Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_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: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1398349 original size:21 final size:21
Alignment explanation
Indices: 1398311--1398350 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1398301 ATGACAATGG
*
1398311 TACTTTACGTGGTAAGGTATC
1 TACTTTACGTGATAAGGTATC
*
1398332 TACTTTACGTGATGAGGTA
1 TACTTTACGTGATAAGGTA
1398351 GCCGCTCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (21 bp):
TACTTTACGTGATAAGGTATC
Found at i:1398701 original size:21 final size:21
Alignment explanation
Indices: 1398647--1398742 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
1398637 ATTCACCTGT
1398647 CATCGTTCAAGAGGCCCC-CC
1 CATCGTTCAAGAGGCCCCTCC
* *
1398667 TATCGTTTAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
1398688 CACCATTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
*
1398709 CATCGTTCAAGAGGCCCCTTC
1 CATCGTTCAAGAGGCCCCTCC
*
1398730 CAGCGTTCAAGAG
1 CATCGTTCAAGAG
1398743 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
20 16 0.25
21 47 0.75
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.21
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:1400270 original size:20 final size:21
Alignment explanation
Indices: 1400245--1400301 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
1400235 GTACACTTTC
1400245 GCAACGCGAATGTCAAAAT-A
1 GCAACGCGAATGTCAAAATCA
*
1400265 GCAACGCGAATATCAAAATCA
1 GCAACGCGAATGTCAAAATCA
* *
1400286 -CAACGCAAAAGTCAAA
1 GCAACGCGAATGTCAAA
1400302 TTCGCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.12
Consensus pattern (21 bp):
GCAACGCGAATGTCAAAATCA
Found at i:1400545 original size:20 final size:20
Alignment explanation
Indices: 1400454--1400538 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
1400444 AAGGTACACT
1400454 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
1400474 TTCGCAACGCTAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* *
1400494 ATCGCAACGCAAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* *
1400514 TTCGTAATGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
1400534 TTCGC
1 TTCGC
1400539 GTTGCGATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:1400863 original size:6 final size:6
Alignment explanation
Indices: 1400854--1400883 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1400844 TTGTGATTGA
*
1400854 GATTTT GATTTT GATTTC GATTTT GATTTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT
1400884 CTTTTGCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (6 bp):
GATTTT
Found at i:1403181 original size:24 final size:24
Alignment explanation
Indices: 1403147--1403201 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1403137 CTGAAACATC
1403147 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1403171 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1403195 AT-AAAAT
1 ATCAAAAT
1403202 TTCGAATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1403970 original size:16 final size:15
Alignment explanation
Indices: 1403948--1403986 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1403938 GAAATCATTG
1403948 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
1403964 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
1403979 AAAAATTA
1 AAAAATTA
1403987 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:1404167 original size:20 final size:20
Alignment explanation
Indices: 1404142--1404231 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
1404132 AAATAAAAGC
1404142 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
1404162 TGTTGCG-AATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTCG
* **
1404182 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
* * *
1404202 TGTTGCG-ATTTAGAAAGTCT
1 TGTTGCGAAATTA-AAATTCG
1404222 TGTTGCGAAA
1 TGTTGCGAAA
1404232 AGGAAACTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
19 10 0.19
20 37 0.69
21 7 0.13
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:1404227 original size:40 final size:40
Alignment explanation
Indices: 1404142--1404232 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
1404132 AAATAAAAGC
** *
1404142 TGTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCG
1 TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
* * * *
1404182 AGTTGCGAAAACAAAATTCGTGTTGCGATTTAGAAAGTCT
1 TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
1404222 TGTTGCGAAAA
1 TGTTGCGAAAA
1404233 GGAAACTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (40 bp):
TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
Found at i:1404280 original size:20 final size:20
Alignment explanation
Indices: 1404255--1404355 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
1404245 TATGAAAAAT
*
1404255 AAATTCGCGTTGCGAATTTG
1 AAATTCGTGTTGCGAATTTG
1404275 AAATTCCGTGTTGCGAA-TTG
1 AAATT-CGTGTTGCGAATTTG
*
1404295 -ACTTCTGTGTTGCGAATTTG
1 AAATTC-GTGTTGCGAATTTG
* * * *
1404315 GAA-CCTGTGCTGCGAAATTGG
1 AAATTC-GTGTTGCG-AATTTG
* *
1404336 AGATTCGCGTTGCGAATTTG
1 AAATTCGTGTTGCGAATTTG
1404356 TTGGTAATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
18 1 0.02
19 13 0.21
20 25 0.40
21 23 0.37
22 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.35
Consensus pattern (20 bp):
AAATTCGTGTTGCGAATTTG
Found at i:1404289 original size:21 final size:21
Alignment explanation
Indices: 1404255--1404314 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 21
1404245 TATGAAAAAT
*
1404255 AAATT-CGCGTTGCGAATTTG
1 AAATTCCGTGTTGCGAATTTG
1404275 AAATTCCGTGTTGCGAA-TTG
1 AAATTCCGTGTTGCGAATTTG
* *
1404295 -ACTTCTGTGTTGCGAATTTG
1 AAATTCCGTGTTGCGAATTTG
1404315 GAACCTGTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 14 0.40
20 11 0.31
21 10 0.29
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (21 bp):
AAATTCCGTGTTGCGAATTTG
Found at i:1406314 original size:63 final size:62
Alignment explanation
Indices: 1406239--1406564 Score: 191
Period size: 63 Copynumber: 5.4 Consensus size: 62
1406229 TGGTGGTGGA
*
1406239 GGTAGTGTAGGTGGATATGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGAGCT
1 GGTAGTGCAGGTGGATATGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGAG-T
* *** * * * * * * *
1406302 GGTAGTGCAGGTGGGTATGGA---GGAGCCGGTGGACATGGAGGTGGTGATGG-AAACG-GT
1 GGTAGTGCAGGTGGATATGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGAGT
* * * * **
1406359 GGT-G-GC-GG-AGCTAGTGAAGGTGGGGCTTCTGGATATGGGACCGGAGGTGGTGAAGGAGGT
1 GGTAGTGCAGGTGGATA-TGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGA-GT
* * * * * * **
1406419 GGATCTGGAGCCGGTGGATATGGAGAAGCTGGTG--T-TGG---TGGAGGTGGAGGTGGTGGTGG
1 GG---TAGTGCAGGTGGATATGGAG--G-TGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGG
1406478 A--
60 AGT
*
1406479 GGTAGTGTAGGTGGATATGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGAGCT
1 GGTAGTGCAGGTGGATATGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGAG-T
*
1406542 GGTAGTGCAGGTGGTTATGGAGG
1 GGTAGTGCAGGTGGATATGGAGG
1406565 AGCCGGTGGA
Statistics
Matches: 188, Mismatches: 49, Indels: 52
0.65 0.17 0.18
Matches are distributed among these distances:
53 3 0.02
54 9 0.05
55 3 0.02
56 2 0.01
57 41 0.22
58 4 0.02
59 3 0.02
60 45 0.24
63 57 0.30
64 1 0.01
65 2 0.01
66 9 0.05
67 4 0.02
68 1 0.01
69 4 0.02
ACGTcount: A:0.19, C:0.07, G:0.52, T:0.22
Consensus pattern (62 bp):
GGTAGTGCAGGTGGATATGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGAGT
Found at i:1406464 original size:6 final size:6
Alignment explanation
Indices: 1406455--1406506 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
1406445 AGCTGGTGTT
* **
1406455 GGTGGA GGTGGA GGTGGT GGTGGA GGTAGTGTA GGTGGA TATGGA GGTGGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGT-G-G-A GGTGGA GGTGGA GGTGGA
1406506 G
1 G
1406507 CTTCTGGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 29 0.78
7 2 0.05
8 2 0.05
9 4 0.11
ACGTcount: A:0.17, C:0.00, G:0.60, T:0.23
Consensus pattern (6 bp):
GGTGGA
Found at i:1406588 original size:123 final size:125
Alignment explanation
Indices: 1406242--1406644 Score: 293
Period size: 123 Copynumber: 3.3 Consensus size: 125
1406232 TGGTGGAGGT
* **
1406242 AGTGTAGGTGGATATGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGAGCTGG-TA
1 AGTGCAGGT-GATATGGAGGTGGAGCTTCTGGATATGGGACCGGAGGTGGTGAAGGAGCTGGATA
* * * * * * ** * *
1406306 GTGCAGGTGGGTATGGAGGAGCCGGTGGACATGGAGGTGGTGATGGAAACGGTGGTGGCGGAGC-
65 GAGCAGGTGGATATGGAGAAGCCGGT-G--ATGGAGGAGGTGGTAG-AGTGGTGGAGGAGGAGCA
* *
1406370 --T--A-GTG--A---AGGTGGGGCTTCTGGATATGGGACCGGAGGTGGTGAAGGAGGTGGATCT
1 AGTGCAGGTGATATGGAGGTGGAGCTTCTGGATATGGGACCGGAGGTGGTGAAGGAGCTGGA--T
* * * * * * *
1406425 GGAGCCGGTGGATATGGAGAAGCTGGTGTTGGTGGAGGTGG-AG-GTGGTGGTGGA-G-G-T
64 AGAGCAGGTGGATATGGAGAAGCCGGTGATGGAGGAGGTGGTAGAGTGGTGGAGGAGGAGCA
* **
1406482 AGTGTAGGTGGATATGGAGGTGGAGCTTCTGGATATGGGGGCGGAGGTGGTGAAGGAGCTGG-TA
1 AGTGCAGGT-GATATGGAGGTGGAGCTTCTGGATATGGGACCGGAGGTGGTGAAGGAGCTGGATA
* * * * *
1406546 GTGCAGGTGGTTATGGAGGAGCCGGTGGACATGGAGGTGGTGGTGGCAGTGGTGGAGGAGGAGCA
65 GAGCAGGTGGATATGGAGAAGCCGGT-G--ATGGAGGAGGTGGTAG-AGTGGTGGAGGAGGAGCA
*
1406611 AGTGCAGGTGATATGGAGATGGAGCTTCTGGATA
1 AGTGCAGGTGATATGGAGGTGGAGCTTCTGGATA
1406645 CGGAAGTGGA
Statistics
Matches: 215, Mismatches: 36, Indels: 48
0.72 0.12 0.16
Matches are distributed among these distances:
112 1 0.00
113 1 0.00
114 9 0.04
116 2 0.01
117 52 0.24
118 1 0.00
119 1 0.00
120 46 0.21
121 1 0.00
122 1 0.00
123 53 0.25
124 2 0.01
126 11 0.05
127 1 0.00
128 25 0.12
129 8 0.04
ACGTcount: A:0.20, C:0.08, G:0.51, T:0.22
Consensus pattern (125 bp):
AGTGCAGGTGATATGGAGGTGGAGCTTCTGGATATGGGACCGGAGGTGGTGAAGGAGCTGGATAG
AGCAGGTGGATATGGAGAAGCCGGTGATGGAGGAGGTGGTAGAGTGGTGGAGGAGGAGCA
Found at i:1406861 original size:126 final size:125
Alignment explanation
Indices: 1406577--1406842 Score: 478
Period size: 126 Copynumber: 2.1 Consensus size: 125
1406567 CCGGTGGACA
* *
1406577 TGGAGGTGGTGGTGGCAGTGGTGGAGGAGGAGCAAGTGCAGGTGATATGGAGATGGAGCTTCTGG
1 TGGAAGTGGTGGTGGCAGTGGTGGAGGAGGAGCAAGCGCAGGTGATATGGAGATGGAGCTTCTGG
1406642 ATACGGAAGTGGAGGCGGTACAGGTGGTGGATCTGGAGGTGCAGGTGGTTACGGAGGAGG
66 ATACGGAAGTGGAGGCGGTACAGGTGGTGGATCTGGAGGTGCAGGTGGTTACGGAGGAGG
* *
1406702 TGGAAGTGGTGGTGGCAGTGGTGGAGGAGGAGCAAGCGCAGGTGGTTATGGAGGTGGAGCTTCTG
1 TGGAAGTGGTGGTGGCAGTGGTGGAGGAGGAGCAAGCGCAGGT-GATATGGAGATGGAGCTTCTG
*
1406767 GATACGGAAGTGGAGGCGGTGCAGGTGGTGGATCTGGAGGTGCAGGTGGTTACGGAGGAGG
65 GATACGGAAGTGGAGGCGGTACAGGTGGTGGATCTGGAGGTGCAGGTGGTTACGGAGGAGG
1406828 TGGAAGTGGTGGTGG
1 TGGAAGTGGTGGTGG
1406843 GAGCGGAGGT
Statistics
Matches: 135, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
125 41 0.30
126 94 0.70
ACGTcount: A:0.20, C:0.09, G:0.52, T:0.20
Consensus pattern (125 bp):
TGGAAGTGGTGGTGGCAGTGGTGGAGGAGGAGCAAGCGCAGGTGATATGGAGATGGAGCTTCTGG
ATACGGAAGTGGAGGCGGTACAGGTGGTGGATCTGGAGGTGCAGGTGGTTACGGAGGAGG
Found at i:1412257 original size:25 final size:24
Alignment explanation
Indices: 1412229--1412300 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 24
1412219 TTATATTCAT
1412229 AATATTTTATATATATTAACTTAAA
1 AATATTTT-TATATATTAACTTAAA
*
1412254 AATATTTTT-TATATTAACTTATTA
1 AATATTTTTATATATTAACTTA-AA
1412278 AATATATTTTAT-TATTAACTTAA
1 AATAT-TTTTATATATTAACTTAA
1412301 TTTTAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 12 0.29
24 7 0.17
25 22 0.52
26 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
AATATTTTTATATATTAACTTAAA
Found at i:1414393 original size:143 final size:142
Alignment explanation
Indices: 1414147--1414409 Score: 384
Period size: 143 Copynumber: 1.8 Consensus size: 142
1414137 AGTGATATAT
** *
1414147 CACTGAAAAGTTTCTTTCATTCTACATTAAATGGCCTATGAGAAATGGACGTTTTTCTAAAATGA
1 CACTGAAAAGTTTCTGCCATTCTA-ATTAAATGGCCTATGAGAAATGGACGTTTTTCTAAAATAA
* *
1414212 ATTAATATATCACAACTAAAAAGTTTTCTGAAATGAGTTGATATATCACTAAAAAAATTCTAAAG
65 AGTAATATATCACAACTAAAAAGTTTTCTAAAATGAGTTGATATATCACTAAAAAAATTCTAAAG
1414277 AGAAGTTATTGGG
130 AGAAGTTATTGGG
* * *
1414290 CACTGAAAAGTTTCTGCCATTGCGT-ATTAAGTGGCCTATGAGAAATGGACGTTTTTCTTATATA
1 CACTGAAAAGTTTCTGCCATT-C-TAATTAAATGGCCTATGAGAAATGGACGTTTTTCTAAAATA
* * * *
1414354 AAGTGATATATCACTACTGAAAAGTTTTCTAAAATGAGTTGATATATCACTGAAAA
64 AAGTAATATATCACAACTAAAAAGTTTTCTAAAATGAGTTGATATATCACTAAAAA
1414410 GTTTTTGTCA
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
143 104 0.98
144 1 0.01
145 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (142 bp):
CACTGAAAAGTTTCTGCCATTCTAATTAAATGGCCTATGAGAAATGGACGTTTTTCTAAAATAAA
GTAATATATCACAACTAAAAAGTTTTCTAAAATGAGTTGATATATCACTAAAAAAATTCTAAAGA
GAAGTTATTGGG
Found at i:1417426 original size:3 final size:3
Alignment explanation
Indices: 1417412--1417461 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
1417402 GATTGGTAAG
1417412 TCT TCAT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1417458 TCT T
1 TCT T
1417462 ATGTTGATCA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1420260 original size:13 final size:12
Alignment explanation
Indices: 1420253--1420326 Score: 53
Period size: 12 Copynumber: 5.8 Consensus size: 12
1420243 CTAAAAGAAT
1420253 AAAATAAAAT-A
1 AAAATAAAATAA
1420264 AAAATAATAAGTAAA
1 AAAATAA-AA-T-AA
1420279 AAACATAAAATAA
1 AAA-ATAAAATAA
*
1420292 ATAATAATAA-AA
1 AAAATAA-AATAA
*
1420304 AATACTAAAAATAA
1 AA-AAT-AAAATAA
1420318 AAAATAAAA
1 AAAATAAAA
1420327 CCAACTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
11 7 0.14
12 13 0.26
13 13 0.26
14 7 0.14
15 6 0.12
16 4 0.08
ACGTcount: A:0.77, C:0.03, G:0.01, T:0.19
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:1420314 original size:26 final size:25
Alignment explanation
Indices: 1420256--1420324 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
1420246 AAAGAATAAA
1420256 ATAAAATAAAAATAATAAGTAAAAAAC
1 ATAAAAT--AAATAATAAGTAAAAAAC
*
1420283 ATAAAATAAATAATAA-TAAAAAAT
1 ATAAAATAAATAATAAGTAAAAAAC
*
1420307 ACTAAAAATAAAAAATAA
1 A-T-AAAATAAATAATAA
1420325 AACCAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 8 0.21
25 10 0.26
26 13 0.34
27 7 0.18
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.20
Consensus pattern (25 bp):
ATAAAATAAATAATAAGTAAAAAAC
Found at i:1420315 original size:22 final size:22
Alignment explanation
Indices: 1420261--1420326 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 22
1420251 ATAAAATAAA
1420261 ATAAAAATAATAAGTAAAAAACAT
1 ATAAAAATAATAA-T-AAAAACAT
*
1420285 AAAATAAATAATAATAAAAA-AT
1 ATAA-AAATAATAATAAAAACAT
*
1420307 ACTAAAAATAAAAAATAAAA
1 A-TAAAAAT-AATAATAAAA
1420327 CCAACTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 7 0.19
23 16 0.44
24 4 0.11
25 9 0.25
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.20
Consensus pattern (22 bp):
ATAAAAATAATAATAAAAACAT
Found at i:1420318 original size:31 final size:27
Alignment explanation
Indices: 1420244--1420319 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
1420234 TGTTAAATTC
* *
1420244 TAAAAGAATAAAATAAAATAAAAATAA
1 TAAAAAAAAAAAATAAAATAAAAATAA
** *
1420271 TAAGTAAAAAACATAAAATAAATAATAA
1 TAAAAAAAAAAAATAAAATAAA-AATAA
1420299 TAAAAAATACTAAAAATAAAA
1 TAAAAAA-A--AAAAATAAAA
1420320 AATAAAACCA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
27 17 0.46
28 10 0.27
29 1 0.03
31 9 0.24
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (27 bp):
TAAAAAAAAAAAATAAAATAAAAATAA
Found at i:1420326 original size:7 final size:7
Alignment explanation
Indices: 1420258--1420326 Score: 50
Period size: 7 Copynumber: 9.3 Consensus size: 7
1420248 AGAATAAAAT
1420258 AAAAT-A
1 AAAATAA
1420264 AAAATAA
1 AAAATAA
* *
1420271 TAAGTAA
1 AAAATAA
* *
1420278 AAAACAT
1 AAAATAA
1420285 AAAATAAA
1 AAAAT-AA
1420293 TAATAATAA
1 -AA-AATAA
1420302 AAAATACTA
1 AAAATA--A
1420311 AAAATAA
1 AAAATAA
1420318 AAAATAA
1 AAAATAA
1420325 AA
1 AA
1420327 CCAACTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
6 5 0.10
7 27 0.55
8 3 0.06
9 11 0.22
10 3 0.06
ACGTcount: A:0.77, C:0.03, G:0.01, T:0.19
Consensus pattern (7 bp):
AAAATAA
Found at i:1420998 original size:3 final size:3
Alignment explanation
Indices: 1420973--1421023 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
1420963 GGCCTACAAA
* *
1420973 AAT AAT AA- AAT AAA AAT ATT AAT AAT AAT AAT AAAT AAAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT
1421018 AAT AAT
1 AAT AAT
1421024 TTTTTTTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 30 0.73
4 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1421006 original size:26 final size:25
Alignment explanation
Indices: 1420973--1421023 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1420963 GGCCTACAAA
1420973 AATAATAAAATAAA-AATATTAATAAT
1 AATAAT-AAATAAATAATA-TAATAAT
1420999 AATAATAAATAAATAATATAATAAT
1 AATAATAAATAAATAATATAATAAT
1421024 TTTTTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AATAATAAATAAATAATATAATAAT
Found at i:1424654 original size:3 final size:3
Alignment explanation
Indices: 1424629--1424689 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
1424619 AGTTTGTAAA
* *
1424629 AAT AAT AA- AAT AAA AAT ATT AAT AAT AAT AAT AATT AAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT -AAT -AAT
1424676 AAT -AT AAT AA- AAT A
1 AAT AAT AAT AAT AAT A
1424690 TTTTTGTAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 6 0.12
3 33 0.67
4 10 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1424662 original size:26 final size:25
Alignment explanation
Indices: 1424629--1424689 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
1424619 AGTTTGTAAA
1424629 AATAATAAAATAA-AAATATTAATAAT
1 AATAATAAAATAATAAATA--AATAAT
*
1424655 AATAAT-AATTAATAAATAAATAAT
1 AATAATAAAATAATAAATAAATAAT
1424679 -ATAATAAAATA
1 AATAATAAAATA
1424690 TTTTTGTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 5 0.16
24 10 0.32
25 5 0.16
26 11 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AATAATAAAATAATAAATAAATAAT
Found at i:1424672 original size:20 final size:20
Alignment explanation
Indices: 1424628--1424686 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1424618 GAGTTTGTAA
1424628 AAATAATAA-AATAA-AAAT
1 AAATAATAATAATAATAAAT
*
1424646 ATTAATAATAATAATAATTAAT
1 A--AATAATAATAATAATAAAT
1424668 AAATAAATAAT-ATAATAAA
1 AAAT-AATAATAATAATAAA
1424687 ATATTTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.03
20 18 0.53
21 11 0.32
22 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATAATAATAATAATAAAT
Found at i:1426054 original size:23 final size:23
Alignment explanation
Indices: 1426010--1426057 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1426000 CAAGTTCGAA
*
1426010 CTTGAGTTTCAGCTTAAATCAAG
1 CTTGAGTTTCAACTTAAATCAAG
* * *
1426033 CTTGAGTTTGAACTTCAGTCAAG
1 CTTGAGTTTCAACTTAAATCAAG
1426056 CT
1 CT
1426058 ACAACTAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (23 bp):
CTTGAGTTTCAACTTAAATCAAG
Found at i:1426069 original size:21 final size:21
Alignment explanation
Indices: 1426043--1426086 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1426033 CTTGAGTTTG
1426043 AACTTCAGTCAAGCTACAACT
1 AACTTCAGTCAAGCTACAACT
1426064 AACTTCAGTCAAGCTACAACT
1 AACTTCAGTCAAGCTACAACT
1426085 AA
1 AA
1426087 AAATATTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.27, G:0.09, T:0.23
Consensus pattern (21 bp):
AACTTCAGTCAAGCTACAACT
Found at i:1427021 original size:2 final size:2
Alignment explanation
Indices: 1427014--1427058 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1427004 TAACCAAAAT
1427014 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1427056 TA T
1 TA T
1427059 TTAGCTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1432888 original size:32 final size:31
Alignment explanation
Indices: 1432800--1432925 Score: 182
Period size: 31 Copynumber: 4.0 Consensus size: 31
1432790 CCCGAAGGAC
*
1432800 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
1432831 CAGTTCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1432862 CAATCCATATGTCCCAAAAGAACATAGGTAAA
1 CAGTCCATATGTCCC-GAAGAACATAGGTAAA
1432894 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1432925 C
1 C
1432926 CCTCGACCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 55 0.65
32 29 0.35
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1434218 original size:3 final size:3
Alignment explanation
Indices: 1434210--1434252 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1434200 TCTCTCGTAC
1434210 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1434253 GAATATCTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1434994 original size:59 final size:59
Alignment explanation
Indices: 1434921--1435250 Score: 552
Period size: 59 Copynumber: 5.6 Consensus size: 59
1434911 GGTGATTACC
*
1434921 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
* * *
1434980 AAATGCTAATGAATTCATACTAAGTGTATGAATCTCCACATAGGGCACTCCGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
* *
1435039 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTTCATATAGGGCACTCCGTGTGATA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
*
1435098 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
* *
1435157 AAATGCTAAGGAATTCATACTAAGTGTATGAATCTCCATATAGGGCACTCTGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
* **
1435216 AAATGATAATAAATTCATACTAAGTGTATGAATTT
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTT
1435251 TTGTATGGGA
Statistics
Matches: 252, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 252 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (59 bp):
AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
Found at i:1440160 original size:59 final size:59
Alignment explanation
Indices: 1440058--1440393 Score: 537
Period size: 59 Copynumber: 5.7 Consensus size: 59
1440048 GGTGATTACC
* * *
1440058 AAATGTTAAGGAATTCATACTAAGTGTATAAATTTCCATATAGGGAACTCCGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
* * * * *
1440117 AAATGCTAATGAATTCATACTAAGTGTATGAATCTGCACATAGGGCATTCCGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
*
1440176 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTTCATATAGGGCACTCCGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
**
1440235 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTTGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
* *
1440294 AAATGCTAAGGAATTCATACTAAGTGTACGAATCTCCATATAGGGCACTCCGTGTGCTA
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
* *
1440353 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATAT
1 AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1440394 GGGAAATGTA
Statistics
Matches: 253, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 253 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (59 bp):
AAATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTCCGTGTGCTA
Found at i:1442018 original size:44 final size:44
Alignment explanation
Indices: 1441949--1442100 Score: 223
Period size: 45 Copynumber: 3.4 Consensus size: 44
1441939 TATAAAATTT
* *
1441949 CTTATCATTTATCCGATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTTTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
*
1441994 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTAACAATATA
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
1442038 CTTACAATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTT-TTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
1442083 CTTGCCATTATTCCATAA
1 CTTACCATTTTTCCATAA
1442101 CCATATACCA
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 46 0.47
45 51 0.53
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (44 bp):
CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:1442068 original size:45 final size:44
Alignment explanation
Indices: 1441955--1442100 Score: 211
Period size: 44 Copynumber: 3.3 Consensus size: 44
1441945 ATTTCTTATC
* *
1441955 ATTTATCCGATAAGCTCGTAAGCTTATTTTACCAATATACTTACC
1 ATTTTTCC-ATAAGCTCGTAAGCTTATTTTACCAATATACTTACA
*
1442000 ATTTTTCCATAAGCTCGTAAGCTTATTTTAACAATATACTTACA
1 ATTTTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACA
* * *
1442044 ATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCC
1 ATTT-TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACA
*
1442089 ATTATTCCATAA
1 ATTTTTCCATAA
1442101 CCATATACCA
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 46 0.50
45 46 0.50
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (44 bp):
ATTTTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACA
Found at i:1442378 original size:21 final size:21
Alignment explanation
Indices: 1442354--1442422 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
1442344 CCTGCAGCTG
*
1442354 CTATACTCTATGGCATGCCAG
1 CTATACTCTATGGCATGCCAA
1442375 CTATACTCTATGGCATGCCAA
1 CTATACTCTATGGCATGCCAA
1442396 CTATACTCTATGGCATGCCAA
1 CTATACTCTATGGCATGCCAA
1442417 CTATAC
1 CTATAC
1442423 CCTGTCCCTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (21 bp):
CTATACTCTATGGCATGCCAA
Found at i:1445150 original size:26 final size:26
Alignment explanation
Indices: 1445114--1445168 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
1445104 AACATCTGTA
1445114 TACTTTGTCCAACTCTAGATCCCAAT
1 TACTTTGTCCAACTCTAGATCCCAAT
*
1445140 TACTTTGTCCAACTCTAGATCTCAAT
1 TACTTTGTCCAACTCTAGATCCCAAT
1445166 TAC
1 TAC
1445169 CTCCAGAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.36
Consensus pattern (26 bp):
TACTTTGTCCAACTCTAGATCCCAAT
Found at i:1446281 original size:2 final size:2
Alignment explanation
Indices: 1446276--1446325 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1446266 CACAAATGAA
1446276 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
1446318 AT AT AT AT
1 AT AT AT AT
1446326 TAATCATCTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1446366 original size:15 final size:15
Alignment explanation
Indices: 1446336--1446376 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1446326 TAATCATCTC
1446336 TCATTTTTTTC-TTT
1 TCATTTTTTTCATTT
*
1446350 TTATTTTCTTTCATTT
1 TCATTTT-TTTCATTT
1446366 TCATTTTTTTC
1 TCATTTTTTTC
1446377 TTATTCGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
16 9 0.39
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TCATTTTTTTCATTT
Found at i:1446393 original size:27 final size:26
Alignment explanation
Indices: 1446363--1446432 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
1446353 TTTTCTTTCA
1446363 TTTTCATTTTTTTCTTATTCGTTT-CCT
1 TTTTCATTTTTTTCTTATT--TTTCCCT
* * *
1446390 TTTTCCTTTTCTTCTTGTTTTTCCCT
1 TTTTCATTTTTTTCTTATTTTTCCCT
*
1446416 TTTTCTGTTTTTTTCTT
1 TTTTC-ATTTTTTTCTT
1446433 CTTATATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.08
26 8 0.22
27 25 0.69
ACGTcount: A:0.03, C:0.20, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTCATTTTTTTCTTATTTTTCCCT
Found at i:1446430 original size:18 final size:18
Alignment explanation
Indices: 1446389--1446427 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1446379 ATTCGTTTCC
*
1446389 TTTTTCCTTTTCTTCTTG
1 TTTTTCCCTTTCTTCTTG
1446407 TTTTTCCCTTT-TTC-TG
1 TTTTTCCCTTTCTTCTTG
1446423 TTTTT
1 TTTTT
1446428 TTCTTCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 10 0.50
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTTCCCTTTCTTCTTG
Found at i:1447156 original size:16 final size:16
Alignment explanation
Indices: 1447135--1447166 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1447125 AATCATAATC
1447135 ATTGATGATATCACTT
1 ATTGATGATATCACTT
*
1447151 ATTGATGATTTCACTT
1 ATTGATGATATCACTT
1447167 TTTCATCAAT
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:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (16 bp):
ATTGATGATATCACTT
Found at i:1448956 original size:45 final size:45
Alignment explanation
Indices: 1448889--1449030 Score: 223
Period size: 45 Copynumber: 3.2 Consensus size: 45
1448879 GAACTCTTTA
1448889 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTG
1 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTG
*
1448934 TTCCATAAGCTCGTAAGTTTATTTTACCAATATACTTACCATTTG
1 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTG
* * * * *
1448979 TTCCATAAGTTTGTAAGCTTATTTTACCAATACACTTGCCA-TTA
1 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTG
1449023 TTCCATAA
1 TTCCATAA
1449031 CCATATACCA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 10 0.11
45 80 0.89
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (45 bp):
TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTG
Found at i:1449052 original size:20 final size:20
Alignment explanation
Indices: 1449027--1449069 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1449017 CCATTATTCC
* *
1449027 ATAACCATATACCATAGACA
1 ATAACCATAAACAATAGACA
*
1449047 ATAACCATAAACAATCGACA
1 ATAACCATAAACAATAGACA
1449067 ATA
1 ATA
1449070 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:1455320 original size:25 final size:26
Alignment explanation
Indices: 1455282--1455330 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1455272 TTTATTAGAA
1455282 AATTAATAGATTAGTAAATTAGTAGT
1 AATTAATAGATTAGTAAATTAGTAGT
* *
1455308 AATTATTA-ATTAGTAATTTAGTA
1 AATTAATAGATTAGTAAATTAGTA
1455331 TCTTTCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (26 bp):
AATTAATAGATTAGTAAATTAGTAGT
Found at i:1456333 original size:16 final size:16
Alignment explanation
Indices: 1456289--1456340 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1456279 ACTGAAATTG
*
1456289 AAATTAACCCAAACCA
1 AAATTAACCCGAACCA
** * *
1456305 AAAGCAACTCGAATCA
1 AAATTAACCCGAACCA
1456321 AAATTAACCCGAACCGA
1 AAATTAACCCGAACC-A
1456338 AAA
1 AAA
1456341 AACCCCGAAC
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.54, C:0.27, G:0.08, T:0.12
Consensus pattern (16 bp):
AAATTAACCCGAACCA
Found at i:1457035 original size:32 final size:31
Alignment explanation
Indices: 1456992--1457064 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
1456982 ACCTAAACCG
*
1456992 AAAATCAACCAATCTGATATTGACCCGACCC
1 AAAATCAACCAATCTGATATTAACCCGACCC
* *
1457023 AAAATCTAACCAATTTGGTATTAACCCGACCC
1 AAAATC-AACCAATCTGATATTAACCCGACCC
1457055 AAAAATCAAC
1 -AAAATCAAC
1457065 TGATATGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 6 0.16
32 25 0.68
33 6 0.16
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (31 bp):
AAAATCAACCAATCTGATATTAACCCGACCC
Found at i:1457234 original size:15 final size:15
Alignment explanation
Indices: 1457211--1457245 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1457201 ATTTAATCTA
* *
1457211 GACCTGAAATGACCT
1 GACCCGAAATGACCC
1457226 GACCCGAAATGACCC
1 GACCCGAAATGACCC
1457241 GACCC
1 GACCC
1457246 AAACCTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.37, G:0.20, T:0.11
Consensus pattern (15 bp):
GACCCGAAATGACCC
Found at i:1460211 original size:3 final size:3
Alignment explanation
Indices: 1460193--1460236 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1460183 TTTGTTTTAA
* * *
1460193 ATT ATT TTT AATT ATT ATT ATT ATT ATT ATT AAT ATT AAT ATT A
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1460237 ATTTTCATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1461901 original size:2 final size:2
Alignment explanation
Indices: 1461894--1461935 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1461884 ATTATTGTAC
1461894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1461936 AATGTATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1462231 original size:21 final size:22
Alignment explanation
Indices: 1462198--1462240 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1462188 TATTGAAATC
*
1462198 TTATCTTTCTTTATCTT-TTATT
1 TTATCTTTATTTAT-TTGTTATT
1462220 TTAT-TTTATTTATTTGTTATT
1 TTATCTTTATTTATTTGTTATT
1462241 ATTCTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 13 0.68
22 4 0.21
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (22 bp):
TTATCTTTATTTATTTGTTATT
Found at i:1462439 original size:82 final size:82
Alignment explanation
Indices: 1462346--1462510 Score: 330
Period size: 82 Copynumber: 2.0 Consensus size: 82
1462336 CATGATTTTA
1462346 TTCTATGTTTTTTTTCTATATCATTTTTTAGTAATTCGAAGATAGACTATTCTTTACGGATAAGA
1 TTCTATGTTTTTTTTCTATATCATTTTTTAGTAATTCGAAGATAGACTATTCTTTACGGATAAGA
1462411 AATAGGCGAGATAGCTT
66 AATAGGCGAGATAGCTT
1462428 TTCTATGTTTTTTTTCTATATCATTTTTTAGTAATTCGAAGATAGACTATTCTTTACGGATAAGA
1 TTCTATGTTTTTTTTCTATATCATTTTTTAGTAATTCGAAGATAGACTATTCTTTACGGATAAGA
1462493 AATAGGCGAGATAGCTT
66 AATAGGCGAGATAGCTT
1462510 T
1 T
1462511 CCCGATGGAG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (82 bp):
TTCTATGTTTTTTTTCTATATCATTTTTTAGTAATTCGAAGATAGACTATTCTTTACGGATAAGA
AATAGGCGAGATAGCTT
Found at i:1473360 original size:14 final size:14
Alignment explanation
Indices: 1473332--1473372 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1473322 AAAAAGGAAA
1473332 AAATAAGA-AATAAG
1 AAATAAGAGAA-AAG
1473346 AAATAAGAGAAAAG
1 AAATAAGAGAAAAG
1473360 AGAA-AAGAGAAAA
1 A-AATAAGAGAAAA
1473373 AAAGAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (14 bp):
AAATAAGAGAAAAG
Found at i:1474604 original size:137 final size:137
Alignment explanation
Indices: 1474350--1474834 Score: 543
Period size: 137 Copynumber: 3.5 Consensus size: 137
1474340 ATGAATCAGT
* * *
1474350 GCGTCATCCTTAGATAACCAGAAT-TCCTCATCACGTAGGAACCGTGTTAACTTA-ACTTATCCC
1 GCGTCAACCTTAGATAACCA-AATGTCCTCATCACGTAGGAACCATGTTATC-TACA-TTATCCC
* * * ** *
1474413 TAAAGATGGCCAGCCATCCTCATCACATAGGAATTGTTTCATCCACCGACCAGATCTCCTAATCA
63 TAAAGATGGCTAGCCATCATCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTAATCA
*
1474478 CGTAAGAGTC
128 CGTAGGAGTC
* * * *
1474488 GCATCAACCTTAGGTAACCAACTGTCCTCATCACGTAGGAACTATGTTATCTACATTATCCCTAA
1 GCGTCAACCTTAGATAACCAAATGTCCTCATCACGTAGGAACCATGTTATCTACATTATCCCTAA
* * * * *
1474553 AGATGGCTAGCCATCTTCATCATGTAGGAACCATGTCATCCATCGACCAGATCTCCTCATCACGT
66 AGATGGCTAGCCATCATCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTAATCACGT
1474618 AGGAGTC
131 AGGAGTC
* *
1474625 GCGTCAACCTTAGATAACC-AATCGTCCTCATCACGTAGGAACCGTGTTATCTACCTTATCCCTA
1 GCGTCAACCTTAGATAACCAAAT-GTCCTCATCACGTAGGAACCATGTTATCTACATTATCCCTA
* * * * *
1474689 AAGATGG-TCAGTCGTCCAT-ATCGCGTAGGAGCCGTGTCATCCACCGACCAGATATCC-ATATC
65 AAGATGGCT-AGCCAT-CATCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTA-ATC
1474751 ACGTAGGAGTC
127 ACGTAGGAGTC
* * ** * * *
1474762 ACGTCAACCTTAGATAACCAAATTTAATAATCACTTAGGAACCATGTTATCTCCAAATT-TCCCT
1 GCGTCAACCTTAGATAACCAAATGTCCTCATCACGTAGGAACCATGTTATCT--ACATTATCCCT
1474826 AAAGATGGC
64 AAAGATGGC
1474835 CAGAACCCTT
Statistics
Matches: 294, Mismatches: 43, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
136 3 0.01
137 228 0.78
138 60 0.20
139 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (137 bp):
GCGTCAACCTTAGATAACCAAATGTCCTCATCACGTAGGAACCATGTTATCTACATTATCCCTAA
AGATGGCTAGCCATCATCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTAATCACGT
AGGAGTC
Found at i:1475105 original size:3 final size:3
Alignment explanation
Indices: 1475072--1475132 Score: 50
Period size: 3 Copynumber: 19.3 Consensus size: 3
1475062 TTTATTTTAA
* * **
1475072 ATT ATT TTT AATT AATT AGT ATT ATT AATT ATT ATT ATT GCT ATT ATT
1 ATT ATT ATT -ATT -ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
*
1475120 ATT ATT AAT ATT A
1 ATT ATT ATT ATT A
1475133 ATTTACATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
3 37 0.80
4 9 0.20
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1477025 original size:5 final size:5
Alignment explanation
Indices: 1477015--1477046 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1477005 AATCATTATC
1477015 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1477047 CTTTGTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1477040 original size:9 final size:9
Alignment explanation
Indices: 1477016--1477046 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1477006 ATCATTATCT
1477016 TTTATTTTA
1 TTTATTTTA
1477025 TTTTATTTTA
1 -TTTATTTTA
1477035 TTTATTTTA
1 TTTATTTTA
1477044 TTT
1 TTT
1477047 CTTTGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1478434 original size:14 final size:14
Alignment explanation
Indices: 1478415--1478441 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1478405 GGATCCGGAA
1478415 CTAATTTGAACTCT
1 CTAATTTGAACTCT
1478429 CTAATTTGAACTC
1 CTAATTTGAACTC
1478442 ATATTCAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (14 bp):
CTAATTTGAACTCT
Found at i:1483971 original size:26 final size:26
Alignment explanation
Indices: 1483935--1484004 Score: 140
Period size: 26 Copynumber: 2.7 Consensus size: 26
1483925 GAATGACCAC
1483935 TATGTCCCGAAGGACCACATATCACA
1 TATGTCCCGAAGGACCACATATCACA
1483961 TATGTCCCGAAGGACCACATATCACA
1 TATGTCCCGAAGGACCACATATCACA
1483987 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
1484005 TCCTTAAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (26 bp):
TATGTCCCGAAGGACCACATATCACA
Found at i:1484871 original size:21 final size:21
Alignment explanation
Indices: 1484845--1484894 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1484835 TGTTTCCTGA
*
1484845 TATCGATACCCTCCACATTGG
1 TATCGATACCCTCCACATTAG
1484866 TATCGATACCCTCCACATTAG
1 TATCGATACCCTCCACATTAG
1484887 TATCGATA
1 TATCGATA
1484895 ATCCTTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (21 bp):
TATCGATACCCTCCACATTAG
Found at i:1484998 original size:21 final size:19
Alignment explanation
Indices: 1484972--1485011 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
1484962 TTTGCCTTGT
1484972 AGTATCGATACTCACTCAACC
1 AGTATCGATACT-AC-CAACC
1484993 AGTATCGATACTACCAACC
1 AGTATCGATACTACCAACC
1485012 CAGAATCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.23
Consensus pattern (19 bp):
AGTATCGATACTACCAACC
Found at i:1494196 original size:55 final size:55
Alignment explanation
Indices: 1494110--1494677 Score: 755
Period size: 55 Copynumber: 10.3 Consensus size: 55
1494100 ACAATGGTAT
* *
1494110 GTACATGCACTATGTGTGCAAATCCATGGAATTTATCATCAGTTGATGAATAACC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
* *
1494165 GTACATGCACTATGTGTGCAAATGCACGGAATTCATCATGAGTTGATGAATAACC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
* * * ** *
1494220 GTATAGGCACTATGTGTGCAAATCTACAGAAATCATCATGAGTTGATGAATAACC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
*
1494275 GTACATGTACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
* * * * *
1494330 GTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAATTGATGAATTATC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
* * * * *
1494385 GTATATACACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGACGAATAACC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
* * *
1494440 GTACAGGCACTACGTGTGCAAATCCATGAAATTCATCATGAGTTGATGAATAACC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
* * *
1494495 GTACA-GTCACTATGTGTGCAAATCCATGGAATTCATTATAAATTGATGAATAACC
1 GTACATG-CACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
* * * *
1494550 GTATAGGCACTATGTGTGCAAATCCTTGGAATTCATCATTAGTTGATGAATAACC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
* * * *
1494605 GTACAAGCACGATGTGTGC-AACCCAAGGAATTCATCATGAGTTGATGAACT-ACC
1 GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAA-TAACC
* * *
1494659 GTATAGGCACTACGTGTGC
1 GTACATGCACTATGTGTGC
1494678 CTCTTAATAA
Statistics
Matches: 454, Mismatches: 56, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
54 45 0.10
55 408 0.90
56 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (55 bp):
GTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACC
Found at i:1500799 original size:20 final size:20
Alignment explanation
Indices: 1500763--1500810 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1500753 ATGCAATCAA
1500763 TATCGATACTGAAAGG-AGAG
1 TATCGATACTGAAAGGAAG-G
**
1500783 TATCGATACTGTGAGGAAGG
1 TATCGATACTGAAAGGAAGG
1500803 TATCGATA
1 TATCGATA
1500811 TCATTGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.25
Consensus pattern (20 bp):
TATCGATACTGAAAGGAAGG
Found at i:1501697 original size:29 final size:29
Alignment explanation
Indices: 1501655--1501723 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
1501645 CAATCTATAT
1501655 GTGACGAAATAGATATCGTCACATTTTTA
1 GTGACGAAATAGATATCGTCACATTTTTA
1501684 GTGACGAAATAGATATCGTCACATTTTTA
1 GTGACGAAATAGATATCGTCACATTTTTA
*
1501713 GTGACGTAATA
1 GTGACGAAATA
1501724 TAACATTACC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (29 bp):
GTGACGAAATAGATATCGTCACATTTTTA
Found at i:1502661 original size:29 final size:29
Alignment explanation
Indices: 1502619--1502687 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
1502609 CAATCTATAT
1502619 GTGACGAAATAGATATCGTCACATTTTTA
1 GTGACGAAATAGATATCGTCACATTTTTA
1502648 GTGACGAAATAGATATCGTCACATTTTTA
1 GTGACGAAATAGATATCGTCACATTTTTA
*
1502677 GTGACGTAATA
1 GTGACGAAATA
1502688 TAACATTACC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (29 bp):
GTGACGAAATAGATATCGTCACATTTTTA
Found at i:1503139 original size:3 final size:3
Alignment explanation
Indices: 1503122--1503162 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
1503112 ATATTATAAA
*
1503122 TAT TAAT TA- TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1503163 ATACAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1506390 original size:55 final size:55
Alignment explanation
Indices: 1506260--1506745 Score: 692
Period size: 55 Copynumber: 8.9 Consensus size: 55
1506250 ACAATGGTAT
*
1506260 GTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAG-T--TGAATAACC
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
* * * *
1506312 GTACATGCATTATGTGTGTAAATCCACAGAATTCATCATGAGTTGATGAATAACC
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
* ** * *
1506367 GTATAAACACTATGTGTGCAAATCTACGGAATTTATCATGAGTTGATGAATAACC
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
* * *
1506422 GTACAGGAACTATGTGTGCAAATCCACGGAATTCATCTTGAGTTGATGAATAACG
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
* * *
1506477 GTACGGGCACTATGTGTACAAATCCACAGAATTCATCATGAGTTGATGAATAACC
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
* *
1506532 ATACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACT
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
* ** *
1506587 GTACATGCACTATGTGTGCAAATCCACATAATTCATCATAAGTTGATGAATAACC
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
* * *
1506642 GTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATTAGTTGATGAGTAACC
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
* * *
1506697 GTACAGGCACGATGTGTGC-AACCCAGGGAATTCATCATGAGTTGATGAA
1 GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA
1506746 CTATCGTATA
Statistics
Matches: 382, Mismatches: 49, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
52 37 0.10
53 1 0.00
54 25 0.07
55 319 0.84
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (55 bp):
GTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC
Found at i:1510594 original size:21 final size:21
Alignment explanation
Indices: 1510558--1510609 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1510548 GTTTCTATTT
*
1510558 TTTCTA-TTTAGCCCCTTAAG
1 TTTCTATTTTAGCCCCTGAAG
*
1510578 TTTCTATTTTAGTCCCTGAAG
1 TTTCTATTTTAGCCCCTGAAG
*
1510599 TTTATATTTTA
1 TTTCTATTTTA
1510610 TCTATTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (21 bp):
TTTCTATTTTAGCCCCTGAAG
Found at i:1528310 original size:34 final size:34
Alignment explanation
Indices: 1528272--1528338 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1528262 TGGTGTTTTG
*
1528272 TTTCTAAAAACAAATTTTGTCTCACTTGAGACAA
1 TTTCTAAAAACAAATTTCGTCTCACTTGAGACAA
* *
1528306 TTTCTCAAAACAAATTTCGTCTCGCTTGAGACA
1 TTTCTAAAAACAAATTTCGTCTCACTTGAGACA
1528339 TTTTTCCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (34 bp):
TTTCTAAAAACAAATTTCGTCTCACTTGAGACAA
Found at i:1528697 original size:33 final size:33
Alignment explanation
Indices: 1528658--1528743 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
1528648 AAATTCTGAA
* *
1528658 ATTGTTTCACTTGAAATAAAAATCATATTTGAG
1 ATTGTTTCACTTGAAACAAAAACCATATTTGAG
* * *
1528691 -TCTGTTTCACTGGAAACAACAACCATCTTTGAG
1 AT-TGTTTCACTTGAAACAAAAACCATATTTGAG
*
1528724 ATTGTTTCTCTTGAAACAAA
1 ATTGTTTCACTTGAAACAAA
1528744 TCTTATTTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
32 1 0.02
33 41 0.95
34 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (33 bp):
ATTGTTTCACTTGAAACAAAAACCATATTTGAG
Found at i:1529377 original size:135 final size:128
Alignment explanation
Indices: 1529061--1529388 Score: 322
Period size: 129 Copynumber: 2.5 Consensus size: 128
1529051 GTCGCTGTCC
* * * * * * *
1529061 TCATCACGTAGGAATTGTGTCAT-CCCTCGACCAGACCTCCTCATCACGTAGCAGCCGTATCAAC
1 TCATCACGTATGAGTCGTGTCATCCCCT-GACCAGATCTCCTCATCACGTAGGAGTCGTGTC-AC
* * * * *
1529125 ACCAGATAACCAGCCGTCCTTATCACGTAGGAACCATGTTATCACCCTTAGATGGCCAGAACTCT
64 CCCAGATAACCAACCGTCCTCATCACGTAGGAACCATGTTATCACCCTAAGATGGCCAAAACTCT
* * * * * **
1529190 TCATCACGTATGAGTCGTGTCATCACCC-GGCCTGATTTACTCGTCATATAGGAGTCGTGTCACC
1 TCATCACGTATGAGTCGTGTCATC-CCCTGACCAGATCTCCTCATCACGTAGGAGTCGTGTCACC
* * *
1529254 CTCAGATAACCAATCTTCCTCATCACGTAGGAACTGA-GTTATCACCTTTCGTAAAGATGGCCAA
65 C-CAGATAACCAACCGTCCTCATCACGTAGGAAC-CATGTTATCACC---C-T-AAGATGGCC-A
1529318 AAACTCT
122 AAACTCT
1529325 TCATCACGTATGAG-CAGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGTCGTGTCACC
1 TCATCACGTATGAGTC-GTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGTCGTGTCACC
1529389 TTTAGACGAC
Statistics
Matches: 158, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
128 3 0.02
129 79 0.50
130 1 0.01
131 3 0.02
132 1 0.01
133 1 0.01
134 12 0.08
135 58 0.37
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (128 bp):
TCATCACGTATGAGTCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGTCGTGTCACCC
CAGATAACCAACCGTCCTCATCACGTAGGAACCATGTTATCACCCTAAGATGGCCAAAACTCT
Found at i:1529600 original size:3 final size:3
Alignment explanation
Indices: 1529592--1529670 Score: 149
Period size: 3 Copynumber: 26.0 Consensus size: 3
1529582 CAAAAAATAT
1529592 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
1529638 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1529671 CATGTTTTGC
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 72 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1531126 original size:30 final size:30
Alignment explanation
Indices: 1531056--1531153 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
1531046 TACTATTATG
* *
1531056 GTCCCTGAAGTTTTTGTTTT-TGCTA-TTTA
1 GTCCCTAAAGTTTATGTTTTAT-CTATTTTA
*
1531085 GCCCCCT-AAGTTTATGTTTTATCTATTTTA
1 G-TCCCTAAAGTTTATGTTTTATCTATTTTA
* * *
1531115 GTCCCTAAAGTTTCTATTTTATCTATTTTG
1 GTCCCTAAAGTTTATGTTTTATCTATTTTA
*
1531145 GTCCTTAAA
1 GTCCCTAAA
1531154 TTTCTATTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
29 20 0.34
30 38 0.66
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.51
Consensus pattern (30 bp):
GTCCCTAAAGTTTATGTTTTATCTATTTTA
Found at i:1531175 original size:30 final size:30
Alignment explanation
Indices: 1531092--1531211 Score: 100
Period size: 30 Copynumber: 4.0 Consensus size: 30
1531082 TTAGCCCCCT
* * * * *
1531092 AAGTTTATGTTTTATCTATTTTAGTCCCTA
1 AAGTTTCTATTTTATCCATTTTGGTCCTTA
*
1531122 AAGTTTCTATTTTATCTATTTTGGTCCTTA
1 AAGTTTCTATTTTATCCATTTTGGTCCTTA
* *
1531152 AA-TTTCTATTTTTTGCCATTTTGGTCCTTT
1 AAGTTTCTATTTTAT-CCATTTTGGTCCTTA
* * *
1531182 GAGTTTGTGTTTT-TCTTCATTTTGGTCCTT
1 AAGTTTCTATTTTATC--CATTTTGGTCCTT
1531212 GTAAGTTCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
29 12 0.16
30 43 0.57
31 21 0.28
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.57
Consensus pattern (30 bp):
AAGTTTCTATTTTATCCATTTTGGTCCTTA
Found at i:1534268 original size:30 final size:30
Alignment explanation
Indices: 1534232--1534297 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1534222 GATTAAATAG
* *
1534232 CAAAAACATAAATTTATAA-GATTAAAACAA
1 CAAAAACAAAAACTTA-AATGATTAAAACAA
*
1534262 CAAAAACAAAAACTTAAATGATTAAAATAA
1 CAAAAACAAAAACTTAAATGATTAAAACAA
*
1534292 TAAAAA
1 CAAAAA
1534298 TAGAAAGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.67, C:0.09, G:0.03, T:0.21
Consensus pattern (30 bp):
CAAAAACAAAAACTTAAATGATTAAAACAA
Found at i:1535904 original size:3 final size:3
Alignment explanation
Indices: 1535896--1535972 Score: 84
Period size: 3 Copynumber: 25.0 Consensus size: 3
1535886 ATGGATAAAT
* *
1535896 TAA TAA TAA TATA TAC TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1535942 -AA TAA CTAA TAA TAG TAT TAA TAAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA
1535973 AAAACCCGGA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 2 0.03
3 52 0.83
4 9 0.14
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1536400 original size:131 final size:131
Alignment explanation
Indices: 1536215--1536493 Score: 323
Period size: 131 Copynumber: 2.1 Consensus size: 131
1536205 TAGTTCTTGG
* *
1536215 CCATCTTTAGGGAGGGTGATAACTCAGTTCCTACGCGATGAGGACGACTAGTTATCTAGGGGTGA
1 CCATCTTTAGGGA---TGATAACACAGTTCCTACACGATGAGGACGACTAGTTATCTAGGGGTGA
* * * *
1536280 CACGGCTCATACGTTATGAGGAGGTCTGGTCGGGGGAT-A-ACATGGTTCCTACGTGATGAGGAT
63 CACGACTCATACGTGATAAGGAGGTATGGTCGGGGGATGACACAT--TTCCTACGTGATGAGGAT
1536343 GG-TAGA
126 GGCT-GA
* * * * *
1536349 CCATCTTTAGGGATGATAACACGGTTCTTACATGATGAGGATGAC-AGGTTATCTAGGTGTGACA
1 CCATCTTTAGGGATGATAACACAGTTCCTACACGATGAGGACGACTA-GTTATCTAGGGGTGACA
* * * *
1536413 CGACTCCTACGTGATAATGAGGTATGGTCGGTGGATGACGCATTTCCTACGTGATGAGGATGGCT
65 CGACTCATACGTGATAAGGAGGTATGGTCGGGGGATGACACATTTCCTACGTGATGAGGATGGCT
*
1536478 GG
130 GA
1536480 CCATCTTTAGGGAT
1 CCATCTTTAGGGAT
1536494 TATGGTTTCA
Statistics
Matches: 125, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
130 1 0.01
131 106 0.85
132 2 0.02
133 3 0.02
134 13 0.10
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (131 bp):
CCATCTTTAGGGATGATAACACAGTTCCTACACGATGAGGACGACTAGTTATCTAGGGGTGACAC
GACTCATACGTGATAAGGAGGTATGGTCGGGGGATGACACATTTCCTACGTGATGAGGATGGCTG
A
Found at i:1536538 original size:28 final size:28
Alignment explanation
Indices: 1536498--1536597 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
1536488 AGGGATTATG
* **
1536498 GTTTCAAGAGAAACCGACCCAAAGATTT
1 GTTTCAAAAGAAACAAACCCAAAGATTT
*
1536526 GTTTCAAAAGAAACAAACTCAAAGATTT
1 GTTTCAAAAGAAACAAACCCAAAGATTT
*
1536554 GTTTCAAGAA-AAACAAAGCCAAAGATAATGT
1 GTTTCAA-AAGAAACAAACCCAAAGAT--T-T
1536585 GTTTCAAAAGAAA
1 GTTTCAAAAGAAA
1536598 TTGTCTTAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
28 45 0.74
29 2 0.03
30 3 0.05
31 11 0.18
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (28 bp):
GTTTCAAAAGAAACAAACCCAAAGATTT
Found at i:1536785 original size:66 final size:65
Alignment explanation
Indices: 1536609--1536778 Score: 171
Period size: 67 Copynumber: 2.6 Consensus size: 65
1536599 TGTCTTAAAA
* * * * *
1536609 GAGACAAAATTTGTTTCAAGGGAAAC-GACTCAAAGATGACGTTTAAAGGGAAACTGTCTCAAGC
1 GAGACAAAATTTGTTTCAAGGGAAACGGTCTCAAAGATGATGTTTAAAGGGAAACTATCACAAAC
* * * * * * * *
1536673 GAGACAAAATTTGTTTTTAAAGGAAACGTTTTCAAAGGTCGGTGTTTCATGGGAAACTATCACAA
1 GAGACAAAATTTG-TTTCAAGGGAAACGGTCTCAAAGAT-GATGTTTAAAGGGAAACTATCACAA
*
1536738 AT
64 AC
* *
1536740 GAGATAAAATTCGTTTCAAGGGAAACGGTCTCAAAGATG
1 GAGACAAAATTTGTTTCAAGGGAAACGGTCTCAAAGATG
1536779 TTTGTTTTGT
Statistics
Matches: 82, Mismatches: 21, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
64 13 0.16
65 12 0.15
66 27 0.33
67 30 0.37
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (65 bp):
GAGACAAAATTTGTTTCAAGGGAAACGGTCTCAAAGATGATGTTTAAAGGGAAACTATCACAAAC
Found at i:1537169 original size:31 final size:33
Alignment explanation
Indices: 1537090--1537183 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 33
1537080 ATCTCAAAGA
* *
1537090 AAAAATGTCTCAAGCAAGACGAAATTTGTTTTGAG
1 AAAAATGTCTCAAGCGAGACAAAATTTG--TTGAG
*
1537125 AGAAATTGTCTCAAGCGAGACAAAATTTG-TG-G
1 A-AAAATGTCTCAAGCGAGACAAAATTTGTTGAG
1537157 AAAAATGTCTCAAGCGAGACAAAATTT
1 AAAAATGTCTCAAGCGAGACAAAATTT
1537184 TATTTCAAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
31 25 0.46
32 2 0.04
33 2 0.04
35 1 0.02
36 24 0.44
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (33 bp):
AAAAATGTCTCAAGCGAGACAAAATTTGTTGAG
Found at i:1537528 original size:10 final size:10
Alignment explanation
Indices: 1537491--1537539 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
1537481 TTATGTATCA
1537491 TGTATGTGTG
1 TGTATGTGTG
*
1537501 TGTGTGTGTG
1 TGTATGTGTG
*
1537511 TGTGTGTGTG
1 TGTATGTGTG
*
1537521 TGCATGTGT-
1 TGTATGTGTG
1537530 TG-ATGTGTG
1 TGTATGTGTG
1537539 T
1 T
1537540 TTTTCTCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
8 6 0.17
9 3 0.09
10 26 0.74
ACGTcount: A:0.06, C:0.02, G:0.43, T:0.49
Consensus pattern (10 bp):
TGTATGTGTG
Found at i:1537539 original size:2 final size:2
Alignment explanation
Indices: 1537495--1537522 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1537485 GTATCATGTA
1537495 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1537523 CATGTGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1538540 original size:2 final size:2
Alignment explanation
Indices: 1538533--1538588 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1538523 AGCTTTATTG
1538533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1538575 TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA T
1538589 TTTGGGTATA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1540474 original size:32 final size:32
Alignment explanation
Indices: 1540433--1540513 Score: 153
Period size: 32 Copynumber: 2.5 Consensus size: 32
1540423 ATCATGATAT
1540433 CTACCCGAACATGCTTTTAATAAATAGCAATC
1 CTACCCGAACATGCTTTTAATAAATAGCAATC
1540465 CTACCCGAACATGCTTTTAATAAATAGCAATC
1 CTACCCGAACATGCTTTTAATAAATAGCAATC
*
1540497 CTACCCGGACATGCTTT
1 CTACCCGAACATGCTTT
1540514 CTACCCACAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.28
Consensus pattern (32 bp):
CTACCCGAACATGCTTTTAATAAATAGCAATC
Found at i:1542133 original size:30 final size:30
Alignment explanation
Indices: 1542099--1542225 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 30
1542089 AAACAAAAAC
*
1542099 TTAAAGGATTAAAATAATAAAAATAGAAAG
1 TTAAAGGACTAAAATAATAAAAATAGAAAG
* ** * *
1542129 TTAAATGACTAAAAT-AGCAAAATCATATAG
1 TTAAAGGACTAAAATAATAAAAAT-AGAAAG
* ** *
1542159 TTTAAGGACTAAAATTGTAAAAATAGTAAG
1 TTAAAGGACTAAAATAATAAAAATAGAAAG
* * * * *
1542189 TTAAAGGACCAAAATAGTTAAAACAAAAAG
1 TTAAAGGACTAAAATAATAAAAATAGAAAG
1542219 TTAAAGG
1 TTAAAGG
1542226 GCTGAACAAT
Statistics
Matches: 74, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
29 6 0.08
30 63 0.85
31 5 0.07
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (30 bp):
TTAAAGGACTAAAATAATAAAAATAGAAAG
Found at i:1542142 original size:60 final size:60
Alignment explanation
Indices: 1542086--1542225 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
1542076 AATAAAACAA
* * *
1542086 CAAAAACAAAAACTTAAAGGATTAAAATAATAAAAATAGAAAGTTAAATGACTAAAATAG
1 CAAAAACAAAAAGTTAAAGGACTAAAATAATAAAAATAGAAAGTTAAAGGACTAAAATAG
* * * * ** * *
1542146 CAAAATCATATAGTTTAAGGACTAAAATTGTAAAAATAGTAAGTTAAAGGACCAAAATAG
1 CAAAAACAAAAAGTTAAAGGACTAAAATAATAAAAATAGAAAGTTAAAGGACTAAAATAG
**
1542206 TTAAAACAAAAAGTTAAAGG
1 CAAAAACAAAAAGTTAAAGG
1542226 GCTGAACAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.58, C:0.07, G:0.13, T:0.22
Consensus pattern (60 bp):
CAAAAACAAAAAGTTAAAGGACTAAAATAATAAAAATAGAAAGTTAAAGGACTAAAATAG
Found at i:1543703 original size:3 final size:3
Alignment explanation
Indices: 1543695--1543765 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
1543685 ATGGATAAAT
* * *
1543695 TAA TAA TAA T-A TAC TAA TAA TAA TAA TAA TAA TAG TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1543742 -AA TAA CTAA TAA TAG TAT TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA
1543766 ATAAATAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1543771 original size:27 final size:25
Alignment explanation
Indices: 1543689--1543773 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 25
1543679 AATGTAATGG
*
1543689 ATAAATTAATAATAATA-TACTAATA
1 ATAAA-TAATAATAATAGTAATAATA
*
1543714 AT-AATAATAATAATAGTAATAGTA
1 ATAAATAATAATAATAGTAATAATA
*
1543738 ATAAAATAACTAATAATAGTATTAATAA
1 AT-AAATAA-TAATAATAGTAATAAT-A
1543766 ATAAATAA
1 ATAAATAA
1543774 ATAAAAGACC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
23 11 0.22
24 10 0.20
25 2 0.04
26 5 0.10
27 20 0.39
28 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (25 bp):
ATAAATAATAATAATAGTAATAATA
Found at i:1546771 original size:83 final size:82
Alignment explanation
Indices: 1546676--1546868 Score: 323
Period size: 83 Copynumber: 2.3 Consensus size: 82
1546666 TGTATTTTTG
* *
1546676 TTTAATATTTTAAATTTAAAAGATGTTATTATCTGTTTAAATTTAGATATTAAAATATGTTTAGT
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAAATGTTTAGT
1546741 TGGAGTAAAGCTCGCAGA
66 TGGAGT-AAGCTCGCAGA
*
1546759 TTTAATAGTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAAATGTTTAGT
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAAATGTTTAGT
* *
1546824 TGGAGTAAGCTCTCATA
66 TGGAGTAAGCTCGCAGA
*
1546841 TTTAATATTTTAAATTTAAAATATATTA
1 TTTAATATTTTAAATTTAAAAGATATTA
1546869 AATCTATTTA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 35 0.34
83 68 0.66
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.45
Consensus pattern (82 bp):
TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAAATGTTTAGT
TGGAGTAAGCTCGCAGA
Found at i:1547277 original size:95 final size:95
Alignment explanation
Indices: 1547113--1547305 Score: 282
Period size: 95 Copynumber: 2.0 Consensus size: 95
1547103 CTGATCTGAT
* ** *
1547113 CTTCTGCTAGAAATATGTTGTCTCTGCCAATCCTAGTTTTGATCCTCCTGCTTCTTAGTACCTTA
1 CTTCTGCTAGAAATATGTTGCCTCTGCCAATCCTAGTCCTGATCCTCCTACTTCTTAGTACCTTA
1547178 GTGTGAAACACTCACACGCTAAGTCACAGA
66 GTGTGAAACACTCACACGCTAAGTCACAGA
* * *
1547208 CTTCTGGTAGAAATATGTTGCCTCTTCCAATCCTAGTCCTGATCCTCTTACTTCTTCA-TACC-T
1 CTTCTGCTAGAAATATGTTGCCTCTGCCAATCCTAGTCCTGATCCTCCTACTTCTT-AGTACCTT
*
1547271 ACGTGTGAAACACTCACAGGCTAAGTCACAGA
65 A-GTGTGAAACACTCACACGCTAAGTCACAGA
1547303 CTT
1 CTT
1547306 AGTGAGGCAT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 2 0.02
95 85 0.97
96 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (95 bp):
CTTCTGCTAGAAATATGTTGCCTCTGCCAATCCTAGTCCTGATCCTCCTACTTCTTAGTACCTTA
GTGTGAAACACTCACACGCTAAGTCACAGA
Found at i:1552034 original size:27 final size:27
Alignment explanation
Indices: 1551971--1552059 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 27
1551961 TTAAATTCAT
*
1551971 AATATTTTATATATTTTAACTTA--AAA
1 AATATTTTAT-TATATTAACTTATTAAA
1551997 AATA-TTT-TTATATTAACTTATTAAA
1 AATATTTTATTATATTAACTTATTAAA
* *
1552022 CATATTTTA-T-TATCAACTTAATTTAAA
1 AATATTTTATTATATTAACTT-A-TTAAA
1552049 AATATTTTATT
1 AATATTTTATT
1552060 TTTATTTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
23 11 0.21
24 1 0.02
25 17 0.33
26 9 0.17
27 13 0.25
28 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTTTATTATATTAACTTATTAAA
Found at i:1559522 original size:20 final size:20
Alignment explanation
Indices: 1559485--1559523 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1559475 AGATTGAGTG
* * *
1559485 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
1559505 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1559524 AGTTTAGGAG
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:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:1559729 original size:22 final size:23
Alignment explanation
Indices: 1559678--1559728 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1559668 CCAGAACCCC
*
1559678 AGGGGGGTATCGGTTCCCCTTCA
1 AGGGGGGAATCGGTTCCCCTTCA
*
1559701 AAGGGGGAATCGGTT-CCC-TCA
1 AGGGGGGAATCGGTTCCCCTTCA
1559722 AGGGGGG
1 AGGGGGG
1559729 GTCGATTCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.18, C:0.22, G:0.41, T:0.20
Consensus pattern (23 bp):
AGGGGGGAATCGGTTCCCCTTCA
Found at i:1562754 original size:2 final size:2
Alignment explanation
Indices: 1562747--1562771 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1562737 ATGCATCATG
1562747 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 T
1562772 CCCTATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1567895 original size:9 final size:9
Alignment explanation
Indices: 1567881--1567915 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1567871 ACTTTATATG
*
1567881 CTTCTTCTT
1 CTTCTTCAT
1567890 CTTCTTCAT
1 CTTCTTCAT
*
1567899 CATCTTCAT
1 CTTCTTCAT
1567908 CTTCTTCA
1 CTTCTTCA
1567916 GAAACACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.11, C:0.34, G:0.00, T:0.54
Consensus pattern (9 bp):
CTTCTTCAT
Found at i:1571565 original size:59 final size:57
Alignment explanation
Indices: 1571458--1571570 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 57
1571448 GAATCTAATA
*
1571458 AGCGATGGATTAAGGGGCGGGTGGGGCAGTAAACCCTTTAAAAATTTAAAATTAACT
1 AGCGATGGATTAAGGGGCGGGTGGGGCAGTAAACCCCTTAAAAATTTAAAATTAACT
* * * *
1571515 AGCGATGGATTAAGGGGACGGGTGGGGGCAGTTACCCCCTTCAAAATTTAAGATTA
1 AGCGATGGATTAAGGGG-CGGGT-GGGGCAGTAAACCCCTTAAAAATTTAAAATTA
1571571 TTATATATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 17 0.35
58 5 0.10
59 27 0.55
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (57 bp):
AGCGATGGATTAAGGGGCGGGTGGGGCAGTAAACCCCTTAAAAATTTAAAATTAACT
Found at i:1578029 original size:36 final size:35
Alignment explanation
Indices: 1577982--1578052 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
1577972 GATTAACTGT
1577982 TCTAATGCTTCATCTTTAGTACTTAAAAATAGAACC
1 TCTAATGCTTCATCTTTAGTACTT-AAAATAGAACC
1578018 TCTAATGCTTCATCTTTAGTACTTAAAATAGAACC
1 TCTAATGCTTCATCTTTAGTACTTAAAATAGAACC
1578053 CAAGTATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 11 0.31
36 24 0.69
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (35 bp):
TCTAATGCTTCATCTTTAGTACTTAAAATAGAACC
Found at i:1590021 original size:18 final size:18
Alignment explanation
Indices: 1589979--1590024 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1589969 TAGTTTGATG
*
1589979 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
1589997 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
1590015 AATGAACTAA
1 AATGAACTAA
1590025 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:1590100 original size:17 final size:17
Alignment explanation
Indices: 1590080--1590121 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1590070 AATATTTCCC
1590080 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
*
1590097 TAAAT-ACAATGCATGCT
1 TAAATGA-AATACATGCT
*
1590114 TTAATGAA
1 TAAATGAA
1590122 CAATATACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:1591368 original size:22 final size:22
Alignment explanation
Indices: 1591343--1591387 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1591333 TATGCCCCTC
* *
1591343 ATCCATATAAATCTTTTCAAAA
1 ATCCATATAAAGCTTCTCAAAA
1591365 ATCCATATAAAGCTTCTCAAAA
1 ATCCATATAAAGCTTCTCAAAA
1591387 A
1 A
1591388 AGTTAATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (22 bp):
ATCCATATAAAGCTTCTCAAAA
Found at i:1592717 original size:21 final size:21
Alignment explanation
Indices: 1592692--1592732 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1592682 TTCTGGGAAA
* *
1592692 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
1592713 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
1592733 ACGAACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:1594583 original size:103 final size:103
Alignment explanation
Indices: 1594255--1594575 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
1594245 GTTGAGGGTC
1594255 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1594320 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1594358 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGGAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1594423 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1594461 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1594526 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1594564 TATGTGGTCCTT
1 TATGTGGTCCTT
1594576 ATGGACATTA
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1594643 original size:23 final size:23
Alignment explanation
Indices: 1594590--1594651 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1594580 ACATTATTAT
*
1594590 ATGGCACTACGGTCCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
* * *
1594613 ACGACACTACGGTGCAATTCTAT
1 ATGGCACTACGGTGCAATTCTAC
* *
1594636 GTGGCACTTCGGTGCA
1 ATGGCACTACGGTGCA
1594652 TTTATATGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:1595676 original size:24 final size:24
Alignment explanation
Indices: 1595649--1595697 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1595639 CTCGTATAAG
* *
1595649 TTGCA-CTGAAGTGCCGCGTAGAAA
1 TTGCACCT-AAGTGCCACATAGAAA
1595673 TTGCACCTAAGTGCCACATAGAAA
1 TTGCACCTAAGTGCCACATAGAAA
1595697 T
1 T
1595698 GTCCAGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (24 bp):
TTGCACCTAAGTGCCACATAGAAA
Found at i:1595715 original size:23 final size:23
Alignment explanation
Indices: 1595686--1595779 Score: 102
Period size: 23 Copynumber: 4.1 Consensus size: 23
1595676 CACCTAAGTG
1595686 CCACATAGAAATGTC-CAGAAGGA
1 CCACATAGAAATGTCTC-GAAGGA
* *
1595709 CCACATAGTATTGTCTCGAAGGA
1 CCACATAGAAATGTCTCGAAGGA
* * *
1595732 CCGCGTAGAAATTTCTCGAAGGA
1 CCACATAGAAATGTCTCGAAGGA
*
1595755 CCACATA-AAATTGTCCCGAAGGA
1 CCACATAGAAA-TGTCTCGAAGGA
1595778 CC
1 CC
1595780 GCGTAGAACC
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
22 3 0.05
23 54 0.93
24 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (23 bp):
CCACATAGAAATGTCTCGAAGGA
Found at i:1597368 original size:4 final size:4
Alignment explanation
Indices: 1597359--1597476 Score: 164
Period size: 4 Copynumber: 29.5 Consensus size: 4
1597349 CAATATATGT
* * *
1597359 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
1597407 ATGC ATAC ATGC ATAC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1597455 ATAC ATAC ATAC ATGC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC AT
1597477 GCACGCACGC
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 102 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:1597484 original size:4 final size:4
Alignment explanation
Indices: 1597477--1597969 Score: 921
Period size: 4 Copynumber: 125.0 Consensus size: 4
1597467 ATGCATACAT
1597477 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597525 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAAC GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GC-AC GCAC GCAC GCAC
1597574 GCAC GCAC G--C GCAC GCAC GCAC GCAC GCAC GCAC GCA- GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597619 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597667 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597715 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597763 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCA- GCAC GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597810 GCAC GCAC GCA- GCAC GCAC GCAC GCAC GCAC GCA- GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597856 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597904 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCA- -CAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1597950 GCAC GCAC GCAC GCAC GCAC
1 GCAC GCAC GCAC GCAC GCAC
1597970 ATACATACAT
Statistics
Matches: 480, Mismatches: 0, Indels: 18
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.01
3 12 0.03
4 460 0.96
5 4 0.01
ACGTcount: A:0.25, C:0.49, G:0.25, T:0.00
Consensus pattern (4 bp):
GCAC
Found at i:1597975 original size:4 final size:4
Alignment explanation
Indices: 1597968--1599467 Score: 2537
Period size: 4 Copynumber: 382.0 Consensus size: 4
1597958 GCACGCACGC
* * ** *
1597968 ACAT ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT GCAT ATGT -TAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* ** *
1598015 A-AT -CAAT ATAT GTAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT
1 ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* ** * * **
1598062 ACAT ACAT ACAT ACAT GCAT ATGT -TAT A-AT -CAAT ATAT GTAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT
*
1598108 ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598156 ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598203 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT
1598252 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598300 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598348 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598396 ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598442 ACAT ACAT -CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACATT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T
1598490 ACAT ACAT ACA- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598537 AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598583 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACCAT ACAT ACA- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-CAT ACAT ACAT ACAT
1598631 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598679 ACAT -CAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598724 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598771 ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1598817 AC-T ACAT ACAT ACAT ACAT ACAT A-AA ACA- ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598862 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1598910 ACA- ACAT ACAT -CAT ACAT ACAT ACA- ACTAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT
1598956 ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1599003 ACCT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T AC-T ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599049 ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599096 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599144 ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599191 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599237 ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599284 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599332 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599380 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599428 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1599468 GTGAATATAT
Statistics
Matches: 1430, Mismatches: 27, Indels: 78
0.93 0.02 0.05
Matches are distributed among these distances:
2 8 0.01
3 66 0.05
4 1342 0.94
5 14 0.01
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:1603989 original size:11 final size:11
Alignment explanation
Indices: 1603973--1603997 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1603963 GTATCTGTAA
1603973 TAAAATAATAT
1 TAAAATAATAT
1603984 TAAAATAATAT
1 TAAAATAATAT
1603995 TAA
1 TAA
1603998 TAACAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:1603993 original size:3 final size:3
Alignment explanation
Indices: 1603970--1604048 Score: 69
Period size: 3 Copynumber: 27.0 Consensus size: 3
1603960 GTTGTATCTG
* * *
1603970 TAA TAA -AA TAA TAT TAA -AA TAA TAT TAA TAA CAA -AA CTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
1604013 TAA TAA TAA TAA TAA -ATA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA
1604049 AACCAAATGT
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
2 8 0.13
3 51 0.81
4 4 0.06
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1604034 original size:24 final size:25
Alignment explanation
Indices: 1603970--1604048 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 25
1603960 GTTGTATCTG
*
1603970 TAATAA-AAT-AATATTAA-AATAA
1 TAATAATAATAAATACTAATAATAA
* *
1603992 TATTAATAACAAA-ACTAATAATAA
1 TAATAATAATAAATACTAATAATAA
1604016 TAATAATAATAAATA-TAATAA-ATA
1 TAATAATAATAAATACTAATAATA-A
1604040 TAATAATAA
1 TAATAATAA
1604049 AACCAAATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
22 5 0.11
23 7 0.15
24 34 0.72
25 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (25 bp):
TAATAATAATAAATACTAATAATAA
Found at i:1604395 original size:124 final size:119
Alignment explanation
Indices: 1604190--1604472 Score: 345
Period size: 124 Copynumber: 2.3 Consensus size: 119
1604180 GTTGAATAAA
* *
1604190 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGTTGACCTA
1 TTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTAACCTA
* * * * *
1604255 TTTCCTTATGTGATAGAGTCATTCAAAAGGTTAAATAAGCTCTTCTCATTATGAAC
64 TCTACTTATGTGATAGAATCATACAAAAGGTTAAACAAGCTCTTCTCATTATGAAC
* *
1604311 TTTTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTT-TTCTGGAAAGGTTGATGCTAA
1 ---TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGG---GGATGATGCTAA
* * * * *
1604375 TCTATCTACTTCTGTGATAGAATTATACAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC
60 CCTATCTACTTATGTGATAGAATCATACAAAAGGTTAAACAAGCTCTTCTCATTATGAAC
*
1604435 TTC-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTT
1604473 CTTTTTCTTC
Statistics
Matches: 141, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
120 34 0.24
121 8 0.06
122 30 0.21
123 5 0.04
124 64 0.45
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (119 bp):
TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTAACCTATC
TACTTATGTGATAGAATCATACAAAAGGTTAAACAAGCTCTTCTCATTATGAAC
Found at i:1604459 original size:36 final size:36
Alignment explanation
Indices: 1604419--1604507 Score: 151
Period size: 36 Copynumber: 2.5 Consensus size: 36
1604409 TTGAACAAGC
* *
1604419 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAAT
*
1604455 TCTTCTCATTATGAACTTCTTTTTCTTCAGATGAAT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAAT
1604491 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
1604508 CTACCTGGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.48
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAAT
Found at i:1604636 original size:38 final size:39
Alignment explanation
Indices: 1604561--1604663 Score: 136
Period size: 38 Copynumber: 2.6 Consensus size: 39
1604551 AGGTTGAACA
1604561 AATTCTTCTCATTATGAACTTATTCTTCATTCTTCAGATGACG
1 AATTCTTCTCATTATGAAC----TCTTCATTCTTCAGATGACG
1604604 AATTCTTCTCATTATGAACTCTTC-TTCTTCAGATGACG
1 AATTCTTCTCATTATGAACTCTTCATTCTTCAGATGACG
** *
1604642 GGTTCTTCTGATTATGAACTCT
1 AATTCTTCTCATTATGAACTCT
1604664 ATCTGGCAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
38 33 0.58
39 5 0.09
43 19 0.33
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (39 bp):
AATTCTTCTCATTATGAACTCTTCATTCTTCAGATGACG
Found at i:1604683 original size:154 final size:147
Alignment explanation
Indices: 1604401--1604770 Score: 545
Period size: 154 Copynumber: 2.5 Consensus size: 147
1604391 ATAGAATTAT
* *
1604401 ACAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC---TTCTTCTTCTTCAGATGAGTTCTTCTCA
1 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCTTCTTCAGATGAGTTCTTCTCA
*
1604463 TTATGAACTTCTTTTTCTTCAGATGAATTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCC
66 TTATGAAC-TCTTCTTCTTCAGATGAATTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCC
1604528 ATCAAATGATGAATTTAA
130 ATCAAATGATGAATTTAA
*
1604546 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCATTCTTCAGATGACGAATTCTT
1 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTC-TTCTTCAGATGA-G--TTCTT
* * *
1604611 CTCATTATGAACTCTTCTTCTTCAGATGACGGGTTCTTCTGATTATGAACTCTATCTGGCAATGT
62 CTCATTATGAACTCTTCTTCTTCAGATGA---ATTCTTCTCATTATGAACTCTACCTGGCAATGT
*
1604676 TAATCCATCAATTGATGAATTTAA
124 TAATCCATCAAATGATGAATTTAA
*
1604700 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTA-T-TT-TTCTTCATATGAGTTCTTCTCA
1 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCTTCTTCAGATGAGTTCTTCTCA
1604762 TTATGAACT
66 TTATGAACT
1604771 TTTTCTGGAA
Statistics
Matches: 205, Mismatches: 10, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
145 31 0.15
147 18 0.09
148 6 0.03
149 13 0.06
150 12 0.06
151 16 0.08
152 19 0.09
153 1 0.00
154 89 0.43
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (147 bp):
ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTTCTTCTTCAGATGAATTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
TCAAATGATGAATTTAA
Found at i:1604883 original size:222 final size:222
Alignment explanation
Indices: 1604604--1605240 Score: 1005
Period size: 222 Copynumber: 2.9 Consensus size: 222
1604594 TCAGATGACG
* *
1604604 AATTCTTCTCATTATGAA---C-TCTT-CTTCTTCAGATGACGGGTTCTTCTGATTATGAACTCT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA---GTTCTTCTCATTATGAACTTT
* * * * * * * **
1604664 ATCTGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTA
63 CTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTA
*
1604729 TGAACTTATTTTTCTTCATATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAGGCTGATCCATC
128 TGAACTTATTTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAGGCTGATCCATC
1604794 AATTGATGAATTCAGGCAAAAGGTTGAACA
193 AATTGATGAATTCAGGCAAAAGGTTGAACA
*
1604824 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
1604889 TGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGA
66 TGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGA
*
1604954 ACTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAGGCTGATCCATCAAT
131 ACTTATTTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAGGCTGATCCATCAAT
1605019 TGATGAATTCAGGCAAAAGGTTGAACA
196 TGATGAATTCAGGCAAAAGGTTGAACA
1605046 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1605111 TGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGA
66 TGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGA
* * * *
1605176 ACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCAT
131 AC-TTAT-TT--TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAGGCTGATCCAT
1605241 TGTTATGGAT
Statistics
Matches: 387, Mismatches: 21, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
220 17 0.04
222 297 0.77
223 4 0.01
224 6 0.02
225 13 0.03
226 50 0.13
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (222 bp):
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGA
ACTTATTTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAGGCTGATCCATCAAT
TGATGAATTCAGGCAAAAGGTTGAACA
Found at i:1604914 original size:113 final size:112
Alignment explanation
Indices: 1604606--1605240 Score: 939
Period size: 113 Copynumber: 5.7 Consensus size: 112
1604596 AGATGACGAA
* * *
1604606 TTCTTCTCATTATGAA---C-TCTTCTTCTTCAGATGACGGGTTCTTCTGATTATGAACTCTATC
1 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGA---GTTCTTCTCATTATGAACTTTCTC
* * * * * **
1604667 TGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACAAG
63 TGGAAAAGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
* * *
1604717 TTCTTCTCATTATGAACTT-AT-TT-TTCTTCATATGAGTTCTTCTCATTATGAACTTTTTCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
1604779 AAAGGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
66 AAAAGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
1604826 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
1604891 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
65 GAAAAGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
*
1604939 TTCTTCTCATTATGAACTTC-T-TT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
1605001 AAAGGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAA
66 AAAAGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
1605048 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
1605113 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAG
65 GAAAAGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
*
1605161 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
1605226 GAAATGTTGATCCAT
65 GAAAAGCTGATCCAT
1605241 TGTTATGGAT
Statistics
Matches: 485, Mismatches: 27, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
109 186 0.38
110 2 0.00
111 22 0.05
112 12 0.02
113 262 0.54
114 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
Found at i:1606099 original size:111 final size:115
Alignment explanation
Indices: 1605947--1606242 Score: 467
Period size: 115 Copynumber: 2.6 Consensus size: 115
1605937 TCATCTTTTA
* * *
1605947 AATGATTGGTTCTGTAG-TTCCTACCAAACCAGATCAGATAACTCAAAGTACACTTCCAGAAGAT
1 AATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1606011 GCTATTGAGTCTCCTTA-TT-T-CTATGAGCAAATTCATC-TTCAAATCC
66 GCTATTGAGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCC
*
1606057 AATGATTGGTTCTGTGGTTTCATACCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGAT
1 AATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
**
1606122 GCTATTGAGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATTT
66 GCTATTGAGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCC
* * * *
1606172 GATGATTGGTTTTGTGGTTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGAT
1 AATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1606237 GCTATT
66 GCTATT
1606243 AGCACATTTA
Statistics
Matches: 170, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
110 16 0.09
111 61 0.36
112 2 0.01
113 1 0.01
114 17 0.10
115 73 0.43
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (115 bp):
AATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
GCTATTGAGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCC
Done.