATTATTTTAAATA
Found at i:1676417 original size:35 final size:35
Alignment explanation
Indices: 1676360--1676450 Score: 175
Period size: 35 Copynumber: 2.6 Consensus size: 35
1676350 TTGAAATTAT
1676360 ATTATTTATTT-ATTTTAAATAATATTATTTTTAA
1 ATTATTTATTTAATTTTAAATAATATTATTTTTAA
1676394 ATTATTTATTTAATTTTAAATAATATTATTTTTAA
1 ATTATTTATTTAATTTTAAATAATATTATTTTTAA
1676429 ATTATTTATTTAATTTTAAATA
1 ATTATTTATTTAATTTTAAATA
1676451 TTTTTTAAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 11 0.20
35 45 0.80
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (35 bp):
ATTATTTATTTAATTTTAAATAATATTATTTTTAA
Found at i:1677808 original size:25 final size:25
Alignment explanation
Indices: 1677780--1677831 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1677770 TCATATTCAT
1677780 ATTATATTATGTTTTATATAAATAA
1 ATTATATTATGTTTTATATAAATAA
1677805 ATTATATTATGTTTTATATAAATAA
1 ATTATATTATGTTTTATATAAATAA
1677830 AT
1 AT
1677832 ATGATACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTATATTATGTTTTATATAAATAA
Found at i:1684990 original size:19 final size:19
Alignment explanation
Indices: 1684966--1685008 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1684956 AAACACCATA
1684966 AAAACTGAGTGATTTTAAT
1 AAAACTGAGTGATTTTAAT
*
1684985 AAAACTGGGTGATTTTAAT
1 AAAACTGAGTGATTTTAAT
1685004 AAAAC
1 AAAAC
1685009 ATTCTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (19 bp):
AAAACTGAGTGATTTTAAT
Found at i:1686189 original size:5 final size:5
Alignment explanation
Indices: 1686179--1686243 Score: 82
Period size: 5 Copynumber: 13.4 Consensus size: 5
1686169 TTTAAATGCA
*
1686179 AAAAT AAAAT AAAAT AAAAT -AAA- CAAAT AAAAT AAAAT AAAAT AAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
1686226 ATAAAT AAGAT AAAAT AA
1 A-AAAT AAAAT AAAAT AA
1686244 GCACAAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
4 7 0.13
5 45 0.85
6 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1686206 original size:18 final size:18
Alignment explanation
Indices: 1686185--1686219 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1686175 TGCAAAAATA
1686185 AAATAAAATAAAATAAAC
1 AAATAAAATAAAATAAAC
1686203 AAATAAAATAAAATAAA
1 AAATAAAATAAAATAAA
1686220 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATAAAATAAAATAAAC
Found at i:1686206 original size:23 final size:22
Alignment explanation
Indices: 1686178--1686243 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 22
1686168 ATTTAAATGC
1686178 AAAAATAAAATAAAATAAAATA
1 AAAAATAAAATAAAATAAAATA
1686200 AACAAATAAAATAAAATAAAAT-
1 AA-AAATAAAATAAAATAAAATA
*
1686222 AAAAAT-AAATAAGATAAAATA
1 AAAAATAAAATAAAATAAAATA
1686243 A
1 A
1686244 GCACAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 13 0.32
21 5 0.12
22 4 0.10
23 19 0.46
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (22 bp):
AAAAATAAAATAAAATAAAATA
Found at i:1696046 original size:18 final size:19
Alignment explanation
Indices: 1696023--1696061 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1696013 TTTAAATAGT
*
1696023 AATAAAAACGATTAAA-TA
1 AATAAAAACAATTAAAGTA
1696041 AATAAAAACAATTAAAGTA
1 AATAAAAACAATTAAAGTA
1696060 AA
1 AA
1696062 AATAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:1701267 original size:13 final size:13
Alignment explanation
Indices: 1701199--1701274 Score: 52
Period size: 12 Copynumber: 6.0 Consensus size: 13
1701189 CTACAACAGA
*
1701199 ATTAAAGTATAAT
1 ATTAAAATATAAT
*
1701212 ATT-AGATATAAT
1 ATTAAAATATAAT
* * *
1701224 TTTTAAAGA-AAT
1 ATTAAAATATAAT
*
1701236 AGTTATAAA-ATAGT
1 A-TTA-AAATATAAT
1701250 ATTAAAATATAAT
1 ATTAAAATATAAT
1701263 ATT-AAATATAAT
1 ATTAAAATATAAT
1701275 TTTTAAAGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
12 24 0.49
13 19 0.39
14 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTAAAATATAAT
Found at i:1701271 original size:12 final size:12
Alignment explanation
Indices: 1701199--1701274 Score: 55
Period size: 13 Copynumber: 6.0 Consensus size: 12
1701189 CTACAACAGA
1701199 ATTAAAGTATAAT
1 ATTAAA-TATAAT
*
1701212 ATTAGATATAATT
1 ATTAAATATAA-T
* *
1701225 TTTAAAGA-AAT
1 ATTAAATATAAT
* *
1701236 AGTTATAAAATAGT
1 A-TTA-AATATAAT
1701250 ATTAAAATATAAT
1 ATT-AAATATAAT
1701263 ATTAAATATAAT
1 ATTAAATATAAT
1701275 TTTTAAAGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
11 1 0.02
12 19 0.39
13 25 0.51
14 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (12 bp):
ATTAAATATAAT
Found at i:1708405 original size:2 final size:2
Alignment explanation
Indices: 1708398--1708436 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1708388 AACATCTTAA
1708398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1708437 CAAAAGACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1718388 original size:3 final size:3
Alignment explanation
Indices: 1718380--1718439 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1718370 GATTAAGCTT
1718380 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1718428 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1718440 ATTTGGAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1719652 original size:30 final size:32
Alignment explanation
Indices: 1719600--1719659 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
1719590 GCAATGTATG
*
1719600 AGATGGAATATGAGTGAAAGCTTAGAAAAGCT
1 AGATAGAATATGAGTGAAAGCTTAGAAAAGCT
* *
1719632 AGATAGAAT-TGAGT-ACAGCTTAGCAAAG
1 AGATAGAATATGAGTGAAAGCTTAGAAAAG
1719660 TTTAGAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.48
31 5 0.20
32 8 0.32
ACGTcount: A:0.43, C:0.08, G:0.27, T:0.22
Consensus pattern (32 bp):
AGATAGAATATGAGTGAAAGCTTAGAAAAGCT
Found at i:1723333 original size:21 final size:21
Alignment explanation
Indices: 1723309--1723349 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1723299 GTTATATGTT
* *
1723309 ATAATCAAGATGAAGATGGCC
1 ATAATCAAAATAAAGATGGCC
1723330 ATAATCAAAATAAAGATGGC
1 ATAATCAAAATAAAGATGGC
1723350 TACAATAGTG
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:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (21 bp):
ATAATCAAAATAAAGATGGCC
Found at i:1727819 original size:21 final size:20
Alignment explanation
Indices: 1727785--1727863 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 20
1727775 ACCCTTGGGG
* *
1727785 GAAATGATCGATCCCTTACC
1 GAAAGGATCAATCCCTTACC
1727805 -AAAGAGAATCAATCCCTTAACC
1 GAAAG-G-ATCAATCCCTT-ACC
* **
1727827 GAAAGGATCGATCCCTTAGGG
1 GAAAGGATCAATCCCTTA-CC
*
1727848 GAAAGGATGAATCCCT
1 GAAAGGATCAATCCCT
1727864 CGAAAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.06
20 2 0.04
21 34 0.72
22 4 0.09
23 4 0.09
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
GAAAGGATCAATCCCTTACC
Found at i:1735156 original size:13 final size:13
Alignment explanation
Indices: 1735116--1735158 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1735106 ATAATATTAA
1735116 AAATCCTAAAATAT
1 AAATCCTAAAAT-T
* * *
1735130 AATTCTTGAAATT
1 AAATCCTAAAATT
1735143 AAATCCTAAAATT
1 AAATCCTAAAATT
1735156 AAA
1 AAA
1735159 GATAAATCTT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (13 bp):
AAATCCTAAAATT
Found at i:1735626 original size:23 final size:21
Alignment explanation
Indices: 1735587--1735628 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1735577 AATTTTTTTG
1735587 TAAAATAAAATATTTTAAATC
1 TAAAATAAAATATTTTAAATC
*
1735608 TAAAATATAATAATATTTAAA
1 TAAAATAAAAT-AT-TTTAAA
1735629 AAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 2 0.11
23 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATAAAATATTTTAAATC
Found at i:1738982 original size:26 final size:26
Alignment explanation
Indices: 1738914--1738986 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 26
1738904 AACTAAATTG
1738914 ATGTAAGCAATGACATCATTAATTAA
1 ATGTAAGCAATGACATCATTAATTAA
*
1738940 ATGATATAAGCAATGACATCTTTAATTAA
1 ATG---TAAGCAATGACATCATTAATTAA
*
1738969 ATGTAAGTAATGACATCA
1 ATGTAAGCAATGACATCA
1738987 ATTTAGTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 16 0.39
29 25 0.61
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (26 bp):
ATGTAAGCAATGACATCATTAATTAA
Found at i:1739727 original size:40 final size:40
Alignment explanation
Indices: 1739683--1739761 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
1739673 CGTCTTTTTT
*
1739683 CCATTTTCCGGGAAAATGTTTATAGAATGCTTTTACCGCG
1 CCATTTTCCGGGAAAATGTTCATAGAATGCTTTTACCGCG
1739723 CCATTTTCCGGGAAAATGTTCATAGAATGCTTTTACCGC
1 CCATTTTCCGGGAAAATGTTCATAGAATGCTTTTACCGC
1739762 ACCTGCTACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (40 bp):
CCATTTTCCGGGAAAATGTTCATAGAATGCTTTTACCGCG
Found at i:1745833 original size:18 final size:19
Alignment explanation
Indices: 1745801--1745838 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1745791 TCAAAGTCAC
*
1745801 TTTCATTCTTCTTTTTTCT
1 TTTCATTCTTCTTTTGTCT
*
1745820 TTTCTTTCTT-TTTTGTCT
1 TTTCATTCTTCTTTTGTCT
1745838 T
1 T
1745839 CAACGTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTCATTCTTCTTTTGTCT
Found at i:1748980 original size:541 final size:531
Alignment explanation
Indices: 1748204--1749274 Score: 1984
Period size: 541 Copynumber: 2.0 Consensus size: 531
1748194 TGCATCAGCG
1748204 TGGCTGACTGCCCTGGTAATTGCTAGTCAGATTTGAAAATTTTACACTCTAATTATGATTTTTTT
1 TGGCTGACTGCCCTGGTAATTGCTAGTCAGATTTGAAAATTTTA-ACTCTAATTATGATTTTTTT
*
1748269 TTGTCACTCTCTTAATAGCCAGGAGTCAAAGGGTACAGAAACAAGAAGCCCATCATCCATGTCTG
65 TGGTCACTCTCTTAATAGCCAGGAGTCAAAGGGTACAGAAACAAGAAGCCCATCATCCATGTCTG
1748334 ACAACTTTACACTGTTCATAGGGTATAAAGTTTGTATTACTAATCAACAGTAGGAAAAGTCTTAA
130 ACAACTTTACACTGTTCATAGGGTATAAAGTTTGTATTACTAATCAACAGTAGGAAAAGTCTTAA
1748399 GTAAATATACAACAAAGGGAAACTGCATATTGTAAGAAAATGAAAATATTTAAATCCATTAAACA
195 GTAAATATACAACAAAGGGAAACTGCATATTGTAAGAAAATGAAAATATTTAAATCCATTAAACA
1748464 GATCCAACAAGACTACTGCCAGAATTGTCTATAGTTCAGAAATAATCCAGAGAAACATTACTTTT
260 GATCCAACAAGACTACTGCCAGAATTGTCTATAGTTCAGAAATAATCCAGAGAAACATTACTTTT
1748529 TAAATTTAACAGCTCAGGAAAATAAAAGGAAAAATAAAAGCAAAAAGGATTTAAATTGGTGATTC
325 TAAATTTAACAGCTC-----------AGG-AAAATAAAAGCAAAAAGGATTTAAATTGGTGATTC
1748594 AACAACATTCCTCAAATCATCAATCCAACATGTCATTGTCACAAAGAATGAAAAACTCCATTTAA
378 AACAACATTCCTCAAATCATCAATCCAACATGTCATTGTCACAAAGAATGAAAAACTCCATTTAA
*
1748659 GATCAAGGCGAGCAAATTTAGCATTTTAAGGATATATGTTTGTGGGTTCATGTATGAATAAAATG
443 GATCAAGGCGAGCAAATTTAGCATTCTAAGGATATATGTTTGTGGGTTCATGTATGAATAAAATG
1748724 ACCTTTTGCTTTGGGAACAAGGCA
508 ACCTTTTGCTTTGGGAACAAGGCA
*
1748748 TGGCTGACTGCCCTGGTAATTGCTAGTCAGATTTGAAAATTTT-ACTCTCATTATGA-TTTTTTT
1 TGGCTGACTGCCCTGGTAATTGCTAGTCAGATTTGAAAATTTTAACTCTAATTATGATTTTTTTT
1748811 GGTCACTCTCTTAATAGCCAGGAGTCAAAGGGTACAGAAACAAGAAGCCCATCATCCATGTCTGA
66 GGTCACTCTCTTAATAGCCAGGAGTCAAAGGGTACAGAAACAAGAAGCCCATCATCCATGTCTGA
1748876 CAACTTTACACTGTTCATAGGGTATAAAGTTTGTATTACTAATCAACAGTAGGAAAAGTCTTAAG
131 CAACTTTACACTGTTCATAGGGTATAAAGTTTGTATTACTAATCAACAGTAGGAAAAGTCTTAAG
1748941 TAAATATACAACAAAGGGAAACTGCATATTGTAAGAAAATGAAAATATTTAAATCCATTAAACAG
196 TAAATATACAACAAAGGGAAACTGCATATTGTAAGAAAATGAAAATATTTAAATCCATTAAACAG
1749006 ATCCAACAAGACTACTGCCAGAATTGTCTATAGTTCAGAAATAATCCAGAGAAACATTACTTTTT
261 ATCCAACAAGACTACTGCCAGAATTGTCTATAGTTCAGAAATAATCCAGAGAAACATTACTTTTT
1749071 AAATTTAACAGCTCAGGAAAATAAAAGCAAAAAGGATTTAAATTGGTGATTCAACAACATTCCTC
326 AAATTTAACAGCTCAGGAAAATAAAAGCAAAAAGGATTTAAATTGGTGATTCAACAACATTCCTC
1749136 AAATCATCAATCCAACATGTCATTGTCACAAAGAATGAAAAACTCCATTTAAGATCAAGGCGAGC
391 AAATCATCAATCCAACATGTCATTGTCACAAAGAATGAAAAACTCCATTTAAGATCAAGGCGAGC
1749201 AAATTTAGCATTCTAAGGATATATGTTTGTGGGTTCATGTATGAATAAAATGACCTTTTGCTTTG
456 AAATTTAGCATTCTAAGGATATATGTTTGTGGGTTCATGTATGAATAAAATGACCTTTTGCTTTG
1749266 GGAACAAGG
521 GGAACAAGG
1749275 TGAGGACTCC
Statistics
Matches: 524, Mismatches: 3, Indels: 15
0.97 0.01 0.03
Matches are distributed among these distances:
529 186 0.35
530 3 0.01
541 280 0.53
542 12 0.02
544 43 0.08
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (531 bp):
TGGCTGACTGCCCTGGTAATTGCTAGTCAGATTTGAAAATTTTAACTCTAATTATGATTTTTTTT
GGTCACTCTCTTAATAGCCAGGAGTCAAAGGGTACAGAAACAAGAAGCCCATCATCCATGTCTGA
CAACTTTACACTGTTCATAGGGTATAAAGTTTGTATTACTAATCAACAGTAGGAAAAGTCTTAAG
TAAATATACAACAAAGGGAAACTGCATATTGTAAGAAAATGAAAATATTTAAATCCATTAAACAG
ATCCAACAAGACTACTGCCAGAATTGTCTATAGTTCAGAAATAATCCAGAGAAACATTACTTTTT
AAATTTAACAGCTCAGGAAAATAAAAGCAAAAAGGATTTAAATTGGTGATTCAACAACATTCCTC
AAATCATCAATCCAACATGTCATTGTCACAAAGAATGAAAAACTCCATTTAAGATCAAGGCGAGC
AAATTTAGCATTCTAAGGATATATGTTTGTGGGTTCATGTATGAATAAAATGACCTTTTGCTTTG
GGAACAAGGCA
Found at i:1756080 original size:45 final size:46
Alignment explanation
Indices: 1755998--1756091 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 46
1755988 TAAAATAGTA
* * * *
1755998 TTTTTTATTGAAAATATTAATATTAGGTATTATCT-AAATATTATT
1 TTTTTTATCGAAAATATTAATATTAGGCACTACCTAAAATATTATT
* *
1756043 TTTTTTATCGAAAATATTAATATTGGGCGCTACCTAAAATATTATT
1 TTTTTTATCGAAAATATTAATATTAGGCACTACCTAAAATATTATT
1756089 TTT
1 TTT
1756092 CTACAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 29 0.69
46 13 0.31
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (46 bp):
TTTTTTATCGAAAATATTAATATTAGGCACTACCTAAAATATTATT
Found at i:1756151 original size:12 final size:12
Alignment explanation
Indices: 1756134--1756158 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1756124 TTGATAAAAC
1756134 AAATAATATTTT
1 AAATAATATTTT
1756146 AAATAATATTTT
1 AAATAATATTTT
1756158 A
1 A
1756159 CCAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:1757449 original size:33 final size:33
Alignment explanation
Indices: 1757407--1757473 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1757397 TTACTGCATA
*
1757407 ATATTTCAGTTCAACTGAAAAAGTTAAAAAATT
1 ATATTTCAGTTCAACCGAAAAAGTTAAAAAATT
* *
1757440 ATATTTCAGTTTAACCGATAAAGTTAAAAAATT
1 ATATTTCAGTTCAACCGAAAAAGTTAAAAAATT
1757473 A
1 A
1757474 ACATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (33 bp):
ATATTTCAGTTCAACCGAAAAAGTTAAAAAATT
Found at i:1760009 original size:59 final size:59
Alignment explanation
Indices: 1759943--1760062 Score: 145
Period size: 59 Copynumber: 2.0 Consensus size: 59
1759933 GTACACATGC
* * * *
1759943 TCCCCCAACTATAAGG-TATTGTTTTGTTGAGTTCCTCGACTATT-AAAGTTAGAAAATGG
1 TCCCCCAACTAT-AGGACATTGTTTTGTTGAG-TCCCCGACTATTAAAAATTAAAAAATGG
* * *
1760002 TCCCCCAATTATAGGACATTGTTTTGTTGCGTCCCCGGCTATTAAAAATTAAAAAATGG
1 TCCCCCAACTATAGGACATTGTTTTGTTGAGTCCCCGACTATTAAAAATTAAAAAATGG
1760061 TC
1 TC
1760063 ACCCTATAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 13 0.25
59 39 0.75
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (59 bp):
TCCCCCAACTATAGGACATTGTTTTGTTGAGTCCCCGACTATTAAAAATTAAAAAATGG
Found at i:1763473 original size:20 final size:20
Alignment explanation
Indices: 1763418--1763474 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
1763408 TTTTCACATT
1763418 CTTTAATTGACCTTCTAAAG
1 CTTTAATTGACCTTCTAAAG
* ** **
1763438 CATTACA-AAAAATTCTAAAG
1 CTTTA-ATTGACCTTCTAAAG
1763458 CTTTAATTGACCTTCTA
1 CTTTAATTGACCTTCTA
1763475 GAATCTGTCT
Statistics
Matches: 25, Mismatches: 10, Indels: 4
0.64 0.26 0.10
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (20 bp):
CTTTAATTGACCTTCTAAAG
Found at i:1764789 original size:17 final size:17
Alignment explanation
Indices: 1764737--1764789 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1764727 TGAATAAAGT
1764737 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* * *
1764754 TAGTTTATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
1764771 TAGTTCATTTATTAGAC
1 TAGTTCATTAATTAAAC
1764788 TA
1 TA
1764790 ACTCTTAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:1767052 original size:6 final size:6
Alignment explanation
Indices: 1767032--1767066 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
1767022 TATCTCCTGC
1767032 TCTCCAT TC-CCT TCTCCT TCTCCT TCTCCT TCTCC
1 TCTCC-T TCTCCT TCTCCT TCTCCT TCTCCT TCTCC
1767067 AAATCGGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 3 0.11
6 22 0.81
7 2 0.07
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.46
Consensus pattern (6 bp):
TCTCCT
Found at i:1773613 original size:2 final size:2
Alignment explanation
Indices: 1773606--1773634 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1773596 GCAACAAGTA
1773606 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1773635 CTCCACAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1775611 original size:43 final size:43
Alignment explanation
Indices: 1775539--1775627 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
1775529 CAAGATTACT
* ** *
1775539 ATTGGATTAGAAAGTTAAATTATTTAATTAAATTAAAGTTATG
1 ATTGAATTAGAAAGTTAAATTATCGAATTAAATTAAAATTATG
*
1775582 ATTGAATTATAAAGTTAAATTATCGAATTAAATTAAAATTATG
1 ATTGAATTAGAAAGTTAAATTATCGAATTAAATTAAAATTATG
1775625 ATT
1 ATT
1775628 AAATCAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.42
Consensus pattern (43 bp):
ATTGAATTAGAAAGTTAAATTATCGAATTAAATTAAAATTATG
Found at i:1782329 original size:20 final size:20
Alignment explanation
Indices: 1782292--1782330 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1782282 AGAGCTCATA
* *
1782292 TAGGATCATGTAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1782312 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1782331 GTGGTGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1786247 original size:32 final size:32
Alignment explanation
Indices: 1786206--1786269 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1786196 GAATCGAAGA
*
1786206 TATCATCGTGAGGGTTGACAAGTTCGTTTTTC
1 TATCATCGTGAGGGTTGACAAGTTCATTTTTC
1786238 TATCATCGTGAGGGTTGACAAGTTCATTTTTC
1 TATCATCGTGAGGGTTGACAAGTTCATTTTTC
1786270 CTGTTGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (32 bp):
TATCATCGTGAGGGTTGACAAGTTCATTTTTC
Found at i:1790231 original size:15 final size:17
Alignment explanation
Indices: 1790213--1790245 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1790203 CCCACTTTGT
1790213 AAAAG-AAA-GAAAAAA
1 AAAAGAAAATGAAAAAA
1790228 AAAAGAAAATGAAAAAA
1 AAAAGAAAATGAAAAAA
1790245 A
1 A
1790246 TGAAGTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 3 0.19
17 8 0.50
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAGAAAATGAAAAAA
Found at i:1790883 original size:20 final size:20
Alignment explanation
Indices: 1790855--1790898 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1790845 GTCTAAGAGC
*
1790855 GCATATAGGATCATATAGAT
1 GCATATAGGAGCATATAGAT
* *
1790875 GCATTTAGGAGCATATAGTT
1 GCATATAGGAGCATATAGAT
1790895 GCAT
1 GCAT
1790899 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (20 bp):
GCATATAGGAGCATATAGAT
Found at i:1794753 original size:32 final size:32
Alignment explanation
Indices: 1794712--1794775 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1794702 GAATCGAAGA
*
1794712 TATCATCGTGAGGGTTGACAAGTTCGTTTTTC
1 TATCATCGTGAGGGTTGACAAGTTCATTTTTC
1794744 TATCATCGTGAGGGTTGACAAGTTCATTTTTC
1 TATCATCGTGAGGGTTGACAAGTTCATTTTTC
1794776 CTGTCGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (32 bp):
TATCATCGTGAGGGTTGACAAGTTCATTTTTC
Found at i:1798709 original size:14 final size:16
Alignment explanation
Indices: 1798690--1798721 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1798680 CCCACTTTGT
1798690 AAAAG-AAA-GAAAAA
1 AAAAGAAAATGAAAAA
1798704 AAAAGAAAATGAAAAA
1 AAAAGAAAATGAAAAA
1798720 AA
1 AA
1798722 TGAAGTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAGAAAATGAAAAA
Found at i:1803899 original size:33 final size:32
Alignment explanation
Indices: 1803832--1803902 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1803822 CCTTTACAAC
* *
1803832 TCCCTAGTTTTTCAGGGCTAAACTAGAACTTT
1 TCCCTAGCTTTTCAGGGATAAACTAGAACTTT
* *
1803864 TCCCTAGCTTTTCACGGGATCAGCTAGAATCTTT
1 TCCCTAGCTTTTCA-GGGATAAACTAGAA-CTTT
*
1803898 CCCCT
1 TCCCT
1803903 TTACAAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 13 0.41
33 11 0.34
34 8 0.25
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.35
Consensus pattern (32 bp):
TCCCTAGCTTTTCAGGGATAAACTAGAACTTT
Found at i:1807260 original size:22 final size:22
Alignment explanation
Indices: 1807200--1807254 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1807190 TTGAGCCTTT
1807200 ATAGGGGTATCGATACCCATTC
1 ATAGGGGTATCGATACCCATTC
1807222 ATAGGGGTATCGATACCCATTC
1 ATAGGGGTATCGATACCCATTC
1807244 ATAGGGGTATC
1 ATAGGGGTATC
1807255 AGTACCTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (22 bp):
ATAGGGGTATCGATACCCATTC
Found at i:1811735 original size:29 final size:29
Alignment explanation
Indices: 1811693--1811750 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1811683 TCCTTAATCT
*
1811693 TTTCAAAGATTATACTTTAGCCACTAAAC
1 TTTCAAAGATTATACTTTAGCCAATAAAC
* *
1811722 TTTCAAA-ATTTATATTTTAGTCAATAAAC
1 TTTCAAAGA-TTATACTTTAGCCAATAAAC
1811751 AAAATTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (29 bp):
TTTCAAAGATTATACTTTAGCCAATAAAC
Found at i:1813237 original size:20 final size:20
Alignment explanation
Indices: 1813191--1813248 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 20
1813181 TTGTTAATGA
1813191 TAAAAAATTAAACAAATTAT
1 TAAAAAATTAAACAAATTAT
**
1813211 T---TGATTAAACAAATTAT
1 TAAAAAATTAAACAAATTAT
*
1813228 TAAAAAATTAAATAAATTAT
1 TAAAAAATTAAACAAATTAT
1813248 T
1 T
1813249 CACGACTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 15 0.50
20 15 0.50
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAAATTAAACAAATTAT
Found at i:1813509 original size:29 final size:29
Alignment explanation
Indices: 1813435--1813511 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
1813425 TTCGGTTCGG
*
1813435 TTAACCGAACCAAAATTTATTTGAAAATTA
1 TTAACCGAACC-AAATTAATTTGAAAATTA
**
1813465 TTAACCGAACTTAATTAATTTGAAAATTA
1 TTAACCGAACCAAATTAATTTGAAAATTA
*
1813494 TTAACCGAACCGAATTAA
1 TTAACCGAACCAAATTAA
1813512 CCGAATATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 32 0.76
30 10 0.24
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (29 bp):
TTAACCGAACCAAATTAATTTGAAAATTA
Found at i:1813551 original size:141 final size:139
Alignment explanation
Indices: 1813335--1813779 Score: 622
Period size: 141 Copynumber: 3.2 Consensus size: 139
1813325 ATCGAACCAA
* * *
1813335 AATTTATTTAAAAATTATTAACCGAACCGAATTAACCGAAACATTTTTGAAAATTATTAACCGAA
1 AATTAATTTGAAAATTATTAACCGAACCGAATTAACCG-AATATTTTTGAAAATTATTAACCGAA
* *
1813400 TTAATCGAAGCAAAAATTTGGTTAATTCGGTTCGGTTAACCGAACCAAAATTTATTTGAAAATTA
65 TTAATTGAAGCAAAAA-TT-GTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTA
**
1813465 TTAACCGAACTT
128 TTAACCGAACCG
1813477 AATTAATTTGAAAATTATTAACCGAACCGAATTAACCGAATATTTTTGAAAAGTT-TTAACCGAA
1 AATTAATTTGAAAATTATTAACCGAACCGAATTAACCGAATATTTTTGAAAA-TTATTAACCGAA
*
1813541 TTAATTGAAGCAAAAATTAAGTTAATTCGGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTA
65 TTAATTGAAGCAAAAATT--GTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTA
1813606 TTAACCGAACCG
128 TTAACCGAACCG
* * * *
1813618 AATTAATTTGAAAATTATTAATCGGACCGAATTAACC-AAT-TTTTTTAAAATTATTAATCGAAT
1 AATTAATTTGAAAATTATTAACCGAACCGAATTAACCGAATATTTTTGAAAATTATTAACCGAAT
* * * *
1813681 TAATTGAAGC--AAA-----AATTCGATTAGGTTAATCGAACCAAAATTTAGTTAAAAATTATTA
66 TAATTGAAGCAAAAATTGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTA
1813739 ACCGAACCG
131 ACCGAACCG
1813748 AATTAATTTGAAAATTATTAACCGAACCGAAT
1 AATTAATTTGAAAATTATTAACCGAACCGAAT
1813780 AAATTTCGAT
Statistics
Matches: 280, Mismatches: 20, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
130 79 0.28
137 3 0.01
138 2 0.01
139 28 0.10
140 5 0.02
141 125 0.45
142 38 0.14
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (139 bp):
AATTAATTTGAAAATTATTAACCGAACCGAATTAACCGAATATTTTTGAAAATTATTAACCGAAT
TAATTGAAGCAAAAATTGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTA
ACCGAACCG
Found at i:1813610 original size:74 final size:73
Alignment explanation
Indices: 1813380--1813614 Score: 229
Period size: 74 Copynumber: 3.3 Consensus size: 73
1813370 CCGAAACATT
* * * *
1813380 TTTGAAAATTATTAACCGAATTAATCGAAGCAAAAATTTGGTTAATTCGGTTCGGTTAACCGAAC
1 TTTGAAAATTATTAACCGAATTAATTGAAGCAAAAA-TTAGTTAATTCGGTTCGGTTAATCAAAC
1813445 CAAAATTTA
65 CAAAATTTA
*** * ** * *
1813454 TTTGAAAATTATTAACCGAACTTAATT-AATTTGAAAATTA-TTAA--CCGAACCG--AAT-TAA
1 TTTGAAAATTATTAACCGAA-TTAATTGAA-GCAAAAATTAGTTAATTCGGTTCGGTTAATCAAA
*
1813512 CC-GAATATT-
64 CCAAAAT-TTA
1813521 TTTGAAAAGTT-TTAACCGAATTAATTGAAGCAAAAATTAAGTTAATTCGGTTCGGTTAATCAAA
1 TTTGAAAA-TTATTAACCGAATTAATTGAAGCAAAAATT-AGTTAATTCGGTTCGGTTAATCAAA
1813585 CCAAAATTTA
64 CCAAAATTTA
1813595 TTTGAAAATTATTAACCGAA
1 TTTGAAAATTATTAACCGAA
1813615 CCGAATTAAT
Statistics
Matches: 125, Mismatches: 21, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
66 12 0.10
67 23 0.18
68 12 0.10
69 2 0.02
70 4 0.03
71 4 0.03
72 3 0.02
73 12 0.10
74 44 0.35
75 9 0.07
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (73 bp):
TTTGAAAATTATTAACCGAATTAATTGAAGCAAAAATTAGTTAATTCGGTTCGGTTAATCAAACC
AAAATTTA
Found at i:1813631 original size:29 final size:29
Alignment explanation
Indices: 1813589--1813652 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1813579 ATCAAACCAA
*
1813589 AATTTATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
* *
1813618 AATTAATTTGAAAATTATTAATCGGACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
1813647 AATTAA
1 AATTAA
1813653 CCAATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:1813761 original size:29 final size:29
Alignment explanation
Indices: 1813729--1813785 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1813719 AATTTAGTTA
*
1813729 AAAATTATTAACCGAACCGAATTAATTTG
1 AAAATTATTAACCGAACCGAATAAATTTG
1813758 AAAATTATTAACCGAACCGAATAAATTT
1 AAAATTATTAACCGAACCGAATAAATTT
1813786 CGATTAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (29 bp):
AAAATTATTAACCGAACCGAATAAATTTG
Found at i:1834444 original size:20 final size:20
Alignment explanation
Indices: 1834421--1834458 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1834411 GACTAAGATA
1834421 AAAATAATAAAA-TAATAATT
1 AAAAT-ATAAAAGTAATAATT
1834441 AAAATATAAAAGTAATAA
1 AAAATATAAAAGTAATAA
1834459 AATTGCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATATAAAAGTAATAATT
Found at i:1835836 original size:3 final size:3
Alignment explanation
Indices: 1835828--1835911 Score: 55
Period size: 3 Copynumber: 28.0 Consensus size: 3
1835818 GTCTGTTTTG
* * * *
1835828 TAA TAA TAA TATT TAT TAA TAA TAA TAA AAA T-A TAA TAA TAA TCA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1835873 TAA TTA TAA TAA -ATA TAA TTA TAA AAA TTA TAA AAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1835912 AAGTAAAATG
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
2 3 0.05
3 55 0.90
4 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1836804 original size:2 final size:2
Alignment explanation
Indices: 1836797--1836825 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1836787 ACATATTTAT
1836797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1836826 TACATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1837465 original size:42 final size:42
Alignment explanation
Indices: 1837268--1837609 Score: 319
Period size: 43 Copynumber: 7.9 Consensus size: 42
1837258 AACTTTCAAT
* * *
1837268 AGGTCGAGATCTATAGCGGCATTTTTAGAAAAAACGCCGCAAAA
1 AGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCGC-AAA
* * * * *
1837312 AGTTGAGATCTATAGTGGCG--TTTGAGAACAAAAAACGGCACAAA
1 AGGTCAGATCTATAGCGGCGTTTTTG-GAAC---AAACGCCGCAAA
* * * * *
1837356 AAGTCTAGATCTATAGCGGCATTTTTGGAACAAAAGTCACAAA
1 AGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *** **
1837399 ATGTCGAGATCTATAGCAATGTTTTTGGAACAAACGCCATAAA
1 AGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * *
1837442 ATGTCAGATCTATAGCGGCGTTTTTGAAACAAACGCCGTAAA
1 AGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * *
1837484 AGGTCAGATCTATAGCGGCATTTTTGAAACAAACGCCGCAGA
1 AGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
*
1837526 AGGTCGAGATCTATAGCGGCGTTTTTCGAACAAACGCCGCAAA
1 AGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *
1837569 AGGTCATATCTATAGCGGCGTTTTTTAGATACAAACGCCGC
1 AGGTCAGATCTATAGCGGCG-TTTTTGGA-ACAAACGCCGC
1837610 TAATTACCTT
Statistics
Matches: 249, Mismatches: 39, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
41 3 0.01
42 92 0.37
43 107 0.43
44 19 0.08
45 20 0.08
46 4 0.02
47 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (42 bp):
AGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
Found at i:1837532 original size:127 final size:130
Alignment explanation
Indices: 1837268--1837608 Score: 350
Period size: 127 Copynumber: 2.6 Consensus size: 130
1837258 AACTTTCAAT
** * * * * * * *
1837268 AGGTCGAGATCTATAGCGGCATTTTTAGAAAAAACGCCGCAAAAAGTTGAGATCTATAGTGGCG-
1 AGGTCGAGATCTATAGCAACGTTTTTCGAACAAACGCCAC-AAAAGGTCAGATCTATAGCGGCGT
* * * ** * *
1837332 -TTTGAGAACAAAAAACGGCACAAAAAGTCTAGATCTATAGCGGCATTTTTGGAACAAAAGTCAC
65 TTTTTAG-A-AACAAACGCCGTAAAAAGTCTAGATCTATAGCGGCATTTTTGAAACAAAAGCCAC
1837396 AAA
128 AAA
* * * * *
1837399 ATGTCGAGATCTATAGCAATGTTTTTGGAACAAACGCCATAAAATGTCAGATCTATAGCGGCG-T
1 AGGTCGAGATCTATAGCAACGTTTTTCGAACAAACGCCACAAAAGGTCAGATCTATAGCGGCGTT
* * * *
1837463 TTTT-GAAACAAACGCCGTAAAAGGTC-AGATCTATAGCGGCATTTTTGAAACAAACGCCGCAGA
66 TTTTAGAAACAAACGCCGTAAAAAGTCTAGATCTATAGCGGCATTTTTGAAACAAAAGCCACAAA
** * *
1837526 AGGTCGAGATCTATAGCGGCGTTTTTCGAACAAACGCCGCAAAAGGTCATATCTATAGCGGCGTT
1 AGGTCGAGATCTATAGCAACGTTTTTCGAACAAACGCCACAAAAGGTCAGATCTATAGCGGCGTT
*
1837591 TTTTAGATACAAACGCCG
66 TTTTAGAAACAAACGCCG
1837609 CTAATTACCT
Statistics
Matches: 173, Mismatches: 34, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
127 86 0.50
128 20 0.12
129 13 0.08
130 20 0.12
131 34 0.20
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (130 bp):
AGGTCGAGATCTATAGCAACGTTTTTCGAACAAACGCCACAAAAGGTCAGATCTATAGCGGCGTT
TTTTAGAAACAAACGCCGTAAAAAGTCTAGATCTATAGCGGCATTTTTGAAACAAAAGCCACAAA
Found at i:1837585 original size:85 final size:84
Alignment explanation
Indices: 1837268--1837607 Score: 331
Period size: 85 Copynumber: 3.9 Consensus size: 84
1837258 AACTTTCAAT
* * * *
1837268 AGGTCGAGATCTATAGCGGCATTTTTAGAAAAAACGCCGCAAAAAGTTGAGATCTATAGTGGCGT
1 AGGTCGAGATCTATAGCGGCATTTTT-GAACAAACGCCGC-AAAAGGTCAGATCTATAGCGGCGT
** * *
1837333 TTGAGAACAAAAAACGGCACAAA
64 TTTTG-A-AACAAACGCCACAAA
* * * * * * ***
1837356 AAGTCTAGATCTATAGCGGCATTTTTGGAACAAAAGTCACAAAATGTCGAGATCTATAGCAATGT
1 AGGTCGAGATCTATAGCGGCATTTTT-GAACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGT
* *
1837421 TTTTGGAACAAACGCCATAAA
64 TTTTGAAACAAACGCCACAAA
* * * *
1837442 ATGTC-AGATCTATAGCGGCGTTTTTGAAACAAACGCCGTAAAAGGTCAGATCTATAGCGGCATT
1 AGGTCGAGATCTATAGCGGCATTTTTG-AACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTT
* *
1837506 TTTGAAACAAACGCCGCAGA
65 TTTGAAACAAACGCCACAAA
* *
1837526 AGGTCGAGATCTATAGCGGCGTTTTTCGAACAAACGCCGCAAAAGGTCATATCTATAGCGGCGTT
1 AGGTCGAGATCTATAGCGGCATTTTT-GAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG-T
*
1837591 TTTTAGATACAAACGCC
64 TTTT-GAAACAAACGCC
1837608 GCTAATTACC
Statistics
Matches: 206, Mismatches: 40, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
84 34 0.17
85 86 0.42
86 22 0.11
87 16 0.08
88 48 0.23
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (84 bp):
AGGTCGAGATCTATAGCGGCATTTTTGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTT
TTGAAACAAACGCCACAAA
Found at i:1845931 original size:41 final size:40
Alignment explanation
Indices: 1845884--1846019 Score: 112
Period size: 41 Copynumber: 3.4 Consensus size: 40
1845874 ATTTTAACGG
* *
1845884 CGTTTTTACAAAAACACCACTATATATCTGGCTATCGCGA
1 CGTTTTTACAAAAACGCCACTATATATCTGGATATCGCGA
* * * * * * *
1845924 CATTTTTTATATAAACGCCACTA-AAATACTCGGTTATTGCGG
1 C-GTTTTTACAAAAACGCCACTATATAT-CT-GGATATCGCGA
* * *
1845966 CGTTTTTCCAAAAACGCCACTATATATTTGGATATCGCGG
1 CGTTTTTACAAAAACGCCACTATATATCTGGATATCGCGA
* *
1846006 CGTTTGTCCAAAAA
1 CGTTTTTACAAAAA
1846020 GTTCGCTATA
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
40 26 0.35
41 37 0.49
42 12 0.16
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (40 bp):
CGTTTTTACAAAAACGCCACTATATATCTGGATATCGCGA
Found at i:1846016 original size:40 final size:40
Alignment explanation
Indices: 1845881--1846019 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 40
1845871 GAGATTTTAA
* * * *
1845881 CGGCGTTTTTACAAAAACACCACTATATATCTGGCTATCG
1 CGGCGTTTTTCCAAAAACGCCACTATATATTTGGATATCG
* * * * * * * *
1845921 CGACATTTTT-TATATAAACGCCACTAAAATACTCGGTTATTG
1 CGGCGTTTTTCCA-A-AAACGCCACT-ATATATTTGGATATCG
1845963 CGGCGTTTTTCCAAAAACGCCACTATATATTTGGATATCG
1 CGGCGTTTTTCCAAAAACGCCACTATATATTTGGATATCG
*
1846003 CGGCGTTTGTCCAAAAA
1 CGGCGTTTTTCCAAAAA
1846020 GTTCGCTATA
Statistics
Matches: 76, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
39 1 0.01
40 36 0.47
41 19 0.25
42 19 0.25
43 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (40 bp):
CGGCGTTTTTCCAAAAACGCCACTATATATTTGGATATCG
Found at i:1852793 original size:23 final size:22
Alignment explanation
Indices: 1852734--1852776 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1852724 AAAGTTATTC
1852734 AAATATTCAAAAAATAAAAATAA
1 AAATATT-AAAAAATAAAAATAA
*
1852757 AAATACTAAAAAATAAAAAT
1 AAATATTAAAAAATAAAAAT
1852777 TTGAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (22 bp):
AAATATTAAAAAATAAAAATAA
Found at i:1853280 original size:24 final size:24
Alignment explanation
Indices: 1853209--1853281 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 24
1853199 TCCATTAAAA
*
1853209 ATATTTTGTATAAGTGTTGATGATAT
1 ATATTTTG--TAATTGTTGATGATAT
* * * * *
1853235 ACA-TAT-TAATTATTTATAATAT
1 ATATTTTGTAATTGTTGATGATAT
1853257 ATATTTTGTAATTGTTGATGATAT
1 ATATTTTGTAATTGTTGATGATAT
1853281 A
1 A
1853282 CATATTAATT
Statistics
Matches: 34, Mismatches: 11, Indels: 6
0.67 0.22 0.12
Matches are distributed among these distances:
22 14 0.41
23 2 0.06
24 14 0.41
25 2 0.06
26 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (24 bp):
ATATTTTGTAATTGTTGATGATAT
Found at i:1853290 original size:22 final size:22
Alignment explanation
Indices: 1853223--1853291 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
1853213 TTTGTATAAG
1853223 TGTTGATGATATACATATTAAT
1 TGTTGATGATATACATATTAAT
* * * * *
1853245 TATTTATAATATATATTTTGTAAT
1 TGTTGATGATATACA-TAT-TAAT
1853269 TGTTGATGATATACATATTAAT
1 TGTTGATGATATACATATTAAT
1853291 T
1 T
1853292 CAAGCATTAC
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
22 16 0.46
23 4 0.11
24 15 0.43
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (22 bp):
TGTTGATGATATACATATTAAT
Found at i:1855736 original size:21 final size:22
Alignment explanation
Indices: 1855696--1855736 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1855686 ATTAGTAAAT
**
1855696 AAATAAATATATAGGTAATATG
1 AAATAAATATATAGAAAATATG
1855718 AAAT-AATATATAGAAAATA
1 AAATAAATATATAGAAAATA
1855737 CAGGCATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (22 bp):
AAATAAATATATAGAAAATATG
Found at i:1855752 original size:3 final size:3
Alignment explanation
Indices: 1855744--1855816 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
1855734 ATACAGGCAT
1855744 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1855790 ATA ATA ATA ATA ATA AT- ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1855817 CATCTAAATA
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 6 0.09
3 61 0.91
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1855864 original size:17 final size:18
Alignment explanation
Indices: 1855837--1855872 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1855827 TATACATGGT
1855837 AAAATGAAAATAAATAAA
1 AAAATGAAAATAAATAAA
*
1855855 AAAATG-AAATATATAAA
1 AAAATGAAAATAAATAAA
1855872 A
1 A
1855873 TATAAGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (18 bp):
AAAATGAAAATAAATAAA
Found at i:1861531 original size:6 final size:6
Alignment explanation
Indices: 1861507--1861553 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
1861497 ATGTATAAAT
*
1861507 AAATGC -AATGC AGAATGC AAATGC AAAGATGC AAATGC AAATAC AAA
1 AAATGC AAATGC A-AATGC AAATGC -AA-ATGC AAATGC AAATGC AAA
1861554 AGGTGTTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
5 5 0.14
6 17 0.47
7 10 0.28
8 4 0.11
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (6 bp):
AAATGC
Found at i:1861540 original size:14 final size:13
Alignment explanation
Indices: 1861507--1861547 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
1861497 ATGTATAAAT
1861507 AAATGC-AATGCA
1 AAATGCAAATGCA
*
1861519 GAATGCAAATGCA
1 AAATGCAAATGCA
1861532 AAGATGCAAATGCA
1 AA-ATGCAAATGCA
1861546 AA
1 AA
1861548 TACAAAAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 5 0.20
13 7 0.28
14 13 0.52
ACGTcount: A:0.51, C:0.15, G:0.20, T:0.15
Consensus pattern (13 bp):
AAATGCAAATGCA
Found at i:1863536 original size:2 final size:2
Alignment explanation
Indices: 1863524--1863579 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
1863514 AAAACATTTA
1863524 AT AT A- AT AT AT AT AT AT AT AT AT AT -T 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 AT AT AT
1863564 -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1863580 ACACTGATAC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1863550 original size:36 final size:35
Alignment explanation
Indices: 1863495--1863579 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 35
1863485 TTTTAACAAA
* *
1863495 ATATATATTTATA-AGTATTAAAACATTTAATATAAT
1 ATATATATATATATAGTATT-AAACATAT-ATATAAT
* * *
1863531 ATATATATATATATA-TATTATATATATATATATT
1 ATATATATATATATAGTATTAAACATATATATAAT
1863565 ATATATATATATATA
1 ATATATATATATATA
1863580 ACACTGATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
34 21 0.49
35 5 0.12
36 16 0.37
37 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (35 bp):
ATATATATATATATAGTATTAAACATATATATAAT
Found at i:1863552 original size:15 final size:15
Alignment explanation
Indices: 1863524--1863578 Score: 96
Period size: 15 Copynumber: 3.8 Consensus size: 15
1863514 AAAACATTTA
1863524 ATATA-ATATA-TAT
1 ATATATATATATTAT
1863537 ATATATATATATTAT
1 ATATATATATATTAT
1863552 ATATATATATATTAT
1 ATATATATATATTAT
1863567 ATATATATATAT
1 ATATATATATAT
1863579 AACACTGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.12
14 5 0.12
15 30 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATATATTAT
Found at i:1863883 original size:13 final size:13
Alignment explanation
Indices: 1863867--1863897 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1863857 TATATCAGGT
1863867 AAAATGAAAAATA
1 AAAATGAAAAATA
*
1863880 AAAATGAAATATA
1 AAAATGAAAAATA
1863893 AAAAT
1 AAAAT
1863898 ATAGCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (13 bp):
AAAATGAAAAATA
Found at i:1867623 original size:44 final size:44
Alignment explanation
Indices: 1867568--1867665 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
1867558 TTATTTATAA
1867568 TATATATTTTTTATTTTTGAATGGTTAAAAGATAAATATATCAT
1 TATATATTTTTTATTTTTGAATGGTTAAAAGATAAATATATCAT
1867612 TATATATTTTTTATTTTTGAATGGTTAAAAGATAAATATATCAT
1 TATATATTTTTTATTTTTGAATGGTTAAAAGATAAATATATCAT
* *
1867656 TTTAAATTTT
1 TATATATTTT
1867666 AAAGGAATGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (44 bp):
TATATATTTTTTATTTTTGAATGGTTAAAAGATAAATATATCAT
Found at i:1870366 original size:20 final size:20
Alignment explanation
Indices: 1870338--1870385 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1870328 CGATATTCGA
1870338 CTCGAAAAGTTCGTGAGCAG
1 CTCGAAAAGTTCGTGAGCAG
*
1870358 CTTGAAAAGTTCGTGAGCAG
1 CTCGAAAAGTTCGTGAGCAG
1870378 CTCGAAAA
1 CTCGAAAA
1870386 AATGTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
CTCGAAAAGTTCGTGAGCAG
Found at i:1880562 original size:19 final size:19
Alignment explanation
Indices: 1880538--1880575 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1880528 TTTTGGTGCA
*
1880538 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
1880557 GAGGGAACCGATTCCCCCT
1 GAGGGAACCGATCCCCCCT
1880576 TTGAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:1886003 original size:22 final size:23
Alignment explanation
Indices: 1885985--1886039 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
1885975 AGAGGGAATT
1885985 GATACCCCC-TTGAAGGGGAACC
1 GATACCCCCTTTGAAGGGGAACC
*
1886007 GATTCCCCCTTTGAAGGGGAACC
1 GATACCCCCTTTGAAGGGGAACC
1886030 GAGT-CCCCCT
1 GA-TACCCCCT
1886040 GGGGTTCTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 8 0.27
23 21 0.70
24 1 0.03
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (23 bp):
GATACCCCCTTTGAAGGGGAACC
Found at i:1890971 original size:16 final size:16
Alignment explanation
Indices: 1890950--1890981 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1890940 ACTATTCACA
*
1890950 TGAATAGTAAATTTCG
1 TGAATAGTAAAATTCG
1890966 TGAATAGTAAAATTCG
1 TGAATAGTAAAATTCG
1890982 GTCGCCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (16 bp):
TGAATAGTAAAATTCG
Found at i:1903613 original size:3 final size:3
Alignment explanation
Indices: 1903605--1903660 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
1903595 TTTGTCTCAT
*
1903605 TTA TTA TTA TTA TTA -TA TTA TTA TTA -TA TTA TTA TTA TT- TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1903650 TTA -TA TTA TTA
1 TTA TTA TTA TTA
1903661 ATGGTAAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
2 8 0.17
3 40 0.83
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1903625 original size:11 final size:11
Alignment explanation
Indices: 1903609--1903660 Score: 86
Period size: 11 Copynumber: 4.7 Consensus size: 11
1903599 TCTCATTTAT
1903609 TATTATTATTA
1 TATTATTATTA
1903620 TATTATTATTA
1 TATTATTATTA
1903631 TATTATTATTA
1 TATTATTATTA
* *
1903642 TTTTTTTATTA
1 TATTATTATTA
1903653 TATTATTA
1 TATTATTA
1903661 ATGGTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATTATTA
Found at i:1904641 original size:14 final size:15
Alignment explanation
Indices: 1904622--1904657 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1904612 AATATTTGAT
1904622 TTTTAATCTT-ATTA
1 TTTTAATCTTCATTA
*
1904636 TTTTAATCTTCTTTA
1 TTTTAATCTTCATTA
1904651 TTTTAAT
1 TTTTAAT
1904658 TACTAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATCTTCATTA
Found at i:1904695 original size:13 final size:13
Alignment explanation
Indices: 1904672--1904707 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1904662 AAAATCATAT
1904672 TTTACGATTTTTAA
1 TTTA-GATTTTTAA
1904686 TTTAGATTTTTAA
1 TTTAGATTTTTAA
1904699 TTTA-ATTTT
1 TTTAGATTTT
1904708 ATTTTAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 13 0.59
14 4 0.18
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (13 bp):
TTTAGATTTTTAA
Found at i:1904708 original size:24 final size:24
Alignment explanation
Indices: 1904680--1904728 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1904670 ATTTTACGAT
*
1904680 TTTTAATTTAGAT-TTTTAATTTAA
1 TTTTAATTTA-ATCATTTAATTTAA
*
1904704 TTTTATTTTAATCATTTAATTTAA
1 TTTTAATTTAATCATTTAATTTAA
1904728 T
1 T
1904729 GTAATTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTAATTTAATCATTTAATTTAA
Found at i:1904713 original size:11 final size:11
Alignment explanation
Indices: 1904680--1904728 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 11
1904670 ATTTTACGAT
1904680 TTTTAATTTAGA
1 TTTTAATTTA-A
1904692 TTTTTAATTTAA
1 -TTTTAATTTAA
*
1904704 TTTTATTTTAA
1 TTTTAATTTAA
1904715 TCATTTAATTTAA
1 T--TTTAATTTAA
1904728 T
1 T
1904729 GTAATTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 11 0.34
12 1 0.03
13 20 0.62
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:1906313 original size:30 final size:29
Alignment explanation
Indices: 1906275--1906344 Score: 113
Period size: 30 Copynumber: 2.4 Consensus size: 29
1906265 AACTAAATTA
1906275 AACGGGGACGGGAAAAAATCGTTTATGCT
1 AACGGGGACGGGAAAAAATCGTTTATGCT
*
1906304 AACCGGGGACGGGAAAAAATCGTTTATGTT
1 AA-CGGGGACGGGAAAAAATCGTTTATGCT
*
1906334 AAAGGGGACGG
1 AACGGGGACGG
1906345 AGACGGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 10 0.26
30 28 0.74
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.19
Consensus pattern (29 bp):
AACGGGGACGGGAAAAAATCGTTTATGCT
Done.