Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 24
Found at i:1236551 original size:19 final size:17
Alignment explanation
Indices: 1236527--1236561 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
1236517 TTCAATTTAA
1236527 TTCAAATTAATTCAAAATT
1 TTCAAATT--TTCAAAATT
1236546 TTCAAATTTTCAAAAT
1 TTCAAATTTTCAAAAT
1236562 AAAAGTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
TTCAAATTTTCAAAATT
Found at i:1237050 original size:30 final size:32
Alignment explanation
Indices: 1237016--1237082 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
1237006 ATGTCATCTA
**
1237016 TTAATAACTC-AAATTTATTTTA-TTTATATT
1 TTAATAACTCAAAATTTAAATTACTTTATATT
*
1237046 TTAATAACTCAAAATTTAAATTACTTTTTATT
1 TTAATAACTCAAAATTTAAATTACTTTATATT
1237078 TTAAT
1 TTAAT
1237083 GTATTTGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 10 0.31
31 10 0.31
32 12 0.38
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (32 bp):
TTAATAACTCAAAATTTAAATTACTTTATATT
Found at i:1239161 original size:24 final size:24
Alignment explanation
Indices: 1239103--1239170 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
1239093 AAACAGAGAT
*
1239103 ATCAGAAATCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATCCAA
* * * *
1239127 AACA-AATATCATAATAGAATCCAG
1 ATCAGAA-ATCAAAACAGAATCCAA
*
1239151 ATCAGAAATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAAT
1239171 TCAGGTCATG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.06
24 30 0.88
25 2 0.06
ACGTcount: A:0.56, C:0.16, G:0.10, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAA
Found at i:1239174 original size:12 final size:12
Alignment explanation
Indices: 1239105--1239174 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
1239095 ACAGAGATAT
* *
1239105 CAGAAATCAAAA
1 CAGAATTCAGAA
*
1239117 CAGAATTCAAAA
1 CAGAATTCAGAA
*
1239129 CA-AATATCATAA
1 CAGAAT-TCAGAA
* * *
1239141 TAGAATCCAGAT
1 CAGAATTCAGAA
*
1239153 CAGAAATCAGAA
1 CAGAATTCAGAA
1239165 CAGAATTCAG
1 CAGAATTCAG
1239175 GTCATGTATC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 3 0.07
12 39 0.87
13 3 0.07
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1239185 original size:48 final size:47
Alignment explanation
Indices: 1239103--1239211 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 47
1239093 AAACAGAGAT
* * * *
1239103 ATCAGAAATCAAAACAGAATTCAAAACAAATATCATAATAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAAAACAAATATCAGAACAAAATCCA
*** ** *
1239150 GATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAAAATTCA
1 -ATCAGAAATCAGAACAGAATTCAAAACAAATATCAGAACAAAATCCA
1239198 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
1239212 TAAAATATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAAAACAAATATCAGAACAAAATCCA
Found at i:1239209 original size:24 final size:24
Alignment explanation
Indices: 1239152--1239211 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1239142 AGAATCCAGA
* *
1239152 TCAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCAGAACAAAATTCAAG
*
1239176 TCATG-TATCAGAACAAAATTCAAG
1 TCA-GAAATCAGAACAAAATTCAAG
1239200 TCAGAAATCAGA
1 TCAGAAATCAGA
1239212 TAAAATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAAAATTCAAG
Found at i:1241697 original size:12 final size:13
Alignment explanation
Indices: 1241678--1241712 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1241668 TATCACCATA
1241678 ACAGAAATTAATT
1 ACAGAAATTAATT
1241691 A-AGAAATTAATT
1 ACAGAAATTAATT
1241703 ACA-AAATTAA
1 ACAGAAATTAA
1241713 CACCCAGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 19 0.90
13 2 0.10
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (13 bp):
ACAGAAATTAATT
Found at i:1244932 original size:20 final size:19
Alignment explanation
Indices: 1244907--1244951 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1244897 TGAGGTGCTA
*
1244907 GAAATTAAAGTTAGAGTGTT
1 GAAATTAAAGTTAGAATG-T
* *
1244927 GAAATTTATGTTAGAATGT
1 GAAATTAAAGTTAGAATGT
1244946 GAAATT
1 GAAATT
1244952 GGATCCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (19 bp):
GAAATTAAAGTTAGAATGT
Found at i:1247532 original size:32 final size:32
Alignment explanation
Indices: 1247491--1247556 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
1247481 ATCGGCAGCT
**
1247491 TATGTTAGGATAGGAAACCGTATAAAACTATC
1 TATGTTAGGATAGGAAACAATATAAAACTATC
1247523 TATGTTAGGATAGGAAACAATATAAAACTATC
1 TATGTTAGGATAGGAAACAATATAAAACTATC
1247555 TA
1 TA
1247557 GTTGATGCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.29
Consensus pattern (32 bp):
TATGTTAGGATAGGAAACAATATAAAACTATC
Found at i:1254129 original size:2 final size:2
Alignment explanation
Indices: 1254122--1254197 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1254112 TTAGATTGCG
1254122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1254164 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1254198 CTTGAGCAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1257864 original size:22 final size:22
Alignment explanation
Indices: 1257839--1257883 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1257829 ATCATAGACT
*
1257839 CATTTGATAGGAAATCTAGATC
1 CATTTGATACGAAATCTAGATC
1257861 CATTTGATACGAAATCTAGATC
1 CATTTGATACGAAATCTAGATC
1257883 C
1 C
1257884 GTCACCATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (22 bp):
CATTTGATACGAAATCTAGATC
Found at i:1268181 original size:182 final size:178
Alignment explanation
Indices: 1267853--1268232 Score: 579
Period size: 182 Copynumber: 2.1 Consensus size: 178
1267843 ATTAAATTTT
* * *
1267853 AAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTGAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1267918 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
66 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
*
1267983 TATTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATT-AA
131 TATTTATAATTATATA-T-TTTAAATTAATTATAAAC---TTTTTTAATTAAA
*
1268035 AAATATTAAATATATTATATATAACATATG-GACTAAGCCCAAATCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGAG-CTAAGCCCAAACCATTTAAAACCCAATTAATA
* * *
1268099 ATTTAATATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATATATCTGAAATT
65 ATTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT-TATATAAAATT
1268164 TTTATTTATAA-TATATATTTTAAATTAATTATAAACTTTTTTAATTAAA
129 TTTATTTATAATTATATATTTTAAATTAATTATAAACTTTTTTAATTAAA
* *
1268213 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1268233 AATTAGAAAA
Statistics
Matches: 185, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
177 18 0.10
178 12 0.06
180 17 0.09
181 2 0.01
182 116 0.63
183 20 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (178 bp):
AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTATAATTATATATTTTAAATTAATTATAAACTTTTTTAATTAAA
Found at i:1277566 original size:11 final size:11
Alignment explanation
Indices: 1277537--1277570 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
1277527 GATTCCTCAA
1277537 TTATATTTTATT
1 TTATATTTT-TT
1277549 TTAATATTTTTT
1 TT-ATATTTTTT
1277561 TTATATTTTT
1 TTATATTTTT
1277571 AAATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.38
12 6 0.29
13 7 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATATTTTTT
Found at i:1281439 original size:14 final size:15
Alignment explanation
Indices: 1281420--1281448 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1281410 CCATTTATTG
1281420 TACTTCG-ATTAATT
1 TACTTCGAATTAATT
1281434 TACTTCGAATTAATT
1 TACTTCGAATTAATT
1281449 AATTAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (15 bp):
TACTTCGAATTAATT
Found at i:1283238 original size:3 final size:3
Alignment explanation
Indices: 1283230--1283277 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
1283220 TTTGTATTAA
* *
1283230 AAT AAT AAT AA- AA- AAT AAT AGT AAT AAT AAT AAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1283276 AA
1 AA
1283278 AGTTAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1286672 original size:2 final size:2
Alignment explanation
Indices: 1286667--1286711 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1286657 GTTGGGCTGC
1286667 AT 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 AT AT
1286708 AT AT
1 AT AT
1286712 TTAAATCTCG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1289202 original size:2 final size:2
Alignment explanation
Indices: 1289197--1289226 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1289187 AAAAGAAAAC
*
1289197 AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1289227 GAGGATAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1289954 original size:5 final size:5
Alignment explanation
Indices: 1289944--1289974 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1289934 ATGAGTTCGG
1289944 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA A
1289975 GATCCCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:1291001 original size:2 final size:2
Alignment explanation
Indices: 1290994--1291041 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1290984 AATATGGATA
1290994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1291036 AT AT AT
1 AT AT AT
1291042 GTTTAATACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1292534 original size:6 final size:6
Alignment explanation
Indices: 1292523--1292586 Score: 121
Period size: 6 Copynumber: 10.8 Consensus size: 6
1292513 ACAAAATAAT
1292523 AAAATA AAAATA AAAATA AAAAT- AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1292570 AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAAT
1292587 TGAAAATTGA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.09
6 52 0.91
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:1292550 original size:23 final size:23
Alignment explanation
Indices: 1292520--1292586 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
1292510 AAAACAAAAT
1292520 AATAAAATAAAAATAAAAATAAA
1 AATAAAATAAAAATAAAAATAAA
1292543 AATAAAATAAAAATAAAAATAAA
1 AATAAAATAAAAATAAAAATAAA
1292566 AATAAAAATAAAAATAAAAAT
1 AAT-AAAATAAAAATAAAAAT
1292587 TGAAAATTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 26 0.60
24 17 0.40
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (23 bp):
AATAAAATAAAAATAAAAATAAA
Found at i:1292592 original size:7 final size:7
Alignment explanation
Indices: 1292582--1292691 Score: 220
Period size: 7 Copynumber: 15.7 Consensus size: 7
1292572 AATAAAAATA
1292582 AAAATTG
1 AAAATTG
1292589 AAAATTG
1 AAAATTG
1292596 AAAATTG
1 AAAATTG
1292603 AAAATTG
1 AAAATTG
1292610 AAAATTG
1 AAAATTG
1292617 AAAATTG
1 AAAATTG
1292624 AAAATTG
1 AAAATTG
1292631 AAAATTG
1 AAAATTG
1292638 AAAATTG
1 AAAATTG
1292645 AAAATTG
1 AAAATTG
1292652 AAAATTG
1 AAAATTG
1292659 AAAATTG
1 AAAATTG
1292666 AAAATTG
1 AAAATTG
1292673 AAAATTG
1 AAAATTG
1292680 AAAATTG
1 AAAATTG
1292687 AAAAT
1 AAAAT
1292692 AAATAAATAA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 103 1.00
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (7 bp):
AAAATTG
Found at i:1292697 original size:4 final size:4
Alignment explanation
Indices: 1292688--1292718 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1292678 TGAAAATTGA
1292688 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1292719 AGGACGACCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1293088 original size:132 final size:130
Alignment explanation
Indices: 1292910--1293397 Score: 527
Period size: 132 Copynumber: 3.7 Consensus size: 130
1292900 TCAAATCAAG
* * * * *
1292910 AAAGGGGATATGCTCCGGTGCTTCTCCAGGGTAGATCAAATCTGGAAACTTTGATTCATTCCATT
1 AAAGGGGATATGCTCCGCTACTTCTTCAGGGTAAATCAAATCTGGAAACTTTGATTCATTCCACT
* *
1292975 GTTCTTCAGGGAATATTGAATCGAAGTATATTTGTTCCATTGTTCCTTAGGAAAGATCAAATCTG
66 GTTCTTCAGGGAAGATTGAATCGAAGTAGATTTGTTCCATTGTT-CTTAGG-AAGATCAAATCTG
1293040 GA
129 GA
* * *
1293042 AAAGGTGATCTGCTCCGCTACTTCTTCAGGGTAAAT-AAGATCTGGAAATTTTGATTCATTCCAC
1 AAAGGGGATATGCTCCGCTACTTCTTCAGGGTAAATCAA-ATCTGGAAACTTTGATTCATTCCAC
* * * *
1293106 TGTTCTTCAGGGAAGATTAAATCGAGGTAGATTTGTTCCACTGCTTCTTCAGGGAAGATCAAATA
65 TGTTCTTCAGGGAAGATTGAATCGAAGTAGATTTGTTCCATTG-TTCTT-A-GGAAGATCAAATC
*
1293171 TGAAAA
127 TG--GA
* * * *
1293177 AAAGGGGGTTATACTCTGCTACTTCTTCAGGGTAAATCAAATCTGGAAACATTGATTCATTCCAC
1 AAA-GGGGATATGCTCCGCTACTTCTTCAGGGTAAATCAAATCTGGAAACTTTGATTCATTCCAC
* * * * * * *
1293242 TATTCTTCAAGGAATATTGAATCGAATTAGATTTGTTTCACTACTTTTTC-AATGAAGATCAAAT
65 TGTTCTTCAGGGAAGATTGAATCGAAGTAGATTTG-TTC-C-A-TTGTTCTTAGGAAGATCAAAT
1293306 CT-GA
126 CTGGA
* * * * * *
1293310 AAAGGGGATCTGCTAC-ATACTTCTTCAGGGTAAATCAGATATGGAAA-TGTTGATTCATGCCAC
1 AAAGGGGATATGCTCCGCTACTTCTTCAGGGTAAATCAAATCTGGAAACT-TTGATTCATTCCAC
1293373 TGTTCTTCAGGGAAGATTGAATCGA
65 TGTTCTTCAGGGAAGATTGAATCGA
1293398 GTTTGATTTG
Statistics
Matches: 296, Mismatches: 47, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
131 65 0.22
132 102 0.34
133 19 0.06
134 2 0.01
135 4 0.01
136 92 0.31
137 6 0.02
138 1 0.00
139 4 0.01
140 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (130 bp):
AAAGGGGATATGCTCCGCTACTTCTTCAGGGTAAATCAAATCTGGAAACTTTGATTCATTCCACT
GTTCTTCAGGGAAGATTGAATCGAAGTAGATTTGTTCCATTGTTCTTAGGAAGATCAAATCTGGA
Found at i:1293236 original size:136 final size:130
Alignment explanation
Indices: 1292930--1293397 Score: 525
Period size: 136 Copynumber: 3.5 Consensus size: 130
1292920 TGCTCCGGTG
* * * *
1292930 CTTCTCCAGGGTAGATCAAATCTGGAAACTTTGATTCATTCCATTGTTCTTCAGGGAATATTGAA
1 CTTCTTCAGGGTAAATCAAATCTGGAAACTTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA
* * * *
1292995 TCGAAGTATATTTGTTCCATTG-TTCCTT-AGGAAAGATCAAATCTGGAAAAGGTG-ATCTGCTC
66 TCGAAGTAGATTTGTTCCACTGCTT-CTTCAGGGAAGATCAAATCT-GAAAAGGGGTATCT-CT-
1293057 CGCTA
127 -GCTA
* *
1293062 CTTCTTCAGGGTAAAT-AAGATCTGGAAATTTTGATTCATTCCACTGTTCTTCAGGGAAGATTAA
1 CTTCTTCAGGGTAAATCAA-ATCTGGAAACTTTGATTCATTCCACTGTTCTTCAGGGAAGATTGA
* *
1293126 ATCGAGGTAGATTTGTTCCACTGCTTCTTCAGGGAAGATCAAATATGAAAAAAAGGGGGTTATAC
65 ATCGAAGTAGATTTGTTCCACTGCTTCTTCAGGGAAGATCAAATCTG---AAAA-GGGG-TAT-C
1293191 TCTGCTA
124 TCTGCTA
* * * *
1293198 CTTCTTCAGGGTAAATCAAATCTGGAAACATTGATTCATTCCACTATTCTTCAAGGAATATTGAA
1 CTTCTTCAGGGTAAATCAAATCTGGAAACTTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA
* * * * ** *
1293263 TCGAATTAGATTTGTTTCACTACTTTTTCAATGAAGATCAAATCTGAAAAGGGG-ATCTGCTACA
66 TCGAAGTAGATTTGTTCCACTGCTTCTTCAGGGAAGATCAAATCTGAAAAGGGGTATCT-CTGC-
1293327 TA
129 TA
* * *
1293329 CTTCTTCAGGGTAAATCAGATATGGAAA-TGTTGATTCATGCCACTGTTCTTCAGGGAAGATTGA
1 CTTCTTCAGGGTAAATCAAATCTGGAAACT-TTGATTCATTCCACTGTTCTTCAGGGAAGATTGA
1293393 ATCGA
65 ATCGA
1293398 GTTTGATTTG
Statistics
Matches: 288, Mismatches: 34, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
129 2 0.01
130 5 0.02
131 65 0.23
132 83 0.29
133 20 0.07
135 4 0.01
136 101 0.35
137 2 0.01
138 4 0.01
139 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (130 bp):
CTTCTTCAGGGTAAATCAAATCTGGAAACTTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA
TCGAAGTAGATTTGTTCCACTGCTTCTTCAGGGAAGATCAAATCTGAAAAGGGGTATCTCTGCTA
Found at i:1293730 original size:63 final size:62
Alignment explanation
Indices: 1293631--1293754 Score: 196
Period size: 63 Copynumber: 2.0 Consensus size: 62
1293621 TTTAAATTGG
* *
1293631 TTACTTTTCAAAAATTTCATTTTCAGAAATGATTTAAATGAAAAACTTTG-GAAATCGTTTTA
1 TTACTTTTAAAAAATTTCATTTTCAGAAAAGATTTAAATGAAAAACTTTGAG-AATCGTTTTA
*
1293693 TTACTTTTAAAAAATTTCAATTTTCAGAAAAGATTTAAATGAGAAACTTTGAGAATCGTTTT
1 TTACTTTTAAAAAATTTC-ATTTTCAGAAAAGATTTAAATGAAAAACTTTGAGAATCGTTTT
1293755 CTCATTTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
62 17 0.30
63 39 0.68
64 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (62 bp):
TTACTTTTAAAAAATTTCATTTTCAGAAAAGATTTAAATGAAAAACTTTGAGAATCGTTTTA
Found at i:1294248 original size:4 final size:4
Alignment explanation
Indices: 1294239--1296070 Score: 3201
Period size: 4 Copynumber: 466.0 Consensus size: 4
1294229 CTATAAGAAT
1294239 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294287 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294335 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294383 TATG TATG TATG TATG -ATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1294430 TA-- TATG TATG TATG TATG TCTG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294476 TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294522 TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294568 TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1294615 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TCTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294663 TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294710 TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294756 TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1294802 TATG TATG GATG TATG TATG TATG TATG --TG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294848 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294896 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294944 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1294992 TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295039 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295087 TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295133 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1295181 TATG TATG GATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295229 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295277 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295325 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295373 TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295419 TATG TATG TTATG TATG TATG TATG TATG T-TG TATG TATG TATG TATG
1 TATG TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295467 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295514 TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295560 TATG TATG TATG TATG TATG TATG TATG TATG TATG T-TG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1295607 TATG TCTG TATG TA-G TATG TA-G TATG --TG TATG TATG TATG T-TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1295650 T-TG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
1295695 TATG TATG TATG CATG TCTG TATG TATG TA-G TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295742 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
1295790 TATG TATG CATG TATG TATG TATG CATG TATG TATG CATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * *
1295838 CATG CATGG CATG TATG CATG CATG CATG TATG TATG TATG TATG CATG
1 TATG TAT-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
1295887 TATG TATG TATG TATG TATG TATG TATG CATA TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1295935 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1295983 TATG TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1296031 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1296071 AAATGATGTG
Statistics
Matches: 1761, Mismatches: 32, Indels: 70
0.95 0.02 0.04
Matches are distributed among these distances:
2 22 0.01
3 36 0.02
4 1695 0.96
5 8 0.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1303356 original size:2 final size:2
Alignment explanation
Indices: 1303344--1303379 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1303334 ACGTAAGTAA
1303344 AT AT A- 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 A
1303380 CATAACGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1305949 original size:2 final size:2
Alignment explanation
Indices: 1305942--1305983 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1305932 AAATTATAAC
1305942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1305983 A
1 A
1305984 GTTAATATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1310268 original size:18 final size:19
Alignment explanation
Indices: 1310226--1310269 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1310216 GATATTTGCT
* *
1310226 TTATTTATAATTTTTTACA
1 TTATTTATAATTTTTAAAA
1310245 TCTATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
1310264 TTATTT
1 TTATTT
1310270 TATATGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:1312823 original size:14 final size:14
Alignment explanation
Indices: 1312804--1312831 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1312794 ATACTCTGGT
1312804 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
1312818 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
1312832 CTAAGCTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:1321515 original size:7 final size:7
Alignment explanation
Indices: 1321499--1321555 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
1321489 ACAAATAAAA
1321499 AAATAA-
1 AAATAAT
1321505 AAATAAT
1 AAATAAT
1321512 AAATAAT
1 AAATAAT
**
1321519 AAACCAT
1 AAATAAT
1321526 AATATAAT
1 AA-ATAAT
1321534 AAATAAT
1 AAATAAT
1321541 ATACATAAT
1 A-A-ATAAT
1321550 ATAATA
1 A-AATA
1321556 CCATAATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
6 6 0.14
7 20 0.47
8 9 0.21
9 8 0.19
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:1321548 original size:13 final size:14
Alignment explanation
Indices: 1321524--1321570 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 14
1321514 ATAATAAACC
1321524 ATAATATA-ATAA-
1 ATAATATACATAAT
1321536 ATAATATACATAAT
1 ATAATATACATAAT
*
1321550 ATAATA-CCATAAT
1 ATAATATACATAAT
1321563 ATAATATA
1 ATAATATA
1321571 TGTACAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.27
13 16 0.53
14 6 0.20
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATATACATAAT
Found at i:1321561 original size:22 final size:22
Alignment explanation
Indices: 1321507--1321565 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
1321497 AAAAATAAAA
*
1321507 ATAATAAATAATAAACCATAAT
1 ATAATAAATAATATACCATAAT
1321529 ATAATAAATAATATA-CATAAT
1 ATAATAAATAATATACCATAAT
*
1321550 ATAATACCATAATATA
1 ATAATA-AATAATATA
1321566 ATATATGTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 12 0.35
22 22 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAATAAATAATATACCATAAT
Found at i:1321561 original size:29 final size:29
Alignment explanation
Indices: 1321517--1321584 Score: 75
Period size: 34 Copynumber: 2.2 Consensus size: 29
1321507 ATAATAAATA
1321517 ATAA-ACCATAATATAATAAATAATATACATAAT
1 ATAATACCATAATATAAT--AT-ATATAC--AAT
*
1321550 ATAATACCATAATATAATATATGTACAAT
1 ATAATACCATAATATAATATATATACAAT
1321579 ATAATA
1 ATAATA
1321585 TATGATATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 9 0.27
31 5 0.15
32 2 0.06
33 4 0.12
34 13 0.39
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.32
Consensus pattern (29 bp):
ATAATACCATAATATAATATATATACAAT
Found at i:1321587 original size:18 final size:18
Alignment explanation
Indices: 1321561--1321600 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
1321551 TAATACCATA
*
1321561 ATATAATATATG-TACA-
1 ATATAATATATGATATAC
1321577 ATATAATATATGATATAC
1 ATATAATATATGATATAC
1321595 ATATAA
1 ATATAA
1321601 ATACTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 3 0.14
18 6 0.29
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
ATATAATATATGATATAC
Found at i:1321668 original size:36 final size:35
Alignment explanation
Indices: 1321609--1321745 Score: 145
Period size: 36 Copynumber: 3.9 Consensus size: 35
1321599 AAATACTTTC
*
1321609 AAAAACTA--TATAATATATATTTTCAAACAGTTTT
1 AAAAACTATGTATTATATATATTTTCAAA-AGTTTT
* *
1321643 CAAAACTATGTATTATATAAATTTTCAAAA-TATTT
1 AAAAACTATGTATTATATATATTTTCAAAAGT-TTT
* *
1321678 AAAAAAACTATGTAATATATATGTTTTCAAAATGTTTT
1 --AAAAACTATGTATTATATATATTTTCAAAA-GTTTT
* *
1321716 AAAAACTATATATTATATATGTTTTCAAAA
1 AAAAACTATGTATTATATATATTTTCAAAA
1321746 ACTATATATT
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
34 8 0.09
35 4 0.05
36 45 0.52
37 26 0.30
38 3 0.03
39 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (35 bp):
AAAAACTATGTATTATATATATTTTCAAAAGTTTT
Found at i:1321697 original size:37 final size:36
Alignment explanation
Indices: 1321644--1321745 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 36
1321634 AACAGTTTTC
**
1321644 AAAACTATGTATTATATAAATTTTCAAAATATTTAAA
1 AAAACTATGTATTATATATGTTTTCAAAATATTT-AA
* * *
1321681 AAAACTATGTAATATATATGTTTTCAAAATGTTTTA
1 AAAACTATGTATTATATATGTTTTCAAAATATTTAA
*
1321717 AAAACTATATATTATATATGTTTTCAAAA
1 AAAACTATGTATTATATATGTTTTCAAAA
1321746 ACTATATATT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 28 0.48
37 30 0.52
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (36 bp):
AAAACTATGTATTATATATGTTTTCAAAATATTTAA
Found at i:1321715 original size:73 final size:71
Alignment explanation
Indices: 1321609--1321745 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 71
1321599 AAATACTTTC
* *
1321609 AAAAACTATATAATATATATTTTCAAACAGTTTTCAAAACTATGTATTATATAAATTTTCAAAAT
1 AAAAACTATATAATATATATTTTCAAACAGTTTTAAAAACTATATATTATATAAATTTTCAAAAT
1321674 ATTTAA
66 ATTTAA
* **
1321680 AAAAACTATGTAATATATATGTTTTCAAA-ATGTTTTAAAAACTATATATTATATATGTTTTCAA
1 AAAAACTATATAATATATA--TTTTCAAACA-GTTTTAAAAACTATATATTATATAAATTTTCAA
1321744 AA
63 AA
1321746 ACTATATATT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 18 0.31
72 1 0.02
73 39 0.67
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (71 bp):
AAAAACTATATAATATATATTTTCAAACAGTTTTAAAAACTATATATTATATAAATTTTCAAAAT
ATTTAA
Found at i:1321765 original size:30 final size:26
Alignment explanation
Indices: 1321709--1321761 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1321699 TGTTTTCAAA
1321709 ATGTTTT-AAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
1321734 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
1321760 AT
1 AT
1321762 ATATATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATATTATAT
Found at i:1323343 original size:43 final size:43
Alignment explanation
Indices: 1323272--1323428 Score: 224
Period size: 43 Copynumber: 3.7 Consensus size: 43
1323262 AGCGGCGTTT
* *
1323272 ACAAACGCCGCAATAGGTGTTGAGATTTAGTGGCGTTTTTCTC
1 ACAAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCTC
* * *
1323315 ACAAACGCCGTAATAGGTTTTGACATTTAGCGGCGTTTTTATC
1 ACAAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCTC
* **
1323358 ACAAACGCCGTAATATGTGTTGAGATTTAGCGATGTTTTTCTC
1 ACAAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCTC
* *
1323401 ACAAACGCAGTAATACGTGTTGAGATTT
1 ACAAACGCCGTAATAGGTGTTGAGATTT
1323429 CGTGACCTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (43 bp):
ACAAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCTC
Found at i:1323440 original size:86 final size:86
Alignment explanation
Indices: 1323271--1323455 Score: 228
Period size: 86 Copynumber: 2.1 Consensus size: 86
1323261 TAGCGGCGTT
* * * * *
1323271 TACAAACGCCGCAATAGGTGTTGAGATTTAGTGGCGTTTTTCTCACAAACGCCGTAATAGGTTTT
1 TACAAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTCTCACAAACGCAGTAATACGTGTT
* *
1323336 GACATTTAGCG-GCGTTTTTA
66 GACATTTAGCGACCTTTTTTA
* * *
1323356 TCACAAACGCCGTAATATGTGTTGAGATTTAGCGATGTTTTTCTCACAAACGCAGTAATACGTGT
1 T-ACAAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTCTCACAAACGCAGTAATACGTGT
* * *
1323421 TGAGATTTCGTGACCTTTTTTTA
65 TGACATTTAGCGACC-TTTTTTA
1323444 TACAAACGCCGC
1 TACAAACGCCGC
1323456 TAAAGGTATG
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
85 1 0.01
86 64 0.77
87 11 0.13
88 7 0.08
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (86 bp):
TACAAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTCTCACAAACGCAGTAATACGTGTT
GACATTTAGCGACCTTTTTTA
Found at i:1329377 original size:29 final size:29
Alignment explanation
Indices: 1329346--1329461 Score: 169
Period size: 29 Copynumber: 4.0 Consensus size: 29
1329336 ATAACATTGT
* *
1329346 TTTTAAAAATATTTACCAAAATATCACCT
1 TTTTAAAAATAATTACCAAAATATCACCG
* *
1329375 TTTTAAAAATAACTCCCAAAATATCACCG
1 TTTTAAAAATAATTACCAAAATATCACCG
* *
1329404 TTTTAAAAATAATTACTAAAATATCTCCG
1 TTTTAAAAATAATTACCAAAATATCACCG
*
1329433 TTTTAACAATAATTACCAAAATATCACCG
1 TTTTAAAAATAATTACCAAAATATCACCG
1329462 GGTCGGGTCG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTAAAAATAATTACCAAAATATCACCG
Found at i:1330197 original size:2 final size:2
Alignment explanation
Indices: 1330190--1330257 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1330180 ACCAATTTAA
1330190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1330232 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1330258 GGGTTGTTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1336876 original size:29 final size:29
Alignment explanation
Indices: 1336836--1336995 Score: 212
Period size: 29 Copynumber: 5.5 Consensus size: 29
1336826 CACAACAATT
* * * * *
1336836 ATTACGAAAATAACACTGTTTTTAAAGTA
1 ATTACCAAAATATCACCGTTTTAAAAATA
* *
1336865 TTTACCAAAATATCACCTTTTTAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
*
1336894 ATTCCCAAAATATCACCGTTTTAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
** **
1336923 ATTAGTAAAATATCACCGTTTTAGCAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
1336952 ATTACCAAAATATCACCGTTTTAAAAATA
1 ATTACCAAAATATCACCGTTTTAAAAATA
1336981 ATTACCAAAATATCA
1 ATTACCAAAATATCA
1336996 ACGGGTCGGG
Statistics
Matches: 112, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 112 1.00
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (29 bp):
ATTACCAAAATATCACCGTTTTAAAAATA
Found at i:1343116 original size:134 final size:134
Alignment explanation
Indices: 1342872--1343119 Score: 397
Period size: 134 Copynumber: 1.9 Consensus size: 134
1342862 GCCACTAAAT
* * *
1342872 TACAACTCTATTGCGGCGTTTATGTCAAAAATGCCACTAAAGTACAACTTTTTAGCGGCATTTGT
1 TACAACTCTATTGCGGCGTTTATGTCAAAAACGCCACTAAAGTACAACTTTTTAGCGACATTTGG
* ** *
1342937 TACCAAACGCCACTAAATTAAGAGTATTTTACGGTGTTTGCTTAAAAAACACCCTTATAAATGAC
66 TAACAAACGCCACTAAATTAAGAGTATTTTACGACGTTTGATTAAAAAACACCCTTATAAATGAC
1343002 AATA
131 AATA
* * *
1343006 TACAACTCTATTGCGGCGTTTATGTCAAAAACGCCATTAAAGTACAACTTTTTTGCGACGTTTGG
1 TACAACTCTATTGCGGCGTTTATGTCAAAAACGCCACTAAAGTACAACTTTTTAGCGACATTTGG
*
1343071 TAACAAACGCCACTAAATTAAGAGTATTTTGCGACGTTTGATTAAAAAA
66 TAACAAACGCCACTAAATTAAGAGTATTTTACGACGTTTGATTAAAAAA
1343120 TGCCACTAAA
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
134 103 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (134 bp):
TACAACTCTATTGCGGCGTTTATGTCAAAAACGCCACTAAAGTACAACTTTTTAGCGACATTTGG
TAACAAACGCCACTAAATTAAGAGTATTTTACGACGTTTGATTAAAAAACACCCTTATAAATGAC
AATA
Found at i:1344896 original size:208 final size:206
Alignment explanation
Indices: 1344604--1345151 Score: 767
Period size: 208 Copynumber: 2.6 Consensus size: 206
1344594 ACAAACGCTG
* * * * * *
1344604 CTAAATTACCACTATATTACGGTGTTTGGG-TTAAACGCCATAAAATTTATTCTCTATTACGGCG
1 CTAAATTACCACTATATTGCGGCGTTTGGGCTAAAACGCC--GAAATTTATTCTATATTGCGGCG
* *
1344668 TTTTTACAATAAATGCCGCTATTGATTAACCCTTCTGTGGCGTTTGTCTAAACATGACGCAAAAG
64 TTTTTACAATAAACGCCGCTATTGATTAACCCTTCTGTGGCGTTTGTCTAAACACGACGCAAAAG
** * *
1344733 TATTATCCCCTTGCGGCGTTTGAGAAATAAATGCCGCTAAATTATCACTCTATTGCGGTGTTAGT
129 TATTATCCCCTTGCGGCGTTTGAGAAATAAACACCGCTAAATTACCACTCTATTACGGTGTTAGT
1344798 GGTATAAAC-ACCA
194 GGTATAAACGA-CA
* * *
1344811 CTAAATTACCACTATATTGCAGCGTTTGGGCTAAAATGCCGCCAAATTTATTCTGTATTGCGGCG
1 CTAAATTACCACTATATTGCGGCGTTTGGGCTAAAACGCCG--AAATTTATTCTATATTGCGGCG
*
1344876 TTTTTACAATAAACGCCGCTATTGATTAACCCTTCTGTGGCGTTTATCTAAACACGACGCAAAAG
64 TTTTTACAATAAACGCCGCTATTGATTAACCCTTCTGTGGCGTTTGTCTAAACACGACGCAAAAG
** * *
1344941 TATTATCCCCTTGCGGCGTTTGAGTTATAAACACCGCTAATTTACCACTCTATTACGGTGTTTGT
129 TATTATCCCCTTGCGGCGTTTGAGAAATAAACACCGCTAAATTACCACTCTATTACGGTGTTAGT
* *
1345006 TGTATAAACGACT
194 GGTATAAACGACA
* ** * *
1345019 CTAAATTATCACTATATTGCGGCAATTGGGCTAAAACGCCGAATTTTTTTTCTATATTGCGGCGT
1 CTAAATTACCACTATATTGCGGCGTTTGGGCTAAAACGCCGAA-ATTTATTCTATATTGCGGCGT
* *
1345084 TTTTACAATAAACGCCGCTATTGATTAACCCTTCTGTGGCGTTTGTCTAAAAACGACGCAAAGGT
65 TTTTACAATAAACGCCGCTATTGATTAACCCTTCTGTGGCGTTTGTCTAAACACGACGCAAAAGT
1345149 ATT
130 ATT
1345152 CTTCATTATT
Statistics
Matches: 304, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
206 2 0.01
207 110 0.36
208 191 0.63
209 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (206 bp):
CTAAATTACCACTATATTGCGGCGTTTGGGCTAAAACGCCGAAATTTATTCTATATTGCGGCGTT
TTTACAATAAACGCCGCTATTGATTAACCCTTCTGTGGCGTTTGTCTAAACACGACGCAAAAGTA
TTATCCCCTTGCGGCGTTTGAGAAATAAACACCGCTAAATTACCACTCTATTACGGTGTTAGTGG
TATAAACGACA
Found at i:1346080 original size:3 final size:3
Alignment explanation
Indices: 1346072--1346149 Score: 61
Period size: 3 Copynumber: 26.0 Consensus size: 3
1346062 TTTTAATTGT
* * * * *
1346072 TTA TTA TTA AT- TTA TAA TTA TTAA TTA TTA ATA TTA ATA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* *
1346117 TTA TTA TTA CTT- TTA TTA CTA TTA ATA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
1346150 CAATTTTGCA
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
2 3 0.05
3 50 0.86
4 5 0.09
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1346122 original size:24 final size:23
Alignment explanation
Indices: 1346072--1346149 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 23
1346062 TTTTAATTGT
1346072 TTATTATTAATTT-ATA--ATTA
1 TTATTATTAATTTAATACTATTA
1346092 TTAATTATTAATATTAATACTATTA
1 TT-ATTATTAAT-TTAATACTATTA
* *
1346117 TTATTATTACTTTTATTACTATTA
1 TTATTATTA-ATTTAATACTATTA
*
1346141 ATATTATTA
1 TTATTATTA
1346150 CAATTTTGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.04
21 9 0.18
22 2 0.04
23 3 0.06
24 26 0.53
25 7 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATTATTAATTTAATACTATTA
Found at i:1346655 original size:15 final size:16
Alignment explanation
Indices: 1346620--1346676 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
1346610 GAAAAGCAGA
1346620 GAAAAAAGAGAGCATTC
1 GAAAAAAGA-AGCATTC
*
1346637 GAAAAAAGAAGC-TTT
1 GAAAAAAGAAGCATTC
*
1346652 GAAAAATAGAAACATATTC
1 GAAAAA-AGAAGC--ATTC
1346671 GAAAAA
1 GAAAAA
1346677 GGAAAACAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.24
16 8 0.24
17 9 0.27
19 8 0.24
ACGTcount: A:0.58, C:0.09, G:0.18, T:0.16
Consensus pattern (16 bp):
GAAAAAAGAAGCATTC
Found at i:1351726 original size:10 final size:10
Alignment explanation
Indices: 1351711--1351742 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1351701 CATCGCTGTT
1351711 ATGCGCAGCC
1 ATGCGCAGCC
1351721 ATGCGCAGCC
1 ATGCGCAGCC
1351731 ATGCGCAGCC
1 ATGCGCAGCC
1351741 AT
1 AT
1351743 ACGCCGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.22, C:0.38, G:0.28, T:0.12
Consensus pattern (10 bp):
ATGCGCAGCC
Found at i:1351862 original size:20 final size:20
Alignment explanation
Indices: 1351816--1351872 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
1351806 GGTTTGGACC
* *
1351816 GACCCGAACCGA-CCAACCA
1 GACCCGAACCAAGTCAACCA
*
1351835 G-TCCGAACCAAGTCAACCA
1 GACCCGAACCAAGTCAACCA
**
1351854 GACCCGAACTTAGTCAACC
1 GACCCGAACCAAGTCAACC
1351873 CAACCCGACA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 8 0.27
19 8 0.27
20 14 0.47
ACGTcount: A:0.35, C:0.40, G:0.16, T:0.09
Consensus pattern (20 bp):
GACCCGAACCAAGTCAACCA
Found at i:1352458 original size:33 final size:33
Alignment explanation
Indices: 1352411--1352476 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1352401 GAGAGGTATT
1352411 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCC
1 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCC
*
1352444 AATTTTGGGTGCTTTGGGAGTTCTTACCCTTCC
1 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCC
1352477 TATGTGTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41
Consensus pattern (33 bp):
AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCC
Found at i:1353627 original size:3 final size:3
Alignment explanation
Indices: 1353613--1353664 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
1353603 TTAATTTTAA
* * * *
1353613 ATT ATT AAT ATT ATT ACT ATT ATT ATT ACTT -TT ATT ACT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
1353658 ATT ATT A
1 ATT ATT A
1353665 CAATTTTTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1353639 original size:21 final size:21
Alignment explanation
Indices: 1353613--1353661 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1353603 TTAATTTTAA
1353613 ATTATTAATATTATTACTATT
1 ATTATTAATATTATTACTATT
* *
1353634 ATTATTACTTTTATTACTATT
1 ATTATTAATATTATTACTATT
*
1353655 AATATTA
1 ATTATTA
1353662 TTACAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTAATATTATTACTATT
Found at i:1360310 original size:33 final size:33
Alignment explanation
Indices: 1360273--1360340 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
1360263 TTGAGAGGTA
*
1360273 CCAATTTTGGGTGCTTTGGGAGTTCTTACCCTT
1 CCAATTTTGGGTGCTTTGGGAGCTCTTACCCTT
1360306 CCAATTTTGGGTGCTTTGGGAGCTCTTACCCTT
1 CCAATTTTGGGTGCTTTGGGAGCTCTTACCCTT
1360339 CC
1 CC
1360341 CATGTATAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.40
Consensus pattern (33 bp):
CCAATTTTGGGTGCTTTGGGAGCTCTTACCCTT
Found at i:1361708 original size:21 final size:21
Alignment explanation
Indices: 1361682--1361722 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1361672 TCATTTTAAA
1361682 TTATTAATATTATTACTATTT
1 TTATTAATATTATTACTATTT
* *
1361703 TTATTACTTTTATTACTATT
1 TTATTAATATTATTACTATT
1361723 ACTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTAATATTATTACTATTT
Found at i:1361716 original size:15 final size:15
Alignment explanation
Indices: 1361692--1361733 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1361682 TTATTAATAT
1361692 TATTACTATT-TT--
1 TATTACTATTATTAC
*
1361704 TATTACTTTTATTAC
1 TATTACTATTATTAC
1361719 TATTACTATTATTAC
1 TATTACTATTATTAC
1361734 ATTTTTGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.36
13 2 0.08
15 14 0.56
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTACTATTATTAC
Found at i:1363057 original size:11 final size:11
Alignment explanation
Indices: 1363041--1363067 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1363031 TTATGTTGCT
1363041 TTATTTTTTTA
1 TTATTTTTTTA
1363052 TTATTTTTTTA
1 TTATTTTTTTA
1363063 TTATT
1 TTATT
1363068 CTGAACCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:1365984 original size:20 final size:20
Alignment explanation
Indices: 1365955--1365993 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1365945 ATTCGATCCA
*
1365955 TTTTTTAGAATTAAGCTCCG
1 TTTTTCAGAATTAAGCTCCG
1365975 TTTTTCAGAATTAAGCTCC
1 TTTTTCAGAATTAAGCTCC
1365994 ATTGACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTTTCAGAATTAAGCTCCG
Found at i:1368010 original size:24 final size:24
Alignment explanation
Indices: 1367907--1368013 Score: 144
Period size: 24 Copynumber: 4.5 Consensus size: 24
1367897 ATTACTTATT
* *
1367907 TGATACTCGACATGGATTCTGATC
1 TGATACTTGACATGGATTCTGATA
*
1367931 TGATA-TCTGACATGGATTTTGATA
1 TGATACT-TGACATGGATTCTGATA
*
1367955 TGATACTTGACTTGGATTCTGATA
1 TGATACTTGACATGGATTCTGATA
* *
1367979 TGATACTTGACCTGGATTTTGATA
1 TGATACTTGACATGGATTCTGATA
1368003 TGATACTTGAC
1 TGATACTTGAC
1368014 GTGAATTATG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
23 1 0.01
24 72 0.97
25 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (24 bp):
TGATACTTGACATGGATTCTGATA
Found at i:1368010 original size:48 final size:48
Alignment explanation
Indices: 1367907--1368013 Score: 162
Period size: 48 Copynumber: 2.2 Consensus size: 48
1367897 ATTACTTATT
* *
1367907 TGATACTCGACATGGATTCTGATCTGATATCTGACATGGATTTTGATA
1 TGATACTTGACATGGATTCTGATATGATATCTGACATGGATTTTGATA
* *
1367955 TGATACTTGACTTGGATTCTGATATGATA-CTTGACCTGGATTTTGATA
1 TGATACTTGACATGGATTCTGATATGATATC-TGACATGGATTTTGATA
1368003 TGATACTTGAC
1 TGATACTTGAC
1368014 GTGAATTATG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 1 0.02
48 53 0.98
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (48 bp):
TGATACTTGACATGGATTCTGATATGATATCTGACATGGATTTTGATA
Found at i:1368025 original size:24 final size:24
Alignment explanation
Indices: 1367907--1368030 Score: 124
Period size: 24 Copynumber: 5.2 Consensus size: 24
1367897 ATTACTTATT
* * * *
1367907 TGATACTCGACATGGATTCTGATC
1 TGATACTTGACCTGGATTATGATA
* *
1367931 TGATA-TCTGACATGGATTTTGATA
1 TGATACT-TGACCTGGATTATGATA
* *
1367955 TGATACTTGACTTGGATTCTGATA
1 TGATACTTGACCTGGATTATGATA
*
1367979 TGATACTTGACCTGGATTTTGATA
1 TGATACTTGACCTGGATTATGATA
* * *
1368003 TGATACTTGACGTGAATTATGATT
1 TGATACTTGACCTGGATTATGATA
1368027 TGAT
1 TGAT
1368031 TTTTTATATA
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 85 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (24 bp):
TGATACTTGACCTGGATTATGATA
Found at i:1368238 original size:2 final size:2
Alignment explanation
Indices: 1368231--1368270 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1368221 GATGGTGGTA
1368231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1368271 TTTAAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1370266 original size:10 final size:10
Alignment explanation
Indices: 1370253--1370280 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1370243 TGTTGACATG
1370253 CGTTGACCGA
1 CGTTGACCGA
1370263 CGTTGACCGA
1 CGTTGACCGA
1370273 CGTTGACC
1 CGTTGACC
1370281 AGAACTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (10 bp):
CGTTGACCGA
Found at i:1372773 original size:12 final size:12
Alignment explanation
Indices: 1372736--1372798 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
1372726 ATTTGATACT
1372736 TGACATGGATTC
1 TGACATGGATTC
*
1372748 TGATAT-GATATC
1 TGACATGGAT-TC
1372760 TGACATGGATTC
1 TGACATGGATTC
* *
1372772 TGATAT-GATAC
1 TGACATGGATTC
*
1372783 TTGACTTGGATTC
1 -TGACATGGATTC
1372796 TGA
1 TGA
1372799 TCTGATACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1372852 original size:24 final size:24
Alignment explanation
Indices: 1372721--1372835 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
1372711 TCGATTTGAT
*
1372721 TTCTGATTTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
1372745 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
*
1372769 TTCTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* *
1372793 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
1372817 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
1372836 GTGAATTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:1373023 original size:2 final size:2
Alignment explanation
Indices: 1373016--1373046 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1373006 CGGATGGGGG
1373016 TA 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 TA T
1373047 GTTTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1373804 original size:29 final size:29
Alignment explanation
Indices: 1373756--1373811 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1373746 CCACAAGAAA
* *
1373756 TATAAGGAAGTGAGCTTAATTTATACACC
1 TATAAGGAAGTGAGCATAATTCATACACC
1373785 TATAAGGAAGTGATG-ATAATTCATACA
1 TATAAGGAAGTGA-GCATAATTCATACA
1373812 TATTTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (29 bp):
TATAAGGAAGTGAGCATAATTCATACACC
Found at i:1374362 original size:21 final size:21
Alignment explanation
Indices: 1374336--1374384 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1374326 TTAATTTTAA
*
1374336 ATTATTAATATTATTACTATT
1 ATTATTAATATTATTACAATT
* *
1374357 ATTATTACTTTTATTACAATT
1 ATTATTAATATTATTACAATT
*
1374378 AATATTA
1 ATTATTA
1374385 TTACATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTAATATTATTACAATT
Found at i:1374951 original size:18 final size:20
Alignment explanation
Indices: 1374914--1374954 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1374904 AAAAACAGAG
1374914 AAAAAAGAGAGCATTCGAAA
1 AAAAAAGAGAGCATTCGAAA
*
1374934 AAAAAAGA-AGC-TTTGAAA
1 AAAAAAGAGAGCATTCGAAA
1374952 AAA
1 AAA
1374955 TAGAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 3 0.15
20 8 0.40
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAAAAGAGAGCATTCGAAA
Found at i:1379615 original size:33 final size:33
Alignment explanation
Indices: 1379578--1379642 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1379568 TGAGAGGTGC
*
1379578 CAATTTTGGGTGCTTTGGGAGTTCTTACCCTTA
1 CAATTTTGGGTGCTTTGGGAGCTCTTACCCTTA
1379611 CAATTTTGGGTGCTTTGGGAGCTCTTACCCTT
1 CAATTTTGGGTGCTTTGGGAGCTCTTACCCTT
1379643 CCCATGTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (33 bp):
CAATTTTGGGTGCTTTGGGAGCTCTTACCCTTA
Found at i:1380980 original size:20 final size:20
Alignment explanation
Indices: 1380955--1380996 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1380945 TTTTATCCGG
*
1380955 ATTTTAATTGTT-TATTATTA
1 ATTTTAATT-TTAAATTATTA
1380975 ATTTTAATTTTAAATTATTA
1 ATTTTAATTTTAAATTATTA
1380995 AT
1 AT
1380997 ATTATTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTAATTTTAAATTATTA
Found at i:1381014 original size:21 final size:21
Alignment explanation
Indices: 1380988--1381036 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1380978 TTAATTTTAA
1380988 ATTATTAATATTATTACTATT
1 ATTATTAATATTATTACTATT
* *
1381009 ATTATTACTTTTATTACTATT
1 ATTATTAATATTATTACTATT
*
1381030 AATATTA
1 ATTATTA
1381037 TAACATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTAATATTATTACTATT
Found at i:1385855 original size:20 final size:20
Alignment explanation
Indices: 1385832--1385878 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1385822 ATCCGAACCA
* *
1385832 AGTCAACCATACTCGAACTG
1 AGTCAACCAGACCCGAACTG
1385852 AGTCAACCAGACCCGAACTG
1 AGTCAACCAGACCCGAACTG
1385872 AGTCAAC
1 AGTCAAC
1385879 TCGACTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.17, T:0.15
Consensus pattern (20 bp):
AGTCAACCAGACCCGAACTG
Found at i:1386467 original size:33 final size:33
Alignment explanation
Indices: 1386418--1386482 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1386408 GAGAGGTACG
1386418 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCT
1 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCT
* *
1386451 AATTTTGGGTGTTTTGGGAGTTCTTACCCTTC
1 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTC
1386483 CCATGTGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.45
Consensus pattern (33 bp):
AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCT
Found at i:1387854 original size:21 final size:21
Alignment explanation
Indices: 1387828--1387876 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1387818 TTTAATTTAA
1387828 ATTATTAATATTATTACTATT
1 ATTATTAATATTATTACTATT
* *
1387849 ATTATTACTTTTATTACTATT
1 ATTATTAATATTATTACTATT
*
1387870 AATATTA
1 ATTATTA
1387877 CTACATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTAATATTATTACTATT
Found at i:1387877 original size:12 final size:11
Alignment explanation
Indices: 1387839--1387879 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
1387829 TTATTAATAT
1387839 TATTACTATTA
1 TATTACTATTA
1387850 TTATTACT-TT-
1 -TATTACTATTA
1387860 TATTACTATTAA
1 TATTACTATT-A
1387872 TATTACTA
1 TATTACTA
1387880 CATTTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 2 0.08
12 15 0.58
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTACTATTA
Found at i:1387877 original size:21 final size:21
Alignment explanation
Indices: 1387838--1387878 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1387828 ATTATTAATA
*
1387838 TTATTACTATTATTATTACTT
1 TTATTACTATTAATATTACTT
1387859 TTATTACTATTAATATTACT
1 TTATTACTATTAATATTACT
1387879 ACATTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTACTATTAATATTACTT
Found at i:1388964 original size:15 final size:16
Alignment explanation
Indices: 1388933--1388967 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1388923 AGATTTACAA
1388933 AAATCTGAGACTTTAT
1 AAATCTGAGACTTTAT
1388949 AAATCTGAGA-TTTAT
1 AAATCTGAGACTTTAT
1388964 AAAT
1 AAAT
1388968 TTGGTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (16 bp):
AAATCTGAGACTTTAT
Found at i:1389296 original size:8 final size:7
Alignment explanation
Indices: 1389219--1389302 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 7
1389209 TTTTATTACT
1389219 TTTTATA
1 TTTTATA
1389226 TTTTA-A
1 TTTTATA
**
1389232 TACTATA
1 TTTTATA
*
1389239 GTTTA-A
1 TTTTATA
1389245 TTTTATTAA
1 TTTTA-T-A
1389254 TTTTAGTCA
1 TTTTA-T-A
*
1389263 TTTTTTA
1 TTTTATA
1389270 -TTTATA
1 TTTTATA
1389276 -TTTATA
1 TTTTATA
1389282 TTTTATA
1 TTTTATA
1389289 TGTTTATA
1 T-TTTATA
1389297 TATTTA
1 T-TTTA
1389303 ATTATTATTG
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
6 20 0.33
7 16 0.27
8 12 0.20
9 12 0.20
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (7 bp):
TTTTATA
Found at i:1389301 original size:23 final size:22
Alignment explanation
Indices: 1389272--1389314 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1389262 ATTTTTTATT
1389272 TATATTTATATT-TTATATGTTTA
1 TATATTTA-ATTATTAT-TGTTTA
1389295 TATATTTAATTATTATTGTT
1 TATATTTAATTATTATTGTT
1389315 ATTATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TATATTTAATTATTATTGTTTA
Found at i:1389704 original size:9 final size:9
Alignment explanation
Indices: 1389686--1389714 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1389676 AATATCTTAT
1389686 TTAT-AAAA
1 TTATAAAAA
1389694 TTATAAAAA
1 TTATAAAAA
1389703 TTATAAAAA
1 TTATAAAAA
1389712 TTA
1 TTA
1389715 ATATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:1389716 original size:147 final size:147
Alignment explanation
Indices: 1389445--1389724 Score: 365
Period size: 147 Copynumber: 1.9 Consensus size: 147
1389435 TAATCATATT
* * *
1389445 TTAATATTTATTTATTTTTTAATATTAAGATATGGGCTATCTTAAAGCACCTAGAAGTCATTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTATCTTAAAGAACCTAGAAGTCATTTTC
* * **
1389510 TGATATTCTTAAATAAATAAATATTCTATTTTTATAAATTATATATTAATTTATTTTAAT-TATT
66 TGATATTCTTAAATAAATAAATATTCTATTTATATAAATTATATATAAATTTAAATTAATATATT
1389574 TTTAGAGAAATGTTTTA
131 TTTAGAGAAATGTTTTA
* * *
1389591 TTAATATTTATTTAATTTTTTAATATTAAGAAATTAGCTGTCTTAAAGAACCTAGAAGTCCTTTT
1 TTAATATTTATTT-ATTTTTTAATATTAAGAAATGAGCTATCTTAAAGAACCTAGAAGTCATTTT
*
1389656 CTGATATT-TCTAAGTAAATAAATA-TCTTATTTATA-AAATTATA-A-AAATTATAAAAATTAA
65 CTGATATTCT-TAAATAAATAAATATTC-TATTTATATAAATTATATATAAATT-T--AAATTAA
1389716 TATATTTTT
125 TATATTTTT
1389725 TTCTTAAAAT
Statistics
Matches: 116, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
144 4 0.03
145 2 0.02
146 24 0.21
147 79 0.68
148 7 0.06
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (147 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTATCTTAAAGAACCTAGAAGTCATTTTC
TGATATTCTTAAATAAATAAATATTCTATTTATATAAATTATATATAAATTTAAATTAATATATT
TTTAGAGAAATGTTTTA
Found at i:1390276 original size:26 final size:25
Alignment explanation
Indices: 1390232--1390294 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
1390222 TTTCTTTCAA
*
1390232 ATATTTTATTACTTATAATATTTATT
1 ATATTTTTTTACTTATAATATTT-TT
*
1390258 ATATTTTTTTA-TTATTAATGTTTTT
1 ATATTTTTTTACTTA-TAATATTTTT
*
1390283 ATTTTATTTTTA
1 ATATT-TTTTTA
1390295 GATATTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 9 0.28
26 23 0.72
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (25 bp):
ATATTTTTTTACTTATAATATTTTT
Found at i:1390283 original size:15 final size:16
Alignment explanation
Indices: 1390253--1390289 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1390243 CTTATAATAT
*
1390253 TTATTATATTTTTTTA
1 TTATTATATGTTTTTA
1390269 TTATTA-ATGTTTTTA
1 TTATTATATGTTTTTA
1390284 TT-TTAT
1 TTATTAT
1390290 TTTTAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 10 0.53
16 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTATTATATGTTTTTA
Found at i:1391737 original size:43 final size:44
Alignment explanation
Indices: 1391676--1391762 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
1391666 TGGCTTTAGA
* * *
1391676 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
* *
1391719 GAAGTTAGGACTGAAAGTTGTCCCCTACATATAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
1391763 TGATGCACGG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 27 0.71
44 11 0.29
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
Found at i:1397988 original size:75 final size:75
Alignment explanation
Indices: 1397865--1398049 Score: 221
Period size: 75 Copynumber: 2.5 Consensus size: 75
1397855 TTGCTAGGGT
* * ** * *
1397865 ATGCTGAAAGCCTATTTCAATC-ATAATCAAGAATATTGACGTATTTTGAATGT-TCACATCAAC
1 ATGCTGAAAGCCCATTTCAATCAAAAAT-TGGAATATTGACGCATTTTGAACGTCT-ACATCAAC
1397928 AAATGTTGGGGC
64 AAATGTTGGGGC
* ** * *
1397940 ATGCTGAAAGCCCATTTCAATCAAAAATTGGAATATTGGCGCATTTTGAACGTCTTTATTAGCAA
1 ATGCTGAAAGCCCATTTCAATCAAAAATTGGAATATTGACGCATTTTGAACGTCTACATCAACAA
1398005 ATGTTGGGGC
66 ATGTTGGGGC
* *
1398015 ATGCTGAAAGCCCTTTTCAATCAGAAATTGGAATA
1 ATGCTGAAAGCCCATTTCAATCAAAAATTGGAATA
1398050 ATATTTTGAA
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
75 90 0.95
76 5 0.05
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (75 bp):
ATGCTGAAAGCCCATTTCAATCAAAAATTGGAATATTGACGCATTTTGAACGTCTACATCAACAA
ATGTTGGGGC
Found at i:1399050 original size:54 final size:54
Alignment explanation
Indices: 1398991--1399128 Score: 154
Period size: 54 Copynumber: 2.6 Consensus size: 54
1398981 CATAGAAAAT
*
1398991 GATGAATGTGTTGTCAAATGCTTTACAAACATCT-GGACATAAGCCACAAGAAAG
1 GATGAATGTGTTGTCAAATGCTTTACAAACATCTAGG-CAGAAGCCACAAGAAAG
* * * * *
1399045 GATGAATGTGTTATCAAAAGCTTTACGAAA-ATCTAGGTAGAAGCCACGAGAAAT
1 GATGAATGTGTTGTCAAATGCTTTAC-AAACATCTAGGCAGAAGCCACAAGAAAG
* * * *
1399099 GATGAATATATTGTCACATGTTTTACAAAC
1 GATGAATGTGTTGTCAAATGCTTTACAAAC
1399129 CATTGATTAT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
53 3 0.04
54 61 0.88
55 5 0.07
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (54 bp):
GATGAATGTGTTGTCAAATGCTTTACAAACATCTAGGCAGAAGCCACAAGAAAG
Found at i:1400309 original size:74 final size:74
Alignment explanation
Indices: 1400196--1400438 Score: 378
Period size: 74 Copynumber: 3.3 Consensus size: 74
1400186 GTGTCATCCA
* * *
1400196 TAAGACCTATAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1400261 GGTCATCTG
66 GGTCATCTG
*
1400270 TAAGACCTACAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
*
1400335 GGCCATCTG
66 GGTCATCTG
* * * * *
1400344 TAAAACCTTCAGTGCATGATGTTTTCAAAAAGCATTCGAGAGCTTTTTGATATTTGAAGCCTCCG
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1400409 GGTCATCTG
66 GGTCATCTG
* *
1400418 TAATACCTACAGTGCAAGATG
1 TAAGACCTACAGTGCATGATG
1400439 ATAAGACCTA
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 154 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (74 bp):
TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
GGTCATCTG
Found at i:1400637 original size:118 final size:118
Alignment explanation
Indices: 1400329--1400703 Score: 540
Period size: 118 Copynumber: 3.2 Consensus size: 118
1400319 ATATTTAAAG
* ** * * * *
1400329 CCTCCGGGCCATCTGTAAAACCTTCAGTGCATGATGTTTTCAAAAAGCATTCGAGAGCTTTTTGA
1 CCTCAGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
* *
1400394 TA-TTT-GAAGCCTCCGGGTCATCTGTAATACCTACAGTGCAAGATGATAAGA
66 TATTTTCAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGA
* *
1400445 CCT-AGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGATTTTTGA
1 CCTCAGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
* * *
1400509 TATTTTTCAAAGCCTCTGGGTTATCTGTAAGACCTACAGTGCAAGCTGATAAGA
66 TA-TTTTCAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGA
* * *
1400563 CCTCAAGGCCATCCATAAGACCTACAGTGCAGGATGTTTTTAAAAAGCCTTCGGGAGCTTTTTGA
1 CCTCAGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
*
1400628 TATTTTCAAAGCCTCCAGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGA
66 TATTTTCAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGA
* *
1400681 CCTCAGGGCCATTCATATGACCT
1 CCTCAGGGCCATCCATAAGACCT
1400704 CTGGGCAGAA
Statistics
Matches: 229, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
115 54 0.24
116 3 0.01
117 3 0.01
118 111 0.48
119 58 0.25
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (118 bp):
CCTCAGGGCCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
TATTTTCAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGA
Found at i:1400855 original size:3 final size:3
Alignment explanation
Indices: 1400849--1400880 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1400839 TTCATCATCA
*
1400849 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1400881 AATAAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1402164 original size:28 final size:31
Alignment explanation
Indices: 1402099--1402198 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 31
1402089 GAATTAGAGC
* *
1402099 ACTA-AGTTTAAATA-TTTT-ACATTTTAAT
1 ACTATAGTTTTAATACTTTTCATATTTTAAT
1402127 CACTA-A-TTTTAATAC-TTTCAT-TTTTAACT
1 -ACTATAGTTTTAATACTTTTCATATTTTAA-T
* *
1402156 AC-A-AGTTTTATTACTTTTTATATTTTAAT
1 ACTATAGTTTTAATACTTTTCATATTTTAAT
1402185 ACTATAGTTTTAAT
1 ACTATAGTTTTAAT
1402199 TTTATTTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
27 2 0.03
28 26 0.45
29 15 0.26
30 7 0.12
31 8 0.14
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.53
Consensus pattern (31 bp):
ACTATAGTTTTAATACTTTTCATATTTTAAT
Found at i:1402257 original size:22 final size:21
Alignment explanation
Indices: 1402226--1402267 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1402216 TTTTTTATTA
1402226 ATATTTTAATT-TTATATGTTT
1 ATATTTTAATTATTAT-TGTTT
1402247 ATATATTTAATTATTATTGTT
1 ATAT-TTTAATTATTATTGTT
1402268 ATTATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
ATATTTTAATTATTATTGTTT
Found at i:1402636 original size:9 final size:9
Alignment explanation
Indices: 1402618--1402646 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1402608 AATATCTTAT
1402618 TTAT-AAAA
1 TTATAAAAA
1402626 TTATAAAAA
1 TTATAAAAA
1402635 TTATAAAAA
1 TTATAAAAA
1402644 TTA
1 TTA
1402647 ATATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:1403218 original size:17 final size:17
Alignment explanation
Indices: 1403182--1403225 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1403172 AAAAATAGAG
1403182 AAAAAAGAGAGCATTCAA
1 AAAAAAGA-AGCATTCAA
* *
1403200 AAAAAAGAAGCTTTGAA
1 AAAAAAGAAGCATTCAA
*
1403217 AAAATAGAA
1 AAAAAAGAA
1403226 ACATATTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.64, C:0.07, G:0.16, T:0.14
Consensus pattern (17 bp):
AAAAAAGAAGCATTCAA
Found at i:1406166 original size:14 final size:16
Alignment explanation
Indices: 1406143--1406181 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
1406133 GCCTTCGGGC
1406143 TATATA-ATAATATT-
1 TATATATATAATATTA
1406157 TATA-ATATAATATTA
1 TATATATATAATATTA
1406172 TATATATATA
1 TATATATATA
1406182 TAACAACGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.05
14 12 0.55
15 4 0.18
16 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATATATAATATTA
Found at i:1406166 original size:17 final size:18
Alignment explanation
Indices: 1406143--1406184 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
1406133 GCCTTCGGGC
*
1406143 TATATAATAATATTTATA
1 TATATAATAATATATATA
*
1406161 -ATATAATATTATATATA
1 TATATAATAATATATATA
1406178 TATATAA
1 TATATAA
1406185 CAACGTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATAATAATATATATA
Found at i:1406818 original size:236 final size:230
Alignment explanation
Indices: 1406529--1407094 Score: 850
Period size: 236 Copynumber: 2.4 Consensus size: 230
1406519 AGAATCTAAT
* * ** * * *
1406529 TTCACTACTCTTTCGTAAAAATCAGACTCACAA-TTGGATTACTTCACTACTCTTCCATGAAGAT
1 TTCACTACTCTTCCGTGAAGTTCAGATTCA-AACTTGAATTTCTTCACTACTCTTCCATGAAGAT
* * **
1406593 CTCATACTTTGCTGAAAAATATGTTCCACTACTCTTCCGTGGAGTTCGAATTTTATTTGGGTTCT
65 CTCATACTTTGCTGAAAAATCTGTTCCACTACTCTTCCCTGGAGTTCGAATTTTATCCGGGTTCT
* *
1406658 TGCTTTTTGCTTCACTACTCTTCTGTGAAGTTTGAATATGATTGCTAAAAAAT-TCGTTCCACTA
130 TGCTTTTCGCTTCACTACTCTTCCGTGAAGTTTGAATATGATTGCTAAAAAATCT-GTTCCACTA
* *
1406722 TTATTCCGTGAAAACTGAATTTTATTCTGGTTTCTGCTTCTGC
194 CTATTCCGTGAAAACTGAATTTTATTATGG----T--TTCTGC
*
1406765 TTCACTACTTTTCCGTGAAGTTCAGATTCAAACTTGAATTTCTTCACTACTCTTCCATGAAGATC
1 TTCACTACTCTTCCGTGAAGTTCAGATTCAAACTTGAATTTCTTCACTACTCTTCCATGAAGATC
1406830 TCATACTTTGCT-AAAACATCTGTTCCACTACTCTTCCCTGGAGTTCGAATTTTATCCGGGTTCT
66 TCATACTTTGCTGAAAA-ATCTGTTCCACTACTCTTCCCTGGAGTTCGAATTTTATCCGGGTTCT
*
1406894 TGCTTTTCGCTTCACTACTCTTCCGTGAAGTTTGAATATGATTGCTAAAAAATCTGTTCCACTCC
130 TGCTTTTCGCTTCACTACTCTTCCGTGAAGTTTGAATATGATTGCTAAAAAATCTGTTCCACTAC
*
1406959 TCTTCCGTGAAAACTGAATTTTATTATGGTTTCTGC
195 TATTCCGTGAAAACTGAATTTTATTATGGTTTCTGC
* *
1406995 TTCACTACTCTTCCGTGAAGTTCAGATTTAAACTTGAATTTCTTCACTACTCTTCCGTGAAGATC
1 TTCACTACTCTTCCGTGAAGTTCAGATTCAAACTTGAATTTCTTCACTACTCTTCCATGAAGATC
1407060 TCATACTTTGCTGAAAAATCTGTTCCACTACTCTT
66 TCATACTTTGCTGAAAAATCTGTTCCACTACTCTT
1407095 TTGTGGAAAG
Statistics
Matches: 305, Mismatches: 21, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
230 98 0.32
231 4 0.01
232 1 0.00
235 6 0.02
236 195 0.64
237 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (230 bp):
TTCACTACTCTTCCGTGAAGTTCAGATTCAAACTTGAATTTCTTCACTACTCTTCCATGAAGATC
TCATACTTTGCTGAAAAATCTGTTCCACTACTCTTCCCTGGAGTTCGAATTTTATCCGGGTTCTT
GCTTTTCGCTTCACTACTCTTCCGTGAAGTTTGAATATGATTGCTAAAAAATCTGTTCCACTACT
ATTCCGTGAAAACTGAATTTTATTATGGTTTCTGC
Found at i:1407333 original size:20 final size:20
Alignment explanation
Indices: 1407308--1407417 Score: 107
Period size: 20 Copynumber: 5.5 Consensus size: 20
1407298 CCAAAGGAAT
1407308 TTTACAAATTACCCAGAGGC
1 TTTACAAATTACCCAGAGGC
* **
1407328 TTTACAAATTACCCAAAGAA
1 TTTACAAATTACCCAGAGGC
* * *
1407348 TTTACAAAATA-CTAGGAGGA
1 TTTACAAATTACCCA-GAGGC
*
1407368 TTTACAAATTACCCGGAGGC
1 TTTACAAATTACCCAGAGGC
* *
1407388 TTTATAAATGACCC-GAAGGC
1 TTTACAAATTACCCAG-AGGC
1407408 TTTACAAATT
1 TTTACAAATT
1407418 TTTGGAAATA
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
19 3 0.04
20 68 0.94
21 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (20 bp):
TTTACAAATTACCCAGAGGC
Found at i:1414991 original size:20 final size:20
Alignment explanation
Indices: 1414968--1415014 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1414958 ATCCGAACCA
* *
1414968 AGTCAACCATACTCGAACTG
1 AGTCAACCAGACCCGAACTG
1414988 AGTCAACCAGACCCGAACTG
1 AGTCAACCAGACCCGAACTG
1415008 AGTCAAC
1 AGTCAAC
1415015 TCGACTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.17, T:0.15
Consensus pattern (20 bp):
AGTCAACCAGACCCGAACTG
Found at i:1415596 original size:33 final size:33
Alignment explanation
Indices: 1415547--1415611 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1415537 ATTGGAGTAG
1415547 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCT
1 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCT
* *
1415580 AATTTTGGGTGTTTTGGGAGTTCTTACCCTTC
1 AATTTTGGGCGCTTTGGGAGTTCTTACCCTTC
1415612 CCATGTGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.45
Consensus pattern (33 bp):
AATTTTGGGCGCTTTGGGAGTTCTTACCCTTCT
Found at i:1416461 original size:13 final size:13
Alignment explanation
Indices: 1416443--1416469 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1416433 CATAGTTGAA
1416443 CAGTCTTCATATG
1 CAGTCTTCATATG
1416456 CAGTCTTCATATG
1 CAGTCTTCATATG
1416469 C
1 C
1416470 GCGTCTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1418244 original size:19 final size:20
Alignment explanation
Indices: 1418222--1418261 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1418212 ACCAACCGGT
1418222 CCGAACCAAGTCAA-CCGAC
1 CCGAACCAAGTCAACCCGAC
**
1418241 CCGAACTGAGTCAACCCGAC
1 CCGAACCAAGTCAACCCGAC
1418261 C
1 C
1418262 TGTTGACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.33, C:0.42, G:0.17, T:0.07
Consensus pattern (20 bp):
CCGAACCAAGTCAACCCGAC
Found at i:1418807 original size:33 final size:33
Alignment explanation
Indices: 1418765--1418832 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1418755 TCGAGAGGTA
* *
1418765 CCAATTTTGGGCGCTTTGGGAGTTCTTACGCTT
1 CCAATTTTGGGCGCTTTGGGAATTCTTACCCTT
*
1418798 CCAATTTTGGGTGCTTTGGGAATTCTTACCCTT
1 CCAATTTTGGGCGCTTTGGGAATTCTTACCCTT
1418831 CC
1 CC
1418833 TATGTGTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.40
Consensus pattern (33 bp):
CCAATTTTGGGCGCTTTGGGAATTCTTACCCTT
Found at i:1419944 original size:3 final size:3
Alignment explanation
Indices: 1419936--1419975 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1419926 TTAATTTCAA
*
1419936 ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ACTT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT A
1419976 CTACAAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1419958 original size:15 final size:15
Alignment explanation
Indices: 1419938--1419975 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1419928 AATTTCAAAT
1419938 TATTATTATTATTAC
1 TATTATTATTATTAC
1419953 TATTATTATTATTAC
1 TATTATTATTATTAC
*
1419968 TTTTATTA
1 TATTATTA
1419976 CTACAAAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:1422251 original size:2 final size:2
Alignment explanation
Indices: 1422239--1422277 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1422229 CTTAATACAC
1422239 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1422278 TTACTATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1422429 original size:44 final size:43
Alignment explanation
Indices: 1422379--1422463 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 43
1422369 ATTATTATGG
* *
1422379 TCATTTCATTTATTTTCTTTATTATTGCATCTTTATTTTTATTT
1 TCATTTCATTTATTTTCTTTA-TATTACATATTTATTTTTATTT
* * *
1422423 TCATTTCCTTTATTTTGTTTATATTACTTATTTATTTTTAT
1 TCATTTCATTTATTTTCTTTATATTACATATTTATTTTTAT
1422464 CTTATTCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 17 0.47
44 19 0.53
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.68
Consensus pattern (43 bp):
TCATTTCATTTATTTTCTTTATATTACATATTTATTTTTATTT
Found at i:1422479 original size:19 final size:18
Alignment explanation
Indices: 1422432--1422479 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1422422 TTCATTTCCT
*
1422432 TTATTTTGTTTATATTAC
1 TTATTTTTTTTATATTAC
* *
1422450 TTATTTATTTTTATCTTAT
1 TTATTT-TTTTTATATTAC
1422469 TCTATTTTTTT
1 T-TATTTTTTT
1422480 ATTTTTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (18 bp):
TTATTTTTTTTATATTAC
Found at i:1422508 original size:24 final size:24
Alignment explanation
Indices: 1422447--1422509 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 24
1422437 TTGTTTATAT
* *
1422447 TACTTATTTATTTTTATCTTATTC
1 TACTTATTTTTTTTTTTCTTATTC
*
1422471 TA-TT-TTTTTATTTTTCTT-TTC
1 TACTTATTTTTTTTTTTCTTATTC
1422492 TACTTATTTCTTTTTTTT
1 TACTTATTT-TTTTTTTT
1422510 TCCTTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 5 0.16
22 13 0.41
23 5 0.16
24 9 0.28
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (24 bp):
TACTTATTTTTTTTTTTCTTATTC
Found at i:1422529 original size:31 final size:29
Alignment explanation
Indices: 1422450--1422541 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 29
1422440 TTTATATTAC
*
1422450 TTATTTATTTTTATCTTA-TTCTATTTTT
1 TTATTTATTTTTTTCTTATTTCTATTTTT
*
1422478 TTATTT-TTCTTTTCTACTTATTTCTTTTTTT
1 TTATTTATT-TTTT-T-CTTATTTCTATTTTT
*
1422509 TTCCTTTATTTTTTTCCTTATTT-TATTTATT
1 TT-ATTTATTTTTTT-CTTATTTCTATTT-TT
1422540 TT
1 TT
1422542 TCATCATCTC
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
27 2 0.04
28 9 0.17
29 1 0.02
30 8 0.15
31 23 0.44
32 7 0.13
33 2 0.04
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (29 bp):
TTATTTATTTTTTTCTTATTTCTATTTTT
Found at i:1426747 original size:95 final size:94
Alignment explanation
Indices: 1426553--1426739 Score: 270
Period size: 95 Copynumber: 2.0 Consensus size: 94
1426543 ACATTATAAT
* * *
1426553 ATTATATATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGTCTTTATG
1 ATTATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGTCTTTATG
* * *
1426618 GATAATATTCAGCTAGCCTGATAAAGGCG
66 CATAAGATTCAGCTAACCTGATAAAGGCG
1426647 ATTATACTATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCAGT-TTT
1 ATTATA-TATACAATAAAGCTTGAGCTGTCCCTCTAGA-GCAATTGGTTAAACGCCCC-GTCTTT
*
1426710 ATGCATAAGATTCAGCTAACCTGATGAAGG
63 ATGCATAAGATTCAGCTAACCTGATAAAGG
1426740 TATTTATATA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
94 7 0.08
95 74 0.89
96 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (94 bp):
ATTATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGTCTTTATG
CATAAGATTCAGCTAACCTGATAAAGGCG
Found at i:1428170 original size:21 final size:20
Alignment explanation
Indices: 1428145--1428207 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
1428135 CGAGATAGTT
1428145 TCTCTTAAAACAAATTTTATC
1 TCTCTTAAAACAAATTTT-TC
*
1428166 TCTCTTAAGAC--A--TTT-
1 TCTCTTAAAACAAATTTTTC
1428181 TCTCTTAAAACAAATTTTGTC
1 TCTCTTAAAACAAATTTT-TC
1428202 TCTCTT
1 TCTCTT
1428208 GAGACGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 10 0.29
16 1 0.03
17 3 0.09
19 3 0.09
20 1 0.03
21 16 0.47
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.46
Consensus pattern (20 bp):
TCTCTTAAAACAAATTTTTC
Found at i:1428197 original size:17 final size:17
Alignment explanation
Indices: 1428143--1428198 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 17
1428133 CTCGAGATAG
1428143 TTTCTCTTAAAACAAATTT
1 TTTCTCTTAAAACAAA--T
*
1428162 TATCTCTCTTAAGAC--AT
1 T-T-TCTCTTAAAACAAAT
1428179 TTTCTCTTAAAACAAAT
1 TTTCTCTTAAAACAAAT
1428196 TTT
1 TTT
1428199 GTCTCTCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
15 10 0.32
16 1 0.03
17 7 0.23
19 2 0.06
20 1 0.03
21 10 0.32
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTCTCTTAAAACAAAT
Found at i:1428311 original size:36 final size:36
Alignment explanation
Indices: 1428114--1428230 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 36
1428104 TAACTTACTC
* *
1428114 AAAACAAATTTTTGTCTCTCTCGAGATAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
1428151 AAAACAAATTTTATCTCTCTTAAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
1428187 AAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
1428223 GAAACAAA
1 AAAACAAA
1428231 AACTTTGAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
36 61 0.88
37 8 0.12
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:1428335 original size:34 final size:36
Alignment explanation
Indices: 1428253--1428353 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 36
1428243 GTTTTCCTTG
* * *
1428253 AAACAAAGTTTTATCTCTCTTGACACAGTTTCTCTTA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTATCTTA
*
1428290 AAACAAATTTTGTCTCTCTTGAGACATTTTATCTT-
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTATCTTA
**
1428325 AAA-ATTTTTTGTCTCTCTTGAGACAGTTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTT
1428354 CCCTTGAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
34 23 0.40
35 3 0.05
36 24 0.42
37 7 0.12
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.45
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTATCTTA
Found at i:1428414 original size:66 final size:65
Alignment explanation
Indices: 1428331--1428493 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
1428321 TCTTAAAATT
*
1428331 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACCAAAATATTTGAATCTATTTCCCTTGAAACAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-CAAAATATTTGAATCTGTTTCCCTTGAAACAA
1428396 A
65 A
* * * * * * *
1428397 TTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATCTTTTAATTTGTTTTCCTTTAAACACA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATCTGTTTCCCTTGAAACAAA
* * * *
1428462 TTTCGTCTCTCTCGAGACTGTTTCTCTTGAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1428494 ATTTTTGTCT
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
65 53 0.63
66 31 0.37
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.42
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATCTGTTTCCCTTGAAACAAA
Found at i:1428417 original size:136 final size:138
Alignment explanation
Indices: 1428115--1428432 Score: 446
Period size: 138 Copynumber: 2.3 Consensus size: 138
1428105 AACTTACTCA
* * *
1428115 AAACAAATTTTTGTCTCTCTCGAGATAGTTTCTCTTAAAACAAATTTTATCTCTCTTAAGACATT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTATCTCTCTTAAGACATT
* * * *
1428180 TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTGT
66 TTATCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATCTAT
*
1428245 TTTCCTTG
131 TTCCCTTG
* * * *
1428253 AAACAAAGTTTTATCTCTCTTGACACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTATCTCTCTTAAGACATT
**
1428318 TTATCTT-AAA-ATTTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACCAAAATA-TTTGAATCT
66 TTATCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-CAAAA-ACTTTGAATCT
1428380 ATTTCCCTTG
129 ATTTCCCTTG
* *
1428390 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAA
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAA
1428433 ATCTTTTAAT
Statistics
Matches: 160, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
136 64 0.40
137 31 0.19
138 65 0.41
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (138 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTATCTCTCTTAAGACATT
TTATCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATCTAT
TTCCCTTG
Found at i:1428432 original size:36 final size:36
Alignment explanation
Indices: 1428243--1428363 Score: 129
Period size: 34 Copynumber: 3.4 Consensus size: 36
1428233 CTTTGAATTT
* * *
1428243 GTTTTCCTTGAAACAAAGTTTTATCTCTCTTGACACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* *
1428280 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* ** **
1428316 TTTTATCTT-AAA-ATTTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1428350 GTTTCCCTTGAAAC
1 GTTTCCCTTGAAAC
1428364 CAAAATATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
34 26 0.37
35 6 0.09
36 24 0.34
37 14 0.20
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.44
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Done.